Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 4 of 173
Found at i:1012560 original size:13 final size:13
Alignment explanation
Indices: 1012463--1012614 Score: 67
Period size: 13 Copynumber: 11.1 Consensus size: 13
1012453 CTTAAACCAA
* *
1012463 ACTTTTCAAAAGT
1 ACTTTTTAAAAGC
* * *
1012476 ACTTCTCAAAATC
1 ACTTTTTAAAAGC
1012489 A-TTTTTCAAAAGC
1 ACTTTTT-AAAAGC
*
1012502 ACTTTTTAAAAGT
1 ACTTTTTAAAAGC
*
1012515 ACTTCTTTCTCAAAATC
1 AC-T-TTT-T-AAAAGC
1012532 A-TTTTTCGAAAA-C
1 ACTTTTT--AAAAGC
1012545 ACTTTTTAAAAGC
1 ACTTTTTAAAAGC
*
1012558 ACTTCTTTCTCAAAATC
1 AC-T-TTT-T-AAAAGC
* **
1012575 AATTTTCGAAAGC
1 ACTTTTTAAAAGC
1012588 ACTTTTTAAAAGC
1 ACTTTTTAAAAGC
* *
1012601 ACTTCTCAAAAGC
1 ACTTTTTAAAAGC
1012614 A
1 A
1012615 ATGCTAAACT
Statistics
Matches: 106, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
12 7 0.07
13 56 0.53
14 19 0.18
15 10 0.09
16 3 0.03
17 11 0.10
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (13 bp):
ACTTTTTAAAAGC
Found at i:1016864 original size:27 final size:26
Alignment explanation
Indices: 1016834--1016894 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
1016824 ATTAATATGC
1016834 AATAAAATA-A-AAAAATAGAAAATAGAA
1 AATAAAATATATAAAAAT--AAAATA-AA
*
1016861 AATAAAATATATATAAATAAAATAAA
1 AATAAAATATATAAAAATAAAATAAA
1016887 AATAAAAT
1 AATAAAAT
1016895 TGGGTTGCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 10 0.32
27 15 0.48
28 1 0.03
29 5 0.16
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (26 bp):
AATAAAATATATAAAAATAAAATAAA
Found at i:1016891 original size:15 final size:15
Alignment explanation
Indices: 1016837--1016892 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1016827 AATATGCAAT
1016837 AAAATAAA-AAAATA
1 AAAATAAATAAAATA
1016851 GAAAATAGAAAATAAAATA
1 -AAAAT---AAATAAAATA
* *
1016870 TATATAAATAAAATA
1 AAAATAAATAAAATA
1016885 AAAATAAA
1 AAAATAAA
1016893 ATTGGGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 21 0.64
18 6 0.18
19 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (15 bp):
AAAATAAATAAAATA
Found at i:1020945 original size:33 final size:33
Alignment explanation
Indices: 1020875--1020948 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
1020865 TTCCTTTTGA
* * **
1020875 AAATCAAGAGTTTGTTGTTGTATTTGTTGTTAG
1 AAATCAAGAGTTTGTCGTTGTATCTACTGTTAG
*
1020908 AAATCAATAGTTTGTCGTTGTATCTACTGTT-G
1 AAATCAAGAGTTTGTCGTTGTATCTACTGTTAG
1020940 CAAATCAAG
1 -AAATCAAG
1020949 CAGATTAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (33 bp):
AAATCAAGAGTTTGTCGTTGTATCTACTGTTAG
Found at i:1023184 original size:19 final size:18
Alignment explanation
Indices: 1023135--1023190 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
1023125 ATTTGTTCCT
1023135 AATTAAACTCTAAAAGATA
1 AATTAAA-TCTAAAAGATA
** *
1023154 AA-TAAAGATAAAAGCTAA
1 AATTAAATCTAAAAGAT-A
*
1023172 AATTAAATCTAAAAAATA
1 AATTAAATCTAAAAGATA
1023190 A
1 A
1023191 TCCTAACAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
17 7 0.25
18 9 0.32
19 12 0.43
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.23
Consensus pattern (18 bp):
AATTAAATCTAAAAGATA
Found at i:1026005 original size:30 final size:31
Alignment explanation
Indices: 1025981--1026039 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1025971 GTAAATACTC
*
1025981 AAAATTTGAGGGGTTAA-AATGTAAATATAA
1 AAAATTTGAAGGGTTAATAATGTAAATATAA
*
1026011 AAAATTTGAAGGGTTAATAGTGTAAATAT
1 AAAATTTGAAGGGTTAATAATGTAAATAT
1026040 TTTAAGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.32
Consensus pattern (31 bp):
AAAATTTGAAGGGTTAATAATGTAAATATAA
Found at i:1028605 original size:53 final size:54
Alignment explanation
Indices: 1028542--1028649 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
1028532 ATTGGTACAA
1028542 GAATTAAATTGTAAAGCATG-AAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1028595 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1028649 G
1 G
1028650 CATGCATGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 20 0.37
54 34 0.63
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (54 bp):
GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
Found at i:1029055 original size:51 final size:49
Alignment explanation
Indices: 1028917--1029094 Score: 189
Period size: 51 Copynumber: 3.5 Consensus size: 49
1028907 CTAGGCCACG
*
1028917 TGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGA-ATGATCGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTAC-GGATA-GATCGGTCACA
* * * * * *
1028967 TGTGTAGTACTATATGCAGGCTACTATGCGTACCGGATAGCTTCGATCACT
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATAG-ATCGGTCACA
* * *
1029018 TGTGTGGTACTATGTGCAGGCTACTACATGTATCGGATGGAAAT-GGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGAT--AGATCGGTCACA
1029069 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
1029095 TGTGAACTGG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
50 33 0.31
51 70 0.67
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACGGATAGATCGGTCACA
Found at i:1041028 original size:24 final size:24
Alignment explanation
Indices: 1041001--1041069 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
1040991 ATAATACTTA
1041001 ATTTCAAATTAATTTTTATTAAAT
1 ATTTCAAATTAATTTTTATTAAAT
* *
1041025 ATTT---GTT-A---TTATTAAGT
1 ATTTCAAATTAATTTTTATTAAAT
*
1041042 CTTTCAAATTAATTTTTATTAAAT
1 ATTTCAAATTAATTTTTATTAAAT
1041066 ATTT
1 ATTT
1041070 GTTATTATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
17 11 0.34
20 3 0.09
21 3 0.09
24 15 0.47
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (24 bp):
ATTTCAAATTAATTTTTATTAAAT
Found at i:1041059 original size:41 final size:41
Alignment explanation
Indices: 1041002--1041084 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
1040992 TAATACTTAA
1041002 TTTCAAATTAATTTTTATTAAATATTTGTTATTATTAAGTC
1 TTTCAAATTAATTTTTATTAAATATTTGTTATTATTAAGTC
1041043 TTTCAAATTAATTTTTATTAAATATTTGTTATTATTAAGTC
1 TTTCAAATTAATTTTTATTAAATATTTGTTATTATTAAGTC
1041084 T
1 T
1041085 ATATAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (41 bp):
TTTCAAATTAATTTTTATTAAATATTTGTTATTATTAAGTC
Found at i:1041139 original size:22 final size:20
Alignment explanation
Indices: 1041089--1041139 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1041079 AAGTCTATAT
* *
1041089 AAAATATTATGTTATCATAG
1 AAAATATTTTGTTATCAAAG
*
1041109 AACATATTTTGATTATCAAAG
1 AAAATATTTTG-TTATCAAAG
1041130 CAAAATATTT
1 -AAAATATTT
1041140 CTACAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 9 0.36
21 8 0.32
22 8 0.32
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (20 bp):
AAAATATTTTGTTATCAAAG
Found at i:1056518 original size:22 final size:22
Alignment explanation
Indices: 1056493--1056535 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1056483 TTTTAAAATA
* *
1056493 TAAAAAATAGGGACTAAATTTC
1 TAAAAAACAAGGACTAAATTTC
*
1056515 TAAAATACAAGGACTAAATTT
1 TAAAAAACAAGGACTAAATTT
1056536 TTAATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (22 bp):
TAAAAAACAAGGACTAAATTTC
Found at i:1060657 original size:27 final size:27
Alignment explanation
Indices: 1060622--1060675 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1060612 GAAGCAACTT
* * *
1060622 TCTCGCTGTTGTTGGCTTCGTGTTGAA
1 TCTCACTGTTGTTCGCTTCATGTTGAA
1060649 TCTCACTGTTGTTCGCTTCATGTTGAA
1 TCTCACTGTTGTTCGCTTCATGTTGAA
1060676 GTTCGAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (27 bp):
TCTCACTGTTGTTCGCTTCATGTTGAA
Found at i:1072702 original size:26 final size:26
Alignment explanation
Indices: 1072654--1072729 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
1072644 TTTCTCACCT
*
1072654 AATTTTACCC-CAATAAAATTTTGAC
1 AATTTTACCCTCGATAAAATTTTGAC
*
1072679 AATTTTACCCTCGGTAAAATTTTGAC
1 AATTTTACCCTCGATAAAATTTTGAC
*
1072705 GATTTTACCACT-GATAAAATTTTGA
1 AATTTTACC-CTCGATAAAATTTTGA
1072730 GAAAATTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
25 10 0.22
26 33 0.73
27 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (26 bp):
AATTTTACCCTCGATAAAATTTTGAC
Found at i:1073066 original size:24 final size:25
Alignment explanation
Indices: 1073011--1073079 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
1073001 TTCGTTCATT
*
1073011 TGTGGTGTAATATGAAAGAAAAAGCTTT
1 TGTGGTGTAATATG-AA-AAAAAGC-TC
1073039 TGTGGTGTAATATGAAAAAAAGC-C
1 TGTGGTGTAATATGAAAAAAAGCTC
* *
1073063 TGTGGCGGAATATGAAA
1 TGTGGTGTAATATGAAA
1073080 GGAATGCCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 15 0.39
26 7 0.18
27 2 0.05
28 14 0.37
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (25 bp):
TGTGGTGTAATATGAAAAAAAGCTC
Found at i:1074483 original size:20 final size:19
Alignment explanation
Indices: 1074437--1074475 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1074427 TTCAAAATAT
1074437 AAATAAATAAATTTCTAAA
1 AAATAAATAAATTTCTAAA
1074456 AAATTAAATTAAATTT-TAAA
1 AAA-TAAA-TAAATTTCTAAA
1074476 TATATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 8 0.44
21 7 0.39
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAAATAAATTTCTAAA
Found at i:1075156 original size:30 final size:28
Alignment explanation
Indices: 1075076--1075156 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
1075066 CCTTTCAATG
* *
1075076 TTTACAGATTCTATCAATTTAGTCATAA
1 TTTACAAATTCTATCAATTTAGCCATAA
* *
1075104 TTCTAAAAAATCTA-CAAATTTAGCCATCAA
1 TT-TACAAATTCTATC-AATTTAGCCAT-AA
*
1075134 CTTTACACATTCTATCAATTTAG
1 -TTTACAAATTCTATCAATTTAG
1075157 TTTTATTTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
28 3 0.07
29 18 0.44
30 17 0.41
31 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (28 bp):
TTTACAAATTCTATCAATTTAGCCATAA
Found at i:1075172 original size:59 final size:60
Alignment explanation
Indices: 1075056--1075181 Score: 159
Period size: 59 Copynumber: 2.1 Consensus size: 60
1075046 TGAAATAACA
* * *
1075056 ACAAATTTAGCCTTTCAATGTTTACAGATTCTATCAATTTAGTCATAATTCTAAAAAATCT
1 ACAAATTTAGCCTATCAATCTTTACACATTCTATCAATTTAGTCATAATTCTAAAAAA-CT
** * *
1075117 ACAAATTTAGCC-ATCAA-CTTTACACATTCTATCAATTTAGTTTTATTTCTTAAAAACT
1 ACAAATTTAGCCTATCAATCTTTACACATTCTATCAATTTAGTCATAATTCTAAAAAACT
1075175 -CAAATTT
1 ACAAATTT
1075182 TAAATTTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 7 0.12
58 2 0.03
59 33 0.57
60 4 0.07
61 12 0.21
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.40
Consensus pattern (60 bp):
ACAAATTTAGCCTATCAATCTTTACACATTCTATCAATTTAGTCATAATTCTAAAAAACT
Found at i:1075210 original size:17 final size:17
Alignment explanation
Indices: 1075176--1075215 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1075166 TTAAAAACTC
** *
1075176 AAATTTTAAATTTTAAA
1 AAATTTTAAAAGTAAAA
1075193 AAATTTTAAAAGTAAAA
1 AAATTTTAAAAGTAAAA
1075210 AAATTT
1 AAATTT
1075216 ATTTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AAATTTTAAAAGTAAAA
Found at i:1075841 original size:20 final size:20
Alignment explanation
Indices: 1075816--1075857 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1075806 CCTTGAATTG
1075816 TTTATTTATA-AGATTATTAT
1 TTTATTTATACA-ATTATTAT
1075836 TTTATTTATACAATTATTAT
1 TTTATTTATACAATTATTAT
1075856 TT
1 TT
1075858 AAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATTTATACAATTATTAT
Found at i:1076385 original size:27 final size:27
Alignment explanation
Indices: 1076347--1076399 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1076337 TCTATACTCC
*
1076347 TTGTAATTATCCCGAAAGGGTTTCCAT
1 TTGTAACTATCCCGAAAGGGTTTCCAT
1076374 TTGTAACTATCCCGAAAGGGTTTCCA
1 TTGTAACTATCCCGAAAGGGTTTCCA
1076400 CTTATCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
TTGTAACTATCCCGAAAGGGTTTCCAT
Found at i:1081098 original size:16 final size:18
Alignment explanation
Indices: 1081079--1081117 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1081069 TATAAAAAAA
*
1081079 TAAAAATA-TAA-TACAT
1 TAAAAATACTAAGAACAT
1081095 TAAAAATACTAAGAACAT
1 TAAAAATACTAAGAACAT
1081113 TAAAA
1 TAAAA
1081118 TAAATGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAATACTAAGAACAT
Found at i:1081114 original size:18 final size:16
Alignment explanation
Indices: 1081068--1081117 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1081058 TTAATTTTTT
* *
1081068 ATATAAAAAAATAAAA
1 ATATAAAACATTAAAA
*
1081084 ATATAATACATTAAAA
1 ATATAAAACATTAAAA
1081100 ATACTAAGAACATTAAAA
1 ATA-TAA-AACATTAAAA
1081118 TAAATGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 16 0.57
17 3 0.11
18 9 0.32
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (16 bp):
ATATAAAACATTAAAA
Found at i:1081850 original size:5 final size:5
Alignment explanation
Indices: 1081840--1081869 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1081830 AATTATGTTT
1081840 TTATA TTATA TTATA TTATTA TTATA TTAT
1 TTATA TTATA TTATA TTA-TA TTATA TTAT
1081870 TATATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:1081944 original size:40 final size:40
Alignment explanation
Indices: 1081887--1081982 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
1081877 ATGACAAAGA
1081887 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
1081928 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
1081968 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
1081983 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:1082978 original size:13 final size:13
Alignment explanation
Indices: 1082960--1082991 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1082950 TTTCCAGCAA
1082960 TTATGAATTTATT
1 TTATGAATTTATT
1082973 TTATGAATTTATT
1 TTATGAATTTATT
*
1082986 TGATGA
1 TTATGA
1082992 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1083199 original size:50 final size:50
Alignment explanation
Indices: 1083086--1083327 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
1083076 ATTTGGGTAA
* * *
1083086 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
1083142 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
1083192 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
1083242 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGTATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
1083292 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
1083328 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.55
51 28 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1083270 original size:100 final size:103
Alignment explanation
Indices: 1083086--1083335 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
1083076 ATTTGGGTAA
1083086 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
1083151 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* *
1083192 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
*
1083254 TAAGACCATGTCTGGGACATGGTATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
1083292 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1083336 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 39 0.29
105 2 0.02
106 41 0.31
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:1086282 original size:20 final size:22
Alignment explanation
Indices: 1086257--1086305 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
1086247 CAAAATTTAT
1086257 ATTTAAAAAAAT-TATAAA-AA
1 ATTTAAAAAAATATATAAAGAA
*
1086277 ATTT-AAAGAATATATAAAGAA
1 ATTTAAAAAAATATATAAAGAA
*
1086298 AGTTAAAA
1 ATTTAAAA
1086306 CTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 10 0.42
21 5 0.21
22 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
ATTTAAAAAAATATATAAAGAA
Found at i:1089026 original size:21 final size:23
Alignment explanation
Indices: 1088990--1089031 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1088980 TGTAAAAAGT
*
1088990 AAAATATACTTAA-TTTAAATCC
1 AAAATATACATAATTTTAAATCC
1089012 AAAATAT-CATAATTTTAAAT
1 AAAATATACATAATTTTAAAT
1089032 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATATACATAATTTTAAATCC
Found at i:1089103 original size:23 final size:23
Alignment explanation
Indices: 1089068--1089111 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1089058 ATAGAAAAAA
1089068 AATAAAAGAGT-AAGAGTAAATTG
1 AATAAAAGAGTAAAG-GTAAATTG
* *
1089091 AATAAATGTGTAAAGGTAAAT
1 AATAAAAGAGTAAAGGTAAAT
1089112 GCTAAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (23 bp):
AATAAAAGAGTAAAGGTAAATTG
Found at i:1090016 original size:11 final size:11
Alignment explanation
Indices: 1090002--1090027 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1089992 TTTTTTTTAA
1090002 TTTTAAAATAC
1 TTTTAAAATAC
1090013 TTTTAAAATAC
1 TTTTAAAATAC
1090024 TTTT
1 TTTT
1090028 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:1090087 original size:29 final size:32
Alignment explanation
Indices: 1090053--1090125 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 32
1090043 TTTTAAATTT
1090053 TTTTTAAAATACTTTTTTTAA-TTT-TTTTAA
1 TTTTTAAAATACTTTTTTTAACTTTGTTTTAA
1090083 -TTTTAAAATACTTTTTTTAACTTTTGTTTTAA
1 TTTTTAAAATACTTTTTTTAAC-TTTGTTTTAA
1090115 TTTTTAAAATA
1 TTTTTAAAATA
1090126 AATTTTTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
29 20 0.51
31 3 0.08
32 6 0.15
33 10 0.26
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (32 bp):
TTTTTAAAATACTTTTTTTAACTTTGTTTTAA
Found at i:1090098 original size:41 final size:41
Alignment explanation
Indices: 1089985--1090098 Score: 160
Period size: 41 Copynumber: 2.8 Consensus size: 41
1089975 AAATATTTTA
*
1089985 TTTTTTATTTTTTTTAATTTTAAAATAC-TTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATACTTTTTAAAATACT
* * **
1090025 TTTTTAAAATTTTTTAAATTTT-AAATTTTTTTTAAAATACT
1 TTTTT-TAATTTTTTTAATTTTAAAATACTTTTTAAAATACT
1090066 TTTTTTAATTTTTTTAATTTTAAAATACTTTTT
1 TTTTTTAATTTTTTTAATTTTAAAATACTTTTT
1090099 TTAACTTTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
40 23 0.37
41 39 0.63
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (41 bp):
TTTTTTAATTTTTTTAATTTTAAAATACTTTTTAAAATACT
Found at i:1090113 original size:41 final size:40
Alignment explanation
Indices: 1089985--1090119 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 40
1089975 AAATATTTTA
* ***
1089985 TTTTTTATTTTTTTTAATTTTAAAATACTTTTAAAATACTT
1 TTTTTTAATTTTTTTAATTTTAAAATACTTTTTTTA-ACTT
** * *
1090026 TTTTAAAATTTTTTAAATTTT-AAAT--TTTTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATACTTTTTTT-AACT--T
1090066 TTTTTTAATTTTTTTAATTTTAAAATACTTTTTTTAACTT
1 TTTTTTAATTTTTTTAATTTTAAAATACTTTTTTTAACTT
1090106 TTGTTTTAATTTTT
1 TT-TTTTAATTTTT
1090120 AAAATAAATT
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
38 6 0.08
39 1 0.01
40 26 0.35
41 32 0.43
42 3 0.04
43 7 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (40 bp):
TTTTTTAATTTTTTTAATTTTAAAATACTTTTTTTAACTT
Found at i:1090119 original size:40 final size:39
Alignment explanation
Indices: 1089985--1090119 Score: 114
Period size: 40 Copynumber: 3.3 Consensus size: 39
1089975 AAATATTTTA
* ***
1089985 TTTTTTATTTTTTTTAATTTTAAAATACTTTTAAAATACTT
1 TTTTTTA-ATTTTTTAATTTTAAAATACTTTTTTTA-ACTT
** *
1090026 TTTTAAAATTTTTTAAATTTT-AAAT--TTTTTTTAAAATACT
1 TTTTTTAATTTTTT-AATTTTAAAATACTTTTTTT-AACT--T
1090066 TTTTTTAATTTTTTTAATTTTAAAATACTTTTTTTAACTT
1 TTTTTTAA-TTTTTTAATTTTAAAATACTTTTTTTAACTT
1090106 TTGTTTTAATTTTT
1 TT-TTTTAATTTTT
1090120 AAAATAAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
38 6 0.08
39 1 0.01
40 31 0.41
41 27 0.36
42 3 0.04
43 7 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (39 bp):
TTTTTTAATTTTTTAATTTTAAAATACTTTTTTTAACTT
Found at i:1090524 original size:11 final size:11
Alignment explanation
Indices: 1090503--1090541 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1090493 AAACAGTAGC
*
1090503 AAACAATAACA
1 AAACAACAACA
*
1090514 AAGCAACAACA
1 AAACAACAACA
*
1090525 AAACATCAACA
1 AAACAACAACA
1090536 AAACAA
1 AAACAA
1090542 TAGTAGGGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.69, C:0.23, G:0.03, T:0.05
Consensus pattern (11 bp):
AAACAACAACA
Found at i:1091163 original size:20 final size:17
Alignment explanation
Indices: 1091130--1091181 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
1091120 TTAAAATTGA
*
1091130 TATAAAATTTATAAATAT
1 TATAAAATTAATAAA-AT
1091148 TATAATAATATAAT-AAAT
1 TATAA-AAT-TAATAAAAT
1091166 TATAAAATTAATAAAA
1 TATAAAATTAATAAAA
1091182 AATATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.13
17 6 0.20
18 12 0.40
19 5 0.17
20 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAAATTAATAAAAT
Found at i:1091184 original size:47 final size:45
Alignment explanation
Indices: 1091095--1091192 Score: 112
Period size: 47 Copynumber: 2.2 Consensus size: 45
1091085 GATTATAAAA
* *
1091095 TATAAATATTAAATATTAAAAAATGTTAAAATTGATATAAAAT-T
1 TATAAATATTAAATATTAAAAAATGTTAAAATTAATAAAAAATAT
*
1091139 TATAAATATTATAATAATATAATAAAT-TATAAAATTAATAAAAAATAT
1 TATAAATATTA-AAT-AT-TAAAAAATGT-TAAAATTAATAAAAAATAT
1091187 T-TAAAT
1 TATAAAT
1091193 TAAAAATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
44 11 0.24
45 3 0.07
46 3 0.07
47 27 0.59
48 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (45 bp):
TATAAATATTAAATATTAAAAAATGTTAAAATTAATAAAAAATAT
Found at i:1091238 original size:10 final size:10
Alignment explanation
Indices: 1091225--1091278 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
1091215 AAAATGCAAT
1091225 AAAAATTATA
1 AAAAATTATA
*
1091235 AAAAAATAT-
1 AAAAATTATA
1091244 AAAAATTGATA
1 AAAAATT-ATA
* *
1091255 TAAATTTATA
1 AAAAATTATA
*
1091265 AAAAATCATA
1 AAAAATTATA
1091275 AAAA
1 AAAA
1091279 CTTAAACTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
9 6 0.17
10 24 0.69
11 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:1091249 original size:30 final size:30
Alignment explanation
Indices: 1091223--1091278 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1091213 TAAAAATGCA
1091223 ATAAAAA-TTATAAAAAAAT-ATAAAAATTG
1 ATAAAAATTTAT-AAAAAATCATAAAAATTG
*
1091252 ATATAAATTTATAAAAAATCATAAAAA
1 ATAAAAATTTATAAAAAATCATAAAAA
1091279 CTTAAACTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (30 bp):
ATAAAAATTTATAAAAAATCATAAAAATTG
Found at i:1091759 original size:20 final size:21
Alignment explanation
Indices: 1091736--1091782 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
1091726 TTTTATAATT
1091736 TTTTATAAAATTTT-AATATG
1 TTTTATAAAATTTTAAATATG
*
1091756 TTTTACAAAATTTTAAATATG
1 TTTTATAAAATTTTAAATATG
1091777 TTTTAT
1 TTTTAT
1091783 TTATTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTATAAAATTTTAAATATG
Found at i:1091895 original size:19 final size:19
Alignment explanation
Indices: 1091873--1091923 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1091863 TAATAATATT
* *
1091873 TTTTTATAATTTTATCTAA
1 TTTTTATGATTTTATATAA
1091892 TTTTTATGATTTTATATAA
1 TTTTTATGATTTTATATAA
*
1091911 TATTTATGATTTT
1 TTTTTATGATTTT
1091924 TAATAACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTTATGATTTTATATAA
Found at i:1097089 original size:11 final size:10
Alignment explanation
Indices: 1097067--1097117 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
1097057 GAATGGTTTT
*
1097067 TAAATAATTA
1 TAAAAAATTA
1097077 TAAAAACATTA
1 TAAAAA-ATTA
1097088 TAAAAAATTA
1 TAAAAAATTA
*
1097098 T-TAAAATTA
1 TAAAAAATTA
* *
1097107 TGAGAAATTA
1 TAAAAAATTA
1097117 T
1 T
1097118 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 8 0.23
10 17 0.49
11 10 0.29
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:1104774 original size:25 final size:25
Alignment explanation
Indices: 1104723--1104776 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1104713 GTTACTGGAG
* *
1104723 GTTGTTAGCTATTTTCTTATTTCTA
1 GTTGTTAGCTACTTCCTTATTTCTA
*
1104748 GTTGTTAGCTGCTTCCTT-TTTCTTA
1 GTTGTTAGCTACTTCCTTATTTC-TA
1104773 GTTG
1 GTTG
1104777 AGTAGTTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (25 bp):
GTTGTTAGCTACTTCCTTATTTCTA
Found at i:1126885 original size:16 final size:18
Alignment explanation
Indices: 1126858--1126891 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1126848 AATAAACATC
1126858 TTAAATTAA-TTTCTCAA
1 TTAAATTAATTTTCTCAA
1126875 TTAAA-TAATTTTCTCAA
1 TTAAATTAATTTTCTCAA
1126892 CTCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTAATTTTCTCAA
Found at i:1128964 original size:73 final size:73
Alignment explanation
Indices: 1128827--1128967 Score: 178
Period size: 73 Copynumber: 1.9 Consensus size: 73
1128817 GGCTCTTTGT
* * * *
1128827 GAGCTTCATGATTAATGGCTCTTCGGAGCTTTCCGATATGGCTCGCTTGAACTTCCAGATATATG
1 GAGCTTCATGATTAATGGCTCTTCAGAGCTTACCGATATGGCTCACATGAACTTCCAGATATATG
1128892 GCTATCCG
66 GCTATCCG
* * * *
1128900 GAGCTTCTTGATTAATGGCTCTTCAGAGC-TACCTGTTATTGGCTCACATGAGCTTCCTGA-ATA
1 GAGCTTCATGATTAATGGCTCTTCAGAGCTTACC-GATA-TGGCTCACATGAACTTCCAGATATA
1128963 TGGCT
64 TGGCT
1128968 TTTATGAGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
72 3 0.05
73 38 0.66
74 17 0.29
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (73 bp):
GAGCTTCATGATTAATGGCTCTTCAGAGCTTACCGATATGGCTCACATGAACTTCCAGATATATG
GCTATCCG
Found at i:1128977 original size:73 final size:73
Alignment explanation
Indices: 1128817--1128978 Score: 166
Period size: 73 Copynumber: 2.2 Consensus size: 73
1128807 CCCGGTTAAA
* * * * *
1128817 GGCTCTTTGTGAGCTTCATGATTAATGGCTCTTCGGAGCTTTCCGATATGGCTCGCTTGAACTTC
1 GGCT-TTTATGAGCTTCATGATTAATGGCTCTTCAGAGCTTACCGATATGGCTCACATGAACTTC
1128882 CAGATATAT
65 CAGATATAT
* *** * * *
1128891 GGCTATCCGGAGCTTCTTGATTAATGGCTCTTCAGAGC-TACCTGTTATTGGCTCACATGAGCTT
1 GGCTTTTATGAGCTTCATGATTAATGGCTCTTCAGAGCTTACC-GATA-TGGCTCACATGAACTT
*
1128955 CCTGA-ATAT
64 CCAGATATAT
1128964 GGCTTTTATGAGCTT
1 GGCTTTTATGAGCTT
1128979 TCCATTATAT
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
72 3 0.04
73 46 0.66
74 21 0.30
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (73 bp):
GGCTTTTATGAGCTTCATGATTAATGGCTCTTCAGAGCTTACCGATATGGCTCACATGAACTTCC
AGATATAT
Found at i:1134313 original size:18 final size:17
Alignment explanation
Indices: 1134292--1134326 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1134282 TTATTATTAA
*
1134292 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1134310 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1134327 TCTTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1134379 original size:157 final size:157
Alignment explanation
Indices: 1134179--1134495 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
1134169 TAGAATACCC
*
1134179 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
1134244 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
1134309 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
1134336 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1134401 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
1134466 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
1134493 TTA
1 TTA
1134496 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:1134466 original size:16 final size:16
Alignment explanation
Indices: 1134429--1134470 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1134419 TTAATCATAT
*
1134429 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
1134445 TT-AAATATATTATAA
1 TTAAAATATATTATAA
1134460 TTAAAATATAT
1 TTAAAATATAT
1134471 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:1134477 original size:14 final size:15
Alignment explanation
Indices: 1134438--1134479 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1134428 TTTAAACATA
*
1134438 ATTATTATTAAATAT
1 ATTATAATTAAATAT
1134453 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
1134467 A-TATAATTTAATA
1 ATTATAATTAAATA
1134480 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:1134492 original size:82 final size:82
Alignment explanation
Indices: 1134249--1134498 Score: 215
Period size: 76 Copynumber: 3.1 Consensus size: 82
1134239 TATTATTATC
* *
1134249 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
1134314 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
* * * *
1134331 AATAATTAGCAGA-AATTT-GT--T-TTGGT-AA-ATTATTATTGTT--AT-TGTTAT--TTAAA
1 AATAA-TA--A-ATAATTTAATCATATT--TAAACATAATTATTATTAAATATATTATAATTAAA
* * * * *
1134384 TTTTAATAAGATTATTAATA-TC--
60 ATAT-ATAA-TTTAATAAAATTCTT
1134406 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
1134471 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
*
1134488 AATAATTAATA
1 AATAATAAATA
1134499 TTCTTATATG
Statistics
Matches: 124, Mismatches: 21, Indels: 46
0.65 0.11 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 3 0.02
75 8 0.06
76 19 0.15
77 6 0.05
78 13 0.10
79 14 0.11
80 6 0.05
81 19 0.15
82 18 0.15
83 3 0.02
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (82 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
AATTTAATAAAATTCTT
Found at i:1134567 original size:120 final size:121
Alignment explanation
Indices: 1134427--1134723 Score: 496
Period size: 120 Copynumber: 2.5 Consensus size: 121
1134417 ATTTAATCAT
*
1134427 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
1134492 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATATTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
1134549 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1134612 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* *
1134668 ATTTGAA-ATAATTAATATTAAATATATT-TAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
1134724 TAAAATAATT
Statistics
Matches: 168, Mismatches: 4, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
119 34 0.20
120 129 0.77
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:1134597 original size:14 final size:15
Alignment explanation
Indices: 1134548--1134599 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1134538 GTAAAATATA
1134548 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
1134563 TATTAAATATATTAT
1 AATTAAATATATTAT
1134578 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
1134591 AATTTAATA
1 AATTAAATA
1134600 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:1134720 original size:17 final size:17
Alignment explanation
Indices: 1134689--1134722 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1134679 TTAATATTAA
1134689 ATATATTTAATTAAAAT
1 ATATATTTAATTAAAAT
1134706 ATATGATTTAA-TAAAAT
1 ATAT-ATTTAATTAAAAT
1134723 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATATTTAATTAAAAT
Found at i:1134810 original size:24 final size:25
Alignment explanation
Indices: 1134764--1134811 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1134754 TATGAATTTG
1134764 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
1134790 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
1134812 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:1134836 original size:92 final size:91
Alignment explanation
Indices: 1134739--1134947 Score: 262
Period size: 92 Copynumber: 2.3 Consensus size: 91
1134729 TAATTATAAC
* * * *
1134739 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAAT-A
* *
1134803 TTAATAT-TAAATTTCATAAAATTCTTGA
64 GTAATATAT-AATTTCATAAAATTCTTAA
* *
1134831 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
*
1134896 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
1134922 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
1134948 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
91 28 0.27
92 72 0.69
93 4 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
AATATATAATTTCATAAAATTCTTAA
Found at i:1140953 original size:8 final size:9
Alignment explanation
Indices: 1140938--1140962 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1140928 AGGTCAGAAC
1140938 TAAAAAAAA
1 TAAAAAAAA
1140947 TAAAAAAAA
1 TAAAAAAAA
1140956 TAAAAAA
1 TAAAAAA
1140963 TGCTACAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1142494 original size:46 final size:46
Alignment explanation
Indices: 1142423--1142511 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 46
1142413 TAAGTAATAA
* * *
1142423 ATTTTAAGAATTTAGAGATTTTAAGTTTATCA-TTTTATTAAAATTAT
1 ATTTAAAGAATTTAGAGATTATAAGTGTAT-AGTTTT-TTAAAATTAT
*
1142470 ATTTAAAGAATTTATAG-TTATAAGTGTATAGTTTTTTAAAAT
1 ATTTAAAGAATTTAGAGATTATAAGTGTATAGTTTTTTAAAAT
1142512 GATAGTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 8 0.22
46 14 0.38
47 15 0.41
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.49
Consensus pattern (46 bp):
ATTTAAAGAATTTAGAGATTATAAGTGTATAGTTTTTTAAAATTAT
Found at i:1142974 original size:18 final size:18
Alignment explanation
Indices: 1142932--1142980 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1142922 ACTATTAAAA
1142932 ATAATAAAAATAT-ATAT
1 ATAATAAAAATATAATAT
* **
1142949 TTTTTAAAAATATAATAT
1 ATAATAAAAATATAATAT
*
1142967 ATAATAAAATTATA
1 ATAATAAAAATATA
1142981 TAAAAATATT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATAAAAATATAATAT
Found at i:1159472 original size:2 final size:2
Alignment explanation
Indices: 1159465--1159499 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1159455 AACAAGTAAA
1159465 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1159500 AGAAGATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1165988 original size:16 final size:18
Alignment explanation
Indices: 1165959--1165993 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1165949 AAAATTGCTT
1165959 TTATATACATATTATAGA
1 TTATATACATATTATAGA
1165977 TTATATA-A-ATTATAGA
1 TTATATACATATTATAGA
1165993 T
1 T
1165994 AGATTTAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TTATATACATATTATAGA
Found at i:1182955 original size:7 final size:8
Alignment explanation
Indices: 1182919--1182956 Score: 53
Period size: 7 Copynumber: 4.9 Consensus size: 8
1182909 AGTTTTAATA
1182919 ATTTTTAT
1 ATTTTTAT
1182927 ATTTTTAT
1 ATTTTTAT
1182935 GATTTTT-T
1 -ATTTTTAT
1182943 ATTTTT-T
1 ATTTTTAT
1182950 ATTTTTA
1 ATTTTTA
1182957 CTTTTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 13 0.46
8 9 0.32
9 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (8 bp):
ATTTTTAT
Found at i:1193123 original size:125 final size:125
Alignment explanation
Indices: 1192921--1193170 Score: 491
Period size: 125 Copynumber: 2.0 Consensus size: 125
1192911 GTGGGCCAAG
1192921 ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
1 ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
1192986 AGATTTGGCGACGTTCCCAGAGCTTGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
66 AGATTTGGCGACGTTCCCAGAGCTTGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
1193046 ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
1 ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
*
1193111 AGATTTGGCGACGTTCCCGGAGCTTGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
66 AGATTTGGCGACGTTCCCAGAGCTTGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
1193171 TATATTTCAG
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (125 bp):
ACTCACACACTAAGCTTTTTAGCTCACTCTGTTGTTTAACATTTTTCAAGTGATCCTCAGACTTA
AGATTTGGCGACGTTCCCAGAGCTTGGTTCGGTTTATTGAATTTTAGTATTTCTGAACTT
Found at i:1197309 original size:21 final size:22
Alignment explanation
Indices: 1197280--1197326 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1197270 CAGAAGGAGT
*
1197280 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1197302 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1197323 GAGT
1 GAGT
1197327 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:1201077 original size:18 final size:18
Alignment explanation
Indices: 1201054--1201098 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1201044 TTCTTAAAAG
*
1201054 TGTAAAATCTTC-CCATCA
1 TGTAAAAT-TTCACAATCA
1201072 TGTAAAATTTCACAATCA
1 TGTAAAATTTCACAATCA
*
1201090 TGTATAATT
1 TGTAAAATT
1201099 ATTTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (18 bp):
TGTAAAATTTCACAATCA
Found at i:1201338 original size:25 final size:25
Alignment explanation
Indices: 1201296--1201350 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1201286 TAAATTCAAA
*
1201296 TAAAAAAATAATTAAATT-TAAATT
1 TAAAAAAATAATAAAATTATAAATT
* *
1201320 TAAATAAATTAATAAAATTATAGATT
1 TAAA-AAAATAATAAAATTATAAATT
1201346 TAAAA
1 TAAAA
1201351 TTATTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 4 0.15
25 13 0.50
26 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
TAAAAAAATAATAAAATTATAAATT
Found at i:1201732 original size:13 final size:13
Alignment explanation
Indices: 1201699--1201749 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
1201689 AATATTAAGC
1201699 ATTATA-TATTTAT
1 ATTATATTATTT-T
*
1201712 ATTTTATTATTTT
1 ATTATATTATTTT
1201725 ATTATATTGATTTT
1 ATTATATT-ATTTT
1201739 ATTCATATTAT
1 ATT-ATATTAT
1201750 ATCAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 13 0.39
14 15 0.45
15 5 0.15
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (13 bp):
ATTATATTATTTT
Found at i:1203728 original size:6 final size:7
Alignment explanation
Indices: 1203711--1203735 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1203701 TTCCTTTGAT
1203711 TTTTTTA
1 TTTTTTA
1203718 TTTTTTA
1 TTTTTTA
1203725 TTTTTTA
1 TTTTTTA
1203732 TTTT
1 TTTT
1203736 CAGCAACCTA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:1203978 original size:12 final size:12
Alignment explanation
Indices: 1203940--1203980 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1203930 ACAATTTTAG
1203940 TACTTATTAAAT
1 TACTTATTAAAT
*
1203952 TA-TT-TTAATT
1 TACTTATTAAAT
1203962 TACTTATTAAAT
1 TACTTATTAAAT
*
1203974 AACTTAT
1 TACTTAT
1203981 ATCACTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.29
11 4 0.17
12 13 0.54
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (12 bp):
TACTTATTAAAT
Found at i:1204184 original size:9 final size:8
Alignment explanation
Indices: 1204169--1204212 Score: 52
Period size: 9 Copynumber: 5.0 Consensus size: 8
1204159 ATATAATCTA
1204169 AAAAAAAT
1 AAAAAAAT
1204177 ATAAAAAAT
1 A-AAAAAAT
1204186 AAGAAAAAT
1 AA-AAAAAT
1204195 AAAAAAATT
1 AAAAAAA-T
1204204 GAAAAAAAT
1 -AAAAAAAT
1204213 CTCAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.22
9 18 0.56
10 7 0.22
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1211532 original size:5 final size:5
Alignment explanation
Indices: 1211515--1211544 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1211505 TCAAAGATCA
1211515 CATTT CAATTT CATTT CATTT CATTT CATT
1 CATTT C-ATTT CATTT CATTT CATTT CATT
1211545 CATCATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (5 bp):
CATTT
Found at i:1213330 original size:25 final size:24
Alignment explanation
Indices: 1213274--1213330 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
1213264 TTAGTTAGAA
* *
1213274 ATAAAATAATTATTTAGTGTTACC
1 ATAAAATAATTAGTTAGTGGTACC
* *
1213298 ATTTAAATAATTTAGTTAGTGGTACT
1 A-TAAAATAA-TTAGTTAGTGGTACC
1213324 ATAAAAT
1 ATAAAAT
1213331 TTTATTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 12 0.46
26 13 0.50
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (24 bp):
ATAAAATAATTAGTTAGTGGTACC
Found at i:1219961 original size:21 final size:22
Alignment explanation
Indices: 1219922--1219963 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1219912 GATTAATACT
1219922 AAAAATAAAATAAACAAACAAG
1 AAAAATAAAATAAACAAACAAG
1219944 AAAAATTAAAA-AAA-AAACAA
1 AAAAA-TAAAATAAACAAACAA
1219964 AAAGTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAAATAAAATAAACAAACAAG
Found at i:1231430 original size:15 final size:15
Alignment explanation
Indices: 1231405--1231439 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1231395 GACTCTATTT
*
1231405 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
1231419 TAATTAATATTAAGA
1 TAATTAATATTAAGA
1231434 TAATTA
1 TAATTA
1231440 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:1236741 original size:15 final size:15
Alignment explanation
Indices: 1236721--1236770 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1236711 TATTTCTTAA
1236721 TATATATTATAATAT
1 TATATATTATAATAT
1236736 TATATATT-TAACT-T
1 TATATATTATAA-TAT
*
1236750 TCATATAATATAATAT
1 T-ATATATTATAATAT
*
1236766 GATAT
1 TATAT
1236771 GAAATAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 5 0.17
15 20 0.69
16 4 0.14
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (15 bp):
TATATATTATAATAT
Found at i:1239691 original size:22 final size:22
Alignment explanation
Indices: 1239664--1239709 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1239654 GAATGCATGA
1239664 AATATAAAATGCGTATGAACGG
1 AATATAAAATGCGTATGAACGG
1239686 AATATAAAATGCGTATGAACGG
1 AATATAAAATGCGTATGAACGG
1239708 AA
1 AA
1239710 GAAGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.22
Consensus pattern (22 bp):
AATATAAAATGCGTATGAACGG
Found at i:1248740 original size:30 final size:30
Alignment explanation
Indices: 1248706--1248785 Score: 151
Period size: 30 Copynumber: 2.7 Consensus size: 30
1248696 TTGTTAAACC
*
1248706 CAAATAAGCCCTTAAACTTTAATTGGTACT
1 CAAATAAGCCCTTAAACTTCAATTGGTACT
1248736 CAAATAAGCCCTTAAACTTCAATTGGTACT
1 CAAATAAGCCCTTAAACTTCAATTGGTACT
1248766 CAAATAAGCCCTTAAACTTC
1 CAAATAAGCCCTTAAACTTC
1248786 TATGGGTCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.30
Consensus pattern (30 bp):
CAAATAAGCCCTTAAACTTCAATTGGTACT
Found at i:1253832 original size:32 final size:32
Alignment explanation
Indices: 1253796--1253858 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1253786 TTTGTTAAGT
* *
1253796 ATACCAGGTTATTACTGGTCTGATATTTATCC
1 ATACCAGATTATTACAGGTCTGATATTTATCC
*
1253828 ATACCAGATTGTTACAGGTCTGATATTTATC
1 ATACCAGATTATTACAGGTCTGATATTTATC
1253859 GAACTGTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (32 bp):
ATACCAGATTATTACAGGTCTGATATTTATCC
Found at i:1267214 original size:40 final size:40
Alignment explanation
Indices: 1267170--1267248 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
1267160 AGTATACTAC
* * *
1267170 TAAGGCACATTGCACTTTTAAAAGAGAATACAAATTCAAA
1 TAAGGCACACTGCACTCTTAAAAGAGAACACAAATTCAAA
* *
1267210 TAAGGCACACTGCACTCTTAATAGAGAACGCAAATTCAA
1 TAAGGCACACTGCACTCTTAAAAGAGAACACAAATTCAA
1267249 TCTTAGAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (40 bp):
TAAGGCACACTGCACTCTTAAAAGAGAACACAAATTCAAA
Found at i:1270190 original size:35 final size:35
Alignment explanation
Indices: 1270151--1270311 Score: 216
Period size: 35 Copynumber: 4.6 Consensus size: 35
1270141 GTTGATATTC
1270151 TGATTCACATGTTAAGCATGTCATTATACTGATTA
1 TGATTCACATGTTAAGCATGTCATTATACTGATTA
* * *
1270186 TGATTCACATGTTAAGCATGCCATTGCT-CTGATTC
1 TGATTCACATGTTAAGCATGTCATT-ATACTGATTA
* *
1270221 TGTTTCACATGTTAAGCATGTCAGTATACTGATTA
1 TGATTCACATGTTAAGCATGTCATTATACTGATTA
* * *
1270256 TGATTCTCATGTTAAGCATGCCATTATACTGATTC
1 TGATTCACATGTTAAGCATGTCATTATACTGATTA
* *
1270291 TGATTCGCATGTTAAACATGT
1 TGATTCACATGTTAAGCATGT
1270312 TGCTATACTG
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
34 1 0.01
35 106 0.98
36 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (35 bp):
TGATTCACATGTTAAGCATGTCATTATACTGATTA
Found at i:1270228 original size:70 final size:70
Alignment explanation
Indices: 1270147--1270311 Score: 260
Period size: 70 Copynumber: 2.4 Consensus size: 70
1270137 ATTTGTTGAT
*
1270147 ATTCTGATTCACATGTTAAGCATGTCATTATACTGATTATGATTCACATGTTAAGCATGCCATTG
1 ATTCTGATTCACATGTTAAGCATGTCAGTATACTGATTATGATTCACATGTTAAGCATGCCATT-
*
1270212 CT-CTG
65 ATACTG
* *
1270217 ATTCTGTTTCACATGTTAAGCATGTCAGTATACTGATTATGATTCTCATGTTAAGCATGCCATTA
1 ATTCTGATTCACATGTTAAGCATGTCAGTATACTGATTATGATTCACATGTTAAGCATGCCATTA
1270282 TACTG
66 TACTG
* *
1270287 ATTCTGATTCGCATGTTAAACATGT
1 ATTCTGATTCACATGTTAAGCATGT
1270312 TGCTATACTG
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
69 1 0.01
70 86 0.99
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (70 bp):
ATTCTGATTCACATGTTAAGCATGTCAGTATACTGATTATGATTCACATGTTAAGCATGCCATTA
TACTG
Found at i:1270319 original size:35 final size:35
Alignment explanation
Indices: 1270147--1270331 Score: 178
Period size: 35 Copynumber: 5.3 Consensus size: 35
1270137 ATTTGTTGAT
**
1270147 ATTCTGATTCACATGTTAAGCATGTCATTATACTG
1 ATTCTGATTCACATGTTAAGCATGTCGCTATACTG
* * ** *
1270182 ATTATGATTCACATGTTAAGCATGCCATTGCT-CTG
1 ATTCTGATTCACATGTTAAGCATGTCGCT-ATACTG
*
1270217 ATTCTGTTTCACATGTTAAGCATGTCAG-TATACTG
1 ATTCTGATTCACATGTTAAGCATGTC-GCTATACTG
* * * **
1270252 ATTATGATTCTCATGTTAAGCATGCCATTATACTG
1 ATTCTGATTCACATGTTAAGCATGTCGCTATACTG
* * *
1270287 ATTCTGATTCGCATGTTAAACATGTTGCTATACTGG
1 ATTCTGATTCACATGTTAAGCATGTCGCTATACT-G
1270323 ATT-TGATTC
1 ATTCTGATTC
1270332 GCATACCTAC
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.01
35 119 0.95
36 5 0.04
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (35 bp):
ATTCTGATTCACATGTTAAGCATGTCGCTATACTG
Found at i:1270319 original size:70 final size:69
Alignment explanation
Indices: 1270147--1270331 Score: 248
Period size: 70 Copynumber: 2.6 Consensus size: 69
1270137 ATTTGTTGAT
*
1270147 ATTCTGATTCACATGTTAAGCATGTCATTATACTGATTATGATTCACATGTTAAGCATGCCATTG
1 ATTCTGATTCACATGTTAAGCATGT-AGTATACTGATTATGATTCACATGTTAAGCATGCCATTG
*
1270212 CTCTG
65 ATCTG
* *
1270217 ATTCTGTTTCACATGTTAAGCATGTCAGTATACTGATTATGATTCTCATGTTAAGCATGCCATT-
1 ATTCTGATTCACATGTTAAGCATGT-AGTATACTGATTATGATTCACATGTTAAGCATGCCATTG
1270281 ATACTG
65 AT-CTG
* * *
1270287 ATTCTGATTCGCATGTTAAACATGTTGCTATACTGGATT-TGATTC
1 ATTCTGATTCACATGTTAAGCATGTAG-TATACT-GATTATGATTC
1270332 GCATACCTAC
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
69 2 0.02
70 98 0.94
71 4 0.04
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (69 bp):
ATTCTGATTCACATGTTAAGCATGTAGTATACTGATTATGATTCACATGTTAAGCATGCCATTGA
TCTG
Found at i:1272823 original size:16 final size:16
Alignment explanation
Indices: 1272799--1272829 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1272789 GTTTGAAAGA
1272799 AAAAAAAAAGAGAATC
1 AAAAAAAAAGAGAATC
*
1272815 AAAATAAAAGAGAAT
1 AAAAAAAAAGAGAAT
1272830 GAGGTGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAAAAAAAGAGAATC
Found at i:1291241 original size:58 final size:58
Alignment explanation
Indices: 1291151--1291267 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
1291141 GAACATTCAA
1291151 GTGGAAATTACAACACTTACCTTGTTCATAGGTGAGCATTTAACTAACAAATGTTTTG
1 GTGGAAATTACAACACTTACCTTGTTCATAGGTGAGCATTTAACTAACAAATGTTTTG
1291209 GTGGAAATTACAACACTTACCTTGTTCATAGGTGAGCATTTAACTAACAAATGTTTTG
1 GTGGAAATTACAACACTTACCTTGTTCATAGGTGAGCATTTAACTAACAAATGTTTTG
1291267 G
1 G
1291268 CATACATTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (58 bp):
GTGGAAATTACAACACTTACCTTGTTCATAGGTGAGCATTTAACTAACAAATGTTTTG
Found at i:1292895 original size:20 final size:19
Alignment explanation
Indices: 1292872--1292910 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1292862 ACTGATGTTC
1292872 TGCATG-ATATGTATGATTAA
1 TGCATGCATAT-TATG-TTAA
1292892 TGCATGCATATTATGTTAA
1 TGCATGCATATTATGTTAA
1292911 GGGTGACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (19 bp):
TGCATGCATATTATGTTAA
Found at i:1293254 original size:45 final size:45
Alignment explanation
Indices: 1293156--1293277 Score: 147
Period size: 45 Copynumber: 2.7 Consensus size: 45
1293146 ATGCCTAAAT
*
1293156 TGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGACAAAAA
1 TGAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGACAAAAA
* * * ** *
1293201 TGAGTAAGACCATGGCTGAAAGACGTCATGGCATCATGGTAAACGA
1 TGAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGACAAA-AA
* *
1293247 -GATTAAGACCATAACTAAAAGACGTTATGGC
1 TGAGTAAGACCATAGCTAAAAGACGTTATGGC
1293278 TTTTTGGTAG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 63 0.98
46 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (45 bp):
TGAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGACAAAAA
Found at i:1293776 original size:12 final size:12
Alignment explanation
Indices: 1293736--1293792 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 12
1293726 TCAACTATGA
1293736 TTAAACTTAATCACT
1 TTAAA-TTAAT-A-T
1293751 TTAATATTAA-AT
1 TTAA-ATTAATAT
1293763 TTAAATTAATAT
1 TTAAATTAATAT
1293775 TTAAATTTAATA-
1 TTAAA-TTAATAT
1293787 TTAAAT
1 TTAAAT
1293793 CTTATTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.15
12 17 0.44
13 7 0.18
15 8 0.21
16 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAATTAATAT
Found at i:1294335 original size:9 final size:9
Alignment explanation
Indices: 1294321--1294414 Score: 118
Period size: 9 Copynumber: 10.4 Consensus size: 9
1294311 TGGTTAAAAA
1294321 TTAACCGAT
1 TTAACCGAT
*
1294330 TTAACCTAT
1 TTAACCGAT
1294339 TTAACCGA-
1 TTAACCGAT
1294347 TTAACCGAT
1 TTAACCGAT
*
1294356 TTAACCGAC
1 TTAACCGAT
*
1294365 TTAACCAAT
1 TTAACCGAT
* *
1294374 CTAACCTAT
1 TTAACCGAT
1294383 TTAACCGAT
1 TTAACCGAT
*
1294392 TTAACCCGAC
1 TTAA-CCGAT
1294402 TTAACCGAT
1 TTAACCGAT
1294411 TTAA
1 TTAA
1294415 ATCACTATAT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
8 8 0.11
9 56 0.78
10 8 0.11
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (9 bp):
TTAACCGAT
Found at i:1294379 original size:44 final size:46
Alignment explanation
Indices: 1294321--1294414 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
1294311 TGGTTAAAAA
* * *
1294321 TTAACCGATTTAACCTATTTAACCGA-TTAA-CCGATTTAACCGAC
1 TTAACCAATCTAACCTATTTAACCGATTTAACCCGACTTAACCGAC
*
1294365 TTAACCAATCTAACCTATTTAACCGATTTAACCCGACTTAACCGAT
1 TTAACCAATCTAACCTATTTAACCGATTTAACCCGACTTAACCGAC
1294411 TTAA
1 TTAA
1294415 ATCACTATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 24 0.55
45 4 0.09
46 16 0.36
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (46 bp):
TTAACCAATCTAACCTATTTAACCGATTTAACCCGACTTAACCGAC
Found at i:1296915 original size:18 final size:19
Alignment explanation
Indices: 1296880--1296931 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1296870 AACCGATCGA
**
1296880 TTAACCGAATTCGGTCGG-
1 TTAACCGAATTTTGTCGGT
*
1296898 TTAACCGAATTTTTTCGGTT
1 TTAACCGAATTTTGTCGG-T
1296918 TTAACCGAATTTTG
1 TTAACCGAATTTTG
1296932 CACACCCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (19 bp):
TTAACCGAATTTTGTCGGT
Found at i:1306520 original size:32 final size:32
Alignment explanation
Indices: 1306484--1306544 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1306474 TTTTTTGTCC
*
1306484 AATTTGGTACCTAAACTTGACACTTTTTCCCT
1 AATTTAGTACCTAAACTTGACACTTTTTCCCT
*
1306516 AATTTAGTACCTAAATTTGACACTTTTTC
1 AATTTAGTACCTAAACTTGACACTTTTTC
1306545 TTAAGTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (32 bp):
AATTTAGTACCTAAACTTGACACTTTTTCCCT
Found at i:1306616 original size:89 final size:89
Alignment explanation
Indices: 1306428--1306618 Score: 226
Period size: 90 Copynumber: 2.1 Consensus size: 89
1306418 TTAATATAAT
* ** * *
1306428 ATTTGGTACTTAAATTTGACATTCTTTTAATTTGGTACTTAAAACTTTTTTTGTCCAATTTGGTA
1 ATTTGGTACCTAAATTTGACATTCTTTTAATTTGGTACTTAAAACTTTTTGGGACAAATTTGGTA
1306493 CCTAAACTTGACACTTTTTCCCTA
66 CCTAAACTTGACACTTTTTCCCTA
* * * *
1306517 ATTTAGTACCTAAATTTGACACTTTTTCTTAAGTTT-GTATTTAATA-TTTTTGGGACAAATTTG
1 ATTTGGTACCTAAATTTGACA-TTCTT-TTAA-TTTGGTACTTAAAACTTTTTGGGACAAATTTG
* * *
1306580 GTACCTGAACTTTACTCTTTTT-CCTA
63 GTACCTAAACTTGACACTTTTTCCCTA
1306606 ATTTGGTACCTAA
1 ATTTGGTACCTAA
1306619 TTTTTTTTTG
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
89 35 0.41
90 36 0.42
91 12 0.14
92 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (89 bp):
ATTTGGTACCTAAATTTGACATTCTTTTAATTTGGTACTTAAAACTTTTTGGGACAAATTTGGTA
CCTAAACTTGACACTTTTTCCCTA
Found at i:1307350 original size:21 final size:21
Alignment explanation
Indices: 1307320--1307375 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1307310 AATAGCGGTG
*
1307320 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
1307341 GCGGTAAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
1307362 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
1307376 AACAATAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:1307772 original size:143 final size:141
Alignment explanation
Indices: 1307506--1307773 Score: 312
Period size: 143 Copynumber: 1.9 Consensus size: 141
1307496 TTACTTTTTT
*
1307506 AAAATTATTAAAATATGTGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTCCAATA
1 AAAATAATTAAAATATGTGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTCCAATA
* ** * ** **
1307571 TTTTATTATAAATATATTAATGAATTATATAATCAATTTAAATTATTTATTAGATAAAATGATAA
66 TTTTATTATAAATAAAAAAATAAATTATATAATCAAAATAAATTATAAATT--ATAAAATGATAA
1307636 TTATTTTTAAATC
129 TTATTTTTAAATC
* *
1307649 AAAATAATTAAAAATATGTGAATTTATAAATTCATTTAAT-AAATATTAAAATGTATCTTTCGAT
1 AAAATAATT-AAAATATGTGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTCCAAT
*
1307713 ATTTTACTATATAAAGTAAAAAAAATAACATT-TTTAAATCAAAAT-AATTA-AAATT-TAAAAT
65 ATTTTA-T-TATAAA-T-AAAAAAATAA-ATTATAT-AATCAAAATAAATTATAAATTATAAAAT
1307774 AAATAATCTA
Statistics
Matches: 106, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
143 42 0.40
144 31 0.29
145 6 0.06
146 4 0.04
147 13 0.12
148 10 0.09
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (141 bp):
AAAATAATTAAAATATGTGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTCCAATA
TTTTATTATAAATAAAAAAATAAATTATATAATCAAAATAAATTATAAATTATAAAATGATAATT
ATTTTTAAATC
Found at i:1311080 original size:23 final size:23
Alignment explanation
Indices: 1311054--1311175 Score: 165
Period size: 23 Copynumber: 5.3 Consensus size: 23
1311044 ATAAGTGCCT
1311054 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1311077 CACTGATATGCAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1311100 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
1311123 CATTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1311146 CACT-AAATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
1311169 CACTGAT
1 CACTGAT
1311176 CAATAACACT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
22 2 0.02
23 80 0.96
24 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1311121 original size:46 final size:46
Alignment explanation
Indices: 1311054--1311175 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
1311044 ATAAGTGCCT
*
1311054 CACTGATATGTAGCCGAAGCTACCACTGATATGCAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGCAGCCGTAGCTAC
* * *
1311100 CACTGAAATGTAGCCGAAGCTACCATTGATATGTAGCTGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGCAGCCGTAGCTAC
1311146 CACT-AAATTGTAGCCGAAGCTACCACTGAT
1 CACTGAAA-TGTAGCCGAAGCTACCACTGAT
1311176 CAATAACACT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 3 0.04
46 67 0.96
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGCAGCCGTAGCTAC
Found at i:1311427 original size:18 final size:17
Alignment explanation
Indices: 1311401--1311439 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1311391 ATTTTCCTTC
1311401 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
1311418 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
1311436 CACA
1 CACA
1311440 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:1313162 original size:14 final size:14
Alignment explanation
Indices: 1313145--1313182 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1313135 TAAAAATTTA
1313145 TAATAAATGTTAAT
1 TAATAAATGTTAAT
* *
1313159 TAATAAATATTAGT
1 TAATAAATGTTAAT
1313173 TAA-AAATGTT
1 TAATAAATGTT
1313183 TGGGAATGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (14 bp):
TAATAAATGTTAAT
Found at i:1313530 original size:9 final size:9
Alignment explanation
Indices: 1313516--1313555 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1313506 ATTAAAATAT
1313516 TAATTAAAC
1 TAATTAAAC
1313525 TAATTAAAC
1 TAATTAAAC
* *
1313534 CAATTAAAG
1 TAATTAAAC
*
1313543 TAATTAACC
1 TAATTAAAC
1313552 TAAT
1 TAAT
1313556 GGAATTTCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (9 bp):
TAATTAAAC
Found at i:1321085 original size:16 final size:18
Alignment explanation
Indices: 1321052--1321085 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1321042 ATGGCTTTTG
1321052 AAAGTCTATTATAAAATA
1 AAAGTCTATTATAAAATA
1321070 AAAGT-TATTA-AAAATA
1 AAAGTCTATTATAAAATA
1321086 TTATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (18 bp):
AAAGTCTATTATAAAATA
Found at i:1321189 original size:25 final size:28
Alignment explanation
Indices: 1321143--1321201 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 28
1321133 AGAATTTAAA
1321143 AATAAGTAATCGAAAATGTAACCAAAT-AT
1 AATAAGTAATCGAAAA-GTAA-CAAATAAT
1321172 AATAA-TAAT-GAAAA-TAACAAATAAT
1 AATAAGTAATCGAAAAGTAACAAATAAT
1321197 AATAA
1 AATAA
1321202 CAAATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 5 0.17
25 10 0.34
27 5 0.17
28 4 0.14
29 5 0.17
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (28 bp):
AATAAGTAATCGAAAAGTAACAAATAAT
Found at i:1321202 original size:13 final size:14
Alignment explanation
Indices: 1321184--1321232 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
1321174 TAATAATGAA
1321184 AATAACAAA-TAAT
1 AATAACAAATTAAT
1321197 AATAACAAATTAAT
1 AATAACAAATTAAT
* *
1321211 ATTAAACTAATTAAT
1 AAT-AACAAATTAAT
1321226 AA-AACAA
1 AATAACAA
1321233 TGGGCTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 13 0.43
14 6 0.20
15 11 0.37
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAACAAATTAAT
Found at i:1322391 original size:13 final size:13
Alignment explanation
Indices: 1322366--1322399 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1322356 AACATTGGAC
1322366 TATTATTTTTATT
1 TATTATTTTTATT
1322379 TATT-TTTTGTATT
1 TATTATTTT-TATT
1322392 TATTATTT
1 TATTATTT
1322400 AATTTGGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 12 0.63
14 3 0.16
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TATTATTTTTATT
Found at i:1330842 original size:37 final size:37
Alignment explanation
Indices: 1330801--1330877 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
1330791 ATTTTTTCCC
1330801 AATGGTTCTTAATATAAATTTTGAACTTTTCTGGCTA
1 AATGGTTCTTAATATAAATTTTGAACTTTTCTGGCTA
1330838 AATGGTTCTTAATATAAATTTTGAACTTTTCTGGCTA
1 AATGGTTCTTAATATAAATTTTGAACTTTTCTGGCTA
1330875 AAT
1 AAT
1330878 TATTGTTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (37 bp):
AATGGTTCTTAATATAAATTTTGAACTTTTCTGGCTA
Found at i:1338054 original size:66 final size:66
Alignment explanation
Indices: 1337967--1338173 Score: 362
Period size: 66 Copynumber: 3.1 Consensus size: 66
1337957 CCTCATCTTC
1337967 ATGGCGTTCACCTTCTCAAGTCATGACAGGGTTCGATGGTACTCAGACCATGGACTACATGAGCG
1 ATGG-GTTCACCTTCTCAAGTCATGACAGGGTTCGATGGTACTCAGACCATGGACTACATGAGCG
1338032 GA
65 GA
* *
1338034 ATGGGTTCACCTTCTCAAGTCATGACAGGGTTCAATGGTACTCAGACAATGGACTACATGAGCGG
1 ATGGGTTCACCTTCTCAAGTCATGACAGGGTTCGATGGTACTCAGACCATGGACTACATGAGCGG
1338099 A
66 A
*
1338100 ATGGGTTCACCTTCTCAAGTCATGACAGGGTT-GAATGGTACTCCGACCATGGACTACATGAGCG
1 ATGGGTTCACCTTCTCAAGTCATGACAGGGTTCG-ATGGTACTCAGACCATGGACTACATGAGCG
1338164 GA
65 GA
1338166 ATGGGTTC
1 ATGGGTTC
1338174 TCATTATGCT
Statistics
Matches: 134, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
66 130 0.97
67 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (66 bp):
ATGGGTTCACCTTCTCAAGTCATGACAGGGTTCGATGGTACTCAGACCATGGACTACATGAGCGG
A
Found at i:1338533 original size:42 final size:42
Alignment explanation
Indices: 1338474--1338564 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
1338464 CATTGGAGTA
1338474 TGAGAGGTTTCAACCTGAAAGCAATGCAGCAGCAGCAGCTAC
1 TGAGAGGTTTCAACCTGAAAGCAATGCAGCAGCAGCAGCTAC
** *
1338516 TGAGAGGTTTGGACCTGAAAGCAATGTAGCAGCAGCAGCTAC
1 TGAGAGGTTTCAACCTGAAAGCAATGCAGCAGCAGCAGCTAC
1338558 TGAGAGG
1 TGAGAGG
1338565 AGGCAGAAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.18
Consensus pattern (42 bp):
TGAGAGGTTTCAACCTGAAAGCAATGCAGCAGCAGCAGCTAC
Found at i:1339387 original size:19 final size:19
Alignment explanation
Indices: 1339349--1339392 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
1339339 TGAGAAAACA
1339349 ATAAAAACTAAAATAATAT
1 ATAAAAACTAAAATAATAT
1339368 A-AAAAACTAAAA-AATGTAT
1 ATAAAAACTAAAATAA--TAT
1339387 ATAAAA
1 ATAAAA
1339393 TTAACTGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 5 0.23
20 4 0.18
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (19 bp):
ATAAAAACTAAAATAATAT
Found at i:1353135 original size:5 final size:5
Alignment explanation
Indices: 1353127--1353156 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1353117 AATCAAATCA
1353127 AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT
1353157 CATGCAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:1356411 original size:5 final size:5
Alignment explanation
Indices: 1356401--1356428 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1356391 GCTGTAACCC
1356401 TCCTA TCCTA TCCTA TCCTA TCCTA TCC
1 TCCTA TCCTA TCCTA TCCTA TCCTA TCC
1356429 CTTCCTCTGG
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:0.18, C:0.43, G:0.00, T:0.39
Consensus pattern (5 bp):
TCCTA
Found at i:1357751 original size:4 final size:4
Alignment explanation
Indices: 1357742--1357826 Score: 170
Period size: 4 Copynumber: 21.2 Consensus size: 4
1357732 TTTTTAAAAA
1357742 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1357790 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1357827 TCACACGTTA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 81 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1359153 original size:17 final size:17
Alignment explanation
Indices: 1359128--1359177 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
1359118 TATCAGATTT
1359128 TGATACTCATATCTTTC
1 TGATACTCATATCTTTC
*
1359145 TGATGCTCATATCTTTC
1 TGATACTCATATCTTTC
1359162 TGATACTCATATCTTT
1 TGATACTCATATCTTT
1359178 GACTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (17 bp):
TGATACTCATATCTTTC
Found at i:1364982 original size:48 final size:48
Alignment explanation
Indices: 1364921--1365015 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
1364911 AGAAGCCGAG
1364921 GCAACGAGAAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGTC
1 GCAACGAGAAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGTC
*
1364969 GCAACGAGGAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGT
1 GCAACGAGAAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGT
1365016 TGCGAGAATG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (48 bp):
GCAACGAGAAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGTC
Found at i:1366324 original size:27 final size:27
Alignment explanation
Indices: 1366294--1366383 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
1366284 TAAAAGAGAG
1366294 TTTTTTTTAGGTAATGGCTTATTTGAC
1 TTTTTTTTAGGTAATGGCTTATTTGAC
*** ** * *
1366321 TTTTTAATTTTACAAAAAAT-AATTATTTTAG
1 -TTTT--TTTT--AGGTAATGGCTTATTTGAC
1366352 TTTTTTTTAGGTAATGGCTTATTTGAC
1 TTTTTTTTAGGTAATGGCTTATTTGAC
1366379 TTTTT
1 TTTTT
1366384 AATTTTACAA
Statistics
Matches: 43, Mismatches: 14, Indels: 11
0.63 0.21 0.16
Matches are distributed among these distances:
26 4 0.09
27 12 0.28
28 8 0.19
30 8 0.19
31 7 0.16
32 4 0.09
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.57
Consensus pattern (27 bp):
TTTTTTTTAGGTAATGGCTTATTTGAC
Found at i:1366347 original size:31 final size:31
Alignment explanation
Indices: 1366312--1366406 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
1366302 AGGTAATGGC
1366312 TTATTTGACTTTTTAATTTTACAAAAAATAA
1 TTATTTGACTTTTTAATTTTACAAAAAATAA
* * *** **
1366343 TTATTTTA-GTTTT--TTTT--AGGTAATGGC
1 TTATTTGACTTTTTAATTTTACAAAAAAT-AA
1366370 TTATTTGACTTTTTAATTTTACAAAAAATAA
1 TTATTTGACTTTTTAATTTTACAAAAAATAA
1366401 TTATTT
1 TTATTT
1366407 TAGTTTTATA
Statistics
Matches: 44, Mismatches: 14, Indels: 12
0.63 0.20 0.17
Matches are distributed among these distances:
26 4 0.09
27 7 0.16
28 8 0.18
30 8 0.18
31 13 0.30
32 4 0.09
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (31 bp):
TTATTTGACTTTTTAATTTTACAAAAAATAA
Found at i:1366356 original size:58 final size:58
Alignment explanation
Indices: 1366292--1366413 Score: 244
Period size: 58 Copynumber: 2.1 Consensus size: 58
1366282 CTTAAAAGAG
1366292 AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
1 AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
1366350 AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
1 AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
1366408 AGTTTT
1 AGTTTT
1366414 ATATTTAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (58 bp):
AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
Found at i:1368381 original size:31 final size:31
Alignment explanation
Indices: 1368343--1368402 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1368333 TTGGTCACTG
*
1368343 AACTATTCGAAAGTTTTCATTTAAATCACAT
1 AACTATTCAAAAGTTTTCATTTAAATCACAT
* *
1368374 AACTATTCAAAAGTTTTTATTTAAGTCAC
1 AACTATTCAAAAGTTTTCATTTAAATCAC
1368403 TAAGTTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAATCACAT
Found at i:1377878 original size:8 final size:8
Alignment explanation
Indices: 1377867--1377927 Score: 63
Period size: 8 Copynumber: 7.6 Consensus size: 8
1377857 ATGTTTTAAA
1377867 TATATTAT
1 TATATTAT
1377875 TATATTAT
1 TATATTAT
*
1377883 TTTATTAT
1 TATATTAT
* *
1377891 AAAATATAT
1 TATAT-TAT
1377900 TATATTA-
1 TATATTAT
1377907 TAT-TATAT
1 TATAT-TAT
1377915 TATATTAT
1 TATATTAT
1377923 TATAT
1 TATAT
1377928 AAAATAAACC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 1 0.02
7 5 0.12
8 30 0.70
9 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTAT
Done.