Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 211 of 221
Found at i:61781502 original size:3 final size:3
Alignment explanation
Indices: 61781473--61781533 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
61781463 TTTACTCCTC
61781473 ATT ATT A-T ATT A-T ATT AATGT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -AT-T ATT ATT ATT ATT ATT ATT ATT ATT
61781517 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
61781534 CATCATATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 2 0.04
5 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:61782055 original size:15 final size:16
Alignment explanation
Indices: 61782023--61782055 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61782013 CATACATACT
*
61782023 TACATATATTTTTACA
1 TACATAGATTTTTACA
61782039 TACATAGATTTTT-CA
1 TACATAGATTTTTACA
61782054 TA
1 TA
61782056 TTTTCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (16 bp):
TACATAGATTTTTACA
Found at i:61784942 original size:13 final size:15
Alignment explanation
Indices: 61784918--61784951 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
61784908 GTTAATTTTC
61784918 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
61784932 AAAATTT-AAAAATA
1 AAAATTTCAAAAATA
61784946 AAAATT
1 AAAATT
61784952 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:61784981 original size:30 final size:30
Alignment explanation
Indices: 61784947--61785062 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
61784937 TTAAAAATAA
*
61784947 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCACT
* **
61784977 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCACT
* * *
61785007 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCACT
* *
61785037 AAATTTCATTTT-AACCCTAAATTTTC
1 AAATTTCATTTTGACCCCTAAACTTTC
61785063 TAAAAATTAC
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.22
30 58 0.78
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCACT
Found at i:61785069 original size:29 final size:29
Alignment explanation
Indices: 61784944--61785076 Score: 94
Period size: 30 Copynumber: 4.5 Consensus size: 29
61784934 AATTTAAAAA
* *
61784944 TAAAAATTGCATTTTGACCCCTAAACTTTTCC
1 TAAAAATTTCATTTT-AACCCTAAAC-TTT-C
*
61784976 T--AAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTTCATTTTAACCC-TAAACTTTC
** *
61785004 TTTAAATTTCA-CTTAGACCCCTAAACTTTC
1 TAAAAATTTCATTTTA-A-CCCTAAACTTTC
* *
61785034 -ATTAAATTTCATTTTAACCCTAAATTTTC
1 TA-AAAATTTCATTTTAACCCTAAACTTTC
*
61785063 TAAAAATTACATTT
1 TAAAAATTTCATTT
61785077 AGCCCCAGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
28 2 0.02
29 29 0.35
30 45 0.54
31 6 0.07
32 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAAAATTTCATTTTAACCCTAAACTTTC
Found at i:61785628 original size:13 final size:13
Alignment explanation
Indices: 61785574--61785629 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
61785564 AGGCCAGCCC
61785574 AAAAAAAACA-AAG
1 AAAAAAAA-AGAAG
* *
61785587 CAAAAAAAAGTAG
1 AAAAAAAAAGAAG
* *
61785600 CAAAAAAGAAGCAG
1 -AAAAAAAAAGAAG
61785614 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
61785627 AAA
1 AAA
61785630 GAAGCAGCCC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
12 1 0.03
13 23 0.68
14 10 0.29
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:61786257 original size:17 final size:17
Alignment explanation
Indices: 61786214--61786261 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
61786204 AGAAAAAAAT
61786214 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
61786233 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
61786249 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
61786262 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:61786345 original size:17 final size:18
Alignment explanation
Indices: 61786325--61786389 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 18
61786315 AAAAAAAATC
61786325 CGTG-TTTCAAAAATTCT
1 CGTGATTTCAAAAATTCT
* **
61786342 CGTGAATAAAAAAATT-T
1 CGTGATTTCAAAAATTCT
* *
61786359 CGTGTTTTCAAAAATTCC
1 CGTGATTTCAAAAATTCT
*
61786377 CGTG-TTTTAAAAA
1 CGTGATTTCAAAAA
61786390 AAATTTCGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
17 25 0.68
18 12 0.32
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (18 bp):
CGTGATTTCAAAAATTCT
Found at i:61786368 original size:35 final size:36
Alignment explanation
Indices: 61786314--61786404 Score: 114
Period size: 37 Copynumber: 2.6 Consensus size: 36
61786304 TTTCTTTCTT
* * *
61786314 TAAAAAAAATCCGTG-TTTCAAAAATTCTCGTG-AA
1 TAAAAAAATTTCGTGTTTTCAAAAATTCCCGTGTAA
**
61786348 TAAAAAAATTTCGTGTTTTCAAAAATTCCCGTGTTT
1 TAAAAAAATTTCGTGTTTTCAAAAATTCCCGTGTAA
61786384 TAAAAAAAATTTCGTGTTTTC
1 T-AAAAAAATTTCGTGTTTTC
61786405 GTGTTTTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 13 0.27
35 16 0.33
36 1 0.02
37 19 0.39
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (36 bp):
TAAAAAAATTTCGTGTTTTCAAAAATTCCCGTGTAA
Found at i:61786371 original size:18 final size:18
Alignment explanation
Indices: 61786350--61786660 Score: 95
Period size: 17 Copynumber: 16.3 Consensus size: 18
61786340 CTCGTGAATA
61786350 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
61786368 -AAAAATTCCCGTGTTTTAA
1 AAAAAATT-TCGTGTTTT-C
61786387 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
61786405 GTGTTTTAAAAAAAAATTCTCGTG-TTTC
1 ---------AA-AAAATT-TCGTGTTTTC
*
61786433 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
*
61786451 AAAATTTTCATGTTTTCGTGTTTTC
1 AAAA-----A-ATT-TCGTGTTTTC
* *
61786476 AAAAAATTCTCATGTTTTTTTT
1 AAAAAATT-TC--G-TGTTTTC
** *
61786498 AAAAAAAATCATGTTTT-
1 AAAAAATTTCGTGTTTTC
* *
61786515 AAAAAAATTCATGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
61786533 -GAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
** *
61786550 --AAAATTTTTTG-TGTC
1 AAAAAATTTCGTGTTTTC
* *
61786565 AAAAAATTCTCATG-TATC
1 AAAAAATT-TCGTGTTTTC
* *
61786583 -GAAAATTTCCTTGTTTTC
1 AAAAAATTT-CGTGTTTTC
*
61786601 AAAAAAATTCCGTGTTTTC
1 -AAAAAATTTCGTGTTTTC
61786620 AAAAAATTTTCGTG-TTTC
1 AAAAAA-TTTCGTGTTTTC
61786638 -AAAAATCTTCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
61786656 AAAAA
1 AAAAA
61786661 TTATTATTGT
Statistics
Matches: 223, Mismatches: 33, Indels: 73
0.68 0.10 0.22
Matches are distributed among these distances:
15 3 0.01
16 10 0.04
17 67 0.30
18 49 0.22
19 32 0.14
20 14 0.06
21 3 0.01
22 11 0.05
23 1 0.00
24 2 0.01
25 14 0.06
27 2 0.01
28 10 0.04
29 5 0.02
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (18 bp):
AAAAAATTTCGTGTTTTC
Found at i:61786371 original size:19 final size:19
Alignment explanation
Indices: 61786349--61786404 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
61786339 TCTCGTGAAT
61786349 AAAAAAATTTCGTGTTTTC
1 AAAAAAATTTCGTGTTTTC
* *
61786368 --AAAAATTCCCGTGTTTTA
1 AAAAAAATT-TCGTGTTTTC
61786386 AAAAAAATTTCGTGTTTTC
1 AAAAAAATTTCGTGTTTTC
61786405 GTGTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.23
18 8 0.27
19 8 0.27
20 7 0.23
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (19 bp):
AAAAAAATTTCGTGTTTTC
Found at i:61786407 original size:27 final size:29
Alignment explanation
Indices: 61786377--61786431 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
61786367 CAAAAATTCC
61786377 CGTGTTTT-AAAAAAAATT-TCGTGTTTT
1 CGTGTTTTAAAAAAAAATTCTCGTGTTTT
61786404 CGTGTTTTAAAAAAAAATTCTCGTGTTT
1 CGTGTTTTAAAAAAAAATTCTCGTGTTT
61786432 CAAAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 8 0.31
28 10 0.38
29 8 0.31
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (29 bp):
CGTGTTTTAAAAAAAAATTCTCGTGTTTT
Found at i:61786433 original size:65 final size:63
Alignment explanation
Indices: 61786349--61786481 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 63
61786339 TCTCGTGAAT
*
61786349 AAAAAAATTTCGTGTTTTCAAAAATTCCCGTGTTTTAAAAAAAATTTCGTGTTTTCGTGTTTTAA
1 AAAAAAATTTCGTGTTTTCAAAAATTCCCGTGTTTT--AAAAAATTTCATGTTTTCGTGTTTTAA
** * * *
61786414 AAAAAAATTCTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCA
1 AAAAAAATT-TCGTGTTTTCAAAAATTCCCGTGTTTTAAAAAATTTCATGTTTTCGTGTTTTAA
61786477 AAAAA
1 AAAAA
61786482 TTCTCATGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
63 28 0.46
65 28 0.46
66 5 0.08
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (63 bp):
AAAAAAATTTCGTGTTTTCAAAAATTCCCGTGTTTTAAAAAATTTCATGTTTTCGTGTTTTAA
Found at i:61786467 original size:25 final size:26
Alignment explanation
Indices: 61786438--61786493 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
61786428 GTTTCAAAAA
*
61786438 TTTTCGTGTTTTC-AAAATTTTCATG
1 TTTTCGTGTTTTCAAAAATTCTCATG
61786463 TTTTCGTGTTTTCAAAAAATTCTCATG
1 TTTTCGTGTTTTC-AAAAATTCTCATG
61786490 TTTT
1 TTTT
61786494 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 13 0.46
27 15 0.54
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.55
Consensus pattern (26 bp):
TTTTCGTGTTTTCAAAAATTCTCATG
Found at i:61786651 original size:36 final size:38
Alignment explanation
Indices: 61786593--61786678 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
61786583 GAAAATTTCC
61786593 TTGT-TTTCAAAAAAATTCCGTGTTTTCAAAAA-ATT-
1 TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
**
61786628 TTCGTGTTTCAAAAATCTT-CGTGTTTTCAAAAATTATTA
1 TT-GTGTTTCAAAAAAATTCCGTGTTTTCAAAAA-TATTA
61786667 TTGTGTTTCAAA
1 TTGTGTTTCAAA
61786679 GTTCTCGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 16 0.36
37 11 0.25
38 13 0.30
39 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (38 bp):
TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
Found at i:61786661 original size:18 final size:18
Alignment explanation
Indices: 61786594--61786661 Score: 84
Period size: 18 Copynumber: 3.7 Consensus size: 18
61786584 AAAATTTCCT
*
61786594 TGTTTTCAAAAAAATTCCG
1 TGTTTTCAAAAATATT-CG
*
61786613 TGTTTTCAAAAAATTTTCG
1 TGTTTTC-AAAAATATTCG
*
61786632 TG-TTTCAAAAATCTTCG
1 TGTTTTCAAAAATATTCG
61786649 TGTTTTCAAAAAT
1 TGTTTTCAAAAAT
61786662 TATTATTGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
17 12 0.27
18 14 0.32
19 11 0.25
20 7 0.16
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (18 bp):
TGTTTTCAAAAATATTCG
Found at i:61806998 original size:21 final size:21
Alignment explanation
Indices: 61806956--61806998 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
61806946 TTCTAAAAGA
*
61806956 AAAATAATAAATAAAAATTTT
1 AAAATAATAAATAAAAACTTT
61806977 AAAATATATAAAT-AAAACTTT
1 AAAATA-ATAAATAAAAACTTT
61806998 A
1 A
61806999 TCAAATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATAATAAATAAAAACTTT
Found at i:61807019 original size:20 final size:20
Alignment explanation
Indices: 61806996--61807046 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
61806986 AAATAAAACT
* *
61806996 TTATCAAATTTTCAAAAATA
1 TTATAAAATTTTCAAAAAAA
**
61807016 TTATAAAACATTCAAAAAAA
1 TTATAAAATTTTCAAAAAAA
61807036 TTATAAAATTT
1 TTATAAAATTT
61807047 ACTGAAATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
TTATAAAATTTTCAAAAAAA
Found at i:61809765 original size:30 final size:31
Alignment explanation
Indices: 61809731--61809832 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
61809721 AAAAAAATAA
*
61809731 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
61809761 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
61809791 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
61809821 AAATTTCATTTT
1 AAATTTCATTTT
61809833 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:61810112 original size:10 final size:10
Alignment explanation
Indices: 61810093--61810135 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
61810083 TTTTTCGAAG
*
61810093 GAAAAAAGAA
1 GAAAAGAGAA
61810103 GAAAAGAGAA
1 GAAAAGAGAA
61810113 GAAAAGAGAA
1 GAAAAGAGAA
* *
61810123 -AGAGGAGAA
1 GAAAAGAGAA
61810132 GAAA
1 GAAA
61810136 GAAAGAGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:61810126 original size:16 final size:17
Alignment explanation
Indices: 61810098--61810142 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
61810088 CGAAGGAAAA
61810098 AAGAAGA-AAAGAGAAG
1 AAGAAGAGAAAGAGAAG
*
61810114 AA-AAGAGAAAGAGGAG
1 AAGAAGAGAAAGAGAAG
61810130 AAGAA-AGAAAGAG
1 AAGAAGAGAAAGAG
61810143 TACCGGCGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 4 0.15
16 20 0.77
17 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAGAAGAGAAAGAGAAG
Found at i:61810130 original size:19 final size:18
Alignment explanation
Indices: 61810096--61810135 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
61810086 TTCGAAGGAA
61810096 AAAAGAAGAAAAGAGAAG
1 AAAAGAAGAAAAGAGAAG
61810114 AAAAG-AGAAAGAGGAGAAG
1 AAAAGAAGAAA-A-GAGAAG
61810133 AAA
1 AAA
61810136 GAAAGAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AAAAGAAGAAAAGAGAAG
Found at i:61810203 original size:3 final size:3
Alignment explanation
Indices: 61810197--61810268 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
61810187 GCTAGACTTT
*
61810197 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
*
61810244 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
61810269 ATAATAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:61810215 original size:10 final size:10
Alignment explanation
Indices: 61810200--61810228 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
61810190 AGACTTTGAA
61810200 GAAGAAGAAG
1 GAAGAAGAAG
61810210 GAAGAAGAAG
1 GAAGAAGAAG
61810220 GAAGAAGAA
1 GAAGAAGAA
61810229 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:61810215 original size:13 final size:13
Alignment explanation
Indices: 61810197--61810242 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
61810187 GCTAGACTTT
61810197 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
61810210 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
61810223 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
61810234 GAAGAAGAA
1 GAAGAAGAA
61810243 AGAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:61810418 original size:23 final size:23
Alignment explanation
Indices: 61810392--61810436 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
61810382 AAAAAGTAGC
61810392 AAAAAGAAGAAGAAAGAAGCAGA
1 AAAAAGAAGAAGAAAGAAGCAGA
61810415 AAAAAGAAGAAGAAAGAAGCAG
1 AAAAAGAAGAAGAAAGAAGCAG
61810437 CCCAAATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.69, C:0.04, G:0.27, T:0.00
Consensus pattern (23 bp):
AAAAAGAAGAAGAAAGAAGCAGA
Found at i:61810571 original size:10 final size:9
Alignment explanation
Indices: 61810555--61810611 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 9
61810545 CAGCCCAGCA
61810555 AAAAAAAAG
1 AAAAAAAAG
61810564 AGAAAAAAAG
1 A-AAAAAAAG
*
61810574 AAAAAGAGAGAA
1 AAAAA-A-A-AG
61810586 AAGAAAAAAG
1 AA-AAAAAAG
61810596 AAAAAACAAG
1 AAAAAA-AAG
61810606 AAAAAA
1 AAAAAA
61810612 GAGGTTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.22
10 22 0.55
11 2 0.05
12 4 0.10
13 3 0.08
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:61810579 original size:16 final size:16
Alignment explanation
Indices: 61810554--61810601 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 16
61810544 CCAGCCCAGC
61810554 AAAA-AAAAAGAGAAA
1 AAAAGAAAAAGAGAAA
*
61810569 AAAAGAAAAAGAG-AG
1 AAAAGAAAAAGAGAAA
61810584 AAAAGAAAAA-AGAAA
1 AAAAGAAAAAGAGAAA
61810599 AAA
1 AAA
61810602 CAAGAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 2 0.07
15 19 0.66
16 8 0.28
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAGAAA
Found at i:61810607 original size:22 final size:22
Alignment explanation
Indices: 61810567--61810609 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
61810557 AAAAAAGAGA
*
61810567 AAAAAAGAAAAAGAGAGAAAAG
1 AAAAAAGAAAAAGAAAGAAAAG
61810589 AAAAAAGAAAAA-ACAAGAAAA
1 AAAAAAGAAAAAGA-AAGAAAA
61810610 AAGAGGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAGAAAGAAAAG
Found at i:61810609 original size:16 final size:15
Alignment explanation
Indices: 61810554--61810610 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
61810544 CCAGCCCAGC
61810554 AAAA-AAAAAGAGAAA
1 AAAAGAAAAAGA-AAA
* *
61810569 AAAAGAAAAAGAGAG
1 AAAAGAAAAAGAAAA
61810584 AAAAGAAAAAAGAAAA
1 AAAAG-AAAAAGAAAA
61810600 AACAAGAAAAA
1 AA-AAGAAAAA
61810611 AGAGGTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 10 0.29
16 22 0.63
17 3 0.09
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:61810986 original size:18 final size:18
Alignment explanation
Indices: 61810942--61811456 Score: 261
Period size: 17 Copynumber: 29.8 Consensus size: 18
61810932 TCAATAATCC
*
61810942 TCGTGCTTTT-AAAAATTC
1 TCGTG-TTTTCAAAAATTT
* *
61810960 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
61810977 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTT
*
61810994 TAGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
61811011 TCTTGTTTTCAGAAAAAATTT
1 TCGTGTTTTC---AAAAATTT
*
61811032 TCGTGTTTT-ATAAATTT
1 TCGTGTTTTCAAAAATTT
* * **
61811049 CCGTATTTTCAAAAA-AA
1 TCGTGTTTTCAAAAATTT
*
61811066 TCATGTCTTTCAAAAATTT
1 TCGTGT-TTTCAAAAATTT
**
61811085 TCGTGTTTTCAAAAAAAATGA
1 TCGTGTTTTC---AAAAATTT
*
61811106 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* *** *
61811123 CCGTGTTAAAAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
61811141 TCGTATTTTCAAAAAATTT
1 TCGTGTTTTC-AAAAATTT
*
61811160 TCGTG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
61811177 TCGTGTTTTCAAAAA-TT
1 TCGTGTTTTCAAAAATTT
*
61811194 TCGGTGTTTT-AAAGATTT
1 TC-GTGTTTTCAAAAATTT
*
61811212 TCGTGTTTTCAAAAA-CT
1 TCGTGTTTTCAAAAATTT
* * **
61811229 CCGGTGATTT-AAAAA-AA
1 TC-GTGTTTTCAAAAATTT
*
61811246 TCGT-TTTCTAAAAAATTT
1 TCGTGTTT-TCAAAAATTT
*
61811264 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
61811281 TCGTGTTTT--AAAATTT
1 TCGTGTTTTCAAAAATTT
*
61811297 TCGTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
*
61811314 TCGTATTTT---AAA-TT
1 TCGTGTTTTCAAAAATTT
*** **
61811328 T--T-TTAAGAAAAAAAT
1 TCGTGTTTTCAAAAATTT
* *
61811343 T-GTG-TTTCAAAAAATG
1 TCGTGTTTTCAAAAATTT
* *
61811359 TCTTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
61811376 TCGTG-TTTCAAAAAATG
1 TCGTGTTTTCAAAAATTT
61811393 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
**
61811410 TCGTGTTTT-TGAAATTT
1 TCGTGTTTTCAAAAATTT
* *
61811427 CCGTG-TTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
61811443 TCGTGTTTT-AAAAA
1 TCGTGTTTTCAAAAA
61811457 AAAAACTTTC
Statistics
Matches: 379, Mismatches: 81, Indels: 75
0.71 0.15 0.14
Matches are distributed among these distances:
11 2 0.01
12 1 0.00
14 5 0.01
15 7 0.02
16 50 0.13
17 178 0.47
18 90 0.24
19 16 0.04
20 4 0.01
21 26 0.07
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:61811004 original size:16 final size:16
Alignment explanation
Indices: 61810953--61811006 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
61810943 CGTGCTTTTA
61810953 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
61810969 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
61810987 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
61811003 AAAA
1 AAAA
61811007 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:61811083 original size:36 final size:38
Alignment explanation
Indices: 61811043--61811126 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 38
61811033 CGTGTTTTAT
*
61811043 AAATTTCCGTATTTTC-AAAAAAATCA-TGTCTTTCAA
1 AAATTTCCGTATTTTCAAAAAAAATCACCGTCTTTCAA
* * * *
61811079 AAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAA
1 AAATTTCCGTATTTTCAAAAAAAATCACCGTCTTTCAA
61811117 AAATTTCCGT
1 AAATTTCCGT
61811127 GTTAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
36 14 0.35
37 9 0.22
38 17 0.43
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (38 bp):
AAATTTCCGTATTTTCAAAAAAAATCACCGTCTTTCAA
Found at i:61811094 original size:74 final size:73
Alignment explanation
Indices: 61810999--61811201 Score: 209
Period size: 74 Copynumber: 2.8 Consensus size: 73
61810989 AATTCTAGTG
* * * * *
61810999 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTGTTTTATAAATTTCCGTATTTTCAAAAA
1 TTTCAAAAATTTTCGTGTTTTCA-AAAAAATCTTCGTGTTTTAAAAATTTCCG--TGTTAAAAAA
61811064 AATCAT-GT-C
63 AATCATCGTAC
*** *
61811073 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
1 TTTCAAAAATTTTCGTGTTTTC-AAAAAAATCTTCGTGTTTTAAAAATTTCCGTGTTAAAAAAAA
* *
61811138 TCTTCGTAT
65 TCATCGTAC
*
61811147 TTTCAAAAAATTTTCGTG-TTTC--AAAAATCTTCGTGTTTTCAAAAATTTCGGTGTT
1 TTTC-AAAAATTTTCGTGTTTTCAAAAAAATCTTCGTGTTTT-AAAAATTTCCGTGTT
61811202 TTAAAGATTT
Statistics
Matches: 109, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
71 13 0.12
72 27 0.25
73 2 0.02
74 53 0.49
75 14 0.13
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (73 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAATCTTCGTGTTTTAAAAATTTCCGTGTTAAAAAAAAT
CATCGTAC
Found at i:61811155 original size:54 final size:55
Alignment explanation
Indices: 61811077--61811183 Score: 137
Period size: 54 Copynumber: 1.9 Consensus size: 55
61811067 CATGTCTTTC
* *
61811077 AAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAAT-TTCCGTGTTAAA
1 AAAAATCTTCGTATTTTC-AAAAAAATGACCGTGTTTCAAAAATCTT-CGTGTTAAA
***
61811133 AAAAATCTTCGTATTTTC-AAAAAATTTTCGTGTTTCAAAAATCTTCGTGTT
1 AAAAATCTTCGTATTTTCAAAAAAATGACCGTGTTTCAAAAATCTTCGTGTT
61811184 TTCAAAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
54 27 0.60
55 2 0.04
56 16 0.36
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (55 bp):
AAAAATCTTCGTATTTTCAAAAAAATGACCGTGTTTCAAAAATCTTCGTGTTAAA
Found at i:61811471 original size:20 final size:20
Alignment explanation
Indices: 61811448--61811486 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61811438 AATTCTCGTG
61811448 TTTTAAAAAAAAAACTTTCA
1 TTTTAAAAAAAAAACTTTCA
** *
61811468 TTTTTTAAAAAAAATTTTC
1 TTTTAAAAAAAAAACTTTC
61811487 GTGCTTCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTAAAAAAAAAACTTTCA
Found at i:61811497 original size:17 final size:17
Alignment explanation
Indices: 61811477--61811514 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
61811467 ATTTTTTAAA
*
61811477 AAAAATTTTCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
61811493 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
61811510 AAAAA
1 AAAAA
61811515 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:61819834 original size:54 final size:54
Alignment explanation
Indices: 61819770--61819975 Score: 160
Period size: 54 Copynumber: 3.5 Consensus size: 54
61819760 TTTTAAATTG
61819770 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
* ***** ***
61819824 ACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAA
1 ACTCATATTGCGAG--A-G-G-TGAG--TTA----A-GCCTTTTAATTTTT-GTTT-T-TCAAAA
**
61819889 ATTG
51 ATCA
61819893 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
* *
61819947 ACTCATATTGCAAGAGGTGAGTTGAGCCT
1 ACTCATATTGCGAGAGGTGAGTTAAGCCT
61819976 CGGGTCACAT
Statistics
Matches: 113, Mismatches: 24, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
54 46 0.41
55 1 0.01
56 5 0.04
57 10 0.09
58 2 0.02
59 4 0.04
61 2 0.02
62 2 0.02
64 4 0.04
65 2 0.02
66 10 0.09
67 5 0.04
68 1 0.01
69 19 0.17
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (54 bp):
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
Found at i:61819912 original size:123 final size:122
Alignment explanation
Indices: 61819693--61820011 Score: 539
Period size: 123 Copynumber: 2.6 Consensus size: 122
61819683 ATTTTTTAAA
61819693 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTAGTTTA
61819758 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
65 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
61819816 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTAGTTTA
61819881 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
65 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* * * * *
61819939 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGG-CAC--GCCGAGGTATTTTTAGTT
61820004 TATGTTTT
63 TATGTTTT
61820012 TTTTCAATCT
Statistics
Matches: 185, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
122 3 0.02
123 159 0.86
125 23 0.12
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (122 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCACGCCGAGGTATTTTTAGTTTAT
GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:61820017 original size:17 final size:18
Alignment explanation
Indices: 61819995--61820029 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
61819985 TGCTGAGGTA
*
61819995 TTTTCAATTTATG-TTTT
1 TTTTCAATCTATGCTTTT
61820012 TTTTCAATCTATGCTTTT
1 TTTTCAATCTATGCTTTT
61820030 CAAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTCAATCTATGCTTTT
Found at i:61820206 original size:72 final size:73
Alignment explanation
Indices: 61820013--61820645 Score: 1015
Period size: 72 Copynumber: 8.7 Consensus size: 73
61820003 TTATGTTTTT
* * * ** *
61820013 TTTCAATCTATGCTTTTCAAAAATT-AACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACG
1 TTTCAATTTCTGCTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
61820077 TTGAGGTAA
65 TTGAGGTAA
*
61820086 TTTTCAATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
1 -TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
61820151 TTGAGGTAA
65 TTGAGGTAA
*
61820160 TTTCAATTTTTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
61820224 TGAGGTAA
66 TGAGGTAA
* * * * *
61820232 TTTCAATTTTTG-TTTTCAAAATTCAACTCATAATGCGAGAAATGAGTTGAGCCTCAGGACATGC
1 TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
61820296 TGAGGTAA
66 TGAGGTAA
*
61820304 TTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACAT
1 TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
*
61820368 TGAGGTAT
66 TGAGGTAA
*
61820376 TTTCAATTTTTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
61820441 TGAGGTAA
66 TGAGGTAA
61820449 TTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
*
61820513 TGAGGTAT
66 TGAGGTAA
61820521 TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
*
61820586 TGAGGTAT
66 TGAGGTAA
* * **
61820594 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAG
61820646 ACTTTTAATT
Statistics
Matches: 527, Mismatches: 29, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
72 274 0.52
73 194 0.37
74 59 0.11
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (73 bp):
TTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
TGAGGTAA
Found at i:61820469 original size:145 final size:145
Alignment explanation
Indices: 61820026--61820645 Score: 1037
Period size: 145 Copynumber: 4.3 Consensus size: 145
61820016 CAATCTATGC
* ** *
61820026 TTTTCAAAAATT-AACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGTTGAGGTAATTTT
1 TTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT-ATTTT
*
61820090 CAATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
64 CAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
*
61820155 GGTAATTTCAATTTTTG
129 GGTAATTTCAATTTCTG
*
61820172 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
* * * * *
61820237 ATTTTTG-TTTTCAAAATTCAACTCATAATGCGAGAAATGAGTTGAGCCTCAGGACATGCTGAGG
66 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
61820301 TAATTTCAATTTCTG
131 TAATTTCAATTTCTG
*
61820316 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
*
61820381 ATTTTTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
66 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
61820446 TAATTTCAATTTCTG
131 TAATTTCAATTTCTG
61820461 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
61820526 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
66 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
61820591 TATTTTCAATTTCTG
131 TAATTTCAATTTCTG
* **
61820606 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAG
61820646 ACTTTTAATT
Statistics
Matches: 447, Mismatches: 24, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
144 136 0.30
145 228 0.51
146 83 0.19
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (145 bp):
TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTCAATTTCTG
Found at i:61820668 original size:54 final size:54
Alignment explanation
Indices: 61820593--61821248 Score: 1015
Period size: 54 Copynumber: 12.0 Consensus size: 54
61820583 CGTTGAGGTA
*
61820593 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGAC
1 TTTT-AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
61820648 TTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
61820702 TTTTAATTTCTGATTTTCACTGATTTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCC
1 TTTTAATTTCTG--------T--TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
61820766 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
61820820 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGAC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* *
61820874 TTTTAATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
61820928 --TT--TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
61820978 TTTTAATTTCTGATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
61821032 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
61821086 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
61821140 --TT--TTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * *
61821192 TTTTGTAAATTCTG-TTTTCAAAAATCAACTTATATTGCGAGAAGTGAGTTGAGCC
1 -TTT-TAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
61821247 TT
1 TT
61821249 GGCTCACGTG
Statistics
Matches: 561, Mismatches: 18, Indels: 45
0.90 0.03 0.07
Matches are distributed among these distances:
50 57 0.10
52 42 0.07
54 359 0.64
55 39 0.07
56 2 0.00
57 5 0.01
58 4 0.01
62 1 0.00
64 52 0.09
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (54 bp):
TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
Found at i:61821092 original size:212 final size:211
Alignment explanation
Indices: 61820593--61821248 Score: 1051
Period size: 212 Copynumber: 3.0 Consensus size: 211
61820583 CGTTGAGGTA
61820593 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTTTTAATTTC
1 TTTT-AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTTTTAATTTC
61820658 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGATTTTCACT
65 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC--TT--TTTCTG--------T
*
61820723 GATTTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTTTAATTTCTGTTTTTCAAAA
118 --TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTG-TTTTCAAAA
61820788 ATCAACTCATATTGCGAGAGGTGAGTTGAGCC
180 ATCAACTCATATTGCGAGAGGTGAGTTGAGCC
61820820 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTTTTAATTTCT
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTTTTAATTTCT
*
61820885 ATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCTGTTTTTCAAAAATCA
66 ATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCTGTTTTTCAAAAATCA
61820950 ACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGATTTTCAAAAATCAACTCATATTGC
131 ACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTG-TTTTCAAAAATCAACTCATATTGC
61821015 GAGAGGTGAGTTGAGCC
195 GAGAGGTGAGTTGAGCC
*
61821032 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCT
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTTTTAATTTCT
* *
61821097 GTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCTATTTTTCAAAAAAAT
66 ATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCTGTTTTTC--AAAAAT
* *
61821162 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTGTAAATTCTGTTTTCAAAAATCAACTTATAT
129 CAACTCATATTGCGAGAGGTGAGTTGAGCC-TTT-TAATTTCTGTTTTCAAAAATCAACTCATAT
*
61821227 TGCGAGAAGTGAGTTGAGCC
192 TGCGAGAGGTGAGTTGAGCC
61821247 TT
1 TT
61821249 GGCTCACGTG
Statistics
Matches: 415, Mismatches: 10, Indels: 20
0.93 0.02 0.04
Matches are distributed among these distances:
212 211 0.51
214 37 0.09
215 44 0.11
216 8 0.02
222 6 0.01
224 2 0.00
226 103 0.25
227 4 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (211 bp):
TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTTTTAATTTCT
ATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCTGTTTTTCAAAAATCA
ACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTCAAAAATCAACTCATATTGCG
AGAGGTGAGTTGAGCC
Found at i:61821506 original size:13 final size:14
Alignment explanation
Indices: 61821488--61821520 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
61821478 GTTAATTTTC
*
61821488 AAAATTTCAAAA-A
1 AAAATTTAAAAATA
61821501 AAAATTTAAAAATA
1 AAAATTTAAAAATA
61821515 AAAATT
1 AAAATT
61821521 GCATTTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTTAAAAATA
Found at i:61821554 original size:29 final size:30
Alignment explanation
Indices: 61821516--61821630 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
61821506 TTAAAAATAA
* *
61821516 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
61821546 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
61821575 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
61821605 AAATTTCATTTT-AACCCTAAATTTTC
1 AAATTTCATTTTGACCCCTAAACTTTC
61821631 TAAAAATTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.06
29 33 0.46
30 35 0.49
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:61821582 original size:30 final size:30
Alignment explanation
Indices: 61821516--61821631 Score: 130
Period size: 29 Copynumber: 3.9 Consensus size: 30
61821506 TTAAAAATAA
* *
61821516 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
61821546 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* * *
61821575 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* *
61821605 AAATTTCATTTT-AACCCTAAATTTTCT
1 AAATTTCATTTTGACCCCTAAACTTTCT
61821632 AAAAATTACA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 36 0.50
30 36 0.50
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:61821637 original size:29 final size:29
Alignment explanation
Indices: 61821513--61821644 Score: 90
Period size: 29 Copynumber: 4.5 Consensus size: 29
61821503 AATTTAAAAA
* *
61821513 TAAAAATTGCATTTTGACCCCTAAACTTT-
1 TAAAAATTTCATTTT-AACCCTAAACTTTC
*** *
61821542 TCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTTCATTTTAACCC-TAAACTTTC
** *
61821572 TTTAAATTTCA-CTTAGACCCCTAAACTTTC
1 TAAAAATTTCATTTTA-A-CCCTAAACTTTC
* *
61821602 -ATTAAATTTCATTTTAACCCTAAATTTTC
1 TA-AAAATTTCATTTTAACCCTAAACTTTC
*
61821631 TAAAAATTACATTT
1 TAAAAATTTCATTT
61821645 AGCCCCAGAA
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
28 3 0.04
29 42 0.52
30 29 0.36
31 6 0.08
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAAAATTTCATTTTAACCCTAAACTTTC
Found at i:61821638 original size:59 final size:59
Alignment explanation
Indices: 61821513--61821638 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
61821503 AATTTAAAAA
* * *
61821513 TAAAAATTGCATTTTGACCCCTAAACTTTTCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
** * * *
61821572 TTTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTCATTTTAACCC-TAAATTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTC-CT-AATTTCATTTTAACCCTTAAACTTTC
61821631 TAAAAATT
1 TAAAAATT
61821639 ACATTTAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 4 0.07
59 36 0.65
60 15 0.27
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (59 bp):
TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
Found at i:61822174 original size:24 final size:24
Alignment explanation
Indices: 61822147--61822200 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
61822137 CAAAAAAACA
*
61822147 AAGCA-AAAAAAAGTAGCAAAAAAG
1 AAGCAGAAAAAAAGAAG-AAAAAAG
*
61822171 AAGCAGAAAAAAAGAAGAAGAAAG
1 AAGCAGAAAAAAAGAAGAAAAAAG
61822195 AAGCAG
1 AAGCAG
61822201 CCCACTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.69, C:0.07, G:0.22, T:0.02
Consensus pattern (24 bp):
AAGCAGAAAAAAAGAAGAAAAAAG
Found at i:61822341 original size:11 final size:11
Alignment explanation
Indices: 61822324--61822363 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
61822314 ACGCCCAGCA
61822324 AAAAAAAATAAG
1 AAAAAAAA-AAG
61822336 AAAAAAAAAAG
1 AAAAAAAAAAG
61822347 AAAAGAAAAAAGG
1 AAAA-AAAAAA-G
61822360 AAAA
1 AAAA
61822364 GGGGGCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.27
12 14 0.54
13 5 0.19
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:61822344 original size:16 final size:16
Alignment explanation
Indices: 61822323--61822357 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
61822313 AACGCCCAGC
*
61822323 AAAAAAAA-ATAAGAA
1 AAAAAAAAGAAAAGAA
61822338 AAAAAAAAGAAAAGAA
1 AAAAAAAAGAAAAGAA
61822354 AAAA
1 AAAA
61822358 GGAAAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGAAAAGAA
Found at i:61822828 original size:17 final size:17
Alignment explanation
Indices: 61822785--61822832 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
61822775 AGAAAAAAAT
61822785 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
61822804 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
61822820 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
61822833 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:61822915 original size:17 final size:18
Alignment explanation
Indices: 61822895--61822973 Score: 56
Period size: 18 Copynumber: 4.5 Consensus size: 18
61822885 TAAAAAAATC
61822895 CGTG-TTTCAAAAATTCT
1 CGTGATTTCAAAAATTCT
* **
61822912 CGTGAATAAAAAAATT-T
1 CGTGATTTCAAAAATTCT
* *
61822929 CGTGTTTTCAAAAATTCC
1 CGTGATTTCAAAAATTCT
* *
61822947 CGTGTTTTAAAAAAATT-T
1 CGTGATTT-CAAAAATTCT
*
61822965 CGTGTTTTC
1 CGTGATTTC
61822974 GTGTTTTAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
17 17 0.35
18 24 0.50
19 7 0.15
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (18 bp):
CGTGATTTCAAAAATTCT
Found at i:61822965 original size:36 final size:35
Alignment explanation
Indices: 61822883--61822973 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 35
61822873 TGTTTCTTTC
* *
61822883 TTTAAAAAAA-TCCGTG-TTTCAAAAATTCTCGTG
1 TTTAAAAAAATTTCGTGTTTTCAAAAATTCCCGTG
**
61822916 AATAAAAAAATTTCGTGTTTTCAAAAATTCCCGTG
1 TTTAAAAAAATTTCGTGTTTTCAAAAATTCCCGTG
61822951 TTTTAAAAAAATTTCGTGTTTTC
1 -TTTAAAAAAATTTCGTGTTTTC
61822974 GTGTTTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
33 8 0.16
34 5 0.10
35 16 0.33
36 20 0.41
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (35 bp):
TTTAAAAAAATTTCGTGTTTTCAAAAATTCCCGTG
Found at i:61822976 original size:26 final size:28
Alignment explanation
Indices: 61822947--61822999 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
61822937 CAAAAATTCC
61822947 CGTGTTTT-AAAAAAATT-TCGTGTTTT
1 CGTGTTTTAAAAAAAATTCTCGTGTTTT
61822973 CGTGTTTTAAAAAAAATTCTCGTGTTT
1 CGTGTTTTAAAAAAAATTCTCGTGTTT
61823000 CAAAATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 8 0.32
27 9 0.36
28 8 0.32
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.47
Consensus pattern (28 bp):
CGTGTTTTAAAAAAAATTCTCGTGTTTT
Found at i:61822987 original size:28 final size:27
Alignment explanation
Indices: 61822947--61823060 Score: 90
Period size: 27 Copynumber: 4.0 Consensus size: 27
61822937 CAAAAATTCC
61822947 CGTGTTTTAAAAAAATT-TCGTGTTTT
1 CGTGTTTTAAAAAAATTCTCGTGTTTT
61822973 CGTGTTTTAAAAAAAATTCTCGTGTTTCAAAATTTT
1 CGTGTTTT-AAAAAAATTCTCGTG--------TTTT
* * *
61823009 CGTGTTTT--CAAAATTTTCATGTTTT
1 CGTGTTTTAAAAAAATTCTCGTGTTTT
*
61823034 CGTGTTTTCAAAAAATTCTCGTGTTTT
1 CGTGTTTTAAAAAAATTCTCGTGTTTT
61823061 TTTTAAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
25 12 0.17
26 8 0.11
27 23 0.33
28 5 0.07
33 10 0.14
36 12 0.17
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (27 bp):
CGTGTTTTAAAAAAATTCTCGTGTTTT
Found at i:61823010 original size:44 final size:44
Alignment explanation
Indices: 61822926--61823017 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
61822916 AATAAAAAAA
*
61822926 TTTCGTGTTTTCAAAAATTCCCGTGTTTTAAAAAAATTTCGTGT
1 TTTCGTGTTTTAAAAAATTCCCGTGTTTTAAAAAAATTTCGTGT
* * *
61822970 TTTCGTGTTTTAAAAAAAATTCTCGTG-TTT-CAAAATTTTCGTGT
1 TTTCGTGTTTT--AAAAAATTCCCGTGTTTTAAAAAAATTTCGTGT
61823014 TTTC
1 TTTC
61823018 AAAATTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 27 0.64
45 3 0.07
46 12 0.29
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (44 bp):
TTTCGTGTTTTAAAAAATTCCCGTGTTTTAAAAAAATTTCGTGT
Found at i:61823013 original size:62 final size:61
Alignment explanation
Indices: 61822918--61823059 Score: 189
Period size: 61 Copynumber: 2.3 Consensus size: 61
61822908 TTCTCGTGAA
*
61822918 TAAAAAAATT-TCGTGTTTTCAAAAATTCCCGTGTTTTAAAAAAATTTCGTGTTTTCGTGTTT
1 TAAAAAAATTCTCGTG-TTTCAAAAATTCCCGTGTTTT-AAAAAATTTCATGTTTTCGTGTTT
** * *
61822980 TAAAAAAAATTCTCGTGTTTC-AAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTT
1 T-AAAAAAATTCTCGTGTTTCAAAAATTCCCGTGTTTTAAAAAATTTCATGTTTTCGTGTTT
*
61823041 TCAAAAAATTCTCGTGTTT
1 TAAAAAAATTCTCGTGTTT
61823060 TTTTTAAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
60 17 0.24
61 22 0.31
62 15 0.21
63 13 0.18
64 5 0.07
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (61 bp):
TAAAAAAATTCTCGTGTTTCAAAAATTCCCGTGTTTTAAAAAATTTCATGTTTTCGTGTTT
Found at i:61823205 original size:17 final size:18
Alignment explanation
Indices: 61822920--61823224 Score: 118
Period size: 17 Copynumber: 16.3 Consensus size: 18
61822910 CTCGTGAATA
61822920 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
61822938 -AAAAATTCCCGTGTTTTA
1 AAAAAATT-TCGTGTTTTC
61822956 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
61822974 GTGTTTTAAAAAAAATTCTCGTG-TTTC
1 ---------AAAAAATT-TCGTGTTTTC
*
61823001 -AAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
*
61823018 AAAATTTTCATGTTTTCGTGTTTTC
1 AAAA-----A--ATTTCGTGTTTTC
*
61823043 AAAAAATTCTCGTGTTTTTTTT
1 AAAAAATT-TCGTG---TTTTC
*
61823065 AAAAAA-TTCATGTTTT-
1 AAAAAATTTCGTGTTTTC
* *
61823081 AAAAAAATTCATGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
61823099 -GAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
*
61823116 --AAAATTT--TG-TGTC
1 AAAAAATTTCGTGTTTTC
* *
61823129 AAAAAATTCTCATG-TATC
1 AAAAAATT-TCGTGTTTTC
* *
61823147 -GAAAATTTCCTTGTTTTC
1 AAAAAATTT-CGTGTTTTC
*
61823165 AAAAAAATTCCGTGTTTTC
1 -AAAAAATTTCGTGTTTTC
61823184 AAAAAAATTTCGTG-TTTC
1 -AAAAAATTTCGTGTTTTC
61823202 -AAAAATCTTCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
61823220 AAAAA
1 AAAAA
61823225 TTATTATTGT
Statistics
Matches: 226, Mismatches: 22, Indels: 77
0.70 0.07 0.24
Matches are distributed among these distances:
13 3 0.01
14 2 0.01
15 6 0.03
16 25 0.11
17 59 0.26
18 37 0.16
19 37 0.16
20 11 0.05
21 1 0.00
22 10 0.04
23 1 0.00
25 17 0.08
27 12 0.05
28 5 0.02
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (18 bp):
AAAAAATTTCGTGTTTTC
Found at i:61823215 original size:36 final size:39
Alignment explanation
Indices: 61823161--61823242 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 39
61823151 ATTTCCTTGT
61823161 TTTCAAAAAAATTCCGTGTTTTCAAAAA-AATT-TCGTG
1 TTTCAAAAAAATTCCGTGTTTTCAAAAATAATTATCGTG
** * *
61823198 TTTCAAAAATCTT-CGTGTTTTCAAAAATTATTATTGTG
1 TTTCAAAAAAATTCCGTGTTTTCAAAAATAATTATCGTG
61823236 TTTCAAA
1 TTTCAAA
61823243 GTTCTCGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 14 0.36
37 14 0.36
38 11 0.28
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (39 bp):
TTTCAAAAAAATTCCGTGTTTTCAAAAATAATTATCGTG
Found at i:61824194 original size:12 final size:12
Alignment explanation
Indices: 61824177--61824206 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
61824167 GTGGTTGAGT
61824177 ATTCAAAACAAA
1 ATTCAAAACAAA
61824189 ATTCAAAACAAA
1 ATTCAAAACAAA
61824201 A-TCAAA
1 ATTCAAA
61824207 CTTTGCAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (12 bp):
ATTCAAAACAAA
Found at i:61826190 original size:9 final size:9
Alignment explanation
Indices: 61826176--61826212 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
61826166 TATAGTTTAA
61826176 TATTCGAAT
1 TATTCGAAT
61826185 TATTCGAAT
1 TATTCGAAT
* *
61826194 TATTTGAGT
1 TATTCGAAT
61826203 TATTCGAAT
1 TATTCGAAT
61826212 T
1 T
61826213 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:61828859 original size:17 final size:17
Alignment explanation
Indices: 61828839--61828876 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
61828829 TTTGATTATA
61828839 AAATATGA-AAAATGTAT
1 AAATATGATAAAA-GTAT
*
61828856 AAATATTATAAAAGTAT
1 AAATATGATAAAAGTAT
61828873 AAAT
1 AAAT
61828877 GTACATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (17 bp):
AAATATGATAAAAGTAT
Found at i:61829023 original size:3 final size:3
Alignment explanation
Indices: 61829015--61829060 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
61829005 ATATGTAAGT
* *
61829015 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
61829061 AGTCATAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:61829070 original size:14 final size:15
Alignment explanation
Indices: 61829019--61829070 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
61829009 GTAAGTATAA
* *
61829019 TAATAATAATAATAA
1 TAATAGTAATAATAG
*
61829034 TAATAATAATAATAG
1 TAATAGTAATAATAG
61829049 TAATAGTAATAA-AG
1 TAATAGTAATAATAG
*
61829063 TCATAGTA
1 TAATAGTA
61829071 TAACATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 9 0.26
15 25 0.74
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (15 bp):
TAATAGTAATAATAG
Found at i:61830701 original size:45 final size:44
Alignment explanation
Indices: 61830576--61830758 Score: 249
Period size: 44 Copynumber: 4.1 Consensus size: 44
61830566 TTGTATATTC
* * *
61830576 GATCTACTTCACGCTAATAAATGAAGACAAGACCTGCTATCTTT
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTT
*
61830620 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTT
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTT
* * * ***
61830664 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTT
1 GATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTATCTTT
* *
61830709 GATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTT
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTT
61830753 GATCTA
1 GATCTA
61830759 TTCCACTGCC
Statistics
Matches: 119, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 82 0.69
45 37 0.31
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (44 bp):
GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTT
Found at i:61830822 original size:44 final size:44
Alignment explanation
Indices: 61830772--61831218 Score: 153
Period size: 44 Copynumber: 10.2 Consensus size: 44
61830762 CACTGCCGAC
*
61830772 CAGGGAGATAGAAT-TACTGGCTTCAATATACTCCACTGTAACCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
* * *** * *
61830816 CAGGGAGGTAAAATCTACCATCTTCGATCTACTCCAC--TACTGT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTAC-CT
* * *
61830859 CTGGGGAGATA-AGATCTGTAAT--CTTCAATCTATTCCACTGCTACC-
1 C-AGGGAGATAGA-ATC--TACTGGCTTCAATCTACTCCACTG-TACCT
* *
61830904 CAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGTAACAT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
* * * **** ** * *
61830948 CAGGGAGGTAAAATCCACCATATTTGATTTGCTCCAC--TACTGCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTAC--CT
* * * *
61830992 TAGGGAGATA-AGATCTGTAAT--CTTCAATCTATTCCACTGCTGCC-
1 CAGGGAGATAGA-ATC--TACTGGCTTCAATCTACTCCACTG-TACCT
*
61831036 CAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGTAACCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
* * * *** * *
61831080 AAGGGAGGTAAAATCTACCATCTTCGATCTGCTCCAC--TACTGCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTAC--CT
* * * * * *
61831124 TAGGGAGATA-AGATCT-GTGAACTTTAATCTATTCCACTTCTACC-
1 CAGGGAGATAGA-ATCTACTG-GCTTCAATCTACTCCAC-TGTACCT
*
61831168 CAGGGAGATAGAAT-TACTGGCTTCAATATACTCCACTGTAACCT
1 CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGT-ACCT
*
61831212 TAGGGAG
1 CAGGGAG
61831219 GTAAAATCCG
Statistics
Matches: 287, Mismatches: 76, Indels: 80
0.65 0.17 0.18
Matches are distributed among these distances:
41 6 0.02
42 10 0.03
43 61 0.21
44 147 0.51
45 52 0.18
46 3 0.01
47 8 0.03
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (44 bp):
CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTACCT
Found at i:61830940 original size:132 final size:132
Alignment explanation
Indices: 61830754--61831226 Score: 763
Period size: 132 Copynumber: 3.6 Consensus size: 132
61830744 GTTTTCTTTG
*
61830754 ATCTATTCCACTGCCGA-CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCA
1 ATCTATTCCACTG-CTACCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCA
* *
61830818 GGGAGGTAAAATCTACCATCTTCGATCTACTCCACTACTG-TCTGGGGAGATAAGATCTGTAATC
65 GGGAGGTAAAATCTACCATCTTCGATCTGCTCCACTACTGCT-TAGGGAGATAAGATCTGTAATC
61830882 TTCA
129 TTCA
* *
61830886 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACATCAG
1 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAG
* * * *
61830951 GGAGGTAAAATCCACCATATTTGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
66 GGAGGTAAAATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
61831016 CA
131 CA
* * *
61831018 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTAAG
1 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAG
61831083 GGAGGTAAAATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGAA-CT
66 GGAGGTAAAATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-AATCT
*
61831147 TTA
130 TCA
* *
61831150 ATCTATTCCACTTCTACCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTTAG
1 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAG
61831215 GGAGGTAAAATC
66 GGAGGTAAAATC
61831227 CGCCATCAAC
Statistics
Matches: 317, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
131 2 0.01
132 312 0.98
133 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAG
GGAGGTAAAATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
CA
Found at i:61831103 original size:88 final size:88
Alignment explanation
Indices: 61830754--61831133 Score: 204
Period size: 88 Copynumber: 4.3 Consensus size: 88
61830744 GTTTTCTTTG
* * *
61830754 ATCTATTCCACTGCCGACCAGGGAGATAGAAT-TACTGGCTTCAATATACTCCACTGTAACCTCA
1 ATCTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAATATACTCCACTGT-ACCTCA
* *
61830818 GGGAGGTAAAATCTACCATCTTCG
65 GGGAGATAAAATCTACCATCTTCA
* * ** * * *
61830842 ATCTACTCCACTACTGTCTGGGGAGATA-AGATCTGTAAT--CTTCAATCTATTCCACTGCTACC
1 ATCTACTCCACTGCTGCCCAGGGAGATAGA-ATC--TACTGGCTTCAATATACTCCACTG-TACC
* ***
61830904 -CAGGGAGATAGAAT-TACTGGCTTCA
62 TCAGGGAGATAAAATCTACCATCTTCA
* * * * * * **** ** * *
61830929 ATGTACTCCACTG-TAACATCAGGGAGGTAAAATCCACCATATTTGATTTGCTCCAC--TACTGC
1 ATCTACTCCACTGCT-GC-CCAGGGAGATAGAATCTACTGGCTTCAATATACTCCACTGTAC--C
* * ***
61830991 TTAGGGAGATAAGATCTGTAATCTTCA
62 TCAGGGAGATAAAATCTACCATCTTCA
* * *
61831018 ATCTATTCCACTGCTGCCCAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGTAACCTAA
1 ATCTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAATATACTCCACTGT-ACCTCA
* *
61831082 GGGAGGTAAAATCTACCATCTTCG
65 GGGAGATAAAATCTACCATCTTCA
* * **
61831106 ATCTGCTCCACTACTGCTTAGGGAGATA
1 ATCTACTCCACTGCTGCCCAGGGAGATA
61831134 AGATCTGTGA
Statistics
Matches: 207, Mismatches: 67, Indels: 36
0.67 0.22 0.12
Matches are distributed among these distances:
85 3 0.01
86 2 0.01
87 33 0.16
88 123 0.59
89 39 0.19
90 4 0.02
91 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (88 bp):
ATCTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAATATACTCCACTGTACCTCAG
GGAGATAAAATCTACCATCTTCA
Found at i:61831321 original size:45 final size:45
Alignment explanation
Indices: 61831270--61831410 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 45
61831260 GTAAGGCTGG
61831270 TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
1 TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
* * * * * * **
61831315 TATCTTTAA-CTTACTCCACT-ACAACT-AAGGGAGGCAAGGCTT--
1 TATCTTTAATC-TGCTTCGCTGTCAA-TGTAGGAAGGCAAGATTTGC
* *
61831357 TAT-TTTCGATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATTTGC
1 TATCTTT-AATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
61831402 TATCTTTAA
1 TATCTTTAA
61831411 CTTGCTCCAC
Statistics
Matches: 68, Mismatches: 19, Indels: 18
0.65 0.18 0.17
Matches are distributed among these distances:
41 3 0.04
42 11 0.16
43 15 0.22
44 16 0.24
45 20 0.29
46 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (45 bp):
TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
Found at i:61831387 original size:87 final size:87
Alignment explanation
Indices: 61831278--61831446 Score: 302
Period size: 87 Copynumber: 1.9 Consensus size: 87
61831268 GGTATCTTTA
61831278 ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGCTATCTTTAACTTACTCCACTACAACTAA
1 ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGCTATCTTTAACTTACTCCACTACAACTAA
61831343 GGGAGGCAAGGCTTTATTTTCG
66 GGGAGGCAAGGCTTTATTTTCG
* * * *
61831365 ATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATTTGCTATCTTTAACTTGCTCCACTGCAACTGA
1 ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGCTATCTTTAACTTACTCCACTACAACTAA
61831430 GGGAGGCAAGGCTTTAT
66 GGGAGGCAAGGCTTTAT
61831447 AATTTCACTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (87 bp):
ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGCTATCTTTAACTTACTCCACTACAACTAA
GGGAGGCAAGGCTTTATTTTCG
Found at i:61835699 original size:13 final size:13
Alignment explanation
Indices: 61835681--61835706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61835671 TGTTCAATTT
61835681 TTTACTAGAAAAC
1 TTTACTAGAAAAC
61835694 TTTACTAGAAAAC
1 TTTACTAGAAAAC
61835707 AAATCTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:61837490 original size:17 final size:17
Alignment explanation
Indices: 61837470--61837507 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
61837460 TTTGATTATA
61837470 AAATATGA-AAAATGTAT
1 AAATATGATAAAA-GTAT
*
61837487 AAATATTATAAAAGTAT
1 AAATATGATAAAAGTAT
61837504 AAAT
1 AAAT
61837508 GTACATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (17 bp):
AAATATGATAAAAGTAT
Found at i:61838824 original size:16 final size:16
Alignment explanation
Indices: 61838799--61838829 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61838789 AAATAAAAAA
61838799 ACATAGATATATATAC
1 ACATAGATATATATAC
*
61838815 ACATATATATATATA
1 ACATAGATATATATA
61838830 AATATAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (16 bp):
ACATAGATATATATAC
Found at i:61838912 original size:27 final size:28
Alignment explanation
Indices: 61838848--61838912 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 28
61838838 AATATTCATT
61838848 AAAAAATATATACATGTACATATATAAAGA
1 AAAAAATATATACA-GTA-ATATATAAAGA
*
61838878 AAATAAATATATACA-T-ATATATAAATTA
1 AAA-AAATATATACAGTAATATATAAA-GA
61838906 AAAAAAT
1 AAAAAAT
61838913 TAATTACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
27 13 0.41
28 4 0.12
29 1 0.03
30 3 0.09
31 11 0.34
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAAAATATATACAGTAATATATAAAGA
Found at i:61838912 original size:31 final size:31
Alignment explanation
Indices: 61838851--61838912 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
61838841 ATTCATTAAA
* *
61838851 AAATATATACATGTACATATATAAAGAAAAT
1 AAATATATACATATACATAAATAAAGAAAAT
*
61838882 AAATATATACATATATATAAATTAAA-AAAAT
1 AAATATATACATATACATAAA-TAAAGAAAAT
61838913 TAATTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (31 bp):
AAATATATACATATACATAAATAAAGAAAAT
Found at i:61840789 original size:43 final size:43
Alignment explanation
Indices: 61840644--61840804 Score: 157
Period size: 43 Copynumber: 3.8 Consensus size: 43
61840634 CTTTCTTGAG
* * * * *
61840644 TCTGCTCCACTGCAAATTCAG-GAAGATAAGA--CCTAATATGA
1 TCTGCTCCACTGCAACTTCAGAG-AGATAAGATTACTACTTTAA
* * * *
61840685 TCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TACTACTTTAA
* * *
61840729 TCCGCTCCACTGCAACTTCAGAGAGATAGGATTACTGCTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATTACTACTTTAA
* *
61840772 TCTGCTCCACTGTAACTTCAGGGAGATAAGATT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATT
61840805 CGCCATATTA
Statistics
Matches: 97, Mismatches: 19, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
41 26 0.27
42 1 0.01
43 37 0.38
44 33 0.34
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGATTACTACTTTAA
Found at i:61841988 original size:25 final size:26
Alignment explanation
Indices: 61841960--61842008 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
61841950 GTGTCTTGAA
61841960 AAGAA-AAAGGTATT-CAAGAACAACG
1 AAGAATAAA-GTATTGCAAGAACAACG
61841985 AAGAATAAAGTATTGCAAGAACAA
1 AAGAATAAAGTATTGCAAGAACAA
61842009 ACAAATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.14
Consensus pattern (26 bp):
AAGAATAAAGTATTGCAAGAACAACG
Found at i:61855098 original size:25 final size:25
Alignment explanation
Indices: 61855064--61855112 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
61855054 GGAATAAAAC
61855064 TGTATTATTATTGT-AATTATATTTT
1 TGTATTATTATTGTCAA-TATATTTT
61855089 TGTATTATTATTGTCAATATATTT
1 TGTATTATTATTGTCAATATATTT
61855113 CTATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (25 bp):
TGTATTATTATTGTCAATATATTTT
Found at i:61855121 original size:25 final size:25
Alignment explanation
Indices: 61855066--61855122 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
61855056 AATAAAACTG
* *
61855066 TATTATTATTGTAATTATATTTTTG
1 TATTATTATTGTAATTATATTTCTA
61855091 TATTATTATTGTCAA-TATATTTCTA
1 TATTATTATTGT-AATTATATTTCTA
*
61855116 TTTTATT
1 TATTATT
61855123 TATTTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (25 bp):
TATTATTATTGTAATTATATTTCTA
Found at i:61855169 original size:3 final size:3
Alignment explanation
Indices: 61855161--61855248 Score: 58
Period size: 3 Copynumber: 30.0 Consensus size: 3
61855151 TCTTTTAACC
* ** *
61855161 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTG TT- TTA AAA TTA TAA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * *
61855208 TTA TTA TCA GTA TTA TAA AT- TTA TTA TGTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
61855249 AGTTTCTTCA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
2 7 0.11
3 53 0.82
4 5 0.08
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:61855270 original size:23 final size:22
Alignment explanation
Indices: 61855239--61855286 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
61855229 TATTATGTAT
*
61855239 TATTATA-TTAAGTTTCTTCATA
1 TATTATATTTAA-TTTCGTCATA
61855261 TATTAATATTTAATTTCGTCATA
1 TATT-ATATTTAATTTCGTCATA
61855284 TAT
1 TAT
61855287 CGTCTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.54
Consensus pattern (22 bp):
TATTATATTTAATTTCGTCATA
Found at i:61855444 original size:49 final size:47
Alignment explanation
Indices: 61855343--61855447 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 47
61855333 TTTTATAATT
*
61855343 CATACGTACATACATTTTTTATATATATTTTATAACTTAAAACTATA
1 CATACATACATACATTTTTTATATATATTTTATAACTTAAAACTATA
* * *
61855390 TATACATACATATATTCTTTT-TATATATTTTATAGTCTTAAAA-TATA
1 CATACATACATACATT-TTTTATATATATTTTATA-ACTTAAAACTATA
61855437 C--ACATACATAC
1 CATACATACATAC
61855448 TTACATATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
45 9 0.18
47 30 0.60
48 11 0.22
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (47 bp):
CATACATACATACATTTTTTATATATATTTTATAACTTAAAACTATA
Found at i:61855540 original size:4 final size:4
Alignment explanation
Indices: 61855531--61855557 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
61855521 TTTTTATAAT
61855531 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
61855558 TTCATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:61857785 original size:6 final size:6
Alignment explanation
Indices: 61857768--61857797 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
61857758 TCTTCACTAT
*
61857768 TCACCA TTACCA TCACCA TCACCA TCACCA
1 TCACCA TCACCA TCACCA TCACCA TCACCA
61857798 ACAAAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (6 bp):
TCACCA
Found at i:61862746 original size:19 final size:18
Alignment explanation
Indices: 61862718--61862753 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
61862708 AAGAAGAAAG
61862718 AAAAGAAAAAATAAAAAA
1 AAAAGAAAAAATAAAAAA
61862736 AAAACGAAAAAATAAAAA
1 AAAA-GAAAAAATAAAAA
61862754 TAATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.86, C:0.03, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAATAAAAAA
Found at i:61862934 original size:21 final size:23
Alignment explanation
Indices: 61862884--61862937 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
61862874 AATCCAGCGT
* *
61862884 AGGCCCAGTGCAGCAGCAGGCTCC
1 AGGCCCAGCGCAGCAGCAAGC-CC
61862908 AGGCCCAGCGCAGCAGCAAG-CC
1 AGGCCCAGCGCAGCAGCAAGCCC
61862930 A-GCCCAGC
1 AGGCCCAGC
61862938 AGGCCCACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.25
22 3 0.11
24 18 0.64
ACGTcount: A:0.24, C:0.41, G:0.31, T:0.04
Consensus pattern (23 bp):
AGGCCCAGCGCAGCAGCAAGCCC
Found at i:61863607 original size:17 final size:18
Alignment explanation
Indices: 61863538--61863814 Score: 146
Period size: 19 Copynumber: 14.8 Consensus size: 18
61863528 CAAAAATTCC
61863538 CGTGTTTT-AAAAAATATT
1 CGTGTTTTCAAAAAA-ATT
* *
61863556 CATGTTTTTTAAAAAAATT
1 CGTG-TTTTCAAAAAAATT
61863575 CCCGTG-TTTCAAAAAATATT
1 --CGTGTTTTCAAAAAA-ATT
61863595 CGTGTTTTCAAAAAAAATT
1 CGTGTTTTC-AAAAAAATT
61863614 C-TCGTGTTTCAAAAAATATT
1 CGT-GT-TTTCAAAAAA-ATT
*
61863634 CATGTTTTCAAAAAAAAATT
1 CGTGTTTTC--AAAAAAATT
**
61863654 CCCGTG-TTTCAAAAATTTT
1 --CGTGTTTTCAAAAAAATT
61863673 CGTGTTTTC--AAAAATT
1 CGTGTTTTCAAAAAAATT
**
61863689 CCCGTG-TTTCAAAAATTTT
1 --CGTGTTTTCAAAAAAATT
* *
61863708 TGTGTTGTCAAAAAAATT
1 CGTGTTTTCAAAAAAATT
* *
61863726 CCCT-TGTTTC-AAAAATTT
1 -CGTGT-TTTCAAAAAAATT
61863744 CCGTGTTTTCAAAAAAAATTT
1 -CGTGTTTTC-AAAAAAA-TT
61863765 CGTG-TTTC-AAAAAATT
1 CGTGTTTTCAAAAAAATT
* **
61863781 C-TCATATTTCAAAAATTTT
1 CGT-GT-TTTCAAAAAAATT
61863800 CGTGTTTTCAAAAAA
1 CGTGTTTTCAAAAAA
61863815 TATTATTGTG
Statistics
Matches: 202, Mismatches: 25, Indels: 64
0.69 0.09 0.22
Matches are distributed among these distances:
15 1 0.00
16 8 0.04
17 17 0.08
18 54 0.27
19 65 0.32
20 38 0.19
21 16 0.08
22 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (18 bp):
CGTGTTTTCAAAAAAATT
Found at i:61863734 original size:37 final size:38
Alignment explanation
Indices: 61863529--61863777 Score: 301
Period size: 39 Copynumber: 6.6 Consensus size: 38
61863519 TTCTTGTTTC
* * * **
61863529 AAAAATTCCCGTGTTTTAAAAAATATTCATGTTTTTTAA
1 AAAAATTCCCGTG-TTTCAAAAATTTTCGTGTTTTCAAA
*
61863568 AAAAATTCCCGTGTTTCAAAAAATATTCGTGTTTTCAAA
1 AAAAATTCCCGTGTTTC-AAAAATTTTCGTGTTTTCAAA
* * *
61863607 AAAAATTCTCGTGTTTCAAAAAATATTCATGTTTTCAAAA
1 AAAAATTCCCGTGTTTC-AAAAATTTTCGTGTTTTC-AAA
61863647 AAAAATTCCCGTGTTTCAAAAATTTTCGTGTTTTC---
1 AAAAATTCCCGTGTTTCAAAAATTTTCGTGTTTTCAAA
* *
61863682 AAAAATTCCCGTGTTTCAAAAATTTTTGTGTTGTC-AA
1 AAAAATTCCCGTGTTTCAAAAATTTTCGTGTTTTCAAA
* *
61863719 AAAAATTCCCTTGTTTCAAAAATTTCCGTGTTTTCAAA
1 AAAAATTCCCGTGTTTCAAAAATTTTCGTGTTTTCAAA
*
61863757 AAAAATT-TCGTGTTTCAAAAA
1 AAAAATTCCCGTGTTTCAAAAA
61863778 ATTCTCATAT
Statistics
Matches: 188, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
35 33 0.18
37 43 0.23
38 12 0.06
39 81 0.43
40 19 0.10
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (38 bp):
AAAAATTCCCGTGTTTCAAAAATTTTCGTGTTTTCAAA
Found at i:61863777 original size:55 final size:55
Alignment explanation
Indices: 61863568--61863849 Score: 249
Period size: 55 Copynumber: 5.1 Consensus size: 55
61863558 TGTTTTTTAA
* *
61863568 AAAAATTCCCGTG-TTTCAAAAAATA-TTCGTGTTTTCAAAAAAAATTCTCGTGTTTC
1 AAAAATTTCCGTGTTTTCAAAAAAAATTTCGTG-TTTC--AAAAAATTCTCGTGTTTC
* * *
61863624 AAAAAATATT-CATGTTTTCAAAAAAAAATTCCCGTGTTTC-AAAAATTTTCGTGTTTTC
1 -AAAAAT-TTCCGTGTTTTC-AAAAAAAATT-TCGTGTTTCAAAAAATTCTCGTG-TTTC
* * * * *
61863682 AAAAATTCCCGTG-TTTC--AAAAATTTTTGTGTTGTCAAAAAAATTCCCTTGTTTC
1 AAAAATTTCCGTGTTTTCAAAAAAAATTTCGTGTT-TC-AAAAAATTCTCGTGTTTC
* *
61863736 AAAAATTTCCGTGTTTTCAAAAAAAATTTCGTGTTTCAAAAAATTCTCATATTTC
1 AAAAATTTCCGTGTTTTCAAAAAAAATTTCGTGTTTCAAAAAATTCTCGTGTTTC
* * * * *
61863791 AAAAATTTTCGTGTTTTCAAAAAATATTATTGTGCTTC--AAAATTCTCGTGTTTT
1 AAAAATTTCCGTGTTTTCAAAAAAAATT-TCGTGTTTCAAAAAATTCTCGTGTTTC
61863845 AAAAA
1 AAAAA
61863850 AAATCATGCT
Statistics
Matches: 185, Mismatches: 26, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
52 5 0.03
53 9 0.05
54 34 0.18
55 55 0.30
56 14 0.08
57 43 0.23
58 9 0.05
59 7 0.04
60 5 0.03
61 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (55 bp):
AAAAATTTCCGTGTTTTCAAAAAAAATTTCGTGTTTCAAAAAATTCTCGTGTTTC
Found at i:61863850 original size:18 final size:18
Alignment explanation
Indices: 61863529--61863850 Score: 133
Period size: 18 Copynumber: 17.3 Consensus size: 18
61863519 TTCTTGTTTC
*
61863529 AAAAATTCCCGTGTTTTA
1 AAAAATTCTCGTGTTTTA
*
61863547 AAAAATAT-TCATGTTTTTTAA
1 AAAAAT-TCTC--GTGTTTT-A
* *
61863568 AAAAATTCCCGTGTTTCA
1 AAAAATTCTCGTGTTTTA
61863586 AAAAATAT-TCGTGTTTTCAAA
1 AAAAAT-TCTCGTGTTTT---A
*
61863607 AAAAATTCTCGTGTTTCA
1 AAAAATTCTCGTGTTTTA
*
61863625 AAAAATAT-TCATGTTTTCAAAA
1 AAAAAT-TCTCGTGTTTT----A
* *
61863647 AAAAATTCCCGTG-TTTC
1 AAAAATTCTCGTGTTTTA
* *
61863664 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTA
* *
61863682 AAAAATTCCCGTG-TTTC
1 AAAAATTCTCGTGTTTTA
* * *
61863699 AAAAATTTTTGTGTTGTCAA
1 AAAAATTCTCGTGTT-T-TA
* * *
61863719 AAAAATTCCCTTGTTTCA
1 AAAAATTCTCGTGTTTTA
*
61863737 AAAATTTC-CGTGTTTTCAAA
1 AAAAATTCTCGTGTTTT---A
*
61863757 AAAAATT-TCGTGTTTCA
1 AAAAATTCTCGTGTTTTA
* * *
61863774 AAAAATTCTCAT-ATTTC
1 AAAAATTCTCGTGTTTTA
*
61863791 AAAAATTTTCGTGTTTTCA
1 AAAAATTCTCGTGTTTT-A
** *
61863810 AAAAATAT-TATTGTGCTT-
1 AAAAAT-TCTCGTGT-TTTA
*
61863828 CAAAATTCTCGTGTTTTA
1 AAAAATTCTCGTGTTTTA
61863846 AAAAA
1 AAAAA
61863851 AATCATGCTT
Statistics
Matches: 225, Mismatches: 48, Indels: 62
0.67 0.14 0.19
Matches are distributed among these distances:
17 54 0.24
18 78 0.35
19 20 0.09
20 36 0.16
21 27 0.12
22 10 0.04
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTA
Found at i:61871196 original size:46 final size:45
Alignment explanation
Indices: 61871143--61871468 Score: 386
Period size: 46 Copynumber: 7.6 Consensus size: 45
61871133 TTTGAGTACT
* *
61871143 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
61871189 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
61871225 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
61871271 TCTGATCAAGTGAAAAAGTGATAAGT-G-A---TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
61871307 TCTGATTAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
61871353 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
61871399 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
61871444 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
61871469 ATCATACGTA
Statistics
Matches: 245, Mismatches: 15, Indels: 43
0.81 0.05 0.14
Matches are distributed among these distances:
36 59 0.24
37 2 0.01
38 2 0.01
40 4 0.02
42 4 0.02
43 12 0.05
44 7 0.03
45 23 0.09
46 132 0.54
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:61871220 original size:36 final size:36
Alignment explanation
Indices: 61871179--61871333 Score: 166
Period size: 36 Copynumber: 4.0 Consensus size: 36
61871169 GGTAGCTTTA
61871179 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
61871215 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
61871260 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * * *
61871297 GATATACTTATCTGATTAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
61871333 G
1 G
61871334 TTAGCCTTAG
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 63 0.62
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 30 0.30
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:61871280 original size:82 final size:82
Alignment explanation
Indices: 61871143--61871468 Score: 433
Period size: 82 Copynumber: 3.9 Consensus size: 82
61871133 TTTGAGTACT
*
61871143 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
61871208 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
61871225 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
61871290 GATAAGTGATATACTTA
66 GATAAGTGCTACACTTA
* * * * *
61871307 TCTGATTAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
61871372 GATAAGTGGTAGCCTTAGCTACACTTA
66 GAT-A-----AG---T-GCTACACTTA
* * * *
61871399 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AG-GGACAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
61871461 GATAAGTG
66 GATAAGTG
61871469 ATCATACGTA
Statistics
Matches: 218, Mismatches: 16, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
79 1 0.00
80 1 0.00
82 142 0.65
83 3 0.01
88 3 0.01
89 8 0.04
90 2 0.01
91 20 0.09
92 38 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:61871461 original size:128 final size:126
Alignment explanation
Indices: 61871143--61871468 Score: 383
Period size: 128 Copynumber: 2.6 Consensus size: 126
61871133 TTTGAGTACT
* * *
61871143 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAG-GGAAAAGT
*
61871208 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
64 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* * * * ** * *
61871271 TCTGATCAAGTGAAAAAGTGATAAGTGATATACTTATCT-GA-TTAAGTGA-CAAAGTGATAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTA-GCTTAGCTACACTTATCTGATC-AAGGGAAAAGT
* * *
61871333 G-TTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACT
64 GATAAG---T-GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACT
61871397 TA
125 TA
* * *
61871399 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AGGGACAAGTGA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGA
61871463 TAAGTG
66 TAAGTG
61871469 ATCATACGTA
Statistics
Matches: 162, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
124 3 0.02
125 8 0.05
126 10 0.06
127 7 0.04
128 123 0.76
129 10 0.06
130 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (126 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGA
TAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:61873701 original size:80 final size:80
Alignment explanation
Indices: 61873528--61874623 Score: 1360
Period size: 80 Copynumber: 13.8 Consensus size: 80
61873518 GTTTTTTTTT
* * * * *
61873528 AAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTTGGGCACACGCCGAGGTATTTC--TT-AAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
61873590 TTCTGTTTTTTC--AA
66 TTCTG-TTTTTCAAAA
* *
61873604 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAAC-CATGCCGATGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
61873668 TTCTGTTTTTCAAAAA
66 TTCTGTTTTTC-AAAA
* *
61873684 AAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTTGGAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
* *
61873748 TTCTATTTTTCCAAA
66 TTCTGTTTTTCAAAA
* * * * *
61873763 AAATCAACTCATATTGTGAAAGGTAAGTTGAGCCTCGGGTCACATACCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTTAAA
*
61873828 TTTTTGTTTTTC-AAA
65 TTTCTGTTTTTCAAAA
*
61873843 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
* *
61873908 TTTTATTTTTC--AA
66 TTCTGTTTTTCAAAA
* * * * *
61873921 AAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGATATTT-TTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTT-AA
*
61873985 ATTTCTATTTTTTTTCAAAA
64 ATTTC---TGTTTTTCAAAA
*
61874005 AAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
61874069 TTCTGTTTTTCAAAA
66 TTCTGTTTTTCAAAA
* * *
61874084 AAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGGACACATACCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
*
61874149 TTCTATTTTTC-AAA
66 TTCTGTTTTTCAAAA
* * * * *
61874163 AAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATACCAAGGTGTTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTTAAA
*
61874228 TTTCTATTTTTCAAAA
65 TTTCTGTTTTTCAAAA
*
61874244 AAATCAACTCATATTGCGAGA---G-G-T-AGCCTCGGACACATACCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
61874303 TTCTGTTTTTC--AA
66 TTCTGTTTTTCAAAA
** * * **
61874316 AAATCAACTCATATTGTTAAAGGTGAGTTGAGCCTCAGGTCACATGTTGAGGTATTT-TTTT-AA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTTAAA
*
61874379 TTTCTATTTTTTTTCAAAA
65 TTTC---TGTTTTTCAAAA
*
61874398 AAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
*
61874462 TTTTGTTTTTCAAAAA
66 TTCTGTTTTTC-AAAA
* *
61874478 AAATCAACTCATATTGCGAAATGG-GAGTTGAGCCTCGGACACATACCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGA-GGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAA
*
61874542 TTTTTGTTTTTTTTTCAAAA
65 TTTCTG----TTTTTCAAAA
* ***
61874562 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGGACACATAATGAGGTATTTCTTTTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTA
61874624 CATTAATCAA
Statistics
Matches: 895, Mismatches: 84, Indels: 74
0.85 0.08 0.07
Matches are distributed among these distances:
72 20 0.02
74 36 0.04
75 21 0.02
76 37 0.04
77 16 0.02
78 60 0.07
79 198 0.22
80 240 0.27
81 92 0.10
82 65 0.07
83 9 0.01
84 95 0.11
85 6 0.01
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (80 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
TTCTGTTTTTCAAAA
Found at i:61874875 original size:30 final size:30
Alignment explanation
Indices: 61874834--61874970 Score: 145
Period size: 30 Copynumber: 4.6 Consensus size: 30
61874824 TTGTGTTAAA
* *
61874834 AAAATTGCATTTTAACCCTTAAACTTTTTC
1 AAAATTACATTTTGACCCTTAAACTTTTTC
* * *
61874864 AAAATTACATTTTAACCCCTAAACTTTCAT-
1 AAAATTACATTTTGACCCTTAAACTTT-TTC
* *
61874894 AAAATTACATTTTGACCCTTGAACTTTCTC
1 AAAATTACATTTTGACCCTTAAACTTTTTC
**
61874924 AAAATTATC-TTTTGACCC-TAATTTTTTTC
1 AAAATTA-CATTTTGACCCTTAAACTTTTTC
*
61874953 AAAATTACGTTTTGACCC
1 AAAATTACATTTTGACCC
61874971 CAAAATTTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.01
29 24 0.26
30 65 0.71
31 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTTAAACTTTTTC
Found at i:61875332 original size:3 final size:3
Alignment explanation
Indices: 61875324--61875371 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
61875314 AGGTTTTGAG
*
61875324 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
61875372 ATGAAAAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:61876236 original size:18 final size:18
Alignment explanation
Indices: 61876206--61876448 Score: 139
Period size: 19 Copynumber: 13.2 Consensus size: 18
61876196 AAAAAAATCG
*
61876206 AAAA-ATTCTTGTTTCAA
1 AAAATATTCGTGTTTCAA
* *
61876223 AAAATATTCATGTTTTTTAA
1 AAAATATTC--GTGTTTCAA
61876243 AAAA-ATTCCAGTGTTTCAA
1 AAAATATT-C-GTGTTTCAA
61876262 AAAATATTCGTGTTTTCAA
1 AAAATATTCGTG-TTTCAA
61876281 AAAA-ATTCCCGTGTTTCAA
1 AAAATATT--CGTGTTTCAA
* *
61876300 AAAATATTCGTTTTTTTAA
1 AAAATATTCG-TGTTTCAA
*
61876319 AAAATTTCTCGTGTTTC-A
1 AAAATAT-TCGTGTTTCAA
* *
61876337 AAAATTTTTGTGTTTTCAA
1 AAAATATTCGTG-TTTCAA
61876356 AAAA-ATTCCCGTGTTTC-A
1 AAAATATT--CGTGTTTCAA
* *
61876374 AAAAT-TTCATTATTTTC-A
1 AAAATATTC-GT-GTTTCAA
*
61876392 AAAATTTTCGTGTTTCAA
1 AAAATATTCGTGTTTCAA
* *
61876410 AAAAT-TCTCTTATTTC-A
1 AAAATAT-TCGTGTTTCAA
*
61876427 AAAAT-TTCCGTGTTTTAA
1 AAAATATT-CGTGTTTCAA
61876445 AAAA
1 AAAA
61876449 ATTATTATTG
Statistics
Matches: 180, Mismatches: 23, Indels: 45
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.01
17 26 0.14
18 62 0.34
19 63 0.35
20 27 0.15
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (18 bp):
AAAATATTCGTGTTTCAA
Found at i:61876283 original size:37 final size:36
Alignment explanation
Indices: 61876206--61876448 Score: 212
Period size: 37 Copynumber: 6.6 Consensus size: 36
61876196 AAAAAAATCG
* * *
61876206 AAAAATT-CTTGTTTCAAAAAATATTCATGTTTTTTAA
1 AAAAATTCCGTGTTTCAAAAAATATTC--GTGTTTTCA
61876243 AAAAATTCCAGTGTTTCAAAAAATATTCGTGTTTTCAA
1 AAAAATTCC-GTGTTTCAAAAAATATTCGTGTTTTC-A
* *
61876281 AAAAATTCCCGTGTTTCAAAAAATATTCGTTTTTTTA
1 AAAAATT-CCGTGTTTCAAAAAATATTCGTGTTTTCA
* *
61876318 AAAAATTTCTCGTGTTTC-AAAAATTTTTGTGTTTTCAA
1 AAAAA-TTC-CGTGTTTCAAAAAATATTCGTGTTTTC-A
* *
61876356 AAAAATTCCCGTGTTTC-AAAAAT-TTCATTATTTTCA
1 AAAAATT-CCGTGTTTCAAAAAATATTC-GTGTTTTCA
* *
61876392 AAAATTTTCGTGTTTCAAAAAAT-TCTC-T-TATTTCA
1 AAAAATTCCGTGTTTCAAAAAATAT-TCGTGT-TTTCA
* *
61876427 AAAATTTCCGTGTTTTAAAAAA
1 AAAAATTCCGTGTTTCAAAAAA
61876449 ATTATTATTG
Statistics
Matches: 178, Mismatches: 16, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
34 1 0.01
35 34 0.19
36 16 0.09
37 58 0.33
38 50 0.28
39 19 0.11
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (36 bp):
AAAAATTCCGTGTTTCAAAAAATATTCGTGTTTTCA
Found at i:61876283 original size:38 final size:37
Alignment explanation
Indices: 61876206--61876448 Score: 225
Period size: 38 Copynumber: 6.6 Consensus size: 37
61876196 AAAAAAATCG
* * *
61876206 AAAAATT-CTTGTTTCAAAAAATATTCATGTTTTTTAA
1 AAAAATTCCGTGTTTCAAAAAATATTCGTG-TTTTCAA
61876243 AAAAATTCCAGTGTTTCAAAAAATATTCGTGTTTTCAA
1 AAAAATTCC-GTGTTTCAAAAAATATTCGTGTTTTCAA
* *
61876281 AAAAATTCCCGTGTTTCAAAAAATATTCGTTTTTTTAA
1 AAAAATT-CCGTGTTTCAAAAAATATTCGTGTTTTCAA
* * *
61876319 AAAATTTCTCGTGTTTC-AAAAATTTTTGTGTTTTCAA
1 AAAAATTC-CGTGTTTCAAAAAATATTCGTGTTTTCAA
* *
61876356 AAAAATTCCCGTGTTTC-AAAAAT-TTCATTATTTTC-A
1 AAAAATT-CCGTGTTTCAAAAAATATTC-GTGTTTTCAA
* *
61876392 AAAATTTTCGTGTTTCAAAAAAT-TCTC-T-TATTTC-A
1 AAAAATTCCGTGTTTCAAAAAATAT-TCGTGT-TTTCAA
* *
61876427 AAAATTTCCGTGTTTTAAAAAA
1 AAAAATTCCGTGTTTCAAAAAA
61876449 ATTATTATTG
Statistics
Matches: 179, Mismatches: 18, Indels: 20
0.82 0.08 0.09
Matches are distributed among these distances:
34 1 0.01
35 34 0.19
36 16 0.09
37 52 0.29
38 55 0.31
39 21 0.12
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (37 bp):
AAAAATTCCGTGTTTCAAAAAATATTCGTGTTTTCAA
Found at i:61876448 original size:35 final size:35
Alignment explanation
Indices: 61876215--61876457 Score: 172
Period size: 35 Copynumber: 6.6 Consensus size: 35
61876205 GAAAAATTCT
* * *
61876215 TGTTTCAAAAAATATTCATGTTTTTTAAAAAAATTCCAG
1 TGTTTCAAAAAAT-TTCA--TTATTTCAAAAATTTCC-G
* *
61876254 TGTTTCAAAAAATATTCGTGT-TTTCAAAAAAATTCCCG
1 TGTTTCAAAAAAT-TTCAT-TATTTC--AAAAATTTCCG
* * *
61876292 TGTTTCAAAAAATATTCGTTTTTTTAAAAAATTTCTCG
1 TGTTTCAAAAAAT-TTC-ATTATTTCAAAAATTTC-CG
* ** *
61876330 TGTTTCAAAAATTTTTGTGT-TTTCAAAAAAATTCCCG
1 TGTTTCAAAAAATTTCAT-TATTTC--AAAAATTTCCG
*
61876367 TGTTTC-AAAAATTTCATTATTTTCAAAAATTTTCG
1 TGTTTCAAAAAATTTCATTA-TTTCAAAAATTTCCG
61876402 TGTTTCAAAAAATTCTC-TTATTTCAAAAATTTCCG
1 TGTTTCAAAAAATT-TCATTATTTCAAAAATTTCCG
* *
61876437 TGTTTTAAAAAAATT-ATTATT
1 TGTTTCAAAAAATTTCATTATT
61876458 GTGCTTCAAA
Statistics
Matches: 170, Mismatches: 20, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
34 6 0.04
35 42 0.25
36 22 0.13
37 29 0.17
38 42 0.25
39 29 0.17
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (35 bp):
TGTTTCAAAAAATTTCATTATTTCAAAAATTTCCG
Found at i:61876988 original size:26 final size:26
Alignment explanation
Indices: 61876925--61877019 Score: 84
Period size: 26 Copynumber: 3.5 Consensus size: 26
61876915 AAAAAAATCT
* * *
61876925 AAAATAAATAATAAATATAAAACAGTTT
1 AAAATAAATAAT--ATATGAAACAATTC
* *
61876953 AAGATAAAATAATATA-GAAAGTAATTC
1 AAAAT-AAATAATATATGAAA-CAATTC
*
61876980 AAAATAAATAATATATGAAACAATTT
1 AAAATAAATAATATATGAAACAATTC
*
61877006 AAAATAGATAATAT
1 AAAATAAATAATAT
61877020 CAAACAGCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
26 30 0.55
27 14 0.25
28 4 0.07
29 7 0.13
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (26 bp):
AAAATAAATAATATATGAAACAATTC
Found at i:61882393 original size:23 final size:23
Alignment explanation
Indices: 61882362--61882412 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
61882352 TTAATAAGAT
61882362 TATTATTAAATATAA-T-TTTTTAA
1 TATTATT-AATATAAGTATTTTT-A
*
61882385 TATTTTTAATATAAGTATTTTTA
1 TATTATTAATATAAGTATTTTTA
61882408 TATTA
1 TATTA
61882413 AATCATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTATTAATATAAGTATTTTTA
Found at i:61884306 original size:29 final size:29
Alignment explanation
Indices: 61884269--61884373 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
61884259 CGTTTTCTTT
* *
61884269 AATTATATTTTAACCCCTCAACTTTTTAA
1 AATTGTATTTTAACCCCTAAACTTTTTAA
* *
61884298 AATTGTA-TTTGACCCCTAAAATTTTTAAA
1 AATTGTATTTTAACCCCTAAACTTTTT-AA
* * * *
61884327 AATTGCATTTTGACCCTTAAACTTTTTTA
1 AATTGTATTTTAACCCCTAAACTTTTTAA
*
61884356 AATTTTATTTTAACCCCT
1 AATTGTATTTTAACCCCT
61884374 GGACTTTCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
28 16 0.26
29 29 0.47
30 17 0.27
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (29 bp):
AATTGTATTTTAACCCCTAAACTTTTTAA
Found at i:61884660 original size:20 final size:20
Alignment explanation
Indices: 61884637--61884696 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 20
61884627 AAAAACTTGC
61884637 GAAAAAGAGAAAAAGAAGAG
1 GAAAAAGAGAAAAAGAAGAG
*
61884657 GAAAAAAGAGAGAAAG-AGAG
1 G-AAAAAGAGAAAAAGAAGAG
* *
61884677 GAGAAAG-G-AGAAGAAGAG
1 GAAAAAGAGAAAAAGAAGAG
61884695 GA
1 GA
61884697 GAGGGTCCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 5 0.15
20 6 0.18
21 13 0.38
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
GAAAAAGAGAAAAAGAAGAG
Found at i:61884662 original size:21 final size:21
Alignment explanation
Indices: 61884638--61884693 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
61884628 AAAACTTGCG
61884638 AAAAAGAGAAAAAGAAGAGGA
1 AAAAAGAGAAAAAGAAGAGGA
*
61884659 AAAAAGAGAGAAAG-AGAGGA
1 AAAAAGAGAAAAAGAAGAGGA
* * *
61884679 GAAAGGAGAAGAAGA
1 AAAAAGAGAAAAAGA
61884694 GGAGAGGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAAAAGAAGAGGA
Found at i:61884687 original size:18 final size:19
Alignment explanation
Indices: 61884649--61884698 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
61884639 AAAAGAGAAA
*
61884649 AAGAAGAGGAAAAAAGAGAG
1 AAGAAGAGG-AGAAAGAGAG
61884669 AA-AGAGAGGAGAAAG-GAG
1 AAGA-AGAGGAGAAAGAGAG
61884687 AAGAAGAGGAGA
1 AAGAAGAGGAGA
61884699 GGGTCCTACG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 13 0.48
19 7 0.26
20 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (19 bp):
AAGAAGAGGAGAAAGAGAG
Found at i:61884920 original size:19 final size:19
Alignment explanation
Indices: 61884893--61884934 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 19
61884883 AGGAGCAGCC
61884893 CAAAAAAAAGGAAAAAGAAAG
1 CAAAAAAAA--AAAAAGAAAG
61884914 CAAAAAAAAAAAAAGAAAG
1 CAAAAAAAAAAAAAGAAAG
61884933 CA
1 CA
61884935 GGCTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAAGAAAG
Found at i:61885091 original size:11 final size:11
Alignment explanation
Indices: 61885073--61885117 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
61885063 CAGTAGAGAA
61885073 AAAAGAAAAAG
1 AAAAGAAAAAG
*
61885084 AGAAGAAAAAAG
1 AAAAG-AAAAAG
61885096 AAAAGAAAAAG
1 AAAAGAAAAAG
*
61885107 AAAAAAAAAAG
1 AAAAGAAAAAG
61885118 GGTTTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:61885092 original size:18 final size:19
Alignment explanation
Indices: 61885069--61885116 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
61885059 GGCCCAGTAG
*
61885069 AGAAAAAAGAAAAAG-AGA
1 AGAAAAAAGAAAAAGAAAA
61885087 AGAAAAAAG-AAAAGAAAA
1 AGAAAAAAGAAAAAGAAAA
61885105 AGAAAAAA-AAAA
1 AGAAAAAAGAAAA
61885117 GGGTTTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AGAAAAAAGAAAAAGAAAA
Found at i:61885101 original size:23 final size:22
Alignment explanation
Indices: 61885073--61885117 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
61885063 CAGTAGAGAA
*
61885073 AAAAGAAAAAGAGAAGAAAAAAG
1 AAAAGAAAAAGA-AAAAAAAAAG
61885096 AAAAGAAAAAGAAAAAAAAAAG
1 AAAAGAAAAAGAAAAAAAAAAG
61885118 GGTTTCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAGAAAAAAAAAAG
Found at i:61885295 original size:21 final size:22
Alignment explanation
Indices: 61885258--61885307 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
61885248 ATTTTTTTGT
61885258 ATTTATATTTTTAATTTAATTTA
1 ATTTA-ATTTTTAATTTAATTTA
* *
61885281 ATTTAATTTTT-ATTTTATTTT
1 ATTTAATTTTTAATTTAATTTA
61885302 ATTTAA
1 ATTTAA
61885308 ATAATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.56
22 6 0.24
23 5 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTTAATTTTTAATTTAATTTA
Found at i:61885527 original size:18 final size:18
Alignment explanation
Indices: 61885504--61885538 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61885494 AAATTTTTTC
61885504 TCGTGTTTCAAAAAATAT
1 TCGTGTTTCAAAAAATAT
*
61885522 TCGTGTTTTAAAAAATA
1 TCGTGTTTCAAAAAATA
61885539 AGGCAACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (18 bp):
TCGTGTTTCAAAAAATAT
Found at i:61885667 original size:18 final size:18
Alignment explanation
Indices: 61885644--61885886 Score: 261
Period size: 17 Copynumber: 13.9 Consensus size: 18
61885634 AAAAGAATCG
*
61885644 AAAATTTTCATGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
61885662 AAAATTCTCGTGTTTT-A
1 AAAATTTTCGTGTTTTCA
*
61885679 AAAATTTCCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
61885697 AAAATTTTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
61885714 AAAATTTTTGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
* * *
61885732 ACAATTCTCGTGTTTTAAA
1 AAAATTTTCGTGTTTT-CA
* *
61885751 AAAATTTTGGTGTTTTGA
1 AAAATTTTCGTGTTTTCA
*
61885769 CAAAATTCTCGTG-TTTCA
1 -AAAATTTTCGTGTTTTCA
*
61885787 AAAATTATCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
61885804 AAAA-TTTCGTGTTTTTA
1 AAAATTTTCGTGTTTTCA
*
61885821 AAAA-TAT-GTGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
61885837 AAAATTCTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
61885855 AAAATTCTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
61885872 AAAACTTTCGT-TTTT
1 AAAATTTTCGTGTTTT
61885887 TTTTTATTTT
Statistics
Matches: 192, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
16 18 0.09
17 80 0.42
18 70 0.36
19 24 0.12
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:61885693 original size:35 final size:35
Alignment explanation
Indices: 61885644--61885875 Score: 276
Period size: 35 Copynumber: 6.6 Consensus size: 35
61885634 AAAAGAATCG
*
61885644 AAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
* * *
61885679 AAAATTTCCGTGTTTTCAAAAATTTTCGTGTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
* *
61885714 AAAATTTTTGTGTTTTCAACAATTCTCGTGTTTTAAA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT--A
* * *
61885751 AAAATTTTGGTGTTTTGACAAAATTCTCGTGTTTCA
1 AAAATTTTCGTGTTTTCA-AAAATTCTCGTGTTTTA
*
61885787 AAAATTATCGTG-TTTCAAAAATT-TCGTGTTTTTA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTG-TTTTA
*
61885821 AAAA-TAT-GTGTTTTCAAAAATTCTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT-A
*
61885855 AAAATTCTCGTG-TTTCAAAAA
1 AAAATTTTCGTGTTTTCAAAAA
61885876 CTTTCGTTTT
Statistics
Matches: 170, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.02
33 23 0.14
34 24 0.14
35 75 0.44
36 14 0.08
37 17 0.10
38 14 0.08
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
Found at i:61888881 original size:23 final size:23
Alignment explanation
Indices: 61888855--61888900 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
61888845 TGAGCAAGGT
61888855 AAACAAATTATTCAAAATTTCAA
1 AAACAAATTATTCAAAATTTCAA
*
61888878 AAACAAGTTATTCAAAATTTCAA
1 AAACAAATTATTCAAAATTTCAA
61888901 CTCGAGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
AAACAAATTATTCAAAATTTCAA
Found at i:61891678 original size:20 final size:20
Alignment explanation
Indices: 61891653--61891694 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
61891643 GGAGTCGATT
61891653 ACGCACGAGGAAGAATTAGC
1 ACGCACGAGGAAGAATTAGC
61891673 ACGCACGAGGAAGAATTAGC
1 ACGCACGAGGAAGAATTAGC
61891693 AC
1 AC
61891695 CCTCGATACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.29, T:0.10
Consensus pattern (20 bp):
ACGCACGAGGAAGAATTAGC
Found at i:61895976 original size:20 final size:20
Alignment explanation
Indices: 61895951--61895990 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
61895941 GGCATTTATA
61895951 CAATTC-ACATATACAACATT
1 CAATTCAACATATA-AACATT
61895971 CAATTCAAACATATAAACAT
1 CAATTC-AACATATAAACAT
61895991 ACACAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
CAATTCAACATATAAACATT
Done.