Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 134 of 199
Found at i:40550111 original size:18 final size:16
Alignment explanation
Indices: 40550087--40550130 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 16
40550077 AAATGACTCA
40550087 GAAATTAATTTATATAT
1 GAAATTAATTTA-ATAT
40550104 GTAAATTATTATTTAATAT
1 G-AAATTA--ATTTAATAT
40550123 GAAATTAA
1 GAAATTAA
40550131 ATAATTGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 1 0.04
18 12 0.50
19 5 0.21
20 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (16 bp):
GAAATTAATTTAATAT
Found at i:40554095 original size:17 final size:17
Alignment explanation
Indices: 40554075--40554109 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40554065 TAACAAGCAC
40554075 ATTAA-TTACTTTATTTT
1 ATTAACTTA-TTTATTTT
40554092 ATTAACTTATTTATTTT
1 ATTAACTTATTTATTTT
40554109 A
1 A
40554110 AGTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTAACTTATTTATTTT
Found at i:40561294 original size:2 final size:2
Alignment explanation
Indices: 40561287--40561312 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40561277 AGTAAACGCA
40561287 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
40561313 CTTTTTGCTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40568978 original size:41 final size:41
Alignment explanation
Indices: 40568933--40569077 Score: 229
Period size: 41 Copynumber: 3.5 Consensus size: 41
40568923 GACTTTAAGT
*
40568933 CTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
40568974 CTAGCAGGCTAAATGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
40569015 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
*
40569056 CTAGCAGGGTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
40569078 ATATGTTAAA
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 1 0.01
41 96 0.99
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:40569109 original size:18 final size:18
Alignment explanation
Indices: 40569088--40569125 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
40569078 ATATGTTAAA
40569088 TTAAGTGATTATATGCAT
1 TTAAGTGATTATATGCAT
40569106 TTAAGTGATTATATGCAT
1 TTAAGTGATTATATGCAT
40569124 TT
1 TT
40569126 GATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (18 bp):
TTAAGTGATTATATGCAT
Found at i:40569179 original size:2 final size:2
Alignment explanation
Indices: 40569127--40569159 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40569117 TATGCATTTG
40569127 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 A
40569160 AATGATTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40574785 original size:17 final size:18
Alignment explanation
Indices: 40574763--40574797 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40574753 ATTTGGGTCA
40574763 TGTGGG-CTACACGGGCG
1 TGTGGGCCTACACGGGCG
40574780 TGTGGGCCTACACGGGCG
1 TGTGGGCCTACACGGGCG
40574798 AACATCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.11, C:0.26, G:0.46, T:0.17
Consensus pattern (18 bp):
TGTGGGCCTACACGGGCG
Found at i:40575775 original size:18 final size:18
Alignment explanation
Indices: 40575731--40575775 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
40575721 CAATAAGAAA
40575731 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAATTGAAT
*
40575749 AACGATTTGTAAA-TGAAT
1 AACGTTTTG-AAATTGAAT
*
40575767 AATGTTTTG
1 AACGTTTTG
40575776 GAAACGAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (18 bp):
AACGTTTTGAAATTGAAT
Found at i:40576853 original size:3 final size:3
Alignment explanation
Indices: 40576845--40576885 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
40576835 AAACTAACCA
40576845 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40576886 CTACATTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40577531 original size:20 final size:19
Alignment explanation
Indices: 40577503--40577563 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
40577493 ATAGATGCAA
40577503 AATAGGGGCACAGATGTGC
1 AATAGGGGCACAGATGTGC
* * * *
40577522 AGTCAGGGGCACCGAAGTGGA
1 AAT-AGGGGCACAGATGT-GC
40577543 AATAGGGGCACAGATGTGC
1 AATAGGGGCACAGATGTGC
40577562 AA
1 AA
40577564 GCATAAATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.33, C:0.16, G:0.38, T:0.13
Consensus pattern (19 bp):
AATAGGGGCACAGATGTGC
Found at i:40579678 original size:25 final size:24
Alignment explanation
Indices: 40579637--40579684 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
40579627 TTATAAATTA
* *
40579637 GAAAAATATCTCTAGAAATTTTTT
1 GAAAAATATCTCCAGAAAATTTTT
*
40579661 GAAATAATCTCTCCAGAAAATTTT
1 GAAA-AATATCTCCAGAAAATTTT
40579685 CTCTCTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (24 bp):
GAAAAATATCTCCAGAAAATTTTT
Found at i:40579942 original size:20 final size:18
Alignment explanation
Indices: 40579895--40579943 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
40579885 CAATATAAAC
40579895 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
40579912 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
40579932 ATTAAATTAATA
1 ATTAAATTAATA
40579944 AAATACTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:40584374 original size:20 final size:20
Alignment explanation
Indices: 40584351--40584389 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40584341 TTTGCTATTG
40584351 TTTCCATTATTTTGCTGCTA
1 TTTCCATTATTTTGCTGCTA
* * *
40584371 TTTCTATTGTTTTGTTGCT
1 TTTCCATTATTTTGCTGCT
40584390 GTGTTTTTTT
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:0.10, C:0.15, G:0.13, T:0.62
Consensus pattern (20 bp):
TTTCCATTATTTTGCTGCTA
Found at i:40585262 original size:19 final size:20
Alignment explanation
Indices: 40585229--40585267 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40585219 AAATGTGTAA
40585229 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
40585249 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
40585268 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:40585298 original size:3 final size:3
Alignment explanation
Indices: 40585290--40585326 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
40585280 AGTAAATATA
*
40585290 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT AAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40585327 AAACAAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:40586416 original size:40 final size:40
Alignment explanation
Indices: 40586299--40586438 Score: 126
Period size: 40 Copynumber: 3.5 Consensus size: 40
40586289 ATCTTTGAGT
* **
40586299 CGATGAGACACT-GAGTGTCAATTTATTACTTCGAATTAATT
1 CGATGAGACACTAG-GTGTCAAATTATTACTTCGAATT-ACC
* * * **
40586340 TGATGAGGCACTAGGTG-CCAA-T-TTACTTCGGTTTACC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTACC
*
40586377 CGAAGAGACACTAGGTGTCAAATTATTACTTCGAATTACC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTACC
* * *
40586417 CGATGAGGCACTGGGTGACAAA
1 CGATGAGACACTAGGTGTCAAA
40586439 CTGGTGTGTT
Statistics
Matches: 77, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 15 0.19
38 13 0.17
39 2 0.03
40 33 0.43
41 13 0.17
42 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTACC
Found at i:40590795 original size:27 final size:27
Alignment explanation
Indices: 40590670--40590811 Score: 151
Period size: 27 Copynumber: 5.3 Consensus size: 27
40590660 ATTCATGGGC
40590670 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* ** * *
40590697 AAATAACTAAAATACCCTCAAATGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * * *
40590724 AAATAACCGAAATATCCTTGAAGGATA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
40590751 AAATGACCGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
40590778 AAATGATCGAAATACCC-CCATTGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
40590805 AAATGAC
1 AAATGAC
40590812 TGTTATACCC
Statistics
Matches: 93, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
26 2 0.02
27 91 0.98
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:40591235 original size:28 final size:28
Alignment explanation
Indices: 40591202--40591268 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
40591192 CTCATATTAC
40591202 ACTGTTACTGCTTAAGGCTAAGGCCCAG
1 ACTGTTACTGCTTAAGGCTAAGGCCCAG
*
40591230 ACTGTTACTGCTTAAGGCTCAGGCCCAG
1 ACTGTTACTGCTTAAGGCTAAGGCCCAG
*
40591258 ACTATTACTGC
1 ACTGTTACTGC
40591269 ATGTCGTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (28 bp):
ACTGTTACTGCTTAAGGCTAAGGCCCAG
Found at i:40592052 original size:18 final size:18
Alignment explanation
Indices: 40592031--40592069 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40592021 ACTCTTAAGT
*
40592031 TAGAGAAAACT-GAGACTG
1 TAGA-AAAACTGGAAACTG
40592049 TAGAAAAACTGGAAACTG
1 TAGAAAAACTGGAAACTG
40592067 TAG
1 TAG
40592070 GGAGACTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.46, C:0.10, G:0.26, T:0.18
Consensus pattern (18 bp):
TAGAAAAACTGGAAACTG
Found at i:40593708 original size:41 final size:41
Alignment explanation
Indices: 40593663--40593817 Score: 238
Period size: 41 Copynumber: 3.8 Consensus size: 41
40593653 TTATATAAAA
* * *
40593663 CACCGGCATAAAGCCTGCTAGACACAAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
40593704 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
40593745 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCAATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCCGATACATTT
*
40593786 CATCGGCACAAAGCCTGCTAGGCATAAAGCCC
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCC
40593818 AAACTTACAA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.17
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCCGATACATTT
Found at i:40594457 original size:47 final size:47
Alignment explanation
Indices: 40594370--40594468 Score: 108
Period size: 47 Copynumber: 2.1 Consensus size: 47
40594360 ATATATATAT
** * * ** *
40594370 ATATACATTCGGCCATAGTTTAATTTATTTCTCTGCATAACAATTAA
1 ATATACATTCAACCATAGATTAATTCATTTCAATGCATAACAAATAA
* * *
40594417 ATATACATTCAACTATAGATTAATTCATTTCAATGTATAACAAATAT
1 ATATACATTCAACCATAGATTAATTCATTTCAATGCATAACAAATAA
40594464 ATATA
1 ATATA
40594469 TATGTATATA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.39
Consensus pattern (47 bp):
ATATACATTCAACCATAGATTAATTCATTTCAATGCATAACAAATAA
Found at i:40594583 original size:47 final size:47
Alignment explanation
Indices: 40594521--40594636 Score: 135
Period size: 47 Copynumber: 2.4 Consensus size: 47
40594511 AAATAATTTA
* *
40594521 TTTCAATGCATAACAAATATATATACATTCGGCCATAGTTTAATTCAT
1 TTTC-ATGCATAACAAATATATATACATTCAGCCATAGATTAATTCAT
* * * *
40594569 TTCTC-TGCATAACAATTACATATACATTCAGCTATAGATTGATTCAT
1 TT-TCATGCATAACAAATATATATACATTCAGCCATAGATTAATTCAT
* *
40594616 TTTCACGCATAAAAAATATAT
1 TTTCATGCATAACAAATATAT
40594637 TTATATATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
46 2 0.04
47 50 0.89
48 2 0.04
49 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (47 bp):
TTTCATGCATAACAAATATATATACATTCAGCCATAGATTAATTCAT
Found at i:40598536 original size:51 final size:51
Alignment explanation
Indices: 40598460--40598559 Score: 200
Period size: 51 Copynumber: 2.0 Consensus size: 51
40598450 TCCTGGTAAG
40598460 GCTAACATAGTAGCGGACGCACTGGGCCGTAGGGCTGTATCTAATTTGAGA
1 GCTAACATAGTAGCGGACGCACTGGGCCGTAGGGCTGTATCTAATTTGAGA
40598511 GCTAACATAGTAGCGGACGCACTGGGCCGTAGGGCTGTATCTAATTTGA
1 GCTAACATAGTAGCGGACGCACTGGGCCGTAGGGCTGTATCTAATTTGA
40598560 AAGCGATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (51 bp):
GCTAACATAGTAGCGGACGCACTGGGCCGTAGGGCTGTATCTAATTTGAGA
Found at i:40599315 original size:17 final size:17
Alignment explanation
Indices: 40599293--40599328 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40599283 CTAATTTAGT
* *
40599293 AATTGAATCTATGATAC
1 AATTGAACCTACGATAC
40599310 AATTGAACCTACGATAC
1 AATTGAACCTACGATAC
40599327 AA
1 AA
40599329 AAGAAGTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (17 bp):
AATTGAACCTACGATAC
Found at i:40602039 original size:68 final size:68
Alignment explanation
Indices: 40601908--40602070 Score: 184
Period size: 68 Copynumber: 2.4 Consensus size: 68
40601898 TCACCTGACA
* * * * ** *
40601908 CCATAGCCGAGCTATGGTCTTACACAATATAGTCCCATGTTTAACATCCTGGTGAACTTCCTTTA
1 CCATAGCCGAGCTATGGTCTTACATATTATAGTCCCATATTGAACATCCTGACGAACTCCCTTTA
40601973 TTG
66 TTG
* * * *
40601976 CCATAGCCGAG-TAATGGTCTTACATATTATGGTCCCATATTGAACGTTCTGACGGACTCCCTTT
1 CCATAGCCGAGCT-ATGGTCTTACATATTATAGTCCCATATTGAACATCCTGACGAACTCCCTTT
*
40602040 GTTG
65 ATTG
* *
40602044 CCATAGTCGAGCTATTGTCTTACATAT
1 CCATAGCCGAGCTATGGTCTTACATAT
40602071 GAAACCTCTT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
67 1 0.01
68 77 0.97
69 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (68 bp):
CCATAGCCGAGCTATGGTCTTACATATTATAGTCCCATATTGAACATCCTGACGAACTCCCTTTA
TTG
Found at i:40610795 original size:19 final size:19
Alignment explanation
Indices: 40610771--40610881 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
40610761 AATCTTCAGG
40610771 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40610790 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
40610809 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40610828 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
** *
40610847 GATATATAATTTTAGATAT
1 GATATGCAATCTTAGATAT
40610866 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40610882 AGATATGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40610821 original size:38 final size:38
Alignment explanation
Indices: 40610778--40610881 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
40610768 AGGGATATGC
40610778 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
40610816 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
40610854 AATTTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
40610882 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:40610907 original size:22 final size:22
Alignment explanation
Indices: 40610771--40610904 Score: 75
Period size: 19 Copynumber: 6.7 Consensus size: 22
40610761 AATCTTCAGG
40610771 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
40610790 GATATGCAATCTTAG-ATATAAT
1 GATATGCAATCTTAGAAGAT-AT
40610812 -ATAT--AATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
40610828 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
** * *
40610847 GATATATAATTTTAG-A-T-AT
1 GATATGCAATCTTAGAAGATAT
40610866 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
40610888 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
40610905 GATTTAATTT
Statistics
Matches: 91, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
16 2 0.02
17 7 0.08
19 55 0.60
20 1 0.01
21 8 0.09
22 6 0.07
23 12 0.13
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:40630315 original size:11 final size:11
Alignment explanation
Indices: 40630301--40630339 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40630291 TAAAAAGAAA
40630301 AGAAAAATGAT
1 AGAAAAATGAT
40630312 AGAAAAATGAT
1 AGAAAAATGAT
* * *
40630323 AAAAAAACGAG
1 AGAAAAATGAT
40630334 AGAAAA
1 AGAAAA
40630340 GAAACTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (11 bp):
AGAAAAATGAT
Found at i:40630873 original size:18 final size:17
Alignment explanation
Indices: 40630852--40630886 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
40630842 GGACTTTTGG
40630852 ACTTTTTAATTTATTTTT
1 ACTTTTTAA-TTATTTTT
40630870 ACTTTTTAATTATTTTT
1 ACTTTTTAATTATTTTT
40630887 GTAAAGGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
ACTTTTTAATTATTTTT
Found at i:40637627 original size:41 final size:41
Alignment explanation
Indices: 40637573--40637650 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
40637563 AAAACAGGTC
40637573 TTTAGCAGCGTTTT-TTCTAAGCGCCACTAAAGAACATTATA
1 TTTAGCAGCGTTTTATT-TAAGCGCCACTAAAGAACATTATA
* * *
40637614 TTTATCAGTGTTTTATTTAAGCGCCGCTAAAGAACAT
1 TTTAGCAGCGTTTTATTTAAGCGCCACTAAAGAACAT
40637651 GTTCGTTAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 31 0.94
42 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (41 bp):
TTTAGCAGCGTTTTATTTAAGCGCCACTAAAGAACATTATA
Found at i:40638026 original size:21 final size:21
Alignment explanation
Indices: 40637988--40638055 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
40637978 TTCTCTGCTT
* * *
40637988 TGCTTCTCTCGCTACAGCCTC
1 TGCTTCCCTCACTGCAGCCTC
* *
40638009 CGCTTCCCTCACTGCAGCCGC
1 TGCTTCCCTCACTGCAGCCTC
* *
40638030 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCCCTCACTGCAGCCTC
40638051 TGCTT
1 TGCTT
40638056 TAAGTTGTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.06, C:0.47, G:0.18, T:0.29
Consensus pattern (21 bp):
TGCTTCCCTCACTGCAGCCTC
Found at i:40639539 original size:9 final size:9
Alignment explanation
Indices: 40639528--40639592 Score: 85
Period size: 9 Copynumber: 7.2 Consensus size: 9
40639518 ATCCAATTGC
*
40639528 AAGTTATGC
1 AAGTTATGT
*
40639537 AAGTTATGC
1 AAGTTATGT
*
40639546 AAGTTATTT
1 AAGTTATGT
*
40639555 AATTTATGT
1 AAGTTATGT
40639564 AAGTTATGT
1 AAGTTATGT
*
40639573 AATTTATGT
1 AAGTTATGT
40639582 AAGTTATGT
1 AAGTTATGT
40639591 AA
1 AA
40639593 TTAGAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (9 bp):
AAGTTATGT
Found at i:40639548 original size:18 final size:18
Alignment explanation
Indices: 40639525--40639594 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
40639515 AAGATCCAAT
* *
40639525 TGCAAGTTATGCAAGTTA
1 TGCAAGTTATGTAATTTA
*
40639543 TGCAAGTTATTTAATTTA
1 TGCAAGTTATGTAATTTA
*
40639561 TGTAAGTTATGTAATTTA
1 TGCAAGTTATGTAATTTA
*
40639579 TGTAAGTTATGTAATT
1 TGCAAGTTATGTAATT
40639595 AGAAATTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (18 bp):
TGCAAGTTATGTAATTTA
Found at i:40639624 original size:37 final size:37
Alignment explanation
Indices: 40639572--40639659 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
40639562 GTAAGTTATG
* *
40639572 TAAT-TTATGTAAGTTATGTAATTAGAAATTTTATCA
1 TAATATTATATAAGTTATGTAATTAGAAATTTGATCA
* *
40639608 TAATATTATATAAGTTATGTAATTCGAAATTTGATCT
1 TAATATTATATAAGTTATGTAATTAGAAATTTGATCA
*
40639645 TAATATTATAAAAGT
1 TAATATTATATAAGT
40639660 AATCTTAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 4 0.09
37 42 0.91
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (37 bp):
TAATATTATATAAGTTATGTAATTAGAAATTTGATCA
Found at i:40639666 original size:20 final size:20
Alignment explanation
Indices: 40639641--40639679 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40639631 TCGAAATTTG
40639641 ATCTTAATATTATAAAAGTA
1 ATCTTAATATTATAAAAGTA
*
40639661 ATCTTAATATTATATAAGT
1 ATCTTAATATTATAAAAGT
40639680 TATGTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
ATCTTAATATTATAAAAGTA
Found at i:40639714 original size:37 final size:37
Alignment explanation
Indices: 40639661--40639947 Score: 239
Period size: 37 Copynumber: 7.7 Consensus size: 37
40639651 TATAAAAGTA
40639661 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
* *
40639698 ATCTTAGTATTGTATAAGTTATGTAATTCGATAA-TTT
1 ATCTTAATATTATATAAGTTATGTAATTCGA-AATTTT
* * *
40639735 ATTTTAATATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
* * **
40639772 ATCTTAACATTATATAAGTTATGTAATAT-TATATAAGTT
1 ATCTTAATATTATATAAGTTATGTAAT-TCGA-A-ATTTT
* * * * ** *
40639811 AT-GTAAT-TCGATAT--TTTATCTTAACATTATATAA-GTT
1 ATCTTAATAT-TATATAAGTTAT-GT-A-ATTCGA-AATTTT
* * *
40639848 AT-GTAATATTACATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
* *
40639884 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
*
40639921 ATCTTAACATTATATAAGTTATGTAAT
1 ATCTTAATATTATATAAGTTATGTAAT
40639948 ATTATATAAG
Statistics
Matches: 205, Mismatches: 30, Indels: 30
0.77 0.11 0.11
Matches are distributed among these distances:
35 1 0.00
36 13 0.06
37 161 0.79
38 15 0.07
39 15 0.07
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.49
Consensus pattern (37 bp):
ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
Found at i:40639822 original size:93 final size:90
Alignment explanation
Indices: 40639558--40640091 Score: 575
Period size: 93 Copynumber: 5.7 Consensus size: 90
40639548 GTTATTTAAT
* * * * * * *
40639558 TTATGTAAGTTATGTAATTTATGTAAGTTATGTAATTAGAAATTTTATCATAATATTATATAAGT
1 TTATATAAGTTATGTAATTCA--TATGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGT
* * *
40639623 TATGTAATTCGAAATTTGATCTTAATA
64 TATGTAATTCGATATTTTATCTTAACA
* * * * * *
40639650 TTATAAAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAGTATTGTATAA
1 TTATATAAGTTAT-GTAAT-TCATAT--GTTATGTAATTCGATATTTTATCTTAATATTGTATAA
* * *
40639715 GTTATGTAATTCGATAATTTATTTTAATA
62 GTTATGTAATTCGATATTTTATCTTAACA
* * * ** ** * *
40639744 TTGTATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTAT-GTAATATTATATAA
1 TTATATAAGTTATGTAATTC-ATATGTTAT-GT-A-ATTCGATATTTTATCTTAATATTGTATAA
40639808 GTTATGTAATTCGATATTTTATCTTAACA
62 GTTATGTAATTCGATATTTTATCTTAACA
*
40639837 TTATATAAGTTATGTAATATTACATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAG
1 TTATATAAGTTATGT-A-ATT-CATATGTTATGTAATTCGATATTTTATCTTAATATTGTATAAG
40639902 TTATGTAATTCGATATTTTATCTTAACA
63 TTATGTAATTCGATATTTTATCTTAACA
*
40639930 TTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAG
1 TTATATAAGTTATGTAAT-TCATAT--GTTATGTAATTCGATATTTTATCTTAATATTGTATAAG
40639995 TTATGTAATTCGATATTTTATCTTAACA
63 TTATGTAATTCGATATTTTATCTTAACA
* * * * *
40640023 TTATATAAGTTATGTAATATTTTATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAG
1 TTATATAAGTTATGT-A-A-TTCATATGTTATGTAATTCGATATTTTATCTTAATATTGTATAAG
40640088 TTAT
63 TTAT
40640092 CTTAATATTA
Statistics
Matches: 377, Mismatches: 47, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
91 9 0.02
92 26 0.07
93 241 0.64
94 83 0.22
95 16 0.04
96 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (90 bp):
TTATATAAGTTATGTAATTCATATGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTA
TGTAATTCGATATTTTATCTTAACA
Found at i:40639825 original size:56 final size:56
Alignment explanation
Indices: 40639739--40639910 Score: 308
Period size: 56 Copynumber: 3.1 Consensus size: 56
40639729 TAATTTATTT
*
40639739 TAATATTGTATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
40639795 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
* * *
40639851 TAATATTACATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTATG
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
40639907 TAAT
1 TAAT
40639911 TCGATATTTT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 112 1.00
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (56 bp):
TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
Found at i:40639871 original size:149 final size:147
Alignment explanation
Indices: 40639711--40640110 Score: 579
Period size: 149 Copynumber: 2.7 Consensus size: 147
40639701 TTAGTATTGT
40639711 ATAAGTTATGTAATTCGATAATTTATTTTAATATTGTATAAGTTATGTAATTCGATATTTTATCT
1 ATAAGTTATGTAATTCGATAATTTATTTTAATATTGTATAAGTTATGTAATTCGATATTTTATCT
40639776 TAACATTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTAT
66 TAACATTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTAT
40639841 ATAAGTTATGTAATATTAC-
131 ATAAGTTATGT-A-ATT-CG
* *
40639860 ATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTATGTAATTCGATATTTTATCT
1 ATAAGTTATGTAATTCGATAATTTATTTTAATATTGTATAAGTTATGTAATTCGATATTTTATCT
* *
40639925 TAACATTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGATATTTTATCTTAATATTGT
66 TAACATTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTAT
40639990 ATAAGTTATGTAATTCG
131 ATAAGTTATGTAATTCG
** * ** * * * * *
40640007 ATATTTTATCTTAACATTATATAAGTTA-TGTAATATTTTATAAGTTATGTAATTAGAAATTTTA
1 ATAAGTTAT-GT-A-ATTCGATAATTTATTTTAATATTGTATAAGTTATGTAATTCGATATTTTA
* *
40640071 TCTTAATATTATATAAGTTATCTTAATATTATATAAGTTA
63 TCTTAACATTATATAAGTTAT-GTAATATTATATAAGTTA
40640111 AGAAATTTTA
Statistics
Matches: 228, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
146 1 0.00
147 10 0.04
148 2 0.01
149 189 0.83
150 26 0.11
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (147 bp):
ATAAGTTATGTAATTCGATAATTTATTTTAATATTGTATAAGTTATGTAATTCGATATTTTATCT
TAACATTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTAT
ATAAGTTATGTAATTCG
Found at i:40639948 original size:56 final size:56
Alignment explanation
Indices: 40639888--40640003 Score: 205
Period size: 56 Copynumber: 2.1 Consensus size: 56
40639878 TATTTTATCT
*
40639888 TAATATTGTATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
* *
40639944 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTATG
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
40640000 TAAT
1 TAAT
40640004 TCGATATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.49
Consensus pattern (56 bp):
TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
Found at i:40639994 original size:37 final size:37
Alignment explanation
Indices: 40639944--40640040 Score: 176
Period size: 37 Copynumber: 2.6 Consensus size: 37
40639934 ATAAGTTATG
40639944 TAATATTATATAAGTTATGTAATTCGATATTTTATCT
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCT
*
40639981 TAATATTGTATAAGTTATGTAATTCGATATTTTATCT
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCT
*
40640018 TAACATTATATAAGTTATGTAAT
1 TAATATTATATAAGTTATGTAAT
40640041 ATTTTATAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.49
Consensus pattern (37 bp):
TAATATTATATAAGTTATGTAATTCGATATTTTATCT
Found at i:40640041 original size:56 final size:57
Alignment explanation
Indices: 40639975--40640110 Score: 202
Period size: 56 Copynumber: 2.4 Consensus size: 57
40639965 ATTCGATATT
* * * *
40639975 TTATCTTAATATTGTATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAG
1 TTATCGTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAG
* *
40640032 TTAT-GTAATATTTTATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAG
1 TTATCGTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAG
*
40640088 TTATCTTAATATTATATAAGTTA
1 TTATCGTAATATTATATAAGTTA
40640111 AGAAATTTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
56 51 0.72
57 20 0.28
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (57 bp):
TTATCGTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAG
Found at i:40641544 original size:23 final size:23
Alignment explanation
Indices: 40641514--40641558 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
40641504 GGAGAATAAA
40641514 TTTTGGGGGATAACTGATGGAGG
1 TTTTGGGGGATAACTGATGGAGG
40641537 TTTTGGGGGATAACTGATGGAG
1 TTTTGGGGGATAACTGATGGAG
40641559 AAAAATGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.04, G:0.42, T:0.31
Consensus pattern (23 bp):
TTTTGGGGGATAACTGATGGAGG
Found at i:40642017 original size:147 final size:147
Alignment explanation
Indices: 40641763--40642029 Score: 338
Period size: 147 Copynumber: 1.8 Consensus size: 147
40641753 TCGTATCGAT
* * * * *
40641763 AAATGTTAAAACATTTTTGCGGCGTTTTAATTAAAGCGCCACTAACTATAAATCAAAACGCAGTC
1 AAATGTTAAAACAATTTTGCGGCGTTTTAAGTAAAGCACCACTAAATATAAATCAAAACGAAGTC
* * * * * * *
40641828 GCTTCATCAACACTTACCTCAAACCAGTGGCGTTTTCGAAAAATCGCCACTAATAACATTTAAAA
66 GCTTCACCAAAACTTAACTCAAACCAGTGGCATTTCCAAAAAAACGCCACTAATAACATTTAAAA
40641893 AACGGCAGCGTTTTTAA
131 AACGGCAGCGTTTTTAA
* *
40641910 AAATGTTAGAACAATTTTGTGGCGTTTTAAGTAAAGCACCACTAAATATAAGATC-AAACGAAGT
1 AAATGTTAAAACAATTTTGCGGCGTTTTAAGTAAAGCACCACTAAATATAA-ATCAAAACGAAGT
* * * * **
40641974 CGTTTCCCCAAAAGTTAACTCAATCTTGTGGCATTTCCAAAAAAACGCCACTAATA
65 CGCTTCACCAAAACTTAACTCAAACCAGTGGCATTTCCAAAAAAACGCCACTAATA
40642030 CCATAGACAA
Statistics
Matches: 99, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
147 96 0.97
148 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (147 bp):
AAATGTTAAAACAATTTTGCGGCGTTTTAAGTAAAGCACCACTAAATATAAATCAAAACGAAGTC
GCTTCACCAAAACTTAACTCAAACCAGTGGCATTTCCAAAAAAACGCCACTAATAACATTTAAAA
AACGGCAGCGTTTTTAA
Found at i:40643610 original size:114 final size:111
Alignment explanation
Indices: 40643419--40643799 Score: 399
Period size: 114 Copynumber: 3.4 Consensus size: 111
40643409 GCTTGTTAAT
* * * *
40643419 AAACGCCGCTAAATCCCCCAATGCTAAGTAAAACGACCTCGTTGGGCTTAGGTTT-TTGGCGGCG
1 AAACGCCGCTAAATCCCCGAATGCTCAG-AAAACGACGTCGTT-GGCTTAGGTTTCTTTGCGGCG
* *
40643483 CTTTCCAAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTCTCCAT
64 C-TTCC-AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAA
* * * * *
40643533 AAACGCCGCTAAATCCTCGAATACTCAGAGAACGGCGTCGTTCGGCTTATGTTTCTTTGCGGCGC
1 AAACGCCGCTAAATCCCCGAATGCTCAGAAAACGACGTCGTT-GGCTTAGGTTTCTTTGCGGCGC
** * * *
40643598 TTCCACAGAAACGCCGCTAAAGTACTGAACATTGGCGGCGCTAC-CTCAA
65 TTCCA-A-AAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC-CAA
* * *
40643647 AAACGTCGCTAAGTCACCGAATGCTCAGAAAACGACGTCGTTGGTCTTAGGTTTCTTTGCGGCGA
1 AAACGCCGCTAAATCCCCGAATGCTCAGAAAACGACGTCGTTGG-CTTAGGTTTCTTTGCGGCG-
* * * *
40643712 ATTCTCAAAAACGCCGCTAAATCCCTGAGCTTTAGCGGCGCTTCAT-AAA
64 CTTC-CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC-TCCAA
* * *
40643761 AAACGTCGCTAAATCCCCGAATGCGCGGAAAACGACGTC
1 AAACGCCGCTAAATCCCCGAATGCTCAGAAAACGACGTC
40643800 ATTCGACCGA
Statistics
Matches: 220, Mismatches: 38, Indels: 18
0.80 0.14 0.07
Matches are distributed among these distances:
112 1 0.00
113 29 0.13
114 184 0.84
115 4 0.02
116 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (111 bp):
AAACGCCGCTAAATCCCCGAATGCTCAGAAAACGACGTCGTTGGCTTAGGTTTCTTTGCGGCGCT
TCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAA
Found at i:40643751 original size:41 final size:40
Alignment explanation
Indices: 40643701--40643777 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
40643691 TCTTAGGTTT
*
40643701 CTTTGCGGCGAATTC-TCAAAAACGCCGCTAAATCCCTGAG
1 CTTTGCGGCG-ATTCATAAAAAACGCCGCTAAATCCCTGAG
* *
40643741 CTTTAGCGGCGCTTCATAAAAAACGTCGCTAAATCCC
1 CTTT-GCGGCGATTCATAAAAAACGCCGCTAAATCCC
40643778 CGAATGCGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 7 0.22
41 25 0.78
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (40 bp):
CTTTGCGGCGATTCATAAAAAACGCCGCTAAATCCCTGAG
Found at i:40643894 original size:40 final size:40
Alignment explanation
Indices: 40643839--40643925 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
40643829 AGAAATCGCC
40643839 GCTAATGCTTATTCTTCAGCAGCGTTTTCCGTAAAGCGCA
1 GCTAATGCTTATTCTTCAGCAGCGTTTTCCGTAAAGCGCA
* *
40643879 GCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAGCGCC
1 GCTAATGCTTATTCTTCAGCAGCGTTTTCCGTAAAGCGCA
40643919 GCTAATG
1 GCTAATG
40643926 ATTGATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (40 bp):
GCTAATGCTTATTCTTCAGCAGCGTTTTCCGTAAAGCGCA
Found at i:40643940 original size:40 final size:40
Alignment explanation
Indices: 40643839--40643941 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 40
40643829 AGAAATCGCC
* * *
40643839 GCTAATGCTTATTCTTCAGCAGCGTTTTCCGTAAAGCGCA
1 GCTAATGATTATTCTACAGCGGCGTTTTCCGTAAAGCGCA
* * *
40643879 GCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAGCGCC
1 GCTAATGATTATTCTACAGCGGCGTTTTCCGTAAAGCGCA
*
40643919 GCTAATGATTGA-TCTAGAGCGGC
1 GCTAATGATT-ATTCTACAGCGGC
40643942 ATTTGTTATC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 56 0.98
41 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (40 bp):
GCTAATGATTATTCTACAGCGGCGTTTTCCGTAAAGCGCA
Found at i:40644642 original size:2 final size:2
Alignment explanation
Indices: 40644635--40644672 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
40644625 CTATACTGTA
40644635 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
40644673 GGGGTTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40645856 original size:18 final size:17
Alignment explanation
Indices: 40645829--40645863 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40645819 CTTAAATATA
40645829 GAAGAAGAAGATGGAGGG
1 GAAGAAGAAGAT-GAGGG
*
40645847 GAAGACGAAGATGAGGG
1 GAAGAAGAAGATGAGGG
40645864 TGGAAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.03, G:0.49, T:0.06
Consensus pattern (17 bp):
GAAGAAGAAGATGAGGG
Found at i:40663186 original size:16 final size:18
Alignment explanation
Indices: 40663167--40663199 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
40663157 ATAAATGTAA
40663167 AATTAAC-C-AAATTTAC
1 AATTAACACTAAATTTAC
40663183 AATTAACACTAAATTTA
1 AATTAACACTAAATTTA
40663200 TTCTATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAACACTAAATTTAC
Found at i:40664401 original size:23 final size:21
Alignment explanation
Indices: 40664375--40664416 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
40664365 TTTTTTATAA
40664375 AATTTTTAATATTTTTATTGACG
1 AATTTTT--TATTTTTATTGACG
*
40664398 AATTTTTTATTTTTTTTGA
1 AATTTTTTATTTTTATTGA
40664417 TTTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (21 bp):
AATTTTTTATTTTTATTGACG
Found at i:40672837 original size:95 final size:95
Alignment explanation
Indices: 40672674--40672865 Score: 375
Period size: 95 Copynumber: 2.0 Consensus size: 95
40672664 AATTGGTCAT
*
40672674 TCGCTAGCTTGGTATAACCTTGATGGTTTGTATTAATCGCTAATATGGAAAAATATGAAATGACG
1 TCGCTAGCTTGGTATAACCTTGATGGTTTGCATTAATCGCTAATATGGAAAAATATGAAATGACG
40672739 AACTAGAGACATAGATCGTCTGTATCACTG
66 AACTAGAGACATAGATCGTCTGTATCACTG
40672769 TCGCTAGCTTGGTATAACCTTGATGGTTTGCATTAATCGCTAATATGGAAAAATATGAAATGACG
1 TCGCTAGCTTGGTATAACCTTGATGGTTTGCATTAATCGCTAATATGGAAAAATATGAAATGACG
40672834 AACTAGAGACATAGATCGTCTGTATCACTG
66 AACTAGAGACATAGATCGTCTGTATCACTG
40672864 TC
1 TC
40672866 TGCAATAAAT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (95 bp):
TCGCTAGCTTGGTATAACCTTGATGGTTTGCATTAATCGCTAATATGGAAAAATATGAAATGACG
AACTAGAGACATAGATCGTCTGTATCACTG
Found at i:40676882 original size:15 final size:15
Alignment explanation
Indices: 40676862--40676890 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40676852 AAATTAATTG
40676862 AGAATTCTCATTTAA
1 AGAATTCTCATTTAA
40676877 AGAATTCTCATTTA
1 AGAATTCTCATTTA
40676891 TTGCTTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (15 bp):
AGAATTCTCATTTAA
Found at i:40678866 original size:17 final size:19
Alignment explanation
Indices: 40678827--40678867 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
40678817 ATACGTGTAC
*
40678827 TTTTTTTTCTTCACTAAGA
1 TTTTTTTTCTCCACTAAGA
*
40678846 TTTTTTTTC-CCAC-AAGG
1 TTTTTTTTCTCCACTAAGA
40678863 TTTTT
1 TTTTT
40678868 ATCTTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 9 0.45
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTTTTTTCTCCACTAAGA
Found at i:40680235 original size:14 final size:14
Alignment explanation
Indices: 40680216--40680245 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40680206 AAAAGTGAAA
40680216 AAATGAGAGTTTTT
1 AAATGAGAGTTTTT
40680230 AAATGAGAGTTTTT
1 AAATGAGAGTTTTT
40680244 AA
1 AA
40680246 CTTTAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (14 bp):
AAATGAGAGTTTTT
Found at i:40684797 original size:20 final size:21
Alignment explanation
Indices: 40684741--40684807 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
40684731 AAACAAGAAG
*
40684741 ATTCAGCCTAGTGGAGGTATT
1 ATTCGGCCTAGTGGAGGTATT
40684762 ATTCGGCCTAGTGGAGGTATT
1 ATTCGGCCTAGTGGAGGTATT
*
40684783 ATTCGG-CTAGCGGAGGTATT
1 ATTCGGCCTAGTGGAGGTATT
40684803 ATTCG
1 ATTCG
40684808 ACAAACCCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (21 bp):
ATTCGGCCTAGTGGAGGTATT
Found at i:40690852 original size:30 final size:30
Alignment explanation
Indices: 40690808--40690865 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40690798 TTCAAACTGC
*
40690808 ACACACACAAACAAACGCACATACACACGG
1 ACACACACAAACAAACGCACACACACACGG
* * *
40690838 ACACATACATACAAACGCAGACACACAC
1 ACACACACAAACAAACGCACACACACAC
40690866 ACACCGACGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.50, C:0.36, G:0.09, T:0.05
Consensus pattern (30 bp):
ACACACACAAACAAACGCACACACACACGG
Found at i:40693632 original size:16 final size:17
Alignment explanation
Indices: 40693611--40693647 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
40693601 TGATTTTCGA
40693611 TTTTCTTTTTTCTTTT-
1 TTTTCTTTTTTCTTTTC
40693627 TTTTCTTTTTTCTTTTC
1 TTTTCTTTTTTCTTTTC
40693644 TTTT
1 TTTT
40693648 GGCTATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTTC
Found at i:40695053 original size:9 final size:9
Alignment explanation
Indices: 40695028--40695061 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
40695018 TTCAAAACAA
40695028 ATAAATTATT
1 ATAAATT-TT
40695038 AATAAATTTT
1 -ATAAATTTT
40695048 ATAAATTTT
1 ATAAATTTT
40695057 ATAAA
1 ATAAA
40695062 ATTCAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 2 0.09
11 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATAAATTTT
Found at i:40695662 original size:21 final size:21
Alignment explanation
Indices: 40695638--40695696 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
40695628 CCAATTTCTG
40695638 ATTTTATATTTTCAATCTTAA
1 ATTTTATATTTTCAATCTTAA
* *
40695659 ATTTT-TAATTTTCAATTTTTA
1 ATTTTAT-ATTTTCAATCTTAA
* *
40695680 ATTTCAGATTTTCAATC
1 ATTTTATATTTTCAATC
40695697 CTCAATCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTATATTTTCAATCTTAA
Found at i:40695676 original size:28 final size:28
Alignment explanation
Indices: 40695609--40695677 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
40695599 TTCCTTCCTA
* *
40695609 AATTTTCAATCTTCAATCCCCAATTTCT
1 AATTTTCAATTTTCAATCCCAAATTTCT
* ** *
40695637 GATTTT-ATATTTTCAATCTTAAATTTTT
1 AATTTTCA-ATTTTCAATCCCAAATTTCT
40695665 AATTTTCAATTTT
1 AATTTTCAATTTT
40695678 TAATTTCAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
27 1 0.03
28 30 0.94
29 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.01, T:0.54
Consensus pattern (28 bp):
AATTTTCAATTTTCAATCCCAAATTTCT
Found at i:40698192 original size:18 final size:18
Alignment explanation
Indices: 40698156--40698193 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40698146 GTAAATTTAC
*
40698156 AATTCGAATAACTAGAAT
1 AATTCGAATAACTAAAAT
*
40698174 AATTCGAATAATTAAAAT
1 AATTCGAATAACTAAAAT
40698192 AA
1 AA
40698194 CAAATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (18 bp):
AATTCGAATAACTAAAAT
Found at i:40700322 original size:23 final size:24
Alignment explanation
Indices: 40700296--40700341 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
40700286 ATCCATCAAT
*
40700296 TTAACAATAGAAATAT-TAATAAA
1 TTAACAATAAAAATATCTAATAAA
* *
40700319 TTAATATTAAAAATATCTAATAA
1 TTAACAATAAAAATATCTAATAA
40700342 CATAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TTAACAATAAAAATATCTAATAAA
Found at i:40700414 original size:25 final size:26
Alignment explanation
Indices: 40700386--40700437 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
40700376 CACTTCTTAT
40700386 AAAA-TATT-TATCATTTCAAA-AATTA
1 AAAATTATTATAT-ATTT-AAATAATTA
40700411 AAAATTATTATATATTTAAATAATTA
1 AAAATTATTATATATTTAAATAATTA
40700437 A
1 A
40700438 TTGATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.29
26 14 0.58
27 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAATTATTATATATTTAAATAATTA
Found at i:40700701 original size:21 final size:21
Alignment explanation
Indices: 40700660--40700701 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40700650 ACAAATATAG
**
40700660 GTTCTGAAAAAATTATTAAAA
1 GTTCTGAAAAAATTAAAAAAA
40700681 GTTCT-AAAAAATATAAAAAAA
1 GTTCTGAAAAAAT-TAAAAAAA
40700702 ATCTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (21 bp):
GTTCTGAAAAAATTAAAAAAA
Found at i:40701610 original size:5 final size:5
Alignment explanation
Indices: 40701600--40701625 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40701590 TGAGCATTCG
40701600 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
40701626 AATGTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:40702419 original size:30 final size:31
Alignment explanation
Indices: 40702374--40702433 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
40702364 GGAGGTGGGA
*
40702374 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
40702405 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
40702434 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:40702660 original size:9 final size:9
Alignment explanation
Indices: 40702646--40702682 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40702636 TATAGTTTGA
40702646 TATTCGAAT
1 TATTCGAAT
40702655 TATTCGAAT
1 TATTCGAAT
*
40702664 TATTCGAGT
1 TATTCGAAT
40702673 TATTCGAAT
1 TATTCGAAT
40702682 T
1 T
40702683 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40707546 original size:51 final size:51
Alignment explanation
Indices: 40707491--40707751 Score: 383
Period size: 51 Copynumber: 5.3 Consensus size: 51
40707481 AATCACATTT
* * *
40707491 ATCACTTGTCACTTGTCTCTGATTAGATAAGTGTAGCTAAAGCTACCACAC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
40707542 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCA--C
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
40707591 -TCA----TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
* * * *
40707637 ATCACTTGTCACTTGTCACTGATTAGATAGGTGTAGCTAAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
* *
40707688 ATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
40707739 ATCACTTGTCACT
1 ATCACTTGTCACT
40707752 GATCAGAAGT
Statistics
Matches: 191, Mismatches: 12, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
44 39 0.20
46 1 0.01
47 3 0.02
48 3 0.02
49 1 0.01
51 144 0.75
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
Found at i:40707600 original size:44 final size:44
Alignment explanation
Indices: 40707550--40707758 Score: 240
Period size: 44 Copynumber: 4.4 Consensus size: 44
40707540 ACATCACTTG
40707550 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
*
40707594 TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTCA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
*
40707638 TCACTTGTCACTTG-TCACTGATTAGATAGGTGTAGCTAAAGCTATCACTTATCA
1 TCACTTGTCAC-TGATCA--GA-T--A-A-GTGTAGCTAAAGCTACCAC---TCA
* *
40707692 CTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTA
1 ----TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
40707740 TCACTTGTCACTGATCAGA
1 TCACTTGTCACTGATCAGA
40707759 AGTACTCAAA
Statistics
Matches: 142, Mismatches: 7, Indels: 32
0.78 0.04 0.18
Matches are distributed among these distances:
44 75 0.53
45 2 0.01
46 2 0.01
47 1 0.01
48 2 0.01
49 1 0.01
50 1 0.01
51 35 0.25
52 1 0.01
53 1 0.01
54 3 0.02
55 1 0.01
56 2 0.01
57 1 0.01
58 14 0.10
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (44 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
Found at i:40707661 original size:146 final size:146
Alignment explanation
Indices: 40707491--40707758 Score: 473
Period size: 146 Copynumber: 1.8 Consensus size: 146
40707481 AATCACATTT
*
40707491 ATCACTTGTCACTTGTCTCTGATTAGATAAGTGTAGCTAAAGCTACCACACATCACTTGTCACTT
1 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACACATCACTTGTCACTT
*
40707556 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTGATCAGATAAATGTA
66 GTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTGATCAGATAAATGTA
40707621 GCTAAAGCTACCACTC
131 GCTAAAGCTACCACTC
* * **
40707637 ATCACTTGTCACTTGTCACTGATTAGATAGGTGTAGCTAAAGCTATCACTTATCACTTGTCACTT
1 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACACATCACTTGTCACTT
*
40707702 GTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTGATCAGA
66 GTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTGATCAGA
40707759 AGTACTCAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
146 115 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (146 bp):
ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACACATCACTTGTCACTT
GTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTGATCAGATAAATGTA
GCTAAAGCTACCACTC
Found at i:40707665 original size:95 final size:97
Alignment explanation
Indices: 40707499--40707751 Score: 366
Period size: 95 Copynumber: 2.6 Consensus size: 97
40707489 TTATCACTTG
* * *
40707499 TCACTTGTCTCTGATTAGATAAGTGTAGCTAAAGCTACCACACATCACTTGTCACTTGTCACTGA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTTGTCACTGA
40707564 TCAGATAAGTGTAGCTAAAGCTACCAC-TCA-
66 TCAGATAAGTGTAGCTAAAGCTACCACTTCAT
*
40707594 TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTCATCACTTGTCACTTGTCACTGA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTTGTCACTGA
* * *
40707659 TTAGATAGGTGTAGCTAAAGCTATCACTTATCACTT
66 TCAGATAAGTGTAGCTAAAGCTACCAC-T-TCA--T
* *
40707695 GTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT
1 -TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACT
40707752 GATCAGAAGT
Statistics
Matches: 141, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
95 85 0.60
98 3 0.02
102 53 0.38
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (97 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTGTCACTTGTCACTGA
TCAGATAAGTGTAGCTAAAGCTACCACTTCAT
Found at i:40710737 original size:33 final size:33
Alignment explanation
Indices: 40710700--40710767 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
40710690 TCAAAAAACA
40710700 TGCAGTAGATGCTGTTTCGACCCAAAATGACTT
1 TGCAGTAGATGCTGTTTCGACCCAAAATGACTT
40710733 TGCAGTAGATGCTGTTTCGACCCAAAATGACTT
1 TGCAGTAGATGCTGTTTCGACCCAAAATGACTT
40710766 TG
1 TG
40710768 GTAATTTGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (33 bp):
TGCAGTAGATGCTGTTTCGACCCAAAATGACTT
Found at i:40713102 original size:48 final size:48
Alignment explanation
Indices: 40713033--40713125 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
40713023 AATTCAAACA
**
40713033 AAATGTGTGCCCAACACTAGTCAGATAAACTAACGGAAGTTGCGCGAC
1 AAATGTGCACCCAACACTAGTCAGATAAACTAACGGAAGTTGCGCGAC
* *
40713081 AAATGTGCACCCAGCACTAGTCAGATAAACTGACGGAAGTTGCGC
1 AAATGTGCACCCAACACTAGTCAGATAAACTAACGGAAGTTGCGC
40713126 CTAGCACTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (48 bp):
AAATGTGCACCCAACACTAGTCAGATAAACTAACGGAAGTTGCGCGAC
Found at i:40713200 original size:74 final size:74
Alignment explanation
Indices: 40713120--40713306 Score: 275
Period size: 74 Copynumber: 2.5 Consensus size: 74
40713110 CTGACGGAAG
* * * * *
40713120 TTGCGCCTAGCACTAGTCAGATAAACCGACAAATAAATAGTGAGCCCAGCTCTAGTTGGATATAC
1 TTGCGCCTAGCGCTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTCGATACAC
40713185 CAACGATAT
66 CAACGATAT
* *
40713194 TTGCGCCTAACGCTAGTCGGATAAGCCGACGAATAAATAGTGAGCCCAGCTCTAGTTCGATACAC
1 TTGCGCCTAGCGCTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTCGATACAC
40713259 CAACGATAT
66 CAACGATAT
* * * *
40713268 TTGTGCCCAGTGTTAGTCGGATAAACCGACGAATAAATA
1 TTGCGCCTAGCGCTAGTCGGATAAACCGACGAATAAATA
40713307 ATTATTTATT
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 100 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (74 bp):
TTGCGCCTAGCGCTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTCGATACAC
CAACGATAT
Found at i:40713249 original size:39 final size:38
Alignment explanation
Indices: 40713132--40713306 Score: 100
Period size: 35 Copynumber: 4.7 Consensus size: 38
40713122 GCGCCTAGCA
* *
40713132 CTAGTCAGATAAACCGACAAATAAATAGTGAGCCCAGCT
1 CTAGTCGGAT-AACCGACGAATAAATAGTGAGCCCAGCT
* * * * * * *
40713171 CTAGTTGGATATACCAACG-AT--AT-TTGCGCCTAACG
1 CTAGTCGGATA-ACCGACGAATAAATAGTGAGCCCAGCT
40713206 CTAGTCGGATAAGCCGACGAATAAATAGTGAGCCCAGCT
1 CTAGTCGGATAA-CCGACGAATAAATAGTGAGCCCAGCT
* * *
40713245 CTAGTTC-GATACACCAACG-AT--AT-TTGTGCCCAG-T
1 CTAG-TCGGATA-ACCGACGAATAAATAGTGAGCCCAGCT
*
40713279 GTTAGTCGGATAAACCGACGAATAAATA
1 -CTAGTCGGAT-AACCGACGAATAAATA
40713307 ATTATTTATT
Statistics
Matches: 100, Mismatches: 21, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
34 4 0.04
35 42 0.42
36 9 0.09
38 9 0.09
39 33 0.33
40 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (38 bp):
CTAGTCGGATAACCGACGAATAAATAGTGAGCCCAGCT
Found at i:40731979 original size:26 final size:26
Alignment explanation
Indices: 40731939--40731989 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40731929 ACACATTTAT
40731939 TTTCTTATTTATTTTCA-TTCTTTTCA
1 TTTCTTATTTATTTTCACTT-TTTTCA
* *
40731965 TTTCTTTTTTTTTTTCACTTTTTTC
1 TTTCTTATTTATTTTCACTTTTTTC
40731990 CTAGTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTCTTATTTATTTTCACTTTTTTCA
Found at i:40740409 original size:2 final size:2
Alignment explanation
Indices: 40740402--40740427 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40740392 TAGTTTAAGC
40740402 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
40740428 CTTTGGATTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40741012 original size:21 final size:21
Alignment explanation
Indices: 40740972--40741017 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40740962 ACGATCTAAG
*
40740972 CACATAGGCGTGTGGAGTAGT
1 CACATAGGCGTGTGGAGTAGC
*
40740993 CACATGGGCGTGT-GAGGTAGC
1 CACATAGGCGTGTGGA-GTAGC
40741014 CACA
1 CACA
40741018 CAGCCATGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.20
Consensus pattern (21 bp):
CACATAGGCGTGTGGAGTAGC
Found at i:40743986 original size:12 final size:12
Alignment explanation
Indices: 40743969--40743993 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40743959 TTCTTCTCCT
40743969 CTTTCCCCTTCC
1 CTTTCCCCTTCC
40743981 CTTTCCCCTTCC
1 CTTTCCCCTTCC
40743993 C
1 C
40743994 CTTGGGTTGC
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:0.60, G:0.00, T:0.40
Consensus pattern (12 bp):
CTTTCCCCTTCC
Found at i:40746256 original size:21 final size:21
Alignment explanation
Indices: 40746232--40746284 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
40746222 CACTGTTTCT
* *
40746232 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
40746253 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
40746274 AATCTCACCGC
1 AATCTCACCGC
40746285 CACCGCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:40765723 original size:16 final size:16
Alignment explanation
Indices: 40765702--40765750 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
40765692 TAAAACATTA
40765702 TTAAAATTTATAAAAT
1 TTAAAATTTATAAAAT
*
40765718 TTAAAATGTTCAAAAAAT
1 TTAAAAT-TT-ATAAAAT
* *
40765736 TAAAAATTAATAAAA
1 TTAAAATTTATAAAA
40765751 ACCATTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 12 0.44
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TTAAAATTTATAAAAT
Found at i:40765738 original size:17 final size:16
Alignment explanation
Indices: 40765701--40765751 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
40765691 TTAAAACATT
40765701 ATTAAAATTTATAAAA
1 ATTAAAATTTATAAAA
*
40765717 TTTAAAATGTTCA-AAAA
1 ATTAAAAT-TT-ATAAAA
*
40765734 ATTAAAAATTAATAAAA
1 ATT-AAAATTTATAAAA
40765751 A
1 A
40765752 CCATTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 8 0.29
17 14 0.50
18 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTAAAATTTATAAAA
Found at i:40772801 original size:66 final size:67
Alignment explanation
Indices: 40772707--40772914 Score: 197
Period size: 66 Copynumber: 3.1 Consensus size: 67
40772697 ACCAAAAAAG
* * * * *
40772707 GTACATGACTTAGGAAGGTCATGAACTTTGAAAAGTT-GTGTTTGAA-AAGGTAAGGCACTTTAA
1 GTACGTGACTTGGGAAGGTCACGAACTTTGAAAAGTTAGTGCTT-AAGAAGGTAAGGCACTCTAA
40772770 GAA
65 GAA
* * * *
40772773 GTACGTGATTTGGGAAGGTTACGAACTTTGAAAAGTTAAGTGCTTAAGAAGGTGAGGTACTCTAA
1 GTACGTGACTTGGGAAGGTCACGAACTTTGAAAAGTT-AGTGCTTAAGAAGGTAAGGCACTCTAA
40772838 GAA
65 GAA
* * ** * * * * * *
40772841 GTATGTGACTTGGGAA-GACACGTGCTTTGAAAACTCAATGCTTAAGAAGGCAAGGTACTTTAAG
1 GTACGTGACTTGGGAAGGTCACGAACTTTGAAAAGTTAGTGCTTAAGAAGGTAAGGCACTCTAAG
40772905 AA
66 AA
*
40772907 GTATGTGA
1 GTACGTGA
40772915 TCTGGAAAGG
Statistics
Matches: 118, Mismatches: 21, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
66 66 0.56
67 16 0.14
68 36 0.31
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (67 bp):
GTACGTGACTTGGGAAGGTCACGAACTTTGAAAAGTTAGTGCTTAAGAAGGTAAGGCACTCTAAG
AA
Found at i:40774697 original size:108 final size:107
Alignment explanation
Indices: 40774530--40774822 Score: 331
Period size: 108 Copynumber: 2.7 Consensus size: 107
40774520 AAGTTCAAAG
** * * ** *
40774530 ATACCTTAAGAGATATGTGACCT-AAAATGGTCAAAAGCTTTGGAAAGCTTGACACTTGAGAATG
1 ATACCTTAA-AGATATGTGACCTGAAAA-GACCAAAAGCTTTCGAAAACTCAACACTTGAGAAGG
* * **
40774594 CAAGGTGTATCTTAAATGATACAAGGTGTATCTTAAGAGATGCA
64 CGAGGTGTATCTTAAAAGATACAAGGTGTATCTTAAGAGACACA
*
40774638 ATACCTTAAACGATATGTGACCTGAAAAGACCAAAAGCTTTCGAAAACTCAACCCTTGAGAAGGC
1 ATACCTTAAA-GATATGTGACCTGAAAAGACCAAAAGCTTTCGAAAACTCAACACTTGAGAAGGC
**
40774703 GAGGTGTATCTTAAAAGATATGAGGTGTATCTTAAGAGACACA
65 GAGGTGTATCTTAAAAGATACAAGGTGTATCTTAAGAGACACA
* * * * * *
40774746 ATACCTTAAAAGGTATATGACTTGAAAA-AGCTAACAGCTTTC-AAAAGCTCAACACTTCAGAAG
1 ATACCTT-AAAGATATGTGACCTGAAAAGA-CCAAAAGCTTTCGAAAA-CTCAACACTTGAGAAG
40774809 GCGAGGTGTATCTT
63 GCGAGGTGTATCTT
40774823 GAGAGATATG
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
107 6 0.04
108 146 0.92
109 7 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (107 bp):
ATACCTTAAAGATATGTGACCTGAAAAGACCAAAAGCTTTCGAAAACTCAACACTTGAGAAGGCG
AGGTGTATCTTAAAAGATACAAGGTGTATCTTAAGAGACACA
Found at i:40774948 original size:87 final size:86
Alignment explanation
Indices: 40774727--40775026 Score: 271
Period size: 87 Copynumber: 3.5 Consensus size: 86
40774717 AAGATATGAG
* * ** * * * * *
40774727 GTGTATCTTAAGAGACACAATACCTTAAAAGGTATATGACTTGAAAAA-GCTAACAGCTTTCAAA
1 GTGTATCTTAAAAGATATGATACCTT-AAAGGCATGTGACAT-AAAAAGGCTAAAAGCTTTAAAA
* * * * *
40774791 AGCTCAACACTTCAGAAGGCGAG
64 AGCTCAACGCTTGAAAAGGCAAT
* * * * * *
40774814 GTGTATCTTGAGAGATATGATACCTTAAGAGGTACGTGACCTGAAAAGGCTAAAAGCTTTAAAAA
1 GTGTATCTTAAAAGATATGATACCTTAA-AGGCATGTGACATAAAAAGGCTAAAAGCTTTAAAAA
* *
40774879 GCTTAACGCGTGAAAAGGCAAT
65 GCTCAACGCTTGAAAAGGCAAT
* * *
40774901 GTGTATCTTAAAAGATATGATACCTTAATAGGCATGTGTCATAAAAAGG-TCAAGAGCTTTGAAA
1 GTGTATCTTAAAAGATATGATACCTTAA-AGGCATGTGACATAAAAAGGCT-AAAAGCTTTAAAA
*
40774965 AGCTCGACGCTTGAAAAGGCAAT
64 AGCTCAACGCTTGAAAAGGCAAT
* * * *
40774988 GTATATATTAAAAGATACGATACCTTAAAAGCATGTGAC
1 GTGTATCTTAAAAGATATGATACCTTAAAGGCATGTGAC
40775027 CTGAAAATGT
Statistics
Matches: 175, Mismatches: 35, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
86 16 0.09
87 159 0.91
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (86 bp):
GTGTATCTTAAAAGATATGATACCTTAAAGGCATGTGACATAAAAAGGCTAAAAGCTTTAAAAAG
CTCAACGCTTGAAAAGGCAAT
Found at i:40775063 original size:86 final size:87
Alignment explanation
Indices: 40774868--40775069 Score: 262
Period size: 87 Copynumber: 2.3 Consensus size: 87
40774858 AAAGGCTAAA
* ** * * * * *
40774868 AGCTTTAAAAAGCTTAACGCGTGAAAAGGCAATGTGTATCTTAAAAGATATGATACCTTAATAGG
1 AGCTTTGAAAAGCTCGACGCTTGAAAAGGCAATGTATATATTAAAAGATACGATACCTTAATAAG
*
40774933 CATGTGTCATAAAAAGGTCAAG
66 CATGTGACATAAAAAGGTCAAG
40774955 AGCTTTGAAAAGCTCGACGCTTGAAAAGGCAATGTATATATTAAAAGATACGATACCTTAA-AAG
1 AGCTTTGAAAAGCTCGACGCTTGAAAAGGCAATGTATATATTAAAAGATACGATACCTTAATAAG
* * *
40775019 CATGTGACCTGAAAATGTCAAG
66 CATGTGACATAAAAAGGTCAAG
* *
40775041 AGCTTTGAAAGGCTCGATGCTTGAGAAAG
1 AGCTTTGAAAAGCTCGACGCTTGA-AAAG
40775070 TGAGGTATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 42 0.42
87 58 0.58
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (87 bp):
AGCTTTGAAAAGCTCGACGCTTGAAAAGGCAATGTATATATTAAAAGATACGATACCTTAATAAG
CATGTGACATAAAAAGGTCAAG
Found at i:40777517 original size:59 final size:55
Alignment explanation
Indices: 40777426--40777538 Score: 172
Period size: 59 Copynumber: 2.0 Consensus size: 55
40777416 TGATATACAA
*
40777426 AAAAGAAGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACG
1 AAAAGAAGAAAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACG
*
40777481 AAAAGAAGGAAAAAAAAATTTTTTGGGTGCTAGCCTGTCAATGGTCGGCACCCAGTAC
1 AAAAGAA-G-AAAAAAAA--TTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTAC
40777539 AGTAAAAAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 7 0.13
56 1 0.02
57 8 0.15
59 36 0.69
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (55 bp):
AAAAGAAGAAAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACG
Found at i:40777586 original size:108 final size:107
Alignment explanation
Indices: 40777477--40777784 Score: 329
Period size: 108 Copynumber: 2.8 Consensus size: 107
40777467 CGGCACCCAG
* * * * *
40777477 TACGAAAAGAAGGAAAAAAAAATTTTTTGGGTGCTAGCCTGTCAATGGTCGGCACCCAGTACAGT
1 TACGAAAAAAAGTAAAAAAAAA--TTTT-GGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
*
40777542 AAAAAGTTTTTTTTACTTTTTTT-GTGTCAGTATC-AGGTATCAGTA
63 AAAAA-TTTTTTTTACTTTTTTTCGTGTCAATATCAAGGTATCAG-A
* *
40777587 TAC-AAAAAAAGTAAAAAAAAAAAATTTGGTACTGGCCTGTCAATGGCCGGCACCCAGCACAGTA
1 TACGAAAAAAAGT--AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTA
**
40777651 AATTTTTTTTTTTTTTACTTTTTTTCGTGTCAATATCAAGGTATCAGTA
64 AA----AATTTTTTTTACTTTTTTTCGTGTCAATATCAAGGTATCAG-A
* * *
40777700 TAACGAAAAAAAGTAAAAAATAATTTTGTTGCTGGGCCTGTCAATTGGCCAGCACCCAGCACAGT
1 T-ACGAAAAAAAGTAAAAAAAAATTTTGGTGCT-GGCCTGTCAA-TGGCCGGCACCCAGCACAGT
40777765 -AAAA-TTTTTTTACTTTTTTT
63 AAAAATTTTTTTTACTTTTTTT
40777785 TCNNNNNNNN
Statistics
Matches: 169, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
108 35 0.21
109 26 0.15
110 3 0.02
111 26 0.15
112 10 0.06
113 27 0.16
114 14 0.08
115 28 0.17
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (107 bp):
TACGAAAAAAAGTAAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
AATTTTTTTTACTTTTTTTCGTGTCAATATCAAGGTATCAGA
Found at i:40777765 original size:115 final size:111
Alignment explanation
Indices: 40777548--40777784 Score: 325
Period size: 115 Copynumber: 2.1 Consensus size: 111
40777538 CAGTAAAAAG
*
40777548 TTTTTTTTACTTTTTTTGTGTCAGTATCAGGTATCAGTATACAAAAAAAGTAAAAAAAAAAAATT
1 TTTTTTTTACTTTTTTTGTGTCAATATCAGGTATCAGTATACAAAAAAAGT-AAAAAAAAAAATT
*
40777613 TGGTACTGGCCTGTCAATGGCCGGCACCCAGCACAGT-AAATTTTTT
65 TGGTACTGGCCTGTCAATGGCCAGCACCCAGCACAGTAAAATTTTTT
*
40777659 TTTTTTTTACTTTTTTTCGTGTCAATATCAAGGTATCAGTATAACGAAAAAAAGT-AAAAAATAA
1 TTTTTTTTACTTTTTTT-GTGTCAATATC-AGGTATCAGTAT-AC-AAAAAAAGTAAAAAAAAAA
* * *
40777723 TTTTGTTGCTGGGCCTGTCAATTGGCCAGCACCCAGCACAGTAAAATTTTTT
62 ATTTGGTACT-GGCCTGTCAA-TGGCCAGCACCCAGCACAGTAAAATTTTTT
40777775 TACTTTTTTT
1 T--TTTTTTT
40777785 TCNNNNNNNN
Statistics
Matches: 111, Mismatches: 6, Indels: 11
0.87 0.05 0.09
Matches are distributed among these distances:
111 17 0.15
112 10 0.09
113 27 0.24
114 12 0.11
115 28 0.25
116 10 0.09
118 7 0.06
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (111 bp):
TTTTTTTTACTTTTTTTGTGTCAATATCAGGTATCAGTATACAAAAAAAGTAAAAAAAAAAATTT
GGTACTGGCCTGTCAATGGCCAGCACCCAGCACAGTAAAATTTTTT
Found at i:40778051 original size:19 final size:18
Alignment explanation
Indices: 40778027--40778069 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40778017 TCCATTAAAT
40778027 AAATATTAAAAAAAGAAAA
1 AAATATTAAAAAAA-AAAA
* *
40778046 AAATA-TAAAAATAAAAG
1 AAATATTAAAAAAAAAAA
40778063 AAATATT
1 AAATATT
40778070 TACATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATATTAAAAAAAAAAA
Found at i:40778111 original size:13 final size:13
Alignment explanation
Indices: 40778093--40778117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40778083 TTAAGAAAGT
40778093 AAAAATTAAAATA
1 AAAAATTAAAATA
40778106 AAAAATTAAAAT
1 AAAAATTAAAAT
40778118 TGTCGTGATC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAAATA
Found at i:40779243 original size:14 final size:15
Alignment explanation
Indices: 40779211--40779243 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
40779201 GAAAAAGATT
40779211 GAAAATAGAGATAAA
1 GAAAATAGAGATAAA
40779226 -AAAATAGAGA-AAA
1 GAAAATAGAGATAAA
40779239 GAAAA
1 GAAAA
40779244 GTTTGAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (15 bp):
GAAAATAGAGATAAA
Found at i:40779294 original size:15 final size:16
Alignment explanation
Indices: 40779260--40779296 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40779250 ATAAAAGGTG
*
40779260 ATTTTTTGTGTTTATC
1 ATTTTTTATGTTTATC
40779276 ATTTTTTATGTTTAT-
1 ATTTTTTATGTTTATC
40779291 ATTTTT
1 ATTTTT
40779297 ATGCATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.73
Consensus pattern (16 bp):
ATTTTTTATGTTTATC
Found at i:40779929 original size:3 final size:3
Alignment explanation
Indices: 40779921--40779975 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
40779911 ATTTTTACAC
* * * * *
40779921 TAT TAT TAT TAT TAT TGT T-T TA- AAT TAT TAT TAT TAC TAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40779967 TAT TAT TAT
1 TAT TAT TAT
40779976 AACCATGCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 3 0.07
3 40 0.93
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:40780060 original size:2 final size:2
Alignment explanation
Indices: 40780055--40780123 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
40780045 ACATTTTCTT
* * * *
40780055 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA CA TT TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
40780097 TA CA TA TT TT TA CA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40780124 CTTCATGGTT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40785350 original size:13 final size:13
Alignment explanation
Indices: 40785321--40785358 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
40785311 GTGATGTGAA
40785321 AAAATGAAAAGATG
1 AAAATGAAAA-ATG
40785335 AAAATGAAAAATG
1 AAAATGAAAAATG
40785348 AAAATGAAAAA
1 AAAATGAAAAA
40785359 GTAAAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:40785364 original size:13 final size:14
Alignment explanation
Indices: 40785321--40785367 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
40785311 GTGATGTGAA
40785321 AAAATG-AAAAGATG
1 AAAATGAAAAAG-TG
40785335 AAAATGAAAAA-TG
1 AAAATGAAAAAGTG
*
40785348 AAAATGAAAAAGTA
1 AAAATGAAAAAGTG
40785362 AAAATG
1 AAAATG
40785368 GAGAGGCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 13 0.43
14 13 0.43
15 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (14 bp):
AAAATGAAAAAGTG
Found at i:40786968 original size:50 final size:50
Alignment explanation
Indices: 40786901--40787291 Score: 262
Period size: 50 Copynumber: 7.8 Consensus size: 50
40786891 TTTGGCATTA
* * * * *
40786901 CAGTAGAATAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAGCGGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTG
* * * * ** * ***
40786951 TAGTGGAACAGATTGAAGCTACAACAGCAGATCTGGTTTCCCCGATATTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTG
* ** * * *
40787001 CAATTAAAAATATTAAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTG
* * * *
40787051 TAGTGGAACAGATTGAAGCCACAACGGCGGATC-TAGTTTCCCCGACATTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTA-TTTCCCTGGCGTTG
* ** * * * *
40787101 CAATTAAAAAGATTGAAGCCACAACGGCTGATCTTACTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTG
* * * ** ** *
40787151 CAGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTG
** * * * *** * *
40787201 CAGTTAAATAGATTGAAGCCACAATGGCGAATCTTGCCTCCCTGGTGGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTG
* * * * * *
40787251 TAGTGGAACAAATTGAAGTCACAACGACGAATCTTGTTTCC
1 CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTATTTCC
40787292 TCGACATTGC
Statistics
Matches: 249, Mismatches: 90, Indels: 4
0.73 0.26 0.01
Matches are distributed among these distances:
49 2 0.01
50 245 0.98
51 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTG
Found at i:40787032 original size:100 final size:100
Alignment explanation
Indices: 40786910--40787307 Score: 519
Period size: 100 Copynumber: 4.0 Consensus size: 100
40786900 ACAGTAGAAT
*
40786910 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACAA
* * *
40786975 CAGCAGATCTGGTTTCCCCGATATTGCAATTAAAA
66 CGGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
* * * * *
40787010 ATATTAAAGCCACAACGGCGGATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTGAAGCCACAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACAA
*
40787075 CGGCGGATCTAGTTTCCCCGACATTGCAATTAAAA
66 CGGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
* * * *
40787110 AGATTGAAGCCACAACGGCTGATCTTACTTCCCTGGCGGTGCAGTGGAATAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACAA
** * *
40787175 CGGCGGATCTGGTTTCCCTAACATTGCAGTTAAAT
66 CGGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
* * * * * *
40787210 AGATTGAAGCCACAATGGCGAATCTTGCCTCCCTGGTGGTGTAGTGGAACAAATTGAAG-TCACA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCT-ACA
* * * * *
40787274 ACGACGAATCTTGTTTCCTCGACATTGCAGTTAA
65 ACGGCGGATCTGGTTTCCCCGACATTGCAATTAA
40787308 GCAAATTGAA
Statistics
Matches: 257, Mismatches: 40, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
99 1 0.00
100 256 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (100 bp):
AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACAA
CGGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
Found at i:40787428 original size:41 final size:42
Alignment explanation
Indices: 40787329--40787430 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
40787319 AAAATAATCC
*
40787329 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCAGATCT
** ***
40787371 TATCTTTCTGAAGTTGCAGTAGAGCGGA-TCGCATGCAG-TCT
1 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAAT-CAGATCT
*
40787412 TATCTCCCTGAGGTTGCAG
1 TATCTCCCTGAAGTTGCAG
40787431 CGGAGTAGAC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
41 22 0.44
42 28 0.56
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (42 bp):
TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCAGATCT
Found at i:40788869 original size:3 final size:3
Alignment explanation
Indices: 40788861--40788912 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
40788851 ATTTTTACAC
* * * *
40788861 TAT TAT TAT TAT TGT T-T TA- AAT TAT TAT TAT TAT TAT AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40788907 TAT TAT
1 TAT TAT
40788913 AACCATGCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 3 0.07
3 39 0.93
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:40788879 original size:22 final size:22
Alignment explanation
Indices: 40788853--40788895 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40788843 CTTCTGTTAT
*
40788853 TTTTACACTATTATTATTATTG
1 TTTTAAACTATTATTATTATTG
*
40788875 TTTTAAATTATTATTATTATT
1 TTTTAAACTATTATTATTATT
40788896 ATAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTAAACTATTATTATTATTG
Found at i:40788979 original size:32 final size:29
Alignment explanation
Indices: 40788942--40789007 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
40788932 TACATTTGAA
* *
40788942 ATATACGTACATATTGTTTTTATAGTTTATAT
1 ATATACGTACAT-TT-TCTTTATA-TATATAT
*
40788974 ATATACTTACATTTTCTTTATATATATAT
1 ATATACGTACATTTTCTTTATATATATAT
40789003 ATATA
1 ATATA
40789008 TTTATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.35
30 7 0.23
31 2 0.06
32 11 0.35
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.53
Consensus pattern (29 bp):
ATATACGTACATTTTCTTTATATATATAT
Found at i:40789013 original size:12 final size:12
Alignment explanation
Indices: 40788992--40789027 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40788982 ACATTTTCTT
*
40788992 TATATATATATA
1 TATATTTATATA
40789004 TATATTTATATA
1 TATATTTATATA
*
40789016 TACATTTATATA
1 TATATTTATATA
40789028 CATACATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATTTATATA
Found at i:40796644 original size:217 final size:217
Alignment explanation
Indices: 40796269--40796662 Score: 664
Period size: 217 Copynumber: 1.8 Consensus size: 217
40796259 GCAATTTAAA
*
40796269 AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATTCT
1 AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* *
40796334 ATCTCCCTAAAGTCGTAGTGGAGCGGATTAAAATAACAGATCTTATCTCTCTGAAGTTGTAGAGA
66 ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATAACAGATCTTATCTCTCTGAAGTTGCAGAGA
*
40796399 GCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAGCCTTAT
131 GCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAGCCTTAT
40796464 CCTCCTGAATTTGTAGTGAGGC
196 CCTCCTGAATTTGTAGTGAGGC
*
40796486 AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCAATAATCCT
1 AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* * * *
40796551 ATCTCCTTGAAA-TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAG
66 ATCTCCCT-AAAGTCGCAGTGGAGCGGATTAAAATAACAGATCTTATCTCTCTGAAGTTGCAGAG
* * *
40796615 AGCAGATCGCATCGGGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGAC
130 AGCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGAC
40796663 CCAAGAAAGC
Statistics
Matches: 164, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
217 161 0.98
218 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (217 bp):
AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATAACAGATCTTATCTCTCTGAAGTTGCAGAGA
GCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAGCCTTAT
CCTCCTGAATTTGTAGTGAGGC
Found at i:40796681 original size:45 final size:44
Alignment explanation
Indices: 40796286--40796791 Score: 265
Period size: 44 Copynumber: 11.6 Consensus size: 44
40796276 AGATGGCGAA
* * * * *
40796286 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAACAAG
* * * * * *
40796331 TC-TATCTCCCTAAAGTCGTAGTGGAGCGGA-TTAAAATAAC-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGA-AACAAG
* * * * * *
40796373 ATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TC--GCATCTAG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAACAAG
* *
40796414 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACT-AAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAACAAG
* * * * **
40796458 CCTTATC-CTCCTGAATTTGTAGT-GAGGCAGACTGAAGATGGCGAA-
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGA-AAC-AAG
** * * *
40796503 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCAATAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAACAAG
* * * ** * *
40796547 TCCTATCTCCTTGAAATTGCAGTGGAGTGGA-TTAA-AATCACAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAACA-AG
* * * * **
40796590 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TC--GCATCGGG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAACAAG
* * *
40796631 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAAAGCGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA-CAAG
*
40796676 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTCAAGAAATCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA-CAAG
* * * * * *
40796721 TCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAAATAAACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAACAAG
* * *
40796765 TCTCATCTCCCTAAAGTTGTAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
40796792 TGGATTAGAA
Statistics
Matches: 349, Mismatches: 86, Indels: 53
0.72 0.18 0.11
Matches are distributed among these distances:
40 41 0.12
41 19 0.05
42 7 0.02
43 27 0.08
44 140 0.40
45 110 0.32
46 5 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAACAAG
Found at i:40797328 original size:19 final size:19
Alignment explanation
Indices: 40797304--40797376 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
40797294 AATCTTCAAG
40797304 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40797323 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40797342 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40797361 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40797377 AGATGTGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40797627 original size:23 final size:23
Alignment explanation
Indices: 40797583--40797627 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40797573 TCTTATTTTG
* *
40797583 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
40797606 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
40797628 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:40797673 original size:15 final size:16
Alignment explanation
Indices: 40797647--40797679 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
40797637 TTTTCCCTTA
40797647 TTATTAATTTTCAAAT
1 TTATTAATTTTCAAAT
40797663 TTATT-ATTTTCAAAT
1 TTATTAATTTTCAAAT
40797678 TT
1 TT
40797680 GTTTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTAATTTTCAAAT
Found at i:40797881 original size:7 final size:7
Alignment explanation
Indices: 40797865--40797902 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
40797855 CATCATCATC
40797865 ATTA-TT
1 ATTATTT
40797871 ATTATTT
1 ATTATTT
40797878 ATTATTT
1 ATTATTT
40797885 ATTATTT
1 ATTATTT
40797892 ATTTATTT
1 A-TTATTT
40797900 ATT
1 ATT
40797903 TATTCATGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTATTT
Found at i:40797886 original size:4 final size:4
Alignment explanation
Indices: 40797872--40797906 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
40797862 ATCATTATTA
40797872 TTAT TTA- TTAT TTA- TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
40797907 CATGCGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:40801751 original size:9 final size:9
Alignment explanation
Indices: 40801676--40801904 Score: 76
Period size: 10 Copynumber: 23.8 Consensus size: 9
40801666 AATATTTTCA
*
40801676 ATAAGAAATC
1 ATAA-AAATT
40801686 ATAAAAATT
1 ATAAAAATT
*
40801695 AATAAAATATA
1 -ATAAAA-ATT
40801706 ATAAAAATAT
1 ATAAAAAT-T
**
40801716 ATTGAAATT
1 ATAAAAATT
*
40801725 ATTAAAATT
1 ATAAAAATT
*
40801734 GACACAAAATT
1 -ATA-AAAATT
40801745 ATAAAAA--
1 ATAAAAATT
* *
40801752 ACTATATATT
1 A-TAAAAATT
40801762 ATAAAAA-T
1 ATAAAAATT
40801770 ATAATAAATT
1 ATAA-AAATT
*
40801780 CTAATAAATT
1 ATAA-AAATT
* *
40801790 TTTAAAATT
1 ATAAAAATT
40801799 AATAAAACAAATT
1 -AT--AA-AAATT
40801812 -T-AAAATAT
1 ATAAAAAT-T
*
40801820 ATAAAATTTT
1 ATAAAA-ATT
* *
40801830 ACAAAAACGT
1 ATAAAAA-TT
*
40801840 AAAAGAAATT
1 ATAA-AAATT
40801850 ATTAAAAACTT
1 A-TAAAAA-TT
40801861 ATAAAAATT
1 ATAAAAATT
40801870 ATTAAAAA-T
1 A-TAAAAATT
40801879 ATAAAAA-T
1 ATAAAAATT
40801887 ATAAAAAATT
1 AT-AAAAATT
40801897 ATTAAAAA
1 A-TAAAAA
40801905 AATATATTTA
Statistics
Matches: 168, Mismatches: 25, Indels: 52
0.69 0.10 0.21
Matches are distributed among these distances:
7 5 0.03
8 20 0.12
9 42 0.25
10 76 0.45
11 19 0.11
12 1 0.01
13 5 0.03
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:40801892 original size:7 final size:8
Alignment explanation
Indices: 40801860--40801893 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
40801850 ATTAAAAACT
40801860 TATAAAAA
1 TATAAAAA
40801868 TTATTAAAAA
1 -TA-TAAAAA
40801878 TATAAAAA
1 TATAAAAA
40801886 TATAAAAA
1 TATAAAAA
40801894 ATTATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 14 0.58
9 4 0.17
10 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TATAAAAA
Found at i:40802632 original size:20 final size:21
Alignment explanation
Indices: 40802592--40802634 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
40802582 TTAAAAATAT
* *
40802592 TTATAAGGTTTTATTATTTTA
1 TTATAAGGTTTTATAAGTTTA
40802613 TTATAA-GTTTTATAAGTTTA
1 TTATAAGGTTTTATAAGTTTA
40802633 TT
1 TT
40802635 TAAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
TTATAAGGTTTTATAAGTTTA
Found at i:40804456 original size:11 final size:11
Alignment explanation
Indices: 40804410--40804475 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
40804400 AAATAAAAGG
40804410 AAAAGAAAGAA
1 AAAAGAAAGAA
** * *
40804421 AGGACAAACAA
1 AAAAGAAAGAA
* * *
40804432 AATAGAAGGGA
1 AAAAGAAAGAA
40804443 AAAAGAAAGAA
1 AAAAGAAAGAA
*
40804454 AAAGGAAAGAA
1 AAAAGAAAGAA
40804465 AAAGAGAAAGA
1 AAA-AGAAAGA
40804476 CCAAAGCTAG
Statistics
Matches: 39, Mismatches: 15, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
11 33 0.85
12 6 0.15
ACGTcount: A:0.71, C:0.03, G:0.24, T:0.02
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:40806278 original size:57 final size:60
Alignment explanation
Indices: 40806185--40806324 Score: 189
Period size: 57 Copynumber: 2.4 Consensus size: 60
40806175 ACCCTAATTC
* * * *
40806185 GGATTACCCGTCCGGGTTAAATCTATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGAGCTATTTTCCACATATTCTTCGGGAGGGCTATATCGATA
40806243 -GATCACCCGTCCGGGCTAGAGCT-TTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGAGCTATTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA
40806304 GGATCACCCGTCCGGGCTAGA
1 GGATCACCCGTCCGGGCTAGA
40806325 TCCTTTTTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
56 5 0.07
57 45 0.62
60 1 0.01
61 1 0.01
62 20 0.28
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGAGCTATTTTCCACATATTCTTCGGGAGGGCTATATCGATA
Found at i:40810338 original size:20 final size:20
Alignment explanation
Indices: 40810313--40810357 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
40810303 TGATAAGATT
*
40810313 GATACCAAGATATAAT-TATC
1 GATACCAA-ATAAAATGTATC
40810333 GATACCAAATAAAATGTATC
1 GATACCAAATAAAATGTATC
40810353 GATAC
1 GATAC
40810358 TGGATTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (20 bp):
GATACCAAATAAAATGTATC
Done.