Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 29 of 52
Found at i:5073329 original size:43 final size:43
Alignment explanation
Indices: 5073264--5073356 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
5073254 AAATATATTC
5073264 ATACATTGAGCCCAACGACTATAAATTTCAAATGCATGTATCA
1 ATACATTGAGCCCAACGACTATAAATTTCAAATGCATGTATCA
* * *
5073307 ATACATTGAGCCTAACGGCTATAAATTTCAAATGCATGTATCG
1 ATACATTGAGCCCAACGACTATAAATTTCAAATGCATGTATCA
5073350 ATACATT
1 ATACATT
5073357 ATGAATTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (43 bp):
ATACATTGAGCCCAACGACTATAAATTTCAAATGCATGTATCA
Found at i:5073735 original size:23 final size:23
Alignment explanation
Indices: 5073708--5073751 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5073698 GTATTCAACC
*
5073708 TTGGGTTATAATCTCTT-AAGAAT
1 TTGGGATATAAT-TCTTGAAGAAT
5073731 TTGGGATATAATTCTTGAAGA
1 TTGGGATATAATTCTTGAAGA
5073752 GATTGAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (23 bp):
TTGGGATATAATTCTTGAAGAAT
Found at i:5081299 original size:18 final size:19
Alignment explanation
Indices: 5081274--5081326 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
5081264 AATAAATTTG
* *
5081274 TAAAAAAGGGGAGAGTTGA
1 TAAAAAGGGGGAGAGTTAA
*
5081293 TAAAAAGGGGGAAAGTTAA
1 TAAAAAGGGGGAGAGTTAA
5081312 TAAAAAGGGGGAGAG
1 TAAAAAGGGGGAGAG
5081327 ATATTTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (19 bp):
TAAAAAGGGGGAGAGTTAA
Found at i:5081452 original size:21 final size:22
Alignment explanation
Indices: 5081417--5081459 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
5081407 AAAGCATATT
5081417 AAAATATTATATTAAGGGGGAG
1 AAAATATTATATTAAGGGGGAG
*
5081439 AAAA-ATTTTATTAAGGGGGAG
1 AAAATATTATATTAAGGGGGAG
5081460 TTATATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (22 bp):
AAAATATTATATTAAGGGGGAG
Found at i:5082191 original size:13 final size:13
Alignment explanation
Indices: 5082173--5082209 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
5082163 AAACTCACAT
5082173 TGTATCGATACAA
1 TGTATCGATACAA
5082186 TGTATCGATACAA
1 TGTATCGATACAA
5082199 TGTATCGATAC
1 TGTATCGATAC
5082210 CTGAAGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5087727 original size:58 final size:57
Alignment explanation
Indices: 5087615--5087771 Score: 147
Period size: 58 Copynumber: 2.7 Consensus size: 57
5087605 TTAGATCATA
* * * * * *
5087615 AAAATTACTTAAATGGCCTAACAATGTATGAAATTGCATGATAGTCCCTTAAACATTG
1 AAAATTACTAAAATGGCCTAA-AATGCATAAAATTGCATAAAAGTCCCTTAAACATGG
* *
5087673 AAAATGACTAAAATGGTCCTAAAATGCATAAAATTGCATAAAAGT-CTTTAAAACATGG
1 AAAATTACTAAAATGG-CCTAAAATGCATAAAATTGCATAAAAGTCCCTT-AAACATGG
* * * * *
5087731 TAAATTACTAGAATGACCCTAAAA-ACATAAAAATGCATAAA
1 AAAATTACTAAAATG-GCCTAAAATGCATAAAATTGCATAAA
5087772 TGGTCATGAA
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
57 18 0.22
58 59 0.72
59 5 0.06
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (57 bp):
AAAATTACTAAAATGGCCTAAAATGCATAAAATTGCATAAAAGTCCCTTAAACATGG
Found at i:5090464 original size:24 final size:23
Alignment explanation
Indices: 5090437--5090482 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
5090427 GAAAAAAAGG
5090437 ATAAA-AAGGAGAAGAAAGAAAAAA
1 ATAAAGAA-GAGAAG-AAGAAAAAA
5090461 ATAAAGAAGAGAAGAAGAAAAA
1 ATAAAGAAGAGAAGAAGAAAAA
5090483 TGAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 11 0.52
25 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (23 bp):
ATAAAGAAGAGAAGAAGAAAAAA
Found at i:5090502 original size:27 final size:27
Alignment explanation
Indices: 5090426--5090502 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 27
5090416 GAAATAAAAG
* * *
5090426 AGAAAAAAAGGATAAAAAGGAGAAGAA
1 AGAAAAAAATGAAAAAAAGAAGAAGAA
*
5090453 AGAAAAAAAT-AAAGAAGAGAAGAAGAAAA
1 AGAAAAAAATGAAA-AAAAGAAGAAG--AA
5090482 ATGAAAAAAATGAAAAAAAGA
1 A-GAAAAAAATGAAAAAAAGA
5090503 TGGCCTGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
26 2 0.05
27 18 0.45
29 3 0.08
30 14 0.35
31 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (27 bp):
AGAAAAAAATGAAAAAAAGAAGAAGAA
Found at i:5105961 original size:33 final size:33
Alignment explanation
Indices: 5105917--5105980 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5105907 AAATTCCCAG
5105917 ATGTATCGATACAAAGA-TCAATGTATCGATATA
1 ATGTATCGATACAAAGAGT-AATGTATCGATATA
* **
5105950 ATGTATTGATACATTGAGTAATGTATCGATA
1 ATGTATCGATACAAAGAGTAATGTATCGATA
5105981 CATTTCCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATATA
Found at i:5106043 original size:19 final size:19
Alignment explanation
Indices: 5106016--5106077 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 19
5106006 CGATACATTA
*
5106016 TATCAATACAACACTTATG
1 TATCGATACAACACTTATG
5106035 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
5106048 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
*
5106067 TATTGATACAA
1 TATCGATACAA
5106078 TTATTGTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
16 6 0.17
18 1 0.03
19 18 0.51
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (19 bp):
TATCGATACAACACTTATG
Found at i:5106051 original size:13 final size:13
Alignment explanation
Indices: 5106033--5106057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5106023 ACAACACTTA
5106033 TGTATCGATACAT
1 TGTATCGATACAT
5106046 TGTATCGATACA
1 TGTATCGATACA
5106058 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5106057 original size:32 final size:32
Alignment explanation
Indices: 5106001--5106081 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
5105991 GCAGTAGCTT
*
5106001 TGTAGCGATACATTATATCAATACAACACTTA
1 TGTATCGATACATTATATCAATACAACACTTA
* *
5106033 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTATATCAATACAACACTTA
*
5106065 TGTATTGATACAATTAT
1 TGTATCGATAC-ATTAT
5106082 TGTTTGTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 39 0.91
33 4 0.09
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATTATATCAATACAACACTTA
Found at i:5106104 original size:19 final size:20
Alignment explanation
Indices: 5106045--5106104 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
5106035 TATCGATACA
* *
5106045 TTGTATCGATACAACACT-T
1 TTGTATCGATACAATATTGT
* *
5106064 ATGTATTGATACAATTATTGT
1 TTGTATCGATACAA-TATTGT
5106085 TTGTATCGATACAA-ATTGT
1 TTGTATCGATACAATATTGT
5106104 T
1 T
5106105 GAAATTCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.55
20 2 0.06
21 13 0.39
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACAATATTGT
Found at i:5107958 original size:52 final size:53
Alignment explanation
Indices: 5107888--5107996 Score: 184
Period size: 52 Copynumber: 2.1 Consensus size: 53
5107878 CAAGTGAAAA
5107888 AAATATTTTTAGGAAAGTCCAAAATGCCTATGAATCGTATTAAAGAAAAATGT
1 AAATATTTTTAGGAAAGTCCAAAATGCCTATGAATCGTATTAAAGAAAAATGT
* * *
5107941 AAAT-TTTTTGGGAAAGTCCAAAATGCTTATGAATTGTATTAAAGAAAAATGT
1 AAATATTTTTAGGAAAGTCCAAAATGCCTATGAATCGTATTAAAGAAAAATGT
5107993 AAAT
1 AAAT
5107997 GATTCATCGA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 49 0.92
53 4 0.08
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (53 bp):
AAATATTTTTAGGAAAGTCCAAAATGCCTATGAATCGTATTAAAGAAAAATGT
Found at i:5110797 original size:51 final size:51
Alignment explanation
Indices: 5110601--5110817 Score: 213
Period size: 52 Copynumber: 4.2 Consensus size: 51
5110591 AATGAGATTA
* * * * * * *
5110601 GAGTATCCTCGATTGTGAAAAATTAGTGTTTTTAGAAATAAAATCAGAGTTG
1 GAGTATCCCCGATTATGAGAAATTAGT-ATTTTAGAAATAAAACCGGGGTTG
* * * * *
5110653 GAGTATCCCCGATTAAAGAAAAATTGGTATTTT-GAAAATAAAATCGAGGTTG
1 GAGTATCCCCGATT-ATGAGAAATTAGTATTTTAG-AAATAAAACCGGGGTTG
* *
5110705 GAGTATCTCCCGATTGTG-GAAAATTAGTGTTTTAGAAATAAAACCGGGGTTG
1 GAGTATC-CCCGATTATGAG-AAATTAGTATTTTAGAAATAAAACCGGGGTTG
* * * *
5110757 GAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTG
1 GAGTATCCCCGATTATGAGAAATTAGTATTTTAGAAATAAAACCGGGGTTG
5110808 GAGTATCCCC
1 GAGTATCCCC
5110818 TCGGAGGTAA
Statistics
Matches: 138, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
51 47 0.34
52 73 0.53
53 18 0.13
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAGAAATTAGTATTTTAGAAATAAAACCGGGGTTG
Found at i:5110840 original size:28 final size:27
Alignment explanation
Indices: 5110800--5110874 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
5110790 GAAATAAAGC
*
5110800 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCTAGGA-GTAA
* * *
5110828 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCTAGGAGTAA
5110855 CGGGGTTGGAGTATCCCCTA
1 CGGGGTTGGAGTATCCCCTA
5110875 ATGAAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 22 0.52
28 20 0.48
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCTAGGAGTAA
Found at i:5110933 original size:104 final size:105
Alignment explanation
Indices: 5110749--5110952 Score: 275
Period size: 104 Copynumber: 1.9 Consensus size: 105
5110739 GAAATAAAAC
* * * * *
5110749 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCC-ATAATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTGGAGTAT
* ** *
5110814 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGATTAA
65 CCCCTCAGAAATAACGGGGTTGGAATATCCCCGATGATTAA
** * *
5110855 CGGGGTTGGAGTATCCCC-TAATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTGTC
1 CGGGGTTGGAGTATCCCCATAATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTGGAGTATC
5110919 CCCTCAGAAATAACGGGGTTGGAATATCCCCGAT
66 CCCTCAGAAATAACGGGGTTGGAATATCCCCGAT
5110953 TGTGAAAAGT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 67 0.79
106 18 0.21
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (105 bp):
CGGGGTTGGAGTATCCCCATAATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTGGAGTATC
CCCTCAGAAATAACGGGGTTGGAATATCCCCGATGATTAA
Found at i:5111003 original size:51 final size:51
Alignment explanation
Indices: 5110936--5111056 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
5110926 AAATAACGGG
* *
5110936 GTTGGAATATCCCCGATTGT-GAAAAGTCGGTGCTTTGA-AAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGGAAAA-TCGGTG-TTTGAGAAATAAAATCAGA
* * * *
5110987 GTTGGAGTATCACCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTGAGAAATAAAATCAGA
5111038 GTTGGAGTATCCCCGATTA
1 GTTGGAGTATCCCCGATTA
5111057 AGAGAAGTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
50 4 0.07
51 52 0.85
52 5 0.08
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTGAGAAATAAAATCAGA
Found at i:5111072 original size:51 final size:51
Alignment explanation
Indices: 5110974--5111101 Score: 143
Period size: 51 Copynumber: 2.5 Consensus size: 51
5110964 GGTGCTTTGA
* * * *
5110974 AAATAAAATCAGAGTTGGAGTATCACCGATTATGGAAAATGGGTGTTTTAG
1 AAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGAAAATGGATGTTTTAG
* * *
5111025 AAATAAAATCGGAGTTGGAGTATCCCCGATTAA-GAGAAGTTGATGTTTTGG
1 AAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGA-AAATGGATGTTTTAG
* *
5111076 AAATGAAACCGG-GATTGGAGTATCCC
1 AAATAAAATCGGAG-TTGGAGTATCCC
5111102 TTCGAAAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 3 0.05
51 63 0.95
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (51 bp):
AAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGAAAATGGATGTTTTAG
Found at i:5111128 original size:79 final size:79
Alignment explanation
Indices: 5111038--5111212 Score: 210
Period size: 79 Copynumber: 2.2 Consensus size: 79
5111028 TAAAATCGGA
* ** * * *
5111038 GTTGGAGTATCCCCGATTAAGAGAAGTTGATGTTTT-GGAAATGAAA-CCGGGATTGGAGTATCC
1 GTTGGAGTATCCCCGATTAAGAGAAATCAATATTTTAAG-AAT-AAAGCAGGGATTGGAGTATCC
*
5111101 CTTCGAAAATAACGGG
64 CCTCGAAAATAACGGG
* * *
5111117 GTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGTAGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTAAGAGAAATCAATATTTTAAGAATAAAGCAGGGATTGGAGTATCCCC
* *
5111182 TCGGAAATAATGGG
66 TCGAAAATAACGGG
5111196 GTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCGAT
5111213 GATTAACGGG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
78 3 0.04
79 78 0.95
80 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.27
Consensus pattern (79 bp):
GTTGGAGTATCCCCGATTAAGAGAAATCAATATTTTAAGAATAAAGCAGGGATTGGAGTATCCCC
TCGAAAATAACGGG
Found at i:5111231 original size:27 final size:28
Alignment explanation
Indices: 5111165--5111239 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
5111155 GAATAAAGTA
*** *
5111165 GGGGTTGGAGTATCCCCTCGGAAATAAT
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
5111193 GGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
5111220 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
5111240 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.25
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:5111338 original size:51 final size:52
Alignment explanation
Indices: 5111223--5111344 Score: 176
Period size: 51 Copynumber: 2.3 Consensus size: 52
5111213 GATTAACGGG
* * *
5111223 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTTGAAAATAAAATCGGA
5111276 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTTGAAAATAAAATCGGA
*
5111327 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
5111345 GCGGAGAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
51 35 0.55
52 1 0.02
53 28 0.44
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:5113714 original size:21 final size:21
Alignment explanation
Indices: 5113690--5113731 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5113680 GTATCGATAC
*
5113690 AATGTATCGATATATTTCCTT
1 AATGTATCGATACATTTCCTT
5113711 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
5113732 GGTAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:5113766 original size:13 final size:13
Alignment explanation
Indices: 5113748--5113799 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
5113738 AGCTTCGTAG
5113748 CGATACATTGTAT
1 CGATACATTGTAT
5113761 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
5113780 CGATACATTGTAT
1 CGATACATTGTAT
5113793 CGATACA
1 CGATACA
5113800 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:5113780 original size:19 final size:18
Alignment explanation
Indices: 5113756--5113818 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
5113746 AGCGATACAT
5113756 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
5113775 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
5113788 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
5113807 TGTATCGATACA
1 TGTATCGATACA
5113819 TTTTCTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:5113789 original size:32 final size:32
Alignment explanation
Indices: 5113748--5113820 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
5113738 AGCTTCGTAG
5113748 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
5113780 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
5113812 CGATACATT
1 CGATACATT
5113821 TTCTGTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:5113847 original size:19 final size:19
Alignment explanation
Indices: 5113787--5113848 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
5113777 TATCGATACA
5113787 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ACTGT
* **
5113806 ATGTATCGATACATTTTCTGT
1 TTGTATCGATACA--AACTGT
5113827 TTGTATCGATACAAACTGT
1 TTGTATCGATACAAACTGT
5113846 TTG
1 TTG
5113849 AAGTTCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:5113902 original size:21 final size:21
Alignment explanation
Indices: 5113878--5113953 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
5113868 ATTGGGACCT
5113878 TGTATCGAAACATTCTACAAA
1 TGTATCGAAACATTCTACAAA
5113899 TGTATC-AATACATTCTACAAA
1 TGTATCGAA-ACATTCTACAAA
*
5113920 TGTATCG--ATATTCTACAAA
1 TGTATCGAAACATTCTACAAA
* *
5113939 AGTATCGATACATTC
1 TGTATCGAAACATTC
5113954 GTCCCCACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 17 0.35
20 2 0.04
21 29 0.60
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (21 bp):
TGTATCGAAACATTCTACAAA
Found at i:5113934 original size:19 final size:19
Alignment explanation
Indices: 5113889--5113948 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
5113879 GTATCGAAAC
*
5113889 ATTCTACAAATGTATCAAT
1 ATTCTACAAATGTATCGAT
5113908 ACATTCTACAAATGTATCGAT
1 --ATTCTACAAATGTATCGAT
*
5113929 ATTCTACAAAAGTATCGAT
1 ATTCTACAAATGTATCGAT
5113948 A
1 A
5113949 CATTCGTCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 19 0.51
21 18 0.49
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (19 bp):
ATTCTACAAATGTATCGAT
Found at i:5115398 original size:90 final size:90
Alignment explanation
Indices: 5115304--5115529 Score: 296
Period size: 90 Copynumber: 2.5 Consensus size: 90
5115294 AAAACTCAAG
* * * * *
5115304 TTTTCTCTTCGTATAATTTTA-CCTTCGGGAAACCTCCATCCCCATTATTCTAAGGGGATACTCT
1 TTTTCCCTTTGTATAATTTTATCCTT-GGGAAA-CTCCATCCCCACTACTCTAAGGGGATACTCC
* *
5115368 AACCCCGTTCTATCAA-AAAATTTAAA
64 AACCCCGTCCTACCAACAAAATTTAAA
*
5115394 TTTTCCCTTTGTATAATTTTATCCTTAGGGAAACTTCATCCCCACTACTCTAAGGGGATACTCCA
1 TTTTCCCTTTGTATAATTTTATCCTT-GGGAAACTCCATCCCCACTACTCTAAGGGGATACTCCA
*
5115459 ATCCCGTCCTACCAACAAAATTTAAA
65 ACCCCGTCCTACCAACAAAATTTAAA
* *
5115485 -TTTCCCTTTTTATAATTTTATCCTTGTGGTAACTCCATCCCCACT
1 TTTTCCCTTTGTATAATTTTATCCTTG-GGAAACTCCATCCCCACT
5115530 CGTCCGTTGA
Statistics
Matches: 120, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
89 1 0.01
90 99 0.82
91 20 0.17
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.37
Consensus pattern (90 bp):
TTTTCCCTTTGTATAATTTTATCCTTGGGAAACTCCATCCCCACTACTCTAAGGGGATACTCCAA
CCCCGTCCTACCAACAAAATTTAAA
Found at i:5115544 original size:90 final size:90
Alignment explanation
Indices: 5115304--5115674 Score: 279
Period size: 90 Copynumber: 4.1 Consensus size: 90
5115294 AAAACTCAAG
* * * * * * * *
5115304 TTTTCTCTTCGTATAATTTTA-CCTTCGGGAAACCTCCATCCCCATTATTCTAAGGGGATACTCT
1 TTTTCCCTTTGTATAATTTTATCCTTAGGGAAA-CTCCATCCCCACTACTCCAAGGAGATACTCC
* *
5115368 AACCCCGTTCTATCAAAAAATTTAAA
65 AACCCCGTCCTACCAAAAAATTTAAA
* * *
5115394 TTTTCCCTTTGTATAATTTTATCCTTAGGGAAACTTCATCCCCACTACTCTAAGGGGATACTCCA
1 TTTTCCCTTTGTATAATTTTATCCTTAGGGAAACTCCATCCCCACTACTCCAAGGAGATACTCCA
*
5115459 ATCCCGTCCTACCAACAAAATTTAAA
66 ACCCCGTCCTACCAA-AAAATTTAAA
* * ***
5115485 -TTTCCCTTTTTATAATTTTATCCTT-GTGGTAACTCCATCCCCACT-CGTCCGTTGAGATACTC
1 TTTTCCCTTTGTATAATTTTATCCTTAG-GGAAACTCCATCCCCACTAC-TCCAAGGAGATACTC
* ** * * * *
5115547 TAACCTTGTTCTTTA-TAAAAAACTTAAT
64 CAACCCCG-TC-CTACCAAAAAATTTAAA
* * * * * * *
5115575 TTTTCTCC-TTGTATGATTTTATCTTTAGGAAAAATCCATTCCCGCTACTTCGAAGG-GATACTC
1 TTTTC-CCTTTGTATAATTTTATCCTTAGGGAAACTCCATCCCCACTAC-TCCAAGGAGATACTC
* * *
5115638 CAACCTCGTTCTACCAAAAAAATTTATA
64 CAACCCCGTCCTACC-AAAAAATTTAAA
*
5115666 TTTTTCCTT
1 TTTTCCCTT
5115675 CGCACCACAT
Statistics
Matches: 220, Mismatches: 48, Indels: 25
0.75 0.16 0.09
Matches are distributed among these distances:
89 4 0.02
90 124 0.56
91 83 0.38
92 9 0.04
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (90 bp):
TTTTCCCTTTGTATAATTTTATCCTTAGGGAAACTCCATCCCCACTACTCCAAGGAGATACTCCA
ACCCCGTCCTACCAAAAAATTTAAA
Found at i:5117154 original size:28 final size:28
Alignment explanation
Indices: 5117079--5117229 Score: 85
Period size: 28 Copynumber: 5.5 Consensus size: 28
5117069 ACACGAATCT
* * * *
5117079 AAGCCTACATTAGCTAGCAT-TCACGTTA
1 AAGCCCACATTAGCTCGCATAT-AAGTCA
* * *
5117107 AAGCCCATATTAGTTTGCATATGAA-TCA
1 AAGCCCACATTAGCTCGCATAT-AAGTCA
* *
5117135 AAGCCCACATTAGCTCGCATCTAAGTCT
1 AAGCCCACATTAGCTCGCATATAAGTCA
* * **
5117163 AAGCCCACACTAGCTAGCACCTAAGT--
1 AAGCCCACATTAGCTCGCATATAAGTCA
* * * * * *
5117189 AAGCCCCCACTAACTAGCATATGAGTCG
1 AAGCCCACATTAGCTCGCATATAAGTCA
5117217 AAGCCCACATTAG
1 AAGCCCACATTAG
5117230 TTGGCATTTG
Statistics
Matches: 96, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
26 21 0.22
27 2 0.02
28 71 0.74
29 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (28 bp):
AAGCCCACATTAGCTCGCATATAAGTCA
Found at i:5117167 original size:56 final size:55
Alignment explanation
Indices: 5117050--5117171 Score: 129
Period size: 56 Copynumber: 2.2 Consensus size: 55
5117040 GGCACCTAAG
* * *
5117050 TAAGCCCACAGTAGTTGGCACACGAATCTAAGCCTACATTAGCTAGCATTCACGT
1 TAAGCCCACAGTAGTTGGCACACGAATCAAAGCCCACATTAGCTAGCATTCAAGT
* * * * * *
5117105 TAAAGCCCATATTAGTTTGCATATGAATCAAAGCCCACATTAGCTCGCA-TCTAAGT
1 T-AAGCCCACAGTAGTTGGCACACGAATCAAAGCCCACATTAGCTAGCATTC-AAGT
5117161 CTAAGCCCACA
1 -TAAGCCCACA
5117172 CTAGCTAGCA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
55 3 0.06
56 50 0.93
57 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (55 bp):
TAAGCCCACAGTAGTTGGCACACGAATCAAAGCCCACATTAGCTAGCATTCAAGT
Found at i:5117236 original size:28 final size:28
Alignment explanation
Indices: 5117106--5117431 Score: 124
Period size: 28 Copynumber: 11.7 Consensus size: 28
5117096 CATTCACGTT
* * * *
5117106 AAAGCCCATATTAGTTTGCATATGAATC
1 AAAGCCCACATTAGTTGGCATCTGAGTC
* * *
5117134 AAAGCCCACATTAGCTCGCATCTAAGTC
1 AAAGCCCACATTAGTTGGCATCTGAGTC
* * * * * *
5117162 TAAGCCCACACTAGCTAGCACCTAAGT-
1 AAAGCCCACATTAGTTGGCATCTGAGTC
* * ** * *
5117189 -AAGCCCCCACTAACTAGCATATGAGTC
1 AAAGCCCACATTAGTTGGCATCTGAGTC
* * *
5117216 GAAGCCCACATTAGTTGGCATTTGCA-TT
1 AAAGCCCACATTAGTTGGCATCTG-AGTC
* * * * *
5117244 AAAGCCCACTTTAATTGGCATATGAATT
1 AAAGCCCACATTAGTTGGCATCTGAGTC
* * * *
5117272 GAAGCCCACACTAGTTGGCACCTTAGTCC
1 AAAGCCCACATTAGTTGGCATCTGAGT-C
* * * * *
5117301 AAA-CCTATACTAGTTGGCACCTTAGTC
1 AAAGCCCACATTAGTTGGCATCTGAGTC
* * *
5117328 CAAGCCCACATTAGTTGGTA-CTTAAGTC
1 AAAGCCCACATTAGTTGGCATC-TGAGTC
* * * *
5117356 GAAA-CCCATACTAGTTAGCATCTAAGTC
1 -AAAGCCCACATTAGTTGGCATCTGAGTC
* * * * * *
5117384 AAAGTCTACACTAGCTGGCAACTAAGTC
1 AAAGCCCACATTAGTTGGCATCTGAGTC
*
5117412 AAAGCCCACACTAGTTGGCA
1 AAAGCCCACATTAGTTGGCA
5117432 CCTCGTAGAA
Statistics
Matches: 230, Mismatches: 58, Indels: 20
0.75 0.19 0.06
Matches are distributed among these distances:
26 21 0.09
27 8 0.03
28 195 0.85
29 6 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (28 bp):
AAAGCCCACATTAGTTGGCATCTGAGTC
Found at i:5117250 original size:138 final size:138
Alignment explanation
Indices: 5117002--5117281 Score: 319
Period size: 138 Copynumber: 2.0 Consensus size: 138
5116992 ACCTAATCCA
* * * * ** *
5117002 CACATTAGATAGCATCTAAGTCTACGCCTACACTAACTGGCACCTAAGTAAGCCCACAGTAGTTG
1 CACATTAGATAGCATCTAAGTCTAAGCCCACACTAACTAGCACCTAAGTAAGCCCACACTAACTA
* * * * *
5117067 GCACACGAATCTAAGCCTACATTAGCTAGCATTCACGTTAAAGCCCA-TATTAGTTTGCATATGA
66 GCACACGAATCGAAGCCCACATTAGCTAGCATTCACATTAAAGCCCACT-TTAATTGGCATATGA
5117131 ATCAAAGCC
130 ATCAAAGCC
* * * *
5117140 CACATTAGCTCGCATCTAAGTCTAAGCCCACACTAGCTAGCACCTAAGTAAGCCCCCACTAACTA
1 CACATTAGATAGCATCTAAGTCTAAGCCCACACTAACTAGCACCTAAGTAAGCCCACACTAACTA
* * * * * **
5117205 GCATATGAGTCGAAGCCCACATTAGTTGGCATTTGCATTAAAGCCCACTTTAATTGGCATATGAA
66 GCACACGAATCGAAGCCCACATTAGCTAGCATTCACATTAAAGCCCACTTTAATTGGCATATGAA
**
5117270 TTGAAGCC
131 TCAAAGCC
5117278 CACA
1 CACA
5117282 CTAGTTGGCA
Statistics
Matches: 116, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
138 115 0.99
139 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (138 bp):
CACATTAGATAGCATCTAAGTCTAAGCCCACACTAACTAGCACCTAAGTAAGCCCACACTAACTA
GCACACGAATCGAAGCCCACATTAGCTAGCATTCACATTAAAGCCCACTTTAATTGGCATATGAA
TCAAAGCC
Found at i:5117333 original size:56 final size:55
Alignment explanation
Indices: 5117273--5117434 Score: 164
Period size: 56 Copynumber: 2.9 Consensus size: 55
5117263 ATATGAATTG
* * *
5117273 AAGCCCACACTAGTTGGCACCTTAGTCCAAACCTATACTAGTTGGCACCTTAGTCC
1 AAGCCCACACTAGTTGGCA-CTTAGTCCAAACCCATACTAGTTGGCACCTAAGTCA
* * * * *
5117329 AAGCCCACATTAGTTGGTACTTAAGTCGAAACCCATACTAGTTAGCATCTAAGTCA
1 AAGCCCACACTAGTTGGCACTT-AGTCCAAACCCATACTAGTTGGCACCTAAGTCA
* * * * *
5117385 AAGTCTACACTAGCTGGCAACTAAGT-CAAAGCCCACACTAGTTGGCACCT
1 AAGCCCACACTAGTTGGC-ACTTAGTCCAAA-CCCATACTAGTTGGCACCT
5117435 CGTAGAAATT
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
55 6 0.07
56 76 0.89
57 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (55 bp):
AAGCCCACACTAGTTGGCACTTAGTCCAAACCCATACTAGTTGGCACCTAAGTCA
Found at i:5128654 original size:36 final size:35
Alignment explanation
Indices: 5128593--5128692 Score: 143
Period size: 36 Copynumber: 2.9 Consensus size: 35
5128583 GTATACATAA
*
5128593 TAAATAATAATAAA-ATATTAAAATTATATTTATGT
1 TAAATAATAA-AAATATATTAAAATTATATTTATAT
5128628 TAAATAATAAAATATATATTAAAATTATATTTATAT
1 TAAATAATAAAA-ATATATTAAAATTATATTTATAT
*
5128664 TAAA-AATAATAAT-TATTAAAATTATATTT
1 TAAATAATAAAAATATATTAAAATTATATTT
5128693 TTTTCAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
33 16 0.26
34 4 0.07
35 17 0.28
36 24 0.39
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (35 bp):
TAAATAATAAAAATATATTAAAATTATATTTATAT
Found at i:5132623 original size:28 final size:26
Alignment explanation
Indices: 5132573--5132643 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 26
5132563 TATGATTTAA
*
5132573 AAATAAATATTTATATTATTATAATT-G
1 AAATAAAT-TTTTTATTATTAT-ATTAG
* *
5132600 AATTAAATTTTTTATTAGTATATATTAT
1 AAATAAATTTTTTATTA-T-TATATTAG
5132628 AAATAAATTTTTTATT
1 AAATAAATTTTTTATT
5132644 TTTTTTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.22
27 11 0.30
28 18 0.49
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
AAATAAATTTTTTATTATTATATTAG
Found at i:5133321 original size:15 final size:16
Alignment explanation
Indices: 5133301--5133331 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5133291 TGATTTGATC
5133301 ATATAATTT-ATTTAA
1 ATATAATTTAATTTAA
5133316 ATATAATTTAATTTAA
1 ATATAATTTAATTTAA
5133332 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATTTAATTTAA
Found at i:5133381 original size:15 final size:15
Alignment explanation
Indices: 5133356--5133407 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5133346 AAATTGAATA
5133356 TAAATTAATTTAAATT
1 TAAA-TAATTTAAATT
* * *
5133372 TAAATGATTTTAACT
1 TAAATAATTTAAATT
*
5133387 TGAATAATTTAAATTT
1 TAAATAATTTAAA-TT
5133403 TAAAT
1 TAAAT
5133408 TCAAAATGAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (15 bp):
TAAATAATTTAAATT
Found at i:5134253 original size:11 final size:11
Alignment explanation
Indices: 5134237--5134261 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5134227 TCGTAATCAC
5134237 TAAAATAATAA
1 TAAAATAATAA
5134248 TAAAATAATAA
1 TAAAATAATAA
5134259 TAA
1 TAA
5134262 TAATTTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:5135090 original size:5 final size:5
Alignment explanation
Indices: 5135077--5135140 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
5135067 TATTTTTTAA
* * * **
5135077 AAATA AAATT AAATAT AATATA AAATT AAATT AATTT AAATT AAATT TTATT
1 AAATT AAATT AAAT-T AA-ATT AAATT AAATT AAATT AAATT AAATT AAATT
*
5135129 AATTT AAATT AA
1 AAATT AAATT AA
5135141 TTTAGTTTAA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
5 39 0.85
6 5 0.11
7 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:5135119 original size:15 final size:16
Alignment explanation
Indices: 5135082--5135141 Score: 70
Period size: 15 Copynumber: 3.8 Consensus size: 16
5135072 TTTAAAAATA
*
5135082 AAATTAAATATAATATA
1 AAATTAAAT-TAATATT
5135099 AAATTAAATTAAT-TT
1 AAATTAAATTAATATT
*
5135114 AAATTAAATT-TTATT
1 AAATTAAATTAATATT
*
5135129 AATTTAAATTAAT
1 AAATTAAATTAAT
5135142 TTAGTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 1 0.03
15 22 0.59
16 5 0.14
17 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTAAATTAATATT
Found at i:5135149 original size:15 final size:15
Alignment explanation
Indices: 5135102--5135150 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5135092 TAATATAAAA
*
5135102 TTAAATTAATTTAAA
1 TTAAATTAATTTAAT
*
5135117 TTAAATT-TTATTAAT
1 TTAAATTAAT-TTAAT
*
5135132 TTAAATTAATTTAGT
1 TTAAATTAATTTAAT
5135147 TTAA
1 TTAA
5135151 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TTAAATTAATTTAAT
Found at i:5135262 original size:18 final size:18
Alignment explanation
Indices: 5135239--5135273 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5135229 TTTTATATTA
*
5135239 TAAAAATTAAAAATTAAG
1 TAAAAAATAAAAATTAAG
*
5135257 TAAAAAATAAAATTTAA
1 TAAAAAATAAAAATTAA
5135274 TTTAATTAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAAAATAAAAATTAAG
Found at i:5135671 original size:19 final size:20
Alignment explanation
Indices: 5135649--5135688 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
5135639 TAAAATTTAA
5135649 TTAT-AATAAAATAATTATT
1 TTATAAATAAAATAATTATT
5135668 TTATAAGAATAAAATAATTAT
1 TTAT-A-AATAAAATAATTAT
5135689 AATAACAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
22 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TTATAAATAAAATAATTATT
Found at i:5146541 original size:32 final size:34
Alignment explanation
Indices: 5146501--5146566 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 34
5146491 AAAATCATAT
5146501 ATTAAAATTTATAT-AATATA-AATTATTAAAAA
1 ATTAAAATTTATATAAATATATAATTATTAAAAA
*
5146533 ATTAAAATTTATATAAATATATAATTTTTAAAAA
1 ATTAAAATTTATATAAATATATAATTATTAAAAA
5146567 CAATTATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.45
33 6 0.19
34 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
ATTAAAATTTATATAAATATATAATTATTAAAAA
Found at i:5147337 original size:18 final size:18
Alignment explanation
Indices: 5147314--5147366 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
5147304 ATTTATTAAA
5147314 ATATTAAAATATTAATTT
1 ATATTAAAATATTAATTT
* *
5147332 ATATTAATATATT-TTTT
1 ATATTAAAATATTAATTT
*
5147349 ATTAATAAAATATTAATT
1 A-TATTAAAATATTAATT
5147367 CAAATCATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 4 0.14
18 22 0.79
19 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAAAATATTAATTT
Found at i:5147569 original size:14 final size:14
Alignment explanation
Indices: 5147552--5147597 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
5147542 TATAATTATT
*
5147552 TTTAAAAAATAATA
1 TTTAAAAATTAATA
*
5147566 TTTAAAAATTTAAAA
1 TTTAAAAA-TTAATA
*
5147581 TTTAAATATTAATA
1 TTTAAAAATTAATA
5147595 TTT
1 TTT
5147598 TTTATCTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTAAAAATTAATA
Found at i:5147819 original size:7 final size:7
Alignment explanation
Indices: 5147807--5147835 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5147797 TATTTGGTCA
5147807 TCATAAT
1 TCATAAT
5147814 TCATAAT
1 TCATAAT
5147821 TCATAAT
1 TCATAAT
5147828 TCATAAT
1 TCATAAT
5147835 T
1 T
5147836 ATATGTTAAT
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:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (7 bp):
TCATAAT
Found at i:5148375 original size:18 final size:17
Alignment explanation
Indices: 5148347--5148382 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5148337 AAATTAATTG
*
5148347 ATTTTTTATATTTTATA
1 ATTTTTTATATTTAATA
5148364 ATTTTATTATATTTAATA
1 ATTTT-TTATATTTAATA
5148382 A
1 A
5148383 ATTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTTATATTTAATA
Found at i:5148390 original size:18 final size:18
Alignment explanation
Indices: 5148352--5148391 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5148342 AATTGATTTT
* * *
5148352 TTATATTTTATAATTTTA
1 TTATATTTAATAAATTAA
5148370 TTATATTTAATAAATTAA
1 TTATATTTAATAAATTAA
5148388 TTAT
1 TTAT
5148392 TAAATTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTTAATAAATTAA
Found at i:5148393 original size:21 final size:21
Alignment explanation
Indices: 5148352--5148411 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
5148342 AATTGATTTT
*
5148352 TTATATTTTAT-AATT--TTA
1 TTATATTTAATAAATTAATTA
5148370 TTATATTTAATAAATTAATTA
1 TTATATTTAATAAATTAATTA
* * *
5148391 TTAAATTTAACAAAATAATTA
1 TTATATTTAATAAATTAATTA
5148412 CATTCATTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.29
19 4 0.11
21 21 0.60
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATTTAATAAATTAATTA
Found at i:5150857 original size:21 final size:22
Alignment explanation
Indices: 5150831--5150875 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5150821 AAATAAATAT
*
5150831 AAATAAATTA-AAATTTATAAA
1 AAATAAATTATAAATATATAAA
*
5150852 AAATAAATTATTAATATATAAA
1 AAATAAATTATAAATATATAAA
5150874 AA
1 AA
5150876 TTTATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAAATTATAAATATATAAA
Found at i:5150876 original size:21 final size:20
Alignment explanation
Indices: 5150819--5150876 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
5150809 TATGAACAAA
* *
5150819 TAAAATAAATATAAATAAAT
1 TAAAATATATAAAAATAAAT
*
5150839 TAAAATTTATAAAAAATAAAT
1 TAAAATATAT-AAAAATAAAT
*
5150860 TATTAATATATAAAAAT
1 TA-AAATATATAAAAAT
5150877 TTATATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 8 0.26
21 17 0.55
22 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAATATATAAAAATAAAT
Found at i:5150905 original size:21 final size:21
Alignment explanation
Indices: 5150879--5150937 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
5150869 ATAAAAATTT
5150879 ATATAATAATATATATTTTAA
1 ATATAATAATATATATTTTAA
* * *
5150900 ATATAAAAACATAAATTTTAA
1 ATATAATAATATATATTTTAA
5150921 ATATAATATATATATAT
1 ATATAATA-ATATATAT
5150938 ATATAACACA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAATAATATATATTTTAA
Found at i:5151893 original size:5 final size:5
Alignment explanation
Indices: 5151883--5151913 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
5151873 TTCTTGTATA
5151883 TTATT TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT T
5151914 GTTGGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:5154021 original size:41 final size:39
Alignment explanation
Indices: 5153956--5154037 Score: 103
Period size: 41 Copynumber: 2.1 Consensus size: 39
5153946 TACAATTTAC
5153956 AAATTAATAAAAATTTAAAAAATATTTTCA-TATTAATAT
1 AAATTAATAAAAATTTAAAAAATATTTTCATTATTAA-AT
* * *
5153995 AAATATAATTAAATTTTAAATAAATATTTTTATTATTAAAT
1 AAAT-TAATAAAAATTTAAA-AAATATTTTCATTATTAAAT
5154036 AA
1 AA
5154038 TAATTGAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 4 0.11
40 13 0.35
41 14 0.38
42 6 0.16
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (39 bp):
AAATTAATAAAAATTTAAAAAATATTTTCATTATTAAAT
Found at i:5154277 original size:21 final size:23
Alignment explanation
Indices: 5154253--5154295 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
5154243 ATATAATACA
5154253 AAAAAAAT-TAAA-ACATAATAT
1 AAAAAAATATAAACACATAATAT
*
5154274 AAAAAAATATAAACAGATAATA
1 AAAAAAATATAAACACATAATA
5154296 ATATACGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (23 bp):
AAAAAAATATAAACACATAATAT
Found at i:5154286 original size:22 final size:22
Alignment explanation
Indices: 5154235--5154295 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
5154225 TATAATTGTT
*
5154235 AAATAT-AAATATAATACAAAA
1 AAATATAAAACATAATACAAAA
*
5154256 AAA-ATTAAAACATAATATAAAA
1 AAATA-TAAAACATAATACAAAA
*
5154278 AAATATAAACAGATAATA
1 AAATATAAA-ACATAATA
5154296 ATATACGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 4 0.12
22 20 0.61
23 8 0.24
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATATAAAACATAATACAAAA
Found at i:5156931 original size:173 final size:173
Alignment explanation
Indices: 5156642--5156973 Score: 637
Period size: 173 Copynumber: 1.9 Consensus size: 173
5156632 AGAATGCAGA
*
5156642 GAGGATGTCTAAGGCTCTCGGCTCCTTAAGACTTGTAATATATTAACTTACTATTTTATTCTCAA
1 GAGGATGTCTAAGGCTCTCAGCTCCTTAAGACTTGTAATATATTAACTTACTATTTTATTCTCAA
*
5156707 GCACACCTTAACTTGATACCGATTCATGATTACGTTAATAAATATTGGCAGAGGATCATGCAATA
66 GCACACCTTAACTTGATACCGATTCATGATTACGTCAATAAATATTGGCAGAGGATCATGCAATA
5156772 TTTCTCTTATAAATGAGGGCTGTAAAGAACGCAAGGATGTAGG
131 TTTCTCTTATAAATGAGGGCTGTAAAGAACGCAAGGATGTAGG
5156815 GAGGATGTCTAAGGCTCTCAGCTCCTTAAGACTTGTAATATATTAACTTACTATTTTATTCTCAA
1 GAGGATGTCTAAGGCTCTCAGCTCCTTAAGACTTGTAATATATTAACTTACTATTTTATTCTCAA
5156880 GCACACCTTAACTTGATACCGATTCATGATTACGTCAATAAATATTGGCAGAGGATCATGCAATA
66 GCACACCTTAACTTGATACCGATTCATGATTACGTCAATAAATATTGGCAGAGGATCATGCAATA
*
5156945 TTTCTCTTATAAATGAGTGCTGTAAAGAA
131 TTTCTCTTATAAATGAGGGCTGTAAAGAA
5156974 AGCATTGACT
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 156 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (173 bp):
GAGGATGTCTAAGGCTCTCAGCTCCTTAAGACTTGTAATATATTAACTTACTATTTTATTCTCAA
GCACACCTTAACTTGATACCGATTCATGATTACGTCAATAAATATTGGCAGAGGATCATGCAATA
TTTCTCTTATAAATGAGGGCTGTAAAGAACGCAAGGATGTAGG
Found at i:5159790 original size:11 final size:11
Alignment explanation
Indices: 5159774--5159804 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5159764 TTGCTTCTAA
5159774 ACTCTAAATTT
1 ACTCTAAATTT
5159785 ACTCTAAATTT
1 ACTCTAAATTT
5159796 ACTCTAAAT
1 ACTCTAAAT
5159805 GAGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (11 bp):
ACTCTAAATTT
Found at i:5159827 original size:139 final size:138
Alignment explanation
Indices: 5159661--5160060 Score: 698
Period size: 139 Copynumber: 3.0 Consensus size: 138
5159651 ACCCTATCAA
5159661 CTAAATGAGAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
1 CTAAATGAGAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
5159726 AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACTCTA
66 AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACTCTA
5159791 AATTTACT
131 AATTTACT
5159799 CTAAATGAGAAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACAT
1 CTAAATGAG-AAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACAT
5159864 AAAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTG---CT----TCT-AA---ACTCT
65 AAAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACTCT
5159918 AAATTTACT
130 AAATTTACT
*
5159927 CTGAATGAG-AAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
1 CTAAATGAGAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
5159991 AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACTCTA
66 AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACTCTA
5160056 AATTT
131 AATTT
5160061 TCATATTATT
Statistics
Matches: 249, Mismatches: 1, Indels: 25
0.91 0.00 0.09
Matches are distributed among these distances:
126 96 0.39
128 22 0.09
129 2 0.01
131 2 0.01
132 3 0.01
133 3 0.01
134 2 0.01
136 2 0.01
137 11 0.04
138 9 0.04
139 97 0.39
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (138 bp):
CTAAATGAGAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACTCTA
AATTTACT
Found at i:5159975 original size:126 final size:127
Alignment explanation
Indices: 5159661--5160058 Score: 672
Period size: 126 Copynumber: 3.0 Consensus size: 127
5159651 ACCCTATCAA
5159661 CTAAATGAGAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
1 CTAAATGAGAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
5159726 AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACTCTA
66 AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTG---CT----TCT-AA---ACTCTA
5159791 AATTTACT
120 AATTTACT
5159799 CTAAATGAGAAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACAT
1 CTAAATGAG-AAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACAT
5159864 AAAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACT
65 AAAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACT
*
5159927 CTGAATGAG-AAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
1 CTAAATGAGAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
5159991 AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACT
66 AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACT
5160053 CTAAAT
1 CTAAAT
5160059 TTTCATATTA
Statistics
Matches: 257, Mismatches: 2, Indels: 14
0.94 0.01 0.05
Matches are distributed among these distances:
126 122 0.47
128 22 0.09
131 2 0.01
132 3 0.01
136 2 0.01
138 9 0.04
139 97 0.38
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.35
Consensus pattern (127 bp):
CTAAATGAGAAAAAAAAAACATTTTTCCATTCTAAAACTATTTTATGGATGAACAGATTAACATA
AAAAATTGCCTTAATACATATAATAATATGAGATTTAGTTGCTTCTAAACTCTAAATTTACT
Found at i:5161593 original size:15 final size:15
Alignment explanation
Indices: 5161575--5161605 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5161565 AAGCAAAGAT
*
5161575 TATATCATATATATA
1 TATATAATATATATA
5161590 TATATAATATATATA
1 TATATAATATATATA
5161605 T
1 T
5161606 GCTTTAATCA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATAATATATATA
Found at i:5165463 original size:2 final size:2
Alignment explanation
Indices: 5165456--5165486 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5165446 ATTCATTATT
5165456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5165487 CAAGGACCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5166744 original size:22 final size:22
Alignment explanation
Indices: 5166712--5166756 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5166702 TGTATAAATT
*
5166712 AAAAATAAAAAATTATATAATAA
1 AAAAATAAAAAAATATAT-ATAA
5166735 AAAAAT-AAAAAATATATATAA
1 AAAAATAAAAAAATATATATAA
5166756 A
1 A
5166757 TATATCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAATAAAAAAATATATATAA
Found at i:5167211 original size:3 final size:3
Alignment explanation
Indices: 5167203--5167249 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
5167193 CAAGTTTTGA
* * *
5167203 ATG ATG ATG ATG ATG ATG ATA ATA AT- AGTA ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A-TG ATG ATG ATG ATG ATG
5167248 AT
1 AT
5167250 AGTAATCTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:5167238 original size:21 final size:21
Alignment explanation
Indices: 5167212--5167255 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5167202 AATGATGATG
5167212 ATGATGATGATAATAATAGTA
1 ATGATGATGATAATAATAGTA
* *
5167233 ATGATGATGATGATGATAGTA
1 ATGATGATGATAATAATAGTA
5167254 AT
1 AT
5167256 CTATATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (21 bp):
ATGATGATGATAATAATAGTA
Found at i:5167875 original size:32 final size:32
Alignment explanation
Indices: 5167839--5167922 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
5167829 TTTATCTATT
* *
5167839 TTTATAGATTCAAATATTATAAATTTGAATAA
1 TTTATAGATTCAAATATTACAAATTTAAATAA
* *
5167871 TTTAT-GAATTTAAATATTACAAATTTAAATGA
1 TTTATAG-ATTCAAATATTACAAATTTAAATAA
*
5167903 TTTGTAGGATTCAAATATTA
1 TTTATA-GATTCAAATATTA
5167923 GATTATTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
31 1 0.02
32 30 0.70
33 11 0.26
34 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTATAGATTCAAATATTACAAATTTAAATAA
Found at i:5169961 original size:16 final size:16
Alignment explanation
Indices: 5169942--5169972 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5169932 ATATTGTTAA
5169942 ATTTATTTATTTTTAC
1 ATTTATTTATTTTTAC
5169958 ATTTATTTATTTTTA
1 ATTTATTTATTTTTA
5169973 TTATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTATTTATTTTTAC
Found at i:5172385 original size:16 final size:17
Alignment explanation
Indices: 5172357--5172416 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 17
5172347 TGTAAATTAA
*
5172357 AAAATTATT-TAAATTT
1 AAAATAATTCTAAATTT
*
5172373 AAAATAA-TCTAAATAT
1 AAAATAATTCTAAATTT
5172389 AAAATAATTCT-AATTT
1 AAAATAATTCTAAATTT
5172405 -AAA-AATTCTAAA
1 AAAATAATTCTAAA
5172417 CATCAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.16
15 6 0.16
16 23 0.61
17 3 0.08
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATAATTCTAAATTT
Found at i:5172425 original size:31 final size:31
Alignment explanation
Indices: 5172368--5172437 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
5172358 AAATTATTTA
*
5172368 AATTTAAAATAATCTAAATATAAAATAATTCT-
1 AATTTAAAATAATCTAAACATAAAAT-A-TCTG
* *
5172400 AATTTAAAA-ATTCTAAACATCAAATATCTG
1 AATTTAAAATAATCTAAACATAAAATATCTG
5172430 AATTTAAA
1 AATTTAAA
5172438 TTTTAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.09
30 9 0.26
31 13 0.38
32 9 0.26
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (31 bp):
AATTTAAAATAATCTAAACATAAAATATCTG
Found at i:5172926 original size:16 final size:16
Alignment explanation
Indices: 5172907--5173001 Score: 75
Period size: 16 Copynumber: 5.9 Consensus size: 16
5172897 TAATTCGAAT
*
5172907 TAAAAATAATTTTAAC
1 TAAAAATAATTTAAAC
*
5172923 TAAAAAT-GTATTAAAC
1 TAAAAATAAT-TTAAAC
* * *
5172939 TCAAAATTATTTAAAT
1 TAAAAATAATTTAAAC
* *
5172955 TAAAAATAAATTAAAT
1 TAAAAATAATTTAAAC
* *
5172971 TTAAAATAATTTAATC
1 TAAAAATAATTTAAAC
* *
5172987 TGAAAATAATCTAAA
1 TAAAAATAATTTAAA
5173002 TCCTACAATT
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
15 1 0.02
16 60 0.97
17 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAAATAATTTAAAC
Found at i:5172959 original size:32 final size:32
Alignment explanation
Indices: 5172909--5172995 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
5172899 ATTCGAATTA
* **
5172909 AAAATAATTTTAACTAAAAATGTATTAAACTC
1 AAAATAATTTAAACTAAAAATAAATTAAACTC
* * * *
5172941 AAAATTATTTAAATTAAAAATAAATTAAATTT
1 AAAATAATTTAAACTAAAAATAAATTAAACTC
* *
5172973 AAAATAATTTAATCTGAAAATAA
1 AAAATAATTTAAACTAAAAATAA
5172996 TCTAAATCCT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (32 bp):
AAAATAATTTAAACTAAAAATAAATTAAACTC
Found at i:5175431 original size:21 final size:22
Alignment explanation
Indices: 5175395--5175449 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
5175385 ATTTAATGTT
*
5175395 AAATTTAATTAAAAATTATT-AAA
1 AAATTTAA--AAAAATAATTAAAA
*
5175418 AATTTTAAAAAAATAATTAAAA
1 AAATTTAAAAAAATAATTAAAA
5175440 AAATTTAAAA
1 AAATTTAAAA
5175450 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.32
22 12 0.43
23 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATTTAAAAAAATAATTAAAA
Found at i:5175457 original size:22 final size:23
Alignment explanation
Indices: 5175401--5175460 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
5175391 TGTTAAATTT
*
5175401 AATTAAAAATTATTAAAAATTTTAA
1 AATT-AAAATTA-TAAAAAATTTAA
*
5175426 AA-AAATAATTA-AAAAAATTTAA
1 AATTAA-AATTATAAAAAATTTAA
5175448 AATTAAAATTATA
1 AATTAAAATTATA
5175461 TAAATCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
22 17 0.59
23 5 0.17
24 5 0.17
25 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AATTAAAATTATAAAAAATTTAA
Found at i:5175800 original size:25 final size:24
Alignment explanation
Indices: 5175772--5175827 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
5175762 TATCAAATCG
*
5175772 ATTAAAAAATTTAA-AGTATAATTAT
1 ATTAAAAAATTTAATAAT-TAATT-T
**
5175797 ATTATTAAATTTAATAATTAATTT
1 ATTAAAAAATTTAATAATTAATTT
5175821 ATTAAAA
1 ATTAAAA
5175828 TATTAATCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 6 0.24
25 17 0.68
26 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTAAAAAATTTAATAATTAATTT
Found at i:5177920 original size:23 final size:21
Alignment explanation
Indices: 5177874--5177916 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5177864 TATAATATTA
*
5177874 AAATTTATATATTTTATAATT
1 AAATTTAAATATTTTATAATT
5177895 AAATTTAAATATTTT-TAATT
1 AAATTTAAATATTTTATAATT
5177915 AA
1 AA
5177917 TAAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATTTAAATATTTTATAATT
Found at i:5178274 original size:68 final size:67
Alignment explanation
Indices: 5178163--5178298 Score: 202
Period size: 67 Copynumber: 2.0 Consensus size: 67
5178153 GATAACTAAG
* * *
5178163 ATTGCATATATAATTTTTAAATTAATAAATATTTTTTAATTTAAAGTGTATATAATTTTTAAATT
1 ATTGCATAGATAATTTTTAAATTAATAAAGATTTTTTAATTTAAAG-ATATATAATTTTTAAATT
5178228 GAT
65 GAT
* *
5178231 ATTGCTTAGATAATTTTTAAATTAAT-AAGATTTTTTAATTTTAAAGATATATATTTTTTAAATT
1 ATTGCATAGATAATTTTTAAATTAATAAAGATTTTTTAA-TTTAAAGATATATAATTTTTAAATT
5178295 GAT
65 GAT
5178298 A
1 A
5178299 AGATAGTATT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
67 31 0.50
68 31 0.50
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (67 bp):
ATTGCATAGATAATTTTTAAATTAATAAAGATTTTTTAATTTAAAGATATATAATTTTTAAATTG
AT
Found at i:5181022 original size:6 final size:6
Alignment explanation
Indices: 5181011--5181035 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5181001 AAATATCCGA
5181011 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
5181036 TTTCTTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:5185087 original size:16 final size:17
Alignment explanation
Indices: 5185066--5185099 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5185056 ATACAAATAT
*
5185066 AAATA-TTAATATTTAA
1 AAATATTTAATATCTAA
5185082 AAATATTTAATATCTAA
1 AAATATTTAATATCTAA
5185099 A
1 A
5185100 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAATATCTAA
Found at i:5185506 original size:15 final size:15
Alignment explanation
Indices: 5185482--5185534 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5185472 TATTAACTTA
5185482 AATA-TTAAAATATT
1 AATATTTAAAATATT
* *
5185496 TATTTTTAAAATATT
1 AATATTTAAAATATT
*
5185511 AATATTT-AAATAAT
1 AATATTTAAAATATT
5185525 AATAGTTTAA
1 AATA-TTTAA
5185535 GCATAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 12 0.39
15 18 0.58
16 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTAAAATATT
Found at i:5185527 original size:14 final size:13
Alignment explanation
Indices: 5185505--5185553 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
5185495 TTATTTTTAA
*
5185505 AATATTAATATTT
1 AATAATAATATTT
5185518 AAATAATAATAGTTT
1 -AATAATAATA-TTT
**
5185533 AAGCATAATATTT
1 AATAATAATATTT
5185546 AATAATAA
1 AATAATAA
5185554 AATATTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 9 0.31
14 17 0.59
15 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (13 bp):
AATAATAATATTT
Found at i:5185603 original size:48 final size:46
Alignment explanation
Indices: 5185540--5185653 Score: 117
Period size: 45 Copynumber: 2.5 Consensus size: 46
5185530 TTTAAGCATA
* * *
5185540 ATATTTAATAATAAAATATTATATTAGTATTAAATA-CTTAAAATAAT
1 ATATTTATTATTAAAATATTATATTA-TA-TAAATATCTTAAAACAAT
* * *
5185587 ACTATTTATTATTAAAACATT-TATTATATAAATATTTTAAAACATT
1 A-TATTTATTATTAAAATATTATATTATATAAATATCTTAAAACAAT
5185633 ATAATTT-TTATTAAAATATTA
1 AT-ATTTATTATTAAAATATTA
5185654 ATTTACAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
45 19 0.34
46 15 0.27
47 6 0.11
48 16 0.29
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (46 bp):
ATATTTATTATTAAAATATTATATTATATAAATATCTTAAAACAAT
Found at i:5185924 original size:15 final size:15
Alignment explanation
Indices: 5185903--5185935 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5185893 TATAAAAATA
*
5185903 TAAAAATTTTAT-AT
1 TAAAAAATTTATCAT
5185917 TAAAAAATTTATCAT
1 TAAAAAATTTATCAT
5185932 TAAA
1 TAAA
5185936 CAACTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAAAATTTATCAT
Found at i:5186694 original size:15 final size:16
Alignment explanation
Indices: 5186654--5186688 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
5186644 TATAAAATTA
5186654 ATTTAATTTA-TTTTT
1 ATTTAATTTATTTTTT
5186669 ATTTAATTTATTTTTT
1 ATTTAATTTATTTTTT
5186685 ATTT
1 ATTT
5186689 GATTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTAATTTATTTTTT
Found at i:5187204 original size:70 final size:72
Alignment explanation
Indices: 5187099--5187280 Score: 176
Period size: 70 Copynumber: 2.5 Consensus size: 72
5187089 TAGAGTTATT
* * *
5187099 ATTTATTTCTATTTGTAGAAGTTTAAATTTA-TTTTTATTTAATTAT-ATA-G-GTTTAAATTTT
1 ATTTATTT-TATTTGTAAAAATTT-AATTTATTTTTTA-TTAAGTATGATATGTGTTTAAATTTT
5187160 T-AGGGTATA
63 TAAGGGTATA
* *
5187169 ATTTATTTTGATTTGTAAAAATTTAATTGTGTTTTTTATTAGGTATGATATGTGTTTAAATTTTT
1 ATTTATTTT-ATTTGTAAAAATTTAATT-TATTTTTTATTAAGTATGATATGTGTTTAAATTTTT
* *
5187234 AATGGTGTA
64 AAGGGTATA
* *
5187243 ATCTAATTTTATTTATAAAAATTTATGATTTATTTTTT
1 AT-TTATTTTATTTGTAAAAATTTA--ATTTATTTTTT
5187281 TAGTTTGATT
Statistics
Matches: 92, Mismatches: 10, Indels: 15
0.79 0.09 0.13
Matches are distributed among these distances:
69 5 0.05
70 27 0.29
71 9 0.10
72 1 0.01
73 12 0.13
74 22 0.24
75 13 0.14
76 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.57
Consensus pattern (72 bp):
ATTTATTTTATTTGTAAAAATTTAATTTATTTTTTATTAAGTATGATATGTGTTTAAATTTTTAA
GGGTATA
Found at i:5187279 original size:74 final size:68
Alignment explanation
Indices: 5187124--5187283 Score: 153
Period size: 74 Copynumber: 2.2 Consensus size: 68
5187114 TAGAAGTTTA
** * *
5187124 AATTTATTTTTATTTAATTATATAGGTTTAAATTTTTAGGGTATAATTTATTTTGATTTGTAAAA
1 AATTTATTTTTA-TTAGGTATATAGGTTTAAATTTTTAGGGTATAATTAATTTTGATTTATAAAA
5187189 ATTT
65 ATTT
* * *
5187193 AATTGTGTTTTTTATTAGGTATGATATGTGTTTAAATTTTTAATGGTGTAATCTAATTTT-ATTT
1 AATT-T-ATTTTTATTAGGTAT-ATA-G-GTTTAAATTTTT-AGGGTATAAT-TAATTTTGATTT
5187257 ATAAAAATTT
59 ATAAAAATTT
5187267 ATGATTTATTTTT-TTAG
1 A--ATTTATTTTTATTAG
5187284 TTTGATTATA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
69 4 0.05
70 7 0.09
71 9 0.12
72 1 0.01
73 16 0.22
74 27 0.36
75 7 0.09
76 3 0.04
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (68 bp):
AATTTATTTTTATTAGGTATATAGGTTTAAATTTTTAGGGTATAATTAATTTTGATTTATAAAAA
TTT
Found at i:5187470 original size:12 final size:13
Alignment explanation
Indices: 5187453--5187484 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5187443 TGTCTCGCAC
5187453 GTCGACCT-GTGA
1 GTCGACCTCGTGA
5187465 GTCGA-CTCGTGA
1 GTCGACCTCGTGA
5187477 GTCGACCT
1 GTCGACCT
5187485 TATTCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.16, C:0.28, G:0.31, T:0.25
Consensus pattern (13 bp):
GTCGACCTCGTGA
Found at i:5190523 original size:13 final size:13
Alignment explanation
Indices: 5190505--5190530 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5190495 TACAGCAAGT
5190505 ATGTATCGATACA
1 ATGTATCGATACA
5190518 ATGTATCGATACA
1 ATGTATCGATACA
5190531 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5192778 original size:21 final size:21
Alignment explanation
Indices: 5192745--5192789 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5192735 TTGCAAGTTG
*
5192745 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5192767 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
5192787 AAA
1 AAA
5192790 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:5194613 original size:15 final size:15
Alignment explanation
Indices: 5194593--5194623 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5194583 TAAAAATGTC
*
5194593 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
5194608 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
5194623 C
1 C
5194624 CACAAGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:5196719 original size:13 final size:13
Alignment explanation
Indices: 5196701--5196739 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
5196691 TACATTTTCT
5196701 TTGTATCGATACA
1 TTGTATCGATACA
5196714 TTGTATCGATACA
1 TTGTATCGATACA
5196727 TTGTATCGATACA
1 TTGTATCGATACA
5196740 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5196884 original size:21 final size:21
Alignment explanation
Indices: 5196860--5196906 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5196850 AAATCTTTTG
5196860 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
5196881 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
5196901 CAAAAT
1 CAAAAT
5196907 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:5196903 original size:20 final size:19
Alignment explanation
Indices: 5196862--5196904 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
5196852 ATCTTTTGCA
5196862 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
5196882 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
5196902 AAA
1 AAA
5196905 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:5199289 original size:13 final size:13
Alignment explanation
Indices: 5199271--5199296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5199261 TACAGCAAGT
5199271 ATGTATCGATACA
1 ATGTATCGATACA
5199284 ATGTATCGATACA
1 ATGTATCGATACA
5199297 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5204336 original size:32 final size:32
Alignment explanation
Indices: 5204282--5204344 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
5204272 CAATTCAGTG
*
5204282 TGTATCAATACCAAGAACATGTATTGATACAA
1 TGTATCAATACCAAGAACATGTATCGATACAA
* * * *
5204314 TGTATCGATACTAAGCATATGTATCGATACA
1 TGTATCAATACCAAGAACATGTATCGATACA
5204345 TTTGGGTATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCAATACCAAGAACATGTATCGATACAA
Found at i:5204485 original size:14 final size:14
Alignment explanation
Indices: 5204466--5204494 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5204456 AACATTATTT
5204466 TTTTGCTTGAAAAA
1 TTTTGCTTGAAAAA
5204480 TTTTGCTTGAAAAA
1 TTTTGCTTGAAAAA
5204494 T
1 T
5204495 ATTTATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (14 bp):
TTTTGCTTGAAAAA
Found at i:5204493 original size:15 final size:15
Alignment explanation
Indices: 5204466--5204498 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
5204456 AACATTATTT
5204466 TTTTGCTTGAAAA-A
1 TTTTGCTTGAAAATA
5204480 TTTTGCTTGAAAAATA
1 TTTTGCTTG-AAAATA
5204496 TTT
1 TTT
5204499 ATACTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (15 bp):
TTTTGCTTGAAAATA
Found at i:5206878 original size:15 final size:15
Alignment explanation
Indices: 5206858--5206908 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
5206848 TTGCTGTTCG
5206858 TCTTGCTATTTTGTT
1 TCTTGCTATTTTGTT
* *
5206873 TCTTGCTGTTTTTTTT
1 TCTTGCT-ATTTTGTT
5206889 GTCTTGCTATTTTGTT
1 -TCTTGCTATTTTGTT
5206905 TCTT
1 TCTT
5206909 ATTTTGATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.37
16 12 0.40
17 7 0.23
ACGTcount: A:0.04, C:0.14, G:0.14, T:0.69
Consensus pattern (15 bp):
TCTTGCTATTTTGTT
Found at i:5206886 original size:17 final size:17
Alignment explanation
Indices: 5206857--5206901 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
5206847 GTTGCTGTTC
*
5206857 GTCTTGCTA-TTTTGTT
1 GTCTTGCTATTTTTTTT
*
5206873 -TCTTGCTGTTTTTTTT
1 GTCTTGCTATTTTTTTT
5206889 GTCTTGCTATTTT
1 GTCTTGCTATTTT
5206902 GTTTCTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.04, C:0.13, G:0.16, T:0.67
Consensus pattern (17 bp):
GTCTTGCTATTTTTTTT
Found at i:5207167 original size:8 final size:8
Alignment explanation
Indices: 5207154--5207217 Score: 80
Period size: 8 Copynumber: 8.0 Consensus size: 8
5207144 ATTATGCATA
5207154 TATATTTT
1 TATATTTT
5207162 TATATTTT
1 TATATTTT
5207170 CT-TA-TTT
1 -TATATTTT
5207177 TATATTTTT
1 TATA-TTTT
5207186 ATATATTTT
1 -TATATTTT
5207195 TATATTTT
1 TATATTTT
5207203 TATA-TTT
1 TATATTTT
5207210 TATATTTT
1 TATATTTT
5207218 GAGACAAGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
6 1 0.02
7 12 0.24
8 25 0.50
9 8 0.16
10 4 0.08
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TATATTTT
Found at i:5207174 original size:10 final size:10
Alignment explanation
Indices: 5207152--5207207 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
5207142 TTATTATGCA
5207152 TATATATTTT
1 TATATATTTT
5207162 TATAT-TTTCT
1 TATATATTT-T
5207172 TATTTTATATTTT
1 TA---TATATTTT
5207185 TATATA-TTT
1 TATATATTTT
5207194 T-TATATTTT
1 TATATATTTT
5207203 TATAT
1 TATAT
5207208 TTTATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
8 4 0.10
9 11 0.28
10 15 0.38
13 6 0.15
14 3 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TATATATTTT
Found at i:5207180 original size:23 final size:23
Alignment explanation
Indices: 5207154--5207217 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
5207144 ATTATGCATA
5207154 TATATTTTTATATTTTCTTAT-TT
1 TATATTTTTATATTTT-TTATATT
5207177 TATATTTTTATATATTTTTATATT
1 TATATTTTTATAT-TTTTTATATT
*
5207201 TTTATATTTTATATTTT
1 TATAT-TTTTATATTTT
5207218 GAGACAAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 17 0.46
24 12 0.32
25 8 0.22
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TATATTTTTATATTTTTTATATT
Found at i:5207180 original size:25 final size:25
Alignment explanation
Indices: 5207152--5207217 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
5207142 TTATTATGCA
5207152 TATATATTTTTATATTTTCT-TATTT
1 TATATATTTTTATATTTT-TATATTT
5207177 TATAT-TTTTATATATTTTTATATTT
1 TATATATTTT-TATATTTTTATATTT
5207202 T-TATA-TTTTATATTTT
1 TATATATTTTTATATTTT
5207218 GAGACAAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
23 8 0.21
24 11 0.29
25 19 0.50
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (25 bp):
TATATATTTTTATATTTTTATATTT
Found at i:5207189 original size:33 final size:33
Alignment explanation
Indices: 5207152--5207217 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
5207142 TTATTATGCA
5207152 TATATATTTTTATATTTTCT-TATTTTATATTTT
1 TATATATTTTTATATTTT-TATATTTTATATTTT
5207185 TATATATTTTTATATTTTTATATTTTATATTTT
1 TATATATTTTTATATTTTTATATTTTATATTTT
5207218 GAGACAAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (33 bp):
TATATATTTTTATATTTTTATATTTTATATTTT
Found at i:5207494 original size:103 final size:104
Alignment explanation
Indices: 5207309--5207521 Score: 306
Period size: 103 Copynumber: 2.0 Consensus size: 104
5207299 TACTATTTCG
* * * *
5207309 ATTATGAATGTGTGAAGTCCATTTGTTGGAAGTGGATTTCTATTATAATGGCTACTATATCGAAT
1 ATTA-GAATGTGTGAAGTCCATTTGATGGAAGTGAATTTCTATTATAATGACTACTATATCAAAT
* *
5207374 CTCAGATAATCCGAAA-TTCTAAGAAAAAGACTC-GACGAA
65 CTCAGATAATCCAAAATTTC-AAGAAAAAGACCCAGACGAA
*
5207413 ATTAGAATGTGTGAAGTCCATTTGATGGAATTGAATTT-TCATTATAATGACTACTATATCAAAT
1 ATTAGAATGTGTGAAGTCCATTTGATGGAAGTGAATTTCT-ATTATAATGACTACTATATCAAAT
*
5207477 CTCGGATAATCCAAAATTTCAAGAAAAAGACCCAGACGAA
65 CTCAGATAATCCAAAATTTCAAGAAAAAGACCCAGACGAA
5207517 ATTAG
1 ATTAG
5207522 GTGTCTACAC
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
102 1 0.01
103 79 0.81
104 18 0.18
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (104 bp):
ATTAGAATGTGTGAAGTCCATTTGATGGAAGTGAATTTCTATTATAATGACTACTATATCAAATC
TCAGATAATCCAAAATTTCAAGAAAAAGACCCAGACGAA
Found at i:5208078 original size:33 final size:33
Alignment explanation
Indices: 5208041--5208107 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5208031 TTCAACGATT
5208041 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
5208074 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
5208107 T
1 T
5208108 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:5208079 original size:13 final size:13
Alignment explanation
Indices: 5208061--5208085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5208051 CATAAAATGT
5208061 TGTATCGATACAA
1 TGTATCGATACAA
5208074 TGTATCGATACA
1 TGTATCGATACA
5208086 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5208168 original size:13 final size:13
Alignment explanation
Indices: 5208150--5208174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5208140 ATTACTCACA
5208150 TGTATCGATACAT
1 TGTATCGATACAT
5208163 TGTATCGATACA
1 TGTATCGATACA
5208175 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5208311 original size:52 final size:52
Alignment explanation
Indices: 5208183--5208303 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
5208173 CACTGATCTT
*
5208183 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
5208235 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
5208287 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
5208304 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:5215489 original size:1 final size:1
Alignment explanation
Indices: 5215483--5215518 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
5215473 GTTCTTTTCC
* *
5215483 AAAAAAAGAAACAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5215519 CCCCTTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.03, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:5216598 original size:30 final size:30
Alignment explanation
Indices: 5216465--5216646 Score: 197
Period size: 31 Copynumber: 5.9 Consensus size: 30
5216455 AAAAAAAAAA
*
5216465 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
* *
5216496 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
* *
5216527 AAAGTCCACGACGCAGTGGCATCTTTTCCTTT
1 AAAGTCCACGACTCAGTGGCATCTTTT-C-TC
5216559 AAAGTCCACGACTCAGTGGCAT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTT-TCTC
* *
5216589 AAGGTCCACGACTCAGTGGCATTTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATCTTTTC-TC
* * *
5216620 AAAGCCCACAACTTC-GTGGCACCTTTT
1 AAAGTCCACGAC-TCAGTGGCATCTTTT
5216647 AAAGCCCACA
Statistics
Matches: 132, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
30 29 0.22
31 78 0.59
32 25 0.19
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTC
Found at i:5216639 original size:93 final size:94
Alignment explanation
Indices: 5216465--5216646 Score: 228
Period size: 93 Copynumber: 1.9 Consensus size: 94
5216455 AAAAAAAAAA
5216465 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAA
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAA
* * *
5216530 GTCCACGACGCAGTGGCATCTTTTCCTTT
66 GCCCACAACGCAGTGGCACCTTTTCCTTT
* * * * *
5216559 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTCAAGGTCCACGACTCAGTGGC-ATTTTTTCTTCA
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTCAAAGTCCACGACTCAGTGGCAATCTCTGC-TCA
*
5216621 AAGCCCACAACTTC-GTGGCACCTTTT
64 AAGCCCACAAC-GCAGTGGCACCTTTT
5216647 AAAGCCCACA
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
92 7 0.09
93 48 0.63
94 21 0.28
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (94 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAA
GCCCACAACGCAGTGGCACCTTTTCCTTT
Found at i:5216684 original size:34 final size:35
Alignment explanation
Indices: 5216643--5217414 Score: 797
Period size: 34 Copynumber: 22.9 Consensus size: 35
5216633 TCGTGGCACC
*
5216643 TTTTAAAGCCCACAACTCCGTGGCAC-CTTCTTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
*
5216677 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT--CT
*
5216714 TTTCAAAGCCCACAACTCCGTGGCAC-CTTTTTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
*
5216748 GTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
*
5216783 CTTTTCAAAGCCCACGACTCCGTGGCA--C----TC-
1 -TTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCT
*
5216813 -TTTAAAGCCCACAACTCCGTGGCAC-CTTCTTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
*
5216846 TTTCAAAGCCCACAACTCCGTGGCA--CTTTTTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
5216879 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT--CT
*
5216916 TTTCAAAGCCCACAACTCCGTGGCAC-CTTTTTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
5216950 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT--CT
5216987 TTTTAAAGCCCACAACTCCGTGGCAC-C-----C-
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
* * *
5217015 TTTT-AAGTCCACGACTCCGTGGCACTC-TTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
*
5217048 TTCT-AAGCCCACAACTCCGTGGCACTCTTTTTTTCCT
1 TTTTAAAGCCCACAACTCCGTGGCACTC--TTTTT-CT
*
5217085 TTTTAAAGCCCACAACTCCGTGGCAC-CTTCTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCACTC-T-TTTTCT
*
5217121 TTCT-AAGCCCACAACTCCGTGGCAC-C-----C-
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
* * *
5217148 TTTT-AAGTCCACGACTCCGTGGCACTC-TTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
* *
5217181 TTTT-AAGTCCACGACTCCGTGGCACTC-TTTTC-
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
* * *
5217213 CTTTAAAGCCCACAACTACGTGGCACTC-TTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
* *
5217247 TTCT-AAGCCCACAACTCCGTGGCACTCTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
* * *
5217281 TTCT-AAGCCCACAACTCTGTGGCACTCTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
*
5217315 TTCT-AAGCCCACAACTCCGTGGCACTCTTTTTTTCCT
1 TTTTAAAGCCCACAACTCCGTGGCACTC--TTTTT-CT
* *
5217352 TTTTAAAGCCCACAACTCTGTGGCAC-CTTGTTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
* *
5217386 TTTT-AAGTCCACAACTTCGTGGCA-TCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTT
5217415 CACCCTTTCT
Statistics
Matches: 649, Mismatches: 43, Indels: 93
0.83 0.05 0.12
Matches are distributed among these distances:
27 61 0.09
28 11 0.02
29 1 0.00
31 2 0.00
32 7 0.01
33 154 0.24
34 174 0.27
35 52 0.08
36 31 0.05
37 115 0.18
38 41 0.06
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.33
Consensus pattern (35 bp):
TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
Found at i:5216725 original size:71 final size:70
Alignment explanation
Indices: 5216641--5217414 Score: 846
Period size: 71 Copynumber: 11.5 Consensus size: 70
5216631 CTTCGTGGCA
* *
5216641 CCTTTT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCTGTGGCACTC
1 CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTC
5216705 TTTTT
66 TTTTT
*
5216710 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACT
1 -CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
5216775 CTTTTT
65 CTTTTT
*
5216781 CTCTTTTCAAAGCCCACGACTCCGTGGCA-C----TC--TTTAAAGCCCACAACTCCGTGGCAC-
1 C-CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
*
5216838 CTTCTT
65 CTTTTT
5216844 -CTTTTCAAAGCCCACAACTCCGTGGCA-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTC
1 CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTC
5216907 TTTTT
66 TTTTT
5216912 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
1 -CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
5216977 CTTTTT
65 CTTTTT
* * *
5216983 CCCTTTTTAAAGCCCACAACTCCGTGGCACC-----C-TTTT-AAGTCCACGACTCCGTGGCACT
1 -CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
5217041 C-TTTT
65 CTTTTT
*
5217046 CC--TTCTAAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTTAAAGCCCACAACTCCGTGGC
1 CCTTTTCAAAGCCCACAACTCCGTGGCAC-C--TTTTT-CTTTTTAAAGCCCACAACTCCGTGGC
5217109 AC-CTTCTTTT
62 ACTC-T-TTTT
* * *
5217119 CC--TTCTAAGCCCACAACTCCGTGGCACC-----C-TTTT-AAGTCCACGACTCCGTGGCACTC
1 CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTC
5217175 -TTTT
66 TTTTT
* * * *
5217179 CCTTTT--AAGTCCACGACTCCGTGGCA-CTCTTTTC-CTTTAAAGCCCACAACTACGTGGCACT
1 CCTTTTCAAAGCCCACAACTCCGTGGCACCT-TTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
5217240 C-TTTT
65 CTTTTT
* * * *
5217245 CC--TTCTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCTGTGGCACT
1 CCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
5217307 CTTTTT
65 CTTTTT
* *
5217313 CC--TTCTAAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTTAAAGCCCACAACTCTGTGGC
1 CCTTTTCAAAGCCCACAACTCCGTGGCAC-C--TTTTT-CTTTTTAAAGCCCACAACTCCGTGGC
*
5217376 AC-CTTGTT
62 ACTCTTTTT
* * * *
5217384 -CTTTT-TAAGTCCACAACTTCGTGGCATCTTT
1 CCTTTTCAAAGCCCACAACTCCGTGGCACCTTT
5217415 CACCCTTTCT
Statistics
Matches: 622, Mismatches: 34, Indels: 98
0.82 0.05 0.13
Matches are distributed among these distances:
59 1 0.00
60 47 0.08
61 28 0.05
62 23 0.04
63 14 0.02
64 49 0.08
65 10 0.02
66 47 0.08
67 51 0.08
68 45 0.07
69 1 0.00
70 47 0.08
71 204 0.33
72 24 0.04
73 31 0.05
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.33
Consensus pattern (70 bp):
CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTC
TTTTT
Found at i:5217026 original size:27 final size:28
Alignment explanation
Indices: 5216987--5217078 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 28
5216977 CTTTTTCCCT
5216987 TTTTAAAGCCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACCC
* * *
5217015 TTTT-AAGTCCACGACTCCGTGGCACTCTT
1 TTTTAAAGCCCACAACTCCGTGGCAC-C-C
* *
5217044 TTCCTTCTAAGCCCACAACTCCGTGGCACTC
1 TT--TT-AAAGCCCACAACTCCGTGGCACCC
5217075 TTTT
1 TTTT
5217079 TTTCCTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
27 19 0.37
28 5 0.10
29 4 0.08
31 4 0.08
33 19 0.37
ACGTcount: A:0.20, C:0.36, G:0.14, T:0.30
Consensus pattern (28 bp):
TTTTAAAGCCCACAACTCCGTGGCACCC
Found at i:5217159 original size:27 final size:27
Alignment explanation
Indices: 5217119--5217211 Score: 96
Period size: 27 Copynumber: 3.2 Consensus size: 27
5217109 ACCTTCTTTT
* * *
5217119 CCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACGACTCCGTGGCAC
5217146 CCTTTTAAGTCCACGACTCCGTGGCACTC
1 CCTTTTAAGTCCACGACTCCGTGGCA--C
5217175 TTTTCCTTTTAAGTCCACGACTCCGTGGCAC
1 ----CCTTTTAAGTCCACGACTCCGTGGCAC
*
5217206 TCTTTT
1 CCTTTT
5217212 CCTTTAAAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
27 28 0.50
29 1 0.02
31 1 0.02
33 26 0.46
ACGTcount: A:0.17, C:0.37, G:0.15, T:0.31
Consensus pattern (27 bp):
CCTTTTAAGTCCACGACTCCGTGGCAC
Found at i:5217165 original size:133 final size:133
Alignment explanation
Indices: 5216648--5217409 Score: 772
Period size: 133 Copynumber: 5.7 Consensus size: 133
5216638 GCACCTTTTA
* *
5216648 AAGCCCACAACTCCGTGGCAC-CTTCTT-CTTTTTAAAGCCCACAACTCTGTGGCACTCTT-TTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTTT
* * *
5216710 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACT
65 TCC--TTCTAAGCCCACAACTCCGTGGCA-C---TCCT-TTT-AAGCCCACAACTCCGTGGCACT
*
5216775 CTTTTTCTCTTTTCA
122 CTTTTTC-C--TTCT
*
5216790 AAGCCCACGACTCCGTGGCA--C----T-C--TTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTT-T
* *
5216846 T--TTCAAAGCCCACAACTCCGTGGCACTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTT
65 TCCTTCTAAGCCCACAACTCCGTGGCAC----TCCTTTT-AAGCCCACAACTCCGTGGCACTCTT
*
5216909 TTTCCCTTTTCA
125 TTT-CC--TTCT
5216921 AAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTTAAAGCCCACAACTCCGTGGCACTCTT-TTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTTT
* * * *
5216983 CCCTTTTTAAAGCCCACAACTCCGTGGCAC-CCTTTTAAGTCCACGACTCCGTGGCACTC-TTTT
65 TCC-TTCT-AAGCCCACAACTCCGTGGCACTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
5217046 CCTTCT
128 CCTTCT
5217052 AAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTT
1 AAGCCCACAACTCCGTGGCACTC--TTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTT
* *
5217117 TTCCTTCTAAGCCCACAACTCCGTGGCAC-CCTTTTAAGTCCACGACTCCGTGGCACTC-TTTTC
64 TTCCTTCTAAGCCCACAACTCCGTGGCACTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTC
*
5217180 CTTTT
129 CTTCT
* * *
5217185 AAGTCCACGACTCCGTGGCACTC-TTTTCC--TTTAAAGCCCACAACTACGTGGCA-C-TCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTTT
* *
5217245 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCACTCTT
66 CCTTCTAAGCCCACAACTCCGTGGCA--C----TCCTTTTAAGCCCACAACTCCGTGGCACTCTT
5217310 TTTCCTTCT
125 TTTCCTTCT
* *
5217319 AAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCACCTTGTT
1 AAGCCCACAACTCCGTGGCACTC--TTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTT
* *
5217384 CTT--TT-TAAGTCCACAACTTCGTGGCA
64 -TTCCTTCTAAGCCCACAACTCCGTGGCA
5217410 TCTTTCACCC
Statistics
Matches: 552, Mismatches: 31, Indels: 77
0.84 0.05 0.12
Matches are distributed among these distances:
126 32 0.06
127 1 0.00
128 24 0.04
130 6 0.01
131 83 0.15
132 32 0.06
133 107 0.19
134 48 0.09
135 80 0.14
136 8 0.01
137 9 0.02
138 27 0.05
139 44 0.08
140 5 0.01
141 25 0.05
142 21 0.04
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.33
Consensus pattern (133 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTTT
CCTTCTAAGCCCACAACTCCGTGGCACTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TCT
Done.