Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1853
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: 113052
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3187 original size:1 final size:1
Alignment explanation
Indices: 3181--3213 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
3171 TTAAATTCGT
3181 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3214 GGCCTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:4239 original size:57 final size:57
Alignment explanation
Indices: 4146--4255 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
4136 CTTCCTGCCT
4146 AACCCCTTGTGAGGTTGTTCACATGTAGGCCCTTGTTGAGCTACAGGTGAGGTTGAC
1 AACCCCTTGTGAGGTTGTTCACATGTAGGCCCTTGTTGAGCTACAGGTGAGGTTGAC
* ** * *
4203 AACCCTTTGTGAGGTTGTTTGCATGTAGGCCTTTGTTGAGCTGCAGGTGAGGT
1 AACCCCTTGTGAGGTTGTTCACATGTAGGCCCTTGTTGAGCTACAGGTGAGGT
4256 GGAATTGGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.17, C:0.18, G:0.32, T:0.33
Consensus pattern (57 bp):
AACCCCTTGTGAGGTTGTTCACATGTAGGCCCTTGTTGAGCTACAGGTGAGGTTGAC
Found at i:7833 original size:3 final size:3
Alignment explanation
Indices: 7825--7860 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
7815 TTAATTTGGT
*
7825 ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7861 TACCCAGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12452 original size:97 final size:96
Alignment explanation
Indices: 12286--12524 Score: 277
Period size: 97 Copynumber: 2.5 Consensus size: 96
12276 TTTTTGGTTC
* ***
12286 AAAAATGGGATTGGAGTATTCC-CTTG-GAGAAATGGGGTTGGAGTATCCCTGACGATTTTAATT
1 AAAAATGGGATTGGAGTA-TCCTC-TGAAAG-AATGGGGTTGGAGTATCCCTGACGATGACAATT
* * *
12349 TAAGCAAAGATAAGATTCAAATCTTGACAAGTTT
63 CAAGCAAAAATAAGATTCAAATCTTAACAAGTTT
* *
12383 AAAAATGGGATTGGAATATCCTCTCGAAAGAATGGGGTTGGAGTATCCCTGATGATGACAATTCA
1 AAAAATGGGATTGGAGTATCCTCT-GAAAGAATGGGGTTGGAGTATCCCTGACGATGACAATTCA
* *
12448 AGCAAAAATAAGATTTAAATTTTAACAAGTTT
65 AGCAAAAATAAGATTCAAATCTTAACAAGTTT
* * * *
12480 -AAAACGGGGTTGGAGTATCCTCTTAGAAGAATGAGGTTGGAGTAT
1 AAAAATGGGATTGGAGTATCCTCTGA-AAGAATGGGGTTGGAGTAT
12525 TCCCGATAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
95 1 0.01
96 42 0.34
97 77 0.63
98 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (96 bp):
AAAAATGGGATTGGAGTATCCTCTGAAAGAATGGGGTTGGAGTATCCCTGACGATGACAATTCAA
GCAAAAATAAGATTCAAATCTTAACAAGTTT
Found at i:14762 original size:51 final size:52
Alignment explanation
Indices: 14642--14780 Score: 201
Period size: 51 Copynumber: 2.7 Consensus size: 52
14632 AATTTCCTAC
* *
14642 ATGTATCGATACATTGAATAATGTATCAATACATTTGGGTCAAAAACCCAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATTTGGGTCAAAAACCCAGA
* * *
14694 ATGTATCGATACGATGAATAATATATCGATA-AGTTTGGGT-TAAAACCCAGA
1 ATGTATCGATACAATGAATAATGTATCGATACA-TTTGGGTCAAAAACCCAGA
*
14745 ATGTATCGATACAATGAAAAATGTATCGATACATTT
1 ATGTATCGATACAATGAATAATGTATCGATACATTT
14781 TCTTTCTAGA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
51 42 0.55
52 35 0.45
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACAATGAATAATGTATCGATACATTTGGGTCAAAAACCCAGA
Found at i:14841 original size:21 final size:21
Alignment explanation
Indices: 14817--14890 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
14807 GACATGGTCC
*
14817 TGTATCGATACATTTCAGACA
1 TGTATCGATACATTTCACACA
**
14838 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACACA
**
14858 TGTATCGATACATTT-ACTTA
1 TGTATCGATACATTTCACACA
14878 TTGTATCGATACA
1 -TGTATCGATACA
14891 AATTATAGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
20 22 0.46
21 26 0.54
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCACACA
Found at i:14860 original size:20 final size:20
Alignment explanation
Indices: 14817--14890 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
14807 GACATGGTCC
***
14817 TGTATCGATACATTTCAGACA
1 TGTATCGATACA-TTCACTTA
14838 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
*
14858 TGTATCGATACATTTACTTA
1 TGTATCGATACATTCACTTA
14878 TTGTATCGATACA
1 -TGTATCGATACA
14891 AATTATAGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 24 0.50
21 24 0.50
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:17763 original size:21 final size:23
Alignment explanation
Indices: 17718--17763 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
17708 TGGAAAATGT
17718 GATAATCATACAATGAACTGATG
1 GATAATCATACAATGAACTGATG
* *
17741 GATAA-CATTCAATG-ACTGCTG
1 GATAATCATACAATGAACTGATG
17762 GA
1 GA
17764 CATATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (23 bp):
GATAATCATACAATGAACTGATG
Found at i:18687 original size:20 final size:20
Alignment explanation
Indices: 18662--18786 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
18652 TTTTAACTAG
18662 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
18682 ATGTATCGATACATATGGGTAAAAAGACAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
*
18713 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
18733 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
* *
18753 ATGTACCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
18773 ATGTATCGATACAT
1 ATGTATCGATACAT
18787 CTGGGTACTT
Statistics
Matches: 83, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 59 0.71
21 1 0.01
22 1 0.01
23 2 0.02
28 2 0.02
29 1 0.01
30 2 0.02
31 15 0.18
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:19578 original size:48 final size:48
Alignment explanation
Indices: 19516--19729 Score: 290
Period size: 48 Copynumber: 4.5 Consensus size: 48
19506 AGAGGAGTGC
** * *
19516 CAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
* *
19564 CAATGTGCTGATTCAAGGCTAGCGACATTAAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
* *
19612 CAATGTGCTGATTCAAGGCCAGCGACATTGAGGTAAGAGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
* * *
19660 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA--TAAAGGT-GC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
* *
19705 CAATATGCTGATTCAATGCCAGCGA
1 CAATGTGCTGATTCAAGGCCAGCGA
19730 TATCAGACTT
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
45 24 0.16
46 5 0.03
48 121 0.81
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
Found at i:19895 original size:28 final size:28
Alignment explanation
Indices: 19832--20059 Score: 285
Period size: 28 Copynumber: 7.8 Consensus size: 28
19822 GGCTTTAAAA
* *
19832 CCACCGACTTGTGTAGGATTTGAAAAGGGTTG
1 CCACTGACTTGTG--GGCTTTG-AAAGGG-TG
* *
19864 CCACTGACTTGTGGGCTTTGAAGGGGTA
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
19892 CCACTGACTTGTGGGCTTTGAAAGGGGATG
1 CCACTGACTTGTGGGCTTTGAAA-GGG-TG
19922 CCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
19950 CCATTGACTTGTGTGCTTTGGAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
19978 CCACTGATTTGTGTGGGTTTGAAAGGGTATG
1 CCACTGACTTGTG-GGCTTTGAAAGGG--TG
20009 CCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
20037 CCACTAACTTGTGGGCTTTGAAA
1 CCACTGACTTGTGGGCTTTGAAA
20060 AGATGAATGT
Statistics
Matches: 174, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
28 85 0.49
29 21 0.12
30 42 0.24
31 14 0.08
32 12 0.07
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGAAAGGGTG
Found at i:19925 original size:58 final size:56
Alignment explanation
Indices: 19831--20059 Score: 287
Period size: 58 Copynumber: 3.9 Consensus size: 56
19821 GGGCTTTAAA
* * *
19831 ACCACCGACTTGTGTAGGATTTGAAAAGGGTTGCCACTGACTTGTGGGCTTTGAAGGGGT
1 ACCACTGACTTGTG--GGCTTTG-AAAGGG-TGCCACTGACTTGTGGGCTTTGAAAGGGT
19891 ACCACTGACTTGTGGGCTTTGAAAGGGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
1 ACCACTGACTTGTGGGCTTTGAAA-GGG-TGCCACTGACTTGTGGGCTTTGAAAGGGT
* * * * * *
19949 GCCATTGACTTGTGTGCTTTGGAAGGGTGCCACTGATTTGTGTGGGTTTGAAAGGGT
1 ACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG-GGCTTTGAAAGGGT
*
20006 ATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAA
1 A--CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
20060 AGATGAATGT
Statistics
Matches: 148, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
56 14 0.09
57 19 0.13
58 66 0.45
59 36 0.24
60 13 0.09
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (56 bp):
ACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
Found at i:20014 original size:87 final size:87
Alignment explanation
Indices: 19832--20056 Score: 310
Period size: 87 Copynumber: 2.6 Consensus size: 87
19822 GGCTTTAAAA
* *
19832 CCACCGACTTGTGTAGGATTTGAAAAGGGTTGCCACTGACTTGTGGGCTTT-GAAGGGGTACCAC
1 CCACTGACTTGTG--GGCTTTG-AAAGGG-TGCCACTGACTTGTGGGCTTTGGAAGGGGTACCAC
19896 TGACTTGTGGGCTTTGAAAGGGGATG
62 TGACTTGTGGGCTTTGAAAGGGGATG
* * * *
19922 CCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGTGCTTTGGAA-GGGTGCCACTGAT
1 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGGAAGGGGTACCACTGAC
* *
19986 TTGTGTGGGTTTGAAAGGGTATG
66 TTGTG-GGCTTTGAAAGGGGATG
*
20009 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
20057 AAAAGATGAA
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
86 35 0.29
87 69 0.57
88 6 0.05
90 12 0.10
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (87 bp):
CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGGAAGGGGTACCACTGAC
TTGTGGGCTTTGAAAGGGGATG
Found at i:20519 original size:108 final size:107
Alignment explanation
Indices: 20360--20553 Score: 334
Period size: 108 Copynumber: 1.8 Consensus size: 107
20350 TTGGTTTCAC
*
20360 TAGAGATTAGGACTTTTTTATTCCATTAGGGATTGTAAACTGTTCAACTCCACTGGGGGTTATAG
1 TAGAGATTAGGACTTTTTTATCCCATTAGGGATTGTAAACTGTTCAACTCCACTGGGGGTTATAG
* * *
20425 GCTATATAGACCTTTTTTGGATTGTAAATTGTTTAACTCTAT
66 ACTATACAAACCTTTTTTGGATTGTAAATTGTTTAACTCTAT
*
20467 TAGAGATTAGGACCTTTTTTATCCCATTAGGGATTGTAAACTGTTCAACTCCACTGGGGGTTGTA
1 TAGAGATTAGGA-CTTTTTTATCCCATTAGGGATTGTAAACTGTTCAACTCCACTGGGGGTTATA
20532 GACTATACAAACCTTTTTTGGA
65 GACTATACAAACCTTTTTTGGA
20554 AATATGACAC
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 12 0.15
108 69 0.85
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (107 bp):
TAGAGATTAGGACTTTTTTATCCCATTAGGGATTGTAAACTGTTCAACTCCACTGGGGGTTATAG
ACTATACAAACCTTTTTTGGATTGTAAATTGTTTAACTCTAT
Found at i:21423 original size:22 final size:21
Alignment explanation
Indices: 21386--21466 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
21376 ACCCCTTTCT
21386 GTTTTTTTGTTATTTTTTTCTTG
1 GTTTTTTTGTT-TTTTTTT-TTG
*
21409 GTTTTTTTG---TTTTTTTAG
1 GTTTTTTTGTTTTTTTTTTTG
* *
21427 GTTTTTTT-TTGGGTTTTTTTAG
1 GTTTTTTTGTT--TTTTTTTTTG
21449 GTTTTTTTGTTTTTTTTT
1 GTTTTTTTGTTTTTTTTT
21467 GGTATGAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
18 10 0.20
19 6 0.12
21 6 0.12
22 17 0.34
23 11 0.22
ACGTcount: A:0.04, C:0.01, G:0.16, T:0.79
Consensus pattern (21 bp):
GTTTTTTTGTTTTTTTTTTTG
Found at i:21432 original size:30 final size:28
Alignment explanation
Indices: 21389--21469 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 28
21379 CCTTTCTGTT
*
21389 TTTTTGTTATTTTTTTCTTGGTTTTTTT-G
1 TTTTT-TTGTTTTTTT-TTGGTTTTTTTAG
21418 TTTTTTTAGGTTTTTTTTTGGGTTTTTTTAGG
1 TTTTTTT--GTTTTTTTTT-GGTTTTTTTA-G
21450 TTTTTTTGTTTTTTTTTGGT
1 TTTTTTTGTTTTTTTTTGGT
21470 ATGAAGAACG
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
28 2 0.04
29 10 0.22
30 26 0.57
32 8 0.17
ACGTcount: A:0.04, C:0.01, G:0.17, T:0.78
Consensus pattern (28 bp):
TTTTTTTGTTTTTTTTTGGTTTTTTTAG
Found at i:21465 original size:10 final size:10
Alignment explanation
Indices: 21387--21467 Score: 65
Period size: 10 Copynumber: 7.8 Consensus size: 10
21377 CCCCTTTCTG
21387 TTTTTTTGTT
1 TTTTTTTGTT
*
21397 ATTTTTTTCTT
1 -TTTTTTTGTT
21408 GGTTTTTTTGTT
1 --TTTTTTTGTT
**
21420 TTTTTAGGTT
1 TTTTTTTGTT
*
21430 TTTTTTTGGGT
1 TTTTTTT-GTT
* *
21441 TTTTTTAG-G
1 TTTTTTTGTT
21450 TTTTTTTGTT
1 TTTTTTTGTT
21460 TTTTTTTG
1 TTTTTTTG
21468 GTATGAAGAA
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
9 7 0.13
10 22 0.40
11 17 0.31
12 9 0.16
ACGTcount: A:0.04, C:0.01, G:0.16, T:0.79
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:27993 original size:52 final size:52
Alignment explanation
Indices: 27727--28036 Score: 232
Period size: 52 Copynumber: 6.0 Consensus size: 52
27717 GATGACAAAG
* * *** * * ** * *
27727 GTGCCAATATACTGATTCAAGGCCAACAATATTAGACTTAAATATTAGAAGA
1 GTGCCAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGAAGATAAAA
* * * ** *
27779 GTACCAATGTGCTGATTCAAGGCCAGCAATATTGTACTTAAAGATA-ATAAAAA
1 GTGCCAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGA-AGAT-AAAA
* * * * ** * *
27832 GTGCTAATATGCTGATTTAAAGCTAATGATATCAGACTTAAAGATGAGAAAA
1 GTGCCAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGAAGATAAAA
* * * * *
27884 GTGCCAATGTGTTGATTCAAGGCTAG-CACATTAGGA-TTAAAGATA-ACAAAA
1 GTGCCAATATGCTGATTCAAGGCTAGTGATATT-GGACTTAAAGA-AGATAAAA
* *
27935 GTGCCAATATGCTTATTCAAGGCTAGTGATATTGGACTTAAAGAAGATAAAG
1 GTGCCAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGAAGATAAAA
* * * *
27987 GTGCCAATATGCTGATTCAAGACCAGTGATATCGGACTTAAAGATGATAA
1 GTGCCAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGAAGATAA
28037 TGTTAGGATC
Statistics
Matches: 202, Mismatches: 48, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
51 42 0.21
52 124 0.61
53 36 0.18
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (52 bp):
GTGCCAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGAAGATAAAA
Found at i:28263 original size:20 final size:20
Alignment explanation
Indices: 28238--28287 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
28228 AAACTTCAAA
28238 GTATCGATACTTAGGTATAT
1 GTATCGATACTTAGGTATAT
*
28258 GTATCGATACTTAGGTATTT
1 GTATCGATACTTAGGTATAT
28278 GTATCGATAC
1 GTATCGATAC
28288 ATTATAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (20 bp):
GTATCGATACTTAGGTATAT
Found at i:28408 original size:19 final size:20
Alignment explanation
Indices: 28380--28431 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
28370 ATCGATAAAA
**
28380 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGGACAAT
*
28399 TGTATTGATACATGGACAAT
1 TGTATCGATACATGGACAAT
28419 TGTATCGATACAT
1 TGTATCGATACAT
28432 AAAACTGGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGGACAAT
Found at i:28486 original size:20 final size:20
Alignment explanation
Indices: 28461--28592 Score: 108
Period size: 20 Copynumber: 7.7 Consensus size: 20
28451 TTACCATTGT
28461 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGGTACA
28481 TTGTATCGATAC-----A-A
1 TTGTATCGATACATGGTACA
28495 -TGTATCGATACATGGTACA
1 TTGTATCGATACATGGTACA
28514 TTGTATCGATAC-----A-A
1 TTGTATCGATACATGGTACA
28528 -TGTATCGATACATGGTACA
1 TTGTATCGATACATGGTACA
28547 TTGTATCGATAC-----A-A
1 TTGTATCGATACATGGTACA
28561 -TGTATCGATACATGGTACA
1 TTGTATCGATACATGGTACA
*
28580 TTGTATTGATACA
1 TTGTATCGATACA
28593 ATGTATTGAT
Statistics
Matches: 90, Mismatches: 1, Indels: 42
0.68 0.01 0.32
Matches are distributed among these distances:
13 33 0.37
14 3 0.03
15 3 0.03
18 3 0.03
19 3 0.03
20 45 0.50
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGTACA
Found at i:28498 original size:13 final size:13
Alignment explanation
Indices: 28477--28572 Score: 81
Period size: 13 Copynumber: 8.3 Consensus size: 13
28467 CGATACATGG
*
28477 TACATTGTATCGA
1 TACAATGTATCGA
28490 TACAATGTATCGA
1 TACAATGTATCGA
28503 TAC-ATG----G-
1 TACAATGTATCGA
*
28510 TACATTGTATCGA
1 TACAATGTATCGA
28523 TACAATGTATCGA
1 TACAATGTATCGA
28536 TAC-ATG----G-
1 TACAATGTATCGA
*
28543 TACATTGTATCGA
1 TACAATGTATCGA
28556 TACAATGTATCGA
1 TACAATGTATCGA
28569 TACA
1 TACA
28573 TGGTACATTG
Statistics
Matches: 66, Mismatches: 5, Indels: 24
0.69 0.05 0.25
Matches are distributed among these distances:
7 6 0.09
8 6 0.09
12 8 0.12
13 46 0.70
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:28504 original size:33 final size:33
Alignment explanation
Indices: 28462--28625 Score: 292
Period size: 33 Copynumber: 5.0 Consensus size: 33
28452 TACCATTGTT
28462 TGTATCGATACATGGTACATTGTATCGATACAA
1 TGTATCGATACATGGTACATTGTATCGATACAA
28495 TGTATCGATACATGGTACATTGTATCGATACAA
1 TGTATCGATACATGGTACATTGTATCGATACAA
28528 TGTATCGATACATGGTACATTGTATCGATACAA
1 TGTATCGATACATGGTACATTGTATCGATACAA
*
28561 TGTATCGATACATGGTACATTGTATTGATACAA
1 TGTATCGATACATGGTACATTGTATCGATACAA
* * *
28594 TGTATTGATACATGATAAATTGTATCGATACA
1 TGTATCGATACATGGTACATTGTATCGATACA
28626 TTGCTTCAAA
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 126 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGGTACATTGTATCGATACAA
Found at i:28597 original size:13 final size:13
Alignment explanation
Indices: 28576--28605 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28566 CGATACATGG
*
28576 TACATTGTATTGA
1 TACAATGTATTGA
28589 TACAATGTATTGA
1 TACAATGTATTGA
28602 TACA
1 TACA
28606 TGATAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (13 bp):
TACAATGTATTGA
Found at i:30490 original size:29 final size:29
Alignment explanation
Indices: 30448--30505 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
30438 CCAAAGAAGA
30448 AAGCCATGGCAGCCACATGGAGTGATAGC
1 AAGCCATGGCAGCCACATGGAGTGATAGC
30477 AAGCCATGGCAGCCACATGGAGTGATAGC
1 AAGCCATGGCAGCCACATGGAGTGATAGC
30506 GACTCATCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.31, T:0.14
Consensus pattern (29 bp):
AAGCCATGGCAGCCACATGGAGTGATAGC
Found at i:37296 original size:13 final size:13
Alignment explanation
Indices: 37278--37302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37268 CACTATGCTT
37278 TGTATCGATACAA
1 TGTATCGATACAA
37291 TGTATCGATACA
1 TGTATCGATACA
37303 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:37389 original size:13 final size:13
Alignment explanation
Indices: 37368--37397 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
37358 CGATATATGG
*
37368 TACATTGTATCGA
1 TACAATGTATCGA
37381 TACAATGTATCGA
1 TACAATGTATCGA
37394 TACA
1 TACA
37398 TGATGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:37395 original size:33 final size:33
Alignment explanation
Indices: 37353--37417 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
37343 TACCACTGTT
* * *
37353 TGTATCGATATATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGATGA-ATTATATCGATACAA
37386 TGTATCGATACATGATGAATTATATCGATACA
1 TGTATCGATACATGATGAATTATATCGATACA
37418 TTGCTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTATATCGATACAA
Found at i:38389 original size:52 final size:52
Alignment explanation
Indices: 38149--38403 Score: 285
Period size: 52 Copynumber: 4.9 Consensus size: 52
38139 TGAACTTTCA
* * * *
38149 GATAAAAGTGCCAATATGTTGATTTAGGGCCAGCGATATCAGACTTAAAAAT
1 GATAAAGGTGCCAATATGTTGATTTAAGGCCAACGATATTAGACTTAAAAAT
* *
38201 GATAAAGGTGCCAATATGTTGATTTAAGGCCAGCGATATCAGACTTAAAAAT
1 GATAAAGGTGCCAATATGTTGATTTAAGGCCAACGATATTAGACTTAAAAAT
* * * *
38253 GATAAAGGTGCCAATATGTTGATTTAAGGCCAAAGATATTAGTCTTGAAGAT
1 GATAAAGGTGCCAATATGTTGATTTAAGGCCAACGATATTAGACTTAAAAAT
* * ** * * * * *
38305 GATAAATGTGCTAATATACTAATTCAAGGCCAACAATATTGGACTTAAAGAT
1 GATAAAGGTGCCAATATGTTGATTTAAGGCCAACGATATTAGACTTAAAAAT
* * * * * *
38357 GAGAAGGGTGCCAATATGCTAATTTAAGGCCAACGACATTGGACTTA
1 GATAAAGGTGCCAATATGTTGATTTAAGGCCAACGATATTAGACTTA
38404 GAAGGAGATG
Statistics
Matches: 176, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 176 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (52 bp):
GATAAAGGTGCCAATATGTTGATTTAAGGCCAACGATATTAGACTTAAAAAT
Found at i:38537 original size:31 final size:31
Alignment explanation
Indices: 38469--38556 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 31
38459 ATTAAAAGGA
38469 GTTGCCACCAACTTGCGTGGGCTTTTGAGAGG
1 GTTGCCACCAACTTG-GTGGGCTTTTGAGAGG
* *
38501 GTTGCCATCGACTTGTGTGGGCTTTTGAG-GG
1 GTTGCCACCAACTTG-GTGGGCTTTTGAGAGG
*
38532 GTTGCCACCTACTTGGATGGGCTTT
1 GTTGCCACCAACTTGG-TGGGCTTT
38557 AAAAAGGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 1 0.02
31 23 0.46
32 26 0.52
ACGTcount: A:0.12, C:0.20, G:0.34, T:0.33
Consensus pattern (31 bp):
GTTGCCACCAACTTGGTGGGCTTTTGAGAGG
Found at i:40105 original size:21 final size:21
Alignment explanation
Indices: 40051--40108 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
40041 TTTTTAATTA
***
40051 TTTTTGATTGATTTTTATTTTT
1 TTTTTGATTGATTTTT-TGCCT
*
40073 TTTTTGA--AATTTTTTGCCT
1 TTTTTGATTGATTTTTTGCCT
40092 TTTTTGATTGATTTTTT
1 TTTTTGATTGATTTTTT
40109 TTGATATGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 9 0.31
20 6 0.21
21 7 0.24
22 7 0.24
ACGTcount: A:0.14, C:0.03, G:0.10, T:0.72
Consensus pattern (21 bp):
TTTTTGATTGATTTTTTGCCT
Found at i:40107 original size:22 final size:19
Alignment explanation
Indices: 40051--40110 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 19
40041 TTTTTAATTA
40051 TTTTTGATTGATTTTTATTT
1 TTTTTGATTGATTTTT-TTT
*
40071 TTTTT--TTGAAATTTTTTGCCT
1 TTTTTGATTG--ATTTTTT--TT
40092 TTTTTGATTGATTTTTTTT
1 TTTTTGATTGATTTTTTTT
40111 GATATGATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 13
0.68 0.04 0.28
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 11 0.34
21 13 0.41
23 3 0.09
ACGTcount: A:0.13, C:0.03, G:0.10, T:0.73
Consensus pattern (19 bp):
TTTTTGATTGATTTTTTTT
Found at i:47380 original size:150 final size:149
Alignment explanation
Indices: 46941--47448 Score: 452
Period size: 155 Copynumber: 3.3 Consensus size: 149
46931 ATGCCCCGAG
* * * * *
46941 GGGATACCTTTGACGTAAAAGTACCTTATACCTCTAAATAACTTAAAAAGGATTATAGATGAGAT
1 GGGATACTTTTGACGTAAAAGTACCTGATACCCCTAAAAAACTTAAAAAGG--TA-A-AAG-GAT
* * * *
47006 GAACCTATCCTAAATACCCACCTTCGGCATAAAAGTGGACTTGACGACAACCTGGGACTCGGTTC
61 GAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACTCGATGACAACCTAGGACTCGGTTC
47071 TAGAAAATTATCAAAATACCCTTA
126 TAGAAAATTATCAAAATACCCTTA
* * * * *
47095 GGGAATA-TCTTTGACGTAGAAGT-GCTCGATATCCCTAAAAGACTTAAAAATGTTACAAAATAG
1 GGG-ATACT-TTTGACGTAAAAGTACCT-GATACCCCTAAAAAACTTAAAAA-GGT---AAA-AG
* * * * * *
47158 GATGAACATATCCTAAATACCCACCTTCGGCATTAAGGCGGACTCAATGACAATCTAGGACTGGG
58 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACTCGATGACAACCTAGGACTCGG
* * *
47223 TTCTAGAAATTTA-CAAAAATGCCTTTA
123 TTCTAGAAAATTATC-AAAATACCCTTA
* * *
47250 GAGGATACTTTTGACATAAAAGTACCTGACACCCCTAAAAAACTTGAAAAGGTAAAAGGATGAAC
1 G-GGATACTTTTGACGTAAAAGTACCTGATACCCCTAAAAAACTTAAAAAGGTAAAAGGATGAAC
* * * * * * *
47315 CTATCCTAAATGCACACCTTCGGAATAAAAGCAGACTCGGTGACAACCTAGGACTCGATTTTAGA
65 CTATCCTAAATACCCACCTTCGGCATAAAAGCGGACTCGATGACAACCTAGGACTCGGTTCTAG-
*
47380 AAAATTATGAAAATAGCCC-TA
129 AAAATTATCAAAATA-CCCTTA
* ** * **
47401 GGGGATACCTGCGACGTAAAAGTGCCTG--ACCCCTAAATGACTTAAAAA
1 -GGGATACTTTTGACGTAAAAGTACCTGATACCCCTAAAAAACTTAAAAA
47449 AGGATTTATA
Statistics
Matches: 282, Mismatches: 56, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
149 17 0.06
150 60 0.21
151 37 0.13
152 3 0.01
154 9 0.03
155 147 0.52
156 8 0.03
157 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (149 bp):
GGGATACTTTTGACGTAAAAGTACCTGATACCCCTAAAAAACTTAAAAAGGTAAAAGGATGAACC
TATCCTAAATACCCACCTTCGGCATAAAAGCGGACTCGATGACAACCTAGGACTCGGTTCTAGAA
AATTATCAAAATACCCTTA
Found at i:49619 original size:166 final size:165
Alignment explanation
Indices: 49413--50058 Score: 845
Period size: 167 Copynumber: 3.9 Consensus size: 165
49403 GATTTTTCCG
* * * *
49413 AAAAAAAGGG-ATTTCAA-AGAAAAACT-ATAAAACTCATGAAAATGAATGAAATTTTGAAAATT
1 AAAAAAAGGGAATTTCAAGA-AAAAATTCA-AAAACCCATGAAAATGAATGAATTTTTGAAAAAT
* * * * * *
49475 GATTTAAAATTAAATAAATAATAATATTTTATGGATTCTAAAAATTAAAAACTAAGAAAAATCCT
64 AATTTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCT
49540 CTCAAAAAAATTTACGGAGTAAAAAACTCTATTTTTT
129 CTCAAAAAAATTTACGGAGTAAAAAACTCTATTTTTT
*
49577 AAAAACAAGGGAATTTCAAGAAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAATA
1 AAAAA-AAGGGAATTTCAAGAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAAATA
* * *
49642 ATTTATTATAAAATCAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCC-C
65 ATTTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTC
*
49706 TCCAAAAAAATTTACGGAGTAGAAAACTCTATTTTTT
130 T-CAAAAAAATTTACGGAGTAAAAAACTCTATTTTTT
** * * *
49743 GGAAATAGGGAAATTTCACGGAAAAAATTCAAAAACCTATGAAAATGAATGAATTTTTGAAAAAT
1 AAAAAAAGGG-AATTTCA-AGAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAAAT
* * *
49808 AATTTATTATGAAATAAATAATAATATTTTAAGAATTTTAAAAATTAAAAACCAAGAAAAATCCC
64 AATTTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCT
* *
49873 CTCAAAAAAATTTACGGACTAGAAAAA-TCTATTTTTCG
129 CTCAAAAAAATTTACGGAGTA-AAAAACTCTATTTTT-T
* * * *
49911 AAAATAAGAGAATTTCAAGAAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAACTG
1 AAAAAAAGGGAATTTCAAG-AAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAAATA
* * * * * *
49976 ATTTAATATGAATTAAATAGTAATATTTGATGAATTTTAAAAATTTTAAACCCATG-AAAATCCT
65 ATTTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAA-TTAAAAACCAAGAAAAATCCT
50040 CTCAAAAAAATTTACGGAG
129 CTCAAAAAAATTTACGGAG
50059 AAGAGAACTC
Statistics
Matches: 425, Mismatches: 45, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
164 5 0.01
165 11 0.03
166 144 0.34
167 245 0.58
168 20 0.05
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (165 bp):
AAAAAAAGGGAATTTCAAGAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAAATAA
TTTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCT
CAAAAAAATTTACGGAGTAAAAAACTCTATTTTTT
Found at i:49825 original size:333 final size:334
Alignment explanation
Indices: 49448--50068 Score: 917
Period size: 333 Copynumber: 1.9 Consensus size: 334
49438 TATAAAACTC
* * * * *
49448 ATGAAAATGAATGAAATTTTGAAAATTGATTTAAAATTAAATAAATAATAATATTTTATGGATTC
1 ATGAAAATGAATGAAATTTTGAAAAATAATTTAAAATGAAATAAATAATAATATTTTAAGAATTC
* * * *
49513 TAAAAATTAAAAACTAAGAAAAATCCTCTCAAAAAAATTTACGGAGTA-AAAAACTCTATTTTTT
66 TAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTAGAAAAA-TCTATTTTTC
*
49577 AAAAACAAGGGAATTTCAAG-AAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAAT
130 AAAAACAAGAGAATTTCAAGAAAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAAT
* * *
49641 AATTTATTATAAAATCAATAATAATATTTTATGAATTTTAAAAA-TTAAAAACCAAGAAAAATCC
195 AATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTTAAAAACCAAG-AAAATCC
*
49705 -CTCCAAAAAAATTTACGGAGTAGAAAACTCTATTTTTTGGAAATAGGGAAATTTCACGGAAAAA
259 TCT-CAAAAAAATTTACGGAGAAGAAAACTCTATTTTTTGGAAATAGGGAAATTTCACGGAAAAA
49769 ATTCAAAAACCT
323 ATTCAAAAACCT
* ** *
49781 ATGAAAATGAATGAATTTTTGAAAAATAATTTATTATGAAATAAATAATAATATTTTAAGAATTT
1 ATGAAAATGAATGAAATTTTGAAAAATAATTTAAAATGAAATAAATAATAATATTTTAAGAATTC
*
49846 TAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTAGAAAAATCTATTTTTCG
66 TAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTAGAAAAATCTATTTTTCA
* * * *
49911 AAAATAAGAGAATTTCAAGAAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAACTG
131 AAAACAAGAGAATTTCAAGAAAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAATA
* * * * * *
49976 ATTTAATATGAATTAAATAGTAATATTTGATGAATTTTAAAAATTTTAAACCCATGAAAATCCTC
196 ATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTTAAAAACCAAGAAAATCCTC
*
50041 TCAAAAAAATTTACGGAGAAGAGAACTC
261 TCAAAAAAATTTACGGAGAAGAAAACTC
50069 CGTAATTTGA
Statistics
Matches: 254, Mismatches: 30, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
333 127 0.50
334 116 0.46
335 11 0.04
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (334 bp):
ATGAAAATGAATGAAATTTTGAAAAATAATTTAAAATGAAATAAATAATAATATTTTAAGAATTC
TAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTAGAAAAATCTATTTTTCA
AAAACAAGAGAATTTCAAGAAAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAATA
ATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTTAAAAACCAAGAAAATCCTC
TCAAAAAAATTTACGGAGAAGAAAACTCTATTTTTTGGAAATAGGGAAATTTCACGGAAAAAATT
CAAAAACCT
Found at i:50167 original size:333 final size:332
Alignment explanation
Indices: 49486--50169 Score: 821
Period size: 333 Copynumber: 2.1 Consensus size: 332
49476 ATTTAAAATT
* * * *
49486 AAATAAATAATAATATTTTATGGATTCTAAAAATTAAAAACTAAGAAAAATCCTCTCAAAAAAAT
1 AAATAAATAATAATATTTTAAGAATTCTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAAT
* * *
49551 TTACGGAGTAAAAAACTCTATTTTTTAAAAACAAGGGAATTTCAAGAAAAAATTCAAAAACCCAT
66 TTACGGACTAAAAAACTCTATTTTTCAAAAACAAGAGAATTTCAAGAAAAAATTCAAAAACCCAT
* * *
49616 GAAAATAAATGAATTTTTGAAAAATAATTTATTATAAAATCAATAATAATATTTTATGAATTTTA
131 GAAAATAAATGAATTTTTGAAAAATAATTTAATATAAAATAAATAATAATATTTGATGAATTTTA
* * ** *
49681 AAAATTAAAAACCAAGAAAAATCCCTCCAAAAAAATTTACGGAGTAGAAAACTCTATTTTTTGGA
196 AAAATTAAAAACCAAGAAAAATCCCTCCAAAAAAATTTACGGAGAAGAAAACTCCATAATTTGAA
* * * * * * *
49746 AATAGGGAAATTTCACGGAAAAAATTCAAAAACCTATGAAAATGAATGAATTTTTGAAAAATAAT
261 AATAGGGAAATTTCACGAAAAAAAATCAAAAACCTATAAAAATAAAAGAAATTTTCAAAAATAAT
49811 TTATTATG
326 TTA-TATG
*
49819 AAATAAATAATAATATTTTAAGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAAT
1 AAATAAATAATAATATTTTAAGAATTCTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAAT
* *
49884 TTACGGACTAGAAAAA-TCTATTTTTCGAAAATAAGAGAATTTCAAGAAAAAAATTCAAAAACCC
66 TTACGGACTA-AAAAACTCTATTTTTCAAAAACAAGAGAATTTCAAG-AAAAAATTCAAAAACCC
* * * * * *
49948 ATGAAAATGAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAGTAATATTTGATGAATTT
129 ATGAAAATAAATGAATTTTTGAAAAATAATTTAATATAAAATAAATAATAATATTTGATGAATTT
* * * * *
50013 TAAAAATTTTAAACCCATG-AAAAT-CCTCTCAAAAAAATTTACGGAGAAGAGAACTCCGTAATT
194 TAAAAA-TTAAAAACCAAGAAAAATCCCTC-CAAAAAAATTTACGGAGAAGAAAACTCCATAATT
*
50076 TGAAAATATGAGG-AA-TTC-C-AAAAGAAAATCAATAA-CTCA-AAAAATAAAAGAAAATTTTC
257 TGAAAATA-G-GGAAATTTCACGAAAA-AAAATCAAAAACCT-ATAAAAATAAAAG-AAATTTTC
* *
50135 AAAACTGATTTA-ATG
317 AAAAATAATTTATATG
* *
50150 AGATTTAAATTATAATATTT
1 A-A-ATAAATAATAATATTT
50170 GAAAACTTTT
Statistics
Matches: 299, Mismatches: 41, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
331 4 0.01
332 14 0.05
333 140 0.47
334 127 0.42
335 12 0.04
336 2 0.01
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (332 bp):
AAATAAATAATAATATTTTAAGAATTCTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAAT
TTACGGACTAAAAAACTCTATTTTTCAAAAACAAGAGAATTTCAAGAAAAAATTCAAAAACCCAT
GAAAATAAATGAATTTTTGAAAAATAATTTAATATAAAATAAATAATAATATTTGATGAATTTTA
AAAATTAAAAACCAAGAAAAATCCCTCCAAAAAAATTTACGGAGAAGAAAACTCCATAATTTGAA
AATAGGGAAATTTCACGAAAAAAAATCAAAAACCTATAAAAATAAAAGAAATTTTCAAAAATAAT
TTATATG
Found at i:51726 original size:13 final size:13
Alignment explanation
Indices: 51708--51764 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
51698 TTCAACAATT
51708 TGTATCGATACAA
1 TGTATCGATACAA
51721 TGTATCGATACATAA
1 TGTATCGATAC--AA
51736 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
51753 TGTATCGATACA
1 TGTATCGATACA
51765 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:51745 original size:19 final size:18
Alignment explanation
Indices: 51721--51783 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
51711 ATCGATACAA
51721 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
51740 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
51753 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
51772 TGTATCGATACA
1 TGTATCGATACA
51784 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:51748 original size:32 final size:32
Alignment explanation
Indices: 51707--51791 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
51697 TTTCAACAAT
51707 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
51739 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
51771 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
51792 CTACGAAGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:55584 original size:20 final size:20
Alignment explanation
Indices: 55559--55610 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
55549 TTACCCAGAT
55559 GTATCGATACATTATTCAAG
1 GTATCGATACATTATTCAAG
* *
55579 GTATCGATATATTATTCAAT
1 GTATCGATACATTATTCAAG
*
55599 GTATTGATACAT
1 GTATCGATACAT
55611 GCAGGCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (20 bp):
GTATCGATACATTATTCAAG
Found at i:61689 original size:27 final size:24
Alignment explanation
Indices: 61647--61701 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 24
61637 ACTATTTTGA
61647 TTTCGAGGATACTCCAACCTCGCT
1 TTTCGAGGATACTCCAACCTCGCT
61671 CTTTCGAGGGAATACTCCAACCTCGCT
1 -TTTCGA-GG-ATACTCCAACCTCGCT
61698 TTTC
1 TTTC
61702 TTCAAGATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 6 0.21
26 6 0.21
27 16 0.57
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (24 bp):
TTTCGAGGATACTCCAACCTCGCT
Found at i:66932 original size:86 final size:86
Alignment explanation
Indices: 66799--66958 Score: 221
Period size: 86 Copynumber: 1.9 Consensus size: 86
66789 CCCCTCGGAG
* * **** * * *
66799 GAATGGGGTTGGAGTATCCCTGATGATTTTGATTCAGGCAAAGATAAGAATCAAATCTTGACAAG
1 GAATAGGGTTGGAGTATCCCTAATGATAACAATTCAAGCAAAAATAAGAATCAAATCATGACAAG
66864 TTTAAAAATATCCTCTTAGAA
66 TTTAAAAATATCCTCTTAGAA
* *
66885 GAATAGGGTTGGAGTATCCCTAATGATAACAATTCAAGCAAAAATAAGATTTAAATCATGACAAG
1 GAATAGGGTTGGAGTATCCCTAATGATAACAATTCAAGCAAAAATAAGAATCAAATCATGACAAG
66950 TTTAAAAAT
66 TTTAAAAAT
66959 GGGGTTGGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 63 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (86 bp):
GAATAGGGTTGGAGTATCCCTAATGATAACAATTCAAGCAAAAATAAGAATCAAATCATGACAAG
TTTAAAAATATCCTCTTAGAA
Found at i:69241 original size:52 final size:51
Alignment explanation
Indices: 69182--69320 Score: 197
Period size: 51 Copynumber: 2.7 Consensus size: 51
69172 AATTACCTGC
*
69182 ATGTATCGATACATTGAAAAATGTATTGATATATTTAGGTCAAAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATTGATATATTTAGGTC-AAAACCCAAA
* * * * *
69234 ATGTATCGATACAATGAATAATGTATCGATAAATTTAGGTCAAAACCTAGA
1 ATGTATCGATACAATGAAAAATGTATTGATATATTTAGGTCAAAACCCAAA
* *
69285 ATGTATCGATACAATGAAAAATGGATTGATGTATTT
1 ATGTATCGATACAATGAAAAATGTATTGATATATTT
69321 TCTTTCTAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 39 0.51
52 37 0.49
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAAATGTATTGATATATTTAGGTCAAAACCCAAA
Found at i:69298 original size:51 final size:52
Alignment explanation
Indices: 69182--69307 Score: 191
Period size: 52 Copynumber: 2.4 Consensus size: 52
69172 AATTACCTGC
* * *
69182 ATGTATCGATACATTGAAAAATGTATTGATATATTTAGGTCAAAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATAAATTTAGGTCAAAAACCCAAA
* * *
69234 ATGTATCGATACAATGAATAATGTATCGATAAATTTAGGTC-AAAACCTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATAAATTTAGGTCAAAAACCCAAA
69285 ATGTATCGATACAATGAAAAATG
1 ATGTATCGATACAATGAAAAATG
69308 GATTGATGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
51 30 0.45
52 37 0.55
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCGATAAATTTAGGTCAAAAACCCAAA
Found at i:69402 original size:20 final size:20
Alignment explanation
Indices: 69377--69423 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
69367 CATTTTAGAC
69377 ATGTATCAATACATTCAATT
1 ATGTATCAATACATTCAATT
* *
69397 ATGTATCGATACATTCACTT
1 ATGTATCAATACATTCAATT
69417 ATTGTAT
1 A-TGTAT
69424 AGATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (20 bp):
ATGTATCAATACATTCAATT
Found at i:69428 original size:21 final size:20
Alignment explanation
Indices: 69385--69428 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
69375 ACATGTATCA
*
69385 ATACATTCAATTATGTATCG
1 ATACATTCAATTATGTATAG
*
69405 ATACATTCACTTATTGTATAG
1 ATACATTCAATTA-TGTATAG
69426 ATA
1 ATA
69429 AAAATTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (20 bp):
ATACATTCAATTATGTATAG
Found at i:72069 original size:27 final size:27
Alignment explanation
Indices: 72030--72082 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
72020 ATTAAAAAAG
* *
72030 AGTCCAACTTAAAAAATCAAAGTCAAA
1 AGTCAAACATAAAAAATCAAAGTCAAA
**
72057 AGTCAAACATAAAAGGTCAAAGTCAA
1 AGTCAAACATAAAAAATCAAAGTCAA
72083 CAAAGAGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.17
Consensus pattern (27 bp):
AGTCAAACATAAAAAATCAAAGTCAAA
Found at i:73865 original size:20 final size:20
Alignment explanation
Indices: 73840--73879 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
73830 TAACTAAGAT
73840 AATTCGGGATATGTCTCGAA
1 AATTCGGGATATGTCTCGAA
73860 AATTCGGGATATGTCTCGAA
1 AATTCGGGATATGTCTCGAA
73880 TTGTCATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
AATTCGGGATATGTCTCGAA
Found at i:82524 original size:23 final size:23
Alignment explanation
Indices: 82496--82553 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
82486 CATCAATCGA
** *
82496 TTTTTCCAAATTTTTAAAATATT
1 TTTTTCCAAAAGTTTAAAATATC
* *
82519 TTTTTCAAAAAGTTTACAATATC
1 TTTTTCCAAAAGTTTAAAATATC
*
82542 TCTTTCCAAAAG
1 TTTTTCCAAAAG
82554 GGAATGGTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (23 bp):
TTTTTCCAAAAGTTTAAAATATC
Found at i:83248 original size:87 final size:86
Alignment explanation
Indices: 83115--83340 Score: 242
Period size: 87 Copynumber: 2.6 Consensus size: 86
83105 TTAGTATTAC
* * *
83115 TTTATCCTTAGGGAAACTCCATCCCTACTCCTCTGAAGAGACACTCCAACCCCACTCTTCAA-AA
1 TTTATCCTTGGGGAAACTCCATCCCTACTCTTC-GAAGAGATACTCCAACCCCACTC-T-AACAA
**
83179 AAATTCAAATTTT-TTTGTACAAT
63 AAATTCAAATTTTCTTCATACAAT
* * * * *
83202 TTTATCCTTGGGGAAACTCCATCCTTACTGTTCCAAGGAGATACTCCAACCCTATTCTAACAAAA
1 TTTATCCTTGGGGAAACTCCATCCCTACTCTTCGAA-GAGATACTCCAACCCCACTCTAACAAAA
* *
83267 ATTTAAATTTTCCTTCATATAAT
65 ATTCAAATTTT-CTTCATACAAT
* * *
83290 TTTATCCTCGGGAAAACTCTATCCCTACTACTTCGAAG-GATACTCCAACCC
1 TTTATCCTTGGGGAAACTCCATCCCTACT-CTTCGAAGAGATACTCCAACCC
83341 TTTTTTCCAT
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
85 2 0.02
86 17 0.15
87 59 0.51
88 33 0.28
89 5 0.04
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (86 bp):
TTTATCCTTGGGGAAACTCCATCCCTACTCTTCGAAGAGATACTCCAACCCCACTCTAACAAAAA
TTCAAATTTTCTTCATACAAT
Found at i:83369 original size:87 final size:87
Alignment explanation
Indices: 83115--83397 Score: 222
Period size: 87 Copynumber: 3.3 Consensus size: 87
83105 TTAGTATTAC
* * * * *
83115 TTTATCCTTAGGG-AAACTCCATCCCTACTCCTCTGAA-GAGACACTCCAACCCCACTCTTCAA-
1 TTTATCCTT-GGGAAAACTCCATCCCTACTCTTC-CAAGGAGATACTCCAACCCTATTC-T-AAC
* *** * *
83177 AAAAATTCAAAT-TTTTTTGTACAAT
62 AAAAATTTAAATCTACCTTCTATAAT
* * *
83202 TTTATCCTTGGGGAAACTCCATCCTTACTGTTCCAAGGAGATACTCCAACCCTATTCTAACAAAA
1 TTTATCCTTGGGAAAACTCCATCCCTACTCTTCCAAGGAGATACTCCAACCCTATTCTAACAAAA
* *
83267 ATTTAAATTTTCCTTCATATAAT
66 ATTTAAATCTACCTTC-TATAAT
* * * * ** *
83290 TTTATCCTCGGGAAAACTCTATCCCTACTACTTCGAA-G-GATACTCCAACCCT-TTTTTCCATA
1 TTTATCCTTGGGAAAACTCCATCCCTACT-CTTCCAAGGAGATACTCCAACCCTATTCTAACAAA
*
83352 AATTTCAAATCTACCTTCTATAGT
65 AATTT-AAATCTACCTTCTATAAT
83376 TTTAT-CTATGGGAAAACTCCAT
1 TTTATCCT-TGGGAAAACTCCAT
83398 TTTCATTATT
Statistics
Matches: 161, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
85 4 0.02
86 50 0.31
87 71 0.44
88 31 0.19
89 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (87 bp):
TTTATCCTTGGGAAAACTCCATCCCTACTCTTCCAAGGAGATACTCCAACCCTATTCTAACAAAA
ATTTAAATCTACCTTCTATAAT
Found at i:84224 original size:13 final size:13
Alignment explanation
Indices: 84206--84230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84196 GTTTTGAGTT
84206 TCCTGAGGCATTA
1 TCCTGAGGCATTA
84219 TCCTGAGGCATT
1 TCCTGAGGCATT
84231 CGAAACCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (13 bp):
TCCTGAGGCATTA
Found at i:88556 original size:13 final size:13
Alignment explanation
Indices: 88528--88583 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
88518 TGCTTGGAAT
88528 TTTCTTTTTTT-C
1 TTTCTTTTTTTCC
88540 --TCTTTTTTTCC
1 TTTCTTTTTTTCC
*
88551 TTTCTTTTTTTCT
1 TTTCTTTTTTTCC
88564 TTTCTTTTTTGTCAC
1 TTTCTTTTTT-TC-C
88579 TTTCT
1 TTTCT
88584 GCCAACCTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 20 0.54
14 2 0.05
15 5 0.14
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTCTTTTTTTCC
Found at i:88558 original size:23 final size:24
Alignment explanation
Indices: 88528--88572 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
88518 TGCTTGGAAT
88528 TTTCTTTTTTTCTCTT-TTTTTCC
1 TTTCTTTTTTTCTCTTCTTTTTCC
*
88551 TTTCTTTTTTTCTTTTCTTTTT
1 TTTCTTTTTTTCTCTTCTTTTT
88573 TGTCACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTCTTTTTTTCTCTTCTTTTTCC
Found at i:88567 original size:28 final size:28
Alignment explanation
Indices: 88527--88583 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
88517 ATGCTTGGAA
*
88527 TTTTCTTTTTTTCTCTTTTTTTC-CTTTC
1 TTTTCTTTTTTTCT-TTTTTGTCACTTTC
88555 TTTT-TTTCTTTTCTTTTTTGTCACTTTC
1 TTTTCTTT-TTTTCTTTTTTGTCACTTTC
88583 T
1 T
88584 GCCAACCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (28 bp):
TTTTCTTTTTTTCTTTTTTGTCACTTTC
Found at i:91321 original size:13 final size:13
Alignment explanation
Indices: 91303--91327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
91293 AATTTTTTGT
91303 GTATCGATACATC
1 GTATCGATACATC
91316 GTATCGATACAT
1 GTATCGATACAT
91328 ACTTGCTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACATC
Found at i:93704 original size:21 final size:21
Alignment explanation
Indices: 93680--93726 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
93670 TTTAATGCTG
93680 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
93700 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
93721 ATTTTG
1 ATTTTG
93727 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:93865 original size:13 final size:13
Alignment explanation
Indices: 93847--93885 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
93837 ATAATCACCC
*
93847 TGTATCGATACAG
1 TGTATCGATACAA
93860 TGTATCGATACAA
1 TGTATCGATACAA
93873 TGTATCGATACAA
1 TGTATCGATACAA
93886 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:93896 original size:20 final size:20
Alignment explanation
Indices: 93871--93949 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
93861 GTATCGATAC
93871 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
93891 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
93916 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
93936 CATGTATCGATACA
1 AATGTATCGATACA
93950 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:95985 original size:15 final size:15
Alignment explanation
Indices: 95965--95995 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
95955 ATTTCGTTTG
*
95965 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
95980 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
95995 G
1 G
95996 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:97827 original size:21 final size:21
Alignment explanation
Indices: 97798--97842 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
97788 AAGTTTTCAT
*
97798 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAACTTCATTA
*
97818 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
97840 TTT
1 TTT
97843 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:100079 original size:13 final size:13
Alignment explanation
Indices: 100061--100086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100051 CAATTTTTTG
100061 TGTATCGATACAT
1 TGTATCGATACAT
100074 TGTATCGATACAT
1 TGTATCGATACAT
100087 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:103012 original size:52 final size:52
Alignment explanation
Indices: 102862--102992 Score: 226
Period size: 52 Copynumber: 2.5 Consensus size: 52
102852 CCCGAAATAT
*
102862 GAAAATTTGTCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
*
102914 GAAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
* *
102966 GCAAATTTGCCTGTATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
102993 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:103019 original size:13 final size:13
Alignment explanation
Indices: 103001--103025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
102991 CAAAGATCAG
103001 TGTATCGATACAA
1 TGTATCGATACAA
103014 TGTATCGATACA
1 TGTATCGATACA
103026 TTTGAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:103100 original size:32 final size:33
Alignment explanation
Indices: 103064--103194 Score: 203
Period size: 33 Copynumber: 4.0 Consensus size: 33
103054 AGTAGCTTAT
* *
103064 ATTGTTTCAATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
103096 ATTGTTTCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
103128 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
103161 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
103194 A
1 A
103195 AATCGTTGAA
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 47 0.49
33 48 0.51
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:103135 original size:13 final size:13
Alignment explanation
Indices: 103117--103174 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
103107 ACAAAACTTA
103117 TGTATCGATACAT
1 TGTATCGATACAT
103130 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
103149 ATGTATCGATACAT
1 -TGTATCGATACAT
103163 TGTATCGATACA
1 TGTATCGATACA
103175 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:103155 original size:20 final size:20
Alignment explanation
Indices: 103130--103195 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
103120 ATCGATACAT
103130 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
103150 TGTATCGAT---ACA---T-
1 TGTATCGATACAACACTTTA
103163 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
103183 TGTATCGATACAA
1 TGTATCGATACAA
103196 ATCGTTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 22 0.56
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACACTTTA
Found at i:109702 original size:42 final size:42
Alignment explanation
Indices: 109647--109756 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
109637 TTCTTCTCTC
* * **
109647 CTCCTCCTGTCATCCCTCCTCTTTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACGATCTCTCCTGTCT
*
109689 CTCCTCCTATCATCCCTCCTATCTCTACGATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACGATCTCTCCTGTCT
*
109731 CTCCTTCTATCATCCCTCCTCTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCT
109757 TCTTTCTCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.09, C:0.45, G:0.04, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACGATCTCTCCTGTCT
Found at i:109707 original size:24 final size:24
Alignment explanation
Indices: 109671--109756 Score: 67
Period size: 24 Copynumber: 3.8 Consensus size: 24
109661 CCTCCTCTTT
* * *
109671 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTA
*
109695 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTA
* *
109716 CGATC-T--CTCCTGTCTCTCCTT
1 CTATCATCCCTCCTGTCTCTCCTA
*
109737 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
109757 TCTTTCTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 4 0.09
20 5 0.11
21 12 0.26
22 5 0.11
24 21 0.45
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTA
Done.