Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 130 of 190
Found at i:38608091 original size:108 final size:106
Alignment explanation
Indices: 38607789--38608108 Score: 381
Period size: 106 Copynumber: 3.0 Consensus size: 106
38607779 ACGACGTGGA
* *
38607789 TTAAAA-TTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGG
1 TTAAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGG
* * *
38607853 CACGTTCTCTCGAATTTCCAAACGCAAAACATTACCTTGTT
66 CACGTTTTCTCGAATTTCCAAACGCAAAACATGACCTTATT
** * * * * *
38607894 TTAAAATTTCGAAAGGATATTTGACTATTTGGCCAAACGAGTAATCGAAACCCAACACGTTAGGG
1 TTAAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGG
* * * * **
38607959 CACGTTTTTTCGAATTTCCGAACGCGAAATATGGTCTTATT
66 CACGTTTTCTCGAATTTCCAAACGCAAAACATGACCTTATT
* * *
38608000 TTGAAAGTTTTAAAAGGGTATTTGGCTATTTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAT
1 TT-AAAATTTTAAAAGGATATTTGGCTA-TTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAG
* * * * *
38608065 GGTACATTTTCTCGATTTTCTAAACGCAAAACATTACCTTATT
64 GGCACGTTTTCTCGAATTTCCAAACGCAAAACATGACCTTATT
38608108 T
1 T
38608109 AGAAAAATTT
Statistics
Matches: 173, Mismatches: 39, Indels: 3
0.80 0.18 0.01
Matches are distributed among these distances:
105 6 0.03
106 83 0.48
107 20 0.12
108 64 0.37
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (106 bp):
TTAAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGG
CACGTTTTCTCGAATTTCCAAACGCAAAACATGACCTTATT
Found at i:38608641 original size:31 final size:30
Alignment explanation
Indices: 38608596--38608653 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
38608586 ATAAAGTTTA
*
38608596 AAATAAAGATATAAATAAGCAAAAAAAAACT
1 AAATAAAGAAATAAATAAG-AAAAAAAAACT
* *
38608627 AAATAAATAAATAAATAAGATAAAAAA
1 AAATAAAGAAATAAATAAGAAAAAAAA
38608654 GGGTTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (30 bp):
AAATAAAGAAATAAATAAGAAAAAAAAACT
Found at i:38613092 original size:27 final size:27
Alignment explanation
Indices: 38613028--38613112 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
38613018 GCTGTGGGCC
*
38613028 CCACCATTGGCGCCTCTCA-ACATGGCA
1 CCACCATTGGCGCCTCTCAGATA-GGCA
* * * *
38613055 CAACTAGTGGCGCCTCTCAGATAGGCT
1 CCACCATTGGCGCCTCTCAGATAGGCA
*
38613082 CCACCATTGGCGCCTCTGAGATAGGCA
1 CCACCATTGGCGCCTCTCAGATAGGCA
38613109 CCAC
1 CCAC
38613113 TACTCTTGTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 45 0.96
28 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.19
Consensus pattern (27 bp):
CCACCATTGGCGCCTCTCAGATAGGCA
Found at i:38614829 original size:31 final size:31
Alignment explanation
Indices: 38614793--38614851 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
38614783 TAATGATTAC
38614793 TGAACTACTCGAAAGTTTTCATTTAAGTCAT
1 TGAACTACTCGAAAGTTTTCATTTAAGTCAT
** *
38614824 TGAACTTGTCGAAAGTTTTTATTTAAGT
1 TGAACTACTCGAAAGTTTTCATTTAAGT
38614852 GGGCTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (31 bp):
TGAACTACTCGAAAGTTTTCATTTAAGTCAT
Found at i:38617151 original size:140 final size:140
Alignment explanation
Indices: 38616899--38617180 Score: 564
Period size: 140 Copynumber: 2.0 Consensus size: 140
38616889 TTTAAAATCT
38616899 GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
1 GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
38616964 AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
66 AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
38617029 AATTTGGGTG
131 AATTTGGGTG
38617039 GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
1 GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
38617104 AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
66 AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
38617169 AATTTGGGTG
131 AATTTGGGTG
38617179 GG
1 GG
38617181 AAATATTTCC
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.35
Consensus pattern (140 bp):
GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
AATTTGGGTG
Found at i:38620111 original size:17 final size:18
Alignment explanation
Indices: 38620089--38620129 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38620079 GTCTTTATAC
*
38620089 TTTACAAATT-TTAAATT
1 TTTACAAATTCTTAAAGT
*
38620106 TTTACAAATTCTTTAAGT
1 TTTACAAATTCTTAAAGT
38620124 TTTACA
1 TTTACA
38620130 TATCATCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTACAAATTCTTAAAGT
Found at i:38625303 original size:3 final size:3
Alignment explanation
Indices: 38625297--38625321 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38625287 CATAATAAAA
38625297 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
38625322 AGAGATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:38632378 original size:31 final size:31
Alignment explanation
Indices: 38632342--38632400 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
38632332 AGATAATTTT
38632342 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
38632373 AAAGAGTTTTATTAGGATTCAATTACTC
1 AAAGAGTTTTATTAGGATTCAATTACTC
38632401 GTGTAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:38632705 original size:3 final size:3
Alignment explanation
Indices: 38632697--38632740 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
38632687 ATCTATCCTT
38632697 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38632741 TAACTAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38642034 original size:10 final size:10
Alignment explanation
Indices: 38642016--38642075 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
38642006 CTATTTAGAT
*
38642016 TTATTAAAAA
1 TTATAAAAAA
*
38642026 TTAGAAAAAA
1 TTATAAAAAA
*
38642036 ATAT-AAAAA
1 TTATAAAAAA
*
38642045 TTGTAAAAAAA
1 TTAT-AAAAAA
38642056 TTATAAAAAA
1 TTATAAAAAA
38642066 TTATAAAAAA
1 TTATAAAAAA
38642076 ATTTTAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 7 0.17
10 26 0.63
11 8 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:38642064 original size:21 final size:21
Alignment explanation
Indices: 38642016--38642105 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
38642006 CTATTTAGAT
* *
38642016 TTATTAAAAATTAGAAAAAAA
1 TTATAAAAAATTATAAAAAAA
*
38642037 -TAT-AAAAATTGTAAAAAAA
1 TTATAAAAAATTATAAAAAAA
38642056 TTATAAAAAATTATAAAAAAA
1 TTATAAAAAATTATAAAAAAA
* **
38642077 TT-TTAAATTTTATAAAAAAAA
1 TTATAAAAAATTAT-AAAAAAA
38642098 TTATAAAA
1 TTATAAAA
38642106 TACATCAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
19 14 0.24
20 14 0.24
21 26 0.45
22 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TTATAAAAAATTATAAAAAAA
Found at i:38642083 original size:11 final size:11
Alignment explanation
Indices: 38642021--38642105 Score: 74
Period size: 11 Copynumber: 8.2 Consensus size: 11
38642011 TAGATTTATT
*
38642021 AAAAATTAGAA
1 AAAAATTATAA
38642032 AAAAA-TAT--
1 AAAAATTATAA
*
38642040 AAAAATTGTAA
1 AAAAATTATAA
38642051 AAAAATTAT-A
1 AAAAATTATAA
38642061 AAAAATTATAA
1 AAAAATTATAA
*
38642072 AAAAATT-T-T
1 AAAAATTATAA
**
38642081 AAATTTTATAAA
1 AAAAATTAT-AA
38642093 AAAAATTATAA
1 AAAAATTATAA
38642104 AA
1 AA
38642106 TACATCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
8 5 0.09
9 7 0.12
10 14 0.24
11 25 0.43
12 7 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:38642321 original size:19 final size:18
Alignment explanation
Indices: 38642297--38642361 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
38642287 GTACGATAAT
38642297 TTTTATAATTTTTTACGAA
1 TTTTATAATTTTTTAC-AA
* *
38642316 TTTTAT-ATTTCTTTATATT
1 TTTTATAATTT-TTTACA-A
38642335 TTTTATAATTTTCTTACAA
1 TTTTATAATTTT-TTACAA
*
38642354 CTTTATAA
1 TTTTATAA
38642362 AACTTATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 5 0.14
19 24 0.65
20 8 0.22
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTTTACAA
Found at i:38645044 original size:89 final size:87
Alignment explanation
Indices: 38644932--38645121 Score: 246
Period size: 89 Copynumber: 2.2 Consensus size: 87
38644922 TTTTTTCTTT
* * *
38644932 AAAAAGCAATTAAG-TCCC-CT-TTTTTT-CACTCAATT-GAGCACTTAAACTTTTAAAATGCAT
1 AAAAAGCAATTAAGCCCCCGCTCTTTTTTCCACTCAATTGGA-CACCTAAACTTTCAAAATGCAT
* *
38644992 CAAAAAGGCCCTCAAACTTCTTCAA
65 CAAAAA-ACCCTCAAAATTCTTC-A
* *
38645017 AAAAAGCAATTAAGCCCCCGCTCTTTTTTCCACTCAATTGGATACCTGAACTTTCAAAATGCATC
1 AAAAAGCAATTAAGCCCCCGCTCTTTTTTCCACTCAATTGGACACCTAAACTTTCAAAATGCATC
*
38645082 AAAAAACCCTCAAAATTTTTCA
66 AAAAAACCCTCAAAATTCTTCA
38645104 AAAAAGCAATTAAGCCCC
1 AAAAAGCAATTAAGCCCC
38645122 TACTCTTATT
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
85 14 0.15
86 3 0.03
87 21 0.23
88 19 0.21
89 33 0.36
90 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.28
Consensus pattern (87 bp):
AAAAAGCAATTAAGCCCCCGCTCTTTTTTCCACTCAATTGGACACCTAAACTTTCAAAATGCATC
AAAAAACCCTCAAAATTCTTCA
Found at i:38645465 original size:44 final size:44
Alignment explanation
Indices: 38645397--38645486 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
38645387 TTATATTTCT
*
38645397 TTATATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATAA
1 TTATATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAA
* **
38645441 TTATATATTT-TATAATTTTTTTACGTTTTTATAAAATTTTACAA
1 TTATAT-TTTGTATAATTTTCTTACGACTTTATAAAATTTTACAA
38645485 TT
1 TT
38645487 TTTTTATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 38 0.93
45 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (44 bp):
TTATATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAA
Found at i:38645472 original size:19 final size:19
Alignment explanation
Indices: 38645448--38645520 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
38645438 TAATTATATA
38645448 TTTTATAATTTTTTTACGT
1 TTTTATAATTTTTTTACGT
** *
38645467 TTTTATAA-AATTTTACAAT
1 TTTTATAATTTTTTTAC-GT
*
38645486 TTTT-TTATATTTTTTACGAT
1 TTTTATAAT-TTTTTTACG-T
38645506 TTTTAT-ATTTTTTTA
1 TTTTATAATTTTTTTA
38645521 TTAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
18 8 0.19
19 20 0.48
20 13 0.31
21 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTTTTACGT
Found at i:38650726 original size:47 final size:46
Alignment explanation
Indices: 38650565--38650729 Score: 177
Period size: 47 Copynumber: 3.5 Consensus size: 46
38650555 GCTTGACCGA
* * * * *
38650565 TGGTTTATCCACAACGTATTTTACTCGGCATTCACCTGTTCGACTAG
1 TGGTTTATCCACAACATATTTTAGTC-ACAATCACCTGCTCGACTAG
* * * *
38650612 TGGTTTGTCCACAACATATCTTAATCGACAATCATCTGCTCGACTAG
1 TGGTTTATCCACAACATATTTTAGTC-ACAATCACCTGCTCGACTAG
* * *
38650659 TGGTTTATCCACAACATATTTTAGTCATCAGTCACCTGCTCTACCAG
1 TGGTTTATCCACAACATATTTTAGTCA-CAATCACCTGCTCGACTAG
* *
38650706 TGGTATATCCACAACGTATTTTAG
1 TGGTTTATCCACAACATATTTTAG
38650730 CAGCTTTTAT
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 1 0.01
47 99 0.99
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (46 bp):
TGGTTTATCCACAACATATTTTAGTCACAATCACCTGCTCGACTAG
Found at i:38652415 original size:44 final size:44
Alignment explanation
Indices: 38652352--38652438 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
38652342 GTTGAAATAA
* *
38652352 AATAGAAGTTGCAAAAATTATACATTAAAAAATAATTATAATTT
1 AATAGAAGTTGCAAAAATTACACATTAAAAAATAATTAAAATTT
** *
38652396 AATAGAAGTTGTGATAATTACACATTAAAAAATAATTAAAATT
1 AATAGAAGTTGCAAAAATTACACATTAAAAAATAATTAAAATT
38652439 ATTAATTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (44 bp):
AATAGAAGTTGCAAAAATTACACATTAAAAAATAATTAAAATTT
Found at i:38653967 original size:24 final size:24
Alignment explanation
Indices: 38653925--38653976 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38653915 AATCAAAATC
** *
38653925 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
38653949 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
38653973 AAAT
1 AAAT
38653977 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:38658317 original size:23 final size:24
Alignment explanation
Indices: 38658269--38658319 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38658259 AGTCAAAGTC
* *
38658269 AAATATATTATGTTAATAAATGCT
1 AAATATATTATCTTAATAAATACT
38658293 AAATATATTATCTT-ATAAATACT
1 AAATATATTATCTTAATAAATACT
38658316 AAAT
1 AAAT
38658320 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATATATTATCTTAATAAATACT
Found at i:38659193 original size:2 final size:2
Alignment explanation
Indices: 38659186--38659211 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38659176 CATACCATAT
38659186 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
38659212 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:38659216 original size:2 final size:2
Alignment explanation
Indices: 38659211--38659235 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38659201 ACACACACAC
38659211 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38659236 CACCACCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38661371 original size:31 final size:31
Alignment explanation
Indices: 38661336--38661398 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
38661326 ATTTAACCAC
38661336 TAAGTTTTCATTTTACGCGATTAAGCCCTTT
1 TAAGTTTTCATTTTACGCGATTAAGCCCTTT
*
38661367 TAAGTTTTCATTTTACTCGATTAAGCCCTTT
1 TAAGTTTTCATTTTACGCGATTAAGCCCTTT
38661398 T
1 T
38661399 CTCAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (31 bp):
TAAGTTTTCATTTTACGCGATTAAGCCCTTT
Found at i:38661460 original size:14 final size:15
Alignment explanation
Indices: 38661441--38661469 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38661431 TCACGAAACT
38661441 TTCACACAT-ATAAA
1 TTCACACATAATAAA
38661455 TTCACACATAATAAA
1 TTCACACATAATAAA
38661470 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:38666200 original size:10 final size:10
Alignment explanation
Indices: 38666185--38666213 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
38666175 AAATTACTAT
38666185 GGGCGGGCCG
1 GGGCGGGCCG
38666195 GGGCGGGCCG
1 GGGCGGGCCG
38666205 GGGCGGGCC
1 GGGCGGGCC
38666214 TGGATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.69, T:0.00
Consensus pattern (10 bp):
GGGCGGGCCG
Found at i:38667715 original size:31 final size:31
Alignment explanation
Indices: 38667671--38667734 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
38667661 ATCACTCAAC
*
38667671 TTCAAAAGGTTTTAAAATAA-TCATTGAACTA
1 TTCAAAAAGTTTT-AAATAAGTCATTGAACTA
* **
38667702 TTCAAAAATTTTTATTTAAGTCATTGAACTA
1 TTCAAAAAGTTTTAAATAAGTCATTGAACTA
38667733 TT
1 TT
38667735 ACATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (31 bp):
TTCAAAAAGTTTTAAATAAGTCATTGAACTA
Found at i:38667788 original size:2 final size:2
Alignment explanation
Indices: 38667781--38667812 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
38667771 ACTATTTATC
38667781 AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38667813 TGGCCATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38667796 original size:12 final size:12
Alignment explanation
Indices: 38667781--38667812 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
38667771 ACTATTTATC
38667781 ATATATATATAT
1 ATATATATATAT
38667793 ATATATA-ATAT
1 ATATATATATAT
38667804 A-ATATATAT
1 ATATATATAT
38667813 TGGCCATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 7 0.37
12 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATATAT
Found at i:38669152 original size:24 final size:24
Alignment explanation
Indices: 38669098--38669144 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
38669088 ACAAATATGC
*
38669098 AAATATATATATATAAAATGTTTA
1 AAATATATATATATAAAATGTATA
38669122 AAATATATATATAT-AAATGTATA
1 AAATATATATATATAAAATGTATA
38669145 TATTTATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATATATATAAAATGTATA
Found at i:38669224 original size:26 final size:27
Alignment explanation
Indices: 38669195--38669248 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
38669185 ATACATATAT
* *
38669195 TATAGGAAACATATGTATA-TATAAAA
1 TATAGAAAACATATATATATTATAAAA
**
38669221 TATAGAAAATGTATATATATTATAAAA
1 TATAGAAAACATATATATATTATAAAA
38669248 T
1 T
38669249 GTATATGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (27 bp):
TATAGAAAACATATATATATTATAAAA
Found at i:38669401 original size:3 final size:3
Alignment explanation
Indices: 38669393--38669460 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
38669383 TACATATAGA
38669393 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38669441 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
38669461 ATAGTGATAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38672373 original size:14 final size:14
Alignment explanation
Indices: 38672319--38672375 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
38672309 AATGGTCAAA
38672319 TTATAGTTTTAATCCTT
1 TTATA-TTTTAAT-C-T
38672336 TTATATTTTCAA-CT
1 TTATATTTT-AATCT
* *
38672350 TTAAAATTTAATCT
1 TTATATTTTAATCT
38672364 TTATATTTTAAT
1 TTATATTTTAAT
38672376 TTTTGACATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 20 0.59
15 1 0.03
16 4 0.12
17 7 0.21
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.58
Consensus pattern (14 bp):
TTATATTTTAATCT
Found at i:38675262 original size:20 final size:20
Alignment explanation
Indices: 38675226--38675263 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38675216 CTTAATTAGT
*
38675226 TTATAAAATTTAAAAAAGCA
1 TTATAAAATGTAAAAAAGCA
38675246 TTAT-AAATGTAACAAAAG
1 TTATAAAATGTAA-AAAAG
38675264 GAAATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (20 bp):
TTATAAAATGTAAAAAAGCA
Found at i:38677236 original size:167 final size:164
Alignment explanation
Indices: 38676498--38677309 Score: 773
Period size: 167 Copynumber: 4.9 Consensus size: 164
38676488 TTCGAAATTG
* * * * * *
38676498 TTGTGTCAAATCTTTTGAATTTTGAATTCTTCGCGTAGTTTAATCTGATCTAAATCTCGGAAGCG
1 TTGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTAAATCTCAGAAGCG
* * * *
38676563 TCGTGAGTTCGTTCGTTTGCTCAGATTTGTATTTCTCAAATTGAATTTATGTTTGTTATAGATTG
65 -C-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATTG
**
38676628 GATTTAGATTTCTCCTTTAAGTGTTGATCTGCTCAGAAAT
128 GATTTAGA-TTCT--TTTTTGTGTTGATCTGCTCAGAAAT
* * * * *
38676668 TGATGTGTCAAATCTTTTGAATTCTGAATTATTCGCGTAGTGGT-ATCTGATCTGAATCTCTG-A
1 T--TGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGT-GTCATCTGATCTAAATCTCAGAA
* * * *
38676731 TC-TTGAGTTCGTTGGTTTG-T---A-----A-TTCTCGAACTGAATTTATGTTTGTTACAGATT
62 GCGCTGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATT
* *
38676785 GGATTTAGATTATTTTTTACATGTT-ACTCTGCTCAGAAATT
127 GGATTTAGATTCTTTTTT--GTGTTGA-TCTGCTCAGAAA-T
* *
38676826 GTTGTGTCAAATCATTTTGAA---T---TATTCGA-GTAGAGTCATCTGATCTAAATCTCGGAA-
1 -TTGTGTCAAAT-ATTTTGAATTTTGAATATTC-ACGTAGTGTCATCTGATCTAAATCTCAGAAG
*
38676883 -G-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTTTCGAATTGAATTTATGTTTGTTACAGATTG
63 CGCTGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATTG
38676946 GATTTAGATTATCTTCTTTTG-GTTGATCTGCTCAGAAAT
128 GATTTAGA-T-TCTT-TTTTGTGTTGATCTGCTCAGAAAT
* * *
38676985 TGTCGTGTCAAATCTTTTGAATTTTGAATTATTCGCGTAGTGTCATCTGATCTAATTCTCAGAAG
1 T-T-GTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTAAATCTCAGAAG
* * * * * *
38677050 CGTCGTGAGTTCCTTGGTTTGCTCGGATTTGTATTTCTCTATTTGAATTTATGTTTGTTACGGAT
63 CG-C-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGAT
*
38677115 TGGATTTAGCTTCTTTTTATGTGTTGATCTGCTCAGAAA-
126 TGGATTTAGATTCTTTTT-TGTGTTGATCTGCTCAGAAAT
38677154 TTGTGTCAAATATTTTGAATTTTGAACTATTCACGTAGTGTCATCTGATC-AGAATCTCAGAAGC
1 TTGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTA-AATCTCAGAAGC
* * *
38677218 GACTTGGGCTCGTTGGTTTGCTCAGATTTGTATATCTCGAAATGAATTTATGTTTGTTACAGATT
64 G-C-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATT
* **
38677283 GGACTT-GGGT-TTTTTTGTGTTGATCTG
127 GGATTTAGATTCTTTTTTGTGTTGATCTG
38677310 GTCAATTCTG
Statistics
Matches: 541, Mismatches: 56, Indels: 96
0.78 0.08 0.14
Matches are distributed among these distances:
150 17 0.03
151 26 0.05
152 1 0.00
154 1 0.00
155 4 0.01
156 1 0.00
157 29 0.05
158 47 0.09
159 12 0.02
160 63 0.12
161 2 0.00
162 4 0.01
163 4 0.01
164 13 0.02
165 5 0.01
166 33 0.06
167 116 0.21
168 20 0.04
169 7 0.01
170 19 0.04
171 64 0.12
172 52 0.10
173 1 0.00
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (164 bp):
TTGTGTCAAATATTTTGAATTTTGAATATTCACGTAGTGTCATCTGATCTAAATCTCAGAAGCGC
TGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATTGGAT
TTAGATTCTTTTTTGTGTTGATCTGCTCAGAAAT
Found at i:38679628 original size:18 final size:18
Alignment explanation
Indices: 38679596--38679650 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
38679586 ATTTAATATT
**
38679596 ATAATTTTATTTTTTATA
1 ATAATTTTAAATTTTATA
38679614 ATAATTTTAAATTTTA-A
1 ATAATTTTAAATTTTATA
38679631 ATAATATTTTAATATTTTAT
1 AT-A-ATTTTAA-ATTTTAT
38679651 TAAAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 3 0.10
18 15 0.48
19 7 0.23
20 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAATTTTAAATTTTATA
Found at i:38679634 original size:20 final size:20
Alignment explanation
Indices: 38679611--38679666 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
38679601 TTTATTTTTT
38679611 ATAATAATTTTAA-ATTTTAA
1 ATAAT-ATTTTAATATTTTAA
38679631 ATAATATTTTAATATTTTATTA
1 ATAATATTTTAATATTTTA--A
*
38679653 AAAATATTTTAATA
1 ATAATATTTTAATA
38679667 ATAAATATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.22
20 11 0.34
22 14 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATATTTTAATATTTTAA
Found at i:38679660 original size:14 final size:15
Alignment explanation
Indices: 38679641--38679674 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
38679631 ATAATATTTT
*
38679641 AATATTTTATTAA-A
1 AATATTTTAATAATA
38679655 AATATTTTAATAATA
1 AATATTTTAATAATA
38679670 AATAT
1 AATAT
38679675 GTAGCTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:38680757 original size:3 final size:3
Alignment explanation
Indices: 38680749--38680825 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
38680739 TTGTGGAGTT
38680749 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38680797 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38680826 TAAATTTACT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38684800 original size:21 final size:21
Alignment explanation
Indices: 38684776--38684818 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
38684766 ACCTTTTCTG
*
38684776 AAGTTAAAAGTCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
*
38684797 AAGTTAAAAGGCAAATCCATT
1 AAGTTAAAAGGCAAAACCATT
38684818 A
1 A
38684819 TATTGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACCATT
Found at i:38685148 original size:16 final size:17
Alignment explanation
Indices: 38685127--38685165 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
38685117 AGTTGAAAAA
38685127 AGATAAAAAAAT-TATT
1 AGATAAAAAAATATATT
*
38685143 AGATAAAATAATATATT
1 AGATAAAAAAATATATT
38685160 A-ATAAA
1 AGATAAA
38685166 GTTGTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AGATAAAAAAATATATT
Found at i:38707459 original size:50 final size:50
Alignment explanation
Indices: 38707397--38707978 Score: 497
Period size: 50 Copynumber: 11.6 Consensus size: 50
38707387 CGTAACTTTT
* * *
38707397 GGAAGTAAGATTCG-TCATTGTGGCTTTAATCTTTTTAACTACAATGTCGG
1 GGAAGCAAGATTCGCT-GTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * ** ** * *
38707447 GGAAGCATGATTCACTGTTGTGGCTTTAATCTATTCCACTGCACCGCCTG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* *
38707497 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * ** ** * *
38707547 GGAAGCATGATTCGCTGTTGTGGCCTTAATCTATTCCACTGCACCGCCTG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * * *
38707597 TGAGGCAAGATTCGCCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGA
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * ** ** * *
38707647 GGAAGCAAGATTTGCCGTTGTGGCTTTAATCTCTTCCACTGCACCGCCTG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * *
38707697 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGTAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * * ** * * *
38707747 GGAAGCATGATTCGCTGTTATGGTTTTAATCTGTTCCACTGCATTGCCTG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * *
38707797 GGAGGCAAGATTCACTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * * ** * *
38707847 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGC-ATCGCCTGA
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAAT-GTC-GG
* * *
38707898 GG-AGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* *
38707947 GGAAGCAAGATTC-ATCGATGTGGCTTTAATCT
1 GGAAGCAAGATTCGCT-GTTGTGGCTTTAATCT
38707979 GTTCGACTGC
Statistics
Matches: 402, Mismatches: 124, Indels: 12
0.75 0.23 0.02
Matches are distributed among these distances:
49 6 0.01
50 390 0.97
51 6 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (50 bp):
GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
Found at i:38707570 original size:100 final size:100
Alignment explanation
Indices: 38707397--38708014 Score: 819
Period size: 100 Copynumber: 6.2 Consensus size: 100
38707387 CGTAACTTTT
* * * * *
38707397 GGAAGTAAGATTCG-TCATTGTGGCTTTAATCTTTTTAACTACAATGTCGGGGAAGCATGATTCA
1 GGAAGTAAGATTCGCT-GTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCG
*
38707461 CTGTTGTGGCTTTAATCTATTCCACTGCACCGCCTG
65 CTGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
*
38707497 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCGC
1 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
* *
38707562 TGTTGTGGCCTTAATCTATTCCACTGCACCGCCTG
66 TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
* * * * * * * *
38707597 TGAGGCAAGATTCGCCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGAGGAAGCAAGATTTGC
1 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
* *
38707662 CGTTGTGGCTTTAATCTCTTCCACTGCACCGCCTG
66 TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
* * *
38707697 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGTAATGTCGGGGAAGCATGATTCGC
1 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
* * **
38707762 TGTTATGGTTTTAATCTGTTCCACTGCATTGCCTG
66 TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
* * * * *
38707797 GGAGGCAAGATTCACTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCGGGGAAGCAAGATTCAC
1 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
* * *
38707862 CGATGTGGCTTTAATCTGTTCCACTGCATCGCCTG
66 TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
*
38707897 AGG-AGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTC-
1 -GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCG
* * * * *
38707960 ATCGATGTGGCTTTAATCTGTTCGACTGCAGCGCCAG
65 CT-GTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
*
38707997 GGAAATAAGATTCGCTGT
1 GGAAGTAAGATTCGCTGT
38708015 CTTCACCGAT
Statistics
Matches: 458, Mismatches: 56, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
99 2 0.00
100 453 0.99
101 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (100 bp):
GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
Found at i:38712115 original size:47 final size:47
Alignment explanation
Indices: 38712054--38712143 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
38712044 TCATTTTTCA
* * *
38712054 TTTTTTGGATTCAAAGTGCCCTTTGAGGATTTTCACTTTGATCATTT
1 TTTTTTGGACTCAAAGCGCCCTTTGAGGATTTTCACCTTGATCATTT
* *
38712101 TTTTTTGGACTCAAAGCGCCCTTTGTGGGTTTTCACCTTGATC
1 TTTTTTGGACTCAAAGCGCCCTTTGAGGATTTTCACCTTGATC
38712144 CTTTCTCTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.46
Consensus pattern (47 bp):
TTTTTTGGACTCAAAGCGCCCTTTGAGGATTTTCACCTTGATCATTT
Found at i:38722808 original size:14 final size:13
Alignment explanation
Indices: 38722785--38722828 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
38722775 CCTGCGGTAG
*
38722785 GGTTTTGGGTTATT
1 GGTTTAGGGTT-TT
*
38722799 GGTTTAGGGTTTAG
1 GGTTTAGGGTTT-T
38722813 GGTTTAGGGTTTT
1 GGTTTAGGGTTTT
38722826 GGT
1 GGT
38722829 ATTTTTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (13 bp):
GGTTTAGGGTTTT
Found at i:38722809 original size:7 final size:7
Alignment explanation
Indices: 38722799--38722824 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38722789 TTGGGTTATT
38722799 GGTTTAG
1 GGTTTAG
38722806 GGTTTAG
1 GGTTTAG
38722813 GGTTTAG
1 GGTTTAG
38722820 GGTTT
1 GGTTT
38722825 TGGTATTTTT
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:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:38722823 original size:21 final size:21
Alignment explanation
Indices: 38722782--38722824 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
38722772 TCTCCTGCGG
* *
38722782 TAGGGTTTTGGGTTATTGGTT
1 TAGGGTTTAGGGTTATGGGTT
38722803 TAGGGTTTAGGGTT-TAGGGTT
1 TAGGGTTTAGGGTTAT-GGGTT
38722824 T
1 T
38722825 TGGTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.49
Consensus pattern (21 bp):
TAGGGTTTAGGGTTATGGGTT
Found at i:38723092 original size:46 final size:46
Alignment explanation
Indices: 38723042--38723210 Score: 132
Period size: 46 Copynumber: 3.6 Consensus size: 46
38723032 GTTTTTAAGG
*
38723042 AAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
1 AAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
* * ** * * *
38723088 AAAAAAATTGAAAATCATATTAGGATTTAAAGTTA--AGAGT-TTTTAATA
1 --AAAAATT--AAAT-AAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
* * *
38723136 AAAAATTAAATAAATTAGAGTTCAGGGTTACTTGAGTAAATTAATT
1 AAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
*
38723182 ATAAATTTATAATAAATTA--GTTTAGGGTT
1 A-AAAATTA-AATAAATTAGGGTTTAGGGTT
38723211 TAGTGTTTAG
Statistics
Matches: 93, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
43 13 0.14
44 4 0.04
45 4 0.04
46 22 0.24
47 6 0.06
48 21 0.23
49 4 0.04
50 4 0.04
51 15 0.16
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (46 bp):
AAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
Found at i:38723133 original size:94 final size:92
Alignment explanation
Indices: 38722947--38723255 Score: 344
Period size: 86 Copynumber: 3.3 Consensus size: 92
38722937 GTGTATATTA
*
38722947 TTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTTA
1 TTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTTA
*
38723012 AAAATCAAATTAGGA--T-AAG---GG
66 AAAATCATATTAGGATTTAAAGTTAGG
* * *
38723033 TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTG
1 TTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTTA
38723098 AAAATCATATTAGGATTTAAAGTTAAGAG
66 AAAATCATATTAGGATTTAAAGTT-AG-G
* * * * * * *
38723127 TTTTTAATAAAAAATTAAATAAATTAGAGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTAT
1 TTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATT-T
* * **
38723192 AATAAATTAGT-TTAGGGTTTAGTGTTTAGGG
65 AA-AAATCA-TATTAGGATTTAAAG-TTA-GG
*
38723223 TTTTTAAGTAAAAACTCAAATAAATTAGGGTTT
1 TTTTTAAG-AAAAAATCAAATAAATTAGGGTTT
38723256 GGGATTTACG
Statistics
Matches: 185, Mismatches: 24, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
86 75 0.41
88 1 0.01
89 3 0.02
93 1 0.01
94 55 0.30
95 2 0.01
96 24 0.13
97 24 0.13
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (92 bp):
TTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTTA
AAAATCATATTAGGATTTAAAGTTAGG
Found at i:38723573 original size:125 final size:126
Alignment explanation
Indices: 38723298--38723720 Score: 722
Period size: 126 Copynumber: 3.4 Consensus size: 126
38723288 TAATTTAAAG
* * * *
38723298 AAGCTCGCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAGAAAATAATTTCAAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
*
38723363 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* *
38723424 AAGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTACTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
*
38723489 CTGAGCAAACAGTGTC-AAAATGCTTTAAGCAGGATGTTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
**
38723549 AAGCTTTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
* *
38723614 TTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAG
66 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
*
38723675 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTACCTCCTGAAAAAA
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAA
38723721 GCTCCTACGT
Statistics
Matches: 278, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 118 0.42
126 160 0.58
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:38726051 original size:41 final size:41
Alignment explanation
Indices: 38726001--38726088 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
38725991 GGCTTAGCAC
* * *
38726001 CTAGAAGGCTTATTGCCAGTGAAACAATTCAGACTTTATGT
1 CTAGCAGGCTTACTGCCAGTGAAACAATTCAGACTATATGT
* *
38726042 CTAGCAGGCTTACTGCCGGTGAAACATTTCAGACTATATGT
1 CTAGCAGGCTTACTGCCAGTGAAACAATTCAGACTATATGT
38726083 CTAGCA
1 CTAGCA
38726089 AGCTAAGTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (41 bp):
CTAGCAGGCTTACTGCCAGTGAAACAATTCAGACTATATGT
Found at i:38726100 original size:41 final size:41
Alignment explanation
Indices: 38726014--38726100 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
38726004 GAAGGCTTAT
* * * *
38726014 TGCCAGTGAAACAATTCAGACTTTATGTCTAGCAGGCTTAC
1 TGCCGGTGAAACAATTCAGACTATATGTCTAGCAAGCTAAC
* *
38726055 TGCCGGTGAAACATTTCAGACTATATGTCTAGCAAGCTAAG
1 TGCCGGTGAAACAATTCAGACTATATGTCTAGCAAGCTAAC
38726096 TGCCG
1 TGCCG
38726101 ATGTATTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (41 bp):
TGCCGGTGAAACAATTCAGACTATATGTCTAGCAAGCTAAC
Found at i:38728508 original size:70 final size:70
Alignment explanation
Indices: 38728295--38728625 Score: 281
Period size: 72 Copynumber: 4.6 Consensus size: 70
38728285 ACCGATGGTA
* * * * * * * * *
38728295 TGAGATCCGACATATGTTGCGAATTCTCTCAAGCTTGTGAGAGCAGAATGGAATCTTTCTTT-GC
1 TGAGATCTGGCATATGTTGC--ATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATC
38728359 TGATGGCT
64 TG-TGGCT
* * * * *
38728367 TGAGATC-GGACATATGTTACGAATTCTTTAAAGCTTGTGTGAGCAGCATCGAACCATTCTTTAT
1 TGAGATCTGG-CATATGTT--GCATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTAT
38728431 -TGATGGCT
63 CTG-TGGCT
* * * * *
38728439 TGAGATCTGGCATATGTTGCATTCTCTGAAGTTTGTGTAAGCATCGTGGAATCATTCTTCATCTG
1 TGAGATCTGGCATATGTTGCATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATCTG
38728504 TGGCT
66 TGGCT
* **
38728509 TGAGATTTAACATATGTTGCGGATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATC
1 TGAGATCTGGCATATGTTGC--ATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATC
*
38728574 GGTGGCT
64 TGTGGCT
*** * * *
38728581 TGAGATCCAACACATGTTATGGATTCTCTGAAGCTTGTGTGAGCA
1 TGAGATCTGGCATATG-T-TGCATTCTCTGAAGTTTGTGTGAGCA
38728626 ACACCCAATA
Statistics
Matches: 215, Mismatches: 34, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
70 56 0.26
71 3 0.01
72 150 0.70
73 3 0.01
74 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (70 bp):
TGAGATCTGGCATATGTTGCATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATCTG
TGGCT
Found at i:38728598 original size:142 final size:144
Alignment explanation
Indices: 38728362--38728625 Score: 352
Period size: 142 Copynumber: 1.8 Consensus size: 144
38728352 TCTTTGCTGA
* *
38728362 TGGCTTGAGATCGGACATATGTTACGAATTCTTTAAAGCTTGTGTGAGCAGCATCGAACCATTCT
1 TGGCTTGAGATCGAACATATGTTACGAATTCTCTAAAGCTTGTGTGAGCAGCATCGAACCATTCT
* *** * *
38728427 TTATTGATGGCTTGAGATCTGGCATATG-T-TGCATTCTCTGAAGTTTGTGTAAGCATCGTGGAA
66 TTATCGATGGCTTGAGATCCAACACATGTTATGCATTCTCTGAAGCTTGTGTAAGCATCGTGGAA
38728490 TCATTCTTCATCTG
131 TCATTCTTCATCTG
** * * * * *
38728504 TGGCTTGAGATTTAACATATGTTGCGGATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCT
1 TGGCTTGAGATCGAACATATGTTACGAATTCTCTAAAGCTTGTGTGAGCAGCATCGAACCATTCT
* * *
38728569 TTATCGGTGGCTTGAGATCCAACACATGTTATGGATTCTCTGAAGCTTGTGTGAGCA
66 TTATCGATGGCTTGAGATCCAACACATGTTATGCATTCTCTGAAGCTTGTGTAAGCA
38728626 ACACCCAATA
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
142 78 0.76
143 1 0.01
144 23 0.23
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (144 bp):
TGGCTTGAGATCGAACATATGTTACGAATTCTCTAAAGCTTGTGTGAGCAGCATCGAACCATTCT
TTATCGATGGCTTGAGATCCAACACATGTTATGCATTCTCTGAAGCTTGTGTAAGCATCGTGGAA
TCATTCTTCATCTG
Found at i:38731551 original size:27 final size:27
Alignment explanation
Indices: 38731490--38731544 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
38731480 AATTGATAAA
38731490 TATAGAACATGGCCACGGGTTGTTTGT
1 TATAGAACATGGCCACGGGTTGTTTGT
38731517 TATAGAACATGGCCACGGGTTGTTTGT
1 TATAGAACATGGCCACGGGTTGTTTGT
38731544 T
1 T
38731545 CTCGAACGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.35
Consensus pattern (27 bp):
TATAGAACATGGCCACGGGTTGTTTGT
Found at i:38735329 original size:2 final size:2
Alignment explanation
Indices: 38735322--38735347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38735312 TTCAATAAAC
38735322 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38735348 GGTGGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38738393 original size:17 final size:16
Alignment explanation
Indices: 38738371--38738403 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
38738361 ACATGAATAC
38738371 TATAAAAATTTATAAAT
1 TATAAAAATTT-TAAAT
38738388 TATAAAAATTTTAAAT
1 TATAAAAATTTTAAAT
38738404 AGATATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAAAATTTTAAAT
Found at i:38739196 original size:20 final size:20
Alignment explanation
Indices: 38739146--38739196 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
38739136 TCAAATAAAA
*
38739146 AACCCTAAACCTTAAACATAG
1 AACCCTAAA-CTCAAACATAG
* *
38739167 AATCCC-AAACTCCAACATGG
1 AA-CCCTAAACTCAAACATAG
38739187 AACCCTAAAC
1 AACCCTAAAC
38739197 CCTAATCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 5 0.20
22 3 0.12
ACGTcount: A:0.45, C:0.33, G:0.06, T:0.16
Consensus pattern (20 bp):
AACCCTAAACTCAAACATAG
Found at i:38745498 original size:30 final size:30
Alignment explanation
Indices: 38745462--38745524 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
38745452 ACTTATTTTA
38745462 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
38745492 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
38745522 TTG
1 TTG
38745525 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:38750418 original size:10 final size:10
Alignment explanation
Indices: 38750403--38750427 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38750393 AATTTAATTA
38750403 TTAAAAAAAT
1 TTAAAAAAAT
38750413 TTAAAAAAAT
1 TTAAAAAAAT
38750423 TTAAA
1 TTAAA
38750428 TATTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:38750674 original size:24 final size:24
Alignment explanation
Indices: 38750646--38750716 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
38750636 AAGGGTTTAC
*
38750646 AAGAAGATGAAAGGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
* *
38750670 AAGAAGATGAAATGTGGAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
* *
38750694 AGGGAGATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTGAAAGGTT
38750717 GAATATCCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTA
Found at i:38755901 original size:4 final size:4
Alignment explanation
Indices: 38755892--38755916 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
38755882 GAACGAAACT
38755892 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
38755917 AAAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:38765524 original size:3 final size:3
Alignment explanation
Indices: 38765516--38765543 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38765506 TATGTCCATC
38765516 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
38765544 CAACTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:38775110 original size:29 final size:30
Alignment explanation
Indices: 38775051--38775108 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38775041 TCCAAGCCTT
*
38775051 GGGGAAAAAATGTAATTATGTAAAAGTTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTTA
* * *
38775081 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAAATGTAATTATGAAAAAGTT
38775109 AGAGTTGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAATGTAATTATGAAAAAGTTTA
Found at i:38775340 original size:13 final size:13
Alignment explanation
Indices: 38775322--38775346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38775312 TCCAGCAACT
38775322 ATGAATTTATTTC
1 ATGAATTTATTTC
38775335 ATGAATTTATTT
1 ATGAATTTATTT
38775347 GATGTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:38775558 original size:50 final size:50
Alignment explanation
Indices: 38775446--38775694 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
38775436 ATTTGGGTAA
*
38775446 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC---A-A-CACG
* * *
38775502 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACACG
* * * *
38775552 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACACG
* * * * *
38775602 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACACG
** *
38775652 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
38775695 TGTTATTATC
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 95 0.55
51 35 0.20
52 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACACG
Found at i:38775635 original size:100 final size:103
Alignment explanation
Indices: 38775446--38775695 Score: 335
Period size: 100 Copynumber: 2.4 Consensus size: 103
38775436 ATTTGGGTAA
*
38775446 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCACGAGAGGTCTC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGAT--CGAGAGGTCCC
* * * *
38775511 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGACG
63 ATATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * *
38775552 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-CC-GAGAT-GAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCGAGAGGTCCCATA
* *
38775614 TAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
38775652 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
38775696 GTTATTATCA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
100 45 0.35
101 36 0.28
103 5 0.04
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCGAGAGGTCCCATA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:38789327 original size:12 final size:12
Alignment explanation
Indices: 38789310--38789335 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38789300 CTCGATTTTT
38789310 TTTAAAAATTTA
1 TTTAAAAATTTA
38789322 TTTAAAAATTTA
1 TTTAAAAATTTA
38789334 TT
1 TT
38789336 ATTCCATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTAAAAATTTA
Found at i:38789544 original size:15 final size:16
Alignment explanation
Indices: 38789521--38789553 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38789511 TACATTATTT
38789521 TATTTTTTTATGTAAA
1 TATTTTTTTATGTAAA
38789537 TATTTTTTTATGTAAA
1 TATTTTTTTATGTAAA
38789553 T
1 T
38789554 TCAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATTTTTTTATGTAAA
Found at i:38801128 original size:18 final size:19
Alignment explanation
Indices: 38801107--38801148 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
38801097 TAAAAATTCT
*
38801107 AAAATT-TATAATTTTTAA
1 AAAATTATAAAATTTTTAA
38801125 AAAATTATAAAATTTTTAA
1 AAAATTATAAAATTTTTAA
38801144 AAAAT
1 AAAAT
38801149 CTAACATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTATAAAATTTTTAA
Found at i:38801574 original size:2 final size:2
Alignment explanation
Indices: 38801567--38801602 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
38801557 TGATTTTAGA
38801567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38801603 AAAGAAGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38801900 original size:2 final size:2
Alignment explanation
Indices: 38801893--38801917 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38801883 GAGATAAAAT
38801893 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38801918 TTAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38814894 original size:21 final size:23
Alignment explanation
Indices: 38814859--38814902 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
38814849 TGGTATTAAA
38814859 TTTAAATAGATTTAATTAAAAAT
1 TTTAAATAGATTTAATTAAAAAT
*
38814882 TTTAAA-A-ATTTAATTAGAAAT
1 TTTAAATAGATTTAATTAAAAAT
38814903 AAATTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTAAATAGATTTAATTAAAAAT
Found at i:38820115 original size:5 final size:5
Alignment explanation
Indices: 38820105--38820140 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
38820095 GGATGTATGG
38820105 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT A
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT A
38820141 ATGTATGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.58
Consensus pattern (5 bp):
ATGTT
Found at i:38822134 original size:7 final size:7
Alignment explanation
Indices: 38822122--38822156 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
38822112 AAATGGTTGC
38822122 TTGAAAG
1 TTGAAAG
38822129 TTGAAAG
1 TTGAAAG
38822136 TTGAAAG
1 TTGAAAG
38822143 TTGAAAG
1 TTGAAAG
38822150 TTGAAAG
1 TTGAAAG
38822157 GTTTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
TTGAAAG
Found at i:38822239 original size:20 final size:20
Alignment explanation
Indices: 38822216--38822253 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38822206 TTTATCTTTA
38822216 TTATTTTTA-ATATAAAATAC
1 TTATTTTTACATA-AAAATAC
38822236 TTATTTTTACATAAAAAT
1 TTATTTTTACATAAAAAT
38822254 TAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTTTTACATAAAAATAC
Found at i:38824950 original size:207 final size:210
Alignment explanation
Indices: 38824703--38825110 Score: 660
Period size: 211 Copynumber: 2.0 Consensus size: 210
38824693 CCGCTAATCC
38824703 AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTA-TTT-TTAAAT-GTTTTTTCACAT
1 AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTCTTAAATCGTTTTTTCACAT
* * * *
38824765 ATTATATACAACCACTTCTTAAGAAATTTTATGGAATAAATAGGGATAAAATAAGTATGTAAACT
66 ATTATATAAAACCACCTCCTAAGAAATTTTATGGAATAAATAGGGATAAAATAAGTATATAAACT
* * * *
38824830 TAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAATATTTTTTATTAGAATTATAATTGT
131 TAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAAATTAT
38824895 TTTTATATAATATCA
196 TTTTATATAATATCA
* *
38824910 AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTTCTTTAATCTTTTTTTCACA
1 AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTA-TTTTCTTAAATCGTTTTTTCACA
* * * *
38824975 TGTTATATAAAACCACCTCCTAGGAAATTTTATGGAATAAATAGGGGTAAAATAGGTATATAAAC
65 TATTATATAAAACCACCTCCTAAGAAATTTTATGGAATAAATAGGGATAAAATAAGTATATAAAC
38825040 TTAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAAATTA
130 TTAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAAATTA
38825105 TTTTTA
195 TTTTTA
38825111 AATTTATTAT
Statistics
Matches: 183, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
207 41 0.22
209 3 0.02
210 5 0.03
211 134 0.73
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (210 bp):
AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTCTTAAATCGTTTTTTCACAT
ATTATATAAAACCACCTCCTAAGAAATTTTATGGAATAAATAGGGATAAAATAAGTATATAAACT
TAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAAATTAT
TTTTATATAATATCA
Found at i:38825169 original size:2 final size:2
Alignment explanation
Indices: 38825162--38825187 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38825152 CTTAATATCA
38825162 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38825188 TAGAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38827091 original size:57 final size:56
Alignment explanation
Indices: 38827004--38827114 Score: 177
Period size: 57 Copynumber: 2.0 Consensus size: 56
38826994 AGTATAAATC
* * * *
38827004 AAAATTGGTCCTCCGAAATCTATACGTCGGTGGATTAATTGCTGAATTTTGCCTCT
1 AAAATTGGTCCTCCAAAATCTATACGTCGGTGGATTAATTCCTCAACTTTGCCTCT
38827060 AAAATTGGTCCTCCAAAAATCTATACGTCGGTGGATTAATTCCTCAACTTTGCCT
1 AAAATTGGTCCTCC-AAAATCTATACGTCGGTGGATTAATTCCTCAACTTTGCCT
38827115 TTGGATAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 14 0.28
57 36 0.72
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (56 bp):
AAAATTGGTCCTCCAAAATCTATACGTCGGTGGATTAATTCCTCAACTTTGCCTCT
Found at i:38827911 original size:36 final size:36
Alignment explanation
Indices: 38827870--38827941 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
38827860 ATTAGAACGA
38827870 TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
1 TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
38827906 TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
1 TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
38827942 GGAGTCGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (36 bp):
TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
Found at i:38828659 original size:20 final size:20
Alignment explanation
Indices: 38828618--38828659 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
38828608 ATTAAAGGAC
*
38828618 AAAATATAAATAATGAATTA
1 AAAATATAAATAATGAAATA
*
38828638 AAAATACTAAA-AATTAAATA
1 AAAATA-TAAATAATGAAATA
38828658 AA
1 AA
38828660 TAAAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAATATAAATAATGAAATA
Found at i:38830215 original size:22 final size:22
Alignment explanation
Indices: 38830182--38830231 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
38830172 ACAATAATAT
38830182 TTAATA-T-TTAATTATTTTTA
1 TTAATATTATTAATTATTTTTA
* *
38830202 TTGATATTATTAATTGTTTTTA
1 TTAATATTATTAATTATTTTTA
38830224 TTAATATT
1 TTAATATT
38830232 TTTATTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.20
21 1 0.04
22 19 0.76
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTAATATTATTAATTATTTTTA
Found at i:38831714 original size:17 final size:18
Alignment explanation
Indices: 38831692--38831728 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
38831682 ATGAAGTGTA
38831692 AAGTATATATATC-ATAT
1 AAGTATATATATCTATAT
*
38831709 AAGTATTTATATCTATAT
1 AAGTATATATATCTATAT
38831727 AA
1 AA
38831729 AATAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
AAGTATATATATCTATAT
Found at i:38831788 original size:2 final size:2
Alignment explanation
Indices: 38831781--38831806 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38831771 GTATGCGCAC
38831781 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38831807 TAACAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38831897 original size:3 final size:3
Alignment explanation
Indices: 38831815--38831877 Score: 117
Period size: 3 Copynumber: 20.7 Consensus size: 3
38831805 ATTAACAAGA
38831815 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38831861 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
38831878 CTTATTAGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38832382 original size:17 final size:17
Alignment explanation
Indices: 38832353--38832556 Score: 91
Period size: 18 Copynumber: 11.6 Consensus size: 17
38832343 ACACAATAAT
38832353 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
38832370 AGATTTTTG-AAACACGA
1 A-ATTTTTGAAAACACGA
38832387 AATTTTTTTGAAAACACGGA
1 AA--TTTTTGAAAACAC-GA
* *
38832407 ATTTTTTTTGAAAACAAGGA
1 A--ATTTTTGAAAAC-ACGA
* * *
38832427 AATTTTCG-ATACATGA
1 AATTTTTGAAAACACGA
38832443 GAATTTTTTG---ACACGAA
1 -AA-TTTTTGAAAACACG-A
* *
38832460 AAATTTTGAAAACCCGA
1 AATTTTTGAAAACACGA
* * **
38832477 AATTCTTCGAACACGGGA
1 AATT-TTTGAAAACACGA
*
38832495 ATTTTTTTGAAAACACGAA
1 A-ATTTTTGAAAACACG-A
**
38832514 AATTTTT--ATTCACGA
1 AATTTTTGAAAACACGA
38832529 GAATTTTTG-AAACACGA
1 -AATTTTTGAAAACACGA
*
38832546 AAATTTTGAAA
1 AATTTTTGAAA
38832557 TACGATTTTT
Statistics
Matches: 141, Mismatches: 26, Indels: 40
0.68 0.13 0.19
Matches are distributed among these distances:
15 6 0.04
16 29 0.21
17 28 0.20
18 50 0.35
19 10 0.07
20 17 0.12
21 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:38832395 original size:19 final size:18
Alignment explanation
Indices: 38832355--38832601 Score: 76
Period size: 18 Copynumber: 13.9 Consensus size: 18
38832345 ACAATAATAA
38832355 TTTTTGAAAACACGAAGA--
1 TTTTTG-AAACACGAA-ATT
38832373 TTTTTGAAACACGAAATT
1 TTTTTGAAACACGAAATT
*
38832391 TTTTTGAAAACACGGAATTT
1 TTTTTG-AAACAC-GAAATT
*
38832411 TTTTTGAAAACAAGGAAA--
1 TTTTTG-AAAC-ACGAAATT
* * *
38832429 TTTTCGATACATGAGAA-T
1 TTTTTGAAACACGA-AATT
*
38832447 TTTTTG--ACACGAAA-A
1 TTTTTGAAACACGAAATT
* *
38832462 ATTTTGAAAACCCGAAA-T
1 TTTTTG-AAACACGAAATT
* * *
38832480 TCTTCG-AACACGGGAATT
1 TTTTTGAAACAC-GAAATT
*
38832498 TTTTTGAAAACACGAAA-A
1 TTTTTG-AAACACGAAATT
**
38832516 TTTTT-ATTCACGAGAA--
1 TTTTTGAAACACGA-AATT
38832532 TTTTTGAAACACGAAA--
1 TTTTTGAAACACGAAATT
* * **
38832548 ATTTTGAAATACGATTTT
1 TTTTTGAAACACGAAATT
* * *
38832566 TTTTTAAAACGCAAAAATT
1 TTTTTGAAACAC-GAAATT
38832585 TCTTTTGAAACACGAAA
1 T-TTTTGAAACACGAAA
38832602 ACTCTTGAAA
Statistics
Matches: 170, Mismatches: 39, Indels: 39
0.69 0.16 0.16
Matches are distributed among these distances:
15 7 0.04
16 38 0.22
17 25 0.15
18 50 0.29
19 16 0.09
20 33 0.19
21 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (18 bp):
TTTTTGAAACACGAAATT
Found at i:38832413 original size:36 final size:38
Alignment explanation
Indices: 38832337--38832412 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 38
38832327 ACACGAGAAC
38832337 TTTGAAACACAATAATAATTTTTGAAAACACGAAGATT
1 TTTGAAACACAATAATAATTTTTGAAAACACGAAGATT
* * *
38832375 TTTGAAACACGA-AAT-TTTTTTGAAAACACGGA-ATT
1 TTTGAAACACAATAATAATTTTTGAAAACACGAAGATT
38832410 TTT
1 TTT
38832413 TTTGAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 6 0.17
36 15 0.43
37 3 0.09
38 11 0.31
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (38 bp):
TTTGAAACACAATAATAATTTTTGAAAACACGAAGATT
Found at i:38832414 original size:20 final size:19
Alignment explanation
Indices: 38832355--38832422 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 19
38832345 ACAATAATAA
**
38832355 TTTTTGAAAACACGAA-GA
1 TTTTTGAAAACACGAATTT
*
38832373 TTTTTG-AAACACGAAATT
1 TTTTTGAAAACACGAATTT
38832391 TTTTTGAAAACACGGAATTT
1 TTTTTGAAAACAC-GAATTT
38832411 TTTTTGAAAACA
1 TTTTTGAAAACA
38832423 AGGAAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 9 0.20
18 12 0.27
19 6 0.14
20 17 0.39
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (19 bp):
TTTTTGAAAACACGAATTT
Found at i:38832427 original size:20 final size:21
Alignment explanation
Indices: 38832373--38832432 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
38832363 AACACGAAGA
*
38832373 TTTTTG-AAAC-ACGAAA-TT
1 TTTTTGAAAACAAGGAAATTT
*
38832391 TTTTTGAAAACACGG-AATTT
1 TTTTTGAAAACAAGGAAATTT
38832411 TTTTTGAAAACAAGGAAATTT
1 TTTTTGAAAACAAGGAAATTT
38832432 T
1 T
38832433 CGATACATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 17 0.49
21 6 0.17
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (21 bp):
TTTTTGAAAACAAGGAAATTT
Found at i:38832569 original size:33 final size:34
Alignment explanation
Indices: 38832496--38832585 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 34
38832486 AACACGGGAA
* *
38832496 TTTTTTTGAAAACACGAAAATTTTTATTCACGAG
1 TTTTTTTGAAAACACGAAAATTTTAAATCACGAG
** *
38832530 AATTTTTG-AAACACGAAAATTTTGAAAT-ACGAT
1 TTTTTTTGAAAACACGAAAATTTT-AAATCACGAG
* * *
38832563 TTTTTTTTAAAACGCAAAAATTT
1 TTTTTTTGAAAACACGAAAATTT
38832586 CTTTTGAAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
33 24 0.55
34 20 0.45
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (34 bp):
TTTTTTTGAAAACACGAAAATTTTAAATCACGAG
Found at i:38832602 original size:21 final size:21
Alignment explanation
Indices: 38832561--38832602 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
38832551 TTGAAATACG
* *
38832561 ATTTTTTTTTAAAACGCAAAA
1 ATTTCTTTTGAAAACGCAAAA
38832582 ATTTCTTTTGAAACACG-AAAA
1 ATTTCTTTTGAAA-ACGCAAAA
38832603 CTCTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (21 bp):
ATTTCTTTTGAAAACGCAAAA
Found at i:38833187 original size:16 final size:16
Alignment explanation
Indices: 38833166--38833245 Score: 81
Period size: 16 Copynumber: 4.9 Consensus size: 16
38833156 TGGAGTCTTT
38833166 TTTTTTCTTTTTTTTC
1 TTTTTTCTTTTTTTTC
* *
38833182 TTTTTTC-CTTTTTCC
1 TTTTTTCTTTTTTTTC
* *
38833197 TTCTTTCTCTTTTTTC
1 TTTTTTCTTTTTTTTC
* *
38833213 TTTTTTCCTTTCTTTC
1 TTTTTTCTTTTTTTTC
38833229 TCTTTTTCTTTCTTTTT
1 T-TTTTTCTTT-TTTTT
38833246 TATTTTTGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
15 12 0.24
16 27 0.53
17 8 0.16
18 4 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTC
Found at i:38833193 original size:24 final size:23
Alignment explanation
Indices: 38833166--38833252 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 23
38833156 TGGAGTCTTT
38833166 TTTTTTCTTTTTTTTCTTTTTTCC
1 TTTTTTCTTTTTTTTCTTTTTT-C
* * *
38833190 TTTTTCCTTCTTTCTCTTTTTTC
1 TTTTTTCTTTTTTTTCTTTTTTC
* *
38833213 TTTTTTCCTTTCTTTCTCTTTTTC
1 TTTTTTCTTTTTTTTCT-TTTTTC
38833237 TTTCTTT-TTTATTTTT
1 TTT-TTTCTTT-TTTTT
38833253 GGTCTCTTGG
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
23 13 0.26
24 30 0.60
25 7 0.14
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTCTTTTTTTTCTTTTTTC
Found at i:38833210 original size:25 final size:25
Alignment explanation
Indices: 38833166--38833235 Score: 99
Period size: 24 Copynumber: 2.9 Consensus size: 25
38833156 TGGAGTCTTT
* *
38833166 TTTTTTCTTT-TTTTTCTTTTTTCC
1 TTTTTCCTTTCTTTCTCTTTTTTCC
*
38833190 TTTTTCC-TTCTTTCTCTTTTTTCT
1 TTTTTCCTTTCTTTCTCTTTTTTCC
38833214 TTTTTCCTTTCTTTCTCTTTTT
1 TTTTTCCTTTCTTTCTCTTTTT
38833236 CTTTCTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.05
24 25 0.61
25 14 0.34
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTCCTTTCTTTCTCTTTTTTCC
Found at i:38833534 original size:6 final size:6
Alignment explanation
Indices: 38833525--38833607 Score: 75
Period size: 6 Copynumber: 14.5 Consensus size: 6
38833515 TTGTTTTAAT
* *
38833525 TTTTTC TTTTT- TTTCTC TTTTTC -TTTTC TTTTTC -TTTT- TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * * *
38833569 TTTTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT
38833608 CTTTAGCTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
5 16 0.24
6 51 0.76
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:38833538 original size:9 final size:9
Alignment explanation
Indices: 38833524--38833607 Score: 62
Period size: 9 Copynumber: 9.1 Consensus size: 9
38833514 ATTGTTTTAA
38833524 TTTTTTCTT
1 TTTTTTCTT
38833533 TTTTTTCTCT
1 TTTTTTCT-T
38833543 TTTTCTT-TT
1 TTTT-TTCTT
*
38833552 CTTTTTCTT
1 TTTTTTCTT
38833561 TTTTCTTCTT
1 TTTT-TTCTT
*
38833571 TTTCTTCTT
1 TTTTTTCTT
* *
38833580 CTTCTTCTT
1 TTTTTTCTT
* *
38833589 CTTCTTCTT
1 TTTTTTCTT
* *
38833598 CTTCTTCTT
1 TTTTTTCTT
38833607 T
1 T
38833608 CTTTAGCTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
8 2 0.03
9 48 0.73
10 14 0.21
11 2 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:38833543 original size:11 final size:10
Alignment explanation
Indices: 38833524--38833576 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 10
38833514 ATTGTTTTAA
38833524 TTTTTTCTTT
1 TTTTTTCTTT
38833534 TTTTTCTCTTT
1 TTTTT-TCTTT
38833545 TTCTTTTCTTT
1 TT-TTTTCTTT
38833556 TTCTTTT-TTCT
1 TT-TTTTCTT-T
38833567 TCTTTTTCTT
1 T-TTTTTCTT
38833577 CTTCTTCTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.18
11 25 0.66
12 6 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:38833578 original size:3 final size:3
Alignment explanation
Indices: 38833540--38833606 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
38833530 CTTTTTTTTC
* * *
38833540 TCT TTT TCT T-T TCT TTT TCT T-T T-T TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
38833585 TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT T
38833607 TCTTTAGCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 6 0.11
3 50 0.89
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TCT
Found at i:38833982 original size:29 final size:29
Alignment explanation
Indices: 38833942--38834056 Score: 108
Period size: 30 Copynumber: 3.9 Consensus size: 29
38833932 AAATGCAGGA
*
38833942 AAAGTTTTAGGGCTAAAACGTAATTTTGAG
1 AAAG-TTTAGGGCTAAAATGTAATTTTGAG
* *
38833972 AAAGTTTAGGGGTCAAAATGTAATTTCGAG
1 AAAGTTTAGGGCT-AAAATGTAATTTTGAG
* * *
38834002 AAAGTCTAGGGGTCAAAAATGAAATTTT-A-
1 AAAGTTTA-GGG-CTAAAATGTAATTTTGAG
* *
38834031 AAAGTTTGGGGGTAAAATGTAATTTT
1 AAAGTTTAGGGCTAAAATGTAATTTT
38834057 TTATTTTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
27 12 0.17
28 3 0.04
29 14 0.20
30 26 0.38
31 14 0.20
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (29 bp):
AAAGTTTAGGGCTAAAATGTAATTTTGAG
Found at i:38834074 original size:18 final size:19
Alignment explanation
Indices: 38834048--38834085 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
38834038 GGGGGTAAAA
38834048 TGTAATTTTTT-ATTTTTT
1 TGTAATTTTTTGATTTTTT
*
38834066 TGTATTTTTTTGATTTTTT
1 TGTAATTTTTTGATTTTTT
38834085 T
1 T
38834086 TAAAAACACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (19 bp):
TGTAATTTTTTGATTTTTT
Found at i:38834086 original size:10 final size:10
Alignment explanation
Indices: 38834053--38834085 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
38834043 TAAAATGTAA
38834053 TTTTT-TATT
1 TTTTTGTATT
38834062 TTTTTGTATT
1 TTTTTGTATT
38834072 TTTTTG-ATT
1 TTTTTGTATT
38834081 TTTTT
1 TTTTT
38834086 TAAAAACACG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.57
10 10 0.43
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (10 bp):
TTTTTGTATT
Found at i:38835573 original size:20 final size:21
Alignment explanation
Indices: 38835548--38835588 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
38835538 TGGGAGTTAG
38835548 TGGGGATATGAGTGG-TTTAA
1 TGGGGATATGAGTGGCTTTAA
*
38835568 TGGGGATATGGGTGGCTTTAA
1 TGGGGATATGAGTGGCTTTAA
38835589 AAAATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.22, C:0.02, G:0.41, T:0.34
Consensus pattern (21 bp):
TGGGGATATGAGTGGCTTTAA
Found at i:38836189 original size:24 final size:24
Alignment explanation
Indices: 38836157--38836216 Score: 104
Period size: 23 Copynumber: 2.5 Consensus size: 24
38836147 TATATTAAAT
38836157 ATATATATTTTTATTTTTAATCAA
1 ATATATATTTTTATTTTTAATCAA
38836181 ATATATA-TTTTATTTTTAATCAA
1 ATATATATTTTTATTTTTAATCAA
*
38836204 ATATATATATTTA
1 ATATATATTTTTA
38836217 ATATGGGCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 23 0.68
24 11 0.32
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATATATTTTTATTTTTAATCAA
Found at i:38836854 original size:6 final size:6
Alignment explanation
Indices: 38836843--38836914 Score: 144
Period size: 6 Copynumber: 12.0 Consensus size: 6
38836833 ATAAATTAAT
38836843 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
38836891 AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC
38836915 CTATTTTGTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:38837898 original size:35 final size:35
Alignment explanation
Indices: 38837822--38837948 Score: 175
Period size: 35 Copynumber: 3.6 Consensus size: 35
38837812 ACTTTCTGTT
38837822 TTGGTGTGTTTCGGATGGA-TAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
* * * *
38837856 TTAGTGTGTTTTGGATGGATTAGCCCTTATGAACA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
*
38837891 TTGGTGTGTTCCGGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
* *
38837926 TCTGGTGTGTTTTGGTTGGATTA
1 T-TGGTGTGTTTCGGATGGATTA
38837949 TTGATGTACT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 17 0.22
35 44 0.56
36 18 0.23
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.41
Consensus pattern (35 bp):
TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
Found at i:38841958 original size:10 final size:9
Alignment explanation
Indices: 38841940--38841991 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 9
38841930 AAACTCCTTT
38841940 AAAATTTAA
1 AAAATTTAA
38841949 AAAATATTAA
1 AAAAT-TTAA
38841959 AAAATTATAAGA
1 AAAATT-T-A-A
*
38841971 AAAATGTATA
1 AAAATTTA-A
38841981 AAAATTTAA
1 AAAATTTAA
38841990 AA
1 AA
38841992 TTTCTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 9 0.25
10 19 0.53
11 2 0.06
12 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAATTTAA
Found at i:38842117 original size:21 final size:21
Alignment explanation
Indices: 38842091--38842145 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
38842081 TGATATTTTT
38842091 ATTTTTAATAAAAAATTTATA
1 ATTTTTAATAAAAAATTTATA
** * * *
38842112 ATTTTTTTTATAAATTTTATG
1 ATTTTTAATAAAAAATTTATA
38842133 ATTTTATAATAAA
1 ATTTT-TAATAAA
38842146 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTTAATAAAAAATTTATA
Found at i:38842895 original size:37 final size:37
Alignment explanation
Indices: 38842810--38842933 Score: 158
Period size: 37 Copynumber: 3.3 Consensus size: 37
38842800 GGTAACCACT
** * *
38842810 CAAAACACACCTGAACGCTCAAACGAACTATATACTATC
1 CAAAACACACCTGATGGCTCGAACGAGCTATAT--TATC
38842849 CAAAACACACCTGATGGCTCGAACGAGCTATATTATC
1 CAAAACACACCTGATGGCTCGAACGAGCTATATTATC
* * **
38842886 CAAAACACACCTAATGGCTCGAATGAGCTATACCATC
1 CAAAACACACCTGATGGCTCGAACGAGCTATATTATC
38842923 CAAAACACACC
1 CAAAACACACC
38842934 AGGGCACTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
37 48 0.62
39 29 0.38
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.18
Consensus pattern (37 bp):
CAAAACACACCTGATGGCTCGAACGAGCTATATTATC
Found at i:38843573 original size:50 final size:49
Alignment explanation
Indices: 38843514--38843663 Score: 158
Period size: 49 Copynumber: 3.0 Consensus size: 49
38843504 ATTATGTGTG
* *
38843514 TTGCA-TTTAATTAAGTCATGCATAAAAGCATCTCATATGTTAATTAAGT
1 TTGCATTTTAATTAAGTCATGCAT-TATGCATCTCATATGTTAATTAAGT
** * * * * *
38843563 TTGTGTTTTAATTATGTAATGCATTATGAAACTCATATGTTAAATAAGT
1 TTGCATTTTAATTAAGTCATGCATTATGCATCTCATATGTTAATTAAGT
* * * *
38843612 TTGCATTTTAATTAAGCCATGCATTTATGCATCTTATAAGTTAATTATGT
1 TTGCATTTTAATTAAGTCATGCA-TTATGCATCTCATATGTTAATTAAGT
38843662 TT
1 TT
38843664 AAGAATAGGT
Statistics
Matches: 79, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
49 41 0.52
50 38 0.48
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (49 bp):
TTGCATTTTAATTAAGTCATGCATTATGCATCTCATATGTTAATTAAGT
Found at i:38844708 original size:23 final size:20
Alignment explanation
Indices: 38844659--38844696 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38844649 TACCAATTTG
*
38844659 CAAACATTTTAAAATACATT
1 CAAACATTATAAAATACATT
38844679 CAAACATTATAAAATACA
1 CAAACATTATAAAATACA
38844697 CAATTCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (20 bp):
CAAACATTATAAAATACATT
Found at i:38849076 original size:27 final size:27
Alignment explanation
Indices: 38849030--38849084 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
38849020 TATCATCACC
*
38849030 TTAATTTTTATAATTTC-TTTATGATTT
1 TTAATTTTTATAATTACTTTTA-GATTT
38849057 TTAATTTTT-TAATATACTTTTAGATTT
1 TTAATTTTTATAAT-TACTTTTAGATTT
38849084 T
1 T
38849085 ATATAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 4 0.16
27 17 0.68
28 4 0.16
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (27 bp):
TTAATTTTTATAATTACTTTTAGATTT
Found at i:38850992 original size:2 final size:2
Alignment explanation
Indices: 38850987--38851041 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
38850977 TTGCAGCCCT
38850987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38851029 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
38851042 CTTTTAAACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38852893 original size:24 final size:24
Alignment explanation
Indices: 38852866--38852916 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
38852856 CCTCCACCAA
* * *
38852866 CACCACCACCAGCTCCTACCCCTC
1 CACCACCACCAGCCCCAACACCTC
* *
38852890 CACCTCCACTAGCCCCAACACCTC
1 CACCACCACCAGCCCCAACACCTC
38852914 CAC
1 CAC
38852917 TTGCTGCAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.61, G:0.04, T:0.12
Consensus pattern (24 bp):
CACCACCACCAGCCCCAACACCTC
Found at i:38852965 original size:12 final size:12
Alignment explanation
Indices: 38852950--38853007 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
38852940 CCTGTTGCAA
38852950 CACCTCCACCAG
1 CACCTCCACCAG
* *
38852962 CACCACCTCCAG
1 CACCTCCACCAG
* *
38852974 CACCTCCGCCAA
1 CACCTCCACCAG
* *
38852986 CACCACCTCCAG
1 CACCTCCACCAG
38852998 CACCTCCACC
1 CACCTCCACC
38853008 TCCACTAACT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.24, C:0.60, G:0.07, T:0.09
Consensus pattern (12 bp):
CACCTCCACCAG
Found at i:38852977 original size:24 final size:24
Alignment explanation
Indices: 38852950--38853097 Score: 140
Period size: 24 Copynumber: 6.2 Consensus size: 24
38852940 CCTGTTGCAA
*
38852950 CACCTCCACCAGCACCACCTCCAG
1 CACCTCCACCAACACCACCTCCAG
*
38852974 CACCTCCGCCAACACCACCTCCAG
1 CACCTCCACCAACACCACCTCCAG
** * *
38852998 CACCTCCACCTCCACTAACTCCTA-
1 CACCTCCACCAACACCACCTCC-AG
* *
38853022 CTCCTCCACCAGCACC-CACTCCAG
1 CACCTCCACCAACACCAC-CTCCAG
*
38853046 CACCTCCGCCAACACCACCTCCTA-
1 CACCTCCACCAACACCACCTCC-AG
* * *
38853070 CACCTCCACCACCACCACCACCAC
1 CACCTCCACCAACACCACCTCCAG
38853094 CACC
1 CACC
38853098 ACCTCCTCCT
Statistics
Matches: 100, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.02
24 95 0.95
25 3 0.03
ACGTcount: A:0.25, C:0.59, G:0.05, T:0.11
Consensus pattern (24 bp):
CACCTCCACCAACACCACCTCCAG
Found at i:38853002 original size:48 final size:48
Alignment explanation
Indices: 38852950--38853097 Score: 156
Period size: 48 Copynumber: 3.1 Consensus size: 48
38852940 CCTGTTGCAA
* *
38852950 CACCTCCACCAGCACCACCTCC-AGCACCTCCGCCAACACCACCTCCAG
1 CACCTCCACCAACACCACCTCCTA-CACCTCCACCAACACCACCTCCAG
** * * * *
38852998 CACCTCCACCTCCACTAACTCCTACTCCTCCACCAGCACC-CACTCCAG
1 CACCTCCACCAACACCACCTCCTACACCTCCACCAACACCAC-CTCCAG
* * * *
38853046 CACCTCCGCCAACACCACCTCCTACACCTCCACCACCACCACCACCAC
1 CACCTCCACCAACACCACCTCCTACACCTCCACCAACACCACCTCCAG
38853094 CACC
1 CACC
38853098 ACCTCCTCCT
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
47 1 0.01
48 78 0.96
49 2 0.02
ACGTcount: A:0.25, C:0.59, G:0.05, T:0.11
Consensus pattern (48 bp):
CACCTCCACCAACACCACCTCCTACACCTCCACCAACACCACCTCCAG
Found at i:38853116 original size:72 final size:71
Alignment explanation
Indices: 38852967--38853384 Score: 202
Period size: 72 Copynumber: 5.9 Consensus size: 71
38852957 ACCAGCACCA
* * * * * * * *
38852967 CCTCCAGCACCTCCGCCAACACCACCTCCAGCACCTCCACCTCCACTAACTCCTA-CTCCTCCAC
1 CCTCCAGCACCTCCGCCAACACCACCTCCACCACCTCCACCACCACCACCACC-ACCACCACCTC
** *
38853031 CAGCACC
65 CTCCACG
38853038 CACTCCAGCACCTCCGCCAACACCACCTCCTA-CACCTCCACCACCACCACCACCACCACCACCT
1 C-CTCCAGCACCTCCGCCAACACCACCTCC-ACCACCTCCACCACCACCACCACCACCACCACCT
38853102 CCTCCTACG
64 CCTCC-ACG
* * * * **
38853111 CCTCCACCACCACCAGCTC--CTA-CTCCTCCACCAGCC-CCAACACCACCACCAATACCTGCAC
1 CCTCCAGCACCTCC-GC-CAAC-ACCACCTCCACCA-CCTCCACCACCACCACC---ACCACCAC
** *
38853172 C-CACTCCAGCACCT
59 CAC-CTCCTCCA-CG
* * * * *
38853186 CCTCCTGCACCTCCGCCAACACTACCTCCACCACCTCCACCACCTCCACCACCAACTCCTA-CTC
1 CCTCCAGCACCTCCGCCAACACCACCTCCACCACCTCCACCACCACCACCACCACCACC-ACCTC
38853250 CTCCACCG
65 CTCCA-CG
* * * * * *
38853258 CCTCCAGCACCTCCACCAGCTCCTA-CTCCTCCA-C-CAACC-CCGA-CACCACCACTACCACCT
1 CCTCCAGCACCTCCGCCAACACC-ACCTCCACCACCTCCACCACC-ACCACCACCACCACCACCT
*
38853318 ACTCC-C-
64 CCTCCACG
* * * * * * * *
38853324 ACTCCAGCACCTCCTCCTACACCACCACCAACACCACCTCCACCACC-CCTAGCACCACCAC
1 CCTCCAGCACCTCCGCCAACACCACCTCCACCACCTCCACCACCACCACC-ACCACCACCAC
38853385 TTGCACCTCC
Statistics
Matches: 262, Mismatches: 56, Indels: 60
0.69 0.15 0.16
Matches are distributed among these distances:
65 1 0.00
66 23 0.09
67 2 0.01
68 7 0.03
69 30 0.11
70 4 0.02
71 4 0.02
72 126 0.48
73 11 0.04
74 8 0.03
75 46 0.18
ACGTcount: A:0.24, C:0.59, G:0.05, T:0.13
Consensus pattern (71 bp):
CCTCCAGCACCTCCGCCAACACCACCTCCACCACCTCCACCACCACCACCACCACCACCACCTCC
TCCACG
Found at i:38853120 original size:3 final size:3
Alignment explanation
Indices: 38853070--38853100 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
38853060 CCACCTCCTA
*
38853070 CAC CTC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
38853101 TCCTCCTACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.68, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:38853120 original size:24 final size:24
Alignment explanation
Indices: 38852952--38853143 Score: 95
Period size: 24 Copynumber: 8.4 Consensus size: 24
38852942 TGTTGCAACA
* *
38852952 CCTCCACCAGCACCACCTCC-AGCA
1 CCTCCACCACCACCACCTCCTA-CG
* * *
38852976 CCTCCGCCAACACCACCTCC-AGCA
1 CCTCCACCACCACCACCTCCTA-CG
* * * *
38853000 CCTCCACCTCCACTAACTCCTACT
1 CCTCCACCACCACCACCTCCTACG
* *
38853024 CCTCCACCAGCACC-CACTCC-AGCA
1 CCTCCACCACCACCAC-CTCCTA-CG
* * *
38853048 CCTCCGCCAACACCACCTCCTACA
1 CCTCCACCACCACCACCTCCTACG
38853072 CCTCCACCACCACCA---CC-A--
1 CCTCCACCACCACCACCTCCTACG
* *
38853090 CCACCACCACC-TC--CTCCTACG
1 CCTCCACCACCACCACCTCCTACG
* *
38853111 CCTCCACCACCACCAGCTCCTACT
1 CCTCCACCACCACCACCTCCTACG
38853135 CCTCCACCA
1 CCTCCACCA
38853144 GCCCCAACAC
Statistics
Matches: 133, Mismatches: 22, Indels: 26
0.73 0.12 0.14
Matches are distributed among these distances:
17 1 0.01
18 12 0.09
19 1 0.01
20 1 0.01
21 12 0.09
22 1 0.01
23 1 0.01
24 101 0.76
25 3 0.02
ACGTcount: A:0.23, C:0.59, G:0.05, T:0.12
Consensus pattern (24 bp):
CCTCCACCACCACCACCTCCTACG
Found at i:38853155 original size:36 final size:36
Alignment explanation
Indices: 38853115--38853309 Score: 110
Period size: 36 Copynumber: 5.2 Consensus size: 36
38853105 CCTACGCCTC
*
38853115 CACCACCACCAGCTCCTACTCCTCCACCAGCC-CCAA
1 CACCACCACCAACTCCTACTCCTCCACC-GCCTCCAA
* * **
38853151 CACCACCACCAA-TACCTGCACCCACTCCAGCACCTCCTCCTG
1 CACCACCACCAACT-CCT--ACTC-CT-C--CACCGCCTCCAA
* * * * * * *
38853193 CACCTCCGCCAAC-ACTACCTCCACCACCTCCACCAC
1 CACCACCACCAACTCCTA-CTCCTCCACCGCCTCCAA
* *
38853229 CTCCACCACCAACTCCTACTCCTCCACCGCCTCCAG
1 CACCACCACCAACTCCTACTCCTCCACCGCCTCCAA
* * * *
38853265 CACCTCCACCAGCTCCTACTCCTCCACCAACC-CCGA
1 CACCACCACCAACTCCTACTCCTCCACC-GCCTCCAA
38853301 CACCACCAC
1 CACCACCAC
38853310 TACCACCTAC
Statistics
Matches: 119, Mismatches: 28, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
35 1 0.01
36 82 0.69
37 5 0.04
38 4 0.03
39 4 0.03
40 3 0.03
41 4 0.03
42 16 0.13
ACGTcount: A:0.24, C:0.58, G:0.05, T:0.13
Consensus pattern (36 bp):
CACCACCACCAACTCCTACTCCTCCACCGCCTCCAA
Done.