Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold50
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: 2541760
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Warning! 26494 characters in sequence are not A, C, G, or T
File 3 of 16
Found at i:504551 original size:33 final size:33
Alignment explanation
Indices: 504455--504732 Score: 263
Period size: 31 Copynumber: 8.7 Consensus size: 33
504445 TACTGAGTGG
* ** *
504455 TGCCACGGAGTCGTGGACTTAAAAG-AAAAAGG
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * ** *
504487 TGTCACGGAGTTATGGACTTT-CAG--AAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * *
504517 TACTACTGAGTGGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
504550 TACCACTGAGTCGGGGACTTTG-A-AAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
504581 TGCCACTGAGTCGTGGACATT--AG-AAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
504611 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * *
504644 TGCCATTGAGTCATGGACTTTGGAAAGAGAAAAGA
1 TGCCACTGAGTCGTGGACTTT-G-AAGAAAAAAGA
* *
504679 TGCCACTAAGTTGTGGACTTTGAAG--AAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
504710 TGCCACTGAGTCATGGACTTTGA
1 TGCCACTGAGTCGTGGACTTTGA
504733 GAAGAGAGAT
Statistics
Matches: 205, Mismatches: 32, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
30 47 0.23
31 56 0.27
32 20 0.10
33 53 0.26
34 2 0.01
35 27 0.13
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (33 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
Found at i:504741 original size:68 final size:68
Alignment explanation
Indices: 504511--504741 Score: 234
Period size: 68 Copynumber: 3.5 Consensus size: 68
504501 GGACTTTCAG
* * ** * * * *
504511 AAAAGATACTACTGAGTGGTGGACTTT-G-AAGA-AAAAAGATACCACTGAGTCGGGGACTTTGA
1 AAAAGATGCCACTGAGTCATGGACTTTGGAAAGAGAAAGAGATGCCACTAAGTCGTGGACTTTGA
504573 A-A
66 AGA
* * *
504575 AAAAGATGCCACTGAGTCGTGGACATT------AGAAAGAGATGCCACTGAGTCGTGGACTTTGA
1 AAAAGATGCCACTGAGTCATGGACTTTGGAAAGAGAAAGAGATGCCACTAAGTCGTGGACTTTGA
504634 AGAA
66 AG-A
* *
504638 AAAAGATGCCATTGAGTCATGGACTTTGGAAAGAGAAA-AGATGCCACTAAGTTGTGGACTTTGA
1 AAAAGATGCCACTGAGTCATGGACTTTGGAAAGAGAAAGAGATGCCACTAAGTCGTGGACTTTGA
504702 AG-
66 AGA
504704 AAAAGATGCCACTGAGTCATGGACTTTGAGAAGAGAGA
1 AAAAGATGCCACTGAGTCATGGACTTTG-GAA-AGAGA
504742 TTTGAAGAAT
Statistics
Matches: 143, Mismatches: 13, Indels: 18
0.82 0.07 0.10
Matches are distributed among these distances:
60 1 0.01
61 28 0.20
63 25 0.17
64 23 0.16
66 27 0.19
67 3 0.02
68 31 0.22
69 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (68 bp):
AAAAGATGCCACTGAGTCATGGACTTTGGAAAGAGAAAGAGATGCCACTAAGTCGTGGACTTTGA
AGA
Found at i:511369 original size:24 final size:24
Alignment explanation
Indices: 511341--511391 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
511331 ATAATGTATG
*
511341 GATACATGAACAGTGATGAATAGT
1 GATACATGAACAGTGATGAACAGT
* *
511365 GATACTTGAACAGTTATGAACAGT
1 GATACATGAACAGTGATGAACAGT
511389 GAT
1 GAT
511392 GTATCGATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (24 bp):
GATACATGAACAGTGATGAACAGT
Found at i:515044 original size:20 final size:20
Alignment explanation
Indices: 515006--515045 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
514996 TTACAAATTT
515006 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
515027 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
515046 TATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:516816 original size:15 final size:16
Alignment explanation
Indices: 516789--516824 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
516779 ATCAAGGGGG
516789 AGAAATGTTTTTTTAA
1 AGAAATGTTTTTTTAA
516805 AGAAAT-TTTTTTTAA
1 AGAAATGTTTTTTTAA
*
516820 CGAAA
1 AGAAA
516825 GCCTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (16 bp):
AGAAATGTTTTTTTAA
Found at i:517450 original size:20 final size:19
Alignment explanation
Indices: 517404--517462 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 19
517394 TTGTATTGAT
* *
517404 ACATTATATCGATACATGT
1 ACATTGTATCGATACATGA
*
517423 TCATTGTATCGATACATGA
1 ACATTGTATCGATACATGA
517442 ACAATTGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
517462 A
1 A
517463 ACTGGCAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:521965 original size:34 final size:32
Alignment explanation
Indices: 521922--521986 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
521912 TACAAGCCAA
521922 TGTATCGATACAAT-TTGGTCATGTATCGATACAT
1 TGTATCGATAC-ATCTT-GT-ATGTATCGATACAT
521956 TGTATCGATACATCTTGTATGTATCGATACA
1 TGTATCGATACATCTTGTATGTATCGATACA
521987 AATAGTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 4 0.13
34 13 0.43
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTGTATGTATCGATACAT
Found at i:521975 original size:15 final size:13
Alignment explanation
Indices: 521943--521968 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
521933 AATTTGGTCA
521943 TGTATCGATACAT
1 TGTATCGATACAT
521956 TGTATCGATACAT
1 TGTATCGATACAT
521969 CTTGTATGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:522079 original size:20 final size:21
Alignment explanation
Indices: 522028--522080 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
522018 GCCAATCAAC
*
522028 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
* *
522049 AGTATCAATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
522069 TGTATCGATACA
1 TGTATCGATACA
522081 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 13 0.50
21 12 0.46
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:522086 original size:13 final size:13
Alignment explanation
Indices: 522068--522092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
522058 ACATTTGGTC
522068 ATGTATCGATACA
1 ATGTATCGATACA
522081 ATGTATCGATAC
1 ATGTATCGATAC
522093 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:529859 original size:33 final size:32
Alignment explanation
Indices: 529817--529880 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
529807 TACAAGCCAA
*
529817 TGTATCGATACATTTTGGGATGTATCAATACAT
1 TGTATCGATACATCTTGGG-TGTATCAATACAT
* *
529850 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCAATACA
529881 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCAATACAT
Found at i:529969 original size:20 final size:20
Alignment explanation
Indices: 529944--530007 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
529934 TTCTTAACAA
529944 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
529964 GTATCGATACA-------AT
1 GTATCGATACATTTGGTCAT
529977 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
529997 GTATCGATACA
1 GTATCGATACA
530008 ATGTATCGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 13 0.35
20 24 0.65
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (20 bp):
GTATCGATACATTTGGTCAT
Found at i:529980 original size:13 final size:12
Alignment explanation
Indices: 529961--530019 Score: 63
Period size: 13 Copynumber: 5.1 Consensus size: 12
529951 TACATTTGGT
529961 CATGTATCGATA
1 CATGTATCGATA
529973 CAATGTATCGATA
1 C-ATGTATCGATA
*
529986 CAT-T-T-GGT-
1 CATGTATCGATA
529994 CATGTATCGATA
1 CATGTATCGATA
530006 CAATGTATCGATA
1 C-ATGTATCGATA
530019 C
1 C
530020 TGTGCAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 2 0.05
11 3 0.08
12 4 0.10
13 24 0.62
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:529986 original size:33 final size:33
Alignment explanation
Indices: 529940--530019 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
529930 TACATTCTTA
529940 ACAA-GTATCGATACATTTGGTCATGTATCGAT
1 ACAATGTATCGATACATTTGGTCATGTATCGAT
529972 ACAATGTATCGATACATTTGGTCATGTATCGAT
1 ACAATGTATCGATACATTTGGTCATGTATCGAT
530005 ACAATGTATCGATAC
1 ACAATGTATCGATAC
530020 TGTGCAATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 4 0.09
33 43 0.91
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (33 bp):
ACAATGTATCGATACATTTGGTCATGTATCGAT
Found at i:530033 original size:33 final size:33
Alignment explanation
Indices: 529940--530040 Score: 127
Period size: 33 Copynumber: 3.1 Consensus size: 33
529930 TACATTCTTA
* *
529940 ACAA-GTATCGATACATTTGGTCATGTATCGAT
1 ACAATGTATCGATACATGTGATCATGTATCGAT
* *
529972 ACAATGTATCGATACATTTGGTCATGTATCGAT
1 ACAATGTATCGATACATGTGATCATGTATCGAT
530005 ACAATGTATCGATAC-TGTGCAATC-TGTATCGAT
1 ACAATGTATCGATACATGTG--ATCATGTATCGAT
530038 ACA
1 ACA
530041 TTTAAAGGTG
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
32 7 0.11
33 55 0.86
34 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (33 bp):
ACAATGTATCGATACATGTGATCATGTATCGAT
Found at i:531975 original size:21 final size:21
Alignment explanation
Indices: 531951--531999 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
531941 TGAATTGGAA
*
531951 GTGTTTTGGTACAAAATCGAG
1 GTGTTTCGGTACAAAATCGAG
531972 GTGTTTCGGTACAAAATCGAG
1 GTGTTTCGGTACAAAATCGAG
531993 GTGTTTC
1 GTGTTTC
532000 AGATTTTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (21 bp):
GTGTTTCGGTACAAAATCGAG
Found at i:532725 original size:8 final size:8
Alignment explanation
Indices: 532712--532737 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
532702 TTCATCATTC
532712 ATCACAAA
1 ATCACAAA
532720 ATCACAAA
1 ATCACAAA
532728 ATCACAAA
1 ATCACAAA
532736 AT
1 AT
532738 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:541496 original size:13 final size:13
Alignment explanation
Indices: 541478--541508 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
541468 ACATTTCTTC
541478 ATGTATCGATACA
1 ATGTATCGATACA
541491 ATGTATCGATACA
1 ATGTATCGATACA
*
541504 TTGTA
1 ATGTA
541509 CCATGTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:541598 original size:19 final size:20
Alignment explanation
Indices: 541574--541627 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
541564 ACAATTTGTC
*
541574 CATGTATCGATACATTG-AA
1 CATGTATCGATACATAGCAA
* *
541593 CATGTATCGATACAAAGCAG
1 CATGTATCGATACATAGCAA
541613 CATGTATCGATACAT
1 CATGTATCGATACAT
541628 CTGGGTGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACATAGCAA
Found at i:542173 original size:17 final size:17
Alignment explanation
Indices: 542147--542211 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
542137 GTTTTCGCTT
542147 TTCT-CCCCTTAAAAAA
1 TTCTCCCCCTTAAAAAA
**
542163 TTCTCCCCCTTAAACGA
1 TTCTCCCCCTTAAAAAA
* *
542180 TTATCTCCTCTTAAAAAA
1 TTCTC-CCCCTTAAAAAA
542198 TTCTCCCCCTTAAA
1 TTCTCCCCCTTAAA
542212 CGATTATCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
16 4 0.10
17 22 0.56
18 13 0.33
ACGTcount: A:0.31, C:0.34, G:0.02, T:0.34
Consensus pattern (17 bp):
TTCTCCCCCTTAAAAAA
Found at i:542194 original size:18 final size:18
Alignment explanation
Indices: 542148--542220 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 18
542138 TTTTCGCTTT
** *
542148 TCTCCCCTTAAAAAATTC
1 TCTCCCCTTAAACGATTA
542166 TC-CCCCTTAAACGATTA
1 TCTCCCCTTAAACGATTA
* ** *
542183 TCTCCTCTTAAAAAATTC
1 TCTCCCCTTAAACGATTA
542201 TC-CCCCTTAAACGATTA
1 TCTCCCCTTAAACGATTA
542218 TCT
1 TCT
542221 TCTCCCCTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
17 27 0.64
18 15 0.36
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.34
Consensus pattern (18 bp):
TCTCCCCTTAAACGATTA
Found at i:542194 original size:35 final size:35
Alignment explanation
Indices: 542148--542220 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
542138 TTTTCGCTTT
542148 TCTCCCCTTAAAAAATTCTCCCCCTTAAACGATTA
1 TCTCCCCTTAAAAAATTCTCCCCCTTAAACGATTA
*
542183 TCTCCTCTTAAAAAATTCTCCCCCTTAAACGATTA
1 TCTCCCCTTAAAAAATTCTCCCCCTTAAACGATTA
542218 TCT
1 TCT
542221 TCTCCCCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.34
Consensus pattern (35 bp):
TCTCCCCTTAAAAAATTCTCCCCCTTAAACGATTA
Found at i:542242 original size:21 final size:19
Alignment explanation
Indices: 542216--542255 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
542206 CTTAAACGAT
542216 TATCTTC-TCCCCTTTTTA
1 TATCTTCTTCCCCTTTTTA
542234 TATCTTCTTCCCCTTTTTA
1 TATCTTCTTCCCCTTTTTA
542253 TAT
1 TAT
542256 AAAAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.12, C:0.30, G:0.00, T:0.57
Consensus pattern (19 bp):
TATCTTCTTCCCCTTTTTA
Found at i:549303 original size:13 final size:13
Alignment explanation
Indices: 549285--549309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
549275 ATATTGCACA
549285 GTATCGATACATT
1 GTATCGATACATT
549298 GTATCGATACAT
1 GTATCGATACAT
549310 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:549322 original size:20 final size:21
Alignment explanation
Indices: 549297--549349 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
549287 ATCGATACAT
*
549297 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
549317 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
549338 TGTATCGATACA
1 TGTATCGATACA
549350 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:549427 original size:13 final size:13
Alignment explanation
Indices: 549409--549434 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
549399 TACACATAAG
549409 ATGTATCGATACA
1 ATGTATCGATACA
549422 ATGTATCGATACA
1 ATGTATCGATACA
549435 TCCCAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:549451 original size:33 final size:32
Alignment explanation
Indices: 549391--549454 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
549381 CTTAACTGTT
* *
549391 TGTATCGATACACATAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
549423 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
549455 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:549541 original size:73 final size:73
Alignment explanation
Indices: 549417--549602 Score: 327
Period size: 73 Copynumber: 2.5 Consensus size: 73
549407 AGATGTATCG
549417 ATACAATGTATCGATACATCCCAAAATGTATCGATACATTGGCTTGTAACGGCTAGTAACAGCTA
1 ATAC-ATGTATCGATACATCCCAAAATGTATCGATACATTGGCTTGTAACGGCTAGTAACAGCTA
549482 TATTTTCAA
65 TATTTTCAA
* * *
549491 ATGCATGTATCGATACATCCCAAAATGTATCGATACATTGGCTTGTAACGGCTAGTAACGGTTAT
1 ATACATGTATCGATACATCCCAAAATGTATCGATACATTGGCTTGTAACGGCTAGTAACAGCTAT
549556 ATTTTCAA
66 ATTTTCAA
*
549564 ATACATGTATCGATACATCCCAAATTGTATCGATACATT
1 ATACATGTATCGATACATCCCAAAATGTATCGATACATT
549603 AACATGGGAT
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 104 0.97
74 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (73 bp):
ATACATGTATCGATACATCCCAAAATGTATCGATACATTGGCTTGTAACGGCTAGTAACAGCTAT
ATTTTCAA
Found at i:557600 original size:22 final size:22
Alignment explanation
Indices: 557575--557619 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
557565 CGAAATTGTT
557575 AAATTGCTTT-ATTAAGGGGGAG
1 AAATT-CTTTGATTAAGGGGGAG
*
557597 AAATTTTTTGATTAAGGGGGAG
1 AAATTCTTTGATTAAGGGGGAG
557619 A
1 A
557620 GATAAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (22 bp):
AAATTCTTTGATTAAGGGGGAG
Found at i:558193 original size:13 final size:13
Alignment explanation
Indices: 558175--558199 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
558165 ATATTGCACA
558175 GTATCGATACATT
1 GTATCGATACATT
558188 GTATCGATACAT
1 GTATCGATACAT
558200 GACCAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:558294 original size:19 final size:19
Alignment explanation
Indices: 558270--558328 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
558260 CTTAACTGTT
558270 TGTATCGATGCACACAAGA
1 TGTATCGATGCACACAAGA
558289 TGTATC---G-ACAC-A-A
1 TGTATCGATGCACACAAGA
558302 TGTATCGAT-CTACACAAGA
1 TGTATCGATGC-ACACAAGA
558321 TGTATCGA
1 TGTATCGA
558329 CACAATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
13 7 0.21
14 1 0.03
15 4 0.12
16 1 0.03
17 4 0.12
18 1 0.03
19 15 0.45
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (19 bp):
TGTATCGATGCACACAAGA
Found at i:558301 original size:15 final size:15
Alignment explanation
Indices: 558281--558341 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
558271 GTATCGATGC
558281 ACACAAGATGTATCG
1 ACACAAGATGTATCG
*
558296 ACACAATGTATCG-ATCT
1 ACACAA-G-AT-GTATCG
558313 ACACAAGATGTATCG
1 ACACAAGATGTATCG
558328 ACAC-A-ATGTATCG
1 ACACAAGATGTATCG
558341 A
1 A
558342 TACATCCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 9 0.22
14 2 0.05
15 15 0.38
16 2 0.05
17 11 0.28
18 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (15 bp):
ACACAAGATGTATCG
Found at i:558306 original size:13 final size:13
Alignment explanation
Indices: 558288--558341 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 13
558278 TGCACACAAG
558288 ATGTATCGACACA
1 ATGTATCGACACA
558301 ATGTATCGATCTACACAA
1 ATGTATCG----ACAC-A
558319 GATGTATCGACACA
1 -ATGTATCGACACA
558333 ATGTATCGA
1 ATGTATCGA
558342 TACATCCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 17 0.49
14 1 0.03
15 4 0.11
17 4 0.11
18 1 0.03
19 8 0.23
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (13 bp):
ATGTATCGACACA
Found at i:558317 original size:32 final size:32
Alignment explanation
Indices: 558270--558361 Score: 132
Period size: 32 Copynumber: 2.8 Consensus size: 32
558260 CTTAACTGTT
558270 TGTATCGATGCACACAAGATGTATCGACACAA
1 TGTATCGATGCACACAAGATGTATCGACACAA
558302 TGTATCGAT-CTACACAAGATGTATCGACACAA
1 TGTATCGATGC-ACACAAGATGTATCGACACAA
* * *
558334 TGTATCGATACATCCCAAAATGTATCGA
1 TGTATCGATGCA-CACAAGATGTATCGA
558362 TACATTGGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 40 0.73
33 14 0.25
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (32 bp):
TGTATCGATGCACACAAGATGTATCGACACAA
Found at i:560433 original size:13 final size:13
Alignment explanation
Indices: 560415--560445 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
560405 ACATTTCTTC
560415 ATGTATCGATACA
1 ATGTATCGATACA
560428 ATGTATCGATACA
1 ATGTATCGATACA
*
560441 TTGTA
1 ATGTA
560446 CAATGTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:560452 original size:33 final size:33
Alignment explanation
Indices: 560395--560461 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
560385 GTTACAAGCT
*
560395 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTCTACATGTATCGATACA
* *
560428 ATGTATCGATACA-TTGTACAATGTATTGATACA
1 ATGTATCGATACATTTCTAC-ATGTATCGATACA
560461 A
1 A
560462 ATAGTGATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTTCTACATGTATCGATACA
Found at i:560520 original size:21 final size:20
Alignment explanation
Indices: 560494--560543 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
560484 CAATTTCATA
**
560494 TATCGATACAATTTGTCCATG
1 TATCGATACAA-TTGAACATG
560515 TATCGATAC-ATTGAACATG
1 TATCGATACAATTGAACATG
560534 TATCGATACA
1 TATCGATACA
560544 TTGCATCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 16 0.62
20 1 0.04
21 9 0.35
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
TATCGATACAATTGAACATG
Found at i:562623 original size:102 final size:102
Alignment explanation
Indices: 562403--562628 Score: 326
Period size: 102 Copynumber: 2.2 Consensus size: 102
562393 GAGGTTGAAA
* * ** *
562403 TATCCCCGATGGTGAAAAATCAATATTTTGGAAACAAAAATGGGGTTGAAGTATCCCTGATGGTG
1 TATCCCCGATGGTGAAAAATCAATAGTTTGGAAACAAAAATAGGGTTGAAGTATCCCCAACGGTG
*
562468 AAAAGTTGATATTTTGGAAATAATATCAGGGTTGGAG
66 AAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAG
* * * *
562505 TATCCCCAATGGTGAAAAATCGATAGTTTGGAAATAAAAATAGGGTTGGAGTATCCCCAACGGTG
1 TATCCCCGATGGTGAAAAATCAATAGTTTGGAAACAAAAATAGGGTTGAAGTATCCCCAACGGTG
562570 AAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAG
66 AAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAG
*** *
562607 TATTTTCGATGATGAAAAATCA
1 TATCCCCGATGGTGAAAAATCA
562629 GTGTTTTAGA
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 108 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (102 bp):
TATCCCCGATGGTGAAAAATCAATAGTTTGGAAACAAAAATAGGGTTGAAGTATCCCCAACGGTG
AAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAG
Found at i:562624 original size:51 final size:51
Alignment explanation
Indices: 562403--562609 Score: 256
Period size: 51 Copynumber: 4.1 Consensus size: 51
562393 GAGGTTGAAA
* * ** * * *
562403 TATCCCCGATGGTGAAAAATCAATATTTTGGAAACAAAAAT-GGGGTTGAAG
1 TATCCCCAATGGTGAAAAGTTGATATTTTGGAAA-TAAAATCAGGGTTGGAG
** *
562454 TATCCCTGATGGTGAAAAGTTGATATTTTGGAAATAATATCAGGGTTGGAG
1 TATCCCCAATGGTGAAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAG
* * *
562505 TATCCCCAATGGTGAAAAATCGATAGTTTGGAAATAAAAAT-AGGGTTGGAG
1 TATCCCCAATGGTGAAAAGTTGATATTTTGGAAAT-AAAATCAGGGTTGGAG
*
562556 TATCCCCAACGGTGAAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAG
1 TATCCCCAATGGTGAAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAG
562607 TAT
1 TAT
562610 TTTCGATGAT
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 9 0.07
51 122 0.90
52 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (51 bp):
TATCCCCAATGGTGAAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAG
Found at i:562659 original size:102 final size:102
Alignment explanation
Indices: 562464--562662 Score: 260
Period size: 102 Copynumber: 2.0 Consensus size: 102
562454 TATCCCTGAT
* *
562464 GGTGAAAAGTTGATATTTTGGAAATAATATCAGGGTTGGAGTATCCCCAATGGTGAAAAATCGAT
1 GGTGAAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAGTATCCCCAATGATGAAAAATCGAT
* * * *
562529 AGTTTGGAAATAAAAATAGGGTTGGAGTATCCCCAAC
66 AGTTTAGAAATAAAAATAAGATTAGAGTATCCCCAAC
*** *
562566 GGTGAAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAGTATTTTCGATGATGAAAAATC-AG
1 GGTGAAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAGTATCCCCAATGATGAAAAATCGA-
562630 T-GTTTTAGAAAT-AAAATCAAGATTAGAGTATCC
65 TAG-TTTAGAAATAAAAAT-AAGATTAGAGTATCC
562663 ACTCAAAAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 7 0.08
102 77 0.92
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.30
Consensus pattern (102 bp):
GGTGAAAAGTTGATATTTTGGAAATAAAATCAGGGTTGGAGTATCCCCAATGATGAAAAATCGAT
AGTTTAGAAATAAAAATAAGATTAGAGTATCCCCAAC
Found at i:562705 original size:79 final size:78
Alignment explanation
Indices: 562622--562766 Score: 184
Period size: 79 Copynumber: 1.8 Consensus size: 78
562612 TCGATGATGA
* *
562622 AAAATCAGTGTTTTAGAAATAAAATCAAGATTAGAGTATCCAC-TCAAAAATAATGGGGTTGGAG
1 AAAATCAATGTTTTAGAAATAAAACCAAGATTAGAGTATCC-CTTCAAAAATAAT-GGGTTGGAG
562686 TATCCATGATAGTGG
64 TATCCATGATAGTGG
* * ** * * *
562701 AAAATCAATGTTTTGGAAATAGAACCGGGGTTGGAGTATCCCTTCGAAAATAATGGGTTGGAGTA
1 AAAATCAATGTTTTAGAAATAAAACCAAGATTAGAGTATCCCTTCAAAAATAATGGGTTGGAGTA
562766 T
66 T
562767 TCCCTTGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
78 13 0.23
79 43 0.77
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (78 bp):
AAAATCAATGTTTTAGAAATAAAACCAAGATTAGAGTATCCCTTCAAAAATAATGGGTTGGAGTA
TCCATGATAGTGG
Found at i:562766 original size:27 final size:27
Alignment explanation
Indices: 562727--562797 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
562717 AAATAGAACC
562727 GGGGTTGGAGTATCCCTTCGAAAATAAT
1 GGGGTTGGAGTATCCCTT-GAAAATAAT
*
562755 -GGGTTGGAGTATTCCCTTGAAAGTAAT
1 GGGGTTGGAGTA-TCCCTTGAAAATAAT
562782 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
562798 CAATGGTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCTTGAAAATAAT
Found at i:565177 original size:20 final size:20
Alignment explanation
Indices: 565152--565226 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
565142 AATTGCCTGC
*
565152 ATGTATCTATACATTGAAAA
1 ATGTATCGATACATTGAAAA
* *
565172 ATGTATCGATACAATGATAA
1 ATGTATCGATACATTGAAAA
* ***
565192 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTGAAAA
565212 ATGTATCGATACATT
1 ATGTATCGATACATT
565227 TCCTTGGCAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:565782 original size:24 final size:22
Alignment explanation
Indices: 565749--565798 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 22
565739 TCATAAAATC
565749 AATAAAATTT-TAAAAACTGATTT
1 AATAAAATTTATAAAAA-T-ATTT
565772 AATACAAATTTAATAAAAATATTT
1 AATA-AAATTT-ATAAAAATATTT
565796 AAT
1 AAT
565799 GAATTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.17
24 13 0.54
25 1 0.04
26 6 0.25
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
AATAAAATTTATAAAAATATTT
Found at i:565869 original size:18 final size:18
Alignment explanation
Indices: 565848--565884 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
565838 AAATTTACGG
565848 AATA-GAAAATATTTTAAA
1 AATAGGAAAA-ATTTTAAA
565866 AATAGGAAAAATTTTAAA
1 AATAGGAAAAATTTTAAA
565884 A
1 A
565885 CTCATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (18 bp):
AATAGGAAAAATTTTAAA
Found at i:566073 original size:152 final size:148
Alignment explanation
Indices: 565734--566147 Score: 449
Period size: 152 Copynumber: 2.8 Consensus size: 148
565724 AAACAAATGC
* * * * ** * * *
565734 AAAACTCATAAAATCAA-TAAAATTTTAAAAACTGATTTAATACAAATTTAATAAAAATATTT-A
1 AAAACCCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATGAATTAAACAATAATATTTGA
* * * * * *
565797 ATGAATTTCAAAAATTATAAACTCAGAAAAATCTCACAAAAAAATTTACGGAATAGAAAATATTT
66 A-GAATTTTAAAAATTATAAACTCAAAAAAATCTTACAGAAAAATTTATGGAATAGAAAATATCT
* *
565862 TAAAAATAGGAAAAATTTT
130 TAAAAATAGAAAAAACTTT
* * * *
565881 AAAACTCATAAATTAAATTAAAATTTTCAAAACTATTTTAATATTAATTAAACAATAATA-TTGA
1 AAAACCCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATGAATTAAACAATAATATTTGA
* *
565945 A-AATTTTTAAAAATTATAAACTCAAAAAAATCTTACTGAAAAATTTATGGAGTAGAAAACTCTG
66 AGAA-TTTTAAAAATTATAAACTCAAAAAAATCTTACAGAAAAATTTATGGAATAGAAAA-----
* *
566009 TATCTTGATAATAGAAAAAACTTT
125 TATCTTAAAAATAGAAAAAACTTT
** *
566033 AAAACCCATAAAATAAATTAATTTTTTTAAAACTAATTTAATATGAATTAAACAATAATATTTGA
1 AAAACCCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATGAATTAAACAATAATATTTGA
* * *
566098 AGAATTTTAAAAATTATAAACTTAAAAAAATCCTATCAGAGAAATTTATG
66 AGAATTTTAAAAATTATAAACTCAAAAAAATCTTA-CAGAAAAATTTATG
566148 AGGCAAAAAA
Statistics
Matches: 223, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
146 2 0.01
147 65 0.29
148 36 0.16
152 72 0.32
153 34 0.15
154 14 0.06
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (148 bp):
AAAACCCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATGAATTAAACAATAATATTTGA
AGAATTTTAAAAATTATAAACTCAAAAAAATCTTACAGAAAAATTTATGGAATAGAAAATATCTT
AAAAATAGAAAAAACTTT
Found at i:566203 original size:152 final size:151
Alignment explanation
Indices: 565880--566189 Score: 351
Period size: 152 Copynumber: 2.0 Consensus size: 151
565870 GGAAAAATTT
* * *
565880 TAAAACTCATAAATTAAATTAAAATTTTCAAAACTATTTTAATATTAATTAAACAATAATATTGA
1 TAAAAC-CATAAAATAAATTAAAATTTTCAAAACTAATTTAATATGAATTAAACAATAATATTGA
* * * * **
565945 AAATTTTTAAAAATTATAAACTCAAAAAAATCTTACTGAAAAATTTATGGAGTAGAAAACTCTGT
65 AAATTTTTAAAAATTATAAACTCAAAAAAATCCTACAGAAAAATTTATGGAGCAAAAAACTCTAC
* * *
566010 ATCTTGATAATAGAAAAAACTT
130 ATCTTGATAATACAAAAAAATC
** *
566032 TAAAACCCATAAAATAAATTAATTTTTTTAAAACTAATTTAATATGAATTAAACAATAATATTTG
1 TAAAA-CCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATGAATTAAACAATAATA-TTG
* *
566097 AAGAA-TTTTAAAAATTATAAACTTAAAAAAATCCTATCAGAGAAATTTAT-GAGGCAAAAAACT
64 AA-AATTTTTAAAAATTATAAACTCAAAAAAATCCTA-CAGAAAAATTTATGGA-GCAAAAAACT
*
566160 -TCACATTTTGA-AA-ACAAGAAAAATC
126 CT-ACATCTTGATAATACAA-AAAAATC
566185 TAAAA
1 TAAAA
566190 GAAAATTCAA
Statistics
Matches: 133, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
152 56 0.42
153 50 0.38
154 27 0.20
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (151 bp):
TAAAACCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATGAATTAAACAATAATATTGAA
AATTTTTAAAAATTATAAACTCAAAAAAATCCTACAGAAAAATTTATGGAGCAAAAAACTCTACA
TCTTGATAATACAAAAAAATC
Found at i:572689 original size:23 final size:23
Alignment explanation
Indices: 572663--572706 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
572653 TATAATTATT
572663 TTTAAAATAT-AATATTTAATAAA
1 TTTAAAATATAAAT-TTTAATAAA
*
572686 TTTAAAATTTAAATTTTAATA
1 TTTAAAATATAAATTTTAATA
572707 TATGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAAAATATAAATTTTAATAAA
Found at i:574323 original size:2 final size:2
Alignment explanation
Indices: 574316--574347 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
574306 ATCTAAGATT
574316 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
574348 GAAAATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:574421 original size:27 final size:27
Alignment explanation
Indices: 574355--574424 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
574345 ATAGAAAATG
574355 TTTATAAAAAAA-TTATAAATGTTAAAA
1 TTTA-AAAAAAATTTATAAATGTTAAAA
** *
574382 TTTAAATCTAAATTTATAGAATGTT-AAC
1 TTTAAA-AAAAATTTATA-AATGTTAAAA
574410 TTTAAAAAAAATTTA
1 TTTAAAAAAAATTTA
574425 CATAAATCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.06
27 14 0.40
28 13 0.37
29 6 0.17
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (27 bp):
TTTAAAAAAAATTTATAAATGTTAAAA
Found at i:574651 original size:19 final size:20
Alignment explanation
Indices: 574629--574673 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
574619 TATTTAAAAA
574629 ATATTAAAAAATTAT-TTTT
1 ATATTAAAAAATTATATTTT
*
574648 ATATT-AAAATTTATATTTT
1 ATATTAAAAAATTATATTTT
574667 -TATTAAA
1 ATATTAAA
574674 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTAAAAAATTATATTTT
Found at i:576055 original size:12 final size:12
Alignment explanation
Indices: 576014--576055 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
576004 AGCACAGTCT
576014 TATTTAAATATAA
1 TATTTAAAT-TAA
*
576027 TATATTATATT-A
1 TAT-TTAAATTAA
576039 TATTTAAATTAA
1 TATTTAAATTAA
576051 TATTT
1 TATTT
576056 TTCTCTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.24
12 10 0.40
13 4 0.16
14 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTTAAATTAA
Found at i:576871 original size:13 final size:13
Alignment explanation
Indices: 576853--576879 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
576843 ACATTATGCT
576853 TTGTATCGATACA
1 TTGTATCGATACA
576866 TTGTATCGATACA
1 TTGTATCGATACA
576879 T
1 T
576880 GTTAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:576889 original size:19 final size:19
Alignment explanation
Indices: 576865--576920 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
576855 GTATCGATAC
**
576865 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
576884 ATTGTATCGATACATTGACA
1 ATTGTATCGATACA-TGACA
576904 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
576921 GAATGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:576908 original size:20 final size:20
Alignment explanation
Indices: 576865--576918 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
576855 GTATCGATAC
**
576865 ATTGTATCGATACA-TGTTA
1 ATTGTATCGATACATTGACA
576884 ATTGTATCGATACATTGACA
1 ATTGTATCGATACATTGACA
576904 ATTGTATCGATACAT
1 ATTGTATCGATACAT
576919 GAGAATGGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (20 bp):
ATTGTATCGATACATTGACA
Found at i:578695 original size:33 final size:33
Alignment explanation
Indices: 578658--578724 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
578648 TTCAACGATC
578658 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
578691 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
578724 T
1 T
578725 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:578696 original size:13 final size:13
Alignment explanation
Indices: 578678--578702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
578668 CATAAAATGT
578678 TGTATCGATACAA
1 TGTATCGATACAA
578691 TGTATCGATACA
1 TGTATCGATACA
578703 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:578783 original size:13 final size:13
Alignment explanation
Indices: 578765--578789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
578755 ATTACTCAAA
578765 TGTATCGATACAT
1 TGTATCGATACAT
578778 TGTATCGATACA
1 TGTATCGATACA
578790 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:578891 original size:52 final size:52
Alignment explanation
Indices: 578798--578925 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
578788 CACTGATCTT
*
578798 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
*
578849 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
578901 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
578926 TCATATTTCG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 19 0.26
52 51 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:582798 original size:21 final size:20
Alignment explanation
Indices: 582774--582815 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
582764 ATATTAAAAG
582774 ATTAGCTAATGAA-AATGAAGA
1 ATTAGCTAA-GAATAAT-AAGA
582795 ATTAGCTAAGAATAATAAGA
1 ATTAGCTAAGAATAATAAGA
582815 A
1 A
582816 CTTGCATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (20 bp):
ATTAGCTAAGAATAATAAGA
Found at i:587577 original size:52 final size:52
Alignment explanation
Indices: 587479--587597 Score: 136
Period size: 52 Copynumber: 2.3 Consensus size: 52
587469 TGAAAATAAT
* *
587479 GGGGTTAGAGTGTCCCCGATTATGGAAAATCAGTGTTCTAAAAAATAAAATC
1 GGGGTTAGAGTATCCCCGATTATGAAAAATCAGTGTTCTAAAAAATAAAATC
* * **
587531 GGGGTTAGAGTATCCCCGATTGTGAAAAAATC-GATGCTT-T-AGAAATAAGGTC
1 GGGGTTAGAGTATCCCCGATTATG-AAAAATCAG-TG-TTCTAAAAAATAAAATC
587583 GGGGTTAGAGTATCC
1 GGGGTTAGAGTATCC
587598 TCGTAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
52 47 0.81
53 9 0.16
54 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (52 bp):
GGGGTTAGAGTATCCCCGATTATGAAAAATCAGTGTTCTAAAAAATAAAATC
Found at i:587596 original size:132 final size:132
Alignment explanation
Indices: 587354--587690 Score: 446
Period size: 132 Copynumber: 2.6 Consensus size: 132
587344 AATAGGGCTG
**
587354 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTATCCCAAAT
1 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTATCCCCGAT
* * * **
587419 TGTGAAAAAATCGATTCTTTAGAAATAAGGCCGGGGTTGGAGTATCC-CTGTGAAAATAATGGGG
66 TGTGAAAAAATCGATGCTTTAGAAATAAGGCCGGGGTTAGAGTATCCTC-GTAAAAATAACAGGG
587483 TTA
130 TTA
* *
587486 GAGTGTCCCCGATTATGGAAAATCAGTGTTCTAAAAAATAAAATCGGGGTTAGAGTATCCCCGAT
1 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTATCCCCGAT
*
587551 TGTGAAAAAATCGATGCTTTAGAAATAAGGTCGGGGTTAGAGTATCCTCGTAAAAATAACAGGGT
66 TGTGAAAAAATCGATGCTTTAGAAATAAGGCCGGGGTTAGAGTATCCTCGTAAAAATAACAGGGT
*
587616 TG
131 TA
* * * *** * ** *
587618 GAGTATCCCCAATTGT-GAGAAATTGGTGTT-TTGGAACTAAAATCGAAGTTGGAGTATCCCCGA
1 GAGTATCCCCGATTATGGA-AAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTATCCCCGA
587681 TTGTGAAAAA
65 TTGTGAAAAA
587691 TTGGTATTTT
Statistics
Matches: 180, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
131 38 0.21
132 141 0.78
133 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (132 bp):
GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTATCCCCGAT
TGTGAAAAAATCGATGCTTTAGAAATAAGGCCGGGGTTAGAGTATCCTCGTAAAAATAACAGGGT
TA
Found at i:587684 original size:51 final size:51
Alignment explanation
Indices: 587614--587729 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
587604 AAATAACAGG
* * *
587614 GTTGGAGTATCCCCAATTGTGAGAAATTGGTGTTTTGGAACTAAAATC-GAA
1 GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAATCAG-A
* *
587665 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTGGAAATAAAATCAGG
1 GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAATCAGA
*
587716 GTTGAAGTATCCCC
1 GTTGGAGTATCCCC
587730 TCGGAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 57 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAATCAGA
Found at i:587827 original size:109 final size:107
Alignment explanation
Indices: 587695--587945 Score: 297
Period size: 109 Copynumber: 2.3 Consensus size: 107
587685 GAAAAATTGG
* * *
587695 TATTTTGGAAATAAAATCAGGGTTGAAGTATCCCCTCGGAAATAATGAGATTGGAGTATCCCCGA
1 TATTTTGGAAATAAAATCGGGGTTGAAGTATCCCCTCAGAAATAACGAGATTGGAGTATCCCCGA
* *
587760 TGACATAACGGGGTTAGAGTACCCCCCGATTATGAAAGAATCAA
66 TGAAATAACGGGGTTAGAGTA-CCCCCAATTATGAAA-AATCAA
* * * * * *
587804 TATTTTGGATATAAAGTCGGGGTTGGAGTATCCCTTCAGAAATAACGGGGTTGGAGTATCCCCGA
1 TATTTTGGAAATAAAATCGGGGTTGAAGTATCCCCTCAGAAATAACGAGATTGGAGTATCCCCGA
* * * * * *
587869 TGAAATGACGGGGTTGGAGTATCCCCAATTGTGAAAAATTAG
66 TGAAATAACGGGGTTAGAGTACCCCCAATTATGAAAAATCAA
* *
587911 TATTTTGAAAATAAAATCGGAGTT-AGAGTATCCCC
1 TATTTTGGAAATAAAATCGGGGTTGA-AGTATCCCC
587946 GATTAAGAAA
Statistics
Matches: 118, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
107 32 0.27
108 12 0.10
109 74 0.63
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (107 bp):
TATTTTGGAAATAAAATCGGGGTTGAAGTATCCCCTCAGAAATAACGAGATTGGAGTATCCCCGA
TGAAATAACGGGGTTAGAGTACCCCCAATTATGAAAAATCAA
Found at i:587861 original size:28 final size:28
Alignment explanation
Indices: 587821--587894 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
587811 GATATAAAGT
587821 CGGGGTTGGAGTATCCCTTC-A-GAAATAA
1 CGGGGTTGGAGTATCCC--CGATGAAATAA
*
587849 CGGGGTTGGAGTATCCCCGATGAAATGA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
587877 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
587895 AATTGTGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 41 0.95
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:590350 original size:20 final size:20
Alignment explanation
Indices: 590304--590396 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
590294 AAATGCCTGT
* ** *
590304 ATGTATCGATACATTATAAA
1 ATGTATCGATACAATGCAGA
*
590324 ATATATCGATACAATG-AGCA
1 ATGTATCGATACAATGCAG-A
*
590344 AAGTATCGATACAATGCAGA
1 ATGTATCGATACAATGCAGA
590364 ATGTATCGATACAATGCAGA
1 ATGTATCGATACAATGCAGA
590384 ATGTATCGATACA
1 ATGTATCGATACA
590397 TCTGTGTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
19 1 0.02
20 61 0.95
21 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACAATGCAGA
Found at i:591071 original size:40 final size:41
Alignment explanation
Indices: 591022--591314 Score: 124
Period size: 42 Copynumber: 7.1 Consensus size: 41
591012 CCACTTTTTA
* * * *
591022 AGGATAAAGGAAAAGAG-AATGAAATAG-GTCTTGCTCCTTG
1 AGGACAAAGGAAAAAAGAAAAGAAA-AGTGTCCTGCTCCTTG
* *
591062 AGGACAAAGGAAAAAAGAAAAGGAAAGTGTCCTGCTTCTTG
1 AGGACAAAGGAAAAAAGAAAAGAAAAGTGTCCTGCTCCTTG
* * *
591103 AGGACAAAGTG-AAAAAG---AG--TA-CGTCCTGCT-TTTCG
1 AGGACAAAG-GAAAAAAGAAAAGAAAAGTGTCCTGCTCCTT-G
* * * ** *
591138 AAGATAAAGGAAAAAAGGAAAACGAAATGCATCCTGCTCTTTG
1 AGGACAAAGGAAAAAA-GAAAA-GAAAAGTGTCCTGCTCCTTG
* * * * *
591181 AGGACAAATGAAAGAAGAAAA-TAAAGTGCGTTCTGCTCTTTG
1 AGGACAAAGGAAAAAAGAAAAGAAAAGT--GTCCTGCTCCTTG
* * ** *
591223 AGGACAAAAGAGAAAAGAAGGGAATGAAGTGTGTCCTGCTCTTTG
1 AGGAC-AAAG-GAAAA-AA-GAAAAGAAAAGTGTCCTGCTCCTTG
* * * *
591268 AGGACAAAGGAAAGAGGAAAA-TAAAGTGCATCCTGCTCTTTG
1 AGGACAAAGGAAAAAAGAAAAGAAAAGTG--TCCTGCTCCTTG
591310 AGGAC
1 AGGAC
591315 TAGAGGGTGC
Statistics
Matches: 192, Mismatches: 38, Indels: 44
0.70 0.14 0.16
Matches are distributed among these distances:
34 3 0.02
35 21 0.11
36 2 0.01
38 2 0.01
39 1 0.01
40 25 0.13
41 34 0.18
42 40 0.21
43 28 0.15
44 11 0.06
45 19 0.10
46 3 0.02
47 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (41 bp):
AGGACAAAGGAAAAAAGAAAAGAAAAGTGTCCTGCTCCTTG
Found at i:591217 original size:42 final size:42
Alignment explanation
Indices: 591169--591314 Score: 186
Period size: 42 Copynumber: 3.4 Consensus size: 42
591159 ACGAAATGCA
*
591169 TCCTGCTCTTTGAGGACAAATGAAAGAAGAAAATAAAGTGCG
1 TCCTGCTCTTTGAGGACAAAAGAAAGAAGAAAATAAAGTGCG
* * *
591211 TTCTGCTCTTTGAGGACAAAAGAGAA-AAGAAGGGAATGAAGTGTG
1 TCCTGCTCTTTGAGGACAAAAGA-AAGAAGAA---AATAAAGTGCG
* * *
591256 TCCTGCTCTTTGAGGACAAAGGAAAGAGGAAAATAAAGTGCA
1 TCCTGCTCTTTGAGGACAAAAGAAAGAAGAAAATAAAGTGCG
591298 TCCTGCTCTTTGAGGAC
1 TCCTGCTCTTTGAGGAC
591315 TAGAGGGTGC
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
42 51 0.57
43 2 0.02
44 2 0.02
45 34 0.38
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (42 bp):
TCCTGCTCTTTGAGGACAAAAGAAAGAAGAAAATAAAGTGCG
Found at i:591509 original size:94 final size:94
Alignment explanation
Indices: 591346--591523 Score: 243
Period size: 94 Copynumber: 1.9 Consensus size: 94
591336 GTGGGCTTTG
* *
591346 AAGGAGAAGGCGTCCTACTCTTTAAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGA
1 AAGGAGAAGGCGTCCTACTCTTTAAGGACTGGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGA
*
591411 CGTCCTGCTCTTTGAGGACTAAAGGGCGA
66 CGTCCTGCTCTTTAAGGACTAAAGGGCGA
* * * * *
591440 AAGGAG-AGAGCGTTCTGCTCTTTGAGGACTGAGAAGG-GCCACCAATTTGTGTGGGCTTTAAAA
1 AAGGAGAAG-GCGTCCTACTCTTTAAGGACTG-GAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
*
591503 GGCGTCCTGCTCTTTAAGGAC
64 GACGTCCTGCTCTTTAAGGAC
591524 CAAAAAAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 2 0.03
94 67 0.92
95 4 0.05
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (94 bp):
AAGGAGAAGGCGTCCTACTCTTTAAGGACTGGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGA
CGTCCTGCTCTTTAAGGACTAAAGGGCGA
Found at i:591576 original size:152 final size:152
Alignment explanation
Indices: 591386--591734 Score: 565
Period size: 152 Copynumber: 2.3 Consensus size: 152
591376 GGAGGGTGCC
* *
591386 ACCAACTCGTGTGGGCTTTGAAAGACGTCCTGCTCTTTGAGGACTAAAGGGCGAAAGGAGAGAGC
1 ACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGCGAAAGGAGAGAGC
* * * *
591451 GTTCTGCTCTTTGAGGACTGAGAAGGGCCACCAATTTGTGTGGGCTTTAAAAGGCGTCCTG-CTC
66 ATTCTGCTCTTTGAGGACTGAGAAGGGCCACCAACTTGTGTGGGCTCTAAAAGGCATCC-GACTC
591515 TTTAAGGACCAAAAAAAAATGCA
130 TTTAAGGACCAAAAAAAAATGCA
* * *
591538 ACCAACTTGTGTGGGCTTTGAAAGGTGTCCTACTCTTTGAGGACTAAAGGGTGAAAGGAGAGAGC
1 ACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGCGAAAGGAGAGAGC
*
591603 ATTCTGCTTTTTGAGGACTGAGAAGGGCCACCAACTTGTGTGGGCTCTAAAAGGCATCCGACTCT
66 ATTCTGCTCTTTGAGGACTGAGAAGGGCCACCAACTTGTGTGGGCTCTAAAAGGCATCCGACTCT
* * *
591668 TTGAGGACTAAAAAAAAATGCC
131 TTAAGGACCAAAAAAAAATGCA
591690 ACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT
1 ACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT
591735 GGAAAATGCC
Statistics
Matches: 181, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
151 1 0.01
152 180 0.99
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (152 bp):
ACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGCGAAAGGAGAGAGC
ATTCTGCTCTTTGAGGACTGAGAAGGGCCACCAACTTGTGTGGGCTCTAAAAGGCATCCGACTCT
TTAAGGACCAAAAAAAAATGCA
Found at i:591764 original size:55 final size:55
Alignment explanation
Indices: 591606--591903 Score: 323
Period size: 55 Copynumber: 5.3 Consensus size: 55
591596 AGAGAGCATT
* ** * * *
591606 CTGCTTTTTGAGGACT-GAGAAGGGCCACCAACTTGTGTGGGCTCTAAAAGGCATC
1 CTGCTCTTTGAGGACTAGA-AAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
*
591661 C-GACTCTTTGAGGACTAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
1 CTG-CTCTTTGAGGACT---AGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
* * * *
591719 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGAGTAGGCTTTGAAAGGAAAGGCATC
1 CTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-----GAAAGGCGTC
*
591779 CTGTTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
1 CTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
* *
591835 CTGCTCTTTGAGGA-TTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
1 CTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
* *
591890 CTACTCTTTAAGGA
1 CTGCTCTTTGAGGA
591904 AAGGTGAAAG
Statistics
Matches: 208, Mismatches: 22, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
54 1 0.00
55 88 0.42
56 22 0.11
58 45 0.22
59 2 0.01
60 29 0.14
61 21 0.10
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (55 bp):
CTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
Found at i:591834 original size:116 final size:117
Alignment explanation
Indices: 591652--591885 Score: 357
Period size: 116 Copynumber: 2.0 Consensus size: 117
591642 GTGGGCTCTA
591652 AAAGGCATCCGACTCTTTGAGGACTAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 AAAGGCATCCGACTCTTTGAGGACT-AAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
591717 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGAGTAGGCTTTGAAAGG
65 TCCTGCTCTTTGAGGA-TGGAAAGATGCCACCAACTTGAGTAGGCTTTGAAAGG
* * *
591770 AAAGGCATCCTG-TTCTTTGAGGACT-AGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 AAAGGCATCC-GACTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
591833 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
65 TCCTGCTCTTTGAGGATGGAAAGATGCCACCAACTTGAGTAGGCTTTGAAAGG
591886 CGTCCTACTC
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
115 5 0.05
116 79 0.74
118 22 0.21
119 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (117 bp):
AAAGGCATCCGACTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGT
CCTGCTCTTTGAGGATGGAAAGATGCCACCAACTTGAGTAGGCTTTGAAAGG
Found at i:592995 original size:14 final size:13
Alignment explanation
Indices: 592972--593050 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 13
592962 CTTAAGCAGA
592972 TTCTTCTTTTTTTT
1 TTCTT-TTTTTTTT
*
592986 CTCTTTTTTTTGTT
1 TTCTTTTTTTT-TT
*
593000 TTGTTTTTTTTTT
1 TTCTTTTTTTTTT
593013 TGT-TTTTTTGTTTT
1 T-TCTTTTTT-TTTT
*
593027 TT-TTGTTGGTTTTTG
1 TTCTT-TT--TTTTTT
593042 TTCTTTTTT
1 TTCTTTTTT
593051 GAAAAAGAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
13 20 0.37
14 23 0.43
15 7 0.13
16 4 0.07
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:593006 original size:25 final size:24
Alignment explanation
Indices: 592978--593030 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
592968 CAGATTCTTC
*
592978 TTTTTTTTCTCT-TTTTTTTGTTT
1 TTTTTTTTTTCTGTTTTTTTGTTT
*
593001 TGTTTTTTTTTTTGTTTTTTTGTTT
1 T-TTTTTTTTTCTGTTTTTTTGTTT
593026 TTTTT
1 TTTTT
593031 GTTGGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 1 0.04
24 13 0.50
25 12 0.46
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.89
Consensus pattern (24 bp):
TTTTTTTTTTCTGTTTTTTTGTTT
Found at i:593009 original size:17 final size:17
Alignment explanation
Indices: 592989--593051 Score: 83
Period size: 17 Copynumber: 3.5 Consensus size: 17
592979 TTTTTTTCTC
592989 TTTTTTTTGTTTTGTTT-
1 TTTTTTTTGTTTT-TTTG
593006 TTTTTTTTGTTTTTTTG
1 TTTTTTTTGTTTTTTTG
593023 TTTTTTTTGTTGGTTTTTG
1 TTTTTTTTGTT--TTTTTG
593042 TTCTTTTTTG
1 TT-TTTTTTG
593052 AAAAAGAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.07
17 24 0.57
19 8 0.19
20 7 0.17
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (17 bp):
TTTTTTTTGTTTTTTTG
Found at i:593012 original size:20 final size:20
Alignment explanation
Indices: 592989--593050 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
592979 TTTTTTTCTC
*
592989 TTTTTT-TTGTTTTGTTTTT
1 TTTTTTGTTTTTTTGTTTTT
593008 TTTTTTGTTTTTTTGTTTTT
1 TTTTTTGTTTTTTTGTTTTT
* *
593028 TTTGTTG-GTTTTTGTTCTTT
1 TTTTTTGTTTTTTTGTT-TTT
593048 TTT
1 TTT
593051 GAAAAAGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.37
20 24 0.63
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (20 bp):
TTTTTTGTTTTTTTGTTTTT
Found at i:593050 original size:1 final size:1
Alignment explanation
Indices: 592978--593030 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
592968 CAGATTCTTC
* * * * * *
592978 TTTTTTTTCTCTTTTTTTTGTTTTGTTTTTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
593031 GTTGGTTTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:603500 original size:131 final size:132
Alignment explanation
Indices: 603226--603501 Score: 473
Period size: 132 Copynumber: 2.1 Consensus size: 132
603216 AGATAGCAAT
603226 AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTAT
1 AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTAT
*
603291 CCCCGATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAATA
66 CCCCAATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAATA
603356 AC
131 AC
* * *
603358 AGGGATAGAGTATCCCCTATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTAT
1 AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTAT
* * * *
603423 CCCTAATTGTG-AAAAATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTATCTCCGTGAAAATA
66 CCCCAATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAATA
603487 AC
131 AC
603489 AGGGTTAGAGTAT
1 AGGGTTAGAGTAT
603502 TCTCGATTGT
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
131 64 0.47
132 71 0.53
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (132 bp):
AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTAT
CCCCAATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAATA
AC
Found at i:603524 original size:131 final size:131
Alignment explanation
Indices: 603226--603569 Score: 485
Period size: 131 Copynumber: 2.6 Consensus size: 131
603216 AGATAGCAAT
*
603226 AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTAT
1 AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTAT
*
603291 CCCCGATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAATA
66 CCCTGATTGTG-AAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAATA
603356 AC
130 AC
* *
603358 AGGGATAGAGTATCCCCTATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTAT
1 AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTAT
* * * *
603423 CCCTAATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTATCTCCGTGAAAATAA
66 CCCTGATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAATAA
603488 C
131 C
* * * * *** * * * *
603489 AGGGTTAGAGTATTCTCGATTGT-GAGAAATTGGTGTT-TTGGAACTAAAATCAGAGTTGGAGTA
1 AGGGTTAGAGTATCCCCGATTATGGA-AAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTA
603552 TCCCTGATTGTGAAAAAT
65 TCCCTGATTGTGAAAAAT
603570 TGGTATTTTA
Statistics
Matches: 189, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
130 38 0.20
131 80 0.42
132 71 0.38
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (131 bp):
AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTAT
CCCTGATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAATAA
C
Found at i:603603 original size:51 final size:51
Alignment explanation
Indices: 603506--603606 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
603496 GAGTATTCTC
* * * * **
603506 GATTGTGAGAAATTGGTGTTTTGGAACTAAAATCAGAGTTGGAGTATCCCT
1 GATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGAGTTAAAGTATCCCT
*
603557 GATTGTGAAAAATTGGTATTTTAGAAATAAAAT-TGAGGTTAAAGTATCCC
1 GATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGA-GTTAAAGTATCCC
603607 CTTGAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.34
Consensus pattern (51 bp):
GATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGAGTTAAAGTATCCCT
Found at i:603603 original size:130 final size:131
Alignment explanation
Indices: 603226--603621 Score: 420
Period size: 131 Copynumber: 3.0 Consensus size: 131
603216 AGATAGCAAT
*
603226 AGGGTTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATC-GAGGTTAGAGTA
1 AGGGATAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCAGA-GTTAGAGTA
** * ** * **
603290 TCCCCGATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGAGCTTGGAGTATCCCCGTGAAAAT
65 TCCCTAATTGTG-AAAAATCGATACTTTAGAAATAAAACCGAGGTTAAAGTATCCCCGTGAAAAT
603355 AAC
129 AAC
* * *
603358 AGGGATAGAGTATCCCCTATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTAT
1 AGGGATAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCAGAGTTAGAGTAT
* ** * ** *
603423 CCCTAATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTATCTCCGTGAAAATAA
66 CCCTAATTGTGAAAAATCGATACTTTAGAAATAAAACCGAGGTTAAAGTATCCCCGTGAAAATAA
603488 C
131 C
* * * * * *** * *
603489 AGGGTTAGAGTATTCTCGATTGT-GAGAAATTGGTGTT-TTGGAACTAAAATCAGAGTTGGAGTA
1 AGGGATAGAGTATCCCCGATTATGGA-AAATCGGTGTTCTAAAAAATAAAATCAGAGTTAGAGTA
* * * * ** *
603552 TCCCTGATTGTGAAAAATTGGTATTTTAGAAATAAAATTGAGGTTAAAGTATCCCCTTGAAAATA
65 TCCCTAATTGTGAAAAATCGATACTTTAGAAATAAAACCGAGGTTAAAGTATCCCCGTGAAAATA
603617 AC
130 AC
603619 AGG
1 AGG
603622 ATTGGAATAT
Statistics
Matches: 227, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
130 77 0.34
131 80 0.35
132 69 0.30
133 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (131 bp):
AGGGATAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCAGAGTTAGAGTAT
CCCTAATTGTGAAAAATCGATACTTTAGAAATAAAACCGAGGTTAAAGTATCCCCGTGAAAATAA
C
Found at i:603738 original size:28 final size:28
Alignment explanation
Indices: 603698--603771 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
603688 GATATAAAGT
**
603698 CGGGGTTGGAGTAT-CCCTTTAGAAATAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
*
603726 CGGGGTTGGAGTATCCCCGATGAAATGA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
603754 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
603772 AATTGTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 38 0.90
29 4 0.10
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:603772 original size:108 final size:107
Alignment explanation
Indices: 603573--603822 Score: 263
Period size: 108 Copynumber: 2.3 Consensus size: 107
603563 GAAAAATTGG
* * * *
603573 TATTTTAGAAATAAAAT-TGAGGTTAAAGTATCCCCTTGAAAATAACAGGATTGGAATATCCTCG
1 TATTTTGGAAATAAAATCGGA-GTTAGAGTATCCCCTTGAAAATAACAGGATTGGAATATCCCCG
*
603637 ATACATAACGGGGTTAGAGTACCCCCCAATTATGAAAGAATCAA
65 ATAAATAACGGGGTTAGAGTACCCCCCAATTATGAAA-AATCAA
* * * * * * * *
603681 TATTTTGGATATAAAGTCGGGGTTGGAGTAT-CCCTTTAGAAATAACGGGGTTGGAGTATCCCCG
1 TATTTTGGAAATAAAATCGGAGTTAGAGTATCCCCTTGA-AAATAACAGGATTGGAATATCCCCG
* * * * ***
603745 ATGAAATGACGGGGTTGGAGTA-TCCCCAATTGTGAAAAATTGG
65 AT-AAATAACGGGGTTAGAGTACCCCCCAATTATGAAAAATCAA
603788 TATTTTGGAAATAAAATCGGAGTTAGAGTATCCCC
1 TATTTTGGAAATAAAATCGGAGTTAGAGTATCCCC
603823 GATTAAGAAA
Statistics
Matches: 114, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
107 36 0.32
108 61 0.54
109 17 0.15
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (107 bp):
TATTTTGGAAATAAAATCGGAGTTAGAGTATCCCCTTGAAAATAACAGGATTGGAATATCCCCGA
TAAATAACGGGGTTAGAGTACCCCCCAATTATGAAAAATCAA
Found at i:603868 original size:51 final size:51
Alignment explanation
Indices: 603754--603875 Score: 129
Period size: 51 Copynumber: 2.4 Consensus size: 51
603744 GATGAAATGA
* * ** * *
603754 CGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAAT
1 CGGGATTGGAGTATCCCCGATTAAGAAAAATTGATATTTTGGAAATAAAAC
* * **
603805 C-GGAGTTAGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGCAAC
1 CGGGA-TTGGAGTATCCCCGATTAAGAAAAATTGATATTTTGGAAATAAAAC
*
603856 CGGGATTGGAGTATCTCCGA
1 CGGGATTGGAGTATCCCCGA
603876 GATGAAAAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
50 2 0.04
51 52 0.91
52 3 0.05
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
CGGGATTGGAGTATCCCCGATTAAGAAAAATTGATATTTTGGAAATAAAAC
Found at i:605935 original size:20 final size:20
Alignment explanation
Indices: 605910--605984 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
605900 AAAATGCCCG
*
605910 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGCAA
605930 AATGTATCGATACATTGCAA
1 AATGTATCGATACATTGCAA
*
605950 AATGTATCGATACAATGCAA
1 AATGTATCGATACATTGCAA
605970 AATGTATCGATACAT
1 AATGTATCGATACAT
605985 CTGGGTAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:606017 original size:13 final size:13
Alignment explanation
Indices: 605999--606023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
605989 GTAAACCTAG
605999 AATGTATCGATAT
1 AATGTATCGATAT
606012 AATGTATCGATA
1 AATGTATCGATA
606024 CATCTAGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:606034 original size:42 final size:42
Alignment explanation
Indices: 605970--606067 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
605960 TACAATGCAA
* * *
605970 AATGTATCGATACATCTGGGTAAACCTAGAATGTATCGATAT
1 AATGTATCGATACATCTAGGTAAACCCAGAATGTATCGATAC
606012 AATGTATCGATACATCTAGGTAAACCCAGAATGTATCGATAC
1 AATGTATCGATACATCTAGGTAAACCCAGAATGTATCGATAC
606054 AATGTATCGATACA
1 AATGTATCGATACA
606068 ATGAACAATG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (42 bp):
AATGTATCGATACATCTAGGTAAACCCAGAATGTATCGATAC
Found at i:606088 original size:13 final size:13
Alignment explanation
Indices: 606041--606070 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
606031 GTAAACCCAG
606041 AATGTATCGATAC
1 AATGTATCGATAC
606054 AATGTATCGATAC
1 AATGTATCGATAC
606067 AATG
1 AATG
606071 AACAATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:609729 original size:30 final size:30
Alignment explanation
Indices: 609693--609850 Score: 124
Period size: 30 Copynumber: 5.5 Consensus size: 30
609683 CATTGTTCAT
609693 TGTATCGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATTTTGGGTTTTACCCAGA
*
609723 TGTATCGATACA--TT--G--TT---CA-T
1 TGTATCGATACATTTTGGGTTTTACCCAGA
609743 TGTATCGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATTTTGGGTTTTACCCAGA
** * **
609773 TGTATCGATACATTATTCATTGTATTAATACA-A
1 TGTATCGATACATT-TT--GGGT-TTTACCCAGA
* *
609806 TGTATTGATACATTCTGGG-TTTACCCAGA
1 TGTATCGATACATTTTGGGTTTTACCCAGA
609835 TGTATCGATACATTTT
1 TGTATCGATACATTTT
609851 TCAATGTATC
Statistics
Matches: 97, Mismatches: 16, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
20 12 0.12
21 2 0.02
22 2 0.02
24 3 0.03
26 3 0.03
28 7 0.07
29 17 0.18
30 27 0.28
31 2 0.02
32 1 0.01
33 16 0.16
34 5 0.05
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (30 bp):
TGTATCGATACATTTTGGGTTTTACCCAGA
Found at i:609804 original size:50 final size:50
Alignment explanation
Indices: 609673--609797 Score: 232
Period size: 50 Copynumber: 2.5 Consensus size: 50
609663 TTTCACCATT
*
609673 TGTATCGACACATTGTTCATTGTATCGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATTGTTCATTGTATCGATACATTTTGGGTTTTACCCAGA
609723 TGTATCGATACATTGTTCATTGTATCGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATTGTTCATTGTATCGATACATTTTGGGTTTTACCCAGA
*
609773 TGTATCGATACATTATTCATTGTAT
1 TGTATCGATACATTGTTCATTGTAT
609798 TAATACAATG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (50 bp):
TGTATCGATACATTGTTCATTGTATCGATACATTTTGGGTTTTACCCAGA
Found at i:609866 original size:62 final size:63
Alignment explanation
Indices: 609743--609866 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 63
609733 CATTGTTCAT
* * *
609743 TGTATCGATACATTTTGGGTTTTACCCAGATGTATCGATACATTATTCATTGTATTAATACAA
1 TGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTATTCAATGTATCAATACAA
* * *
609806 TGTATTGATACATTCTGGG-TTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACA
1 TGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTATTCAATGTATCAATACA
609867 TTCAAGCATG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 38 0.69
63 17 0.31
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (63 bp):
TGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTATTCAATGTATCAATACAA
Found at i:612304 original size:79 final size:79
Alignment explanation
Indices: 612182--612386 Score: 261
Period size: 79 Copynumber: 2.6 Consensus size: 79
612172 CAGCTCTGAT
* * * * * * * *
612182 TTTATTTTCAAAACACTAATTTTTTACAATCGGGGATGCTCCAACCCCGTTA-TTTCTGAGGGGA
1 TTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCATTATTTTC-GAGGGGA
*
612246 TACTCCAACCCCTGC
65 TACTCCAACCCCGGC
* *
612261 TTTA-TTCTTAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGA
1 TTTATTTC-CAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGA
612325 TACTCCAACCCCGGC
65 TACTCCAACCCCGGC
* *
612340 TTTATTTCCAAAATATTAATTTCTCATAATTGAGGATACTCCAACCC
1 TTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCC
612387 TTGCTTTATT
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
78 2 0.02
79 99 0.92
80 7 0.06
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (79 bp):
TTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGAT
ACTCCAACCCCGGC
Found at i:612381 original size:130 final size:131
Alignment explanation
Indices: 612243--612516 Score: 408
Period size: 130 Copynumber: 2.1 Consensus size: 131
612233 ATTTCTGAGG
* *
612243 GGATACTCCAACCCCTGCTTTA-TTCTTAAAATATTGATTTCTCATAATCGGGGATACTCCAACC
1 GGATACTCCAACCCCTGCTTTATTTC-CAAAATATTAATTTCTCATAATCGGGGATACTCCAACC
* * * * *
612307 CCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTA-TTTCCAAAATATTAATTTCTCATAATT
65 CCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTTCAAAAACATCAATTTCTCACAATC
612371 GA
130 GA
*
612373 GGATACTCCAACCCTTGCTTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCTGCTTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCC
** * * *
612438 TGTTATTTTCGAGGGGATACTCTAACCCCGGTTTTATTTTCAAAAACATCAATTTTTCACAATCG
66 CATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTTCAAAAACATCAATTTCTCACAATCG
612503 A
131 A
612504 GGATACTCCAACC
1 GGATACTCCAACC
612517 TCGTTATTTC
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
130 90 0.70
131 39 0.30
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (131 bp):
GGATACTCCAACCCCTGCTTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCC
CATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTTCAAAAACATCAATTTCTCACAATCG
A
Found at i:612438 original size:51 final size:51
Alignment explanation
Indices: 612320--612439 Score: 204
Period size: 51 Copynumber: 2.4 Consensus size: 51
612310 TTATTTTCGA
* *
612320 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTAATTTCTCATAATT
1 GGGGATACTCCAACCCTGGCTTTATTTCCAAAATATTAATTTCTCATAATC
* *
612371 GAGGATACTCCAACCCTTGCTTTATTTCCAAAATATTAATTTCTCATAATC
1 GGGGATACTCCAACCCTGGCTTTATTTCCAAAATATTAATTTCTCATAATC
612422 GGGGATACTCCAACCCTG
1 GGGGATACTCCAACCCTG
612440 TTATTTTCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGGCTTTATTTCCAAAATATTAATTTCTCATAATC
Found at i:612456 original size:79 final size:80
Alignment explanation
Indices: 612373--612547 Score: 196
Period size: 80 Copynumber: 2.2 Consensus size: 80
612363 TCATAATTGA
** * * * * *
612373 GGATACTCCAACCCTTGCTTTA-TTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACC
1 GGATACTCCAACCCCGGCTTTATTTTCAAAAACATCAATTTCTCACAATCGAGGATACTCCAACC
612437 -CTGTTATTTTCGAGG
66 TC-GTTATTTTCGAGG
* * *
612452 GGATACTCTAACCCCGGTTTTATTTTCAAAAACATCAATTTTTCACAATCGAGGATACTCCAACC
1 GGATACTCCAACCCCGGCTTTATTTTCAAAAACATCAATTTCTCACAATCGAGGATACTCCAACC
612517 TCGTTA-TTTC-ATCGG
66 TCGTTATTTTCGA--GG
*
612532 GGATATTCCAACCCCG
1 GGATACTCCAACCCCG
612548 TTACCTCCGA
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 22 0.28
80 56 0.70
81 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (80 bp):
GGATACTCCAACCCCGGCTTTATTTTCAAAAACATCAATTTCTCACAATCGAGGATACTCCAACC
TCGTTATTTTCGAGG
Found at i:612583 original size:187 final size:184
Alignment explanation
Indices: 612373--612709 Score: 455
Period size: 187 Copynumber: 1.8 Consensus size: 184
612363 TCATAATTGA
*
612373 GGATACTCCAACCCTTGCTTTATTTCC-AAAATATTAATTTCTCATAATCGGGGATACTCCAA-C
1 GGATACTCCAACCCTCGCTTTA-TTCCTAAAATATTAATTTCTCATAATCGGGGATACTCCAATC
* * * * * *
612436 CCTGTTATTTTCGAGGGGATACTCTAACCCCGGTTTTATTTTCAAAAACATCAATTTTTCACAAT
65 CC-GTTATTTCCGAGGAGATACTCCAACCCCGATTTT-TTTT--AAAACATCAATTTCTCACAAC
*
612501 CGAGGATACTCCAACCTCGTTATTTCATCGGGGATATTCCAACCCCGTTACCTCCGAGG
126 CGAGGATACTCCAACCCCGTTATTTCATCGGGGATATTCCAACCCCGTTACCTCCGAGG
* *
612560 GGATACTCCAACCC-CGACTTTATTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAATC
1 GGATACTCCAACCCTCG-CTTTATTCCTAAAATATTAATTTCTCATAATCGGGGATACTCCAATC
* * * * *
612624 CCGTTATTTCCGAGGAGATACTCCAATCCTGATTTTTTTTTAATCATCAATTTCTCACAACCGGG
65 CCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTTTTTAAAACATCAATTTCTCACAACCGAG
*
612689 GATACTCCAGCCCCGTTATTT
130 GATACTCCAACCCCGTTATTT
612710 TCAAGGGGCT
Statistics
Matches: 131, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
184 39 0.30
186 9 0.07
187 80 0.61
188 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (184 bp):
GGATACTCCAACCCTCGCTTTATTCCTAAAATATTAATTTCTCATAATCGGGGATACTCCAATCC
CGTTATTTCCGAGGAGATACTCCAACCCCGATTTTTTTTAAAACATCAATTTCTCACAACCGAGG
ATACTCCAACCCCGTTATTTCATCGGGGATATTCCAACCCCGTTACCTCCGAGG
Found at i:625148 original size:11 final size:11
Alignment explanation
Indices: 625129--625186 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
625119 TTCTCTTTTT
625129 AAAAAAAAAAC
1 AAAAAAAAAAC
*
625140 AAAACAAAAAC
1 AAAAAAAAAAC
**
625151 -AAAAGCAAA-
1 AAAAAAAAAAC
625160 AAAAAAAAAAC
1 AAAAAAAAAAC
*
625171 AAAAAAAAAAG
1 AAAAAAAAAAC
625182 AAAAA
1 AAAAA
625187 GAGAGAAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 13 0.34
11 25 0.66
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:625163 original size:15 final size:14
Alignment explanation
Indices: 625129--625180 Score: 77
Period size: 14 Copynumber: 3.5 Consensus size: 14
625119 TTCTCTTTTT
625129 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
625143 ACAAAAACAAAAGCAAA
1 A-AAAAA-AAAA-CAAA
625160 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
625174 AAAAAAA
1 AAAAAAA
625181 GAAAAAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 12 0.34
15 9 0.26
16 9 0.26
17 5 0.14
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:625201 original size:1 final size:1
Alignment explanation
Indices: 625129--625186 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
625119 TTCTCTTTTT
* * * ** * *
625129 AAAAAAAAAACAAAACAAAAACAAAAGCAAAAAAAAAAAAACAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
625187 GAGAGAAAAG
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:625201 original size:26 final size:26
Alignment explanation
Indices: 625130--625186 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
625120 TCTCTTTTTA
*
625130 AAAAAAAAACAAAACAAAAACAAAAGC
1 AAAAAAAAA-AAAACAAAAAAAAAAGC
625157 AAAAAAAAAAAAACAAAAAAAAAAG-
1 AAAAAAAAAAAAACAAAAAAAAAAGC
625182 AAAAA
1 AAAAA
625187 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 5 0.17
26 15 0.52
27 9 0.31
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAAAACAAAAAAAAAAGC
Found at i:626426 original size:157 final size:149
Alignment explanation
Indices: 626154--626549 Score: 508
Period size: 157 Copynumber: 2.6 Consensus size: 149
626144 CTTCTCCTTC
* * * * *
626154 CATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAAGTTGGTAGCACCTTCTA
1 CATTTTCCAGTCCTTAAAGAGCAAGACGCCTTTTAAAGCCCACAC-AAGTTGGTGGCACCTTCTA
* * * *
626219 GTCCTCAAAGTGCAAGATGCTCTTTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGATGTCTTTCA
65 GTCCTCAAAGAGCAGGACGCTCTTTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGATGCCTTTCA
* **
626284 AAGCCCACACAAGTTCTCCTTT
130 AAGCCCACACAAG-T-TCATGG
* * *
626306 CACTTTT-CAGTCTTTAAAGAGCATGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CA-TTTTCCAGTCCTTAAAGAGCA--A-GAC-GC-C-TTTTAAAGCCCACACAAGTTGGTGGCAC
*
626370 CTTCTAGTCCTCAAAGAGTAGGACGCTCTTTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGATGC
59 CTTCTAGTCCTCAAAGAGCAGGACGCTCTTTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGATGC
* *
626435 CTTTTAAAGCCCACACAAGTTGATGG
124 CTTTCAAAGCCCACACAAGTTCATGG
*
626461 CATTTTCCAGTCCTTAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAG
1 CATTTTCCAGTCCTTAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
*
626526 TCCTCAAAGAGCAGGTCGC-CTTTC
66 TCCTCAAAGAGCAGGACGCTCTTTC
626550 AAAGCCCACA
Statistics
Matches: 212, Mismatches: 24, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
148 5 0.02
149 51 0.24
150 1 0.00
151 1 0.00
152 17 0.08
153 5 0.02
154 4 0.02
155 21 0.10
156 2 0.01
157 91 0.43
158 14 0.07
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (149 bp):
CATTTTCCAGTCCTTAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
TCCTCAAAGAGCAGGACGCTCTTTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAA
AGCCCACACAAGTTCATGG
Found at i:626498 original size:55 final size:55
Alignment explanation
Indices: 626414--626823 Score: 448
Period size: 55 Copynumber: 7.2 Consensus size: 55
626404 TTCACCCTTT
* * *
626414 AGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGATGGCATTTTCC
1 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
626469 AGTCCTTAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT--
1 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA--TTTTCC
* * * **
626524 AGTCCTCAAAGAGCAGGTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * * *
626579 AGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACAAAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
626634 AGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTT-C
1 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
626688 AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCA--AGA-C---GCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * **
626750 AGTCCTCAAAGAGCAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCA--AGAC----GCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
626811 AGTCCTCAAAGAG
1 AGTCCTCAAAGAG
626824 TAGGATGTCT
Statistics
Matches: 315, Mismatches: 27, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
53 4 0.01
54 15 0.05
55 189 0.60
56 2 0.01
57 5 0.02
60 27 0.09
61 20 0.06
62 53 0.17
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:626609 original size:110 final size:111
Alignment explanation
Indices: 626411--626895 Score: 512
Period size: 110 Copynumber: 4.2 Consensus size: 111
626401 CCTTTCACCC
* * *
626411 TTTAGTCCTCAAAGAGCAGGAT-GCCTTTTAAAGCCCACACAAGTTGATGGCATTTTCCAGTCCT
1 TTTAGTCCTCAAAGAGCAGG-TCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCT
* * * *
626475 TAAAGAGCAAGACGCC-TTTTAAAGCCCACACAAGTTGGTGGCACCT
65 CAAAGAGCAGGACGCCATTTCAAAGCCCACACAAGTTGGTGGCACTT
* ** *
626521 TTTAGTCCTCAAAGAGCAGGTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCTTC
1 TTTAGTCCTCAAAGAGCAGGTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTC
*
626586 AAAGAGCAGGACGCC-TTTCAAAGCCCACAAAAGTTGGTGGCA-TT
66 AAAGAGCAGGACGCCATTTCAAAGCCCACACAAGTTGGTGGCACTT
* * * *
626630 TTCTAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCA-CTTTCAGTCCT
1 TT-TAGTCCTCAAAGAGCAGGTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCT
* *
626694 CAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
65 CAAAGAGCAGGACGCCATTT-C----AAAGCCCACACAAGTTGGTGGCACTT
** * *
626746 TTCTAGTCCTCAAAGAGCAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC
1 TT-TAGTCCTCAAAGAGCAGG------TCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCC
* * *
626811 AGTCCTCAAAGAGTAGGATGTCTTTTCATTTCAAAGCCCACACGAGTTGGTGGCACTT
59 AGTCCTCAAAGAGCAGGACG-C----CATTTCAAAGCCCACACAAGTTGGTGGCACTT
* * *
626869 TTTTGTCCTCAAAAAGCAGGACGCCTT
1 TTTAGTCCTCAAAGAGCAGGTCGCCTT
626896 ATCCTTCTCT
Statistics
Matches: 319, Mismatches: 35, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
109 27 0.08
110 146 0.46
111 1 0.00
115 22 0.07
116 26 0.08
122 43 0.13
123 48 0.15
124 1 0.00
127 1 0.00
128 4 0.01
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (111 bp):
TTTAGTCCTCAAAGAGCAGGTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTC
AAAGAGCAGGACGCCATTTCAAAGCCCACACAAGTTGGTGGCACTT
Found at i:626683 original size:165 final size:168
Alignment explanation
Indices: 626411--626900 Score: 592
Period size: 165 Copynumber: 2.8 Consensus size: 168
626401 CCTTTCACCC
* * *
626411 TTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGATGGCATTTTCCAGTCCTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
*
626476 AAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGG
66 AAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGG
*
626541 TCGCCTTT-C-AAAGCCCACACAAGTTGGTGGCA-TTT
131 ACGCCTTTCCTAAAGCCCACACAAGTTGGTGGCACTTT
* * * *
626576 TTTAGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACAAAAGTTGGTGGCATTTTCTAGTCCTC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
* *
626641 AAAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGG
66 AAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGG
*
626705 ACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT
131 ACGCC-TTTCC---TAAAGCCCACACAAGTTGGTGGCACTTT
* * **
626747 TCTAGTCCTCAAAGAGCAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCA
1 TTTAGTCCTCAAAGAGCAGG--AC----GCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * * * * *
626812 GTCCTCAAAGAGTAGGATGTCTTTTCATTTCAAAGCCCACACGAGTTGGTGGCACTTTTTTGTCC
60 GTCCTCAAAGAGCAAGACG-C----C-TTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCC
*
626877 TCAAAAAGCAGGACGCCTTATCCT
119 TCAAAGAGCAGGACGCCTT-TCCT
626901 TCTCTCCTTT
Statistics
Matches: 274, Mismatches: 30, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
164 24 0.09
165 101 0.37
166 1 0.00
170 23 0.08
171 21 0.08
173 2 0.01
177 47 0.17
178 1 0.00
181 1 0.00
182 1 0.00
183 27 0.10
184 25 0.09
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (168 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
AAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGG
ACGCCTTTCCTAAAGCCCACACAAGTTGGTGGCACTTT
Found at i:626999 original size:41 final size:42
Alignment explanation
Indices: 626905--627134 Score: 153
Period size: 44 Copynumber: 5.3 Consensus size: 42
626895 TATCCTTCTC
* * * *
626905 TCCTTTGTCCTCAAAGGGTAGGACACA-TTTCATTTCCTTCTTT
1 TCCTTTGTCCTCAAAGAGCAGGACACACTTT-TTTTTCTT-TTT
* **
626948 TCCTTTTTGTCCTCAAAGAGCATGATGC-CTTTTTTTTCTTTTT
1 TCC--TTTGTCCTCAAAGAGCAGGACACACTTTTTTTTCTTTTT
* *
626991 TCCTTTGTCTTTAAAGAGCAGGACACACTTCATTTCTTTC-TTTT
1 TCCTTTGTCCTCAAAGAGCAGGACACACTT--TTT-TTTCTTTTT
* * * *
627035 CCCTTCTAGTTCTCAAAGAGCAGGACACACTTTATTTTCCTTTT
1 TCCTT-T-GTCCTCAAAGAGCAGGACACACTTTTTTTTCTTTTT
* * * ** *
627079 TCTTTTGTCCTCAAAGGGCATGATGCA-TTTCGTTTTCCTTTTTT
1 TCCTTTGTCCTCAAAGAGCAGGACACACTTT--TTTTTC-TTTTT
627123 TCCTTTGTCCTC
1 TCCTTTGTCCTC
627135 GAAAAATAGG
Statistics
Matches: 146, Mismatches: 28, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
41 21 0.14
42 19 0.13
43 18 0.12
44 41 0.28
45 26 0.18
46 21 0.14
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (42 bp):
TCCTTTGTCCTCAAAGAGCAGGACACACTTTTTTTTCTTTTT
Found at i:627874 original size:30 final size:30
Alignment explanation
Indices: 627838--627946 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 30
627828 TTTCACCATT
627838 TGTATCGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATTTTGGGTTTTACCCAGA
** **
627868 TGTATCGATACATTGTT-CATTGTATCAATACA-A
1 TGTATCGATACATT-TTGGGTT-T-T--ACCCAGA
* *
627901 TGTATTGATACATTCTGGG-TTTACCCAGA
1 TGTATCGATACATTTTGGGTTTTACCCAGA
627930 TGTATCGATACAATTTT
1 TGTATCGATAC-ATTTT
627947 CAATGTATTG
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
28 3 0.05
29 11 0.19
30 21 0.36
31 4 0.07
32 3 0.05
33 14 0.24
34 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (30 bp):
TGTATCGATACATTTTGGGTTTTACCCAGA
Found at i:629531 original size:79 final size:79
Alignment explanation
Indices: 629415--629807 Score: 490
Period size: 79 Copynumber: 5.0 Consensus size: 79
629405 CAGCTCAGAT
* * * * *
629415 TTTATTTTCAAAACACTAATTT-TCTATAATCGAGGATACTCCAACCCCGTTATTTTTGAGGGGA
1 TTTATTTCCAAAATATTAATTTCTC-ATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGA
* *
629479 TACTCCAATCTCTGC
65 TACTCCAACCCCTGC
* *
629494 TTTA-TTCTTAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGA
1 TTTATTTC-CAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGA
*
629558 TACTCCAACCCCAGC
65 TACTCCAACCCCTGC
* * *
629573 TTTATTTCCAAAATATTAATTTCTCATAATTGGGGATTCTCCAACCCTGTTATTTTCGAGGGGAT
1 TTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
629638 ACTCCAACCCCTGC
66 ACTCCAACCCCTGC
* *
629652 TTTATTTCCAAAATATTAATTTCTCATAATCGGAGATACTCTAACCCCGTTATTTTCGAGGGGAT
1 TTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
*
629717 ACTCCAA-CCCTGGG
66 ACTCCAACCCCT-GC
* * * * * * *
629731 TTTATTTTCAAAAACATCAATTTTTCACAATCGAGGATACTCCAACCTCGTTA-TTTC-ATCGGG
1 TTTA-TTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCGA--GGG
629794 GATACTCCAACCCC
63 GATACTCCAACCCC
629808 GTTACCTCCG
Statistics
Matches: 275, Mismatches: 31, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
78 7 0.03
79 208 0.76
80 57 0.21
81 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
ACTCCAACCCCTGC
Found at i:632249 original size:19 final size:19
Alignment explanation
Indices: 632225--632279 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
632215 ACATTATGCT
** *
632225 TTGTATCGATACATGTTAG
1 TTGTATCGATACATGACAA
632244 TTGTATCGATACATGGACAA
1 TTGTATCGATACAT-GACAA
632264 TTGTATCGATACATGA
1 TTGTATCGATACATGA
632280 GATTGGCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGACAA
Found at i:632269 original size:20 final size:20
Alignment explanation
Indices: 632225--632278 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
632215 ACATTATGCT
** *
632225 TTGTATCGATACAT-GTTAG
1 TTGTATCGATACATGGACAA
632244 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
632264 TTGTATCGATACATG
1 TTGTATCGATACATG
632279 AGATTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:634787 original size:151 final size:152
Alignment explanation
Indices: 634510--634787 Score: 387
Period size: 151 Copynumber: 1.8 Consensus size: 152
634500 TATTTATCCT
* * * * * * *
634510 ACATAACCACAAGGCTTAACATCGAGGCATTTTATGAAATATATTACAAATTAATTTTTGGTTAC
1 ACATAACCACAAGGCTTAACATCAAGGCATTTTATGAAATAGATGACAAACTAATATCTGGTGAC
* * * * *
634575 TTAAAAATAGTGCTTATTTAGCCTCATTTGGTCATGACTCCAAATATAAAATGTTTAATTTTCCT
66 TTAAAAACAATGCTTATTTAGCATCATTTGGCCATGACTCCAAATATAAAATGCTTAATTTTCCT
634640 TAAACTAATTTTTTATTTTCTC
131 TAAACTAATTTTTTATTTTCTC
* *
634662 ACATAACCACAAGGCTTAACATCAAGTCATTTTATTAAATAGATGACAAACTAA-ATCTGGTGAC
1 ACATAACCACAAGGCTTAACATCAAGGCATTTTATGAAATAGATGACAAACTAATATCTGGTGAC
* * * *
634726 TTAAAAACAATGCTTGTTTAGCATTATTTGGCCATGACTCCAAGTATAAAATGCTTGATTTT
66 TTAAAAACAATGCTTATTTAGCATCATTTGGCCATGACTCCAAATATAAAATGCTTAATTTT
634788 ACCTAAGCTT
Statistics
Matches: 108, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
151 60 0.56
152 48 0.44
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (152 bp):
ACATAACCACAAGGCTTAACATCAAGGCATTTTATGAAATAGATGACAAACTAATATCTGGTGAC
TTAAAAACAATGCTTATTTAGCATCATTTGGCCATGACTCCAAATATAAAATGCTTAATTTTCCT
TAAACTAATTTTTTATTTTCTC
Found at i:635917 original size:20 final size:20
Alignment explanation
Indices: 635892--635945 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
635882 GTTACAAACA
635892 ATGTATCGATACAAT-TCAT
1 ATGTATCGATACAATGTCAT
*
635911 CATGTATCGATACAATGTCCT
1 -ATGTATCGATACAATGTCAT
635932 ATGTATCGATACAA
1 ATGTATCGATACAA
635946 ACAGTGTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTCAT
Found at i:636019 original size:19 final size:19
Alignment explanation
Indices: 635975--636046 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
635965 TGCTAGTTTC
***
635975 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAAT
635995 ATGTATCGATACAATGAAT
1 ATGTATCGATACAATGAAT
* *
636014 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAATGAAT
636033 AATGTATCGATACA
1 -ATGTATCGATACA
636047 TTCAAGGGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 19 0.41
20 27 0.59
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATGAAT
Found at i:644690 original size:32 final size:32
Alignment explanation
Indices: 644635--644698 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
644625 TGCCAGTTTC
*
644635 ATGTATCGATACAATGAATATGTATCGATACA
1 ATGTATCGATACAAAGAATATGTATCGATACA
*
644667 ATGTATC-ATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-ATGTATCGATACA
644699 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (32 bp):
ATGTATCGATACAAAGAATATGTATCGATACA
Found at i:650516 original size:51 final size:51
Alignment explanation
Indices: 650307--650799 Score: 395
Period size: 51 Copynumber: 9.6 Consensus size: 51
650297 GAAATAACGA
* * * * * * *
650307 GGTTGGAGGATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTG-TTTTGGAAATAAAACCGG
* * * * *
650359 AGTTGGAGTATCCCTGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTGGAAATAAAACCGG
* * * *
650411 GGTTGGAG-ATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGA
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGGAAATAAAACCGG
* * * *
650461 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGGA-AAATTAGTGTTTTGGAAATAAAACCGG
* ** * * * ***** * *
650512 GGTTGGAGTATCCCCTCGGAGGTAATGG--GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTAT-CCC-C-GA--TTATGGAAAATTAGTGTTTTGGAAAT-AAA-ACCGG
* * * * *
650568 GGTTGGAGTATCCTCGATTGA-GAAAAATTGGTATTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTGGAAATAAAACCGG
* * * *
650619 AGTTGGAGTATCCCCGATTATAGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
650670 GGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGGAAATAAAACCGG
* * * *
650721 AGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACTGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGGAAATAAAACCGG
*
650772 GGTTGGAGTATCCCTGATTAT-GAAAATT
1 GGTTGGAGTATCCCCGATTATGGAAAATT
650800 TGAGAAACTT
Statistics
Matches: 347, Mismatches: 79, Indels: 32
0.76 0.17 0.07
Matches are distributed among these distances:
50 44 0.13
51 207 0.60
52 44 0.13
53 22 0.06
54 8 0.02
55 5 0.01
56 16 0.05
57 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:653138 original size:13 final size:13
Alignment explanation
Indices: 653120--653145 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
653110 ACAAAGATCG
653120 ATGTATCGATACA
1 ATGTATCGATACA
653133 ATGTATCGATACA
1 ATGTATCGATACA
653146 TTTCCTTAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:653156 original size:21 final size:21
Alignment explanation
Indices: 653132--653173 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
653122 GTATCGATAC
653132 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
653153 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
653174 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:653257 original size:19 final size:19
Alignment explanation
Indices: 653197--653258 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
653187 TAGTGATACA
653197 TTGTATCGATACAAAACT-T
1 TTGTATCGATAC-AAACTGT
* **
653216 ATGTATCGATACATTTTCTGT
1 TTGTATCGATACA--AACTGT
653237 TTGTATCGATACAAACTGT
1 TTGTATCGATACAAACTGT
653256 TTG
1 TTG
653259 AAGTTCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 2 0.06
21 13 0.38
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:654168 original size:43 final size:42
Alignment explanation
Indices: 653995--654218 Score: 217
Period size: 42 Copynumber: 5.2 Consensus size: 42
653985 CGTCCCATTT
* *
653995 TTTGAGGACAAAGGA-AAAAGGGAAACA-AAATACGTCCCGCTC
1 TTTGAGGACAAAGGAGAAAA-GGAAA-ATAAATGCGTCCTGCTC
* * *
654037 TCTGAGGACAAAAG-GAAAAGGAAAATAAAGTGCGCCCTGCTC
1 TTTGAGGACAAAGGAGAAAAGGAAAATAAA-TGCGTCCTGCTC
* *
654079 TTTGAGGACTAGAAGG-GAAAAGAAGGAAATAAAGAGCGTCCTGCTC
1 TTTGAGGAC-A-AAGGAGAAAAG--GAAAATAAA-TGCGTCCTGCTC
* *
654125 TTTGAAGACAAAGGAGAAAAGGAAAACGAAATGCGTCCTGCTC
1 TTTGAGGACAAAGGAGAAAAGGAAAA-TAAATGCGTCCTGCTC
*
654168 TTTGAGGACAAA--AGAAAGAGGAAAATAAAGTGCGTCTTGCTC
1 TTTGAGGACAAAGGAGAAA-AGGAAAATAAA-TGCGTCCTGCTC
654210 TTTGAGGAC
1 TTTGAGGAC
654219 TACAAAGTGC
Statistics
Matches: 154, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
40 1 0.01
41 16 0.10
42 60 0.39
43 27 0.18
44 16 0.10
45 7 0.05
46 27 0.18
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.17
Consensus pattern (42 bp):
TTTGAGGACAAAGGAGAAAAGGAAAATAAATGCGTCCTGCTC
Found at i:654304 original size:62 final size:59
Alignment explanation
Indices: 654205--654369 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 59
654195 AAGTGCGTCT
* * *
654205 TGCTCTTTGAGGACT-ACAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCC
1 TGCTCCTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTG--AA-AAAAAGGCATCA
* * * * *
654267 TGCTCCTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCCTT----AAAAGGCATTA
1 TGCTCCTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAGGCATCA
*
654322 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
1 TGCTCCTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
654370 GGCGTCCTAC
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
55 48 0.56
62 37 0.44
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (59 bp):
TGCTCCTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAGGCATCA
Found at i:654345 original size:55 final size:55
Alignment explanation
Indices: 654256--654396 Score: 185
Period size: 55 Copynumber: 2.6 Consensus size: 55
654246 TTTGAAAAGA
* * *
654256 AAAAGGCATCCTGCTCCTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCCTT
1 AAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCCTT
** * *
654311 AAAAGGCATTATGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCCTT
* * *
654366 GAAAGGCGTCCTACTCTTTGAGGACT-AAAGG
1 AAAAGGCATCCTGCTCTTTGAGGACTGAAAGG
654397 GTGAAAAGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 5 0.07
55 69 0.93
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (55 bp):
AAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCCTT
Done.