Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 7 of 206
Found at i:2141678 original size:38 final size:38
Alignment explanation
Indices: 2141635--2141762 Score: 184
Period size: 38 Copynumber: 3.3 Consensus size: 38
2141625 AATAAATATA
*
2141635 TTTATTTTTTAATTTTAAAATATTATTAAAATATTTTT
1 TTTATTTTTTAATTTTAAAATATTTTTAAAATATTTTT
2141673 TTTATTTTTTAATTTTAAAATATTTTTAAAATACTTTTT
1 TTTATTTTTTAATTTTAAAATATTTTTAAAATA-TTTTT
*** *
2141712 AAAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTTA-TTTTTTAATTTTAAAATATTTTTAAAATATTTTT
*
2141751 TTTAATTTTTAA
1 TTTATTTTTTAA
2141763 AATAAATTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
38 39 0.49
39 11 0.14
40 29 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTATTTTTTAATTTTAAAATATTTTTAAAATATTTTT
Found at i:2141699 original size:11 final size:11
Alignment explanation
Indices: 2141685--2141751 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
2141675 TATTTTTTAA
2141685 TTTTAAAATAT
1 TTTTAAAATAT
2141696 TTTTAAAATACT
1 TTTTAAAATA-T
2141708 TTTTAAAAT-T
1 TTTTAAAATAT
*
2141718 TTTT----TAA
1 TTTTAAAATAT
2141725 TTTTAAAATAT
1 TTTTAAAATAT
2141736 TTTTAAAATACT
1 TTTTAAAATA-T
2141748 TTTT
1 TTTT
2141752 TTAATTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
10 5 0.11
11 22 0.47
12 15 0.32
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2141732 original size:40 final size:40
Alignment explanation
Indices: 2141639--2141760 Score: 194
Period size: 40 Copynumber: 3.1 Consensus size: 40
2141629 AATATATTTA
* *
2141639 TTTTTTAATTTTAAAATATTATTAAAATA-TTTTTTTTA-
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
**
2141677 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
2141717 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
2141757 TTTT
1 TTTT
2141761 AAAATAAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
38 28 0.37
39 6 0.08
40 42 0.55
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
Found at i:2141772 original size:21 final size:21
Alignment explanation
Indices: 2141734--2141773 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2141724 ATTTTAAAAT
**
2141734 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
2141755 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
2141774 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:2141780 original size:22 final size:21
Alignment explanation
Indices: 2141733--2141791 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
2141723 AATTTTAAAA
* *
2141733 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
2141753 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
2141776 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
2141792 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:2151625 original size:31 final size:31
Alignment explanation
Indices: 2151587--2151650 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
2151577 CCTTGAGTCC
2151587 ATAATGATTTTGTCTATATATAATCTAAAAG
1 ATAATGATTTTGTCTATATATAATCTAAAAG
*
2151618 ATAATGATTTTGTCTATATATAATCTAGAAG
1 ATAATGATTTTGTCTATATATAATCTAAAAG
2151649 AT
1 AT
2151651 TTGAGTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (31 bp):
ATAATGATTTTGTCTATATATAATCTAAAAG
Found at i:2151984 original size:31 final size:30
Alignment explanation
Indices: 2151948--2152014 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
2151938 AAAAATTTTA
*
2151948 ATAAAATTGT-ACTTTTAATTTTTTAAAAATG
1 ATAAAATTGTGA--TTTAATCTTTTAAAAATG
* *
2151979 ATAAAATTTTGATTTAATCTTTTAAAAATT
1 ATAAAATTGTGATTTAATCTTTTAAAAATG
2152009 ATAAAA
1 ATAAAA
2152015 ATTTATACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 22 0.69
31 9 0.28
32 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (30 bp):
ATAAAATTGTGATTTAATCTTTTAAAAATG
Found at i:2160116 original size:12 final size:12
Alignment explanation
Indices: 2160084--2160117 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2160074 AAAAGTATAG
2160084 ATAATAATAACA
1 ATAATAATAACA
* *
2160096 ACAACAATAACA
1 ATAATAATAACA
2160108 ATAATAATAA
1 ATAATAATAA
2160118 TAGTTTTGAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAATAATAACA
Found at i:2164013 original size:12 final size:13
Alignment explanation
Indices: 2163991--2164020 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2163981 GTTTAAATTT
2163991 TTTTATTAATAAA
1 TTTTATTAATAAA
2164004 TTTT-TTAATAAA
1 TTTTATTAATAAA
2164016 TTTTA
1 TTTTA
2164021 AATTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTATTAATAAA
Found at i:2164193 original size:32 final size:31
Alignment explanation
Indices: 2164145--2164274 Score: 94
Period size: 32 Copynumber: 4.3 Consensus size: 31
2164135 TTAATATCAT
* *
2164145 ATTTGGTATCTGAACTTACCACTTTTTTTCTA
1 ATTTGGTACCTAAACTTA-CACTTTTTTTCTA
* * *
2164177 ATTTGGTACATAAAC-T----TTTTTGTCCA
1 ATTTGGTACCTAAACTTACACTTTTTTTCTA
* * *
2164203 ATTTGGTACCCAAGCTTAACACTTTTTTCCTA
1 ATTTGGTACCTAAACTT-ACACTTTTTTTCTA
2164235 ATTTGGTACCTAAACTTGACA--TTTTTTCTTA
1 ATTTGGTACCTAAACTT-ACACTTTTTTTC-TA
*
2164266 AGTTGGTAC
1 ATTTGGTAC
2164275 TTAATCTTTT
Statistics
Matches: 75, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
26 20 0.27
27 1 0.01
30 6 0.08
31 11 0.15
32 37 0.49
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTACACTTTTTTTCTA
Found at i:2164272 original size:31 final size:32
Alignment explanation
Indices: 2164205--2164274 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
2164195 TTTGTCCAAT
* *
2164205 TTGGTACCCAAGCTTAACACTTTTTTCCTAAT
1 TTGGTACCCAAACTTAACACTTTTTTCCTAAG
* * *
2164237 TTGGTACCTAAACTTGACA-TTTTTTCTTAAG
1 TTGGTACCCAAACTTAACACTTTTTTCCTAAG
2164268 TTGGTAC
1 TTGGTAC
2164275 TTAATCTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (32 bp):
TTGGTACCCAAACTTAACACTTTTTTCCTAAG
Found at i:2164346 original size:60 final size:60
Alignment explanation
Indices: 2164233--2164345 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 60
2164223 ACTTTTTTCC
*
2164233 TAATTTGGTACCTAAACTTGACATTTTTTCTTAAGTTGGTACTTAATCTTTTTTGGGGTA
1 TAATTTGGTACCTAAACTTGACATTTTTTCCTAAGTTGGTACTTAATCTTTTTTGGGGTA
* * ** *
2164293 TAATTTGGTACTTGAACTT-ATTTTTTTTCCTAATTTGGTA-TCTAATCTTTTTT
1 TAATTTGGTACCTAAACTTGACATTTTTTCCTAAGTTGGTACT-TAATCTTTTTT
2164346 TTGTTCGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 1 0.02
59 28 0.61
60 17 0.37
ACGTcount: A:0.22, C:0.12, G:0.13, T:0.53
Consensus pattern (60 bp):
TAATTTGGTACCTAAACTTGACATTTTTTCCTAAGTTGGTACTTAATCTTTTTTGGGGTA
Found at i:2164842 original size:26 final size:26
Alignment explanation
Indices: 2164806--2164857 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2164796 GTCAAGTTCA
2164806 TGTATCAAATTAAGCCAAAAAAAATT
1 TGTATCAAATTAAGCCAAAAAAAATT
2164832 TGTATCAAATTAAGCCAAAAAAAATT
1 TGTATCAAATTAAGCCAAAAAAAATT
2164858 AAGTACCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.27
Consensus pattern (26 bp):
TGTATCAAATTAAGCCAAAAAAAATT
Found at i:2164842 original size:57 final size:58
Alignment explanation
Indices: 2164718--2164845 Score: 143
Period size: 58 Copynumber: 2.2 Consensus size: 58
2164708 AAAAGCTCAG
* * * * **
2164718 GTATCATATTAGGAAAAAATATCAAGTTCAAGTACCAAATAGGGCCCAAAAAGTTTAT
1 GTATCAAATTAAGAAAAAATATCAAGTTCAAGTACCAAATAGAGCCAAAAAAAATTAT
* * * *
2164776 GTACCAAATTAAGAAAAAATGTCAAGTTCATGTATCAAATTA-AGCCAAAAAAAATT-T
1 GTATCAAATTAAGAAAAAATATCAAGTTCAAGTACCAAA-TAGAGCCAAAAAAAATTAT
2164833 GTATCAAATTAAG
1 GTATCAAATTAAG
2164846 CCAAAAAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
57 13 0.22
58 43 0.74
59 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (58 bp):
GTATCAAATTAAGAAAAAATATCAAGTTCAAGTACCAAATAGAGCCAAAAAAAATTAT
Found at i:2164870 original size:27 final size:26
Alignment explanation
Indices: 2164811--2164871 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
2164801 GTTCATGTAT
* *
2164811 CAAATTAAGCCAAAAAAAATTTGTAT
1 CAAATTAAGCCAAAAAAAATTAGTAC
2164837 CAAATTAAGCCAAAAAAAATTAAGTAC
1 CAAATTAAGCCAAAAAAAATT-AGTAC
*
2164864 CATATTAA
1 CAAATTAA
2164872 AAAAAATATC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.25
Consensus pattern (26 bp):
CAAATTAAGCCAAAAAAAATTAGTAC
Found at i:2165105 original size:11 final size:11
Alignment explanation
Indices: 2165085--2165153 Score: 58
Period size: 11 Copynumber: 6.4 Consensus size: 11
2165075 TTAAAAATTA
2165085 AAAAAGTATTTT
1 AAAAA-TATTTT
2165097 AAAAATATTTT
1 AAAAATATTTT
2165108 --AAA-A--TT
1 AAAAATATTTT
*
2165114 AAAAAAATTTT
1 AAAAATATTTT
2165125 AAAAAAAGTATTTT
1 --AAAAA-TATTTT
2165139 AAAAATATTTT
1 AAAAATATTTT
2165150 AAAA
1 AAAA
2165154 TTAAAAAATG
Statistics
Matches: 48, Mismatches: 1, Indels: 17
0.73 0.02 0.26
Matches are distributed among these distances:
6 2 0.04
8 4 0.08
9 4 0.08
11 18 0.38
12 10 0.21
13 5 0.10
14 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2165108 original size:31 final size:31
Alignment explanation
Indices: 2165071--2165144 Score: 100
Period size: 30 Copynumber: 2.4 Consensus size: 31
2165061 ACTAAAAATT
2165071 TATTTTAAAAATTAAAAAAGTATTTT-AAAAA-
1 TATTTTAAAAATTAAAAAA--ATTTTAAAAAAG
2165102 TATTTT-AAAATTAAAAAAATTTTAAAAAAAG
1 TATTTTAAAAATTAAAAAAATTTT-AAAAAAG
2165133 TATTTTAAAAAT
1 TATTTTAAAAAT
2165145 ATTTTAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
28 5 0.13
30 17 0.44
31 12 0.31
32 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (31 bp):
TATTTTAAAAATTAAAAAAATTTTAAAAAAG
Found at i:2165117 original size:17 final size:17
Alignment explanation
Indices: 2165095--2165128 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2165085 AAAAAGTATT
*
2165095 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTTAAAA
2165112 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
2165129 AAAGTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:2165171 original size:42 final size:42
Alignment explanation
Indices: 2165084--2165172 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
2165074 TTTAAAAATT
**
2165084 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTTA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAA
2165126 AAAAAAGTATTTTAAAAATATTTTAAAATT-AAAAAATGTAAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAT-TAAA
2165168 AAAAA
1 AAAAA
2165173 TAAATATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 7 0.16
42 37 0.84
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (42 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAA
Found at i:2171193 original size:20 final size:20
Alignment explanation
Indices: 2171155--2171193 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2171145 AACCCCATTT
**
2171155 AAAAAACTAACTTCCTTTTA
1 AAAAAACTAACTTAATTTTA
*
2171175 AAAAAATTAACTTAATTTT
1 AAAAAACTAACTTAATTTT
2171194 CTCCTATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAACTAACTTAATTTTA
Found at i:2175305 original size:29 final size:29
Alignment explanation
Indices: 2175277--2175333 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2175267 GTACTCTTTA
2175277 AAATTTAG-AAGTTAATTTATATATTTTT
1 AAATTTAGAAAGTTAATTTATATATTTTT
** * *
2175305 ATTTTTAGAAATTTAATTTATTTATTTTT
1 AAATTTAGAAAGTTAATTTATATATTTTT
2175334 TAGATTTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (29 bp):
AAATTTAGAAAGTTAATTTATATATTTTT
Found at i:2177304 original size:17 final size:17
Alignment explanation
Indices: 2177282--2177334 Score: 106
Period size: 17 Copynumber: 3.1 Consensus size: 17
2177272 TTTGAGTTGA
2177282 AGCGTGTTTCCTTGGTT
1 AGCGTGTTTCCTTGGTT
2177299 AGCGTGTTTCCTTGGTT
1 AGCGTGTTTCCTTGGTT
2177316 AGCGTGTTTCCTTGGTT
1 AGCGTGTTTCCTTGGTT
2177333 AG
1 AG
2177335 GGATATTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.08, C:0.17, G:0.30, T:0.45
Consensus pattern (17 bp):
AGCGTGTTTCCTTGGTT
Found at i:2177688 original size:40 final size:40
Alignment explanation
Indices: 2177633--2177718 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
2177623 ACATGTTCAC
2177633 TAAATATACAAACTTCTTACTAGCCTAGATTTGCATCTAA
1 TAAATATACAAACTTCTTACTAGCCTAGATTTGCATCTAA
* *
2177673 TAAATATACAAACTTCTTACTTGCCTAGATTTGCATCTGA
1 TAAATATACAAACTTCTTACTAGCCTAGATTTGCATCTAA
2177713 TAAATA
1 TAAATA
2177719 GTTCTCGGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (40 bp):
TAAATATACAAACTTCTTACTAGCCTAGATTTGCATCTAA
Found at i:2179225 original size:36 final size:36
Alignment explanation
Indices: 2179185--2179295 Score: 213
Period size: 36 Copynumber: 3.1 Consensus size: 36
2179175 TCATGTTTCT
2179185 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
1 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
*
2179221 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACCGCA
1 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
2179257 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
1 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
2179293 TCA
1 TCA
2179296 TCGTTTGCAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (36 bp):
TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
Found at i:2186571 original size:65 final size:65
Alignment explanation
Indices: 2186501--2186631 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
2186491 GATTTTGATT
*
2186501 TGATATAATTATATAAATAAAATTTCGATTTAATTTAAAATTTCACATATCTCTAATTAGATTTG
1 TGATATAATTATATAAATAAAATTTCGACTTAATTTAAAATTTCACATATCTCTAATTAGATTTG
* *
2186566 TGATATAATTATATAAATAAAATTTCGACTTAATTTAAAATTTCACATATTTTTAATTAGATTTG
1 TGATATAATTATATAAATAAAATTTCGACTTAATTTAAAATTTCACATATCTCTAATTAGATTTG
2186631 T
1 T
2186632 CTATGGGTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (65 bp):
TGATATAATTATATAAATAAAATTTCGACTTAATTTAAAATTTCACATATCTCTAATTAGATTTG
Found at i:2196032 original size:24 final size:24
Alignment explanation
Indices: 2195969--2196020 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2195959 TTTCTAAAAG
* *
2195969 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
2195993 ATTTAGCATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
2196017 ATTT
1 ATTT
2196021 GACTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:2199927 original size:14 final size:15
Alignment explanation
Indices: 2199900--2199928 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2199890 ACTTGATTTC
2199900 TATTGATGTAATAAT
1 TATTGATGTAATAAT
2199915 TATTGAT-TAATAAT
1 TATTGATGTAATAAT
2199929 ATGCAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TATTGATGTAATAAT
Found at i:2209952 original size:17 final size:17
Alignment explanation
Indices: 2209930--2210007 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 17
2209920 TATCTTCATA
2209930 AATATTAAATTTAATTT
1 AATATTAAATTTAATTT
*
2209947 AATATTAACA-TTAAATT
1 AATATTAA-ATTTAATTT
* * **
2209964 AA-ATTTAATGCTAAGAT
1 AATATTAAAT-TTAATTT
2209981 AATTATTAAATTTAATTT
1 AA-TATTAAATTTAATTT
2209999 AATATTAAA
1 AATATTAAA
2210008 CTATTAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 29 0.62
18 7 0.15
19 6 0.13
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
AATATTAAATTTAATTT
Found at i:2211379 original size:29 final size:29
Alignment explanation
Indices: 2211315--2211381 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
2211305 ATTTAGTCAT
** *
2211315 ATTTAATCTTTTTAATAATAACAAAACTA
1 ATTTAATCCATTTAATAAAAACAAAACTA
** * *
2211344 AAGTAATCCATTTAATAAAAATAAGACTA
1 ATTTAATCCATTTAATAAAAACAAAACTA
2211373 ATTTAATCC
1 ATTTAATCC
2211382 GGTTTTTATA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTTAATCCATTTAATAAAAACAAAACTA
Found at i:2211976 original size:21 final size:20
Alignment explanation
Indices: 2211938--2211977 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2211928 AATTTTAAAA
*
2211938 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTT
2211958 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAAT-AATTTTT
2211978 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTT
Found at i:2217132 original size:28 final size:28
Alignment explanation
Indices: 2217099--2217154 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2217089 AGCATTGGAC
2217099 CTTATCATTGTTGTCAGTTATTGGAAGA
1 CTTATCATTGTTGTCAGTTATTGGAAGA
2217127 CTTATCATTGTTGTCAGTTATTGGAAGA
1 CTTATCATTGTTGTCAGTTATTGGAAGA
2217155 GTAAAAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (28 bp):
CTTATCATTGTTGTCAGTTATTGGAAGA
Found at i:2218923 original size:13 final size:13
Alignment explanation
Indices: 2218905--2218929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2218895 GGTCCTTTTG
2218905 TTATTTTAAATTT
1 TTATTTTAAATTT
2218918 TTATTTTAAATT
1 TTATTTTAAATT
2218930 ATGTTACTTA
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTTAAATTT
Found at i:2223996 original size:15 final size:15
Alignment explanation
Indices: 2223976--2224023 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
2223966 TGTTTATAAA
*
2223976 TATTTAATTATTATT
1 TATTTAAATATTATT
*
2223991 TATTTAAATATTATG
1 TATTTAAATATTATT
* * *
2224006 AATTTCAATAATATT
1 TATTTAAATATTATT
2224021 TAT
1 TAT
2224024 ATCAGCATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TATTTAAATATTATT
Found at i:2224718 original size:83 final size:83
Alignment explanation
Indices: 2224564--2224718 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 83
2224554 CCACCTCGCG
* * * * *
2224564 AGGTGGAGCATAAGGGAGATGCGTGAGCCGCGAGATGGACTGCCTCATCGCGTCTCACATCCCAT
1 AGGTGGAGCACAAGAGAGATGCGTGAGCCGCGAGATGGACTACCTCATCGCGTCTCACACCCCAC
2224629 CAACATGATGACCTGGCT
66 CAACATGATGACCTGGCT
* * * *
2224647 AGGTGGAGCACAAGAGAGATGTGTGAGTCGTGAGATGGA-TCACCTCATTGTC-TCTCACACCCC
1 AGGTGGAGCACAAGAGAGATGCGTGAGCCGCGAGATGGACT-ACCTCATCG-CGTCTCACACCCC
*
2224710 ACCGACATG
64 ACCAACATG
2224719 GCGACCTCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 1 0.02
83 58 0.97
84 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.20
Consensus pattern (83 bp):
AGGTGGAGCACAAGAGAGATGCGTGAGCCGCGAGATGGACTACCTCATCGCGTCTCACACCCCAC
CAACATGATGACCTGGCT
Found at i:2226660 original size:22 final size:22
Alignment explanation
Indices: 2226608--2226660 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
2226598 GTTACTGTTA
* *
2226608 TGTTGTTGTTTTGCTACTATTT
1 TGTTGTTATATTGCTACTATTT
*** *
2226630 CACTATTATATTGCTACTATTT
1 TGTTGTTATATTGCTACTATTT
2226652 TGTTGTTAT
1 TGTTGTTAT
2226661 TGTTTGAATC
Statistics
Matches: 21, Mismatches: 10, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.13, T:0.58
Consensus pattern (22 bp):
TGTTGTTATATTGCTACTATTT
Found at i:2227731 original size:15 final size:16
Alignment explanation
Indices: 2227711--2227746 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2227701 TAAAAAAAAA
2227711 ATTGAGTTATAGCT-G
1 ATTGAGTTATAGCTCG
*
2227726 ATTGAGTTTTAGCTCG
1 ATTGAGTTATAGCTCG
2227742 ATTGA
1 ATTGA
2227747 CATGGGTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (16 bp):
ATTGAGTTATAGCTCG
Found at i:2229948 original size:10 final size:10
Alignment explanation
Indices: 2229933--2229957 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2229923 TTTTAATAAG
2229933 TTTATATATT
1 TTTATATATT
2229943 TTTATATATT
1 TTTATATATT
2229953 TTTAT
1 TTTAT
2229958 TGTTTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATATATT
Found at i:2231010 original size:4 final size:4
Alignment explanation
Indices: 2231001--2231028 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2230991 TACAAACTAA
2231001 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2231029 CTTAAGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:2240370 original size:17 final size:17
Alignment explanation
Indices: 2240330--2240374 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
2240320 CCGATATAAT
* *
2240330 AAATATATTTATTTTTA
1 AAATATTTTTAATTTTA
2240347 AAA-ATTTTTAATTTTA
1 AAATATTTTTAATTTTA
2240363 AAATATTTTTAA
1 AAATATTTTTAA
2240375 AATACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:2240372 original size:11 final size:11
Alignment explanation
Indices: 2240358--2240424 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
2240348 AAATTTTTAA
2240358 TTTTAAAATAT
1 TTTTAAAATAT
2240369 TTTTAAAATACT
1 TTTTAAAATA-T
* *
2240381 TTTT-TATTAT
1 TTTTAAAATAT
*
2240391 TTTT----TAA
1 TTTTAAAATAT
2240398 TTTTAAAATAT
1 TTTTAAAATAT
2240409 TTTTAAAATACT
1 TTTTAAAATA-T
2240421 TTTT
1 TTTT
2240425 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 6 0.13
10 5 0.11
11 25 0.54
12 10 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2240385 original size:40 final size:40
Alignment explanation
Indices: 2240341--2240425 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
2240331 AATATATTTA
2240341 TTTTTAAAAATTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTAAAAATTTTTAATTTTAAAATATTTTTAAAATACT
** *
2240381 TTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTAAAAATTTTTAATTTTAAAATATTTTTAAAATACT
2240421 TTTTT
1 TTTTT
2240426 TAATTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (40 bp):
TTTTTAAAAATTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:2240445 original size:21 final size:21
Alignment explanation
Indices: 2240407--2240446 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2240397 ATTTTAAAAT
**
2240407 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
2240428 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
2240447 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:2240453 original size:22 final size:20
Alignment explanation
Indices: 2240406--2240460 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
2240396 AATTTTAAAA
* *
2240406 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
2240426 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
2240449 TATTTATTAAAA
1 TATTT-TTAAAA
2240461 AATGGACCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:2240783 original size:9 final size:11
Alignment explanation
Indices: 2240761--2240792 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2240751 ATTATTTATT
2240761 TATTTTAAATA
1 TATTTTAAATA
2240772 TATTTTAAATA
1 TATTTTAAATA
*
2240783 TAATTTAAAT
1 TATTTTAAAT
2240793 TAATCCGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTTTAAATA
Found at i:2241563 original size:28 final size:28
Alignment explanation
Indices: 2241521--2241580 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2241511 CTGATTATTC
* *
2241521 AACTAGTAAGTGAAGTACGAGACCATTT
1 AACTAGTAAGCGAAGTACAAGACCATTT
* **
2241549 AACTAGTAGGCGAAGTACAAGATTATTT
1 AACTAGTAAGCGAAGTACAAGACCATTT
2241577 AACT
1 AACT
2241581 TAATGATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (28 bp):
AACTAGTAAGCGAAGTACAAGACCATTT
Found at i:2252917 original size:2 final size:2
Alignment explanation
Indices: 2252910--2252947 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2252900 ATCATTTGAT
2252910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2252948 CCATTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2253205 original size:45 final size:45
Alignment explanation
Indices: 2253143--2253245 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
2253133 AATCAGTAAC
*
2253143 GGTAGCAGTAACAGTAACAGTATTCAACACACAAAGTG-CTGAATAT
1 GGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTC-GAAT-T
* * *
2253189 -GTAACAGTAACGGTAACAGTATTCGACACACAAGGTGTCGAATT
1 GGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATT
2253233 GGTAACAGTAACA
1 GGTAACAGTAACA
2253246 ATAGTCAGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 1 0.02
45 48 0.96
46 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (45 bp):
GGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATT
Found at i:2255024 original size:19 final size:19
Alignment explanation
Indices: 2254994--2255042 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2254984 TTTTAAAATA
2254994 TATTAA-TTTTAT-ATTTAT
1 TATTAATTTTTATCATTT-T
2255012 TATTAATTTTTATCATTTT
1 TATTAATTTTTATCATTTT
2255031 TA-TATATTTTTA
1 TATTA-ATTTTTA
2255043 AATAACATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.29
19 16 0.57
20 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTAATTTTTATCATTTT
Found at i:2260079 original size:51 final size:51
Alignment explanation
Indices: 2260003--2260308 Score: 380
Period size: 51 Copynumber: 6.2 Consensus size: 51
2259993 TAATCAATGA
* **
2260003 CAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATTGGTGACAAGTGG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
* * *
2260054 CAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACATA-TGA
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA-AGTGG
*
2260105 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCAGTGACAAGTGG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
* * * *
2260156 CAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAGCAGTGACATA-TGA
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA-AGTGG
*
2260207 CAAGTGATAAGTGGTAGCTTTAGCTATACTTATCTG---A-T--C-AGTGG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
* * *
2260251 CAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTAATCAGGGACAAGTGA
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
*
2260301 TAAGTGAT
1 CAAGTGAT
2260309 CATACGTAAG
Statistics
Matches: 220, Mismatches: 24, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
43 16 0.07
44 20 0.09
45 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
50 12 0.05
51 165 0.75
52 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (51 bp):
CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
Found at i:2260169 original size:102 final size:101
Alignment explanation
Indices: 2259999--2260308 Score: 449
Period size: 102 Copynumber: 3.1 Consensus size: 101
2259989 CTTCTAATCA
* * *
2259999 ATGACAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATTGGTGACAAGTGGCAAGTGATAA
1 ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTA-TCGTGACAAGTGGCAAGTGATAA
2260064 GTGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
65 GTGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
2260101 ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCAGTGACAAGTGGCAAGTGATAA
1 ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATC-GTGACAAGTGGCAAGTGATAA
*
2260166 GTGATAGCTTCAGCTACACTTATCTGAGCAGTGACAT
65 GTGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
2260203 ATGACAAGTGATAAGTGGTAGCTTTAGCT--A--TA-CTTATC-TGATC-AGTGGCAAGTGATAA
1 ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCGTGA-CAAGTGGCAAGTGATAA
* * *
2260261 GTGGTAGCTT-AGCTACACTTATCTAATCAGGGACA-
65 GTGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
*
2260296 AGTGATAAGTGAT
1 A-TGACAAGTGAT
2260309 CATACGTAAG
Statistics
Matches: 196, Mismatches: 9, Indels: 14
0.89 0.04 0.06
Matches are distributed among these distances:
93 1 0.01
94 32 0.16
95 27 0.14
96 1 0.01
97 6 0.03
98 2 0.01
100 1 0.01
101 1 0.01
102 125 0.64
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (101 bp):
ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCGTGACAAGTGGCAAGTGATAAG
TGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
Found at i:2260290 original size:43 final size:44
Alignment explanation
Indices: 2260205--2260306 Score: 163
Period size: 43 Copynumber: 2.3 Consensus size: 44
2260195 AGTGACATAT
* *
2260205 GACAAGTGATAAGTGGTAGCTTTAGCTATACTTATCTGATCAGTG
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAG-G
2260250 G-CAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTAATCAGG
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGG
2260292 GACAAGTGATAAGTG
1 GACAAGTGATAAGTG
2260307 ATCATACGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
42 2 0.04
43 33 0.61
44 18 0.33
45 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (44 bp):
GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGG
Found at i:2263010 original size:2 final size:2
Alignment explanation
Indices: 2263003--2263044 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2262993 CCCTCTCACC
2263003 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2263045 TACGTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2268758 original size:2 final size:2
Alignment explanation
Indices: 2268751--2268801 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
2268741 NNNNNNNNNN
* * * *
2268751 TC TC TC TC TC TC TC TC TC TC TC TC AC TC AC TC TC TC TC TT TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2268793 TC TC TC TC T
1 TC TC TC TC T
2268802 TTATTACATA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.04, C:0.45, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2269097 original size:17 final size:16
Alignment explanation
Indices: 2269070--2269101 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2269060 TGATTTTTGA
2269070 TAAGGAGGTGACAAAT
1 TAAGGAGGTGACAAAT
2269086 TAAGGTAGGTGACAAA
1 TAAGG-AGGTGACAAA
2269102 ATGCACTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (16 bp):
TAAGGAGGTGACAAAT
Found at i:2278827 original size:2 final size:2
Alignment explanation
Indices: 2278820--2278953 Score: 69
Period size: 2 Copynumber: 68.5 Consensus size: 2
2278810 CATATAAAGA
* * * *
2278820 AT AT AT AT AG GT AT AT AT AT AT AT AT AT AT AT AT TT AT GA- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * * * * *
2278862 AT A- AC AT AT GT AT AT AG AT AT AT AG AT GT GT AT AT AA AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
2278902 AT A- AA AT AT AA AA AT AA AT AT GT AT GT 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 AT
*
2278943 AC AT AT AT AT A
1 AT AT AT AT AT A
2278954 GATAAGCTAT
Statistics
Matches: 98, Mismatches: 29, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
1 4 0.04
2 93 0.95
3 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.41
Consensus pattern (2 bp):
AT
Found at i:2280321 original size:20 final size:22
Alignment explanation
Indices: 2280293--2280344 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
2280283 TTTTTTAAAT
2280293 ATTTG-TATAAAAT-T-TTACA
1 ATTTGTTATAAAATCTGTTACA
*
2280312 ATTTGTTAT-AATTCTGTTACA
1 ATTTGTTATAAAATCTGTTACA
2280333 ATTT-TTATAAAA
1 ATTTGTTATAAAA
2280345 AAATTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 8 0.30
20 8 0.30
21 11 0.41
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (22 bp):
ATTTGTTATAAAATCTGTTACA
Found at i:2285716 original size:22 final size:22
Alignment explanation
Indices: 2285654--2285725 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
2285644 AATATTTAAA
* **
2285654 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
2285676 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
2285698 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
2285720 CATGAG
1 CATGAG
2285726 GGTTTATTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:2286650 original size:31 final size:31
Alignment explanation
Indices: 2286590--2286654 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2286580 AATATCAGTA
*
2286590 TTTTAATTTGATTAATTTTAATCTTTTAATT
1 TTTTAATTTGATTAATTTTAATCTCTTAATT
* *
2286621 TTTTGATTTGGTTAATTTTAAT-TCCTTAATT
1 TTTTAATTTGATTAATTTTAATCT-CTTAATT
2286652 TTT
1 TTT
2286655 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.65
Consensus pattern (31 bp):
TTTTAATTTGATTAATTTTAATCTCTTAATT
Found at i:2287630 original size:20 final size:21
Alignment explanation
Indices: 2287591--2287632 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2287581 ATTAATATTC
2287591 AATAAATTATTCAATATTTTAA
1 AATAAATTA-TCAATATTTTAA
*
2287613 AATAAATTA-CAATTTTTTAA
1 AATAAATTATCAATATTTTAA
2287633 GTGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAAATTATCAATATTTTAA
Found at i:2288526 original size:91 final size:91
Alignment explanation
Indices: 2288408--2288573 Score: 244
Period size: 91 Copynumber: 1.8 Consensus size: 91
2288398 CGAGATTCTT
* ***
2288408 TTTTTGTTCCGTGGTTAAGAAAATGTTTGGCTTGAATTCGCACTAGAATTTTCTGTTT-CTTTGC
1 TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGC-TTGC
*
2288472 TGCGAAACACTGTTTGAATTCTTTTTA
65 TGAGAAACACTGTTTGAATTCTTTTTA
* * *
2288499 TTTTCGTTGCGTGGTTAAGAAACTGTTTAAATTGAATTCGCACTAGAATTTTTTGTTTGCTTGCT
1 TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGCTTGCT
2288564 GAGAAACACT
66 GAGAAACACT
2288574 CTGAGAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
91 65 0.98
92 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (91 bp):
TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGCTTGCT
GAGAAACACTGTTTGAATTCTTTTTA
Found at i:2288775 original size:100 final size:100
Alignment explanation
Indices: 2288475--2288858 Score: 425
Period size: 105 Copynumber: 3.8 Consensus size: 100
2288465 TCTTTGCTGC
* * * *
2288475 GAAACACTGTTTGAATTCTTTTTATTTTCGTTGCGTGGTTAAGAAACTGTTTAAATTGAATTCGC
1 GAAAAACTGTTTGAATTC-TTTT-TTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGC
* *
2288540 ACTAGAATTTTTTGTTTGCTTGCTGAGAAACACTCTGA
64 ACTAGAATTTTCTGATTGCTTGCTGAGAAACACT-TGA
* * * * *
2288578 GAAAAACTGGTTGAATTCCTTTTTTTT-TTTGGTCGCGTGGATAAGAAAATGTTTGATTCGAATT
1 GAAAAACTGTTTGAATT-CTTTTTTTTCGTT-G-CGC--GGTTAAGAAAATGTTTAATTTGAATT
** * *
2288642 CGCGTTAGAGTTTTCTGATTGTTTGCTGAGAAACACTGTGA
61 CGCACTAGAATTTTCTGATTGCTTGCTGAGAAACACT-TGA
* * *
2288683 GAAAAACTGTTTGAGTTCTTTTTTTTCGTTGCGCGGTTAAGAAAATG-TTAGTTTTAATTCGCAC
1 GAAAAACTGTTTGAATTCTTTTTTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGCAC
* *
2288747 TAGAATTATCTGATTGGTTGCTGAGAAACAC-TGA
66 TAGAATTTTCTGATTGCTTGCTGAGAAACACTTGA
* * * *
2288781 GAAAAAATCGTTTGAATT-TTTTTATTTCGTTGCGTGGTTAAGAAATTGTTTAATTTGAACTCGC
1 GAAAAACT-GTTTGAATTCTTTTT-TTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGC
2288845 ACTAGAATTTTCTG
64 ACTAGAATTTTCTG
2288859 TTTTTGGTTG
Statistics
Matches: 235, Mismatches: 37, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
98 15 0.06
99 30 0.13
100 64 0.27
101 14 0.06
102 5 0.02
103 24 0.10
104 11 0.05
105 72 0.31
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.41
Consensus pattern (100 bp):
GAAAAACTGTTTGAATTCTTTTTTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGCAC
TAGAATTTTCTGATTGCTTGCTGAGAAACACTTGA
Found at i:2288871 original size:56 final size:56
Alignment explanation
Indices: 2288809--2288914 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
2288799 TTTTTATTTC
2288809 GTTGCGTGGTTAAGAA-ATTGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTTTG
1 GTTGCGTGGTTAAGAAGA-TGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTTTG
* * * *
2288865 GTTGCGTGGTTAATAAGATGTTTAATTTGAATTCGGATTAGAATTTTCTG
1 GTTGCGTGGTTAAGAAGATGTTTAATTTGAACTCGCACTAGAATTTTCTG
2288915 ATTGTTTCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
56 44 0.98
57 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (56 bp):
GTTGCGTGGTTAAGAAGATGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTTTG
Found at i:2294672 original size:13 final size:13
Alignment explanation
Indices: 2294654--2294680 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2294644 AATTTAAAAG
2294654 TTAGATATGATTA
1 TTAGATATGATTA
2294667 TTAGATATGATTA
1 TTAGATATGATTA
2294680 T
1 T
2294681 ATAATAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TTAGATATGATTA
Found at i:2305163 original size:26 final size:26
Alignment explanation
Indices: 2305127--2305178 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2305117 ATTGTCAATG
2305127 CAAGAGGACGTAAGTTTAAAGTGTAC
1 CAAGAGGACGTAAGTTTAAAGTGTAC
2305153 CAAGAGGACGTAAGTTTAAAGTGTAC
1 CAAGAGGACGTAAGTTTAAAGTGTAC
2305179 TATCCTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (26 bp):
CAAGAGGACGTAAGTTTAAAGTGTAC
Found at i:2307443 original size:21 final size:21
Alignment explanation
Indices: 2307414--2307457 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2307404 ACGTTATCGC
* *
2307414 ATAATTTTTTTAATTTTTTTT
1 ATAAATTTTATAATTTTTTTT
2307435 ATAAATTTTATAATTTTTTTT
1 ATAAATTTTATAATTTTTTTT
2307456 AT
1 AT
2307458 TCTTAGATTG
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATAAATTTTATAATTTTTTTT
Found at i:2311114 original size:9 final size:9
Alignment explanation
Indices: 2311102--2311166 Score: 67
Period size: 9 Copynumber: 7.2 Consensus size: 9
2311092 ATTCGGTCGG
2311102 TTAACCGAA
1 TTAACCGAA
*
2311111 TTAACCGAG
1 TTAACCGAA
*
2311120 TTAACCGGA
1 TTAACCGAA
*
2311129 TTACCCGAA
1 TTAACCGAA
* *
2311138 TTAATCGGA
1 TTAACCGAA
* *
2311147 TTACCCAAA
1 TTAACCGAA
2311156 TTAACCGAA
1 TTAACCGAA
2311165 TT
1 TT
2311167 GAATCACTAC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (9 bp):
TTAACCGAA
Found at i:2311122 original size:18 final size:18
Alignment explanation
Indices: 2311102--2311166 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
2311092 ATTCGGTCGG
* *
2311102 TTAACCGAATTAACCGAG
1 TTAACCGAATTACCCGAA
*
2311120 TTAACCGGATTACCCGAA
1 TTAACCGAATTACCCGAA
* * *
2311138 TTAATCGGATTACCCAAA
1 TTAACCGAATTACCCGAA
2311156 TTAACCGAATT
1 TTAACCGAATT
2311167 GAATCACTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (18 bp):
TTAACCGAATTACCCGAA
Found at i:2311389 original size:125 final size:125
Alignment explanation
Indices: 2311257--2311502 Score: 483
Period size: 125 Copynumber: 2.0 Consensus size: 125
2311247 ATTTGTAATT
*
2311257 TTTATGATTGGGTTGAGTTGGGTAATTGGGTTGGGTTGAATACTTGAGTTTGGATTGGGTTTAGG
1 TTTATGATTGGGTTGAGTTGGGTAATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGG
2311322 TGAATAATGGGCCTATTTATATATTATAATTTTATTTATTAATTTTTTCGGTTAACTGAA
66 TGAATAATGGGCCTATTTATATATTATAATTTTATTTATTAATTTTTTCGGTTAACTGAA
2311382 TTTATGATTGGGTTGAGTTGGGTAATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGG
1 TTTATGATTGGGTTGAGTTGGGTAATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGG
2311447 TGAATAATGGGCCTATTTATATATTATAATTTTATTTATTAATTTTTTCGGTTAAC
66 TGAATAATGGGCCTATTTATATATTATAATTTTATTTATTAATTTTTTCGGTTAAC
2311503 CGAAGAAATT
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.47
Consensus pattern (125 bp):
TTTATGATTGGGTTGAGTTGGGTAATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGG
TGAATAATGGGCCTATTTATATATTATAATTTTATTTATTAATTTTTTCGGTTAACTGAA
Found at i:2312316 original size:3 final size:3
Alignment explanation
Indices: 2312308--2312378 Score: 61
Period size: 3 Copynumber: 23.7 Consensus size: 3
2312298 CGAAGAGGAA
* * * * * * * * *
2312308 GAC GAC GAC GAC GAC GAC GAG GAT GAG GAT GAT GAA GGC GAA GAT GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
2312356 GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GA
2312379 AGGAGAGGAG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.21, G:0.38, T:0.06
Consensus pattern (3 bp):
GAC
Found at i:2312485 original size:9 final size:9
Alignment explanation
Indices: 2312467--2312529 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
2312457 GGATGTTAAA
*
2312467 GACGATGAT
1 GACGACGAT
2312476 GACGACGAT
1 GACGACGAT
**
2312485 GAAGGCGACGGC
1 G-A--CGACGAT
*
2312497 GATGACGAT
1 GACGACGAT
*
2312506 GACGACGAC
1 GACGACGAT
2312515 GACGACGAT
1 GACGACGAT
2312524 GACGAC
1 GACGAC
2312530 AGTGATGAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
9 34 0.81
10 1 0.02
11 1 0.02
12 6 0.14
ACGTcount: A:0.32, C:0.22, G:0.37, T:0.10
Consensus pattern (9 bp):
GACGACGAT
Found at i:2312529 original size:15 final size:15
Alignment explanation
Indices: 2312476--2312528 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2312466 AGACGATGAT
* *
2312476 GACGACGATGAAGGC
1 GACGACGATGACGAC
* *
2312491 GACGGCGATGACGAT
1 GACGACGATGACGAC
*
2312506 GACGACGACGACGAC
1 GACGACGATGACGAC
*
2312521 GATGACGA
1 GACGACGA
2312529 CAGTGATGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.38, T:0.08
Consensus pattern (15 bp):
GACGACGATGACGAC
Found at i:2313289 original size:3 final size:3
Alignment explanation
Indices: 2313277--2313319 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
2313267 AGAAAATGGT
* * * *
2313277 GAA GAG GAA GAA GAA GAA GAA GAA GAT GAA GAC GAT GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2313320 GTAGTGGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.56, C:0.02, G:0.37, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:2313554 original size:13 final size:13
Alignment explanation
Indices: 2313536--2313562 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2313526 GGTGTGTTAG
2313536 AAAAAACAAAAAA
1 AAAAAACAAAAAA
2313549 AAAAAACAAAAAA
1 AAAAAACAAAAAA
2313562 A
1 A
2313563 GTAGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAA
Found at i:2313843 original size:3 final size:3
Alignment explanation
Indices: 2313835--2313875 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2313825 CCATTTTTGC
2313835 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2313876 AGCCATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2320880 original size:60 final size:57
Alignment explanation
Indices: 2320815--2320973 Score: 176
Period size: 60 Copynumber: 2.7 Consensus size: 57
2320805 AAAAGCTTGG
2320815 GTACCAAATTAGAAAAAAATGGCAAGTTCAAGTACCAAATTTGGTCCCAAAAAAAGTTCA
1 GTACCAAATTAGAAAAAAATGGCAAGTTCAAGTACCAAA-TTGG--CCAAAAAAAGTTCA
* * * * *
2320875 GTACCAAATTTTA-AAAAAAATGGCAAGTTCAGGTACCTAATTGGGCAAAAAAATTTTA
1 GTACCAAA--TTAGAAAAAAATGGCAAGTTCAAGTACCAAATTGGCCAAAAAAAGTTCA
* *
2320933 GATACCAAATTAGAAAAAAAAGTGTCAAGTTCAAGAACCAA
1 G-TACCAAATTAG-AAAAAAA-TGGCAAGTTCAAGTACCAA
2320974 TGTTATATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
57 3 0.04
58 12 0.14
59 14 0.17
60 27 0.32
61 25 0.30
62 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (57 bp):
GTACCAAATTAGAAAAAAATGGCAAGTTCAAGTACCAAATTGGCCAAAAAAAGTTCA
Found at i:2326731 original size:14 final size:14
Alignment explanation
Indices: 2326712--2326739 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2326702 GGCCTGTGAT
2326712 TCAAGATTTTAAAC
1 TCAAGATTTTAAAC
2326726 TCAAGATTTTAAAC
1 TCAAGATTTTAAAC
2326740 AACTAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TCAAGATTTTAAAC
Found at i:2330369 original size:2 final size:2
Alignment explanation
Indices: 2330362--2330397 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2330352 CATTTGACTC
2330362 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2330398 TAATATTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2338249 original size:19 final size:21
Alignment explanation
Indices: 2338225--2338270 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2338215 TATTTTTTAA
2338225 TATGAA-CTTTTTT-AAATTT
1 TATGAATCTTTTTTAAAATTT
*
2338244 TATGAATTTTTTTTAAAATTT
1 TATGAATCTTTTTTAAAATTT
2338265 TATGAA
1 TATGAA
2338271 GTATATCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 12 0.50
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TATGAATCTTTTTTAAAATTT
Found at i:2338257 original size:20 final size:21
Alignment explanation
Indices: 2338232--2338270 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2338222 TAATATGAAC
2338232 TTTTTT-AAATTTTATGAATT
1 TTTTTTAAAATTTTATGAATT
2338252 TTTTTTAAAATTTTATGAA
1 TTTTTTAAAATTTTATGAA
2338271 GTATATCTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTTTAAAATTTTATGAATT
Found at i:2338682 original size:30 final size:29
Alignment explanation
Indices: 2338643--2338700 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
2338633 ACAATCATAA
2338643 AAAAATATTTA-TAATATTTTAAAATTAATT
1 AAAAATATTTATTAATA-TTT-AAATTAATT
*
2338673 AAAATTATTTATTTAATATTTAAATTAA
1 AAAAATATTTA-TTAATATTTAAATTAA
2338701 ATATCAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 17 0.68
31 3 0.12
32 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AAAAATATTTATTAATATTTAAATTAATT
Found at i:2342844 original size:26 final size:25
Alignment explanation
Indices: 2342792--2342852 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
2342782 TGCCCATATT
2342792 AAATATATATTTGATTAAAAATAAA
1 AAATATATATTTGATTAAAAATAAA
2342817 AAATATATATTTGATTAAAAATAAA
1 AAATATATATTTGATTAAAAATAAA
2342842 AAA-ATATATTT
1 AAATATATATTT
2342853 AATATATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 8 0.22
25 28 0.78
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
AAATATATATTTGATTAAAAATAAA
Found at i:2356537 original size:17 final size:17
Alignment explanation
Indices: 2356515--2356548 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2356505 ATGAACTTTA
2356515 TTTTATTT-TTTATATAT
1 TTTTATTTATTTA-ATAT
2356532 TTTTATTTATTTAATAT
1 TTTTATTTATTTAATAT
2356549 AAAAAAGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTATTTAATAT
Found at i:2363773 original size:4 final size:4
Alignment explanation
Indices: 2363764--2363790 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2363754 AAGTAAAGTA
2363764 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2363791 AAGGAAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2364607 original size:20 final size:21
Alignment explanation
Indices: 2364582--2364620 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2364572 AATGGAAAAT
2364582 AAAGAA-A-AAAAATAAAGTTA
1 AAAGAACATAAAAA-AAAGTTA
2364602 AAAGAACATAAAAAAAAGT
1 AAAGAACATAAAAAAAAGT
2364621 GCTCAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (21 bp):
AAAGAACATAAAAAAAAGTTA
Found at i:2364747 original size:16 final size:16
Alignment explanation
Indices: 2364723--2364756 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2364713 CTTATCATTA
*
2364723 TACCGTTAAGGGCAAT
1 TACCATTAAGGGCAAT
2364739 TACCATTAAGGGCAAT
1 TACCATTAAGGGCAAT
2364755 TA
1 TA
2364757 ATAGCTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (16 bp):
TACCATTAAGGGCAAT
Found at i:2366845 original size:10 final size:10
Alignment explanation
Indices: 2366826--2366855 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2366816 ATTTTACTAT
2366826 TATATATATG
1 TATATATATG
*
2366836 TATATGTATG
1 TATATATATG
2366846 TATATATATG
1 TATATATATG
2366856 CTTCAGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:2371112 original size:17 final size:18
Alignment explanation
Indices: 2371090--2371124 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2371080 CACTCCTCAC
2371090 AAAACAAAAC-AAAAAAA
1 AAAACAAAACTAAAAAAA
2371107 AAAACAAAACTAAAAAAA
1 AAAACAAAACTAAAAAAA
2371125 CAGTCTTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (18 bp):
AAAACAAAACTAAAAAAA
Found at i:2375462 original size:19 final size:20
Alignment explanation
Indices: 2375452--2375488 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
2375442 TAATTAATAA
2375452 TTATAAAAAT-ATAAAAAAT
1 TTATAAAAATAATAAAAAAT
2375471 TTATAAAAATAATAAAAA
1 TTATAAAAATAATAAAAA
2375489 CATATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TTATAAAAATAATAAAAAAT
Found at i:2376125 original size:19 final size:19
Alignment explanation
Indices: 2376101--2376177 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 19
2376091 TGATTTTTTT
2376101 TATAATTTTTATAAGTTTA
1 TATAATTTTTATAAGTTTA
* *
2376120 TATAA-TTTTA-ATGTTTT
1 TATAATTTTTATAAGTTTA
2376137 TATTAATTTTTAATAA-TTT-
1 TA-TAATTTTT-ATAAGTTTA
*
2376156 TATGATTTTTTATAAGTTTA
1 TAT-AATTTTTATAAGTTTA
2376176 TA
1 TA
2376178 AGAATGTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
17 7 0.15
18 13 0.28
19 20 0.43
20 6 0.13
21 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TATAATTTTTATAAGTTTA
Found at i:2376194 original size:29 final size:28
Alignment explanation
Indices: 2376098--2376199 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
2376088 TTATGATTTT
*
2376098 TTTTATAATTTTTATAAGTTTAT-ATAA
1 TTTTATAGTTTTTATAAGTTTATAATAA
*
2376125 TTTTA-ATGTTTTTATTAA-TTTTTAATAA
1 TTTTATA-GTTTTTA-TAAGTTTATAATAA
* *
2376153 TTTTATGATTTTTTATAAGTTTATAAGAA
1 TTTTAT-AGTTTTTATAAGTTTATAATAA
*
2376182 TGTTATACGTTTTTATAA
1 TTTTATA-GTTTTTATAA
2376200 AATTTTAGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
26 1 0.02
27 15 0.25
28 16 0.26
29 28 0.46
30 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTTATAGTTTTTATAAGTTTATAATAA
Found at i:2376250 original size:18 final size:19
Alignment explanation
Indices: 2376211--2376259 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
2376201 ATTTTAGATA
2376211 TTTTTTATTAATTCTATAAT
1 TTTTTTA-TAATTCTATAAT
*
2376231 TTTTTTATAATT-TATTAT
1 TTTTTTATAATTCTATAAT
2376249 TTTTTTATAAT
1 TTTTTTATAAT
2376260 ATTTATAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 16 0.57
19 5 0.18
20 7 0.25
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTATAATTCTATAAT
Found at i:2376263 original size:20 final size:20
Alignment explanation
Indices: 2376191--2376267 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 20
2376181 ATGTTATACG
*
2376191 TTTTTATAAAATTT-TAGATAT
1 TTTTTATAATATTTATA-AT-T
*
2376212 TTTTTATTAAT-TCTATAATT
1 TTTTTA-TAATATTTATAATT
*
2376232 TTTTTAT-A-ATTTATTATT
1 TTTTTATAATATTTATAATT
2376250 TTTTTATAATATTTATAA
1 TTTTTATAATATTTATAA
2376268 GTTTATATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
18 15 0.33
19 2 0.04
20 14 0.30
21 10 0.22
22 5 0.11
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTTTATAATATTTATAATT
Found at i:2376413 original size:16 final size:17
Alignment explanation
Indices: 2376388--2376424 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2376378 GAATATTAAA
2376388 ATAA-ATTTTATATTTT
1 ATAATATTTTATATTTT
2376404 -TAATATTTTATATTTT
1 ATAATATTTTATATTTT
2376420 ATAAT
1 ATAAT
2376425 TTAAAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATATTTTATATTTT
Found at i:2376514 original size:21 final size:21
Alignment explanation
Indices: 2376490--2376530 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2376480 GATCAAATAG
*
2376490 TAGTTCAATGTGATCTACTTC
1 TAGTTCAATGTGATCCACTTC
2376511 TAGTTCAATGTGATCCACTT
1 TAGTTCAATGTGATCCACTT
2376531 TTAGATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (21 bp):
TAGTTCAATGTGATCCACTTC
Found at i:2377328 original size:54 final size:55
Alignment explanation
Indices: 2377242--2377355 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 55
2377232 TCAAACTTCT
* *
2377242 TCAGCCTCCTTCGAGCACTACTCGTCGGCTAACATTGCTT-ACACCTATGCTCTA
1 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAACACCTATGCTCTA
2377296 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAGACACCTATGCTCTA
1 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTA-ACACCTATGCTCTA
2377352 TCAG
1 TCAG
2377356 GAATTGGTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
54 38 0.68
56 18 0.32
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (55 bp):
TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAACACCTATGCTCTA
Found at i:2381362 original size:29 final size:30
Alignment explanation
Indices: 2381328--2381395 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2381318 TTGAAAATGT
2381328 AAAATTTAGATC-CTATA-TTTTTA-TTTTC
1 AAAATTTAG-TCACTATACTTTTTAGTTTTC
*
2381356 AAGAATTTAGTCACTCTACTTTTTAGTTTTTC
1 AA-AATTTAGTCACTATACTTTTTAG-TTTTC
2381388 AAAATTTA
1 AAAATTTA
2381396 AGTCCAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 4 0.12
29 11 0.32
30 6 0.18
31 6 0.18
32 7 0.21
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (30 bp):
AAAATTTAGTCACTATACTTTTTAGTTTTC
Found at i:2382069 original size:17 final size:17
Alignment explanation
Indices: 2382043--2382085 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
2382033 TAAAAAACCA
2382043 ACTT-AATAATCAAATT
1 ACTTAAATAATCAAATT
*
2382059 ATTTAAATAATCAAATT
1 ACTTAAATAATCAAATT
2382076 ACTTAAATAA
1 ACTTAAATAA
2382086 ACACTCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
ACTTAAATAATCAAATT
Found at i:2385775 original size:13 final size:13
Alignment explanation
Indices: 2385757--2385781 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2385747 CCTTGTTTAA
2385757 ATAAAATACAATG
1 ATAAAATACAATG
2385770 ATAAAATACAAT
1 ATAAAATACAAT
2385782 AAAAGTAAAA
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:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (13 bp):
ATAAAATACAATG
Found at i:2390053 original size:15 final size:17
Alignment explanation
Indices: 2390024--2390055 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2390014 AAATTAAGAT
2390024 TTATCATATTAAATTAA
1 TTATCATATTAAATTAA
2390041 TTATCAT-TT-AATTAA
1 TTATCATATTAAATTAA
2390056 ATTTAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATCATATTAAATTAA
Found at i:2402903 original size:27 final size:27
Alignment explanation
Indices: 2402848--2402904 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
2402838 TATATTTATA
**
2402848 TTTATTTTTTTAATTTTAAAATACTTT
1 TTTATTTTTTTAATTTTAAAATAAATT
*
2402875 TTTATTTTTTTAATTTTACAATAAATT
1 TTTATTTTTTTAATTTTAAAATAAATT
2402902 TTT
1 TTT
2402905 GGTGTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTATTTTTTTAATTTTAAAATAAATT
Found at i:2409852 original size:26 final size:26
Alignment explanation
Indices: 2409800--2409852 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2409790 ATGAGATTAA
*
2409800 TATTCAAAAACAAATCCATAATATTG
1 TATTCAAAAACAAATCCAGAATATTG
*
2409826 TATTCAAGAACAAATCCGAGAAT-TTG
1 TATTCAAAAACAAATCC-AGAATATTG
2409852 T
1 T
2409853 TGTTGGAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (26 bp):
TATTCAAAAACAAATCCAGAATATTG
Found at i:2420851 original size:2 final size:2
Alignment explanation
Indices: 2420844--2420882 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2420834 GTGAATTTAA
2420844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2420883 AGAGAAAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2424111 original size:31 final size:32
Alignment explanation
Indices: 2424047--2424116 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
2424037 TAACAGAGAA
*
2424047 TGACT-AAAATAGAAATGATCTAAATCGTGAG
1 TGACTAAAAATAGAAATGATCTAAATCATGAG
* *
2424078 TGA-TAAAAATAGAAATTATCTAAAAT-ATTAG
1 TGACTAAAAATAGAAATGATCT-AAATCATGAG
2424109 TGACTAAA
1 TGACTAAA
2424117 TTAAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 1 0.03
31 24 0.73
32 8 0.24
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (32 bp):
TGACTAAAAATAGAAATGATCTAAATCATGAG
Found at i:2427354 original size:31 final size:30
Alignment explanation
Indices: 2427311--2427382 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
2427301 GATTGATTCA
* * *
2427311 AAATTAAAGTTTCATATATATATTTGAACC
1 AAATCAAAGTTTCATATAGATAATTGAACC
* *
2427341 ACAATCAAAGTTTCATGTAGATAATTGCACC
1 A-AATCAAAGTTTCATATAGATAATTGAACC
*
2427372 AAATTAAAGTT
1 AAATCAAAGTT
2427383 CGTGTATCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATCAAAGTTTCATATAGATAATTGAACC
Found at i:2442618 original size:2 final size:2
Alignment explanation
Indices: 2442607--2442641 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2442597 TCAATATCTC
2442607 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2442642 ACTAATTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2458508 original size:3 final size:3
Alignment explanation
Indices: 2458500--2458526 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2458490 ATACATAATT
2458500 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
2458527 TAATAATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:2459732 original size:21 final size:23
Alignment explanation
Indices: 2459706--2459752 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
2459696 TATAAAAATT
2459706 TAAAAATAATT-TTAAATT-AAA
1 TAAAAATAATTATTAAATTCAAA
*
2459727 TAAAAATAATTATTCAATTCAAA
1 TAAAAATAATTATTAAATTCAAA
2459750 TAA
1 TAA
2459753 TCGTGATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 6 0.26
23 6 0.26
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAAATAATTATTAAATTCAAA
Found at i:2462142 original size:12 final size:11
Alignment explanation
Indices: 2462127--2462169 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
2462117 GTAATTAAAA
2462127 ACTTGATTAATG
1 ACTTGATTAA-G
*
2462139 ACTTGATACAAG
1 ACTTGAT-TAAG
2462151 ACTTGATTCAAG
1 ACTTGATT-AAG
2462163 ACTTGAT
1 ACTTGAT
2462170 GATAAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 25 0.93
13 2 0.07
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (11 bp):
ACTTGATTAAG
Found at i:2476162 original size:13 final size:13
Alignment explanation
Indices: 2476146--2476182 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2476136 TTTAAACCAA
2476146 ACTTTTCAAAATC
1 ACTTTTCAAAATC
* *
2476159 ACTTTTCCACATC
1 ACTTTTCAAAATC
2476172 ACTTTTCAAAA
1 ACTTTTCAAAA
2476183 GCATTGCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAATC
Found at i:2478717 original size:30 final size:31
Alignment explanation
Indices: 2478664--2478729 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
2478654 GCTATTAAGT
**
2478664 TTTTTTATTTATTTAGAAATTAGTCTATATA
1 TTTTTTATTTATCAAGAAATTAGTCTATATA
* * *
2478695 TTTTTTATTT-TCAAGAATTTAGTCTTTTTA
1 TTTTTTATTTATCAAGAAATTAGTCTATATA
2478725 TTTTT
1 TTTTT
2478730 CAGATTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.26, C:0.05, G:0.06, T:0.64
Consensus pattern (31 bp):
TTTTTTATTTATCAAGAAATTAGTCTATATA
Found at i:2480109 original size:2 final size:2
Alignment explanation
Indices: 2480102--2480133 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2480092 TGAATAAATC
2480102 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
2480134 TTCATAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2481131 original size:4 final size:4
Alignment explanation
Indices: 2481122--2481148 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2481112 TTTCAAAATT
2481122 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
2481149 TCTCAATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2486761 original size:8 final size:8
Alignment explanation
Indices: 2486748--2486778 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
2486738 TAGTATGGAC
2486748 TAAAATTT
1 TAAAATTT
2486756 TAAAATTT
1 TAAAATTT
2486764 TAAAATTT
1 TAAAATTT
2486772 TAAAATT
1 TAAAATT
2486779 AAAAAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TAAAATTT
Found at i:2486784 original size:16 final size:16
Alignment explanation
Indices: 2486749--2486784 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2486739 AGTATGGACT
**
2486749 AAAATTTTAAAATTTT
1 AAAATTTTAAAATTAA
2486765 AAAATTTTAAAATTAA
1 AAAATTTTAAAATTAA
2486781 AAAA
1 AAAA
2486785 GCATAAGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTTTAAAATTAA
Found at i:2491282 original size:20 final size:20
Alignment explanation
Indices: 2491257--2491299 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2491247 AAAAGCATTC
2491257 TATAAATTGATATAGTTTGG
1 TATAAATTGATATAGTTTGG
2491277 TATAAATTGATATAGTTTGG
1 TATAAATTGATATAGTTTGG
2491297 TAT
1 TAT
2491300 TTGAATATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.47
Consensus pattern (20 bp):
TATAAATTGATATAGTTTGG
Found at i:2493599 original size:12 final size:12
Alignment explanation
Indices: 2493584--2493625 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
2493574 ATATTTATTA
2493584 AATTATTATTGT
1 AATTATTATTGT
2493596 AATTATTATTGT
1 AATTATTATTGT
2493608 AATTATT-TT-T
1 AATTATTATTGT
2493618 -ATTATTAT
1 AATTATTAT
2493626 CACAATTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 2 0.07
12 19 0.66
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (12 bp):
AATTATTATTGT
Found at i:2493708 original size:23 final size:23
Alignment explanation
Indices: 2493697--2493775 Score: 78
Period size: 21 Copynumber: 3.7 Consensus size: 23
2493687 ACATTAGGGG
2493697 CTTTATGTGTCGTATCTCAGGCA
1 CTTTATGTGTCGTATCTCAGGCA
*
2493720 CTTTATGTGTCGTA--TCAGGTA
1 CTTTATGTGTCGTATCTCAGGCA
* **
2493741 CCTCGTGTGTCGT-T-TCAGGCA
1 CTTTATGTGTCGTATCTCAGGCA
*
2493762 C-TTATGTGCCGTAT
1 CTTTATGTGTCGTAT
2493776 ACTGATCAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.17
21 24 0.52
23 14 0.30
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (23 bp):
CTTTATGTGTCGTATCTCAGGCA
Found at i:2509457 original size:11 final size:11
Alignment explanation
Indices: 2509441--2509465 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2509431 TAAATATATT
2509441 AATGTATGGTA
1 AATGTATGGTA
2509452 AATGTATGGTA
1 AATGTATGGTA
2509463 AAT
1 AAT
2509466 TTGTTAGGTT
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:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (11 bp):
AATGTATGGTA
Found at i:2509531 original size:13 final size:14
Alignment explanation
Indices: 2509490--2509531 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2509480 TTGAAATTCT
2509490 AATTCTATTAGTTA
1 AATTCTATTAGTTA
*
2509504 AATT-TGTTAGGTTA
1 AATTCTATTA-GTTA
2509518 AATTCTATTA-TTA
1 AATTCTATTAGTTA
2509531 A
1 A
2509532 TCCGGTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 8 0.33
14 12 0.50
15 4 0.17
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (14 bp):
AATTCTATTAGTTA
Found at i:2510030 original size:5 final size:5
Alignment explanation
Indices: 2510022--2510049 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2510012 TCTTTTCAGT
2510022 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
2510050 ACATTATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Done.