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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 31 of 97
Found at i:12933809 original size:17 final size:17
Alignment explanation
Indices: 12933783--12933825 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
12933773 GGATTCAATA
*
12933783 AAAATATAAAAAAAATC
1 AAAATCTAAAAAAAATC
*
12933800 AAAATCT-AAAAGAATC
1 AAAATCTAAAAAAAATC
12933816 AAAATCTAAA
1 AAAATCTAAA
12933826 TTGTGGTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAATCTAAAAAAAATC
Found at i:12940223 original size:31 final size:31
Alignment explanation
Indices: 12940156--12940224 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
12940146 TGAAATTGAT
* *
12940156 ATTGTTTCGACTTTGAACTTTGGATTCGGTA
1 ATTGTTTAGACTTTGAACTTTGGATTCGGCA
* * *
12940187 TTTGTTTAGACTTT-AGTCTTTGGATTTGGCA
1 ATTGTTTAGACTTTGA-ACTTTGGATTCGGCA
12940218 ATTGTTT
1 ATTGTTT
12940225 CAACATTGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.17, C:0.10, G:0.22, T:0.51
Consensus pattern (31 bp):
ATTGTTTAGACTTTGAACTTTGGATTCGGCA
Found at i:12945112 original size:35 final size:35
Alignment explanation
Indices: 12945066--12945132 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
12945056 TTAAAATCTG
12945066 AATAAGCATGCAAATAAAATAAAATCCTAAGTCTA
1 AATAAGCATGCAAATAAAATAAAATCCTAAGTCTA
*
12945101 AATAAGCATGCAAATGAAATAAAATCCTAAGT
1 AATAAGCATGCAAATAAAATAAAATCCTAAGT
12945133 TCCCATAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.22
Consensus pattern (35 bp):
AATAAGCATGCAAATAAAATAAAATCCTAAGTCTA
Found at i:12945399 original size:17 final size:16
Alignment explanation
Indices: 12945330--12945403 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
12945320 ATTTTTTTTG
12945330 AAATAAAT-AAATAAA
1 AAATAAATAAAATAAA
**
12945345 TAAATAGAGATTAATGTAAA
1 -AAATA-A-A-TAAAATAAA
12945365 AATATAAATAAAAT-AA
1 AA-ATAAATAAAATAAA
*
12945381 AAATAACTGAAAATAAA
1 AAATAAAT-AAAATAAA
12945398 AAATAA
1 AAATAA
12945404 GAGTTTCGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
15 5 0.11
16 14 0.30
17 13 0.28
18 2 0.04
19 4 0.09
20 8 0.17
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAATAAAATAAA
Found at i:12949895 original size:35 final size:35
Alignment explanation
Indices: 12949846--12949922 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
12949836 CTTGGTAGAA
* * *
12949846 GTTATGCTTGATCTTATAAAAGGCATGTTGTAAAG
1 GTTACGCTTGATCTTACAAAAGGCATGTCGTAAAG
*
12949881 GTTACGCTTGATCTTGCAAAAGGCATGTCGTAAAG
1 GTTACGCTTGATCTTACAAAAGGCATGTCGTAAAG
12949916 GTTACGC
1 GTTACGC
12949923 CTGACCCTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (35 bp):
GTTACGCTTGATCTTACAAAAGGCATGTCGTAAAG
Found at i:12954897 original size:35 final size:35
Alignment explanation
Indices: 12954858--12954940 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 35
12954848 TAGTGCCTTG
* *
12954858 GTAGAGGTTACGCTTGATCTTGCAAAAGACATGCT
1 GTAGAGGTTACGCCTAATCTTGCAAAAGACATGCT
* * * *
12954893 GTAGAGGTTACACCTAATCTTGGAAAAGGCATGTT
1 GTAGAGGTTACGCCTAATCTTGCAAAAGACATGCT
*
12954928 GTAAAGGTTACGC
1 GTAGAGGTTACGC
12954941 ATGACCCTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (35 bp):
GTAGAGGTTACGCCTAATCTTGCAAAAGACATGCT
Found at i:12955492 original size:16 final size:15
Alignment explanation
Indices: 12955471--12955516 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
12955461 ATTTGGATTC
12955471 AATAAAAATATAAAAA
1 AATAAAAAT-TAAAAA
*
12955487 AATAAAACTCTAAAAA
1 AATAAAAAT-TAAAAA
*
12955503 AATTAAAATTAAAA
1 AATAAAAATTAAAA
12955517 TTTTGATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (15 bp):
AATAAAAATTAAAAA
Found at i:12966295 original size:50 final size:48
Alignment explanation
Indices: 12966220--12966318 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 48
12966210 ATACTTGAAT
*
12966220 ACCTCGAAAAAATCAACAAAGTCGGTAGTGTACCTAGTGGTGCAACTA
1 ACCTCGAAAAAATCAACAAAGTCGGTAGTGTACCTAGTGGTACAACTA
**
12966268 ANCCTCGAAAAAATCGTCAAAAGTCGGTAGTGTACCTAGTGGTACAACTA
1 A-CCTCGAAAAAATCAAC-AAAGTCGGTAGTGTACCTAGTGGTACAACTA
12966318 A
1 A
12966319 GTTGATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 1 0.02
49 14 0.30
50 31 0.67
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.21
Consensus pattern (48 bp):
ACCTCGAAAAAATCAACAAAGTCGGTAGTGTACCTAGTGGTACAACTA
Found at i:12969440 original size:34 final size:34
Alignment explanation
Indices: 12969400--12969475 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
12969390 AACTTGTAAT
* *
12969400 GTTATTTAAGTTGTTGTTTG-GATATTTTCTTTTA
1 GTTATTTAAGTTGATATTTGAGATATTTT-TTTTA
12969434 GTTATTTAAGTTGATATTTGAGATATTTTTTTTA
1 GTTATTTAAGTTGATATTTGAGATATTTTTTTTA
12969468 -TTATTTAA
1 GTTATTTAA
12969476 ATTTAAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
33 8 0.21
34 23 0.59
35 8 0.21
ACGTcount: A:0.24, C:0.01, G:0.14, T:0.61
Consensus pattern (34 bp):
GTTATTTAAGTTGATATTTGAGATATTTTTTTTA
Found at i:12971787 original size:44 final size:44
Alignment explanation
Indices: 12971737--12971824 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
12971727 ATATGGCTAC
* *
12971737 TAGCACTGTAATATGATATATTATATTCCATCCTAAGTAAAGTT
1 TAGCACTATAATATGATATATTATATTCCACCCTAAGTAAAGTT
12971781 TAGCACTATAATATGATATATTATATTCCACCCTAAGTAAAGTT
1 TAGCACTATAATATGATATATTATATTCCACCCTAAGTAAAGTT
12971825 CTAAGTACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (44 bp):
TAGCACTATAATATGATATATTATATTCCACCCTAAGTAAAGTT
Found at i:12984735 original size:34 final size:35
Alignment explanation
Indices: 12984697--12984764 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
12984687 TTCACCAAGC
*
12984697 TTTACAATGGCTTTTCAAG-GCTCAACCAAAACCT
1 TTTACAATAGCTTTTCAAGAGCTCAACCAAAACCT
* * * *
12984731 TTTACACTAGTTTTTCACGAGCTCAACTAAAACC
1 TTTACAATAGCTTTTCAAGAGCTCAACCAAAACC
12984765 CAAAGTGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.31
Consensus pattern (35 bp):
TTTACAATAGCTTTTCAAGAGCTCAACCAAAACCT
Found at i:12994055 original size:329 final size:331
Alignment explanation
Indices: 12993393--12994056 Score: 969
Period size: 330 Copynumber: 2.0 Consensus size: 331
12993383 ACTGAAACTC
* * *
12993393 AGATGTATTACACCACCACTAAAAAAAAAAAACTATTAACTATTGTGTATGCATTTGATAATTTT
1 AGATGCATTACACCACCACT--AAAAAAAAAACTATTAACTATTGTATATGCATTTGATAAGTTT
* *
12993458 AGTTCCTACTTGGTTGGCACTAAGTTTATTGTGTACACTAATCATTCTACAATTAAGTATTTGAT
64 AGTTCCTACTTGGTTGGCACTAAGGTTATTGTGTACACTAATCATTCTACAATTAAATATTTGAT
* * *
12993523 TACCTAAAAAGATGCGAAGCCAAAATTGATAAGATGGATCCTTTTGCTTCAGGAATTTGATTTAG
129 TACCTAAAAAGATGCCAAGCCAAAATTGATAAGATGGATCCTCTTGCTTCAAGAATTTGATTTAG
* *
12993588 AAATTAGAAATAGGAAAGGCACAGAAAATCAAGTAGCAGGCCATCTGTAAAGGTTGACGAATGAT
194 AAATTAGAAATAGGAAAGGCACAGAAAATCAAGTAGCAGACCATATGTAAAGGTTGACGAATGAT
*
12993653 AACCAAGGTAATGATTTAACTTTAACTAATGAAACTTTTCTTAATGAGCAATTGTTGCATGTTGG
259 AACCAAGGTAATGATTTAACTTTAACTAATGAAACTTTTCTTAATGAGCAATTGTTGCACGTTGG
*
12993718 TTAAAAGA
324 TCAAAAGA
* ** * *
12993726 AGATGCATTACACCACCACT-AAAAAAGAACTATTAGTTGTTGTATATGCATTTGATAAGTTTCG
1 AGATGCATTACACCACCACTAAAAAAAAAACTATTAACTATTGTATATGCATTTGATAAGTTTAG
* * *
12993790 TTCTTACTTGGTTGGCACTAAGGTTATTGTGTACACTGATCA-TCTTGCAATTAAATATTTGATT
66 TTCCTACTTGGTTGGCACTAAGGTTATTGTGTACACTAATCATTC-TACAATTAAATATTTGATT
* * * *
12993854 GCC-AAGAAAGATGCCAAGCCAAGATTGATAAGATGGATGCTCTTGCTTCAAGAA-TTGATTTGG
130 ACCTAA-AAAGATGCCAAGCCAAAATTGATAAGATGGATCCTCTTGCTTCAAGAATTTGATTTAG
* * * *
12993917 AGATTAGAGATAGGAAAGGCATAGAAAATCAAGTAGCAGACCATATGTCAAGGTTGGA-GAATGA
194 AAATTAGAAATAGGAAAGGCACAGAAAATCAAGTAGCAGACCATATGTAAAGGTT-GACGAATGA
* * *
12993981 TAACCAAGGTAATGATTTAACTTTGATTAATGAAACTTTTCTTGATGAGCAATTGTTGCACGTTG
258 TAACCAAGGTAATGATTTAACTTTAACTAATGAAACTTTTCTTAATGAGCAATTGTTGCACGTTG
12994046 GTCAAAAGA
323 GTCAAAAGA
12994055 AG
1 AG
12994057 TTACCTTGGT
Statistics
Matches: 297, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
329 138 0.46
330 140 0.47
333 19 0.06
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (331 bp):
AGATGCATTACACCACCACTAAAAAAAAAACTATTAACTATTGTATATGCATTTGATAAGTTTAG
TTCCTACTTGGTTGGCACTAAGGTTATTGTGTACACTAATCATTCTACAATTAAATATTTGATTA
CCTAAAAAGATGCCAAGCCAAAATTGATAAGATGGATCCTCTTGCTTCAAGAATTTGATTTAGAA
ATTAGAAATAGGAAAGGCACAGAAAATCAAGTAGCAGACCATATGTAAAGGTTGACGAATGATAA
CCAAGGTAATGATTTAACTTTAACTAATGAAACTTTTCTTAATGAGCAATTGTTGCACGTTGGTC
AAAAGA
Found at i:13000377 original size:15 final size:16
Alignment explanation
Indices: 13000350--13000379 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13000340 AAAACTTGTA
13000350 ATTTATAAAAATTATC
1 ATTTATAAAAATTATC
13000366 ATTTAT-AAAATTAT
1 ATTTATAAAAATTAT
13000380 TAGTGTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTATAAAAATTATC
Found at i:13001426 original size:23 final size:23
Alignment explanation
Indices: 13001391--13001437 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
13001381 GGATTTGAGA
* *
13001391 GATAGTCCTTAATCTTCTAAAAT
1 GATACTCCGTAATCTTCTAAAAT
*
13001414 GATACTCCGTAATCTTCTCAAAT
1 GATACTCCGTAATCTTCTAAAAT
13001437 G
1 G
13001438 TCATTTGGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (23 bp):
GATACTCCGTAATCTTCTAAAAT
Found at i:13002461 original size:24 final size:25
Alignment explanation
Indices: 13002415--13002462 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
13002405 AACAAACATT
13002415 TCATAAAATTTTCATAATCCATTTC
1 TCATAAAATTTTCATAATCCATTTC
*
13002440 TCATATAA-TTTCATATAT-CATTT
1 TCATAAAATTTTCATA-ATCCATTT
13002463 TACGTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (25 bp):
TCATAAAATTTTCATAATCCATTTC
Found at i:13003918 original size:38 final size:38
Alignment explanation
Indices: 13003863--13004004 Score: 126
Period size: 38 Copynumber: 3.7 Consensus size: 38
13003853 GATTATAAGA
*
13003863 GTGGGTATTCATGCATCCACACTTGCAATATCATAAAG
1 GTGGGTATTCATTCATCCACACTTGCAATATCATAAAG
* ** * *
13003901 GTGGGTATTTATTCATCCACACTCACATTATCATAAAA
1 GTGGGTATTCATTCATCCACACTTGCAATATCATAAAG
* * * *
13003939 GTTGGCATTGATTCATCCACA-TT-CACATTAGCATAAAG
1 GTGGGTATTCATTCATCCACACTTGCA-A-TATCATAAAG
* * *
13003977 ATGGGGTATTCATTTATCCACACATGCA
1 GT-GGGTATTCATTCATCCACACTTGCA
13004005 TTCATCTAGC
Statistics
Matches: 80, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
36 2 0.03
37 1 0.01
38 59 0.74
39 15 0.19
40 1 0.01
41 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (38 bp):
GTGGGTATTCATTCATCCACACTTGCAATATCATAAAG
Found at i:13005055 original size:60 final size:60
Alignment explanation
Indices: 13004980--13005113 Score: 241
Period size: 60 Copynumber: 2.2 Consensus size: 60
13004970 TGTTTCAATG
** *
13004980 ATAAGTGAACATATAATATACTTTTACTCAATAAATTTAATTTAAATTTCTCTTTCTTAA
1 ATAAGTGAATGTATAATATACTTGTACTCAATAAATTTAATTTAAATTTCTCTTTCTTAA
13005040 ATAAGTGAATGTATAATATACTTGTACTCAATAAATTTAATTTAAATTTCTCTTTCTTAA
1 ATAAGTGAATGTATAATATACTTGTACTCAATAAATTTAATTTAAATTTCTCTTTCTTAA
13005100 ATAAGTGAATGTAT
1 ATAAGTGAATGTAT
13005114 GTGATCATTA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.44
Consensus pattern (60 bp):
ATAAGTGAATGTATAATATACTTGTACTCAATAAATTTAATTTAAATTTCTCTTTCTTAA
Found at i:13005651 original size:13 final size:13
Alignment explanation
Indices: 13005633--13005658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13005623 ATGAGATAAG
13005633 TTCAATCAGAAAT
1 TTCAATCAGAAAT
13005646 TTCAATCAGAAAT
1 TTCAATCAGAAAT
13005659 CCCCAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTCAATCAGAAAT
Found at i:13010752 original size:15 final size:15
Alignment explanation
Indices: 13010732--13010762 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13010722 AGACTTGTGT
*
13010732 GAGAAAAATTTGAGA
1 GAGAAAAATTAGAGA
13010747 GAGAAAAATTAGAGA
1 GAGAAAAATTAGAGA
13010762 G
1 G
13010763 TAAAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (15 bp):
GAGAAAAATTAGAGA
Found at i:13011704 original size:27 final size:27
Alignment explanation
Indices: 13011669--13011832 Score: 163
Period size: 26 Copynumber: 6.1 Consensus size: 27
13011659 TGTGCGCGTG
** *
13011669 AAAAAAAGTTGTTGTATGCCATGTTGA
1 AAAAAAAGTTGTTACACGCCATGTTGA
* *
13011696 AAAAAAAGTTGTTGCACACCATGTTGA
1 AAAAAAAGTTGTTACACGCCATGTTGA
* * *
13011723 AAAAAAA-TGGTTACACGCCATATTAAA
1 AAAAAAAGTTGTTACACGCCATGTT-GA
*
13011750 AAAAAAAGTTGTTACATGCCATGTTG-
1 AAAAAAAGTTGTTACACGCCATGTTGA
* **
13011776 AAAAAAAGTTGTTACAAGTAATGTTGA
1 AAAAAAAGTTGTTACACGCCATGTTGA
* * *
13011803 AAAAAAA-TCGTTACAAGCAATGTTGA
1 AAAAAAAGTTGTTACACGCCATGTTGA
13011829 AAAA
1 AAAA
13011833 TTATTATTAC
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
26 57 0.49
27 46 0.39
28 14 0.12
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (27 bp):
AAAAAAAGTTGTTACACGCCATGTTGA
Found at i:13011806 original size:54 final size:53
Alignment explanation
Indices: 13011689--13011832 Score: 157
Period size: 54 Copynumber: 2.7 Consensus size: 53
13011679 GTTGTATGCC
* * *
13011689 ATGTTGAAAAAAAAGTTGTTGCACA-CCATGTTGAAAAAAAATGGTTACACGCC
1 ATGTTGAAAAAAAAGTTGTTACA-AGCCATGTTGAAAAAAAATGGTTACAAGCA
* * * * * *
13011742 ATATTAAAAAAAAAAGTTGTTACATGCCATGTTGAAAAAAAGTTGTTACAAGTA
1 ATGTT-GAAAAAAAAGTTGTTACAAGCCATGTTGAAAAAAAATGGTTACAAGCA
* *
13011796 ATGTTGAAAAAAAA-TCGTTACAAGCAATGTTGAAAAA
1 ATGTTGAAAAAAAAGTTGTTACAAGCCATGTTGAAAAA
13011833 TTATTATTAC
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
52 20 0.27
53 12 0.16
54 43 0.57
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (53 bp):
ATGTTGAAAAAAAAGTTGTTACAAGCCATGTTGAAAAAAAATGGTTACAAGCA
Found at i:13011832 original size:80 final size:81
Alignment explanation
Indices: 13011669--13011832 Score: 215
Period size: 80 Copynumber: 2.0 Consensus size: 81
13011659 TGTGCGCGTG
** * * *
13011669 AAAAAAAGTTGTTGTATGCCATGTTGAAAAAAAAGTTGTTGCACACCATGTTGAAAAAAAATGGT
1 AAAAAAAGTTGTTACATGCCATGTTGAAAAAAAAGTTGTTACACACAATGTTGAAAAAAAATCGT
* *
13011734 TACACGCCATATTAAA
66 TACAAGCAATATTAAA
*
13011750 AAAAAAAGTTGTTACATGCCATGTTG-AAAAAAAGTTGTTACA-AGTAATGTTGAAAAAAAATCG
1 AAAAAAAGTTGTTACATGCCATGTTGAAAAAAAAGTTGTTACACA-CAATGTTGAAAAAAAATCG
* *
13011813 TTACAAGCAATGTTGAA
65 TTACAAGCAATATTAAA
13011830 AAA
1 AAA
13011833 TTATTATTAC
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 47 0.65
81 24 0.33
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (81 bp):
AAAAAAAGTTGTTACATGCCATGTTGAAAAAAAAGTTGTTACACACAATGTTGAAAAAAAATCGT
TACAAGCAATATTAAA
Found at i:13022375 original size:19 final size:21
Alignment explanation
Indices: 13022347--13022387 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13022337 ACATGTTGAA
13022347 TAGTTATA-TT-AAGTTATTT
1 TAGTTATATTTAAAGTTATTT
*
13022366 TAGTTCTATTTAAAGTTATTT
1 TAGTTATATTTAAAGTTATTT
13022387 T
1 T
13022388 GCTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (21 bp):
TAGTTATATTTAAAGTTATTT
Found at i:13023897 original size:28 final size:28
Alignment explanation
Indices: 13023866--13023980 Score: 135
Period size: 28 Copynumber: 4.2 Consensus size: 28
13023856 ACTATGTTAA
* *
13023866 AAAAAAAAAGTTATTACACGCCAAGTTG
1 AAAAAAAAAGTTGTTACACGCCATGTTG
* *
13023894 AAAAAAAAA-TTGTTACATGCTATGTT-
1 AAAAAAAAAGTTGTTACACGCCATGTTG
* *
13023920 AAAAAAAAAGTTGTTATATGCCATGTTG
1 AAAAAAAAAGTTGTTACACGCCATGTTG
* * *
13023948 AAAATAAAATTTGTTACACGCCATGATG
1 AAAAAAAAAGTTGTTACACGCCATGTTG
13023976 AAAAA
1 AAAAA
13023981 GTGTTGCAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 9 0.12
27 28 0.38
28 36 0.49
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (28 bp):
AAAAAAAAAGTTGTTACACGCCATGTTG
Found at i:13023948 original size:54 final size:56
Alignment explanation
Indices: 13023857--13023965 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 56
13023847 CAACAACACA
13023857 CTATGTTAAAAAAAAAAAGTTATTACACGCCAAGTTGAAAA-AAAAATTGTTACATG
1 CTATGTT-AAAAAAAAAAGTTATTACACGCCAAGTTGAAAATAAAAATTGTTACATG
* * * * *
13023913 CTATGTT-AAAAAAAAAGTTGTTATATGCCATGTTGAAAATAAAATTTGTTACA
1 CTATGTTAAAAAAAAAAGTTATTACACGCCAAGTTGAAAATAAAAATTGTTACA
13023966 CGCCATGATG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
54 28 0.60
55 12 0.26
56 7 0.15
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (56 bp):
CTATGTTAAAAAAAAAAGTTATTACACGCCAAGTTGAAAATAAAAATTGTTACATG
Found at i:13023980 original size:54 final size:54
Alignment explanation
Indices: 13023866--13023980 Score: 140
Period size: 54 Copynumber: 2.1 Consensus size: 54
13023856 ACTATGTTAA
* * *
13023866 AAAAAAAAAGTTATTACACGCCAAGTTGAAAAAAAAATTGTTACATGCTATGTT
1 AAAAAAAAAGTTATTACACGCCAAGTTGAAAAAAAAATTGTTACACGCCATGAT
* * * * *
13023920 AAAAAAAAAGTTGTTATATGCCATGTTGAAAATAAAATTTGTTACACGCCATGAT
1 AAAAAAAAAGTTATTACACGCCAAGTTGAAAA-AAAAATTGTTACACGCCATGAT
*
13023975 GAAAAA
1 AAAAAA
13023981 GTGTTGCAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
54 28 0.55
55 23 0.45
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (54 bp):
AAAAAAAAAGTTATTACACGCCAAGTTGAAAAAAAAATTGTTACACGCCATGAT
Found at i:13024490 original size:172 final size:172
Alignment explanation
Indices: 13024246--13024687 Score: 642
Period size: 172 Copynumber: 2.6 Consensus size: 172
13024236 TTTTGCCCAT
* * * * *
13024246 TTTCTCTTTATTTCAATTTTTCACTGAATTTGAAAAATTTGAAATCTTTTGTTTATTTCGAGATG
1 TTTCTCTTTGTTTCAATTTTACACCGAATTTGAAAAAATTGAAATCTTTTGTTTATTTCAAGATG
* * *
13024311 AATGGAAAATCTTGAACCATTCCTTTCCTTTCCTTTACAACTAAAACACAAAAACCGTTTTCTTA
66 GATGGAAAATCTTGAACCATTCCTTTCCTTTCCTCTACAAATAAAACACAAAAACCGTTTTCTTA
*
13024376 CCTACAATTCTTTTTCACCTTCTTCTTCATTCTTTTTTTGCAC
131 CCTACAATTCTTTTTCACCTTCTTCTTC-TTCCTTTTTTGCAC
* *
13024419 TTTCTCTTTGTTTCGA-TTTACACCGAATTTGAAAAAATTGAAATCTTTTGTTTATTTCAATATG
1 TTTCTCTTTGTTTCAATTTTACACCGAATTTGAAAAAATTGAAATCTTTTGTTTATTTCAAGATG
* * * * *
13024483 GATGGAAAATCTTGAACCATTTCTTTCTTTTCCTCTACAAATGAAACACAAAAACTGTTTTCTTT
66 GATGGAAAATCTTGAACCATTCCTTTCCTTTCCTCTACAAATAAAACACAAAAACCGTTTTCTTA
*
13024548 CCTACAGTTCTTTTTCACCTTCTTCTTCTTCCTTTTTTGCAC
131 CCTACAATTCTTTTTCACCTTCTTCTTCTTCCTTTTTTGCAC
* * *
13024590 TTTTTCTTTGTTTCAATTTTACACCAAATTTGAAAAAATTGAAACCTTTTG---ATTT-AAGATG
1 TTTCTCTTTGTTTCAATTTTACACCGAATTTGAAAAAATTGAAATCTTTTGTTTATTTCAAGATG
* *
13024651 GATGCAAAATCTTGAACCATTCCTTTCCTTTTCTCTA
66 GATGGAAAATCTTGAACCATTCCTTTCCTTTCCTCTA
13024688 TTTAAATTCT
Statistics
Matches: 242, Mismatches: 26, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
168 38 0.16
169 4 0.02
171 27 0.11
172 159 0.66
173 14 0.06
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (172 bp):
TTTCTCTTTGTTTCAATTTTACACCGAATTTGAAAAAATTGAAATCTTTTGTTTATTTCAAGATG
GATGGAAAATCTTGAACCATTCCTTTCCTTTCCTCTACAAATAAAACACAAAAACCGTTTTCTTA
CCTACAATTCTTTTTCACCTTCTTCTTCTTCCTTTTTTGCAC
Found at i:13026672 original size:31 final size:31
Alignment explanation
Indices: 13026637--13026736 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
13026627 AGCTTTGCTT
* **
13026637 AATTTAGATC-ATGTACTATAGCATTTTGTTC
1 AATTTAG-TCTATGTACTAAAAAATTTTGTTC
*
13026668 AATTTAGTCTCTGTACTAAAAAATTTTGTTC
1 AATTTAGTCTATGTACTAAAAAATTTTGTTC
* * * ** * *
13026699 AATTTAATCTTTGTATTTCACAATTTTGTTT
1 AATTTAGTCTATGTACTAAAAAATTTTGTTC
13026730 AATTTAG
1 AATTTAG
13026737 CCCTTAGACA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 2 0.04
31 54 0.96
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (31 bp):
AATTTAGTCTATGTACTAAAAAATTTTGTTC
Found at i:13033062 original size:49 final size:49
Alignment explanation
Indices: 13032990--13033091 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
13032980 AAAGATGATT
13032990 GTTTTCTTTAGTTAATTGGAATAGCAAGATATATGAAATCAGCTCCTCG
1 GTTTTCTTTAGTTAATTGGAATAGCAAGATATATGAAATCAGCTCCTCG
13033039 GTTTTCTTTAGTTAATTGGAATAGCAAGATATATGAAATCAGCTCCTCG
1 GTTTTCTTTAGTTAATTGGAATAGCAAGATATATGAAATCAGCTCCTCG
13033088 GTTT
1 GTTT
13033092 ATCTCATGGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (49 bp):
GTTTTCTTTAGTTAATTGGAATAGCAAGATATATGAAATCAGCTCCTCG
Found at i:13033330 original size:3 final size:3
Alignment explanation
Indices: 13033315--13033347 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
13033305 AAAAAATTTA
*
13033315 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13033348 GAATTTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:13048698 original size:19 final size:19
Alignment explanation
Indices: 13048674--13048710 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13048664 CATCTGCGGG
* *
13048674 GCATCTCTGCAAAGCAAAA
1 GCATCTATGAAAAGCAAAA
13048693 GCATCTATGAAAAGCAAA
1 GCATCTATGAAAAGCAAA
13048711 GAAGACAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.16
Consensus pattern (19 bp):
GCATCTATGAAAAGCAAAA
Found at i:13058874 original size:2 final size:2
Alignment explanation
Indices: 13058867--13058930 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
13058857 CCAAAATCAA
* * * * **
13058867 AT AT AT AT AT AT AT GT AT GT AT AT AT AT GT GT AT AT GC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
13058909 AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
13058931 CCAACAAGGA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13058891 original size:18 final size:18
Alignment explanation
Indices: 13058867--13058930 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
13058857 CCAAAATCAA
13058867 ATATATATATATATG--T
1 ATATATATATATATGTAT
* *
13058883 ATGTATATATATGTGTAT
1 ATATATATATATATGTAT
**
13058901 ATGCATATATATATGTAT
1 ATATATATATATATGTAT
13058919 ATATATATATAT
1 ATATATATATAT
13058931 CCAACAAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.32
18 27 0.68
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (18 bp):
ATATATATATATATGTAT
Found at i:13059633 original size:71 final size:72
Alignment explanation
Indices: 13059511--13059651 Score: 185
Period size: 71 Copynumber: 2.0 Consensus size: 72
13059501 AACTATTTCC
* * * * * *
13059511 ACTCACTCAAGTCTTTCAGCTCTCTAAACTGTATCAACTTTGTCAACTCTCTGTTGAGCA-CATT
1 ACTCACTCAACTCTCTCAGCTCTCTAAACTATATCAACTTCGTCAACTCTCTATTGAGCACCATC
13059575 GTCATTA
66 GTCATTA
* * * *
13059582 ACTCTCTCAACTCTCTCAGCTCTTTAAACTATATCAGCTTCGTCAATTCTCTATTGAGCACCATC
1 ACTCACTCAACTCTCTCAGCTCTCTAAACTATATCAACTTCGTCAACTCTCTATTGAGCACCATC
13059647 GTCAT
66 GTCAT
13059652 CATGCTGTGG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
71 51 0.86
72 8 0.14
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (72 bp):
ACTCACTCAACTCTCTCAGCTCTCTAAACTATATCAACTTCGTCAACTCTCTATTGAGCACCATC
GTCATTA
Found at i:13059937 original size:23 final size:25
Alignment explanation
Indices: 13059880--13059944 Score: 89
Period size: 23 Copynumber: 2.7 Consensus size: 25
13059870 ATGTGTTAGC
13059880 ACATGGCATGTAACATTTTTATTGA
1 ACATGGCATGTAACATTTTTATTGA
* * *
13059905 ATATGGCATGTAATA-TTTT-TTGG
1 ACATGGCATGTAACATTTTTATTGA
13059928 ACATGGCATGTAACATT
1 ACATGGCATGTAACATT
13059945 GGCGTGTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 16 0.47
24 5 0.15
25 13 0.38
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (25 bp):
ACATGGCATGTAACATTTTTATTGA
Found at i:13131395 original size:17 final size:19
Alignment explanation
Indices: 13131364--13131409 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
13131354 ACAATTAATT
*
13131364 AAAACTAAATTTAATCAA-
1 AAAACTAAATCTAATCAAC
*
13131382 AAAACTAAA-CTAATTAAC
1 AAAACTAAATCTAATCAAC
13131400 AAAGACTAAA
1 AAA-ACTAAA
13131410 AATCCACTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 12 0.50
19 6 0.25
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAACTAAATCTAATCAAC
Found at i:13133503 original size:127 final size:127
Alignment explanation
Indices: 13133265--13133514 Score: 367
Period size: 127 Copynumber: 2.0 Consensus size: 127
13133255 ATATACTAGG
* * * *
13133265 TTTAGAAACATGGGTTGCCTCCCAAGAAGCGCTCTTTTTATAGTCATTAGCTAGACTCTCTTGTA
1 TTTAGAAACATAGGCTGCCTCCCAAAAAGCGCTCTTTTTATAGTCATTAGCCAGACTCTCTTGTA
* **
13133330 AGCTCATTTGGGATAGAAAAGATTGATGGACGATCATTGATGATCAATGTCACCTCCCAAAT
66 AGCTCATTTGGGATAGAAAAGATTGATGGACAATCATTGACAATCAATGTCACCTCCCAAAT
* * * *
13133392 TTTAGAAACTTAGGCTGCCTCCCAAAAAGTGCTCTTTTTATAGTCGTTAGCCAGACTCTTTTGTA
1 TTTAGAAACATAGGCTGCCTCCCAAAAAGCGCTCTTTTTATAGTCATTAGCCAGACTCTCTTGTA
* *
13133457 AGCTCATTTGGGGTTA-AAAAGATTGATGGACAATCGTTGACAATCAATGTCACCTCCC
66 AGCTCATTT-GGGATAGAAAAGATTGATGGACAATCATTGACAATCAATGTCACCTCCC
13133515 CAATAATGCT
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
127 104 0.95
128 5 0.05
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (127 bp):
TTTAGAAACATAGGCTGCCTCCCAAAAAGCGCTCTTTTTATAGTCATTAGCCAGACTCTCTTGTA
AGCTCATTTGGGATAGAAAAGATTGATGGACAATCATTGACAATCAATGTCACCTCCCAAAT
Found at i:13147308 original size:38 final size:40
Alignment explanation
Indices: 13147266--13147368 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 40
13147256 ATAGTGCCCG
* *
13147266 TGTGCACGATGTGGGAGGATGTACACGACGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGACGGCGACGGATA
* * * * * *
13147304 TGTGCATGATGTGGGGGGATGCACATGATGGCGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGACGGCGACGGATA
13147344 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
13147369 TGAGCCGGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 27 0.51
39 3 0.06
40 23 0.43
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGACGGCGACGGATA
Found at i:13149731 original size:21 final size:21
Alignment explanation
Indices: 13149705--13149768 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
13149695 CCCGGCAATG
*
13149705 ACTTTAGTTAGCTAACTTCAC
1 ACTTTAGTCAGCTAACTTCAC
* *
13149726 ACTTTAGTCAACTAACTTCAT
1 ACTTTAGTCAGCTAACTTCAC
*
13149747 GCTTTAGTCAGCTAACTTCAC
1 ACTTTAGTCAGCTAACTTCAC
13149768 A
1 A
13149769 GATTAAGTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (21 bp):
ACTTTAGTCAGCTAACTTCAC
Found at i:13157061 original size:21 final size:21
Alignment explanation
Indices: 13157035--13157098 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
13157025 CCTGCCAATG
13157035 ACTTTAGTCAGCTAACTTCAC
1 ACTTTAGTCAGCTAACTTCAC
* *
13157056 ACTTTAGTCAACTAACTTCAT
1 ACTTTAGTCAGCTAACTTCAC
* *
13157077 GCTTTAGTAAGCTAACTTCAC
1 ACTTTAGTCAGCTAACTTCAC
13157098 A
1 A
13157099 GATTATGTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34
Consensus pattern (21 bp):
ACTTTAGTCAGCTAACTTCAC
Found at i:13168096 original size:22 final size:22
Alignment explanation
Indices: 13168068--13168132 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
13168058 TTAGATTGGT
13168068 ATCAGAGCTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
13168090 ATCAGAGCTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
* *
13168112 ATTAGAGCTTTTGGGTTTAAA
1 ATCAGAGCTTTTGGTTTTAAA
13168133 ATTGTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (22 bp):
ATCAGAGCTTTTGGTTTTAAAG
Found at i:13173347 original size:17 final size:17
Alignment explanation
Indices: 13173325--13173385 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
13173315 GACACATGGC
13173325 ATATTTATAACCATTAA
1 ATATTTATAACCATTAA
* **
13173342 ATATTTAACTTTAA-AATTNC
1 ATATTT-A---TAACCATTAA
13173362 ATATTTATAACCATTAA
1 ATATTTATAACCATTAA
13173379 ATATTTA
1 ATATTTA
13173386 GCTTTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
16 3 0.09
17 16 0.48
18 1 0.03
19 1 0.03
20 9 0.27
21 3 0.09
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATTTATAACCATTAA
Found at i:13173374 original size:37 final size:36
Alignment explanation
Indices: 13173324--13173396 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 36
13173314 TGACACATGG
13173324 CATATTTATAACCATTAAATATTTAACTTTAAAATT
1 CATATTTATAACCATTAAATATTTAACTTTAAAATT
*
13173360 NCATATTTATAACCATTAAATATTTAGCTTTAAAATT
1 -CATATTTATAACCATTAAATATTTAACTTTAAAATT
13173397 AATACAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.11, G:0.01, T:0.44
Consensus pattern (36 bp):
CATATTTATAACCATTAAATATTTAACTTTAAAATT
Found at i:13175671 original size:28 final size:28
Alignment explanation
Indices: 13175615--13175672 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
13175605 ATTTATAGTA
*
13175615 TAGGGGCGAAATGGTAATTTTGCCACCC
1 TAGGGGCGAAATGGTAATTTTGACACCC
*
13175643 TAGGGGC-AAATCGGTAAATTTTTAC-CCC
1 TAGGGGCGAAAT-GGT-AATTTTGACACCC
13175671 TA
1 TA
13175673 ACACTTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 15 0.58
29 7 0.27
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (28 bp):
TAGGGGCGAAATGGTAATTTTGACACCC
Found at i:13176823 original size:13 final size:13
Alignment explanation
Indices: 13176805--13176829 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13176795 TGAGAAATTG
13176805 TGATTTTATAAAA
1 TGATTTTATAAAA
13176818 TGATTTTATAAA
1 TGATTTTATAAA
13176830 TTTTCTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:13187703 original size:13 final size:13
Alignment explanation
Indices: 13187685--13187709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13187675 TTTCAGAAAA
13187685 TTTATAAAATCAT
1 TTTATAAAATCAT
13187698 TTTATAAAATCA
1 TTTATAAAATCA
13187710 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:13188875 original size:27 final size:27
Alignment explanation
Indices: 13188822--13188875 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
13188812 AAATGTTCTA
* *
13188822 GGGGTGCAACATTACCATTTTGCCCCC
1 GGGGTGCAAAATTACCATTTCGCCCCC
13188849 GGGGTGGCAAAATTACCATTTCGCCCC
1 GGGGT-GCAAAATTACCATTTCGCCCC
13188876 TGTACTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (27 bp):
GGGGTGCAAAATTACCATTTCGCCCCC
Found at i:13188944 original size:19 final size:19
Alignment explanation
Indices: 13188920--13188957 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13188910 ACTTCTAAAC
13188920 CTCAAATCATACCCCAATA
1 CTCAAATCATACCCCAATA
*
13188939 CTCAAATCATACTCCAATA
1 CTCAAATCATACCCCAATA
13188958 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (19 bp):
CTCAAATCATACCCCAATA
Found at i:13200030 original size:73 final size:74
Alignment explanation
Indices: 13199823--13200030 Score: 260
Period size: 73 Copynumber: 2.8 Consensus size: 74
13199813 ATCTTCAAAC
* ** *
13199823 AGAATGCTCTTAGTCGACTAACTATACTTCTTAGTTAATTAAGTCGTCTTTGTCTCTGAAC-CCA
1 AGAA-GCTCTTAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACTCCA
13199887 GTTTCTGGCA
65 GTTTCTGGCA
* * * * * *
13199897 AGAAGCTTTTAGTTGACTAACTATGCTTCTTAATCGATTAATTCGTCTCTATCTCTGAACTCGA-
1 AGAAGCTCTTAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACTCCAG
* *
13199961 TTTTTGG-T
66 TTTCTGGCA
*
13199969 AGTAAGCTCTTAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTTTGAACT
1 AG-AAGCTCTTAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACT
13200031 GACCCATCTT
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
72 2 0.02
73 106 0.93
74 6 0.05
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (74 bp):
AGAAGCTCTTAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACTCCAG
TTTCTGGCA
Found at i:13203434 original size:27 final size:27
Alignment explanation
Indices: 13203383--13203434 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
13203373 ATATCCTGAT
*
13203383 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
*
13203410 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
13203435 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:13203505 original size:20 final size:20
Alignment explanation
Indices: 13203480--13203525 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
13203470 TTTCTAAACC
13203480 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
13203500 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
13203520 TCAAAT
1 TCAAAT
13203526 GGGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:13204952 original size:20 final size:20
Alignment explanation
Indices: 13204914--13204952 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13204904 TCAAGAGTAA
*
13204914 GAAGAATAATAAAAGCTAAG
1 GAAGAATAATAAAAACTAAG
13204934 GAAGAATAA-AATAAACTAA
1 GAAGAATAATAA-AAACTAA
13204953 TTTTTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.64, C:0.05, G:0.15, T:0.15
Consensus pattern (20 bp):
GAAGAATAATAAAAACTAAG
Found at i:13274901 original size:19 final size:20
Alignment explanation
Indices: 13274862--13274902 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13274852 CTTTCTTGTT
13274862 AGTTTTTTGATAACTCAAAA
1 AGTTTTTTGATAACTCAAAA
13274882 AGTTTTTTGATAACTCAAAA
1 AGTTTTTTGATAACTCAAAA
13274902 A
1 A
13274903 ACTAACTTTT
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:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (20 bp):
AGTTTTTTGATAACTCAAAA
Found at i:13283447 original size:19 final size:19
Alignment explanation
Indices: 13283423--13283460 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
13283413 ACTTCTTAAC
13283423 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
13283442 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
13283461 AGTCAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:13283892 original size:19 final size:19
Alignment explanation
Indices: 13283868--13283918 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
13283858 TTAATATTTT
13283868 AATATTATCTTATTA-ATAA
1 AATATTATCTTATTATA-AA
* *
13283887 AATATTATTTTATTTTAAA
1 AATATTATCTTATTATAAA
*
13283906 AATTTTATCTTAT
1 AATATTATCTTAT
13283919 CTCCTTGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTATCTTATTATAAA
Found at i:13293764 original size:28 final size:29
Alignment explanation
Indices: 13293723--13293782 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
13293713 GTCTATGGGC
*
13293723 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
13293751 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
13293781 AA
1 AA
13293783 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:13303330 original size:31 final size:31
Alignment explanation
Indices: 13303287--13303426 Score: 228
Period size: 31 Copynumber: 4.5 Consensus size: 31
13303277 GTGTCAGCGT
*
13303287 TGGCGTGTAACAACATTTGACTTGATATACA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
13303318 TGGCATGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
13303349 TGGCGTGTAACAACATTTGACTTGATACGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
13303380 TGGCGTGTAACAATATTTGACGTT-ATATGCA
1 TGGCGTGTAACAACATTTGAC-TTGATATGCA
13303411 TGGCGTGTAACAACAT
1 TGGCGTGTAACAACAT
13303427 GACTGACAAA
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 99 0.98
32 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTGACTTGATATGCA
Found at i:13307376 original size:86 final size:86
Alignment explanation
Indices: 13307244--13307408 Score: 267
Period size: 86 Copynumber: 1.9 Consensus size: 86
13307234 ACACACTGAG
* * * *
13307244 TGCATGTAGATTTTTGTGGTAATACGCTGACTTCTTGTAGTATTGTGGGGTGACACGGCACGCCT
1 TGCATGTAGATTTCTGTGGTAAGACGCTGACTTATTGTAGTATTGTGGGGTGACACGGCACGCCA
13307309 CAATTCTAGTGACACGTTGAA
66 CAATTCTAGTGACACGTTGAA
* *
13307330 TGCATGTAGATTTCTGTGGTGAGACGCTGACTTATTGTAGTATTGTGGGGTGACACGGCATGCCA
1 TGCATGTAGATTTCTGTGGTAAGACGCTGACTTATTGTAGTATTGTGGGGTGACACGGCACGCCA
*
13307395 CAATTGTAGTGACA
66 CAATTCTAGTGACA
13307409 TGCTGAGTGG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 72 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (86 bp):
TGCATGTAGATTTCTGTGGTAAGACGCTGACTTATTGTAGTATTGTGGGGTGACACGGCACGCCA
CAATTCTAGTGACACGTTGAA
Found at i:13307443 original size:86 final size:86
Alignment explanation
Indices: 13307231--13307445 Score: 218
Period size: 86 Copynumber: 2.5 Consensus size: 86
13307221 GATACTTGGC
* * * * * * * * *
13307231 GTGACACACTGAGTGCATGTAGATTTTTGTGGTAATACGCTGACTTCTTGTAGTATTGTGGGGTG
1 GTGACACGCTGAATGCAAGCAGATCTCTGTGGTGACACGCTGACTTATTGTAGTATTGTGGGGTG
*
13307296 ACACGGCACGCCTCAATTCTA
66 ACACGGCACGCCACAATTCTA
* * * * *
13307317 GTGACACGTTGAATGCATGTAGATTTCTGTGGTGAGACGCTGACTTATTGTAGTATTGTGGGGTG
1 GTGACACGCTGAATGCAAGCAGATCTCTGTGGTGACACGCTGACTTATTGTAGTATTGTGGGGTG
* *
13307382 ACACGGCATGCCACAATTGTA
66 ACACGGCACGCCACAATTCTA
* * *
13307403 GTGACATGCTGAGTGGAAGCAGATACT-TG-GCGTGACACGCTGA
1 GTGACACGCTGAATGCAAGCAGAT-CTCTGTG-GTGACACGCTGA
13307446 GTGCATGCAA
Statistics
Matches: 109, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
85 1 0.01
86 107 0.98
87 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (86 bp):
GTGACACGCTGAATGCAAGCAGATCTCTGTGGTGACACGCTGACTTATTGTAGTATTGTGGGGTG
ACACGGCACGCCACAATTCTA
Found at i:13307465 original size:117 final size:117
Alignment explanation
Indices: 13307317--13307796 Score: 636
Period size: 117 Copynumber: 4.1 Consensus size: 117
13307307 CTCAATTCTA
* * * * * *
13307317 GTGACACGTTGAATGCATGTAGATTTCTGTGGTGAGACGCTGACTTATTGTAGTATTGTGGGGTG
1 GTGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTTTTGCAGTATTGTGGGGTG
* * * * *
13307382 ACACGGCATGCCACAATTGTAGTGACATGCTGAGTGGAAGCAGATACTTGGC
66 ACACAGCACGCCCCAATTCTAGTGACACGCTGAGTGGAAGCAGATACTTGGC
* ** * *
13307434 GTGACACGCTGAGTGCATGCAAATTTCTGTGGTGACACATTGACTTCTTACAGTATTGTGGGGTG
1 GTGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTTTTGCAGTATTGTGGGGTG
* * *
13307499 ACACAGCACGCCCCAATTCTAGTGACACGTTGAGTGGAAACAAATACTTGGC
66 ACACAGCACGCCCCAATTCTAGTGACACGCTGAGTGGAAGCAGATACTTGGC
* * * * * *
13307551 GTGACACACTGAGTACATGTAGATTTCTGTGGTGACATGTTGACTTTTTGCAGTGTTGTGGGGTG
1 GTGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTTTTGCAGTATTGTGGGGTG
* *
13307616 ACACAACACGCCCCATTTCTAGTGACACGCTGAGTGGAAGCAGATACTTGGC
66 ACACAGCACGCCCCAATTCTAGTGACACGCTGAGTGGAAGCAGATACTTGGC
* * * *
13307668 ATAACATGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTTACTTTTTGCAGTATTGTGGGGTG
1 GTGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTTTTGCAGTATTGTGGGGTG
* * * * *
13307733 ACACGGCACTCCCCAATTGTGGTGACACGCTGAGTGGAAGCAGATTCTTGGC
66 ACACAGCACGCCCCAATTCTAGTGACACGCTGAGTGGAAGCAGATACTTGGC
13307785 GTGACACGCTGA
1 GTGACACGCTGA
13307797 CTTGTTACAG
Statistics
Matches: 311, Mismatches: 52, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
117 311 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (117 bp):
GTGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTTTTGCAGTATTGTGGGGTG
ACACAGCACGCCCCAATTCTAGTGACACGCTGAGTGGAAGCAGATACTTGGC
Found at i:13307587 original size:203 final size:203
Alignment explanation
Indices: 13307195--13307587 Score: 454
Period size: 203 Copynumber: 1.9 Consensus size: 203
13307185 CAATGACATC
* * * *
13307195 TTGTGGTGACACGCTGAGTAGAAGTCGATACTTGGCGTGACACACTGAGTGCATGTAGATTTTTG
1 TTGTAGTGACACGCTGAGTAGAAGTCGATACTTGGCGTGACACACTGAGTGCATGCAAATTTCTG
* * ** * *
13307260 TGGTAATACGCTGACTTCTTGTAGTATTGTGGGGTGACACGGCACGCCTCAATTCTAGTGACACG
66 TGGTAACACACTGACTTCTTACAGTATTGTGGGGTGACACAGCACGCCCCAATTCTAGTGACACG
*** * * * * * * *
13307325 TTGAATGCATGTAGATTTCTGTGGTGAGACGCTGACTTATTGTAGTATTGTGGGGTGACACGGCA
131 TTGAATGCAAACAAATCTCTGTGGTGACACACTGACGTAATGTAGTATTCTGGGGTGACACGGCA
13307390 TGCCACAA
196 TGCCACAA
* * *
13307398 TTGTAGTGACATGCTGAGTGGAAG-CAGATACTTGGCGTGACACGCTGAGTGCATGCAAATTTCT
1 TTGTAGTGACACGCTGAGTAGAAGTC-GATACTTGGCGTGACACACTGAGTGCATGCAAATTTCT
* *
13307462 GTGGTGACACATTGACTTCTTACAGTATTGTGGGGTGACACAGCACGCCCCAATTCTAGTGACAC
65 GTGGTAACACACTGACTTCTTACAGTATTGTGGGGTGACACAGCACGCCCCAATTCTAGTGACAC
* * *
13307527 GTTGAGTGGAAACAAATACT-TG-GCGTGACACACTGA-GTACATGTAG-ATTTCTGTGGTGACA
130 GTTGAATGCAAACAAAT-CTCTGTG-GTGACACACTGACGTA-ATGTAGTA-TTCTGGGGTGACA
13307588 TGTTGACTTT
Statistics
Matches: 157, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
202 5 0.03
203 151 0.96
204 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (203 bp):
TTGTAGTGACACGCTGAGTAGAAGTCGATACTTGGCGTGACACACTGAGTGCATGCAAATTTCTG
TGGTAACACACTGACTTCTTACAGTATTGTGGGGTGACACAGCACGCCCCAATTCTAGTGACACG
TTGAATGCAAACAAATCTCTGTGGTGACACACTGACGTAATGTAGTATTCTGGGGTGACACGGCA
TGCCACAA
Found at i:13311575 original size:31 final size:31
Alignment explanation
Indices: 13311540--13311628 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
13311530 AGAAAGAAAT
* * *
13311540 AAATGTTGTTACATGCTATGCATATCTAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* *
13311571 AAATGCTGTTACACGCCATGCATATCAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* *
13311602 AAATGTCGTGACACGCCATGCATATCA
1 AAATGTTGTTACACGCCATGCATATCA
13311629 GTGTTGTGAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (31 bp):
AAATGTTGTTACACGCCATGCATATCAAGTA
Found at i:13311985 original size:104 final size:103
Alignment explanation
Indices: 13311723--13312042 Score: 370
Period size: 104 Copynumber: 3.0 Consensus size: 103
13311713 TAAAAACCCT
* * * * *** * *
13311723 AAAAACTAGTTAACCCACAGCACGCCACGAAGAGCCGTGACACACTAAAAACACAAAAAACTAGT
1 AAAAAATAGTTAACCCACAACACGCCACGAACAACCGTGACACACCCTAAACCCAAAAAACCAGT
* *
13311788 TAACCCACAACACGCCATATGCAATCGTGACACGCTAAAAA
66 TAACCCACAACACGCCATGTGCAACCGTGACACGCT---AA
* *
13311829 CCCAAAAAACTAGTTAACCCACAACATGCCACGAACAACCGTGACACGCCCTAAACCCAAAAAAC
1 ---AAAAAA-TAGTTAACCCACAACACGCCACGAACAACCGTGACACACCCTAAACCCAAAAAAC
* * *
13311894 CAGTTAATCCATAACACGCCATGTGCAGCCGTGACACGCTGAA
62 CAGTTAACCCACAACACGCCATGTGCAACCGTGACACGCT-AA
* * *
13311937 AAAAAATAGCTAACCCACAACACGCCACAAACAACCGTGACACACCCTAAACCCAGAAAACCAGT
1 AAAAAATAGTTAACCCACAACACGCCACGAACAACCGTGACACACCCTAAACCCAAAAAACCAGT
* **
13312002 TAACCCACAACACACCATGAACAACCGTGACACGCTAA
66 TAACCCACAACACGCCATGTGCAACCGTGACACGCTAA
13312040 AAA
1 AAA
13312043 CCCAAAAAAC
Statistics
Matches: 182, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
103 5 0.03
104 84 0.46
105 6 0.03
108 2 0.01
109 5 0.03
110 80 0.44
ACGTcount: A:0.44, C:0.33, G:0.12, T:0.11
Consensus pattern (103 bp):
AAAAAATAGTTAACCCACAACACGCCACGAACAACCGTGACACACCCTAAACCCAAAAAACCAGT
TAACCCACAACACGCCATGTGCAACCGTGACACGCTAA
Found at i:13312102 original size:214 final size:214
Alignment explanation
Indices: 13311723--13312241 Score: 513
Period size: 214 Copynumber: 2.4 Consensus size: 214
13311713 TAAAAACCCT
* * * * * * * *
13311723 AAAAACTAGTTAACCCACAGCACGCCACGAAGAGCCGTGACACACTAAAAACACAAAAAACTAGT
1 AAAAAATAGCTAACCCACAACACGCCACAAACAACCGTGACACACCAAAAACACAAAAAACCAGT
* * * *
13311788 TAACCCACAACACGCCATATGCAATCGTGACACGCTAAAAACCCAAAAAACTAGTTAACCCACAA
66 TAACCCACAACACACCATATACAACCGTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAA
** * ** * *
13311853 CATGCCACGAACAACCGTGACACGCCCTAAACCCAAAAAACCAGTTAATCCATAACACGCCATGT
131 CATGCCACGAACAACAATGACACACCAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATGT
13311918 GCAGCCGTGACACGCTGAA
196 GCAGCCGTGACACGCTGAA
** * *
13311937 AAAAAATAGCTAACCCACAACACGCCACAAACAACCGTGACACACCCTAAACCCAGAAAACCAGT
1 AAAAAATAGCTAACCCACAACACGCCACAAACAACCGTGACACACCAAAAACACAAAAAACCAGT
13312002 TAACCCACAACACACCATGA-ACAACCGTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACA
66 TAACCCACAACACACCAT-ATACAACCGTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACA
* * * * * * * *
13312066 ACATGTCA-TATGCAGCAATGACACACTAAAAACCCAAAAAATCAGTTAACCCACAACATGCCAC
130 ACATGCCACGA-ACAACAATGACACACCAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAT
** * ** *
13312130 GAACAACCGTGACACATTTAAAA
194 GTGCAGCCGTGACAC-GCT-GAA
* * ** ** * *
13312153 CTTAAAAAACTAGTTAACCCACAACACGCCATATGCAATTGTGACACGCTAAAAATC-CAAAAAA
1 ---AAAAAA-TAGCTAACCCACAACACGCCACAAACAACCGTGACACACCAAAAA-CACAAAAAA
* *
13312217 CCAATTAACCCACAACACGCCATAT
61 CCAGTTAACCCACAACACACCATAT
13312242 GCAAACGCAG
Statistics
Matches: 245, Mismatches: 50, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
213 1 0.00
214 170 0.69
215 2 0.01
216 2 0.01
219 7 0.03
220 62 0.25
221 1 0.00
ACGTcount: A:0.45, C:0.32, G:0.11, T:0.13
Consensus pattern (214 bp):
AAAAAATAGCTAACCCACAACACGCCACAAACAACCGTGACACACCAAAAACACAAAAAACCAGT
TAACCCACAACACACCATATACAACCGTGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAA
CATGCCACGAACAACAATGACACACCAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATGT
GCAGCCGTGACACGCTGAA
Found at i:13312184 original size:269 final size:268
Alignment explanation
Indices: 13311716--13312207 Score: 677
Period size: 269 Copynumber: 1.8 Consensus size: 268
13311706 GACACACTAA
* * * * *
13311716 AAACCCTAAAAACTAGTTAACCCACAGCACGCCACGAAGAGCCGTGACACACTAAAAACACAAAA
1 AAACCCTAAAAACCAGTTAACCCACAACACACCACGAACAACCGTGACACACTAAAAACACAAAA
* * * *
13311781 AACTAGTTAACCCACAACACGCCATATGCAATCGTGACACGCTAAAAACCCAAAAAACTAGTTAA
66 AACCAGTTAACCCACAACACGCCATATGCAAGCATGACACACTAAAAACCCAAAAAACTAGTTAA
* * *
13311846 CCCACAACATGCCACGAACAACCGTGACACGCCCTAAACCCAAAAAACCAGTTAATCCATAACAC
131 CCCACAACATGCCACGAACAACCGTGACACGACCTAAACCCAAAAAACCAGTTAACCCACAACAC
* *
13311911 GCCATGTGCAGCCGTGACACGCTGAAAAAAAATAGCTAACCCACAACACGCCACAAACAACCGTG
196 GCCATATGCAACCGTGACACGCT-AAAAAAAATAGCTAACCCACAACACGCCACAAACAACCGTG
13311976 ACACACCCT
260 ACACACCCT
* * *
13311985 AAACCC-AGAAAACCAGTTAACCCACAACACACCATGAACAACCGTGACACGCTAAAAACCCAAA
1 AAACCCTA-AAAACCAGTTAACCCACAACACACCACGAACAACCGTGACACACTAAAAACACAAA
* *
13312049 AAACCAGTTAACCCACAACATGTCATATGC-AGCAATGACACACTAAAAACCCAAAAAA-TCAGT
65 AAACCAGTTAACCCACAACACGCCATATGCAAGC-ATGACACACTAAAAACCCAAAAAACT-AGT
** ** *
13312112 TAACCCACAACATGCCACGAACAACCGTGACAC-ATTTAAAACTTAAAAAACTAGTTAACCCACA
128 TAACCCACAACATGCCACGAACAACCGTGACACGACCT-AAACCCAAAAAACCAGTTAACCCACA
**
13312176 ACACGCCATATGCAATTGTGACACGCTAAAAA
192 ACACGCCATATGCAACCGTGACACGCTAAAAA
13312208 TCCAAAAAAC
Statistics
Matches: 193, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
268 10 0.05
269 183 0.95
ACGTcount: A:0.44, C:0.32, G:0.11, T:0.13
Consensus pattern (268 bp):
AAACCCTAAAAACCAGTTAACCCACAACACACCACGAACAACCGTGACACACTAAAAACACAAAA
AACCAGTTAACCCACAACACGCCATATGCAAGCATGACACACTAAAAACCCAAAAAACTAGTTAA
CCCACAACATGCCACGAACAACCGTGACACGACCTAAACCCAAAAAACCAGTTAACCCACAACAC
GCCATATGCAACCGTGACACGCTAAAAAAAATAGCTAACCCACAACACGCCACAAACAACCGTGA
CACACCCT
Found at i:13312239 original size:55 final size:55
Alignment explanation
Indices: 13311705--13312245 Score: 481
Period size: 55 Copynumber: 9.9 Consensus size: 55
13311695 CGAACAGTCA
* * * * * * *
13311705 TGACACACTAAAAACCCTAAAAACTAGTTAACCCACAGCACGCCACGAAG-AGCCG
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCA-TATGCAACCG
* * * *
13311760 TGACACACTAAAAACACAAAAAACTAGTTAACCCACAACACGCCATATGCAATCG
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATATGCAACCG
* * * *
13311815 TGACACGCTAAAAACCCAAAAAACTAGTTAACCCACAACATGCCACGA-ACAACCG
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCA-TATGCAACCG
*** * * * *
13311870 TGACACGCCCTAAACCCAAAAAACCAGTTAATCCATAACACGCCATGTGCAGCCG
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATATGCAACCG
* * * * **
13311925 TGACACGCT--GAA---AAAAAA-TAGCTAACCCACAACACGCCACAAACAACCG
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATATGCAACCG
* *** * * *
13311974 TGACACACCCTAAACCCAGAAAACCAGTTAACCCACAACACACCATGA-ACAACCG
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAT-ATGCAACCG
* * * **
13312029 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACATGTCATATGCAGCAA
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATATGCAACCG
* * * * *
13312084 TGACACACTAAAAACCCAAAAAATCAGTTAACCCACAACATGCCACGA-ACAACCG
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCA-TATGCAACCG
** * ** * **
13312139 TGACACATTTAAAACTTAAAAAACTAGTTAACCCACAACACGCCATATGCAATTG
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATATGCAACCG
* *
13312194 TGACACGCTAAAAATCCAAAAAACCAATTAACCCACAACACGCCATATGCAA
1 TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATATGCAA
13312246 ACGCAGACCC
Statistics
Matches: 391, Mismatches: 82, Indels: 26
0.78 0.16 0.05
Matches are distributed among these distances:
49 29 0.07
50 6 0.02
51 2 0.01
53 2 0.01
54 9 0.02
55 340 0.87
56 3 0.01
ACGTcount: A:0.45, C:0.32, G:0.11, T:0.13
Consensus pattern (55 bp):
TGACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCATATGCAACCG
Found at i:13312661 original size:23 final size:23
Alignment explanation
Indices: 13312635--13312695 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
13312625 TTCTTTCAGA
13312635 CCATGGCATGTCACATATTCAAC
1 CCATGGCATGTCACATATTCAAC
* *
13312658 CCATGGCATGTCACATGTTCAAG
1 CCATGGCATGTCACATATTCAAC
* *
13312681 CCATGCCGTGTCACA
1 CCATGGCATGTCACA
13312696 CGTTCTGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (23 bp):
CCATGGCATGTCACATATTCAAC
Found at i:13312798 original size:23 final size:23
Alignment explanation
Indices: 13312755--13312799 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13312745 CGTGTTACAT
*
13312755 ATTATCACCGTGCCGTCTCACAC
1 ATTATCACCGTGCCATCTCACAC
*
13312778 ATTATCACTC-TGCCATGTCACA
1 ATTATCAC-CGTGCCATCTCACA
13312800 GATTCCCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.24, C:0.36, G:0.11, T:0.29
Consensus pattern (23 bp):
ATTATCACCGTGCCATCTCACAC
Found at i:13312844 original size:47 final size:47
Alignment explanation
Indices: 13312787--13312891 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 47
13312777 CATTATCACT
* *
13312787 CTGCCATGTCACAGATTCCCTCCATAGAGTGTCACAAACTCTGAACC
1 CTGCCGTGTCACAGATTCCCTCCATAGAGTGTCACAAACTCTAAACC
* * *
13312834 CTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACACACTCTAAACC
1 CTGCCGTGTCACAGATTCCCTCCATAGAGTGTCACAAACTCTAAACC
* *
13312881 TTACCGTGTCA
1 CTGCCGTGTCA
13312892 TAGTCGTGTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (47 bp):
CTGCCGTGTCACAGATTCCCTCCATAGAGTGTCACAAACTCTAAACC
Found at i:13312868 original size:23 final size:23
Alignment explanation
Indices: 13312793--13312869 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
13312783 CACTCTGCCA
* *
13312793 TGTCACAGATTCCCTCCATAGAG
1 TGTCACAGATTCCCTCCATGGCG
* * *** * *
13312816 TGTCACAAACTCTGAACCCTGCCG
1 TGTCACAGATTC-CCTCCATGGCG
13312840 TGTCACAGATTCCCTCCATGGCG
1 TGTCACAGATTCCCTCCATGGCG
13312863 TGTCACA
1 TGTCACA
13312870 CACTCTAAAC
Statistics
Matches: 37, Mismatches: 16, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (23 bp):
TGTCACAGATTCCCTCCATGGCG
Found at i:13312992 original size:24 final size:23
Alignment explanation
Indices: 13312933--13312998 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
13312923 TCACAAATTA
**
13312933 TAACCCT-TCCGTGTCACACGTTC
1 TAACCCTGT-CGTGTCACACACTC
* *
13312956 TAACCATGGCGTGTCACACACTC
1 TAACCCTGTCGTGTCACACACTC
13312979 TAAACCCTGTCGTGTCACAC
1 T-AACCCTGTCGTGTCACAC
13312999 TCGTGTCACA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (23 bp):
TAACCCTGTCGTGTCACACACTC
Found at i:13313030 original size:23 final size:23
Alignment explanation
Indices: 13313004--13313059 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
13312994 CACACTCGTG
* * *
13313004 TCACATATTCTCACCGTGCCGTC
1 TCACACATTCTCACCCTACCGTC
* *
13313027 TCACACATTATCACCCTACCGTG
1 TCACACATTCTCACCCTACCGTC
*
13313050 TCACAGATTC
1 TCACACATTC
13313060 CCTCAATGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.29
Consensus pattern (23 bp):
TCACACATTCTCACCCTACCGTC
Found at i:13313130 original size:23 final size:23
Alignment explanation
Indices: 13313104--13313156 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
13313094 GTGTCACAGC
*
13313104 CGTGTCACATATTCTCACCATGA
1 CGTGTCACACATTCTCACCATGA
* * *
13313127 CGTGTCACACATTGTCATCATGC
1 CGTGTCACACATTCTCACCATGA
13313150 CGTGTCA
1 CGTGTCA
13313157 TAAACTCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (23 bp):
CGTGTCACACATTCTCACCATGA
Found at i:13313153 original size:104 final size:104
Alignment explanation
Indices: 13312831--13313156 Score: 377
Period size: 104 Copynumber: 3.1 Consensus size: 104
13312821 CAAACTCTGA
* ** * *
13312831 ACCCTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACACACTCTAAACCTTACCGTGTCATAGT
1 ACCCTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACAGC
* * * * * * *
13312896 CGTGTCACACATTATCACTGTGTCGTTTCACAAATTATA
66 CGTGTCACATATTCTCACCGTGACGTCTCACACATTATC
* ***
13312935 ACCCTTCCGTGTCACACG-TTCTAACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACA-
1 ACCCTGCCGTGTCACA-GATTCCCTCCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACAG
*
13312998 CTCGTGTCACATATTCTCACCGTGCCGTCTCACACATTATC
65 C-CGTGTCACATATTCTCACCGTGACGTCTCACACATTATC
* * ** *
13313039 ACCCTACCGTGTCACAGATTCCCTCAATGGTATGTCACACACTCTAAACCCTGTTGTGTCACAGC
1 ACCCTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACAGC
* * *
13313104 CGTGTCACATATTCTCACCATGACGTGTCACACATTGTC
66 CGTGTCACATATTCTCACCGTGACGTCTCACACATTATC
* *
13313143 ATCATGCCGTGTCA
1 ACCCTGCCGTGTCA
13313157 TAAACTCTAT
Statistics
Matches: 187, Mismatches: 31, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
103 1 0.01
104 184 0.98
105 2 0.01
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (104 bp):
ACCCTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACAGC
CGTGTCACATATTCTCACCGTGACGTCTCACACATTATC
Found at i:13313156 original size:81 final size:81
Alignment explanation
Indices: 13313038--13313252 Score: 234
Period size: 81 Copynumber: 2.7 Consensus size: 81
13313028 CACACATTAT
* * * * *** * **
13313038 CACCCTACCGTGTCACAGATTCCCTCAATGGTATGTCACACACTCTAAACCCTGTTGTGTCACAG
1 CACCATACCGTGTCACACATTCCCACCATGCCGTGTCACAAACTCTAAACCCTGCCGTGTCACAG
*
13313103 CCGTGTCACATATTCT
66 CCGTGTCACATATTCC
** * * *
13313119 CACCATGA-CGTGTCACACATTGTCATCATGCCGTGTCATAAACTCTATACCCTGCCGTGTCACA
1 CACCAT-ACCGTGTCACACATTCCCACCATGCCGTGTCACAAACTCTAAACCCTGCCGTGTCACA
*
13313183 GTCGTGTCACATATTCC
65 GCCGTGTCACATATTCC
* * *
13313200 CACCATACCGTGTCACACATTCCCACCATGTCGTTTCACAAACTCAAAACCCT
1 CACCATACCGTGTCACACATTCCCACCATGCCGTGTCACAAACTCTAAACCCT
13313253 ACTGTCACAC
Statistics
Matches: 107, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
80 1 0.01
81 105 0.98
82 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.13, T:0.27
Consensus pattern (81 bp):
CACCATACCGTGTCACACATTCCCACCATGCCGTGTCACAAACTCTAAACCCTGCCGTGTCACAG
CCGTGTCACATATTCC
Found at i:13313215 original size:23 final size:23
Alignment explanation
Indices: 13313185--13313228 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
13313175 GTGTCACAGT
*
13313185 CGTGTCACATATTCCCACCATAC
1 CGTGTCACACATTCCCACCATAC
13313208 CGTGTCACACATTCCCACCAT
1 CGTGTCACACATTCCCACCAT
13313229 GTCGTTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.41, G:0.09, T:0.25
Consensus pattern (23 bp):
CGTGTCACACATTCCCACCATAC
Found at i:13313238 original size:23 final size:23
Alignment explanation
Indices: 13313183--13313239 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
13313173 CCGTGTCACA
*
13313183 GTCGTGTCACATATTCCCACCAT
1 GTCGTGTCACACATTCCCACCAT
**
13313206 ACCGTGTCACACATTCCCACCAT
1 GTCGTGTCACACATTCCCACCAT
*
13313229 GTCGTTTCACA
1 GTCGTGTCACA
13313240 AACTCAAAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.37, G:0.12, T:0.28
Consensus pattern (23 bp):
GTCGTGTCACACATTCCCACCAT
Found at i:13313270 original size:81 final size:81
Alignment explanation
Indices: 13313104--13313277 Score: 188
Period size: 81 Copynumber: 2.1 Consensus size: 81
13313094 GTGTCACAGC
* ** * * * *
13313104 CGTGTCACATATTCTCACCATGACGTGTCACACATTGTCATCATGCCGTGTCATAAACTCTATAC
1 CGTGTCACATATTCCCACCATGACGTGTCACACATTCCCACCATGCCGTGTCACAAACTCAAAAC
* ** **
13313169 CCTGCCGTGTCACAGT
66 CCTACCGTCACACAAA
* *
13313185 CGTGTCACATATTCCCACCAT-ACCGTGTCACACATTCCCACCATGTCGTTTCACAAACTCAAAA
1 CGTGTCACATATTCCCACCATGA-CGTGTCACACATTCCCACCATGCCGTGTCACAAACTCAAAA
*
13313249 CCCTACTGTCACACAAA
65 CCCTACCGTCACACAAA
*
13313266 CGTGTCATATAT
1 CGTGTCACATAT
13313278 GGCTTGTTAT
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
80 1 0.01
81 75 0.99
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.28
Consensus pattern (81 bp):
CGTGTCACATATTCCCACCATGACGTGTCACACATTCCCACCATGCCGTGTCACAAACTCAAAAC
CCTACCGTCACACAAA
Found at i:13326221 original size:26 final size:26
Alignment explanation
Indices: 13326192--13326313 Score: 117
Period size: 24 Copynumber: 4.8 Consensus size: 26
13326182 ATGTTAAGCT
13326192 ATATACAATTCCAAATATGCTAGGGC
1 ATATACAATTCCAAATATGCTAGGGC
* * *
13326218 ATAT--AATTCTAGATATGTTAGGGC
1 ATATACAATTCCAAATATGCTAGGGC
* * * *
13326242 ATAAACAACTCTAAATATGCTATGGC
1 ATATACAATTCCAAATATGCTAGGGC
* *
13326268 ATAT--AATTCCAAATATGATAGTGC
1 ATATACAATTCCAAATATGCTAGGGC
* *
13326292 ATATACAACTGCAAATATGCTA
1 ATATACAATTCCAAATATGCTA
13326314 TGAATCACGA
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
24 39 0.52
26 36 0.48
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (26 bp):
ATATACAATTCCAAATATGCTAGGGC
Found at i:13326234 original size:50 final size:50
Alignment explanation
Indices: 13326173--13326313 Score: 167
Period size: 50 Copynumber: 2.8 Consensus size: 50
13326163 AATTTGTATG
* *
13326173 ATTCCCAATATGTTA-AGCTATATACAATTCCAAATATGCTAGGGCATATA
1 ATTCCAAATATGTTAGAGC-ATATACAACTCCAAATATGCTAGGGCATATA
* * * * * *
13326223 ATTCTAGATATGTTAGGGCATAAACAACTCTAAATATGCTATGGCATATA
1 ATTCCAAATATGTTAGAGCATATACAACTCCAAATATGCTAGGGCATATA
* * *
13326273 ATTCCAAATATGATAGTGCATATACAACTGCAAATATGCTA
1 ATTCCAAATATGTTAGAGCATATACAACTCCAAATATGCTA
13326314 TGAATCACGA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
50 73 0.97
51 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (50 bp):
ATTCCAAATATGTTAGAGCATATACAACTCCAAATATGCTAGGGCATATA
Found at i:13328589 original size:22 final size:23
Alignment explanation
Indices: 13328564--13328618 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 23
13328554 GCCTTAACCA
*
13328564 ATCCCAA-TTGACTGCAGGGCTC
1 ATCCCAAGTTGACTACAGGGCTC
13328586 ATCCCAACAGTTTGACTACAGGGCTC
1 ATCCC-A-AG-TTGACTACAGGGCTC
13328612 ATCCCAA
1 ATCCCAA
13328619 CAGTGTGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 5 0.18
23 1 0.04
24 2 0.07
25 1 0.04
26 19 0.68
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (23 bp):
ATCCCAAGTTGACTACAGGGCTC
Found at i:13328600 original size:26 final size:26
Alignment explanation
Indices: 13328571--13328622 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
13328561 CCAATCCCAA
*
13328571 TTGACTGCAGGGCTCATCCCAACAGT
1 TTGACTACAGGGCTCATCCCAACAGT
13328597 TTGACTACAGGGCTCATCCCAACAGT
1 TTGACTACAGGGCTCATCCCAACAGT
13328623 GTGAACCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (26 bp):
TTGACTACAGGGCTCATCCCAACAGT
Found at i:13328869 original size:24 final size:24
Alignment explanation
Indices: 13328824--13328888 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
13328814 GGACACTATA
* *
13328824 GCATATAATTCTAAATAAGCTAAG-
1 GCATATAATTCCAAACAAGCT-AGT
* *
13328848 GCATATGATTCCAAACATGCTAGT
1 GCATATAATTCCAAACAAGCTAGT
13328872 GCATATAA-TCCACAACA
1 GCATATAATTCCA-AACA
13328889 CCAATATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 6 0.18
24 28 0.82
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (24 bp):
GCATATAATTCCAAACAAGCTAGT
Found at i:13330601 original size:6 final size:6
Alignment explanation
Indices: 13330581--13330631 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
13330571 CAATTAGGTG
*
13330581 ATTTTT -TTCTTT ATTTTT ATTTTTT ATTTTG ATTTTT A-TTTT ATTTTT
1 ATTTTT ATT-TTT ATTTTT A-TTTTT ATTTTT ATTTTT ATTTTT ATTTTT
13330629 ATT
1 ATT
13330632 CTATTTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 7 0.18
6 24 0.62
7 8 0.21
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:13330605 original size:17 final size:16
Alignment explanation
Indices: 13330583--13330644 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 16
13330573 ATTAGGTGAT
13330583 TTTTTTCTTTATTTTTA
1 TTTTTT-TTTATTTTTA
13330600 TTTTTTATTTTGATTTTTA
1 -TTTTT-TTTT-ATTTTTA
*
13330619 TTTTATTTTTA-TTCTA
1 TTTT-TTTTTATTTTTA
13330635 TTTATTTTTT
1 TTT-TTTTTT
13330645 GGGACATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
16 12 0.31
17 2 0.05
18 16 0.41
19 9 0.23
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTATTTTTA
Found at i:13330628 original size:11 final size:11
Alignment explanation
Indices: 13330590--13330637 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
13330580 GATTTTTTTC
13330590 TTTATTTTTATTT
1 TTTA-TTTTA-TT
13330603 TTTATTTTGATT
1 TTTATTTT-ATT
13330615 TTTATTTTATT
1 TTTATTTTATT
*
13330626 TTTATTCTATT
1 TTTATTTTATT
13330637 T
1 T
13330638 ATTTTTTGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
11 14 0.42
12 14 0.42
13 5 0.15
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:13330852 original size:165 final size:164
Alignment explanation
Indices: 13330674--13331150 Score: 669
Period size: 165 Copynumber: 2.9 Consensus size: 164
13330664 AGTTTACATG
* *
13330674 ATAAATAAAAATTCTCCGATGAAGGAATTTCAAGAAGGTTATGAATAATAGATTTTTGAAAATTT
1 ATAAATAAAAATTCTCCAATGAAGGAATTTAAAGAAGGTTATGAATAATAG-TTTTTGAAAATTT
* *
13330739 CTAGGTGAGAGATTTTTCTTGAATTCTATCATAAGTGATGGAGTTTTCCAA-GAATATTTCAATA
65 CTAGGTGAGAGATTTTTCTTGAATTCTGTCATAAGTGTTGGAGTTTT-CAAGGAATATTTCAATA
* * *
13330803 TTAATGAGTTTTTGTTTATTTCAA-TCACAGATGTAA
129 TCAAAGAGTTTTTGTTTATTTCAATTCA-AAATGTAA
* * * *
13330839 ATAAATAAAAATTCTCCAATGATGGAATTTTAAGAAAGTTATGAATAATAGCTTCTTGAAAATTT
1 ATAAATAAAAATTCTCCAATGAAGGAATTTAAAGAAGGTTATGAATAATAG-TTTTTGAAAATTT
* * * *
13330904 TTAGGTGAAAGATTTTTTTTGAATTCTGTCATAAGTGTTGGAGTTTTCAAGGAATATTTCAACAT
65 CTAGGTGAGAGATTTTTCTTGAATTCTGTCATAAGTGTTGGAGTTTTCAAGGAATATTTCAATAT
*
13330969 CAAAGAGTTTTTGTTTATTTCAATTGAAAATGTAA
130 CAAAGAGTTTTTGTTTATTTCAATTCAAAATGTAA
* *
13331004 ATAAATAAAAATTCTCTAACGATA-GAATTTAAAGAAGGTTATGAATAATAGTTTCTTGAAAATT
1 ATAAATAAAAATTCTCCAATGA-AGGAATTTAAAGAAGGTTATGAATAATAGTTT-TTGAAAATT
* *
13331068 TCTAAGT--GAGATTTTTCTTGAATTCTGTCATAAATGTTGGAGTTTTCAAGGAATATTTCAATA
64 TCTAGGTGAGAGATTTTTCTTGAATTCTGTCATAAGTGTTGGAGTTTTCAAGGAATATTTCAATA
*
13331131 TCAAAGAATTTTT-TTTATTT
129 TCAAAGAGTTTTTGTTTATTT
13331151 TGGGGAATAA
Statistics
Matches: 279, Mismatches: 29, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
162 7 0.03
163 64 0.23
164 5 0.02
165 201 0.72
166 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (164 bp):
ATAAATAAAAATTCTCCAATGAAGGAATTTAAAGAAGGTTATGAATAATAGTTTTTGAAAATTTC
TAGGTGAGAGATTTTTCTTGAATTCTGTCATAAGTGTTGGAGTTTTCAAGGAATATTTCAATATC
AAAGAGTTTTTGTTTATTTCAATTCAAAATGTAA
Found at i:13332552 original size:35 final size:35
Alignment explanation
Indices: 13332504--13332591 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
13332494 TTTTCAATAG
*
13332504 GATCAAGCATAACCTTTACAACATGCCTTTTGCAA
1 GATCAAGCATAACCTCTACAACATGCCTTTTGCAA
* * *
13332539 GATCAGGCTTAACCTCTCCAACATGCCTTTTGC-A
1 GATCAAGCATAACCTCTACAACATGCCTTTTGCAA
*
13332573 GTATCAAGCGTAACCTCTA
1 G-ATCAAGCATAACCTCTA
13332592 TGAAGACAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 2 0.04
35 43 0.96
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (35 bp):
GATCAAGCATAACCTCTACAACATGCCTTTTGCAA
Found at i:13338338 original size:17 final size:19
Alignment explanation
Indices: 13338300--13338341 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
13338290 CAAGTGAATT
*
13338300 TTTAGTTTTTGTTAATTAA
1 TTTAGTGTTTGTTAATTAA
13338319 TTTAGTGTTTGTT-A-TAA
1 TTTAGTGTTTGTTAATTAA
13338336 TTTAGT
1 TTTAGT
13338342 TTCAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 12 0.55
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (19 bp):
TTTAGTGTTTGTTAATTAA
Found at i:13341379 original size:17 final size:17
Alignment explanation
Indices: 13341352--13341396 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
13341342 TTAATGTAGA
13341352 GAAAT-AAAATACATAAT
1 GAAATGAAAATA-ATAAT
13341369 -AAATGAAAATAAT-AT
1 GAAATGAAAATAATAAT
*
13341384 GAAAAGAAAATAA
1 GAAATGAAAATAA
13341397 ATAAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 17 0.68
17 6 0.24
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (17 bp):
GAAATGAAAATAATAAT
Found at i:13341758 original size:13 final size:13
Alignment explanation
Indices: 13341740--13341802 Score: 65
Period size: 13 Copynumber: 4.5 Consensus size: 13
13341730 AATTTGAATT
13341740 TTTTTTTGAAATA
1 TTTTTTTGAAATA
*
13341753 TTTTTTTGACATGAAA
1 TTTTTTTGA-A--ATA
13341769 TTTTTTTTGAAA-A
1 -TTTTTTTGAAATA
13341782 TTTTTTTGAAATA
1 TTTTTTTGAAATA
13341795 TATTTTTT
1 T-TTTTTT
13341803 TCTTGAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
12 11 0.26
13 12 0.28
14 8 0.19
16 3 0.07
17 9 0.21
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.62
Consensus pattern (13 bp):
TTTTTTTGAAATA
Found at i:13341775 original size:30 final size:30
Alignment explanation
Indices: 13341734--13341821 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
13341724 AAAAAAAATT
*
13341734 TGAATTTTTTTTTGAAATATTTTTTTGACA
1 TGAATTTTTTTTTGAAATATTTTTTTGAAA
*
13341764 TGAAATTTTTTTTGAAA-ATTTTTTTGAAA
1 TGAATTTTTTTTTGAAATATTTTTTTGAAA
*
13341793 T-ATATTTTTTTCTTG-AATTTTTTTTTGAA
1 TGA-ATTTTTTT-TTGAAATATTTTTTTGAA
13341822 TTTTTTTTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
28 1 0.02
29 21 0.41
30 29 0.57
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (30 bp):
TGAATTTTTTTTTGAAATATTTTTTTGAAA
Found at i:13341778 original size:42 final size:42
Alignment explanation
Indices: 13341732--13341829 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
13341722 AAAAAAAAAA
13341732 TTTGAATTTTTTTTTGAAATAT-TTTTTTGACATGAAATTTTT
1 TTTGAATTTTTTTTTGAAATATATTTTTT-ACATGAAATTTTT
** * * *
13341774 TTTGAAAATTTTTTTGAAATATATTTTTTTCTTGAATTTTTT
1 TTTGAATTTTTTTTTGAAATATATTTTTTACATGAAATTTTT
13341816 TTTGAATTTTTTTT
1 TTTGAATTTTTTTT
13341830 ACATGAACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 42 0.88
43 6 0.12
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.65
Consensus pattern (42 bp):
TTTGAATTTTTTTTTGAAATATATTTTTTACATGAAATTTTT
Found at i:13341825 original size:11 final size:12
Alignment explanation
Indices: 13341732--13341829 Score: 61
Period size: 12 Copynumber: 7.2 Consensus size: 12
13341722 AAAAAAAAAA
13341732 TTTGAATTTTTT
1 TTTGAATTTTTT
13341744 TTTGAAATATTTTT
1 TTTG-AAT-TTTTT
*
13341758 TTGACATGAAATTTTT
1 TT----TGAATTTTTT
**
13341774 TTTGAAAATTTT
1 TTTGAATTTTTT
13341786 TTTGAAATATATTTTTT
1 TTTG----A-ATTTTTT
13341803 TCTTGAATTTTTT
1 T-TTGAATTTTTT
13341816 TTTGAATTTTTT
1 TTTGAATTTTTT
13341828 TT
1 TT
13341830 ACATGAACTT
Statistics
Matches: 70, Mismatches: 4, Indels: 24
0.71 0.04 0.24
Matches are distributed among these distances:
12 30 0.43
13 11 0.16
14 8 0.11
16 8 0.11
17 8 0.11
18 5 0.07
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.65
Consensus pattern (12 bp):
TTTGAATTTTTT
Found at i:13342489 original size:21 final size:21
Alignment explanation
Indices: 13342465--13342505 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13342455 TTGAATGATG
13342465 GCATCAATCCTTGTCATGAAA
1 GCATCAATCCTTGTCATGAAA
* **
13342486 GCATCTATTTTTGTCATGAA
1 GCATCAATCCTTGTCATGAA
13342506 TTGTATGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (21 bp):
GCATCAATCCTTGTCATGAAA
Found at i:13343255 original size:23 final size:24
Alignment explanation
Indices: 13343199--13343247 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
13343189 ATAAAAAAGA
13343199 AAAATTAAAACTAATAAACTAAAACT
1 AAAATT-AAA-TAATAAACTAAAACT
13343225 AAAATTAAATAATAAA-TAAAACT
1 AAAATTAAATAATAAACTAAAACT
13343248 CACTTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.30
24 7 0.30
25 3 0.13
26 6 0.26
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATTAAATAATAAACTAAAACT
Found at i:13353143 original size:15 final size:15
Alignment explanation
Indices: 13353123--13353169 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
13353113 TAGAACAACC
*
13353123 TTAAAATCAAAAACT
1 TTAAAATCAAAAGCT
*
13353138 TTAAAATCCAAAGCT
1 TTAAAATCAAAAGCT
*
13353153 TTAAAACCAAAAGCT
1 TTAAAATCAAAAGCT
13353168 TT
1 TT
13353170 GATCTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (15 bp):
TTAAAATCAAAAGCT
Found at i:13356110 original size:28 final size:27
Alignment explanation
Indices: 13356055--13356110 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
13356045 AATGTCTTGG
** *
13356055 TGGTGGAAAATTACTGTTTTGCCCCTA
1 TGGTGGAAAATTACCATTTTACCCCTA
*
13356082 TGGTGGTAAAATTACCATTTTACCTCTA
1 TGGTGG-AAAATTACCATTTTACCCCTA
13356110 T
1 T
13356111 ACTCCAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (27 bp):
TGGTGGAAAATTACCATTTTACCCCTA
Found at i:13363680 original size:37 final size:37
Alignment explanation
Indices: 13363617--13363703 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
13363607 GCATTTTGCC
* * *
13363617 TGATTTAAACCTCTATTGGTTACTTCAATGT-C-GCGCA
1 TGATTTGAACCTCTACTAGTTACTTC-A-GTACTGCGCA
* *
13363654 TGATTTGAACCTCTACTAGTTGCTTCAGTACTGTGCA
1 TGATTTGAACCTCTACTAGTTACTTCAGTACTGCGCA
13363691 TGATTTGAACCTC
1 TGATTTGAACCTC
13363704 CATAGGTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
35 2 0.05
36 2 0.05
37 39 0.91
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (37 bp):
TGATTTGAACCTCTACTAGTTACTTCAGTACTGCGCA
Found at i:13365648 original size:19 final size:19
Alignment explanation
Indices: 13365621--13365657 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13365611 CCATTTGATT
13365621 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
*
13365640 TATTGGAGTATGATTTGA
1 TATTAGAGTATGATTTGA
13365658 AGTTTAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:13365736 original size:26 final size:27
Alignment explanation
Indices: 13365701--13365751 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
13365691 TTGGAGTATA
*
13365701 GGGGCGAAAT-GATAATTTTGTCACCCC
1 GGGGCGAAATCGATAAATTT-TCACCCC
13365728 GGGGC-AAATCGATAAATTTTCACC
1 GGGGCGAAATCGATAAATTTTCACC
13365752 TCCGACACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (27 bp):
GGGGCGAAATCGATAAATTTTCACCCC
Found at i:13370394 original size:9 final size:9
Alignment explanation
Indices: 13370366--13370399 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
13370356 ATTTATATTA
13370366 TTATTTTTT
1 TTATTTTTT
13370375 TATATTTTTT
1 T-TATTTTTT
13370385 TTATTTTTT
1 TTATTTTTT
*
13370394 TCATTT
1 TTATTT
13370400 CTACTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (9 bp):
TTATTTTTT
Found at i:13373815 original size:31 final size:31
Alignment explanation
Indices: 13373772--13373840 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
13373762 TGCGGAATGA
13373772 GGGGG-AGAGAGAGCAATGGGTGGGAGTGGT
1 GGGGGAAGAGAGAGCAATGGGTGGGAGTGGT
13373802 GGGGGAAGAGAGAGCAATGGGTGGGAGTGGT
1 GGGGGAAGAGAGAGCAATGGGTGGGAGTGGT
13373833 GGGGGAAG
1 GGGGGAAG
13373841 GGGAAGGGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.13
31 33 0.87
ACGTcount: A:0.25, C:0.03, G:0.61, T:0.12
Consensus pattern (31 bp):
GGGGGAAGAGAGAGCAATGGGTGGGAGTGGT
Found at i:13377400 original size:19 final size:19
Alignment explanation
Indices: 13377378--13377418 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
13377368 TTTTTTTTCT
*
13377378 AAAAAACAAAATTTAAA-A
1 AAAAAAAAAAATTTAAAGA
*
13377396 AAAAAAAGAAATTTAAAGA
1 AAAAAAAAAAATTTAAAGA
13377415 AAAA
1 AAAA
13377419 GCTCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAAAAAAAATTTAAAGA
Found at i:13381503 original size:68 final size:68
Alignment explanation
Indices: 13381407--13381553 Score: 190
Period size: 68 Copynumber: 2.2 Consensus size: 68
13381397 GTACGTTTTT
* * *
13381407 CCAA-CTTGACCTTGTGGTATTCTTACCCCCACA-TCGGGATTCATAAAAGAAAAAGATGGCACA
1 CCAATCTTGACCTTATGATATTCTCACCCCCACACT-GGGATTCATAAAAGAAAAAGATGGCACA
13381470 TTCA
65 TTCA
* * ** * *
13381474 CTAATCTTGACCTTATGATATTCTCACCCCCACACTGGGATTCATTAGGGAAAAATATGGCACGT
1 CCAATCTTGACCTTATGATATTCTCACCCCCACACTGGGATTCATAAAAGAAAAAGATGGCACAT
13381539 TCA
66 TCA
13381542 CCAATCTTGACC
1 CCAATCTTGACC
13381554 CTGTGGTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
67 3 0.04
68 64 0.94
69 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (68 bp):
CCAATCTTGACCTTATGATATTCTCACCCCCACACTGGGATTCATAAAAGAAAAAGATGGCACAT
TCA
Found at i:13386804 original size:57 final size:57
Alignment explanation
Indices: 13386716--13386834 Score: 238
Period size: 57 Copynumber: 2.1 Consensus size: 57
13386706 CCCGTACTAT
13386716 AGGCATTAGCACTTTAGAAAGATTGCACTTTCATACAATAACAATAATAATATTTGA
1 AGGCATTAGCACTTTAGAAAGATTGCACTTTCATACAATAACAATAATAATATTTGA
13386773 AGGCATTAGCACTTTAGAAAGATTGCACTTTCATACAATAACAATAATAATATTTGA
1 AGGCATTAGCACTTTAGAAAGATTGCACTTTCATACAATAACAATAATAATATTTGA
13386830 AGGCA
1 AGGCA
13386835 ACAAGCCAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (57 bp):
AGGCATTAGCACTTTAGAAAGATTGCACTTTCATACAATAACAATAATAATATTTGA
Found at i:13393539 original size:73 final size:72
Alignment explanation
Indices: 13393441--13393639 Score: 274
Period size: 73 Copynumber: 2.7 Consensus size: 72
13393431 TATGGCTGGT
* * * * *
13393441 TCAGAAACAGAGAAGACTTAGTCGACCAAGAAGCATGGTTAGTCGACTAAGAGCTCACTGTCAGA
1 TCAGAAACAGAGACGACTTAATCGACTAAGAAGCAT-GTTAGTCAACTAAGAGCTCACTGTCAAA
*
13393506 AATTGAGA
65 AACTGAGA
*
13393514 TCAGAAACAAAGACGACTTAATCGACTAAGAAGCATTGTTAGTCAACTAAGAG-TCACTGTCAAA
1 TCAGAAACAGAGACGACTTAATCGACTAAGAAGCA-TGTTAGTCAACTAAGAGCTCACTGTCAAA
13393578 AACTGAGA
65 AACTGAGA
* * *
13393586 TCAGAAGATAGAGCCGACTTAATCGACTAAGAAGTATGTTAGTCAACTAAGAGC
1 TCAGAA-ACAGAGACGACTTAATCGACTAAGAAGCATGTTAGTCAACTAAGAGC
13393640 ATTATATCTG
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
72 40 0.36
73 71 0.63
74 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.21
Consensus pattern (72 bp):
TCAGAAACAGAGACGACTTAATCGACTAAGAAGCATGTTAGTCAACTAAGAGCTCACTGTCAAAA
ACTGAGA
Found at i:13395129 original size:3 final size:3
Alignment explanation
Indices: 13395121--13395151 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
13395111 CTGGAACTTA
13395121 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
13395152 CAAAAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:13403892 original size:20 final size:20
Alignment explanation
Indices: 13403867--13404006 Score: 65
Period size: 20 Copynumber: 6.7 Consensus size: 20
13403857 AAAGGGGAGA
13403867 AAAGAGAGAAAGAAATAGAG
1 AAAGAGAGAAAGAAATAGAG
* * *
13403887 AAAGAGAGAAGGAAGAAAGAA
1 AAAGAGAGAAAGAA-ATAGAG
*
13403908 AAAGGAAAGAAA-AAATGAGAG
1 AAA-GAGAGAAAGAAAT-AGAG
*
13403929 AAGAAGAGAGAAAAGAGAGATCGACG
1 -A-AAGAGAG-AAAGA-A-ATAGA-G
* *
13403955 ACAAGGGAAAAAG-AA-AGAG
1 A-AAGAGAGAAAGAAATAGAG
*
13403974 AAAGAGAGAAAAAGAAAGAGAG
1 AAAGAGAG--AAAGAAATAGAG
13403996 AAA-A-AGAAAGA
1 AAAGAGAGAAAGA
13404007 GAGAAAAGAA
Statistics
Matches: 91, Mismatches: 15, Indels: 30
0.67 0.11 0.22
Matches are distributed among these distances:
18 10 0.11
19 2 0.02
20 22 0.24
21 16 0.18
22 19 0.21
23 5 0.05
24 5 0.05
25 9 0.10
26 3 0.03
ACGTcount: A:0.65, C:0.02, G:0.31, T:0.02
Consensus pattern (20 bp):
AAAGAGAGAAAGAAATAGAG
Found at i:13403999 original size:34 final size:33
Alignment explanation
Indices: 13403867--13404046 Score: 115
Period size: 34 Copynumber: 5.3 Consensus size: 33
13403857 AAAGGGGAGA
* *
13403867 AAAGAGAGAAAGA-AATAGAGAAAGAGAGAAGGAAG
1 AAAGAGA-AAAGAGAA-AAAGAAAGAGAGAA-AAAG
* *
13403902 AAAGA-AAAAG-GAAAGAAAAAATGAGAGAAGAAG
1 AAAGAGAAAAGAGAAA-AAGAAA-GAGAGAAAAAG
* *
13403935 --AGAGAAAAGAGAGATCGACGACAAG-G-GAAAAAG
1 AAAGAGAAAAGAGA-A--AAAGA-AAGAGAGAAAAAG
13403968 AAAGAGAAAGAGAGAAAAAGAAAGAGAGAAAAAG
1 AAAGAGAAA-AGAGAAAAAGAAAGAGAGAAAAAG
* *
13404002 AAAGAGAGAAA-AGAAAAAGAAAAAGAAAAAAAAG
1 AAAGAGA-AAAGAGAAAAAGAAAGAG-AGAAAAAG
13404036 AAAGAGGAAAA
1 AAAGA-GAAAA
13404047 AAACCTCAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 35
0.72 0.06 0.21
Matches are distributed among these distances:
31 3 0.03
32 9 0.08
33 39 0.33
34 40 0.34
35 20 0.17
36 7 0.06
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.02
Consensus pattern (33 bp):
AAAGAGAAAAGAGAAAAAGAAAGAGAGAAAAAG
Found at i:13404032 original size:14 final size:14
Alignment explanation
Indices: 13403962--13404049 Score: 65
Period size: 14 Copynumber: 6.4 Consensus size: 14
13403952 ACGACAAGGG
*
13403962 AAAAAGAAAGAGAA
1 AAAAAGAAAAAGAA
* *
13403976 AGAGAGAAAAAGAA
1 AAAAAGAAAAAGAA
* *
13403990 AGAGAGAAAAAGAA
1 AAAAAGAAAAAGAA
* *
13404004 AGAGAG-AAAAG--
1 AAAAAGAAAAAGAA
13404015 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAG-AA
*
13404030 AAAAAGAAAGAGGAA
1 AAAAAGAAA-AAGAA
13404045 AAAAA
1 AAAAA
13404050 CCTCAAACGG
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
11 4 0.06
12 5 0.08
13 5 0.08
14 31 0.49
15 16 0.25
16 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:13404633 original size:2 final size:2
Alignment explanation
Indices: 13404621--13404666 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
13404611 TTTTAAGGAA
13404621 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13404662 AT AT A
1 AT AT A
13404667 ATAAATGAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13407757 original size:21 final size:20
Alignment explanation
Indices: 13407725--13407764 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
13407715 TAACTTTTCC
13407725 TAAAGTAAATTGAGATAAAT
1 TAAAGTAAATTGAGATAAAT
*
13407745 TAAAGTGAAATTGAGCTAAA
1 TAAAGT-AAATTGAGATAAA
13407765 AACAACTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (20 bp):
TAAAGTAAATTGAGATAAAT
Found at i:13417877 original size:20 final size:20
Alignment explanation
Indices: 13417841--13417878 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13417831 AATATATTTT
*
13417841 ATTTTAATATTTGATTTTCA
1 ATTTTAATATTTAATTTTCA
13417861 ATTTTAA-ATATTAATTTT
1 ATTTTAATAT-TTAATTTT
13417879 TAAATGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
ATTTTAATATTTAATTTTCA
Found at i:13418083 original size:18 final size:19
Alignment explanation
Indices: 13418062--13418107 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
13418052 ATATTAAAAA
13418062 TTTATAATTAAAATTAT-T
1 TTTATAATTAAAATTATAT
13418080 TTTA-AAGTTAAAATTATAT
1 TTTATAA-TTAAAATTATAT
*
13418099 TTTTTAATT
1 TTTATAATT
13418108 TATAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 6 0.25
20 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTATAATTAAAATTATAT
Found at i:13418178 original size:21 final size:22
Alignment explanation
Indices: 13418128--13418178 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
13418118 ATTTTAATTG
13418128 AATTTTTA-AATTTTAAATATA
1 AATTTTTATAATTTTAAATATA
* *
13418149 AATTATTATAATTTGT-ATTAT-
1 AATTTTTATAATTT-TAAATATA
13418170 AATTTTTAT
1 AATTTTTAT
13418179 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 15 0.60
22 9 0.36
23 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTTTTATAATTTTAAATATA
Found at i:13418187 original size:12 final size:12
Alignment explanation
Indices: 13418151--13418197 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
13418141 TAAATATAAA
13418151 TTATTATAATTT
1 TTATTATAATTT
*
13418163 GTATTATAATTT
1 TTATTATAATTT
*
13418175 TTATTAAAATTT
1 TTATTATAATTT
*
13418187 TAATT-TAATTT
1 TTATTATAATTT
13418198 AGAGAGAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 5 0.17
12 25 0.83
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATTATAATTT
Found at i:13420375 original size:2 final size:2
Alignment explanation
Indices: 13420368--13420408 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13420358 GTTTTAAGAT
13420368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13420409 TTGTTATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13425022 original size:35 final size:35
Alignment explanation
Indices: 13424964--13425086 Score: 149
Period size: 35 Copynumber: 3.5 Consensus size: 35
13424954 GTTCATAAAT
* *
13424964 TTCAGTGTAGTATTCTTATCCCCA-AAGTGGGCTTTA
1 TTCA-TGTAGTATTCTTACCCCCATGA-TGGGCTTTA
* *
13425000 TTCATGTGGTATTCTTACCCCCATGATGGACTTTA
1 TTCATGTAGTATTCTTACCCCCATGATGGGCTTTA
* * * *
13425035 TTCATGTGGTACTCTTGCCCCCATGTTGGGCTTTA
1 TTCATGTAGTATTCTTACCCCCATGATGGGCTTTA
13425070 TTCATGTAGTATTCTTA
1 TTCATGTAGTATTCTTA
13425087 TCCCTCACGA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
35 70 0.93
36 5 0.07
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (35 bp):
TTCATGTAGTATTCTTACCCCCATGATGGGCTTTA
Found at i:13428091 original size:19 final size:19
Alignment explanation
Indices: 13428067--13428104 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13428057 CCATTTAACT
*
13428067 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
13428086 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
13428105 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Done.