Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 22 of 54
Found at i:9642189 original size:162 final size:162
Alignment explanation
Indices: 9641897--9642241 Score: 444
Period size: 162 Copynumber: 2.1 Consensus size: 162
9641887 CCCAGACCCC
* * * *
9641897 AGCTGCCGGCCTACCACGCCAAGCTCGTCAGCTGTCGACCTACCACGCCAAGCTCGGGTCCTTCA
1 AGCTGCCGGCCTACCACGCCAACCTCGTCAGCTGCCAACCTACCACGCCAAGCTCAGGTCCTTCA
* * * * * * *** *
9641962 TCGGTTGATCTATCTTTTCTCTCCAACCGGGCAGCCCCAACGATGCCATGCCGGTTGATTGGGTG
66 TCGGTTGATCTACCTTTTCTCTCCAACCAGCCAGCCACAACAAGGCCATGCCAACTGAGTGGGTG
9642027 TCGCCCCAAGC-CCGACGCCGTTGTTCTTCCCT
131 TCGCCCCAAGCTCC-ACGCCGTTGTTCTTCCCT
* *
9642059 AGCTGCCAGCCTACCACGCCAACCTCGTCAGCTGCCAACCTACCACTCCAAGCTCAGGTCCTTCA
1 AGCTGCCGGCCTACCACGCCAACCTCGTCAGCTGCCAACCTACCACGCCAAGCTCAGGTCCTTCA
* * * *
9642124 TCGGTTGATCTGCCTTTTCTCTCCAA-CAGCCTAGCCACAGTCAAGGTC-TGCCAACTGCGTGGG
66 TCGGTTGATCTACCTTTTCTCTCCAACCAGCC-AGCCACA-ACAAGGCCATGCCAACTGAGTGGG
* *
9642187 TGTCTCCCCAAGCTCCACGCCTTTGTTCTTCCCT
129 TGTCGCCCCAAGCTCCACGCCGTTGTTCTTCCCT
9642221 AGCTGCCGGCCTACCACGCCA
1 AGCTGCCGGCCTACCACGCCA
9642242 CGCTCGGCTC
Statistics
Matches: 157, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
161 3 0.02
162 148 0.94
163 6 0.04
ACGTcount: A:0.17, C:0.39, G:0.21, T:0.23
Consensus pattern (162 bp):
AGCTGCCGGCCTACCACGCCAACCTCGTCAGCTGCCAACCTACCACGCCAAGCTCAGGTCCTTCA
TCGGTTGATCTACCTTTTCTCTCCAACCAGCCAGCCACAACAAGGCCATGCCAACTGAGTGGGTG
TCGCCCCAAGCTCCACGCCGTTGTTCTTCCCT
Found at i:9642753 original size:35 final size:36
Alignment explanation
Indices: 9642698--9642777 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
9642688 ATGGTTCCCC
*
9642698 AGATATTTGTTTTTAGTTATTT-AATTTTAAGTTTA
1 AGATTTTTGTTTTTAGTTATTTAAATTTTAAGTTTA
*
9642733 AGATTTTTGTTTTT-GATTATTTAAATTTTAATTTTA
1 AGATTTTTGTTTTTAG-TTATTTAAATTTTAAGTTTA
*
9642769 ATATTTTTG
1 AGATTTTTG
9642778 GGGAAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
34 1 0.03
35 19 0.47
36 20 0.50
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (36 bp):
AGATTTTTGTTTTTAGTTATTTAAATTTTAAGTTTA
Found at i:9642954 original size:31 final size:31
Alignment explanation
Indices: 9642919--9642977 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
9642909 AATGTTTTTC
*
9642919 CGTTGGAAATAAAATTTGCAACGGAAAATTT
1 CGTTGGAAATAAAATTTCCAACGGAAAATTT
**
9642950 CGTTGGAAATAATTTTTCCAACGGAAAA
1 CGTTGGAAATAAAATTTCCAACGGAAAA
9642978 AATTTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (31 bp):
CGTTGGAAATAAAATTTCCAACGGAAAATTT
Found at i:9643961 original size:27 final size:27
Alignment explanation
Indices: 9643930--9644029 Score: 84
Period size: 27 Copynumber: 3.6 Consensus size: 27
9643920 ATCACTTCTC
9643930 ATTTTTATGTAATGAAAGATTAATTTA
1 ATTTTTATGTAATGAAAGATTAATTTA
*
9643957 ATTTTTA---AAGTGTACTAGTATTAATGATT-
1 ATTTTTATGTAA-TG-A-AAG-ATTAAT--TTA
*
9643986 -TTCTTTATCTAATGAAAGATTAATTTA
1 ATT-TTTATGTAATGAAAGATTAATTTA
9644013 ATTTTTATGTAATGAAA
1 ATTTTTATGTAATGAAA
9644030 AATCTTCTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 24
0.68 0.04 0.28
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
26 3 0.05
27 22 0.38
28 16 0.28
29 6 0.10
30 3 0.05
31 2 0.03
32 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (27 bp):
ATTTTTATGTAATGAAAGATTAATTTA
Found at i:9647640 original size:15 final size:15
Alignment explanation
Indices: 9647613--9647650 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
9647603 TTGAAATAAA
9647613 ACTTTCC-TTTTAAG
1 ACTTTCCATTTTAAG
*
9647627 ACTTTCCATTTTAAT
1 ACTTTCCATTTTAAG
*
9647642 TCTTTCCAT
1 ACTTTCCAT
9647651 AATTAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (15 bp):
ACTTTCCATTTTAAG
Found at i:9648023 original size:77 final size:78
Alignment explanation
Indices: 9647909--9648074 Score: 219
Period size: 77 Copynumber: 2.1 Consensus size: 78
9647899 TGAATTTCTT
* *
9647909 AAATTAAAATACTATCCTTAATTTTAGAGATTTCTTTTAAAGTAGGAAACAATTTCCTA-TGTTT
1 AAATTAAAATACTATCCTCAATTTTAGAGATTGCTTTTAAAGTAGGAAACAATTTCCTATTGTTT
*
9647973 TATGAATCACCTA
66 TATGAATCACCCA
** * * *
9647986 AAATTAAAATTGTATCCTCAATTTTAG-GAATTGCTTTTAAAGTAGGAAATAATTTTCTATTTTT
1 AAATTAAAATACTATCCTCAATTTTAGAG-ATTGCTTTTAAAGTAGGAAACAATTTCCTATTGTT
* *
9648050 TTATGTATTACCCA
65 TTATGAATCACCCA
9648064 AAATTAAAATA
1 AAATTAAAATA
9648075 GATGGTATTT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
76 1 0.01
77 51 0.67
78 24 0.32
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.42
Consensus pattern (78 bp):
AAATTAAAATACTATCCTCAATTTTAGAGATTGCTTTTAAAGTAGGAAACAATTTCCTATTGTTT
TATGAATCACCCA
Found at i:9651803 original size:19 final size:19
Alignment explanation
Indices: 9651779--9651816 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
9651769 CTGCCAAACC
*
9651779 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
9651798 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
9651817 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:9654457 original size:29 final size:31
Alignment explanation
Indices: 9654413--9654476 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
9654403 CAAAAGTTTT
*
9654413 AAAATTTTATAATTTT-TT-GTAATTTTTTAA
1 AAAATTTTATAATTTTGTTCCT-ATTTTTTAA
9654443 AAAATTTTAT-ATTTTGTTCCTATTTTTTAA
1 AAAATTTTATAATTTTGTTCCTATTTTTTAA
9654473 AAAA
1 AAAA
9654477 AAATTATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.16
30 25 0.81
31 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (31 bp):
AAAATTTTATAATTTTGTTCCTATTTTTTAA
Found at i:9654821 original size:5 final size:5
Alignment explanation
Indices: 9654811--9654856 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
9654801 TAGACACATA
* *
9654811 AAATT AAATT AAATT AAATC AAATT AAA-T AAA-T AAA-T AAAAT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAAT
9654857 AAAAAAAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
4 12 0.32
5 25 0.68
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (5 bp):
AAATT
Found at i:9655723 original size:15 final size:14
Alignment explanation
Indices: 9655698--9655732 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
9655688 AGCTTGCAAA
9655698 AAATAAAATAAATAAT
1 AAAT-AAATAAAT-AT
9655714 AAATAAATAAATAT
1 AAATAAATAAATAT
9655728 AAATA
1 AAATA
9655733 TACATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 8 0.42
16 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAATAAATAT
Found at i:9655804 original size:25 final size:26
Alignment explanation
Indices: 9655767--9655849 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 26
9655757 TTTGGATAAA
* *
9655767 AAAATTAATTAAATAAA-AAATATAT
1 AAAATAAAATAAATAAATAAATATAT
9655792 AAAATAAAATAAA-AAATAATGATAGTAAT
1 AAAATAAAATAAATAAATAA--ATA-T-AT
9655821 AAAATGAAAA-AAATAAATAAATAATAT
1 AAAAT-AAAATAAATAAATAAAT-ATAT
9655848 AA
1 AA
9655850 TTGGAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 3 0.06
25 13 0.27
27 7 0.15
28 4 0.08
29 11 0.23
30 10 0.21
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAATAAAATAAATAAATAAATATAT
Found at i:9671057 original size:3 final size:3
Alignment explanation
Indices: 9671049--9671083 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
9671039 TTTGTTGGGA
9671049 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
9671084 ATCAACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:9672664 original size:20 final size:20
Alignment explanation
Indices: 9672635--9672673 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9672625 ATGATTAAAT
9672635 TTGAAATT-AATTTATGTATG
1 TTGAAATTAAATTT-TGTATG
*
9672655 TTGAACTTAAATTTTGTAT
1 TTGAAATTAAATTTTGTAT
9672674 TGCATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (20 bp):
TTGAAATTAAATTTTGTATG
Found at i:9674112 original size:22 final size:22
Alignment explanation
Indices: 9674084--9674128 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
9674074 TAAAAATATT
* *
9674084 TTAAATATTTTTATCTTAATTA
1 TTAAATAATTTTATATTAATTA
*
9674106 TTAAATAATTTTCTATTAATTA
1 TTAAATAATTTTATATTAATTA
9674128 T
1 T
9674129 CTTAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAAATAATTTTATATTAATTA
Found at i:9693247 original size:2 final size:2
Alignment explanation
Indices: 9693240--9693290 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
9693230 CATCTCATAC
* * * * *
9693240 AT AT AT AT AC AT AT AT AT GT AT AT AT AC AT GT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9693282 AT AT AT AT A
1 AT AT AT AT A
9693291 CATGTATATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9693257 original size:12 final size:12
Alignment explanation
Indices: 9693250--9693299 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
9693240 ATATATATAC
*
9693250 ATATATATGTAT
1 ATATACATGTAT
*
9693262 ATATACATGTGT
1 ATATACATGTAT
* *
9693274 ATATATATATAT
1 ATATACATGTAT
9693286 ATATACATGTAT
1 ATATACATGTAT
9693298 AT
1 AT
9693300 GCTACATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (12 bp):
ATATACATGTAT
Found at i:9693286 original size:24 final size:24
Alignment explanation
Indices: 9693250--9693295 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
9693240 ATATATATAC
*
9693250 ATATATATGTATATATACATGTGT
1 ATATATATATATATATACATGTGT
9693274 ATATATATATATATATACATGT
1 ATATATATATATATATACATGT
9693296 ATATGCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (24 bp):
ATATATATATATATATACATGTGT
Found at i:9704565 original size:25 final size:25
Alignment explanation
Indices: 9704537--9704604 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
9704527 GCTAATAGAG
*
9704537 AGTGAAACAGGGGAAAAGGAAAGAA
1 AGTGAAATAGGGGAAAAGGAAAGAA
* *
9704562 AGTGAAATAGGCGAATAGGAAAGAA
1 AGTGAAATAGGGGAAAAGGAAAGAA
*
9704587 AGTGAAATAGGGAAAAAG
1 AGTGAAATAGGGGAAAAG
9704605 AACCTTTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.54, C:0.03, G:0.34, T:0.09
Consensus pattern (25 bp):
AGTGAAATAGGGGAAAAGGAAAGAA
Found at i:9710847 original size:15 final size:15
Alignment explanation
Indices: 9710813--9710849 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
9710803 AATTACTATT
9710813 ATATATATACTTTTA
1 ATATATATACTTTTA
*
9710828 GTATATATA-TTTTA
1 ATATATATACTTTTA
9710842 A-ATATATA
1 ATATATATA
9710850 AATATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 7 0.35
14 5 0.25
15 8 0.40
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (15 bp):
ATATATATACTTTTA
Found at i:9711100 original size:34 final size:34
Alignment explanation
Indices: 9711056--9711144 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 34
9711046 AAACTTGTAA
*
9711056 TGTTATTTAAGTTGT-TGTTT-AGATATTTGTTTT
1 TGTTATTTAAGTT-TATATTTGAGATATTTGTTTT
9711089 TAGTTATTTAAGTTTATATTTGAGATATTTGTTTT
1 T-GTTATTTAAGTTTATATTTGAGATATTTGTTTT
* *
9711124 TGATTATTTAAATTTAAATTT
1 TG-TTATTTAAGTTTATATTT
9711145 TATTGTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
33 2 0.04
34 17 0.35
35 30 0.61
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (34 bp):
TGTTATTTAAGTTTATATTTGAGATATTTGTTTT
Found at i:9711984 original size:25 final size:24
Alignment explanation
Indices: 9711948--9712003 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 24
9711938 TCTTGGATAA
*
9711948 AAAGTAAATAAAAAATATTTATAC
1 AAAGAAAATAAAAAATATTTATAC
*
9711972 AAAGAAAAGTAAAAAATATTTATAT
1 AAAGAAAA-TAAAAAATATTTATAC
9711997 AAAGAAA
1 AAAGAAA
9712004 TCAAATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (24 bp):
AAAGAAAATAAAAAATATTTATAC
Found at i:9712414 original size:23 final size:21
Alignment explanation
Indices: 9712372--9712416 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
9712362 TTCTTTCTTT
*
9712372 TCTTTATTGTTCTTTAAGTTA
1 TCTTTATTATTCTTTAAGTTA
9712393 TCTTTATTTATTCTTTTAAGTTA
1 TCTTTA-TTATTC-TTTAAGTTA
9712416 T
1 T
9712417 TTTTCATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 10 0.48
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (21 bp):
TCTTTATTATTCTTTAAGTTA
Found at i:9720066 original size:10 final size:9
Alignment explanation
Indices: 9720022--9720053 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
9720012 AACACTTTGG
9720022 TTTTTGTTT
1 TTTTTGTTT
9720031 TTTTTGTTT
1 TTTTTGTTT
9720040 TTTTTGTTT
1 TTTTTGTTT
9720049 TTTTT
1 TTTTT
9720054 TGTTGTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:9722197 original size:35 final size:35
Alignment explanation
Indices: 9722129--9722197 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
9722119 CCCTAATCTA
* * *
9722129 TGCAATCAAAAGCAAAGCAGGCATATACTTGTTTG
1 TGCAATCAAAAGCAAAACAGACATATACCTGTTTG
* * *
9722164 TGCAATTAAAAGTAAAACAGACATGTACCTGTTT
1 TGCAATCAAAAGCAAAACAGACATATACCTGTTT
9722198 TTTGCCCATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (35 bp):
TGCAATCAAAAGCAAAACAGACATATACCTGTTTG
Found at i:9723894 original size:39 final size:39
Alignment explanation
Indices: 9723840--9724074 Score: 177
Period size: 39 Copynumber: 6.0 Consensus size: 39
9723830 TGTTGATGCC
* *
9723840 TGTGATAACTCAGGGCGAAGGA-AAAAGTCAGAAAACTCT
1 TGTGATAACTCAGGGCCAAAGAGAAAA-TCAGAAAACTCT
** * *
9723879 TGTGATATTTCAGGGCCAAAGAGAAAATCAGAAGATTCT
1 TGTGATAACTCAGGGCCAAAGAGAAAATCAGAAAACTCT
* * * * *
9723918 TGTGATACCACAGGGCCAAAGCA-AAAATCAGAAGATTCC
1 TGTGATAACTCAGGGCCAAAG-AGAAAATCAGAAAACTCT
* * * * ** * *
9723957 TGTGTTATCTCAGCGCTAAAGAGAAAATCAGACGATTCA
1 TGTGATAACTCAGGGCCAAAGAGAAAATCAGAAAACTCT
* ** **
9723996 TGTAATTTCTCAGGGCCAAAGAGAAAATCAGAACCCTCT
1 TGTGATAACTCAGGGCCAAAGAGAAAATCAGAAAACTCT
** * * *
9724035 TGTGATATTTCAGGACCAAATAGAAAATCAGAAGACTCT
1 TGTGATAACTCAGGGCCAAAGAGAAAATCAGAAAACTCT
9724074 T
1 T
9724075 TCTATAAGTC
Statistics
Matches: 159, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
38 1 0.01
39 153 0.96
40 5 0.03
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (39 bp):
TGTGATAACTCAGGGCCAAAGAGAAAATCAGAAAACTCT
Found at i:9724060 original size:78 final size:76
Alignment explanation
Indices: 9723848--9724069 Score: 237
Period size: 78 Copynumber: 2.8 Consensus size: 76
9723838 CCTGTGATAA
* *
9723848 CTCAGGGCGAAGGAAAAAGTCAGAAAACTCTTGTGATATTTCAGGGCCAAAGAGAAAATCAGAAG
1 CTCAGGGCCAAAGAAAAA-TCAGAAAACTCTTGTGATATTTCA-GGCCAAAGAGAAAATCAGAAG
* *
9723913 ATTCTTGTGATAC
64 ATTCATGTAATAC
* * * * * * * *
9723926 CACAGGGCCAAAGCAAAAATCAGAAGATTCCTGTGTTATCTCAGCGCTAAAGAGAAAATCAGACG
1 CTCAGGGCCAAAG-AAAAATCAGAAAACTCTTGTGATATTTCAG-GCCAAAGAGAAAATCAGAAG
**
9723991 ATTCATGTAATTT
64 ATTCATGTAATAC
** *
9724004 CTCAGGGCCAAAGAGAAAATCAGAACCCTCTTGTGATATTTCAGGACCAAATAGAAAATCAGAAG
1 CTCAGGGCCAAAGA-AAAATCAGAAAACTCTTGTGATATTTCAGG-CCAAAGAGAAAATCAGAAG
9724069 A
64 A
9724070 CTCTTTCTAT
Statistics
Matches: 116, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
77 3 0.03
78 108 0.93
79 5 0.04
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (76 bp):
CTCAGGGCCAAAGAAAAATCAGAAAACTCTTGTGATATTTCAGGCCAAAGAGAAAATCAGAAGAT
TCATGTAATAC
Found at i:9736987 original size:5 final size:5
Alignment explanation
Indices: 9736963--9737001 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
9736953 ACCATGCCCA
* *
9736963 TTTTC CTTTC TTGTTA TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTT
9737002 CCTCCACCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:9736997 original size:15 final size:16
Alignment explanation
Indices: 9736962--9737001 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
9736952 GACCATGCCC
*
9736962 ATTTTCCTTTCTTGTT
1 ATTTTCTTTTCTTGTT
9736978 ATTTTCTTTTCTT-TT
1 ATTTTCTTTTCTTGTT
*
9736993 CTTTTCTTT
1 ATTTTCTTT
9737002 CCTCCACCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (16 bp):
ATTTTCTTTTCTTGTT
Found at i:9737562 original size:2 final size:2
Alignment explanation
Indices: 9737551--9737591 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
9737541 TACATATTAG
9737551 TA TA TA -A TA TA TA TA TA TA TA TA TA -A T- TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9737589 TA T
1 TA T
9737592 TATTTTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.11
2 31 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9737573 original size:19 final size:17
Alignment explanation
Indices: 9737538--9737591 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 17
9737528 TAGCTTACTC
9737538 AATTACATAT-TAGTATAT
1 AATTA-ATATATA-TATAT
9737556 AATATATATATATATATAT
1 AAT-TA-ATATATATATAT
9737575 AATTAATATATATATAT
1 AATTAATATATATATAT
9737592 TATTTTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 12 0.36
18 5 0.15
19 14 0.42
20 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
AATTAATATATATATAT
Found at i:9754687 original size:16 final size:18
Alignment explanation
Indices: 9754657--9754693 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
9754647 AATATATGGA
9754657 AAAAAATTATAAAAAGAT
1 AAAAAATTATAAAAAGAT
9754675 AAAAAA-TAT-AAAAGAT
1 AAAAAATTATAAAAAGAT
9754691 AAA
1 AAA
9754694 CCAGCAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 3 0.16
18 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (18 bp):
AAAAAATTATAAAAAGAT
Found at i:9758946 original size:31 final size:31
Alignment explanation
Indices: 9758908--9758989 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
9758898 AATTATATAA
*
9758908 AATATAAGGATTAAAATAAATAAAATTTTAT
1 AATATAAGAATTAAAATAAATAAAATTTTAT
*
9758939 AATATAAGAATTAAATTAAATAAAATTTTAT
1 AATATAAGAATTAAAATAAATAAAATTTTAT
* *
9758970 AATATAAGAATCAAATTAAA
1 AATATAAGAATTAAAATAAA
9758990 CAAATTTCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (31 bp):
AATATAAGAATTAAAATAAATAAAATTTTAT
Found at i:9758976 original size:36 final size:33
Alignment explanation
Indices: 9758897--9758989 Score: 113
Period size: 31 Copynumber: 2.9 Consensus size: 33
9758887 TATAGGAATC
* *
9758897 AAATTATATAAAATATAAGGATTAAAATAAATA
1 AAATTATATATAATATAAGAATTAAAATAAATA
*
9758930 AAATT-T-TATAATATAAGAATTAAATTAAATA
1 AAATTATATATAATATAAGAATTAAAATAAATA
* *
9758961 AAATT-T-TATAATATAAGAATCAAATTAAA
1 AAATTATATATAATATAAGAATTAAAATAAA
9758990 CAAATTTCTA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
31 50 0.89
32 1 0.02
33 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (33 bp):
AAATTATATATAATATAAGAATTAAAATAAATA
Found at i:9759961 original size:31 final size:31
Alignment explanation
Indices: 9759926--9760012 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
9759916 TTACTCTTGA
**
9759926 TATTATAGAGTTTTGTTAAATTTAGTCCATG
1 TATTATAGAGTTTTGTTAAATTTAAACCATG
* * *
9759957 TATTATAAAGTTTTGTTTAATATAAACCATG
1 TATTATAGAGTTTTGTTAAATTTAAACCATG
* *
9759988 TACTATAGAGTTTTGTTCAATTTAA
1 TATTATAGAGTTTTGTTAAATTTAA
9760013 TTTATTCATT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (31 bp):
TATTATAGAGTTTTGTTAAATTTAAACCATG
Found at i:9766522 original size:83 final size:83
Alignment explanation
Indices: 9766383--9766587 Score: 329
Period size: 83 Copynumber: 2.5 Consensus size: 83
9766373 ATGTCTATTA
* * * * * **
9766383 TTACAACATGAATTAGAGAATATTGAACTTGATTTTTAGTTTTTTAGTTTCTTTTCTTTATTAAA
1 TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAGTTATTCAATTAATTTTCTTTATTAAA
9766448 TATTTTTTACATTAATAC
66 TATTTTTTACATTAATAC
*
9766466 TTACAACATGAATTAGAGAAAATTGAACCTGAATTTTAGTTATTCAATTAATTTTCTTTATTAAA
1 TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAGTTATTCAATTAATTTTCTTTATTAAA
9766531 TATTTTTTACATTAATAC
66 TATTTTTTACATTAATAC
*
9766549 TTACAATATGAATTAGAGAAAATTGAACCTGATTTTTAG
1 TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAG
9766588 ATAATGAAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 112 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (83 bp):
TTACAACATGAATTAGAGAAAATTGAACCTGATTTTTAGTTATTCAATTAATTTTCTTTATTAAA
TATTTTTTACATTAATAC
Found at i:9766805 original size:31 final size:31
Alignment explanation
Indices: 9766767--9766828 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
9766757 AGTTTTTATA
*
9766767 TAATTCATAACATACTATCATTGACCAAATT
1 TAATTCATAACATACTATCAATGACCAAATT
9766798 TAATTCATAACATACTATCAATGACCAAATT
1 TAATTCATAACATACTATCAATGACCAAATT
9766829 GATGCTTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (31 bp):
TAATTCATAACATACTATCAATGACCAAATT
Found at i:9771503 original size:2 final size:2
Alignment explanation
Indices: 9771492--9771525 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9771482 AGTAATAGTG
9771492 TA TA -A 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
9771526 TGATAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9772593 original size:11 final size:11
Alignment explanation
Indices: 9772566--9772595 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
9772556 AGTTTTCCCT
9772566 AAAAATCAAATA
1 AAAAAT-AAATA
9772578 AAAAATAAATA
1 AAAAATAAATA
9772589 AAAAATA
1 AAAAATA
9772596 TATATATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:9774413 original size:27 final size:27
Alignment explanation
Indices: 9774383--9774456 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
9774373 AGAGGTACAT
*
9774383 GGATACCTTTA-CTCGCCAAAGGTGGAC
1 GGATACCTTTACCT-ACCAAAGGTGGAC
* *
9774410 GGATATCTTTACCTACCAAAGGTGGAT
1 GGATACCTTTACCTACCAAAGGTGGAC
* * *
9774437 GAATAACTTTACCAACCAAA
1 GGATACCTTTACCTACCAAA
9774457 AATGAATAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 38 0.95
28 2 0.05
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (27 bp):
GGATACCTTTACCTACCAAAGGTGGAC
Found at i:9776218 original size:20 final size:20
Alignment explanation
Indices: 9776190--9776229 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9776180 CTTCAAGTAT
* *
9776190 TATTCTCAATTATCATCAAG
1 TATTATCAATCATCATCAAG
9776210 TATTATCAATCATCATCAAG
1 TATTATCAATCATCATCAAG
9776230 CATTCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (20 bp):
TATTATCAATCATCATCAAG
Found at i:9780751 original size:35 final size:35
Alignment explanation
Indices: 9780712--9780850 Score: 106
Period size: 35 Copynumber: 4.1 Consensus size: 35
9780702 AGTTAGTATT
*
9780712 AGGTTTTGATTGATCTTGTGAAAAACCATTGTTAA
1 AGGTTTTGATTGATCCTGTGAAAAACCATTGTTAA
* * * * *
9780747 AGGTTATGGTTGAGCCTTTGAAAAACTATT-TT--
1 AGGTTTTGATTGATCCTGTGAAAAACCATTGTTAA
* * *
9780779 GGGTTTT-AGTTGATCCCGTGAAAAATCATTGTTAA
1 AGGTTTTGA-TTGATCCTGTGAAAAACCATTGTTAA
* ** * * *
9780814 AGGTTGTGGCTGAGCCTGTGAAAAGCCATTGTAAA
1 AGGTTTTGATTGATCCTGTGAAAAACCATTGTTAA
9780849 AG
1 AG
9780851 CTTGGTGGAA
Statistics
Matches: 76, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
32 21 0.28
33 2 0.03
34 2 0.03
35 51 0.67
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.35
Consensus pattern (35 bp):
AGGTTTTGATTGATCCTGTGAAAAACCATTGTTAA
Found at i:9783261 original size:13 final size:13
Alignment explanation
Indices: 9783243--9783267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9783233 TATTTTTTAT
9783243 AAAATAAAATATA
1 AAAATAAAATATA
9783256 AAAATAAAATAT
1 AAAATAAAATAT
9783268 TTAGATTGAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAAATATA
Found at i:9783884 original size:5 final size:5
Alignment explanation
Indices: 9783874--9783899 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9783864 ATTCAGGAGG
9783874 AAAAC AAAAC AAAAC AAAAC AAAAC A
1 AAAAC AAAAC AAAAC AAAAC AAAAC A
9783900 CAACTCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:9786461 original size:20 final size:20
Alignment explanation
Indices: 9786436--9786473 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9786426 AAAGAGATAC
9786436 CTACTTTATAAGGGAAGGAT
1 CTACTTTATAAGGGAAGGAT
* *
9786456 CTACTTTTTAAGGTAAGG
1 CTACTTTATAAGGGAAGG
9786474 TTTTAGTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (20 bp):
CTACTTTATAAGGGAAGGAT
Found at i:9793544 original size:18 final size:16
Alignment explanation
Indices: 9793521--9793563 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
9793511 TCCCACAGCT
9793521 AAGAAAGAATTGAAGAAG
1 AAGAAAGAATT--AGAAG
*
9793539 AAGAAA-AATTAGGAG
1 AAGAAAGAATTAGAAG
9793554 AAGAAAGAAT
1 AAGAAAGAAT
9793564 CAGGCAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 3 0.13
17 4 0.17
18 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.12
Consensus pattern (16 bp):
AAGAAAGAATTAGAAG
Found at i:9799013 original size:2 final size:2
Alignment explanation
Indices: 9799006--9799046 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9798996 NNNNNNNNNN
9799006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9799047 AAAGTATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9799698 original size:15 final size:15
Alignment explanation
Indices: 9799678--9799710 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
9799668 TTTATATATA
9799678 TTTATAA-TTAATAAT
1 TTTATAAGTT-ATAAT
9799693 TTTATAAGTTATAAT
1 TTTATAAGTTATAAT
9799708 TTT
1 TTT
9799711 TGTAATGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTATAAGTTATAAT
Found at i:9800712 original size:16 final size:16
Alignment explanation
Indices: 9800693--9800755 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
9800683 TCAAGCCCGC
*
9800693 AAAAAGGGAAGAAA-AA
1 AAAAAGAGAA-AAAGAA
9800709 AAAAAGAGAAAAAGAA
1 AAAAAGAGAAAAAGAA
*
9800725 AAAAAAAG-AAAAG-A
1 AAAAAGAGAAAAAGAA
*
9800739 AGAAAGAGAAAAAGAA
1 AAAAAGAGAAAAAGAA
9800755 A
1 A
9800756 GAGAAGAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 7 0.17
15 13 0.32
16 20 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAGAGAAAAAGAA
Found at i:9800726 original size:15 final size:15
Alignment explanation
Indices: 9800693--9800755 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
9800683 TCAAGCCCGC
* *
9800693 AAAAAGGGAAGAAAAA
1 AAAAAGAGAA-AAAGA
9800709 AAAAAGAGAAAAAGA
1 AAAAAGAGAAAAAGA
*
9800724 AAAAA-AAAGAAAAGA
1 AAAAAGAGA-AAAAGA
*
9800739 AGAAAGAGAAAAAGA
1 AAAAAGAGAAAAAGA
9800754 AA
1 AA
9800756 GAGAAGAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 2 0.05
15 26 0.67
16 11 0.28
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAAAGA
Found at i:9800730 original size:21 final size:22
Alignment explanation
Indices: 9800704--9800766 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
9800694 AAAAGGGAAG
9800704 AAAAAAAAAAGAGAA-AAAGAA
1 AAAAAAAAAAGAGAAGAAAGAA
9800725 AAAAAAAGAAA-AGAAGAAAG-A
1 AAAAAAA-AAAGAGAAGAAAGAA
* *
9800746 GAAAAAGAAAGAGAAGAAAGA
1 AAAAAAAAAAGAGAAGAAAGA
9800767 GAGTGGGGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 3 0.08
21 26 0.72
22 7 0.19
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAGAGAAGAAAGAA
Found at i:9800731 original size:24 final size:24
Alignment explanation
Indices: 9800704--9800751 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
9800694 AAAAGGGAAG
9800704 AAAAAAAAAAG-AGAAAAAGAAAA
1 AAAAAAAAAAGAAGAAAAAGAAAA
* *
9800727 AAAAAGAAAAGAAGAAAGAGAAAA
1 AAAAAAAAAAGAAGAAAAAGAAAA
9800751 A
1 A
9800752 GAAAGAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAGAAGAAAAAGAAAA
Found at i:9800767 original size:21 final size:20
Alignment explanation
Indices: 9800700--9800768 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 20
9800690 CGCAAAAAGG
*
9800700 GAAGAAA-AAAAAAAGAGAAA
1 GAAGAAAGAGAAAAAGA-AAA
9800720 -AAGAAA-A-AAAAAGAAAA
1 GAAGAAAGAGAAAAAGAAAA
9800737 GAAGAAAGAGAAAAAGAAAGA
1 GAAGAAAGAGAAAAAGAAA-A
9800758 GAAGAAAGAGA
1 GAAGAAAGAGA
9800769 GTGGGGACCC
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.07
18 13 0.29
19 8 0.18
20 9 0.20
21 12 0.27
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (20 bp):
GAAGAAAGAGAAAAAGAAAA
Found at i:9800853 original size:15 final size:15
Alignment explanation
Indices: 9800835--9800864 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9800825 ACGTCTTGAG
*
9800835 GAGAAGAAAAAGAAA
1 GAGAAAAAAAAGAAA
9800850 GAGAAAAAAAAGAAA
1 GAGAAAAAAAAGAAA
9800865 AAAGAAAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
GAGAAAAAAAAGAAA
Found at i:9800861 original size:11 final size:12
Alignment explanation
Indices: 9800839--9800874 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
9800829 CTTGAGGAGA
9800839 AGAAAAAGAAAG
1 AGAAAAAGAAAG
9800851 AGAAAAA-AAAG
1 AGAAAAAGAAAG
9800862 A-AAAAAGAAAG
1 AGAAAAAGAAAG
9800873 AG
1 AG
9800875 GGAGCAGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.23
11 10 0.45
12 7 0.32
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAAG
Found at i:9800993 original size:20 final size:18
Alignment explanation
Indices: 9800965--9801006 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
9800955 CCAGAGGAGA
9800965 AAGAGGAAAAAGAGAAAAG
1 AAGAGGAAAAAGAG-AAAG
9800984 AAGAGTGAAAAAGAGAAAG
1 AAGAG-GAAAAAGAGAAAG
9801003 AAGA
1 AAGA
9801007 AAAGAAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (18 bp):
AAGAGGAAAAAGAGAAAG
Found at i:9801013 original size:20 final size:20
Alignment explanation
Indices: 9800970--9801018 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
9800960 GGAGAAAGAG
**
9800970 GAAAAAGAGAAAAGAAGAGT
1 GAAAAAGAGAAAAGAAGAAA
9800990 GAAAAAGAG-AAAGAAGAAA
1 GAAAAAGAGAAAAGAAGAAA
*
9801009 -AGAAAGAGAA
1 GAAAAAGAGAA
9801019 GTGCCGGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 9 0.36
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (20 bp):
GAAAAAGAGAAAAGAAGAAA
Found at i:9805022 original size:60 final size:60
Alignment explanation
Indices: 9804921--9805098 Score: 198
Period size: 60 Copynumber: 3.0 Consensus size: 60
9804911 ATTTGATTTA
* * * * **
9804921 AAAGGGGGACCTAAAGCCCCGATTTATATTGGATGACGTGGATAGTTCTTACGAGTAGGT
1 AAAGGGGGACTTGAAGCCCTGATTCATATTGGATGACGTGGATAGTTCCCACGAGTAGGT
* * * **
9804981 AAAGGGGGATTTGAAGCCCTGATTGATATTGGGTGGTGTGGATAGTTCCCACGAGTAGGT
1 AAAGGGGGACTTGAAGCCCTGATTCATATTGGATGACGTGGATAGTTCCCACGAGTAGGT
* * * **
9805041 AAAGGGGGACTTGAAGCCCTAATTCATA-T-GATGGCATGGGCAGTTCCCACGAGTAGGT
1 AAAGGGGGACTTGAAGCCCTGATTCATATTGGATGACGTGGATAGTTCCCACGAGTAGGT
9805099 GATGATGTCT
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 24 0.24
59 1 0.01
60 75 0.75
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (60 bp):
AAAGGGGGACTTGAAGCCCTGATTCATATTGGATGACGTGGATAGTTCCCACGAGTAGGT
Found at i:9806528 original size:18 final size:18
Alignment explanation
Indices: 9806505--9806540 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
9806495 TTTATTTTAC
*
9806505 TATTCCCATTATGAATGT
1 TATTCCAATTATGAATGT
9806523 TATTCCAATTATGAATGT
1 TATTCCAATTATGAATGT
9806541 AACCCCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (18 bp):
TATTCCAATTATGAATGT
Found at i:9812617 original size:14 final size:14
Alignment explanation
Indices: 9812600--9812626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9812590 CAAAATTAAT
9812600 TAATTAACTAAAAC
1 TAATTAACTAAAAC
9812614 TAATTAACTAAAA
1 TAATTAACTAAAA
9812627 TTAAAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:9816386 original size:14 final size:15
Alignment explanation
Indices: 9816380--9816413 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
9816370 AATCAAAATT
9816380 AATTAATTAA-CTAA
1 AATTAATTAATCTAA
9816394 AATTAATTAA-CTAA
1 AATTAATTAATCTAA
9816408 AATTAA
1 AATTAA
9816414 AATCAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTAATTAATCTAA
Found at i:9825596 original size:27 final size:27
Alignment explanation
Indices: 9825562--9825634 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
9825552 TGAGGTTTTT
9825562 TTTTATTGAAATTAAGAAAATGATGTA
1 TTTTATTGAAATTAAGAAAATGATGTA
*
9825589 TTTTATTGAAATTAAAAAAATGATGTA
1 TTTTATTGAAATTAAGAAAATGATGTA
9825616 TTTTATTGAAATTAAGAAA
1 TTTTATTGAAATTAAGAAA
9825635 GAGCAAATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (27 bp):
TTTTATTGAAATTAAGAAAATGATGTA
Found at i:9826032 original size:26 final size:26
Alignment explanation
Indices: 9825979--9826033 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
9825969 ATTAATTATC
* * *
9825979 TTAATTTTTGTATAATTTTAATATAA
1 TTAATTATTATATAATTTTAATAAAA
9826005 TTAATTATTATATAATTATT-ATAAAA
1 TTAATTATTATATAATT-TTAATAAAA
9826031 TTA
1 TTA
9826034 TGGACCTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TTAATTATTATATAATTTTAATAAAA
Found at i:9838757 original size:20 final size:19
Alignment explanation
Indices: 9838724--9838762 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
9838714 GTATTTTGAC
**
9838724 TATACATAGTTATTATTATT
1 TATACATACATATT-TTATT
9838744 TATACATACATATTTTATT
1 TATACATACATATTTTATT
9838763 CATTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (19 bp):
TATACATACATATTTTATT
Found at i:9840140 original size:52 final size:52
Alignment explanation
Indices: 9840026--9840156 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 52
9840016 CTAAGGAGCT
* * * * *
9840026 CGAATCTCTCTCTCTCTCTTCCTCCCTAGTCGGCGGCGCAACCCAAAGGACC
1 CGAATTTCTCTCTCTCTCTTCCTCCCCAATCAGCGACGCAACCCAAAGGACC
* * * *
9840078 C-AAATT-TCTCTCTCTCTTCCTCCCCAATCAGCGATGCAACCTAGAGGACC
1 CGAATTTCTCTCTCTCTCTTCCTCCCCAATCAGCGACGCAACCCAAAGGACC
9840128 CGAATTTCTCTCTCTCTCTTCCTCCCCAA
1 CGAATTTCTCTCTCTCTCTTCCTCCCCAA
9840157 CCGGCGGGTT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 38 0.57
51 7 0.10
52 22 0.33
ACGTcount: A:0.19, C:0.41, G:0.12, T:0.27
Consensus pattern (52 bp):
CGAATTTCTCTCTCTCTCTTCCTCCCCAATCAGCGACGCAACCCAAAGGACC
Found at i:9840648 original size:11 final size:12
Alignment explanation
Indices: 9840630--9840664 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
9840620 TTCATTCATC
9840630 ATTTTTTTATTT
1 ATTTTTTTATTT
*
9840642 A-TTTTTTATTA
1 ATTTTTTTATTT
9840653 ATTTTTTTATTT
1 ATTTTTTTATTT
9840665 TTTGGCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:9854100 original size:60 final size:61
Alignment explanation
Indices: 9854033--9854148 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
9854023 CATTTTGAGT
* *
9854033 ATTTTGGAGTAATTTTTGATACACAAAG-AAAACTTTTGAGCGTTTTGAGCATTTTTAAGC
1 ATTTTGGAGTAATTTTTGATACACAAAGAAAAACCTTTGAGCATTTTGAGCATTTTTAAGC
* * * **
9854093 ATTTTGGAGTGATTTTTTATATATGAAGAAAAACCTTTGAGCATTTTGAGCATTTT
1 ATTTTGGAGTAATTTTTGATACACAAAGAAAAACCTTTGAGCATTTTGAGCATTTT
9854149 GAGTATTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 23 0.48
61 25 0.52
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (61 bp):
ATTTTGGAGTAATTTTTGATACACAAAGAAAAACCTTTGAGCATTTTGAGCATTTTTAAGC
Found at i:9854344 original size:22 final size:22
Alignment explanation
Indices: 9854262--9854345 Score: 64
Period size: 22 Copynumber: 3.9 Consensus size: 22
9854252 AGTTATTAGG
* *
9854262 TTTTAGGTATTGCATGACTGA-
1 TTTTAGGCATTGCATGACTAAT
* * *
9854283 CTTT-GGACATTGCGTGATTAAT
1 TTTTAGG-CATTGCATGACTAAT
* * *
9854305 TTTTAAGCATCGCGTGACTAAT
1 TTTTAGGCATTGCATGACTAAT
*
9854327 TTTTAGGTATTGCATGACT
1 TTTTAGGCATTGCATGACT
9854346 TGTTAGTAAG
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
20 2 0.04
21 13 0.28
22 31 0.66
23 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (22 bp):
TTTTAGGCATTGCATGACTAAT
Found at i:9854524 original size:22 final size:22
Alignment explanation
Indices: 9854456--9854514 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
9854446 TAAGTCACGT
9854456 AATACTTAAAAATCAGTCTCGC
1 AATACTTAAAAATCAGTCTCGC
*
9854478 AATGCTTAAAAATCAGTCTCGC
1 AATACTTAAAAATCAGTCTCGC
9854500 AATACTTAAAAATCA
1 AATACTTAAAAATCA
9854515 ATAACACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.27
Consensus pattern (22 bp):
AATACTTAAAAATCAGTCTCGC
Found at i:9855772 original size:22 final size:23
Alignment explanation
Indices: 9855733--9855781 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
9855723 AGTTAGATTA
* *
9855733 TTACACGTCATGTTC-AAATATG
1 TTACACGTCATATACAAAATATG
9855755 TTACACGTCATATACAAAAATATG
1 TTACACGTCATATAC-AAAATATG
9855779 TTA
1 TTA
9855782 AATGCTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (23 bp):
TTACACGTCATATACAAAATATG
Found at i:9855823 original size:31 final size:31
Alignment explanation
Indices: 9855788--9855889 Score: 120
Period size: 32 Copynumber: 3.4 Consensus size: 31
9855778 GTTAAATGCT
* *
9855788 ATGTTGAAAAAAAATATTATTGTTACACGTC
1 ATGTTGAAAAAAAATATTGTTGTTACACGCC
*
9855819 ATGTTGAAAAAAAAATATTGTTGTTACATGCC
1 ATGTTG-AAAAAAAATATTGTTGTTACACGCC
*
9855851 ATGTT---AAAAAATATTGTTGTTACACACC
1 ATGTTGAAAAAAAATATTGTTGTTACACGCC
* *
9855879 ATATTCAAAAA
1 ATGTTGAAAAA
9855890 CATTTTGTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
28 25 0.41
31 9 0.15
32 27 0.44
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (31 bp):
ATGTTGAAAAAAAATATTGTTGTTACACGCC
Found at i:9855868 original size:28 final size:28
Alignment explanation
Indices: 9855796--9855903 Score: 110
Period size: 28 Copynumber: 3.8 Consensus size: 28
9855786 CTATGTTGAA
* *
9855796 AAAAAATATTATTGTTACACGTCATGTT
1 AAAAAATATTGTTGTTACACGCCATGTT
*
9855824 GAAAAAAAAATATTGTTGTTACATGCCATGTT
1 ----AAAAAATATTGTTGTTACACGCCATGTT
* *
9855856 AAAAAATATTGTTGTTACACACCATATT
1 AAAAAATATTGTTGTTACACGCCATGTT
* *
9855884 CAAAAACATT-TTGTTACACG
1 AAAAAATATTGTTGTTACACG
9855904 TTAATACTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
27 9 0.13
28 33 0.49
32 25 0.37
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (28 bp):
AAAAAATATTGTTGTTACACGCCATGTT
Found at i:9856331 original size:20 final size:20
Alignment explanation
Indices: 9856303--9856351 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
9856293 AGGAAAGAAA
*
9856303 AAATTGAAAGCACGAGATAT
1 AAATCGAAAGCACGAGATAT
9856323 AAATCGAAAGCACGAGATAT
1 AAATCGAAAGCACGAGATAT
9856343 AAATCGAAA
1 AAATCGAAA
9856352 AGAGAAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.16
Consensus pattern (20 bp):
AAATCGAAAGCACGAGATAT
Found at i:9857590 original size:2 final size:2
Alignment explanation
Indices: 9857583--9857619 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9857573 GAAGAGGCAA
9857583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9857620 ACTTAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9865284 original size:35 final size:35
Alignment explanation
Indices: 9865233--9865321 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 35
9865223 TTATTAATGA
*
9865233 GTTACTGGTAGGATTTTCTAT-TATATCAGTAATCG
1 GTTAGTGGTAGGATTTT-TATGTATATCAGTAATCG
* * * *
9865268 GTTTGTGGTAGGATTTTTTTGGTTTATCAGTAATGG
1 GTTAGTGGTAGGATTTTTAT-GTATATCAGTAATCG
*
9865304 GTTAGTGGTATGATTTTT
1 GTTAGTGGTAGGATTTTT
9865322 TTGTGAGTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 2 0.04
35 15 0.33
36 28 0.62
ACGTcount: A:0.20, C:0.06, G:0.26, T:0.48
Consensus pattern (35 bp):
GTTAGTGGTAGGATTTTTATGTATATCAGTAATCG
Found at i:9865312 original size:36 final size:36
Alignment explanation
Indices: 9865256--9865324 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
9865246 TTTTCTATTA
*
9865256 TATCAGTAATCGGTTTGTGGTAGGATTTTTTTGGTT
1 TATCAGTAATCGGTTAGTGGTAGGATTTTTTTGGTT
* *
9865292 TATCAGTAATGGGTTAGTGGTATGATTTTTTTG
1 TATCAGTAATCGGTTAGTGGTAGGATTTTTTTG
9865325 TGAGTAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.19, C:0.04, G:0.28, T:0.49
Consensus pattern (36 bp):
TATCAGTAATCGGTTAGTGGTAGGATTTTTTTGGTT
Found at i:9879454 original size:22 final size:20
Alignment explanation
Indices: 9879426--9879469 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
9879416 GTCATTTATG
*
9879426 AAAGAAAAAAGAGATAGAAAAA
1 AAAGAAAAAA-A-ATACAAAAA
9879448 AAAGAAAAAAAATACAAAAA
1 AAAGAAAAAAAATACAAAAA
9879468 AA
1 AA
9879470 TAAAAATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 10 0.48
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAGAAAAAAAATACAAAAA
Found at i:9879455 original size:9 final size:9
Alignment explanation
Indices: 9879441--9879485 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
9879431 AAAAAGAGAT
9879441 AGAAAAAAA
1 AGAAAAAAA
9879450 AGAAAAAAA
1 AGAAAAAAA
*
9879459 ATACAAAAAA
1 AGA-AAAAAA
* *
9879469 ATAAAAATA
1 AGAAAAAAA
9879478 AGAAAAAA
1 AGAAAAAA
9879486 CCTAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 22 0.71
10 9 0.29
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:9879470 original size:10 final size:9
Alignment explanation
Indices: 9879443--9879508 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
9879433 AAAGAGATAG
*
9879443 AAAAAAAAG
1 AAAAAAAAT
9879452 AAAAAAAAT
1 AAAAAAAAT
9879461 ACAAAAAAAT
1 A-AAAAAAAT
* *
9879471 AAAAATAAG
1 AAAAAAAAT
9879480 AAAAAACCTAAT
1 AAAAAA---AAT
* *
9879492 TAAAAAATT
1 AAAAAAAAT
9879501 AAAAAAAA
1 AAAAAAAA
9879509 GAAGAGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 28 0.64
10 9 0.20
12 7 0.16
ACGTcount: A:0.80, C:0.05, G:0.03, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:9881268 original size:19 final size:19
Alignment explanation
Indices: 9881241--9881283 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9881231 AGAATCTCTA
* * *
9881241 CAAAGGCATTTTTGCAAAG
1 CAAAAGCATTTCTGAAAAG
9881260 CAAAAGCATTTCTGAAAAG
1 CAAAAGCATTTCTGAAAAG
9881279 -AAAAG
1 CAAAAG
9881284 AAAACAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.21
Consensus pattern (19 bp):
CAAAAGCATTTCTGAAAAG
Found at i:9881347 original size:37 final size:37
Alignment explanation
Indices: 9881305--9881406 Score: 195
Period size: 37 Copynumber: 2.8 Consensus size: 37
9881295 ATCCCTAGAA
9881305 CTTGCAAGGCATCTGAAGAAAGAAACTTCCAAAGCAT
1 CTTGCAAGGCATCTGAAGAAAGAAACTTCCAAAGCAT
*
9881342 CTTGCAAGGCATCTGAAGAAAGAAACTTCCCAAGCAT
1 CTTGCAAGGCATCTGAAGAAAGAAACTTCCAAAGCAT
9881379 CTTGCAAGGCATCTGAAGAAAGAAACTT
1 CTTGCAAGGCATCTGAAGAAAGAAACTT
9881407 TCTAGATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (37 bp):
CTTGCAAGGCATCTGAAGAAAGAAACTTCCAAAGCAT
Found at i:9881992 original size:19 final size:19
Alignment explanation
Indices: 9881955--9881992 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9881945 CCATTTAACT
* *
9881955 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATATGAG
9881974 TATTGGAGTATAATATGAG
1 TATTGGAGTATAATATGAG
9881993 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGGAGTATAATATGAG
Found at i:9884611 original size:15 final size:16
Alignment explanation
Indices: 9884591--9884629 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
9884581 CAGAGATTTT
9884591 GATTTTAAAA-CTTTG
1 GATTTTAAAATCTTTG
*
9884606 GATTTTAAAATTTTTG
1 GATTTTAAAATCTTTG
9884622 G-TTTTAAA
1 GATTTTAAA
9884630 GTTGTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (16 bp):
GATTTTAAAATCTTTG
Found at i:9884676 original size:5 final size:5
Alignment explanation
Indices: 9884666--9884696 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
9884656 TTGCGGGCCC
9884666 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTT AA
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AA
9884697 ATCAGGTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:9884691 original size:14 final size:15
Alignment explanation
Indices: 9884666--9884696 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
9884656 TTGCGGGCCC
9884666 AAGTTAAGTTAAGTT
1 AAGTTAAGTTAAGTT
9884681 AAGTT-AGTTAAGTT
1 AAGTTAAGTTAAGTT
9884695 AA
1 AA
9884697 ATCAGGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (15 bp):
AAGTTAAGTTAAGTT
Found at i:9884705 original size:19 final size:19
Alignment explanation
Indices: 9884667--9884706 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9884657 TGCGGGCCCA
* *
9884667 AGTTAAGTTAAGTTAAGTT
1 AGTTAAGTTAAATCAAGTT
*
9884686 AGTTAAGTTAAATCAGGTT
1 AGTTAAGTTAAATCAAGTT
9884705 AG
1 AG
9884707 GTAGAATAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.38
Consensus pattern (19 bp):
AGTTAAGTTAAATCAAGTT
Found at i:9903356 original size:11 final size:11
Alignment explanation
Indices: 9903340--9903369 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9903330 GCTTGTTCTG
*
9903340 ACGGATTTTCA
1 ACGGATTTCCA
9903351 ACGGATTTCCA
1 ACGGATTTCCA
9903362 ACGGATTT
1 ACGGATTT
9903370 ATACTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (11 bp):
ACGGATTTCCA
Found at i:9905017 original size:13 final size:13
Alignment explanation
Indices: 9904999--9905023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9904989 TTCCAGAAAA
9904999 TTTATAAAATCAT
1 TTTATAAAATCAT
9905012 TTTATAAAATCA
1 TTTATAAAATCA
9905024 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:9906412 original size:19 final size:19
Alignment explanation
Indices: 9906388--9906425 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
9906378 CTGCCAAACC
*
9906388 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
9906407 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
9906426 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:9908823 original size:89 final size:89
Alignment explanation
Indices: 9908663--9908871 Score: 285
Period size: 89 Copynumber: 2.3 Consensus size: 89
9908653 ACAAGCGACC
* *
9908663 CCCAACTC-TCTCTCTCTCAACTCCTTCCTTTTCCAACCGACGACACAAGCCCGAAGCCCCAACT
1 CCCAAATCTTCTCTCTCTC-ACTTCTTCCTTTTCCAACCGACGACACAAGCCCGAAGCCCCAACT
* *
9908727 CTTTCTAGAACCGGCGGCATAGGAA
65 CTCTCTAGAACCGGCGGCACAGGAA
* * ** * *
9908752 CCCAAATCTTCTCTCTCTCGCTTCTTCCTTTTTCAACCGGTGACACAAGCTCGAAGCCCCAGCTC
1 CCCAAATCTTCTCTCTCTCACTTCTTCCTTTTCCAACCGACGACACAAGCCCGAAGCCCCAACTC
*
9908817 TCTCTAGAATCGGCGGCACAGGAA
66 TCTCTAGAACCGGCGGCACAGGAA
* *
9908841 CCTAGATCTTCTCTCTCTCACTTCTTCCTTT
1 CCCAAATCTTCTCTCTCTCACTTCTTCCTTT
9908872 CGCAGACGGT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
89 95 0.90
90 10 0.10
ACGTcount: A:0.21, C:0.38, G:0.13, T:0.27
Consensus pattern (89 bp):
CCCAAATCTTCTCTCTCTCACTTCTTCCTTTTCCAACCGACGACACAAGCCCGAAGCCCCAACTC
TCTCTAGAACCGGCGGCACAGGAA
Found at i:9909311 original size:3 final size:3
Alignment explanation
Indices: 9909296--9909347 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
9909286 ATTAGTTAAG
*
9909296 TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9909344 TAT T
1 TAT T
9909348 TAACACCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:9910056 original size:29 final size:28
Alignment explanation
Indices: 9910022--9910092 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 28
9910012 CTAGTATTTG
9910022 TTTTTAGTTATTT-AAT-TTTAAATTTAAGA
1 TTTTTA-TT-TTTGAATATTTAAATTTAA-A
*
9910051 TTTTTATTTTTGATTATTTAAATTTAAA
1 TTTTTATTTTTGAATATTTAAATTTAAA
9910079 TTTTAATATTTTTG
1 TTTT--TATTTTTG
9910093 TGGAAGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 9 0.24
29 17 0.46
30 8 0.22
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (28 bp):
TTTTTATTTTTGAATATTTAAATTTAAA
Found at i:9910191 original size:12 final size:12
Alignment explanation
Indices: 9910174--9910200 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9910164 TCAGGTATAC
9910174 ATGAGTGAATTT
1 ATGAGTGAATTT
9910186 ATGAGTGAATTT
1 ATGAGTGAATTT
9910198 ATG
1 ATG
9910201 GCACGTATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (12 bp):
ATGAGTGAATTT
Found at i:9910583 original size:29 final size:29
Alignment explanation
Indices: 9910547--9910602 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
9910537 AATAGGTCAA
9910547 AATATTTT-CAACGAAAAATTT-CGTTGCT
1 AATATTTTCCAAC-AAAAATTTCCGTTGCT
*
9910575 AATATTTTTCCAACAGAAATTTCCGTTG
1 AATA-TTTTCCAACAAAAATTTCCGTTG
9910603 GAAATGCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 11 0.46
30 9 0.38
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (29 bp):
AATATTTTCCAACAAAAATTTCCGTTGCT
Found at i:9910898 original size:26 final size:26
Alignment explanation
Indices: 9910869--9910923 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
9910859 ATTTCCAACG
* *
9910869 AATTTCTAACGGAATTTTTTGTTGAA
1 AATTTCCAACGGAATTTTCTGTTGAA
* *
9910895 AATTTCCAACGGACTTTTCTGTTGGA
1 AATTTCCAACGGAATTTTCTGTTGAA
9910921 AAT
1 AAT
9910924 CCGTTGGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (26 bp):
AATTTCCAACGGAATTTTCTGTTGAA
Found at i:9926323 original size:34 final size:33
Alignment explanation
Indices: 9926267--9926333 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
9926257 TTTTTATGAC
* *
9926267 TATTTTTTTAGAAAAAAGAGTTTTCCTTGTATT
1 TATTTTTTTAGAAAAAAAAGTTTTCCTTATATT
*
9926300 TATTTTTTTA-AAGGAAAAAAGTTTTTCTTATATT
1 TATTTTTTTAGAA--AAAAAAGTTTTCCTTATATT
9926334 AAAATTCTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 2 0.07
33 10 0.34
34 17 0.59
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.52
Consensus pattern (33 bp):
TATTTTTTTAGAAAAAAAAGTTTTCCTTATATT
Found at i:9929150 original size:13 final size:14
Alignment explanation
Indices: 9929122--9929179 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 14
9929112 TAATTATATT
9929122 AATTATTTAATAAAA
1 AATTATTT-ATAAAA
9929137 AATTATTT-TAAAA
1 AATTATTTATAAAA
9929150 AATTA-TTA-AAAA
1 AATTATTTATAAAA
* * *
9929162 TATAATATATAAAA
1 AATTATTTATAAAA
9929176 AATT
1 AATT
9929180 TCAAAAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 9 0.26
13 12 0.34
14 6 0.17
15 8 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTATTTATAAAA
Found at i:9936740 original size:60 final size:60
Alignment explanation
Indices: 9936672--9936827 Score: 276
Period size: 60 Copynumber: 2.6 Consensus size: 60
9936662 GCCTCGATTC
* * *
9936672 ATATTTGGTGGTGTGGGGAGTTCCCACCAGTAGGTAAAGGGGGACTTGAAGTCTCAACTT
1 ATATTTGGTAGCGTGGGGAGTTCCCACGAGTAGGTAAAGGGGGACTTGAAGTCTCAACTT
9936732 ATATTTGGTAGCGTGGGGAGTTCCCACGAGTAGGTAAAGGGGGACTTGAAGTCTCAACTT
1 ATATTTGGTAGCGTGGGGAGTTCCCACGAGTAGGTAAAGGGGGACTTGAAGTCTCAACTT
*
9936792 ATATTTGGTAGCATGGGGAGTTCCCACGAGTAGGTA
1 ATATTTGGTAGCGTGGGGAGTTCCCACGAGTAGGTA
9936828 TTGATGTTAT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (60 bp):
ATATTTGGTAGCGTGGGGAGTTCCCACGAGTAGGTAAAGGGGGACTTGAAGTCTCAACTT
Found at i:9938175 original size:19 final size:18
Alignment explanation
Indices: 9938139--9938177 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
9938129 AAAAAGGAAA
* *
9938139 GAGAAGAAATTGGGAATG
1 GAGAACAAATTGGCAATG
9938157 GAGAACAAAGTTGGCAATG
1 GAGAACAAA-TTGGCAATG
9938176 GA
1 GA
9938178 TACCAGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.44, C:0.05, G:0.36, T:0.15
Consensus pattern (18 bp):
GAGAACAAATTGGCAATG
Found at i:9938295 original size:17 final size:18
Alignment explanation
Indices: 9938262--9938317 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
9938252 ACTTGGTGGG
9938262 TTGAAAAAGGAAA-GAAAA
1 TTGAAAAA-GAAATGAAAA
9938280 TTGAAAAA-AAATGAAAA
1 TTGAAAAAGAAATGAAAA
*
9938297 TTGAAAAAACAAATGAAAA
1 TTG-AAAAAGAAATGAAAA
9938316 TT
1 TT
9938318 ATATATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.09
17 8 0.23
18 13 0.37
19 11 0.31
ACGTcount: A:0.66, C:0.02, G:0.14, T:0.18
Consensus pattern (18 bp):
TTGAAAAAGAAATGAAAA
Found at i:9938305 original size:19 final size:19
Alignment explanation
Indices: 9938262--9938317 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
9938252 ACTTGGTGGG
**
9938262 TTGAAAAAGGAAA-GAAAA
1 TTGAAAAAAAAAATGAAAA
9938280 TTG--AAAAAAAATGAAAA
1 TTGAAAAAAAAAATGAAAA
*
9938297 TTGAAAAAACAAATGAAAA
1 TTGAAAAAAAAAATGAAAA
9938316 TT
1 TT
9938318 ATATATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.19
17 8 0.25
18 3 0.09
19 15 0.47
ACGTcount: A:0.66, C:0.02, G:0.14, T:0.18
Consensus pattern (19 bp):
TTGAAAAAAAAAATGAAAA
Found at i:9938567 original size:2 final size:2
Alignment explanation
Indices: 9938560--9938602 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
9938550 CTTTTTCACC
9938560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9938602 T
1 T
9938603 CTCTCTCTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9938607 original size:2 final size:2
Alignment explanation
Indices: 9938602--9938637 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9938592 TATATATATA
9938602 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9938638 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9939541 original size:15 final size:15
Alignment explanation
Indices: 9939521--9939581 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 15
9939511 NNNNNNNNNN
9939521 ATTAATATTTAAATT
1 ATTAATATTTAAATT
9939536 ATTAAT-TATTAATATT
1 ATTAATAT-TTAA-ATT
9939552 -TTAATTAATTATAAATT
1 ATTAA-T-ATT-TAAATT
9939569 ATTAATATTTAAA
1 ATTAATATTTAAA
9939582 AATAAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
14 1 0.03
15 18 0.46
16 7 0.18
17 5 0.13
18 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTAATATTTAAATT
Found at i:9939591 original size:26 final size:26
Alignment explanation
Indices: 9939539--9939592 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
9939529 TTAAATTATT
* * *
9939539 AATTATTAATATTTTAATTAATTATA
1 AATTATTAATATTTAAAATAATAATA
9939565 AATTATTAATATTTAAAAATAA-AATA
1 AATTATTAATATTT-AAAATAATAATA
9939591 AA
1 AA
9939593 AATAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTATTAATATTTAAAATAATAATA
Found at i:9940804 original size:21 final size:21
Alignment explanation
Indices: 9940765--9940804 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
9940755 GTTACCAAGT
*
9940765 AGGAAATAATTGAACTTTTAA
1 AGGAAATAAATGAACTTTTAA
9940786 AGGATAATAAATGAA-TTTT
1 AGGA-AATAAATGAACTTTT
9940805 CGAACTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGAAATAAATGAACTTTTAA
Found at i:9947933 original size:20 final size:20
Alignment explanation
Indices: 9947908--9947947 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9947898 TGTTGCATAC
*
9947908 AATATAAAATTAATTTCCAA
1 AATATAAAACTAATTTCCAA
*
9947928 AATATAAGACTAATTTCCAA
1 AATATAAAACTAATTTCCAA
9947948 CTTTAAGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (20 bp):
AATATAAAACTAATTTCCAA
Found at i:9955419 original size:55 final size:55
Alignment explanation
Indices: 9955342--9955448 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
9955332 AATGAGAGGC
* * **
9955342 TTTGGTATATTGTGAGTAAGGTAGGGAGGCTATATTTATAGGTAGGGAATGAGAT
1 TTTGGTATATTGTGAGTAAGGTAGAGAGGATATATTTATAGACAGGGAATGAGAT
* * *
9955397 TTTGGTGTGTTGTGAG-AGAGGTAGAGAGGATGTATTTATAGACAGGGAATGA
1 TTTGGTATATTGTGAGTA-AGGTAGAGAGGATATATTTATAGACAGGGAATGA
9955449 AGTGTATTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 1 0.02
55 43 0.98
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.33
Consensus pattern (55 bp):
TTTGGTATATTGTGAGTAAGGTAGAGAGGATATATTTATAGACAGGGAATGAGAT
Found at i:9955782 original size:15 final size:15
Alignment explanation
Indices: 9955762--9955807 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
9955752 GTTTTGGTGT
9955762 GTTGTGAGTGAGGTA
1 GTTGTGAGTGAGGTA
9955777 GTTGTGAGTG-GTGTA
1 GTTGTGAGTGAG-GTA
9955792 GTTGTGAGTGAGGTA
1 GTTGTGAGTGAGGTA
9955807 G
1 G
9955808 CATGGTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.35
Consensus pattern (15 bp):
GTTGTGAGTGAGGTA
Found at i:9955835 original size:33 final size:33
Alignment explanation
Indices: 9955792--9955856 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
9955782 GAGTGGTGTA
*
9955792 GTTGTGAGTGAGGTAGCATGGTAGAGTACTTGT
1 GTTGTAAGTGAGGTAGCATGGTAGAGTACTTGT
9955825 GTTGTAAGTGAGGTAGCATGGTAGAGTACTTG
1 GTTGTAAGTGAGGTAGCATGGTAGAGTACTTG
9955857 AAAACTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.38, T:0.32
Consensus pattern (33 bp):
GTTGTAAGTGAGGTAGCATGGTAGAGTACTTGT
Found at i:9958432 original size:30 final size:30
Alignment explanation
Indices: 9958396--9958458 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
9958386 GAGTGTGGCA
9958396 CTTAGTTTTCAATAAAGCAAAAAATGTGAG
1 CTTAGTTTTCAATAAAGCAAAAAATGTGAG
* *
9958426 CTTAGTTTTCAATAAAGCGAGAAATGTGAG
1 CTTAGTTTTCAATAAAGCAAAAAATGTGAG
9958456 CTT
1 CTT
9958459 CTCTTCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (30 bp):
CTTAGTTTTCAATAAAGCAAAAAATGTGAG
Found at i:9958814 original size:12 final size:12
Alignment explanation
Indices: 9958797--9958824 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9958787 GTAAGGTTCG
9958797 AATTCTCTAAAT
1 AATTCTCTAAAT
9958809 AATTCTCTAAAT
1 AATTCTCTAAAT
9958821 AATT
1 AATT
9958825 AAACAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (12 bp):
AATTCTCTAAAT
Found at i:9959231 original size:39 final size:39
Alignment explanation
Indices: 9959188--9959326 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 39
9959178 AAATTGATAC
* *
9959188 TCATCATATAAATACACCAAAACATTCATAAATCAATAT
1 TCATCATATGAATAAACCAAAACATTCATAAATCAATAT
** * * * *
9959227 TCATCATATGAATAAACCAAATTACTCGTAAATAAAATTT
1 TCATCATATGAATAAACCAAAACATTCATAAAT-CAATAT
* * * *
9959267 TCATCATATGAATAAACTACAAGATTCATAAATC-ATGT
1 TCATCATATGAATAAACCAAAACATTCATAAATCAATAT
*
9959305 TTATCATATGAATAAACCAAAA
1 TCATCATATGAATAAACCAAAA
9959327 ACAGAAAATA
Statistics
Matches: 80, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
38 22 0.28
39 27 0.34
40 31 0.39
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (39 bp):
TCATCATATGAATAAACCAAAACATTCATAAATCAATAT
Found at i:9966498 original size:22 final size:21
Alignment explanation
Indices: 9966473--9966524 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
9966463 GACTTAATCG
*
9966473 TTACGTGACTGGTTTTTAAGCA
1 TTACGTGA-TGGATTTTAAGCA
* *
9966495 TTACGTGATTGATTTTAGGCA
1 TTACGTGATGGATTTTAAGCA
9966516 TTACGTGAT
1 TTACGTGAT
9966525 TAGCTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (21 bp):
TTACGTGATGGATTTTAAGCA
Found at i:9966535 original size:22 final size:21
Alignment explanation
Indices: 9966486--9966553 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
9966476 CGTGACTGGT
*
9966486 TTTTAAGCATTACGTGATTGA
1 TTTTAGGCATTACGTGATTGA
*
9966507 TTTTAGGCATTACGTGATTAGC
1 TTTTAGGCATTACGTGATT-GA
* * *
9966529 TTTTAGGTATTATGTGACTGA
1 TTTTAGGCATTACGTGATTGA
9966550 TTTT
1 TTTT
9966554 CAAGTAATGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 23 0.57
22 17 0.43
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (21 bp):
TTTTAGGCATTACGTGATTGA
Found at i:9966593 original size:23 final size:23
Alignment explanation
Indices: 9966567--9966687 Score: 149
Period size: 23 Copynumber: 5.3 Consensus size: 23
9966557 GTAATGCCTA
*
9966567 AGTCACACAATGCCTTACTAACT
1 AGTCACACAATACCTTACTAACT
* *
9966590 AGTCACGCAATGCCTTACTAACT
1 AGTCACACAATACCTTACTAACT
9966613 AGTCACACAATACCTTACTAACT
1 AGTCACACAATACCTTACTAACT
* *
9966636 AGTCAAACAATACCTTATTAA-T
1 AGTCACACAATACCTTACTAACT
*
9966658 AAGTCACGCAATACC-TA-TCAACT
1 -AGTCACACAATACCTTACT-AACT
9966681 AGTCACA
1 AGTCACA
9966688 AAATGTCATA
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
21 1 0.01
22 11 0.13
23 75 0.86
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (23 bp):
AGTCACACAATACCTTACTAACT
Found at i:9966750 original size:21 final size:21
Alignment explanation
Indices: 9966719--9966822 Score: 93
Period size: 21 Copynumber: 4.9 Consensus size: 21
9966709 CACAGTACTT
9966719 AAAAATTAGTCACGTAATACC
1 AAAAATTAGTCACGTAATACC
* *
9966740 CAAAGTTAGTCACGTAATACC
1 AAAAATTAGTCACGTAATACC
* * *
9966761 TAAAAATTAGTCACGCAATGCTT
1 -AAAAATTAGTCACGTAATAC-C
* *
9966784 AAAAACTAATCACGTAATATCC
1 AAAAATTAGTCACGTAATA-CC
* *
9966806 -AAAGTTAGTCACATAAT
1 AAAAATTAGTCACGTAAT
9966823 GTCCAAGTCA
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
21 32 0.50
22 31 0.48
23 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (21 bp):
AAAAATTAGTCACGTAATACC
Found at i:9966773 original size:22 final size:22
Alignment explanation
Indices: 9966718--9966802 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
9966708 ACACAGTACT
9966718 TAAAAATTAGTCACGTAATACC
1 TAAAAATTAGTCACGTAATACC
* *
9966740 -CAAAGTTAGTCACGTAATACC
1 TAAAAATTAGTCACGTAATACC
* * *
9966761 TAAAAATTAGTCACGCAATGCT
1 TAAAAATTAGTCACGTAATACC
* *
9966783 TAAAAACTAATCACGTAATA
1 TAAAAATTAGTCACGTAATA
9966803 TCCAAAGTTA
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 19 0.37
22 32 0.63
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (22 bp):
TAAAAATTAGTCACGTAATACC
Found at i:9966835 original size:20 final size:21
Alignment explanation
Indices: 9966793--9966843 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
9966783 TAAAAACTAA
* * *
9966793 TCACGTAATATCCAAAGTTAG
1 TCACATAATGTCCAAAGTCAG
9966814 TCACATAATGTCC-AAGTCAG
1 TCACATAATGTCCAAAGTCAG
9966834 TCACATAATG
1 TCACATAATG
9966844 CCTAAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (21 bp):
TCACATAATGTCCAAAGTCAG
Found at i:9972766 original size:20 final size:20
Alignment explanation
Indices: 9972725--9972762 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9972715 CATGAATAAT
* *
9972725 ACGATTAATATATGATTGAC
1 ACGATAAATATATGAATGAC
9972745 ACGATAAATATAT-AATGA
1 ACGATAAATATATGAATGA
9972763 ACACAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (20 bp):
ACGATAAATATATGAATGAC
Found at i:9978205 original size:74 final size:73
Alignment explanation
Indices: 9978062--9978252 Score: 228
Period size: 74 Copynumber: 2.6 Consensus size: 73
9978052 GTGAGATAGA
* *
9978062 AAGACTTAGTCGACTAAGAAACACTGTTAGTCAACTAAGAGCATACTACCAGAAATCTTAATTAT
1 AAGACTTAATCGACTAAGAAGCA-TGTTAGTCAACTAAGAGCATACTACCAGAAATCTTAATTAT
9978127 AAGACAAAG
65 AAGACAAAG
* ** *
9978136 -AGAACTTAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGC-TCACTGTCAGAGAT-TTCAAT
1 AAG-ACTTAATCGACTAAGAAGCAT-GTTAGTCAACTAAGAGCAT-ACTACCAGAAATCTT-AAT
*
9978198 T-TCAAGACAGAG
62 TAT-AAGACAAAG
9978210 AAGACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGAGCA
1 AAGACTTAATCGACTAAGAAGCAT-GTTAGTCAACTAAGAGCA
9978253 CTCTGTCTGA
Statistics
Matches: 101, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
73 7 0.07
74 92 0.91
75 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (73 bp):
AAGACTTAATCGACTAAGAAGCATGTTAGTCAACTAAGAGCATACTACCAGAAATCTTAATTATA
AGACAAAG
Done.