Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 17 of 66
Found at i:5822637 original size:21 final size:20
Alignment explanation
Indices: 5822607--5822648 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5822597 AATTGTTGTT
*
5822607 AAAAAATAATATATATATAA
1 AAAAAATAATAAATATATAA
*
5822627 AAAATAATAATAAATATGTAA
1 AAAA-AATAATAAATATATAA
5822648 A
1 A
5822649 CAAGGCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAAATAATAAATATATAA
Found at i:5824008 original size:14 final size:15
Alignment explanation
Indices: 5823983--5824011 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5823973 ATTTTCCAAC
5823983 AAAATGTTCCGTTGG
1 AAAATGTTCCGTTGG
5823998 AAAAT-TTCCGTTGG
1 AAAATGTTCCGTTGG
5824012 TAATAGATTT
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:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (15 bp):
AAAATGTTCCGTTGG
Found at i:5824546 original size:12 final size:13
Alignment explanation
Indices: 5824516--5824540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5824506 TATCCGTTGG
5824516 AAATTTCCAACGA
1 AAATTTCCAACGA
5824529 AAATTTCCAACG
1 AAATTTCCAACG
5824541 GAATTTTTTC
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:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
AAATTTCCAACGA
Found at i:5826946 original size:25 final size:25
Alignment explanation
Indices: 5826917--5826980 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
5826907 TTAATGATGT
5826917 ATTTTATCATA-TTATATGATAATAA
1 ATTTTATCATATTTAT-TGATAATAA
* *
5826942 ATTTTA-CATATGTTATTTATATTAA
1 ATTTTATCATAT-TTATTGATAATAA
*
5826967 ATTTTATTATATTT
1 ATTTTATCATATTT
5826981 GATGTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 4 0.12
25 21 0.64
26 8 0.24
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (25 bp):
ATTTTATCATATTTATTGATAATAA
Found at i:5828499 original size:47 final size:48
Alignment explanation
Indices: 5828428--5828524 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 48
5828418 CATAAAAAAG
*
5828428 TATGATAAGATTTTTATTGGTTAGTAT-ATATTTTTATAATATATGTA
1 TATGATAAGATTTTTATTGATTAGTATAATATTTTTATAATATATGTA
* * *
5828475 TATGATAAGATTTTTATTGATTAGTATAATTTTTTTATCATGTATGTA
1 TATGATAAGATTTTTATTGATTAGTATAATATTTTTATAATATATGTA
5828523 TA
1 TA
5828525 AAAATGTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 26 0.58
48 19 0.42
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (48 bp):
TATGATAAGATTTTTATTGATTAGTATAATATTTTTATAATATATGTA
Found at i:5828501 original size:26 final size:26
Alignment explanation
Indices: 5828428--5828502 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 26
5828418 CATAAAAAAG
*
5828428 TATGATAAGATTTTTATTGGTTAG--
1 TATGATAAGATTTTTATTGATTAGTA
*
5828452 TAT-AT---ATTTTTA-TAATATATGTA
1 TATGATAAGATTTTTATTGAT-TA-GTA
5828475 TATGATAAGATTTTTATTGATTAGTA
1 TATGATAAGATTTTTATTGATTAGTA
5828501 TA
1 TA
5828503 ATTTTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
19 2 0.05
20 9 0.23
21 1 0.03
23 5 0.13
24 5 0.13
26 5 0.13
27 9 0.23
28 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (26 bp):
TATGATAAGATTTTTATTGATTAGTA
Found at i:5842300 original size:43 final size:43
Alignment explanation
Indices: 5842239--5842325 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
5842229 TTAAGTACAC
*
5842239 GAAATGGCTTCAACAATAGACATTTTTAGGCAATCTAAGCTTT
1 GAAATGGCTTCAACAATAGACATCTTTAGGCAATCTAAGCTTT
*
5842282 GAAATGGCTTCAACAATAGACATCTTTGGGCAATCTAAGCTTT
1 GAAATGGCTTCAACAATAGACATCTTTAGGCAATCTAAGCTTT
5842325 G
1 G
5842326 TCTTCCCCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (43 bp):
GAAATGGCTTCAACAATAGACATCTTTAGGCAATCTAAGCTTT
Found at i:5843283 original size:2 final size:2
Alignment explanation
Indices: 5843276--5843307 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5843266 AGTTTAAAAC
5843276 AT AT AT 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 AT AT AT
5843308 GCTAGAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5849839 original size:29 final size:29
Alignment explanation
Indices: 5849797--5849874 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
5849787 TCCTCCCAAA
5849797 ATTTTAAAAATTTATAATTTTATT-ATTTT
1 ATTTT-AAAATTTATAATTTTATTAATTTT
* *
5849826 ATTTTAAATATTTAT-CTTTTTTTAATTTT
1 ATTTTAAA-ATTTATAATTTTATTAATTTT
5849855 -TTTTAAAATTTTATAATTTT
1 ATTTTAAAA-TTTATAATTTT
5849875 TATTTTCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.02
28 21 0.50
29 20 0.48
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (29 bp):
ATTTTAAAATTTATAATTTTATTAATTTT
Found at i:5849875 original size:28 final size:28
Alignment explanation
Indices: 5849797--5849885 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
5849787 TCCTCCCAAA
*
5849797 ATTTTAAAAATTTATAATTTTATTATTTT
1 ATTTTAAAATTTTATAATTTT-TTATTTT
**
5849826 ATTTT-AAATATTTATCTTTTTTTAATTTT
1 ATTTTAAAAT-TTTATAATTTTTT-ATTTT
5849855 -TTTTAAAATTTTATAA-TTTTTATTTT
1 ATTTTAAAATTTTATAATTTTTTATTTT
5849881 CATTT
1 -ATTT
5849886 CTTCAAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
26 5 0.10
27 5 0.10
28 17 0.34
29 23 0.46
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
ATTTTAAAATTTTATAATTTTTTATTTT
Found at i:5849885 original size:20 final size:19
Alignment explanation
Indices: 5849807--5849885 Score: 58
Period size: 20 Copynumber: 4.1 Consensus size: 19
5849797 ATTTTAAAAA
5849807 TTTATAATTTTATTATTTTAT
1 TTTATAA-TTT-TTATTTTAT
* *
5849828 TTTA-AATATTTATCTT-T
1 TTTATAATTTTTATTTTAT
*
5849845 TTT-TAATTTTT-TTTAAAAT
1 TTTATAATTTTTATTT--TAT
5849864 TTTATAATTTTTATTTTCAT
1 TTTATAATTTTTATTTT-AT
5849884 TT
1 TT
5849886 CTTCAAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
16 2 0.04
17 10 0.22
18 6 0.13
19 6 0.13
20 14 0.31
21 7 0.16
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATAATTTTTATTTTAT
Found at i:5857404 original size:14 final size:14
Alignment explanation
Indices: 5857385--5857411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5857375 TTGGTTTTAA
5857385 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
5857399 TTTTAGTTAATTA
1 TTTTAGTTAATTA
5857412 ATAAATTTTG
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:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:5861910 original size:13 final size:13
Alignment explanation
Indices: 5861892--5861916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5861882 TTTCAGAAAA
5861892 TTTATAAAATCAT
1 TTTATAAAATCAT
5861905 TTTATAAAATCA
1 TTTATAAAATCA
5861917 GAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5865906 original size:15 final size:15
Alignment explanation
Indices: 5865886--5865968 Score: 62
Period size: 18 Copynumber: 5.3 Consensus size: 15
5865876 ACCTTACTCG
5865886 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
*
5865901 ATTTTATTTTATTTC
1 ATTTTATTTTATTTT
*
5865916 A-TTT-TTTTACTTT
1 ATTTTATTTTATTTT
* *
5865929 CTTATGATTATTATTATT
1 ATT-TTATT-TTATT-TT
5865947 ATTATTATTATTATTATT
1 ATT-TTATT-TTATT-TT
5865965 ATTT
1 ATTT
5865969 AATCTATTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.13
14 4 0.07
15 16 0.29
16 2 0.04
17 5 0.09
18 21 0.38
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (15 bp):
ATTTTATTTTATTTT
Found at i:5865941 original size:3 final size:3
Alignment explanation
Indices: 5865930--5865967 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5865920 TTTTACTTTC
*
5865930 TTA TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5865968 TAATCTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5868344 original size:22 final size:22
Alignment explanation
Indices: 5868304--5868365 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
5868294 GAGGGAGTAG
*
5868304 TTTAGAATTTTG-TTAGTTTATT-
1 TTTAGTATTTTGCTT-GTTT-TTA
5868326 TTTAGTATTTTGCTTGTTTTTA
1 TTTAGTATTTTGCTTGTTTTTA
*
5868348 TTTA-TA-TTTGCATGTTTT
1 TTTAGTATTTTGCTTGTTTT
5868366 GTTGTGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 11 0.31
21 4 0.11
22 19 0.53
23 2 0.06
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.66
Consensus pattern (22 bp):
TTTAGTATTTTGCTTGTTTTTA
Found at i:5870806 original size:14 final size:14
Alignment explanation
Indices: 5870787--5870813 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5870777 TTGGTTTTAA
5870787 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
5870801 TTTTAGTTAATTA
1 TTTTAGTTAATTA
5870814 ATAAATTTTG
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:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:5895412 original size:52 final size:51
Alignment explanation
Indices: 5895348--5895452 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 51
5895338 AAATTATTTC
5895348 TCTAGCTTATTTTTGCTATATTACAATATAACCTAACTAAAATCACTTAAT
1 TCTAGCTTATTTTTGCTATATTACAATATAACCTAACTAAAATCACTTAAT
* *
5895399 TCNTAGCTTATTTTTGCTATATTTCAATATAACTTAACTAAAATCACTTAAT
1 TC-TAGCTTATTTTTGCTATATTACAATATAACCTAACTAAAATCACTTAAT
5895451 TC
1 TC
5895453 AATTAAAATC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 2 0.04
52 49 0.96
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.43
Consensus pattern (51 bp):
TCTAGCTTATTTTTGCTATATTACAATATAACCTAACTAAAATCACTTAAT
Found at i:5903476 original size:40 final size:38
Alignment explanation
Indices: 5903372--5903477 Score: 106
Period size: 40 Copynumber: 2.7 Consensus size: 38
5903362 ATAGTGCCCG
* * *
5903372 TGTGCACGATGTGGAGGGATATACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATATACATGATGGCACGGAT
* * ** *
5903410 TGTGCACAATGTAGGGGGATGCACATGATGGTGC-CGGCT
1 TGTGCACGATGTGGGGGGATATACATGAT-G-GCACGGAT
5903449 ATGTGCACGATGTGGGGGGATATACATGA
1 -TGTGCACGATGTGGGGGGATATACATGA
5903478 GCCGGGTGTG
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
38 23 0.43
39 4 0.08
40 26 0.49
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATATACATGATGGCACGGAT
Found at i:5903897 original size:39 final size:39
Alignment explanation
Indices: 5903828--5903924 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 39
5903818 AGTGAAAAAG
* * *
5903828 GAATCTCGCTACAGCGAAAAACTCTTTGTTTCATCAGTT-
1 GAATTTCGCTGCAGCGAGAAACTCTTTGTTT-ATCAGTTA
* **
5903867 GAATTTCGCTGCAGCGAGAAAC-CTTCTGTTTTTGGGTTA
1 GAATTTCGCTGCAGCGAGAAACTCTT-TGTTTATCAGTTA
*
5903906 CAATTTCGCTGCAGCGAGA
1 GAATTTCGCTGCAGCGAGA
5903925 TTCAAAAAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
38 7 0.14
39 42 0.86
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (39 bp):
GAATTTCGCTGCAGCGAGAAACTCTTTGTTTATCAGTTA
Found at i:5904142 original size:22 final size:22
Alignment explanation
Indices: 5904117--5904159 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5904107 AATCCCAATA
5904117 TCGCTGCAACGAAAATTCATTT
1 TCGCTGCAACGAAAATTCATTT
* *
5904139 TCGCTGCAGCGAAGATTCATT
1 TCGCTGCAACGAAAATTCATT
5904160 GTCATATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (22 bp):
TCGCTGCAACGAAAATTCATTT
Found at i:5929216 original size:31 final size:31
Alignment explanation
Indices: 5929146--5929296 Score: 148
Period size: 31 Copynumber: 4.9 Consensus size: 31
5929136 CCTTTAACAT
* *
5929146 ACTACC-TTTTCTTATAGAGGTATAACCTTTC
1 ACTACCTTTTTC-TATGGAGGTATAACCTTAC
* *
5929177 TCTA-CTTTTTCTATGGAGGTATAAGCTTAC
1 ACTACCTTTTTCTATGGAGGTATAACCTTAC
* ***
5929207 ACTCCCTTTTGAAATGGAGGTATAACCTTAC
1 ACTACCTTTTTCTATGGAGGTATAACCTTAC
* *
5929238 ACTACCTTTTAC-AGTGGAGGTATAACCTTTC
1 ACTACCTTTTTCTA-TGGAGGTATAACCTTAC
**
5929269 TTTACC-TTTTCTATGGAGGTATAACCTT
1 ACTACCTTTTTCTATGGAGGTATAACCTT
5929297 TCAATAGTGG
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
30 39 0.39
31 60 0.61
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (31 bp):
ACTACCTTTTTCTATGGAGGTATAACCTTAC
Found at i:5929230 original size:61 final size:61
Alignment explanation
Indices: 5929162--5929299 Score: 154
Period size: 61 Copynumber: 2.3 Consensus size: 61
5929152 TTTTCTTATA
* * * *
5929162 GAGGTATAACCTTTCTCTA-CTTTTTCTA-TGGAGGTATAAGCTTACACTCCCTTTTGAAATG
1 GAGGTATAACCTTTCACTACCTTTTAC-AGTGGAGGTATAACCTTACACTACCTTTT-AAATG
* * ** **
5929223 GAGGTATAACCTTACACTACCTTTTACAGTGGAGGTATAACCTTTCTTTACCTTTTCTATG
1 GAGGTATAACCTTTCACTACCTTTTACAGTGGAGGTATAACCTTACACTACCTTTTAAATG
5929284 GAGGTATAACCTTTCA
1 GAGGTATAACCTTTCA
5929300 ATAGTGGATT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
61 36 0.56
62 28 0.44
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (61 bp):
GAGGTATAACCTTTCACTACCTTTTACAGTGGAGGTATAACCTTACACTACCTTTTAAATG
Found at i:5929799 original size:73 final size:71
Alignment explanation
Indices: 5929672--5929859 Score: 232
Period size: 73 Copynumber: 2.6 Consensus size: 71
5929662 TATCCTGAGC
* * * *
5929672 CTTTCTATTTTTGAAAATCGATCTTTCCATTCTTGAGGTAGTGATCCTTCTTGTCTCACTTAAAG
1 CTTTCTATTTTTGAGAATCGATCTCTCCATTCTTGAGATA-TGATCCTTATTGTCTCACTTAAAG
5929737 TCTAGAA
65 TCTAGAA
* * *
5929744 CTTTCTCATTTTTGAGAATCGATCTCTCAATTCTTGAGATATCTATCCTTATTGTCTCACTTGAA
1 CTTTCT-ATTTTTGAGAATCGATCTCTCCATTCTTGAGATAT-GATCCTTATTGTCTCACTTAAA
* *
5929809 GTGTAGAG
64 GTCTAGAA
* * *
5929817 CTTTTTGTTTTCTGAGAATCAATCTCTCCATTCTTGAGATATG
1 CTTTCTATTTT-TGAGAATCGATCTCTCCATTCTTGAGATATG
5929860 GATTTTTCTC
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
72 11 0.11
73 88 0.89
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (71 bp):
CTTTCTATTTTTGAGAATCGATCTCTCCATTCTTGAGATATGATCCTTATTGTCTCACTTAAAGT
CTAGAA
Found at i:5929875 original size:73 final size:72
Alignment explanation
Indices: 5929679--5929909 Score: 185
Period size: 73 Copynumber: 3.2 Consensus size: 72
5929669 AGCCTTTCTA
* * * * * * **
5929679 TTTTTGAAAATCGATCTTTCCATTCTTGAGGTAGT-GATCCTTCTTGTCTCACTTAAAGTCTAGA
1 TTTTTGAGAATCAATCTCTCAATTCTTGAGATA-TCGATCCTTATCATCTCACTTAAAGTCTAGA
* **
5929743 ACTTTCTCA
65 GCTTT-TTG
* * ** * *
5929752 TTTTTGAGAATCGATCTCTCAATTCTTGAGATATCTATCCTTATTGTCTCACTTGAAGTGTAGAG
1 TTTTTGAGAATCAATCTCTCAATTCTTGAGATATCGATCCTTATCATCTCACTTAAAGTCTAGAG
5929817 CTTTTTG
66 CTTTTTG
* * ** * *
5929824 TTTTCTGAGAATCAATCTCTCCATTCTTGAGATATGGATTTTTCTCATCTCACTTTTAAGTCTAG
1 TTTT-TGAGAATCAATCTCTCAATTCTTGAGATATCGATCCTTATCATCTCAC-TTAAAGTCTAG
*
5929889 AGCTTTCTG
64 AGCTTTTTG
*
5929898 TTCTTTAAGAAT
1 TT-TTTGAGAAT
5929910 TGATATTTGT
Statistics
Matches: 130, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
72 6 0.05
73 97 0.75
74 25 0.19
75 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (72 bp):
TTTTTGAGAATCAATCTCTCAATTCTTGAGATATCGATCCTTATCATCTCACTTAAAGTCTAGAG
CTTTTTG
Found at i:5933672 original size:116 final size:113
Alignment explanation
Indices: 5933512--5933819 Score: 304
Period size: 116 Copynumber: 2.7 Consensus size: 113
5933502 TAATTTAATA
*
5933512 AAACCTTAATTAATTTAAATAATTATAAATT-CTACTAA-ATTTACTAATTTAATTAATTACTTA
1 AAACCTTAATT-ATTTAAATAATTATAAATTAC-A-TAATA-TTACTAATTTAATTAATTGCTTA
* * ** * *
5933575 ATTACTAACACATGATTC-TT-TTTAATTAGTTAAATTATGCAATTAATTCCCTC
62 ATTACTAACACAT--TACATTACTTAATTAACTAAATTATGCAATTAACT-CATC
* *
5933628 AAACCTTAATTCATTTAAATAATTATAATATTACATAATATTACTTATCTAATTAATTGCTT-A-
1 AAACCTTAATT-ATTTAAATAATTATAA-ATTACATAATATTACTAATTTAATTAATTGCTTAAT
** *
5933691 TACCCTAACACATTACATTACTTAATTAACTAAATTATTTAATTAACTCATG
64 TA--CTAACACATTACATTACTTAATTAACTAAATTATGCAATTAACTCATC
* * * *
5933743 AACACCTTAATTATTTTAAATATTTTTAAATTAAATAATATTACTAATTTAATTAATTGTTTAAT
1 AA-ACCTTAATTA-TTTAAATAATTATAAATTACATAATATTACTAATTTAATTAATTGCTTAAT
*
5933808 TACTAAAACATT
64 TACTAACACATT
5933820 TTTTTTATAA
Statistics
Matches: 161, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
114 4 0.02
115 46 0.29
116 103 0.64
117 7 0.04
118 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (113 bp):
AAACCTTAATTATTTAAATAATTATAAATTACATAATATTACTAATTTAATTAATTGCTTAATTA
CTAACACATTACATTACTTAATTAACTAAATTATGCAATTAACTCATC
Found at i:5939858 original size:12 final size:12
Alignment explanation
Indices: 5939841--5939897 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
5939831 CTTTCACTAA
5939841 GCTTTTACAATG
1 GCTTTTACAATG
*
5939853 GCTTTTACCA-G
1 GCTTTTACAATG
*
5939864 GCTTTCACTAA--
1 GCTTTTAC-AATG
5939875 GCTTTTACAATG
1 GCTTTTACAATG
5939887 GCTTTTACAAT
1 GCTTTTACAAT
5939898 AGCTAAAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
10 2 0.05
11 15 0.39
12 21 0.55
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (12 bp):
GCTTTTACAATG
Found at i:5939868 original size:34 final size:34
Alignment explanation
Indices: 5939830--5939894 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
5939820 AAATTCACAA
5939830 GCTTTCACTAAGCTTTTACAATGGCTTTTACCAG
1 GCTTTCACTAAGCTTTTACAATGGCTTTTACCAG
5939864 GCTTTCACTAAGCTTTTACAATGGCTTTTAC
1 GCTTTCACTAAGCTTTTACAATGGCTTTTAC
5939895 AATAGCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (34 bp):
GCTTTCACTAAGCTTTTACAATGGCTTTTACCAG
Found at i:5954895 original size:22 final size:22
Alignment explanation
Indices: 5954869--5954913 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5954859 TGACAAAAAG
5954869 AAAGAAACAGAACCCTCACTCC
1 AAAGAAACAGAACCCTCACTCC
*
5954891 AAAGAAACAGAACCCTCATTCC
1 AAAGAAACAGAACCCTCACTCC
5954913 A
1 A
5954914 CGAATGTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.33, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAGAAACAGAACCCTCACTCC
Found at i:5959859 original size:19 final size:19
Alignment explanation
Indices: 5959810--5959859 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5959800 GCTATAAATA
*
5959810 TCTTCTCCTTCCAGCAGCT
1 TCTTCTTCTTCCAGCAGCT
* *
5959829 TCTTCAAT-TTCCAGTAGCT
1 TCTTC-TTCTTCCAGCAGCT
5959848 TCTTCTTCTTCC
1 TCTTCTTCTTCC
5959860 TCCTTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.12, C:0.36, G:0.08, T:0.44
Consensus pattern (19 bp):
TCTTCTTCTTCCAGCAGCT
Found at i:5960706 original size:42 final size:41
Alignment explanation
Indices: 5960648--5960854 Score: 200
Period size: 42 Copynumber: 4.9 Consensus size: 41
5960638 GATGTGGACT
* *
5960648 CGGCTATGTGCAAGTAGGAGTGCGCATACGCCGATGATGAC
1 CGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGATGAC
* * *
5960689 CAGGCTCTGTGCGAGTAGAAGTGTGCATAAGCCGATGATGACC
1 C-GGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGATGA-C
* *
5960732 CGACTATGTGCGAGT-GAGAGTGCGCATAAGCCAATGATGAC
1 CGGCTATGTGCGAGTAG-GAGTGCGCATAAGCCGATGATGAC
* * * *
5960773 TCGGCTATATGTGAGTAGGGGTACGCATAAGCCGATGATGACC
1 -CGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGATGA-C
* * * * * *
5960816 CAGCCATGTGCGAGTGGGGAGTGCACATGAGCTGATGAT
1 CGGCTATGTGCGAGT-AGGAGTGCGCATAAGCCGATGAT
5960855 AATGGGACGG
Statistics
Matches: 133, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
41 3 0.02
42 109 0.82
43 21 0.16
ACGTcount: A:0.26, C:0.20, G:0.34, T:0.21
Consensus pattern (41 bp):
CGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGATGAC
Found at i:5960753 original size:84 final size:85
Alignment explanation
Indices: 5960650--5960839 Score: 226
Period size: 84 Copynumber: 2.3 Consensus size: 85
5960640 TGTGGACTCG
* * * * * **
5960650 GCTATGTGCAAGT-AGGAGTGCGCATACGCCGATGATGAC-CAGGCTCTGTGCGAGTAGAAGTGT
1 GCTATGTGCGAGTGAGGAGTGCGCATAAGCCAATGATGACTC-GGCTATATGCGAGTAGAAGTAC
5960713 GCATAAGCCGATGATGACCC-
65 GCATAAGCCGATGATGACCCA
* **
5960733 GACTATGTGCGAGTGA-GAGTGCGCATAAGCCAATGATGACTCGGCTATATGTGAGTAGGGGTAC
1 G-CTATGTGCGAGTGAGGAGTGCGCATAAGCCAATGATGACTCGGCTATATGCGAGTAGAAGTAC
5960797 GCATAAGCCGATGATGACCCA
65 GCATAAGCCGATGATGACCCA
* *
5960818 GCCATGTGCGAGTGGGGAGTGC
1 GCTATGTGCGAGTGAGGAGTGC
5960840 ACATGAGCTG
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
83 1 0.01
84 80 0.89
85 9 0.10
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (85 bp):
GCTATGTGCGAGTGAGGAGTGCGCATAAGCCAATGATGACTCGGCTATATGCGAGTAGAAGTACG
CATAAGCCGATGATGACCCA
Found at i:5962186 original size:22 final size:22
Alignment explanation
Indices: 5962130--5962196 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
5962120 CGTACTGACC
*
5962130 CAACGTCACGCAATACATAACAA
1 CAAC-TCACGCAATACATAAAAA
*
5962153 CAACTCAAGCAATACATAAAAA
1 CAACTCACGCAATACATAAAAA
* *
5962175 CCAA-TCACGCAATGCCTAAAAA
1 -CAACTCACGCAATACATAAAAA
5962197 GTAGTCAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
22 31 0.82
23 7 0.18
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.13
Consensus pattern (22 bp):
CAACTCACGCAATACATAAAAA
Found at i:5962641 original size:22 final size:22
Alignment explanation
Indices: 5962577--5962648 Score: 99
Period size: 22 Copynumber: 3.3 Consensus size: 22
5962567 ACTGGACACG
* *
5962577 TAATGCCTAATATCCATTCAAA
1 TAATGCATAATATCCATTCACA
* *
5962599 CAATGCATCATATCCATTCACA
1 TAATGCATAATATCCATTCACA
*
5962621 TAATGCATAATATCCATTCACT
1 TAATGCATAATATCCATTCACA
5962643 TAATGC
1 TAATGC
5962649 CTATAAATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (22 bp):
TAATGCATAATATCCATTCACA
Found at i:5963475 original size:21 final size:21
Alignment explanation
Indices: 5963445--5963493 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5963435 ACTAAAATTC
5963445 AGTCACGCAATGCCTACAACA
1 AGTCACGCAATGCCTACAACA
* *
5963466 AGTCATGCAATGCCTACAAACT
1 AGTCACGCAATGCCTAC-AACA
5963488 AGTCAC
1 AGTCAC
5963494 ACATTGCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.37, C:0.31, G:0.14, T:0.18
Consensus pattern (21 bp):
AGTCACGCAATGCCTACAACA
Found at i:5967593 original size:32 final size:29
Alignment explanation
Indices: 5967516--5967694 Score: 155
Period size: 29 Copynumber: 6.3 Consensus size: 29
5967506 AGGCATTAAA
* *
5967516 GTGTAACAA-AATA-TTTTTGAATATGGC
1 GTGTAACAACAATATTTTTTCAACATGGC
5967543 GTGTAACAACAATATTTTTTCAACATGGC
1 GTGTAACAACAATATTTTTTCAACATGGC
*
5967572 GTGTAACAACAATATTTTTTTTTCAACATGAC
1 GTGTAACAACAATA---TTTTTTCAACATGGC
* *
5967604 GTGTAACAAC---CTTTTTT-AACCATGGT
1 GTGTAACAACAATATTTTTTCAA-CATGGC
* * *
5967630 GTGT---AAC-ATGTTTTTT-TACATGGT
1 GTGTAACAACAATATTTTTTCAACATGGC
5967654 GTGTAACAACAATATGTTTTTTCAACATGGC
1 GTGTAACAACAATA--TTTTTTCAACATGGC
5967685 GTGTAACAAC
1 GTGTAACAAC
5967695 CTAACCATGG
Statistics
Matches: 126, Mismatches: 11, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
23 3 0.02
24 10 0.08
25 9 0.07
26 14 0.11
27 12 0.10
28 6 0.05
29 26 0.21
30 6 0.05
31 16 0.13
32 24 0.19
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (29 bp):
GTGTAACAACAATATTTTTTCAACATGGC
Found at i:5967643 original size:24 final size:24
Alignment explanation
Indices: 5967615--5967661 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
5967605 TGTAACAACC
5967615 TTTTTTAACCATGGTGTGTAACATG
1 TTTTTTAA-CATGGTGTGTAACATG
*
5967640 TTTTTTTACATGGTGTGTAACA
1 TTTTTTAACATGGTGTGTAACA
5967662 ACAATATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (24 bp):
TTTTTTAACATGGTGTGTAACATG
Found at i:5967734 original size:45 final size:45
Alignment explanation
Indices: 5967680--5967768 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
5967670 TTTTTTCAAC
*
5967680 ATGGCGTGTAACAACCTAACCATGGCTTGTCACAAGTTTTTGTAT
1 ATGGCGTGTAACAACCTAACCATAGCTTGTCACAAGTTTTTGTAT
* * * *
5967725 ATGGCGTGTAACGAGCTAACCATAGCTTGTCATATGTTTTTGTA
1 ATGGCGTGTAACAACCTAACCATAGCTTGTCACAAGTTTTTGTA
5967769 CTTGGCTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (45 bp):
ATGGCGTGTAACAACCTAACCATAGCTTGTCACAAGTTTTTGTAT
Found at i:5967789 original size:69 final size:69
Alignment explanation
Indices: 5967700--5967912 Score: 261
Period size: 69 Copynumber: 3.1 Consensus size: 69
5967690 ACAACCTAAC
* * * *
5967700 CATGGCTTGTCACA-AGTTTTTGTATATGGCGTGTAACGA-GCTAACCATAGCTTGTCATATGTT
1 CATGGCTTGTCATATA-TTTTTGTACATAGCGTGTAAC-ACGCTAACCATAGCTTGTCACATGTT
5967763 TTTGTA
64 TTTGTA
* * * *
5967769 CTTGGCTTGTCATATATTTTTGTACATAGCGTGTAACATGCTAACCATGGCTTGTCACATATTTT
1 CATGGCTTGTCATATATTTTTGTACATAGCGTGTAACACGCTAACCATAGCTTGTCACATGTTTT
5967834 TGTA
66 TGTA
** * * *
5967838 CACAG-TGTGTCATATGTTTTTGTACATAGCGTGTAACACGCTAACCATAACTTGTCACAAGTTT
1 CATGGCT-TGTCATATATTTTTGTACATAGCGTGTAACACGCTAACCATAGCTTGTCACATGTTT
5967902 TTGTA
65 TTGTA
5967907 CATGGC
1 CATGGC
5967913 GTGTAACAAG
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
68 2 0.02
69 119 0.98
70 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (69 bp):
CATGGCTTGTCATATATTTTTGTACATAGCGTGTAACACGCTAACCATAGCTTGTCACATGTTTT
TGTA
Found at i:5967871 original size:24 final size:24
Alignment explanation
Indices: 5967745--5967871 Score: 82
Period size: 24 Copynumber: 5.4 Consensus size: 24
5967735 ACGAGCTAAC
*
5967745 CATAGCTTGTCATATGTTTTTGTA
1 CATAGCGTGTCATATGTTTTTGTA
* * * *
5967769 CTTGGCTTGTCATATATTTTTGTA
1 CATAGCGTGTCATATGTTTTTGTA
* * * *
5967793 CATAGCGTGTAACATG---CT-AA
1 CATAGCGTGTCATATGTTTTTGTA
* * * *
5967813 CCATGGCTTGTCACATATTTTTGTA
1 -CATAGCGTGTCATATGTTTTTGTA
* *
5967838 CACAGTGTGTCATATGTTTTTGTA
1 CATAGCGTGTCATATGTTTTTGTA
5967862 CATAGCGTGT
1 CATAGCGTGT
5967872 AACACGCTAA
Statistics
Matches: 73, Mismatches: 25, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
20 1 0.01
21 13 0.18
24 58 0.79
25 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
CATAGCGTGTCATATGTTTTTGTA
Found at i:5967909 original size:45 final size:45
Alignment explanation
Indices: 5967853--5968044 Score: 262
Period size: 45 Copynumber: 4.3 Consensus size: 45
5967843 TGTGTCATAT
*
5967853 GTTTTTGTACATAGCGTGTAACACGCTAACCATAACTTGTCACAA
1 GTTTTTGTACATAGCGTGTAACACGCTAACCATGACTTGTCACAA
* * *
5967898 GTTTTTGTACATGGCGTGTAACAAGCTAACCATGATTTGTCACATA
1 GTTTTTGTACATAGCGTGTAACACGCTAACCATGACTTGTCACA-A
* *
5967944 -TTTTTATACATAGCGTGTAACACGCTAACCATGATTTGTCACAA
1 GTTTTTGTACATAGCGTGTAACACGCTAACCATGACTTGTCACAA
** * *
5967988 GTTTTTGTTGAT-GACGTGTAACACGCTAACTATGACTTATCACAA
1 GTTTTTGTACATAG-CGTGTAACACGCTAACCATGACTTGTCACAA
5968033 GTTTTTGTACAT
1 GTTTTTGTACAT
5968045 GACGTGTCAC
Statistics
Matches: 129, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
44 2 0.02
45 126 0.98
46 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (45 bp):
GTTTTTGTACATAGCGTGTAACACGCTAACCATGACTTGTCACAA
Found at i:5983664 original size:33 final size:33
Alignment explanation
Indices: 5983622--5983686 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
5983612 TCTATTGTAA
*
5983622 AAACTTTTAATTTTGTTTGTTTCTTTTTAGGCC
1 AAACTTTTAATTTTGTTTGTTTCTTTTCAGGCC
5983655 AAACTTTTAATTTTGTTTGTTTCTTTTCAGGC
1 AAACTTTTAATTTTGTTTGTTTCTTTTCAGGC
5983687 ACTCTCTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.57
Consensus pattern (33 bp):
AAACTTTTAATTTTGTTTGTTTCTTTTCAGGCC
Found at i:5984238 original size:2 final size:2
Alignment explanation
Indices: 5984231--5984260 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5984221 TTCATATTCA
5984231 AT AT 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 AT AT
5984261 TAGACTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5986808 original size:42 final size:42
Alignment explanation
Indices: 5986749--5986931 Score: 294
Period size: 42 Copynumber: 4.4 Consensus size: 42
5986739 GTTGATTTGA
*
5986749 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGTTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
*
5986791 ACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
5986833 ACCCGGCTATGTGCTAGTAGGAGTGCACATAAGTCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
** *
5986875 ACCCGGCTATGTATGAGTGGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
*
5986917 ACCCGGCTATATGCG
1 ACCCGGCTATGTGCG
5986932 CATAAGCCGT
Statistics
Matches: 128, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 128 1.00
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
Found at i:5986938 original size:30 final size:30
Alignment explanation
Indices: 5986902--5986974 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
5986892 TGGGAGTGCA
5986902 CATAAGCCGTTGCTGACCCGGCTATATGCG
1 CATAAGCCGTTGCTGACCCGGCTATATGCG
* * *
5986932 CATAAGCCGTTCCTGACTCGGTTATATGCG
1 CATAAGCCGTTGCTGACCCGGCTATATGCG
*
5986962 CATAAGTCGTTGC
1 CATAAGCCGTTGC
5986975 ATATGAGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (30 bp):
CATAAGCCGTTGCTGACCCGGCTATATGCG
Found at i:5987018 original size:26 final size:26
Alignment explanation
Indices: 5986981--5987042 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
5986971 TTGCATATGA
* *
5986981 GATGATGGTGATTGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAT
5987007 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAT
*
5987033 GTTGATGATG
1 GATGATGATG
5987043 GGTATATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.34
Consensus pattern (26 bp):
GATGATGATGATGGGATGGTGTGCAT
Found at i:5990611 original size:42 final size:42
Alignment explanation
Indices: 5990564--5990831 Score: 421
Period size: 42 Copynumber: 6.4 Consensus size: 42
5990554 TGTTGATTTG
* *
5990564 GACCCGGCTATGTGCGAGTAGGAGTGCATATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* * *
5990606 GACCCGGCTATGTGCTAGTAGGAGTGCAGATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* *
5990648 GACCCGACTATGTG-GAAGTGGGAGTACACATAAGCCGTTGCT
1 GACCCGGCTATGTGCG-AGTGGGAGTGCACATAAGCCGTTGCT
*
5990690 GACCCGGCTATGTGCGAGTGGGAGCGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
*
5990732 GACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
5990774 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* *
5990816 AACCCGGCTATATGCG
1 GACCCGGCTATGTGCG
5990832 CATAAGCCGT
Statistics
Matches: 209, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
42 208 1.00
43 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.22
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
Found at i:5990887 original size:26 final size:26
Alignment explanation
Indices: 5990851--5990912 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
5990841 TTGCATATGA
*
5990851 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAC
5990877 GATGATGATGATGGGATGGTGTGCAC
1 GATGATGATGATGGGATGGTGTGCAC
*
5990903 GTTGATGATG
1 GATGATGATG
5990913 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.23, C:0.05, G:0.42, T:0.31
Consensus pattern (26 bp):
GATGATGATGATGGGATGGTGTGCAC
Found at i:5997698 original size:29 final size:28
Alignment explanation
Indices: 5997660--5997714 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
5997650 AAATCTTTAT
* *
5997660 AATATTCACAGTAGCTAAACAAGATATAC
1 AATATCCACAATAGCT-AACAAGATATAC
*
5997689 AATATCCACAATAGCTAGCAAGATAT
1 AATATCCACAATAGCTAACAAGATAT
5997715 GTTGAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (28 bp):
AATATCCACAATAGCTAACAAGATATAC
Found at i:6015939 original size:2 final size:2
Alignment explanation
Indices: 6015934--6015964 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6015924 TATGTATATA
*
6015934 TG TG TG TG TG TG GG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6015965 ATACATACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
TG
Found at i:6015976 original size:2 final size:2
Alignment explanation
Indices: 6015971--6015995 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6015961 GTGTATACAT
6015971 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
6015996 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6016000 original size:2 final size:2
Alignment explanation
Indices: 6015995--6016026 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6015985 ACACACACAC
*
6015995 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6016027 GTTAGAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6017023 original size:21 final size:20
Alignment explanation
Indices: 6016983--6017037 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
6016973 TGGTCTATGG
6016983 AATTGAATTAATTAATTTAA
1 AATTGAATTAATTAATTTAA
* *
6017003 AATTGAATATGATTCATTT-A
1 AATTGAAT-TAATTAATTTAA
6017023 AATT-AATTAATTAAT
1 AATTGAATTAATTAAT
6017038 AATATTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 6 0.20
19 3 0.10
20 13 0.43
21 8 0.27
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
AATTGAATTAATTAATTTAA
Found at i:6022049 original size:30 final size:30
Alignment explanation
Indices: 6022013--6022072 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6022003 TAGTCCTAAA
6022013 GACTTATTTAACTCAAAATAAAAATATAAG
1 GACTTATTTAACTCAAAATAAAAATATAAG
* *
6022043 GACTTATTTGACTCAAAATAAAAGTATAAG
1 GACTTATTTAACTCAAAATAAAAATATAAG
6022073 AGCTTGATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (30 bp):
GACTTATTTAACTCAAAATAAAAATATAAG
Found at i:6026466 original size:73 final size:73
Alignment explanation
Indices: 6026381--6026552 Score: 218
Period size: 73 Copynumber: 2.4 Consensus size: 73
6026371 CGGTTCATAA
* * * *
6026381 ATAGAGACGACTTAATCGACTTAGAAGCATTGTTAGTCAACTAAGAGCTTATTGCCACAAACTCG
1 ATAGAGATGACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGAGCTTACTGCCACAAACTCG
*
6026446 ATTTAGAG
66 ATTTAAAG
* * * * *
6026454 ATAGAGATGACTTAATTGACTAAGAAGCATAGTTAGTCGACTAAGAGTTTACTGCCAGAAACTTG
1 ATAGAGATGACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGAGCTTACTGCCACAAACTCG
*
6026519 GTTTAAAG
66 ATTTAAAG
* **
6026527 ACAGAGATGACTTAATTAACTAAGAA
1 ATAGAGATGACTTAATCGACTAAGAA
6026553 CATTCTACTT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 86 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (73 bp):
ATAGAGATGACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGAGCTTACTGCCACAAACTCG
ATTTAAAG
Found at i:6030528 original size:14 final size:14
Alignment explanation
Indices: 6030509--6030547 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6030499 TTATATTTGA
*
6030509 TGTTATTATTATTT
1 TGTTATAATTATTT
6030523 TGTTATAATTA-TT
1 TGTTATAATTATTT
6030536 T-TTATAATTATT
1 TGTTATAATTATT
6030548 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 9 0.39
13 4 0.17
14 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TGTTATAATTATTT
Found at i:6031490 original size:38 final size:38
Alignment explanation
Indices: 6031448--6031549 Score: 141
Period size: 38 Copynumber: 2.7 Consensus size: 38
6031438 GCCGTCTAGT
*
6031448 TCTCCAACACCATCAGGGTCTATATCATGCCGTCCTAC
1 TCTCCAACACCATCAGGGTCTATATCATGCCGTCCAAC
* * * **
6031486 TCTCCAACACCGTTAGGGTCCATATTGTGCCGTCCAAC
1 TCTCCAACACCATCAGGGTCTATATCATGCCGTCCAAC
*
6031524 TCTCCAACACCATCAAGGTCTATATC
1 TCTCCAACACCATCAGGGTCTATATC
6031550 GCCATCCAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.25, C:0.35, G:0.14, T:0.26
Consensus pattern (38 bp):
TCTCCAACACCATCAGGGTCTATATCATGCCGTCCAAC
Found at i:6031952 original size:22 final size:21
Alignment explanation
Indices: 6031923--6031979 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
6031913 GCATGATGAG
*
6031923 GTTTTAGGAATTGCTTGACTA
1 GTTTTAGGAATTGCCTGACTA
* *
6031944 GTTTGTAGGCATTGCCTGACTG
1 GTTT-TAGGAATTGCCTGACTA
*
6031966 GTTGTTAGTAATTG
1 GTT-TTAGGAATTG
6031980 TGTTGCTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.14
22 24 0.83
23 1 0.03
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (21 bp):
GTTTTAGGAATTGCCTGACTA
Found at i:6032813 original size:22 final size:22
Alignment explanation
Indices: 6032788--6032844 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
6032778 AGGCATTAAG
*
6032788 TGAATGGATATTATGCATTGTT
1 TGAATGGATATTATGCATTGTA
* *
6032810 TGAATTGTTATTATGCATTGTA
1 TGAATGGATATTATGCATTGTA
*
6032832 TGAATGGACATTA
1 TGAATGGATATTA
6032845 GGTATTGCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (22 bp):
TGAATGGATATTATGCATTGTA
Found at i:6033239 original size:22 final size:23
Alignment explanation
Indices: 6033214--6033261 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
6033204 TGTTTTGAGA
*
6033214 CATTTCT-TGACTACTTTTTATG
1 CATTTCTGTGACTACTTGTTATG
**
6033236 CA-TTCTGTGACTGGTTGTTATG
1 CATTTCTGTGACTACTTGTTATG
6033258 CATT
1 CATT
6033262 GCATGACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.19
22 16 0.76
23 1 0.05
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (23 bp):
CATTTCTGTGACTACTTGTTATG
Found at i:6037206 original size:22 final size:22
Alignment explanation
Indices: 6037178--6037230 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
6037168 AACAAGTAAC
*
6037178 ATGCCTAATATGGGGTCACACA
1 ATGCCTAAAATGGGGTCACACA
** *
6037200 ATGCCTAAAATTTGGTCACGCA
1 ATGCCTAAAATGGGGTCACACA
*
6037222 ATGCATAAA
1 ATGCCTAAA
6037231 CAACATATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (22 bp):
ATGCCTAAAATGGGGTCACACA
Found at i:6039558 original size:23 final size:23
Alignment explanation
Indices: 6039520--6039693 Score: 143
Period size: 23 Copynumber: 7.6 Consensus size: 23
6039510 ACAATAAGTG
* *
6039520 AGTCACGCAATACCATATCAAAT
1 AGTCACGCGATTCCATATCAAAT
* * *
6039543 AGTCGCACGATTCCATATCAACT
1 AGTCACGCGATTCCATATCAAAT
* *
6039566 AGTCACGCAATAT-CATATGAAAT
1 AGTCACGCGAT-TCCATATCAAAT
* *
6039589 AGTTACGTGATTCCATATCAAAT
1 AGTCACGCGATTCCATATCAAAT
* * * * *
6039612 AATCACTCAATTCCACATCAACT
1 AGTCACGCGATTCCATATCAAAT
* *
6039635 AGTCATGCGATTCCATATCAACT
1 AGTCACGCGATTCCATATCAAAT
* * * *
6039658 AGTCATGTGATTTCATATCAACT
1 AGTCACGCGATTCCATATCAAAT
*
6039681 AGTCACGTGATTC
1 AGTCACGCGATTC
6039694 ATACACACCA
Statistics
Matches: 119, Mismatches: 30, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
22 1 0.01
23 117 0.98
24 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.29
Consensus pattern (23 bp):
AGTCACGCGATTCCATATCAAAT
Found at i:6039589 original size:46 final size:46
Alignment explanation
Indices: 6039520--6039693 Score: 170
Period size: 46 Copynumber: 3.8 Consensus size: 46
6039510 ACAATAAGTG
* * *
6039520 AGTCACGCAATACCATATCAAATAGTCGCACGATTCCATATCAACT
1 AGTCACGCAATATCATATCAAATAGTCACGCGATTCCATATCAACT
* * * *
6039566 AGTCACGCAATATCATATGAAATAGTTACGTGATTCCATATCAAAT
1 AGTCACGCAATATCATATCAAATAGTCACGCGATTCCATATCAACT
* * * * *
6039612 AATCACTCAAT-TCCACATCAACTAGTCATGCGATTCCATATCAACT
1 AGTCACGCAATAT-CATATCAAATAGTCACGCGATTCCATATCAACT
* ** * * *
6039658 AGTCATGTGATTTCATATCAACTAGTCACGTGATTC
1 AGTCACGCAATATCATATCAAATAGTCACGCGATTC
6039694 ATACACACCA
Statistics
Matches: 102, Mismatches: 24, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
45 1 0.01
46 100 0.98
47 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.29
Consensus pattern (46 bp):
AGTCACGCAATATCATATCAAATAGTCACGCGATTCCATATCAACT
Found at i:6039652 original size:69 final size:69
Alignment explanation
Indices: 6039532--6039678 Score: 170
Period size: 69 Copynumber: 2.1 Consensus size: 69
6039522 TCACGCAATA
* * * * * *
6039532 CCATATCAAATAGTCGCACGATTCCATATCAACTAGTCACGCAATATCATATGAAATAGTTACGT
1 CCATATCAAATAATCACACAATTCCACATCAACTAGTCACGCAATATCATATCAAATAGTCACGT
6039597 GATT
66 GATT
* * * * *
6039601 CCATATCAAATAATCACTCAATTCCACATCAACTAGTCATGCGAT-TCCATATCAACTAGTCATG
1 CCATATCAAATAATCACACAATTCCACATCAACTAGTCACGCAATAT-CATATCAAATAGTCACG
6039665 TGATT
65 TGATT
*
6039670 TCATATCAA
1 CCATATCAA
6039679 CTAGTCACGT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (69 bp):
CCATATCAAATAATCACACAATTCCACATCAACTAGTCACGCAATATCATATCAAATAGTCACGT
GATT
Found at i:6040060 original size:26 final size:25
Alignment explanation
Indices: 6040016--6040066 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
6040006 TTTCCCTTTG
6040016 TTAAATAATACAAAAAGAATAATTT
1 TTAAATAATACAAAAAGAATAATTT
* *
6040041 TTAAATGATATAACAAAGAATAATTT
1 TTAAATAATACAA-AAAGAATAATTT
6040067 GGAGATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
TTAAATAATACAAAAAGAATAATTT
Found at i:6042040 original size:38 final size:40
Alignment explanation
Indices: 6041951--6042056 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 40
6041941 CACACCCGGC
*
6041951 TCATGTACATCCCCCCACATCGTGCACATAGCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGGCACCA
* * * *
6041991 TCATGTGCATCCCCCCACATCATGCACA-ATCAGTC-CCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGGCACCA
* *
6042029 TCGTGTACATCCCTCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
6042057 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 27 0.47
39 4 0.07
40 26 0.46
ACGTcount: A:0.25, C:0.42, G:0.13, T:0.21
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGCACCA
Found at i:6042049 original size:19 final size:19
Alignment explanation
Indices: 6041954--6042052 Score: 56
Period size: 19 Copynumber: 5.1 Consensus size: 19
6041944 ACCCGGCTCA
6041954 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* * ** *
6041973 TGCACATAGCCGGCACCATCA
1 TGTACAT-CCCCCCA-CATCG
* *
6041994 TGTGCATCCCCCCACATCA
1 TGTACATCCCCCCACATCG
* ***
6042013 TGCACAATCAGTCC-CATCG
1 TGTAC-ATCCCCCCACATCG
*
6042032 TGTACATCCCTCCACATCG
1 TGTACATCCCCCCACATCG
6042051 TG
1 TG
6042053 CACACGGGCA
Statistics
Matches: 57, Mismatches: 19, Indels: 8
0.68 0.23 0.10
Matches are distributed among these distances:
18 6 0.11
19 29 0.51
20 13 0.23
21 9 0.16
ACGTcount: A:0.23, C:0.41, G:0.14, T:0.21
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:6042391 original size:2 final size:2
Alignment explanation
Indices: 6042380--6042408 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6042370 ATTCATCATG
6042380 CA CA -A 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 CA CA
6042409 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6044790 original size:21 final size:21
Alignment explanation
Indices: 6044758--6044808 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
6044748 GGATCTCCAA
*
6044758 CTGCAT-TGCATGTATATGCAT
1 CTGCATGT-CATGCATATGCAT
*
6044779 TTGCATGTCATGCATATGCAT
1 CTGCATGTCATGCATATGCAT
6044800 CTGCATGTC
1 CTGCATGTC
6044809 TCACTCAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (21 bp):
CTGCATGTCATGCATATGCAT
Found at i:6047371 original size:19 final size:19
Alignment explanation
Indices: 6047347--6047396 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
6047337 GCGAATAATA
6047347 ACCACTCCAAAATACTTCT
1 ACCACTCCAAAATACTTCT
*
6047366 ACCACTCCAAAATGCTTCT
1 ACCACTCCAAAATACTTCT
*
6047385 ACCACTACAAAA
1 ACCACTCCAAAA
6047397 AATGCTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.40, C:0.36, G:0.02, T:0.22
Consensus pattern (19 bp):
ACCACTCCAAAATACTTCT
Found at i:6047400 original size:21 final size:19
Alignment explanation
Indices: 6047347--6047402 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
6047337 GCGAATAATA
* *
6047347 ACCACTCCAAAATACTTCT
1 ACCACTCAAAAATGCTTCT
*
6047366 ACCACTCCAAAATGCTTCT
1 ACCACTCAAAAATGCTTCT
6047385 ACCACTACAAAAAATGCT
1 ACCACT-C-AAAAATGCT
6047403 CAAAAGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 24 0.73
20 1 0.03
21 8 0.24
ACGTcount: A:0.39, C:0.34, G:0.04, T:0.23
Consensus pattern (19 bp):
ACCACTCAAAAATGCTTCT
Found at i:6053250 original size:229 final size:228
Alignment explanation
Indices: 6052875--6053301 Score: 570
Period size: 229 Copynumber: 1.9 Consensus size: 228
6052865 ATTGAAGATT
* * * * * *
6052875 ATTGAACTACAACAAAATTTTAGATAATTAACACATGAATCAAGCTATGAAAAAAAAAAAGATCA
1 ATTGAACCACAACAAAATCTCACATAATGAACACATGAATCAAGCTATG--AAAAAAAAAGACCA
* * * *
6052940 CCAACTAGATTGTACATCAAAGAAATTCTCATTATGAGGGTAAGTTATAAACAAATTTCTAATAA
64 CCAACTAGATTGTACATCAAAGAAATTCTCACTACGAGGGCAAGTTATAAACAAATATCTAATAA
* *
6053005 GACTCCAAATTGTATTCTTCCTAGTCTAAAAAGATTACACTTTTCTTTTATTTAACAAACTCATT
129 GACTCCAAATTGTATTCTTCCTACTCTAAAAAGATTACACTTTTCTTTTATTCAACAAACTCATT
6053070 CAATGAAATCAATCATATATAAAAAAAATTTTATC
194 CAATGAAATCAATCATATATAAAAAAAATTTTATC
* *
6053105 ATTGAACCAGAACAAAATCTCACATAATGAACACAAATGAATCAAGCTATG-AAAAAGAAGACCA
1 ATTGAACCACAACAAAATCTCACATAATGAACAC--ATGAATCAAGCTATGAAAAAAAAAGACCA
* * * * * *
6053169 TCAACTAGATTGTATATCAAA-AAACTTCTCACTACGAGGGCAAGTTGTAAATAACTATCTAATG
64 CCAACTAGATTGTACATCAAAGAAA-TTCTCACTACGAGGGCAAGTTATAAACAAATATCTAATA
* * * * *
6053233 AGATTCCAAATTGTATTCTTCCTACTTTAACAAGATTACACTTTTCTTTTATTCAATAAATTCAT
128 AGACTCCAAATTGTATTCTTCCTACTCTAAAAAGATTACACTTTTCTTTTATTCAACAAACTCAT
6053298 TCAA
193 TCAA
6053302 GCAAATGATT
Statistics
Matches: 169, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
228 3 0.02
229 123 0.73
230 28 0.17
232 15 0.09
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (228 bp):
ATTGAACCACAACAAAATCTCACATAATGAACACATGAATCAAGCTATGAAAAAAAAAGACCACC
AACTAGATTGTACATCAAAGAAATTCTCACTACGAGGGCAAGTTATAAACAAATATCTAATAAGA
CTCCAAATTGTATTCTTCCTACTCTAAAAAGATTACACTTTTCTTTTATTCAACAAACTCATTCA
ATGAAATCAATCATATATAAAAAAAATTTTATC
Found at i:6057456 original size:13 final size:13
Alignment explanation
Indices: 6057438--6057514 Score: 70
Period size: 13 Copynumber: 5.8 Consensus size: 13
6057428 ATTTTATTAG
6057438 TAAAAAAAAATCA
1 TAAAAAAAAATCA
*
6057451 TAAAAAATAATCA
1 TAAAAAAAAATCA
*
6057464 TAAACAAAAATCA
1 TAAAAAAAAATCA
*
6057477 CACCAAAAAAAAT-A
1 TA--AAAAAAAATCA
6057491 TAAAAATAAAA--A
1 TAAAAA-AAAATCA
6057503 TAAAATAAAAAT
1 TAAAA-AAAAAT
6057515 AAAATAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
12 14 0.26
13 29 0.55
14 2 0.04
15 8 0.15
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (13 bp):
TAAAAAAAAATCA
Found at i:6057495 original size:11 final size:12
Alignment explanation
Indices: 6057481--6057525 Score: 60
Period size: 11 Copynumber: 3.9 Consensus size: 12
6057471 AAATCACACC
6057481 AAAA-AAAATAT
1 AAAATAAAATAT
6057492 AAAAATAAAA-AT
1 -AAAATAAAATAT
6057504 AAAATAAAA-AT
1 AAAATAAAATAT
6057515 AAAATAAAATA
1 AAAATAAAATA
6057526 AAATAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 20 0.65
12 7 0.23
13 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAATAAAATAT
Found at i:6057501 original size:6 final size:6
Alignment explanation
Indices: 6057481--6057528 Score: 59
Period size: 5 Copynumber: 8.7 Consensus size: 6
6057471 AAATCACACC
*
6057481 AAAAA- AAATAT AAAAAT AAAAAT -AAAAT AAAAAT -AAAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
6057525 AAAA
1 AAAA
6057529 TAAGAGAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
5 19 0.50
6 19 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:6057507 original size:5 final size:5
Alignment explanation
Indices: 6057493--6057531 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
6057483 AAAAAATATA
6057493 AAAAT AAAAAT AAAAT AAAAAT AAAAT AAAAT AAAAT AA
1 AAAAT -AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AA
6057532 GAGAGAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 22 0.69
6 10 0.31
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:6057750 original size:26 final size:25
Alignment explanation
Indices: 6057711--6057766 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
6057701 GCCAAGAACG
* *
6057711 AGCAATCAAAAACCCTAGAAAAT-CCT
1 AGCAACCAAAAA-CC-AAAAAATCCCT
*
6057737 AGCAACCAACAACCAAAAAATCCCT
1 AGCAACCAAAAACCAAAAAATCCCT
6057762 AGCAA
1 AGCAA
6057767 GCTTCCTAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 6 0.23
25 10 0.38
26 10 0.38
ACGTcount: A:0.52, C:0.30, G:0.07, T:0.11
Consensus pattern (25 bp):
AGCAACCAAAAACCAAAAAATCCCT
Found at i:6058658 original size:12 final size:10
Alignment explanation
Indices: 6058623--6058655 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
6058613 CAAAAAAAAC
6058623 AAAAATAT--
1 AAAAATATAA
6058631 AAAAATATAA
1 AAAAATATAA
6058641 AAAAATATAA
1 AAAAATATAA
6058651 AAAAA
1 AAAAA
6058656 AATGAATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
10 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAATATAA
Found at i:6059096 original size:7 final size:7
Alignment explanation
Indices: 6059084--6059165 Score: 55
Period size: 7 Copynumber: 11.6 Consensus size: 7
6059074 TTATTCAATA
6059084 AAATAAT
1 AAATAAT
6059091 AAATAAAT
1 AAAT-AAT
6059099 AACAATAGAT
1 -A-AATA-AT
*
6059109 AAA-AAA
1 AAATAAT
6059115 AAGATAA-
1 AA-ATAAT
6059122 AAATAAT
1 AAATAAT
6059129 AAATAA-
1 AAATAAT
6059135 AAATAAT
1 AAATAAT
**
6059142 TCA-AAT
1 AAATAAT
*
6059148 ATATAAT
1 AAATAAT
6059155 AAATAAT
1 AAATAAT
6059162 AAAT
1 AAAT
6059166 TTGTGAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
6 17 0.28
7 28 0.47
8 7 0.12
9 3 0.05
10 5 0.08
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:6059100 original size:11 final size:11
Alignment explanation
Indices: 6059084--6059165 Score: 54
Period size: 11 Copynumber: 8.0 Consensus size: 11
6059074 TTATTCAATA
6059084 AAATAATAAAT
1 AAATAATAAAT
*
6059095 AAATAA-CAAT
1 AAATAATAAAT
*
6059105 AGATAA-AAA-
1 AAATAATAAAT
*
6059114 AAA-GAT-AA-
1 AAATAATAAAT
6059122 AAATAATAAAT
1 AAATAATAAAT
*
6059133 AAA-AATAATT
1 AAATAATAAAT
6059143 CAAAT-ATATAAT
1 -AAATAATA-AAT
6059155 AAATAATAAAT
1 AAATAATAAAT
6059166 TTGTGAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
8 6 0.11
9 4 0.07
10 18 0.33
11 22 0.40
12 5 0.09
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:6059383 original size:23 final size:21
Alignment explanation
Indices: 6059353--6059411 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
6059343 GGAGAAACTT
6059353 AGAATAAAAAAATAAAATATGGA
1 AGAATAAAAAAATAAAATAT--A
*
6059376 AGAATAAAAAATAGAAAATATA
1 AGAATAAAAAA-ATAAAATATA
*
6059398 AAAATAAAAAAATA
1 AGAATAAAAAAATA
6059412 TATAAAGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 11 0.34
23 11 0.34
24 8 0.25
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (21 bp):
AGAATAAAAAAATAAAATATA
Found at i:6059423 original size:16 final size:16
Alignment explanation
Indices: 6059355--6059423 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 16
6059345 AGAAACTTAG
6059355 AATAAAAAAATA-AAA
1 AATAAAAAAATATAAA
* ** *
6059370 TATGGAAGAATA-AAA
1 AATAAAAAAATATAAA
*
6059385 AAT-AGAAAATATAAA
1 AATAAAAAAATATAAA
6059400 AATAAAAAAATATATAA
1 AATAAAAAAATATA-AA
*
6059417 AGTAAAA
1 AATAAAA
6059424 TAAAATAATA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
14 5 0.12
15 19 0.46
16 9 0.22
17 8 0.20
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
AATAAAAAAATATAAA
Found at i:6059439 original size:22 final size:21
Alignment explanation
Indices: 6059398--6059448 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
6059388 AGAAAATATA
6059398 AAAATAAAAAAATATATAAAGT
1 AAAATAAAAAAATATATAAA-T
*
6059420 AAAATAAAATAATA-ATTAAAT
1 AAAATAAAAAAATATA-TAAAT
6059441 AATAATAA
1 AA-AATAA
6059449 TACTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAATAAAAAAATATATAAAT
Found at i:6059459 original size:9 final size:9
Alignment explanation
Indices: 6059381--6059459 Score: 51
Period size: 9 Copynumber: 8.7 Consensus size: 9
6059371 ATGGAAGAAT
6059381 AAAA-AATA
1 AAAATAATA
6059389 GAAAAT-ATA
1 -AAAATAATA
6059398 AAAATAA-A
1 AAAATAATA
6059406 AAAATATATA
1 AAAATA-ATA
6059416 AAGTAA-AAT-
1 AA--AATAATA
6059425 AAAATAATA
1 AAAATAATA
6059434 ATTAAATAATA
1 A--AAATAATA
* *
6059445 ATAATACTA
1 AAAATAATA
6059454 AAAATA
1 AAAATA
6059460 GTTAATTGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
7 2 0.04
8 15 0.26
9 23 0.40
10 5 0.09
11 10 0.18
12 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (9 bp):
AAAATAATA
Found at i:6062909 original size:17 final size:18
Alignment explanation
Indices: 6062883--6062917 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6062873 TTGATTCGAA
*
6062883 AATATGTATTAAT-AAAT
1 AATATATATTAATGAAAT
6062900 AATATATATTAATGAAAT
1 AATATATATTAATGAAAT
6062918 GTCATAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AATATATATTAATGAAAT
Found at i:6063368 original size:2 final size:2
Alignment explanation
Indices: 6063361--6063385 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6063351 AGAAAAAGTG
6063361 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
6063386 TATTCTTTAT
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:6066214 original size:14 final size:14
Alignment explanation
Indices: 6066195--6066226 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
6066185 TTTGAGTTGA
*
6066195 AGATTTTTTTTTTG
1 AGATTTTTGTTTTG
6066209 AGATTTTTGTTTTG
1 AGATTTTTGTTTTG
6066223 AGAT
1 AGAT
6066227 ATTGTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (14 bp):
AGATTTTTGTTTTG
Found at i:6068018 original size:80 final size:80
Alignment explanation
Indices: 6067885--6068111 Score: 350
Period size: 80 Copynumber: 2.8 Consensus size: 80
6067875 CATGAGCTCC
6067885 ATTTATG-AGATTAT-AACATGCATGCCATGAGATGTATGTGTTGGGATAGTCATATACACTATG
1 ATTTATGAAG-TTATGAA-ATGCATGCCATGAGATGTATGTGTTGGGATAGTCATATACACTATG
6067948 GGCTAAACATGTGAGCT
64 GGCTAAACATGTGAGCT
* *
6067965 ATTTATGAAGTTATGAAATGCATGCCATGAGATGTATGTGTTGGGATAATCATATACATTATGGG
1 ATTTATGAAGTTATGAAATGCATGCCATGAGATGTATGTGTTGGGATAGTCATATACACTATGGG
** *
6068030 CTACGCATGTGAGTT
66 CTAAACATGTGAGCT
* * *
6068045 ATTTATGAGGTTATGAAATGCATGCCATGTGATGTATGTGTTGAGATAGTCATATACACTATGGG
1 ATTTATGAAGTTATGAAATGCATGCCATGAGATGTATGTGTTGGGATAGTCATATACACTATGGG
6068110 CT
66 CT
6068112 TAGTATGATG
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
80 131 0.97
81 4 0.03
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (80 bp):
ATTTATGAAGTTATGAAATGCATGCCATGAGATGTATGTGTTGGGATAGTCATATACACTATGGG
CTAAACATGTGAGCT
Found at i:6072398 original size:14 final size:15
Alignment explanation
Indices: 6072381--6072410 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6072371 TTTAAAGAAT
6072381 AAAATC-TAAAAAAA
1 AAAATCTTAAAAAAA
6072395 AAAATCTTAAAAAAA
1 AAAATCTTAAAAAAA
6072410 A
1 A
6072411 GCTTCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATCTTAAAAAAA
Found at i:6072666 original size:17 final size:17
Alignment explanation
Indices: 6072644--6072676 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6072634 TTATTTCTTT
*
6072644 TTTTTCTTTTTATTTTA
1 TTTTTCATTTTATTTTA
6072661 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
6072677 CCATCGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCATTTTATTTTA
Found at i:6073719 original size:34 final size:34
Alignment explanation
Indices: 6073616--6073722 Score: 97
Period size: 34 Copynumber: 3.1 Consensus size: 34
6073606 GGCGATGTAT
* * * *
6073616 CACTATTTTGTTGCCATGAGTAGAGCGAAAATAC
1 CACTATTTTATTGCCATGAGTGGGGCGGAAATAC
* * * * * * **
6073650 GACTGTTATATAGCCATAAGTGGGGTGGATGTAC
1 CACTATTTTATTGCCATGAGTGGGGCGGAAATAC
*
6073684 CATTATTTTATTGCCATGAGTGGGGCGGAAATAC
1 CACTATTTTATTGCCATGAGTGGGGCGGAAATAC
6073718 CACTA
1 CACTA
6073723 CCCCTGCTTT
Statistics
Matches: 51, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (34 bp):
CACTATTTTATTGCCATGAGTGGGGCGGAAATAC
Found at i:6073979 original size:18 final size:19
Alignment explanation
Indices: 6073948--6073985 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6073938 AATGGAAATC
6073948 AAACAAACAAAAAG-ACAA
1 AAACAAACAAAAAGAACAA
6073966 AAACAAA-ACAAAAGAACAA
1 AAACAAACA-AAAAGAACAA
6073985 A
1 A
6073986 CCAAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 12 0.67
19 5 0.28
ACGTcount: A:0.79, C:0.16, G:0.05, T:0.00
Consensus pattern (19 bp):
AAACAAACAAAAAGAACAA
Found at i:6074173 original size:25 final size:25
Alignment explanation
Indices: 6074121--6074180 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
6074111 ATAAAATTAC
*
6074121 AAATCAA-AAAGTAAAAAAGTAAAG
1 AAATCAAGAAAGTAAAAAAGCAAAG
*
6074145 AAATCAAGAAA-TCAAAAAGCAAAG
1 AAATCAAGAAAGTAAAAAAGCAAAG
*
6074169 AAAATGAAGAAA
1 -AAATCAAGAAA
6074181 AAAGCACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.58
25 13 0.42
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.10
Consensus pattern (25 bp):
AAATCAAGAAAGTAAAAAAGCAAAG
Found at i:6075165 original size:2 final size:2
Alignment explanation
Indices: 6075158--6075185 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6075148 GGTATTTTCA
6075158 AT 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 AT
6075186 TCTACTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6075224 original size:2 final size:2
Alignment explanation
Indices: 6075217--6075246 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6075207 TTACTTTTNA
6075217 AT AT 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 AT AT
6075247 TCCATTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6079570 original size:18 final size:18
Alignment explanation
Indices: 6079539--6079589 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
6079529 TTTTCCTTCC
6079539 CCTTTCTCCTTTCTTTCTTT
1 CCTTTCT-C-TTCTTTCTTT
6079559 CCTTTCTCTTCTTTCTTT
1 CCTTTCTCTTCTTTCTTT
**
6079577 TATTTCTC-TCTTT
1 CCTTTCTCTTCTTT
6079590 TTCTTGCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 5 0.17
18 16 0.55
19 1 0.03
20 7 0.24
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (18 bp):
CCTTTCTCTTCTTTCTTT
Found at i:6079868 original size:16 final size:15
Alignment explanation
Indices: 6079847--6079876 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
6079837 TTATGGCTGC
6079847 CCCCCCCTCCCCCCCG
1 CCCCCCC-CCCCCCCG
6079863 CCCCCCCCCCCCCC
1 CCCCCCCCCCCCCC
6079877 CCTCCAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.93, G:0.03, T:0.03
Consensus pattern (15 bp):
CCCCCCCCCCCCCCG
Found at i:6079878 original size:17 final size:17
Alignment explanation
Indices: 6079845--6079878 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6079835 AGTTATGGCT
*
6079845 GCCCCCCCCTCCCCCCC
1 GCCCCCCCCCCCCCCCC
6079862 GCCCCCCCCCCCCCCCC
1 GCCCCCCCCCCCCCCCC
6079879 TCCAAGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.91, G:0.06, T:0.03
Consensus pattern (17 bp):
GCCCCCCCCCCCCCCCC
Found at i:6088381 original size:43 final size:42
Alignment explanation
Indices: 6088329--6088455 Score: 164
Period size: 43 Copynumber: 3.0 Consensus size: 42
6088319 AATATCATCA
**
6088329 TCATGTGCACTCCCTATTCGCACATAGCTGGGTCATCATTAGC
1 TCATGTGCACTCCC-AAACGCACATAGCTGGGTCATCATTAGC
* *
6088372 TCATGTGCACTCCCACACCGCACATAGCTGGATCATCATTAGC
1 TCATGTGCACTCCCA-AACGCACATAGCTGGGTCATCATTAGC
* * *
6088415 TCATGTGCACTCCCACACTGCACATAGTTGGGTCATTATTA
1 TCATGTGCACTCCCAAAC-GCACATAGCTGGGTCATCATTA
6088456 CCACACAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 2 0.03
43 72 0.97
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (42 bp):
TCATGTGCACTCCCAAACGCACATAGCTGGGTCATCATTAGC
Found at i:6089793 original size:35 final size:34
Alignment explanation
Indices: 6089752--6089875 Score: 131
Period size: 35 Copynumber: 3.5 Consensus size: 34
6089742 TTAATTGTTT
6089752 AATTTAATCAATTAGGCCCAATAATTCAATTAAAA
1 AATTTAATCAATTAGGCCCAATAATT-AATTAAAA
* * *
6089787 AATTTAATTAATTAAGCCCAACAATTTAATTAAAA
1 AATTTAATCAATTAGGCCCAATAA-TTAATTAAAA
* * * *
6089822 AATTCAAATCAATTTGACCCAATGACTTAATTAAACA
1 AATT-TAATCAATTAGGCCCAAT-AATTAATTAAA-A
*
6089859 ATTTTAATCAATTAGGC
1 AATTTAATCAATTAGGC
6089876 TCACTAAGTA
Statistics
Matches: 71, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
35 33 0.46
36 33 0.46
37 5 0.07
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.33
Consensus pattern (34 bp):
AATTTAATCAATTAGGCCCAATAATTAATTAAAA
Found at i:6091452 original size:73 final size:74
Alignment explanation
Indices: 6091345--6091539 Score: 177
Period size: 73 Copynumber: 2.6 Consensus size: 74
6091335 GCAGAATGAT
* * * *
6091345 CTTAATTGACTAACTGCAC-TCTTAGTTGACTAAGTCGTTTCTGTTTTTTG-A-TCCCAG-TTTT
1 CTTAGTTGACTAACT-TACTTCTTAGTCGACTAAGTCGTTTCTG-TTCTTGAAGT-CCAGATTTT
**
6091406 TAGCAGTGGGCA
63 TAGCAGTAAGCA
* * * *
6091418 CTTAGTTGACTAACTTACTTCTTAGTCGATTAAGTTGGTTCTG-TCTTGAAGTCCAGATTTTTGG
1 CTTAGTTGACTAACTTACTTCTTAGTCGACTAAGTCGTTTCTGTTCTTGAAGTCCAGATTTTTAG
*
6091482 CAGTAAGCT
66 CAGTAAGCA
* * *
6091491 CTTAGTCGACTAACTTGCTTCTTGGTCGACTAAGTC-TTCTCTGTCTCTT
1 CTTAGTTGACTAACTTACTTCTTAGTCGACTAAGTCGTT-TCTGT-TCTT
6091540 AAACCTCTTG
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
71 4 0.04
72 8 0.08
73 82 0.84
75 4 0.04
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (74 bp):
CTTAGTTGACTAACTTACTTCTTAGTCGACTAAGTCGTTTCTGTTCTTGAAGTCCAGATTTTTAG
CAGTAAGCA
Found at i:6101126 original size:21 final size:21
Alignment explanation
Indices: 6101102--6101142 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6101092 GCTCATTGCT
6101102 TTAAAAGTATCGATACATTTC
1 TTAAAAGTATCGATACATTTC
*
6101123 TTAAATGTATCGATACATTT
1 TTAAAAGTATCGATACATTT
6101143 TCAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (21 bp):
TTAAAAGTATCGATACATTTC
Found at i:6101148 original size:61 final size:61
Alignment explanation
Indices: 6101049--6101181 Score: 153
Period size: 61 Copynumber: 2.2 Consensus size: 61
6101039 AAACTCAATT
* * * * *
6101049 TATCGATACA-TTCTTAATTGTATCAATAAATATGCAACAGAATGCTCATTGCT-TTAAAAG
1 TATCGATACATTTCTTAAATGTATCAATAAATATGCAACAAAATACTCACT-CTCTCAAAAG
* * * *
6101109 TATCGATACATTTCTTAAATGTATCGATACATTTTCAACAAAATACTCACTCTCTCAAAAG
1 TATCGATACATTTCTTAAATGTATCAATAAATATGCAACAAAATACTCACTCTCTCAAAAG
*
6101170 TATCAATACATT
1 TATCGATACATT
6101182 AGCATATGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
60 12 0.20
61 49 0.80
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (61 bp):
TATCGATACATTTCTTAAATGTATCAATAAATATGCAACAAAATACTCACTCTCTCAAAAG
Found at i:6101261 original size:20 final size:19
Alignment explanation
Indices: 6101236--6101277 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
6101226 CAAGCAAGTT
6101236 CAAATGTATCAATACATGCA
1 CAAATGTATCAATACAT-CA
*
6101256 CAAATGTATCTATACATCA
1 CAAATGTATCAATACATCA
6101275 CAA
1 CAA
6101278 TAAGAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.26
Consensus pattern (19 bp):
CAAATGTATCAATACATCA
Found at i:6104894 original size:26 final size:26
Alignment explanation
Indices: 6104864--6104917 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
6104854 ATTTTAGAGT
6104864 AAGGAATTCATTATAACCTACTCAAG
1 AAGGAATTCATTATAACCTACTCAAG
*
6104890 AAGGAATTCATTATAACCTACTCGAG
1 AAGGAATTCATTATAACCTACTCAAG
6104916 AA
1 AA
6104918 TACATCCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.26
Consensus pattern (26 bp):
AAGGAATTCATTATAACCTACTCAAG
Found at i:6106378 original size:19 final size:21
Alignment explanation
Indices: 6106354--6106406 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
6106344 CCCTAAATTT
*
6106354 TTATTTTATTTGTTTTT-CC-
1 TTATTTTATTTCTTTTTGCCA
6106373 TTATTTT-TTTCTTTTTGCCA
1 TTATTTTATTTCTTTTTGCCA
*
6106393 TTTTTTTA-TTCTTT
1 TTATTTTATTTCTTT
6106407 CTACCTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 8 0.28
19 9 0.31
20 12 0.41
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.75
Consensus pattern (21 bp):
TTATTTTATTTCTTTTTGCCA
Found at i:6112063 original size:15 final size:14
Alignment explanation
Indices: 6112043--6112083 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
6112033 GACACCCCAT
6112043 TTTGTTTTTATTTCA
1 TTTGTTTTTATTT-A
*
6112058 TTTG-TTTTGTTT-
1 TTTGTTTTTATTTA
6112070 TTTGTTTTTATTTA
1 TTTGTTTTTATTTA
6112084 ATTTATTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 7 0.32
15 4 0.18
ACGTcount: A:0.10, C:0.02, G:0.10, T:0.78
Consensus pattern (14 bp):
TTTGTTTTTATTTA
Found at i:6112097 original size:27 final size:27
Alignment explanation
Indices: 6112042--6112097 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
6112032 TGACACCCCA
* * * *
6112042 TTTTGTTTTTATTTCATTTGTTTTGTT
1 TTTTGTTTTTATTTAATTTATTGTATT
6112069 TTTTGTTTTTATTTAATTTATTGTATT
1 TTTTGTTTTTATTTAATTTATTGTATT
6112096 TT
1 TT
6112098 ATTTAATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (27 bp):
TTTTGTTTTTATTTAATTTATTGTATT
Found at i:6115487 original size:12 final size:12
Alignment explanation
Indices: 6115472--6115591 Score: 118
Period size: 12 Copynumber: 10.1 Consensus size: 12
6115462 TTAACATGTT
*
6115472 TACATATATGTA
1 TACATATATATA
*
6115484 TACATGTATATA
1 TACATATATATA
* *
6115496 TGCATGTATATA
1 TACATATATATA
6115508 T--ATATATATA
1 TACATATATATA
*
6115518 TATATATATATA
1 TACATATATATA
*
6115530 TANCATATATGTA
1 TA-CATATATATA
*
6115543 TACATGTATATA
1 TACATATATATA
* *
6115555 TGCATGTATATA
1 TACATATATATA
*
6115567 TATATATATATA
1 TACATATATATA
*
6115579 TATATATATATA
1 TACATATATATA
6115591 T
1 T
6115592 TTAGGCTGCT
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
10 9 0.10
12 74 0.80
13 10 0.11
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (12 bp):
TACATATATATA
Found at i:6115507 original size:2 final size:2
Alignment explanation
Indices: 6115502--6115591 Score: 108
Period size: 2 Copynumber: 44.5 Consensus size: 2
6115492 TATATGCATG
* *
6115502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NCA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
6115545 CA TG TA TA TA TG CA TG 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
6115587 TA TA T
1 TA TA T
6115592 TTAGGCTGCT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
2 72 0.99
3 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6115546 original size:59 final size:58
Alignment explanation
Indices: 6115472--6115590 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 58
6115462 TTAACATGTT
6115472 TACATATATGTATACATGTATATATGCATGTATATATATATATATATATATATATATA
1 TACATATATGTATACATGTATATATGCATGTATATATATATATATATATATATATATA
6115530 TANCATATATGTATACATGTATATATGCATGTATATATATATATATATATATATATATA
1 TA-CATATATGTATACATGTATATATGCATGTATATATATATATATATATATATATATA
6115589 TA
1 TA
6115591 TTTAGGCTGC
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 2 0.03
59 58 0.97
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (58 bp):
TACATATATGTATACATGTATATATGCATGTATATATATATATATATATATATATATA
Found at i:6130769 original size:2 final size:2
Alignment explanation
Indices: 6130762--6130786 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6130752 GAGAAGACTT
6130762 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
6130787 ATTTTTTATC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6142021 original size:2 final size:2
Alignment explanation
Indices: 6142014--6142051 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6142004 ATAATCAATA
6142014 AT AT AT AT AT AT 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 AT AT AT AT AT AT
6142052 GAAATTCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6146766 original size:35 final size:35
Alignment explanation
Indices: 6146717--6146796 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
6146707 ATTTGCTAAA
*
6146717 TTTTATTTTTAA-TTTAATTGAATATCTAAATGTACT
1 TTTTA-TTTTAATTTTAATTG-ATAGCTAAATGTACT
*
6146753 TTTTATTTTAATTTTATTTGATAGCTAAATGTACT
1 TTTTATTTTAATTTTAATTGATAGCTAAATGTACT
*
6146788 TTTAATTTT
1 TTTTATTTT
6146797 TTATGTTGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 28 0.70
36 12 0.30
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (35 bp):
TTTTATTTTAATTTTAATTGATAGCTAAATGTACT
Found at i:6148215 original size:31 final size:30
Alignment explanation
Indices: 6148172--6148275 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
6148162 CATAAAGATC
*
6148172 AAATT-AAAAAAATTATACAGTACAGAGACT
1 AAATTGAACAAAATTATACAGTACA-AGACT
* * *
6148202 AAATTGAACAAAATTGTAGAGTACAATGATT
1 AAATTGAACAAAATTATACAGTACAA-GACT
* * * * *
6148233 ATATTGAACAAAATTTTATAATATAAAGACT
1 AAATTGAACAAAATTATACAGTA-CAAGACT
6148264 AAATTGAACAAA
1 AAATTGAACAAA
6148276 GGTATGTTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
30 6 0.10
31 52 0.87
32 2 0.03
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.28
Consensus pattern (30 bp):
AAATTGAACAAAATTATACAGTACAAGACT
Found at i:6150843 original size:22 final size:22
Alignment explanation
Indices: 6150805--6150868 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
6150795 TAAATAAAAC
6150805 ACTAAATTGAAAAAAAATATTAAT
1 ACTAAATT--AAAAAAATATTAAT
*
6150829 ACTAAATTAAAAAAA-ATTTATT
1 ACTAAATTAAAAAAATA-TTAAT
* *
6150851 ACTAAATTGAGAAAATAT
1 ACTAAATTAAAAAAATAT
6150869 CTTTTGCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
22 25 0.71
23 1 0.03
24 8 0.23
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (22 bp):
ACTAAATTAAAAAAATATTAAT
Found at i:6150850 original size:25 final size:24
Alignment explanation
Indices: 6150805--6150865 Score: 90
Period size: 23 Copynumber: 2.6 Consensus size: 24
6150795 TAAATAAAAC
6150805 ACTAAATTGAAAAAAAATATTAAT
1 ACTAAATTGAAAAAAAATATTAAT
*
6150829 ACTAAATT-AAAAAAAAT-TTATT
1 ACTAAATTGAAAAAAAATATTAAT
*
6150851 ACTAAATTGAGAAAA
1 ACTAAATTGAAAAAA
6150866 TATCTTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 12 0.35
23 14 0.41
24 8 0.24
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (24 bp):
ACTAAATTGAAAAAAAATATTAAT
Found at i:6152687 original size:40 final size:39
Alignment explanation
Indices: 6152666--6152745 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 39
6152656 AATTGACCAT
*
6152666 AAAAATAAAGTTTTCGAGACCACAACTTCATCAAGTTGAA
1 AAAAATAAAGTTTTCGAGACCACAAC-TCATCAAATTGAA
*
6152706 AAAAATAAAGTTTTCGAGACCACAACTTCATCAAGTTGAA
1 AAAAATAAAGTTTTCGAGACCACAAC-TCATCAAATTGAA
6152746 CAAATACCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (39 bp):
AAAAATAAAGTTTTCGAGACCACAACTCATCAAATTGAA
Found at i:6155001 original size:27 final size:29
Alignment explanation
Indices: 6154965--6155018 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
6154955 TCGGAGTATA
**
6154965 GGGGTAAAATC-GTAATTTTTTTGCCCTT
1 GGGGTAAAATCTGTAAAATTTTTGCCCTT
6154993 GGGGT-AAATCTGTAAAATTTTTGCCC
1 GGGGTAAAATCTGTAAAATTTTTGCCC
6155019 CAGCACTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (29 bp):
GGGGTAAAATCTGTAAAATTTTTGCCCTT
Found at i:6155416 original size:20 final size:20
Alignment explanation
Indices: 6155379--6155417 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6155369 GCTTTTGTTC
*
6155379 TTGATTTTCATGGTTGAATA
1 TTGATTTTCATGGATGAATA
6155399 TTGAGTTTTCAT-GATGAAT
1 TTGA-TTTTCATGGATGAAT
6155418 TCAATTCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (20 bp):
TTGATTTTCATGGATGAATA
Done.