Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 31 of 128
Found at i:9454415 original size:39 final size:38
Alignment explanation
Indices: 9454361--9454503 Score: 151
Period size: 39 Copynumber: 3.7 Consensus size: 38
9454351 TGATTATTCA
* *
9454361 GGCTATGTGGCTAGCAGGCTGTGTGCTGGTAATTACTTG
1 GGCTATGTGCCTAGCAGGCTGTGTGCCGGTAATTA-TTG
* * * **
9454400 GGCTATGTGCCTAGCAAGCTGGGTGCCGGTTATTATCCA
1 GGCTATGTGCCTAGCAGGCTGTGTGCCGGTAATTAT-TG
* * * *
9454439 GGTTATGTGTCTAGTAGGCTGTGTGCCGGTGATTATTCG
1 GGCTATGTGCCTAGCAGGCTGTGTGCCGGTAATTATT-G
*
9454478 GGCTATGTGCCTAGCAGGCTATGTGC
1 GGCTATGTGCCTAGCAGGCTGTGTGC
9454504 TGGTGTATTA
Statistics
Matches: 83, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 82 0.99
ACGTcount: A:0.15, C:0.18, G:0.34, T:0.32
Consensus pattern (38 bp):
GGCTATGTGCCTAGCAGGCTGTGTGCCGGTAATTATTG
Found at i:9456951 original size:140 final size:138
Alignment explanation
Indices: 9456556--9456944 Score: 455
Period size: 139 Copynumber: 2.8 Consensus size: 138
9456546 TAATTAGAAA
* *
9456556 AGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCGCAGTTCTAATA-C-TATGGCCTCCAAACAGT
1 AGTTAAAAGCTCCCAGCTGTCATTCTAAGGCTCGCAGTT-TAATATCGCA--GCCTCCAAACAGT
* * * * *
9456619 TAGCGAGAGTTAGAAGCTCTCAGCTATCATTTTAAGGCTTGCAAGTTTAATACTGCGACCTCTAT
63 TAGCGAGAGTTAAAAGCTCCCAGCTATCATTTTAAGGCTCGCAGGTTTAATACCGCGACCTCTAT
* *
9456684 AAATTAGTGAG
128 AAATTAGCGAC
* * * *
9456695 AGTTAAAAGCTCCCAGCTATCATTCTAAGGTTCGCATGTTCAATATCGC-GACCTCTAAACAGTT
1 AGTTAAAAGCTCCCAGCTGTCATTCTAAGGCTCGCA-GTTTAATATCGCAG-CCTCCAAACAGTT
* *
9456759 AGCGAGAGTTAAAAGCTCCCAGCTTTCATTTTAAGGCTCACAGGTTTAATACCGC-AGCCTCTA-
64 AGCGAGAGTTAAAAGCTCCCAGCTATCATTTTAAGGCTCGCAGGTTTAATACCGCGA-CCTCTAT
9456822 AATAGTTAGCGAC
128 AA-A-TTAGCGAC
* * * *
9456835 AGTTAAAAGCTCCTAGCTGTCATTCTAAGGGTCACAGGTTTAATATCGCAGCCTCCAAACTGTTA
1 AGTTAAAAGCTCCCAGCTGTCATTCTAAGGCTCGCA-GTTTAATATCGCAGCCTCCAAACAGTTA
* * * *
9456900 GCAAGAGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGTAGGTT
65 GCGAGAGTTAAAAGCTCCCAGCTATCATTTTAAGGCTCGCAGGTT
9456945 CGATACCATA
Statistics
Matches: 213, Mismatches: 29, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
138 4 0.02
139 104 0.49
140 104 0.49
141 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (138 bp):
AGTTAAAAGCTCCCAGCTGTCATTCTAAGGCTCGCAGTTTAATATCGCAGCCTCCAAACAGTTAG
CGAGAGTTAAAAGCTCCCAGCTATCATTTTAAGGCTCGCAGGTTTAATACCGCGACCTCTATAAA
TTAGCGAC
Found at i:9456964 original size:70 final size:70
Alignment explanation
Indices: 9456556--9456982 Score: 385
Period size: 70 Copynumber: 6.1 Consensus size: 70
9456546 TAATTAGAAA
* * * ***** *
9456556 AGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCGCA-GTTCTAATACTATGGCCTCCAAACAGTT
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCACAGGTTC-AATACCGCAACCTCTAAACAGTT
9456620 AGCGAG
65 AGCGAG
* * * ** * * * *
9456626 AGTTAGAAGCTCTCAGCTATCATTTTAAGGCTTGCAAGTTTAATACTGCGACCTCTATAA-A-TT
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCACAGGTTCAATACCGCAACCTCTA-AACAGTT
*
9456689 AGTGAG
65 AGCGAG
* * * * *
9456695 AGTTAAAAGCTCCCAGCTATCATTCTAAGGTTCGCATGTTCAATATCGCGACCTCTAAACAGTTA
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCACAGGTTCAATACCGCAACCTCTAAACAGTTA
9456760 GCGAG
66 GCGAG
* * * * *
9456765 AGTTAAAAGCTCCCAGCTTTCATTTTAAGGCTCACAGGTTTAATACCGCAGCCTCTAAATAGTTA
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCACAGGTTCAATACCGCAACCTCTAAACAGTTA
*
9456830 GCGAC
66 GCGAG
* * * * * * * *
9456835 AGTTAAAAGCTCCTAGCTGTCATTCTAAGGGTCACAGGTTTAATATCGCAGCCTCCAAACTGTTA
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCACAGGTTCAATACCGCAACCTCTAAACAGTTA
*
9456900 GCAAG
66 GCGAG
* ** * **
9456905 AGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGTAGGTTCGATACCATAACCT-TCAAACAGTT
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCACAGGTTCAATACCGCAACCTCT-AAACAGTT
9456969 AGCGAG
65 AGCGAG
9456975 AGCTTAAA
1 AG-TTAAA
9456983 CTCCTGACTG
Statistics
Matches: 293, Mismatches: 58, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
68 2 0.01
69 56 0.19
70 225 0.77
71 10 0.03
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (70 bp):
AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCACAGGTTCAATACCGCAACCTCTAAACAGTTA
GCGAG
Found at i:9457255 original size:16 final size:16
Alignment explanation
Indices: 9457234--9457264 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9457224 GAGATAGAAT
9457234 ATCATGATATTGACAC
1 ATCATGATATTGACAC
9457250 ATCATGATATTGACA
1 ATCATGATATTGACA
9457265 ATCGAACTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (16 bp):
ATCATGATATTGACAC
Found at i:9460176 original size:20 final size:20
Alignment explanation
Indices: 9460151--9460193 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9460141 TCATAGGAGT
9460151 AGTGGGGTCAAGTCATGAAC
1 AGTGGGGTCAAGTCATGAAC
* * *
9460171 AGTGGGGTTATGTCGTGAAC
1 AGTGGGGTCAAGTCATGAAC
9460191 AGT
1 AGT
9460194 AATAGTATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.37, T:0.26
Consensus pattern (20 bp):
AGTGGGGTCAAGTCATGAAC
Found at i:9461456 original size:16 final size:16
Alignment explanation
Indices: 9461435--9461466 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9461425 CATACCTTAT
9461435 ATCCAAGTTGATCTAA
1 ATCCAAGTTGATCTAA
9461451 ATCCAAGTTGATCTAA
1 ATCCAAGTTGATCTAA
9461467 CAGTCAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
ATCCAAGTTGATCTAA
Found at i:9470399 original size:18 final size:18
Alignment explanation
Indices: 9470376--9470413 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
9470366 TACCAGATGC
*
9470376 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
9470394 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
9470412 GT
1 GT
9470414 TTTCTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:9474795 original size:16 final size:16
Alignment explanation
Indices: 9474771--9474824 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
9474761 TTTGGTTCGC
* *
9474771 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
9474787 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
9474803 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
9474819 TGTAAT
1 TGTAAT
9474825 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:9474908 original size:39 final size:43
Alignment explanation
Indices: 9474803--9474912 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
9474793 GGAATAGAGG
9474803 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * * ***
9474848 TGTAATGGCATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
9474888 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
9474913 TAAAGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 19 0.35
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.40
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:9477895 original size:122 final size:122
Alignment explanation
Indices: 9477678--9477922 Score: 454
Period size: 122 Copynumber: 2.0 Consensus size: 122
9477668 GCTGTAATTG
*
9477678 TGTTATTAATTTATTATTTTAAATTCTAAAACTAAATTCATTAATTTTTATATTTAATTTTAAAG
1 TGTTATTAATTGATTATTTTAAATTCTAAAACTAAATTCATTAATTTTTATATTTAATTTTAAAG
*
9477743 TTAAAATTTTCATAGAAAATTTTATTTAAATAATATTTTTTATCCTTAAAAGTATAT
66 TTAAAATTTTCATAGAAAATTTAATTTAAATAATATTTTTTATCCTTAAAAGTATAT
*
9477800 TGTTATTAATTGATTATTTTAAATTCTAAAACTAAATTTATTAATTTTTATATTTAATTTTAAAG
1 TGTTATTAATTGATTATTTTAAATTCTAAAACTAAATTCATTAATTTTTATATTTAATTTTAAAG
*
9477865 TTAAAATTTTCATAGAGAATTTAATTTAAATAATATTTTTTATCCTTAAAAGTATAT
66 TTAAAATTTTCATAGAAAATTTAATTTAAATAATATTTTTTATCCTTAAAAGTATAT
9477922 T
1 T
9477923 TAAAGTTCAA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (122 bp):
TGTTATTAATTGATTATTTTAAATTCTAAAACTAAATTCATTAATTTTTATATTTAATTTTAAAG
TTAAAATTTTCATAGAAAATTTAATTTAAATAATATTTTTTATCCTTAAAAGTATAT
Found at i:9477952 original size:122 final size:121
Alignment explanation
Indices: 9477704--9477951 Score: 364
Period size: 122 Copynumber: 2.1 Consensus size: 121
9477694 TTTTAAATTC
*
9477704 TAAAACTAAATTCATTAATTTTTATATTTAATTTTAAAGTTAAAATTTTCATAGAAAATTTTATT
1 TAAAACTAAATTCATTAATTTTTATATTTAATTTTAAAGTTAAAATTTTCATAGAAAATTTAATT
* * * **
9477769 TAAATAATATTTTTTATCCTTAAAAGTATATTGTTATTAATTGATTATTTTAAATTC
66 TAAATAATATTTTTTATCCTTAAAAGTATATTGTTA-TAATTCATAATTTAAAATAA
* *
9477826 TAAAACTAAATTTATTAATTTTTATATTTAATTTTAAAGTTAAAATTTTCATAGAGAATTTAATT
1 TAAAACTAAATTCATTAATTTTTATATTTAATTTTAAAGTTAAAATTTTCATAGAAAATTTAATT
9477891 TAAATAATATTTTTTATCCTTAAAAGTATA-T-TTA-AAGTTCA-AATTTAAAA-AA
66 TAAATAATATTTTTTATCCTTAAAAGTATATTGTTATAA-TTCATAATTTAAAATAA
9477943 TAAAA-TAAA
1 TAAAACTAAA
9477952 ATATTTATCA
Statistics
Matches: 117, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
116 4 0.03
117 5 0.04
118 9 0.08
119 3 0.03
120 3 0.03
121 1 0.01
122 92 0.79
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (121 bp):
TAAAACTAAATTCATTAATTTTTATATTTAATTTTAAAGTTAAAATTTTCATAGAAAATTTAATT
TAAATAATATTTTTTATCCTTAAAAGTATATTGTTATAATTCATAATTTAAAATAA
Found at i:9478065 original size:43 final size:43
Alignment explanation
Indices: 9477998--9478227 Score: 311
Period size: 43 Copynumber: 5.4 Consensus size: 43
9477988 ATAATTTTTT
* * * * * *
9477998 TAAAGGTTAT-GTTTTTAGCAGCGTTTTTGTGCAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
9478040 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGTCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
9478083 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGG-AAAGCGCCAC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
9478125 TGAAGGTCTTGGTCATTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
9478168 TGAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
9478211 TAAAGGTCTTGGTCTTT
1 TAAAGGTCATGGTCTTT
9478228 TCGAATTCAC
Statistics
Matches: 169, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 45 0.27
43 124 0.73
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (43 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:9478144 original size:85 final size:85
Alignment explanation
Indices: 9477998--9478224 Score: 321
Period size: 85 Copynumber: 2.7 Consensus size: 85
9477988 ATAATTTTTT
* * * * * *
9477998 TAAAGGTTAT-GTTTTTAGCAGCGTTTTTGTGCAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGG
1 TAAAGGTCATGGTCTTTAGCGGCGTTTTTG-GGAAAGCGCCGCTAAAGGTCTTGGTCATTAGCGG
*
9478062 CGTTTGTGGGAAAAGCGTCGC
65 CGTTTGTGGGAAAAGCGCCGC
* *
9478083 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCACTGAAGGTCTTGGTCATTAGCGGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGGTCATTAGCGGC
9478148 GTTTGTGGGAAAAGCGCCGC
66 GTTTGTGGGAAAAGCGCCGC
* * *
9478168 TGAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
9478225 TTTTCGAATT
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
85 87 0.69
86 39 0.31
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.30
Consensus pattern (85 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGGTCATTAGCGGC
GTTTGTGGGAAAAGCGCCGC
Found at i:9479317 original size:13 final size:13
Alignment explanation
Indices: 9479299--9479325 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9479289 GTAAACGATA
9479299 AAAATTTTCACAC
1 AAAATTTTCACAC
9479312 AAAATTTTCACAC
1 AAAATTTTCACAC
9479325 A
1 A
9479326 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:9480061 original size:125 final size:125
Alignment explanation
Indices: 9479786--9480178 Score: 495
Period size: 126 Copynumber: 3.1 Consensus size: 125
9479776 GTCAAGCAAA
** *
9479786 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAAATTTTTTCAGTAATTTTGCTGACAGTGCAGCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * *
9479851 TGTTTGAAGTTTTTTTACACTATTTTTTTCAAAACCGTC-TTCTAAAATTTATTTTTTCAAG
66 TGTTTGAAGATTTTTTACACTA-TTTTTTCAGAACCGTCTTTTTAAAA-TTATTTTTTCAAG
* * * *
9479912 AACTACTGCAGAAAAAGATG-GTCCACGTGGGAGCTTTTTTCAATAATTCTGTTGACAGTGCATC
1 AACTACTGTAGAAAAAGA-GCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * * *
9479976 CTGCTTGAAGAATTTTGAAACTATTTTTTCAGAATCGTCTTTTTAAAATTATTTTTTCAAG
65 CTGTTTGAAGATTTTTTACACTATTTTTTCAGAACCGTCTTTTTAAAATTATTTTTTCAAG
* * * *
9480037 AACTACTATAGAAAAAGAGCGTCCACATGGGAGCTTTTTTTAGTAATTTTGCTAACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * * * * *
9480102 TGTTTGAAGCGTTTTTTACATTATTTTTTCAGAACCATCTTCTCAAAATTAATTTTTCTAA-
66 TGTTTGAAG-ATTTTTTACACTATTTTTTCAGAACCGTCTTTTTAAAATTATTTTTTC-AAG
9480163 AACTACTGTAGAAAAA
1 AACTACTGTAGAAAAA
9480179 AACAAAATCC
Statistics
Matches: 227, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
124 1 0.00
125 90 0.40
126 133 0.59
127 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (125 bp):
AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
TGTTTGAAGATTTTTTACACTATTTTTTCAGAACCGTCTTTTTAAAATTATTTTTTCAAG
Found at i:9480360 original size:33 final size:33
Alignment explanation
Indices: 9480234--9480359 Score: 134
Period size: 34 Copynumber: 3.8 Consensus size: 33
9480224 CTAAACACAA
*
9480234 AATTATTTTTTTAAAAA--CTAAACCCTAATTT
1 AATTATTTTTTAAAAAACTCTAAACCCTAATTT
9480265 AATTAATTTTCTT-AAAAACTCTAAACCCTAATTTT
1 AATT-ATTTT-TTAAAAAACTCTAAACCCTAA-TTT
* ** *
9480300 ATTTATTTATTTAAAACCCT-TAAAACCTAATTT
1 AATTATTT-TTTAAAAAACTCTAAACCCTAATTT
9480333 AATTATTTTTTAAAAAAACTCTAAACC
1 AATTATTTTTT-AAAAAACTCTAAACC
9480360 TTGATTTATT
Statistics
Matches: 78, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
31 4 0.05
32 13 0.17
33 18 0.23
34 31 0.40
35 12 0.15
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (33 bp):
AATTATTTTTTAAAAAACTCTAAACCCTAATTT
Found at i:9482187 original size:21 final size:21
Alignment explanation
Indices: 9482149--9482188 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9482139 GTCAAGGATG
* *
9482149 CTCAATTTCATGATACCTAGT
1 CTCAATGTCATGACACCTAGT
*
9482170 CTCAATGTCGTGACACCTA
1 CTCAATGTCATGACACCTA
9482189 CATCAAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (21 bp):
CTCAATGTCATGACACCTAGT
Found at i:9490638 original size:20 final size:19
Alignment explanation
Indices: 9490613--9490659 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
9490603 ATTAATTATT
9490613 TATAAAATTTAATTAGAATA
1 TATAAAATTTAATTA-AATA
* * *
9490633 TATAAACTATATTTAAATA
1 TATAAAATTTAATTAAATA
9490652 TA-AAAATT
1 TATAAAATT
9490660 AAATATTTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAATTTAATTAAATA
Found at i:9491923 original size:14 final size:15
Alignment explanation
Indices: 9491904--9491933 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
9491894 CAAATAAATC
9491904 AAAAGTGGCAT-AAA
1 AAAAGTGGCATCAAA
9491918 AAAAGTGGCATCAAA
1 AAAAGTGGCATCAAA
9491933 A
1 A
9491934 TGTAGAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.10, G:0.20, T:0.13
Consensus pattern (15 bp):
AAAAGTGGCATCAAA
Found at i:9491974 original size:75 final size:75
Alignment explanation
Indices: 9491851--9491994 Score: 270
Period size: 75 Copynumber: 1.9 Consensus size: 75
9491841 ATTGAAAGAA
9491851 CATCAAAATGTAGAAGTATCGATTCTGTTCAATAATGCAGATGCAAATAAATCAAAAGTGGCATA
1 CATCAAAATGTAGAAGTATCGATTCTGTTCAATAATGCAGATGCAAATAAATCAAAAGTGGCATA
9491916 AAAAAAGTGG
66 AAAAAAGTGG
* *
9491926 CATCAAAATGTAGAAGTATCGATTTTGTTCAATAATGCAGATGCAAATAAATCAAAAGTGGCATC
1 CATCAAAATGTAGAAGTATCGATTCTGTTCAATAATGCAGATGCAAATAAATCAAAAGTGGCATA
9491991 AAAA
66 AAAA
9491995 TGTAGAAGTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (75 bp):
CATCAAAATGTAGAAGTATCGATTCTGTTCAATAATGCAGATGCAAATAAATCAAAAGTGGCATA
AAAAAAGTGG
Found at i:9498856 original size:21 final size:21
Alignment explanation
Indices: 9498831--9498872 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9498821 ATTATCAGTG
9498831 CAAAAGCAACCAA-AACACCAA
1 CAAAAGCAACCAAGAA-ACCAA
*
9498852 CAAAAGCACCCAAGAAACCAA
1 CAAAAGCAACCAAGAAACCAA
9498873 ATACCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.60, C:0.33, G:0.07, T:0.00
Consensus pattern (21 bp):
CAAAAGCAACCAAGAAACCAA
Found at i:9504935 original size:197 final size:190
Alignment explanation
Indices: 9504587--9504939 Score: 481
Period size: 197 Copynumber: 1.8 Consensus size: 190
9504577 ATCCTATCAC
** * *
9504587 AAATTTAAAACACAAATGTCTGTTTAAAATAACATATAATAAATAATAAAACATATGATTTGAAA
1 AAATTTAAAACACAAATGTCCATTTAAAATAACATAAAACAAATAATAAAACATATGATTTGAAA
* * *
9504652 CTAATTAATAATAATACATGAAATATGTATGTTATTCAAATAAAAAATTAGATTAAATTGTTTAT
66 CTAATTAATAATAACACATGAAATATGTATGTTATTAAAAGAAAAAATTAGATTAAATTGTTTAT
* *
9504717 CATGGTGTTGTCATTAATCTTAAGTCAGTCCTATCATACGTATATGCGTGTGGAGACCTT
131 CATGATGTTGTCATCAATCTTAAGTCAGTCCTATCATACGTATATGCGTGTGGAGACCTT
* * * * * * *
9504777 AAATTTAGAACACAAATTTCCATTTAAAAATAGCATAAAACAAATACTGAAACTTATGGTTTGAA
1 AAATTTAAAACACAAATGTCCATTT-AAAATAACATAAAACAAATAATAAAACATATGATTTGAA
9504842 ACTAATTTAATAATAACACATGAAGTATATATGTATGTTATTAAAAAGAAAAAATTAGATTAAAT
65 ACTAA-TTAATAATAACACATG-A--A-ATATGTATGTTATT-AAAAGAAAAAATTAGATTAAAT
* *
9504907 TGTTTATTATGATGTTGTTATCAATCTTAAGTC
124 TGTTTATCATGATGTTGTCATCAATCTTAAGTC
9504940 GGTGTCGAAT
Statistics
Matches: 138, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
190 21 0.15
191 37 0.27
192 15 0.11
193 1 0.01
195 1 0.01
196 14 0.10
197 49 0.36
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (190 bp):
AAATTTAAAACACAAATGTCCATTTAAAATAACATAAAACAAATAATAAAACATATGATTTGAAA
CTAATTAATAATAACACATGAAATATGTATGTTATTAAAAGAAAAAATTAGATTAAATTGTTTAT
CATGATGTTGTCATCAATCTTAAGTCAGTCCTATCATACGTATATGCGTGTGGAGACCTT
Found at i:9505048 original size:18 final size:19
Alignment explanation
Indices: 9505009--9505052 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
9504999 ATGGATGTAA
9505009 TAAAATGTGCATAATAAAAT
1 TAAAATGT-CATAATAAAAT
9505029 TAAAATGT-ATAA-AAATAT
1 TAAAATGTCATAATAAA-AT
9505047 TAAAAT
1 TAAAAT
9505053 AAAACTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
20 8 0.35
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (19 bp):
TAAAATGTCATAATAAAAT
Found at i:9506913 original size:35 final size:35
Alignment explanation
Indices: 9506859--9506925 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
9506849 CCAATTTGTC
* * *
9506859 ATTTTCTTAATAAAGAATATTTGGAGAAATTACAT
1 ATTTTCTTAAAAAAAAATATTTGGAAAAATTACAT
*
9506894 ATTTTTTTAAAAAAAAATATTTGGAAAAATTA
1 ATTTTCTTAAAAAAAAATATTTGGAAAAATTA
9506926 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.40
Consensus pattern (35 bp):
ATTTTCTTAAAAAAAAATATTTGGAAAAATTACAT
Found at i:9507578 original size:31 final size:31
Alignment explanation
Indices: 9507543--9507645 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 31
9507533 TAATTACATT
*
9507543 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATAATATCTAGATA
** * *
9507574 AATATTAAATT-A-AATTTAATATCTCATATT
1 AATATTAAATTAATAAAATAATATCT-AGATA
* *
9507604 AATATTAAATTAATAAAGTAATAACTAGATA
1 AATATTAAATTAATAAAATAATATCTAGATA
*
9507635 AATATTTAATT
1 AATATTAAATT
9507646 TAATTTAATA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 9 0.16
30 15 0.26
31 25 0.43
32 9 0.16
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (31 bp):
AATATTAAATTAATAAAATAATATCTAGATA
Found at i:9507635 original size:61 final size:61
Alignment explanation
Indices: 9507540--9507655 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
9507530 AATTAATTAC
* *
9507540 ATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTAAATTAATAAAATAATAACTAGATAAATATTAAATTAAATTTAATATCTCAT
* * *
9507601 ATTAATATTAAATTAATAAAGTAATAACTAGATAAATATTTAATTTAATTTAATA
1 ATTAATATTAAATTAATAAAATAATAACTAGATAAATATTAAATTAAATTTAATA
9507656 ATAAATTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATAATAACTAGATAAATATTAAATTAAATTTAATATCTCAT
Found at i:9510892 original size:25 final size:25
Alignment explanation
Indices: 9510855--9510948 Score: 125
Period size: 25 Copynumber: 3.8 Consensus size: 25
9510845 CGGGCACACC
* **
9510855 ACAGCTCGTATGAGCTTCCTATTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
9510880 ACAGCTCGCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
*
9510905 TCAGCTCGCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
* * *
9510930 TCAGCTCGGAGGAGCTTCC
1 ACAGCTCGCATGAGCTTCC
9510949 TGTTTATAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (25 bp):
ACAGCTCGCATGAGCTTCCCGTTAT
Found at i:9518342 original size:25 final size:25
Alignment explanation
Indices: 9518310--9518368 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
9518300 AGCATTAGAT
*
9518310 TTCT-GTTATACAACTCGCATGAGC
1 TTCTCGTTATACAACTCGCACGAGC
** *
9518334 TTCTCGTTATTTAGCTCGCACGAGC
1 TTCTCGTTATACAACTCGCACGAGC
*
9518359 TTCCCGTTAT
1 TTCTCGTTAT
9518369 TTAGCTCGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (25 bp):
TTCTCGTTATACAACTCGCACGAGC
Found at i:9518369 original size:25 final size:25
Alignment explanation
Indices: 9518323--9518391 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
9518313 TGTTATACAA
* *
9518323 CTCGCATGAGCTTCTCGTTATTTAG
1 CTCGCACGAGCTTCCCGTTATTTAG
9518348 CTCGCACGAGCTTCCCGTTATTTAG
1 CTCGCACGAGCTTCCCGTTATTTAG
* *
9518373 CTCGGAGGAGCTTCCCGTT
1 CTCGCACGAGCTTCCCGTT
9518392 TATAGATCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.14, C:0.29, G:0.23, T:0.33
Consensus pattern (25 bp):
CTCGCACGAGCTTCCCGTTATTTAG
Found at i:9534058 original size:5 final size:5
Alignment explanation
Indices: 9534048--9534092 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
9534038 TGAATAGGGA
* *
9534048 CTTTT CTTTT CTTTT CTTTT CTTTT CTCTT CTCTTT CTCTT CTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CT-TTT CTTTT CTTT
9534093 GTTTTGGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (5 bp):
CTTTT
Found at i:9541040 original size:14 final size:13
Alignment explanation
Indices: 9541022--9541082 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
9541012 AAATATAAAC
9541022 AAAAATATATATT
1 AAAAATATATATT
9541035 ACAAAAT-T-TA-T
1 A-AAAATATATATT
9541046 --AAATATATATT
1 AAAAATATATATT
9541057 AAAAATATAT-TAT
1 AAAAATATATAT-T
9541070 AAAAAT-TATATT
1 AAAAATATATATT
9541082 A
1 A
9541083 TTGTGGCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 17
0.70 0.00 0.30
Matches are distributed among these distances:
8 4 0.10
9 1 0.03
10 2 0.05
11 2 0.05
12 8 0.20
13 18 0.45
14 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAAATATATATT
Found at i:9541083 original size:14 final size:13
Alignment explanation
Indices: 9541022--9541083 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 13
9541012 AAATATAAAC
9541022 AAAAATATA-TATT
1 AAAAATATATTA-T
*
9541035 ACAAA-AT-TTAT
1 AAAAATATATTAT
*
9541046 AAATATATA-T-T
1 AAAAATATATTAT
9541057 AAAAATATATTAT
1 AAAAATATATTAT
9541070 AAAAATTATATTAT
1 AAAAA-TATATTAT
9541084 TGTGGCTTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
11 13 0.33
12 8 0.21
13 10 0.26
14 8 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATATATTAT
Found at i:9541134 original size:26 final size:24
Alignment explanation
Indices: 9541105--9541161 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
9541095 TAAAACATAT
9541105 ATTATTAAAATTTATATTATAAAAAA
1 ATTA-TAAAA-TTATATTATAAAAAA
*
9541131 ATTATGAAATTATATTATAAAAAA
1 ATTATAAAATTATATTATAAAAAA
9541155 A-TATAAA
1 ATTATAAA
9541162 TACATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.17
24 16 0.55
25 4 0.14
26 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
ATTATAAAATTATATTATAAAAAA
Found at i:9541168 original size:23 final size:24
Alignment explanation
Indices: 9541118--9541169 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
9541108 ATTAAAATTT
*
9541118 ATATTATAAAAAAATTATGAAATT
1 ATATTATAAAAAAATTATGAAATC
9541142 ATATTATAAAAAAA-TAT-AAATAC
1 ATATTATAAAAAAATTATGAAAT-C
9541165 ATATT
1 ATATT
9541170 TTTATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 8 0.31
24 14 0.54
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
ATATTATAAAAAAATTATGAAATC
Found at i:9547482 original size:12 final size:12
Alignment explanation
Indices: 9547467--9547495 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
9547457 AATATTAGAT
9547467 TAAATTTAATAC
1 TAAATTTAATAC
9547479 TAAATTTAATAC
1 TAAATTTAATAC
9547491 TAAAT
1 TAAAT
9547496 CTTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTTAATAC
Found at i:9547576 original size:74 final size:71
Alignment explanation
Indices: 9547409--9547582 Score: 171
Period size: 74 Copynumber: 2.4 Consensus size: 71
9547399 CAACTATGAT
* * * *
9547409 TAAACTTAATCACTTT-AA-TATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAAT
1 TAAA-TTAATCACTTTAAACTATTAAAATAATAGAATATTTATCAAGATAAACATTAAATTAAAT
9547472 TTAATAC
65 TTAATAC
*
9547479 TAAATTTAAT-AC--TAAATCTTATTAAAATAATAGAATGTTTATCTGCAAGATAAACATTAAAT
1 TAAA-TTAATCACTTTAAA-C-TATTAAAATAATAGAATATTTA--T-CAAGATAAACATTAAAT
*
9547541 TAAATTTAATAT
60 TAAATTTAATAC
*
9547553 TAAGA-TAATCACTTTAAACTATTAAGATAA
1 TAA-ATTAATCACTTTAAACTATTAAAATAA
9547583 GTATTAAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
67 1 0.01
68 2 0.02
69 2 0.02
70 9 0.11
71 19 0.22
73 5 0.06
74 41 0.48
75 2 0.02
76 4 0.05
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (71 bp):
TAAATTAATCACTTTAAACTATTAAAATAATAGAATATTTATCAAGATAAACATTAAATTAAATT
TAATAC
Found at i:9549261 original size:16 final size:16
Alignment explanation
Indices: 9549240--9549270 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9549230 CTATGCATGC
*
9549240 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
9549256 AAAATACAAAAGACA
1 AAAATACAAAAGACA
9549271 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:9554289 original size:17 final size:17
Alignment explanation
Indices: 9554267--9554315 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
9554257 AAGGCCAATC
9554267 TGGGCATGTGGGCCACA
1 TGGGCATGTGGGCCACA
*
9554284 TGGGCATGTTGGCCCACA
1 TGGGCATG-TGGGCCACA
*
9554302 CGGGCATGTGGGCC
1 TGGGCATGTGGGCC
9554316 CAAACTTCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.14, C:0.27, G:0.41, T:0.18
Consensus pattern (17 bp):
TGGGCATGTGGGCCACA
Found at i:9560972 original size:15 final size:15
Alignment explanation
Indices: 9560954--9560986 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
9560944 ATATCACAAT
9560954 TATAAA-ATTATATAA
1 TATAAATATTATA-AA
9560969 TATAAATATTATAAA
1 TATAAATATTATAAA
9560984 TAT
1 TAT
9560987 TATAAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAAATATTATAAA
Found at i:9560983 original size:9 final size:9
Alignment explanation
Indices: 9560952--9560992 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
9560942 ATATATCACA
9560952 ATTATAAA-
1 ATTATAAAT
9560960 ATTAT--AT
1 ATTATAAAT
*
9560967 AATATAAAT
1 ATTATAAAT
9560976 ATTATAAAT
1 ATTATAAAT
9560985 ATTATAAA
1 ATTATAAA
9560993 ACAGATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
6 1 0.04
7 4 0.14
8 5 0.18
9 18 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATTATAAAT
Found at i:9564275 original size:18 final size:17
Alignment explanation
Indices: 9564249--9564296 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
9564239 AATAAAAATA
9564249 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAA-TGAAT
*
9564267 AACGATTTGTAAATGAAT
1 AACGTTTTG-AAATGAAT
*
9564285 AATGTTTTGAAA
1 AACGTTTTGAAA
9564297 ACGAACGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (17 bp):
AACGTTTTGAAATGAAT
Found at i:9566412 original size:29 final size:29
Alignment explanation
Indices: 9566376--9566435 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
9566366 CAGAAAATAC
9566376 AAAAGACATAATAGTGAAATGTGAAATTA
1 AAAAGACATAATAGTGAAATGTGAAATTA
9566405 AAAAGACATAATAGTGAAATGTGAAATTA
1 AAAAGACATAATAGTGAAATGTGAAATTA
9566434 AA
1 AA
9566436 TTTATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.57, C:0.03, G:0.17, T:0.23
Consensus pattern (29 bp):
AAAAGACATAATAGTGAAATGTGAAATTA
Found at i:9566706 original size:18 final size:18
Alignment explanation
Indices: 9566683--9566720 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
9566673 ATAGGTGTCT
*
9566683 TTAATTTTGTCCCAAAAA
1 TTAATTTTGGCCCAAAAA
9566701 TTAATTTTGGCCCAAAAA
1 TTAATTTTGGCCCAAAAA
9566719 TT
1 TT
9566721 TTAGTGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (18 bp):
TTAATTTTGGCCCAAAAA
Found at i:9567708 original size:125 final size:126
Alignment explanation
Indices: 9567481--9567740 Score: 504
Period size: 125 Copynumber: 2.1 Consensus size: 126
9567471 TGAGATGATT
9567481 TAAAGTGTTCGGAACTCATAATTGGAAATAACTTGTTGTAGAGGAAAAAGAAAAGTTACAGATTA
1 TAAA-TGTTCGGAACTCATAATTGGAAATAACTTGTTGTAGAGGAAAAAGAAAAGTTACAGATTA
9567546 GTCCTTGACACTCGTACTATTATTGTTTGTGCCTAGTAAGTTCATACAGTTTTTAAT-ATTA
65 GTCCTTGACACTCGTACTATTATTGTTTGTGCCTAGTAAGTTCATACAGTTTTTAATCATTA
9567607 TAAATGTTCGGAACTCATAATTGGAAATAACTTGTTGTAGAGGAAAAAGAAAAGTTACAGATTAG
1 TAAATGTTCGGAACTCATAATTGGAAATAACTTGTTGTAGAGGAAAAAGAAAAGTTACAGATTAG
9567672 TCCTTGACACTCGTACTATTATTGTTTGTGCCTAGTAAGTTCATACAGTTTTTAATCATTA
66 TCCTTGACACTCGTACTATTATTGTTTGTGCCTAGTAAGTTCATACAGTTTTTAATCATTA
9567733 TAAATGTT
1 TAAATGTT
9567741 GATTAATTGT
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
125 117 0.88
126 16 0.12
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (126 bp):
TAAATGTTCGGAACTCATAATTGGAAATAACTTGTTGTAGAGGAAAAAGAAAAGTTACAGATTAG
TCCTTGACACTCGTACTATTATTGTTTGTGCCTAGTAAGTTCATACAGTTTTTAATCATTA
Found at i:9568047 original size:20 final size:20
Alignment explanation
Indices: 9567990--9568047 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
9567980 TTCGTACTCT
*
9567990 TATTAGCACTACGGTGCTCC
1 TATTAGCACTACGGTGCTCA
* **
9568010 TAATAGCAC-ATCCATGCTCA
1 TATTAGCACTA-CGGTGCTCA
*
9568030 TGTTAGCACTACGGTGCT
1 TATTAGCACTACGGTGCT
9568048 TTTGATGGCA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (20 bp):
TATTAGCACTACGGTGCTCA
Found at i:9575124 original size:18 final size:17
Alignment explanation
Indices: 9575094--9575127 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9575084 TGTTTAATGG
9575094 TAAAGAACGAAATGGAC
1 TAAAGAACGAAATGGAC
*
9575111 TAAATGAACTAAATGGA
1 TAAA-GAACGAAATGGA
9575128 AATGTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (17 bp):
TAAAGAACGAAATGGAC
Found at i:9576578 original size:28 final size:28
Alignment explanation
Indices: 9576538--9576601 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
9576528 TGCTATTTTA
9576538 TTAGTTTAAGAAACCCTAAAAGTATCTC
1 TTAGTTTAAGAAACCCTAAAAGTATCTC
9576566 TTAGTTTAAGAAACCCTAAAAGTATCTC
1 TTAGTTTAAGAAACCCTAAAAGTATCTC
*
9576594 TTATTTTA
1 TTAGTTTA
9576602 CTTTCCTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (28 bp):
TTAGTTTAAGAAACCCTAAAAGTATCTC
Found at i:9577180 original size:13 final size:13
Alignment explanation
Indices: 9577162--9577275 Score: 52
Period size: 13 Copynumber: 8.7 Consensus size: 13
9577152 TAAATGTGTA
9577162 ATATGAAATGATT
1 ATATGAAATGATT
* * *
9577175 ATATGAGACGGTT
1 ATATGAAATGATT
* *
9577188 ATACG-AATGGTT
1 ATATGAAATGATT
* *
9577200 ATATAAAATGAAT
1 ATATGAAATGATT
*
9577213 ATATGAAAGGATT
1 ATATGAAATGATT
* * *
9577226 GTTTG-AATCAATT
1 ATATGAAAT-GATT
*
9577239 ATATGGAAATAATT
1 ATAT-GAAATGATT
* *
9577253 ATATAAAACTGTTT
1 ATATGAAA-TGATT
*
9577267 ATACGAAAT
1 ATATGAAAT
9577276 TTTTATATGG
Statistics
Matches: 72, Mismatches: 24, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
12 10 0.14
13 41 0.57
14 18 0.25
15 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (13 bp):
ATATGAAATGATT
Found at i:9592593 original size:21 final size:21
Alignment explanation
Indices: 9592569--9592610 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9592559 ATTTTCAAAT
*
9592569 TAATTGCACATTGATTTGTAA
1 TAATTGCACATTAATTTGTAA
*
9592590 TAATTGCATATTAATTTGTAA
1 TAATTGCACATTAATTTGTAA
9592611 ATTTTTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (21 bp):
TAATTGCACATTAATTTGTAA
Found at i:9596539 original size:21 final size:22
Alignment explanation
Indices: 9596505--9596558 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
9596495 ATATGTGGAT
*
9596505 TATAAAAATA-ACATAAAATAA
1 TATATAAATATACATAAAATAA
***
9596526 TATAT-AATATACATATTTTAA
1 TATATAAATATACATAAAATAA
9596547 TATATAAATATA
1 TATATAAATATA
9596559 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAATATACATAAAATAA
Found at i:9596752 original size:21 final size:21
Alignment explanation
Indices: 9596720--9596760 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9596710 AATAAAAACC
9596720 TAACAATAATAACAAA-AATAT
1 TAACAATAATAA-AAATAATAT
9596741 TAACGAAT-ATAAAAATAATA
1 TAAC-AATAATAAAAATAATA
9596761 ATAGTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.17
21 12 0.67
22 3 0.17
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
TAACAATAATAAAAATAATAT
Found at i:9596762 original size:3 final size:3
Alignment explanation
Indices: 9596749--9596797 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
9596739 ATTAACGAAT
* * *
9596749 ATA AAA ATA ATA ATA GTA A-A GACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
9596794 ATA A
1 ATA A
9596798 ATTGACCAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:9598607 original size:44 final size:43
Alignment explanation
Indices: 9598535--9598831 Score: 234
Period size: 44 Copynumber: 6.9 Consensus size: 43
9598525 AGATAAGATC
* * * *
9598535 CTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACTAT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACT-T
*
9598579 CTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTT
* * * * *
9598625 CTTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGAC-G
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGA--TTACTT
* ** * *
9598669 C---GATCTACTCTGCTGTAA-CTTCAGAGAGGTAAGA-T-C--
1 CTTTGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACTT
* * *
9598705 CTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACT-T
*
9598749 CTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTT
* * *
9598795 CTTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGA
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
9598832 CCTGACGCGA
Statistics
Matches: 200, Mismatches: 35, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
36 1 0.00
37 1 0.00
39 23 0.12
40 3 0.01
41 25 0.12
44 68 0.34
45 4 0.02
46 68 0.34
47 6 0.03
48 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (43 bp):
CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTT
Found at i:9598646 original size:46 final size:43
Alignment explanation
Indices: 9598544--9598831 Score: 232
Period size: 46 Copynumber: 6.7 Consensus size: 43
9598534 CCTTTAATCC
* * *
9598544 GCTCCACTGTAATCTCAGGGAAATAGGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTCGATCT
* *
9598588 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTTCTTCGATCT
* * * *
9598634 GCTCCACTGTAATCTCAGGGAAATAAGA--CCTGAC-GCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTCGATCT
* ** * * ** *
9598675 ACTCTGCTGTAA-CTTCAGAGAGGTAAGA-T-C--CTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTCGATCT
* *
9598714 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTCGATCT
* *
9598758 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTTCTTCGATCT
*
9598804 GCTCCACTGTAATCTCAGGGAAATAAGA
1 GCTCCACTGTAATCTCAGGGAGATAAGA
9598832 CCTGACGCGA
Statistics
Matches: 193, Mismatches: 35, Indels: 30
0.75 0.14 0.12
Matches are distributed among these distances:
38 1 0.01
39 23 0.12
40 3 0.02
41 29 0.15
42 1 0.01
44 60 0.31
45 2 0.01
46 68 0.35
47 6 0.03
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (43 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTCGATCT
Found at i:9598704 original size:170 final size:170
Alignment explanation
Indices: 9598414--9598877 Score: 838
Period size: 170 Copynumber: 2.7 Consensus size: 170
9598404 ACTGGCTTCA
* * * * * *
9598414 ATCTGCTCCGCTGTAATCTCAGGGAGATAAAATTTGAAATTCTTCGGTCTGTTCCACTGTAACCT
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCT
* *
9598479 CAAGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCATAGAGATAAGATCCTTTAATCC
66 CAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTAATCC
9598544 GCTCCACTGTAATCTCAGGGAAATAGGATTACTATCTTTG
131 GCTCCACTGTAATCTCAGGGAAATAGGATTACTATCTTTG
9598584 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCT
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCT
*
9598649 CAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGGTAAGATCCTTTAATCC
66 CAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTAATCC
*
9598714 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTG
131 GCTCCACTGTAATCTCAGGGAAATAGGATTACTATCTTTG
9598754 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCT
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCT
9598819 CAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTT
66 CAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTT
9598878 NNNNNNNNNN
Statistics
Matches: 283, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 283 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (170 bp):
ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCT
CAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTAATCC
GCTCCACTGTAATCTCAGGGAAATAGGATTACTATCTTTG
Found at i:9610091 original size:102 final size:102
Alignment explanation
Indices: 9609905--9610105 Score: 248
Period size: 101 Copynumber: 2.0 Consensus size: 102
9609895 ACAGACTGAG
** *
9609905 CAATTATAAACCACAATGATGAAAGTTATAATGAAGAATGAAATGCCATGAAAGGATCGTAAATT
1 CAATTATAAACCACAACAATGAAAGTTATAA-GAAGAATGAAATGCAATGAAAGGATC-TAAATT
9609970 TAAAACCAAATTTTCAATTTTCGACAAAAAGACAACACAA
64 TAAAACCAAATTTTCAA-TTTCGACAAAAAGACAACACAA
* *
9610010 CAATTATAAACCACAACAATGACAA-TTAT-A-ACGAATGAAATGCAATGAAAGGAT-TATATCT
1 CAATTATAAACCACAACAATGA-AAGTTATAAGAAGAATGAAATGCAATGAAAGGATCTAAAT-T
* * *
9610071 TTAAATCAAGTTTTCAAATTTCGACAAAAAGACAA
64 TAAAACCAAATTTTC-AATTTCGACAAAAAGACAA
9610106 AAAGTAATCA
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
100 4 0.05
101 30 0.35
102 24 0.28
104 1 0.01
105 24 0.28
106 2 0.02
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.25
Consensus pattern (102 bp):
CAATTATAAACCACAACAATGAAAGTTATAAGAAGAATGAAATGCAATGAAAGGATCTAAATTTA
AAACCAAATTTTCAATTTCGACAAAAAGACAACACAA
Found at i:9611161 original size:21 final size:22
Alignment explanation
Indices: 9611127--9611180 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
9611117 ATATGTGGAT
*
9611127 TATAAAAATA-ACATAAAATAA
1 TATATAAATATACATAAAATAA
***
9611148 TATAT-AATATACATATTTTAA
1 TATATAAATATACATAAAATAA
9611169 TATATAAATATA
1 TATATAAATATA
9611181 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAATATACATAAAATAA
Found at i:9611374 original size:21 final size:21
Alignment explanation
Indices: 9611342--9611382 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9611332 AATAAAAACC
9611342 TAACAATAATAACAAA-AATAT
1 TAACAATAATAA-AAATAATAT
9611363 TAACGAAT-ATAAAAATAATA
1 TAAC-AATAATAAAAATAATA
9611383 ATAGTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.17
21 12 0.67
22 3 0.17
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
TAACAATAATAAAAATAATAT
Found at i:9611397 original size:18 final size:18
Alignment explanation
Indices: 9611371--9611421 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
9611361 ATTAACGAAT
*
9611371 ATAAAAATAATAATAGTA
1 ATAACAATAATAATAGTA
*
9611389 A-AGACAATAATAGTAGTA
1 ATA-ACAATAATAATAGTA
*
9611407 ATAATAATAATAATA
1 ATAACAATAATAATA
9611422 AATTGACCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (18 bp):
ATAACAATAATAATAGTA
Found at i:9640845 original size:13 final size:13
Alignment explanation
Indices: 9640829--9640861 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
9640819 TTTAAACCAA
9640829 ACTTTTCACAAAT-
1 ACTTTTCA-AAATC
9640842 ACTTTTCAAAATC
1 ACTTTTCAAAATC
9640855 ACTTTTC
1 ACTTTTC
9640862 TACAGGACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.42
Consensus pattern (13 bp):
ACTTTTCAAAATC
Found at i:9641361 original size:20 final size:20
Alignment explanation
Indices: 9641315--9641361 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
9641305 TGCTAAACAT
* *
9641315 TAATTT-AATTAAGTTTAAT
1 TAATTTAAATTAAGATTAAG
9641334 TAGA-TTAAATTAAGATTAAG
1 TA-ATTTAAATTAAGATTAAG
9641354 TAATTTAA
1 TAATTTAA
9641362 TTATAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (20 bp):
TAATTTAAATTAAGATTAAG
Found at i:9649694 original size:20 final size:20
Alignment explanation
Indices: 9649669--9649710 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
9649659 TCGGTGCCGC
9649669 CATCTGACAATCTGCACAAA
1 CATCTGACAATCTGCACAAA
9649689 CATCTGACAATCTGCACAAA
1 CATCTGACAATCTGCACAAA
9649709 CA
1 CA
9649711 CTGTGCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.31, G:0.10, T:0.19
Consensus pattern (20 bp):
CATCTGACAATCTGCACAAA
Found at i:9650634 original size:20 final size:22
Alignment explanation
Indices: 9650611--9650653 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9650601 AAACCCGAAT
*
9650611 TTAACTCAA-AAAA-ATAAAAA
1 TTAAATCAACAAAAGATAAAAA
*
9650631 TTAAATTAACAAAAGATAAAAA
1 TTAAATCAACAAAAGATAAAAA
9650653 T
1 T
9650654 ATTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (22 bp):
TTAAATCAACAAAAGATAAAAA
Found at i:9652942 original size:19 final size:19
Alignment explanation
Indices: 9652905--9652942 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9652895 AAGCACCATC
*
9652905 ATAAAATTATAGTTTTTTA
1 ATAAAATTATAGTTATTTA
9652924 ATAAAATTAT-GATTATTTA
1 ATAAAATTATAG-TTATTTA
9652943 TAATAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
ATAAAATTATAGTTATTTA
Found at i:9654859 original size:30 final size:30
Alignment explanation
Indices: 9654797--9654860 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
9654787 TATTATATTT
*
9654797 AAATAAGTCTTTAAATTTTAATTAGTACTC
1 AAATAAGTCTTTAAATTTTAATTAGCACTC
* *
9654827 AAATAAGTTTTTAAATTTTAAGTTA-CATTC
1 AAATAAGTCTTTAAATTTTAA-TTAGCACTC
9654857 AAAT
1 AAAT
9654861 TATAAGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (30 bp):
AAATAAGTCTTTAAATTTTAATTAGCACTC
Found at i:9667886 original size:18 final size:18
Alignment explanation
Indices: 9667865--9667922 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
9667855 AATGCAAAGA
9667865 TTAATAAAAATAAATAAT
1 TTAATAAAAATAAATAAT
*
9667883 TTAATAATATATAAA-AA-
1 TTAATAA-AAATAAATAAT
** *
9667900 TTGGTAAAAATCAATAAT
1 TTAATAAAAATAAATAAT
9667918 TTAAT
1 TTAAT
9667923 CATTTATATG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 5 0.17
17 7 0.23
18 12 0.40
19 6 0.20
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (18 bp):
TTAATAAAAATAAATAAT
Found at i:9671342 original size:17 final size:16
Alignment explanation
Indices: 9671320--9671352 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
9671310 TGAAAGATTG
9671320 ATGTAAATATATGTTAA
1 ATGTAAATATAT-TTAA
9671337 ATGTAAATATATTTAA
1 ATGTAAATATATTTAA
9671353 TTTTTTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (16 bp):
ATGTAAATATATTTAA
Found at i:9671631 original size:20 final size:20
Alignment explanation
Indices: 9671593--9671644 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
9671583 TTTCTCTTCC
*
9671593 AATTATAAAAAAATAAAAA-
1 AATTATAAAAATATAAAAAG
*
9671612 AATTATTAAAAATATGAAAAG
1 AATTA-TAAAAATATAAAAAG
*
9671633 AGTTATAAAAAT
1 AATTATAAAAAT
9671645 TAATGGCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.18
20 19 0.68
21 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AATTATAAAAATATAAAAAG
Found at i:9679842 original size:31 final size:31
Alignment explanation
Indices: 9679807--9679868 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
9679797 GCAATAAGAA
9679807 AGAACCAGTATATTGATTCATTGTGCTTACT
1 AGAACCAGTATATTGATTCATTGTGCTTACT
9679838 AGAACCAGTATATTGATTCATTGTGCTTACT
1 AGAACCAGTATATTGATTCATTGTGCTTACT
9679869 CAGAGGAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
AGAACCAGTATATTGATTCATTGTGCTTACT
Found at i:9682538 original size:29 final size:29
Alignment explanation
Indices: 9682480--9682538 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
9682470 TGGGCAACAG
* * * *
9682480 AAAATAGTTTAGGTATCACTTGTGACAAA
1 AAAAAAGTTTAGGTATAACTAGGGACAAA
9682509 AAAAAAGTTTAGGTACTAACTAGGGA-AAA
1 AAAAAAGTTTAGGTA-TAACTAGGGACAAA
9682538 A
1 A
9682539 TGGTATAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (29 bp):
AAAAAAGTTTAGGTATAACTAGGGACAAA
Found at i:9683534 original size:8 final size:8
Alignment explanation
Indices: 9683521--9683545 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9683511 ATTGGACAAC
9683521 AAAATTTT
1 AAAATTTT
9683529 AAAATTTT
1 AAAATTTT
9683537 AAAATTTT
1 AAAATTTT
9683545 A
1 A
9683546 TAATATAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAAATTTT
Found at i:9685537 original size:11 final size:11
Alignment explanation
Indices: 9685521--9685550 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
9685511 ATTGACCCAT
9685521 ATACAGAAATC
1 ATACAGAAATC
9685532 ATACAGAAATC
1 ATACAGAAATC
9685543 ATACAGAA
1 ATACAGAA
9685551 CATGCTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.10, T:0.17
Consensus pattern (11 bp):
ATACAGAAATC
Found at i:9695019 original size:25 final size:24
Alignment explanation
Indices: 9694991--9695068 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 24
9694981 ATGCTTATAC
*
9694991 GAGCACATAAACGGGAAGCTCATGT
1 GAGC-CATAAACGGGAAGCTCATGA
* * * *
9695016 GAGCCATGTAACGGAAAGCTTATAA
1 GAGCCAT-AAACGGGAAGCTCATGA
* * *
9695041 GAGTCATAATCGGGAAGCTCATGC
1 GAGCCATAAACGGGAAGCTCATGA
9695065 GAGC
1 GAGC
9695069 TAATATTAAG
Statistics
Matches: 39, Mismatches: 13, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
24 17 0.44
25 22 0.56
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (24 bp):
GAGCCATAAACGGGAAGCTCATGA
Found at i:9696002 original size:15 final size:16
Alignment explanation
Indices: 9695982--9696013 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9695972 CCATGGAAAA
9695982 ACCCT-ATACTTTGAT
1 ACCCTAATACTTTGAT
9695997 ACCCTAATACTTTGAT
1 ACCCTAATACTTTGAT
9696013 A
1 A
9696014 ACTTTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
ACCCTAATACTTTGAT
Found at i:9699635 original size:4 final size:4
Alignment explanation
Indices: 9699626--9699657 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
9699616 CATAATAATA
9699626 AAAT AAAT AAAT AAAT AAAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAA
9699658 GAGGGAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:9699644 original size:17 final size:17
Alignment explanation
Indices: 9699622--9699657 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
9699612 TAGGCATAAT
9699622 AATAAAATAAATAAATA
1 AATAAAATAAATAAATA
9699639 AATAAAATAAATAAATA
1 AATAAAATAAATAAATA
9699656 AA
1 AA
9699658 GAGGGAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAAATAAATAAATA
Found at i:9700615 original size:12 final size:12
Alignment explanation
Indices: 9700588--9700630 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
9700578 TTATTTCAAA
9700588 AAAAG-AAAAAC
1 AAAAGAAAAAAC
9700599 AAAAGAAGAAAAC
1 AAAAGAA-AAAAC
*
9700612 -AAAGAAAAAAG
1 AAAAGAAAAAAC
9700623 AAAAGAAA
1 AAAAGAAA
9700631 TTGTGAACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAC
Found at i:9703330 original size:31 final size:31
Alignment explanation
Indices: 9703292--9703385 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
9703282 TAAATAGTGA
**
9703292 AAACCATCATTGTTGGGCAATCCAGGGTGGT
1 AAACCATCATTGTAAGGCAATCCAGGGTGGT
* *
9703323 AAACCATCATTGTAAGGCAATCCGGGGTCGT
1 AAACCATCATTGTAAGGCAATCCAGGGTGGT
*** * *
9703354 ATGTCATCATTGCTAA-TCAATCCAGGATGGT
1 AAACCATCATTG-TAAGGCAATCCAGGGTGGT
9703385 A
1 A
9703386 GAATTGAATG
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 48 0.94
32 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (31 bp):
AAACCATCATTGTAAGGCAATCCAGGGTGGT
Found at i:9703550 original size:31 final size:31
Alignment explanation
Indices: 9703478--9703537 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
9703468 AATGAAAAAA
* * *
9703478 CCATCATAGCCGGGCAATCTAGGGTGGTAAG
1 CCATCATTGCCAGGCAATCTAGGGTAGTAAG
9703509 CCATCATTGCCAGGCAATCTAGGGTAGTA
1 CCATCATTGCCAGGCAATCTAGGGTAGTA
9703538 GATCATCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (31 bp):
CCATCATTGCCAGGCAATCTAGGGTAGTAAG
Found at i:9703557 original size:31 final size:31
Alignment explanation
Indices: 9703478--9703562 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
9703468 AATGAAAAAA
* * *
9703478 CCATCATAGCCGGGCAATCTAGGGTGGTAAG
1 CCATCATTGCCGAGCAATCTAGGGTAGTAAG
9703509 CCATCATTGCC-AGGCAATCTAGGGTAGT-AG
1 CCATCATTGCCGA-GCAATCTAGGGTAGTAAG
* * *
9703539 ATCATCGTTGCCGAGCAATATAGG
1 -CCATCATTGCCGAGCAATCTAGG
9703563 ATGACAGATA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 2 0.04
31 42 0.93
32 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (31 bp):
CCATCATTGCCGAGCAATCTAGGGTAGTAAG
Found at i:9717675 original size:27 final size:27
Alignment explanation
Indices: 9717631--9717724 Score: 134
Period size: 27 Copynumber: 3.5 Consensus size: 27
9717621 CTTGTCAGCT
* * * *
9717631 TTTGTGGCATACTCTGAAAGAATTGCC
1 TTTGTGGCGTACTATGAATGAATCGCC
*
9717658 TTTGTGGCGTATTATGAATGAATCGCC
1 TTTGTGGCGTACTATGAATGAATCGCC
9717685 TTTGTGGCGTACTATGAATGAATCGCC
1 TTTGTGGCGTACTATGAATGAATCGCC
*
9717712 TTTGTGGCATACT
1 TTTGTGGCGTACT
9717725 CTATATAGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (27 bp):
TTTGTGGCGTACTATGAATGAATCGCC
Found at i:9718298 original size:28 final size:28
Alignment explanation
Indices: 9718265--9718321 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
9718255 ATGTCTAAAG
9718265 ATAAAATTAATGGTATCTAGTTCTACAT
1 ATAAAATTAATGGTATCTAGTTCTACAT
9718293 ATAAAATTAATGGTATCTAGTTCTACAT
1 ATAAAATTAATGGTATCTAGTTCTACAT
9718321 A
1 A
9718322 GGTATTTGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (28 bp):
ATAAAATTAATGGTATCTAGTTCTACAT
Found at i:9729963 original size:5 final size:5
Alignment explanation
Indices: 9729953--9729979 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9729943 TTATCTTAAT
9729953 ATTTA ATTTA ATTTA ATTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT
9729980 GTTTATCTTG
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:9736895 original size:43 final size:44
Alignment explanation
Indices: 9736776--9736924 Score: 125
Period size: 42 Copynumber: 3.5 Consensus size: 44
9736766 CCGTTACTCG
* * *
9736776 GTGGATTCAGCACTTAGCAACTACC-TTAAATTC-AGTGATTAC
1 GTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAAGTGATTAC
* * * *
9736818 GGGGAATCAGCACATAACAACC-CCTTTCACAGTCAAG-GA-TAC
1 GTGGAATCAGCACTTAGCAACCACCTTT-AAAGTCAAGTGATTAC
* *
9736860 GATGGAATCAGCACTTAGTAACCACCTTTAAAGTCAA-TAATT-C
1 G-TGGAATCAGCACTTAGCAACCACCTTTAAAGTCAAGTGATTAC
*
9736903 AG-GTAATCAGCACTTAGCAACC
1 -GTGGAATCAGCACTTAGCAACC
9736925 CCTCGAGAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
41 2 0.02
42 41 0.49
43 32 0.38
44 9 0.11
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (44 bp):
GTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAAGTGATTAC
Found at i:9753900 original size:6 final size:6
Alignment explanation
Indices: 9753891--9753922 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
9753881 TCTTCGTCTT
9753891 CATCTC CATCTC CATCTC CATCTC CATCTC CA
1 CATCTC CATCTC CATCTC CATCTC CATCTC CA
9753923 CTTCCACTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.00, T:0.31
Consensus pattern (6 bp):
CATCTC
Found at i:9758795 original size:20 final size:20
Alignment explanation
Indices: 9758770--9758808 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
9758760 AACTTTCTTC
9758770 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
9758790 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
9758809 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:9759136 original size:50 final size:50
Alignment explanation
Indices: 9759073--9759205 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
9759063 AAATGTCATA
* * ** * *
9759073 TCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTGCCAACGCCATG
* * *
9759123 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTGCCAACGCCATG
*
9759173 TCCCAGACATGGTCTTACGTGGA-ACCTCTCATA
1 TCCCAGACATGGTCTTAC-AGGAGACCTCTCATA
9759206 ACCTCAATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
50 68 0.97
51 2 0.03
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTGCCAACGCCATG
Found at i:9763133 original size:9 final size:9
Alignment explanation
Indices: 9763119--9763146 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
9763109 TGCAACTGAG
9763119 CTTTCAATT
1 CTTTCAATT
9763128 CTTTCAATT
1 CTTTCAATT
9763137 CTTTCAATT
1 CTTTCAATT
9763146 C
1 C
9763147 CAACGGGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (9 bp):
CTTTCAATT
Found at i:9766461 original size:20 final size:20
Alignment explanation
Indices: 9766436--9766474 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
9766426 TACTTTCTTC
9766436 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
9766456 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
9766475 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:9770468 original size:12 final size:13
Alignment explanation
Indices: 9770436--9770473 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
9770426 CAAAGAAAGG
*
9770436 ATAGAAAAAGAGA
1 ATAGAAACAGAGA
9770449 ATAGAAACAGAGA
1 ATAGAAACAGAGA
9770462 A-AGAAACAGAGA
1 ATAGAAACAGAGA
9770474 GCAAAACGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.66, C:0.05, G:0.24, T:0.05
Consensus pattern (13 bp):
ATAGAAACAGAGA
Found at i:9771126 original size:24 final size:24
Alignment explanation
Indices: 9771094--9771418 Score: 557
Period size: 24 Copynumber: 13.5 Consensus size: 24
9771084 ACTTTAGCGC
9771094 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771118 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771142 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771166 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771190 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771214 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771238 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771262 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771286 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
9771311 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
9771335 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
***
9771360 GCTCTCTGATATTTAGCACGCCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* *
9771385 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
9771407 GCTCTCTG-TATT
1 GCTCTCTGATATT
9771419 TGTTCCGTAT
Statistics
Matches: 290, Mismatches: 7, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
22 18 0.06
23 2 0.01
24 204 0.70
25 66 0.23
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:9778663 original size:51 final size:51
Alignment explanation
Indices: 9778602--9778708 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
9778592 AGAAATGATG
* * * *
9778602 AAATAGAGAAATAGGAA-CATTTCGAAATGATTATGATTTTCTCCAAAATGA
1 AAATGGAGAAAT-GAAATCATTTCGAAATAAATATGATTTTCTCCAAAATGA
* * *
9778653 AAATGGAGAAATGAAATCATTTGGAAATAAATGTGGTTTTCTCCAAAATGA
1 AAATGGAGAAATGAAATCATTTCGAAATAAATATGATTTTCTCCAAAATGA
9778704 AAATG
1 AAATG
9778709 AAAATGGCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 3 0.06
51 45 0.94
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (51 bp):
AAATGGAGAAATGAAATCATTTCGAAATAAATATGATTTTCTCCAAAATGA
Found at i:9784462 original size:57 final size:57
Alignment explanation
Indices: 9784400--9784517 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 57
9784390 AGAAATGATG
* * *
9784400 AAATAGAGAAATAGGAA-CATTTGGAAATGATTATGATTTTCTCCAAAATGAAAATGA
1 AAATAGAGAAA-AGAAATCATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGA
* * *
9784457 AAATAGAGAAACGAAATCATTTGAAAATGAATGTGGTTTTCTCCAAAATGAAAATGA
1 AAATAGAGAAAAGAAATCATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGA
9784514 AAAT
1 AAAT
9784518 GGCCTGAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 3 0.06
57 51 0.94
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (57 bp):
AAATAGAGAAAAGAAATCATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGA
Found at i:9788122 original size:20 final size:20
Alignment explanation
Indices: 9788097--9788140 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
9788087 AGAAGCATTA
9788097 GGACTTTAATGGTTTAATGT
1 GGACTTTAATGGTTTAATGT
9788117 GGACTTTAATGGTTTAATGT
1 GGACTTTAATGGTTTAATGT
9788137 GGAC
1 GGAC
9788141 ATGGCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (20 bp):
GGACTTTAATGGTTTAATGT
Found at i:9788993 original size:2 final size:2
Alignment explanation
Indices: 9788986--9789018 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9788976 TGCGTGGAGG
*
9788986 TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9789019 TTGTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9793053 original size:57 final size:57
Alignment explanation
Indices: 9792966--9793084 Score: 220
Period size: 57 Copynumber: 2.1 Consensus size: 57
9792956 TGATATGGAG
*
9792966 TTATTTTATTCAAACGATTCAAAATCCCTAGTAGTTGGCTATACTGATACTGGAAAT
1 TTATTTTATTCAAACGATTCAAAATCCCTAGTAGTCGGCTATACTGATACTGGAAAT
*
9793023 TTATTTTATTCAAATGATTCAAAATCCCTAGTAGTCGGCTATACTGATACTGGAAAT
1 TTATTTTATTCAAACGATTCAAAATCCCTAGTAGTCGGCTATACTGATACTGGAAAT
9793080 TTATT
1 TTATT
9793085 GAATCCACAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (57 bp):
TTATTTTATTCAAACGATTCAAAATCCCTAGTAGTCGGCTATACTGATACTGGAAAT
Found at i:9800240 original size:41 final size:41
Alignment explanation
Indices: 9800190--9800295 Score: 169
Period size: 41 Copynumber: 2.6 Consensus size: 41
9800180 CAGACTTTAC
*
9800190 GTCTAGCAGGCTAAGTGCCAGTGATCTGAAACAGGCTATAA
1 GTCTAGCAGGCTAAGTGCCGGTGATCTGAAACAGGCTATAA
*
9800231 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
1 GTCTAGCAGGCTAAGTGCCGGTGATCTGAAACAGGCTATAA
*
9800272 G-CTTAGCAGGTTAAGTGCCGGTGA
1 GTC-TAGCAGGCTAAGTGCCGGTGA
9800296 ATATGTTAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.02
41 60 0.98
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (41 bp):
GTCTAGCAGGCTAAGTGCCGGTGATCTGAAACAGGCTATAA
Found at i:9801216 original size:11 final size:11
Alignment explanation
Indices: 9801202--9801258 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
9801192 ATATCCAAAT
9801202 AATAATAACAA
1 AATAATAACAA
*
9801213 AATATTAACAA
1 AATAATAACAA
*
9801224 TATAATAACAA
1 AATAATAACAA
* *
9801235 AATGATAGCAA
1 AATAATAACAA
* *
9801246 AACAACAACAA
1 AATAATAACAA
9801257 AA
1 AA
9801259 CAACTTATTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.67, C:0.12, G:0.04, T:0.18
Consensus pattern (11 bp):
AATAATAACAA
Found at i:9803375 original size:58 final size:58
Alignment explanation
Indices: 9803292--9803495 Score: 263
Period size: 52 Copynumber: 3.7 Consensus size: 58
9803282 CATTTCCGAG
* **
9803292 TCATTTTCATTT-GGAGAAAACCACATTCGTTTTCAAATGTCCCCTATTTCTCCATTT
1 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
9803349 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTA----T--ATTT
1 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
*
9803401 TCATTTTCATTTGGGATAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
1 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
* *
9803459 TCA---T--TTT-GGAAAAAACCACATCCATTTTCAAATGTTT
1 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTT
9803496 TTCATTTCTT
Statistics
Matches: 134, Mismatches: 6, Indels: 19
0.84 0.04 0.12
Matches are distributed among these distances:
52 78 0.58
53 3 0.02
54 1 0.01
55 1 0.01
56 1 0.01
57 12 0.09
58 38 0.28
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (58 bp):
TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
Found at i:9803511 original size:110 final size:106
Alignment explanation
Indices: 9803292--9803495 Score: 297
Period size: 110 Copynumber: 1.9 Consensus size: 106
9803282 CATTTCCGAG
*
9803292 TCATTTTCATTTGGAGAAAACCACATTCGTTTTCAAATGTCCCCTATTTCTCCATTTTCATTTTC
1 TCATTTTCATTTGGAGAAAACCACATTCATTTTCAAATGTCCCCTATTTCTCCATTTTCA--TT-
* *
9803357 ATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATATTT
63 ATTTGGGAAAAAACCACATCCATTTTCAAATGTTTCCTATATTT
* **
9803401 TCATTTTCATTTGGGATAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTTTCA-T-T
1 TCATTTTCATTT-GGAGAAAACCACATTCATTTTCAAATGTCCCCTATTTCTCCATTTTCATTAT
9803464 TT-GGAAAAAACCACATCCATTTTCAAATGTTT
65 TTGGGAAAAAACCACATCCATTTTCAAATGTTT
9803496 TTCATTTCTT
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
104 28 0.32
105 3 0.03
107 1 0.01
109 12 0.14
110 44 0.50
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (106 bp):
TCATTTTCATTTGGAGAAAACCACATTCATTTTCAAATGTCCCCTATTTCTCCATTTTCATTATT
TGGGAAAAAACCACATCCATTTTCAAATGTTTCCTATATTT
Found at i:9804428 original size:33 final size:33
Alignment explanation
Indices: 9804391--9804458 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
9804381 CGGACATGTT
9804391 TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
1 TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
9804424 TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
1 TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
9804457 TA
1 TA
9804459 TCACGATCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.43
Consensus pattern (33 bp):
TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
Found at i:9807753 original size:12 final size:12
Alignment explanation
Indices: 9807736--9807761 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9807726 CTATTGAGTC
9807736 TAGGTCAACAAT
1 TAGGTCAACAAT
9807748 TAGGTCAACAAT
1 TAGGTCAACAAT
9807760 TA
1 TA
9807762 TGGATGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (12 bp):
TAGGTCAACAAT
Found at i:9820189 original size:8 final size:8
Alignment explanation
Indices: 9820176--9820202 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
9820166 AGTATATTCG
9820176 TTTGTAAA
1 TTTGTAAA
9820184 TTTGTAAA
1 TTTGTAAA
9820192 TTTGTAAA
1 TTTGTAAA
9820200 TTT
1 TTT
9820203 TTTTGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (8 bp):
TTTGTAAA
Found at i:9820487 original size:169 final size:170
Alignment explanation
Indices: 9820183--9820493 Score: 536
Period size: 170 Copynumber: 1.8 Consensus size: 170
9820173 TCGTTTGTAA
* * *
9820183 ATTTGTAAATTTGTAAATTTTTTTGAAAAAATTGTTTTATTAACCAATGTAACAATCAATGAATT
1 ATTTGTAAACTTGTAAACTTTTTCGAAAAAATTGTTTTATTAACCAATGTAACAATCAATGAATT
* *
9820248 TATTTTATTAACCAATCTGTTCAAAAAAAATTACAAGTTTACAGATGAATACACTACACTTAGGG
66 TATTTTATTAACCAATCTGTTCAAAAAAAATTACAAGTTTACAGACGAATACACTACACTCAGGG
9820313 CATTAGATCCAACACTCAGGGCTCTGAGTGTAGTATATTC
131 CATTAGATCCAACACTCAGGGCTCTGAGTGTAGTATATTC
*
9820353 ATTTGTAAACTTGT-AACTTTTTCGAAAAAAATTGTTTTATTAACCAATGTCACAATCAATGAAT
1 ATTTGTAAACTTGTAAACTTTTTCG-AAAAAATTGTTTTATTAACCAATGTAACAATCAATGAAT
*
9820417 TTATTTTATTAACCAATCTGTTCAAAAAAAA-TACAAGTTTACAGACGAATATACTACACTCAGG
65 TTATTTTATTAACCAATCTGTTCAAAAAAAATTACAAGTTTACAGACGAATACACTACACTCAGG
9820481 GCATTAGATCCAA
130 GCATTAGATCCAA
9820494 TAGTCTTTCA
Statistics
Matches: 133, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
169 51 0.38
170 82 0.62
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.35
Consensus pattern (170 bp):
ATTTGTAAACTTGTAAACTTTTTCGAAAAAATTGTTTTATTAACCAATGTAACAATCAATGAATT
TATTTTATTAACCAATCTGTTCAAAAAAAATTACAAGTTTACAGACGAATACACTACACTCAGGG
CATTAGATCCAACACTCAGGGCTCTGAGTGTAGTATATTC
Found at i:9822242 original size:30 final size:33
Alignment explanation
Indices: 9822180--9822242 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 33
9822170 AGTTTTAGGG
* **
9822180 TTAGGTTTTCTTTTCTTTCTTTTTTATTTTAGA
1 TTAGGTTTTCTTCTCTTTCTTTTTTAGATTAGA
9822213 TTAGGTTTT-TTCT-TTTC-TTTTTAGATTAGA
1 TTAGGTTTTCTTCTCTTTCTTTTTTAGATTAGA
9822243 CTCTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 4 0.15
32 3 0.11
33 9 0.33
ACGTcount: A:0.14, C:0.08, G:0.11, T:0.67
Consensus pattern (33 bp):
TTAGGTTTTCTTCTCTTTCTTTTTTAGATTAGA
Found at i:9836069 original size:14 final size:15
Alignment explanation
Indices: 9836043--9836115 Score: 66
Period size: 14 Copynumber: 5.0 Consensus size: 15
9836033 TATAGAATAG
9836043 TATAGATTA-TGAAAC
1 TATAGA-TACTGAAAC
9836058 T-TAGATACTGAAAAC
1 TATAGATACTG-AAAC
*
9836073 TATAGATACTGATAC
1 TATAGATACTGAAAC
9836088 TATAG-TGAC-GAAAC
1 TATAGAT-ACTGAAAC
*
9836102 TTTAGA-ACTGAAAC
1 TATAGATACTGAAAC
9836116 ATTCTGAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.08
14 20 0.41
15 16 0.33
16 9 0.18
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (15 bp):
TATAGATACTGAAAC
Found at i:9836092 original size:15 final size:16
Alignment explanation
Indices: 9836054--9836084 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9836044 ATAGATTATG
9836054 AAACT-TAGATACTGA
1 AAACTATAGATACTGA
9836069 AAACTATAGATACTGA
1 AAACTATAGATACTGA
9836085 TACTATAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (16 bp):
AAACTATAGATACTGA
Found at i:9847939 original size:25 final size:25
Alignment explanation
Indices: 9847890--9847939 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
9847880 GGTTTTTTTA
*
9847890 TTATTTAATATTAACATAATTATTT
1 TTATTTAATATTAACATAATAATTT
*
9847915 TTATTTAAATATTAATATAA-AATTT
1 TTATTT-AATATTAACATAATAATTT
9847940 AAATTTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATTTAATATTAACATAATAATTT
Found at i:9852772 original size:13 final size:13
Alignment explanation
Indices: 9852754--9852779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9852744 ATTTTAACTG
9852754 TTTTCATTTCTAT
1 TTTTCATTTCTAT
9852767 TTTTCATTTCTAT
1 TTTTCATTTCTAT
9852780 AGATAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCATTTCTAT
Found at i:9861046 original size:43 final size:43
Alignment explanation
Indices: 9860980--9861105 Score: 143
Period size: 41 Copynumber: 3.0 Consensus size: 43
9860970 GGCTCGTACA
**
9860980 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTGAACACATATCG
1 ATGCCAATATCCCAGACAG-GGTCTTACATGTGAACACATATCG
* *
9861023 ATGCCACTATCCCAGACAGGGTCTTACA--TGAATCAAATA-CG
1 ATGCCAATATCCCAGACAGGGTCTTACATGTGAA-CACATATCG
* * *
9861064 ATGCCAATGTCCCAGACATGGTCTTACATGTAAACACATATC
1 ATGCCAATATCCCAGACAGGGTCTTACATGTGAACACATATC
9861106 AAAAATCCTA
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
41 31 0.45
42 10 0.14
43 27 0.39
44 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATATCCCAGACAGGGTCTTACATGTGAACACATATCG
Found at i:9861868 original size:10 final size:10
Alignment explanation
Indices: 9861855--9861883 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
9861845 TCAAAAACAT
9861855 AACAAAATCG
1 AACAAAATCG
9861865 AACAAAATCG
1 AACAAAATCG
9861875 AACAAAATC
1 AACAAAATC
9861884 CATACCGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.21, G:0.07, T:0.10
Consensus pattern (10 bp):
AACAAAATCG
Found at i:9875848 original size:25 final size:25
Alignment explanation
Indices: 9875785--9875850 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
9875775 GTACATATAT
** * * *
9875785 GCTCATATGAGCTATGAATCGGTAT
1 GCTCATACAAGCTGTGAATCGATAA
9875810 GCTC-TCACAAGCTGTGAATCGATAA
1 GCTCAT-ACAAGCTGTGAATCGATAA
9875835 GCTCATACAAGCTGTG
1 GCTCATACAAGCTGTG
9875851 GTGTGTTCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
GCTCATACAAGCTGTGAATCGATAA
Found at i:9881366 original size:32 final size:32
Alignment explanation
Indices: 9881330--9881416 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
9881320 ACTTTTCCGA
*
9881330 AAAATATTTTCAGGAAATC-TGCCAAACAACAG
1 AAAATATTTTCAGCAAATCAT-CCAAACAACAG
* *
9881362 AAAATATTTTACA-CAGATTCATCCAAACACCAG
1 AAAATATTTT-CAGCA-AATCATCCAAACAACAG
*
9881395 AAAATATTTTTCAGTAAATCAT
1 AAAATA-TTTTCAGCAAATCAT
9881417 TTTCCAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
32 11 0.24
33 28 0.62
34 6 0.13
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (32 bp):
AAAATATTTTCAGCAAATCATCCAAACAACAG
Found at i:9881432 original size:20 final size:20
Alignment explanation
Indices: 9881407--9881446 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9881397 AATATTTTTC
9881407 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
9881427 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
9881447 TCATTTTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:9881448 original size:34 final size:33
Alignment explanation
Indices: 9881396--9881460 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
9881386 AAACACCAGA
*
9881396 AAATATTTTTCAGTAAATCATTTTCCAGAAAAGT
1 AAATATTTTCCAGTAAATCATTTTCC-GAAAAGT
9881430 AAATCATTTTCCAG-AAATCATTTTCCGAAAA
1 AAAT-ATTTTCCAGTAAATCATTTTCCGAAAA
9881461 ACATTTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 16 0.55
35 8 0.28
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (33 bp):
AAATATTTTCCAGTAAATCATTTTCCGAAAAGT
Found at i:9881449 original size:14 final size:13
Alignment explanation
Indices: 9881430--9881459 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
9881420 CCAGAAAAGT
9881430 AAATCATTTTCCAG
1 AAATCATTTTCC-G
9881444 AAATCATTTTCCG
1 AAATCATTTTCCG
9881457 AAA
1 AAA
9881460 AACATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (13 bp):
AAATCATTTTCCG
Found at i:9884228 original size:63 final size:62
Alignment explanation
Indices: 9884108--9884259 Score: 146
Period size: 63 Copynumber: 2.4 Consensus size: 62
9884098 CTCACACGAA
* * * *
9884108 CTAGGGAAACGGGCGTGTGTCCAGACTGTATAACTCATTGTTTGTAATTGGGCGTCACATAGG
1 CTAGGGACAC-GGCGTGTGTCCAGGCTGTATAACTCATTGTTTGGAATTAGGCGTCACATAGG
* * * * *
9884171 TTAGGGACACGGACGTGTGTCCAGGTTGTGTAACTCACTAT-TTTGGATTTAGG-GTCACATGGG
1 CTAGGGACACGG-CGTGTGTCCAGGCTGTATAACTCA-T-TGTTTGGAATTAGGCGTCACATAGG
* *
9884234 CCAAGGACACAGGCGTGTGTCCAGGC
1 CTAGGGACAC-GGCGTGTGTCCAGGC
9884260 CGTGTGAGGG
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
62 2 0.03
63 57 0.79
64 12 0.17
65 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (62 bp):
CTAGGGACACGGCGTGTGTCCAGGCTGTATAACTCATTGTTTGGAATTAGGCGTCACATAGG
Found at i:9884862 original size:23 final size:23
Alignment explanation
Indices: 9884832--9884882 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
9884822 CCCTATATGG
*
9884832 TGTGTTAGGATGGTCGGGGATGA
1 TGTGTTAGGATGGTCGGAGATGA
*
9884855 TGTGTTAGGATGGTCGGAGATGG
1 TGTGTTAGGATGGTCGGAGATGA
9884878 TGTGT
1 TGTGT
9884883 AGTGGATAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.04, G:0.47, T:0.33
Consensus pattern (23 bp):
TGTGTTAGGATGGTCGGAGATGA
Found at i:9887164 original size:3 final size:3
Alignment explanation
Indices: 9887156--9887196 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
9887146 AATATAAACA
9887156 AAC AAC AAC AAC AAC AAC AAC AAC AAC AGAGC AAC AA- AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC A-A-C AAC AAC AAC A
9887197 GTGACAGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 29 0.83
4 2 0.06
5 2 0.06
ACGTcount: A:0.66, C:0.29, G:0.05, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:9888131 original size:23 final size:22
Alignment explanation
Indices: 9888078--9888139 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
9888068 TTTAAGCTTG
*
9888078 ATATTATTTTAAATTCATCATTA
1 ATATTA-TTTAAATTTATCATTA
9888101 ATA-T-TTTAAATTTATCATATA
1 ATATTATTTAAATTTATCAT-TA
* *
9888122 TTATTATTTACATTTATC
1 ATATTATTTAAATTTATC
9888140 GTCTATTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.39
21 4 0.12
22 2 0.06
23 14 0.42
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTATTTAAATTTATCATTA
Done.