Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold829
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: 69730
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:834 original size:38 final size:38
Alignment explanation
Indices: 731--873 Score: 130
Period size: 38 Copynumber: 3.7 Consensus size: 38
721 TATACCACTA
* * *
731 GTTAAAAATAGTGGTTTTTGTATT-GAACTGTG-TCATTG
1 GTTAAAAATAGTGATTTTTGT-TTCGAATTGTGCT-AATG
* * *
769 GTTAAGAATAATGATTTTTATTTCGAATTGTGCTAATG
1 GTTAAAAATAGTGATTTTTGTTTCGAATTGTGCTAATG
* **
807 GTTAAAAATAGTGATTTTTGTTTCGAATTATGCCTACCG
1 GTTAAAAATAGTGATTTTTGTTTCGAATTGTG-CTAATG
* *
846 GTTTAGAATAGT-AGTTTTTGTTTCGAAT
1 GTTAAAAATAGTGA-TTTTTGTTTCGAAT
874 CATGCCACCA
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
37 2 0.02
38 56 0.64
39 29 0.33
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (38 bp):
GTTAAAAATAGTGATTTTTGTTTCGAATTGTGCTAATG
Found at i:864 original size:39 final size:37
Alignment explanation
Indices: 812--905 Score: 127
Period size: 39 Copynumber: 2.5 Consensus size: 37
802 TAATGGTTAA
* *
812 AAATAGT-GATTTTTGTTTCGAATTATGCCTACCGGTTT
1 AAATAGTAG-TTTTTGTTTCGAATCATGCC-ACCAGTTT
850 AGAATAGTAGTTTTTGTTTCGAATCATGCCACCAGTTT
1 A-AATAGTAGTTTTTGTTTCGAATCATGCCACCAGTTT
*
888 AAATAATAGTTTTTGTTT
1 AAATAGTAGTTTTTGTTT
906 ATAACTTGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
37 16 0.31
38 9 0.18
39 25 0.49
40 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.45
Consensus pattern (37 bp):
AAATAGTAGTTTTTGTTTCGAATCATGCCACCAGTTT
Found at i:1884 original size:29 final size:29
Alignment explanation
Indices: 1844--1901 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1834 ATTAGAATTC
*
1844 TTTTTTTAGCTTCATCTTTGTAAACACCT
1 TTTTTTTAGCTTCATCTTTATAAACACCT
1873 TTTTTTTAGCTTCATCTTTATAAACACCT
1 TTTTTTTAGCTTCATCTTTATAAACACCT
1902 AACATTTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (29 bp):
TTTTTTTAGCTTCATCTTTATAAACACCT
Found at i:1909 original size:29 final size:29
Alignment explanation
Indices: 1848--1910 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1838 GAATTCTTTT
* ****
1848 TTTAGCTTCATCTTTGTAAACACCTTTTT
1 TTTAGCTTCATCTTTATAAACACCTAACA
1877 TTTAGCTTCATCTTTATAAACACCTAACA
1 TTTAGCTTCATCTTTATAAACACCTAACA
1906 TTTAG
1 TTTAG
1911 AGGTATTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (29 bp):
TTTAGCTTCATCTTTATAAACACCTAACA
Found at i:13298 original size:2 final size:2
Alignment explanation
Indices: 13291--13330 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
13281 AGAGCAAATC
13291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13331 GTATGAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14942 original size:21 final size:21
Alignment explanation
Indices: 14901--14942 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
14891 TAAGGATGTG
*
14901 TTTGATAAAATATTAAAAATT
1 TTTGATAAAATATAAAAAATT
*
14922 TTTGATGAAATA-AAAATAATT
1 TTTGATAAAATATAAAA-AATT
14943 CAGCATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTGATAAAATATAAAAAATT
Found at i:15588 original size:19 final size:19
Alignment explanation
Indices: 15566--15612 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
15556 TTAATAAAAA
15566 ATTAATAAATTATATTTAT
1 ATTAATAAATTATATTTAT
*
15585 ATTAAT--ATTATATTTTT
1 ATTAATAAATTATATTTAT
15602 A-TAATTAAATT
1 ATTAA-TAAATT
15613 TATGTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
19 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTAATAAATTATATTTAT
Found at i:16022 original size:13 final size:13
Alignment explanation
Indices: 16001--16030 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15991 CGATACATGG
*
16001 TACATTGTATCGA
1 TACAATGTATCGA
16014 TACAATGTATCGA
1 TACAATGTATCGA
16027 TACA
1 TACA
16031 TGATGAATTG
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:16028 original size:33 final size:33
Alignment explanation
Indices: 15986--16048 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
15976 TACCACTGTT
*
15986 TGTATCGATACATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGATGA-ATTGTATCGATACAA
16019 TGTATCGATACATGATGAATTGTATCGATA
1 TGTATCGATACATGATGAATTGTATCGATA
16049 TATTGCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAA
Found at i:24058 original size:79 final size:79
Alignment explanation
Indices: 23956--24360 Score: 491
Period size: 79 Copynumber: 5.2 Consensus size: 79
23946 AATAATAGGG
** * * * *
23956 TTGGAGTATCTTCTCGAAAATAACGGGGTTGGAGCATCCCCGATTGTGAAAAATCGATGATTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAG
24021 AAATAAAATCGGGA
66 AAATAAAATCGGGA
* *
24035 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGACTATGAAAAATTGATGTTTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAG
*
24100 AAATAAAA-CCGGA
66 AAATAAAATCGGGA
* * * *
24113 GTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCTCGATTAAGAAAAATTGATATTTTA
1 -TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTA
** *
24178 GAAATAAAGCCGGGG
65 GAAATAAAATCGGGA
* *
24193 TTGGGGTATCCCCGT-GAAAATAACGGGGTTGGAGTAT-CCC--TGATGAAAAATTGATGTTTTA
1 TTGGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTA
* *
24254 AAAATAAAATCGGGG
65 GAAATAAAATCGGGA
* * * * * *
24269 TTGGAGTGTCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTG-AAAAGTCAGTGTTTTG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGA-TGTTTTA
24333 GAAATAAAATC-GGA
65 GAAATAAAATCGGGA
24347 GTTGGAGTATCCCC
1 -TTGGAGTATCCCC
24361 AATTATGGAA
Statistics
Matches: 279, Mismatches: 38, Indels: 18
0.83 0.11 0.05
Matches are distributed among these distances:
75 1 0.00
76 62 0.22
77 3 0.01
78 14 0.05
79 195 0.70
80 4 0.01
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAG
AAATAAAATCGGGA
Found at i:24337 original size:155 final size:156
Alignment explanation
Indices: 23953--24360 Score: 543
Period size: 155 Copynumber: 2.6 Consensus size: 156
23943 GATAATAATA
** * *
23953 GGGTTGGAGTATCTTCTCGAAAATAACGGGGTTGGAGCATCCCCGATTGTGAAAAATCGATGATT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTT
* *
24018 TAGAAATAAAATCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGACTATG
66 TAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA--ATG
*
24083 AAAAATTGATGTTTTAGAAATAAAACCG
129 AAAAATTGATGTTTTAAAAATAAAACCG
* * * ** * *
24111 GAGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCTCGATTAAGAAAAATTGATATTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTT
** * *
24176 TAGAAATAAAGCCGGGGTTGGGGTATCCCCGT-GAAAATAACGGGGTTGGAGTATCCCTG-ATGA
66 TAGAAATAAAATCGGGGTTGGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTATCCCCGAATGA
*
24239 AAAATTGATGTTTTAAAAATAAAATCG
130 AAAATTGATGTTTTAAAAATAAAACCG
* * *
24266 GGGTTGGAGTGTCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAGTC-AGTGTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGA-TGTT
* *
24330 TTGGAAATAAAATCGGAGTTGGAGTATCCCC
65 TTAGAAATAAAATCGGGGTTGGAGTATCCCC
24361 AATTATGGAA
Statistics
Matches: 214, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
154 1 0.00
155 107 0.50
158 105 0.49
159 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (156 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTT
TAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAATGAA
AAATTGATGTTTTAAAAATAAAACCG
Found at i:24351 original size:51 final size:49
Alignment explanation
Indices: 24296--24472 Score: 187
Period size: 51 Copynumber: 3.5 Consensus size: 49
24286 AAATAACGGG
*
24296 GTTGGAGTATCCCCGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAA-T-AGTGTTTTGGAAATAAAATCGGA
* * *
24347 GTTGGAGTATCCCCAATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAAT-AGTGTTTTGGAAATAAAATCGGA
* * * * *
24398 GTTAGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTATG-AAAATAG-TGTTTTGGAAATAAAATCGGA
*
24448 GATTGGAGTATCCCCGA-GATGAAAA
1 G-TTGGAGTATCCCCGATTATGAAAA
24473 ATCTAGAAAT
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
49 4 0.04
50 5 0.05
51 93 0.87
52 5 0.05
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (49 bp):
GTTGGAGTATCCCCGATTATGAAAATAGTGTTTTGGAAATAAAATCGGA
Found at i:26780 original size:20 final size:20
Alignment explanation
Indices: 26755--26848 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
26745 AAAATGCCTG
*
26755 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
* *
26775 AATGTATCAATACAATGAGC
1 AATGTATCGATACAATGAGA
*
26795 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
*
26815 AATGTATCGATACAAT-ACAA
1 AATGTATCGATACAATGA-GA
26835 AATGTATCGATACA
1 AATGTATCGATACA
26849 TCTGGGTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 2 0.03
20 64 0.97
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:26910 original size:18 final size:19
Alignment explanation
Indices: 26867--26919 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
26857 AACTTCCTAG
* *
26867 ATGTATCGATACAAAGATCG
1 ATGTATCGATAC-AATATCA
26887 ATGTATCGATACAATA-CA
1 ATGTATCGATACAATATCA
26905 ATGTATCGATACAAT
1 ATGTATCGATACAAT
26920 GTATCGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 16 0.52
19 3 0.10
20 12 0.39
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
ATGTATCGATACAATATCA
Found at i:26918 original size:13 final size:13
Alignment explanation
Indices: 26900--26930 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
26890 TATCGATACA
26900 ATACAATGTATCG
1 ATACAATGTATCG
26913 ATACAATGTATCG
1 ATACAATGTATCG
26926 ATACA
1 ATACA
26931 TTTCCTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (13 bp):
ATACAATGTATCG
Found at i:27612 original size:40 final size:42
Alignment explanation
Indices: 27568--27667 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 42
27558 GCCCCACTTT
* *
27568 TTGAGGACAAAGGAAAAG-AG-AATGAAATAG-GTCTTGCTCC
1 TTGAGGACAAAGGAAAAGAAGAAAAGAAA-AGTGTCATGCTCC
* *
27608 TTGAGGACAAAGGAAGAGAAGAAAAGAAAAGTGTCATGCTTC
1 TTGAGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCATGCTCC
27650 TTGAGGACAAAGTGAAAA
1 TTGAGGACAAAG-GAAAA
27668 AGAGTACGTC
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 17 0.33
41 4 0.08
42 26 0.51
43 4 0.08
ACGTcount: A:0.44, C:0.10, G:0.28, T:0.18
Consensus pattern (42 bp):
TTGAGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCATGCTCC
Found at i:27984 original size:60 final size:60
Alignment explanation
Indices: 27848--28367 Score: 503
Period size: 60 Copynumber: 8.7 Consensus size: 60
27838 AAAATAAAGT
* ** * * **
27848 GCGTCCCGCTCTTTGAGGACTAAAAAGTGTCGCCAACCCGTGTGGGCTTTGAAAAG-GAAA
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAGAAA
* *
27908 GACATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTG-GGGCTTTACAAAGAGAAA
1 G-CGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTA-AAAGAGAAA
* * * *
27969 GCATCCTGCTCTTTGAGGACTGGAAAATACCACCAACTTGTGTGGGCTTTGAAAG-GAAAA
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAG-AAA
* ** * *
28029 GGCGTCTTGCTCTTTGAGGACTAAAAAAGTGCCACTAACTTGTGTGAGCTTTGCAAAA-AGAAA
1 -GCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT--AAAAGAGAAA
* * *
28092 GCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAGAAA
* * *
28153 GTGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTT-AAA-AG---
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAA
* *
28207 GCGTCCTACTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAA-AAAAA
1 GCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAA
* ** ** * * *
28266 GGTGTCCTGCTCTTTGAGGACTGGAGGGTGCCAATAACTCGTGTGGGCTTTGAAGGAG-AA
1 -GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAA
28326 GACGTCCTGCTCTTTGAGGACT--AAAGGGTGCCACCAACTTGT
1 G-CGTCCTGCTCTTTGAGGACTGGAAA--GTGCCACCAACTTGT
28368 CCAATCCTCC
Statistics
Matches: 382, Mismatches: 54, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
54 19 0.05
55 24 0.06
56 5 0.01
57 2 0.01
58 1 0.00
59 12 0.03
60 157 0.41
61 113 0.30
62 42 0.11
63 3 0.01
64 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (60 bp):
GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAA
Found at i:28107 original size:183 final size:174
Alignment explanation
Indices: 27843--28347 Score: 584
Period size: 183 Copynumber: 2.8 Consensus size: 174
27833 GAAAAAAAAT
* * * ** *
27843 AAAGTGCGTCCCGCTCTTTGAGGACTAAAAAGTGTCGCCAACCCGTGTGGGCTTTGAAAAGGAAA
1 AAAG-GCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAGAAA
*
27908 GACATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTG-GGGCTTTACAAAGAGAAAGCA
65 G-CATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTA-AAAGAGAAAGCG
27972 TCCTGCTCTTTGAGGACTGGAAAATACCACCAACTTGTGTGGGCTTTGAAAGGA
128 TCCTGCTCTTTGAGGACT-GAAAATACCACCAACTTGTGTGGGCTTT------A
* * *
28026 AAAGGCGTCTTGCTCTTTGAGGACTAAAAAAGTGCCACTAACTTGTGTGAGCTTTGCAAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAAAGAA
* * * *
28091 AGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTG
64 AGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAGAAAGCG
** * *
28156 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTA
128 TCCTGCTCTTTGAGGACTGAAAATACCACCAACTTGTGTGGGCTTTA
* ** *
28203 AAAGGCGTCCTACTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAAAAAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAGAAA-
** * ** * * *
28267 GTGTCCTGCTCTTTGAGGACTGGAGGGTGCCAATAACTCGTGTGGGCTTTGAAGGAG-AAGACGT
65 GCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAAG-CGT
28331 CCTGCTCTTTGAGGACT
129 CCTGCTCTTTGAGGACT
28348 AAAGGGTGCC
Statistics
Matches: 279, Mismatches: 37, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
173 2 0.01
174 30 0.11
175 44 0.16
176 25 0.09
177 24 0.09
182 19 0.07
183 94 0.34
184 41 0.15
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (174 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAGAAAG
CATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAAGCGTCC
TGCTCTTTGAGGACTGAAAATACCACCAACTTGTGTGGGCTTTA
Found at i:31182 original size:20 final size:19
Alignment explanation
Indices: 31139--31198 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
31129 ACATTATGCT
***
31139 TTGTATCGATACATGTTTA
1 TTGTATCGATACATGACAA
31158 TTGTATCGATACATAGACAA
1 TTGTATCGATACAT-GACAA
31178 TTGTATCGATACATGA-AA
1 TTGTATCGATACATGACAA
31196 TTG
1 TTG
31199 GTAGTAGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.14
19 16 0.43
20 16 0.43
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATGACAA
Found at i:31239 original size:43 final size:43
Alignment explanation
Indices: 31178--31278 Score: 184
Period size: 43 Copynumber: 2.3 Consensus size: 43
31168 ACATAGACAA
* *
31178 TTGTATCGATACATGAAATTGGTAGTAGCTACCCTGCCACTGT
1 TTGTATCGATACATGAAATTGGTAGTAGCCACCCTACCACTGT
31221 TTGTATCGATACATGAAATTGGTAGTAGCCACCCTACCACTGT
1 TTGTATCGATACATGAAATTGGTAGTAGCCACCCTACCACTGT
31264 TTGTATCGATACATG
1 TTGTATCGATACATG
31279 GTATATTGTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (43 bp):
TTGTATCGATACATGAAATTGGTAGTAGCCACCCTACCACTGT
Found at i:31302 original size:33 final size:33
Alignment explanation
Indices: 31265--31329 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
31255 TACCACTGTT
*
31265 TGTATCGATACATGGT-ATATTGTATCAATACAA
1 TGTATCGATACATGATGA-ATTGTATCAATACAA
* *
31298 TGTATTGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGATGAATTGTATCAATACA
31330 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:0.11, G:0.17, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCAATACAA
Found at i:32635 original size:24 final size:23
Alignment explanation
Indices: 32602--32673 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
32592 AAAATAAAAA
32602 TAAATATAAATATATTAACACATTT
1 TAAA-ATAAATATATTAACA-ATTT
* * *
32627 TAAAATAAAATAAAATAATAATTT
1 TAAAAT-AAATATATTAACAATTT
* * *
32651 TTAAATAAATATATAAATAATTT
1 TAAAATAAATATATTAACAATTT
32674 ATTCAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 14 0.36
24 11 0.28
25 14 0.36
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAATAAATATATTAACAATTT
Found at i:32637 original size:25 final size:24
Alignment explanation
Indices: 32603--32666 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
32593 AAATAAAAAT
*
32603 AAATATAAATATATTAACACATTTTA
1 AAATA-AAATATAATAACA-ATTTTA
* * *
32629 AAATAAAATAAAATAATAATTTTT
1 AAATAAAATATAATAACAATTTTA
32653 AAATAAATATATAA
1 AAATAAA-ATATAA
32667 ATAATTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 12 0.38
25 15 0.47
26 5 0.16
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAAAATATAATAACAATTTTA
Found at i:32669 original size:23 final size:23
Alignment explanation
Indices: 32602--32673 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
32592 AAAATAAAAA
* *
32602 TAAATATAAATATATTAACACATTT
1 TAAA-ATAAATATATAAATA-ATTT
*
32627 TAAAATAAA-ATAAAATAATAATTT
1 TAAAATAAATAT-ATA-AATAATTT
*
32651 TTAAATAAATATATAAATAATTT
1 TAAAATAAATATATAAATAATTT
32674 ATTCAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
23 10 0.26
24 20 0.51
25 9 0.23
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAATAAATATATAAATAATTT
Found at i:32710 original size:29 final size:30
Alignment explanation
Indices: 32654--32728 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
32644 ATAATTTTTA
* * * *
32654 AATAAATATATAAATAATTTATT-CAAAAT
1 AATAATTATTTAAATAATTGATTAAAAAAT
*
32683 AATAATTATTTAAATGATTGATTAAAAAAT
1 AATAATTATTTAAATAATTGATTAAAAAAT
*
32713 TATAAACTTATTTAAA
1 AAT-AA-TTATTTAAA
32729 GGCTTTAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 19 0.51
30 7 0.19
31 2 0.05
32 9 0.24
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (30 bp):
AATAATTATTTAAATAATTGATTAAAAAAT
Found at i:32787 original size:6 final size:7
Alignment explanation
Indices: 32771--32795 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32761 ATAAAACTAT
32771 AAAATTA
1 AAAATTA
32778 AAAATTA
1 AAAATTA
32785 AAAATTA
1 AAAATTA
32792 AAAA
1 AAAA
32796 AACAACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:33078 original size:48 final size:48
Alignment explanation
Indices: 33023--33123 Score: 157
Period size: 48 Copynumber: 2.1 Consensus size: 48
33013 TAAAGATCAT
* ** **
33023 AATATAAATCAATATTTAAATTTTAAATTAAGGAATAAATAAATTCAA
1 AATATAAATCAATATTTAAATTTTAAACTAAAAAATAAATAAACCCAA
33071 AATATAAATCAATATTTAAATTTTAAACTAAAAAATAAATAAACCCAA
1 AATATAAATCAATATTTAAATTTTAAACTAAAAAATAAATAAACCCAA
33119 AATAT
1 AATAT
33124 GTGTTTAAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (48 bp):
AATATAAATCAATATTTAAATTTTAAACTAAAAAATAAATAAACCCAA
Found at i:33714 original size:22 final size:22
Alignment explanation
Indices: 33672--33715 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
33662 TTTGAATGGC
*
33672 TTTTAAGAAATGGTAAGTTTTT
1 TTTTAAGAAATGATAAGTTTTT
33694 TTTTAAGAGAAT-ATAA-TTTTT
1 TTTTAAGA-AATGATAAGTTTTT
33715 T
1 T
33716 AAATTTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 11 0.55
23 3 0.15
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TTTTAAGAAATGATAAGTTTTT
Found at i:35900 original size:2 final size:2
Alignment explanation
Indices: 35895--35919 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35885 TTTTTTATTT
35895 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 T
35920 TAAAGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36106 original size:28 final size:29
Alignment explanation
Indices: 36047--36108 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
36037 ATTAACAATA
* *
36047 ATTTATTATATTTTTAAATATTTTATATT
1 ATTTATTATATTTTTAAAAATTTTAGATT
*
36076 ATTTATT-TATTATTTAAAAATTTT-GGTT
1 ATTTATTATATT-TTTAAAAATTTTAGATT
36104 ATTTA
1 ATTTA
36109 AATATTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (29 bp):
ATTTATTATATTTTTAAAAATTTTAGATT
Found at i:36158 original size:18 final size:19
Alignment explanation
Indices: 36137--36172 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36127 TTTTATATTT
*
36137 ATAGATAA-ATAAATATAC
1 ATAGATAATAGAAATATAC
36155 ATAGATAATAGAAATATA
1 ATAGATAATAGAAATATA
36173 TTTACATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (19 bp):
ATAGATAATAGAAATATAC
Found at i:36760 original size:32 final size:33
Alignment explanation
Indices: 36724--36791 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
36714 TTAATTTACT
36724 TAAAATTATTATTTAAAAGC-TTTTTTCTAATA
1 TAAAATTATTATTTAAAAGCTTTTTTTCTAATA
* *
36756 TAAAATTGTTATTTAAAAGCTTTTTTTGTAATA
1 TAAAATTATTATTTAAAAGCTTTTTTTCTAATA
36789 TAA
1 TAA
36792 TCTGAATAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 19 0.58
33 14 0.42
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (33 bp):
TAAAATTATTATTTAAAAGCTTTTTTTCTAATA
Found at i:37116 original size:29 final size:29
Alignment explanation
Indices: 37065--37134 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
37055 AAAATGATAA
* * * *
37065 TTTATATATTCAT-ATCGTGTTTATATTAT
1 TTTATATATT-ATAATCATATTTAAAATAT
37094 TTTATATATTATAATCATATTTAAAATAT
1 TTTATATATTATAATCATATTTAAAATAT
*
37123 TATATA-ATTATA
1 TTTATATATTATA
37135 TAAATTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 8 0.23
29 27 0.77
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTATATATTATAATCATATTTAAAATAT
Found at i:37621 original size:31 final size:32
Alignment explanation
Indices: 37561--37621 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
37551 AATGAATTTT
*
37561 AAATAAAAAGTTATTTTTGTTATGATAAAATA
1 AAATAAAAAGTTATTTTTGTTATAATAAAATA
37593 AAATAAAAAGTT-TTTTTGTTA-AATTAAAA
1 AAATAAAAAGTTATTTTTGTTATAA-TAAAA
37622 ATTAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 1 0.04
31 14 0.52
32 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (32 bp):
AAATAAAAAGTTATTTTTGTTATAATAAAATA
Found at i:44036 original size:59 final size:57
Alignment explanation
Indices: 43913--44219 Score: 266
Period size: 58 Copynumber: 5.3 Consensus size: 57
43903 GGTTATCTTA
* * * * * * *
43913 GTCA-TTTTCTATGACTTAAGAACTTTTATGTAATTTTATATACGTTAGGATCATTTAA
1 GTCATTTTTC-ATGATTTAAGGACTTTTATGCAATTTTATGTATGTT-GGGTCATTTAG
* * *
43971 GTCATTTTGCATGATTTAAGGACTTTTATGCAATTTGATGTAATTTTAGGGTCATTTAG
1 GTCATTTTTCATGATTTAAGGACTTTTATGCAATTTTATGT-ATGTT-GGGTCATTTAG
* * *
44030 GTCATTTTTCATGATCTAAGGACTTTTATGCAAATTTTTTGTGTGTTGGGTCATTTAG
1 GTCATTTTTCATGATTTAAGGACTTTTATGC-AATTTTATGTATGTTGGGTCATTTAG
* * * * *
44088 GTCATTTTTTATGATCTAAGGACTTTTATGTATATTTCATGTAT-TT-TGTCATTTAG
1 GTCATTTTTCATGATTTAAGGACTTTTATGCA-ATTTTATGTATGTTGGGTCATTTAG
* * * * *
44144 GTAATTTTTCATGATTTATA-GAC-CTTATTGCAATTTTATG-ACTGATGATGTCACTTAG
1 GTCATTTTTCATGATTTA-AGGACTTTTA-TGCAATTTTATGTA-TGTTG-GGTCATTTAG
*
44202 GTCATTTTTCATGGTTTA
1 GTCATTTTTCATGATTTA
44220 GTGTTTTGAT
Statistics
Matches: 207, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
54 1 0.00
55 11 0.05
56 31 0.15
57 4 0.02
58 103 0.50
59 49 0.24
60 8 0.04
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (57 bp):
GTCATTTTTCATGATTTAAGGACTTTTATGCAATTTTATGTATGTTGGGTCATTTAG
Found at i:44115 original size:29 final size:29
Alignment explanation
Indices: 44025--44115 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
44015 TTTAGGGTCA
*
44025 TTTAGGTCATTTTTCATGATCTAAGGACT
1 TTTAGGTCATTTTTTATGATCTAAGGACT
* * * ** * *
44054 TTTATG-CAAATTTTTTGTG-TGTTGGGTCA
1 TTTAGGTC--ATTTTTTATGATCTAAGGACT
44083 TTTAGGTCATTTTTTATGATCTAAGGACT
1 TTTAGGTCATTTTTTATGATCTAAGGACT
44112 TTTA
1 TTTA
44116 TGTATATTTC
Statistics
Matches: 43, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
28 10 0.23
29 24 0.56
30 9 0.21
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (29 bp):
TTTAGGTCATTTTTTATGATCTAAGGACT
Found at i:44203 original size:114 final size:115
Alignment explanation
Indices: 43971--44214 Score: 273
Period size: 114 Copynumber: 2.1 Consensus size: 115
43961 GATCATTTAA
* * * *
43971 GTCATTTTGCATGATTTAAGGACTTTTATGCAATTTGATGTAATTTTAGGGTCATTTAGGTCATT
1 GTCATTTTTCATGATCTAAGGACTTTTATGCAATTTCATGTAATTTT--GGTCATTTAGGTAATT
* * ** * *
44036 TTTCATGATCTAAGGACTTTTATGCAAATTTTTTGTGTGTTGGGTCATTTAG
64 TTTCATGATCTAAGGACTTATATGCAAATTTTATGACTGATGGGTCACTTAG
* *
44088 GTCATTTTTTATGATCTAAGGACTTTTATGTATATTTCATGT-ATTTT-GTCATTTAGGTAATTT
1 GTCATTTTTCATGATCTAAGGACTTTTATGCA-ATTTCATGTAATTTTGGTCATTTAGGTAATTT
* *
44151 TTCATGATTTATA-GACCTTAT-TGC-AATTTTATGACTGATGATGTCACTTAG
65 TTCATGATCTA-AGGA-CTTATATGCAAATTTTATGACTGATG-GGTCACTTAG
44202 GTCATTTTTCATG
1 GTCATTTTTCATG
44215 GTTTAGTGTT
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
113 12 0.11
114 50 0.46
115 5 0.05
117 33 0.31
118 8 0.07
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (115 bp):
GTCATTTTTCATGATCTAAGGACTTTTATGCAATTTCATGTAATTTTGGTCATTTAGGTAATTTT
TCATGATCTAAGGACTTATATGCAAATTTTATGACTGATGGGTCACTTAG
Found at i:50386 original size:25 final size:24
Alignment explanation
Indices: 50349--50421 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
50339 TATTTAAATT
50349 TAATTA-ATT-TTTAGTTATTTTTA
1 TAATTAGATTATTTA-TTATTTTTA
*
50372 -AATTAGTTTTATTTATT-TTCTTTA
1 TAATTAG-ATTATTTATTATT-TTTA
*
50396 TAATTAGATTATATATTATTTTTA
1 TAATTAGATTATTTATTATTTTTA
50420 TA
1 TA
50422 TTTTTGTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
22 5 0.12
23 2 0.05
24 22 0.54
25 12 0.29
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (24 bp):
TAATTAGATTATTTATTATTTTTA
Found at i:57943 original size:52 final size:53
Alignment explanation
Indices: 57878--58063 Score: 220
Period size: 52 Copynumber: 3.6 Consensus size: 53
57868 TAGAAGATAA
* *
57878 CGGGGTTGGAGTATCCTCGATT-GTGAAAAATTGGTGTTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAATGAAAAATTGGTGTTTTTAGAAATAAAAT
* * * * *
57930 CGGAGTTGGAGTATCTCCGATTAAAGGAAAATTGGTGTTTTGA-AAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAATGAAAAATTGGTGTTTTTAGAAATAAAAT
* * ** *
57982 CGGGGTTGCAGTATCCCCGATTATTG-AAAATTAATG-TTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAATGAAAAATTGGTGTTTTTAGAAATAAAAT
*
58033 CGGGGTTGGAGTATCCCCGATT-ATGAGAAAT
1 CGGGGTTGGAGTATCCCCGATTAATGAAAAAT
58064 CAATATTTTG
Statistics
Matches: 112, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 6 0.05
51 41 0.37
52 49 0.44
53 16 0.14
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (53 bp):
CGGGGTTGGAGTATCCCCGATTAATGAAAAATTGGTGTTTTTAGAAATAAAAT
Found at i:58037 original size:51 final size:50
Alignment explanation
Indices: 57878--58099 Score: 221
Period size: 51 Copynumber: 4.3 Consensus size: 50
57868 TAGAAGATAA
* * ** *
57878 CGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATTAATG-TTTTAGAAATAAAAC
* * * ** *
57930 CGGAGTTGGAGTATCTCCGATTAAAGGAAAATTGGTGTTTT-GAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATT--ATGAAAATTAATGTTTTAG-AAATAAAAC
*
57982 CGGGGTTGCAGTATCCCCGATTATTGAAAATTAATGTTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTA-TGAAAATTAATGTTTTAGAAATAAAAC
* * * *
58033 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGA-AAATTAATGTTTTAGAAATAAAAC
*
58084 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
58100 TTTCGGAAAT
Statistics
Matches: 146, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
50 4 0.03
51 79 0.54
52 52 0.36
53 10 0.07
54 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAATTAATGTTTTAGAAATAAAAC
Found at i:58127 original size:79 final size:79
Alignment explanation
Indices: 58033--58199 Score: 255
Period size: 79 Copynumber: 2.1 Consensus size: 79
58023 GAAATAAAAC
* * *
58033 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTT-GGAAATAAAGCCGAGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATAAATATTTTAAG-AATAAAGCAGAGGTTGGAGTA
** *
58097 TCCTTTCGGAAATAA
65 TCCCCTCGAAAATAA
*
58112 CGGGGTTGGAGTATCCCCGATTATGAGAAATAAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATAAATATTTTAAGAATAAAGCAGAGGTTGGAGTAT
58177 CCCCTCGAAAATAA
66 CCCCTCGAAAATAA
58191 CGGGGTTGG
1 CGGGGTTGG
58200 TTGGAGTATC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 79 0.99
80 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATAAATATTTTAAGAATAAAGCAGAGGTTGGAGTAT
CCCCTCGAAAATAA
Found at i:58198 original size:28 final size:28
Alignment explanation
Indices: 58164--58267 Score: 124
Period size: 32 Copynumber: 3.6 Consensus size: 28
58154 GAATAAAGCA
58164 GGGGTTGGAGTATCCCCTCGAAAATAAC
1 GGGGTTGGAGTATCCCCTCGAAAATAAC
58192 GGGGTTGGTTGGAGTATCCCCTCGAAAATAAC
1 --GG--GGTTGGAGTATCCCCTCGAAAATAAC
*
58224 GGGGTTGGAGTAT-CCCT--AATGATTAAC
1 GGGGTTGGAGTATCCCCTCGAA--AATAAC
58251 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
58268 GATTGTGAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
25 2 0.03
27 22 0.32
28 14 0.21
30 4 0.06
32 26 0.38
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCTCGAAAATAAC
Found at i:58205 original size:32 final size:32
Alignment explanation
Indices: 58166--58231 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
58156 ATAAAGCAGG
58166 GGTTGGAGTATCCCCTCGAAAATAACGGGGTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTT
58198 GGTTGGAGTATCCCCTCGAAAATAACGGGGTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTT
58230 GG
1 GG
58232 AGTATCCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (32 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGGTT
Found at i:58334 original size:54 final size:51
Alignment explanation
Indices: 58254--58376 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 51
58244 GATTAACGGG
* * *
58254 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG---TTTTGAAAATAAAATCGGA
*
58308 GTTGGAGTATCCCTGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGAAAATAAAATCGGA
* *
58359 GTGGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
58377 GCGGAGAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
51 33 0.54
53 1 0.02
54 27 0.44
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:60761 original size:13 final size:13
Alignment explanation
Indices: 60743--60768 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60733 CAAAGATTTG
60743 ATGTATCGATACA
1 ATGTATCGATACA
60756 ATGTATCGATACA
1 ATGTATCGATACA
60769 CAGAAAAATG
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:60844 original size:19 final size:19
Alignment explanation
Indices: 60820--60909 Score: 103
Period size: 19 Copynumber: 4.7 Consensus size: 19
60810 AGCGATACAT
60820 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
60839 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
* *
60858 TGTATCGAT--AACATTTA
1 TGTATCGATACAAAACTTA
** *
60875 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACT-TA
60896 TGTATCGATACAAA
1 TGTATCGATACAAA
60910 TTATTGGAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
17 15 0.25
19 29 0.49
20 2 0.03
21 13 0.22
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:60877 original size:17 final size:17
Alignment explanation
Indices: 60836--60890 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
60826 GATACAAAAC
* *
60836 TTATGTATCGATACAAAAC
1 TTATGTATCGAT--AACAT
60855 TTATGTATCGATAACAT
1 TTATGTATCGATAACAT
60872 TTATGTATCGAT-ACAT
1 TTATGTATCGATAACAT
60888 TTA
1 TTA
60891 CTGAATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 7 0.21
17 15 0.44
19 12 0.35
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (17 bp):
TTATGTATCGATAACAT
Found at i:62513 original size:18 final size:18
Alignment explanation
Indices: 62470--62565 Score: 51
Period size: 18 Copynumber: 5.5 Consensus size: 18
62460 TCCATCTTCT
*
62470 TCTCTCCTC-CTTCTATCA
1 TCTCTCCTCTC-TCTATTA
62488 TCAT-TCCTCTCTCTATTA
1 TC-TCTCCTCTCTCTATTA
* *
62506 TCTCTCCTATCTC--TTC
1 TCTCTCCTCTCTCTATTA
* *
62522 TC-CT-ATCATCCCTATTA
1 TCTCTCCTC-TCTCTATTA
* * *
62539 TCTCTACTATCTCTCTTA
1 TCTCTCCTCTCTCTATTA
62557 TCTCTCCTC
1 TCTCTCCTC
62566 CTATCATCCA
Statistics
Matches: 57, Mismatches: 13, Indels: 16
0.66 0.15 0.19
Matches are distributed among these distances:
14 1 0.02
15 5 0.09
16 4 0.07
17 5 0.09
18 39 0.68
19 3 0.05
ACGTcount: A:0.14, C:0.40, G:0.00, T:0.47
Consensus pattern (18 bp):
TCTCTCCTCTCTCTATTA
Found at i:62535 original size:21 final size:21
Alignment explanation
Indices: 62511--62574 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
62501 TATTATCTCT
62511 CCTATCTCTTCTCCTATCATC
1 CCTATCTCTTCTCCTATCATC
* *
62532 CCTAT-TATCTCTACTATC-TC
1 CCTATCTCT-TCTCCTATCATC
* *
62552 TCTTATCTCTCCTCCTATCATC
1 -CCTATCTCTTCTCCTATCATC
62574 C
1 C
62575 ATCCTATCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.44
Consensus pattern (21 bp):
CCTATCTCTTCTCCTATCATC
Found at i:62583 original size:42 final size:42
Alignment explanation
Indices: 62463--62583 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
62453 TCACTCTTCC
* * * *
62463 ATCT-TCTTCTCTCCTCCTTCTATCAT-CATTCCTCTCTCTATT
1 ATCTCTCTTATCT-CTCCTCCTATCATCCA-TCCTATCTCTACT
* * * **
62505 ATCTCTCCTATCTCTTCTCCTATCATCCCTATTATCTCTACT
1 ATCTCTCTTATCTCTCCTCCTATCATCCATCCTATCTCTACT
62547 ATCTCTCTTATCTCTCCTCCTATCATCCATCCTATCT
1 ATCTCTCTTATCTCTCCTCCTATCATCCATCCTATCT
62584 TTTTTTTCTC
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 56 0.89
43 7 0.11
ACGTcount: A:0.15, C:0.39, G:0.00, T:0.46
Consensus pattern (42 bp):
ATCTCTCTTATCTCTCCTCCTATCATCCATCCTATCTCTACT
Found at i:63372 original size:10 final size:10
Alignment explanation
Indices: 63359--63398 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
63349 TTTTCCTTTC
63359 TTTTT-TATT
1 TTTTTGTATT
63368 TTTTTGTATCT
1 TTTTTGTAT-T
*
63379 TTTTTTTATT
1 TTTTTGTATT
63389 TTTTTGTATT
1 TTTTTGTATT
63399 CTTGAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 5 0.19
10 13 0.48
11 9 0.33
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (10 bp):
TTTTTGTATT
Found at i:66433 original size:3 final size:3
Alignment explanation
Indices: 66427--66459 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
66417 CTACTACTAC
66427 TAA TAA TAA TATA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
66460 AAAAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:66445 original size:13 final size:12
Alignment explanation
Indices: 66427--66459 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
66417 CTACTACTAC
66427 TAATAATAATATA
1 TAATAATAATA-A
66440 TAATAATAATAA
1 TAATAATAATAA
66452 TAA-AATAA
1 TAATAATAA
66460 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATAATAATAA
Done.