Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 139 of 378
Found at i:39601965 original size:10 final size:10
Alignment explanation
Indices: 39601952--39601985 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
39601942 GAAAAAGGGC
39601952 AAAGAAAACT
1 AAAGAAAACT
39601962 AAAGAAAACCT
1 AAAGAAAA-CT
*
39601973 ATAGAAAACT
1 AAAGAAAACT
39601983 AAA
1 AAA
39601986 TCTAAACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.68, C:0.12, G:0.09, T:0.12
Consensus pattern (10 bp):
AAAGAAAACT
Found at i:39604498 original size:18 final size:18
Alignment explanation
Indices: 39604454--39604489 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
39604444 AAACATATAT
39604454 AAATAAATAATAATAGATA
1 AAAT-AATAATAATAGATA
39604473 AAATAATAATAAT-GATA
1 AAATAATAATAATAGATA
39604490 GTAATAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
AAATAATAATAATAGATA
Found at i:39604581 original size:15 final size:16
Alignment explanation
Indices: 39604557--39604599 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
39604547 ATAAAAATGG
39604557 TTAAAGAAAT-AAATA
1 TTAAAGAAATAAAATA
*
39604572 TTAAATAAATAAAATA
1 TTAAAGAAATAAAATA
39604588 TTAAACGAAATA
1 TTAAA-GAAATA
39604600 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 9 0.38
16 10 0.42
17 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (16 bp):
TTAAAGAAATAAAATA
Found at i:39606203 original size:44 final size:44
Alignment explanation
Indices: 39606079--39606656 Score: 271
Period size: 44 Copynumber: 12.9 Consensus size: 44
39606069 GAAATTGACG
* ** * **
39606079 CTTCAATCTGCT-CACTGCATCTTCTTGGAGATAATAGATG--A
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA
* ** **
39606120 CTTCAATCTG-TCCCACTGTAACTTCAGGG-GTATGGGATTTGTGG
1 CTTCAATCTGCT-CCACTGCAACTTCAGGGAG-ATAAGATTTGTAA
* * * * *
39606164 CTTCAATCTACTCTACCGCAACTTTAGGGAGATAAGATTTGCCT-T
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--TAA
* * * * * *
39606209 CTTTACTCTGCTCCAATGCAACTTCAGGAAGATGAGACTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA
* * * *
39606253 CTTCAACCTGCT-CACTGCAACTTCAGGGAGATAAGGTTTATAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA
* * * * *
39606296 CTTTAGTCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAA
** ** * * *
39606341 CTTTGATCTATTCCACTGCAACTTCAGTGAGATAAGATCTATAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA
* *
39606385 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA
* * * ** * *
39606429 CTTTAATTTGCTCCGCTATAACTTTAGGGAGATAAGATTCGCCATGATGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-----TG-TAA
* * * * * *
39606479 CTT-AATCCGAC-CTACTACAACTTCAGAGGTACAAGATTAGTTATTTATAG
1 CTTCAATCTG-CTCCACTGCAACTTCAG-GG----AGATAAG--ATTTGTAA
* * * *
39606529 CTT-AGATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCGCTATA
1 CTTCA-ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TA-A
* * * * * **
39606575 -TTCAACCTACTCTACTGCAACTTCAGGGAAATAAGGTTAATAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA
* *
39606618 CTTTAATCTAG-TCCACTGCAACTTTAGGGAGATAAGATT
1 CTTCAATCT-GCTCCACTGCAACTTCAGGGAGATAAGATT
39606657 CGCCATGGTA
Statistics
Matches: 397, Mismatches: 107, Indels: 63
0.70 0.19 0.11
Matches are distributed among these distances:
40 1 0.00
41 11 0.03
42 17 0.04
43 35 0.09
44 168 0.42
45 100 0.25
46 7 0.02
49 16 0.04
50 16 0.04
51 17 0.04
54 6 0.02
56 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA
Found at i:39606386 original size:132 final size:133
Alignment explanation
Indices: 39606174--39606420 Score: 342
Period size: 132 Copynumber: 1.9 Consensus size: 133
39606164 CTTCAATCTA
* * *
39606174 CTCTACCGCAACTTTAGGGAGATAAGATTTGCCTTCTTTACTCTGCTCCAATGCAACTTCAGGAA
1 CTCTACCGCAACTTCAGAGAGATAAGATTTGCCTTCTTTACTCTACTCCAATGCAACTTCAGGAA
* *
39606239 GATGAGACTTGTAACTTCAACCTGCT-CACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTAGT
66 GATAAGACTTATAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTAGT
39606303 CTG
131 CTG
* * *
39606306 CTCTACTGCAACTTCAGAGAGATAAGATTTG-CTATCTTTGA-TCTATTCCACTGCAACTTCAGT
1 CTCTACCGCAACTTCAGAGAGATAAGATTTGCCT-TCTTT-ACTCTACTCCAATGCAACTTCAG-
*
39606369 G-AGATAAGA-TCTATAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
63 GAAGATAAGACT-TATAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG
39606421 ATTCGTGACT
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
131 3 0.03
132 73 0.72
133 25 0.25
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (133 bp):
CTCTACCGCAACTTCAGAGAGATAAGATTTGCCTTCTTTACTCTACTCCAATGCAACTTCAGGAA
GATAAGACTTATAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTAGT
CTG
Found at i:39606643 original size:189 final size:189
Alignment explanation
Indices: 39606345--39606699 Score: 457
Period size: 189 Copynumber: 1.9 Consensus size: 189
39606335 TGCTATCTTT
* * * *
39606345 GATCTATTCCACTGCAACTTCAGTGAGATAAGATCTATAACTTCAATCTGCTCCACTGCAACTTC
1 GATCTATTCCACTGCAACTTCAGGGAAATAAGATCTATAACTTCAACCTACTCCACTGCAACTTC
* ** * * * *
39606410 AGGGAGATAAGATTCGTGACTTTAATTTGCTCCGCTATAACTTTAGGGAGATAAGATTCGCCATG
66 AGGGAAATAAGATTAATAACTTTAATTAGCTCCACTACAACTTTAGGGAGATAAGATTCGCCATG
39606475 AT-GACTTAATCCGACCTACTACAACTTCAGAGGTACAAGATTAGTTATTTATAGCTTA
131 ATAGACTTAATCCGACCTACTACAACTTCAGAGGTACAAGATTAGTTATTTATAGCTTA
* * *
39606533 GATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCGCTAT-A-TTCAACCTACTCTACTGCAAC
1 GATCTATTCCACTGCAACTTCAGGGAAATAAGA-T--CTATAACTTCAACCTACTCCACTGCAAC
* *
39606596 TTCAGGGAAATAAGGTTAATAACTTTAATCTAG-TCCACTGCAACTTTAGGGAGATAAGATTCGC
63 TTCAGGGAAATAAGATTAATAACTTTAAT-TAGCTCCACTACAACTTTAGGGAGATAAGATTCGC
* * * * *
39606660 CATGGTAGATTTGATCTGACCTACTACAACTTTAGAGGTA
127 CATGATAGACTTAATCCGACCTACTACAACTTCAGAGGTA
39606700 TAGGATTTAT
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
188 29 0.21
189 76 0.54
190 32 0.23
191 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (189 bp):
GATCTATTCCACTGCAACTTCAGGGAAATAAGATCTATAACTTCAACCTACTCCACTGCAACTTC
AGGGAAATAAGATTAATAACTTTAATTAGCTCCACTACAACTTTAGGGAGATAAGATTCGCCATG
ATAGACTTAATCCGACCTACTACAACTTCAGAGGTACAAGATTAGTTATTTATAGCTTA
Found at i:39618209 original size:15 final size:15
Alignment explanation
Indices: 39618154--39618220 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
39618144 AAAAGGAACA
* *
39618154 TAAATAAATGAATTT
1 TAAATAAATAAATAT
*
39618169 TAATCATAAA-AAAAAGT
1 TAA--ATAAATAAATA-T
*
39618186 TAAAGAAATAAATAT
1 TAAATAAATAAATAT
39618201 TAAATAAATAAAATAT
1 TAAATAAAT-AAATAT
39618217 TAAA
1 TAAA
39618221 CGAAATATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
15 16 0.39
16 16 0.39
17 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (15 bp):
TAAATAAATAAATAT
Found at i:39618216 original size:16 final size:15
Alignment explanation
Indices: 39618185--39618227 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
39618175 TAAAAAAAAG
39618185 TTAAAGAAATAAATA
1 TTAAAGAAATAAATA
*
39618200 TTAAATAAATAAAATA
1 TTAAAGAAAT-AAATA
39618216 TTAAACGAAATA
1 TTAAA-GAAATA
39618228 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 11 0.46
17 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (15 bp):
TTAAAGAAATAAATA
Found at i:39622237 original size:21 final size:21
Alignment explanation
Indices: 39622213--39622252 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39622203 AACTTTTCTA
*
39622213 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
39622234 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
39622253 CATTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATT
Found at i:39634061 original size:19 final size:21
Alignment explanation
Indices: 39634015--39634062 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
39634005 ATTATTTCTT
39634015 TTTTCTTAAAACAATAGTAAA
1 TTTTCTTAAAACAATAGTAAA
* * *
39634036 TTATCTTAATA-AATA-TTAA
1 TTTTCTTAAAACAATAGTAAA
39634055 TTTTCTTA
1 TTTTCTTA
39634063 CCTTTGTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.43
20 4 0.17
21 9 0.39
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTCTTAAAACAATAGTAAA
Found at i:39634654 original size:14 final size:14
Alignment explanation
Indices: 39634635--39634663 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39634625 AGATACAACA
39634635 AACATATATATAAT
1 AACATATATATAAT
39634649 AACATATATATAAT
1 AACATATATATAAT
39634663 A
1 A
39634664 GCATGTCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AACATATATATAAT
Found at i:39637735 original size:6 final size:6
Alignment explanation
Indices: 39637724--39637750 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39637714 TTGCGTGTTC
39637724 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
39637751 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:39646336 original size:39 final size:39
Alignment explanation
Indices: 39646293--39646420 Score: 186
Period size: 39 Copynumber: 3.3 Consensus size: 39
39646283 GGTCTTTAAC
**
39646293 CCGGATATTTTTCTAGCACGTAGCCTGCGGACCTCAAT-T
1 CCGGATATTTTTCTAGCATATAGCCTGCGGACCTC-ATGT
* *
39646332 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCTAGCATATAGCCTGCGGACCTCATGT
*
39646371 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCTAGCATATAGCCTGCGGACCTCATGT
*
39646410 CTGGATATTTT
1 CCGGATATTTT
39646421 CAATCTCATA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 2 0.03
39 78 0.98
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (39 bp):
CCGGATATTTTTCTAGCATATAGCCTGCGGACCTCATGT
Found at i:39654322 original size:39 final size:39
Alignment explanation
Indices: 39654259--39654386 Score: 193
Period size: 39 Copynumber: 3.3 Consensus size: 39
39654249 GGGTCTTTAA
** *
39654259 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
39654298 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
39654337 CCGGATATTTTTCCAGCATATAGCCTGTGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
39654376 CCGGATATTTT
1 CCGGATATTTT
39654387 CAATCTCATA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:39665857 original size:32 final size:32
Alignment explanation
Indices: 39665818--39665945 Score: 229
Period size: 32 Copynumber: 4.0 Consensus size: 32
39665808 CATAAAAAAT
39665818 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
39665850 ATCATACATTAGGTTTACATATAAAAAAGTTG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
*
39665882 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
39665914 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
39665946 TATAGTTATA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 90 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:39666654 original size:7 final size:7
Alignment explanation
Indices: 39666642--39666668 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39666632 CCTACAAAAC
39666642 ATGTTAA
1 ATGTTAA
39666649 ATGTTAA
1 ATGTTAA
39666656 ATGTTAA
1 ATGTTAA
39666663 ATGTTA
1 ATGTTA
39666669 CACTCAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
ATGTTAA
Found at i:39671296 original size:42 final size:42
Alignment explanation
Indices: 39671237--39671324 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
39671227 TACTAAAGAG
39671237 ACATTGTGTTAAAGAAGAGATTTGTAAAATTTATGGTAGCGA
1 ACATTGTGTTAAAGAAGAGATTTGTAAAATTTATGGTAGCGA
39671279 ACATTGTGTTAAAGAAGAGATTTGTAAAATTTATGGTAGCGA
1 ACATTGTGTTAAAGAAGAGATTTGTAAAATTTATGGTAGCGA
39671321 ACAT
1 ACAT
39671325 GTATTTCGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.33
Consensus pattern (42 bp):
ACATTGTGTTAAAGAAGAGATTTGTAAAATTTATGGTAGCGA
Found at i:39671788 original size:42 final size:42
Alignment explanation
Indices: 39671710--39671796 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
39671700 TTTTAGGTTG
** **
39671710 TATCTTAGATAAATAAGTTTTTTTTTTAAATTTAAACTA-TT
1 TATCTTAGATAAATAAGTTTTTTTTAAAAAAATAAACTAGTT
*
39671751 TATCTTAGATAATTAAGGTTTTTTTTAAAAAAATAAACTAGTT
1 TATCTTAGATAAATAA-GTTTTTTTTAAAAAAATAAACTAGTT
39671794 TAT
1 TAT
39671797 TTTGTATTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 15 0.38
42 19 0.49
43 5 0.13
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (42 bp):
TATCTTAGATAAATAAGTTTTTTTTAAAAAAATAAACTAGTT
Found at i:39672828 original size:26 final size:26
Alignment explanation
Indices: 39672765--39673319 Score: 318
Period size: 26 Copynumber: 21.8 Consensus size: 26
39672755 AAACGAAGCA
* * *
39672765 AAATAATATATAAAATAATTT-GAAG
1 AAATAATATATAAAACAATTTAAAAT
*
39672790 AAAT-A-GTATAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* * * *
39672814 AAATAATATGTAAAAGAAATGAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* * *
39672840 AAATAACATACAAAGA-AATTTAACAT
1 AAATAATATATAAA-ACAATTTAAAAT
* *
39672866 AAATAATATA-ATAGACACTTTAAAAT
1 AAATAATATATA-AAACAATTTAAAAT
* ** *
39672892 ACATAA-A-A-AAAGA-GTTTTAAGAT
1 AAATAATATATAAA-ACAATTTAAAAT
* * *
39672915 AAATAACATGTAAAAAGAAATTTAAAAT
1 AAATAATATAT-AAAA-CAATTTAAAAT
* **
39672943 AAATAATATACAAAACGGTTT-AAA-
1 AAATAATATATAAAACAATTTAAAAT
* *
39672967 AAATAATATATATATAAAAATTCAAAAT
1 AAATAATATATA-A-AACAATTTAAAAT
* * *
39672995 AAACAATATATATAACAGTTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
39673021 AAATAATATATAAAA-AATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
** * *
39673046 GGATAATAGTTTAAAATACA--T--AAT
1 AAATAATA-TATAAAACA-ATTTAAAAT
39673070 AAATAATA-ATAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
*
39673095 AAATAATATATGAAAA-AGTTTAAAAT
1 AAATAATATAT-AAAACAATTTAAAAT
*
39673121 AAAAAATATATAAAA-AA-TTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
39673145 AAATAA-AGCATAAAACAATTTGAAAT
1 AAATAATA-TATAAAACAATTTAAAAT
* ** *
39673171 AAATAATTTATAAAGTAATTTTAAAT
1 AAATAATATATAAAACAATTTAAAAT
* * *
39673197 ATATAATACATAAAACAGTTT-AAAT
1 AAATAATATATAAAACAATTTAAAAT
* * * *
39673222 GAACTAATATGTAAAA-AGTCTAAAAT
1 -AAATAATATATAAAACAATTTAAAAT
* ** *
39673248 AAATAATATATAACACTGTTTCAAAT
1 AAATAATATATAAAACAATTTAAAAT
39673274 AAATAATATA-AAAA-AATTATAATAAGT
1 AAATAATATATAAAACAATT-TAA-AA-T
*
39673301 -AA-AATATATGAAACAATTT
1 AAATAATATATAAAACAATTT
39673320 GATATTAAAA
Statistics
Matches: 404, Mismatches: 88, Indels: 75
0.71 0.16 0.13
Matches are distributed among these distances:
21 1 0.00
22 6 0.01
23 27 0.07
24 51 0.13
25 76 0.19
26 195 0.48
27 21 0.05
28 27 0.07
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.29
Consensus pattern (26 bp):
AAATAATATATAAAACAATTTAAAAT
Found at i:39672923 original size:28 final size:28
Alignment explanation
Indices: 39672888--39672957 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
39672878 AGACACTTTA
** *
39672888 AAAT-ACATAAAAAAAGAGTTTTAAGAT
1 AAATAACATAAAAAAAGAAATTTAAAAT
**
39672915 AAATAACATGTAAAAAGAAATTTAAAAT
1 AAATAACATAAAAAAAGAAATTTAAAAT
* *
39672943 AAATAATATACAAAA
1 AAATAACATAAAAAA
39672958 CGGTTTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 4 0.12
28 30 0.88
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.24
Consensus pattern (28 bp):
AAATAACATAAAAAAAGAAATTTAAAAT
Found at i:39673117 original size:75 final size:74
Alignment explanation
Indices: 39672933--39673211 Score: 240
Period size: 75 Copynumber: 3.7 Consensus size: 74
39672923 TGTAAAAAGA
* ** *
39672933 AATTTAAAATAAATAATATACAAAACGGTTTAAAA-AATAATATATATATAAAAATTCAAAATAA
1 AATTTAAAATAAATAATATATAAAA-AATTTAAAATAA-AA-A-ATATAT-AAAATACAAAATAA
* * *
39672997 ACAATATATATAAC
61 ATAATACATAAAAC
* ** * * *
39673011 AGTTTAAAATAAATAATATATAAAAAATTTAAAATGGATAATAGTTTAAAATACATAATAAATAA
1 AATTTAAAATAAATAATATATAAAAAATTTAAAATAAAAAATA-TATAAAATACAAAATAAATAA
39673076 TA-ATAAAAC
65 TACATAAAAC
* * *
39673085 AATTTAAAATAAATAATATATGAAAAAGTTTAAAATAAAAAATATATAAAAAATTAAAATAAATA
1 AATTTAAAATAAATAATATAT-AAAAAATTTAAAATAAAAAATATATAAAATA-CAAAATAAATA
39673150 A-AGCATAAAAC
64 ATA-CATAAAAC
* * * * * * *
39673161 AATTTGAAATAAATAATTTATAAAGTAATTTTAAATATATAATACATAAAA
1 AATTTAAAATAAATAATATATAAA-AAATTTAAAATAAAAAATATATAAAA
39673212 CAGTTTAAAT
Statistics
Matches: 165, Mismatches: 29, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
74 34 0.21
75 51 0.31
76 49 0.30
77 8 0.05
78 23 0.14
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (74 bp):
AATTTAAAATAAATAATATATAAAAAATTTAAAATAAAAAATATATAAAATACAAAATAAATAAT
ACATAAAAC
Found at i:39673217 original size:102 final size:99
Alignment explanation
Indices: 39672967--39673255 Score: 271
Period size: 100 Copynumber: 2.8 Consensus size: 99
39672957 ACGGTTTAAA
* * * *
39672967 AAATAATATATATATAAAAATTCAAAATAAACAATATATATAACAGTTTAAAATAAATAATATAT
1 AAATAATA-ATA-A-AACAATTTAAAATAAATAATATATAAAACAGTTTAAAATAAATAATATAT
** ** *
39673032 AAAAAATTTAAAATGGATAATAGTTTAAAATACATAAT
63 AAAAAA-TTAAAATAAATAATAGCATAAAACACATAAT
*
39673070 AAATAATAATAAAACAATTTAAAATAAATAATATATGAAAA-AGTTTAAAATAAAAAATATATAA
1 AAATAATAATAAAACAATTTAAAATAAATAATATAT-AAAACAGTTTAAAATAAATAATATATAA
39673134 AAAATTAAAATAAATAA-AGCATAAAACA-ATTTGAAAT
65 AAAATTAAAATAAATAATAGCATAAAACACA--T--AAT
* ** * * * * *
39673171 AAATAATTTATAAAGTAATTTTAAATATATAATACATAAAACAGTTT-AAATGAACTAATATGTA
1 AAATAA-TAATAAAACAATTTAAAATAAATAATATATAAAACAGTTTAAAAT-AAATAATATATA
*
39673235 AAAAGTCTAAAATAAATAATA
64 AAAAAT-TAAAATAAATAATA
39673256 TATAACACTG
Statistics
Matches: 156, Mismatches: 20, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
97 1 0.01
98 8 0.05
99 12 0.08
100 47 0.30
101 21 0.13
102 46 0.29
103 20 0.13
104 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (99 bp):
AAATAATAATAAAACAATTTAAAATAAATAATATATAAAACAGTTTAAAATAAATAATATATAAA
AAATTAAAATAAATAATAGCATAAAACACATAAT
Found at i:39673315 original size:102 final size:98
Alignment explanation
Indices: 39672967--39673315 Score: 246
Period size: 100 Copynumber: 3.4 Consensus size: 98
39672957 ACGGTTTAAA
* * *
39672967 AAAT-AATATATATATAAAAATTCAAAATAAACAATATAT-ATAACAGTTTAAAATAAATAATAT
1 AAATAAATA-ATATAAAAAAATTTAAAAT-AA-AATATATGA-AACAGTTTAAAATAAAAAATAT
** ** *
39673030 ATAAAAAATTTAAAATGGATAATAG--TTTAA-AA-TAC
62 ATAAAAAA-TTAAAATAAATAA-AGCATAAAACAATTTC
* *
39673065 ATAATAAATAATAATAAAACAATTTAAAATAAATAATATATGAAAAAGTTTAAAATAAAAAATAT
1 A-AATAAATAAT-ATAAAAAAATTTAAAAT-AA-AATATATGAAACAGTTTAAAATAAAAAATAT
*
39673130 ATAAAAAATTAAAATAAATAAAGCATAAAACAATTTG
62 ATAAAAAATTAAAATAAATAAAGCATAAAACAATTTC
* * * * * **
39673167 AAATAAATAATTTATAAAGTAATTTTAAATATATAATACATAAAACAGTTT-AAATGAACTAATA
1 AAATAAATAA--TATAAA-AAAATTTAAA-ATAAAATATATGAAACAGTTTAAAAT-AAAAAATA
* * * * **
39673231 TGTAAAAAGTCTAAAATAAATAATA-TATAACACTGTTTC
61 TATAAAAAAT-TAAAATAAATAA-AGCATAAAACAATTTC
39673270 AAATAAATAATATAAAAAAATTATAATAAGTAAAATATATGAAACA
1 AAATAAATAATATAAAAAAATT-TAA-AA-TAAAATATATGAAACA
39673316 ATTTGATATT
Statistics
Matches: 200, Mismatches: 33, Indels: 32
0.75 0.12 0.12
Matches are distributed among these distances:
98 3 0.01
99 16 0.08
100 63 0.31
101 26 0.13
102 49 0.25
103 40 0.20
104 3 0.01
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (98 bp):
AAATAAATAATATAAAAAAATTTAAAATAAAATATATGAAACAGTTTAAAATAAAAAATATATAA
AAAATTAAAATAAATAAAGCATAAAACAATTTC
Found at i:39674150 original size:5 final size:5
Alignment explanation
Indices: 39674140--39674181 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
39674130 GATTTGCAAA
*
39674140 AAAAT AAAAT AAAAT AAAAAT AAACAG AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT AAA-AT AAAAT AAAAT AAAAT
39674182 TTGAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 24 0.73
6 9 0.27
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:39674159 original size:11 final size:11
Alignment explanation
Indices: 39674140--39674180 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
39674130 GATTTGCAAA
39674140 AAAAT-AAAAT
1 AAAATAAAAAT
39674150 AAAATAAAAAT
1 AAAATAAAAAT
*
39674161 AAACA-GAAAAT
1 AAA-ATAAAAAT
39674172 AAAATAAAA
1 AAAATAAAA
39674181 TTTGAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 6 0.23
11 19 0.73
12 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:39676362 original size:13 final size:13
Alignment explanation
Indices: 39676323--39676399 Score: 82
Period size: 13 Copynumber: 5.9 Consensus size: 13
39676313 AGTTTGGCAA
* *
39676323 TGCTTTTAAAAAA
1 TGCTTTTGAAAAG
*
39676336 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
*
39676349 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* * *
39676362 TACTGTGGAAAAG
1 TGCTTTTGAAAAG
*
39676375 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
39676388 TGCTTTTGAAAA
1 TGCTTTTGAAAA
39676400 ATTTGGTTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 52 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:39676398 original size:26 final size:26
Alignment explanation
Indices: 39676336--39676399 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
39676326 TTTTAAAAAA
*
39676336 TGCTTTTAAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTGAGAAG
* * *
39676362 TACTGTGGAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTGAGAAG
39676388 TGCTTTTGAAAA
1 TGCTTTTGAAAA
39676400 ATTTGGTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTTTTGAGAAG
Found at i:39677107 original size:14 final size:15
Alignment explanation
Indices: 39677088--39677118 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
39677078 AGATATGTAT
39677088 ATATATATTTTA-AA
1 ATATATATTTTATAA
39677102 ATATATATTTTATAA
1 ATATATATTTTATAA
39677117 AT
1 AT
39677119 TTTTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATTTTATAA
Found at i:39678930 original size:30 final size:30
Alignment explanation
Indices: 39678894--39679053 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
39678884 GACAAGATTG
* * * * *
39678894 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
39678924 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
39678952 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
39678981 GCACTAAGCGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
39679011 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
39679040 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39679054 GATTCACTAT
Statistics
Matches: 118, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.19
29 48 0.41
30 44 0.37
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:39680660 original size:12 final size:12
Alignment explanation
Indices: 39680643--39680667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39680633 ACATCCCGTA
39680643 AGTTAGGACACG
1 AGTTAGGACACG
39680655 AGTTAGGACACG
1 AGTTAGGACACG
39680667 A
1 A
39680668 CACCATGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (12 bp):
AGTTAGGACACG
Found at i:39681110 original size:20 final size:20
Alignment explanation
Indices: 39681085--39681128 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
39681075 ACGTAACATA
39681085 TAAATACTAACACTAATAAT
1 TAAATACTAACACTAATAAT
*
39681105 TAAATATTAACACTAATAAT
1 TAAATACTAACACTAATAAT
39681125 TAAA
1 TAAA
39681129 GAGCAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATACTAACACTAATAAT
Found at i:39682630 original size:8 final size:8
Alignment explanation
Indices: 39682617--39682650 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
39682607 GGTTTGTAGT
39682617 AAAAAATA
1 AAAAAATA
39682625 AAAAAAT-
1 AAAAAATA
39682632 AAAAAATA
1 AAAAAATA
39682640 AAAAAATA
1 AAAAAATA
39682648 AAA
1 AAA
39682651 GAAGAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:39682636 original size:15 final size:15
Alignment explanation
Indices: 39682616--39682650 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
39682606 AGGTTTGTAG
39682616 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
39682631 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
39682646 TAAAA
1 TAAAA
39682651 GAAGAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAAAAATAAAAAAA
Found at i:39697622 original size:29 final size:29
Alignment explanation
Indices: 39697585--39697643 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
39697575 ACTGTCAAAA
*
39697585 GAATGTTGATATAAATGCTTAGCAAATAT
1 GAATGTTGATATAAATACTTAGCAAATAT
*
39697614 GAATTTTGATATAAATACTTAGCAAATAT
1 GAATGTTGATATAAATACTTAGCAAATAT
39697643 G
1 G
39697644 TTCAAATGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (29 bp):
GAATGTTGATATAAATACTTAGCAAATAT
Found at i:39698584 original size:30 final size:30
Alignment explanation
Indices: 39698550--39698628 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
39698540 AAATTTAATT
39698550 TTTGAAAGTATAAGGACTAAAAGTGACCAA
1 TTTGAAAGTATAAGGACTAAAAGTGACCAA
* * *
39698580 TTTGAAAAGTA-CAGGACTAAAATTGATCAA
1 TTTG-AAAGTATAAGGACTAAAAGTGACCAA
*
39698610 -AT-AAAGTATAAGGACTAAA
1 TTTGAAAGTATAAGGACTAAA
39698629 TTTACAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 6 0.14
28 9 0.21
29 1 0.02
30 20 0.48
31 6 0.14
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (30 bp):
TTTGAAAGTATAAGGACTAAAAGTGACCAA
Found at i:39698808 original size:2 final size:2
Alignment explanation
Indices: 39698801--39698825 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39698791 ACATACATGC
39698801 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 A
39698826 AACATGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39701572 original size:29 final size:29
Alignment explanation
Indices: 39701539--39701598 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
39701529 TTTTTTTATG
*
39701539 ATAGTAAATAATAACTTGTAATTACTCTT
1 ATAGTAAATAATAACTTCTAATTACTCTT
39701568 ATAGTAAATAATAACTTCTAATTACTCTT
1 ATAGTAAATAATAACTTCTAATTACTCTT
39701597 AT
1 AT
39701599 TACATATGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (29 bp):
ATAGTAAATAATAACTTCTAATTACTCTT
Found at i:39709821 original size:2 final size:2
Alignment explanation
Indices: 39709814--39709839 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39709804 AATAAGCAAT
39709814 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
39709840 CATCATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39711000 original size:56 final size:56
Alignment explanation
Indices: 39710939--39711197 Score: 360
Period size: 56 Copynumber: 4.6 Consensus size: 56
39710929 TCCCAAACAA
* * * * * *
39710939 GGTCTTACTCGTAAACACATATCGAAATCACATATCGATGCCAACGTATAAAATGT
1 GGTCTTACTCGCACACATATATCGAAGTCACATATCGATGCCAACGTATGAAACGT
* * *
39710995 AGTCTTACTCGCACACTTATATC-AGAGTCACATATCGATGCCAACGTATGAAATGT
1 GGTCTTACTCGCACACATATATCGA-AGTCACATATCGATGCCAACGTATGAAACGT
*
39711051 GGTCTTACTCGCACACATATATC-AGAGTCACATATCGATGCCAACATATGAAACGT
1 GGTCTTACTCGCACACATATATCGA-AGTCACATATCGATGCCAACGTATGAAACGT
* * *
39711107 GGACTTACTCACACACATATATCGGAGTCACATATCGATGCCAACGTATGAAACGT
1 GGTCTTACTCGCACACATATATCGAAGTCACATATCGATGCCAACGTATGAAACGT
*
39711163 GGACTTACTCGCACACATATATCGAAGTCACATAT
1 GGTCTTACTCGCACACATATATCGAAGTCACATAT
39711198 ACTTCCAGGT
Statistics
Matches: 184, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
55 1 0.01
56 183 0.99
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGAAGTCACATATCGATGCCAACGTATGAAACGT
Found at i:39714535 original size:27 final size:28
Alignment explanation
Indices: 39714485--39714610 Score: 132
Period size: 28 Copynumber: 4.6 Consensus size: 28
39714475 ATGTGTTCCC
39714485 TATTTTTCAGATTTTATAGTTTTACCCT
1 TATTTTTCAGATTTTATAGTTTTACCCT
* * *
39714513 TATTTTTCATATTTGATAG-TTTAGCCT
1 TATTTTTCAGATTTTATAGTTTTACCCT
*
39714540 T-TTTTT-AGATTTTATAGTTTTACCCC
1 TATTTTTCAGATTTTATAGTTTTACCCT
* * ** *
39714566 TATTTTTTAGATTTTACAAATTTAACCT
1 TATTTTTCAGATTTTATAGTTTTACCCT
*
39714594 TATTTTTTTAGATTTTA
1 TA-TTTTTCAGATTTTA
39714611 CAGCTTTGTC
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
25 9 0.11
26 12 0.15
27 13 0.16
28 34 0.41
29 14 0.17
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (28 bp):
TATTTTTCAGATTTTATAGTTTTACCCT
Found at i:39722675 original size:31 final size:30
Alignment explanation
Indices: 39722602--39722678 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
39722592 TGGTTGACCC
* *
39722602 ATCCCTTTTCGTAATTCAATAACTGAAGTT
1 ATCCCTTTTCATAATTCAATAACTGAAATT
* * *
39722632 ATCCCTTTTCATAGTTCGATAGCTGAAATT
1 ATCCCTTTTCATAATTCAATAACTGAAATT
39722662 ATCCCTTTTTCATAATT
1 ATCCC-TTTTCATAATT
39722679 TGATGGTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 30 0.75
31 10 0.25
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCAATAACTGAAATT
Found at i:39722845 original size:29 final size:29
Alignment explanation
Indices: 39722813--39722890 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
39722803 TAGTCGAAGT
* *
39722813 TATCCTTTTTCATAGTCGATGGTCGTCAC
1 TATCCTTTTTCATAGTCGATGCTCATCAC
* * * *
39722842 TATCCCTTTTCATTGTTGATGCTCATCTC
1 TATCCTTTTTCATAGTCGATGCTCATCAC
* * *
39722871 CATCCTTTTACATAATCGAT
1 TATCCTTTTTCATAGTCGAT
39722891 AGCTAAAGCT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.44
Consensus pattern (29 bp):
TATCCTTTTTCATAGTCGATGCTCATCAC
Found at i:39722850 original size:60 final size:61
Alignment explanation
Indices: 39722693--39722851 Score: 187
Period size: 61 Copynumber: 2.6 Consensus size: 61
39722683 GGTCATCACC
* * *
39722693 ATCCCTTTTCATTGTTCAATGGCCGTCACTATCCTTTTTTCATAATTTAATAACCGAAGCT
1 ATCCCTTTTCATAGTTCGATGGACGTCACTATCCTTTTTTCATAATTTAATAACCGAAGCT
* * * * ** *
39722754 ATCCCTTTTCATAGTTTGATGGACATCACCATCCTTTTTT-ATAATTTTATAGTCGAAGTT
1 ATCCCTTTTCATAGTTCGATGGACGTCACTATCCTTTTTTCATAATTTAATAACCGAAGCT
* * *
39722814 ATCCTTTTTCATAG-TCGATGGTCGTCACTATCCCTTTT
1 ATCCCTTTTCATAGTTCGATGGACGTCACTATCCTTTTT
39722852 CATTGTTGAT
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
59 19 0.23
60 29 0.35
61 34 0.41
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (61 bp):
ATCCCTTTTCATAGTTCGATGGACGTCACTATCCTTTTTTCATAATTTAATAACCGAAGCT
Found at i:39722922 original size:28 final size:27
Alignment explanation
Indices: 39722889--39722942 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
39722879 TACATAATCG
39722889 ATAGCT-AAAGCTATCCCTTTTCTATTTA
1 ATAGCTGAAA-CTATCCCTTTTC-ATTTA
39722917 ATAGCTGAAACTATCCCTTTTCATTT
1 ATAGCTGAAACTATCCCTTTTCATTT
39722943 GTTGATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 4 0.16
28 18 0.72
29 3 0.12
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (27 bp):
ATAGCTGAAACTATCCCTTTTCATTTA
Found at i:39725052 original size:30 final size:30
Alignment explanation
Indices: 39725018--39725215 Score: 170
Period size: 30 Copynumber: 6.7 Consensus size: 30
39725008 AGCCGGAGCT
* *
39725018 ATCCCTTTTCATAATTTGATGGTTGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * *
39725048 ATCCCTTTCCATTATTCGATGGTCTTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * *** *
39725078 ATCCC-TTTCTATAATTTGATAG-CCAAACTT
1 ATCCCTTTTC-ATAATTCGATGGTCGTCAC-C
* * *
39725108 ATCCCTTTTCATAGTTCGAAGATCGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * *
39725138 ATTCCTTTTCATTATTCGATGGTCGTCGCC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
** *
39725168 ATCCCTTTTCATTGTT-AATGGTCGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
39725197 ATCCCTTTTCATAA-TCGAT
1 ATCCCTTTTCATAATTCGAT
39725216 AGCTGAAGCT
Statistics
Matches: 128, Mismatches: 35, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
28 1 0.01
29 31 0.24
30 89 0.70
31 7 0.05
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATGGTCGTCACC
Found at i:39725082 original size:60 final size:60
Alignment explanation
Indices: 39725018--39725211 Score: 189
Period size: 60 Copynumber: 3.2 Consensus size: 60
39725008 AGCCGGAGCT
* * *
39725018 ATCCCTTTTCATAATTTGATGGTTGTCACCATCCCTTTCCATTATTCGATGGTCTTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACCATCCCTTTTCATTATTCGATGGTCGTCACC
* *** * * *
39725078 ATCCC-TTTCTATAATTTGATAG-CCAAACTTATCCCTTTTCA-TAGTTCGAAGATCGTCACC
1 ATCCCTTTTC-ATAATTTGATGGTCGTCAC-CATCCCTTTTCATTA-TTCGATGGTCGTCACC
* * * * * *
39725138 ATTCCTTTTCATTATTCGATGGTCGTCGCCATCCCTTTTCATTGTT-AATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACCATCCCTTTTCATTATTCGATGGTCGTCACC
39725197 ATCCCTTTTCATAAT
1 ATCCCTTTTCATAAT
39725212 CGATAGCTGA
Statistics
Matches: 103, Mismatches: 25, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
59 31 0.30
60 65 0.63
61 7 0.07
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.41
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATGGTCGTCACCATCCCTTTTCATTATTCGATGGTCGTCACC
Found at i:39725211 original size:25 final size:26
Alignment explanation
Indices: 39725130--39725208 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 26
39725120 AGTTCGAAGA
*
39725130 TCGTCACCATTCCTTTTCATTATTCGATGG
1 TCGTCACCATCCCTTTTCATTA----ATGG
*
39725160 TCGTCGCCATCCCTTTTCATTGTTAATGG
1 TCGTCACCATCCCTTTTCA---TTAATGG
39725189 TCGTCACCATCCCTTTTCAT
1 TCGTCACCATCCCTTTTCAT
39725209 AATCGATAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.02
29 22 0.51
30 17 0.40
33 3 0.07
ACGTcount: A:0.15, C:0.30, G:0.13, T:0.42
Consensus pattern (26 bp):
TCGTCACCATCCCTTTTCATTAATGG
Found at i:39725229 original size:29 final size:29
Alignment explanation
Indices: 39725197--39725266 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
39725187 GGTCGTCACC
* * *
39725197 ATCCCTTTTCATAATCGATAGCTGAAGCT
1 ATCCCTTTTCATAATCGATAACCGAAACT
* *
39725226 ATCCCATTTCATATTCGATAACCGAAACT
1 ATCCCTTTTCATAATCGATAACCGAAACT
*
39725255 ATCGCTTTTCAT
1 ATCCCTTTTCAT
39725267 TTTTCGATGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAACCGAAACT
Found at i:39727556 original size:49 final size:48
Alignment explanation
Indices: 39727383--39727558 Score: 217
Period size: 51 Copynumber: 3.5 Consensus size: 48
39727373 TGAGTACACG
* *
39727383 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA-ATTGTT-GGTCGCA
* * * * * *
39727433 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGGCTTTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAATTG--TTGGTCGCA
*
39727484 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-AATTGTTGGTCGCA
39727533 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
39727559 TGCGTATCAG
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 32 0.30
50 34 0.32
51 39 0.36
52 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAATTGTTGGTCGCA
Found at i:39727564 original size:100 final size:101
Alignment explanation
Indices: 39727379--39727564 Score: 329
Period size: 101 Copynumber: 1.9 Consensus size: 101
39727369 ATTGTGAGTA
*
39727379 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCATGTGTAGTACT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
39727444 AAGTGCAGGCTACTATGCGTACTCAATGGCTTTGAT
66 AAGTGCAGGCTACTATGCGTACTCAATGGCTTTGAT
* * *
39727480 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTT-GGTCGCATGTGTAGTACT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
39727544 AAGTGCAGGCTACTATGCGTA
66 AAGTGCAGGCTACTATGCGTA
39727565 TCAGATAGCT
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 38 0.47
101 43 0.53
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACTCAATGGCTTTGAT
Found at i:39742299 original size:48 final size:48
Alignment explanation
Indices: 39742243--39742340 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
39742233 GGAAAATAAC
39742243 ACAAAGTAAGCATGTCATGCTTAGTAAGTTCGTAACACATACAGGTTA
1 ACAAAGTAAGCATGTCATGCTTAGTAAGTTCGTAACACATACAGGTTA
*
39742291 ACAAAGTAAGCATGTCATGCTTAGTAAGTTTGTAACACATACAGGTTA
1 ACAAAGTAAGCATGTCATGCTTAGTAAGTTCGTAACACATACAGGTTA
39742339 AC
1 AC
39742341 TTTGCCAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (48 bp):
ACAAAGTAAGCATGTCATGCTTAGTAAGTTCGTAACACATACAGGTTA
Found at i:39742643 original size:60 final size:60
Alignment explanation
Indices: 39742581--39742771 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
39742571 AGCTGAAGCT
* * * * * *
39742581 ATCCCTTTTCATAATTTGATGGTCGTCA-CCATCTCTTTCCATTGTTCGATGGTCGTCACT
1 ATCCCTTTTCATAATTTGATAGCCG-AAGCCATCCCTTTTCATTGTTCGATGGTCGTCACC
**
39742641 ATCCCTTTTCATAATTTGATAGCCGAAGTTATCCCTTTTCATAT-TTCGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCAT-TGTTCGATGGTCGTCACC
* *
39742701 ATCCCTTTTCATAATTTGATAGCCGAAGCTATCCCTTTTCATAG-TCGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATTGTTCGATGGTCGTCACC
39742760 ATCCCTTTTCAT
1 ATCCCTTTTCAT
39742772 TGTTGATGGT
Statistics
Matches: 118, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
59 28 0.24
60 89 0.75
61 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.40
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATTGTTCGATGGTCGTCACC
Found at i:39742676 original size:30 final size:30
Alignment explanation
Indices: 39742639--39742858 Score: 143
Period size: 29 Copynumber: 7.5 Consensus size: 30
39742629 ATGGTCGTCA
39742639 CTATCCCTTTTCATAATTTGATAGCCGAAG
1 CTATCCCTTTTCATAATTTGATAGCCGAAG
* * * *
39742669 TTATCCCTTTTCAT-ATTTCGATGGTCGTCA-
1 CTATCCCTTTTCATAATTT-GATAGCCG-AAG
*
39742699 CCATCCCTTTTCATAATTTGATAGCCGAAG
1 CTATCCCTTTTCATAATTTGATAGCCGAAG
* * * * *
39742729 CTATCCCTTTTCAT-AGTCGATGGTCGTCA-
1 CTATCCCTTTTCATAATTTGATAGCCG-AAG
* * * * *
39742758 CCATCCCTTTTCAT--TGTTGATGGTCGTCAT
1 CTATCCCTTTTCATAAT-TTGATAGCCG-AAG
* *
39742788 C-ATCCCTTTTCGTAA-TTGATAGCTGAAG
1 CTATCCCTTTTCATAATTTGATAGCCGAAG
* * *
39742816 CTATCCCTTTTCGT-ATTTGATAGCCAAAA
1 CTATCCCTTTTCATAATTTGATAGCCGAAG
*
39742845 CTATCCATTTTCAT
1 CTATCCCTTTTCAT
39742859 TTGTCGATGA
Statistics
Matches: 150, Mismatches: 29, Indels: 23
0.74 0.14 0.11
Matches are distributed among these distances:
28 3 0.02
29 90 0.60
30 52 0.35
31 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (30 bp):
CTATCCCTTTTCATAATTTGATAGCCGAAG
Found at i:39743645 original size:15 final size:15
Alignment explanation
Indices: 39743625--39743656 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39743615 CTAAAAATGG
39743625 TTTTGTTTTTACTTA
1 TTTTGTTTTTACTTA
*
39743640 TTTTGTTTTTATTTA
1 TTTTGTTTTTACTTA
39743655 TT
1 TT
39743657 AAATTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTGTTTTTACTTA
Found at i:39745770 original size:23 final size:24
Alignment explanation
Indices: 39745740--39745850 Score: 92
Period size: 23 Copynumber: 4.7 Consensus size: 24
39745730 GGACTCACCA
39745740 TAGCTCATAAGAGCTTACT-ATTT
1 TAGCTCATAAGAGCTTACTGATTT
*
39745763 TAGCTCAT-TGTAGCTTACTGA-TT
1 TAGCTCATAAG-AGCTTACTGATTT
39745786 TAGCTCGA-AAGAGCTTACTG--TT
1 TAGCTC-ATAAGAGCTTACTGATTT
* * *
39745808 CAGCTCA-ATAGAGCTAACTGTTTGT
1 TAGCTCATA-AGAGCTTACTGATT-T
39745833 TAGCTCAGTAAGAGCTTA
1 TAGCTCA-TAAGAGCTTA
39745851 TCGACCATGA
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.03
22 18 0.25
23 33 0.46
24 4 0.06
25 7 0.10
26 7 0.10
27 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (24 bp):
TAGCTCATAAGAGCTTACTGATTT
Found at i:39745820 original size:22 final size:22
Alignment explanation
Indices: 39745774--39745829 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
39745764 AGCTCATTGT
*
39745774 AGCTTACTGATTTAGCTCGAAAG
1 AGCTTACTG-TTCAGCTCGAAAG
39745797 AGCTTACTGTTCAGCTC-AATAG
1 AGCTTACTGTTCAGCTCGAA-AG
*
39745819 AGCTAACTGTT
1 AGCTTACTGTT
39745830 TGTTAGCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 19 0.63
23 9 0.30
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (22 bp):
AGCTTACTGTTCAGCTCGAAAG
Found at i:39748913 original size:6 final size:6
Alignment explanation
Indices: 39748904--39748929 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39748894 CACCGTAATG
39748904 GTAACA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GT
39748930 CGGGTACAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:39750007 original size:2 final size:2
Alignment explanation
Indices: 39750000--39750039 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39749990 ATTTACTTGT
39750000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39750040 ATAACATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39750560 original size:15 final size:15
Alignment explanation
Indices: 39750528--39750565 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
39750518 CCAATTATCC
39750528 TTAATTAAGTTAAAT
1 TTAATTAAGTTAAAT
*
39750543 TTACTTAA-TTAAACT
1 TTAATTAAGTTAAA-T
39750558 TTAATTAA
1 TTAATTAA
39750566 CCACTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAATTAAGTTAAAT
Found at i:39756717 original size:22 final size:22
Alignment explanation
Indices: 39756692--39756748 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
39756682 AGCTTGAAAG
39756692 AGCTTACTGTTCAGCTCAATAA
1 AGCTTACTGTTCAGCTCAATAA
* * *
39756714 AGCTTACCGTTTTTAGCTCAATAG
1 AGCTTA-C-TGTTCAGCTCAATAA
39756738 AGCTTACTGTT
1 AGCTTACTGTT
39756749 TATCAGCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 9 0.31
23 2 0.07
24 18 0.62
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (22 bp):
AGCTTACTGTTCAGCTCAATAA
Found at i:39756729 original size:46 final size:45
Alignment explanation
Indices: 39756643--39756773 Score: 120
Period size: 46 Copynumber: 2.8 Consensus size: 45
39756633 CATAGCTCGT
* * ** *
39756643 AAGAGCTTACTATTTCAGCTCATTGTAGCTTACC-AATTTAGCTTGA
1 AAGAGCTTACT-GTTCAGCTCAATAAAGCTTACCGAATTTAGC-TCA
**
39756689 AAGAGCTTACTGTTCAGCTCAATAAAGCTTACCGTTTTTAGCTCA
1 AAGAGCTTACTGTTCAGCTCAATAAAGCTTACCGAATTTAGCTCA
*
39756734 ATAGAGCTTACTGTTTATCAGCTCAGTAAGAGCTTACCGA
1 A-AGAGCTTACTG--T-TCAGCTCAATAA-AGCTTACCGA
39756774 CCATGACTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
45 21 0.30
46 28 0.40
48 1 0.01
49 11 0.16
50 9 0.13
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (45 bp):
AAGAGCTTACTGTTCAGCTCAATAAAGCTTACCGAATTTAGCTCA
Found at i:39756731 original size:24 final size:25
Alignment explanation
Indices: 39756702--39756772 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
39756692 AGCTTACTGT
39756702 TCAGCTCAATAAAGCTTACCGTTT-
1 TCAGCTCAATAAAGCTTACCGTTTA
* * *
39756726 TTAGCTCAATAGAGCTTACTGTTTA
1 TCAGCTCAATAAAGCTTACCGTTTA
*
39756751 TCAGCTCAGTAAGAGCTTACCG
1 TCAGCTCAATAA-AGCTTACCG
39756773 ACCATGACTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 21 0.55
25 9 0.24
26 8 0.21
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (25 bp):
TCAGCTCAATAAAGCTTACCGTTTA
Found at i:39763194 original size:14 final size:14
Alignment explanation
Indices: 39763172--39763216 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
39763162 TTAATTATCA
*
39763172 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
39763186 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* *
39763200 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
39763214 TTA
1 TTA
39763217 GTATTTATGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:39763225 original size:21 final size:21
Alignment explanation
Indices: 39763178--39763254 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
39763168 ATCATTATAG
* *
39763178 TTTAAGGTTTATGGTTTAAGA
1 TTTATGGTTTAGGGTTTAAGA
*
39763199 TATATGGTTTAGGGTTT-AGTA
1 TTTATGGTTTAGGGTTTAAG-A
** *
39763220 TTTATGGGATAGGGGTTAAGAA
1 TTTATGGTTTAGGGTTTAAG-A
*
39763242 GTTTAGGGTTTAG
1 -TTTATGGTTTAG
39763255 ATTAATTAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.05
21 28 0.67
22 3 0.07
23 9 0.21
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (21 bp):
TTTATGGTTTAGGGTTTAAGA
Found at i:39763881 original size:3 final size:3
Alignment explanation
Indices: 39763873--39763904 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
39763863 CATTTTAGTA
*
39763873 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39763905 AAGAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39764258 original size:37 final size:37
Alignment explanation
Indices: 39764193--39764301 Score: 166
Period size: 37 Copynumber: 2.9 Consensus size: 37
39764183 GTGTCAGAAA
* *
39764193 AACCCATCTCCTCCGTCGCCTTCTCCCCGTGCATCGC
1 AACCCATCTCCTCCATCGCCTTCGCCCCGTGCATCGC
* *
39764230 AACTCAT-TCCCTCCATCGTCTTCGCCCCGTGCATCGC
1 AACCCATCT-CCTCCATCGCCTTCGCCCCGTGCATCGC
39764267 AACCCATCTCCTCCATCGCCTTCGCCCCGTGCATC
1 AACCCATCTCCTCCATCGCCTTCGCCCCGTGCATC
39764302 TGCTGCATAG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
36 1 0.02
37 62 0.97
38 1 0.02
ACGTcount: A:0.13, C:0.50, G:0.13, T:0.25
Consensus pattern (37 bp):
AACCCATCTCCTCCATCGCCTTCGCCCCGTGCATCGC
Found at i:39767558 original size:19 final size:19
Alignment explanation
Indices: 39767536--39767576 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39767526 TTTATTGATA
39767536 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
39767554 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
39767573 TTTT
1 TTTT
39767577 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:39768748 original size:28 final size:28
Alignment explanation
Indices: 39768716--39768773 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
39768706 CATTTGTCCT
* *
39768716 TATTTCTTT-GATTTTACAATTTTTCCCC
1 TATTT-TTTAGATTTTACAATCTATCCCC
39768744 TATTTTTTAGATTTTACAATCTATCCCC
1 TATTTTTTAGATTTTACAATCTATCCCC
39768772 TA
1 TA
39768774 CTTTACAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.22, C:0.21, G:0.03, T:0.53
Consensus pattern (28 bp):
TATTTTTTAGATTTTACAATCTATCCCC
Found at i:39768785 original size:28 final size:28
Alignment explanation
Indices: 39768726--39768797 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
39768716 TATTTCTTTG
* * ** *
39768726 ATTTTACAATTTTTCCCCTATTTTTTAG
1 ATTTTACAATCTTTCCCCTACTTTACAA
*
39768754 ATTTTACAATCTATCCCCTACTTTACAA
1 ATTTTACAATCTTTCCCCTACTTTACAA
39768782 ATTTTAC-ATCTTTCCC
1 ATTTTACAATCTTTCCC
39768798 AAAATTTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 8 0.22
28 29 0.78
ACGTcount: A:0.25, C:0.25, G:0.01, T:0.49
Consensus pattern (28 bp):
ATTTTACAATCTTTCCCCTACTTTACAA
Found at i:39773249 original size:72 final size:72
Alignment explanation
Indices: 39773132--39773274 Score: 207
Period size: 72 Copynumber: 2.0 Consensus size: 72
39773122 AGTACTGTCT
* * * *
39773132 GAAGCTGTCTTCTCCCGAATCAATTCAGCTGCTGCTTCTTTGCTCTCCTCAACCATTCAAAACAG
1 GAAGCTGTCTCCTCCCGAATCAATTCAGCCGCTGCTTCCTCGCTCTCCTCAACCATTCAAAACAG
*
39773197 CCAGCCC
66 CAAGCCC
* *
39773204 GAAGCTGTCTCCTCCCG-ATTAGATTCAGCCGCTGCTTCCTCGCTCTCCTCAACCGTTCAAAACA
1 GAAGCTGTCTCCTCCCGAATCA-ATTCAGCCGCTGCTTCCTCGCTCTCCTCAACCATTCAAAACA
39773268 GCAAGCC
65 GCAAGCC
39773275 ATCGCCCCTG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
71 3 0.05
72 60 0.95
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (72 bp):
GAAGCTGTCTCCTCCCGAATCAATTCAGCCGCTGCTTCCTCGCTCTCCTCAACCATTCAAAACAG
CAAGCCC
Found at i:39776117 original size:40 final size:39
Alignment explanation
Indices: 39775967--39776119 Score: 243
Period size: 39 Copynumber: 3.9 Consensus size: 39
39775957 AAATGTTCGA
* *
39775967 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
39776006 GTGACATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
39776045 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
39776084 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
39776120 GGTTACCATA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:39776135 original size:40 final size:39
Alignment explanation
Indices: 39775968--39776150 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
39775958 AATGTTCGAG
* * *
39775968 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
39776007 TGACATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
39776046 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
39776085 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
39776125 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
39776151 GTTTGAACGA
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 87 0.68
40 41 0.32
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:39776186 original size:79 final size:79
Alignment explanation
Indices: 39775974--39776188 Score: 177
Period size: 78 Copynumber: 2.7 Consensus size: 79
39775964 CGAGTGATAT
** * * * * * *
39775974 CCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGACATCCGGGCT-AA-GCCCGAAGGCAATTG
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCC-GGATAAACTCCCGAAGGCAATTG
** *
39776037 TGCGAGTTATGATAT
65 TGCGAGTTACCATAA
** * * * * *
39776052 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGATAAACTCCCGAAGGCAATTGT
*
39776117 GCGGGTTACCATAA
66 GCGAGTTACCATAA
* **
39776131 CCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT-ATATCCGGATAAACT-CCGAAGG
1 CCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-TGATATCCGGATAAACTCCCGAAGG
39776189 TATGTGATTC
Statistics
Matches: 114, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
77 3 0.03
78 40 0.35
79 40 0.35
80 30 0.26
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.22
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGATAAACTCCCGAAGGCAATTGT
GCGAGTTACCATAA
Found at i:39779594 original size:12 final size:12
Alignment explanation
Indices: 39779577--39779605 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
39779567 GCCGTGCCTC
39779577 GCACATGGCCAG
1 GCACATGGCCAG
39779589 GCACATGGCCAG
1 GCACATGGCCAG
39779601 GCACA
1 GCACA
39779606 CACCTGTGTG
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:0.28, C:0.34, G:0.31, T:0.07
Consensus pattern (12 bp):
GCACATGGCCAG
Found at i:39779658 original size:23 final size:24
Alignment explanation
Indices: 39779630--39779684 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
39779620 CGATAATAAG
39779630 GTTTTTCGGCTTTCATCAAAACTC
1 GTTTTTCGGCTTTCATCAAAACTC
39779654 GTTTTTCGGCTTTCATCAAAACTC
1 GTTTTTCGGCTTTCATCAAAACTC
39779678 GTTTTTC
1 GTTTTTC
39779685 TATGTTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (24 bp):
GTTTTTCGGCTTTCATCAAAACTC
Found at i:39794807 original size:40 final size:40
Alignment explanation
Indices: 39794705--39794888 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
39794695 AAATTGAATG
* * * * *
39794705 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
39794745 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
39794785 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
39794825 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
39794865 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
39794889 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:39794913 original size:80 final size:80
Alignment explanation
Indices: 39794747--39794933 Score: 189
Period size: 80 Copynumber: 2.3 Consensus size: 80
39794737 TGAAAATTAT
* * *
39794747 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCTATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCTATATCCGGGCTAAGACCCGAAGGCATT
* *
39794812 CGTGCAAGTTGTTAA
66 CGTGCAAGTTATCAA
* * * * * *
39794827 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCT-ATATCCGGGCTAAGACCCGAAGGCAT
* **
39794891 TGGTGCGGGTTATCATA
65 TCGTGCAAGTTATCA-A
* * *
39794908 A-CCGGGCTATGTCCCGAAGGCGATTG
1 ATCCGGGCTAAGACCCGAAGGCAATTG
39794934 AACGAGTAGC
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
79 1 0.01
80 84 0.97
81 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCTATATCCGGGCTAAGACCCGAAGGCATT
CGTGCAAGTTATCAA
Found at i:39797650 original size:31 final size:31
Alignment explanation
Indices: 39797615--39797690 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
39797605 CATAAAGGGA
*
39797615 CACACGCCCGTGTAGAGGGCTCATGTGGACT
1 CACACGCCCGTGTAGAGGGCCCATGTGGACT
* * * *
39797646 CACACACCCATGTAGGGGGCCCGTGTGGACT
1 CACACGCCCGTGTAGAGGGCCCATGTGGACT
39797677 CACACGCCCGTGTA
1 CACACGCCCGTGTA
39797691 TCTTGGGGCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (31 bp):
CACACGCCCGTGTAGAGGGCCCATGTGGACT
Found at i:39800870 original size:20 final size:20
Alignment explanation
Indices: 39800845--39800889 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
39800835 AATTCAATTG
39800845 AAAGAGGAAATA-AAAAAAGA
1 AAAGAGGAAA-AGAAAAAAGA
*
39800865 AAAGAGGAAAAGAAAGAAGA
1 AAAGAGGAAAAGAAAAAAGA
39800885 AAAGA
1 AAAGA
39800890 AAAGGATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AAAGAGGAAAAGAAAAAAGA
Found at i:39800877 original size:13 final size:13
Alignment explanation
Indices: 39800859--39800893 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
39800849 AGGAAATAAA
*
39800859 AAAAGAAAAGAGG
1 AAAAGAAAAGAAG
39800872 AAAAG-AAAGAAG
1 AAAAGAAAAGAAG
39800884 AAAAGAAAAG
1 AAAAGAAAAG
39800894 GATTTGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAG
Found at i:39801973 original size:9 final size:9
Alignment explanation
Indices: 39801959--39802278 Score: 68
Period size: 10 Copynumber: 33.1 Consensus size: 9
39801949 TATTTTTCTC
39801959 ATAAAAATT
1 ATAAAAATT
*
39801968 ATAAAAATC
1 ATAAAAATT
39801977 ATAAAAGATT
1 ATAAAA-ATT
*
39801987 ATTACAAATT
1 A-TAAAAATT
39801997 -TAAAAA-T
1 ATAAAAATT
39802004 ATTAAAAAATGT
1 A-T-AAAAAT-T
*
39802016 ATGAAATATT
1 AT-AAAAATT
39802026 -TACAGAAACTT
1 ATA-A-AAA-TT
**
39802037 ATAAAAGCTACA
1 ATAAAA---ATT
*
39802049 AAAAAAATT
1 ATAAAAATT
39802058 CATAAAAACTT
1 -ATAAAAA-TT
*
39802069 ATAAATATT
1 ATAAAAATT
39802078 ATAAAAATT
1 ATAAAAATT
39802087 ATAAAAGA-T
1 ATAAAA-ATT
*
39802096 ACTATTAAATT
1 A-TA-AAAATT
39802107 ATAAAAGTAATT
1 AT-AAA--AATT
39802119 ATAAAAA--
1 ATAAAAATT
39802126 ATAAAACATGT
1 ATAAAA-AT-T
39802137 -TAAAAA-T
1 ATAAAAATT
39802144 ATAAAAACATT
1 AT-AAAA-ATT
* *
39802155 CTATAAACTT
1 ATA-AAAATT
*
39802165 ATAAACATT
1 ATAAAAATT
*
39802174 ATCAAAAGTT
1 AT-AAAAATT
39802184 ATAAAAGATT
1 ATAAAA-ATT
**
39802194 CATAATATGTT
1 -ATAA-AAATT
* *
39802205 CTAATGAATT
1 ATAA-AAATT
39802215 ATAAAAAATT
1 AT-AAAAATT
***
39802225 ATAATTTTT
1 ATAAAAATT
39802234 A-AGAAAATT
1 ATA-AAAATT
*
39802243 ATAAATATT
1 ATAAAAATT
*
39802252 A-AAAAGTAT
1 ATAAAAAT-T
*
39802261 GTAAAAA-T
1 ATAAAAATT
39802269 ATAAAAATT
1 ATAAAAATT
39802278 A
1 A
39802279 ATTTATTGGT
Statistics
Matches: 224, Mismatches: 45, Indels: 84
0.63 0.13 0.24
Matches are distributed among these distances:
7 8 0.04
8 20 0.09
9 71 0.32
10 72 0.32
11 36 0.16
12 16 0.07
13 1 0.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:39802064 original size:11 final size:10
Alignment explanation
Indices: 39802050--39802127 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 10
39802040 AAAGCTACAA
39802050 AAAAAATTCAT
1 AAAAAATT-AT
*
39802061 AAAAACTTAT
1 AAAAAATTAT
*
39802071 -AAATATTAT
1 AAAAAATTAT
39802080 -AAAAATTAT
1 AAAAAATTAT
*
39802089 AAAAGA-TACT
1 AAAAAATTA-T
**
39802099 ATTAAATTAT
1 AAAAAATTAT
39802109 AAAAGTAATTAT
1 AAAA--AATTAT
39802121 AAAAAAT
1 AAAAAAT
39802128 AAAACATGTT
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
9 17 0.33
10 16 0.31
11 9 0.17
12 10 0.19
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:39802253 original size:18 final size:18
Alignment explanation
Indices: 39802219--39802253 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39802209 TGAATTATAA
* *
39802219 AAAATTATAATTTTTAAG
1 AAAATTATAAATATTAAG
39802237 AAAATTATAAATATTAA
1 AAAATTATAAATATTAA
39802254 AAAGTATGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAATTATAAATATTAAG
Found at i:39804278 original size:136 final size:140
Alignment explanation
Indices: 39804122--39804377 Score: 376
Period size: 144 Copynumber: 1.8 Consensus size: 140
39804112 ATGGAATTAA
*
39804122 AACTGGATTGAGAAAATTATTTAATTAAAAAATTAATTTAGTTGA-T-TTAATT-AAT-TAATAT
1 AACTGGATTGAAAAAATTATTTAATTAAAAAATTAATTTAGTTGATTATTAATTAAATATAATAT
* *
39804183 TTATTTTGGAAAATAGAAAACAAGTATTGGGTTGGATTAAATTATGAAGTGCAAGATCAAAATTG
66 TAATTTTGGAAAACAGAAAACAAGTATTGGGTTGGATTAAATTATGAAGTGCAAGATCAAAATTG
39804248 GACTGGTTAG
131 GACTGGTTAG
** *
39804258 AACTGGATTGAAAAAATTATTTAATTAGGAAATTAGTTTAGTTGATTTCATTAATTAAATAAATA
1 AACTGGATTGAAAAAATTATTTAATTAAAAAATTAATTTAGTTGA-TT-ATTAATTAAAT--ATA
* *
39804323 ATATTAATTTTGGGAAACAGAAAACAAGTATTGGGTTGGATTAAATTATTAAGTG
62 ATATTAATTTTGGAAAACAGAAAACAAGTATTGGGTTGGATTAAATTATGAAGTG
39804378 GGAGATAAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
136 41 0.39
138 1 0.01
140 6 0.06
141 3 0.03
144 53 0.51
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (140 bp):
AACTGGATTGAAAAAATTATTTAATTAAAAAATTAATTTAGTTGATTATTAATTAAATATAATAT
TAATTTTGGAAAACAGAAAACAAGTATTGGGTTGGATTAAATTATGAAGTGCAAGATCAAAATTG
GACTGGTTAG
Found at i:39808897 original size:13 final size:13
Alignment explanation
Indices: 39808879--39808905 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39808869 ATAGTGTGTA
39808879 AGGATGGACGGAG
1 AGGATGGACGGAG
39808892 AGGATGGACGGAG
1 AGGATGGACGGAG
39808905 A
1 A
39808906 TGGTATTTAG
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:0.33, C:0.07, G:0.52, T:0.07
Consensus pattern (13 bp):
AGGATGGACGGAG
Found at i:39819759 original size:2 final size:2
Alignment explanation
Indices: 39819712--39819742 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39819702 AAATCGATTG
39819712 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
39819743 AATGGTGCTG
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:39849444 original size:10 final size:9
Alignment explanation
Indices: 39849431--39849653 Score: 107
Period size: 10 Copynumber: 23.3 Consensus size: 9
39849421 TAATAATATC
39849431 TAATTTTTCA
1 TAATTTTT-A
39849441 TAATTTTTA
1 TAATTTTTA
39849450 T-ATTATTTA
1 TAATT-TTTA
*
39849459 TAATTTTTT
1 TAATTTTTA
*
39849468 TGAATTTCTA
1 T-AATTTTTA
39849478 TTAAGTTTTTA
1 -TAA-TTTTTA
*
39849489 TAAAATTTTA
1 T-AATTTTTA
39849499 -AATGTTTTAAA
1 TAAT-TTTT--A
*
39849510 TATTTTTTA
1 TAATTTTTA
39849519 TTAATTTTTTTA
1 -TAA--TTTTTA
*
39849531 TAATATATTA
1 TAAT-TTTTA
*
39849541 GAATTTTTA
1 TAATTTTTA
*
39849550 TAAATTTTCA
1 T-AATTTTTA
*
39849560 TAATATTTA
1 TAATTTTTA
39849569 TAAGTTTTTA
1 TAA-TTTTTA
*
39849579 TGATTTTT-
1 TAATTTTTA
39849587 TAATTTTTA
1 TAATTTTTA
* *
39849596 TTAGTTTATA
1 -TAATTTTTA
39849606 TCAA-TTTTA
1 T-AATTTTTA
*
39849615 GT--TTTTTT
1 -TAATTTTTA
39849623 TAATTTTTA
1 TAATTTTTA
*
39849632 GTATTTTTTA
1 -TAATTTTTA
*
39849642 TATTTTTTA
1 TAATTTTTA
39849651 TAA
1 TAA
39849654 ACTTGTTAAT
Statistics
Matches: 163, Mismatches: 26, Indels: 49
0.68 0.11 0.21
Matches are distributed among these distances:
7 1 0.01
8 16 0.10
9 56 0.34
10 66 0.40
11 16 0.10
12 8 0.05
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (9 bp):
TAATTTTTA
Found at i:39849593 original size:17 final size:17
Alignment explanation
Indices: 39849581--39849648 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 17
39849571 AGTTTTTATG
*
39849581 ATTTTTTAATTTTTATT
1 ATTTTTTAATTTTTAGT
*
39849598 AGTTTATATCAA-TTTTAGT
1 A-TTT-T-TTAATTTTTAGT
*
39849617 TTTTTTTAATTTTTAGT
1 ATTTTTTAATTTTTAGT
39849634 ATTTTTTATATTTTT
1 ATTTTTTA-ATTTTT
39849649 TATAAACTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.07
17 16 0.39
18 12 0.29
19 7 0.17
20 3 0.07
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (17 bp):
ATTTTTTAATTTTTAGT
Found at i:39856082 original size:26 final size:26
Alignment explanation
Indices: 39856046--39856155 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
39856036 TGATACAAAT
39856046 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
39856072 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
39856098 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
39856124 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
39856150 TGATAA
1 TGATAA
39856156 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:39857637 original size:28 final size:26
Alignment explanation
Indices: 39857595--39857669 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
39857585 AAAAGTAGCT
* * * *
39857595 AAATTACTATAATACCTCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
*
39857623 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
39857649 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
39857670 GGTTAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 23 0.56
27 1 0.02
28 17 0.41
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:39857814 original size:27 final size:27
Alignment explanation
Indices: 39857773--39857885 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
39857763 GAGGAAGCGT
*
39857773 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
39857800 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
39857827 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
39857855 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
39857881 TCTGG
1 TCTGG
39857886 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:39857878 original size:54 final size:54
Alignment explanation
Indices: 39857771--39857885 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
39857761 TGGAGGAAGC
*
39857771 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
39857825 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
39857879 GTTCTGG
1 GTTCTGG
39857886 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:39860933 original size:9 final size:9
Alignment explanation
Indices: 39860919--39860962 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
39860909 ATTCTCAAAT
39860919 TCGAATAAC
1 TCGAATAAC
*
39860928 TCGAATAAT
1 TCGAATAAC
39860937 TCGAATAAC
1 TCGAATAAC
*
39860946 TCGAATAAT
1 TCGAATAAC
39860955 TCGAATAA
1 TCGAATAA
39860963 ACCGAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (9 bp):
TCGAATAAC
Found at i:39860968 original size:27 final size:27
Alignment explanation
Indices: 39860919--39860970 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
39860909 ATTCTCAAAT
**
39860919 TCGAATAACTCGAATAATTCGAATAAC
1 TCGAATAACTCGAATAAACCGAATAAC
*
39860946 TCGAATAATTCGAATAAACCGAATA
1 TCGAATAACTCGAATAAACCGAATA
39860971 TAAACTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (27 bp):
TCGAATAACTCGAATAAACCGAATAAC
Found at i:39860970 original size:18 final size:18
Alignment explanation
Indices: 39860916--39860962 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
39860906 TGAATTCTCA
39860916 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
39860934 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
39860952 AATTCGAATAA
1 AATTCGAATAA
39860963 ACCGAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:39861676 original size:5 final size:5
Alignment explanation
Indices: 39861666--39861696 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
39861656 CTCAAAAATT
*
39861666 TTCGA TTCGA TTCGA TTCGA TTCTA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
39861697 CGAATGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.45
Consensus pattern (5 bp):
TTCGA
Found at i:39865419 original size:24 final size:24
Alignment explanation
Indices: 39865387--39865433 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
39865377 GATATTTGAC
*
39865387 AGTTATGCTTGACGTCCTTTCTGG
1 AGTTATGCTTGACATCCTTTCTGG
39865411 AGTTATGCTTGACATCCTTTCTG
1 AGTTATGCTTGACATCCTTTCTG
39865434 ATATCCAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (24 bp):
AGTTATGCTTGACATCCTTTCTGG
Found at i:39874278 original size:29 final size:28
Alignment explanation
Indices: 39874246--39874348 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 28
39874236 GTGACGAGAT
* *
39874246 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACT-AGTGTGCGAGCTTGGAATATA
* *
39874275 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACT-AGTGTGCGAGCTTGGAATATA
* **
39874304 TGGCACTATGTGTGCGGGCTT-GAATCACG
1 TGGCACTA-GTGTGCGAGCTTGGAAT-ATA
39874333 TGGCACTAAGTGTGCG
1 TGGCACT-AGTGTGCG
39874349 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.07
29 56 0.92
30 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (28 bp):
TGGCACTAGTGTGCGAGCTTGGAATATA
Found at i:39882278 original size:29 final size:28
Alignment explanation
Indices: 39882216--39882316 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 28
39882206 GTGACGAGAT
* * *
39882216 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-GATATA
* *
39882245 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGA-TATA
* *
39882274 TGGCACTATGTGTGCGGGCTT-GA-ATCA
1 TGGCACTAAGTGTGCGAGCTTGGATAT-A
39882301 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
39882317 TGATTGAGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
26 2 0.03
27 16 0.27
28 3 0.05
29 39 0.65
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGGATATA
Found at i:39882323 original size:27 final size:27
Alignment explanation
Indices: 39882246--39882323 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
39882236 TGTAATGTAC
*
39882246 GGCACTAAGTGTGCGAGTTTGGACTATAT
1 GGCACTAAGTGTGCGAGATT-GAC-ATAT
* * *
39882275 GGCACTATGTGTGCGGGCTTGA-ATCAT
1 GGCACTAAGTGTGCGAGATTGACAT-AT
*
39882302 GGCACTAAGTGTGCGTGATTGA
1 GGCACTAAGTGTGCGAGATTGA
39882324 GTATTAAGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
26 2 0.05
27 21 0.50
28 2 0.05
29 17 0.40
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.29
Consensus pattern (27 bp):
GGCACTAAGTGTGCGAGATTGACATAT
Found at i:39884858 original size:32 final size:32
Alignment explanation
Indices: 39884782--39884862 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 32
39884772 TTCCTGTATT
* * *
39884782 AAAATCCAACCAAATACAACAAATATAATAT-
1 AAAATACAACCAAAAACAACAAATATAACATA
* * * * *
39884813 AAAATGCAGCCAAAAATAGCAAATTTAACATA
1 AAAATACAACCAAAAACAACAAATATAACATA
39884845 AAAATACAACCAAAAACA
1 AAAATACAACCAAAAACA
39884863 TTAATTCTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 24 0.62
32 15 0.38
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.16
Consensus pattern (32 bp):
AAAATACAACCAAAAACAACAAATATAACATA
Found at i:39891856 original size:11 final size:11
Alignment explanation
Indices: 39891842--39891891 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
39891832 AATATTTTAA
39891842 AAATTCTTGAC
1 AAATTCTTGAC
* *
39891853 AAATTATTTTGTC
1 AAA-T-TCTTGAC
39891866 AAATTCTTGAC
1 AAATTCTTGAC
39891877 AAATTCTTGAC
1 AAATTCTTGAC
39891888 AAAT
1 AAAT
39891892 ATACAAGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 23 0.70
12 2 0.06
13 8 0.24
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATTCTTGAC
Found at i:39892291 original size:18 final size:19
Alignment explanation
Indices: 39892270--39892305 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39892260 TTTGAAATTC
39892270 TTCATCTCT-CAATTCTAT
1 TTCATCTCTGCAATTCTAT
*
39892288 TTCATCTTTGCAATTCTA
1 TTCATCTCTGCAATTCTA
39892306 CAGAAAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (19 bp):
TTCATCTCTGCAATTCTAT
Found at i:39893272 original size:2 final size:2
Alignment explanation
Indices: 39893265--39893294 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39893255 TTCAAATAAA
39893265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39893295 TCAAAACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39894353 original size:21 final size:21
Alignment explanation
Indices: 39894327--39894387 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
39894317 GGATTTTGGA
* *
39894327 GTTTATGGTTTAGTGTTTATG
1 GTTTATGGTTTAATGTTTAGG
* **
39894348 GTTTATGTTTTAAAATTTAGG
1 GTTTATGGTTTAATGTTTAGG
*
39894369 GTTTAGGGTTTAATGTTTA
1 GTTTATGGTTTAATGTTTA
39894388 AGATTTAAGG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (21 bp):
GTTTATGGTTTAATGTTTAGG
Found at i:39894359 original size:14 final size:14
Alignment explanation
Indices: 39894327--39894357 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39894317 GGATTTTGGA
39894327 GTTTATGGTTTAGT
1 GTTTATGGTTTAGT
39894341 GTTTATGGTTTA-T
1 GTTTATGGTTTAGT
39894354 GTTT
1 GTTT
39894358 TAAAATTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (14 bp):
GTTTATGGTTTAGT
Found at i:39894366 original size:28 final size:28
Alignment explanation
Indices: 39894335--39894402 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
39894325 GAGTTTATGG
* *
39894335 TTTAGTGTTTATGGTTT-ATGTTTTAAAA
1 TTTAGGGTTTAGGGTTTAATG-TTTAAAA
*
39894363 TTTAGGGTTTAGGGTTTAATGTTTAAGA
1 TTTAGGGTTTAGGGTTTAATGTTTAAAA
39894391 TTTAAGGGTTTA
1 TTT-AGGGTTTA
39894403 CAGAAAGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 24 0.69
29 11 0.31
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (28 bp):
TTTAGGGTTTAGGGTTTAATGTTTAAAA
Found at i:39894734 original size:41 final size:40
Alignment explanation
Indices: 39894689--39895159 Score: 417
Period size: 41 Copynumber: 11.6 Consensus size: 40
39894679 AACTTTTTGC
*
39894689 GGCGTTTGGACCAAAAACGCCGCTATTAATCAGTTTTTAGT
1 GGCGTTTGGA-CAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * *
39894730 GGCGTTTTGGATAAAAACGCCACAATTGATCAGTTTTTTGT
1 GGCG-TTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
** * * * * *
39894771 GGCGTTTTTATCCAAAACGCCACAATTAATAAGTTTTTAGT
1 GGCGTTTGGA-CAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * * *
39894812 GGCATTTTGGATAAAAATGCCACAATTGATCAGTTTTTAGT
1 GGC-GTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
** *
39894853 GGCGTTTGGGATTAAAACGCCGCTATTGATCAGCTTTTAGT
1 GGCGTTT-GGACAAAAACGCCGCTATTGATCAGTTTTTAGT
** * * *
39894894 GGCGTTTGGTGAAAACCACCGCTATTGACCAGTTTTTAGT
1 GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
** *
39894934 GGCGTTTGGGATTAAAACGCCGCTATTGATCAGCTTTTAGT
1 GGCGTTT-GGACAAAAACGCCGCTATTGATCAGTTTTTAGT
** * *
39894975 GGCGTTTGGTGAAAAACACCGCTATTGACCAGTTTTTAGT
1 GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
* * *
39895015 GCCGTTTTGGCCAAAAACGCCGCTATTGACCAGTTTTTAGT
1 GGCG-TTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
* * *
39895056 GGCGTTTTGG-CCAAAACGCCGTTATTGACCAGTTTTTAGT
1 GGCG-TTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
** * * * * *
39895096 GGTATTTTGGCCAAAAACGCTGCTATAGTTTAGTTTTTAGT
1 GG-CGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
*
39895137 GGCATTTCGGAC--AAACGCCGCTA
1 GGCGTTT-GGACAAAAACGCCGCTA
39895160 ATGTTTGTTA
Statistics
Matches: 355, Mismatches: 66, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
39 10 0.03
40 108 0.30
41 227 0.64
42 10 0.03
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (40 bp):
GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
Found at i:39894939 original size:81 final size:80
Alignment explanation
Indices: 39894702--39895159 Score: 434
Period size: 81 Copynumber: 5.6 Consensus size: 80
39894692 GTTTGGACCA
* * * *
39894702 AAAACGCCGCTATTAATCAGTTTTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGTTTT
1 AAAACGCCGCTATTGATCAGTTTTTAGTGGCG-TTTGG-TAAAAACGCCGCTATTGACCAGTTTT
* ** *
39894767 TTGTGGCGTTT-TTATCC
64 TAGTGGCGTTTGGGAT-T
* * * * * * * * *
39894784 AAAACGCCACAATTAATAAGTTTTTAGTGGCATTTTGGATAAAAATGCCACAATTGATCAGTTTT
1 AAAACGCCGCTATTGATCAGTTTTTAGTGGC-GTTTGG-TAAAAACGCCGCTATTGACCAGTTTT
39894849 TAGTGGCGTTTGGGATT
64 TAGTGGCGTTTGGGATT
* * *
39894866 AAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTGGTGAAAACCACCGCTATTGACCAGTTTTT
1 AAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTGGT-AAAAACGCCGCTATTGACCAGTTTTT
39894931 AGTGGCGTTTGGGATT
65 AGTGGCGTTTGGGATT
* *
39894947 AAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTGGTGAAAAACACCGCTATTGACCAGTTTTT
1 AAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTGGT-AAAAACGCCGCTATTGACCAGTTTTT
* * ***
39895012 AGTGCCGTTTTGGCCA
65 AGTGGCGTTTGGGATT
* ** *
39895028 AAAACGCCGCTATTGACCAGTTTTTAGTGGCGTTTTGGCCAAAACGCCGTTATTGACCAGTTTTT
1 AAAACGCCGCTATTGATCAGTTTTTAGTGGCG-TTTGGTAAAAACGCCGCTATTGACCAGTTTTT
** * ***
39895093 AGTGGTATTTTGGCCA
65 AGTGGCGTTTGGGATT
* * * * * *
39895109 AAAACGCTGCTATAGTTTAGTTTTTAGTGGCATTTCGG-ACAAACGCCGCTA
1 AAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTT-GGTAAAAACGCCGCTA
39895160 ATGTTTGTTA
Statistics
Matches: 326, Mismatches: 45, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
80 14 0.04
81 210 0.64
82 100 0.31
83 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (80 bp):
AAAACGCCGCTATTGATCAGTTTTTAGTGGCGTTTGGTAAAAACGCCGCTATTGACCAGTTTTTA
GTGGCGTTTGGGATT
Found at i:39900437 original size:20 final size:20
Alignment explanation
Indices: 39900412--39900461 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
39900402 AGGGACTAAA
* *
39900412 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
39900432 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
39900452 ATGAATAAAT
1 ATGAA-AAAT
39900462 GTGTTGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:39906373 original size:161 final size:161
Alignment explanation
Indices: 39906108--39906428 Score: 570
Period size: 161 Copynumber: 2.0 Consensus size: 161
39906098 CATTGTTGCT
*
39906108 ATTATTGTCTTCTTCAAGCATCCACAAAGAGATTTCTAAGCGTTTCTTAACCTTATTCTTATGCT
1 ATTATTGTCTTCTTCAAGCATCCACAAAGAGATTTCTAAGCGTTTCTTAACCCTATTCTTATGCT
* * *
39906173 TATTTTGATGTATGATTTGAGTATATGTTTGGTTGTTGTGTGCATGAAAATGATGATTTGTAACT
66 TATTTTAATGTATGATTTAAGTATATGTTTGGTTGTTGTGTGCATAAAAATGATGATTTGTAACT
39906238 AAATTTATCGTGGTTGATTGATGTAAATATA
131 AAATTTATCGTGGTTGATTGATGTAAATATA
* * *
39906269 ATTATTGTCTTCTTCAAGCATCCATAAAGAGATTTCTAAGCTTTTGTTAACCCTATTCTTATGCT
1 ATTATTGTCTTCTTCAAGCATCCACAAAGAGATTTCTAAGCGTTTCTTAACCCTATTCTTATGCT
39906334 TATTTTAATGTATGATTTAAGTATATGTTTGGTTGTTGTGTGCATAAAAATGATGATTTGTAACT
66 TATTTTAATGTATGATTTAAGTATATGTTTGGTTGTTGTGTGCATAAAAATGATGATTTGTAACT
*
39906399 AAATTTATCGTGGTTGGTTGATGTAAATAT
131 AAATTTATCGTGGTTGATTGATGTAAATAT
39906429 TATTTGGTTA
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
161 152 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (161 bp):
ATTATTGTCTTCTTCAAGCATCCACAAAGAGATTTCTAAGCGTTTCTTAACCCTATTCTTATGCT
TATTTTAATGTATGATTTAAGTATATGTTTGGTTGTTGTGTGCATAAAAATGATGATTTGTAACT
AAATTTATCGTGGTTGATTGATGTAAATATA
Found at i:39913492 original size:16 final size:16
Alignment explanation
Indices: 39913471--39913502 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39913461 AAATATTAAA
*
39913471 TTTTTAAGTTTTTTAT
1 TTTTTAAATTTTTTAT
39913487 TTTTTAAATTTTTTAT
1 TTTTTAAATTTTTTAT
39913503 GAAGATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTAAATTTTTTAT
Found at i:39914157 original size:7 final size:7
Alignment explanation
Indices: 39914117--39914282 Score: 75
Period size: 7 Copynumber: 22.7 Consensus size: 7
39914107 ATTAACTAAT
39914117 CTAAACC
1 CTAAACC
*
39914124 TTAAACTC
1 CTAAAC-C
*
39914132 CTAATCC
1 CTAAACC
*
39914139 CTAAACA
1 CTAAACC
*
39914146 TTAAACC
1 CTAAACC
*
39914153 CTAAAAC
1 CTAAACC
*
39914160 ATAAACC
1 CTAAACC
*
39914167 CTGAACC
1 CTAAACC
39914174 CTAAACC
1 CTAAACC
* *
39914181 GTGAACC
1 CTAAACC
*
39914188 CTGAACCC
1 CT-AAACC
*
39914196 CTAACCC
1 CTAAACC
39914203 CT-AACAC
1 CTAAAC-C
39914210 CTAAACC
1 CTAAACC
*
39914217 TTAAACC
1 CTAAACC
*
39914224 C-CAACC
1 CTAAACC
39914230 CTTAAACTAC
1 C-TAAAC--C
39914240 CTTTAAACC
1 C--TAAACC
* *
39914249 ATAATCC
1 CTAAACC
39914256 CTAAACC
1 CTAAACC
*
39914263 CATAATCC
1 C-TAAACC
*
39914271 ATAAACC
1 CTAAACC
*
39914278 TTAAA
1 CTAAA
39914283 ATAGTGAGAC
Statistics
Matches: 117, Mismatches: 32, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
6 7 0.06
7 80 0.68
8 21 0.18
9 1 0.01
10 2 0.02
11 6 0.05
ACGTcount: A:0.41, C:0.36, G:0.02, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:39914267 original size:15 final size:15
Alignment explanation
Indices: 39914243--39914277 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
39914233 AAACTACCTT
*
39914243 TAAA-CCATAATCCC
1 TAAACCCATAATCCA
39914257 TAAACCCATAATCCA
1 TAAACCCATAATCCA
39914272 TAAACC
1 TAAACC
39914278 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCATAATCCA
Found at i:39914372 original size:41 final size:41
Alignment explanation
Indices: 39914315--39914395 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
39914305 CTAGTTGGTA
39914315 TCTTTAGCGGTGTTTCACCAAAAGCGCCGCTAATGCTCTGG
1 TCTTTAGCGGTGTTTCACCAAAAGCGCCGCTAATGCTCTGG
*
39914356 TCTTTAGCGGTGTTTCACCAAAAGCGCCGCTAATGTTCTG
1 TCTTTAGCGGTGTTTCACCAAAAGCGCCGCTAATGCTCTG
39914396 TTTTTAGTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (41 bp):
TCTTTAGCGGTGTTTCACCAAAAGCGCCGCTAATGCTCTGG
Found at i:39914418 original size:40 final size:40
Alignment explanation
Indices: 39914317--39914469 Score: 137
Period size: 41 Copynumber: 3.8 Consensus size: 40
39914307 AGTTGGTATC
* * * *
39914317 TTTAGCGGTGTTTCACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTAACAAAAGCGCCGCTAATGCTCT-GTT
* * * *
39914358 TTTAGCGGTGTTTCACCAAAAGCGCCGCTAATGTTCTGTT
1 TTTAGCGGCGTTTTAACAAAAGCGCCGCTAATGCTCTGTT
* * * * *
39914398 TTTAGTGGCGTTTTAACAAAAAACGCGGCTATTGCTCAGTT
1 TTTAGCGGCGTTTTAAC-AAAAGCGCCGCTAATGCTCTGTT
**
39914439 TTTAGCGGCGTTTTTGTCAAAA-CGCCGCTAA
1 TTTAGCGGCG-TTTTAACAAAAGCGCCGCTAA
39914470 AGCCCTATTT
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 22 0.23
41 67 0.71
42 5 0.05
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (40 bp):
TTTAGCGGCGTTTTAACAAAAGCGCCGCTAATGCTCTGTT
Found at i:39918475 original size:23 final size:23
Alignment explanation
Indices: 39918406--39918475 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
39918396 AATCATGACA
39918406 AAATAAAATATTTGCACATTATT
1 AAATAAAATATTTGCACATTATT
** ** *
39918429 AAATTCAACCTTAT-CACA-CA--
1 AAATAAAATATT-TGCACATTATT
39918449 AAATAAAATATTTGCACATTATT
1 AAATAAAATATTTGCACATTATT
39918472 AAAT
1 AAAT
39918476 CTTCTATCTA
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 1 0.03
20 12 0.38
21 1 0.03
22 1 0.03
23 16 0.50
24 1 0.03
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (23 bp):
AAATAAAATATTTGCACATTATT
Found at i:39926097 original size:13 final size:13
Alignment explanation
Indices: 39926079--39926106 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39926069 AGAAGAAAAA
39926079 ATAGACACTGACC
1 ATAGACACTGACC
39926092 ATAGACACTGACC
1 ATAGACACTGACC
39926105 AT
1 AT
39926107 CCATAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (13 bp):
ATAGACACTGACC
Found at i:39927997 original size:31 final size:30
Alignment explanation
Indices: 39927959--39928063 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
39927949 ATAATAAGAA
*
39927959 TTTTTAAAAATTTGAAGAGTTTAATTCAAAT
1 TTTTTAAAAATTTGAAGAG-TTAATTAAAAT
* * ** *
39927990 TTTTTAAAAACTTCAAGAGAAAAATAAAAT
1 TTTTTAAAAATTTGAAGAGTTAATTAAAAT
* *
39928020 TTTATAAAAAAGTTGAAG-GCTTAATTAAAAT
1 TTT-TTAAAAATTTGAAGAG-TTAATTAAAAT
*
39928051 TTTCTAAAAATTT
1 TTTTTAAAAATTT
39928064 CAATGAAAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
30 18 0.32
31 39 0.68
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39
Consensus pattern (30 bp):
TTTTTAAAAATTTGAAGAGTTAATTAAAAT
Found at i:39928028 original size:61 final size:59
Alignment explanation
Indices: 39927951--39928084 Score: 153
Period size: 61 Copynumber: 2.2 Consensus size: 59
39927941 TAAAAGGTAT
* * * *
39927951 AATAAGAATTTTT-AAAAATTTGAAGAGTTTAATTCAAATTTTTTAAAAACTTCAAGAGAAA
1 AATAA-AATTTTTAAAAAAGTTGAAG-GCTTAATTAAAATTTTCTAAAAACTTCAA-AGAAA
* *
39928012 AATAAAATTTTATAAAAAAGTTGAAGGCTTAATTAAAATTTTCTAAAAATTTCAATGAAA
1 AATAAAATTTT-TAAAAAAGTTGAAGGCTTAATTAAAATTTTCTAAAAACTTCAAAGAAA
*
39928072 AATCATAATTTTT
1 AAT-AAAATTTTT
39928085 CAATTCCTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
60 14 0.22
61 38 0.60
62 11 0.17
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.37
Consensus pattern (59 bp):
AATAAAATTTTTAAAAAAGTTGAAGGCTTAATTAAAATTTTCTAAAAACTTCAAAGAAA
Done.