Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 127 of 325
Found at i:40649157 original size:147 final size:142
Alignment explanation
Indices: 40648967--40649600 Score: 849
Period size: 147 Copynumber: 4.4 Consensus size: 142
40648957 ACACGTTTCG
* * * **
40648967 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * * *
40649032 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCAT-GT
66 ATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGGT
40649096 TCACATTCATCA
131 TCACATTCATCA
* * *
40649108 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCACATTGGCCATTC
1 CATTGGCCATTCGGCCTTATCA--C----ACATACACATGTTCACATTCATCACATTGGCCATTC
*
40649173 GGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACG
60 GGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACA
*
40649238 CAT-GTTCACATCCATCA
125 CATGGTTCACATTCATCA
40649255 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTT
* ** * *
40649320 ATCACGCATATATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATA
66 ATCA--C----ACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACA
*
40649385 TATACGGGTTCACATTCATCA
125 CAT---GGTTCACATTCATCA
* *
40649406 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTT
* *
40649471 ATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATATATACG
66 ATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACAT---
40649536 GGTTCACATTCATCA
128 GGTTCACATTCATCA
* * *
40649551 CATTGGTCATTCGGCCTTATCACACATACGCATGTTCACATCCATCACAT
1 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACAT
40649601 AAAATCCTAA
Statistics
Matches: 451, Mismatches: 26, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
141 63 0.14
143 2 0.00
145 121 0.27
147 184 0.41
149 1 0.00
151 80 0.18
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.31
Consensus pattern (142 bp):
CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGGT
TCACATTCATCA
Found at i:40649301 original size:194 final size:194
Alignment explanation
Indices: 40648967--40649600 Score: 1065
Period size: 194 Copynumber: 3.3 Consensus size: 194
40648957 ACACGTTTCG
* * * **
40648967 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * * *
40649032 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
66 ATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
40649097 CACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
131 CACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
40649161 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
40649226 ATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
66 ATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
40649291 CACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
131 CACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
***
40649355 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCACATTGGCCATTCGG
40649420 CCTTATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCA
62 CCTTATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCA
* *
40649485 TGTTCACATTCATCACATTGGCCATTCGGCCTTATCA--CACATATATATACGGGTTCACATTCA
127 TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCA
40649548 TCA
192 TCA
* *
40649551 CATTGGTCATTCGGCCTTATCACACATACGCATGTTCACATCCATCACAT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
40649601 AAAATCCTAA
Statistics
Matches: 415, Mismatches: 21, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
192 16 0.04
194 214 0.52
196 56 0.13
198 129 0.31
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.31
Consensus pattern (194 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
CACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
Found at i:40660478 original size:25 final size:25
Alignment explanation
Indices: 40660447--40660494 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40660437 TTATAACATG
* *
40660447 AAAATGACCGTTTTACCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
40660472 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
40660495 GTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:40660561 original size:20 final size:20
Alignment explanation
Indices: 40660531--40660593 Score: 110
Period size: 20 Copynumber: 3.1 Consensus size: 20
40660521 ATTTTGATAG
40660531 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
40660551 ACATG-TCATGTATGATATGC
1 ACATGAT-ATGTATGATATGC
40660571 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
40660591 ACA
1 ACA
40660594 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40660673 original size:24 final size:24
Alignment explanation
Indices: 40660646--40660727 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
40660636 TGAAGAAGTG
*
40660646 CAAAAGGGCTTATGCCGCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
40660670 C-AAAGGGCTTATGCCTCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
40660693 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
40660717 TAAAAGAGGCT
1 CAAAAG-GGCT
40660728 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 21 0.40
24 27 0.52
25 4 0.08
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:40660737 original size:25 final size:25
Alignment explanation
Indices: 40660647--40660737 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 25
40660637 GAAGAAGTGC
* *
40660647 AAAAGGGCTTATGCC-GCAGTTA-T
1 AAAAGGGCTTAGGCCTCCAGTTATT
* *
40660670 CAAAGGGCTTATGCCT-CAGTTATT
1 AAAAGGGCTTAGGCCTCCAGTTATT
**
40660694 AAAAGGGCTTTTGCC-CCAGTTATT
1 AAAAGGGCTTAGGCCTCCAGTTATT
40660718 AAAAGAGGC-TAGGCCTCCAG
1 AAAAG-GGCTTAGGCCTCCAG
40660738 ATATATGATA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
23 20 0.34
24 31 0.53
25 7 0.12
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTAGGCCTCCAGTTATT
Found at i:40660970 original size:31 final size:31
Alignment explanation
Indices: 40660935--40660998 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40660925 CGATTACAGT
40660935 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
40660966 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
40660997 AA
1 AA
40660999 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:40664140 original size:29 final size:30
Alignment explanation
Indices: 40664083--40664140 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
40664073 TGGAAGGGGA
** * *
40664083 GTAAAAGTTTTGGGGGGAAAGTGAGAAGGG
1 GTAAAAGTTTTGGAAGGAAAGTAAAAAGGG
40664113 GTAAAAGTTTT-GAAGGAAAGTAAAAAGG
1 GTAAAAGTTTTGGAAGGAAAGTAAAAAGG
40664141 TTTGAGAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (30 bp):
GTAAAAGTTTTGGAAGGAAAGTAAAAAGGG
Found at i:40664287 original size:9 final size:9
Alignment explanation
Indices: 40664268--40664300 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
40664258 ATTTGAGTTG
40664268 ACTCGAATA
1 ACTCGAATA
40664277 ACTC-AATTA
1 ACTCGAA-TA
40664286 ACTCGAATA
1 ACTCGAATA
40664295 ACTCGA
1 ACTCGA
40664301 TTCGTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:40665010 original size:66 final size:63
Alignment explanation
Indices: 40664872--40665011 Score: 181
Period size: 66 Copynumber: 2.1 Consensus size: 63
40664862 GTATACTCTA
* * *
40664872 CACGGCCTCACACACGGGCGTGTGACTGGCCGTGTGGCACAAGTCAGTATACCCTCTGAATGG
1 CACGGCCTAACACACGGGCGTGTGACTGGCCGTGTGGCACAACTCAGTATACCCTATGAATGG
* * *
40664935 CACATGGCCTAACACACGGGCGTGTGACTTGGCCGTGTTGCATAACTCAGTATACCCTATAGGAT
1 CAC--GGCCTAACACACGGGCGTGTGAC-TGGCCGTGTGGCACAACTCAGTATACCCTAT--GAA
40665000 TGG
61 TGG
40665003 CACGGCCTA
1 CACGGCCTA
40665012 GTACATGGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
63 3 0.05
65 22 0.33
66 33 0.50
68 8 0.12
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.21
Consensus pattern (63 bp):
CACGGCCTAACACACGGGCGTGTGACTGGCCGTGTGGCACAACTCAGTATACCCTATGAATGG
Found at i:40670680 original size:42 final size:43
Alignment explanation
Indices: 40670621--40670713 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 43
40670611 CGCATCCATT
*
40670621 ATGAACTCGAACCACTTAACAAGCTCAGATGC-CACAGATATC
1 ATGAACTCGAACCACTTAAAAAGCTCAGATGCTCACAGATATC
* * * * *
40670663 ATGAACTTGGACCACTTAAAAAGTTCAGATTCTCACATATATC
1 ATGAACTCGAACCACTTAAAAAGCTCAGATGCTCACAGATATC
40670706 ATGAACTC
1 ATGAACTC
40670714 AGACTGCTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 27 0.63
43 16 0.37
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (43 bp):
ATGAACTCGAACCACTTAAAAAGCTCAGATGCTCACAGATATC
Found at i:40678116 original size:75 final size:75
Alignment explanation
Indices: 40678029--40678178 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
40678019 ACTCATCACA
40678029 ACATGGCCGAATACACATTTCTCCTACTTCCATTCTAAATAAAATTTTATCAAGCTTCCATCTTC
1 ACATGGCCGAATACACATTTCTCCTACTTCCATTCTAAATAAAATTTTATCAAGCTTCCATCTTC
40678094 ATTTAACTAT
66 ATTTAACTAT
*
40678104 ACATGGCTGAATACACATTTCTCCTACTTCCATTCTAAATAAAATTTTATCAAGCTTCCATCTTC
1 ACATGGCCGAATACACATTTCTCCTACTTCCATTCTAAATAAAATTTTATCAAGCTTCCATCTTC
40678169 ATTTAACTAT
66 ATTTAACTAT
40678179 GTACCATTTA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (75 bp):
ACATGGCCGAATACACATTTCTCCTACTTCCATTCTAAATAAAATTTTATCAAGCTTCCATCTTC
ATTTAACTAT
Found at i:40679899 original size:14 final size:16
Alignment explanation
Indices: 40679867--40679899 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40679857 AAGTTGTTAA
40679867 CTTGAGAAGTTATATG
1 CTTGAGAAGTTATATG
40679883 CTTGAGAA-TTA-ATG
1 CTTGAGAAGTTATATG
40679897 CTT
1 CTT
40679900 AATGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 3 0.18
16 8 0.47
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (16 bp):
CTTGAGAAGTTATATG
Found at i:40686248 original size:20 final size:21
Alignment explanation
Indices: 40686225--40686270 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
40686215 AGCTCCAATC
40686225 AGCTCACTTGAGCTTG-ATTT
1 AGCTCACTTGAGCTTGAATTT
**
40686245 AGCTCGTTTGAGCTTGAATTT
1 AGCTCACTTGAGCTTGAATTT
40686266 AGCTC
1 AGCTC
40686271 GTTTCAGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (21 bp):
AGCTCACTTGAGCTTGAATTT
Found at i:40686267 original size:21 final size:20
Alignment explanation
Indices: 40686232--40686279 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
40686222 ATCAGCTCAC
40686232 TTGAGCTTGATTTAGCTCGT
1 TTGAGCTTGATTTAGCTCGT
40686252 TTGAGCTTGAATTTAGCTCGT
1 TTGAGCTTG-ATTTAGCTCGT
*
40686273 TTCAGCT
1 TTGAGCT
40686280 CATTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGAGCTTGATTTAGCTCGT
Found at i:40686982 original size:10 final size:10
Alignment explanation
Indices: 40686967--40686994 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40686957 TTAATGTTTT
40686967 CATTCTAGAA
1 CATTCTAGAA
40686977 CATTCTAGAA
1 CATTCTAGAA
40686987 CATTCTAG
1 CATTCTAG
40686995 TTAATTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (10 bp):
CATTCTAGAA
Found at i:40687668 original size:12 final size:12
Alignment explanation
Indices: 40687637--40687668 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
40687627 GAGTAAAGTA
*
40687637 TTGAGCTCAAAC
1 TTGAGCTTAAAC
40687649 TTGAGCTTAAAC
1 TTGAGCTTAAAC
40687661 TTGAGCTT
1 TTGAGCTT
40687669 CCCACTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (12 bp):
TTGAGCTTAAAC
Found at i:40688302 original size:15 final size:16
Alignment explanation
Indices: 40688282--40688311 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40688272 AGAATATATC
40688282 TTCTTTTT-CTTTTTT
1 TTCTTTTTCCTTTTTT
40688297 TTCTTTTTCCTTTTT
1 TTCTTTTTCCTTTTT
40688312 GATTTTCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTCTTTTTCCTTTTTT
Found at i:40695460 original size:29 final size:28
Alignment explanation
Indices: 40695423--40695479 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
40695413 TGAACTGTTG
* *
40695423 AAGGGAGTTCCTAACCTTGGAACTCGTCA
1 AAGGAAGTTCCTAACCTTAG-ACTCGTCA
40695452 AAGGAAGTTCCTAACCTTAGACTCGTCA
1 AAGGAAGTTCCTAACCTTAGACTCGTCA
40695480 GGAAGGGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (28 bp):
AAGGAAGTTCCTAACCTTAGACTCGTCA
Found at i:40700418 original size:68 final size:68
Alignment explanation
Indices: 40700345--40700483 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 68
40700335 ATTATCTTTT
* *
40700345 TTTTTATTATTTGTTTTATCATAAGTAGCACCAAAGAGATATATGTAGAGTTTGCTAAAATTTAT
1 TTTTTATTATTTCTTTTATCATAAGTAGCACCAAAGAGATATAAGTAGAGTTTGCTAAAATTTAT
40700410 GCG
66 GCG
40700413 TTTTTATTATTTCTTTTATCATAAGTAGCACCAAAGAGATATAAGTAGAGTTTGCTAAAATTTAT
1 TTTTTATTATTTCTTTTATCATAAGTAGCACCAAAGAGATATAAGTAGAGTTTGCTAAAATTTAT
40700478 GCG
66 GCG
40700481 TTT
1 TTT
40700484 CTATGATATA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.43
Consensus pattern (68 bp):
TTTTTATTATTTCTTTTATCATAAGTAGCACCAAAGAGATATAAGTAGAGTTTGCTAAAATTTAT
GCG
Found at i:40702287 original size:30 final size:29
Alignment explanation
Indices: 40702238--40702310 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
40702228 ATTTCATTTC
* *
40702238 AAATATGGGCTTATCTGGATACAAATCAA
1 AAATAAGGGTTTATCTGGATACAAATCAA
* *
40702267 AGAATAAGGGTTTATTTGGATACAAATTAA
1 A-AATAAGGGTTTATCTGGATACAAATCAA
*
40702297 AATATAAGGCTTTA
1 AA-ATAAGGGTTTA
40702311 AGAAAACTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (29 bp):
AAATAAGGGTTTATCTGGATACAAATCAA
Found at i:40703644 original size:18 final size:17
Alignment explanation
Indices: 40703621--40703659 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
40703611 TTCCTTTTTA
40703621 TTTTT-CTTTTTTGATTAT
1 TTTTTCCTTTTTT-ATT-T
40703639 TTTTTCCTTTTTTATTT
1 TTTTTCCTTTTTTATTT
40703656 TTTT
1 TTTT
40703660 ACTTCAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 8 0.40
19 7 0.35
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTCCTTTTTTATTT
Found at i:40704512 original size:73 final size:73
Alignment explanation
Indices: 40704374--40704513 Score: 244
Period size: 73 Copynumber: 1.9 Consensus size: 73
40704364 CGAAAATTTC
* * *
40704374 TCCGAAATTTGGAAATTTGAGTCATTCCGTGAAGTAAAACTAAGATGTATTCTTAGAATAGTTTT
1 TCCGAAATTTAGAAATTTGAGTCATTCCGTGAAGTAAAACTAAGATGTATTCTTAGAAAAATTTT
40704439 TGAGTTTT
66 TGAGTTTT
*
40704447 TCCGAAATTTAGAAATTTGAGTCATTCCGTGAAGTAAAACTAAGATGTATTCTTGGAAAAATTTT
1 TCCGAAATTTAGAAATTTGAGTCATTCCGTGAAGTAAAACTAAGATGTATTCTTAGAAAAATTTT
40704512 TG
66 TG
40704514 GGTTATTCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (73 bp):
TCCGAAATTTAGAAATTTGAGTCATTCCGTGAAGTAAAACTAAGATGTATTCTTAGAAAAATTTT
TGAGTTTT
Found at i:40708852 original size:28 final size:28
Alignment explanation
Indices: 40708804--40708894 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
40708794 GTGACAGAGT
*
40708804 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
40708833 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
40708861 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
40708889 CACCAG
1 CACCAG
40708895 GACGCTTCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:40709047 original size:28 final size:28
Alignment explanation
Indices: 40709003--40709064 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
40708993 TTAACCCTAG
*
40709003 GGGTATAAAGGTCATTTAGCATACATAA
1 GGGTATAAAGGTAATTTAGCATACATAA
* * *
40709031 GGGTATAATGGTAATTTTGCATACATAG
1 GGGTATAAAGGTAATTTAGCATACATAA
40709059 GGGTAT
1 GGGTAT
40709065 TCTAGTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (28 bp):
GGGTATAAAGGTAATTTAGCATACATAA
Found at i:40718184 original size:79 final size:80
Alignment explanation
Indices: 40718076--40718245 Score: 213
Period size: 79 Copynumber: 2.1 Consensus size: 80
40718066 ACTAAGATCA
*
40718076 GAAGGCATTTGTGTGAGATACTAAATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGA-TACTA
1 GAAGGCATTTGTGCGAGATACTAAATCCGGACTAAG-TCCCAAAGGCATTTGTGCGA-ATTACTA
* *
40718139 -ATTCCGGGCTAAG-CCC
64 TA-ACCGAGCTAAGTCCC
* ** *
40718155 GAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATA
1 GAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGTCCCAAAGGCATTTGTGCGAATTACTATA
*
40718220 ACCGAGCTATGTCCC
66 ACCGAGCTAAGTCCC
40718235 GAAGGCATTTG
1 GAAGGCATTTG
40718246 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 62 0.78
80 15 0.19
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (80 bp):
GAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGTCCCAAAGGCATTTGTGCGAATTACTATA
ACCGAGCTAAGTCCC
Found at i:40718209 original size:40 final size:40
Alignment explanation
Indices: 40718021--40718245 Score: 235
Period size: 40 Copynumber: 5.7 Consensus size: 40
40718011 TTGAATGATG
* * * *
40718021 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
40718061 TCCGGACTAAGAT-CAGAAGGCATTTGTGTGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
40718101 TCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
40718141 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40718180 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
40718221 -CCGAGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40718246 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 34 0.21
40 116 0.73
41 9 0.06
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40718267 original size:79 final size:79
Alignment explanation
Indices: 40718095--40718278 Score: 180
Period size: 79 Copynumber: 2.3 Consensus size: 79
40718085 TGTGTGAGAT
** * * *
40718095 ACTAAATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAG
1 ACTAAATCCGGGTTAA-ATCCCGAAGGCATTTGTGCGAGATACTAATACCGAGCTAAGCCCGAAG
** *
40718159 GCATTTGTGCGAGTT
65 GCATTTGAACGAGTG
* *
40718174 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGAGCTATGTCCCGA
1 ACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGAGCTAAG-CCCGA
40718237 AGGCATTTGAACGAG-G
63 AGGCATTTGAACGAGTG
* *
40718253 AGCTATATCC-GGTTAAATTCCGAAGG
1 A-CTAAATCCGGGTTAAATCCCGAAGG
40718279 TACGTGATTT
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
78 4 0.05
79 58 0.67
80 25 0.29
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (79 bp):
ACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTAATACCGAGCTAAGCCCGAAGG
CATTTGAACGAGTG
Found at i:40733009 original size:75 final size:77
Alignment explanation
Indices: 40732890--40733079 Score: 201
Period size: 75 Copynumber: 2.5 Consensus size: 77
40732880 TTGAATGATG
* * * * *
40732890 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA-TCCGGACTAAGATC-AAGGCATT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGC-GAGT-ACTAAATTCCGG-CTAAGACCGAAGGCATT
40732952 TGTGCGAGATACT-AA
62 TGTGCGAGATACTAAA
* *
40732967 TCCGGACTAAG-CCGAAGGCATTTGTGCGAGTACTAAATTCCGGGTAAGCCCGAAGGCATTTGTG
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGTACTAAATTCCGGCTAAGACCGAAGGCATTTGTG
*
40733031 CGAGTTACTAAA
66 CGAGATACTAAA
** *
40733043 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGATTACTA
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGTACTA
40733080 TAACCGGGCT
Statistics
Matches: 96, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
74 9 0.09
75 36 0.38
76 18 0.19
77 10 0.10
78 23 0.24
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (77 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGTACTAAATTCCGGCTAAGACCGAAGGCATTTGTG
CGAGATACTAAA
Found at i:40733078 original size:39 final size:39
Alignment explanation
Indices: 40732890--40733107 Score: 227
Period size: 39 Copynumber: 5.6 Consensus size: 39
40732880 TTGAATGATG
* * * *
40732890 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAA
* ** *
40732930 TCCGGACTAAGATC-AAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40732967 TCCGGACTAAG-CCGAAGGCATTTGTGCGAG-TACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
40733004 TTCCGGG-TAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40733043 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-TTACTATAA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40733083 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
40733108 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
36 5 0.03
37 34 0.22
38 39 0.25
39 48 0.31
40 31 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40733129 original size:78 final size:77
Alignment explanation
Indices: 40732978--40733140 Score: 188
Period size: 78 Copynumber: 2.1 Consensus size: 77
40732968 CCGGACTAAG
** *
40732978 CCGAAGGCATTTGTGCGAGTACTAAATTCCGGGTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGAAGGCATTTGTGCGAGTACTAAA-TCCGGGTAAGCCCGAAGGCATTTGAACGAGTGACTAAA
*
40733043 TCCGGGTTAAGTC
65 TCCGGGTTAAATC
* *
40733056 CCGAAGGCATTTGTGCGATTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCT
1 CCGAAGGCATTTGTGCGAGTACTA-AATCCGGG-TAAG-CCCGAAGGCATTTGAACGAGTGA-CT
* *
40733119 ATATCC-GGTTAAATT
62 AAATCCGGGTTAAATC
40733134 CCGAAGG
1 CCGAAGG
40733141 TACGTGATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
77 5 0.07
78 41 0.56
79 27 0.37
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGTACTAAATCCGGGTAAGCCCGAAGGCATTTGAACGAGTGACTAAAT
CCGGGTTAAATC
Found at i:40734690 original size:28 final size:28
Alignment explanation
Indices: 40734642--40734732 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
40734632 GTGACAGAGT
*
40734642 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
40734671 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
40734699 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
40734727 CACCAG
1 CACCAG
40734733 GACGCTTCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:40734910 original size:28 final size:28
Alignment explanation
Indices: 40734838--40734898 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
40734828 AAATTAACCC
* * *
40734838 TAGGGGTATAAAAGTCATTTAGCATACA
1 TAGGGCTATAATAGTAATTTAGCATACA
* *
40734866 TAGGGCTATAATGGTAATTTTGCATACA
1 TAGGGCTATAATAGTAATTTAGCATACA
40734894 TAGGG
1 TAGGG
40734899 GTATTCTAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (28 bp):
TAGGGCTATAATAGTAATTTAGCATACA
Found at i:40739862 original size:25 final size:26
Alignment explanation
Indices: 40739828--40739888 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
40739818 AAGAAGAAAG
* * *
40739828 AAAATAAAAAAATAAAATCTAATCTA
1 AAAATGAAAAAAGAAAACCTAATCTA
*
40739854 AAAA-GAAAAGAGAAAACCTAATCTA
1 AAAATGAAAAAAGAAAACCTAATCTA
40739879 AAAATGAAAA
1 AAAATGAAAA
40739889 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.69, C:0.08, G:0.07, T:0.16
Consensus pattern (26 bp):
AAAATGAAAAAAGAAAACCTAATCTA
Found at i:40739882 original size:26 final size:25
Alignment explanation
Indices: 40739841--40739890 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
40739831 ATAAAAAAAT
*
40739841 AAAATCTAATCTAAAAAGAAAAGAG
1 AAAACCTAATCTAAAAAGAAAAGAG
40739866 AAAACCTAATCTAAAAATGAAAAGA
1 AAAACCTAATCTAAAAA-GAAAAGA
40739891 AAAGAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.16
Consensus pattern (25 bp):
AAAACCTAATCTAAAAAGAAAAGAG
Found at i:40741955 original size:60 final size:60
Alignment explanation
Indices: 40741883--40742132 Score: 195
Period size: 60 Copynumber: 4.2 Consensus size: 60
40741873 TCATCAACCA
* * *
40741883 ATGAAAAAGGATGCCTTC-GGCTATCAAAATATGGAAAGGGATGGCTTTGACCACCGAATT
1 ATGAAAAGGGATG-CTTCAGGCTATCAAAATATGGAAAGGGATGGCTTCGACCATCGAATT
* ** * * * *
40741943 ATGAATAGGGATGGATCTGGATAT-AAAATTATGGAAAGGGATGGCTTCGACTATCGATTT
1 ATGAAAAGGGATGCTTCAGGCTATCAAAA-TATGGAAAGGGATGGCTTCGACCATCGAATT
* * ** ** * *
40742003 ATGAAAAGGGATAACTTCAGG-TATCAAATTATAAAAAGTTATGG-TGACGACCATCAAATT
1 ATGAAAAGGGAT-GCTTCAGGCTATCAAAATATGGAAAGGGATGGCT-TCGACCATCGAATT
* * * * * * *
40742063 ATGAAAAGGGATGGCTT-TGACTATCAAAACATGGAAAGGGATAGCTTCGGCTATCGAACT
1 ATGAAAAGGGAT-GCTTCAGGCTATCAAAATATGGAAAGGGATGGCTTCGACCATCGAATT
40742123 ATGAAAAGGG
1 ATGAAAAGGG
40742133 GTGGTAACAA
Statistics
Matches: 144, Mismatches: 39, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
59 8 0.06
60 128 0.89
61 8 0.06
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (60 bp):
ATGAAAAGGGATGCTTCAGGCTATCAAAATATGGAAAGGGATGGCTTCGACCATCGAATT
Found at i:40742005 original size:30 final size:30
Alignment explanation
Indices: 40741891--40742132 Score: 123
Period size: 30 Copynumber: 8.1 Consensus size: 30
40741881 CAATGAAAAA
* * * *
40741891 GGATGCCTTCGGCTATCAAAATATGGAAAG
1 GGATGGCTTCGACTATCGAATTATGGAAAG
* * *
40741921 GGATGGCTTTGACCACCGAATTAT-GAATAG
1 GGATGGCTTCGACTATCGAATTATGGAA-AG
* * **
40741951 GGATGGATCTGGA-TATAAAATTATGGAAAG
1 GGATGGCT-TCGACTATCGAATTATGGAAAG
* *
40741981 GGATGGCTTCGACTATCGATTTATGAAAAG
1 GGATGGCTTCGACTATCGAATTATGGAAAG
** * * **
40742011 GGATAACTTC-AGGTATCAAATTATAAAAAG
1 GGATGGCTTCGA-CTATCGAATTATGGAAAG
** * * * *
40742041 TTATGG-TGACGACCATCAAATTATGAAAAG
1 GGATGGCT-TCGACTATCGAATTATGGAAAG
* * **
40742071 GGATGGCTTTGACTATCAAAACATGGAAAG
1 GGATGGCTTCGACTATCGAATTATGGAAAG
* * * *
40742101 GGATAGCTTCGGCTATCGAACTATGAAAAG
1 GGATGGCTTCGACTATCGAATTATGGAAAG
40742131 GG
1 GG
40742133 GTGGTAACAA
Statistics
Matches: 156, Mismatches: 48, Indels: 16
0.71 0.22 0.07
Matches are distributed among these distances:
29 8 0.05
30 140 0.90
31 8 0.05
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (30 bp):
GGATGGCTTCGACTATCGAATTATGGAAAG
Found at i:40745350 original size:26 final size:26
Alignment explanation
Indices: 40745313--40745366 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
40745303 TGCTTCGGAG
*
40745313 ATAGTTTGAGAAGGTTGCCTATTATT
1 ATAGTTTAAGAAGGTTGCCTATTATT
*
40745339 ATAGTTTAAGAAGGTTGCCTATTGTT
1 ATAGTTTAAGAAGGTTGCCTATTATT
40745365 AT
1 AT
40745367 TTCTACTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (26 bp):
ATAGTTTAAGAAGGTTGCCTATTATT
Found at i:40749595 original size:30 final size:28
Alignment explanation
Indices: 40749525--40749599 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 28
40749515 GAATTATGCT
* * *
40749525 ATTATGAAAATGGATGATATGACCATCA
1 ATTATGAAAAGGGATGGTATGACCACCA
** *
40749553 ACAATAAAAAGGGATGGTGATGACCACCGA
1 ATTATGAAAAGGGATGGT-ATGACCACC-A
40749583 ATTATGAAAAGGGATGG
1 ATTATGAAAAGGGATGG
40749600 CTTTGGCTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
28 13 0.36
29 8 0.22
30 15 0.42
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (28 bp):
ATTATGAAAAGGGATGGTATGACCACCA
Found at i:40749615 original size:30 final size:30
Alignment explanation
Indices: 40749581--40749775 Score: 164
Period size: 30 Copynumber: 6.5 Consensus size: 30
40749571 GATGACCACC
*
40749581 GAATTATGAAAAGGGATGGCTTTGGCTATA
1 GAATTATGAAAAGGGATGGCTTCGGCTATA
* * *
40749611 GAATTATGAAAAAGGATGGCTTCAGCTATC
1 GAATTATGAAAAGGGATGGCTTCGGCTATA
* * *
40749641 GAATTATGAAAATGGATAGCTTTGGCTATCA
1 GAATTATGAAAAGGGATGGCTTCGGCTAT-A
** * * *
40749672 G-ATTATGAAAATAGATGG-TGAT-GACCATT
1 GAATTATGAAAAGGGATGGCT--TCGGCTATA
40749701 GAATTATGAAAAGGGATGGCTTCGGCTATCA
1 GAATTATGAAAAGGGATGGCTTCGGCTAT-A
** * * *
40749732 -AAACATGGAAAGGGATAGCTTCGGCTATT
1 GAATTATGAAAAGGGATGGCTTCGGCTATA
*
40749761 GAACTATGAAAAGGG
1 GAATTATGAAAAGGG
40749776 GTGGTAACAA
Statistics
Matches: 130, Mismatches: 27, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
29 3 0.02
30 124 0.95
31 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (30 bp):
GAATTATGAAAAGGGATGGCTTCGGCTATA
Found at i:40749648 original size:60 final size:61
Alignment explanation
Indices: 40749580--40749775 Score: 197
Period size: 60 Copynumber: 3.3 Consensus size: 61
40749570 TGATGACCAC
40749580 CGAATTATGAAAAGGGATGGCTTTGGCTAT-AGAATTATGAAAAAGGATGGCTTCAGCTAT
1 CGAATTATGAAAAGGGATGGCTTTGGCTATCAGAATTATGAAAAAGGATGGCTTCAGCTAT
* * * *
40749640 CGAATTATGAAAATGGATAGCTTTGGCTATCAG-ATTATGAAAATA-GATGG--TGATGACCAT
1 CGAATTATGAAAAGGGATGGCTTTGGCTATCAGAATTATGAAAA-AGGATGGCTTCA-G-CTAT
* * ** * * * *
40749700 TGAATTATGAAAAGGGATGGCTTCGGCTATCA-AAACATGGAAAGGGATAGCTTCGGCTAT
1 CGAATTATGAAAAGGGATGGCTTTGGCTATCAGAATTATGAAAAAGGATGGCTTCAGCTAT
* *
40749760 TGAACTATGAAAAGGG
1 CGAATTATGAAAAGGG
40749776 GTGGTAACAA
Statistics
Matches: 111, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 103 0.93
61 4 0.04
62 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (61 bp):
CGAATTATGAAAAGGGATGGCTTTGGCTATCAGAATTATGAAAAAGGATGGCTTCAGCTAT
Found at i:40749789 original size:90 final size:90
Alignment explanation
Indices: 40749611--40749789 Score: 198
Period size: 90 Copynumber: 2.0 Consensus size: 90
40749601 TTTGGCTATA
* ** * * *
40749611 GAATTATGAAAAAGGATGGCTTCAGCTATCGAATTATGAAAATGGATAGCTTTGGCTATCAGATT
1 GAATTATGAAAAAGGATGGCTTCAGCTATCAAAACATGAAAAGGGATAGCTTCGGCTATCAGACT
* * **
40749676 ATGAAAATAGATGGTGATGACCATT
66 ATGAAAAGAGATGGTAACAACCATT
* * * *
40749701 GAATTATGAAAAGGGATGGCTTCGGCTATCAAAACATGGAAAGGGATAGCTTCGGCTAT-TGAAC
1 GAATTATGAAAAAGGATGGCTTCAGCTATCAAAACATGAAAAGGGATAGCTTCGGCTATCAG-AC
* *
40749765 TATGAAAAGGGGTGGTAACAACCAT
65 TATGAAAAGAGATGGTAACAACCAT
40749790 CGTGATTTTA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
89 1 0.01
90 71 0.99
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (90 bp):
GAATTATGAAAAAGGATGGCTTCAGCTATCAAAACATGAAAAGGGATAGCTTCGGCTATCAGACT
ATGAAAAGAGATGGTAACAACCATT
Found at i:40757028 original size:95 final size:94
Alignment explanation
Indices: 40756917--40757466 Score: 917
Period size: 95 Copynumber: 5.8 Consensus size: 94
40756907 GTATATTTGA
40756917 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* *
40756982 ATATATGTGATAAGGCCGAAT-GCCAATGTG
64 ATATATGTGATAAGGCCTAATGGCCGATGTG
40757012 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
40757077 ATATATGTGATAAGGCCTAATGGCCGATGTG
64 ATATATGTGATAAGGCCTAATGGCCGATGTG
*
40757108 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
40757172 ATATATGTGATAAGGCCTAATGGCCGATGTG
64 ATATATGTGATAAGGCCTAATGGCCGATGTG
40757203 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
40757268 ATATGTGATAAGGCCTAAT-GCCGATGTG
66 ATATGTGATAAGGCCTAATGGCCGATGTG
*
40757296 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
40757361 ATATGTGATAAGGCCTAATGGCCGATGTG
66 ATATGTGATAAGGCCTAATGGCCGATGTG
* * * * * * *
40757390 ATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
40757455 AAATGTGATAAG
66 ATATGTGATAAG
40757467 TCCCGAAGGG
Statistics
Matches: 438, Mismatches: 12, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
93 112 0.26
94 126 0.29
95 157 0.36
96 43 0.10
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (94 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:40757092 original size:142 final size:143
Alignment explanation
Indices: 40756917--40757466 Score: 961
Period size: 142 Copynumber: 3.9 Consensus size: 143
40756907 GTATATTTGA
40756917 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
40756982 ATATATGTGATAAGGCCGAAT-GCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
64 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
40757046 CTAATGGCCGATGTG
129 CTAATGGCCGATGTG
40757061 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
40757126 ATATGTGATAAGGCCGAATGGCC-ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
66 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
40757190 AATGGCCGATGTG
131 AATGGCCGATGTG
40757203 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* *
40757268 ATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCT
66 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
*
40757330 AATGGCCAATGTG
131 AATGGCCGATGTG
40757343 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * *
40757408 ATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
66 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
40757467 TCCCGAAGGG
Statistics
Matches: 392, Mismatches: 9, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
140 111 0.28
141 34 0.09
142 227 0.58
143 5 0.01
144 15 0.04
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (143 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
AATGGCCGATGTG
Found at i:40757098 original size:47 final size:47
Alignment explanation
Indices: 40756917--40757466 Score: 917
Period size: 47 Copynumber: 11.6 Consensus size: 47
40756907 GTATATTTGA
40756917 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
* *
40756966 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT-GCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
40757012 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
40757061 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
40757108 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
40757154 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
40757203 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
40757250 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
40757296 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
40757343 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* * * * * *
40757390 ATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* *
40757437 ATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGAATGTGAAAGTGTATATATGTGATAAG
40757467 TCCCGAAGGG
Statistics
Matches: 476, Mismatches: 18, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
46 89 0.19
47 283 0.59
48 46 0.10
49 58 0.12
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:40757634 original size:37 final size:37
Alignment explanation
Indices: 40757584--40757728 Score: 227
Period size: 37 Copynumber: 3.9 Consensus size: 37
40757574 TCGAGCTCTA
* *
40757584 AAGACCCGATGACTACGTGTGGAGAGTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
*
40757621 AAGACCCGATGACTACGTGTGGAGATTTTGCCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
*
40757658 AAGACCCAATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
* * *
40757695 AAGACCCGATAACTTCGTGTGGAGATTTCGTCCG
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCG
40757729 AGCTAAAGGT
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
Found at i:40759070 original size:40 final size:40
Alignment explanation
Indices: 40758989--40759491 Score: 763
Period size: 40 Copynumber: 12.8 Consensus size: 40
40758979 GAGAATTGAG
*
40758989 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40759028 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40759068 AGTGATATATCCGGGCTAAGTCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40759108 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40759148 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40759188 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
40759228 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
40759268 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
40759308 AGTGATGTATCCGGGCTAAGT-CCAAAGAGCA-TCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
40759346 AGTGATGTATCC-GACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40759385 AGTGATATATCCGGGCTAA-T-CCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40759423 AGTGATATATCCGTGCTAAGT-CCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
40759462 GGTG-TTTATTCGGGCTAGGT-CCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
40759492 ATCATGCTGG
Statistics
Matches: 431, Mismatches: 28, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
37 7 0.02
38 85 0.20
39 70 0.16
40 269 0.62
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:40763230 original size:48 final size:48
Alignment explanation
Indices: 40763166--40763669 Score: 737
Period size: 48 Copynumber: 10.6 Consensus size: 48
40763156 GTATATTTGA
40763166 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTG
* *
40763215 ATGAATGT-AAAGTG-TATATATGTGATAAGGCCGAATGGCCAAATGTG
1 ATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCC-GATGTG
*
40763262 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGTCGATGTG
1 ATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTG
*
40763311 ATGAATGTGAAAGTG-TATATATGTGATAAGGCC-AATAGCCGATGTG
1 ATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTG
* *
40763357 ATGAATGTGAAAGTG-TATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTG
40763404 ATGAATGTGAAAGTGTATATATATGTGAT-AGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTG
40763452 ATGAATGTGAAAGTGA-ATATATGTTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGATATATATG-TGATAAGGCCTAATGGCCGATGTG
40763500 ATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCC-A-GTG
1 ATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTG
40763545 ATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTG
* * * * * *
40763592 ATGAATGTGAAAGTG-TAATATATGTGACAGGGCCGAGTGGCCAACGTG
1 ATGAATGTGAAAGTGAT-ATATATGTGATAAGGCCTAATGGCCGATGTG
* *
40763640 ATGGATGTGAAAGTG-TATAAATGTGATAAG
1 ATGAATGTGAAAGTGATATATATGTGATAAG
40763670 TCCCGAAGGG
Statistics
Matches: 421, Mismatches: 21, Indels: 28
0.90 0.04 0.06
Matches are distributed among these distances:
45 44 0.10
46 78 0.19
47 110 0.26
48 125 0.30
49 40 0.10
50 24 0.06
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (48 bp):
ATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:40763396 original size:143 final size:143
Alignment explanation
Indices: 40763166--40763669 Score: 806
Period size: 143 Copynumber: 3.5 Consensus size: 143
40763156 GTATATTTGA
40763166 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT-AAAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
40763230 ATATATGTGATAAGGCCGAATGGCCAAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
64 ATATATGTGATAAGGCCGAATGGCC-AATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
*
40763295 CCTAATGGTCGATGTG
128 CCTAATGGCCGATGTG
*
40763311 ATGAATGTGAAAGTGTATATATGTGATAAGGCC-AATAGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
40763375 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGAT-AGGCCT
66 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
40763439 AATGGCCGATGTG
131 AATGGCCGATGTG
*
40763452 ATGAATGTGAAAGTGAATATATGTTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 ATGAATGTGAAAGTGTATATATG-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
*
40763517 TATATGTGATAAGGCCTAATGGCC-A-GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
65 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
40763578 TAATGGCCGATGTG
130 TAATGGCCGATGTG
* * * * * * *
40763592 ATGAATGTGAAAGTGTAATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTA
1 ATGAATGTGAAAGTGT-ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
*
40763657 TAAATGTGATAAG
65 TATATGTGATAAG
40763670 TCCCGAAGGG
Statistics
Matches: 340, Mismatches: 14, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
139 12 0.04
140 80 0.24
141 65 0.19
142 66 0.19
143 102 0.30
145 15 0.04
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (143 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
AATGGCCGATGTG
Found at i:40763429 original size:95 final size:94
Alignment explanation
Indices: 40763166--40763669 Score: 757
Period size: 95 Copynumber: 5.3 Consensus size: 94
40763156 GTATATTTGA
40763166 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT-AAAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
40763230 ATATATGTGATAAGGCCGAATGGCCAAATGTG
64 ATATATGTGATAAGGCCGAATGGCC-AATGTG
*
40763262 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* *
40763327 ATATATGTGATAAGGCC-AATAGCCGATGTG
64 ATATATGTGATAAGGCCGAATGGCCAATGTG
* *
40763357 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
* *
40763422 ATATATGTGAT-AGGCCTAATGGCCGATGTG
64 ATATATGTGATAAGGCCGAATGGCCAATGTG
*
40763452 ATGAATGTGAAAGTGAATATATGTTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 ATGAATGTGAAAGTGTATATATG-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
*
40763517 TATATGTGATAAGGCCTAATGGCC-A-GTG
65 TATATGTGATAAGGCCGAATGGCCAATGTG
40763545 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAA
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-A
* * * *
40763610 TATATGTGACAGGGCCGAGTGGCCAACGTG
65 TATATGTGATAAGGCCGAATGGCCAATGTG
* *
40763640 ATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGAATGTGAAAGTGTATATATGTGATAAG
40763670 TCCCGAAGGG
Statistics
Matches: 382, Mismatches: 17, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
92 40 0.10
93 90 0.24
94 19 0.05
95 110 0.29
96 99 0.26
97 24 0.06
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (94 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGATAAGGCCGAATGGCCAATGTG
Found at i:40763839 original size:37 final size:37
Alignment explanation
Indices: 40763789--40763930 Score: 202
Period size: 37 Copynumber: 3.9 Consensus size: 37
40763779 CCGAGCTCTA
* *
40763789 AAGACCCGATGACTACGTGTGGAGAGTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
*
40763826 AAGACCCGATGACTACGTGTGGAGATTTTGCCGCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTC-CGGGT
40763864 AAGACCC-ATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
* *
40763900 AAGA-CCGAT-ACTTCGTGT-GAGATTTCGTCCG
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCG
40763931 AGCTAAAGGT
Statistics
Matches: 97, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
34 12 0.12
35 10 0.10
36 11 0.11
37 52 0.54
38 12 0.12
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
Found at i:40764977 original size:46 final size:46
Alignment explanation
Indices: 40764917--40765087 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
40764907 GGTTTGAGCA
*
40764917 CCGAA-TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGT
* * * *
40764962 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGT
* * * *
40765009 CCAAACTCGTTGAGTTGAGTTCGAGTTCATTTATGGATGCGAACG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGT
*
40765054 CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
40765088 GGGGCAGGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
43 6 0.06
45 12 0.12
46 49 0.48
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGT
Found at i:40765342 original size:18 final size:19
Alignment explanation
Indices: 40765305--40765342 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40765295 CGATAAGGTG
40765305 TAAGATGATGAATGATGTT
1 TAAGATGATGAATGATGTT
40765324 TAAGATG-TGATAT-ATGTT
1 TAAGATGATGA-ATGATGTT
40765342 T
1 T
40765343 TGGTGGTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (19 bp):
TAAGATGATGAATGATGTT
Found at i:40767096 original size:19 final size:19
Alignment explanation
Indices: 40767051--40767096 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
40767041 TATTATGAAA
40767051 AACTAAAATAAAAGTAATT
1 AACTAAAATAAAAGTAATT
*
40767070 AA-TCAAAATAACA-TAAATT
1 AACT-AAAATAAAAGT-AATT
40767089 AACTAAAA
1 AACTAAAA
40767097 ATTAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.09
19 20 0.87
20 1 0.04
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (19 bp):
AACTAAAATAAAAGTAATT
Found at i:40771891 original size:50 final size:49
Alignment explanation
Indices: 40771812--40772178 Score: 265
Period size: 50 Copynumber: 7.6 Consensus size: 49
40771802 CATCAAAGTT
* * *
40771812 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATTGTGGC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTGTTGTGAC
** * *
40771861 TGACACCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTGTAG-GTACC
1 -GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTGTTGTG-A-C
* * * *
40771912 GATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCACCTGTTGGTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTGTT-GTGAC
* ** *
40771962 GATGCCATGTCCCAGACATGGTCTTACACTGACACAT-ATC----AAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTC-TCATCTGTTGTGAC
* * * * * * *
40772007 GATGCCATGTCCCAGACATGGTCTTAAACT-AGCTTTCATATCTCGAGGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATCTGTTG-TGAC
* * * *** *
40772057 GATGCCATGTCCCAGACATGGCCTTACACT-AGTTCTCGTCT-CAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATCTGTTGTGAC
* * * *
40772105 GATGCTATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTTGT--T
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCAT-CTGTTGTGAC
40772153 GATG-CATGTCCCAGACAT-GTCTTACA
1 GATGCCATGTCCCAGACATGGTCTTACA
40772179 TTAGCACACA
Statistics
Matches: 253, Mismatches: 49, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
44 2 0.01
45 34 0.13
46 8 0.03
47 13 0.05
48 39 0.15
49 2 0.01
50 151 0.60
51 3 0.01
52 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTGTTGTGAC
Found at i:40772058 original size:95 final size:98
Alignment explanation
Indices: 40771763--40772189 Score: 424
Period size: 95 Copynumber: 4.4 Consensus size: 98
40771753 GGTAAGATGC
* * * * **
40771763 CGATGCTATGTCCCAGACATGGTCTTACATTAGCTCACACATCAAAGTTGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCTAAGCCGATGCCATGTCCCAGA
*
40771828 CATGGTCTTACACTGACTCTCATATATTGTGG-
66 CATGGTCTTACACTGGCTCTCATATATTGTGGT
** * * * * *
40771860 CTGACACCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTGTAGGTACCGATGCCATGTCCC
1 C-GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCTAAG--CCGATGCCATGTCCC
* ** *
40771925 AGACATAGTCTTACACTGGCTCTCACCTGTTG-GTGT
63 AGACATGGTCTTACACTGGCTCTCATATATTGTG-GT
*
40771961 CGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATATC-AAGCCGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCTAAGCCGATGCCATGTCCCAGA
* * * * * *
40772023 CATGGTCTTAAACTAGCTTTCATATCTCGAGGT
66 CATGGTCTTACACTGGCTCTCATATATTGTGGT
* * * * * *
40772056 CGATGCCATGTCCCAGACATGGCCTTACACTAGTTCTCGTCTC-AATGCCGATGCTATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCTAA-GCCGATGCCATGTCCCAG
*
40772120 ACATGGTCTTACACTGGCTCTCATA-A-TGTTGT
65 ACATGGTCTTACACTGGCTCTCATATATTGTGGT
* * *
40772152 TGATG-CATGTCCCAGACAT-GTCTTACATTAGCACACAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT
40772190 GTCACCCAAA
Statistics
Matches: 268, Mismatches: 53, Indels: 21
0.78 0.15 0.06
Matches are distributed among these distances:
94 13 0.05
95 85 0.32
96 9 0.03
97 10 0.04
98 79 0.29
99 2 0.01
100 69 0.26
101 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (98 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCTAAGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGGCTCTCATATATTGTGGT
Found at i:40772161 original size:145 final size:143
Alignment explanation
Indices: 40771763--40772176 Score: 399
Period size: 145 Copynumber: 2.8 Consensus size: 143
40771753 GGTAAGATGC
* * * * * *
40771763 CGATGCTATGTCCCAGACATGGTCTTACATTAGCTCACACATCAAAGTTGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGTTCACTC-TCAATGTCGATGCCATGTCCCAGA
* * ** * *
40771828 CATGGTCTTACACTGACTCTCATATATTGTGGCTGACACCATGTCCCAGACATGGTCTTACACTG
65 CATGGTCTTACACTGGCTCTCATA-A-TGTAGCTGA-TGCATGTCCCAGACATGGTCTTAAACTA
40771893 GCTCTCATCTGTAGGTA
127 GCTCTCATCTGTAGGTA
* * * ***
40771910 CCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCACCTGTTGGTGTCGATGCCATGTCCC
1 -CGATGCCATGTCCCAGACATGGTCTTACACTAG-T-TCA-CTCTCAATGTCGATGCCATGTCCC
* * ** *
40771975 AGACATGGTCTTACACT-G-ACACAT-ATCAAGCCGATGCCATGTCCCAGACATGGTCTTAAACT
62 AGACATGGTCTTACACTGGCTCTCATAATGTAGCTGATG-CATGTCCCAGACATGGTCTTAAACT
*
40772037 AGCTTTCATATCTCG-AGGT-
126 AGCTCTC--ATCT-GTAGGTA
* * * *
40772056 CGATGCCATGTCCCAGACATGGCCTTACACTAGTTCTCGTCTCAATGCCGATGCTATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGTTCAC-TCTCAATGTCGATGCCATGTCCCAGA
* *
40772121 CATGGTCTTACACTGGCTCTCATAATGTTGTTGATGCATGTCCCAGACAT-GTCTTA
65 CATGGTCTTACACTGGCTCTCATAATGTAGCTGATGCATGTCCCAGACATGGTCTTA
40772177 CATTAGCACA
Statistics
Matches: 214, Mismatches: 41, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
142 1 0.00
143 36 0.17
144 8 0.04
145 82 0.38
146 8 0.04
147 8 0.04
148 34 0.16
150 36 0.17
151 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (143 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGTTCACTCTCAATGTCGATGCCATGTCCCAGAC
ATGGTCTTACACTGGCTCTCATAATGTAGCTGATGCATGTCCCAGACATGGTCTTAAACTAGCTC
TCATCTGTAGGTA
Found at i:40774329 original size:47 final size:48
Alignment explanation
Indices: 40774244--40774454 Score: 134
Period size: 48 Copynumber: 4.5 Consensus size: 48
40774234 TCTGCATATC
* ** *
40774244 GATGCCATATCCTAGTTATGGTCTTATACGAAGTCTCATAACGGTACT
1 GATGCCATATCCCAGACATGGTCTTATACGAAGCCTCATAACGGTACT
*
40774292 GATGCCATATCCCAGACAT-GTCTTATACGGAGCCTCAT-A---T-C-
1 GATGCCATATCCCAGACATGGTCTTATACGAAGCCTCATAACGGTACT
* * ** * * * *
40774333 GGTGCCATGTCCCAGACATGGTCTTATACGAAATCACGTAACGATGCT
1 GATGCCATATCCCAGACATGGTCTTATACGAAGCCTCATAACGGTACT
* * * * * ** *
40774381 GAAGCCATATCCCTA-ATATGGTCTTATACG-GGATCACATATTGGTGCT
1 GATGCCATATCCC-AGACATGGTCTTATACGAAG-CCTCATAACGGTACT
* *
40774429 GATGCCATGTCCCAAACATGGTCTTA
1 GATGCCATATCCCAGACATGGTCTTA
40774455 CACTAGCACA
Statistics
Matches: 128, Mismatches: 25, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
41 17 0.13
42 15 0.12
43 2 0.02
46 2 0.02
47 19 0.15
48 72 0.56
49 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (48 bp):
GATGCCATATCCCAGACATGGTCTTATACGAAGCCTCATAACGGTACT
Found at i:40774357 original size:89 final size:90
Alignment explanation
Indices: 40774203--40774411 Score: 217
Period size: 89 Copynumber: 2.3 Consensus size: 90
40774193 TAGAGTGCCA
* * * * * * * **
40774203 AAGCCATGTCCCTGACATTGTCTTACATGG-GTCTGCATATCGATGCCATATCCTAGTTATGGTC
1 AAGCCATATCCCTAACATGGTCTTATACGGAGCCT-CATATCGATGCCATATCCCAGACATGGTC
* * *
40774267 TTATACGAAGTCTCATAACGGTACTG
65 TTATACGAAATCACATAACGATACTG
* * *
40774293 ATGCCATATCCC-AGACAT-GTCTTATACGGAGCCTCATATCGGTGCCATGTCCCAGACATGGTC
1 AAGCCATATCCCTA-ACATGGTCTTATACGGAGCCTCATATCGATGCCATATCCCAGACATGGTC
* *
40774356 TTATACGAAATCACGTAACGATGCTG
65 TTATACGAAATCACATAACGATACTG
*
40774382 AAGCCATATCCCTAATATGGTCTTATACGG
1 AAGCCATATCCCTAACATGGTCTTATACGG
40774412 GATCACATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
89 68 0.70
90 29 0.30
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (90 bp):
AAGCCATATCCCTAACATGGTCTTATACGGAGCCTCATATCGATGCCATATCCCAGACATGGTCT
TATACGAAATCACATAACGATACTG
Found at i:40774467 original size:48 final size:48
Alignment explanation
Indices: 40774335--40774602 Score: 195
Period size: 48 Copynumber: 5.6 Consensus size: 48
40774325 CTCATATCGG
* * * * * * *
40774335 TGCCATGTCCCAGACATGGTCTTATACGA-AATCACGTAACGATGCTGA
1 TGCCATGTCCCAAACATGGTCTTACACTAGCA-CACATATCGGTGCTGA
* * * * * * * *
40774383 AGCCATATCCCTAATATGGTCTTATAC-GGGATCACATATTGGTGCTGA
1 TGCCATGTCCCAAACATGGTCTTACACTAGCA-CACATATCGGTGCTGA
*
40774431 TGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAACGT-C-GA
1 TGCCATGTCCCAAACATGGTCTTACACTAGCACACATATC--GGTGCTGA
* * *** *
40774479 TGCCATGTCGCAGACATGGTCTTACACTAGCACACATATCAACGTTGA
1 TGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCGGTGCTGA
* * * * *
40774527 TGCCATGTCCCAAACATGGTCTTACA-TGGGATCTCATCTCGGATGCCGA
1 TGCCATGTCCCAAACATGGTCTTACACTAGCA-CACATATCGG-TGCTGA
*
40774576 TGCCATGTCCCAGACATGGTCTTACAC
1 TGCCATGTCCCAAACATGGTCTTACAC
40774603 AGGATCTCAT
Statistics
Matches: 173, Mismatches: 38, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
47 3 0.02
48 137 0.79
49 31 0.18
50 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (48 bp):
TGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCGGTGCTGA
Found at i:40779673 original size:20 final size:19
Alignment explanation
Indices: 40779637--40779687 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
40779627 AAGGGCTATT
*
40779637 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
40779656 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
40779676 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
40779688 GTTACAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:40779864 original size:17 final size:17
Alignment explanation
Indices: 40779832--40779864 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40779822 TTAACTATAG
40779832 AATGTATTAAATAATGT
1 AATGTATTAAATAATGT
40779849 AATG-ATTAAATGAATG
1 AATGTATTAAAT-AATG
40779865 AATTTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
AATGTATTAAATAATGT
Found at i:40780911 original size:13 final size:13
Alignment explanation
Indices: 40780893--40780956 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
40780883 GATTCTTCAT
40780893 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
40780906 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
40780919 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
** *
40780932 TATTTTTGAGAAG
1 TGCTTTTGAAAAG
*
40780945 TGCTTTGGAAAA
1 TGCTTTTGAAAA
40780957 ATTTAAGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:40781221 original size:19 final size:19
Alignment explanation
Indices: 40781186--40781233 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
40781176 AATTATTTAT
40781186 TAAATTTAATTAGAATATA
1 TAAATTTAATTAGAATATA
* *
40781205 TAAACTTTATTTA-AATATT
1 TAAA-TTTAATTAGAATATA
*
40781224 TAAATATAAT
1 TAAATTTAAT
40781234 AATTAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 7 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TAAATTTAATTAGAATATA
Found at i:40785462 original size:7 final size:7
Alignment explanation
Indices: 40785450--40785475 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40785440 CCATTCCTAA
40785450 TCATCCC
1 TCATCCC
40785457 TCATCCC
1 TCATCCC
40785464 TCATCCC
1 TCATCCC
40785471 TCATC
1 TCATC
40785476 ATTTTCTATT
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:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:40793530 original size:16 final size:17
Alignment explanation
Indices: 40793511--40793547 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40793501 ACTAAAAGGT
40793511 TAAACATG-TAAAATAA
1 TAAACATGTTAAAATAA
*
40793527 TAAACATGTTAATATAA
1 TAAACATGTTAAAATAA
40793544 TAAA
1 TAAA
40793548 ACATATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (17 bp):
TAAACATGTTAAAATAA
Found at i:40794595 original size:27 final size:27
Alignment explanation
Indices: 40794564--40794647 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
40794554 TAGTTTACCA
** *
40794564 AATTACCAAAGTACCCCCGATTTATAG
1 AATTACCAATCTACCCTCGATTTATAG
**
40794591 AATTACCGCTCTACCCTCGATTTATAG
1 AATTACCAATCTACCCTCGATTTATAG
* *
40794618 AATTACCATTTTACCCTCGATTTATAG
1 AATTACCAATCTACCCTCGATTTATAG
40794645 AAT
1 AAT
40794648 ACTTTAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (27 bp):
AATTACCAATCTACCCTCGATTTATAG
Found at i:40794718 original size:28 final size:28
Alignment explanation
Indices: 40794659--40794732 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
40794649 CTTTAATTTA
40794659 CAAAATTACTAAAATA-CCCCTAGTTTG
1 CAAAATTACTAAAATACCCCCTAGTTTG
40794686 CAAAATTACTAAAATACCCCCT-GATTTG
1 CAAAATTACTAAAATACCCCCTAG-TTTG
* *
40794714 TAAAATTACTGAAATACCC
1 CAAAATTACTAAAATACCC
40794733 TCAACTTGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 17 0.40
28 26 0.60
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (28 bp):
CAAAATTACTAAAATACCCCCTAGTTTG
Found at i:40794746 original size:28 final size:28
Alignment explanation
Indices: 40794660--40794760 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 28
40794650 TTTAATTTAC
** *
40794660 AAAATTACTAAAATA-CCCCTAGTTTGC
1 AAAATTACTAAAATACCCCCTAACTTGT
* *
40794687 AAAATTACTAAAATACCCCCTGATTTGT
1 AAAATTACTAAAATACCCCCTAACTTGT
* *
40794715 AAAATTACTGAAATACCCTC-AACTTGT
1 AAAATTACTAAAATACCCCCTAACTTGT
* *
40794742 AAAAATTACCAAAGTACCC
1 -AAAATTACTAAAATACCC
40794761 TCGATTTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 20 0.32
28 42 0.68
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAATTACTAAAATACCCCCTAACTTGT
Found at i:40794990 original size:54 final size:54
Alignment explanation
Indices: 40794654--40795029 Score: 206
Period size: 54 Copynumber: 6.9 Consensus size: 54
40794644 GAATACTTTA
* ** * * *
40794654 ATTTACAAAATTACTAAAATACCC-CTAGTTTGCAAAATTACTAAAATACCCCCTG
1 ATTTATAAAATTACCGAAATACCCTC-AATTTGTAAAATTACCAAAATA-CCCCTG
* * * *
40794709 ATTTGTAAAATTACTGAAATACCCTCAACTTGTAAAAATTACCAAAGTA-CCCTCG
1 ATTTATAAAATTACCGAAATACCCTCAATTTGT-AAAATTACCAAAATACCCCT-G
* * ** * * * ***** *
40794764 ATTTATAGAATTA-CTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTG
1 ATTTATAAAATTACCGA-AATACCCTCAATTTGTAAAATTACCAAAATACCCCTG
* *** * * **
40794818 ATTTACAAAATTACCGTTTTACCCTCGA-TTGTGAAATTACTGAAATACCCCT-
1 ATTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTG
*** * * * * *
40794870 ATAGGGTAGAATTACCAAAACACTCCT-AGTTTGTAAAATTACCAAAATACCACTG
1 AT-TTATAAAATTACCGAAATAC-CCTCAATTTGTAAAATTACCAAAATACCCCTG
* * *
40794925 GTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTG
1 ATTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTG
* * ** * * *
40794979 ATTTACAAAATTACAGAAATACCCTTGATTTGTAGATTTACCAAAACACCC
1 ATTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCC
40795030 TTGTAGGATG
Statistics
Matches: 240, Mismatches: 70, Indels: 23
0.72 0.21 0.07
Matches are distributed among these distances:
52 2 0.01
53 30 0.12
54 141 0.59
55 53 0.22
56 14 0.06
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
ATTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTG
Found at i:40795011 original size:81 final size:81
Alignment explanation
Indices: 40794810--40795011 Score: 189
Period size: 81 Copynumber: 2.5 Consensus size: 81
40794800 ATTACTGTTT
* * *** * * *
40794810 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGA-TTGTGAAATTACTGAAATACCCCTATAG
1 TACCCCTGATTTACAAAATTACAGAAATACCCTTGATTTGTGAAATTACCGAAATACCCCAATAG
*
40794874 GGTAGAATTACCAAAA
66 GGTAAAATTACCAAAA
* * ** *
40794890 CACTCCT-AGTTTGTAAAATTACCA-AAATACCAC-TGGTTTGTGAAATTACCGAAATACCCTCA
1 TACCCCTGA-TTTACAAAATTA-CAGAAATACC-CTTGATTTGTGAAATTACCGAAATACCC-CA
**
40794952 AT-TTGTAAAATTACCAAAA
62 ATAGGGTAAAATTACCAAAA
40794971 TACCCCTGATTTACAAAATTACAGAAATACCCTTGATTTGT
1 TACCCCTGATTTACAAAATTACAGAAATACCCTTGATTTGT
40795012 AGATTTACCA
Statistics
Matches: 93, Mismatches: 21, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
79 1 0.01
80 22 0.24
81 66 0.71
82 4 0.04
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (81 bp):
TACCCCTGATTTACAAAATTACAGAAATACCCTTGATTTGTGAAATTACCGAAATACCCCAATAG
GGTAAAATTACCAAAA
Found at i:40795031 original size:27 final size:27
Alignment explanation
Indices: 40794660--40795032 Score: 164
Period size: 27 Copynumber: 13.8 Consensus size: 27
40794650 TTTAATTTAC
* * *
40794660 AAAATTACTAAAATACCCCT-AGTTTGC
1 AAAATTACCAAAATACCCTTGA-TTTGT
* *
40794687 AAAATTACTAAAATACCCCCTGATTTGT
1 AAAATTACCAAAATA-CCCTTGATTTGT
** ** *
40794715 AAAATTACTGAAATACCCTCAACTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* * *
40794742 AAAAATTACCAAAGTACCCTCGATTTAT
1 -AAAATTACCAAAATACCCTTGATTTGT
* * *** * *
40794770 AGAATTACTATTTTACCCTCGATTTAT
1 AAAATTACCAAAATACCCTTGATTTGT
* ***** **
40794797 AGAATTACTGTTTTACCCTTGATTTAC
1 AAAATTACCAAAATACCCTTGATTTGT
**** *
40794824 AAAATTACCGTTTTACCCTCGA-TTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* ** * **
40794850 GAAATTACTGAAATACCCCT-ATAGGGT
1 AAAATTACCAAAATACCCTTGAT-TTGT
* * *
40794877 AGAATTACCAAAACACTCCTAG-TTTGT
1 AAAATTACCAAAATAC-CCTTGATTTGT
*
40794904 AAAATTACCAAAATACCAC-TGGTTTGT
1 AAAATTACCAAAATACC-CTTGATTTGT
* * **
40794931 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* **
40794958 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACCAAAATACCCTTGATTTGT
40794985 AAAATTA-CAGAAATACCCTTGATTTGT
1 AAAATTACCA-AAATACCCTTGATTTGT
* * *
40795012 AGATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
40795033 TAGGATGAAA
Statistics
Matches: 270, Mismatches: 64, Indels: 24
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.00
26 20 0.07
27 199 0.74
28 49 0.18
29 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGATTTGT
Found at i:40795945 original size:26 final size:26
Alignment explanation
Indices: 40795915--40796089 Score: 237
Period size: 26 Copynumber: 6.8 Consensus size: 26
40795905 GAAGAAGTGC
*
40795915 AAAAGGGTTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
40795941 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* *
40795967 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* *
40795993 AAAAGGGTTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* * *
40796019 AAAAGGGCTTATGCCTCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* *
40796045 AAAAGGGCTT-TGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATCG
40796070 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40796090 ATTAAAGAGG
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 30 0.23
26 102 0.77
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:40796044 original size:78 final size:77
Alignment explanation
Indices: 40795915--40796089 Score: 262
Period size: 78 Copynumber: 2.3 Consensus size: 77
40795905 GAAGAAGTGC
* *
40795915 AAAAGGGTTTATGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG
1 AAAAGGGTTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTGAAAAGGGCTT-TG
***
40795980 CCCCAATTTATTG
65 CCCCAATTTACCA
*
40795993 AAAAGGGTTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCTCAATTTATTGAAAAGGGCTTTGC
1 AAAAGGGTTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTGAAAAGGGCTTTGC
*
40796058 CCCAGTTTACCA
66 CCCAATTTACCA
*
40796070 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGTTTATGCCCCAGTT
40796090 ATTAAAGAGG
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
76 10 0.11
77 20 0.22
78 59 0.66
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (77 bp):
AAAAGGGTTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTGAAAAGGGCTTTGC
CCCAATTTACCA
Found at i:40796293 original size:42 final size:42
Alignment explanation
Indices: 40796234--40796325 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
40796224 TAGTCTCCCC
* *
40796234 AAATGGGCTTGCATACATTCATTG-GTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGAG-ATTACATGTGATATTG
40796276 AAATGGGCTTGCATACATCCATTGAGATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGAGATTACATGTGATATTG
40796318 AAATGGGC
1 AAATGGGC
40796326 CTAAGGGCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGAGATTACATGTGATATTG
Found at i:40796426 original size:31 final size:31
Alignment explanation
Indices: 40796340--40796432 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
40796330 GGGCCATACC
* * *
40796340 ATTTATAGTAAAGGCTTCGACCCAATGATATG
1 ATTTAT-GAAAAGGCTTCGGCCCAGTGATATG
40796372 ATTTATGAAAAGGCTTCGGCCCAGTGATATG
1 ATTTATGAAAAGGCTTCGGCCCAGTGATATG
40796403 ATTTATGAAAAGGCTTCGGCCCAGT-ATATG
1 ATTTATGAAAAGGCTTCGGCCCAGTGATATG
40796433 TTAAGACTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 5 0.09
31 47 0.81
32 6 0.10
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (31 bp):
ATTTATGAAAAGGCTTCGGCCCAGTGATATG
Found at i:40797001 original size:16 final size:15
Alignment explanation
Indices: 40796960--40797001 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
40796950 AAATATGAAT
*
40796960 TATATATGCTGAAATG
1 TATATATG-TGAAATA
40796976 TATA-ATGTGATAATA
1 TATATATGTGA-AATA
40796991 TATATATGTGA
1 TATATATGTGA
40797002 GCCGAATGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.40
Consensus pattern (15 bp):
TATATATGTGAAATA
Found at i:40798102 original size:13 final size:14
Alignment explanation
Indices: 40798084--40798118 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
40798074 TATAGACAAA
40798084 ATGTTTGGCTAT-G
1 ATGTTTGGCTATCG
*
40798097 ATGTTTGGCTATCT
1 ATGTTTGGCTATCG
40798111 ATGTTTGG
1 ATGTTTGG
40798119 TTTATAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.14, C:0.09, G:0.29, T:0.49
Consensus pattern (14 bp):
ATGTTTGGCTATCG
Found at i:40802452 original size:27 final size:27
Alignment explanation
Indices: 40802412--40802474 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
40802402 TGTAAGATAG
* *
40802412 GCCACTAAGGCAATCCATTCAGAGTATT
1 GCCACAAAGACAATCCATTCAGAG-ATT
40802440 -CCACAAAGACAATCCATTCAGAGATT
1 GCCACAAAGACAATCCATTCAGAGATT
40802466 GCCACAAAG
1 GCCACAAAG
40802475 GCTATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (27 bp):
GCCACAAAGACAATCCATTCAGAGATT
Found at i:40804741 original size:27 final size:27
Alignment explanation
Indices: 40804700--40804797 Score: 117
Period size: 27 Copynumber: 3.6 Consensus size: 27
40804690 GGAGGGTTAC
*
40804700 ACGATTCATATAGAGTACGCCACAAAG
1 ACGATTCATACAGAGTACGCCACAAAG
40804727 ACGATTCATACAGAGTACGCCACAAAG
1 ACGATTCATACAGAGTACGCCACAAAG
* * * **
40804754 GCGATTCATACACAGTACACCGTAAAGG
1 ACGATTCATACAGAGTACGCCACAAA-G
*
40804782 A-GATTCATTCAGAGTA
1 ACGATTCATACAGAGTA
40804798 TGTTACAAAG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 60 0.98
28 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (27 bp):
ACGATTCATACAGAGTACGCCACAAAG
Found at i:40806354 original size:23 final size:23
Alignment explanation
Indices: 40806324--40806371 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40806314 TATTGGTTGG
40806324 AAGTAATCCCACATCGGGAAGCT
1 AAGTAATCCCACATCGGGAAGCT
40806347 AAGTAATCCCACATCGGGAAGCT
1 AAGTAATCCCACATCGGGAAGCT
40806370 AA
1 AA
40806372 CATGAGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (23 bp):
AAGTAATCCCACATCGGGAAGCT
Found at i:40806785 original size:27 final size:27
Alignment explanation
Indices: 40806747--40806826 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
40806737 AATCTCATAT
40806747 CTGTAGGGTAGAATTACTAAAATACCC
1 CTGTAGGGTAGAATTACTAAAATACCC
* *
40806774 CTGTAGGGTAGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTAAAATACCC
*
40806801 CTGTAGGGTAGAATTACCAAAATACC
1 CTGTAGGGTAGAATTACTAAAATACC
40806827 ATTGGTTTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTAAAATACCC
Found at i:40806870 original size:54 final size:54
Alignment explanation
Indices: 40806812--40807101 Score: 217
Period size: 54 Copynumber: 5.4 Consensus size: 54
40806802 TGTAGGGTAG
* * * *
40806812 AATTACCAAAATACCATTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTGATTTGCAAAATTACCAAAATACCCTTAGTTTGTAA
* * ** * * *
40806866 AATTACCACAATACCCCTGATTTGTGAAATTACCGAAATA-CCTTCGACTTGTAA
1 AATTACCAAAATACCCTTGATTTGCAAAATTACCAAAATACCCTTAG-TTTGTAA
* * * * * *
40806920 AATTACTAAAATACCCTTAATTTGTAAAGTTACCAAAATACCCCT-GATTTGGAA
1 AATTACCAAAATACCCTTGATTTGCAAAATTACCAAAATACCCTTAG-TTTGTAA
* * * * * * **
40806974 AAGTACCGAAATACCCTTAATTTGGAAAATTACAAAAATACCCTTGACTTTCAAA
1 AATTACCAAAATACCCTTGATTTGCAAAATTACCAAAATACCCTT-AGTTTGTAA
* * * ** * *
40807029 AATTA-TAGAAATACCATTGGTTTGCAAAATTACTGAAATACCCTTGGTTTGTAG
1 AATTACCA-AAATACCCTTGATTTGCAAAATTACCAAAATACCCTTAGTTTGTAA
* *
40807083 ATTTACCAAAACACCCTTG
1 AATTACCAAAATACCCTTG
40807102 TAGGATGAAA
Statistics
Matches: 181, Mismatches: 49, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
53 4 0.02
54 133 0.73
55 44 0.24
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (54 bp):
AATTACCAAAATACCCTTGATTTGCAAAATTACCAAAATACCCTTAGTTTGTAA
Found at i:40806897 original size:81 final size:80
Alignment explanation
Indices: 40806812--40807016 Score: 241
Period size: 81 Copynumber: 2.5 Consensus size: 80
40806802 TGTAGGGTAG
* * * * * *
40806812 AATTACCAAAATACCATTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCACAA
1 AATTACCGAAATACC-TTGATTTGCAAAATTACAAAAATACCCCTAATTTGTAAAATTACCAAAA
40806877 TACCCCTGATTTGTG-A
65 TACCCCTGATTTG-GAA
* * * * *
40806893 AATTACCGAAATACCTTCGACTTGTAAAATTACTAAAATACCCTTAATTTGTAAAGTTACCAAAA
1 AATTACCGAAATACCTT-GATTTGCAAAATTACAAAAATACCCCTAATTTGTAAAATTACCAAAA
40806958 TACCCCTGATTTGGAA
65 TACCCCTGATTTGGAA
* * *
40806974 AAGTACCGAAATACCCTTAATTTGGAAAATTACAAAAATACCC
1 AATTACCGAAATA-CCTTGATTTGCAAAATTACAAAAATACCC
40807017 TTGACTTTCA
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
80 3 0.03
81 99 0.93
82 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (80 bp):
AATTACCGAAATACCTTGATTTGCAAAATTACAAAAATACCCCTAATTTGTAAAATTACCAAAAT
ACCCCTGATTTGGAA
Found at i:40807017 original size:81 final size:81
Alignment explanation
Indices: 40806837--40807018 Score: 242
Period size: 81 Copynumber: 2.2 Consensus size: 81
40806827 ATTGGTTTAC
* * * * *
40806837 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCACAATACCCCTGATTTGTGAAATTACCGA
1 AAAATTACAAAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTGATTTGTGAAAGTACCGA
* *
40806902 AATACCTTCGACTTGT
66 AATACCTTCAACTTGG
* *
40806918 AAAATTACTAAAATACCCTTAATTTGTAAAGTTACCAAAATACCCCTGATTTG-GAAAAGTACCG
1 AAAATTACAAAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTGATTTGTG-AAAGTACCG
*
40806982 AAATACCCTT-AATTTGG
65 AAATA-CCTTCAACTTGG
40806999 AAAATTACAAAAATACCCTT
1 AAAATTACAAAAATACCCTT
40807019 GACTTTCAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
80 1 0.01
81 84 0.94
82 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (81 bp):
AAAATTACAAAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTGATTTGTGAAAGTACCGA
AATACCTTCAACTTGG
Found at i:40807029 original size:27 final size:28
Alignment explanation
Indices: 40806812--40807101 Score: 190
Period size: 27 Copynumber: 10.7 Consensus size: 28
40806802 TGTAGGGTAG
* *
40806812 AATTACCAAAATACCATTG-GTTTACAA
1 AATTACCAAAATACCCTTGAGTTTGCAA
* *
40806839 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCTTGAGTTTGCAA
* * **
40806866 AATTACCACAATACCCCTGA-TTTGTGA
1 AATTACCAAAATACCCTTGAGTTTGCAA
* * *
40806893 AATTACCGAAATA-CCTTCGA-CTTGTAA
1 AATTACCAAAATACCCTT-GAGTTTGCAA
* * *
40806920 AATTACTAAAATACCCTT-AATTTGTAA
1 AATTACCAAAATACCCTTGAGTTTGCAA
* * *
40806947 AGTTACCAAAATACCCCTGA-TTTGGAA
1 AATTACCAAAATACCCTTGAGTTTGCAA
* * * *
40806974 AAGTACCGAAATACCCTT-AATTTGGAA
1 AATTACCAAAATACCCTTGAGTTTGCAA
* *
40807001 AATTACAAAAATACCCTTGACTTT-CAAA
1 AATTACCAAAATACCCTTGAGTTTGC-AA
* *
40807029 AATTA-TAGAAATACCATTG-GTTTGCAA
1 AATTACCA-AAATACCCTTGAGTTTGCAA
** * *
40807056 AATTACTGAAATACCCTTG-GTTTGTAG
1 AATTACCAAAATACCCTTGAGTTTGCAA
* *
40807083 ATTTACCAAAACACCCTTG
1 AATTACCAAAATACCCTTG
40807102 TAGGATGAAA
Statistics
Matches: 213, Mismatches: 38, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
26 5 0.02
27 179 0.84
28 29 0.14
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (28 bp):
AATTACCAAAATACCCTTGAGTTTGCAA
Found at i:40807143 original size:27 final size:27
Alignment explanation
Indices: 40807113--40807165 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
40807103 AGGATGAAAT
40807113 GACTAAAATACCCCTAATA-GGTAAAAA
1 GACTAAAATACCCCT-ATAGGGTAAAAA
** *
40807140 GACTGTAATGCCCCTATAGGGTAAAA
1 GACTAAAATACCCCTATAGGGTAAAA
40807166 TGACCGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (27 bp):
GACTAAAATACCCCTATAGGGTAAAAA
Found at i:40807206 original size:27 final size:27
Alignment explanation
Indices: 40807123--40807196 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
40807113 GACTAAAATA
* *
40807123 CCCCTAATAGG-TAAAAAGACTGTAATG
1 CCCCT-ATAGGCTAAAATGACCGTAATG
* *
40807150 CCCCTATAGGGTAAAATGACCGTAAAG
1 CCCCTATAGGCTAAAATGACCGTAATG
*
40807177 CCCCTGTAGGCTAAAATGAC
1 CCCCTATAGGCTAAAATGAC
40807197 GATTATGCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 5 0.12
27 36 0.88
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (27 bp):
CCCCTATAGGCTAAAATGACCGTAATG
Found at i:40807371 original size:27 final size:27
Alignment explanation
Indices: 40807337--40807416 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
40807327 GGAAGTTCTG
*
40807337 TACTGGTGACTATG-T-CATATTCACTGT
1 TACTGGTGACTATGCTACA-ATT-ACTGA
*
40807364 TACTGGTGGCTATGCTACAATTACTGA
1 TACTGGTGACTATGCTACAATTACTGA
* * * *
40807391 TACTGGTGGCTTTGCCACATTTACTG
1 TACTGGTGACTATGCTACAATTACTG
40807417 TTTCTGGTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 40 0.87
28 4 0.09
29 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (27 bp):
TACTGGTGACTATGCTACAATTACTGA
Found at i:40807423 original size:27 final size:27
Alignment explanation
Indices: 40807359--40807432 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
40807349 TGTCATATTC
* *
40807359 ACTGTTACTGGTGGCTATGCTACAATT
1 ACTGTTACTGGTGGCTTTGCCACAATT
* *
40807386 ACTGATACTGGTGGCTTTGCCACATTT
1 ACTGTTACTGGTGGCTTTGCCACAATT
* *
40807413 ACTGTTTCTGGTAGCTTTGC
1 ACTGTTACTGGTGGCTTTGC
40807433 TACGATATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (27 bp):
ACTGTTACTGGTGGCTTTGCCACAATT
Found at i:40813531 original size:16 final size:16
Alignment explanation
Indices: 40813510--40813540 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40813500 ATTTTGGGGG
40813510 CAAAATGTAATTTTTC
1 CAAAATGTAATTTTTC
40813526 CAAAATGTAATTTTT
1 CAAAATGTAATTTTT
40813541 GGGTTGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (16 bp):
CAAAATGTAATTTTTC
Found at i:40818550 original size:19 final size:19
Alignment explanation
Indices: 40818505--40818551 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
40818495 TATTATGAAA
40818505 AACTAAAATAGAAATAATT
1 AACTAAAATAGAAATAATT
*
40818524 AA-TCAAAATA-ACATAAATT
1 AACT-AAAATAGAAAT-AATT
40818543 AACTAAAAT
1 AACTAAAAT
40818552 TAAAGAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 19 0.79
20 1 0.04
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (19 bp):
AACTAAAATAGAAATAATT
Found at i:40836042 original size:53 final size:54
Alignment explanation
Indices: 40835969--40836283 Score: 363
Period size: 55 Copynumber: 5.8 Consensus size: 54
40835959 TTCCTTTCTA
* * *
40835969 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
40836022 AACTCACCAATGCCATGTCTTGGCATGGTCTTAGATGGGA-CCTTTGCCTTATAG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC-TTGCCTTATAG
* *
40836076 TAACTCATCAATGCCATGTCTTGACATGGTCTTACATGGCATCCTTGCCTTAT-G
1 -AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * *
40836130 AACTCACCAATTTCATGCCTTGGCATGGTCTTACATAGG-A-CCTTTGCCTTATAG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACAT-GGTATCC-TTGCCTTATAG
* * *
40836184 TAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAG
1 -AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
40836239 AACTTATCAATGCCATGCCTTGGA-ATGGTCTTACATGATATCCTT
1 AACTCACCAATGCCATGTCTT-GACATGGTCTTACATGGTATCCTT
40836284 ATCTTACCAA
Statistics
Matches: 226, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
52 4 0.02
53 84 0.37
54 45 0.20
55 89 0.39
56 4 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.35
Consensus pattern (54 bp):
AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:40836171 original size:108 final size:108
Alignment explanation
Indices: 40835979--40836274 Score: 475
Period size: 108 Copynumber: 2.7 Consensus size: 108
40835969 AACTTACCAT
* *
40835979 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGTCTTG
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
* *
40836044 GCATGGTCTTAGATGGGACCTTTGCCTTATAGTAACTCATCAA
66 GCATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
* **
40836087 TGCCATGTCTTGACATGGTCTTACATGGCATCCTTGCCTTATGAACTCACCAATTTCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
40836152 GCATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
66 GCATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
* * * *
40836195 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
*
40836260 GGAATGGTCTTACAT
65 GGCATGGTCTTACAT
40836275 GATATCCTTA
Statistics
Matches: 172, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
108 140 0.81
109 32 0.19
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (108 bp):
TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
GCATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
Found at i:40836318 original size:47 final size:47
Alignment explanation
Indices: 40836263--40836383 Score: 215
Period size: 47 Copynumber: 2.6 Consensus size: 47
40836253 ATGCCTTGGA
* *
40836263 ATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAAC
1 ATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAAC
40836310 ATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAAC
1 ATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAAC
*
40836357 ATGGTCTTACATGGTATCATTGTCTTA
1 ATGGTCTTACATGGTATCCTTGTCTTA
40836384 GTGCCAATGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (47 bp):
ATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAAC
Found at i:40843254 original size:43 final size:42
Alignment explanation
Indices: 40843219--40843352 Score: 146
Period size: 42 Copynumber: 3.1 Consensus size: 42
40843209 TCTTCCATGT
* *
40843219 AATCAAATATTGATGCCACTATCCCAAACAGGGTCTTACACGA
1 AATCAAATA-CGATGCCAATATCCCAAACAGGGTCTTACACGA
* *
40843262 AATCAAATACGATGCCAATGTCCCAAACATGGTCTTACACGTA
1 AATCAAATACGATGCCAATATCCCAAACAGGGTCTTACACG-A
** *
40843305 AATCTCAAAT-CGATGCCAACGTCCCATAC-GTGGTCTTACACGA
1 AA--TCAAATACGATGCCAATATCCCAAACAG-GGTCTTACACGA
40843348 AATCA
1 AATCA
40843353 CATATCGGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
41 3 0.04
42 28 0.35
43 15 0.19
44 28 0.35
45 6 0.08
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (42 bp):
AATCAAATACGATGCCAATATCCCAAACAGGGTCTTACACGA
Found at i:40843289 original size:42 final size:43
Alignment explanation
Indices: 40843183--40843352 Score: 172
Period size: 43 Copynumber: 4.0 Consensus size: 43
40843173 CAGAAAGCTC
* * * * *
40843183 ATACAATGCCAACGTCCCAGA-AGTGGTCTTCCATGTAATCAA
1 ATACGATGCCAACGTCCCAAACAGTGGTCTTACACGAAATCAA
* *
40843225 ATATTGATGCC-ACTATCCCAAACAG-GGTCTTACACGAAATCAA
1 ATA-CGATGCCAAC-GTCCCAAACAGTGGTCTTACACGAAATCAA
*
40843268 ATACGATGCCAATGTCCCAAACA-TGGTCTTACACGTAAATCTCAA
1 ATACGATGCCAACGTCCCAAACAGTGGTCTTACACG-AAA--TCAA
*
40843313 AT-CGATGCCAACGTCCCATAC-GTGGTCTTACACGAAATCA
1 ATACGATGCCAACGTCCCAAACAGTGGTCTTACACGAAATCA
40843353 CATATCGGAA
Statistics
Matches: 107, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
41 3 0.03
42 31 0.29
43 36 0.34
44 31 0.29
45 6 0.06
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (43 bp):
ATACGATGCCAACGTCCCAAACAGTGGTCTTACACGAAATCAA
Found at i:40843339 original size:44 final size:44
Alignment explanation
Indices: 40843240--40843351 Score: 158
Period size: 44 Copynumber: 2.6 Consensus size: 44
40843230 GATGCCACTA
* *
40843240 TCCCAAACAGGGTCTTACACGAAA--TCAAATACGATGCCAATG
1 TCCCAAACATGGTCTTACACGAAATCTCAAATACGATGCCAACG
40843282 TCCCAAACATGGTCTTACACGTAAATCTCAAAT-CGATGCCAACG
1 TCCCAAACATGGTCTTACACG-AAATCTCAAATACGATGCCAACG
* *
40843326 TCCCATACGTGGTCTTACACGAAATC
1 TCCCAAACATGGTCTTACACGAAATC
40843352 ACATATCGGA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
42 20 0.32
43 8 0.13
44 29 0.46
45 6 0.10
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (44 bp):
TCCCAAACATGGTCTTACACGAAATCTCAAATACGATGCCAACG
Found at i:40845169 original size:13 final size:12
Alignment explanation
Indices: 40845147--40845188 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
40845137 AATTACAATA
40845147 AAAGAAATAAAG
1 AAAGAAATAAAG
40845159 AAAGAAAATAAAG
1 AAAG-AAATAAAG
**
40845172 AAA-AAGGAAAG
1 AAAGAAATAAAG
40845183 AAAGAA
1 AAAGAA
40845189 GGCCATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 9 0.35
12 6 0.23
13 11 0.42
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (12 bp):
AAAGAAATAAAG
Found at i:40845183 original size:20 final size:21
Alignment explanation
Indices: 40845147--40845185 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40845137 AATTACAATA
40845147 AAAGAAATAAAGAAAGAAAAT
1 AAAGAAATAAAGAAAGAAAAT
*
40845168 AAAGAAA-AAGGAAAGAAA
1 AAAGAAATAAAGAAAGAAA
40845186 GAAGGCCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (21 bp):
AAAGAAATAAAGAAAGAAAAT
Found at i:40845246 original size:18 final size:18
Alignment explanation
Indices: 40845201--40845246 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
40845191 CCATGGTTAG
40845201 AAGGGAAAGAAAGAAGAA
1 AAGGGAAAGAAAGAAGAA
*
40845219 AAGAGAAAAGAAA-AAGAAA
1 AAG-GGAAAGAAAGAAG-AA
40845238 AAGGGAAAG
1 AAGGGAAAG
40845247 CTAGGGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AAGGGAAAGAAAGAAGAA
Found at i:40861107 original size:48 final size:48
Alignment explanation
Indices: 40861025--40861153 Score: 179
Period size: 48 Copynumber: 2.7 Consensus size: 48
40861015 TACCACGGCT
* * *
40861025 ATACGTGTAATGTGGTGCTAAGTGGATTTACCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
* * *
40861073 ATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
* *
40861121 ATTCAT-TAACGTGGTGCTAAGTGGATATTCCAC
1 ATACATGTAACGTGGTGCTAAGTGGATATACCAC
40861154 AGTTAAACAT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
47 26 0.36
48 47 0.64
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (48 bp):
ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
Found at i:40861178 original size:38 final size:38
Alignment explanation
Indices: 40861127--40861203 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
40861117 ATTGATTCAT
*
40861127 TAACGTGGTGCTAAGTGGATATTCCACAGTTAAACATG
1 TAACGTGGTGCTAAGTGGATATGCCACAGTTAAACATG
* *
40861165 TAACGTGGTGCTAAGTGGATATGCCACGGTTATACATG
1 TAACGTGGTGCTAAGTGGATATGCCACAGTTAAACATG
40861203 T
1 T
40861204 TAATTTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATGCCACAGTTAAACATG
Found at i:40862703 original size:25 final size:25
Alignment explanation
Indices: 40862674--40862725 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40862664 TTCAAAGTAT
40862674 ATCTTGTTGTGTTAGCAATTTTGCG
1 ATCTTGTTGTGTTAGCAATTTTGCG
40862699 ATCTTGTTGTGTTAGCAATTTTGCG
1 ATCTTGTTGTGTTAGCAATTTTGCG
40862724 AT
1 AT
40862726 GTATAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.48
Consensus pattern (25 bp):
ATCTTGTTGTGTTAGCAATTTTGCG
Found at i:40866255 original size:44 final size:42
Alignment explanation
Indices: 40866201--40866356 Score: 170
Period size: 43 Copynumber: 3.6 Consensus size: 42
40866191 TTTCGATATG
*
40866201 TGATTTCGTGTAAGACCACGTCTAGGACATTGGCATC-AATT
1 TGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAATT
* * *
40866242 TGAGATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATT
1 T--GATTT-CGTGTAAGACCACGTCTGGGACATTGGCATCGAATT
* ** *
40866287 TGATTTTGTGTAAGACCTTGTCTGGGACAGTGGCATCGATATT
1 TGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGA-ATT
* * *
40866330 TGATTACATGTAAGACCACGTCAGGGA
1 TGATTTCGTGTAAGACCACGTCTGGGA
40866357 TGTCGGCATT
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 28 0.29
43 34 0.36
44 28 0.29
45 4 0.04
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAATT
Found at i:40867327 original size:27 final size:27
Alignment explanation
Indices: 40867263--40867476 Score: 144
Period size: 27 Copynumber: 7.9 Consensus size: 27
40867253 AATACTTTAG
* * ** *
40867263 TTTACCAAATTACTAAAATGTCCTCAA
1 TTTACAAAATTACCAAAATACCCTCGA
** *
40867290 TTTGTAAAATTACCAAAGTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* **** *
40867317 TTTACAGAATTACCGTTTTTACACTCGA
1 TTTACAAAATTACC-AAAATACCCTCGA
* * * *
40867345 TTTACAAAATTACTAAAATACCATTGG
1 TTTACAAAATTACCAAAATACCCTCGA
*
40867372 TTTACAAAATTACCAAAATACCC-CTA
1 TTTACAAAATTACCAAAATACCCTCGA
*** * *
40867398 GTTTGTGAAATTACCGAAATACCCTCAA
1 -TTTACAAAATTACCAAAATACCCTCGA
**
40867426 TTTGTAAAATTACCAAAATACCC-CTGA
1 TTTACAAAATTACCAAAATACCCTC-GA
*
40867453 TTTACAAAATTACAAAAATACCCT
1 TTTACAAAATTACCAAAATACCCT
40867477 TGACTTTCTA
Statistics
Matches: 140, Mismatches: 42, Indels: 9
0.73 0.22 0.05
Matches are distributed among these distances:
26 1 0.01
27 117 0.84
28 22 0.16
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTCGA
Found at i:40867526 original size:27 final size:27
Alignment explanation
Indices: 40867345--40867561 Score: 141
Period size: 27 Copynumber: 8.0 Consensus size: 27
40867335 TTACACTCGA
* *
40867345 TTTACAAAATTACTAAAATACCATTGG
1 TTTACAAAATTACCAAAATACCCTTGG
* *
40867372 TTTACAAAATTACCAAAATACCCCTAG
1 TTTACAAAATTACCAAAATACCCTTGG
*** * ***
40867399 TTTGTGAAATTACCGAAATACCCTCAA
1 TTTACAAAATTACCAAAATACCCTTGG
** * *
40867426 TTTGTAAAATTACCAAAATACCCCTGA
1 TTTACAAAATTACCAAAATACCCTTGG
* *
40867453 TTTACAAAATTACAAAAATACCCTTGAC
1 TTTACAAAATTACCAAAATACCCTTG-G
* *
40867481 TTT-CTAAAAATTA-TAGAAATACCATTGG
1 TTTAC--AAAATTACCA-AAATACCCTTGG
** *
40867509 TTTACAAAATTACTGAAATACCATTGG
1 TTTACAAAATTACCAAAATACCCTTGG
** * * *
40867536 TTTGTAGATTTACCAAAACACCCTTG
1 TTTACAAAATTACCAAAATACCCTTG
40867562 TAGGATGAAA
Statistics
Matches: 151, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
27 125 0.83
28 8 0.05
29 18 0.12
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTTGG
Found at i:40867622 original size:27 final size:27
Alignment explanation
Indices: 40867579--40867652 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
40867569 AAATGACTAA
*
40867579 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
40867606 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
40867633 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
40867653 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:40867656 original size:27 final size:27
Alignment explanation
Indices: 40867592--40867656 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
40867582 ACCCCTAATA
*
40867592 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
40867619 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
40867646 GGTAAAATGAC
1 GGTAAAATGAC
40867657 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:40868535 original size:24 final size:25
Alignment explanation
Indices: 40868464--40868533 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
40868454 AAGAAGTGCT
* * *
40868464 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
40868489 AAAAGGGCTTTACCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
40868514 AAAAGGGCTTTGCCTCAGTT
1 AAAAGGGCTTTGCCCCAGTT
40868534 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:40868546 original size:24 final size:24
Alignment explanation
Indices: 40868514--40868560 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40868504 CAGTTTATCA
**
40868514 AAAAGGGCTTTGCCT-CAGTTATT
1 AAAAGGGCTAGGCCTCCAGTTATT
40868537 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTAGGCCTCCAGTTAT
40868561 ATGATAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 8 0.40
25 7 0.35
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTAGGCCTCCAGTTATT
Found at i:40883806 original size:17 final size:20
Alignment explanation
Indices: 40883771--40883806 Score: 51
Period size: 17 Copynumber: 1.9 Consensus size: 20
40883761 GGAAAGTGAA
40883771 ATAATAAAAGATGATAAATG
1 ATAATAAAAGATGATAAATG
40883791 ATAA-AAAA-ATGA-AAAT
1 ATAATAAAAGATGATAAAT
40883807 ATCATCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 4 0.25
20 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (20 bp):
ATAATAAAAGATGATAAATG
Found at i:40885929 original size:36 final size:37
Alignment explanation
Indices: 40885883--40885962 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 37
40885873 AGGTAATATA
*
40885883 AACATAATATACTACAATTCCATTTAATCACAAGGCT
1 AACACAATATACTACAATTCCATTTAATCACAAGGCT
40885920 AACACATATAATATACTACAATTCCATTTAATCACAAGGCT
1 AACAC----AATATACTACAATTCCATTTAATCACAAGGCT
40885961 AA
1 AA
40885963 TATATATGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
37 4 0.11
41 34 0.89
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (37 bp):
AACACAATATACTACAATTCCATTTAATCACAAGGCT
Found at i:40886512 original size:28 final size:28
Alignment explanation
Indices: 40886481--40886539 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
40886471 TAAAATACAA
40886481 TTATATTAATGCTTATTAACATATGAAC
1 TTATATTAATGCTTATTAACATATGAAC
40886509 TTATATTAATGCTTATTAACATATGAAC
1 TTATATTAATGCTTATTAACATATGAAC
40886537 TTA
1 TTA
40886540 CTTTGGTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (28 bp):
TTATATTAATGCTTATTAACATATGAAC
Found at i:40887900 original size:24 final size:24
Alignment explanation
Indices: 40887859--40887910 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
40887849 CACAAACACA
*
40887859 GCTCTTCATGAGCATCCTGATATAG
1 GCTCTTCATGAGCATCCTGACAT-G
* *
40887884 GCTCTT-ATGATCTTCCTGACATG
1 GCTCTTCATGAGCATCCTGACATG
40887907 GCTC
1 GCTC
40887911 GCTTAAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (24 bp):
GCTCTTCATGAGCATCCTGACATG
Found at i:40887980 original size:23 final size:23
Alignment explanation
Indices: 40887953--40888016 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
40887943 CTGTTACATA
40887953 GCTCTTTGTGAGCTTCCTGATAG
1 GCTCTTTGTGAGCTTCCTGATAG
40887976 GCTCTTTGTGAGCTTCCTGATAG
1 GCTCTTTGTGAGCTTCCTGATAG
*
40887999 GCTCTTTGTGAGTTTCCT
1 GCTCTTTGTGAGCTTCCT
40888017 AATTAAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.11, C:0.22, G:0.25, T:0.42
Consensus pattern (23 bp):
GCTCTTTGTGAGCTTCCTGATAG
Found at i:40888931 original size:16 final size:16
Alignment explanation
Indices: 40888910--40888941 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40888900 TTTGTAACGT
40888910 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
*
40888926 CCCAAAAATCCTGAAA
1 CCCAAAAATCCCGAAA
40888942 TCCCGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.34, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:40890314 original size:29 final size:29
Alignment explanation
Indices: 40890271--40890368 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
40890261 ATTTGACTAC
* *
40890271 GCCTAACGGGTCATATAAATGTGATTTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* * *
40890300 GCCTAATGGGCCATATACAGGTCATTTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* *
40890329 GCC-AATGGGCCATATGAATATGA-TTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
*
40890356 GCTTAATGGGCCA
1 GCCTAATGGGCCA
40890369 GATACAGGTA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
27 6 0.11
28 24 0.42
29 27 0.47
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
GCCTAATGGGCCATATAAATGTGATTTGG
Found at i:40894546 original size:43 final size:43
Alignment explanation
Indices: 40894421--40894575 Score: 161
Period size: 43 Copynumber: 3.6 Consensus size: 43
40894411 AGCCATATCT
* * ** *
40894421 CAGATATGGTCTTACATGTCGTCAC-ATATCAATGCCACTGTCC
1 CAGACATGGTCTTACACGTAATCACAATA-CAATGCCAATGTCC
* ** *
40894464 CAGACATGGTCTTACACGAAAT-TGAATAACGATGCCAATGTCC
1 CAGACATGGTCTTACACGTAATCACAAT-ACAATGCCAATGTCC
*
40894507 CAGACATGGTCTTACACGTAATCACAATACAATGTCAATGTCC
1 CAGACATGGTCTTACACGTAATCACAATACAATGCCAATGTCC
* * *
40894550 TAAACATGGTCTTACATGTAATCACA
1 CAGACATGGTCTTACACGTAATCACA
40894576 TCTCGGTAAC
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
43 88 0.96
44 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
CAGACATGGTCTTACACGTAATCACAATACAATGCCAATGTCC
Found at i:40897834 original size:22 final size:22
Alignment explanation
Indices: 40897804--40897848 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
40897794 ATGACATTAG
*
40897804 TAAGTTTATATCTATTGATGCA
1 TAAGGTTATATCTATTGATGCA
40897826 TAAGGTTATATCTATTGATGCA
1 TAAGGTTATATCTATTGATGCA
40897848 T
1 T
40897849 GAGATAATAC
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:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (22 bp):
TAAGGTTATATCTATTGATGCA
Done.