Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 8 of 198
Found at i:2791039 original size:2 final size:2
Alignment explanation
Indices: 2791032--2791069 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2791022 AAATCTCATC
2791032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2791070 GCGTTGTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2791981 original size:14 final size:14
Alignment explanation
Indices: 2791962--2792000 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2791952 TTGTTTCACT
*
2791962 GAAAATGGCTTCCG
1 GAAAATGACTTCCG
* *
2791976 GAAAATGATTTCTG
1 GAAAATGACTTCCG
2791990 GAAAATGACTT
1 GAAAATGACTT
2792001 ACTTTTCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:2797947 original size:11 final size:11
Alignment explanation
Indices: 2797933--2798015 Score: 70
Period size: 11 Copynumber: 7.9 Consensus size: 11
2797923 TTTTTTTAAA
2797933 TTTTAAAATAT
1 TTTTAAAATAT
2797944 TTTTAAAATACT
1 TTTTAAAATA-T
* *
2797956 TTTT---TTAA
1 TTTTAAAATAT
2797964 TTTTAAAATAT
1 TTTTAAAATAT
2797975 TTTTAAAATACT
1 TTTTAAAATA-T
**
2797987 TTTTTTAAT-T
1 TTTTAAAATAT
2797997 TTTTAAAA-A-
1 TTTTAAAATAT
2798006 TTTTAAAATA
1 TTTTAAAATA
2798016 AAAATGGGTC
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 4 0.07
9 10 0.18
10 8 0.14
11 22 0.39
12 13 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2797959 original size:32 final size:32
Alignment explanation
Indices: 2797923--2798015 Score: 147
Period size: 31 Copynumber: 3.0 Consensus size: 32
2797913 ACTTTTTTAA
2797923 TTTTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAAATTTTAAAATATTTTTAAAATAC
2797955 TTTTTTT-AATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAAATTTTAAAATATTTTTAAAATAC
*
2797986 TTTTTTTAATTTTTTAAAA-A-TTTTAAAATA
1 TTTTTTTAA-ATTTTAAAATATTTTTAAAATA
2798016 AAAATGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
31 41 0.71
32 9 0.16
33 8 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (32 bp):
TTTTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:2798631 original size:29 final size:30
Alignment explanation
Indices: 2798574--2798637 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
2798564 ATTACTCAAT
*
2798574 TATTAGTAAATTTATTTTTGGTCACCCAAC
1 TATTAGTAAATTTAGTTTTGGTCACCCAAC
* *
2798604 TATTAGTAAATTT-GTTTTGGTCATCCAAT
1 TATTAGTAAATTTAGTTTTGGTCACCCAAC
2798633 TATTA
1 TATTA
2798638 AAAGTTACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (30 bp):
TATTAGTAAATTTAGTTTTGGTCACCCAAC
Found at i:2807105 original size:11 final size:12
Alignment explanation
Indices: 2807080--2807110 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2807070 GCGTTTAATA
*
2807080 TTTAATTATTTT
1 TTTAAATATTTT
2807092 TTTAAATATTTT
1 TTTAAATATTTT
2807104 TTTAAAT
1 TTTAAAT
2807111 TATAGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAAATATTTT
Found at i:2807413 original size:24 final size:24
Alignment explanation
Indices: 2807386--2807444 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
2807376 ATTGTAAATC
*
2807386 AATAAAATTAATACAA-ATTTTTAA
1 AATAAAATTAACACAATA-TTTTAA
*
2807410 AATAAAATTAGCACAATATTTTAA
1 AATAAAATTAACACAATATTTTAA
2807434 AATAATAATTA
1 AATAA-AATTA
2807445 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 25 0.81
25 6 0.19
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAAAATTAACACAATATTTTAA
Found at i:2807645 original size:5 final size:5
Alignment explanation
Indices: 2807635--2807665 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
2807625 GTATTACAAT
2807635 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
2807666 AATAAATGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:2807908 original size:21 final size:21
Alignment explanation
Indices: 2807855--2807908 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2807845 CCCTCTTAGA
* *
2807855 TTCATATTTTTATCTTATTTTT
1 TTCA-ATTTTTAACTTATTTTC
**
2807877 TTCAAGATTTAACTTATTTTC
1 TTCAATTTTTAACTTATTTTC
*
2807898 TTCACTTTTTA
1 TTCAATTTTTA
2807909 TATATGAGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.22, C:0.13, G:0.02, T:0.63
Consensus pattern (21 bp):
TTCAATTTTTAACTTATTTTC
Found at i:2809069 original size:4 final size:4
Alignment explanation
Indices: 2809060--2809093 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2809050 ATATACCTAA
2809060 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
2809094 TTGCGGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:2814289 original size:22 final size:22
Alignment explanation
Indices: 2814262--2814305 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2814252 TTCTTTATAT
2814262 ATTTTTATAATTTTTAAAAATAA
1 ATTTTTA-AATTTTTAAAAATAA
*
2814285 ATTTTTAAATTTTTATAAATA
1 ATTTTTAAATTTTTAAAAATA
2814306 TTTTGAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTAAATTTTTAAAAATAA
Found at i:2814323 original size:19 final size:19
Alignment explanation
Indices: 2814281--2814336 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2814271 ATTTTTAAAA
*
2814281 ATAAAT-TTTTAAATTTTT
1 ATAAATATTTTGAATTTTT
2814299 ATAAATATTTTGAATCTTTT
1 ATAAATATTTTGAAT-TTTT
*
2814319 A-AAATTATTCTGAATTTT
1 ATAAA-TATTTTGAATTTT
2814337 CTTTTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 6 0.18
19 13 0.39
20 14 0.42
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (19 bp):
ATAAATATTTTGAATTTTT
Found at i:2821782 original size:28 final size:28
Alignment explanation
Indices: 2821738--2821818 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 28
2821728 TAAATAATTT
2821738 TATATT-TCATTTATTAAAACTTTATA-TA
1 TATATTAT-ATTTATTAAAA-TTTATATTA
* * *
2821766 TATCTTATATTTTTTAATATTTATATTA
1 TATATTATATTTATTAAAATTTATATTA
2821794 TATATTATATATTATTATAAATTTA
1 TATATTATAT-TTATTA-AAATTTA
2821819 GTTTTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 6 0.14
28 25 0.58
29 6 0.14
30 6 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATTATATTTATTAAAATTTATATTA
Found at i:2826509 original size:29 final size:29
Alignment explanation
Indices: 2826476--2826532 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2826466 CTAAAGGCTT
*
2826476 GCCTATAAGGT-TTCACATGCAAGGGGTTC
1 GCCTAT-AGGTGTTCACATACAAGGGGTTC
*
2826505 GCCTATAGGTGTTCGCATACAAGGGGTT
1 GCCTATAGGTGTTCACATACAAGGGGTT
2826533 TACATGCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (29 bp):
GCCTATAGGTGTTCACATACAAGGGGTTC
Found at i:2828916 original size:25 final size:25
Alignment explanation
Indices: 2828855--2828935 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 25
2828845 GCAAGTATGA
*
2828855 AATTGAAAATAAAAATATTAATAATT
1 AATT-AAAATAAAATTATTAATAATT
2828881 AAATTAGAAATAAAATTATTTAATAATT
1 -AATTA-AAATAAAATTA-TTAATAATT
* *
2828909 AATT-AAATAGAATTAATTAGTAATT
1 AATTAAAATAAAATT-ATTAATAATT
2828934 AA
1 AA
2828936 ATTGATTAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 19 0.40
26 2 0.04
27 18 0.38
28 9 0.19
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (25 bp):
AATTAAAATAAAATTATTAATAATT
Found at i:2830317 original size:36 final size:35
Alignment explanation
Indices: 2830223--2830320 Score: 90
Period size: 36 Copynumber: 2.7 Consensus size: 35
2830213 GCGCGGAGCT
* *
2830223 CATATTACTTTGGACATACCGATGAAGTGCGGATCA
1 CATATTACTTTGGACATACCAATG-AGTGCGGAACA
* * ** *
2830259 CACATTACTTCGGTTTATACCAATGAG-GCGTGAAACG
1 CATATTACTTTGG-ACATACCAATGAGTGCG-G-AACA
2830296 CATATTACTTTGGACATACCAATGA
1 CATATTACTTTGGACATACCAATGA
2830321 TGCATTAGGT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
35 3 0.06
36 24 0.50
37 21 0.44
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (35 bp):
CATATTACTTTGGACATACCAATGAGTGCGGAACA
Found at i:2831238 original size:2 final size:2
Alignment explanation
Indices: 2831202--2831226 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2831192 ATGTACATAC
2831202 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2831227 CACTCCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2836258 original size:11 final size:11
Alignment explanation
Indices: 2836242--2836267 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2836232 TGTGAATTTA
2836242 AAAAAAAAAAG
1 AAAAAAAAAAG
2836253 AAAAAAAAAAG
1 AAAAAAAAAAG
2836264 AAAA
1 AAAA
2836268 GGAAGATGAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:2840499 original size:22 final size:23
Alignment explanation
Indices: 2840474--2840516 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2840464 ACTAATGTTC
*
2840474 AATTTGGCACTTG-ATTTTTTCT
1 AATTTGACACTTGAATTTTTTCT
*
2840496 AATTTGATACTTGAATTTTTT
1 AATTTGACACTTGAATTTTTT
2840517 TGCCCTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.23, C:0.09, G:0.12, T:0.56
Consensus pattern (23 bp):
AATTTGACACTTGAATTTTTTCT
Found at i:2841048 original size:531 final size:531
Alignment explanation
Indices: 2840006--2841069 Score: 1871
Period size: 531 Copynumber: 2.0 Consensus size: 531
2839996 TGCTACTACT
* *
2840006 GTGATCGTTTGTTGTTGTATCCTGGGAGACAGACGTCTAACGTTACTCAAAGCATCGAGGAGTGG
1 GTGATCGTTTGTTGTTGTATCCTGGGAGACAGACGTCCAACGTTACTCAAAGCATCGAGGAGAGG
* * * * *
2840071 ATGAATTTGTCTTAAGGAAACTGTTTATATAGGCATCAACAAAATTCTTCTTCTAATTTTTAACT
66 ACGAATTTGTCTTAAAGAAACAGTTTATACAGGCATCAACAAAATTCTTCTTCTAATTTTCAACT
* *
2840136 TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCTACTGCGTTGTATTGCATTGTCATTGTTACT
131 TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCCACTGCATTGTATTGCATTGTCATTGTTACT
*
2840201 GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTTCAATCAAGGTGAAGCTAGAAA
196 GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTCCAATCAAGGTGAAGCTAGAAA
*
2840266 ATTTGTTTGGGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCACAATT
261 ATTTGTTTGAGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCACAATT
* * * *
2840331 TTAATAGCCTATACTTTTTTTTTATAAATTTTAAAGGATTAAATCAATTTTTTAACATTTTGATT
326 TTAATAGCATATACTATATTTTTATAAATTTTAAAGGATTAAATCAAATTTTTAACATTTTGATT
*
2840396 TAAAATTTTATAAATTATAAAAAGGCCTAAATGGAATTTTTTTTTATTTTAAGGGGTCGGGGCAT
391 TAAAATTTTATAAATTATAAAAAGGCCTAAATGGAATATTTTTTTATTTTAAGGGGTCGGGGCAT
* *
2840461 GCCACTAATGTTCAATTTGGCACTTGATTTTTTCTAATTTGATACTTGAATTTTTTTGCCCTGGT
456 GCCACTAATGTTCAAATTGGCACCTGATTTTTTCTAATTTGATACTTGAATTTTTTTGCCCTGGT
2840526 TAAATACCAAA
521 TAAATACCAAA
* *
2840537 GTGATCTTTTGTTGTTGTATCCTGGGAGACAGACGTCCAACGTTACTTAAAGCATCGAGGAGAGG
1 GTGATCGTTTGTTGTTGTATCCTGGGAGACAGACGTCCAACGTTACTCAAAGCATCGAGGAGAGG
2840602 ACGAATTTGTCTTAAAGAAACAGTTTATACAGGCATCAACAAAATTCTTCTTCTAATTTTCAACT
66 ACGAATTTGTCTTAAAGAAACAGTTTATACAGGCATCAACAAAATTCTTCTTCTAATTTTCAACT
2840667 TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCCACTGCATTGTATTGCATTGTCATTGTTACT
131 TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCCACTGCATTGTATTGCATTGTCATTGTTACT
2840732 GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTCCAATCAAGGTGAAGCTAGAAA
196 GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTCCAATCAAGGTGAAGCTAGAAA
* * *
2840797 TTTTGTTTGAGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCTCCATT
261 ATTTGTTTGAGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCACAATT
*
2840862 TTAATAGCATATA-TATATTTTTATAAATTTTAAAGGATTAAATCAAATTTTTATCATTTTGATT
326 TTAATAGCATATACTATATTTTTATAAATTTTAAAGGATTAAATCAAATTTTTAACATTTTGATT
*
2840926 TAAAATTTTATAAATTATAAAAAGGCCTAAATGAGAA-ATTTTTTTATTTTAGGGGGTCGGGGCA
391 TAAAATTTTATAAATTATAAAAAGGCCTAAATG-GAATATTTTTTTATTTTAAGGGGTCGGGGCA
2840990 TGCCACTAATGTTCAAATTGGCACCTGATTTTTTCTAATTTGATACTTGAATTTTTTTTGCCCTG
455 TGCCACTAATGTTCAAATTGGCACCTGATTTTTTCTAATTTGATACTTGAA-TTTTTTTGCCCTG
2841055 GTTAAATACCAAA
519 GTTAAATACCAAA
2841068 GT
1 GT
2841070 TTAAATTCTA
Statistics
Matches: 506, Mismatches: 25, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
530 154 0.30
531 352 0.70
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (531 bp):
GTGATCGTTTGTTGTTGTATCCTGGGAGACAGACGTCCAACGTTACTCAAAGCATCGAGGAGAGG
ACGAATTTGTCTTAAAGAAACAGTTTATACAGGCATCAACAAAATTCTTCTTCTAATTTTCAACT
TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCCACTGCATTGTATTGCATTGTCATTGTTACT
GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTCCAATCAAGGTGAAGCTAGAAA
ATTTGTTTGAGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCACAATT
TTAATAGCATATACTATATTTTTATAAATTTTAAAGGATTAAATCAAATTTTTAACATTTTGATT
TAAAATTTTATAAATTATAAAAAGGCCTAAATGGAATATTTTTTTATTTTAAGGGGTCGGGGCAT
GCCACTAATGTTCAAATTGGCACCTGATTTTTTCTAATTTGATACTTGAATTTTTTTGCCCTGGT
TAAATACCAAA
Found at i:2842983 original size:21 final size:21
Alignment explanation
Indices: 2842937--2842985 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2842927 AAACTATCCA
*
2842937 AAATAATATAAAATATAATAT
1 AAATAATATAAAATATAAAAT
*
2842958 TAATAATATTAAAATA-AAAAT
1 AAATAATA-TAAAATATAAAAT
2842979 AAATAAT
1 AAATAAT
2842986 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAATATAAAATATAAAAT
Found at i:2846629 original size:16 final size:16
Alignment explanation
Indices: 2846610--2846641 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2846600 AACACGAAGG
2846610 GTCAAATGCTGCCATT
1 GTCAAATGCTGCCATT
2846626 GTCAAATGCTGCCATT
1 GTCAAATGCTGCCATT
2846642 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
GTCAAATGCTGCCATT
Found at i:2859230 original size:7 final size:7
Alignment explanation
Indices: 2859218--2859259 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
2859208 TATGATGCAT
2859218 GCAATGG
1 GCAATGG
2859225 GCAATGG
1 GCAATGG
2859232 GCAATGG
1 GCAATGG
2859239 GCAATGG
1 GCAATGG
2859246 GCAATGG
1 GCAATGG
2859253 GCAATGG
1 GCAATGG
2859260 CTGTATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14
Consensus pattern (7 bp):
GCAATGG
Found at i:2870825 original size:3 final size:3
Alignment explanation
Indices: 2870817--2870863 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2870807 TGTCTTGAGG
2870817 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2870864 GATAGGTAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2871577 original size:35 final size:35
Alignment explanation
Indices: 2871524--2871596 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
2871514 TTGGTGTCCA
* * * *
2871524 TTGCATATTAGATGTACAAACACTTAACATATTTG
1 TTGCATATCAAATCTACAAACACCTAACATATTTG
2871559 TTGCATATCAAATCTACAAACACCTAACATATTTG
1 TTGCATATCAAATCTACAAACACCTAACATATTTG
2871594 TTG
1 TTG
2871597 TTATGTCACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (35 bp):
TTGCATATCAAATCTACAAACACCTAACATATTTG
Found at i:2882300 original size:64 final size:64
Alignment explanation
Indices: 2882224--2882351 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
2882214 ATCTACATTA
* *
2882224 ATTTCACGTAAGTGTTATCAAAGGTTTAA-TTTCATAATATGGTTGAGATTAAAGCTAATAATGG
1 ATTTCACATAAGTGTTATCAAAGG-TTAATTTTCATAATATGGCTGAGATTAAAGCTAATAATGG
*
2882288 ATTTCACATAAGTGTTATCAAAGGTTAATTTTCATAATATGGCTGAGATTAGAGCTAATAATGG
1 ATTTCACATAAGTGTTATCAAAGGTTAATTTTCATAATATGGCTGAGATTAAAGCTAATAATGG
2882352 GCCGATTTCG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 4 0.07
64 56 0.93
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (64 bp):
ATTTCACATAAGTGTTATCAAAGGTTAATTTTCATAATATGGCTGAGATTAAAGCTAATAATGG
Found at i:2887776 original size:14 final size:16
Alignment explanation
Indices: 2887741--2887782 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
2887731 TATATATCAT
2887741 TATTAAATTATATTTAA
1 TATT-AATTATATTTAA
2887758 TATTAATTAT-TTTAA
1 TATTAATTATATTTAA
*
2887773 -ATTAGTTATA
1 TATTAATTATA
2887783 AATTCTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
16 6 0.26
17 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATTAATTATATTTAA
Found at i:2888629 original size:16 final size:16
Alignment explanation
Indices: 2888604--2888657 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
2888594 TTGATTTGCT
*
2888604 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
2888620 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
2888636 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
2888652 AATACA
1 ATTACA
2888658 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:2888755 original size:16 final size:16
Alignment explanation
Indices: 2888734--2888773 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2888724 ATATAGTCTA
*
2888734 TTTGAGTTAGGATAAT
1 TTTGAGTTAAGATAAT
*
2888750 TTTGAGTTAAGATAGT
1 TTTGAGTTAAGATAAT
*
2888766 TTCGAGTT
1 TTTGAGTT
2888774 CATGTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.45
Consensus pattern (16 bp):
TTTGAGTTAAGATAAT
Found at i:2906201 original size:31 final size:31
Alignment explanation
Indices: 2906134--2906201 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2906124 TGAAAAACTT
* * * *
2906134 AAAGTTCAGGCCTCAACGTGAGAACAATTGC
1 AAAGTTCAGGCCCCAACATGAGAACAAGTAC
*
2906165 AAAGTTCAGGCCCCAATATGAGAACAAGTAC
1 AAAGTTCAGGCCCCAACATGAGAACAAGTAC
*
2906196 CAAGTT
1 AAAGTT
2906202 TAGGAACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (31 bp):
AAAGTTCAGGCCCCAACATGAGAACAAGTAC
Found at i:2915481 original size:6 final size:6
Alignment explanation
Indices: 2915470--2915495 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2915460 TTTTATTGCC
2915470 AATGCT AATGCT AATGCT AATGCT AA
1 AATGCT AATGCT AATGCT AATGCT AA
2915496 GTGCCAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (6 bp):
AATGCT
Found at i:2922089 original size:30 final size:30
Alignment explanation
Indices: 2922009--2922089 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 30
2921999 AATATGTATG
* *
2922009 ATTGAATCAAATTAAAGTTTTATGTATACA
1 ATTGAACCAAATTAAAGTTTCATGTATACA
* ** * *
2922039 TTTGAACCACAACCAAAGTTTCATGTGTATA
1 ATTGAACCA-AATTAAAGTTTCATGTATACA
*
2922070 ATTGCACCAAATTAAAGTTT
1 ATTGAACCAAATTAAAGTTT
2922090 ACGTACCAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
30 16 0.41
31 23 0.59
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (30 bp):
ATTGAACCAAATTAAAGTTTCATGTATACA
Found at i:2923138 original size:27 final size:25
Alignment explanation
Indices: 2923100--2923153 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
2923090 CACTTACATC
* * *
2923100 TTTTATTAATTTGACTTTTATTCTT
1 TTTTATTAATTTCACCTTTAATCTT
2923125 TTTTAGTTAAATTTCACCTTTAATCTT
1 TTTTA-TT-AATTTCACCTTTAATCTT
2923152 TT
1 TT
2923154 AAAAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 2 0.08
27 17 0.71
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTATTAATTTCACCTTTAATCTT
Found at i:2931773 original size:57 final size:57
Alignment explanation
Indices: 2931680--2931791 Score: 145
Period size: 57 Copynumber: 2.0 Consensus size: 57
2931670 CATGCACCCA
** * * *
2931680 AAAAATAATTTGGATTAAGGGCGTAAAAAGCACTCAAA-TTTAAAAAAATAATAAATT
1 AAAAATAATTACGATTAAGGACATAAAAAACACTCAAACTTTAAAAAAA-AATAAATT
* *
2931737 AAAAATAATTACGATTAAGGATATAAAAAACTCTCAAACTTTAAAAAAAAATAAA
1 AAAAATAATTACGATTAAGGACATAAAAAACACTCAAACTTTAAAAAAAAATAAA
2931792 ACAGAAGCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 37 0.79
58 10 0.21
ACGTcount: A:0.58, C:0.08, G:0.09, T:0.25
Consensus pattern (57 bp):
AAAAATAATTACGATTAAGGACATAAAAAACACTCAAACTTTAAAAAAAAATAAATT
Found at i:2933546 original size:2 final size:2
Alignment explanation
Indices: 2933539--2933565 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2933529 TTTACGGCAC
2933539 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2933566 TTAACATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2933776 original size:6 final size:6
Alignment explanation
Indices: 2933765--2933789 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2933755 CCAGCAGGCC
2933765 TGTATA TGTATA TGTATA TGTATA T
1 TGTATA TGTATA TGTATA TGTATA T
2933790 ATGCCTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:2950212 original size:14 final size:14
Alignment explanation
Indices: 2950185--2950228 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2950175 TTTACAACAC
*
2950185 ATACGAATAAATAT
1 ATACAAATAAATAT
* *
2950199 TTACAAATATATAT
1 ATACAAATAAATAT
2950213 ATACAAATACAATAT
1 ATACAAATA-AATAT
2950228 A
1 A
2950229 CCAGTAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (14 bp):
ATACAAATAAATAT
Found at i:2950982 original size:3 final size:3
Alignment explanation
Indices: 2950913--2950965 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
2950903 TTGATGGTGT
2950913 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2950961 TAA TA
1 TAA TA
2950966 CACAATGCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2955595 original size:13 final size:14
Alignment explanation
Indices: 2955565--2955597 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2955555 CAATATTATT
2955565 ATATTAATAATAAA
1 ATATTAATAATAAA
*
2955579 ATATTAAT-ATCAA
1 ATATTAATAATAAA
2955592 ATATTA
1 ATATTA
2955598 TCTATTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTAATAATAAA
Found at i:2955891 original size:20 final size:18
Alignment explanation
Indices: 2955849--2955897 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
2955839 ATCCTCACCC
2955849 TTAATATTTTCTACTCAT
1 TTAATATTTTCTACTCAT
*
2955867 TTAATTTTTTCTACTCATCT
1 TTAATATTTTCTACTCA--T
2955887 TTAATATTTTC
1 TTAATATTTTC
2955898 AATCTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 16 0.59
20 11 0.41
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTTTCTACTCAT
Found at i:2956402 original size:18 final size:17
Alignment explanation
Indices: 2956379--2956412 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2956369 TTTATTTTTA
2956379 TTTTTAAATTTTAAAATG
1 TTTTT-AATTTTAAAATG
*
2956397 TTTTTATTTTTAAAAT
1 TTTTTAATTTTAAAAT
2956413 AATTTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTTAATTTTAAAATG
Found at i:2958620 original size:24 final size:22
Alignment explanation
Indices: 2958593--2958650 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
2958583 TTTTTATTAA
2958593 AATATTTATATATAAGCACATTGT
1 AATATTTATATATAAGCAC-TT-T
*
2958617 AATATTATATATTATAATCACTTT
1 AATATT-TATA-TATAAGCACTTT
2958641 AAT-TTTATAT
1 AATATTTATAT
2958651 GTTATAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 1 0.03
22 4 0.13
23 2 0.06
24 10 0.32
25 6 0.19
26 8 0.26
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (22 bp):
AATATTTATATATAAGCACTTT
Found at i:2967100 original size:26 final size:26
Alignment explanation
Indices: 2967047--2967100 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
2967037 TAAACTAAAA
**
2967047 TTTTTAAAAGTATTTCTCAAAATTAC
1 TTTTTAAAAGTATTTCTCAAAAGCAC
* * *
2967073 TTTTTTAAAGTATTTTTGAAAAGCAC
1 TTTTTAAAAGTATTTCTCAAAAGCAC
2967099 TT
1 TT
2967101 CTCAAAAGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (26 bp):
TTTTTAAAAGTATTTCTCAAAAGCAC
Found at i:2968049 original size:2 final size:2
Alignment explanation
Indices: 2968042--2968069 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2968032 AAAATTATGA
2968042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2968070 GCTTGTGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2968653 original size:11 final size:11
Alignment explanation
Indices: 2968639--2968693 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
2968629 TAATTTTTAA
2968639 TTTTAAAATAT
1 TTTTAAAATAT
2968650 TTTTAAAATACT
1 TTTTAAAATA-T
* *
2968662 TTTT-TATTAT
1 TTTTAAAATAT
*
2968672 TTTTTAAATAT
1 TTTTAAAATAT
2968683 TTTTAAAATAT
1 TTTTAAAATAT
2968694 ATATATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 5 0.14
11 27 0.73
12 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2972959 original size:37 final size:37
Alignment explanation
Indices: 2972900--2973045 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
2972890 TACGTATGAT
*
2972900 CACTTATCAC-TTG-TCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
2972935 CACCTATCACTTTATTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2972972 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
2973009 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2973046 TAAAGCTATC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 2 0.02
37 92 0.89
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:2973062 original size:46 final size:46
Alignment explanation
Indices: 2973009--2973231 Score: 266
Period size: 52 Copynumber: 4.6 Consensus size: 46
2972999 TAAGTGTAGC
* *
2973009 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* * *
2973055 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
*
2973101 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* *
2973153 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
2973205 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2973232 AGTACTCAAA
Statistics
Matches: 162, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
46 69 0.43
49 1 0.01
50 1 0.01
51 3 0.02
52 88 0.54
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
Found at i:2973128 original size:52 final size:52
Alignment explanation
Indices: 2973052--2973225 Score: 267
Period size: 52 Copynumber: 3.3 Consensus size: 52
2973042 TAGCTAAAGC
* * *
2973052 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
2973105 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* ** *
2973157 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
2973209 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
2973226 ATCAGAAGTA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
52 94 0.84
53 18 0.16
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:2973197 original size:98 final size:98
Alignment explanation
Indices: 2973008--2973231 Score: 253
Period size: 98 Copynumber: 2.3 Consensus size: 98
2972998 ATAAGTGTAG
* * * *
2973008 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
*
2973073 TTGATCAGATAAGTATAGCCGAAGCTATCA-CTTA
66 TTGATCAGATAAGTATAGCCGAAGCTA-AAGC-TA
* * *
2973107 TCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT-CCAC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
* * *
2973170 TTG-TCACTTGATCAG-ATAAG-TGTAGCTAAAGCTA
66 TTGATCA---GATAAGTAT-AGCCGAAGCTAAAGCTA
2973204 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
2973232 AGTACTCAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
96 3 0.03
97 17 0.16
98 70 0.66
99 16 0.15
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
TTGATCAGATAAGTATAGCCGAAGCTAAAGCTA
Found at i:2976094 original size:14 final size:13
Alignment explanation
Indices: 2976074--2976139 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
2976064 TTGCAATTTG
2976074 ATTCTCAATTTCTT
1 ATTCTCAATTT-TT
*
2976088 GTTCTCAATCTTTT
1 ATTCTCAAT-TTTT
**
2976102 ATTCTCAATTGTCA
1 ATTCTCAATT-TTT
*
2976116 ATTCTCGATTTTTT
1 ATTCTC-AATTTTT
*
2976130 ATTCTAAATT
1 ATTCTCAATT
2976140 CCCAATTTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
13 4 0.10
14 31 0.77
15 5 0.12
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (13 bp):
ATTCTCAATTTTT
Found at i:2976120 original size:28 final size:28
Alignment explanation
Indices: 2976089--2976165 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
2976079 CAATTTCTTG
* * **
2976089 TTCTCAATCTTTTATTCTCAATTGTCAA
1 TTCTCAATTTTTTATTCTAAATTCCCAA
*
2976117 TTCTCGATTTTTTATTCTAAATTCCCAA
1 TTCTCAATTTTTTATTCTAAATTCCCAA
*
2976145 TT-TCAATTTTTT-TTTTAAATT
1 TTCTCAATTTTTTATTCTAAATT
2976166 TTTCTAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 8 0.19
27 9 0.21
28 25 0.60
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.56
Consensus pattern (28 bp):
TTCTCAATTTTTTATTCTAAATTCCCAA
Found at i:2976330 original size:52 final size:52
Alignment explanation
Indices: 2976264--2976368 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
2976254 TAACAAACGG
* *
2976264 TAAGAAAATGTTATTAAATTATTTAATTTT-AATCAGTTAGTTATTATGATGT
1 TAAGAAAATATTATTAAATTATTTAATTTTAAAT-AGTTAATTATTATGATGT
* *
2976316 TAAGAAACTATTATTAAATTATTTAATTTTAAATAGTTAATTATTATGTTGT
1 TAAGAAAATATTATTAAATTATTTAATTTTAAATAGTTAATTATTATGATGT
2976368 T
1 T
2976369 TAGATTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 45 0.94
53 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.50
Consensus pattern (52 bp):
TAAGAAAATATTATTAAATTATTTAATTTTAAATAGTTAATTATTATGATGT
Found at i:2980489 original size:6 final size:6
Alignment explanation
Indices: 2980478--2980526 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
2980468 TCTGAAATCG
2980478 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
2980526 A
1 A
2980527 ACTTGTTCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:2982152 original size:13 final size:13
Alignment explanation
Indices: 2982130--2982160 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2982120 TTTTATTTCG
*
2982130 AATAACTAAGGAA
1 AATAAATAAGGAA
2982143 AATAAATAAGGAA
1 AATAAATAAGGAA
2982156 AATAA
1 AATAA
2982161 TGATTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.13, T:0.16
Consensus pattern (13 bp):
AATAAATAAGGAA
Found at i:2982971 original size:31 final size:28
Alignment explanation
Indices: 2982927--2982994 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 28
2982917 AGTAAGAGTA
*
2982927 AAATTATATTTTAATTTTTCAAAAATGATAT
1 AAATTATAATTTAATTTTT-AAAAAT--TAT
*
2982958 AAATTTTAATTTAATTTTTAAAAATTAT
1 AAATTATAATTTAATTTTTAAAAATTAT
2982986 AAATATATA
1 AAAT-TATA
2982995 TTATATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.21
29 3 0.09
30 6 0.18
31 17 0.52
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
AAATTATAATTTAATTTTTAAAAATTAT
Found at i:2986444 original size:21 final size:21
Alignment explanation
Indices: 2986418--2986472 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
2986408 AACAGCGGTG
*
2986418 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
2986439 GCGGTGAGATTAGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
2986460 GCGGTGAGATTAG
1 GCGGTGAGATTAG
2986473 AAATAATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:2990356 original size:31 final size:30
Alignment explanation
Indices: 2990320--2990709 Score: 382
Period size: 30 Copynumber: 12.6 Consensus size: 30
2990310 CTACTTTATA
2990320 ATTTTTTTATTTTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATAT
*
2990350 ATTTTTTTACTTTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATAT
* * ** * *
2990380 ATATATATATATATATATATATATTTAAAATACACTACAT
1 AT-T-T-T-T-T-TATTTTTA-AAATACACTACA-T--AT
* *
2990420 ATATATTTTTTATTTTTAAAATACACTACATAT
1 ATTTTTT---TATTTTTAAAATACACTACATAT
*
2990453 ATTTTTTTACTTTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATAT
*
2990483 A------TATATTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATAT
2990507 ATATTTTTTATTTTTAAAATACACTACATAT
1 AT-TTTTTTATTTTTAAAATACACTACATAT
*
2990538 ATTTTTTTTACTTTTAAAATACACTACATAT
1 A-TTTTTTTATTTTTAAAATACACTACATAT
* * *
2990569 ATATATATA-TTTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATAT
* *
2990598 ATATATTTTT-TATTTTAAAATATAGTACATAT
1 AT-T-TTTTTAT-TTTTAAAATACACTACATAT
2990630 ATTTTTTTTATTTTTAAAATACACTACATAT
1 A-TTTTTTTATTTTTAAAATACACTACATAT
*
2990661 ATTTTTTTATTTTTAAAATACACTACATGT
1 ATTTTTTTATTTTTAAAATACACTACATAT
*
2990691 ATTTTTTAATTTTTAAAAT
1 ATTTTTTTATTTTTAAAAT
2990710 TTTAAATACA
Statistics
Matches: 298, Mismatches: 36, Indels: 52
0.77 0.09 0.13
Matches are distributed among these distances:
24 22 0.07
29 22 0.07
30 105 0.35
31 79 0.27
32 23 0.08
33 9 0.03
34 1 0.00
35 3 0.01
36 14 0.05
37 14 0.05
38 2 0.01
40 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (30 bp):
ATTTTTTTATTTTTAAAATACACTACATAT
Found at i:2990383 original size:2 final size:2
Alignment explanation
Indices: 2990376--2990403 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2990366 AATACACTAC
2990376 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2990404 TTAAAATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2990506 original size:22 final size:23
Alignment explanation
Indices: 2990464--2990512 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
2990454 TTTTTTTACT
2990464 TTTAAAATACACTACATATATATA
1 TTTAAAATACACTACA-ATATATA
2990488 TTTAAAATACACTAC-ATATATA
1 TTTAAAATACACTACAATATATA
2990510 TTT
1 TTT
2990513 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 10 0.40
24 15 0.60
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAAATACACTACAATATATA
Found at i:2990694 original size:30 final size:30
Alignment explanation
Indices: 2990403--2990709 Score: 405
Period size: 31 Copynumber: 10.3 Consensus size: 30
2990393 TATATATATA
2990403 TTTAAAATACACTACATATATATTTTTTATT
1 TTTAAAATACACTACATATAT-TTTTTTATT
*
2990434 TTTAAAATACACTACATATATTTTTTTACT
1 TTTAAAATACACTACATATATTTTTTTATT
*
2990464 TTTAAAATACACTACATATA------TATA
1 TTTAAAATACACTACATATATTTTTTTATT
2990488 TTTAAAATACACTACATATATATTTTTTATT
1 TTTAAAATACACTACATATAT-TTTTTTATT
*
2990519 TTTAAAATACACTACATATATTTTTTTTACT
1 TTTAAAATACACTACATATA-TTTTTTTATT
* * *
2990550 TTTAAAATACACTACATATATATATATA-T
1 TTTAAAATACACTACATATATTTTTTTATT
2990579 TTTAAAATACACTACATATATATATTTTT-TAT
1 TTTAAAATACACTACATATAT-T-TTTTTAT-T
* *
2990611 TTTAAAATATAGTACATATATTTTTTTTATT
1 TTTAAAATACACTACATATA-TTTTTTTATT
2990642 TTTAAAATACACTACATATATTTTTTTATT
1 TTTAAAATACACTACATATATTTTTTTATT
* *
2990672 TTTAAAATACACTACATGTATTTTTTAATT
1 TTTAAAATACACTACATATATTTTTTTATT
2990702 TTTAAAAT
1 TTTAAAAT
2990710 TTTAAATACA
Statistics
Matches: 245, Mismatches: 17, Indels: 29
0.84 0.06 0.10
Matches are distributed among these distances:
24 22 0.09
29 22 0.09
30 79 0.32
31 99 0.40
32 22 0.09
33 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.50
Consensus pattern (30 bp):
TTTAAAATACACTACATATATTTTTTTATT
Found at i:2990776 original size:16 final size:16
Alignment explanation
Indices: 2990737--2990777 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2990727 TTCTCCACTC
2990737 CCATCTCCCCTCTTCCA
1 CCAT-TCCCCTCTTCCA
*
2990754 TCATTCCCCTCTTCCA
1 CCATTCCCCTCTTCCA
*
2990770 CCGTTCCC
1 CCATTCCC
2990778 TCCTCCCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.10, C:0.56, G:0.02, T:0.32
Consensus pattern (16 bp):
CCATTCCCCTCTTCCA
Found at i:2990821 original size:60 final size:60
Alignment explanation
Indices: 2990749--2990931 Score: 232
Period size: 60 Copynumber: 3.1 Consensus size: 60
2990739 ATCTCCCCTC
* *
2990749 TTCCATCATTCCCCTCTTCCACCGTTCCCTCCTCCCATTTCCTATTCCCATGCAATACCCA
1 TTCCAT-ATTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCA
* * * * *
2990810 TTCCA-ATTTCCC-ATTCCACCGTGCCGTCCTCCCATTTCCCATTCCCAT-C--TCCCCTC
1 TTCCATATTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCC-A
2990866 TTCCATCGATTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCA
1 TTCCAT--ATTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCA
2990928 TTCC
1 TTCC
2990932 CATTATCAAC
Statistics
Matches: 102, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
55 4 0.04
56 5 0.05
57 1 0.01
58 32 0.31
59 12 0.12
60 34 0.33
61 6 0.06
62 4 0.04
63 4 0.04
ACGTcount: A:0.15, C:0.49, G:0.05, T:0.32
Consensus pattern (60 bp):
TTCCATATTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCA
Found at i:2990850 original size:28 final size:28
Alignment explanation
Indices: 2990815--2990914 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 28
2990805 ACCCATTCCA
*
2990815 ATTTCCCATTCCACCGTGCCGTCCTCCC
1 ATTTCCCATTCCACCGTGCCCTCCTCCC
* * *
2990843 ATTTCCCATTCCCATC-TCCCCTCTTCCATC
1 ATTTCCCATT-CCACCGTGCCCTCCTCC--C
* *
2990873 GATTCCCCTCTTCCACCGTGCCCTCCTCCC
1 -ATTTCCC-ATTCCACCGTGCCCTCCTCCC
2990903 ATTTCCCATTCC
1 ATTTCCCATTCC
2990915 CATGCAATAC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 22 0.40
29 10 0.18
30 2 0.04
31 10 0.18
32 11 0.20
ACGTcount: A:0.11, C:0.51, G:0.06, T:0.32
Consensus pattern (28 bp):
ATTTCCCATTCCACCGTGCCCTCCTCCC
Found at i:2993659 original size:21 final size:20
Alignment explanation
Indices: 2993635--2993697 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
2993625 GAACAAAGTA
*
2993635 AAAAAGAGGGGAGAAACTAGC
1 AAAAAGA-GGGAGAAACCAGC
* *
2993656 AAAAACGAGGGACAAACCAGT
1 AAAAA-GAGGGAGAAACCAGC
*
2993677 AAACA-AGGGAGAAACCAGC
1 AAAAAGAGGGAGAAACCAGC
2993696 AA
1 AA
2993698 GAACGAGGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 14 0.40
21 19 0.54
22 2 0.06
ACGTcount: A:0.54, C:0.16, G:0.27, T:0.03
Consensus pattern (20 bp):
AAAAAGAGGGAGAAACCAGC
Found at i:2993685 original size:19 final size:19
Alignment explanation
Indices: 2993658--2993694 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2993648 AAACTAGCAA
*
2993658 AAACGAGGGACAAACCAGT
1 AAACAAGGGACAAACCAGT
*
2993677 AAACAAGGGAGAAACCAG
1 AAACAAGGGACAAACCAG
2993695 CAAGAACGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.19, G:0.27, T:0.03
Consensus pattern (19 bp):
AAACAAGGGACAAACCAGT
Found at i:2995559 original size:13 final size:13
Alignment explanation
Indices: 2995541--2995602 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
2995531 TTCTTCATTG
2995541 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
2995554 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
* *
2995567 CTGTGGAAAAGTA
1 CTTTTGAAAAGTA
* *
2995580 CTTTTGAGAAGTG
1 CTTTTGAAAAGTA
*
2995593 TTTTTGAAAA
1 CTTTTGAAAA
2995603 TTTTGAGTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:2997741 original size:72 final size:73
Alignment explanation
Indices: 2997651--2997825 Score: 230
Period size: 72 Copynumber: 2.4 Consensus size: 73
2997641 AAAATCACAT
* * *
2997651 ATAAACAACTATTGATAAAACTAATTTAGTA-AAAAATAAGTAGAATATAAATTCAATATCTAAA
1 ATAAACAACTATTGATAAAACTAATTTAGCACAAAAATAAGTAGAACATAAATTCAATATCCAAA
*
2997715 GACCAAAC
66 AACCAAAC
* * * *
2997723 ATAAACAACTTTTAATAAAACTAGA-TTA-CACATAAATAAGTAGAACATAAGTTCAATATCCAA
1 ATAAACAACTATTGATAAAACTA-ATTTAGCACAAAAATAAGTAGAACATAAATTCAATATCCAA
2997786 AAACCAAAC
65 AAACCAAAC
* *
2997795 ATAAATAACTATTGATAAAACTAGTTTAGCA
1 ATAAACAACTATTGATAAAACTAATTTAGCA
2997826 TTGTTGTTTA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
71 1 0.01
72 83 0.95
73 3 0.03
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (73 bp):
ATAAACAACTATTGATAAAACTAATTTAGCACAAAAATAAGTAGAACATAAATTCAATATCCAAA
AACCAAAC
Found at i:2998271 original size:18 final size:18
Alignment explanation
Indices: 2998250--2998297 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2998240 TCCATCAATT
2998250 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
2998268 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
*
2998286 TAAACATCATTT
1 TGAACATCATTT
2998298 CTCATATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:3000851 original size:25 final size:25
Alignment explanation
Indices: 3000773--3000845 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
3000763 AGAGGAACAA
* *
3000773 AGCACCAGCAGAGGAACAAATAACC
1 AGCACCAGTAGAGGAACAAAGAACC
* *
3000798 AACACCAGTAGAAGAACAAAGAACC
1 AGCACCAGTAGAGGAACAAAGAACC
*
3000823 AGCACCAGTAGAGGATCAAAGAA
1 AGCACCAGTAGAGGAACAAAGAA
3000846 GTAGCAGAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.51, C:0.23, G:0.21, T:0.05
Consensus pattern (25 bp):
AGCACCAGTAGAGGAACAAAGAACC
Found at i:3001341 original size:44 final size:46
Alignment explanation
Indices: 3001254--3001344 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 46
3001244 CTAAAAAACA
*
3001254 ATTAACAATATCATTGAAAAACAAAAAAAAAATTATTAATTTATTTT
1 ATTAACAATATAATT-AAAAACAAAAAAAAAATTATTAATTTATTTT
* *
3001301 ATTAACAATATAATT-AAAA-AATAATAAAATTATTAATTTATTTT
1 ATTAACAATATAATTAAAAACAAAAAAAAAATTATTAATTTATTTT
3001345 TATTGGTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
44 23 0.56
45 4 0.10
47 14 0.34
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (46 bp):
ATTAACAATATAATTAAAAACAAAAAAAAAATTATTAATTTATTTT
Found at i:3003046 original size:26 final size:24
Alignment explanation
Indices: 3003017--3003110 Score: 84
Period size: 26 Copynumber: 3.8 Consensus size: 24
3003007 GGGCTCACCA
3003017 CAGCTCGTATGAGCTTACCTATATAT
1 CAGCTCGTATGAGCTTACCT-T-TAT
** *
3003043 CAGCTTTTATGAGCTTACCGTT-T
1 CAGCTCGTATGAGCTTACCTTTAT
*
3003066 CAGCTCG-ATAGAGCTTATCGTTTAT
1 CAGCTCGTAT-GAGCTTA-CCTTTAT
*
3003091 CAGCTCGGAATGAGCTTACC
1 CAGCTC-GTATGAGCTTACC
3003111 GATCATGGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
22 2 0.04
23 13 0.24
24 4 0.07
25 9 0.16
26 25 0.45
27 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACCTTTAT
Found at i:3003317 original size:20 final size:20
Alignment explanation
Indices: 3003275--3003318 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3003265 GATGAATTAT
* * *
3003275 TGTTGATATGTATAAGTTGC
1 TGTTGATACGGATAAATTGC
*
3003295 TGTTGATACGGATAAATTTC
1 TGTTGATACGGATAAATTGC
3003315 TGTT
1 TGTT
3003319 ATTACTGATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (20 bp):
TGTTGATACGGATAAATTGC
Found at i:3022787 original size:41 final size:41
Alignment explanation
Indices: 3022742--3022824 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
3022732 CAAAACATAA
3022742 CTCACCCTACTCCAACAGACAATCTTAAACATCTACGAAAT
1 CTCACCCTACTCCAACAGACAATCTTAAACATCTACGAAAT
*
3022783 CTCACCCTACTCTAACAGACAATCTTAAACATCTACGAAAT
1 CTCACCCTACTCCAACAGACAATCTTAAACATCTACGAAAT
3022824 C
1 C
3022825 ATCGATGCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.23
Consensus pattern (41 bp):
CTCACCCTACTCCAACAGACAATCTTAAACATCTACGAAAT
Found at i:3022806 original size:23 final size:23
Alignment explanation
Indices: 3022742--3022807 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 23
3022732 CAAAACATAA
*
3022742 CTCACCCTACTCCAACAGACAAT
1 CTCACCCTACTCTAACAGACAAT
* **
3022765 CTTAAAC-A-TCT-AC-GA-AAT
1 CTCACCCTACTCTAACAGACAAT
3022783 CTCACCCTACTCTAACAGACAAT
1 CTCACCCTACTCTAACAGACAAT
3022806 CT
1 CT
3022808 TAAACATCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 5 0.16
21 4 0.13
22 3 0.10
23 9 0.29
ACGTcount: A:0.36, C:0.36, G:0.05, T:0.23
Consensus pattern (23 bp):
CTCACCCTACTCTAACAGACAAT
Found at i:3024903 original size:183 final size:184
Alignment explanation
Indices: 3024709--3025206 Score: 748
Period size: 183 Copynumber: 2.6 Consensus size: 184
3024699 TCAAAGACAT
* * *
3024709 ATACATACATATATATATGCAAAATGATATTTAAGAAAAACCCAAAGAGGTGATTAATGTAAAAC
1 ATACATACATATATATATGCAAAATGATATTTAAG-AAAACCCAAAGAGCTGGTTAATGTAAACC
*
3024774 TTAAGACAGATCACAAATATCACTTAATAACTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGG
65 TTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGG
3024839 GTCATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGACATACCTGC-AA-
130 GTCATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGACATACCTGCAAAC
* *
3024892 ATACATACATATATATATGCAAAATGATATTTAAGGAAAACCCAAAGCGCTGGTTAATGGAAACC
1 ATACATACATATATATATGCAAAATGATATTTAA-GAAAACCCAAAGAGCTGGTTAATGTAAACC
3024957 TTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGG
65 TTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGG
* *
3025022 GTTATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGCCATACCTGCAAATGC
130 GTCATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGACATACCTGCAAA--C
*
3025079 ATACATATATATATGCAAATATATATGCAAAATGATATTTAATGAAAACCCAAAGAGCTGGTTAA
1 ATAC------ATA--CATATATATATGCAAAATGATATTTAA-GAAAACCCAAAGAGCTGGTTAA
* * * *
3025144 TGTAAACCTTAAGACAGATCACAGATATCACTTAATAATTAAGATGGAAGCAAGGTATATCAA
57 TGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAA
3025207 GTATCAATGG
Statistics
Matches: 286, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
183 171 0.60
184 3 0.01
187 4 0.01
193 3 0.01
195 105 0.37
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (184 bp):
ATACATACATATATATATGCAAAATGATATTTAAGAAAACCCAAAGAGCTGGTTAATGTAAACCT
TAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGGG
TCATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGACATACCTGCAAAC
Found at i:3025116 original size:14 final size:12
Alignment explanation
Indices: 3025085--3025109 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3025075 ATGCATACAT
3025085 ATATATATGCAA
1 ATATATATGCAA
3025097 ATATATATGCAA
1 ATATATATGCAA
3025109 A
1 A
3025110 ATGATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
ATATATATGCAA
Found at i:3025690 original size:3 final size:3
Alignment explanation
Indices: 3025682--3025731 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
3025672 GTTACACCTC
* * * * *
3025682 CAT CAT CAT CAT CAT CCT CAT CAT AAT CAT AAC CAT CAT CAC CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3025730 CA
1 CA
3025732 ACTATGGTGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (3 bp):
CAT
Found at i:3031644 original size:3 final size:3
Alignment explanation
Indices: 3031636--3031681 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
3031626 TAAAGTATGT
*
3031636 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3031682 AGACAATCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3037514 original size:33 final size:33
Alignment explanation
Indices: 3037469--3037541 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
3037459 ATGCCATTAA
* ** *
3037469 CAACCACTACTTACTA-CACCATCTTCTTCAACC
1 CAACCACCACTTA-TAGCACCATCAACTCCAACC
3037502 CAACCACCACTTATAGCACCATCAACTCCAACC
1 CAACCACCACTTATAGCACCATCAACTCCAACC
3037535 CAACCAC
1 CAACCAC
3037542 TTTTTCCTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.34, C:0.45, G:0.01, T:0.19
Consensus pattern (33 bp):
CAACCACCACTTATAGCACCATCAACTCCAACC
Found at i:3040088 original size:6 final size:6
Alignment explanation
Indices: 3040077--3040101 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3040067 AATCAAAATT
3040077 ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA A
3040102 AAATAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:3049328 original size:14 final size:14
Alignment explanation
Indices: 3049311--3049340 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3049301 GATTCACGCA
3049311 ATTCTAACATTAAT
1 ATTCTAACATTAAT
*
3049325 ATTCTAACGTTAAT
1 ATTCTAACATTAAT
3049339 AT
1 AT
3049341 ATATAGAAAT
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:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTCTAACATTAAT
Found at i:3051039 original size:41 final size:41
Alignment explanation
Indices: 3050976--3051249 Score: 372
Period size: 41 Copynumber: 6.7 Consensus size: 41
3050966 GTTTTCGGGG
* ** * *
3050976 CTTTAGTGGCGTTTTTCAAAAAGCGCCGCTAAAGATCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
3051017 CTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
3051058 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* * **
3051099 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGTTCTATT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
3051140 CTTTAGCGGCGCTTTTGTGAAAA-CGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTG-GAAAAGCGCCGCTAATGCTCTGGT
* * * * *
3051181 CTTTAGCGGCGTTTTTGTACAAGTGCCGCTATTACTCT-GT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
3051221 CTTTAGCGGCGTTTTTGGGAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
3051250 AAAATGTATT
Statistics
Matches: 205, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
40 30 0.15
41 171 0.83
42 4 0.02
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
Found at i:3051965 original size:7 final size:7
Alignment explanation
Indices: 3051955--3051995 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
3051945 GATTTAAGGT
3051955 TTAGGGG
1 TTAGGGG
*
3051962 TTAGGAG
1 TTAGGGG
3051969 TTAGGGG
1 TTAGGGG
3051976 TTAGGGG
1 TTAGGGG
* *
3051983 TTAAGAG
1 TTAGGGG
3051990 TTAGGG
1 TTAGGG
3051996 ATTTAGGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.49, T:0.29
Consensus pattern (7 bp):
TTAGGGG
Found at i:3052005 original size:21 final size:21
Alignment explanation
Indices: 3051952--3052003 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
3051942 TGGGATTTAA
*
3051952 GGTTTAGGGGTTAGGAGTTAG
1 GGTTTAGGGGTTAAGAGTTAG
*
3051973 GGGTTAGGGGTTAAGAGTTAG
1 GGTTTAGGGGTTAAGAGTTAG
3051994 GGATTTAGGG
1 GG-TTTAGGG
3052004 TTTTAAGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.21, C:0.00, G:0.48, T:0.31
Consensus pattern (21 bp):
GGTTTAGGGGTTAAGAGTTAG
Found at i:3052034 original size:7 final size:7
Alignment explanation
Indices: 3051947--3052043 Score: 51
Period size: 7 Copynumber: 13.9 Consensus size: 7
3051937 AGTGTTGGGA
*
3051947 TTTAAGG
1 TTTAGGG
3051954 TTTAGGG
1 TTTAGGG
*
3051961 GTTAGGAG
1 TTTAGG-G
3051969 -TTAGGG
1 TTTAGGG
*
3051975 GTTAGGGG
1 TTTA-GGG
* *
3051983 TTAAGAG
1 TTTAGGG
3051990 -TTAGGG
1 TTTAGGG
3051996 ATTTAGGG
1 -TTTAGGG
3052004 TTTTAAGGG
1 -TTT-AGGG
*
3052013 --TCGGG
1 TTTAGGG
*
3052018 -TTAAGG
1 TTTAGGG
3052024 TTTAGGG
1 TTTAGGG
3052031 TTTAGGG
1 TTTAGGG
3052038 TTTAGG
1 TTTAGG
3052044 AATTTTTTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
5 3 0.04
6 9 0.13
7 39 0.56
8 15 0.21
9 4 0.06
ACGTcount: A:0.21, C:0.01, G:0.42, T:0.36
Consensus pattern (7 bp):
TTTAGGG
Found at i:3052176 original size:38 final size:38
Alignment explanation
Indices: 3052133--3052214 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
3052123 GAGTATAGTT
3052133 TATATTATTTAAGAGATATATAATAGATAGACTTTATG
1 TATATTATTTAAGAGATATATAATAGATAGACTTTATG
3052171 TATATTATTTAAGAGATATATAATAGATAGACTTTATG
1 TATATTATTTAAGAGATATATAATAGATAGACTTTATG
3052209 TATATT
1 TATATT
3052215 GAATGGTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (38 bp):
TATATTATTTAAGAGATATATAATAGATAGACTTTATG
Found at i:3054832 original size:40 final size:39
Alignment explanation
Indices: 3054741--3054847 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 39
3054731 TGGTTTTTTT
3054741 TTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGA
1 TTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGA
** * *
3054780 TGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGG
1 TTTG-TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGA
*
3054822 TTTGTC-GCTCCGCTACTGCTTAGGGA
1 TTTGTCTGCTCCACTACTGCTTAGGGA
3054848 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
39 2 0.04
40 47 0.82
41 4 0.07
42 4 0.07
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (39 bp):
TTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGA
Found at i:3055208 original size:40 final size:40
Alignment explanation
Indices: 3055089--3055302 Score: 283
Period size: 42 Copynumber: 5.3 Consensus size: 40
3055079 NNNNNNNNNN
*
3055089 AGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTT
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTT
* *
3055129 AGGGAGATAAGATCTGTGGTTCTG-TCTGCTCCACTATTGCTT
1 AGGGAGATAAGA-CT-TGATGC-GATCTGCTCCACTATTGCTT
3055171 AGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTT
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTT
* *
3055211 AGGGAGATAAGATCTGTGGTTCTG-TCTGCTCCACTATTGCTT
1 AGGGAGATAAGA-CT-TGATGC-GATCTGCTCCACTATTGCTT
*
3055253 AGGGAG--AAGACTTGATGCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTT
*
3055291 AGAGAGATAAGA
1 AGGGAGATAAGA
3055303 TCTGGTTTCT
Statistics
Matches: 153, Mismatches: 11, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
37 1 0.01
38 26 0.17
39 3 0.02
40 54 0.35
41 6 0.04
42 61 0.40
43 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (40 bp):
AGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTT
Found at i:3055226 original size:82 final size:82
Alignment explanation
Indices: 3055089--3055319 Score: 396
Period size: 82 Copynumber: 2.9 Consensus size: 82
3055079 NNNNNNNNNN
3055089 AGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTGTGGTTCTGT
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTGTGGTTCTGT
3055154 CTGCTCCACTATTGCTT
66 CTGCTCCACTATTGCTT
*
3055171 AGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGT
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTGTGGTTCTGT
3055236 CTGCTCCACTATTGCTT
66 CTGCTCCACTATTGCTT
* * *
3055253 AGGGAG--AAGACTTGATGCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTG-GTTTCTGT
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTGTGGTTCTGT
*
3055315 TTGCT
66 CTGCT
3055320 AGAGAAGTGA
Statistics
Matches: 144, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
79 11 0.08
80 46 0.32
82 87 0.60
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (82 bp):
AGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTGTGGTTCTGT
CTGCTCCACTATTGCTT
Found at i:3055511 original size:100 final size:99
Alignment explanation
Indices: 3055324--3055908 Score: 633
Period size: 100 Copynumber: 5.9 Consensus size: 99
3055314 TTTGCTAGAG
* * * *
3055324 AAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTT-AATTACAATGTCGGGGAACAAGATTCACCG
1 AAGTAAGATTCGCCGTTGCGGCTTCAATCT-TTTAAATTGCAATGTCGGGAAACAAGATTCACCG
*
3055388 TTGTAGCTTCAATCTGATCCACTGCATCGCCAAGA
65 TTGTAGCTTCAATCTGCTCCACTGCATCGCCAAGA
* *
3055423 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCAGGGAAACAATATTCACCG
1 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTC-GGGAAACAAGATTCACCG
* * * *
3055488 TCGTAGCTTTAATCTGCTGCACTGTA-CTGCCAGAGA
65 TTGTAGCTTCAATCTGCTCCACTGCATC-GCCA-AGA
* * * * * *
3055524 AA-TGAGATTCACCGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGGGAATAAGATTCGCCG
1 AAGTAAGATTCGCCGTTGCGGCTTCAATCT-TTTAAATTGCAATGTCGGGAAACAAGATTCACCG
*
3055587 TTGTAGCTTCAATCTGATCCACTGCATCGCCAAGA
65 TTGTAGCTTCAATCTGCTCCACTGCATCGCCAAGA
* ** *
3055622 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCAAGAAAGCAAGATTCGCCG
1 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGAAA-CAAGATTCACCG
* * * *
3055687 TCGTAGCTTTAATCTGCTACACTGTA-CTGCC-AGA
65 TTGTAGCTTCAATCTGCTCCACTGCATC-GCCAAGA
* * * * * * *
3055721 GAAGTGAGATTCGTCGTTGCGGCTTCAATCTTTTAAATTGTAATGTTGAGGAAGCAAGATTCGCT
1 -AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCG-GGAAACAAGATTCACC
* * * *
3055786 GTTGTAGCTTTAATCTGCCCCACTGCATCGCCATGG
64 GTTGTAGCTTCAATCTGCTCCACTGCATCGCCAAGA
*** * * **
3055822 AAGTAAGATTCATTGTTGCAGCTTCAATCTTTTAAATTGTAATGTCGGGGAAGTAAGATTCACCG
1 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTC-GGGAAACAAGATTCACCG
*
3055887 TTGTAGCTTCAATCTGTTCCAC
65 TTGTAGCTTCAATCTGCTCCAC
3055909 AATATAGGAA
Statistics
Matches: 408, Mismatches: 63, Indels: 29
0.82 0.13 0.06
Matches are distributed among these distances:
98 11 0.03
99 120 0.29
100 263 0.64
101 14 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (99 bp):
AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGAAACAAGATTCACCGT
TGTAGCTTCAATCTGCTCCACTGCATCGCCAAGA
Found at i:3055667 original size:199 final size:199
Alignment explanation
Indices: 3055320--3055902 Score: 846
Period size: 199 Copynumber: 2.9 Consensus size: 199
3055310 TCTGTTTGCT
* *
3055320 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTACAATGTCGGGGAACAAGATTCA
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
3055385 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCCGTTGCGGCTTCAA
66 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCCGTTGCGGCTTCAA
* *
3055450 TCTTTTAAATTGCAATATCAGGGAAACAATATTCACCGTCGTAGCTTTAATCTGCTGCACTGTAC
131 TCTTTTAAATTGCAATATCAGGGAAACAAGATTCACCGTCGTAGCTTTAATCTGCTACACTGTAC
3055515 TGCC
196 TGCC
* * *
3055519 AGAGAAATGAGATTCACCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAATAAGATTCG
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
3055584 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCCGTTGCGGCTTCAA
66 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCCGTTGCGGCTTCAA
* *
3055649 TCTTTTAAATTGCAATATCA-AGAAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTACACTGTA
131 TCTTTTAAATTGCAATATCAGGGAAA-CAAGATTCACCGTCGTAGCTTTAATCTGCTACACTGTA
3055713 CTGCC
195 CTGCC
* * * * *
3055718 AGAGAAGTGAGATTCGTCGTTGCGGCTTCAATCT-TTTAAATTGTAATGTTGAGGAAGCAAGATT
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGGGAA-CAAGATT
* * ** * * *** *
3055782 CGCTGTTGTAGCTTTAATCTGCCCCACTGCATCGCCATGGAAGTAAGATTCATTGTTGCAGCTTC
64 CGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCCGTTGCGGCTTC
* * * ** * *
3055847 AATCTTTTAAATTGTAATGTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTG
129 AATCTTTTAAATTGCAATATCAGGGAAACAAGATTCACCGTCGTAGCTTTAATCTG
3055903 TTCCACAATA
Statistics
Matches: 344, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
198 7 0.02
199 230 0.67
200 104 0.30
201 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (199 bp):
AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCCGTTGCGGCTTCAA
TCTTTTAAATTGCAATATCAGGGAAACAAGATTCACCGTCGTAGCTTTAATCTGCTACACTGTAC
TGCC
Found at i:3055671 original size:50 final size:50
Alignment explanation
Indices: 3055324--3055901 Score: 231
Period size: 50 Copynumber: 11.6 Consensus size: 50
3055314 TTTGCTAGAG
* * ** *
3055324 AAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTT-AATTACAATGTCGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCAAGA
* * * ** ** * *
3055374 AA-CAAGATTCACCGTTGTAGCTTCAATCTGATCCACTGC-ATCGCCAAGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAAT-GTCAAGA
* * *
3055423 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCAGGGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCA-AGA
* * * * * * ** ** * * * *
3055474 AA-CAATATTCACCGTCGTAGCTTTAATCTGCTGCACTGTACTGCCAGAGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCA-AGA
* * ** *
3055524 AA-TGAGATTCACCGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCAAGA
* ** ** * *
3055573 AA-TAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGC-ATCGCCAAGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAAT-GTCAAGA
* *
3055622 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCAAGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAAGA
* * * * ** * * * * *
3055672 AAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTACACTGTACTG-CCAGA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAAGA
* * * * ** *
3055721 GAAGTGAGATTCGTCGTTGCGGCTTCAATCTTTTAAATTGTAATGTTGAGG
1 -AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAAGA
* * * * ***** * * * *
3055772 AAGCAAGATTCGCTGTTGTAGCTTTAATCTGCCCCACTGC-ATCGCCATGG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAAT-GTCAAGA
*** ** * ** *
3055822 AAGTAAGATTCATTGTTGCAGCTTCAATCTTTTAAATTGTAATGTCGGGG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAAGA
* *
3055872 AAGTAAGATTCACCGTTGTAGCTTCAATCT
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCT
3055902 GTTCCACAAT
Statistics
Matches: 372, Mismatches: 142, Indels: 28
0.69 0.26 0.05
Matches are distributed among these distances:
48 6 0.02
49 73 0.20
50 280 0.75
51 13 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (50 bp):
AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAAGA
Found at i:3055975 original size:44 final size:43
Alignment explanation
Indices: 3055908--3056230 Score: 270
Period size: 44 Copynumber: 7.5 Consensus size: 43
3055898 ATCTGTTCCA
*
3055908 CAATATAGGAAGACAAGACCTGCTATCTTCGATCTACTTCACGC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CGC
* * * *
3055952 CAATACATGAAGACAAGATCTGCTTTCTTGGATCTACTT-CGC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCGC
* * *
3055994 CACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTAC
1 CA--A-TATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCC-GC
* * * *
3056040 CAATATAAGAAGATAGGACCTGCTATCTTCGA--T-C-T--GC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCGC
* * * *
3056077 CAACATAGGAAGACAATATCTACTTTCTTCGATCTAC-TCCGCC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCG-C
* * *
3056120 ACTAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTAC
1 -C-AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCC-GC
* *
3056165 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACTGC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-C-GC
* *
3056210 CAACACAGGAAGACAAGATCT
1 CAATATAGGAAGACAAGATCT
3056231 ACTTTAATGA
Statistics
Matches: 218, Mismatches: 43, Indels: 35
0.74 0.15 0.12
Matches are distributed among these distances:
37 25 0.11
39 1 0.00
40 3 0.01
41 1 0.00
42 6 0.03
43 35 0.16
44 84 0.39
45 60 0.28
46 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCGC
Found at i:3056137 original size:125 final size:125
Alignment explanation
Indices: 3055960--3056199 Score: 408
Period size: 125 Copynumber: 1.9 Consensus size: 125
3055950 GCCAATACAT
* * * *
3055960 GAAGACAAGATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTACTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
3056025 CGATCCACTTCCTACCAATATAAGAAGATAGGACCTGCTATCTTCGATCTGCCAACATAG
66 CGATCCACTTCCTACCAATATAAGAAGACAGGACCTGCTATCTTCGATCTGCCAACATAG
* *
3056085 GAAGACAATATCTACTTTCTTCGATCTACTCCGCCACTAATATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTACTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
3056150 CGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCT
66 CGATCCACTTCCTACCAATATAAGAAGACAGGACCTGCTATCTTCGATCT
3056200 ACTTCACTGC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 107 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (125 bp):
GAAGACAAGATCTACTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCTT
CGATCCACTTCCTACCAATATAAGAAGACAGGACCTGCTATCTTCGATCTGCCAACATAG
Found at i:3056437 original size:15 final size:15
Alignment explanation
Indices: 3056397--3056437 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
3056387 TAACTAGATG
3056397 TGTATGAATGATATT
1 TGTATGAATGATATT
*
3056412 TGCATTGAATGATATT
1 TGTA-TGAATGATATT
3056428 TGTATGAATG
1 TGTATGAATG
3056438 CAGAATGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (15 bp):
TGTATGAATGATATT
Found at i:3059183 original size:62 final size:62
Alignment explanation
Indices: 3059081--3059205 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
3059071 CTAAACTTGA
*
3059081 CGTACTTTTGGATTTTAGGAAATTTACTGTATGCAATGAAACGTAATGTTGATGCATGAATG
1 CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
* * * *
3059143 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCGATGAAATGTAATGTTGATGCATGAATG
1 CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
3059205 C
1 C
3059206 AAAAAAGAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (62 bp):
CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
Found at i:3061421 original size:31 final size:29
Alignment explanation
Indices: 3061356--3061430 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
3061346 ATAACGTTTC
* *
3061356 AAATAAATAGAATATATATAAAAATTAGA
1 AAATAAATAGAATATATAGAAAAATTAAA
*
3061385 CAATAAATA-AATAATAATAGAAACAATTAAA
1 AAATAAATAGAAT-AT-ATAGAAA-AATTAAA
*
3061416 AAATAAATAGTATAT
1 AAATAAATAGAATAT
3061431 TTAAAATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 3 0.08
29 10 0.27
30 6 0.16
31 16 0.43
32 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATAAATAGAATATATAGAAAAATTAAA
Found at i:3061531 original size:2 final size:2
Alignment explanation
Indices: 3061524--3061552 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3061514 ATAAGAAATG
3061524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3061553 AGAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3065553 original size:14 final size:14
Alignment explanation
Indices: 3065534--3065563 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3065524 AGTTGCACTA
3065534 TTTGAACTTGAAAT
1 TTTGAACTTGAAAT
*
3065548 TTTGAACTTGTAAT
1 TTTGAACTTGAAAT
3065562 TT
1 TT
3065564 AACATGATTT
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:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (14 bp):
TTTGAACTTGAAAT
Found at i:3065839 original size:43 final size:43
Alignment explanation
Indices: 3065777--3065895 Score: 184
Period size: 43 Copynumber: 2.8 Consensus size: 43
3065767 NNNNNTAATC
*
3065777 AAAGCGTCGCTAAATGTCTTGAGCTATAGCGGCGTTTGTGAAA
1 AAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAA
*
3065820 AAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAA
1 AAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAA
* * * *
3065863 GATGCGTCGCTAAAGGTCCTGATCTATAGCGGC
1 AAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGC
3065896 ATTGACAATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (43 bp):
AAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAA
Found at i:3082720 original size:20 final size:20
Alignment explanation
Indices: 3082681--3082719 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3082671 TAAAAATAAA
*
3082681 AAAATCTAAAAAAGTATTTT
1 AAAATCTAAAAAAATATTTT
3082701 AAAAT-TAAAAAAATATTTT
1 AAAATCTAAAAAAATATTTT
3082720 TTATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATCTAAAAAAATATTTT
Found at i:3082991 original size:18 final size:18
Alignment explanation
Indices: 3082945--3082999 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
3082935 TTTAATGTAC
3082945 TGTGATTGTCAATCTATAAT
1 TGTGATTGT-AAT-TATAAT
*
3082965 T-TGCTTTGTAATTATAAT
1 TGTG-ATTGTAATTATAAT
*
3082983 TGTGATTGTACTTATAA
1 TGTGATTGTAATTATAA
3083000 CAATACTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 18 0.60
19 7 0.23
20 5 0.17
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (18 bp):
TGTGATTGTAATTATAAT
Found at i:3088004 original size:14 final size:16
Alignment explanation
Indices: 3087980--3088011 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3087970 TGTGTCCCTT
3087980 TTTTTTAAATATT-TA
1 TTTTTTAAATATTATA
3087995 TTTTTT-AATATTATA
1 TTTTTTAAATATTATA
3088010 TT
1 TT
3088012 ATAACTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTTAAATATTATA
Found at i:3088654 original size:4 final size:4
Alignment explanation
Indices: 3088647--3088701 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
3088637 TTATACATAC
3088647 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3088695 ATGT ATG
1 ATGT ATG
3088702 AGTCATGTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:3092854 original size:19 final size:18
Alignment explanation
Indices: 3092817--3092856 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3092807 CATAATGATA
* *
3092817 TATATAATATATTTTTAT
1 TATATAATACATATTTAT
3092835 TATATAACTACATATTTAT
1 TATATAA-TACATATTTAT
3092854 TAT
1 TAT
3092857 TTTATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATAATACATATTTAT
Found at i:3099252 original size:16 final size:18
Alignment explanation
Indices: 3099231--3099265 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3099221 TTACAATTTT
3099231 TTAA-TTTA-TTTTATAA
1 TTAATTTTATTTTTATAA
3099247 TTAATTTTATTTTTATAA
1 TTAATTTTATTTTTATAA
3099265 T
1 T
3099266 GTATGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTAATTTTATTTTTATAA
Found at i:3103836 original size:17 final size:17
Alignment explanation
Indices: 3103810--3103856 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
3103800 TCACGTCAAC
3103810 AAATAATTTAAAAATTA
1 AAATAATTTAAAAATTA
3103827 TAAA-AATTTAAAAATTA
1 -AAATAATTTAAAAATTA
*
3103844 AAATAATTCAAAA
1 AAATAATTTAAAA
3103857 TTCAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAATTTAAAAATTA
Found at i:3103844 original size:7 final size:8
Alignment explanation
Indices: 3103814--3103846 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3103804 GTCAACAAAT
3103814 AATTTAAA
1 AATTTAAA
3103822 AATTATAAA
1 AATT-TAAA
3103831 AATTTAAA
1 AATTTAAA
3103839 AA-TTAAA
1 AATTTAAA
3103846 A
1 A
3103847 TAATTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.25
8 10 0.42
9 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATTTAAA
Found at i:3113273 original size:3 final size:3
Alignment explanation
Indices: 3113265--3113309 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3113255 GGATATATGA
3113265 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3113310 TATTGGAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3119346 original size:2 final size:2
Alignment explanation
Indices: 3119339--3119363 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3119329 CGTAACTATG
3119339 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3119364 GTTATGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3121509 original size:7 final size:7
Alignment explanation
Indices: 3121497--3121523 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3121487 CATGCTGTAG
3121497 ACCCTAA
1 ACCCTAA
3121504 ACCCTAA
1 ACCCTAA
3121511 ACCCTAA
1 ACCCTAA
3121518 ACCCTA
1 ACCCTA
3121524 GACCACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:3122405 original size:24 final size:22
Alignment explanation
Indices: 3122378--3122422 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
3122368 TTATAGAGTC
*
3122378 TAAATTGTTTTCAGTAATTTTCTT
1 TAAATTCTTTT-AGT-ATTTTCTT
3122402 TAAATTCTTTTAGTATTTTCT
1 TAAATTCTTTTAGTATTTTCT
3122423 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 10 0.50
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60
Consensus pattern (22 bp):
TAAATTCTTTTAGTATTTTCTT
Found at i:3124989 original size:22 final size:22
Alignment explanation
Indices: 3124955--3124996 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3124945 TTCACTTAGT
*
3124955 CAGGCATCAGTGTCGTGACATC
1 CAGGCATCAGTGTCGCGACATC
* *
3124977 CAGGCTTCGGTGTCGCGACA
1 CAGGCATCAGTGTCGCGACA
3124997 CCCTCGATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.29, G:0.31, T:0.21
Consensus pattern (22 bp):
CAGGCATCAGTGTCGCGACATC
Found at i:3126461 original size:21 final size:20
Alignment explanation
Indices: 3126428--3126469 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
3126418 TTTGTAATGA
3126428 GATATGATGATAGGAGATTAT
1 GATATGATGATA-GAGATTAT
*
3126449 GATATG-TGCATAGATATTAT
1 GATATGATG-ATAGAGATTAT
3126469 G
1 G
3126470 TTAAACGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (20 bp):
GATATGATGATAGAGATTAT
Found at i:3127521 original size:2 final size:2
Alignment explanation
Indices: 3127516--3127569 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
3127506 CCCCCCCCCC
*
3127516 CT CT CT CT CT CT CT CA 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
3127558 CT CT CT CT CT CT
1 CT CT CT CT CT CT
3127570 TGTTTACTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3132915 original size:27 final size:28
Alignment explanation
Indices: 3132871--3132926 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
3132861 TATCGTTATA
3132871 AAAATAAAAATAATTATTTTATGA-AAAT
1 AAAATAAAAATAATTATTTTA-GATAAAT
*
3132899 AAAAT-AAACTAATTATTTTAGATAAAT
1 AAAATAAAAATAATTATTTTAGATAAAT
3132926 A
1 A
3132927 TTCAAATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 2 0.08
27 19 0.73
28 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATAAAAATAATTATTTTAGATAAAT
Found at i:3138265 original size:22 final size:22
Alignment explanation
Indices: 3138237--3138289 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
3138227 ATAATTACAT
3138237 TTAGTACGTGAAACATGAGAGC
1 TTAGTACGTGAAACATGAGAGC
* **
3138259 TTAGTACGTTAGCCATGAGAGC
1 TTAGTACGTGAAACATGAGAGC
3138281 TTAGTACGT
1 TTAGTACGT
3138290 TAGCCATGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (22 bp):
TTAGTACGTGAAACATGAGAGC
Found at i:3138312 original size:22 final size:22
Alignment explanation
Indices: 3138250--3138299 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
3138240 GTACGTGAAA
3138250 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
3138272 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
3138294 CATGAG
1 CATGAG
3138300 GGTTTAGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:3138360 original size:25 final size:25
Alignment explanation
Indices: 3138330--3138381 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3138320 TTTTTAAATA
3138330 TTTAACATATATATT-AT-AATATATT
1 TTTAAC-TAT-TATTAATAAATATATT
*
3138355 TTTAACTATTTTTAATAAATATATT
1 TTTAACTATTATTAATAAATATATT
3138380 TT
1 TT
3138382 ATTACAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.12
24 5 0.21
25 16 0.67
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTAACTATTATTAATAAATATATT
Found at i:3138766 original size:2 final size:2
Alignment explanation
Indices: 3138754--3138798 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3138744 ACATGAAAAT
3138754 TA TA T- 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
3138795 TA TA
1 TA TA
3138799 GGTAGAGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.