Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 4 of 208
Found at i:1203668 original size:16 final size:16
Alignment explanation
Indices: 1203647--1203680 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1203637 ACCTGTCCAT
*
1203647 GGGCCGGGATGGGTTC
1 GGGCCGGGACGGGTTC
*
1203663 GGGCCGGGCCGGGTTC
1 GGGCCGGGACGGGTTC
1203679 GG
1 GG
1203681 AAAAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.24, G:0.59, T:0.15
Consensus pattern (16 bp):
GGGCCGGGACGGGTTC
Found at i:1203807 original size:25 final size:26
Alignment explanation
Indices: 1203772--1203833 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
1203762 CGGCCCGGCC
* * *
1203772 TATTTTTAAAAT-AAACATTAAAAAT
1 TATTTTAAAAATAAAAAATAAAAAAT
1203797 TATTTTAAAAATAAAAAAATAAAAAAT
1 TATTTTAAAAAT-AAAAAATAAAAAAT
1203824 TATTTTAAAA
1 TATTTTAAAA
1203834 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 11 0.34
27 21 0.66
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TATTTTAAAAATAAAAAATAAAAAAT
Found at i:1203820 original size:38 final size:38
Alignment explanation
Indices: 1203778--1203862 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
1203768 GGCCTATTTT
*
1203778 TAAAATAAACA-TTAAAAATTATTTTAAAAATAAAAAAA
1 TAAAATAAACATTTAAAAAGTATTTT-AAAATAAAAAAA
** * *
1203816 TAAAA-AATTATTTTAAAAGTATTTTAAAATTAAAAAA
1 TAAAATAAACATTTAAAAAGTATTTTAAAATAAAAAAA
1203853 TAAAAATAAA
1 T-AAAATAAA
1203863 AATATATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
37 15 0.39
38 21 0.55
39 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (38 bp):
TAAAATAAACATTTAAAAAGTATTTTAAAATAAAAAAA
Found at i:1205588 original size:24 final size:24
Alignment explanation
Indices: 1205537--1205594 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1205527 CAGCTCGAAA
* * *
1205537 GAGCGTCCCGTTATTAGCTCTCAT
1 GAGCATCCCGTTAATAGCTCTCAG
*
1205561 GAGCTTCCCGTTAATAGCTCTTC-G
1 GAGCATCCCGTTAATAGCTC-TCAG
1205585 GAGCATCCCG
1 GAGCATCCCG
1205595 ATTGGTTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.17, C:0.31, G:0.22, T:0.29
Consensus pattern (24 bp):
GAGCATCCCGTTAATAGCTCTCAG
Found at i:1212150 original size:32 final size:32
Alignment explanation
Indices: 1212114--1212190 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 32
1212104 ATTTTAAATT
1212114 TTAAAAATAACATATAAAAC-TTAAAATATATA
1 TTAAAAATAACATAT-AAACTTTAAAATATATA
1212146 TTAAAAA-ATAC--ATAAACTTTAAAATATATA
1 TTAAAAATA-ACATATAAACTTTAAAATATATA
*
1212176 -TATAAAATAAAATAT
1 TTA-AAAATAACATAT
1212191 TTTAAAACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
29 6 0.16
30 19 0.50
31 2 0.05
32 11 0.29
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (32 bp):
TTAAAAATAACATATAAACTTTAAAATATATA
Found at i:1218492 original size:26 final size:26
Alignment explanation
Indices: 1218434--1218486 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1218424 TGATTCCTTG
*
1218434 TGGAACTCTAAGGGAATTGCCTACCT
1 TGGAACTCTAAGGGAATTGCCCACCT
* *
1218460 TGGAACTCTAAGGGAGTTGCCCCCCT
1 TGGAACTCTAAGGGAATTGCCCACCT
1218486 T
1 T
1218487 TTAACTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (26 bp):
TGGAACTCTAAGGGAATTGCCCACCT
Found at i:1226706 original size:4 final size:4
Alignment explanation
Indices: 1226697--1226727 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1226687 AAAAGCCGCA
*
1226697 TGAC TGAC TGAC TGAC TAAC TGAC TGAC TGA
1 TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGA
1226728 TGATGTCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (4 bp):
TGAC
Found at i:1231725 original size:73 final size:73
Alignment explanation
Indices: 1231642--1231838 Score: 236
Period size: 72 Copynumber: 2.7 Consensus size: 73
1231632 ATTATTAACT
* * *
1231642 ACTCTAACATTACTAAATATATTTCACTTAAATTGCAATTTAAATTTATACAATTTTGTTCATCC
1 ACTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTCATCC
**
1231707 ATGGAACC
66 ATAAAACC
* * *
1231715 ACTCTGACATTATTAAATATATGTT-ATTTAAA-TACAATTCAAATTTATACAATTTTGTTGATC
1 ACTCTGACATTACTAAATATAT-TTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTCATC
*
1231778 CATAAAACT
65 CATAAAACC
* * **
1231787 ATTGTTTGACATTACTAAATGCATTTCATTTAAATTGCAATTCAAATTTATA
1 A--CTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATA
1231839 AGAAATTTAA
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
72 35 0.34
73 28 0.27
74 25 0.24
75 16 0.15
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (73 bp):
ACTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTCATCC
ATAAAACC
Found at i:1232306 original size:26 final size:26
Alignment explanation
Indices: 1232271--1232332 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
1232261 ATAAAAAATA
1232271 ACCAAAATATTATAATTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTATTT
*
1232297 ATCAAAATATTATAATTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTATTT
1232323 ACCAAAATAT
1 ACCAAAATAT
1232333 ACCAAAACAA
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:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (26 bp):
ACCAAAATATTATAATTTTTTTATTT
Found at i:1232418 original size:27 final size:27
Alignment explanation
Indices: 1232388--1232439 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1232378 GGCCAATCAC
1232388 ATTGGCGGCACCAAAGGTGCCAATGTA
1 ATTGGCGGCACCAAAGGTGCCAATGTA
*
1232415 ATTGGCGGCACCAATGGTGCCAATG
1 ATTGGCGGCACCAAAGGTGCCAATG
1232440 AACTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAATGTA
Found at i:1232767 original size:19 final size:19
Alignment explanation
Indices: 1232743--1232806 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
1232733 ATTAAAATAG
1232743 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
1232762 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
1232780 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
1232799 TTTAATTT
1 TTTAATTT
1232807 TAAAAAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:1233065 original size:19 final size:18
Alignment explanation
Indices: 1233041--1233099 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
1233031 ATTTTATATT
1233041 TTAAATGAAAATAAAGTTA
1 TTAAATGAAAAT-AAGTTA
*
1233060 TTAAATGAGAAT-AGTTTA
1 TTAAATGAAAATAAG-TTA
*
1233078 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATA-AGTTA
1233097 TTA
1 TTA
1233100 CTGAATTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 13 0.38
19 17 0.50
20 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (18 bp):
TTAAATGAAAATAAGTTA
Found at i:1233090 original size:18 final size:18
Alignment explanation
Indices: 1233041--1233091 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1233031 ATTTTATATT
1233041 TTAAATGAAAATAAAG-TTA
1 TTAAATGAAAAT--AGTTTA
*
1233060 TTAAATGAGAATAGTTTA
1 TTAAATGAAAATAGTTTA
*
1233078 TTAAATTAAAATAG
1 TTAAATGAAAATAG
1233092 AGTTATTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.07
18 15 0.54
19 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (18 bp):
TTAAATGAAAATAGTTTA
Found at i:1233708 original size:27 final size:27
Alignment explanation
Indices: 1233648--1233699 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1233638 CATTTTAGTC
1233648 CATTGGCACCATTGGTGCCGCCAATCA
1 CATTGGCACCATTGGTGCCGCCAATCA
*
1233675 CATTGGCACCTTTGGTGCCGCCAAT
1 CATTGGCACCATTGGTGCCGCCAAT
1233700 GTGATTGGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.33, G:0.23, T:0.25
Consensus pattern (27 bp):
CATTGGCACCATTGGTGCCGCCAATCA
Found at i:1233788 original size:26 final size:28
Alignment explanation
Indices: 1233759--1233822 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
1233749 TTTTTTTAGT
1233759 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
1233785 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
1233813 ATATTTTGGT
1 ATATTTTGGT
1233823 TATTTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 14 0.39
27 7 0.19
28 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:1235854 original size:3 final size:3
Alignment explanation
Indices: 1235846--1235875 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1235836 CCTGTTCCTG
1235846 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1235876 GATGGATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1236764 original size:2 final size:2
Alignment explanation
Indices: 1236757--1236787 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1236747 AGAAAAGGGC
1236757 AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1236788 GAGCTTATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1249379 original size:30 final size:32
Alignment explanation
Indices: 1249331--1249393 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
1249321 TAATAATGTT
*
1249331 AAAATTATACTTTGATTTTTTAAAAATAATAA
1 AAAATTATACTTTAATTTTTTAAAAATAATAA
*
1249363 AAAATTA-A-TTTAATTTTTTAAAAATTATAA
1 AAAATTATACTTTAATTTTTTAAAAATAATAA
1249393 A
1 A
1249394 GATAAGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 21 0.72
31 1 0.03
32 7 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
AAAATTATACTTTAATTTTTTAAAAATAATAA
Found at i:1250134 original size:24 final size:25
Alignment explanation
Indices: 1250084--1250137 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1250074 ATTATATACA
* *
1250084 AATAAATTTAACAAAAATAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
*
1250109 AATAAATTCAAC-ACAAGAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
1250133 AATAA
1 AATAA
1250138 CCCATCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.67, C:0.15, G:0.02, T:0.17
Consensus pattern (25 bp):
AATAAATTCAACAAAAAGAAAACAC
Found at i:1254531 original size:3 final size:3
Alignment explanation
Indices: 1254512--1254549 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1254502 ATGATATCTT
* *
1254512 AGC ATC AGC AAC AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1254550 ATGATGCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.37, C:0.32, G:0.29, T:0.03
Consensus pattern (3 bp):
AGC
Found at i:1254976 original size:20 final size:20
Alignment explanation
Indices: 1254933--1254976 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1254923 CTTTTTTATT
*
1254933 TTTAAAATTTCAATTTTAAT
1 TTTAAAATTTCAATTTTAAA
*
1254953 TTTAAAATTT-ATTTATTAAA
1 TTTAAAATTTCAATT-TTAAA
1254973 TTTA
1 TTTA
1254977 TTGATGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAAAATTTCAATTTTAAA
Found at i:1259224 original size:51 final size:51
Alignment explanation
Indices: 1259162--1259297 Score: 164
Period size: 51 Copynumber: 2.7 Consensus size: 51
1259152 TGGAAACATG
*
1259162 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * * ** * * **
1259213 ATCTTATAAGATATTATTTTATAAGATTATATATCTTATCTAAGATATGGA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* *
1259264 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATATTATAATCTTAGAGAT
1259298 TTGATGGTAG
Statistics
Matches: 67, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (51 bp):
ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:1272748 original size:75 final size:75
Alignment explanation
Indices: 1272625--1272767 Score: 225
Period size: 75 Copynumber: 1.9 Consensus size: 75
1272615 CAGGCTATGC
* *
1272625 TCCTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAGGACCTGGTCATCCTCCAAGTCCACCAC
1 TCCTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCAC
1272690 ATGCCGAGCA
66 ATGCCGAGCA
* * *
1272700 TCCTCCTCCAAGGCCAAGT-CTCTATGCGCCACCACCAAGACCAGGTCATCCTCCAGGTCCACTA
1 TCCTCCTCCAAGGCCAAGTCCTC-AAGCGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCA
1272764 CATG
65 CATG
1272768 AGCATCCTCC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 3 0.05
75 59 0.95
ACGTcount: A:0.24, C:0.43, G:0.17, T:0.17
Consensus pattern (75 bp):
TCCTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCAC
ATGCCGAGCA
Found at i:1272785 original size:99 final size:99
Alignment explanation
Indices: 1272671--1272853 Score: 269
Period size: 99 Copynumber: 1.8 Consensus size: 99
1272661 AGGACCTGGT
* *
1272671 CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCCAAG-TCTCTATGCGCCACCAC
1 CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGG-CAAGATCCCCATGCGCCACCAC
1272735 CAAGACCAGGTCATCCTCCAGGTCCACTACATGAG
65 CAAGACCAGGTCATCCTCCAGGTCCACTACATGAG
** * ***
1272770 CATCCTCCAAGTCCACCACATGTTGAGCATCCTCCTCCAAGGCTAGATCCCCATGCGCCACCGTT
1 CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCAAGATCCCCATGCGCCACCACC
*
1272835 AGGACCAGGTCATCCTCCA
66 AAGACCAGGTCATCCTCCA
1272854 AGCCCACCAC
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
98 3 0.04
99 71 0.96
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (99 bp):
CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCAAGATCCCCATGCGCCACCACC
AAGACCAGGTCATCCTCCAGGTCCACTACATGAG
Found at i:1272804 original size:27 final size:24
Alignment explanation
Indices: 1272746--1272791 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1272736 AAGACCAGGT
* *
1272746 CATCCTCCAGGTCCACTACATGAG
1 CATCCTCCAAGTCCACCACATGAG
1272770 CATCCTCCAAGTCCACCACATG
1 CATCCTCCAAGTCCACCACATG
1272792 TTGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (24 bp):
CATCCTCCAAGTCCACCACATGAG
Found at i:1273124 original size:93 final size:92
Alignment explanation
Indices: 1272799--1273131 Score: 321
Period size: 93 Copynumber: 3.6 Consensus size: 92
1272789 ATGTTGAGCA
* * *** * *
1272799 TCCTCCTCCAAGGCTAGATCCCCATGCGCCACCGTTAGGACCAGGTCATCCTCCAAGCCCACCAC
1 TCCTCCTCCAAGGCCAGGTCCCCATGCGCCACCACCAGAACCAGGTCATCCTCCAAG-TCACCAC
* * *
1272864 ATAATGATCATCTTCATCCAGACCATGC
65 ATAATGGTCATCCTCATCCAGGCCATGC
* * * * * * *
1272892 TCCCCCTCCAGGGCCAGGTCCCCATGTGCCACCACCA-AGACCTGGACATCCTCCAGGTGCATCA
1 TCCTCCTCCAAGGCCAGGTCCCCATGCGCCACCACCAGA-ACCAGGTCATCCTCCAAGT-CACCA
** *
1272956 CATGCTGAG-CATTCTCATCCAGGCCATGC
64 CATAATG-GTCATCCTCATCCAGGCCATGC
* * *
1272985 TCCTCCTCC-AGGACCAAGTCCCCATACGCCACCACCAGAACCAGGTCATCTTCCAAGTCAACCA
1 TCCTCCTCCAAGG-CCAGGTCCCCATGCGCCACCACCAGAACCAGGTCATCCTCCAAGTC-ACCA
* *
1273049 CATATTGGTCATCCTCATCCAGGCCACGC
64 CATAATGGTCATCCTCATCCAGGCCATGC
* * ** *
1273078 TCCTCCTCCAAGGCCAGGTCCCCATGCACCACTACCAGGTCTAGGTCATCCTCC
1 TCCTCCTCCAAGGCCAGGTCCCCATGCGCCACCACCAGAACCAGGTCATCCTCC
1273132 TGAGCCACAC
Statistics
Matches: 190, Mismatches: 42, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
92 4 0.02
93 182 0.96
94 4 0.02
ACGTcount: A:0.23, C:0.41, G:0.17, T:0.19
Consensus pattern (92 bp):
TCCTCCTCCAAGGCCAGGTCCCCATGCGCCACCACCAGAACCAGGTCATCCTCCAAGTCACCACA
TAATGGTCATCCTCATCCAGGCCATGC
Found at i:1274501 original size:15 final size:14
Alignment explanation
Indices: 1274468--1274519 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 14
1274458 GAACGAAAAT
1274468 AAAATAAAATAAA-A
1 AAAATAAAA-AAACA
*
1274482 TAAAATAAACAAACCA
1 -AAAATAAA-AAAACA
1274498 AAAATAAAAAAACA
1 AAAATAAAAAAACA
1274512 AATAATAA
1 AA-AATAA
1274520 GGATAACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 7 0.22
15 23 0.72
16 2 0.06
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAAAAAAACA
Found at i:1274506 original size:5 final size:5
Alignment explanation
Indices: 1274463--1274490 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1274453 ATAAAGAACG
1274463 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1274491 CAAACCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1274713 original size:3 final size:3
Alignment explanation
Indices: 1274705--1274808 Score: 60
Period size: 3 Copynumber: 35.0 Consensus size: 3
1274695 TAAGAGAAAT
* * *
1274705 ATA ATA ATA ATA ATA GTA ATA ATA ATGCA A-A TTA ATTA AT- TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT--A ATA ATA A-TA ATA ATA ATA
*
1274751 AT- ATA ATA ATA ACA AGTAA ATAA ATA A-A A-A AT- ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA A-T-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA
*
1274794 ATA GTA ATA ATA ATA
1 ATA ATA ATA ATA ATA
1274809 TTAAATTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
2 12 0.15
3 56 0.70
4 8 0.10
5 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1288925 original size:82 final size:82
Alignment explanation
Indices: 1288788--1288950 Score: 281
Period size: 82 Copynumber: 2.0 Consensus size: 82
1288778 GGAAGACTCA
* *
1288788 CAATTTGATAAGCTTCTTCCACTGTAAAGGTTGATTAAATGAGGTCTCTATTCCATCGCTTAGGA
1 CAATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTCTATATTCCATCGCTTAGGA
*
1288853 TTCTGCAAAATCAAATG
66 TTCTACAAAATCAAATG
*
1288870 CAATTTGATAATCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTCTATATTCCATCGCTTAGGA
1 CAATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTCTATATTCCATCGCTTAGGA
*
1288935 TTTTACAAAATCAAAT
66 TTCTACAAAATCAAAT
1288951 CAGACACAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (82 bp):
CAATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTCTATATTCCATCGCTTAGGA
TTCTACAAAATCAAATG
Found at i:1290272 original size:17 final size:17
Alignment explanation
Indices: 1290250--1290310 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
1290240 TAAAGAATGA
1290250 CCTAAATAGCAATTATG
1 CCTAAATAGCAATTATG
** * *
1290267 CCTAAATAAAAAGATAAGG
1 CCTAAAT-AGCA-ATTATG
1290286 CCTAAATAGCAATTATG
1 CCTAAATAGCAATTATG
1290303 CCTAAATA
1 CCTAAATA
1290311 AAAAGATGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 19 0.56
18 4 0.12
19 11 0.32
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (17 bp):
CCTAAATAGCAATTATG
Found at i:1290293 original size:36 final size:36
Alignment explanation
Indices: 1290250--1290322 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1290240 TAAAGAATGA
1290250 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
1 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
*
1290286 CCTAAATAGCAATTATGCCTAAATAAAAAGATGAGG
1 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
1290322 C
1 C
1290323 AACATAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (36 bp):
CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
Found at i:1295184 original size:23 final size:23
Alignment explanation
Indices: 1295134--1295177 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1295124 AATAGTCCAG
1295134 AAGAAAAAGCGCGTCAAAAGACA
1 AAGAAAAAGCGCGTCAAAAGACA
* *
1295157 AAGAAAAAGTGTGTCAAAAGA
1 AAGAAAAAGCGCGTCAAAAGA
1295178 TAGAGAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.23, T:0.09
Consensus pattern (23 bp):
AAGAAAAAGCGCGTCAAAAGACA
Found at i:1301865 original size:30 final size:31
Alignment explanation
Indices: 1301796--1301865 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1301786 ATACTCAATT
* ** *
1301796 ACTTAAATTTACCTATTTAATCCATCTCATT
1 ACTTAAATTTACCTATTTAACCCATAGCATA
**
1301827 GGTTAAATTTACCTATTTAACCCA-AGCATA
1 ACTTAAATTTACCTATTTAACCCATAGCATA
1301857 ACTTAAATT
1 ACTTAAATT
1301866 ACTTAAATTC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (31 bp):
ACTTAAATTTACCTATTTAACCCATAGCATA
Found at i:1304979 original size:21 final size:21
Alignment explanation
Indices: 1304881--1304995 Score: 72
Period size: 21 Copynumber: 5.5 Consensus size: 21
1304871 GCTTAACTCA
1304881 TATGAGTTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * * **
1304902 AATGGGTTTCCATT-AAGCTAT
1 TATGAGTTTCCGTTCAA-CCCT
* * * *
1304923 TTTGAGCTTCTGTTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * * *
1304944 TTTGAGATTT-TGTTCAGCTCT
1 TATGAG-TTTCCGTTCAACCCT
1304965 TATGAGTTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
*
1304986 TATGGGTTTC
1 TATGAGTTTC
1304996 TCTTTAGCAC
Statistics
Matches: 68, Mismatches: 22, Indels: 8
0.69 0.22 0.08
Matches are distributed among these distances:
20 5 0.07
21 59 0.87
22 4 0.06
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.43
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAACCCT
Found at i:1305009 original size:42 final size:42
Alignment explanation
Indices: 1304881--1305010 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 42
1304871 GCTTAACTCA
*
1304881 TATGAGTTTCCGTTCAACCCTAATGGGTTTC-CATTAAGCTA-T
1 TATGAGTTTCCGTTCAACCCTTATGGGTTTCTC-TTAAGC-ACT
* * * * * * * * *
1304923 TTTGAGCTTCTGTTTAACCCTTTTGAGATTT-TGTTCAGCTCT
1 TATGAGTTTCCGTTCAACCCTTATG-GGTTTCTCTTAAGCACT
*
1304965 TATGAGTTTCCGTTCAACCCTTATGGGTTTCTCTTTAGCACT
1 TATGAGTTTCCGTTCAACCCTTATGGGTTTCTCTTAAGCACT
1305007 TATG
1 TATG
1305011 TGCTTCTATT
Statistics
Matches: 65, Mismatches: 19, Indels: 8
0.71 0.21 0.09
Matches are distributed among these distances:
41 4 0.06
42 57 0.88
43 4 0.06
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TATGAGTTTCCGTTCAACCCTTATGGGTTTCTCTTAAGCACT
Found at i:1309002 original size:20 final size:20
Alignment explanation
Indices: 1308973--1309020 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1308963 CTGCATCTAA
*
1308973 GAAAAATTTTGAACTTTTGG
1 GAAAAATTTTGAAATTTTGG
*
1308993 GAAAATTTTTGAAATTTTGG
1 GAAAAATTTTGAAATTTTGG
1309013 GAAAAATT
1 GAAAAATT
1309021 CTCTAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
GAAAAATTTTGAAATTTTGG
Found at i:1309350 original size:58 final size:58
Alignment explanation
Indices: 1309249--1309396 Score: 188
Period size: 58 Copynumber: 2.6 Consensus size: 58
1309239 ACCAATTTGT
* * * *
1309249 TCAAGCCTTAATATAGGTACAATTGCCAAGTTCAAATATTAACTTGGACAAAAAAAAA
1 TCAAGCCTTAATATAGGTACAATTGTCAAGTTCAAAGACTAACTTGAACAAAAAAAAA
* * * *
1309307 TTAAGCCCTAATATAGGTACAATTGTCAAGTTCAGAGACTAACTTTAACAAAAAAAAA
1 TCAAGCCTTAATATAGGTACAATTGTCAAGTTCAAAGACTAACTTGAACAAAAAAAAA
* * * *
1309365 TCAAACCTTAATATAAGAACAATTATCAAGTT
1 TCAAGCCTTAATATAGGTACAATTGTCAAGTT
1309397 TAGGTCCTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 76 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (58 bp):
TCAAGCCTTAATATAGGTACAATTGTCAAGTTCAAAGACTAACTTGAACAAAAAAAAA
Found at i:1309407 original size:58 final size:58
Alignment explanation
Indices: 1309288--1309418 Score: 149
Period size: 58 Copynumber: 2.3 Consensus size: 58
1309278 GTTCAAATAT
* * * * * *
1309288 TAACTTGGACAAAAAAAAATTAAGCCCTAATATAGGTACAATTGTCAAGTTCAGAGAC
1 TAACTTGAACAAAAAAAAATCAAACCCTAATATAAGAACAATTATCAAGTTCAGAGAC
* * * *
1309346 TAACTTTAACAAAAAAAAATCAAACCTTAATATAAGAACAATTATCAAGTTTAG-GTCC
1 TAACTTGAACAAAAAAAAATCAAACCCTAATATAAGAACAATTATCAAGTTCAGAG-AC
1309404 TAACTTGAA-AAAAAA
1 TAACTTGAACAAAAAA
1309419 TAATTGAAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
57 7 0.11
58 54 0.89
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.25
Consensus pattern (58 bp):
TAACTTGAACAAAAAAAAATCAAACCCTAATATAAGAACAATTATCAAGTTCAGAGAC
Found at i:1310395 original size:27 final size:26
Alignment explanation
Indices: 1310344--1310396 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1310334 TGACTATTTT
**
1310344 TTAAAAGATTAATAATTAATTTAAAC
1 TTAAAAGATTAATAATTAAAATAAAC
1310370 TTAAAA-ATTAATAATATTAAAATAAAC
1 TTAAAAGATTAAT-A-ATTAAAATAAAC
1310397 AAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.26
26 7 0.30
27 10 0.43
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
TTAAAAGATTAATAATTAAAATAAAC
Found at i:1325183 original size:7 final size:7
Alignment explanation
Indices: 1325171--1325208 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
1325161 TTAAACAAGG
1325171 TTTTCTT
1 TTTTCTT
1325178 TTTTC-T
1 TTTTCTT
1325184 TTTTCTT
1 TTTTCTT
*
1325191 TTTTTTT
1 TTTTCTT
1325198 TTTTACTT
1 TTTT-CTT
1325206 TTT
1 TTT
1325209 GGCGTAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 6 0.22
7 16 0.59
8 5 0.19
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:1325200 original size:13 final size:13
Alignment explanation
Indices: 1325171--1325199 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1325161 TTAAACAAGG
1325171 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
1325184 TTTTCTTTTTT-T
1 TTTTCTTTTTTCT
1325196 TTTT
1 TTTT
1325200 TTACTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:1325718 original size:20 final size:20
Alignment explanation
Indices: 1325667--1325718 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
1325657 TAATCATTGC
1325667 AATATATGTAAAAATAATTT
1 AATATATGTAAAAATAATTT
* *
1325687 AA-A-ATATAAAAAT-TTATT
1 AATATATGTAAAAATAAT-TT
1325705 AATATATGTAAAAA
1 AATATATGTAAAAA
1325719 CAACTTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.04
18 13 0.50
19 2 0.08
20 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AATATATGTAAAAATAATTT
Found at i:1325814 original size:14 final size:15
Alignment explanation
Indices: 1325792--1325868 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
1325782 CAATCAAACA
1325792 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
1325806 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
1325821 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
1325841 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
1325855 ACAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
1325869 ACTGGCAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 22 0.43
15 15 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:1325833 original size:20 final size:20
Alignment explanation
Indices: 1325808--1325847 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1325798 AATATTTTCC
*
1325808 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1325828 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1325848 TCATTTTACA
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1325853 original size:34 final size:35
Alignment explanation
Indices: 1325796--1325862 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
1325786 CAAACACCAG
*
1325796 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
1325831 AAAACATTTTCCAG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1325863 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1326105 original size:19 final size:19
Alignment explanation
Indices: 1326081--1326117 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1326071 ACAAATATTC
1326081 ATAAAAA-TTCAAATAAAAA
1 ATAAAAAGTTCAAA-AAAAA
1326100 ATAAAAAGTTCAAAAAAA
1 ATAAAAAGTTCAAAAAAA
1326118 TTATTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (19 bp):
ATAAAAAGTTCAAAAAAAA
Found at i:1326815 original size:21 final size:20
Alignment explanation
Indices: 1326789--1326828 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1326779 TAGTGTTTAC
1326789 TTTAATGTATATATACAAGGA
1 TTTAATGTATATATA-AAGGA
*
1326810 TTTAATGTGTATATAAAGG
1 TTTAATGTATATATAAAGG
1326829 CATATATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTAATGTATATATAAAGGA
Found at i:1332181 original size:10 final size:10
Alignment explanation
Indices: 1332166--1332223 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
1332156 TAAAGTAAAT
*
1332166 GAAATAAAAA
1 GAAAGAAAAA
*
1332176 GAAATAAAAA
1 GAAAGAAAAA
* *
1332186 CAAAGCAAAA
1 GAAAGAAAAA
1332196 GAAAGAAGAAA
1 GAAAGAA-AAA
1332207 G-AAGAAAAA
1 GAAAGAAAAA
1332216 G-AAGAAAA
1 GAAAGAAAA
1332224 TAGGGAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
9 11 0.26
10 27 0.64
11 4 0.10
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
GAAAGAAAAA
Found at i:1332909 original size:12 final size:12
Alignment explanation
Indices: 1332863--1332911 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
1332853 GTGAGGTAAG
*
1332863 TATTAATATTAG
1 TATTAATATTAT
1332875 TATTAAT-TTAT
1 TATTAATATTAT
**
1332886 TATTCGTATTAT
1 TATTAATATTAT
*
1332898 TATTATTATTAT
1 TATTAATATTAT
1332910 TA
1 TA
1332912 GTGGGAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 8 0.26
12 23 0.74
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:1333322 original size:37 final size:39
Alignment explanation
Indices: 1333263--1333358 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
1333253 CGGATAGATT
* * * *
1333263 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
1333300 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
1333339 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
1333359 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:1334866 original size:16 final size:16
Alignment explanation
Indices: 1334845--1334905 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
1334835 AATAGTAGAA
1334845 AAAAAATTAGAGGTGT
1 AAAAAATTAGAGGTGT
* * *
1334861 AAAAAATTCAAAATAGTAGAA
1 AAAAAATT--AGA-GGT-G-T
1334882 AAAAAATTAGAGGTGT
1 AAAAAATTAGAGGTGT
1334898 AAAAAATT
1 AAAAAATT
1334906 CTCTAACTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
16 16 0.47
17 1 0.03
18 4 0.12
19 4 0.12
20 1 0.03
21 8 0.24
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.23
Consensus pattern (16 bp):
AAAAAATTAGAGGTGT
Found at i:1334879 original size:37 final size:37
Alignment explanation
Indices: 1334833--1334906 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1334823 ACATATATTA
1334833 AAAATAGTAGAAAAAAAATTAGAGGTGTAAAAAATTC
1 AAAATAGTAGAAAAAAAATTAGAGGTGTAAAAAATTC
1334870 AAAATAGTAGAAAAAAAATTAGAGGTGTAAAAAATTC
1 AAAATAGTAGAAAAAAAATTAGAGGTGTAAAAAATTC
1334907 TCTAACTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.59, C:0.03, G:0.16, T:0.22
Consensus pattern (37 bp):
AAAATAGTAGAAAAAAAATTAGAGGTGTAAAAAATTC
Found at i:1335473 original size:19 final size:19
Alignment explanation
Indices: 1335449--1335499 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1335439 GTTTTTGATG
* *
1335449 TATTTTTATAGATTTTTAC
1 TATTTTTATAAAATTTTAC
1335468 TATTTTTATAAAATTTTAC
1 TATTTTTATAAAATTTTAC
*
1335487 AATTTTTTATAAA
1 TA-TTTTTATAAA
1335500 TGTTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTTTTATAAAATTTTAC
Found at i:1344012 original size:21 final size:21
Alignment explanation
Indices: 1343986--1344028 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1343976 ATTTTAAAAG
1343986 TAAAAATTATATTGCATTGAA
1 TAAAAATTATATTGCATTGAA
1344007 TAAAAATTATATTGCATTGAA
1 TAAAAATTATATTGCATTGAA
1344028 T
1 T
1344029 CTTCAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
TAAAAATTATATTGCATTGAA
Found at i:1350831 original size:13 final size:14
Alignment explanation
Indices: 1350813--1350864 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1350803 TTATATTTAC
1350813 ACAAATATATAT-T
1 ACAAATATATATAT
*
1350826 ACAAATATATCTAT
1 ACAAATATATATAT
* *
1350840 ATAAATATATTTAT
1 ACAAATATATATAT
1350854 ATCTAAATATA
1 A-C-AAATATA
1350865 AGTTTCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.34
14 14 0.44
16 7 0.22
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (14 bp):
ACAAATATATATAT
Found at i:1352917 original size:17 final size:17
Alignment explanation
Indices: 1352887--1352932 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1352877 CAACATTTTT
1352887 AAAAGTATTT-TAAATTC
1 AAAA-TATTTATAAATTC
1352904 AAAATATTTATAAAATTC
1 AAAATATTTAT-AAATTC
*
1352922 TAAAT-TTTATA
1 AAAATATTTATA
1352933 TTTTTTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.23
17 10 0.38
18 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AAAATATTTATAAATTC
Found at i:1352921 original size:18 final size:17
Alignment explanation
Indices: 1352898--1352932 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1352888 AAAGTATTTT
1352898 AAATTCAAAATATTTATA
1 AAATTCAAAAT-TTTATA
*
1352916 AAATTCTAAATTTTATA
1 AAATTCAAAATTTTATA
1352933 TTTTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTCAAAATTTTATA
Found at i:1359493 original size:69 final size:69
Alignment explanation
Indices: 1359382--1359524 Score: 286
Period size: 69 Copynumber: 2.1 Consensus size: 69
1359372 TGAAAAATTA
1359382 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAATG
1 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAATG
1359447 GTTG
66 GTTG
1359451 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAATG
1 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAATG
1359516 GTTG
66 GTTG
1359520 GACCT
1 GACCT
1359525 TTCATACAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (69 bp):
GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAATG
GTTG
Found at i:1372319 original size:91 final size:91
Alignment explanation
Indices: 1372185--1372369 Score: 352
Period size: 91 Copynumber: 2.0 Consensus size: 91
1372175 TAGATGACCT
1372185 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCAGAGTTATTTCTGACTTA
1 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCAGAGTTATTTCTGACTTA
1372250 ATCTGGAAAGTCTCTACTTATCTTTG
66 ATCTGGAAAGTCTCTACTTATCTTTG
* *
1372276 TTTTAGCTTATCAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCAGAGTTATTTCTGACTTA
1372341 ATCTGGAAAGTCTCTACTTATCTTTG
66 ATCTGGAAAGTCTCTACTTATCTTTG
1372367 TTT
1 TTT
1372370 GATGAAGATG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (91 bp):
TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCAGAGTTATTTCTGACTTA
ATCTGGAAAGTCTCTACTTATCTTTG
Found at i:1373046 original size:21 final size:21
Alignment explanation
Indices: 1373022--1373083 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1373012 TGGTGAGAGT
* * *
1373022 GACGAAGAGGATGACGATGAC
1 GACGATGATGATGACGATGAA
**
1373043 GACGATGATGATGGGGATGAA
1 GACGATGATGATGACGATGAA
*
1373064 GATGATGATGATGACGATGA
1 GACGATGATGATGACGATGA
1373084 TGGTGAGGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.08, G:0.39, T:0.18
Consensus pattern (21 bp):
GACGATGATGATGACGATGAA
Found at i:1373112 original size:15 final size:15
Alignment explanation
Indices: 1373088--1373122 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1373078 CGATGATGGT
*
1373088 GAGGATGAAGAAGAG
1 GAGGACGAAGAAGAG
*
1373103 GAGGACGAAGAAGAT
1 GAGGACGAAGAAGAG
1373118 GAGGA
1 GAGGA
1373123 TGATGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06
Consensus pattern (15 bp):
GAGGACGAAGAAGAG
Found at i:1382351 original size:18 final size:18
Alignment explanation
Indices: 1382328--1382367 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1382318 TGCTAAAAAG
*
1382328 AAAAATT-CATAATTGATT
1 AAAAATTCCA-AAATGATT
1382346 AAAAATTCCAAAATGATT
1 AAAAATTCCAAAATGATT
1382364 AAAA
1 AAAA
1382368 TTAGCCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATTCCAAAATGATT
Found at i:1383487 original size:18 final size:17
Alignment explanation
Indices: 1383444--1383499 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
1383434 TATCAATAAA
*
1383444 AAAATTATTTAAAAACTC
1 AAAATTATTTAAAAA-TT
**
1383462 AATTTTATTTAAAAATAT
1 AAAATTATTTAAAAAT-T
*
1383480 AAAATTA-TAAAAAATT
1 AAAATTATTTAAAAATT
1383496 AAAA
1 AAAA
1383500 CCTCAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 5 0.16
17 8 0.26
18 18 0.58
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTATTTAAAAATT
Found at i:1387809 original size:46 final size:45
Alignment explanation
Indices: 1387742--1388021 Score: 312
Period size: 46 Copynumber: 6.6 Consensus size: 45
1387732 TTTGAGTACT
* *
1387742 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1387788 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1387824 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
1387860 TATGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
* *
1387906 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
1387952 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
1387997 TCTTATCAAG-G-ACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
1388022 ATCATACGTA
Statistics
Matches: 212, Mismatches: 11, Indels: 25
0.85 0.04 0.10
Matches are distributed among these distances:
36 63 0.30
38 1 0.00
39 2 0.01
40 4 0.02
42 4 0.02
43 15 0.07
44 2 0.01
45 21 0.10
46 99 0.47
47 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:1387824 original size:36 final size:36
Alignment explanation
Indices: 1387778--1387886 Score: 191
Period size: 36 Copynumber: 3.0 Consensus size: 36
1387768 GGTAGCTTTA
*
1387778 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1387814 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
1387850 GCTATACTTATATGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1387886 G
1 G
1387887 GTAGCTTTAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:1389307 original size:13 final size:14
Alignment explanation
Indices: 1389282--1389335 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
1389272 ATAATATATG
1389282 TATAATAATAATAA
1 TATAATAATAATAA
1389296 TATAAT-ATAATAA
1 TATAATAATAATAA
1389309 TA-AATGCTAATAATAA
1 TATAA---TAATAATAA
*
1389325 TATAGTAATAA
1 TATAATAATAA
1389336 ACAATTTAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 9 0.26
14 12 0.35
15 1 0.03
16 9 0.26
17 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (14 bp):
TATAATAATAATAA
Found at i:1389321 original size:16 final size:17
Alignment explanation
Indices: 1389283--1389335 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
1389273 TAATATATGT
1389283 ATAATAATAATAATATA
1 ATAATAATAATAATATA
*
1389300 AT-ATAATAATAA-ATG
1 ATAATAATAATAATATA
*
1389315 CTAATAATAAT-ATAGTA
1 ATAATAATAATAATA-TA
1389332 ATAA
1 ATAA
1389336 ACAATTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 4 0.14
16 19 0.66
17 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATATA
Found at i:1398459 original size:24 final size:25
Alignment explanation
Indices: 1398415--1398468 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
1398405 TCACAACAAG
1398415 AAAAAAGAAAGTTTCATTTTTAGTC
1 AAAAAAGAAAGTTTCATTTTTAGTC
1398440 AAAAAAGAAAGTTTCATTTTTAGTC
1 AAAAAAGAAAGTTTCATTTTTAGTC
1398465 AAAA
1 AAAA
1398469 CTAATTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.33
Consensus pattern (25 bp):
AAAAAAGAAAGTTTCATTTTTAGTC
Found at i:1405198 original size:9 final size:10
Alignment explanation
Indices: 1405176--1405232 Score: 61
Period size: 9 Copynumber: 6.2 Consensus size: 10
1405166 TTTTGGTTAA
1405176 AAATTAACCG
1 AAATTAACCG
1405186 -AATT-ACCG
1 AAATTAACCG
1405194 AAATTAACC-
1 AAATTAACCG
*
1405203 AAATTAATCG
1 AAATTAACCG
*
1405213 -AATTACCCG
1 AAATTAACCG
1405222 -AATTAACCG
1 AAATTAACCG
1405231 AA
1 AA
1405233 CTAAATCACT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 4 0.10
9 31 0.79
10 4 0.10
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (10 bp):
AAATTAACCG
Found at i:1405199 original size:18 final size:19
Alignment explanation
Indices: 1405176--1405232 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
1405166 TTTTGGTTAA
1405176 AAATTAACCGAATT-ACCG
1 AAATTAACCGAATTAACCG
* *
1405194 AAATTAACCAAATTAATCG
1 AAATTAACCGAATTAACCG
*
1405213 -AATTACCCGAATTAACCG
1 AAATTAACCGAATTAACCG
1405231 AA
1 AA
1405233 CTAAATCACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (19 bp):
AAATTAACCGAATTAACCG
Found at i:1405209 original size:27 final size:27
Alignment explanation
Indices: 1405176--1405229 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1405166 TTTTGGTTAA
1405176 AAATTAACCGAATTA-CCGAAATTAACC
1 AAATTAACCGAATTACCCG-AATTAACC
*
1405203 AAATTAATCGAATTACCCGAATTAACC
1 AAATTAACCGAATTACCCGAATTAACC
1405230 GAACTAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.24
Consensus pattern (27 bp):
AAATTAACCGAATTACCCGAATTAACC
Found at i:1421590 original size:41 final size:41
Alignment explanation
Indices: 1421435--1421580 Score: 217
Period size: 41 Copynumber: 3.6 Consensus size: 41
1421425 TGATTCAGTA
1421435 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1421476 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* * *
1421517 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-AAT-TACTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA--T
1421558 CACCGGCATTAAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
1421581 GTAACGTCTG
Statistics
Matches: 98, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 91 0.93
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:1462198 original size:17 final size:18
Alignment explanation
Indices: 1462148--1462202 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
1462138 GTCAACAAAT
* *
1462148 AATTTAAAAATTATAGAAA
1 AATTCAAAAATTA-AAAAA
* *
1462167 TATTCAAAAAATAAAAAA
1 AATTCAAAAATTAAAAAA
1462185 AATTC-AAAATTAAAAAA
1 AATTCAAAAATTAAAAAA
1462202 A
1 A
1462203 TTAAAAGTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 12 0.40
18 8 0.27
19 10 0.33
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (18 bp):
AATTCAAAAATTAAAAAA
Found at i:1462199 original size:16 final size:15
Alignment explanation
Indices: 1462174--1462208 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1462164 AAATATTCAA
1462174 AAAATAAAAAAAATT
1 AAAATAAAAAAAATT
*
1462189 CAAAATTAAAAAAATT
1 -AAAATAAAAAAAATT
1462205 AAAA
1 AAAA
1462209 GTTCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATAAAAAAAATT
Found at i:1467335 original size:30 final size:31
Alignment explanation
Indices: 1467274--1467350 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
1467264 TTACAATTTG
1467274 GTCACTGAACTATTAAAAAATTTTCATTTAA
1 GTCACTGAACTATTAAAAAATTTTCATTTAA
* * *
1467305 GTCACTAAACTATTCAAAAGTTTT-ATTTAA
1 GTCACTGAACTATTAAAAAATTTTCATTTAA
*
1467335 GTCATTGAACTATTAA
1 GTCACTGAACTATTAA
1467351 GTTTTTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (31 bp):
GTCACTGAACTATTAAAAAATTTTCATTTAA
Found at i:1471705 original size:67 final size:67
Alignment explanation
Indices: 1471592--1471726 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 67
1471582 TTCATTAAAC
*
1471592 TATTACGACAAAAAGATCTTATCTCAGATACCAAAAAAAAAAGATTCTCAGGTCAGTTGAATTTA
1 TATTACGACAAAAAGATCTTATCTCAGATACCAAAAAAAAAAGATTCTCAAGTCAGTTGAATTTA
1471657 CA
66 CA
* * * *
1471659 TATTACGACAAAAAGATCTTATTTCAGATGCCAAAAAAAAATGATTCTCAAGTCAGTTTAATTTA
1 TATTACGACAAAAAGATCTTATCTCAGATACCAAAAAAAAAAGATTCTCAAGTCAGTTGAATTTA
1471724 CA
66 CA
1471726 T
1 T
1471727 GATATAATTC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.30
Consensus pattern (67 bp):
TATTACGACAAAAAGATCTTATCTCAGATACCAAAAAAAAAAGATTCTCAAGTCAGTTGAATTTA
CA
Found at i:1475441 original size:23 final size:22
Alignment explanation
Indices: 1475412--1475457 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1475402 AAATGGTAAT
1475412 TTTTTTTTAAAGTAAGAAAATGA
1 TTTTTTTT-AAGTAAGAAAATGA
* *
1475435 TTTTTTTTAGGTAAGATAATGA
1 TTTTTTTTAAGTAAGAAAATGA
1475457 T
1 T
1475458 AATTTTAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (22 bp):
TTTTTTTTAAGTAAGAAAATGA
Found at i:1475463 original size:23 final size:23
Alignment explanation
Indices: 1475414--1475463 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1475404 ATGGTAATTT
1475414 TTTTTTAAAGTAAGAAAATGAT-
1 TTTTTTAAAGTAAGAAAATGATA
* * *
1475436 TTTTTTTAGGTAAGATAATGATA
1 TTTTTTAAAGTAAGAAAATGATA
*
1475459 ATTTT
1 TTTTT
1475464 AGATATGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (23 bp):
TTTTTTAAAGTAAGAAAATGATA
Found at i:1476026 original size:43 final size:43
Alignment explanation
Indices: 1475978--1476077 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
1475968 AGAGTAATAC
* *
1475978 CTTTAGCGGCGTTTTTGGTATAAGCACTGCTATAGA-CTAGGGT
1 CTTTAGCGGCGTTTTTGGTAAAAGCACCGCTATAGATC-AGGGT
* *
1476021 CTTTAGCGACGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTGGTAAAAGCACCGCTATAGATCAGGGT
*
1476064 CTTTAGTGGCGTTT
1 CTTTAGCGGCGTTT
1476078 GTGACCAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 49 0.98
44 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGGTAAAAGCACCGCTATAGATCAGGGT
Found at i:1476092 original size:43 final size:43
Alignment explanation
Indices: 1476006--1476102 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 43
1475996 TATAAGCACT
* **
1476006 GCTATAGACTAGGGTCTTTAGCGACGTTTTTGGTAAAAGCGCC
1 GCTATAGACTAGGGTCTTTAGCGACGTTTGTGCCAAAAGCGCC
* *
1476049 GCTATAGA-TCAGGGTCTTTAGTGGCGTTTGTGACCAAAA-CGCC
1 GCTATAGACT-AGGGTCTTTAGCGACGTTTGTG-CCAAAAGCGCC
*
1476092 GCTAAAGACTA
1 GCTATAGACTA
1476103 ACACCTTTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
42 1 0.02
43 39 0.87
44 5 0.11
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (43 bp):
GCTATAGACTAGGGTCTTTAGCGACGTTTGTGCCAAAAGCGCC
Found at i:1476284 original size:19 final size:18
Alignment explanation
Indices: 1476250--1476285 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1476240 TATATATTAA
1476250 ACAAATAATATAATAAAT
1 ACAAATAATATAATAAAT
*
1476268 ACAAATAAATATTATAAA
1 ACAAAT-AATATAATAAA
1476286 ATTCGTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
ACAAATAATATAATAAAT
Found at i:1476478 original size:21 final size:21
Alignment explanation
Indices: 1476449--1476503 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1476439 TTTGACGCTG
1476449 CTCTGCTTCCCTCGCTTCAGC
1 CTCTGCTTCCCTCGCTTCAGC
* *
1476470 CTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTTCAGC
1476491 CTCTGCTTCCCTC
1 CTCTGCTTCCCTC
1476504 TTAGCAGCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.05, C:0.47, G:0.11, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTTCAGC
Found at i:1480444 original size:37 final size:37
Alignment explanation
Indices: 1480387--1480589 Score: 338
Period size: 37 Copynumber: 5.5 Consensus size: 37
1480377 TGCCTCATGT
* *
1480387 AAGAGACAAAGTGATGAGTGGCTACACTTATCTGATC
1 AAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC
1480424 AAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC
1 AAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC
*
1480461 AAGAAACAAAGTGATAAGTGGCTATACTTATCTGATC
1 AAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC
1480498 AAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC
1 AAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC
*
1480535 AAGAAACAAAGTGATAGGTGGCTACACTTATCTGATC
1 AAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC
**
1480572 -AGGGAC-AAGTGATAAGTG
1 AAGAAACAAAGTGATAAGTG
1480590 ATCATACGTA
Statistics
Matches: 158, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
35 11 0.07
36 4 0.03
37 143 0.91
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (37 bp):
AAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC
Found at i:1481920 original size:58 final size:58
Alignment explanation
Indices: 1481843--1482010 Score: 237
Period size: 58 Copynumber: 3.0 Consensus size: 58
1481833 CATGTGAACA
1481843 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1481902 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATA--
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
* * *
1481958 TGTG--A--T--TT-CGTGTAAGACCATAGTTGGGCTATGGCATCGGTATGTGATTTG
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1482009 TG
1 TG
1482011 ATTACGTGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
49 38 0.37
50 2 0.02
51 2 0.02
52 1 0.01
54 1 0.01
56 4 0.04
58 51 0.49
59 5 0.05
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (58 bp):
TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:1481952 original size:28 final size:28
Alignment explanation
Indices: 1481862--1481952 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
1481852 GTGATTCCGT
1481862 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
1481890 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
1481919 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
1481948 GTAAG
1 GTAAG
1481953 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:1481975 original size:49 final size:49
Alignment explanation
Indices: 1481903--1482045 Score: 232
Period size: 49 Copynumber: 2.9 Consensus size: 49
1481893 AGTGATATGT
* *
1481903 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
1481952 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
1482001 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
1482046 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:1485252 original size:52 final size:46
Alignment explanation
Indices: 1485233--1485472 Score: 273
Period size: 46 Copynumber: 5.3 Consensus size: 46
1485223 TGACAAGTGG
* *
1485233 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1485279 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
* *
1485325 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
** * *
1485377 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
**
1485423 AAAGTG---A-TG--AG--T-GGCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1485460 AAAGTGATAAGTG
1 AAAGTGATAAGTG
1485473 GCTACACTTA
Statistics
Matches: 173, Mismatches: 11, Indels: 25
0.83 0.05 0.12
Matches are distributed among these distances:
37 28 0.16
38 1 0.01
40 3 0.02
41 2 0.01
42 2 0.01
43 1 0.01
46 92 0.53
52 44 0.25
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
Found at i:1485287 original size:98 final size:98
Alignment explanation
Indices: 1485167--1485418 Score: 450
Period size: 98 Copynumber: 2.6 Consensus size: 98
1485157 TTTGAGTACT
*
1485167 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
1485232 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
1485265 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
1485330 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
1485363 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
1485419 AGATAAAGTG
Statistics
Matches: 146, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 146 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:1485442 original size:37 final size:36
Alignment explanation
Indices: 1485399--1485527 Score: 213
Period size: 37 Copynumber: 3.5 Consensus size: 36
1485389 GATAGCTTTA
* *
1485399 GCTACACTTATCTGATCAAGAGATAAAGTGATGAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGTG
1485436 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGTG
1485473 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATA-GTG
1485510 GCTACACTTATCTGATCA
1 GCTACACTTATCTGATCA
1485528 GGGACAAGTG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
36 1 0.01
37 87 0.99
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAGTG
Found at i:1485520 original size:74 final size:72
Alignment explanation
Indices: 1485399--1485544 Score: 222
Period size: 74 Copynumber: 2.0 Consensus size: 72
1485389 GATAGCTTTA
* *
1485399 GCTACACTTATCTGATCAAGAGATAAAGTGATGAGTGGCTACACTTATCTGATCAAGAAACAAAG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATGAGTGGCTACACTTATCTGATC-AGAAAC-AAG
1485464 TGATAAGTG
64 TGATAAGTG
**
1485473 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGGTGGCTACACTTATCTGATCAGGGACAAGT
1 GCTACACTTATCTGATCAAGAAACAAAGTGATGA-GTGGCTACACTTATCTGATCAGAAACAAGT
1485537 GATAAGTG
65 GATAAGTG
1485545 ATCATACGTA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
72 12 0.18
73 5 0.07
74 50 0.75
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (72 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATGAGTGGCTACACTTATCTGATCAGAAACAAGTG
ATAAGTG
Found at i:1486499 original size:9 final size:9
Alignment explanation
Indices: 1486463--1486890 Score: 203
Period size: 9 Copynumber: 49.8 Consensus size: 9
1486453 AATTGCACGG
1486463 GTAAGTTAT
1 GTAAGTTAT
*
1486472 GT-A-TTGT
1 GTAAGTTAT
*
1486479 GTAAGCTAT
1 GTAAGTTAT
*
1486488 GTAAGTTGT
1 GTAAGTTAT
1486497 GT-A-TTAT
1 GTAAGTTAT
1486504 GTAAGTTAT
1 GTAAGTTAT
1486513 -T-A-TTAT
1 GTAAGTTAT
1486519 GCTTTAAGTTAT
1 G---TAAGTTAT
*
1486531 GTAAGTAAT
1 GTAAGTTAT
1486540 GT-A-TTAT
1 GTAAGTTAT
*
1486547 GTAAGTTGT
1 GTAAGTTAT
*
1486556 GT-A-TAAT
1 GTAAGTTAT
*
1486563 GTTAGTTAT
1 GTAAGTTAT
1486572 GTAAGTTAT
1 GTAAGTTAT
1486581 GTAAGTTAT
1 GTAAGTTAT
1486590 GT-A---A-
1 GTAAGTTAT
1486594 GTAAGTTAT
1 GTAAGTTAT
1486603 GTAAGTTAT
1 GTAAGTTAT
** *
1486612 CAAAGTAAT
1 GTAAGTTAT
*
1486621 GTATGTTAT
1 GTAAGTTAT
1486630 GTAAG-T-T
1 GTAAGTTAT
1486637 GTAAGTTAT
1 GTAAGTTAT
*
1486646 -TATGTATTAT
1 GTAAG--TTAT
*
1486656 GTAAGTTAA
1 GTAAGTTAT
* *
1486665 G-ATGGATTAC
1 GTA-AG-TTAT
1486675 GTAAGTTAT
1 GTAAGTTAT
1486684 GTAAGTTAAAT
1 GTAAGTT--AT
1486695 GT-A-TTAT
1 GTAAGTTAT
1486702 GTAAG-T-T
1 GTAAGTTAT
1486709 GTAAGTTAGAT
1 GTAAGTT--AT
1486720 GT-A-TTAT
1 GTAAGTTAT
1486727 GTAAG-T-T
1 GTAAGTTAT
1486734 GTAAGTTAGAT
1 GTAAGTT--AT
1486745 GT-A-TTAT
1 GTAAGTTAT
1486752 GTAAG-T-T
1 GTAAGTTAT
1486759 GTAAGTTAT
1 GTAAGTTAT
*
1486768 -TATGTATTAT
1 GTAAG--TTAT
1486778 GTAAGTTAT
1 GTAAGTTAT
1486787 GTAAGTTAAAT
1 GTAAGTT--AT
1486798 GT-A-TTAT
1 GTAAGTTAT
1486805 G-AAGGTTAT
1 GTAA-GTTAT
*
1486814 GTAAGTTGT
1 GTAAGTTAT
**
1486823 GTAAGAGAT
1 GTAAGTTAT
*
1486832 TTAAGTTAT
1 GTAAGTTAT
* *
1486841 GTGAGTTTT
1 GTAAGTTAT
1486850 GT-A-TTAT
1 GTAAGTTAT
1486857 GTAAGTTAT
1 GTAAGTTAT
*
1486866 GTAGGTTAT
1 GTAAGTTAT
* *
1486875 TTAGGTTAT
1 GTAAGTTAT
1486884 GTAAGTT
1 GTAAGTT
1486891 TTGAGTTGTT
Statistics
Matches: 318, Mismatches: 45, Indels: 112
0.67 0.09 0.24
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 4 0.01
7 65 0.20
8 31 0.10
9 167 0.53
10 20 0.06
11 22 0.07
12 5 0.02
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:1486536 original size:43 final size:42
Alignment explanation
Indices: 1486463--1486636 Score: 148
Period size: 43 Copynumber: 4.2 Consensus size: 42
1486453 AATTGCACGG
* *
1486463 GTAAGTTATGTAT--TGTGTAAGCTATGTAAGTTGTGTATTAT
1 GTAAGTTATGTATAATGT-TAAGTTATGTAAGTTATGTATTAT
* *
1486504 GTAAGTTAT-TATTATGCTTTAAGTTATGTAAGTAATGTATTAT
1 GTAAGTTATGTATAATG--TTAAGTTATGTAAGTTATGTATTAT
*
1486547 GTAAGTTGTGTATAATGTT-AGTTATGTAAGTTATGTAAGTTAT
1 GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGT-A-TTAT
* ** *
1486590 GTAAG-TAAGT-T-ATG-TAAGTTATCAAAGTAATGTATGTTAT
1 GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGTA--TTAT
1486630 GTAAGTT
1 GTAAGTT
1486637 GTAAGTTATT
Statistics
Matches: 112, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
39 2 0.02
40 30 0.27
41 27 0.24
42 8 0.07
43 38 0.34
44 7 0.06
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (42 bp):
GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGTATTAT
Found at i:1486556 original size:59 final size:56
Alignment explanation
Indices: 1486479--1486862 Score: 180
Period size: 53 Copynumber: 7.0 Consensus size: 56
1486469 TATGTATTGT
* *
1486479 GTAAGCTATGTAAGTTGTGTATTATGTAAGTTAT-T-A-TTATGCTTTAAGTTATGTAA
1 GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATG---TAAGTTATGTAA
*
1486535 GTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATGTAAGTTATGTAAGTTATGTAA
1 GTAA-G--TTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
* ** * *
1486594 GTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTAT-TAT
1 GTAAGTTATGTAAGTTGT-GTA-TAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
* * * *
1486649 GT-A-TTATGTAAGTTAAGATGGATTACGTAAGTTATGTAAGTTA---AA-TGTAT-TAT
1 GTAAGTTATGTAAGTT--G-TGTATAATGTAAGTTATGTAAGTTATGTAAGT-TATGTAA
*
1486702 GTAAG-T-TGTAAGTTAGATGTATTATGTAAG-T-TGTAAGTTAGATGT-A-TTATGTAA
1 GTAAGTTATGTAAGTT-G-TGTATAATGTAAGTTATGTAAGTT--ATGTAAGTTATGTAA
* * * * *
1486756 GT-TG-TAAGTTA-TTATGTATTATGTAAGTTATGTAAGTTAAATGT-A-TTATG-AA
1 GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTT--ATGTAAGTTATGTAA
* * * *
1486808 G---GTTATGTAAGTTGTGTAAGAGATTTAAGTTATGTGAGTTTTGT-A-TTATGTAA
1 GTAAGTTATGTAAGTTGTGT-ATA-ATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
1486861 GT
1 GT
1486863 TATGTAGGTT
Statistics
Matches: 266, Mismatches: 31, Indels: 64
0.74 0.09 0.18
Matches are distributed among these distances:
50 9 0.03
51 19 0.07
52 34 0.13
53 59 0.22
54 43 0.16
55 6 0.02
56 27 0.10
57 3 0.01
58 17 0.06
59 42 0.16
60 1 0.00
61 1 0.00
62 5 0.02
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.45
Consensus pattern (56 bp):
GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
Found at i:1486558 original size:25 final size:26
Alignment explanation
Indices: 1486500--1486890 Score: 274
Period size: 25 Copynumber: 15.1 Consensus size: 26
1486490 AAGTTGTGTA
1486500 TTATGTAAGTT-AT-TATTATGCTTTAAG
1 TTATGTAAGTTAATGTATTATG---TAAG
1486527 TTATGTAAG-TAATGTATTATGTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
*
1486552 TTGTGT-A--TAATGTTAGTTATGTAAG
1 TTATGTAAGTTAATG-TA-TTATGTAAG
1486577 TTATGTAAGTT-ATGTA--A-GTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
* *
1486599 TTATGTAAGTTATCAAAGTA--ATGTATG
1 TTATGTAAG-T-T-AATGTATTATGTAAG
1486626 TTATGTAAGTTGTAA-GTTATTATGT-A-
1 TTATGTAAG-T-TAATG-TATTATGTAAG
* *
1486652 TTATGTAAGTTAAGATGGATTACGTAAG
1 TTATGTAAGTT-A-ATGTATTATGTAAG
1486680 TTATGTAAGTTAAATGTATTATGTAAG
1 TTATGTAAGTT-AATGTATTATGTAAG
1486707 -T-TGTAAGTTAGATGTATTATGTAAG
1 TTATGTAAGTTA-ATGTATTATGTAAG
1486732 -T-TGTAAGTTAGATGTATTATGTAAG
1 TTATGTAAGTTA-ATGTATTATGTAAG
1486757 -T-TGTAAGTTATTATGTATTATGTAAG
1 TTATGTAAGTTA--ATGTATTATGTAAG
1486783 TTATGTAAGTTAAATGTATTATG-AAGG
1 TTATGTAAGTT-AATGTATTATGTAA-G
* ** *
1486810 TTATGTAAGTT-GTGTAAGAGATTTAAG
1 TTATGTAAGTTAATGT-A-TTATGTAAG
* *
1486837 TTATGTGAGTT-TTGTATTATGTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
* *
1486862 TTATGTAGGTT-ATTTAGGTTATGTAAG
1 TTATGTAAGTTAATGTA--TTATGTAAG
1486889 TT
1 TT
1486891 TTGAGTTGTT
Statistics
Matches: 309, Mismatches: 24, Indels: 62
0.78 0.06 0.16
Matches are distributed among these distances:
22 14 0.05
23 7 0.02
24 6 0.02
25 104 0.34
26 48 0.16
27 94 0.30
28 35 0.11
29 1 0.00
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (26 bp):
TTATGTAAGTTAATGTATTATGTAAG
Found at i:1486597 original size:13 final size:13
Alignment explanation
Indices: 1486581--1486608 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1486571 TGTAAGTTAT
1486581 GTAAGTTATGTAA
1 GTAAGTTATGTAA
1486594 GTAAGTTATGTAA
1 GTAAGTTATGTAA
1486607 GT
1 GT
1486609 TATCAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (13 bp):
GTAAGTTATGTAA
Found at i:1486597 original size:22 final size:22
Alignment explanation
Indices: 1486572--1486661 Score: 82
Period size: 22 Copynumber: 4.1 Consensus size: 22
1486562 TGTTAGTTAT
1486572 GTAAGTTATGTAAGTTATGTAA
1 GTAAGTTATGTAAGTTATGTAA
1486594 GTAAGTTATGTAAGTTATCAAAGTAA
1 GTAAGTTATGTAAGTTAT----GTAA
*
1486620 TGTATGTTATGTAAG-T-TGTAA
1 -GTAAGTTATGTAAGTTATGTAA
*
1486641 GTTA-TTATGT-A-TTATGTAA
1 GTAAGTTATGTAAGTTATGTAA
1486660 GT
1 GT
1486662 TAAGATGGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
18 2 0.03
19 13 0.22
20 2 0.03
21 4 0.07
22 18 0.31
25 1 0.02
26 5 0.09
27 13 0.22
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.43
Consensus pattern (22 bp):
GTAAGTTATGTAAGTTATGTAA
Found at i:1486658 original size:19 final size:19
Alignment explanation
Indices: 1486636--1486786 Score: 62
Period size: 19 Copynumber: 8.5 Consensus size: 19
1486626 TTATGTAAGT
1486636 TGTAAGTTATTATGTATTA
1 TGTAAGTTATTATGTATTA
** *
1486655 TGTAAGTTAAGATGGATTA
1 TGTAAGTTATTATGTATTA
*
1486674 CGTAAG---TTATGTA--A
1 TGTAAGTTATTATGTATTA
* *
1486688 -GTTAAATGTATTATGTAAGT-
1 TG-TAAGT-TATTATGT-ATTA
*
1486708 TGTAAGTTA-GATGTATTA
1 TGTAAGTTATTATGTATTA
* *
1486726 TGTAAGTT-GTAAG--TTA
1 TGTAAGTTATTATGTATTA
* *
1486742 -G-ATG-TATTATGTAAGT-
1 TGTAAGTTATTATGT-ATTA
1486758 TGTAAGTTATTATGTATTA
1 TGTAAGTTATTATGTATTA
1486777 TGTAAGTTAT
1 TGTAAGTTAT
1486787 GTAAGTTAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 38
0.62 0.13 0.25
Matches are distributed among these distances:
13 2 0.02
14 9 0.10
15 1 0.01
16 7 0.07
17 4 0.04
18 24 0.26
19 42 0.45
20 4 0.04
21 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (19 bp):
TGTAAGTTATTATGTATTA
Found at i:1486857 original size:43 final size:43
Alignment explanation
Indices: 1486810--1486893 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
1486800 ATTATGAAGG
* *
1486810 TTATGTAAGTTGTGTAAGAGATTTAAGTTATGTGAGTTTTGTA
1 TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
* ** *
1486853 TTATGTAAGTTATGTAGGTTATTTAGGTTATGTAAGTTTTG
1 TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTG
1486894 AGTTGTTCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
Found at i:1487090 original size:92 final size:92
Alignment explanation
Indices: 1486977--1487184 Score: 391
Period size: 92 Copynumber: 2.3 Consensus size: 92
1486967 AAAATAAATA
*
1486977 ATTTAATTAT-ATTTTAACATAATTATTGTTAAGTACAATTTAATAAAATAATATATAATTTAAT
1 ATTTAATAATAATTTTAACATAATTATTGTTAAGTACAATTTAATAAAATAATATATAATTTAAT
1487041 AACATTACTAATATAATTATTAATAAT
66 AACATTACTAATATAATTATTAATAAT
1487068 ATTTAATAATAATTTTAACATAATTATTGTTAAGTACAATTTAATAAAATAATATATAATTTAAT
1 ATTTAATAATAATTTTAACATAATTATTGTTAAGTACAATTTAATAAAATAATATATAATTTAAT
1487133 AACATTACTAATATAATTATTAATAAT
66 AACATTACTAATATAATTATTAATAAT
*
1487160 ATTTAATAATAATTTTAATATAATT
1 ATTTAATAATAATTTTAACATAATT
1487185 TTATTATTAA
Statistics
Matches: 114, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
91 9 0.08
92 105 0.92
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (92 bp):
ATTTAATAATAATTTTAACATAATTATTGTTAAGTACAATTTAATAAAATAATATATAATTTAAT
AACATTACTAATATAATTATTAATAAT
Found at i:1489572 original size:40 final size:42
Alignment explanation
Indices: 1489523--1489604 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 42
1489513 TTGTCGATTC
*
1489523 CAACTTTTACGGCG-CTT-ACAATCAAACGCCACTAAT-TTTA
1 CAACATTTACGGCGTCTTGACAAT-AAACGCCACTAATATTTA
* *
1489563 CAACATTTACGGCGTTTTGAGAATAAACGCCACTAATATTTA
1 CAACATTTACGGCGTCTTGACAATAAACGCCACTAATATTTA
1489605 ATTCGTCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 13 0.36
41 15 0.42
42 8 0.22
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.30
Consensus pattern (42 bp):
CAACATTTACGGCGTCTTGACAATAAACGCCACTAATATTTA
Found at i:1490347 original size:39 final size:39
Alignment explanation
Indices: 1490283--1490368 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
1490273 AATTCCTAAC
*
1490283 CCAT-AACCCCTAAATCCCCTAAACCCTTAAAGCATAAA
1 CCATAAACCCCTAAATCCCCTAAACCCCTAAAGCATAAA
*
1490321 CCATAAACCCCTAAATCTCCCT-AACCCCTAAAGCATAAC
1 CCATAAACCCCTAAATC-CCCTAAACCCCTAAAGCATAAA
*
1490360 CCCTAAACC
1 CCATAAACC
1490369 ATTCCAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 4 0.09
39 35 0.81
40 4 0.09
ACGTcount: A:0.40, C:0.41, G:0.02, T:0.17
Consensus pattern (39 bp):
CCATAAACCCCTAAATCCCCTAAACCCCTAAAGCATAAA
Found at i:1491152 original size:31 final size:32
Alignment explanation
Indices: 1491080--1491154 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 32
1491070 TAACCCATAT
* * *
1491080 ATAACCCCTAAATCCCCTTTAACCCTTAAAGC
1 ATAACCCCTAAATCCCCTCTAACCCCTAAACC
* **
1491112 ATAAACCCTAAA-CTTCTCTAACCCCTAAACC
1 ATAACCCCTAAATCCCCTCTAACCCCTAAACC
*
1491143 GTAACCCCTAAA
1 ATAACCCCTAAA
1491155 AAATTTATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.23
Consensus pattern (32 bp):
ATAACCCCTAAATCCCCTCTAACCCCTAAACC
Found at i:1491450 original size:22 final size:22
Alignment explanation
Indices: 1491425--1491478 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1491415 CTTACCGTTC
*
1491425 AAACCCTAAACCAAAAATCCCT
1 AAACCCTAAACCAAAAACCCCT
**
1491447 AAACCCTAAACCCTAAACCCCT
1 AAACCCTAAACCAAAAACCCCT
*
1491469 AAACCATAAA
1 AAACCCTAAA
1491479 TCTTAAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (22 bp):
AAACCCTAAACCAAAAACCCCT
Found at i:1491468 original size:15 final size:14
Alignment explanation
Indices: 1491425--1491478 Score: 63
Period size: 15 Copynumber: 3.7 Consensus size: 14
1491415 CTTACCGTTC
**
1491425 AAACCCTAAACCAA
1 AAACCCTAAACCCT
1491439 AAATCCCTAAACCCT
1 AAA-CCCTAAACCCT
1491454 AAACCCTAAACCCCT
1 AAACCCTAAA-CCCT
*
1491469 AAACCATAAA
1 AAACCCTAAA
1491479 TCTTAAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.29
15 25 0.71
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (14 bp):
AAACCCTAAACCCT
Found at i:1491470 original size:8 final size:7
Alignment explanation
Indices: 1491425--1491478 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
1491415 CTTACCGTTC
1491425 AAACCCT
1 AAACCCT
**
1491432 AAACCAA
1 AAACCCT
1491439 AAATCCCT
1 AAA-CCCT
1491447 AAACCCT
1 AAACCCT
1491454 AAACCCT
1 AAACCCT
1491461 AAACCCCT
1 AAA-CCCT
*
1491469 AAACCAT
1 AAACCCT
1491476 AAA
1 AAA
1491479 TCTTAAATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 28 0.70
8 12 0.30
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:1491996 original size:113 final size:112
Alignment explanation
Indices: 1491763--1492311 Score: 465
Period size: 114 Copynumber: 4.8 Consensus size: 112
1491753 AATCCCTGAT
* * * * *
1491763 CATTAGCTGCGCTTTTCTAAAAACGCCGCTAAATCCCTCAAAAGCACAGAAAACGACGACGTTGC
1 CATTAGCGGCGCTTTAC-AAAAACGCCGCTAAATCCC-CGAAAGCTCAGAAAACGACGTCGTTGC
* *
1491828 GCTTAGTTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGAC-TGAA
64 GCTTAG-GTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGACTTCAA
* *
1491877 CATTAGCGGCGCTTTAACAAAAACGCCGCTAAAATCCCCGAAAGC-CAGAAAACGGCGTCGTTGG
1 CATTAGCGGCGCTTT-ACAAAAACGCCGCT-AAATCCCCGAAAGCTCAGAAAACGACGTCGTTGC
* *
1491941 GCTTAGGTTTTTTGCGGCGCATT-AACAAAAACGCCGCTAAAGACTTCAA
64 GCTTAGGTTTTTTGCGGCGCTTTCCA-AAAAACGCCGCTAAAGACTTCAA
* * * * * * *
1491990 CATTAGCGGCGCTTT-CTGTAAAAGCGCCACTAAATCCCTGAAAGCTCGGGAGACGACGTCATTG
1 CATTAGCGGCGCTTTAC---AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTG
* * * * *
1492054 CGC-TA-GTATTAAGTAGCGGCGCTTTTCC-AGAAACGCTGCTAAAGACCT-AA
63 CGCTTAGGT-TT--TTTGCGGCGC-TTTCCAAAAAACGCCGCTAAAGACTTCAA
* * * * *
1492104 CCATTAGCGGCGCTTTATAGAAAGCGCCGCTACATCCCTGAAAGCTC-GAGAAACGACATCGTTG
1 -CATTAGCGGCGCTTTACA-AAAACGCCGCTAAATCCCCGAAAGCTCAGA-AAACGACGTCGTTG
* * * * * * *
1492168 GGCTTAGTTATTTTTCCGGCGCTTTCCTAGAAACGCCGCTAAAGCCTTCAG
63 CGCTTAGGT-TTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGACTTCAA
* * * * * *
1492219 CATTAGCGGCGC-TTACTGAAAAAAGCCGCTAAATCACCGAATGCT-GGGAAACGGCGTCGTTGC
1 CATTAGCGGCGCTTTAC--AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGC
1492282 GC-TAGGTTTTTTGCGGCGCTTTCTCAAAAA
64 GCTTAGGTTTTTTGCGGCGCTTTC-CAAAAA
1492312 TGCCGGTAAT
Statistics
Matches: 353, Mismatches: 57, Indels: 52
0.76 0.12 0.11
Matches are distributed among these distances:
111 17 0.05
112 43 0.12
113 81 0.23
114 154 0.44
115 52 0.15
116 6 0.02
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (112 bp):
CATTAGCGGCGCTTTACAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGCGC
TTAGGTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGACTTCAA
Found at i:1492168 original size:228 final size:226
Alignment explanation
Indices: 1491842--1492286 Score: 537
Period size: 228 Copynumber: 2.0 Consensus size: 226
1491832 AGTTTTTTTT
1491842 GCGGCGCTTTCCAAAAAACGCCGCTAAAGACTGAACATTAGCGGCGCTTTAACAAAAACGCCGCT
1 GCGGCGCTTTCCAAAAAACGCCGCTAAAGACTGAACATTAGCGGCGCTTTAACAAAAACGCCGCT
* * *
1491907 AAAATCCCCGAAAGCCAGAAAACGGCGTCGTTGGGCTTAGGT-TTTTTGCGGCGCATTAAC-AAA
66 AAAATCCCCGAAAGCCAGAAAACGACATCGTTGGGCTTAGGTATTTTTCCGGCGC-TTAACTAAA
* **
1491970 AACGCCGCTAAAGACTTCAACATTAGCGGCGCTTTCTGTAAAAGCGCCACTAAATC-CCTGAAAG
130 AACGCCGCTAAAGACTTCAACATTAGCGGCGCTTACTG-AAAAAAGCCACTAAATCACC-GAAAG
*
1492034 CTCGGGAGACGACGTCATTGCGCTAGTATTAAGTA
193 CT-GGGAAACGACGTCATTGCGCTAGTATTAAGTA
* * * *
1492069 GCGGCGCTTTTCC-AGAAACGCTGCTAAAGACCT-AACCATTAGCGGCGCTTTATA-GAAAGCGC
1 GCGGCGC-TTTCCAAAAAACGCCGCTAAAGA-CTGAA-CATTAGCGGCGCTTTA-ACAAAAACGC
* * * **
1492131 CGCT-ACATCCCTGAAAGCTC-GAGAAACGACATCGTTGGGCTTAGTTATTTTTCCGGCGCTTTC
62 CGCTAAAATCCCCGAAAGC-CAGA-AAACGACATCGTTGGGCTTAGGTATTTTTCCGGCGCTTAA
* * * *
1492194 CTAGAAACGCCGCTAAAGCCTTCAGCATTAGCGGCGCTTACTGAAAAAAGCCGCTAAATCACCGA
125 CTAAAAACGCCGCTAAAGACTTCAACATTAGCGGCGCTTACTGAAAAAAGCCACTAAATCACCGA
* * *
1492259 ATGCTGGGAAACGGCGTCGTTGCGCTAG
190 AAGCTGGGAAACGACGTCATTGCGCTAG
1492287 GTTTTTTGCG
Statistics
Matches: 186, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
227 58 0.31
228 77 0.41
229 51 0.27
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.22
Consensus pattern (226 bp):
GCGGCGCTTTCCAAAAAACGCCGCTAAAGACTGAACATTAGCGGCGCTTTAACAAAAACGCCGCT
AAAATCCCCGAAAGCCAGAAAACGACATCGTTGGGCTTAGGTATTTTTCCGGCGCTTAACTAAAA
ACGCCGCTAAAGACTTCAACATTAGCGGCGCTTACTGAAAAAAGCCACTAAATCACCGAAAGCTG
GGAAACGACGTCATTGCGCTAGTATTAAGTA
Found at i:1493046 original size:16 final size:17
Alignment explanation
Indices: 1493021--1493053 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1493011 CTTTTAATTT
*
1493021 TTTTATAATTTATAATA
1 TTTTATAATTAATAATA
1493038 TTTTA-AATTAATAATA
1 TTTTATAATTAATAATA
1493054 GTAAAATTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATAATTAATAATA
Found at i:1500638 original size:4 final size:4
Alignment explanation
Indices: 1500629--1500673 Score: 81
Period size: 4 Copynumber: 11.2 Consensus size: 4
1500619 ACCCCTATAC
*
1500629 GTAT GTAT GTGT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1500674 CATAGTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:1505607 original size:47 final size:47
Alignment explanation
Indices: 1505554--1505647 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1505544 AAACTGAGCA
*
1505554 GAAGTATTAATGGATAGATTTGCAAAATAGCTAACAATGAATGCACT
1 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1505601 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1505648 TACTTTCTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (47 bp):
GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
Found at i:1512981 original size:24 final size:20
Alignment explanation
Indices: 1512936--1512976 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1512926 AACCCCTTAA
1512936 AATAATTTTTTATTTAATTT
1 AATAATTTTTTATTTAATTT
1512956 AATAATTTTTTATTTAATTT
1 AATAATTTTTTATTTAATTT
1512976 A
1 A
1512977 TTTAAAATTT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATAATTTTTTATTTAATTT
Found at i:1528708 original size:3 final size:3
Alignment explanation
Indices: 1528702--1528726 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1528692 ACCACCACAA
1528702 CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG C
1528727 TCTAGCGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1530338 original size:27 final size:28
Alignment explanation
Indices: 1530308--1530361 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
1530298 TAAAATTGAC
*
1530308 TAATTCAA-AAAGTATAGAAGA-TAAAAT
1 TAATTAAATAAAGTATA-AAGACTAAAAT
1530335 TAATTAAATTAAAGTATAAAGACTAAA
1 TAATTAAA-TAAAGTATAAAGACTAAA
1530362 TTCATAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 7 0.30
28 4 0.17
29 12 0.52
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (28 bp):
TAATTAAATAAAGTATAAAGACTAAAAT
Found at i:1531901 original size:35 final size:35
Alignment explanation
Indices: 1531852--1531963 Score: 133
Period size: 34 Copynumber: 3.3 Consensus size: 35
1531842 AAAATATATC
* *
1531852 AGGGTTT-GGAGTTTTTTAAAAAATTAATTAAGTT
1 AGGGTTTATGAGTTTTTTAAAAAATTAATTAAATT
* *
1531886 AGGTTTTATG-G-GTTTTAAATAAATTAATTAAATT
1 AGGGTTTATGAGTTTTTTAAA-AAATTAATTAAATT
*
1531920 AGGGTTTA-GAGTTTTTAAAAAAAATTAATTAAATT
1 AGGGTTTATGAGTTTTT-TAAAAAATTAATTAAATT
1531955 AGGGTTTAT
1 AGGGTTTAT
1531964 TTTAAAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
33 8 0.12
34 28 0.43
35 26 0.40
36 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (35 bp):
AGGGTTTATGAGTTTTTTAAAAAATTAATTAAATT
Found at i:1532193 original size:124 final size:123
Alignment explanation
Indices: 1532050--1532423 Score: 541
Period size: 124 Copynumber: 3.0 Consensus size: 123
1532040 GTAGTTTCAA
* *
1532050 AAAAATTAATTTTGAGAAGACAGTTCTGAAAAAATGGTGTCAAAAACGCTTTAAGCAAGATGCAC
1 AAAAA-TAATTTTGAGAAGACGGTTCTGAAAAAATGGTGTCAAAAACGCTTCAAGCAAGATGCAC
** *
1532115 TGTCAGCAAAAATATTGAAAAAAGCTCTCATATGACGCTCTTTTTCTACATTAGTTCTTG
65 TGTCAGCAAAAATA-TGAAAAAAGCTCTCACGTGACGCTCTTTTTCTACAGTAGTTCTTG
* * *
1532175 AAAAATAATTTTGAGAAGACGGTTTTGAAGAAATGGTGTCAAAAATGCTTCAAGCAAGATGCACT
1 AAAAATAATTTTGAGAAGACGGTTCTGAAAAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
* * *
1532240 GTCAGCAAAAATACTGAAAAAAGCTCCCACGTGGCGCTCTTTTTATACAGTAGTTCTTG
66 GTCAGCAAAAATA-TGAAAAAAGCTCTCACGTGACGCTCTTTTTCTACAGTAGTTCTTG
* * * * *
1532299 AAAAATAATTTTGAGAAGATGGTTCTGAACAAATTGTGTCAAAAACACTTCAAGCAAGATGCATT
1 AAAAATAATTTTGAGAAGACGGTTCTGAAAAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
* *
1532364 GTTAGCAAAATTGATGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCTTG
66 GTCAGCAAAAAT-ATGAAAAAAGCTCTCACGT-GACGCTCTTTTTCTACAGTAGTTCTTG
1532424 TTTGGCCTTA
Statistics
Matches: 223, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
124 192 0.86
125 31 0.14
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (123 bp):
AAAAATAATTTTGAGAAGACGGTTCTGAAAAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
GTCAGCAAAAATATGAAAAAAGCTCTCACGTGACGCTCTTTTTCTACAGTAGTTCTTG
Found at i:1535485 original size:15 final size:15
Alignment explanation
Indices: 1535447--1535488 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1535437 TTTGTACAAA
*
1535447 TATATTAAAACAATT
1 TATATTAAAATAATT
1535462 TATATTAAAATAATT
1 TATATTAAAATAATT
1535477 TACTA-TAAAATA
1 TA-TATTAAAATA
1535489 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATTAAAATAATT
Found at i:1536534 original size:7 final size:7
Alignment explanation
Indices: 1536524--1536548 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1536514 TTATATACAT
1536524 AATACTA
1 AATACTA
1536531 AATACTA
1 AATACTA
1536538 AATACTA
1 AATACTA
1536545 AATA
1 AATA
1536549 TGAAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:1537011 original size:26 final size:27
Alignment explanation
Indices: 1536974--1537025 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1536964 TAAATATATA
1536974 TTTTTTATTTTTTAATTTTAAAATACT
1 TTTTTTATTTTTTAATTTTAAAATACT
*
1537001 TTTTTTATTTTTTATTTTTAAAATA
1 TTTTTTATTTTTTAATTTTAAAATA
1537026 AATTTTTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTTATTTTTTAATTTTAAAATACT
Found at i:1537031 original size:27 final size:27
Alignment explanation
Indices: 1536964--1537032 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
1536954 GAATATATAA
*
1536964 TAAATATATATTTTTTATTTTTTAATTT
1 TAAA-ATAAATTTTTTATTTTTTAATTT
** *
1536992 TAAAATACTTTTTTTATTTTTTATTTT
1 TAAAATAAATTTTTTATTTTTTAATTT
1537019 TAAAATAAATTTTT
1 TAAAATAAATTTTT
1537033 GGTGTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 32 0.89
28 4 0.11
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (27 bp):
TAAAATAAATTTTTTATTTTTTAATTT
Done.