Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 80 of 106
Found at i:30455346 original size:47 final size:47
Alignment explanation
Indices: 30455289--30455439 Score: 205
Period size: 47 Copynumber: 3.2 Consensus size: 47
30455279 ACACATTATC
*
30455289 ACCCTACCGTGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAA
1 ACCCTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAA
* * * * *
30455336 ACCCTGCCGTGTCACAAATCCCCTCCATGACGTGTCACAAACTCTGA
1 ACCCTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAA
* * *
30455383 ACCCTGTC-TATCACAGATTCCCTCCATGGCATGTCACACACTCTAA
1 ACCCTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAA
*
30455429 ACCTTGCCGTG
1 ACCCTGCCGTG
30455440 CCTCAGTCGT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
46 37 0.43
47 49 0.57
ACGTcount: A:0.25, C:0.37, G:0.14, T:0.24
Consensus pattern (47 bp):
ACCCTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAA
Found at i:30455353 original size:24 final size:24
Alignment explanation
Indices: 30455321--30455388 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 24
30455311 CTCCATGGCA
*
30455321 TGTCACAAACTCTAAACCCTGCCG
1 TGTCACAAACTCTAAACCCTGACG
**** *
30455345 TGTCACAAA-TCCCCTCCATGACG
1 TGTCACAAACTCTAAACCCTGACG
*
30455368 TGTCACAAACTCTGAACCCTG
1 TGTCACAAACTCTAAACCCTG
30455389 TCTATCACAG
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.28, C:0.37, G:0.13, T:0.22
Consensus pattern (24 bp):
TGTCACAAACTCTAAACCCTGACG
Found at i:30455507 original size:197 final size:197
Alignment explanation
Indices: 30455209--30455581 Score: 496
Period size: 197 Copynumber: 1.9 Consensus size: 197
30455199 CACGTTCTCA
* * *
30455209 CCATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACCCATGTCACATATTATCACTGTGCT
1 CCATGGCATGTCACACACTCTAAACCCTGCCGTGCCACACCCATGTCACATATTATCACCGTGCT
* *
30455274 GTCACACACATTATCACCCTACCGTGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAAACC
66 ATCACACACATTATCACCCTACCATGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAAACC
* *
30455339 CTGCCGTGTCACAAATCCCCTCCATGACGTGTCACAAACTCTGAACCCTGTCTATCACAGATTCC
131 CTGCCATGTCACAAATCCCCTCCATGACATGTCACAAACTCTGAACCCTGTCTATCACAGATTCC
30455404 CT
196 CT
* * ** * *
30455406 CCATGGCATGTCACACACTCTAAACCTTGCCGTGCCTCAGTCGTGTCACATATTCTCACCGTG-T
1 CCATGGCATGTCACACACTCTAAACCCTGCCGTGCCACACCCATGTCACATATTATCACCGTGCT
* * * * * * **
30455470 CATCTCACACATTATCACCTTGCCATGTCATAGATTCCCTCCATGGCGTGTCACAAACTTTCGAC
66 -ATCACACACATTATCACCCTACCATGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAAAC
* * * * *
30455535 CCTGTCATGTCACAAATTCCCTTCATGGCATGTCACAAATTCTGAAC
130 CCTGCCATGTCACAAATCCCCTCCATGACATGTCACAAACTCTGAAC
30455582 ACTGCCATGT
Statistics
Matches: 149, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
196 1 0.01
197 148 0.99
ACGTcount: A:0.25, C:0.35, G:0.14, T:0.27
Consensus pattern (197 bp):
CCATGGCATGTCACACACTCTAAACCCTGCCGTGCCACACCCATGTCACATATTATCACCGTGCT
ATCACACACATTATCACCCTACCATGTCACAGATTCCCTCCATGGCATGTCACAAACTCTAAACC
CTGCCATGTCACAAATCCCCTCCATGACATGTCACAAACTCTGAACCCTGTCTATCACAGATTCC
CT
Found at i:30455525 original size:150 final size:150
Alignment explanation
Indices: 30455356--30455651 Score: 364
Period size: 150 Copynumber: 2.0 Consensus size: 150
30455346 GTCACAAATC
*
30455356 CCCTCCATGACGTGTCACAAACTCT-GAACCCTGTC-TATCACAGATTCCCTCCATGGCATGTCA
1 CCCTCCATGACGTGTCACAAACTCTCG-ACCCTGTCATATCACAAATTCCCTCCATGGCATGTCA
* * * * * * *
30455419 CACACTCTAAAC-CTTGCCGTGCCTCAGTCGTGTCACATATTCTCACCGTGTCATCTCACACATT
65 CAAACTCTAAACAC-TGCCATGCCACAGCCGTGTCACATA-GCTCACCATGCCATCTCACACATT
*
30455483 ATCACCTTGCCATGTCATAGATT
128 ATCACCATGCCATGTCATAGATT
* * * *
30455506 CCCTCCATGGCGTGTCACAAACTTTCGACCCTGTCATGTCACAAATTCCCTTCATGGCATGTCAC
1 CCCTCCATGACGTGTCACAAACTCTCGACCCTGTCATATCACAAATTCCCTCCATGGCATGTCAC
* * * * * *
30455571 AAATTCTGAACACTGCCATGTCACAGCCGTGTCACATAGCTCACCATGCCGTCTCACATATTCTC
66 AAACTCTAAACACTGCCATGCCACAGCCGTGTCACATAGCTCACCATGCCATCTCACACATTATC
*
30455636 ACCATGGCATGTCATA
131 ACCATGCCATGTCATA
30455652 TATGAACACC
Statistics
Matches: 123, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
150 66 0.54
151 56 0.46
152 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (150 bp):
CCCTCCATGACGTGTCACAAACTCTCGACCCTGTCATATCACAAATTCCCTCCATGGCATGTCAC
AAACTCTAAACACTGCCATGCCACAGCCGTGTCACATAGCTCACCATGCCATCTCACACATTATC
ACCATGCCATGTCATAGATT
Found at i:30455591 original size:47 final size:47
Alignment explanation
Indices: 30455490--30455595 Score: 126
Period size: 47 Copynumber: 2.3 Consensus size: 47
30455480 ATTATCACCT
* * * *
30455490 TGCCATGTCATAGATTCCCTCCATGGCGTGTCACAAACTTTCGACCC
1 TGCCATGTCACAAATTCCCTCCATGGCATGTCACAAACTTTCGACAC
* *
30455537 TGTCATGTCACAAATTCCCTTCATGGCATGTCACAAA--TTCTGAACAC
1 TGCCATGTCACAAATTCCCTCCATGGCATGTCACAAACTTTC-G-ACAC
30455584 TGCCATGTCACA
1 TGCCATGTCACA
30455596 GCCGTGTCAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 3 0.06
46 1 0.02
47 46 0.92
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.28
Consensus pattern (47 bp):
TGCCATGTCACAAATTCCCTCCATGGCATGTCACAAACTTTCGACAC
Found at i:30455621 original size:22 final size:23
Alignment explanation
Indices: 30455596--30455641 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
30455586 CCATGTCACA
*
30455596 GCCGTGTCACATA-GCTCACCAT
1 GCCGTCTCACATATGCTCACCAT
*
30455618 GCCGTCTCACATATTCTCACCAT
1 GCCGTCTCACATATGCTCACCAT
30455641 G
1 G
30455642 GCATGTCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (23 bp):
GCCGTCTCACATATGCTCACCAT
Found at i:30455654 original size:23 final size:23
Alignment explanation
Indices: 30455600--30455854 Score: 188
Period size: 23 Copynumber: 11.3 Consensus size: 23
30455590 GTCACAGCCG
* * *
30455600 TGTCACATA-GCTCACCATGCCG
1 TGTCACATATTCTCACCATGGCA
*
30455622 TCTCACATATTCTCACCATGGCA
1 TGTCACATATTCTCACCATGGCA
* ***
30455645 TGTCATATATGAACACCATGGCA
1 TGTCACATATTCTCACCATGGCA
* *
30455668 TG-C-CACATTCTTACACTAT--CA
1 TGTCACATATTC-T-CACCATGGCA
*
30455689 TGTCACATATTCTCACCATGTCA
1 TGTCACATATTCTCACCATGGCA
* * *
30455712 TGTCACATATGCACACCATGGCG
1 TGTCACATATTCTCACCATGGCA
*
30455735 TG-C-CACATTCTCA-CATTGGCA
1 TGTCACATATTCTCACCA-TGGCA
30455756 TGTCACATATTCTCACCATGGCA
1 TGTCACATATTCTCACCATGGCA
* * **
30455779 TGTCACATATTCCCTCCGA-GTTA
1 TGTCACATATTCTCACC-ATGGCA
* *
30455802 GGTCACATATTCTCACTC-TGTCA
1 TGTCACATATTCTCAC-CATGGCA
* *
30455825 TGTCACATATTCCCTCCATGGCA
1 TGTCACATATTCTCACCATGGCA
30455848 TGTCACA
1 TGTCACA
30455855 AACTCTAAAC
Statistics
Matches: 180, Mismatches: 38, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.01
21 25 0.14
22 14 0.08
23 135 0.75
24 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.30
Consensus pattern (23 bp):
TGTCACATATTCTCACCATGGCA
Found at i:30455732 original size:67 final size:67
Alignment explanation
Indices: 30455624--30455788 Score: 258
Period size: 67 Copynumber: 2.5 Consensus size: 67
30455614 CCATGCCGTC
* * *
30455624 TCACATATTCTCACCATGGCATGTCATATATGAACACCATGGCATGCCACATTCTTACACTATCA
1 TCACATATTCTCACCATGGCATGTCACATATGAACACCATGGCATGCCACATTCTCACACTAGCA
30455689 TG
66 TG
* * * * *
30455691 TCACATATTCTCACCATGTCATGTCACATATGCACACCATGGCGTGCCACATTCTCACATTGGCA
1 TCACATATTCTCACCATGGCATGTCACATATGAACACCATGGCATGCCACATTCTCACACTAGCA
30455756 TG
66 TG
30455758 TCACATATTCTCACCATGGCATGTCACATAT
1 TCACATATTCTCACCATGGCATGTCACATAT
30455789 TCCCTCCGAG
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 89 1.00
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.30
Consensus pattern (67 bp):
TCACATATTCTCACCATGGCATGTCACATATGAACACCATGGCATGCCACATTCTCACACTAGCA
TG
Found at i:30455745 original size:44 final size:44
Alignment explanation
Indices: 30455697--30455786 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
30455687 CATGTCACAT
* *
30455697 ATTCTCACCA-TGTCATGTCACATATGCACACCATGGCGTGCCAC
1 ATTCTCA-CATTGGCATGTCACATATGCACACCATGGCATGCCAC
* * *
30455741 ATTCTCACATTGGCATGTCACATATTCTCACCATGGCATGTCAC
1 ATTCTCACATTGGCATGTCACATATGCACACCATGGCATGCCAC
30455785 AT
1 AT
30455787 ATTCCCTCCG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (44 bp):
ATTCTCACATTGGCATGTCACATATGCACACCATGGCATGCCAC
Found at i:30455809 original size:67 final size:67
Alignment explanation
Indices: 30455624--30455854 Score: 220
Period size: 67 Copynumber: 3.4 Consensus size: 67
30455614 CCATGCCGTC
* * * * * * **
30455624 TCACATATTCTCACCATGGCATGTCATATATGAACACCATGGCATGCCAC-ATTCTTACACTATC
1 TCACATATTCTCACCATGGCATGTCACATATGCACACCATAGCGT-CCACAATTCTCACTCTGGC
30455688 ATG
65 ATG
* *
30455691 TCACATATTCTCACCATGTCATGTCACATATGCACACCATGGCGTGCCAC-ATTCTCACAT-TGG
1 TCACATATTCTCACCATGGCATGTCACATATGCACACCATAGCGT-CCACAATTCTCAC-TCTGG
30455754 CATG
64 CATG
* * *
30455758 TCACATATTCTCACCATGGCATGTCACATATTCCCTCCGAGTTAG-GT-CACATATTCTCACTCT
1 TCACATATTCTCACCATGGCATGTCACATATGCACACC-A--TAGCGTCCACA-ATTCTCACTCT
*
30455821 GTCATG
62 GGCATG
* *
30455827 TCACATATTCCCTCCATGGCATGTCACA
1 TCACATATTCTCACCATGGCATGTCACA
30455855 AACTCTAAAC
Statistics
Matches: 141, Mismatches: 16, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
67 95 0.67
68 2 0.01
69 42 0.30
70 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (67 bp):
TCACATATTCTCACCATGGCATGTCACATATGCACACCATAGCGTCCACAATTCTCACTCTGGCA
TG
Found at i:30455917 original size:23 final size:23
Alignment explanation
Indices: 30455881--30455944 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
30455871 GTGTCACAGT
* * *
30455881 CGTGTCATATATTCTCACAATGA
1 CGTGTCACACATTCCCACAATGA
* *
30455904 CGTGTCACACATTCCCACCATGC
1 CGTGTCACACATTCCCACAATGA
*
30455927 CATGTCACACATTCCCAC
1 CGTGTCACACATTCCCAC
30455945 CATGCTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.36, G:0.11, T:0.27
Consensus pattern (23 bp):
CGTGTCACACATTCCCACAATGA
Found at i:30455958 original size:23 final size:23
Alignment explanation
Indices: 30455906--30455949 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
30455896 CACAATGACG
30455906 TGTCACACATTCCCACCATGCCA
1 TGTCACACATTCCCACCATGCCA
30455929 TGTCACACATTCCCACCATGC
1 TGTCACACATTCCCACCATGC
30455950 TGTTTCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.43, G:0.09, T:0.23
Consensus pattern (23 bp):
TGTCACACATTCCCACCATGCCA
Found at i:30465868 original size:15 final size:16
Alignment explanation
Indices: 30465848--30465890 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
30465838 ATATAAAATT
*
30465848 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
30465863 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
30465880 AAAATAACTAA
1 AAAATAACTAA
30465891 AATAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:30468602 original size:46 final size:47
Alignment explanation
Indices: 30468549--30468701 Score: 136
Period size: 47 Copynumber: 3.3 Consensus size: 47
30468539 TTAATTTTTG
30468549 CTTAGGAAAATATT-TT-ATCTTAATTCATTATTT-TGC-TTGCACTTGA
1 CTTAGGAAAATATTCTTAAT-TTAATTCATTATTTGTGCATT--ACTTGA
* * *
30468595 CTTAGGAAAATATTCTTAATTTGATTTATTATTTGTTCATTACTTGA
1 CTTAGGAAAATATTCTTAATTTAATTCATTATTTGTGCATTACTTGA
* * * * * * *
30468642 CTTGGGAAAATATTATT-ACTCATATTTATTATTTGTTCATTATTTGA
1 CTTAGGAAAATATTCTTAATTTA-ATTCATTATTTGTGCATTACTTGA
*
30468689 CTAAGGAAAATAT
1 CTTAGGAAAATAT
30468702 CTTTACTTTG
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
46 16 0.18
47 69 0.76
48 4 0.04
49 2 0.02
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.48
Consensus pattern (47 bp):
CTTAGGAAAATATTCTTAATTTAATTCATTATTTGTGCATTACTTGA
Found at i:30468642 original size:47 final size:47
Alignment explanation
Indices: 30468589--30468729 Score: 187
Period size: 47 Copynumber: 3.0 Consensus size: 47
30468579 TTTTGCTTGC
*
30468589 ACTTGACTTAGGAAAATATTCTTAATTTGATTTATTATTTGTTCATT
1 ACTTGACTTAGGAAAATATTCTTACTTTGATTTATTATTTGTTCATT
* * *
30468636 ACTTGACTTGGGAAAATATTATTACTCAT-ATTTATTATTTGTTCATT
1 ACTTGACTTAGGAAAATATTCTTACT-TTGATTTATTATTTGTTCATT
* * *
30468683 ATTTGACTAAGGAAAATA-TCTTTACTTTGATGTATTATTTGTTCATT
1 ACTTGACTTAGGAAAATATTC-TTACTTTGATTTATTATTTGTTCATT
30468730 TCAACTTTCT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
46 2 0.02
47 78 0.96
48 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (47 bp):
ACTTGACTTAGGAAAATATTCTTACTTTGATTTATTATTTGTTCATT
Found at i:30469697 original size:22 final size:22
Alignment explanation
Indices: 30469646--30469700 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
30469636 CCATTTCAAG
* *
30469646 CATTC-TCAAAACCTCTGGGTA
1 CATTCTTCAAAACCCCTAGGTA
*
30469667 C-CTCTTCAAAACCCCTAGGTA
1 CATTCTTCAAAACCCCTAGGTA
30469688 CATTCTTCAAAAC
1 CATTCTTCAAAAC
30469701 TTCCAACTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 10 0.36
ACGTcount: A:0.31, C:0.33, G:0.09, T:0.27
Consensus pattern (22 bp):
CATTCTTCAAAACCCCTAGGTA
Found at i:30469785 original size:21 final size:21
Alignment explanation
Indices: 30469755--30469795 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30469745 TTTGGGTAAC
30469755 AATTTTAAAACCT-CAAGTAG
1 AATTTTAAAACCTCCAAGTAG
30469775 AATTTGTAAAACCTCCAAGTA
1 AATTT-TAAAACCTCCAAGTA
30469796 ACCTTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (21 bp):
AATTTTAAAACCTCCAAGTAG
Found at i:30477831 original size:20 final size:20
Alignment explanation
Indices: 30477806--30477845 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30477796 ATAAGCCTTG
*
30477806 TTGATTTTTACGAAATGAAA
1 TTGATTTATACGAAATGAAA
*
30477826 TTGATTTATATGAAATGAAA
1 TTGATTTATACGAAATGAAA
30477846 AGAGATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGATTTATACGAAATGAAA
Found at i:30479050 original size:29 final size:29
Alignment explanation
Indices: 30479007--30479065 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
30478997 ATTCACACAT
* *
30479007 TGAAAAAATATAATAAATAATGATAATAA
1 TGAAAAAATATAATAAATAATAAAAATAA
30479036 TGAATAAAATA-AATAAATAATAAAAATAA
1 TGAA-AAAATATAATAAATAATAAAAATAA
30479065 T
1 T
30479066 TAGAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (29 bp):
TGAAAAAATATAATAAATAATAAAAATAA
Found at i:30481217 original size:15 final size:15
Alignment explanation
Indices: 30481189--30481260 Score: 81
Period size: 15 Copynumber: 4.8 Consensus size: 15
30481179 TTAACAATGC
* *
30481189 AATGTGATTACAGGT
1 AATGTGATTGCAAGT
* *
30481204 AATGTAATTGCAGGT
1 AATGTGATTGCAAGT
*
30481219 AATGTTATTGCAAGT
1 AATGTGATTGCAAGT
* *
30481234 AATATGATTGCAAGC
1 AATGTGATTGCAAGT
30481249 AATGTGATTGCA
1 AATGTGATTGCA
30481261 TGGAAAATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:30481486 original size:18 final size:18
Alignment explanation
Indices: 30481463--30481497 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30481453 CTATTAAATA
30481463 TATTTTAATGTCATATTT
1 TATTTTAATGTCATATTT
* *
30481481 TATTTTCATGTCTTATT
1 TATTTTAATGTCATATT
30481498 ATAATCTTAT
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:0.23, C:0.09, G:0.06, T:0.63
Consensus pattern (18 bp):
TATTTTAATGTCATATTT
Found at i:30482393 original size:17 final size:17
Alignment explanation
Indices: 30482371--30482407 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30482361 AAGAGGAAAA
*
30482371 TATGGCTATATATAAAT
1 TATGGCAATATATAAAT
*
30482388 TATGGCAATATATTAAT
1 TATGGCAATATATAAAT
30482405 TAT
1 TAT
30482408 TGACCTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (17 bp):
TATGGCAATATATAAAT
Found at i:30484250 original size:16 final size:16
Alignment explanation
Indices: 30484229--30484266 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
30484219 AGAGAAGGAA
30484229 AAGCTCCTATGTCCTT
1 AAGCTCCTATGTCCTT
*
30484245 AAGCTCCTGTGTCCTT
1 AAGCTCCTATGTCCTT
30484261 AAGCTC
1 AAGCTC
30484267 TTTTTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (16 bp):
AAGCTCCTATGTCCTT
Found at i:30485905 original size:3 final size:3
Alignment explanation
Indices: 30485897--30485943 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
30485887 AAAAATGATC
*
30485897 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30485944 GGATAAACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:30493834 original size:8 final size:9
Alignment explanation
Indices: 30493813--30493839 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
30493803 AGAATATATA
30493813 AAAAATTTT
1 AAAAATTTT
30493822 AAAAATTTT
1 AAAAATTTT
30493831 AAAAATTTT
1 AAAAATTTT
30493840 GGAGGCCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAAATTTT
Found at i:30500594 original size:17 final size:19
Alignment explanation
Indices: 30500548--30500594 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
30500538 GGAAATTTTT
*
30500548 TATTTTTTTGT-TTGTATA
1 TATTTTTTTATATTGTATA
*
30500566 TATTTATTTATATTGTAT-
1 TATTTTTTTATATTGTATA
30500584 T-TTTTTTTATA
1 TATTTTTTTATA
30500595 AATCAATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 10 0.40
19 6 0.24
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
TATTTTTTTATATTGTATA
Found at i:30500770 original size:33 final size:33
Alignment explanation
Indices: 30500732--30500830 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 33
30500722 ATTAACAATA
30500732 TTCAACAATGGATAAAAACAATAACAAATAGTC
1 TTCAACAATGGATAAAAACAATAACAAATAGTC
* ** *
30500765 TTCAACAA---ATAACAGGA-AATAATTAACAGTC
1 TTCAACAATGGATAA-A-AACAATAACAAATAGTC
* *
30500796 TTCAACAATGGATAAAAGCAACAACAAATAGTC
1 TTCAACAATGGATAAAAACAATAACAAATAGTC
30500829 TT
1 TT
30500831 AAATGGAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
30 4 0.08
31 20 0.40
32 1 0.02
33 21 0.42
34 4 0.08
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (33 bp):
TTCAACAATGGATAAAAACAATAACAAATAGTC
Found at i:30505953 original size:20 final size:20
Alignment explanation
Indices: 30505908--30505945 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
30505898 CTTTGGCCCC
30505908 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
30505928 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
30505946 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:30506029 original size:27 final size:27
Alignment explanation
Indices: 30505999--30506056 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
30505989 TTGGAGTAAA
*
30505999 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGGTAATTTT-CCACCACC
*
30506026 AGGGGCAAAATTGTAATTTTCCACCACC
1 A-GGGCAAAATGGTAATTTTCCACCACC
30506054 AGG
1 AGG
30506057 ACATTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACC
Found at i:30512108 original size:20 final size:20
Alignment explanation
Indices: 30512093--30512130 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30512083 CCTCAAATCT
30512093 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
*
30512113 TACTCCAATAAGTTAAAT
1 TACTCCAATAAGTCAAAT
30512131 GGAGCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:30519964 original size:20 final size:20
Alignment explanation
Indices: 30519947--30519984 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
30519937 CCTCAAATCT
30519947 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
30519967 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
30519985 GGAGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:30522986 original size:18 final size:19
Alignment explanation
Indices: 30522939--30522986 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
30522929 TTAATATTTT
30522939 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
* *
30522958 AATAATATTTTATT-TTAA
1 AATATTATTTTATTCATAA
*
30522976 AATATTCTTTT
1 AATATTATTTT
30522987 CACTCGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:30527982 original size:47 final size:47
Alignment explanation
Indices: 30527882--30527974 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
30527872 AATGCAAACA
* *
30527882 AACTAGGGAACTCATGTTTAAGTATCATACCTTTCAGCTATGCATCG
1 AACTAGAGAACTCATATTTAAGTATCATACCTTTCAGCTATGCATCG
*
30527929 AACTAGAGAACTCATATTTAAGTATCATGCCTTTCAGCTATGCATC
1 AACTAGAGAACTCATATTTAAGTATCATACCTTTCAGCTATGCATC
30527975 ATGCTAGAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (47 bp):
AACTAGAGAACTCATATTTAAGTATCATACCTTTCAGCTATGCATCG
Found at i:30548027 original size:19 final size:19
Alignment explanation
Indices: 30548003--30548039 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30547993 CATTTAACTT
*
30548003 ATTGGAGTATGATTTGAGC
1 ATTGGAGTATAATTTGAGC
30548022 ATTGGAGTATAATTTGAG
1 ATTGGAGTATAATTTGAG
30548040 GGTTTGGCAG
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:0.03, G:0.30, T:0.38
Consensus pattern (19 bp):
ATTGGAGTATAATTTGAGC
Found at i:30548246 original size:28 final size:29
Alignment explanation
Indices: 30548205--30548265 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 29
30548195 TTCTATGGGC
*
30548205 AATTTTTCAGTTTTT-GGGGCAAAAATGT
1 AATTTTTCACTTTTTAGGGGCAAAAATGT
* *
30548233 AATTTTTGACTTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTTA--GGGGCAAAAATGT
30548264 AA
1 AA
30548266 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.48
31 14 0.52
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (29 bp):
AATTTTTCACTTTTTAGGGGCAAAAATGT
Found at i:30552963 original size:204 final size:203
Alignment explanation
Indices: 30552610--30553018 Score: 773
Period size: 204 Copynumber: 2.0 Consensus size: 203
30552600 TCAGTGAGTA
*
30552610 AACAAAGTCCGTCATTAACTTCTAAAGCTGAGTAAATGGAGACAGTTAACTTTTCATCATACCAT
1 AACAAAGTCCGTCATTAACTTCTAAAGCCGAGTAAATGGAGACAGTTAACTTTTCATCATACCAT
30552675 AATCCACAACATTTTGTACTTGTTTCAAATCATATAAAACAACACATTTCATTATAATACACATC
66 AATCCACAACATTTTGTACTTGTTTCAAATCATATAAAACAACACATTTCATTATAATACACATC
*
30552740 ACGACTTATGATTTTCTTAAAAACTTGGCTCATGCCAAAAATCATACTCGGTGATACCTTGGCCG
131 ACGACTTATGATTTTCTTAAAAACTTAGCTCATGCCAAAAATCATACTCGGTGATACCTTGGCCG
30552805 AGGCATTC
196 AGGCATTC
30552813 AACNAAAGTCCGTCATTAACTTCTAAAGCCGAGTAAATGGAGACAGTTAACTTTTCATCATACCA
1 AAC-AAAGTCCGTCATTAACTTCTAAAGCCGAGTAAATGGAGACAGTTAACTTTTCATCATACCA
30552878 TAATCCACAACATTTTGTACTTGTTTCAAATCATATAAAACAACACATTTCATTATAATACACAT
65 TAATCCACAACATTTTGTACTTGTTTCAAATCATATAAAACAACACATTTCATTATAATACACAT
* *
30552943 CACGACTTATGATTTTCTTAAAAACTTAGCTCGTGCCAAAAATCATACTTGGTGATACCTTGGCC
130 CACGACTTATGATTTTCTTAAAAACTTAGCTCATGCCAAAAATCATACTCGGTGATACCTTGGCC
30553008 GAGGCATTC
195 GAGGCATTC
30553017 AA
1 AA
30553019 TCGAGTCCAC
Statistics
Matches: 201, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
203 3 0.01
204 198 0.99
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (203 bp):
AACAAAGTCCGTCATTAACTTCTAAAGCCGAGTAAATGGAGACAGTTAACTTTTCATCATACCAT
AATCCACAACATTTTGTACTTGTTTCAAATCATATAAAACAACACATTTCATTATAATACACATC
ACGACTTATGATTTTCTTAAAAACTTAGCTCATGCCAAAAATCATACTCGGTGATACCTTGGCCG
AGGCATTC
Found at i:30561701 original size:20 final size:20
Alignment explanation
Indices: 30561673--30561718 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
30561663 TTTTGGCCCC
*
30561673 ATTTAACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
30561693 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
30561713 ATTTGA
1 ATTTGA
30561719 GGTTTATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:30563562 original size:2 final size:2
Alignment explanation
Indices: 30563555--30563585 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30563545 TGTATTGTTT
30563555 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 T
30563586 GATTTGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30566380 original size:18 final size:20
Alignment explanation
Indices: 30566343--30566380 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30566333 GGTATTTTCG
*
30566343 TAATTTGCTATCAGCACTGA
1 TAATTTGCTACCAGCACTGA
30566363 TAATTTGC-ACCA-CACTGA
1 TAATTTGCTACCAGCACTGA
30566381 GAGACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (20 bp):
TAATTTGCTACCAGCACTGA
Found at i:30568591 original size:27 final size:27
Alignment explanation
Indices: 30568550--30568620 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
30568540 ATTATTCATT
*
30568550 CACTTCTGGTAGGTTAAAAGTATCCATC
1 CACTT-TGGTGGGTTAAAAGTATCCATC
*
30568578 CACTTTGGTGGGTTACAAGTATCCATC
1 CACTTTGGTGGGTTAAAAGTATCCATC
*
30568605 CACCTCTGGTGGGTTA
1 CA-CTTTGGTGGGTTA
30568621 TCCAATTCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (27 bp):
CACTTTGGTGGGTTAAAAGTATCCATC
Found at i:30568680 original size:26 final size:26
Alignment explanation
Indices: 30568650--30568758 Score: 110
Period size: 26 Copynumber: 4.2 Consensus size: 26
30568640 TGGGTTAAGA
* *
30568650 TATCCGTCCACTTTTAGTAGTAAAAT
1 TATCCATCCACTTCTAGTAGTAAAAT
* * * *
30568676 TATCCATCAACATCTGGTGGTAAAAT
1 TATCCATCCACTTCTAGTAGTAAAAT
* * * *
30568702 TATCTATCCACTTATGGTGGTAAAAT
1 TATCCATCCACTTCTAGTAGTAAAAT
* *
30568728 TATCCATTCACTTCTAGTAATAAAAT
1 TATCCATCCACTTCTAGTAGTAAAAT
30568754 TATCC
1 TATCC
30568759 TTAAAATTGA
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (26 bp):
TATCCATCCACTTCTAGTAGTAAAAT
Found at i:30569265 original size:11 final size:11
Alignment explanation
Indices: 30569249--30569273 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30569239 TTAAAAGAAC
30569249 AAATATAAAAG
1 AAATATAAAAG
30569260 AAATATAAAAG
1 AAATATAAAAG
30569271 AAA
1 AAA
30569274 GTATTTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAATATAAAAG
Found at i:30569614 original size:21 final size:22
Alignment explanation
Indices: 30569585--30569627 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
30569575 ATACCATTTT
*
30569585 ATTATAATATTTAAT-TTTTAA
1 ATTAAAATATTTAATATTTTAA
*
30569606 ATTAAAATATTTATTATTTTAA
1 ATTAAAATATTTAATATTTTAA
30569628 TAATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAAAATATTTAATATTTTAA
Found at i:30569796 original size:15 final size:15
Alignment explanation
Indices: 30569776--30569818 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
30569766 CATTATTCAT
30569776 TTTAAAATATTAAAA
1 TTTAAAATATTAAAA
* * *
30569791 TTTAAAAAATTTATA
1 TTTAAAATATTAAAA
*
30569806 TTTAAAATTTTAA
1 TTTAAAATATTAA
30569819 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAAATATTAAAA
Found at i:30570362 original size:19 final size:17
Alignment explanation
Indices: 30570339--30570383 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
30570329 AATTTGAATT
30570339 ATATTAAAAACAGTAAAA
1 ATATTAAAAACAG-AAAA
*
30570357 ATTATTAAAAATAGAAAA
1 A-TATTAAAAACAGAAAA
30570375 ATATTAAAA
1 ATATTAAAA
30570384 TTATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 6 0.24
19 11 0.44
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (17 bp):
ATATTAAAAACAGAAAA
Found at i:30570440 original size:25 final size:22
Alignment explanation
Indices: 30570412--30570463 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 22
30570402 GATATTTTAT
*
30570412 AAAAATGAAAAATAAAGAACAAAAG
1 AAAAATAAAAAAT-AA-AA-AAAAG
30570437 AAAAATAAAAAATAAAAAAAAG
1 AAAAATAAAAAATAAAAAAAAG
30570459 AAAAA
1 AAAAA
30570464 ATAATTGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.38
23 2 0.08
24 2 0.08
25 12 0.46
ACGTcount: A:0.83, C:0.02, G:0.08, T:0.08
Consensus pattern (22 bp):
AAAAATAAAAAATAAAAAAAAG
Found at i:30570453 original size:18 final size:18
Alignment explanation
Indices: 30570413--30570467 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 18
30570403 ATATTTTATA
* *
30570413 AAAATGAAAAATAAAGAAC
1 AAAA-GAAAAATAAAAAAT
30570432 AAAAGAAAAATAAAAAAT
1 AAAAGAAAAATAAAAAAT
*
30570450 -AAA-AAAAAGAAAAAAT
1 AAAAGAAAAATAAAAAAT
30570466 AA
1 AA
30570468 TTGGATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 12 0.38
17 4 0.12
18 12 0.38
19 4 0.12
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAATAAAAAAT
Found at i:30573838 original size:646 final size:641
Alignment explanation
Indices: 30572608--30574102 Score: 1992
Period size: 646 Copynumber: 2.3 Consensus size: 641
30572598 CAAGTTCATG
* *
30572608 CAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATCCTCTAGGTATTAAAAGT
1 CAAAAAATAATATTAAATTGTAATTGAAAAATATTAAATGAATCTATCCTCTAGGCATTAAAAGT
* **
30572673 TAAAAATTATTATCTTCAAATATTTTTTACTGAAATAAATAAAAGTAAAAAAAACCCTTCAACTG
66 TAAAAATTATTATTTTCAAATATTTTTTACTGAAATAAATAAAAGTAAAAAAAACCCTTCAAAAG
* * * * *
30572738 TAAAAAACAACACAA-TTTGACGTAAAGTGTAAAAAAAATTAATTCAATTGAAAATAACAGATGT
131 TAAAAAATAACGCAATTTTGACATAAAGTGTAAAAAAAATTAATTCAATTGAGAATGACAGATGT
* * *
30572802 CAACCAATTGACCTAACAGTTATCCTATTTAAAATTGTATTTATTTAAAGAAGATAATAATCCTA
196 CAACCAATTGACCTAACAGTTATCCTATTTAAAATTGTACTTATTCAAAGAAGACAATAATCCTA
* * * * **
30572867 TCAAAAATTGTTAGATGTATAATAAAATGTTAAGAAATGAAAGAGTATATACCTTGTACTATTAG
261 TCAAAAATTATTAAATGTACAATAAAATATTAAGAAATGAAAGAGTATATACCAAGTACTATTAG
* * * * *
30572932 CAGATTAAGATAAACAATTGTATAATATAAGACAACAGTATAATGTAAAGATCCTATCAATGTAA
326 CAGATTAAAATAAACAATTATAGAATATAAAACAACAGTATAATGTAAAGATCCTATCAATATAA
* * * * *
30572997 AATAGTTATTAATTTCTAATAGCGTATGTCTTATATATATAAAATGAATGGTTAAAGGTTATCAA
391 AATAGTTACTAATTTCTAATAGCATATGTCTTATATATATAAAATAAATGGCTAAAGGTTACCAA
** * * * *
30573062 ATTTAGTTGATTTGTTTATTCAATGATGGTTGTGTGCTATGTATATTGAGAAATGAGTAGACCTT
456 ATTTAGTTGATTTGTTTATTCAATGATGACTGTATACTATGTATATAGAGAAATGAGTAAACCTT
* * * *
30573127 CTTAACTTTTTTATTTTGTTCAATAGATTAAATGGATATTAATTTGAATTTAAACATTCATGTAT
521 CTTAACTTTTTTAATTTATGCAATAGATTAAATGGATATTAATTAGAATTTAAACATTCATGTAT
* * * * * *
30573192 AATAGAGATGTCTAAATACTATGAATTCAGGTTCATGCAAAAAAAAAAGATATAGA
586 AAAAGAAATGTCTAAATACTATAAATTAAAGTTCATGCAAAAAAAAAAGATATAAA
* * *
30573248 CAAAAAATAGTATTAAATTATAATTGACAAATATTAAATGAATCTATCCTCTAGGCATTAAAAGT
1 CAAAAAATAATATTAAATTGTAATTGAAAAATATTAAATGAATCTATCCTCTAGGCATTAAAAGT
** * *
30573313 TAGTAATTATTGTTTTCAAATA-TTTTTATTGAAATAAATAAAAGTAAAAAACAAAAAACCCCTT
66 TAAAAATTATTATTTTCAAATATTTTTTACTGAAATAAATAAAAGT----AA-AAAAAA-CCCTT
*
30573377 CAAAAGTAAAAAATAACGCAATTTTGACATAATGTGTAAAAAAAATTAATTCAATTGAGAATGAC
125 CAAAAGTAAAAAATAACGCAATTTTGACATAAAGTGTAAAAAAAATTAATTCAATTGAGAATGAC
* * * *
30573442 AGGTGTCAATCAATTGACCTAACAGTTATCCTATTTAAAATTGTACTTATTCAAATAATACAATA
190 AGATGTCAACCAATTGACCTAACAGTTATCCTATTTAAAATTGTACTTATTCAAAGAAGACAATA
* *
30573507 ATCCTATCAAAGATTATTAAATGTACAATAAAATATTAAGAAATGAAAGAGTATATAGCAAGTAC
255 ATCCTATCAAAAATTATTAAATGTACAATAAAATATTAAGAAATGAAAGAGTATATACCAAGTAC
* *
30573572 TATT-GTCAGATTAAAATAAACAGTTATAGAATATAAAACAATAGTATAATGTAAAGATCCTATC
320 TATTAG-CAGATTAAAATAAACAATTATAGAATATAAAACAACAGTATAATGTAAAGATCCTATC
* * ** * *
30573636 AATATAAAATAGTTACTAATTTTTAGTATTATCTGTCTTTTATATATAAAATAAATGGCTAAAGG
384 AATATAAAATAGTTACTAATTTCTAATAGCATATGTCTTATATATATAAAATAAATGGCTAAAGG
*
30573701 TTACCAAATTTAGTTGATTTGTTTATTCAATGATGACTGTATATTATGTATATAGAGAAATGAGT
449 TTACCAAATTTAGTTGATTTGTTTATTCAATGATGACTGTATACTATGTATATAGAGAAATGAGT
* * * ** ** * *
30573766 AAACTTTTTTTACTTTTTTAATTTATGCAAT-GAATTGGATGGATATTTGTTAGGATTTCAACAT
514 AAACCTTCTTAACTTTTTTAATTTATGCAATAG-ATTAAATGGATATTAATTAGAATTTAAACAT
* * * * *
30573830 TTATGTATAAAAGAAATGTCTAAATACTATAAATTAAAGTTCATGCAGAATAAGAGGATATAAA
578 TCATGTATAAAAGAAATGTCTAAATACTATAAATTAAAGTTCATGCAAAAAAAAAAGATATAAA
* *
30573894 TAAAAAATAATATTAAATTGTAATTGAAAAATATTAAATGAATCTATCCTCTAAGCATTAAAAGT
1 CAAAAAATAATATTAAATTGTAATTGAAAAATATTAAATGAATCTATCCTCTAGGCATTAAAAGT
** * * * *
30573959 TAAAAATTATTATTTTCATGTATTTTTTACAGCAATAAAAAAAAGTGAAAAAAAA-CCTTCAAAC
66 TAAAAATTATTATTTTCAAATATTTTTTACTGAAATAAATAAAAGT-AAAAAAAACCCTTCAAAA
* * * * * *
30574023 GTCAAAAATAACGTAATTTTGACATAAGGTGTACAAAAAAAATTAATTTATTTGAGAATGACAAA
130 GTAAAAAATAACGCAATTTTGACATAAAGTGT--AAAAAAAATTAATTCAATTGAGAATGACAGA
30574088 TGTCAACCAATTGAC
193 TGTCAACCAATTGAC
30574103 TTAATTAATT
Statistics
Matches: 738, Mismatches: 105, Indels: 21
0.85 0.12 0.02
Matches are distributed among these distances:
639 22 0.03
640 79 0.11
641 37 0.05
643 49 0.07
644 8 0.01
645 24 0.03
646 500 0.68
647 19 0.03
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.35
Consensus pattern (641 bp):
CAAAAAATAATATTAAATTGTAATTGAAAAATATTAAATGAATCTATCCTCTAGGCATTAAAAGT
TAAAAATTATTATTTTCAAATATTTTTTACTGAAATAAATAAAAGTAAAAAAAACCCTTCAAAAG
TAAAAAATAACGCAATTTTGACATAAAGTGTAAAAAAAATTAATTCAATTGAGAATGACAGATGT
CAACCAATTGACCTAACAGTTATCCTATTTAAAATTGTACTTATTCAAAGAAGACAATAATCCTA
TCAAAAATTATTAAATGTACAATAAAATATTAAGAAATGAAAGAGTATATACCAAGTACTATTAG
CAGATTAAAATAAACAATTATAGAATATAAAACAACAGTATAATGTAAAGATCCTATCAATATAA
AATAGTTACTAATTTCTAATAGCATATGTCTTATATATATAAAATAAATGGCTAAAGGTTACCAA
ATTTAGTTGATTTGTTTATTCAATGATGACTGTATACTATGTATATAGAGAAATGAGTAAACCTT
CTTAACTTTTTTAATTTATGCAATAGATTAAATGGATATTAATTAGAATTTAAACATTCATGTAT
AAAAGAAATGTCTAAATACTATAAATTAAAGTTCATGCAAAAAAAAAAGATATAAA
Found at i:30576045 original size:50 final size:50
Alignment explanation
Indices: 30575991--30576090 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
30575981 TTAATGAAAG
*
30575991 TTAGTCAACAATTAGTGAAAATAGCTTATTTGATTTAAAATACAAGTTTA
1 TTAGTCAACAATTAGTGAAAATAGCTTATTTAATTTAAAATACAAGTTTA
*
30576041 TTAGTTAACAATTAGTGAAAATAGCTTATTTAATTTAAAATACAAGTTTA
1 TTAGTCAACAATTAGTGAAAATAGCTTATTTAATTTAAAATACAAGTTTA
30576091 AGGAACAGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (50 bp):
TTAGTCAACAATTAGTGAAAATAGCTTATTTAATTTAAAATACAAGTTTA
Found at i:30591064 original size:2 final size:2
Alignment explanation
Indices: 30591044--30591132 Score: 73
Period size: 2 Copynumber: 45.5 Consensus size: 2
30591034 TTATTTATCA
* *
30591044 AT AT TT AT AT TT A- 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
*
30591085 -T GT -T NACT AT AT -T ACT -T AT CA- AT AT AT AT AT AT AT AT AT
1 AT AT AT -A-T AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT
30591124 AT AT AT AT A
1 AT AT AT AT A
30591133 ATGTTCTATT
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
1 6 0.08
2 63 0.86
3 3 0.04
4 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30597825 original size:27 final size:25
Alignment explanation
Indices: 30597782--30597835 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
30597772 TGCATTTGCA
30597782 TCTTTATGTGTCACTGTGTGTATGTGT
1 TCTTTATGTGTCAC--TGTGTATGTGT
*
30597809 TCTTTATTTGTGC-CTGTGTATGTGT
1 TCTTTATGTGT-CACTGTGTATGTGT
30597834 TC
1 TC
30597836 CATCTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 13 0.52
27 11 0.44
28 1 0.04
ACGTcount: A:0.09, C:0.13, G:0.24, T:0.54
Consensus pattern (25 bp):
TCTTTATGTGTCACTGTGTATGTGT
Found at i:30605548 original size:98 final size:98
Alignment explanation
Indices: 30605338--30605549 Score: 259
Period size: 98 Copynumber: 2.2 Consensus size: 98
30605328 TGGATTTTCG
* * *
30605338 ACGGAAATGATTCCGTTGGAAATCCGTTAGAAACAATTTTGGTGCAAAAAAAATTAATCGTGTCA
1 ACGGAAATCATTCTGTTGGAAATCCGTTAGAAACAATTTTGGTGCAAAAAAAATTAATCGCGTCA
* * * *
30605403 AATTTTTCGATGGATTTCCGATGGAAATTTCCA
66 AAATTTCCAATGGATTTCCGATAGAAATTTCCA
* * * *
30605436 ACGG-AATCATTTCTGTTGGAAATCCGTTGGAAATAGTTTTGGTGGAAAAAAAATTAATC-CGTC
1 ACGGAAATCA-TTCTGTTGGAAATCCGTTAGAAACAATTTTGGTGCAAAAAAAATTAATCGCGTC
*
30605499 AAAATTTCCAATGGAACTTT-CGATAGAAATTTCTA
65 AAAATTTCCAATGG-A-TTTCCGATAGAAATTTCCA
*
30605534 ACGGAAATTATTCTGT
1 ACGGAAATCATTCTGT
30605550 CAGAAAGTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
97 18 0.19
98 72 0.74
99 7 0.07
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (98 bp):
ACGGAAATCATTCTGTTGGAAATCCGTTAGAAACAATTTTGGTGCAAAAAAAATTAATCGCGTCA
AAATTTCCAATGGATTTCCGATAGAAATTTCCA
Found at i:30607145 original size:16 final size:15
Alignment explanation
Indices: 30607108--30607148 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
30607098 ATAAATTTAA
*
30607108 AATCAATATTTGTTT
1 AATCAATTTTTGTTT
*
30607123 TATCAATTTTTGTATT
1 AATCAATTTTTGT-TT
30607139 AATCAATTTT
1 AATCAATTTT
30607149 CATGCATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (15 bp):
AATCAATTTTTGTTT
Found at i:30607996 original size:13 final size:13
Alignment explanation
Indices: 30607978--30608016 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
30607968 GTGTTTGTGC
30607978 GTGATTGTGGATT
1 GTGATTGTGGATT
30607991 GTGATTGTGGATT
1 GTGATTGTGGATT
30608004 GTGATTGT-GATT
1 GTGATTGTGGATT
30608016 G
1 G
30608017 CTCTGCTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (13 bp):
GTGATTGTGGATT
Found at i:30607998 original size:6 final size:6
Alignment explanation
Indices: 30607978--30608016 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
30607968 GTGTTTGTGC
30607978 GTGATT GTGGATT GTGATT GTGGATT GTGATT GTGATT G
1 GTGATT GT-GATT GTGATT GT-GATT GTGATT GTGATT G
30608017 CTCTGCTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 19 0.61
7 12 0.39
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (6 bp):
GTGATT
Found at i:30614062 original size:32 final size:33
Alignment explanation
Indices: 30614008--30614074 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
30613998 GATATTTGAG
* *
30614008 TTATTTGTTTTGCTTATTTAAATTTAATTTTTA
1 TTATTTGTTGTGCTTATTTAAATTTAATTATTA
30614041 TTATTTG-TGTGCTT-TTATAAATTTAATTATTA
1 TTATTTGTTGTGCTTATT-TAAATTTAATTATTA
30614073 TT
1 TT
30614075 GAATTATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 2 0.06
32 22 0.71
33 7 0.23
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.64
Consensus pattern (33 bp):
TTATTTGTTGTGCTTATTTAAATTTAATTATTA
Found at i:30614233 original size:36 final size:36
Alignment explanation
Indices: 30614193--30614264 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
30614183 AAGCGGGTTT
*
30614193 GGGTAATTATCGGGTAGTGTGTATGTATTAGAGTTC
1 GGGTAATTATCGAGTAGTGTGTATGTATTAGAGTTC
* *
30614229 GGGTAATTATTGAGTAGTGTGTATGTATTAGGGTTC
1 GGGTAATTATCGAGTAGTGTGTATGTATTAGAGTTC
30614265 AGGTTAGGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.04, G:0.33, T:0.40
Consensus pattern (36 bp):
GGGTAATTATCGAGTAGTGTGTATGTATTAGAGTTC
Found at i:30617612 original size:19 final size:19
Alignment explanation
Indices: 30617584--30617621 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30617574 CCATTTAACT
* *
30617584 TATTGGAGTATGATTTGAG
1 TATTGAAGTATAATTTGAG
30617603 TATTGAAGTATAATTTGAG
1 TATTGAAGTATAATTTGAG
30617622 GGTTTGGCAG
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:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTGAAGTATAATTTGAG
Found at i:30619015 original size:13 final size:13
Alignment explanation
Indices: 30618997--30619021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30618987 AGAGAAATTG
30618997 TGATTTTATAAAA
1 TGATTTTATAAAA
30619010 TGATTTTATAAA
1 TGATTTTATAAA
30619022 TTTTCTAGAA
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:30621419 original size:15 final size:15
Alignment explanation
Indices: 30621395--30621431 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
30621385 GCTAGCTAGG
30621395 GGAAGAAAAGAAGAA
1 GGAAGAAAAGAAGAA
*
30621410 GGAAGGAAAGAAGAA
1 GGAAGAAAAGAAGAA
30621425 -GAAGAAA
1 GGAAGAAA
30621432 TAAAAGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GGAAGAAAAGAAGAA
Found at i:30621425 original size:18 final size:18
Alignment explanation
Indices: 30621402--30621442 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
30621392 AGGGGAAGAA
* *
30621402 AAGAAGAAGGAAGGAAAG
1 AAGAAGAAGAAAGAAAAG
*
30621420 AAGAAGAAGAAATAAAAG
1 AAGAAGAAGAAAGAAAAG
30621438 AAGAA
1 AAGAA
30621443 CTGCCACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (18 bp):
AAGAAGAAGAAAGAAAAG
Found at i:30621583 original size:27 final size:26
Alignment explanation
Indices: 30621545--30621604 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
30621535 GAAGAAAAGA
*
30621545 AAGAAAAAGGAGCAGTTGATTGGGGGG
1 AAGAAAAAGGAGCAGTTGATT-AGGGG
* * *
30621572 AAGAAGAAGGAGCGGTTGGTTAGGGG
1 AAGAAAAAGGAGCAGTTGATTAGGGG
30621598 AAGAAAA
1 AAGAAAA
30621605 GAAGAGAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.40, C:0.03, G:0.43, T:0.13
Consensus pattern (26 bp):
AAGAAAAAGGAGCAGTTGATTAGGGG
Found at i:30621859 original size:16 final size:16
Alignment explanation
Indices: 30621825--30621867 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
30621815 TATATATATA
30621825 TTATAA-TTAAAAATT
1 TTATAAGTTAAAAATT
* *
30621840 TTATAAGTTACAATTT
1 TTATAAGTTAAAAATT
30621856 TTATAATGTTAA
1 TTATAA-GTTAA
30621868 CATGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 6 0.26
16 13 0.57
17 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (16 bp):
TTATAAGTTAAAAATT
Found at i:30621924 original size:21 final size:21
Alignment explanation
Indices: 30621878--30621926 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
30621868 CATGAAATAA
* *
30621878 AAAGTAAATATATTTATATTT
1 AAAGTATATATATATATATTT
30621899 AAAGTATATATATATATA-TT
1 AAAGTATATATATATATATTT
30621919 ACAAGTAT
1 A-AAGTAT
30621927 TTTAGTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
AAAGTATATATATATATATTT
Found at i:30622452 original size:344 final size:347
Alignment explanation
Indices: 30621819--30622464 Score: 962
Period size: 344 Copynumber: 1.9 Consensus size: 347
30621809 AAAGCGTATA
* *
30621819 TATATATTATAATTAAAAATTTTATAAGTTACAATTTTTATAATGTTAACATGAAATAAAAAGTA
1 TATATATTATAATTAAAAATTTTACAAGTTACAATTTTTATAATGTTAACATCAAATAAAAAGTA
* * *
30621884 AATATATTTATATTTAAAGTATATATATATATATTACAAGTATTTTAGTGTATATATAAAATAAT
66 AATATATGTATATTTAAAG-ATATATATACATA-TACAAGTA-TTTAGTATATATATAAAATAAT
* *
30621949 AATTATATTTCTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAGCT
128 AATTATATTTCTTATAAATGAACCCAATATATATAAAGTAAACATATTAAAAAACATTACAAGCT
*
30622014 AATTAATAATCATAGTTTCATGAATTAATTTAATTAATTATATGGGTTTGTCCTTAATTACATCA
193 AATTAATAATCATAGTTTCATGAATTAATTTAATTAATTATATGGATTTGTCCTTAATTACATCA
*
30622079 AATTAAAAAAAATAATTAAGTTTCAAAACTATTCTAATCTCACAACTTCTCTGAAAGTTTGTATA
258 AATTAAAAAAAACAATTAAGTTTCAAAACTATTCTAATCTCACAACTTCTCTGAAAGTTTGTATA
30622144 TTATAAGTTTATATAAACAAATGTG
323 TTATAAGTTTATATAAACAAATGTG
* * * *
30622169 TATATATTATAATTAATAATTTTACAAGTTATAATTTTTGTAATGTTAA-ATTCAAATAGAAAGT
1 TATATATTATAATTAAAAATTTTACAAGTTACAATTTTTATAATGTTAACA-TCAAATAAAAAGT
* * *
30622233 AAATATATGTATATTTAAA-ATATATATACACTA-A-TAGTA-TTAGTATATATATAATATAGTA
65 AAATATATGTATATTTAAAGATATATATACA-TATACAAGTATTTAGTATATATATAAAATAATA
* * * * *
30622294 ATTATCTTTCTTATAAATGAACCCAATATATATAATGTATACATTTTAAAAAACATTACAAGTTA
129 ATTATATTTCTTATAAATGAACCCAATATATATAAAGTAAACATATTAAAAAACATTACAAGCTA
* * *
30622359 ATTAATAATCATAGTTTTATGAATTAATTTAATTAATTATATGGATTTGTCTTTAATTACATGAA
194 ATTAATAATCATAGTTTCATGAATTAATTTAATTAATTATATGGATTTGTCCTTAATTACATCAA
* *
30622424 ATTAAAAAAAACAGTT-AGATTTCAAAACTATTTTAATCTCA
259 ATTAAAAAAAACAATTAAG-TTTCAAAACTATTCTAATCTCA
30622465 AAGACTCTAA
Statistics
Matches: 267, Mismatches: 26, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
343 2 0.01
344 173 0.65
346 4 0.01
347 1 0.00
348 10 0.04
349 3 0.01
350 74 0.28
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (347 bp):
TATATATTATAATTAAAAATTTTACAAGTTACAATTTTTATAATGTTAACATCAAATAAAAAGTA
AATATATGTATATTTAAAGATATATATACATATACAAGTATTTAGTATATATATAAAATAATAAT
TATATTTCTTATAAATGAACCCAATATATATAAAGTAAACATATTAAAAAACATTACAAGCTAAT
TAATAATCATAGTTTCATGAATTAATTTAATTAATTATATGGATTTGTCCTTAATTACATCAAAT
TAAAAAAAACAATTAAGTTTCAAAACTATTCTAATCTCACAACTTCTCTGAAAGTTTGTATATTA
TAAGTTTATATAAACAAATGTG
Found at i:30628487 original size:20 final size:20
Alignment explanation
Indices: 30628459--30628502 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
30628449 TCTAAACTTG
30628459 AAATCATACTCCAATAAGTC
1 AAATCATACTCCAATAAGTC
* *
30628479 AAATTATACTCTAATAAGTC
1 AAATCATACTCCAATAAGTC
30628499 AAAT
1 AAAT
30628503 GGGGTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (20 bp):
AAATCATACTCCAATAAGTC
Found at i:30629849 original size:23 final size:23
Alignment explanation
Indices: 30629823--30629884 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
30629813 ACGTTTGTTG
*
30629823 AAACATAACAGACATATCTGTAA
1 AAACATAACAGACACATCTGTAA
* * * **
30629846 AAACTTTACGGACACATCTGTTG
1 AAACATAACAGACACATCTGTAA
*
30629869 AAACAGAACAGACACA
1 AAACATAACAGACACA
30629885 ACTTTTCAGT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (23 bp):
AAACATAACAGACACATCTGTAA
Found at i:30638687 original size:2 final size:2
Alignment explanation
Indices: 30638680--30638743 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
30638670 TCATGAGTAC
30638680 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30638722 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
30638744 NNNNNNNNNN
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30641770 original size:15 final size:15
Alignment explanation
Indices: 30641737--30641770 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30641727 AAATTATAAA
*
30641737 TTATAAAAAAAACAC
1 TTATAAAAAAAAAAC
*
30641752 TTATAAAAAAAAAAT
1 TTATAAAAAAAAAAC
30641767 TTAT
1 TTAT
30641771 CAAATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
TTATAAAAAAAAAAC
Found at i:30643378 original size:16 final size:17
Alignment explanation
Indices: 30643357--30643388 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30643347 TTGATTTTTG
30643357 ATAGTG-AAATAAAAAC
1 ATAGTGAAAATAAAAAC
30643373 ATAGTGAAAATAAAAA
1 ATAGTGAAAATAAAAA
30643389 TTAACAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.03, G:0.12, T:0.19
Consensus pattern (17 bp):
ATAGTGAAAATAAAAAC
Found at i:30644046 original size:36 final size:36
Alignment explanation
Indices: 30643998--30644084 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
30643988 TAATTGTTTA
*
30643998 ATTTAATCAATTAGGCCCAATGACTTAATTAAAATT
1 ATTTAATTAATTAGGCCCAATGACTTAATTAAAATT
*
30644034 ATTTAATTAATTAGGCTCAATGACTTAATTAAAATT
1 ATTTAATTAATTAGGCCCAATGACTTAATTAAAATT
*
30644070 GTTTAATTAATTAGG
1 ATTTAATTAATTAGG
30644085 TTTTAATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.40
Consensus pattern (36 bp):
ATTTAATTAATTAGGCCCAATGACTTAATTAAAATT
Found at i:30644091 original size:15 final size:15
Alignment explanation
Indices: 30644071--30644099 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30644061 ATTAAAATTG
30644071 TTTAATTAATTAGGT
1 TTTAATTAATTAGGT
30644086 TTTAATTAATTAGG
1 TTTAATTAATTAGG
30644100 CTCAATGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
TTTAATTAATTAGGT
Found at i:30644097 original size:51 final size:51
Alignment explanation
Indices: 30644035--30644135 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
30644025 ATTAAAATTA
* *
30644035 TTTAATTAATTAGGCTCAATGACTTAATTAAA-ATTGTTTAATTAATTAGGT
1 TTTAATTAATTAGGCTCAATGACTTAATTAAACAAT-TTTAATCAATTAGGT
30644086 TTTAATTAATTAGGCTCAATGACTTAATTAAACAATTTTAATCAATTAGG
1 TTTAATTAATTAGGCTCAATGACTTAATTAAACAATTTTAATCAATTAGG
30644136 CCTAATGACT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 45 0.96
52 2 0.04
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.43
Consensus pattern (51 bp):
TTTAATTAATTAGGCTCAATGACTTAATTAAACAATTTTAATCAATTAGGT
Found at i:30644133 original size:36 final size:36
Alignment explanation
Indices: 30644085--30644201 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 36
30644075 ATTAATTAGG
*
30644085 TTTTAATTAATTAGGCTCAATGACTTAATTAAACAA
1 TTTTAATCAATTAGGCTCAATGACTTAATTAAACAA
30644121 TTTTAATCAATTAGGC-CTAATGACTTAATTAAACAA
1 TTTTAATCAATTAGGCTC-AATGACTTAATTAAACAA
* * ** **
30644157 -TTTAATTAATTAAG-TCCAACAACTTACGTAAACAA
1 TTTTAATCAATTAGGCT-CAATGACTTAATTAAACAA
30644192 TTTTAATCAA
1 TTTTAATCAA
30644202 GTACTTGAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
35 27 0.39
36 42 0.61
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.37
Consensus pattern (36 bp):
TTTTAATCAATTAGGCTCAATGACTTAATTAAACAA
Found at i:30644818 original size:19 final size:20
Alignment explanation
Indices: 30644791--30644836 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
30644781 AAGAGACAAG
*
30644791 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
30644810 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
30644829 ATAATATT
1 ATAATATT
30644837 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:30652762 original size:119 final size:119
Alignment explanation
Indices: 30652530--30652754 Score: 396
Period size: 119 Copynumber: 1.9 Consensus size: 119
30652520 TCAAAGACAG
*
30652530 AGCAAGTGATGTGAGACACACTAGACATTGAGGCAAGGCCCACTAGATTTGTAATTTCCTTTCCT
1 AGCAAGTGATGTGAGACACACTAGACATTGAGGAAAGGCCCACTAGATTTGTAATTTCCTTTCCT
* *
30652595 AGTGGCTTGCAGTTGTTGCTGTAGGAGGGTAGTGCCATTTTACCAAAAAACCAA
66 AGCGGCTTGCAGTTGTCGCTGTAGGAGGGTAGTGCCATTTTACCAAAAAACCAA
*
30652649 AGCAAGTGATGTGAGACACATTAGACATTGAGGAAAGGCCCACTAGATTTGTAATTTCCTTTCCT
1 AGCAAGTGATGTGAGACACACTAGACATTGAGGAAAGGCCCACTAGATTTGTAATTTCCTTTCCT
* *
30652714 TGCGGCTTGTAGTTGTCGCTGTAGGAGGGTAGTGCCATTTT
66 AGCGGCTTGCAGTTGTCGCTGTAGGAGGGTAGTGCCATTTT
30652755 GCGAAAAACA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 100 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (119 bp):
AGCAAGTGATGTGAGACACACTAGACATTGAGGAAAGGCCCACTAGATTTGTAATTTCCTTTCCT
AGCGGCTTGCAGTTGTCGCTGTAGGAGGGTAGTGCCATTTTACCAAAAAACCAA
Found at i:30665192 original size:27 final size:27
Alignment explanation
Indices: 30665154--30665294 Score: 144
Period size: 27 Copynumber: 5.3 Consensus size: 27
30665144 GGGACGAGAT
*
30665154 GTTCCCAAGTGCGTAAAGCATAGGGAC
1 GTTCCCAAGTGCGTAATGCATAGGGAC
** *
30665181 GTTCCCAAGTGC-TAACACATA-GGAT
1 GTTCCCAAGTGCGTAATGCATAGGGAC
* * *
30665206 GTT-CTAAGTGTGTAATGCATAGAGAC
1 GTTCCCAAGTGCGTAATGCATAGGGAC
*
30665232 GTTCCCAAGTGCGTAATGTATAGGGAC
1 GTTCCCAAGTGCGTAATGCATAGGGAC
* * * *
30665259 ATTCCCAAGTGTGTAATGCTTAGGTGAT
1 GTTCCCAAGTGCGTAATGCATAGG-GAC
30665287 GTTCCCAA
1 GTTCCCAA
30665295 ATACATAGCA
Statistics
Matches: 91, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
24 6 0.07
25 13 0.14
26 12 0.13
27 51 0.56
28 9 0.10
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (27 bp):
GTTCCCAAGTGCGTAATGCATAGGGAC
Found at i:30668834 original size:47 final size:47
Alignment explanation
Indices: 30668765--30668858 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
30668755 CCTTGAACTA
30668765 TAGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATC
1 TAGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATC
30668812 TAGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATC
1 TAGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATC
30668859 CATAACAAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.32
Consensus pattern (47 bp):
TAGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATC
Found at i:30668866 original size:47 final size:47
Alignment explanation
Indices: 30668766--30668871 Score: 185
Period size: 47 Copynumber: 2.2 Consensus size: 47
30668756 CTTGAACTAT
*
30668766 AGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATCT
1 AGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATCC
30668813 AGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATCC
1 AGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATCC
*
30668860 ATAACAAGCTTG
1 AGAACAA-CTTG
30668872 AGATTCAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (47 bp):
AGAACAACTTGTTGATTTGGGGTGTGAAAATACAAAGTTGTGAATCC
Found at i:30674205 original size:15 final size:15
Alignment explanation
Indices: 30674185--30674223 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
30674175 GTATAATTTG
*
30674185 ATTTTTATGTTTTAT
1 ATTTTTATATTTTAT
*
30674200 ATTTTTATATTTTTT
1 ATTTTTATATTTTAT
*
30674215 ATTATTATA
1 ATTTTTATA
30674224 AACAAACGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
ATTTTTATATTTTAT
Found at i:30674505 original size:2 final size:2
Alignment explanation
Indices: 30674498--30674530 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30674488 AACCATACAA
*
30674498 AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30674531 TTCTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:30675073 original size:15 final size:15
Alignment explanation
Indices: 30675053--30675093 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
30675043 AAGAGAACAA
*
30675053 AAGAAATGTAGGAAG
1 AAGAAATGGAGGAAG
30675068 AAGAAATGGAGGAAG
1 AAGAAATGGAGGAAG
*
30675083 AAGGAATGGAG
1 AAGAAATGGAG
30675094 AGGTGAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.39, T:0.10
Consensus pattern (15 bp):
AAGAAATGGAGGAAG
Found at i:30675284 original size:40 final size:38
Alignment explanation
Indices: 30675211--30675309 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 38
30675201 CTTTTTTTAG
* *
30675211 TTTTTTCATTTTTGATTTTTCCTTTTATTTTTTTCATTCA
1 TTTTTTCATTTTTGA--TTTCCTTTTATTTTTTTAATTAA
30675251 TTTTTTCATCTTTTGATTTCCATTTT-TTATTTTTAATTAA
1 TTTTTTCAT-TTTTGATTTCC-TTTTATT-TTTTTAATTAA
*
30675291 TTTATTTAATTTTTGATTT
1 TTT-TTTCATTTTTGATTT
30675310 ATACTTTTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
39 7 0.13
40 34 0.65
41 11 0.21
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (38 bp):
TTTTTTCATTTTTGATTTCCTTTTATTTTTTTAATTAA
Found at i:30676461 original size:13 final size:13
Alignment explanation
Indices: 30676440--30676489 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
30676430 CCAAAAAAGG
*
30676440 GAGAGGAAAGAAA
1 GAGAAGAAAGAAA
30676453 GAGAAGAAAGAAA
1 GAGAAGAAAGAAA
*
30676466 AAGAAGAAAGAAA
1 GAGAAGAAAGAAA
30676479 G-GAAG-AAGAAA
1 GAGAAGAAAGAAA
30676490 AGGTAGGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 24 0.71
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
GAGAAGAAAGAAA
Found at i:30676585 original size:3 final size:3
Alignment explanation
Indices: 30676574--30676684 Score: 76
Period size: 3 Copynumber: 37.3 Consensus size: 3
30676564 GAAAGAGAGG
* *
30676574 GAA GAAA GAA GAA -AGA GAA -AA GAA GAA GAA GAGA GAA GTA GCAA CGGTA
1 GAA G-AA GAA GAA GA-A GAA GAA GAA GAA GAA GA-A GAA GAA G-AA --GAA
*
30676623 GAA G-A GAA GAA -AGA GAG GAA GAA GAA GAA -AA GAA -AA GAA GAA
1 GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
30676665 GAA GAA -AA GAA -AA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA G
30676685 CTGGCTTTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
2 14 0.16
3 62 0.71
4 9 0.10
5 1 0.01
6 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:30676597 original size:31 final size:30
Alignment explanation
Indices: 30676562--30676661 Score: 78
Period size: 34 Copynumber: 3.2 Consensus size: 30
30676552 TCTCGGGGAG
30676562 AAGAAAGAGAGGGAAGAAAGAAGAAAGAGAA
1 AAGAAAGAGAGGGAAG-AAGAAGAAAGAGAA
* * ** *
30676593 AAGAAGAAGAAGAGAGAAGTAGCAACGGTAGAAGAG
1 AAG-A-AAG-AGAGGGAAGAAG-AA-GAAAG-AGAA
30676629 AAGAAAGAGA-GGAAGAAGAAGAAA-AGAA
1 AAGAAAGAGAGGGAAGAAGAAGAAAGAGAA
30676657 AAGAA
1 AAGAA
30676662 GAAGAAGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
28 8 0.15
30 2 0.04
31 5 0.09
32 7 0.13
33 8 0.15
34 13 0.25
35 4 0.08
36 6 0.11
ACGTcount: A:0.62, C:0.02, G:0.34, T:0.02
Consensus pattern (30 bp):
AAGAAAGAGAGGGAAGAAGAAGAAAGAGAA
Found at i:30676602 original size:20 final size:20
Alignment explanation
Indices: 30676560--30676684 Score: 91
Period size: 19 Copynumber: 6.1 Consensus size: 20
30676550 CATCTCGGGG
**
30676560 AGAAGAAAGAG-AGGGAAGAA
1 AGAAGAAAGAGAAAAGAAG-A
30676580 AGAAGAAAGAGAAAAGAAGA
1 AGAAGAAAGAGAAAAGAAGA
*
30676600 AGAAGAGAGAAGTAGCAACGGTAGAAG-
1 AG-A-AGA-AAG-AG-AA---AAGAAGA
*
30676627 AGAAGAAAGAG--AGGAAGA
1 AGAAGAAAGAGAAAAGAAGA
30676645 AGAAGAAA-AGAAAAGAAGA
1 AGAAGAAAGAGAAAAGAAGA
30676664 AGAAGAAA-AGAAAAGAAGA
1 AGAAGAAAGAGAAAAGAAGA
30676683 AG
1 AG
30676685 CTGGCTTTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 25
0.74 0.05 0.21
Matches are distributed among these distances:
17 6 0.07
18 8 0.09
19 27 0.31
20 14 0.16
21 6 0.07
22 3 0.03
23 5 0.06
24 5 0.06
25 5 0.06
26 1 0.01
27 2 0.02
28 5 0.06
ACGTcount: A:0.63, C:0.02, G:0.34, T:0.02
Consensus pattern (20 bp):
AGAAGAAAGAGAAAAGAAGA
Found at i:30676662 original size:19 final size:19
Alignment explanation
Indices: 30676622--30676684 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
30676612 TAGCAACGGT
*
30676622 AGAAG-AGAAG-AAAGAGA
1 AGAAGAAGAAGAAAAGAAA
*
30676639 GGAAGAAGAAGAAAAGAAA
1 AGAAGAAGAAGAAAAGAAA
30676658 AGAAGAAGAAGAAAAGAAA
1 AGAAGAAGAAGAAAAGAAA
30676677 AGAAGAAG
1 AGAAGAAG
30676685 CTGGCTTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 4 0.10
18 5 0.12
19 32 0.78
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AGAAGAAGAAGAAAAGAAA
Found at i:30676662 original size:31 final size:31
Alignment explanation
Indices: 30676560--30676664 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 31
30676550 CATCTCGGGG
30676560 AGAAGAAAGAGAGGGAAGAAAGAAGAAAGAGAAA
1 AGAAGAAAGAGA-GGAAG-AAGAAGAAA-AGAAA
* ** *
30676594 AGAAG-AAGAAGAGAGAAGTAGCAACG-GTAGAAG
1 AGAAGAAAG-AGAG-GAAGAAG-AA-GAAAAGAAA
30676627 AGAAGAAAGAGAGGAAGAAGAAGAAAAGAAA
1 AGAAGAAAGAGAGGAAGAAGAAGAAAAGAAA
30676658 AGAAGAA
1 AGAAGAA
30676665 GAAGAAAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
30 1 0.02
31 13 0.23
32 6 0.11
33 19 0.33
34 17 0.30
35 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.34, T:0.02
Consensus pattern (31 bp):
AGAAGAAAGAGAGGAAGAAGAAGAAAAGAAA
Found at i:30676668 original size:42 final size:46
Alignment explanation
Indices: 30676574--30676675 Score: 111
Period size: 48 Copynumber: 2.2 Consensus size: 46
30676564 GAAAGAGAGG
* *
30676574 GAAGAA-AGAAGAAAGAGAAAAGAAGAAGAAGAGAGAAGTAGCAAC
1 GAAGAAGAGAAGAAAGAGAGAAGAAGAAGAAGAGAGAAGAAGCAAC
* * *
30676619 GGTAGAAGAGAAGAAAGAGAGGAAGAAGAAGAAAAGAAAAGAAG-AA-
1 -GAAGAAGAGAAGAAAGAGA-GAAGAAGAAGAAGAGAGAAGAAGCAAC
*
30676665 GAAGAAAAGAA
1 GAAGAAGAGAA
30676676 AAGAAGAAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
45 9 0.19
46 5 0.11
47 14 0.30
48 19 0.40
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (46 bp):
GAAGAAGAGAAGAAAGAGAGAAGAAGAAGAAGAGAGAAGAAGCAAC
Found at i:30677631 original size:60 final size:60
Alignment explanation
Indices: 30677413--30677650 Score: 307
Period size: 61 Copynumber: 3.9 Consensus size: 60
30677403 GATTGTAAAG
* * * * *
30677413 GGGGACTTGAAGCCTCGATTTATATTGGGTGGCATGGACAGTTCCCATGAGTAGGTAAAAA
1 GGGGACTTGAAGCCCCGATTTATATT-GGTGACGTGGGCAGTTCCCACGAGTAGGTAAAAA
* *
30677474 GGGGACTTGAAGCCCCGATTTATATTGGTTAGTGTGGGCAGTTCCCACGAGTAGGTAAAAA
1 GGGGACTTGAAGCCCCGATTTATATTGGTGA-CGTGGGCAGTTCCCACGAGTAGGTAAAAA
* * * *
30677535 GGGGACTTGAAGCCCTGATTTAAATTGTGTGGCGTGGGCAGATCCCACGAGTAGGT-AAAA
1 GGGGACTTGAAGCCCCGATTTATATTG-GTGACGTGGGCAGTTCCCACGAGTAGGTAAAAA
* * *
30677595 GGGGACTTGAAGTCTCGATTTATATATGCTGACGTGGGCAGTTCCCACGAGTAGGT
1 GGGGACTTGAAGCCCCGATTTATAT-TGGTGACGTGGGCAGTTCCCACGAGTAGGT
30677651 GATGATGTTT
Statistics
Matches: 154, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
60 53 0.34
61 99 0.64
62 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (60 bp):
GGGGACTTGAAGCCCCGATTTATATTGGTGACGTGGGCAGTTCCCACGAGTAGGTAAAAA
Found at i:30683844 original size:69 final size:70
Alignment explanation
Indices: 30683809--30683973 Score: 221
Period size: 69 Copynumber: 2.4 Consensus size: 70
30683799 GGTGTCTCAG
*
30683809 GGAGAAGAAATAGAGGGAAA-AAAGAAGAAAAAG-AAAGAGAAGAAGAAAGAGAGAAGGAGCAGT
1 GGAGAAGAAAAAGA-GGAAAGAAAGAAGAAAAAGAAAAGAGAAGAAGAAAGAGAGAAGGAGCAGT
30683872 GACAGA
65 GACAGA
* * *
30683878 GGAGAAGAAAAAGAGGAAAGAAAGAAGAAAAAGAAAA-AGAAGAATAAGGAGAGAAGGAGCAGCG
1 GGAGAAGAAAAAGAGGAAAGAAAGAAGAAAAAGAAAAGAGAAGAAGAAAGAGAGAAGGAGCAGTG
*
30683942 ACGGA
66 ACAGA
*
30683947 GGAGAAGAAGGAAAG-GGAAAAAAAGAA
1 GGAGAAGAA--AAAGAGGAAAGAAAGAA
30683974 AATAGCTAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
68 5 0.06
69 63 0.73
70 14 0.16
71 4 0.05
ACGTcount: A:0.60, C:0.03, G:0.35, T:0.02
Consensus pattern (70 bp):
GGAGAAGAAAAAGAGGAAAGAAAGAAGAAAAAGAAAAGAGAAGAAGAAAGAGAGAAGGAGCAGTG
ACAGA
Found at i:30685139 original size:13 final size:13
Alignment explanation
Indices: 30685090--30685140 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 13
30685080 AGCACAAAAT
30685090 AAAATAACTTATTA
1 AAAATAAC-TATTA
30685104 AAAATAAACTAATTA
1 AAAAT-AACT-ATTA
* *
30685119 GAAA-AACTACTA
1 AAAATAACTATTA
30685131 AAAATAACTA
1 AAAATAACTA
30685141 AAAGCTAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.19
13 9 0.29
14 6 0.19
15 10 0.32
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (13 bp):
AAAATAACTATTA
Found at i:30686500 original size:470 final size:469
Alignment explanation
Indices: 30685621--30686562 Score: 1760
Period size: 470 Copynumber: 2.0 Consensus size: 469
30685611 TATCAAAACT
* *
30685621 TAATTTGACCCTAATTTTACAAAACCCATGCATCAAAACACTCCAAAAACTATAAAATCTAGATC
1 TAATTTGACCCTAATTTTACAAAACCCATGCATCAAAACACTCCAAAAACTACAAAATCTAGACC
30685686 AATTGTCAAGAACTAGATTTTATTGGTCCTTATAATATGTGCTAAAAGGGGGTGAATAACACAAT
66 AATTGTCAAGAACTAGATTTTATTGGTCCTTATAATATGTGCTAAAAGGGGGTGAATAACACAAT
* * *
30685751 TTGGCTCTTGACAAGATTATAAAGTAATTTTCAAAACTTAAGAAAACAAAAATAGAGTATAAAAT
131 TTGGCTCTTGACAAGATTAGAAACTAATTTCCAAAACTTAAGAAAACAAAAATAGAGTATAAAAT
30685816 GCACAGCAATTTAAGGTGGTTTAGTCCAAGACCTACATCCATTACCTTGATTATCCAACCAAGGA
196 GCACAGCAATTTAAGGTGGTTTAGTCCAAGACCTACATCCATTACCTTGATTATCCAACCAAGGA
30685881 TTTTCTTACAAACTCACTAACAACCGGTGAAATTCACAAGCTTCCACCAAGCTTTTACAATGACT
261 TTTTCTTACAAACTCACTAACAACCGGTGAAATTCACAAGCTTCCACCAAGCTTTTACAATGACT
30685946 TTTACCAGGCTCAGCCACAACCTTTTACATTAGTTTTACATGGGTTCAACTAAAACCCAAAGAGG
326 TTTACCAGGCTCAGCCACAACCTTTTACATTAGTTTTACATGGGTTCAACTAAAACCCAAAGAGG
*
30686011 TTTTCCAAGGCTCAACCACAAACTTTAACAATCAAGCTATCCTAAACTTGAACAACCTCGTAGAG
391 TTTTCCAAGGCTCAACCACAAACTTTAACAATCAAGCTATCCCAAACTTGAACAACCTCGTAGAG
*
30686076 TGACTCCTTCACTC
456 TGACTCCCTCACTC
30686090 TAATTTGACCCTAATTTTACAAAACCCATGCATCAAAACACTCCAAAAACTACAAAATCTAGACC
1 TAATTTGACCCTAATTTTACAAAACCCATGCATCAAAACACTCCAAAAACTACAAAATCTAGACC
** *
30686155 AATTGTCAAGAACTAGATTTTATTGGTCCTTATAATATGTGCTAGAGGGGGGGTGAATAGCACAA
66 AATTGTCAAGAACTAGATTTTATTGGTCCTTATAATATGTGCTA-AAAGGGGGTGAATAACACAA
*
30686220 TTTGGCTCTTGACAAGATTAGAAACTAATTTCCAGAACTTAAGAAAACAAAAATAGAGTATAAAA
130 TTTGGCTCTTGACAAGATTAGAAACTAATTTCCAAAACTTAAGAAAACAAAAATAGAGTATAAAA
30686285 TGCACAGCAATTT-AGAGTGGTTTAGTCCAAGACCTACATCCATTACCTTGATTATCCAACCAAG
195 TGCACAGCAATTTAAG-GTGGTTTAGTCCAAGACCTACATCCATTACCTTGATTATCCAACCAAG
30686349 GATTTTCTTACAAACTCACTAACAACCGGTGAAATTCACAAGCTTCCACCAAGCTTTTACAATGA
259 GATTTTCTTACAAACTCACTAACAACCGGTGAAATTCACAAGCTTCCACCAAGCTTTTACAATGA
30686414 CTTTTACCAGGCTCAGCCACAACCTTTTACATTAGTTTTACATGGGTTCAACTAAAACCCAAAGA
324 CTTTTACCAGGCTCAGCCACAACCTTTTACATTAGTTTTACATGGGTTCAACTAAAACCCAAAGA
30686479 GGTTTTCCAAGGCTCAACCACAAACTTTAACAATCAAGCTATCCCAAACTTGAACAACCTCGTAG
389 GGTTTTCCAAGGCTCAACCACAAACTTTAACAATCAAGCTATCCCAAACTTGAACAACCTCGTAG
30686544 AGTGACTCCCTCACTC
454 AGTGACTCCCTCACTC
30686560 TAA
1 TAA
30686563 GAATACAAGA
Statistics
Matches: 460, Mismatches: 11, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
469 109 0.24
470 351 0.76
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (469 bp):
TAATTTGACCCTAATTTTACAAAACCCATGCATCAAAACACTCCAAAAACTACAAAATCTAGACC
AATTGTCAAGAACTAGATTTTATTGGTCCTTATAATATGTGCTAAAAGGGGGTGAATAACACAAT
TTGGCTCTTGACAAGATTAGAAACTAATTTCCAAAACTTAAGAAAACAAAAATAGAGTATAAAAT
GCACAGCAATTTAAGGTGGTTTAGTCCAAGACCTACATCCATTACCTTGATTATCCAACCAAGGA
TTTTCTTACAAACTCACTAACAACCGGTGAAATTCACAAGCTTCCACCAAGCTTTTACAATGACT
TTTACCAGGCTCAGCCACAACCTTTTACATTAGTTTTACATGGGTTCAACTAAAACCCAAAGAGG
TTTTCCAAGGCTCAACCACAAACTTTAACAATCAAGCTATCCCAAACTTGAACAACCTCGTAGAG
TGACTCCCTCACTC
Found at i:30687485 original size:61 final size:61
Alignment explanation
Indices: 30687401--30687642 Score: 281
Period size: 61 Copynumber: 4.0 Consensus size: 61
30687391 ATTTGATTGT
* * *
30687401 AAAGGGGGACCTGAATCCCCGATTTATATTGAGTGGCGTGGGCAGTTCTCACGAGTAGGTA
1 AAAGGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGCAGTTCCCACGAGTAGGTA
* * * * *
30687462 AAAGAGGGACCTAAAGCCCCGATTTATATAGGGTGGCGTGGACAGTTCCCACGAGTAAGTA
1 AAAGGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGCAGTTCCCACGAGTAGGTA
** * * * * * * * *
30687523 AAAGGAAGACTTGAAGTCCCGATTTATATTGGGTGACATAGGTAGATCCCACGAATAGGT-
1 AAAGGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGCAGTTCCCACGAGTAGGTA
* *
30687583 AAAGGGGGACTTGAAGCCCCGATTTATATAT-GGTGGCGTGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTTATAT-TGGGTGGCGTGGGCAGTTCCCACGAGTAGGT
30687643 GATGATGTAT
Statistics
Matches: 149, Mismatches: 31, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
60 50 0.34
61 99 0.66
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (61 bp):
AAAGGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGCAGTTCCCACGAGTAGGTA
Found at i:30687618 original size:121 final size:122
Alignment explanation
Indices: 30687418--30687639 Score: 311
Period size: 121 Copynumber: 1.8 Consensus size: 122
30687408 GACCTGAATC
* * * * * *
30687418 CCCGATTTATATTGAGTGGCGTGGGCAGTTCTCACGAGTAGGTAAAAGAGGGACCTAAAGCCCCG
1 CCCGATTTATATTGAGTGACATAGGCAGATCCCACGAATAGGTAAAAGAGGGACCTAAAGCCCCG
30687483 ATTTATATAGGGTGGCGTGGACAGTTCCCACGAGTAAGTAAAAGGAAGACTTGAAGT
66 ATTTATATAGGGTGGCGTGGACAGTTCCCACGAGTAAGTAAAAGGAAGACTTGAAGT
* * * * *
30687540 CCCGATTTATATTGGGTGACATAGGTAGATCCCACGAATAGGT-AAAGGGGGACTTGAAGCCCCG
1 CCCGATTTATATTGAGTGACATAGGCAGATCCCACGAATAGGTAAAAGAGGGACCTAAAGCCCCG
* **
30687604 ATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTA
66 ATTTATATAGGGTGGCGTGGACAGTTCCCACGAGTA
30687640 GGTGATGATG
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
121 51 0.59
122 35 0.41
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (122 bp):
CCCGATTTATATTGAGTGACATAGGCAGATCCCACGAATAGGTAAAAGAGGGACCTAAAGCCCCG
ATTTATATAGGGTGGCGTGGACAGTTCCCACGAGTAAGTAAAAGGAAGACTTGAAGT
Found at i:30692247 original size:18 final size:18
Alignment explanation
Indices: 30692197--30692250 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
30692187 ACACCATCAG
30692197 GGTCTATATCTTGCCATCTA
1 GGTCTATATC--GCCATCTA
* ** *
30692217 GCTCTCCAACGCCATCTA
1 GGTCTATATCGCCATCTA
30692235 GGTCTATATCGCCATC
1 GGTCTATATCGCCATC
30692251 CAATTTTCTC
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
18 20 0.77
20 6 0.23
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.31
Consensus pattern (18 bp):
GGTCTATATCGCCATCTA
Found at i:30692629 original size:22 final size:23
Alignment explanation
Indices: 30692604--30692673 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
30692594 TGAGTTGTGC
30692604 ATTGCATGA-TGAGGTTTTAGGA
1 ATTGCATGACTGAGGTTTTAGGA
* *
30692626 ATTGCTTGACT-A-GTTTGTAGGT
1 ATTGCATGACTGAGGTTT-TAGGA
* *
30692648 ATTGCATGACTG-GTTTTTAGTA
1 ATTGCATGACTGAGGTTTTAGGA
30692670 ATTG
1 ATTG
30692674 TGTTGTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
21 4 0.11
22 30 0.79
23 4 0.11
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (23 bp):
ATTGCATGACTGAGGTTTTAGGA
Found at i:30693496 original size:22 final size:22
Alignment explanation
Indices: 30693463--30693519 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 22
30693453 ATATTATTTT
30693463 ATATATAGGCATTA-AGTGAATGG
1 ATAT-TAGGCATTATA-TGAATGG
*
30693486 ATATTATGCATTATATGAATGG
1 ATATTAGGCATTATATGAATGG
30693508 ATATTAGGCATT
1 ATATTAGGCATT
30693520 GCATGTCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (22 bp):
ATATTAGGCATTATATGAATGG
Found at i:30693757 original size:22 final size:22
Alignment explanation
Indices: 30693732--30693781 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
30693722 TTAGGCATTG
* *
30693732 TGTGACTGGTTGTTATGTATTC
1 TGTGACTGGTAGTGATGTATTC
* *
30693754 TGTGACTTGTAGTGATGTATTG
1 TGTGACTGGTAGTGATGTATTC
30693776 TGTGAC
1 TGTGAC
30693782 GTTGGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.16, C:0.08, G:0.30, T:0.46
Consensus pattern (22 bp):
TGTGACTGGTAGTGATGTATTC
Found at i:30697654 original size:22 final size:22
Alignment explanation
Indices: 30697626--30697694 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
30697616 ATGAGTAACG
30697626 TGCTTAATATGGGGTCACACAA
1 TGCTTAATATGGGGTCACACAA
* * *
30697648 TGCTTAATAAGGGGTCTCAAAA
1 TGCTTAATATGGGGTCACACAA
* * * *
30697670 TGCCTAAAATTGGGTCACTCAA
1 TGCTTAATATGGGGTCACACAA
30697692 TGC
1 TGC
30697695 ATAAACAACG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCTTAATATGGGGTCACACAA
Found at i:30699741 original size:2 final size:2
Alignment explanation
Indices: 30699734--30699780 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
30699724 ACCGAGGTAC
30699734 AT AT AT 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
30699776 AT AT A
1 AT AT A
30699781 GATTTCTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30702634 original size:45 final size:46
Alignment explanation
Indices: 30702550--30702716 Score: 205
Period size: 46 Copynumber: 3.7 Consensus size: 46
30702540 TTGAAGCCAT
* * * *
30702550 GCAATACCATATCAAATAGTTACAC-ACTTCCATATCAAATAGTCAC
1 GCAATTCCATATCAACTAGTCACGCGA-TTCCATATCAAATAGTCAC
*
30702596 GCAATTCCATA-CAACTAGTC-CTGCGATTTCATATCAAATAGTCAC
1 GCAATTCCATATCAACTAGTCAC-GCGATTCCATATCAAATAGTCAC
* *
30702641 GCAATTCCATATCAACTAGTCACGCTATTCCATATCAAATAATCAC
1 GCAATTCCATATCAACTAGTCACGCGATTCCATATCAAATAGTCAC
* * *
30702687 GCGATTCCATATCAACAAGTCACGTGATTC
1 GCAATTCCATATCAACTAGTCACGCGATTC
30702717 ATACACACCC
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
44 1 0.01
45 37 0.35
46 66 0.63
47 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.10, T:0.28
Consensus pattern (46 bp):
GCAATTCCATATCAACTAGTCACGCGATTCCATATCAAATAGTCAC
Found at i:30702634 original size:68 final size:69
Alignment explanation
Indices: 30702556--30702709 Score: 197
Period size: 68 Copynumber: 2.2 Consensus size: 69
30702546 CCATGCAATA
* * * *
30702556 CCATATCAAATAGTTACACACTTCCATATCAAATAGTCACGCAATTCCATA-CAACTAGTC-CTG
1 CCATATCAAATAGTCACACAATTCCATATCAAATAGTCACGCAATTCCATATCAAATAATCAC-G
30702619 CGATT
65 CGATT
* * * *
30702624 TCATATCAAATAGTCACGCAATTCCATATCAACTAGTCACGCTATTCCATATCAAATAATCACGC
1 CCATATCAAATAGTCACACAATTCCATATCAAATAGTCACGCAATTCCATATCAAATAATCACGC
30702689 GATT
66 GATT
30702693 CCATATCAACA-AGTCAC
1 CCATATCAA-ATAGTCAC
30702710 GTGATTCATA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
68 45 0.61
69 27 0.36
70 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.27
Consensus pattern (69 bp):
CCATATCAAATAGTCACACAATTCCATATCAAATAGTCACGCAATTCCATATCAAATAATCACGC
GATT
Found at i:30702715 original size:23 final size:23
Alignment explanation
Indices: 30702556--30702716 Score: 177
Period size: 23 Copynumber: 7.0 Consensus size: 23
30702546 CCATGCAATA
* *
30702556 CCATATCAAATAGTTACAC-ACTT
1 CCATATCAAATAGTCACGCGA-TT
*
30702579 CCATATCAAATAGTCACGCAATT
1 CCATATCAAATAGTCACGCGATT
*
30702602 CCATA-CAACTAGTC-CTGCGATT
1 CCATATCAAATAGTCAC-GCGATT
* *
30702624 TCATATCAAATAGTCACGCAATT
1 CCATATCAAATAGTCACGCGATT
* *
30702647 CCATATCAACTAGTCACGCTATT
1 CCATATCAAATAGTCACGCGATT
*
30702670 CCATATCAAATAATCACGCGATT
1 CCATATCAAATAGTCACGCGATT
*
30702693 CCATATCAACA-AGTCACGTGATT
1 CCATATCAA-ATAGTCACGCGATT
30702716 C
1 C
30702717 ATACACACCC
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.01
22 17 0.14
23 97 0.82
24 3 0.03
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.28
Consensus pattern (23 bp):
CCATATCAAATAGTCACGCGATT
Found at i:30705111 original size:27 final size:27
Alignment explanation
Indices: 30705081--30705190 Score: 114
Period size: 27 Copynumber: 4.1 Consensus size: 27
30705071 TGAGAAACAA
* *
30705081 GAGAAGTAACATCGAA-AGCAGCATGAG
1 GAGAAGCAACATC-AAGAGCACCATGAG
*
30705108 GAGAAGCAACATCAAGAGTACCATGAG
1 GAGAAGCAACATCAAGAGCACCATGAG
* * * *
30705135 GAGAAACAGCATCAAGAGTACCATGAA
1 GAGAAGCAACATCAAGAGCACCATGAG
* * *
30705162 GAGAAACAGCATCAAGAGCAACATGAG
1 GAGAAGCAACATCAAGAGCACCATGAG
30705189 GA
1 GA
30705191 ATAGTAGATG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
26 2 0.03
27 71 0.97
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (27 bp):
GAGAAGCAACATCAAGAGCACCATGAG
Found at i:30706952 original size:23 final size:23
Alignment explanation
Indices: 30706926--30706975 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
30706916 TGAACCTTAT
30706926 TCACCTAATGACCTATCAACCAC
1 TCACCTAATGACCTATCAACCAC
* * *
30706949 TCACGTAATGACTTATCAACCAG
1 TCACCTAATGACCTATCAACCAC
30706972 TCAC
1 TCAC
30706976 ACAATGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.08, T:0.24
Consensus pattern (23 bp):
TCACCTAATGACCTATCAACCAC
Found at i:30706981 original size:23 final size:23
Alignment explanation
Indices: 30706932--30706981 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
30706922 TTATTCACCT
**
30706932 AATGACCTATCAACCACTCACGT
1 AATGACCTATCAACCACTCACAC
* *
30706955 AATGACTTATCAACCAGTCACAC
1 AATGACCTATCAACCACTCACAC
30706978 AATG
1 AATG
30706982 TTAAAACCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.22
Consensus pattern (23 bp):
AATGACCTATCAACCACTCACAC
Found at i:30709528 original size:26 final size:26
Alignment explanation
Indices: 30709488--30709630 Score: 72
Period size: 26 Copynumber: 5.6 Consensus size: 26
30709478 TTAAAGGAAA
*
30709488 AAAAATTAAAATAAAATATATAATAT
1 AAAAATTATAATAAAATATATAATAT
* *
30709514 AAAAATTATATTAAAA-ATA-AAAAT
1 AAAAATTATAATAAAATATATAATAT
*
30709538 -AAAA--AT-ATAAGAT-TATAATA-
1 AAAAATTATAATAAAATATATAATAT
* *
30709558 AAAAATAAAAATAAAATATATGACAT-T
1 AAAAATTATAATAAAATATAT-A-ATAT
* *
30709585 AAAAATATATTTAA-AAGATGATATTATAT
1 AAAAAT-TA--TAATAAAAT-ATATAATAT
*
30709614 AAAAATTAACAATAAAA
1 AAAAATT-ATAATAAAA
30709631 AATACAAGTA
Statistics
Matches: 86, Mismatches: 14, Indels: 32
0.65 0.11 0.24
Matches are distributed among these distances:
20 6 0.07
21 9 0.10
23 5 0.06
24 10 0.12
25 6 0.07
26 15 0.17
27 10 0.12
28 7 0.08
29 12 0.14
30 6 0.07
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (26 bp):
AAAAATTATAATAAAATATATAATAT
Found at i:30709533 original size:32 final size:32
Alignment explanation
Indices: 30709495--30709578 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 32
30709485 AAAAAAAATT
*
30709495 AAAATAAAATATATAATATA-AAAATTAT-ATTA
1 AAAATAAAA-ATA-AATATATAAAATTATAATAA
* *
30709527 AAAATAAAAATAAAAATATAAGATTATAATAA
1 AAAATAAAAATAAATATATAAAATTATAATAA
30709559 AAAATAAAAATAAAATATAT
1 AAAATAAAAAT-AAATATAT
30709579 GACATTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
30 5 0.11
31 10 0.22
32 23 0.51
33 7 0.16
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (32 bp):
AAAATAAAAATAAATATATAAAATTATAATAA
Found at i:30709541 original size:5 final size:6
Alignment explanation
Indices: 30709488--30709573 Score: 64
Period size: 6 Copynumber: 13.7 Consensus size: 6
30709478 TTAAAGGAAA
* * * * *
30709488 AAAAAT TAAAAT AAAATAT ATAATAT AAAAAT TATATT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * *
30709538 AAAAAT ATAAGAT TATAAT AAAAAAT AAAAAT AAAA
1 AAAAAT A-AAAAT AAAAAT -AAAAAT AAAAAT AAAA
30709574 TATATGACAT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
6 44 0.73
7 14 0.23
8 2 0.03
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (6 bp):
AAAAAT
Found at i:30709812 original size:15 final size:15
Alignment explanation
Indices: 30709792--30709852 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 15
30709782 TGTTATTTTC
*
30709792 CTTATAATCACATTG
1 CTTATAATCACATTA
* *
30709807 CTTATAATTATATTA
1 CTTATAATCACATTA
* * *
30709822 CTTGTAATTATATTA
1 CTTATAATCACATTA
30709837 CTTATAATCACATTA
1 CTTATAATCACATTA
30709852 C
1 C
30709853 ATTGTAAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (15 bp):
CTTATAATCACATTA
Found at i:30710259 original size:17 final size:16
Alignment explanation
Indices: 30710227--30710260 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
30710217 GGTTGAATTG
*
30710227 AAATTTAAAATTAAAA
1 AAATTTAAAATAAAAA
30710243 AAATTTGAAAATAAAAA
1 AAATTT-AAAATAAAAA
30710260 A
1 A
30710261 GATTGACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATTTAAAATAAAAA
Found at i:30710266 original size:16 final size:17
Alignment explanation
Indices: 30710227--30710260 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
30710217 GGTTGAATTG
30710227 AAATTT-AAAATTAAAA
1 AAATTTGAAAATTAAAA
30710243 AAATTTGAAAA-TAAAA
1 AAATTTGAAAATTAAAA
30710259 AA
1 AA
30710261 GATTGACCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATTTGAAAATTAAAA
Found at i:30719941 original size:32 final size:32
Alignment explanation
Indices: 30719888--30719948 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
30719878 GCATGGCTTA
* *
30719888 TGTTTAGACCTGTATATTTTCGAATAAGAGAG
1 TGTTTAGACCTGTACACTTTCGAATAAGAGAG
* *
30719920 TGTTTAGACTTGTACACTTTCGGATAAGA
1 TGTTTAGACCTGTACACTTTCGAATAAGA
30719949 TGAAAAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (32 bp):
TGTTTAGACCTGTACACTTTCGAATAAGAGAG
Found at i:30721073 original size:28 final size:29
Alignment explanation
Indices: 30721032--30721091 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
30721022 GTCTATGGGC
* *
30721032 AATTTTTTAGTTTT-TGGGGCAAAAATGT
1 AATTTTTGAGTTTTAAGGGGCAAAAATGT
* *
30721060 AATTTTTGATTTTTACAGGGGCAAAAGTGT
1 AATTTTTGAGTTTTA-AGGGGCAAAAATGT
30721090 AA
1 AA
30721092 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:0.05, G:0.22, T:0.42
Consensus pattern (29 bp):
AATTTTTGAGTTTTAAGGGGCAAAAATGT
Found at i:30722246 original size:13 final size:13
Alignment explanation
Indices: 30722228--30722252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30722218 AGAGAAATTG
30722228 TGATTTTATAAAA
1 TGATTTTATAAAA
30722241 TGATTTTATAAA
1 TGATTTTATAAA
30722253 TTTTCTGAAA
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:30723495 original size:15 final size:15
Alignment explanation
Indices: 30723451--30723496 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
30723441 AGATCAGAGA
* *
30723451 TTTTGATTTGAAAGC
1 TTTTGATTTTAAAGT
*
30723466 TTTGGATTTTAAAGT
1 TTTTGATTTTAAAGT
30723481 TTTTGATTTTAAAGT
1 TTTTGATTTTAAAGT
30723496 T
1 T
30723497 GTTTTAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.54
Consensus pattern (15 bp):
TTTTGATTTTAAAGT
Found at i:30723541 original size:5 final size:5
Alignment explanation
Indices: 30723531--30723563 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
30723521 TACGTGGCCC
30723531 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTT AAGT
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGT
30723564 CAGGCTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:30723556 original size:14 final size:15
Alignment explanation
Indices: 30723531--30723563 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
30723521 TACGTGGCCC
30723531 AAGTTAAGTTAAGTT
1 AAGTTAAGTTAAGTT
30723546 AAGTT-AGTTAAGTT
1 AAGTTAAGTTAAGTT
30723560 AAGT
1 AAGT
30723564 CAGGCTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (15 bp):
AAGTTAAGTTAAGTT
Done.