Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006691.1 Hibiscus syriacus cultivar Beakdansim tig00016637_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1195339
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:525711 original size:15 final size:15
Alignment explanation
Indices: 525681--525724 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
525671 GGTCAACAGT
525681 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
* *
525698 GGTCAATGGGTCAAT
1 GGTCAACGGGTCAAC
525713 GGTCAACGGGTC
1 GGTCAACGGGTC
525725 GGGTAAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 17 0.71
17 7 0.29
ACGTcount: A:0.23, C:0.25, G:0.34, T:0.18
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:525750 original size:13 final size:13
Alignment explanation
Indices: 525713--525768 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
525703 ATGGGTCAAT
525713 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
525726 GGTAAATGGGTCG
1 GGTCAACGGGTCG
*
525739 GGTCAACAGGTCG
1 GGTCAACGGGTCG
*
525752 GGTCAACTGGTCG
1 GGTCAACGGGTCG
525765 GGTC
1 GGTC
525769 GGGTCGGGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:526823 original size:90 final size:89
Alignment explanation
Indices: 526708--526884 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
526698 TAATCCCAAA
* *
526708 TATTTAATTTCAATTAATTAAATATAGATTTAATTATTTTAAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
*
526773 TAGGGTAACTTGGATATAAAAGGAT
65 CAGGGTAACTTGGATATAAAAGGAT
*
526798 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATC
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATC
*
526863 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
526885 GTGTGTTAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 33 0.40
90 49 0.60
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATC
AGGGTAACTTGGATATAAAAGGAT
Found at i:541029 original size:26 final size:24
Alignment explanation
Indices: 540992--541041 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
540982 TTTTGTAACA
*
540992 TTAAACATCTAAATTGACAAAAAAAT
1 TTAAACACCTAAA-T-ACAAAAAAAT
541018 TTAAACACCTAAATACAAAAAAAT
1 TTAAACACCTAAATACAAAAAAAT
541042 ATATAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
26 12 0.52
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
TTAAACACCTAAATACAAAAAAAT
Found at i:541956 original size:34 final size:33
Alignment explanation
Indices: 541909--541975 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
541899 CTTGCAGTTG
** *
541909 TTTTAATTGGGATTCGTGTTTAAAGATGAAGAT
1 TTTTAATTGGGATTAATATTTAAAGATGAAGAT
*
541942 TTTTGAATTGGGATTAATATTTAAAGATGGAGAT
1 TTTT-AATTGGGATTAATATTTAAAGATGAAGAT
541976 GAAACTCACC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.33, C:0.01, G:0.24, T:0.42
Consensus pattern (33 bp):
TTTTAATTGGGATTAATATTTAAAGATGAAGAT
Found at i:542170 original size:28 final size:28
Alignment explanation
Indices: 542138--542192 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
542128 ATTTTAGATA
542138 TTATACATCATAATTAAATATTAATAAT
1 TTATACATCATAATTAAATATTAATAAT
* * **
542166 TTATATATCATTATTATGTATTAATAA
1 TTATACATCATAATTAAATATTAATAA
542193 AAAACCACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
TTATACATCATAATTAAATATTAATAAT
Found at i:542598 original size:11 final size:11
Alignment explanation
Indices: 542582--542636 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
542572 GTGTTATTTA
542582 ATATATATAAT
1 ATATATATAAT
542593 ATATATATAAT
1 ATATATATAAT
* *
542604 -TTTGA-AAACAT
1 ATAT-ATATA-AT
542615 ATATATATAAT
1 ATATATATAAT
542626 ATATATATAAT
1 ATATATATAAT
542637 TTTGAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 4 0.11
11 28 0.78
12 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
ATATATATAAT
Found at i:542623 original size:33 final size:33
Alignment explanation
Indices: 542582--542647 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
542572 GTGTTATTTA
542582 ATATATATAATATATATATAATTTTGAAAACAT
1 ATATATATAATATATATATAATTTTGAAAACAT
542615 ATATATATAATATATATATAATTTTGAAAACAT
1 ATATATATAATATATATATAATTTTGAAAACAT
542648 GAAAACCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (33 bp):
ATATATATAATATATATATAATTTTGAAAACAT
Found at i:542723 original size:28 final size:27
Alignment explanation
Indices: 542691--542773 Score: 105
Period size: 26 Copynumber: 3.1 Consensus size: 27
542681 TAGTTTGAAA
*
542691 ATATATAATATAAAGGTTTTGAAAACAT
1 ATATATAATATATAGGTTTTGAAAA-AT
* *
542719 GTATATAATATATAGTTTTTG-AAAAT
1 ATATATAATATATAGGTTTTGAAAAAT
* *
542745 AAATATAATATATAGGTTTTTAAAAAT
1 ATATATAATATATAGGTTTTGAAAAAT
542772 AT
1 AT
542774 TTTGAAAACA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 19 0.41
27 9 0.20
28 18 0.39
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (27 bp):
ATATATAATATATAGGTTTTGAAAAAT
Found at i:542789 original size:38 final size:38
Alignment explanation
Indices: 542735--542812 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 38
542725 AATATATAGT
*
542735 TTTTGAAAA-TAAATATAATATATAGGTTTTTA-AAAATA
1 TTTTGAAAACAAAATATAATATATA-G-TTTTAGAAAATA
*
542773 TTTTGAAAACATATATATAATATATAGTTTTAGAAAATA
1 TTTTGAAAACA-AAATATAATATATAGTTTTAGAAAATA
542812 T
1 T
542813 GTATATGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 14 0.40
39 8 0.23
40 13 0.37
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (38 bp):
TTTTGAAAACAAAATATAATATATAGTTTTAGAAAATA
Found at i:542904 original size:21 final size:20
Alignment explanation
Indices: 542862--542905 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
542852 TTATTGTAAA
542862 TTTATTATTTTCATTTTCTTT
1 TTTATTATTTTCA-TTTCTTT
542883 TTTATTTATTTTC-TTTCATTT
1 TTTA-TTATTTTCATTTC-TTT
542904 TT
1 TT
542906 GTGTTATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTATTTTCATTTCTTT
Found at i:542912 original size:25 final size:25
Alignment explanation
Indices: 542861--542913 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
542851 ATTATTGTAA
* *
542861 ATTTATTATTTTCATTTTCTTTTTT
1 ATTTATTATTTTCATTTTCTGTGTT
*
542886 ATTTATTTTCTTTCATTTT-TGTGTT
1 ATTTATTAT-TTTCATTTTCTGTGTT
542911 ATT
1 ATT
542914 CGGCCTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.74
Consensus pattern (25 bp):
ATTTATTATTTTCATTTTCTGTGTT
Found at i:542913 original size:21 final size:21
Alignment explanation
Indices: 542862--542905 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
542852 TTATTGTAAA
*
542862 TTTA-TTATTTTCATTTTCTTT
1 TTTATTTATTTTCA-TTTCATT
542883 TTTATTTATTTTC-TTTCATT
1 TTTATTTATTTTCATTTCATT
542903 TTT
1 TTT
542906 GTGTTATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTATTTATTTTCATTTCATT
Found at i:556134 original size:29 final size:26
Alignment explanation
Indices: 556094--556150 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
556084 TATTTAATAA
556094 ATATAATATATATAAAATTTTGAAAAC
1 ATATAATATATAT-AAATTTTGAAAAC
**
556121 ATATATATAATATATAGTTTTTGAAAAC
1 ATATA-AT-ATATATAAATTTTGAAAAC
556149 AT
1 AT
556151 TTTGAAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
28 15 0.58
29 6 0.23
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (26 bp):
ATATAATATATATAAATTTTGAAAAC
Found at i:556154 original size:39 final size:37
Alignment explanation
Indices: 556110--556366 Score: 256
Period size: 35 Copynumber: 7.1 Consensus size: 37
556100 TATATATAAA
556110 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
1 ATTTTG-AAA-ATATATATAATATATAGTTTTTGAAAAC
* *
556149 ATTTTGAAAACCTATGTATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAA--TATATATAATATATAGTTTTTGAAAAC
* *
556188 AGTTTG-AAA-ATATATAATATATAGTTTTCT-AAAAT
1 ATTTTGAAAATATATATAATATATAGTTTT-TGAAAAC
*
556223 AGTTTG-AAA-ATATATAATATATAGTTTTTGAAAA-
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
556257 A---TG------TATATAATATATAGTTTTTGAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
*
556285 ATTTTGAAAATATATATCATATATAGTTTTTGAATAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTG-A-AAAC
* *
556324 ATTTTGAAAACATATATATAATATATAGTTTTAGAAAAT
1 ATTTTG-AAA-ATATATATAATATATAGTTTTTGAAAAC
556363 ATTT
1 ATTT
556367 ATATGTATAA
Statistics
Matches: 192, Mismatches: 8, Indels: 36
0.81 0.03 0.15
Matches are distributed among these distances:
27 24 0.12
28 1 0.01
31 4 0.02
34 2 0.01
35 55 0.29
36 1 0.01
37 20 0.10
38 7 0.04
39 53 0.28
40 4 0.02
41 21 0.11
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (37 bp):
ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
Found at i:556263 original size:25 final size:26
Alignment explanation
Indices: 556225--556283 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
556215 TCTAAAATAG
556225 TTTG-AAAAT-ATATAATATATAGTT
1 TTTGAAAAATAATATAATATATAGTT
*
556249 TTTGAAAAATGTATATAATATATAGTT
1 TTTGAAAAAT-AATATAATATATAGTT
556276 TTTGAAAA
1 TTTGAAAA
556284 CATTTTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 4 0.12
25 5 0.16
27 23 0.72
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (26 bp):
TTTGAAAAATAATATAATATATAGTT
Found at i:556271 original size:62 final size:63
Alignment explanation
Indices: 556198--556318 Score: 192
Period size: 62 Copynumber: 1.9 Consensus size: 63
556188 AGTTTGAAAA
*
556198 TATATAATATATAGTTTTCT-AAAATAGTTTGAAAATATATA-ATATATAGTTTTTGAAAAATG
1 TATATAATATATAGTTTT-TGAAAACAGTTTGAAAATATATACATATATAGTTTTTGAAAAATG
*
556260 TATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATCATATATAGTTTTTGAA
1 TATATAATATATAGTTTTTGAAAACAGTTTGAAAATATATA-CATATATAGTTTTTGAA
556319 TAAACATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 1 0.02
62 37 0.69
64 16 0.30
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (63 bp):
TATATAATATATAGTTTTTGAAAACAGTTTGAAAATATATACATATATAGTTTTTGAAAAATG
Found at i:556297 original size:28 final size:27
Alignment explanation
Indices: 556233--556300 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
556223 AGTTTGAAAA
*
556233 TATATAATATATAGTTTTTGAAAAATG
1 TATAAAATATATAGTTTTTGAAAAATG
*
556260 TATATAATATATAGTTTTTGAAAACAT-
1 TATAAAATATATAGTTTTTGAAAA-ATG
*
556287 TTTGAAAATATATA
1 TAT-AAAATATATA
556301 TCATATATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 26 0.70
28 11 0.30
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (27 bp):
TATAAAATATATAGTTTTTGAAAAATG
Found at i:556383 original size:41 final size:36
Alignment explanation
Indices: 556248--556366 Score: 139
Period size: 37 Copynumber: 3.1 Consensus size: 36
556238 AATATATAGT
*
556248 TTTTGAAAAATGTATATAATATATAGTTTTTGAAAACA
1 TTTTG-AAAATATATATAATATATAGTTTTTGAAAA-A
*
556286 TTTTGAAAATATATATCATATATAGTTTTTGAATAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTG-A-AAA-A
*
556325 TTTTGAAAACATATATATAATATATAGTTTTAGAAAATA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAA-A
556364 TTT
1 TTT
556367 ATATGTATAA
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
37 24 0.33
38 6 0.08
39 17 0.24
40 4 0.06
41 21 0.29
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAAA
Found at i:556388 original size:9 final size:9
Alignment explanation
Indices: 556361--556408 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
556351 GTTTTAGAAA
556361 ATAT-TTAT
1 ATATATTAT
* *
556369 ATGTATAAT
1 ATATATTAT
556378 ATATATTAT
1 ATATATTAT
556387 ATATATTAT
1 ATATATTAT
556396 -T-TATTAT
1 ATATATTAT
556403 AT-TATT
1 ATATATT
556409 GTAATTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 6 0.18
8 9 0.26
9 19 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
ATATATTAT
Found at i:556424 original size:7 final size:7
Alignment explanation
Indices: 556390--556449 Score: 52
Period size: 7 Copynumber: 8.1 Consensus size: 7
556380 ATATTATATA
556390 TATTATT
1 TATTATT
556397 TATTATAT
1 TATTAT-T
556405 TATTGTAATT
1 TA-T-T-ATT
556415 TATTATT
1 TATTATT
556422 TATTATT
1 TATTATT
*
556429 T-TCATT
1 TATTATT
556435 T-TTATT
1 TATTATT
556441 TATTTATT
1 TA-TTATT
556449 T
1 T
556450 TCTTTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
6 10 0.22
7 17 0.38
8 10 0.22
9 2 0.04
10 4 0.09
11 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (7 bp):
TATTATT
Found at i:556457 original size:20 final size:19
Alignment explanation
Indices: 556395--556456 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
556385 ATATATATTA
* *
556395 TTTATTATATTATTGTAATT
1 TTTATT-TATTATTTTCATT
556415 TATTATTTATTATTTTCATT
1 T-TTATTTATTATTTTCATT
556435 TTTATTTATTTATTTTC-TT
1 TTTATTTA-TTATTTTCATT
556454 TTT
1 TTT
556457 TTTGTGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 12 0.32
20 21 0.55
21 5 0.13
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTATTATTTTCATT
Found at i:556467 original size:19 final size:20
Alignment explanation
Indices: 556412--556456 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
556402 TATTATTGTA
556412 ATTTATTATTTA-TTATTTTC
1 ATTT-TTATTTATTTATTTTC
556432 ATTTTTATTTATTTATTTTC
1 ATTTTTATTTATTTATTTTC
556452 -TTTTT
1 ATTTTT
556457 TTTGTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTTATTTATTTATTTTC
Found at i:557980 original size:20 final size:20
Alignment explanation
Indices: 557955--558009 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
557945 ACTTCGACTA
557955 TCGCATTGCGATTTACATA-T
1 TCGCATTGCGATTTACA-AGT
* *
557975 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGAT-TTACAAGT
557996 TCGCATTGCGATTT
1 TCGCATTGCGATTT
558010 TCCAAATTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAGT
Found at i:558000 original size:21 final size:21
Alignment explanation
Indices: 557974--558234 Score: 236
Period size: 21 Copynumber: 12.6 Consensus size: 21
557964 GATTTACATA
*
557974 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
557995 TTCGCATTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
558016 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
558035 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
558058 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
558077 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
558100 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
558119 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
558142 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
558161 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
558182 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
558203 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
558222 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
558235 TTATTCCAAA
Statistics
Matches: 192, Mismatches: 32, Indels: 32
0.75 0.12 0.12
Matches are distributed among these distances:
19 55 0.29
21 112 0.58
23 25 0.13
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:558056 original size:42 final size:42
Alignment explanation
Indices: 557980--558173 Score: 347
Period size: 42 Copynumber: 4.7 Consensus size: 42
557970 CATATTCGCA
*
557980 TTGCGATAGTCCAAGTTCGCATTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
558020 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
558062 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
558104 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
558146 TTGCGATAGTCCAAGTTCGCGTTGCGAT
1 TTGCGATAGTCCAAGTTCGCGTTGCGAT
558174 AGTCGAAGTT
Statistics
Matches: 149, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
40 25 0.17
41 2 0.01
42 122 0.82
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:558127 original size:63 final size:60
Alignment explanation
Indices: 557980--558234 Score: 237
Period size: 61 Copynumber: 4.1 Consensus size: 60
557970 CATATTCGCA
* ** * *
557980 TTGCGATAGTCCAAGTTCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTCGTTGCGATAGTCCAAATTC-CG
* * * * *
558041 TTGCGATTTATTCCAAATT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-C
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCCAAATT--CGTTGCGA--TAGTCCAAATTCC
558103 G
60 G
* *
558104 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAATTCGTTGCGATAGTCCAAATTC-CG
* ** * *
558167 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTCGTTGCGATAGTCCAAATTC-CG
558228 TTGCGAT
1 TTGCGAT
558235 TTATTCCAAA
Statistics
Matches: 162, Mismatches: 20, Indels: 24
0.79 0.10 0.12
Matches are distributed among these distances:
61 77 0.48
63 69 0.43
65 16 0.10
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (60 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTCGTTGCGATAGTCCAAATTCCG
Found at i:558218 original size:40 final size:42
Alignment explanation
Indices: 558165--558248 Score: 154
Period size: 40 Copynumber: 2.0 Consensus size: 42
558155 TCCAAGTTCG
558165 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
558205 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
558247 CG
1 CG
558249 CAACGACTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 29 0.69
41 2 0.05
42 11 0.26
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:558231 original size:103 final size:105
Alignment explanation
Indices: 558060--558248 Score: 355
Period size: 103 Copynumber: 1.8 Consensus size: 105
558050 ATTCCAAATT
558060 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
558125 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
66 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
*
558165 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
558228 TTGCGATTTATTCCAAATTCG
66 TTGCGATTTATTCCAAATTCG
558249 CAACGACTGG
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 52 0.63
104 2 0.02
105 29 0.35
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (105 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:559638 original size:19 final size:19
Alignment explanation
Indices: 559614--559733 Score: 96
Period size: 19 Copynumber: 5.9 Consensus size: 19
559604 TCGTTGCGAT
*
559614 TTTGGAGTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
559633 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* *
559656 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
559675 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* * * *
559698 CTTCGACTATCGCAAAGAA
1 TTTGGAATATCGCAACGAA
*
559717 TTTGGAAAATCGCAACG
1 TTTGGAATATCGCAACG
559734 CGAACTTCGA
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
19 32 0.41
21 28 0.35
23 19 0.24
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:559648 original size:21 final size:21
Alignment explanation
Indices: 559622--559693 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
559612 ATTTTGGAGT
559622 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
559643 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
559664 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
559685 ATCGCAACG
1 ATCGCAACG
559694 CGAACTTCGA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 10 0.23
21 23 0.53
23 10 0.23
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:559674 original size:42 final size:42
Alignment explanation
Indices: 559621--559752 Score: 232
Period size: 42 Copynumber: 3.2 Consensus size: 42
559611 GATTTTGGAG
*
559621 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAC
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
559663 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
*
559705 TATCGCAAAGAATTTGG-A-AAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
559745 TATCGCAA
1 TATCGCAA
559753 TGCGAATATG
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
40 30 0.34
41 1 0.01
42 57 0.65
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
Found at i:559709 original size:21 final size:21
Alignment explanation
Indices: 559643--559758 Score: 105
Period size: 21 Copynumber: 5.6 Consensus size: 21
559633 TTTGGAATAA
559643 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
559664 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
559683 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
* * **
559706 ATCGCAA--AGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
559725 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
559746 ATCGCAATGCGAA
1 ATCGCAACGCGAA
559759 TATGTAAATC
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
19 24 0.33
21 40 0.55
23 9 0.12
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:564504 original size:25 final size:27
Alignment explanation
Indices: 564476--564525 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
564466 CAAAACACAA
*
564476 TAATTT-GAAAA-TTAACATTTTTTTT
1 TAATTTCGAAAATTTAAAATTTTTTTT
564501 TAATTTCGAAAATTTAAAATTTTTT
1 TAATTTCGAAAATTTAAAATTTTTT
564526 GGAAAATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 5 0.23
27 11 0.50
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (27 bp):
TAATTTCGAAAATTTAAAATTTTTTTT
Found at i:564955 original size:22 final size:21
Alignment explanation
Indices: 564908--564970 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
564898 TTCCCCTGTG
564908 GGGGGAATCGGTTCCTCTTCAAA
1 GGGGGAATCGGTTCC-C-TCAAA
*
564931 GGGGGAATCGGTTCCCTCATGA
1 GGGGGAATCGGTTCCCTCA-AA
* *
564953 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
564971 TGCATCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.08
22 18 0.50
23 15 0.42
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:564957 original size:23 final size:21
Alignment explanation
Indices: 564907--564970 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 21
564897 ATTCCCCTGT
564907 GGGGGGAATCGGTTCCTCTTCAA
1 GGGGGGAATCGGTTCC-C-TCAA
*
564930 AGGGGGAATCGGTTCCCTCATGA
1 GGGGGGAATCGGTTCCCTCA--A
*
564953 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
564971 TGCATCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.08
22 12 0.33
23 21 0.58
ACGTcount: A:0.17, C:0.23, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:571229 original size:2 final size:2
Alignment explanation
Indices: 571222--571248 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
571212 CCCCAACTTT
571222 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
571249 TATTATGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:573642 original size:15 final size:15
Alignment explanation
Indices: 573622--573655 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
573612 TTATTATCAC
573622 TTTATCAAAAAATAA
1 TTTATCAAAAAATAA
573637 TTTATCAAAAAATAA
1 TTTATCAAAAAATAA
573652 TTTA
1 TTTA
573656 AACCTGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTATCAAAAAATAA
Found at i:576057 original size:36 final size:36
Alignment explanation
Indices: 576010--576098 Score: 178
Period size: 36 Copynumber: 2.5 Consensus size: 36
576000 ATATACCATA
576010 ATTCGTGTATCAATGTTATCATATCAGCTTTGGTAC
1 ATTCGTGTATCAATGTTATCATATCAGCTTTGGTAC
576046 ATTCGTGTATCAATGTTATCATATCAGCTTTGGTAC
1 ATTCGTGTATCAATGTTATCATATCAGCTTTGGTAC
576082 ATTCGTGTATCAATGTT
1 ATTCGTGTATCAATGTT
576099 CAGCACCGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (36 bp):
ATTCGTGTATCAATGTTATCATATCAGCTTTGGTAC
Found at i:583815 original size:23 final size:23
Alignment explanation
Indices: 583762--583816 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
583752 TCATGTCACT
583762 TTTCAACCATTATTGGTGCCAAC
1 TTTCAACCATTATTGGTGCCAAC
* * *
583785 TATGAACCATTATTGTTGCCAAC
1 TTTCAACCATTATTGGTGCCAAC
583808 TTTCAACCA
1 TTTCAACCA
583817 CCTAAAGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (23 bp):
TTTCAACCATTATTGGTGCCAAC
Found at i:588469 original size:23 final size:23
Alignment explanation
Indices: 588412--588476 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
588402 GTCACTTTTC
* *
588412 AACCATTATTGGTGCCAACTATG
1 AACCATTATTGTTGTCAACTATG
588435 AACCATTATTGTTGTCAACTATG
1 AACCATTATTGTTGTCAACTATG
588458 AACCATTATTGTTGT-AACT
1 AACCATTATTGTTGTCAACT
588477 TTCAACCACC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 4 0.10
23 36 0.90
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (23 bp):
AACCATTATTGTTGTCAACTATG
Found at i:590337 original size:24 final size:24
Alignment explanation
Indices: 590310--590355 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
590300 CGAACCTTGC
*
590310 GCCTAGGCTCCAGAGATCCTTTGT
1 GCCTAGGCTCCAGAGACCCTTTGT
*
590334 GCCTAGGCTCTAGAGACCCTTT
1 GCCTAGGCTCCAGAGACCCTTT
590356 ACGCCTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.30, G:0.24, T:0.28
Consensus pattern (24 bp):
GCCTAGGCTCCAGAGACCCTTTGT
Found at i:590361 original size:24 final size:24
Alignment explanation
Indices: 590309--590361 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
590299 ACGAACCTTG
* *
590309 CGCCTAGGCTCCAGAGATCCTTTG
1 CGCCTAGGCTCCAGAGACCCTTTA
* *
590333 TGCCTAGGCTCTAGAGACCCTTTA
1 CGCCTAGGCTCCAGAGACCCTTTA
590357 CGCCT
1 CGCCT
590362 CATTGCGTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.34, G:0.23, T:0.26
Consensus pattern (24 bp):
CGCCTAGGCTCCAGAGACCCTTTA
Found at i:595400 original size:18 final size:18
Alignment explanation
Indices: 595374--595414 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
595364 TCGAAAGGAC
* *
595374 TGAAGTAAATGATAAGAT
1 TGAATTAAATAATAAGAT
595392 TGAATTAAATAATAAGAT
1 TGAATTAAATAATAAGAT
*
595410 CGAAT
1 TGAAT
595415 GGAAGGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAATTAAATAATAAGAT
Found at i:600389 original size:18 final size:18
Alignment explanation
Indices: 600363--600397 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
600353 TCGAAAGGAC
*
600363 TGAAATAAATGATAAGAT
1 TGAAATAAATAATAAGAT
*
600381 TGAATTAAATAATAAGA
1 TGAAATAAATAATAAGA
600398 CCGAATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (18 bp):
TGAAATAAATAATAAGAT
Found at i:605279 original size:18 final size:18
Alignment explanation
Indices: 605253--605287 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
605243 TCGAAAGGAC
*
605253 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
605271 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
605288 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:606879 original size:32 final size:31
Alignment explanation
Indices: 606796--606880 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
606786 CTAATGTGAC
* *
606796 TCTTAGGTAGG-CTCTACGGCCGTGAGATCAT
1 TCTTAGGTAGGCCTC-ACGGCCCTAAGATCAT
* ** **
606827 TCTTGGGTAGGCCTTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCTCACGGCCCTAAGAT-CAT
606859 TCTTAGGTAGGCCTCACGGCCC
1 TCTTAGGTAGGCCTCACGGCCC
606881 CGAAATCTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
31 20 0.48
32 22 0.52
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCTCACGGCCCTAAGATCAT
Found at i:607957 original size:2 final size:2
Alignment explanation
Indices: 607950--608011 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
607940 GTAACTTATC
607950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
607992 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
608012 GTGGAATGCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:609872 original size:23 final size:24
Alignment explanation
Indices: 609827--609880 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
609817 ATGAGAAAAA
*
609827 AGAAAAAAAATAATTTATATATTT
1 AGAAATAAAATAATTTATATATTT
* *
609851 ATAAATAAAAT-ATTTATTTATTT
1 AGAAATAAAATAATTTATATATTT
609874 AGAAATA
1 AGAAATA
609881 TCAGAAAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
AGAAATAAAATAATTTATATATTT
Found at i:611460 original size:3 final size:3
Alignment explanation
Indices: 611452--611507 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
611442 GTAAATTTTT
611452 TAA TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
611497 T-A TAAA TAA TA
1 TAA T-AA TAA TA
611508 TTTAAATGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 40 0.82
4 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:611842 original size:122 final size:116
Alignment explanation
Indices: 611712--611928 Score: 285
Period size: 122 Copynumber: 1.8 Consensus size: 116
611702 ACCTATTTCC
* * * *
611712 TTCTGTGATAGAGTCATTCAAAAGATTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTCCT
1 TTCTGTGATAGAATCATGCAAAAGATTGAATAAGATATTCTCATTATGAA---C-T-TTT-T-CT
611777 TCAGATGAGTTC-T-TCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTGT
59 TCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAGGTTGATGCTAATCTATCTGT
* * *
611834 TTCTGTGATAGAATTATGCAAAAGGTTGAATAAGATATTCTCATTGTGAACTTTTTCTTCAGATG
1 TTCTGTGATAGAATCATGCAAAAGATTGAATAAGATATTCTCATTATGAACTTTTTCTTCAGATG
611899 AGTTCTTCTCATTATGAACTTCTCTGGAAA
66 AGTTCTTCTCATTATGAACTTCTCTGGAAA
611929 AGCTGCTCCA
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
115 14 0.16
116 13 0.15
117 14 0.16
118 1 0.01
119 1 0.01
122 43 0.50
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (116 bp):
TTCTGTGATAGAATCATGCAAAAGATTGAATAAGATATTCTCATTATGAACTTTTTCTTCAGATG
AGTTCTTCTCATTATGAACTTCTCTGGAAAGGTTGATGCTAATCTATCTGT
Found at i:612189 original size:113 final size:112
Alignment explanation
Indices: 611888--612376 Score: 630
Period size: 113 Copynumber: 4.3 Consensus size: 112
611878 TGTGAACTTT
* *
611888 TTCTTCAGATGAGTTCTTCTCATTATGAACTT-CTCTGGAAAAGCTGCTCCATCAAGTGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGCTGATCCATCAAATGATGGAT
*
611952 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC
66 TTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC
* * * * *
611999 TTCTTCAGATTACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGAT
1 TTCTTCAGA-T--GAGTTCTTCTCATTATGAACT-TCCTCTGGAAAAGCTGATCCATCAAATGAT
* * * *
612063 GAATTTAAACAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC
62 GGATTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-C
*
612115 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGCTGATCCATCAAATGATGGAT
*
612180 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC
66 TTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-C
* * * * * * *
612228 TTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGG-AAAGTTTGTTCCATCGAGTGATGGT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAG-CTGATCCATCAAATGATGGA
* *
612292 TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTATTC
65 TTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC
*
612337 TTCTTCAGATGACGAATTCTTCTCATTACGAACTTCCTCT
1 TTCTTCAGATGA-G--TTCTTCTCATTATGAACTTCCTCT
612377 TCCTTCTTCA
Statistics
Matches: 334, Mismatches: 33, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
109 13 0.04
110 4 0.01
111 10 0.03
112 31 0.09
113 177 0.53
114 21 0.06
115 67 0.20
116 11 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGCTGATCCATCAAATGATGGAT
TTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC
Found at i:612202 original size:228 final size:222
Alignment explanation
Indices: 611888--612376 Score: 680
Period size: 228 Copynumber: 2.2 Consensus size: 222
611878 TGTGAACTTT
* *
611888 TTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGCTGCTCCATCAAGTGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
*
611952 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATTACGAGT
66 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGA-T--GAAT
* * *
612016 TCTTCTCATTATGAACTCTAC-CTGGCAA-TGTTAATCCATCAAATGATGAATTTAAACAAAAGG
128 TCTTCTCATTACGAACT-TACTCTGGAAAGT-TTAATCCATCAAATGATGAATTTAAACAAAAAG
* *
612079 TTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC
191 TTGAACAAATTCTTCTCATTATGAA--T-TTATT-C
612115 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
612180 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCT
66 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCT
* ** * * ** *
612245 TCTCATTACGAACTTCCTCTGGAAAGTTTGTTCCATCGAGTGATGGTTTTGAACAAAAAGTTGAA
131 TCTCATTACGAACTTACTCTGGAAAGTTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAA
612310 CAAATTCTTCTCATTATGAATTTATTC
196 CAAATTCTTCTCATTATGAATTTATTC
* *
612337 TTCTTCAGATGACGAATTCTTCTCATTACGAACTTCCTCT
1 TTCTTCAGATGA-G--TTCTTCTCATTATGAACTTTCTCT
612377 TCCTTCTTCA
Statistics
Matches: 237, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
222 13 0.05
223 5 0.02
224 1 0.00
225 24 0.10
226 74 0.31
227 31 0.13
228 79 0.33
229 10 0.04
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (222 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCT
TCTCATTACGAACTTACTCTGGAAAGTTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAA
CAAATTCTTCTCATTATGAATTTATTC
Found at i:612410 original size:40 final size:39
Alignment explanation
Indices: 612313--612410 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 39
612303 AGTTGAACAA
612313 ATTCTTCTCATTATGAA-TTTATTCTTCTTCAGATGACG
1 ATTCTTCTCATTATGAACTTTATTCTTCTTCAGATGACG
* *
612351 AATTCTTCTCATTACGAACTTCCTCTTCCTTCTTCAGATGA-G
1 -ATTCTTCTCATTATGAACTT--TATT-CTTCTTCAGATGACG
612393 -TTCTTCTCATTATGAACT
1 ATTCTTCTCATTATGAACT
612411 CGACCTAGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
39 16 0.31
40 19 0.37
42 4 0.08
43 13 0.25
ACGTcount: A:0.22, C:0.23, G:0.09, T:0.45
Consensus pattern (39 bp):
ATTCTTCTCATTATGAACTTTATTCTTCTTCAGATGACG
Found at i:613418 original size:93 final size:93
Alignment explanation
Indices: 613175--613782 Score: 1092
Period size: 93 Copynumber: 6.5 Consensus size: 93
613165 GTTTTATATT
613175 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
*
613240 TCAATGATTGGTTTTTCGGGGTTCATACC
66 TCAATGATTGGTTTTT-GTGGTTCATACC
*
613269 AAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
613334 TCAATGATTGGTTTTTGTGGTTCATACC
66 TCAATGATTGGTTTTTGTGGTTCATACC
*
613362 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
613427 TCAATGATTGGTTTTTGTGGTTCATACC
66 TCAATGATTGGTTTTTGTGGTTCATACC
*
613455 AAACCAGATCAGATAAGTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
* *
613520 TCAATGATTGGTTTTT-CGGTTCATATC
66 TCAATGATTGGTTTTTGTGGTTCATACC
* * * *
613547 AAACCATATAAGATAACTCAAAGAACATTTCCAGAAGATGATATGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
613612 TCAATGATTGGTTTTTGTGGTTCATACC
66 TCAATGATTGGTTTTTGTGGTTCATACC
*
613640 AAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
*
613705 TCAATGATTGGTTTTTGTGGTTCATATC
66 TCAATGATTGGTTTTTGTGGTTCATACC
613733 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAC
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAC
613783 TTGTTCTACT
Statistics
Matches: 491, Mismatches: 22, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
92 85 0.17
93 326 0.66
94 80 0.16
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (93 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
TCAATGATTGGTTTTTGTGGTTCATACC
Found at i:613629 original size:185 final size:186
Alignment explanation
Indices: 613144--613782 Score: 1104
Period size: 185 Copynumber: 3.4 Consensus size: 186
613134 TTCATCTTTT
* * *
613144 AATTCCAATGATTGG-TTCTG-GGTTTTATATTAAACCAGATCAGATAACTCAAAGAACACTTCC
1 AATT-CAATGATTGGTTTTTGTGG-TTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCC
*
613207 AGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTCGGGGTTCATACCAAA
64 AGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTT-GTGGTTCATACCAAA
* *
613272 CCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
128 CCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
*
613331 AATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
*
613396 AAGATGCTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCA
66 AAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCA
*
613461 GATCAGATAAGTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
131 GATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
* * * *
613517 AATTCAATGATTGGTTTTT-CGGTTCATATCAAACCATATAAGATAACTCAAAGAACATTTCCAG
1 AATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
*
613581 AAGATGATATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCA
66 AAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCA
613646 GATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
131 GATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
613702 AATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
613767 AAGATGCTATGAGCAC
66 AAGATGCTATGAGCAC
613783 TTGTTCTACT
Statistics
Matches: 428, Mismatches: 21, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
185 177 0.41
186 156 0.36
187 93 0.22
188 2 0.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (186 bp):
AATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
AAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCA
GATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
Found at i:613674 original size:278 final size:279
Alignment explanation
Indices: 613133--613782 Score: 1121
Period size: 278 Copynumber: 2.3 Consensus size: 279
613123 CGATCATGCA
* * * *
613133 ATTCATCTT-TTAATTCCAATGATTGG-TTCTG-GGTTTTATATTAAACCAGATCAGATAACTCA
1 ATTCATCTTCTAAATT-CAATGATTGGTTTTTGTGG-TTCATATCAAACCAGATCAGATAACTCA
613195 AAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTCGGG
64 AAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTC-GG
*
613260 GTTCATACCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
128 GTTCATACCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGATATGAGCACATTCAT
*
613325 CTTCCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
193 CTTCCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAAATCAAAGAACAC
613390 TTCCAGAAGATGCTATGAGCAC
258 TTCCAGAAGATGCTATGAGCAC
* *
613412 ATTCATCTTCTAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAAGTCAAA
1 ATTCATCTTCTAAATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAA
613477 GAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTC-GGTT
66 GAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTCGGGTT
* * *
613541 CATATCAAACCATAT-AAGATAACTCAAAGAACATTTCCAGAAGATGATATGAGCACATTCATCT
131 CATACCAAACCAGATCAA-ATAACTCAAAGAACACTTCCAGAAGATGATATGAGCACATTCATCT
613605 TCCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAAATCAAAGAACACTT
195 TCCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAAATCAAAGAACACTT
613670 CCAGAAGATGCTATGAGCAC
260 CCAGAAGATGCTATGAGCAC
*
613690 ATTCATCTTCCAAATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAA
1 ATTCATCTTCTAAATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAA
613755 GAACACTTCCAGAAGATGCTATGAGCAC
66 GAACACTTCCAGAAGATGCTATGAGCAC
613783 TTGTTCTACT
Statistics
Matches: 353, Mismatches: 14, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
277 2 0.01
278 235 0.67
279 19 0.05
280 95 0.27
281 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (279 bp):
ATTCATCTTCTAAATTCAATGATTGGTTTTTGTGGTTCATATCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTCGGGTT
CATACCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGATATGAGCACATTCATCTT
CCAAATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAAATCAAAGAACACTTC
CAGAAGATGCTATGAGCAC
Found at i:614744 original size:71 final size:71
Alignment explanation
Indices: 614636--614768 Score: 257
Period size: 71 Copynumber: 1.9 Consensus size: 71
614626 GGTTCAATCG
*
614636 CCAGATGCCTAATATCAATATGCATTTGAGTCGCCCATTCAGGTTTTCAACTCAAATCCTTCCTT
1 CCAGATGCCTAATATCAATATGCATTTGAGCCGCCCATTCAGGTTTTCAACTCAAATCCTTCCTT
614701 CAATTT
66 CAATTT
614707 CCAGATGCCTAATATCAATATGCATTTGAGCCGCCCATTCAGGTTTTCAACTCAAATCCTTC
1 CCAGATGCCTAATATCAATATGCATTTGAGCCGCCCATTCAGGTTTTCAACTCAAATCCTTC
614769 ATTTGGTTAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (71 bp):
CCAGATGCCTAATATCAATATGCATTTGAGCCGCCCATTCAGGTTTTCAACTCAAATCCTTCCTT
CAATTT
Found at i:614784 original size:71 final size:71
Alignment explanation
Indices: 614638--614786 Score: 235
Period size: 71 Copynumber: 2.1 Consensus size: 71
614628 TTCAATCGCC
* *
614638 AGATGCCTAATATCAATATGCATTTGAGTCGCCCATTCAGGTTTTCAACTCAAATCCTTCCTTCA
1 AGATGCCTAATATCAATATGCATTTGAGCCGCCCATTCAGGTTTTCAACTCAAATCCTTCATTCA
* *
614703 ATTTCC
66 ATTACA
**
614709 AGATGCCTAATATCAATATGCATTTGAGCCGCCCATTCAGGTTTTCAACTCAAATCCTTCATTTG
1 AGATGCCTAATATCAATATGCATTTGAGCCGCCCATTCAGGTTTTCAACTCAAATCCTTCATTCA
*
614774 GTTACA
66 ATTACA
614780 AGATGCC
1 AGATGCC
614787 CTTTGCGGGT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (71 bp):
AGATGCCTAATATCAATATGCATTTGAGCCGCCCATTCAGGTTTTCAACTCAAATCCTTCATTCA
ATTACA
Found at i:622177 original size:15 final size:15
Alignment explanation
Indices: 622154--622185 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
622144 TGAAATGAAT
622154 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
622169 AATGCATGTATGCAA
1 AATGAATGTATGCAA
622184 AA
1 AA
622186 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:625536 original size:18 final size:20
Alignment explanation
Indices: 625491--625537 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
625481 TGAAATATTA
625491 ATAAGAAAATATATAAATACT
1 ATAA-AAAATATATAAATACT
*
625512 AT-GAAAATA-ATAAATA-T
1 ATAAAAAATATATAAATACT
625529 ATAAAAAAT
1 ATAAAAAAT
625538 TTGAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 6 0.26
21 2 0.09
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (20 bp):
ATAAAAAATATATAAATACT
Found at i:626077 original size:23 final size:24
Alignment explanation
Indices: 626033--626085 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
626023 ATGAGAAAAA
626033 AGAAA-AAAATAATTTATATATTT
1 AGAAATAAAATAATTTATATATTT
* *
626056 ATAAATAAAAT-ATTTATTTATTT
1 AGAAATAAAATAATTTATATATTT
626079 AGAAATA
1 AGAAATA
626086 TCAGAAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AGAAATAAAATAATTTATATATTT
Found at i:627666 original size:3 final size:3
Alignment explanation
Indices: 627658--627729 Score: 87
Period size: 3 Copynumber: 23.7 Consensus size: 3
627648 GTAAATTTTT
627658 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TA-A TAA
627704 TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TA
627730 TTTAAATGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 14
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.10
3 45 0.73
4 11 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:631452 original size:34 final size:33
Alignment explanation
Indices: 631405--631471 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
631395 CTTCTTGTTG
*
631405 TTTTAATTGGGATTAGTGTTTAAAGATGAAGAT
1 TTTTAATTGGGATTAATGTTTAAAGATGAAGAT
*
631438 TTTTGAATTGGGATTAATGTTTAAAGATGGAGAT
1 TTTT-AATTGGGATTAATGTTTAAAGATGAAGAT
631472 GAAACTCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (33 bp):
TTTTAATTGGGATTAATGTTTAAAGATGAAGAT
Found at i:631617 original size:2 final size:2
Alignment explanation
Indices: 631610--631648 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
631600 TAAATTAATA
631610 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT -T AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
631649 TAATAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:633981 original size:17 final size:17
Alignment explanation
Indices: 633956--633989 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
633946 AACTTTTGCA
* *
633956 CTCATTTGTTGTTATTT
1 CTCAATTGTTCTTATTT
633973 CTCAATTGTTCTTATTT
1 CTCAATTGTTCTTATTT
633990 GTTCTTGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.62
Consensus pattern (17 bp):
CTCAATTGTTCTTATTT
Found at i:635205 original size:15 final size:15
Alignment explanation
Indices: 635185--635218 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
635175 TTATTATCAT
635185 TTTATCGAAAA-ATAA
1 TTTATC-AAAATATAA
635200 TTTATCAAAATATAA
1 TTTATCAAAATATAA
635215 TTTA
1 TTTA
635219 AACCTGAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TTTATCAAAATATAA
Found at i:636307 original size:14 final size:14
Alignment explanation
Indices: 636262--636298 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
636252 GAATTAAAAT
636262 AAATAAATAATAT-
1 AAATAAATAATATA
*
636275 -AATAGATAATATA
1 AAATAAATAATATA
636288 AAATAAATAAT
1 AAATAAATAAT
636299 TTAAGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AAATAAATAATATA
Found at i:637140 original size:23 final size:23
Alignment explanation
Indices: 637110--637172 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
637100 TCTTAATTTT
637110 CACCGAAGTGCCACATAGGTTTG
1 CACCGAAGTGCCACATAGGTTTG
637133 CACCGAAGTGCCACATAGGTTTG
1 CACCGAAGTGCCACATAGGTTTG
*
637156 CACCGAAGTGTCACATA
1 CACCGAAGTGCCACATA
637173 ATTGTCCCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.21
Consensus pattern (23 bp):
CACCGAAGTGCCACATAGGTTTG
Found at i:637762 original size:18 final size:19
Alignment explanation
Indices: 637724--637764 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
637714 TCTAAGAGCT
*
637724 CATTTAGGACCGTATAGATG
1 CATTTAGGACCG-ACAGATG
637744 CATTTAGGACCG-CAGATG
1 CATTTAGGACCGACAGATG
637762 CAT
1 CAT
637765 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (19 bp):
CATTTAGGACCGACAGATG
Found at i:639798 original size:43 final size:43
Alignment explanation
Indices: 639720--640108 Score: 570
Period size: 43 Copynumber: 9.1 Consensus size: 43
639710 GCAAAAGCGA
* * * *
639720 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGGAACTG
* * * *
639764 TAAGGCTTACCCTTGTACACAACAAAGGAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
* * * *
639806 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GAGAAATTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
*
639848 TAAGGCTTACCCTTGCACACAGCAAAGGGACATGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
639891 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
639934 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
* *
639977 TAAGGCTTACCCTTGCACCCA-CTAAAGGGACCTGGGGGAGCTG
1 TAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGGGGAACTG
640020 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
* *
640063 TAAGGCTTACCCTTGCACACATCAAAAGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
640106 TAA
1 TAA
640109 CGGTAATTAA
Statistics
Matches: 319, Mismatches: 22, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
42 79 0.25
43 233 0.73
44 7 0.02
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
Found at i:646894 original size:20 final size:20
Alignment explanation
Indices: 646869--646911 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
646859 TATAAGAGCT
*
646869 CATTTAGGACCATATAGATG
1 CATTTAAGACCATATAGATG
* *
646889 CATTTAAGAGCATATAGTTG
1 CATTTAAGACCATATAGATG
646909 CAT
1 CAT
646912 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
CATTTAAGACCATATAGATG
Found at i:652723 original size:44 final size:44
Alignment explanation
Indices: 652673--652756 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
652663 CAGCTCGTAA
** *
652673 TTTGCACTGAAGTGCAACATAATTATCCTGAAGGAGCACAAAGG
1 TTTGCACCAAAGTGCAACATAATTATCCTGAAGGACCACAAAGG
* * *
652717 TTTGCACCAAAGTGCCATATAATTGTCCTGAAGGACCACA
1 TTTGCACCAAAGTGCAACATAATTATCCTGAAGGACCACA
652757 TAGAACCCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (44 bp):
TTTGCACCAAAGTGCAACATAATTATCCTGAAGGACCACAAAGG
Found at i:653946 original size:13 final size:13
Alignment explanation
Indices: 653928--653953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
653918 TTAATTTCCA
653928 TATAATCATATAC
1 TATAATCATATAC
653941 TATAATCATATAC
1 TATAATCATATAC
653954 ACTCACCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TATAATCATATAC
Found at i:662583 original size:29 final size:29
Alignment explanation
Indices: 662542--662609 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
662532 ATAAAACATT
662542 ACAT-GGAATGAGATTCCCGGCCAACCAA
1 ACATGGGAATGAGATTCCCGGCCAACCAA
* * *
662570 ACATGGGAATGAGATTCTCGGCTAACTAA
1 ACATGGGAATGAGATTCCCGGCCAACCAA
*
662599 ACACGGGAATG
1 ACATGGGAATG
662610 TGGATTCCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (29 bp):
ACATGGGAATGAGATTCCCGGCCAACCAA
Found at i:672020 original size:16 final size:18
Alignment explanation
Indices: 671999--672032 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
671989 TTCATACTTT
671999 TATA-TTTTA-GATTTGG
1 TATATTTTTATGATTTGG
672015 TATATTTTTATGATTTGG
1 TATATTTTTATGATTTGG
672033 ATGATTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (18 bp):
TATATTTTTATGATTTGG
Found at i:681242 original size:11 final size:10
Alignment explanation
Indices: 681221--681283 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
681211 AGGGGAGGAT
681221 AGAGAGAAAA
1 AGAGAGAAAA
*
681231 AGAGAGGAAA
1 AGAGAGAAAA
681241 A-AGAGAAAA
1 AGAGAGAAAA
681250 AGAGA-ATAAA
1 AGAGAGA-AAA
681260 ATG-GA-AAAA
1 A-GAGAGAAAA
*
681269 AGAAAGAAAA
1 AGAGAGAAAA
681279 AGAGA
1 AGAGA
681284 ACATATTAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.02
9 14 0.32
10 28 0.64
11 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (10 bp):
AGAGAGAAAA
Found at i:681245 original size:19 final size:19
Alignment explanation
Indices: 681223--681284 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
681213 GGGAGGATAG
*
681223 AGAGAAAAAGAGAGGAAAA
1 AGAGAAAAAGAGAAGAAAA
*
681242 AGAGAAAAAGAGAATAAAA
1 AGAGAAAAAGAGAAGAAAA
*
681261 TG-GAAAAA-AGAAAGAAAA
1 AGAGAAAAAGAG-AAGAAAA
681279 AGAGAA
1 AGAGAA
681285 CATATTAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 2 0.06
18 13 0.36
19 21 0.58
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (19 bp):
AGAGAAAAAGAGAAGAAAA
Found at i:684661 original size:18 final size:18
Alignment explanation
Indices: 684638--684680 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
684628 CTTTATAGTA
* *
684638 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATAT
*
684656 TTTATTTAATTCTTATAT
1 TTTATTTAATTATTATAT
684674 TTTATTT
1 TTTATTT
684681 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:693257 original size:18 final size:18
Alignment explanation
Indices: 693234--693276 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
693224 CTTTAGATTA
*
693234 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
693252 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
693270 TTTATTT
1 TTTATTT
693277 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:693355 original size:18 final size:17
Alignment explanation
Indices: 693329--693384 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
693319 TTATTTATTA
* *
693329 TTTTCTTATTTTTCCTT
1 TTTTATTATTTTTACTT
*
693346 TTTTATTTATTATTACTT
1 TTTTA-TTATTTTTACTT
*
693364 ATTTTATTATTTTTTCTT
1 -TTTTATTATTTTTACTT
693382 TTT
1 TTT
693385 AAATTATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 7 0.22
18 20 0.62
19 5 0.16
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTATTTTTACTT
Found at i:693376 original size:29 final size:29
Alignment explanation
Indices: 693319--693378 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
693309 TTTACTACTA
* *
693319 TTATTTATTATTTTCTTATTTTTCCTTTT
1 TTATTTATTATTTACTTATTTTTCATTTT
*
693348 TTATTTATTA-TTACTTATTTTATTATTTT
1 TTATTTATTATTTACTTATTTT-TCATTTT
693377 TT
1 TT
693379 CTTTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (29 bp):
TTATTTATTATTTACTTATTTTTCATTTT
Found at i:693404 original size:36 final size:35
Alignment explanation
Indices: 693323--693407 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 35
693313 CTACTATTAT
* * * *
693323 TTATTATTTTCTTATTTTTCCTTTTTTATTTATTA
1 TTATTATTTTATTATTTTTCCTTTTTAAATTATAA
*
693358 TTACTTATTTTATTATTTTTTCTTTTTAAATTATAA
1 TTA-TTATTTTATTATTTTTCCTTTTTAAATTATAA
693394 TTATTAATTTTATT
1 TTATT-ATTTTATT
693408 TTATTTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 5 0.12
36 38 0.88
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (35 bp):
TTATTATTTTATTATTTTTCCTTTTTAAATTATAA
Found at i:698911 original size:5 final size:5
Alignment explanation
Indices: 698901--698951 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
698891 ACCCATTTCG
**
698901 TTTTA TTTTA TTTTA TTCCA TTTTA TTTTCA TTTTA TTTTCA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT-A TTTTA TTTT
698952 TAAGGAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
5 30 0.75
6 10 0.25
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:698935 original size:11 final size:11
Alignment explanation
Indices: 698896--698951 Score: 80
Period size: 11 Copynumber: 5.3 Consensus size: 11
698886 AGGCAACCCA
*
698896 TTTCGTTTTAT
1 TTTCATTTTAT
698907 TTT-ATTTTA-
1 TTTCATTTTAT
*
698916 TTCCATTTTAT
1 TTTCATTTTAT
698927 TTTCATTTTAT
1 TTTCATTTTAT
698938 TTTCATTTTAT
1 TTTCATTTTAT
698949 TTT
1 TTT
698952 TAAGGAAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
9 2 0.05
10 11 0.28
11 27 0.68
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:707661 original size:21 final size:23
Alignment explanation
Indices: 707635--707686 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
707625 AGGGTATCGA
707635 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
**
707656 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
707679 TCCCCCCA
1 TCCCCCCA
707687 CAGGGGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.17
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:707693 original size:21 final size:21
Alignment explanation
Indices: 707667--707706 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
707657 CCCCCTTTGA
*
707667 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
707688 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
707707 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:711183 original size:37 final size:35
Alignment explanation
Indices: 711130--711226 Score: 112
Period size: 37 Copynumber: 2.8 Consensus size: 35
711120 TTATCTTTAC
711130 TATTATTATTTATTATTTTATTATTTTTCTCTTTTT
1 TATTATTATTTATTATTTTATTATTTTT-TCTTTTT
711166 TATTCATTA-TTACTTATTTTATTATTTTTTC-TTTT
1 TATT-ATTATTTA-TTATTTTATTATTTTTTCTTTTT
* *
711201 TA-AATTA-TAATTATTTATATTATTTT
1 TATTATTATTTATTATTT-TATTATTTT
711227 ATTTCAAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
32 6 0.11
33 15 0.27
35 6 0.11
36 9 0.16
37 20 0.36
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (35 bp):
TATTATTATTTATTATTTTATTATTTTTTCTTTTT
Found at i:711200 original size:15 final size:15
Alignment explanation
Indices: 711117--711200 Score: 50
Period size: 15 Copynumber: 5.7 Consensus size: 15
711107 TAAAAACCCC
*
711117 TTTTTATCTTTACTA-
1 TTTTTAT-TTTATTAT
*
711132 TTATTA-TTTATTAT
1 TTTTTATTTTATTAT
*
711146 TTTATTATTTT-TCTCT
1 TTT-TTATTTTAT-TAT
*
711162 TTTTTA-TTCATTAT
1 TTTTTATTTTATTAT
**
711176 TACTTATTTTATTAT
1 TTTTTATTTTATTAT
*
711191 TTTTTCTTTT
1 TTTTTATTTT
711201 TAAATTATAA
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
13 6 0.12
14 10 0.20
15 27 0.53
16 8 0.16
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTATTTTATTAT
Found at i:711224 original size:36 final size:37
Alignment explanation
Indices: 711142--711224 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 37
711132 TTATTATTTA
* *
711142 TTATTTTATTATTTTTCTCTTTTTTATTCATTATTAC
1 TTATTTTATTATTTTTCTCTTTTTAATTCATAATTAC
*
711179 TTATTTTATTATTTTT-TCTTTTTAAATT-ATAATTAT
1 TTATTTTATTATTTTTCTCTTTTT-AATTCATAATTAC
*
711215 TTATATTATT
1 TTATTTTATT
711225 TTATTTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 22 0.54
37 19 0.46
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (37 bp):
TTATTTTATTATTTTTCTCTTTTTAATTCATAATTAC
Found at i:711669 original size:67 final size:67
Alignment explanation
Indices: 711584--712098 Score: 739
Period size: 67 Copynumber: 7.7 Consensus size: 67
711574 TTCCTAAAAT
* * * *
711584 AAGTTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAACCCTTTGAGATTGTTTCTCTCGTAA
1 AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAA
711649 CA
66 CA
* *
711651 AAGTTTTGTCTCGTTTGAGACAATTTCTGTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAA
1 AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAA
711716 CA
66 CA
* * *
711718 AAGTTTTGTATCGCTTGAGACAATTTCTCTTGAAACATAAACATTTGAGATTGCTTCTCTCGAAA
1 AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAA
711783 CA
66 CA
* * *
711785 AAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAAACATAAACCTTTGATATTGTTTCACTCGAAA
1 AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAA
711850 CA
66 CA
* * * *
711852 AAGTTTTGTCTCGCTAGAGAC-AGTTCTCTTGAAACATAAAACCTTTTAGATTGTTTCTCTTGAA
1 AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACAT-AAACCTTTGAGATTGTTTCTCTCGAA
711916 ACA
65 ACA
* * * * *
711919 AA-TGTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGATATTGTTTATCTTGAAA
1 AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAA
711983 C-
66 CA
* * * * *
711984 AAGTGTTATCTCGCTTGAGACAAATTCTCTTGAAACGTAAACCTTTGATATTGTTTCTCTCGAAA
1 AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAA
712049 CA
66 CA
* * *
712051 AAGTTTTGTCTCACTTGAGGCAATTTCTCTTGAAAAATAAACCTTTGA
1 AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGA
712099 CGAAACAAAG
Statistics
Matches: 402, Mismatches: 42, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
65 2 0.00
66 113 0.28
67 287 0.71
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (67 bp):
AAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAA
CA
Found at i:711952 original size:36 final size:36
Alignment explanation
Indices: 711905--712019 Score: 100
Period size: 36 Copynumber: 3.4 Consensus size: 36
711895 TTTTAGATTG
711905 TTTCTCTTGAAACAAATGTTATCTCGCTTGAGACAA
1 TTTCTCTTGAAACAAATGTTATCTCGCTTGAGACAA
* * ***
711941 TTTCTCTTGAAACATAA----A-C-C-TTTGATATTG
1 TTTCTCTTGAAACA-AATGTTATCTCGCTTGAGACAA
* *
711971 TTTATCTTGAAACAAGTGTTATCTCGCTTGAGACAA
1 TTTCTCTTGAAACAAATGTTATCTCGCTTGAGACAA
*
712007 ATTCTCTTGAAAC
1 TTTCTCTTGAAAC
712020 GTAAACCTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
29 1 0.02
30 18 0.32
31 1 0.02
32 1 0.02
33 2 0.04
34 1 0.02
35 1 0.02
36 30 0.53
37 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATGTTATCTCGCTTGAGACAA
Found at i:712803 original size:139 final size:138
Alignment explanation
Indices: 712488--712853 Score: 380
Period size: 139 Copynumber: 2.6 Consensus size: 138
712478 ATCATTGGTT
* * * * *
712488 ACCGACCAGATCTCCTCAA-AATGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTGCTCATCA
1 ACCGACCAGATCTCCTCAACAA-GAAAGAG-TGTGTCATCCTTAGACAATCAGACTTCCTCATCA
* * * *
712552 TGTAGGAACCTTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGATGTCCTCATCACGTAGGAAC
64 CGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAAGAAC
*
712617 AATGTCGTCC
129 AATGTCATCC
** * * * *
712627 ACTAACCAGATCTCCTCATGGCATAGGAACA-T-CGTCATCCTTAGACAATCAGACTTCCTCATC
1 ACCGACCAGATCTCCTCA--ACA-AGAAAGAGTGTGTCATCCTTAGACAATCAGACTTCCTCATC
* * * * * *
712690 ACGTAGGAATCGTGTTGTCTCTAAATTATCCTTAAATATGGCTATACGTCCTCATCACGTAAGAA
63 ACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAAGAA
712755 CAATGTCATCC
128 CAATGTCATCC
* * * *
712766 ACCGACCAAATCTCCTCAACACGAAAGAGTTGTGTCATCCTTAGACAATCTGACTTCCTCAAT-G
1 ACCGACCAGATCTCCTCAACAAGAAAGAG-TGTGTCATCCTTAGACAATCAGACTTCCTC-ATCA
* * *
712830 CGTAAGAACCCTGTTATCTCCAAA
64 CGTAGGAACCGTGTTGTCTCCAAA
712854 ATCATCTCCA
Statistics
Matches: 182, Mismatches: 37, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
136 4 0.02
137 2 0.01
138 1 0.01
139 168 0.92
140 2 0.01
142 4 0.02
143 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (138 bp):
ACCGACCAGATCTCCTCAACAAGAAAGAGTGTGTCATCCTTAGACAATCAGACTTCCTCATCACG
TAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAAGAACAA
TGTCATCC
Found at i:713300 original size:3 final size:3
Alignment explanation
Indices: 713209--713288 Score: 133
Period size: 3 Copynumber: 26.7 Consensus size: 3
713199 TTTTAATTGT
* * *
713209 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA CTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
713257 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
713289 TCTGTTATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:723192 original size:18 final size:18
Alignment explanation
Indices: 723169--723216 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
723159 AAATTGTCCT
* *
723169 TATTATATATTTGTATAA
1 TATTATATATTTATAAAA
*
723187 TATTATA-AATTATAAAA
1 TATTATATATTTATAAAA
723204 TATTTATATATTT
1 TA-TTATATATTT
723217 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTATATATTTATAAAA
Found at i:723274 original size:32 final size:31
Alignment explanation
Indices: 723193--723274 Score: 83
Period size: 37 Copynumber: 2.4 Consensus size: 31
723183 ATAATATTAT
723193 AAATTATAAAATATTTATATATTTTCTTTAAA
1 AAATTA-AAAATATTTATATATTTTCTTTAAA
* *
723225 AAATTAAATTCATAATATTTATATAATTTTTTTTACA
1 AAATT-AA---A-AATATTTATAT-ATTTTCTTTAAA
723262 AAATTAAAAATAT
1 AAATTAAAAATAT
723275 AAAAAAGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
32 11 0.26
33 2 0.05
35 1 0.02
36 13 0.31
37 15 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATTAAAAATATTTATATATTTTCTTTAAA
Found at i:727186 original size:25 final size:26
Alignment explanation
Indices: 727158--727210 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
727148 TCCAATGTTC
727158 AAATG-ACCAAAATACCCTAAACTCT
1 AAATGAACCAAAATACCCTAAACTCT
* * *
727183 AAATGAACCAGAATACCTTAAAGTCT
1 AAATGAACCAAAATACCCTAAACTCT
727209 AA
1 AA
727211 GATGGTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.21
Consensus pattern (26 bp):
AAATGAACCAAAATACCCTAAACTCT
Found at i:731050 original size:18 final size:18
Alignment explanation
Indices: 731024--731080 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
731014 ACCGGTTACA
*
731024 ACCCGACCTGACCCGTTT
1 ACCCGACCTGACCCGTTG
* *
731042 ACCCAACCTGACCCATTG
1 ACCCGACCTGACCCGTTG
*
731060 ACCCGACCCGACCCGTTG
1 ACCCGACCTGACCCGTTG
731078 ACC
1 ACC
731081 TTTGACAGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.21, C:0.47, G:0.16, T:0.16
Consensus pattern (18 bp):
ACCCGACCTGACCCGTTG
Found at i:734431 original size:15 final size:16
Alignment explanation
Indices: 734407--734439 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
734397 TAAATCAACG
734407 TTTGTCTTTGTCTTGT
1 TTTGTCTTTGTCTTGT
*
734423 TTTGT-TTTGTTTTGT
1 TTTGTCTTTGTCTTGT
734438 TT
1 TT
734440 CAATAGTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.00, C:0.06, G:0.18, T:0.76
Consensus pattern (16 bp):
TTTGTCTTTGTCTTGT
Found at i:741594 original size:22 final size:22
Alignment explanation
Indices: 741567--741616 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
741557 CATTGTTCAA
*
741567 TGTTCACAGTATTGTTTATTAC
1 TGTTCACAGTATTGTTCATTAC
*
741589 TGTTCACGGTATTGTTCATTAC
1 TGTTCACAGTATTGTTCATTAC
741611 TGTTCA
1 TGTTCA
741617 AAAATACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (22 bp):
TGTTCACAGTATTGTTCATTAC
Found at i:748821 original size:36 final size:36
Alignment explanation
Indices: 748781--748919 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
748771 ACGGTACTAG
748781 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
748817 ACATTGATACACGAATATACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
748853 ACATTGATACACGAATGTACCAAAGTTGATATAATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
748889 ACATTGATACACGAATGTATCAAATCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
748920 ATAGATAAAT
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 96 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:754338 original size:19 final size:19
Alignment explanation
Indices: 754314--754417 Score: 127
Period size: 19 Copynumber: 5.3 Consensus size: 19
754304 TCTGCAATTG
754314 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
754333 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
*
754352 TCGTTACGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
754371 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
754392 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
754412 TCGTTG
1 TCGTTG
754418 TGAAAATTCG
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
19 50 0.71
20 5 0.07
21 5 0.07
22 10 0.14
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:754342 original size:41 final size:40
Alignment explanation
Indices: 754293--754417 Score: 164
Period size: 41 Copynumber: 3.1 Consensus size: 40
754283 TTGAAAATCG
*
754293 CGTTGCGATAATCTGCAATTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGAT-ATCTACAATTGTCGTTGCGATTTTCCAAATT
* * * *
754334 CGTTGCGAT-TTTTCAAAT-TCGTTACGATTTTCCAAATT
1 CGTTGCGATATCTACAATTGTCGTTGCGATTTTCCAAATT
*
754372 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATA-TCTACAATTGTCGTTGCGATTTTCCAAATT
754413 CGTTG
1 CGTTG
754418 TGAAAATTCG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
38 28 0.39
39 6 0.08
40 5 0.07
41 33 0.46
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (40 bp):
CGTTGCGATATCTACAATTGTCGTTGCGATTTTCCAAATT
Found at i:754426 original size:13 final size:13
Alignment explanation
Indices: 754408--754433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
754398 GCGATTTTCC
754408 AAATTCGTTGTGA
1 AAATTCGTTGTGA
754421 AAATTCGTTGTGA
1 AAATTCGTTGTGA
754434 TAGTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
AAATTCGTTGTGA
Found at i:754548 original size:10 final size:11
Alignment explanation
Indices: 754517--754550 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
754507 GACACGTATT
754517 ACCACGACCACG
1 ACCACGACC-CG
754529 ACCACGACCCG
1 ACCACGACCCG
754540 ACC-CGACCCG
1 ACCACGACCCG
754550 A
1 A
754551 GACGTGACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:755071 original size:6 final size:6
Alignment explanation
Indices: 755045--755116 Score: 123
Period size: 6 Copynumber: 12.5 Consensus size: 6
755035 TCTCGTCTCG
755045 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
755090 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
755117 AATGGTAATG
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.23
6 51 0.77
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:755122 original size:6 final size:6
Alignment explanation
Indices: 755113--755143 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
755103 GTCGTGGTCG
755113 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
755144 ACGTGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:755293 original size:41 final size:41
Alignment explanation
Indices: 755247--755695 Score: 835
Period size: 41 Copynumber: 11.0 Consensus size: 41
755237 GCAATGAATT
755247 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
*
755288 TGGAAAATCGCAAAGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
* *
755329 TGGAAAAGCGCAACGCGATTTTTAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
*
755370 TGGAAAAGCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
* *
755411 TGGAAAAGCGCAACGCGATTTTCAACTATAGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
*
755452 TGGAAAATCGCAACGCGATTTTCAACTTTCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
755493 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
755534 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
755575 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
755616 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
755657 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGA
755696 TTTTCAACTA
Statistics
Matches: 398, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 398 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
Found at i:755729 original size:41 final size:41
Alignment explanation
Indices: 755684--755761 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
755674 ATTTTCAACT
*
755684 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTAACGCAACGCGAAATGGAAA
*
755725 ATCGCAACGCGATTTTCAACTAACGCAATGCGAAATG
1 ATCGCAACGCGATTTTCAACTAACGCAACGCGAAATG
755762 CAACGCGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTAACGCAACGCGAAATGGAAA
Found at i:764811 original size:15 final size:15
Alignment explanation
Indices: 764791--764841 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
764781 GGCCGGTTAT
764791 ATATATTTAAATTAA
1 ATATATTTAAATTAA
* *
764806 ATATA-TAAATATTAT
1 ATATATTTAA-ATTAA
764821 ATATATTTAAATTAA
1 ATATATTTAAATTAA
764836 ATATAT
1 ATATAT
764842 AAATATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 3 0.10
15 24 0.80
16 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATTTAAATTAA
Found at i:764811 original size:17 final size:17
Alignment explanation
Indices: 764789--764842 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
764779 CGGGCCGGTT
764789 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
764806 ATATATA---AATATT--
1 ATATATATTTAA-ATTAA
764819 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
764836 ATATATA
1 ATATATA
764843 AATATTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 7 0.23
14 2 0.06
15 6 0.19
16 2 0.06
17 14 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:764814 original size:13 final size:13
Alignment explanation
Indices: 764793--764845 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
764783 CCGGTTATAT
*
764793 ATATTTAAATTAA
1 ATATATAAATTAA
764806 ATATATAAATATTATA
1 ATATAT-AA-ATTA-A
*
764822 TATATTTAAATTAA
1 -ATATATAAATTAA
764836 ATATATAAAT
1 ATATATAAAT
764846 ATTATATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 14 0.42
14 3 0.09
15 8 0.24
16 3 0.09
17 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATAAATTAA
Found at i:764823 original size:30 final size:30
Alignment explanation
Indices: 764787--764854 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
764777 ATCGGGCCGG
764787 TTATATATATTTAAATTAAATATATAAATA
1 TTATATATATTTAAATTAAATATATAAATA
764817 TTATATATATTTAAATTAAATATATAAATA
1 TTATATATATTTAAATTAAATATATAAATA
764847 TTATATAT
1 TTATATAT
764855 TTTTTTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTATATATATTTAAATTAAATATATAAATA
Found at i:764849 original size:15 final size:15
Alignment explanation
Indices: 764801--764854 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
764791 ATATATTTAA
764801 ATTAAATATATAAAT
1 ATTAAATATATAAAT
* *
764816 ATTATATATATTTAA-
1 ATTAAATATA-TAAAT
764831 ATTAAATATATAAAT
1 ATTAAATATATAAAT
*
764846 ATTATATAT
1 ATTAAATAT
764855 TTTTTTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 3 0.09
15 26 0.81
16 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATATATAAAT
Found at i:768271 original size:2 final size:2
Alignment explanation
Indices: 768264--768311 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
768254 GTTCCTTATT
768264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
768306 TA TA TA
1 TA TA TA
768312 GAACTTTTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:769996 original size:12 final size:12
Alignment explanation
Indices: 769979--770003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
769969 AGTGTTGGAG
769979 TAACATAGAACA
1 TAACATAGAACA
769991 TAACATAGAACA
1 TAACATAGAACA
770003 T
1 T
770004 CAGAGGTGAA
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:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (12 bp):
TAACATAGAACA
Found at i:772688 original size:3 final size:3
Alignment explanation
Indices: 772675--772730 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
772665 GAACTCAAAT
*
772675 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
772723 TTA TTA TT
1 TTA TTA TT
772731 TGGTGTGACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:778658 original size:23 final size:23
Alignment explanation
Indices: 778640--778728 Score: 151
Period size: 23 Copynumber: 3.9 Consensus size: 23
778630 GAAGTGTCAT
*
778640 GTAGAATTGCACCGAAGTGTCGC
1 GTAGAATTGCACCGAAGTGCCGC
778663 GTAGAATTGCACCGAAGTGCCGC
1 GTAGAATTGCACCGAAGTGCCGC
778686 GTAGAATTGCACCGAAGTGCCGC
1 GTAGAATTGCACCGAAGTGCCGC
* *
778709 GTAGAATTGCAGCGTAGTGC
1 GTAGAATTGCACCGAAGTGC
778729 TATATAAGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.20
Consensus pattern (23 bp):
GTAGAATTGCACCGAAGTGCCGC
Found at i:783372 original size:23 final size:23
Alignment explanation
Indices: 783346--783392 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
783336 TTTGTATAAA
783346 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
* *
783369 TGCACCGAAGTGCCGTGTATAAT
1 TGCACCGAAGTGCCATGTAGAAT
783392 T
1 T
783393 ACACTGTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:786656 original size:72 final size:72
Alignment explanation
Indices: 786539--786688 Score: 282
Period size: 72 Copynumber: 2.1 Consensus size: 72
786529 AACAATCCTC
* *
786539 TGAACAACATCCTCTTCCAGCAATTTCTGGATCTCGTGAGTATTCCAATTCCCCATATCAGTTAC
1 TGAACAACATCCTCTTCCAGCAATTTCTGGATCTCGTGAATATTCCAATTCCCCATATCAGTAAC
786604 GTAATCA
66 GTAATCA
786611 TGAACAACATCCTCTTCCAGCAATTTCTGGATCTCGTGAATATTCCAATTCCCCATATCAGTAAC
1 TGAACAACATCCTCTTCCAGCAATTTCTGGATCTCGTGAATATTCCAATTCCCCATATCAGTAAC
786676 GTAATCA
66 GTAATCA
786683 TGAACA
1 TGAACA
786689 GTGGCATGGG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (72 bp):
TGAACAACATCCTCTTCCAGCAATTTCTGGATCTCGTGAATATTCCAATTCCCCATATCAGTAAC
GTAATCA
Done.