Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 98 of 141
Found at i:27813026 original size:16 final size:16
Alignment explanation
Indices: 27813005--27813072 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
27812995 TTTGGTTCGC
27813005 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
27813021 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
27813037 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
27813053 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
27813069 TGTA
1 TGTA
27813073 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:27813328 original size:16 final size:16
Alignment explanation
Indices: 27813288--27813342 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
27813278 TTAATCATAT
*
27813288 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
27813304 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
27813319 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
27813337 -TAAAAT
1 TTAAAAT
27813343 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:27813335 original size:18 final size:17
Alignment explanation
Indices: 27813308--27813342 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27813298 TTTTTATTAA
*
27813308 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
27813326 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
27813343 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:27813455 original size:18 final size:17
Alignment explanation
Indices: 27813428--27813462 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27813418 TTACTATTAA
*
27813428 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
27813446 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
27813463 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:27813504 original size:120 final size:120
Alignment explanation
Indices: 27813291--27813761 Score: 861
Period size: 120 Copynumber: 3.9 Consensus size: 120
27813281 ATCATATTTA
*
27813291 AACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
27813356 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
27813411 AACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
27813476 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
27813531 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
27813596 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
27813651 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
27813716 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAA
27813762 NNNNNNNNNN
Statistics
Matches: 338, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 338 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:27815973 original size:15 final size:15
Alignment explanation
Indices: 27815949--27815978 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27815939 GGAGGGTAAA
*
27815949 ACAGAGAGCAAATCG
1 ACAGAAAGCAAATCG
27815964 ACAGAAAGCAAATCG
1 ACAGAAAGCAAATCG
27815979 GCCAAAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.20, G:0.23, T:0.07
Consensus pattern (15 bp):
ACAGAAAGCAAATCG
Found at i:27818298 original size:28 final size:28
Alignment explanation
Indices: 27818266--27818353 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
27818256 GCGGTGCCAT
27818266 CTCGCATCTTGCCTCTTTACAGAGTCAG
1 CTCGCATCTTGCCTCTTTACAGAGTCAG
** * * ** * * * *
27818294 CTCGCCCCCTGCCACTTCGCGGTGCCAT
1 CTCGCATCTTGCCTCTTTACAGAGTCAG
27818322 CTCGCATCTTGCCTCTTTACAGAGTCAG
1 CTCGCATCTTGCCTCTTTACAGAGTCAG
27818350 CTCG
1 CTCG
27818354 TCAGCTCGCA
Statistics
Matches: 40, Mismatches: 20, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.14, C:0.39, G:0.19, T:0.28
Consensus pattern (28 bp):
CTCGCATCTTGCCTCTTTACAGAGTCAG
Found at i:27818330 original size:56 final size:56
Alignment explanation
Indices: 27818244--27818430 Score: 266
Period size: 56 Copynumber: 3.2 Consensus size: 56
27818234 GCAGTTCACA
27818244 CCCTGCCACTTCGCGGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTCGCC
1 CCCTGCCACTTCGCGGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTCGCC
27818300 CCCTGCCACTTCGCGGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTCGTCAGCTCGC
1 CCCTGCCACTTCGCGGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAG--C-TC-G--C-C
* * *
27818363 ACCCTGCCACTTCGCAGTGCCATCTCGCATCTTGCCTCTTTGCAGAGTCAGCTCGCA
1 -CCCTGCCACTTCGCGGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTCGCC
*
27818420 CCTTGCCACTT
1 CCCTGCCACTT
27818431 TGTGGAGTCA
Statistics
Matches: 119, Mismatches: 4, Indels: 16
0.86 0.03 0.12
Matches are distributed among these distances:
56 60 0.50
58 2 0.02
59 2 0.02
60 2 0.02
61 2 0.02
62 2 0.02
63 1 0.01
64 48 0.40
ACGTcount: A:0.13, C:0.40, G:0.19, T:0.27
Consensus pattern (56 bp):
CCCTGCCACTTCGCGGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTCGCC
Found at i:27818369 original size:64 final size:64
Alignment explanation
Indices: 27818289--27818417 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
27818279 TCTTTACAGA
* *
27818289 GTCAGCTCGCCCCCTGCCACTTCGCGGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTC
1 GTCAGCTCGCACCCTGCCACTTCGCAGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTC
*
27818353 GTCAGCTCGCACCCTGCCACTTCGCAGTGCCATCTCGCATCTTGCCTCTTTGCAGAGTCAGCTC
1 GTCAGCTCGCACCCTGCCACTTCGCAGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTC
27818417 G
1 G
27818418 CACCTTGCCA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.13, C:0.40, G:0.21, T:0.26
Consensus pattern (64 bp):
GTCAGCTCGCACCCTGCCACTTCGCAGTGCCATCTCGCATCTTGCCTCTTTACAGAGTCAGCTC
Found at i:27818440 original size:28 final size:28
Alignment explanation
Indices: 27818353--27818432 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
27818343 GAGTCAGCTC
* * *
27818353 GTCAGCTCGCACCCTGCCACTTCGCAGT
1 GTCAGCTCGCACCTTGCCACTTTGCAGA
* * * *
27818381 GCCATCTCGCATCTTGCCTCTTTGCAGA
1 GTCAGCTCGCACCTTGCCACTTTGCAGA
27818409 GTCAGCTCGCACCTTGCCACTTTG
1 GTCAGCTCGCACCTTGCCACTTTG
27818433 TGGAGTCAAC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.14, C:0.39, G:0.20, T:0.28
Consensus pattern (28 bp):
GTCAGCTCGCACCTTGCCACTTTGCAGA
Found at i:27818452 original size:28 final size:28
Alignment explanation
Indices: 27818353--27818457 Score: 86
Period size: 28 Copynumber: 3.8 Consensus size: 28
27818343 GAGTCAGCTC
* * * * *
27818353 GTCAGCTCGCACCCTGCCACTTCGCAGT
1 GTCAACTCGCATCTTGCCACTTTGCAGA
* * *
27818381 GCCATCTCGCATCTTGCCTCTTTGCAGA
1 GTCAACTCGCATCTTGCCACTTTGCAGA
* * **
27818409 GTCAGCTCGCACCTTGCCACTTTGTGGA
1 GTCAACTCGCATCTTGCCACTTTGCAGA
*
27818437 GTCAACTTGCATCTTG-CACTT
1 GTCAACTCGCATCTTGCCACTT
27818458 GACACTTCGC
Statistics
Matches: 61, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
27 5 0.08
28 56 0.92
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.30
Consensus pattern (28 bp):
GTCAACTCGCATCTTGCCACTTTGCAGA
Found at i:27823594 original size:21 final size:21
Alignment explanation
Indices: 27823556--27823652 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
27823546 ACGTCGACAG
*
27823556 AAGCTCA-AA-AGCTGAATAA
1 AAGCTCATAAGAGCTAAATAA
*
27823575 AAGCTCATAAGAGCTAAATAG
1 AAGCTCATAAGAGCTAAATAA
* * * *
27823596 AAGCTCGTAAGAACTAAACAG
1 AAGCTCATAAGAGCTAAATAA
* *
27823617 AAGCTCGTAAGAACTAAA-AA
1 AAGCTCATAAGAGCTAAATAA
27823637 GAAGCTCATAAGAGCT
1 -AAGCTCATAAGAGCT
27823653 GATCCACCCA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.10
20 3 0.04
21 57 0.85
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (21 bp):
AAGCTCATAAGAGCTAAATAA
Found at i:27824169 original size:17 final size:16
Alignment explanation
Indices: 27824149--27824196 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
27824139 CTTAATTAGT
27824149 TAATCTATCAAATTAA
1 TAATCTATCAAATTAA
* *
27824165 CTAATTTTCTCAAATTAA
1 -TAA-TCTATCAAATTAA
27824183 TAATCTATCTAAAT
1 TAATCTATC-AAAT
27824197 ATTATATGCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.16
17 10 0.40
18 11 0.44
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATCTATCAAATTAA
Found at i:27828420 original size:19 final size:19
Alignment explanation
Indices: 27828396--27828449 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
27828386 TTATAAATTT
27828396 ATTTTACGATTTTTATAAA
1 ATTTTACGATTTTTATAAA
* *
27828415 ATTTTACAATTTTTTTATAAT
1 ATTTTACGA--TTTTTATAAA
*
27828436 TTTTTACGATTTTT
1 ATTTTACGATTTTT
27828450 GATATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 13 0.45
21 16 0.55
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (19 bp):
ATTTTACGATTTTTATAAA
Found at i:27828438 original size:9 final size:9
Alignment explanation
Indices: 27828426--27828508 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 9
27828416 TTTTACAATT
27828426 TTTTTATAA
1 TTTTTATAA
27828435 TTTTT-TACGA
1 TTTTTATA--A
27828445 TTTTTGAT-A
1 TTTTT-ATAA
*
27828454 TTTTTATAT
1 TTTTTATAA
27828463 TTTTTATTAAA
1 TTTTTA-T-AA
* *
27828474 ATTTAATAA
1 TTTTTATAA
27828483 TTTTTATAA
1 TTTTTATAA
* *
27828492 CTTTTATTGA
1 TTTTTA-TAA
27828502 TTTTTAT
1 TTTTTAT
27828509 CTTCTTCTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
8 4 0.07
9 32 0.56
10 15 0.26
11 5 0.09
12 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:27828456 original size:19 final size:19
Alignment explanation
Indices: 27828397--27828458 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
27828387 TATAAATTTA
**
27828397 TTTTACGATTTTTATAAAA
1 TTTTACGATTTTTATAATT
*
27828416 TTTTACAATTTTTTTATAATT
1 TTTTACGA--TTTTTATAATT
27828437 TTTTACGATTTTTGAT-ATT
1 TTTTACGATTTTT-ATAATT
27828456 TTT
1 TTT
27828459 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 18 0.50
20 2 0.06
21 16 0.44
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTACGATTTTTATAATT
Found at i:27828477 original size:40 final size:40
Alignment explanation
Indices: 27828378--27828498 Score: 99
Period size: 40 Copynumber: 3.1 Consensus size: 40
27828368 TCTATATTCC
* *
27828378 TATATATTTTA-TAAATTTATTTTACGATTTTTATAAAATTT
1 TATATTTTTTATTAAAATT-TTTTACGATTTTTAT-AAATTT
* * * *
27828419 TACAATTTTT-TTATAATTTTTTACGATTTTTGAT-ATTTT
1 TATATTTTTTATTAAAATTTTTTACGATTTTT-ATAAATTT
** *
27828458 TATATTTTTTATTAAAATTTAATA--ATTTTTATAACTTT
1 TATATTTTTTATTAAAATTTTTTACGATTTTTATAAATTT
27828496 TAT
1 TAT
27828499 TGATTTTTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
37 2 0.03
38 13 0.20
39 12 0.19
40 23 0.36
41 14 0.22
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (40 bp):
TATATTTTTTATTAAAATTTTTTACGATTTTTATAAATTT
Found at i:27829287 original size:21 final size:20
Alignment explanation
Indices: 27829245--27829284 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
27829235 AGCCTGGCCA
27829245 TAAATATATATTTTTATTTT
1 TAAATATATATTTTTATTTT
*
27829265 TAAA-ATATTTTTTTATTTT
1 TAAATATATATTTTTATTTT
27829284 T
1 T
27829285 TTATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TAAATATATATTTTTATTTT
Found at i:27829313 original size:26 final size:27
Alignment explanation
Indices: 27829257--27829315 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
27829247 AATATATATT
* ** *
27829257 TTTATTTTTAAAATATTTTTTTATTTT
1 TTTATTTTTAAAATAATTTTTTAGGTG
27829284 TTTATTTTTAAAATAATTTTTT-GGTG
1 TTTATTTTTAAAATAATTTTTTAGGTG
27829310 TTTATT
1 TTTATT
27829316 AAAAATGGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTATTTTTAAAATAATTTTTTAGGTG
Found at i:27831707 original size:10 final size:10
Alignment explanation
Indices: 27831692--27831719 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
27831682 GTACTATGAT
27831692 TGATATTGGA
1 TGATATTGGA
27831702 TGATATTGGA
1 TGATATTGGA
27831712 TGATATTG
1 TGATATTG
27831720 AATGTGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (10 bp):
TGATATTGGA
Found at i:27838178 original size:29 final size:29
Alignment explanation
Indices: 27838146--27838242 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
27838136 ATAGGTTAGA
27838146 GGCTTATTTAACTACAAAAATAGTATAAG
1 GGCTTATTTAACTACAAAAATAGTATAAG
* *
27838175 GGCTTCTTTAA--A-AAAATTATAG-ACTAGG
1 GGCTTATTTAACTACAAAA--ATAGTA-TAAG
* *
27838203 GGCTTATTAAACTACGAAAATAGTATAAG
1 GGCTTATTTAACTACAAAAATAGTATAAG
*
27838232 GGCTTCTTTAA
1 GGCTTATTTAA
27838243 ACAAAGAGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 16 0.30
29 26 0.49
30 2 0.04
31 3 0.06
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (29 bp):
GGCTTATTTAACTACAAAAATAGTATAAG
Found at i:27846989 original size:26 final size:26
Alignment explanation
Indices: 27846960--27847018 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
27846950 CATTGCTTTT
*
27846960 GAAAAATGTTTTTGAGAAGTGCTCTG
1 GAAAAATGCTTTTGAGAAGTGCTCTG
* * *
27846986 GAAAAGTGCTTTTGAGAAGTGCTTTT
1 GAAAAATGCTTTTGAGAAGTGCTCTG
27847012 GAAAAAT
1 GAAAAAT
27847019 TTGAGTGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.34
Consensus pattern (26 bp):
GAAAAATGCTTTTGAGAAGTGCTCTG
Found at i:27847005 original size:13 final size:13
Alignment explanation
Indices: 27846953--27847016 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
27846943 AGTTCTTCAT
*
27846953 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
* *
27846966 TGTTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
27846979 TGCTCTGGAAAAG
1 TGCTTTTGAAAAG
*
27846992 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
27847005 TGCTTTTGAAAA
1 TGCTTTTGAAAA
27847017 ATTTGAGTGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:27849615 original size:31 final size:33
Alignment explanation
Indices: 27849577--27849639 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
27849567 GAGACGAGGG
* *
27849577 CAAAGAACCAGC-G-TAGCAGAGAGCAGAGAAA
1 CAAAGAACCAGCAGAGAGCAGAGAGCAAAGAAA
27849608 CAAAGAACCAGCAGAGAGCAGAGAGCAAAGAA
1 CAAAGAACCAGCAGAGAGCAGAGAGCAAAGAA
27849640 GGGCGTTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 12 0.43
32 1 0.04
33 15 0.54
ACGTcount: A:0.51, C:0.19, G:0.29, T:0.02
Consensus pattern (33 bp):
CAAAGAACCAGCAGAGAGCAGAGAGCAAAGAAA
Found at i:27849623 original size:26 final size:25
Alignment explanation
Indices: 27849591--27849639 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
27849581 GAACCAGCGT
27849591 AGCAGAGAGCAGAGAAACAAAGAACC
1 AGCAGAGAGCAGAG-AACAAAGAACC
*
27849617 AGCAGAGAGCAGAGAGCAAAGAA
1 AGCAGAGAGCAGAGAACAAAGAA
27849640 GGGCGTTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.53, C:0.16, G:0.31, T:0.00
Consensus pattern (25 bp):
AGCAGAGAGCAGAGAACAAAGAACC
Found at i:27854312 original size:21 final size:22
Alignment explanation
Indices: 27854282--27854326 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
27854272 GAGCAAATTG
27854282 TTGATTCTATTTCCTTTTTG-AT
1 TTGATTCTA-TTCCTTTTTGTAT
*
27854304 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
27854325 TT
1 TT
27854327 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:27855073 original size:35 final size:34
Alignment explanation
Indices: 27854986--27855085 Score: 141
Period size: 32 Copynumber: 3.0 Consensus size: 34
27854976 TTGTTCTACA
* *
27854986 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAG
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
*
27855020 AAATGAT--GTGAACAGGAAAGATTCCCTGCAAC
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
*
27855052 AGAATAATGCGTGAACAGGAAATATTCCCTGCAA
1 A-AATAATGCGTGAACAGGAAAGATTCCCTGCAA
27855086 GAAAAGACAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
32 24 0.41
33 5 0.09
34 6 0.10
35 23 0.40
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (34 bp):
AAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
Found at i:27858635 original size:21 final size:22
Alignment explanation
Indices: 27858611--27858655 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
27858601 AGAAAAAGAG
27858611 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
27858632 AAATCAAAAAGGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
27858654 AA
1 AA
27858656 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:27861543 original size:35 final size:33
Alignment explanation
Indices: 27861456--27861694 Score: 277
Period size: 35 Copynumber: 7.1 Consensus size: 33
27861446 GTCCAAAAAG
* *
27861456 AAATAATACATGAACAGGAGAGATTCCCTGCAAG
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAA
*
27861490 AAATGAT-GTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAA-A
*
27861523 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAG
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAA
* *
27861557 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAA-A
*
27861590 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAG
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAA
* *
27861624 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAA-A
* * *
27861657 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGA
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAA-A
27861692 AAA
1 AAA
27861695 GACAAGTGAA
Statistics
Matches: 177, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
32 69 0.39
33 17 0.10
34 18 0.10
35 73 0.41
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (33 bp):
AAATAATCGTGAACAGGAGAGATTCCCTGCAAA
Found at i:27861564 original size:67 final size:67
Alignment explanation
Indices: 27861456--27861693 Score: 422
Period size: 67 Copynumber: 3.6 Consensus size: 67
27861446 GTCCAAAAAG
* * *
27861456 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
27861521 CA
66 CA
27861523 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
27861588 CA
66 CA
27861590 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
27861655 CA
66 CA
* * *
27861657 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAA
27861694 AGACAAGTGA
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 165 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (67 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
CA
Found at i:27862405 original size:18 final size:17
Alignment explanation
Indices: 27862382--27862439 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 17
27862372 TTTTGTTTAA
*
27862382 AATTAACCAAATTAGCCG
1 AATTAACCGAATTA-CCG
27862400 AATTAACCGAATTACCTG
1 AATTAACCGAATTACC-G
*
27862418 AATTACCCGAATTAACCG
1 AATTAACCGAATT-ACCG
27862436 AATT
1 AATT
27862440 GAATCACTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.06
18 31 0.86
19 3 0.08
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.26
Consensus pattern (17 bp):
AATTAACCGAATTACCG
Found at i:27862413 original size:27 final size:27
Alignment explanation
Indices: 27862382--27862439 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
27862372 TTTTGTTTAA
*
27862382 AATTAACC-AAATTAGCCGAATTAACCG
1 AATT-ACCTAAATTACCCGAATTAACCG
*
27862409 AATTACCTGAATTACCCGAATTAACCG
1 AATTACCTAAATTACCCGAATTAACCG
27862436 AATT
1 AATT
27862440 GAATCACTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.26
Consensus pattern (27 bp):
AATTACCTAAATTACCCGAATTAACCG
Found at i:27862420 original size:9 final size:8
Alignment explanation
Indices: 27862391--27862439 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 8
27862381 AAATTAACCA
27862391 AATTAGCCG
1 AATTA-CCG
27862400 AATTAACCG
1 AATT-ACCG
27862409 AATTACCTG
1 AATTACC-G
27862418 AATTACCCG
1 AATTA-CCG
27862427 AATTAACCG
1 AATT-ACCG
27862436 AATT
1 AATT
27862440 GAATCACTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 3 0.08
9 29 0.81
10 4 0.11
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (8 bp):
AATTACCG
Found at i:27862479 original size:37 final size:37
Alignment explanation
Indices: 27862438--27862512 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
27862428 ATTAACCGAA
* *
27862438 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAAAATTACATAAGTCT
*
27862475 TTGAATCAGTACATAATTAAAAAAATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAAAATTACATAAGTCT
27862512 T
1 T
27862513 GAAATTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAAAATTACATAAGTCT
Found at i:27862526 original size:37 final size:37
Alignment explanation
Indices: 27862438--27862529 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
27862428 ATTAACCGAA
* * * *
27862438 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATAAGTACATAATTAAAAAAATTACATAAGTCT
*
27862475 TTGAATCAGTACATAATTAAAAAAATTACATAAGTC-
1 TTGAATAAGTACATAATTAAAAAAATTACATAAGTCT
27862511 TTGAAATTAAG-ACATAATT
1 TTG-AA-TAAGTACATAATT
27862530 GAAATGTAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 3 0.06
37 43 0.88
38 3 0.06
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.34
Consensus pattern (37 bp):
TTGAATAAGTACATAATTAAAAAAATTACATAAGTCT
Found at i:27862670 original size:24 final size:23
Alignment explanation
Indices: 27862623--27862670 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
27862613 AACATGTGCC
* * *
27862623 TATTTATATATTATTTTTATTTT
1 TATTTATAAATTATTTGTAATTT
27862646 TATTTATTAAATTATTTGTAATTT
1 TATTTA-TAAATTATTTGTAATTT
27862670 T
1 T
27862671 TATGATTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTATAAATTATTTGTAATTT
Found at i:27862698 original size:18 final size:18
Alignment explanation
Indices: 27862675--27862728 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
27862665 AATTTTTATG
*
27862675 ATTGGGTTAGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
27862693 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
*
27862711 CTTGGGTTGGGATTGGGT
1 ATTGGGTTGGG-TTGGGT
27862729 TTAGGTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.13, C:0.02, G:0.46, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:27863057 original size:32 final size:32
Alignment explanation
Indices: 27862975--27863100 Score: 146
Period size: 32 Copynumber: 3.8 Consensus size: 32
27862965 TCGCACTATT
27862975 TGGCACGCATATTTGAACAAAACTCGCACATTCTA
1 TGGCACGCATA-TTGAAC--AACTCGCACATTCTA
* *
27863010 TGGCACACA-ATTTGAATAACTCGCACATTCTA
1 TGGCACGCATA-TTGAACAACTCGCACATTCTA
* * *
27863042 TGGCATGCATATTGAACAACTCACACATTTTA
1 TGGCACGCATATTGAACAACTCGCACATTCTA
* *
27863074 CGGCACGCATATTGAACAACTTGCACA
1 TGGCACGCATATTGAACAACTCGCACA
27863101 ACGATACGAC
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
32 63 0.80
33 1 0.01
34 7 0.09
35 8 0.10
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (32 bp):
TGGCACGCATATTGAACAACTCGCACATTCTA
Found at i:27863444 original size:51 final size:51
Alignment explanation
Indices: 27863375--27863603 Score: 287
Period size: 51 Copynumber: 4.5 Consensus size: 51
27863365 CAATGCCAGA
* * * * *
27863375 TCACACATAAAATTTTTACATAATTAGTATGCACAAACCTTGCATTCACAAT
1 TCACACATAGAA-CTTTACATAATTAGTACGCACATATCTTGCATTCACAAT
* * * *
27863427 TCACAGATAGAACTTTACATAATTAGTACACGCATATCTTGCATTCACAGT
1 TCACACATAGAACTTTACATAATTAGTACGCACATATCTTGCATTCACAAT
* * *
27863478 TCACACATAGAACTTTACAAAATCAGTATGCACATATCTTGCATTCACAAT
1 TCACACATAGAACTTTACATAATTAGTACGCACATATCTTGCATTCACAAT
* * * * *
27863529 TCATATATATAACTTTACATAATCAGTACGCACATATCTTGCATTCACAGT
1 TCACACATAGAACTTTACATAATTAGTACGCACATATCTTGCATTCACAAT
*
27863580 TCATACATAGAACTTTACATAATT
1 TCACACATAGAACTTTACATAATT
27863604 GACTGCCCAC
Statistics
Matches: 152, Mismatches: 25, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 142 0.93
52 10 0.07
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (51 bp):
TCACACATAGAACTTTACATAATTAGTACGCACATATCTTGCATTCACAAT
Found at i:27863565 original size:102 final size:102
Alignment explanation
Indices: 27863375--27863598 Score: 322
Period size: 102 Copynumber: 2.2 Consensus size: 102
27863365 CAATGCCAGA
* * * *
27863375 TCACACATAAAATTTTTACATAATTAGTATGCACAAACCTTGCATTCACAATTCACAGATAGAAC
1 TCACACATAGAA-CTTTACAAAATCAGTATGCACAAACCTTGCATTCACAATTCACAGATAGAAC
* *
27863440 TTTACATAATTAGTACACGCATATCTTGCATTCACAGT
65 TTTACATAATCAGTACACACATATCTTGCATTCACAGT
* * * * *
27863478 TCACACATAGAACTTTACAAAATCAGTATGCACATATCTTGCATTCACAATTCATATATATAACT
1 TCACACATAGAACTTTACAAAATCAGTATGCACAAACCTTGCATTCACAATTCACAGATAGAACT
*
27863543 TTACATAATCAGTACGCACATATCTTGCATTCACAGT
66 TTACATAATCAGTACACACATATCTTGCATTCACAGT
*
27863580 TCATACATAGAACTTTACA
1 TCACACATAGAACTTTACA
27863599 TAATTGACTG
Statistics
Matches: 108, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
102 97 0.90
103 11 0.10
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (102 bp):
TCACACATAGAACTTTACAAAATCAGTATGCACAAACCTTGCATTCACAATTCACAGATAGAACT
TTACATAATCAGTACACACATATCTTGCATTCACAGT
Found at i:27872574 original size:36 final size:36
Alignment explanation
Indices: 27872525--27872606 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
27872515 CATAGTTTGA
* * * *
27872525 CAAATTAATACAGTTTTCCGTATTAATATAGA-TCAC
1 CAAATTAACACAGTTTGCCATAATAATATA-ATTCAC
27872561 CAAATTAACACAGTTTGCCATAATAATATAATTCAC
1 CAAATTAACACAGTTTGCCATAATAATATAATTCAC
*
27872597 CAAGTTAACA
1 CAAATTAACA
27872607 TGGTTCACAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 1 0.03
36 39 0.98
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (36 bp):
CAAATTAACACAGTTTGCCATAATAATATAATTCAC
Found at i:27874901 original size:17 final size:18
Alignment explanation
Indices: 27874879--27874913 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27874869 ATTTGGGCCA
*
27874879 TGTGGG-CCACTCGAGTG
1 TGTGGGCCCACACGAGTG
27874896 TGTGGGCCCACACGAGTG
1 TGTGGGCCCACACGAGTG
27874914 AACTTCTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.20
Consensus pattern (18 bp):
TGTGGGCCCACACGAGTG
Found at i:27877166 original size:15 final size:15
Alignment explanation
Indices: 27877110--27877166 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
27877100 TTTAACCTAA
27877110 AATTA-TTAATTC-T
1 AATTATTTAATTCTT
*
27877123 AATTATTTTAATATTTT
1 AATTA-TTTAAT-TCTT
* *
27877140 ATTTAATTAATTCTT
1 AATTATTTAATTCTT
27877155 AATTATTTAATT
1 AATTATTTAATT
27877167 ATCTAATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 5 0.15
15 18 0.53
16 6 0.18
17 5 0.15
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTATTTAATTCTT
Found at i:27877179 original size:32 final size:31
Alignment explanation
Indices: 27877114--27877180 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
27877104 ACCTAAAATT
* * *
27877114 ATTAATTCTAATTATTTTAATATTTTATTTA
1 ATTAATTCTAATTATTTTAATATCTAATATA
27877145 ATTAATTCTTAATTA-TTTAATTATCTAATATA
1 ATTAATTC-TAATTATTTTAA-TATCTAATATA
27877177 ATTA
1 ATTA
27877181 CGATTTTCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTAATTCTAATTATTTTAATATCTAATATA
Found at i:27878382 original size:29 final size:30
Alignment explanation
Indices: 27878349--27878405 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
27878339 CAATTTGTGC
* *
27878349 TTTATTTTAAGTAATA-TATATGTTAAAAT
1 TTTATTTAAACTAATATTATATGTTAAAAT
*
27878378 TTTATTTAAACTATTATTATATGTTAAA
1 TTTATTTAAACTAATATTATATGTTAAA
27878406 GTTAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTATTTAAACTAATATTATATGTTAAAAT
Found at i:27885838 original size:66 final size:66
Alignment explanation
Indices: 27885728--27885867 Score: 219
Period size: 66 Copynumber: 2.1 Consensus size: 66
27885718 GAATACTATA
* *
27885728 TTTTGCAACGAAAATTTATGAGTTCTTAAATTTGAAAATTGTGATTTAGTTTGTAAAATCAGATA
1 TTTTGCAACGAAAATTTATGAGTTCTTAAATTTGAAAATCGTGATTTAGTTTGTAAAACCAGATA
27885793 G
66 G
* *
27885794 TTTTGCAGCGAAAAGTTT-TGAGTTCTTAAATTTGAAAATCGTGATTTAGTTTGTAAAACCATAT
1 TTTTGCAACGAAAA-TTTATGAGTTCTTAAATTTGAAAATCGTGATTTAGTTTGTAAAACCAGAT
27885858 AG
65 AG
*
27885860 GTTTGCAA
1 TTTTGCAA
27885868 TTTAAAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 64 0.96
67 3 0.04
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (66 bp):
TTTTGCAACGAAAATTTATGAGTTCTTAAATTTGAAAATCGTGATTTAGTTTGTAAAACCAGATA
G
Found at i:27889169 original size:24 final size:24
Alignment explanation
Indices: 27889140--27889193 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
27889130 ATTTTAACCC
*
27889140 ATAATTATTTGTATACAATTTTTA
1 ATAATTATTTGTATACAATGTTTA
27889164 ATAATTATTTGTATACAATGTTTA
1 ATAATTATTTGTATACAATGTTTA
27889188 ATAATT
1 ATAATT
27889194 TTTCAAAGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (24 bp):
ATAATTATTTGTATACAATGTTTA
Found at i:27900662 original size:18 final size:17
Alignment explanation
Indices: 27900639--27900691 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
27900629 AATCGTGTCG
27900639 TTCATTTCCAAAATATTA
1 TTCATTT-CAAAATATTA
*
27900657 TTCATTT-ACAAATCGTTA
1 TTCATTTCA-AAAT-ATTA
27900675 TTCAATTTCAAAATATT
1 TTC-ATTTCAAAATATT
27900692 TTCTTATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 1 0.03
17 4 0.14
18 15 0.52
19 8 0.28
20 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (17 bp):
TTCATTTCAAAATATTA
Found at i:27907500 original size:187 final size:187
Alignment explanation
Indices: 27907185--27907557 Score: 728
Period size: 187 Copynumber: 2.0 Consensus size: 187
27907175 TTGGTAAGCA
*
27907185 TGATACATGAATAAATGTTATGCTCATCCGTGCTTATAATGCTTATGCTATATGTGTATTTGGCT
1 TGATACATGAATAAATGTTATGCTCATCCATGCTTATAATGCTTATGCTATATGTGTATTTGGCT
27907250 AACATATTTGGTGTACATGCTTAGGCTTTGGCCAAGTAGTGGCTGGATTATGCCACGTTAAATTT
66 AACATATTTGGTGTACATGCTTAGGCTTTGGCCAAGTAGTGGCTGGATTATGCCACGTTAAATTT
27907315 ATAAGTTATGCATTGAAATGGCAAGTGCCTAATTGGACATATGCTTGTGATCATAAG
131 ATAAGTTATGCATTGAAATGGCAAGTGCCTAATTGGACATATGCTTGTGATCATAAG
*
27907372 TGATACATGAATAAATGTTGTGCTCATCCATGCTTATAATGCTTATGCTATATGTGTATTTGGCT
1 TGATACATGAATAAATGTTATGCTCATCCATGCTTATAATGCTTATGCTATATGTGTATTTGGCT
27907437 AACATATTTGGTGTACATGCTTAGGCTTTGGCCAAGTAGTGGCTGGATTATGCCACGTTAAATTT
66 AACATATTTGGTGTACATGCTTAGGCTTTGGCCAAGTAGTGGCTGGATTATGCCACGTTAAATTT
27907502 ATAAGTTATGCATTGAAATGGCAAGTGCCTAATTGGACATATGCTTGTGATCATAA
131 ATAAGTTATGCATTGAAATGGCAAGTGCCTAATTGGACATATGCTTGTGATCATAA
27907558 AAAGGGTTGT
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 184 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (187 bp):
TGATACATGAATAAATGTTATGCTCATCCATGCTTATAATGCTTATGCTATATGTGTATTTGGCT
AACATATTTGGTGTACATGCTTAGGCTTTGGCCAAGTAGTGGCTGGATTATGCCACGTTAAATTT
ATAAGTTATGCATTGAAATGGCAAGTGCCTAATTGGACATATGCTTGTGATCATAAG
Found at i:27907941 original size:43 final size:44
Alignment explanation
Indices: 27907880--27907991 Score: 190
Period size: 44 Copynumber: 2.6 Consensus size: 44
27907870 TTTGAGTACT
* *
27907880 TCTGATTAGTGACAAGTGATAAGTGGTCGC-TTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
27907923 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
27907967 TCTGATCAGTGACAAGTGACAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
27907992 ACAAGTGATA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
43 28 0.43
44 37 0.57
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:27907986 original size:7 final size:7
Alignment explanation
Indices: 27907974--27907999 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27907964 TTATCTGATC
27907974 AGTGACA
1 AGTGACA
27907981 AGTGACA
1 AGTGACA
27907988 AGTGACA
1 AGTGACA
27907995 AGTGA
1 AGTGA
27908000 TAAATGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (7 bp):
AGTGACA
Found at i:27910098 original size:43 final size:44
Alignment explanation
Indices: 27910037--27910148 Score: 190
Period size: 44 Copynumber: 2.6 Consensus size: 44
27910027 TTTGAGTACT
* *
27910037 TCTGATTAGTGACAAGTGATAAGTGGTCGC-TTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
27910080 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
27910124 TCTGATCAGTGACAAGTGACAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
27910149 ACAAGTGATA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
43 28 0.43
44 37 0.57
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:27910143 original size:7 final size:7
Alignment explanation
Indices: 27910131--27910156 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27910121 TTATCTGATC
27910131 AGTGACA
1 AGTGACA
27910138 AGTGACA
1 AGTGACA
27910145 AGTGACA
1 AGTGACA
27910152 AGTGA
1 AGTGA
27910157 TAAATGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (7 bp):
AGTGACA
Found at i:27915519 original size:51 final size:50
Alignment explanation
Indices: 27915420--27915538 Score: 193
Period size: 51 Copynumber: 2.4 Consensus size: 50
27915410 ACTTCTGATC
* *
27915420 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTGTCTGATCGGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
27915470 AGTGACAATTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
*
27915521 AGTGACAAGTGACAAGTG
1 AGTGACAAGTGATAAGTG
27915539 ATAAATGTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
50 22 0.35
51 41 0.65
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:27915526 original size:7 final size:7
Alignment explanation
Indices: 27915514--27915539 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27915504 TTATCTGATC
27915514 AGTGACA
1 AGTGACA
27915521 AGTGACA
1 AGTGACA
27915528 AGTGACA
1 AGTGACA
27915535 AGTGA
1 AGTGA
27915540 TAAATGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (7 bp):
AGTGACA
Found at i:27920756 original size:4 final size:4
Alignment explanation
Indices: 27920747--27921121 Score: 741
Period size: 4 Copynumber: 93.8 Consensus size: 4
27920737 TTCCCAACAT
27920747 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27920795 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27920843 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27920891 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27920939 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27920987 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
27921035 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27921083 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
27921122 TGGAGATTTT
Statistics
Matches: 369, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 369 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:27923165 original size:32 final size:32
Alignment explanation
Indices: 27923124--27923185 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
27923114 TTGGTTGGGG
*
27923124 TGAATGGAATAAGGCTGTAATGAAATAGAAAT
1 TGAATGGAATAAAGCTGTAATGAAATAGAAAT
*
27923156 TGAATGGAATAAAGCTGTAATGGAATAGAA
1 TGAATGGAATAAAGCTGTAATGAAATAGAA
27923186 CTGCAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.26, T:0.24
Consensus pattern (32 bp):
TGAATGGAATAAAGCTGTAATGAAATAGAAAT
Found at i:27923177 original size:16 final size:16
Alignment explanation
Indices: 27923126--27923182 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
27923116 GGTTGGGGTG
*
27923126 AATGGAATAAGGCTGT
1 AATGGAATAAAGCTGT
* **
27923142 AATGAAATAGAAATTG-
1 AATGGAATA-AAGCTGT
27923158 AATGGAATAAAGCTGT
1 AATGGAATAAAGCTGT
27923174 AATGGAATA
1 AATGGAATA
27923183 GAACTGCAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 4 0.12
16 25 0.78
17 3 0.09
ACGTcount: A:0.47, C:0.04, G:0.25, T:0.25
Consensus pattern (16 bp):
AATGGAATAAAGCTGT
Found at i:27923484 original size:17 final size:17
Alignment explanation
Indices: 27923429--27923491 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 17
27923419 ATATTTTAAC
27923429 ATAATTATTATT-AAAT
1 ATAATTATTATTAAAAT
*
27923445 ATAATTTAATAATATTCATAAT
1 ATAA-TT-AT--TATT-AAAAT
27923467 ATAATTATTATTAAAAT
1 ATAATTATTATTAAAAT
27923484 ATGAATTA
1 AT-AATTA
27923492 ATAAAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
16 4 0.11
17 8 0.21
18 11 0.29
20 6 0.16
21 2 0.05
22 7 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
ATAATTATTATTAAAAT
Found at i:27923591 original size:100 final size:100
Alignment explanation
Indices: 27923373--27923591 Score: 256
Period size: 100 Copynumber: 2.2 Consensus size: 100
27923363 TAATGAGATT
*
27923373 ATTATTAA-AT-ATAATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTTTAACATAATTA
1 ATTATTAATATAATAA-TTAATAAAAATAAAAAGTAAATAATTTAATCATATTTTAACAGAATTA
* *
27923436 TTATTAAATATAATTTAATAATATTCATAATATAATT
65 TTAATAAATATAA-TTAATAATATTCATAATATAATC
*
27923473 ATTATTAAAAT-ATGAATTAATAAAAATAAAAA-TAAATAATTTAATCATATTTTAACAGAATTA
1 ATTATTAATATAAT-AATTAATAAAAATAAAAAGTAAATAATTTAATCATATTTTAACAGAATTA
*
27923536 TTAATACAATTTAA-TAA-AATATAT-ATAACT-TAATAGC
65 TTAATA-AATATAATTAATAATAT-TCATAA-TATAAT--C
*
27923573 ATTCTTAATATAATAATTA
1 ATTATTAATATAATAATTA
27923592 TTATTTTAGG
Statistics
Matches: 105, Mismatches: 6, Indels: 16
0.83 0.05 0.13
Matches are distributed among these distances:
98 13 0.12
99 5 0.05
100 57 0.54
101 28 0.27
102 2 0.02
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (100 bp):
ATTATTAATATAATAATTAATAAAAATAAAAAGTAAATAATTTAATCATATTTTAACAGAATTAT
TAATAAATATAATTAATAATATTCATAATATAATC
Found at i:27932552 original size:146 final size:148
Alignment explanation
Indices: 27932286--27932579 Score: 538
Period size: 146 Copynumber: 2.0 Consensus size: 148
27932276 GGTGAAAAGC
*
27932286 ATCCGAATGCCATAGGTAACAACATAATTGAGTTCACAGAGGCAATATTTTCTATACCCCTCTTC
1 ATCCGAATGCCACAGGTAACAACATAATTGAGTTCACAGAGGCAATATTTTCTATACCCCTCTTC
*
27932351 TTTTTTATATTGATTACTGCTTTCAATTTTAGATGATTAAATCGAATAAGAAGTTTAAATTCTTT
66 GTTTTTATATTGATTACTGCTTTCAATTTTAGATGATTAAATCGAATAAGAAGTTTAAATTCTTT
*
27932416 TTCTGAGGAACTTGCCTG
131 TTCTGAGAAACTTGCCTG
*
27932434 ATCCGAATGCCACAGGTAACAACATAATT-A-TTCATAGAGGCAATATTTTCTATACCCCTCTTC
1 ATCCGAATGCCACAGGTAACAACATAATTGAGTTCACAGAGGCAATATTTTCTATACCCCTCTTC
27932497 GTTTTTATATTGATTACTGCTTTCAATTTTAGATGATTAAATCGAATAAGAAGTTTAAATTCTTT
66 GTTTTTATATTGATTACTGCTTTCAATTTTAGATGATTAAATCGAATAAGAAGTTTAAATTCTTT
27932562 TTCTGAGAAACTTGCCTG
131 TTCTGAGAAACTTGCCTG
27932580 CTCATCAAAA
Statistics
Matches: 142, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
146 113 0.80
147 1 0.01
148 28 0.20
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (148 bp):
ATCCGAATGCCACAGGTAACAACATAATTGAGTTCACAGAGGCAATATTTTCTATACCCCTCTTC
GTTTTTATATTGATTACTGCTTTCAATTTTAGATGATTAAATCGAATAAGAAGTTTAAATTCTTT
TTCTGAGAAACTTGCCTG
Found at i:27952329 original size:20 final size:20
Alignment explanation
Indices: 27952306--27952371 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
27952296 ACATATATGT
27952306 CCCTGTTTGTACTTCGGTAC
1 CCCTGTTTGTACTTCGGTAC
** * ** *
27952326 CCCTAAATTGTACATATGTGC
1 CCCT-GTTTGTACTTCGGTAC
* *
27952347 CCCTGTTTATACTTCGATAC
1 CCCTGTTTGTACTTCGGTAC
27952367 CCCTG
1 CCCTG
27952372 AATTACACAT
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.36
Consensus pattern (20 bp):
CCCTGTTTGTACTTCGGTAC
Found at i:27952351 original size:41 final size:41
Alignment explanation
Indices: 27952290--27952436 Score: 161
Period size: 41 Copynumber: 3.6 Consensus size: 41
27952280 TTATTCCTTG
* * *
27952290 AATTGTACATATATGTCCCTGTTTGTACTTCGGTACCCCTA
1 AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTA
* * * *
27952331 AATTGTACATATGTGCCCCTGTTTATACTTCGATACCCCTG
1 AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTA
* * * * *
27952372 AATTACACATACGTGCCCTTTTTTGTACTTCAGTACCCCTA
1 AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTA
*
27952413 AATTGCACATCA-GTGCCCTTGTTT
1 AATTGCACAT-ATGTGCCCCTGTTT
27952437 ACACTCCGGT
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 88 0.99
42 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (41 bp):
AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTA
Found at i:27954834 original size:9 final size:9
Alignment explanation
Indices: 27954820--27954846 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
27954810 AGTGGGGTAA
27954820 GCATGAATT
1 GCATGAATT
27954829 GCATGAATT
1 GCATGAATT
27954838 GCATGAATT
1 GCATGAATT
27954847 TTCATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (9 bp):
GCATGAATT
Found at i:27955310 original size:31 final size:30
Alignment explanation
Indices: 27955236--27955314 Score: 108
Period size: 29 Copynumber: 2.6 Consensus size: 30
27955226 TTCGGCTATC
*
27955236 AAATTATGAAAAGGGATGGTGATGACCATCA
1 AAATTA-GAAAAGGGATGGTGACGACCATCA
27955267 ACAA-T-GAAAAGGGATGGTGACGACCATCA
1 A-AATTAGAAAAGGGATGGTGACGACCATCA
27955296 AAATTACGAAAAGGGATGG
1 AAATTA-GAAAAGGGATGG
27955315 CTTCGGCTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
28 2 0.05
29 25 0.58
31 14 0.33
32 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.18
Consensus pattern (30 bp):
AAATTAGAAAAGGGATGGTGACGACCATCA
Found at i:27955401 original size:120 final size:120
Alignment explanation
Indices: 27955183--27955465 Score: 381
Period size: 120 Copynumber: 2.4 Consensus size: 120
27955173 ATCGAACTAT
* * * * * **
27955183 GAAAAGGGGTGGCTTCAACTGTCGATTCATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAA
1 GAAAAGGGATGGCTTCGACTGTTGAATCATGAAAAGGGATAGCTCCAACTATCAAATTATGAAAA
** *
27955248 GGGATGGTGATGACCATCAACAATGAAAAGGGATGGTGACGACCATCAAAATTAC
66 GGGATGGTGACAACCATCAACAATGAAAAGGGATAGTGACGACCATCAAAATTAC
* * *
27955303 GAAAAGGGATGGCTTCGGCTGTTGAATCATGAAAAAGGATAGCTCCAATTATCAAATTATGAAAA
1 GAAAAGGGATGGCTTCGACTGTTGAATCATGAAAAGGGATAGCTCCAACTATCAAATTATGAAAA
* *
27955368 GGGATGGTGACAACCATTAACAAT-AAAAGGGGATAGTGACGACCATCAAAATTAT
66 GGGATGGTGACAACCATCAACAATGAAAA-GGGATAGTGACGACCATCAAAATTAC
* *
27955423 GAAAAGGGATAGCTTCGACTGTTGAA-CTATGGAAAGGGATAGC
1 GAAAAGGGATGGCTTCGACTGTTGAATC-ATGAAAAGGGATAGC
27955466 AAGTTCAGCT
Statistics
Matches: 142, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
119 5 0.04
120 137 0.96
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (120 bp):
GAAAAGGGATGGCTTCGACTGTTGAATCATGAAAAGGGATAGCTCCAACTATCAAATTATGAAAA
GGGATGGTGACAACCATCAACAATGAAAAGGGATAGTGACGACCATCAAAATTAC
Found at i:27955420 original size:60 final size:60
Alignment explanation
Indices: 27955211--27955432 Score: 188
Period size: 60 Copynumber: 3.7 Consensus size: 60
27955201 CTGTCGATTC
* * * * *
27955211 ATGAAAAGGGATAGCT-TCGGCTATC-AAATTATGAAAAGGGATGGTGATGACCATCAACA
1 ATGAAAAGGGATAG-TGACGACCATCAAAATTATGAAAAGGGATGGTGACGACCATTAACA
* * * * **
27955270 ATGAAAAGGGATGGTGACGACCATCAAAATTACGAAAAGGGATGGCT-TCGGCTGTTGAATC-
1 ATGAAAAGGGATAGTGACGACCATCAAAATTATGAAAAGGGATGG-TGACGACCATT-AA-CA
* * * ** *
27955331 ATGAAAAAGGATAGCT-CCAATTATC-AAATTATGAAAAGGGATGGTGACAACCATTAACA
1 ATGAAAAGGGATAG-TGACGACCATCAAAATTATGAAAAGGGATGGTGACGACCATTAACA
27955390 AT-AAAAGGGGATAGTGACGACCATCAAAATTATGAAAAGGGAT
1 ATGAAAA-GGGATAGTGACGACCATCAAAATTATGAAAAGGGAT
27955433 AGCTTCGACT
Statistics
Matches: 124, Mismatches: 28, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
58 7 0.06
59 35 0.28
60 60 0.48
61 20 0.16
62 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (60 bp):
ATGAAAAGGGATAGTGACGACCATCAAAATTATGAAAAGGGATGGTGACGACCATTAACA
Found at i:27964858 original size:21 final size:21
Alignment explanation
Indices: 27964832--27964871 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
27964822 CTACAGTTTT
*
27964832 AAAAA-TCTTTAATATTTTCTA
1 AAAAATTCTATAA-ATTTTCTA
27964853 AAAAATTCTATAAATTTTC
1 AAAAATTCTATAAATTTTC
27964872 GATTTAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATTCTATAAATTTTCTA
Found at i:27970981 original size:41 final size:41
Alignment explanation
Indices: 27970865--27971012 Score: 170
Period size: 41 Copynumber: 3.6 Consensus size: 41
27970855 GTTAATTATT
* * * *
27970865 CCCTGAATTGCACATACGTGCCCTTGTTTGTACTCCGGTAC
1 CCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
* * * *
27970906 CCCTAAATTACAGATATGTGCCACTATTTGTACTTCGGTAC
1 CCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
* * * *
27970947 CCCTGAATTGCATATATGTGCCCCTCTTTGTACTTTGATAC
1 CCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
* *
27970988 CCCTGAATTGCACATAAGTGTCCCT
1 CCCTGAATTGCACATATGTGCCCCT
27971013 GTTTACACTC
Statistics
Matches: 89, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (41 bp):
CCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
Found at i:27973143 original size:24 final size:23
Alignment explanation
Indices: 27973070--27973143 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 23
27973060 AGAAGTTTTG
*
27973070 ATAATTATACATCTAAAAATAATT
1 ATAATTATACAT-TAAAAATAGTT
* *
27973094 ATAATT-TA-A-TAAAAATTGTG
1 ATAATTATACATTAAAAATAGTT
* *
27973114 ACAATTACACATTTAAAAATAGTT
1 ATAATTATACA-TTAAAAATAGTT
27973138 ATAATT
1 ATAATT
27973144 TAATTTTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 13 0.34
21 1 0.03
22 2 0.05
23 2 0.05
24 20 0.53
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (23 bp):
ATAATTATACATTAAAAATAGTT
Found at i:27974012 original size:11 final size:11
Alignment explanation
Indices: 27973996--27974033 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27973986 GAGAGAATAT
27973996 AAAAAAATTTC
1 AAAAAAATTTC
27974007 AAAAAAATTT-
1 AAAAAAATTTC
* *
27974017 AGAAAAATCTC
1 AAAAAAATTTC
27974028 AAAAAA
1 AAAAAA
27974034 TTTTAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.21
Consensus pattern (11 bp):
AAAAAAATTTC
Found at i:27974024 original size:21 final size:21
Alignment explanation
Indices: 27973998--27974038 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27973988 GAGAATATAA
*
27973998 AAAAATTTCAAAAAAATTTAG
1 AAAAATCTCAAAAAAATTTAG
*
27974019 AAAAATCTCAAAAAATTTTA
1 AAAAATCTCAAAAAAATTTA
27974039 ACAATTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATCTCAAAAAAATTTAG
Found at i:27975416 original size:8 final size:8
Alignment explanation
Indices: 27975405--27975438 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
27975395 AATCTAACAT
*
27975405 ACAAACAA
1 ACAAATAA
27975413 ACAAATAA
1 ACAAATAA
27975421 ACAAATAA
1 ACAAATAA
27975429 ACAAATAA
1 ACAAATAA
27975437 AC
1 AC
27975439 GATGTGAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.74, C:0.18, G:0.00, T:0.09
Consensus pattern (8 bp):
ACAAATAA
Found at i:27981706 original size:78 final size:78
Alignment explanation
Indices: 27981613--27981847 Score: 461
Period size: 78 Copynumber: 3.0 Consensus size: 78
27981603 ATCAGCCAGA
27981613 AATACCGTCTCTTGAACCTCTAAAGGAACATCCCTTTACAGTTTGCTAACTCTAAAAGATTGCCC
1 AATACCGTCTCTTGAACCTCTAAAGGAACATCCCTTTACAGTTTGCTAACTCTAAAAGATTGCCC
27981678 CAGTGGGCTCAGT
66 CAGTGGGCTCAGT
27981691 AATACCGTCTCTTGAACCTCTAAAGGAACATCCCTTTACAGTTTGCTAACTCTAAAAGATTGCCC
1 AATACCGTCTCTTGAACCTCTAAAGGAACATCCCTTTACAGTTTGCTAACTCTAAAAGATTGCCC
27981756 CAGTGGGCTCAGT
66 CAGTGGGCTCAGT
27981769 AATACCGTCTCTTGAACCTCTAAAGGAACATCCCTTTACAGTTTGCTAACTCTAAAAGATTGCCC
1 AATACCGTCTCTTGAACCTCTAAAGGAACATCCCTTTACAGTTTGCTAACTCTAAAAGATTGCCC
*
27981834 CAGCGGGCTCAGT
66 CAGTGGGCTCAGT
27981847 A
1 A
27981848 CAATCACCTC
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 156 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (78 bp):
AATACCGTCTCTTGAACCTCTAAAGGAACATCCCTTTACAGTTTGCTAACTCTAAAAGATTGCCC
CAGTGGGCTCAGT
Found at i:27983861 original size:35 final size:35
Alignment explanation
Indices: 27983822--27983908 Score: 138
Period size: 37 Copynumber: 2.4 Consensus size: 35
27983812 TGAAAAACAT
*
27983822 TAGTTTTTAGAAAAACATCGTGTTTTGTGGAATTG
1 TAGTTTTTAAAAAAACATCGTGTTTTGTGGAATTG
*
27983857 TAGTTTTTAAAAAAAAATATCGTGTTTTGTGGAATTG
1 TAGTTTTT--AAAAAAACATCGTGTTTTGTGGAATTG
27983894 TAGTTTTTAAAAAAA
1 TAGTTTTTAAAAAAA
27983909 TCCATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
35 15 0.31
37 33 0.69
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (35 bp):
TAGTTTTTAAAAAAACATCGTGTTTTGTGGAATTG
Found at i:27983882 original size:37 final size:37
Alignment explanation
Indices: 27983832--27983908 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
27983822 TAGTTTTTAG
27983832 AAAAACATCGTGTTTTGTGGAATTGTAGTTTTTAAAA
1 AAAAACATCGTGTTTTGTGGAATTGTAGTTTTTAAAA
*
27983869 AAAAATATCGTGTTTTGTGGAATTGTAGTTTTTAAAA
1 AAAAACATCGTGTTTTGTGGAATTGTAGTTTTTAAAA
27983906 AAA
1 AAA
27983909 TCCATAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (37 bp):
AAAAACATCGTGTTTTGTGGAATTGTAGTTTTTAAAA
Found at i:27987141 original size:16 final size:17
Alignment explanation
Indices: 27987120--27987151 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27987110 ACGTTCACTT
27987120 TTAAGCATAT-ATCACA
1 TTAAGCATATAATCACA
27987136 TTAAGCATATAATCAC
1 TTAAGCATATAATCAC
27987152 GTAACATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (17 bp):
TTAAGCATATAATCACA
Found at i:27987184 original size:39 final size:39
Alignment explanation
Indices: 27987122--27987376 Score: 357
Period size: 39 Copynumber: 6.5 Consensus size: 39
27987112 GTTCACTTTT
* ** * *
27987122 AAGCATATATCACATTAAGCATATAATCACGTAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * ** * *
27987161 AAGCAAATACCACAACACTCATATTTTCACATAATATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
27987200 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
27987239 AAGCATATATTACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
27987278 AAGCATATATCATAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
27987317 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * *
27987356 AAGCATTTATTATAATACTCA
1 AAGCATATATCACAATACTCA
27987377 AATACATGTT
Statistics
Matches: 192, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 192 1.00
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.31
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:27994241 original size:137 final size:138
Alignment explanation
Indices: 27993994--27994242 Score: 365
Period size: 137 Copynumber: 1.8 Consensus size: 138
27993984 GGGCCTACTT
* * *
27993994 ACACAAGCTGTCGGTCAGAATGTAAGCTACACGATGCTGCTCACACAAGATGTCGAGTATCCGCA
1 ACACAAGCTGTCGGTCAGAATGTAAGCTACACGATACTACTCACACAAGATGTCAAGTATCCGCA
* * * *
27994059 ACTAATGTTGGACCTCAACCATAGGTAGGACATTCAAGACTAGCACCCAAAATATAGTAACCTGG
66 ACTAATGTCGGAACTCAACCACAGGTAGGACATTCAAGACCAGCACCCAAAATATAGTAACCTGG
27994124 GTCTGCTC
131 GTCTGCTC
** * *
27994132 ACACAAGCTGTCGGTTGGAATGT-AGCTACACGATACTACTCACACAAGCTGTCAAGTATCTGCA
1 ACACAAGCTGTCGGTCAGAATGTAAGCTACACGATACTACTCACACAAGATGTCAAGTATCCGCA
* * *
27994196 ACTAATGTCGGAACTCAGCCACCGGTAGGACATTCATGACCAGCACC
66 ACTAATGTCGGAACTCAACCACAGGTAGGACATTCAAGACCAGCACC
27994243 TGAAACATGG
Statistics
Matches: 97, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
137 76 0.78
138 21 0.22
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (138 bp):
ACACAAGCTGTCGGTCAGAATGTAAGCTACACGATACTACTCACACAAGATGTCAAGTATCCGCA
ACTAATGTCGGAACTCAACCACAGGTAGGACATTCAAGACCAGCACCCAAAATATAGTAACCTGG
GTCTGCTC
Found at i:28001625 original size:27 final size:27
Alignment explanation
Indices: 28001593--28001929 Score: 320
Period size: 27 Copynumber: 12.5 Consensus size: 27
28001583 AAACCCCAAA
* *
28001593 ATAGGGTAAAATGACTGAAGTACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
* * *
28001620 ATAGGGTAAAATGACCGAAATATCTCC
1 ATAGGGTAAAATGACTGAAATACCCCC
* * **
28001647 ACAGGATAAAATGA-TCGAAATACCCTT
1 ATAGGGTAAAATGACT-GAAATACCCCC
** * *
28001674 ACGGGGTAAAATGATTGAAATACACCC
1 ATAGGGTAAAATGACTGAAATACCCCC
** * *
28001701 GCAGGGTAAAATAACCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
* * * *
28001728 ACACGATAAAATGA-TCGAAATACCCCT
1 ATAGGGTAAAATGACT-GAAATACCCCC
*
28001755 ATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
* *
28001782 ACAGGGTAAAAT-AATCGAAATACCCCC
1 ATAGGGTAAAATGACT-GAAATACCCCC
* *
28001809 ACAGGGTAAAATGAATGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
* * *
28001836 ATAGGGTAAAATAACCGAAATACCTCC
1 ATAGGGTAAAATGACTGAAATACCCCC
** *
28001863 ATAGGGTAAAATGACCAAAATACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
* *
28001890 ATAGTGTAAAATAACTGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
28001917 ATAGGGTAAAATG
1 ATAGGGTAAAATG
28001930 TTAGTTATAC
Statistics
Matches: 251, Mismatches: 53, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
26 2 0.01
27 244 0.97
28 5 0.02
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
ATAGGGTAAAATGACTGAAATACCCCC
Found at i:28004999 original size:14 final size:14
Alignment explanation
Indices: 28004977--28005010 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
28004967 TAATCAAATT
28004977 TAAAATTTTCCACA
1 TAAAATTTTCCACA
*
28004991 TAAAGTTTTCCACA
1 TAAAATTTTCCACA
28005005 TAAAAT
1 TAAAAT
28005011 AAAGAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (14 bp):
TAAAATTTTCCACA
Found at i:28027689 original size:6 final size:6
Alignment explanation
Indices: 28027678--28027705 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28027668 GTGATTAACA
28027678 TGAAAT TGAAAT TGAAAT TGAAAT TGAA
1 TGAAAT TGAAAT TGAAAT TGAAAT TGAA
28027706 TGTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (6 bp):
TGAAAT
Found at i:28029655 original size:46 final size:46
Alignment explanation
Indices: 28029604--28029696 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
28029594 TGAATCATAT
*
28029604 ACATTATTTTTCCAACATTTGATATATCATCACCTTTTCATTTACA
1 ACATTATTTTGCCAACATTTGATATATCATCACCTTTTCATTTACA
28029650 ACATTATTTTGCCAACATTTGATATATCATCACCTTTTCATTTACA
1 ACATTATTTTGCCAACATTTGATATATCATCACCTTTTCATTTACA
28029696 A
1 A
28029697 TTTTTACCCG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (46 bp):
ACATTATTTTGCCAACATTTGATATATCATCACCTTTTCATTTACA
Found at i:28037123 original size:2 final size:2
Alignment explanation
Indices: 28037116--28037141 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28037106 TGAGATAATT
28037116 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28037142 AAAGAAGAAT
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):
TA
Found at i:28037632 original size:43 final size:44
Alignment explanation
Indices: 28037547--28037633 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
28037537 AAAAATATTT
* *
28037547 AATTTAATAAAATATTTGCATATTTTTAATTCATTTTATTTTCA
1 AATTAAATAAAATATTTGCATATTTTTAATTCATTTGATTTTCA
** * *
28037591 AATTAAAT-AAATATTTTTATATTTTTATTTCATTTGGTTTTCA
1 AATTAAATAAAATATTTGCATATTTTTAATTCATTTGATTTTCA
28037634 TTCAATGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 30 0.81
44 7 0.19
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (44 bp):
AATTAAATAAAATATTTGCATATTTTTAATTCATTTGATTTTCA
Found at i:28037662 original size:48 final size:43
Alignment explanation
Indices: 28037552--28037663 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 43
28037542 TATTTAATTT
* *
28037552 AATAAAATATTTGCATATTTTTAATTCATTTTATTTTCAAATTA
1 AATAAAATATTT-CATATTTTTAATTCATTTGATTTTCAAATGA
* * *
28037596 AAT-AAATATTTTTATATTTTTATTTCATTTGGTTTTCATTCAATGA
1 AATAAAATA-TTTCATATTTTTAATTCATTTGATTTTCA---AATGA
28037642 AATAATAATATTTCAATATTTT
1 AATAA-AATATTTC-ATATTTT
28037664 AAATATGTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
43 27 0.49
44 6 0.11
46 7 0.13
47 4 0.07
48 11 0.20
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (43 bp):
AATAAAATATTTCATATTTTTAATTCATTTGATTTTCAAATGA
Found at i:28045680 original size:27 final size:27
Alignment explanation
Indices: 28045642--28045705 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
28045632 TAAAAAAATA
28045642 ACCAAAATATTATAACTTTTTTTATTC
1 ACCAAAATATTATAACTTTTTTTATTC
* *
28045669 ACCAAAATATTATAATTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTC
*
28045696 ACTAAAATAT
1 ACCAAAATAT
28045706 ACCAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTC
Found at i:28046403 original size:18 final size:18
Alignment explanation
Indices: 28046382--28046465 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 18
28046372 AGTAATAACT
28046382 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
** * **
28046400 CTATCCTCATTTAA-ACT
1 CTATTTTAATTTAATAAA
*
28046417 CTATTGTAATTTAATAAA
1 CTATTTTAATTTAATAAA
*
28046435 CTATTCTT-ATTTAATAACT
1 CTATT-TTAATTTAATAA-A
*
28046454 CTATTTTCATTT
1 CTATTTTAATTT
28046466 GAAATATAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
17 12 0.24
18 28 0.56
19 10 0.20
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.50
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:28046427 original size:35 final size:37
Alignment explanation
Indices: 28046374--28046458 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 37
28046364 TCTAATTAAG
*
28046374 TAATAACTCTATTTTAATTTAATAAACTATCCTCATT
1 TAATAACTCTATTGTAATTTAATAAACTATCCTCATT
* *
28046411 T-A-AACTCTATTGTAATTTAATAAACTATTCTTATT
1 TAATAACTCTATTGTAATTTAATAAACTATCCTCATT
28046446 TAATAACTCTATT
1 TAATAACTCTATT
28046459 TTCATTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 31 0.72
36 2 0.05
37 10 0.23
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (37 bp):
TAATAACTCTATTGTAATTTAATAAACTATCCTCATT
Found at i:28046639 original size:19 final size:19
Alignment explanation
Indices: 28046615--28046680 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
28046605 ATTTATTTTT
28046615 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
28046634 TTAAATGAGAATA-ATTTA
1 TTAAATTAAAATAGAGTTA
*
28046652 TTACATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
28046671 TTAAATTAAA
1 TTAAATTAAA
28046681 CTATTTTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:28047122 original size:27 final size:28
Alignment explanation
Indices: 28047098--28047162 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
28047088 TTTTTTTAGT
28047098 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAATTTATA
* *
28047125 ATATTTTGGTATATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAATTTATA
28047153 ATATTTTGGT
1 ATATTTTGGT
28047163 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 13 0.37
28 22 0.63
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAATTTATA
Found at i:28054966 original size:29 final size:30
Alignment explanation
Indices: 28054912--28054974 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
28054902 TTTAATATGC
28054912 AATTGTATACATGAACTTTGATTTTG-TGCA
1 AATTGTATACATGAACTTTGATTTTGAT-CA
*
28054942 AATT-TATACATGAGATTTTGA-TTTGATCA
1 AATTGTATACATGA-ACTTTGATTTTGATCA
28054971 AATT
1 AATT
28054975 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
AATTGTATACATGAACTTTGATTTTGATCA
Found at i:28055505 original size:30 final size:30
Alignment explanation
Indices: 28055445--28055507 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
28055435 TGCCAATATT
* *
28055445 TTTTGAAATTTTCATTAAACACCTTAAAAA
1 TTTTGAAATTTTAATTAAACACCTCAAAAA
* * *
28055475 TTTTGAAATTTTAATTAGATACCTCCAAAA
1 TTTTGAAATTTTAATTAAACACCTCAAAAA
28055505 TTT
1 TTT
28055508 ATTGCTAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.43
Consensus pattern (30 bp):
TTTTGAAATTTTAATTAAACACCTCAAAAA
Found at i:28057036 original size:20 final size:19
Alignment explanation
Indices: 28057011--28057048 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
28057001 TTACATTAAA
*
28057011 TATTATTTATATATTATTTG
1 TATTATCTATA-ATTATTTG
28057031 TATTATCTATAATTATTT
1 TATTATCTATAATTATTT
28057049 TTTAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (19 bp):
TATTATCTATAATTATTTG
Found at i:28058734 original size:41 final size:40
Alignment explanation
Indices: 28058683--28059207 Score: 217
Period size: 41 Copynumber: 12.6 Consensus size: 40
28058673 CTTTGAATGT
*
28058683 AAGGGGTTGCTAAGTGCAGATTCCCCGAATGATTGATGAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGAT-AAA
* * * * *
28058724 AAGGAGTTGCTATGTGCTA-ATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGC-AGATTCCCCGAATCATTGATAAA
* * * * **
28058764 AAGGTGGTTGCTAAGTGCTGATTCCACTGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCAGATTCC-CCGAATCATTGA-T-AAA
* * * * *
28058808 AAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGA-TAAA
* * * * * **
28058849 AAGTGGTTGCTAAGTGCTGGTTCCACCGTATCCTTGATTGTGA
1 AAGGGGTTGCTAAGTGCAGATTCC-CCGAATCATTGA-T-AAA
* * * * * * * *
28058892 AATGGGTTGCTATGTGCTGATTCCCTGTATCATAGATTAT
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATAAA
* * * * **
28058932 AAGGTGGTTGCTAAGTGCTGATTCCACTGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCAGATTCC-CCGAATCATTGA-T-AAA
* * * * * * *
28058976 AAGGGGTTGCTATGTGCTGATTCCCTGTATCATAGATTAT
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATAAA
* * * ***
28059016 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTG
1 AAGG-GGTTGCTAAGTGCAGATTCC-CCGAATCATTGA-TAAA
* ** * * *
28059059 AAGGGGTTGCTATGTGCTA-ATTCCTTGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGC-AGATTCCCCGAATCATTGATAAA
** * * *
28059099 AAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCTTGACTGTAA
1 AAGG-GGTTGCTAAGTGCAGATTCC-CCGAATCATTGA-T-AAA
* * * * *
28059143 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATAAA
*
28059183 AAGGTGGTTGCTAAGTGCTGATTCC
1 AAGG-GGTTGCTAAGTGCAGATTCC
28059208 ACTGTATCCT
Statistics
Matches: 391, Mismatches: 71, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
40 25 0.06
41 154 0.39
42 111 0.28
43 85 0.22
44 16 0.04
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (40 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATAAA
Found at i:28058831 original size:84 final size:84
Alignment explanation
Indices: 28058723--28059295 Score: 932
Period size: 84 Copynumber: 6.8 Consensus size: 84
28058713 GATTGATGAA
* * *
28058723 AAAGGAGTTGCTATGTGCTAATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28058788 CACTGTATCCTTGATTGTG
66 CACTGTATCCTTGATTGTG
* *
28058807 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAAGTGGTTGCTAAGTGCTGGTTC
1 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
*
28058872 CACCGTATCCTTGATTGTG
66 CACTGTATCCTTGATTGTG
* *
28058891 AAATGGGTTGCTATGTGCTGATTCCCTGTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28058956 CACTGTATCCTTGATTGTG
66 CACTGTATCCTTGATTGTG
*
28058975 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
*
28059040 CACCGTATCCTTGATTGTG
66 CACTGTATCCTTGATTGTG
* * *
28059059 -AAGGGGTTGCTATGTGCTAATTCCTTGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
* * *
28059123 CACCGTATCCTTGACTGTA
66 CACTGTATCCTTGATTGTG
*
28059142 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28059207 CACTGTATCCTTGATTGTG
66 CACTGTATCCTTGATTGTG
* * * * * *
28059226 AAAGTGGTTGCTATGTACTGATTCCCCGTATAATTAATTATAAGGTGGTTGCAAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28059291 CACTG
66 CACTG
28059296 GGGTCCTTTG
Statistics
Matches: 457, Mismatches: 31, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
83 77 0.17
84 380 0.83
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
CACTGTATCCTTGATTGTG
Found at i:28059175 original size:251 final size:252
Alignment explanation
Indices: 28058723--28059293 Score: 948
Period size: 251 Copynumber: 2.3 Consensus size: 252
28058713 GATTGATGAA
* * *
28058723 AAAGGAGTTGCTATGTGCTAATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTC
* *
28058788 CACTGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAAGT
66 CACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTAATTCCCTGTATCATTGATTATAAAGT
* * * * *
28058853 GGTTGCTAAGTGCTGGTTCCACCGTATCCTTGATTGTGAAATGGGTTGCTATGTGCTGATTCCCT
131 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGACTGTAAAAGGGGTTGCTATGTGCTGATTCCCC
28058918 GTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTCCACTGTATCCTTGATTGTG
196 GTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTCCACTGTATCCTTGATTGTG
*
28058975 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTC
* *
28059040 CACCGTATCCTTGATTGTG-AAGGGGTTGCTATGTGCTAATTCCTTGTATCATTGATTATAAGGT
66 CACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTAATTCCCTGTATCATTGATTATAAAGT
*
28059104 GGTTGCTAAGTGTTGATTCCACCGTATCCTTGACTGTAAAAGGGGTTGCTATGTGCTGATTCCCC
131 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGACTGTAAAAGGGGTTGCTATGTGCTGATTCCCC
*
28059169 GTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACTGTATCCTTGATTGTG
196 GTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTCCACTGTATCCTTGATTGTG
* * * *
28059226 AAAGTGGTTGCTATGTACTGATTCCCCGTATAATTA-ATTATAAGGTGGTTGCAAAGTGCTGATT
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCA-TAGATTATAAGGTGGTTGCTAAGTGCTGATT
28059290 CCAC
65 CCAC
28059294 TGGGGTCCTT
Statistics
Matches: 298, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
251 217 0.73
252 81 0.27
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (252 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTC
CACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTAATTCCCTGTATCATTGATTATAAAGT
GGTTGCTAAGTGCTGATTCCACCGTATCCTTGACTGTAAAAGGGGTTGCTATGTGCTGATTCCCC
GTATCATAGATTATAAGGTGGTTGCTAAGTGCTGATTCCACTGTATCCTTGATTGTG
Found at i:28060397 original size:117 final size:117
Alignment explanation
Indices: 28060234--28060467 Score: 450
Period size: 117 Copynumber: 2.0 Consensus size: 117
28060224 TAGAAATGAT
28060234 GCTTACATTTGCGTATTATTGATCATGATTTAAGCTCATATGGGAAAATAAAGTTTCATAGTATG
1 GCTTACATTTGCGTATTATTGATCATGATTTAAGCTCATATGGGAAAATAAAGTTTCATAGTATG
28060299 TGAGTGTGGTATATTTGGTATATGATTTGGTATGAAGTAAAGCCACGAATGG
66 TGAGTGTGGTATATTTGGTATATGATTTGGTATGAAGTAAAGCCACGAATGG
28060351 GCTTACATTTGCGTATTATTGATCATGATTTAAGCTCATATGGGAAAATAAAGTTTCATAGTATG
1 GCTTACATTTGCGTATTATTGATCATGATTTAAGCTCATATGGGAAAATAAAGTTTCATAGTATG
* *
28060416 TGAGTGTGGTATATTTGGTATATGATTTGGTATGAAGTAAGGCCATGAATGG
66 TGAGTGTGGTATATTTGGTATATGATTTGGTATGAAGTAAAGCCACGAATGG
28060468 TTTATGGATT
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.37
Consensus pattern (117 bp):
GCTTACATTTGCGTATTATTGATCATGATTTAAGCTCATATGGGAAAATAAAGTTTCATAGTATG
TGAGTGTGGTATATTTGGTATATGATTTGGTATGAAGTAAAGCCACGAATGG
Found at i:28061663 original size:33 final size:33
Alignment explanation
Indices: 28061602--28061665 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
28061592 TATATTAATG
* *
28061602 TTTCTATTTTATTCAATAATTTATCTTTATTTT
1 TTTCTATTTTATTAAATAATTTACCTTTATTTT
* *
28061635 TTTCTATTTTATTAAATATTTTCCCTTTATT
1 TTTCTATTTTATTAAATAATTTACCTTTATT
28061666 CTTTGAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTCTATTTTATTAAATAATTTACCTTTATTTT
Found at i:28062996 original size:14 final size:14
Alignment explanation
Indices: 28062977--28063004 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28062967 TCATTTGCCA
28062977 GTAAAATATTTTCC
1 GTAAAATATTTTCC
28062991 GTAAAATATTTTCC
1 GTAAAATATTTTCC
28063005 TTATTTTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
GTAAAATATTTTCC
Found at i:28065271 original size:14 final size:14
Alignment explanation
Indices: 28065252--28065279 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28065242 TCATTTGCCA
28065252 GTAAAATATTTTCC
1 GTAAAATATTTTCC
28065266 GTAAAATATTTTCC
1 GTAAAATATTTTCC
28065280 TTATTTTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
GTAAAATATTTTCC
Found at i:28069866 original size:16 final size:16
Alignment explanation
Indices: 28069842--28069889 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
28069832 TTCGCTGTAT
28069842 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
* *
28069858 TGGATTAGAGGTGTAA
1 TGGAATAGAGGCGTAA
28069874 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28069890 CAGCAAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.38, T:0.23
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:28069933 original size:45 final size:44
Alignment explanation
Indices: 28069869--28069959 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 44
28069859 GGATTAGAGG
28069869 TGTAATGGAATAGAGGCGTAACAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAACAG-AAATC-ATGTGTTTGGTTGAA
* * *
28069914 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAACAGAAATCATGTGTTTGGTTGAA
28069958 TG
1 TG
28069960 GAATAGAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.43
45 23 0.55
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAACAGAAATCATGTGTTTGGTTGAA
Found at i:28070140 original size:16 final size:16
Alignment explanation
Indices: 28070103--28070144 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28070093 TTAATCATAT
*
28070103 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28070119 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28070134 TTAAAATATAT
1 TTAAAATATAT
28070145 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28070151 original size:14 final size:15
Alignment explanation
Indices: 28070112--28070153 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28070102 TTTAAACATA
*
28070112 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28070127 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28070141 A-TATAATTTAATA
1 ATTATAATTAAATA
28070154 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28070203 original size:61 final size:61
Alignment explanation
Indices: 28070138--28070328 Score: 196
Period size: 61 Copynumber: 3.2 Consensus size: 61
28070128 TTATAATTAA
* *
28070138 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATGAATTTACTCAAAGCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATGAATTTACTAAAATCAT
* * * * * * * * * *
28070199 AATATATGATACT-ATAAAA-T-ATAAT-TTAACATAATTATTAT-TAAATATATTATAATAAA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATTCTTATATGAATTTACTAAAATCAT
28070258 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
28070319 AATATATAAT
1 AATATATAAT
28070329 ACTAAAATCA
Statistics
Matches: 99, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
57 2 0.02
58 2 0.02
59 31 0.31
60 16 0.16
61 43 0.43
62 5 0.05
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:28070245 original size:120 final size:121
Alignment explanation
Indices: 28070101--28070332 Score: 405
Period size: 120 Copynumber: 1.9 Consensus size: 121
28070091 ATTTAATCAT
*
28070101 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATAAAAATATATAATTTAATAAAATTCTTAAT-
* *
28070166 ATT-AATATTCTTATATGAATTTACTCAAAGCATAATATATGATACTATAAAATATA
65 ATTAAATATTCTTATATGAATTTACTAAAAGCATAATATATAATACTATAAAATATA
28070222 ATTT-AACATAATTATTATTAAATATATTATAATAAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATAAAAATATATAATTTAATAAAATTCTTAATA
*
28070286 TTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
66 TTAAATATTCTTATATGAATTTACTAAAAGCATAATATATAATACTA
28070333 AAATCATAAT
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
119 3 0.03
120 99 0.93
121 4 0.04
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATAAAAATATATAATTTAATAAAATTCTTAATA
TTAAATATTCTTATATGAATTTACTAAAAGCATAATATATAATACTATAAAATATA
Found at i:28070324 original size:59 final size:58
Alignment explanation
Indices: 28070141--28070324 Score: 155
Period size: 59 Copynumber: 3.1 Consensus size: 58
28070131 TAATTAAAAT
*
28070141 ATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATGAATTTACTCAAAGCATA
1 ATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATGAATTTACT-AAAACATA
* * * * * * *
28070200 ATAT-ATGATACTATAAAATATAATTTAACA-TAATTATTATTAAAT-ATATTATAATAAAA-AT
1 ATATAAT-TTA--ATAAAAT-T--CTTAATATTAAATATTCTTATATGA-ATT-TACTAAAACAT
28070261 -
58 A
28070261 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAA-CATA
28070320 ATATA
1 ATATA
28070325 TAATACTAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
56 12 0.13
57 15 0.16
58 6 0.06
59 18 0.19
61 13 0.14
62 7 0.07
63 17 0.18
64 7 0.07
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (58 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAACATA
Found at i:28070351 original size:23 final size:21
Alignment explanation
Indices: 28070307--28070347 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28070297 TATATGAATT
28070307 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATATAA
28070328 TACTAAAATCATAATATATA
1 TACTAAAATCATAATATATA
28070348 TAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAAAATCATAATATATAA
Found at i:28079357 original size:25 final size:25
Alignment explanation
Indices: 28079311--28079366 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
28079301 TTGCTAACTA
* *
28079311 AATGAAGGGAAAATGGAGGGTTTA-TG
1 AATG-AGGGAAAATGAAAGG-TTAGTG
28079337 AATGAGGGAAAATGAAAGGTTAGTG
1 AATGAGGGAAAATGAAAGGTTAGTG
28079362 AATGA
1 AATGA
28079367 TGAGAGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 3 0.11
25 20 0.74
26 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (25 bp):
AATGAGGGAAAATGAAAGGTTAGTG
Found at i:28090071 original size:12 final size:12
Alignment explanation
Indices: 28090054--28090083 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28090044 AAGAACACAC
*
28090054 CCGTGTGCTAGG
1 CCGTGTGCTAAG
28090066 CCGTGTGCTAAG
1 CCGTGTGCTAAG
28090078 CCGTGT
1 CCGTGT
28090084 AACAGCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.27, G:0.37, T:0.27
Consensus pattern (12 bp):
CCGTGTGCTAAG
Found at i:28094683 original size:11 final size:11
Alignment explanation
Indices: 28094663--28094706 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
28094653 AGATAAATGT
*
28094663 TATTTAATTAA
1 TATTTTATTAA
28094674 TATTTTATTAA
1 TATTTTATTAA
*
28094685 TATTATTATTAT
1 TATT-TTATTAA
28094697 TATTTTATTA
1 TATTTTATTA
28094707 TTAAATGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:28094693 original size:3 final size:3
Alignment explanation
Indices: 28094669--28094709 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
28094659 ATGTTATTTA
* *
28094669 ATT AAT ATT -TT ATT AAT ATT ATT ATT ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
28094710 AATGATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28096949 original size:12 final size:12
Alignment explanation
Indices: 28096932--28096982 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
28096922 TTTTAATAAG
28096932 ATTTAATATTAA
1 ATTTAATATTAA
*
28096944 ATTTAATCTAATAA
1 ATTTAA--TATTAA
*
28096958 ATATT-AGATTAA
1 AT-TTAATATTAA
28096970 ATTTAATATTAA
1 ATTTAATATTAA
28096982 A
1 A
28096983 GTGATTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
11 2 0.06
12 19 0.61
14 8 0.26
15 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:28096960 original size:21 final size:21
Alignment explanation
Indices: 28096936--28096977 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28096926 AATAAGATTT
*
28096936 AATATTAAATTTAATCTAATA
1 AATATTAAATTAAATCTAATA
* *
28096957 AATATTAGATTAAATTTAATA
1 AATATTAAATTAAATCTAATA
28096978 TTAAAGTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATTAAATTAAATCTAATA
Found at i:28102059 original size:4 final size:4
Alignment explanation
Indices: 28102050--28102079 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
28102040 TACCACCAAC
28102050 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
28102080 ATATAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:28104817 original size:27 final size:26
Alignment explanation
Indices: 28104787--28104837 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
28104777 TGTGACAAAT
28104787 TCTAAATGGAATGCCTTG-GTGGCGTAC
1 TCTAAAT-GAATG-CTTGTGTGGCGTAC
*
28104814 TCTATATGAATGCTTGTGTGGCGT
1 TCTAAATGAATGCTTGTGTGGCGT
28104838 GTTCTGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (26 bp):
TCTAAATGAATGCTTGTGTGGCGTAC
Found at i:28105377 original size:22 final size:23
Alignment explanation
Indices: 28105328--28105378 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
28105318 AAGATTCATA
*
28105328 ATACCAATCACATATACATATTC
1 ATACCATTCACATATACATATTC
28105351 A-ACCATTCA-ATATAGCATATT-
1 ATACCATTCACATATA-CATATTC
28105372 ATACCAT
1 ATACCAT
28105379 CCAGTTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.24
22 18 0.72
23 1 0.04
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (23 bp):
ATACCATTCACATATACATATTC
Found at i:28105643 original size:28 final size:28
Alignment explanation
Indices: 28105612--28105672 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
28105602 AAGTTTTTAT
*
28105612 TTATGAAATGGCTTACACAAGCCTTAGG
1 TTATGAAATGGCTCACACAAGCCTTAGG
*
28105640 TTATGAAATGGCTCACACAAGCTTTAGG
1 TTATGAAATGGCTCACACAAGCCTTAGG
28105668 TTATG
1 TTATG
28105673 GTATCCGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (28 bp):
TTATGAAATGGCTCACACAAGCCTTAGG
Found at i:28123300 original size:14 final size:14
Alignment explanation
Indices: 28123281--28123307 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28123271 CCTTGACTGT
28123281 GAAGATTGTCTAGA
1 GAAGATTGTCTAGA
28123295 GAAGATTGTCTAG
1 GAAGATTGTCTAG
28123308 GATGGTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (14 bp):
GAAGATTGTCTAGA
Done.