Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 48 of 126
Found at i:9455992 original size:69 final size:68
Alignment explanation
Indices: 9455902--9456102 Score: 260
Period size: 69 Copynumber: 2.9 Consensus size: 68
9455892 AAGGTCTTAG
* * *
9455902 AAATCTCAAATTCATTGAATGCTCCTCTAATCAGAGGTCATGAAACTTTAAAAT-TTTAAAATGT
1 AAATCTCAAAATCTTTGAATGCTCCTCTAATCAGAGG-CATGAAACTTTAAAATCTTT-AAATGG
*
9455966 TTTGC
64 TTCGC
* * *
9455971 AAATCTCAAAATCTTTGAATGCCCCTCCAATCAGAGGCTATGAAACTTTAAAATCTTTGAATGGT
1 AAATCTCAAAATCTTTGAATGCTCCTCTAATCAGAGGC-ATGAAACTTTAAAATCTTTAAATGGT
9456036 TCGC
65 TCGC
* * * *
9456040 AAATCTCAAAACCTTTTAATGCTCTTCTAATCAGAGGCCATGAAACTTTAAAATCTTTGAATG
1 AAATCTCAAAATCTTTGAATGCTCCTCTAATCAGAGG-CATGAAACTTTAAAATCTTTAAATG
9456103 CTCCTCCAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
68 1 0.01
69 112 0.96
70 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (68 bp):
AAATCTCAAAATCTTTGAATGCTCCTCTAATCAGAGGCATGAAACTTTAAAATCTTTAAATGGTT
CGC
Found at i:9456122 original size:42 final size:42
Alignment explanation
Indices: 9456047--9456134 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
9456037 CGCAAATCTC
* * * *
9456047 AAAACCTTTTAATGCTCTTCTAATCAGAGGCCATGAAACTTT
1 AAAACCTTTGAATGCTCCTCCAATCAAAGGCCATGAAACTTT
* *
9456089 AAAATCTTTGAATGCTCCTCCAATCAAATGCCATGAAACTTT
1 AAAACCTTTGAATGCTCCTCCAATCAAAGGCCATGAAACTTT
9456131 AAAA
1 AAAA
9456135 ATTAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.31
Consensus pattern (42 bp):
AAAACCTTTGAATGCTCCTCCAATCAAAGGCCATGAAACTTT
Found at i:9456562 original size:11 final size:10
Alignment explanation
Indices: 9456539--9456579 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
9456529 CATCAATCTC
*
9456539 TTTTTTTTCT
1 TTTTTTTTAT
9456549 TTTTTTATTAT
1 TTTTTT-TTAT
9456560 TTTTTTGTTAT
1 TTTTTT-TTAT
9456571 TTTTTTTTA
1 TTTTTTTTA
9456580 AACAATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:9456775 original size:20 final size:20
Alignment explanation
Indices: 9456752--9456792 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
9456742 TTTGTTTCGT
9456752 TATTT-TTTTGTTATGTTTTC
1 TATTTATTTT-TTATGTTTTC
*
9456772 TATTTATTTTTTATTTTTTC
1 TATTTATTTTTTATGTTTTC
9456792 T
1 T
9456793 TCTTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (20 bp):
TATTTATTTTTTATGTTTTC
Found at i:9457285 original size:11 final size:11
Alignment explanation
Indices: 9457269--9457312 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
9457259 CTCCTTCATT
9457269 TTTATTTTTTA
1 TTTATTTTTTA
9457280 TTTATTTTTTA
1 TTTATTTTTTA
9457291 --TATTTTTTA
1 TTTATTTTTTA
9457300 TTT-TTTTTTA
1 TTTATTTTTTA
9457310 TTT
1 TTT
9457313 TTTCTTAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.29
10 10 0.32
11 12 0.39
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:9457315 original size:7 final size:7
Alignment explanation
Indices: 9457267--9457305 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
9457257 TCCTCCTTCA
9457267 TTTTTAT
1 TTTTTAT
9457274 TTTTTAT
1 TTTTTAT
*
9457281 TTATT-T
1 TTTTTAT
*
9457287 TTTATAT
1 TTTTTAT
9457294 TTTTTAT
1 TTTTTAT
9457301 TTTTT
1 TTTTT
9457306 TTTATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:9471403 original size:19 final size:20
Alignment explanation
Indices: 9471373--9471430 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
9471363 AACCAAGTGT
* *
9471373 TTTCCTAGTCAAGGTAGGAA
1 TTTCCAAGTCAAAGTAGGAA
9471393 TTT-CAAGTCAAAGTAGG-A
1 TTTCCAAGTCAAAGTAGGAA
* *
9471411 TTTCCAAGTTAATGTAGGAA
1 TTTCCAAGTCAAAGTAGGAA
9471431 AACCTTCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.12
19 24 0.75
20 4 0.12
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (20 bp):
TTTCCAAGTCAAAGTAGGAA
Found at i:9473818 original size:145 final size:144
Alignment explanation
Indices: 9473591--9474079 Score: 529
Period size: 145 Copynumber: 3.4 Consensus size: 144
9473581 TGAAATTCTA
* * * * * *
9473591 AGCTCAAAAAGGCTAAATTACAATAATACCCTTATGAGGGTATTTTAGTAATTTCATACTTTTCG
1 AGCTCGAAAAGGCCAAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCATACTTTTTG
* * * * *
9473656 GGGTACTGTTATAATTTCAAATGCATCATAAATCATTAAATATTATAAAACTAAGATATGAAAAG
66 GGGTACTGATATGATTTCAAATGAATCAAAAATCATAAAATATTATAAAA-TAAGATATGAAAAG
**
9473721 TTTTATGAAATTTTG
130 TTTTACAAAATTTTG
* * * *
9473736 AGCACGAAAAGGCCAAATTACGAAAATACCCCTTA-AAGGGTATTTTGGTAATTTCACATTTTTT
1 AGCTCGAAAAGGCCAAATTACAAAAATA-CCCTTATAAGGGTATTTTGGTAATTTCATACTTTTT
* * * * * **
9473800 GGGGTACTAATATGATTTCAAACTAAAT-AAAAAT-AAAGAAATATTACAAAAGTGAGACCTGAA
65 GGGGTACTGATATGATTTCAAA-TGAATCAAAAATCATA-AAATATTATAAAA-TAAGATATGAA
9473863 AA-TTTTCACAAAATTTTG
127 AAGTTTT-ACAAAATTTTG
** * *
9473881 AGCTCGGGAAGGCCAAATTACAAAAATACCCTTGTAAGGGTATTTTGGTAATTTCATACTTTTTA
1 AGCTCGAAAAGGCCAAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCATACTTTTTG
* * * *
9473946 GGGTACGGCTATGATTTCAAGTGTA-CTAAAAATCATAAAATATTATAAAATAGAGATATGAAAA
66 GGGTACTGATATGATTTCAAATGAATC-AAAAATCATAAAATATTATAAAATA-AGATATGAAAA
* **
9474010 GTTTCACAAAATTTCA
129 GTTTTACAAAATTTTG
** *
9474026 AGCTCGAAAAGATCAAATTACAAAAATACCCTTATAAGGGTATTTTGATAATTT
1 AGCTCGAAAAGGCCAAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTT
9474080 AGCCTTTCCC
Statistics
Matches: 281, Mismatches: 53, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
144 13 0.05
145 254 0.90
146 14 0.05
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33
Consensus pattern (144 bp):
AGCTCGAAAAGGCCAAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCATACTTTTTG
GGGTACTGATATGATTTCAAATGAATCAAAAATCATAAAATATTATAAAATAAGATATGAAAAGT
TTTACAAAATTTTG
Found at i:9474852 original size:121 final size:121
Alignment explanation
Indices: 9474632--9474903 Score: 373
Period size: 121 Copynumber: 2.2 Consensus size: 121
9474622 AGCTTTTGAA
* * * * * *
9474632 TGCTCTTTTAATTAGAGGCCACAAAACTTTGAATTTAAAATGGTTGGAGATTATGCCCGATGGTC
1 TGCTCCTTTAATTAGAGGCCATAAAACTTTAAATTTAAAATGGTTGAAGATTATGCCCAAAGGTC
*
9474697 TTACAAATCTTAAAATCTTTAAATACTCATCCAATCAGAGGCCATGAAACTTTAAG
66 TTACAAATCTCAAAATCTTTAAATACTCATCCAATCAGAGGCCATGAAACTTTAAG
* * * *
9474753 TGCTTCTTTAATCAGAGGCCATAAAACTTTAAATTTAAAATGTTTGAAGATTATGCTCAAAGGTC
1 TGCTCCTTTAATTAGAGGCCATAAAACTTTAAATTTAAAATGGTTGAAGATTATGCCCAAAGGTC
* * * * * *
9474818 TTATAAATCTCAAATTCTTTAAATGCTCCTCCAATCAGAGGTCATGAAACTTTGAG
66 TTACAAATCTCAAAATCTTTAAATACTCATCCAATCAGAGGCCATGAAACTTTAAG
* *
9474874 TGCTCCTCTAATTAGAGGCCATGAAACTTT
1 TGCTCCTTTAATTAGAGGCCATAAAACTTT
9474904 GAATGCTTCT
Statistics
Matches: 130, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
121 130 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (121 bp):
TGCTCCTTTAATTAGAGGCCATAAAACTTTAAATTTAAAATGGTTGAAGATTATGCCCAAAGGTC
TTACAAATCTCAAAATCTTTAAATACTCATCCAATCAGAGGCCATGAAACTTTAAG
Found at i:9474879 original size:33 final size:33
Alignment explanation
Indices: 9474834--9475071 Score: 341
Period size: 33 Copynumber: 7.2 Consensus size: 33
9474824 ATCTCAAATT
* *
9474834 CTTTAAATGCTCCTCCAATCAGAGGTCATGAAA
1 CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
* * *
9474867 CTTTGAGTGCTCCTCTAATTAGAGGCCATGAAA
1 CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
* * *
9474900 CTTTGAATGCTTCTCTAATTAGAGGCCATGAAA
1 CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
*
9474933 CTTTAAATGCTCCTCTAATCAAAGGCCATGAAA
1 CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
* *
9474966 CTTTAAGTGTTCCTCTAATCAGAGGCCATGAAA
1 CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
** * *
9474999 CTTTAAATATTCCTCTAATCAAAGGCCATTAAA
1 CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
9475032 CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
1 CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
9475065 CTTTAAA
1 CTTTAAA
9475072 AATTAAAAAT
Statistics
Matches: 183, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 183 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (33 bp):
CTTTAAATGCTCCTCTAATCAGAGGCCATGAAA
Found at i:9475728 original size:37 final size:38
Alignment explanation
Indices: 9475646--9475747 Score: 107
Period size: 37 Copynumber: 2.6 Consensus size: 38
9475636 CTTTTTTAGG
* *
9475646 ATGCAAATGCAAGTGATGCAAATACGAATGTTTTTTTCATG
1 ATGCAAATGCAAGTGATGCAAAT--G-ATCTTTTTTTCATC
* **
9475687 ATGCAAATGCAAGTGTTGCAAATG-TCTTTTTTTTTTC
1 ATGCAAATGCAAGTGATGCAAATGATCTTTTTTTCATC
* *
9475724 ATGCAGATGTAAGTGATGCAAATG
1 ATGCAAATGCAAGTGATGCAAATG
9475748 CAAATGTCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
37 30 0.57
39 1 0.02
41 22 0.42
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (38 bp):
ATGCAAATGCAAGTGATGCAAATGATCTTTTTTTCATC
Found at i:9476828 original size:17 final size:17
Alignment explanation
Indices: 9476787--9476828 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
9476777 TTTCTTTTTC
*
9476787 TTTTTC-TTTCTTTTAT
1 TTTTTCTTTTCTTTCAT
* *
9476803 TCTTACTTTTCTTTCAT
1 TTTTTCTTTTCTTTCAT
9476820 TTTTTCTTT
1 TTTTTCTTT
9476829 CCTTCTTTCT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTCTTTCAT
Found at i:9477343 original size:7 final size:6
Alignment explanation
Indices: 9477329--9477403 Score: 55
Period size: 6 Copynumber: 11.8 Consensus size: 6
9477319 TCATAACCAT
*
9477329 TTTTTC TTCTTTC TTTTCTC TTTTTTTC TTTTT- TTTTTT TTTTTC ATTTTTC
1 TTTTTC TT-TTTC TTTT-TC --TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC
* *
9477381 ATTTTTC ATTTT- TTCTTC TTTTT
1 -TTTTTC TTTTTC TTTTTC TTTTT
9477404 TTTGGTTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
5 8 0.14
6 22 0.39
7 21 0.37
8 2 0.04
9 4 0.07
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:9477378 original size:6 final size:7
Alignment explanation
Indices: 9477368--9477393 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9477358 TTTTTTTTTT
9477368 TTTTTCA
1 TTTTTCA
9477375 TTTTTCA
1 TTTTTCA
9477382 TTTTTCA
1 TTTTTCA
9477389 TTTTT
1 TTTTT
9477394 TCTTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:9477393 original size:39 final size:39
Alignment explanation
Indices: 9477328--9477406 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 39
9477318 GTCATAACCA
* *
9477328 TTTTTTCTTCTTTCTTTTCTCTTTTTTTCTTTTTTTTTT
1 TTTTTTCTTCTTTCTTTTCTCATTTTTTCTTCTTTTTTT
9477367 TTTTTTCATT-TTTCATTTT-TCATTTTTTCTTCTTTTTTT
1 TTTTTTC-TTCTTTC-TTTTCTCATTTTTTCTTCTTTTTTT
9477406 T
1 T
9477407 GGTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 30 0.83
40 6 0.17
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (39 bp):
TTTTTTCTTCTTTCTTTTCTCATTTTTTCTTCTTTTTTT
Found at i:9479987 original size:30 final size:30
Alignment explanation
Indices: 9479951--9480021 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
9479941 ATGTGCATAA
*
9479951 AATGGGATGCATGTACTATCTATTGATGTG
1 AATGGGATGCATGTACTATCCATTGATGTG
9479981 AATGGGATGCATGTACTATCCATTGATGTG
1 AATGGGATGCATGTACTATCCATTGATGTG
*
9480011 GATGGGATGCA
1 AATGGGATGCA
9480022 ATACATGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.32
Consensus pattern (30 bp):
AATGGGATGCATGTACTATCCATTGATGTG
Found at i:9484997 original size:146 final size:142
Alignment explanation
Indices: 9484560--9485033 Score: 461
Period size: 146 Copynumber: 3.3 Consensus size: 142
9484550 CGAAAATGCT
* * * * **** *
9484560 AAATTACGAAAATACCCATATGAGGGTATTTTGGTAATTTCACACTTTTCGGGGTGTTGTTATAA
1 AAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCACACTTTTCAGGGT-ACAATATGA
* * * ** *
9484625 TTTCAAA-TACATCAAAAATCATGAAATATTAAAAATAG-GATCTGGAAAGTTTAATGAAATTTT
65 TTTCAAACTAC-T-AAAAATCATGAAATATTAAAAATTGAGATCTGAAAAGTTTCACAAAATTTC
*
9484688 GAGCTCAGAAAGGCC
128 GAGCTCAGGAAGGCC
* ** * * *
9484703 AAATTACGAAAATACCCCCA-AAGGGTATTTTGGTATTTTCACACTTTTCTGCGGTACTGATATG
1 AAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCACACTTTTCAG-GGTAC-AATATG
* * * * *
9484767 ATTTTAAACTCACCAAAAATCATAAAATATTACAAAAATGAGAGCTGAAAAGTTTCACAAAA-TT
64 ATTTCAAACT-ACTAAAAATCATGAAATATTA-AAAATTGAGATCTGAAAAGTTTCACAAAATTT
*
9484831 CTGAGCTCATGAAGGCC
127 C-GAGCTCAGGAAGGCC
*
9484848 AAATTACCAAAAATACCCTTGTAAGGGTATTTTGGTAATTTCACACTTTTCAGGGTACAACTATG
1 AAATTA-CAAAAATACCCTTATAAGGGTATTTTGGTAATTTCACACTTTTCAGGGTACAA-TATG
*
9484913 ATTTCAAACGTACTAAAAATCATGAAATATTATAACATTGAGATCTGAAAAGTTTCACAAAATTT
64 ATTTCAAAC-TACTAAAAATCATGAAATATTA-AAAATTGAGATCTGAAAAGTTTCACAAAATTT
* ***
9484978 CGAGCTTAGGAATATC
127 CGAGCTCAGGAAGGCC
* * * * *
9484994 AAATTAGAAAAATACCTTTATAGGGGTATCTTGATAATTT
1 AAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTT
9485034 GGCCTTTCTT
Statistics
Matches: 272, Mismatches: 47, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
142 28 0.10
143 49 0.18
144 8 0.03
145 66 0.24
146 88 0.32
147 33 0.12
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (142 bp):
AAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCACACTTTTCAGGGTACAATATGAT
TTCAAACTACTAAAAATCATGAAATATTAAAAATTGAGATCTGAAAAGTTTCACAAAATTTCGAG
CTCAGGAAGGCC
Found at i:9487885 original size:17 final size:18
Alignment explanation
Indices: 9487865--9487901 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9487855 ATTTTCTATT
9487865 ATTTGATT-TTTTTTAAA
1 ATTTGATTCTTTTTTAAA
*
9487882 ATTTGATTCTTTTTTTAA
1 ATTTGATTCTTTTTTAAA
9487900 AT
1 AT
9487902 ACTATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTTGATTCTTTTTTAAA
Found at i:9488166 original size:15 final size:16
Alignment explanation
Indices: 9488148--9488187 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
9488138 TTATAGTAGT
9488148 AATATTTAT-TATGAA
1 AATATTTATATATGAA
*
9488163 AATATTTATACTATTAA
1 AATATTTATA-TATGAA
9488180 AATATTTA
1 AATATTTA
9488188 AATTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
17 13 0.59
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
AATATTTATATATGAA
Found at i:9492592 original size:10 final size:10
Alignment explanation
Indices: 9492577--9492609 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
9492567 TTAGCAATTT
9492577 CATATATATA
1 CATATATATA
9492587 CATATATATA
1 CATATATATA
9492597 CATATATATA
1 CATATATATA
9492607 CAT
1 CAT
9492610 GGACAAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (10 bp):
CATATATATA
Found at i:9497605 original size:215 final size:215
Alignment explanation
Indices: 9497234--9497663 Score: 781
Period size: 215 Copynumber: 2.0 Consensus size: 215
9497224 GTGTCTAGAA
*
9497234 TATTCAATCTTTAAAGGTACATTGTAACTCCTTGCTCTAGCACATTTATAGTAGACATTAATCAT
1 TATTCAATCTTTAAAGGTACATTGTAACTCCTTGCTCTAGCACATTTATAATAGACATTAATCAT
*
9497299 TTGAATTTTAGTATCCAAATTACTTTGGGTCTTTAAGAGTTAGTCACAATATTTCTTGTTCCTTA
66 TTGAATTTTAGTATCCAAATTACTTTGGGTCTTTAAGAGTTAGTCACAATATTTCTTATTCCTTA
*
9497364 TGATTGGGTCAATCTACAAGTGCATAGACCGTACAAGTAATAATAATGACCTTTC-GATCAAGAT
131 AGATTGGGTCAATCTACAAGTGCATAGACCGTACAAGTAATAATAATGACCTTTCAG-TCAAGAT
9497428 ATCATCCTACAAAGATTAGGT
195 ATCATCCTACAAAGATTAGGT
* * *
9497449 TATTCAATTTTTAAAGGTATATTGTAACTTCTTGCTCTAGCACATTTATAATAGACATTAATCAT
1 TATTCAATCTTTAAAGGTACATTGTAACTCCTTGCTCTAGCACATTTATAATAGACATTAATCAT
*
9497514 TTGAATTTTAGTATCCAAATTGCTTTGGGTCTTTAAGAGTTAGTCACAATATTTCTTATTCCTTA
66 TTGAATTTTAGTATCCAAATTACTTTGGGTCTTTAAGAGTTAGTCACAATATTTCTTATTCCTTA
9497579 AGATTGGGTCAATCTACAAGTGCATAGACCGTACAAGTAATAATAATGACCTTTCAGTCAAGATA
131 AGATTGGGTCAATCTACAAGTGCATAGACCGTACAAGTAATAATAATGACCTTTCAGTCAAGATA
9497644 TCATCCTACAAAGATTAGGT
196 TCATCCTACAAAGATTAGGT
9497664 AAAGAAATTA
Statistics
Matches: 207, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
215 206 1.00
216 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (215 bp):
TATTCAATCTTTAAAGGTACATTGTAACTCCTTGCTCTAGCACATTTATAATAGACATTAATCAT
TTGAATTTTAGTATCCAAATTACTTTGGGTCTTTAAGAGTTAGTCACAATATTTCTTATTCCTTA
AGATTGGGTCAATCTACAAGTGCATAGACCGTACAAGTAATAATAATGACCTTTCAGTCAAGATA
TCATCCTACAAAGATTAGGT
Found at i:9501234 original size:21 final size:21
Alignment explanation
Indices: 9501188--9501235 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
9501178 AGCATTCAAG
**
9501188 GCTTTAGGGATCAATCCTTTT
1 GCTTTAGGGATCAATCCTCAT
* *
9501209 TCTTTAGGGATCGATCCTCAT
1 GCTTTAGGGATCAATCCTCAT
9501230 GCTTTA
1 GCTTTA
9501236 AAAAAGAGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (21 bp):
GCTTTAGGGATCAATCCTCAT
Found at i:9502107 original size:2 final size:2
Alignment explanation
Indices: 9502100--9502135 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9502090 CCATATCGTT
9502100 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
9502136 ACAGGATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9502488 original size:18 final size:18
Alignment explanation
Indices: 9502465--9502499 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9502455 TTTGATTAAA
*
9502465 TTTCTTTTTTTCTTTTTC
1 TTTCTTTCTTTCTTTTTC
9502483 TTTCTTTCTTTCTTTTT
1 TTTCTTTCTTTCTTTTT
9502500 TAACAAACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTCTTTCTTTCTTTTTC
Found at i:9503697 original size:1 final size:1
Alignment explanation
Indices: 9503693--9503722 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
9503683 ATAAAAATGC
*
9503693 AAAAAAAGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9503723 CAAAGCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:9504848 original size:15 final size:14
Alignment explanation
Indices: 9504808--9504850 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
9504798 TTCGTATTTC
9504808 AAATATATTTTCTAAA
1 AAATATA-TTT-TAAA
*
9504824 AAATAAATTTTAAA
1 AAATATATTTTAAA
9504838 ATAATATATTTTA
1 A-AATATATTTTA
9504851 TATTTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATATTTTAAA
Found at i:9505009 original size:19 final size:20
Alignment explanation
Indices: 9504977--9505020 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
9504967 TAAATCATAA
*
9504977 CAAAAAATATTATTTTCTAT
1 CAAAAAATACTATTTTCTAT
9504997 CAAAAAAT-CTATTTTCTAT
1 CAAAAAATACTATTTTCTAT
*
9505016 TAAAA
1 CAAAA
9505021 GATTACATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (20 bp):
CAAAAAATACTATTTTCTAT
Found at i:9505284 original size:64 final size:64
Alignment explanation
Indices: 9505211--9505351 Score: 146
Period size: 64 Copynumber: 2.2 Consensus size: 64
9505201 AAATTTTAGA
* * * *
9505211 AAAT-AAAATTAAGTTA-A-AATTTTCAAAATTATTTTTAAAAAATTCTATATCATTTTAAAA-A
1 AAATAAAAATT-AGTTATATAATTTTAAAAATT-TATATAAAAAATTCCATAT-ATTTTAAAATA
9505272 TT
63 TT
* * * *
9505274 AATTAAAAATTATTTATATCATTTTAAAAATTTATATAAAAAATTCCATATTTTTTAAAATATT
1 AAATAAAAATTAGTTATATAATTTTAAAAATTTATATAAAAAATTCCATATATTTTAAAATATT
9505338 AAATAAAAAATTAG
1 AAAT-AAAAATTAG
9505352 ATATTATTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
63 15 0.24
64 29 0.46
65 19 0.30
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (64 bp):
AAATAAAAATTAGTTATATAATTTTAAAAATTTATATAAAAAATTCCATATATTTTAAAATATT
Found at i:9505333 original size:31 final size:32
Alignment explanation
Indices: 9505246--9505349 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 32
9505236 AAATTATTTT
*
9505246 TAAAAAATTCTATATCATTTTAAAAATTAAT-
1 TAAAAAATTCTATATCATTTTAAAAATTTATA
9505277 TAAAAATTATT-TATATCATTTTAAAAATTTATA
1 TAAAAA--ATTCTATATCATTTTAAAAATTTATA
* * *
9505310 TAAAAAATTCCATAT--TTTTTAAAATATTAAA
1 TAAAAAATTCTATATCATTTTAAAAAT-TTATA
9505341 TAAAAAATT
1 TAAAAAATT
9505350 AGATATTATT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
30 9 0.14
31 22 0.34
32 24 0.38
33 9 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (32 bp):
TAAAAAATTCTATATCATTTTAAAAATTTATA
Found at i:9505356 original size:31 final size:30
Alignment explanation
Indices: 9505295--9505356 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
9505285 ATTTATATCA
* *
9505295 TTTTAAAAATTTATATAAAAAATTCCATAT
1 TTTTAAAAATTTAAATAAAAAATTACATAT
* *
9505325 TTTTTAAAATATTAAATAAAAAATTAGATAT
1 TTTTAAAAAT-TTAAATAAAAAATTACATAT
9505356 T
1 T
9505357 ATTGTAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTTAAAAATTTAAATAAAAAATTACATAT
Found at i:9505366 original size:31 final size:31
Alignment explanation
Indices: 9505300--9505372 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
9505290 TATCATTTTA
* * *
9505300 AAAAT-TTATATAAAAAATTCCATATTTTTT
1 AAAATATTAAATAAAAAATTACATATTTTGT
*
9505330 AAAATATTAAATAAAAAATTAGATATTATTGT
1 AAAATATTAAATAAAAAATTACATATT-TTGT
*
9505362 -AAATAATAAAT
1 AAAATATTAAAT
9505373 TTATTAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 5 0.14
31 28 0.78
32 3 0.08
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (31 bp):
AAAATATTAAATAAAAAATTACATATTTTGT
Found at i:9507714 original size:58 final size:58
Alignment explanation
Indices: 9507630--9507774 Score: 247
Period size: 58 Copynumber: 2.5 Consensus size: 58
9507620 AAAAAAAACC
* *
9507630 TTTTTAGAAAA-TTATTTTAAAAAAAAATTGATACTTTCAACTTCTCCTCAAAAATAT
1 TTTTTAGAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTCTCCTCAAAAATAT
*
9507687 TTTTTAGAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAT
1 TTTTTAGAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTCTCCTCAAAAATAT
*
9507745 TTTTTAGAAAACTTATTTTCAAGGAAAATT
1 TTTTTAGAAAACTTATTTTCAAGAAAAATT
9507775 TTCAAGGAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
57 11 0.13
58 72 0.87
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (58 bp):
TTTTTAGAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTCTCCTCAAAAATAT
Found at i:9507777 original size:13 final size:13
Alignment explanation
Indices: 9507759--9507787 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9507749 TAGAAAACTT
9507759 ATTTTCAAGGAAA
1 ATTTTCAAGGAAA
9507772 ATTTTCAAGGAAA
1 ATTTTCAAGGAAA
9507785 ATT
1 ATT
9507788 GATACTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (13 bp):
ATTTTCAAGGAAA
Found at i:9507909 original size:3 final size:3
Alignment explanation
Indices: 9507901--9507934 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9507891 TAATCTAAAC
9507901 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9507935 ATGAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9508753 original size:17 final size:17
Alignment explanation
Indices: 9508718--9508807 Score: 62
Period size: 17 Copynumber: 5.4 Consensus size: 17
9508708 TAACTAAAAG
*
9508718 AAAATAATTAGATAAATAA
1 AAAAT-ATTA-ATAGATAA
9508737 AAAATATTAATAGATAA
1 AAAATATTAATAGATAA
* *
9508754 ATAATAATAA-AG-T-A
1 AAAATATTAATAGATAA
* *
9508768 TATATATTAATAGATAA
1 AAAATATTAATAGATAA
* **
9508785 ATAATAACAATA-ATAA
1 AAAATATTAATAGATAA
9508801 AAAATAT
1 AAAATAT
9508808 ATATTAATAA
Statistics
Matches: 54, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
14 7 0.13
15 3 0.06
16 12 0.22
17 23 0.43
18 4 0.07
19 5 0.09
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (17 bp):
AAAATATTAATAGATAA
Found at i:9508754 original size:21 final size:22
Alignment explanation
Indices: 9508697--9508757 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
9508687 TAAAGATAAT
*
9508697 ATATTAATAGATAACTAAAAGA
1 ATATTAATAGATAAATAAAAGA
*
9508719 A-AATAATTAGATAAATAAAA-A
1 ATATTAA-TAGATAAATAAAAGA
9508740 ATATTAATAGATAAATAA
1 ATATTAATAGATAAATAA
9508758 TAATAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.28
Consensus pattern (22 bp):
ATATTAATAGATAAATAAAAGA
Found at i:9508761 original size:14 final size:14
Alignment explanation
Indices: 9508738--9508791 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
9508728 GATAAATAAA
*
9508738 AAATATTAATAGAT
1 AAATAATAATAGAT
9508752 AAATAATAATAAAGTAT
1 AAATAATAAT--AG-AT
* *
9508769 ATATATTAATAGAT
1 AAATAATAATAGAT
9508783 AAATAATAA
1 AAATAATAA
9508792 CAATAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.56
15 2 0.06
16 2 0.06
17 10 0.31
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (14 bp):
AAATAATAATAGAT
Found at i:9508778 original size:20 final size:19
Alignment explanation
Indices: 9508755--9508817 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
9508745 AATAGATAAA
9508755 TAATAATAAAGTATATATAT
1 TAATAATAAA-TATATATAT
9508775 TAATAGATAAATA-ATA-A-
1 TAATA-ATAAATATATATAT
* *
9508792 CAATAATAAAAAATATATAT
1 TAATAAT-AAATATATATAT
9508812 TAATAA
1 TAATAA
9508818 ATAGTAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.06
17 8 0.23
18 4 0.11
19 4 0.11
20 12 0.34
21 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (19 bp):
TAATAATAAATATATATAT
Found at i:9508806 original size:27 final size:26
Alignment explanation
Indices: 9508726--9508858 Score: 76
Period size: 27 Copynumber: 4.9 Consensus size: 26
9508716 AGAAAATAAT
* * *
9508726 TAGATAAATAA-AAAATATTAATAGA
1 TAGATAAATAATAAAATAATAAAAAA
* * **
9508751 TAAAT-AATAATAAAGTATATATATTAA
1 TAGATAAATAATAAAATA-ATA-AAAAA
9508778 TAGATAAATAATAACAATAATAAAAAA
1 TAGATAAATAATAA-AATAATAAAAAA
* *
9508805 TATATATTAATAAATAGTAATAATAAATAAA
1 TAGATA--AAT-AATA-AAATAATAAA-AAA
9508836 TAAGATAAA-AATAAAA-AATAAAA
1 T-AGATAAATAATAAAATAATAAAA
9508859 TAAAATAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
24 5 0.06
25 10 0.12
26 8 0.10
27 17 0.20
28 15 0.18
29 6 0.07
30 15 0.18
31 4 0.05
32 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.29
Consensus pattern (26 bp):
TAGATAAATAATAAAATAATAAAAAA
Found at i:9508833 original size:17 final size:17
Alignment explanation
Indices: 9508729--9508867 Score: 89
Period size: 17 Copynumber: 8.5 Consensus size: 17
9508719 AAATAATTAG
* *
9508729 ATAAATAAAAAATATTA
1 ATAAATAAATAATAATA
*
9508746 ATAGATAAATAATAATA
1 ATAAATAAATAATAATA
* * *
9508763 A-AGTATATATATTAATA
1 ATA-AATAAATAATAATA
*
9508780 GATAAAT-AATAACAATA
1 -ATAAATAAATAATAATA
9508797 ATAAA-AAAT-AT-AT-
1 ATAAATAAATAATAATA
* *
9508810 ATTAATAAATAGTAATA
1 ATAAATAAATAATAATA
*
9508827 ATAAATAAATAA-GATA
1 ATAAATAAATAATAATA
*
9508843 A-AAATAAAAAATAA-A
1 ATAAATAAATAATAATA
9508858 ATAAAATAAA
1 AT-AAATAAA
9508868 ATAAAATGAA
Statistics
Matches: 93, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
13 4 0.04
14 6 0.06
15 13 0.14
16 16 0.17
17 50 0.54
18 3 0.03
19 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.28
Consensus pattern (17 bp):
ATAAATAAATAATAATA
Found at i:9508834 original size:37 final size:38
Alignment explanation
Indices: 9508679--9508834 Score: 116
Period size: 37 Copynumber: 4.2 Consensus size: 38
9508669 AAAATAAACA
* *
9508679 AAATAA-AATAAAGATAATATATTAATAGATA-ACTAA-
1 AAATAATAATAAAGAT-ATATATTAATAAATATAATAAT
* * *
9508715 AAGAAAATAAT-TAGATA-A-A-TAAAAAATATTAATAGAT
1 AA-ATAATAATAAAGATATATATTAATAAATA-TAATA-AT
*
9508752 AAATAATAATAAAGTATATATATTAATAGATA-AATAAT
1 AAATAATAATAAAG-ATATATATTAATAAATATAATAAT
9508790 AACAATAATAA-AAA-ATATATATTAATAAATAGTAATAAT
1 -A-AATAATAATAAAGATATATATTAATAAATA-TAATAAT
9508829 AAATAA
1 AAATAA
9508835 ATAAGATAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 29
0.71 0.07 0.22
Matches are distributed among these distances:
33 7 0.07
34 1 0.01
35 4 0.04
36 11 0.12
37 32 0.34
38 9 0.09
39 15 0.16
40 9 0.09
41 7 0.07
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (38 bp):
AAATAATAATAAAGATATATATTAATAAATATAATAAT
Found at i:9508849 original size:22 final size:23
Alignment explanation
Indices: 9508823--9508873 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
9508813 AATAAATAGT
* *
9508823 AATAATAAAT-AAATAAGATAAA
1 AATAAAAAATAAAATAAAATAAA
9508845 AATAAAAAATAAAATAAAAT-AA
1 AATAAAAAATAAAATAAAATAAA
9508867 AATAAAA
1 AATAAAA
9508874 TGAAAATGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
AATAAAAAATAAAATAAAATAAA
Found at i:9508851 original size:5 final size:5
Alignment explanation
Indices: 9508829--9508880 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
9508819 TAGTAATAAT
* *
9508829 AAAT- AAATA AGATA AAA-A TAA-A AAATA AAATA AAATA AAATA AAATGA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A
9508877 AAAT
1 AAAT
9508881 GGGCTTACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 10 0.24
5 26 0.63
6 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:9509186 original size:44 final size:43
Alignment explanation
Indices: 9509063--9509194 Score: 185
Period size: 43 Copynumber: 3.1 Consensus size: 43
9509053 ACCTTTATGT
* ** *
9509063 AGAGGTTCAATGACTTT-AAAAATAAGTAAAGCTCTTCTAAAC
1 AGAGGCTCAATGACTTTGAAAAATAAACAAAGCTCCTCTAAAC
*
9509105 AGAGGCTCGATGACTTTGAAAAATAAACAAAGCTCCTCTAAAC
1 AGAGGCTCAATGACTTTGAAAAATAAACAAAGCTCCTCTAAAC
* *
9509148 AGAGGCTCCATGACTTTGAAAAAATAAACAAAGCTCCTCTAAGC
1 AGAGGCTCAATGACTTTG-AAAAATAAACAAAGCTCCTCTAAAC
9509192 AGA
1 AGA
9509195 TAAACAAAGC
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 15 0.19
43 39 0.48
44 27 0.33
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (43 bp):
AGAGGCTCAATGACTTTGAAAAATAAACAAAGCTCCTCTAAAC
Found at i:9509201 original size:23 final size:23
Alignment explanation
Indices: 9509171--9509215 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
9509161 CTTTGAAAAA
9509171 ATAAACAAAGCTCCTCTAAGCAG
1 ATAAACAAAGCTCCTCTAAGCAG
9509194 ATAAACAAAGCTCCTCTAAGCA
1 ATAAACAAAGCTCCTCTAAGCA
9509216 AAGGCTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.27, G:0.11, T:0.18
Consensus pattern (23 bp):
ATAAACAAAGCTCCTCTAAGCAG
Found at i:9509238 original size:67 final size:67
Alignment explanation
Indices: 9509127--9509261 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 67
9509117 ACTTTGAAAA
* *
9509127 ATAAACAAAGCTCCTCTAAACAGAGGCTCCATGACTTTGAAAAAATAAACAAAGCTCCTCTAAGC
1 ATAAACAAAGCTCCTCTAAACAAAGGCTCCACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGC
9509192 AG
66 AG
* *
9509194 ATAAACAAAGCTCCTCTAAGCAAAGGCTCCACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGC
1 ATAAACAAAGCTCCTCTAAACAAAGGCTCCACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGC
9509259 AG
66 AG
9509261 A
1 A
9509262 GGCTCCACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (67 bp):
ATAAACAAAGCTCCTCTAAACAAAGGCTCCACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGC
AG
Found at i:9509257 original size:44 final size:45
Alignment explanation
Indices: 9509194--9509321 Score: 206
Period size: 44 Copynumber: 2.9 Consensus size: 45
9509184 CTCTAAGCAG
*
9509194 ATAAACAAAGCTCCTCTAAGCAAAGGCTCCACGACTTTGG-AAAA
1 ATAAACAAAGCTCCTCTAAGCAGAGGCTCCACGACTTTGGAAAAA
*
9509238 ATAAACAAAGCTCCTCTAAGCAGAGGCTCCACAAC-TTGGAAAAA
1 ATAAACAAAGCTCCTCTAAGCAGAGGCTCCACGACTTTGGAAAAA
* *
9509282 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGG
1 ATAAACAAAGCTCCTCTAAGCAGAGGCTCCACGACTTTGG
9509322 GAACAATGAA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
43 4 0.05
44 69 0.90
45 4 0.05
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (45 bp):
ATAAACAAAGCTCCTCTAAGCAGAGGCTCCACGACTTTGGAAAAA
Found at i:9509283 original size:111 final size:110
Alignment explanation
Indices: 9509090--9509305 Score: 333
Period size: 111 Copynumber: 2.0 Consensus size: 110
9509080 AAAAATAAGT
* * * *
9509090 AAAGCTCTTCTAAACAGAGGCTCGATGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAGGCT
1 AAAGCTCCTCTAAACAAAGGCTCCACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAGGCT
** * *
9509155 CCATGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGATAAAC
66 CCACAACTTGGAAAAAATAAACAAAGCTCCTCTAAACAGATAAAC
* *
9509200 AAAGCTCCTCTAAGCAAAGGCTCCACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGCAGAGGC
1 AAAGCTCCTCTAAACAAAGGCTCCACGACTTT-GAAAAATAAACAAAGCTCCTCTAAACAGAGGC
9509265 TCCACAACTTGGAAAAAATAAACAAAGCTCCTCTAAACAGA
65 TCCACAACTTGGAAAAAATAAACAAAGCTCCTCTAAACAGA
9509306 GGCTCAACGA
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
110 27 0.28
111 68 0.72
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.19
Consensus pattern (110 bp):
AAAGCTCCTCTAAACAAAGGCTCCACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAGGCT
CCACAACTTGGAAAAAATAAACAAAGCTCCTCTAAACAGATAAAC
Found at i:9509377 original size:43 final size:41
Alignment explanation
Indices: 9509247--9509423 Score: 122
Period size: 43 Copynumber: 4.1 Consensus size: 41
9509237 AATAAACAAA
* * **
9509247 GCTCCTCTAAGCAGAGGCTCCACAA-CTTGGAAAAAATAAACAAA
1 GCTCCTCTAAACAGAGGCACCACAACCTT-G-AAAAAT-AA-ATT
* * * * * *
9509291 GCTCCTCTAAACAGAGGCTCAACGACTTTGGGAACAATGAATT
1 GCTCCTCTAAACAGAGGCACCACAACCTT--GAAAAATAAATT
* * * *
9509334 GCTCTTCTAAACGGAGGCAACCACGACTGTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGC-ACCACAAC-CTTGAAAAATAAATT
* * *
9509377 GCTCCTCTAAATAGAGGCATCACAACCTTGAACAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACCTTGAAAAATAAATT
9509418 GCTCCT
1 GCTCCT
9509424 TGACGATCAA
Statistics
Matches: 107, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
41 19 0.18
42 6 0.06
43 42 0.39
44 29 0.27
45 9 0.08
46 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACAACCTTGAAAAATAAATT
Found at i:9509420 original size:41 final size:41
Alignment explanation
Indices: 9509291--9509423 Score: 133
Period size: 43 Copynumber: 3.1 Consensus size: 41
9509281 AATAAACAAA
* *
9509291 GCTCCTCTAAACAGAGGC-TCAACGACTTTGGGAACAATGAATT
1 GCTCCTCTAAACAGAGGCATC-ACGACCTT--GAACAATAAATT
* * * * *
9509334 GCTCTTCTAAACGGAGGCAACCACGACTGTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGC-ATCACGAC-CTTGAACAATAAATT
* *
9509377 GCTCCTCTAAATAGAGGCATCACAACCTTGAACAATAAATT
1 GCTCCTCTAAACAGAGGCATCACGACCTTGAACAATAAATT
9509418 GCTCCT
1 GCTCCT
9509424 TGACGATCAA
Statistics
Matches: 74, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
41 19 0.26
42 6 0.08
43 41 0.55
44 5 0.07
45 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCATCACGACCTTGAACAATAAATT
Found at i:9510455 original size:13 final size:13
Alignment explanation
Indices: 9510439--9510500 Score: 81
Period size: 13 Copynumber: 4.6 Consensus size: 13
9510429 TCATTCACTT
9510439 TTTTTTCTTTTCA
1 TTTTTTCTTTTCA
9510452 TTTTCTT-TTTTCA
1 TTTT-TTCTTTTCA
9510465 TTTTTTTCTTTTTCA
1 -TTTTTTC-TTTTCA
*
9510480 TTTTTTCATTTCA
1 TTTTTTCTTTTCA
9510493 TTTTTTCT
1 TTTTTTCT
9510501 CTTTTTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
13 24 0.56
14 13 0.30
15 6 0.14
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTCTTTTCA
Found at i:9510477 original size:28 final size:28
Alignment explanation
Indices: 9510425--9510506 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 28
9510415 TGAGTCCTCC
9510425 TTTTTCA-TTCACTTTTTTT-TCTTTTCAT
1 TTTTTCATTTCA-TTTTTTTCT-TTTTCAT
*
9510453 TTTCTT-TTTTCATTTTTTTCTTTTTCAT
1 TTT-TTCATTTCATTTTTTTCTTTTTCAT
9510481 TTTTTCATTTCATTTTTTCTCTTTTT
1 TTTTTCATTTCATTTTTT-TCTTTTT
9510507 TTTCAAGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
27 2 0.04
28 31 0.66
29 14 0.30
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTTCATTTCATTTTTTTCTTTTTCAT
Found at i:9510487 original size:23 final size:22
Alignment explanation
Indices: 9510425--9510490 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 22
9510415 TGAGTCCTCC
**
9510425 TTTTTCATTCACTTTTTT--TT
1 TTTTTCATTTTCTTTTTTCATT
*
9510445 CTTTTCATTTTCTTTTTTCATT
1 TTTTTCATTTTCTTTTTTCATT
*
9510467 TTTTTCTTTTTCATTTTTTCATT
1 TTTTTCATTTTC-TTTTTTCATT
9510490 T
1 T
9510491 CATTTTTTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 15 0.39
22 12 0.32
23 11 0.29
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTCATTTTCTTTTTTCATT
Found at i:9521034 original size:60 final size:58
Alignment explanation
Indices: 9520963--9521187 Score: 256
Period size: 60 Copynumber: 3.8 Consensus size: 58
9520953 TACTTTTATA
*
9520963 CAAGGAAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTCTAAAACTTTAATTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTT-TAAAAC-TTATTTT
* * ** *
9521023 CAAGGAAAATTGATACTTTCAATTTTTCCTACAAAAAAACCTTTTTTAGAAAATTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTTA-AAACTTATTTT
* ** **
9521083 CAAAGAAAATTGATACTTTCAACTTCTT-CTTGAAAATATTTTTTAGAAAACTTATTTT
1 CAAGGAAAATTGATACTTTCAACTT-TTCCTCAAAAATATTTTTTTTAAAACTTATTTT
* * *
9521141 CAAGAAAAATTGATACTTTCAACTTCTCCTCAAAAATATATTTTTTA
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTA
9521188 GAATTTTTAT
Statistics
Matches: 136, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
57 1 0.01
58 47 0.35
59 10 0.07
60 61 0.45
61 16 0.12
62 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (58 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAAAACTTATTTT
Found at i:9521199 original size:118 final size:120
Alignment explanation
Indices: 9520967--9521190 Score: 312
Period size: 118 Copynumber: 1.9 Consensus size: 120
9520957 TTTATACAAG
** *
9520967 GAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTCTAAAACTTTAATTTCAAGGAAAA
1 GAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTAGAAAACTTTAATTTCAAGAAAAA
* * *
9521032 TTGATACTTTCAATTTTTCCTACAAAAAAACCTTTTTTAGAAAATTATTTTCAAA
66 TTGATACTTTCAACTTCTCCTACAAAAAAACATTTTTTAGAAAATTATTTTCAAA
* * *
9521087 GAAAATTGATACTTTCAACTTCTT-CTTGAAAATA-TTTTTTAGAAAAC-TTATTTTCAAGAAAA
1 GAAAATTGATACTTTCAACTT-TTCCCTAAAAATATTTTTTTAGAAAACTTTAATTTCAAGAAAA
* *
9521149 ATTGATACTTTCAACTTCTCCT-CAAAAATATATTTTTTAGAA
65 ATTGATACTTTCAACTTCTCCTACAAAAAAACATTTTTTAGAA
9521191 TTTTTATTTA
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
117 17 0.18
118 33 0.36
119 11 0.12
120 29 0.32
121 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (120 bp):
GAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTAGAAAACTTTAATTTCAAGAAAAA
TTGATACTTTCAACTTCTCCTACAAAAAAACATTTTTTAGAAAATTATTTTCAAA
Found at i:9522148 original size:43 final size:42
Alignment explanation
Indices: 9522094--9522187 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 42
9522084 TAAAATAAAG
* *
9522094 ATAATATATTAATAGATAACTAAAAGAAAATAATTAGATAAATA
1 ATAAAATATTAATAGATAAATAAAA-AAAATAA-TAGATAAATA
* *
9522138 A-AAAATATTAATAGATAAATAACAATAATAATAGATAAATA
1 ATAAAATATTAATAGATAAATAAAAAAAATAATAGATAAATA
9522179 ATAAAATAT
1 ATAAAATAT
9522188 ATATATTAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 11 0.24
42 13 0.29
43 20 0.44
44 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (42 bp):
ATAAAATATTAATAGATAAATAAAAAAAATAATAGATAAATA
Found at i:9522155 original size:17 final size:17
Alignment explanation
Indices: 9522120--9522181 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 17
9522110 TAACTAAAAG
*
9522120 AAAATAATTAGATAAATAA
1 AAAAT-ATTA-ATAGATAA
9522139 AAAATATTAATAGATAAA
1 AAAATATTAATAGAT-AA
*
9522157 TAACAATAATAATAGATAA
1 -AA-AATATTAATAGATAA
*
9522176 ATAATA
1 AAAATA
9522182 AAATATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.24
18 7 0.19
19 9 0.24
20 12 0.32
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAATATTAATAGATAA
Found at i:9522169 original size:20 final size:20
Alignment explanation
Indices: 9522103--9522248 Score: 96
Period size: 21 Copynumber: 6.8 Consensus size: 20
9522093 GATAATATAT
* *
9522103 TAATAGATAACTAAAAGAAAA
1 TAATAGATAAATAAAA-ATAA
*
9522124 TAATTAGATAAATAAAAAATAT
1 TAA-TAGATAAAT-AAAAATAA
*
9522146 TAATAGATAAATAACAATAA
1 TAATAGATAAATAAAAATAA
9522166 TAATAGATAAATAATAAAATATA
1 TAATAGATAAAT-A-AAAATA-A
*
9522189 TATATTAACAGATAAATAATAATAA
1 TA-A-T---AGATAAATAAAAATAA
* * *
9522214 T-ATATATTAATAAATAGTAA
1 TAATAGATAAATAAA-AATAA
*
9522234 TAATAAATAAATAAA
1 TAATAGATAAATAAA
9522249 TAAGATACAA
Statistics
Matches: 100, Mismatches: 13, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
19 8 0.08
20 23 0.23
21 24 0.24
22 19 0.19
23 8 0.08
24 1 0.01
25 3 0.03
26 5 0.05
27 1 0.01
28 8 0.08
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
TAATAGATAAATAAAAATAA
Found at i:9522240 original size:13 final size:12
Alignment explanation
Indices: 9522204--9522247 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
9522194 TAACAGATAA
9522204 ATAATAATAATAT
1 ATAATAATAA-AT
*
9522217 ATATTAATAAAT
1 ATAATAATAAAT
9522229 AGTAATAATAAAT
1 A-TAATAATAAAT
9522242 A-AATAA
1 ATAATAA
9522248 ATAAGATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 5 0.18
12 3 0.11
13 20 0.71
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:9522282 original size:14 final size:14
Alignment explanation
Indices: 9522242--9522294 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
9522232 AATAATAAAT
9522242 AAATAAATAAGATACAA
1 AAATAAA-AA-ATAC-A
*
9522259 AAATTAAAAATACA
1 AAATAAAAAATACA
* *
9522273 AAATACAAAATAAA
1 AAATAAAAAATACA
9522287 AAATAAAA
1 AAATAAAA
9522295 TAAAATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 19 0.61
15 4 0.13
16 2 0.06
17 6 0.19
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (14 bp):
AAATAAAAAATACA
Found at i:9523077 original size:19 final size:20
Alignment explanation
Indices: 9523055--9523092 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
9523045 AGAATTTCAT
*
9523055 AAATTGATT-TTTATAAAAA
1 AAATTGATTATTAATAAAAA
*
9523074 AAATTTATTATTAATAAAA
1 AAATTGATTATTAATAAAA
9523093 TATTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATTGATTATTAATAAAAA
Found at i:9526548 original size:21 final size:22
Alignment explanation
Indices: 9526524--9526564 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9526514 CTTAGAAATG
*
9526524 CATAA-TAGTATGTTATTTAGT
1 CATAATTAGGATGTTATTTAGT
*
9526545 CATAATTAGGATTTTATTTA
1 CATAATTAGGATGTTATTTA
9526565 TTATTAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (22 bp):
CATAATTAGGATGTTATTTAGT
Found at i:9529419 original size:21 final size:20
Alignment explanation
Indices: 9529376--9529413 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9529366 TTTTTTATCT
9529376 AAATTCATATTCTTTCTCTAA
1 AAATTCATA-TCTTTCTCTAA
9529397 AAATTCATA-CTTTCTCT
1 AAATTCATATCTTTCTCT
9529414 TTAAAACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTCATATCTTTCTCTAA
Found at i:9529451 original size:22 final size:23
Alignment explanation
Indices: 9529409--9529453 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
9529399 ATTCATACTT
*
9529409 TCTCTTTAAAACTGAACCAATTC
1 TCTCTTTAAAACTCAACCAATTC
9529432 TCTCTTT-AAACTCAGA-CAATTC
1 TCTCTTTAAAACTCA-ACCAATTC
9529454 ACAAACAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (23 bp):
TCTCTTTAAAACTCAACCAATTC
Found at i:9535120 original size:37 final size:37
Alignment explanation
Indices: 9535065--9535155 Score: 130
Period size: 37 Copynumber: 2.4 Consensus size: 37
9535055 TTTAAGGTAT
* *
9535065 AACCTTTACAATCCTTATCTTTTGAAAGG-TAAGATAAC
1 AACCTTTAC-CTCTTTATCTTTTG-AAGGTTAAGATAAC
9535103 AACCTTTACCTCTTTATCTTTTGAAGGTTAAGATAAC
1 AACCTTTACCTCTTTATCTTTTGAAGGTTAAGATAAC
*
9535140 AACCTTTACCTTTTTA
1 AACCTTTACCTCTTTA
9535156 AAGATTTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 4 0.08
37 36 0.73
38 9 0.18
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.40
Consensus pattern (37 bp):
AACCTTTACCTCTTTATCTTTTGAAGGTTAAGATAAC
Found at i:9537633 original size:42 final size:42
Alignment explanation
Indices: 9537582--9537690 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
9537572 TTGTTGGTTC
*
9537582 AAACACCACTAAAAATTGGTAAATAGCAGCAT-TT-TAGAATGT
1 AAACGCCACTAAAAATTGGTAAATAGC-G-ATGTTATAGAATGT
* *
9537624 AAACGCCACTAAAATTTGGTAAATAGCGATGTTATGGAATGT
1 AAACGCCACTAAAAATTGGTAAATAGCGATGTTATAGAATGT
* * *
9537666 AAATGCCACTAAATATTAGTAAATA
1 AAACGCCACTAAAAATTGGTAAATA
9537691 ATGGCATTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 2 0.03
41 3 0.05
42 53 0.91
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (42 bp):
AAACGCCACTAAAAATTGGTAAATAGCGATGTTATAGAATGT
Found at i:9538545 original size:19 final size:20
Alignment explanation
Indices: 9538508--9538547 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9538498 CAGGTTCAGT
* *
9538508 TTTTTTTTATTAATTTAAAA
1 TTTTTTTAATTAATCTAAAA
9538528 TTTTTTTAATT-ATCTAAAA
1 TTTTTTTAATTAATCTAAAA
9538547 T
1 T
9538548 AATTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTAATTAATCTAAAA
Found at i:9546938 original size:150 final size:153
Alignment explanation
Indices: 9546661--9546995 Score: 434
Period size: 150 Copynumber: 2.2 Consensus size: 153
9546651 ACTATGTTTC
* * * * *
9546661 TAATTGCAAGATAGATGTTAATTTCCCTTCCATTCTATCAGCAATCATAATTACGTTACAAGTAT
1 TAATTGCAAGACAGATATTAATTTCCCTTCCATTCTA-CAGCAACCATAATTACCTTACAAGCAT
* * *
9546726 TAATTGCAAATTTATGACTAAATAATAAATGCTCACAAATATTTCAAATTTATGATTTAAATATT
65 TAATTGCAAATTTATGACTAAATAATAAATGCTCAAAAATATTTCAAATTTATGACTCAAATATT
*
9546791 ACGTTTCTATTCATAGAAATGCAA
130 ACATTTCTATTCATAGAAATGCAA
*
9546815 TAATTGCAAGACAGATATTAATTTCCCTATCCA-TC-A-A-CAACCATAATTGCCTTACAAGCAT
1 TAATTGCAAGACAGATATTAATTTCCCT-TCCATTCTACAGCAACCATAATTACCTTACAAGCAT
* *
9546876 TAATTGTAAATTTATGACTAAATAATAGATGGC-CATAAAAT-TTTCAAATTTACT-ACTCAAAT
65 TAATTGCAAATTTATGACTAAATAATAAAT-GCTCA-AAAATATTTCAAATTTA-TGACTCAAAT
* *
9546938 ATTGCATTTCTATTCATAGAAATGCAG
127 ATTACATTTCTATTCATAGAAATGCAA
*
9546965 TAATTGTAAGACAGATATTAA-TTCCCTTCCA
1 TAATTGCAAGACAGATATTAATTTCCCTTCCA
9546996 ATAATATAAA
Statistics
Matches: 162, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
148 4 0.02
149 6 0.04
150 111 0.69
151 8 0.05
153 1 0.01
154 28 0.17
155 4 0.02
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (153 bp):
TAATTGCAAGACAGATATTAATTTCCCTTCCATTCTACAGCAACCATAATTACCTTACAAGCATT
AATTGCAAATTTATGACTAAATAATAAATGCTCAAAAATATTTCAAATTTATGACTCAAATATTA
CATTTCTATTCATAGAAATGCAA
Found at i:9561846 original size:21 final size:21
Alignment explanation
Indices: 9561804--9561846 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9561794 GCAACAAATT
** * *
9561804 AATGACCAGGAGCAACGCCTC
1 AATGACCAACAGCAAAGACTC
9561825 AATGACCAACAGCAAAGACTC
1 AATGACCAACAGCAAAGACTC
9561846 A
1 A
9561847 TTGTTTTGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.19, T:0.09
Consensus pattern (21 bp):
AATGACCAACAGCAAAGACTC
Found at i:9568171 original size:14 final size:13
Alignment explanation
Indices: 9568152--9568195 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
9568142 AAACAAAGCC
9568152 TAAAAAATTAAATA
1 TAAAAAATTAAA-A
9568166 TAAAAAATATAAAA
1 TAAAAAAT-TAAAA
*
9568180 -AAAAAATCAAAA
1 TAAAAAATTAAAA
9568192 TAAA
1 TAAA
9568196 TTAAAAGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 4 0.15
13 10 0.37
14 9 0.33
15 4 0.15
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAAATTAAAA
Found at i:9568630 original size:43 final size:45
Alignment explanation
Indices: 9568573--9568663 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 45
9568563 AAACACAGAT
* * **
9568573 AAAAAAAACAACTGCTGCAGAAATTA-GGAAAC-AGATCAGAAAA
1 AAAAAAAAAAACTGCAGCAGAAACCAGGGAAACAAGATCAGAAAA
9568616 AAAAAAAAAAACTGCAGCAGAAACCAGGGAAACATAGATCAGAAAA
1 AAAAAAAAAAACTGCAGCAGAAACCAGGGAAACA-AGATCAGAAAA
9568662 AA
1 AA
9568664 CTGCAGTAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 22 0.54
44 6 0.15
46 13 0.32
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.09
Consensus pattern (45 bp):
AAAAAAAAAAACTGCAGCAGAAACCAGGGAAACAAGATCAGAAAA
Found at i:9568694 original size:35 final size:36
Alignment explanation
Indices: 9568621--9568719 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 36
9568611 GAAAAAAAAA
* *
9568621 AAAAAACTGCAGCAGAAACCAGGGAAACATAGATCAG
1 AAAAAACTGCAGCAGAAACTA-GGAAACATAGACCAG
*
9568658 AAAAAACTGCAGTAGAAA-TAGGAAACACTA-ACCAG
1 AAAAAACTGCAGCAGAAACTAGGAAACA-TAGACCAG
* *
9568693 AAAATATTGCAGCAGAAACT-GGAAACA
1 AAAAAACTGCAGCAGAAACTAGGAAACA
9568720 GAAACTAGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
35 33 0.61
36 4 0.07
37 17 0.31
ACGTcount: A:0.53, C:0.17, G:0.19, T:0.11
Consensus pattern (36 bp):
AAAAAACTGCAGCAGAAACTAGGAAACATAGACCAG
Found at i:9568780 original size:35 final size:34
Alignment explanation
Indices: 9568687--9568768 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
9568677 AGGAAACACT
* * **
9568687 AACCAGAAAATATTGCAGCAGAAACTGGAAACAGA
1 AACCAGAAGATACTGCAGCAG-AACAAGAAACAGA
*
9568722 AACTAGAAGTATACTGCAGCAGAACAAGAAACAGA
1 AACCAGAAG-ATACTGCAGCAGAACAAGAAACAGA
9568757 AACCAGAA-ATAC
1 AACCAGAAGATAC
9568769 GTTGTAGCAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 4 0.10
35 25 0.62
36 11 0.28
ACGTcount: A:0.52, C:0.18, G:0.18, T:0.11
Consensus pattern (34 bp):
AACCAGAAGATACTGCAGCAGAACAAGAAACAGA
Found at i:9569558 original size:16 final size:16
Alignment explanation
Indices: 9569537--9569568 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9569527 AGCTAAAAGA
9569537 AGGTTTCATAGAAATG
1 AGGTTTCATAGAAATG
9569553 AGGTTTCATAGAAATG
1 AGGTTTCATAGAAATG
9569569 GTTTGCCTAA
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:0.06, G:0.25, T:0.31
Consensus pattern (16 bp):
AGGTTTCATAGAAATG
Found at i:9570229 original size:12 final size:13
Alignment explanation
Indices: 9570202--9570244 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
9570192 AAAATCGAAT
9570202 TCCTAAATTAAAA
1 TCCTAAATTAAAA
*
9570215 TCCTAAA-TGAAA
1 TCCTAAATTAAAA
9570227 TCCTAAATTAAAA
1 TCCTAAATTAAAA
*
9570240 CCCTA
1 TCCTA
9570245 GAATGAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (13 bp):
TCCTAAATTAAAA
Found at i:9570236 original size:25 final size:25
Alignment explanation
Indices: 9570184--9570258 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
9570174 AACCCTAACC
* *
9570184 AAAATCTTAAAATCGAATTCCTAAATT
1 AAAATCCT-AAAT-GAAATCCTAAATT
9570211 AAAATCCTAAATGAAATCCTAAATT
1 AAAATCCTAAATGAAATCCTAAATT
* *
9570236 AAAACCCTAGAATGAAACCCTAA
1 AAAATCCTA-AATGAAATCCTAA
9570259 TCTGCAACCT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 20 0.47
26 16 0.37
27 7 0.16
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.25
Consensus pattern (25 bp):
AAAATCCTAAATGAAATCCTAAATT
Found at i:9570253 original size:13 final size:12
Alignment explanation
Indices: 9570216--9570258 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
9570206 AAATTAAAAT
*
9570216 CCTAAATGAAAT
1 CCTAAATGAAAC
*
9570228 CCTAAATTAAAAC
1 CCTAAA-TGAAAC
9570241 CCTAGAATGAAAC
1 CCTA-AATGAAAC
9570254 CCTAA
1 CCTAA
9570259 TCTGCAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 7 0.27
13 17 0.65
14 2 0.08
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (12 bp):
CCTAAATGAAAC
Found at i:9570352 original size:20 final size:21
Alignment explanation
Indices: 9570295--9570361 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 21
9570285 AATGAAATCC
9570295 TAGGTGAAAAC-C-AAAACCT
1 TAGGTGAAAACTCGAAAACCT
*
9570314 TAGTTGAAAACT-G-AAACCT
1 TAGGTGAAAACTCGAAAACCT
9570333 TAGGT-AAAACTCGAAAACC-
1 TAGGTGAAAACTCGAAAACCT
9570352 TAGGT-AAAAC
1 TAGGTGAAAAC
9570362 CCTAAATCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.14
19 31 0.74
20 5 0.12
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.19
Consensus pattern (21 bp):
TAGGTGAAAACTCGAAAACCT
Found at i:9571136 original size:15 final size:15
Alignment explanation
Indices: 9571112--9571141 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9571102 ATAATATTCC
9571112 TAAATAAATTTTTTT
1 TAAATAAATTTTTTT
*
9571127 TAAATTAATTTTTTT
1 TAAATAAATTTTTTT
9571142 CTTAAAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TAAATAAATTTTTTT
Found at i:9575388 original size:6 final size:7
Alignment explanation
Indices: 9575347--9575396 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
9575337 GTTTTTCTTT
9575347 AAAAGGAA
1 AAAAGG-A
*
9575355 AAATAGAA
1 AAA-AGGA
9575363 AAAAGGAA
1 AAAAGG-A
9575371 AAATAGGA
1 AAA-AGGA
9575379 AAAAGGA
1 AAAAGGA
9575386 AAAAGGA
1 AAAAGGA
9575393 AAAA
1 AAAA
9575397 ATTGTTAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
7 17 0.46
8 15 0.41
9 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (7 bp):
AAAAGGA
Found at i:9575389 original size:8 final size:8
Alignment explanation
Indices: 9575347--9575397 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
9575337 GTTTTTCTTT
9575347 AAAAGGAA
1 AAAAGGAA
9575355 AAATA-GAA
1 AAA-AGGAA
9575363 AAAAGGAA
1 AAAAGGAA
9575371 AAATAGG-A
1 AAA-AGGAA
9575379 AAAAGG-A
1 AAAAGGAA
9575386 AAAAGGAA
1 AAAAGGAA
9575394 AAAA
1 AAAA
9575398 TTGTTAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 11 0.28
8 24 0.62
9 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.04
Consensus pattern (8 bp):
AAAAGGAA
Found at i:9575397 original size:16 final size:16
Alignment explanation
Indices: 9575347--9575389 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
9575337 GTTTTTCTTT
9575347 AAAAGGAAAAATAGAA
1 AAAAGGAAAAATAGAA
*
9575363 AAAAGGAAAAATAGGA
1 AAAAGGAAAAATAGAA
9575379 AAAAGGAAAAA
1 AAAAGGAAAAA
9575390 GGAAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (16 bp):
AAAAGGAAAAATAGAA
Found at i:9576040 original size:25 final size:25
Alignment explanation
Indices: 9576011--9576059 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
9576001 CTTTAAATGA
9576011 GTTTATTCCACATGAACT-TTTTCTT
1 GTTTATTCCACATG-ACTCTTTTCTT
*
9576036 GTTTATTCTACATGACTCTTTTCT
1 GTTTATTCCACATGACTCTTTTCT
9576060 CATAATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.18, C:0.20, G:0.08, T:0.53
Consensus pattern (25 bp):
GTTTATTCCACATGACTCTTTTCTT
Found at i:9576709 original size:17 final size:17
Alignment explanation
Indices: 9576687--9576750 Score: 58
Period size: 22 Copynumber: 3.5 Consensus size: 17
9576677 GAATTTACTT
9576687 AAAGAAAAGAAAAAGTG
1 AAAGAAAAGAAAAAGTG
9576704 AAAGAATGAAAAAGAAAAAGTG
1 --A-AA-G-AAAAGAAAAAGTG
*
9576726 -AAGAAAAGAGAAAAATG
1 AAAGAAAAGA-AAAAGTG
9576743 AAAGAAAA
1 AAAGAAAA
9576751 AAGAAAAAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 6 0.15
17 7 0.18
18 9 0.23
19 1 0.03
20 2 0.05
21 1 0.03
22 13 0.33
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (17 bp):
AAAGAAAAGAAAAAGTG
Found at i:9576717 original size:22 final size:19
Alignment explanation
Indices: 9576691--9576759 Score: 88
Period size: 18 Copynumber: 3.6 Consensus size: 19
9576681 TTACTTAAAG
9576691 AAAAGAAAAAGTGAAAGAATGA
1 AAAAGAAAAAGTGAAAG-A--A
9576713 AAAAGAAAAAGTG-AAGAA
1 AAAAGAAAAAGTGAAAGAA
*
9576731 AAGAGAAAAA-TGAAAGAA
1 AAAAGAAAAAGTGAAAGAA
9576749 AAAAGAAAAAG
1 AAAAGAAAAAG
9576760 AAAAGAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 2 0.05
18 24 0.56
20 1 0.02
21 3 0.07
22 13 0.30
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAAGTGAAAGAA
Found at i:9576737 original size:7 final size:6
Alignment explanation
Indices: 9576687--9576763 Score: 52
Period size: 6 Copynumber: 12.3 Consensus size: 6
9576677 GAATTTACTT
* *
9576687 AAAG-A AAAGAA AAAGTGAA AGAATGAA AAAGAA AAAG-T GAAGAA AAGAGAA
1 AAAGAA AAAGAA AAA--GAA A-AA-GAA AAAGAA AAAGAA AAAGAA AA-AGAA
*
9576738 AAATGAA AGA-AA AAAGAA AAAGAA AA
1 AAA-GAA AAAGAA AAAGAA AAAGAA AA
9576764 GAAGAAAACA
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
5 11 0.19
6 23 0.40
7 13 0.22
8 9 0.16
9 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:9576748 original size:11 final size:11
Alignment explanation
Indices: 9576734--9576805 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
9576724 TGAAGAAAAG
*
9576734 AGAAAAATGAA
1 AGAAAAAAGAA
9576745 AGAAAAAAGAA
1 AGAAAAAAGAA
9576756 A-AAGAAAAG-A
1 AGAA-AAAAGAA
9576766 AGAAAACAAAGAA
1 AG-AAA-AAAGAA
* * *
9576779 AGATATAAGGA
1 AGAAAAAAGAA
9576790 A-AAAAAAGAA
1 AGAAAAAAGAA
*
9576800 ATAAAA
1 AGAAAA
9576806 TGAAATGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
10 11 0.23
11 26 0.54
12 8 0.17
13 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (11 bp):
AGAAAAAAGAA
Found at i:9576759 original size:13 final size:13
Alignment explanation
Indices: 9576726--9576771 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
9576716 AGAAAAAGTG
9576726 AAGAAAAGAGAAAA
1 AAGAAAA-AGAAAA
*
9576740 ATG--AAAGAAAA
1 AAGAAAAAGAAAA
9576751 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
9576764 GAAGAAAA
1 -AAGAAAA
9576772 CAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
13 8 0.30
14 9 0.33
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:9578054 original size:33 final size:33
Alignment explanation
Indices: 9577999--9578067 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
9577989 GCACCCAGGT
* ** *
9577999 TTTAAGCCTAGATTAGTTGGCACCTA-GTGAAAA
1 TTTAAGCCCAGATTAGCGGGCA-CTACATGAAAA
*
9578032 TTTAAGCCCAGTTTAGCGGGCACTACATGAAAA
1 TTTAAGCCCAGATTAGCGGGCACTACATGAAAA
9578065 TTT
1 TTT
9578068 TAAACCTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (33 bp):
TTTAAGCCCAGATTAGCGGGCACTACATGAAAA
Found at i:9578119 original size:33 final size:33
Alignment explanation
Indices: 9578066--9578657 Score: 140
Period size: 33 Copynumber: 18.0 Consensus size: 33
9578056 ACATGAAAAT
** * * *
9578066 TTTAAACCTAACTTAGCTAGCATCTAGTGAAGT
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
*
9578099 TTTAAACCTAGTTTAACTAGCA-CCAATGAAGA
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
* * * * *
9578131 TTT-AAGCTCAATTTATC-AGGCATTTCATGAAAAGA
1 TTTAAACCT-AGTTTAACTA-GCATCTAATG--AAGA
* * * * *
9578166 TTTAAACCTAGTCTATCTAGCACCTAGTGAAGT
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
* * * *
9578199 TTTAAGCATAGTTTAATTTGCA-CTAATGAAGA
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
* ** * * * *
9578231 TTTAAGCCTAGTTTAGTTGGCACCTATTGAAGT
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
* * * *
9578264 TTTAAGCATAGTTTAATTTGCATC-AATGAAGA
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
* * * *
9578296 TTTAAGCCCAGTTTAA-TTGACA-CGAATGAAGA
1 TTTAAACCTAGTTTAACTAG-CATCTAATGAAGA
** * * *
9578328 TTT-AAGTTCAGTTTATCTGACCCTC-AATGAA-A
1 TTTAAACCT-AGTTTAACT-AGCATCTAATGAAGA
* * * * *
9578360 TTTTAAGCCTAGCTTATCTAGTAT-TCATGAAAAGA
1 -TTTAAACCTAGTTTAACTAGCATCTAATG--AAGA
* * * *
9578395 TTT-AAGCTCAGTTTAACTGGC-GCTATTGAAGA
1 TTTAAACCT-AGTTTAACTAGCATCTAATGAAGA
* * * * * * *
9578427 TTTAATCCCAGTTTATCTAGTACCCAATGAAAA
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
* * * * *
9578460 TTTAAACCCAGTTTAGCTAGCACCCAATAAAAAGA
1 TTTAAACCTAGTTTAACTAGCATCTAAT--GAAGA
* * * * * *
9578495 TTTAAGCCTAATTTGATTGGCA-CTAATAAAGA
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
* * * * *
9578527 TTTAAGTCC-AATTTATCTAGCACCTAATAAAGA
1 TTTAA-ACCTAGTTTAACTAGCATCTAATGAAGA
* * * * **
9578560 TTTTAGCCCAATTTAGTTAGCATC-AATGAAGA
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
* * * * * *
9578592 TTTAAGCCTTGTTTATA-TGGCACCCAGTGAAGA
1 TTTAAACCTAGTTTA-ACTAGCATCTAATGAAGA
* * *
9578625 TTTAAGCCCAGTTTAACTAGCA-CTACTGAAGA
1 TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
9578657 T
1 T
9578658 ATAAGCCCAA
Statistics
Matches: 414, Mismatches: 113, Indels: 65
0.70 0.19 0.11
Matches are distributed among these distances:
31 10 0.02
32 161 0.39
33 177 0.43
34 23 0.06
35 38 0.09
36 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (33 bp):
TTTAAACCTAGTTTAACTAGCATCTAATGAAGA
Found at i:9578122 original size:100 final size:101
Alignment explanation
Indices: 9578018--9578246 Score: 268
Period size: 100 Copynumber: 2.3 Consensus size: 101
9578008 AGATTAGTTG
* * * *
9578018 GCACCTAGTGAAAATTTAAGCCCAGTTTAGCGGGCACTACATGAAAA-TTTTAAACCTAACT-TA
1 GCACCTAATGAAGATTTAAGCCCAGTTTAGCAGGCACTACATGAAAAGATTTAAACCT-ACTCTA
* *
9578081 GCTAGCATCTAGTGAAGTTTTAAACCTAGTTTAACTA
65 GCTAGCACCTAGTGAAGTTTTAAACATAGTTTAACTA
* * * * * * *
9578118 GCACC-AATGAAGATTTAAGCTCAATTTATCAGGCATTTCATGAAAAGATTTAAACCTAGTCTAT
1 GCACCTAATGAAGATTTAAGCCCAGTTTAGCAGGCACTACATGAAAAGATTTAAACCTACTCTAG
* * *
9578182 CTAGCACCTAGTGAAGTTTTAAGCATAGTTTAATTT
66 CTAGCACCTAGTGAAGTTTTAAACATAGTTTAACTA
*
9578218 GCA-CTAATGAAGATTTAAGCCTAGTTTAG
1 GCACCTAATGAAGATTTAAGCCCAGTTTAG
9578247 TTGGCACCTA
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
99 36 0.34
100 70 0.66
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (101 bp):
GCACCTAATGAAGATTTAAGCCCAGTTTAGCAGGCACTACATGAAAAGATTTAAACCTACTCTAG
CTAGCACCTAGTGAAGTTTTAAACATAGTTTAACTA
Found at i:9578135 original size:32 final size:32
Alignment explanation
Indices: 9578093--9578870 Score: 248
Period size: 32 Copynumber: 23.8 Consensus size: 32
9578083 TAGCATCTAG
* *
9578093 TGAAGTTTTAAACCTAGTTTAACTAGCACCAA
1 TGAAGATTTAAGCCTAGTTTAACTAGCACCAA
* * *
9578125 TGAAGATTTAAG-CTCAATTTATC-AGGCATTTC-A
1 TGAAGATTTAAGCCT-AGTTTAACTA-GCA--CCAA
* * * *
9578158 TGAAAAGATTTAAACCTAGTCTATCTAGCACCTAG
1 TG--AAGATTTAAGCCTAGTTTAACTAGCACC-AA
* * * * *
9578193 TGAAGTTTTAAGCATAGTTTAATTTGCACTAA
1 TGAAGATTTAAGCCTAGTTTAACTAGCACCAA
** * *
9578225 TGAAGATTTAAGCCTAGTTTAGTTGGCACCTAT
1 TGAAGATTTAAGCCTAGTTTAACTAGCACC-AA
* * * * *
9578258 TGAAGTTTTAAGCATAGTTTAATTTGCATCAA
1 TGAAGATTTAAGCCTAGTTTAACTAGCACCAA
* * *
9578290 TGAAGATTTAAGCCCAGTTTAA-TTGACACGAA
1 TGAAGATTTAAGCCTAGTTTAACTAG-CACCAA
* * *
9578322 TGAAGATTTAAG-TTCAGTTTATCT-GACCCTCAA
1 TGAAGATTTAAGCCT-AGTTTAACTAG-CAC-CAA
* * * *
9578355 TGAA-ATTTTAAGCCTAGCTTATCTAGTATTC-A
1 TGAAGA-TTTAAGCCTAGTTTAACTAGCA-CCAA
* * * *
9578387 TGAAAAGATTTAAG-CTCAGTTTAACTGGCGCTAT
1 TG--AAGATTTAAGCCT-AGTTTAACTAGCACCAA
* * * *
9578421 TGAAGATTTAATCCCAGTTTATCTAGTACCCAA
1 TGAAGATTTAAGCCTAGTTTAACTAGCA-CCAA
* * * *
9578454 TGAAAATTTAAACCCAGTTTAGCTAGCACCCAA
1 TGAAGATTTAAGCCTAGTTTAACTAGCA-CCAA
* * * * * *
9578487 TAAAAAGATTTAAGCCTAATTTGATTGGCACTAA
1 T--GAAGATTTAAGCCTAGTTTAACTAGCACCAA
* * *
9578521 TAAAGATTTAAGTCC-AATTTATCTAGCACCTAA
1 TGAAGATTTAAG-CCTAGTTTAACTAGCACC-AA
* * * * ** *
9578554 TAAAGATTTTAGCCCAATTTAGTTAGCATCAA
1 TGAAGATTTAAGCCTAGTTTAACTAGCACCAA
* * *
9578586 TGAAGATTTAAGCCTTGTTTATA-TGGCACCCAG
1 TGAAGATTTAAGCCTAGTTTA-ACTAGCA-CCAA
* * *
9578619 TGAAGATTTAAGCCCAGTTTAACTAGCACTAC
1 TGAAGATTTAAGCCTAGTTTAACTAGCACCAA
* * * * *
9578651 TGAAGATATAAGCCCAATTTAGCT-GACACATAA
1 TGAAGATTTAAGCCTAGTTTAACTAG-CAC-CAA
* * *
9578684 TGAAAAAATTTAAGCCCAGTTTAGCTAGCACC--
1 TG--AAGATTTAAGCCTAGTTTAACTAGCACCAA
* * * * * *
9578716 T-AGGTTTTAAGCCCAATATTCACTGGCACCAA
1 TGAAGATTTAAGCCTAGT-TTAACTAGCACCAA
* *
9578748 TGGAA-ATCTAAG-CTAGTTTATCT-GACATCTC-A
1 T-GAAGATTTAAGCCTAGTTTAACTAG-CA-C-CAA
* * *
9578780 TGAAAAGATTTAAGCCCAGTTTAGCTAGCATCAA
1 TG--AAGATTTAAGCCTAGTTTAACTAGCACCAA
* * * *
9578814 TGAAAAATTTAATCC-AGTTTGA-TAGCATCAA
1 TG-AAGATTTAAGCCTAGTTTAACTAGCACCAA
* *
9578845 TGAAAATTTAAGCCTAGTTTGACTAG
1 TGAAGATTTAAGCCTAGTTTAACTAG
9578871 TATTAATAAA
Statistics
Matches: 561, Mismatches: 130, Indels: 110
0.70 0.16 0.14
Matches are distributed among these distances:
29 12 0.02
30 21 0.04
31 32 0.06
32 201 0.36
33 183 0.33
34 35 0.06
35 72 0.13
36 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (32 bp):
TGAAGATTTAAGCCTAGTTTAACTAGCACCAA
Found at i:9578254 original size:65 final size:65
Alignment explanation
Indices: 9578162--9578310 Score: 221
Period size: 65 Copynumber: 2.3 Consensus size: 65
9578152 ATTTCATGAA
* *
9578162 AAGATTTAAACCTAGTCTATCTAGCACCTAGTGAAGTTTTAAGCATAGTTTAATTTGCA-CTAAT
1 AAGATTTAAGCCTAGTTTATCTAGCACCTAGTGAAGTTTTAAGCATAGTTTAATTTGCATC-AAT
9578226 G
65 G
* *
9578227 AAGATTTAAGCCTAGTTTAGT-TGGCACCTATTGAAGTTTTAAGCATAGTTTAATTTGCATCAAT
1 AAGATTTAAGCCTAGTTTA-TCTAGCACCTAGTGAAGTTTTAAGCATAGTTTAATTTGCATCAAT
9578291 G
65 G
*
9578292 AAGATTTAAGCCCAGTTTA
1 AAGATTTAAGCCTAGTTTA
9578311 ATTGACACGA
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
65 75 0.97
66 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (65 bp):
AAGATTTAAGCCTAGTTTATCTAGCACCTAGTGAAGTTTTAAGCATAGTTTAATTTGCATCAATG
Found at i:9578457 original size:67 final size:67
Alignment explanation
Indices: 9578324--9578459 Score: 150
Period size: 67 Copynumber: 2.0 Consensus size: 67
9578314 GACACGAATG
* * * **
9578324 AAGATTTAAGTTCAGTTTATCTGACCCTCAATGAAATTTTAAGCCTAGCTTATCTAGTATTCATG
1 AAGATTTAAGCTCAGTTTAACTGACCCTCAATGAAATTTTAAGCCCAGCTTATCTAGTACCCATG
9578389 AA
66 AA
* * * * *
9578391 AAGATTTAAGCTCAGTTTAACTGGCGCT-ATTGAAGA-TTTAATCCCAGTTTATCTAGTACCCAA
1 AAGATTTAAGCTCAGTTTAACTGACCCTCAATGAA-ATTTTAAGCCCAGCTTATCTAGTACCC-A
9578454 TGAA
64 TGAA
9578458 AA
1 AA
9578460 TTTAAACCCA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
66 25 0.44
67 32 0.56
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (67 bp):
AAGATTTAAGCTCAGTTTAACTGACCCTCAATGAAATTTTAAGCCCAGCTTATCTAGTACCCATG
AA
Found at i:9578594 original size:65 final size:65
Alignment explanation
Indices: 9578451--9578701 Score: 177
Period size: 65 Copynumber: 3.8 Consensus size: 65
9578441 ATCTAGTACC
* * * * *
9578451 CAATGAAAATTTAAACCCAGTTTAGCTAGCACCCAATAAAAAGATTTAAGCCTAATTTGATTGGC
1 CAATGAAGATTTAAGCCCAATTTAGCTAGCACCCAAT-AAAAGATTTAAGCCCAATTTGATTAGC
9578516 A
65 A
* * * * *
9578517 CTAATAAAGATTTAAGTCCAATTTATCTAGCACCTAAT-AAAGATTTTAGCCCAATTT-AGTTAG
1 C-AATGAAGATTTAAGCCCAATTTAGCTAGCACCCAATAAAAGATTTAAGCCCAATTTGA-TTAG
9578580 CA
64 CA
*** ** * * * * * *
9578582 TCAATGAAGATTTAAGCCTTGTTTATATGGCACCCAGT-GAAGATTTAAGCCCAGTTTAACTAGC
1 -CAATGAAGATTTAAGCCCAATTTAGCTAGCACCCAATAAAAGATTTAAGCCCAATTTGATTAGC
9578646 A
65 A
* * ** *
9578647 CTACTGAAGATATAAGCCCAATTTAGCT-GACACATAATGAAAAAATTTAAGCCCA
1 C-AATGAAGATTTAAGCCCAATTTAGCTAG-CACCCAAT-AAAAGATTTAAGCCCA
9578702 GTTTAGCTAG
Statistics
Matches: 142, Mismatches: 35, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
64 3 0.02
65 94 0.66
66 3 0.02
67 42 0.30
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (65 bp):
CAATGAAGATTTAAGCCCAATTTAGCTAGCACCCAATAAAAGATTTAAGCCCAATTTGATTAGCA
Found at i:9578853 original size:30 final size:31
Alignment explanation
Indices: 9578779--9578866 Score: 115
Period size: 31 Copynumber: 2.7 Consensus size: 31
9578769 CTGACATCTC
*
9578779 ATGAAAAGATTTAAGCCCAGTTTAGCTAGCATCA
1 ATGAAAA-ATTTAAG-CCAGTTT-GATAGCATCA
*
9578813 ATGAAAAATTTAATCCAGTTTGATAGCATCA
1 ATGAAAAATTTAAGCCAGTTTGATAGCATCA
9578844 ATG-AAAATTTAAGCCTAGTTTGA
1 ATGAAAAATTTAAGCC-AGTTTGA
9578867 CTAGTATTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 11 0.22
31 19 0.38
32 7 0.14
33 6 0.12
34 7 0.14
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (31 bp):
ATGAAAAATTTAAGCCAGTTTGATAGCATCA
Found at i:9579014 original size:33 final size:33
Alignment explanation
Indices: 9578193--9579028 Score: 238
Period size: 32 Copynumber: 25.5 Consensus size: 33
9578183 TAGCACCTAG
* ** * *
9578193 TGAAGTTTTAAGCATAGTTTAATTTGCACT-AA
1 TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* *
9578225 TGAAGATTTAAGCCTAGTTTAGTTGGCAC-CTAT
1 TGAAGATTTAAGCCCAGTTTAGTTGGCACTC-AA
* ** * *
9578258 TGAAGTTTTAAGCATAGTTTAATTTGCA-TCAA
1 TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* * *
9578290 TGAAGATTTAAGCCCAGTTTAATTGACAC-GAA
1 TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
** * *
9578322 TGAAGATTTAAGTTCAGTTTA-TCTGACCCTCAA
1 TGAAGATTTAAGCCCAGTTTAGT-TGGCACTCAA
* * * * *
9578355 TGAA-ATTTTAAGCCTAGCTTA-TCTAGTATTC-A
1 TGAAGA-TTTAAGCCCAGTTTAGT-TGGCACTCAA
* ** * *
9578387 TGAAAAGATTTAAGCTCAGTTTAACTGGCGCT-AT
1 TG--AAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* * * *
9578421 TGAAGATTTAATCCCAGTTTA-TCTAGTACCCAA
1 TGAAGATTTAAGCCCAGTTTAGT-TGGCACTCAA
* * * * *
9578454 TGAAAATTTAAACCCAGTTTAGCTAGCACCCAA
1 TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* * *
9578487 TAAAAAGATTTAAGCCTAATTT-GATTGGCACT-AA
1 T--GAAGATTTAAGCCCAGTTTAG-TTGGCACTCAA
* * * *
9578521 TAAAGATTTAAGTCCAATTTA-TCTAGCAC-CTAA
1 TGAAGATTTAAGCCCAGTTTAGT-TGGCACTC-AA
* * * *
9578554 TAAAGATTTTAGCCCAATTTAGTTAGCA-TCAA
1 TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
** * *
9578586 TGAAGATTTAAGCCTTGTTTA-TATGGCACCCAG
1 TGAAGATTTAAGCCCAGTTTAGT-TGGCACTCAA
** * *
9578619 TGAAGATTTAAGCCCAGTTTAACTAGCACT-AC
1 TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* * * *
9578651 TGAAGATATAAGCCCAATTTAGCTGACACAT-AA
1 TGAAGATTTAAGCCCAGTTTAGTTGGCAC-TCAA
* * *
9578684 TGAAAAAATTTAAGCCCAGTTTAGCTAGCAC-C--
1 TG--AAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* * * *
9578716 T-AGGTTTTAAGCCCAATATTCA-CTGGCAC-CAA
1 TGAAGATTTAAGCCCAGT-TT-AGTTGGCACTCAA
* * *
9578748 TGGAA-ATCTAAG-CTAGTTTA-TCTGACATCTC-A
1 T-GAAGATTTAAGCCCAGTTTAGT-TGGCA-CTCAA
* *
9578780 TGAAAAGATTTAAGCCCAGTTTAGCTAGCA-TCAA
1 TG--AAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* * * *
9578814 TGAAAAATTTAA-TCCAGTTT-GATAGCA-TCAA
1 TG-AAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* * * * * *
9578845 TGAAAATTTAAGCCTAGTTT-GACTAGTA-TTAA
1 TGAAGATTTAAGCCCAGTTTAG-TTGGCACTCAA
* * ** *
9578877 TAAAAGAGTTAAGCTTAATTTAGTTGGCACATC-A
1 T-GAAGATTTAAGCCCAGTTTAGTTGGCAC-TCAA
* * * *
9578911 TGAAAAGATTTAAACCCAGTTTAGCTAGTACTCAA
1 TG--AAGATTTAAGCCCAGTTTAGTTGGCACTCAA
* * * * *
9578946 T-AAAAATTAAGCCTAGATTA-TCAGGTC-CT-AA
1 TGAAGATTTAAGCCCAGTTTAGT-TGG-CACTCAA
9578977 TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
1 TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
9579010 TGAAGAATTTAAGCCCAGT
1 TGAAG-ATTTAAGCCCAGT
9579029 ATAAGTAGCA
Statistics
Matches: 597, Mismatches: 145, Indels: 122
0.69 0.17 0.14
Matches are distributed among these distances:
29 12 0.02
30 19 0.03
31 34 0.06
32 227 0.38
33 179 0.30
34 52 0.09
35 74 0.12
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (33 bp):
TGAAGATTTAAGCCCAGTTTAGTTGGCACTCAA
Found at i:9579043 original size:33 final size:34
Alignment explanation
Indices: 9578975--9579051 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
9578965 ATCAGGTCCT
* *
9578975 AATGAAG-ATTTAAGCCCAGTTTAGTTGGCACTC
1 AATGAAGAATTTAAGCCCAGTTAAGTTAGCACTC
9579008 AATGAAGAATTTAAGCCCAGTATAAG-TAGCA-TC
1 AATGAAGAATTTAAGCCCAGT-TAAGTTAGCACTC
9579041 AATGAA-AATTT
1 AATGAAGAATTT
9579052 TGTTCCAGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 5 0.12
33 15 0.38
34 17 0.43
35 3 0.08
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (34 bp):
AATGAAGAATTTAAGCCCAGTTAAGTTAGCACTC
Found at i:9579258 original size:10 final size:10
Alignment explanation
Indices: 9579239--9579307 Score: 50
Period size: 10 Copynumber: 6.5 Consensus size: 10
9579229 GGTGTTGTAA
9579239 AAAAAAAAAC
1 AAAAAAAAAC
*
9579249 AAAAACAAAC
1 AAAAAAAAAC
9579259 AAATAAACAAA-
1 AAA-AAA-AAAC
**
9579270 AAATTAAAAC
1 AAAAAAAAAC
*
9579280 AAAAAAAATGAA
1 AAAAAAAA--AC
9579292 AAACAAAAAAC
1 AAA-AAAAAAC
9579303 AAAAA
1 AAAAA
9579308 CCAAAGAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
9 3 0.07
10 21 0.47
11 9 0.20
12 7 0.16
13 5 0.11
ACGTcount: A:0.83, C:0.10, G:0.01, T:0.06
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:9579317 original size:15 final size:13
Alignment explanation
Indices: 9579237--9579322 Score: 68
Period size: 15 Copynumber: 6.4 Consensus size: 13
9579227 GTGGTGTTGT
9579237 AAAAA-AAAAAAC
1 AAAAACAAAAAAC
*
9579249 AAAAACAAACAA-
1 AAAAACAAAAAAC
* *
9579261 ATAAACAAAAAATT
1 AAAAACAAAAAA-C
* *
9579275 AAAACAAAAAAAATG
1 AAAA-ACAAAAAA-C
9579290 AAAAACAAAAAAC
1 AAAAACAAAAAAC
9579303 AAAAACCAAAGAAAC
1 AAAAA-CAAA-AAAC
9579318 AAAAA
1 AAAAA
9579323 TGAAAGGAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
12 15 0.25
13 10 0.17
14 14 0.23
15 21 0.35
ACGTcount: A:0.81, C:0.12, G:0.02, T:0.05
Consensus pattern (13 bp):
AAAAACAAAAAAC
Found at i:9579322 original size:29 final size:28
Alignment explanation
Indices: 9579237--9579322 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 28
9579227 GTGGTGTTGT
9579237 AAAAAAAAAAACAAAAACAAACAAATAAAC
1 AAAAAAAAAAACAAAAA-AAACAAA-AAAC
* **
9579267 AAAAAATTAAAACAAAAAAAATGAAAAAC
1 AAAAAA-AAAAACAAAAAAAACAAAAAAC
* *
9579296 AAAAAACAAAAACCAAAGAAACAAAAA
1 AAAAAA-AAAAACAAAAAAAACAAAAA
9579323 TGAAAGGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 25 0.54
30 11 0.24
31 10 0.22
ACGTcount: A:0.81, C:0.12, G:0.02, T:0.05
Consensus pattern (28 bp):
AAAAAAAAAAACAAAAAAAACAAAAAAC
Found at i:9579622 original size:26 final size:27
Alignment explanation
Indices: 9579593--9579653 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
9579583 AAGAAAAGCC
*
9579593 CAAAATAAATTAAAGA-GCCCAAAGTA
1 CAAAATAAATAAAAGAGGCCCAAAGTA
* * *
9579619 CAAAAGAAATAAAATAGGCCCTAAGTA
1 CAAAATAAATAAAAGAGGCCCAAAGTA
*
9579646 TAAAATAA
1 CAAAATAA
9579654 TAGGAAGACA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.59, C:0.13, G:0.11, T:0.16
Consensus pattern (27 bp):
CAAAATAAATAAAAGAGGCCCAAAGTA
Found at i:9580225 original size:35 final size:35
Alignment explanation
Indices: 9580181--9580254 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
9580171 AACATAAATA
*
9580181 AAAAAATATTACAATAGAAA-TAGGAAATAGAAACC
1 AAAAAATATTACAATAAAAACT-GGAAATAGAAACC
* * *
9580216 AAAACATATTATAGTAAAAACTGGAAATAGAAACC
1 AAAAAATATTACAATAAAAACTGGAAATAGAAACC
9580251 AAAA
1 AAAA
9580255 GTATAATACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (35 bp):
AAAAAATATTACAATAAAAACTGGAAATAGAAACC
Found at i:9583357 original size:36 final size:36
Alignment explanation
Indices: 9583331--9583421 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 36
9583321 ATTGAGAAGT
*
9583331 TACTATCTTAGCCTTGAAAGATAAGGAGTTAGAATC
1 TACTACCTTAGCCTTGAAAGATAAGGAGTTAGAATC
* * *
9583367 TGCTACCTTAGCCTTGAAA-AGTATGGAGTTAGAGGT-
1 TACTACCTTAGCCTTGAAAGA-TAAGGAGTTAGA-ATC
*
9583403 TA-TACTTTAGCCTTGAAAG
1 TACTACCTTAGCCTTGAAAG
9583422 GTAGGGATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
35 16 0.35
36 29 0.63
37 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (36 bp):
TACTACCTTAGCCTTGAAAGATAAGGAGTTAGAATC
Found at i:9583420 original size:35 final size:35
Alignment explanation
Indices: 9583374--9583442 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
9583364 ATCTGCTACC
*
9583374 TTAGCCTTGAAAAGTATGGAGTTAGAGGTTATACT
1 TTAGCCTTGAAAAGTAGGGAGTTAGAGGTTATACT
* * *
9583409 TTAGCCTTGAAAGGTAGGGATTTAGTGGTTATAC
1 TTAGCCTTGAAAAGTAGGGAGTTAGAGGTTATAC
9583443 CTTGGTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.35
Consensus pattern (35 bp):
TTAGCCTTGAAAAGTAGGGAGTTAGAGGTTATACT
Found at i:9593010 original size:19 final size:19
Alignment explanation
Indices: 9592983--9593300 Score: 93
Period size: 19 Copynumber: 17.3 Consensus size: 19
9592973 ATTCAGGTTT
*
9592983 GCAAAAAATTCAAAGATTC
1 GCAAGAAATTCAAAGATTC
*
9593002 GCAAGAAATTCAAATATTC
1 GCAAGAAATTCAAAGATTC
** *
9593021 ATAAAAAATTC-AA-ATTC
1 GCAAGAAATTCAAAGATTC
* *
9593038 GTAA-AAACTTCAAAAATTC
1 GCAAGAAA-TTCAAAGATTC
* *
9593057 ACAA-AAACTTTAAAGATTC
1 GCAAGAAA-TTCAAAGATTC
* **
9593076 ACAAGTGATTC-AAGA-TC
1 GCAAGAAATTCAAAGATTC
* * * *
9593093 TCAAAAAATTC--AGGTTT
1 GCAAGAAATTCAAAGATTC
* *
9593110 GTAAGAAATTC-AA-ATTT
1 GCAAGAAATTCAAAGATTC
*
9593127 GCAA-AAACTTCAAAGATTT
1 GCAAGAAA-TTCAAAGATTC
* *
9593146 GGAAGAGCTTCACATTCAAAGATTT
1 GCAAGA-----A-ATTCAAAGATTC
*
9593171 GCAAGAAATTC--ATATTC
1 GCAAGAAATTCAAAGATTC
* * *
9593188 AC-AGAACTTTAAAGATTC
1 GCAAGAAATTCAAAGATTC
* *
9593206 ACAAGAACTTCAAAGATTC
1 GCAAGAAATTCAAAGATTC
*
9593225 GCAAGATATTC-AAG-TTC
1 GCAAGAAATTCAAAGATTC
* * *
9593242 ACAAGAAATT--TAG-GTC
1 GCAAGAAATTCAAAGATTC
*
9593258 TGCAAGATATTC-AA-ATTC
1 -GCAAGAAATTCAAAGATTC
*
9593276 GCAAGAACTTCAAAGATTC
1 GCAAGAAATTCAAAGATTC
*
9593295 ACAAGA
1 GCAAGA
9593301 GCTTCAAATT
Statistics
Matches: 228, Mismatches: 47, Indels: 48
0.71 0.15 0.15
Matches are distributed among these distances:
16 18 0.08
17 70 0.31
18 26 0.11
19 93 0.41
20 3 0.01
25 17 0.07
26 1 0.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.27
Consensus pattern (19 bp):
GCAAGAAATTCAAAGATTC
Found at i:9593038 original size:36 final size:38
Alignment explanation
Indices: 9592984--9593075 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 38
9592974 TTCAGGTTTG
*
9592984 CAAAAAATTCAAAGATTCGCAAGAAA-TTCAAATATTCA
1 CAAAAAATTCAAAGATTCGCAA-AAACTTCAAAAATTCA
* *
9593022 TAAAAAATTC-AA-ATTCGTAAAAACTTCAAAAATTCA
1 CAAAAAATTCAAAGATTCGCAAAAACTTCAAAAATTCA
* *
9593058 CAAAAACTTTAAAGATTC
1 CAAAAAATTCAAAGATTC
9593076 ACAAGTGATT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
35 3 0.07
36 25 0.56
37 4 0.09
38 13 0.29
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.26
Consensus pattern (38 bp):
CAAAAAATTCAAAGATTCGCAAAAACTTCAAAAATTCA
Found at i:9593182 original size:25 final size:25
Alignment explanation
Indices: 9593135--9593188 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
9593125 TTGCAAAAAC
* **
9593135 TTCAAAGATTTGGAAGAGCTTCACA
1 TTCAAAGATTTGCAAGAAATTCACA
*
9593160 TTCAAAGATTTGCAAGAAATTCATA
1 TTCAAAGATTTGCAAGAAATTCACA
9593185 TTCA
1 TTCA
9593189 CAGAACTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (25 bp):
TTCAAAGATTTGCAAGAAATTCACA
Found at i:9593270 original size:149 final size:149
Alignment explanation
Indices: 9593007--9593337 Score: 378
Period size: 149 Copynumber: 2.2 Consensus size: 149
9592997 GATTCGCAAG
* * * * * *
9593007 AAATTCAAATATTCATAAAAAATTCAAATTCGTA-AAAACTTCAAAAATTCACAAAAACTTTAAA
1 AAATTCAAAGATTCACAAGAAATTCAGATTC--ACAGAACTTCAAAAATTCACAAAAACTTCAAA
* * * *
9593071 GATTCACAAGTGATTCAAGATCTCAAAAAATTCAGGTTTGTAAGAAATTCAAATTTGCAAAAACT
64 GATTCACAAGTGATTCAAGATCACAAAAAATTCAGGTCTGCAAGAAATTCAAATTCGCAAAAACT
***
9593136 TCAAAGATTTGGAAGAGCTTC
129 TCAAAGATTCACAAGAGCTTC
* ** * * * *
9593157 ACATTCAAAGATTTGCAAGAAATTCATATTCACAGAACTTTAAAGATTCACAAGAACTTCAAAGA
1 AAATTCAAAGATTCACAAGAAATTCAGATTCACAGAACTTCAAAAATTCACAAAAACTTCAAAGA
* * * * * *
9593222 TTCGCAAGAT-ATTCAAGTTCACAAGAAATTTAGGTCTGCAAGATATTCAAATTCGCAAGAACTT
66 TTCACAAG-TGATTCAAGATCACAAAAAATTCAGGTCTGCAAGAAATTCAAATTCGCAAAAACTT
9593286 CAAAGATTCACAAGAGCTTC
130 CAAAGATTCACAAGAGCTTC
*
9593306 AAATTCAAAGATTCATAAGAAATTCAGATTCA
1 AAATTCAAAGATTCACAAGAAATTCAGATTCA
9593338 AACATTCGTA
Statistics
Matches: 149, Mismatches: 30, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
148 1 0.01
149 123 0.83
150 25 0.17
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (149 bp):
AAATTCAAAGATTCACAAGAAATTCAGATTCACAGAACTTCAAAAATTCACAAAAACTTCAAAGA
TTCACAAGTGATTCAAGATCACAAAAAATTCAGGTCTGCAAGAAATTCAAATTCGCAAAAACTTC
AAAGATTCACAAGAGCTTC
Found at i:9593279 original size:17 final size:17
Alignment explanation
Indices: 9593221--9593281 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
9593211 AACTTCAAAG
9593221 ATTCGCAAGATATTCAA
1 ATTCGCAAGATATTCAA
* * * *
9593238 GTTCACAAGAAATT-TA
1 ATTCGCAAGATATTCAA
**
9593254 GGTCTGCAAGATATTCAA
1 ATTC-GCAAGATATTCAA
9593272 ATTCGCAAGA
1 ATTCGCAAGA
9593282 ACTTCAAAGA
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
16 4 0.12
17 25 0.78
18 3 0.09
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (17 bp):
ATTCGCAAGATATTCAA
Found at i:9593305 original size:19 final size:19
Alignment explanation
Indices: 9593272--9593308 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9593262 AGATATTCAA
*
9593272 ATTCGCAAGAACTTCAAAG
1 ATTCACAAGAACTTCAAAG
*
9593291 ATTCACAAGAGCTTCAAA
1 ATTCACAAGAACTTCAAA
9593309 TTCAAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (19 bp):
ATTCACAAGAACTTCAAAG
Found at i:9593312 original size:25 final size:25
Alignment explanation
Indices: 9593284--9593362 Score: 104
Period size: 25 Copynumber: 3.2 Consensus size: 25
9593274 TCGCAAGAAC
* **
9593284 TTCAAAGATTCACAAGAGCTTCAAA
1 TTCAAAGATTCATAAGAAATTCAAA
*
9593309 TTCAAAGATTCATAAGAAATTCAGA
1 TTCAAAGATTCATAAGAAATTCAAA
* *
9593334 TTCAAACATTCGTAAGAAATTCAAA
1 TTCAAAGATTCATAAGAAATTCAAA
9593359 TTCA
1 TTCA
9593363 TAAAACTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (25 bp):
TTCAAAGATTCATAAGAAATTCAAA
Found at i:9593632 original size:46 final size:45
Alignment explanation
Indices: 9593555--9593655 Score: 139
Period size: 46 Copynumber: 2.2 Consensus size: 45
9593545 GTTTCAAATA
* *
9593555 TGAAAAATTTTGGGATTCGCATCCAAAATTTCAAAGATTCTTATT
1 TGAAAATTTTTGGGATTCACATCCAAAATTTCAAAGATTCTTATT
* *
9593600 TGAAAATTTTATGGGTTTCACATCCAACATTTCAAAGATTCTTATT
1 TGAAAATTTT-TGGGATTCACATCCAAAATTTCAAAGATTCTTATT
**
9593646 CAAAAATTTT
1 TGAAAATTTT
9593656 CTTTAAACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
45 9 0.18
46 40 0.82
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (45 bp):
TGAAAATTTTTGGGATTCACATCCAAAATTTCAAAGATTCTTATT
Found at i:9593972 original size:23 final size:23
Alignment explanation
Indices: 9593935--9593981 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
9593925 GCATGCTTTA
* *
9593935 ACAATGATGTAAATGTAATTATC
1 ACAATGATGTAAATGCAAATATC
9593958 ACAATGTATGT-AATGCAAATATC
1 ACAATG-ATGTAAATGCAAATATC
9593981 A
1 A
9593982 TTAAATCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (23 bp):
ACAATGATGTAAATGCAAATATC
Found at i:9597969 original size:9 final size:9
Alignment explanation
Indices: 9597942--9597975 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
9597932 TGCTAGATAT
9597942 ATAAAATAA
1 ATAAAATAA
9597951 AT-AAATAA
1 ATAAAATAA
*
9597959 ATAAAACAA
1 ATAAAATAA
9597968 ATAAAATA
1 ATAAAATA
9597976 CAAACATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAAAATAA
Found at i:9598766 original size:14 final size:15
Alignment explanation
Indices: 9598749--9598794 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
9598739 TTAGCATAAA
9598749 CAAA-AACTATCATG
1 CAAAGAACTATCATG
9598763 CAAAGAA-TATCATG
1 CAAAGAACTATCATG
*
9598777 CAAATATAC-ATCATG
1 CAAAGA-ACTATCATG
9598792 CAA
1 CAA
9598795 TAATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.22
Consensus pattern (15 bp):
CAAAGAACTATCATG
Found at i:9606369 original size:22 final size:25
Alignment explanation
Indices: 9606324--9606369 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
9606314 TCTTCGACCA
9606324 AAATAGTCATTTATTTTATGTTAACT
1 AAATAGTCATTTATTTTA-GTTAACT
9606350 AAATAGTC-TTT-TTTTA-TTAA
1 AAATAGTCATTTATTTTAGTTAA
9606370 GTTTGGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
24 5 0.25
25 3 0.15
26 8 0.40
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (25 bp):
AAATAGTCATTTATTTTAGTTAACT
Found at i:9608495 original size:10 final size:10
Alignment explanation
Indices: 9608480--9608506 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9608470 ATTATGGATG
9608480 AGCTCTCTTA
1 AGCTCTCTTA
9608490 AGCTCTCTTA
1 AGCTCTCTTA
9608500 AGCTCTC
1 AGCTCTC
9608507 AAGTTGCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.33, G:0.11, T:0.37
Consensus pattern (10 bp):
AGCTCTCTTA
Found at i:9612641 original size:2 final size:2
Alignment explanation
Indices: 9612634--9612664 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9612624 TTGAAATTTA
9612634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9612665 AAAGCAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9620248 original size:37 final size:37
Alignment explanation
Indices: 9620196--9620266 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
9620186 ACTTAGAAAA
*
9620196 ATAATGAATAGACAAGTGTTGGATGCATACTGATATG
1 ATAATGAATACACAAGTGTTGGATGCATACTGATATG
*
9620233 ATAATGAATACACAAGTGTTGGATGCATATTGAT
1 ATAATGAATACACAAGTGTTGGATGCATACTGAT
9620267 GTCCAACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (37 bp):
ATAATGAATACACAAGTGTTGGATGCATACTGATATG
Done.