Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold127
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: 3416254
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 147187 characters in sequence are not A, C, G, or T
File 9 of 10
Found at i:2911864 original size:29 final size:30
Alignment explanation
Indices: 2911797--2911869 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
2911787 TATAATTACC
*
2911797 ATAATTATAATAATGTTTGACTGAAAAATT
1 ATAATTATAATAATATTTGACTGAAAAATT
*
2911827 ATAATTATAATAATATTTGA-TCG-TAAATT
1 ATAATTATAATAATATTTGACT-GAAAAATT
2911856 ATAATTATAATAAT
1 ATAATTATAATAAT
2911870 TATAACAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 20 0.50
30 20 0.50
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (30 bp):
ATAATTATAATAATATTTGACTGAAAAATT
Found at i:2927687 original size:26 final size:26
Alignment explanation
Indices: 2927658--2927719 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
2927648 TACCTACAGT
2927658 AGTTTCAGAATATCATAACA-GATATC
1 AGTTTCAGAATATCATAACATG-TATC
* *
2927684 AGTTTCAGAATATTATAGCATGTATC
1 AGTTTCAGAATATCATAACATGTATC
2927710 AGTTTCAGAA
1 AGTTTCAGAA
2927720 CACTTACAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATGTATC
Found at i:2936267 original size:120 final size:119
Alignment explanation
Indices: 2936080--2936344 Score: 327
Period size: 120 Copynumber: 2.2 Consensus size: 119
2936070 GAACTAAAGT
* ** *
2936080 ACAAATAGGGGCATGTATGTGCATTCAGGGGTACCGAAGTATAAACAGGGGCAAGTATGTGCATT
1 ACAAATAGGGGCACGTATGTGCATTCAGGGGTACAAAAGTACAAACAGGGGCAAGTATGTGCATT
* ** *
2936145 CAGGGGTATCGAAGTACAAACAGGGGCACCTATG-TGCATTTAAGGGTATCGAAGC
66 CAGGGGTACCGAAGTACAAACAAAGGCA--TATGATACATTTAAGGGTATCGAAGC
* * **
2936200 ACAAACAGGGGCACGTATGTGCATTCAGGGGTACAAAAGTACAAATC-GGGGCATGTATGTGTGT
1 ACAAATAGGGGCACGTATGTGCATTCAGGGGTACAAAAGTACAAA-CAGGGGCAAGTATGTGCAT
* *
2936264 TCAGGGGTACCGAAGTACAAACAAAGGCATATGTATACATTTACGGGTATCGAAGT
65 TCAGGGGTACCGAAGTACAAACAAAGGCATATG-ATACATTTAAGGGTATCGAAGC
* * *
2936320 ACGAGTAGGGGCACGTATATGCATT
1 ACAAATAGGGGCACGTATGTGCATT
2936345 ATATAATAAT
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
118 4 0.03
120 119 0.96
121 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (119 bp):
ACAAATAGGGGCACGTATGTGCATTCAGGGGTACAAAAGTACAAACAGGGGCAAGTATGTGCATT
CAGGGGTACCGAAGTACAAACAAAGGCATATGATACATTTAAGGGTATCGAAGC
Found at i:2936293 original size:40 final size:40
Alignment explanation
Indices: 2936023--2936286 Score: 298
Period size: 40 Copynumber: 6.6 Consensus size: 40
2936013 ATACTATTTG
* * * *
2936023 ATTCAGGGCTACCAAAGTATAAATA-GGGCATGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGC
* * ** *
2936062 ATTCAAGGGAACTAAAGTACAAATAGGGGCATGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGC
* *
2936102 ATTCAGGGGTACCGAAGTATAAACAGGGGCAAGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGC
* **
2936142 ATTCAGGGGTATCGAAGTACAAACAGGGGCACCTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGC
* * * * *
2936182 ATTTAAGGGTATCGAAGCACAAACAGGGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGC
** *
2936222 ATTCAGGGGTACAAAAGTACAAATC-GGGGCATGTATGTGT
1 ATTCAGGGGTACCGAAGTACAAA-CAGGGGCATGTATGTGC
*
2936262 GTTCAGGGGTACCGAAGTACAAACA
1 ATTCAGGGGTACCGAAGTACAAACA
2936287 AAGGCATATG
Statistics
Matches: 191, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
39 21 0.11
40 169 0.88
41 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (40 bp):
ATTCAGGGGTACCGAAGTACAAACAGGGGCATGTATGTGC
Found at i:2936312 original size:80 final size:80
Alignment explanation
Indices: 2936023--2936344 Score: 246
Period size: 80 Copynumber: 4.0 Consensus size: 80
2936013 ATACTATTTG
* * * * * * * * *
2936023 ATTCAGGGCTACCAAAGTATAAATA-GGGCATGTATGTGCATTCAAGGG-AACTAAAGTACAAAT
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATATGTATGCATTCAGGGGTATC-AAAGTACAAAT
*
2936086 AGGGGCATGTATGTGC
65 CGGGGCATGTATGTGC
* *
2936102 ATTCAGGGGTACCGAAGTATAAACAGGGGCA-A-GTATGTGCATTCAGGGGTATCGAAGTACAAA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATATGTA--TGCATTCAGGGGTATCAAAGTACAAA
**
2936165 -CAGGGGCACCTATGTGC
64 TC-GGGGCATGTATGTGC
* * * *
2936182 ATTTAAGGGTATCGAAGCACAAACAGGGGCACGTATG--TGCATTCAGGGGTA-CAAAAGTACAA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCA--TATGTATGCATTCAGGGGTATC-AAAGTACAA
*
2936244 ATCGGGGCATGTATGTGT
63 ATCGGGGCATGTATGTGC
* ** * * * * * * *
2936262 GTTCAGGGGTACCGAAGTACAAACAAAGGCATATGTATACATTTACGGGTATCGAAGTACGAGTA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCATATGTATGCATTCAGGGGTATCAAAGTACAAATC
* *
2936327 GGGGCACGTATATGC
66 GGGGCATGTATGTGC
2936342 ATT
1 ATT
2936345 ATATAATAAT
Statistics
Matches: 190, Mismatches: 39, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
78 5 0.03
79 23 0.12
80 156 0.82
81 4 0.02
83 1 0.01
84 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (80 bp):
ATTCAGGGGTACCGAAGTACAAACAGGGGCATATGTATGCATTCAGGGGTATCAAAGTACAAATC
GGGGCATGTATGTGC
Found at i:2941272 original size:28 final size:23
Alignment explanation
Indices: 2941204--2941260 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
2941194 TGAATTTTTT
*
2941204 AATTGATAATAATATATGGAATG
1 AATTGATGATAATATATGGAATG
2941227 AATTGATGATAATATATGGAATG
1 AATTGATGATAATATATGGAATG
2941250 AATTGATGATA
1 AATTGATGATA
2941261 TAGAATTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (23 bp):
AATTGATGATAATATATGGAATG
Found at i:2957783 original size:41 final size:41
Alignment explanation
Indices: 2957736--2957904 Score: 194
Period size: 41 Copynumber: 4.1 Consensus size: 41
2957726 ACAGAAATAC
** * * * *
2957736 ATTCAAGGGTACTGAATTATAAATAGGGGCACATATGTGCA
1 ATTCAAGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
*
2957777 ATTCAAGGGTACCAAAGTACAGACAGGGGCACGTATGTGCA
1 ATTCAAGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
* * * *
2957818 ATTTAGGGGTACCAAAGTACAAACAGAGGCACTTATGTGCA
1 ATTCAAGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
* * * * *
2957859 ATTCAGGGGTACCGAAGTACAAATAGTGGCATGTATGTGCA
1 ATTCAAGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
2957900 ATTCA
1 ATTCA
2957905 GAAGTAATCT
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 110 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (41 bp):
ATTCAAGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
Found at i:2957905 original size:41 final size:41
Alignment explanation
Indices: 2957760--2957905 Score: 202
Period size: 41 Copynumber: 3.6 Consensus size: 41
2957750 AATTATAAAT
* * *
2957760 AGGGGCACATATGTGCAATTCAAGGGTACCAAAGTACAGAC
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAC
*
2957801 AGGGGCACGTATGTGCAATTTAGGGGTACCAAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAC
* * * *
2957842 AGAGGCACTTATGTGCAATTCAGGGGTACCGAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAC
* *
2957883 AGTGGCATGTATGTGCAATTCAG
1 AGGGGCACGTATGTGCAATTCAG
2957906 AAGTAATCTT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAC
Found at i:2958133 original size:21 final size:21
Alignment explanation
Indices: 2958109--2958151 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2958099 TAATCCATTT
2958109 AATACCTCTAGCATTCAATTA
1 AATACCTCTAGCATTCAATTA
2958130 AATACCTCTAGCATTCAATTA
1 AATACCTCTAGCATTCAATTA
2958151 A
1 A
2958152 GTCCACATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (21 bp):
AATACCTCTAGCATTCAATTA
Found at i:2961234 original size:49 final size:49
Alignment explanation
Indices: 2961181--2961333 Score: 109
Period size: 49 Copynumber: 3.1 Consensus size: 49
2961171 TTAAATTGAT
2961181 ATTTTTTAAGCTAGAAATGGAAAATGATTAAATTGTAGAATAAATATAA
1 ATTTTTTAAGCTAGAAATGGAAAATGATTAAATTGTAGAATAAATATAA
* * *** * ** * * * *
2961230 A--TTTT-GGTTTTTATTGTTAAATAGTTTTAGTATTAG-AGATTAAAT-TGAT
1 ATTTTTTAAGCTAGAAATGGAAAAT-G-ATTA-AATT-GTAGAATAAATAT-AA
2961279 ATTTTTTAAGCTAGAAATGGAAAATGATTAAATTGTAGAATAAATTATAA
1 ATTTTTTAAGCTAGAAATGGAAAATGATTAAATTGTAGAATAAA-TATAA
2961329 ATTTT
1 ATTTT
2961334 GAGTAATAGG
Statistics
Matches: 69, Mismatches: 24, Indels: 21
0.61 0.21 0.18
Matches are distributed among these distances:
46 9 0.13
47 5 0.07
48 5 0.07
49 24 0.35
50 11 0.16
51 6 0.09
52 9 0.13
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.42
Consensus pattern (49 bp):
ATTTTTTAAGCTAGAAATGGAAAATGATTAAATTGTAGAATAAATATAA
Found at i:2961307 original size:98 final size:99
Alignment explanation
Indices: 2961138--2961334 Score: 387
Period size: 98 Copynumber: 2.0 Consensus size: 99
2961128 GATTTTAGAT
2961138 GTTTTTATTGTTAAATAGTTTTAGTATTAGAGATTAAATTGATATTTTTTAAGCTAGAAATGGAA
1 GTTTTTATTGTTAAATAGTTTTAGTATTAGAGATTAAATTGATATTTTTTAAGCTAGAAATGGAA
2961203 AATGATTAAATTGTAGAATAAA-TATAAATTTTG
66 AATGATTAAATTGTAGAATAAATTATAAATTTTG
2961236 GTTTTTATTGTTAAATAGTTTTAGTATTAGAGATTAAATTGATATTTTTTAAGCTAGAAATGGAA
1 GTTTTTATTGTTAAATAGTTTTAGTATTAGAGATTAAATTGATATTTTTTAAGCTAGAAATGGAA
2961301 AATGATTAAATTGTAGAATAAATTATAAATTTTG
66 AATGATTAAATTGTAGAATAAATTATAAATTTTG
2961335 AGTAATAGGG
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 87 0.89
99 11 0.11
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (99 bp):
GTTTTTATTGTTAAATAGTTTTAGTATTAGAGATTAAATTGATATTTTTTAAGCTAGAAATGGAA
AATGATTAAATTGTAGAATAAATTATAAATTTTG
Found at i:2968018 original size:18 final size:20
Alignment explanation
Indices: 2967995--2968032 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2967985 ATGATGGGGC
2967995 CGAAAT-TAAT-TTAAGAAA
1 CGAAATATAATGTTAAGAAA
*
2968013 CGAAATATATTGTTAAGAAA
1 CGAAATATAATGTTAAGAAA
2968033 ATTCGAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.53, C:0.05, G:0.13, T:0.29
Consensus pattern (20 bp):
CGAAATATAATGTTAAGAAA
Found at i:2968942 original size:15 final size:15
Alignment explanation
Indices: 2968924--2968962 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
2968914 ATTATAATAA
2968924 TAATAATAATAAAAG
1 TAATAATAATAAAAG
2968939 TAATAATAATAAAAG
1 TAATAATAATAAAAG
*
2968954 AAATAATAA
1 TAATAATAA
2968963 AGAAAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (15 bp):
TAATAATAATAAAAG
Found at i:2968962 original size:3 final size:3
Alignment explanation
Indices: 2968917--2968950 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
2968907 TATGAAGATT
2968917 ATA ATA ATA ATA ATA ATA A-A AGTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
2968951 AAGAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2972113 original size:33 final size:32
Alignment explanation
Indices: 2972071--2972155 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 32
2972061 TTAAATCCGT
*
2972071 TGTCGCCTCTCTCTCACCCTCCACTGCCACCAA
1 TGTCGCCTCTCTCTCACCCTCCACTGAC-CCAA
* *
2972104 TGTCGCCTCTCCCTCACCCTCCACTTACCCAA
1 TGTCGCCTCTCTCTCACCCTCCACTGACCCAA
*
2972136 TGCCGCCTCTCTCTCACCCT
1 TGTCGCCTCTCTCTCACCCT
2972156 TCACAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 22 0.47
33 25 0.53
ACGTcount: A:0.13, C:0.53, G:0.08, T:0.26
Consensus pattern (32 bp):
TGTCGCCTCTCTCTCACCCTCCACTGACCCAA
Found at i:2972143 original size:32 final size:33
Alignment explanation
Indices: 2972074--2972155 Score: 121
Period size: 32 Copynumber: 2.5 Consensus size: 33
2972064 AATCCGTTGT
* *
2972074 CGCCTCTCTCTCACCCTCCACTGCCACCAATGT
1 CGCCTCTCTCTCACCCTCCACTGACACCAATGC
* *
2972107 CGCCTCTCCCTCACCCTCCACTTAC-CCAATGC
1 CGCCTCTCTCTCACCCTCCACTGACACCAATGC
2972139 CGCCTCTCTCTCACCCT
1 CGCCTCTCTCTCACCCT
2972156 TCACAATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 22 0.50
33 22 0.50
ACGTcount: A:0.13, C:0.55, G:0.07, T:0.24
Consensus pattern (33 bp):
CGCCTCTCTCTCACCCTCCACTGACACCAATGC
Found at i:2977128 original size:20 final size:22
Alignment explanation
Indices: 2977103--2977162 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 22
2977093 AAGCTTATGC
2977103 TAAGTAAATGGAATGGAAAGTAAG
1 TAAGTAAATGGAATGG-AAG-AAG
2977127 TAAGTAAAT-GAAGTGG-A-AAG
1 TAAGTAAATGGAA-TGGAAGAAG
2977147 TAAGTAAATGGAATGG
1 TAAGTAAATGGAATGG
2977163 TTCATCGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 15 0.44
21 3 0.09
22 1 0.03
23 3 0.09
24 12 0.35
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.22
Consensus pattern (22 bp):
TAAGTAAATGGAATGGAAGAAG
Found at i:2977130 original size:24 final size:24
Alignment explanation
Indices: 2977103--2977153 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
2977093 AAGCTTATGC
2977103 TAAGTAAATGGAA-TGGAAAGTAAG
1 TAAGTAAAT-GAAGTGGAAAGTAAG
2977127 TAAGTAAATGAAGTGGAAAGTAAG
1 TAAGTAAATGAAGTGGAAAGTAAG
2977151 TAA
1 TAA
2977154 ATGGAATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (24 bp):
TAAGTAAATGAAGTGGAAAGTAAG
Found at i:2978658 original size:24 final size:24
Alignment explanation
Indices: 2978605--2978659 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
2978595 TGAGTTGGTT
* *
2978605 GTGGAGGATATCAAGGAGGGGTGA
1 GTGGAGAAAATCAAGGAGGGGTGA
* *
2978629 GCGGAGAAAATCAAGGAGAGGG-GG
1 GTGGAGAAAATCAAGGAG-GGGTGA
2978653 GTGGAGA
1 GTGGAGA
2978660 TTTTCAAGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.05, G:0.51, T:0.11
Consensus pattern (24 bp):
GTGGAGAAAATCAAGGAGGGGTGA
Found at i:2978968 original size:41 final size:41
Alignment explanation
Indices: 2978922--2979008 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
2978912 GCTGATCCTC
2978922 TCTTTTACTTTCATCTGTACTTATTTTCAAATTCAATTTTT
1 TCTTTTACTTTCATCTGTACTTATTTTCAAATTCAATTTTT
* * * *
2978963 TCTTTTGCTTTCATCTGTACTTCTTTTCCAATTCCATTTTT
1 TCTTTTACTTTCATCTGTACTTATTTTCAAATTCAATTTTT
*
2979004 CCTTT
1 TCTTT
2979009 CTCTGTTAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (41 bp):
TCTTTTACTTTCATCTGTACTTATTTTCAAATTCAATTTTT
Found at i:2980065 original size:27 final size:27
Alignment explanation
Indices: 2980035--2980165 Score: 113
Period size: 27 Copynumber: 4.9 Consensus size: 27
2980025 CCCAATATTT
*
2980035 GTAACATGATCGTAATACCCTTGTAAG
1 GTAAAATGATCGTAATACCCTTGTAAG
* * * * * *
2980062 GTAAAATAACCGAAAAACCCTTATAGG
1 GTAAAATGATCGTAATACCCTTGTAAG
* *
2980089 GTAAAATGA-CAGTAATA-CCTTCATAGG
1 GTAAAATGATC-GTAATACCCTT-GTAAG
* * *
2980116 GTTAAATGATCGAAATACCCCTGTAAG
1 GTAAAATGATCGTAATACCCTTGTAAG
*
2980143 GTAAAATGATCGTAATGCCCTTG
1 GTAAAATGATCGTAATACCCTTG
2980166 GAGGTTAAAA
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
26 5 0.06
27 72 0.89
28 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (27 bp):
GTAAAATGATCGTAATACCCTTGTAAG
Found at i:2980158 original size:54 final size:54
Alignment explanation
Indices: 2980035--2980164 Score: 129
Period size: 54 Copynumber: 2.4 Consensus size: 54
2980025 CCCAATATTT
* * * *
2980035 GTAACATGATCGTAATACCCTTGTAAGGTAAAATAACCGAAAAACCCTTATAGG
1 GTAAAATGATCGTAATACCCTTATAAGGTAAAATAACCGAAAAACCCCTATAAG
* * * * * *
2980089 GTAAAATGA-CAGTAATA-CCTTCATAGGGTTAAATGATCGAAATACCCCTGTAAG
1 GTAAAATGATC-GTAATACCCTT-ATAAGGTAAAATAACCGAAAAACCCCTATAAG
*
2980143 GTAAAATGATCGTAATGCCCTT
1 GTAAAATGATCGTAATACCCTT
2980165 GGAGGTTAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
53 5 0.08
54 51 0.84
55 5 0.08
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (54 bp):
GTAAAATGATCGTAATACCCTTATAAGGTAAAATAACCGAAAAACCCCTATAAG
Found at i:2980289 original size:24 final size:24
Alignment explanation
Indices: 2980199--2980304 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
2980189 TCGAGTGTAA
* * * **
2980199 ATGATTGATTTGTCCGTGATGTAA
1 ATGACTGATTTGTCTGTGATTTGT
**
2980223 ATGACTGATTTGTCTGTGATTTAA
1 ATGACTGATTTGTCTGTGATTTGT
* * *
2980247 ATAACTGATTTGTCAGTGATTGGT
1 ATGACTGATTTGTCTGTGATTTGT
*
2980271 ATGACTGATTTGTTTGTGATTTGT
1 ATGACTGATTTGTCTGTGATTTGT
2980295 ATGACTGATT
1 ATGACTGATT
2980305 CTGCGCATGG
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTGATTTGT
Found at i:2980518 original size:32 final size:32
Alignment explanation
Indices: 2980476--2980664 Score: 252
Period size: 32 Copynumber: 5.9 Consensus size: 32
2980466 GTTGCGATGC
*
2980476 TACTGATGGCTTTGTGCCGGTCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
2980508 TACTGGTGGCTTTGTGCCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
2980540 TACTGATGGCTTTGTACCGATTATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
2980572 TACTAATAGCTTTGTGCCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * *
2980604 TACTGATGGCTGTGTGTCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
2980636 TACTGATGGCTTTGTGCCAATCATATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
2980665 TGTAGTTATA
Statistics
Matches: 133, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 133 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:2982363 original size:21 final size:21
Alignment explanation
Indices: 2982325--2982365 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2982315 GAGTGCCGTA
* * *
2982325 TTAAAATTTGGCTCGTTAATT
1 TTAAAATTTAGATAGTTAATT
2982346 TTAAAATTTAGATAGTTAAT
1 TTAAAATTTAGATAGTTAAT
2982366 CAAAGGAAAA
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:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (21 bp):
TTAAAATTTAGATAGTTAATT
Found at i:2989363 original size:16 final size:16
Alignment explanation
Indices: 2989333--2989371 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2989323 ATTCAGGTGA
*
2989333 AATGCTCATATCAAAAT
1 AATG-TCATAGCAAAAT
2989350 AATGTCATAGCAAAAT
1 AATGTCATAGCAAAAT
*
2989366 ATTGTC
1 AATGTC
2989372 TAATCAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (16 bp):
AATGTCATAGCAAAAT
Found at i:2991842 original size:22 final size:22
Alignment explanation
Indices: 2991787--2991832 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2991777 AAGAGCTCCT
2991787 CTTAGTGACTGGGAATCCCGAG
1 CTTAGTGACTGGGAATCCCGAG
*
2991809 CTTAGTGACTGGGAATCTCGAG
1 CTTAGTGACTGGGAATCCCGAG
2991831 CT
1 CT
2991833 ATTGAGCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (22 bp):
CTTAGTGACTGGGAATCCCGAG
Found at i:2992671 original size:29 final size:29
Alignment explanation
Indices: 2992606--2992661 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2992596 TTATTCAATA
* *
2992606 TGTAATGTCATATATGAATTTTGATTTTG
1 TGTAATTTTATATATGAATTTTGATTTTG
*
2992635 TGTGATTTTATATATGAATTTTGATTT
1 TGTAATTTTATATATGAATTTTGATTT
2992662 GATTCAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (29 bp):
TGTAATTTTATATATGAATTTTGATTTTG
Found at i:2994831 original size:30 final size:30
Alignment explanation
Indices: 2994795--2994851 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2994785 TAGTATGAGG
*
2994795 AAAAATTTA-TACATATTTAATGTACTATAT
1 AAAAATTTACT-CATACTTAATGTACTATAT
2994825 AAAAATTTACTCATACTTAATGTACTA
1 AAAAATTTACTCATACTTAATGTACTA
2994852 ATTTCTATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAAATTTACTCATACTTAATGTACTATAT
Found at i:2997503 original size:13 final size:13
Alignment explanation
Indices: 2997479--2997513 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2997469 AATACAAAAA
*
2997479 AAAATTAATTTTT
1 AAAATTATTTTTT
2997492 AAAA-TATTTTTT
1 AAAATTATTTTTT
2997504 AAAATTATTT
1 AAAATTATTT
2997514 ATGTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:2999456 original size:22 final size:21
Alignment explanation
Indices: 2999430--2999470 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2999420 ATTTAAAAAT
*
2999430 TATTTTATACTAATATTTTATA
1 TATTTTATAATAA-ATTTTATA
2999452 TATTTTATAATAAATTTTA
1 TATTTTATAATAAATTTTA
2999471 CATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATAATAAATTTTATA
Found at i:3000080 original size:12 final size:13
Alignment explanation
Indices: 3000055--3000089 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3000045 AATACAAAAA
*
3000055 AAAATTAATTTTT
1 AAAATTATTTTTT
3000068 AAAA-TATTTTTT
1 AAAATTATTTTTT
3000080 AAAATTATTT
1 AAAATTATTT
3000090 ATGTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:3000337 original size:22 final size:22
Alignment explanation
Indices: 3000312--3000354 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3000302 TTTTTTAATA
3000312 TTTTTA-AATAATTTTAATAACT
1 TTTTTATAAT-ATTTTAATAACT
*
3000334 TTTTTATAATATTTTACTAAC
1 TTTTTATAATATTTTAATAAC
3000355 AAGTGTTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTATAATATTTTAATAACT
Found at i:3014172 original size:15 final size:15
Alignment explanation
Indices: 3014152--3014180 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3014142 ATGCTTGACA
3014152 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
3014167 CACCGTGTTATCAA
1 CACCGTGTTATCAA
3014181 GCAACAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:3015009 original size:31 final size:31
Alignment explanation
Indices: 3014968--3015037 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
3014958 AAATCAATTA
*
3014968 TTAGCGTGTTCAATTTAATGTGACAAGATGC
1 TTAGTGTGTTCAATTTAATGTGACAAGATGC
3014999 TTAGTGTGTTCAATTTAATGTGACAAGATGC
1 TTAGTGTGTTCAATTTAATGTGACAAGATGC
3015030 TTA-TGTGT
1 TTAGTGTGT
3015038 AACATGTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 5 0.13
31 33 0.87
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (31 bp):
TTAGTGTGTTCAATTTAATGTGACAAGATGC
Found at i:3024240 original size:24 final size:25
Alignment explanation
Indices: 3024188--3024241 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
3024178 AAATGAATAG
* *
3024188 AAATTGAGAAATGAAAAACATTCAG
1 AAATGGAGAAATGAAAAACATTCAA
* *
3024213 AAATGGAGAAATG-AAATCATTTAA
1 AAATGGAGAAATGAAAAACATTCAA
3024237 AAATG
1 AAATG
3024242 AACGTGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (25 bp):
AAATGGAGAAATGAAAAACATTCAA
Found at i:3035230 original size:50 final size:50
Alignment explanation
Indices: 3035150--3035295 Score: 166
Period size: 50 Copynumber: 2.9 Consensus size: 50
3035140 GGGATGTTTT
* * * **
3035150 TGCCAATGCCATATCCCAGATATAGTCTTACAAGGGAGTTATCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAAGGGACCTATCATATCGG
* ** * *
3035200 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAAGGGACCTATCATATCGG
* * * *
3035250 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAAGGGACCTATCATA
3035296 ATCTCAACGA
Statistics
Matches: 80, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAAGGGACCTATCATATCGG
Found at i:3039017 original size:210 final size:210
Alignment explanation
Indices: 3038653--3039077 Score: 787
Period size: 210 Copynumber: 2.0 Consensus size: 210
3038643 TTGGATAGTG
* * * *
3038653 CATCTAATGTTATTTCGTCTATGCCAAGACAGAAATATGGTAGAAAAGGTAGTGAAACGTATCTT
1 CATCTAATGTTATTTCGGCTATGCCAACACAGAAATATGGTAGAAAAGGCAGTGAAAAGTATCTT
3038718 GCTTATATATTTGATTCTAGAGTTTCTAAACTAAAGCTAGAATTGGTTCTTGTGGTATGCGAGTA
66 GCTTATATATTTGATTCTAGAGTTTCTAAACTAAAGCTAGAATTGGTTCTTGTGGTATGCGAGTA
* * *
3038783 TACTGGACTATTTCTAGTAGAATTACCTGGGTTACAGTTAATCAGAGAGGTTGAGTTTGCTATTG
131 TACTGGACTATTTCTAGAAGAATTACCTAGGTTACAGCTAATCAGAGAGGTTGAGTTTGCTATTG
3038848 AGTTAGTGTAGGGAA
196 AGTTAGTGTAGGGAA
3038863 CATCTAATGTTATTTCGGCTATGCCAACACAGAAATATGGTAGAAAAGGCAGTGAAAAGTATCTT
1 CATCTAATGTTATTTCGGCTATGCCAACACAGAAATATGGTAGAAAAGGCAGTGAAAAGTATCTT
3038928 GCTTATATATTTGATTCTAGAGTTTCTAAACTAAAGCTAGAATTGGTTCTTGTGGTATGCGAGTA
66 GCTTATATATTTGATTCTAGAGTTTCTAAACTAAAGCTAGAATTGGTTCTTGTGGTATGCGAGTA
3038993 TACTGGACTATTTCTAGAAGAATTACCTAGGTTACAGCTAATCAGAGAGGTTGAGTTTGCTATTG
131 TACTGGACTATTTCTAGAAGAATTACCTAGGTTACAGCTAATCAGAGAGGTTGAGTTTGCTATTG
3039058 AGTTAGTGTAGGGAA
196 AGTTAGTGTAGGGAA
3039073 CATCT
1 CATCT
3039078 CTGATATCGA
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
210 208 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (210 bp):
CATCTAATGTTATTTCGGCTATGCCAACACAGAAATATGGTAGAAAAGGCAGTGAAAAGTATCTT
GCTTATATATTTGATTCTAGAGTTTCTAAACTAAAGCTAGAATTGGTTCTTGTGGTATGCGAGTA
TACTGGACTATTTCTAGAAGAATTACCTAGGTTACAGCTAATCAGAGAGGTTGAGTTTGCTATTG
AGTTAGTGTAGGGAA
Found at i:3050016 original size:3 final size:3
Alignment explanation
Indices: 3050008--3050045 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3049998 GGAACTATAG
* *
3050008 TGA TGA TGA TGA TAA TGA TGA TGA TGA TGA TAA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
3050046 CTTTTTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:3050333 original size:15 final size:16
Alignment explanation
Indices: 3050313--3050343 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3050303 GAGGCAAAGT
3050313 AAAATA-TTTAAAAAA
1 AAAATATTTTAAAAAA
3050328 AAAATATTTTAAAAAA
1 AAAATATTTTAAAAAA
3050344 GAGGTATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATTTTAAAAAA
Found at i:3060950 original size:50 final size:49
Alignment explanation
Indices: 3060895--3061116 Score: 201
Period size: 50 Copynumber: 4.3 Consensus size: 49
3060885 CATCCTAGAT
** * *
3060895 ATGGTCTTACATGGGAGTTCTCATATAGGTGCCCATGCGATGTCCCAGAT
1 ATGGTCTTACATGGGACCTCTCATATAGGTGCCAATGC-ATGTCCCAGAC
** * * *
3060945 ATGGTCTTACGGGGGACCTCACATATTGGTGCCAATGCCATGTCCTAGAC
1 ATGGTCTTACATGGGACCTCTCATATAGGTGCCAATG-CATGTCCCAGAC
* * * * *
3060995 ATGGTCTTACATGGGACCTCTCATCTCGGTGCAAACGTCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATATAGGTGCCAATG-CATGTCCCAGAC
* * *
3061045 ATGGTCTTACATGGGACCTCTCATTATCTCAATGATGGCAATGCCATGTCCCAGGC
1 ATGGTCTTACATGGGACCTCTCA-TA--T--A-GGTGCCAATG-CATGTCCCAGAC
3061101 ATGGTCTTACATGGGA
1 ATGGTCTTACATGGGA
3061117 TCTCATCCTC
Statistics
Matches: 137, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
50 102 0.74
51 2 0.01
53 1 0.01
56 32 0.23
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (49 bp):
ATGGTCTTACATGGGACCTCTCATATAGGTGCCAATGCATGTCCCAGAC
Found at i:3061017 original size:100 final size:103
Alignment explanation
Indices: 3060876--3061116 Score: 247
Period size: 100 Copynumber: 2.3 Consensus size: 103
3060866 TCTTGTACTT
** * ** ** *
3060876 CCAATGCCACATCCTAGATATGGTCTTACATGGGAGTTCTCATATAGGTGCCCATG-CGATGTCC
1 CCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATAGGTGCAAACGTC-ATGTCC
* * * *
3060940 CAGATATGGTCTTACGGGGGACCTCACA-TA-T-TGGTG
65 CAAACATGGTCTTACAGGGGACCTCACATTACTATGATG
* *
3060976 CCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCAAACGTCATGTCCC
1 CCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATAGGTGCAAACGTCATGTCCC
* *
3061041 AAACATGGTCTTACATGGGACCTCTCATTATCTCAATGATG
66 AAACATGGTCTTACAGGGGACCTCACATTA-CT--ATGATG
* * *
3061082 GCAATGCCATGTCCCAGGCATGGTCTTACATGGGA
1 CCAATGCCATGTCCTAGACATGGTCTTACATGGGA
3061117 TCTCATCCTC
Statistics
Matches: 115, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
100 75 0.65
101 3 0.03
103 1 0.01
106 36 0.31
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (103 bp):
CCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATAGGTGCAAACGTCATGTCCC
AAACATGGTCTTACAGGGGACCTCACATTACTATGATG
Found at i:3067956 original size:50 final size:50
Alignment explanation
Indices: 3067884--3068126 Score: 227
Period size: 50 Copynumber: 4.7 Consensus size: 50
3067874 TTTCTTGTAC
** * **
3067884 TGCCAATGCCACATCCCAGATATGGTCTTACATGGGAGTTCTCATATAAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAAG
* * * ** * * *
3067934 TGCCCATGCGATGTCCCAGATATGGTCTTACGGGGGACGTCACATAT-CG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAAG
* * **
3067983 CTGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAAG
* * * *
3068034 TGCCAACGCCATGTCTCAGACATGGTTTTACATGGGACCTCTCATAATCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-AG
3068090 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
3068127 TCTCATCCTC
Statistics
Matches: 154, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.01
50 117 0.76
51 1 0.01
53 1 0.01
56 34 0.22
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAAG
Found at i:3068027 original size:100 final size:101
Alignment explanation
Indices: 3067883--3068126 Score: 256
Period size: 100 Copynumber: 2.4 Consensus size: 101
3067873 GTTTCTTGTA
** * ** * * *
3067883 CTGCCAATGCCACATCCCAGATATGGTCTTACATGGGAGTTCTCATATAAGTGCCCATGCGATGT
1 CTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAAGTGCCAACGCCATGT
* * *
3067948 CCCAGATATGGTCTTACGGGGGACGTCACAT-ATCG
66 CCCAGACATGGTCTTACAGGGGACCTCACATAATCG
* * **
3067983 CTGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGT
1 CTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAAGTGCCAACGCCATGT
* * * * *
3068048 CTCAGACATGGTTTTACATGGGACCTCTCATAATCT
66 CCCAGACATGGTCTTACAGGGGACCTCACATAATCG
3068084 CAATAATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 C-----TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
3068127 TCTCATCCTC
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
100 77 0.66
101 4 0.03
106 36 0.31
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (101 bp):
CTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAAGTGCCAACGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCACATAATCG
Found at i:3068505 original size:30 final size:30
Alignment explanation
Indices: 3068470--3068527 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3068460 CCTCGACTCT
3068470 AACTTTGACAAAATTACAATTTTGCCCCTA
1 AACTTTGACAAAATTACAATTTTGCCCCTA
* * *
3068500 AACTTTTACATAATTACACTTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
3068528 AAAGCTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:3073220 original size:14 final size:15
Alignment explanation
Indices: 3073201--3073230 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3073191 GAATCCACTA
3073201 ATCATTTTCTT-ACC
1 ATCATTTTCTTCACC
3073215 ATCATTTTCTTCACC
1 ATCATTTTCTTCACC
3073230 A
1 A
3073231 CTTCTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (15 bp):
ATCATTTTCTTCACC
Found at i:3076249 original size:18 final size:18
Alignment explanation
Indices: 3076208--3076249 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3076198 TCTAATTATA
*
3076208 TAAAAATTTTAACAAATT
1 TAAAATTTTTAACAAATT
*
3076226 TGAAATTTTTAA-AAATAT
1 TAAAATTTTTAACAAAT-T
3076244 TAAAAT
1 TAAAAT
3076250 AAAAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAAATTTTTAACAAATT
Found at i:3080072 original size:13 final size:13
Alignment explanation
Indices: 3080056--3080108 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
3080046 TTTAAACCAA
3080056 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
3080069 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* **
3080082 ACTTTTCCACTGC
1 ACTTTTCAAAAGC
3080095 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
3080108 A
1 A
3080109 ATGAAGAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:3080248 original size:23 final size:23
Alignment explanation
Indices: 3080222--3080343 Score: 154
Period size: 23 Copynumber: 5.3 Consensus size: 23
3080212 ATAAGTGCCA
3080222 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
3080245 CACTAATACGTAGCCGTAGCTAG
1 CACTGATATGTAGCCGAAGCTAC
* *
3080268 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3080291 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
3080314 CACCGAAATGTAGCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
3080337 CACTGAT
1 CACTGAT
3080344 CAATAACACT
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 80 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3080341 original size:46 final size:46
Alignment explanation
Indices: 3080229--3080343 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
3080219 CCACACTGAT
* * *
3080229 ATGTAGCCGAAGCTACCACTAATACGTAGCCGTAGCTAGCACTGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACCGAA
* *
3080275 ATGTAGCCAAAGCTACCACTGATATGTAGCCGTAGCTACCACCGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACCGAA
*
3080321 ATGTAGCCGAAGTTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAT
3080344 CAATAACACT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACCGAA
Found at i:3085960 original size:23 final size:23
Alignment explanation
Indices: 3085934--3085979 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3085924 AGTCTTTTTA
3085934 TTAATATATGAATATTATGTTTG
1 TTAATATATGAATATTATGTTTG
3085957 TTAATATATGAATATTATGTTTG
1 TTAATATATGAATATTATGTTTG
3085980 GATATTATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (23 bp):
TTAATATATGAATATTATGTTTG
Found at i:3086463 original size:45 final size:44
Alignment explanation
Indices: 3086379--3086471 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 44
3086369 ATTACAACAT
* *
3086379 CATTTCATTCAACCAAACACAAGAATACTATTATAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
3086423 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
3086468 CATT
1 CATT
3086472 ACAGCTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 22 0.50
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:3086474 original size:16 final size:16
Alignment explanation
Indices: 3086453--3086492 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3086443 TTGAATTACT
*
3086453 ATTACAG-TTCTATTCC
1 ATTACAGCTT-TATTCA
3086469 ATTACAGCTTTATTCA
1 ATTACAGCTTTATTCA
3086485 ATTACAGC
1 ATTACAGC
3086493 AAACCAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTACAGCTTTATTCA
Found at i:3091814 original size:42 final size:42
Alignment explanation
Indices: 3091750--3091830 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
3091740 TTTATAGCTT
* *
3091750 TTTTCCAACAACCCATGTTTATCTTCTCCTATTTTTAAATTCA
1 TTTTCCAACAACCCAAGATTATCTTCTCCT-TTTTTAAATTCA
*
3091793 TTTT-CAACAACGCAAGATTATCTTCTCCTTTTTTAAAT
1 TTTTCCAACAACCCAAGATTATCTTCTCCTTTTTTAAAT
3091831 GTTTTTCTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 9 0.26
42 22 0.63
43 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (42 bp):
TTTTCCAACAACCCAAGATTATCTTCTCCTTTTTTAAATTCA
Found at i:3107128 original size:41 final size:42
Alignment explanation
Indices: 3107065--3107143 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 42
3107055 ATAGCTTTCT
* *
3107065 TTTTCCAACAACCCATGTTTATCTTGTCA-TCTTTTTAAGTTC
1 TTTTCCAACAACCCATGATTATCTTCT-ATTCTTTTTAAGTTC
3107107 TTTT-CAACAACCC-TAGATTATCTTCTATTCTTTTTAA
1 TTTTCCAACAACCCAT-GATTATCTTCTATTCTTTTTAA
3107144 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
40 2 0.06
41 27 0.82
42 4 0.12
ACGTcount: A:0.24, C:0.23, G:0.05, T:0.48
Consensus pattern (42 bp):
TTTTCCAACAACCCATGATTATCTTCTATTCTTTTTAAGTTC
Found at i:3110298 original size:32 final size:31
Alignment explanation
Indices: 3110234--3110448 Score: 157
Period size: 32 Copynumber: 6.8 Consensus size: 31
3110224 TACAGTAATG
* * * *
3110234 TGATTGGCAAAAAGCCAT-AGTAGCAATGATA
1 TGATCGGCACAAAGCCATCAGTAGTAGT-ATA
3110265 TGATCGGCACAAAGCCATCAGTAGTAGTCATA
1 TGATCGGCACAAAGCCATCAGTAGTAGT-ATA
* * ** * *
3110297 TGACCAGCACGCAGCCATCAGTAATAGTGAAA
1 TGATCGGCACAAAGCCATCAGTAGTAGT-ATA
* * * *
3110329 TGACCAGCACACAGCCATCGGTA--ACGATAATA
1 TGATCGGCACAAAGCCATCAGTAGTA-G-T-ATA
* *
3110361 TGATCGGCACAAAGCCATCAGTAATGGTACTA
1 TGATCGGCACAAAGCCATCAGTAGTAGTA-TA
* **
3110393 TAATCGGCACAAAGCCATCAGTAGCGGTACTA
1 TGATCGGCACAAAGCCATCAGTAGTAGTA-TA
*
3110425 TGATCGGTACAAAGCCATCAGTAG
1 TGATCGGCACAAAGCCATCAGTAG
3110449 CATCGCAGCA
Statistics
Matches: 152, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
30 1 0.01
31 18 0.12
32 132 0.87
33 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (31 bp):
TGATCGGCACAAAGCCATCAGTAGTAGTATA
Found at i:3110449 original size:32 final size:32
Alignment explanation
Indices: 3110263--3110447 Score: 158
Period size: 32 Copynumber: 5.8 Consensus size: 32
3110253 GTAGCAATGA
***
3110263 TATGATCGGCACAAAGCCATCAGTAGTAGT-C
1 TATGATCGGCACAAAGCCATCAGTAACGGTAC
* * ** **
3110294 ATATGACCAGCACGCAGCCATCAGTAATAGTGA-
1 -TATGATCGGCACAAAGCCATCAGTAACGGT-AC
* * * * * * *
3110327 AATGACCAGCACACAGCCATCGGTAACGATAA
1 TATGATCGGCACAAAGCCATCAGTAACGGTAC
*
3110359 TATGATCGGCACAAAGCCATCAGTAATGGTAC
1 TATGATCGGCACAAAGCCATCAGTAACGGTAC
* *
3110391 TATAATCGGCACAAAGCCATCAGTAGCGGTAC
1 TATGATCGGCACAAAGCCATCAGTAACGGTAC
*
3110423 TATGATCGGTACAAAGCCATCAGTA
1 TATGATCGGCACAAAGCCATCAGTA
3110448 GCATCGCAGC
Statistics
Matches: 126, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
31 1 0.01
32 125 0.99
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (32 bp):
TATGATCGGCACAAAGCCATCAGTAACGGTAC
Found at i:3110530 original size:21 final size:20
Alignment explanation
Indices: 3110505--3110547 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
3110495 TAATGTATAT
*
3110505 GTGGCCAAGCCACCAGTAACA
1 GTGGCAAAGCCACCAGT-ACA
3110526 GTGGCAAAGCCACCAGTACA
1 GTGGCAAAGCCACCAGTACA
3110546 GT
1 GT
3110548 ACTTCCTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.30, G:0.26, T:0.12
Consensus pattern (20 bp):
GTGGCAAAGCCACCAGTACA
Found at i:3110644 original size:24 final size:23
Alignment explanation
Indices: 3110612--3110670 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
3110602 CCATGCTTAG
3110612 AATCAGTCATTCAAATCACAAACA
1 AATCAGTCATTCAAA-CACAAACA
* * *
3110636 AATCAGTCATACCAAACACAGATA
1 AATCAGTCAT-TCAAACACAAACA
3110660 AATCAGTCATT
1 AATCAGTCATT
3110671 TAACCACAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (23 bp):
AATCAGTCATTCAAACACAAACA
Found at i:3110773 original size:27 final size:27
Alignment explanation
Indices: 3110734--3110870 Score: 150
Period size: 27 Copynumber: 5.1 Consensus size: 27
3110724 ACACCAGGGA
*
3110734 ATTACGGTTATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** * *
3110761 ATTACTCTCATTTTACCCTATAAGGG-
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * *
3110787 CTTATGATCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
3110814 ATTACGGTCATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* **
3110841 TTTACGGTCATTTTACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
3110868 ATT
1 ATT
3110871 TTAGTATTCT
Statistics
Matches: 88, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
26 20 0.23
27 68 0.77
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:3110800 original size:53 final size:54
Alignment explanation
Indices: 3110743--3110870 Score: 168
Period size: 53 Copynumber: 2.4 Consensus size: 54
3110733 AATTACGGTT
* * *
3110743 ATTTTACCCTACAGGGGTATTACTCTCATTTTACCCTATAAGGG-CTTATGATC
1 ATTTTACCCTACAGGGGTATTACGCTCATTTTACCCTACAAGGGTCTTACGATC
* * * *
3110796 ATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAAGGGTTTTACGGTC
1 ATTTTACCCTACAGGGGTATTACGCTCATTTTACCCTACAAGGGTCTTACGATC
**
3110850 ATTTTACCCTATGGGGGTATT
1 ATTTTACCCTACAGGGGTATT
3110871 TTAGTATTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
53 40 0.62
54 24 0.38
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.37
Consensus pattern (54 bp):
ATTTTACCCTACAGGGGTATTACGCTCATTTTACCCTACAAGGGTCTTACGATC
Found at i:3110892 original size:27 final size:27
Alignment explanation
Indices: 3110847--3110964 Score: 102
Period size: 26 Copynumber: 4.4 Consensus size: 27
3110837 GGGTTTTACG
* *
3110847 GTCATTTTACCCTATGGGGGTATTTTA
1 GTCATTCTACCCCATGGGGGTATTTTA
3110874 GT-ATTCTACCCCATGGGGGTATTTTA
1 GTCATTCTACCCCATGGGGGTATTTTA
* * *
3110900 GTCATTTTA-CCCATCGAGGGTA-TTTC
1 GTCATTCTACCCCAT-GGGGGTATTTTA
* *
3110926 GATCATTTTA--CCATCGAGGGTATTTTA
1 G-TCATTCTACCCCAT-GGGGGTATTTTA
*
3110953 GTCATTTTACCC
1 GTCATTCTACCC
3110965 TTTTAGGGTA
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
26 53 0.67
27 25 0.32
28 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (27 bp):
GTCATTCTACCCCATGGGGGTATTTTA
Found at i:3110907 original size:53 final size:54
Alignment explanation
Indices: 3110847--3110992 Score: 144
Period size: 53 Copynumber: 2.8 Consensus size: 54
3110837 GGGTTTTACG
* *
3110847 GTCATTTTACCCTAT-GGGGGTATTTTAG-T-ATTCTACCCCAT-GGGGGTATTTTA
1 GTCATTTTACCCTATCGAGGGTA-TTTAGATCATTCTA--CCATCGAGGGTATTTTA
* *
3110900 GTCATTTTACCC-ATCGAGGGTATTTCGATCATTTTACCATCGAGGGTATTTTA
1 GTCATTTTACCCTATCGAGGGTATTTAGATCATTCTACCATCGAGGGTATTTTA
** *
3110953 GTCATTTTACCCT-TTTAGGGTATTTCAG-TCATTTTACCAT
1 GTCATTTTACCCTATCGAGGGTATTT-AGATCATTCTACCAT
3110993 TTGAGGATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
52 10 0.12
53 64 0.80
54 6 0.08
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTATCGAGGGTATTTAGATCATTCTACCATCGAGGGTATTTTA
Found at i:3110982 original size:27 final size:27
Alignment explanation
Indices: 3110820--3111004 Score: 144
Period size: 27 Copynumber: 6.9 Consensus size: 27
3110810 GGGCATTACG
*** *
3110820 GTCATTTTACCCTACAAGGGT-TTTACG
1 GTCATTTTACCCTTTGAGGGTATTT-CA
* * *
3110847 GTCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTTTGAGGGTATTTCA
* ** * *
3110874 GT-ATTCTACCCCATGGGGGTATTTTA
1 GTCATTTTACCCTTTGAGGGTATTTCA
* *
3110900 GTCATTTTACCCATCGAGGGTATTTC-
1 GTCATTTTACCCTTTGAGGGTATTTCA
* * *
3110926 GATCATTTTA-CCATCGAGGGTATTTTA
1 G-TCATTTTACCCTTTGAGGGTATTTCA
*
3110953 GTCATTTTACCCTTTTAGGGTATTTCA
1 GTCATTTTACCCTTTGAGGGTATTTCA
* *
3110980 GTCATTTTACCATTTGAGGATATTT
1 GTCATTTTACCCTTTGAGGGTATTT
3111005 TGGTCCAGAT
Statistics
Matches: 132, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 48 0.36
27 81 0.61
28 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTTTGAGGGTATTTCA
Found at i:3118176 original size:25 final size:25
Alignment explanation
Indices: 3118141--3118190 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3118131 CCGTACCTCC
* *
3118141 CTCGGGGAGGCTTACCGGATAATAA
1 CTCGGGCAGGCTTACCGGACAATAA
3118166 CTCGGGCAGGCTTACCGGACAATAA
1 CTCGGGCAGGCTTACCGGACAATAA
3118191 ACTCAGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.24, G:0.30, T:0.18
Consensus pattern (25 bp):
CTCGGGCAGGCTTACCGGACAATAA
Found at i:3121582 original size:20 final size:21
Alignment explanation
Indices: 3121553--3121597 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
3121543 TCTCTATATA
3121553 TTAA-ATTAAAGTGATTAA-T
1 TTAATATTAAAGTGATTAAGT
3121572 TTAATATTAAAGTGATTAAGT
1 TTAATATTAAAGTGATTAAGT
3121593 TTAAT
1 TTAAT
3121598 GATAGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (21 bp):
TTAATATTAAAGTGATTAAGT
Found at i:3123058 original size:75 final size:75
Alignment explanation
Indices: 3122931--3123073 Score: 234
Period size: 75 Copynumber: 1.9 Consensus size: 75
3122921 GGAAAACCAA
* * *
3122931 GATTATTCCCTTATTAATAGATAAGGCAAATGGAAAGTTAGAAAAAGAAATTATATTCTTTTCAA
1 GATTATTCCCTTATTAATAGAGAAGGCAAATGGAAACTTAGAAAAAGAAATTATATTCTTTCCAA
3122996 AAGAGCATAG
66 AAGAGCATAG
*
3123006 GATTATTCCCTTATTAATAGAGAAGGCAAATGGAAACTTTGAAAAATG-AATTATATTCTTTCCA
1 GATTATTCCCTTATTAATAGAGAAGGCAAATGGAAACTTAGAAAAA-GAAATTATATTCTTTCCA
3123070 AAAG
65 AAAG
3123074 GATATTAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 62 0.98
76 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.31
Consensus pattern (75 bp):
GATTATTCCCTTATTAATAGAGAAGGCAAATGGAAACTTAGAAAAAGAAATTATATTCTTTCCAA
AAGAGCATAG
Found at i:3123241 original size:71 final size:70
Alignment explanation
Indices: 3123163--3123378 Score: 180
Period size: 71 Copynumber: 3.1 Consensus size: 70
3123153 TATACATTTA
3123163 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATG
1 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCAT-
3123228 TCTTTT
65 TCTTTT
* * * * * * ** *
3123234 ATATTTTG-ACCGAAT-TAATT-A-ATA-TAATTGT-TTATATT--AATAA-ATTCAATAAAATA
1 ATATTTTGTA-TGAATCAAATTCATATATTAATTATATTCT-TTCCAA-AAGAAT-ATTAATTTT
* * *
3123290 CATACAATTA
62 CATTC-TTTT
*
3123300 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTTATA
1 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCAT-
3123365 TCTTTT
65 TCTTTT
*
3123371 ACATTTTG
1 ATATTTTG
3123379 ACTTAAATTA
Statistics
Matches: 104, Mismatches: 26, Indels: 30
0.65 0.16 0.19
Matches are distributed among these distances:
65 5 0.05
66 27 0.26
67 13 0.12
68 4 0.04
69 4 0.04
70 13 0.12
71 33 0.32
72 5 0.05
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (70 bp):
ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATT
CTTTT
Found at i:3123305 original size:137 final size:137
Alignment explanation
Indices: 3123054--3123467 Score: 636
Period size: 137 Copynumber: 3.0 Consensus size: 137
3123044 TTGAAAAATG
* *
3123054 AATTATATTCTTTCCAAAAGGATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTG-AATTAATTAA
* * * *
3123119 TATAATTTTTTACATTAATAAATTCGTTAAAATATATACATTTAATATTTTGTATGAATCAAATT
65 TATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
3123184 CATATATT
130 CATATATT
*
3123192 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAATTAATTAAT
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAATTAATTAAT
* *
3123257 ATAATTGTTTATATTAATAAATTCAATAAAATACATACAATTAATATTTTGTATGAATCAAATTC
66 ATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
3123322 ATATATT
131 ATATATT
* * * *
3123329 AATTATATTCTTTCCAAAAGAATATTAATTTTTATATCTTTTACATTTTGACTTAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGAC-TGAATTAATTAA
* * *
3123394 TATAATCGTTTATATTAATAAA-T-GGTAAAATATATGCAATTAATATTTT-TATGAATCAAATT
65 TATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
3123456 GATATATT
130 CATATATT
3123464 AATT
1 AATT
3123468 TATCTATATT
Statistics
Matches: 255, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
135 24 0.09
136 22 0.09
137 127 0.50
138 82 0.32
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAATTAATTAAT
ATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATT
Found at i:3142677 original size:30 final size:30
Alignment explanation
Indices: 3142641--3142703 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
3142631 TGAAACCAAA
3142641 CTTATTCAAGAGACTTCCAGACACTAAATT
1 CTTATTCAAGAGACTTCCAGACACTAAATT
*
3142671 CTTATTCAAGAGACTTCTAGACACTAAATT
1 CTTATTCAAGAGACTTCCAGACACTAAATT
3142701 CTT
1 CTT
3142704 CCTAACTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (30 bp):
CTTATTCAAGAGACTTCCAGACACTAAATT
Found at i:3155349 original size:38 final size:38
Alignment explanation
Indices: 3155305--3155380 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3155295 CATGTGAGAA
3155305 AAGGAAAAGCAAGATTTAGTTAACAAACATAGAGAAAT
1 AAGGAAAAGCAAGATTTAGTTAACAAACATAGAGAAAT
3155343 AAGGAAAAGCAAGATTTAGTTAACAAACATAGAGAAAT
1 AAGGAAAAGCAAGATTTAGTTAACAAACATAGAGAAAT
3155381 GTTGCTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.18
Consensus pattern (38 bp):
AAGGAAAAGCAAGATTTAGTTAACAAACATAGAGAAAT
Found at i:3157057 original size:23 final size:24
Alignment explanation
Indices: 3157018--3157062 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3157008 AGATGGACGA
*
3157018 AAAATTTTTATTTGTAACTTAAGT
1 AAAATTTTTATTAGTAACTTAAGT
3157042 AAAA-TTTTATTAGTAACTTAA
1 AAAATTTTTATTAGTAACTTAA
3157063 TTAATGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (24 bp):
AAAATTTTTATTAGTAACTTAAGT
Found at i:3157848 original size:396 final size:396
Alignment explanation
Indices: 3157111--3157887 Score: 1473
Period size: 396 Copynumber: 2.0 Consensus size: 396
3157101 TATGCTAAGG
*
3157111 TACCATTTGTCATTTGGTTACTGTTTTTGCCGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAT
1 TACCATTTGTCATTTGGTTACTGTTTTTGCCGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAC
*
3157176 TTGGATAGGAAAGAAAATAAAATAATTAAAAGTATTTATATATATCATTTATTTTAGAACAAAAT
66 TTGGATAGGAAAGAAAATAAAATAATTAAAAGTACTTATATATATCATTTATTTTAGAACAAAAT
* *
3157241 AATTTGATTTTTCTTTTAATAGAACAGTTATTCTAGAAATTTCGTTACATTTTAGTCATATATTT
131 AATTTGATTTTTCTTTTAATAGAACAGTTATACTAGAAATTTCGTTACAGTTTAGTCATATATTT
*
3157306 TCAATCAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAGGC
196 TCAATCAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAAGC
3157371 TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
261 TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
3157436 GAACACAGACCATAAAATGGACATGGAGAATACCAAAATACAAGAAACAAAAAGCAAAAATACAT
326 GAACACAGACCATAAAATGGACATGGAGAATACCAAAATACAAGAAACAAAAAGCAAAAATACAT
3157501 GGAGAA
391 GGAGAA
* *
3157507 TACCGTTTGTCATTTGGTTACTGTTTTTGCTGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAC
1 TACCATTTGTCATTTGGTTACTGTTTTTGCCGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAC
3157572 TTGGATAGGAAAGAAAATAAAATAATTAAAAGTACTTATATATATCATTTATTTTAGAACAAAAT
66 TTGGATAGGAAAGAAAATAAAATAATTAAAAGTACTTATATATATCATTTATTTTAGAACAAAAT
3157637 AATTTGATTTTTCTTTTAATAGAACAGTTATACTAGAAATTTCGTTACAGTTTAGTCATATATTT
131 AATTTGATTTTTCTTTTAATAGAACAGTTATACTAGAAATTTCGTTACAGTTTAGTCATATATTT
3157702 TCAATCAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAAGC
196 TCAATCAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAAGC
3157767 TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
261 TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
**
3157832 GAACATGGACCATAAAATGGACATGGAGAATACCAAAATACAAGAAACAAAAAGCA
326 GAACACAGACCATAAAATGGACATGGAGAATACCAAAATACAAGAAACAAAAAGCA
3157888 TATTCGCGGA
Statistics
Matches: 372, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
396 372 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (396 bp):
TACCATTTGTCATTTGGTTACTGTTTTTGCCGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAC
TTGGATAGGAAAGAAAATAAAATAATTAAAAGTACTTATATATATCATTTATTTTAGAACAAAAT
AATTTGATTTTTCTTTTAATAGAACAGTTATACTAGAAATTTCGTTACAGTTTAGTCATATATTT
TCAATCAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAAGC
TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
GAACACAGACCATAAAATGGACATGGAGAATACCAAAATACAAGAAACAAAAAGCAAAAATACAT
GGAGAA
Found at i:3162012 original size:15 final size:15
Alignment explanation
Indices: 3161992--3162021 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3161982 TTTGTAAATG
*
3161992 TTCTTTACCTGAGGA
1 TTCTTTACCTCAGGA
3162007 TTCTTTACCTCAGGA
1 TTCTTTACCTCAGGA
3162022 ACAGTTATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (15 bp):
TTCTTTACCTCAGGA
Found at i:3173247 original size:24 final size:25
Alignment explanation
Indices: 3173184--3173247 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
3173174 TTACTGATAC
*
3173184 TCAGCTCGTATGAGATAACCATTAT
1 TCAGCTCGTATGAGCTAACCATTAT
* * *
3173209 TCAGCTCGGAGGAGCTTACCATT-T
1 TCAGCTCGTATGAGCTAACCATTAT
3173233 ATC-GCTCGTATGAGC
1 -TCAGCTCGTATGAGC
3173248 AAAAATGTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 11 0.34
25 21 0.66
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (25 bp):
TCAGCTCGTATGAGCTAACCATTAT
Found at i:3174358 original size:112 final size:112
Alignment explanation
Indices: 3174161--3174377 Score: 434
Period size: 112 Copynumber: 1.9 Consensus size: 112
3174151 TGTAAATTGT
3174161 TGAGCTTAGGTTAAAACCAAATTGAGTTAGAAATATGGCTTGGAAAATGACTTATTTTTGTCTAG
1 TGAGCTTAGGTTAAAACCAAATTGAGTTAGAAATATGGCTTGGAAAATGACTTATTTTTGTCTAG
3174226 ACGAGCAGAGACACGGGCGTGTGTCTCAGTCGTATGTGACGGCCAGG
66 ACGAGCAGAGACACGGGCGTGTGTCTCAGTCGTATGTGACGGCCAGG
3174273 TGAGCTTAGGTTAAAACCAAATTGAGTTAGAAATATGGCTTGGAAAATGACTTATTTTTGTCTAG
1 TGAGCTTAGGTTAAAACCAAATTGAGTTAGAAATATGGCTTGGAAAATGACTTATTTTTGTCTAG
3174338 ACGAGCAGAGACACGGGCGTGTGTCTCAGTCGTATGTGAC
66 ACGAGCAGAGACACGGGCGTGTGTCTCAGTCGTATGTGAC
3174378 ACACGGCCAG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 105 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (112 bp):
TGAGCTTAGGTTAAAACCAAATTGAGTTAGAAATATGGCTTGGAAAATGACTTATTTTTGTCTAG
ACGAGCAGAGACACGGGCGTGTGTCTCAGTCGTATGTGACGGCCAGG
Found at i:3176545 original size:45 final size:45
Alignment explanation
Indices: 3176481--3176645 Score: 179
Period size: 45 Copynumber: 3.7 Consensus size: 45
3176471 TCTTACAAAT
** *
3176481 ACCATAGCTGAAAGATGTTATGGTGTCACTG-CAAAAATGAGTAAG
1 ACCATAGCTGAAAGATGTTATGGCATCA-TGAAAAAAATGAGTAAG
*
3176526 ACCATAGTTGAAAGATGTTATGGCATCATGAAAAAAATGAGTAAG
1 ACCATAGCTGAAAGATGTTATGGCATCATGAAAAAAATGAGTAAG
* * * ** * *
3176571 ACCATAGCCGAAAGACGCTATGGCATCATGGTAGAAATAAGTAAG
1 ACCATAGCTGAAAGATGTTATGGCATCATGAAAAAAATGAGTAAG
* ***
3176616 ACCATAGCTAAAAGACACTATGGCATCATG
1 ACCATAGCTGAAAGATGTTATGGCATCATG
3176646 TGAAAGCACG
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 2 0.02
45 102 0.98
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (45 bp):
ACCATAGCTGAAAGATGTTATGGCATCATGAAAAAAATGAGTAAG
Found at i:3197195 original size:13 final size:13
Alignment explanation
Indices: 3197160--3197196 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3197150 ACTTTGTATA
3197160 ATTTTCTCTTTAG
1 ATTTTCTCTTTAG
**
3197173 ATTTAGTCTTTAG
1 ATTTTCTCTTTAG
3197186 ATTTTCTCTTT
1 ATTTTCTCTTT
3197197 TCTTAGGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTTTCTCTTTAG
Found at i:3198860 original size:19 final size:19
Alignment explanation
Indices: 3198844--3198891 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3198834 ATATTAGCGA
3198844 ATGAAGTGCATCCTAGCAC
1 ATGAAGTGCATCCTAGCAC
*
3198863 ACGAAGTGCATCCTAGCAC
1 ATGAAGTGCATCCTAGCAC
3198882 AT-AAGTGCAT
1 ATGAAGTGCAT
3198892 AAACTCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (19 bp):
ATGAAGTGCATCCTAGCAC
Found at i:3200149 original size:20 final size:20
Alignment explanation
Indices: 3200124--3200175 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3200114 AATAAAAATA
3200124 GTGGTATCGATAATTAATTT
1 GTGGTATCGATAATTAATTT
*
3200144 GTGGTATTGATAATTAATTT
1 GTGGTATCGATAATTAATTT
*
3200164 GTTGTATCGATA
1 GTGGTATCGATA
3200176 CTTTATATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (20 bp):
GTGGTATCGATAATTAATTT
Found at i:3203913 original size:21 final size:21
Alignment explanation
Indices: 3203887--3203927 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3203877 CCAGCTTCTG
* *
3203887 GCGAGGGTTATGGTTGCTCCA
1 GCGAGGATTATGGTTCCTCCA
*
3203908 GCGAGGATTCTGGTTCCTCC
1 GCGAGGATTATGGTTCCTCC
3203928 GGTAGGGGAT
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:0.12, C:0.24, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGAGGATTATGGTTCCTCCA
Found at i:3204211 original size:18 final size:18
Alignment explanation
Indices: 3204185--3204227 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3204175 GACTAGAAAA
* *
3204185 AGGAAACATAAAAGGGTT
1 AGGATACATAAAAGGGCT
3204203 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
3204221 AGGATAC
1 AGGATAC
3204228 GCACCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:3204314 original size:30 final size:30
Alignment explanation
Indices: 3204280--3204352 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
3204270 GGTTGAACTA
* *
3204280 CTGGGTCGGGTGACTGTGTCGGTGCTGTTG
1 CTGGGTCGGGTGACTGTATCGGTGCTGATG
* *
3204310 CTGGGT-GTGGTGATTGTATGGGTGCTGATG
1 CTGGGTCG-GGTGACTGTATCGGTGCTGATG
* *
3204340 ATGGGCCGGGTGA
1 CTGGGTCGGGTGA
3204353 TTGTCTGGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 1 0.03
30 33 0.94
31 1 0.03
ACGTcount: A:0.08, C:0.12, G:0.48, T:0.32
Consensus pattern (30 bp):
CTGGGTCGGGTGACTGTATCGGTGCTGATG
Found at i:3206079 original size:11 final size:11
Alignment explanation
Indices: 3206063--3206130 Score: 86
Period size: 11 Copynumber: 6.2 Consensus size: 11
3206053 TTTTTTAAAT
*
3206063 AGGAATTTGAG
1 AGGAAATTGAG
*
3206074 AGGAATTTGAG
1 AGGAAATTGAG
3206085 AGGAAATTGAG
1 AGGAAATTGAG
3206096 AGGAAATTGAG
1 AGGAAATTGAG
3206107 A-GAATATT-AG
1 AGGAA-ATTGAG
3206117 AGAGAAATTGAG
1 AG-GAAATTGAG
3206129 AG
1 AG
3206131 AAAGGATTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
10 6 0.12
11 39 0.75
12 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:3206100 original size:33 final size:33
Alignment explanation
Indices: 3206063--3206130 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3206053 TTTTTTAAAT
*
3206063 AGGAATTTGAGAGGAAT-TTGAGAG-GAAATTGAG
1 AGGAAATTGAGA-GAATATT-AGAGAGAAATTGAG
3206096 AGGAAATTGAGAGAATATTAGAGAGAAATTGAG
1 AGGAAATTGAGAGAATATTAGAGAGAAATTGAG
3206129 AG
1 AG
3206131 AAAGGATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 8 0.25
33 24 0.75
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (33 bp):
AGGAAATTGAGAGAATATTAGAGAGAAATTGAG
Found at i:3207074 original size:21 final size:21
Alignment explanation
Indices: 3207050--3207105 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
3207040 CATCATTATT
*
3207050 TCTAATCTCACTGCTACAATA
1 TCTAATCTCACCGCTACAATA
* *
3207071 TCTAATCTCACCGCTATAGTA
1 TCTAATCTCACCGCTACAATA
*
3207092 TCTAATTTCACCGC
1 TCTAATCTCACCGC
3207106 CACCGCTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAATA
Found at i:3207445 original size:6 final size:6
Alignment explanation
Indices: 3207425--3207468 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
3207415 ACCCTTCTTC
* *
3207425 TCCCCTT TCCTCT TCCCCT TCCCCT TCCCTT TCCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
3207469 GGGTTGCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
TCCCCT
Found at i:3207452 original size:18 final size:18
Alignment explanation
Indices: 3207425--3207468 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
3207415 ACCCTTCTTC
*
3207425 TCCCCTTTCCTCTTCCCCT
1 TCCCCTTCCCT-TTCCCCT
3207444 TCCCCTTCCCTTTCCCCT
1 TCCCCTTCCCTTTCCCCT
3207462 TCCCCTT
1 TCCCCTT
3207469 GGGTTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (18 bp):
TCCCCTTCCCTTTCCCCT
Found at i:3207587 original size:25 final size:27
Alignment explanation
Indices: 3207527--3207587 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
3207517 CCAGGTAAGG
3207527 CTTCTTCTTCTTCATCCGTTCTTCATTC
1 CTTC-TCTTCTTCATCCGTTCTTCATTC
*
3207555 CTT-T-TTCTTCTTCCGTTCTTCA-T-
1 CTTCTCTTCTTCATCCGTTCTTCATTC
3207578 CTTCTCTTCT
1 CTTCTCTTCT
3207588 CAGCATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.10
24 2 0.07
25 21 0.70
26 1 0.03
28 3 0.10
ACGTcount: A:0.05, C:0.34, G:0.03, T:0.57
Consensus pattern (27 bp):
CTTCTCTTCTTCATCCGTTCTTCATTC
Found at i:3207723 original size:12 final size:12
Alignment explanation
Indices: 3207692--3207724 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3207682 CGTTCTCACT
*
3207692 AAAATCGATAAA
1 AAAATCGGTAAA
3207704 AAAATCGGTAAA
1 AAAATCGGTAAA
3207716 AAAATCGGT
1 AAAATCGGT
3207725 GGTTCCAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.18
Consensus pattern (12 bp):
AAAATCGGTAAA
Found at i:3208072 original size:14 final size:13
Alignment explanation
Indices: 3208046--3208070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3208036 TCAATGAACC
3208046 CTTAATTTTTTTG
1 CTTAATTTTTTTG
3208059 CTTAATTTTTTT
1 CTTAATTTTTTT
3208071 TGGTACAGAA
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:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
CTTAATTTTTTTG
Found at i:3210619 original size:12 final size:12
Alignment explanation
Indices: 3210589--3210621 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3210579 ATGCAACAGG
3210589 AAACCAGCA-GC
1 AAACCAGCATGC
3210600 AAACCAGCATGC
1 AAACCAGCATGC
*
3210612 AGACCAGCAT
1 AAACCAGCAT
3210622 CCAAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:3214494 original size:22 final size:22
Alignment explanation
Indices: 3214469--3214511 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3214459 TAATTTCAAG
3214469 TTTAAATT-TGTACTAACTATTC
1 TTTAAATTATGT-CTAACTATTC
**
3214491 TTTATTTTATGTCTAACTATT
1 TTTAAATTATGTCTAACTATT
3214512 GTGATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTAAATTATGTCTAACTATTC
Found at i:3217369 original size:3 final size:3
Alignment explanation
Indices: 3217355--3217394 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
3217345 AGTTGTGCCC
* *
3217355 GCT GCT GGT GCT GCT GGT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
3217395 AAAGTTCGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.28, G:0.40, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:3220889 original size:21 final size:20
Alignment explanation
Indices: 3220859--3220897 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3220849 AAATAGTTAT
*
3220859 TTTTATTTATCTCATATTTTA
1 TTTTAATTAT-TCATATTTTA
*
3220880 TTTTAATTATTTATATTT
1 TTTTAATTATTCATATTT
3220898 AAAATATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTAATTATTCATATTTTA
Found at i:3221123 original size:25 final size:25
Alignment explanation
Indices: 3221074--3221123 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3221064 TTTTGAGTAA
* *
3221074 TTTAAATTTTTTTGTTTTATGTTTT
1 TTTAAATTTTTTTCTTTTATATTTT
* *
3221099 TTTAACTTTTTTTCTTTTTTATTTT
1 TTTAAATTTTTTTCTTTTATATTTT
3221124 CTATTCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (25 bp):
TTTAAATTTTTTTCTTTTATATTTT
Found at i:3222867 original size:11 final size:11
Alignment explanation
Indices: 3222853--3222897 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
3222843 AGATAAATAT
3222853 TATTTTATTAA
1 TATTTTATTAA
*
3222864 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
3222877 TATTTTACTAA
1 TATTTTATTAA
3222888 TATTTTATTA
1 TATTTTATTA
3222898 TAAATAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 16 0.57
12 5 0.18
13 7 0.25
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:3222939 original size:2 final size:2
Alignment explanation
Indices: 3222932--3222963 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3222922 GAAGATGAAA
3222932 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
3222964 GATCCTCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3224108 original size:2 final size:2
Alignment explanation
Indices: 3224101--3224127 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3224091 AACTATATGA
3224101 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3224128 GTAGATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3226737 original size:17 final size:17
Alignment explanation
Indices: 3226692--3226738 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
3226682 ATAAGCAAAA
* *
3226692 AAAATTAGTTTTTGCTC
1 AAAAGTAGTTTTTGCCC
*
3226709 AAAAGTACTTTTTGGCCC
1 AAAAGTAGTTTTT-GCCC
3226727 AAAAGT-GTTTTT
1 AAAAGTAGTTTTT
3226739 AAGAAGCGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (17 bp):
AAAAGTAGTTTTTGCCC
Found at i:3235080 original size:35 final size:36
Alignment explanation
Indices: 3235039--3235106 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
3235029 GTTTTTTATT
3235039 TAAATTT-AAAAAAACCCTTATTTCGACCCTTTAAA
1 TAAATTTAAAAAAAACCCTTATTTCGACCCTTTAAA
*
3235074 TAAATTTAAAAAAAACCCTTATTTCGGCCCTTT
1 TAAATTTAAAAAAAACCCTTATTTCGACCCTTT
3235107 GTTAGTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (36 bp):
TAAATTTAAAAAAAACCCTTATTTCGACCCTTTAAA
Found at i:3235234 original size:189 final size:189
Alignment explanation
Indices: 3234905--3235253 Score: 508
Period size: 189 Copynumber: 1.8 Consensus size: 189
3234895 AACATGTTCG
* *
3234905 TATTTCAGCCCTTTGTTCGTAATTTTTTCCCCGGATTTTATTACTTTAAAAAATATACTATTTTC
1 TATTTCAGCCCTTTGTTAGTAATTTTTTCCCCGGATTTTATTACTTAAAAAAATATACTATTTTC
* * * * *
3234970 TAGTTTTATTATTTTATATTATTTTAGTACATTATGTTTGAAATTTATTCATTTAGTGTGTTTTT
66 TAGTTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGTTTTT
* ** *
3235035 TATTTAAA-TTTAAAAAAACCCTTATTTCGACCCTTTAAATAAATTTAAAAAAAACCCT
131 GAAATAAATTTTAAAAAAACCATTATTTCGACCCTTTAAATAAATTTAAAAAAAACCCT
* * *
3235093 TATTTCGGCCCTTTGTTAGT-ATTTTTT-TCCGGATTTTATTACTTCCAATAAAAATATATTATT
1 TATTTCAGCCCTTTGTTAGTAATTTTTTCCCCGGATTTTATTACTT--AA-AAAAATATACTATT
3235156 TTCGTA-TTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGT
63 TTC-TAGTTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGT
3235220 TTTTGAAATAAATTTTAAAAAAACCATTATTTCG
127 TTTTGAAATAAATTTTAAAAAAACCATTATTTCG
3235254 GCCATTTGTT
Statistics
Matches: 142, Mismatches: 14, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
186 16 0.11
187 7 0.05
188 19 0.13
189 78 0.55
190 22 0.15
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (189 bp):
TATTTCAGCCCTTTGTTAGTAATTTTTTCCCCGGATTTTATTACTTAAAAAAATATACTATTTTC
TAGTTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGTTTTT
GAAATAAATTTTAAAAAAACCATTATTTCGACCCTTTAAATAAATTTAAAAAAAACCCT
Found at i:3235250 original size:154 final size:153
Alignment explanation
Indices: 3235068--3235606 Score: 809
Period size: 152 Copynumber: 3.5 Consensus size: 153
3235058 ATTTCGACCC
*
3235068 TTTAAATAAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTAGTATTTTTTTCCGGATTTTATT
1 TTTAAATAAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCGGATTTTATT
* *
3235133 ACTTCCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATATTT
66 ACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTT
* *
3235198 GAAATGTATTAATTTACTGTGTT
131 GAAATGTATTCATTTAGTGTGTT
* * *
3235221 TTTGAAATAAATTTTAAAAAAACCATTATTTCGGCCATTTGTTCGTATTTTTTTCCGGATTTTAT
1 TTT-AAATAAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCGGATTTTAT
*
3235286 TACTTT-TA-AAAAATATATTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGT
65 TACTTTCAATAAAAATATATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGT
*
3235348 TTGAAATTTATTCATTTAGTGTGTTT
129 TTGAAATGTATTCATTTAGTGTG-TT
** * *
3235374 TTTATTTAAATTT-AAAAAAACCCTTATTTCGACCCTTTATTCGTATTTTTTT-CGGATTTTATT
1 TTTAAATAAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCGGATTTTATT
* *
3235437 ACTTTCAATAAAAATATATTATTTTCGTATTCTATTATTTTAAATTATTTTAGTACATTATGTTT
66 ACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTT
3235502 GAAATGTATTCATTTAGTGTGTGT
131 GAAATGTATTCATTTAGTGTGT-T
** *
3235526 TTTATTTAAATTTAAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTACCGAATTTTA
1 TTTAAATAAATTT-AAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTT-CCGGATTTTA
*
3235591 TTGCTTTCAATAAAAA
64 TTACTTTCAATAAAAA
3235607 ACACACTAAA
Statistics
Matches: 351, Mismatches: 24, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
150 16 0.05
151 38 0.11
152 165 0.47
153 10 0.03
154 99 0.28
156 23 0.07
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (153 bp):
TTTAAATAAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCGGATTTTATT
ACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTT
GAAATGTATTCATTTAGTGTGTT
Found at i:3236290 original size:433 final size:433
Alignment explanation
Indices: 3235484--3236347 Score: 1728
Period size: 433 Copynumber: 2.0 Consensus size: 433
3235474 TTTTAAATTA
3235484 TTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTGTTTTATTTAAATTTAAAAAAAAAC
1 TTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTGTTTTATTTAAATTTAAAAAAAAAC
3235549 CCTTATTTCGGCCCTTTGTTCGTATTTTTTTACCGAATTTTATTGCTTTCAATAAAAAACACACT
66 CCTTATTTCGGCCCTTTGTTCGTATTTTTTTACCGAATTTTATTGCTTTCAATAAAAAACACACT
3235614 AAATGAATACATTTCAAGCATAATGTACTAAAATAATATAAAATAATAAATTATAAAATAGTATT
131 AAATGAATACATTTCAAGCATAATGTACTAAAATAATATAAAATAATAAATTATAAAATAGTATT
3235679 TTTTTAAAGTAATAAAATTTGGGGAAAAAATACGAACAAAGGGCTGAAATACGAACATGTTGGTG
196 TTTTTAAAGTAATAAAATTTGGGGAAAAAATACGAACAAAGGGCTGAAATACGAACATGTTGGTG
3235744 CCGCCTTTGCCACAGGCACCATTGGTGCCGCCTAGACTTGTCCATGGGCTGGGCCGGGCCCAGAA
261 CCGCCTTTGCCACAGGCACCATTGGTGCCGCCTAGACTTGTCCATGGGCTGGGCCGGGCCCAGAA
3235809 AAATTTCAACCCGCTTCCTAGGCCCGGCCCGGCCCAAAATATGGGCCTGAGATTTTGTCCAGGCC
326 AAATTTCAACCCGCTTCCTAGGCCCGGCCCGGCCCAAAATATGGGCCTGAGATTTTGTCCAGGCC
3235874 CGGCCTGAAGAAAAAATATGGGGCCCGAGCCCGGCCCGGCCTT
391 CGGCCTGAAGAAAAAATATGGGGCCCGAGCCCGGCCCGGCCTT
3235917 TTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTGTTTTATTTAAATTTAAAAAAAAAC
1 TTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTGTTTTATTTAAATTTAAAAAAAAAC
3235982 CCTTATTTCGGCCCTTTGTTCGTATTTTTTTACCGAATTTTATTGCTTTCAATAAAAAACACACT
66 CCTTATTTCGGCCCTTTGTTCGTATTTTTTTACCGAATTTTATTGCTTTCAATAAAAAACACACT
3236047 AAATGAATACATTTCAAGCATAATGTACTAAAATAATATAAAATAATAAATTATAAAATAGTATT
131 AAATGAATACATTTCAAGCATAATGTACTAAAATAATATAAAATAATAAATTATAAAATAGTATT
3236112 TTTTTAAAGTAATAAAATTTGGGGAAAAAATACGAACAAAGGGCTGAAATACGAACATGTTGGTG
196 TTTTTAAAGTAATAAAATTTGGGGAAAAAATACGAACAAAGGGCTGAAATACGAACATGTTGGTG
3236177 CCGCCTTTGCCACAGGCACCATTGGTGCCGCCTAGACTTGTCCATGGGCTGGGCCGGGCCCAGAA
261 CCGCCTTTGCCACAGGCACCATTGGTGCCGCCTAGACTTGTCCATGGGCTGGGCCGGGCCCAGAA
3236242 AAATTTCAACCCGCTTCCTAGGCCCGGCCCGGCCCAAAATATGGGCCTGAGATTTTGTCCAGGCC
326 AAATTTCAACCCGCTTCCTAGGCCCGGCCCGGCCCAAAATATGGGCCTGAGATTTTGTCCAGGCC
3236307 CGGCCTGAAGAAAAAATATGGGGCCCGAGCCCGGCCCGGCC
391 CGGCCTGAAGAAAAAATATGGGGCCCGAGCCCGGCCCGGCC
3236348 CGTTTTTAAT
Statistics
Matches: 431, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
433 431 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (433 bp):
TTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTGTTTTATTTAAATTTAAAAAAAAAC
CCTTATTTCGGCCCTTTGTTCGTATTTTTTTACCGAATTTTATTGCTTTCAATAAAAAACACACT
AAATGAATACATTTCAAGCATAATGTACTAAAATAATATAAAATAATAAATTATAAAATAGTATT
TTTTTAAAGTAATAAAATTTGGGGAAAAAATACGAACAAAGGGCTGAAATACGAACATGTTGGTG
CCGCCTTTGCCACAGGCACCATTGGTGCCGCCTAGACTTGTCCATGGGCTGGGCCGGGCCCAGAA
AAATTTCAACCCGCTTCCTAGGCCCGGCCCGGCCCAAAATATGGGCCTGAGATTTTGTCCAGGCC
CGGCCTGAAGAAAAAATATGGGGCCCGAGCCCGGCCCGGCCTT
Found at i:3236418 original size:15 final size:16
Alignment explanation
Indices: 3236382--3236420 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3236372 TTGATAAAAT
* *
3236382 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3236398 TAAAATTAATTG-TAG
1 TAAAATTAATTGTTAG
3236413 TAAAATTA
1 TAAAATTA
3236421 TTAATTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3236515 original size:40 final size:36
Alignment explanation
Indices: 3236471--3236569 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 36
3236461 AAATTATATC
*
3236471 AAATTATTAATTATTAATTGTTACTAACATTTCTTTAGTA
1 AAATTATTAATTATTAATTGTTA-TAA-A-TT-GTTAGTA
* *
3236511 AAATTATTAATTGTTAATTG-TATTAATTGTTAGTA
1 AAATTATTAATTATTAATTGTTATAAATTGTTAGTA
*
3236546 AAATTATCAAATTATTAATTGTTA
1 AAATTAT-TAATTATTAATTGTTA
3236570 ATTGTTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 13 0.25
36 13 0.25
37 3 0.06
38 2 0.04
39 2 0.04
40 19 0.37
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (36 bp):
AAATTATTAATTATTAATTGTTATAAATTGTTAGTA
Found at i:3236536 original size:16 final size:16
Alignment explanation
Indices: 3236515--3236584 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 16
3236505 TTAGTAAAAT
3236515 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
3236531 TATTAATTGTT-A--G
1 TATTAATTGTTAATTG
* * * *
3236544 TA-AAATTATCAAAT-
1 TATTAATTGTTAATTG
3236558 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
*
3236574 TTTTAATTGTT
1 TATTAATTGTT
3236585 GTAACAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 2 0.05
15 9 0.22
16 21 0.51
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (16 bp):
TATTAATTGTTAATTG
Found at i:3239059 original size:43 final size:42
Alignment explanation
Indices: 3238963--3239189 Score: 221
Period size: 43 Copynumber: 5.4 Consensus size: 42
3238953 CTCGGTGGAT
3238963 TCAGCACTTAGCAACCACC-TTA-AATTC-AGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAA-TCAAG-GATACGGGGAA
*
3239004 TCAGCACATAGCAACC-CCTTTCACAATCAAGGATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAAGGATACGG-GGAA
* * * * *
3239047 TCAACACTTAGCAACCACCTATATATTCAATGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAAGGATACGGGGAA
* * *
3239089 TCAGCACGTAGCAACC-CCTTTCACAATAAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAAGGATACGG-GGAA
* * * ** **
3239132 TTAGCACTTAGCAACCACCTTTAGAGTCAATAATTTGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAAGGATACGGGGAA
3239174 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
3239190 CCTCGGGGAA
Statistics
Matches: 153, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
40 2 0.01
41 21 0.14
42 59 0.39
43 62 0.41
44 9 0.06
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTACAATCAAGGATACGGGGAA
Found at i:3239101 original size:85 final size:84
Alignment explanation
Indices: 3238955--3239192 Score: 332
Period size: 85 Copynumber: 2.8 Consensus size: 84
3238945 ATCTGTTACT
* *
3238955 CGGTGGATTCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAATGATACGGGGAATCAGCACATAGCAACC
* *
3239020 CCTTTCACAATCAAGGATA
66 CCTTTCACAATAAAAGATA
* * *
3239039 CGGTGGAATCAACACTTAGCAACCACCTATATATTCAATGATACGGGGAATCAGCACGTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCT-TAAATTCAATGATACGGGGAATCAGCACATAGCAAC
3239104 CCCTTTCACAATAAAAGATA
65 CCCTTTCACAATAAAAGATA
* * * * ** *
3239124 CGGTGGAATTAGCACTTAGCAACCACCTTTAGAGTCAATAATTTGGGGAATCAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACC-TTAAATTCAATGATACGGGGAATCAGCACATAGCAAC
3239189 CCCT
65 CCCT
3239193 CGGGGAATCT
Statistics
Matches: 137, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 26 0.19
85 110 0.80
86 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAATGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATAAAAGATA
Found at i:3239102 original size:42 final size:42
Alignment explanation
Indices: 3238963--3239189 Score: 237
Period size: 42 Copynumber: 5.4 Consensus size: 42
3238953 CTCGGTGGAT
*
3238963 TCAGCACTTAGCAACCACC-TTA-AATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAA-TCAATGATACGGGGAA
* *
3239004 TCAGCACATAGCAACC-CCTTTCACAATCAAGGATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAATGATACGG-GGAA
* * * *
3239047 TCAACACTTAGCAACCACCTATATATTCAATGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
* * *
3239089 TCAGCACGTAGCAACC-CCTTTCACAATAAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAATGATACGG-GGAA
* * * * **
3239132 TTAGCACTTAGCAACCACCTTTAGAGTCAATAATTTGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
3239174 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
3239190 CCTCGGGGAA
Statistics
Matches: 152, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.01
41 21 0.14
42 60 0.39
43 60 0.39
44 9 0.06
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
Found at i:3239197 original size:26 final size:26
Alignment explanation
Indices: 3239168--3239218 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3239158 TCAATAATTT
3239168 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACTTAGCAACCCCTC
* *
3239194 GGGGAATCTGCACTTAGCGACCCCT
1 GGGGAATCAGCACTTAGCAACCCCT
3239219 TTTTATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (26 bp):
GGGGAATCAGCACTTAGCAACCCCTC
Found at i:3245410 original size:24 final size:23
Alignment explanation
Indices: 3245367--3245414 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
3245357 TCTTAAATTA
*
3245367 ATTATATATATATATTTTATTTG
1 ATTATATATAAATATTTTATTTG
3245390 ATTA-ATATAAATACTTATTATTTG
1 ATTATATATAAATA-TT-TTATTTG
3245414 A
1 A
3245415 AATGAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 6 0.27
24 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTATATATAAATATTTTATTTG
Found at i:3246878 original size:31 final size:29
Alignment explanation
Indices: 3246811--3246884 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
3246801 ACTTAAGGTT
* *
3246811 ACATTTTAGTCACTTATATTTAAAATGTT
1 ACATTTTAGTCACTTACATTTAAAATGTA
*
3246840 ACATTTTAGTCACTTACA-TTAACGAGTTGTA
1 ACATTTTAGTCACTTACATTTAA--A-ATGTA
3246871 ACATTTTAGTCACT
1 ACATTTTAGTCACT
3246885 AAGCCGTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 4 0.10
29 17 0.44
30 1 0.03
31 17 0.44
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
ACATTTTAGTCACTTACATTTAAAATGTA
Found at i:3247480 original size:24 final size:23
Alignment explanation
Indices: 3247437--3247484 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
3247427 TCTTAAATTA
*
3247437 ATTATATATATATATTTTATTTG
1 ATTATATATAAATATTTTATTTG
3247460 ATTA-ATATAAATACTTATTATTTG
1 ATTATATATAAATA-TT-TTATTTG
3247484 A
1 A
3247485 CGTGGCACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 6 0.27
24 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTATATATAAATATTTTATTTG
Found at i:3248266 original size:12 final size:13
Alignment explanation
Indices: 3248244--3248269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3248234 ATGAGAAGAG
3248244 AATGAAAAAAAAA
1 AATGAAAAAAAAA
3248257 AATGAAAAAAAAA
1 AATGAAAAAAAAA
3248270 GGATAGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AATGAAAAAAAAA
Found at i:3248342 original size:170 final size:165
Alignment explanation
Indices: 3248120--3248480 Score: 595
Period size: 170 Copynumber: 2.2 Consensus size: 165
3248110 AAAGAAATAC
*
3248120 AAAAG-AAAAAAAATTAGATTGTTCAAAAAAAAGTATAGGGACTAGTTTTAACAAATGGAAAACT
1 AAAAGAAAAAAAAATTAAATTGTTCAAAAAAAAGTATAGGGACTAGTTTTAACAAATGGAAAACT
3248184 TAGAAAAACTACGTTAAAAGAAATGAAGAT-GAGAGGAAAACTGAGAAAGAATGAGAAGAGAATG
66 TAGAAAAACTACGTTAAAAGAAATGAAGATAG-GAGGAAAACTGAGAAAGAATGAGAAGAGAATG
*
3248248 AAAAAAAAAAATGAAAAAAAAAGGATAGTTTAAAGAACAT
130 --AAAAAAAAA-G-AAAAAAAAGGATAGTATAAAGAACAT
3248288 AAAAGAAAAAAAAAATTAAATTGTTCAAAAAAAAGTATAGGGACTAGTTTTAACAAATGGAAAAC
1 AAAAG-AAAAAAAAATTAAATTGTTCAAAAAAAAGTATAGGGACTAGTTTTAACAAATGGAAAAC
**
3248353 TTAGAAAAACTACGTTAAAAGAAATGAAGATAGGAGGAAAACTGAGGGAGAATGAGAAGAGAATG
65 TTAGAAAAACTACGTTAAAAGAAATGAAGATAGGAGGAAAACTGAGAAAGAATGAGAAGAGAATG
*
3248418 AAAAAAAAAGAAAAAAGAGGATAGTATAAAGAACAT
130 AAAAAAAAAGAAAAAAAAGGATAGTATAAAGAACAT
3248454 AAAAG-AAAAAAAA-TAAATTGTTCAAAA
1 AAAAGAAAAAAAAATTAAATTGTTCAAAA
3248481 CGAAAAAAAT
Statistics
Matches: 185, Mismatches: 5, Indels: 11
0.92 0.02 0.05
Matches are distributed among these distances:
163 14 0.08
164 8 0.04
166 29 0.16
167 1 0.01
168 14 0.08
170 118 0.64
171 1 0.01
ACGTcount: A:0.59, C:0.05, G:0.19, T:0.17
Consensus pattern (165 bp):
AAAAGAAAAAAAAATTAAATTGTTCAAAAAAAAGTATAGGGACTAGTTTTAACAAATGGAAAACT
TAGAAAAACTACGTTAAAAGAAATGAAGATAGGAGGAAAACTGAGAAAGAATGAGAAGAGAATGA
AAAAAAAAGAAAAAAAAGGATAGTATAAAGAACAT
Found at i:3252324 original size:53 final size:53
Alignment explanation
Indices: 3252258--3252363 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
3252248 CCATGACACT
*
3252258 AAAGAAGACCATATCATGTAAGACCATAACTT-GTGGGTTATGGCATCATATGG
1 AAAGAAGACCATATCATGTAAGACCATAA-TTGGTGGGTTATGACATCATATGG
* ** * *
3252311 AAAGAATACCATATTGTGTAAGATCGTAATTGGTGGGTTATGACATCATATGG
1 AAAGAAGACCATATCATGTAAGACCATAATTGGTGGGTTATGACATCATATGG
3252364 GAAAAATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 2 0.04
53 44 0.96
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (53 bp):
AAAGAAGACCATATCATGTAAGACCATAATTGGTGGGTTATGACATCATATGG
Found at i:3252582 original size:29 final size:28
Alignment explanation
Indices: 3252539--3252614 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 28
3252529 ATTGAATGTT
3252539 AAGGAATGCCTTTGTGGCAAACCTCTAG
1 AAGGAATGCCTTTGTGGCAAACCTCTAG
* *
3252567 AAGGAAATGCCTTTGTGACAAATCTCTAG
1 AAGG-AATGCCTTTGTGGCAAACCTCTAG
3252596 ACATGGAA-GCCTTTGTGGC
1 A-A-GGAATGCCTTTGTGGC
3252615 TATCTCTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.10
29 33 0.79
30 3 0.07
31 2 0.05
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (28 bp):
AAGGAATGCCTTTGTGGCAAACCTCTAG
Found at i:3257309 original size:26 final size:26
Alignment explanation
Indices: 3257176--3257296 Score: 226
Period size: 26 Copynumber: 4.7 Consensus size: 26
3257166 CTTGTCAAAA
3257176 TTTTACTAGGGGTAAAATCGTTAAAG
1 TTTTACTAGGGGTAAAATCGTTAAAG
3257202 TTTTACTAGGGGTAAAATCGTTAAAG
1 TTTTACTAGGGGTAAAATCGTTAAAG
3257228 TTTTACTAGGGGTAAAATCGTTAAAG
1 TTTTACTAGGGGTAAAATCGTTAAAG
*
3257254 TTTTACTAGGGGTAAAATCGTTAAAC
1 TTTTACTAGGGGTAAAATCGTTAAAG
3257280 TTTTACTA-GGGTAAAAT
1 TTTTACTAGGGGTAAAAT
3257297 AGGGATAAAT
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
25 9 0.10
26 85 0.90
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (26 bp):
TTTTACTAGGGGTAAAATCGTTAAAG
Found at i:3265267 original size:19 final size:22
Alignment explanation
Indices: 3265231--3265278 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
3265221 ATAGTGAGAA
*
3265231 TTTATTTTCTAAGTAT-A-AAT
1 TTTATTTTCTAAGAATAACAAT
*
3265251 TTTATTTTCT-GGAATAACAAT
1 TTTATTTTCTAAGAATAACAAT
3265272 TTTATTT
1 TTTATTT
3265279 CCCATTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 11 0.46
21 10 0.42
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTATTTTCTAAGAATAACAAT
Done.