Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1179
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1367275
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 72735 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:607649 original size:1 final size:1
Alignment explanation
Indices: 607643--607667 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
607633 GCAGGCAGGG
607643 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
607668 GTTGACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:608444 original size:6 final size:6
Alignment explanation
Indices: 608433--608470 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
608423 TGCTATACCC
608433 TCGGCG TCGGCG TCGGCGG T-GGCG TCGGCG TCGGCG TC
1 TCGGCG TCGGCG TCGGC-G TCGGCG TCGGCG TCGGCG TC
608471 CGGACCTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.00, C:0.32, G:0.50, T:0.18
Consensus pattern (6 bp):
TCGGCG
Found at i:608806 original size:177 final size:175
Alignment explanation
Indices: 608608--609156 Score: 715
Period size: 177 Copynumber: 3.1 Consensus size: 175
608598 GGGTCCTAAA
* * * *
608608 TTTCAGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCAT-
1 TTTCGGATGCTGGAGGAGGTTAAGGTT-TTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCC-TC
* * * *
608672 TGATAGCA-ATATCTAACTTACTACTAGTCCTAACTTCACCAAACTTGTATGAATGATGCGTCTT
64 TGAT-G-ATATATCTTAGTTACTACTAGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTT
* *
608736 ATGATATTAATGCACCTGACAAGCTTGAATGCTGAATATGAGCAATAGG
127 ATGATACTGATGCACCTGACAAGCTTGAATGCTGAATATGAGCAATAGG
* *
608785 TTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGTTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGG-TTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
*
608850 GATGATTATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTAT
65 GATGA-TATATCTTAGTTACTACTAGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTAT
*
608915 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
129 GATACTGATGCACCTGACAAGCTTGAATGCTGAATATGAGCAATAGG
* ***
608962 TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAAAGCTGGTTAAATAAAGTTTTTGAAACAGGTGCC
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTT-AGAGCTGG-T---TAAAGTTTTTGTTGCAGGTGCC
* * * * ** *
609027 CTCTGATGATGATATCTTAGTTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTC
61 CTCTGATGAT-ATATCTTAGTTACTACTAGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTC
* * * *
609092 TTATGATACTGATGCACCTGACAGGCTTGAATGCTGAGTGTGAGCCATAGG
125 TTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATATGAGCAATAGG
609143 TTTCGGATGCTGGA
1 TTTCGGATGCTGGA
609157 TAAAGTTAAG
Statistics
Matches: 331, Mismatches: 31, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
175 1 0.00
176 6 0.02
177 185 0.56
178 3 0.01
180 1 0.00
181 135 0.41
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (175 bp):
TTTCGGATGCTGGAGGAGGTTAAGGTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTG
ATGATATATCTTAGTTACTACTAGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGA
TACTGATGCACCTGACAAGCTTGAATGCTGAATATGAGCAATAGG
Found at i:609110 original size:181 final size:177
Alignment explanation
Indices: 608689--609156 Score: 675
Period size: 181 Copynumber: 2.6 Consensus size: 177
608679 AATATCTAAC
* * * *
608689 TTACTACTAGTCCTAACTTCACCAAACTTGTATGAATGATGCGTCTTATGATATTAATGCACCTG
1 TTACTACTAGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTG
* *
608754 ACAAGCTTGAATGCTGAATATGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAG
66 ACAAGCTTGAATGCTGAATATGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTAAAAG
*** * *
608819 CTGGTTAAAGTTTTTGTTGCAGTTGCCCTCTGATGATTATATCTTAG
131 CTGGTTAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAG
*
608866 TTACTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTG
1 TTACTACTAGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTG
* *
608931 ACAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAAAG
66 ACAAGCTTGAATGCTGAATATGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTAAAAG
608996 CTGGTTAAATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAG
131 CTGG-T---TAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAG
* * * * ** *
609047 TTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCTG
1 TTACTACTAGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTG
* * * *
609112 ACAGGCTTGAATGCTGAGTGTGAGCCATAGGTTTCGGATGCTGGA
66 ACAAGCTTGAATGCTGAATATGAGCAATAGGTTTCGGATGCTGGA
609157 TAAAGTTAAG
Statistics
Matches: 262, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
177 125 0.48
178 1 0.00
181 136 0.52
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (177 bp):
TTACTACTAGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTG
ACAAGCTTGAATGCTGAATATGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTAAAAG
CTGGTTAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAG
Found at i:609819 original size:20 final size:20
Alignment explanation
Indices: 609794--609837 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
609784 GATTCCTATG
609794 ATATTGTATGATATGAAACA
1 ATATTGTATGATATGAAACA
* *
609814 ATATTGTTTGATATGATACA
1 ATATTGTATGATATGAAACA
609834 ATAT
1 ATAT
609838 GAAATCATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (20 bp):
ATATTGTATGATATGAAACA
Found at i:609948 original size:28 final size:28
Alignment explanation
Indices: 609899--609952 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
609889 TCAATTTTTT
609899 TGATATTTTATGATATGATATTGTATCA
1 TGATATTTTATGATATGATATTGTATCA
609927 TGATATTGTTATG-TAT-AGTATTGTAT
1 TGATATT-TTATGATATGA-TATTGTAT
609953 ATTATGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.04
28 18 0.75
29 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (28 bp):
TGATATTTTATGATATGATATTGTATCA
Found at i:610115 original size:15 final size:15
Alignment explanation
Indices: 610058--610107 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
610048 GTATCCTATG
610058 ATACAATATTGTATA
1 ATACAATATTGTATA
* * *
610073 TTCTATAATATTGTATC
1 --ATACAATATTGTATA
610090 ATACAATATTGTATA
1 ATACAATATTGTATA
610105 ATA
1 ATA
610108 TGATATTGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 15 0.56
17 12 0.44
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (15 bp):
ATACAATATTGTATA
Found at i:620162 original size:2 final size:2
Alignment explanation
Indices: 620155--620185 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
620145 AGATCTTATA
620155 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
620186 AGAGATATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:622783 original size:21 final size:21
Alignment explanation
Indices: 622757--622806 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
622747 TTGCCATATT
*
622757 AGTTGCATGTCAACATAACTA
1 AGTTGCATGTCAACATAAATA
*
622778 AGTTGCATGTCGACATAAATA
1 AGTTGCATGTCAACATAAATA
*
622799 AGTAGCAT
1 AGTTGCAT
622807 CTAGCACGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (21 bp):
AGTTGCATGTCAACATAAATA
Found at i:627509 original size:18 final size:18
Alignment explanation
Indices: 627473--627523 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
627463 GTCCTCCTCC
* *
627473 TTCTT-TTCCTCTGTCTT
1 TTCTTCTTCTTCTTTCTT
627490 TTCTTCTTCTTCTTTCTT
1 TTCTTCTTCTTCTTTCTT
* *
627508 TTCCTCCTCTTCTTTC
1 TTCTTCTTCTTCTTTC
627524 ACTGCCTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (18 bp):
TTCTTCTTCTTCTTTCTT
Found at i:637046 original size:17 final size:17
Alignment explanation
Indices: 637024--637058 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
637014 ACCGTAATGT
637024 CTCGTGTATAATACGCA
1 CTCGTGTATAATACGCA
637041 CTCGTGTATAATACGCA
1 CTCGTGTATAATACGCA
637058 C
1 C
637059 CCCCAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (17 bp):
CTCGTGTATAATACGCA
Found at i:637327 original size:108 final size:107
Alignment explanation
Indices: 637128--637329 Score: 260
Period size: 108 Copynumber: 1.9 Consensus size: 107
637118 AAAAAATGGT
** * * * *
637128 AAAATCAACGGCCGCCATTTTCCCCCAAACTATCGATGTTTCATGTTAATTTTATAATCCATGCG
1 AAAATCAACGGCCGCCATTTTCCCAAAAACTATCGATGTTTAATGATAATTTTATAACCCAAGCG
* * * *
637193 CAATTTCTTTAATTTTGAGATTGGAACATAGCACAGACGATG
66 CAATTACTGTAATTTCGAGATCGGAACATAGCACAGACGATG
* * *
637235 AAAATCGACGGCCGCCATTTTCCCAAATAACTATCGATGTTTAATGATGATTTTCTAACCCAAGC
1 AAAATCAACGGCCGCCATTTTCCCAAA-AACTATCGATGTTTAATGATAATTTTATAACCCAAGC
* *
637300 GTAATTACTGTAATTTCGTGATCGGAACAT
65 GCAATTACTGTAATTTCGAGATCGGAACAT
637330 GGCCTAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
107 24 0.30
108 55 0.70
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (107 bp):
AAAATCAACGGCCGCCATTTTCCCAAAAACTATCGATGTTTAATGATAATTTTATAACCCAAGCG
CAATTACTGTAATTTCGAGATCGGAACATAGCACAGACGATG
Found at i:645169 original size:2 final size:2
Alignment explanation
Indices: 645162--645235 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
645152 GACCATTATT
645162 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
645204 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
645236 AATATCTACA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:645787 original size:2 final size:2
Alignment explanation
Indices: 645780--645814 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
645770 GACCATTATT
645780 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
645815 TTAAATTTTG
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:647978 original size:11 final size:11
Alignment explanation
Indices: 647948--647981 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
647938 AACCACCAAA
647948 AAAACAAA-AC
1 AAAACAAACAC
647958 AAAAACAAACAC
1 -AAAACAAACAC
647970 AAAACAAACAC
1 AAAACAAACAC
647981 A
1 A
647982 CTCATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 20 0.91
12 2 0.09
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAACAC
Found at i:656089 original size:11 final size:11
Alignment explanation
Indices: 656073--656097 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
656063 TTAGGATTTA
656073 TTGTCAGTTTT
1 TTGTCAGTTTT
656084 TTGTCAGTTTT
1 TTGTCAGTTTT
656095 TTG
1 TTG
656098 ATTAAGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (11 bp):
TTGTCAGTTTT
Found at i:661048 original size:1 final size:1
Alignment explanation
Indices: 661013--661040 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
661003 TTGAGTGTAA
661013 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
661041 ACATTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:663757 original size:11 final size:11
Alignment explanation
Indices: 663741--663765 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
663731 TAATTGTATT
663741 CCTATTTGTCC
1 CCTATTTGTCC
663752 CCTATTTGTCC
1 CCTATTTGTCC
663763 CCT
1 CCT
663766 TAGAACACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.40, G:0.08, T:0.44
Consensus pattern (11 bp):
CCTATTTGTCC
Found at i:668244 original size:12 final size:12
Alignment explanation
Indices: 668198--668248 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
668188 TTAAAAAGTG
*
668198 AAAAAA-AAATA
1 AAAAAAGAAACA
*
668209 AAAAAATAAAACA
1 AAAAAA-GAAACA
*
668222 AAAAAATAAACA
1 AAAAAAGAAACA
*
668234 AAAACAGAAACA
1 AAAAAAGAAACA
668246 AAA
1 AAA
668249 CGAAGTTGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 6 0.18
12 18 0.53
13 10 0.29
ACGTcount: A:0.84, C:0.08, G:0.02, T:0.06
Consensus pattern (12 bp):
AAAAAAGAAACA
Found at i:668244 original size:24 final size:21
Alignment explanation
Indices: 668200--668248 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
668190 AAAAAGTGAA
*
668200 AAAAAAATAAAAAAATAAAAC
1 AAAAAAATAAAAAAACAAAAC
668221 AAAAAAATAAACAAAAACAGAAAC
1 AAAAAAAT-AA-AAAAACA-AAAC
668245 AAAA
1 AAAA
668249 CGAAGTTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 2 0.08
23 6 0.25
24 8 0.33
ACGTcount: A:0.84, C:0.08, G:0.02, T:0.06
Consensus pattern (21 bp):
AAAAAAATAAAAAAACAAAAC
Found at i:675583 original size:19 final size:19
Alignment explanation
Indices: 675545--675589 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
675535 TACGATATTA
*
675545 TATATATTCTTTTTATAAG
1 TATATATTCTTATTATAAG
*
675564 TCTATATTCTGTATTA-AAG
1 TATATATTCT-TATTATAAG
675583 TATATAT
1 TATATAT
675590 ATTCTGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (19 bp):
TATATATTCTTATTATAAG
Found at i:677800 original size:2 final size:2
Alignment explanation
Indices: 677793--677832 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
677783 TTATGTACAC
677793 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
677833 TAAATTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:686151 original size:16 final size:15
Alignment explanation
Indices: 686130--686160 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
686120 TCTATATCAG
686130 TTATATTATATCAATA
1 TTATATTA-ATCAATA
686146 TTATATTAATCAATA
1 TTATATTAATCAATA
686161 CTTGAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATATTAATCAATA
Found at i:686367 original size:22 final size:24
Alignment explanation
Indices: 686329--686380 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 24
686319 AAGTCGCAAA
686329 GATAAATTTAAATAATC-TTAGTTT
1 GATAAATTTAAATAATCTTTA-TTT
686353 GATAAA-TT-AATAATCTTTATTT
1 GATAAATTTAAATAATCTTTATTT
686375 GATAAA
1 GATAAA
686381 CTTGTACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 16 0.59
23 5 0.19
24 6 0.22
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (24 bp):
GATAAATTTAAATAATCTTTATTT
Found at i:687253 original size:35 final size:36
Alignment explanation
Indices: 687177--687254 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 36
687167 ACATTGTCAA
**
687177 ACATTCTACAAATAATCGATACAATCACATCTTCAG
1 ACATTCTACAAATAATCGATACAATCACATCGGCAG
* * *
687213 ACATTCTAC-ATTAATCGATATATTCACATCGGCAG
1 ACATTCTACAAATAATCGATACAATCACATCGGCAG
*
687248 TCATTCT
1 ACATTCT
687255 GCGACAGACA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 27 0.75
36 9 0.25
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (36 bp):
ACATTCTACAAATAATCGATACAATCACATCGGCAG
Found at i:694744 original size:2 final size:2
Alignment explanation
Indices: 694737--694791 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
694727 TAAAAGAATT
694737 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
694779 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
694792 TAAATCGATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:695085 original size:2 final size:2
Alignment explanation
Indices: 695080--695115 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
695070 AAACATTTAT
695080 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
695116 TTTGATTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:697520 original size:8 final size:7
Alignment explanation
Indices: 697509--697602 Score: 65
Period size: 7 Copynumber: 13.4 Consensus size: 7
697499 CGTTTATGAG
*
697509 TTTTCGT
1 TTTTTGT
697516 TTTTTGT
1 TTTTTGT
697523 TTTTT-T
1 TTTTTGT
*
697529 TTGTTTTT
1 TT-TTTGT
697537 TGTTTTGT
1 T-TTTTGT
697545 TTTGTT-T
1 TTT-TTGT
697552 TGTTTTGT
1 T-TTTTGT
697560 TTTTTGT
1 TTTTTGT
697567 TTTGTT-T
1 TTT-TTGT
*
697574 TGTTTG-
1 TTTTTGT
697580 TTTTTGT
1 TTTTTGT
697587 TTTCTT-T
1 TTT-TTGT
697594 TTTTT-T
1 TTTTTGT
697600 TTT
1 TTT
697603 ACAAAACTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 21
0.74 0.04 0.21
Matches are distributed among these distances:
6 16 0.22
7 39 0.53
8 17 0.23
9 1 0.01
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (7 bp):
TTTTTGT
Found at i:697526 original size:1 final size:1
Alignment explanation
Indices: 697515--697602 Score: 59
Period size: 1 Copynumber: 88.0 Consensus size: 1
697505 TGAGTTTTCG
* * * * * * * * * * *
697515 TTTTTTGTTTTTTTTTGTTTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGTTTTGTTTTGTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
697580 TTTTTGTTTTCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTT
697603 ACAAAACTTT
Statistics
Matches: 61, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (1 bp):
T
Found at i:697530 original size:10 final size:10
Alignment explanation
Indices: 697515--697602 Score: 97
Period size: 10 Copynumber: 8.4 Consensus size: 10
697505 TGAGTTTTCG
697515 TTTTTTGTTT
1 TTTTTTGTTT
697525 TTTTTTGTTTT
1 TTTTTTG-TTT
697536 TTGTTTTGTTT
1 TT-TTTTGTTT
*
697547 TGTTTTGTTTT
1 TTTTTTG-TTT
697558 GTTTTTTGTTT
1 -TTTTTTGTTT
*
697569 TGTTTTGTTT
1 TTTTTTGTTT
*
697579 GTTTTTGTTT
1 TTTTTTGTTT
697589 TCTTTTT-TTT
1 T-TTTTTGTTT
697599 TTTT
1 TTTT
697603 ACAAAACTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
9 3 0.04
10 33 0.49
11 20 0.30
12 11 0.16
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:697547 original size:27 final size:27
Alignment explanation
Indices: 697517--697589 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
697507 AGTTTTCGTT
697517 TTTTGTTTTTTTTTGTTTTTTGTTTTG
1 TTTTGTTTTTTTTTGTTTTTTGTTTTG
*
697544 TTTTGTTTTGTTTTGTTTTTTGTTTTG
1 TTTTGTTTTTTTTTGTTTTTTGTTTTG
*
697571 TTTTGTTTGTTTTTGTTTT
1 TTTTGTTTTTTTTTGTTTT
697590 CTTTTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (27 bp):
TTTTGTTTTTTTTTGTTTTTTGTTTTG
Found at i:699213 original size:2 final size:2
Alignment explanation
Indices: 699206--699259 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
699196 AGGAGATAAT
699206 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
699248 GA GA GA GA GA GA
1 GA GA GA GA GA GA
699260 TTCCCATTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:707711 original size:27 final size:27
Alignment explanation
Indices: 707676--707728 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
707666 AAAAGTGAAC
*
707676 GTATCATCTTAAGAATATATTTGATAG
1 GTATAATCTTAAGAATATATTTGATAG
*
707703 GTATAATCTTTAGAATATATTTGATA
1 GTATAATCTTAAGAATATATTTGATA
707729 ACAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (27 bp):
GTATAATCTTAAGAATATATTTGATAG
Found at i:708119 original size:19 final size:19
Alignment explanation
Indices: 708003--709373 Score: 939
Period size: 19 Copynumber: 72.2 Consensus size: 19
707993 AGTTATTACA
*
708003 AACAGACAAC-AGAACATGT
1 AACAGAC-ACTAGGACATGT
** * *
708022 AACCTACACTAGTACATGC
1 AACAGACACTAGGACATGT
* ** *
708041 AACAAACACTAGTTCATGC
1 AACAGACACTAGGACATGT
* *
708060 AACAGGCACTAGGACATAT
1 AACAGACACTAGGACATGT
* * **
708079 AGCTGACACTAGTTCATGT
1 AACAGACACTAGGACATGT
* *
708098 AACAGAGACTAGGACATAT
1 AACAGACACTAGGACATGT
* * *
708117 AACAGGCATTAGGACGTGT
1 AACAGACACTAGGACATGT
* * * *
708136 AATAGGCATTAGGATATGT
1 AACAGACACTAGGACATGT
* * *
708155 ACCAGACACTAGAACATTT
1 AACAGACACTAGGACATGT
*
708174 TACAGACACTAGGACATGT
1 AACAGACACTAGGACATGT
* *
708193 AACCGACACTAGGGCATGT
1 AACAGACACTAGGACATGT
* *
708212 AACAGACACTAGTACACGT
1 AACAGACACTAGGACATGT
* *
708231 AACAGACACTACTG-CATAT
1 AACAGACACTA-GGACATGT
* * *
708250 AACAGGCACTAGAACGTGT
1 AACAGACACTAGGACATGT
* *
708269 ACCAGACACTAGGATATGT
1 AACAGACACTAGGACATGT
* *
708288 AACAGACACTAGGGCGTGT
1 AACAGACACTAGGACATGT
* *
708307 AACAAACACAAGGACATGT
1 AACAGACACTAGGACATGT
* ** *
708326 AACAGGCACGACTAGTATGTTT
1 AACA-G-AC-ACTAGGACATGT
* *
708348 AACAGGCACTTGGACATGT
1 AACAGACACTAGGACATGT
* * * *
708367 TACAGGCACTAGTACGTGT
1 AACAGACACTAGGACATGT
* * * *
708386 TACAGACTCTAGTACATGC
1 AACAGACACTAGGACATGT
*
708405 AACAGGCACTAGGACATGT
1 AACAGACACTAGGACATGT
* * **
708424 AATAGGCA-TCAGGATGTGT
1 AACAGACACT-AGGACATGT
* * *
708443 ACCTGA-A-TAGAACATGT
1 AACAGACACTAGGACATGT
*
708460 TACAGACACTAGGACATGT
1 AACAGACACTAGGACATGT
708479 AACAGACACTAAGG-CATGT
1 AACAGACACT-AGGACATGT
* *
708498 AACAGGCATTAGGACATGT
1 AACAGACACTAGGACATGT
*
708517 AACAGACATTAGGACATGT
1 AACAGACACTAGGACATGT
* *
708536 AGCTGACACTAGGACATGT
1 AACAGACACTAGGACATGT
* *
708555 TACATG-CACTAGGACGTGT
1 AACA-GACACTAGGACATGT
* * * * *
708574 ACCAGGCACTTGTACTTGT
1 AACAGACACTAGGACATGT
* *
708593 AACAAACACTAGTACATGT
1 AACAGACACTAGGACATGT
*
708612 AACAGACACTAGGACATAT
1 AACAGACACTAGGACATGT
* * *
708631 AACTGACACTAAGATATGTATGTTT
1 AACAGACACT-AG-GA--CATG--T
* *
708656 AACAGGCACT-TGATCATGT
1 AACAGACACTAGGA-CATGT
* * *
708675 AATAGGCACTAGAACATGT
1 AACAGACACTAGGACATGT
*
708694 AACAGACACTAGGGCATGT
1 AACAGACACTAGGACATGT
*
708713 AACAGGCACTAGGACATGT
1 AACAGACACTAGGACATGT
* * *
708732 AACAGGCACGAGGACGTGT
1 AACAGACACTAGGACATGT
* *
708751 ACCAGACAATAGGACATGT
1 AACAGACACTAGGACATGT
*
708770 AACATG-CACTAGTACATGT
1 AACA-GACACTAGGACATGT
* * ** *
708789 AACAAACATTAATATATGT
1 AACAGACACTAGGACATGT
* * **
708808 AACAGGCATTAGTTCATGT
1 AACAGACACTAGGACATGT
708827 AACAGACACTAGGA-ATGT
1 AACAGACACTAGGACATGT
708845 AACAGACACTAGGA-A--T
1 AACAGACACTAGGACATGT
* *
708861 AACTGACACTAGGGCATGT
1 AACAGACACTAGGACATGT
*** * *
708880 AACAGGTTCTTGTACATGT
1 AACAGACACTAGGACATGT
* * * *
708899 AGCAAACACTTGTACATGT
1 AACAGACACTAGGACATGT
*
708918 AACAGACACTAGGACATAT
1 AACAGACACTAGGACATGT
* *
708937 AACTGACACTATGACATGT
1 AACAGACACTAGGACATGT
* *
708956 AATAGGCACTAGGACATGT
1 AACAGACACTAGGACATGT
* * *
708975 AATAGGCACTAGAACATGT
1 AACAGACACTAGGACATGT
708994 AACAGACACTAGGACATGT
1 AACAGACACTAGGACATGT
*
709013 AACAGGCACTAGGACATGT
1 AACAGACACTAGGACATGT
* * *
709032 AACAGGCACGAGGACGTGT
1 AACAGACACTAGGACATGT
* *
709051 ACCAGACAATAGGACATGT
1 AACAGACACTAGGACATGT
*
709070 AACATG-CACTAGTACATGT
1 AACA-GACACTAGGACATGT
* * ** *
709089 AACAAACATTAATATATGT
1 AACAGACACTAGGACATGT
* * **
709108 AACAGGCATTAGTTCATGT
1 AACAGACACTAGGACATGT
709127 AACAGACACTAGGA-ATGT
1 AACAGACACTAGGACATGT
709145 AACAGACACTAGGA-A--T
1 AACAGACACTAGGACATGT
* *
709161 AACTGACACTAGGGCATGT
1 AACAGACACTAGGACATGT
*** * *
709180 AACAGGTTCTTGTACATGT
1 AACAGACACTAGGACATGT
* * * *
709199 AGCAAACACTTGTACATGT
1 AACAGACACTAGGACATGT
*
709218 AACAGACACTAGGACATAT
1 AACAGACACTAGGACATGT
* *
709237 AACTGACACTATGACATGT
1 AACAGACACTAGGACATGT
* *
709256 AATAGGCACTAGGACATGT
1 AACAGACACTAGGACATGT
* * *
709275 AATAGGCACTAGAACATGT
1 AACAGACACTAGGACATGT
709294 AACAGACACTAGGACATGT
1 AACAGACACTAGGACATGT
*
709313 AACA-AGCACTAGGACGTGT
1 AACAGA-CACTAGGACATGT
* * *
709332 -ACTAGACAATAGCATATGT
1 AAC-AGACACTAGGACATGT
709351 AACATG-CACTAGGACATGT
1 AACA-GACACTAGGACATGT
709370 AACA
1 AACA
709374 AACATTAGTA
Statistics
Matches: 1047, Mismatches: 270, Indels: 70
0.75 0.19 0.05
Matches are distributed among these distances:
16 26 0.02
17 11 0.01
18 51 0.05
19 915 0.87
20 14 0.01
21 7 0.01
22 12 0.01
23 2 0.00
25 9 0.01
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (19 bp):
AACAGACACTAGGACATGT
Found at i:709023 original size:300 final size:300
Alignment explanation
Indices: 708351--709332 Score: 1427
Period size: 300 Copynumber: 3.2 Consensus size: 300
708341 TATGTTTAAC
* * * * * * * * *
708351 AGGCACTTGGACATGTTACAGGCACTAGTACGTGTTACAGACTCTAGTACATGCAACAGGCACTA
1 AGGCACTAGGACATGTAATAGGCACTAGAACATGTAACAGACACTAGGACATGTAACAGGCACTA
* * * * * *
708416 GGACATGTAATAGGCATC-AGGATGTGTACCTG--AATAGAACATGTTACA-GACACTAGGACAT
66 GGACATGTAACAGGCA-CGAGGACGTGTACCAGACAATAGGACATGTAACATG-CACTAGTACAT
* * *** ** * * *
708477 GTAACAGACACTAAGGCATGTAACAGGCATTAGGACATGTAACAGACATTAGGACATGTAGCTGA
129 GTAACAAACATTAATATATGTAACAGGCATTAGTTCATGTAACAGACACTAGGA-ATGTAACAGA
* * * * ** * * *
708542 CACTAGGACATGTTACATG-CACTAGGACGTGTACCAGGCACTTGTACTTGTAACAAACACTAGT
193 CACTAGGA-A--TAAC-TGACACTAGGGCATGTAACAGGTTCTTGTACATGTAGCAAACACTTGT
* * *
708606 ACATGTAACAGACACTAGGACATATAACTGACACTAAGATATGTATGTTTAAC
254 ACATGTAACAGACACTAGGACATATAACTGACACTATG--A--CATG--TAAT
* *
708659 AGGCACT-TGATCATGTAATAGGCACTAGAACATGTAACAGACACTAGGGCATGTAACAGGCACT
1 AGGCACTAGGA-CATGTAATAGGCACTAGAACATGTAACAGACACTAGGACATGTAACAGGCACT
708723 AGGACATGTAACAGGCACGAGGACGTGTACCAGACAATAGGACATGTAACATGCACTAGTACATG
65 AGGACATGTAACAGGCACGAGGACGTGTACCAGACAATAGGACATGTAACATGCACTAGTACATG
708788 TAACAAACATTAATATATGTAACAGGCATTAGTTCATGTAACAGACACTAGGAATGTAACAGACA
130 TAACAAACATTAATATATGTAACAGGCATTAGTTCATGTAACAGACACTAGGAATGTAACAGACA
708853 CTAGGAATAACTGACACTAGGGCATGTAACAGGTTCTTGTACATGTAGCAAACACTTGTACATGT
195 CTAGGAATAACTGACACTAGGGCATGTAACAGGTTCTTGTACATGTAGCAAACACTTGTACATGT
708918 AACAGACACTAGGACATATAACTGACACTATGACATGTAAT
260 AACAGACACTAGGACATATAACTGACACTATGACATGTAAT
708959 AGGCACTAGGACATGTAATAGGCACTAGAACATGTAACAGACACTAGGACATGTAACAGGCACTA
1 AGGCACTAGGACATGTAATAGGCACTAGAACATGTAACAGACACTAGGACATGTAACAGGCACTA
709024 GGACATGTAACAGGCACGAGGACGTGTACCAGACAATAGGACATGTAACATGCACTAGTACATGT
66 GGACATGTAACAGGCACGAGGACGTGTACCAGACAATAGGACATGTAACATGCACTAGTACATGT
709089 AACAAACATTAATATATGTAACAGGCATTAGTTCATGTAACAGACACTAGGAATGTAACAGACAC
131 AACAAACATTAATATATGTAACAGGCATTAGTTCATGTAACAGACACTAGGAATGTAACAGACAC
709154 TAGGAATAACTGACACTAGGGCATGTAACAGGTTCTTGTACATGTAGCAAACACTTGTACATGTA
196 TAGGAATAACTGACACTAGGGCATGTAACAGGTTCTTGTACATGTAGCAAACACTTGTACATGTA
709219 ACAGACACTAGGACATATAACTGACACTATGACATGTAAT
261 ACAGACACTAGGACATATAACTGACACTATGACATGTAAT
*
709259 AGGCACTAGGACATGTAATAGGCACTAGAACATGTAACAGACACTAGGACATGTAACAAGCACTA
1 AGGCACTAGGACATGTAATAGGCACTAGAACATGTAACAGACACTAGGACATGTAACAGGCACTA
*
709324 GGACGTGTA
66 GGACATGTA
709333 CTAGACAATA
Statistics
Matches: 625, Mismatches: 42, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
300 370 0.59
301 2 0.00
302 3 0.00
304 1 0.00
305 2 0.00
306 77 0.12
307 3 0.00
308 80 0.13
309 16 0.03
310 70 0.11
311 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (300 bp):
AGGCACTAGGACATGTAATAGGCACTAGAACATGTAACAGACACTAGGACATGTAACAGGCACTA
GGACATGTAACAGGCACGAGGACGTGTACCAGACAATAGGACATGTAACATGCACTAGTACATGT
AACAAACATTAATATATGTAACAGGCATTAGTTCATGTAACAGACACTAGGAATGTAACAGACAC
TAGGAATAACTGACACTAGGGCATGTAACAGGTTCTTGTACATGTAGCAAACACTTGTACATGTA
ACAGACACTAGGACATATAACTGACACTATGACATGTAAT
Found at i:716375 original size:16 final size:16
Alignment explanation
Indices: 716354--716384 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
716344 TATTGGGAAA
716354 GAAAATGAATAAAAAG
1 GAAAATGAATAAAAAG
*
716370 GAAAATGGATAAAAA
1 GAAAATGAATAAAAA
716385 CATTCGAAAA
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:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (16 bp):
GAAAATGAATAAAAAG
Found at i:722885 original size:13 final size:13
Alignment explanation
Indices: 722863--722903 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
722853 ACCACGAAAC
722863 AAAC-AAAAACAA
1 AAACAAAAAACAA
722875 AAACAAAAAAC-A
1 AAACAAAAAACAA
*
722887 AAACGAAAAAATAA
1 AAAC-AAAAAACAA
722901 AAA
1 AAA
722904 TTCTAACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 9 0.36
13 12 0.48
14 4 0.16
ACGTcount: A:0.83, C:0.12, G:0.02, T:0.02
Consensus pattern (13 bp):
AAACAAAAAACAA
Found at i:727510 original size:18 final size:18
Alignment explanation
Indices: 727483--727534 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
727473 AAAGTCCTAA
*
727483 TTCCTTTAGGAATTATAT
1 TTCCTGTAGGAATTATAT
**
727501 TTCCTGTAGGAGAATGGTAT
1 TTCCTGTA-G-GAATTATAT
727521 TTCCTGTAGGAATT
1 TTCCTGTAGGAATT
727535 TGATTCAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.39
19 2 0.07
20 15 0.54
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (18 bp):
TTCCTGTAGGAATTATAT
Found at i:731967 original size:14 final size:13
Alignment explanation
Indices: 731939--731963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
731929 AAACGAAAAC
731939 TTATTCATTTTTA
1 TTATTCATTTTTA
731952 TTATTCATTTTT
1 TTATTCATTTTT
731964 TATTTTATTT
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTCATTTTTA
Found at i:735517 original size:22 final size:22
Alignment explanation
Indices: 735492--735535 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
735482 CAAAAGACAT
*
735492 ACTCTATACGTTTAGTATATAA
1 ACTCTATAAGTTTAGTATATAA
735514 ACTCTATAAGTTTAGTATATAA
1 ACTCTATAAGTTTAGTATATAA
735536 TAGAGCCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (22 bp):
ACTCTATAAGTTTAGTATATAA
Found at i:736128 original size:20 final size:20
Alignment explanation
Indices: 736103--736141 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
736093 GCAAACCTGT
736103 TTAATGTTGAATGTGTAATG
1 TTAATGTTGAATGTGTAATG
736123 TTAATGTTGAATGTGTAAT
1 TTAATGTTGAATGTGTAAT
736142 TTTTCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (20 bp):
TTAATGTTGAATGTGTAATG
Found at i:736395 original size:12 final size:12
Alignment explanation
Indices: 736378--736403 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
736368 TCTTTTCTTC
736378 TACATTCTAATA
1 TACATTCTAATA
736390 TACATTCTAATA
1 TACATTCTAATA
736402 TA
1 TA
736404 TGCTCAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
TACATTCTAATA
Found at i:761781 original size:2 final size:2
Alignment explanation
Indices: 761774--761804 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
761764 GTGAACATCA
761774 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 T
761805 GGCGGACACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:766292 original size:2 final size:2
Alignment explanation
Indices: 766285--766335 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
766275 CGGAGTAACT
766285 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
766327 GA GA GA GA G
1 GA GA GA GA G
766336 TGATGACTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:767120 original size:2 final size:2
Alignment explanation
Indices: 767113--767157 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
767103 ATGAAACAGA
767113 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
767155 TC T
1 TC T
767158 GAGACTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:787061 original size:17 final size:17
Alignment explanation
Indices: 787029--787061 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
787019 TTTAAACAAA
787029 CTGCTTATTTTCTCTCG
1 CTGCTTATTTTCTCTCG
787046 CTGCTGTATTTT-TCTC
1 CTGCT-TATTTTCTCTC
787062 TTTTGGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.27, G:0.12, T:0.55
Consensus pattern (17 bp):
CTGCTTATTTTCTCTCG
Found at i:796602 original size:16 final size:16
Alignment explanation
Indices: 796573--796625 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
796563 TACTTTGTAC
*
796573 ATGTAACAGTCTTTGT
1 ATGTAACCGTCTTTGT
* * *
796589 ATTTATCTGTCTTTGT
1 ATGTAACCGTCTTTGT
796605 ATGTAACCGTCTTTGT
1 ATGTAACCGTCTTTGT
796621 ATGTA
1 ATGTA
796626 CATTGTACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (16 bp):
ATGTAACCGTCTTTGT
Found at i:808570 original size:58 final size:61
Alignment explanation
Indices: 808443--808568 Score: 234
Period size: 61 Copynumber: 2.1 Consensus size: 61
808433 TAAAATATTT
* *
808443 TATTATTTTGTAAAGAAATAATAATATATTATATAATAAAGCGTTTCTCAAATGTAAAAAA
1 TATTATTTTGTAAAGAAATAATAATATATTAAATAATAAAGCGTTTCTCAAAAGTAAAAAA
808504 TATTATTTTGTAAAGAAATAATAATATATTAAATAATAAAGCGTTTCTCAAAAGTAAAAAA
1 TATTATTTTGTAAAGAAATAATAATATATTAAATAATAAAGCGTTTCTCAAAAGTAAAAAA
808565 TATT
1 TATT
808569 TTTGAAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (61 bp):
TATTATTTTGTAAAGAAATAATAATATATTAAATAATAAAGCGTTTCTCAAAAGTAAAAAA
Found at i:812513 original size:2 final size:2
Alignment explanation
Indices: 812506--812555 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
812496 TCAAATGAAA
812506 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
812548 AG AG AG AG
1 AG AG AG AG
812556 GGGGTGGGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:846156 original size:14 final size:14
Alignment explanation
Indices: 846137--846163 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
846127 TTTATTAAAA
846137 GCGATGTCAAAGTT
1 GCGATGTCAAAGTT
846151 GCGATGTCAAAGT
1 GCGATGTCAAAGT
846164 CGTAATACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (14 bp):
GCGATGTCAAAGTT
Found at i:849259 original size:2 final size:2
Alignment explanation
Indices: 849252--849292 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
849242 ACAAACGAGC
* *
849252 AG AG AG AG AG AT AG AT 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 AG AG AG A
849293 TATGTAGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.44, T:0.05
Consensus pattern (2 bp):
AG
Found at i:852482 original size:17 final size:16
Alignment explanation
Indices: 852457--852491 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
852447 TAGCGCGATA
852457 TAATTTTTTTATTTGC
1 TAATTTTTTTATTTGC
852473 TAATTTTTTTATTTGC
1 TAATTTTTTTATTTGC
852489 TAA
1 TAA
852492 GCGAGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
TAATTTTTTTATTTGC
Found at i:853916 original size:2 final size:2
Alignment explanation
Indices: 853909--853950 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
853899 AGCTGATTTT
853909 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
853951 TTATGCAGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:856445 original size:165 final size:165
Alignment explanation
Indices: 856219--856545 Score: 593
Period size: 165 Copynumber: 2.0 Consensus size: 165
856209 CACCCCCCCC
*
856219 CCCCCCATGTGGCCTCACACTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACACTACC
1 CCCCCCATGTGGCCCCACACTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACACTACC
856284 TGAGGATACTTCCACACAAGTTTCAACTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAA
66 TGAGGATACTTCCACACAAGTTTCAACTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAA
856349 AGATTTACTCTATATATTCCTATGTAAAACTTCGA
131 AGATTTACTCTATATATTCCTATGTAAAACTTCGA
*
856384 CCCCCCAT-TGTGCCCCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACACTAC
1 CCCCCCATGTG-GCCCCACACTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACACTAC
* * *
856448 CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTA
65 CTGAGGATACTTCCACACAAGTTTCAACTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTA
856513 AAGATTTACTCTATATATTCCTATGTAAAACTT
130 AAGATTTACTCTATATATTCCTATGTAAAACTT
856546 NCGTTTATCC
Statistics
Matches: 156, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
164 2 0.01
165 154 0.99
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (165 bp):
CCCCCCATGTGGCCCCACACTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACACTACC
TGAGGATACTTCCACACAAGTTTCAACTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAA
AGATTTACTCTATATATTCCTATGTAAAACTTCGA
Found at i:859922 original size:2 final size:2
Alignment explanation
Indices: 859915--859959 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
859905 GAAAGCGTAC
859915 TA TA TA TA TA TA 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
859957 TA T
1 TA T
859960 GCCATTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:878301 original size:18 final size:18
Alignment explanation
Indices: 878278--878314 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
878268 TCGAGAGAGG
878278 AGATTAGATCAAAAAAGT
1 AGATTAGATCAAAAAAGT
*
878296 AGATTAGATCGAAAAAGT
1 AGATTAGATCAAAAAAGT
878314 A
1 A
878315 AGTAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (18 bp):
AGATTAGATCAAAAAAGT
Found at i:881021 original size:20 final size:20
Alignment explanation
Indices: 880996--881038 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
880986 TGACGCTAAT
*
880996 TTTTGCAGGGAATCAGTCTG
1 TTTTGCAGGGAATCAGTATG
881016 TTTTGCAGGGAATCAGTATG
1 TTTTGCAGGGAATCAGTATG
881036 TTT
1 TTT
881039 ACGGCGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.40
Consensus pattern (20 bp):
TTTTGCAGGGAATCAGTATG
Found at i:887934 original size:12 final size:12
Alignment explanation
Indices: 887917--887951 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
887907 CCAAGGGTCA
887917 TTGACAGAAAAC
1 TTGACAGAAAAC
887929 TTGACAGAAAAC
1 TTGACAGAAAAC
887941 TTGACAGAAAA
1 TTGACAGAAAA
887952 GTCCGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (12 bp):
TTGACAGAAAAC
Found at i:889599 original size:177 final size:176
Alignment explanation
Indices: 889381--890153 Score: 953
Period size: 177 Copynumber: 4.4 Consensus size: 176
889371 ACTTGAAAGA
* ** * * * *
889381 CTTGGATGCTGAATCTGAGTCC-TAAATTTTAGATGCTGGAGGAGATTAAGGTTGTTGGACCAGG
1 CTTGAATGCTGAATCTGAG-CCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGG
* * *
889445 TTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCTAAGTTACTACAGGTCCGT-ACTTCA
65 TTAAAGTTTTTGTTACAGGTGCCCTCTGAT-GCAATATCTAAGTTACTACTGGTCC-TAACTTCA
* * *
889509 CCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCACCCGACAGG
128 CCAAACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGG
* * * *
889558 CTTGAGTGCTGAATATGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGT
1 CTTGAATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGT
* * * * *
889623 TAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCTAAGTTACTGCTGGT-CTGTACTCCAC
66 TAAAGTTTTTGTTACAGGTGCCCTCTGAT-GCAATATCTAAGTTACTACTGGTCCT-AACTTCAC
* * * *
889687 CAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCACCAGGCAGG
129 CAAACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGG
** * * * * *
889735 CTTGGGTGCTGAATCTGAGCTATAGGTTACAGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGT
1 CTTGAATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGT
* * *
889800 TAAAGTTTTTGTTACAGGTGCCCTCTGATGATAATATCTTAGTTACTACTTGTCCTAACTTCACC
66 TAAAGTTTTTGTTACAGGTGCCCTCTGATG-CAATATCTAAGTTACTACTGGTCCTAACTTCACC
* *
889865 AGACCTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGG
130 AAACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGG
* * *
889912 CTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGCAGGTTAAGGTTTTTGGAGCTGGT
1 CTTGAATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGT
* ** * * *
889977 AAAAGTTTTTGAAACAGGTGCCCTCTGATG-ATTATATCTTAGTTATTACTTGTCCTAACTTCAC
66 TAAAGTTTTTGTTACAGGTGCCCTCTGATGCA--ATATCTAAGTTACTACTGGTCCTAACTTCAC
* *
890041 CAGACTTCCATGGATGGTGCGTCTTTTGATACTGATGCACCTGACAGG
129 CAAACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGG
* * * *
890089 CTTGAATGCTGAGTCTGAGCCATAGGTTTCAGATGCTGGA-TATGGTTAAGTTTTTTGGAACAGG
1 CTTGAATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGA-GGTTAAGGTTTTTGGAGCAGG
890153 T
65 T
890154 CACATGTTTA
Statistics
Matches: 531, Mismatches: 57, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
175 2 0.00
176 4 0.01
177 523 0.98
178 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (176 bp):
CTTGAATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGT
TAAAGTTTTTGTTACAGGTGCCCTCTGATGCAATATCTAAGTTACTACTGGTCCTAACTTCACCA
AACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGG
Found at i:889641 original size:19 final size:19
Alignment explanation
Indices: 889594--889633 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
889584 TTTCGGATGC
* *
889594 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
889613 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
889632 TG
1 TG
889634 TTGCAGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:889970 original size:19 final size:19
Alignment explanation
Indices: 889948--889987 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
889938 TTTCGGATGC
* *
889948 TGGAGCAGGTTAAGGTTTT
1 TGGAGCAGGTAAAAGTTTT
*
889967 TGGAGCTGGTAAAAGTTTT
1 TGGAGCAGGTAAAAGTTTT
889986 TG
1 TG
889988 AAACAGGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.35, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTAAAAGTTTT
Found at i:891091 original size:214 final size:214
Alignment explanation
Indices: 890722--891152 Score: 817
Period size: 214 Copynumber: 2.0 Consensus size: 214
890712 TAGATAGATG
890722 TGTTTGTTGATAAATGATATAACATGATTCCTATGATATAGTATTGTATGGTATGAAACAATATT
1 TGTTTGTTGATAAATGATATAACATGATTCCTATGATATAGTATTGTATGGTATGAAACAATATT
*
890787 GTTTAATATGATACAATATAATATCATATGTAATATTATAAAAAGTTATATGATACGATATGATA
66 GTTGAATATGATACAATATAATATCATATGTAATATTATAAAAAGTTATATGATACGATATGATA
*
890852 TTATATCAATTTTTTTTATATTTTATGTTATGATATTGTATCATGATATCGTTATGTAAAGTATT
131 TTATATCAATTTTTTTGATATTTTATGTTATGATATTGTATCATGATATCGTTATGTAAAGTATT
890917 GTATATAATGATACAATAT
196 GTATATAATGATACAATAT
* *
890936 TGTTTGTTGATAAATGATATAACATGATTCCTATGATATGGTATTGTATGGTATGGAACAATATT
1 TGTTTGTTGATAAATGATATAACATGATTCCTATGATATAGTATTGTATGGTATGAAACAATATT
*
891001 GTTGAATATGATACAATATAATATCATATTTAATATTATAAAAAGTTATATGATACGATATGATA
66 GTTGAATATGATACAATATAATATCATATGTAATATTATAAAAAGTTATATGATACGATATGATA
891066 TTATATCAATTTTTTTGATATTTTATGTTATGATATTGTATCATGATATCGTTATGTAAAGTATT
131 TTATATCAATTTTTTTGATATTTTATGTTATGATATTGTATCATGATATCGTTATGTAAAGTATT
891131 GTATATAATGATACAATAT
196 GTATATAATGATACAATAT
891150 TGT
1 TGT
891153 ATAATATTAT
Statistics
Matches: 212, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
214 212 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (214 bp):
TGTTTGTTGATAAATGATATAACATGATTCCTATGATATAGTATTGTATGGTATGAAACAATATT
GTTGAATATGATACAATATAATATCATATGTAATATTATAAAAAGTTATATGATACGATATGATA
TTATATCAATTTTTTTGATATTTTATGTTATGATATTGTATCATGATATCGTTATGTAAAGTATT
GTATATAATGATACAATAT
Found at i:891416 original size:98 final size:99
Alignment explanation
Indices: 891252--891497 Score: 241
Period size: 98 Copynumber: 2.5 Consensus size: 99
891242 ACAATATTGT
* * * * * * *
891252 ATATTCTATAATATTGTATCATACGATATTTTAAAATATGATATTAGTTTCTGTAATTTAGAATT
1 ATATTTTATAATATCGTATCATACGATATTGTATAATATGATATT-GGTTCTATAATTGAGAATT
*
891317 AT-ATCACATGAAATTGTA-TAATATGATACTGT-A
65 ATCATCACATGAAATTGTACT-ATAAGATACTGTAA
*
891350 ATATTTTATAATATCGTATCATACGATATTGTATAATATGATATTGGTT-TATAATATGATATAT
1 ATATTTTATAATATCGTATCATACGATATTGTATAATATGATATTGGTTCTATAAT-TGAGA-AT
* *
891414 TATCACATCACATGAAATTGTACTGTAAGATATTGTAAA
64 TAT--CATCACATGAAATTGTACTATAAGATACTGT-AA
* ** * * *
891453 ATATATTATTGTATCATATGATACAATA-TGTATAATATGATATTG
1 ATATTTTATAATATCGTATCATACGATATTGTATAATATGATATTG
891498 TATTATACAA
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
96 5 0.04
97 6 0.05
98 46 0.37
101 25 0.20
102 18 0.15
103 23 0.19
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (99 bp):
ATATTTTATAATATCGTATCATACGATATTGTATAATATGATATTGGTTCTATAATTGAGAATTA
TCATCACATGAAATTGTACTATAAGATACTGTAA
Found at i:891900 original size:16 final size:15
Alignment explanation
Indices: 891870--891915 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
891860 ATTTAATATG
891870 ATAAAGGTG-GTCTC
1 ATAAAGGTGAGTCTC
891884 ATAAAGGTGAAGTCTC
1 ATAAAGGTG-AGTCTC
*
891900 ATAAGGGTGATGTCTC
1 ATAAAGGTGA-GTCTC
891916 GTCTCGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 18 0.64
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (15 bp):
ATAAAGGTGAGTCTC
Found at i:892528 original size:31 final size:31
Alignment explanation
Indices: 892491--892611 Score: 206
Period size: 31 Copynumber: 3.9 Consensus size: 31
892481 GTGTTATTGC
892491 ATATAACGTTTAAAATTTTCTTCTCTACTGT
1 ATATAACGTTTAAAATTTTCTTCTCTACTGT
* *
892522 ATATAACGTTTAAAATGTTCTTCTCTATTGT
1 ATATAACGTTTAAAATTTTCTTCTCTACTGT
*
892553 ATATAACGTTTAAAATTTTCTTCTCTATTGT
1 ATATAACGTTTAAAATTTTCTTCTCTACTGT
*
892584 ATATAACGTTTAAAGTTTTCTTCTCTAC
1 ATATAACGTTTAAAATTTTCTTCTCTAC
892612 ATCTGCTGAC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (31 bp):
ATATAACGTTTAAAATTTTCTTCTCTACTGT
Found at i:899480 original size:31 final size:31
Alignment explanation
Indices: 899430--899493 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
899420 TGTGGTTGCA
* *
899430 TTAGCGCGACGGCATGTTGT-CTGCAGTTGTG
1 TTAGCGCGACGGCAGGTTGTGC-GAAGTTGTG
* *
899461 TTAGCGCGTCGGCGGGTTGTGCGAAGTTGTG
1 TTAGCGCGACGGCAGGTTGTGCGAAGTTGTG
899492 TT
1 TT
899494 TCCGCGACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.11, C:0.17, G:0.39, T:0.33
Consensus pattern (31 bp):
TTAGCGCGACGGCAGGTTGTGCGAAGTTGTG
Found at i:902432 original size:14 final size:14
Alignment explanation
Indices: 902398--902434 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
902388 GAAGGCTCAC
902398 TCGAGATTCGAAAT
1 TCGAGATTCGAAAT
* *
902412 ACAAGATTCGAAAT
1 TCGAGATTCGAAAT
902426 TCGAGATTC
1 TCGAGATTC
902435 AATATCTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (14 bp):
TCGAGATTCGAAAT
Found at i:903201 original size:30 final size:30
Alignment explanation
Indices: 903166--903226 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
903156 ATTTTGAACG
903166 GCCGGTCAATAGACTGCGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
*
903196 GCCGGTCAATAGACTGTGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
903226 G
1 G
903227 GCAACGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (30 bp):
GCCGGTCAATAGACTGCGATCTATTGGACC
Found at i:903991 original size:49 final size:51
Alignment explanation
Indices: 903931--904039 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 51
903921 GGGAAGAGCT
* * *
903931 TGTTAAGCCAAAGGAAG-T-TATACAAATATGTCCTTTTTCGGGATGTAAA
1 TGTTAAGCCAAAGGAAGTTATATACAAATATGTCATTCTTCGGGAAGTAAA
* * *
903980 TGTTTAGCCAAAGGAAGTTATATACAATTTTGTCATTCTTCGGGAAGTAAA
1 TGTTAAGCCAAAGGAAGTTATATACAAATATGTCATTCTTCGGGAAGTAAA
904031 TGTTAAGCC
1 TGTTAAGCC
904040 TTATGTTTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 16 0.31
50 1 0.02
51 34 0.67
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (51 bp):
TGTTAAGCCAAAGGAAGTTATATACAAATATGTCATTCTTCGGGAAGTAAA
Found at i:905837 original size:19 final size:20
Alignment explanation
Indices: 905810--905943 Score: 87
Period size: 19 Copynumber: 6.5 Consensus size: 20
905800 GAATTCAGCG
*
905810 AATTTGTTATAACAGATT-A
1 AATTCGTTATAACAGATTAA
905829 AATTCGTTATAAC-GAATTCCTAA
1 AATTCGTTATAACAG-A-T--TAA
* * *
905852 AATTTGTTATAACAAATT-T
1 AATTCGTTATAACAGATTAA
* *
905871 GATTCGTTATAACGGATTCAAA
1 AATTCGTTATAACAGATT--AA
*
905893 AATTCGTTATAAC-GATTGA
1 AATTCGTTATAACAGATTAA
* *
905912 AATTCGTTTTAACAAATTTAA
1 AATTCGTTATAACAGA-TTAA
905933 GAATTCGTTAT
1 -AATTCGTTAT
905944 CTCAAATTCA
Statistics
Matches: 88, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.01
19 40 0.45
20 3 0.03
21 7 0.08
22 23 0.26
23 14 0.16
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (20 bp):
AATTCGTTATAACAGATTAA
Found at i:905845 original size:42 final size:41
Alignment explanation
Indices: 905795--905943 Score: 147
Period size: 42 Copynumber: 3.6 Consensus size: 41
905785 AAAATTTGAA
**
905795 ATAACGAATTCAGCGAATTTGTTATAACAGATTAAATTCGTT
1 ATAACGAATTCA-AAAATTTGTTATAACAGATTAAATTCGTT
* * **
905837 ATAACGAATTCCTAAAATTTGTTATAACAAATTTGATTCGTT
1 ATAACGAATT-CAAAAATTTGTTATAACAGATTAAATTCGTT
* *
905879 ATAACGGATTCAAAAATTCGTTATAAC-GATTGAAATTCGTT
1 ATAACGAATTCAAAAATTTGTTATAACAGATT-AAATTCGTT
* * * * *
905920 TTAACAAATTTAAGAATTCGTTAT
1 ATAACGAATTCAAAAATTTGTTAT
905944 CTCAAATTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
40 3 0.03
41 41 0.47
42 43 0.49
43 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (41 bp):
ATAACGAATTCAAAAATTTGTTATAACAGATTAAATTCGTT
Found at i:905917 original size:41 final size:42
Alignment explanation
Indices: 905795--905943 Score: 144
Period size: 41 Copynumber: 3.6 Consensus size: 42
905785 AAAATTTGAA
** *
905795 ATAACGAATTCAGCGAATTTGTTATAACAGATT-AAATTCGTT
1 ATAACGAATTCA-AAAATTCGTTATAACAGATTGAAATTCGTT
* * *
905837 ATAACGAATTCCTAAAATTTGTTATAACAAATTTG--ATTCGTT
1 ATAACGAATT-CAAAAATTCGTTATAACAGA-TTGAAATTCGTT
*
905879 ATAACGGATTCAAAAATTCGTTATAAC-GATTGAAATTCGTT
1 ATAACGAATTCAAAAATTCGTTATAACAGATTGAAATTCGTT
* * * *
905920 TTAACAAATTTAAGAATTCGTTAT
1 ATAACGAATTCAAAAATTCGTTAT
905944 CTCAAATTCA
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
39 3 0.03
40 1 0.01
41 41 0.46
42 41 0.46
43 3 0.03
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (42 bp):
ATAACGAATTCAAAAATTCGTTATAACAGATTGAAATTCGTT
Found at i:913714 original size:20 final size:20
Alignment explanation
Indices: 913689--913727 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
913679 CTAAATATAG
*
913689 ATTTACATTTGGAAACTATC
1 ATTTACATTCGGAAACTATC
*
913709 ATTTACATTCGGTAACTAT
1 ATTTACATTCGGAAACTAT
913728 AGTTAAGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTTACATTCGGAAACTATC
Found at i:919713 original size:69 final size:63
Alignment explanation
Indices: 919451--919712 Score: 416
Period size: 63 Copynumber: 4.1 Consensus size: 63
919441 ATATTTCGTA
919451 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTCCTCTATT
1 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTCCTCTATT
* *
919514 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCTATG
1 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTCCTCTATT
*** *
919577 ATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCTATTAT
1 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTCCTC------
919642 TATT
60 TATT
919646 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTCCTCTATT
1 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTCCTCTATT
919709 ATTA
1 ATTA
919713 TAATTCTTTT
Statistics
Matches: 183, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
63 125 0.68
69 58 0.32
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.48
Consensus pattern (63 bp):
ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTCCTCTATT
Found at i:932428 original size:33 final size:32
Alignment explanation
Indices: 932337--932415 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
932327 CCTAGCCATC
*
932337 TTTCCCCCCGGAAAAATGGCTATGTAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
932369 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
932401 TTTCCCCCACGGAAA
1 TTTCCCCC-CGGAAA
932416 GCTGACTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 39 0.87
33 6 0.13
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
Found at i:932437 original size:33 final size:32
Alignment explanation
Indices: 932337--932441 Score: 120
Period size: 32 Copynumber: 3.2 Consensus size: 32
932327 CCTAGCCATC
* * *
932337 TTTCCCCCCGGAAAAATGGCTATGTAGCAGTT
1 TTTCCCCCCGGAAAAATGACTATATAGCAGGT
* *
932369 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGACTATATAGCAGGT
** **
932401 TTTCCCCCACGGAAAGCTGACTATATAGTGGGT
1 TTTCCCCC-CGGAAAAATGACTATATAGCAGGT
932434 TTTCCCCC
1 TTTCCCCC
932442 GTTTTATAGC
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 39 0.60
33 26 0.40
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGACTATATAGCAGGT
Found at i:960295 original size:1 final size:1
Alignment explanation
Indices: 960289--960332 Score: 70
Period size: 1 Copynumber: 44.0 Consensus size: 1
960279 TATCCGGTGT
**
960289 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
960333 TTAGGATGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.95, C:0.02, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:984999 original size:70 final size:72
Alignment explanation
Indices: 984883--985020 Score: 163
Period size: 70 Copynumber: 1.9 Consensus size: 72
984873 CAAATGACAC
* * * * *
984883 ATTTTCTCAAATATTATATATGGCGATTCTAAAAAGTTCGAGCTTGCTTTATATGTTGACTTTAG
1 ATTTTCTCAAATATTATATATGGCGATTCCAAAAAGGTCGAACTTGCATTATATGTTGACTTAAG
984948 AAATCAT
66 AAATCAT
* ** * * *
984955 ATTTTCTCAATTA-TAT-TATGTTGATTCCAAAGAGGTCGAACTTGCATTATTTGTTGAGTTAAG
1 ATTTTCTCAAATATTATATATGGCGATTCCAAAAAGGTCGAACTTGCATTATATGTTGACTTAAG
985018 AAA
66 AAA
985021 AATATGAATC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
70 40 0.73
71 3 0.05
72 12 0.22
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (72 bp):
ATTTTCTCAAATATTATATATGGCGATTCCAAAAAGGTCGAACTTGCATTATATGTTGACTTAAG
AAATCAT
Found at i:985069 original size:17 final size:17
Alignment explanation
Indices: 985047--985554 Score: 716
Period size: 17 Copynumber: 29.9 Consensus size: 17
985037 TGATCAGTGT
985047 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
985064 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
* *
985081 -TCCATATTGTATACATG
1 TTCC-TACTGTACACATG
985098 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
* *
985115 TCCCTATTGTACACATG
1 TTCCTACTGTACACATG
985132 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
*
985149 -TCCATATTGTACACATG
1 TTCC-TACTGTACACATG
985166 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
985183 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
*
985200 TTCCTACTGTTCACATG
1 TTCCTACTGTACACATG
985217 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
* *
985234 TTCTTATTGTACACATG
1 TTCCTACTGTACACATG
*
985251 TTCCTAATGTACACATG
1 TTCCTACTGTACACATG
* *
985268 TTCCTATTGTACACGTG
1 TTCCTACTGTACACATG
* *
985285 TTCTTACTGTACACGTG
1 TTCCTACTGTACACATG
985302 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
*
985319 -TCCATATTGTACACATG
1 TTCC-TACTGTACACATG
985336 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
* *
985353 TCCCTATTGTACACATG
1 TTCCTACTGTACACATG
* *
985370 TCCCTATTGTACACATG
1 TTCCTACTGTACACATG
* *
985387 TTCCTATTGTACACGTG
1 TTCCTACTGTACACATG
985404 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
985421 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
*
985438 TTCCTATTGTACACATG
1 TTCCTACTGTACACATG
* *
985455 TTCCTATTGTACACGTG
1 TTCCTACTGTACACATG
*
985472 TTCTTACTGTACACATG
1 TTCCTACTGTACACATG
985489 TTCCTACTGTACACATG
1 TTCCTACTGTACACATG
*
985506 TTCCTATTGTACACATG
1 TTCCTACTGTACACATG
* *
985523 TTCCTATTGTACACGTG
1 TTCCTACTGTACACATG
*
985540 TTCCTACTGTGCACA
1 TTCCTACTGTACACA
985555 CTAAGTTTGT
Statistics
Matches: 444, Mismatches: 41, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
16 9 0.02
17 426 0.96
18 9 0.02
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.38
Consensus pattern (17 bp):
TTCCTACTGTACACATG
Found at i:1009792 original size:2 final size:2
Alignment explanation
Indices: 1009785--1009827 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1009775 TCTCAAAACT
*
1009785 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1009827 G
1 G
1009828 GGTTGATGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1017206 original size:21 final size:21
Alignment explanation
Indices: 1017182--1017222 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1017172 GTTATTTAAA
1017182 CGTGCAATAAAATTACATTTT
1 CGTGCAATAAAATTACATTTT
* **
1017203 CGTGTAATAATGTTACATTT
1 CGTGCAATAAAATTACATTT
1017223 GTGTGTTTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (21 bp):
CGTGCAATAAAATTACATTTT
Found at i:1029927 original size:16 final size:16
Alignment explanation
Indices: 1029890--1029921 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1029880 ACACTGACTG
*
1029890 AATCAAAAAATATCAA
1 AATCATAAAATATCAA
1029906 AATCATAAAATATCAA
1 AATCATAAAATATCAA
1029922 TTTCATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (16 bp):
AATCATAAAATATCAA
Found at i:1034682 original size:12 final size:11
Alignment explanation
Indices: 1034667--1034701 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1034657 TTTTTTTGTG
1034667 TTTGTTTGTTTT
1 TTTGTTT-TTTT
1034679 TTTGTTTTTTT
1 TTTGTTTTTTT
*
1034690 TTTGGTTTTTT
1 TTTGTTTTTTT
1034701 T
1 T
1034702 GCTGTAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:1034691 original size:11 final size:11
Alignment explanation
Indices: 1034667--1034701 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
1034657 TTTTTTTGTG
1034667 TTTGTTTGTTTT
1 TTTGTTT-TTTT
1034679 TTTGTTTTTTT
1 TTTGTTTTTTT
1034690 TTTGGTTTTTTT
1 TTT-GTTTTTTT
1034702 GCTGTAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:1035510 original size:2 final size:2
Alignment explanation
Indices: 1035503--1035557 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1035493 AATATCAAAG
1035503 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1035545 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
1035558 AAGTGTGTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1036792 original size:2 final size:2
Alignment explanation
Indices: 1036787--1036832 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1036777 TCTTTTTTTC
1036787 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1036829 AG AG
1 AG AG
1036833 TTCAAACAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1040777 original size:14 final size:14
Alignment explanation
Indices: 1040758--1040787 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1040748 CCGTTTTTAT
1040758 TTGTTAACATCAAG
1 TTGTTAACATCAAG
1040772 TTGTTAACATCAAG
1 TTGTTAACATCAAG
1040786 TT
1 TT
1040788 TAAAGTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (14 bp):
TTGTTAACATCAAG
Found at i:1045257 original size:21 final size:21
Alignment explanation
Indices: 1045231--1045284 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1045221 AAATATTTGT
1045231 ATCTCGTAATTACGAAAAAAG
1 ATCTCGTAATTACGAAAAAAG
** * *
1045252 ATCTCGTAAAAACGAGAAAAT
1 ATCTCGTAATTACGAAAAAAG
*
1045273 ATCTCGTTATTA
1 ATCTCGTAATTA
1045285 TGAGTTAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (21 bp):
ATCTCGTAATTACGAAAAAAG
Found at i:1050055 original size:37 final size:33
Alignment explanation
Indices: 1050028--1050092 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1050018 CAAGAGTTTT
1050028 CAAATGTAATTAATTAAATTACAATTAC-TTTG
1 CAAATGTAATTAATTAAATTACAATTACATTTG
*
1050060 CAGATGTAATTAATTAAATTACAAATTACATTT
1 CAAATGTAATTAATTAAATTAC-AATTACATTT
1050093 TCATCAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 21 0.70
33 6 0.20
34 3 0.10
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (33 bp):
CAAATGTAATTAATTAAATTACAATTACATTTG
Found at i:1051177 original size:13 final size:13
Alignment explanation
Indices: 1051159--1051183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1051149 AATTACACTC
1051159 AATTACCATTACA
1 AATTACCATTACA
1051172 AATTACCATTAC
1 AATTACCATTAC
1051184 CCCATCCCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTACCATTACA
Found at i:1066785 original size:2 final size:2
Alignment explanation
Indices: 1066773--1066829 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1066763 TTAAAAGCAT
1066773 GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1066814 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
1066830 TTGTCAGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1070078 original size:22 final size:21
Alignment explanation
Indices: 1070026--1070103 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
1070016 TAAAAGATAT
* *
1070026 ATTTTGTGATATCAGAAAATC
1 ATTTTATGATATCACAAAATC
*
1070047 ATTTTATGATATCACAAATTC
1 ATTTTATGATATCACAAAATC
* *
1070068 GATTTCT-TGATATCAAAAAATT
1 -ATTT-TATGATATCACAAAATC
*
1070090 ATTTTCTGATATCA
1 ATTTTATGATATCA
1070104 TAAGATAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 30 0.62
22 16 0.33
23 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (21 bp):
ATTTTATGATATCACAAAATC
Found at i:1070115 original size:43 final size:42
Alignment explanation
Indices: 1070019--1070126 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 42
1070009 ATTGATATAA
* *
1070019 AAGATATATTTTGTGATATCAGAAAATCATTTTATGATATCAC
1 AAGATAGATTTT-TGATATCAAAAAATCATTTTATGATATCAC
* * * *
1070062 AA-ATTCGATTTCTTGATATCAAAAAATTATTTTCTGATATCAT
1 AAGA-TAGATTT-TTGATATCAAAAAATCATTTTATGATATCAC
*
1070105 AAGATAGATTTTTTTATATCAA
1 AAGATAGA-TTTTTGATATCAA
1070127 GAATTAAAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
42 1 0.02
43 47 0.89
44 5 0.09
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (42 bp):
AAGATAGATTTTTGATATCAAAAAATCATTTTATGATATCAC
Found at i:1070161 original size:22 final size:22
Alignment explanation
Indices: 1070078--1070161 Score: 55
Period size: 22 Copynumber: 3.6 Consensus size: 22
1070068 GATTTCTTGA
*
1070078 TATCAAAAAATT-ATTTTCTGA
1 TATCAAAAAATTGATTTTCTGT
* * * *
1070099 TATCATAAGATAGATTTT-TTT
1 TATCAAAAAATTGATTTTCTGT
1070120 ATATCAAGAATTAAAGTTGATTTTCTGT
1 -TATC-A-AA--AAA-TTGATTTTCTGT
1070148 TATCAAAAAATTGA
1 TATCAAAAAATTGA
1070162 ATTATTGATA
Statistics
Matches: 46, Mismatches: 9, Indels: 15
0.66 0.13 0.21
Matches are distributed among these distances:
21 10 0.22
22 13 0.28
23 4 0.09
24 1 0.02
25 2 0.04
26 3 0.07
27 11 0.24
28 2 0.04
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (22 bp):
TATCAAAAAATTGATTTTCTGT
Found at i:1078033 original size:165 final size:165
Alignment explanation
Indices: 1077663--1078701 Score: 1361
Period size: 166 Copynumber: 6.3 Consensus size: 165
1077653 TAAAGAGCAT
* *
1077663 CTGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACCCTATATATTCCTTTGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
* * * *
1077725 TTGACCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATGATTTTCACAACTATGAATCTACA
66 TCGACCTCCCATTGTGGCCCCACCCTACCCCCGGGG-TCATGATTTTCACAACTTTGAATCTACA
*
1077790 CTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
130 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * * *
1077826 CTGGCTGATTAGTTTCTGATAAGAAGATTTTTAAAGATTTACTCTGTTTATTCCTATGTAAAAAC
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGT-TAAAC
* * * * * * *
1077891 ATCGACCTCCCATTGTGGCCCAAACCTACCCCCAGGGTTATGATTTTCAAAAATTTGAATCTACA
65 TTCGACCTCCCATTGTGGCCCCACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATCTACA
1077956 CTACCTGAGGATGC-TCCACACAAGTTTCAGCTTTC
130 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * *
1077991 CTGGCTAATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTA--CTATATAATCATATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
** * * *
1078054 TCGACC-CCCATTTGTGGCCCCATTCTACCCCCAGGGGTTATTATTTTCACAACTTTGAATCAAC
66 TCGACCTCCCA-TTGTGGCCCCACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATCTAC
*
1078118 ACTACCTGAGGATGCTTCCGA-ACAAGTTTCAGCATTGC
129 ACTACCTGAGGATGCTTCC-ACACAAGTTTCAGC-TTTC
* *
1078156 C-GGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACTCTTTATATTCCTATGTTTAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
* *
1078217 TCGATCCT-TCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATTTAC
66 TCGA-CCTCCCATTGTGGCCCCACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATCTAC
* *
1078281 ACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
129 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * *
1078318 CTGGCTGATAATTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAACCT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
* * * * *
1078383 TCGATCC-CCCATTATGGCCCTACCGTACCCCGGGGGTCATGGTTTTCACAACTTTGAATCTACA
66 TCGA-CCTCCCATTGTGGCCCCACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATCTACA
* * *
1078447 CTACATGAGGATCCTTCCACACAAGTGTCAGCTTTC
130 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * * *
1078483 CTGGCCGTTTAGTTTCTGAGAAGAAGATTTTTTAAGATTTAATCTATATATTCCTATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
* ** * *
1078548 TCGA-CTCCCCATTGTGGCCCCGCCCTACCATCGGGGATCATGATTTTCACAAATTTGTATCTAC
66 TCGACCT-CCCATTGTGGCCCCACCCTACCCCCGGGG-TCATGATTTTCACAACTTTGAATCTAC
* * * *
1078612 ATTACCTGATGATGCTTTCACACAAGTTTCATCTTTC
129 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1078649 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTC
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTC
1078702 NNNNNNNNNN
Statistics
Matches: 760, Mismatches: 94, Indels: 41
0.85 0.11 0.05
Matches are distributed among these distances:
161 24 0.03
162 34 0.04
163 181 0.24
164 33 0.04
165 212 0.28
166 242 0.32
167 34 0.04
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (165 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
TCGACCTCCCATTGTGGCCCCACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATCTACAC
TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
Found at i:1089343 original size:15 final size:15
Alignment explanation
Indices: 1089320--1089354 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1089310 TTTACACATG
*
1089320 ACTTGGTTTTAAAGT
1 ACTTTGTTTTAAAGT
*
1089335 ACTTTGTTTTTAAGT
1 ACTTTGTTTTAAAGT
1089350 ACTTT
1 ACTTT
1089355 TTAGTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (15 bp):
ACTTTGTTTTAAAGT
Found at i:1097073 original size:16 final size:16
Alignment explanation
Indices: 1097048--1097082 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1097038 ATCAATGAAC
* *
1097048 AAGTATTTAGTGCTGA
1 AAGTAGTTAGTACTGA
1097064 AAGTAGTTAGTACTGA
1 AAGTAGTTAGTACTGA
1097080 AAG
1 AAG
1097083 AAGTACTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (16 bp):
AAGTAGTTAGTACTGA
Found at i:1098383 original size:47 final size:47
Alignment explanation
Indices: 1098329--1098435 Score: 171
Period size: 47 Copynumber: 2.3 Consensus size: 47
1098319 CAAAACTGAA
*
1098329 ATAAAACCTTTCCATATTTCATATAACTTTTCATCATTAATTCCA-TC
1 ATAAAACCTTTCCATATTTCATATAACTTTTCATCATGAATT-CATTC
1098376 ATAAAACCTTTCCATATTTCATATAACTTTTCATCATGAATTCATTC
1 ATAAAACCTTTCCATATTTCATATAACTTTTCATCATGAATTCATTC
*
1098423 ATATAAAACTTTC
1 ATA-AAACCTTTC
1098436 TGGTTACAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
46 2 0.04
47 46 0.82
48 8 0.14
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.42
Consensus pattern (47 bp):
ATAAAACCTTTCCATATTTCATATAACTTTTCATCATGAATTCATTC
Found at i:1098407 original size:20 final size:20
Alignment explanation
Indices: 1098337--1098407 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 20
1098327 AAATAAAACC
1098337 TTTCCATATTTCATATAACT
1 TTTCCATATTTCATATAACT
* *
1098357 TTTCATCATTAATTCCATCATAAAACC
1 TTTC--CA-T-ATT---TCATATAACT
1098384 TTTCCATATTTCATATAACT
1 TTTCCATATTTCATATAACT
1098404 TTTC
1 TTTC
1098408 ATCATGAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
20 16 0.40
22 2 0.05
23 4 0.10
24 4 0.10
25 2 0.05
27 12 0.30
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTCCATATTTCATATAACT
Found at i:1102891 original size:161 final size:161
Alignment explanation
Indices: 1102620--1103022 Score: 641
Period size: 161 Copynumber: 2.5 Consensus size: 161
1102610 GAATTTTTCT
* *
1102620 ACCTAGATATTGTCATGATAAACCTGTATACCAAATTTCATTTCAATATG-TC--CCTTCTGGGA
1 ACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAATATGTTCATCC-TCTGCGA
* * *
1102682 AGAAATTGAGCGGAAACTGCAAAAAACTAGAATTTTTCTACGTCCAAGGGTCATAACTCTGTCGA
65 AGAAAATGAGCGGAAACTGCAAAAAACTAGAATTTTTCTACGTCCAAGGGCCATAACTATGTCGA
*
1102747 AAATAGCTCTATCATACCCAATATCGAACTTG
130 AAATAGCTCAATCATACCCAATATCGAACTTG
* *
1102779 ACCTAGATATTATCATGATAAACCTGTATACCAAATTTCGTTTCAATATGTTCATCCTCTGTGAA
1 ACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAA
* *
1102844 GAAAATGAGCGGAAACTGCAAAAACCTAGAATTTTTCTACGTCCAAGGGCCATAACTATGTGGAA
66 GAAAATGAGCGGAAACTGCAAAAAACTAGAATTTTTCTACGTCCAAGGGCCATAACTATGTCGAA
* * * *
1102909 AATTGCTCAATCGTACCCAATATTGGACTTG
131 AATAGCTCAATCATACCCAATATCGAACTTG
1102940 ACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAA
1 ACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAA
*
1103005 GAAAATGAACGGAAACTG
66 GAAAATGAGCGGAAACTG
1103023 TTGGTGGACC
Statistics
Matches: 225, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
159 48 0.21
160 2 0.01
161 173 0.77
162 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (161 bp):
ACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAA
GAAAATGAGCGGAAACTGCAAAAAACTAGAATTTTTCTACGTCCAAGGGCCATAACTATGTCGAA
AATAGCTCAATCATACCCAATATCGAACTTG
Found at i:1106873 original size:18 final size:18
Alignment explanation
Indices: 1106837--1106879 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1106827 TATGCCCCCT
* *
1106837 TCTTCTTCTCCTTCCTCC
1 TCTTCTTCACCCTCCTCC
*
1106855 TCTTCTTCACCCTCTTCC
1 TCTTCTTCACCCTCCTCC
1106873 TGCTTCT
1 T-CTTCT
1106880 CCTCTGGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (18 bp):
TCTTCTTCACCCTCCTCC
Found at i:1111020 original size:17 final size:18
Alignment explanation
Indices: 1110993--1111026 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1110983 ATCGCATAGC
1110993 CCCCTAACTCCGTCACTA
1 CCCCTAACTCCGTCACTA
1111011 CCCC-AACTCCGTCACT
1 CCCCTAACTCCGTCACT
1111027 TTCGGGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.21, C:0.53, G:0.06, T:0.21
Consensus pattern (18 bp):
CCCCTAACTCCGTCACTA
Found at i:1112069 original size:14 final size:14
Alignment explanation
Indices: 1112050--1112084 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1112040 CAGCATTATG
*
1112050 ACTGTTGGACTGGA
1 ACTGTTAGACTGGA
*
1112064 ACTGTTAGATTGGA
1 ACTGTTAGACTGGA
1112078 ACTGTTA
1 ACTGTTA
1112085 AAATCGACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (14 bp):
ACTGTTAGACTGGA
Found at i:1113219 original size:24 final size:24
Alignment explanation
Indices: 1113192--1113243 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1113182 AAGATGGAAA
*
1113192 AAGCAATGCAGGCAGTGATGTTGG
1 AAGCAATGCAGGCAGTGATGATGG
* *
1113216 AAGCGATGTAGGCAGTGATGATGG
1 AAGCAATGCAGGCAGTGATGATGG
1113240 AAGC
1 AAGC
1113244 GAAGAAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.38, T:0.19
Consensus pattern (24 bp):
AAGCAATGCAGGCAGTGATGATGG
Found at i:1115132 original size:12 final size:12
Alignment explanation
Indices: 1115115--1115150 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1115105 TGGTTTCACC
1115115 CTGTCCGTCTGT
1 CTGTCCGTCTGT
1115127 CTGTCCGTCTGT
1 CTGTCCGTCTGT
* *
1115139 CCGTCTGTCTGT
1 CTGTCCGTCTGT
1115151 AGACGCAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42
Consensus pattern (12 bp):
CTGTCCGTCTGT
Found at i:1130031 original size:27 final size:27
Alignment explanation
Indices: 1130001--1130088 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
1129991 CAAGATTATA
1130001 TTACATTAGTTACAATATCTATTGACT
1 TTACATTAGTTACAATATCTATTGACT
* ***
1130028 TTACATGTATGTATATAA-AAAGATT-A-T
1 TTACAT-TA-GT-TACAATATCTATTGACT
1130055 ATTACATTAGTTACAATATCTATTGACT
1 -TTACATTAGTTACAATATCTATTGACT
1130083 TTACAT
1 TTACAT
1130089 GTATGTATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
25 4 0.09
26 6 0.13
27 16 0.35
28 10 0.22
29 6 0.13
30 4 0.09
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (27 bp):
TTACATTAGTTACAATATCTATTGACT
Found at i:1130076 original size:55 final size:55
Alignment explanation
Indices: 1129992--1130103 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
1129982 TACTGTAGCC
1129992 AAGATTATATTACATTAGTTACAATATCTATTGACTTTACATGTATGTATATAAA
1 AAGATTATATTACATTAGTTACAATATCTATTGACTTTACATGTATGTATATAAA
1130047 AAGATTATATTACATTAGTTACAATATCTATTGACTTTACATGTATGTATATAAA
1 AAGATTATATTACATTAGTTACAATATCTATTGACTTTACATGTATGTATATAAA
1130102 AA
1 AA
1130104 TTTAACAGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (55 bp):
AAGATTATATTACATTAGTTACAATATCTATTGACTTTACATGTATGTATATAAA
Found at i:1131076 original size:14 final size:14
Alignment explanation
Indices: 1131057--1131086 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1131047 TTCCAAACCT
1131057 TCAATTAATCATAA
1 TCAATTAATCATAA
*
1131071 TCAATTAATGATAA
1 TCAATTAATCATAA
1131085 TC
1 TC
1131087 CAAAAGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (14 bp):
TCAATTAATCATAA
Found at i:1148878 original size:16 final size:16
Alignment explanation
Indices: 1148854--1148886 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1148844 CTGGGGCTAG
1148854 TTTGATATCTAAAAAT
1 TTTGATATCTAAAAAT
*
1148870 TTTGTTATCTAAAAAT
1 TTTGATATCTAAAAAT
1148886 T
1 T
1148887 CGGGTGGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTGATATCTAAAAAT
Found at i:1149016 original size:2 final size:2
Alignment explanation
Indices: 1149011--1149069 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1149001 AAACAAAATA
1149011 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1149053 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
1149070 GTAATAATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1174317 original size:165 final size:164
Alignment explanation
Indices: 1173967--1174538 Score: 739
Period size: 165 Copynumber: 3.5 Consensus size: 164
1173957 GAAACATCCA
* * * * * * ** *
1173967 CAAAGAAAATGAACATAACCTGCAAATACCTGGAATTTTTGTAAGTCCAAGGGGTATAACTCTGC
1 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
* * *** * * * * *
1174032 CGAAAATTGCTCTATCAAATCCAAAATCAAACTTGATCTAGACA--AT-AT-TTAGATAAACCTG
66 CGAAAATTGTTCGATTGTACCCAATATCAAACTTGACCTAGATATTATCATGATA-ATAAACCTG
* * * *
1174093 TATGCCAAATTTCATATCAATATGTGCACCCTCTG
130 TATACCAAATTTCATTTCAATATGTTCATCCTCTG
* * *
1174128 CGAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTGTTCTACGTCCAAGGGCCATTACTCTGT
1 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
1174193 CGAAAATTGTTCGATTGTACCCAATATCAAACTTGACCTAGATATTATCATGATAATTAAACCTG
66 CGAAAATTGTTCGATTGTACCCAATATCAAACTTGACCTAGATATTATCATGATAA-TAAACCTG
* * * *
1174258 TATACCAAATTTCATTTGAATGTGTTTATCCGCTG
130 TATACCAAATTTCATTTCAATATGTTCATCCTCTG
*
1174293 CAAAGAAAATGAGCAGATACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
* *
1174358 CGAAAATTGCTC-ATTGTACCCAATATCAAACTTGACCTAGATATTATTATGATAAT---CCTGT
66 CGAAAATTGTTCGATTGTACCCAATATCAAACTTGACCTAGATATTATCATGATAATAAACCTGT
*
1174419 ATACCAAATCTCATTTCAATATGTTCATCCTCTG
131 ATACCAAATTTCATTTCAATATGTTCATCCTCTG
1174453 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
*
1174518 CTAAAATTGCTT-GATTGTACC
66 CGAAAATTG-TTCGATTGTACC
1174539 TATATATATA
Statistics
Matches: 360, Mismatches: 44, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
160 106 0.29
161 97 0.27
163 3 0.01
164 45 0.12
165 109 0.30
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (164 bp):
CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
CGAAAATTGTTCGATTGTACCCAATATCAAACTTGACCTAGATATTATCATGATAATAAACCTGT
ATACCAAATTTCATTTCAATATGTTCATCCTCTG
Found at i:1174490 original size:160 final size:161
Alignment explanation
Indices: 1173967--1174538 Score: 761
Period size: 160 Copynumber: 3.5 Consensus size: 161
1173957 GAAACATCCA
* * * * * * ** *
1173967 CAAAGAAAATGAACATAACCTGCAAATACCTGGAATTTTTGTAAGTCCAAGGGGTATAACTCTGC
1 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
* *** * * * * * *
1174032 CGAAAATTGCTCTATCAAATCCAAAATCAAACTTGATCTAGACAATATT-TAGATAAACCTGTAT
66 CGAAAATTGCTCGATTGTACCCAATATCAAACTTGACCTAGATATTATTAT-GATAATCCTGTAT
* * * *
1174096 GCCAAATTTCATATCAATATGTGCACCCTCTG
130 ACCAAATTTCATTTCAATATGTTCATCCTCTG
* * *
1174128 CGAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTGTTCTACGTCCAAGGGCCATTACTCTGT
1 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
* *
1174193 CGAAAATTGTTCGATTGTACCCAATATCAAACTTGACCTAGATATTATCATGATAATTAAACCTG
66 CGAAAATTGCTCGATTGTACCCAATATCAAACTTGACCTAGATATTATTATGATAA-T---CCTG
* * * *
1174258 TATACCAAATTTCATTTGAATGTGTTTATCCGCTG
127 TATACCAAATTTCATTTCAATATGTTCATCCTCTG
*
1174293 CAAAGAAAATGAGCAGATACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
1174358 CGAAAATTGCTC-ATTGTACCCAATATCAAACTTGACCTAGATATTATTATGATAATCCTGTATA
66 CGAAAATTGCTCGATTGTACCCAATATCAAACTTGACCTAGATATTATTATGATAATCCTGTATA
*
1174422 CCAAATCTCATTTCAATATGTTCATCCTCTG
131 CCAAATTTCATTTCAATATGTTCATCCTCTG
1174453 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
* *
1174518 CTAAAATTGCTTGATTGTACC
66 CGAAAATTGCTCGATTGTACC
1174539 TATATATATA
Statistics
Matches: 359, Mismatches: 46, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
160 108 0.30
161 104 0.29
162 1 0.00
163 1 0.00
164 42 0.12
165 103 0.29
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (161 bp):
CAAAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
CGAAAATTGCTCGATTGTACCCAATATCAAACTTGACCTAGATATTATTATGATAATCCTGTATA
CCAAATTTCATTTCAATATGTTCATCCTCTG
Found at i:1176492 original size:14 final size:14
Alignment explanation
Indices: 1176473--1176503 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1176463 ATTTCATTTA
1176473 TCATTATTTTCAAT
1 TCATTATTTTCAAT
1176487 TCATTATTTTCAAT
1 TCATTATTTTCAAT
1176501 TCA
1 TCA
1176504 CCTAGTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (14 bp):
TCATTATTTTCAAT
Found at i:1184318 original size:2 final size:2
Alignment explanation
Indices: 1184311--1184361 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1184301 AGAAGATTTC
1184311 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1184353 AG AG AG AG A
1 AG AG AG AG A
1184362 ATTTTTAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1188870 original size:18 final size:18
Alignment explanation
Indices: 1188847--1188881 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1188837 TTTAACACAT
1188847 GATATGACATTGTATCAA
1 GATATGACATTGTATCAA
*
1188865 GATATGATATTGTATCA
1 GATATGACATTGTATCA
1188882 TATAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (18 bp):
GATATGACATTGTATCAA
Found at i:1191320 original size:16 final size:16
Alignment explanation
Indices: 1191301--1191334 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1191291 AAAAGGGTGT
1191301 CAGGAGAAAACGTACC
1 CAGGAGAAAACGTACC
1191317 CAGGAGAAAACGTACC
1 CAGGAGAAAACGTACC
1191333 CA
1 CA
1191335 ATCTCTAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.24, T:0.06
Consensus pattern (16 bp):
CAGGAGAAAACGTACC
Found at i:1191380 original size:31 final size:31
Alignment explanation
Indices: 1191342--1191403 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1191332 CCAATCTCTA
1191342 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
*
1191373 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
1191404 TATGAAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (31 bp):
GGGTACGTTTTCTCCAGGAGAAAACGTACCC
Found at i:1192290 original size:31 final size:31
Alignment explanation
Indices: 1192252--1192313 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1192242 TATTTCCATA
*
1192252 GGGTACGTTTTCTCTTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1192283 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1192314 TATAAATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGTACGTTTTCTCCTGGAGAAAACGTACCC
Found at i:1192340 original size:16 final size:16
Alignment explanation
Indices: 1192321--1192368 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
1192311 CCCTATAAAT
1192321 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
1192337 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
1192353 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
1192369 AGCATTCGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.06, C:0.25, G:0.25, T:0.44
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:1195988 original size:2 final size:2
Alignment explanation
Indices: 1195981--1196073 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
1195971 CAAGTAGGGA
1195981 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1196023 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1196065 CT CT CT CT C
1 CT CT CT CT C
1196074 CATTTACTTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Done.