Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 118 of 172
Found at i:39337485 original size:136 final size:131
Alignment explanation
Indices: 39337161--39337602 Score: 344
Period size: 136 Copynumber: 3.4 Consensus size: 131
39337151 AATGAAATTA
* * * *** * *
39337161 AGTTTCAGCTAGAAGATAGAGCTGAATAGCATCAAAACCAAGT-GAAAAACATAAA-AATTTTCA
1 AGTTTCAGCTA-AAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAAATAAACGATTTTCA
* * ** * * * * *
39337224 GTTTCAGATAAAACATAAACTAAATAGCGTAAAAAATGAGTGAAAAAAAACATAATGA--T----
65 G-TACAGATAAAAGATAAAGAAAATAGCATCAAAATTGAGTG-AAAAAGACATAAAGATTTACAG
39337283 TTTC
128 TTTC
* * *
39337287 AGTTTCAGCTAAAAGGTAAAGCTTAATAGCGTCAAAATTGAGT-GAAAAAACA-AAACGGTTTTC
1 AGTTTCAGCT-AAAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAA-ATAAACGATTTTC
* * * * * * *
39337350 AGTTTCAGCTAAAAAGATAAAGCTAAATAG-AGTCAAATTTTAGT-TAAAAGTACATTAAGATTT
64 AG-TACAGAT-AAAAGATAAAG-AAAATAGCA-TCAAAATTGAGTGAAAAAG-ACATAAAGATTT
39337413 ACAGTTTC
124 ACAGTTTC
**
39337421 AGATTTTCAGCTCAAAGATAAAGCTAAATAGCGTCAAAATTTTGTGGAAAAAAATAAA-GATTTT
1 AG--TTTCAGCT-AAAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAAATAAACGATTTT
* *
39337485 CAGTACAGATAAAAGATAAAGAAAATAGCATCAAAATTGAGTGAAAAAGACGTAAAGATTTTCAG
63 CAGTACAGATAAAAGATAAAGAAAATAGCATCAAAATTGAGTGAAAAAGACATAAAGATTTACAG
39337550 TTTC
128 TTTC
* *
39337554 AG-TT-A---AAAGATAAAGATAAATAACGTCAAAATTGAGTGGAAAAAAATAA
1 AGTTTCAGCTAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAAATAA
39337603 TAAAATAAAA
Statistics
Matches: 256, Mismatches: 41, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
125 40 0.16
126 43 0.17
127 20 0.08
128 16 0.06
129 16 0.06
130 3 0.01
133 35 0.14
134 23 0.09
135 5 0.02
136 45 0.18
137 10 0.04
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (131 bp):
AGTTTCAGCTAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAAATAAACGATTTTCAG
TACAGATAAAAGATAAAGAAAATAGCATCAAAATTGAGTGAAAAAGACATAAAGATTTACAGTTT
C
Found at i:39339341 original size:91 final size:91
Alignment explanation
Indices: 39339202--39339474 Score: 305
Period size: 91 Copynumber: 3.0 Consensus size: 91
39339192 ATACGTCAAT
*
39339202 TTGCTCATAAGAGCTTTCCAACTGATAACATGTCAGATGCACATAGTGCAAAGCCCATAGACTAA
1 TTGCTCATAAGAGCTTTCCAACTGATAACATGCCAGATGCACATAGTGCAAAGCCCATAGACTAA
* *
39339267 ATAATCTCTCTCAATAACACGCC-GAA
66 ATAATCTCCCCCAATAACACGCCAG-A
* * * * ** *
39339293 TTGCTTATAAGAGCTTTCCAACTGATAGCATGCCATACGCACATAGTGCAAAGCCCATAGGTTGA
1 TTGCTCATAAGAGCTTTCCAACTGATAACATGCCAGATGCACATAGTGCAAAGCCCATAGACTAA
* **
39339358 ATATTCTCCCCCAATAACACTTCAGA
66 ATAATCTCCCCCAATAACACGCCAGA
** * * *** ** *
39339384 TTGCTCATAAGAGCTTTCCAACCAATAACACGCTAGATGCACATAGTGCAAAGCTTGTAGGTTGA
1 TTGCTCATAAGAGCTTTCCAACTGATAACATGCCAGATGCACATAGTGCAAAGCCCATAGACTAA
* *
39339449 ATATTCTCCCCCGATAACACGCCAGA
66 ATAATCTCCCCCAATAACACGCCAGA
39339475 ATCTCTGAAA
Statistics
Matches: 154, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
91 153 0.99
92 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (91 bp):
TTGCTCATAAGAGCTTTCCAACTGATAACATGCCAGATGCACATAGTGCAAAGCCCATAGACTAA
ATAATCTCCCCCAATAACACGCCAGA
Found at i:39342380 original size:24 final size:25
Alignment explanation
Indices: 39342352--39342399 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
39342342 GATAAATGAA
39342352 ATACATGTGTAATAAATAT-TGTAC
1 ATACATGTGTAATAAATATATGTAC
* *
39342376 ATACATTTGTAATACATATATGTA
1 ATACATGTGTAATAAATATATGTA
39342400 TTTACTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (25 bp):
ATACATGTGTAATAAATATATGTAC
Found at i:39343913 original size:18 final size:18
Alignment explanation
Indices: 39343856--39343915 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
39343846 GATTGTTTGC
* *
39343856 TACTGAATAATTGACTGT
1 TACTGAATAAATGACTAT
* *
39343874 TACGGAATAAACGACTGA-
1 TACTGAATAAATGACT-AT
39343892 TACTGAATAAATGACTAT
1 TACTGAATAAATGACTAT
39343910 TACTGA
1 TACTGA
39343916 TTAACCAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (18 bp):
TACTGAATAAATGACTAT
Found at i:39352131 original size:25 final size:25
Alignment explanation
Indices: 39352103--39352194 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 25
39352093 AATATACATT
*
39352103 TTATGCATCACATCTTCAACATGTA
1 TTATTCATCACATCTTCAACATGTA
* *
39352128 TTATTCATCCATATCAAT-ATACAT-T-
1 TTATTCAT-CACATC-TTCA-ACATGTA
39352153 TTATTCATCACATCTTCAACATGTA
1 TTATTCATCACATCTTCAACATGTA
39352178 TTATTCATC-CAT-TTCAA
1 TTATTCATCACATCTTCAA
39352195 AGCATTTATA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
23 10 0.18
24 10 0.18
25 24 0.43
26 7 0.12
27 5 0.09
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (25 bp):
TTATTCATCACATCTTCAACATGTA
Found at i:39352142 original size:50 final size:50
Alignment explanation
Indices: 39352087--39352194 Score: 198
Period size: 50 Copynumber: 2.2 Consensus size: 50
39352077 ATATTAGGAA
39352087 CATATCAATATACATTTTATGCATCACATCTTCAACATGTATTATTCATC
1 CATATCAATATACATTTTATGCATCACATCTTCAACATGTATTATTCATC
*
39352137 CATATCAATATACATTTTATTCATCACATCTTCAACATGTATTATTCATC
1 CATATCAATATACATTTTATGCATCACATCTTCAACATGTATTATTCATC
*
39352187 CATTTCAA
1 CATATCAA
39352195 AGCATTTATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (50 bp):
CATATCAATATACATTTTATGCATCACATCTTCAACATGTATTATTCATC
Found at i:39366241 original size:293 final size:293
Alignment explanation
Indices: 39365709--39366294 Score: 1127
Period size: 293 Copynumber: 2.0 Consensus size: 293
39365699 TTAATATCTT
*
39365709 CAAATGGTTCAAATGGTAGTATAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
1 CAAATGGTTCAAATGGTAGTACAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
39365774 AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCCAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
66 AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCCAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
*
39365839 GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGTTGGCTGATTTATTTAGTTTTTGAAG
131 GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGCTGGCTGATTTATTTAGTTTTTGAAG
*
39365904 TTTCTTTTCATATGATTGCTTGAAGCAAATTATGGCTTGCTTGGTCTTTTCTAAGAACATTTATG
196 TTTCTTTTCATATGATTGCTTGAAGCAAATTATGGCTCGCTTGGTCTTTTCTAAGAACATTTATG
39365969 AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
261 AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
39366002 CAAATGGTTCAAATGGTAGTACAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
1 CAAATGGTTCAAATGGTAGTACAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
*
39366067 AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCTAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
66 AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCCAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
39366132 GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGCTGGCTGATTTATTTAGTTTTTGAAG
131 GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGCTGGCTGATTTATTTAGTTTTTGAAG
*
39366197 TTTCTTTTCATATGATTGCTTGGAGCAAATTATGGCTCGCTTGGTCTTTTCTAAGAACATTTATG
196 TTTCTTTTCATATGATTGCTTGAAGCAAATTATGGCTCGCTTGGTCTTTTCTAAGAACATTTATG
39366262 AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
261 AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
39366295 TTAATCAATG
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
293 288 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (293 bp):
CAAATGGTTCAAATGGTAGTACAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCCAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGCTGGCTGATTTATTTAGTTTTTGAAG
TTTCTTTTCATATGATTGCTTGAAGCAAATTATGGCTCGCTTGGTCTTTTCTAAGAACATTTATG
AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
Found at i:39367378 original size:18 final size:17
Alignment explanation
Indices: 39367343--39367384 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
39367333 ATTTTTATGC
39367343 AAATAAATAAAAACAAT
1 AAATAAATAAAAACAAT
* *
39367360 AAATAACATAAATATAAT
1 AAATAA-ATAAAAACAAT
39367378 AAA-AAAT
1 AAATAAAT
39367385 TTATGAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 12 0.55
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAATAAAAACAAT
Found at i:39367788 original size:21 final size:20
Alignment explanation
Indices: 39367764--39367818 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
39367754 TTTTAAAATT
39367764 ATACATAATATAATAAATAAG
1 ATACATAA-ATAATAAATAAG
*
39367785 ATACAATAAA-ATATAAATAAT
1 ATAC-ATAAATA-ATAAATAAG
39367806 ATA-ATAAATAATA
1 ATACATAAATAATA
39367819 CAAATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 8 0.27
20 2 0.07
21 16 0.53
22 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
ATACATAAATAATAAATAAG
Found at i:39367805 original size:33 final size:32
Alignment explanation
Indices: 39367757--39367829 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
39367747 TACAAATTTT
*
39367757 TAAAATTATACATAATATAATAAATAAGATAC-AA
1 TAAAA-TATAAATAATATAATAAAT-A-ATACAAA
39367791 TAAAATATAAATAATATAATAAATAATACAAA
1 TAAAATATAAATAATATAATAAATAATACAAA
39367823 TAAAATA
1 TAAAATA
39367830 AATATTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 4 0.11
32 10 0.27
33 18 0.49
34 5 0.14
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (32 bp):
TAAAATATAAATAATATAATAAATAATACAAA
Found at i:39367814 original size:12 final size:11
Alignment explanation
Indices: 39367763--39367818 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 11
39367753 TTTTTAAAAT
*
39367763 TATACATAATA
1 TATAAATAATA
*
39367774 TAATAAATAAGA
1 T-ATAAATAATA
* *
39367786 TA-CAATAAAA
1 TATAAATAATA
39367796 TATAAATAATA
1 TATAAATAATA
39367807 TAATAAATAATA
1 T-ATAAATAATA
39367819 CAAATAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 8 0.22
11 9 0.25
12 19 0.53
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (11 bp):
TATAAATAATA
Found at i:39367876 original size:30 final size:28
Alignment explanation
Indices: 39367842--39367908 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
39367832 TATTTTTTAC
* *
39367842 ATATAAATAAGGTTTAAAGTAAAATAAATA
1 ATATAAA-AAGATTTAAAAT-AAATAAATA
* *
39367872 ATATACAAAATATTTAAAATAAATAAATT
1 ATATA-AAAAGATTTAAAATAAATAAATA
39367901 ATATAAAA
1 ATATAAAA
39367909 TATATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 13 0.41
30 14 0.44
31 2 0.06
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
ATATAAAAAGATTTAAAATAAATAAATA
Found at i:39367889 original size:25 final size:27
Alignment explanation
Indices: 39367861--39367911 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39367851 AGGTTTAAAG
39367861 TAAAATAAAT-AA-TATACAAAATATT
1 TAAAATAAATAAATTATACAAAATATT
*
39367886 TAAAATAAATAAATTATATAAAATAT
1 TAAAATAAATAAATTATACAAAATAT
39367912 ATATAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.43
26 2 0.09
27 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAAATAAATAAATTATACAAAATATT
Found at i:39367890 original size:9 final size:9
Alignment explanation
Indices: 39367871--39367914 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
39367861 TAAAATAAAT
*
39367871 AATATACAA
1 AATATATAA
*
39367880 AATATTTAA
1 AATATATAA
*
39367889 AATAAATAA
1 AATATATAA
*
39367898 ATTATATAA
1 AATATATAA
39367907 AATATATA
1 AATATATA
39367915 TAAAAAGGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AATATATAA
Found at i:39367904 original size:29 final size:30
Alignment explanation
Indices: 39367854--39367919 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
39367844 ATAAATAAGG
*
39367854 TTTAAAGTAAAATAAATAATATACAAA-ATA
1 TTTAAAATAAAATAAATAATATA-AAATATA
*
39367884 TTTAAAAT-AAATAAATTATATAAAATATA
1 TTTAAAATAAAATAAATAATATAAAATATA
*
39367913 TATAAAA
1 TTTAAAA
39367920 AGGATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 3 0.09
29 22 0.69
30 7 0.22
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
TTTAAAATAAAATAAATAATATAAAATATA
Found at i:39371837 original size:26 final size:26
Alignment explanation
Indices: 39371806--39371965 Score: 275
Period size: 26 Copynumber: 6.2 Consensus size: 26
39371796 TGAAATGCCC
* *
39371806 ATCATGGAACATTTATCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
39371832 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
39371858 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
39371884 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
39371910 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
39371936 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39371962 ATCA
1 ATCA
39371966 ATTTGTACCA
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 126 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39373151 original size:19 final size:19
Alignment explanation
Indices: 39373127--39373164 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39373117 CATCCAAACA
39373127 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
*
39373146 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATCATTT
39373165 TTCGGAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:39377828 original size:8 final size:8
Alignment explanation
Indices: 39377811--39377869 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
39377801 GATTCGAGTA
*
39377811 ATATATAT
1 ATATACAT
39377819 ATATACAT
1 ATATACAT
39377827 ATATACAT
1 ATATACAT
39377835 ATATACAT
1 ATATACAT
* *
39377843 ATACATAT
1 ATATACAT
* **
39377851 ACATATGT
1 ATATACAT
39377859 ATATACAT
1 ATATACAT
39377867 ATA
1 ATA
39377870 CACACATGCA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (8 bp):
ATATACAT
Found at i:39377870 original size:6 final size:6
Alignment explanation
Indices: 39377813--39377871 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
39377803 TTCGAGTAAT
* * * **
39377813 ATATAT ATATAC ATAT-- ATACAT ATATAC ATATAC ATATAC ATATGT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
39377859 ATATAC ATATAC A
1 ATATAC ATATAC A
39377872 CACATGCATG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 3 0.07
6 40 0.93
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:39379750 original size:2 final size:2
Alignment explanation
Indices: 39379743--39379776 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39379733 TGCTTTTTAA
39379743 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39379777 TTTGTTGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:39382065 original size:5 final size:5
Alignment explanation
Indices: 39382055--39382090 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
39382045 TTTTTTGAAC
* *
39382055 ATTAA AATAA AATAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
39382091 GTTAGAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
ATTAA
Found at i:39386267 original size:12 final size:12
Alignment explanation
Indices: 39386250--39386274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39386240 TGCGCCTACG
39386250 CGCCGTCTCGAA
1 CGCCGTCTCGAA
39386262 CGCCGTCTCGAA
1 CGCCGTCTCGAA
39386274 C
1 C
39386275 TCAAAAATTT
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:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (12 bp):
CGCCGTCTCGAA
Found at i:39387262 original size:87 final size:88
Alignment explanation
Indices: 39387160--39387766 Score: 402
Period size: 87 Copynumber: 7.0 Consensus size: 88
39387150 GTTTTTTGAC
* *
39387160 AACACAA-AGATGCCAAATCATCTTAGATCTGCTTCAGCGT-AAACA-CGTGAAAGCCAAATCTG
1 AACACAAGA-ATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAACATC-TGAAAGCCAAATCTG
* *
39387222 CTGTGTCTTTGATTTGCTCCTTGTG
64 CTATGTCTTCGATTTGCTCCTTGTG
* * ** *
39387247 AACACAAGAATGCCAAATCCTCTTGGATCTGCTTCA--GTAAAATCATCTGAAGGTTAGATCTGC
1 AACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAA-CATCTGAAAGCCAAATCTGC
* *
39387310 TATG---T--ATCTGCT-CTCCGTCG
65 TATGTCTTCGATTTGCTCCT-TGT-G
** * * ** * *
39387330 AA-A-TGGAGATGCCAGATCTGTTATCTTGGATCTACTTTGGTGTAAGAACATCCGAAAGTCAAA
1 AACACAAGA-ATGCCAAATC----ATCTTGGATCTGCTTCAGTGTAA-AACATCTGAAAGCCAAA
*
39387393 TCTGCTATGTCTTCGATTTGTTCCTTGT-
60 TCTGCTATGTCTTCGATTTGCTCCTTGTG
* * *
39387421 AAGCACAAGAACGCCAAATCATCTTGGATCTGCTTCAGTAT-AAACATCTGAAAGCCAAATCTGT
1 AA-CACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAACATCTGAAAGCCAAATCTGC
*
39387485 TGTGTCTTCGATTTGCTCCTTGTG
65 TATGTCTTCGATTTGCTCCTTGTG
* * * ** *
39387509 AACACAAGGATGCCAAATCATCTTGGATTTGCTTCA--GTAAAATCATCTGAAGGTTAGATCTGC
1 AACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAA-CATCTGAAAGCCAAATCTGC
*
39387572 TATG---T--ATCTGCT-CTCTGTCG
65 TATGTCTTCGATTTGCTCCT-TGT-G
** * ** * * *
39387592 AA-A-TGGAGATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAA
1 AACACAAGA-ATGCCAAATC----ATCTTGGATCTGCTTCAGTGT-AAAACATCTGAAAGCCAAA
* * *
39387655 TCTGCTATGTCTTCGATTTGTTCCCTGTA
60 TCTGCTATGTCTTCGATTTGCTCCTTGTG
* * * *
39387684 AACACAAGAATGCCAACTCATCTTGGATCTGCTTCAGTAT-AAACATCTGAAAGCCAAATTTGTT
1 AACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAACATCTGAAAGCCAAATCTGCT
* * *
39387748 GTTTCTTCGATTTTCTCCT
66 ATGTCTTCGATTTGCTCCT
39387767 CGTCGAAGAT
Statistics
Matches: 396, Mismatches: 80, Indels: 88
0.70 0.14 0.16
Matches are distributed among these distances:
81 7 0.02
82 37 0.09
83 6 0.02
84 2 0.01
85 3 0.01
86 33 0.08
87 171 0.43
88 51 0.13
89 40 0.10
91 4 0.01
92 2 0.01
93 33 0.08
94 7 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (88 bp):
AACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAACATCTGAAAGCCAAATCTGCT
ATGTCTTCGATTTGCTCCTTGTG
Found at i:39387605 original size:262 final size:262
Alignment explanation
Indices: 39387171--39387766 Score: 1014
Period size: 262 Copynumber: 2.3 Consensus size: 262
39387161 ACACAAAGAT
* ** * *
39387171 GCCAAATCATCTTAGATCTGCTTCAGCGTAAACA-CGTGAAAGCCAAATCTGCTGTGTCTTTGAT
1 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATC-TGAAAGCCAAATCTGTTGTGTCTTCGAT
*
39387235 TTGCTCCTTGTGAACACAAGAATGCCAAATCCTCTTGGATCTGCTTCAGTAAAATCATCTGAAGG
65 TTGCTCCTTGTGAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGG
39387300 TTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTAC
130 TTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTAC
* *
39387365 TTTGGTGTAAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAG
195 TTTGGTGTAAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCCTGTAAACACAAG
39387430 AAC
260 AAC
39387433 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATCTGTTGTGTCTTCGATT
1 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATCTGTTGTGTCTTCGATT
* *
39387498 TGCTCCTTGTGAACACAAGGATGCCAAATCATCTTGGATTTGCTTCAGTAAAATCATCTGAAGGT
66 TGCTCCTTGTGAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGT
* *
39387563 TAGATCTGCTATGTATCTGCTCTCTGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTGCT
131 TAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTACT
*
39387628 TTGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCCTGTAAACACAAGA
196 TTGGTGTAAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCCTGTAAACACAAGA
*
39387693 AT
261 AC
* * *
39387695 GCCAACTCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATTTGTTGTTTCTTCGATT
1 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATCTGTTGTGTCTTCGATT
*
39387760 TTCTCCT
66 TGCTCCT
39387767 CGTCGAAGAT
Statistics
Matches: 315, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
262 314 1.00
263 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (262 bp):
GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATCTGTTGTGTCTTCGATT
TGCTCCTTGTGAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGT
TAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTACT
TTGGTGTAAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCCTGTAAACACAAGA
AC
Found at i:39390359 original size:4 final size:4
Alignment explanation
Indices: 39390344--39390373 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
39390334 GCTTGGGCCT
39390344 TAAA TCAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA T-AAA TAAA TAAA TAAA TAAA TAAA T
39390374 GTTTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:39391659 original size:19 final size:19
Alignment explanation
Indices: 39391635--39391679 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
39391625 TATAGTCCTT
*
39391635 TTAAATATTTTTTTATCTA
1 TTAAATATTTTTATATCTA
*
39391654 TTAAATA-CTTTATATCTA
1 TTAAATATTTTTATATCTA
39391672 -TAAATATT
1 TTAAATATT
39391680 AATTATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 6 0.27
18 9 0.41
19 7 0.32
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAAATATTTTTATATCTA
Found at i:39391713 original size:13 final size:13
Alignment explanation
Indices: 39391695--39391733 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
39391685 TAAAAAATAG
39391695 TATATATTATTTT
1 TATATATTATTTT
*
39391708 TATATATTATTTA
1 TATATATTATTTT
39391721 T-TATATTATTTT
1 TATATATTATTTT
39391733 T
1 T
39391734 TACTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATATTATTTT
Found at i:39391727 original size:12 final size:12
Alignment explanation
Indices: 39391697--39391762 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 12
39391687 AAAAATAGTA
*
39391697 TATATTATTTTT
1 TATATTATTTAT
39391709 ATATATTATTTAT
1 -TATATTATTTAT
39391722 TATATTATTT-T
1 TATATTATTTAT
**
39391733 T-TACTTATAAAT
1 TATA-TTATTTAT
39391745 TATATTTATTTA-
1 TATA-TTATTTAT
39391757 TATATT
1 TATATT
39391763 TCATATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 2 0.05
11 8 0.18
12 16 0.36
13 18 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTATTTAT
Found at i:39391753 original size:43 final size:43
Alignment explanation
Indices: 39391695--39391776 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
39391685 TAAAAAATAG
* *
39391695 TATATATTATTTTTATATAT-TATTT-ATTATATTATTTTTTACT
1 TATAAATTATATTTATATATATATTTCA-TATA-TATTTTTTACT
*
39391738 TATAAATTATATTTATTTATATATTTCATATATATTTTT
1 TATAAATTATATTTATATATATATTTCATATATATTTTT
39391777 AAAAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 24 0.71
44 9 0.26
45 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (43 bp):
TATAAATTATATTTATATATATATTTCATATATATTTTTTACT
Found at i:39392104 original size:35 final size:35
Alignment explanation
Indices: 39392058--39392128 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
39392048 TTTTTTCTTT
*
39392058 TTATTCTGTCACGGTTGGAGTCGTGGGCACGACGC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
39392093 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
39392128 T
1 T
39392129 GGGCACGACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (35 bp):
TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
Found at i:39393576 original size:22 final size:22
Alignment explanation
Indices: 39393550--39393591 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39393540 TTTTAATACG
**
39393550 TATTAAATTTTTTATATATTGT
1 TATTAAATCATTTATATATTGT
*
39393572 TATTATATCATTTATATATT
1 TATTAAATCATTTATATATT
39393592 AAATGCTAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTAAATCATTTATATATTGT
Found at i:39408635 original size:13 final size:13
Alignment explanation
Indices: 39408617--39408646 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
39408607 ATCAAATCAG
39408617 TCAAACCGATAAA
1 TCAAACCGATAAA
39408630 TCAAACCGATAAA
1 TCAAACCGATAAA
39408643 TCAA
1 TCAA
39408647 TGACCTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.17
Consensus pattern (13 bp):
TCAAACCGATAAA
Found at i:39422693 original size:23 final size:23
Alignment explanation
Indices: 39422667--39422712 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
39422657 ACACATAGCC
39422667 TGCTATTCAATAGACATCTTATG
1 TGCTATTCAATAGACATCTTATG
39422690 TGCTATTCAATAGACATCTTATG
1 TGCTATTCAATAGACATCTTATG
39422713 ATCACGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
TGCTATTCAATAGACATCTTATG
Found at i:39424547 original size:12 final size:14
Alignment explanation
Indices: 39424521--39424552 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
39424511 AATTATTTTT
39424521 ATTTTTTTAATTTA
1 ATTTTTTTAATTTA
39424535 ATTTTTTT-A-TTA
1 ATTTTTTTAATTTA
39424547 ATTTTT
1 ATTTTT
39424553 AAAGGGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTTTTTAATTTA
Found at i:39425825 original size:16 final size:16
Alignment explanation
Indices: 39425804--39425834 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39425794 CATTTTATTT
*
39425804 ATATTAGGATAATTAA
1 ATATTAAGATAATTAA
39425820 ATATTAAGATAATTA
1 ATATTAAGATAATTA
39425835 TTATGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
ATATTAAGATAATTAA
Found at i:39431798 original size:9 final size:9
Alignment explanation
Indices: 39431786--39431851 Score: 71
Period size: 9 Copynumber: 7.3 Consensus size: 9
39431776 AAAAGTATAA
39431786 AATTAACCG
1 AATTAACCG
**
39431795 AATTAATTG
1 AATTAACCG
39431804 AATTAACCG
1 AATTAACCG
*
39431813 AATTACCCG
1 AATTAACCG
39431822 AATT-ACTCG
1 AATTAAC-CG
*
39431831 AATTAACAG
1 AATTAACCG
*
39431840 AATTAACTG
1 AATTAACCG
39431849 AAT
1 AAT
39431852 CATTTGTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
8 1 0.02
9 44 0.94
10 2 0.04
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:39431816 original size:27 final size:27
Alignment explanation
Indices: 39431786--39431851 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
39431776 AAAAGTATAA
* *
39431786 AATTAACCGAATTAATTGAATTAACCG
1 AATTAACCGAATTAATCGAATTAACAG
* *
39431813 AATTACCCGAATTACTCGAATTAACAG
1 AATTAACCGAATTAATCGAATTAACAG
*
39431840 AATTAACTGAAT
1 AATTAACCGAAT
39431852 CATTTGTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (27 bp):
AATTAACCGAATTAATCGAATTAACAG
Found at i:39432173 original size:18 final size:18
Alignment explanation
Indices: 39432123--39432175 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
39432113 CTGAACCCTG
*
39432123 ACCGAATTAATTCGGTTA
1 ACCGAATTTATTCGGTTA
* *
39432141 ACAGAATTTAGTCGGTTA
1 ACCGAATTTATTCGGTTA
*
39432159 ACCGAATTTTTTCGGTT
1 ACCGAATTTATTCGGTT
39432176 TTACCTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (18 bp):
ACCGAATTTATTCGGTTA
Found at i:39436347 original size:157 final size:157
Alignment explanation
Indices: 39436118--39436432 Score: 630
Period size: 157 Copynumber: 2.0 Consensus size: 157
39436108 TACTTATCAA
39436118 TAATAATCTAATATTGCTACCATAATACTCATGAAGTTATATTTAACAACTCACTAAGTGAATAA
1 TAATAATCTAATATTGCTACCATAATACTCATGAAGTTATATTTAACAACTCACTAAGTGAATAA
39436183 ATCTACAATATCACTTATACATAATATTCCTAACATCGTAGGATTTTAAACAACTTTAACTCTTC
66 ATCTACAATATCACTTATACATAATATTCCTAACATCGTAGGATTTTAAACAACTTTAACTCTTC
39436248 CAAAATTTCTTTATTTTCATTTGCGTT
131 CAAAATTTCTTTATTTTCATTTGCGTT
39436275 TAATAATCTAATATTGCTACCATAATACTCATGAAGTTATATTTAACAACTCACTAAGTGAATAA
1 TAATAATCTAATATTGCTACCATAATACTCATGAAGTTATATTTAACAACTCACTAAGTGAATAA
39436340 ATCTACAATATCACTTATACATAATATTCCTAACATCGTAGGATTTTAAACAACTTTAACTCTTC
66 ATCTACAATATCACTTATACATAATATTCCTAACATCGTAGGATTTTAAACAACTTTAACTCTTC
39436405 CAAAATTTCTTTATTTTCATTTGCGTT
131 CAAAATTTCTTTATTTTCATTTGCGTT
39436432 T
1 T
39436433 CTTTACTTTC
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (157 bp):
TAATAATCTAATATTGCTACCATAATACTCATGAAGTTATATTTAACAACTCACTAAGTGAATAA
ATCTACAATATCACTTATACATAATATTCCTAACATCGTAGGATTTTAAACAACTTTAACTCTTC
CAAAATTTCTTTATTTTCATTTGCGTT
Found at i:39439875 original size:33 final size:33
Alignment explanation
Indices: 39439838--39440081 Score: 136
Period size: 33 Copynumber: 7.3 Consensus size: 33
39439828 TGGCCCTGCC
*
39439838 ATGGTCTTACATTAGTAGTGCCATAGCCCAGTT
1 ATGGTCTTACATTAATAGTGCCATAGCCCAGTT
* * * * *
39439871 ATGGTCTTATCGTCAA-AATACCATAGCCCAGCT
1 ATGGTCTTA-CATTAATAGTGCCATAGCCCAGTT
* * * * ***
39439904 ATGGTCTTACATATAATTACTACCATGGTCCAACC
1 ATGGTCTTACAT-TAA-TAGTGCCATAGCCCAGTT
* *
39439939 ATGGTCTTACGTTCAA-AGTGCCATAACCCAGTT
1 ATGGTCTTACATT-AATAGTGCCATAGCCCAGTT
* * *
39439972 ATAGTCTT--ATCAATAGAATGCCATAACCCAGTT
1 ATGGTCTTACATTAATAG--TGCCATAGCCCAGTT
* * * * ***
39440005 ATGGTCTTACATATAAACACTGCCATGGTCCAACC
1 ATGGTCTTACAT-T-AATAGTGCCATAGCCCAGTT
* * *
39440040 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACATTAATAGTGCCATAGCCCAGTT
39440073 ATGGTCTTA
1 ATGGTCTTA
39440082 TCCGTCAATT
Statistics
Matches: 154, Mismatches: 45, Indels: 24
0.69 0.20 0.11
Matches are distributed among these distances:
30 2 0.01
31 3 0.02
32 2 0.01
33 92 0.60
34 5 0.03
35 47 0.31
37 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (33 bp):
ATGGTCTTACATTAATAGTGCCATAGCCCAGTT
Found at i:39439969 original size:101 final size:101
Alignment explanation
Indices: 39439836--39440089 Score: 359
Period size: 101 Copynumber: 2.5 Consensus size: 101
39439826 TATGGCCCTG
* * *
39439836 CCATGGTCTTACATT-AGTAGTGCCATAGCCCAGTTATGGTCTTATCGTCAAAATACCATAGCCC
1 CCATGGTCTTACGTTCA-TAGTGCCATAACCCAGTTATGGTCTTATCGTCAAAATACCATAACCC
**
39439900 AGCTATGGTCTTACATATAATTACTACCATGGTCCAA
65 AGCTATGGTCTTACATATAAACACTACCATGGTCCAA
* * * * *
39439937 CCATGGTCTTACGTTCAAAGTGCCATAACCCAGTTATAGTCTTATCAAT-AGAATGCCATAACCC
1 CCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC-GTCAAAATACCATAACCC
* *
39440001 AGTTATGGTCTTACATATAAACACTGCCATGGTCCAA
65 AGCTATGGTCTTACATATAAACACTACCATGGTCCAA
39440038 CCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCCGTCAA
1 CCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTAT-CGTCAA
39440090 TTCATCTTTT
Statistics
Matches: 133, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
101 129 0.97
102 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (101 bp):
CCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCGTCAAAATACCATAACCCA
GCTATGGTCTTACATATAAACACTACCATGGTCCAA
Found at i:39441263 original size:14 final size:15
Alignment explanation
Indices: 39441232--39441266 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
39441222 TTTATTTCTA
39441232 TTAAAAATATAGAAT
1 TTAAAAATATAGAAT
*
39441247 TTAAATATATA-AAT
1 TTAAAAATATAGAAT
39441261 TTAAAA
1 TTAAAA
39441267 CCCTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TTAAAAATATAGAAT
Found at i:39444922 original size:19 final size:19
Alignment explanation
Indices: 39444884--39444923 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39444874 AAAATATCAT
*
39444884 ATTAATTTAAATTGATTTG
1 ATTAATTTAAATTGACTTG
* *
39444903 ATTAATTTAATTTTACTTG
1 ATTAATTTAAATTGACTTG
39444922 AT
1 AT
39444924 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAATTGACTTG
Found at i:39452848 original size:29 final size:29
Alignment explanation
Indices: 39452816--39452893 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
39452806 AATACTGATA
*
39452816 TCATGGCCCGAAGCTAAATTAGCCAATAT
1 TCATGGCCCGAAGCCAAATTAGCCAATAT
* * * *
39452845 TCATGGCCTGAAGCCAAATCAGTCGATAT
1 TCATGGCCCGAAGCCAAATTAGCCAATAT
*
39452874 TCATGGCTCGAAGCCAAATT
1 TCATGGCCCGAAGCCAAATT
39452894 GGTATAACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (29 bp):
TCATGGCCCGAAGCCAAATTAGCCAATAT
Found at i:39457677 original size:26 final size:26
Alignment explanation
Indices: 39457648--39457723 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
39457638 TCTTATCCCT
*
39457648 ATTTTACCCTTAATAAAATTTTGACG
1 ATTTTACCCTTGATAAAATTTTGACG
*
39457674 ATTTTA-CCTCTGATAAAATTTTAACG
1 ATTTTACCCT-TGATAAAATTTTGACG
*
39457700 ATTTTACCCTTGGTAAAATTTTGA
1 ATTTTACCCTTGATAAAATTTTGA
39457724 GAAAATATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.07
26 38 0.86
27 3 0.07
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.43
Consensus pattern (26 bp):
ATTTTACCCTTGATAAAATTTTGACG
Found at i:39457883 original size:12 final size:12
Alignment explanation
Indices: 39457866--39457890 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39457856 TGCAAATGAA
39457866 TCATTTCCATTT
1 TCATTTCCATTT
39457878 TCATTTCCATTT
1 TCATTTCCATTT
39457890 T
1 T
39457891 GAAAACTCAC
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:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:39461265 original size:31 final size:33
Alignment explanation
Indices: 39461208--39461274 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
39461198 GGAAACACCC
*
39461208 AAAAATTGAATATAGTTTAGTCACCAAAAAAGA
1 AAAAATTGAATATAGTTGAGTCACCAAAAAAGA
* *
39461241 AAAAATTG-A-ATAGTTGAGTGACCAAAAATGA
1 AAAAATTGAATATAGTTGAGTCACCAAAAAAGA
39461272 AAA
1 AAA
39461275 TTACTAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 22 0.71
32 1 0.03
33 8 0.26
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.22
Consensus pattern (33 bp):
AAAAATTGAATATAGTTGAGTCACCAAAAAAGA
Found at i:39461864 original size:12 final size:12
Alignment explanation
Indices: 39461847--39461886 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
39461837 TTAAAAGATA
39461847 TTTTTA-AAATAT
1 TTTTTATAAAT-T
39461859 TTTTTATAAATT
1 TTTTTATAAATT
39461871 TTTTTATAAATT
1 TTTTTATAAATT
39461883 TTTT
1 TTTT
39461887 GAATTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTATAAATT
Found at i:39463474 original size:6 final size:6
Alignment explanation
Indices: 39463463--39463490 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39463453 CCGAAAAGAG
39463463 TGAAAA TGAAAA TGAAAA TGAAAA TGAA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAA
39463491 GAGGAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (6 bp):
TGAAAA
Found at i:39485524 original size:21 final size:21
Alignment explanation
Indices: 39485499--39485550 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
39485489 TGTTTTGAGG
39485499 TAAAAAAATATTTAGAATAA-T
1 TAAAAAAATATTTA-AATAATT
*
39485520 TAAAAATATTATTTAAATAATT
1 TAAAAA-AATATTTAAATAATT
*
39485542 TGAAAAAAT
1 TAAAAAAAT
39485551 TATCCAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
TAAAAAAATATTTAAATAATT
Found at i:39485552 original size:22 final size:21
Alignment explanation
Indices: 39485499--39485553 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
39485489 TGTTTTGAGG
*
39485499 TAAAAAAATATTTAGAATAAT
1 TAAAAAATTATTTAGAATAAT
39485520 TAAAAATATTATTTA-AATAATT
1 TAAAAA-ATTATTTAGAATAA-T
39485542 TGAAAAAATTAT
1 T-AAAAAATTAT
39485554 CCAAATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.37
22 14 0.47
23 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAAAATTATTTAGAATAAT
Found at i:39490487 original size:17 final size:18
Alignment explanation
Indices: 39490455--39490489 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39490445 GGAATTTGGG
*
39490455 GAGTTTTGTCTTTTTATT
1 GAGTTTTCTCTTTTTATT
39490473 GAGTTTTCT-TTTTTATT
1 GAGTTTTCTCTTTTTATT
39490490 ATCCTATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (18 bp):
GAGTTTTCTCTTTTTATT
Found at i:39494119 original size:12 final size:12
Alignment explanation
Indices: 39494102--39494128 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39494092 CATTCTGTAA
39494102 CAACTCAATTTT
1 CAACTCAATTTT
39494114 CAACTCAATTTT
1 CAACTCAATTTT
39494126 CAA
1 CAA
39494129 TGGTGTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (12 bp):
CAACTCAATTTT
Found at i:39498353 original size:22 final size:21
Alignment explanation
Indices: 39498328--39498386 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
39498318 CGACTCGTAT
39498328 GAGCTTACTGTTCAGCTCAATA
1 GAGCTTACT-TTCAGCTCAATA
* *
39498350 GAGCTTACCATTTTAGCTCATTA
1 GAGCTTA-C-TTTCAGCTCAATA
39498373 GAGCTTACTATTCA
1 GAGCTTACT-TTCA
39498387 TCAGCTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.35
23 18 0.58
24 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAGCTTACTTTCAGCTCAATA
Found at i:39505155 original size:25 final size:24
Alignment explanation
Indices: 39505127--39505345 Score: 86
Period size: 25 Copynumber: 8.7 Consensus size: 24
39505117 CTATTATTTA
*
39505127 GCTCTCATGAGCATCCCGTTAGATG
1 GCTCTCATGAGCTTCCCGTTA-ATG
* * *
39505152 GCTCTGACGAGCTTCTCGATTAATG
1 GCTCTCATGAGCTTCCCG-TTAATG
* * *
39505177 GCTCTCTTGAGCTTCCCGTTTACG
1 GCTCTCATGAGCTTCCCGTTAATG
* * * *
39505201 GCT-TATATGAGCTTTCTGATAATTG
1 GCTCT-CATGAGCTTCCCGTTAA-TG
* * * * *
39505226 GATCTCCA-AAGCTTCCCAATAAAAG
1 GCTCT-CATGAGCTTCCC-GTTAATG
* *
39505251 GCTCTCACATGAGCTTCCCGATAAAAG
1 GCTCT--CATGAGCTTCCCG-TTAATG
39505278 GCTCTCACATGAGCTTCCCGATTAATG
1 GCTCT--CATGAGCTTCCCG-TTAATG
* * * *
39505305 GCTCTC-TGAAGCTACTCGATATTG
1 GCTCTCATG-AGCTTCCCGTTAATG
39505329 GCT-TGCATGAGCTTCCC
1 GCTCT-CATGAGCTTCCC
39505346 TATATTTCGC
Statistics
Matches: 144, Mismatches: 39, Indels: 23
0.70 0.19 0.11
Matches are distributed among these distances:
23 2 0.01
24 34 0.24
25 55 0.38
26 9 0.06
27 44 0.31
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (24 bp):
GCTCTCATGAGCTTCCCGTTAATG
Found at i:39505181 original size:50 final size:50
Alignment explanation
Indices: 39505101--39505196 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
39505091 CTTGATAATA
* *
39505101 GGCTCTCACGAGCTTCCTATTATTTAGCTCTCATGAGCATCCCGTTAGAT
1 GGCTCTCACGAGCTTCCGATTATATAGCTCTCATGAGCATCCCGTTAGAT
* * * *
39505151 GGCTCTGACGAGCTTCTCGATTA-ATGGCTCTCTTGAGCTTCCCGTT
1 GGCTCTCACGAGCTTC-CGATTATATAGCTCTCATGAGCATCCCGTT
39505197 TACGGCTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 34 0.87
51 5 0.13
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (50 bp):
GGCTCTCACGAGCTTCCGATTATATAGCTCTCATGAGCATCCCGTTAGAT
Found at i:39505269 original size:27 final size:27
Alignment explanation
Indices: 39505235--39505310 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
39505225 GGATCTCCAA
*
39505235 AGCTTCCCAATAAAAGGCTCTCACATG
1 AGCTTCCCGATAAAAGGCTCTCACATG
39505262 AGCTTCCCGATAAAAGGCTCTCACATG
1 AGCTTCCCGATAAAAGGCTCTCACATG
* *
39505289 AGCTTCCCGATTAATGGCTCTC
1 AGCTTCCCGATAAAAGGCTCTC
39505311 TGAAGCTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (27 bp):
AGCTTCCCGATAAAAGGCTCTCACATG
Found at i:39507388 original size:22 final size:23
Alignment explanation
Indices: 39507363--39507408 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
39507353 CAACCAAATC
39507363 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
39507385 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
39507408 A
1 A
39507409 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:39507414 original size:23 final size:23
Alignment explanation
Indices: 39507370--39507414 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39507360 ATCAATTCAA
*
39507370 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
39507393 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
39507415 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:39515410 original size:49 final size:50
Alignment explanation
Indices: 39515304--39515399 Score: 124
Period size: 49 Copynumber: 1.9 Consensus size: 50
39515294 TCCTGATATT
* * *
39515304 TAGCTCCCATGAGCATCCCGTTATATGGCTCTCACGAGCTTCTCAATTAA
1 TAGCTCTCTTGAGCATCCCGTTATATGGCTCTCACGAGCTTCCCAATTAA
* *
39515354 TAGCTCTCTTGAGCTTCCCGTT-TATGGCTCGT-ATGAGCTTCCCAAT
1 TAGCTCTCTTGAGCATCCCGTTATATGGCTC-TCACGAGCTTCCCAAT
39515400 AATTGGCTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
49 20 0.50
50 20 0.50
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (50 bp):
TAGCTCTCTTGAGCATCCCGTTATATGGCTCTCACGAGCTTCCCAATTAA
Found at i:39515410 original size:74 final size:74
Alignment explanation
Indices: 39515329--39515481 Score: 197
Period size: 74 Copynumber: 2.1 Consensus size: 74
39515319 TCCCGTTATA
* * *
39515329 TGGCTCTCACG-AGCTT-CTCAATTAATAGCTCTCTT-GAGCTTCCCG-TTTATGGCTCGTATGA
1 TGGCTCTC-CGAAGCTTCCT-AATTAATAGCTC-CTTAGAGCTACCCGATAT-TGGCTCGCATGA
39515390 GCTTCCCAATAAT
62 GCTTCCCAATAAT
*
39515403 TGGCTCTCCGAAGCTTCCTGATTAATAGCTCCTTAGAGCTACCCGATATTGGCTCGCATGAGCTT
1 TGGCTCTCCGAAGCTTCCTAATTAATAGCTCCTTAGAGCTACCCGATATTGGCTCGCATGAGCTT
*
39515468 CCCAATATT
66 CCCAATAAT
39515477 TGGCT
1 TGGCT
39515482 TGCAAGAGCT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
73 5 0.07
74 61 0.87
75 4 0.06
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.33
Consensus pattern (74 bp):
TGGCTCTCCGAAGCTTCCTAATTAATAGCTCCTTAGAGCTACCCGATATTGGCTCGCATGAGCTT
CCCAATAAT
Found at i:39515490 original size:25 final size:24
Alignment explanation
Indices: 39515437--39515519 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 24
39515427 ATAGCTCCTT
* * *
39515437 AGAGCTACCCGATATTGGCTCGCA
1 AGAGCTTCCCAATATTGGCTTGCA
*
39515461 TGAGCTTCCCAATATTTGGCTTGCA
1 AGAGCTTCCCAATA-TTGGCTTGCA
* * *
39515486 AGAGCTTCCCATTACATGGCTTACA
1 AGAGCTTCCCAATA-TTGGCTTGCA
*
39515511 TGAGCTTCC
1 AGAGCTTCC
39515520 TGTTACATGG
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 11 0.23
25 37 0.77
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (24 bp):
AGAGCTTCCCAATATTGGCTTGCA
Found at i:39515516 original size:74 final size:74
Alignment explanation
Indices: 39515378--39515516 Score: 158
Period size: 74 Copynumber: 1.9 Consensus size: 74
39515368 TTCCCGTTTA
* * * * *
39515378 TGGCTCGTATGAGCTTCCCAATAATTGGCTCTCCGAAGCTTCCTGATTAATAGCTCCTTAGAGCT
1 TGGCTCGCATGAGCTTCCCAATAATTGGCTCTCCAAAGCTTCCTCATTAATAGCTACATAGAGCT
39515443 ACCCGATAT
66 ACCCGATAT
* * *
39515452 TGGCTCGCATGAGCTTCCCAATATTTGGCT-TGCAAGAGCTTCC-CATTACATGGCTTACAT-GA
1 TGGCTCGCATGAGCTTCCCAATAATTGGCTCTCCAA-AGCTTCCTCATTA-ATAGC-TACATAGA
39515514 GCT
63 GCT
39515517 TCCTGTTACA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
73 7 0.13
74 44 0.81
75 3 0.06
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (74 bp):
TGGCTCGCATGAGCTTCCCAATAATTGGCTCTCCAAAGCTTCCTCATTAATAGCTACATAGAGCT
ACCCGATAT
Found at i:39515525 original size:25 final size:25
Alignment explanation
Indices: 39515462--39515531 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
39515452 TGGCTCGCAT
* ** *
39515462 GAGCTTCCCAATATTTGGCTTGCAA
1 GAGCTTCCCATTACATGGCTTACAA
*
39515487 GAGCTTCCCATTACATGGCTTACAT
1 GAGCTTCCCATTACATGGCTTACAA
**
39515512 GAGCTTCCTGTTACATGGCT
1 GAGCTTCCCATTACATGGCT
39515532 CGAAACAGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCATTACATGGCTTACAA
Found at i:39516798 original size:20 final size:19
Alignment explanation
Indices: 39516775--39516828 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
39516765 TAGACTATGA
39516775 ACCACTTCATTTACATACTT
1 ACCA-TTCATTTACATACTT
*
39516795 ACCATTCCATTTACTTACTT
1 ACCATT-CATTTACATACTT
*
39516815 TCCATTCTATTTAC
1 ACCATTC-ATTTAC
39516829 TTAGCATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (19 bp):
ACCATTCATTTACATACTT
Found at i:39516829 original size:20 final size:20
Alignment explanation
Indices: 39516782--39516831 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
39516772 TGAACCACTT
*
39516782 CATTTACATACTTACCATTC
1 CATTTACTTACTTACCATTC
*
39516802 CATTTACTTACTTTCCATTC
1 CATTTACTTACTTACCATTC
*
39516822 TATTTACTTA
1 CATTTACTTA
39516832 GCATAAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (20 bp):
CATTTACTTACTTACCATTC
Found at i:39523368 original size:7 final size:7
Alignment explanation
Indices: 39523356--39523394 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
39523346 TTTCTCATAT
39523356 AAAATGA
1 AAAATGA
39523363 AAAATGA
1 AAAATGA
39523370 AAAATGA
1 AAAATGA
39523377 AAAATGA
1 AAAATGA
39523384 AAAATGA
1 AAAATGA
39523391 AAAA
1 AAAA
39523395 GAATTAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAATGA
Found at i:39530201 original size:31 final size:31
Alignment explanation
Indices: 39530166--39530227 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
39530156 CATGAAATAA
39530166 GTATGGATGTTTGCTAATTACTCGGTAAGTT
1 GTATGGATGTTTGCTAATTACTCGGTAAGTT
39530197 GTATGGATGTTTGCTAATTACTCGGTAAGTT
1 GTATGGATGTTTGCTAATTACTCGGTAAGTT
39530228 TACTTTCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (31 bp):
GTATGGATGTTTGCTAATTACTCGGTAAGTT
Found at i:39531144 original size:21 final size:22
Alignment explanation
Indices: 39531111--39531151 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39531101 ACAATTTATG
*
39531111 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
39531132 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
39531152 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:39532877 original size:98 final size:98
Alignment explanation
Indices: 39532766--39532961 Score: 347
Period size: 98 Copynumber: 2.0 Consensus size: 98
39532756 TTAGTCCTTT
* * *
39532766 TTGCTTAATTAACTATCGAAACGATAAAATTTTTCAACGAAACTTTAATACCATCTTATTGCCAC
1 TTGCTCAATTAACTATCGAAACAATAAAATTTTTCAACGAAAATTTAATACCATCTTATTGCCAC
39532831 TACGTAAATATTTATAAAAATATTTACGACTCG
66 TACGTAAATATTTATAAAAATATTTACGACTCG
*
39532864 TTGCTCAATTAACTATCGAAACAATAAAATTTTTCAACGAAAATTTAATACCATCTTATTTCCAC
1 TTGCTCAATTAACTATCGAAACAATAAAATTTTTCAACGAAAATTTAATACCATCTTATTGCCAC
*
39532929 TATGTAAATATTTATAAAAATATTTACGACTCG
66 TACGTAAATATTTATAAAAATATTTACGACTCG
39532962 ATTTATAGGA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (98 bp):
TTGCTCAATTAACTATCGAAACAATAAAATTTTTCAACGAAAATTTAATACCATCTTATTGCCAC
TACGTAAATATTTATAAAAATATTTACGACTCG
Found at i:39534189 original size:383 final size:382
Alignment explanation
Indices: 39533342--39534493 Score: 2205
Period size: 383 Copynumber: 3.0 Consensus size: 382
39533332 AATCATTAGT
* *
39533342 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTACTGGTTGTTTATGATGAATTAA
1 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
*
39533407 CATGGAATTGAAGCTTTAACTTAGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
66 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
* *
39533472 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTTTAAATATCGAAG
131 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
39533537 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTGGA
196 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTGGA
*
39533602 AAATTGATATGGGACTAAATTGTTAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAATT
261 AAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAATT
*
39533667 AAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
326 GAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
39533724 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
1 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
39533789 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
66 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
39533854 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
131 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
39533919 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTAGG
196 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGT-GG
39533984 AAAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAAT
260 AAAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAAT
39534049 TGAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
325 TGAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
39534107 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
1 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
39534172 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
66 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
39534237 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
131 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
*
39534302 GCTGTATAGTAGCCTAAAATAATTAGGGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTGGG
196 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGT-GG
39534367 AAAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAAT
260 AAAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAAT
*
39534432 TGAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATAAATAA
325 TGAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
39534490 TTTT
1 TTTT
39534494 ATATTATAGA
Statistics
Matches: 759, Mismatches: 10, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
382 252 0.33
383 507 0.67
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.35
Consensus pattern (382 bp):
TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTGGA
AAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAATT
GAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
Found at i:39534980 original size:33 final size:33
Alignment explanation
Indices: 39534907--39534984 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
39534897 ATATATATAT
* *
39534907 GTGTAAGACCATAGCTGGGCTATGGCATCATGA
1 GTGTAAGACCATAACTGGGCTATGGCATCACGA
* *
39534940 -TGATAAGACCATAACTGGGTTGTGGCA-CTACGA
1 GTG-TAAGACCATAACTGGGCTATGGCATC-ACGA
39534973 GTGTAAGACCAT
1 GTGTAAGACCAT
39534985 GGCAATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 3 0.08
33 33 0.87
34 2 0.05
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (33 bp):
GTGTAAGACCATAACTGGGCTATGGCATCACGA
Found at i:39540574 original size:80 final size:80
Alignment explanation
Indices: 39540441--39540601 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
39540431 TAGAATCGAT
39540441 GAGATGATGATCGGGAATAATGGAAACGGTAAGAATGTGATTTTTGGCATTCTCGGTAAGTTGGG
1 GAGATGATGATCGGGAATAATGGAAACGGTAAGAATGTGATTTTTGGCATTCTCGGTAAGTTGGG
*
39540506 CCTCGAGGGGCCGAA
66 CCTCAAGGGGCCGAA
39540521 GAGATGATGATCGGGAATAATGGAAACGGTAAGAATGTGATTTTTGGCATTCTCGGTAAGTTGGG
1 GAGATGATGATCGGGAATAATGGAAACGGTAAGAATGTGATTTTTGGCATTCTCGGTAAGTTGGG
39540586 CCTCAAGGGGCCGAA
66 CCTCAAGGGGCCGAA
39540601 G
1 G
39540602 TAAGGCCCAT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.28, C:0.12, G:0.35, T:0.25
Consensus pattern (80 bp):
GAGATGATGATCGGGAATAATGGAAACGGTAAGAATGTGATTTTTGGCATTCTCGGTAAGTTGGG
CCTCAAGGGGCCGAA
Found at i:39540915 original size:25 final size:25
Alignment explanation
Indices: 39540886--39540933 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39540876 TTATAACATG
* * *
39540886 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
39540911 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
39540934 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:39541017 original size:11 final size:11
Alignment explanation
Indices: 39540981--39541036 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
39540971 CATGGTATGT
39540981 ATGATATGCAC
1 ATGATATGCAC
* *
39540992 ATGACATG--T
1 ATGATATGCAC
39541001 ATGATATGCAC
1 ATGATATGCAC
*
39541012 ATGATATG--T
1 ATGATATGCAC
39541021 ATGATATGCAC
1 ATGATATGCAC
39541032 ATGAT
1 ATGAT
39541037 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:39541036 original size:20 final size:20
Alignment explanation
Indices: 39540970--39541036 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
39540960 ATTTTGATAA
*
39540970 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
39540990 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
39541010 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
39541030 ACATGAT
1 ACATGAT
39541037 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:39541120 original size:23 final size:23
Alignment explanation
Indices: 39541087--39541204 Score: 175
Period size: 23 Copynumber: 5.1 Consensus size: 23
39541077 AGGAAGTGAA
* *
39541087 AAAGGGATTATGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
39541110 AAAGGGCTTATGTCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
39541133 AAAGGGCTTATACCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
39541156 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
39541178 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
39541202 AAA
1 AAA
39541205 AGAGGCTAGG
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.12
23 66 0.77
24 10 0.12
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:39541221 original size:25 final size:24
Alignment explanation
Indices: 39541086--39541221 Score: 129
Period size: 23 Copynumber: 5.8 Consensus size: 24
39541076 GAGGAAGTGA
* * *
39541086 AAAAGGGATTATGCCCCAATTATT
1 AAAAGGGCTTAGGCCCCAGTTATT
* *
39541110 -AAAGGGCTTATGTCCCAGTTATT
1 AAAAGGGCTTAGGCCCCAGTTATT
**
39541133 -AAAGGGCTTATACCCCAGTTATT
1 AAAAGGGCTTAGGCCCCAGTTATT
*
39541156 -AAAGGGCTTATG-CCCAGTTATT
1 AAAAGGGCTTAGGCCCCAGTTATT
**
39541178 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTAGGCCCCAGTTATT
39541202 AAAAGAGGC-TAGGCCTCCAG
1 AAAAG-GGCTTAGGCC-CCAG
39541222 ATATATGATA
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
22 10 0.10
23 63 0.64
24 19 0.19
25 7 0.07
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTAGGCCCCAGTTATT
Found at i:39541455 original size:31 final size:31
Alignment explanation
Indices: 39541420--39541483 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
39541410 CGTTTACAGT
39541420 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
39541451 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
39541482 AA
1 AA
39541484 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:39547980 original size:25 final size:25
Alignment explanation
Indices: 39547951--39547998 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
39547941 TTATAACATG
* *
39547951 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
39547976 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
39547999 GTTTATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:39548082 original size:11 final size:11
Alignment explanation
Indices: 39548046--39548101 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
39548036 CATGGTATGT
39548046 ATGATATGCAC
1 ATGATATGCAC
* *
39548057 ATGACATG--T
1 ATGATATGCAC
39548066 ATGATATGCAC
1 ATGATATGCAC
*
39548077 ATGATATG--T
1 ATGATATGCAC
39548086 ATGATATGCAC
1 ATGATATGCAC
39548097 ATGAT
1 ATGAT
39548102 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:39548101 original size:20 final size:20
Alignment explanation
Indices: 39548035--39548101 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
39548025 ATTTTGATAG
*
39548035 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
39548055 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
39548075 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
39548095 ACATGAT
1 ACATGAT
39548102 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:39548182 original size:23 final size:22
Alignment explanation
Indices: 39548152--39548246 Score: 145
Period size: 23 Copynumber: 4.1 Consensus size: 22
39548142 AGGAAGTGAA
39548152 AAAGGGCTTATGTCCCAGTTATT
1 AAAGGGCTTATG-CCCAGTTATT
39548175 AAAGGGCTTATGCCCGAGTTATT
1 AAAGGGCTTATGCCC-AGTTATT
39548198 AAAGGGCTTATGCCCAGTTATT
1 AAAGGGCTTATGCCCAGTTATT
*
39548220 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATG-CCCAGTTATT
39548244 AAA
1 AAA
39548247 ATAGGCTAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
22 10 0.15
23 48 0.71
24 10 0.15
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (22 bp):
AAAGGGCTTATGCCCAGTTATT
Found at i:39548496 original size:31 final size:31
Alignment explanation
Indices: 39548461--39548524 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
39548451 CGTTTACAGT
39548461 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
39548492 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
39548523 AA
1 AA
39548525 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:39551129 original size:21 final size:24
Alignment explanation
Indices: 39551086--39551134 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 24
39551076 GTTTGAAGCA
39551086 CTTCATAAAATTAAAAGTTATAAAC
1 CTTCATAAAATT-AAAGTTATAAAC
39551111 CTTCATAAAA-T-AAG-TATAAAC
1 CTTCATAAAATTAAAGTTATAAAC
39551132 CTT
1 CTT
39551135 TACTAATGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
24 1 0.04
25 10 0.42
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (24 bp):
CTTCATAAAATTAAAGTTATAAAC
Found at i:39555764 original size:37 final size:37
Alignment explanation
Indices: 39555714--39555787 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
39555704 ATAACGGAAC
39555714 ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
1 ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
39555751 ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
1 ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
39555788 CTGATAAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (37 bp):
ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
Found at i:39558079 original size:38 final size:38
Alignment explanation
Indices: 39558017--39558139 Score: 185
Period size: 38 Copynumber: 3.2 Consensus size: 38
39558007 GGTCCTTAAC
*
39558017 CCGGATATTTTTCCAGCACT-TAGCCTGCGGACTTTAAGT
1 CCGGAT-TTATTCCAGCA-TATAGCCTGCGGACTTTAAGT
* * *
39558056 CCGAATTTATTCCATCATATAGCCTGCAGACTTTAAGT
1 CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
39558094 CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
1 CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
39558132 CCGGATTT
1 CCGGATTT
39558140 CTTCTTTTAC
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
37 1 0.01
38 70 0.92
39 5 0.07
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (38 bp):
CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
Found at i:39562645 original size:46 final size:44
Alignment explanation
Indices: 39562586--39562700 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
39562576 ACAGGACAGA
* *
39562586 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
39562632 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
39562676 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
39562701 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:39562681 original size:44 final size:45
Alignment explanation
Indices: 39562586--39562719 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
39562576 ACAGGACAGA
* *
39562586 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
39562632 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
39562676 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
39562720 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:39564662 original size:79 final size:79
Alignment explanation
Indices: 39564543--39564701 Score: 210
Period size: 79 Copynumber: 2.0 Consensus size: 79
39564533 TTATGCATGC
* * * * *
39564543 AAAACATGAAAGATAGAAACACAAAGGGCATAATACTGAAATGTGAAATTAACTTTATCTATTTA
1 AAAACATGAAAGACACAAACACAAAAGACATAATACTGAAATGTAAAATTAACTTTATCTATTTA
39564608 TTCATAGTTCAAAT
66 TTCATAGTTCAAAT
* * * * * *
39564622 AAAACATGAAAGACACAAATATAAAAGACATAATAGTGAAATGTAAAATTAAGTTTGTTTATTTA
1 AAAACATGAAAGACACAAACACAAAAGACATAATACTGAAATGTAAAATTAACTTTATCTATTTA
*
39564687 TTCATTGTTCAAAT
66 TTCATAGTTCAAAT
39564701 A
1 A
39564702 CATAAAAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (79 bp):
AAAACATGAAAGACACAAACACAAAAGACATAATACTGAAATGTAAAATTAACTTTATCTATTTA
TTCATAGTTCAAAT
Found at i:39568584 original size:52 final size:52
Alignment explanation
Indices: 39568498--39568605 Score: 191
Period size: 52 Copynumber: 2.1 Consensus size: 52
39568488 ATAGAAGTTC
*
39568498 ACTTCCTC-ATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
1 ACTTCATCTATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
*
39568549 TCTTCATCTATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
1 ACTTCATCTATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
39568601 ACTTC
1 ACTTC
39568606 TACTAGATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 6 0.11
52 47 0.89
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (52 bp):
ACTTCATCTATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
Found at i:39569838 original size:20 final size:20
Alignment explanation
Indices: 39569815--39569852 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39569805 TTATTTTTTT
39569815 AATT-TATTGATGCTTTTTAG
1 AATTATATTGAT-CTTTTTAG
*
39569835 AATTATATTTATCTTTTT
1 AATTATATTGATCTTTTT
39569853 TTTCTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (20 bp):
AATTATATTGATCTTTTTAG
Found at i:39570376 original size:36 final size:36
Alignment explanation
Indices: 39570336--39570408 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
39570326 AATAGTTTTC
*
39570336 TATATTATAGGAAGTAGATGGCGAG-TAGGAGTAGTT
1 TATATTATAGGAAGTAGAGGGCG-GTTAGGAGTAGTT
* *
39570372 TATATTTTAGGAAGTAGAGGGTGGTTAGGAGTAGTT
1 TATATTATAGGAAGTAGAGGGCGGTTAGGAGTAGTT
39570408 T
1 T
39570409 TCCTATTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 32 0.97
ACGTcount: A:0.30, C:0.01, G:0.34, T:0.34
Consensus pattern (36 bp):
TATATTATAGGAAGTAGAGGGCGGTTAGGAGTAGTT
Found at i:39572320 original size:699 final size:693
Alignment explanation
Indices: 39571338--39572729 Score: 2209
Period size: 697 Copynumber: 2.0 Consensus size: 693
39571328 AGAAGCCTAG
*
39571338 AGATTCTTTTTCTTTACGTAATAATAAAACATCAAAAATTTTTGAATTACTACAGTGTGATTTAT
1 AGATTCTTTTTCTTTACGTAATAATAAAACATCAAAAATTTTTGAATTAATACAGTGTGATTTAT
*
39571403 TGGGACCTTATAAACCCTCGTCTTCCTGTGGAGCAATATATTTTTTTGACATTAGTTGATGATTT
66 TGGGACCTTATAAACCCTCGTCTTCCTGTGGAGCAATAGATTTTTTTGACATTAGTTGATGATTT
*
39571468 TTCACTTGTTGTATGAGTAAATTTATTGGTTGATGAAATCGAGGTTTTTCAATTTTTTATGTCCT
131 TTCACTTGTTGTATGAGTAAATTTATTGGTTGATGAAATAGAGGTTTTTCAATTTTTTATGTCCT
39571533 TTATTTCCATGAATGAGTGCCAATTTTCCAAGAAAATCAAGATAGTACAGAGTGATAATGGTACT
196 TTATTTCCATGAATGAGTGCCAATTTTCCAAGAAAATCAAGATAGTACAGAGTGATAATGGTACT
* * * *
39571598 GGTTTTAATTGCATGAAGGACTATTTTTTTTGGCTAATGGCATCTTATGCCAATCTTCTTATGTT
261 GGGTTTAATTGCATAAAGGACTA--TTTTTTGGCTAATGGCATCTTATGCCAAACTTCTTATGCT
* * *
39571663 GGCACTCCTCAACAAAATGGAGGAGTGGAGAGAAAACATCAACATATTTTAAATGCTGTTGATAT
324 GGCACTCCTCAACAAAATAGACGAGTGGAGAGAAAACATCAACATATTTTAAATGCTGTTCATAT
** ** * * *
39571728 TTTATGTTTTCAAGGGAACTTACTGATTATGTTTTAGGGGGAGTGTGTTTTAGCTGCGGCACATC
389 TTTACATTTTCAAGGGAACTTACCAATTATGTTTTACGGGGAGTGTGTTTTAGCTACGACACATC
39571793 TAATTAATAAAACTCCCTCTAGTGTACTTCATAATAAAACTCGTTATGACATTTTGTTTGGCTCT
454 TAATTAATAAAACTCCCTCTAGTGTACTTCATAATAAAACTC---ATGACATTTTGTTTGGCTCT
* * * *
39571858 CCACTCTCGTATGATAGCTTGTGTGTTTTAGGTTATTTGTGTTTTGCTCATAATCAACGAGCAAA
516 CCACTCTCGTATAATAGCTTGTGTGTTTTAGATTATTTGTGCTTTACTCATAATCAACGAGCAAA
* * * * * *
39571923 AGGTGAGAAATTTGCAAGTCGAAGTTGAAAATATGCATTTTTTGGGTATCCTTTTGGG-AAAAAG
581 AGCTAAGAAATTTGCAAGTCGAAG-TAAAAAAATGCATTTGTTAGGTATCCTTTTGGGAAAAAAG
**
39571987 GTTGGATGTTATATGATTTGGAGAGAAGGGTTTTTTTCACATCTAGGGA
645 GTTGGATGTTATATGATTTGGAGAGAAAAGTTTTTTTCACATCTAGGGA
** * * * *
39572036 AGATTCTTTTTCTTTGTGTAATAATAAAATATCAGAAATTTTTGAATTAATACATTGTTATTTAT
1 AGATTCTTTTTCTTTACGTAATAATAAAACATCAAAAATTTTTGAATTAATACAGTGTGATTTAT
* *
39572101 TGGGACCTTATAATCCCTTGTCTTCCTGTGGAGC-A-AGATTTTTTTGACATTAGTTGATGATTT
66 TGGGACCTTATAAACCCTCGTCTTCCTGTGGAGCAATAGATTTTTTTGACATTAGTTGATGATTT
* *
39572164 TTCACTTGTTGTATGAGTAAATTTATTGGTTGATGAAATAGAGTTTTTTTTTAATTTTTTTATGT
131 TTCACTTGTTGTATGAGTAAATTTATTGGTTGATGAAATAGAG--GTTTTTCAA-TTTTTTATGT
39572229 CCTTTATTTCCAT-AATTGA-TCGCCAATTTTCCAAGAAAATCAAGATAGTACAGAGTGATAATG
193 CCTTTATTTCCATGAA-TGAGT-GCCAATTTTCCAAGAAAATCAAGATAGTACAGAGTGATAATG
*
39572292 GTATTGGGTTTAATTGCATAAAGGACTATTTTTTGGCTAATGGCATCTTATGCCAAACTTCTTAT
256 GTACTGGGTTTAATTGCATAAAGGACTATTTTTTGGCTAATGGCATCTTATGCCAAACTTCTTAT
*
39572357 GCTGGCACTCCTCAACAAAATAGACGAGTGGAGAGAAAACATCAACATATTTTAAATGTTGTTCA
321 GCTGGCACTCCTCAACAAAATAGACGAGTGGAGAGAAAACATCAACATATTTTAAATGCTGTTCA
* *
39572422 TATTTTGCATTTTCAAGGGAACTTACCAATTCTGTTTTACGGGGAGTGTGTTTTAGCTACGACAC
386 TATTTTACATTTTCAAGGGAACTTACCAATTATGTTTTACGGGGAGTGTGTTTTAGCTACGACAC
* *
39572487 ATCTGATTAATAAAACTCCCTCTAGTGTACTTCATAATAAAACTCCTGACATTTTGTTTGGCTCT
451 ATCTAATTAATAAAACTCCCTCTAGTGTACTTCATAATAAAACTCATGACATTTTGTTTGGCTCT
* * *
39572552 CCACTCTTGTATAATGGCTTGTGTGTTTTCGATTATTTGTGCTTTACTCATAATCAACGAGCAAA
516 CCACTCTCGTATAATAGCTTGTGTGTTTTAGATTATTTGTGCTTTACTCATAATCAACGAGCAAA
*
39572617 AGCTAAGAAATTTGCAAGTTGAAGTAAAAAAATGCATTTGTTAGGTATCCTTTTGGGAAAAAAGG
581 AGCTAAGAAATTTGCAAGTCGAAGTAAAAAAATGCATTTGTTAGGTATCCTTTTGGGAAAAAAGG
39572682 TTGGATGTTATATGATTTGGAGAGAAAAGTTTTTTTCACATCTAGGGA
646 TTGGATGTTATATGATTTGGAGAGAAAAGTTTTTTTCACATCTAGGGA
39572730 TGTTCGATTT
Statistics
Matches: 639, Mismatches: 49, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
693 29 0.05
694 151 0.24
696 69 0.11
697 197 0.31
698 100 0.16
699 93 0.15
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (693 bp):
AGATTCTTTTTCTTTACGTAATAATAAAACATCAAAAATTTTTGAATTAATACAGTGTGATTTAT
TGGGACCTTATAAACCCTCGTCTTCCTGTGGAGCAATAGATTTTTTTGACATTAGTTGATGATTT
TTCACTTGTTGTATGAGTAAATTTATTGGTTGATGAAATAGAGGTTTTTCAATTTTTTATGTCCT
TTATTTCCATGAATGAGTGCCAATTTTCCAAGAAAATCAAGATAGTACAGAGTGATAATGGTACT
GGGTTTAATTGCATAAAGGACTATTTTTTGGCTAATGGCATCTTATGCCAAACTTCTTATGCTGG
CACTCCTCAACAAAATAGACGAGTGGAGAGAAAACATCAACATATTTTAAATGCTGTTCATATTT
TACATTTTCAAGGGAACTTACCAATTATGTTTTACGGGGAGTGTGTTTTAGCTACGACACATCTA
ATTAATAAAACTCCCTCTAGTGTACTTCATAATAAAACTCATGACATTTTGTTTGGCTCTCCACT
CTCGTATAATAGCTTGTGTGTTTTAGATTATTTGTGCTTTACTCATAATCAACGAGCAAAAGCTA
AGAAATTTGCAAGTCGAAGTAAAAAAATGCATTTGTTAGGTATCCTTTTGGGAAAAAAGGTTGGA
TGTTATATGATTTGGAGAGAAAAGTTTTTTTCACATCTAGGGA
Found at i:39579103 original size:7 final size:7
Alignment explanation
Indices: 39579093--39579117 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39579083 TGGGGCTTAG
39579093 GTGGGTA
1 GTGGGTA
39579100 GTGGGTA
1 GTGGGTA
39579107 GTGGGTA
1 GTGGGTA
39579114 GTGG
1 GTGG
39579118 ACAGTGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.60, T:0.28
Consensus pattern (7 bp):
GTGGGTA
Found at i:39579123 original size:14 final size:14
Alignment explanation
Indices: 39579093--39579126 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39579083 TGGGGCTTAG
**
39579093 GTGGGTAGTGGGTA
1 GTGGGTAGTGGACA
39579107 GTGGGTAGTGGACA
1 GTGGGTAGTGGACA
39579121 GTGGGT
1 GTGGGT
39579127 TAATTGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.56, T:0.26
Consensus pattern (14 bp):
GTGGGTAGTGGACA
Found at i:39585701 original size:8 final size:8
Alignment explanation
Indices: 39585690--39585719 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
39585680 AAAATTTTTT
39585690 TTTTTATA
1 TTTTTATA
39585698 TTTTTATA
1 TTTTTATA
39585706 TGTTTTATA
1 T-TTTTATA
39585715 TTTTT
1 TTTTT
39585720 GCACTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (8 bp):
TTTTTATA
Found at i:39586785 original size:73 final size:73
Alignment explanation
Indices: 39586680--39586837 Score: 194
Period size: 73 Copynumber: 2.2 Consensus size: 73
39586670 AAAAGGAATT
** *
39586680 AAAATACCTCAGCGTGACCTGAGGCTTGACTCACCTCTCGCAATATGAG-TCAATTTTTG-AAAC
1 AAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTCAATTTTTGAAAAC
39586743 ATAAACTA
66 ATAAACTA
** * *
39586751 AAAATACCTCAGCGTGTGACCTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTGAAA
1 AAAATACCTCAGC--GTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTCAATTTTTGAAA
* *
39586816 ACATGAATTA
64 ACATAAACTA
*
39586826 AAGATACCTCAG
1 AAAATACCTCAG
39586838 AGTACCCAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 13 0.18
73 31 0.42
74 8 0.11
75 21 0.29
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (73 bp):
AAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTCAATTTTTGAAAAC
ATAAACTA
Found at i:39594836 original size:18 final size:18
Alignment explanation
Indices: 39594815--39594858 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
39594805 GTTTGGGTTG
39594815 CGGGTCGGGTCACCGGAT
1 CGGGTCGGGTCACCGGAT
* *
39594833 CGGGTCGTGTCGCCGGAT
1 CGGGTCGGGTCACCGGAT
39594851 CGGGTCGG
1 CGGGTCGG
39594859 TTTGACCCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.27, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCACCGGAT
Found at i:39594912 original size:6 final size:6
Alignment explanation
Indices: 39594902--39594979 Score: 68
Period size: 6 Copynumber: 12.3 Consensus size: 6
39594892 ATTTTTTATT
*
39594902 TTTTTCC TTTTTC -TTTTC TTTTTC TTTTTC TTTTTTC TTCTTCTCC TTCTTC
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TT-TT-T-C TTTTTC
* * *
39594954 TTCTTC TTCTTC TTTTTC TTCTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TT
39594980 CACGAGCCCT
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
5 5 0.08
6 39 0.62
7 14 0.22
8 2 0.03
9 3 0.05
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:39594944 original size:3 final size:3
Alignment explanation
Indices: 39594912--39594980 Score: 81
Period size: 3 Copynumber: 24.0 Consensus size: 3
39594902 TTTTTCCTTT
* * *
39594912 TTC TT- TTC TTT TTC TTT TTC TT- TT- TTC TTC TTC TCC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
39594957 TTC TTC TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC
39594981 ACGAGCCCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 6 0.11
3 50 0.89
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:39595037 original size:18 final size:18
Alignment explanation
Indices: 39594997--39595039 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
39594987 CCTAGCCGCC
39594997 GCGCCG-CGCCGTCGCTT
1 GCGCCGTCGCCGTCGCTT
*
39595014 GTGCCGTCGCCGTCGTCTT
1 GCGCCGTCGCCGTCG-CTT
39595033 -CGCCGTC
1 GCGCCGTC
39595040 AAGCCGCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 14 0.64
19 3 0.14
ACGTcount: A:0.00, C:0.44, G:0.33, T:0.23
Consensus pattern (18 bp):
GCGCCGTCGCCGTCGCTT
Found at i:39595091 original size:20 final size:20
Alignment explanation
Indices: 39595058--39595115 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
39595048 GTCGGAGGCT
39595058 CTCTTC-TTCTTCTCCTTTCTC
1 CTCTTCTTTC-TCTCCTTT-TC
39595079 CTC-TCTTTCTCTCCTTTTC
1 CTCTTCTTTCTCTCCTTTTC
*
39595098 CTCTTCTTTTTCT-CTTTT
1 CTCTTCTTTCTCTCCTTTT
39595116 TTGCAAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 10 0.29
20 18 0.53
21 6 0.18
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTCTTTCTCTCCTTTTC
Found at i:39595398 original size:30 final size:30
Alignment explanation
Indices: 39595358--39595452 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
39595348 ATTTAGGATT
*
39595358 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * * *
39595388 TAAGTGAAATTTAAAGAAAGTTTAAGTGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
39595418 AAAATGGAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
39595448 AAAAT
1 AAAAT
39595453 ACAATTTTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 2 0.04
30 51 0.96
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:39595507 original size:25 final size:25
Alignment explanation
Indices: 39595455--39595508 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
39595445 GTCAAAATAC
**
39595455 AATTTTTATTTTTTTAAATTTTTTA
1 AATTTTTATTTTTTTAAATTTTGAA
39595480 AATTTTT-TTTTTTTGAAATTTTGAA
1 AATTTTTATTTTTTT-AAATTTTGAA
39595505 AATT
1 AATT
39595509 AAACACAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
AATTTTTATTTTTTTAAATTTTGAA
Found at i:39604370 original size:119 final size:119
Alignment explanation
Indices: 39604154--39604631 Score: 814
Period size: 119 Copynumber: 4.0 Consensus size: 119
39604144 AAATAAATTG
* ** **
39604154 AAGACAGCAGATCTAGA-CTTCAGACATTTATGTTGAAGCAGATCCAAGATGATTTGGTATTCTT
1 AAGATAGCAGATCTA-ACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTT
*
39604218 GTGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
65 GTGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGATTCTCAGACGTTCTCA
* *
39604273 AAGATAGCAGATCTAACCTTCAGATGATTATACTGAAGCAGATCCAGGATGATTTGGTATTCTTG
1 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
39604338 TGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGATTCTCAGACGTTCTCA
66 TGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGATTCTCAGACGTTCTCA
*
39604392 AAGATAGCAGACCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
1 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
39604457 TGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGATTCTCAGACGTTCTCA
66 TGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGATTCTCAGACGTTCTCA
* *
39604511 AAGATAGCAGATCTAACCTTCAGATGTTTATATTGAAGCAGATCCAAGATGATTTGGCATTCTTG
1 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
* * *
39604576 TATTTACAAGGAACAAATCGAGGACATAGCAGATTTGATTCTCAGATGTTCTCA
66 TGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGATTCTCAGACGTTCTCA
39604630 AA
1 AA
39604632 CAGACTCAAG
Statistics
Matches: 341, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
118 1 0.00
119 340 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (119 bp):
AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
TGTTTACAAGGAGCAAATCGAGGACATAGCAGATTTGATTCTCAGACGTTCTCA
Found at i:39604659 original size:83 final size:83
Alignment explanation
Indices: 39604555--39604824 Score: 360
Period size: 83 Copynumber: 3.2 Consensus size: 83
39604545 GAAGCAGATC
* ** * * *
39604555 CAAGATGATTTGGCATTCTTGTATTTACAAGGAACAAATCGAGGACATAGCAGATTTGATTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
*
39604620 GATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* *
39604638 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATAACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
39604703 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* * * * * * *
39604721 CAAGATGGTTTAAGTACCCTCGTGCTTACAAGGAACAAGTCGAGGACCTTGCAGATATGACTCTC
1 CAAGATGATTT-GGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTC
* *
39604786 AAATGTTTTCAGACAGACT
65 AAATGTTCTCAAACAGACT
*
39604805 CAAGATGATTTGACATCCTT
1 CAAGATGATTTGGCATCCTT
39604825 ACAAATCGAA
Statistics
Matches: 162, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
83 89 0.55
84 73 0.45
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (83 bp):
CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
AATGTTCTCAAACAGACT
Found at i:39604776 original size:84 final size:83
Alignment explanation
Indices: 39604579--39604811 Score: 340
Period size: 84 Copynumber: 2.8 Consensus size: 83
39604569 ATTCTTGTAT
* * * *
39604579 TTACAAGGAACAAATCGAGGACATAGCAGATTTGATTCTCAGATGTTCTCAAACAGACTCAAGAT
1 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAAGAT
* * *
39604644 GGTTTGGCATCCTTGTGC
66 GGTTTAGCACCCTCGTGC
*
39604662 TTACAAGGAACAAATCGAGGACATTGCAGATATAACTCTCAAATGTTCTCAAACAGACTCAAGAT
1 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAAGAT
*
39604727 GGTTTAAGTACCCTCGTGC
66 GGTTT-AGCACCCTCGTGC
* * * *
39604746 TTACAAGGAACAAGTCGAGGACCTTGCAGATATGACTCTCAAATGTTTTCAGACAGACTCAAGAT
1 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAAGAT
39604811 G
66 G
39604812 ATTTGACATC
Statistics
Matches: 135, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 65 0.48
84 70 0.52
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (83 bp):
TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAAGAT
GGTTTAGCACCCTCGTGC
Found at i:39606330 original size:17 final size:18
Alignment explanation
Indices: 39606308--39606348 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39606298 TATATTATAT
*
39606308 ATTATAA-AATTATTTTG
1 ATTATAAGAATTATTTTA
*
39606325 ATTATAAGTATTATTTTA
1 ATTATAAGAATTATTTTA
39606343 ATTATA
1 ATTATA
39606349 TATTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTATAAGAATTATTTTA
Found at i:39606337 original size:18 final size:19
Alignment explanation
Indices: 39606316--39606358 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
39606306 ATATTATAAA
*
39606316 ATTATTTTGATTATA-AGT
1 ATTATTTTAATTATATAGT
*
39606334 ATTATTTTAATTATATATT
1 ATTATTTTAATTATATAGT
39606353 ATTATT
1 ATTATT
39606359 ACTTATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTATTTTAATTATATAGT
Found at i:39606354 original size:16 final size:16
Alignment explanation
Indices: 39606316--39606394 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 16
39606306 ATATTATAAA
*
39606316 ATTATTTTGATTATAAGT
1 ATTATTTTAATTAT-A-T
39606334 ATTATTTTAATTATAT
1 ATTATTTTAATTATAT
*
39606350 ATTATTATTACTTATTATGT
1 ATTATT-TTA---ATTATAT
** *
39606370 ATTATTTTTCTTAAAT
1 ATTATTTTAATTATAT
39606386 ATTATTTTA
1 ATTATTTTA
39606395 CATCTCTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
16 19 0.38
17 4 0.08
18 13 0.26
19 2 0.04
20 12 0.24
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (16 bp):
ATTATTTTAATTATAT
Found at i:39606469 original size:12 final size:12
Alignment explanation
Indices: 39606425--39606476 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
39606415 ATATTTTCAC
39606425 ATATATTATATTT
1 ATATATTAT-TTT
*
39606438 AT-TAATTA-TAT
1 ATAT-ATTATTTT
39606449 ATATATTATTTT
1 ATATATTATTTT
*
39606461 ATATGTTATTTT
1 ATATATTATTTT
39606473 ATAT
1 ATAT
39606477 TATATCTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 8 0.24
12 19 0.58
13 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
ATATATTATTTT
Found at i:39606489 original size:12 final size:12
Alignment explanation
Indices: 39606428--39606489 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
39606418 TTTTCACATA
39606428 TATTATATTTAT
1 TATTATATTTAT
*
39606440 TAATTATATATA-
1 T-ATTATATTTAT
39606452 TATTAT-TTTAT
1 TATTATATTTAT
*
39606463 ATGTTAT-TTTA-
1 -TATTATATTTAT
*
39606474 TATTATATCTAT
1 TATTATATTTAT
39606486 TATT
1 TATT
39606490 TTTCTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
10 8 0.20
11 8 0.20
12 15 0.38
13 9 0.22
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:39606552 original size:18 final size:19
Alignment explanation
Indices: 39606529--39606576 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
39606519 ATATAATCTT
39606529 TATTATGTT-TTATTTTTA
1 TATTATGTTATTATTTTTA
* *
39606547 TATTAT-TTATTGTTTTTT
1 TATTATGTTATTATTTTTA
39606565 TATATATGTTAT
1 TAT-TATGTTAT
39606577 ATATATCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 3 0.12
20 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (19 bp):
TATTATGTTATTATTTTTA
Found at i:39609515 original size:22 final size:22
Alignment explanation
Indices: 39609488--39609531 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39609478 ATTATTATTG
*
39609488 ATTAATTAGTTTAATTAGATAA
1 ATTAATTAGTTTAATTAAATAA
**
39609510 ATTAATTTTTTTAATTAAATAA
1 ATTAATTAGTTTAATTAAATAA
39609532 TTTTCTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTAATTAGTTTAATTAAATAA
Found at i:39609534 original size:17 final size:18
Alignment explanation
Indices: 39609507--39609540 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39609497 TTTAATTAGA
*
39609507 TAAATTAATTTTTTTAAT
1 TAAATTAATTTTCTTAAT
39609525 TAAA-TAATTTTCTTAA
1 TAAATTAATTTTCTTAA
39609541 CCCAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTAATTTTCTTAAT
Found at i:39612310 original size:18 final size:18
Alignment explanation
Indices: 39612287--39612323 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39612277 TATCATGCCA
*
39612287 TTTATATCTTTTAATAAT
1 TTTATATCTTTTAAAAAT
*
39612305 TTTATATTTTTTAAAAAT
1 TTTATATCTTTTAAAAAT
39612323 T
1 T
39612324 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATATCTTTTAAAAAT
Found at i:39617294 original size:21 final size:21
Alignment explanation
Indices: 39617270--39617322 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
39617260 CACTGTTTCT
*
39617270 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
39617291 AATCTCACCGCTTCAGTAACT
1 AATCTCACCGCTACAGTAACC
39617312 AATCTCACCGC
1 AATCTCACCGC
39617323 CACCGCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:39626285 original size:46 final size:46
Alignment explanation
Indices: 39626232--39626450 Score: 209
Period size: 46 Copynumber: 4.7 Consensus size: 46
39626222 GTTATTGTTG
* *
39626232 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCATTGAGATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATGAGA
*
39626278 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATG-AGA
* * * * *
39626324 GCCAGTGTAAGACATATTTGGGATATGCATCGGC-TACGAGATGATA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGATGAGA
*
39626370 G-TCAGTGTAAGACCATGT-TAGGGACATGGCATC-G-ATTTGAGAT-ATGA
1 GCT-AGTGTAAGA-CATGTCT-GGGACAT-GCATCGGCA-TCGAGATGA-GA
*
39626417 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCG
39626451 TCACCTTACC
Statistics
Matches: 147, Mismatches: 13, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
45 2 0.01
46 91 0.62
47 47 0.32
48 7 0.05
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATGAGA
Found at i:39630622 original size:21 final size:21
Alignment explanation
Indices: 39630598--39630659 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
39630588 AGTTTATTTA
*
39630598 ATATTT-AATATTTTATCTTTT
1 ATATTTAAATATTAT-TCTTTT
39630619 ATATTTAAATATTATTCTTTT
1 ATATTTAAATATTATTCTTTT
**
39630640 GATA-GAAAATATTATTCTTT
1 -ATATTTAAATATTATTCTTT
39630660 AATAGTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 26 0.72
22 10 0.28
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (21 bp):
ATATTTAAATATTATTCTTTT
Done.