Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 130 of 325
Found at i:40544655 original size:29 final size:29
Alignment explanation
Indices: 40544613--40544670 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40544603 GAAATAACAA
40544613 CAAATATGTGCTATAATAGGGTTCCAAAT
1 CAAATATGTGCTATAATAGGGTTCCAAAT
40544642 CAAATATGTGCTATAATAGGGTTCCAAAT
1 CAAATATGTGCTATAATAGGGTTCCAAAT
40544671 AATTCGGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (29 bp):
CAAATATGTGCTATAATAGGGTTCCAAAT
Found at i:40546228 original size:44 final size:44
Alignment explanation
Indices: 40546179--40546269 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
40546169 TTTGAAAATG
*
40546179 GTTTGAAGGTGATTTGGTAAGTATATGTTATGTAAGTTAACTAT
1 GTTTGAAGGTGATTTGGTAAGTATACGTTATGTAAGTTAACTAT
40546223 GTTTGAAGGTGATTTGGTAAGTATACGTTATGTAAGTTAACTAT
1 GTTTGAAGGTGATTTGGTAAGTATACGTTATGTAAGTTAACTAT
40546267 GTT
1 GTT
40546270 GGTACATTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.03, G:0.25, T:0.43
Consensus pattern (44 bp):
GTTTGAAGGTGATTTGGTAAGTATACGTTATGTAAGTTAACTAT
Found at i:40546673 original size:15 final size:15
Alignment explanation
Indices: 40546653--40546686 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40546643 AAACACTAGC
40546653 GTGTGAC-TCAGCCAT
1 GTGTGACAT-AGCCAT
40546668 GTGTGACATAGCCAT
1 GTGTGACATAGCCAT
40546683 GTGT
1 GTGT
40546687 CCCCTGTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.94
16 1 0.06
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (15 bp):
GTGTGACATAGCCAT
Found at i:40547736 original size:47 final size:46
Alignment explanation
Indices: 40547671--40547770 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
40547661 GTTTAACCAT
* **
40547671 ATATCTATTTTGGCAGCTTGGTTGCAATTATAGTGGCTTAACCACAC
1 ATATCTGTTTTGGCAGCTTGACTGCAA-TATAGTGGCTTAACCACAC
* * * *
40547718 ATATCTGTTTTGGTAGCTTGACTGCAATGTAGTGGCTTGACCACAT
1 ATATCTGTTTTGGCAGCTTGACTGCAATATAGTGGCTTAACCACAC
40547764 ATATCTG
1 ATATCTG
40547771 ATAAATCGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 23 0.50
47 23 0.50
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (46 bp):
ATATCTGTTTTGGCAGCTTGACTGCAATATAGTGGCTTAACCACAC
Found at i:40547768 original size:46 final size:47
Alignment explanation
Indices: 40547656--40547770 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 47
40547646 CTGCACTATC
* * **
40547656 TAGTGGTTTAA-C-CATATATCTATTTTGGCAGCTTGGTTGCAATTA
1 TAGTGGCTTAACCACATATATCTGTTTTGGCAGCTTGACTGCAATTA
* * *
40547701 TAGTGGCTTAACCACACATATCTGTTTTGGTAGCTTGACTGCAA-TG
1 TAGTGGCTTAACCACATATATCTGTTTTGGCAGCTTGACTGCAATTA
*
40547747 TAGTGGCTTGACCACATATATCTG
1 TAGTGGCTTAACCACATATATCTG
40547771 ATAAATCGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 10 0.17
46 24 0.41
47 25 0.42
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (47 bp):
TAGTGGCTTAACCACATATATCTGTTTTGGCAGCTTGACTGCAATTA
Found at i:40558195 original size:86 final size:86
Alignment explanation
Indices: 40558093--40558262 Score: 322
Period size: 86 Copynumber: 2.0 Consensus size: 86
40558083 CGTTATAAGG
40558093 GCCTACGAGGCCTTAAACATGCTTCAAAAGTGGTTCGGGACTAAACCAATAAATATGAAAATTTT
1 GCCTACGAGGCCTTAAACATGCTTCAAAAGTGGTTCGGGACTAAACCAATAAATATGAAAATTTT
40558158 GGAAACTTAGAAAAAATCTAA
66 GGAAACTTAGAAAAAATCTAA
* *
40558179 GCCTACGAGGCCTTAAACATGCTTTAGAAGTGGTTCGGGACTAAACCAATAAATATGAAAATTTT
1 GCCTACGAGGCCTTAAACATGCTTCAAAAGTGGTTCGGGACTAAACCAATAAATATGAAAATTTT
40558244 GGAAACTTAGAAAAAATCT
66 GGAAACTTAGAAAAAATCT
40558263 CAACCATACA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (86 bp):
GCCTACGAGGCCTTAAACATGCTTCAAAAGTGGTTCGGGACTAAACCAATAAATATGAAAATTTT
GGAAACTTAGAAAAAATCTAA
Found at i:40570674 original size:37 final size:37
Alignment explanation
Indices: 40570629--40570701 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
40570619 TGAAAATCGT
40570629 GATCACTCTACTGACACTTTTCTGACCCACTCAAATC
1 GATCACTCTACTGACACTTTTCTGACCCACTCAAATC
*
40570666 GATCACTCTGCTGACACTTTTCTGACCCACTCAAAT
1 GATCACTCTACTGACACTTTTCTGACCCACTCAAAT
40570702 TTAACATCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.34, G:0.10, T:0.30
Consensus pattern (37 bp):
GATCACTCTACTGACACTTTTCTGACCCACTCAAATC
Found at i:40573994 original size:40 final size:43
Alignment explanation
Indices: 40573946--40574039 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
40573936 GTGAATTGAA
*
40573946 ATAGCTTTGGTTC-A-TG-TGGCACTAAGTGTGTGATACCGAG
1 ATAGCTTTGGTTCAAGTGATGGCACTAAGTGTGCGATACCGAG
* **
40573986 ATAGCTTTGGTTCAATGTGATGGCACTAAGTGTGCGATATCGCT
1 ATAGCTTTGGTTCAA-GTGATGGCACTAAGTGTGCGATACCGAG
40574030 ATAGCTTTGG
1 ATAGCTTTGG
40574040 CTAAACATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 13 0.28
41 1 0.02
43 2 0.04
44 30 0.65
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (43 bp):
ATAGCTTTGGTTCAAGTGATGGCACTAAGTGTGCGATACCGAG
Found at i:40574223 original size:40 final size:40
Alignment explanation
Indices: 40574188--40574266 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
40574178 TTGATACTAT
*
40574188 GTGTATGAAACTTGATGAAATGGTATATACATGATAAATC
1 GTGTATAAAACTTGATGAAATGGTATATACATGATAAATC
*
40574228 GTGTATAAAACTTGATGAAATGGTTTATACATGATAAAT
1 GTGTATAAAACTTGATGAAATGGTATATACATGATAAAT
40574267 GGTTATGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (40 bp):
GTGTATAAAACTTGATGAAATGGTATATACATGATAAATC
Found at i:40574268 original size:18 final size:19
Alignment explanation
Indices: 40574200--40574270 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
40574190 GTATGAAACT
*
40574200 TGATGAAATGGTATATACA
1 TGATGAAATGGTTTATACA
* * *
40574219 TGAT-AAATCGTGTATAAAACT
1 TGATGAAAT-G-GT-TTATACA
40574240 TGATGAAATGGTTTATACA
1 TGATGAAATGGTTTATACA
40574259 TGAT-AAATGGTT
1 TGATGAAATGGTT
40574271 ATGAATTAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 12 0.29
19 13 0.32
20 4 0.10
21 8 0.20
22 4 0.10
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (19 bp):
TGATGAAATGGTTTATACA
Found at i:40578093 original size:32 final size:32
Alignment explanation
Indices: 40578052--40578114 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
40578042 TTGATCGAAG
*
40578052 CTCCAGTGTTAGTTCAGTTAGAACCAGGAAAT
1 CTCCAGTGTTAGTTCAGCTAGAACCAGGAAAT
40578084 CTCCAGTGTTAGTTCAGCTAGAACCAGGAAA
1 CTCCAGTGTTAGTTCAGCTAGAACCAGGAAA
40578115 AGAATTTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (32 bp):
CTCCAGTGTTAGTTCAGCTAGAACCAGGAAAT
Found at i:40581867 original size:17 final size:17
Alignment explanation
Indices: 40581845--40581879 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
40581835 TAGAAATGGT
40581845 AAGTTTTATGTCATATA
1 AAGTTTTATGTCATATA
40581862 AAGTTTTATGTCATATA
1 AAGTTTTATGTCATATA
40581879 A
1 A
40581880 TAGGTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (17 bp):
AAGTTTTATGTCATATA
Found at i:40593048 original size:19 final size:20
Alignment explanation
Indices: 40593024--40593061 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40593014 GGTACCACCA
40593024 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
40593043 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
40593062 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:40593357 original size:46 final size:46
Alignment explanation
Indices: 40593290--40593455 Score: 185
Period size: 46 Copynumber: 3.6 Consensus size: 46
40593280 CGCCCCTAAG
* *
40593290 TGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
* * * * *
40593336 TGAACTCAGACTCAACTCAACGAGTTCGAATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCG---GAC-ATTTGCATCCATAAA
* * *
40593383 CGAACTCGGACTCAACTCAACGAGTTTGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
40593429 TGAACTCGGACTCAACTCAACGAGTTC
1 TGAACTCGGACTCAACTCAACGAGTTC
40593456 TGATGCTCAA
Statistics
Matches: 97, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 1 0.01
46 51 0.53
47 26 0.27
48 1 0.01
49 3 0.03
50 6 0.06
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
Found at i:40597130 original size:46 final size:48
Alignment explanation
Indices: 40596945--40597130 Score: 168
Period size: 46 Copynumber: 3.9 Consensus size: 48
40596935 GTGGGAAAGT
* * *
40596945 GCCGATGCCATGTCCCAGACGTGGTCTTACACTAGCTCTCGCCT-ATCTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG--CTCACATAATCTG
* * * * *
40596994 TGTCGATGCCATGTCCCAGACATGGTATTACACTA--ACACA-ACTCTTA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATC-TG
* * * ** *
40597041 GCCGATGCCATGTCCCAGGCATAGTCTTACACTGGCTTTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATCTG
40597089 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCACATAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAA
40597131 GTGACCCAAA
Statistics
Matches: 108, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
46 51 0.47
47 14 0.13
48 10 0.09
49 2 0.02
50 31 0.29
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATCTG
Found at i:40603423 original size:22 final size:23
Alignment explanation
Indices: 40603381--40603423 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
40603371 TGGGTAGGAA
40603381 GTTTTCTAGAAAATTTGCATTTT
1 GTTTTCTAGAAAATTTGCATTTT
40603404 GTTTTCT--AAAATATTGCATT
1 GTTTTCTAGAAAAT-TTGCATT
40603424 AGCATAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (23 bp):
GTTTTCTAGAAAATTTGCATTTT
Found at i:40604096 original size:30 final size:29
Alignment explanation
Indices: 40604060--40604117 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
40604050 GTAATTTCTG
*
40604060 AAAATTGAATC-AAATCAAATTTTCATGTAT
1 AAAATTGAA-CAAAATCAAA-GTTCATGTAT
*
40604090 AAAATTGCACAAAATCAAAGTTCATGTA
1 AAAATTGAACAAAATCAAAGTTCATGTA
40604118 CGACATTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (29 bp):
AAAATTGAACAAAATCAAAGTTCATGTAT
Found at i:40604114 original size:29 final size:30
Alignment explanation
Indices: 40604071--40604148 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
40604061 AAATTGAATC
* *
40604071 AAATCAAATTTTCATGTATAAAATTGCACA-
1 AAATCAAA-GTTCATGTACAAAATTGCACAT
* * *
40604101 AAATCAAAGTTCATGTACGACATTGCATATT
1 AAATCAAAGTTCATGTACAAAATTGCACA-T
40604132 AAATCAAAGTTCATGTA
1 AAATCAAAGTTCATGTA
40604149 GATATTCATC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.39
30 8 0.20
31 17 0.41
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATGTACAAAATTGCACAT
Found at i:40607384 original size:19 final size:19
Alignment explanation
Indices: 40607362--40607421 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
40607352 TAAGTGCTTA
40607362 AGGGGTACCGAAGTACAAC
1 AGGGGTACCGAAGTACAAC
* *
40607381 AGGGGCA-CGTAAGTACATTC
1 AGGGGTACCG-AAGTACA-AC
*
40607401 AGGGGTACCAAAGTACAAC
1 AGGGGTACCGAAGTACAAC
40607420 AG
1 AG
40607422 AGGCACGTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.06
19 16 0.48
20 14 0.42
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (19 bp):
AGGGGTACCGAAGTACAAC
Found at i:40607405 original size:20 final size:20
Alignment explanation
Indices: 40607345--40607405 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
40607335 AGTACAACAA
* *
40607345 GGGCACGTAAGTGC-TTAAG
1 GGGCACGTAAGTACATTCAG
* *
40607364 GGGTACCG-AAGTACA-ACAG
1 GGGCA-CGTAAGTACATTCAG
40607383 GGGCACGTAAGTACATTCAG
1 GGGCACGTAAGTACATTCAG
40607403 GGG
1 GGG
40607406 TACCAAAGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.06
19 22 0.69
20 8 0.25
ACGTcount: A:0.30, C:0.18, G:0.36, T:0.16
Consensus pattern (20 bp):
GGGCACGTAAGTACATTCAG
Found at i:40607416 original size:39 final size:39
Alignment explanation
Indices: 40607328--40607454 Score: 175
Period size: 39 Copynumber: 3.3 Consensus size: 39
40607318 ACTATCAGGA
* *
40607328 GTACTGAAGTACAACAAGGGCACGTAAGTGC-TTAAGGG
1 GTACCGAAGTACAACAGGGGCACGTAAGTGCATTAAGGG
* *
40607366 GTACCGAAGTACAACAGGGGCACGTAAGTACATTCAGGG
1 GTACCGAAGTACAACAGGGGCACGTAAGTGCATTAAGGG
* * * *
40607405 GTACCAAAGTACAACAGAGGCACGTACGTGCATTTAGGG
1 GTACCGAAGTACAACAGGGGCACGTAAGTGCATTAAGGG
40607444 GTACCGAAGTA
1 GTACCGAAGTA
40607455 AAATTTTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 28 0.36
39 50 0.64
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (39 bp):
GTACCGAAGTACAACAGGGGCACGTAAGTGCATTAAGGG
Found at i:40615552 original size:20 final size:20
Alignment explanation
Indices: 40615527--40615567 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40615517 AATGAATGTC
40615527 TATATGAATTCTCAATTAAT
1 TATATGAATTCTCAATTAAT
40615547 TATATGAATTCTCAATTAAT
1 TATATGAATTCTCAATTAAT
40615567 T
1 T
40615568 TTCGTATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (20 bp):
TATATGAATTCTCAATTAAT
Found at i:40623515 original size:18 final size:18
Alignment explanation
Indices: 40623494--40623532 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
40623484 AATAAAAATT
40623494 TAAAAATCAAATTTAAAC
1 TAAAAATCAAATTTAAAC
*
40623512 TAAAGATCAAATTTAAAC
1 TAAAAATCAAATTTAAAC
40623530 TAA
1 TAA
40623533 TTACAGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAAATCAAATTTAAAC
Found at i:40623609 original size:29 final size:29
Alignment explanation
Indices: 40623566--40623629 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
40623556 AAATAATATG
*
40623566 ATCTTTATCCGGCCAA-TTTCAAATCTTTA
1 ATCTTTATCCAGCCAACTTT-AAATCTTTA
40623595 ATCTTTATCCAGCCAACTTTAAATCTTTA
1 ATCTTTATCCAGCCAACTTTAAATCTTTA
40623624 ATCTTT
1 ATCTTT
40623630 CAATCTACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 30 0.91
30 3 0.09
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (29 bp):
ATCTTTATCCAGCCAACTTTAAATCTTTA
Found at i:40629772 original size:21 final size:21
Alignment explanation
Indices: 40629756--40629818 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
40629746 GCCCATTTAG
40629756 AGGCCACACACGCCCATGTGA
1 AGGCCACACACGCCCATGTGA
* * * *
40629777 AGGCCACACAAGCTCGTGTGG
1 AGGCCACACACGCCCATGTGA
* *
40629798 AGGGCACACACGCCCGTGTGA
1 AGGCCACACACGCCCATGTGA
40629819 GCACTCTTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.33, G:0.30, T:0.11
Consensus pattern (21 bp):
AGGCCACACACGCCCATGTGA
Found at i:40631089 original size:43 final size:43
Alignment explanation
Indices: 40631042--40631212 Score: 168
Period size: 43 Copynumber: 4.0 Consensus size: 43
40631032 GGTTCTGAGA
*
40631042 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
* *
40631085 TGTGATTACATGTAAGACCATGTCTACGACATTGGCATTGTTAA
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTG-TAT
* *** * * * *
40631129 T-CGATTTTGTGTAAGACCCTGTCTAGGAAAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
* * * *
40631170 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
1 -TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
40631213 GAGCTATATG
Statistics
Matches: 101, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 89 0.88
44 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
Found at i:40632058 original size:47 final size:47
Alignment explanation
Indices: 40632000--40632092 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
40631990 GCCGTGTGCG
* * * *
40632000 ACACACTGTCATGTTACACGGCCGTGTGTCCCCTGGGGCAGCCCTTT
1 ACACACGGTCATGTTACACAGCCATGTGCCCCCTGGGGCAGCCCTTT
* *
40632047 ACACACGGTCATTTTACACAGCCATGTGCCCCCTGGGGTAGCCCTT
1 ACACACGGTCATGTTACACAGCCATGTGCCCCCTGGGGCAGCCCTT
40632093 CGAATTTAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.17, C:0.34, G:0.24, T:0.25
Consensus pattern (47 bp):
ACACACGGTCATGTTACACAGCCATGTGCCCCCTGGGGCAGCCCTTT
Found at i:40633329 original size:19 final size:18
Alignment explanation
Indices: 40633296--40633361 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
40633286 TAAAAATACC
40633296 ATAAAATAAATAACATAA
1 ATAAAATAAATAACATAA
*
40633314 ATAAATATATATAACATAAA
1 ATAAA-ATAAATAACAT-AA
*
40633334 ATAATAATAAA-AACAAAA
1 ATAA-AATAAATAACATAA
*
40633352 ATCAAATAAA
1 ATAAAATAAA
40633362 ATTAATTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
17 6 0.15
18 10 0.24
19 14 0.34
20 10 0.24
21 1 0.02
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAATAAATAACATAA
Found at i:40633362 original size:17 final size:17
Alignment explanation
Indices: 40633299--40633361 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
40633289 AAATACCATA
*
40633299 AAATAAATAACATAAAT
1 AAATAAATAACAAAAAT
40633316 AAATATATATAACATAAAAT
1 AAATA-A-ATAACA-AAAAT
40633336 AATAATAAA-AACAAAAAT
1 -A-AATAAATAACAAAAAT
40633354 CAAATAAA
1 -AAATAAA
40633362 ATTAATTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 11 0.28
18 7 0.18
19 10 0.26
20 5 0.13
21 2 0.05
22 4 0.10
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAAATAACAAAAAT
Found at i:40635899 original size:20 final size:20
Alignment explanation
Indices: 40635876--40635933 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
40635866 GTCATGTTCT
40635876 AAGCCACACGGGCGTGTGCC
1 AAGCCACACGGGCGTGTGCC
40635896 AAGCCACACGGGCGTGTGCC
1 AAGCCACACGGGCGTGTGCC
*
40635916 AAGCCACACGGGTGTGTG
1 AAGCCACACGGGCGTGTG
40635934 ACTCACTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.21, C:0.31, G:0.36, T:0.12
Consensus pattern (20 bp):
AAGCCACACGGGCGTGTGCC
Found at i:40639598 original size:31 final size:31
Alignment explanation
Indices: 40639546--40639655 Score: 139
Period size: 31 Copynumber: 3.5 Consensus size: 31
40639536 TTTAACGGTT
* *
40639546 ACTGGGCCGAATCCTTTTCATAAACCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
40639577 ACTGGGCTGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
40639608 ACTAGGCCAAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* * *
40639639 ATTAGACCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
40639656 ACTGTAAACG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:40639904 original size:25 final size:25
Alignment explanation
Indices: 40639876--40639945 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
40639866 CTCTTTTAAT
*
40639876 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
40639901 AACTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
40639926 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40639946 AGCACTTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:40640795 original size:27 final size:26
Alignment explanation
Indices: 40640758--40640836 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 26
40640748 TATTCGCTAT
*
40640758 TTTACCATACAGGGGTATTACGGTCAC
1 TTTACCCTACAGGGGT-TTACGGTCAC
*
40640785 TTTACCCTACAAGGGCTTTACGGTCAC
1 TTTACCCTAC-AGGGGTTTACGGTCAC
* *
40640812 TTCACCCTACAGGGGCTTTATGGTC
1 TTTACCCTACAGGGG-TTTACGGTC
40640837 TTTTTACCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 4 0.09
27 36 0.80
28 5 0.11
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (26 bp):
TTTACCCTACAGGGGTTTACGGTCAC
Found at i:40641140 original size:27 final size:26
Alignment explanation
Indices: 40640877--40641164 Score: 202
Period size: 27 Copynumber: 10.6 Consensus size: 26
40640867 TCATCCGACA
* * *
40640877 AGGGTGTTTTGGTAAATCTACAAACC
1 AGGGTATTTTGGTAATTTTACAAACC
**
40640903 AAGGGTATTTCAGTAATTTT-CTAAACC
1 -AGGGTATTTTGGTAATTTTAC-AAACC
* * * *
40640930 AATGGTATTTCT-ATAATTTTTAGAAAGGCA
1 -AGGGTATTT-TGGTAA-TTTTACAAA--CC
* * ** *
40640960 AGGGTATTTTTGTAACTTTGTAAATC
1 AGGGTATTTTGGTAATTTTACAAACC
* **
40640986 AGGGGTATTTTGGTAATTTTATAAATTG
1 A-GGGTATTTTGGTAATTTTACAAA-CC
* *
40641014 AGGGTATTTCGGTAATTTCACAAACC
1 AGGGTATTTTGGTAATTTTACAAACC
*
40641040 AGTGGTATTTTGGTAATTTTACAAACT
1 AG-GGTATTTTGGTAATTTTACAAACC
40641067 AGGGGTATTTTGGTAATTTTACAAACC
1 A-GGGTATTTTGGTAATTTTACAAACC
* * *
40641094 AGGGGTATTTTAGCAATTTTACAGACC
1 A-GGGTATTTTGGTAATTTTACAAACC
* * *
40641121 AGGGTATTTTGGTAATTTTTACTGATCG
1 AGGGTATTTTGGTAA-TTTTAC-AAACC
40641149 AGGGTATTTTGGTAAT
1 AGGGTATTTTGGTAAT
40641165 ATTGTAAACT
Statistics
Matches: 209, Mismatches: 39, Indels: 26
0.76 0.14 0.09
Matches are distributed among these distances:
26 16 0.08
27 148 0.71
28 33 0.16
29 11 0.05
30 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACC
Found at i:40641287 original size:81 final size:81
Alignment explanation
Indices: 40641192--40641395 Score: 327
Period size: 81 Copynumber: 2.5 Consensus size: 81
40641182 TTAGTAGTTT
* * *
40641192 TGTAAATCGGGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATAAATTGAG
1 TGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAG
40641257 GGTAAAACGGTAATTC
66 GGTAAAACGGTAATTC
* * * *
40641273 TGTAAATTGAGGGTAAAACAGTAATTCTGTAAGTCGAGGGTAAAATGGTAATTCTATAAATCGAG
1 TGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAG
40641338 GGTAAAACGGTAATTC
66 GGTAAAACGGTAATTC
* *
40641354 TATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
1 TGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTA
40641396 CTTTGGTAAT
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 111 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (81 bp):
TGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAG
GGTAAAACGGTAATTC
Found at i:40641406 original size:27 final size:27
Alignment explanation
Indices: 40641194--40641395 Score: 296
Period size: 27 Copynumber: 7.5 Consensus size: 27
40641184 AGTAGTTTTG
* *
40641194 TAAATCGGGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
* **
40641221 TAAATCAAGGGTAAAATAGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
* *
40641248 TAAATTGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTA
* * *
40641275 TAAATTGAGGGTAAAACAGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTA
* *
40641302 TAAGTCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
40641329 TAAATCGAGGGTAAAACGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
40641356 TAAATCGAGGGTAAAACGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
40641383 TAAATCGAGGGTA
1 TAAATCGAGGGTA
40641396 CTTTGGTAAT
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 159 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACGGTAATTCTA
Found at i:40643731 original size:31 final size:31
Alignment explanation
Indices: 40643693--40643802 Score: 168
Period size: 31 Copynumber: 3.6 Consensus size: 31
40643683 TTTAATGGTT
*
40643693 ACTGGGCCGAAGCCTTTTCATAAATCATATA
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
40643724 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
40643755 ACTGGGCCAAAGCCTTTTCATAAATGATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
40643786 ATTGGGCCGAAG-CTTTT
1 ACTGGGCCGAAGCCTTTT
40643803 ATTGTAAACG
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 5 0.07
31 67 0.93
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:40644061 original size:25 final size:25
Alignment explanation
Indices: 40644027--40644117 Score: 146
Period size: 25 Copynumber: 3.6 Consensus size: 25
40644017 TTTAATAACC
* *
40644027 GGGGCAAAGCCCTTTTTGATAAACT
1 GGGGCAAAGCCCTTTTCGGTAAACT
40644052 GGGGCAAAGCCCTTTTCGGTAAACT
1 GGGGCAAAGCCCTTTTCGGTAAACT
*
40644077 GGGGCAAAGCCCTTTTCGGTAAACC
1 GGGGCAAAGCCCTTTTCGGTAAACT
*
40644102 GGGGCATAGCCCTTTT
1 GGGGCAAAGCCCTTTT
40644118 AGCACTTCCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.25
Consensus pattern (25 bp):
GGGGCAAAGCCCTTTTCGGTAAACT
Found at i:40645398 original size:27 final size:27
Alignment explanation
Indices: 40645345--40645704 Score: 199
Period size: 27 Copynumber: 13.3 Consensus size: 27
40645335 TTTCATCCTA
* * * * *
40645345 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *
40645372 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
40645399 CAATGGTATTTCTA-TAATTTTTAGAAAGT
1 CAAGGGTATTT-TAGTAA-TTTTATAAA-C
* * *
40645428 CAAGGGTATTTCTA-TAACTTTGTAAAT
1 CAAGGGTATTT-TAGTAATTTTATAAAC
* * * *
40645455 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
** ** * *
40645482 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *
40645509 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTAGTAATTTTATAAAC
* * * *
40645536 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * * *
40645563 CAGGGGTATTTTAGCAATTTTACAGAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
40645590 C-AGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTAGTAATTTTA-TAAAC
* * *
40645616 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *
40645643 CAAGGGTATTTTAGTAGTTTTATAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *** * * *
40645670 CGAGGGTAAAATAGTAATTCTGTAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
40645697 CAAGGGTA
1 CAAGGGTA
40645705 AAACAGTAAT
Statistics
Matches: 267, Mismatches: 57, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
26 24 0.09
27 212 0.79
28 15 0.06
29 16 0.06
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTATAAAC
Found at i:40645664 original size:80 final size:81
Alignment explanation
Indices: 40645456--40645664 Score: 260
Period size: 80 Copynumber: 2.6 Consensus size: 81
40645446 TTTGTAAATC
*** ** *
40645456 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAACCAGTGGTATTTT
*
40645521 GGTAATTTTACAAACT
66 GGTAATTTTACAAACG
* * *
40645537 AGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAGACCAG-GGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAACCAGTGGTATTTT
* *
40645601 GGTAATTTTACTGATCG
66 GGTAATTTTAC-AAACG
** *
40645618 A-GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAGTTTTA
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTA
40645665 TAAATCGAGG
Statistics
Matches: 110, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
80 60 0.55
81 50 0.45
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.40
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAACCAGTGGTATTTT
GGTAATTTTACAAACG
Found at i:40645687 original size:54 final size:54
Alignment explanation
Indices: 40645629--40645866 Score: 208
Period size: 54 Copynumber: 4.4 Consensus size: 54
40645619 GGGTATTTTG
* **** * * *
40645629 GTAATTTTGTAAACCAAGGGTATTTTAGTAGTTTTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA
* *
40645683 GTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAATTGAGGGTAAAACA
1 GTAATTCTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA
* *** * * **
40645737 GTAATTCTATAAATTGAGGGTAAAAC-GATAATTCTCTAAGTCGAGGGTAAAATG
1 GTAATTCTGTAAACCAAGGGTAAAACAG-TAATTCTATAAATCGAGGGTAAAACA
* * * * * * *
40645791 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA
* * *
40645845 GTAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAACCAAGGGTA
40645867 CTTTGGTAAT
Statistics
Matches: 159, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 157 0.99
55 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (54 bp):
GTAATTCTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA
Found at i:40645704 original size:134 final size:134
Alignment explanation
Indices: 40645458--40645704 Score: 282
Period size: 134 Copynumber: 1.8 Consensus size: 134
40645448 TGTAAATCAG
* *
40645458 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTAG
* *** * * *
40645523 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAG
66 TAATTTTACAAACGAGGGGTAAAATAGTAATTCTACAAACCAAGGGTATTTTAGCAATTTTACAG
40645588 ACCA
131 ACCA
** * ***
40645592 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAG-GGTATTTTA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTTTA
* * ** *
40645656 GTAGTTTTATAAATCGA-GGGTAAAATAGTAATTCTGTAAATCAAGGGTA
65 GTAATTTTACAAA-CGAGGGGTAAAATAGTAATTCTACAAACCAAGGGTA
40645705 AAACAGTAAT
Statistics
Matches: 91, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
134 87 0.96
135 4 0.04
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.38
Consensus pattern (134 bp):
GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTAG
TAATTTTACAAACGAGGGGTAAAATAGTAATTCTACAAACCAAGGGTATTTTAGCAATTTTACAG
ACCA
Found at i:40645705 original size:27 final size:27
Alignment explanation
Indices: 40645654--40645866 Score: 266
Period size: 27 Copynumber: 7.9 Consensus size: 27
40645644 AAGGGTATTT
* *
40645654 TAGTAGTTTTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* *
40645681 TAGTAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* *
40645708 CAGTAATTCTATAAATTGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* *
40645735 CAGTAATTCTATAAATTGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* * *
40645762 -CGATAATTCTCTAAGTCGAGGGTAAAA
1 TAG-TAATTCTATAAATCGAGGGTAAAA
*
40645789 TGGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
** * *
40645816 CGGTAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
40645843 TAGTAATTCTATAAATCGAGGGTA
1 TAGTAATTCTATAAATCGAGGGTA
40645867 CTTTGGTAAT
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 160 0.99
28 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (27 bp):
TAGTAATTCTATAAATCGAGGGTAAAA
Found at i:40645877 original size:54 final size:54
Alignment explanation
Indices: 40645663--40645866 Score: 300
Period size: 54 Copynumber: 3.8 Consensus size: 54
40645653 TTAGTAGTTT
* * *
40645663 TATAAATCGAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTC
1 TATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATTC
* * * *
40645717 TATAAATTGAGGGTAAAACAGTAATTCTATAAATTGAGGGTAAAACGATAATTC
1 TATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATTC
* * *
40645771 TCTAAGTCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTC
1 TATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATTC
* *
40645825 TGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTA
1 TATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTA
40645867 CTTTGGTAAT
Statistics
Matches: 132, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 132 1.00
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (54 bp):
TATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATTC
Found at i:40647242 original size:30 final size:29
Alignment explanation
Indices: 40647199--40647259 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
40647189 TAAGTAGCCG
* *
40647199 AAGCTAGTTAAATCGCATACTTAGTGCCA
1 AAGCTAGTTAAATCACACACTTAGTGCCA
40647228 AAGCTAGTTTAAATCACACACTTAGTGCCA
1 AAGCTAG-TTAAATCACACACTTAGTGCCA
40647258 AA
1 AA
40647260 ACTTCCGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (29 bp):
AAGCTAGTTAAATCACACACTTAGTGCCA
Found at i:40656868 original size:6 final size:6
Alignment explanation
Indices: 40656859--40656900 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
40656849 GAAGTCTAAG
**
40656859 AAAATA AAAATA ATCATA AAAATA AAAAT- AAAAT- AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
40656901 TGGACTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:40658474 original size:3 final size:3
Alignment explanation
Indices: 40658461--40658511 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
40658451 ATAAAGAGAA
*
40658461 AAT AA- AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
40658506 AAT AAT
1 AAT AAT
40658512 GAGAAAAGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:40658478 original size:31 final size:31
Alignment explanation
Indices: 40658443--40658507 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
40658433 GTAAAACTAG
*
40658443 TAAAACTAATAA-AGAGAA-AATAAAATAATAA
1 TAAAAATAATAATA-AGAATAAT-AAATAATAA
*
40658474 TAAAAATAATAATAATAATAATAAATAATAA
1 TAAAAATAATAATAAGAATAATAAATAATAA
40658505 TAA
1 TAA
40658508 TAATGAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.25
Consensus pattern (31 bp):
TAAAAATAATAATAAGAATAATAAATAATAA
Found at i:40658918 original size:17 final size:17
Alignment explanation
Indices: 40658896--40658930 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
40658886 AGAAGAGAAT
40658896 AGGGAAAGGAGAAGGGA
1 AGGGAAAGGAGAAGGGA
*
40658913 AGGGAAAGGAGAGGGGA
1 AGGGAAAGGAGAAGGGA
40658930 A
1 A
40658931 AGGTCGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (17 bp):
AGGGAAAGGAGAAGGGA
Found at i:40661839 original size:14 final size:14
Alignment explanation
Indices: 40661820--40661846 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40661810 GAACCTCGTG
40661820 GTATAGCTATGGTA
1 GTATAGCTATGGTA
40661834 GTATAGCTATGGT
1 GTATAGCTATGGT
40661847 GAGTCGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (14 bp):
GTATAGCTATGGTA
Found at i:40665297 original size:15 final size:15
Alignment explanation
Indices: 40665277--40665308 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40665267 TATCACAAAT
40665277 TACTATGAATACAAC
1 TACTATGAATACAAC
40665292 TACTATGAATACAAC
1 TACTATGAATACAAC
40665307 TA
1 TA
40665309 GGCATTACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (15 bp):
TACTATGAATACAAC
Found at i:40670043 original size:47 final size:47
Alignment explanation
Indices: 40669987--40670089 Score: 136
Period size: 47 Copynumber: 2.2 Consensus size: 47
40669977 GTCGATGAGA
* * *
40669987 CACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTTCGATGAAG
1 CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTCCAATGAAG
* * *
40670034 TACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTCCAATGAAG
1 CACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTCCAATGAAG
40670081 CACTATGTG
1 CACTATGTG
40670090 CTTATCTCGG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 45 0.96
48 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (47 bp):
CACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTCCAATGAAG
Found at i:40676373 original size:47 final size:47
Alignment explanation
Indices: 40676314--40676575 Score: 234
Period size: 47 Copynumber: 5.6 Consensus size: 47
40676304 ATCCATAAGT
*
40676314 GAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
* * * * * * * * *
40676361 GAACTCGGACTCAACTCAACAAGTTCAGACG-TTCGCATCCA--TAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACATTTCA-C
**
40676407 GAACTTAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
* * * * * *
40676454 AAATTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--TTCA-C
40676500 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
* *
40676547 GAACTCGGACTCAACTTAACAAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
40676576 CGTTCGCATC
Statistics
Matches: 164, Mismatches: 37, Indels: 28
0.72 0.16 0.12
Matches are distributed among these distances:
42 2 0.01
43 4 0.02
44 1 0.01
45 5 0.03
46 57 0.35
47 83 0.51
48 5 0.03
49 1 0.01
50 4 0.02
51 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40676401 original size:93 final size:93
Alignment explanation
Indices: 40676267--40676625 Score: 558
Period size: 93 Copynumber: 3.9 Consensus size: 93
40676257 CGCCCATAAG
** * *
40676267 CGAACTCGGACTCAACTCAATGAGCTT-GGGCATTCGTATCCATAAGTGAACTCAGACTCAACTC
1 CGAACTCGGACTCAACTCAACAAG-TTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTC
40676331 AACGAGTTCGGATGCCTAGTTACATTTCA
65 AACGAGTTCGGATGCCTAGTTACATTTCA
* * *
40676360 CGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCATAAGTGAACTTAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
40676425 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* * * * *
40676453 CAAATTCGGACTCAACTCAACGAGTTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
40676518 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* * *
40676546 CGAACTCGGACTCAACTTAACAAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
40676611 ACGAGTTTGGATGCC
66 ACGAGTTCGGATGCC
40676626 CAAATATCCG
Statistics
Matches: 243, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
92 2 0.01
93 241 0.99
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:40676524 original size:46 final size:46
Alignment explanation
Indices: 40676260--40676617 Score: 231
Period size: 46 Copynumber: 7.7 Consensus size: 46
40676250 TGTAACCCGC
* * *
40676260 CCATAAGCGAACTCGGACTCAACTCAATGAGCTT-GGGCATTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGGCATTCGCAT
* *
40676306 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCAT
* * * * * * *
40676356 --TTCA-CGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
** *
40676399 CCATAAGTGAACTTAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCA-T
* * *
40676450 TCA-CA---AATTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
*
40676492 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCAT
* * * * * * *
40676542 --TTCA-CGAACTCGGACTCAACTTAACAAGTTCGGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
40676585 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
40676618 TGGATGCCCA
Statistics
Matches: 235, Mismatches: 47, Indels: 60
0.69 0.14 0.18
Matches are distributed among these distances:
42 9 0.04
43 10 0.04
44 3 0.01
45 7 0.03
46 103 0.44
47 75 0.32
48 6 0.03
49 3 0.01
50 10 0.04
51 9 0.04
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
Found at i:40676561 original size:186 final size:186
Alignment explanation
Indices: 40676272--40676625 Score: 620
Period size: 186 Copynumber: 1.9 Consensus size: 186
40676262 ATAAGCGAAC
* *
40676272 TCGGACTCAACTCAATGAGCTTGGGCATTCGTATCCATAAGTGAACTCAGACTCAACTCAACGAG
1 TCGGACTCAACTCAACGAGCTTGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAG
40676337 TTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCA
66 TTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCA
*
40676402 TAAGTGAACTTAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCACAAAT
131 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCACAAAT
*
40676458 TCGGACTCAACTCAACGAG-TTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA
1 TCGGACTCAACTCAACGAGCTT-GGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA
* *
40676522 GTTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTTAACAAGTTCGGACGTTCGCATCC
65 GTTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCC
* *
40676587 ATAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCC
130 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCC
40676626 CAAATATCCG
Statistics
Matches: 159, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
185 2 0.01
186 157 0.99
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (186 bp):
TCGGACTCAACTCAACGAGCTTGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAG
TTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACAAGTTCAGACGTTCGCATCCA
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCACAAAT
Found at i:40683368 original size:22 final size:22
Alignment explanation
Indices: 40683326--40683369 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40683316 TATGTGAAAC
**
40683326 CTCTTTTCTTTTTTTCTTTTTT
1 CTCTTTTCTTTTTTGATTTTTT
40683348 CTCTTTT-TTTTTTGATATTTTT
1 CTCTTTTCTTTTTTGAT-TTTTT
40683370 TAAAGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80
Consensus pattern (22 bp):
CTCTTTTCTTTTTTGATTTTTT
Found at i:40704455 original size:4 final size:4
Alignment explanation
Indices: 40704446--40704475 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
40704436 AAGGGAGCGT
40704446 GGCA GGCA GGCA GGCA GGCA GGCA GGCA GG
1 GGCA GGCA GGCA GGCA GGCA GGCA GGCA GG
40704476 TTCGTCACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.53, T:0.00
Consensus pattern (4 bp):
GGCA
Found at i:40705581 original size:16 final size:16
Alignment explanation
Indices: 40705560--40705591 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40705550 TAACAGATTA
*
40705560 AATTGACTAAAAAATT
1 AATTGAATAAAAAATT
40705576 AATTGAATAAAAAATT
1 AATTGAATAAAAAATT
40705592 GAACTAAATA
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:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
AATTGAATAAAAAATT
Found at i:40709492 original size:43 final size:43
Alignment explanation
Indices: 40709431--40709516 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
40709421 TCCATGTCGC
* *
40709431 AACACCATATCTGTAAAGTCATGACATTGAAACTGGACAATCA
1 AACACCACATCTGTAAAGTCAAGACATTGAAACTGGACAATCA
40709474 AACACCACATCTGTAAAGTCAAGACATTGAAACTGGACAATCA
1 AACACCACATCTGTAAAGTCAAGACATTGAAACTGGACAATCA
40709517 CTTGGGACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (43 bp):
AACACCACATCTGTAAAGTCAAGACATTGAAACTGGACAATCA
Found at i:40711456 original size:46 final size:45
Alignment explanation
Indices: 40711393--40711557 Score: 159
Period size: 46 Copynumber: 3.5 Consensus size: 45
40711383 CTAATTGTTT
* *
40711393 TGTAGGTTCAACCCTTACGAGTGATTAGACACTATTATCCGATTTG
1 TGTAGGTTCAACCCTTACG-GTGACTAGACACTATTATACGATTTG
* ** * **
40711439 TGTAGGTTCAACCCTTACGGTTGACCAGGGACTATGATTTATTATTTG
1 TGTAGGTTCAACCCTTACGG-TGACTAGACACTAT--TATACGATTTG
* * * * *
40711487 TGTAGGTTTAACCCTTATGGGTGACTAGACAATATTATTCGATTCG
1 TGTAGGTTCAACCCTTA-CGGTGACTAGACACTATTATACGATTTG
40711533 TGTAGGTTCAACCCTTACGTGTGAC
1 TGTAGGTTCAACCCTTACG-GTGAC
40711558 CAAGAATTAT
Statistics
Matches: 93, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
45 2 0.02
46 56 0.60
48 33 0.35
49 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (45 bp):
TGTAGGTTCAACCCTTACGGTGACTAGACACTATTATACGATTTG
Found at i:40711503 original size:48 final size:47
Alignment explanation
Indices: 40711434--40711594 Score: 150
Period size: 48 Copynumber: 3.4 Consensus size: 47
40711424 CTATTATCCG
40711434 ATTTGTGTAGGTTCAACCCTTACGGTTGACCAGGGACTATGATTTATT
1 ATTTGTGTAGGTTCAACCCTTACGGTTGACCA-GGACTATGATTTATT
* * * * *
40711482 ATTTGTGTAGGTTTAACCCTTATGGGTGACTA-GACAAT-A-TTATT
1 ATTTGTGTAGGTTCAACCCTTACGGTTGACCAGGACTATGATTTATT
* * * *
40711526 CGATTCGTGTAGGTTCAACCCTTAC-GTGTGACCAAGAATTATGATTCATT
1 --ATTTGTGTAGGTTCAACCCTTACGGT-TGACC-AGGACTATGATTTATT
* *
40711576 ATTTGTTTAGGTTTAACCC
1 ATTTGTGTAGGTTCAACCC
40711595 AAATGGGTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
44 5 0.06
45 2 0.02
46 29 0.33
47 1 0.01
48 47 0.53
49 1 0.01
50 4 0.04
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (47 bp):
ATTTGTGTAGGTTCAACCCTTACGGTTGACCAGGACTATGATTTATT
Found at i:40711558 original size:94 final size:94
Alignment explanation
Indices: 40711393--40711617 Score: 290
Period size: 94 Copynumber: 2.4 Consensus size: 94
40711383 CTAATTGTTT
* * * * *
40711393 TGTAGGTTCAACCCTTACGAGTGATTAGACACTATTATCCGATTTGTGTAGGTTCAACCCTTACG
1 TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCGTGTAGGTTCAACCCTTACG
* * *
40711458 GTTGACCAGGGACTATGATTTATTATTTG
66 GTTGACCAAGAACTATGATTCATTATTTG
* *
40711487 TGTAGGTTTAACCCTTATGGGTGACTAGACAATATTATTCGATTCGTGTAGGTTCAACCCTTAC-
1 TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCGTGTAGGTTCAACCCTTACG
*
40711551 GTGTGACCAAGAATTATGATTCATTATTTG
66 GT-TGACCAAGAACTATGATTCATTATTTG
* ** * *
40711581 TTTAGGTTTAACCCAAATGGGTAACCAGACACTATTA
1 TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTA
40711618 CTTTTACCTA
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
93 2 0.02
94 111 0.98
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (94 bp):
TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCGTGTAGGTTCAACCCTTACG
GTTGACCAAGAACTATGATTCATTATTTG
Found at i:40714136 original size:24 final size:24
Alignment explanation
Indices: 40714109--40714158 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
40714099 CGATGTACTA
* *
40714109 TCAGTCTAATCATTCACATTTATG
1 TCAGTCTAATCAATCACATCTATG
40714133 TCAGTCTAATCAATCACATCTATG
1 TCAGTCTAATCAATCACATCTATG
40714157 TC
1 TC
40714159 TTTATTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (24 bp):
TCAGTCTAATCAATCACATCTATG
Found at i:40721738 original size:43 final size:42
Alignment explanation
Indices: 40721691--40721788 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
40721681 CCCAGACGTT
40721691 GTCTTACATGTAATCAAATATCAATGCC-ACTATCCCAAACAGG
1 GTCTTACATGTAATCAAATAT-AATGCCGA-TATCCCAAACAGG
*** * * * *
40721734 GTCTTACACAAAATCAAATATGATGCCGATGTCCCAGACATG
1 GTCTTACATGTAATCAAATATAATGCCGATATCCCAAACAGG
40721776 GTCTTACATGTAA
1 GTCTTACATGTAA
40721789 ATCATAAGTT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 25 0.57
43 19 0.43
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (42 bp):
GTCTTACATGTAATCAAATATAATGCCGATATCCCAAACAGG
Found at i:40721812 original size:44 final size:43
Alignment explanation
Indices: 40721671--40721829 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
40721661 AACTCGTACA
* * * *
40721671 ATGCCAAAGTCCCAGACGTTGTCTTACATGT-AATCAAATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCAAATAT-G
* * * **
40721714 ATGCC-ACTATCCCAAACAGGGTCTTACA-CAAAATCAAATATG
1 ATGCCAAC-GTCCCAGACATGGTCTTACATGTAAATCAAATATG
* *
40721756 ATGCCGATGTCCCAGACATGGTCTTACATGTAAATCATAAGT-TG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCA-AA-TATG
*
40721800 ATGCCAACGTCCCAGACGTGGTCTTACATG
1 ATGCCAACGTCCCAGACATGGTCTTACATG
40721830 ATAACACATA
Statistics
Matches: 92, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 23 0.25
43 37 0.40
44 31 0.34
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCAAATATG
Found at i:40726602 original size:43 final size:42
Alignment explanation
Indices: 40726514--40726602 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 42
40726504 CATGCAATTA
* * *
40726514 GGGACATTGGCATCATATTTGATTTCATGTAAGACCCTGTTT
1 GGGACAGTGGCATCATATTTGATTACATGTAAGACCCTGTCT
40726556 GGGACAGTGGCATCAATATTTGATTACATGTAAGACCAC-GTCT
1 GGGACAGTGGCATC-ATATTTGATTACATGTAAGACC-CTGTCT
40726599 GGGA
1 GGGA
40726603 TGTTGGCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 13 0.31
43 28 0.67
44 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (42 bp):
GGGACAGTGGCATCATATTTGATTACATGTAAGACCCTGTCT
Found at i:40734198 original size:3 final size:3
Alignment explanation
Indices: 40734175--40734236 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
40734165 AGTAGCTTTT
* *
40734175 TTA TT- TTA ATA TTA ATA TTA TTA -TA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
40734219 TTA TT- TGTA TATA TTA TT
1 TTA TTA T-TA T-TA TTA TT
40734237 CATACTATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
2 5 0.10
3 37 0.76
4 7 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:40734236 original size:13 final size:13
Alignment explanation
Indices: 40734184--40734224 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
40734174 TTTATTTTAA
*
40734184 TATTAATATTATT
1 TATTATTATTATT
40734197 ATATTATTATTATT
1 -TATTATTATTATT
40734211 TATTATTATTATT
1 TATTATTATTATT
40734224 T
1 T
40734225 GTATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:40737770 original size:20 final size:20
Alignment explanation
Indices: 40737745--40737784 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40737735 CGTAAAATGA
*
40737745 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
40737765 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40737785 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:40737774 original size:34 final size:35
Alignment explanation
Indices: 40737730--40737796 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40737720 CAGTAAAATA
*
40737730 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
40737764 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
40737797 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:40737800 original size:14 final size:15
Alignment explanation
Indices: 40737724--40737800 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
40737714 GATTGCCAGT
* *
40737724 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
40737738 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
40737752 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
40737772 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
40737787 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
40737801 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:40747449 original size:76 final size:75
Alignment explanation
Indices: 40747295--40747481 Score: 191
Period size: 76 Copynumber: 2.5 Consensus size: 75
40747285 TTCTGTTTTC
** ** ** *
40747295 AAAAATTAACTCATATTATGAGAGGCAAGTTGAGCGTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCCCAAGACACGCTGAGGTATTTTCAATTTC
*
40747360 TGTCTTTCGAA
66 TGTCTATC-AA
* *
40747371 AAAAATTGACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTAATTTT-AATTT
1 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCCCAAGACACGCTGAGGT-ATTTTCAATTT
40747435 -T-TACTCATCAA
65 CTGT-CT-ATCAA
* * * *
40747446 AAAAATCAACTCATATTGCAAAAGATGAGTTGAGCC
1 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
40747482 TCGGGCCACA
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
74 1 0.01
75 36 0.39
76 51 0.55
77 5 0.05
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (75 bp):
AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCCCAAGACACGCTGAGGTATTTTCAATTTC
TGTCTATCAA
Found at i:40747663 original size:90 final size:89
Alignment explanation
Indices: 40747446--40747852 Score: 357
Period size: 88 Copynumber: 4.6 Consensus size: 89
40747436 TACTCATCAA
* * * * * *
40747446 AAAAATCAACTCATATTGCAAAAGATGAGTTGAGCCTCGGGC-CACATGCCGAAGTATTTTCAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGCTCACATGCTGAGGTATTTTC--A
*
40747510 ATT-TCG-TTTTTCAATTTCTGTTTCTTCC
63 ATTAT-GTTTTTTCAATTTCTGCTT-TT-C
*
40747538 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACATGTTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTATTTTCAATT
* *
40747603 GATGTTTTTTCAGTTTATGCTTTTC
66 -ATGTTTTTTCAATTTCTGCTTTTC
* * * * *
40747628 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCAGAGGTATTTTCAA-A
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTATTTTCAATT
* * *
40747692 ATCTGTTTTGCAAATTCTGC-TTTC
66 ATGT-TTTTTCAATTTCTGCTTTTC
** * * * *
40747716 AAAAATCAACTCATATTTTGAGAAGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTATTTTCAATT
* *
40747781 -TCTATTTTT-AATGTCTAG-TTTT-
66 ATGT-TTTTTCAATTTCT-GCTTTTC
* * ** *
40747803 AAAGAGTCAATTCATATTGCGAGAAATGAGTTGAG-CTCAGGATCACATGC
1 AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GCTCACATGC
40747853 CGAGTAAAGA
Statistics
Matches: 262, Mismatches: 43, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
87 11 0.04
88 106 0.40
89 11 0.04
90 63 0.24
91 5 0.02
92 66 0.25
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (89 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTATTTTCAATT
ATGTTTTTTCAATTTCTGCTTTTC
Found at i:40747774 original size:88 final size:88
Alignment explanation
Indices: 40747446--40747778 Score: 346
Period size: 92 Copynumber: 3.7 Consensus size: 88
40747436 TACTCATCAA
* * * * * * *
40747446 AAAAATCAACTCATATTGCAAAAGATGAGTTGAGCCTCGGGC-CACATGCCGAAGTATTTTCAAA
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-AGCTCACATGCTGAGGTATTTTCAAA
* *
40747510 ATTTCGTTTTTCAATTTCTGTTTCTTCC
65 ATAT-GTTTTTCAATTTCTG---CTTTC
* * *
40747538 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACATGTTGAGGTATTTTC-AAT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTATTTTCAAAA
* *
40747602 TGATGTTTTTTCAGTTTATGCTTTTC
66 T-ATG-TTTTTCAATTTCTGC-TTTC
* * *
40747628 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCAGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTATTTTCAAAA
* * *
40747693 TCTGTTTTGCAAATTCTGCTTTC
66 TATGTTTTTCAATTTCTGCTTTC
** * * * *
40747716 AAAAATCAACTCATATTTTGAGAAGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTCAA
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTATTTTCAA
40747779 TTTCTATTTT
Statistics
Matches: 204, Mismatches: 32, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
88 58 0.28
89 12 0.06
90 61 0.30
91 9 0.04
92 64 0.31
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (88 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTATTTTCAAAA
TATGTTTTTCAATTTCTGCTTTC
Found at i:40749006 original size:28 final size:28
Alignment explanation
Indices: 40748974--40749033 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
40748964 CATATTAATG
40748974 GGGTATAAGAAAAGTTTCATAACTTATA
1 GGGTATAAGAAAAGTTTCATAACTTATA
* * * *
40749002 GGGTATAGGAAGAGTTTTATAACTTATG
1 GGGTATAAGAAAAGTTTCATAACTTATA
40749030 GGGT
1 GGGT
40749034 TGATAATGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (28 bp):
GGGTATAAGAAAAGTTTCATAACTTATA
Found at i:40754424 original size:28 final size:28
Alignment explanation
Indices: 40754384--40754446 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
40754374 TCCTATATTA
40754384 ATGGGGTATAGGAAAAGTCACATAACTT
1 ATGGGGTATAGGAAAAGTCACATAACTT
* ***
40754412 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTCACATAACTT
40754440 ATGGGGT
1 ATGGGGT
40754447 TGATAATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTCACATAACTT
Found at i:40755247 original size:38 final size:38
Alignment explanation
Indices: 40755196--40755272 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
40755186 TATATGTGTA
40755196 AGAAAATTTTGTGTATTTTGTGATTTTGTGAATTAGGG
1 AGAAAATTTTGTGTATTTTGTGATTTTGTGAATTAGGG
40755234 AGAAAATTTTGTGTATTTTGTGATTTTGTGAATTAGGG
1 AGAAAATTTTGTGTATTTTGTGATTTTGTGAATTAGGG
40755272 A
1 A
40755273 CTAAAGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (38 bp):
AGAAAATTTTGTGTATTTTGTGATTTTGTGAATTAGGG
Found at i:40755788 original size:42 final size:42
Alignment explanation
Indices: 40755693--40755836 Score: 123
Period size: 42 Copynumber: 3.4 Consensus size: 42
40755683 CCACATTTGA
* * *
40755693 GACATTGGCATCG-ACTTATGATTTACGTGTAAGACCATGTCTGG
1 GACAGTGGCATCGTA-TT-TGATTT-CATGTAAGACCATGTCTAG
* * *
40755737 GACATTGGCATCGTATTTGATTTCATGTAAGCCCTTGTCTAG
1 GACAGTGGCATCGTATTTGATTTCATGTAAGACCATGTCTAG
* * * *
40755779 GATAGTGGCATCGATATTTGATTACATGTAAGATCA-CTCTAG
1 GACAGTGGCATCG-TATTTGATTTCATGTAAGACCATGTCTAG
*
40755821 GAC-GTTGGCATTGTAT
1 GACAG-TGGCATCGTAT
40755837 GAGCTTTCTG
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
41 4 0.05
42 40 0.48
43 24 0.29
44 15 0.18
45 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (42 bp):
GACAGTGGCATCGTATTTGATTTCATGTAAGACCATGTCTAG
Found at i:40755797 original size:43 final size:43
Alignment explanation
Indices: 40755693--40755811 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 43
40755683 CCACATTTGA
* * * *
40755693 GACATTGGCATCGACT-TATGATTTACGTGTAAGACCATGTCTGG
1 GACAGTGGCATCGA-TATTTGATTT-CATGTAAGACCATGTCTAG
* * *
40755737 GACATTGGCATCG-TATTTGATTTCATGTAAGCCCTTGTCTAG
1 GACAGTGGCATCGATATTTGATTTCATGTAAGACCATGTCTAG
* *
40755779 GATAGTGGCATCGATATTTGATTACATGTAAGA
1 GACAGTGGCATCGATATTTGATTTCATGTAAGA
40755812 TCACTCTAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 27 0.42
43 24 0.38
44 13 0.20
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
GACAGTGGCATCGATATTTGATTTCATGTAAGACCATGTCTAG
Found at i:40758203 original size:41 final size:40
Alignment explanation
Indices: 40758124--40758207 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
40758114 TAATATACAT
* *
40758124 ATATTAGTAATTATTATATATTTACTTATAATTTAAGTAA
1 ATATTAGTAATTATTATATATTTAATTATAATTGAAGTAA
*
40758164 ATATTATTATATTATTATATTATATTAATTA-AA-TGAAGTAA
1 ATATTAGTA-ATTATTATA-TAT-TTAATTATAATTGAAGTAA
40758205 ATA
1 ATA
40758208 AATTAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
40 8 0.21
41 19 0.50
42 5 0.13
43 6 0.16
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (40 bp):
ATATTAGTAATTATTATATATTTAATTATAATTGAAGTAA
Found at i:40758413 original size:29 final size:27
Alignment explanation
Indices: 40758354--40758425 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
40758344 AATAAACAAA
*
40758354 AGAAACAAAAGAAAAAAAAGGAAGAAC
1 AGAAAGAAAAGAAAAAAAAGGAAGAAC
* *
40758381 AGAATGAAAACGAAAAAAACAGGGGAGAA-
1 AGAAAGAAAA-GAAAAAAA-A-GGAAGAAC
*
40758410 AGAAAGAAAGGAAAAA
1 AGAAAGAAAAGAAAAA
40758426 GGGAAAGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 8 0.22
28 14 0.38
29 9 0.24
30 6 0.16
ACGTcount: A:0.69, C:0.06, G:0.24, T:0.01
Consensus pattern (27 bp):
AGAAAGAAAAGAAAAAAAAGGAAGAAC
Found at i:40759345 original size:40 final size:40
Alignment explanation
Indices: 40759301--40759411 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 40
40759291 TCGAGAATTA
* *
40759301 AAAGTGAATAGGATCTATTCTTGATTCACTA-AAAGAAACT
1 AAAGTGAATAGGATTTATTCCTGATTCACTAGAAAGAAA-T
* * *
40759341 AAAGTGAATAGGATTTATTCCTGATGCACTAGAAATATAT
1 AAAGTGAATAGGATTTATTCCTGATTCACTAGAAAGAAAT
* *
40759381 AAAGTGGATAGGATTTGTTCCTGATTCACTA
1 AAAGTGAATAGGATTTATTCCTGATTCACTA
40759412 TGGTAAGTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 57 0.92
41 5 0.08
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (40 bp):
AAAGTGAATAGGATTTATTCCTGATTCACTAGAAAGAAAT
Found at i:40780002 original size:40 final size:40
Alignment explanation
Indices: 40779937--40780112 Score: 205
Period size: 40 Copynumber: 4.4 Consensus size: 40
40779927 GATGATAACT
* * * *
40779937 GGGCCAAGTCCCGAAGGCATTTGTGCGAGTGACTATTTCC
1 GGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
40779977 GGGCTAAGTTCCGAAGGCATTTGTGCTAGTTACTATATCT
1 GGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40780017 GGGCTAAG-TCCTGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTTCC-GAAGGCATTTGTGCGAGTTACTATATCC
* * *
40780057 GGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTTCCGAAGGCATTTGTGCGAGTTA-CTATATCC
* *
40780097 -GGCTAAATTCTGAAGG
1 GGGCTAAGTTCCGAAGG
40780113 TACTTGGTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
39 17 0.15
40 97 0.84
41 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
GGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:40788034 original size:40 final size:40
Alignment explanation
Indices: 40787971--40788079 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
40787961 TATTCGGATG
* *
40787971 ATAACCGGGCCAAGTCCCAAAGGCATTTGTGCGAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
** *
40788011 ATTTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
40788051 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
40788080 AGTGAGTAGC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
Found at i:40788112 original size:39 final size:40
Alignment explanation
Indices: 40787975--40788112 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
40787965 CGGATGATAA
* * *
40787975 CCGGGCCAAGTCCCAAAGGCATTTGTGCGAGT-GACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAG-CTATAT
*
40788015 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATAT
* *
40788055 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATAT
* *
40788095 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40788113 TACTTGGTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 16 0.19
40 69 0.80
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATAT
Found at i:40798617 original size:33 final size:33
Alignment explanation
Indices: 40798577--40798653 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
40798567 TGGCCAGGTA
* * *
40798577 GGCTGTGT-GTGACACATAGGCTGGACTGATTTT
1 GGCTGTGTAG-GACACACAGGCTAGACTGATTTG
* *
40798610 GGTTGTGTAGGCCACACAGGCTAGACTGATTTG
1 GGCTGTGTAGGACACACAGGCTAGACTGATTTG
40798643 GGCTGTGTAGG
1 GGCTGTGTAGG
40798654 TCATACTAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 36 0.97
34 1 0.03
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (33 bp):
GGCTGTGTAGGACACACAGGCTAGACTGATTTG
Found at i:40798773 original size:17 final size:18
Alignment explanation
Indices: 40798747--40798782 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40798737 CAAATAGGGC
*
40798747 CGTGTGGGCCA-CACGGG
1 CGTGTAGGCCAGCACGGG
40798764 CGTGTAGGCCAGCACGGG
1 CGTGTAGGCCAGCACGGG
40798782 C
1 C
40798783 AGGCCACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.14, C:0.31, G:0.44, T:0.11
Consensus pattern (18 bp):
CGTGTAGGCCAGCACGGG
Found at i:40804258 original size:29 final size:28
Alignment explanation
Indices: 40804206--40804354 Score: 172
Period size: 29 Copynumber: 5.1 Consensus size: 28
40804196 GTATAGACGC
* *
40804206 CCATCGAATATGAAAAGGGTTGGTTTCA
1 CCATCAAATATGAAAAGGGATGGTTTCA
* **
40804234 TCTATCAAATATGAAAAGGGATGGTGACGA
1 -CCATCAAATATGAAAAGGGATGGTTTC-A
*
40804264 CCATCAAATAAGAAAAGGGATGGTTTCAA
1 CCATCAAATATGAAAAGGGATGGTTTC-A
* **
40804293 CCATCGAATATGAAAAGGGATGGTGACGA
1 CCATCAAATATGAAAAGGGATGGTTTC-A
40804322 CCATCAAATATGAAAAGGGATGGTTTCAA
1 CCATCAAATATGAAAAGGGATGGTTTC-A
40804351 CCAT
1 CCAT
40804355 TGATTAAAGA
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
29 99 0.99
30 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (28 bp):
CCATCAAATATGAAAAGGGATGGTTTCA
Found at i:40804282 original size:58 final size:58
Alignment explanation
Indices: 40804201--40804354 Score: 245
Period size: 58 Copynumber: 2.7 Consensus size: 58
40804191 ATGAAGTATA
* * * * *
40804201 GACGCCCATCGAATATGAAAAGGGTTGGTTTCATCTATCAAATATGAAAAGGGATGGT
1 GACGACCATCAAATATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGGATGGT
* *
40804259 GACGACCATCAAATAAGAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGGATGGT
1 GACGACCATCAAATATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGGATGGT
40804317 GACGACCATCAAATATGAAAAGGGATGGTTTCAACCAT
1 GACGACCATCAAATATGAAAAGGGATGGTTTCAACCAT
40804355 TGATTAAAGA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 88 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (58 bp):
GACGACCATCAAATATGAAAAGGGATGGTTTCAACCATCAAATATGAAAAGGGATGGT
Found at i:40804354 original size:87 final size:88
Alignment explanation
Indices: 40804206--40804385 Score: 229
Period size: 87 Copynumber: 2.1 Consensus size: 88
40804196 GTATAGACGC
* ** * *
40804206 CCATCGAATATGAAAAGGGTTGGTTTCATCTATCAAATATGAAAAGGGATGGTGACGACCATCAA
1 CCATCGAATATGAAAAGGGATGGTGACATCCATCAAATATGAAAAGGGATGGTGACAACCATCAA
* *
40804271 AT-AAGAAAAGGGATGGTTTCAA
66 ATAAAGAAAAGAGATAGTTTCAA
** **
40804293 CCATCGAATATGAAAAGGGATGGTGACGA-CCATCAAATATGAAAAGGGATGGTTTCAACCATTG
1 CCATCGAATATGAAAAGGGATGGTGAC-ATCCATCAAATATGAAAAGGGATGGTGACAACCATCA
*
40804357 ATTAAAGAAAAGAGATAGTTTCAA
65 AATAAAGAAAAGAGATAGTTTCAA
40804381 CCATC
1 CCATC
40804386 ATTTAGCACA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 55 0.70
88 24 0.30
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (88 bp):
CCATCGAATATGAAAAGGGATGGTGACATCCATCAAATATGAAAAGGGATGGTGACAACCATCAA
ATAAAGAAAAGAGATAGTTTCAA
Found at i:40810309 original size:27 final size:27
Alignment explanation
Indices: 40810255--40810314 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
40810245 AATATAATAT
*
40810255 AATTATAAAATAATTAAATTGTACTTA
1 AATTATAAAATAATTAAATTGTAATTA
*
40810282 AATTATAAACAT-ATTAAATTTTAATTA
1 AATTATAAA-ATAATTAAATTGTAATTA
*
40810309 ATTTAT
1 AATTAT
40810315 TAATAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTATAAAATAATTAAATTGTAATTA
Found at i:40814331 original size:9 final size:9
Alignment explanation
Indices: 40814289--40814329 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
40814279 GTTAATTTCA
40814289 GTTAAATTG
1 GTTAAATTG
40814298 GTTAAATTG
1 GTTAAATTG
40814307 GTTAAATTG
1 GTTAAATTG
*
40814316 ATT-AATTCG
1 GTTAAATT-G
40814325 GTTAA
1 GTTAA
40814330 TTTTTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 4 0.14
9 23 0.82
10 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (9 bp):
GTTAAATTG
Found at i:40814558 original size:21 final size:20
Alignment explanation
Indices: 40814527--40814572 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
40814517 TTTTTTCTTT
* * *
40814527 TAAAATTTTATGTCTTTTTA
1 TAAAATTTTATATATATTTA
40814547 TAAAACTTTTATATATATTTA
1 TAAAA-TTTTATATATATTTA
40814568 TAAAA
1 TAAAA
40814573 AGATTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
TAAAATTTTATATATATTTA
Found at i:40815594 original size:20 final size:21
Alignment explanation
Indices: 40815571--40815610 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40815561 AAATAACGAA
*
40815571 AAAATAGTA-AAAAAAACAAG
1 AAAATAATATAAAAAAACAAG
*
40815591 AAAATAATATAACAAAACAA
1 AAAATAATATAAAAAAACAA
40815611 CAATTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAATAATATAAAAAAACAAG
Found at i:40818687 original size:46 final size:48
Alignment explanation
Indices: 40818587--40818689 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 48
40818577 ATAGTAAAAC
* * * *
40818587 TATGGTCTTGCACATAGTCATATATCACACACTGAAGCCATAGCCCAGC
1 TATGGTCTTACACAGAGTCACATAT-ACACACTGAAGCCATAGCCCAGA
* * * *
40818636 CATGGTCTTACACAGA-TCACATAT-CACACTGATGCCATATCCCATA
1 TATGGTCTTACACAGAGTCACATATACACACTGAAGCCATAGCCCAGA
40818682 TATGGTCT
1 TATGGTCT
40818690 ATATTGAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
46 25 0.56
48 7 0.16
49 13 0.29
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (48 bp):
TATGGTCTTACACAGAGTCACATATACACACTGAAGCCATAGCCCAGA
Found at i:40819710 original size:22 final size:24
Alignment explanation
Indices: 40819683--40819811 Score: 128
Period size: 25 Copynumber: 5.4 Consensus size: 24
40819673 CACTAATGAA
40819683 CAGAGAGCACTGAAGTGCT-ATA-
1 CAGAGAGCACTGAAGTGCTAATAT
*
40819705 CAGAGAGCAC-AAATGTGCT-A-AT
1 CAGAGAGCACTGAA-GTGCTAATAT
40819727 CAGAGAGCACTGACA-TGCTAAATAT
1 CAGAGAGCACTGA-AGTGCT-AATAT
*
40819752 CAGATAGCACTGACA-TGCTAAATAT
1 CAGAGAGCACTGA-AGTGCT-AATAT
*
40819777 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGAAGTGCT-AATAT
40819802 CAGAGAGCAC
1 CAGAGAGCAC
40819812 AAATGTTATA
Statistics
Matches: 94, Mismatches: 5, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.03
22 30 0.32
23 1 0.01
24 2 0.02
25 58 0.62
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (24 bp):
CAGAGAGCACTGAAGTGCTAATAT
Found at i:40819760 original size:25 final size:25
Alignment explanation
Indices: 40819725--40819811 Score: 156
Period size: 25 Copynumber: 3.5 Consensus size: 25
40819715 AAATGTGCTA
40819725 ATCAGAGAGCACTGACATGCTAAAT
1 ATCAGAGAGCACTGACATGCTAAAT
*
40819750 ATCAGATAGCACTGACATGCTAAAT
1 ATCAGAGAGCACTGACATGCTAAAT
*
40819775 ATCAGAGAGCACTGACGTGCTAAAT
1 ATCAGAGAGCACTGACATGCTAAAT
40819800 ATCAGAGAGCAC
1 ATCAGAGAGCAC
40819812 AAATGTTATA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (25 bp):
ATCAGAGAGCACTGACATGCTAAAT
Found at i:40832531 original size:11 final size:11
Alignment explanation
Indices: 40832515--40832547 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
40832505 CTTAGAACAG
40832515 ATCCCTTAGTA
1 ATCCCTTAGTA
40832526 ATCCCTTAGTA
1 ATCCCTTAGTA
40832537 AGT-CCTTAGTA
1 A-TCCCTTAGTA
40832548 CTCTTGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.95
12 1 0.05
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCCCTTAGTA
Found at i:40834273 original size:46 final size:46
Alignment explanation
Indices: 40834220--40834340 Score: 172
Period size: 46 Copynumber: 2.6 Consensus size: 46
40834210 TTTTGCATGA
* *
40834220 TTCCATAGTGTCTTTCAACTATAGTCTTATTCATTTCCCGTCATAT
1 TTCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCCATCATAT
* *
40834266 TTCCATAGTGTCTTTCAAAC-ATGGTCTTATTCATTTCCTATCATGT
1 TTCCATAGTGTCTTTC-AACTATGGTCTTATTCATTTCCCATCATAT
* *
40834312 TGCCGTAGTGTCTTTCAACTATGGTCTTA
1 TTCCATAGTGTCTTTCAACTATGGTCTTA
40834341 CACGTTTAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
45 3 0.04
46 61 0.91
47 3 0.04
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (46 bp):
TTCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCCATCATAT
Found at i:40834372 original size:45 final size:45
Alignment explanation
Indices: 40834275--40834525 Score: 152
Period size: 45 Copynumber: 5.6 Consensus size: 45
40834265 TTTCCATAGT
* ** * * **
40834275 GTCTTTCAAAC-ATGGTCTTATTCATTTCCTATCATGTTGCCGTAGT
1 GTCTTTC-AACTATGGTCTTACTCATTT-AAATCATGATGCCATAAC
* * *
40834321 GTCTTTCAACTATGGTCTTACACGTTTAAGTCATGATGCCATAAC
1 GTCTTTCAACTATGGTCTTACTCATTTAAATCATGATGCCATAAC
* * * **
40834366 GTCTTTCAGCTATCGTCTTACTTATTTAAATCATGATATCAT-AC
1 GTCTTTCAACTATGGTCTTACTCATTTAAATCATGATGCCATAAC
** * ** *
40834410 TGTCTTT--TTTATGGTCTTACTCATCTAAATTGTGATGTCATAAC
1 -GTCTTTCAACTATGGTCTTACTCATTTAAATCATGATGCCATAAC
* ** *** * **
40834454 GTCTTTCAATTATGGTCTTACTTGTTTTTGGT-ATGGTGCCATAGT
1 GTCTTTCAACTATGGTCTTAC-TCATTTAAATCATGATGCCATAAC
*
40834499 GTCTTTCAACTATGGTCTTATTCATTT
1 GTCTTTCAACTATGGTCTTACTCATTT
40834526 TCCGGTATAG
Statistics
Matches: 157, Mismatches: 42, Indels: 14
0.74 0.20 0.07
Matches are distributed among these distances:
43 32 0.20
44 8 0.05
45 93 0.59
46 24 0.15
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.45
Consensus pattern (45 bp):
GTCTTTCAACTATGGTCTTACTCATTTAAATCATGATGCCATAAC
Found at i:40834548 original size:46 final size:45
Alignment explanation
Indices: 40834454--40834571 Score: 166
Period size: 46 Copynumber: 2.6 Consensus size: 45
40834444 ATGTCATAAC
* * * *
40834454 GTCTTTCAATTATGGTCTTACTT-GTTTTTGGTATGGTGCCATAGT
1 GTCTTTCAACTATGGTCTTA-TTCATTTTCGGTATAGTGCCATAGT
40834499 GTCTTTCAACTATGGTCTTATTCATTTTCCGGTATAGTGCCATAGT
1 GTCTTTCAACTATGGTCTTATTCATTTT-CGGTATAGTGCCATAGT
*
40834545 GTCTTTCAACTATGGTCTTAATCATTT
1 GTCTTTCAACTATGGTCTTATTCATTT
40834572 CCTTAGTGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 2 0.03
45 23 0.35
46 41 0.62
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.47
Consensus pattern (45 bp):
GTCTTTCAACTATGGTCTTATTCATTTTCGGTATAGTGCCATAGT
Found at i:40834579 original size:34 final size:34
Alignment explanation
Indices: 40834541--40834609 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
40834531 TATAGTGCCA
40834541 TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
1 TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
40834575 TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
1 TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
40834609 T
1 T
40834610 CAAGCCAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (34 bp):
TAGTGTCTTTCAACTATGGTCTTAATCATTTCCT
Found at i:40839713 original size:30 final size:30
Alignment explanation
Indices: 40839672--40839737 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
40839662 TTTTTGGCTT
40839672 AGGGACTAAATTGAATAAAAGTAAAATTTTA
1 AGGG-CTAAATTGAATAAAAGTAAAATTTTA
40839703 AGGGCTAAATTGAATAAAAGTAAAATTTTA
1 AGGGCTAAATTGAATAAAAGTAAAATTTTA
*
40839733 GGGGC
1 AGGGC
40839738 AATTTTGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (30 bp):
AGGGCTAAATTGAATAAAAGTAAAATTTTA
Found at i:40840263 original size:25 final size:25
Alignment explanation
Indices: 40840224--40840316 Score: 98
Period size: 25 Copynumber: 3.7 Consensus size: 25
40840214 GTTTCAACCC
* *
40840224 ACAGCTCGTGTGAGCATATCGATTT
1 ACAGCTCATATGAGCATATCGATTT
* * * *
40840249 ATAGCTCATAAGAGCATATCAATCT
1 ACAGCTCATATGAGCATATCGATTT
*
40840274 ACAGCTCA-AGTGAGCATATCGATTC
1 ACAGCTCATA-TGAGCATATCGATTT
*
40840299 ACAGCTTATATGAGCATA
1 ACAGCTCATATGAGCATA
40840317 CATGTACTGG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 1 0.02
25 52 0.96
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (25 bp):
ACAGCTCATATGAGCATATCGATTT
Found at i:40841436 original size:20 final size:20
Alignment explanation
Indices: 40841403--40841441 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40841393 GCCATATGGT
40841403 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
40841423 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
40841442 TTTCAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:40843506 original size:25 final size:25
Alignment explanation
Indices: 40843478--40843543 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 25
40843468 CGATATATGT
*
40843478 CTCTTTAGAGCTTCCTAATTAAAGG
1 CTCTTTAGAGCTTCCCAATTAAAGG
* *
40843503 CTCTTCTATAAGCTTCCCAATTAATGG
1 CTCTT-TA-GAGCTTCCCAATTAAAGG
* *
40843530 CTCTCTGGAGCTTC
1 CTCTTTAGAGCTTC
40843544 TCGATATTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 11 0.33
26 3 0.09
27 19 0.58
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (25 bp):
CTCTTTAGAGCTTCCCAATTAAAGG
Found at i:40843556 original size:24 final size:24
Alignment explanation
Indices: 40843527--40843615 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
40843517 TCCCAATTAA
40843527 TGGCTCTCTGGAGCTTCTCGATAT
1 TGGCTCTCTGGAGCTTCTCGATAT
* * *
40843551 TGGCTCGCTTGAACTTCTCGATAT
1 TGGCTCTCTGGAGCTTCTCGATAT
* * * *
40843575 TGGCTCATATGG-GCTTCCCGTTAA
1 TGGCTC-TCTGGAGCTTCTCGATAT
*
40843599 TGGCTCTCCGGAGCTTC
1 TGGCTCTCTGGAGCTTC
40843616 CTGTTACATA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 3 0.06
24 46 0.90
25 2 0.04
ACGTcount: A:0.13, C:0.27, G:0.25, T:0.35
Consensus pattern (24 bp):
TGGCTCTCTGGAGCTTCTCGATAT
Found at i:40851252 original size:25 final size:25
Alignment explanation
Indices: 40851220--40851292 Score: 121
Period size: 25 Copynumber: 3.0 Consensus size: 25
40851210 TTAACTCTCA
*
40851220 TGAGCTTCCCATTATATAGTTCTTT
1 TGAGCTTCCCATTATATAGTTCTTG
40851245 TGAGCTTCCCATTATATAGTTCTTG
1 TGAGCTTCCCATTATATAGTTCTTG
*
40851270 TGAGCTTCCCATTA-ATAGCTCTT
1 TGAGCTTCCCATTATATAGTTCTT
40851293 CGAAGCATCT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 8 0.17
25 38 0.83
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (25 bp):
TGAGCTTCCCATTATATAGTTCTTG
Found at i:40851395 original size:25 final size:26
Alignment explanation
Indices: 40851367--40851458 Score: 84
Period size: 27 Copynumber: 3.7 Consensus size: 26
40851357 CACAAAATAT
*
40851367 GGCTCTTC-GGAGCTTCCCAATTAAA
1 GGCTCTTCAAGAGCTTCCCAATTAAA
* *
40851392 GGCTCTTTCATGAGCTTCCCGATTAAA
1 GGCTC-TTCAAGAGCTTCCCAATTAAA
* * *
40851419 GGCT-TTCTAGAGCTT-TCAATTAAT
1 GGCTCTTCAAGAGCTTCCCAATTAAA
*
40851443 GGCTCTCCAAG-GCTTC
1 GGCTCTTCAAGAGCTTC
40851459 TCGTTACGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
24 14 0.26
25 18 0.33
26 3 0.06
27 19 0.35
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (26 bp):
GGCTCTTCAAGAGCTTCCCAATTAAA
Found at i:40854820 original size:20 final size:21
Alignment explanation
Indices: 40854795--40854837 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
40854785 ATTTTAGATA
*
40854795 TTTATGTATTTTTGT-TTTAT
1 TTTATGTATTTATGTATTTAT
40854815 TTTATGTATTTATGTATTTAT
1 TTTATGTATTTATGTATTTAT
40854836 TT
1 TT
40854838 ATCTTATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTATGTATTTATGTATTTAT
Found at i:40855930 original size:12 final size:12
Alignment explanation
Indices: 40855913--40855938 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40855903 GCATTTCTAA
40855913 TTTCGTACTTTG
1 TTTCGTACTTTG
40855925 TTTCGTACTTTG
1 TTTCGTACTTTG
40855937 TT
1 TT
40855939 ATATCTAATC
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:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTCGTACTTTG
Found at i:40857569 original size:43 final size:44
Alignment explanation
Indices: 40857518--40857708 Score: 205
Period size: 43 Copynumber: 4.4 Consensus size: 44
40857508 TATTGAGATG
*
40857518 TGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
* * * **
40857562 TG-TTACATGTAAGACCATGTTTGAGACATTGGAAAGGTATTGA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
*
40857605 -GATTACATGTAAGACCATGTCTGGGACATTGGCATCG--TTAA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
* * * * *
40857646 TCGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATCG-ATATG-
1 T-GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TGA
*
40857690 TGATAACATGTAAGACCAT
1 TGATTACATGTAAGACCAT
40857709 ATTTGGCATA
Statistics
Matches: 120, Mismatches: 22, Indels: 11
0.78 0.14 0.07
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 111 0.93
44 4 0.03
45 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (44 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
Found at i:40861161 original size:37 final size:37
Alignment explanation
Indices: 40861111--40861223 Score: 199
Period size: 37 Copynumber: 3.1 Consensus size: 37
40861101 TTTTAGCTCA
* *
40861111 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
40861148 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
40861185 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
40861222 GA
1 GA
40861224 ATATATTTCC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.22
Consensus pattern (37 bp):
GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:40861489 original size:98 final size:98
Alignment explanation
Indices: 40861370--40861580 Score: 386
Period size: 98 Copynumber: 2.2 Consensus size: 98
40861360 GCACATCGCC
* *
40861370 TACATATTTCACACTAGCCATTCGGCTTTCCCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
40861435 GACCATTCGGCTGTACCACATATGCATATCTCA
66 GACCATTCGGCTGTACCACATATGCATATCTCA
*
40861468 TACATATTTCACATTATCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
*
40861533 GACCATTCGGCTTTACCACATATGCATATCTCA
66 GACCATTCGGCTGTACCACATATGCATATCTCA
40861566 TACATATTTCACATT
1 TACATATTTCACATT
40861581 CACATTCATC
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 109 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (98 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
GACCATTCGGCTGTACCACATATGCATATCTCA
Found at i:40861494 original size:48 final size:49
Alignment explanation
Indices: 40861370--40861580 Score: 295
Period size: 50 Copynumber: 4.3 Consensus size: 49
40861360 GCACATCGCC
* *
40861370 TACATATTTCACACT-AGCCATTCGGCTTTCCCACATATACATATCTCATA
1 TACATATTTCACATTGA-CCATTCGGCTTTACCACATATACATATCTCA-A
* * *
40861420 TATATATTTCACATTGACCATTCGGCTGTACCACATATGCATATCTC-A
1 TACATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCAA
40861468 TACATATTTCACATT-ATCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTGA-CCATTCGGCTTTACCACATATACATATCTCA-A
* *
40861518 TATATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCAA
40861566 TACATATTTCACATT
1 TACATATTTCACATT
40861581 CACATTCATC
Statistics
Matches: 145, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
47 1 0.01
48 58 0.40
50 84 0.58
51 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (49 bp):
TACATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCAA
Found at i:40862265 original size:21 final size:20
Alignment explanation
Indices: 40862239--40862279 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40862229 AAATTTTATC
40862239 TTATAACCATTTTTCTAAAAA
1 TTATAACCA-TTTTCTAAAAA
**
40862260 TTATAATGATTTTCTAAAAA
1 TTATAACCATTTTCTAAAAA
40862280 CAGAACAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (20 bp):
TTATAACCATTTTCTAAAAA
Found at i:40863940 original size:11 final size:11
Alignment explanation
Indices: 40863924--40863948 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40863914 AGGATGAAGC
40863924 CTTTTTTTTTT
1 CTTTTTTTTTT
40863935 CTTTTTTTTTT
1 CTTTTTTTTTT
40863946 CTT
1 CTT
40863949 CTAGGTACGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:40882321 original size:28 final size:27
Alignment explanation
Indices: 40882273--40882378 Score: 128
Period size: 27 Copynumber: 3.9 Consensus size: 27
40882263 CTGCCAGAAT
*
40882273 AGATAATGTGACAGA-CTCACCAGATAC
1 AGATAATGTGGCAGAGC-CACCAGATAC
40882300 AGATAATCGTGGCAGAGCCACCAGA-AC
1 AGATAAT-GTGGCAGAGCCACCAGATAC
40882327 AGATATATGTGGCAGAGCCACCAGAT-C
1 AGATA-ATGTGGCAGAGCCACCAGATAC
*
40882354 AGATAATTTGTGGCATAGCCACCAG
1 AGATAA--TGTGGCAGAGCCACCAG
40882379 GACGCTTCCT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
26 1 0.01
27 37 0.52
28 32 0.45
29 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
AGATAATGTGGCAGAGCCACCAGATAC
Found at i:40882350 original size:55 final size:54
Alignment explanation
Indices: 40882266--40882378 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 54
40882256 AGCATGGCTG
*
40882266 CCAGAATAGATAATGTGACAGACTCACCAGATACAGATAA-TCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGACTCACCAGAT-CAGATAATTCGTGGCAGAGCCA
* * *
40882320 CCAGAACAGATATATGTGGCAGAGC-CACCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGA-CTCACCAGATCAGATAATTCGTGGCAGAGCCA
40882375 CCAG
1 CCAG
40882379 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
54 18 0.35
55 33 0.63
56 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGACTCACCAGATCAGATAATTCGTGGCAGAGCCA
Done.