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 76 of 106
Found at i:28997203 original size:67 final size:67
Alignment explanation
Indices: 28997129--28997267 Score: 210
Period size: 67 Copynumber: 2.1 Consensus size: 67
28997119 TGATTATTGT
* *
28997129 AGGTTGTGGTTGAGCCTT-TGAAAAATCACTTTGGGTTTTGGTTGAGCCC-GTGAAAAACCATTG
1 AGGTTGTGGTTGAG-CTTGTGAAAAACCACTTTGGATTTTGGTTGAGCCCGGT-AAAAACCATTG
28997192 TGAA
64 TGAA
* *
28997196 AGGTTGTGGTTGAGCTTGTGAAAAACCACTTTGGATTTTGGTTGATCCTGGTAAAAACCATTGTG
1 AGGTTGTGGTTGAGCTTGTGAAAAACCACTTTGGATTTTGGTTGAGCCCGGTAAAAACCATTGTG
28997261 AA
66 AA
28997263 AGGTT
1 AGGTT
28997268 TTGGCTAGGC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
66 3 0.05
67 61 0.92
68 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (67 bp):
AGGTTGTGGTTGAGCTTGTGAAAAACCACTTTGGATTTTGGTTGAGCCCGGTAAAAACCATTGTG
AA
Found at i:28997208 original size:35 final size:33
Alignment explanation
Indices: 28997129--28997255 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 33
28997119 TGATTATTGT
* *
28997129 AGGTTGTGGTTGAGCCTTTGAAAAATCACTTTG
1 AGGTTGTGGTTGAGCCTGTGAAAAACCACTTTG
* *
28997162 -GGTTTTGGTTGAGCCCGTGAAAAACCA-TTGTG
1 AGGTTGTGGTTGAGCCTGTGAAAAACCACTT-TG
*
28997194 AAAGGTTGTGGTTGAGCTTGTGAAAAACCACTTTG
1 --AGGTTGTGGTTGAGCCTGTGAAAAACCACTTTG
* * *
28997229 -GATTTTGGTTGATCCTG-GTAAAAACCA
1 AGGTTGTGGTTGAGCCTGTG-AAAAACCA
28997256 TTGTGAAAGG
Statistics
Matches: 77, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
31 3 0.04
32 46 0.60
35 26 0.34
36 2 0.03
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (33 bp):
AGGTTGTGGTTGAGCCTGTGAAAAACCACTTTG
Found at i:29002650 original size:16 final size:16
Alignment explanation
Indices: 29002629--29002659 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29002619 CTAAAATTTA
*
29002629 GATTTTAATTCTTTTG
1 GATTTTAATTATTTTG
29002645 GATTTTAATTATTTT
1 GATTTTAATTATTTT
29002660 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (16 bp):
GATTTTAATTATTTTG
Found at i:29002887 original size:21 final size:21
Alignment explanation
Indices: 29002863--29002935 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
29002853 TTTTCATAAA
29002863 CAAATGTATCAATACATGGCC
1 CAAATGTATCAATACATGGCC
* *
29002884 CAAATATATCAAAACATGGCC
1 CAAATGTATCAATACATGGCC
* *
29002905 CAAATGTATCAATACATAGCT
1 CAAATGTATCAATACATGGCC
29002926 CAAATGTATC
1 CAAATGTATC
29002936 GACACACTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (21 bp):
CAAATGTATCAATACATGGCC
Found at i:29005463 original size:316 final size:319
Alignment explanation
Indices: 29004831--29005464 Score: 963
Period size: 320 Copynumber: 2.0 Consensus size: 319
29004821 AAGAATGCTG
* * * * *
29004831 TTTTGAGACCTTATTTTTTTGAAGGAAATAAAAGGTGAATATTTAAACCATATTATAGGTTAAGG
1 TTTTGAGACCTTATTATCTTGAAGGAAATAAAAGGTGAATATTCAAACCACATTAAAGGTTAAGG
* *
29004896 ATGACAAAGCTAAGGACTTAGGGCTTTAGGGTAGGAGTTTTTTGTTTTTTTAACAAGAGTCTTTT
66 ATGACAAAGCTAAGGACTTAAGGCTTTAGGGTAGGAGGTTTTTGTTTTTTTAACAAGAG-CTTTT
* ** *
29004961 TTGTGAGTGTGATGAAAATTGTCTTATGCCTTTCAAAGTCGTAAGACAATTTTCCAAGTTAGCGG
130 TTGTGAGTGTGATGAAAATTGTCTTATACCCCTCAAAGTCGTAAGACAATTTTCCAAGTTAACGG
** * * *
29005026 GTCTTTTACCTATTAATGCGTAAAACTTTTACTCTTAGAATTTCATTTTCAGTCATCCAAATACC
195 GTCTTTTACCTATTAACACATAAAACTTTTACTCTTAGAATTTCATTTTCAGCCATCCAAACACC
*
29005091 ATTATGTCGTGAAAATGTTTTCTCAAAAAACTTTTACTTCCAAACAAACACACCCTTTCT
260 ATTATGTCGTGAAAATGTATTCTCAAAAAACTTTTACTTCCAAACAAACACACCCTTTCT
* *
29005151 TTTTGAGACCTTATTATCTTGAAGGAAATAAAAGGTGAATGTTCAAACCACATTAAAGGTTAGGG
1 TTTTGAGACCTTATTATCTTGAAGGAAATAAAAGGTGAATATTCAAACCACATTAAAGGTTAAGG
* *
29005216 ATGACAGAGCTAAGGACTTAAGGCTTTAGGGTAGGAGGTTTTTGTTTTTTTAACAGGAG-TTTTT
66 ATGACAAAGCTAAGGACTTAAGGCTTTAGGGTAGGAGGTTTTTGTTTTTTTAACAAGAGCTTTTT
*
29005280 T-TGAGTGTGATGAAAATTGTCTTA-ACCCCTCAAAGTCTTAAGACAA-TTTCCATAGTTAACGG
131 TGTGAGTGTGATGAAAATTGTCTTATACCCCTCAAAGTCGTAAGACAATTTTCCA-AGTTAACGG
* * *
29005342 GTCTTTTACGTGTTAACACATAAAACTTTTACTCTTAGAATTTCATTTTTCAGCCATCTAAACAC
195 GTCTTTTACCTATTAACACATAAAACTTTTACTCTTAGAATTTCA-TTTTCAGCCATCCAAACAC
* *
29005407 CATTATGTCGTGAAAATGTATTCT-AAAAAACTTTTACTTTCAAACAAACGCACCCTTT
259 CATTATGTCGTGAAAATGTATTCTCAAAAAACTTTTACTTCCAAACAAACACACCCTTT
29005465 GATATCTTAA
Statistics
Matches: 285, Mismatches: 27, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
315 6 0.02
316 98 0.34
317 62 0.22
318 6 0.02
320 113 0.40
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (319 bp):
TTTTGAGACCTTATTATCTTGAAGGAAATAAAAGGTGAATATTCAAACCACATTAAAGGTTAAGG
ATGACAAAGCTAAGGACTTAAGGCTTTAGGGTAGGAGGTTTTTGTTTTTTTAACAAGAGCTTTTT
TGTGAGTGTGATGAAAATTGTCTTATACCCCTCAAAGTCGTAAGACAATTTTCCAAGTTAACGGG
TCTTTTACCTATTAACACATAAAACTTTTACTCTTAGAATTTCATTTTCAGCCATCCAAACACCA
TTATGTCGTGAAAATGTATTCTCAAAAAACTTTTACTTCCAAACAAACACACCCTTTCT
Found at i:29010683 original size:21 final size:21
Alignment explanation
Indices: 29010658--29010708 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
29010648 GATAGGTGGA
*
29010658 GAAGACTCGTGTTTATATACT
1 GAAGACTCATGTTTATATACT
* *
29010679 GAAGATTCATGTTTATATATT
1 GAAGACTCATGTTTATATACT
*
29010700 TAAGACTCA
1 GAAGACTCA
29010709 CTCCATCTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (21 bp):
GAAGACTCATGTTTATATACT
Found at i:29012850 original size:18 final size:17
Alignment explanation
Indices: 29012823--29012859 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
29012813 ATTTGATAAA
*
29012823 TTGTTGAAAATGTTCAAT
1 TTGTTAAAAATGTT-AAT
29012841 TTGTTAAAAATGTTAAT
1 TTGTTAAAAATGTTAAT
29012858 TT
1 TT
29012860 TAGTGATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.49
Consensus pattern (17 bp):
TTGTTAAAAATGTTAAT
Found at i:29016803 original size:24 final size:24
Alignment explanation
Indices: 29016776--29016829 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
29016766 ATGTTCTTGG
29016776 TCAATGTATCATTCAGATTGGACA
1 TCAATGTATCATTCAGATTGGACA
29016800 TCAATGTATCATTCAGATTGGACA
1 TCAATGTATCATTCAGATTGGACA
29016824 TCAATG
1 TCAATG
29016830 ATGCTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (24 bp):
TCAATGTATCATTCAGATTGGACA
Found at i:29017847 original size:70 final size:68
Alignment explanation
Indices: 29017718--29017932 Score: 202
Period size: 71 Copynumber: 3.1 Consensus size: 68
29017708 TAAGCACTTG
**
29017718 ATTAAAATTGTTTAATTAAGTTATGCCTAATTAATTAAATTGTTTAATTATTTCATTGGG-CTTA
1 ATTAAAATTGTTTAATTAAGTTATGCCTAATTAATTAAATTGTTTAATTAAGTCATTGGGTC-TA
29017782 A-TA
65 ATTA
* * *
29017785 ATT-AAATTGTTTAATTAAGTCATTTAGCCTAGTTAATTAAAATTGTTTGATTAAGTCATTGGGT
1 ATTAAAATTGTTTAATTAAGT--TAT-GCCTAATTAATT-AAATTGTTTAATTAAGTCATTGGGT
*
29017849 CTAATTG
62 CTAATTA
** ** * * * *
29017856 ATTAAAATTGTTTAATTAAATTGTTGGGTTTAATTAATTAAATTATTTAATTAAGTTATTAGGCC
1 ATTAAAATTGTTTAATT-AA--GTTATGCCTAATTAATTAAATTGTTTAATTAAGTCATTGGGTC
*
29017921 TAATTG
63 TAATTA
29017927 ATTAAA
1 ATTAAA
29017933 TTAAATAATT
Statistics
Matches: 122, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
66 17 0.14
67 3 0.02
68 2 0.02
69 11 0.09
70 24 0.20
71 38 0.31
72 22 0.18
73 3 0.02
75 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.47
Consensus pattern (68 bp):
ATTAAAATTGTTTAATTAAGTTATGCCTAATTAATTAAATTGTTTAATTAAGTCATTGGGTCTAA
TTA
Found at i:29017935 original size:35 final size:35
Alignment explanation
Indices: 29017722--29017934 Score: 211
Period size: 36 Copynumber: 6.1 Consensus size: 35
29017712 CACTTGATTA
29017722 AAATTGTTTAATTAAGTTA-T--GCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* *
29017754 AAATTGTTTAATT-ATTTCATTGGGCTTAA-TAATT
1 AAATTGTTTAATTAAGTT-ATTGGGCCTAATTAATT
* ** *
29017788 AAATTGTTTAATTAAGTCATTTAGCCTAGTTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
29017823 AAAATTGTTTGATTAAGTCATTGGGTCTAATTGATT
1 -AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * **
29017859 AAAATTGTTTAATTAAATTGTTGGGTTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
29017895 AAATTATTTAATTAAGTTATTAGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
29017930 AAATT
1 AAATT
29017935 AAATAATTAA
Statistics
Matches: 147, Mismatches: 27, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
31 3 0.02
32 14 0.10
33 1 0.01
34 25 0.17
35 45 0.31
36 59 0.40
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:29020914 original size:10 final size:10
Alignment explanation
Indices: 29020893--29020935 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
29020883 CATTACAACC
29020893 ATATACCATAT
1 ATATA-CATAT
*
29020904 ATGTACATAT
1 ATATACATAT
*
29020914 ATATATATAT
1 ATATACATAT
*
29020924 ATATATATAT
1 ATATACATAT
29020934 AT
1 AT
29020936 CAATAATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 25 0.86
11 4 0.14
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (10 bp):
ATATACATAT
Found at i:29020915 original size:2 final size:2
Alignment explanation
Indices: 29020900--29020935 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
29020890 ACCATATACC
* *
29020900 AT AT AT GT AC 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
29020936 CAATAATCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29026097 original size:23 final size:23
Alignment explanation
Indices: 29026063--29026122 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
29026053 TGAGCTGGTG
* *
29026063 ATGATGATGATGGGATGGTGTGC
1 ATGATGATGATGGGATGGTATGA
*
29026086 ATGATGACGATGGGATGGTATGA
1 ATGATGATGATGGGATGGTATGA
*
29026109 ATAATGATGATGGG
1 ATGATGATGATGGG
29026123 TATATACGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.03, G:0.40, T:0.28
Consensus pattern (23 bp):
ATGATGATGATGGGATGGTATGA
Found at i:29030687 original size:2 final size:2
Alignment explanation
Indices: 29030680--29030713 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29030670 ACTTACTCCC
29030680 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
29030714 TCACAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29030811 original size:2 final size:2
Alignment explanation
Indices: 29030804--29030836 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29030794 TACTTACTAC
29030804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29030837 TCACAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29030847 original size:123 final size:122
Alignment explanation
Indices: 29030681--29030915 Score: 461
Period size: 123 Copynumber: 1.9 Consensus size: 122
29030671 CTTACTCCCA
29030681 TATATATATATATATATATATATATATATATATTCACAAATATGACGTCAAACTTTGATCAAAAC
1 TATATATATATATATATATATATATATATATATTCACAAATATGACGTCAAACTTTGATCAAAAC
29030746 TTCAAATTATGGGATTTATCACATATTTCATCAAAATTTTCCTAAGNTTACTTACTAC
66 TTCAAATTATGGGATTTATCACATATTTCATCAAAATTTTCCTAAG-TTACTTACTAC
29030804 TATATATATATATATATATATATATATATATATTCACAAATATGACGTCAAACTTTGATCAAAAC
1 TATATATATATATATATATATATATATATATATTCACAAATATGACGTCAAACTTTGATCAAAAC
29030869 TTCAAATTATGGGATTTATCACATATTTCATCAAAATTTTCCTAAGT
66 TTCAAATTATGGGATTTATCACATATTTCATCAAAATTTTCCTAAGT
29030916 GTCAATATGT
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 1 0.01
123 111 0.99
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (122 bp):
TATATATATATATATATATATATATATATATATTCACAAATATGACGTCAAACTTTGATCAAAAC
TTCAAATTATGGGATTTATCACATATTTCATCAAAATTTTCCTAAGTTACTTACTAC
Found at i:29033197 original size:42 final size:42
Alignment explanation
Indices: 29033150--29033400 Score: 322
Period size: 42 Copynumber: 6.0 Consensus size: 42
29033140 CATCTCATAT
* * * *
29033150 GCAACGGCTTATGCGTACTCCCACTCACATATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * *
29033192 GCAACGGCTTATGTCCACTCCCACTTGCACATAGCCGAGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * * *
29033234 GCAATGGCTTATGTGCATTCCCATTCGCACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* ***
29033276 GCAACGGCTTATGTGCACTCCTACTCGCACATAGTTAGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
29033318 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCGGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
** *
29033360 GCAACGGCTTATGTGCACTCTTACTCGCACATAGCTGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
29033401 CACATCAACA
Statistics
Matches: 184, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 184 1.00
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:29041880 original size:21 final size:21
Alignment explanation
Indices: 29041850--29041891 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29041840 TAGTTGGGTT
* *
29041850 AGCAATGGCTTATGTGTACTC
1 AGCAACGGCTTATGTGCACTC
29041871 AGCAACGGCTTATGTGCACTC
1 AGCAACGGCTTATGTGCACTC
29041892 CCACTAGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
AGCAACGGCTTATGTGCACTC
Found at i:29041925 original size:63 final size:63
Alignment explanation
Indices: 29041806--29041933 Score: 166
Period size: 63 Copynumber: 2.0 Consensus size: 63
29041796 TATAGCCGAG
* ** * * *** *
29041806 TCAGCAACAGCTTATGTGCACTCCTACTCTCACATAGTTGGGTTAGCAATGGCTTATGTGTAC
1 TCAGCAACAGCTTATGTGCACTCCCACTAGCACATAGTCGGGTCAGCAACAACTTATGTGCAC
*
29041869 TCAGCAACGGCTTATGTGCACTCCCACTAGCACATAGTCGGGTCAGCAACAACTTATGTGCAC
1 TCAGCAACAGCTTATGTGCACTCCCACTAGCACATAGTCGGGTCAGCAACAACTTATGTGCAC
29041932 TC
1 TC
29041934 CCACTCGCAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (63 bp):
TCAGCAACAGCTTATGTGCACTCCCACTAGCACATAGTCGGGTCAGCAACAACTTATGTGCAC
Found at i:29041928 original size:42 final size:42
Alignment explanation
Indices: 29041869--29041996 Score: 177
Period size: 42 Copynumber: 3.0 Consensus size: 42
29041859 TTATGTGTAC
* *
29041869 TCAGCAACGGCTTATGTGCACTCCCACTAGCACATAGTCGGG
1 TCAGCAACGACTTATGTGCACTCCCACTAGCACATAGCCGGG
* *
29041911 TCAGCAACAACTTATGTGCACTCCCACTCGCACATAGCCGGG
1 TCAGCAACGACTTATGTGCACTCCCACTAGCACATAGCCGGG
* * *
29041953 TTAGCAACGACTTATGTGCACTCCTACTCA-CACATGGCCGGG
1 TCAGCAACGACTTATGTGCACTCCCACT-AGCACATAGCCGGG
29041995 TC
1 TC
29041997 CACATCAACA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (42 bp):
TCAGCAACGACTTATGTGCACTCCCACTAGCACATAGCCGGG
Found at i:29041954 original size:105 final size:105
Alignment explanation
Indices: 29041767--29041975 Score: 292
Period size: 105 Copynumber: 2.0 Consensus size: 105
29041757 CATCTCATAT
* * * * *
29041767 GCAACGGCTTATGCGTACTCCCACTCGCATATAGCCGAGTCAGCAACAGCTTATGTGCACTCCTA
1 GCAACGGCTTATGCGCACTCCCACTAGCACATAGCCGAGTCAGCAACAACTTATGTGCACTCCCA
* ** * * *
29041832 CTCTCACATAGTTGGGTTAGCAATGGCTTATGTGTACTCA
66 CTCGCACATAGCCGGGTTAGCAACGACTTATGTGCACTCA
* * *
29041872 GCAACGGCTTATGTGCACTCCCACTAGCACATAGTCGGGTCAGCAACAACTTATGTGCACTCCCA
1 GCAACGGCTTATGCGCACTCCCACTAGCACATAGCCGAGTCAGCAACAACTTATGTGCACTCCCA
29041937 CTCGCACATAGCCGGGTTAGCAACGACTTATGTGCACTC
66 CTCGCACATAGCCGGGTTAGCAACGACTTATGTGCACTC
29041976 CTACTCACAC
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 90 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (105 bp):
GCAACGGCTTATGCGCACTCCCACTAGCACATAGCCGAGTCAGCAACAACTTATGTGCACTCCCA
CTCGCACATAGCCGGGTTAGCAACGACTTATGTGCACTCA
Found at i:29044781 original size:21 final size:20
Alignment explanation
Indices: 29044757--29044804 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
29044747 ATTTTCATTT
29044757 TTTCTTAACTGATTACCATC
1 TTTCTTAACTGATTACCATC
*
29044777 ATTTCTTGACTGATTACCATC
1 -TTTCTTAACTGATTACCATC
29044798 -TTCTTAA
1 TTTCTTAA
29044805 TGGAAGCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
21 19 0.76
ACGTcount: A:0.25, C:0.23, G:0.06, T:0.46
Consensus pattern (20 bp):
TTTCTTAACTGATTACCATC
Found at i:29047176 original size:20 final size:20
Alignment explanation
Indices: 29047151--29047196 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
29047141 TTTTGACCCC
*
29047151 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTAAG
29047171 ATTTGACTTATTGGAGTAAG
1 ATTTGACTTATTGGAGTAAG
29047191 ATTTGA
1 ATTTGA
29047197 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.24, T:0.43
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTAAG
Found at i:29047272 original size:28 final size:27
Alignment explanation
Indices: 29047241--29047293 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
29047231 TTTGGAGTAA
*
29047241 AAGGGTAAAATGGTAATTTTGCCACCTT
1 AAGGGCAAAATGGTAATTTT-CCACCTT
*
29047269 AAGGGCAAAATTGTAATTTTCCACC
1 AAGGGCAAAATGGTAATTTTCCACC
29047294 ATTAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (27 bp):
AAGGGCAAAATGGTAATTTTCCACCTT
Found at i:29053151 original size:56 final size:56
Alignment explanation
Indices: 29053046--29053216 Score: 209
Period size: 56 Copynumber: 3.0 Consensus size: 56
29053036 TTAAGACAAC
* ** * *
29053046 TCTTGTCTTTAATTAAGATAAAAATATTTTATCTTATTTAAATTGAGACAAATATGTTT
1 TCTTGTC-TAAATTAAGACCAAAATA-TTT-TCTTATTTAAATTAAGACAAACATGTTT
* * *
29053105 TCTTGTCTAGATTAAGA-CAAAATATTTTCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTCTAAATTAAGACCAAAATATTTTCTTAT-TTAAATTAAGACAAACATGTTT
*
29053161 TCTTGTCTAAATTAAGACCAAACATGTTTTCTTATTTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACCAAA-ATATTTTCTTATTTAAATTAAGACAAACATGTT
29053217 AAAACTACCA
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
55 5 0.05
56 38 0.39
57 30 0.31
58 18 0.18
59 7 0.07
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (56 bp):
TCTTGTCTAAATTAAGACCAAAATATTTTCTTATTTAAATTAAGACAAACATGTTT
Found at i:29053165 original size:29 final size:29
Alignment explanation
Indices: 29053046--29053213 Score: 184
Period size: 28 Copynumber: 5.9 Consensus size: 29
29053036 TTAAGACAAC
* * *
29053046 TCTTGTCTTTAATTAAGATAAAAATATTTT
1 TCTTGTCTTAAATTAAGACAAACATA-TTT
* * * *
29053076 ATCTTAT-TTAAATTGAGACAAATATGTTT
1 -TCTTGTCTTAAATTAAGACAAACATATTT
*
29053105 TCTTGTC-TAGATTAAGACAAA-ATATTT
1 TCTTGTCTTAAATTAAGACAAACATATTT
29053132 TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTCTTAAATTAAGACAAACATATTT
*
29053161 TCTTGTC-TAAATTAAGACCAAACATGTTT
1 TCTTGTCTTAAATTAAGA-CAAACATATTT
*
29053190 TCTTAT-TTAAATTAAGACAAACAT
1 TCTTGTCTTAAATTAAGACAAACAT
29053214 GTTAAAACTA
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.10
28 47 0.39
29 41 0.34
30 14 0.12
31 5 0.04
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (29 bp):
TCTTGTCTTAAATTAAGACAAACATATTT
Found at i:29058580 original size:26 final size:27
Alignment explanation
Indices: 29058551--29058603 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
29058541 GCTAAGCCCA
29058551 TTTATCTCCTA-TTGGGCCATCCCCTT
1 TTTATCTCCTACTTGGGCCATCCCCTT
* * *
29058577 TTTATTTTCTACTTGGGCCATGCCCTT
1 TTTATCTCCTACTTGGGCCATCCCCTT
29058604 GTTTTTTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.11, C:0.30, G:0.13, T:0.45
Consensus pattern (27 bp):
TTTATCTCCTACTTGGGCCATCCCCTT
Found at i:29058593 original size:27 final size:26
Alignment explanation
Indices: 29058562--29058612 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
29058552 TTATCTCCTA
*
29058562 TTGGGCCATCCCCTTTTTATTTTCTAC
1 TTGGGCCATCCCCTTGTT-TTTTCTAC
*
29058589 TTGGGCCATGCCCTTGTTTTTTCT
1 TTGGGCCATCCCCTTGTTTTTTCT
29058613 CTCATCCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.08, C:0.27, G:0.16, T:0.49
Consensus pattern (26 bp):
TTGGGCCATCCCCTTGTTTTTTCTAC
Found at i:29061285 original size:32 final size:31
Alignment explanation
Indices: 29061237--29061296 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
29061227 ACAACACAAA
*
29061237 ACTCACCTTTCAAGCATAACCATAAATCAAC
1 ACTCACATTTCAAGCATAACCATAAATCAAC
*
29061268 ACTCACATTTCTAAGCATAATCATAAATC
1 ACTCACATTTC-AAGCATAACCATAAATC
29061297 TTCACTAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.42, C:0.28, G:0.03, T:0.27
Consensus pattern (31 bp):
ACTCACATTTCAAGCATAACCATAAATCAAC
Found at i:29066747 original size:2 final size:2
Alignment explanation
Indices: 29066740--29066774 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29066730 CCAAAACCTC
29066740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29066775 GTAACCACCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29066858 original size:42 final size:42
Alignment explanation
Indices: 29066812--29066928 Score: 191
Period size: 42 Copynumber: 2.8 Consensus size: 42
29066802 ATCTCAACTT
29066812 ATGTGCACTACC-ACACCGCACATGGCTGGGTCAGCACAGCTC
1 ATGTGCACT-CCTACACCGCACATGGCTGGGTCAGCACAGCTC
* *
29066854 ATGTGCACTCCTACACCACACATGGTTGGGTCAGCACAGCTC
1 ATGTGCACTCCTACACCGCACATGGCTGGGTCAGCACAGCTC
*
29066896 ATGTGCACTCCTACACGGCACATGGCTGGGTCA
1 ATGTGCACTCCTACACCGCACATGGCTGGGTCA
29066929 TAATTATCAC
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
41 2 0.03
42 67 0.97
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.20
Consensus pattern (42 bp):
ATGTGCACTCCTACACCGCACATGGCTGGGTCAGCACAGCTC
Found at i:29078548 original size:42 final size:41
Alignment explanation
Indices: 29078502--29078621 Score: 132
Period size: 42 Copynumber: 2.9 Consensus size: 41
29078492 TATGCATCAA
* *
29078502 CTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCATTGG
1 CTTATGT-CACTCCCACTCGCACATAGCCGGGTCAACATCGG
* * **
29078544 CTTATGCTCACTCTCACTTGCACATAGCCAAGTCAACATCGG
1 CTTATG-TCACTCCCACTCGCACATAGCCGGGTCAACATCGG
* * *
29078586 CTTATGCACACTCCTACTCACACATAGCCGGGTCAA
1 CTTATG-TCACTCCCACTCGCACATAGCCGGGTCAA
29078622 TATCATTACA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 63 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (41 bp):
CTTATGTCACTCCCACTCGCACATAGCCGGGTCAACATCGG
Found at i:29078649 original size:2 final size:2
Alignment explanation
Indices: 29078642--29078669 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29078632 AAACATTATT
29078642 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
29078670 CATAATGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29081381 original size:58 final size:57
Alignment explanation
Indices: 29081272--29081433 Score: 193
Period size: 58 Copynumber: 2.8 Consensus size: 57
29081262 TGGTAGTTTT
* * * *
29081272 AACATGTTTGTCTTAATTTAAACAAG--AAATCATGTTTGGTCTTAGTTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAAT-AT-TTTTGTCTTAATGTAGACAAGAA
* *
29081329 AATATGTTTGTCTTAATTTAGGACAAGAAAAATATTTTTATCTTAATGTAGACAAGAA
1 AACATGTTTGTCTTAATTTA-GACAAGAAAAATATTTTTGTCTTAATGTAGACAAGAA
* * *
29081387 AACATATTTGTCTCAATTTAGACAAGATAAACTATTTTTGTCTTAAT
1 AACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTGTCTTAAT
29081434 TAAAAATAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
57 26 0.29
58 58 0.64
59 2 0.02
60 4 0.04
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (57 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTGTCTTAATGTAGACAAGAA
Found at i:29081409 original size:28 final size:28
Alignment explanation
Indices: 29081272--29081434 Score: 182
Period size: 28 Copynumber: 5.6 Consensus size: 28
29081262 TGGTAGTTTT
*
29081272 AACATGTTTGTCTTAATTTAAACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* *
29081300 ATCATGTTTGGTCTTAGTTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
29081329 AATATGTTTGTCTTAATTTAGGACAAGAAA
1 AACATGTTTGTCTTAATTTA-GACAAG-AA
* * * *
29081359 AATATTTTTATCTTAATGTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* *
29081387 AACATATTTGTCTCAATTTAGACAAGATA
1 AACATGTTTGTCTTAATTTAGACAAGA-A
*
29081416 AACTATTTTTGTCTTAATT
1 AAC-ATGTTTGTCTTAATT
29081435 AAAAATAAGA
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
28 42 0.37
29 40 0.35
30 32 0.28
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:29082145 original size:42 final size:42
Alignment explanation
Indices: 29082086--29082168 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
29082076 GGTGTGGTGG
* *
29082086 TGTCCAAAAATAAGAATCTAAAAAAAGGGTACCTTTTTTTTT
1 TGTCCAAAAATAAGAATCTAAAAAAAAGGTACCGTTTTTTTT
29082128 TGTCCAAAAATAAGAATCTAAAAAAAAGGTACCGTTTTTTT
1 TGTCCAAAAATAAGAATCTAAAAAAAAGGTACCGTTTTTTT
29082169 CTTACTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (42 bp):
TGTCCAAAAATAAGAATCTAAAAAAAAGGTACCGTTTTTTTT
Found at i:29087366 original size:16 final size:16
Alignment explanation
Indices: 29087345--29087376 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29087335 CATGTGTGAG
29087345 TTATAAATAACTCTAT
1 TTATAAATAACTCTAT
29087361 TTATAAATAACTCTAT
1 TTATAAATAACTCTAT
29087377 GGGTAGATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
TTATAAATAACTCTAT
Found at i:29089601 original size:59 final size:60
Alignment explanation
Indices: 29089528--29089647 Score: 154
Period size: 59 Copynumber: 2.0 Consensus size: 60
29089518 ATAGAGGCTT
*
29089528 TATAGTCAATCCTTGG-TCAAAACCCTTGACTCCTCTTAC-TTCACTTCACAAGATTGACC
1 TATAGTCAATCCTTGGCT-AAAACCCTTGACTCCTCCTACTTTCACTTCACAAGATTGACC
* * * * *
29089587 TATAGTCGATCCTTGGCTAGAACCTTTGTCTTCTCCTACTTTTCACTTCACAAGATTGACC
1 TATAGTCAATCCTTGGCTAAAACCCTTGACTCCTCCTAC-TTTCACTTCACAAGATTGACC
29089648 CTTTATGCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 31 0.60
60 1 0.02
61 20 0.38
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (60 bp):
TATAGTCAATCCTTGGCTAAAACCCTTGACTCCTCCTACTTTCACTTCACAAGATTGACC
Found at i:29096052 original size:36 final size:36
Alignment explanation
Indices: 29095985--29096073 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 36
29095975 GTTTTTTAAC
* *
29095985 AAGATGAAGCGATAACCCTTACAACGACTTTTTCAG
1 AAGATCAAGCAATAACCCTTACAACGACTTTTTCAG
* *
29096021 AAGATCAAGCAATAACCCTTAC-ACCAGCTTTTTCAT
1 AAGATCAAGCAATAACCCTTACAACGA-CTTTTTCAG
* *
29096057 AGGATCTAGCAATAACC
1 AAGATCAAGCAATAACC
29096074 TTCACACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 3 0.07
36 43 0.93
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (36 bp):
AAGATCAAGCAATAACCCTTACAACGACTTTTTCAG
Found at i:29097549 original size:56 final size:55
Alignment explanation
Indices: 29097405--29097573 Score: 196
Period size: 56 Copynumber: 3.0 Consensus size: 55
29097395 GCATAGGATG
* *
29097405 GCCGCGGTGGGGTAAAAATACTTCTTGAGTAAGGGTCGGAGTAACTAATTAGCATA
1 GCCGCGGTGGGGTAAAAATAC-TATTGAGTAAGGGTCGGAGTACCTAATTAGCATA
** * * *
29097461 GCTACGGTGGGGTAAAAACCAC-ACTGATGTAAGGGTCGGAGTACCCAATTAGCATA
1 GCCGCGGTGGGGTAAAAA-TACTATTGA-GTAAGGGTCGGAGTACCTAATTAGCATA
* ** *
29097517 GCCGCGGTGGGGTAGAAATACTATTGGAGTAAGGGTCAAAGCACCTAATTAGCATA
1 GCCGCGGTGGGGTAAAAATACTATT-GAGTAAGGGTCGGAGTACCTAATTAGCATA
29097573 G
1 G
29097574 TCGTGGAAGG
Statistics
Matches: 93, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
55 5 0.05
56 84 0.90
57 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (55 bp):
GCCGCGGTGGGGTAAAAATACTATTGAGTAAGGGTCGGAGTACCTAATTAGCATA
Found at i:29097615 original size:112 final size:112
Alignment explanation
Indices: 29097405--29097648 Score: 246
Period size: 112 Copynumber: 2.2 Consensus size: 112
29097395 GCATAGGATG
* * ** *
29097405 GCCGCGGTGGGGTAAAAATACTTCTTGAGTAAGGGTCGGAGTAACTAATTAGCATAGCTACGGTG
1 GCCGCGGTGGGGTAGAAATACTTCTGGAGTAAGGGTCAAAGCAACTAATTAGCATAGCTACGGTG
* * * *
29097470 GGGTAAAAACCACACTGATGTAAGGGTCGGAGTACCCAAT-TAGCATA
66 GGGAAAAAAACACACTGACGTAAAGGTCGGAGTACCCAATGT-GCATA
*
29097517 GCCGCGGTGGGGTAGAAATACTAT-TGGAGTAAGGGTCAAAGCACCTAATTAGCATAG-T-C-GT
1 GCCGCGGTGGGGTAGAAATACT-TCTGGAGTAAGGGTCAAAGCAACTAATTAGCATAGCTACGGT
* * * ** *
29097578 GGAAGGAAAAAAATACCACTGGCGTAAAGGTCTGAGTACCTTATGTGCATG
65 GG--GGAAAAAAACA-CACTGACGTAAAGGTCGGAGTACCCAATGTGCATA
* *
29097629 GCCACTGTGGGGTAGAAATA
1 GCCGCGGTGGGGTAGAAATA
29097649 GCACTGATTC
Statistics
Matches: 109, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
109 4 0.04
110 1 0.01
111 9 0.08
112 93 0.85
113 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (112 bp):
GCCGCGGTGGGGTAGAAATACTTCTGGAGTAAGGGTCAAAGCAACTAATTAGCATAGCTACGGTG
GGGAAAAAAACACACTGACGTAAAGGTCGGAGTACCCAATGTGCATA
Found at i:29101784 original size:27 final size:27
Alignment explanation
Indices: 29101719--29101784 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
29101709 ATTTATAAAT
29101719 TATA-AAAATAAT-TTTTAAAATTTTAA
1 TATATAAAA-AATATTTTAAAATTTTAA
* * *
29101745 AAT-TAAATTAATATTTTAATATTTTAA
1 TATATAAA-AAATATTTTAAAATTTTAA
29101772 TATATAAAAAATA
1 TATATAAAAAATA
29101785 AAGAAGAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
26 8 0.26
27 19 0.61
28 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TATATAAAAAATATTTTAAAATTTTAA
Found at i:29101958 original size:21 final size:21
Alignment explanation
Indices: 29101914--29101963 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
29101904 ATTGATTTTT
29101914 TTATAAATTATAAAAATAAATA
1 TTAT-AATTATAAAAATAAATA
* *
29101936 TTTTAATT-TAAAAATCAAGTA
1 TTATAATTATAAAAAT-AAATA
29101957 TTATAAT
1 TTATAAT
29101964 AAAGAGAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 14 0.58
22 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTATAATTATAAAAATAAATA
Found at i:29102468 original size:11 final size:11
Alignment explanation
Indices: 29102452--29102488 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
29102442 TTTTTACTTT
*
29102452 TCATGTTAGTG
1 TCATGTTAATG
29102463 TCATGTTAATG
1 TCATGTTAATG
*
29102474 TCATGTTAATA
1 TCATGTTAATG
29102485 TCAT
1 TCAT
29102489 ATGGGCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (11 bp):
TCATGTTAATG
Found at i:29104921 original size:24 final size:23
Alignment explanation
Indices: 29104890--29104943 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
29104880 TTAAGTGAGA
29104890 TTTATTTAATA-TT-TAATTTTAGT
1 TTTATTTAATAGTTATAATTTT--T
*
29104913 TTTAGTTTATTAGTTATAATTTTT
1 TTTA-TTTAATAGTTATAATTTTT
29104937 TTTATTT
1 TTTATTT
29104944 TAATTGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 7 0.26
24 11 0.41
25 2 0.07
26 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (23 bp):
TTTATTTAATAGTTATAATTTTT
Found at i:29105656 original size:21 final size:21
Alignment explanation
Indices: 29105630--29105697 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
29105620 GTTCATACAA
*
29105630 TTCATGACAAAGACTGATGCT
1 TTCATGACAAAGACTGATGCC
*
29105651 TTCATGACAAAGACAGATGCC
1 TTCATGACAAAGACTGATGCC
* *
29105672 TTCATGACAAGGATTGATGCC
1 TTCATGACAAAGACTGATGCC
*
29105693 ATCAT
1 TTCAT
29105698 TCAAAGTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (21 bp):
TTCATGACAAAGACTGATGCC
Found at i:29106305 original size:16 final size:15
Alignment explanation
Indices: 29106270--29106304 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
29106260 TTTTAAATTT
29106270 AAAAACAAATTAAAA
1 AAAAACAAATTAAAA
29106285 AAAAACAAATTAAAA
1 AAAAACAAATTAAAA
29106300 AAAAA
1 AAAAA
29106305 AGTGGCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAACAAATTAAAA
Found at i:29106635 original size:8 final size:8
Alignment explanation
Indices: 29106622--29106667 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
29106612 GACTAACCAT
29106622 TTACCCAC
1 TTACCCAC
29106630 TTACCCAC
1 TTACCCAC
* *
29106638 TAACCCAT
1 TTACCCAC
*
29106646 TTACCCAT
1 TTACCCAC
29106654 TTACCCA-
1 TTACCCAC
29106661 TTACCCA
1 TTACCCA
29106668 ACAAAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
7 7 0.20
8 28 0.80
ACGTcount: A:0.28, C:0.43, G:0.00, T:0.28
Consensus pattern (8 bp):
TTACCCAC
Found at i:29106648 original size:24 final size:23
Alignment explanation
Indices: 29106613--29106660 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
29106603 TTTTATTTGG
29106613 ACTAACCATTTACCCACTTACCC
1 ACTAACCATTTACCCACTTACCC
*
29106636 ACTAACCCATTTACCCATTTACCC
1 ACTAA-CCATTTACCCACTTACCC
29106660 A
1 A
29106661 TTACCCAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (23 bp):
ACTAACCATTTACCCACTTACCC
Found at i:29109117 original size:40 final size:41
Alignment explanation
Indices: 29109041--29109204 Score: 168
Period size: 43 Copynumber: 3.9 Consensus size: 41
29109031 TCATTCATCA
* ** * ** *
29109041 TCATGTGCACTCCTTACTCGCACATTTCAACATCATCA-AC
1 TCATGTGCACTCCCTACTCGCACATAGCTAGGTCATCACGC
*
29109081 TCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCATCGGC
1 TCATGTGCACTCCCTACTCGCACATAGCTAGGTCATCA-C-GC
* *
29109124 TCATGTGCACTCCCTACTCGCACATAACCAGGTCATCATCGGC
1 TCATGTGCACTCCCTACTCGCACATAGCTAGGTCATCA-C-GC
* * *
29109167 TCATGTACACTCCCTACTCGCCCATAGCTGGGTCATCA
1 TCATGTGCACTCCCTACTCGCACATAGCTAGGTCATCA
29109205 TCATCACATA
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
40 31 0.30
43 74 0.70
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (41 bp):
TCATGTGCACTCCCTACTCGCACATAGCTAGGTCATCACGC
Found at i:29109132 original size:43 final size:43
Alignment explanation
Indices: 29109071--29109206 Score: 209
Period size: 43 Copynumber: 3.2 Consensus size: 43
29109061 CACATTTCAA
**
29109071 CATCATCAACTCATGTGCACTCCCTACTCGCACATAGCTGGGT
1 CATCATCGGCTCATGTGCACTCCCTACTCGCACATAGCTGGGT
* **
29109114 CATCATCGGCTCATGTGCACTCCCTACTCGCACATAACCAGGT
1 CATCATCGGCTCATGTGCACTCCCTACTCGCACATAGCTGGGT
* *
29109157 CATCATCGGCTCATGTACACTCCCTACTCGCCCATAGCTGGGT
1 CATCATCGGCTCATGTGCACTCCCTACTCGCACATAGCTGGGT
29109200 CATCATC
1 CATCATC
29109207 ATCACATAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.25
Consensus pattern (43 bp):
CATCATCGGCTCATGTGCACTCCCTACTCGCACATAGCTGGGT
Found at i:29109193 original size:86 final size:83
Alignment explanation
Indices: 29109041--29109206 Score: 233
Period size: 86 Copynumber: 2.0 Consensus size: 83
29109031 TCATTCATCA
* ** *
29109041 TCATGTGCACTCCTTACTCGCACATTTCAACATCATCAACTCATGTGCACTCCCTACTCGCACAT
1 TCATGTGCACTCCCTACTCGCACATACCAACATCATCAACTCATGTACACTCCCTACTCGCACAT
29109106 AGCTGGGTCATCATCGGC
66 AGCTGGGTCATCATCGGC
* ** *
29109124 TCATGTGCACTCCCTACTCGCACATAACCAGGTCATCATCGGCTCATGTACACTCCCTACTCGCC
1 TCATGTGCACTCCCTACTCGCACAT-ACCA--ACATCATCAACTCATGTACACTCCCTACTCGCA
29109189 CATAGCTGGGTCATCATC
63 CATAGCTGGGTCATCATC
29109207 ATCACATAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
83 24 0.33
84 2 0.03
86 46 0.64
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.27
Consensus pattern (83 bp):
TCATGTGCACTCCCTACTCGCACATACCAACATCATCAACTCATGTACACTCCCTACTCGCACAT
AGCTGGGTCATCATCGGC
Found at i:29110713 original size:3 final size:3
Alignment explanation
Indices: 29110705--29110754 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
29110695 ACTTTATCTC
* * * * *
29110705 TAG TAG TAG TAA TAG TAA TAG TAA TAG TAG TAC TAG TAG TAG TAG GAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
29110753 TA
1 TA
29110755 ATTATATTTA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (3 bp):
TAG
Found at i:29110754 original size:12 final size:12
Alignment explanation
Indices: 29110705--29110749 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
29110695 ACTTTATCTC
29110705 TAGTAGTAGTAA
1 TAGTAGTAGTAA
*
29110717 TAGTAATAGTAA
1 TAGTAGTAGTAA
* *
29110729 TAGTAGTACTAG
1 TAGTAGTAGTAA
29110741 TAGTAGTAG
1 TAGTAGTAG
29110750 GAGTAATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.33
Consensus pattern (12 bp):
TAGTAGTAGTAA
Found at i:29123076 original size:18 final size:19
Alignment explanation
Indices: 29123053--29123089 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29123043 CAAGTAGAAA
29123053 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
*
29123071 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
29123090 GTCAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:29123635 original size:20 final size:20
Alignment explanation
Indices: 29123612--29123673 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
29123602 CATACTTTTG
29123612 GAAAGAAAGAAAGGAGAAAA
1 GAAAGAAAGAAAGGAGAAAA
*
29123632 GAAAGAAAGAAAGGAGAAAG
1 GAAAGAAAGAAAGGAGAAAA
*
29123652 GAAAAGAGAGAAAGGATGAAAA
1 G-AAAGAAAGAAAGGA-GAAAA
29123674 AGCTTGGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 20 0.54
21 13 0.35
22 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (20 bp):
GAAAGAAAGAAAGGAGAAAA
Found at i:29123649 original size:7 final size:7
Alignment explanation
Indices: 29123619--29123672 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
29123609 TTGGAAAGAA
29123619 AGAAAGG
1 AGAAAGG
29123626 AGAAA--
1 AGAAAGG
*
29123631 AGAAAGAA
1 AGAAAG-G
29123639 AGAAAGG
1 AGAAAGG
29123646 AGAAAGG
1 AGAAAGG
29123653 A-AAAGAG
1 AGAAAG-G
29123660 AGAAAGG
1 AGAAAGG
29123667 ATGAAA
1 A-GAAA
29123673 AAGCTTGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
5 5 0.12
6 4 0.10
7 17 0.43
8 14 0.35
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (7 bp):
AGAAAGG
Found at i:29130343 original size:26 final size:26
Alignment explanation
Indices: 29130314--29130366 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
29130304 CAATAGCAAG
29130314 CAAGAGTTCCAATTCTAGAAAATAAA
1 CAAGAGTTCCAATTCTAGAAAATAAA
*
29130340 CAAGAGTTCCAATTCTATAAAATAAA
1 CAAGAGTTCCAATTCTAGAAAATAAA
29130366 C
1 C
29130367 CATCTATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (26 bp):
CAAGAGTTCCAATTCTAGAAAATAAA
Found at i:29132789 original size:35 final size:35
Alignment explanation
Indices: 29132686--29132798 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
29132676 GATGTGGGTA
** * *
29132686 GGAGTGCATGTGATGGTATTGAAATGTGCGTGCAG
1 GGAGTGCACATGATGATATTGAAATGTGCGTGTAG
*
29132721 GGAGTGCACATGATGATATTGAAATGTGTGTGTAG
1 GGAGTGCACATGATGATATTGAAATGTGCGTGTAG
*** *
29132756 GGAGTGCACATGATGATATTGCCTTGTGCGTGTAA
1 GGAGTGCACATGATGATATTGAAATGTGCGTGTAG
29132791 GGAGTGCA
1 GGAGTGCA
29132799 TAAGAGCTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.25, C:0.10, G:0.36, T:0.29
Consensus pattern (35 bp):
GGAGTGCACATGATGATATTGAAATGTGCGTGTAG
Found at i:29142995 original size:19 final size:19
Alignment explanation
Indices: 29142971--29143008 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29142961 TGCTAAACCC
*
29142971 TCAAATTATACTCCAATAA
1 TCAAATCATACTCCAATAA
29142990 TCAAATCATACTCCAATAA
1 TCAAATCATACTCCAATAA
29143009 GTTAGATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (19 bp):
TCAAATCATACTCCAATAA
Found at i:29146754 original size:5 final size:5
Alignment explanation
Indices: 29146746--29146778 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
29146736 ACCTAACCTG
29146746 ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
29146779 GGGCCACGCA
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:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ACTTA
Found at i:29146765 original size:14 final size:15
Alignment explanation
Indices: 29146746--29146778 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
29146736 ACCTAACCTG
29146746 ACTTAACTTAAC-TA
1 ACTTAACTTAACTTA
29146760 ACTTAACTTAACTTA
1 ACTTAACTTAACTTA
29146775 ACTT
1 ACTT
29146779 GGGCCACGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (15 bp):
ACTTAACTTAACTTA
Found at i:29146833 original size:15 final size:15
Alignment explanation
Indices: 29146813--29146858 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29146803 TTCTTAAAAC
29146813 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
29146828 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
29146843 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
29146858 A
1 A
29146859 TCTCTGATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.89
16 2 0.07
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:29152256 original size:19 final size:19
Alignment explanation
Indices: 29152232--29152269 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29152222 TGCTAAACCC
*
29152232 TCAAATTATACTCCAATAA
1 TCAAATCATACTCCAATAA
29152251 TCAAATCATACTCCAATAA
1 TCAAATCATACTCCAATAA
29152270 GTTAGATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (19 bp):
TCAAATCATACTCCAATAA
Found at i:29155459 original size:21 final size:19
Alignment explanation
Indices: 29155403--29155468 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 19
29155393 CTACAAAAGC
29155403 ATAAAAACT-AATAAATAATA
1 ATAAAAA-TAAATAAATAA-A
*
29155423 ATAAAACTAAAGTAAATAAA
1 ATAAAAATAAA-TAAATAAA
29155443 CATAAAAATAATATAAAATAAA
1 -ATAAAAATAA-AT-AAATAAA
29155465 ATAA
1 ATAA
29155469 CTTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 9 0.23
21 21 0.54
22 8 0.21
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.23
Consensus pattern (19 bp):
ATAAAAATAAATAAATAAA
Found at i:29155466 original size:15 final size:15
Alignment explanation
Indices: 29155415--29155468 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
29155405 AAAAACTAAT
29155415 AAATAATAATAAAACTA
1 AAATAAT-ATAAAA-TA
*
29155432 AAGTAA-ATAAACATAA
1 AAATAATATAAA-AT-A
29155448 AAATAATATAAAATA
1 AAATAATATAAAATA
29155463 AAATAA
1 AAATAA
29155469 CTTAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 13 0.41
16 9 0.28
17 10 0.31
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (15 bp):
AAATAATATAAAATA
Found at i:29156338 original size:21 final size:21
Alignment explanation
Indices: 29156314--29156395 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 21
29156304 CTTTTACCTA
*
29156314 AATTAACACAACTCTTGTCTT
1 AATTAACACAATTCTTGTCTT
*
29156335 AATTAATGCAACATATTTACCTTGTCTA
1 AATTAA--C-ACA-A-TT--CTTGTCTT
*
29156363 AATTAAGACAATTCTTGTCTT
1 AATTAACACAATTCTTGTCTT
*
29156384 AATTAAGACAAT
1 AATTAACACAAT
29156396 ATCTAAAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
21 25 0.50
23 3 0.06
24 4 0.08
25 4 0.08
26 1 0.02
28 13 0.26
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (21 bp):
AATTAACACAATTCTTGTCTT
Found at i:29161128 original size:25 final size:25
Alignment explanation
Indices: 29161094--29161141 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
29161084 GGTTTTTCTA
* *
29161094 CTCTTTCTTT-TCTTGCTTTCTTTTT
1 CTCTTGCTTTCTCTCGC-TTCTTTTT
29161119 CTCTTGCTTTCTCTCGCTTCTTT
1 CTCTTGCTTTCTCTCGCTTCTTT
29161142 CTTCCCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.00, C:0.29, G:0.06, T:0.65
Consensus pattern (25 bp):
CTCTTGCTTTCTCTCGCTTCTTTTT
Found at i:29161444 original size:74 final size:74
Alignment explanation
Indices: 29161346--29161506 Score: 175
Period size: 74 Copynumber: 2.2 Consensus size: 74
29161336 TAAGGTGTCA
* *
29161346 ATTCTCCTTGTCCCATATCAAAGGTAGCA-CTATTTTG-T-TTTTCTAAGAATCAACCTTTATAG
1 ATTCTACTTGTCCCATATCAAAGGTAGCACCT-TTCTGTTCTTTTC-AA-AATCAACCTTTATAG
29161408 CTTGAAGCATCG
63 CTTGAAGCATCG
* * * ** *
29161420 ATTCTACTTGTCTCATCTCTAAGGTAGCACCTTTCTGTTCTTTTCAAAATTGACCTTTGTAGCTT
1 ATTCTACTTGTCCCATATCAAAGGTAGCACCTTTCTGTTCTTTTCAAAATCAACCTTTATAGCTT
** *
29161485 GAAGTGTTG
66 GAAGCATCG
29161494 ATTCTACTTGTCC
1 ATTCTACTTGTCC
29161507 ATTAAATGCC
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
74 62 0.86
75 5 0.07
76 5 0.07
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (74 bp):
ATTCTACTTGTCCCATATCAAAGGTAGCACCTTTCTGTTCTTTTCAAAATCAACCTTTATAGCTT
GAAGCATCG
Found at i:29162268 original size:21 final size:20
Alignment explanation
Indices: 29162230--29162269 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29162220 TACATTTTGT
**
29162230 TTCAAATGTATCGTTACATG
1 TTCAAATGTATCAATACATG
29162250 TTCATAATGTATCAATACAT
1 TTCA-AATGTATCAATACAT
29162270 ATGGTCATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
TTCAAATGTATCAATACATG
Found at i:29173840 original size:25 final size:24
Alignment explanation
Indices: 29173797--29173857 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
29173787 CCATTTATTT
*
29173797 TTATTTCCTATTGGGCATGCGC-AC
1 TTATTTTCTATTGGGCATGC-CAAC
* *
29173821 TTATTTTCTATTAGGTCATGCCAAT
1 TTATTTTCTATT-GGGCATGCCAAC
29173846 TTATTTTCTATT
1 TTATTTTCTATT
29173858 TATTTTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.38
25 20 0.62
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (24 bp):
TTATTTTCTATTGGGCATGCCAAC
Found at i:29186600 original size:5 final size:5
Alignment explanation
Indices: 29186596--29186625 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
29186586 CTATTCAACC
*
29186596 TAACC TAACT TAACT TAACT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT TAACT
29186626 AGGGGCCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (5 bp):
TAACT
Found at i:29189184 original size:28 final size:27
Alignment explanation
Indices: 29189140--29189192 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
29189130 TGTGCTGGTG
29189140 GTGGAAAATTACTATTTTGCCCCTAAA
1 GTGGAAAATTACTATTTTGCCCCTAAA
29189167 GTGGTAAAATTA-TCATTTTGCCCCTA
1 GTGG-AAAATTACT-ATTTTGCCCCTA
29189193 TGCTCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (27 bp):
GTGGAAAATTACTATTTTGCCCCTAAA
Found at i:29192786 original size:33 final size:33
Alignment explanation
Indices: 29192749--29192819 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
29192739 CAACAACATC
*
29192749 AACATACCACATCATCATCGATTATGACATGTT
1 AACATACCACATCATAATCGATTATGACATGTT
**
29192782 AACATACCACATCATAATTTATTATGACATGTT
1 AACATACCACATCATAATCGATTATGACATGTT
29192815 AACAT
1 AACAT
29192820 GCCATGTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.32
Consensus pattern (33 bp):
AACATACCACATCATAATCGATTATGACATGTT
Found at i:29208027 original size:35 final size:35
Alignment explanation
Indices: 29207986--29208179 Score: 199
Period size: 35 Copynumber: 5.5 Consensus size: 35
29207976 ATTAAGTTGT
* *
29207986 GCCTAATTAATTAAATTGTTTAATTAAATCATTGG
1 GCCTAATTAATTAAATTGTTTAATTAAGTTATTGG
**** * *
29208021 GCCTAATTAATTAAATTAAACAATTAAGTTACTCG
1 GCCTAATTAATTAAATTGTTTAATTAAGTTATTGG
* * * *
29208056 GCCTAATTGATTAAATTTGTTTAATTACGTCATTGC
1 GCCTAATTAATTAAA-TTGTTTAATTAAGTTATTGG
* * *
29208092 GCCTAATTGATTAACATTGTTTAATTAAATTGTTGG
1 GCCTAATTAATTAA-ATTGTTTAATTAAGTTATTGG
* *
29208128 GCTTAATTAATTAAATTGTTTAATTAAGTTATTAG
1 GCCTAATTAATTAAATTGTTTAATTAAGTTATTGG
* *
29208163 GCGTAATTGATTAAATT
1 GCCTAATTAATTAAATT
29208180 AAACAATTAA
Statistics
Matches: 127, Mismatches: 30, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
35 74 0.58
36 52 0.41
37 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (35 bp):
GCCTAATTAATTAAATTGTTTAATTAAGTTATTGG
Found at i:29208120 original size:107 final size:106
Alignment explanation
Indices: 29207986--29208179 Score: 280
Period size: 107 Copynumber: 1.8 Consensus size: 106
29207976 ATTAAGTTGT
29207986 GCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAATTAAATTAAACAATTAAGTT
1 GCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAATTAAATTAAACAATTAAGTT
*
29208051 ACTCGGCCTAATTGATTAAATTTGTTTAATTACGTCATTGC
66 ACTAGGCCTAATTGATTAAATTTGTTTAATTACGTCATTGC
* ** * ****
29208092 GCCTAATTGATTAACATTGTTTAATTAAATTGTTGGGCTTAATTAATTAAATTGTTTAATTAAGT
1 GCCTAATTAATTAA-ATTGTTTAATTAAATCATTGGGCCTAATTAATTAAATTAAACAATTAAGT
* *
29208157 TATTAGGCGTAATTGATTAAATT
65 TACTAGGCCTAATTGATTAAATT
29208180 AAACAATTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
106 13 0.17
107 63 0.83
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (106 bp):
GCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAATTAAATTAAACAATTAAGTT
ACTAGGCCTAATTGATTAAATTTGTTTAATTACGTCATTGC
Found at i:29208193 original size:35 final size:34
Alignment explanation
Indices: 29207961--29208179 Score: 185
Period size: 35 Copynumber: 6.3 Consensus size: 34
29207951 TCTCAAGCAT
*
29207961 TTGATTAAAATTG--TAATTAAGTT-GT-GCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGCCTAA
* * *
29207992 TTAATTAAATTGTTTAATTAAATCATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATT-GGCCTAA
* **** *
29208027 TTAATTAAATTAAACAATTAAGTTACTCGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTA-TTGGCCTAA
* *
29208062 TTGATTAAATTTGTTTAATTACGTCATTGCGCCTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTG-GCCTAA
* * *
29208098 TTGATTAACATTGTTTAATTAAATTGTTGGGCTTAA
1 TTGATTAA-ATTGTTTAATTAAGTTATT-GGCCTAA
* *
29208134 TTAATTAAATTGTTTAATTAAGTTATTAGGCGTAA
1 TTGATTAAATTGTTTAATTAAGTTATT-GGCCTAA
29208169 TTGATTAAATT
1 TTGATTAAATT
29208180 AAACAATTAA
Statistics
Matches: 148, Mismatches: 30, Indels: 16
0.76 0.15 0.08
Matches are distributed among these distances:
30 6 0.04
31 5 0.03
32 8 0.05
33 1 0.01
35 75 0.51
36 51 0.34
37 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.43
Consensus pattern (34 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGCCTAA
Found at i:29208431 original size:27 final size:27
Alignment explanation
Indices: 29208401--29208454 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29208391 TTTTTCATTT
29208401 ACTTGATTTCTTATATGTGTTCAACCC
1 ACTTGATTTCTTATATGTGTTCAACCC
*
29208428 ACTTGATTTCTTATGTGTGTTCAACCC
1 ACTTGATTTCTTATATGTGTTCAACCC
29208455 CAAAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (27 bp):
ACTTGATTTCTTATATGTGTTCAACCC
Found at i:29210621 original size:140 final size:139
Alignment explanation
Indices: 29210470--29210747 Score: 538
Period size: 140 Copynumber: 2.0 Consensus size: 139
29210460 TAATTAAAAT
29210470 AATTTTTTTAAAAAAATAAAAATCTGTTTAATAGGTTAACATGTAAACAATATAAATAATTTTTA
1 AATTTTTTTAAAAAAATAAAAATCTGTTTAATAGGTTAACATGTAAACAATATAAATAATTTTTA
29210535 AACTTATTCATTTTTTATTAACAATATAGATAATTCTTAAATTAATTTAATTTATTTTAAACATC
66 AACTTATTCATTTTTTATTAACAATATAGATAATTCTTAAATTAATTTAATTTATTTTAAACATC
29210600 ANTAAAATTA
131 A-TAAAATTA
29210610 AATTTTTTTAAAAAAATAAAAATCTGTTTAATAGGTTAACATGTAAACAATATAAATAATTTTTA
1 AATTTTTTTAAAAAAATAAAAATCTGTTTAATAGGTTAACATGTAAACAATATAAATAATTTTTA
29210675 AACTTATTCATTTTTTATTAACAATATAGATAATTCTTAAATTAATTTAATTTATTTTAAACATC
66 AACTTATTCATTTTTTATTAACAATATAGATAATTCTTAAATTAATTTAATTTATTTTAAACATC
*
29210740 ATATAATT
131 ATAAAATT
29210748 TTTATTTTTA
Statistics
Matches: 137, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
139 6 0.04
140 131 0.96
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (139 bp):
AATTTTTTTAAAAAAATAAAAATCTGTTTAATAGGTTAACATGTAAACAATATAAATAATTTTTA
AACTTATTCATTTTTTATTAACAATATAGATAATTCTTAAATTAATTTAATTTATTTTAAACATC
ATAAAATTA
Found at i:29211412 original size:252 final size:251
Alignment explanation
Indices: 29210982--29211837 Score: 1064
Period size: 252 Copynumber: 3.4 Consensus size: 251
29210972 TAATTCTTTT
** * * * * * *
29210982 TATTTACGCATAAATTAATTTTTGTAAGCTATAAATCACTCTAAACTTGAGAATAAAAATTTAAT
1 TATTTACGCATAAATTAAAATTTGTAAGCCATAAAACACTTTAAACTTAAGAATAACAATTTAAA
* * * * * * * *
29211047 TGTATAATTTTTTCAAAAATTATA-TTATTTGACACAATTGACTTATTATATTAAATGTCACATA
66 TGTTTAATTTCTTCAAAAATTATATTTATTAGACATAATTGACTTGTTACATTAAATATCACACA
*
29211111 TTTACATCAATATTTTGACAAT-CCTTTCTCCACCTTTATAA-GATTTTATGTTAATTCTTACCA
131 TTTACATCAATATTTTGA-AATGCCTGT-TCCACCTTTATAATG-TTTTATGTTAATTCTTACCA
29211174 CTTTACGTTAATGCTTTTTAAATATTAATTTTCATCGTAATTCTTTTTACCCTTACTAC
193 CTTTACGTTAATGCTTTTTAAATATTAATTTTCATCGTAATTCTTTTTACCCTTACTAC
* * ** *
29211233 TATTTACGCATAAATTAAAATTTGTAAGCCGTAGAACACTTTAAACTCGAGAATAACAATTTCAA
1 TATTTACGCATAAATTAAAATTTGTAAGCCATAAAACACTTTAAACTTAAGAATAACAATTTAAA
* *
29211298 TGTTTAATTTCTCCAAAAATGATATTTATTAGACATAATTGACTTGTTACATTAAATATCACACA
66 TGTTTAATTTCTTCAAAAATTATATTTATTAGACATAATTGACTTGTTACATTAAATATCACACA
* * *
29211363 TTTACGTCAATATTTTGCAAATGCGTGTTCCACCTTTATAATGTTTTATGTTAATTATTACCACT
131 TTTACATCAATATTTTG-AAATGCCTGTTCCACCTTTATAATGTTTTATGTTAATTCTTACCACT
* * *
29211428 TTACGTTAACGCATTTTAAATATCAATTTTCATCGTAATTCTTTTTACCCTTACTAC
195 TTACGTTAATGCTTTTTAAATATTAATTTTCATCGTAATTCTTTTTACCCTTACTAC
* * *
29211485 TATTTACGCATAGATTAAAATTTGCAAGCCATAAAATACTTTAAACTTAAGAATAACAATTTAAA
1 TATTTACGCATAAATTAAAATTTGTAAGCCATAAAACACTTTAAACTTAAGAATAACAATTTAAA
* * *
29211550 TGTTTAATTTC-TCTAAAATTATATTTATTAGACATAATTGACTTGTTACCTTAAATCT-AGCAC
66 TGTTTAATTTCTTCAAAAATTATATTTATTAGACATAATTGACTTGTTACATTAAATATCA-CAC
* * * * * **
29211613 GTTTACATCAATAATTTGAAAATGCTTGTTCCA-C--TCTAATGTTTTATATTAATTCTTATTAC
130 ATTTACATCAATATTTTG-AAATGCCTGTTCCACCTTTATAATGTTTTATGTTAATTCTTACCAC
* * * * *
29211675 TTTATGTCAATGCTTTTTAAATACTAATTTTCACCGTAATTCTTTTTATCCTTACTA-
194 TTTACGTTAATGCTTTTTAAATATTAATTTTCATCGTAATTCTTTTTACCCTTACTAC
* * * * * *
29211732 TAATTCATGCATAGATTAAAATTTATAAGCCATAAAATACTTTAAACTTAAAAATAACAATTTAA
1 T-ATTTACGCATAAATTAAAATTTGTAAGCCATAAAACACTTTAAACTTAAGAATAACAATTTAA
* * * *
29211797 ATATTTTATTTCTTCAAAAATTATGTTTATTAGATATAATT
65 ATGTTTAATTTCTTCAAAAATTATATTTATTAGACATAATT
29211838 TGTCAAGCCC
Statistics
Matches: 529, Mismatches: 69, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
247 1 0.00
248 140 0.26
249 25 0.05
250 2 0.00
251 147 0.28
252 209 0.40
253 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (251 bp):
TATTTACGCATAAATTAAAATTTGTAAGCCATAAAACACTTTAAACTTAAGAATAACAATTTAAA
TGTTTAATTTCTTCAAAAATTATATTTATTAGACATAATTGACTTGTTACATTAAATATCACACA
TTTACATCAATATTTTGAAATGCCTGTTCCACCTTTATAATGTTTTATGTTAATTCTTACCACTT
TACGTTAATGCTTTTTAAATATTAATTTTCATCGTAATTCTTTTTACCCTTACTAC
Found at i:29215053 original size:27 final size:27
Alignment explanation
Indices: 29215002--29215053 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
29214992 ATGTCCTGAT
*
29215002 GGTGGAAAATTACAATTTTGCCCCTGG
1 GGTGGAAAATTACAATTTTGACCCTGG
29215029 GGTGGCAAAATTATC-ATTTT-ACCCT
1 GGTGG-AAAATTA-CAATTTTGACCCT
29215054 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.41
28 12 0.55
29 1 0.05
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTGG
Found at i:29215145 original size:20 final size:20
Alignment explanation
Indices: 29215099--29215145 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
29215089 CTTCTAAACC
*
29215099 TCAAATCATACTCCAATAAG
1 TCAAATTATACTCCAATAAG
*
29215119 TCAAATTATACTCTAATAAG
1 TCAAATTATACTCCAATAAG
29215139 TCAAATT
1 TCAAATT
29215146 GGGTCAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (20 bp):
TCAAATTATACTCCAATAAG
Found at i:29217193 original size:28 final size:29
Alignment explanation
Indices: 29217152--29217211 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
29217142 GTCTATGGGC
*
29217152 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
29217180 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
29217210 AA
1 AA
29217212 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:29225373 original size:28 final size:29
Alignment explanation
Indices: 29225332--29225391 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
29225322 GTCTATGGGC
*
29225332 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
29225360 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
29225390 AA
1 AA
29225392 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:29233554 original size:28 final size:29
Alignment explanation
Indices: 29233513--29233572 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
29233503 GTCTATGGGC
*
29233513 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
29233541 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
29233571 AA
1 AA
29233573 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:29241735 original size:28 final size:29
Alignment explanation
Indices: 29241694--29241753 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
29241684 GTCTATGGGC
*
29241694 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
29241722 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
29241752 AA
1 AA
29241754 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:29249915 original size:28 final size:29
Alignment explanation
Indices: 29249874--29249933 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
29249864 GTCTATGGGC
*
29249874 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
29249902 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
29249932 AA
1 AA
29249934 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:29258095 original size:28 final size:29
Alignment explanation
Indices: 29258054--29258113 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
29258044 GTCTATGGGC
*
29258054 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
29258082 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
29258112 AA
1 AA
29258114 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:29262072 original size:251 final size:252
Alignment explanation
Indices: 29260683--29263181 Score: 2726
Period size: 251 Copynumber: 9.9 Consensus size: 252
29260673 ACTTCATGAC
* * * * * *** *
29260683 TTTTCAACCAATAATTTTCATCATAATTCTTTTTATCCTTTCTATTATTCACAAATAAATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCATGCATAGATTAAAA
* * * * ** **
29260748 TTTGTCAGTTGTAAAATACTTTAAACTCGAGAA-AAAAACTTTAAATGTTTTATTTTTTTGAAAA
66 TTTGTAAGTCGTAAAACACTTTAAACTCGAGAATAAAAA-TTTAAATGTTTAATTTCCTCAAAAA
* * * * *
29260812 TTATGTTTATTTGACATAATTGACTTGTTACATTAAATCTCATACATTTACGTCAATATTTTAAC
130 TTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGAC
* * *
29260877 ATTGCTTCTTCCACCTTTATAATGTTTTAC-TTGAATTCTTATCA-CTTTACGTCAAGGG
195 AATGCTTGTTCCACCTTTATAATGTTTTACATT-AATTCTTA-CAGCTTTACGTCAAGGT
* * * * *
29260935 TTTTC-ACTTACTAAATTTCAACACAATTCTTTATATCCTTACCATTATTCTTGCATAGATTAAA
1 TTTTCAAC-TACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCATGCATAGATTAAA
* * * * **
29260999 ATTTGTTAGTCGTAAAACACTTTAAACTCAAAAATAAAAATTTAAATATTTAATTTTTTCAAAAA
65 ATTTGTAAGTCGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCTCAAAAA
* *
29261064 TTATGTTTATTTGACATAATTGACTTATTACGTTAAATCTCACACATTTATGTTAATATTTTGAT
130 TTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGAC
* * * * *
29261129 AATGCTTCTTTCATCGTTATAATGTTTTATATTAATTCTTACCA-CTTTACGTCAAGGT
195 AATGCTTGTTCCACCTTTATAATGTTTTACATTAATTCTTA-CAGCTTTACGTCAAGGT
*
29261187 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTAATGCATAGATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCATGCATAGATTAAAA
* * * **
29261252 TTTGTAAGTTGTTAAACACTTTAAACTCGAGAACAAAAATTTAAATGTTTAACTTTTTTCAAAAA
66 TTTGTAAGTCGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAA-TTTCCTCAAAAA
* * * *
29261317 TTATGTTTGTTTGACATAATTGACTTGTTAAGTTAAATCTCATACATTTACGTTAATATTTTGAC
130 TTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGAC
* * * ** * **
29261382 AATGTTTGTTCCATCTTGATAATGTTTTACGCTAATTCTTATAATTTTACGTCAAGGT
195 AATGCTTGTTCCACCTTTATAATGTTTTACATTAATTCTTACAGCTTTACGTCAAGGT
* * * * * * * *
29261440 TTTTTAACTAGTAAATTTGACCGTAATTTTTTTTATCCTTACTATGATTCACGCATAAATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCATGCATAGATTAAAA
* * * * * * *
29261505 TTTGTCAGCCATAAAACACTTTAAACTCAAGAATAAAGATTTAAATGTTTAATTTCCT-ACACAT
66 TTTGTAAGTCGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCTCAAAAAT
* * * * * * *
29261569 TATATTTATTTGACATAATTGACTTTTTAAGTTTAATCTCACATATTTATGTCAATATTTTGATA
131 TATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGACA
* * * ** *
29261634 ATGCTTATTCCATCTTTATAATG-TTTACGTTAATTCTTACAATTTTACATCAAGGT
196 ATGCTTGTTCCACCTTTATAATGTTTTACATTAATTCTTACAGCTTTACGTCAAGGT
* * * **
29261690 TTTTCAACTAGTAAATTTCACCATAATTCTTTTTATCTTTACTATGATTCACACATAGATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCATGCATAGATTAAAA
* * * ** * * *
29261755 TTTGTCAGCCGTAGAACACTTTAAACTTTAGAATAAAGATTTAAATGTTTAATTTTCTAAAAAAT
66 TTTGTAAGTCGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCTCAAAAAT
* * * * * * *
29261820 TATG-CTGTTTGACATAATTGACTTTTTATGTTAAATCTTACATATTTATGTTAATATTTTGACC
131 TATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGACA
* * * **
29261884 ATGCTTGTTCTACCTTTATAATGTTTTACATTAATTCTTACAGCCTTACGTCATGAC
196 ATGCTTGTTCCACCTTTATAATGTTTTACATTAATTCTTACAGCTTTACGTCAAGGT
* * * * *
29261941 TTTTCAACTATTAATTTTCATCGTAATTCTTTATATCCTTACTATTATTCATGCATAGATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCATGCATAGATTAAAA
* * * * * *
29262006 CTTGTTAGTCATAAAA-AGCTTTAAACTCGAGAATAAAAATTCAAATGTTCAATTTCCTCGAAAA
66 TTTGTAAGTCGTAAAACA-CTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCTCAAAAA
* * * * *
29262070 TTATGTTTATTTGATATAATTGTCTTGTTAAGTTAAAACTCACTCATTTATGTTAATATTTTGAC
130 TTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGAC
* * * *
29262135 AATG-TTGGTTCCATCTTTATAATGTTTTACATTAATCCTTGCCA-CTTTATGTCAAGG-
195 AATGCTT-GTTCCACCTTTATAATGTTTTACATTAATTCTT-ACAGCTTTACGTCAAGGT
*
29262192 TTTTCAACTACTAAATTTCACCATAATTCTTGTTATCCTTACTATTATTCATGCATAGATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCATGCATAGATTAAAA
* *
29262257 TTTGTAAG-CTGTAAAAGACTTTAAACTTGAGAATAAAAATTTAAATGTTTAATTTTCC-CAAAA
66 TTTGTAAGTC-GTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAA-TTTCCTCAAAA
* * * * * *
29262320 ATTATGTTTATTTGACCTAATTGATTTGTTATGTGAAATCTCACACATTTATGTCAATATTTTGT
129 ATTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGA
* * * * * *
29262385 CAATGGTTGTTCCCCCTTTATAACGTTTTACGTTAATTCTTAC-GTTTTTATGTCAAGGT
194 CAATGCTTGTTCCACCTTTATAATGTTTTACATTAATTCTTACAG-CTTTACGTCAAGGT
* * * *
29262444 TTTTCAACTATTAAATTTCACCATGATTCTTTTTA-CCTTTACTATTATTTATGTATAGATTAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCC-TTACTATTATTCATGCATAGATTAAA
* * * * *
29262508 ATTTGTCAA-TCATAAAACACTTTAAACTTGAGAATAACAATTTAAATTTTTAATTTCCTCGAAA
65 ATTTGT-AAGTCGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCTCAAAA
* * * *
29262572 ATTATGTTTATTTAACATAATTGACTTGTTACATTAAATGTCACACATTTATATTAATATTTTGA
129 ATTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGA
* * * * * ****
29262637 AAATGCTTGTTCCACCTTTGTAATGTTTTATATTAATTCTTATAGCCTTACGTCATTAC
194 CAATGCTTGTTCCACCTTTATAATGTTTTACATTAATTCTTACAGCTTTACGTCAAGGT
* * ** * *
29262696 TTTTCAACTGCTAATTTTTGCCATAATTCTTTGTATCCTTACTATTATTC-TCACATAGATT-AA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCAT-GCATAGATTAAA
* * *
29262759 ATTTGAAAGTCGTAAAACACTTTGAACTTGAGAATAAAAATTTAAATGTTTAATTAT-CTCAAAA
65 ATTTGTAAGTCGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATT-TCCTCAAAA
* * * * * * *
29262823 ATTATATTTATTTGACATAATTGACCTATTATGTTAAATCTCACGCATTTATGTCAATATTTTGT
129 ATTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGA
* * ** * * * *
29262888 TAAT-CTTTGTTCCACCTTTATAATGTTGTACGCTAATTCTCACTGTTTTACGTGAAGGT
194 CAATGC-TTGTTCCACCTTTATAATGTTTTACATTAATTCTTACAGCTTTACGTCAAGGT
* * **
29262947 TTTTCAACTACT-AATTAAT-ACTATAATT-ATTTTATCCTTA-TAATTATTCATTTATAGATTA
1 TTTTCAACTACTAAATT--TCACCATAATTCTTTTTATCCTTACT-ATTATTCATGCATAGATTA
* * *
29263008 AAATTTGTAAGTCGTAAAACACTTTAAACTTGAAAATAAAATTTTAAATGTTTAATTTCCTCAAA
63 AAATTTGTAAGTCGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCTCAAA
* * * *
29263073 AATTATGTTTATTTTACATAATTGACTTGTTACGTTAAATCTGACATATTTAAGTTAATATTTTG
128 AATTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTG
** ** * * *
29263138 TTAATTTTTGTTTCACTTTTATAATGTTTTAAATTAATTCTTAC
193 ACAATGCTTGTTCCACCTTTATAATGTTTTACATTAATTCTTAC
29263182 GATATTACAT
Statistics
Matches: 1897, Mismatches: 314, Indels: 73
0.83 0.14 0.03
Matches are distributed among these distances:
249 1 0.00
250 247 0.13
251 757 0.40
252 658 0.35
253 234 0.12
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (252 bp):
TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCATGCATAGATTAAAA
TTTGTAAGTCGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCTCAAAAAT
TATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTTAATATTTTGACA
ATGCTTGTTCCACCTTTATAATGTTTTACATTAATTCTTACAGCTTTACGTCAAGGT
Found at i:29262417 original size:754 final size:752
Alignment explanation
Indices: 29260683--29263201 Score: 2914
Period size: 754 Copynumber: 3.3 Consensus size: 752
29260673 ACTTCATGAC
* * * * * **
29260683 TTTTCAACCAATAATTTTCATCATAATTCTTTTTATCCTTTCTATTATTCACAAATAAATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCACGCATAAATTAAAA
* * * * ****
29260748 TTTGTCAGTTGTAAAATACTTTAAACTCGAGAA-AAAAACTTTAAATGTTTTATTTTTTTGAAAA
66 TTTGTAAGCTGTAAAACACTTTAAACTCGAGAATAAAAA-TTTAAATG-TTTAATTTCCCAAAAA
* * * **
29260812 TTATGTTTATTTGACATAATTGACTTGTTACATTAAATCTCATACATTTACGTCAATATTTTAAC
129 TTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTCAATATTTTGTC
* * * * *
29260877 ATTGCTTCTTCCACCTTTATAATGTTTTAC-TTGAATTCTTATC-ACTTTACGTCAAGGGTTTTC
194 AATGCTTGTTCCACCTTTATAATGTTTTACGTT-AATTCTTA-CGATTTTACATCAAGGTTTTTC
* * * * * *
29260940 -ACTTACTAAATTTCAACACAATTCTTTATATCCTTACCATTATTCTTGCATAGATTAAAATTTG
257 AAC-TACTAAATTTCACCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTG
* * * *
29261004 TTAGTCGTAAAACACTTTAAACTCAAAAATAAAAATTTAAATATTTAATTTTTTCAAAAATTATG
321 TCAGTCGTAAAACACTTTAAACTTAAGAAT-AAAATTTAAATATTTAATTTTCTCAAAAATTATG
*
29261069 TTTATTTGACATAATTGACTTATTACGTTAAATCTCACACATTTATGTTAATATTTTGATAATGC
385 TTTATTTGACATAATTGACTTATTACGTTAAATCTCACACATTTATGTTAATATTTTGAAAATGC
* * * * * **
29261134 TTCTT-TCATCGTTATAATGTTTTATATTAATTCTTACCA-CTTTACGTCAAGGTTTTTCAACTA
450 TTGTTCT-ACCTTTATAATGTTTTATATTAATTCTTA-CAGCCTTACGTCATGACTTTTCAACTA
* * *
29261197 CTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTAATGCATAGATTAAAATTTGTAAGTT
513 CTAATTTTCACCATAATTCTTTATATCCTTACTATTATTCATGCATAGATTAAAATTTGTAAG-T
** * * * *
29261262 GTTAAACACTTTAAACTCGAGAACAAAAATTTAAATGTTTAACTTTTTTCAAAAATTATGTTTGT
577 CATAAAAACTTTAAACTCGAGAATAAAAATTTAAATGTTTAA--TTTCTCAAAAATTATGTTTAT
*
29261327 TTGACATAATTGACTTGTTAAGTTAAATCTCA-TACATTTACGTTAATATTTTGACAATGTTTGT
640 TTGACATAATTGACTTGTTAAGTTAAATCTCACT-CATTTATGTTAATATTTTGACAATGTTTGT
* *
29261391 TCCATCTTGATAATGTTTTACGCTAATTCTTATAATTTTACGTCAAGGT
704 TCCATCTTTATAATGTTTTACGCTAATTCTTACAATTTTACGTCAAGGT
* * * * * *
29261440 TTTTTAACTAGTAAATTTGACCGTAATTTTTTTTATCCTTACTATGATTCACGCATAAATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCACGCATAAATTAAAA
* ** * * * * *
29261505 TTTGTCAGCCATAAAACACTTTAAACTCAAGAATAAAGATTTAAATGTTTAATTTCCTACACATT
66 TTTGTAAGCTGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCCAAAAATT
* * * * *
29261570 ATATTTATTTGACATAATTGACTTTTTAAGTTTAATCTCACATATTTATGTCAATATTTTGAT-A
131 ATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTCAATATTTTG-TCA
* * *
29261634 ATGCTTATTCCATCTTTATAATG-TTTACGTTAATTCTTACAATTTTACATCAAGGTTTTTCAAC
195 ATGCTTGTTCCACCTTTATAATGTTTTACGTTAATTCTTACGATTTTACATCAAGGTTTTTCAAC
* * **
29261698 TAGTAAATTTCACCATAATTCTTTTTATCTTTACTATGATTCACACATAGATTAAAATTTGTCAG
260 TACTAAATTTCACCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTCAG
* * * * * * *
29261763 CCGTAGAACACTTTAAACTTTAGAATAAAGATTTAAATGTTTAATTTTCTAAAAAATTATG-CTG
325 TCGTAAAACACTTTAAACTTAAGAATAAA-ATTTAAATATTTAATTTTCTCAAAAATTATGTTTA
* * * * **
29261827 TTTGACATAATTGACTTTTTATGTTAAATCTTACATATTTATGTTAATATTTTGACCATGCTTGT
389 TTTGACATAATTGACTTATTACGTTAAATCTCACACATTTATGTTAATATTTTGAAAATGCTTGT
* *
29261892 TCTACCTTTATAATGTTTTACATTAATTCTTACAGCCTTACGTCATGACTTTTCAACTATTAATT
454 TCTACCTTTATAATGTTTTATATTAATTCTTACAGCCTTACGTCATGACTTTTCAACTACTAATT
* * * *
29261957 TTCATCGTAATTCTTTATATCCTTACTATTATTCATGCATAGATTAAAACTTGTTAGTCATAAAA
519 TTCACCATAATTCTTTATATCCTTACTATTATTCATGCATAGATTAAAATTTGTAAGTCATAAAA
* * * *
29262022 AGCTTTAAACTCGAGAATAAAAATTCAAATGTTCAATTTCCTCGAAAATTATGTTTATTTGATAT
584 A-CTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTT-CTCAAAAATTATGTTTATTTGACAT
* * *
29262087 AATTGTCTTGTTAAGTTAAAACTCACTCATTTATGTTAATATTTTGACAATGTTGGTTCCATCTT
647 AATTGACTTGTTAAGTTAAATCTCACTCATTTATGTTAATATTTTGACAATGTTTGTTCCATCTT
** * * * * *
29262152 TATAATGTTTTACATTAATCCTTGCCACTTTATGTCAAGG-
712 TATAATGTTTTACGCTAATTCTTACAATTTTACGTCAAGGT
* * *
29262192 TTTTCAACTACTAAATTTCACCATAATTCTTGTTATCCTTACTATTATTCATGCATAGATTAAAA
1 TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCACGCATAAATTAAAA
* *
29262257 TTTGTAAGCTGTAAAAGACTTTAAACTTGAGAATAAAAATTTAAATGTTTAATTTTCCCAAAAAT
66 TTTGTAAGCTGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAA-TTTCCCAAAAAT
* * * *
29262322 TATGTTTATTTGACCTAATTGATTTGTTATGTGAAATCTCACACATTTATGTCAATATTTTGTCA
130 TATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTCAATATTTTGTCA
* * * * **
29262387 ATGGTTGTTCCCCCTTTATAACGTTTTACGTTAATTCTTACGTTTTTATGTCAAGGTTTTTCAAC
195 ATGCTTGTTCCACCTTTATAATGTTTTACGTTAATTCTTACGATTTTACATCAAGGTTTTTCAAC
* * * * * *
29262452 TATTAAATTTCACCATGATTCTTTTTACCTTTACTATTATTTATGTATAGATTAAAATTTGTCAA
260 TACTAAATTTCACCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTCAG
* * * * *
29262517 TCATAAAACACTTTAAACTTGAGAATAACAATTTAAATTTTTAATTTCCTCGAAAATTATGTTTA
325 TCGTAAAACACTTTAAACTTAAGAATAA-AATTTAAATATTTAATTTTCTCAAAAATTATGTTTA
* * * * *
29262582 TTTAACATAATTGACTTGTTACATTAAATGTCACACATTTATATTAATATTTTGAAAATGCTTGT
389 TTTGACATAATTGACTTATTACGTTAAATCTCACACATTTATGTTAATATTTTGAAAATGCTTGT
* * * * *
29262647 TCCACCTTTGTAATGTTTTATATTAATTCTTATAGCCTTACGTCATTACTTTTCAACTGCTAATT
454 TCTACCTTTATAATGTTTTATATTAATTCTTACAGCCTTACGTCATGACTTTTCAACTACTAATT
** * * * *
29262712 TTTGCCATAATTCTTTGTATCCTTACTATTATTC-TCACATAGATT-AAATTTGAAAGTCGTAAA
519 TTCACCATAATTCTTTATATCCTTACTATTATTCAT-GCATAGATTAAAATTTGTAAGTCATAAA
* * *
29262775 ACACTTTGAACTTGAGAATAAAAATTTAAATGTTTAATTATCTCAAAAATTATATTTATTTGACA
583 A-ACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATT-TCTCAAAAATTATGTTTATTTGACA
* * * * * ** * *
29262840 TAATTGACCTATTATGTTAAATCTCACGCATTTATGTCAATATTTTGTTAATCTTTGTTCCACCT
646 TAATTGACTTGTTAAGTTAAATCTCACTCATTTATGTTAATATTTTGACAATGTTTGTTCCATCT
* * ** *
29262905 TTATAATGTTGTACGCTAATTCTCACTGTTTTACGTGAAGGT
711 TTATAATGTTTTACGCTAATTCTTACAATTTTACGTCAAGGT
* * *** *
29262947 TTTTCAACTACT-AATTAAT-ACTATAATT-ATTTTATCCTTA-TAATTATTCATTTATAGATTA
1 TTTTCAACTACTAAATT--TCACCATAATTCTTTTTATCCTTACT-ATTATTCACGCATAAATTA
* * *
29263008 AAATTTGTAAG-TCGTAAAACACTTTAAACTTGAAAATAAAATTTTAAATGTTTAATTTCCTCAA
63 AAATTTGTAAGCT-GTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCC-CAA
* * * * *
29263072 AAATTATGTTTATTTTACATAATTGACTTGTTACGTTAAATCTGACATATTTAAGTTAATATTTT
126 AAATTATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTCAATATTTT
* ** * * ** * *
29263137 GTTAATTTTTGTTTCACTTTTATAATGTTTTAAATTAATTCTTACGATATTACATCAAAGTTTTT
191 GTCAATGCTTGTTCCACCTTTATAATGTTTTACGTTAATTCTTACGATTTTACATCAAGGTTTTT
29263202 AAATGTTCAA
Statistics
Matches: 1488, Mismatches: 249, Indels: 53
0.83 0.14 0.03
Matches are distributed among these distances:
752 105 0.07
753 208 0.14
754 684 0.46
755 308 0.21
756 90 0.06
757 89 0.06
758 4 0.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.45
Consensus pattern (752 bp):
TTTTCAACTACTAAATTTCACCATAATTCTTTTTATCCTTACTATTATTCACGCATAAATTAAAA
TTTGTAAGCTGTAAAACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCCCAAAAATT
ATGTTTATTTGACATAATTGACTTGTTACGTTAAATCTCACACATTTATGTCAATATTTTGTCAA
TGCTTGTTCCACCTTTATAATGTTTTACGTTAATTCTTACGATTTTACATCAAGGTTTTTCAACT
ACTAAATTTCACCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTCAGT
CGTAAAACACTTTAAACTTAAGAATAAAATTTAAATATTTAATTTTCTCAAAAATTATGTTTATT
TGACATAATTGACTTATTACGTTAAATCTCACACATTTATGTTAATATTTTGAAAATGCTTGTTC
TACCTTTATAATGTTTTATATTAATTCTTACAGCCTTACGTCATGACTTTTCAACTACTAATTTT
CACCATAATTCTTTATATCCTTACTATTATTCATGCATAGATTAAAATTTGTAAGTCATAAAAAC
TTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTCTCAAAAATTATGTTTATTTGACATAATT
GACTTGTTAAGTTAAATCTCACTCATTTATGTTAATATTTTGACAATGTTTGTTCCATCTTTATA
ATGTTTTACGCTAATTCTTACAATTTTACGTCAAGGT
Found at i:29282576 original size:18 final size:17
Alignment explanation
Indices: 29282549--29282583 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
29282539 TTGTGGCCAC
29282549 CATCAATTTCATATCAT
1 CATCAATTTCATATCAT
29282566 CATCTAATTTCATATCAT
1 CATC-AATTTCATATCAT
29282584 TAAGTGTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (17 bp):
CATCAATTTCATATCAT
Found at i:29292675 original size:91 final size:92
Alignment explanation
Indices: 29292513--29292890 Score: 376
Period size: 91 Copynumber: 4.0 Consensus size: 92
29292503 CAACGATAAC
* * **
29292513 CTCATACTCC-ATTTGTTTCTTTTTTACTTTCAGCTTTTGATTATTTTTATCATACTATAATAAT
1 CTCATACTCCTA-TTG-TTCTCTTTT-CTTTTAGCTTTTGA-T-TTTTTATCATACTCCAATAAT
29292577 C-CTTTCAA-TCTTTCAATTTCACACTTCAAACT
61 CTC-TTCAACT-TTTCAATTTCACACTTCAAACT
* *
29292609 CTCATACTCCTATTGCTTCTCTTCTTCTTTTAGC-TTT-A-TTTTTATCATGCTGCAATAATCTC
1 CTCATACTCCTATTG-TTCTCTT-TTCTTTTAGCTTTTGATTTTTTATCATACTCCAATAATCTC
*
29292671 TTCAACTTTTCTATTTCACACTTCAAACT
64 TTCAACTTTTCAATTTCACACTTCAAACT
* * * *
29292700 CTCATACTCCCATTGTTTCTCCTTTTCTTTTAACTTTTGATTATTTTATCATAATCCAATAATTT
1 CTCATACTCCTATTG-TTCT-CTTTTCTTTTAGCTTTTGATT-TTTTATCATACTCCAATAATCT
* * * *
29292765 CTTTAACTTTTCAATTTTACACTTGAAGCT
63 CTTCAACTTTTCAATTTCACACTTCAAACT
* * * *
29292795 CTCATACTCTTGTTGTT-TCTTTTTTTTTCAGCTTTTGATTGTTTTTATCATACTCCAGTAAT-T
1 CTCATACTCCTATTGTTCTCTTTTCTTTT-AGCTTTTGA-T-TTTTTATCATACTCCAATAATCT
*
29292858 CCTTCAACTTTTCAATTTTACACTTCAAACT
63 -CTTCAACTTTTCAATTTCACACTTCAAACT
29292889 CT
1 CT
29292891 TAATTTCACT
Statistics
Matches: 240, Mismatches: 29, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
91 72 0.30
92 17 0.07
93 11 0.05
94 52 0.22
95 59 0.25
96 26 0.11
97 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.04, T:0.50
Consensus pattern (92 bp):
CTCATACTCCTATTGTTCTCTTTTCTTTTAGCTTTTGATTTTTTATCATACTCCAATAATCTCTT
CAACTTTTCAATTTCACACTTCAAACT
Found at i:29297516 original size:61 final size:61
Alignment explanation
Indices: 29297353--29297516 Score: 256
Period size: 61 Copynumber: 2.7 Consensus size: 61
29297343 AGCTGATGTG
* * * *
29297353 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACAATTATAAATATCATGATAG
1 CATCATTATCGGCATGTGCACTGCCCACTCCGCACATGCACGATTATAAATATCATGACAA
* **
29297414 CATCATTATTGATATGTGCACTGCCCACTCCGCACATGCACGATTATAAATATCATGACAA
1 CATCATTATCGGCATGTGCACTGCCCACTCCGCACATGCACGATTATAAATATCATGACAA
*
29297475 CATCATTATCGGCATGTGCACTGTCCACTCCGCACATGCACG
1 CATCATTATCGGCATGTGCACTGCCCACTCCGCACATGCACG
29297517 GTTGGGCTCC
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 92 1.00
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (61 bp):
CATCATTATCGGCATGTGCACTGCCCACTCCGCACATGCACGATTATAAATATCATGACAA
Found at i:29313622 original size:15 final size:15
Alignment explanation
Indices: 29313602--29313642 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
29313592 TTCTTAAAAC
29313602 AACTTTAAAA-CCAAA
1 AACTTTAAAATCC-AA
29313617 AACTTTAAAATCCAA
1 AACTTTAAAATCCAA
*
29313632 AGCTTTAAAAT
1 AACTTTAAAAT
29313643 GAAAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (15 bp):
AACTTTAAAATCCAA
Found at i:29316254 original size:19 final size:19
Alignment explanation
Indices: 29316230--29316267 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29316220 CTACCAAACC
* *
29316230 CTCAAATTATACTCTAATA
1 CTCAAATCATACTCCAATA
29316249 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
29316268 AGTTAAATGG
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:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:29323491 original size:3 final size:3
Alignment explanation
Indices: 29323483--29323512 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
29323473 TACGAAGAGC
*
29323483 AAG AAG AAG AAG AAG AAG AGG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
29323513 TGGAGGAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29334496 original size:13 final size:13
Alignment explanation
Indices: 29334478--29334502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29334468 TTTGTAATGG
29334478 TCTATTTGTTGTA
1 TCTATTTGTTGTA
29334491 TCTATTTGTTGT
1 TCTATTTGTTGT
29334503 TCTCTCAATT
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:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (13 bp):
TCTATTTGTTGTA
Found at i:29343953 original size:71 final size:71
Alignment explanation
Indices: 29343829--29343990 Score: 216
Period size: 71 Copynumber: 2.3 Consensus size: 71
29343819 CTTGAAGTAT
* * * * * * *
29343829 ACAAAGCCATAATCGACTCTAGATTGGTTATAGTCGACCCCAAAGTAGGAAGCTCGAAAATTTGG
1 ACAAAACCATAGTCGACCCTAAAGTGGTTATAGTCGACCCCAAAGCAGAAAGCTCGAAAATTTGG
29343894 AGAACA
66 AGAACA
* * *
29343900 ACAAAACCATAGTCGACCCTAAAGTGGTTATATTCGACCCTAAAGCAGAAAGCTTGAAAATTTGG
1 ACAAAACCATAGTCGACCCTAAAGTGGTTATAGTCGACCCCAAAGCAGAAAGCTCGAAAATTTGG
29343965 AGAACA
66 AGAACA
* *
29343971 ATACAACCATAGTCGACCCT
1 ACAAAACCATAGTCGACCCT
29343991 GGAATAGTAG
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 79 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (71 bp):
ACAAAACCATAGTCGACCCTAAAGTGGTTATAGTCGACCCCAAAGCAGAAAGCTCGAAAATTTGG
AGAACA
Found at i:29344641 original size:34 final size:34
Alignment explanation
Indices: 29344597--29344744 Score: 183
Period size: 34 Copynumber: 4.3 Consensus size: 34
29344587 ATTATTGAAA
*
29344597 GGTTTTGCTTGATTTCGTGAAAAAGCATTGTAAG
1 GGTTTTGCTTGATCTCGTGAAAAAGCATTGTAAG
* **
29344631 GGTTTCGCTTGATCAAGTGAAAAAGCATTGTAAG
1 GGTTTTGCTTGATCTCGTGAAAAAGCATTGTAAG
* *
29344665 GGTTTCGCTTGATC-CAGTGAAAAAGCTATTGTTAG
1 GGTTTTGCTTGATCTC-GTGAAAAAGC-ATTGTAAG
* *
29344700 GATTTTGCTTGATCTCGT-AAAAAGCCATTGTGAG
1 GGTTTTGCTTGATCTCGTGAAAAAG-CATTGTAAG
29344734 GGTTTTGCTTG
1 GGTTTTGCTTG
29344745 GACCCATAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
34 77 0.77
35 22 0.22
36 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (34 bp):
GGTTTTGCTTGATCTCGTGAAAAAGCATTGTAAG
Found at i:29344736 original size:69 final size:68
Alignment explanation
Indices: 29344613--29344744 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 68
29344603 GCTTGATTTC
*
29344613 GTGAAAAAGCATTGTAAGGGTTTCGCTTGATCAAGTGAAAAAGCATTGTAAGGGTTTCGCTTGAT
1 GTGAAAAAGCATTGTAAGGATTTCGCTTGATCAAGTGAAAAAGCATTGTAAGGGTTTCGCTTGAT
29344678 CCA
66 CCA
* * ** * *
29344681 GTGAAAAAGCTATTGTTAGGATTTTGCTTGATCTCGT-AAAAAGCCATTGTGAGGGTTTTGCTTG
1 GTGAAAAAGC-ATTGTAAGGATTTCGCTTGATCAAGTGAAAAAG-CATTGTAAGGGTTTCGCTTG
29344745 GACCCATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
68 16 0.29
69 39 0.71
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (68 bp):
GTGAAAAAGCATTGTAAGGATTTCGCTTGATCAAGTGAAAAAGCATTGTAAGGGTTTCGCTTGAT
CCA
Found at i:29354330 original size:22 final size:23
Alignment explanation
Indices: 29354302--29354389 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 23
29354292 TGGTCGAAAC
*
29354302 TCGCTGCAGCGAGGATG-CATTT
1 TCGCTGCAGCGAGAATGACATTT
*
29354324 TCGCTGCATCGAGAATGACATTGTAGCT
1 TCGCTGCAGCGAGAATGACA-T-T---T
*
29354352 TCTTGCTGCAGCGA-AATG-CATTC
1 TC--GCTGCAGCGAGAATGACATTT
29354375 TCGCTGCAGCGAGAA
1 TCGCTGCAGCGAGAA
29354390 ACTTTTTGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
21 10 0.19
22 17 0.32
23 4 0.08
24 1 0.02
25 1 0.02
26 1 0.02
27 1 0.02
28 5 0.09
29 4 0.08
30 9 0.17
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (23 bp):
TCGCTGCAGCGAGAATGACATTT
Found at i:29357957 original size:24 final size:26
Alignment explanation
Indices: 29357913--29357961 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 26
29357903 TCGGCCGAAC
29357913 TTCCTTCTCTCTTTTTCTTTCCTTTG
1 TTCCTTCTCTCTTTTTCTTTCCTTTG
29357939 TTCCTTCT-TCTTTTT-TTTCCTTT
1 TTCCTTCTCTCTTTTTCTTTCCTTT
29357962 CTTTTCTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.35
25 7 0.30
26 8 0.35
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (26 bp):
TTCCTTCTCTCTTTTTCTTTCCTTTG
Found at i:29358295 original size:3 final size:3
Alignment explanation
Indices: 29358282--29358312 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
29358272 AATTTTTTTA
29358282 ATT ATT CATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
29358313 TATCTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:29361080 original size:2 final size:2
Alignment explanation
Indices: 29361073--29361112 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
29361063 TGTTATGTTG
* *
29361073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29361113 GTATGATATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29361374 original size:2 final size:2
Alignment explanation
Indices: 29361367--29361397 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29361357 GTTATGTATG
29361367 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
29361398 TTATGCAATA
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:29361803 original size:19 final size:19
Alignment explanation
Indices: 29361779--29361815 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29361769 GGGGTTTTAG
29361779 TGAGAAACCCTCGGCCAGC
1 TGAGAAACCCTCGGCCAGC
*
29361798 TGAGAAACCCTTGGCCAG
1 TGAGAAACCCTCGGCCAG
29361816 TTGATAATTT
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:0.27, C:0.32, G:0.27, T:0.14
Consensus pattern (19 bp):
TGAGAAACCCTCGGCCAGC
Found at i:29362666 original size:20 final size:20
Alignment explanation
Indices: 29362638--29362679 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29362628 TTAGGTTACC
29362638 TTTAAGTTAGTTATTTTAAT
1 TTTAAGTTAGTTATTTTAAT
* * *
29362658 TTTATGTTATTTCTTTTAAT
1 TTTAAGTTAGTTATTTTAAT
29362678 TT
1 TT
29362680 GTTTATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTAAGTTAGTTATTTTAAT
Found at i:29369515 original size:16 final size:16
Alignment explanation
Indices: 29369488--29369532 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
29369478 GTTTTGGTTT
29369488 ATTTTA-TTTTATTTC
1 ATTTTATTTTTATTTC
*
29369503 ATTTTATTTTTATTTT
1 ATTTTATTTTTATTTC
29369519 ATTTTATTTTTATT
1 ATTTTATTTTTATT
29369533 ATTTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 6 0.21
16 22 0.79
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTTATTTTTATTTC
Found at i:29369536 original size:9 final size:9
Alignment explanation
Indices: 29369486--29369602 Score: 117
Period size: 9 Copynumber: 13.9 Consensus size: 9
29369476 CAGTTTTGGT
29369486 TTATT-TTA
1 TTATTATTA
29369494 TT-TTATT-
1 TTATTATTA
*
29369501 TCATT-TTA
1 TTATTATTA
*
29369509 TTTTTATT-
1 TTATTATTA
29369517 TTATT-TTA
1 TTATTATTA
*
29369525 TTTTTATTA
1 TTATTATTA
*
29369534 TTTTTATTA
1 TTATTATTA
29369543 TT-TT-TTA
1 TTATTATTA
*
29369550 CT-TTATTA
1 TTATTATTA
29369558 TTATTATTA
1 TTATTATTA
29369567 TTATTATTA
1 TTATTATTA
29369576 TTATTATTA
1 TTATTATTA
29369585 TTATTATTA
1 TTATTATTA
29369594 TTATCTATT
1 TTAT-TATT
29369603 CTTTTCCCTT
Statistics
Matches: 93, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
7 13 0.14
8 23 0.25
9 53 0.57
10 4 0.04
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.73
Consensus pattern (9 bp):
TTATTATTA
Found at i:29369596 original size:6 final size:6
Alignment explanation
Indices: 29369486--29369602 Score: 117
Period size: 6 Copynumber: 20.8 Consensus size: 6
29369476 CAGTTTTGGT
* * *
29369486 TTATT- TTATT- TTATT- TCATT- TTATTT TTATT- TTATT- TTATTT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* *
29369528 TTATTA TTTTTA TTATT- TT-TTA CT-TTA TTATTA TTATTA TTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
29369573 TTATTA TTATTA TTATTA TTATTA TCTATT
1 TTATTA TTATTA TTATTA TTATTA T-TATT
29369603 CTTTTCCCTT
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
4 2 0.02
5 35 0.35
6 59 0.59
7 4 0.04
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.73
Consensus pattern (6 bp):
TTATTA
Found at i:29369841 original size:37 final size:37
Alignment explanation
Indices: 29369731--29369831 Score: 202
Period size: 37 Copynumber: 2.7 Consensus size: 37
29369721 GTTTAGAATT
29369731 TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
1 TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
29369768 TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
1 TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
29369805 TTGTTAGTTTATTTACATGTTTTATTT
1 TTGTTAGTTTATTTACATGTTTTATTT
29369832 ATATTTTGCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.19, C:0.05, G:0.15, T:0.61
Consensus pattern (37 bp):
TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
Found at i:29371132 original size:20 final size:20
Alignment explanation
Indices: 29371103--29371146 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
29371093 ATTAGGTTAC
29371103 TTTTAAGTTAGTTATTTTAA
1 TTTTAAGTTAGTTATTTTAA
* * *
29371123 TTTTATGTTATTTCTTTTAA
1 TTTTAAGTTAGTTATTTTAA
29371143 TTTT
1 TTTT
29371147 TTTTTTATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTAAGTTAGTTATTTTAA
Found at i:29388408 original size:13 final size:13
Alignment explanation
Indices: 29388390--29388414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29388380 GGAGAAATTG
29388390 TGATTTTATAAAA
1 TGATTTTATAAAA
29388403 TGATTTTATAAA
1 TGATTTTATAAA
29388415 TTTTTTGAAA
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:29396887 original size:29 final size:28
Alignment explanation
Indices: 29396842--29397013 Score: 166
Period size: 29 Copynumber: 5.9 Consensus size: 28
29396832 GGCAACTTTG
*
29396842 ACATGTTTATCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
*
29396870 ACATGTTTGGTCTTAATTTAGATAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* *
29396899 ATATGTTTTTCTTAATTTAAGACAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAA
* * *
29396928 ATTAT-TTTGTCTTAATTTAGTCAAAAAA
1 A-CATGTTTGTCTTAATTTAGACAAGAAA
* *
29396956 ACATATTTGTCTCAATTTAGACAAGATAAA
1 ACATGTTTGTCTTAATTTAGACAAG--AAA
* * *
29396986 ATATTTTTTGTCTTAATTACAGACAAGA
1 ACA-TGTTTGTCTTAATT-TAGACAAGA
29397014 GTTGTCTTAA
Statistics
Matches: 120, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.02
28 43 0.36
29 47 0.39
30 9 0.08
31 12 0.10
32 7 0.06
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:29396940 original size:57 final size:56
Alignment explanation
Indices: 29396842--29397003 Score: 175
Period size: 57 Copynumber: 2.8 Consensus size: 56
29396832 GGCAACTTTG
* *
29396842 ACATGTTTATCTTAATTTAGACAAGAAAA-CATGTTTGGTCTTAATTTAGAT-AAGAAA
1 ACATGTTTATCTTAATTTAGACAAGAAAATTAT-TTT-GTCTTAATTTAG-TCAAAAAA
* *
29396899 ATATGTTTTTCTTAATTTAAGACAAGAAAATTATTTTGTCTTAATTTAGTCAAAAAA
1 ACATGTTTATCTTAATTT-AGACAAGAAAATTATTTTGTCTTAATTTAGTCAAAAAA
* * * *
29396956 ACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTTGTCTTAATT
1 ACATGTTTATCTTAATTTAGACAAG--AAAAT-TATTTTGTCTTAATT
29397004 ACAGACAAGA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
56 8 0.09
57 47 0.52
58 19 0.21
59 16 0.18
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (56 bp):
ACATGTTTATCTTAATTTAGACAAGAAAATTATTTTGTCTTAATTTAGTCAAAAAA
Found at i:29397177 original size:17 final size:17
Alignment explanation
Indices: 29397155--29397187 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29397145 ATAATAATAA
29397155 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
29397172 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
29397188 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:29398413 original size:39 final size:38
Alignment explanation
Indices: 29398344--29398425 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 38
29398334 TGCTGCCGGG
* * *
29398344 CAGCACACAACCCTTGTTATGTGCCGTTCGACAGCACA
1 CAGCACACAACCATTGCTATGTGCCATTCGACAGCACA
*
29398382 CAGCACACAACACATTGCTGTGTGCCATTCGACAGCACA
1 CAGCACACAAC-CATTGCTATGTGCCATTCGACAGCACA
29398421 CAGCA
1 CAGCA
29398426 GCAGTGTGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 11 0.28
39 28 0.72
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (38 bp):
CAGCACACAACCATTGCTATGTGCCATTCGACAGCACA
Found at i:29398433 original size:28 final size:28
Alignment explanation
Indices: 29398401--29398462 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
29398391 ACACATTGCT
29398401 GTGTGCCATTCGACAGCACACAGCAGCA
1 GTGTGCCATTCGACAGCACACAGCAGCA
* *
29398429 GTGTGCCGTTTGACAGCACACAGCAGCA
1 GTGTGCCATTCGACAGCACACAGCAGCA
*
29398457 ATGTGC
1 GTGTGC
29398463 TGCTGTCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.27, T:0.18
Consensus pattern (28 bp):
GTGTGCCATTCGACAGCACACAGCAGCA
Found at i:29409567 original size:22 final size:21
Alignment explanation
Indices: 29409516--29409567 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
29409506 AAAACCCTAG
*
29409516 GTGGAAAAATTCAAGGGAAAA
1 GTGGAAAAATTCAAGGAAAAA
29409537 GTGTG-AAAATTCAAGGAAACAA
1 GTG-GAAAAATTCAAGGAAA-AA
29409559 GTGGAAAAA
1 GTGGAAAAA
29409568 GGTAAGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.52, C:0.06, G:0.27, T:0.15
Consensus pattern (21 bp):
GTGGAAAAATTCAAGGAAAAA
Found at i:29410928 original size:19 final size:20
Alignment explanation
Indices: 29410904--29410942 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29410894 CCTATAAATA
29410904 TCTTG-AATTTCCAGCAGCT
1 TCTTGAAATTTCCAGCAGCT
*
29410923 TCTTGAAATTTTCAGCAGCT
1 TCTTGAAATTTCCAGCAGCT
29410943 AGTCTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (20 bp):
TCTTGAAATTTCCAGCAGCT
Done.