Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 101 of 106
Found at i:38558232 original size:29 final size:29
Alignment explanation
Indices: 38558185--38558254 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 29
38558175 CAATTTTATT
38558185 TAATTTAGTTCACTTA-TTT-AAAATTGAAG
1 TAATTTAG-TCACTTATTTTAAAAATT-AAG
* *
38558214 TAATTTAGTCTCTTAATTTTAAAAATTACG
1 TAATTTAGTCACTT-ATTTTAAAAATTAAG
38558244 TCAATTTAGTC
1 T-AATTTAGTC
38558255 CCCTAACGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.14
29 9 0.26
30 6 0.17
31 15 0.43
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.46
Consensus pattern (29 bp):
TAATTTAGTCACTTATTTTAAAAATTAAG
Found at i:38559445 original size:108 final size:109
Alignment explanation
Indices: 38559292--38559502 Score: 327
Period size: 108 Copynumber: 1.9 Consensus size: 109
38559282 TATAAGAAAT
** *
38559292 TTTGAGTAAATTTAAATAAAAAGGTGTATTGGCTAAGAGTTGAATAATTAT-AAAAGAATGTGTA
1 TTTGAGTAAATTTAAATAAAAAGGTAAATTGGCTAAGACTTGAATAATT-TCAAAAGAATGTGTA
* *
38559356 TTTGTAAATTGTGAAAGTTGTAACTAAATCAACATATTTTGCTAA
65 TTTGTAAATTATAAAAGTTGTAACTAAATCAACATATTTTGCTAA
* *
38559401 TTTGAGTAAATTTAAATAAAAA-GTAAATTGGGTAAGACTTGAATAATTTCAAATGAATGTGTAT
1 TTTGAGTAAATTTAAATAAAAAGGTAAATTGGCTAAGACTTGAATAATTTCAAAAGAATGTGTAT
*
38559465 TTGTAAATTATAAAAGTTGTAATTAAATCAACATATTT
66 TTGTAAATTATAAAAGTTGTAACTAAATCAACATATTT
38559503 AGTCATTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
107 1 0.01
108 70 0.75
109 22 0.24
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (109 bp):
TTTGAGTAAATTTAAATAAAAAGGTAAATTGGCTAAGACTTGAATAATTTCAAAAGAATGTGTAT
TTGTAAATTATAAAAGTTGTAACTAAATCAACATATTTTGCTAA
Found at i:38560943 original size:2 final size:2
Alignment explanation
Indices: 38560936--38560971 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
38560926 TTTTAAGTCC
*
38560936 AT AT AT AT AT AA 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
38560972 GTTCATAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38561658 original size:1 final size:1
Alignment explanation
Indices: 38561652--38561699 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
38561642 CCTTTGTTGC
* * * *
38561652 TTTTTTTTTTTTTTTTATTTTATTTTTTTTTTGTTTTTATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38561700 CTTTGTCTNT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.06, C:0.00, G:0.02, T:0.92
Consensus pattern (1 bp):
T
Found at i:38561677 original size:17 final size:17
Alignment explanation
Indices: 38561652--38561699 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
38561642 CCTTTGTTGC
38561652 TTTTT-TTTTTTTTTT-
1 TTTTTATTTTTTTTTTG
38561667 TATTTTATTTTTTTTTTG
1 T-TTTTATTTTTTTTTTG
38561685 TTTTTATTTTTTTTT
1 TTTTTATTTTTTTTT
38561700 CTTTGTCTNT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.03
16 4 0.13
17 24 0.80
18 1 0.03
ACGTcount: A:0.06, C:0.00, G:0.02, T:0.92
Consensus pattern (17 bp):
TTTTTATTTTTTTTTTG
Found at i:38561680 original size:22 final size:21
Alignment explanation
Indices: 38561652--38561699 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
38561642 CCTTTGTTGC
38561652 TTTTTTTTTTT-TTTTTATTT
1 TTTTTTTTTTTGTTTTTATTT
38561672 TATTTTTTTTTTGTTTTTATTT
1 T-TTTTTTTTTTGTTTTTATTT
38561694 TTTTTT
1 TTTTTT
38561700 CTTTGTCTNT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.04
21 15 0.58
22 10 0.38
ACGTcount: A:0.06, C:0.00, G:0.02, T:0.92
Consensus pattern (21 bp):
TTTTTTTTTTTGTTTTTATTT
Found at i:38561712 original size:21 final size:19
Alignment explanation
Indices: 38561652--38561705 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
38561642 CCTTTGTTGC
*
38561652 TTTTTTTTTTTT-TTTTATT
1 TTTTTTTTTTTTGTTTT-TA
38561671 TTATTTTTTTTTTGTTTTTA
1 TT-TTTTTTTTTTGTTTTTA
38561691 TTTTTTTTTCTTTGT
1 TTTTTTTTT-TTTGT
38561706 CTNTTATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 9 0.29
20 18 0.58
21 4 0.13
ACGTcount: A:0.06, C:0.02, G:0.04, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTTTTGTTTTTA
Found at i:38564816 original size:14 final size:13
Alignment explanation
Indices: 38564792--38564825 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
38564782 AATACCATCA
*
38564792 TTTTGTTTTTCTT
1 TTTTTTTTTTCTT
38564805 TTCTTTTTTTTCTT
1 TT-TTTTTTTTCTT
38564819 TTTTTTT
1 TTTTTTT
38564826 ATACTAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:38565059 original size:280 final size:278
Alignment explanation
Indices: 38564558--38565114 Score: 1080
Period size: 280 Copynumber: 2.0 Consensus size: 278
38564548 CTTTAATTAC
38564558 TATCAAATTAAATTTTAAATAGGTTAAATTATATTTTCATTATGTATGAAATATATCAAATTATA
1 TATCAAATTAAATTTTAAATAGGTTAAATTATATTTTCATTATGTATGAAATATATCAAATTATA
38564623 AATAATTTAATTAGAAAAAATAATTTTCACAAGGTTTTTTTTAAAAATAAATTACTCTTATTAGT
66 AATAATTTAATTAGAAAAAATAATTTTCACAAGGTTTTTTTTAAAAATAAATTACTCTTATTAGT
38564688 TTGAAAAACATTCTTTATCTCTCTAAAAAATGTAAATTATGTTAGATTCCGTTAATCAAACTAAT
131 TTGAAAAACATTCTTTATCTCTCTAAAAAATGTAAATTATGTTAGATTCCGTTAATCAAACTAAT
38564753 ATTGATTCTAACGTACTTTAAATATTAAAAATACCATCATTTTGTTTT-TCTTTTCTTTTTTTTC
196 ATTGATTCTAACGTACTTTAAATATTAAAAATACCATCATTTTGTTTTCT-TTTTCTTTTTTTTC
38564817 TTTTTTTTTATACTAGAGGA
260 -TTTTTTTTATACTAGAGGA
38564837 NTATCAAATTAAATTTTAAATAGGTTAAATTATATTTTCATTATGTATGAAATATATCAAATTAT
1 -TATCAAATTAAATTTTAAATAGGTTAAATTATATTTTCATTATGTATGAAATATATCAAATTAT
38564902 AAATAATTTAATTAGAAAAAATAATTTTCACAAGGTTTTTTTTAAAAATAAATTACTCTTATTAG
65 AAATAATTTAATTAGAAAAAATAATTTTCACAAGGTTTTTTTTAAAAATAAATTACTCTTATTAG
38564967 TTTGAAAAACATTCTTTATCTCTCTAAAAAATGTAAATTATGTTAGATTCCGTTAATCAAACTAA
130 TTTGAAAAACATTCTTTATCTCTCTAAAAAATGTAAATTATGTTAGATTCCGTTAATCAAACTAA
38565032 TATTGATTCTAACGTACTTTAAATATTAAAAATACCATCATTTTGTTTTCTTTTTCTTTTTTTTC
195 TATTGATTCTAACGTACTTTAAATATTAAAAATACCATCATTTTGTTTTCTTTTTCTTTTTTTTC
38565097 TTTTTTTTATACTAGAGG
260 TTTTTTTTATACTAGAGG
38565115 TAAATTTGTG
Statistics
Matches: 276, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
279 18 0.07
280 257 0.93
281 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (278 bp):
TATCAAATTAAATTTTAAATAGGTTAAATTATATTTTCATTATGTATGAAATATATCAAATTATA
AATAATTTAATTAGAAAAAATAATTTTCACAAGGTTTTTTTTAAAAATAAATTACTCTTATTAGT
TTGAAAAACATTCTTTATCTCTCTAAAAAATGTAAATTATGTTAGATTCCGTTAATCAAACTAAT
ATTGATTCTAACGTACTTTAAATATTAAAAATACCATCATTTTGTTTTCTTTTTCTTTTTTTTCT
TTTTTTTATACTAGAGGA
Found at i:38565097 original size:15 final size:16
Alignment explanation
Indices: 38565072--38565101 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38565062 AATACCATCA
38565072 TTTTGTTTTCTTTTTC
1 TTTTGTTTTCTTTTTC
38565088 TTTT-TTTTCTTTTT
1 TTTTGTTTTCTTTTT
38565102 TTTATACTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (16 bp):
TTTTGTTTTCTTTTTC
Found at i:38566511 original size:30 final size:30
Alignment explanation
Indices: 38566472--38566539 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
38566462 TCATAAGGGC
*
38566472 TTATTTGACTAAAAATAAAAATATAAAATT
1 TTATTTGACTAAAAATAAAAATATAAAAAT
* *
38566502 TTGTTTGACTCAAAATAAAAATATAAAAAT
1 TTATTTGACTAAAAATAAAAATATAAAAAT
38566532 TTATTTGA
1 TTATTTGA
38566540 ATTCTCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.38
Consensus pattern (30 bp):
TTATTTGACTAAAAATAAAAATATAAAAAT
Found at i:38567688 original size:38 final size:38
Alignment explanation
Indices: 38567637--38567714 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
38567627 TCTCAATAAC
38567637 CATTAACATATTTGACTAATTATTTCAATCATAATCAA
1 CATTAACATATTTGACTAATTATTTCAATCATAATCAA
38567675 CATTAACATATTTGACTAATTATTTCAATCATAATCAA
1 CATTAACATATTTGACTAATTATTTCAATCATAATCAA
38567713 CA
1 CA
38567715 AATATTGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (38 bp):
CATTAACATATTTGACTAATTATTTCAATCATAATCAA
Found at i:38567863 original size:13 final size:13
Alignment explanation
Indices: 38567847--38567873 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38567837 AAATAAAATG
38567847 AAAAACAAAATAA
1 AAAAACAAAATAA
38567860 AAAAACAAAATAA
1 AAAAACAAAATAA
38567873 A
1 A
38567874 TAATACTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAACAAAATAA
Found at i:38568254 original size:55 final size:55
Alignment explanation
Indices: 38568177--38568291 Score: 221
Period size: 55 Copynumber: 2.1 Consensus size: 55
38568167 AAAGCCAATA
38568177 ACCACTAAAACTATTCACACTAAGAAAGATGTGGACTCCATTAAACGATAACTGT
1 ACCACTAAAACTATTCACACTAAGAAAGATGTGGACTCCATTAAACGATAACTGT
*
38568232 ACCACTAAAACTATTCATACTAAGAAAGATGTGGACTCCATTAAACGATAACTGT
1 ACCACTAAAACTATTCACACTAAGAAAGATGTGGACTCCATTAAACGATAACTGT
38568287 ACCAC
1 ACCAC
38568292 CAAGACTCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (55 bp):
ACCACTAAAACTATTCACACTAAGAAAGATGTGGACTCCATTAAACGATAACTGT
Found at i:38569868 original size:20 final size:21
Alignment explanation
Indices: 38569829--38569868 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38569819 TATGAATCCC
38569829 TTATTGAGCATCTCATATAAT
1 TTATTGAGCATCTCATATAAT
* *
38569850 TTATTTAGCATGT-ATATAA
1 TTATTGAGCATCTCATATAA
38569869 CCCAACGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (21 bp):
TTATTGAGCATCTCATATAAT
Found at i:38570670 original size:23 final size:23
Alignment explanation
Indices: 38570623--38570691 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
38570613 TGTATTATAT
* *
38570623 TAAAATTTTAATATTTGT-AAGAA
1 TAAAATTTTAAAATTT-TAAAAAA
38570646 TAAAATTTTAAAATTTTAAAAAA
1 TAAAATTTTAAAATTTTAAAAAA
**
38570669 TAAAAAAAATTAAAATTTTAAAA
1 T--AAAATTTTAAAATTTTAAAA
38570692 CTTTGAGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 20 0.51
25 18 0.46
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (23 bp):
TAAAATTTTAAAATTTTAAAAAA
Found at i:38572696 original size:29 final size:28
Alignment explanation
Indices: 38572637--38572725 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 28
38572627 AAGTATTAAA
* *
38572637 GTGTAACAA-ATTTTTTTTGAACATGAC
1 GTGTAACAATAATTTTTTTCAACATGAC
**
38572664 GTGTAACAATAATATTTTTTCAACATGGT
1 GTGTAACAATAAT-TTTTTTCAACATGAC
*
38572693 GTGTAACAAT-ATTTTTTTTAACATGAC
1 GTGTAACAATAATTTTTTTCAACATGAC
*
38572720 ATGTAA
1 GTGTAA
38572726 TATGTTTTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
27 26 0.50
28 4 0.08
29 22 0.42
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (28 bp):
GTGTAACAATAATTTTTTTCAACATGAC
Found at i:38572740 original size:24 final size:24
Alignment explanation
Indices: 38572700--38572749 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
38572690 GGTGTGTAAC
* *
38572700 AATATTTTTTTTAACATGACATGT
1 AATATTTTTTGTAACATAACATGT
*
38572724 AATATGTTTTTGT-ACATAACGTGT
1 AATAT-TTTTTGTAACATAACATGT
38572748 AA
1 AA
38572750 CAACAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (24 bp):
AATATTTTTTGTAACATAACATGT
Found at i:38572843 original size:44 final size:44
Alignment explanation
Indices: 38572755--38572843 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
38572745 TGTAACAACA
*
38572755 ATATTTTTTTTTGACATAACGTGTAACAATATTTCTTAATCATG
1 ATATTTTTTTTTGACATAACGTGTAACAATATTTCTTAACCATG
* *
38572799 ATATTTTTTTTTGACATAACTTGTAACAA-ATTTTTTTAACCATG
1 ATATTTTTTTTTGACATAACGTGTAACAATA-TTTCTTAACCATG
38572843 A
1 A
38572844 CTTATAACAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (44 bp):
ATATTTTTTTTTGACATAACGTGTAACAATATTTCTTAACCATG
Found at i:38572846 original size:26 final size:25
Alignment explanation
Indices: 38572804--38572852 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
38572794 TCATGATATT
* *
38572804 TTTTTTTGACATAACTTGTAACAAA
1 TTTTTTTAACATAACTTATAACAAA
*
38572829 TTTTTTTAACCATGACTTATAACA
1 TTTTTTTAA-CATAACTTATAACA
38572853 TGTTTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTTTTAACATAACTTATAACAAA
Found at i:38572977 original size:29 final size:29
Alignment explanation
Indices: 38572929--38573024 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 29
38572919 CTATAATGTG
**
38572929 TAATATGTTTTTGTACATAACGTATAACAA
1 TAATAT-TTTTTCAACATAACGTATAACAA
38572959 TAATATTTTTTCAACATAACGTATAAC-A
1 TAATATTTTTTCAACATAACGTATAACAA
* *
38572987 T-AT-TTTTGT-AA-GTAACGTATAACAA
1 TAATATTTTTTCAACATAACGTATAACAA
*
38573012 TAATTTTTTTTCA
1 TAATATTTTTTCA
38573025 GTATAACACG
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 11 0.19
25 4 0.07
26 7 0.12
27 7 0.12
28 3 0.05
29 19 0.33
30 6 0.11
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (29 bp):
TAATATTTTTTCAACATAACGTATAACAA
Found at i:38573039 original size:53 final size:53
Alignment explanation
Indices: 38572936--38573040 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 53
38572926 GTGTAATATG
**
38572936 TTTTTGTACATAACGTATAACAATAATATTTTTTCAACATAACGTATAACATA
1 TTTTTGTACATAACGTATAACAATAATATTTTTTCAACATAACACATAACATA
* ** *
38572989 TTTTTGTA-AGTAACGTATAACAATAATTTTTTTTCAGTATAACACGTAACAT
1 TTTTTGTACA-TAACGTATAACAATAATATTTTTTCAACATAACACATAACAT
38573041 CACATGCATT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 1 0.02
53 44 0.98
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (53 bp):
TTTTTGTACATAACGTATAACAATAATATTTTTTCAACATAACACATAACATA
Found at i:38579040 original size:2 final size:2
Alignment explanation
Indices: 38579033--38579067 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
38579023 TTTGGGGTCC
* *
38579033 CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT TT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
38579068 ATACATCCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:38580955 original size:2 final size:2
Alignment explanation
Indices: 38580948--38581013 Score: 80
Period size: 2 Copynumber: 32.5 Consensus size: 2
38580938 CATTTCAATA
** *
38580948 CT CT CT CT CT CT CT CT C- CT CT CT CT NG CT CC CT ACT ACT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT -CT CT CT
38580991 CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
38581014 CCCCTGTGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 1 0.02
2 50 0.89
3 5 0.09
ACGTcount: A:0.03, C:0.50, G:0.02, T:0.44
Consensus pattern (2 bp):
CT
Found at i:38589768 original size:2 final size:2
Alignment explanation
Indices: 38589761--38589792 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38589751 AACAAAAGCC
38589761 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
38589793 TATTTTGTAG
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:38589836 original size:2 final size:2
Alignment explanation
Indices: 38589829--38589863 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
38589819 TAATTAAGTN
*
38589829 AT AT AT AT AT AT AT AT AT AT AT AT A- AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38589864 TTTTGAGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38589838 original size:68 final size:64
Alignment explanation
Indices: 38589761--38589892 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 64
38589751 AACAAAAGCC
38589761 ATATATATATATATATATATATAT-ATATATAT-TATTTTGTAGGCACATGACAAACAAGTAATT
1 ATATATATATATATATATATATATAATATATATAT-TTTTG-AGGCACATG-CAAACAAG--ATT
38589824 AAGT
61 AAGT
*
38589828 NATATATATATATATATATATATATAATCTATATATTTTTGAGGCACATGCAAACAAGATTAAGT
1 -ATATATATATATATATATATATATAATATATATATTTTTGAGGCACATGCAAACAAGATTAAGT
38589893 CATGCTTTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
65 7 0.11
67 8 0.13
68 33 0.54
69 12 0.20
70 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (64 bp):
ATATATATATATATATATATATATAATATATATATTTTTGAGGCACATGCAAACAAGATTAAGT
Found at i:38594235 original size:41 final size:41
Alignment explanation
Indices: 38594178--38594258 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
38594168 ATGATTCCAG
*
38594178 GGTCAATTGCACTAACCAGAATCAAGTTGACAAGAACCTGC
1 GGTCAATTACACTAACCAGAATCAAGTTGACAAGAACCTGC
* *
38594219 GGTCAATTACACTAACCAGGATCAAGTTGACAAGTACCTG
1 GGTCAATTACACTAACCAGAATCAAGTTGACAAGAACCTG
38594259 TAGTTCATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (41 bp):
GGTCAATTACACTAACCAGAATCAAGTTGACAAGAACCTGC
Found at i:38602557 original size:2 final size:2
Alignment explanation
Indices: 38602515--38602542 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38602505 ATAAAAATTA
38602515 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
38602543 TCAGTTTTAT
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:38605597 original size:2 final size:2
Alignment explanation
Indices: 38605585--38605632 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
38605575 GAATAAAAAT
* *
38605585 TA TA AA TA TA TA TA TA TA TA TA TA TA TG 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
*
38605627 GA TA TA
1 TA TA TA
38605633 AACAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:38608585 original size:13 final size:13
Alignment explanation
Indices: 38608567--38608591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38608557 TATAAGATAA
38608567 TTAGAGAGAGAAT
1 TTAGAGAGAGAAT
38608580 TTAGAGAGAGAA
1 TTAGAGAGAGAA
38608592 GCTCTCAAGT
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:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
TTAGAGAGAGAAT
Found at i:38608833 original size:29 final size:29
Alignment explanation
Indices: 38608800--38608855 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
38608790 GAGGTGTACA
*
38608800 AGAATAGGTACGAGAGAAGAAGCTGTATG
1 AGAATAGGTACAAGAGAAGAAGCTGTATG
*
38608829 AGAATAGGTACAAGAGAATAAGCTGTA
1 AGAATAGGTACAAGAGAAGAAGCTGTA
38608856 CATGAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.30, T:0.18
Consensus pattern (29 bp):
AGAATAGGTACAAGAGAAGAAGCTGTATG
Found at i:38608862 original size:29 final size:28
Alignment explanation
Indices: 38608794--38608863 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
38608784 AGAAAAGAGG
*
38608794 TGTACAAGAATAGGTACGAGAGAAGAAGC
1 TGTAC-AGAATAGGTACAAGAGAAGAAGC
* *
38608823 TGTATGAGAATAGGTACAAGAGAATAAGC
1 TGTA-CAGAATAGGTACAAGAGAAGAAGC
38608852 TGTACATGAATA
1 TGTACA-GAATA
38608864 AGTATACGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.44, C:0.09, G:0.27, T:0.20
Consensus pattern (28 bp):
TGTACAGAATAGGTACAAGAGAAGAAGC
Found at i:38609172 original size:26 final size:26
Alignment explanation
Indices: 38609143--38609217 Score: 150
Period size: 26 Copynumber: 2.9 Consensus size: 26
38609133 AAGTAATACT
38609143 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
38609169 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
38609195 TGAAGTAGCGCTTCACTTGTTCT
1 TGAAGTAGCGCTTCACTTGTTCT
38609218 CTATATAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (26 bp):
TGAAGTAGCGCTTCACTTGTTCTGCG
Found at i:38618829 original size:26 final size:26
Alignment explanation
Indices: 38618774--38618829 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
38618764 AGATGTAATC
38618774 AAAA-TATATTGTTTTTTTAATATCT
1 AAAATTATATTGTTTTTTTAATATCT
* *
38618799 GAAATTATATT-TTATTTTTAATATTT
1 AAAATTATATTGTT-TTTTTAATATCT
38618825 AAAAT
1 AAAAT
38618830 CATGGTACGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (26 bp):
AAAATTATATTGTTTTTTTAATATCT
Found at i:38620487 original size:43 final size:44
Alignment explanation
Indices: 38620428--38620512 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 44
38620418 AGCAAGTAGG
*
38620428 AAAAAAACTTAGAATGAGATTTTG-TTTCTTTTTATTTTTAAGA
1 AAAAAAACCTAGAATGAGATTTTGTTTTCTTTTTATTTTTAAGA
*
38620471 AAAAAAACCTAGAATGAGATTTTGTTTTTTTTTTATTTTTAA
1 AAAAAAACCTAGAATGAGATTTTGTTTTCTTTTTATTTTTAA
38620513 AGTGACATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 23 0.59
44 16 0.41
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (44 bp):
AAAAAAACCTAGAATGAGATTTTGTTTTCTTTTTATTTTTAAGA
Found at i:38639908 original size:2 final size:2
Alignment explanation
Indices: 38639901--38640013 Score: 111
Period size: 2 Copynumber: 56.0 Consensus size: 2
38639891 CACCCTATGA
*
38639901 AT AT AT AT AT AT AT AT AT AC 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 AT AT
** ** * * * * *
38639943 AT AT AT NNN NN CT CT CAC CT AG A- 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 AT AT
38639986 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
38640014 GTATGTATAG
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.01
2 95 0.99
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:38641599 original size:17 final size:17
Alignment explanation
Indices: 38641577--38641623 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
38641567 TTAACCTGAT
*
38641577 AAATTTATCAGAAAGCA
1 AAATTTATCAAAAAGCA
*
38641594 AAATTTATCAAAAAGTA
1 AAATTTATCAAAAAGCA
38641611 AAATTTATCAAAA
1 AAATTTATCAAAA
38641624 TAAACATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (17 bp):
AAATTTATCAAAAAGCA
Found at i:38643300 original size:25 final size:25
Alignment explanation
Indices: 38643272--38643322 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
38643262 TCCTTTTCAG
38643272 TGTTGTGTATGCTTTTAAGCGTGTC
1 TGTTGTGTATGCTTTTAAGCGTGTC
38643297 TGTTGTGTATGCTTTTAAGCGTGTC
1 TGTTGTGTATGCTTTTAAGCGTGTC
38643322 T
1 T
38643323 CAGTTCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.49
Consensus pattern (25 bp):
TGTTGTGTATGCTTTTAAGCGTGTC
Found at i:38660512 original size:29 final size:29
Alignment explanation
Indices: 38660467--38660522 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
38660457 CGTGCCTTCT
* *
38660467 TTTGAATTAATTGGTTTAAAGGGTATTTA
1 TTTGAATTAATTAGTTTAAAAGGTATTTA
38660496 TTTGAATTAATTAGTTTAAAAGGTATT
1 TTTGAATTAATTAGTTTAAAAGGTATT
38660523 CTTATTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (29 bp):
TTTGAATTAATTAGTTTAAAAGGTATTTA
Found at i:38663860 original size:43 final size:43
Alignment explanation
Indices: 38663799--38663882 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
38663789 ATTAAGTCCA
*
38663799 TGTTGGCTTTTAAAAGCCTTACCCTAAT-TCGCCCCATAACCCG
1 TGTTGACTTTTAAAAGCCTTACCCTAATCT-GCCCCATAACCCG
*
38663842 TGTTGACTTTTAAAAGCCTTACCCTAATCTGCTCCATAACC
1 TGTTGACTTTTAAAAGCCTTACCCTAATCTGCCCCATAACC
38663883 AAATGTAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (43 bp):
TGTTGACTTTTAAAAGCCTTACCCTAATCTGCCCCATAACCCG
Found at i:38666187 original size:17 final size:17
Alignment explanation
Indices: 38666165--38666198 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38666155 ATAAGTCAGT
38666165 AGTGTATAAAAATTATA
1 AGTGTATAAAAATTATA
* *
38666182 AGTGTATCAAATTTATA
1 AGTGTATAAAAATTATA
38666199 TTATACATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (17 bp):
AGTGTATAAAAATTATA
Found at i:38671887 original size:2 final size:2
Alignment explanation
Indices: 38671880--38671916 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
38671870 ACCCCAGTAA
* *
38671880 AC AC AC AC AC AC GC AC AC GC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
38671917 TCATACATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.49, G:0.05, T:0.00
Consensus pattern (2 bp):
AC
Found at i:38672052 original size:142 final size:142
Alignment explanation
Indices: 38671900--38672185 Score: 563
Period size: 142 Copynumber: 2.0 Consensus size: 142
38671890 ACGCACACGC
38671900 ACACACACACACACACATCATACATGATGGTAGCCTAAGTTGTTAAATTCACCAGCAGAGCTGTC
1 ACACACACACACACACATCATACATGATGGTAGCCTAAGTTGTTAAATTCACCAGCAGAGCTGTC
*
38671965 CAAAGTTCTATGCTAGGCTAACTCATTTTTTTGTTTCGCTGAAAATTTTTCCAAAAGCATATGCA
66 CAAAGTTCTATGCTAGGCTAACTCATTTTTTTGTTTCGCTGAAAATTTTTCCAAAAGCACATGCA
38672030 TACCTCACATCA
131 TACCTCACATCA
38672042 ACACACACACACACACATCATACATGATGGTAGCCTAAGTTGTTAAATTCACCAGCAGAGCTGTC
1 ACACACACACACACACATCATACATGATGGTAGCCTAAGTTGTTAAATTCACCAGCAGAGCTGTC
38672107 CAAAGTTCTATGCTAGGCTAACTCATTTTTTTGTTTCGCTGAAAATTTTTCCAAAAGCACATGCA
66 CAAAGTTCTATGCTAGGCTAACTCATTTTTTTGTTTCGCTGAAAATTTTTCCAAAAGCACATGCA
38672172 TACCTCACATCA
131 TACCTCACATCA
38672184 AC
1 AC
38672186 TAACATCCTC
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 143 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (142 bp):
ACACACACACACACACATCATACATGATGGTAGCCTAAGTTGTTAAATTCACCAGCAGAGCTGTC
CAAAGTTCTATGCTAGGCTAACTCATTTTTTTGTTTCGCTGAAAATTTTTCCAAAAGCACATGCA
TACCTCACATCA
Found at i:38675505 original size:6 final size:6
Alignment explanation
Indices: 38675494--38675527 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
38675484 AAGAATAAAC
38675494 TGATTT TGATTT TGATTT TGATTT TGATTT TGAT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGAT
38675528 CCAAATGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (6 bp):
TGATTT
Found at i:38677573 original size:22 final size:22
Alignment explanation
Indices: 38677514--38677591 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
38677504 TTGTCATTAA
* *
38677514 TATATTTTTATTAGTTTAATATA-
1 TATAATTTTATT-TTTTAATA-AG
* * *
38677537 TATACTTTCATTTTTTATTAAG
1 TATAATTTTATTTTTTAATAAG
*
38677559 TGATAATTTTATTTTTTAATATG
1 T-ATAATTTTATTTTTTAATAAG
38677582 TATAATTTTA
1 TATAATTTTA
38677592 AATTACATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
21 1 0.02
22 16 0.36
23 28 0.62
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (22 bp):
TATAATTTTATTTTTTAATAAG
Found at i:38678200 original size:2 final size:2
Alignment explanation
Indices: 38678193--38678222 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38678183 TAACCAACAA
38678193 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
38678223 GATTAAAATT
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:38681733 original size:30 final size:30
Alignment explanation
Indices: 38681697--38681759 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
38681687 ACCATTAATC
**
38681697 ATAAAAACTAATTTGGCTCAAAATAAAAAT
1 ATAAAAACTAATTTAACTCAAAATAAAAAT
* * *
38681727 ATAAAAATTTATTTAACTTAAAATAAAAAT
1 ATAAAAACTAATTTAACTCAAAATAAAAAT
38681757 ATA
1 ATA
38681760 GAGACTTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (30 bp):
ATAAAAACTAATTTAACTCAAAATAAAAAT
Found at i:38681800 original size:10 final size:9
Alignment explanation
Indices: 38681786--38681826 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
38681776 TAATAAAAAA
38681786 TAAATTTTT
1 TAAATTTTT
38681795 TAAAATTTTT
1 T-AAATTTTT
**
38681805 TAAATAATT
1 TAAATTTTT
38681814 TAAATTTTT
1 TAAATTTTT
38681823 TAAA
1 TAAA
38681827 ATATTATATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAAATTTTT
Found at i:38687061 original size:13 final size:13
Alignment explanation
Indices: 38687045--38687080 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
38687035 TCCTTTTCCT
38687045 TTTTTTTTTTTTA
1 TTTTTTTTTTTTA
*
38687058 TTTTTTATTTTTA
1 TTTTTTTTTTTTA
38687071 TTTTTCTTTT
1 TTTTT-TTTT
38687081 GGGCTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.08, C:0.03, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTTA
Found at i:38692158 original size:3 final size:3
Alignment explanation
Indices: 38692150--38692197 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
38692140 AATCATGCAT
* *
38692150 ATA ATA ATA ATA ATA ATA ATA ATA ATG ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38692198 TTATTATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:38692311 original size:22 final size:22
Alignment explanation
Indices: 38692285--38692327 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
38692275 AATTATGGAG
* *
38692285 AAATTTTTTAAAATTTAAAATT
1 AAATTTTATAAAATGTAAAATT
38692307 AAATTTTATAAAATGTAAAAT
1 AAATTTTATAAAATGTAAAAT
38692328 AAAAATTATG
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:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATTTTATAAAATGTAAAATT
Found at i:38703383 original size:25 final size:24
Alignment explanation
Indices: 38703347--38703402 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
38703337 AAGTTAAATA
*
38703347 AATTTTTATAATTAATAAT-TAATT
1 AATTATTATAATTAA-AATATAATT
38703371 AATTATTATTAATTAAAATATAATT
1 AATTATTA-TAATTAAAATATAATT
*
38703396 TATTATT
1 AATTATT
38703403 TTATGTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTATTATAATTAAAATATAATT
Found at i:38712928 original size:49 final size:49
Alignment explanation
Indices: 38712875--38712972 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
38712865 GATTGAAAAA
38712875 CAATCAATAACATATTCCAAAAGAATTTAAGGCTTTATCCTCAAACCAC
1 CAATCAATAACATATTCCAAAAGAATTTAAGGCTTTATCCTCAAACCAC
38712924 CAATCAATAACATATTCCAAAAGAATTTAAGGCTTTATCCTCAAACCAC
1 CAATCAATAACATATTCCAAAAGAATTTAAGGCTTTATCCTCAAACCAC
38712973 GTGAAAGGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (49 bp):
CAATCAATAACATATTCCAAAAGAATTTAAGGCTTTATCCTCAAACCAC
Found at i:38715760 original size:31 final size:30
Alignment explanation
Indices: 38715715--38715773 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
38715705 AAATAGATAA
*
38715715 ATATTTTATTAATT-ATTTTAATTTTTATAT
1 ATATTTAATTAATTAATTTT-ATTTTTATAT
38715745 ATATTTAATATAATTAATTTTATTTTTAT
1 ATATTTAAT-TAATTAATTTTATTTTTAT
38715774 TATTATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 13 0.50
32 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
ATATTTAATTAATTAATTTTATTTTTATAT
Found at i:38717437 original size:15 final size:15
Alignment explanation
Indices: 38717417--38717446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38717407 ACTTTTTGAA
38717417 TTATTTATTTATTTT
1 TTATTTATTTATTTT
*
38717432 TTATTTTTTTATTTT
1 TTATTTATTTATTTT
38717447 GTTTAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTATTTATTTATTTT
Found at i:38717848 original size:107 final size:108
Alignment explanation
Indices: 38717674--38717882 Score: 339
Period size: 107 Copynumber: 1.9 Consensus size: 108
38717664 TATAAGAAAT
* *
38717674 TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAGTTGAATAATTTCAAAAAAATGTGTGTT
1 TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAGTTGAATAATTTCAAAAAAACGTGTATT
* * * * *
38717739 TGTAAATTGTGAAAGTTGTAACTAAATTAACATATTTTGCTAA
66 TGTAAATTCTAAAAATTATAACTAAATCAACATATTTTGCTAA
*
38717782 TTTGAGTAAATTTAAATAAAAAGTAAATT-GGTAAGAGTTGAATAATTTCAAAAGAACGTGTATT
1 TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAGTTGAATAATTTCAAAAAAACGTGTATT
38717846 TGTAAATTCTAAAAATTATAACTAAATCAACATATTT
66 TGTAAATTCTAAAAATTATAACTAAATCAACATATTT
38717883 AGTTGTTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 64 0.69
108 29 0.31
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.36
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAGTTGAATAATTTCAAAAAAACGTGTATT
TGTAAATTCTAAAAATTATAACTAAATCAACATATTTTGCTAA
Found at i:38729086 original size:26 final size:26
Alignment explanation
Indices: 38729024--38729074 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
38729014 TATTAAATTT
*
38729024 TTAAATAAATTTTTATTTTTATTATA
1 TTAAATAAATTTTTATATTTATTATA
*
38729050 TTTAATCAAATTTTTATATTT-TTAT
1 TTAAAT-AAATTTTTATATTTATTAT
38729075 TTCAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTAAATAAATTTTTATATTTATTATA
Found at i:38729560 original size:20 final size:21
Alignment explanation
Indices: 38729525--38729569 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
38729515 CTTAAAAAAA
38729525 TAAAAAATAAATAACA-AAACC
1 TAAAAAATAAATAACATAAA-C
*
38729546 TAAATAATAAA-AACATAAAC
1 TAAAAAATAAATAACATAAAC
38729566 TAAA
1 TAAA
38729570 CAAGAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAAAAATAAATAACATAAAC
Found at i:38734336 original size:24 final size:24
Alignment explanation
Indices: 38734309--38734358 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
38734299 ATTTCTTTCT
38734309 TTAGTCTCTCAGTGCTATTTACTG
1 TTAGTCTCTCAGTGCTATTTACTG
38734333 TTAGTCTCTCAGTGCTATTTACTG
1 TTAGTCTCTCAGTGCTATTTACTG
38734357 TT
1 TT
38734359 CTTTCTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (24 bp):
TTAGTCTCTCAGTGCTATTTACTG
Found at i:38799158 original size:23 final size:23
Alignment explanation
Indices: 38799106--38799190 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
38799096 AATTATTTTT
* * *
38799106 TTTCCTTTTAGAGTAAACCC-AT
1 TTTCCTTATAAAGTAAACCCAAA
38799128 TTTCCTTATAAAGTAAACCCAAA
1 TTTCCTTATAAAGTAAACCCAAA
**
38799151 TTTCCTTATAAAGTAAATTCAAA
1 TTTCCTTATAAAGTAAACCCAAA
* *
38799174 TTTTCTTATAGAGTAAA
1 TTTCCTTATAAAGTAAA
38799191 AGATGCATTG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 18 0.33
23 37 0.67
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (23 bp):
TTTCCTTATAAAGTAAACCCAAA
Found at i:38805663 original size:20 final size:20
Alignment explanation
Indices: 38805638--38805683 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
38805628 CTTCTAAACC
*
38805638 TCAAATCCTACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
38805658 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
38805678 TCAAAT
1 TCAAAT
38805684 GGGGCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:38807071 original size:5 final size:5
Alignment explanation
Indices: 38807063--38807104 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
38807053 TTTCTGGTTA
* *
38807063 TTTTC TTTTC CTTTC CTTTC TTTTC TTTTC TTTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
38807105 CNNNNNNNNN
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:38812695 original size:19 final size:20
Alignment explanation
Indices: 38812661--38812705 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
38812651 AGATCTAATA
38812661 TGAAAAGATAATTTTT-TATT
1 TGAAAAGATAATTTTTAT-TT
*
38812681 TGAAAAGA-CATTTTTATTT
1 TGAAAAGATAATTTTTATTT
38812700 TGAAAA
1 TGAAAA
38812706 TACAATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (20 bp):
TGAAAAGATAATTTTTATTT
Found at i:38814643 original size:23 final size:23
Alignment explanation
Indices: 38814594--38814667 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
38814584 TTCCTTACCG
*
38814594 AGTAAACCC-ATTTTCATTATAA
1 AGTAAACCCAAATTTCATTATAA
* *
38814616 AGTAAACCCAAATTTCCTTGTAA
1 AGTAAACCCAAATTTCATTATAA
* * *
38814639 TGTAAATCCAAATTTTC-TTATAG
1 AGTAAACCCAAA-TTTCATTATAA
38814662 AGTAAA
1 AGTAAA
38814668 AGATGCATTG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 9 0.21
23 29 0.69
24 4 0.10
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (23 bp):
AGTAAACCCAAATTTCATTATAA
Found at i:38814742 original size:128 final size:128
Alignment explanation
Indices: 38814512--38814758 Score: 359
Period size: 128 Copynumber: 1.9 Consensus size: 128
38814502 TTCTTATAGA
* * *
38814512 GTAAACCCAAATTTCCTTATAGAATAAACGATGCATTGCTTAATTGCCTAAATTTGAAATTATTT
1 GTAAACCCAAATTTCCTTATAGAATAAAAGATGCATTGCTTAACTACCTAAATTTGAAATTATTT
* * *
38814577 TTCTTTATTCCTTACCGAGTAAACCCATTTTCATTATAAAGTAAACCCAAATTTCCTTGTAAT
66 GTCTTTATTCCTTACAGAATAAACCCATTTTCATTATAAAGTAAACCCAAATTTCCTTGTAAT
* * * *
38814640 GTAAATCCAAATTTTCTTATAGAGTAAAAGATGCATTGCTTAACTATCTAAATTTGAAATTATTT
1 GTAAACCCAAATTTCCTTATAGAATAAAAGATGCATTGCTTAACTACCTAAATTTGAAATTATTT
* * * * *
38814705 GTCTTTTTTCGTTATAGAATAAACCCATTTTCCTTATAGAGTAAACCCAAATTT
66 GTCTTTATTCCTTACAGAATAAACCCATTTTCATTATAAAGTAAACCCAAATTT
38814759 TAAAATTATT
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
128 104 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (128 bp):
GTAAACCCAAATTTCCTTATAGAATAAAAGATGCATTGCTTAACTACCTAAATTTGAAATTATTT
GTCTTTATTCCTTACAGAATAAACCCATTTTCATTATAAAGTAAACCCAAATTTCCTTGTAAT
Found at i:38814758 original size:24 final size:22
Alignment explanation
Indices: 38814710--38814753 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
38814700 TATTTGTCTT
*
38814710 TTTTCGTTATAGAATAAACCCA
1 TTTTCCTTATAGAATAAACCCA
*
38814732 TTTTCCTTATAGAGTAAACCCA
1 TTTTCCTTATAGAATAAACCCA
38814754 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTTCCTTATAGAATAAACCCA
Found at i:38819482 original size:20 final size:21
Alignment explanation
Indices: 38819456--38819562 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 21
38819446 ATTTTTCTTT
38819456 TTTCCTTATAAAGTAAACCCA
1 TTTCCTTATAAAGTAAACCCA
* ** *
38819477 -TTCCTTGTCGAGTAAATCCAAA
1 TTTCCTTATAAAGTAAA-CC-CA
38819499 TTTCCTTATAAAGTAAACCCA
1 TTTCCTTATAAAGTAAACCCA
* * *
38819520 -TTCCTTGTAGAGTAAATCCAAA
1 TTTCCTTATAAAGTAAA-CC-CA
38819542 TTTCCTTATAAAGTAAACCCA
1 TTTCCTTATAAAGTAAACCCA
38819563 AATTTTCTTA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
20 27 0.41
21 6 0.09
22 6 0.09
23 27 0.41
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.33
Consensus pattern (21 bp):
TTTCCTTATAAAGTAAACCCA
Found at i:38819505 original size:23 final size:23
Alignment explanation
Indices: 38819456--38819581 Score: 111
Period size: 23 Copynumber: 5.7 Consensus size: 23
38819446 ATTTTTCTTT
* *
38819456 TTTCCTTATAAAGTAAA-CC-CA
1 TTTCCTTATAGAGTAAATCCAAA
* *
38819477 -TTCCTTGTCGAGTAAATCCAAA
1 TTTCCTTATAGAGTAAATCCAAA
* *
38819499 TTTCCTTATAAAGTAAA-CC-CA
1 TTTCCTTATAGAGTAAATCCAAA
*
38819520 -TTCCTTGTAGAGTAAATCCAAA
1 TTTCCTTATAGAGTAAATCCAAA
* *
38819542 TTTCCTTATAAAGTAAACCCAAA
1 TTTCCTTATAGAGTAAATCCAAA
* *
38819565 TTTTCTTATCGAGTAAA
1 TTTCCTTATAGAGTAAA
38819582 AAATGCATTG
Statistics
Matches: 82, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
20 27 0.33
21 5 0.06
22 4 0.05
23 46 0.56
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (23 bp):
TTTCCTTATAGAGTAAATCCAAA
Found at i:38819517 original size:43 final size:43
Alignment explanation
Indices: 38819456--38819562 Score: 205
Period size: 43 Copynumber: 2.5 Consensus size: 43
38819446 ATTTTTCTTT
*
38819456 TTTCCTTATAAAGTAAACCCATTCCTTGTCGAGTAAATCCAAA
1 TTTCCTTATAAAGTAAACCCATTCCTTGTAGAGTAAATCCAAA
38819499 TTTCCTTATAAAGTAAACCCATTCCTTGTAGAGTAAATCCAAA
1 TTTCCTTATAAAGTAAACCCATTCCTTGTAGAGTAAATCCAAA
38819542 TTTCCTTATAAAGTAAACCCA
1 TTTCCTTATAAAGTAAACCCA
38819563 AATTTTCTTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.33
Consensus pattern (43 bp):
TTTCCTTATAAAGTAAACCCATTCCTTGTAGAGTAAATCCAAA
Found at i:38819672 original size:24 final size:22
Alignment explanation
Indices: 38819624--38819673 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
38819614 TATTTTTCTT
*
38819624 TTTTCCTTATAGAGTAAACCCA
1 TTTTCCTTATAGAGTAAACCAA
38819646 TTTTCCTTATAGAGTAAACTCAAA
1 TTTTCCTTATAGAGTAAAC-C-AA
38819670 TTTT
1 TTTT
38819674 GAAACTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 19 0.76
23 1 0.04
24 5 0.20
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (22 bp):
TTTTCCTTATAGAGTAAACCAA
Found at i:38821148 original size:13 final size:13
Alignment explanation
Indices: 38821130--38821154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38821120 TCTTCTTTCC
38821130 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
38821143 TTTTTCTTTTTT
1 TTTTTCTTTTTT
38821155 GTCTTTTGGA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:38827762 original size:20 final size:19
Alignment explanation
Indices: 38827718--38827763 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
38827708 CTTCTAAACC
38827718 TCAAATCATACTCCAATAA
1 TCAAATCATACTCCAATAA
* *
38827737 TCCAAATTATGCTCCAATAA
1 T-CAAATCATACTCCAATAA
38827757 GTCAAAT
1 -TCAAAT
38827764 GGGGACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.28
Consensus pattern (19 bp):
TCAAATCATACTCCAATAA
Found at i:38834834 original size:19 final size:20
Alignment explanation
Indices: 38834800--38834844 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
38834790 AGACATGATA
38834800 TGAAAAGATAATTTTT-TATT
1 TGAAAAGATAATTTTTAT-TT
*
38834820 TGAAAAGA-CATTTTTATTT
1 TGAAAAGATAATTTTTATTT
38834839 TGAAAA
1 TGAAAA
38834845 TACAACAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (20 bp):
TGAAAAGATAATTTTTATTT
Found at i:38838414 original size:23 final size:23
Alignment explanation
Indices: 38838362--38838446 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
38838352 ATTTTTCTTT
*
38838362 TTTCCTTATAGAGTAAACCC-AT
1 TTTCCTTATAGAGTAAACCCAAA
*
38838384 TTTCCTTATAAAGTAAACCCAAA
1 TTTCCTTATAGAGTAAACCCAAA
* *
38838407 TTTCCTTATAGAGTCAATCCAAA
1 TTTCCTTATAGAGTAAACCCAAA
*
38838430 TTTTCTTATAGAGTAAA
1 TTTCCTTATAGAGTAAA
38838447 AGATGCATCG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 19 0.35
23 36 0.65
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (23 bp):
TTTCCTTATAGAGTAAACCCAAA
Found at i:38844125 original size:20 final size:20
Alignment explanation
Indices: 38844100--38844145 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
38844090 TTTTGGCCCC
38844100 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
38844120 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
38844140 ATTTGA
1 ATTTGA
38844146 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:38849212 original size:2 final size:2
Alignment explanation
Indices: 38849205--38849255 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
38849195 TGGCATTTAC
*
38849205 AT AT AT AT CT 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 AT AT
38849247 AT AT AT AT A
1 AT AT AT AT A
38849256 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38849319 original size:2 final size:2
Alignment explanation
Indices: 38849312--38849352 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38849302 NNNNNNNNNN
38849312 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
38849353 GAAAGTGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38849670 original size:20 final size:21
Alignment explanation
Indices: 38849644--38849707 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
38849634 ATTTTTCTTT
38849644 TTTCCTTATAAAGTAAACCCA
1 TTTCCTTATAAAGTAAACCCA
* * *
38849665 -TTCCTTGTAGAGTAAATCCAAA
1 TTTCCTTATAAAGTAAA-CC-CA
38849687 TTTCCTTATAAAGTAAACCCA
1 TTTCCTTATAAAGTAAACCCA
38849708 AATTTTCTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 3 0.09
23 14 0.41
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.33
Consensus pattern (21 bp):
TTTCCTTATAAAGTAAACCCA
Found at i:38849693 original size:23 final size:23
Alignment explanation
Indices: 38849644--38849726 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
38849634 ATTTTTCTTT
*
38849644 TTTCCTTATAAAGTAAACCC--A
1 TTTCCTTATAGAGTAAACCCAAA
* *
38849665 -TTCCTTGTAGAGTAAATCCAAA
1 TTTCCTTATAGAGTAAACCCAAA
*
38849687 TTTCCTTATAAAGTAAACCCAAA
1 TTTCCTTATAGAGTAAACCCAAA
* *
38849710 TTTTCTTATCGAGTAAA
1 TTTCCTTATAGAGTAAA
38849727 AAATGTATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
20 16 0.32
22 1 0.02
23 33 0.66
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
TTTCCTTATAGAGTAAACCCAAA
Found at i:38849811 original size:24 final size:22
Alignment explanation
Indices: 38849763--38849812 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
38849753 AGAAAATTTT
**
38849763 TTTTCCTTATAGAGTAAACCCA
1 TTTTCCTTATAGAGTAAACAAA
38849785 TTTTCCTTATAGAGTAAATTCAAA
1 TTTTCCTTATAGAGTAAA--CAAA
38849809 TTTT
1 TTTT
38849813 GAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.75
24 6 0.25
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (22 bp):
TTTTCCTTATAGAGTAAACAAA
Found at i:38852444 original size:19 final size:19
Alignment explanation
Indices: 38852420--38852457 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
38852410 CCATTTAACT
*
38852420 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
38852439 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
38852458 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:38855984 original size:13 final size:13
Alignment explanation
Indices: 38855966--38855990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38855956 TTTCAGAAAA
38855966 TTTATAAAATCAT
1 TTTATAAAATCAT
38855979 TTTATAAAATCA
1 TTTATAAAATCA
38855991 CAATTTCTCC
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:38857176 original size:30 final size:28
Alignment explanation
Indices: 38857142--38857201 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
38857132 TTTTTGAAAT
*
38857142 TTACACTTTTACCCTCATAAAAGTAAAAAA
1 TTACACTTTTA-CCTCA-AAAACTAAAAAA
* *
38857172 TTACATTTTTACCTCAAAAACTGAAAAA
1 TTACACTTTTACCTCAAAAACTAAAAAA
38857200 TT
1 TT
38857202 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 5 0.19
30 10 0.37
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.33
Consensus pattern (28 bp):
TTACACTTTTACCTCAAAAACTAAAAAA
Found at i:38857389 original size:19 final size:19
Alignment explanation
Indices: 38857367--38857404 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38857357 CTGCCAAACC
*
38857367 CTCAAATTATACTCAAATA
1 CTCAAATCATACTCAAATA
*
38857386 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCAAATA
38857405 AGTTAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCAAATA
Found at i:38861047 original size:2 final size:2
Alignment explanation
Indices: 38861042--38861106 Score: 87
Period size: 2 Copynumber: 32.5 Consensus size: 2
38861032 ATATANNNAC
* *
38861042 TA TA TA TA TA GTC TT TA T- 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
*
38861084 CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
38861107 TTGAAGCCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
1 1 0.02
2 54 0.96
3 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38861937 original size:8 final size:8
Alignment explanation
Indices: 38861910--38861952 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
38861900 CTTTTTCTTT
38861910 TTTC-TCC
1 TTTCTTCC
*
38861917 TTTCTTTC
1 TTTCTTCC
*
38861925 ATTCTTCC
1 TTTCTTCC
38861933 TTTC-TCC
1 TTTCTTCC
38861940 TTTCTTCC
1 TTTCTTCC
38861948 TTTCT
1 TTTCT
38861953 CTCTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 11 0.37
8 19 0.63
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTCTTCC
Found at i:38861944 original size:15 final size:16
Alignment explanation
Indices: 38861910--38861958 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 16
38861900 CTTTTTCTTT
*
38861910 TTTC-TCCTTTCTTTC
1 TTTCTTCCTTTCTCTC
*
38861925 ATTCTTCCTTTCTC-C
1 TTTCTTCCTTTCTCTC
38861940 TTTCTTCCTTTCTCTC
1 TTTCTTCCTTTCTCTC
38861956 TTT
1 TTT
38861959 GTTTCCAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTCTTCCTTTCTCTC
Found at i:38867057 original size:23 final size:22
Alignment explanation
Indices: 38867005--38867089 Score: 107
Period size: 23 Copynumber: 3.8 Consensus size: 22
38866995 ATTTTTCTTT
* * *
38867005 TTTCCTTATAGAGTAAACCCAT
1 TTTCCTTATAAAGTAAACCAAA
38867027 TTTCCTTATAAAGTAAACCTAAA
1 TTTCCTTATAAAGTAAACC-AAA
38867050 TTTCCTTATAAAGTAAATCCAAA
1 TTTCCTTATAAAGTAAA-CCAAA
* *
38867073 TTTTCTTATAGAGTAAA
1 TTTCCTTATAAAGTAAA
38867090 AGATGCATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
22 18 0.32
23 36 0.64
24 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (22 bp):
TTTCCTTATAAAGTAAACCAAA
Found at i:38867154 original size:128 final size:128
Alignment explanation
Indices: 38866926--38867180 Score: 379
Period size: 128 Copynumber: 2.0 Consensus size: 128
38866916 TATTTTTTTT
** * *
38866926 CTTATAAAGTAAACCCAAATTTCCTTATAGAATAAAAGATGCATTGTTTAATTGCCTAAATTTGA
1 CTTATAAAGTAAACCCAAATTTCCTTATAGAATAAAAGATGCATTACTTAACTACCTAAATTTGA
* *
38866991 AATTATTTTTCTTTTTTCCTTATAGAGTAAACCCATTTTCCTTATA-AAGTAAACCTAAATTTC
66 AATTATTTTTCTTTTTTCCTTATAGAATAAACCCATTTTCCTTATAGAA-TAAACCCAAATTTC
* * * *
38867054 CTTATAAAGTAAATCCAAATTTTCTTATAGAGTAAAAGATGCATTACTTAACTATCTAAATTTGA
1 CTTATAAAGTAAACCCAAATTTCCTTATAGAATAAAAGATGCATTACTTAACTACCTAAATTTGA
*
38867119 AATT-TTTTTTTTTTTGTCCTTATAGAATAAACCCATTTTCCTTATAGAATAAACCCAAATTT
66 AATTATTTTTCTTTTT-TCCTTATAGAATAAACCCATTTTCCTTATAGAATAAACCCAAATTT
38867181 TGAAATTATT
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
127 10 0.09
128 102 0.89
129 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.41
Consensus pattern (128 bp):
CTTATAAAGTAAACCCAAATTTCCTTATAGAATAAAAGATGCATTACTTAACTACCTAAATTTGA
AATTATTTTTCTTTTTTCCTTATAGAATAAACCCATTTTCCTTATAGAATAAACCCAAATTTC
Found at i:38870686 original size:21 final size:21
Alignment explanation
Indices: 38870658--38870706 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
38870648 TGCAAAGATA
38870658 TTAG-GTGTATAGACAAAACT
1 TTAGAGTGTATAGACAAAACT
*
38870678 TTAGAGTGTTTAGACAAAACT
1 TTAGAGTGTATAGACAAAACT
38870699 TTAGAGTG
1 TTAGAGTG
38870707 CCTAGATGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (21 bp):
TTAGAGTGTATAGACAAAACT
Found at i:38870712 original size:21 final size:21
Alignment explanation
Indices: 38870667--38870712 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
38870657 ATTAGGTGTA
**
38870667 TAGACAAAACTTTAGAGTGTT
1 TAGACAAAACTTTAGAGTGCC
38870688 TAGACAAAACTTTAGAGTGCC
1 TAGACAAAACTTTAGAGTGCC
38870709 TAGA
1 TAGA
38870713 TGGCCAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGACAAAACTTTAGAGTGCC
Found at i:38871426 original size:19 final size:19
Alignment explanation
Indices: 38871404--38871441 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38871394 ATAAGCATAA
*
38871404 TATTAAAAAAATTTTAAAT
1 TATTAAAAAAATTTCAAAT
*
38871423 TATTCAAAAAATTTCAAAT
1 TATTAAAAAAATTTCAAAT
38871442 AAATCTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAAAAAATTTCAAAT
Found at i:38871714 original size:23 final size:23
Alignment explanation
Indices: 38871688--38871757 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
38871678 TGTAGATATG
* *
38871688 TCTGTTGATATACAACAGACACA
1 TCTGTTGAAATACAAAAGACACA
38871711 TCTGTTGAAAATA-AAAAGGACACA
1 TCTGTTG-AAATACAAAA-GACACA
* *
38871735 TCTGTTGAAAGACAATAGACACA
1 TCTGTTGAAATACAAAAGACACA
38871758 ACCTCTCACT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (23 bp):
TCTGTTGAAATACAAAAGACACA
Found at i:38872251 original size:24 final size:24
Alignment explanation
Indices: 38872218--38872272 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
38872208 ACTAAATTTT
*
38872218 ATATT-AAATAGCCTCATTGTAGA
1 ATATTCAAATAGCCTCATTCTAGA
38872241 ATATTCAAATAGCCTCATTCTAGA
1 ATATTCAAATAGCCTCATTCTAGA
*
38872265 ACATTCAA
1 ATATTCAA
38872273 TGTGACTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (24 bp):
ATATTCAAATAGCCTCATTCTAGA
Found at i:38872823 original size:23 final size:23
Alignment explanation
Indices: 38872795--38872887 Score: 93
Period size: 23 Copynumber: 4.0 Consensus size: 23
38872785 TGTAGATACG
38872795 TCTGTTGAAATACAACAGACACA
1 TCTGTTGAAATACAACAGACACA
38872818 TCTGTT-AAA-ACAGTACAGACACA
1 TCTGTTGAAATACA--ACAGACACA
*
38872841 TCTGTTGAAAATA-AAAAGGACACA
1 TCTGTTG-AAATACAACA-GACACA
* * *
38872865 TTTGTTAAAAGACAACAGACACA
1 TCTGTTGAAATACAACAGACACA
38872888 ACCTCTCACT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
21 3 0.05
22 3 0.05
23 33 0.57
24 14 0.24
25 4 0.07
26 1 0.02
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (23 bp):
TCTGTTGAAATACAACAGACACA
Found at i:38872883 original size:47 final size:46
Alignment explanation
Indices: 38872795--38872887 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 46
38872785 TGTAGATACG
* **
38872795 TCTGTTGAAATACAACAGACACATCTGTTAAAACAGTACAGACACA
1 TCTGTTGAAATACAAAAGACACATCTGTTAAAACACAACAGACACA
* *
38872841 TCTGTTGAAAATA-AAAAGGACACATTTGTTAAAAGACAACAGACACA
1 TCTGTTG-AAATACAAAA-GACACATCTGTTAAAACACAACAGACACA
38872888 ACCTCTCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
46 10 0.25
47 30 0.75
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (46 bp):
TCTGTTGAAATACAAAAGACACATCTGTTAAAACACAACAGACACA
Found at i:38873497 original size:23 final size:22
Alignment explanation
Indices: 38873437--38873522 Score: 91
Period size: 23 Copynumber: 3.8 Consensus size: 22
38873427 TATTTTTCTT
* *
38873437 TTTTCCTTATAGAGTAAACCCAC
1 TTTT-CTTATAGAGTAAACCAAA
*
38873460 TTTCCTTATAGAGTAAATCCAAA
1 TTTTCTTATAGAGTAAA-CCAAA
*
38873483 TTTTCTTATAAAGTAAACCCAAA
1 TTTTCTTATAGAGTAAA-CCAAA
* *
38873506 TTTTTTTATCGAGTAAA
1 TTTTCTTATAGAGTAAA
38873523 AAATGCATTG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.25
23 40 0.75
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.38
Consensus pattern (22 bp):
TTTTCTTATAGAGTAAACCAAA
Found at i:38874137 original size:23 final size:23
Alignment explanation
Indices: 38874107--38874152 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38874097 CTATGCTTCC
*
38874107 GATTTCTCTATCTCACGTTTTCA
1 GATTTCTCTATCTCACGCTTTCA
* *
38874130 GATTTCTCTTTCTTACGCTTTCA
1 GATTTCTCTATCTCACGCTTTCA
38874153 AGACACCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.09, T:0.50
Consensus pattern (23 bp):
GATTTCTCTATCTCACGCTTTCA
Found at i:38874566 original size:21 final size:21
Alignment explanation
Indices: 38874540--38874619 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
38874530 GGCTTTTGTA
38874540 CATGACGTGTCACACGCTAAC
1 CATGACGTGTCACACGCTAAC
* * *
38874561 CATGACTTGTCACAGGCTTTTGTA-
1 CATGACGTGTCACACGC---T-AAC
*
38874585 CATGGCGTGTCACACGCTAAC
1 CATGACGTGTCACACGCTAAC
* *
38874606 CATGGCTTGTCACA
1 CATGACGTGTCACA
38874620 GGTTTTTGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.02
21 29 0.63
24 15 0.33
25 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (21 bp):
CATGACGTGTCACACGCTAAC
Found at i:38874572 original size:45 final size:45
Alignment explanation
Indices: 38874516--38874643 Score: 220
Period size: 45 Copynumber: 2.8 Consensus size: 45
38874506 GGTTTTTGTA
*
38874516 CATGGCTTGTCACAGGCTTTTGTACATGACGTGTCACACGCTAAC
1 CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
*
38874561 CATGACTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
1 CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
* *
38874606 CATGGCTTGTCACAGGTTTTTGTACATGGTGTGTCACA
1 CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACA
38874644 TGTTTTTGTA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (45 bp):
CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
Found at i:38874641 original size:69 final size:69
Alignment explanation
Indices: 38874568--38874846 Score: 423
Period size: 69 Copynumber: 4.0 Consensus size: 69
38874558 AACCATGACT
* * *
38874568 TGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTGTCACAGGTTTTTGTACAT
1 TGTCACAGGTTTTTGTACATGGCGTGTCACACGCTAACCATAGCTTGTCACAGATTTTTGTACAT
*
38874633 GGTG
66 GGCG
* * *
38874637 TGTCACATGTTTTTGTACATGACGTGTCACACGCTAACCATAGCTTATCACAGATTTTTGTACAT
1 TGTCACAGGTTTTTGTACATGGCGTGTCACACGCTAACCATAGCTTGTCACAGATTTTTGTACAT
38874702 GGCG
66 GGCG
* * *
38874706 TGTCACATGTTTTTGTACATGGCGTGTCATACGCTAACCATGGCTTGTCACAGATTTTTGTACAT
1 TGTCACAGGTTTTTGTACATGGCGTGTCACACGCTAACCATAGCTTGTCACAGATTTTTGTACAT
38874771 GGCG
66 GGCG
* * * *
38874775 TGTCACAGATTTTTCTACATGGCGTGTAACACGCTAACCATAGCTTGTTACAGATTTTTGTACAT
1 TGTCACAGGTTTTTGTACATGGCGTGTCACACGCTAACCATAGCTTGTCACAGATTTTTGTACAT
*
38874840 GACG
66 GGCG
38874844 TGT
1 TGT
38874847 AACATCATAG
Statistics
Matches: 191, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 191 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (69 bp):
TGTCACAGGTTTTTGTACATGGCGTGTCACACGCTAACCATAGCTTGTCACAGATTTTTGTACAT
GGCG
Found at i:38874701 original size:114 final size:114
Alignment explanation
Indices: 38874501--38874712 Score: 347
Period size: 114 Copynumber: 1.9 Consensus size: 114
38874491 ATTTGAAGTT
38874501 TCACAGGTTTTTGTACATGGCTTGTCACAGGCTTTTGTACATGACGTGTCACACGCTAACCATGA
1 TCACAGGTTTTTGTACATGGCTTGTCACAGGCTTTTGTACATGACGTGTCACACGCTAACCATGA
* *
38874566 CTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTG
66 CTTATCACAGACTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTG
* *
38874615 TCACAGGTTTTTGTACATGG-TGTGTCACATGTTTTTGTACATGACGTGTCACACGCTAACCAT-
1 TCACAGGTTTTTGTACATGGCT-TGTCACAGGCTTTTGTACATGACGTGTCACACGCTAACCATG
*
38874678 AGCTTATCACAGATTTTTGTACATGGCGTGTCACA
65 A-CTTATCACAGACTTTTGTACATGGCGTGTCACA
38874713 TGTTTTTGTA
Statistics
Matches: 91, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
113 2 0.02
114 89 0.98
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (114 bp):
TCACAGGTTTTTGTACATGGCTTGTCACAGGCTTTTGTACATGACGTGTCACACGCTAACCATGA
CTTATCACAGACTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTG
Found at i:38874748 original size:114 final size:111
Alignment explanation
Indices: 38874515--38874781 Score: 274
Period size: 114 Copynumber: 2.3 Consensus size: 111
38874505 AGGTTTTTGT
* * *
38874515 ACATGGCTTGTCACAGGCTTTTGTACATGACGTGTCACACGCTAACCATGACTTGTCACAGGCTT
1 ACATGGCTTGTCACA-GTTTTTGTACATGACGTGTCACACGCTAACCATGACTTATCACAGACTT
* * * *
38874580 TTGTACATGGCGTGTCACACGCTAACCATGGCTTGTCACAGGTTTTTGT
65 TTGTACATGGCGTGTCACACGCTAACCATGGCGTGTCACACG--TCTGA
*
38874629 ACATGG-TGTGTCACATGTTTTTGTACATGACGTGTCACACGCTAACCAT-AGCTTATCACAGAT
1 ACATGGCT-TGTCACA-GTTTTTGTACATGACGTGTCACACGCTAACCATGA-CTTATCACAGAC
* * * *
38874692 TTTTGTACATGGCGTGTCACATGTTTTTGTA-CATGGCGTGTCATACG-CT-A
63 TTTTGTACATGGCGTGTCACACG---CT-AACCATGGCGTGTCACACGTCTGA
*
38874742 ACCATGGCTTGTCACAGATTTTTGTACATGGCGTGTCACA
1 A-CATGGCTTGTCACAG-TTTTTGTACATGACGTGTCACA
38874782 GATTTTTCTA
Statistics
Matches: 130, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
113 4 0.03
114 110 0.85
115 1 0.01
117 14 0.11
118 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (111 bp):
ACATGGCTTGTCACAGTTTTTGTACATGACGTGTCACACGCTAACCATGACTTATCACAGACTTT
TGTACATGGCGTGTCACACGCTAACCATGGCGTGTCACACGTCTGA
Found at i:38874798 original size:24 final size:24
Alignment explanation
Indices: 38874606--38874801 Score: 128
Period size: 24 Copynumber: 8.4 Consensus size: 24
38874596 ACACGCTAAC
* *
38874606 CATGGCTTGTCACAGGTTTTTGTA
1 CATGGCGTGTCACAGATTTTTGTA
*
38874630 CATGGTGTGTCACATG-TTTTTGTA
1 CATGGCGTGTCACA-GATTTTTGTA
* * *
38874654 CATGACGTGTCACACG----CT-AA
1 CATGGCGTGTCACA-GATTTTTGTA
* * *
38874674 CCATAGCTTATCACAGATTTTTGTA
1 -CATGGCGTGTCACAGATTTTTGTA
38874699 CATGGCGTGTCACATG-TTTTTGTA
1 CATGGCGTGTCACA-GATTTTTGTA
* * *
38874723 CATGGCGTGTCATACG----CT-AA
1 CATGGCGTGTCACA-GATTTTTGTA
*
38874743 CCATGGCTTGTCACAGATTTTTGTA
1 -CATGGCGTGTCACAGATTTTTGTA
*
38874768 CATGGCGTGTCACAGATTTTTCTA
1 CATGGCGTGTCACAGATTTTTGTA
38874792 CATGGCGTGT
1 CATGGCGTGT
38874802 AACACGCTAA
Statistics
Matches: 132, Mismatches: 26, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
20 4 0.03
21 24 0.18
24 100 0.76
25 4 0.03
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (24 bp):
CATGGCGTGTCACAGATTTTTGTA
Found at i:38875734 original size:16 final size:17
Alignment explanation
Indices: 38875713--38875750 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
38875703 AATATGAAGG
38875713 AAGAAAAG-GAACAAAC
1 AAGAAAAGAGAACAAAC
*
38875729 AAGAAAAGAGAACAATC
1 AAGAAAAGAGAACAAAC
38875746 AAGAA
1 AAGAA
38875751 TTTTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.68, C:0.11, G:0.18, T:0.03
Consensus pattern (17 bp):
AAGAAAAGAGAACAAAC
Found at i:38915214 original size:191 final size:191
Alignment explanation
Indices: 38914890--38915272 Score: 649
Period size: 191 Copynumber: 2.0 Consensus size: 191
38914880 GAAGCCGAGC
*
38914890 ATGTAATGCATGAGGATTTATTGCAGGATCTTTCTCTGCATCTCTCCTCATAATATCAACAACTC
1 ATGTAATGCATAAGGATTTATTGCAGGATCTTTCTCTGCATCTCTCCTCATAATATCAACAACTC
* * *
38914955 TGCACCAGAATAGCAAATTGATATAGATAACTCTATGAGAGAATATTGCTTTGGTAAACTCAAAA
66 TGCACCAGAATAGCAAATTGAGATAGATAACTCTATAAGAGAACATTGCTTTGGTAAACTCAAAA
* *
38915020 TTCCAAGATGATTTTTATACAAGTTTGAGGAAACATGGTAAAACATTTATCCAATCAAGCA
131 TTCCAAGACGATTTTTACACAAGTTTGAGGAAACATGGTAAAACATTTATCCAATCAAGCA
* *
38915081 ATGTAATGCATAAGGATTTGTTGCAGGATCTTTCTCTGCATCTCTCCTCATAATATCAAGAACTC
1 ATGTAATGCATAAGGATTTATTGCAGGATCTTTCTCTGCATCTCTCCTCATAATATCAACAACTC
*
38915146 TGCACCAGAATAGCAAATTGAGATAGATAACTCTATAAGAGACCATTGCTTTGGTAAACTCAAAA
66 TGCACCAGAATAGCAAATTGAGATAGATAACTCTATAAGAGAACATTGCTTTGGTAAACTCAAAA
* ** *
38915211 TTCCAAGACGATTTTTACACAAGTTTGAGGAAACATGGTGAATTATTTATCTAATCAAGCA
131 TTCCAAGACGATTTTTACACAAGTTTGAGGAAACATGGTAAAACATTTATCCAATCAAGCA
38915272 A
1 A
38915273 AATAAGCAAA
Statistics
Matches: 179, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
191 179 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (191 bp):
ATGTAATGCATAAGGATTTATTGCAGGATCTTTCTCTGCATCTCTCCTCATAATATCAACAACTC
TGCACCAGAATAGCAAATTGAGATAGATAACTCTATAAGAGAACATTGCTTTGGTAAACTCAAAA
TTCCAAGACGATTTTTACACAAGTTTGAGGAAACATGGTAAAACATTTATCCAATCAAGCA
Found at i:38917422 original size:2 final size:2
Alignment explanation
Indices: 38917417--38917446 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38917407 AAACACACAC
38917417 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
38917447 ACATACATAC
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:38925654 original size:27 final size:27
Alignment explanation
Indices: 38925622--38925677 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
38925612 TTCGTTTTGA
38925622 TTGATGTTTTTGTTATTTATCTTTTAT
1 TTGATGTTTTTGTTATTTATCTTTTAT
38925649 TTGATGTTTTTGTTATTTATCTTTTAT
1 TTGATGTTTTTGTTATTTATCTTTTAT
38925676 TT
1 TT
38925678 TATATATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.04, G:0.11, T:0.71
Consensus pattern (27 bp):
TTGATGTTTTTGTTATTTATCTTTTAT
Found at i:38925680 original size:16 final size:15
Alignment explanation
Indices: 38925643--38925690 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
38925633 GTTATTTATC
*
38925643 TTTTATTTGATGTTTT
1 TTTTATTT-ATCTTTT
*
38925659 TGTTATTTATCTTTT
1 TTTTATTTATCTTTT
*
38925674 ATTTTATATATCTTTT
1 -TTTTATTTATCTTTT
38925690 T
1 T
38925691 ATCTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTTATTTATCTTTT
Found at i:38926893 original size:23 final size:23
Alignment explanation
Indices: 38926841--38926893 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
38926831 ATATTTTATC
* *
38926841 CAAAATCACTCTTAATAGTTTTT
1 CAAATTCACTCTTAATAGTTTCT
38926864 CATAAATTCACTCTTAATAGTTTCT
1 C--AAATTCACTCTTAATAGTTTCT
38926889 CAAAT
1 CAAAT
38926894 CAATCCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
25 21 0.81
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.42
Consensus pattern (23 bp):
CAAATTCACTCTTAATAGTTTCT
Found at i:38937764 original size:30 final size:30
Alignment explanation
Indices: 38937724--38937780 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
38937714 CAATGCTCTT
* *
38937724 TCTTGATTTCTCTTTTTTGTCAGTGCTGGC
1 TCTTGATTTCTCTCTATTGTCAGTGCTGGC
* *
38937754 TCTTGCTTTCTCTCTATTGTCTGTGCT
1 TCTTGATTTCTCTCTATTGTCAGTGCT
38937781 TAGCCTAGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.05, C:0.23, G:0.18, T:0.54
Consensus pattern (30 bp):
TCTTGATTTCTCTCTATTGTCAGTGCTGGC
Found at i:38938951 original size:2 final size:2
Alignment explanation
Indices: 38938944--38938976 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38938934 ATATCTCCAG
38938944 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38938977 TTTGACTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38943980 original size:2 final size:2
Alignment explanation
Indices: 38943963--38944015 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
38943953 TATATTCTTG
* *
38943963 TA TA AA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38944005 TA TA TA TA TA T
1 TA TA TA TA TA T
38944016 GAGAAAAAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38948480 original size:35 final size:34
Alignment explanation
Indices: 38948434--38948520 Score: 129
Period size: 35 Copynumber: 2.5 Consensus size: 34
38948424 GAAATGGATC
*
38948434 AGAAGAAATGGGGCTTTTTTTTTTTTCTGAAAGTT
1 AGAAGAAATGGGGCTTTTTTTCTTTT-TGAAAGTT
*
38948469 AGAAGAAATGGGGCATTTTTTTCTTTTTGAAGGTT
1 AGAAGAAATGGGGC-TTTTTTTCTTTTTGAAAGTT
*
38948504 AGAAGAAATGGGACTTT
1 AGAAGAAATGGGGCTTT
38948521 GTTCAAGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
34 3 0.06
35 34 0.71
36 11 0.23
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.40
Consensus pattern (34 bp):
AGAAGAAATGGGGCTTTTTTTCTTTTTGAAAGTT
Found at i:38969115 original size:13 final size:13
Alignment explanation
Indices: 38969097--38969121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38969087 TTTCATTAGT
38969097 TTAATCTAAAATA
1 TTAATCTAAAATA
38969110 TTAATCTAAAAT
1 TTAATCTAAAAT
38969122 GGGATTTCTT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAATCTAAAATA
Found at i:38982714 original size:15 final size:15
Alignment explanation
Indices: 38982694--38982728 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
38982684 TAAATATATT
*
38982694 TATATCTAAAGTATA
1 TATATCAAAAGTATA
38982709 TATATCAAAAGTATA
1 TATATCAAAAGTATA
38982724 TATAT
1 TATAT
38982729 AATAGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (15 bp):
TATATCAAAAGTATA
Found at i:38982725 original size:17 final size:17
Alignment explanation
Indices: 38982688--38982729 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
38982678 AGAAAGTAAA
* *
38982688 TATATTTATATCTAAAG
1 TATATATATATCAAAAG
38982705 --TATATATATCAAAAG
1 TATATATATATCAAAAG
38982720 TATATATATA
1 TATATATATA
38982730 ATAGTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 13 0.62
17 8 0.38
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (17 bp):
TATATATATATCAAAAG
Found at i:38983337 original size:2 final size:2
Alignment explanation
Indices: 38983330--38983363 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
38983320 TGATCTACAT
*
38983330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38983364 GACTTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38988640 original size:2 final size:2
Alignment explanation
Indices: 38988633--38988659 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38988623 TGACTTAATC
38988633 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38988660 ATAACTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.