Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 68 of 433
Found at i:19572752 original size:29 final size:30
Alignment explanation
Indices: 19572705--19572772 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
19572695 TGGCCCAAGA
* *
19572705 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
19572735 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
19572765 GTAAATAT
1 GTAAATAT
19572773 TTTAAGGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.29
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:19575253 original size:46 final size:46
Alignment explanation
Indices: 19575196--19575423 Score: 359
Period size: 46 Copynumber: 5.0 Consensus size: 46
19575186 AGTGTGCTCT
* *
19575196 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
19575242 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
19575288 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
19575334 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
19575380 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
19575424 TCATGTCAAA
Statistics
Matches: 171, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
45 1 0.01
46 170 0.99
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:19585174 original size:28 final size:28
Alignment explanation
Indices: 19585142--19585206 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
19585132 ATTTACTAGA
*
19585142 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* * *
19585170 ATACCCTTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
19585198 ATACCCCTA
1 ATACCCCTA
19585207 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:19587074 original size:40 final size:40
Alignment explanation
Indices: 19587015--19587121 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 40
19587005 CAATTGAATG
* * * *
19587015 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTAACT
* * * *
19587055 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTAACT
*
19587095 ACATCCGGGCTAAGA-CCGAAGGCATTT
1 ATATCCGGGCTAAGACCCGAAGGCATTT
19587122 GTGCAAATTG
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
39 11 0.20
40 45 0.80
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTAACT
Found at i:19589104 original size:19 final size:19
Alignment explanation
Indices: 19589080--19589118 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19589070 TTTTAATTAT
* *
19589080 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
19589099 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
19589118 T
1 T
19589119 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:19591740 original size:42 final size:42
Alignment explanation
Indices: 19591678--19591770 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
19591668 TTCAATCTTA
* * * *
19591678 ATGGGATTCCGTTCAGCTCTTTTGAGC-TTCTATTTAACCCTT
1 ATGGGTTTCCGTTCAACTCTTATGAGCTTTC-ATTCAACCCTT
* *
19591720 ATGGGTTTCCGTTCAACTCTTATGAGCTTTCGTTCAATCCTT
1 ATGGGTTTCCGTTCAACTCTTATGAGCTTTCATTCAACCCTT
19591762 ATGGGTTTC
1 ATGGGTTTC
19591771 TGTTTAGCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
42 41 0.93
43 3 0.07
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (42 bp):
ATGGGTTTCCGTTCAACTCTTATGAGCTTTCATTCAACCCTT
Found at i:19591743 original size:21 final size:21
Alignment explanation
Indices: 19591661--19591770 Score: 82
Period size: 21 Copynumber: 5.2 Consensus size: 21
19591651 ACTCATAAGA
19591661 GTTTCCGTTCAA-TCTTAATGG
1 GTTTCCGTTCAACTCTT-ATGG
* * * *
19591682 GATTCCGTTCAGCTCTTTTGA
1 GTTTCCGTTCAACTCTTATGG
* ** * *
19591703 GCTTCTATTTAACCCTTATGG
1 GTTTCCGTTCAACTCTTATGG
19591724 GTTTCCGTTCAACTCTTATGAG
1 GTTTCCGTTCAACTCTTATG-G
*
19591746 CTTT-CGTTCAA-TCCTTATGG
1 GTTTCCGTTCAACT-CTTATGG
19591766 GTTTC
1 GTTTC
19591771 TGTTTAGCAC
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
20 5 0.08
21 53 0.80
22 8 0.12
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (21 bp):
GTTTCCGTTCAACTCTTATGG
Found at i:19591783 original size:21 final size:21
Alignment explanation
Indices: 19591759--19591811 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
19591749 TCGTTCAATC
*
19591759 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGCTTCTGTTTAGCA
*
19591780 CTTATGTGCTTCTGTTTAGC-
1 CTTATGGGCTTCTGTTTAGCA
*
19591800 CTT-CGGGCTTCT
1 CTTATGGGCTTCT
19591812 AAAAACGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.25
20 3 0.11
21 18 0.64
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (21 bp):
CTTATGGGCTTCTGTTTAGCA
Found at i:19594919 original size:18 final size:18
Alignment explanation
Indices: 19594896--19594931 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19594886 CAAACTCCAG
*
19594896 CAAACTCTAGCAAGGAAC
1 CAAACTCCAGCAAGGAAC
19594914 CAAACTCCAGCAAGGAAC
1 CAAACTCCAGCAAGGAAC
19594932 AACAAGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.17, T:0.08
Consensus pattern (18 bp):
CAAACTCCAGCAAGGAAC
Found at i:19602696 original size:18 final size:17
Alignment explanation
Indices: 19602654--19602701 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
19602644 TTTTTTACTG
* *
19602654 TATATTATTATAATTTTT
1 TATATT-TTAAAATTTTA
19602672 TATATTTTAAAATTTTA
1 TATATTTTAAAATTTTA
19602689 TATAATTTTAAAA
1 TAT-ATTTTAAAA
19602702 ATTCATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTAAAATTTTA
Found at i:19612140 original size:26 final size:26
Alignment explanation
Indices: 19612104--19612187 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
19612094 CATGAAATTT
*
19612104 TTATCATGAAACATTTGCCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
19612130 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
19612156 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
19612182 TTATCA
1 TTATCA
19612188 AATTATATCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:19613357 original size:2 final size:2
Alignment explanation
Indices: 19613344--19613387 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
19613334 TACAATGTTG
19613344 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19613387 T
1 T
19613388 GTATGTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19615061 original size:27 final size:27
Alignment explanation
Indices: 19615027--19615129 Score: 118
Period size: 27 Copynumber: 3.8 Consensus size: 27
19615017 AAGGCAAACC
19615027 ATACAGAGTATACCACAAAGGCCATAT
1 ATACAGAGTATACCACAAAGGCCATAT
* * **
19615054 ATATAGAGTATGCCACAAAGGTTATAT
1 ATACAGAGTATACCACAAAGGCCATAT
**
19615081 ATACAGAGTATACCACAAAGGTGAT-T
1 ATACAGAGTATACCACAAAGGCCATAT
* *
19615107 CATTCAGAGTACACCACAAAGGC
1 -ATACAGAGTATACCACAAAGGC
19615130 TGATAGGATG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 1 0.02
27 64 0.98
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.21
Consensus pattern (27 bp):
ATACAGAGTATACCACAAAGGCCATAT
Found at i:19618533 original size:31 final size:31
Alignment explanation
Indices: 19618491--19618552 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
19618481 TGATGAATGG
*
19618491 GAAATTAATACTCAAAGTAAGCCACTTGTGA
1 GAAATTAATACTCAAAATAAGCCACTTGTGA
* *
19618522 GAAATTGATACTCAAAATAAGCTACTTGTGA
1 GAAATTAATACTCAAAATAAGCCACTTGTGA
19618553 ATTATGTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (31 bp):
GAAATTAATACTCAAAATAAGCCACTTGTGA
Found at i:19619209 original size:64 final size:65
Alignment explanation
Indices: 19619107--19619236 Score: 208
Period size: 64 Copynumber: 2.0 Consensus size: 65
19619097 GTCCGATAAA
* * *
19619107 CATTGGACTGTCATTGCACATTCCCCATAACGCTCGTTAACC-AAACCGCTTGGGTCCAAATCAT
1 CATTGGACTGTCATTGCACACTCCCCATAACGCGCGTTAACCAAAACAGCTTGGGTCCAAATCAT
* *
19619171 CATTGGGCTGTCATTGCACACTCCCCCTAACGCGCGTTAACCAAAACAGCTTGGGTCCAAATCAT
1 CATTGGACTGTCATTGCACACTCCCCATAACGCGCGTTAACCAAAACAGCTTGGGTCCAAATCAT
19619236 C
1 C
19619237 TGATAGTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
64 38 0.63
65 22 0.37
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (65 bp):
CATTGGACTGTCATTGCACACTCCCCATAACGCGCGTTAACCAAAACAGCTTGGGTCCAAATCAT
Found at i:19620721 original size:27 final size:27
Alignment explanation
Indices: 19620691--19620746 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
19620681 AACTTGTTAC
*
19620691 TGATATGTATATCTTTATCATTGATCT
1 TGATATGTACATCTTTATCATTGATCT
19620718 TGATATGTACATCTTTATCATTGATCT
1 TGATATGTACATCTTTATCATTGATCT
19620745 TG
1 TG
19620747 TAGGTTCTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (27 bp):
TGATATGTACATCTTTATCATTGATCT
Found at i:19624764 original size:6 final size:6
Alignment explanation
Indices: 19624757--19624789 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
19624747 GTCCTTAATT
*
19624757 TCAATT TCAATC TCAATC TCAATC TCAATC TCA
1 TCAATC TCAATC TCAATC TCAATC TCAATC TCA
19624790 TGCTCTTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (6 bp):
TCAATC
Found at i:19624802 original size:5 final size:5
Alignment explanation
Indices: 19624792--19624821 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
19624782 CAATCTCATG
19624792 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT
1 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT
19624822 TGTTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTCTT
Found at i:19626028 original size:29 final size:27
Alignment explanation
Indices: 19625966--19626028 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
19625956 ATTTGGGCTT
*
19625966 ATTTGATTCATTTTAATAGTAGGACTA
1 ATTTGATCCATTTTAATAGTAGGACTA
*
19625993 AATTGATCCA-TTTAATAGTAAAGGAACTA
1 ATTTGATCCATTTTAATAGT--AGG-ACTA
19626022 ATTTGAT
1 ATTTGAT
19626029 GAGGTCCCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 9 0.30
27 8 0.27
28 3 0.10
29 10 0.33
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (27 bp):
ATTTGATCCATTTTAATAGTAGGACTA
Found at i:19638728 original size:499 final size:501
Alignment explanation
Indices: 19637781--19638793 Score: 1904
Period size: 499 Copynumber: 2.0 Consensus size: 501
19637771 AACGTGTTAT
* *
19637781 AATATTTTAGTCACTGAGTTGTAAATTGCCGTTAACGGTTTAAGGGTAAGCTAACATGGCACGTT
1 AATATTATAGTCACTGAGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACATGGCACGTT
19637846 AAATCATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTTGT
66 AAATCATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTTGT
19637911 TTTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTTCTTTTTTTTCCA
131 TTTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTTCTTTTTTTTCCA
*
19637976 TTCTCCCTCTGTTTTCATCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCATT
196 TTCTCCCTCTATTTTCATCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCATT
19638041 TATTAAAACTGTTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGC
261 TATTAAAACTGTTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGC
*
19638106 TTCGTGAGGGTGTGCCTCATATTTACGAGACGGTGTCGTGATGACGTGACAAACGACGTCCCAAC
326 TTCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAAC
19638171 GAGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAG
391 GAGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAG
19638236 TTAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
456 TTAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
* *
19638282 AATATTATAGTCACTGGGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACGTGGCACGTT
1 AATATTATAGTCACTGAGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACATGGCACGTT
*
19638347 AAATTATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATA-TTTTTTTTGT
66 AAATCATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTTGT
19638411 TTTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTTC-TTTTTTTCCA
131 TTTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTTCTTTTTTTTCCA
19638475 TTCTCCCTCTATTTTCATCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCATT
196 TTCTCCCTCTATTTTCATCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCATT
*
19638540 TGTTAAAACTGTTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGC
261 TATTAAAACTGTTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGC
*
19638605 TTCGTGTGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAAC
326 TTCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAAC
* *
19638670 GAGAGGAAAACAATGTCGCGACTTGGTGATGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAG
391 GAGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAG
*
19638735 TTAAACTCTACTATTTATTCTTTAATTAAACTTTGATTATTCTAGG
456 TTAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
19638781 AATATTATAGTCA
1 AATATTATAGTCA
19638794 TATTAGGACT
Statistics
Matches: 500, Mismatches: 12, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
499 322 0.64
500 64 0.13
501 114 0.23
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (501 bp):
AATATTATAGTCACTGAGTTGTAAATTGCCATTAACGGTTTAAGGGTAAGCTAACATGGCACGTT
AAATCATCATTTCAAACAAAAATTTTAAGTTAAAGTATACAATTGATCCTCATATTTTTTTTTGT
TTTGAGTAATCTATTTTTTTCTTTTATATTCTTTTAACTTTCCTTTTTTTTTTCTTTTTTTTCCA
TTCTCCCTCTATTTTCATCCCTCCCTCTCTCTCTCTTTTAACGTAGTTTTTCTATATTTTCCATT
TATTAAAACTGTTTTATGTTTATGAAAAAAGAAAAGGCGAACGTTGAAACCAAAATAACACTTGC
TTCGTGAGGGTGTGCCTCATATTTACGAGACGGCGTCGTGATGACGTGACAAACGACGTCCCAAC
GAGAGGAAAACAATGTCGCGACGTGGTGACGTGTTCCCAAATTCAATTGGGTTTTCTTCTCCTAG
TTAAACTCTACTATTTATTCTTTAATTAAACTCTGATTATTCTAGG
Found at i:19640435 original size:3 final size:3
Alignment explanation
Indices: 19640427--19640465 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
19640417 GTGACTATTT
19640427 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19640466 GTTGTCGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19641419 original size:19 final size:19
Alignment explanation
Indices: 19641395--19641444 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
19641385 CCATTTTCCA
*
19641395 TCCCTCTCTCCCATCCCTC
1 TCCCTCTCTACCATCCCTC
19641414 TCCCTCTCCCTACCATCCCTC
1 TCCCTCT--CTACCATCCCTC
19641435 -CCCTACTCTA
1 TCCCT-CTCTA
19641445 ATTCTTTCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
20 4 0.15
21 13 0.48
ACGTcount: A:0.10, C:0.60, G:0.00, T:0.30
Consensus pattern (19 bp):
TCCCTCTCTACCATCCCTC
Found at i:19645347 original size:32 final size:32
Alignment explanation
Indices: 19645298--19645358 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
19645288 TAGCCGTGTG
* *
19645298 GGCCACATGGGCTAGGCCAAGT-TGGGCGTATA
1 GGCCACACGGGCAAGGCCAA-TCTGGGCGTATA
19645330 GGCCACACGGGCAAGGCCAATCTGGGCGT
1 GGCCACACGGGCAAGGCCAATCTGGGCGT
19645359 GTGGACCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (32 bp):
GGCCACACGGGCAAGGCCAATCTGGGCGTATA
Found at i:19647476 original size:16 final size:16
Alignment explanation
Indices: 19647451--19647482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19647441 TATCTTAATT
*
19647451 AAAATGATTAAAATAA
1 AAAATAATTAAAATAA
19647467 AAAATAATTAAAATAA
1 AAAATAATTAAAATAA
19647483 GATAAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
AAAATAATTAAAATAA
Found at i:19647479 original size:9 final size:9
Alignment explanation
Indices: 19647446--19647482 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
19647436 ATAGTTATCT
19647446 TAATTAAAA
1 TAATTAAAA
*
19647455 TGATTAAAA
1 TAATTAAAA
19647464 TAA--AAAA
1 TAATTAAAA
19647471 TAATTAAAA
1 TAATTAAAA
19647480 TAA
1 TAA
19647483 GATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 7 0.29
9 17 0.71
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (9 bp):
TAATTAAAA
Found at i:19650826 original size:15 final size:15
Alignment explanation
Indices: 19650808--19650849 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
19650798 CATAGTTTTG
19650808 TTCTGCTCTGCTCTA
1 TTCTGCTCTGCTCTA
* *
19650823 TTCTGTTCTGTTCTA
1 TTCTGCTCTGCTCTA
*
19650838 CTCTGCTCTGCT
1 TTCTGCTCTGCT
19650850 TGATTTGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.31, G:0.14, T:0.50
Consensus pattern (15 bp):
TTCTGCTCTGCTCTA
Found at i:19651787 original size:16 final size:17
Alignment explanation
Indices: 19651749--19651792 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
19651739 ATTTATCTAA
19651749 TTATATTTAATAATTTT
1 TTATATTTAATAATTTT
** *
19651766 ACATATTTAA-ATTTTT
1 TTATATTTAATAATTTT
19651782 TTATATTTAAT
1 TTATATTTAAT
19651793 TAGTAATATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTAATAATTTT
Found at i:19651793 original size:15 final size:15
Alignment explanation
Indices: 19651723--19651793 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 15
19651713 TAAAAAATTG
*
19651723 AATTTTTTTATTTTT
1 AATTTTTTTATATTT
19651738 AATTTATCTAATTATATTT
1 AATTT-T-T--TTATATTT
**
19651757 AATAATTTTACATATTT
1 AAT--TTTTTTATATTT
19651774 AAATTTTTTTATATTT
1 -AATTTTTTTATATTT
19651790 AATT
1 AATT
19651794 AGTAATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
15 9 0.20
16 11 0.25
17 7 0.16
18 3 0.07
19 11 0.25
20 1 0.02
21 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTTTTTATATTT
Found at i:19651946 original size:2 final size:2
Alignment explanation
Indices: 19651941--19651978 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
19651931 ATATAATTCC
19651941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19651979 GGAATAGTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19652318 original size:14 final size:15
Alignment explanation
Indices: 19652286--19652320 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19652276 ATTGATGTGC
*
19652286 TTTATTTTTTATATA
1 TTTATTTTTAATATA
19652301 TTTATTTTTAATAT-
1 TTTATTTTTAATATA
19652315 TTTATT
1 TTTATT
19652321 ATACCTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTTAATATA
Found at i:19658354 original size:2 final size:2
Alignment explanation
Indices: 19658317--19658343 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19658307 AGCAAAATTC
19658317 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19658344 TCAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19663234 original size:20 final size:20
Alignment explanation
Indices: 19663209--19663248 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19663199 ACACTACATC
*
19663209 TCTATTAAGAAAATATGAAA
1 TCTATTAAGAAAATACGAAA
19663229 TCTATTAAGAAAATACGAAA
1 TCTATTAAGAAAATACGAAA
19663249 GAACATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (20 bp):
TCTATTAAGAAAATACGAAA
Found at i:19665388 original size:46 final size:46
Alignment explanation
Indices: 19665321--19665497 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
19665311 TGTAACCCGC
* * *
19665321 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
* * *
19665367 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-TTCGCAT
* ***** **
19665413 ACATCTCACAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
19665459 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
19665498 CTCAACCATC
Statistics
Matches: 104, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
45 2 0.02
46 100 0.96
47 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
Found at i:19665487 original size:92 final size:92
Alignment explanation
Indices: 19665330--19665498 Score: 302
Period size: 92 Copynumber: 1.8 Consensus size: 92
19665320 CCCATAAGCG
***
19665330 AACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
19665395 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
*
19665422 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
19665487 GAGTTCGGATGC
66 GAGTTCGGATGC
19665499 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19672968 original size:93 final size:93
Alignment explanation
Indices: 19672855--19673026 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
19672845 CGCCCATAAG
* *
19672855 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19672920 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
19672948 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19673013 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
19673027 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:19673023 original size:46 final size:46
Alignment explanation
Indices: 19672848--19673023 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
19672838 TGTAACCCGC
* * *
19672848 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
19672894 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
19672944 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
19672987 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
19673024 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:19676926 original size:22 final size:22
Alignment explanation
Indices: 19676901--19676974 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
19676891 GCTAAAACGA
* *
19676901 TAAGCTCTATCCAGTTTAACAG
1 TAAGCTCTATCCAGCTGAACAG
**
19676923 TAAGCTCTATGGAGCTGAACAG
1 TAAGCTCTATCCAGCTGAACAG
* *
19676945 TAAGCTC-ATACGAGCTGAAACGG
1 TAAGCTCTAT-CCAGCTG-AACAG
19676968 TAAGCTC
1 TAAGCTC
19676975 CAATAAGCTG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.05
22 31 0.70
23 11 0.25
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
TAAGCTCTATCCAGCTGAACAG
Found at i:19677009 original size:26 final size:23
Alignment explanation
Indices: 19676934--19677010 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
19676924 AAGCTCTATG
*
19676934 GAGCTG-AACAGTAAGCTCATAC
1 GAGCTGAAACGGTAAGCTCATAC
19676956 GAGCTGAAACGGTAAGCTCCAATA-
1 GAGCTGAAACGGTAAGCT-C-ATAC
19676980 -AGCTGATATATCGGTAAGCTCATAC
1 GAGCTGA-A-A-CGGTAAGCTCATAC
19677005 GAGCTG
1 GAGCTG
19677011 TGATGAGTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
22 6 0.13
23 16 0.35
24 5 0.11
25 5 0.11
26 14 0.30
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (23 bp):
GAGCTGAAACGGTAAGCTCATAC
Found at i:19678365 original size:43 final size:43
Alignment explanation
Indices: 19678316--19678466 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 43
19678306 TATCCCATAT
* * * * *
19678316 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGAA
1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCTAGAC
* * * *
19678359 AGGGTCTTATACGTAATCGA-TTAACGATGCCAATGTCCTAGAC
1 ATGGTCTTACACGTAATC-ACATATCGATGCCAATGTCCTAGAC
* *
19678402 ATGGTCTTACACGTAATCACA-ATACAATGCCAATGTCTTAGAC
1 ATGGTCTTACACGTAATCACATAT-CGATGCCAATGTCCTAGAC
*
19678445 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACACGTAATCACAT
19678467 CTCGGTAACC
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
42 2 0.02
43 85 0.97
44 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCTAGAC
Found at i:19686536 original size:18 final size:19
Alignment explanation
Indices: 19686515--19686572 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
19686505 AAAAAATTCT
19686515 AATTTTTAATAAATTTA-A
1 AATTTTTAATAAATTTATA
*
19686533 AATTTTTAA-AATTTTATTA
1 AATTTTTAATAAATTTA-TA
*
19686552 AA-TTTTAATAATTTTTATA
1 AATTTTTAATAA-ATTTATA
19686571 AA
1 AA
19686573 ATTTAATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 6 0.17
18 15 0.43
19 9 0.26
20 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTTTTAATAAATTTATA
Found at i:19686539 original size:46 final size:47
Alignment explanation
Indices: 19686471--19686592 Score: 115
Period size: 46 Copynumber: 2.6 Consensus size: 47
19686461 ATAACCAAAA
* * *
19686471 TTTATAAAAGTTTACAATTTTTTATGATTTTTATAAAAAATT-CTAATT
1 TTTATAAAA-TTTA-AAATTTTTATAATTTTTATAAAAAATTAATAATT
* * **
19686519 TTTA-ATAAATTTAAAATTTTTA-AAATTTTATTAAATTTTAATAATT
1 TTTATA-AAATTTAAAATTTTTATAATTTTTATAAAAAATTAATAATT
* *
19686565 TTTATAAAATTTAATATTTTTATTATTT
1 TTTATAAAATTTAAAATTTTTATAATTT
19686593 ATAATTTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
45 12 0.20
46 32 0.53
47 9 0.15
48 7 0.12
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (47 bp):
TTTATAAAATTTAAAATTTTTATAATTTTTATAAAAAATTAATAATT
Found at i:19686540 original size:9 final size:9
Alignment explanation
Indices: 19686515--19686586 Score: 51
Period size: 9 Copynumber: 7.9 Consensus size: 9
19686505 AAAAAATTCT
19686515 AATTTTTAA
1 AATTTTTAA
*
19686524 TAA-ATTTAA
1 -AATTTTTAA
19686533 AATTTTTAA
1 AATTTTTAA
*
19686542 AATTTTATTA
1 AATTTT-TAA
19686552 AA-TTTTAA
1 AATTTTTAA
19686560 TAATTTTTATA
1 -AATTTTTA-A
*
19686571 AA-ATTTAA
1 AATTTTTAA
*
19686579 TATTTTTA
1 AATTTTTA
19686587 TTATTTATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
8 6 0.12
9 29 0.59
10 13 0.27
11 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTTAA
Found at i:19686556 original size:10 final size:10
Alignment explanation
Indices: 19686530--19686576 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
19686520 TTAATAAATT
19686530 TAAAATTTT-
1 TAAAATTTTA
19686539 TAAAATTTTA
1 TAAAATTTTA
*
19686549 TTAAATTTTA
1 TAAAATTTTA
*
19686559 -ATAATTTTTA
1 TA-AAATTTTA
19686569 TAAAATTT
1 TAAAATTT
19686577 AATATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 9 0.29
10 21 0.68
11 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TAAAATTTTA
Found at i:19686577 original size:19 final size:18
Alignment explanation
Indices: 19686544--19686587 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
19686534 ATTTTTAAAA
*
19686544 TTTTATTAAATTTTAATAAT
1 TTTTA-TAAAATTTAAT-AT
19686564 TTTTATAAAATTTAATAT
1 TTTTATAAAATTTAATAT
19686582 TTTTAT
1 TTTTAT
19686588 TATTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATAAAATTTAATAT
Found at i:19686827 original size:89 final size:88
Alignment explanation
Indices: 19686622--19686828 Score: 233
Period size: 89 Copynumber: 2.3 Consensus size: 88
19686612 TAATAAGAGT
* *
19686622 AGGGGCTTAATT-TTTTTTTGAAAAATTTTGAGGGTCTTTTTGATATATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTCTTTTTTTGAAAAAGTTTGAGAGTCTTTTTGATATATTTTGAAAGTTCAAGTA
* * ** *
19686686 CCCAATTGAGTGGGAAAAAAAGT
66 CACAATTGAATGAAAAAAAAAGA
* *
19686709 A-GGGCTTAATTACTTTTTTTTGAAGAAGTTTGAGAG-CTTTTT-TTATGCATTTTGAAAGTTCA
1 AGGGGCTTAATT-C-TTTTTTTGAAAAAGTTTGAGAGTCTTTTTGATAT--ATTTTGAAAGTTCA
*
19686771 AGTGCACAATTGAATGAAAAAAAAAGA
62 AGTACACAATTGAATGAAAAAAAAAGA
* *
19686798 AGGGGCTTAATTGCTTTTTTCGAATAAGTTT
1 AGGGGCTTAATT-CTTTTTTTGAAAAAGTTT
19686829 AAGGACTTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
86 10 0.10
87 4 0.04
88 6 0.06
89 70 0.69
90 11 0.11
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (88 bp):
AGGGGCTTAATTCTTTTTTTGAAAAAGTTTGAGAGTCTTTTTGATATATTTTGAAAGTTCAAGTA
CACAATTGAATGAAAAAAAAAGA
Found at i:19691167 original size:30 final size:30
Alignment explanation
Indices: 19691127--19691199 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
19691117 TATCGACACC
*
19691127 ACACGGCCGTGTGGTAGGCCATGTACAATG
1 ACACGGCCGTGTGGTAGGCCATGAACAATG
* * *
19691157 ACACGACCGTGTGGTAGGCCGTGAACGATG
1 ACACGGCCGTGTGGTAGGCCATGAACAATG
19691187 ACACGGCCGTGTG
1 ACACGGCCGTGTG
19691200 AATGACCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.36, T:0.18
Consensus pattern (30 bp):
ACACGGCCGTGTGGTAGGCCATGAACAATG
Found at i:19696033 original size:71 final size:71
Alignment explanation
Indices: 19695947--19696110 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
19695937 CGATTTGTCT
19695947 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
19696012 CTTTCA
66 CTTTCA
19696018 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
19696083 CTTTCA
66 CTTTCA
19696089 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
19696111 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:19696148 original size:71 final size:70
Alignment explanation
Indices: 19695947--19696144 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
19695937 CGATTTGTCT
* * * *
19695947 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
19696012 CTTTCA
65 CTTTCA
* * * *
19696018 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
19696083 CTTTCA
65 CTTTCA
* *
19696089 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
19696145 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:19708567 original size:22 final size:20
Alignment explanation
Indices: 19708526--19708597 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
19708516 GAGCGTTACA
**
19708526 AAAACAGCACCAAAGCAGCATC
1 AAAACAGCA-CAAAATAGCA-C
19708548 AAAACAGCATCAAAATAGCAC
1 AAAACAGCA-CAAAATAGCAC
* *
19708569 CAAACAGCAAAAAATAGCAC
1 AAAACAGCACAAAATAGCAC
19708589 AAAACAGCA
1 AAAACAGCA
19708598 GCAGTGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.41
21 9 0.20
22 17 0.39
ACGTcount: A:0.57, C:0.26, G:0.11, T:0.06
Consensus pattern (20 bp):
AAAACAGCACAAAATAGCAC
Found at i:19708587 original size:10 final size:10
Alignment explanation
Indices: 19708526--19708597 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 10
19708516 GAGCGTTACA
19708526 AAAACAGCACC
1 AAAACAGCA-C
*
19708537 AAAGCAGCATC
1 AAAACAGCA-C
19708548 AAAACAGCATC
1 AAAACAGCA-C
*
19708559 AAAATAGCAC
1 AAAACAGCAC
* *
19708569 CAAACAGCAA
1 AAAACAGCAC
*
19708579 AAAATAGCAC
1 AAAACAGCAC
19708589 AAAACAGCA
1 AAAACAGCA
19708598 GCAGTGAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
10 23 0.46
11 27 0.54
ACGTcount: A:0.57, C:0.26, G:0.11, T:0.06
Consensus pattern (10 bp):
AAAACAGCAC
Found at i:19708802 original size:9 final size:9
Alignment explanation
Indices: 19708785--19708820 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
19708775 ATCGAAGAAA
*
19708785 CATCATCCT
1 CATCGTCCT
19708794 CATCGTCCT
1 CATCGTCCT
*
19708803 CATCGTCAT
1 CATCGTCCT
19708812 CATCGTCCT
1 CATCGTCCT
19708821 TGCAACCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.17, C:0.42, G:0.08, T:0.33
Consensus pattern (9 bp):
CATCGTCCT
Found at i:19712487 original size:30 final size:31
Alignment explanation
Indices: 19712452--19712515 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
19712442 ACGAAATGAC
19712452 AAAATGAAAGTGG-AAAAAAGGAGAAAAGTT
1 AAAATGAAAGTGGAAAAAAAGGAGAAAAGTT
19712482 AAAATGAAAGTGGAAAAAAAGGAGAAAAGTT
1 AAAATGAAAGTGGAAAAAAAGGAGAAAAGTT
19712513 AAA
1 AAA
19712516 GTTAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (31 bp):
AAAATGAAAGTGGAAAAAAAGGAGAAAAGTT
Found at i:19729729 original size:26 final size:27
Alignment explanation
Indices: 19729678--19729730 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
19729668 TTGCCTTAAA
*
19729678 TTCAAATCTTTTTGAGTCATTAAATAT
1 TTCAAATCTTTTTGAGTCAGTAAATAT
*
19729705 TTCAAA-CTTTTGTGA-TCAGTGAATAT
1 TTCAAATCTTTT-TGAGTCAGTAAATAT
19729731 GTGGCACTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (27 bp):
TTCAAATCTTTTTGAGTCAGTAAATAT
Found at i:19735067 original size:53 final size:54
Alignment explanation
Indices: 19734975--19735187 Score: 249
Period size: 53 Copynumber: 4.0 Consensus size: 54
19734965 TACGTGGTAT
* * *
19734975 CCTTTTGAAACTTACCATTGCCAT-TCTTGACATGGTCTTACATGGTATCCTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* *
19735028 CCTTATG-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGG-A-CCTTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTG
* * * *
19735080 CCTTATAGTAACTTA-CAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTG
1 CCTTAT-GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* *
19735134 CCTTA-GAAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 CCTTATGAAA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
19735188 AAACCCTAAT
Statistics
Matches: 135, Mismatches: 16, Indels: 16
0.81 0.10 0.10
Matches are distributed among these distances:
51 2 0.01
52 27 0.20
53 58 0.43
54 16 0.12
55 32 0.24
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (54 bp):
CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
Found at i:19735132 original size:106 final size:108
Alignment explanation
Indices: 19734983--19735180 Score: 305
Period size: 106 Copynumber: 1.9 Consensus size: 108
19734973 ATCCTTTTGA
* *
19734983 AACTTACCATTGCCATTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA-
1 AACTTACCAATGCCATTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAAT
19735045 TGCCATGCCTTGGCATGGTCTTACATGGACCTTTGCCTTATAGT
65 TGCCATGCCTTGGCATGGTCTTACATGGACCTTTGCCTTATAGT
* *
19735089 AACTTA-CAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCAT-TCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
19735153 TTCCATGCCTTGGCATGGTCTTACATGG
65 TGCCATGCCTTGGCATGGTCTTACATGG
19735181 TATCCTTAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
105 9 0.11
106 40 0.48
107 7 0.08
108 27 0.33
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.35
Consensus pattern (108 bp):
AACTTACCAATGCCATTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAATT
GCCATGCCTTGGCATGGTCTTACATGGACCTTTGCCTTATAGT
Found at i:19738928 original size:16 final size:16
Alignment explanation
Indices: 19738907--19738941 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19738897 TGGTTCACTA
*
19738907 TAATGGAATAGAGTTG
1 TAATGGAATAGAGCTG
19738923 TAATGGAATAGAGCTG
1 TAATGGAATAGAGCTG
19738939 TAA
1 TAA
19738942 ATAATAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.29
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:19739286 original size:23 final size:21
Alignment explanation
Indices: 19739255--19739297 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19739245 TATAATATGA
19739255 ATTACAAAATCATAATATATAAT
1 ATTACAAAA--ATAATATATAAT
*
19739278 ATTATAAAAATAATATATAA
1 ATTACAAAAATAATATATAA
19739298 CCTACGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTACAAAAATAATATATAAT
Found at i:19742661 original size:17 final size:17
Alignment explanation
Indices: 19742620--19742662 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19742610 ACGCTCAACA
*
19742620 AAACAATTTACGAAAAC
1 AAACATTTTACGAAAAC
** *
19742637 AATGATTTTACGTAAAC
1 AAACATTTTACGAAAAC
19742654 AAACATTTT
1 AAACATTTT
19742663 TGAGAACACA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (17 bp):
AAACATTTTACGAAAAC
Found at i:19743138 original size:19 final size:20
Alignment explanation
Indices: 19743114--19743156 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
19743104 AGTTAGGGAC
*
19743114 TGAAACTCCTGA-AAATTTT
1 TGAAACTCCTGATAAATATT
*
19743133 TGAAACTTCTGATAAATATT
1 TGAAACTCCTGATAAATATT
19743153 TGAA
1 TGAA
19743157 GCTAAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAACTCCTGATAAATATT
Found at i:19751777 original size:28 final size:28
Alignment explanation
Indices: 19751708--19751808 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
19751698 GACAAGATTG
* * * *
19751708 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
19751738 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
19751766 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
19751795 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
19751809 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:19751802 original size:29 final size:28
Alignment explanation
Indices: 19751737--19751808 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
19751727 AAAATTGTAC
*
19751737 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
19751765 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
19751794 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
19751809 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:19759574 original size:28 final size:28
Alignment explanation
Indices: 19759505--19759605 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
19759495 GACAAGATTG
* * * *
19759505 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
19759535 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
19759563 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
19759592 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
19759606 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:19759599 original size:29 final size:28
Alignment explanation
Indices: 19759534--19759605 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
19759524 AAAATTGTAC
*
19759534 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
19759562 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
19759591 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
19759606 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:19763600 original size:47 final size:48
Alignment explanation
Indices: 19763572--19763676 Score: 151
Period size: 47 Copynumber: 2.2 Consensus size: 48
19763562 TAGTATTAAT
**
19763572 TATGTGATAAGGCCGAATGGCCAATGTG-ATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGAAAAGATGTGAAAGTGTATA
**
19763619 TATGTGATAAGGCCGAATGGCCAATGTGATGA-ATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGAAAAGATGTGAAAGTGTATA
*
19763666 AATGTGATAAG
1 TATGTGATAAG
19763677 TCCCGAAGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (48 bp):
TATGTGATAAGGCCGAATGGCCAATGTGAAAAGATGTGAAAGTGTATA
Found at i:19767356 original size:38 final size:38
Alignment explanation
Indices: 19767254--19767358 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 38
19767244 AATCCGAGTT
* * * *
19767254 TAAAGACCCGCTGACTATATGTAGAGATTATGTCCGGG
1 TAAAGACCCGATGGCTATATATAGAGATTATGTCCGGA
* *
19767292 TAAAGACCCGATGGCTATGTACAGAGATTATGTCCGGA
1 TAAAGACCCGATGGCTATATATAGAGATTATGTCCGGA
*
19767330 TTAAGACCC-ACTGGCT-TCATATAGAGATT
1 TAAAGACCCGA-TGGCTAT-ATATAGAGATT
19767359 TCATCCGAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 2 0.04
38 54 0.96
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (38 bp):
TAAAGACCCGATGGCTATATATAGAGATTATGTCCGGA
Found at i:19767449 original size:40 final size:40
Alignment explanation
Indices: 19767386--19767618 Score: 382
Period size: 40 Copynumber: 5.9 Consensus size: 40
19767376 CTCGACGATG
*
19767386 ATCCGGGCTAAGT-CCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
19767425 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
* * *
19767465 ATCCGGGCTAAGTCCCGAAGGGCATTGGTTCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
19767505 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
* *
19767545 ATCCGGGCTAAATCCC-AAGGGTATTCGTGCCGATGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
*
19767584 ATCCGGGCTAAGT-CCGAAGGGCATTCGTGCCGGTG
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTG
19767619 ATGTGTATTC
Statistics
Matches: 180, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
38 2 0.01
39 62 0.34
40 116 0.64
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
Found at i:19772071 original size:47 final size:47
Alignment explanation
Indices: 19772020--19772124 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
19772010 TAGTATTAAT
*
19772020 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
19772067 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
*
19772114 AATGTGATAAG
1 TATGTGATAAG
19772125 TCCCGAAGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
Found at i:19780288 original size:49 final size:50
Alignment explanation
Indices: 19780126--19780349 Score: 328
Period size: 49 Copynumber: 4.5 Consensus size: 50
19780116 ATACCCGATA
* * * *
19780126 GCCTGCACATAGTACCA-ACCTTGTAGTCAAAGCTACCTTCTTCACAAAGTG
1 GCCTTCACATAGTACCACA-CTTGT-GACCAAGCTATCTTCTTCACAAAGTG
*
19780177 TCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCACAAAGTG
1 GCCTTCACATAGTACCACACTTGTGACC-AAGCTATC-TTCTTCACAAAGTG
*
19780229 GCCTTCACATAGTACCACACTTGTGACCAAGCTATC-TCTTCTCAAAGTG
1 GCCTTCACATAGTACCACACTTGTGACCAAGCTATCTTCTTCACAAAGTG
*
19780278 GCCTTCACATAGTACCACACTTGTGACCAAGCTATC-TCTTCTCAAAGTG
1 GCCTTCACATAGTACCACACTTGTGACCAAGCTATCTTCTTCACAAAGTG
19780327 GCCTTCACATAGTACCACACTTG
1 GCCTTCACATAGTACCACACTTG
19780350 AGTCACTAGT
Statistics
Matches: 163, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
49 84 0.52
50 2 0.01
51 35 0.21
52 42 0.26
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (50 bp):
GCCTTCACATAGTACCACACTTGTGACCAAGCTATCTTCTTCACAAAGTG
Found at i:19781906 original size:41 final size:41
Alignment explanation
Indices: 19781780--19782063 Score: 342
Period size: 41 Copynumber: 7.0 Consensus size: 41
19781770 TTTTAAAATA
* * * *
19781780 CAGAGCAATAGCGGCG-TTTTAAGAAAAACACCGCTAAAAA-
1 CAGAGCATTAGCGGCGCTTTT-GGTAAAACGCCGCTAAAAAC
** * *
19781820 CAGAGCAACAGCGGCG-TTTTAGTAAAAAACGCCACTAAAAA-
1 CAGAGCATTAGCGGCGCTTTTGGT--AAAACGCCGCTAAAAAC
* *
19781861 CAGAGCATTAGCGGCGCCTTCGGTAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
** * *
19781902 CAGAGCATTAGCAACGCTTTTGGTAAAACACAGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
*
19781943 CAGAGCATTACCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
*
19781984 CAGAGCATTAGTGGCGCTTTTGGTAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
* * *
19782025 CAAAGCATTAGCGGCGCTTTTGGTAAAACGTCTCTAAAA
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
19782064 GTCATATAAC
Statistics
Matches: 213, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 2 0.01
40 34 0.16
41 173 0.81
42 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (41 bp):
CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
Found at i:19782863 original size:2 final size:2
Alignment explanation
Indices: 19782858--19782896 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19782848 TATATATATA
19782858 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
19782897 TTTTAATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:19783178 original size:15 final size:15
Alignment explanation
Indices: 19783158--19783189 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19783148 TTTAATTTAG
*
19783158 AAGATAAATGTATAT
1 AAGATAAATATATAT
19783173 AAGATAAATATATAT
1 AAGATAAATATATAT
19783188 AA
1 AA
19783190 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:19783228 original size:24 final size:23
Alignment explanation
Indices: 19783161--19783228 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
19783151 AATTTAGAAG
*
19783161 ATAAATGTATATAAGATAAATATAT
1 ATAAAT-TATATATGA-AAATATAT
* *
19783186 ATAAATTATTATTTTAAAATATAT
1 ATAAATTA-TATATGAAAATATAT
19783210 ATAAATATATATATGAAAA
1 ATAAAT-TATATATGAAAA
19783229 GTGGTTTAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
ATAAATTATATATGAAAATATAT
Found at i:19792682 original size:29 final size:30
Alignment explanation
Indices: 19792635--19792705 Score: 126
Period size: 29 Copynumber: 2.4 Consensus size: 30
19792625 AGATATTTAG
19792635 ATTTATGATGTAGTAAGATTTTATGATTTTT
1 ATTTAT-ATGTAGTAAGATTTTATGATTTTT
19792666 ATTTATATGTA-TAAGATTTTATGATTTTT
1 ATTTATATGTAGTAAGATTTTATGATTTTT
19792695 ATTTATATGTA
1 ATTTATATGTA
19792706 ATGTTATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 29 0.73
30 5 0.12
31 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
ATTTATATGTAGTAAGATTTTATGATTTTT
Found at i:19794735 original size:43 final size:43
Alignment explanation
Indices: 19794671--19795036 Score: 373
Period size: 43 Copynumber: 8.5 Consensus size: 43
19794661 ACTCGGCAAA
* * *
19794671 TTAGCGGCGTTTTTTAAAAAAGTGCCGCTAAAAGTAGATGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACATGTCT
* *
19794714 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGT-CCTCGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAT-GTCT
* * *
19794757 TTAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTAAAGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACATGTCT
* * * * * *
19794800 CTAGCAGCATTTTTTATAAAAGCGCCACTAAAGGT-CCTGGT-T
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAT-GTCT
* * * * *
19794842 TCTAGTGGCGTTTTTTACAAAAGCGCCTCTAAAAGTACAGGTAT
1 T-TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACATGTCT
*
19794886 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACA-GCTAT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACATG-TCT
* * * *
19794929 TTAGCGGCATTTTTTATAAAAGCGCCGCTAAAGGTCCTTGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACATGTCT
* * * *
19794972 TTAGCAGTGTTTTTTTATAAAAGCGCCGCTAAAGGT-CCTGGTCT
1 TTAGCGGCG-TTTTTTATAAAAGCGCCGCTAAAAGTACAT-GTCT
* *
19795016 TTACCGGCGTTTTTTCTAAAA
1 TTAGCGGCGTTTTTTATAAAA
19795037 AACGGCGCTA
Statistics
Matches: 269, Mismatches: 44, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
42 3 0.01
43 226 0.84
44 40 0.15
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACATGTCT
Found at i:19794816 original size:86 final size:86
Alignment explanation
Indices: 19794671--19795030 Score: 452
Period size: 86 Copynumber: 4.2 Consensus size: 86
19794661 ACTCGGCAAA
* * * * *
19794671 TTAGCGGCGTTTTTTAAAAAAGTGCCGCTAAAAGTAGATGTCTTTAGCGGCGTTTTTTATAAAAG
1 TTAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTTTAGCAGCGTTTTTTATAAAAG
*
19794736 CGCCGCTAAAGGTCCTCGTCT
66 CGCCGCTAAAGGTCCTGGTCT
* * *
19794757 TTAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTAAAGGTCTCTAGCAGCATTTTTTATAAAAG
1 TTAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTTTAGCAGCGTTTTTTATAAAAG
*
19794822 CGCCACTAAAGGTCCTGGT-T
66 CGCCGCTAAAGGTCCTGGTCT
* * * *
19794842 TCTAGTGGCGTTTTTTACAAAAGCGCCTCTAAAAGTACAGGTATTTAGCGGCGTTTTTTATAAAA
1 T-TAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTTTAGCAGCGTTTTTTATAAAA
* * * * *
19794907 GCGCCGCTAAAAGTACAGCTAT
65 GCGCCGCTAAAGGTCCTGGTCT
* * * * ** *
19794929 TTAGCGGCATTTTTTATAAAAGCGCCGCTAAAGGTCCTTGTCTTTAGCAGTGTTTTTTTATAAAA
1 TTAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTTTAGCAGCG-TTTTTTATAAAA
19794994 GCGCCGCTAAAGGTCCTGGTCT
65 GCGCCGCTAAAGGTCCTGGTCT
*
19795016 TTACCGGCGTTTTTT
1 TTAGCGGCGTTTTTT
19795031 CTAAAAAACG
Statistics
Matches: 232, Mismatches: 39, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
85 2 0.01
86 186 0.80
87 44 0.19
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (86 bp):
TTAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTTTAGCAGCGTTTTTTATAAAAG
CGCCGCTAAAGGTCCTGGTCT
Found at i:19794874 original size:129 final size:129
Alignment explanation
Indices: 19794710--19795030 Score: 446
Period size: 129 Copynumber: 2.5 Consensus size: 129
19794700 AAAAGTAGAT
*
19794710 GTCTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTCGTCTTTAGCGGCGTTTTTTACA
1 GTCTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTTTTACA
* *
19794775 AAAGCGCCGCTAAAAGTAAAGGTCTCTAGCAGCATTTTTTATAAAAGCGCCACTAAAGGTCCTG
66 AAAGCGCCGCTAAAAGTAAAGCTATCTAGCAGCATTTTTTATAAAAGCGCCACTAAAGGTCCTG
* * * * * * * *
19794839 GT-TTCTAGTGGCGTTTTTTACAAAAGCGCCTCTAAAAGTACAGGTATTTAGCGGCGTTTTTTAT
1 GTCTT-TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTTTTAC
* * * * *
19794903 AAAAGCGCCGCTAAAAGTACAGCTATTTAGCGGCATTTTTTATAAAAGCGCCGCTAAAGGTCCTT
65 AAAAGCGCCGCTAAAAGTAAAGCTATCTAGCAGCATTTTTTATAAAAGCGCCACTAAAGGTCCTG
* * *
19794968 GTCTTTAGCAGTGTTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCTTTACCGGCGTTTTTT
1 GTCTTTAGCGGCG-TTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTTTT
19795031 CTAAAAAACG
Statistics
Matches: 163, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
128 2 0.01
129 117 0.72
130 44 0.27
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (129 bp):
GTCTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTTTTACA
AAAGCGCCGCTAAAAGTAAAGCTATCTAGCAGCATTTTTTATAAAAGCGCCACTAAAGGTCCTG
Found at i:19795903 original size:22 final size:22
Alignment explanation
Indices: 19795875--19795922 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
19795865 AACGTGTTGC
19795875 TAGAAAATCAACCCAACCCAAT
1 TAGAAAATCAACCCAACCCAAT
19795897 TAGAAAATCAACCCAACCCAAT
1 TAGAAAATCAACCCAACCCAAT
19795919 TAGA
1 TAGA
19795923 GTAACTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.50, C:0.29, G:0.06, T:0.15
Consensus pattern (22 bp):
TAGAAAATCAACCCAACCCAAT
Found at i:19798258 original size:49 final size:49
Alignment explanation
Indices: 19798198--19798330 Score: 162
Period size: 49 Copynumber: 2.7 Consensus size: 49
19798188 CTTGTTGTGT
* * *
19798198 GTCAGTGTAAGACCTGTATGGGACATGACATCGACAC-CGATAGATGAGA
1 GTCAGTGTAAGACCTGTCTGGGACATGACATCGAC-CTCGATAGATAAAA
* * *
19798247 G-CTAGTGTAAGACCTGTCTGGGACACGACATCGGCCTCGATATATAAAA
1 GTC-AGTGTAAGACCTGTCTGGGACATGACATCGACCTCGATAGATAAAA
* *
19798296 GTCAGTGTAAAACCTGTCTGGGACATGGCATCGAC
1 GTCAGTGTAAGACCTGTCTGGGACATGACATCGAC
19798331 TTTGATGTGC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 2 0.03
49 68 0.96
50 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (49 bp):
GTCAGTGTAAGACCTGTCTGGGACATGACATCGACCTCGATAGATAAAA
Found at i:19803185 original size:40 final size:39
Alignment explanation
Indices: 19803020--19803203 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
19803010 AAATTGAATG
* * *
19803020 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
19803060 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
19803100 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
19803140 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
19803179 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
19803204 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:19803228 original size:80 final size:81
Alignment explanation
Indices: 19803060--19803248 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
19803050 GCTGGAAATT
* * * *
19803060 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
19803125 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
19803141 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
19803204 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
19803220 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
19803249 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:19811292 original size:40 final size:39
Alignment explanation
Indices: 19811127--19811310 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
19811117 AAATTGAATG
* * *
19811127 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
19811167 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
19811207 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
19811247 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
19811286 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
19811311 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:19811335 original size:80 final size:81
Alignment explanation
Indices: 19811167--19811355 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
19811157 GCTGGAAATT
* * * *
19811167 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
19811232 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
19811248 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
19811311 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
19811327 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
19811356 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:19813178 original size:39 final size:38
Alignment explanation
Indices: 19813129--19813236 Score: 146
Period size: 39 Copynumber: 2.8 Consensus size: 38
19813119 AATCACGATT
* *
19813129 GCACAAATGCCTTCGGGTCTTAGCCCGGATAG-AATACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GTAACACTA
19813168 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAACACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGTAACACTA
*
19813207 GCACAATTGCCTTCGGGTCTTAACCCGGAT
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGAT
19813237 TATAATTTCC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
38 3 0.05
39 60 0.95
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGTAACACTA
Found at i:19820304 original size:78 final size:80
Alignment explanation
Indices: 19820124--19820319 Score: 285
Period size: 78 Copynumber: 2.5 Consensus size: 80
19820114 TCGAATGATG
* * * *
19820124 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGATAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGATCCGAAGGCATT
19820188 TGTGCGAGTTACTAAA
65 TGTGCGAGTTACTAAA
19820204 TCC-GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCA-
1 TCCGGGA-TAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCAT
19820266 TT-TGCGAGTTACTAAA
64 TTGTGCGAGTTACTAAA
*
19820282 TCCGGGATAAGTCCCGAAGGCATTTGTGCGAGCTACTA
1 TCCGGGATAAGTCCCGAAGGCATTTGTGCGAGTTACTA
19820320 TAACCGGGCT
Statistics
Matches: 106, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
77 1 0.01
78 45 0.42
79 7 0.07
80 45 0.42
81 8 0.08
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (80 bp):
TCCGGGATAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:19820347 original size:40 final size:40
Alignment explanation
Indices: 19820124--19820319 Score: 269
Period size: 40 Copynumber: 5.0 Consensus size: 40
19820114 TCGAATGATG
* * * *
19820124 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
19820164 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
19820204 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
19820244 TCCGGACTAAGATCCGAAGGCA-TT-TGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
*
19820282 TCCGGGA-TAAG-TCCCGAAGGCATTTGTGCGAGCTACTA
1 TCC-GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
19820320 TAACCGGGCT
Statistics
Matches: 145, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
37 1 0.01
38 30 0.21
39 7 0.05
40 99 0.68
41 8 0.06
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:19821656 original size:48 final size:48
Alignment explanation
Indices: 19821600--19822021 Score: 353
Period size: 48 Copynumber: 8.8 Consensus size: 48
19821590 TGAATTGCTG
* * * * * * *
19821600 ATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATGTTGAGGCTA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
* * * * * ** *
19821648 ATGCCATGTCCCAGACATGCTCTTACACTAGCTCTCGTCTCAATACCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
* * * * **
19821696 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATGTTGTGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
* * ** * ** **
19821744 ATGTCATGTACCAGACATGGTCTTACACTAGGACACATATCAATACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
* * * * ** *
19821792 ATGCCATGTCCCAGATATGTTCTTACACTGGCTCTCATATTGTGGCAA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
* * *
19821840 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
* * * ** *
19821888 ATGTCATGTTCCAGACATGGTCTTACACTAGCTCTCATATTGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
* * * *
19821936 ACGCCATGTCCCAGACATGGTCTTGCACTAGC-CACATATTAATGCTA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
* * *
19821983 ATGCCATGTCCC-GGCATGGTGTTACACTAGCTCTCATAT
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAT
19822022 CACCCAAGTG
Statistics
Matches: 286, Mismatches: 87, Indels: 3
0.76 0.23 0.01
Matches are distributed among these distances:
46 16 0.06
47 26 0.09
48 244 0.85
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTAAGGCCA
Found at i:19821768 original size:96 final size:96
Alignment explanation
Indices: 19821599--19822021 Score: 499
Period size: 96 Copynumber: 4.4 Consensus size: 96
19821589 GTGAATTGCT
* * * * * *
19821599 GATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATGTTGAGGCTAATGCCATGTCCCAGAC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCAATGCCATGTCCCAGAC
* * * * *
19821664 ATGCTCTTACACTAGCTCTCGTCTCAATACC
66 ATGGTCTTACACTAGCACACATATCAATACC
* * *
19821695 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATGTTGTGGCCAATGTCATGTACCAGAC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCAATGCCATGTCCCAGAC
* *
19821760 ATGGTCTTACACTAGGACACATATCAATACT
66 ATGGTCTTACACTAGCACACATATCAATACC
* * * *
19821791 GATGCCATGTCCCAGATATGTTCTTACACTGGCTCTCATATTGTGGCAAATGCCATGTCCCAGAC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCAATGCCATGTCCCAGAC
**
19821856 ATGGTCTTACACTAGCACACATATCAAGGCC
66 ATGGTCTTACACTAGCACACATATCAATACC
* * * * * *
19821887 GATGTCATGTTCCAGACATGGTCTTACACTAGCTCTCATATTGTGGCCGACGCCATGTCCCAGAC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCAATGCCATGTCCCAGAC
* * * *
19821952 ATGGTCTTGCACTAGC-CACATATTAATGCT
66 ATGGTCTTACACTAGCACACATATCAATACC
* ** * *
19821982 AATGCCATGTCCC-GGCATGGTGTTACACTAGCTCTCATAT
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAT
19822022 CACCCAAGTG
Statistics
Matches: 285, Mismatches: 42, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
94 25 0.09
95 21 0.07
96 239 0.84
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (96 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCAATGCCATGTCCCAGAC
ATGGTCTTACACTAGCACACATATCAATACC
Found at i:19825665 original size:28 final size:28
Alignment explanation
Indices: 19825596--19825696 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
19825586 GACAAGATTG
* * * *
19825596 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
19825626 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
19825654 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
19825683 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
19825697 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:19825690 original size:29 final size:28
Alignment explanation
Indices: 19825625--19825696 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
19825615 AAAATTGTAC
*
19825625 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
19825653 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
19825682 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
19825697 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:19833470 original size:28 final size:28
Alignment explanation
Indices: 19833401--19833501 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
19833391 GACAAGATTG
* * * *
19833401 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
19833431 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
19833459 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
19833488 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
19833502 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:19833495 original size:29 final size:28
Alignment explanation
Indices: 19833430--19833501 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
19833420 AAAATTGTAC
*
19833430 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
19833458 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
19833487 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
19833502 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:19836420 original size:5 final size:5
Alignment explanation
Indices: 19836410--19836436 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19836400 CAAAATAGAA
19836410 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
19836437 TGTGTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:19837384 original size:29 final size:27
Alignment explanation
Indices: 19837328--19837387 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
19837318 TAACATAAAG
*
19837328 TAAAAATATCAAAAATAAAAATAGTTT
1 TAAAAATATCAAAAATAAAAATAATTT
* *
19837355 TAAAATATATTAAAAGATTAAAATAATTT
1 TAAAA-ATATCAAAA-ATAAAAATAATTT
19837384 TAAA
1 TAAA
19837388 TGAAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 8 0.29
29 15 0.54
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (27 bp):
TAAAAATATCAAAAATAAAAATAATTT
Found at i:19837388 original size:28 final size:27
Alignment explanation
Indices: 19837328--19837388 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
19837318 TAACATAAAG
* *
19837328 TAAAAATATCAAAAATAAAAATAGTTT
1 TAAATATATCAAAAATAAAAATAATTT
* *
19837355 TAAAATATATTAAAAGATTAAAATAATTT
1 T-AAATATATCAAAA-ATAAAAATAATTT
19837384 TAAAT
1 TAAAT
19837389 GAAATATATC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.04
28 15 0.54
29 12 0.43
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (27 bp):
TAAATATATCAAAAATAAAAATAATTT
Found at i:19839128 original size:38 final size:38
Alignment explanation
Indices: 19839084--19839159 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
19839074 GAGTTGGAGT
19839084 ATAGTTCAAGGGCCAATTTACTAATAAATCCTATTATA
1 ATAGTTCAAGGGCCAATTTACTAATAAATCCTATTATA
19839122 ATAGTTCAAGGGCCAATTTACTAATAAATCCTATTATA
1 ATAGTTCAAGGGCCAATTTACTAATAAATCCTATTATA
19839160 TTATACATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (38 bp):
ATAGTTCAAGGGCCAATTTACTAATAAATCCTATTATA
Found at i:19843178 original size:21 final size:21
Alignment explanation
Indices: 19843152--19843192 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19843142 AGACGAGCGA
* *
19843152 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
19843173 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
19843193 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:19847646 original size:40 final size:40
Alignment explanation
Indices: 19847591--19847754 Score: 177
Period size: 40 Copynumber: 4.1 Consensus size: 40
19847581 TGAATGATAC
* *
19847591 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
19847631 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * * * ** *
19847671 CTGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
19847711 CCGGGTTAAGACCCGAAGGCAGTTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
19847751 CCGG
1 CCGG
19847755 TTAAATCCCG
Statistics
Matches: 100, Mismatches: 22, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.97
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:19857528 original size:31 final size:32
Alignment explanation
Indices: 19857493--19857555 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
19857483 ATAATTATTT
19857493 TAATTAAAATGATTAAATTG-AAAAAAATTAA
1 TAATTAAAATGATTAAATTGAAAAAAAATTAA
19857524 TAATTAAAATGATTAAATTGAAAAAAAATTAA
1 TAATTAAAATGATTAAATTGAAAAAAAATTAA
19857556 AGTGATTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (32 bp):
TAATTAAAATGATTAAATTGAAAAAAAATTAA
Found at i:19857542 original size:14 final size:15
Alignment explanation
Indices: 19857494--19857547 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
19857484 TAATTATTTT
19857494 AATT-AAAATGATTA
1 AATTGAAAATGATTA
**
19857508 AATTGAAAAAAATTAA
1 AATTGAAAATGATT-A
19857524 TAATT-AAAATGATTA
1 -AATTGAAAATGATTA
19857539 AATTGAAAA
1 AATTGAAAA
19857548 AAAATTAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 8 0.25
15 12 0.38
16 8 0.25
17 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AATTGAAAATGATTA
Found at i:19857554 original size:16 final size:15
Alignment explanation
Indices: 19857504--19857556 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
19857494 AATTAAAATG
19857504 ATTAAATTGAAAAAA
1 ATTAAATTGAAAAAA
**
19857519 ATTAATAATT-AAAATG
1 ATT-A-AATTGAAAAAA
19857535 ATTAAATTGAAAAAAA
1 ATTAAATTG-AAAAAA
19857551 ATTAAA
1 ATTAAA
19857557 GTGATTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.13
15 4 0.13
16 18 0.60
17 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (15 bp):
ATTAAATTGAAAAAA
Found at i:19857763 original size:2 final size:2
Alignment explanation
Indices: 19857756--19857813 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
19857746 TCGCTTTAGG
19857756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19857798 TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA
19857814 GTTTAATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19858798 original size:20 final size:20
Alignment explanation
Indices: 19858753--19858799 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
19858743 TTTTTAATCC
* *
19858753 ATTAAATAATATATTTTATA
1 ATTAAAAAACATATTTTATA
19858773 ATTTAAAAAACATA-TTTACTA
1 A-TTAAAAAACATATTTTA-TA
19858794 ATTAAA
1 ATTAAA
19858800 TTAGAGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTAAAAAACATATTTTATA
Found at i:19859353 original size:18 final size:21
Alignment explanation
Indices: 19859330--19859375 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
19859320 ACTATTTCTC
19859330 TAATAATAA-AA-AT-ATTAT
1 TAATAATAACAATATAATTAT
19859348 TAATAA-AACAATTATAATTAT
1 TAATAATAACAA-TATAATTAT
19859369 TAATAAT
1 TAATAAT
19859376 TTGTTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.09
18 8 0.35
20 2 0.09
21 11 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATAATAACAATATAATTAT
Found at i:19859434 original size:15 final size:16
Alignment explanation
Indices: 19859414--19859444 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
19859404 TGGAAGATTT
19859414 AATAAAAT-ATTATTA
1 AATAAAATAATTATTA
19859429 AATAAAATAATTATTA
1 AATAAAATAATTATTA
19859445 TCATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAAATAATTATTA
Found at i:19859966 original size:19 final size:19
Alignment explanation
Indices: 19859942--19859978 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19859932 AATATAAATT
*
19859942 ATTTATAAATTTTATTTAA
1 ATTTATAAATTATATTTAA
19859961 ATTTATAAATTATATTTA
1 ATTTATAAATTATATTTA
19859979 TGATTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTATAAATTATATTTAA
Found at i:19864633 original size:13 final size:14
Alignment explanation
Indices: 19864608--19864636 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19864598 ATTTGGGTTT
19864608 ATGAAGCCCAAAAC
1 ATGAAGCCCAAAAC
19864622 ATGAAG-CCAAAAC
1 ATGAAGCCCAAAAC
19864635 AT
1 AT
19864637 ACTTAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.24, G:0.14, T:0.10
Consensus pattern (14 bp):
ATGAAGCCCAAAAC
Found at i:19866565 original size:26 final size:26
Alignment explanation
Indices: 19866529--19866638 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
19866519 TGATACAAAT
19866529 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
19866555 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
19866581 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
19866607 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
19866633 TGATAA
1 TGATAA
19866639 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:19868332 original size:40 final size:39
Alignment explanation
Indices: 19868288--19868480 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
19868278 GTTCAAAACA
* * ** * *
19868288 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
19868328 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
19868368 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
19868407 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
19868446 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
19868481 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:19868399 original size:39 final size:39
Alignment explanation
Indices: 19868318--19868480 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
19868308 TATGGTAACC
* *
19868318 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
19868358 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
19868397 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
19868436 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
19868475 CGCACA
1 CGCACA
19868481 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:19876219 original size:40 final size:39
Alignment explanation
Indices: 19876175--19876367 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
19876165 GTTCAAAACA
* * ** * *
19876175 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
19876215 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
19876255 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
19876294 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
19876333 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
19876368 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:19876286 original size:39 final size:39
Alignment explanation
Indices: 19876205--19876367 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
19876195 TATGGTAACC
* *
19876205 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
19876245 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
19876284 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
19876323 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
19876362 CGCACA
1 CGCACA
19876368 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:19881382 original size:24 final size:26
Alignment explanation
Indices: 19881355--19881414 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 26
19881345 TTCATGTTTT
*
19881355 CATGGTAAAAATT-A-ACATATAATA
1 CATGGTAAAAATTAAGACACATAATA
*
19881379 CAT-G-AAACATTAAGACACATAATA
1 CATGGTAAAAATTAAGACACATAATA
*
19881403 CATGGTAGAAAT
1 CATGGTAAAAAT
19881415 GAAATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
22 6 0.21
23 2 0.07
24 15 0.54
25 1 0.04
26 4 0.14
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.25
Consensus pattern (26 bp):
CATGGTAAAAATTAAGACACATAATA
Found at i:19886368 original size:18 final size:19
Alignment explanation
Indices: 19886335--19886370 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19886325 TATGTATAAC
*
19886335 ATGTTTAACTTAATGTTTG
1 ATGTTTAACATAATGTTTG
19886354 ATGTTTAA-ATAATGTTT
1 ATGTTTAACATAATGTTT
19886371 AAATAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (19 bp):
ATGTTTAACATAATGTTTG
Found at i:19892837 original size:8 final size:8
Alignment explanation
Indices: 19892826--19892850 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19892816 GGTGGTTAAG
19892826 TGGAGTGT
1 TGGAGTGT
19892834 TGGAGTGT
1 TGGAGTGT
19892842 TGGAGTGT
1 TGGAGTGT
19892850 T
1 T
19892851 AGAGGTCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (8 bp):
TGGAGTGT
Found at i:19896386 original size:29 final size:28
Alignment explanation
Indices: 19896352--19896454 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
19896342 TACTCAATCA
*
19896352 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
19896381 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
19896410 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
19896439 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
19896455 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:19904379 original size:29 final size:28
Alignment explanation
Indices: 19904345--19904447 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
19904335 TACTCAATCA
*
19904345 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
19904374 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
19904403 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
19904432 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
19904448 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:19909416 original size:25 final size:25
Alignment explanation
Indices: 19909357--19909426 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
19909347 CAGGCCCATT
* *
19909357 TCACAACTCGTGTGAGCATTTACAA
1 TCACAACTTGTCTGAGCATTTACAA
* **
19909382 TCACAGCTTGTCTGAGCATTTACCG
1 TCACAACTTGTCTGAGCATTTACAA
* *
19909407 TCATAACTTGTTTGAGCATT
1 TCACAACTTGTCTGAGCATT
19909427 GCTTCTACAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (25 bp):
TCACAACTTGTCTGAGCATTTACAA
Found at i:19909548 original size:13 final size:13
Alignment explanation
Indices: 19909485--19909551 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
19909475 TGAGTAAACA
*
19909485 GAAATGGTAATAT
1 GAAATGGTTATAT
*
19909498 G-AATGGATATACT
1 GAAATGGTTATA-T
*
19909511 -AAATGTTTATAT
1 GAAATGGTTATAT
* *
19909523 GAAAATAGATATAT
1 G-AAATGGTTATAT
19909537 GAAATGGTTATAT
1 GAAATGGTTATAT
19909550 GA
1 GA
19909552 GTTGTTTATG
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
12 9 0.22
13 22 0.54
14 10 0.24
ACGTcount: A:0.45, C:0.01, G:0.19, T:0.34
Consensus pattern (13 bp):
GAAATGGTTATAT
Found at i:19909593 original size:27 final size:27
Alignment explanation
Indices: 19909511--19909593 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
19909501 TGGATATACT
* *
19909511 AAATGTTTATATGAAAATAGATATATG
1 AAATGTTTATATGAATATAGATATGTG
* * * *
19909538 AAATGGTTATATGAGT-T-GTTTATGCG
1 AAATGTTTATATGAATATAG-ATATGTG
*
19909564 AAATATTTATATGAATATAGATATGTG
1 AAATGTTTATATGAATATAGATATGTG
19909591 AAA
1 AAA
19909594 AGGAGCATTG
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
25 1 0.02
26 18 0.43
27 22 0.52
28 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.18, T:0.39
Consensus pattern (27 bp):
AAATGTTTATATGAATATAGATATGTG
Found at i:19913704 original size:13 final size:13
Alignment explanation
Indices: 19913686--19913716 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19913676 TTCTTATTGG
19913686 AAAAAATAAAAAC
1 AAAAAATAAAAAC
*
19913699 AAAAAATAAAAAT
1 AAAAAATAAAAAC
19913712 AAAAA
1 AAAAA
19913717 GAATCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAATAAAAAC
Done.