Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 36 of 344
Found at i:12152176 original size:32 final size:32
Alignment explanation
Indices: 12152139--12152215 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
12152129 ATGCATGTGT
* * **
12152139 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
12152171 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
12152203 GTAACTTTTCATA
1 GTAACTTTTCATA
12152216 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:12153304 original size:20 final size:21
Alignment explanation
Indices: 12153266--12153346 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 21
12153256 ATTAATTTTT
**
12153266 TAAAATTTTTAAATTTTAAAA
1 TAAAATTTTTAAAAATTAAAA
12153287 TAAAA-TTTTAAAAATTAAAAA
1 TAAAATTTTTAAAAATT-AAAA
12153308 TCACAAAATTATTTAAAAA-TATAAA
1 T---AAAATT-TTTAAAAATTA-AAA
*
12153333 -AAAATTGTTAAAAA
1 TAAAATTTTTAAAAA
12153347 ATATTTATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
20 16 0.32
21 16 0.32
24 5 0.10
25 5 0.10
26 8 0.16
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (21 bp):
TAAAATTTTTAAAAATTAAAA
Found at i:12153307 original size:21 final size:21
Alignment explanation
Indices: 12153266--12153308 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12153256 ATTAATTTTT
* * *
12153266 TAAAATTTTTAAATTTTAAAA
1 TAAAATTTTAAAAATTAAAAA
12153287 TAAAATTTTAAAAATTAAAAA
1 TAAAATTTTAAAAATTAAAAA
12153308 T
1 T
12153309 CACAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAATTTTAAAAATTAAAAA
Found at i:12153457 original size:21 final size:21
Alignment explanation
Indices: 12153433--12153474 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12153423 TTGAAATGAT
12153433 TTTATAAAAAT-ATAAATTAAA
1 TTTA-AAAAATAATAAATTAAA
* *
12153454 TTTAAAGAATAATATATTAAA
1 TTTAAAAAATAATAAATTAAA
12153475 ATATACTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAAAAAATAATAAATTAAA
Found at i:12157115 original size:17 final size:17
Alignment explanation
Indices: 12157077--12157114 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12157067 TATATAGTGC
*
12157077 AAAAATATAAAACATAT
1 AAAAATATAAAAAATAT
12157094 AAAAATATAAAAAA-AT
1 AAAAATATAAAAAATAT
12157110 AAAAA
1 AAAAA
12157115 AAAATCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAATATAAAAAATAT
Found at i:12157116 original size:8 final size:8
Alignment explanation
Indices: 12157077--12157114 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
12157067 TATATAGTGC
12157077 AAAAATAT
1 AAAAATAT
12157085 AAAACATAT
1 AAAA-ATAT
12157094 AAAAATAT
1 AAAAATAT
*
12157102 AAAAAAAT
1 AAAAATAT
12157110 AAAAA
1 AAAAA
12157115 AAAATCAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAATAT
Found at i:12157249 original size:16 final size:16
Alignment explanation
Indices: 12157230--12157265 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12157220 CCTTTTCCCC
12157230 CTCTCCTTCCTCCCTT
1 CTCTCCTTCCTCCCTT
* *
12157246 CTCTCTTTTCTCCCTT
1 CTCTCCTTCCTCCCTT
12157262 CTCT
1 CTCT
12157266 TTCTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (16 bp):
CTCTCCTTCCTCCCTT
Found at i:12157808 original size:14 final size:14
Alignment explanation
Indices: 12157789--12157819 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12157779 TTATCCACTT
12157789 TTATATTATTATTA
1 TTATATTATTATTA
*
12157803 TTATATTATTTTTA
1 TTATATTATTATTA
12157817 TTA
1 TTA
12157820 CTATGGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:12157815 original size:25 final size:25
Alignment explanation
Indices: 12157747--12157817 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
12157737 ACCTATTACT
* *
12157747 TTATTCTTATTTTATTTTTATATCA
1 TTATTATTATATTATTTTTATATCA
* * * *
12157772 TTA-TATTTTATCCACTTTTATATTA
1 TTATTATTATAT-TATTTTTATATCA
12157797 TTATTATTATATTATTTTTAT
1 TTATTATTATATTATTTTTAT
12157818 TACTATGGTT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
24 5 0.14
25 23 0.66
26 7 0.20
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (25 bp):
TTATTATTATATTATTTTTATATCA
Found at i:12170987 original size:70 final size:70
Alignment explanation
Indices: 12170856--12171029 Score: 237
Period size: 72 Copynumber: 2.5 Consensus size: 70
12170846 TTAAGCTTTT
* * *
12170856 AATTTTTGTTTTTCAAAATCAACTCATATTG-TAGAGTGAGTTGAGCCTCAGGACACGCTGA-GT
1 AATTTTTG-TTTTAAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAGGACACGCTGAGGT
12170919 AATTTC
65 AATTTC
12170925 -ATTTTTGTTGTTAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTTTGTT-TTAAAAATCAACTCATATTGCGAG-AATGAGTTGAGCCTCAGGACACGCTGAGG
12170989 TAATTTC
64 TAATTTC
* * *
12170996 AATTTCTGTTTTCAAAATTCAACTTATATTGCGA
1 AATTTTTGTTTT-AAAAATCAACTCATATTGCGA
12171030 TGATGACTCA
Statistics
Matches: 93, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
67 2 0.02
68 26 0.28
69 2 0.02
70 26 0.28
71 10 0.11
72 27 0.29
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (70 bp):
AATTTTTGTTTTAAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAGGACACGCTGAGGTA
ATTTC
Found at i:12171399 original size:67 final size:70
Alignment explanation
Indices: 12171266--12171506 Score: 297
Period size: 67 Copynumber: 3.5 Consensus size: 70
12171256 TTTGAAAGAA
*
12171266 TCAACT-ATATTGCGAGAAATGAGTTGAGCCTCA-AGACATG-GGTAATTTCAA-TTCTGTTTTC
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACATGAGGTAATTTCAATTTCTGTTTTC
12171327 AAAAT
66 AAAAT
*
12171332 TCAACTCATATTGCGAG-AATGAGTTGAG-CTCAGA-ACTTGAAGGT-A-TTCAATTTCTGCTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACATG-AGGTAATTTCAATTTCTG-TTT
12171392 TCAAAAT
64 TCAAAAT
* *
12171399 TCAA-TCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-GACAC-ATGAGGTAATTTCAATTTCTGTTT
*
12171463 TCAAAAAAA
64 TC--AAAAT
12171472 TCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCAG
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAG
12171507 TTCATATGTT
Statistics
Matches: 154, Mismatches: 4, Indels: 27
0.83 0.02 0.15
Matches are distributed among these distances:
65 13 0.08
66 36 0.23
67 38 0.25
68 4 0.03
69 2 0.01
70 6 0.04
71 7 0.05
72 11 0.07
73 12 0.08
74 25 0.16
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (70 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACATGAGGTAATTTCAATTTCTGTTTTC
AAAAT
Found at i:12172867 original size:28 final size:31
Alignment explanation
Indices: 12172800--12172868 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 31
12172790 AGGTAACTGA
12172800 AAAGAAAAAAGAAGAGAAGAAACAGAAAGAT
1 AAAGAAAAAAGAAGAGAAGAAACAGAAAGAT
* * * *
12172831 GAAGGAAAAAG-AGAGAA-AAAGATAAA-AT
1 AAAGAAAAAAGAAGAGAAGAAACAGAAAGAT
12172859 AAAGAAAAAA
1 AAAGAAAAAA
12172869 AATAAAAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 10 0.31
29 7 0.22
30 6 0.19
31 9 0.28
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.04
Consensus pattern (31 bp):
AAAGAAAAAAGAAGAGAAGAAACAGAAAGAT
Found at i:12173490 original size:17 final size:17
Alignment explanation
Indices: 12173468--12173506 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12173458 TCGTTTTTAA
12173468 AAAATTT-TCATGTCTTC
1 AAAATTTCTCATGT-TTC
*
12173485 AAAATTTCTCGTGTTTC
1 AAAATTTCTCATGTTTC
12173502 AAAAT
1 AAAAT
12173507 AATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (17 bp):
AAAATTTCTCATGTTTC
Found at i:12173605 original size:17 final size:17
Alignment explanation
Indices: 12173553--12173608 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
12173543 TTCGTGTTTC
*
12173553 TTTCTAAAAAAAATCGTG
1 TTTC-AAAAAAATTCGTG
12173571 TTTTC--AAAAATTCCCGTG
1 -TTTCAAAAAAATT--CGTG
12173589 TTTCAAAAAAATTCGTG
1 TTTCAAAAAAATTCGTG
12173606 TTT
1 TTT
12173609 TCGTGTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 11 0.34
18 4 0.12
19 11 0.34
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (17 bp):
TTTCAAAAAAATTCGTG
Found at i:12173610 original size:18 final size:18
Alignment explanation
Indices: 12173553--12173610 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
12173543 TTCGTGTTTC
*
12173553 TTTCTAAAAAAAATCGTGT
1 TTTC-AAAAAAATTCGTGT
12173572 TTTC--AAAAATTCCCGTG-
1 TTTCAAAAAAATT--CGTGT
12173589 TTTCAAAAAAATTCGTGT
1 TTTCAAAAAAATTCGTGT
12173607 TTTC
1 TTTC
12173611 GTGTTTTCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
16 6 0.18
17 8 0.24
18 8 0.24
19 11 0.33
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (18 bp):
TTTCAAAAAAATTCGTGT
Found at i:12173631 original size:27 final size:25
Alignment explanation
Indices: 12173585--12173635 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
12173575 CAAAAATTCC
12173585 CGTGTTTCAAAAAAATTCGTGTTTT
1 CGTGTTTCAAAAAAATTCGTGTTTT
* *
12173610 CGTGTTTTCGAAAACATCTCGTGTTT
1 CGTG-TTTCAAAAAAAT-TCGTGTTT
12173636 CAAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 10 0.45
27 8 0.36
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (25 bp):
CGTGTTTCAAAAAAATTCGTGTTTT
Found at i:12173739 original size:18 final size:18
Alignment explanation
Indices: 12173718--12174145 Score: 198
Period size: 17 Copynumber: 25.0 Consensus size: 18
12173708 AAATTTTGTG
12173718 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
12173736 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
12173754 -TCT-GTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
12173770 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
12173787 TTTTCGTGTTTTAAAAAAA
1 TTTTCGTGTTTT-CAAAAA
* * *
12173806 ATTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
12173824 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
12173841 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
12173859 -CTCCG-GTATTTC-AAAG
1 TTTTCGTGT-TTTCAAAAA
* *
12173875 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * **
12173893 TTCTCGCGTTTAAAAAAAA
1 TTTTCGTGTTT-TCAAAAA
**
12173912 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
12173930 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
12173944 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
12173959 ---TCGTG-TTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
12173974 ATGTCGTGTTTT--AAAA
1 TTTTCGTGTTTTCAAAAA
*
12173990 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
12174007 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
12174024 --TTCCTGTGTTTCAAAAAA
1 TTTTCGTGT-TTTC-AAAAA
* * *
12174042 ATGTCGTGTTTTAAAAAAA
1 TTTTCGTGTTTT-CAAAAA
*
12174061 ATTT-GT-TTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
12174078 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
12174095 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
12174111 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
12174129 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
12174146 AAACTTTTCG
Statistics
Matches: 313, Mismatches: 59, Indels: 77
0.70 0.13 0.17
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 6 0.02
15 15 0.05
16 41 0.13
17 101 0.32
18 100 0.32
19 38 0.12
20 5 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:12173842 original size:54 final size:52
Alignment explanation
Indices: 12173718--12174145 Score: 216
Period size: 54 Copynumber: 8.3 Consensus size: 52
12173708 AAATTTTGTG
*
12173718 TTTTCGTGTTTTCAAAAATTTTCGTGTTTT-CAAAAATCTGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTAAAAAAATCTGTGTTTTCAAAAA
* * * *
12173770 TTCTGGCGTTTCAAAAATTTTCGTGTTTTAAAAAAAAT-TACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTT-AAAAAAATCT--GTGTTTTCAAAAA
* * * * * *
12173824 TTTTCGTGTTTCACAAATTCTCGTGTTTTCAAAAACTCCG-GTATTTC-AAAG
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAAAATCTGTGT-TTTCAAAAA
* * * * *
12173875 TTTCCATGTTTTCAAAAATTCTCGCGTTTAAAAAAAAAAT-TCGTG-TTTCAAAATA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTT--TAAAAAAATCT-GTGTTTTCAAAA-A
* ** **
12173930 TTCTCGCATTTC---AATTTT--TGTTTT--TTAAATC-GTG-TTTCAAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAAAATCTGTGTTTTC-AAAAA
* * * ** **
12173974 ATGTCGTGTTT-TAAAATTTTCGTGTTTCT-AAAATTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTT-TAAAAAAATCTGTGTTTTCAAAAA
* * * *
12174024 -TTCCTGTGTTTCAAAAAAATGTCGTGTTTTAAAAAAAATTTGT-TTTTCTAAAAA
1 TTTTC-GTGTTTC-AAAAATTTTCGTGTTTT-AAAAAAATCTGTGTTTTC-AAAAA
* * *
12174078 TTTTCGTGTTTCTAAAATTTTCGTG-TTT-ACAAATTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAAAATCT-GTGTTTTCAAAAA
* *
12174129 TTCTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
12174146 AAACTTTTCG
Statistics
Matches: 279, Mismatches: 63, Indels: 69
0.68 0.15 0.17
Matches are distributed among these distances:
44 15 0.05
45 8 0.03
46 6 0.02
48 5 0.02
49 7 0.03
50 20 0.07
51 60 0.22
52 57 0.20
53 32 0.11
54 62 0.22
55 7 0.03
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (52 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAAAATCTGTGTTTTCAAAAA
Found at i:12173885 original size:88 final size:88
Alignment explanation
Indices: 12173722--12173892 Score: 220
Period size: 88 Copynumber: 1.9 Consensus size: 88
12173712 TTTGTGTTTT
* * *
12173722 CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAATTCTGGCGTTTCAAAAA
1 CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAACTCCGGCATTTCAAAAA
* *
12173787 TTTTCGTGTTTTAAAAAAAATTA
66 TTTCCATGTTTTAAAAAAAATTA
* * *
12173810 CGTGTTTTCACAAATTTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAACTCCGGTATTTC-AA
1 CGTGTTTTCAAAAATTTTCGTGTTTTCA-AAAATCT-GTGTTTTCAAAAACTCCGGCATTTCAAA
* *
12173873 AGTTTCCATGTTTTCAAAAA
64 AATTTCCATGTTTTAAAAAA
12173893 TTCTCGCGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
87 5 0.07
88 45 0.63
89 21 0.30
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (88 bp):
CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAACTCCGGCATTTCAAAAA
TTTCCATGTTTTAAAAAAAATTA
Found at i:12173989 original size:16 final size:16
Alignment explanation
Indices: 12173970--12174145 Score: 124
Period size: 18 Copynumber: 10.3 Consensus size: 16
12173960 CGTGTTTCAA
*
12173970 AAAAATGTCGTGTTTT
1 AAAAATTTCGTGTTTT
*
12173986 AAAATTTTCGTGTTTCT
1 AAAAATTTCGTGTTT-T
*
12174003 -AAAATTTCCCTGTTTT
1 AAAAATTT-CGTGTTTT
* *
12174019 AAAAATTCCTGTGTTTCAA
1 AAAAATTTC-GTGTTT--T
*
12174038 AAAAATGTCGTGTTTT
1 AAAAATTTCGTGTTTT
*
12174054 AAAAAAAATTT-GTTTTTCT
1 ---AAAAATTTCGTGTTT-T
12174073 AAAAATTTTCGTGTTTCT
1 AAAAA-TTTCGTGTTT-T
*
12174091 AAAATTTTCGTG-TTT
1 AAAAATTTCGTGTTTT
*
12174106 ACAAATTCTCGTGTTTT
1 AAAAATT-TCGTGTTTT
12174123 CAAAAATTCTCGTGTTTT
1 -AAAAATT-TCGTGTTTT
12174141 AAAAA
1 AAAAA
12174146 AAACTTTTCG
Statistics
Matches: 128, Mismatches: 17, Indels: 29
0.74 0.10 0.17
Matches are distributed among these distances:
15 6 0.05
16 33 0.26
17 36 0.28
18 38 0.30
19 15 0.12
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (16 bp):
AAAAATTTCGTGTTTT
Found at i:12174043 original size:19 final size:18
Alignment explanation
Indices: 12174019--12174063 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12174009 TCCCTGTTTT
*
12174019 AAAAATTCCTGTGTTTCAA
1 AAAAATTCCTGT-TTTAAA
*
12174038 AAAAATGTCGTGTTTTAAA
1 AAAAAT-TCCTGTTTTAAA
12174057 AAAAATT
1 AAAAATT
12174064 TGTTTTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAATTCCTGTTTTAAA
Found at i:12174156 original size:21 final size:20
Alignment explanation
Indices: 12174124--12174171 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
12174114 TCGTGTTTTC
*
12174124 AAAAA-TTCTCGTGTTTTAAA
1 AAAAACTTCTCGT-TTTAAAA
*
12174144 AAAAACTTTTCGTTTTAAAA
1 AAAAACTTCTCGTTTTAAAA
12174164 AAGAAACT
1 AA-AAACT
12174172 GCGCTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (20 bp):
AAAAACTTCTCGTTTTAAAA
Found at i:12190573 original size:38 final size:38
Alignment explanation
Indices: 12190523--12190595 Score: 89
Period size: 40 Copynumber: 1.9 Consensus size: 38
12190513 AGCAATTTAA
*
12190523 TTTTTTTTATTCT-TT-TGACTT-TCCCTTTTTTTTTCT
1 TTTTTTTTATTCTCTTCTG-CTTCTCCCTTTGTTTTTCT
12190559 TTTTTTTTCCATTCTCTTCTGCTTCTCCCTTTGTTTT
1 TTTTTTTT--ATTCTCTTCTGCTTCTCCCTTTGTTTT
12190596 CCTCCCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
36 8 0.26
38 5 0.16
39 5 0.16
40 13 0.42
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (38 bp):
TTTTTTTTATTCTCTTCTGCTTCTCCCTTTGTTTTTCT
Found at i:12192078 original size:23 final size:23
Alignment explanation
Indices: 12192042--12192100 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 23
12192032 GGGTTTAGGG
*
12192042 TTTTAGATAGTTCAGCTCTAGCCT
1 TTTTAAATA-TTCAGCTCTAGCCT
12192066 TTTTAAATATTCAGCTCTAGCCT
1 TTTTAAATATTCAGCTCTAGCCT
12192089 TTTTAAATATTC
1 TTTTAAATATTC
12192101 GCGGAGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 26 0.76
24 8 0.24
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (23 bp):
TTTTAAATATTCAGCTCTAGCCT
Found at i:12203495 original size:22 final size:21
Alignment explanation
Indices: 12203455--12203495 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12203445 ATATTATAAT
*
12203455 ATTAAAATCAAATCAAATTGC
1 ATTAAAATCAAACCAAATTGC
*
12203476 ATTAAAATCCAAACCCAATT
1 ATTAAAAT-CAAACCAAATT
12203496 CATATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (21 bp):
ATTAAAATCAAACCAAATTGC
Found at i:12203765 original size:4 final size:4
Alignment explanation
Indices: 12203756--12203785 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
12203746 CTAAGCGTAT
12203756 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
12203786 GTTTAAGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:12204972 original size:3 final size:3
Alignment explanation
Indices: 12204966--12205018 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
12204956 CATTATTAAC
12204966 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12205014 ATT AT
1 ATT AT
12205019 GTTACAGTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12210750 original size:28 final size:28
Alignment explanation
Indices: 12210710--12210768 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
12210700 TGTATGAAAT
12210710 ATAAATTTTAAATATTTTTAAGTAATAA
1 ATAAATTTTAAATATTTTTAAGTAATAA
12210738 ATAAATTTTAAATATTTTTAAGTAATAA
1 ATAAATTTTAAATATTTTTAAGTAATAA
12210766 ATA
1 ATA
12210769 TTAATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
ATAAATTTTAAATATTTTTAAGTAATAA
Found at i:12210764 original size:24 final size:26
Alignment explanation
Indices: 12210710--12210778 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 26
12210700 TGTATGAAAT
12210710 ATAAATTTTAAATATTTTTAAGTAATAA
1 ATAAATTTTAAATATTTTTAAG--ATAA
12210738 ATAAATTTTAAATATTTTTAAG-T-A
1 ATAAATTTTAAATATTTTTAAGATAA
* *
12210762 ATAAATATTAATTATTT
1 ATAAATTTTAAATATTT
12210779 ATAAAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.41
25 1 0.03
28 22 0.56
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
ATAAATTTTAAATATTTTTAAGATAA
Found at i:12212482 original size:57 final size:57
Alignment explanation
Indices: 12212421--12212547 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
12212411 TTTTTTCAGG
* * **
12212421 TCATTTTCATTTTGGAGAAAATCACATTCATTTTCAAATGA-TTCTATTTCTCCATTT
1 TCATTTTCATTTTGGAGAAAACCACAATCATTTGAAAATGATTTC-ATTTCTCCATTT
* * *
12212478 TCATTTTTATTTTGGAGAAAACCATAATCATTTGAAAATGATTTCATTTCTCTATTT
1 TCATTTTCATTTTGGAGAAAACCACAATCATTTGAAAATGATTTCATTTCTCCATTT
12212535 TCATTTTCATTTT
1 TCATTTTCATTTT
12212548 TATTTTCGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 58 0.95
58 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (57 bp):
TCATTTTCATTTTGGAGAAAACCACAATCATTTGAAAATGATTTCATTTCTCCATTT
Found at i:12212490 original size:63 final size:57
Alignment explanation
Indices: 12212422--12212612 Score: 168
Period size: 57 Copynumber: 3.2 Consensus size: 57
12212412 TTTTTCAGGT
* * *
12212422 CATTTTCATTTTGGAGAAAATCACATTCATTTTCAAATGATTCTATTTCTCCATTTTCA
1 CATTTT-ATTTTGGAGAAAATCATAATCATTTCCAAATGATT-TATTTCTCCATTTTCA
* * ** *
12212481 -TTTTTATTTTGGAGAAAACCATAATCATTTGAAAATGATTTCATTTCTCTATTTTCA
1 CATTTTATTTTGGAGAAAATCATAATCATTTCCAAATGATTT-ATTTCTCCATTTTCA
* * *
12212538 TTTTCATTTTTATTTTCGAGAAAATCATAATCATTTCCGAATGTTTTATATTTCTCCATTTTCA
1 ----CA-TTTTATTTTGGAGAAAATCATAATCATTTCCAAATG-ATT-TATTTCTCCATTTTCA
12212602 CCATTTCTATT
1 -CATTT-TATT
12212613 CATTTTTGTT
Statistics
Matches: 106, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
56 1 0.01
57 44 0.42
58 4 0.04
60 3 0.03
61 6 0.06
63 31 0.29
64 16 0.15
65 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (57 bp):
CATTTTATTTTGGAGAAAATCATAATCATTTCCAAATGATTTATTTCTCCATTTTCA
Found at i:12217240 original size:31 final size:30
Alignment explanation
Indices: 12217170--12217244 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
12217160 AAATTATTCA
* *
12217170 AAAGTTTTCATTTAAGTCATTGAACTATTTT
1 AAAGTTTTTATTTAAATCATTGAAC-ATTTT
*
12217201 AAAGTTTTTATTTAAATCATTGAGC-TTTT
1 AAAGTTTTTATTTAAATCATTGAACATTTT
12217230 AAATGTTTTT-TTTAA
1 AAA-GTTTTTATTTAA
12217245 GTTTCGCCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 12 0.30
30 6 0.15
31 22 0.55
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (30 bp):
AAAGTTTTTATTTAAATCATTGAACATTTT
Found at i:12225997 original size:422 final size:422
Alignment explanation
Indices: 12225213--12226053 Score: 1549
Period size: 422 Copynumber: 2.0 Consensus size: 422
12225203 ACATTTTAGG
12225213 CTGCATAATTGATAAATTGCTCTGAACCTTCCCTACTCTCTCTGCAGAAAGACTTCTTGTATTAA
1 CTGCATAATTGATAAATTGCTCTGAACCTTCCCTACTCTCTCTGCAGAAAGACTTCTTGTATTAA
* * *
12225278 CTGTCTGAGTAGGCAAGTTTAATTTGTTGCCTTAAGCTACATTCTAATTGTACAAAAAAGTTGAT
66 CTGCCTGAGTAGACAAGTTTAATTTGTTGCCTTAAGCTACATTCTAATTGTACAAAAAAGGTGAT
*
12225343 GTTGAACTAGTTGAAATTGATGTTTCCATACCATGATCAAATGGTGTTTTATCTTCATTGTTGGT
131 GTTGAACTAGTTGAAATTGATGTTTCCATACCATGATCAAATGGTGTTTTAACTTCATTGTTGGT
12225408 TGCTTGATATTACGAGATGGGTATTTTTGAGCCCCTTCAAGCAACTCCCAGTTTGAAAATCATCA
196 TGCTTGATATTACGAGATGGGTATTTTTGAGCCCCTTCAAGCAACTCCCAGTTTGAAAATCATCA
*
12225473 CCTGCCCATGAAAATTCTGTAAGAAAAATTCTTTCATTATGTACTATTATTTATTTTTCTTTTTT
261 CCTGCCCATGAAAATTCTGTAAGAAAAATTCTTGCATTATGTACTATTATTTATTTTTCTTTTTT
12225538 TATGGATTCTGTTTGAGAAAAGATCATTGTTGTGTTTAACGGGTTGGTTTTCCCTGATTATGTAC
326 TATGGATTCTGTTTGAGAAAAGATCATTGTTGTGTTTAACGGGTTGGTTTTCCCTGATTATGTAC
12225603 AGTGCATGAGAATCCATCATGCAGGTAACTGC
391 AGTGCATGAGAATCCATCATGCAGGTAACTGC
*
12225635 CTGCATAATTGATAAATTGCTCTGGACCTTCCCTACTCTCTCTGCAGAAAGACTTCTTGTATTAA
1 CTGCATAATTGATAAATTGCTCTGAACCTTCCCTACTCTCTCTGCAGAAAGACTTCTTGTATTAA
* *
12225700 CTGCCTGAGTAGACAAGTTTAATTTGTTGCCTTAAGCTACATTCTAATTGTATAAACAAGGTG-T
66 CTGCCTGAGTAGACAAGTTTAATTTGTTGCCTTAAGCTACATTCTAATTGTACAAAAAAGGTGAT
* * *
12225764 GTTGAGCTAGTTGAAATTGATGTTTCCATGCCATGATCAAATGGTGTTTTAACTTCATTTTTGGT
131 GTTGAACTAGTTGAAATTGATGTTTCCATACCATGATCAAATGGTGTTTTAACTTCATTGTTGGT
*
12225829 TGCTTGATATTATGAGATGGGTATTTTTGAGCCCCTTCAAGCAACTCCCAGTTTGAAAATCATCA
196 TGCTTGATATTACGAGATGGGTATTTTTGAGCCCCTTCAAGCAACTCCCAGTTTGAAAATCATCA
*
12225894 CCTGCCCATGAAAGTTCTGTAAGAAAAATTCTTGCATTATGTACTATTATTTATTTTTCTCTTTT
261 CCTGCCCATGAAAATTCTGTAAGAAAAATTCTTGCATTATGTACTATTATTTATTTTTCT-TTTT
12225959 TTATGGATTCTGTTTGAGAAAAGATCATTGTTGTGTTTAACGGGTTGGTTTTCCCTGATTATGTA
325 TTATGGATTCTGTTTGAGAAAAGATCATTGTTGTGTTTAACGGGTTGGTTTTCCCTGATTATGTA
12226024 CAGTGCATGAGAATCCATCATGCAGGTAAC
390 CAGTGCATGAGAATCCATCATGCAGGTAAC
12226054 ATGTTCTTTC
Statistics
Matches: 405, Mismatches: 13, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
421 184 0.45
422 221 0.55
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (422 bp):
CTGCATAATTGATAAATTGCTCTGAACCTTCCCTACTCTCTCTGCAGAAAGACTTCTTGTATTAA
CTGCCTGAGTAGACAAGTTTAATTTGTTGCCTTAAGCTACATTCTAATTGTACAAAAAAGGTGAT
GTTGAACTAGTTGAAATTGATGTTTCCATACCATGATCAAATGGTGTTTTAACTTCATTGTTGGT
TGCTTGATATTACGAGATGGGTATTTTTGAGCCCCTTCAAGCAACTCCCAGTTTGAAAATCATCA
CCTGCCCATGAAAATTCTGTAAGAAAAATTCTTGCATTATGTACTATTATTTATTTTTCTTTTTT
TATGGATTCTGTTTGAGAAAAGATCATTGTTGTGTTTAACGGGTTGGTTTTCCCTGATTATGTAC
AGTGCATGAGAATCCATCATGCAGGTAACTGC
Found at i:12230043 original size:19 final size:17
Alignment explanation
Indices: 12230005--12230044 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
12229995 TTATATATGG
*
12230005 ATTAATTATTTAGTTGA
1 ATTAATTATTTAGTTAA
12230022 ATTAATTAATTTAAGTTAA
1 ATTAATT-ATTT-AGTTAA
12230041 ATTA
1 ATTA
12230045 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
ATTAATTATTTAGTTAA
Found at i:12232911 original size:18 final size:18
Alignment explanation
Indices: 12232888--12232925 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12232878 AAAATGAAAG
12232888 AGAAGCACGCAAAGCAGA
1 AGAAGCACGCAAAGCAGA
12232906 AGAAGCACGCAAAGCAGA
1 AGAAGCACGCAAAGCAGA
12232924 AG
1 AG
12232926 GAAAACAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.21, G:0.29, T:0.00
Consensus pattern (18 bp):
AGAAGCACGCAAAGCAGA
Found at i:12234245 original size:23 final size:22
Alignment explanation
Indices: 12234201--12234282 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
12234191 TATATATTAT
*
12234201 ATATTTTAAACTATTTATTTTAA
1 ATATTTTATA-TATTTATTTTAA
*
12234224 ATTATTTTATATATATATTTTAA
1 A-TATTTTATATATTTATTTTAA
* * *
12234247 A-ACTCTATTTATTTATTTTAAA
1 ATATTTTATATATTTATTTT-AA
*
12234269 ATATTTTATTTATT
1 ATATTTTATATATT
12234283 ATCCATTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 14 0.29
22 3 0.06
23 23 0.48
24 8 0.17
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTATATATTTATTTTAA
Found at i:12238515 original size:20 final size:20
Alignment explanation
Indices: 12238490--12238539 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
12238480 TGGCTTAAAA
12238490 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
12238510 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
12238527 GTGGTAGTGGATT
1 TTGGTAGTGGATT
12238540 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:12243154 original size:20 final size:20
Alignment explanation
Indices: 12243129--12243178 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
12243119 TGGCTTAAAA
12243129 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
12243149 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
12243166 GTGGTAGTGGATT
1 TTGGTAGTGGATT
12243179 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:12251848 original size:7 final size:7
Alignment explanation
Indices: 12251836--12251947 Score: 61
Period size: 7 Copynumber: 15.7 Consensus size: 7
12251826 ACTAATTAAT
12251836 CTAAACC
1 CTAAACC
12251843 CTAAACC
1 CTAAACC
*
12251850 TCTTAACCC
1 -C-TAAACC
*
12251859 CT-ATCC
1 CTAAACC
*
12251865 CATAAACA
1 C-TAAACC
12251873 CTAAACC
1 CTAAACC
12251880 CTAAACC
1 CTAAACC
*
12251887 CTTAACC
1 CTAAACC
*
12251894 CTTAACTC
1 CTAAAC-C
*
12251902 CAAAACC
1 CTAAACC
* *
12251909 TTACACC
1 CTAAACC
*
12251916 TTAAACTC
1 CTAAAC-C
12251924 C--AACC
1 CTAAACC
12251929 CT-AACC
1 CTAAACC
12251935 CATAAACC
1 C-TAAACC
12251943 CTAAA
1 CTAAA
12251948 TCATAATCCT
Statistics
Matches: 83, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
5 2 0.02
6 12 0.14
7 48 0.58
8 16 0.19
9 5 0.06
ACGTcount: A:0.39, C:0.40, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:12251997 original size:26 final size:26
Alignment explanation
Indices: 12251963--12252014 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12251953 ATCCTTAAAC
12251963 CCATAATTTATCATAAAACTTCAAAT
1 CCATAATTTATCATAAAACTTCAAAT
12251989 CCATAATTTATCATAAAACTTCAAAT
1 CCATAATTTATCATAAAACTTCAAAT
12252015 ACTAGTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (26 bp):
CCATAATTTATCATAAAACTTCAAAT
Found at i:12252084 original size:25 final size:25
Alignment explanation
Indices: 12251948--12252086 Score: 85
Period size: 26 Copynumber: 5.6 Consensus size: 25
12251938 AAACCCTAAA
* *
12251948 TCATAATCCTTAAACCCATAATTTA-
1 TCATAAACCTTAAA-CCATAATTAAC
* *
12251973 TCATAAAACTTCAAATCCATAATTTA-
1 TCATAAACCTT-AAA-CCATAATTAAC
* * *
12251999 TCATAAAACTTCAAA-TACTAGTTAAC
1 TCATAAACCTT-AAACCA-TAATTAAC
* *
12252025 TCCTAAACCTTAAACCCT-A--AAC
1 TCATAAACCTTAAACCATAATTAAC
* *
12252047 T-ATATATCTTAAACCATAATTAAC
1 TCATAAACCTTAAACCATAATTAAC
12252071 TCATAAACCTTAAACC
1 TCATAAACCTTAAACC
12252087 CTAAACCATC
Statistics
Matches: 89, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
21 12 0.13
22 5 0.06
24 5 0.06
25 30 0.34
26 37 0.42
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.32
Consensus pattern (25 bp):
TCATAAACCTTAAACCATAATTAAC
Found at i:12252121 original size:14 final size:14
Alignment explanation
Indices: 12252028--12252121 Score: 61
Period size: 14 Copynumber: 6.7 Consensus size: 14
12252018 AGTTAACTCC
* *
12252028 TAAACCTTAAACCC
1 TAAACCATAAACCT
* * *
12252042 TAAACTATATATCT
1 TAAACCATAAACCT
12252056 TAAACCAT-AA--T
1 TAAACCATAAACCT
12252067 T-AACTCATAAACCT
1 TAAAC-CATAAACCT
*
12252081 TAAACCCTAAACCATCT
1 TAAACCATAAA-C--CT
12252098 TAAACCATAAACCT
1 TAAACCATAAACCT
*
12252112 TAAACTATAA
1 TAAACCATAA
12252122 TGATAATTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
10 3 0.05
11 5 0.08
12 2 0.03
13 1 0.02
14 34 0.55
15 4 0.06
16 1 0.02
17 12 0.19
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:12252334 original size:41 final size:41
Alignment explanation
Indices: 12252275--12252373 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 41
12252265 GGAGTTATAC
*
12252275 GGTTTTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCT
1 GGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT
* * *
12252316 GGTTTTTAGCGGCATTTTATCAAAAGCGCCGCTATTGCTCT
1 GGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT
*
12252357 -ATTTTTAGCGGCGTTTT
1 GGTTTTTAGCGGCGTTTT
12252374 TGGTAAAACG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 15 0.29
41 37 0.71
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
GGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT
Found at i:12252386 original size:40 final size:40
Alignment explanation
Indices: 12252277--12252397 Score: 138
Period size: 41 Copynumber: 3.0 Consensus size: 40
12252267 AGTTATACGG
* * * *
12252277 TTTTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTT-TCAAAAGCGCCGCTATTGCTCTGA
*
12252318 TTTTTAGCGGCATTTTATCAAAAGCGCCGCTATTGCTCT-A
1 TTTTTAGCGGCGTTTT-TCAAAAGCGCCGCTATTGCTCTGA
*
12252358 TTTTTAGCGGCGTTTTTGGTAAAA-CGCCGCTATTGCTCTG
1 TTTTTAGCGGCGTTTTT--CAAAAGCGCCGCTATTGCTCTG
12252398 TGTTTTACAA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
39 1 0.01
40 30 0.43
41 39 0.56
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCAAAAGCGCCGCTATTGCTCTGA
Found at i:12256632 original size:23 final size:23
Alignment explanation
Indices: 12256600--12256653 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
12256590 TTACTTAGGA
* **
12256600 AAAAACTAATTATTATTGCATTT
1 AAAAATTAATTATTATTAAATTT
12256623 AAAAATTAATTATTATTAAATTT
1 AAAAATTAATTATTATTAAATTT
12256646 AAAAATTA
1 AAAAATTA
12256654 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
AAAAATTAATTATTATTAAATTT
Found at i:12256682 original size:40 final size:42
Alignment explanation
Indices: 12256636--12256728 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 42
12256626 AATTAATTAT
12256636 TATTAAATTTAAAAATT-ATTTTAAA-ATATA-TTGAACTACA
1 TATTAAATTTAAAAATTAATTTTAAATATATAGTTGAA-TACA
* * *
12256676 TATTAAATTT-TAAATTAATTTTAAATATGTAGTTGAATATA
1 TATTAAATTTAAAAATTAATTTTAAATATATAGTTGAATACA
*
12256717 TTTTAAATTTAA
1 TATTAAATTTAA
12256729 TAATAATGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 5 0.11
40 18 0.41
41 16 0.36
42 5 0.11
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (42 bp):
TATTAAATTTAAAAATTAATTTTAAATATATAGTTGAATACA
Found at i:12256723 original size:41 final size:40
Alignment explanation
Indices: 12256633--12256728 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 40
12256623 AAAAATTAAT
12256633 TATTATTAAATTTAAAAATTATTTTAAAATATATTGAACTA
1 TATT-TTAAATTTAAAAATTATTTTAAAATATATTGAACTA
* * * *
12256674 CATATTAAATTT-TAAATTAATTTTAAATATGTAGTTGAA-TA
1 TATTTTAAATTTAAAAATT-ATTTTAAA-ATATA-TTGAACTA
12256715 TATTTTAAATTTAA
1 TATTTTAAATTTAA
12256729 TAATAATGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
39 5 0.11
40 16 0.36
41 18 0.41
42 5 0.11
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (40 bp):
TATTTTAAATTTAAAAATTATTTTAAAATATATTGAACTA
Found at i:12260561 original size:7 final size:7
Alignment explanation
Indices: 12260549--12260577 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12260539 ATAAATAAGT
12260549 AAATATA
1 AAATATA
12260556 AAATATA
1 AAATATA
12260563 AAATATA
1 AAATATA
12260570 AAATATA
1 AAATATA
12260577 A
1 A
12260578 CAAAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATATA
Found at i:12260602 original size:3 final size:3
Alignment explanation
Indices: 12260596--12260705 Score: 58
Period size: 3 Copynumber: 36.0 Consensus size: 3
12260586 AAATGACAAC
* * * * * *
12260596 AAT AAT AAT AAT AAT AAT AAAG AAC AGT AAT AAA AAT AGT AAT AAA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * ** * *
12260642 AAT AAT ATT AAC AGT AAA AAT AAT GGT GAT AAT AAAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* *
12260688 AAT AGT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT
12260706 TAATTAATTA
Statistics
Matches: 76, Mismatches: 29, Indels: 4
0.70 0.27 0.04
Matches are distributed among these distances:
3 71 0.93
4 5 0.07
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:12260621 original size:25 final size:25
Alignment explanation
Indices: 12260593--12260641 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12260583 TATAAATGAC
*
12260593 AACAATAATAATAATAATAATAAAG
1 AACAATAATAAAAATAATAATAAAG
* *
12260618 AACAGTAATAAAAATAGTAATAAA
1 AACAATAATAAAAATAATAATAAA
12260642 AATAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22
Consensus pattern (25 bp):
AACAATAATAAAAATAATAATAAAG
Found at i:12260680 original size:16 final size:16
Alignment explanation
Indices: 12260596--12260705 Score: 68
Period size: 16 Copynumber: 6.8 Consensus size: 16
12260586 AAATGACAAC
*
12260596 AATAATAATAATAAT-
1 AATAATAGTAATAATA
*
12260611 AATAA-AGAACAGTAATA
1 AATAATAGTA-A-TAATA
12260628 AA-AATAGTAATAA-A
1 AATAATAGTAATAATA
*
12260642 AATAATATTAACAGTAA-A
1 AATAATAGT-A-A-TAATA
* *
12260660 AATAATGGTGATAATA
1 AATAATAGTAATAATA
12260676 AATAATAGTAATAATA
1 AATAATAGTAATAATA
*
12260692 GTAATAATATTAAT
1 --AATAATAGTAAT
12260706 TAATTAATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
14 5 0.07
15 17 0.23
16 24 0.32
17 6 0.08
18 22 0.30
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (16 bp):
AATAATAGTAATAATA
Found at i:12265903 original size:93 final size:95
Alignment explanation
Indices: 12265716--12265916 Score: 250
Period size: 93 Copynumber: 2.1 Consensus size: 95
12265706 AAGTTGTCAC
* * * * *
12265716 TGCCATGTCCCAGACATGGTCTTACGCTGGCTATCTCCATCGAGGCCGATGCCATGTCCCAGACA
1 TGCCATGTCCCAGACATCGTCTTACACTGGCTAACTCCATCGAGGCCGATGACATGTCCCAAACA
12265781 TGGTCTTACACTAGCACGAAACTTAGCCGA
66 TGGTCTTACACTAGCACGAAACTTAGCCGA
*
12265811 TG-CATGTCTCAGACA-CGTCTTACACTGGCTAACAT-CATCGAGGCCGAT-ACATGTCCCAAAC
1 TGCCATGTCCCAGACATCGTCTTACACTGGCTAAC-TCCATCGAGGCCGATGACATGTCCCAAAC
* ** *
12265872 AT-GTCTTACACTGGCACTCACCTCTACGCCGA
65 ATGGTCTTACACTAGCACGAAACT-TA-GCCGA
12265904 TGCCATGTCCCAG
1 TGCCATGTCCCAG
12265917 CCGTGGTCTT
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
91 17 0.19
92 15 0.16
93 35 0.38
94 22 0.24
95 2 0.02
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (95 bp):
TGCCATGTCCCAGACATCGTCTTACACTGGCTAACTCCATCGAGGCCGATGACATGTCCCAAACA
TGGTCTTACACTAGCACGAAACTTAGCCGA
Found at i:12265911 original size:47 final size:49
Alignment explanation
Indices: 12265716--12265929 Score: 189
Period size: 47 Copynumber: 4.5 Consensus size: 49
12265706 AAGTTGTCAC
* *
12265716 TGCCATGTCCCAGACATGGTCTTACGCTGGCTATCTC-CATCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTA-CTCACCTCGAGGCCGA
* ** * *
12265765 TGCCATGTCCCAGACATGGTCTTACACTAGC-ACGAAACT-TA-GCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTACTCACCTCGAGGCCGA
* *
12265811 TG-CATGTCTCAGACA-CGTCTTACACTGGCTAACATCA--TCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGGCT-AC-TCACCTCGAGGCCGA
* * * *
12265858 T-ACATGTCCCAAACAT-GTCTTACACTGGC-ACTCACCTCTACGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTACTCACCTCGAGGCCGA
* *
12265904 TGCCATGTCCCAGCCGTGGTCTTACA
1 TGCCATGTCCCAGACATGGTCTTACA
12265930 TGGGCTATCA
Statistics
Matches: 132, Mismatches: 21, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
44 15 0.11
45 15 0.11
46 19 0.14
47 44 0.33
48 10 0.08
49 29 0.22
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (49 bp):
TGCCATGTCCCAGACATGGTCTTACACTGGCTACTCACCTCGAGGCCGA
Found at i:12267715 original size:35 final size:36
Alignment explanation
Indices: 12267676--12267749 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 36
12267666 AAATTTTATA
12267676 AAAAATGATATAAAAACTAAATG-TAACTTTGGTTG
1 AAAAATGATATAAAAACTAAATGTTAACTTTGGTTG
*
12267711 AAAAATGATATAAAAATTAAATGTTAACTTTGGTTG
1 AAAAATGATATAAAAACTAAATGTTAACTTTGGTTG
12267747 AAA
1 AAA
12267750 TTGTAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 22 0.59
36 15 0.41
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (36 bp):
AAAAATGATATAAAAACTAAATGTTAACTTTGGTTG
Found at i:12270189 original size:21 final size:22
Alignment explanation
Indices: 12270151--12270194 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 22
12270141 GAATGAACCC
12270151 AAAATCAGAGAATCAGAAAACAA
1 AAAATCAGAGAATCAG-AAACAA
12270174 AAAATCA-A-AATCAGAAACAA
1 AAAATCAGAGAATCAGAAACAA
12270194 A
1 A
12270195 GGTGATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 1 0.05
23 7 0.33
ACGTcount: A:0.68, C:0.14, G:0.09, T:0.09
Consensus pattern (22 bp):
AAAATCAGAGAATCAGAAACAA
Found at i:12270955 original size:86 final size:86
Alignment explanation
Indices: 12270846--12271004 Score: 191
Period size: 86 Copynumber: 1.8 Consensus size: 86
12270836 TCATTTTTTC
* * * *
12270846 TCATTATTTTATTTTAATTTTAATA-TTATTCATACTATTATA-TTTTATT-ACTGTTATTATTA
1 TCATTATTTTATTTTAATCTTAATACTTATT-ATACTA-TATAGTATTATTAACAGTTATTAATA
12270908 TTATATATTTTATTTATTAGCATT
64 TTAT-TATTTTATTTATTAGCATT
* * *
12270932 TCATTATTATTATTTTTA-CTTAATACTTATTATATTATATAGTATTATTAACAGTTTTTAATAT
1 TCATTATT-TTATTTTAATCTTAATACTTATTATACTATATAGTATTATTAACAGTTATTAATAT
12270996 TATTATTTT
65 TATTATTTT
12271005 TGTTAATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
85 4 0.06
86 31 0.50
87 27 0.44
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (86 bp):
TCATTATTTTATTTTAATCTTAATACTTATTATACTATATAGTATTATTAACAGTTATTAATATT
ATTATTTTATTTATTAGCATT
Found at i:12271001 original size:3 final size:3
Alignment explanation
Indices: 12270848--12270981 Score: 52
Period size: 3 Copynumber: 45.3 Consensus size: 3
12270838 ATTTTTTCTC
* *
12270848 ATT ATT -TT ATT -TT AATT -TT AAT ATT ATT CA-T ACT ATT A-T ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
* * ** *
12270890 -TT ATT ACT GTT ATT ATT ATT ATAT ATT -TT ATTT ATT AGC ATT -TC
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT A-TT ATT ATT ATT ATT
* * *
12270934 ATT ATT ATT ATT TTT ACTT AAT ACTT ATT A-T ATT ATAT AGT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT ATT AT-T ATT ATT ATT
12270981 A
1 A
12270982 ACAGTTTTTA
Statistics
Matches: 96, Mismatches: 19, Indels: 32
0.65 0.13 0.22
Matches are distributed among these distances:
2 16 0.17
3 64 0.67
4 16 0.17
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:12271121 original size:17 final size:17
Alignment explanation
Indices: 12271101--12271134 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12271091 ATGTATATTA
12271101 TTTTTTAAATATTATGT
1 TTTTTTAAATATTATGT
*
12271118 TTTTTTATATATTATGT
1 TTTTTTAAATATTATGT
12271135 ATATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTTTTTAAATATTATGT
Found at i:12271163 original size:25 final size:25
Alignment explanation
Indices: 12271126--12271294 Score: 156
Period size: 26 Copynumber: 6.9 Consensus size: 25
12271116 GTTTTTTTAT
12271126 ATATTATGTATATATTTTTAATATC
1 ATATTATGTATATATTTTTAATATC
12271151 ATATTAT-TCATATA-TTTT-AT-T-
1 ATATTATGT-ATATATTTTTAATATC
*
12271172 ATATTATGTATATATTTTTAATAGC
1 ATATTATGTATATATTTTTAATATC
* *
12271197 TATATTATGTATGTATTTTTAACA-C
1 -ATATTATGTATATATTTTTAATATC
* * *
12271222 TATATTACGTACATACTTTTAATATC
1 -ATATTATGTATATATTTTTAATATC
*
12271248 ATTATTATGTATATATTTTT-ACAT-
1 A-TATTATGTATATATTTTTAATATC
* * *
12271272 GTATTATGTACATATTTTCAATA
1 ATATTATGTATATATTTTTAATA
12271295 ACTACATCAT
Statistics
Matches: 118, Mismatches: 16, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
21 12 0.10
22 6 0.05
23 20 0.17
24 7 0.06
25 36 0.31
26 37 0.31
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.53
Consensus pattern (25 bp):
ATATTATGTATATATTTTTAATATC
Found at i:12271200 original size:26 final size:25
Alignment explanation
Indices: 12271125--12271314 Score: 155
Period size: 26 Copynumber: 7.6 Consensus size: 25
12271115 TGTTTTTTTA
12271125 TATATTATGTATATATTTTTAATA-
1 TATATTATGTATATATTTTTAATAC
12271149 TCATATTAT-TCATATA-TTTT-AT--
1 T-ATATTATGT-ATATATTTTTAATAC
12271171 TATATTATGTATATATTTTTAATAGC
1 TATATTATGTATATATTTTTAATA-C
* *
12271197 TATATTATGTATGTATTTTTAACAC
1 TATATTATGTATATATTTTTAATAC
* * *
12271222 TATATTACGTACATACTTTTAATA-
1 TATATTATGTATATATTTTTAATAC
*
12271246 TCATTATTATGTATATATTTTT-ACA-
1 T-A-TATTATGTATATATTTTTAATAC
* * *
12271271 TGTATTATGTACATATTTTCAATAAC
1 TATATTATGTATATATTTTTAAT-AC
*
12271297 TACATCATATGTATATAT
1 TATAT--TATGTATATAT
12271315 ATTATGTGCA
Statistics
Matches: 133, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
21 12 0.09
22 6 0.05
23 20 0.15
24 8 0.06
25 37 0.28
26 40 0.30
28 10 0.08
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (25 bp):
TATATTATGTATATATTTTTAATAC
Found at i:12271243 original size:51 final size:48
Alignment explanation
Indices: 12271124--12271294 Score: 163
Period size: 51 Copynumber: 3.5 Consensus size: 48
12271114 ATGTTTTTTT
* *
12271124 ATATATTATGTATATATTTTTAATATCA-TATTAT-TCATATA-TTTTA-
1 ATATATTATGTACATA-TTTTAATAGCATTATTATGT-ATATATTTTTAC
* * *
12271170 TTATATTATGTATATATTTTTAATAGC-TATATTATGTATGTATTTTTAAC
1 ATATATTATGTACATA-TTTTAATAGCAT-TATTATGTATATATTTTT-AC
* *
12271220 ACTATATTACGTACATACTTTTAATATCATTATTATGTATATATTTTTAC
1 A-TATATTATGTACATA-TTTTAATAGCATTATTATGTATATATTTTTAC
*
12271270 ATGTATTATGTACATATTTTCAATA
1 ATATATTATGTACATATTTT-AATA
12271295 ACTACATCAT
Statistics
Matches: 105, Mismatches: 11, Indels: 15
0.80 0.08 0.11
Matches are distributed among these distances:
46 25 0.24
47 10 0.10
48 9 0.09
49 18 0.17
50 3 0.03
51 39 0.37
52 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (48 bp):
ATATATTATGTACATATTTTAATAGCATTATTATGTATATATTTTTAC
Found at i:12271308 original size:51 final size:51
Alignment explanation
Indices: 12271171--12271314 Score: 138
Period size: 51 Copynumber: 2.8 Consensus size: 51
12271161 TATATTTTAT
* * * *
12271171 TATATTATGTATATATTTTTAATAGCTATAT-TATGTATGTATTTTTAACAC
1 TATATTATGTACATA-TTTTAATAACTACATATATGTATATATTTTTAACAC
*
12271222 TATATTACGTACATACTTTTAAT-A-T-CATTATTATGTATATATTTTT-ACA-
1 TATATTATGTACATA-TTTTAATAACTACA-TA-TATGTATATATTTTTAACAC
*
12271271 TGTATTATGTACATATTTTCAATAACTACATCATATGTATATAT
1 TATATTATGTACATATTTT-AATAACTACAT-ATATGTATATAT
12271315 ATTATGTGCA
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
48 5 0.06
49 18 0.23
50 4 0.05
51 47 0.61
52 3 0.04
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (51 bp):
TATATTATGTACATATTTTAATAACTACATATATGTATATATTTTTAACAC
Found at i:12271478 original size:18 final size:20
Alignment explanation
Indices: 12271457--12271501 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
12271447 ATTTCTATTT
12271457 TATTTTT-TTATTTGTC-AA
1 TATTTTTATTATTTGTCTAA
*
12271475 TATTATTTATTATTTTTCTAA
1 TATT-TTTATTATTTGTCTAA
12271496 TATTTT
1 TATTTT
12271502 GATATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 3 0.13
20 10 0.43
21 6 0.26
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTTTTATTATTTGTCTAA
Found at i:12271508 original size:8 final size:7
Alignment explanation
Indices: 12271495--12271528 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
12271485 TATTTTTCTA
12271495 ATATTTT
1 ATATTTT
12271502 GATATTTT
1 -ATATTTT
12271510 AATATTTT
1 -ATATTTT
12271518 ATATTTT
1 ATATTTT
12271525 ATAT
1 ATAT
12271529 ACTTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (7 bp):
ATATTTT
Found at i:12271514 original size:16 final size:15
Alignment explanation
Indices: 12271493--12271538 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
12271483 ATTATTTTTC
12271493 TAATATTTTGATATTT
1 TAATATTTT-ATATTT
12271509 TAATATTTTATATTT
1 TAATATTTTATATTT
12271524 TATATACTTTT-TATT
1 TA-ATA-TTTTATATT
12271539 ATTCGCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.29
16 16 0.57
17 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TAATATTTTATATTT
Found at i:12275774 original size:27 final size:27
Alignment explanation
Indices: 12275751--12275806 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
12275741 AAAGAAAGGC
12275751 TCAAGGCGATAGAAGGTGCTGAAACCT
1 TCAAGGCGATAGAAGGTGCTGAAACCT
12275778 TCAAGGCGATAGAAGGTGCTGAAACCT
1 TCAAGGCGATAGAAGGTGCTGAAACCT
12275805 TC
1 TC
12275807 TCTACACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20
Consensus pattern (27 bp):
TCAAGGCGATAGAAGGTGCTGAAACCT
Found at i:12283669 original size:160 final size:161
Alignment explanation
Indices: 12283336--12283724 Score: 540
Period size: 160 Copynumber: 2.4 Consensus size: 161
12283326 GGTATTTTGA
* * * * *
12283336 TGTTTTT--ATTTCTGTTTT-C-AAAAATTAATTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA
1 TGTTTTTCAATTTATGTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
** * * * * * *
12283397 CACGTTGAGGTATTTTCAATTTCTGTCTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGA
66 CACACTAAGGTAATCTCAATTTATG-CTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
*
12283462 GCCTCGGTTCACATGCCGAGATATTTTCAAATTC
130 ACCTCGG-T-ACATGCCGAGATATTTTCAAATTC
*
12283496 TATTTTTCAATTTATGTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
1 TGTTTTTCAATTTATGTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
12283561 CACACTAAGGTAATCTCAATTTATG-TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
66 CACACTAAGGTAATCTCAATTTATGCTTTC-AAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
*
12283625 ACCTCGG-ACATGCCGAGGTATTTTCAAATTC
130 ACCTCGGTACATGCCGAGATATTTTCAAATTC
12283656 TGTTTTTCAATTTATGTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGT
1 TGTTTTTCAATTTATGTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-
12283720 TCACA
65 TCACA
12283725 TGCCGAGATA
Statistics
Matches: 206, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
159 2 0.01
160 94 0.46
162 14 0.07
163 39 0.19
164 57 0.28
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (161 bp):
TGTTTTTCAATTTATGTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
CACACTAAGGTAATCTCAATTTATGCTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAA
CCTCGGTACATGCCGAGATATTTTCAAATTC
Found at i:12283789 original size:89 final size:89
Alignment explanation
Indices: 12283586--12283813 Score: 327
Period size: 89 Copynumber: 2.6 Consensus size: 89
12283576 TCAATTTATG
* * * *
12283586 TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGG--ACATGCCGAGGTATTTT
1 TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGATATTTC
**
12283649 CAAATTCTGTTTTTCAATTTATGTT
65 CAAATTCTGTTTTTCAAACTATGTT
*
12283674 TTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCCGAGATATTTC
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-TCACATGCCGAGATATTTC
12283739 CAAATTCTG-TTTTCAAACTATGTT
65 CAAATTCTGTTTTTCAAACTATGTT
* *
12283763 TTTCAAAAAATTAACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGTCACA
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACA
12283814 CTGAGGTATT
Statistics
Matches: 126, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
87 39 0.31
88 3 0.02
89 58 0.46
90 26 0.21
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (89 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGATATTTCC
AAATTCTGTTTTTCAAACTATGTT
Found at i:12283848 original size:249 final size:250
Alignment explanation
Indices: 12283409--12284006 Score: 905
Period size: 249 Copynumber: 2.4 Consensus size: 250
12283399 CGTTGAGGTA
* *
12283409 TTTTCAATTTCTGTCTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCAC
1 TTTTCAATTTATGTCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCAC
* **
12283474 ATGCCGAGATATTTTCAAATTCTATTTTTCAATTTATGTTTTCCAAAAAATCAACTCATATTGCG
66 ATGCCGAGATATTTCCAAATTCT-TTTTTCAAACTATGTTTTCCAAAAAATCAACTCATATTGCG
*
12283539 AGAGGTGAGTTGAGCCTCAGGTCACACTAAGGTAATCTCAATTTATGTTTCAAAAAAATCAACTC
130 AGAGCTGAGTTGAGCCTCAGGTCACACTAAGGTAATCTCAATTTATGTTTCAAAAAAATCAACTC
* * *
12283604 ATATTGCGAGAAGTGAGTTGAACCTCGG-ACATGCCGAGGTATTTTCAAATTCTGT
195 ATATTGCGAGAAGTAAGTTGAACCTCGGCACACGCCGAGGTATTTTCAAATTCTGC
12283659 TTTTCAATTTATGT-TTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCA
1 TTTTCAATTTATGTCTTT-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCA
* * *
12283723 CATGCCGAGATATTTCCAAATTCTGTTTTCAAACTATGTTTTTCAAAAAATTAACTCATATTGCG
65 CATGCCGAGATATTTCCAAATTCTTTTTTCAAACTATGTTTTCCAAAAAATCAACTCATATTGCG
* *
12283788 AGAGCTGAGTTGAGCCTCAGGTCACACTGAGGTATTCTCAATTTATGTTTCAAAAAAATCAACTC
130 AGAGCTGAGTTGAGCCTCAGGTCACACTAAGGTAATCTCAATTTATGTTTCAAAAAAATCAACTC
* * * * *
12283853 ATATTGCGAGAGGTAAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAATTTCTGC
195 ATATTGCGAGAAGTAAGTTGAACCTCGG--CACACGCCGAGGTATTTTCAAATTCTGC
* * *
12283911 TTTTCAATTTATGTGTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGATCAC
1 TTTTCAATTTATGTCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCAC
* * * *
12283975 ACGCTGAGGTATTTCCAATTTCTTTTTTCAAA
66 ATGCCGAGATATTTCCAAATTCTTTTTTCAAA
12284007 AAAAAAAATC
Statistics
Matches: 317, Mismatches: 26, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
249 125 0.39
250 81 0.26
251 70 0.22
252 38 0.12
253 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (250 bp):
TTTTCAATTTATGTCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCAC
ATGCCGAGATATTTCCAAATTCTTTTTTCAAACTATGTTTTCCAAAAAATCAACTCATATTGCGA
GAGCTGAGTTGAGCCTCAGGTCACACTAAGGTAATCTCAATTTATGTTTCAAAAAAATCAACTCA
TATTGCGAGAAGTAAGTTGAACCTCGGCACACGCCGAGGTATTTTCAAATTCTGC
Found at i:12283876 original size:162 final size:162
Alignment explanation
Indices: 12283660--12284040 Score: 480
Period size: 162 Copynumber: 2.3 Consensus size: 162
12283650 AAATTCTGTT
* *
12283660 TTTCAATTTATGTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACA
1 TTTCAATTTATG-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACA
* * *
12283725 TGCCGAGATATTTCCAAATTCTG-TTTTCAAACTATGTTTTTCAAAAAATTAACTCATATTGCGA
65 CGCCGAGATATTTCCAAATTCTGCTTTTCAAACTATGTGTTTC-AAAAATCAACTCATATTGCGA
12283789 GAGCTGAGTTGAGCCTCAGG-TCACA-CTGAGGTA
129 GAGCTGAGTTGAGCCT-AGGATCACACCTGAGGTA
* *
12283822 TTCTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGCTCACA
1 TT-TCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACA
* * * * **
12283887 CGCTGAGGTATTTTCAATTTCTGCTTTTCAATTTATGTGTTTCAAAAATCAACTCATATTGCGAG
65 CGCCGAGATATTTCCAAATTCTGCTTTTCAAACTATGTGTTTCAAAAATCAACTCATATTGCGAG
* *
12283952 AGGTGAGTTGAGCCTTGGATCACACGCTGAGGTA
130 AGCTGAGTTGAGCCTAGGATCACAC-CTGAGGTA
* * *
12283986 TTTCCAATTTCTTTTTTCAAAAAAAAAAATCAACTCATATTGCTAGAGGTGAGTT
1 TTT-CAATTT-ATGTTTC----AAAAAAATCAACTCATATTGCGAGAGGTGAGTT
12284041 AAGTCCTAGG
Statistics
Matches: 189, Mismatches: 19, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
161 2 0.01
162 108 0.57
163 27 0.14
164 16 0.08
165 5 0.03
169 31 0.16
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (162 bp):
TTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAC
GCCGAGATATTTCCAAATTCTGCTTTTCAAACTATGTGTTTCAAAAATCAACTCATATTGCGAGA
GCTGAGTTGAGCCTAGGATCACACCTGAGGTA
Found at i:12283877 original size:73 final size:73
Alignment explanation
Indices: 12283763--12283906 Score: 202
Period size: 73 Copynumber: 2.0 Consensus size: 73
12283753 AAACTATGTT
* *
12283763 TTTCAAAAAATTAACTCATATTGCGAGAGCTGAGTTGAGCCTCAGG-TCACA-CTGAGGTATTCT
1 TTTCAAAAAATCAACTCATATTGCGAGAGCTAAGTTGAGCCT-AGGCTCACACCTGAGGTATTCT
12283826 CAATTTATG
65 CAATTTATG
* * *
12283835 TTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGCTCACACGCTGAGGTATTT
1 TTTC-AAAAAATCAACTCATATTGCGAGAGCTAAGTTGAGCCTAGGCTCACAC-CTGAGGTATTC
12283900 TCAATTT
64 TCAATTT
12283907 CTGCTTTTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
72 6 0.10
73 40 0.63
75 17 0.27
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (73 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGCTAAGTTGAGCCTAGGCTCACACCTGAGGTATTCTC
AATTTATG
Found at i:12283976 original size:89 final size:87
Alignment explanation
Indices: 12283825--12284005 Score: 283
Period size: 89 Copynumber: 2.0 Consensus size: 87
12283815 TGAGGTATTC
*
12283825 TCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGCTCACACGC
1 TCAATTTATGTTTC-AAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGATCACACGC
*
12283890 TGAGGTATTTTCAATTTCTGCTTT
65 TGAGGTATTTCCAATTTCT-CTTT
*
12283914 TCAATTTATGTGTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGATCACACG
1 TCAATTTA--TGTTTCAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGATCACACG
*
12283978 CTGAGGTATTTCCAATTTCTTTTT
64 CTGAGGTATTTCCAATTTCTCTTT
12284002 TCAA
1 TCAA
12284006 AAAAAAAAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
88 7 0.08
89 73 0.85
91 6 0.07
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (87 bp):
TCAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGATCACACGCT
GAGGTATTTCCAATTTCTCTTT
Found at i:12284569 original size:25 final size:25
Alignment explanation
Indices: 12284535--12284582 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12284525 AAAAGTCTTT
*
12284535 ACTCTATTCTCGTTACACGACAACA
1 ACTCTATTCTCGTGACACGACAACA
12284560 ACTCTATTCTCGTGACACGACAA
1 ACTCTATTCTCGTGACACGACAA
12284583 TGAGTAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.27
Consensus pattern (25 bp):
ACTCTATTCTCGTGACACGACAACA
Found at i:12285121 original size:21 final size:22
Alignment explanation
Indices: 12285083--12285126 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 22
12285073 GAACGAACCC
12285083 AAAATCAGAGAATCAGAAAACAA
1 AAAATCAGAGAATCAG-AAACAA
12285106 AAAATCA-A-AATCAGAAACAA
1 AAAATCAGAGAATCAGAAACAA
12285126 A
1 A
12285127 GGTGATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 1 0.05
23 7 0.33
ACGTcount: A:0.68, C:0.14, G:0.09, T:0.09
Consensus pattern (22 bp):
AAAATCAGAGAATCAGAAACAA
Found at i:12285829 original size:17 final size:16
Alignment explanation
Indices: 12285796--12285829 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12285786 ATATTATTCA
*
12285796 TACTGTTATATTTTAT
1 TACTGTTATATTATAT
12285812 TACTGTTATTATTATAT
1 TACTGTTA-TATTATAT
12285829 T
1 T
12285830 TTTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TACTGTTATATTATAT
Found at i:12285990 original size:46 final size:46
Alignment explanation
Indices: 12285936--12286025 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
12285926 TAATATATTA
12285936 GTATGTCATATATATATTCTTTTAATATATATATTATACTCCATTC
1 GTATGTCATATATATATTCTTTTAATATATATATTATACTCCATTC
12285982 GTATGTCATATATATATTCTTTTAATATATATATTATACTCCAT
1 GTATGTCATATATATATTCTTTTAATATATATATTATACTCCAT
12286026 ATTACGCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.50
Consensus pattern (46 bp):
GTATGTCATATATATATTCTTTTAATATATATATTATACTCCATTC
Found at i:12286036 original size:44 final size:45
Alignment explanation
Indices: 12285940--12286043 Score: 158
Period size: 46 Copynumber: 2.3 Consensus size: 45
12285930 ATATTAGTAT
*
12285940 GTCATATATATATTCTTTTAATATATATATTATACTCCATTCGTAT
1 GTCATATATATATTCTTTTAATATATATATTATACTCCATTC-TAC
12285986 GTCATATATATATTCTTTTAATATATATATTATACTCCATAT-TAC
1 GTCATATATATATTCTTTTAATATATATATTATACTCCAT-TCTAC
*
12286031 G-CATATATGTATT
1 GTCATATATATATT
12286044 AATATTATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
44 11 0.20
45 3 0.05
46 40 0.73
47 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (45 bp):
GTCATATATATATTCTTTTAATATATATATTATACTCCATTCTAC
Found at i:12286117 original size:26 final size:24
Alignment explanation
Indices: 12286077--12286252 Score: 147
Period size: 26 Copynumber: 7.4 Consensus size: 24
12286067 TTTTAAATAT
*
12286077 TATATTTTT-TTATATATTATGTA
1 TATATTTTTATCATATATTATGTA
*
12286100 TATATTTTAAT-ATCATATTAT-TCA
1 TATATTTTTATCAT-ATATTATGT-A
12286124 TATA-TTTTAT--TATATTATGTA
1 TATATTTTTATCATATATTATGTA
*
12286145 TATATTTTTAATAACTATATTATGTA
1 TATATTTTT-ATCA-TATATTATGTA
* *
12286171 TGTATTTTTAACACTATATTACT-TA
1 TATATTTTTATCA-TATATTA-TGTA
*
12286196 CATATTTTTAAT-ATCATTATTATGTA
1 TATATTTTT-ATCAT-A-TATTATGTA
12286222 TATATTTTTA--ATATATTATGTA
1 TATATTTTTATCATATATTATGTA
12286244 TATATTTTT
1 TATATTTTT
12286253 GTAATATTAT
Statistics
Matches: 130, Mismatches: 9, Indels: 29
0.77 0.05 0.17
Matches are distributed among these distances:
21 12 0.09
22 24 0.18
23 19 0.15
24 16 0.12
25 23 0.18
26 36 0.28
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (24 bp):
TATATTTTTATCATATATTATGTA
Found at i:12286263 original size:47 final size:46
Alignment explanation
Indices: 12286049--12286264 Score: 170
Period size: 51 Copynumber: 4.7 Consensus size: 46
12286039 GTATTAATAT
*
12286049 TATATTATGTATATTGTTTTTTAA-A-TATTA--TAT-T-TTTTT-A
1 TATATTATGTATA-TATTTTTTAATATTATTATGTATATATTTTTAA
*
12286089 TATATTATGTATATA--TTTTAATATCATATTAT-TCATATA-TTTTAT
1 TATATTATGTATATATTTTTTAATAT--TATTATGT-ATATATTTTTAA
*
12286134 TATATTATGTATATA-TTTTTAATAACTATATTATGTATGTATTTTTAACA
1 TATATTATGTATATATTTTTTAAT-A-T-TATTATGTATATATTTTT-A-A
* *
12286184 CTATATTACT-TACATATTTTTAATATCATTATTATGTATATATTTTTAA
1 -TATATTA-TGTATATATTTTTTA-AT-ATTATTATGTATATATTTTTAA
12286233 TATATTATGTATATATTTTTGTAATATTATTA
1 TATATTATGTATATATTTTT-TAATATTATTA
12286265 ATAATTTTTT
Statistics
Matches: 144, Mismatches: 10, Indels: 37
0.75 0.05 0.19
Matches are distributed among these distances:
37 6 0.04
38 1 0.01
39 1 0.01
40 13 0.09
41 5 0.03
42 1 0.01
43 2 0.01
44 5 0.03
45 15 0.10
46 7 0.05
47 20 0.14
48 25 0.17
49 3 0.02
50 1 0.01
51 29 0.20
52 7 0.05
53 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (46 bp):
TATATTATGTATATATTTTTTAATATTATTATGTATATATTTTTAA
Found at i:12286398 original size:223 final size:214
Alignment explanation
Indices: 12286098--12286508 Score: 460
Period size: 215 Copynumber: 1.9 Consensus size: 214
12286088 ATATATTATG
* * * *
12286098 TATATATTTTAATATCATATTATTCATATATTTTATTATATTATGTATATATTTTTAATAACTAT
1 TATATATTTTAATATCATATTATTCATATATTTTAATATATTATGTACATATTTTCAATAACTAC
* *
12286163 ATTATGTATGTATTTTTAACACTATATTACT-TACATATTTTTAATATCATTATTATGTATATAT
66 ATCA-GTATGTA----T---A-TATATTA-TGTACATACTTTT-A-AT-ATTATTATGTATATAT
* * * * *
12286227 TTTTAATATATTATGTATATATTTTTGTAATATTATTAATA-ATT-TTTTT-AACATTATTATTA
118 TTTTAATATA-TATGTACATATTTATGTAATATTACTAATAGATTGTTTTTAAACATCATTAATA
12286289 TTTCTTAGATGTATATATCATATCTATAAATAC
182 TTTCTTAGATGTATATATCATATCTATAAATAC
*
12286322 TATAT-TTTTAATA-CTATATTATGT-ATATATTTTTACATGTATTATGTACATATTTTCAATAA
1 TATATATTTTAATATC-ATATTAT-TCATATA-TTTTA-ATATATTATGTACATATTTTCAATAA
* *
12286384 CTACATCA-TATGTATATATATTATGTGCATACTTTTAATATTATTATGTATTTATTTTTAATAT
62 CTACATCAGTATGTATATATATTATGTACATACTTTTAATATTATTATGTATATATTTTTAATAT
*
12286448 ATATGTACATATTTATGTAGTATTACTAATAGTATTGTTTTTAAACATCATTAATATTTCT
127 ATATGTACATATTTATGTAATATTACTAATAG-ATTGTTTTTAAACATCATTAATATTTCT
12286509 AATATATATA
Statistics
Matches: 163, Mismatches: 15, Indels: 27
0.80 0.07 0.13
Matches are distributed among these distances:
211 26 0.16
212 25 0.15
213 5 0.03
214 7 0.04
215 32 0.20
216 1 0.01
219 1 0.01
222 1 0.01
223 26 0.16
224 11 0.07
225 28 0.17
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.54
Consensus pattern (214 bp):
TATATATTTTAATATCATATTATTCATATATTTTAATATATTATGTACATATTTTCAATAACTAC
ATCAGTATGTATATATATTATGTACATACTTTTAATATTATTATGTATATATTTTTAATATATAT
GTACATATTTATGTAATATTACTAATAGATTGTTTTTAAACATCATTAATATTTCTTAGATGTAT
ATATCATATCTATAAATAC
Found at i:12286460 original size:25 final size:23
Alignment explanation
Indices: 12286416--12286463 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12286406 ATGTGCATAC
**
12286416 TTTTAATATTATTATGTATTTAT
1 TTTTAATATTATTACATATTTAT
12286439 TTTTAATATATATGTACATATTTAT
1 TTTTAATAT-TAT-TACATATTTAT
12286464 GTAGTATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 3 0.14
25 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTAATATTATTACATATTTAT
Found at i:12286563 original size:18 final size:18
Alignment explanation
Indices: 12286529--12286647 Score: 70
Period size: 18 Copynumber: 6.7 Consensus size: 18
12286519 TTATGTACAC
12286529 TTTTTTATT-TCTATTTTAT
1 TTTTTTATTAT-T-TTTTAT
12286548 TTTTTTATTATTTTTTAT
1 TTTTTTATTATTTTTTAT
** *
12286566 TTGTCAATATTATTTATTAT
1 TT-T-TTTATTATTTTTTAT
* * *
12286586 TTTTCTAATA-TTTTGAT
1 TTTTTTATTATTTTTTAT
* * *
12286603 ATTTTGA-TA--TTTTAA
1 TTTTTTATTATTTTTTAT
12286618 TTTTTTA-TATTTTTTAT
1 TTTTTTATTATTTTTTAT
12286635 ATTTTTTATTATT
1 -TTTTTTATTATT
12286648 CACATCATTA
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
15 11 0.14
16 2 0.03
17 14 0.18
18 19 0.25
19 16 0.21
20 15 0.19
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTTATTATTTTTTAT
Found at i:12286578 original size:20 final size:21
Alignment explanation
Indices: 12286553--12286597 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
12286543 TTTATTTTTT
*
12286553 TATTATTTTTTATTTGTC-AA
1 TATTATTTATTATTTGTCTAA
*
12286573 TATTATTTATTATTTTTCTAA
1 TATTATTTATTATTTGTCTAA
12286594 TATT
1 TATT
12286598 TTGATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTATTTATTATTTGTCTAA
Found at i:12286623 original size:24 final size:24
Alignment explanation
Indices: 12286591--12286639 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
12286581 ATTATTTTTC
12286591 TAATATTTTGATA-TTTTGATATTT
1 TAATATTTT-ATATTTTTGATATTT
* *
12286615 TAATTTTTTATATTTTTTATATTT
1 TAATATTTTATATTTTTGATATTT
12286639 T
1 T
12286640 TTATTATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
TAATATTTTATATTTTTGATATTT
Found at i:12286631 original size:9 final size:9
Alignment explanation
Indices: 12286542--12286643 Score: 65
Period size: 9 Copynumber: 11.7 Consensus size: 9
12286532 TTTATTTCTA
12286542 TTTTAT-TT
1 TTTTATATT
12286550 TTTTATTATT
1 TTTTA-TATT
12286560 TTTTAT-TT
1 TTTTATATT
* **
12286568 GTCAATATT
1 TTTTATATT
*
12286577 ATTTATTATT
1 TTTTA-TATT
12286587 TTTCTA-ATAT
1 TTT-TATAT-T
*
12286597 TTTGATA-T
1 TTTTATATT
*
12286605 TTTGATA--
1 TTTTATATT
12286612 TTTTA-ATT
1 TTTTATATT
12286620 TTTTATATT
1 TTTTATATT
12286629 TTTTATATT
1 TTTTATATT
12286638 TTTTAT
1 TTTTAT
12286644 TATTCACATC
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 23 0.31
9 27 0.36
10 18 0.24
11 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:12290189 original size:21 final size:21
Alignment explanation
Indices: 12290165--12290208 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12290155 ATAATAATAT
* * *
12290165 AATATAATAGAAGAATAAAGA
1 AATAAAATAGAAAAAGAAAGA
12290186 AATAAAATAGAAAAAGAAAGA
1 AATAAAATAGAAAAAGAAAGA
12290207 AA
1 AA
12290209 GAACAGACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AATAAAATAGAAAAAGAAAGA
Found at i:12291116 original size:6 final size:6
Alignment explanation
Indices: 12291107--12291138 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12291097 CCTGACTATG
*
12291107 ACTGTT ACTGTT ACTGTC ACTGTT ACTGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT AC
12291139 CCTACAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.44
Consensus pattern (6 bp):
ACTGTT
Found at i:12299177 original size:19 final size:19
Alignment explanation
Indices: 12299155--12299193 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12299145 AGAATAATTG
*
12299155 AAAGCATCTTTCGATAGGC
1 AAAGCATCGTTCGATAGGC
12299174 AAAGCATCGTTCGATAGGC
1 AAAGCATCGTTCGATAGGC
12299193 A
1 A
12299194 GAAATTGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (19 bp):
AAAGCATCGTTCGATAGGC
Found at i:12300089 original size:21 final size:21
Alignment explanation
Indices: 12300065--12300108 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12300055 ATAATAATAT
* * *
12300065 AATATAATAGAAGAATAAAGA
1 AATAAAATAGAAAAAGAAAGA
12300086 AATAAAATAGAAAAAGAAAGA
1 AATAAAATAGAAAAAGAAAGA
12300107 AA
1 AA
12300109 GAACAGACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AATAAAATAGAAAAAGAAAGA
Found at i:12302954 original size:22 final size:19
Alignment explanation
Indices: 12302927--12303037 Score: 54
Period size: 19 Copynumber: 5.8 Consensus size: 19
12302917 AAATATGTTT
12302927 TTATTTATAAATATATATATA
1 TTATTT-TAAATAT-TATATA
*
12302948 TTGATTTGT-TATATTATATA
1 TT-ATTT-TAAATATTATATA
*
12302968 TTATTTTAAA-ATTAGTATG
1 TTATTTTAAATATTA-TATA
* *
12302987 TTA-TAT-AATATT-TAAA
1 TTATTTTAAATATTATATA
* * * *
12303003 TTGTTTTATAAAAATGTATA
1 TTATTTTA-AATATTATATA
12303023 TT-TTTTAAATATTAT
1 TTATTTTAAATATTAT
12303038 TACATATGTG
Statistics
Matches: 67, Mismatches: 15, Indels: 19
0.66 0.15 0.19
Matches are distributed among these distances:
16 4 0.06
17 4 0.06
18 15 0.22
19 20 0.30
20 13 0.19
21 6 0.09
22 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTATTTTAAATATTATATA
Found at i:12305954 original size:16 final size:18
Alignment explanation
Indices: 12305928--12305965 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
12305918 TGTTTTTATG
12305928 TTTTAAAAATAATTTT-A
1 TTTTAAAAATAATTTTAA
*
12305945 TTTT-AAAATATTTTTAA
1 TTTTAAAAATAATTTTAA
12305962 TTTT
1 TTTT
12305966 TTTAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAAAAATAATTTTAA
Found at i:12327048 original size:27 final size:27
Alignment explanation
Indices: 12327010--12327065 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
12327000 TTAATTTATA
12327010 TAAAATATGTTACTATTATTATTCATT
1 TAAAATATGTTACTATTATTATTCATT
12327037 TAAAATATGTTACTATTATTATTCATT
1 TAAAATATGTTACTATTATTATTCATT
12327064 TA
1 TA
12327066 TTTATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.52
Consensus pattern (27 bp):
TAAAATATGTTACTATTATTATTCATT
Found at i:12327095 original size:14 final size:12
Alignment explanation
Indices: 12327062--12327088 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12327052 TTATTATTCA
12327062 TTTATTTATATT
1 TTTATTTATATT
12327074 TTTATTTATATT
1 TTTATTTATATT
12327086 TTT
1 TTT
12327089 TAATTTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTATATT
Found at i:12330964 original size:35 final size:35
Alignment explanation
Indices: 12330925--12330994 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
12330915 AGGTATGAGA
* * *
12330925 TAGTTTGAAAATATTCTTGATTTCATATAGATAAC
1 TAGTTCGAAAATATTCCTGATTTCATATAAATAAC
12330960 TAGTTCGAAAATATTCCTGATTTCATATAAATAAC
1 TAGTTCGAAAATATTCCTGATTTCATATAAATAAC
12330995 GGTATCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (35 bp):
TAGTTCGAAAATATTCCTGATTTCATATAAATAAC
Found at i:12333942 original size:21 final size:21
Alignment explanation
Indices: 12333918--12333961 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12333908 TGTTTCTTTT
* *
12333918 ATATTTTATTTTATTATAATA
1 ATATTATATTATATTATAATA
*
12333939 ATATTATATTATATTATATTA
1 ATATTATATTATATTATAATA
12333960 AT
1 AT
12333962 TTCTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTATATTATATTATAATA
Found at i:12333947 original size:5 final size:5
Alignment explanation
Indices: 12333916--12333959 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
12333906 TTTGTTTCTT
* * *
12333916 TTATA TTTTA TTTTA TTATAA TAATA TTATA TTATA TTATA TTA
1 TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTA
12333960 ATTTCTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:12339355 original size:56 final size:56
Alignment explanation
Indices: 12339269--12339381 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
12339259 AATTATTGCG
12339269 AAAGTCTTGGTGAAACGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
1 AAAGTCTTGGTGAAACGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
*
12339325 AAAGTCTTGGTGAAGCGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
1 AAAGTCTTGGTGAAACGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
12339381 A
1 A
12339382 TAGGCTTTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (56 bp):
AAAGTCTTGGTGAAACGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
Found at i:12340702 original size:15 final size:17
Alignment explanation
Indices: 12340682--12340715 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12340672 CTTTTTACTT
12340682 TTCCTC-AAA-TTTTTA
1 TTCCTCAAAACTTTTTA
12340697 TTCCTCAAAACTTTTTA
1 TTCCTCAAAACTTTTTA
12340714 TT
1 TT
12340716 TTCCCCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (17 bp):
TTCCTCAAAACTTTTTA
Found at i:12340887 original size:17 final size:18
Alignment explanation
Indices: 12340865--12340909 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
12340855 TTATTTATAT
12340865 TATTGAATTTT-TTGTCA
1 TATTGAATTTTATTGTCA
*
12340882 TATTGAATATTTATTTTCA
1 TATTGAAT-TTTATTGTCA
*
12340901 AATTGAATT
1 TATTGAATT
12340910 ATTAATTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 4 0.17
19 12 0.50
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (18 bp):
TATTGAATTTTATTGTCA
Found at i:12350445 original size:26 final size:26
Alignment explanation
Indices: 12350416--12350466 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
12350406 AGGTTTTTTA
* *
12350416 TTTTTAAAGTATTAAAATTTTAAAAC
1 TTTTGAAAGTATTAAAATTTGAAAAC
* *
12350442 TTTTGATAGTGTTAAAATTTGAAAA
1 TTTTGAAAGTATTAAAATTTGAAAA
12350467 AAGATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
TTTTGAAAGTATTAAAATTTGAAAAC
Found at i:12361593 original size:28 final size:28
Alignment explanation
Indices: 12361537--12361597 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
12361527 TCTATGAATT
* * *
12361537 AAAAGTTGTAAAATTATTTCTACTAAAA
1 AAAAGTTGTAAAACTATCTCAACTAAAA
*
12361565 AAAAGTTGTAAAACTATCTGAACTTAAAA
1 AAAAGTTGTAAAACTATCTCAAC-TAAAA
12361594 AAAA
1 AAAA
12361598 AAAATGACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAAGTTGTAAAACTATCTCAACTAAAA
Found at i:12364228 original size:12 final size:12
Alignment explanation
Indices: 12364211--12364240 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
12364201 TCAAAATGTT
12364211 ATATTTTTATAA
1 ATATTTTTATAA
12364223 ATA-TTTTATAA
1 ATATTTTTATAA
12364234 ATATTTT
1 ATATTTT
12364241 AATACTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTTTTATAA
Found at i:12364231 original size:11 final size:11
Alignment explanation
Indices: 12364215--12364241 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12364205 AATGTTATAT
12364215 TTTTATAAATA
1 TTTTATAAATA
12364226 TTTTATAAATA
1 TTTTATAAATA
12364237 TTTTA
1 TTTTA
12364242 ATACTTACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTATAAATA
Found at i:12366916 original size:171 final size:171
Alignment explanation
Indices: 12366631--12366976 Score: 595
Period size: 171 Copynumber: 2.0 Consensus size: 171
12366621 GTTTGAAGTA
* * *
12366631 ATATGCGCTCTGTGCCTTATCGATATAAATCGACGTAAACCCCATACATTAATCTTATGACATGC
1 ATATGCGCTCTGTGCCTCATCGATATAAATCGAAGTAAACCCCATACATTAATCCTATGACATGC
* ** *
12366696 CAATTATACGCGACTCTGTTTGAGACTGTTTAATAAAGTATTCAATGATTCTATTCATACATGTC
66 CAATTATACGCAACTCTGTTCAAGACTGTTTAATAAAGAATTCAATGATTCTATTCATACATGTC
12366761 CACATATCATTCATATCACTTTTAATCACATTAACATTAGC
131 CACATATCATTCATATCACTTTTAATCACATTAACATTAGC
*
12366802 ATATGCGCTCTGTGCCTCATCGATATAAATCGAAGTAAACCCCATACATTAATCCTATGGCATGC
1 ATATGCGCTCTGTGCCTCATCGATATAAATCGAAGTAAACCCCATACATTAATCCTATGACATGC
12366867 CAATTATAC-CTAACTCTGTTCAAGACTGTTTAATAAAGAATTCAATGATTCTATTCATACATGT
66 CAATTATACGC-AACTCTGTTCAAGACTGTTTAATAAAGAATTCAATGATTCTATTCATACATGT
*
12366931 CCACATATCATTCATATCACTTTTAATTACATTAACATTAGC
130 CCACATATCATTCATATCACTTTTAATCACATTAACATTAGC
12366973 ATAT
1 ATAT
12366977 CAATATCTTA
Statistics
Matches: 165, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
170 1 0.01
171 164 0.99
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (171 bp):
ATATGCGCTCTGTGCCTCATCGATATAAATCGAAGTAAACCCCATACATTAATCCTATGACATGC
CAATTATACGCAACTCTGTTCAAGACTGTTTAATAAAGAATTCAATGATTCTATTCATACATGTC
CACATATCATTCATATCACTTTTAATCACATTAACATTAGC
Found at i:12369601 original size:24 final size:25
Alignment explanation
Indices: 12369573--12369633 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 25
12369563 AGTAAATTAG
*
12369573 TTATTTTATTACAAGTGTA-C-ATA
1 TTATTTTATTACAAATGTACCAATA
12369596 TCTA-TTTATTACAAATGTACCAATA
1 T-TATTTTATTACAAATGTACCAATA
12369621 TT-TTTTATTACAA
1 TTATTTTATTACAA
12369634 TTGTCATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 15 0.45
24 14 0.42
25 4 0.12
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (25 bp):
TTATTTTATTACAAATGTACCAATA
Found at i:12369885 original size:27 final size:28
Alignment explanation
Indices: 12369829--12369919 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 28
12369819 TTTAATTTAT
* *
12369829 TTAATAATAATACCAATTAAATAATTATAAC
1 TTAAT-ATAAAACCAA-T-AATAATAATAAC
* *
12369860 TTAATATGAAACCATAATAATAATAATAAT
1 TTAATATAAAACC--AATAATAATAATAAC
12369890 TTAATATAAAACCATACTAATAATTAATAA
1 TTAATATAAAACCA-A-TAATAA-TAATAA
12369920 TAATAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 34 0.68
31 12 0.24
32 2 0.04
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (28 bp):
TTAATATAAAACCAATAATAATAATAAC
Found at i:12369894 original size:30 final size:30
Alignment explanation
Indices: 12369848--12369920 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
12369838 ATACCAATTA
* * *
12369848 AATAATTATAACTTAATATGAAACCATAAT
1 AATAATAATAATTTAATATAAAACCATAAT
*
12369878 AATAATAATAATTTAATATAAAACCATACT
1 AATAATAATAATTTAATATAAAACCATAAT
12369908 AATAATTAATAAT
1 AATAA-TAATAAT
12369921 AATAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 31 0.82
31 7 0.18
ACGTcount: A:0.56, C:0.08, G:0.01, T:0.34
Consensus pattern (30 bp):
AATAATAATAATTTAATATAAAACCATAAT
Found at i:12369929 original size:30 final size:30
Alignment explanation
Indices: 12369848--12369930 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
12369838 ATACCAATTA
*
12369848 AATAATT-ATAACTTAATATGAAACCATAAT
1 AATAATTAATAA-TTAATATAAAACCATAAT
*
12369878 AATAA-TAATAATTTAATATAAAACCATACT
1 AATAATTAATAA-TTAATATAAAACCATAAT
12369908 AATAATTAATAA-TAATAATAAAA
1 AATAATTAATAATTAAT-ATAAAA
12369931 TCTTAGATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 5 0.11
30 36 0.77
31 6 0.13
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (30 bp):
AATAATTAATAATTAATATAAAACCATAAT
Found at i:12375501 original size:53 final size:53
Alignment explanation
Indices: 12375421--12375534 Score: 201
Period size: 53 Copynumber: 2.2 Consensus size: 53
12375411 ACTCGGGAAA
* * *
12375421 GCTCACACGAAGTGTGCCTTTACATATAATCGTAACCTTTCTTTTACATCAAT
1 GCTCACACAAAGTGTGCCTTTACATATAACCGTAACCTTTCCTTTACATCAAT
12375474 GCTCACACAAAGTGTGCCTTTACATATAACCGTAACCTTTCCTTTACATCAAT
1 GCTCACACAAAGTGTGCCTTTACATATAACCGTAACCTTTCCTTTACATCAAT
12375527 GCTCACAC
1 GCTCACAC
12375535 GAGCTATAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (53 bp):
GCTCACACAAAGTGTGCCTTTACATATAACCGTAACCTTTCCTTTACATCAAT
Found at i:12377987 original size:109 final size:109
Alignment explanation
Indices: 12377851--12378052 Score: 352
Period size: 109 Copynumber: 1.9 Consensus size: 109
12377841 TAAATTCAAT
*
12377851 AGGATATTTGACAATTTGGTTAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
12377916 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
* *
12377960 AGGATATTT-AGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTTGA-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
*
12378024 ATTTCCAAACGCAAAATATTGCCTTATTT
65 ATTTCCAAACGCAAAACATTGCCTTATTT
12378053 GGAAATATTT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
108 1 0.01
109 87 0.99
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (109 bp):
AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
Found at i:12378666 original size:24 final size:22
Alignment explanation
Indices: 12378639--12378689 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
12378629 ATATATGCAC
*
12378639 ATATATATATTAAGATATATGG
1 ATATATATAATAAGATATATGG
* *
12378661 ATATATATAATAAGATACATAG
1 ATATATATAATAAGATATATGG
12378683 ATATATA
1 ATATATA
12378690 ACTAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (22 bp):
ATATATATAATAAGATATATGG
Found at i:12388090 original size:13 final size:13
Alignment explanation
Indices: 12388072--12388099 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12388062 TATATATATA
12388072 CAAACTAATTTTG
1 CAAACTAATTTTG
12388085 CAAACTAATTTTG
1 CAAACTAATTTTG
12388098 CA
1 CA
12388100 GTTTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (13 bp):
CAAACTAATTTTG
Found at i:12394647 original size:31 final size:30
Alignment explanation
Indices: 12394612--12394674 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
12394602 CAATTTAACA
12394612 AATAAATGCCTCTAAAATAATAATAAAAATT
1 AATAAATGCCTCTAAAATAATAA-AAAAATT
* *
12394643 AATAAATGCCTTTAAAATAATAACAAAATT
1 AATAAATGCCTCTAAAATAATAAAAAAATT
12394673 AA
1 AA
12394675 CAAGAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AATAAATGCCTCTAAAATAATAAAAAAATT
Found at i:12394732 original size:22 final size:22
Alignment explanation
Indices: 12394707--12394749 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12394697 TATCCAAACA
12394707 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
12394729 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
12394750 AATAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:12394762 original size:22 final size:22
Alignment explanation
Indices: 12394714--12394762 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
12394704 ACAATAACAA
* *
12394714 TAAAATAGTAGCAACATAATAG
1 TAAAATAGTAGCAAAATAAGAG
*
12394736 TAAAATGGTAGCAAAATAGAGAG
1 TAAAATAGTAGCAAAATA-AGAG
12394759 -AAAA
1 TAAAA
12394763 CAACAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.57, C:0.06, G:0.18, T:0.18
Consensus pattern (22 bp):
TAAAATAGTAGCAAAATAAGAG
Found at i:12396898 original size:16 final size:16
Alignment explanation
Indices: 12396877--12396911 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12396867 AGATCGACTG
12396877 ATTGACGTGGGTTTGA
1 ATTGACGTGGGTTTGA
12396893 ATTGACGTGGGTTTGA
1 ATTGACGTGGGTTTGA
12396909 ATT
1 ATT
12396912 TTTTCGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.06, G:0.34, T:0.40
Consensus pattern (16 bp):
ATTGACGTGGGTTTGA
Found at i:12397089 original size:19 final size:19
Alignment explanation
Indices: 12397067--12397104 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12397057 TATTTATATA
*
12397067 TTTTAATAATTTTTGTGAT
1 TTTTAATAATTTTTATGAT
12397086 TTTTAATAATTTTTATGAT
1 TTTTAATAATTTTTATGAT
12397105 AAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTTAATAATTTTTATGAT
Found at i:12399482 original size:32 final size:32
Alignment explanation
Indices: 12399386--12399468 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
12399376 TATCCAAATG
* *
12399386 GTACAATTTGAAAATGTTATGTACACTTTGTAT
1 GTACAA-TTGAAAAGGTTATGTACACTTTGTGT
*
12399419 GTACACTTGAAAAGGTTATGTACACTTTGTGT
1 GTACAATTGAAAAGGTTATGTACACTTTGTGT
*
12399451 GTACAATTGGAAAGGTTA
1 GTACAATTGAAAAGGTTA
12399469 GATATGCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 40 0.89
33 5 0.11
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (32 bp):
GTACAATTGAAAAGGTTATGTACACTTTGTGT
Found at i:12400152 original size:12 final size:11
Alignment explanation
Indices: 12400133--12400163 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
12400123 TGTATAAAAC
12400133 TTATTTTATTA
1 TTATTTTATTA
12400144 TTAATTTTATTA
1 TT-ATTTTATTA
12400156 TTATTTTA
1 TTATTTTA
12400164 AAGGCATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:12400178 original size:30 final size:30
Alignment explanation
Indices: 12400144--12400203 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
12400134 TATTTTATTA
12400144 TTAATTTTATTATTATTTTAAAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
* *
12400174 TTAATTTTATTATTATTTTAGAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
12400204 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGCATTTG
Done.