Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 92 of 279
Found at i:30041601 original size:4 final size:4
Alignment explanation
Indices: 30041592--30041625 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
30041582 CCATCAACAT
30041592 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
30041626 CTTCTCATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:30044832 original size:19 final size:21
Alignment explanation
Indices: 30044804--30044845 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
30044794 TGATTGTGTG
*
30044804 TACATGTGTA-AAAATAA-AA
1 TACATATGTATAAAATAATAA
30044823 TACATATGTATAAAATAATAA
1 TACATATGTATAAAATAATAA
30044844 TA
1 TA
30044846 TATGAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (21 bp):
TACATATGTATAAAATAATAA
Found at i:30048840 original size:16 final size:16
Alignment explanation
Indices: 30048831--30048869 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
30048821 TATTATATTG
30048831 TTATTATATTATTATA
1 TTATTATATTATTATA
30048847 TTATTATA-TATTATCA
1 TTATTATATTATTAT-A
30048863 -TATTATA
1 TTATTATA
30048870 ATTAAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTATATTATTATA
Found at i:30048842 original size:8 final size:8
Alignment explanation
Indices: 30048831--30048869 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
30048821 TATTATATTG
30048831 TTATTATA
1 TTATTATA
30048839 TTATTATA
1 TTATTATA
30048847 TTATTATA
1 TTATTATA
30048855 -TATTATCA
1 TTATTAT-A
30048863 -TATTATA
1 TTATTATA
30048870 ATTAAAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTATA
Found at i:30051365 original size:18 final size:18
Alignment explanation
Indices: 30051344--30051398 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 18
30051334 ATGTAAAATA
30051344 TTTCAAATATCATTGTTT
1 TTTCAAATATCATTGTTT
**
30051362 TTTCATCTA-CA-T-TTT
1 TTTCAAATATCATTGTTT
30051377 TTT-AAATATCATTGTTT
1 TTTCAAATATCATTGTTT
30051394 TTTCA
1 TTTCA
30051399 TCTACATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 2 0.07
17 8 0.28
18 8 0.28
ACGTcount: A:0.25, C:0.13, G:0.04, T:0.58
Consensus pattern (18 bp):
TTTCAAATATCATTGTTT
Found at i:30051379 original size:17 final size:17
Alignment explanation
Indices: 30051354--30051406 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
30051344 TTTCAAATAT
30051354 CATTGTTTTTTCATCTA
1 CATTGTTTTTTCATCTA
** *
30051371 CATT-TTTTTAAATAT-
1 CATTGTTTTTTCATCTA
30051386 CATTGTTTTTTCATCTA
1 CATTGTTTTTTCATCTA
30051403 CATT
1 CATT
30051407 TACATTGTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 4 0.14
16 16 0.57
17 8 0.29
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (17 bp):
CATTGTTTTTTCATCTA
Found at i:30055035 original size:61 final size:62
Alignment explanation
Indices: 30054875--30055053 Score: 225
Period size: 62 Copynumber: 2.9 Consensus size: 62
30054865 TACGAACGGC
* * * * *
30054875 CGTGTAACTTACTGTTCATGGTATAAAACCACATGGCCAGGGACACGGGTGTGTGCCCAGGT
1 CGTGTAACTCACTGTTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
* * * ** *
30054937 CGTGTAACTCACTTTTTATAGTGTAAAACCATGCGACCAGGGACATGGGCGTGTGCCCAGG-
1 CGTGTAACTCACTGTTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
* * *
30054998 CGTGTAACTCACTGTTCATTGTATAAAACCACACGACCAGGGACACGAGCATGTGC
1 CGTGTAACTCACTGTTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGC
30055054 ATCACTGTTG
Statistics
Matches: 97, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
61 47 0.48
62 50 0.52
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (62 bp):
CGTGTAACTCACTGTTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
Found at i:30062767 original size:30 final size:30
Alignment explanation
Indices: 30062731--30062838 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
30062721 TCGCCATGTC
** **
30062731 TATAATGCTGGTCAATCTGATGGTTAAGTT
1 TATAATGCTGGTCAAAATGATGGTTAAAAT
*
30062761 TATAATGCTGGTCAAAATGCTGGTTAAAAT
1 TATAATGCTGGTCAAAATGATGGTTAAAAT
* * * *
30062791 TATAATCCTGGTTAAAATGCTGGTCAAAAT
1 TATAATGCTGGTCAAAATGATGGTTAAAAT
* *
30062821 TATCATACTGGTCAAAAT
1 TATAATGCTGGTCAAAAT
30062839 TGGTCTCTGC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (30 bp):
TATAATGCTGGTCAAAATGATGGTTAAAAT
Found at i:30067591 original size:26 final size:27
Alignment explanation
Indices: 30067554--30067623 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 27
30067544 ATAAATATTT
30067554 AATTATCT-ATATTTAATCA-TATAATA
1 AATTAT-TAATATTTAATCATTATAATA
* *
30067580 AATTATTAATATAGTTTATCATTTTAATA
1 AATTATTAATAT--TTAATCATTATAATA
*
30067609 AATTTCTTAATATTT
1 AA-TTATTAATATTT
30067624 TAATTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.03
26 10 0.28
28 8 0.22
29 8 0.22
30 9 0.25
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTATTAATATTTAATCATTATAATA
Found at i:30067592 original size:28 final size:30
Alignment explanation
Indices: 30067561--30067627 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
30067551 TTTAATTATC
30067561 TATATTTAATCA-TATAATAAA-TTATTAA
1 TATATTTAATCATTATAATAAATTTATTAA
* *
30067589 TATAGTTT-ATCATTTTAATAAATTTCTTAA
1 TATA-TTTAATCATTATAATAAATTTATTAA
30067619 TAT-TTTAAT
1 TATATTTAAT
30067628 TTTATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 11 0.33
29 13 0.39
30 9 0.27
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (30 bp):
TATATTTAATCATTATAATAAATTTATTAA
Found at i:30073422 original size:34 final size:34
Alignment explanation
Indices: 30073382--30073492 Score: 134
Period size: 34 Copynumber: 3.3 Consensus size: 34
30073372 GAAGTACATA
*
30073382 AATATATATGTATGGCTTGGCATAATCGAAGATG
1 AATATATATGTATGGCTTGGTATAATCGAAGATG
* * *
30073416 ATTATATATGTATAGCTTGGTATAATC-AAAAGTG
1 AATATATATGTATGGCTTGGTATAATCGAAGA-TG
* * * *
30073450 AATATATATGTATGGTTTGATATAACCGAAGGTG
1 AATATATATGTATGGCTTGGTATAATCGAAGATG
30073484 AATATATAT
1 AATATATAT
30073493 ACATTTATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 3 0.05
34 59 0.92
35 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (34 bp):
AATATATATGTATGGCTTGGTATAATCGAAGATG
Found at i:30073690 original size:59 final size:61
Alignment explanation
Indices: 30073563--30073700 Score: 167
Period size: 59 Copynumber: 2.3 Consensus size: 61
30073553 TAAGCTTGAG
* * *
30073563 ATGAGCACTAAGTGTGCGAAATGAAATTGGTACTGAGTACTAAGTGTACGAAATTGGTCAT
1 ATGAGCACTAAGTGTGCGAAATGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
* * * * *
30073624 TTG-GCACTAAGGGTGC-AAATTG-AATTTATACCGAGTACTAAGTGTACGAGATCGGTTA-
1 ATGAGCACTAAGTGTGCGAAA-TGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
30073682 ATGAGCACTAAGTGTGCGA
1 ATGAGCACTAAGTGTGCGA
30073701 GTTTATCTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 2 0.03
59 45 0.70
60 15 0.23
61 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.28
Consensus pattern (61 bp):
ATGAGCACTAAGTGTGCGAAATGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
Found at i:30078295 original size:15 final size:15
Alignment explanation
Indices: 30078275--30078343 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
30078265 GTATCTTGGG
30078275 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
30078290 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
30078305 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
30078320 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
30078335 TTTCTTTAT
1 TTTCTTTAT
30078344 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:30078344 original size:30 final size:30
Alignment explanation
Indices: 30078266--30078353 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
30078256 CATAGTATCG
* * * *
30078266 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
30078296 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
30078326 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
30078354 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:30088120 original size:25 final size:25
Alignment explanation
Indices: 30088092--30088140 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
30088082 ATAGTTAAAC
* * *
30088092 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
30088117 CCTAGGGGCAAAATAGTCATTTTT
1 CCTAGGGGCAAAATAGTCATTTTT
30088141 CATATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:30091353 original size:34 final size:34
Alignment explanation
Indices: 30091315--30091422 Score: 144
Period size: 34 Copynumber: 3.2 Consensus size: 34
30091305 GTACATAAAA
* * *
30091315 ATATATGTATAGCTTGGCATAATCGAAGGTGATT
1 ATATATGTATAGTTTGGTATAATCGAAGGTGAAT
* *
30091349 ATATATGTATAGTTTGGTATAATCAAAAGTGAAT
1 ATATATGTATAGTTTGGTATAATCGAAGGTGAAT
* * *
30091383 ATATATGTATGGTTTGATATAACCGAAGGTGAAT
1 ATATATGTATAGTTTGGTATAATCGAAGGTGAAT
30091417 ATATAT
1 ATATAT
30091423 ATACATTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (34 bp):
ATATATGTATAGTTTGGTATAATCGAAGGTGAAT
Found at i:30091622 original size:59 final size:61
Alignment explanation
Indices: 30091495--30091632 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 61
30091485 TAAGCTTGAG
* ** *
30091495 ATGAGCACTAAGTGTGCGAAATGAAATTGGTACTGAGTACTAAGTGTACGAAATTGGTCAT
1 ATGAGCACTAAGTGTGCGAAATGAAATTGATACCAAGTACTAAGTGTACGAAATCGGTCAT
* * * * *
30091556 TTG-GCACTAAGGGTGC-AAATTG-AATTTATACCAAGTACTAAGTGTACGAGATCGGTTA-
1 ATGAGCACTAAGTGTGCGAAA-TGAAATTGATACCAAGTACTAAGTGTACGAAATCGGTCAT
30091614 ATGAGCACTAAGTGTGCGA
1 ATGAGCACTAAGTGTGCGA
30091633 GTTTATCTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
58 2 0.03
59 44 0.70
60 15 0.24
61 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (61 bp):
ATGAGCACTAAGTGTGCGAAATGAAATTGATACCAAGTACTAAGTGTACGAAATCGGTCAT
Found at i:30095079 original size:106 final size:106
Alignment explanation
Indices: 30094880--30095072 Score: 248
Period size: 106 Copynumber: 1.8 Consensus size: 106
30094870 CAATATAAAC
* * * * * * *
30094880 TACATGCTTTAACATTTTATGCAACTATAATATAGAAAATGATGAATAACAACTTAAATTATATA
1 TACATGCATTAACATTTCATGCAAATATAACATAGAAAATAATGAATAACAACATAAATTACATA
*
30094945 ATATACATTAACCTTTCATGCAGATATAAATAACATAAATA
66 ATATACATTAACATTTCATGCAGATATAAATAACATAAATA
*
30094986 TACATGCATTAATATTTCATGCAAAATATAACATAGAAAATAATGAATATAACAACATAAATTAC
1 TACATGCATTAACATTTCATGC-AAATATAACATAGAAAATAATG-A-ATAACAACATAAATTAC
*
30095051 AT-ATATA-A-TAATATTTCATGCA
63 ATAATATACATTAACATTTCATGCA
30095073 AGTATAACTT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
106 31 0.42
107 20 0.27
108 6 0.08
109 17 0.23
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (106 bp):
TACATGCATTAACATTTCATGCAAATATAACATAGAAAATAATGAATAACAACATAAATTACATA
ATATACATTAACATTTCATGCAGATATAAATAACATAAATA
Found at i:30095141 original size:18 final size:18
Alignment explanation
Indices: 30095118--30095152 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30095108 ATGCGAATAT
*
30095118 ATAAAAACAATAAATAAC
1 ATAAAAACAACAAATAAC
*
30095136 ATAAAAATAACAAATAA
1 ATAAAAACAACAAATAA
30095153 TTTATGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAACAACAAATAAC
Found at i:30095258 original size:15 final size:15
Alignment explanation
Indices: 30095238--30095269 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30095228 GAACATATAT
30095238 AAAATATAAGTAAAA
1 AAAATATAAGTAAAA
*
30095253 AAAATATAATTAAAA
1 AAAATATAAGTAAAA
30095268 AA
1 AA
30095270 TATTGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AAAATATAAGTAAAA
Found at i:30095362 original size:20 final size:18
Alignment explanation
Indices: 30095320--30095381 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
30095310 AATGATTAAT
30095320 ATATATATATAAAACATA
1 ATATATATATAAAACATA
* *
30095338 CTATATGATATAATAACTTA
1 ATATAT-ATATAA-AACATA
*
30095358 ATATATTTATAAAA-ATA
1 ATATATATATAAAACATA
30095375 ATA-ATAT
1 ATATATAT
30095382 GTTAAATAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 7 0.19
19 11 0.31
20 10 0.28
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATATATATAAAACATA
Found at i:30095575 original size:18 final size:18
Alignment explanation
Indices: 30095552--30095586 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30095542 ATGCGAATAT
*
30095552 ATAAAAACAATAAATAAC
1 ATAAAAACAACAAATAAC
*
30095570 ATAAAAATAACAAATAA
1 ATAAAAACAACAAATAA
30095587 TTTATGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAACAACAAATAAC
Found at i:30095781 original size:20 final size:18
Alignment explanation
Indices: 30095739--30095800 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
30095729 CGATTAATAT
30095739 ATATATATATAAAACATA
1 ATATATATATAAAACATA
* *
30095757 CTATATGATATAATAACTTA
1 ATATAT-ATATAA-AACATA
*
30095777 ATATATTTATAAAA-ATA
1 ATATATATATAAAACATA
30095794 ATA-ATAT
1 ATATATAT
30095801 GTTAAATAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 7 0.19
19 11 0.31
20 10 0.28
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATATATATAAAACATA
Found at i:30095854 original size:7 final size:7
Alignment explanation
Indices: 30095839--30095874 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
30095829 ATTTAAGAAC
*
30095839 ATTAGAT
1 ATTAAAT
30095846 ATTAAAT
1 ATTAAAT
30095853 ATTAAAT
1 ATTAAAT
30095860 ATTAAAT
1 ATTAAAT
*
30095867 ATTTAAT
1 ATTAAAT
30095874 A
1 A
30095875 ATGATATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (7 bp):
ATTAAAT
Found at i:30096003 original size:19 final size:19
Alignment explanation
Indices: 30095981--30096068 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 19
30095971 AATATAAGGA
30095981 ATAATATATATAATAAAAT
1 ATAATATATATAATAAAAT
*
30096000 AT-A-ATATGTAATAAAAT
1 ATAATATATATAATAAAAT
*
30096017 AT-ATA-ATAAAATACAAAT
1 ATAATATATATAATA-AAAT
* *
30096035 A-ACCTGATAAATAATAAAAT
1 ATA-AT-ATATATAATAAAAT
30096055 -TAATATATAATAAT
1 ATAATATAT-ATAAT
30096069 TTTTACATGT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
17 22 0.42
18 10 0.19
19 9 0.17
20 6 0.11
21 6 0.11
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAATATATATAATAAAAT
Found at i:30096118 original size:18 final size:18
Alignment explanation
Indices: 30096091--30096133 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30096081 AAATAATGTT
*
30096091 TATA-AAAATAATTAATA
1 TATATAAAATAATTAAAA
*
30096108 TATATAAAATATTTAAAA
1 TATATAAAATAATTAAAA
*
30096126 TAAATAAA
1 TATATAAA
30096134 TTGTATGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATATAAAATAATTAAAA
Found at i:30100365 original size:12 final size:14
Alignment explanation
Indices: 30100343--30100387 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
30100333 AAAAATAGTG
30100343 ATAAAAGGATAAT-
1 ATAAAAGGATAATA
30100356 ATAAAA-GATAATA
1 ATAAAAGGATAATA
*
30100369 ATAATAATGATAATA
1 ATAA-AAGGATAATA
30100384 ATAA
1 ATAA
30100388 TAATAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.21
13 10 0.34
14 2 0.07
15 11 0.38
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (14 bp):
ATAAAAGGATAATA
Found at i:30100371 original size:3 final size:3
Alignment explanation
Indices: 30100363--30100395 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
30100353 AATATAAAAG
*
30100363 ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30100396 TACCTATGAT
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:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30100391 original size:15 final size:15
Alignment explanation
Indices: 30100350--30100391 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
30100340 GTGATAAAAG
30100350 GATAAT-ATAA-AA-
1 GATAATAATAATAAT
30100362 GATAATAATAATAAT
1 GATAATAATAATAAT
30100377 GATAATAATAATAAT
1 GATAATAATAATAAT
30100392 AATATACCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.22
13 4 0.15
14 2 0.07
15 15 0.56
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
GATAATAATAATAAT
Found at i:30100745 original size:11 final size:11
Alignment explanation
Indices: 30100683--30100800 Score: 53
Period size: 11 Copynumber: 10.1 Consensus size: 11
30100673 TTATATATGC
30100683 ACATATATATATT
1 ACATA-ATATA-T
30100696 A-ATAAGTATAT
1 ACATAA-TATAT
30100707 ACATAATAATGAT
1 ACATAAT-AT-AT
* *
30100720 ATTAAAATATAT
1 A-CATAATATAT
*
30100732 ACATAATATGT
1 ACATAATATAT
30100743 ACATGATATATAT
1 ACAT-A-ATATAT
* * *
30100756 AAAGAAAAATAT
1 ACA-TAATATAT
*
30100768 ACATAGTATATT
1 ACATAATATA-T
*
30100780 A-A-AATATAG
1 ACATAATATAT
30100789 ACATAATATAT
1 ACATAATATAT
30100800 A
1 A
30100801 TAAAAAATAT
Statistics
Matches: 78, Mismatches: 16, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
9 1 0.01
10 6 0.08
11 27 0.35
12 26 0.33
13 14 0.18
14 4 0.05
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (11 bp):
ACATAATATAT
Found at i:30100792 original size:21 final size:21
Alignment explanation
Indices: 30100760--30100806 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
30100750 ATATATAAAG
* *
30100760 AAAAATATACATAGTATAT-T
1 AAAAATAGACATAATATATAT
30100780 AAAATATAGACATAATATATAT
1 AAAA-ATAGACATAATATATAT
30100802 AAAAA
1 AAAAA
30100807 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 14 0.61
22 5 0.22
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (21 bp):
AAAAATAGACATAATATATAT
Found at i:30103309 original size:174 final size:171
Alignment explanation
Indices: 30103081--30103512 Score: 509
Period size: 174 Copynumber: 2.5 Consensus size: 171
30103071 TTCGTCGTCT
* * * * * *
30103081 TTTGATCTGCTTCCCTACTGCTTATGGTGATGAGATCTATAAATCTTCAGCCTGTTACCCTACTG
1 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
* * * * *
30103146 CTTAGGAGGTTAAGGCTTGTTACCTTTGATCTGTTTCC-CTACTGCTTAGGGGGATAAGATCTAT
66 CTTAGGAGGTTAAGGCTTGTT--CTTCGATCTG-CTCCACTACTACTTAGGGAGATAAGATCTAC
* **
30103210 AATCTTCGGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCCATC-
128 AA--TTCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
* * *
30103255 TTTGATTTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATCTTTAGCCTGTTACCCTACTG
1 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
*
30103320 CTTAGG-GGTTTAAGGCCCTTCG-TCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTG
66 CTTAGGAGG-TTAAGG--CTT-GTTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTA
* * *
30103383 CAATTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCG
127 CAATTCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
30103428 TCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA--TTCAGCCTGTTACCCTAC
1 T-TT-GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTAC
*
30103491 TGCTTATGGA-GATAAGGCTTGT
64 TGCTTA-GGAGGTTAAGGCTTGT
30103513 GAATTCACCG
Statistics
Matches: 222, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
170 1 0.00
171 3 0.01
172 35 0.16
173 34 0.15
174 106 0.48
175 38 0.17
176 4 0.02
177 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (171 bp):
TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
CTTAGGAGGTTAAGGCTTGTTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAAT
TCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
Found at i:30103396 original size:86 final size:87
Alignment explanation
Indices: 30103075--30103496 Score: 429
Period size: 86 Copynumber: 4.8 Consensus size: 87
30103065 GCAAGATTCG
* * * * * *
30103075 TCGTCTTTTGATCTGCTTCCCTACTGCTTATGGTGATGAGATCTATAAATCTTC-AGCCTGTTAC
1 TCGTC-TTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCT-GAAA--TTCGAGCCTGTTAC
30103139 CCTACTGCTTAGGAGG-TTAAGG--CT
62 CCTACTGCTTAGG-GGTTTAAGGCCCT
*
30103163 T-GTTACCTTTGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCT-ATAATCTTCG-GCCTGTT
1 TCG-T--CTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGA-AA--TTCGAGCCTGTT
* * *
30103225 ACCCTACTGCTTAGGGGGTTAAGGTCCA
60 ACCCTACTGCTTAGGGGTTTAAGGCCCT
* * **
30103253 TC-T-TT-GATTTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATCTTTAGCCTGTTACCC
1 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCT-GAAAT-TCGAGCCTGTTACCC
30103315 TACTGCTTAGGGGTTTAAGGCCCT
64 TACTGCTTAGGGGTTTAAGGCCCT
* * * * *
30103339 TCGTCTTCGATCTG-CTCCACTACTACTTAGGGAGATAAGATCTGCAATTCGA-TCTGTTACCCT
1 TCGTCTTCGATCTGTTTCC-CTACTGCTTAGGGGGATAAGATCTGAAATTCGAGCCTGTTACCCT
*
30103402 ACTGCTTAGGGGTTTAAGACCCT
65 ACTGCTTAGGGGTTTAAGGCCCT
*
30103425 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTC-AGCCTGTTACCCT
1 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTG-AAATTCGAGCCTGTTACCCT
30103489 ACTGCTTA
65 ACTGCTTA
30103497 TGGAGATAAG
Statistics
Matches: 286, Mismatches: 28, Indels: 41
0.81 0.08 0.12
Matches are distributed among these distances:
84 1 0.00
85 34 0.12
86 107 0.37
87 34 0.12
88 46 0.16
89 61 0.21
90 3 0.01
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (87 bp):
TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGAAATTCGAGCCTGTTACCCTA
CTGCTTAGGGGTTTAAGGCCCT
Found at i:30103464 original size:44 final size:43
Alignment explanation
Indices: 30103132--30103464 Score: 216
Period size: 44 Copynumber: 7.7 Consensus size: 43
30103122 AATCTTCAGC
* * * *
30103132 CTGTTACCCTACTGCTTAGGAGGTTAAG-GCTT-GTTACCTTTGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCG-T--CTTCGAT
* * ** **
30103176 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTATAATCTTCGGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCT-TCGTCTTCGAT
* * *
30103220 CTGTTACCCTACTGCTTAGGGGGTTAAGGTCCATC-T-TT-GAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAA-GACCTTCGTCTTCGAT
* * * * *
30103261 TTGTTTCCCTACTGCTTAGGGGGTTAAGATC-TGGAAATCTT-TAGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCG---TCTTCGA-T
* * *
30103306 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAA-GACCTTCGTCTTCGAT
* * * * * * **
30103350 CTG-CTCCACTACTACTTAGGGAGATAAGATCTGC-AATTCGAT
1 CTGTTTCC-CTACTGCTTAGGGGGTTAAGACCTTCGTCTTCGAT
* *
30103392 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGA-CCTTCGTCTTCGAT
30103436 CTGTTTCCCTACTGCTTAGGGGGTTAAGA
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGA
30103465 TCTGTAAATT
Statistics
Matches: 218, Mismatches: 54, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 26 0.12
42 28 0.13
43 13 0.06
44 113 0.52
45 29 0.13
46 4 0.02
47 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (43 bp):
CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCGTCTTCGAT
Found at i:30103684 original size:64 final size:64
Alignment explanation
Indices: 30103583--30103706 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
30103573 GTATCTATGT
*
30103583 TTATGCCAAATAATTAGGATGATATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
1 TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
* * * * *
30103647 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAACTGCTCCTAATTAGATGTG
1 TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTG
30103707 TTATGAATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (64 bp):
TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
Found at i:30116030 original size:10 final size:10
Alignment explanation
Indices: 30116017--30116055 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
30116007 AAAAACCTAT
*
30116017 AAAAATATAC
1 AAAAAAATAC
30116027 AAAAAAATA-
1 AAAAAAATAC
*
30116036 AAAAAAATAA
1 AAAAAAATAC
30116046 AAAAAAATAC
1 AAAAAAATAC
30116056 CTTTTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:30116039 original size:9 final size:9
Alignment explanation
Indices: 30116017--30116051 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
30116007 AAAAACCTAT
*
30116017 AAAAATATA
1 AAAAAAATA
30116026 CAAAAAAATA
1 -AAAAAAATA
30116036 AAAAAAATA
1 AAAAAAATA
30116045 AAAAAAA
1 AAAAAAA
30116052 ATACCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATA
Found at i:30116039 original size:19 final size:19
Alignment explanation
Indices: 30116017--30116054 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30116007 AAAAACCTAT
* *
30116017 AAAAATATACAAAAAAATA
1 AAAAAAATAAAAAAAAATA
30116036 AAAAAAATAAAAAAAAATA
1 AAAAAAATAAAAAAAAATA
30116055 CCTTTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAAAAATAAAAAAAAATA
Found at i:30116901 original size:3 final size:3
Alignment explanation
Indices: 30116895--30117028 Score: 51
Period size: 3 Copynumber: 44.0 Consensus size: 3
30116885 TTTTGTTTTT
* * * **
30116895 TTA TTA TCA TTA TTA -TA TCA TTA TTA TTT TTCA TGTA CACA TTA TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA -TTA TTA TT-A
* * * * * *
30116943 -TA TTA TTT TTA TAA TTA TTA TTA TT- GTA TTTA TTT TTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * *
30116987 TTA -TA TTTA TTA TTA GTA TTA ATA TTA TAA TTA CTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30117029 CACTTATATG
Statistics
Matches: 93, Mismatches: 28, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
2 6 0.06
3 78 0.84
4 8 0.09
5 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:30116967 original size:21 final size:21
Alignment explanation
Indices: 30116895--30117028 Score: 64
Period size: 21 Copynumber: 6.4 Consensus size: 21
30116885 TTTTGTTTTT
* *
30116895 TTATTATCATTATTAT-ATCA
1 TTATTATTATTATTATAATTA
* *
30116915 TTATTATTTTTCATGTACACATTA
1 TTATTATTATT-AT-TATA-ATTA
*
30116939 TTCA-TATTATTTTTATAATTA
1 TT-ATTATTATTATTATAATTA
* *
30116960 TTATTATT-GTATT-T-ATTT
1 TTATTATTATTATTATAATTA
* * *
30116978 TTACTACTATTA-TATTTATTA
1 TTATTATTATTATTA-TAATTA
* *
30116999 TTAGTATTAATATTATAATTA
1 TTATTATTATTATTATAATTA
*
30117020 CTATTATTA
1 TTATTATTA
30117029 CACTTATATG
Statistics
Matches: 83, Mismatches: 20, Indels: 21
0.67 0.16 0.17
Matches are distributed among these distances:
18 10 0.12
19 3 0.04
20 14 0.17
21 36 0.43
22 7 0.08
23 1 0.01
24 11 0.13
25 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTATTATTATTATAATTA
Found at i:30116975 original size:15 final size:15
Alignment explanation
Indices: 30116943--30117028 Score: 59
Period size: 15 Copynumber: 5.7 Consensus size: 15
30116933 ACATTATTCA
*
30116943 TATTATTTTTATAAT
1 TATTATTATTATAAT
* *
30116958 TATTATTATTGTATT
1 TATTATTATTATAAT
* *
30116973 TATTTTTACTACT-AT
1 TATTATTATTA-TAAT
* *
30116988 TA-TATTTATTATTAG
1 TATTA-TTATTATAAT
*
30117003 TATTAATATTATAAT
1 TATTATTATTATAAT
*
30117018 TACTATTATTA
1 TATTATTATTA
30117029 CACTTATATG
Statistics
Matches: 52, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
14 2 0.04
15 47 0.90
16 3 0.06
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTATTATTATAAT
Found at i:30117157 original size:20 final size:20
Alignment explanation
Indices: 30117132--30117177 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
30117122 ATGTATGTAT
*
30117132 ATATTTATGTAATATTATTA
1 ATATTTATGTAACATTATTA
* *
30117152 ATATTTTTTTAACATTATTA
1 ATATTTATGTAACATTATTA
*
30117172 TTATTT
1 ATATTT
30117178 CTTAGATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATATTTATGTAACATTATTA
Found at i:30117217 original size:14 final size:14
Alignment explanation
Indices: 30117198--30117227 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30117188 TACATCATGT
30117198 TTTTTAATACTATA
1 TTTTTAATACTATA
30117212 TTTTTAATACTATA
1 TTTTTAATACTATA
30117226 TT
1 TT
30117228 ATGTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTAATACTATA
Found at i:30117335 original size:25 final size:24
Alignment explanation
Indices: 30117302--30117349 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
30117292 ATGTACATAC
*
30117302 TTTTAATATTAT-TATGTATTTATT
1 TTTTAATA-TATGTATATATTTATT
30117326 TTTTATATATATGTATATATTTAT
1 TTTTA-ATATATGTATATATTTAT
30117350 GTAGTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTAATATATGTATATATTTATT
Found at i:30117432 original size:24 final size:22
Alignment explanation
Indices: 30117389--30117449 Score: 59
Period size: 24 Copynumber: 2.7 Consensus size: 22
30117379 TTCTAATATG
* * *
30117389 TATATACTATGTAAATATTTTAA
1 TATATATTATGTATACATTTT-A
*
30117412 TACTATATTATGTATACATTTTT
1 TA-TATATTATGTATACATTTTA
*
30117435 TATATATTACGTATA
1 TATATATTATGTATA
30117450 TATATATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 12 0.38
23 4 0.12
24 16 0.50
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.51
Consensus pattern (22 bp):
TATATATTATGTATACATTTTA
Found at i:30117606 original size:25 final size:25
Alignment explanation
Indices: 30117515--30117606 Score: 94
Period size: 25 Copynumber: 3.5 Consensus size: 25
30117505 TATATTACTT
* *
30117515 TTTTTACATATTATCTTATGTATATA
1 TTTTTA-ATACTATATTATGTATATA
*
30117541 TTTTTTTAATAACTATATTATGTATGTA
1 --TTTTTAAT-ACTATATTATGTATATA
** *
30117569 TTTTTAACGCTATATTATGTACATA
1 TTTTTAATACTATATTATGTATATA
30117594 TTTTTAATACTAT
1 TTTTTAATACTAT
30117607 GTATATACCT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
25 25 0.46
26 7 0.13
27 2 0.04
28 20 0.37
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (25 bp):
TTTTTAATACTATATTATGTATATA
Found at i:30130131 original size:163 final size:168
Alignment explanation
Indices: 30129838--30130252 Score: 431
Period size: 163 Copynumber: 2.4 Consensus size: 168
30129828 TTTCTAGTTC
** * *
30129838 AAAAATCAACTCATATTGTAATAGGTGAGTTGAGCCTCAAG-ACACGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCACA-GCTGAGGTATTTTCAATTT
* * *
30129902 TTATTTTTCAATTTCTGTCTTTCGGAAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCT
64 CTGTTTTTCAATTTC--TCTTTCGG-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
30129967 CAAGACATGCTGAGGTAATTTT-AATTT-C-TGTTC-AT-C-AA
126 CAAGACACGCTGAGGT-ATTTTCAATTTCCGTGTTCTATGCTAA
30130005 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACA-GCTGAGGTATTTTCAATT
** *
30130070 TCTGTTTTTCAA-TTC-CTATTC-G-TTAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC
63 TCTGTTTTTCAATTTCTCT-TTCGGAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * **
30130131 AGGACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCTTC
127 AAGACACGCTGAGGTATTTTCAATTTCCG-TGTTC----TATGCTAA
* * *
30130178 AAAAATCAACTCATATTGCGAGAGATGAATTGAGCCTCGGGACACA-CTAAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-CACAGCTGAGGTATTTTCAATTT
30130242 CTGTTTTTCAA
64 CTGTTTTTCAA
30130253 AAAAATCAAG
Statistics
Matches: 212, Mismatches: 20, Indels: 28
0.82 0.08 0.11
Matches are distributed among these distances:
162 5 0.02
163 53 0.25
164 1 0.00
165 3 0.01
166 8 0.04
167 35 0.17
168 3 0.01
169 31 0.15
171 30 0.14
172 1 0.00
173 40 0.19
174 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (168 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACAGCTGAGGTATTTTCAATTTCT
GTTTTTCAATTTCTCTTTCGGAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA
CACGCTGAGGTATTTTCAATTTCCGTGTTCTATGCTAA
Found at i:30130215 original size:85 final size:85
Alignment explanation
Indices: 30130005--30130382 Score: 345
Period size: 85 Copynumber: 4.5 Consensus size: 85
30129995 TGTTCATCAA
*
30130005 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTATTTTCAATT
*
30130070 TCTGTTTTTCAATTCCTATTCGTT
63 TCTGTTTTTCAATT-CTATGCGTT
*
30130094 -AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAATTTC
*
30130158 CGTTTTTCAATT-TATGC-TT
65 TGTTTTTCAATTCTATGCGTT
* * * *
30130177 CAAAAATCAACTCATATTGCGAGAGATGAATTGAGCCTCGGGACACACTAAGGTATTTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAATTT
30130242 CTGTTTTTC-A----A------
64 CTGTTTTTCAATTCTATGCGTT
* * * * * * *
30130253 AAAAATCAAGCTTATATTGCGAGAGGTGAGATGAACCTTGGGACACGTTGAGGTATTTTTAGTTT
1 AAAAATCAA-CTCATATTGCGAGAGGTGAGTTGAGCC-TCGGACACGCTGAGGTATTTTCAATTT
* **
30130318 CTGTTTTTCGAATTCTGT-TTTT
64 CTGTTTTTC-AATTCTATGCGTT
* * *
30130340 ATCAAAAGTCAGCTCATATCGCGAGAGGTGATTTGAGCCTCGG
1 A--AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
30130383 GTCACATGCC
Statistics
Matches: 240, Mismatches: 30, Indels: 39
0.78 0.10 0.13
Matches are distributed among these distances:
75 9 0.04
76 51 0.21
77 1 0.00
78 1 0.00
81 1 0.00
83 2 0.01
84 5 0.02
85 65 0.27
86 34 0.14
87 1 0.00
88 39 0.16
89 28 0.12
90 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (85 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTCAATTTCT
GTTTTTCAATTCTATGCGTT
Found at i:30130296 original size:76 final size:75
Alignment explanation
Indices: 30130178--30130326 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 75
30130168 TTTATGCTTC
*
30130178 AAAAATCAACTCATATTGCGAGAGATGAATTGAGCCTCGGGACACACTAAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGATGAATTGAACCTCGGGACACACTAAGGTATTTTCAATTTC
30130243 TGTTTTTCAA
66 TGTTTTTCAA
* * * ** * * *
30130253 AAAAATCAAGCTTATATTGCGAGAGGTGAGA-TGAACCTTGGGACACGTTGAGGTATTTTTAGTT
1 AAAAATCAA-CTCATATTGCGAGAGATGA-ATTGAACCTCGGGACACACTAAGGTATTTTCAATT
30130317 TCTGTTTTTC
64 TCTGTTTTTC
30130327 GAATTCTGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
75 9 0.14
76 53 0.84
77 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGATGAATTGAACCTCGGGACACACTAAGGTATTTTCAATTTC
TGTTTTTCAA
Found at i:30130299 original size:161 final size:164
Alignment explanation
Indices: 30130094--30130388 Score: 382
Period size: 161 Copynumber: 1.8 Consensus size: 164
30130084 CCTATTCGTT
* * *
30130094 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCC
1 AAAATCAACTCATATTGCGAGAGGTGAGATGAACCTCAGGACACGCTGAGGTATTTTCAATTTCC
*
30130159 GTTTTTC-AATT-T-ATGCT-TCAAAAATCAACTCATATTGCGAGAGATGAATTGAGCCTCGGGA
66 GTTTTTCGAATTCTGATGCTATCAAAAATCAACTCATATCGCGAGAGATGAATTGAGCCTCGGGA
30130220 CACACTAAGGTATTTTCAATTTCTGTTTTTCAAA
131 CACACTAAGGTATTTTCAATTTCTGTTTTTCAAA
* ** * * *
30130254 AAAATCAAGCTTATATTGCGAGAGGTGAGATGAACCTTGGGACACGTTGAGGTATTTTTAGTTTC
1 AAAATCAA-CTCATATTGCGAGAGGTGAGATGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
* * ** * * * *
30130319 TGTTTTTCGAATTCTGTTTTTATCAAAAGTCAGCTCATATCGCGAGAGGTGATTTGAGCCTCGGG
65 CGTTTTTCGAATTCTGATGCTATCAAAAATCAACTCATATCGCGAGAGATGAATTGAGCCTCGGG
*
30130384 TCACA
130 ACACA
30130389 TGCCGAGGAT
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
160 8 0.07
161 54 0.49
162 4 0.04
163 1 0.01
164 2 0.02
165 42 0.38
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (164 bp):
AAAATCAACTCATATTGCGAGAGGTGAGATGAACCTCAGGACACGCTGAGGTATTTTCAATTTCC
GTTTTTCGAATTCTGATGCTATCAAAAATCAACTCATATCGCGAGAGATGAATTGAGCCTCGGGA
CACACTAAGGTATTTTCAATTTCTGTTTTTCAAA
Found at i:30132053 original size:27 final size:27
Alignment explanation
Indices: 30132015--30132072 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
30132005 ATATTTTAAA
* * *
30132015 TATTATTTATATTATCCTTATGACTAT
1 TATTATTAATATTATCATTATCACTAT
* *
30132042 TATTATTAATATTCTTATTATCACTAT
1 TATTATTAATATTATCATTATCACTAT
30132069 TATT
1 TATT
30132073 TTTATTCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (27 bp):
TATTATTAATATTATCATTATCACTAT
Found at i:30132078 original size:24 final size:26
Alignment explanation
Indices: 30132015--30132098 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 26
30132005 ATATTTTAAA
* *
30132015 TATTATTTATATT-ATCCTTATGACTAT
1 TATTA-TTATATTCAT-TTTATCACTAT
30132042 TATTATTAATATTC-TTATTATCACTAT
1 TATTATT-ATATTCATT-TTATCACTAT
*
30132069 TATT-TT-TATTCATTTTATCAATA-
1 TATTATTATATTCATTTTATCACTAT
30132092 TATTATT
1 TATTATT
30132099 TCTACAGTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
23 4 0.08
24 15 0.31
25 2 0.04
26 4 0.08
27 24 0.49
ACGTcount: A:0.31, C:0.10, G:0.01, T:0.58
Consensus pattern (26 bp):
TATTATTATATTCATTTTATCACTAT
Found at i:30132346 original size:24 final size:24
Alignment explanation
Indices: 30132282--30132361 Score: 63
Period size: 24 Copynumber: 3.1 Consensus size: 24
30132272 TGTTTTTTTA
*
30132282 TTATCATTATTATATCATTATTATTT
1 TTATGATTATTAT-TCA-TATTATTT
**
30132308 TTCATGTACACATTATTCATATTATTT
1 TT-ATG-A-TTATTATTCATATTATTT
*
30132335 TTATGATTATTATT-GTATTTATTT
1 TTATGATTATTATTCATA-TTATTT
30132359 TTA
1 TTA
30132362 CTACTATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.05
24 15 0.34
25 1 0.02
26 5 0.11
27 12 0.27
28 4 0.09
29 5 0.11
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATGATTATTATTCATATTATTT
Found at i:30132380 original size:24 final size:23
Alignment explanation
Indices: 30132300--30132381 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 23
30132290 ATTATATCAT
* *
30132300 TATTATTTTTCATGTACACATTATTCA
1 TATTATTTTT-ATG-AC-TATTATT-G
*
30132327 TATTATTTTTATGATTATTATTG
1 TATTATTTTTATGACTATTATTG
*
30132350 TATTTATTTTTACT-ACTATTATATT
1 TA-TTATTTTTA-TGACTATTAT-TG
30132375 TATTATT
1 TATTATT
30132382 AGTATTAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.04
24 27 0.57
25 5 0.11
26 3 0.06
27 10 0.21
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (23 bp):
TATTATTTTTATGACTATTATTG
Found at i:30132601 original size:14 final size:14
Alignment explanation
Indices: 30132582--30132608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30132572 ACATCATGTT
30132582 TTTTAATACTATAC
1 TTTTAATACTATAC
30132596 TTTTAATACTATA
1 TTTTAATACTATA
30132609 TTATGTATAT
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:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTAATACTATAC
Found at i:30132689 original size:64 final size:58
Alignment explanation
Indices: 30132605--30132737 Score: 135
Period size: 64 Copynumber: 2.2 Consensus size: 58
30132595 CTTTTAATAC
* *
30132605 TATA-TTATGTATATATTTTTACAT-GCATTATGTACATATTTTCAATAACTATATCATATGTA
1 TATATTTATGTACATACTTTTA-ATAGCATTATGTACATATTTT---TAA-TATAT-ATATGTA
** **
30132667 TATATTTTATGTACATACTTTTAATATTATTATGTATTTATTTTTAATATATATATGTA
1 TATA-TTTATGTACATACTTTTAATAGCATTATGTACATATTTTTAATATATATATGTA
30132726 TATATTTATGTA
1 TATATTTATGTA
30132738 GTATTATTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
58 8 0.13
59 11 0.18
60 5 0.08
61 3 0.05
62 4 0.06
63 2 0.03
64 29 0.47
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (58 bp):
TATATTTATGTACATACTTTTAATAGCATTATGTACATATTTTTAATATATATATGTA
Found at i:30132700 original size:23 final size:23
Alignment explanation
Indices: 30132668--30132725 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
30132658 TCATATGTAT
30132668 ATATT-TTATGTACATACTTTTA
1 ATATTATTATGTACATACTTTTA
** *
30132690 ATATTATTATGTATTTATTTTTA
1 ATATTATTATGTACATACTTTTA
30132713 ATA-TATATATGTA
1 ATATTAT-TATGTA
30132726 TATATTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (23 bp):
ATATTATTATGTACATACTTTTA
Found at i:30132732 original size:23 final size:23
Alignment explanation
Indices: 30132591--30132674 Score: 53
Period size: 23 Copynumber: 3.3 Consensus size: 23
30132581 TTTTTAATAC
*
30132591 TATACTTTTAATACTATATTATGTA
1 TATATTTTTAATA-TATA-TATGTA
**
30132616 TATATTTTTACATGCAT-TATGTA
1 TATATTTTTA-ATATATATATGTA
*
30132639 CATATTTTCAATAACTATATCATATGTA
1 TATATTTT---TAA-TATAT-ATATGTA
30132667 TATATTTT
1 TATATTTT
30132675 ATGTACATAC
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
23 13 0.29
25 12 0.27
26 7 0.16
28 13 0.29
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.51
Consensus pattern (23 bp):
TATATTTTTAATATATATATGTA
Found at i:30132996 original size:25 final size:25
Alignment explanation
Indices: 30132860--30133054 Score: 105
Period size: 25 Copynumber: 8.2 Consensus size: 25
30132850 TTTAATATTG
* *
30132860 TATTTTT-ATA-TATGTCATGTATA
1 TATTTTTAATACTATATTATGTATA
* *
30132883 TATTTCTAATACTATATTA---CT-
1 TATTTTTAATACTATATTATGTATA
* *
30132904 T-TTTTTACATATTATCTTATGTATA
1 TATTTTTA-ATACTATATTATGTATA
*
30132929 TATTTTTTTAATAACTATATTATGTATG
1 TA--TTTTTAAT-ACTATATTATGTATA
** *
30132957 TATTTTTAACGCTATATTATGTACA
1 TATTTTTAATACTATATTATGTATA
30132982 TATTTTTAATAC-----TATGTATA
1 TATTTTTAATACTATATTATGTATA
* * * *
30133002 TACCTTTTATTCCTATTATTACGTATA
1 TA-TTTTTAATACTA-TATTATGTATA
30133029 TA-TTTTAATAC-ATA-TATGTATA
1 TATTTTTAATACTATATTATGTATA
30133051 TATT
1 TATT
30133055 CATATATCGT
Statistics
Matches: 128, Mismatches: 25, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
20 14 0.11
21 17 0.13
22 10 0.08
23 9 0.07
24 5 0.04
25 35 0.27
26 7 0.05
27 11 0.09
28 20 0.16
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (25 bp):
TATTTTTAATACTATATTATGTATA
Found at i:30136386 original size:20 final size:20
Alignment explanation
Indices: 30136337--30136384 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
30136327 TAAATTCTAA
**
30136337 AAAGATAAATAAATTTAATT
1 AAAGATAAATAAATAAAATT
30136357 AAAGATAAATAAATAAAATT
1 AAAGATAAATAAATAAAATT
30136377 AAA-ATAAA
1 AAAGATAAA
30136385 ATTCTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAATAAAATT
Found at i:30137324 original size:23 final size:23
Alignment explanation
Indices: 30137293--30137346 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
30137283 AATTAATTAC
30137293 TAACTAATGCCACCTTTATTGACT
1 TAAC-AATGCCACCTTTATTGACT
30137317 TAACAATGCCACCTTTATTGACT
1 TAACAATGCCACCTTTATTGACT
30137340 TAACAAT
1 TAACAAT
30137347 CTCTTGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.35
Consensus pattern (23 bp):
TAACAATGCCACCTTTATTGACT
Found at i:30138961 original size:16 final size:16
Alignment explanation
Indices: 30138929--30138979 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
30138919 GGTTGAGGTG
30138929 AATGGAATA-AGACTGT
1 AATGGAATAGAGA-TGT
* *
30138945 AATGTAATTGAGATGT
1 AATGGAATAGAGATGT
*
30138961 AATGGAATAGAGTTGT
1 AATGGAATAGAGATGT
30138977 AAT
1 AAT
30138980 CAATAACTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 26 0.90
17 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.31
Consensus pattern (16 bp):
AATGGAATAGAGATGT
Found at i:30139258 original size:57 final size:59
Alignment explanation
Indices: 30139144--30139264 Score: 183
Period size: 60 Copynumber: 2.1 Consensus size: 59
30139134 TTGTTATTAA
* *
30139144 ATTTTAATAAAATTATTATTAAGTATAATTTAATAAAAATAAAATAAATAATTTAATCAT
1 ATTTTAACAAAATTATTATTAAATATAATTTAATAAAAAT-AAATAAATAATTTAATCAT
* *
30139204 ATTTTAACATAATTATTATTAAATATAATTTAAT-AAAAT-AATATATAATTTAATCAT
1 ATTTTAACAAAATTATTATTAAATATAATTTAATAAAAATAAATAAATAATTTAATCAT
30139261 ATTT
1 ATTT
30139265 CAATTTATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
57 21 0.37
59 5 0.09
60 31 0.54
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (59 bp):
ATTTTAACAAAATTATTATTAAATATAATTTAATAAAAATAAATAAATAATTTAATCAT
Found at i:30139277 original size:57 final size:59
Alignment explanation
Indices: 30139154--30139267 Score: 178
Period size: 57 Copynumber: 1.9 Consensus size: 59
30139144 ATTTTAATAA
* *
30139154 AATTATTATTAAGTATAATTTAATAAAAATAAAATAAATAATTTAATCATATTTTAACAT
1 AATTATTATTAAATATAATTTAATAAAAAT-AAATAAATAATTTAATCATATTTCAACAT
*
30139214 AATTATTATTAAATATAATTTAAT-AAAAT-AATATATAATTTAATCATATTTCAA
1 AATTATTATTAAATATAATTTAATAAAAATAAATAAATAATTTAATCATATTTCAA
30139268 TTTATTTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
57 23 0.45
59 5 0.10
60 23 0.45
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (59 bp):
AATTATTATTAAATATAATTTAATAAAAATAAATAAATAATTTAATCATATTTCAACAT
Found at i:30164757 original size:20 final size:20
Alignment explanation
Indices: 30164723--30164773 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
30164713 AACAAGTCAT
30164723 TATAGAAAA-TTTTTAAAAAA
1 TATA-AAAATTTTTTAAAAAA
* * *
30164743 TGTATAAATTTTTTAAAGAA
1 TATAAAAATTTTTTAAAAAA
30164763 TATAAAAATTT
1 TATAAAAATTT
30164774 CAAAAGAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (20 bp):
TATAAAAATTTTTTAAAAAA
Found at i:30167766 original size:17 final size:17
Alignment explanation
Indices: 30167738--30167780 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
30167728 TAAAAAATTC
30167738 AAATATTAAAAATTAGAAA
1 AAATA-TAAAAA-TAGAAA
* *
30167757 AAATATAAAAATCGTAA
1 AAATATAAAAATAGAAA
30167774 AAATATA
1 AAATATA
30167781 TATAATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 6 0.27
19 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
AAATATAAAAATAGAAA
Found at i:30167776 original size:19 final size:19
Alignment explanation
Indices: 30167754--30167841 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 19
30167744 TAAAAATTAG
30167754 AAAAAATATAAAAATCGTA
1 AAAAAATATAAAAATCGTA
* * * *
30167773 AAAATATATATAATTTGTA
1 AAAAAATATAAAAATCGTA
***
30167792 AAATTTTATAAAAATCGTA
1 AAAAAATATAAAAATCGTA
* *
30167811 AAACAAT-TATAAAAT-AT-
1 AAAAAATATA-AAAATCGTA
30167828 AAAAAATATAAAAA
1 AAAAAATATAAAAA
30167842 AAATTATAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
17 10 0.19
18 5 0.09
19 38 0.72
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAAATATAAAAATCGTA
Found at i:30168277 original size:85 final size:86
Alignment explanation
Indices: 30168178--30168342 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 86
30168168 AAGAGTAGGA
* * *
30168178 GTTTAATTGCTTTTTTGAAA-AATTTTAAGGGTCTTTTTT-ATGCATTTTGAAAGTTCAAGAGCC
1 GTTTAATTGCTTTTTTGAAAGAAATTTAAGAG-CTTTTTTGATGCATTCTGAAAGTTCAAGAGCC
*
30168241 CAATTGAGTGAAAAAATCAAGG
65 CAATTAAGTGAAAAAATCAAGG
* * * * ** *
30168263 GTTTAATTGTTTTTTTTAAAGAAATTTGAGAGCTTTTTTGATGCATTCTGAAAGTTTAATTGCTC
1 GTTTAATTGCTTTTTTGAAAGAAATTTAAGAGCTTTTTTGATGCATTCTGAAAGTTCAAGAGCCC
30168328 AATTAAGTGAAAAAA
66 AATTAAGTGAAAAAA
30168343 AAAAAGAGAG
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
85 25 0.37
86 42 0.63
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (86 bp):
GTTTAATTGCTTTTTTGAAAGAAATTTAAGAGCTTTTTTGATGCATTCTGAAAGTTCAAGAGCCC
AATTAAGTGAAAAAATCAAGG
Found at i:30170873 original size:31 final size:31
Alignment explanation
Indices: 30170826--30170900 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
30170816 TTTTAATGAT
* *
30170826 AGAGTTACT-AAATTGACAACTTATCTAATA
1 AGAGTGACTAAAATTGACAACTTATCTAACA
30170856 AGAGTGACTAAAATTGACAACTTATCTAACA
1 AGAGTGACTAAAATTGACAACTTATCTAACA
*
30170887 TGAGTGACTAAAAT
1 AGAGTGACTAAAAT
30170901 AGTAAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 8 0.20
31 33 0.80
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (31 bp):
AGAGTGACTAAAATTGACAACTTATCTAACA
Found at i:30176001 original size:24 final size:25
Alignment explanation
Indices: 30175973--30176024 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
30175963 ACTATCTTAA
*
30175973 AATAAAAAT-ATATATT-AAAATGTG
1 AATAAAAATGAAAT-TTAAAAATGTG
30175997 AAT-AAAATGAAATTTAAAAATGTG
1 AATAAAAATGAAATTTAAAAATGTG
30176021 AATA
1 AATA
30176025 CATTATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (25 bp):
AATAAAAATGAAATTTAAAAATGTG
Found at i:30180429 original size:3 final size:3
Alignment explanation
Indices: 30180409--30180456 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
30180399 CTGAAGGAAG
*
30180409 GAA GAAA GAA GGA GAA GAA GAA -AA GAA G-A GAA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
30180453 GAA G
1 GAA G
30180457 GAGGAGGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:30180446 original size:22 final size:21
Alignment explanation
Indices: 30180410--30180452 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
30180400 TGAAGGAAGG
*
30180410 AAGAAAGAAGGAGAAGAAGAA
1 AAGAAAGAAGAAGAAGAAGAA
30180431 AAGAAGAGAAGAAGAAGAAGAA
1 AAGAA-AGAAGAAGAAGAAGAA
30180453 GAAGGAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAGAAGAAGAAGAA
Found at i:30180449 original size:25 final size:24
Alignment explanation
Indices: 30180409--30180455 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
30180399 CTGAAGGAAG
*
30180409 GAAGAAAGAAGGAGAAGAAGAAAA
1 GAAGAAAGAAGAAGAAGAAGAAAA
30180433 GAAGAGAAGAAGAAGAAGAAGAA
1 GAAGA-AAGAAGAAGAAGAAGAA
30180456 GGAGGAGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (24 bp):
GAAGAAAGAAGAAGAAGAAGAAAA
Found at i:30180954 original size:17 final size:16
Alignment explanation
Indices: 30180924--30181006 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
30180914 TTTTTTTACA
* *
30180924 AAAATAGTATAAAATAT
1 AAAATACTA-AAAAAAT
30180941 AAAATACTAAAAAAAT
1 AAAATACTAAAAAAAT
*** * *
30180957 ATCTTAATGAAAAAAT
1 AAAATACTAAAAAAAT
*
30180973 AAAATACGAAAAGAAAT
1 AAAATACTAAAA-AAAT
*
30180990 AAAATA-TGAAAAAAT
1 AAAATACTAAAAAAAT
30181005 AA
1 AA
30181007 CTTTTTGGGG
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
15 6 0.12
16 26 0.52
17 18 0.36
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAATACTAAAAAAAT
Found at i:30183558 original size:32 final size:32
Alignment explanation
Indices: 30183477--30183591 Score: 133
Period size: 33 Copynumber: 3.5 Consensus size: 32
30183467 ATCTTTAGAT
*
30183477 CGTATCCACTGCAGTACAGCACTA-CCCTCGACC
1 CGTATCCACCGCAGTACAGCACTACCCCT-G-CC
* *
30183510 CGTATCCATCGTAGTACAGCACTACCCCTGCC
1 CGTATCCACCGCAGTACAGCACTACCCCTGCC
* * *
30183542 CGAATCCACCACAGTACAGCACTACTCCCGGCC
1 CGTATCCACCGCAGTACAGCACTAC-CCCTGCC
*
30183575 CGTATCAACCGCAGTAC
1 CGTATCCACCGCAGTAC
30183592 TCCACTCCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 23 0.33
33 42 0.61
34 4 0.06
ACGTcount: A:0.25, C:0.42, G:0.16, T:0.17
Consensus pattern (32 bp):
CGTATCCACCGCAGTACAGCACTACCCCTGCC
Found at i:30189477 original size:45 final size:42
Alignment explanation
Indices: 30189392--30189477 Score: 109
Period size: 45 Copynumber: 2.0 Consensus size: 42
30189382 TACAACATAA
* *
30189392 ACCCAATAACCCAAAGCCCAAATACTTAAAATTAAACCCAAG
1 ACCCAATAACCCAAAACCCAAATACTTAAAACTAAACCCAAG
* *
30189434 ACCCACTAACACCTAAAACCCAAATACATTATAACTAAACCCAA
1 ACCCAATAAC-CC-AAAACCCAAATAC-TTAAAACTAAACCCAA
30189478 CACTCATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 9 0.24
43 2 0.05
44 12 0.32
45 14 0.38
ACGTcount: A:0.50, C:0.33, G:0.02, T:0.15
Consensus pattern (42 bp):
ACCCAATAACCCAAAACCCAAATACTTAAAACTAAACCCAAG
Found at i:30190573 original size:3 final size:3
Alignment explanation
Indices: 30190567--30190612 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
30190557 ACTACTATAT
30190567 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
30190613 GTGTATACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:30190756 original size:3 final size:3
Alignment explanation
Indices: 30190750--30190883 Score: 50
Period size: 3 Copynumber: 46.7 Consensus size: 3
30190740 TTTATAATAC
* * * * * *
30190750 TAT TAT TA- TAA TCT TAT T-T TAT TAT TAT CAT TCT TAT TAA TA- CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * ** *
30190795 TAT TAT TAT T-T TAC CA- TAT TAT TAT T-T TAT ATAT TAT TGC TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * *
30190838 TAT TAA CA- TAC TAT TAT TAT TAT TA- TACT TAT TAA TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
30190882 TA
1 TA
30190884 GTACTAGTAT
Statistics
Matches: 98, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
2 13 0.13
3 80 0.82
4 5 0.05
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:30190774 original size:19 final size:20
Alignment explanation
Indices: 30190750--30190787 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30190740 TTTATAATAC
30190750 TATTATTAT-AATCTTATTT
1 TATTATTATCAATCTTATTT
*
30190769 TATTATTATCATTCTTATT
1 TATTATTATCAATCTTATT
30190788 AATACATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATTATCAATCTTATTT
Found at i:30190816 original size:16 final size:15
Alignment explanation
Indices: 30190790--30190832 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
30190780 TTCTTATTAA
30190790 TACATTATTATTATTT
1 TACA-TATTATTATTT
30190806 TACCATATTATTATTT
1 TA-CATATTATTATTT
*
30190822 TATATATTATT
1 TACATATTATT
30190833 GCTGTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 15 0.60
17 2 0.08
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TACATATTATTATTT
Found at i:30193748 original size:64 final size:64
Alignment explanation
Indices: 30193681--30193802 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
30193671 AAAATAACAA
* * *
30193681 AAAAGAATA-TACCT-TTTCTTTCTTCTCTTTTCCCTCTCTTCTTCTATAATTTTTTTTTACTGG
1 AAAA-AATATTACCTCTTTCTTTCTTCTCTTCTCCCTCTCTTCTTCCACAATTTTTTTTTACTGG
*** *
30193744 AAAAAATATTTTTTCTTTCTTTCTTCTCTTCTCCCTCTCTTCTTCCGCAATTTTTTTTT
1 AAAAAATATTACCTCTTTCTTTCTTCTCTTCTCCCTCTCTTCTTCCACAATTTTTTTTT
30193803 TTGCTGGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 4 0.08
63 6 0.12
64 40 0.80
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.56
Consensus pattern (64 bp):
AAAAAATATTACCTCTTTCTTTCTTCTCTTCTCCCTCTCTTCTTCCACAATTTTTTTTTACTGG
Found at i:30195027 original size:22 final size:22
Alignment explanation
Indices: 30194999--30195040 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30194989 TTGAAAATGA
30194999 ATTGATTCT-TTATTATTTTTGG
1 ATTGATT-TGTTATTATTTTTGG
*
30195021 ATTGATTTGTTTTTATTTTT
1 ATTGATTTGTTATTATTTTT
30195041 TAATTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.69
Consensus pattern (22 bp):
ATTGATTTGTTATTATTTTTGG
Found at i:30195260 original size:16 final size:16
Alignment explanation
Indices: 30195231--30195264 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
30195221 TAATTCACTT
30195231 TTCAATTTTCAATTAA
1 TTCAATTTTCAATTAA
30195247 TTCATATTTT-AATTAA
1 TTCA-ATTTTCAATTAA
30195263 TT
1 TT
30195265 AACTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCAATTTTCAATTAA
Found at i:30196655 original size:4 final size:4
Alignment explanation
Indices: 30196648--30196677 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
30196638 ACACGCAAGC
*
30196648 AAAT AAAT AAAT GAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
30196678 TGGTAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:30196750 original size:26 final size:28
Alignment explanation
Indices: 30196699--30196750 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
30196689 AATGATAACG
*
30196699 AAAACAATAATAACGATATGAGTAAAGA
1 AAAACAATAATAACGATATGAATAAAGA
30196727 AAAACGAATAA-AACGA-AT-AATAAA
1 AAAAC-AATAATAACGATATGAATAAA
30196751 ATAATGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 5 0.23
27 2 0.09
28 10 0.45
29 5 0.23
ACGTcount: A:0.65, C:0.08, G:0.12, T:0.15
Consensus pattern (28 bp):
AAAACAATAATAACGATATGAATAAAGA
Found at i:30196958 original size:62 final size:62
Alignment explanation
Indices: 30196861--30196995 Score: 243
Period size: 62 Copynumber: 2.2 Consensus size: 62
30196851 TATTAATAGT
* *
30196861 AATAATACAGGTAATGCTTTAGAAATGATGTATGAAAGTGTATATACGTACATGTATAAATA
1 AATAATATACGTAATGCTTTAGAAATGATGTATGAAAGTGTATATACGTACATGTATAAATA
*
30196923 AATAATATACGTAATGCTTTAGAAATGATGTATGAAAGTGTATATACGTACGTGTATAAATA
1 AATAATATACGTAATGCTTTAGAAATGATGTATGAAAGTGTATATACGTACATGTATAAATA
30196985 AATAATATACG
1 AATAATATACG
30196996 ATGTGGGTGA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.33
Consensus pattern (62 bp):
AATAATATACGTAATGCTTTAGAAATGATGTATGAAAGTGTATATACGTACATGTATAAATA
Found at i:30197446 original size:21 final size:23
Alignment explanation
Indices: 30197420--30197468 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
30197410 AGGTATTACA
*
30197420 TAAAAATATATACAT-AT-ATAT
1 TAAAAATAAATACATGATAATAT
*
30197441 TAAAAATAAATATATGATAATAT
1 TAAAAATAAATACATGATAATAT
30197464 TAAAA
1 TAAAA
30197469 GTATGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 2 0.08
23 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAATAAATACATGATAATAT
Found at i:30199610 original size:44 final size:44
Alignment explanation
Indices: 30199549--30199747 Score: 154
Period size: 43 Copynumber: 4.6 Consensus size: 44
30199539 AACGTCAGCT
* * * ** * *
30199549 TGTTACCCTACTACTTAGGGAGTTAAAGCTC-GTTGCCTTCGATC
1 TGTTTCCCTACTGCTTAGGGAGTTAAAGATCTG-TGAATTCAACC
* *
30199593 TGTTTCCCTACTGCTTAGGGGGTT-AAGATCTGTGAATTTAACC
1 TGTTTCCCTACTGCTTAGGGAGTTAAAGATCTGTGAATTCAACC
* * * *
30199636 TGTTTCCCTACTGCTTAGGGA-TTTAAGGTCTGTAAATTTAACC
1 TGTTTCCCTACTGCTTAGGGAGTTAAAGATCTGTGAATTCAACC
* * * * *** *
30199679 TGTTTCCTTACTGCTTAGGGA-TTTAAGGTCTGTAAATTTGGCT
1 TGTTTCCCTACTGCTTAGGGAGTTAAAGATCTGTGAATTCAACC
* *
30199722 TGTTACCCTACTGCTTAGGGGGTTAA
1 TGTTTCCCTACTGCTTAGGGAGTTAA
30199748 GCCCATCATC
Statistics
Matches: 132, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
42 2 0.02
43 105 0.80
44 25 0.19
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (44 bp):
TGTTTCCCTACTGCTTAGGGAGTTAAAGATCTGTGAATTCAACC
Found at i:30199648 original size:43 final size:43
Alignment explanation
Indices: 30199592--30199748 Score: 215
Period size: 43 Copynumber: 3.7 Consensus size: 43
30199582 TGCCTTCGAT
* * *
30199592 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTGAATTTAAC
1 CTGTTTCCCTACTGCTTAGGGAGTTAAGGTCTGTAAATTTAAC
*
30199635 CTGTTTCCCTACTGCTTAGGGATTTAAGGTCTGTAAATTTAAC
1 CTGTTTCCCTACTGCTTAGGGAGTTAAGGTCTGTAAATTTAAC
* * **
30199678 CTGTTTCCTTACTGCTTAGGGATTTAAGGTCTGTAAATTTGGC
1 CTGTTTCCCTACTGCTTAGGGAGTTAAGGTCTGTAAATTTAAC
* * *
30199721 TTGTTACCCTACTGCTTAGGGGGTTAAG
1 CTGTTTCCCTACTGCTTAGGGAGTTAAG
30199749 CCCATCATCT
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 102 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (43 bp):
CTGTTTCCCTACTGCTTAGGGAGTTAAGGTCTGTAAATTTAAC
Found at i:30199768 original size:86 final size:86
Alignment explanation
Indices: 30199500--30199794 Score: 256
Period size: 86 Copynumber: 3.4 Consensus size: 86
30199490 GCTGTTTTTT
* * * * * * *
30199500 GATCTGCTTCCCTACTGTTTAGGGTGATAAGATCT-TATGAACGTCAGCTTGTTACCCTACTACT
1 GATCTGTTTCCCTACTGCTTAGGGAGTTAAGATCTGTA--AA-TTTAGCTTGTTACCCTACTGCT
* ***
30199564 TAGGGAGTTAAAGCTCGTTGCCTTC
63 TAGGGAGTT-AAGCCCGTAATCTTC
* * * * *
30199589 GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTGAATTTAACCTGTTTCCCTACTGCTTAG
1 GATCTGTTTCCCTACTGCTTAGGGAGTTAAGATCTGTAAATTTAGCTTGTTACCCTACTGCTTAG
* * *
30199654 GGATTTAAGGTCTGTAAAT-TT-
66 GGAGTTAA-GCCCGT-AATCTTC
* * * * * *
30199675 AACCTGTTTCCTTACTGCTTAGGGATTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAG
1 GATCTGTTTCCCTACTGCTTAGGGAGTTAAGATCTGTAAATTTAGCTTGTTACCCTACTGCTTAG
* * *
30199740 GGGGTTAAGCCCATCATCTTC
66 GGAGTTAAGCCCGTAATCTTC
30199761 GATCTGTTTCCCTACTGCTTAGGG-GTTAAGATCT
1 GATCTGTTTCCCTACTGCTTAGGGAGTTAAGATCT
30199795 TATAAATTCA
Statistics
Matches: 161, Mismatches: 40, Indels: 14
0.75 0.19 0.07
Matches are distributed among these distances:
84 2 0.01
85 13 0.08
86 83 0.52
87 29 0.18
88 2 0.01
89 31 0.19
90 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (86 bp):
GATCTGTTTCCCTACTGCTTAGGGAGTTAAGATCTGTAAATTTAGCTTGTTACCCTACTGCTTAG
GGAGTTAAGCCCGTAATCTTC
Found at i:30202854 original size:90 final size:90
Alignment explanation
Indices: 30202701--30202879 Score: 340
Period size: 90 Copynumber: 2.0 Consensus size: 90
30202691 GTCAAAGTTC
*
30202701 AGAGGCTCGTAGTCCTCTAGGGTTCTACTGGCTAGGAAATCTACTATCGCACTCCCTTTTACGGC
1 AGAGGCTCGTAGTCCTCTAGGGCTCTACTGGCTAGGAAATCTACTATCGCACTCCCTTTTACGGC
30202766 CTTCTGGTTCACATAGATTATATCT
66 CTTCTGGTTCACATAGATTATATCT
*
30202791 AGAGGCTCGTAGTCCTCTAGGGCTCTGCTGGCTAGGAAATCTACTATCGCACTCCCTTTTACGGC
1 AGAGGCTCGTAGTCCTCTAGGGCTCTACTGGCTAGGAAATCTACTATCGCACTCCCTTTTACGGC
30202856 CTTCTGGTTCACATAGATTATATC
66 CTTCTGGTTCACATAGATTATATC
30202880 GAACTCAGAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (90 bp):
AGAGGCTCGTAGTCCTCTAGGGCTCTACTGGCTAGGAAATCTACTATCGCACTCCCTTTTACGGC
CTTCTGGTTCACATAGATTATATCT
Found at i:30203887 original size:96 final size:96
Alignment explanation
Indices: 30203723--30203914 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 96
30203713 GCAAAAGGTT
30203723 CCCCACATGGTCACAAATGTGGTTTTATTCATGTCTTCAGGATGCATCTTGATCTGATTGTACCC
1 CCCCACATGGTCACAAATGTGGTTTTATTCATGTCTTCAGGATGCATCTTGATCTGATTGTACCC
*
30203788 TGAGAGACCATCCATGAAGGAGAAGAGTGAG
66 TGAGAAACCATCCATGAAGGAGAAGAGTGAG
30203819 CCCCACATGGTCACAAATGTGGTTTTATTCATGTCTTCAGGATGCATCTTGATCTGATTGTACCC
1 CCCCACATGGTCACAAATGTGGTTTTATTCATGTCTTCAGGATGCATCTTGATCTGATTGTACCC
30203884 TGAGAAACCATCCATGAAGGAGAAGAGTGAG
66 TGAGAAACCATCCATGAAGGAGAAGAGTGAG
30203915 TAACCTGCTG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (96 bp):
CCCCACATGGTCACAAATGTGGTTTTATTCATGTCTTCAGGATGCATCTTGATCTGATTGTACCC
TGAGAAACCATCCATGAAGGAGAAGAGTGAG
Found at i:30206598 original size:11 final size:11
Alignment explanation
Indices: 30206582--30206609 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
30206572 TTCCACCATT
30206582 TTCTTCCAAAC
1 TTCTTCCAAAC
30206593 TTCTTCCAAAC
1 TTCTTCCAAAC
30206604 TTCTTC
1 TTCTTC
30206610 TAACGGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (11 bp):
TTCTTCCAAAC
Found at i:30212076 original size:4 final size:4
Alignment explanation
Indices: 30212069--30212098 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
30212059 ACACGCAAGC
*
30212069 AAAT AAAT AAAT GAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
30212099 TGGTAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:30212587 original size:19 final size:19
Alignment explanation
Indices: 30212563--30212601 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30212553 AAAATAGACA
30212563 TAACAATA-ATATGATATAT
1 TAACAATATATAT-ATATAT
30212582 TAACAATATATATATATAT
1 TAACAATATATATATATAT
30212601 T
1 T
30212602 TATATGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (19 bp):
TAACAATATATATATATAT
Found at i:30212824 original size:21 final size:23
Alignment explanation
Indices: 30212798--30212846 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
30212788 AGGTATTACA
*
30212798 TAAAAATATATACAT-AT-ATAT
1 TAAAAATAAATACATGATAATAT
*
30212819 TAAAAATAAATATATGATAATAT
1 TAAAAATAAATACATGATAATAT
30212842 TAAAA
1 TAAAA
30212847 GTATGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 2 0.08
23 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAATAAATACATGATAATAT
Found at i:30213899 original size:32 final size:32
Alignment explanation
Indices: 30213829--30213899 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
30213819 TTTGTTTGAA
* * * * *
30213829 CTGTTTTTTGCCTTTTGATTTTGCTGAGATTT
1 CTGTTTTTTACCTTTTGATGTTGATGAAATCT
* *
30213861 CAGTTTTTTACTTTTTGATGTTGATGAAATCT
1 CTGTTTTTTACCTTTTGATGTTGATGAAATCT
30213893 CTGTTTT
1 CTGTTTT
30213900 GTATTCTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58
Consensus pattern (32 bp):
CTGTTTTTTACCTTTTGATGTTGATGAAATCT
Found at i:30216285 original size:26 final size:26
Alignment explanation
Indices: 30216256--30216365 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
30216246 TGGTACAAAT
30216256 TGATAATAGGTTAGGTAAATG-TTCGA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
30216282 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
30216308 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
30216334 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
30216360 TGATAA
1 TGATAA
30216366 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:30217848 original size:28 final size:26
Alignment explanation
Indices: 30217817--30217876 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
30217807 AATAACTATA
* *
30217817 ATACCCCTATGTATGGAAAATTACTGTT
1 ATACCCCTA-G-ATGCAAAATTACCGTT
* *
30217845 ATACCCTTAGGTGCAAAATTACCGTT
1 ATACCCCTAGATGCAAAATTACCGTT
30217871 ATACCC
1 ATACCC
30217877 GTAGGGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.68
27 1 0.04
28 8 0.29
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (26 bp):
ATACCCCTAGATGCAAAATTACCGTT
Found at i:30218046 original size:27 final size:27
Alignment explanation
Indices: 30217984--30218050 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
30217974 GAGGAAGCGT
* *
30217984 TCTGGTGGCTATGCCACAAATATTTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
30218011 TCTGATGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
30218038 TTTGGTGGCTCTG
1 TCTGGTGGCTCTG
30218051 TCACGATGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:30233966 original size:43 final size:43
Alignment explanation
Indices: 30233918--30234006 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
30233908 CAATGAAAAG
*
30233918 TATGATTTGGAACTAATTAATAGTAATACATGAGTATATACCA
1 TATGATTTGGAACTAATTAATAGTAATACATGAATATATACCA
* *
30233961 TATGATTTGGAACTAATTAATAGTAATCCATGAATATATACTA
1 TATGATTTGGAACTAATTAATAGTAATACATGAATATATACCA
30234004 TAT
1 TAT
30234007 TAAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (43 bp):
TATGATTTGGAACTAATTAATAGTAATACATGAATATATACCA
Found at i:30235788 original size:40 final size:39
Alignment explanation
Indices: 30235721--30235857 Score: 104
Period size: 37 Copynumber: 3.5 Consensus size: 39
30235711 ACTAGAATGG
30235721 CACCCAGTGCCTCATCGGA--TAGTTCGAAGCAATATAGTGA
1 CACCCAGTGCCTCATC-GACCTAG-TCGAAG-AATATAGTGA
* * *
30235761 CACCCAGTGTCTCATCGACCTAGTCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGACCTAGTCGAAGAATATAGTGA
* * * * *
30235798 TACCCAGTACCTCATCGAATCTA-TCTGAAAAAATATAGTAA
1 CACCCAGTGCCTCATCG-ACCTAGTC-G-AAGAATATAGTGA
*
30235839 CACCCAGTGTCTCATCGAC
1 CACCCAGTGCCTCATCGAC
30235858 TTGAGGTCGA
Statistics
Matches: 75, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
37 22 0.29
38 5 0.07
39 4 0.05
40 22 0.29
41 22 0.29
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGACCTAGTCGAAGAATATAGTGA
Found at i:30236476 original size:42 final size:41
Alignment explanation
Indices: 30236430--30236559 Score: 123
Period size: 42 Copynumber: 3.3 Consensus size: 41
30236420 TTGAATTTCT
30236430 ATTCAATTTACACCTTATTTTCAATTAGGTCCTAGCTGATTC
1 ATTCAATTTACACCTTATTTTCAATTAGGTCCTA-CTGATTC
* * * *
30236472 ATTCACTTTACTAACTTA-ATTC-A-TA-CT-CTA-T--TTC
1 ATTCAATTTAC-ACCTTATTTTCAATTAGGTCCTACTGATTC
30236506 TATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTC
1 -ATTCAATTTACACCTTATTTTCAATTAGGTCCT-ACTGATTC
*
30236549 ATTCACTTTAC
1 ATTCAATTTAC
30236560 TAACTTAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
34 8 0.12
35 13 0.19
36 2 0.03
37 2 0.03
38 4 0.06
39 3 0.04
40 3 0.04
41 2 0.03
42 23 0.34
43 8 0.12
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (41 bp):
ATTCAATTTACACCTTATTTTCAATTAGGTCCTACTGATTC
Found at i:30236511 original size:77 final size:77
Alignment explanation
Indices: 30236424--30236589 Score: 323
Period size: 77 Copynumber: 2.2 Consensus size: 77
30236414 AAATAATTGA
*
30236424 ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAGCTGATTCATTCACTTTACTAACTT
1 ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTCATTCACTTTACTAACTT
30236489 AATTCATACTCT
66 AATTCATACTCT
30236501 ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTCATTCACTTTACTAACTT
1 ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTCATTCACTTTACTAACTT
30236566 AATTCATACTCT
66 AATTCATACTCT
30236578 ATTTCTATTCAA
1 ATTTCTATTCAA
30236590 GTTCCATCCA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 88 1.00
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (77 bp):
ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTCATTCACTTTACTAACTT
AATTCATACTCT
Found at i:30237904 original size:26 final size:26
Alignment explanation
Indices: 30237875--30237924 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
30237865 TGTGAGACCT
*
30237875 TAGTGT-TAGAACCCTTAAGTGCGAGC
1 TAGTGTGT-GAACCCCTAAGTGCGAGC
*
30237901 TAGTGTGTGAACCCCTATGTGCGA
1 TAGTGTGTGAACCCCTAAGTGCGA
30237925 ACCCTTATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (26 bp):
TAGTGTGTGAACCCCTAAGTGCGAGC
Found at i:30238066 original size:28 final size:28
Alignment explanation
Indices: 30237963--30238066 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 28
30237953 TCCTACGTGT
* *
30237963 AAACCCTTATGTGTGAACTTGTATCTGC
1 AAACCCTTATGTGTGAACCTGTATGTGC
* * *
30237991 AAACCCCTATGTGTGAGCTCTAGGTGTGTG-
1 AAACCCTTATGTGTGAAC-CT--GTATGTGC
** *
30238021 -AACCCTTATACGTAAACCTGTATGTGC
1 AAACCCTTATGTGTGAACCTGTATGTGC
*
30238048 AAACCCTTATGTGTCAACC
1 AAACCCTTATGTGTGAACC
30238067 CTATAGTTTA
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
26 6 0.11
28 33 0.58
29 13 0.23
31 5 0.09
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (28 bp):
AAACCCTTATGTGTGAACCTGTATGTGC
Found at i:30238182 original size:36 final size:36
Alignment explanation
Indices: 30238097--30238174 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
30238087 ACCCTAGGTT
* *
30238097 ATGTTATGTGAACCTTGTATGTGTCATATGCAAGCC
1 ATGTTATGTGAACCTAGTATGTGTCATATACAAGCC
* *
30238133 ATGATATCTGAACCTAGTATGTGTCATATACGAA-CC
1 ATGTTATGTGAACCTAGTATGTGTCATATAC-AAGCC
30238169 ATGTTA
1 ATGTTA
30238175 GGAGAACCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (36 bp):
ATGTTATGTGAACCTAGTATGTGTCATATACAAGCC
Found at i:30240058 original size:17 final size:19
Alignment explanation
Indices: 30240023--30240066 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
30240013 TATTATTTTT
30240023 ATATTTTATATTATTAATA
1 ATATTTTATATTATTAATA
30240042 ATATTTTATA-T-TTAATA
1 ATATTTTATATTATTAATA
*
30240059 ATTTTTTA
1 ATATTTTA
30240067 ATAACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 1 0.04
19 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTATATTATTAATA
Found at i:30242560 original size:226 final size:217
Alignment explanation
Indices: 30242165--30242568 Score: 504
Period size: 226 Copynumber: 1.8 Consensus size: 217
30242155 GAAGTTGTCG
* * * * * *
30242165 AAATTATGATATAATGTTGAAAATTTTAAATTTTTTTGGTTAAAGAACTGGTTTTAGGTGAGGAA
1 AAATTATGATATAAGGTTCAAAAATTTAAATTTTTTTGGTTAAAGAACTGATATTAGGTGAAGAA
* * * *
30242230 TTTATTTGAATTTATATTTTAAAAGCTCCAATTTTAAAGAAAATGTAAGATGCTTGATCTCAATA
66 TTTATATGAATTTAGATTATAAAAGCTCCAATTTTAAAGAAAATGCAAGATGCTTGATCTCAATA
* * *
30242295 TTTTAATTTTATTTTGTTTGATTTGGATTCTTGTGAGCTTGTTTATTTAAATTTTTTTTCTTTTG
131 TTTTAATTTTATTTTGTTTAATTTGGATTATTGTGAGCTTATTTATTTAAATTTTTTTTCTTTTG
30242360 GGTTAAATTGGCTTCTTTTGTT
196 GGTTAAATTGGCTTCTTTTGTT
** *
30242382 AAATTATGATATGCGGTTCAAAAATTTAAGTTTTTTTGGGTTAAAGAACTGATATTAGGT-AAGA
1 AAATTATGATATAAGGTTCAAAAATTTAAATTTTTTT-GGTTAAAGAACTGATATTAGGTGAAGA
* *
30242446 ATATATATATGAGTTTAGATTATAAAAGCTCCTATTGTTTAAAAAAGAAAAGTTGCAAGATGCTT
65 AT-T-TATATGAATTTAGATTATAAAAGCTCC-AAT-TTT---AAAGAAAA--TGCAAGATGCTT
* * * * *
30242511 GATCTTAATATTTTTATTTTGTTTTGTTTAATTTGGCTTATTTTGAGCTTATTTATTT
121 GATCTCAATATTTTAATTTTATTTTGTTTAATTTGGATTATTGTGAGCTTATTTATTT
30242569 GGATTTATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
217 36 0.23
218 21 0.14
219 23 0.15
220 2 0.01
221 3 0.02
224 8 0.05
226 61 0.40
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.48
Consensus pattern (217 bp):
AAATTATGATATAAGGTTCAAAAATTTAAATTTTTTTGGTTAAAGAACTGATATTAGGTGAAGAA
TTTATATGAATTTAGATTATAAAAGCTCCAATTTTAAAGAAAATGCAAGATGCTTGATCTCAATA
TTTTAATTTTATTTTGTTTAATTTGGATTATTGTGAGCTTATTTATTTAAATTTTTTTTCTTTTG
GGTTAAATTGGCTTCTTTTGTT
Found at i:30253622 original size:41 final size:40
Alignment explanation
Indices: 30253554--30253655 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 40
30253544 CACCCATTTC
** *
30253554 CTCATTGGGTAATTCGAAGTAATAAATTGACAC-CTAGTGT
1 CTCATTGAATAATTCGAAGTAATAAATTAACACAC-AGTGT
30253594 CTCATTGAATAATTCTGAAGTAATAAATTAACACACAGTGT
1 CTCATTGAATAATTC-GAAGTAATAAATTAACACACAGTGT
* *
30253635 CTCATTG-GTAAATCGAAGTAA
1 CTCATTGAATAATTCGAAGTAA
30253656 ATTGGAACCC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
39 7 0.13
40 18 0.33
41 29 0.53
42 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (40 bp):
CTCATTGAATAATTCGAAGTAATAAATTAACACACAGTGT
Found at i:30254014 original size:5 final size:5
Alignment explanation
Indices: 30254004--30254041 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
30253994 TAAAATTCAT
30254004 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAA
1 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAA
30254042 TTCAATTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (5 bp):
CAACA
Found at i:30254121 original size:19 final size:19
Alignment explanation
Indices: 30254099--30254137 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
30254089 TTTTCAATTT
*
30254099 AGTCCCTAAATCGAGACTA
1 AGTCCCTAAACCGAGACTA
30254118 AGTCCCTAAACCGAGACTA
1 AGTCCCTAAACCGAGACTA
30254137 A
1 A
30254138 CTTTTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (19 bp):
AGTCCCTAAACCGAGACTA
Found at i:30254695 original size:19 final size:20
Alignment explanation
Indices: 30254663--30254701 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
30254653 AAACATATTT
*
30254663 TATTAATATATACATATGTA
1 TATTAATATATACACATGTA
*
30254683 TATTAA-ATTTACACATGTA
1 TATTAATATATACACATGTA
30254702 ATCAGTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (20 bp):
TATTAATATATACACATGTA
Found at i:30258318 original size:24 final size:24
Alignment explanation
Indices: 30258291--30258402 Score: 91
Period size: 24 Copynumber: 4.6 Consensus size: 24
30258281 AGAAATTTCA
* *
30258291 GCACTATGTGTGCGAGGTTATGCG
1 GCACTATGTGTGCGAGATTATACG
* * * * *
30258315 GCACTATGTGTGCAAAAACTACATG
1 GCACTATGTGTGC-GAGATTATACG
* **
30258340 GCACTATGTGGGCGAGATTATATA
1 GCACTATGTGTGCGAGATTATACG
* *
30258364 GCACTATGTGTGCGAGGA-AATGCG
1 GCACTATGTGTGCGA-GATTATACG
30258388 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
30258403 ATGAGTAAGA
Statistics
Matches: 68, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
24 50 0.74
25 18 0.26
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (24 bp):
GCACTATGTGTGCGAGATTATACG
Found at i:30263743 original size:14 final size:14
Alignment explanation
Indices: 30263724--30263761 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
30263714 CATATCTTCC
*
30263724 AATTTTGAACTCAA
1 AATTTTAAACTCAA
30263738 AATTTTAAACTCAA
1 AATTTTAAACTCAA
30263752 AATTTTAAAC
1 AATTTTAAAC
30263762 AGACTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (14 bp):
AATTTTAAACTCAA
Found at i:30265660 original size:20 final size:20
Alignment explanation
Indices: 30265635--30265679 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
30265625 CCATATATAA
*
30265635 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTCA-AAATTAT
30265655 TTTG-AATTTTCAAAATTAT
1 TTTGAAATTTTCAAAATTAT
30265674 TTTGAA
1 TTTGAA
30265680 TTATTTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTGAAATTTTCAAAATTAT
Found at i:30267484 original size:18 final size:16
Alignment explanation
Indices: 30267461--30267496 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
30267451 TTAATGAATG
30267461 TTTTTATTATTTATGTAA
1 TTTTTATT-TTTAT-TAA
30267479 TTTTTATTTTTATTAA
1 TTTTTATTTTTATTAA
30267495 TT
1 TT
30267497 AATGCTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTATTTTTATTAA
Found at i:30270012 original size:35 final size:36
Alignment explanation
Indices: 30269942--30270012 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
30269932 TATTGAAAAT
* * *
30269942 AAAATATATTAATTTATCAATTCAAATATTATAATA
1 AAAAAATATTAAATAATCAATTCAAATATTATAATA
*
30269978 AAAAAATATTAAATAAT-AATT-AAAGTATTTTAATA
1 AAAAAATATTAAATAATCAATTCAAA-TATTATAATA
30270013 TATTTAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
34 3 0.10
35 13 0.43
36 14 0.47
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (36 bp):
AAAAAATATTAAATAATCAATTCAAATATTATAATA
Found at i:30271094 original size:19 final size:20
Alignment explanation
Indices: 30271053--30271094 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
30271043 TATTGTAATT
* * *
30271053 AATTTTTAATTTATTATTTA
1 AATTTTTAATATATAATTAA
30271073 AATTTTTAA-ATATAATTAA
1 AATTTTTAATATATAATTAA
30271092 AAT
1 AAT
30271095 ATATTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTTTAATATATAATTAA
Found at i:30273473 original size:62 final size:62
Alignment explanation
Indices: 30273366--30273541 Score: 210
Period size: 62 Copynumber: 2.8 Consensus size: 62
30273356 TGTGGCCCAT
* * * **
30273366 ACAGCTTGGACACACGTCCGTGTCTCTGACCCGTGTGACTCAAATTCTAAACTAATATGTTAC
1 ACAGCTTGGACACACGTCCGTGTCTCTAACCCGTGTGACTTAAATTCAAAAC-AATAAATTAC
* * * *
30273429 AC-GGTTGGACACACGTCCGTTTCTCTAACTCGTGTGACTTAAATTCCAAAACAGTAAATTAC
1 ACAGCTTGGACACACGTCCGTGTCTCTAACCCGTGTGACTTAAATT-CAAAACAATAAATTAC
* * * *
30273491 ACAGCCTGGACACACGCCCGTGTCTCTAACCCATGTGAATTAAATTCAAAA
1 ACAGCTTGGACACACGTCCGTGTCTCTAACCCGTGTGACTTAAATTCAAAA
30273542 ATAGTGAGTT
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
62 52 0.55
63 43 0.45
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (62 bp):
ACAGCTTGGACACACGTCCGTGTCTCTAACCCGTGTGACTTAAATTCAAAACAATAAATTAC
Done.