Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009628.1 Hibiscus syriacus cultivar Beakdansim tig00117021_pilon, whole genome shotgun sequence
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: 2284295
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:2060900 original size:17 final size:18
Alignment explanation
Indices: 2060867--2060900 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2060857 TCTCTATTAG
2060867 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
2060885 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
2060901 GACCGGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:2063421 original size:20 final size:20
Alignment explanation
Indices: 2063396--2063433 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2063386 AAGACTATTA
2063396 AAACAGGAATTTTAAGGGAT
1 AAACAGGAATTTTAAGGGAT
2063416 AAACAGGAATTTTAAGGG
1 AAACAGGAATTTTAAGGG
2063434 GTCAATATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.26, T:0.24
Consensus pattern (20 bp):
AAACAGGAATTTTAAGGGAT
Found at i:2065322 original size:17 final size:16
Alignment explanation
Indices: 2065285--2065323 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2065275 TAAAAATAAG
2065285 ATTATTAAAATATTAT
1 ATTATTAAAATATTAT
* *
2065301 ATTATTAAGAATGTTGT
1 ATTATTAA-AATATTAT
2065318 ATTATT
1 ATTATT
2065324 TAGGATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
ATTATTAAAATATTAT
Found at i:2065645 original size:17 final size:18
Alignment explanation
Indices: 2065620--2065664 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
2065610 TTTAATATAC
2065620 ATATATATAATTTTAATA
1 ATATATATAATTTTAATA
2065638 ATAT-TATAATTTTAATA
1 ATATATATAATTTTAATA
*
2065655 TTATAT-TAAT
1 ATATATATAAT
2065665 ATATACTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATATAATTTTAATA
Found at i:2065664 original size:49 final size:50
Alignment explanation
Indices: 2065554--2065667 Score: 121
Period size: 49 Copynumber: 2.4 Consensus size: 50
2065544 TTTATACATA
* ** *
2065554 TAATATTAAATTAATAT-TTTAATATCATTTTAATAAAAATATCAATTAT
1 TAATATTATATTAATATACATAATATAATTTTAATAAAAATATCAATTAT
* * *
2065603 TAA-AATAT-TTAATATACATATATATAATTTTAATAATATTAT-AATT-T
1 TAATATTATATTAATATACATA-ATATAATTTTAATAAAAATATCAATTAT
2065650 TAATATTATATTAATATA
1 TAATATTATATTAATATA
2065668 TACTCATATA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
47 11 0.21
48 13 0.25
49 29 0.55
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (50 bp):
TAATATTATATTAATATACATAATATAATTTTAATAAAAATATCAATTAT
Found at i:2065835 original size:30 final size:27
Alignment explanation
Indices: 2065738--2065838 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 27
2065728 TATTGTTTTC
* *
2065738 ATAATATAATATTATTAAAT-TATTAATA
1 ATAATATAATAAT-TTATATAT-TTAATA
2065766 ATAAGTAATAATAATTTATATATTTAA-A
1 ATAA-T-ATAATAATTTATATATTTAATA
2065794 ATTAATATAATAATTTAGTATTATGTTAATA
1 A-TAATATAATAATTTA-TA-TAT-TTAATA
2065825 A-AATACTAATAATT
1 ATAATA-TAATAATT
2065839 AAAGGTGTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
27 11 0.18
28 9 0.15
29 20 0.32
30 20 0.32
31 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (27 bp):
ATAATATAATAATTTATATATTTAATA
Found at i:2066149 original size:29 final size:29
Alignment explanation
Indices: 2066094--2066186 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
2066084 TTCTAAAAAT
* * * **
2066094 GTAATTCATTTTACGTTAAACGGTTTTAG
1 GTAATTAATTTAACGTAAAACAATTTTAG
* * *
2066123 GTAATTCATTTAATGTAAAATAATTTTAG
1 GTAATTAATTTAACGTAAAACAATTTTAG
* *
2066152 GTAATTAATTTTACGTAAAACAGTTTTCAG
1 GTAATTAATTTAACGTAAAACAATTTT-AG
2066182 GTAAT
1 GTAAT
2066187 CTATTTTACA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 45 0.87
30 7 0.13
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (29 bp):
GTAATTAATTTAACGTAAAACAATTTTAG
Found at i:2066162 original size:14 final size:14
Alignment explanation
Indices: 2066117--2066169 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
2066107 CGTTAAACGG
*
2066117 TTTTAGGTAATTCA
1 TTTTAGGTAATTAA
* * *
2066131 TTTAATGTAAAATAA
1 TTTTAGGT-AATTAA
2066146 TTTTAGGTAATTAA
1 TTTTAGGTAATTAA
*
2066160 TTTTACGTAA
1 TTTTAGGTAA
2066170 AACAGTTTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (14 bp):
TTTTAGGTAATTAA
Found at i:2070710 original size:16 final size:17
Alignment explanation
Indices: 2070686--2070718 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2070676 AAAAATAATT
*
2070686 AAGTAAAATATTAAATA
1 AAGTAAAATATAAAATA
2070703 AAGT-AAATATAAAATA
1 AAGTAAAATATAAAATA
2070719 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
AAGTAAAATATAAAATA
Found at i:2071704 original size:3 final size:3
Alignment explanation
Indices: 2071696--2071722 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2071686 TCAAAGTGAC
2071696 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
2071723 TTTTGAGTTG
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:2077418 original size:9 final size:9
Alignment explanation
Indices: 2077404--2077502 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
2077394 GCTGCTGGAA
2077404 ACCGGTTTG
1 ACCGGTTTG
*
2077413 ACCGGTTTTCA
1 ACCGG-TTT-G
2077424 ACCGGTTCTG
1 ACCGGTT-TG
2077434 ACCGGTTTG
1 ACCGGTTTG
*
2077443 ACCGGTTTCA
1 ACCGGTTT-G
*
2077453 ACCGGTTCG
1 ACCGGTTTG
2077462 AACCGGTTTG
1 -ACCGGTTTG
*
2077472 ACCGGTCTG
1 ACCGGTTTG
*
2077481 AATCGGTTTG
1 -ACCGGTTTG
*
2077491 ACCGGTCTG
1 ACCGGTTTG
2077500 ACC
1 ACC
2077503 CGACCCGACC
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.47
11 6 0.08
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2077448 original size:19 final size:19
Alignment explanation
Indices: 2077404--2077502 Score: 89
Period size: 19 Copynumber: 5.2 Consensus size: 19
2077394 GCTGCTGGAA
* *
2077404 ACCGGTTTGACCGGTTTTCA
1 ACCGGTTTGACCGGTTCT-G
2077424 ACCGGTTCTGACCGGTT-TG
1 ACCGGTT-TGACCGGTTCTG
*
2077443 ACCGGTTTCAACCGGTTC-G
1 ACCGGTTT-GACCGGTTCTG
2077462 AACCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
*
2077481 AATCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
2077500 ACC
1 ACC
2077503 CGACCCGACC
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.07
19 39 0.57
20 16 0.23
21 9 0.13
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (19 bp):
ACCGGTTTGACCGGTTCTG
Found at i:2077466 original size:29 final size:30
Alignment explanation
Indices: 2077403--2077502 Score: 127
Period size: 29 Copynumber: 3.4 Consensus size: 30
2077393 GGCTGCTGGA
2077403 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
2077434 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
2077462 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
2077491 -ACCGGTCTGACC
1 AACCGGTTTGACC
2077503 CGACCCGACC
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
28 12 0.19
29 37 0.59
30 14 0.22
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:2077509 original size:5 final size:5
Alignment explanation
Indices: 2077499--2077556 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
2077489 TGACCGGTCT
* * *
2077499 GACCC GACCC GACCGTT GACCC GACCC GACCC AACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
2077548 GACCC GACC
1 GACCC GACC
2077557 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 36 0.84
7 7 0.16
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:2077525 original size:22 final size:22
Alignment explanation
Indices: 2077499--2077563 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
2077489 TGACCGGTCT
2077499 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
2077521 GACCCGACCCAACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2077543 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
2077564 GTTGACCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:2077565 original size:7 final size:7
Alignment explanation
Indices: 2077553--2077590 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
2077543 GACCCGACCC
2077553 GACCGTT
1 GACCGTT
2077560 GACCGTT
1 GACCGTT
2077567 GACCGTT
1 GACCGTT
2077574 GACCGTT
1 GACCGTT
2077581 GACCGTT
1 GACCGTT
2077588 GAC
1 GAC
2077591 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:2084772 original size:9 final size:9
Alignment explanation
Indices: 2084758--2084856 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
2084748 GCTGCTGGAA
2084758 ACCGGTTTG
1 ACCGGTTTG
*
2084767 ACCGGTTTTCA
1 ACCGG-TTT-G
2084778 ACCGGTTCTG
1 ACCGGTT-TG
2084788 ACCGGTTTG
1 ACCGGTTTG
*
2084797 ACCGGTTTCA
1 ACCGGTTT-G
*
2084807 ACCGGTTCG
1 ACCGGTTTG
2084816 AACCGGTTTG
1 -ACCGGTTTG
*
2084826 ACCGGTCTG
1 ACCGGTTTG
*
2084835 AATCGGTTTG
1 -ACCGGTTTG
*
2084845 ACCGGTCTG
1 ACCGGTTTG
2084854 ACC
1 ACC
2084857 CGACCCGACC
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.47
11 6 0.08
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2084802 original size:19 final size:19
Alignment explanation
Indices: 2084758--2084856 Score: 89
Period size: 19 Copynumber: 5.2 Consensus size: 19
2084748 GCTGCTGGAA
* *
2084758 ACCGGTTTGACCGGTTTTCA
1 ACCGGTTTGACCGGTTCT-G
2084778 ACCGGTTCTGACCGGTT-TG
1 ACCGGTT-TGACCGGTTCTG
*
2084797 ACCGGTTTCAACCGGTTC-G
1 ACCGGTTT-GACCGGTTCTG
2084816 AACCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
*
2084835 AATCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
2084854 ACC
1 ACC
2084857 CGACCCGACC
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.07
19 39 0.57
20 16 0.23
21 9 0.13
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (19 bp):
ACCGGTTTGACCGGTTCTG
Found at i:2084820 original size:29 final size:30
Alignment explanation
Indices: 2084757--2084856 Score: 127
Period size: 29 Copynumber: 3.4 Consensus size: 30
2084747 GGCTGCTGGA
2084757 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
2084788 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
2084816 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
2084845 -ACCGGTCTGACC
1 AACCGGTTTGACC
2084857 CGACCCGACC
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
28 12 0.19
29 37 0.59
30 14 0.22
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:2084863 original size:5 final size:5
Alignment explanation
Indices: 2084853--2084905 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
2084843 TGACCGGTCT
* *
2084853 GACCC GACCC GACCGTT GACCC GACCC GACCGTT GACCC GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACC--C GACCC GACCC GACCC
2084902 GACC
1 GACC
2084906 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:2084879 original size:22 final size:22
Alignment explanation
Indices: 2084870--2084912 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2084860 CCCGACCGTT
2084870 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2084892 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
2084913 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:2084912 original size:17 final size:17
Alignment explanation
Indices: 2084852--2084900 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
2084842 TTGACCGGTC
2084852 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2084869 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2084886 TGACCCGACCCGACC
1 TGACCCGACCCGACC
2084901 CGACCGTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:2085863 original size:63 final size:63
Alignment explanation
Indices: 2085795--2085918 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
2085785 CTAATGTGAC
* ** * *
2085795 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
2085858 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
2085919 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:2087960 original size:24 final size:24
Alignment explanation
Indices: 2087928--2087978 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2087918 TACTAAATAA
*
2087928 ATTATTTTAATATTTAAA-AATATT
1 ATTATTTTAATA-ATAAATAATATT
*
2087952 ATTATTTTATTAATAAATAATATT
1 ATTATTTTAATAATAAATAATATT
2087976 ATT
1 ATT
2087979 TATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTATTTTAATAATAAATAATATT
Found at i:2087962 original size:21 final size:21
Alignment explanation
Indices: 2087941--2087983 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2087931 ATTTTAATAT
*
2087941 TTAA-AAATATTATTATTTTA
1 TTAATAAATAATATTATTTTA
2087961 TTAATAAATAATATTA-TTTA
1 TTAATAAATAATATTATTTTA
2087981 TTA
1 TTA
2087984 TATTTGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATAAATAATATTATTTTA
Found at i:2088191 original size:3 final size:3
Alignment explanation
Indices: 2088183--2088212 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2088173 AATTACTTTA
2088183 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2088213 AAACATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2093959 original size:35 final size:35
Alignment explanation
Indices: 2093918--2093999 Score: 146
Period size: 35 Copynumber: 2.3 Consensus size: 35
2093908 AATCTACCAC
*
2093918 GGAGAAAACAATGATAATTATCTCTTGATAAAAAA
1 GGAGAAAACAACGATAATTATCTCTTGATAAAAAA
2093953 GGAGAAAACAACGATAATTATCTCTTGATAAAAAA
1 GGAGAAAACAACGATAATTATCTCTTGATAAAAAA
*
2093988 GAAGAAAACAAC
1 GGAGAAAACAAC
2094000 TCACAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.21
Consensus pattern (35 bp):
GGAGAAAACAACGATAATTATCTCTTGATAAAAAA
Found at i:2095053 original size:25 final size:24
Alignment explanation
Indices: 2095024--2095093 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 24
2095014 ATTGATATAT
2095024 TAATTTTATATATTATAATATTAA
1 TAATTTTATATATTATAATATTAA
*
2095048 TAAATTTAAATATAATT-TAA-ATTAA
1 T-AATTT-TATAT-ATTATAATATTAA
* * *
2095073 TATTTTTAAATTTTATAATAT
1 TAATTTTATATATTATAATAT
2095094 AAGGTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
22 2 0.06
23 6 0.17
24 7 0.19
25 11 0.31
26 7 0.19
27 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATTTTATATATTATAATATTAA
Found at i:2095074 original size:15 final size:14
Alignment explanation
Indices: 2095012--2095084 Score: 55
Period size: 13 Copynumber: 5.4 Consensus size: 14
2095002 ATTTAAATTA
*
2095012 AAATTGATATA-TT
1 AAATTAATATATTT
* *
2095025 AATTTTATATATTAT
1 AAATTAATATATT-T
*
2095040 AATATTAATAAATTT
1 AA-ATTAATATATTT
2095055 AAA-T-ATA-ATTT
1 AAATTAATATATTT
*
2095066 AAATTAATATTTTT
1 AAATTAATATATTT
2095080 AAATT
1 AAATT
2095085 TTATAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
11 7 0.15
12 4 0.08
13 13 0.27
14 10 0.21
15 6 0.12
16 8 0.17
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (14 bp):
AAATTAATATATTT
Found at i:2098053 original size:8 final size:8
Alignment explanation
Indices: 2098040--2098071 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
2098030 TGAAACATCC
2098040 GACAAACG
1 GACAAACG
2098048 GACAAACG
1 GACAAACG
2098056 GACAAACG
1 GACAAACG
2098064 GACAAACG
1 GACAAACG
2098072 TTTTCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.25, T:0.00
Consensus pattern (8 bp):
GACAAACG
Found at i:2105001 original size:20 final size:20
Alignment explanation
Indices: 2104952--2105062 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
2104942 AAATGACTAA
* *
2104952 CAAATTCGCAACGC-GAACT
1 CAAATTCGCAACACAGAAGT
* *
2104971 CCAATTTCGCAACCCAGAAGT
1 -CAAATTCGCAACACAGAAGT
* **
2104992 CAAATCCGCAACAC-GATTT
1 CAAATTCGCAACACAGAAGT
*
2105011 CCAAATTCGCAACACATAAGT
1 -CAAATTCGCAACACAGAAGT
*
2105032 CAAATTCGCAACATAGAAGT
1 CAAATTCGCAACACAGAAGT
2105052 CAAATTCGCAA
1 CAAATTCGCAA
2105063 AGCACGTTTA
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 3 0.04
20 65 0.88
21 6 0.08
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:2105014 original size:40 final size:40
Alignment explanation
Indices: 2104952--2105062 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 40
2104942 AAATGACTAA
* * *
2104952 CAAATTCGCAACGCGAACTCCAATTTCGCAACCCAGAAGT
1 CAAATTCGCAACACGAACTCCAAATTCGCAACACAGAAGT
* ** *
2104992 CAAATCCGCAACACGATTTCCAAATTCGCAACACATAAGT
1 CAAATTCGCAACACGAACTCCAAATTCGCAACACAGAAGT
* *
2105032 CAAATTCGCAACATAGAAGT-CAAATTCGCAA
1 CAAATTCGCAACA-CGAACTCCAAATTCGCAA
2105063 AGCACGTTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 56 0.95
41 3 0.05
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACACGAACTCCAAATTCGCAACACAGAAGT
Found at i:2105268 original size:22 final size:22
Alignment explanation
Indices: 2105210--2105268 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
2105200 TCACTCTCTA
* *
2105210 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCCGTCTCCATCTC
* *
2105232 CGACAAAATCCGTCTCCATCTC
1 CGGCGAAATCCGTCTCCATCTC
2105254 CGGCGAAATCCGTCT
1 CGGCGAAATCCGTCT
2105269 ATCTCCATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.42, G:0.17, T:0.20
Consensus pattern (22 bp):
CGGCGAAATCCGTCTCCATCTC
Found at i:2105636 original size:20 final size:20
Alignment explanation
Indices: 2105613--2105654 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2105603 AAACTTAAAT
*
2105613 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATAAAAA
*
2105633 TCGCAACGCGAAAATAAAAA
1 TCGCAACACGAAAATAAAAA
2105653 TC
1 TC
2105655 ACAATGCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.12
Consensus pattern (20 bp):
TCGCAACACGAAAATAAAAA
Found at i:2105663 original size:20 final size:20
Alignment explanation
Indices: 2105616--2105663 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2105606 CTTAAATTCG
* * *
2105616 CAACACGAAAATGAAAATCG
1 CAACGCGAAAATAAAAATCA
2105636 CAACGCGAAAATAAAAATCA
1 CAACGCGAAAATAAAAATCA
*
2105656 CAATGCGA
1 CAACGCGA
2105664 TTTTAGTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.54, C:0.21, G:0.15, T:0.10
Consensus pattern (20 bp):
CAACGCGAAAATAAAAATCA
Found at i:2105695 original size:20 final size:19
Alignment explanation
Indices: 2105659--2105713 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
2105649 AAAATCACAA
*
2105659 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTATTTTCGCGT
2105678 TGCGATTTTCATTTTCGCGT
1 TGCGATTTT-ATTTTCGCGT
*
2105698 TGCGAATTTAATTTTC
1 TGCG-ATTTTATTTTC
2105714 AGAAACTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 9 0.28
20 19 0.59
21 4 0.12
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.49
Consensus pattern (19 bp):
TGCGATTTTATTTTCGCGT
Found at i:2107988 original size:18 final size:18
Alignment explanation
Indices: 2107965--2108001 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2107955 ATTTATATAT
2107965 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2107983 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2108001 A
1 A
2108002 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2108421 original size:25 final size:25
Alignment explanation
Indices: 2108387--2108436 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2108377 TATTATTTTC
*
2108387 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2108412 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2108437 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2108561 original size:29 final size:29
Alignment explanation
Indices: 2108515--2108575 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
2108505 AATTCGCAAC
*
2108515 GCGAAAGTAAAATTCGCATTGCGATTGTT
1 GCGAAAGTAAAATACGCATTGCGATTGTT
* * *
2108544 GCGAAAGTCAAATACGCATTGTGATTTTT
1 GCGAAAGTAAAATACGCATTGCGATTGTT
2108573 GCG
1 GCG
2108576 TTGCGAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (29 bp):
GCGAAAGTAAAATACGCATTGCGATTGTT
Found at i:2108976 original size:18 final size:18
Alignment explanation
Indices: 2108950--2108990 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2108940 AGGTGAAGTC
*
2108950 GATTGTGATTGAGAATTT
1 GATTTTGATTGAGAATTT
* *
2108968 GATTTTGATTGCGATTTT
1 GATTTTGATTGAGAATTT
2108986 GATTT
1 GATTT
2108991 CCTTTTGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.24, T:0.51
Consensus pattern (18 bp):
GATTTTGATTGAGAATTT
Found at i:2111069 original size:3 final size:3
Alignment explanation
Indices: 2111061--2111085 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2111051 TCTTCGGGAA
2111061 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
2111086 AGAGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2112309 original size:19 final size:20
Alignment explanation
Indices: 2112249--2112360 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
2112239 ACTAAAACCT
* *
2112249 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
2112268 GTTGTGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGA
2112288 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
*
2112307 GTTGCGAATTTGAAATTCAA
1 GTTGCGAATTTGAAATTCGA
*
2112327 TGTTGCGAATTTGGAAA-TCGC
1 -GTTGCGAATTT-GAAATTCGA
2112348 GTTGCGAATTTGA
1 GTTGCGAATTTGA
2112361 CTTATGTGTT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
19 29 0.37
20 33 0.42
21 13 0.16
22 4 0.05
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:2112331 original size:60 final size:58
Alignment explanation
Indices: 2112249--2112360 Score: 152
Period size: 60 Copynumber: 1.9 Consensus size: 58
2112239 ACTAAAACCT
* *
2112249 GTTGCGAAATTAAATTCGTGTTGTGAATTCGAAAATCGAGTTGCGAATTTGAAATTCA
1 GTTGCGAAATTAAATTCATGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCA
* * * *
2112307 GTTGCGAATTTGAAATTCAATGTTGCGAATTTGGAAATCGCGTTGCGAATTTGA
1 GTTGCGAAATT-AAATTC-ATGTTGCGAATTCGAAAATCGAGTTGCGAATTTGA
2112361 CTTATGTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 10 0.22
59 6 0.13
60 30 0.65
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (58 bp):
GTTGCGAAATTAAATTCATGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCA
Found at i:2112371 original size:40 final size:41
Alignment explanation
Indices: 2112248--2112439 Score: 132
Period size: 40 Copynumber: 4.8 Consensus size: 41
2112238 AACTAAAACC
* * * * * *
2112248 TGTTGCGAAATT-AAATTCGTGTTGTGAATTCGAAAATCGA
1 TGTTGCGAATTTGAAATTCGCGTTGCGAATTTGAAATTCAA
*
2112288 -GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCAA
1 TGTTGCGAATTTGAAATTCGCGTTGCGAATTTGAAATTCAA
* *
2112327 TGTTGCGAATTTGGAAA-TCGCGTTGCGAATTTG-ACTT-ATG
1 TGTTGCGAATTT-GAAATTCGCGTTGCGAATTTGAAATTCA-A
* * *
2112367 TGTTGTG-ATTTACAAATTCGCGTTGCGAATTTGGAAA--CTA
1 TGTTGCGAATTT-GAAATTCGCGTTGCGAATTT-GAAATTCAA
* * * * *
2112407 GGTTGCGAAATTGGAGTTCGCGTTGTGAATTTG
1 TGTTGCGAATTTGAAATTCGCGTTGCGAATTTG
2112440 TTAGTCATTT
Statistics
Matches: 120, Mismatches: 22, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
39 35 0.29
40 64 0.53
41 20 0.17
42 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (41 bp):
TGTTGCGAATTTGAAATTCGCGTTGCGAATTTGAAATTCAA
Found at i:2116908 original size:29 final size:29
Alignment explanation
Indices: 2116847--2116913 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
2116837 TTATACAGTG
* * *
2116847 ACCAAAGAGGTCGCCATGCACGCCCAACG
1 ACCAAGGAGGTCGCCATGCACGCACAACA
* * *
2116876 ACCAAGGAGGTCGCCATGCACTCAGAGCA
1 ACCAAGGAGGTCGCCATGCACGCACAACA
2116905 ACCAAGGAG
1 ACCAAGGAG
2116914 CGGGAGCTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.33, G:0.27, T:0.07
Consensus pattern (29 bp):
ACCAAGGAGGTCGCCATGCACGCACAACA
Found at i:2117194 original size:65 final size:65
Alignment explanation
Indices: 2117106--2117231 Score: 216
Period size: 65 Copynumber: 1.9 Consensus size: 65
2117096 TGCACCACAC
* *
2117106 CCAAACTTTAACCCTATCCCTCATGCATGTGTTGCATCCATAGCTGGGAGATTCCTGCATCGCGA
1 CCAAACTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGCTGGGAGATTCCTGCATCGCGA
* *
2117171 CCAAGCTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGTTGGGAGATTCCTGCATC
1 CCAAACTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGCTGGGAGATTCCTGCATC
2117232 CGTAGCTGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (65 bp):
CCAAACTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGCTGGGAGATTCCTGCATCGCGA
Found at i:2117657 original size:21 final size:21
Alignment explanation
Indices: 2117632--2117675 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2117622 AATCTAGTTA
2117632 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
*
2117653 ATTAGTTTGTTAGTTTAAATT
1 ATTAGTTTGTTAGTATAAATT
2117674 AT
1 AT
2117676 ATATTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:2121574 original size:17 final size:18
Alignment explanation
Indices: 2121548--2121582 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2121538 AATGATTAGT
2121548 AATTATTAATAATAATGA
1 AATTATTAATAATAATGA
2121566 AATTA-TAATAATAATGA
1 AATTATTAATAATAATGA
2121583 TTTACTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTATTAATAATAATGA
Found at i:2121799 original size:12 final size:11
Alignment explanation
Indices: 2121778--2122081 Score: 83
Period size: 12 Copynumber: 24.6 Consensus size: 11
2121768 AATAATCATT
2121778 ATAATGATTTA
1 ATAATGATTTA
2121789 ATAATGAATTTA
1 ATAATG-ATTTA
* * * *
2121801 ATATTTAATGA
1 ATAATGATTTA
* *
2121812 TTTGATGATTTA
1 -ATAATGATTTA
*
2121824 GTAATGATATGATA
1 ATAATGAT-T--TA
* *
2121838 ATAATCAATATA
1 ATAAT-GATTTA
2121850 ATAATGATTTGATA
1 ATAATGA-TT--TA
*
2121864 ATAATCATTATA
1 ATAATGATT-TA
2121876 ATAATGATTTAGTA
1 ATAATGA-TT--TA
*
2121890 ATAATCATTATA
1 ATAATGATT-TA
2121902 ATAATGATTTA
1 ATAATGATTTA
*
2121913 ACAATGATTT-
1 ATAATGATTTA
2121923 A-AAT-ATTTA
1 ATAATGATTTA
2121932 ATGATTTGATGATTTA
1 AT-A----ATGATTTA
*
2121948 GTAATGATTTGATA
1 ATAATGA-TT--TA
*
2121962 ATAATCATTATA
1 ATAATGATT-TA
2121974 ATAATGATTTAATA
1 ATAATGA-TT--TA
*
2121988 ATAATCATTATA
1 ATAATGATT-TA
*
2122000 ATAATTATTATA
1 ATAATGATT-TA
*
2122012 ATAATAATTTA
1 ATAATGATTTA
*
2122023 ATAATAATGTAATA
1 ATAATGAT-T--TA
2122037 ATAATGATTTGA
1 ATAATGATTT-A
*
2122049 TTGTAATGATTTA
1 --ATAATGATTTA
*
2122062 GTAATGATTAGTA
1 ATAATGATT--TA
2122075 ATAATGA
1 ATAATGA
2122082 AATTATTATT
Statistics
Matches: 227, Mismatches: 34, Indels: 62
0.70 0.11 0.19
Matches are distributed among these distances:
8 4 0.02
9 4 0.02
10 1 0.00
11 52 0.23
12 77 0.34
13 22 0.10
14 56 0.25
15 5 0.02
16 6 0.03
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (11 bp):
ATAATGATTTA
Found at i:2121855 original size:26 final size:26
Alignment explanation
Indices: 2121825--2122041 Score: 123
Period size: 26 Copynumber: 8.7 Consensus size: 26
2121815 GATGATTTAG
2121825 TAATGATATGATAATAATCAATATAA
1 TAATGATATGATAATAATCAATATAA
* *
2121851 TAATGATTTGATAATAATCATTATAA
1 TAATGATATGATAATAATCAATATAA
* *
2121877 TAATGAT-TTAGTAATAATCATTATAA
1 TAATGATATGA-TAATAATCAATATAA
* * *
2121903 TAATGAT-T--TAACAAT-GATTTAAA
1 TAATGATATGATAATAATCAATAT-AA
* * * * * * *
2121926 TATTTA-ATGAT-TTGAT-GATTTAG
1 TAATGATATGATAATAATCAATATAA
* *
2121949 TAATGATTTGATAATAATCATTATAA
1 TAATGATATGATAATAATCAATATAA
* * *
2121975 TAATGATTTAATAATAATCATTATAA
1 TAATGATATGATAATAATCAATATAA
* *
2122001 TAAT--TATTATAATAAT-AATTTAA
1 TAATGATATGATAATAATCAATATAA
* * *
2122024 TAATAATGTAATAATAAT
1 TAATGATATGATAATAAT
2122042 GATTTGATTG
Statistics
Matches: 152, Mismatches: 29, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
22 2 0.01
23 27 0.18
24 21 0.14
25 16 0.11
26 86 0.57
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (26 bp):
TAATGATATGATAATAATCAATATAA
Found at i:2121930 original size:124 final size:123
Alignment explanation
Indices: 2121752--2122027 Score: 420
Period size: 124 Copynumber: 2.3 Consensus size: 123
2121742 TCAATTAACC
* *
2121752 ATAAAAATGATTT-GATAATAATCA-TT-ATAATGATTTAATAATGAATTTAATATTTAATGATT
1 ATAATAATGATTTAG-TAATAATCATTTAATAATGATTTAACAATGAATTTAATATTTAATGATT
*
2121814 TGATGATTTAGTAATGATATGATAATAATCAATATAATAATGATTTGATAATAATCATT
65 TGATGATTTAGTAATGATATGATAATAATCAATATAATAATGATTTAATAATAATCATT
2121873 ATAATAATGATTTAGTAATAATCATTATAATAATGATTTAACAATG-ATTTAAATATTTAATGAT
1 ATAATAATGATTTAGTAATAATCATT-TAATAATGATTTAACAATGAATTT-AATATTTAATGAT
* *
2121937 TTGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATT
64 TTGATGATTTAGTAATGATATGATAATAATCAATATAATAATGATTTAATAATAATCATT
* *
2121997 ATAATAATTA-TTA-TAATAATAATTTAATAAT
1 ATAATAATGATTTAGTAATAATCATTTAATAAT
2122028 AATGTAATAA
Statistics
Matches: 143, Mismatches: 7, Indels: 10
0.89 0.04 0.06
Matches are distributed among these distances:
121 28 0.20
122 12 0.08
123 8 0.06
124 95 0.66
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (123 bp):
ATAATAATGATTTAGTAATAATCATTTAATAATGATTTAACAATGAATTTAATATTTAATGATTT
GATGATTTAGTAATGATATGATAATAATCAATATAATAATGATTTAATAATAATCATT
Found at i:2121977 original size:3 final size:3
Alignment explanation
Indices: 2121959--2122041 Score: 55
Period size: 3 Copynumber: 28.7 Consensus size: 3
2121949 TAATGATTTG
* * * * * * *
2121959 ATA ATA ATC ATT ATA ATA ATG AT- TTA ATA ATA ATC ATT ATA ATA ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
2122006 ATT ATA ATA ATA AT- TTA ATA ATA AT- GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2122042 GATTTGATTG
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
2 3 0.05
3 59 0.95
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:2122076 original size:21 final size:20
Alignment explanation
Indices: 2122046--2122137 Score: 57
Period size: 21 Copynumber: 4.6 Consensus size: 20
2122036 AATAATGATT
2122046 TGATT-GTAATGATTTAGTAA
1 TGATTAGTAAT-ATTTAGTAA
* *
2122066 TGATTAGTAATA-AT-GAAA
1 TGATTAGTAATATTTAGTAA
* * * *
2122084 TTATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAGT-A-A
*
2122106 TGA-TATTAATGATTTAGTAA
1 TGATTAGTAAT-ATTTAGTAA
2122126 TGATTAGTAATA
1 TGATTAGTAATA
2122138 ATGAAATTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
18 13 0.25
19 2 0.04
20 10 0.19
21 20 0.38
22 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (20 bp):
TGATTAGTAATATTTAGTAA
Found at i:2122076 original size:124 final size:122
Alignment explanation
Indices: 2121752--2122060 Score: 405
Period size: 124 Copynumber: 2.5 Consensus size: 122
2121742 TCAATTAACC
* * *
2121752 ATAAAAATGATTTGATAATAATCA-T-T-ATAATGATTTAATAATGAATTTAATATTTAATGATT
1 ATAATAATGATTTAATAATAAT-ATTATAATAATGATATAATAATG-ATTTAATATTTAATGATT
*
2121814 TGATGATTTAGTAATGATATGATAATAATCAATATAATAATGATTTGATAATAATCATT
64 TGATGATTTAGTAATGATATGATAATAATCAATATAATAATGATTTAATAATAATCATT
* * *
2121873 ATAATAATGATTTAGTAATAATCATTATAATAATGATTTAACAATGATTTAAATATTTAATGATT
1 ATAATAATGATTTAATAATAAT-ATTATAATAATGATATAATAATGATTT-AATATTTAATGATT
* *
2121938 TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATT
64 TGATGATTTAGTAATGATATGATAATAATCAATATAATAATGATTTAATAATAATCATT
* * *
2121997 ATAATAATTATTATAATAATAAT-TTAATAATAATG-TAATAATAATGATTTGAT-TGTAATGAT
1 ATAATAATGATT-TAATAATAATATT-ATAATAATGAT-ATAATAATGATTTAATATTTAATGAT
2122059 TT
63 TT
2122061 AGTAATGATT
Statistics
Matches: 168, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
121 21 0.12
122 11 0.07
123 10 0.06
124 117 0.70
125 9 0.05
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (122 bp):
ATAATAATGATTTAATAATAATATTATAATAATGATATAATAATGATTTAATATTTAATGATTTG
ATGATTTAGTAATGATATGATAATAATCAATATAATAATGATTTAATAATAATCATT
Found at i:2122077 original size:60 final size:60
Alignment explanation
Indices: 2121787--2122185 Score: 228
Period size: 60 Copynumber: 6.5 Consensus size: 60
2121777 TATAATGATT
* * * * * *
2121787 TAATAATGAATTTAATATTTAATGATTT-G--ATGATTTAGTAATGATATGATAATAATCAATA
1 TAATAATG-ATTTGAT-TATAATGATTTAGTAATGATTTAGTAATAATTTAATAATAAT-TA-A
* * * * *
2121848 TAATAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATT-ATAATAATGATT
1 TAATAATGATTTGATTATAATGATT-TAGTAATGATTTAGTAATAAT--TTAATAATAATTA-A
* * * * * *
2121911 TAACAATGATTTAAATATTTAATGATTT-G--ATGATTTAGTAATGATTTGATAATAATCATTA
1 TAATAATGATTT-GAT-TATAATGATTTAGTAATGATTTAGTAATAATTTAATAATAAT--TAA
* * * * * *
2121972 TAATAATGATTTAATAATAATCATTATAATAATTATTATAATAATAATTTAATAATAATGTAA
1 TAATAATGATTTGATTATAATGATT-TAGTAATGATT-TAGTAATAATTTAATAATAAT-TAA
* ** * *
2122035 TAATAATGATTTGATTGTAATGATTTAGTAATGA-TTAGTAATAATGAAATTATTATTAA
1 TAATAATGATTTGATTATAATGATTTAGTAATGATTTAGTAATAATTTAATAATAATTAA
* ** * *
2122094 TATTTAATGATTTGA-TATTAATGATTTAGTAATGA-TTAGTAATAATGAAATTATTATTAA
1 TA-ATAATGATTTGATTA-TAATGATTTAGTAATGATTTAGTAATAATTTAATAATAATTAA
**
2122154 TTTTTAATGATTTGA-TAGTAATGA-TTAGTAAT
1 -TAATAATGATTTGATTA-TAATGATTTAGTAAT
2122186 AATAATTTAT
Statistics
Matches: 274, Mismatches: 45, Indels: 40
0.76 0.13 0.11
Matches are distributed among these distances:
59 30 0.11
60 108 0.39
61 36 0.13
62 7 0.03
63 56 0.20
64 29 0.11
65 8 0.03
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (60 bp):
TAATAATGATTTGATTATAATGATTTAGTAATGATTTAGTAATAATTTAATAATAATTAA
Found at i:2122185 original size:24 final size:24
Alignment explanation
Indices: 2122158--2122233 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
2122148 TATTAATTTT
2122158 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
* * *
2122182 TAATAATAATTTATTATTAAT-ATT--
1 TAATGAT--TTGA-TAGTAATGATTAG
2122206 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
2122230 TAAT
1 TAAT
2122234 AATAATTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
21 6 0.15
22 6 0.15
24 16 0.40
26 6 0.15
27 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:2122224 original size:108 final size:108
Alignment explanation
Indices: 2122060--2122882 Score: 714
Period size: 108 Copynumber: 7.6 Consensus size: 108
2122050 TGTAATGATT
2122060 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAAT-AAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
*
2122125 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
65 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* *
2122169 TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAATGA-TTAGTAA
1 TAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
* * * * * * * * *
2122233 TAATAATTTATTATTAATATT-TAATGAATTAATACTAATGATTT-A
66 TGATTAGTAATAATGAA-ATTATTATTAA-T-AT-TTAATGATTTGA
* *
2122278 -A-TAATGATTAGTAATATTGAAATTATTATTAATATTTAATGATTTGATAGTAATGA-TTAGTA
1 TAGTAATGATTAGTAATAAT-AAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
* * *
2122340 ATGATTAGTAATAAT-AATTTATTATTAATATCTAATAATTTGA
65 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * * * * *
2122383 TATTAATGATTTAGTAATGAT---TTGA-TAGTAATGATTT-ACGACTTGA-A-CAATGA---A-
1 TAGTAATGA-TTAGTAATAATAAATT-ATTATTAAT-ATTTAATGATTTGATATTAATGATTTAG
* * * ** * * * *
2122437 CAATGTTTGGTTCAATTAACCATATT-TTCGTTACATAACTAGTAATGAAATT-A
63 TAATGATTAG-T-AA-TAATGAAATTATT-ATTA-AT-A-T-TTAATG-ATTTGA
* *
2122490 TAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAAT-AAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
2122555 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
65 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * * * * * * *
2122599 TAGTAATGATTTAGTAATGAT-TAGTAATAATAA-AATT-ATTA-TTAATATTTAATGATTTGAT
1 TAGTAATGA-TTAGTAATAATAAATTATTATTAATATTTAATGATTTGATA-TTAATGA-TT--T
*
2122660 AGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
61 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * * * * * * * *
2122707 TAATAATGATTTAGTAATGATTAGTAATAATGAA-A-TT-ATTA-TTAATATTTAATGATTTAGT
1 TAGTAATGA-TTAGTAATAATAAATTATTATTAATATTTAATGATTTGATA-TTAATGATTTAGT
2122768 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
64 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
** *
2122813 TAGTAATGATTAGTAATAATATTTTATTATTAATATTTAATGATTTGATATTAATGATTTAATAA
1 TAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
2122878 TGATT
66 TGATT
2122883 TGATAGTAAT
Statistics
Matches: 581, Mismatches: 86, Indels: 95
0.76 0.11 0.12
Matches are distributed among these distances:
99 7 0.01
100 2 0.00
101 2 0.00
102 10 0.02
103 7 0.01
104 26 0.04
105 51 0.09
106 60 0.10
107 74 0.13
108 204 0.35
109 71 0.12
110 35 0.06
111 2 0.00
112 7 0.01
113 10 0.02
114 4 0.01
115 2 0.00
116 7 0.01
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.45
Consensus pattern (108 bp):
TAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
TGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:2122263 original size:18 final size:18
Alignment explanation
Indices: 2122242--2122319 Score: 50
Period size: 18 Copynumber: 4.0 Consensus size: 18
2122232 ATAATAATTT
2122242 ATTATTAATATTTAATGA
1 ATTATTAATATTTAATGA
*
2122260 ATTAATACTAATGATTTAATAA
1 ATT-AT--TAAT-ATTTAATGA
* * *
2122282 TGATTAGTAATATTGAAAT-T
1 --ATTATTAATATT-TAATGA
2122302 ATTATTAATATTTAATGA
1 ATTATTAATATTTAATGA
2122320 TTTGATAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
17 3 0.07
18 14 0.31
19 2 0.04
20 3 0.07
21 11 0.24
22 8 0.18
23 1 0.02
24 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (18 bp):
ATTATTAATATTTAATGA
Found at i:2122292 original size:59 final size:59
Alignment explanation
Indices: 2122197--2122404 Score: 258
Period size: 59 Copynumber: 3.5 Consensus size: 59
2122187 ATAATTTATT
2122197 ATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGA
1 ATTAATA-TTAATGATTT-A-A-TAATGATTAGTAATAATAATTTATTATTAATATTTAATGA
* * *
2122260 ATTAATACTAATGATTTAATAATGATTAGTAATATTGAAATTATTATTAATATTTAATGA
1 ATTAATATTAATGATTTAATAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGA
* * * * *
2122320 TTTGATAGTAATGA-TTAGTAATGATTAGTAATAATAATTTATTATTAATATCTAAT-A
1 ATTAATATTAATGATTTAATAATGATTAGTAATAATAATTTATTATTAATATTTAATGA
* *
2122377 ATTTGATATTAATGATTTAGTAATGATT
1 A-TTAATATTAATGATTTAATAATGATT
2122405 TGATAGTAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
57 1 0.01
58 31 0.24
59 47 0.36
60 34 0.26
61 1 0.01
62 9 0.07
63 7 0.05
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (59 bp):
ATTAATATTAATGATTTAATAATGATTAGTAATAATAATTTATTATTAATATTTAATGA
Found at i:2122340 original size:10 final size:10
Alignment explanation
Indices: 2122325--2122351 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2122315 AATGATTTGA
2122325 TAGTAATGAT
1 TAGTAATGAT
2122335 TAGTAATGAT
1 TAGTAATGAT
2122345 TAGTAAT
1 TAGTAAT
2122352 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:2122394 original size:14 final size:14
Alignment explanation
Indices: 2122372--2122419 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2122362 TATTAATATC
* *
2122372 TAATAATTTGATAT
1 TAATGATTTGATAG
2122386 TAATGA-TT--TAG
1 TAATGATTTGATAG
2122397 TAATGATTTGATAG
1 TAATGATTTGATAG
2122411 TAATGATTT
1 TAATGATTT
2122420 ACGACTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 2 0.07
14 17 0.59
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:2122402 original size:274 final size:272
Alignment explanation
Indices: 2122038--2122882 Score: 932
Period size: 274 Copynumber: 3.1 Consensus size: 272
2122028 AATGTAATAA
* *
2122038 TAATGATTTGATTGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
2122103 ATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
66 ATTTGATATTAATGATTTAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGA-TT-
2122168 ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
128 ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGA-TT-ATAGTAATGATTAGTAA
* * * * *
2122233 TAAT-AATTTATTATTAATATTTAATGAATTAATACTAATGATTTAATAATGATTAGTAATATTG
191 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATAATGATTAGTAATAATG
2122297 AAATTATTATTAATATT
256 AAATTATTATTAATATT
* * *
2122314 TAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATCTAATA
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
* * * ** * **
2122377 ATTTGATATTAATGATTTAGTAATGATTTGATAGTAATGATTTACGACTTGAA----CAATGAAC
66 ATTTGATATTAATGATTTAGTAATGATTAG-TAATAATGAATTATTA-TT-AATTTTTAATGATT
* * * ** * * * * *
2122438 A-ATGT-TTGGTTCAATTAACCATATTTTCGTTACATAACTA-GTAATGAAATTATAATAATGAT
128 ATA-GTAATGATT--AGTAATAATAATTT-ATTA-TTAA-TATTTAATG--ATTATAGTAATGAT
*
2122500 TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
185 TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATAATGATTAGTA
2122565 ATAATGAAATTATTATTAATATT
250 ATAATGAAATTATTATTAATATT
2122588 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
* * * * * * * * *
2122653 ATTTGATAGTAATGA-TTAGTAATAATAATTTATTATTAA-TATTTAATGATTTGATAATAATGA
66 ATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAATTA-TTATTAATTT--T--TAATGA
*
2122716 TT-TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATT-TAGTAATGATTAGTA
126 TTATAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTATAGTAATGATTAGTA
*
2122779 ATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA-TTAGTAAT-A--A-T-AT--T
190 ATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATAATGATTAGTAATAAT
2122836 ----TTATTATTAATATT
255 GAAATTATTATTAATATT
* *
2122850 TAATGATTTGATATTAATGATTTAATAATGATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATT
2122883 TGATAGTAAT
Statistics
Matches: 481, Mismatches: 61, Indels: 68
0.79 0.10 0.11
Matches are distributed among these distances:
262 45 0.09
266 1 0.00
268 2 0.00
269 6 0.01
270 4 0.01
271 10 0.02
272 10 0.02
273 39 0.08
274 211 0.44
275 65 0.14
276 56 0.12
277 8 0.02
278 9 0.02
279 5 0.01
280 10 0.02
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (272 bp):
TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
ATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAATTATTATTAATTTTTAATGATTATA
GTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTATAGTAATGATTAGTAATAATG
AAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATAATGATTAGTAATAATGAAATT
ATTATTAATATT
Found at i:2122405 original size:25 final size:25
Alignment explanation
Indices: 2122372--2122420 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2122362 TATTAATATC
*
2122372 TAATAATTTGATATTAATGATTTAG
1 TAATAATTTGATAGTAATGATTTAG
*
2122397 TAATGATTTGATAGTAATGATTTA
1 TAATAATTTGATAGTAATGATTTA
2122421 CGACTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (25 bp):
TAATAATTTGATAGTAATGATTTAG
Found at i:2122508 original size:13 final size:12
Alignment explanation
Indices: 2122486--2122739 Score: 51
Period size: 11 Copynumber: 21.1 Consensus size: 12
2122476 TAGTAATGAA
2122486 ATTATAATAATG
1 ATTATAATAATG
2122498 ATTAGTAATAATG
1 ATTA-TAATAATG
*
2122511 AAATTATTATTAAT-
1 --ATTA-TAATAATG
*
2122525 ATT-TAATGAT-
1 ATTATAATAATG
*
2122535 -TTGATAGTAATG
1 ATT-ATAATAATG
*
2122547 ATT-TAGTAATG
1 ATTATAATAATG
2122558 ATTAGTAATAATG
1 ATTA-TAATAATG
*
2122571 AAATTATTATTAAT-
1 --ATTA-TAATAATG
*
2122585 ATT-TAATGAT-
1 ATTATAATAATG
*
2122595 -TTGATAGTAATG
1 ATT-ATAATAATG
*
2122607 ATT-TAGTAATG
1 ATTATAATAATG
2122618 ATTAGTAATAAT-
1 ATTA-TAATAATG
* *
2122630 A--A-AATTATT
1 ATTATAATAATG
*
2122639 ATTAATATTTAATG
1 ATT-ATA-ATAATG
*
2122653 ATTTGATAGTAATG
1 A-TT-ATAATAATG
*
2122667 ATTAGTAATAATA
1 ATTA-TAATAATG
*
2122680 ATTTATTATTAAT-
1 A-TTA-TAATAATG
*
2122693 ATT-TAATGAT-
1 ATTATAATAATG
2122703 -TTGATAATAATG
1 ATT-ATAATAATG
*
2122715 ATT-TAGTAATG
1 ATTATAATAATG
2122726 ATTAGTAATAATG
1 ATTA-TAATAATG
2122739 A
1 A
2122740 AATTATTATT
Statistics
Matches: 181, Mismatches: 29, Indels: 63
0.66 0.11 0.23
Matches are distributed among these distances:
8 5 0.03
9 7 0.04
10 16 0.09
11 48 0.27
12 15 0.08
13 46 0.25
14 19 0.10
15 25 0.14
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:2122547 original size:490 final size:483
Alignment explanation
Indices: 2122038--2123096 Score: 1643
Period size: 490 Copynumber: 2.2 Consensus size: 483
2122028 AATGTAATAA
*
2122038 TAATGATTTGATTGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
* * *
2122103 ATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
66 ATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTG
*
2122168 ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAATGA-TTAGTA
131 ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAATAATGATTTAGTA
* * * * *
2122232 ATAATAATTTATTATTAATATTTAATGAATTAATA-CTAATGATTTAATAATGATTAGTAATATT
196 ATAATAAGTAATAATGAA-A-TT-AT-AATTAATATCTAATGATTTAATAATGATTAGTAATAAT
2122296 GAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAATTTA
257 GAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAG---T-A--A-TAAT-AT--TTTA
*
2122361 TTATTAATATCTAATAATTTGATATTAATGATTTAGTAATGATTTGATAGTAATGATTTACGACT
312 TTATTAATATCTAATAATTTGATATTAATGATTTAATAATGATTTGATAGTAATGATTTACGACT
* *
2122426 TGAACAATGAACAATGTTTGGTTCAATTAACCATATTTTCGTTACATAACTAGTAATGAAATTAT
377 TGAACAATGAACAATGTTTGATTCAATTAACCATATTTCCGTTACATAACTAGTAATGAAATTAT
2122491 AAT-A-A-T-G-ATTAGTAATAATGAAATTATTATTAATATT
442 AATAAGATTAGTATTAGTAATAATGAAATTATTATTAATATT
2122528 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
2122593 ATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTG
66 ATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTG
2122658 ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAATAATGATTTAGTA
131 ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAATAATGATTTAGTA
* * * * *
2122723 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAGTAATGATTAGTAATAATGAAA
196 ATAATAAGTAATAATGAAATTATAATTAATATCTAATGATTTAATAATGATTAGTAATAATGAAA
*
2122788 TTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATATTTTATTATTAATATTTAA
261 TTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATATTTTATTATTAATATCTAA
* *
2122853 TGATTTGATATTAATGATTTAATAATGATTTGATAGTAATGATTTATGACTTGAACAATGAACAA
326 TAATTTGATATTAATGATTTAATAATGATTTGATAGTAATGATTTACGACTTGAACAATGAACAA
*
2122918 TGTTTTATTCAATTAACCATATTTCCGTTACATAACTAGTAATGAAATTATAATAATGATTTAGT
391 TGTTTGATTCAATTAACCATATTTCCGTTACATAACTAGTAATGAAATTATAATAA-GA-TTAG-
2122983 AATTATTAGTAATAATGAAATTATTATTAATATT
453 ---TATTAGTAATAATGAAATTATTATTAATATT
* * *
2123017 TAATGATTTGATATTAATGATTTAATAATAATTAGTAATAATGAAATTATTATTAATATTTAATG
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
2123082 A-TT--TAGTAATGATTT
66 ATTTGATAGTAATGATTT
2123097 GTTAAGGTTT
Statistics
Matches: 531, Mismatches: 25, Indels: 30
0.91 0.04 0.05
Matches are distributed among these distances:
478 130 0.24
479 1 0.00
480 2 0.00
481 5 0.01
482 1 0.00
483 1 0.00
484 2 0.00
485 1 0.00
486 12 0.02
487 7 0.01
488 72 0.14
489 95 0.18
490 184 0.35
491 18 0.03
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (483 bp):
TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
ATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTG
ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAATAATGATTTAGTA
ATAATAAGTAATAATGAAATTATAATTAATATCTAATGATTTAATAATGATTAGTAATAATGAAA
TTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATATTTTATTATTAATATCTAA
TAATTTGATATTAATGATTTAATAATGATTTGATAGTAATGATTTACGACTTGAACAATGAACAA
TGTTTGATTCAATTAACCATATTTCCGTTACATAACTAGTAATGAAATTATAATAAGATTAGTAT
TAGTAATAATGAAATTATTATTAATATT
Found at i:2122555 original size:11 final size:10
Alignment explanation
Indices: 2122539--2122626 Score: 51
Period size: 10 Copynumber: 8.7 Consensus size: 10
2122529 AATGATTTGA
2122539 TAGTAATGATT
1 TAGTAATGA-T
2122550 TAGTAATGAT
1 TAGTAATGAT
*
2122560 TAGTAAT-AA
1 TAGTAATGAT
* *
2122569 T-GAAATTAT
1 TAGTAATGAT
*
2122578 TATTAAT-AT
1 TAGTAATGAT
2122587 T--TAATGATTT
1 TAGTAATGA--T
2122597 GATAGTAATGATT
1 --TAGTAATGA-T
2122610 TAGTAATGAT
1 TAGTAATGAT
2122620 TAGTAAT
1 TAGTAAT
2122627 AATAAAATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
7 4 0.06
8 5 0.08
9 7 0.11
10 20 0.32
11 18 0.29
12 1 0.02
13 2 0.03
14 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:2122561 original size:60 final size:60
Alignment explanation
Indices: 2122493--2122780 Score: 446
Period size: 60 Copynumber: 5.1 Consensus size: 60
2122483 GAAATTATAA
2122493 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG
2122553 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG
*
2122613 TAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGA-TTAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG
*
2122672 ---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATAATAATGATTTAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG
2122721 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGA-TT--TAGTAATGA-TTAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG
2122777 TAAT
1 TAAT
2122781 AATGAAATTA
Statistics
Matches: 213, Mismatches: 3, Indels: 28
0.87 0.01 0.11
Matches are distributed among these distances:
48 33 0.15
49 4 0.02
52 8 0.04
53 2 0.01
55 2 0.01
56 16 0.08
57 8 0.04
59 6 0.03
60 134 0.63
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (60 bp):
TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG
Found at i:2122665 original size:21 final size:21
Alignment explanation
Indices: 2122496--2122876 Score: 90
Period size: 21 Copynumber: 17.9 Consensus size: 21
2122486 ATTATAATAA
* *
2122496 TGATTAGTAATAATGAA-A-T
1 TGATTAGTAATATTTAATATT
*
2122515 T-ATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAAT-ATT
* *
2122536 TGA-TAGTAATGATTTAGTA-A
1 TGATTAGTAAT-ATTTAATATT
* *
2122556 TGATTAGTAATAATGAA-A-T
1 TGATTAGTAATATTTAATATT
*
2122575 T-ATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAAT-ATT
* *
2122596 TGA-TAGTAATGATTTAGTA-A
1 TGATTAGTAAT-ATTTAATATT
* *
2122616 TGATTAGTAATA-ATAA-AAT
1 TGATTAGTAATATTTAATATT
*
2122635 T-ATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAAT-ATT
2122656 TGA-TAGTAATGATTAGTAATAATAAT
1 TGATTAGTAAT-ATT--TAAT-AT--T
* *
2122682 TTATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAAT-ATT
* * *
2122704 TGA-TAATAATGATTTAGTA-A
1 TGATTAGTAAT-ATTTAATATT
* *
2122724 TGATTAGTAATAATGAA-A-T
1 TGATTAGTAATATTTAATATT
*
2122743 T-ATTATTAATATTTAATGATTTAGT
1 TGATTAGTAATATTTAAT-A--T--T
* *
2122768 AATGATTAGTAATAATGAA-A-T
1 --TGATTAGTAATATTTAATATT
*
2122789 T-ATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAAT-ATT
2122810 TGA-TAGTAATGATTAGTAATAATATT
1 TGATTAGTAAT-A-T--T--TAATATT
* *
2122836 TTATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAAT-ATT
*
2122858 TGA-TATTAATGATTTAATA
1 TGATTAGTAAT-ATTTAATA
2122877 ATGATTTGAT
Statistics
Matches: 265, Mismatches: 49, Indels: 94
0.65 0.12 0.23
Matches are distributed among these distances:
18 58 0.22
19 12 0.05
20 20 0.08
21 75 0.28
22 41 0.15
23 2 0.01
24 12 0.05
25 3 0.01
26 13 0.05
27 17 0.06
28 12 0.05
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.46
Consensus pattern (21 bp):
TGATTAGTAATATTTAATATT
Found at i:2122732 original size:10 final size:10
Alignment explanation
Indices: 2122710--2122780 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
2122700 GATTTGATAA
2122710 TAATGATTTAG
1 TAATGA-TTAG
2122721 TAATGATTAG
1 TAATGATTAG
*
2122731 TAAT-AAT-G
1 TAATGATTAG
* * *
2122739 AAATTATTAT
1 TAATGATTAG
2122749 TAAT-ATT--
1 TAATGATTAG
2122756 TAATGATTTAG
1 TAATGA-TTAG
2122767 TAATGATTAG
1 TAATGATTAG
2122777 TAAT
1 TAAT
2122781 AATGAAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
7 4 0.08
8 5 0.10
9 9 0.18
10 19 0.39
11 12 0.24
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (10 bp):
TAATGATTAG
Found at i:2122760 original size:154 final size:154
Alignment explanation
Indices: 2122602--2123095 Score: 561
Period size: 154 Copynumber: 3.1 Consensus size: 154
2122592 GATTTGATAG
2122602 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATG
* *
2122667 ATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAATAATGATTTAGTAATGATTAGT
66 ATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAATAATGATTAGT
2122732 AATAATGAAATTATTATTAATATT
131 AATAATGAAATTATTATTAATATT
*
2122756 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATG
* *
2122821 ATTAGTAATAATATTTTATTATTAATATTTAATGATTTGATATTAATGATTTAATAATGATTTGA
66 ATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAATAATGATTAG-
* * * * *
2122886 TAGTAATG-ATTTATGACTTGAACAATGAA
130 TAATAATGAAATTATTA-TT-AA-TAT--T
* * * * * * * * *
2122915 CAATGTTTTATTCAATTAACCATATTTCCGTTACATAACTAGTAATGA-AATT-ATA-ATAATGA
1 TAATGATTTAGT-AA-T-----GA-TT-AG-TA-ATAA-TA-AAATTATTATTAATATTTAATGA
* *
2122977 -TT--TAGTAATTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
53 TTTGATAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATT
*
2123039 TAATAATAATTAGTAATAATGAAATTATTATTAATATT
117 TAATAATGATTAGTAATAATGAAATTATTATTAATATT
2123077 TAATGATTTAGTAATGATT
1 TAATGATTTAGTAATGATT
2123096 TGTTAAGGTT
Statistics
Matches: 285, Mismatches: 34, Indels: 42
0.79 0.09 0.12
Matches are distributed among these distances:
154 132 0.46
155 10 0.04
156 2 0.01
157 2 0.01
159 9 0.03
160 3 0.01
161 3 0.01
162 9 0.03
164 2 0.01
165 2 0.01
166 29 0.10
167 56 0.20
168 3 0.01
169 8 0.03
170 7 0.02
171 4 0.01
172 4 0.01
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (154 bp):
TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATG
ATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAATAATGATTAGT
AATAATGAAATTATTATTAATATT
Found at i:2122866 original size:14 final size:14
Alignment explanation
Indices: 2122849--2122897 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
2122839 TTATTAATAT
2122849 TTAATGATTTGATA
1 TTAATGATTTGATA
2122863 TTAATGATTT-A-A
1 TTAATGATTTGATA
2122875 -TAATGATTTGATA
1 TTAATGATTTGATA
*
2122888 GTAATGATTT
1 TTAATGATTT
2122898 ATGACTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.28
12 2 0.06
13 2 0.06
14 19 0.59
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (14 bp):
TTAATGATTTGATA
Found at i:2123008 original size:21 final size:21
Alignment explanation
Indices: 2122984--2123071 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
2122974 TGATTTAGTA
2122984 ATTATTAGTAATAATGAAATT
1 ATTATTAGTAATAATGAAATT
* *
2123005 ATTATTAATATTTAATG--ATT
1 ATTATTAGTA-ATAATGAAATT
* * * ** *
2123025 -TGA-TATTAATGATTTAATA
1 ATTATTAGTAATAATGAAATT
*
2123044 ATAATTAGTAATAATGAAATT
1 ATTATTAGTAATAATGAAATT
2123065 ATTATTA
1 ATTATTA
2123072 ATATTTAATG
Statistics
Matches: 47, Mismatches: 15, Indels: 10
0.65 0.21 0.14
Matches are distributed among these distances:
17 3 0.06
18 4 0.09
19 4 0.09
20 5 0.11
21 26 0.55
22 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (21 bp):
ATTATTAGTAATAATGAAATT
Found at i:2123035 original size:60 final size:60
Alignment explanation
Indices: 2122971--2123085 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 60
2122961 GAAATTATAA
* *
2122971 TAATGATTTAGTAATTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAATAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
2123031 TAATGATTTAATAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTT
1 TAATGATTTAATAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTT
2123086 AGTAATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (60 bp):
TAATGATTTAATAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
Found at i:2124000 original size:23 final size:23
Alignment explanation
Indices: 2123974--2124018 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2123964 AAAATTACGA
*
2123974 AAATAATAAAATTTATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
2123997 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
2124019 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:2125329 original size:22 final size:22
Alignment explanation
Indices: 2125304--2125352 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2125294 ACAACTAATA
* *
2125304 AACTATTTTTTAATATAACTTT
1 AACTATTCTTTAATATAACGTT
2125326 AACTATTCTTTAATATAACGTT
1 AACTATTCTTTAATATAACGTT
2125348 AACTA
1 AACTA
2125353 ATAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (22 bp):
AACTATTCTTTAATATAACGTT
Found at i:2125369 original size:29 final size:29
Alignment explanation
Indices: 2125326--2125420 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 29
2125316 ATATAACTTT
2125326 AACTATTCTTTAATATAACGTT-AACTAATA
1 AACTATT-TTTAATATAAC-TTAAACTAATA
2125356 AACTATTTTTAATATAACTTAAACTAATA
1 AACTATTTTTAATATAACTTAAACTAATA
* * *
2125385 AA-TGATTTTTAATTATAATTTATTACTAAAA
1 AACT-ATTTTTAA-TATAACTTA-AACTAATA
2125416 AACTA
1 AACTA
2125421 ATTAACTAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
28 3 0.05
29 29 0.51
30 15 0.26
31 9 0.16
32 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.42
Consensus pattern (29 bp):
AACTATTTTTAATATAACTTAAACTAATA
Found at i:2125700 original size:29 final size:29
Alignment explanation
Indices: 2125667--2125760 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 29
2125657 TGTTTTACCC
2125667 TAATTTATAATAATAAACTAATTAACTAA
1 TAATTTATAATAATAAACTAATTAACTAA
* * *
2125696 TAATTTATAACAATTAACTAATTTAAATAA
1 TAATTTATAATAATAAACTAA-TTAACTAA
* *
2125726 TTATTCTTTTATATAACTTAAACTAATTAACTAA
1 -TAAT-TTATA-ATAA--TAAACTAATTAACTAA
2125760 T
1 T
2125761 TTTTTTATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
29 19 0.37
30 7 0.14
31 3 0.06
32 4 0.08
33 4 0.08
34 7 0.14
35 7 0.14
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (29 bp):
TAATTTATAATAATAAACTAATTAACTAA
Found at i:2125761 original size:34 final size:31
Alignment explanation
Indices: 2125670--2125778 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
2125660 TTTACCCTAA
*
2125670 TTTATAATAA-TAAACTAATTAACTAATAATT
1 TTTAT-ATAATTAAACTAATTAACTAATATTT
* * *
2125701 TATA-ACAATT-AACTAATTTAAATAATTATTCT
1 TTTATATAATTAAACTAA-TTAACTAA-TATT-T
2125733 TTTATATAACTTAAACTAATTAACTAAT-TTT
1 TTTATATAA-TTAAACTAATTAACTAATATTT
2125764 TTTATATAATATAAA
1 TTTATATAAT-TAAA
2125779 TTCAACAACC
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
29 9 0.14
30 9 0.14
31 20 0.32
32 6 0.10
33 4 0.06
34 9 0.14
35 6 0.10
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTATATAATTAAACTAATTAACTAATATTT
Found at i:2126129 original size:11 final size:11
Alignment explanation
Indices: 2126113--2126148 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2126103 CTGAAGGACT
2126113 GCAATAATGCA
1 GCAATAATGCA
*
2126124 GCAATAAGTGCT
1 GCAATAA-TGCA
2126136 GCAATAATGCA
1 GCAATAATGCA
2126147 GC
1 GC
2126149 TGAATTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:2128738 original size:2 final size:2
Alignment explanation
Indices: 2128731--2128758 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2128721 GATTCCTTCC
2128731 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
2128759 TCCATAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2129007 original size:37 final size:37
Alignment explanation
Indices: 2128959--2129029 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
2128949 GATCAAACTG
* *
2128959 AGGGATCGATACACAGGTTAAGTTATTAAGCTGAGGT
1 AGGGATCGATACACAGGTCAAGATATTAAGCTGAGGT
* *
2128996 AGGGATTGATACACTGGTCAAGATATTAAGCTGA
1 AGGGATCGATACACAGGTCAAGATATTAAGCTGA
2129030 TGGAACAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (37 bp):
AGGGATCGATACACAGGTCAAGATATTAAGCTGAGGT
Found at i:2129782 original size:20 final size:20
Alignment explanation
Indices: 2129745--2129784 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2129735 TTCCCCTTCA
*
2129745 TTTTCTTCTCTTTCTTCCTC
1 TTTTCTTCTCATTCTTCCTC
2129765 TTTTCTTCTCCATT-TTCCTC
1 TTTTCTTCT-CATTCTTCCTC
2129785 CCTTTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTCTTCTCATTCTTCCTC
Found at i:2129792 original size:22 final size:22
Alignment explanation
Indices: 2129755--2129800 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2129745 TTTTCTTCTC
*
2129755 TTTCTTCCTCTTTTCTTCTCCAT
1 TTTCCTCCTCTTTTC-TCTCCAT
*
2129778 TTTCCTCC-CTTTTCTCTTCAT
1 TTTCCTCCTCTTTTCTCTCCAT
2129799 TT
1 TT
2129801 ATTTCCTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTCCTCCTCTTTTCTCTCCAT
Found at i:2131347 original size:183 final size:182
Alignment explanation
Indices: 2131040--2131399 Score: 641
Period size: 183 Copynumber: 2.0 Consensus size: 182
2131030 TATAATTAAA
*
2131040 ATAAAAAATTAAATTTGAGAGTTGAGTGATTAAATTAGGAGTAATTTGAAAGTTAAATAATTAAA
1 ATAAAAAATTAAATTTGAGAGTTGAGTAATTAAATTAGGAGTAATTTGAAAGTTAAATAATTAAA
*
2131105 TCAAAATAATTAAAATTTCAGTGACCAAAACAATAATGATAAGATAGTCGAGTGATTAATGATTG
66 TCAAAATAATTAAAATTTCAGTGACCAAAACAAGAATGATAAGATAGTCGAGTGATTAATGATTG
2131170 AATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTACCCCC
131 AATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTACCCCC
* *
2131222 ATAAAAAATTAAATTTGAGTGTTAGAGTAATTAAATTATGAGTAATTTGAAAGTTAAATAATTAA
1 ATAAAAAATTAAATTTGAGAGTT-GAGTAATTAAATTAGGAGTAATTTGAAAGTTAAATAATTAA
*
2131287 ATCAAAATAATTAAAACTTT-AGTGACCAAAACAAGAATGATAAGATAGTTGAGTGATTAATGAT
65 ATCAAAATAATTAAAA-TTTCAGTGACCAAAACAAGAATGATAAGATAGTCGAGTGATTAATGAT
*
2131351 TGAATTTACGCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTA
129 TGAATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTA
2131400 AAGGGGAAGT
Statistics
Matches: 170, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
182 22 0.13
183 145 0.85
184 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (182 bp):
ATAAAAAATTAAATTTGAGAGTTGAGTAATTAAATTAGGAGTAATTTGAAAGTTAAATAATTAAA
TCAAAATAATTAAAATTTCAGTGACCAAAACAAGAATGATAAGATAGTCGAGTGATTAATGATTG
AATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTACCCCC
Found at i:2131899 original size:15 final size:15
Alignment explanation
Indices: 2131879--2131912 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2131869 TATCGGCTTG
*
2131879 TCTTCTTATTTTTCT
1 TCTTCTTATTTTTAT
*
2131894 TCTTCTTCTTTTTAT
1 TCTTCTTATTTTTAT
2131909 TCTT
1 TCTT
2131913 AGGATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTCTTATTTTTAT
Found at i:2132254 original size:29 final size:29
Alignment explanation
Indices: 2132188--2132255 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
2132178 ACTCTTATTT
* *
2132188 ACTGAACTTTACTTTCTTTCATTTTACTC
1 ACTGAACTTTAATTTCTTTCAATTTACTC
* * *
2132217 ACCGTACTTTCAATTT-TTTCAATTTGCTC
1 ACTGAACTTT-AATTTCTTTCAATTTACTC
2132246 ACTGAACTTT
1 ACTGAACTTT
2132256 GTATATTGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.22, C:0.24, G:0.06, T:0.49
Consensus pattern (29 bp):
ACTGAACTTTAATTTCTTTCAATTTACTC
Found at i:2132333 original size:46 final size:46
Alignment explanation
Indices: 2132261--2132352 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
2132251 ACTTTGTATA
* *
2132261 TTGAATTTTTTTAATCACTCAGCCGTTTTCTCAGTTATACCATGAT
1 TTGAATTTTTTTAATCACTCAACCGTTTTCTCAGTTACACCATGAT
* *
2132307 TTGAATTTTTTTAATCATTCAACCGTTTTCTCAGTTACACCGTGAT
1 TTGAATTTTTTTAATCACTCAACCGTTTTCTCAGTTACACCATGAT
2132353 GATGTGGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (46 bp):
TTGAATTTTTTTAATCACTCAACCGTTTTCTCAGTTACACCATGAT
Found at i:2132423 original size:28 final size:28
Alignment explanation
Indices: 2132391--2132446 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2132381 GACACACAGG
*
2132391 ATTTACATTTAAAATAAAAGCTTCTTTT
1 ATTTACATTTAAAATAAAAGCTGCTTTT
*
2132419 ATTTACATTTAAAATAAATGCTGCTTTT
1 ATTTACATTTAAAATAAAAGCTGCTTTT
2132447 GCTTTACTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (28 bp):
ATTTACATTTAAAATAAAAGCTGCTTTT
Found at i:2135466 original size:163 final size:163
Alignment explanation
Indices: 2135196--2135522 Score: 627
Period size: 163 Copynumber: 2.0 Consensus size: 163
2135186 ATGGAGATAG
2135196 GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCGTTCGCGGTAGGAGAACT
1 GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCGTTCGCGGTAGGAGAACT
2135261 CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAATTTGAGTTGTGGAAAC
66 CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAATTTGAGTTGTGGAAAC
2135326 AATCCTTTTAGTCTAACAACATCTCATGTAGTT
131 AATCCTTTTAGTCTAACAACATCTCATGTAGTT
* *
2135359 GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCTTTTGCGGTAGGAGAACT
1 GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCGTTCGCGGTAGGAGAACT
*
2135424 CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAGTTTGAGTTGTGGAAAC
66 CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAATTTGAGTTGTGGAAAC
2135489 AATCCTTTTAGTCTAACAACATCTCATGTAGTT
131 AATCCTTTTAGTCTAACAACATCTCATGTAGTT
2135522 G
1 G
2135523 CTTCAAGTCA
Statistics
Matches: 161, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 161 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (163 bp):
GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCGTTCGCGGTAGGAGAACT
CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAATTTGAGTTGTGGAAAC
AATCCTTTTAGTCTAACAACATCTCATGTAGTT
Found at i:2141007 original size:22 final size:22
Alignment explanation
Indices: 2140959--2141012 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
2140949 TTCAGCTGTT
* *
2140959 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
2140981 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
2141003 ATAACTCCTG
1 ATAACTCCTG
2141013 TAACTCCCGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:2141331 original size:20 final size:20
Alignment explanation
Indices: 2141303--2141350 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2141293 ACCACGACCA
* *
2141303 CGAGTCGAGTCAAGCCGAAC
1 CGAGCCGAGCCAAGCCGAAC
* **
2141323 CGAGCCGAGCCATGCCGTGC
1 CGAGCCGAGCCAAGCCGAAC
2141343 CGAGCCGA
1 CGAGCCGA
2141351 ACCGAGACGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.35, G:0.33, T:0.08
Consensus pattern (20 bp):
CGAGCCGAGCCAAGCCGAAC
Found at i:2141333 original size:15 final size:15
Alignment explanation
Indices: 2141315--2141356 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2141305 AGTCGAGTCA
2141315 AGCCGAACCGAGCCG
1 AGCCGAACCGAGCCG
* *
2141330 AGCC-ATGCCGTGCCG
1 AGCCGA-ACCGAGCCG
2141345 AGCCGAACCGAG
1 AGCCGAACCGAG
2141357 ACGGACGGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.24, C:0.38, G:0.33, T:0.05
Consensus pattern (15 bp):
AGCCGAACCGAGCCG
Found at i:2146124 original size:22 final size:22
Alignment explanation
Indices: 2146076--2146129 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
2146066 TTCAGGTGTT
* *
2146076 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
2146098 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
2146120 ATAACTCCTG
1 ATAACTCCTG
2146130 TAACTCCCAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:2147312 original size:11 final size:11
Alignment explanation
Indices: 2147286--2147338 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
2147276 AAAACACGTT
2147286 TATA-ATAATA
1 TATATATAATA
* *
2147296 TTTATACAATA
1 TATATATAATA
2147307 TATATATAATA
1 TATATATAATA
2147318 TATATATAA-A
1 TATATATAATA
2147328 TATATA-AATA
1 TATATATAATA
2147338 T
1 T
2147339 GTAAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 2 0.05
10 12 0.32
11 23 0.62
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
TATATATAATA
Found at i:2147332 original size:8 final size:8
Alignment explanation
Indices: 2147298--2147348 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
2147288 TAATAATATT
2147298 TATACAATA
1 TATA-AATA
*
2147307 TATATATA
1 TATAAATA
*
2147315 -ATATATA
1 TATAAATA
2147322 TATAAATA
1 TATAAATA
2147330 TATAAATA
1 TATAAATA
*
2147338 TGTAAATA
1 TATAAATA
2147346 TAT
1 TAT
2147349 GTTCATTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
7 7 0.19
8 26 0.70
9 4 0.11
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (8 bp):
TATAAATA
Found at i:2148050 original size:106 final size:101
Alignment explanation
Indices: 2147860--2148218 Score: 379
Period size: 106 Copynumber: 3.5 Consensus size: 101
2147850 ACTGCTCCAA
* * * * *
2147860 GTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGTTCTGGAACTGGAAAATTGTTTGTTGACAGT
1 GTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGATATGAAATTGG-GAA-T-TTT-TTGACAGT
2147924 CAGCCACCCCTTCGCTGTAAAGTTGAGCTTGTGCTGTCTTGG
61 CAGCCACCCCTTCGC-GTAAAGTTGAGCTTGTGCTGTCTTGG
*
2147966 GTCCAATATTCTTCGCTGTGAAGTTGAAATTGGATATGAAATTGGGGAATTATTTACTGACAGTC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATATGAAATT-GGGAATT-TTT--TGACAGTC
* * *
2148031 AGCCGCCCCTTCGCAGTAAAGTTGAGATTGTGCTGTCTTGA
62 AGCCACCCCTTCGC-GTAAAGTTGAGCTTGTGCTGTCTTGG
* * * * *
2148072 GTCCAATATCATTCGTTGTGAAGTTGAAATT-GACTCTGAAAGTT--G--TTTGTTGACAATCAG
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGA-TATGAAA-TTGGGAATTTTTTGACAGTCAG
* * *
2148132 CCACCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGG
64 CCACCCCTTC-GCGTAAAGTTGAGCTTGTGCTGTCTTGG
* *
2148171 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTATGAAATTAGGAA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATATGAAATTGGGAA
2148219 GCCCCTTCGT
Statistics
Matches: 214, Mismatches: 26, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
98 2 0.01
99 75 0.35
100 3 0.01
101 2 0.01
102 2 0.01
104 3 0.01
105 5 0.02
106 117 0.55
107 5 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (101 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATATGAAATTGGGAATTTTTTGACAGTCAGCC
ACCCCTTCGCGTAAAGTTGAGCTTGTGCTGTCTTGG
Found at i:2148175 original size:99 final size:96
Alignment explanation
Indices: 2148023--2148213 Score: 231
Period size: 99 Copynumber: 1.9 Consensus size: 96
2148013 AATTATTTAC
* * * *
2148023 TGACAGTCAGCCGCCCCTTCGCAGTAAAGTTGAGATTGTGCTGTCTTGAGTCCAATATCATTCGT
1 TGACAGTCAGCCACCCCTTCGCAGTAAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATC-TTCGC
*
2148088 TGTGAAGTTGAAATTGACTCTGAAAGTTGTTTGT
65 TGTGAAGTTGAAATTGA-TATGAAA-TTGTTTGT
* * * *
2148122 TGACAATCAGCCACCCCTTCATC-GTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCG
1 TGACAGTCAGCCACCCCTTC-GCAGTAAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT-CTTCG
*
2148186 CTGTGAAGTTGAAATTGGTTATGAAATT
64 CTGTGAAGTTGAAATT-GATATGAAATT
2148214 AGGAAGCCCC
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
98 2 0.03
99 74 0.94
100 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (96 bp):
TGACAGTCAGCCACCCCTTCGCAGTAAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCTTCGCT
GTGAAGTTGAAATTGATATGAAATTGTTTGT
Found at i:2149380 original size:16 final size:16
Alignment explanation
Indices: 2149361--2149397 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2149351 ACCCTAAAAG
2149361 TTTTTCTTTTTCTTGT
1 TTTTTCTTTTTCTTGT
2149377 TTTTTCTTTTTCTTGT
1 TTTTTCTTTTTCTTGT
2149393 TTTTT
1 TTTTT
2149398 TTCCGACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTTCTTGT
Found at i:2159897 original size:13 final size:12
Alignment explanation
Indices: 2159879--2159919 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
2159869 ACAACTAATG
2159879 AATAAATAAATA
1 AATAAATAAATA
2159891 CAATAAATAAATA
1 -AATAAATAAATA
2159904 AATAAAATAAAATA
1 AAT-AAAT-AAATA
2159918 AA
1 AA
2159920 ATGATCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.12
13 16 0.62
14 7 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (12 bp):
AATAAATAAATA
Found at i:2159901 original size:17 final size:18
Alignment explanation
Indices: 2159879--2159919 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
2159869 ACAACTAATG
*
2159879 AATAAATAAATACAAT-A
1 AATAAATAAATAAAATAA
2159896 AATAAATAAATAAAATAA
1 AATAAATAAATAAAATAA
2159914 AATAAA
1 AATAAA
2159920 ATGATCATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (18 bp):
AATAAATAAATAAAATAA
Found at i:2159921 original size:5 final size:4
Alignment explanation
Indices: 2159879--2159919 Score: 55
Period size: 4 Copynumber: 9.5 Consensus size: 4
2159869 ACAACTAATG
2159879 AATA AATA AATA CAATA AATA AATA AATAA AATAA AATA AA
1 AATA AATA AATA -AATA AATA AATA AAT-A AAT-A AATA AA
2159920 ATGATCATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 22 0.63
5 13 0.37
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:2161789 original size:30 final size:29
Alignment explanation
Indices: 2161748--2161835 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 29
2161738 AATCTCATGC
*
2161748 AGATGTCAGAATGGAGAATTTATCCTATGT
1 AGATGTTAGAATGG-GAATTTATCCTATGT
* *
2161778 AGATGTTAGAATGGGGAGTTTATCCAATGT
1 AGATGTTAGAAT-GGGAATTTATCCTATGT
2161808 AGATGTTAGAAATGGGAA-TTAGTCCTAT
1 AGATGTTAG-AATGGGAATTTA-TCCTAT
2161836 ACAAAATCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.06
30 42 0.84
31 5 0.10
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (29 bp):
AGATGTTAGAATGGGAATTTATCCTATGT
Found at i:2164405 original size:23 final size:23
Alignment explanation
Indices: 2164379--2164423 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2164369 CCCTCTAGAT
*
2164379 TACACCAGGTAATATTAAAACGA
1 TACACCAGGTAATATCAAAACGA
*
2164402 TACATCAGGTAATATCAAAACG
1 TACACCAGGTAATATCAAAACG
2164424 TAAAAAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (23 bp):
TACACCAGGTAATATCAAAACGA
Found at i:2164692 original size:30 final size:30
Alignment explanation
Indices: 2164658--2164734 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
2164648 ATATAATCTC
*
2164658 ATGCAGATGTCAAAAC-GGGAAATTTATCCT
1 ATGCAGATGTCAAAACAGAG-AATTTATCCT
* * * *
2164688 ATGCAGATGCCAGAACATAGAGTTTATCCT
1 ATGCAGATGTCAAAACAGAGAATTTATCCT
*
2164718 ATGCAGATGTCAGAACA
1 ATGCAGATGTCAAAACA
2164735 TGGATGAGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 39 0.98
31 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (30 bp):
ATGCAGATGTCAAAACAGAGAATTTATCCT
Found at i:2166970 original size:2 final size:2
Alignment explanation
Indices: 2166963--2166988 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2166953 ATTTTATCTC
2166963 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
2166989 CATTAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2168052 original size:14 final size:13
Alignment explanation
Indices: 2168035--2168068 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2168025 TTCTATCATC
2168035 TTAAATCTTAAGCT
1 TTAAATCTTAA-CT
2168049 TTAAATCTTAACT
1 TTAAATCTTAACT
*
2168062 TAAAATC
1 TTAAATC
2168069 CTAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (13 bp):
TTAAATCTTAACT
Found at i:2168094 original size:21 final size:21
Alignment explanation
Indices: 2168068--2168107 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2168058 AACTTAAAAT
* *
2168068 CCTAAATTTTAAACCCTAACA
1 CCTAAACTTTAAACACTAACA
2168089 CCTAAACTTTAAACACTAA
1 CCTAAACTTTAAACACTAA
2168108 TTTAAAATCC
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:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (21 bp):
CCTAAACTTTAAACACTAACA
Found at i:2169809 original size:20 final size:20
Alignment explanation
Indices: 2169761--2169813 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2169751 TAATACAAAA
* *
2169761 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
2169781 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
2169801 TCGCAACGCGATT
1 TCGCAACGCGATT
2169814 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:2170495 original size:20 final size:19
Alignment explanation
Indices: 2170387--2170518 Score: 139
Period size: 19 Copynumber: 7.1 Consensus size: 19
2170377 GAAAACAAAA
*
2170387 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2170406 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2170425 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2170444 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
**
2170460 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
2170477 TCCGCGTTACGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2170497 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2170517 TC
1 TC
2170519 AACCAAAAGA
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
19 48 0.51
20 28 0.29
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2172686 original size:42 final size:42
Alignment explanation
Indices: 2172640--2172812 Score: 172
Period size: 42 Copynumber: 4.1 Consensus size: 42
2172630 CCTATCGTTG
*
2172640 AAGAGGCCCCTATCATTCCTCGAGAGTCCCATCCCACCATTC
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCATCCCACCATTC
* * * * * * *
2172682 AAGAGGCCACTGTCATCCCTCAAGAGT-CCACTCCTATCGTTG
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCA-TCCCACCATTC
* * *
2172724 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCATCCCACCATTC
* * *
2172766 AAGAGGCCACTGTCA-TCGTTGAAGAGGTCCC-TCCCACCATTC
1 AAGAGGCCACTATCATTCCTCG-AGA-GTCCCATCCCACCATTC
2172808 AAGAG
1 AAGAG
2172813 CCCGATTCAC
Statistics
Matches: 106, Mismatches: 21, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
41 7 0.07
42 92 0.87
43 7 0.07
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.21
Consensus pattern (42 bp):
AAGAGGCCACTATCATTCCTCGAGAGTCCCATCCCACCATTC
Found at i:2172770 original size:21 final size:21
Alignment explanation
Indices: 2172746--2172812 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2172736 TCATTCCTCG
2172746 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2172767 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2172788 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2172809 AGAG
1 AGAG
2172813 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2172791 original size:84 final size:84
Alignment explanation
Indices: 2172607--2172782 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
2172597 CCCGACTCGC
2172607 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCAT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCAT
2172672 CCCACCATTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
*
2172691 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCAT
*
2172756 CCCACCGTTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
2172775 CTGTCATC
1 CTGTCATC
2172783 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCAT
CCCACCATTCAAGAGGCCA
Found at i:2172812 original size:84 final size:84
Alignment explanation
Indices: 2172607--2172812 Score: 279
Period size: 84 Copynumber: 2.5 Consensus size: 84
2172597 CCCGACTCGC
* * * *
2172607 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCAT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCAT
2172672 CCCACCATTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
* * * * *
2172691 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCAT
*
2172756 CCCACCGTTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
** *
2172775 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
2172813 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCAT
CCCACCATTCAAGAGGCCA
Found at i:2174182 original size:14 final size:14
Alignment explanation
Indices: 2174163--2174198 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2174153 ATTGTTTAAT
2174163 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2174177 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2174191 TGATTTGT
1 TGATTTGT
2174199 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2174344 original size:14 final size:14
Alignment explanation
Indices: 2174325--2174414 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
2174315 ACGAAATGAA
2174325 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2174339 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2174358 AATCGCAACGACAG
1 AATCGCAACGAGAG
*
2174372 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2174391 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2174405 AATCGCAACG
1 AATCGCAACG
2174415 CGAAATTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 19 0.32
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2174353 original size:33 final size:33
Alignment explanation
Indices: 2174307--2174429 Score: 201
Period size: 33 Copynumber: 3.7 Consensus size: 33
2174297 AAAAAGTACT
**
2174307 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
2174340 ATCGCAACGCGAAATGAAAATCGCAACGACAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2174373 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
2174406 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
2174430 GTTGCGATTT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 84 1.00
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2174399 original size:19 final size:19
Alignment explanation
Indices: 2174316--2174400 Score: 82
Period size: 19 Copynumber: 5.0 Consensus size: 19
2174306 TATCGCAATA
2174316 CGAAATGAAAATCGCAA--
1 CGAAATGAAAATCGCAACG
*
2174333 CG--A-GAGAATCGCAACG
1 CGAAATGAAAATCGCAACG
2174349 CGAAATGAAAATCGCAA--
1 CGAAATGAAAATCGCAACG
*
2174366 CGACA-G--AATCGCAACG
1 CGAAATGAAAATCGCAACG
2174382 CGAAATGAAAATCGCAACG
1 CGAAATGAAAATCGCAACG
2174401 AGAGAATCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
14 18 0.33
15 1 0.02
16 7 0.13
17 7 0.13
18 1 0.02
19 20 0.37
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (19 bp):
CGAAATGAAAATCGCAACG
Found at i:2174447 original size:19 final size:19
Alignment explanation
Indices: 2174425--2174575 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
2174415 CGAAATTAAA
2174425 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2174444 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2174459 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
2174477 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
2174491 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2174510 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2174525 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
2174543 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2174562 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2174576 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2174471 original size:33 final size:32
Alignment explanation
Indices: 2174429--2174555 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
2174419 ATTAAATTCG
2174429 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
2174462 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2174495 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
2174528 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2174556 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2174507 original size:66 final size:66
Alignment explanation
Indices: 2174422--2174554 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2174412 ACGCGAAATT
*
2174422 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2174487 G
66 G
*
2174488 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2174553 G
66 G
2174554 A
1 A
2174555 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Done.