Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 104 of 135
Found at i:38612404 original size:26 final size:26
Alignment explanation
Indices: 38612368--38612417 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
38612358 TACAGAGGTT
* *
38612368 TGCCATAAAGGTTTTTCTTTTATATA
1 TGCCACAAAGGTTTTTCCTTTATATA
38612394 TGCCACAAAGGTTTTTCCTTTATA
1 TGCCACAAAGGTTTTTCCTTTATA
38612418 GGGATTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (26 bp):
TGCCACAAAGGTTTTTCCTTTATATA
Found at i:38612602 original size:30 final size:31
Alignment explanation
Indices: 38612563--38612643 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
38612553 TATTCAGTGG
* *
38612563 TTCGTCACAAAGGTTTTTC-CTTTACAGAGA
1 TTCGCCACAAAGGCTTTTCTCTTTACAGAGA
* * *
38612593 TTCGCCACAAAGGCTCTTCTTTTTACAGAGG
1 TTCGCCACAAAGGCTTTTCTCTTTACAGAGA
*
38612624 TTTGCCACAAAGGCTTTTCT
1 TTCGCCACAAAGGCTTTTCT
38612644 ATTTTCTGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 16 0.37
31 27 0.63
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (31 bp):
TTCGCCACAAAGGCTTTTCTCTTTACAGAGA
Found at i:38620133 original size:26 final size:26
Alignment explanation
Indices: 38620104--38620158 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
38620094 AGGATTCTTG
38620104 CATGGCTATCTTGATAAGACCATTTA
1 CATGGCTATCTTGATAAGACCATTTA
*
38620130 CATGGCTATCTTGATGAGACCATTTA
1 CATGGCTATCTTGATAAGACCATTTA
38620156 CAT
1 CAT
38620159 AGCTCAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (26 bp):
CATGGCTATCTTGATAAGACCATTTA
Found at i:38623245 original size:62 final size:59
Alignment explanation
Indices: 38623169--38623295 Score: 157
Period size: 62 Copynumber: 2.1 Consensus size: 59
38623159 ATAATTTTAT
* * *
38623169 TTTAAT-AGATTTAATATTAAACTTAATTTAATATTAATCTTGTAAATAAATATTCTATTAA
1 TTTAATAAGATTTAATATTAAACTTAATCTAATATTAATCTT-T--ATAAATATTATACTAA
* * * *
38623230 TTTAATAATATTTAATATTAAATTTAATCTAATATTTATCTTTATAAGTATTATACTAA
1 TTTAATAAGATTTAATATTAAACTTAATCTAATATTAATCTTTATAAATATTATACTAA
38623289 TTTAATA
1 TTTAATA
38623296 TTAAAGTGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 20 0.34
61 7 0.12
62 31 0.53
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (59 bp):
TTTAATAAGATTTAATATTAAACTTAATCTAATATTAATCTTTATAAATATTATACTAA
Found at i:38623432 original size:26 final size:22
Alignment explanation
Indices: 38623403--38623450 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 22
38623393 AGTTGTAGAG
38623403 AGAAAATTCTCTGAACAGATTATTTT
1 AGAAAATT-TCT-AA-AGA-TATTTT
38623429 AGAAAATTTCTAAAGATATTTT
1 AGAAAATTTCTAAAGATATTTT
38623451 TCTTATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 3 0.14
24 2 0.09
25 3 0.14
26 8 0.36
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (22 bp):
AGAAAATTTCTAAAGATATTTT
Found at i:38625911 original size:25 final size:24
Alignment explanation
Indices: 38625851--38625912 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
38625841 TAAAATACTC
**
38625851 TCCAC-AAGGCTTTCCAGAGGATT
1 TCCACAAAGGCTTTCCAGAAAATT
* *
38625874 CCCACAAATGCTTTCCAGAAAATTT
1 TCCACAAAGGCTTTCCAGAAAA-TT
38625899 TCCACAAAGGCTTT
1 TCCACAAAGGCTTT
38625913 ACATGAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 4 0.13
24 13 0.42
25 14 0.45
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (24 bp):
TCCACAAAGGCTTTCCAGAAAATT
Found at i:38628337 original size:27 final size:27
Alignment explanation
Indices: 38628305--38628580 Score: 290
Period size: 27 Copynumber: 10.3 Consensus size: 27
38628295 TTAACCCGAA
* *
38628305 GGTATTTCGATAATTTTACCCTTCGGG
1 GGTATTTCGATAATTTTACCCATCGAG
**
38628332 GGTATTTCGATAATTTTACCC-TTTAGG
1 GGTATTTCGATAATTTTACCCATCGA-G
* *
38628359 GGTATTT-TAGTAATTTTATCCATC-AG
1 GGTATTTCGA-TAATTTTACCCATCGAG
*
38628385 GGTATTTCTATAATTTTACCCATCGAG
1 GGTATTTCGATAATTTTACCCATCGAG
* *
38628412 GGTATTTTGGTAATTTTACCCATCGAG
1 GGTATTTCGATAATTTTACCCATCGAG
* *
38628439 GGTATTTCGTTCATTTTACCCATCGAG
1 GGTATTTCGATAATTTTACCCATCGAG
* ** * *
38628466 GCTATTTTAATAATTTTACCAATCAAG
1 GGTATTTCGATAATTTTACCCATCGAG
38628493 GGTATTTCGATAATTTTACCCATCGAG
1 GGTATTTCGATAATTTTACCCATCGAG
* * * *
38628520 GGTATTTCGGTCATTGTACCTATCGAG
1 GGTATTTCGATAATTTTACCCATCGAG
** *
38628547 GGTATTTC-AGTCTTTTTAGCCATCGAG
1 GGTATTTCGA-TAATTTTACCCATCGAG
38628574 GGTATTT
1 GGTATTT
38628581 TAGTAATTTT
Statistics
Matches: 209, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
26 23 0.11
27 185 0.89
28 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACCCATCGAG
Found at i:38628374 original size:54 final size:54
Alignment explanation
Indices: 38628315--38628591 Score: 326
Period size: 54 Copynumber: 5.1 Consensus size: 54
38628305 GGTATTTCGA
* * **
38628315 TAATTTTACCCTTCGGGGGTATTTCGATAATTTTACCC-TTTAGGGGTATTTTAG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGA-GGGTATTTTAG
* * *
38628369 TAATTTTATCCATC-AGGGTATTTCTATAATTTTACCCATCGAGGGTATTTTGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAG
* * * *
38628422 TAATTTTACCCATCGAGGGTATTTCGTTCATTTTACCCATCGAGGCTATTTTAA
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAG
* * **
38628476 TAATTTTACCAATCAAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAG
* * * ** *
38628530 TCATTGTACCTATCGAGGGTATTTC-AGTCTTTTTAGCCATCGAGGGTATTTTAG
1 TAATTTTACCCATCGAGGGTATTTCGA-TAATTTTACCCATCGAGGGTATTTTAG
38628584 TAATTTTA
1 TAATTTTA
38628592 GAGGCCCAAT
Statistics
Matches: 187, Mismatches: 33, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
53 45 0.24
54 142 0.76
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (54 bp):
TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAG
Found at i:38633535 original size:20 final size:20
Alignment explanation
Indices: 38633489--38633536 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
38633479 ATTTGAATGG
*
38633489 TCGATTCATTATGGTTTAAA
1 TCGATTCATTATGGATTAAA
* * * *
38633509 TCAATTCTTTTTGGATTAAC
1 TCGATTCATTATGGATTAAA
38633529 TCGATTCA
1 TCGATTCA
38633537 AAAACCCAAC
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (20 bp):
TCGATTCATTATGGATTAAA
Found at i:38634216 original size:44 final size:46
Alignment explanation
Indices: 38634167--38634259 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
38634157 TATAATATCT
*
38634167 ATTCCATTTAACCAAATACAA-T-AA-TACT-ATTACAGTTCTATTCC
1 ATTCCATTTAACC-AA-ACAATTGAATTACTGATTACAGCTCTATTCC
*
38634211 ATTCCATTTAATCAAACAATTGAATTACTGATTACAGCTCTATTCC
1 ATTCCATTTAACCAAACAATTGAATTACTGATTACAGCTCTATTCC
38634257 ATT
1 ATT
38634260 ACAACTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
42 4 0.09
43 3 0.07
44 14 0.33
45 4 0.09
46 18 0.42
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.38
Consensus pattern (46 bp):
ATTCCATTTAACCAAACAATTGAATTACTGATTACAGCTCTATTCC
Found at i:38634262 original size:16 final size:16
Alignment explanation
Indices: 38634241--38634292 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
38634231 TGAATTACTG
*
38634241 ATTACAGCTCTATTCC
1 ATTACAACTCTATTCC
* *
38634257 ATTACAACTTTATTCT
1 ATTACAACTCTATTCC
38634273 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
38634289 ATTA
1 ATTA
38634293 GAGTGAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:38638223 original size:39 final size:38
Alignment explanation
Indices: 38638174--38638251 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
38638164 TAAATATATT
* * *
38638174 TATATCGATGTAATTGAGATATATTATGAATATATAACA
1 TATATCGATGTAACTGAGATAAATCATGAAT-TATAACA
* *
38638213 TATATGGATGTAACTGAGATAAATCATGTATTATAACA
1 TATATCGATGTAACTGAGATAAATCATGAATTATAACA
38638251 T
1 T
38638252 TTAATTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 8 0.24
39 26 0.76
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.37
Consensus pattern (38 bp):
TATATCGATGTAACTGAGATAAATCATGAATTATAACA
Found at i:38639394 original size:3 final size:3
Alignment explanation
Indices: 38639335--38639382 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
38639325 NNNNNNNNNN
38639335 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38639383 AAAAGATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:38639953 original size:194 final size:194
Alignment explanation
Indices: 38639617--38640006 Score: 622
Period size: 194 Copynumber: 2.0 Consensus size: 194
38639607 TACCTAAGTT
* * * *
38639617 TTCATTCGTCCTAATTTGCTACCTGAGTTTGGCTTCAATGCTCACTTTGGTACCTAAACCAAATG
1 TTCATTCATCCTAATTTGCTACCTGAGTTTGACTTCAATACTCAATTTGGTACCTAAACCAAATG
38639682 GCATCATGTGGTCCAACGAGTATTTGATGTCTAATCTAGAAAAAAGAATATGAATACTTAATTGG
66 GCATCATGTGGTCCAACGAGTATTTGATGTCTAATCTAGAAAAAAGAATATGAATACTTAATTGG
*
38639747 GACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAACTTGGGTACTTGGGAAAAATA
131 GACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAAATTGGGTACTTGGGAAAAATA
* *
38639811 TTCATTCATCCTAATTTGCTACCTGAGTTTGATTTCAATATTCAATTTGGTACCTAAACCAAATG
1 TTCATTCATCCTAATTTGCTACCTGAGTTTGACTTCAATACTCAATTTGGTACCTAAACCAAATG
* * * *
38639876 GCATCATGTGGTCCAACGAGTCTTTGATGTCTAATCTAGTAAAAAA-ATTAT-AGATGCTTACTT
66 GCATCATGTGGTCCAACGAGTATTTGATGTCTAATCTAG-AAAAAAGAATATGA-ATACTTAATT
* * *
38639939 GGGACCATAACATTCTCGGATACTAAATAGAACATTGAAGTCAAAATTGGTTACTTGGTAAAAAT
129 GGGACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAAATTGGGTACTTGGGAAAAAT
38640004 A
194 A
38640005 TT
1 TT
38640007 AGTATCAAAT
Statistics
Matches: 180, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
193 1 0.01
194 173 0.96
195 6 0.03
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (194 bp):
TTCATTCATCCTAATTTGCTACCTGAGTTTGACTTCAATACTCAATTTGGTACCTAAACCAAATG
GCATCATGTGGTCCAACGAGTATTTGATGTCTAATCTAGAAAAAAGAATATGAATACTTAATTGG
GACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAAATTGGGTACTTGGGAAAAATA
Found at i:38640989 original size:18 final size:17
Alignment explanation
Indices: 38640966--38641010 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 17
38640956 TTATGTATTT
38640966 AATATTTAATTATTTTTA
1 AATA-TTAATTATTTTTA
38640984 AATATT-A-TATTTTTA
1 AATATTAATTATTTTTA
38640999 ACATATTAATTA
1 A-ATATTAATTA
38641011 ACATGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 9 0.38
16 6 0.25
17 3 0.12
18 6 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AATATTAATTATTTTTA
Found at i:38641950 original size:21 final size:22
Alignment explanation
Indices: 38641926--38641966 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38641916 ATATGAAGAA
38641926 AATT-AAAGAGTATTTTCAATC
1 AATTCAAAGAGTATTTTCAATC
*
38641947 AATTCAAAGAGTTTTTTCAA
1 AATTCAAAGAGTATTTTCAA
38641967 ACTCATGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
AATTCAAAGAGTATTTTCAATC
Found at i:38650682 original size:92 final size:92
Alignment explanation
Indices: 38650570--38651235 Score: 1071
Period size: 92 Copynumber: 7.2 Consensus size: 92
38650560 GTTTTATACA
* * * *
38650570 TTGCCGAACTAATTCGTATATAATTGTACATTACTGAAATTTATTTGTATATGGTTATATATTAT
1 TTGCCGAATTGATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
38650635 CGAAATTGATTTGTATATGAAGATAAG
66 CGAAATTGATTTGTATATGAAGATAAG
* *
38650662 TTGCCGAATTGATTCTTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATACATTAT
1 TTGCCGAATTGATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
*
38650727 CGAAATTGATATGTATATGAAGATAAG
66 CGAAATTGATTTGTATATGAAGATAAG
* *
38650754 TTGCCGAATTGATTCGTATATGATTATACATTGCTAAAATTTATTTGTATATGGTTATATATTAT
1 TTGCCGAATTGATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
* *
38650819 CAAAATTGATTTGTATATAAAGATAAG
66 CGAAATTGATTTGTATATGAAGATAAG
*
38650846 TTGCCGAATTGATTCGTAAATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
1 TTGCCGAATTGATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
*
38650911 CGAAATTGATTTGTATATAAAGATAAG
66 CGAAATTGATTTGTATATGAAGATAAG
* * * *
38650938 TTGCCGAATTAATTCGTATATAATTAAACATTGTTGAAATTCATTTGTATATGGTTATATATTAT
1 TTGCCGAATTGATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
*
38651003 CAAAATTGATTTGTATATGAAGATAAG
66 CGAAATTGATTTGTATATGAAGATAAG
* * * *
38651030 TTGCCAAATTGATTCATATATAATTATACATTGCTAAAATTTATTTGTATATGGTTATACATTAT
1 TTGCCGAATTGATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
38651095 CGAAATTGATTTGTATATGAAGATAAG
66 CGAAATTGATTTGTATATGAAGATAAG
** * *
38651122 TTGTTGAATTGATTCGTATATGATTATACATTGCTGAAATTTATTTGTATATGGTTATACATTAT
1 TTGCCGAATTGATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
38651187 CGAAATTGATTTGTATATGAAGATAAG
66 CGAAATTGATTTGTATATGAAGATAAG
**
38651214 TTTTCGAACTTGATTCGTATAT
1 TTGCCGAA-TTGATTCGTATAT
38651236 GACTATATAT
Statistics
Matches: 531, Mismatches: 42, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
92 518 0.98
93 13 0.02
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (92 bp):
TTGCCGAATTGATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATATATTAT
CGAAATTGATTTGTATATGAAGATAAG
Found at i:38651491 original size:41 final size:42
Alignment explanation
Indices: 38651389--38651505 Score: 128
Period size: 41 Copynumber: 2.8 Consensus size: 42
38651379 TGATTTTGTG
* *
38651389 TAAGACCATGTCTGGGACATTGGCATCGAAGTAAGAAAACGTG
1 TAAGACCATGTCTGGGACATTGGCATCGTA-TAAGAAAACGTA
* * * **
38651432 TAAGACTATGTCTGGGACATTGTCATCGTATATG-ATTCGTA
1 TAAGACCATGTCTGGGACATTGGCATCGTATAAGAAAACGTA
* *
38651473 TAAGACCATGTCTAGGACAGTGGCATCGATATA
1 TAAGACCATGTCTGGGACATTGGCATCG-TATA
38651506 CGTTAACATG
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 28 0.45
42 7 0.11
43 27 0.44
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATTGGCATCGTATAAGAAAACGTA
Found at i:38658931 original size:39 final size:39
Alignment explanation
Indices: 38658878--38658954 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
38658868 ACCATAAGTA
38658878 AAAAAAAAATACATCCATCATTTACCTCATTACTCAAAT
1 AAAAAAAAATACATCCATCATTTACCTCATTACTCAAAT
38658917 AAAAAAAAATACATCCATCATTTACCTCATTACTCAAA
1 AAAAAAAAATACATCCATCATTTACCTCATTACTCAAA
38658955 CCAAATTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.27
Consensus pattern (39 bp):
AAAAAAAAATACATCCATCATTTACCTCATTACTCAAAT
Found at i:38667497 original size:15 final size:15
Alignment explanation
Indices: 38667477--38667505 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38667467 TCTCTCATTC
38667477 ATTCTCTCTTTCATA
1 ATTCTCTCTTTCATA
38667492 ATTCTCTCTTTCAT
1 ATTCTCTCTTTCAT
38667506 TTCCCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTCTCTCTTTCATA
Found at i:38681094 original size:9 final size:9
Alignment explanation
Indices: 38681080--38681133 Score: 67
Period size: 9 Copynumber: 6.0 Consensus size: 9
38681070 TTCAAATAAA
38681080 AATTGAGAG
1 AATTGAGAG
38681089 AATTGAGA-
1 AATTGAGAG
*
38681097 AAGTTGAAAG
1 AA-TTGAGAG
38681107 AATTGAGA-
1 AATTGAGAG
38681115 AAGTTGAGAG
1 AA-TTGAGAG
38681125 AATTGAGAG
1 AATTGAGAG
38681134 TTTACAGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 4 0.10
9 31 0.79
10 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.22
Consensus pattern (9 bp):
AATTGAGAG
Found at i:38681108 original size:18 final size:18
Alignment explanation
Indices: 38681082--38681132 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
38681072 CAAATAAAAA
38681082 TTGAGAGAATTGAGAAAG
1 TTGAGAGAATTGAGAAAG
*
38681100 TTGAAAGAATTGAGAAAG
1 TTGAGAGAATTGAGAAAG
38681118 TTGAGAGAATTGAGA
1 TTGAGAGAATTGAGA
38681133 GTTTACAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (18 bp):
TTGAGAGAATTGAGAAAG
Found at i:38681145 original size:36 final size:35
Alignment explanation
Indices: 38681082--38681156 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
38681072 CAAATAAAAA
*
38681082 TTGAGAGAATTGAGAAAGTTGAAAGAATTGAGAAAG
1 TTGAGAGAATTGAG-AAGTTGAAAGAATAGAGAAAG
* *
38681118 TTGAGAGAATTGAG-AGTTTACAGAGAATAGAGAGAG
1 TTGAGAGAATTGAGAAGTTGA-A-AGAATAGAGAAAG
38681154 TTG
1 TTG
38681157 GATTTGAGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 5 0.15
35 1 0.03
36 28 0.82
ACGTcount: A:0.43, C:0.01, G:0.32, T:0.24
Consensus pattern (35 bp):
TTGAGAGAATTGAGAAGTTGAAAGAATAGAGAAAG
Found at i:38681893 original size:43 final size:43
Alignment explanation
Indices: 38681844--38681931 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
38681834 TATTAGCACG
* * *
38681844 ATCTTGCTCAAAGTGATAGATCATTTTATCAACAATCAAATTT
1 ATCTTGCTCAAAGTGATAAAACATTTTATCAACAATAAAATTT
* * *
38681887 ATCTTGCTCAAAGTGATAAAACCTTTTATCGACTATAAAATTT
1 ATCTTGCTCAAAGTGATAAAACATTTTATCAACAATAAAATTT
38681930 AT
1 AT
38681932 TCTCCATGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (43 bp):
ATCTTGCTCAAAGTGATAAAACATTTTATCAACAATAAAATTT
Found at i:38683182 original size:51 final size:49
Alignment explanation
Indices: 38683127--38683383 Score: 219
Period size: 51 Copynumber: 5.1 Consensus size: 49
38683117 TGTGTAGGTC
* *
38683127 ACTATGTGAAAGTGAAAGTGATGGTCACGTGTGTAGTACTATGTGTAGGCT
1 ACTATGTGAACG-GAAAGT-ATGGTCACGTGTGTAGTACTATGTGCAGGCT
* * * * * * *
38683178 ACTATGTGTACCGGAATGAAAGGTCGCATGTGTAGTACTATATGCAGGCT
1 ACTATGTG-AACGGAAAGTATGGTCACGTGTGTAGTACTATGTGCAGGCT
* * * * *
38683228 ACTATACGT-ACCGGATAGCTACGATCACGTGTGTAGTACTATGTGCAGGAT
1 ACTAT--GTGAACGGAAAG-TATGGTCACGTGTGTAGTACTATGTGCAGGCT
* * * * *
38683279 ACTACGTGTATCGGATATTAATGGTCACGTGTGTAGTACCATGTGCAGGCT
1 ACTATGTG-AACGGAAAGT-ATGGTCACGTGTGTAGTACTATGTGCAGGCT
* * * *
38683330 ACTACGTGAACCGGAAAGTTTGATCACGTGTGTAGTACTATGTGAAGGCT
1 ACTATGTGAA-CGGAAAGTATGGTCACGTGTGTAGTACTATGTGCAGGCT
38683380 ACTA
1 ACTA
38683384 CTTGTATCGA
Statistics
Matches: 166, Mismatches: 32, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
49 2 0.01
50 71 0.43
51 89 0.54
52 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (49 bp):
ACTATGTGAACGGAAAGTATGGTCACGTGTGTAGTACTATGTGCAGGCT
Found at i:38683390 original size:101 final size:100
Alignment explanation
Indices: 38683151--38683397 Score: 295
Period size: 101 Copynumber: 2.5 Consensus size: 100
38683141 AAAGTGATGG
* * *
38683151 TCACGTGTGTAGTACTATGTGTAGGCTACTA-TGTGTACCGGAATGAAAGGTCGCATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACT-TGTATCGGAATGAAAGGTCACATGTGTAGTA
* *
38683215 CTATATGCAGGCTACTATACGTACCGGATAGCTACGA
65 CCATATGCAGGCTAC-ATACGTACCGGAAAGCTACGA
* * * * * *
38683252 TCACGTGTGTAGTACTATGTGCAGGATACTACGTGTATCGGATATTAATGGTCACGTGTGTAGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACTTGTATCGGA-ATGAAAGGTCACATGTGTAGTA
* **
38683317 CCATGTGCAGGCTAC-TACGTGAACCGGAAAG-TTTGA
65 CCATATGCAGGCTACATACGT--ACCGGAAAGCTACGA
38683353 TCACGTGTGTAGTACTATGTGAAGGCTACTACTTGTATC-GAATGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACTTGTATCGGAATGA
38683398 TAATAGTTAA
Statistics
Matches: 125, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
99 3 0.02
100 7 0.06
101 76 0.61
102 39 0.31
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACTTGTATCGGAATGAAAGGTCACATGTGTAGTAC
CATATGCAGGCTACATACGTACCGGAAAGCTACGA
Found at i:38683424 original size:101 final size:101
Alignment explanation
Indices: 38683151--38683426 Score: 294
Period size: 101 Copynumber: 2.7 Consensus size: 101
38683141 AAAGTGATGG
* * *
38683151 TCACGTGTGTAGTACTATGTGTAGGCTACTA-TGTGTACCGGAATGA-AA-GGTCGCATGTGTAG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACT-TGTATC-GAATGATAATGGTCACATGTGTAG
* *
38683213 TACTATATGCAGGCTACTATACGTACCGGATAGCTACGA
64 TACTATGTGCAGGCTAC-ATACGTACCGGAAAGCTACGA
* * * * *
38683252 TCACGTGTGTAGTACTATGTGCAGGATACTACGTGTATCGGAT-ATTAATGGTCACGTGTGTAGT
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACTTGTATCGAATGA-TAATGGTCACATGTGTAGT
* **
38683316 ACCATGTGCAGGCTAC-TACGTGAACCGGAAAG-TTTGA
65 ACTATGTGCAGGCTACATACGT--ACCGGAAAGCTACGA
* * * * *
38683353 TCACGTGTGTAGTACTATGTGAAGGCTACTACTTGTATCGAATGATAATAGTTAAATGAGTGGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACTTGTATCGAATGATAATGGTCACATGTGTAGTA
38683418 CTATGTGCA
66 CTATGTGCA
38683427 AACTACCAAA
Statistics
Matches: 145, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
99 1 0.01
100 8 0.06
101 100 0.69
102 36 0.25
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACTTGTATCGAATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACATACGTACCGGAAAGCTACGA
Found at i:38689902 original size:46 final size:46
Alignment explanation
Indices: 38689835--38690050 Score: 362
Period size: 46 Copynumber: 4.7 Consensus size: 46
38689825 CTATAGCTCG
38689835 GTATGGTTTTCTTCACGGAAATACCATACCTACTATTCACAACTCA
1 GTATGGTTTTCTTCACGGAAATACCATACCTACTATTCACAACTCA
38689881 GTATGGTTTTCTTCACGGAAATACCATACCTACTATTCACAACTCA
1 GTATGGTTTTCTTCACGGAAATACCATACCTACTATTCACAACTCA
38689927 GTATGGTTTTCTTCACGGAAATACCATACCTACT-TGTCACAACTCA
1 GTATGGTTTTCTTCACGGAAATACCATACCTACTAT-TCACAACTCA
* * * * *
38689973 GTATGGTTTTCATCACTGAAACACCATACCTGCTTTTCACAACTCA
1 GTATGGTTTTCTTCACGGAAATACCATACCTACTATTCACAACTCA
*
38690019 GTATGGTTTTCTTCACTGAAATACCATACCTA
1 GTATGGTTTTCTTCACGGAAATACCATACCTA
38690051 AGTTTCACAC
Statistics
Matches: 161, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
45 1 0.01
46 159 0.99
47 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (46 bp):
GTATGGTTTTCTTCACGGAAATACCATACCTACTATTCACAACTCA
Found at i:38690856 original size:16 final size:17
Alignment explanation
Indices: 38690810--38690857 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
38690800 AAATTCTTTT
38690810 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
38690827 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
38690844 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
38690858 TTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:38692568 original size:17 final size:17
Alignment explanation
Indices: 38692537--38692569 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38692527 CTTAAAATGT
38692537 TTTAAAATATATGTTTG
1 TTTAAAATATATGTTTG
38692554 TTTATAAATAT-TGTTT
1 TTTA-AAATATATGTTT
38692570 TACAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (17 bp):
TTTAAAATATATGTTTG
Found at i:38694204 original size:20 final size:20
Alignment explanation
Indices: 38694147--38694204 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
38694137 GATATAAATA
38694147 TTAA-AATATTATTAA-TTAT
1 TTAATAATATT-TTAATTTAT
38694166 TTAAT--TATTTTATATTTTAT
1 TTAATAATATTTTA-A-TTTAT
38694186 TTAATAATATTTTAATTTA
1 TTAATAATATTTTAATTTA
38694205 GTTTGTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
17 3 0.09
18 5 0.15
19 4 0.12
20 13 0.39
21 1 0.03
22 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATAATATTTTAATTTAT
Found at i:38694750 original size:20 final size:20
Alignment explanation
Indices: 38694693--38694750 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
38694683 GATATAAATA
38694693 TTAA-AATATTATTAA-TTAT
1 TTAATAATATT-TTAATTTAT
38694712 TTAAT--TATTTTATATTTTAT
1 TTAATAATATTTTA-A-TTTAT
38694732 TTAATAATATTTTAATTTA
1 TTAATAATATTTTAATTTA
38694751 GTTTGTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
17 3 0.09
18 5 0.15
19 4 0.12
20 13 0.39
21 1 0.03
22 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATAATATTTTAATTTAT
Found at i:38695055 original size:546 final size:546
Alignment explanation
Indices: 38694023--38695115 Score: 2186
Period size: 546 Copynumber: 2.0 Consensus size: 546
38694013 GTCTACTTCT
38694023 ATCCATAAACCCTCTTTAACCCTTAAATCGAGGGAAAGTATGGCTCAAACCCACATCCTCCGAGT
1 ATCCATAAACCCTCTTTAACCCTTAAATCGAGGGAAAGTATGGCTCAAACCCACATCCTCCGAGT
38694088 TGTTCCAATAGCAGCGATGCCAACTAAAATACTAAGGCTCAATCGAATAGATATAAATATTAAAA
66 TGTTCCAATAGCAGCGATGCCAACTAAAATACTAAGGCTCAATCGAATAGATATAAATATTAAAA
38694153 TATTATTAATTATTTAATTATTTTATATTTTATTTAATAATATTTTAATTTAGTTTGTTAATTTT
131 TATTATTAATTATTTAATTATTTTATATTTTATTTAATAATATTTTAATTTAGTTTGTTAATTTT
38694218 TAAAGTTTTTATATATACATGGACTATTATAATGTCGTATAAAATTTAAAAATTAGTTTTTAATT
196 TAAAGTTTTTATATATACATGGACTATTATAATGTCGTATAAAATTTAAAAATTAGTTTTTAATT
38694283 TATTTTAATTATTAAAAATATTTTTATTTTTATGGTTTTTTAATAATTTAGTAAACTATTTGGTA
261 TATTTTAATTATTAAAAATATTTTTATTTTTATGGTTTTTTAATAATTTAGTAAACTATTTGGTA
38694348 AATTGAGAAATTTTAATTGAATATTATGTTATTACGATTTTATTGTTAAATAGAACAATTGTGTT
326 AATTGAGAAATTTTAATTGAATATTATGTTATTACGATTTTATTGTTAAATAGAACAATTGTGTT
38694413 TTGATTTAATCACAAAATTATTTTATTTATTTAAAATATTTTAAATCATTTCAAAACTAATGTTT
391 TTGATTTAATCACAAAATTATTTTATTTATTTAAAATATTTTAAATCATTTCAAAACTAATGTTT
38694478 AATTTTTAATAATTTCTTAATATATATAACTTTACAAAAAGTGCTCTAAACTATAATTTAGAATA
456 AATTTTTAATAATTTCTTAATATATATAACTTTACAAAAAGTGCTCTAAACTATAATTTAGAATA
38694543 TTTATATTTGAAACGTTTTTTTTTCA
521 TTTATATTTGAAACGTTTTTTTTTCA
38694569 ATCCATAAACCCTCTTTAACCCTTAAATCGAGGGAAAGTATGGCTCAAACCCACATCCTCCGAGT
1 ATCCATAAACCCTCTTTAACCCTTAAATCGAGGGAAAGTATGGCTCAAACCCACATCCTCCGAGT
38694634 TGTTCCAATAGCAGCGATGCCAACTAAAATACTAAGGCTCAATCGAATAGATATAAATATTAAAA
66 TGTTCCAATAGCAGCGATGCCAACTAAAATACTAAGGCTCAATCGAATAGATATAAATATTAAAA
38694699 TATTATTAATTATTTAATTATTTTATATTTTATTTAATAATATTTTAATTTAGTTTGTTAATTTT
131 TATTATTAATTATTTAATTATTTTATATTTTATTTAATAATATTTTAATTTAGTTTGTTAATTTT
38694764 TAAAGTTTTTATATATACATGGACTATTATAATGTCGTATAAAATTTAAAAATTAGTTTTTAATT
196 TAAAGTTTTTATATATACATGGACTATTATAATGTCGTATAAAATTTAAAAATTAGTTTTTAATT
38694829 TATTTTAATTATTAAAAATATTTTTATTTTTATGGTTTTTTAATAATTTAGTAAACTATTTGGTA
261 TATTTTAATTATTAAAAATATTTTTATTTTTATGGTTTTTTAATAATTTAGTAAACTATTTGGTA
38694894 AATTGAGAAATTTTAATTGAATATTATGTTATTACGATTTTATTGTTAAATAGAACAATTGTGTT
326 AATTGAGAAATTTTAATTGAATATTATGTTATTACGATTTTATTGTTAAATAGAACAATTGTGTT
38694959 TTGATTTAATCACAAAATTATTTTATTTATTTAAAATATTTTAAATCATTTCAAAACTAATGTTT
391 TTGATTTAATCACAAAATTATTTTATTTATTTAAAATATTTTAAATCATTTCAAAACTAATGTTT
38695024 AATTTTTAATAATTTCTTAATATATATAACTTTACAAAAAGTGCTCTAAACTATAATTTAGAATA
456 AATTTTTAATAATTTCTTAATATATATAACTTTACAAAAAGTGCTCTAAACTATAATTTAGAATA
38695089 TTTATATTTGAAACGTTTTTTTTTCA
521 TTTATATTTGAAACGTTTTTTTTTCA
38695115 A
1 A
38695116 AATATATTTT
Statistics
Matches: 547, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
546 547 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (546 bp):
ATCCATAAACCCTCTTTAACCCTTAAATCGAGGGAAAGTATGGCTCAAACCCACATCCTCCGAGT
TGTTCCAATAGCAGCGATGCCAACTAAAATACTAAGGCTCAATCGAATAGATATAAATATTAAAA
TATTATTAATTATTTAATTATTTTATATTTTATTTAATAATATTTTAATTTAGTTTGTTAATTTT
TAAAGTTTTTATATATACATGGACTATTATAATGTCGTATAAAATTTAAAAATTAGTTTTTAATT
TATTTTAATTATTAAAAATATTTTTATTTTTATGGTTTTTTAATAATTTAGTAAACTATTTGGTA
AATTGAGAAATTTTAATTGAATATTATGTTATTACGATTTTATTGTTAAATAGAACAATTGTGTT
TTGATTTAATCACAAAATTATTTTATTTATTTAAAATATTTTAAATCATTTCAAAACTAATGTTT
AATTTTTAATAATTTCTTAATATATATAACTTTACAAAAAGTGCTCTAAACTATAATTTAGAATA
TTTATATTTGAAACGTTTTTTTTTCA
Found at i:38720282 original size:3 final size:3
Alignment explanation
Indices: 38720274--38720335 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
38720264 GTCAATTCCT
38720274 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38720322 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
38720336 TGGTAAAAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:38728507 original size:29 final size:29
Alignment explanation
Indices: 38728472--38728589 Score: 88
Period size: 29 Copynumber: 4.2 Consensus size: 29
38728462 TTAAATAATA
38728472 AAAATATTTTAATTATAAATTTAATTATC
1 AAAATATTTTAATTATAAATTTAATTATC
* * * **
38728501 AAAATATGTAAAATACCAA--TAA--A--
1 AAAATATTTTAATTATAAATTTAATTATC
* * * *
38728524 AATATATTTTTAATCT-TCAATTTAAATATA
1 AAAATA-TTTTAAT-TATAAATTTAATTATC
38728554 AAAATATTTTAATTATAAATTTAATTATC
1 AAAATATTTTAATTATAAATTTAATTATC
38728583 AAAATAT
1 AAAATAT
38728590 GTAAAATACC
Statistics
Matches: 66, Mismatches: 14, Indels: 18
0.67 0.14 0.18
Matches are distributed among these distances:
23 5 0.08
24 7 0.11
25 2 0.03
26 3 0.05
27 3 0.05
28 2 0.03
29 39 0.59
30 5 0.08
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (29 bp):
AAAATATTTTAATTATAAATTTAATTATC
Found at i:38728563 original size:82 final size:83
Alignment explanation
Indices: 38728456--38728622 Score: 327
Period size: 82 Copynumber: 2.0 Consensus size: 83
38728446 GTAATCTAAA
38728456 TTCAATTTAAATAATAAAAATATTTTAATTATAAATTTAATTATCAAAATATGTAAAATACCAAT
1 TTCAATTTAAATAATAAAAATATTTTAATTATAAATTTAATTATCAAAATATGTAAAATACCAAT
38728521 AAAAATATATTTTTAATC
66 AAAAATATATTTTTAATC
38728539 TTCAATTTAAAT-ATAAAAATATTTTAATTATAAATTTAATTATCAAAATATGTAAAATACCAAT
1 TTCAATTTAAATAATAAAAATATTTTAATTATAAATTTAATTATCAAAATATGTAAAATACCAAT
38728603 AAAAATATATTTTTAATC
66 AAAAATATATTTTTAATC
38728621 TT
1 TT
38728623 TTATTAATTT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 72 0.86
83 12 0.14
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (83 bp):
TTCAATTTAAATAATAAAAATATTTTAATTATAAATTTAATTATCAAAATATGTAAAATACCAAT
AAAAATATATTTTTAATC
Found at i:38728618 original size:41 final size:41
Alignment explanation
Indices: 38728491--38728619 Score: 124
Period size: 41 Copynumber: 3.1 Consensus size: 41
38728481 TAATTATAAA
38728491 TTTAATTATCAAAATATGTAAAATACCAATAAAAATATATT
1 TTTAATTATCAAAATATGTAAAATACCAATAAAAATATATT
** * * **
38728532 TTTAATCT-TC--AAT-T-TAAATATAAAAATATTTTAATTATAAA
1 TTTAAT-TATCAAAATATGTAAA-ATACCAATA---AAAATATATT
38728573 TTTAATTATCAAAATATGTAAAATACCAATAAAAATATATT
1 TTTAATTATCAAAATATGTAAAATACCAATAAAAATATATT
38728614 TTTAAT
1 TTTAAT
38728620 CTTTTATTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
37 4 0.06
38 8 0.12
39 3 0.05
40 1 0.02
41 34 0.52
42 1 0.02
43 3 0.05
44 8 0.12
45 4 0.06
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (41 bp):
TTTAATTATCAAAATATGTAAAATACCAATAAAAATATATT
Found at i:38730819 original size:4 final size:4
Alignment explanation
Indices: 38730810--38730835 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
38730800 ATTTTTCCCT
38730810 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
38730836 CATCATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:38730903 original size:14 final size:14
Alignment explanation
Indices: 38730886--38730921 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38730876 TTTTTTTATA
38730886 TTTTATATTTTAGT
1 TTTTATATTTTAGT
38730900 TTTTAGT-TTTTAGT
1 TTTTA-TATTTTAGT
38730914 TTTTATAT
1 TTTTATAT
38730922 ATATGTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.05
14 18 0.90
15 1 0.05
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (14 bp):
TTTTATATTTTAGT
Found at i:38730909 original size:6 final size:7
Alignment explanation
Indices: 38730893--38730918 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38730883 ATATTTTATA
38730893 TTTTAGT
1 TTTTAGT
38730900 TTTTAGT
1 TTTTAGT
38730907 TTTTAGT
1 TTTTAGT
38730914 TTTTA
1 TTTTA
38730919 TATATATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (7 bp):
TTTTAGT
Found at i:38730952 original size:18 final size:18
Alignment explanation
Indices: 38730931--38731005 Score: 72
Period size: 18 Copynumber: 4.3 Consensus size: 18
38730921 TATATGTATA
38730931 TGTATATATTTATCTTAT
1 TGTATATATTTATCTTAT
38730949 TGTATCAT-TTTAT-TT-T
1 TGTAT-ATATTTATCTTAT
38730965 T-TAT-TATTTA-CTTGTAT
1 TGTATATATTTATC-T-TAT
38730982 ATGTATATATTTATCTTAT
1 -TGTATATATTTATCTTAT
38731001 TGTAT
1 TGTAT
38731006 CATTTTATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 20
0.70 0.00 0.30
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 4 0.09
16 3 0.06
17 3 0.06
18 16 0.34
19 8 0.17
20 7 0.15
21 1 0.02
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.63
Consensus pattern (18 bp):
TGTATATATTTATCTTAT
Found at i:38730983 original size:52 final size:52
Alignment explanation
Indices: 38730925--38731029 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
38730915 TTTATATATA
*
38730925 TGTATATGTATATATTTATCTTATTGTATCATTTTATTTTTTATTATTTACT
1 TGTATATGTATATATTTATCTTATTGTATCATTTTATTATTTATTATTTACT
38730977 TGTATATGTATATATTTATCTTATTGTATCATTTTATTATTTATTATTTACT
1 TGTATATGTATATATTTATCTTATTGTATCATTTTATTATTTATTATTTACT
38731029 T
1 T
38731030 CTTGCTTTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (52 bp):
TGTATATGTATATATTTATCTTATTGTATCATTTTATTATTTATTATTTACT
Found at i:38731012 original size:18 final size:18
Alignment explanation
Indices: 38730939--38731013 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
38730929 TATGTATATA
38730939 TTTATCTTATTGTATCAT
1 TTTATCTTATTGTATCAT
*
38730957 TTTAT-TT-TT-TATTA-
1 TTTATCTTATTGTATCAT
38730971 TTTA-CTTGTATATGTAT-AT
1 TTTATC-T-TAT-TGTATCAT
38730990 ATTTATCTTATTGTATCAT
1 -TTTATCTTATTGTATCAT
38731009 TTTAT
1 TTTAT
38731014 TATTTATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 20
0.69 0.01 0.30
Matches are distributed among these distances:
14 4 0.09
15 5 0.11
16 3 0.07
17 3 0.07
18 17 0.37
19 8 0.17
20 5 0.11
21 1 0.02
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTATCTTATTGTATCAT
Found at i:38731067 original size:3 final size:3
Alignment explanation
Indices: 38731059--38731227 Score: 79
Period size: 3 Copynumber: 53.7 Consensus size: 3
38731049 ATATTTTCAA
* * * *
38731059 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TC GTT ACT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * ** * *
38731106 GTT ATT ACT ATT ACT ATT TTT ACT ACC ATT ATT ATT ATT AAT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
38731154 CTT ATTT ATTT ATTT ACT ACT ATT ATT CGGTT ATT AATGT ATG ATT ATTT
1 ATT A-TT A-TT A-TT ATT ATT ATT ATT --ATT ATT -AT-T ATT ATT A-TT
*
38731204 ATT ATT ATT CTT AGTT ATT ATT AT
1 ATT ATT ATT ATT A-TT ATT ATT AT
38731228 GATCACTATG
Statistics
Matches: 125, Mismatches: 33, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
2 1 0.01
3 100 0.80
4 21 0.17
5 3 0.02
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:38732072 original size:107 final size:106
Alignment explanation
Indices: 38731810--38732126 Score: 404
Period size: 107 Copynumber: 3.0 Consensus size: 106
38731800 CCATACTTTG
* * * * * * * *
38731810 AAGTTTTAAGAGGGTATTTAGCTATTTAGTCGAATGAGAAATCAAAACCCAGCATGTTAGGGCAT
1 AAGTTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* * * * *
38731875 GTTTTCTCGAATTTTCAAACGCAAAATATTGCCTCACTTTGA
66 GTTTCCTCG-ATTTTCAAACGCGAAATATTGCCTTATTTTAA
* * * * *
38731917 AA-TTTTAAAAGGATATTTGGCTATTTGGTCAAACAATG-AGTCGAAACCCAACACGTTAAGGCA
1 AAGTTTTAAAAGGATATTTGGCTATTTGGTCGAACGA-GAAATCGAAACCCAGCACGTTAGGGCA
38731980 CGTTTCCTCGATTTTCTAAACGCGAAATATTGCCTTATTTTAA
65 CGTTTCCTCGATTTTC-AAACGCGAAATATTGCCTTATTTTAA
* *
38732023 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCTGCACGTTAGGGCAC
1 AAGTTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
38732088 GTTTCCTCGATTTTCCAAACGCGAAATATTGCCTTATTT
66 GTTTCCTCGATTTT-CAAACGCGAAATATTGCCTTATTT
38732127 AGAAAAAACC
Statistics
Matches: 180, Mismatches: 25, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
105 6 0.03
106 80 0.44
107 93 0.52
108 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (106 bp):
AAGTTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
GTTTCCTCGATTTTCAAACGCGAAATATTGCCTTATTTTAA
Found at i:38732455 original size:18 final size:18
Alignment explanation
Indices: 38732429--38732498 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
38732419 ATATAAATCG
38732429 TAAAGTATAAAAATGTATA
1 TAAA-TATAAAAATGTATA
* *
38732448 TAAATATAAATATATATA
1 TAAATATAAAAATGTATA
* * *
38732466 TTAA-ATAAAAATCTGTA
1 TAAATATAAAAATGTATA
* *
38732483 AAAAAATAAAAATGTA
1 TAAATATAAAAATGTA
38732499 AGTATGTTCA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
17 12 0.30
18 24 0.60
19 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (18 bp):
TAAATATAAAAATGTATA
Found at i:38734350 original size:44 final size:44
Alignment explanation
Indices: 38734301--38734980 Score: 652
Period size: 44 Copynumber: 15.6 Consensus size: 44
38734291 TCCACTTCCT
*
38734301 ACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
38734345 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
38734390 ACCAATATGGGAAGACAAGATCTGC-ATCTTCGACCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
38734432 TACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAT
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
38734477 GCCAATACATGAAGACAAGATTTGCTATCTTCGATCTACTTCAT
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
38734521 GCCATTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* *
38734566 ACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
38734608 TACCCATATAGGAAGATAGGACCTGCTATATTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
38734653 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
38734698 ACCAATATGGGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
38734743 ACCAATATGGGAAGACAAGATCTGCT-TC-T--A-CTTC-GC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
38734780 ACCAGTATGGGAAGACAAAATC-ACTATCTTTGATCTACTTCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
38734823 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
*
38734868 ACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCTACTTTGC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTAC-TT-CAC
* *
38734912 ACCAATATGGGAAGACGAGATCTGC-ATCTTCGATCTACTTCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
38734955 GCCAATACATGAAGACAAGATCTGCT
1 ACCAATATAGGAAGACAAGATCTGCT
38734981 TTAATGACTT
Statistics
Matches: 526, Mismatches: 88, Indels: 44
0.80 0.13 0.07
Matches are distributed among these distances:
36 2 0.00
37 23 0.04
38 1 0.00
39 1 0.00
40 4 0.01
41 4 0.01
42 4 0.01
43 82 0.16
44 269 0.51
45 135 0.26
46 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
Found at i:38734606 original size:176 final size:176
Alignment explanation
Indices: 38734302--38734952 Score: 889
Period size: 176 Copynumber: 3.7 Consensus size: 176
38734292 CCACTTCCTA
* * *
38734302 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCA--ATACAT-GAAGACAAG
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTT--CGCCACCA-ACATGGAAGACAAG
*
38734364 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGACCCACT
63 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACT
*
38734429 TCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCATG
128 TCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
* **
38734478 CCAATACATGAAGACAAGATTTGCTATCTTCGATCTACTTCATGCCA-TTACAT-GAAGACAAGA
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC--GCCACCAACATGGAAGACAAGA
38734541 TCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTT
64 TCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTT
* *
38734606 CCTACCCATATAGGAAGATAGGACCTGCTATATTCGATCTACTTCACG
129 CCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
* *
38734654 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAACAT-GGAAGACAAGAT
38734719 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG---CTTC--T--ACTTC
65 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC
* * * * ** * * *
38734777 GCCACCAGTATGGGAAGACAAAATC-ACTATCTTTGATCTACTTCACG
130 -CTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
* *
38734824 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAACAT-GGAAGACAAGAT
* * * *
38734889 CTGC-ATCTTCGATCTACTTTGCCACCAATATGGGAAGACGAGATCTGCATCTTCGATCTACTTC
65 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC
38734953 ACGCCAATAC
Statistics
Matches: 433, Mismatches: 28, Indels: 28
0.89 0.06 0.06
Matches are distributed among these distances:
169 40 0.09
170 93 0.21
171 16 0.04
172 5 0.01
174 10 0.02
175 3 0.01
176 207 0.48
177 59 0.14
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (176 bp):
CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAACATGGAAGACAAGATC
TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCC
TACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
Found at i:38734858 original size:214 final size:212
Alignment explanation
Indices: 38734372--38734981 Score: 552
Period size: 214 Copynumber: 2.8 Consensus size: 212
38734362 AGATCTGCTT
* * * ** * * * *
38734372 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGACCCACTTC--CTA
1 TCTTCGATCCACTTC-CTACCCATACAGGAAGACAAGACCTGCTATATTCGATCTACTTCGAC-A
* * * * *** ***
38734434 CCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTC-ATGCCAATACATGAAGACAAGAT
64 CCAATACAGGAAGACAAGATCTGC-ATCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGAT
* ** * *
38734498 TTGCTATCTTCGATCTACTTCATGCCATTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC
128 CTGC-ATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTG----C-T---TCTACTTC
* *
38734563 GCCACCAATATGGGAAGACAAGATCTGCA
184 GCCACCAATATGGGAAGACAAAATCTACA
* * * *
38734592 TCTTCGATCCACTTCCTACCCATATAGGAAGATAGGACCTGCTATATTCGATCTACTTC-ACGCC
1 TCTTCGATCCACTTCCTACCCATACAGGAAGACAAGACCTGCTATATTCGATCTACTTCGACACC
* *
38734656 AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
66 AATACAGGAAGACAAGATCTGC-ATCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
* * ** *
38734721 GCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTTCTACTTCGCCACCAGT
130 GC-ATCTTCGATCTACTTC-ACACCAATACAGGAAGACAAGATCTGCTTCTACTTCGCCACCAAT
38734786 ATGGGAAGACAAAATC-ACTA
193 ATGGGAAGACAAAATCTAC-A
* * * * * * *
38734806 TCTTTGATCTACTT-C-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
1 TCTTCGATCCACTTCCTAC-CC-ATACAGGAAGACAAGACCTGCTATATTCGATCTACTTCGACA
** * *
38734869 CCAATATGGGAAGACAAGATCTGCATCTTCGATCTACTTTGCCACCAATATGGGAAGACGAGATC
64 CCAATACAGGAAGACAAGATCTGCATCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATC
* *
38734934 TGCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
129 TGCATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTT
38734982 TAATGACTTC
Statistics
Matches: 324, Mismatches: 58, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
212 26 0.08
213 19 0.06
214 116 0.36
215 22 0.07
217 1 0.00
218 1 0.00
219 21 0.06
220 62 0.19
221 37 0.11
222 19 0.06
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (212 bp):
TCTTCGATCCACTTCCTACCCATACAGGAAGACAAGACCTGCTATATTCGATCTACTTCGACACC
AATACAGGAAGACAAGATCTGCATCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG
CATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTTCTACTTCGCCACCAATATG
GGAAGACAAAATCTACA
Found at i:38735945 original size:11 final size:11
Alignment explanation
Indices: 38735931--38735969 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
38735921 CCCTCTCCTT
*
38735931 TTTTTATTTCC
1 TTTTTATTTTC
38735942 TTTTTTATTTTC
1 -TTTTTATTTTC
38735954 TTTTTATTTTC
1 TTTTTATTTTC
38735965 TTTTT
1 TTTTT
38735970 TCCTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATTTTC
Found at i:38735947 original size:12 final size:12
Alignment explanation
Indices: 38735930--38735970 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
38735920 GCCCTCTCCT
*
38735930 TTTTTTATTTCC
1 TTTTTTATTTTC
38735942 TTTTTTATTTTC
1 TTTTTTATTTTC
38735954 -TTTTTATTTTC
1 TTTTTTATTTTC
38735965 TTTTTT
1 TTTTTT
38735971 CCTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTATTTTC
Found at i:38735980 original size:23 final size:22
Alignment explanation
Indices: 38735929--38735981 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
38735919 TGCCCTCTCC
38735929 TTTTTTTATTTCCTTTTTTATT
1 TTTTTTTATTTCCTTTTTTATT
* **
38735951 TTCTTTTTATTTTCTTTTTTCCT
1 TT-TTTTTATTTCCTTTTTTATT
38735974 TTTTTTTA
1 TTTTTTTA
38735982 GGCAAAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTTATTTCCTTTTTTATT
Found at i:38739876 original size:11 final size:11
Alignment explanation
Indices: 38739856--38739890 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
38739846 GGGGAAAGGT
38739856 CATT-GGTTCC
1 CATTCGGTTCC
38739866 CATTCGGTTCC
1 CATTCGGTTCC
*
38739877 CATTCGGTTTC
1 CATTCGGTTCC
38739888 CAT
1 CAT
38739891 CCCGCTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.11, C:0.31, G:0.17, T:0.40
Consensus pattern (11 bp):
CATTCGGTTCC
Found at i:38747199 original size:106 final size:106
Alignment explanation
Indices: 38747013--38747330 Score: 420
Period size: 106 Copynumber: 3.0 Consensus size: 106
38747003 GGGAAACCAT
* * * * * *
38747013 ACTTTGAAGTTTTAAGAGGGTATTTAGCTATTTAGTCGAACGAGAAATCAAAACCCAGCACGTTA
1 ACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTA
* * * * *
38747078 GGGCATGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTC
66 GGGCACGTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTC
* * * * * *
38747119 ACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACAAGGAGTCGGAACCCAACACGTTA
1 ACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTA
* *
38747184 AGGCACGTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTT
66 GGGCACGTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTC
* * * *
38747225 ATTTTAAAAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCTGCACGTT
1 ACTTTGAAA-TTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTT
38747290 AGGGCACGTTTCCTCGATTTTCCAAGCGCGAAATATTGCCT
65 AGGGCACGTTTCCTCGATTTTCCAAGCGCGAAATATTGCCT
38747331 TATTTAGAAA
Statistics
Matches: 181, Mismatches: 30, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
106 94 0.52
107 87 0.48
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (106 bp):
ACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTA
GGGCACGTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTC
Found at i:38747289 original size:107 final size:107
Alignment explanation
Indices: 38747019--38747335 Score: 429
Period size: 107 Copynumber: 3.0 Consensus size: 107
38747009 CCATACTTTG
* * * * * *
38747019 AAGTTTTAAGAGGGTATTTAGCTATTTAGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCAT
1 AAGTTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* * * * * * *
38747084 GTTTTCTCGAATTTCCAAACGCAAAATATTGCCTCACTTTGA
66 GTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTTATTTTAA
* * * * * * *
38747126 AA-TTTTAAAAGGATATTTGGCTATTTGGTCAAACAAGGAGTCGGAACCCAACACGTTAAGGCAC
1 AAGTTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
38747190 GTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTTATTTTAA
66 GTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTTATTTTAA
* *
38747232 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCTGCACGTTAGGGCAC
1 AAGTTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
38747297 GTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTTATTT
66 GTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTTATTT
38747336 AGAAAAAACC
Statistics
Matches: 180, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
106 86 0.48
107 94 0.52
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (107 bp):
AAGTTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
GTTTCCTCGATTTTCCAAGCGCGAAATATTGCCTTATTTTAA
Found at i:38747664 original size:18 final size:18
Alignment explanation
Indices: 38747638--38747707 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
38747628 ATATAAATCG
38747638 TAAAGTATAAAAATGTATA
1 TAAA-TATAAAAATGTATA
* *
38747657 TAAATATAAATATATATA
1 TAAATATAAAAATGTATA
38747675 TTAAATA-AAAATATGTA-A
1 -TAAATATAAAA-ATGTATA
*
38747693 -AAAAATAAAAATGTA
1 TAAATATAAAAATGTA
38747708 AGTATGTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 9 0.21
17 4 0.09
18 16 0.37
19 14 0.33
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
TAAATATAAAAATGTATA
Found at i:38747679 original size:19 final size:18
Alignment explanation
Indices: 38747638--38747688 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
38747628 ATATAAATCG
* *
38747638 TAAAGTATAAAAATGTATA
1 TAAA-TATAAATATATATA
38747657 TAAATATAAATATATATA
1 TAAATATAAATATATATA
*
38747675 TTAAATAAAAATAT
1 -TAAATATAAATAT
38747689 GTAAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
TAAATATAAATATATATA
Found at i:38750466 original size:17 final size:17
Alignment explanation
Indices: 38750444--38750483 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
38750434 AAAATTTAGC
*
38750444 TTTGAACCTTTTTAAAA
1 TTTGAACCTTTTAAAAA
38750461 TTTGAACCTTTTAAAAA
1 TTTGAACCTTTTAAAAA
38750478 TTTGAA
1 TTTGAA
38750484 TTTACATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (17 bp):
TTTGAACCTTTTAAAAA
Found at i:38753257 original size:5 final size:5
Alignment explanation
Indices: 38753247--38753280 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
38753237 NNNNNNNNNN
38753247 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
38753281 AAACCAAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:38753483 original size:23 final size:22
Alignment explanation
Indices: 38753445--38753498 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
38753435 AGGAGTAAAG
* *
38753445 AAATAATTAAATGAATGAATAT
1 AAATAATAAAATGAATGAAAAT
38753467 AAATAAATAAAATGAATGAAAAT
1 AAAT-AATAAAATGAATGAAAAT
38753490 AAAATAATA
1 -AAATAATA
38753499 TCATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 20 0.71
24 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
AAATAATAAAATGAATGAAAAT
Found at i:38754513 original size:22 final size:23
Alignment explanation
Indices: 38754481--38754526 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
38754471 TTCTTTTTTT
*
38754481 TGCTATTGTTTGCT-TAC-ATTTC
1 TGCTATCGTTT-CTCTACTATTTC
38754503 TGCTATCGTTTCTCTACTATTTC
1 TGCTATCGTTTCTCTACTATTTC
38754526 T
1 T
38754527 TTGTTGCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 13 0.62
23 6 0.29
ACGTcount: A:0.13, C:0.22, G:0.11, T:0.54
Consensus pattern (23 bp):
TGCTATCGTTTCTCTACTATTTC
Found at i:38758282 original size:3 final size:3
Alignment explanation
Indices: 38758274--38758315 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
38758264 TTCTTGAACT
* * *
38758274 TTA TTA TTA TTA TCA TTA TTA TTA TTA GTA ATA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38758316 GGTTTCCATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:38759911 original size:5 final size:5
Alignment explanation
Indices: 38759901--38759926 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38759891 TGAGCATTCG
38759901 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
38759927 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:38772405 original size:65 final size:65
Alignment explanation
Indices: 38772325--38772507 Score: 330
Period size: 65 Copynumber: 2.8 Consensus size: 65
38772315 AATAAAACAA
* * *
38772325 ATATAAAATTGAGGTATTTAAAAAATAAAAGAATAATAAATAAATAGATAAAACAAATGCAAATC
1 ATATTAAATTTAGGTATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAACAAATGCAAATC
38772390 ATATTAAATTTAGGTATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAACAAATGCAAATC
1 ATATTAAATTTAGGTATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAACAAATGCAAATC
*
38772455 ATATTAAATTTAGGTATTTAAAAAGTAAAAGAATAATAAATAAATAAATAAAA
1 ATATTAAATTTAGGTATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAA
38772508 TATAAAATTG
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 114 1.00
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (65 bp):
ATATTAAATTTAGGTATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAACAAATGCAAATC
Found at i:38772412 original size:35 final size:35
Alignment explanation
Indices: 38772373--38772477 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 35
38772363 AATAAATAGA
38772373 TAAAACAAATGCAAATCATATTAAATTTAGGTATT
1 TAAAACAAATGCAAATCATATTAAATTTAGGTATT
* * ** * ** **
38772408 T-AAA-AAGT-AAAAGAATAATAAA--TAAATAGA
1 TAAAACAAATGCAAATCATATTAAATTTAGGTATT
38772438 TAAAACAAATGCAAATCATATTAAATTTAGGTATT
1 TAAAACAAATGCAAATCATATTAAATTTAGGTATT
38772473 TAAAA
1 TAAAA
38772478 AGTAAAAGAA
Statistics
Matches: 47, Mismatches: 18, Indels: 10
0.63 0.24 0.13
Matches are distributed among these distances:
30 5 0.11
31 3 0.06
32 13 0.28
33 13 0.28
34 3 0.06
35 10 0.21
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.30
Consensus pattern (35 bp):
TAAAACAAATGCAAATCATATTAAATTTAGGTATT
Found at i:38772430 original size:32 final size:32
Alignment explanation
Indices: 38772394--38772495 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 32
38772384 CAAATCATAT
38772394 TAAATTTAGGTATTTAAAAAGTAAAAGAATAA
1 TAAATTTAGGTATTTAAAAAGTAAAAGAATAA
* * * * ** *
38772426 TAAATAAATA-G-A-TAAAACAAATGCAAATCATAT
1 TAAAT--TTAGGTATTTAAA-AAGT-AAAAGAATAA
38772459 TAAATTTAGGTATTTAAAAAGTAAAAGAATAA
1 TAAATTTAGGTATTTAAAAAGTAAAAGAATAA
38772491 TAAAT
1 TAAAT
38772496 AAATAAATAA
Statistics
Matches: 49, Mismatches: 14, Indels: 14
0.64 0.18 0.18
Matches are distributed among these distances:
31 6 0.12
32 21 0.43
33 16 0.33
34 6 0.12
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.29
Consensus pattern (32 bp):
TAAATTTAGGTATTTAAAAAGTAAAAGAATAA
Found at i:38776712 original size:114 final size:113
Alignment explanation
Indices: 38776539--38776751 Score: 304
Period size: 114 Copynumber: 1.9 Consensus size: 113
38776529 AAAATAAGCA
* * *
38776539 TTAGCGGCGTTTTCCGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTCCGGAAAGCACCGCAAAAAACATAAGCCCAACAACGCCGTTTTCTGAGCTTT
*
38776604 CGGGGATTTAGCGGCGTTTTT-AGGAAAGCGCCGCTAATGCCCAGGGCT
66 CGGGGATTTAGCGGCGTTTTTGA-CAAAGCGCCGCTAATGCCCAGGGCT
** * *
38776652 TTAGCGGCGTTTT-TTGAGAAGCACCGCAAAAAAACATAAGCCTAACAACGTCGTTTTCTGAGCT
1 TTAGCGGCGTTTTCCGGA-AAGCACCGC-AAAAAACATAAGCCCAACAACGCCGTTTTCTGAGCT
*
38776716 TTCGTGGATTTAGCGGCGTTTTTGACAAAGCGCCGC
64 TTCGGGGATTTAGCGGCGTTTTTGACAAAGCGCCGC
38776752 AAAAAAACTT
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
112 2 0.02
113 21 0.24
114 64 0.73
115 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.25
Consensus pattern (113 bp):
TTAGCGGCGTTTTCCGGAAAGCACCGCAAAAAACATAAGCCCAACAACGCCGTTTTCTGAGCTTT
CGGGGATTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCCCAGGGCT
Found at i:38776801 original size:72 final size:72
Alignment explanation
Indices: 38776652--38776820 Score: 205
Period size: 73 Copynumber: 2.3 Consensus size: 72
38776642 GCCCAGGGCT
* * * **
38776652 TTAGCGGCGTTTTTTGAGAAGCACCGCAAAAAAACATAAGCCTAACAACGTCGTTTTCTGAGCTT
1 TTAGCGGCG-TTTTTGAAAAGCGCCGCAAAAAAACATAAGCCCAACAACCCCGTTTTCTGAGCTT
* *
38776717 TCGTGGAT
65 TCGGGGAC
* *
38776725 TTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACTTAAGCCCAACGACCCCGTTTTCTG-GCTT
1 TTAGCGGCGTTTTTGA-AAAGCGCCGCAAAAAAACATAAGCCCAACAACCCCGTTTTCTGAGCTT
38776789 TCGGGGAC
65 TCGGGGAC
* *
38776797 TTAGCGGCATTTTTTAGAAAGCGC
1 TTAGCGGCGTTTTTGA-AAAGCGC
38776821 TGCTAATGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
72 38 0.46
73 45 0.54
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (72 bp):
TTAGCGGCGTTTTTGAAAAGCGCCGCAAAAAAACATAAGCCCAACAACCCCGTTTTCTGAGCTTT
CGGGGAC
Found at i:38776867 original size:186 final size:186
Alignment explanation
Indices: 38776539--38776938 Score: 556
Period size: 186 Copynumber: 2.1 Consensus size: 186
38776529 AAAATAAGCA
* *
38776539 TTAGCGGCGTTTTCCG-GAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTT-TGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACCCCGTTTTCTGAGCTT
* *
38776603 TCGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCGTTTTTTG
65 TCGGGGACTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGACGTTTTTTG
* * *
38776668 AGAAGCACCGCAAAAAAACATAAGCCTAACAACGTCGTTTTCTGAGCTTTCGTGGAT
130 AGAAGCACCGCAAAAAAACATAAACCTAACAACGCCGTTTTCTGAGCTTTCGGGGAT
* *
38776725 TTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACTTAAGCCCAACGACCCCGTTTTCTG-GCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACCCCGTTTTCTGAGCTT
* * ** *
38776789 TCGGGGACTTAGCGGCATTTTTTA-GAAAGCGCTGCTAATGTTCAGTGCTTTAGCGACGTTTTTG
65 TCGGGGACTTAGCGGC-GTTTTTAGGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGACGTTTTT-
* * * *
38776853 TG-GAAGCGCCGCAAAGAAACATAAACCTAACGACGCCGTTTTCTGAGTTTTCGGGGAT
128 TGAGAAGCACCGCAAAAAAACATAAACCTAACAACGCCGTTTTCTGAGCTTTCGGGGAT
*
38776911 TTAGCGGCGTTTCTTTAGAAAGCGCCGC
1 TTAGCGGCGTTT-TTGAGAAAGCGCCGC
38776939 TAATGCTAAG
Statistics
Matches: 189, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
185 1 0.01
186 137 0.72
187 51 0.27
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (186 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACCCCGTTTTCTGAGCTTT
CGGGGACTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGACGTTTTTTGA
GAAGCACCGCAAAAAAACATAAACCTAACAACGCCGTTTTCTGAGCTTTCGGGGAT
Found at i:38777089 original size:114 final size:114
Alignment explanation
Indices: 38776724--38777215 Score: 646
Period size: 115 Copynumber: 4.3 Consensus size: 114
38776714 CTTTCGTGGA
* * *
38776724 TTTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACTTAAGCCCAACGACCCCGTTTTCTG-GCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
* * * * *
38776788 TTCGGGGACTTAGCGGCATTTTTTAGAAAGCGCTGCTAATGTTCAGTGC
66 TTCGGGGATTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGGC
* * * * * * *
38776837 TTTAGCGACGTTTTTGTGGAAGCGCCGCAAAGAAACATAAACCTAACGACGCCGTTTTCTGAGTT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
*
38776902 TTCGGGGATTTAGCGGCGTTTCTTTAGAAAGCGCCGCTAATGCTAAGGGC
66 TTCGGGGATTTAGCGGCGTTT-TTTAGAAAGCGCCGCTAATGCTCAGGGC
* * *
38776952 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAATAAAC-TAAGCCCAATGACGTCGTTTTCTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAA-AAACATAAGCCCAACGACGCCGTTTTCTGAGC
* * * *
38777016 TTTCGCGGATTTAGTGGCGTTTTTTAGGAAGTGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
38777066 TTTAGCGACGTTTTTGAGAAAGCGTCGCAAAAAGACATAAGCCCAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
38777131 TTCGGGGATTTAGCGGCGTTGTTTAGGAAAGCGCCACTAATACTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTTA-GAAAGCGCCGCTAATGCTCAGGGC
* *
38777181 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAAA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAA
38777216 AACATAGGGT
Statistics
Matches: 323, Mismatches: 51, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
113 55 0.17
114 122 0.38
115 142 0.44
116 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:38777136 original size:229 final size:228
Alignment explanation
Indices: 38776724--38777215 Score: 675
Period size: 229 Copynumber: 2.2 Consensus size: 228
38776714 CTTTCGTGGA
*
38776724 TTTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACTTAAGCCCAACGACCCCGTTTTCTGGCTT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACTTAAGCCCAACGACCCCGTTTTCTGGCTT
* * * * *
38776789 TCGGGGACTTAGCGGCATTTTTTAGAAAGCGCTGCTAATGTTCAGTGCTTTAGCGACGTTTTTGT
66 TCGCGGACTTAGCGGCATTTTTTAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGACGTTTTTGA
* * *
38776854 GGAAGCGCCGCAAAGAAACATAAACCTAACGACGCCGTTTTCTGAGTTTTCGGGGATTTAGCGGC
131 GAAAGCGCCGCAAAGAAACATAAACCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
* *
38776919 GTTTCTTTA-GAAAGCGCCGCTAATGCTAAGGGC
196 G-TTCTTTAGGAAAGCGCCACTAATACTAAGGGC
* * **
38776952 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAATAAAC-TAAGCCCAATGACGTCGTTTTCTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAA-AAACTTAAGCCCAACGACCCCGTTTTCTG-GC
* * * * *
38777016 TTTCGCGGATTTAGTGGCGTTTTTTAGGAAGTGCCGCTAATGCTCAGGGCTTTAGCGACGTTTTT
64 TTTCGCGGACTTAGCGGCATTTTTTAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGACGTTTTT
* * *
38777081 GAGAAAGCGTCGCAAA-AAGACATAAGCCCAACGACGCCGTTTTTTGAGCTTTCGGGGATTTAGC
129 GAGAAAGCGCCGCAAAGAA-ACATAAACCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGC
* * *
38777145 GGCGTTGTTTAGGAAAGCGCCACTAATACTCAGGTC
193 GGCGTTCTTTAGGAAAGCGCCACTAATACTAAGGGC
* *
38777181 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAAA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAA
38777216 AACATAGGGT
Statistics
Matches: 231, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
228 62 0.27
229 169 0.73
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (228 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACTTAAGCCCAACGACCCCGTTTTCTGGCTT
TCGCGGACTTAGCGGCATTTTTTAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGACGTTTTTGA
GAAAGCGCCGCAAAGAAACATAAACCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
GTTCTTTAGGAAAGCGCCACTAATACTAAGGGC
Found at i:38777325 original size:14 final size:14
Alignment explanation
Indices: 38777306--38777332 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38777296 GAGTATGGGT
38777306 TTAGGGATTATGGA
1 TTAGGGATTATGGA
38777320 TTAGGGATTATGG
1 TTAGGGATTATGG
38777333 TTTAAGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:38777632 original size:15 final size:15
Alignment explanation
Indices: 38777594--38777628 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38777584 TATATTTTAA
38777594 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
38777609 GGTTTAGGGATTAT-
1 GGTTTAGGGAGTATG
38777623 GGTTTA
1 GGTTTA
38777629 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:38777649 original size:21 final size:20
Alignment explanation
Indices: 38777615--38777655 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
38777605 TATGGGTTTA
*
38777615 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
38777635 GGGATTTAAGGTTTAAGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
38777656 AGGGNNNNNN
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:38777833 original size:40 final size:39
Alignment explanation
Indices: 38777789--38777900 Score: 145
Period size: 38 Copynumber: 2.8 Consensus size: 39
38777779 ATAATGTTTT
38777789 GCGGCGTTTCTATGACAAACGCCGCAAAAGATAACCAATA
1 GCGGCGTTTCTATGA-AAACGCCGCAAAAGATAACCAATA
* *
38777829 GCGGCGTTT-TCTGAAAACGCCGCAAAAGATAAGCAATA
1 GCGGCGTTTCTATGAAAACGCCGCAAAAGATAACCAATA
* * * *
38777867 GCAGCGTTTTCTATAAAAATGCCGCAAAATATAA
1 GCGGCG-TTTCTATGAAAACGCCGCAAAAGATAA
38777901 ATAAAATTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
38 28 0.44
39 7 0.11
40 28 0.44
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (39 bp):
GCGGCGTTTCTATGAAAACGCCGCAAAAGATAACCAATA
Found at i:38777922 original size:22 final size:21
Alignment explanation
Indices: 38777892--38777932 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
38777882 AAAATGCCGC
*
38777892 AAAATATAAATAAAATTATAA
1 AAAATATAAAAAAAATTATAA
38777913 AAAATGATAAAAAAAATTAT
1 AAAAT-ATAAAAAAAATTAT
38777933 TTGCATAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATATAAAAAAAATTATAA
Found at i:38777992 original size:106 final size:105
Alignment explanation
Indices: 38777863--38778181 Score: 423
Period size: 106 Copynumber: 3.0 Consensus size: 105
38777853 AAAGATAAGC
* * * * *
38777863 AATAGCAGCG-TTTTCTATAAAAATGCCGCAAAATATAAATAAAATTATAAAAAATGATAA-AAA
1 AATAGCGGCGTTTTTC-ATAAAAATGCCGCAAAA-ATAAATCAATTTATAAAAAA-CAAAATAAA
38777926 AAATTATT-TGCATAGCAAAACGGCGTCATTTTGTTCAAAATGA
63 AAATT-TTCTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGA
* **
38777969 AATAGCGGCGTTTTTCATAAAAATGTCG-GGAAA-AAATCAATTTATAAAAAACAAAATAAAAAA
1 AATAGCGGCGTTTTTCATAAAAATGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAAA
38778032 TTTTCTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGA
66 TTTTCTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGA
* * * *
38778072 AATTGCGGCGTTTTCCATAAAAACGCCGCAAAAAATAAATCAATTTAAAAAAAACAAAATAAAAA
1 AATAGCGGCGTTTTTCATAAAAATGCCGC-AAAAATAAATCAATTTATAAAAAACAAAATAAAAA
* * *
38778137 ATTTTGTGCAGAGCAAAACGGCGTCATTTTGTTTAAAATGA
65 ATTTTCTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGA
38778178 AATA
1 AATA
38778182 ATATCAAAAA
Statistics
Matches: 188, Mismatches: 19, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
102 5 0.03
103 83 0.44
104 1 0.01
105 5 0.03
106 89 0.47
107 5 0.03
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (105 bp):
AATAGCGGCGTTTTTCATAAAAATGCCGCAAAAATAAATCAATTTATAAAAAACAAAATAAAAAA
TTTTCTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGA
Found at i:38782279 original size:21 final size:21
Alignment explanation
Indices: 38782249--38782319 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
38782239 CTACAACTTA
*
38782249 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
38782270 AAGTAGAGGCTGCAGCGAGGA
1 AAGCAGAGGCTGCAGCGAGGG
*
38782291 AAGCAGAGGCTGTAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
38782312 AAGCAGAG
1 AAGCAGAG
38782320 CAAAGTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.32, C:0.15, G:0.46, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:38783254 original size:16 final size:16
Alignment explanation
Indices: 38783220--38783254 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38783210 CTCAAAAATG
**
38783220 ATTGTTAATTAATGTT
1 ATTGTTAATTAATACT
38783236 ATTGTTAATTAATACT
1 ATTGTTAATTAATACT
38783252 ATT
1 ATT
38783255 AAGTGATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (16 bp):
ATTGTTAATTAATACT
Found at i:38786753 original size:13 final size:13
Alignment explanation
Indices: 38786737--38786787 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
38786727 TAAACCAAAT
38786737 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
38786750 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
* *
38786763 TTTTTAAAAACAC
1 TTTTCAAAAGCAC
38786776 TTTTCAAAAGCA
1 TTTTCAAAAGCA
38786788 TTGCCAAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 4 0.13
13 21 0.70
14 5 0.17
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:38789830 original size:20 final size:20
Alignment explanation
Indices: 38789805--38789845 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
38789795 AATGTGTTTA
38789805 GATCAAGAATTAAAGAAATC
1 GATCAAGAATTAAAGAAATC
38789825 GATCAAGAATTAAAGAAATC
1 GATCAAGAATTAAAGAAATC
38789845 G
1 G
38789846 GACTTGGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.20
Consensus pattern (20 bp):
GATCAAGAATTAAAGAAATC
Found at i:38790150 original size:43 final size:42
Alignment explanation
Indices: 38790103--38790203 Score: 114
Period size: 43 Copynumber: 2.4 Consensus size: 42
38790093 TTATATAAAC
38790103 GGCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAATAAAAG
1 GGCACTAAGTGTGCGAAACTAAAATGGA-GAGGTTG-ATAAAAG
* * * * * *
38790146 GGCACTGAGTGTGTGAAATTAAAATGGAGATGTTGATTAACG
1 GGCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGATAAAAG
*
38790188 GGCATTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
38790204 TACCGAGAGC
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 18 0.38
43 28 0.58
44 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.31, T:0.24
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGATAAAAG
Found at i:38790919 original size:2 final size:2
Alignment explanation
Indices: 38790912--38790948 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
38790902 AATAATACTA
*
38790912 AT AT AT AT AT AT GT 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 AT AT AT A
38790949 GGATTTGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38792776 original size:31 final size:29
Alignment explanation
Indices: 38792738--38792836 Score: 92
Period size: 31 Copynumber: 3.3 Consensus size: 29
38792728 CTAACGGCTC
* *
38792738 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
38792769 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
*
38792798 AGTGACTAAAATGTAAC-CTGTGCCAAACAAA
1 AGTGACTAAAATGTAACAC-GT--CAAACATA
38792829 AGTGACTA
1 AGTGACTA
38792837 TTTTGGTAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 23 0.41
30 3 0.05
31 30 0.54
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:38793868 original size:28 final size:28
Alignment explanation
Indices: 38793814--38793879 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
38793804 TACGATAATA
*
38793814 TATATATATATATATAAAAGTATGTATG
1 TATATATATATATATAAAAGTACGTATG
* *
38793842 TATATATATCTGTCATAAAA-TACGTATG
1 TATATATATATAT-ATAAAAGTACGTATG
* *
38793870 CATGTATATA
1 TATATATATA
38793880 AATGTATTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 25 0.81
29 6 0.19
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (28 bp):
TATATATATATATATAAAAGTACGTATG
Found at i:38794135 original size:10 final size:10
Alignment explanation
Indices: 38794120--38794144 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38794110 ATATAAAAGG
38794120 TATATATGTA
1 TATATATGTA
38794130 TATATATGTA
1 TATATATGTA
38794140 TATAT
1 TATAT
38794145 GATGAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (10 bp):
TATATATGTA
Found at i:38794308 original size:27 final size:26
Alignment explanation
Indices: 38794244--38794311 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
38794234 ATATAGGAAT
*
38794244 ATAATAAATAATAATGATACAATGCTA
1 ATAATAAAT-ATAATAATACAATGCTA
* * *
38794271 ATAGTATAATATAATAATATAATGGTA
1 ATAATA-AATATAATAATACAATGCTA
38794298 ATGAATAAATATAA
1 AT-AATAAATATAA
38794312 AAAAATTTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 28 0.82
28 6 0.18
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (26 bp):
ATAATAAATATAATAATACAATGCTA
Found at i:38795156 original size:6 final size:7
Alignment explanation
Indices: 38795141--38795165 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38795131 TTTAATATAC
38795141 AAAATAA
1 AAAATAA
38795148 AAAATAA
1 AAAATAA
38795155 AAAATAA
1 AAAATAA
38795162 AAAA
1 AAAA
38795166 AAGAAGTGTG
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:38796250 original size:45 final size:45
Alignment explanation
Indices: 38796153--38796270 Score: 141
Period size: 45 Copynumber: 2.6 Consensus size: 45
38796143 TTTTAATCCG
* * * *
38796153 CTCCACTACAACTTCAGGGAGATAGGA-TTAGTAGCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTCACTAGCTTCAGTCTA
* *
38796197 CTCCACTGCAACTTCAGGGACATAAGACTCACTATCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTCACTAGCTTCAGTCTA
* *
38796242 CTCTACTGCAACCTT-AGTGAGATAAGACT
1 CTCCACTGCAA-CTTCAGGGAGATAAGACT
38796271 TGTTATGATA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 24 0.38
45 36 0.57
46 3 0.05
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTCACTAGCTTCAGTCTA
Found at i:38796596 original size:43 final size:42
Alignment explanation
Indices: 38796538--38796683 Score: 105
Period size: 43 Copynumber: 3.4 Consensus size: 42
38796528 CCCCACTGCA
*
38796538 ACTTCAGGGGGATAAGGTTGGTGCTTTCGATCTGCTCCACTACT
1 ACTT-AGGGAGATAAGGTTGGTGCTTT-GATCTGCTCCACTACT
* ** * * * *
38796582 ACTTAGGGAGATAAGATCTACAAT-CTTTGACCTACTCCGCTGCT
1 ACTTAGGGAGATAAGGT-T--GGTGCTTTGATCTGCTCCACTACT
* * * * *
38796626 ACTCAAGGAGATAGGGCTGGTGCCTTTGATCTGTTCCACTACT
1 ACTTAGGGAGATAAGGTTGGTG-CTTTGATCTGCTCCACTACT
*
38796669 GCTTAGGGAGATAAG
1 ACTTAGGGAGATAAG
38796684 ATCTAATATA
Statistics
Matches: 73, Mismatches: 24, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
41 1 0.01
43 38 0.52
44 29 0.40
45 4 0.05
46 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.29
Consensus pattern (42 bp):
ACTTAGGGAGATAAGGTTGGTGCTTTGATCTGCTCCACTACT
Found at i:38796664 original size:87 final size:85
Alignment explanation
Indices: 38796541--38796859 Score: 291
Period size: 87 Copynumber: 3.7 Consensus size: 85
38796531 CACTGCAACT
* * * * *
38796541 TCAGGGGGATAAGGTTGGTGCTTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAAT
1 TCAGGGAGATAGGGCTGGTGCTTT-GATCTG-TTCACTACTACTTAGGAAGATAAGATCTACAAT
*
38796606 CTTTGACCTACTCCGCTGCTAC
64 CTTCGACCTACTCCGCTGCTAC
* * *
38796628 TCAAGGAGATAGGGCTGGTGCCTTTGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTA-ATA
1 TCAGGGAGATAGGGCTGGTG-CTTTGATCTGTT-CACTACTACTTAGGAAGATAAGATCTACA-A
* * * * *
38796692 TATTCAACCTACTCAGTTGCTGC
63 TCTTCGACCTACTCCGCTGCTAC
* * * * * * * * *
38796715 TCAGGGAGATAAGGCTTGTAGCTTCGATCTGTTCACTGCCAGTATAGAAAGACAAGATCTGCAAT
1 TCAGGGAGATAGGGCTGGT-GCTTTGATCTGTTCACTACTACT-TAGGAAGATAAGATCTACAAT
*
38796780 CTTCGACCTACTCCACTGCTAC
64 CTTCGACCTACTCCGCTGCTAC
* **
38796802 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTC-CTACTATCTTAGGAAGATAAGAT
1 TCAGGGAGATAGGGCTGGT-GCTTTGATCTG-TTCACTACTA-CTTAGGAAGATAAGAT
38796860 TCACCGTCTT
Statistics
Matches: 183, Mismatches: 41, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
86 8 0.04
87 165 0.90
88 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (85 bp):
TCAGGGAGATAGGGCTGGTGCTTTGATCTGTTCACTACTACTTAGGAAGATAAGATCTACAATCT
TCGACCTACTCCGCTGCTAC
Found at i:38797036 original size:89 final size:89
Alignment explanation
Indices: 38796932--38797190 Score: 277
Period size: 89 Copynumber: 2.9 Consensus size: 89
38796922 TCCAATGTTG
* * * *
38796932 CTCAGGGAGATAAGGCTTGTGTCTTCAATTTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCT
1 CTCAGGGAGACAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCT
* * ** *
38796997 CCTTCTAGTCTGTTCTGTTGTAAA
66 GCTTCTAGTCTGCTCCATTGCAAA
* * * **
38797021 CTCAGGGAGACAAGGCTGGTGTTTTCGATCTGCTTCACTCCCGGTACAGGAAGACAAGATCTATT
1 CTCAGGGAGACAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCT
* *
38797086 GTTTTTAGTCTGCTCCATTGCAAA
66 GCTTCTAGTCTGCTCCATTGCAAA
* * * * * * * *
38797110 CTCAGGAAGGTC-AGACTTGTGTTTTTGATCTGCTTCACTGCCAATACAAGAAGACAAAATTTGC
1 CTCAGGGA-GACAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGC
*
38797174 TGCTTCTAGTCTACTCC
65 TGCTTCTAGTCTGCTCC
38797191 TCTGTAATTT
Statistics
Matches: 137, Mismatches: 32, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
89 135 0.99
90 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (89 bp):
CTCAGGGAGACAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCT
GCTTCTAGTCTGCTCCATTGCAAA
Found at i:38797576 original size:24 final size:24
Alignment explanation
Indices: 38797544--38797599 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
38797534 GATTGCCCCT
*
38797544 ACTGTAATCTTCAAGGTTCAATCC
1 ACTGTAATCTTCAAGGTTAAATCC
38797568 ACTGTAATCTTCAAGGTTAAATCC
1 ACTGTAATCTTCAAGGTTAAATCC
*
38797592 ACGGTAAT
1 ACTGTAAT
38797600 TTTGGGACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (24 bp):
ACTGTAATCTTCAAGGTTAAATCC
Found at i:38798255 original size:105 final size:107
Alignment explanation
Indices: 38798066--38798387 Score: 481
Period size: 105 Copynumber: 3.0 Consensus size: 107
38798056 AAATGCTTGA
* * *
38798066 AAAAGATTATCA-AGATGGACAAGATGGAATTTTATTGAGAATAAGGCTCAAAATGAATAAATTA
1 AAAAGATTATCACA-ATGGACAAGATGGAATTTTATTGAGAACAAAGCTCGAAATGAATAAATTA
* * *
38798130 ATCAAGATAGCAAATTTTGCTCAGATACGAACTGAATAAGATG
65 ATCAAGATAGCAAATTTTGCTAAGATACAAAATGAATAAGATG
* *
38798173 AAAA-A-TATCACAATGGATAAGATGGAATTTTATTGAGAGCAAAGCTCGAAATGAATAAATTAA
1 AAAAGATTATCACAATGGACAAGATGGAATTTTATTGAGAACAAAGCTCGAAATGAATAAATTAA
* *
38798236 TCAGGATAGCAAATTTTGCTAAGATCCAAAATGAATAAGATG
66 TCAAGATAGCAAATTTTGCTAAGATACAAAATGAATAAGATG
* * *
38798278 AAAAGGATTATCACAATGGACAGGATGGAATTTTATTGAGAACAAAGCTCGAAATAAACAAA-TA
1 AAAA-GATTATCACAATGGACAAGATGGAATTTTATTGAGAACAAAGCTCGAAATGAATAAATTA
38798342 ATCAAGATAGCAAATTTTGCTAAGATACAAAATGAATAAGATG
65 ATCAAGATAGCAAATTTTGCTAAGATACAAAATGAATAAGATG
38798385 AAA
1 AAA
38798388 GCAGGTGCCC
Statistics
Matches: 194, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
105 92 0.47
106 2 0.01
107 51 0.26
108 49 0.25
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.25
Consensus pattern (107 bp):
AAAAGATTATCACAATGGACAAGATGGAATTTTATTGAGAACAAAGCTCGAAATGAATAAATTAA
TCAAGATAGCAAATTTTGCTAAGATACAAAATGAATAAGATG
Found at i:38798677 original size:11 final size:11
Alignment explanation
Indices: 38798654--38798704 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
38798644 TCTCTCCTTT
38798654 TTCTTTTTCTTC
1 TTCTTTTT-TTC
38798666 TTCTTTTTTTC
1 TTCTTTTTTTC
*
38798677 TT-TTCTTTTC
1 TTCTTTTTTTC
38798687 TT-TTTCTTTTC
1 TTCTTT-TTTTC
38798698 TTCTTTT
1 TTCTTTT
38798705 CTTTTTGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 11 0.31
11 13 0.37
12 11 0.31
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:38798682 original size:5 final size:5
Alignment explanation
Indices: 38798652--38798709 Score: 61
Period size: 5 Copynumber: 11.8 Consensus size: 5
38798642 GGTCTCTCCT
38798652 TTTTC TTTTTC TTCTTC -TTT- TTTTC TTTTC TTTTC TTTTTC TTTTC
1 TTTTC -TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC
38798698 --TTC TTTTC TTTT
1 TTTTC TTTTC TTTT
38798710 TGAACATCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
3 3 0.07
4 5 0.11
5 25 0.54
6 13 0.28
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:38798690 original size:16 final size:16
Alignment explanation
Indices: 38798652--38798699 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
38798642 GGTCTCTCCT
38798652 TTTTCTTTTTC--TTC
1 TTTTCTTTTTCTTTTC
38798666 TTCTT-TTTTTCTTTTC
1 TT-TTCTTTTTCTTTTC
38798682 TTTTCTTTTTCTTTTC
1 TTTTCTTTTTCTTTTC
38798698 TT
1 TT
38798700 CTTTTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.27
15 4 0.13
16 18 0.60
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:38798693 original size:24 final size:24
Alignment explanation
Indices: 38798652--38798709 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
38798642 GGTCTCTCCT
*
38798652 TTTTCTTTTTCTTCTTCTTTTTTTC
1 TTTTC-TTTTCTTCTTCTTTTCTTC
*
38798677 TTTTCTTTTCTTTTTCTTTTCTTC
1 TTTTCTTTTCTTCTTCTTTTCTTC
38798701 TTTTCTTTT
1 TTTTCTTTT
38798710 TGAACATCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTCTTTTCTTCTTCTTTTCTTC
Found at i:38798703 original size:19 final size:18
Alignment explanation
Indices: 38798650--38798710 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
38798640 TTGGTCTCTC
38798650 CTTTTTC-TTTTTCTTCTT
1 CTTTTTCTTTTTTCTT-TT
38798668 CTTTTT-TTCTTTTCTTTT
1 CTTTTTCTT-TTTTCTTTT
38798686 CTTTTTCTTTTCTTCTTTT
1 CTTTTTCTTTT-TTCTTTT
38798705 CTTTTT
1 CTTTTT
38798711 GAACATCCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 17 0.44
19 22 0.56
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
CTTTTTCTTTTTTCTTTT
Found at i:38803455 original size:20 final size:20
Alignment explanation
Indices: 38803432--38803469 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38803422 AAAACAAGTG
38803432 TAATGGAA-TAAAAATGATGA
1 TAATGGAAGT-AAAATGATGA
*
38803452 TAATGTAAGTAAAATGAT
1 TAATGGAAGTAAAATGAT
38803470 ATGAGCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (20 bp):
TAATGGAAGTAAAATGATGA
Found at i:38804322 original size:10 final size:10
Alignment explanation
Indices: 38804307--38804331 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38804297 ATATAAAAGG
38804307 TATATATGTA
1 TATATATGTA
38804317 TATATATGTA
1 TATATATGTA
38804327 TATAT
1 TATAT
38804332 GAAGTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (10 bp):
TATATATGTA
Found at i:38806272 original size:27 final size:24
Alignment explanation
Indices: 38806216--38806276 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
38806206 TTTTAAAATT
38806216 AATATTATTTTAATGATCAAGCTC
1 AATATTATTTTAATGATCAAGCTC
38806240 AATATTATTTTAATGATCAAGCTC
1 AATATTATTTTAATGATCAAGCTC
*
38806264 AACATTATTTTAA
1 AATATTATTTTAA
38806277 ATTTATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (24 bp):
AATATTATTTTAATGATCAAGCTC
Found at i:38806433 original size:18 final size:19
Alignment explanation
Indices: 38806387--38806433 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
38806377 TTATATATTA
38806387 ATATTTTAATTTCCATATAT
1 ATATTTT-ATTTCCATATAT
* *
38806407 ATATATTATTT-CATATGT
1 ATATTTTATTTCCATATAT
*
38806425 TTATTTTAT
1 ATATTTTAT
38806434 GTAAATTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 6 0.26
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATTTTATTTCCATATAT
Found at i:38806561 original size:64 final size:64
Alignment explanation
Indices: 38806491--38806617 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
38806481 ATATACTTTT
*
38806491 AAAATCCACTTTTATATATTTCATTTTTAAAGTTTTATACGATAATATTCTTATGCAATATTTA
1 AAAATCCACTTTTATATATTTCATCTTTAAAGTTTTATACGATAATATTCTTATGCAATATTTA
38806555 AAAATCCACTTTTATATATTTCATCTTTAAAGTTTTATACGATAATATTCTTATGCAATATTT
1 AAAATCCACTTTTATATATTTCATCTTTAAAGTTTTATACGATAATATTCTTATGCAATATTT
38806618 GCTTGAAAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (64 bp):
AAAATCCACTTTTATATATTTCATCTTTAAAGTTTTATACGATAATATTCTTATGCAATATTTA
Found at i:38808193 original size:43 final size:42
Alignment explanation
Indices: 38808140--38808246 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 42
38808130 CTATAGTTAT
* * *
38808140 ATAAACGGCACTAAGTGTGCGGAACTAAAAT-GATGAGGTTGA
1 ATAAAGGGCACTAAGTGTGCGAAACTAAAATGGA-GAGATTGA
* *
38808182 ATAAAAGGGCACTAAGTGTGCGAAATTAAAATGGAGATATTGA
1 AT-AAAGGGCACTAAGTGTGCGAAACTAAAATGGAGAGATTGA
* *
38808225 ATAACGGGCACTAAGAGTGCGA
1 ATAAAGGGCACTAAGTGTGCGA
38808247 TACCGGAGCA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 20 0.36
43 34 0.61
44 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (42 bp):
ATAAAGGGCACTAAGTGTGCGAAACTAAAATGGAGAGATTGA
Found at i:38815681 original size:194 final size:194
Alignment explanation
Indices: 38815347--38815762 Score: 616
Period size: 194 Copynumber: 2.1 Consensus size: 194
38815337 AGTCATTATG
* * * * * * *
38815347 GCGAATCTTATTTTCCTAGAGATGCCGTGGAATAAATTAAAGCTGAAGGCAGCGAATCTTATTTC
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTGAAGGCAGCAAATCTTATTTC
* * *
38815412 CCTGGCGTTGTAGTAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGTAGTAAATT
66 CCTAGCATTGTAATAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGTAGTAAATT
38815477 AAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCATTGCAATGGAACAGATTAAAGCTGAAAGAA
131 AAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCATTGCAATGGAACAGATTAAAGCTGAAAGAA
* * * * *
38815541 GTGAGTCTTATTTCCTTGGCGTTGCAGTGGAACAAATTAAAGTTGAATGCAGCAAATCTTATTTC
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTGAAGGCAGCAAATCTTATTTC
* * *
38815606 CCTAGCATTGTAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGTAGTAGATT
66 CCTAGCATTGTAATAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGTAGTAAATT
* * * * * *
38815671 AAAGCTGAAGGCATCGAATCTTATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTGAAGGCA
131 AAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCATTGCAATGGAACAGATTAAAGCTGAAAGAA
38815735 GCGAATCTTATTTCCCTGGCGTTGCAGT
1 GCGAATCTTATTTCCCTGGCGTTGCAGT
38815763 AGATTAGAGC
Statistics
Matches: 195, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
194 195 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (194 bp):
GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTGAAGGCAGCAAATCTTATTTC
CCTAGCATTGTAATAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGTAGTAAATT
AAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCATTGCAATGGAACAGATTAAAGCTGAAAGAA
Found at i:38815718 original size:97 final size:97
Alignment explanation
Indices: 38815379--38815824 Score: 543
Period size: 97 Copynumber: 4.6 Consensus size: 97
38815369 TGCCGTGGAA
*
38815379 TAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGTAGT---A-A-ATTAAAGCTGA
1 TAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
*
38815439 AGGCAGCGAATCTTATTTCCCTGGCGTTGTAG
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAG
* * * *
38815471 TAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCATTGCAATGGAACAGATTAAAGCTGA
1 TAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
* * * * *
38815536 AAGAAGTGAGTCTTATTTCCTTGGCGTTGCAG
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAG
* * * * *
38815568 TGGAACAAATTAAAGTTGAATGCAGCAAATCTTATTTCCCTAGCATT---GT--AATAGATTAAA
1 T-----AAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAA
* *
38815628 GCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGTAG
61 GCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAG
* * *
38815665 TAGATTAAAGCTGAAGGCATCGAATCTTATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTGA
1 TAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
38815730 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAG
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAG
* * * * *
38815762 TAGATTAGAGCTGAATGCAGCGAACCTTATTTCCCTAGCGTTGCAGTGGAATAGATTAAAGCT
1 TAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCT
38815825 ACAAATTATG
Statistics
Matches: 301, Mismatches: 38, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
92 76 0.25
95 3 0.01
96 1 0.00
97 184 0.61
99 1 0.00
102 36 0.12
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (97 bp):
TAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
AGGCAGCGAATCTTATTTCCCTGGCGTTGCAG
Found at i:38815805 original size:46 final size:46
Alignment explanation
Indices: 38815382--38815808 Score: 467
Period size: 46 Copynumber: 9.0 Consensus size: 46
38815372 CGTGGAATAA
* *
38815382 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGTAGTAA
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTAG
* *
38815428 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGTAGTAA
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTAG
* * *
38815474 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCATTGCAATGGAACAG
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGC-A--G--TAG
* * * * * *
38815525 ATTAAAGCTGAAAGAAGTGAGTCTTATTTCCTTGGCGTTGCAGTGGAACAA
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGT-----AG
* * * * * * *
38815576 ATTAAAGTTGAATGCAGCAAATCTTATTTCCCTAGCATTGTAATAG
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTAG
* *
38815622 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGTAGTAG
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTAG
* *
38815668 ATTAAAGCTGAAGGCATCGAATCTTATTTCCTTGGCGTTGCAGTGGAATAG
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCA---G--TAG
38815719 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTAG
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTAG
* * * *
38815765 ATTAGAGCTGAATGCAGCGAACCTTATTTCCCTAGCGTTGCAGT
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGT
38815809 GGAATAGATT
Statistics
Matches: 327, Mismatches: 39, Indels: 30
0.83 0.10 0.08
Matches are distributed among these distances:
46 207 0.63
47 1 0.00
48 2 0.01
49 2 0.01
50 1 0.00
51 114 0.35
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (46 bp):
ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTAG
Found at i:38815817 original size:194 final size:192
Alignment explanation
Indices: 38815380--38815824 Score: 605
Period size: 194 Copynumber: 2.3 Consensus size: 192
38815370 GCCGTGGAAT
* *
38815380 AAATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGTAGT-A-A-ATTAAAGCTGAAGG
1 AAATTAAAGCTGAATGCAGCGAATCTTATTTCCCTAGCGTTG-AGTAATAGATTAAAGCTGAAGG
38815442 CAGCGAATCTTATTTCCCTGGCGTTGTAGTAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCTT
65 CAGCGAATCTTATTTCCCTGGCGTTGTAGTAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCTT
* * *
38815507 GGCATTGCAATGGAACAGATTAAAGCTGAAAGAAGTGAGTCTTATTTCCTTGGCGTTGCAGTGGA
130 GGCATTGCAATGGAACAGATTAAAGCTGAAAGAAGCGAATCTTATTTCCCTGGCGTTGCAGT---
38815572 A
192 A
* * *
38815573 CAAATTAAAGTTGAATGCAGCAAATCTTATTTCCCTAGCATT--GTAATAGATTAAAGCTGAAGG
1 -AAATTAAAGCTGAATGCAGCGAATCTTATTTCCCTAGCGTTGAGTAATAGATTAAAGCTGAAGG
* * *
38815636 CAGCGAATCTTATTTCCTTGGCGTTGTAGTAGATTAAAGCTGAAGGCATCGAATCTTATTTCCTT
65 CAGCGAATCTTATTTCCCTGGCGTTGTAGTAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCTT
* * * * *
38815701 GGCGTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGT-
130 GGCATTGCAATGGAACAGATTAAAGCTGAAAGAAGCGAATCTTATTTCCCTGGCGTTGCAGTA
* * *
38815763 AGATTAGAGCTGAATGCAGCGAACCTTATTTCCCTAGCGTTGCAGTGGAATAGATTAAAGCT
1 AAATTAAAGCTGAATGCAGCGAATCTTATTTCCCTAGCGTTG-AGT--AATAGATTAAAGCT
38815825 ACAAATTATG
Statistics
Matches: 221, Mismatches: 22, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
189 35 0.16
191 2 0.01
192 3 0.01
193 1 0.00
194 180 0.81
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (192 bp):
AAATTAAAGCTGAATGCAGCGAATCTTATTTCCCTAGCGTTGAGTAATAGATTAAAGCTGAAGGC
AGCGAATCTTATTTCCCTGGCGTTGTAGTAAATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTG
GCATTGCAATGGAACAGATTAAAGCTGAAAGAAGCGAATCTTATTTCCCTGGCGTTGCAGTA
Found at i:38819835 original size:27 final size:24
Alignment explanation
Indices: 38819779--38819839 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
38819769 TTTTAAAATT
38819779 AATATTATTTTAATGATCAAGCTC
1 AATATTATTTTAATGATCAAGCTC
38819803 AATATTATTTTAATGATCAAGCTC
1 AATATTATTTTAATGATCAAGCTC
*
38819827 AACATTATTTTAA
1 AATATTATTTTAA
38819840 ATTTATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (24 bp):
AATATTATTTTAATGATCAAGCTC
Found at i:38819957 original size:24 final size:24
Alignment explanation
Indices: 38819830--38819979 Score: 91
Period size: 23 Copynumber: 6.3 Consensus size: 24
38819820 CAAGCTCAAC
**
38819830 ATTATTTTAAATTTATTAT-TAAC
1 ATTATTTTAAATTTATTATATATT
* **
38819853 ATT-GTTTAAATTTATCGTATATT
1 ATTATTTTAAATTTATTATATATT
*
38819876 ATTATTTT-AATTT-TGTATGTATT
1 ATTATTTTAAATTTAT-TATATATT
* *
38819899 ATT-TTTCTAAGCTTTTCATGTAT-TAAT
1 ATTATTT-TAA--ATTT-AT-TATATATT
*
38819926 ATTTTTTTAAATTTATTATATATT
1 ATTATTTTAAATTTATTATATATT
*
38819950 ATTATTTT-AATTTCCTTATATA-T
1 ATTATTTTAAATTT-ATTATATATT
38819973 ATTATTT
1 ATTATTT
38819980 CATATTTTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
22 16 0.16
23 38 0.38
24 23 0.23
25 3 0.03
26 3 0.03
27 9 0.09
28 8 0.08
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTATTTTAAATTTATTATATATT
Found at i:38819992 original size:24 final size:24
Alignment explanation
Indices: 38819941--38819986 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
38819931 TTTAAATTTA
*
38819941 TTATATATTATTATTTTAATTTCC
1 TTATATATTATTATTTCAATTTCC
38819965 TTATATA-TATTATTTCATATTT
1 TTATATATTATTATTTCA-ATTT
38819987 TTTTATGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATATATTATTATTTCAATTTCC
Found at i:38820379 original size:17 final size:18
Alignment explanation
Indices: 38820347--38820380 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38820337 GCTCTTGTGT
38820347 GTATTGTATTGCTTATTG
1 GTATTGTATTGCTTATTG
*
38820365 GTATT-TATTGGTTATT
1 GTATTGTATTGCTTATT
38820381 TGTAGTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.59
Consensus pattern (18 bp):
GTATTGTATTGCTTATTG
Found at i:38844039 original size:24 final size:24
Alignment explanation
Indices: 38844012--38844069 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
38844002 AAACCTAATT
38844012 CTAATCAAA-ATCAAATATATTATG
1 CTAAT-AAATATCAAATATATTATG
* * *
38844036 CTAATAAATGTTAAATATATTATA
1 CTAATAAATATCAAATATATTATG
*
38844060 CTTATAAATA
1 CTAATAAATA
38844070 CTAAATCTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (24 bp):
CTAATAAATATCAAATATATTATG
Found at i:38844074 original size:24 final size:24
Alignment explanation
Indices: 38844024--38844075 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38844014 AATCAAAATC
* **
38844024 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
38844048 AAATATATTATACTTATAAATACT
1 AAATATATTATACTAATAAATACT
38844072 AAAT
1 AAAT
38844076 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:38854087 original size:241 final size:241
Alignment explanation
Indices: 38853664--38854147 Score: 968
Period size: 241 Copynumber: 2.0 Consensus size: 241
38853654 TCTCGTCACC
38853664 AAATTACTTTGCACTAGCGGTTTGTAATTACACCAACTCTCATAAGCCTTAATCGCTCTATTGGT
1 AAATTACTTTGCACTAGCGGTTTGTAATTACACCAACTCTCATAAGCCTTAATCGCTCTATTGGT
38853729 GTAAACCGTAGCCATGTTGATGACAACGATTAGAATTGGGGTTCTTCCCTCGAAAATAACCTAGT
66 GTAAACCGTAGCCATGTTGATGACAACGATTAGAATTGGGGTTCTTCCCTCGAAAATAACCTAGT
38853794 TTTCTTGGTTTCAAATACTCCATAAGTTTGAGGTAAACAATAAGAAGTTGTCCCTATCCTCCTTT
131 TTTCTTGGTTTCAAATACTCCATAAGTTTGAGGTAAACAATAAGAAGTTGTCCCTATCCTCCTTT
38853859 TCTGATTTAATTCGCCTTAACATTGGGAGAATCCACTCAATAGGAG
196 TCTGATTTAATTCGCCTTAACATTGGGAGAATCCACTCAATAGGAG
38853905 AAATTACTTTGCACTAGCGGTTTGTAATTACACCAACTCTCATAAGCCTTAATCGCTCTATTGGT
1 AAATTACTTTGCACTAGCGGTTTGTAATTACACCAACTCTCATAAGCCTTAATCGCTCTATTGGT
38853970 GTAAACCGTAGCCATGTTGATGACAACGATTAGAATTGGGGTTCTTCCCTCGAAAATAACCTAGT
66 GTAAACCGTAGCCATGTTGATGACAACGATTAGAATTGGGGTTCTTCCCTCGAAAATAACCTAGT
38854035 TTTCTTGGTTTCAAATACTCCATAAGTTTGAGGTAAACAATAAGAAGTTGTCCCTATCCTCCTTT
131 TTTCTTGGTTTCAAATACTCCATAAGTTTGAGGTAAACAATAAGAAGTTGTCCCTATCCTCCTTT
38854100 TCTGATTTAATTCGCCTTAACATTGGGAGAATCCACTCAATAGGAG
196 TCTGATTTAATTCGCCTTAACATTGGGAGAATCCACTCAATAGGAG
38854146 AA
1 AA
38854148 TTCATCTTCA
Statistics
Matches: 243, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
241 243 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (241 bp):
AAATTACTTTGCACTAGCGGTTTGTAATTACACCAACTCTCATAAGCCTTAATCGCTCTATTGGT
GTAAACCGTAGCCATGTTGATGACAACGATTAGAATTGGGGTTCTTCCCTCGAAAATAACCTAGT
TTTCTTGGTTTCAAATACTCCATAAGTTTGAGGTAAACAATAAGAAGTTGTCCCTATCCTCCTTT
TCTGATTTAATTCGCCTTAACATTGGGAGAATCCACTCAATAGGAG
Found at i:38857268 original size:21 final size:21
Alignment explanation
Indices: 38857221--38857269 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
38857211 AAACCCAAAC
*
38857221 TTTTT-CTATAAAAATTCATG
1 TTTTTCCTATAAAAATTCAAG
* *
38857241 TAATTTCCTATAAAATTTCAAG
1 T-TTTTCCTATAAAAATTCAAG
38857263 TTTTTCC
1 TTTTTCC
38857270 CTATTACAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 8 0.35
22 14 0.61
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTTTCCTATAAAAATTCAAG
Found at i:38859835 original size:21 final size:22
Alignment explanation
Indices: 38859806--38859850 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
38859796 TATAATAATC
*
38859806 AATAGAAATAATAA-AACAACAA
1 AATAGAAATAA-AATAAAAACAA
38859828 AATA-AAATAAAATAAAAACAA
1 AATAGAAATAAAATAAAAACAA
38859849 AA
1 AA
38859851 AAATGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 15 0.71
22 4 0.19
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (22 bp):
AATAGAAATAAAATAAAAACAA
Found at i:38865637 original size:11 final size:11
Alignment explanation
Indices: 38865621--38865653 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
38865611 TTCGGGAGTC
38865621 GGTTACGCACG
1 GGTTACGCACG
38865632 GGTTACGCACG
1 GGTTACGCACG
38865643 GGTTACGCACG
1 GGTTACGCACG
38865654 AGGAAGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.36, T:0.18
Consensus pattern (11 bp):
GGTTACGCACG
Found at i:38866206 original size:3 final size:3
Alignment explanation
Indices: 38866198--38867028 Score: 1662
Period size: 3 Copynumber: 277.0 Consensus size: 3
38866188 TATGCTAGTG
38866198 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866246 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866294 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866342 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866390 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866438 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866486 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866534 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866582 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866630 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866678 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866726 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866774 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866822 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866870 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866918 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38866966 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38867014 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
38867029 NNNNNNNNNN
Statistics
Matches: 828, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 828 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.