Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 68 of 208
Found at i:19791823 original size:30 final size:26
Alignment explanation
Indices: 19791761--19791825 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
19791751 AAATATGATA
*
19791761 TTTTTATTTCTTTTATTTTTAATTTT
1 TTTTTATTTATTTTATTTTTAATTTT
*
19791787 TGTTTATTTATTGTTATTTGTTTAATTTCT
1 TTTTTATTTATT-TTA-TT-TTTAATTT-T
19791817 TTTTTATTT
1 TTTTTATTT
19791826 GTAGGTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.31
27 3 0.09
28 2 0.06
29 8 0.25
30 9 0.28
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTTATTTATTTTATTTTTAATTTT
Found at i:19793541 original size:5 final size:5
Alignment explanation
Indices: 19793531--19793574 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
19793521 CTACACCACC
*
19793531 CTCCT CTCCT CGCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCC
1 CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCC
19793575 ATTTTCTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.00, C:0.61, G:0.02, T:0.36
Consensus pattern (5 bp):
CTCCT
Found at i:19801157 original size:33 final size:33
Alignment explanation
Indices: 19801120--19801396 Score: 160
Period size: 33 Copynumber: 7.5 Consensus size: 33
19801110 ATTGGTGGAT
*
19801120 TCAGCACTTAGCAACCACCAGTGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
*
19801153 TCAGCACTTAGCAACCCCTTTCACATTCAAAGATAT-GGTGGAA
1 TCAGCACTTAGCAA---C---CAC---CAATGAT-TCGG-GGAA
**
19801196 TCAGCACTTAGCAACCACCAATGATTTAGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* * *
19801229 TCAGCGCTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAA
1 TCAGCACTTAGCAA-CCAC--CA-A--T---GATTCGG-GGAA
* *
19801272 TCAACACTTAGCAACCACCAATGAATCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* *
19801305 TCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCACC---A-A--T---GATTCGG-GGAA
*
19801348 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
19801381 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
19801397 CCTTCATATT
Statistics
Matches: 191, Mismatches: 21, Indels: 64
0.69 0.08 0.23
Matches are distributed among these distances:
33 73 0.38
34 20 0.10
36 4 0.02
37 7 0.04
39 7 0.04
40 4 0.02
42 19 0.10
43 57 0.30
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGATTCGGGGAA
Found at i:19801210 original size:43 final size:42
Alignment explanation
Indices: 19801149--19801363 Score: 153
Period size: 43 Copynumber: 5.5 Consensus size: 42
19801139 AGTGATTCGG
19801149 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGT
1 GGAATCAGCACTTAGCAACCCC-TTCACATTCAAAGATATGGT
* * *
19801192 GGAATCAGCACTTAGCAA---C--CAC---CAATGATTTAG-
1 GGAATCAGCACTTAGCAACCCCTTCACATTCAAAGATATGGT
* * *
19801225 GGAATCAGCGCTTAGCAACCCCCTTCACATTTAAAGATACGGT
1 GGAATCAGCACTTAGCAA-CCCCTTCACATTCAAAGATATGGT
* *
19801268 GGAATCAACACTTAGCAA---C--CAC---CAATGA-ATCGG-
1 GGAATCAGCACTTAGCAACCCCTTCACATTCAAAGATAT-GGT
* * * *
19801301 GGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGT
1 GGAATCAGCACTTAGCAA-CCCCTTCACATTCAAAGATATGGT
19801344 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
19801364 ACCAATGAGT
Statistics
Matches: 130, Mismatches: 20, Indels: 45
0.67 0.10 0.23
Matches are distributed among these distances:
33 35 0.27
34 14 0.11
37 8 0.06
39 5 0.04
40 1 0.01
42 14 0.11
43 53 0.41
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCTTCACATTCAAAGATATGGT
Found at i:19801239 original size:76 final size:76
Alignment explanation
Indices: 19801113--19801409 Score: 445
Period size: 76 Copynumber: 3.9 Consensus size: 76
19801103 AACCGTTATT
* *
19801113 GGTGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACA
1 GGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACA
*
19801178 TTCAAAGATAT
66 TTCAAAGATAC
** * *
19801189 GGTGGAATCAGCACTTAGCAACCACCAATGATTTAGGGAATCAGCGCTTAGCAACCCCCTTCACA
1 GGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACA
*
19801254 TTTAAAGATAC
66 TTCAAAGATAC
* * *
19801265 GGTGGAATCAACACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTT-AT
1 GGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAA-CCCCTTTCAC
*
19801329 ATTTAAAGATAC
65 ATTCAAAGATAC
* *
19801341 GGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCC-TTCATA
1 GGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACA
19801405 TTCAA
66 TTCAA
19801410 TGTACTCCGG
Statistics
Matches: 201, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
74 2 0.01
75 11 0.05
76 182 0.91
77 6 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (76 bp):
GGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACA
TTCAAAGATAC
Found at i:19814663 original size:20 final size:19
Alignment explanation
Indices: 19814638--19814679 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19814628 CCAATATAGT
*
19814638 GGTCAATGCTCTTAGTTGAA
1 GGTCAATGCTC-GAGTTGAA
*
19814658 GGTCAATGTTCGAGTTGAA
1 GGTCAATGCTCGAGTTGAA
19814677 GGT
1 GGT
19814680 GATTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.24, C:0.12, G:0.31, T:0.33
Consensus pattern (19 bp):
GGTCAATGCTCGAGTTGAA
Found at i:19825235 original size:13 final size:14
Alignment explanation
Indices: 19825217--19825245 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19825207 TATTCTTCTA
19825217 AAAAATAGTT-ATT
1 AAAAATAGTTAATT
19825230 AAAAATAGTTAATT
1 AAAAATAGTTAATT
19825244 AA
1 AA
19825246 TTTTAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
AAAAATAGTTAATT
Found at i:19825354 original size:18 final size:18
Alignment explanation
Indices: 19825320--19825354 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19825310 TTAGAGTTTA
* *
19825320 TATCTAAATTTATTTAAT
1 TATCTAAATTAAATTAAT
19825338 TATCTAAATTAAATTAA
1 TATCTAAATTAAATTAA
19825355 ACTATGATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TATCTAAATTAAATTAAT
Found at i:19829856 original size:18 final size:20
Alignment explanation
Indices: 19829819--19829863 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
19829809 AAATAAATTC
19829819 ATTCAAT-T-AAGTACTTCA
1 ATTCAATCTCAAGTACTTCA
19829837 ATT-AATCTCAAGTA-TTCA
1 ATTCAATCTCAAGTACTTCA
19829855 ATTCAATCT
1 ATTCAATCT
19829864 ATAATTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 11 0.46
19 10 0.42
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (20 bp):
ATTCAATCTCAAGTACTTCA
Found at i:19830632 original size:8 final size:8
Alignment explanation
Indices: 19830621--19830645 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19830611 AACATTAAAT
19830621 AAATATTA
1 AAATATTA
19830629 AAATATTA
1 AAATATTA
19830637 AAATATTA
1 AAATATTA
19830645 A
1 A
19830646 CTCCCTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATATTA
Found at i:19833102 original size:92 final size:91
Alignment explanation
Indices: 19832886--19833113 Score: 307
Period size: 92 Copynumber: 2.5 Consensus size: 91
19832876 AATAATATTA
* * *
19832886 GTTGTGATATTAAATTAGTGAGCTATTTGGAGTAACGATAGTAAATAAGCTAACTCAAAGATTTT
1 GTTGTGATCTTAAATTAGTGAGCTATTTGGAGTAACGATAGAAAACAAGCTAACTCAAAGATTTT
19832951 TCATGATAGTAAATCAATGAACTTAG
66 TCATGATAGTAAATCAATGAACTTAG
* * ** * *
19832977 GCTGTGATCTTAAATCAGTGAGCTATTCAGAGTAACGGA-AGAAAACCAGTTAACTCAGAAGATT
1 GTTGTGATCTTAAATTAGTGAGCTATTTGGAGTAAC-GATAGAAAACAAGCTAACTCA-AAGATT
19833041 ATTT-ATGATAGTAAATCAATGAACTTAG
64 -TTTCATGATAGTAAATCAATGAACTTAG
* * *
19833069 GTTGTGATCTTAAATTAGTGAGCTGTTTGGAGTAGCGATACAAAA
1 GTTGTGATCTTAAATTAGTGAGCTATTTGGAGTAACGATAGAAAA
19833114 TCAACTGTTA
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
91 47 0.40
92 67 0.57
93 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (91 bp):
GTTGTGATCTTAAATTAGTGAGCTATTTGGAGTAACGATAGAAAACAAGCTAACTCAAAGATTTT
TCATGATAGTAAATCAATGAACTTAG
Found at i:19835065 original size:23 final size:23
Alignment explanation
Indices: 19835038--19835084 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
19835028 GAGCTCTTTT
19835038 TTGTTGAGCTGGTGAGTTTCCCC
1 TTGTTGAGCTGGTGAGTTTCCCC
19835061 TTGTTGAGCTGGTGAGTTTCCCC
1 TTGTTGAGCTGGTGAGTTTCCCC
19835084 T
1 T
19835085 AGATAACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.09, C:0.21, G:0.30, T:0.40
Consensus pattern (23 bp):
TTGTTGAGCTGGTGAGTTTCCCC
Found at i:19840604 original size:16 final size:14
Alignment explanation
Indices: 19840569--19840611 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
19840559 AAGGGAAGGG
19840569 AAAAAG-AAAG-AA
1 AAAAAGAAAAGAAA
19840581 AAAAAGAAAAGGAAA
1 AAAAAGAAAA-GAAA
19840596 AAAATAGAAAAGAAA
1 AAAA-AGAAAAGAAA
19840611 A
1 A
19840612 GATAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.22
13 3 0.11
14 1 0.04
15 11 0.41
16 6 0.22
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:19840953 original size:16 final size:17
Alignment explanation
Indices: 19840932--19840966 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
19840922 GTTATTTTGA
19840932 TTATTTTAATATT-TTT
1 TTATTTTAATATTGTTT
19840948 TTATTTTAATATTGTTT
1 TTATTTTAATATTGTTT
19840965 TT
1 TT
19840967 TTATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTATTTTAATATTGTTT
Found at i:19843072 original size:12 final size:12
Alignment explanation
Indices: 19843057--19843115 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
19843047 TATAGAGGTC
* *
19843057 GAGCCAGAGCTA
1 GAGCCCGAGCCA
* *
19843069 GAGCCTGAGCCG
1 GAGCCCGAGCCA
*
19843081 GAGCCTGAGCCA
1 GAGCCCGAGCCA
19843093 GAGCCCGAGCTC-
1 GAGCCCGAGC-CA
19843105 GAGCCCGAGCC
1 GAGCCCGAGCC
19843116 TGATAGGTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.02
12 39 0.95
13 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.36, T:0.07
Consensus pattern (12 bp):
GAGCCCGAGCCA
Found at i:19843078 original size:18 final size:17
Alignment explanation
Indices: 19843057--19843115 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
19843047 TATAGAGGTC
*
19843057 GAGCCAGAGCTAGAGCCT
1 GAGCCAGAGCT-GAGCCA
*
19843075 GAGCCGGAGCCTGAGCCA
1 GAGCCAGAG-CTGAGCCA
* *
19843093 GAGCCCGAGCTCGAGCCC
1 GAGCCAGAGCT-GAGCCA
19843111 GAGCC
1 GAGCC
19843116 TGATAGGTCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 2 0.06
18 31 0.89
19 2 0.06
ACGTcount: A:0.22, C:0.36, G:0.36, T:0.07
Consensus pattern (17 bp):
GAGCCAGAGCTGAGCCA
Found at i:19843731 original size:62 final size:62
Alignment explanation
Indices: 19843650--19843768 Score: 202
Period size: 62 Copynumber: 1.9 Consensus size: 62
19843640 TTTGTTTGTA
* *
19843650 ATATAAATTAAATACATTACATCACTAAAAATTGGAACCAACATTGTAATATAAATTGTGTT
1 ATATAAATTAAATACATTACAACACTAAAAATTGGAACAAACATTGTAATATAAATTGTGTT
* *
19843712 ATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATT
1 ATATAAATTAAATACATTACAACACTAAAAATTGGAACAAACATTGTAATATAAATT
19843769 AGGTACATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.34
Consensus pattern (62 bp):
ATATAAATTAAATACATTACAACACTAAAAATTGGAACAAACATTGTAATATAAATTGTGTT
Found at i:19847016 original size:27 final size:27
Alignment explanation
Indices: 19846985--19847047 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
19846975 CTAGGTGTGT
19846985 CGCCTATCAGATAGGCACCACTAGTGC
1 CGCCTATCAGATAGGCACCACTAGTGC
*** *
19847012 CGCCTATCAGATAGGGGTCACTGGTGC
1 CGCCTATCAGATAGGCACCACTAGTGC
19847039 CGCCTATCA
1 CGCCTATCA
19847048 AGTAGACACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.21
Consensus pattern (27 bp):
CGCCTATCAGATAGGCACCACTAGTGC
Found at i:19847951 original size:25 final size:26
Alignment explanation
Indices: 19847905--19847957 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
19847895 ATCAAATAAA
*
19847905 AAATATATATAATTTTAAATTTTATCT
1 AAATATATATAAATTT-AATTTTATCT
* *
19847932 AAATATTTATAAATTT-ATTTTTTCT
1 AAATATATATAAATTTAATTTTATCT
19847957 A
1 A
19847958 CTCACATTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
AAATATATATAAATTTAATTTTATCT
Found at i:19848373 original size:20 final size:22
Alignment explanation
Indices: 19848348--19848395 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
19848338 GTTAGCGAAC
19848348 AAATATGAATAT-AAATAAAA-
1 AAATATGAATATAAAATAAAAT
**
19848368 AAATATTTATATAAAATAAAAT
1 AAATATGAATATAAAATAAAAT
19848390 AAATAT
1 AAATAT
19848396 TTATATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 8 0.33
22 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATATGAATATAAAATAAAAT
Found at i:19848396 original size:22 final size:20
Alignment explanation
Indices: 19848356--19848401 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 20
19848346 ACAAATATGA
19848356 ATATAAATAAAAAAATATTT
1 ATATAAATAAAAAAATATTT
19848376 ATATAAAATAAAATAAATATTT
1 ATAT-AAATAAAA-AAATATTT
19848398 ATAT
1 ATAT
19848402 TTAGAATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 8 0.33
22 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAAATAAAAAAATATTT
Found at i:19848850 original size:20 final size:20
Alignment explanation
Indices: 19848825--19848873 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
19848815 AGGAGTCATT
*
19848825 AAATCAATTTGATTAAAATC
1 AAATCAAATTGATTAAAATC
*
19848845 AAATCAAATTGATTAGAATC
1 AAATCAAATTGATTAAAATC
*
19848865 AAATAAAAT
1 AAATCAAAT
19848874 CAAGATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATC
Found at i:19851012 original size:18 final size:17
Alignment explanation
Indices: 19850985--19851018 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19850975 TGTCTCAAAG
*
19850985 TTTTCAAAAATTACAAT
1 TTTTCAAAAATAACAAT
19851002 TTTTCCAAAAATAACAA
1 TTTT-CAAAAATAACAA
19851019 ATATTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTTCAAAAATAACAAT
Found at i:19851490 original size:18 final size:18
Alignment explanation
Indices: 19851469--19851503 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19851459 TCTAAGTTTT
*
19851469 TATTTTATTTATAAAATC
1 TATTTTATTTAAAAAATC
19851487 TATTTTATTTAAAAAAT
1 TATTTTATTTAAAAAAT
19851504 TATCATCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTTATTTAAAAAATC
Found at i:19853575 original size:13 final size:15
Alignment explanation
Indices: 19853557--19853588 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
19853547 ATGGAATGCT
19853557 TATGATAG-A-TTAA
1 TATGATAGCATTTAA
19853570 TATGATAGCATTTAA
1 TATGATAGCATTTAA
19853585 TATG
1 TATG
19853589 CTTATAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.41
Consensus pattern (15 bp):
TATGATAGCATTTAA
Found at i:19853620 original size:34 final size:34
Alignment explanation
Indices: 19853568--19853733 Score: 122
Period size: 34 Copynumber: 4.9 Consensus size: 34
19853558 ATGATAGATT
* ** *
19853568 AATATGATAGCATTTAATATGCTTATAATAGTTC
1 AATATGGTAGCAAATAATATGCTTATAACAGTTC
* * *
19853602 AATATGGTAGCAAATAATATACTTACAACGGATT-
1 AATATGGTAGCAAATAATATGCTTATAACAG-TTC
* * * * *
19853636 AATACGGTAGTAATTAATATGCTTCTAACAGATC
1 AATATGGTAGCAAATAATATGCTTATAACAGTTC
* * * *
19853670 AATAAGGTA-AAAACTAACATGCTTATAACAGATC
1 AATATGGTAGCAAA-TAATATGCTTATAACAGTTC
* *
19853704 AATGTGGT-GCCAAATAATATGTTTATAACA
1 AATATGGTAG-CAAATAATATGCTTATAACA
19853734 AATCACTATA
Statistics
Matches: 102, Mismatches: 25, Indels: 10
0.74 0.18 0.07
Matches are distributed among these distances:
33 3 0.03
34 94 0.92
35 5 0.05
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (34 bp):
AATATGGTAGCAAATAATATGCTTATAACAGTTC
Found at i:19864864 original size:41 final size:43
Alignment explanation
Indices: 19864818--19864899 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
19864808 CCATAAATTT
*
19864818 TTTGCAGAT-AAACTACCA-ATGGTTGTGGACACACAACAGAA
1 TTTGCAAATAAAACTACCACATGGTTGTGGACACACAACAGAA
* * *
19864859 TTTGCAAATGAAAACTGCCACATGGTTTTGGATACACAACA
1 TTTGCAAAT-AAAACTACCACATGGTTGTGGACACACAACA
19864900 AAATATCGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 8 0.24
43 8 0.24
44 18 0.53
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (43 bp):
TTTGCAAATAAAACTACCACATGGTTGTGGACACACAACAGAA
Found at i:19865220 original size:67 final size:68
Alignment explanation
Indices: 19865111--19865242 Score: 160
Period size: 67 Copynumber: 2.0 Consensus size: 68
19865101 TTCGACACAG
* * ***
19865111 TAGCAAATAATATGATCATAATGGATCAATACGGTGGTAATTAATATACTTATAACAGAAT-AAT
1 TAGCAAATAACATGATCATAATAGATCAATACGGTAACAATTAATATACTTATAACA-AATCAAT
19865175 ACGT
65 ACGT
* * **
19865179 TAGC-AATAACATGATTATAATAGATCAATGCGGTAACAATTAATATGTTTATAACAAATCAATA
1 TAGCAAATAACATGATCATAATAGATCAATACGGTAACAATTAATATACTTATAACAAATCAATA
19865243 TAGTAGCAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
66 3 0.06
67 47 0.87
68 4 0.07
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (68 bp):
TAGCAAATAACATGATCATAATAGATCAATACGGTAACAATTAATATACTTATAACAAATCAATA
CGT
Found at i:19865240 original size:34 final size:34
Alignment explanation
Indices: 19865135--19865242 Score: 87
Period size: 34 Copynumber: 3.2 Consensus size: 34
19865125 ATCATAATGG
***
19865135 ATCAATACGGTGGTAATTAATAT-ACTTATAACAGA
1 ATCAATACGGTAACAATTAATATGA-TTATAACA-A
* * * * *
19865170 AT-AATACGTTAGCAA-TAACATGATTATAATAG
1 ATCAATACGGTAACAATTAATATGATTATAACAA
* *
19865202 ATCAATGCGGTAACAATTAATATGTTTATAACAA
1 ATCAATACGGTAACAATTAATATGATTATAACAA
19865236 ATCAATA
1 ATCAATA
19865243 TAGTAGCAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
32 2 0.04
33 22 0.39
34 30 0.54
35 2 0.04
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (34 bp):
ATCAATACGGTAACAATTAATATGATTATAACAA
Found at i:19866110 original size:22 final size:22
Alignment explanation
Indices: 19866085--19866129 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
19866075 GATTCGATTA
19866085 ATGATAATTCTAAAATCGATGG
1 ATGATAATTCTAAAATCGATGG
*
19866107 ATGATAATTCTAAAATTGATGG
1 ATGATAATTCTAAAATCGATGG
19866129 A
1 A
19866130 AAGAACGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (22 bp):
ATGATAATTCTAAAATCGATGG
Found at i:19867767 original size:7 final size:7
Alignment explanation
Indices: 19867755--19867780 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19867745 TCAAATATAT
19867755 TAAAATG
1 TAAAATG
19867762 TAAAATG
1 TAAAATG
19867769 TAAAATG
1 TAAAATG
19867776 TAAAA
1 TAAAA
19867781 AATATTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
TAAAATG
Found at i:19871710 original size:10 final size:10
Alignment explanation
Indices: 19871695--19871720 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19871685 TTAATTTTAA
19871695 TTTTTAGAAT
1 TTTTTAGAAT
19871705 TTTTTAGAAT
1 TTTTTAGAAT
19871715 TTTTTA
1 TTTTTA
19871721 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (10 bp):
TTTTTAGAAT
Found at i:19882670 original size:20 final size:20
Alignment explanation
Indices: 19882647--19882684 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19882637 GCCTAGGTCG
*
19882647 CATTCTATTAGCCTTTGTGA
1 CATTATATTAGCCTTTGTGA
*
19882667 CATTATGTTAGCCTTTGT
1 CATTATATTAGCCTTTGT
19882685 AGTGTACTCT
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:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (20 bp):
CATTATATTAGCCTTTGTGA
Found at i:19889031 original size:26 final size:25
Alignment explanation
Indices: 19888963--19889036 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
19888953 ATATTTTCTA
* *
19888963 AAAATTTTACTGAAGGCAAAATCATC
1 AAAATTTTA-TGAGGGTAAAATCATC
**
19888989 AAAATTTTACCAGGGGTAAAATCATC
1 AAAATTTTATGA-GGGTAAAATCATC
19889015 AAAATTTTGATGAGGGTAAAAT
1 AAAATTTT-ATGAGGGTAAAAT
19889037 AGGGATAAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.03
26 37 0.93
27 2 0.05
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (25 bp):
AAAATTTTATGAGGGTAAAATCATC
Found at i:19892375 original size:27 final size:27
Alignment explanation
Indices: 19892345--19892411 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
19892335 AATGCACCAG
*
19892345 AGTGCCAATATCAATGAGTTGCATTGA
1 AGTGCCAATATCAATGAGTTGCATCGA
* * *
19892372 AGTGCCAATAACATTGTGTTGCATCGA
1 AGTGCCAATATCAATGAGTTGCATCGA
*
19892399 AGGGCCAATATCA
1 AGTGCCAATATCA
19892412 CTAATTTGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (27 bp):
AGTGCCAATATCAATGAGTTGCATCGA
Found at i:19893814 original size:13 final size:14
Alignment explanation
Indices: 19893782--19893813 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
19893772 AATTATCATG
19893782 ATTTTATATGAAAA
1 ATTTTATATGAAAA
19893796 ATTTTATATGAAAA
1 ATTTTATATGAAAA
19893810 ATTT
1 ATTT
19893814 AACACCACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
ATTTTATATGAAAA
Found at i:19898098 original size:13 final size:13
Alignment explanation
Indices: 19898080--19898105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19898070 TATCATGTGG
19898080 CATGTTTTATATA
1 CATGTTTTATATA
19898093 CATGTTTTATATA
1 CATGTTTTATATA
19898106 TCAATTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
CATGTTTTATATA
Found at i:19898809 original size:22 final size:22
Alignment explanation
Indices: 19898765--19898809 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19898755 AAATGCTGGG
**
19898765 CAATAGGCACCGTAATGTGAAT
1 CAATAGGCACCGTAATGCAAAT
*
19898787 CAATAGGCACCGTAGTGCAAAT
1 CAATAGGCACCGTAATGCAAAT
19898809 C
1 C
19898810 CTGTAAAAGC
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:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (22 bp):
CAATAGGCACCGTAATGCAAAT
Found at i:19910363 original size:12 final size:13
Alignment explanation
Indices: 19910342--19910375 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
19910332 GAAGTAAAAC
*
19910342 AAAGAAAAAAAATA
1 AAAGAAAAAATA-A
19910356 AAAGAAAAAATAA
1 AAAGAAAAAATAA
19910369 AAAGAAA
1 AAAGAAA
19910376 GAAGAAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (13 bp):
AAAGAAAAAATAA
Found at i:19921007 original size:49 final size:49
Alignment explanation
Indices: 19920964--19921074 Score: 150
Period size: 49 Copynumber: 2.3 Consensus size: 49
19920954 AAAAAGGTGG
* * ** *
19920964 GACCAAGGTGAAAGCCTACAAAGGGTGTTTTGAGTCAAAAAAAAAAAGA
1 GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAAAAGA
*
19921013 GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAAAAGA
1 GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAAAAGA
* *
19921062 GGCTAAGGTGAAA
1 GACCAAGGTGAAA
19921075 ACTCGTAAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.47, C:0.14, G:0.26, T:0.14
Consensus pattern (49 bp):
GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAAAAGA
Found at i:19922998 original size:50 final size:50
Alignment explanation
Indices: 19922544--19923006 Score: 374
Period size: 50 Copynumber: 9.3 Consensus size: 50
19922534 TTAAATCTTG
* * *
19922544 GAACAGATTGAAGCTACGACGGCGGATTTGGTTTCCATGATATTGCAATT
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATT
* * * * * *** * * * *
19922594 AAAGAGATTGAAGCCACAACGGTGGATCTTACTT-CCTTAGCAGTGCAGTG
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-CATTGCAATT
* *
19922644 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAATATTGCAATT
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATT
* * * * *** * * * *
19922694 AAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAGTG
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-CATTGCAATT
* * *
19922744 GAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATATTGTAATT
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATT
* * * * *** * * * *
19922794 AAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAGTG
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-CATTGCAATT
*
19922844 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATT
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATT
* * * * *** ** *
19922894 AAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCAATG
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATT
* *
19922944 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTGCAGTT
1 GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATT
*
19922994 GAACAAATTGAAG
1 GAACAGATTGAAG
19923007 ATTACAGATC
Statistics
Matches: 303, Mismatches: 104, Indels: 12
0.72 0.25 0.03
Matches are distributed among these distances:
49 11 0.04
50 280 0.92
51 12 0.04
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (50 bp):
GAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATT
Found at i:19923006 original size:100 final size:100
Alignment explanation
Indices: 19922542--19922990 Score: 774
Period size: 100 Copynumber: 4.5 Consensus size: 100
19922532 GATTAAATCT
* * *
19922542 TGGAACAGATTGAAGCTACGACGGCGGATTTGGTTTCCATGATATTGCAATTAAAGAGATTGAAG
1 TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAG
*
19922607 CCACAACGGTGGATCTTACTTCCTTAGCAGTGCAG
66 CCACAACGGCGGATCTTACTTCCTTAGCAGTGCAG
*
19922642 TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAATATTGCAATTAAAAAGATTGAAG
1 TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAG
19922707 CCACAACGGCGGATCTTACTTCCTTAGCAGTGCAG
66 CCACAACGGCGGATCTTACTTCCTTAGCAGTGCAG
* *
19922742 TGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATATTGTAATTAAAAAGATTGAAG
1 TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAG
19922807 CCACAACGGCGGATCTTACTTCCTTAGCAGTGCAG
66 CCACAACGGCGGATCTTACTTCCTTAGCAGTGCAG
19922842 TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAG
1 TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAG
* * *
19922907 CCACAACGGCGGATCTTACTTCCCT-GACGGTGCAA
66 CCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAG
* *
19922942 TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTGCA
1 TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCA
19922991 GTTGAACAAA
Statistics
Matches: 333, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
99 1 0.00
100 332 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (100 bp):
TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAG
CCACAACGGCGGATCTTACTTCCTTAGCAGTGCAG
Found at i:19923287 original size:132 final size:132
Alignment explanation
Indices: 19923011--19923287 Score: 362
Period size: 132 Copynumber: 2.1 Consensus size: 132
19923001 TTGAAGATTA
*
19923011 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGTGAATTTTACCTCCCTGTGGT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGTGAATTTTACCTCCCTGAGGT
* * *
19923076 TACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGAT
66 TACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGAGCAGCAATGGAATAGATTAAAGAC
*
19923141 TG
131 CG
* * * *
19923143 CATATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTTCCTGAGGT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGTGAATTTTACCTCCCTGAGGT
* * * * *
19923208 TACAGTGGAGTACATTGAAGCCAG-TATTCCTA-TCTCCTTGAAGCTGCAATGGAGTGGATTAAA
66 TACAGTGGAGTACATTGAAGCCAGCAATT-CTACT-TCCCTG-AGCAGCAATGGAATAGATTAAA
19923271 -ACCG
128 GACCG
* *
19923275 TAGATCTCATCTC
1 CAGATCTTATCTC
19923288 TCTGAAATTG
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
131 4 0.03
132 104 0.83
133 17 0.14
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (132 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGTGAATTTTACCTCCCTGAGGT
TACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGAGCAGCAATGGAATAGATTAAAGAC
CG
Found at i:19925272 original size:16 final size:15
Alignment explanation
Indices: 19925251--19925280 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19925241 TTAAACATTT
19925251 TTTATATACTCTATTA
1 TTTATATACT-TATTA
19925267 TTTATATACTTATT
1 TTTATATACTTATT
19925281 GCACATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTATATACTTATTA
Found at i:19926118 original size:37 final size:37
Alignment explanation
Indices: 19926068--19926142 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
19926058 CCGATTTTGG
19926068 GCGTTACGAGGGTGCTAACCCTTCCTCGTACGTAACT
1 GCGTTACGAGGGTGCTAACCCTTCCTCGTACGTAACT
*
19926105 GCGTTACGAGGGTGCTAACCCTTCCTCGTGCGTAACT
1 GCGTTACGAGGGTGCTAACCCTTCCTCGTACGTAACT
19926142 G
1 G
19926143 ACTCCCGAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (37 bp):
GCGTTACGAGGGTGCTAACCCTTCCTCGTACGTAACT
Found at i:19932365 original size:44 final size:43
Alignment explanation
Indices: 19932315--19932457 Score: 139
Period size: 44 Copynumber: 3.2 Consensus size: 43
19932305 TCTGCTCTAC
19932315 TGCAACTTCAGAGAGATGAGATCTGCGATTTTAATCCACTCCAT
1 TGCAACTTCAGAGAGAT-AGATCTGCGATTTTAATCCACTCCAT
* * ** *
19932359 TGCAACTTCA-AGGAGATAGGAT-TG-GCTTACTTCAGTCTGCTCCAC
1 TGCAACTTCAGA-GAGATA-GATCTGCGATT--TT-AATCCACTCCAT
* *
19932404 TGCAACTTCAGGGAGATAAGATCTGCGATTTTAATCCACTCCGT
1 TGCAACTTCAGAGAGAT-AGATCTGCGATTTTAATCCACTCCAT
19932448 TGCAACTTCA
1 TGCAACTTCA
19932458 AGAAGATTGG
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
42 3 0.04
43 4 0.05
44 37 0.47
45 28 0.36
46 3 0.04
47 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (43 bp):
TGCAACTTCAGAGAGATAGATCTGCGATTTTAATCCACTCCAT
Found at i:19932456 original size:89 final size:88
Alignment explanation
Indices: 19932305--19932512 Score: 344
Period size: 89 Copynumber: 2.4 Consensus size: 88
19932295 TCTGATGCGA
* * *
19932305 TCTGCTCTACTGCAACTTCAGAGAGATGAGATCTGCGATTTTAATCCACTCCATTGCAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCGATTTTAATCCACTCCATTGCAACTTCAA
*
19932370 GGAGATAGGATTGGCTTACTTCAG
66 GAAGATAGGATTGG-TTACTTCAG
*
19932394 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCGATTTTAATCCACTCCGTTGCAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCGATTTTAATCCACTCCATTGCAACTTCAA
*
19932459 GAAGATTGGATTGGTTACTTCAG
66 GAAGATAGGATTGGTTACTTCAG
*
19932482 TCTGCTCCACTGCAATTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
19932513 CTTGTATCTT
Statistics
Matches: 112, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
88 39 0.35
89 73 0.65
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (88 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCGATTTTAATCCACTCCATTGCAACTTCAA
GAAGATAGGATTGGTTACTTCAG
Found at i:19932496 original size:44 final size:45
Alignment explanation
Indices: 19932353--19932509 Score: 151
Period size: 44 Copynumber: 3.5 Consensus size: 45
19932343 TTTTAATCCA
* *
19932353 CTCCATTGCAACTTCAAGGAGATAGGATTGGCTTACTTCAGTCTG
1 CTCCACTGCAACTTCAAGGAGATAGGATTGGATTACTTCAGTCTG
* * * **
19932398 CTCCACTGCAACTTCAGGGAGATAAGATCTGCGATT--TT-AATCCA
1 CTCCACTGCAACTTCAAGGAGATAGGAT-TG-GATTACTTCAGTCTG
** * *
19932442 CTCCGTTGCAACTTCAAGAAGATTGGATTGG-TTACTTCAGTCTG
1 CTCCACTGCAACTTCAAGGAGATAGGATTGGATTACTTCAGTCTG
* *
19932486 CTCCACTGCAATTTCAGGGAGATA
1 CTCCACTGCAACTTCAAGGAGATA
19932510 AGACTTGTAT
Statistics
Matches: 85, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 4 0.05
44 46 0.54
45 27 0.32
46 2 0.02
47 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (45 bp):
CTCCACTGCAACTTCAAGGAGATAGGATTGGATTACTTCAGTCTG
Found at i:19932831 original size:50 final size:50
Alignment explanation
Indices: 19932770--19932918 Score: 156
Period size: 50 Copynumber: 3.0 Consensus size: 50
19932760 CAATGTCGGG
*
19932770 GAAACCAGATCCGCCGTCGTAGCTTCAATCTTTTCCACTGCACTGCTAAC
1 GAAACAAGATCCGCCGTCGTAGCTTCAATCTTTTCCACTGCACTGCTAAC
* * * ** * * * * **
19932820 GAAATAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTACAAT-ATCAGG
1 GAAACAAGATCCGCCGTCGTAGCTTCAATCTTTTCCACTGCACTGCT-AAC
* *
19932870 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAA
1 GAAACAAGATCCGCCGTCGTAGCTTCAATCTTTTCCACTGCACTGCTAA
19932919 GGAAGTAAAA
Statistics
Matches: 73, Mismatches: 24, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
49 1 0.01
50 71 0.97
51 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (50 bp):
GAAACAAGATCCGCCGTCGTAGCTTCAATCTTTTCCACTGCACTGCTAAC
Found at i:19933008 original size:44 final size:44
Alignment explanation
Indices: 19932960--19933174 Score: 162
Period size: 44 Copynumber: 4.9 Consensus size: 44
19932950 ATGCAACTTC
* *
19932960 AGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCAATCTTCAATCTGCTCCACTACTGCTT
* * * ** * **
19933004 AGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGGTAAAATCTGCAATCTTCAATCTGCTCCACTACTGCTT
* * * *** * * * * **
19933048 AGGGAAGTAGAAT-TACTGGCTTCAATGTACTTCACTGCAACTT
1 AGGGAGGTAAAATCTGCAATCTTCAATCTGCTCCACTACTGCTT
* *
19933091 CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTT
1 -AGGGAGGTAAAATCTGCAATCTTCAATCTGCTCCACTACTGCTT
* * * *
19933136 AGGGAGGCAAGATCTGAAATCTTCAACCTGCTCCACTAC
1 AGGGAGGTAAAATCTGCAATCTTCAATCTGCTCCACTAC
19933175 CTCCGAGGGA
Statistics
Matches: 124, Mismatches: 45, Indels: 4
0.72 0.26 0.02
Matches are distributed among these distances:
43 18 0.15
44 87 0.70
45 19 0.15
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (44 bp):
AGGGAGGTAAAATCTGCAATCTTCAATCTGCTCCACTACTGCTT
Found at i:19933097 original size:132 final size:131
Alignment explanation
Indices: 19932892--19933161 Score: 461
Period size: 132 Copynumber: 2.0 Consensus size: 131
19932882 GCCGTCGTAG
* *
19932892 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAAATTACTGGCTTCAATGTACTCCATGCAAC
1 CTTCAATCTATTCCACTG-ACTGCCAAGGAAGTAAAATTACTGGCTTCAATGTACTCCATGCAAC
19932957 TTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAA
65 TTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAA
19933022 AT
130 AT
* * *
19933024 CTTCAATCTATTCCACTG-CTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTTCACTGCAA
1 CTTCAATCTATTCCACTGACTG-CCAAGGAAGTAAAATTACTGGCTTCAATGTACTCCA-TGCAA
19933088 CTTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGA
64 CTTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGA
19933153 AAT
129 AAT
19933156 CTTCAA
1 CTTCAA
19933162 CCTGCTCCAC
Statistics
Matches: 131, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
130 3 0.02
131 32 0.24
132 96 0.73
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (131 bp):
CTTCAATCTATTCCACTGACTGCCAAGGAAGTAAAATTACTGGCTTCAATGTACTCCATGCAACT
TCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAA
T
Found at i:19933184 original size:44 final size:44
Alignment explanation
Indices: 19933092--19933187 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
19933082 CTGCAACTTC
* ** * * **
19933092 AGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGGCAAAATCTGAAATCTTCAACCTGCTCCACTACTGCCG
*
19933136 AGGGAGGCAAGATCTGAAATCTTCAACCTGCTCCACTACCT-CCG
1 AGGGAGGCAAAATCTGAAATCTTCAACCTGCTCCACTA-CTGCCG
19933180 AGGGAGGC
1 AGGGAGGC
19933188 GAGGTTGGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 41 0.95
45 2 0.05
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (44 bp):
AGGGAGGCAAAATCTGAAATCTTCAACCTGCTCCACTACTGCCG
Found at i:19938373 original size:20 final size:20
Alignment explanation
Indices: 19938348--19938385 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19938338 TAAAGAAATT
19938348 AAATGC-AATGGAAAATAATG
1 AAATGCAAAT-GAAAATAATG
19938368 AAATGCAAATGAAAATAA
1 AAATGCAAATGAAAATAA
19938386 CAAAACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (20 bp):
AAATGCAAATGAAAATAATG
Found at i:19943177 original size:51 final size:50
Alignment explanation
Indices: 19943113--19943229 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 50
19943103 AATTTCCACG
19943113 TCATTT-TCATTTTCATTTTGGAGAAAA-CTACATTCATTTCGAAATGTTT
1 TCATTTCTCATTTTCATTTTGGAGAAAATC-ACATTCATTTCGAAATGTTT
*
19943162 TCATTTCTCTATTTTCATTTTGGAGAAAATCACATTCATTTCTAAATGTTT
1 TCATTTCTC-ATTTTCATTTTGGAGAAAATCACATTCATTTCGAAATGTTT
19943213 TCATTTCTCCATTTTCA
1 TCATTTCT-CATTTTCA
19943230 CCATTTCTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
49 6 0.10
50 2 0.03
51 53 0.84
52 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (50 bp):
TCATTTCTCATTTTCATTTTGGAGAAAATCACATTCATTTCGAAATGTTT
Found at i:19948421 original size:21 final size:22
Alignment explanation
Indices: 19948385--19948425 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19948375 TGATTGTTTG
19948385 TATATTTTAAAAAATTTTAATA
1 TATATTTTAAAAAATTTTAATA
*
19948407 TATATTTT-TAAAATTTTAA
1 TATATTTTAAAAAATTTTAA
19948426 AATTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATATTTTAAAAAATTTTAATA
Found at i:19948425 original size:8 final size:8
Alignment explanation
Indices: 19948412--19948437 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
19948402 TAATATATAT
19948412 TTTTAAAA
1 TTTTAAAA
19948420 TTTTAAAA
1 TTTTAAAA
19948428 TTTTAAAA
1 TTTTAAAA
19948436 TT
1 TT
19948438 ATTTTTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTTAAAA
Found at i:19950208 original size:14 final size:14
Alignment explanation
Indices: 19950164--19950214 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
19950154 CCAATTTTTT
*
19950164 ATTTTAAATCTTCAA
1 ATTTTCAAT-TTCAA
19950179 ATTTT-AACTTTC-A
1 ATTTTCAA-TTTCAA
19950192 ATTTTCAATTTCAA
1 ATTTTCAATTTCAA
19950206 ATTTTCAAT
1 ATTTTCAAT
19950215 CATCAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 10 0.30
14 17 0.52
15 6 0.18
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTCAATTTCAA
Found at i:19950241 original size:13 final size:13
Alignment explanation
Indices: 19950219--19950248 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19950209 TTCAATCATC
*
19950219 AATTATTTTTTTA
1 AATTAGTTTTTTA
19950232 AATTAGTTTTTTA
1 AATTAGTTTTTTA
19950245 AATT
1 AATT
19950249 TATTATCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
AATTAGTTTTTTA
Found at i:19951984 original size:63 final size:63
Alignment explanation
Indices: 19951908--19952066 Score: 185
Period size: 63 Copynumber: 2.5 Consensus size: 63
19951898 TTTTTTTTGT
* * * * *** *
19951908 CACAATCATCACAACACGCACACTCATTCCCTGCATTATCACCTTC-AGTTTCGGTTTATTTTA
1 CACAATCACCACAACACGCACAATCATTCCCTGCATTAACACATTCAACACT-AGTTTATTTTA
*
19951971 CACAATCACCACAACACACACAATCATTCCCTGCATTAACACATTCAACACTAGTTTATTTTA
1 CACAATCACCACAACACGCACAATCATTCCCTGCATTAACACATTCAACACTAGTTTATTTTA
* * * *
19952034 CACAAGCACCACAACACGCCCCATCTTTCCCTG
1 CACAATCACCACAACACGCACAATCATTCCCTG
19952067 TAACAACATC
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 79 0.98
64 2 0.02
ACGTcount: A:0.31, C:0.35, G:0.06, T:0.27
Consensus pattern (63 bp):
CACAATCACCACAACACGCACAATCATTCCCTGCATTAACACATTCAACACTAGTTTATTTTA
Found at i:19957053 original size:41 final size:41
Alignment explanation
Indices: 19956989--19957129 Score: 156
Period size: 41 Copynumber: 3.4 Consensus size: 41
19956979 ATTATACTTG
** *
19956989 AATTGCACATACGTGCCATTGTTTGTTCTTCGATACCCCTA
1 AATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTA
* * *
19957030 AATTGAACATACATGCCCCTGTTTGTACTTCGATACCCTTA
1 AATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTA
* * * * * * *
19957071 AATTGCATATACGTTCCCCTGTTTATACTTTGGTACCCTTG
1 AATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTA
*
19957112 AATTACACATACGTGCCC
1 AATTGCACATACGTGCCC
19957130 TAATTCAGAT
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.35
Consensus pattern (41 bp):
AATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTA
Found at i:19959638 original size:41 final size:41
Alignment explanation
Indices: 19959581--19959956 Score: 466
Period size: 41 Copynumber: 9.2 Consensus size: 41
19959571 TAATTATACT
* *
19959581 TGAATTACACATACGTGCCCCTATTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
*
19959622 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCA
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
19959663 TAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* **
19959704 TGAATTGCATATTTGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
19959745 TAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
19959786 TAAATTGCATATTCGTGCCCCTATTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
19959827 TAAATTTCACATACGTGCCCCTATTTGTACTTCGGTACCTC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* ** *
19959868 TGAATTGCACATACGTGCCCCTATTTGTACTAGGGTA-CTC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * * * *
19959908 TGTATAGCACTTACGTGCCCCTGTTTATACATCTGGTAACCT
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTC-GGTACCCC
19959950 TGAATTG
1 TGAATTG
19959957 AATAATATAT
Statistics
Matches: 291, Mismatches: 42, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
40 28 0.10
41 257 0.88
42 6 0.02
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:19959705 original size:20 final size:19
Alignment explanation
Indices: 19959598--19959786 Score: 74
Period size: 20 Copynumber: 9.3 Consensus size: 19
19959588 CACATACGTG
*
19959598 CCCCTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTC-GTA
* * * *
19959618 CCCCTGAATTGCACATACGTG
1 CCCCTG-TTTGTAC-TTCGTA
19959639 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTC-GTA
* ** * * *
19959659 CCCATAAATTGCACATACGTG
1 CCCCT-GTTTGTAC-TTCGTA
19959680 CCCCTGTTTGTACTTCGATA
1 CCCCTGTTTGTACTTCG-TA
* * *
19959700 CCCCTGAATTGCATA-TTTGTG
1 CCCCTG-TTTG--TACTTCGTA
19959721 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTC-GTA
** * * *
19959741 CCCCTAAATTGCACATACGTG
1 CCCCT-GTTTGTAC-TTCGTA
19959762 CCCCTGTTTGTACTTCGATA
1 CCCCTGTTTGTACTTCG-TA
19959782 CCCCT
1 CCCCT
19959787 AAATTGCATA
Statistics
Matches: 118, Mismatches: 37, Indels: 28
0.64 0.20 0.15
Matches are distributed among these distances:
18 2 0.02
19 10 0.08
20 49 0.42
21 46 0.39
22 9 0.08
23 2 0.02
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (19 bp):
CCCCTGTTTGTACTTCGTA
Found at i:19970961 original size:13 final size:13
Alignment explanation
Indices: 19970945--19970995 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
19970935 TTTAAACCAA
19970945 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
19970958 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
19970971 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
19970984 ATTTTTCAAAAG
1 ACTTTTCAAAAG
19970996 TAATGAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:19972037 original size:30 final size:30
Alignment explanation
Indices: 19972002--19972065 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
19971992 TTTGATGAAC
19972002 TTAATTAGTTAAATTATTTTAAACAAAAAA
1 TTAATTAGTTAAATTATTTTAAACAAAAAA
19972032 TTAATTAGTTAAATTATTTTAAACAAAAAA
1 TTAATTAGTTAAATTATTTTAAACAAAAAA
19972062 TTAA
1 TTAA
19972066 CTAATATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
TTAATTAGTTAAATTATTTTAAACAAAAAA
Found at i:19972737 original size:6 final size:6
Alignment explanation
Indices: 19972726--19972772 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
19972716 AGCCAAAAAA
* * *
19972726 AAATAT AAATAT AAATAA AAATTT ATATAT AAA-AT AAAATAT AAATA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT -AAATAT AAATA
19972773 GCATAATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 2 0.06
6 29 0.88
7 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:19972745 original size:18 final size:17
Alignment explanation
Indices: 19972721--19972772 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
19972711 ATGTTAGCCA
19972721 AAAAAAAATATAAATAT
1 AAAAAAAATATAAATAT
* *
19972738 AAATAAAAATTTATATAT
1 AAA-AAAAATATAAATAT
19972756 AAAATAAAATATAAATA
1 AAAA-AAAATATAAATA
19972773 GCATAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAAAATATAAATAT
Found at i:19973766 original size:16 final size:17
Alignment explanation
Indices: 19973732--19973771 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
19973722 TATTTTATAT
*
19973732 AATATAA-TATGTACTA
1 AATATAATTATGTACAA
19973748 AATATAATTATGT-CAA
1 AATATAATTATGTACAA
19973764 AATA-AATT
1 AATATAATT
19973772 CATATCATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (17 bp):
AATATAATTATGTACAA
Found at i:19977799 original size:22 final size:23
Alignment explanation
Indices: 19977760--19977875 Score: 137
Period size: 22 Copynumber: 5.1 Consensus size: 23
19977750 CCCACAAATT
*
19977760 ACAACCAAACATAGCCTCCAAAC
1 ACAACCAAATATAGCCTCCAAAC
*
19977783 ACAACC-AATTTAGCCTCCAAAC
1 ACAACCAAATATAGCCTCCAAAC
* *
19977805 ACAACCAAACATACCCTCC-AAC
1 ACAACCAAATATAGCCTCCAAAC
* *
19977827 ATAACCAAATATAGCCTCCAAGC
1 ACAACCAAATATAGCCTCCAAAC
* * *
19977850 ACCACCAAATATACCCTTCAAAC
1 ACAACCAAATATAGCCTCCAAAC
19977873 ACA
1 ACA
19977876 TCTATTTAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
22 39 0.51
23 37 0.49
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.14
Consensus pattern (23 bp):
ACAACCAAATATAGCCTCCAAAC
Found at i:19977824 original size:45 final size:46
Alignment explanation
Indices: 19977760--19977875 Score: 155
Period size: 45 Copynumber: 2.6 Consensus size: 46
19977750 CCCACAAATT
* *
19977760 ACAACCAAACATAGCCTCCAAACACAACC-AATTTAGCCTCCAAAC
1 ACAACCAAACATACCCTCCAAACACAACCAAATATAGCCTCCAAAC
* *
19977805 ACAACCAAACATACCCTCC-AACATAACCAAATATAGCCTCCAAGC
1 ACAACCAAACATACCCTCCAAACACAACCAAATATAGCCTCCAAAC
* * *
19977850 ACCACCAAATATACCCTTCAAACACA
1 ACAACCAAACATACCCTCCAAACACA
19977876 TCTATTTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 8 0.13
45 48 0.79
46 5 0.08
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.14
Consensus pattern (46 bp):
ACAACCAAACATACCCTCCAAACACAACCAAATATAGCCTCCAAAC
Found at i:19980082 original size:44 final size:44
Alignment explanation
Indices: 19980019--19980103 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
19980009 GTGTTATATT
*
19980019 TCAAATGATGTAAACATCTTATTGGAGTTTTTATGCCATTTGGC
1 TCAAATGATGTAAACATCTTATTGGAGTTTTTATCCCATTTGGC
*
19980063 TCAAATGATGTAAATATCTTATTGGAGTTTTTATCCCATTT
1 TCAAATGATGTAAACATCTTATTGGAGTTTTTATCCCATTT
19980104 AGGTCATACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (44 bp):
TCAAATGATGTAAACATCTTATTGGAGTTTTTATCCCATTTGGC
Found at i:19985834 original size:231 final size:231
Alignment explanation
Indices: 19985431--19985895 Score: 912
Period size: 231 Copynumber: 2.0 Consensus size: 231
19985421 ACAAAGTAAG
19985431 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
1 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
19985496 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
66 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
19985561 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
131 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
19985626 TAAGGCACTTCAATACTTATCACATACCACATATCA
196 TAAGGCACTTCAATACTTATCACATACCACATATCA
19985662 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
1 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
*
19985727 GAAAATGTCATACGTCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
66 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
19985792 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
131 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
*
19985857 TAAGGCACTTCAATACTTATCACATATCACATATCA
196 TAAGGCACTTCAATACTTATCACATACCACATATCA
19985893 AAT
1 AAT
19985896 ATAAAACATA
Statistics
Matches: 232, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
231 232 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (231 bp):
AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
TAAGGCACTTCAATACTTATCACATACCACATATCA
Found at i:19989074 original size:25 final size:25
Alignment explanation
Indices: 19989046--19989110 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
19989036 CTGTTTTTGA
*
19989046 TAGTATATCCTAAAACTACTATATG
1 TAGTATATACTAAAACTACTATATG
* * *
19989071 TAGTGTATACTGAGACTACTATA-G
1 TAGTATATACTAAAACTACTATATG
**
19989095 ATAGGCTATACTAAAA
1 -TAGTATATACTAAAA
19989111 ACACTCAAGT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
24 1 0.03
25 30 0.97
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (25 bp):
TAGTATATACTAAAACTACTATATG
Found at i:20014381 original size:24 final size:24
Alignment explanation
Indices: 20014350--20014397 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
20014340 AATGCATTCA
* *
20014350 TTTGAATTT-TGGAAATTTTATGT
1 TTTGAATTTATGAAAATTGTATGT
20014373 TTTGCAATTTATGAAAATTGTATGT
1 TTTG-AATTTATGAAAATTGTATGT
20014398 GACTATAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 12 0.57
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (24 bp):
TTTGAATTTATGAAAATTGTATGT
Found at i:20016324 original size:31 final size:31
Alignment explanation
Indices: 20016281--20016346 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
20016271 AACTCTAATT
** *
20016281 GTTA-TGTAACACCCCTCACCCGATCTAGAA
1 GTTATTGTAACACCCCAAACCCGACCTAGAA
* *
20016311 GTTATTGTCACACCCCAAACCCGACCTAGAC
1 GTTATTGTAACACCCCAAACCCGACCTAGAA
20016342 GTTAT
1 GTTAT
20016347 GGCCGAATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (31 bp):
GTTATTGTAACACCCCAAACCCGACCTAGAA
Found at i:20019482 original size:12 final size:12
Alignment explanation
Indices: 20019467--20019575 Score: 92
Period size: 12 Copynumber: 9.1 Consensus size: 12
20019457 CCAGAGACAA
20019467 ATACAGATGCAG
1 ATACAGATGCAG
**
20019479 ATACAGACCCAG
1 ATACAGATGCAG
* **
20019491 ATATAGATATAG
1 ATACAGATGCAG
*
20019503 ATACAGATGCGG
1 ATACAGATGCAG
* *
20019515 ATACAGATGTAA
1 ATACAGATGCAG
* *
20019527 ACACAGATTCAG
1 ATACAGATGCAG
*
20019539 ATACAAATGCAG
1 ATACAGATGCAG
* *
20019551 ACACAGATTCAG
1 ATACAGATGCAG
*
20019563 TTACAGATGCAG
1 ATACAGATGCAG
20019575 A
1 A
20019576 CACCAATCCT
Statistics
Matches: 70, Mismatches: 27, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 70 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.19
Consensus pattern (12 bp):
ATACAGATGCAG
Found at i:20019485 original size:6 final size:6
Alignment explanation
Indices: 20019467--20019575 Score: 56
Period size: 6 Copynumber: 18.2 Consensus size: 6
20019457 CCAGAGACAA
* ** * * * *
20019467 ATACAG ATGCAG ATACAG ACCCAG ATATAG ATATAG ATACAG ATGCGG
1 ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG
** * * * * * * *
20019515 ATACAG ATGTAA ACACAG ATTCAG ATACAA ATGCAG ACACAG ATTCAG
1 ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG
* *
20019563 TTACAG ATGCAG A
1 ATACAG ATACAG A
20019576 CACCAATCCT
Statistics
Matches: 70, Mismatches: 33, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.19
Consensus pattern (6 bp):
ATACAG
Found at i:20019789 original size:25 final size:27
Alignment explanation
Indices: 20019730--20019789 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 27
20019720 TGCGGTAAAT
20019730 TACCA-AAATCAAATAAGTGTGGTCAA
1 TACCACAAATCAAATAAGTGTGGTCAA
* *
20019756 -GCCATCAAATCAAAT-A-TGTGGTTAA
1 TACCA-CAAATCAAATAAGTGTGGTCAA
20019781 TACCACAAA
1 TACCACAAA
20019790 ATAAGTCATC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
25 15 0.54
26 4 0.14
27 9 0.32
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (27 bp):
TACCACAAATCAAATAAGTGTGGTCAA
Found at i:20021389 original size:21 final size:21
Alignment explanation
Indices: 20021365--20021407 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
20021355 GAGATATCAA
20021365 AAATACAGTAGGTGATAAGGT
1 AAATACAGTAGGTGATAAGGT
20021386 AAATACAGTAGGTGATAAGGT
1 AAATACAGTAGGTGATAAGGT
20021407 A
1 A
20021408 TTCTTGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATACAGTAGGTGATAAGGT
Found at i:20022892 original size:15 final size:15
Alignment explanation
Indices: 20022872--20022904 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
20022862 AGATACAATT
20022872 TTTTTAATTT-TTTAA
1 TTTTT-ATTTGTTTAA
20022887 TTTTTATTTGTTTAA
1 TTTTTATTTGTTTAA
20022902 TTT
1 TTT
20022905 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTATTTGTTTAA
Found at i:20026489 original size:24 final size:23
Alignment explanation
Indices: 20026456--20026500 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
20026446 ATTCTGAACA
20026456 TTTTTATTT-ATTTATATTTGGAC
1 TTTTTATTTAATTT-TATTTGGAC
20026479 TTTTTACTTTAATTTTATTTGG
1 TTTTTA-TTTAATTTTATTTGG
20026501 GATGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.20, C:0.04, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTTTATTTAATTTTATTTGGAC
Found at i:20028415 original size:32 final size:32
Alignment explanation
Indices: 20028375--20028498 Score: 158
Period size: 32 Copynumber: 3.9 Consensus size: 32
20028365 ATAAGTATAA
* * *
20028375 TAATATGATTGGCATAAAGCCATCAGTAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * * *
20028407 TGATATGATCAGCACACAGCCATCAGTAATAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* *
20028439 TAATATGATCGGTACAAAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
*
20028471 TAATATAATCGGCACAAAGCCATCAGTA
1 TAATATGATCGGCACAAAGCCATCAGTA
20028499 GCATCGTAGC
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAACAG
Found at i:20028461 original size:64 final size:64
Alignment explanation
Indices: 20028360--20028498 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 64
20028350 GAATGGCTAC
* * * * * *
20028360 AAGCCATAAGT-ATAATAATATGATTGGCATAAAGCCATCAGTAGCAGTGATATGATCAGCACA
1 AAGCCATCAGTAATAATAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACA
* * * * *
20028423 CAGCCATCAGTAATAGTAATATGATCGGTACAAAGCCATCAGTAACGGTAATATAATCGGCACA
1 AAGCCATCAGTAATAATAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACA
20028487 AAGCCATCAGTA
1 AAGCCATCAGTA
20028499 GCATCGTAGC
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
63 9 0.14
64 54 0.86
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (64 bp):
AAGCCATCAGTAATAATAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACA
Found at i:20028693 original size:11 final size:11
Alignment explanation
Indices: 20028677--20028722 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
20028667 CAGAATCAGT
20028677 CATACAAATCA
1 CATACAAATCA
20028688 CATACAAATCAA
1 CATACAAATC-A
*
20028700 TCATACTAATCA
1 -CATACAAATCA
*
20028712 CAGACAAATCA
1 CATACAAATCA
20028723 ATCATTTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 19 0.63
12 2 0.07
13 9 0.30
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (11 bp):
CATACAAATCA
Found at i:20028703 original size:24 final size:24
Alignment explanation
Indices: 20028670--20028751 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
20028660 CCATGCTCAG
* *
20028670 AATCAGTCATACAAATCACATACA
1 AATCAATCATACAAATCACAGACA
*
20028694 AATCAATCATACTAATCACAGACA
1 AATCAATCATACAAATCACAGACA
** * *
20028718 AATCAATCATTTACATCACGGACA
1 AATCAATCATACAAATCACAGACA
*
20028742 AATAAATCAT
1 AATCAATCAT
20028752 TTACACTCGA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (24 bp):
AATCAATCATACAAATCACAGACA
Found at i:20028752 original size:24 final size:24
Alignment explanation
Indices: 20028684--20028756 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
20028674 AGTCATACAA
* *
20028684 ATCACATACAAATCAATCATACTA-
1 ATCACAGACAAATCAATCAT-TTAC
20028708 ATCACAGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
* *
20028732 ATCACGGACAAATAAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
20028756 A
1 A
20028757 CTCGAGAGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:20028825 original size:27 final size:27
Alignment explanation
Indices: 20028771--20029155 Score: 237
Period size: 27 Copynumber: 14.4 Consensus size: 27
20028761 AGAGGAAAAA
* * * *
20028771 GTCA-TTTACCCTTCAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTTCG
* *
20028797 GTCATTTTACCTTACAGTGGTATTTCG
1 GTCATTTTACCCTACAGGGGTATTTCG
* * *
20028824 GTCATTTAACCCTA-TGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTTCG
* *
20028850 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTTCG
* **
20028877 GTTATTTTACCCTATGGGGGT-TTTCG
1 GTCATTTTACCCTACAGGGGTATTTCG
*
20028903 GT-ATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTTCG
**
20028929 GTCATTTTA-CCTATCAATGGTA-TTCTG
1 GTCATTTTACCCTA-CAGGGGTATTTC-G
* * *
20028956 ATAATTTTA-TCTATC-GAGGGTATTTCG
1 GTCATTTTACCCTA-CAG-GGGTATTTCG
* *
20028983 GTCATTTTACCC-ATTAGGGGTATTT-T
1 GTCATTTTACCCTA-CAGGGGTATTTCG
** **
20029009 GAAATTTTACCC-ATC-GAGGGTATTTTA
1 GTCATTTTACCCTA-CAG-GGGTATTTCG
* *
20029036 GTCATTTTACCC-ATC-GAGGATAATTCG
1 GTCATTTTACCCTA-CAG-GGGTATTTCG
* * *
20029063 GTCATTTTACCCTTCAGGGGTAATTCA
1 GTCATTTTACCCTACAGGGGTATTTCG
* * *
20029090 GTCATTTTACCCTTCAGGGGTAATTCA
1 GTCATTTTACCCTACAGGGGTATTTCG
20029117 GTCATTTTACCCCT-C-GAGGGTAATTT-G
1 GTCATTTTA-CCCTACAG-GGGT-ATTTCG
20029144 GTCATTTTACCC
1 GTCATTTTACCC
20029156 CTCGGGGGTA
Statistics
Matches: 292, Mismatches: 50, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
25 17 0.06
26 68 0.23
27 194 0.66
28 13 0.04
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTTCG
Found at i:20028829 original size:53 final size:53
Alignment explanation
Indices: 20028771--20028935 Score: 167
Period size: 53 Copynumber: 3.1 Consensus size: 53
20028761 AGAGGAAAAA
* * * *
20028771 GTCATTTACCCTTCA-AGGGCATTACGGTCATTTTACCTTACAGTGGTATTTCG
1 GTCATTTACCCTT-ATAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACG
* *
20028824 GTCATTTAACCC-TATGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACG
1 GTCATTT-ACCCTTATAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACG
* * ** * *
20028877 GTTATTTTACCC-TATGGGGGTTTTCGGT-ATTTTACCCTACAGGGGTATTACG
1 GTCA-TTTACCCTTATAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACG
20028929 GTCATTT
1 GTCATTT
20028936 TACCTATCAA
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
51 3 0.03
52 27 0.28
53 60 0.62
54 7 0.07
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (53 bp):
GTCATTTACCCTTATAGGGCATTACGGTCATTTTACCCTACAGGGGCATTACG
Found at i:20028963 original size:79 final size:80
Alignment explanation
Indices: 20028771--20029155 Score: 244
Period size: 80 Copynumber: 4.8 Consensus size: 80
20028761 AGAGGAAAAA
* * * *
20028771 GTCA-TTTACCCTTCAAGGGCATTACGGTCATTTTACCT-TAC-AGTGGTATTTCGGTCATTTAA
1 GTCATTTTACCCTACAAGGGCATTACGATAATTTTACCTAT-CGAG-GGTATTTCGGTCATTTTA
*
20028833 CCCTATGGGGTATTACG
64 CCCTAAGGGGTATTACG
* * * *
20028850 GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTAT-GGGGGT-TTTCGGT-ATTTTAC
1 GTCATTTTACCCTACAAGGGCATTACGATAATTTTA-CCTATCGAGGGTATTTCGGTCATTTTAC
20028912 CCTACAGGGGTATTACG
65 CCTA-AGGGGTATTACG
* * *
20028929 GTCATTTTA-CCTATCAATGGTATT-CTGATAATTTTATCTATCGAGGGTATTTCGGTCATTTTA
1 GTCATTTTACCCTA-CAAGGGCATTAC-GATAATTTTACCTATCGAGGGTATTTCGGTCATTTTA
* **
20028992 CCCATTAGGGGTATT-TT
64 CCC-TAAGGGGTATTACG
** * * * * * *
20029009 GAAATTTTACCC-ATCGAGGGTATTTTA-G-TCATTTTACCCATCGAGGATAATTCGGTCATTTT
1 GTCATTTTACCCTA-CAAGGGCA--TTACGATAATTTTACCTATCGAGGGTATTTCGGTCATTTT
* *
20029071 ACCCTTCAGGGGTAATT-CA
63 ACCC-TAAGGGGT-ATTACG
* * * * **
20029090 GTCATTTTACCCTTCAGGGGTAATT-C-AGTCATTTTACCCCTCGAGGGTAATTT-GGTCATTTT
1 GTCATTTTACCCTACAAGGG-CATTACGA-TAATTTTACCTATCGAGGGT-ATTTCGGTCATTTT
20029152 ACCC
63 ACCC
20029156 CTCGGGGGTA
Statistics
Matches: 246, Mismatches: 38, Indels: 42
0.75 0.12 0.13
Matches are distributed among these distances:
78 19 0.08
79 51 0.21
80 95 0.39
81 73 0.30
82 8 0.03
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (80 bp):
GTCATTTTACCCTACAAGGGCATTACGATAATTTTACCTATCGAGGGTATTTCGGTCATTTTACC
CTAAGGGGTATTACG
Found at i:20029134 original size:81 final size:80
Alignment explanation
Indices: 20028815--20029177 Score: 278
Period size: 81 Copynumber: 4.5 Consensus size: 80
20028805 ACCTTACAGT
* * * * * *
20028815 GGTATTTCGGTCATTTAACCC-T-ATGGGGTATTACGGTCATTTTACCCTACAGGGG-CATTACG
1 GGTAATTCGGTCATTTTACCCTTCA-GGGGTATT-CAGTCATTTTACCCTTCAGGGGTAATT-CA
* *
20028877 GTTATTTTACCCTAT-GGG
63 GTCATTTTACCC-ATCGAG
* * * ** *
20028895 GGT-TTTCGGT-ATTTTACCCTACAGGGGTATTACGGTCATTTTA-CCTATCAATGGT-ATTCTG
1 GGTAATTCGGTCATTTTACCCTTCAGGGGTATT-CAGTCATTTTACCCT-TCAGGGGTAATTCAG
* * *
20028956 ATAATTTTATCTATCGAG
64 -TCATTTTACCCATCGAG
* ** ** * * *
20028974 GGTATTTCGGTCATTTTACCCATT-AGGGGTATTTTGAAATTTTACCCATC-GAGGGTATTTTAG
1 GGTAATTCGGTCATTTTACCC-TTCAGGGGTATTCAGTCATTTTACCCTTCAG-GGGTAATTCAG
20029037 TCATTTTACCCATCGAG
64 TCATTTTACCCATCGAG
*
20029054 GATAATTCGGTCATTTTACCCTTCAGGGGTAATTCAGTCATTTTACCCTTCAGGGGTAATTCAGT
1 GGTAATTCGGTCATTTTACCCTTCAGGGGT-ATTCAGTCATTTTACCCTTCAGGGGTAATTCAGT
*
20029119 CATTTTACCCCTCGAG
65 CATTTTACCCATCGAG
* * * *
20029135 GGTAATTTGGTCATTTTACCCCTCGGGGGTAATTCAATCATTT
1 GGTAATTCGGTCATTTTACCCTTCAGGGGT-ATTCAGTCATTT
20029178 AACAAATATT
Statistics
Matches: 229, Mismatches: 39, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
78 15 0.07
79 49 0.21
80 62 0.27
81 101 0.44
82 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (80 bp):
GGTAATTCGGTCATTTTACCCTTCAGGGGTATTCAGTCATTTTACCCTTCAGGGGTAATTCAGTC
ATTTTACCCATCGAG
Found at i:20029156 original size:27 final size:27
Alignment explanation
Indices: 20028959--20029177 Score: 178
Period size: 27 Copynumber: 8.1 Consensus size: 27
20028949 TATTCTGATA
* * *
20028959 ATTTTATCTATCGAGGGT-ATTTCGGTC
1 ATTTTACCCATCGAGGGTAATTT-AGTC
* * **
20028986 ATTTTACCCAT-TAGGGGT-ATTTTGAA
1 ATTTTACCCATCGA-GGGTAATTTAGTC
*
20029012 ATTTTACCCATCGAGGGTATTTTAGTC
1 ATTTTACCCATCGAGGGTAATTTAGTC
* **
20029039 ATTTTACCCATCGAGGATAATTCGGTC
1 ATTTTACCCATCGAGGGTAATTTAGTC
* *
20029066 ATTTTACCCTTC-AGGGGTAATTCAGTC
1 ATTTTACCCATCGA-GGGTAATTTAGTC
* *
20029093 ATTTTACCCTTC-AGGGGTAATTCAGTC
1 ATTTTACCCATCGA-GGGTAATTTAGTC
* *
20029120 ATTTTACCCCTCGAGGGTAATTTGGTC
1 ATTTTACCCATCGAGGGTAATTTAGTC
* * * *
20029147 ATTTTACCCCTCGGGGGTAATTCAATC
1 ATTTTACCCATCGAGGGTAATTTAGTC
20029174 ATTT
1 ATTT
20029178 AACAAATATT
Statistics
Matches: 162, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
26 18 0.11
27 143 0.88
28 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTAATTTAGTC
Found at i:20029164 original size:54 final size:54
Alignment explanation
Indices: 20028959--20029177 Score: 212
Period size: 54 Copynumber: 4.1 Consensus size: 54
20028949 TATTCTGATA
* * * * ** **
20028959 ATTTTATCTATCGAGGGT-ATTTCGGTCATTTTACCCATTAGGGGT-ATTTTGAA
1 ATTTTACCCATCGAGGGTAATTT-AGTCATTTTACCCATCAGGGGTAATTCAGTC
* * *
20029012 ATTTTACCCATCGAGGGTATTTTAGTCATTTTACCCATC-GAGGATAATTCGGTC
1 ATTTTACCCATCGAGGGTAATTTAGTCATTTTACCCATCAG-GGGTAATTCAGTC
* * *
20029066 ATTTTACCCTTC-AGGGGTAATTCAGTCATTTTACCCTTCAGGGGTAATTCAGTC
1 ATTTTACCCATCGA-GGGTAATTTAGTCATTTTACCCATCAGGGGTAATTCAGTC
* * * * *
20029120 ATTTTACCCCTCGAGGGTAATTTGGTCATTTTACCCCTCGGGGGTAATTCAATC
1 ATTTTACCCATCGAGGGTAATTTAGTCATTTTACCCATCAGGGGTAATTCAGTC
20029174 ATTT
1 ATTT
20029178 AACAAATATT
Statistics
Matches: 138, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
52 1 0.01
53 34 0.25
54 101 0.73
55 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (54 bp):
ATTTTACCCATCGAGGGTAATTTAGTCATTTTACCCATCAGGGGTAATTCAGTC
Found at i:20029845 original size:12 final size:13
Alignment explanation
Indices: 20029828--20029856 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20029818 ACTAAAACTT
20029828 AAAAGAAAGAAA-
1 AAAAGAAAGAAAG
20029840 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
20029853 AAAA
1 AAAA
20029857 AACCTAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:20030778 original size:41 final size:41
Alignment explanation
Indices: 20030698--20030806 Score: 121
Period size: 41 Copynumber: 2.7 Consensus size: 41
20030688 TCGGGCTCTG
* * *
20030698 TGCCTAGCAAGCTTTATGCCGGTGAATTATAGCAGGCTTTA
1 TGCCTAGCAGGCTTTATGCCGGTGTATCATAGCAGGCTTTA
** * *
20030739 TGCCTAGCAGGCTTCGTGCCGGTGTATCATATCTA-GCTTTG
1 TGCCTAGCAGGCTTTATGCCGGTGTATCATAGC-AGGCTTTA
* *
20030780 TGCCTAGAAGGATTTATGCCGGTGTAT
1 TGCCTAGCAGGCTTTATGCCGGTGTAT
20030807 TTTAATAAGC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 55 0.98
42 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (41 bp):
TGCCTAGCAGGCTTTATGCCGGTGTATCATAGCAGGCTTTA
Found at i:20031499 original size:12 final size:12
Alignment explanation
Indices: 20031482--20031507 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20031472 TTATATCTCG
20031482 TGTCTAGAAATA
1 TGTCTAGAAATA
20031494 TGTCTAGAAATA
1 TGTCTAGAAATA
20031506 TG
1 TG
20031508 GTGTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (12 bp):
TGTCTAGAAATA
Found at i:20031726 original size:2 final size:2
Alignment explanation
Indices: 20031719--20031761 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
20031709 ATGGAATGTT
20031719 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
20031761 T
1 T
20031762 GTTATGTTTA
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:20034923 original size:41 final size:40
Alignment explanation
Indices: 20034855--20035013 Score: 149
Period size: 41 Copynumber: 3.9 Consensus size: 40
20034845 TGAAAATAAG
* * *
20034855 ATGTTTCAGACTTTACGTCCAAGAGGCTTGATGCCGATGAA
1 ATGTTTCAGACTTTATGT-CTACAGGCTTGATGCCGATGAA
20034896 ATGTTTCAGACTTTATGTCTACTAGGCTTGATGCCGATGAA
1 ATGTTTCAGACTTTATGTCTAC-AGGCTTGATGCCGATGAA
* ** *
20034937 TTACTTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTA-CAGGC-TTGATGCCGATGAA
* * * * * *
20034978 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCG
1 ATGTTTCAGACTTTATGTCTA-CAGGCTTGATGCCG
20035014 GTGTTTTATA
Statistics
Matches: 98, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 4 0.04
41 90 0.92
42 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (40 bp):
ATGTTTCAGACTTTATGTCTACAGGCTTGATGCCGATGAA
Found at i:20035005 original size:82 final size:82
Alignment explanation
Indices: 20034859--20035013 Score: 181
Period size: 82 Copynumber: 1.9 Consensus size: 82
20034849 AATAAGATGT
* *
20034859 TTCAGACTTTACGTCCAAGAGGCTTGATGCCGATGAAATGTTTCAGACTTTATGTCTACTAGGCT
1 TTCAGACTTTACGTCCAAGAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTACTAGGCT
20034924 TGATGCCGATGAATTAC
66 TGATGCCGATGAATTAC
* * * * * *
20034941 TTCAGACTTTATGT-CTAGCAGGCTTTG-TGCCGGTGAAATGTATCGGGCTTTGTGCCTAGC-AG
1 TTCAGACTTTACGTCCAAG-AGGC-TTGATGCCGATGAAATGTATCAGACTTTATGCCTA-CTAG
*
20035003 GCTTTATGCCG
63 GCTTGATGCCG
20035014 GTGTTTTATA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
81 3 0.05
82 54 0.89
83 4 0.07
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (82 bp):
TTCAGACTTTACGTCCAAGAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTACTAGGCT
TGATGCCGATGAATTAC
Found at i:20036935 original size:74 final size:74
Alignment explanation
Indices: 20036814--20036963 Score: 300
Period size: 74 Copynumber: 2.0 Consensus size: 74
20036804 GTTCTGCAGA
20036814 GAAAGAAAAATGAAACCAAAAAGAAAGTTACCTATACGGCAAATGAAGGAATGAGGAGAAGTAGT
1 GAAAGAAAAATGAAACCAAAAAGAAAGTTACCTATACGGCAAATGAAGGAATGAGGAGAAGTAGT
20036879 GGAAATTTT
66 GGAAATTTT
20036888 GAAAGAAAAATGAAACCAAAAAGAAAGTTACCTATACGGCAAATGAAGGAATGAGGAGAAGTAGT
1 GAAAGAAAAATGAAACCAAAAAGAAAGTTACCTATACGGCAAATGAAGGAATGAGGAGAAGTAGT
20036953 GGAAATTTT
66 GGAAATTTT
20036962 GA
1 GA
20036964 TCACTTCAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.50, C:0.08, G:0.25, T:0.17
Consensus pattern (74 bp):
GAAAGAAAAATGAAACCAAAAAGAAAGTTACCTATACGGCAAATGAAGGAATGAGGAGAAGTAGT
GGAAATTTT
Found at i:20038957 original size:46 final size:46
Alignment explanation
Indices: 20038890--20038977 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
20038880 CAATATGCAG
* * *
20038890 TGTGGGCCTTAGCCCATTACAGT-ATCAGAATCAGAAATAGAATACA
1 TGTGGGCCTAAGCCCAATACAGTGA-CAAAATCAGAAATAGAATACA
*
20038936 TGTGGGCCTAAGCCCAATACAGTGACAAAATCAGTAATAGAA
1 TGTGGGCCTAAGCCCAATACAGTGACAAAATCAGAAATAGAA
20038978 ACGCAACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (46 bp):
TGTGGGCCTAAGCCCAATACAGTGACAAAATCAGAAATAGAATACA
Found at i:20039248 original size:32 final size:31
Alignment explanation
Indices: 20039193--20039331 Score: 118
Period size: 32 Copynumber: 4.4 Consensus size: 31
20039183 GAACGCCTAC
*
20039193 AAGCCATAAGT-ACAGTAATATGATTAGCACA
1 AAGCCATCAGTAACAGTAATATGA-TAGCACA
* * * *
20039224 AAGCCATCAGTAGCAGTGATATGATCGATACA
1 AAGCCATCAGTAACAGTAATATGATAG-CACA
* ** * *
20039256 CAGCCATCAGTAATGGTAATATGATAGGTATA
1 AAGCCATCAGTAACAGTAATATGATA-GCACA
** *
20039288 AAGCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGAT-AGCACA
20039320 AAGCCATCAGTA
1 AAGCCATCAGTA
20039332 GCATCGCAGC
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
31 12 0.14
32 75 0.85
33 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (31 bp):
AAGCCATCAGTAACAGTAATATGATAGCACA
Found at i:20039503 original size:24 final size:24
Alignment explanation
Indices: 20039476--20039557 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
20039466 ACATTTTCAG
* *
20039476 AATCAGTCATACGAATCACAGACA
1 AATCAGTCATACAAATCATAGACA
*
20039500 AATCAGTCATACCAATCATAGACA
1 AATCAGTCATACAAATCATAGACA
**
20039524 AATCAGTCATTTAAATCATAGACA
1 AATCAGTCATACAAATCATAGACA
*
20039548 AATCAATCAT
1 AATCAGTCAT
20039558 TTACATCACG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (24 bp):
AATCAGTCATACAAATCATAGACA
Found at i:20039558 original size:24 final size:24
Alignment explanation
Indices: 20039489--20039584 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
20039479 CAGTCATACG
* ***
20039489 AATCACAGACAAATCAGTCATACC
1 AATCACAGACAAATCAATCATTTA
* *
20039513 AATCATAGACAAATCAGTCATTTA
1 AATCACAGACAAATCAATCATTTA
*
20039537 AATCATAGACAAATCAATCATTTA
1 AATCACAGACAAATCAATCATTTA
* * *
20039561 CATCACGGACAAATAAATCATTTA
1 AATCACAGACAAATCAATCATTTA
20039585 CACTCGAAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (24 bp):
AATCACAGACAAATCAATCATTTA
Found at i:20039660 original size:27 final size:27
Alignment explanation
Indices: 20039630--20039937 Score: 142
Period size: 27 Copynumber: 11.4 Consensus size: 27
20039620 GGCATTACGG
* *
20039630 TCATTTTACCTTACAGTGGTATTTCGA
1 TCATTTTACCCTACAGGGGTATTTCGA
* ** *
20039657 TCATTTAACCCTATGGGGGTATTAT-GG
1 TCATTTTACCCTACAGGGGTATT-TCGA
** *
20039684 TCATTTTACCCTATGGGGGTTTTTCGA
1 TCATTTTACCCTACAGGGGTATTTCGA
*
20039711 TCATTTTACCCTACAGGGGTATTACGA
1 TCATTTTACCCTACAGGGGTATTTCGA
* *
20039738 TTATTTTA-CCTATC-GAGGGTATTTCAA
1 TCATTTTACCCTA-CAG-GGGTATTTCGA
* * *
20039765 TCATTTTACCC-ATCAAGGGTATTTTGG
1 TCATTTTACCCTA-CAGGGGTATTTCGA
* * *
20039792 TAATTTTACCC-ATCAAGGGTATTT-TA
1 TCATTTTACCCTA-CAGGGGTATTTCGA
*
20039818 GTAATTTTACCC-ATC-GAGGGTATTTC-A
1 -TCATTTTACCCTA-CAG-GGGTATTTCGA
* *
20039845 GTAATTTTACCC-ATC-GAGGGTAATTC-A
1 -TCATTTTACCCTA-CAG-GGGTATTTCGA
* *
20039872 GTCATTTTACCCTTC-GGAGGTAATTC-A
1 -TCATTTTACCCTACAGG-GGTATTTCGA
** *
20039899 GTCATTTTACCCTATGGGGGTAATTT-GG
1 -TCATTTTACCCTACAGGGGT-ATTTCGA
20039927 TCATTTTACCC
1 TCATTTTACCC
20039938 CTCGAAGCTA
Statistics
Matches: 235, Mismatches: 32, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.03
27 220 0.94
28 8 0.03
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTTCGA
Found at i:20039686 original size:54 final size:52
Alignment explanation
Indices: 20039623--20039909 Score: 163
Period size: 54 Copynumber: 5.3 Consensus size: 52
20039613 CTTTAAGGGC
* *
20039623 ATTACGGTCATTTTACCTTACAGTGGTATTTCGATCATTTAACCCTATGGGGGT
1 ATTACGGTCATTTTACC-TACAG-GGTATTTCGATCATTTTACCCTATAGGGGT
* ** * *
20039677 ATTATGGTCATTTTACCCTATGGGGGTTTTTCGATCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTA-CCTA-CAGGGTATTTCGATCATTTTACCCTATAGGGGT
* * * *
20039731 ATTACGATTATTTTACCTATCGAGGGTATTTCAATCATTTTACCC-ATCAAGGGT
1 ATTACGGTCATTTTACCTA-C-AGGGTATTTCGATCATTTTACCCTAT-AGGGGT
** * * * * *
20039785 ATTTTGGTAATTTTACCCATCAAGGGTATTT-TAGTAATTTTACCC-ATCGAGGGT
1 ATTACGGTCATTTTACCTA-C-AGGGTATTTCGA-TCATTTTACCCTATAG-GGGT
* * * * * *
20039839 ATTTCAGTAATTTTACCCATCGAGGGTAATTC-AGTCATTTTACCCT-TCGGAGGT
1 ATTACGGTCATTTTACCTA-C-AGGGTATTTCGA-TCATTTTACCCTATAGG-GGT
*
20039893 AATT-CAGTCATTTTACC
1 -ATTACGGTCATTTTACC
20039910 CTATGGGGGT
Statistics
Matches: 191, Mismatches: 32, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
53 8 0.04
54 177 0.93
55 6 0.03
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (52 bp):
ATTACGGTCATTTTACCTACAGGGTATTTCGATCATTTTACCCTATAGGGGT
Found at i:20039769 original size:81 final size:81
Alignment explanation
Indices: 20039630--20039884 Score: 211
Period size: 81 Copynumber: 3.1 Consensus size: 81
20039620 GGCATTACGG
* * * * * * *
20039630 TCATTTTACCTTACAGTGGTATTTCGATCATTTAACCCTAT-GGGGGTATTAT-GGTCATTTTAC
1 TCATTTTACCCTACAGGGGTATTACGATAATTTTA-CCTATCGAGGGTATT-TCAGTCATTTTAC
**
20039693 CCTAT-GGGGGT-TTTTCGA
64 CC-ATCAAGGGTATTTT-GA
* *
20039711 TCATTTTACCCTACAGGGGTATTACGATTATTTTACCTATCGAGGGTATTTCAATCATTTTACCC
1 TCATTTTACCCTACAGGGGTATTACGATAATTTTACCTATCGAGGGTATTTCAGTCATTTTACCC
*
20039776 ATCAAGGGTATTTTGG
66 ATCAAGGGTATTTTGA
* * * *
20039792 TAATTTTACCC-ATCAAGGGTATTTTA-G-TAATTTTACCCATCGAGGGTATTTCAGTAATTTTA
1 TCATTTTACCCTA-CAGGGGTA--TTACGATAATTTTACCTATCGAGGGTATTTCAGTCATTTTA
* * *
20039854 CCCATCGAGGGTA-ATTCA
63 CCCATCAAGGGTATTTTGA
20039872 GTCATTTTACCCT
1 -TCATTTTACCCT
20039885 TCGGAGGTAA
Statistics
Matches: 143, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
80 11 0.08
81 124 0.87
82 5 0.03
83 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (81 bp):
TCATTTTACCCTACAGGGGTATTACGATAATTTTACCTATCGAGGGTATTTCAGTCATTTTACCC
ATCAAGGGTATTTTGA
Found at i:20039906 original size:81 final size:81
Alignment explanation
Indices: 20039740--20039959 Score: 230
Period size: 81 Copynumber: 2.7 Consensus size: 81
20039730 TATTACGATT
* * * * ** *
20039740 ATTTTACCTATCGAGGGTATTTCAATCATTTTACCCATCAAGGGTATTTTGGTAATTTTACCCAT
1 ATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCAT
* *
20039805 CAAGGGTATTTTAGTA
66 CAAGGGTAATTCAGTA
* *
20039821 ATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCTT
1 ATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCAT
* *
20039886 C-GGAGGTAATTCAGTC
66 CAAG-GGTAATTCAGTA
* * * * *
20039902 ATTTTACCCTAT-GGGGGTAATTT-GGTCATTTTACCCCTCGAAGCTAATTCAGTCATTT
1 ATTTTACCC-ATCGAGGGT-ATTTCAGTCATTTTACCCATCGAGGGTAATTCAGTCATTT
20039960 AACAAATATT
Statistics
Matches: 117, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
80 1 0.01
81 110 0.94
82 6 0.05
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (81 bp):
ATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCAT
CAAGGGTAATTCAGTA
Found at i:20039910 original size:54 final size:54
Alignment explanation
Indices: 20039740--20039959 Score: 203
Period size: 54 Copynumber: 4.1 Consensus size: 54
20039730 TATTACGATT
* * * * **
20039740 ATTTTACCTATCGAGGGTATTTCAATCATTTTACCCATCAAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCATCAAGGGTAATTCAGTA
* * * * * *
20039794 ATTTTACCCATCAAGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCATCAAGGGTAATTCAGTA
* * *
20039848 ATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCTTC-GGAGGTAATTCAGTC
1 ATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCATCAAG-GGTAATTCAGTA
* ** * * *
20039902 ATTTTACCCTAT-GGGGGTAATTTGGTCATTTTACCCCTCGAA-GCTAATTCAGTC
1 ATTTTACCC-ATCGAGGGTAATTCAGTCATTTTACCCATC-AAGGGTAATTCAGTA
20039956 ATTT
1 ATTT
20039960 AACAAATATT
Statistics
Matches: 140, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
53 1 0.01
54 137 0.98
55 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (54 bp):
ATTTTACCCATCGAGGGTAATTCAGTCATTTTACCCATCAAGGGTAATTCAGTA
Found at i:20040494 original size:8 final size:8
Alignment explanation
Indices: 20040481--20040516 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
20040471 AATCATCGTA
20040481 TTTTTGGC
1 TTTTTGGC
20040489 TTTTTGGC
1 TTTTTGGC
20040497 TTTTTGGC
1 TTTTTGGC
*
20040505 TTTTCGGC
1 TTTTTGGC
20040513 TTTT
1 TTTT
20040517 GCCGATTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.00, C:0.14, G:0.22, T:0.64
Consensus pattern (8 bp):
TTTTTGGC
Found at i:20047690 original size:159 final size:159
Alignment explanation
Indices: 20047494--20047805 Score: 493
Period size: 159 Copynumber: 2.0 Consensus size: 159
20047484 AAAGATACAT
* * *
20047494 AATTTAAAACATTATGGTTCTAAAGGACCTAAGTGAATATGTGCATACCATGTTTTAATTACAAG
1 AATTTAAAACATTACGGTTCTAAAAGACCTAAGTGAATATGTGCATACCATGTTTTAAATA-AAG
*
20047559 -TTTTATATGCTTGATGATAAGAATATA-ACATTGTTTCTTTATTGAAATTATCGTACGTAGTTA
65 TTTTTATATGCTTGATGATAAGAATA-ACACATTGTTTCTTTATTGAAATTATCATACGTAGTTA
* *
20047622 AAATCGATGCCATTCTATTGAAAGATGTAAG
129 AAATCGATGCCAGTCTATCGAAAGATGTAAG
* * * *
20047653 AATTTAGAACATTGCGGTTCTAAAATACCTAAGTGAATATGTGCATACCATGTTTTAAATATAGT
1 AATTTAAAACATTACGGTTCTAAAAGACCTAAGTGAATATGTGCATACCATGTTTTAAATAAAGT
*
20047718 TTTTATATGCTTGATGATGAGAATAACACATTGTTTCTTTATTGAAATTATCATACGTAGTTAAA
66 TTTTATATGCTTGATGATAAGAATAACACATTGTTTCTTTATTGAAATTATCATACGTAGTTAAA
20047783 ATCGATGCCAGTCTATCGAAAGA
131 ATCGATGCCAGTCTATCGAAAGA
20047806 CAAAGGGAAA
Statistics
Matches: 140, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
158 3 0.02
159 137 0.98
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (159 bp):
AATTTAAAACATTACGGTTCTAAAAGACCTAAGTGAATATGTGCATACCATGTTTTAAATAAAGT
TTTTATATGCTTGATGATAAGAATAACACATTGTTTCTTTATTGAAATTATCATACGTAGTTAAA
ATCGATGCCAGTCTATCGAAAGATGTAAG
Found at i:20049574 original size:13 final size:13
Alignment explanation
Indices: 20049556--20049632 Score: 136
Period size: 13 Copynumber: 5.9 Consensus size: 13
20049546 AGTTCTTCAT
20049556 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
20049569 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
20049582 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
20049595 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
20049608 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
20049621 TGCTTTTGAGAA
1 TGCTTTTGAGAA
20049633 ATTTGAGTGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 60 1.00
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:20052551 original size:32 final size:32
Alignment explanation
Indices: 20052510--20052571 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
20052500 AAGGTTAACA
20052510 TATTTAATATTTATATATAAATATAGGATAGT
1 TATTTAATATTTATATATAAATATAGGATAGT
20052542 TATTTAATATTTATATATAAATATAGGATA
1 TATTTAATATTTATATATAAATATAGGATA
20052572 ATCATGGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
TATTTAATATTTATATATAAATATAGGATAGT
Found at i:20055403 original size:143 final size:143
Alignment explanation
Indices: 20055145--20055433 Score: 479
Period size: 143 Copynumber: 2.0 Consensus size: 143
20055135 TAAATACGTA
20055145 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
1 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
* *
20055210 CCATTGGCTGAGTTACGTAGGAGTACCTGACGAGTTAGAAAACATTAGGCTACTGTTAGATCAAT
66 CCATGGGCCGAGTTACGTAGGAGTACCTGACGAGTTAGAAAACATTAGGCTACTGTTAGATCAAT
*
20055275 GCCCGAAACCAAG
131 ACCCGAAACCAAG
*
20055288 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTATAGGTGGAA
1 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
* * * ** *
20055353 CCATGGGCCGAGTTACGTGGGAGTACCTGACGATTTGGAAAATGTTAGGCTGCTGTTAGATCAAT
66 CCATGGGCCGAGTTACGTAGGAGTACCTGACGAGTTAGAAAACATTAGGCTACTGTTAGATCAAT
*
20055418 ACTCGAAACCAAG
131 ACCCGAAACCAAG
20055431 GTT
1 GTT
20055434 AATTACCTAT
Statistics
Matches: 135, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
143 135 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (143 bp):
GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
CCATGGGCCGAGTTACGTAGGAGTACCTGACGAGTTAGAAAACATTAGGCTACTGTTAGATCAAT
ACCCGAAACCAAG
Found at i:20060646 original size:7 final size:8
Alignment explanation
Indices: 20060616--20060663 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
20060606 CTTTCAAAAT
20060616 ACCCTAAA
1 ACCCTAAA
20060624 ACCCTAAA
1 ACCCTAAA
*
20060632 ATCCTAAA
1 ACCCTAAA
20060640 A-CCTAAAA
1 ACCCT-AAA
20060648 ACCCTAAA
1 ACCCTAAA
20060656 A-CCTAAA
1 ACCCTAAA
20060663 A
1 A
20060664 AAAATAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
7 10 0.27
8 24 0.65
9 3 0.08
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (8 bp):
ACCCTAAA
Found at i:20060664 original size:16 final size:16
Alignment explanation
Indices: 20060611--20060664 Score: 74
Period size: 16 Copynumber: 3.3 Consensus size: 16
20060601 AAATACTTTC
20060611 AAAATACCCTAAAACCCT
1 AAAA-ACCCTAAAA-CCT
*
20060629 -AAAATCCTAAAACCT
1 AAAAACCCTAAAACCT
20060644 AAAAACCCTAAAACCT
1 AAAAACCCTAAAACCT
20060660 AAAAA
1 AAAAA
20060665 AAATAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 3 0.09
16 27 0.82
17 3 0.09
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAACCCTAAAACCT
Found at i:20060672 original size:24 final size:25
Alignment explanation
Indices: 20060620--20060672 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
20060610 CAAAATACCC
***
20060620 TAAAACCCTAAAATCCTAAAACCTA
1 TAAAACCCTAAAATCCTAAAAAAAA
20060645 -AAAACCCTAAAA-CCTAAAAAAAA
1 TAAAACCCTAAAATCCTAAAAAAAA
20060668 TAAAA
1 TAAAA
20060673 AGTCCTAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (25 bp):
TAAAACCCTAAAATCCTAAAAAAAA
Found at i:20061950 original size:10 final size:11
Alignment explanation
Indices: 20061925--20061950 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20061915 TTTCTTTATG
20061925 AAAAATAAATT
1 AAAAATAAATT
20061936 AAAAATAAATT
1 AAAAATAAATT
20061947 AAAA
1 AAAA
20061951 GGCGGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAAATT
Found at i:20070164 original size:12 final size:12
Alignment explanation
Indices: 20070149--20070210 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
20070139 AAATTCTCTC
20070149 AATTCCTTTCAA
1 AATTCCTTTCAA
* *
20070161 AATTTCTCTC--
1 AATTCCTTTCAA
20070171 AATTCCTTTCAA
1 AATTCCTTTCAA
* *
20070183 AATTTCTATC-A
1 AATTCCTTTCAA
*
20070194 AATTCCTTCCAA
1 AATTCCTTTCAA
20070206 AATTC
1 AATTC
20070211 TCTCAAACTC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
10 8 0.21
11 8 0.21
12 22 0.58
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (12 bp):
AATTCCTTTCAA
Found at i:20070217 original size:22 final size:22
Alignment explanation
Indices: 20070125--20070216 Score: 132
Period size: 22 Copynumber: 4.2 Consensus size: 22
20070115 AAATTCAATA
* *
20070125 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCTTTCAAAATTTCTC
20070147 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCTTTCAAAATTTCTC
*
20070169 TCAATTCCTTTCAAAATTTCTA
1 TCAATTCCTTTCAAAATTTCTC
*
20070191 TCAAATTCCTTCCAAAA-TTCTC
1 TC-AATTCCTTTCAAAATTTCTC
20070213 TCAA
1 TCAA
20070217 ACTCTCAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
21 2 0.03
22 49 0.77
23 13 0.20
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCTTTCAAAATTTCTC
Found at i:20070254 original size:52 final size:51
Alignment explanation
Indices: 20070166--20070268 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 51
20070156 TTCAAAATTT
* * * *
20070166 CTCTCAATTCCTTTCAAAATTTCTATCAAATTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCTTCCAAAATTCCTATCAAATTCCTTCAAAAAATCTC-CAAA
* *
20070218 CTCTCAAATTCCTTCCAAAA-TCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCTTCCAAAATTCCTATCAAATTCCTTCAAAAAATCTCCAAA
20070269 TCCATATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 4 0.09
52 27 0.61
53 13 0.30
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCTTCCAAAATTCCTATCAAATTCCTTCAAAAAATCTCCAAA
Found at i:20070257 original size:21 final size:22
Alignment explanation
Indices: 20070218--20070259 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20070208 TTCTCTCAAA
20070218 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
20070240 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
20070260 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Done.