Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_pilon, whole genome shotgun sequence
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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 27
Found at i:3065745 original size:23 final size:23
Alignment explanation
Indices: 3065718--3065807 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
3065708 CATTTTATAT
* *
3065718 GGCACTTTGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTATACGC
* *
3065741 GGCACTTCGGTGTATTTATATGC
1 GGCACTTCGGTGCATTTATACGC
* * * *
3065764 GACACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTATACGC
*
3065787 AGCAC-TCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTATACG
3065808 AGTTGTGGTG
Statistics
Matches: 53, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
22 14 0.26
23 39 0.74
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTATACGC
Found at i:3065776 original size:46 final size:43
Alignment explanation
Indices: 3065711--3065805 Score: 118
Period size: 46 Copynumber: 2.1 Consensus size: 43
3065701 TTATGGACAT
* * * *
3065711 TTTATATGGCACTTTGGTGCATTTCTACGCGGCACTTCGGTGTA
1 TTTATATGGCACTTCGGTGCAATTCTACGCAGCAC-TCGGTGCA
*
3065755 TTTATATGCGACACTTCGGTGCAATTCTACGTAGCACTCGGTGCA
1 TTTATATG-G-CACTTCGGTGCAATTCTACGCAGCACTCGGTGCA
3065800 TTTATA
1 TTTATA
3065806 CGAGTTGTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
44 8 0.18
45 14 0.32
46 22 0.50
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (43 bp):
TTTATATGGCACTTCGGTGCAATTCTACGCAGCACTCGGTGCA
Found at i:3066379 original size:19 final size:20
Alignment explanation
Indices: 3066342--3066379 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3066332 ATAGGTGATA
*
3066342 GTATGAATAAGATATGAGTG
1 GTATGAATAAGATAGGAGTG
*
3066362 GTATG-ATATGATAGGAGT
1 GTATGAATAAGATAGGAGT
3066380 AATTATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (20 bp):
GTATGAATAAGATAGGAGTG
Found at i:3068044 original size:20 final size:19
Alignment explanation
Indices: 3068008--3068056 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3067998 GTAGCTCTAT
*
3068008 ATGAGAGTAATATAATAATA
1 ATGAGA-TAATACAATAATA
*
3068028 ATGAGATAATAACAATAATT
1 ATGAGATAAT-ACAATAATA
*
3068048 GTGAGATAA
1 ATGAGATAA
3068057 CCATAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (19 bp):
ATGAGATAATACAATAATA
Found at i:3071904 original size:2 final size:2
Alignment explanation
Indices: 3071897--3071926 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3071887 GTCTAGTTGA
3071897 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
3071927 TTCTTTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3084980 original size:15 final size:15
Alignment explanation
Indices: 3084960--3084994 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3084950 TCACATCAAA
*
3084960 CCTTCACCTTCTCCT
1 CCTTCACCGTCTCCT
3084975 CCTTCACCGTCTCCT
1 CCTTCACCGTCTCCT
*
3084990 TCTTC
1 CCTTC
3084995 GCCCTGTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.51, G:0.03, T:0.40
Consensus pattern (15 bp):
CCTTCACCGTCTCCT
Found at i:3093600 original size:21 final size:21
Alignment explanation
Indices: 3093575--3093619 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3093565 ACTTAACGCG
3093575 TTTAGTACCTAAACTATCATT
1 TTTAGTACCTAAACTATCATT
*
3093596 TTTAGTACCTAAACTTTCATT
1 TTTAGTACCTAAACTATCATT
3093617 TTT
1 TTT
3093620 CCCCCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCATT
Found at i:3096139 original size:3 final size:3
Alignment explanation
Indices: 3096131--3096158 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3096121 CTTTACTCAA
3096131 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3096159 TACAAAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3096876 original size:2 final size:2
Alignment explanation
Indices: 3096822--3096859 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3096812 GTTACACACA
3096822 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
3096860 TTAAAAAAAT
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:3097072 original size:16 final size:16
Alignment explanation
Indices: 3097051--3097089 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3097041 TTTTATTTAT
3097051 CTTCTTAGAAATGATA
1 CTTCTTAGAAATGATA
3097067 CTTCTTAGAAATGATA
1 CTTCTTAGAAATGATA
*
3097083 TTTCTTA
1 CTTCTTA
3097090 TCATTTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (16 bp):
CTTCTTAGAAATGATA
Found at i:3102193 original size:20 final size:20
Alignment explanation
Indices: 3102168--3102206 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3102158 TGAAAATTAA
*
3102168 ATATA-TATTCTGTTTATAAG
1 ATATATTATT-TGATTATAAG
3102188 ATATATTATTTGATTATAA
1 ATATATTATTTGATTATAA
3102207 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (20 bp):
ATATATTATTTGATTATAAG
Found at i:3113925 original size:19 final size:18
Alignment explanation
Indices: 3113901--3113938 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
3113891 TATATGTGTG
3113901 TATAAGTATTTATTACATA
1 TATAAGTATTTATT-CATA
3113920 TATAAGTATTTATTCATA
1 TATAAGTATTTATTCATA
3113938 T
1 T
3113939 CCATGCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (18 bp):
TATAAGTATTTATTCATA
Found at i:3116105 original size:15 final size:15
Alignment explanation
Indices: 3116085--3116114 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3116075 CAAGCCCCCT
3116085 TACCATCCTCTACAA
1 TACCATCCTCTACAA
3116100 TACCATCCTCTACAA
1 TACCATCCTCTACAA
3116115 GAATAACTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (15 bp):
TACCATCCTCTACAA
Found at i:3130096 original size:2 final size:2
Alignment explanation
Indices: 3130089--3130114 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3130079 ATTTATTTCA
3130089 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
3130115 TCTAATAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3136310 original size:71 final size:76
Alignment explanation
Indices: 3136156--3136311 Score: 187
Period size: 78 Copynumber: 2.1 Consensus size: 76
3136146 TTTGAATTTA
* * *
3136156 TAATAAACTATGATAATTAATATGATTACTTTTTAAAAGTTAAAACAAATTGTTAGTTGTGATGA
1 TAATAAACTATAATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATTGTTAGCTGTGATGA
****
3136221 TTTTTTGACAAT
66 -TTAACCACAAT
*
3136233 TAAATAAACTATAATAATTAATATGCTTACTCTTTAAAAGTTAAAACAAATTGTTA-CT-T-ATG
1 T-AATAAACTATAATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATTGTTAGCTGTGATG
3136295 A-TAACCA-AAT
65 ATTAACCACAAT
3136305 TAATAAA
1 TAATAAA
3136312 TTTACTTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
71 6 0.09
72 4 0.06
73 2 0.03
75 4 0.06
76 1 0.01
77 2 0.03
78 51 0.73
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (76 bp):
TAATAAACTATAATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATTGTTAGCTGTGATGA
TTAACCACAAT
Found at i:3136356 original size:21 final size:20
Alignment explanation
Indices: 3136317--3136356 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3136307 ATAAATTTAC
*
3136317 TTTATATATTAATTGTAATA
1 TTTATATATAAATTGTAATA
*
3136337 TTTATATTATAAATTTTAAT
1 TTTATA-TATAAATTGTAAT
3136357 TATAATCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTATATATAAATTGTAATA
Found at i:3137110 original size:10 final size:10
Alignment explanation
Indices: 3137092--3137138 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
3137082 TATTATACGT
*
3137092 TATACTTATA
1 TATATTTATA
3137102 TATATTTATA
1 TATATTTATA
3137112 TATACTTATATA
1 TATA-TT-TATA
*
3137124 CATATTTATA
1 TATATTTATA
3137134 TATAT
1 TATAT
3137139 ATATGTGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 21 0.66
11 4 0.12
12 7 0.22
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (10 bp):
TATATTTATA
Found at i:3137115 original size:20 final size:21
Alignment explanation
Indices: 3137092--3137137 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
3137082 TATTATACGT
3137092 TATACTTATAT-ATATTTATA
1 TATACTTATATAATATTTATA
3137112 TATACTTATATACATATTTATA
1 TATACTTATATA-ATATTTATA
3137134 TATA
1 TATA
3137138 TATATGTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 11 0.46
22 13 0.54
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TATACTTATATAATATTTATA
Found at i:3137235 original size:34 final size:32
Alignment explanation
Indices: 3137172--3137248 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 32
3137162 TAAGTATACA
*
3137172 TATACTTATATTATATACTAATAAATATAATG
1 TATACTTATATTATACACTAATAAATATAATG
* * *
3137204 TATAGTTATATATATACACTTATTAAGTATAATG
1 TATACTTATAT-TATACAC-TAATAAATATAATG
3137238 TATACATTATA
1 TATAC-TTATA
3137249 AATATAATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 10 0.27
33 6 0.16
34 16 0.43
35 5 0.14
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (32 bp):
TATACTTATATTATACACTAATAAATATAATG
Found at i:3137274 original size:20 final size:20
Alignment explanation
Indices: 3137216--3137267 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
3137206 TAGTTATATA
*
3137216 TATACACTTATTAAGTATAATG
1 TATACA-TTA-TAAATATAATG
3137238 TATACATTATAAATATAATG
1 TATACATTATAAATATAATG
3137258 TATAC-TTATA
1 TATACATTATA
3137268 TTATATACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.17
20 15 0.52
21 3 0.10
22 6 0.21
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (20 bp):
TATACATTATAAATATAATG
Found at i:3137290 original size:16 final size:13
Alignment explanation
Indices: 3137258--3137296 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
3137248 AAATATAATG
3137258 TATACTTATATTA
1 TATACTTATATTA
3137271 TATACTTATATAAGTA
1 TATACTTATAT---TA
3137287 TATACTTATA
1 TATACTTATA
3137297 ATGTATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.48
16 12 0.52
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (13 bp):
TATACTTATATTA
Found at i:3137666 original size:71 final size:70
Alignment explanation
Indices: 3137585--3137721 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 70
3137575 TTAATTTTAT
*
3137585 ATTTATTCAATTTAGTCCTTAAAATTATAT-TTGTATATGAAATTGGCACATACTTATTTATATT
1 ATTTATTCAATTTAGTCCTTAAAATTATATATT-TATATGAAATTGACACATACTTATTTATATT
3137649 TTTGTA
65 TTTGTA
*
3137655 ATTTACTTCAATTTAGTCCTTAAAATTATATATTTATATGAAATTGACCCATACTTATTTATATT
1 ATTTA-TTCAATTTAGTCCTTAAAATTATATATTTATATGAAATTGACACATACTTATTTATATT
3137720 TT
65 TT
3137722 GATTTGATCC
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
70 5 0.08
71 56 0.89
72 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.50
Consensus pattern (70 bp):
ATTTATTCAATTTAGTCCTTAAAATTATATATTTATATGAAATTGACACATACTTATTTATATTT
TTGTA
Found at i:3138586 original size:2 final size:2
Alignment explanation
Indices: 3138579--3138613 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3138569 ATTAAAAATA
3138579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3138614 TAATAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3138617 original size:6 final size:7
Alignment explanation
Indices: 3138576--3138618 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 7
3138566 AATATTAAAA
3138576 ATAATAT
1 ATAATAT
3138583 ATATATAT
1 ATA-ATAT
3138591 ATATATAT
1 ATA-ATAT
3138599 ATATATAT
1 ATA-ATAT
3138607 ATAATAT
1 ATAATAT
3138614 -TAATA
1 ATAATA
3138619 AATTTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 5 0.14
7 7 0.20
8 23 0.66
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATAATAT
Found at i:3139376 original size:16 final size:16
Alignment explanation
Indices: 3139355--3139386 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3139345 TACTAACCCC
3139355 TTCTATTATTACTGCA
1 TTCTATTATTACTGCA
3139371 TTCTATTATTACTGCA
1 TTCTATTATTACTGCA
3139387 GATATCTTAA
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:0.19, G:0.06, T:0.50
Consensus pattern (16 bp):
TTCTATTATTACTGCA
Found at i:3150549 original size:12 final size:12
Alignment explanation
Indices: 3150534--3150565 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3150524 GTTATTTAAA
3150534 CGGGTATTAGGT
1 CGGGTATTAGGT
3150546 CGGGTATTAGGT
1 CGGGTATTAGGT
*
3150558 TGGGTATT
1 CGGGTATT
3150566 GGATCGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.41, T:0.38
Consensus pattern (12 bp):
CGGGTATTAGGT
Found at i:3150657 original size:24 final size:24
Alignment explanation
Indices: 3150597--3150657 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
3150587 TCGGGCCAGG
3150597 TATATATATA-TATTTAAATTAAA
1 TATATATATATTATTTAAATTAAA
*
3150620 TATATATATTTTATTTAAATTAAA
1 TATATATATATTATTTAAATTAAA
*
3150644 TTTAT-TAATATTAT
1 TATATAT-ATATTAT
3150658 ATATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.30
24 23 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATATATATTATTTAAATTAAA
Found at i:3151169 original size:18 final size:17
Alignment explanation
Indices: 3151122--3151169 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
3151112 AAGGAGGAGA
3151122 CCGTGGTGGAAGGGGTGG
1 CCGTGGTGG-AGGGGTGG
* **
3151140 CGGTGGAAGAGGTGGTGG
1 CCGTGGTGGAGG-GGTGG
3151158 CCGTGGTGGAGG
1 CCGTGGTGGAGG
3151170 ACGCAGAGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.12, C:0.10, G:0.60, T:0.17
Consensus pattern (17 bp):
CCGTGGTGGAGGGGTGG
Found at i:3159177 original size:18 final size:17
Alignment explanation
Indices: 3159154--3159187 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3159144 TAGTCTGTTT
3159154 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
3159172 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
3159188 TTAGTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:3161677 original size:19 final size:19
Alignment explanation
Indices: 3161653--3161696 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
3161643 AATTCAATTA
*
3161653 GAGAATATTCTGACAGTTT
1 GAGAATATTCTGACAGTTC
3161672 GAGAATATTCTGACAGTTC
1 GAGAATATTCTGACAGTTC
3161691 GAGAAT
1 GAGAAT
3161697 TTTTAGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (19 bp):
GAGAATATTCTGACAGTTC
Found at i:3175683 original size:18 final size:17
Alignment explanation
Indices: 3175660--3175693 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3175650 CAGTCTGTTT
3175660 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
3175678 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
3175694 TTAGTATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:3176211 original size:29 final size:29
Alignment explanation
Indices: 3176174--3176236 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
3176164 AATGAAACAA
3176174 ATTTTTAGGCAAATTTAAGTTCAGTAAAT
1 ATTTTTAGGCAAATTTAAGTTCAGTAAAT
3176203 ATTTTTAGGCAAATTTAAGTTCAGTAAAT
1 ATTTTTAGGCAAATTTAAGTTCAGTAAAT
3176232 ATTTT
1 ATTTT
3176237 GAAGTTGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (29 bp):
ATTTTTAGGCAAATTTAAGTTCAGTAAAT
Found at i:3183600 original size:18 final size:17
Alignment explanation
Indices: 3183577--3183610 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3183567 CAGTCTGTTT
3183577 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
3183595 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
3183611 TTAGTATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:3186953 original size:21 final size:20
Alignment explanation
Indices: 3186881--3186953 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
3186871 AGCCGTAGAA
* *
3186881 TATCGATACCCAAGGGGCGAG
1 TATCGATA-CCAAGAGGCTAG
*
3186902 TATCGATACTCAAGA-GTTAG
1 TATCGATAC-CAAGAGGCTAG
3186922 TATCGATACCAAGAGGCCTAG
1 TATCGATACCAAGAGG-CTAG
3186943 TATCGATACCA
1 TATCGATACCA
3186954 TCATACATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.11
20 14 0.31
21 26 0.58
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (20 bp):
TATCGATACCAAGAGGCTAG
Found at i:3187254 original size:28 final size:28
Alignment explanation
Indices: 3187200--3187256 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3187190 GATATATCTA
* * **
3187200 AGTGTGTGAGGCACTTTAATGTTTAACT
1 AGTGCGTGAGGCACTCTAATGACTAACT
*
3187228 AGTGCGTGAGGCACTCTGATGACTAACT
1 AGTGCGTGAGGCACTCTAATGACTAACT
3187256 A
1 A
3187257 TGGCGCAAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (28 bp):
AGTGCGTGAGGCACTCTAATGACTAACT
Found at i:3188398 original size:22 final size:22
Alignment explanation
Indices: 3188368--3188410 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3188358 ATGTAGTAAC
*
3188368 ATAACAAAATAAGTTATAAACG
1 ATAACAAAATAAATTATAAACG
*
3188390 ATAAGAAAATAAATTATAAAC
1 ATAACAAAATAAATTATAAAC
3188411 AGTAAACGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (22 bp):
ATAACAAAATAAATTATAAACG
Found at i:3188708 original size:77 final size:77
Alignment explanation
Indices: 3188542--3188744 Score: 187
Period size: 77 Copynumber: 2.7 Consensus size: 77
3188532 AATGTCATGG
* ** * * ** *
3188542 TTCACTAAAAAATAAGGTGCGATCTGG-ATGTTAATATTTTTATTAATAAAATGGGTTACGCCTA
1 TTCACTAAGAAATAAATTACGATATGGAATGTTAATATTTTTATTAATAAAATAAGTTACGCCAA
* *
3188606 ATAATACCATAG
66 AAAATACCATAA
* *
3188618 TTCACTAAGAAATAAATTACGATTTGGAATGTTAATATTTTTATTAATAAAATAAGTTCCGCCAA
1 TTCACTAAGAAATAAATTACGATATGGAATGTTAATATTTTTATTAATAAAATAAGTTACGCCAA
**
3188683 AAAATATTATAA
66 AAAATACCATAA
* ** ** * *
3188695 TTC-TTAAGAAAATATGTTGTGATATGAAATATTAATATTTTTATT-ATAAA
1 TTCACTAAG-AAATAAATTACGATATGGAATGTTAATATTTTTATTAATAAA
3188745 TAATTTGAAG
Statistics
Matches: 104, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
76 31 0.30
77 73 0.70
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (77 bp):
TTCACTAAGAAATAAATTACGATATGGAATGTTAATATTTTTATTAATAAAATAAGTTACGCCAA
AAAATACCATAA
Found at i:3194345 original size:41 final size:43
Alignment explanation
Indices: 3194265--3194345 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
3194255 AAATTAGAAA
* * * * *
3194265 ATATTTATATATTTTCTTTTAAAAAATTTAAATTCATAAATAT
1 ATATATATATATATTCTTTTAAAAAAGTGAAAATCATAAATAT
3194308 ATATATATATATATT-TTTTAAAAAAGTGAAAAT-ATAAA
1 ATATATATATATATTCTTTTAAAAAAGTGAAAATCATAAA
3194346 AAGGTTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 5 0.15
42 15 0.45
43 13 0.39
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (43 bp):
ATATATATATATATTCTTTTAAAAAAGTGAAAATCATAAATAT
Found at i:3194577 original size:26 final size:26
Alignment explanation
Indices: 3194543--3194592 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3194533 TAAAATGCCA
*
3194543 GTAAACCAATAATACATAAGGAAATG
1 GTAAACCAACAATACATAAGGAAATG
* *
3194569 GTAATCCAACAATACCTAAGGAAA
1 GTAAACCAACAATACATAAGGAAA
3194593 AGGAGGTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (26 bp):
GTAAACCAACAATACATAAGGAAATG
Found at i:3195003 original size:39 final size:39
Alignment explanation
Indices: 3194923--3195004 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
3194913 AACAAGTTAG
* * * *
3194923 AAAATATTTATATATTTTATTTAAAAAATTTAAATTCAT
1 AAAATATATATATATTATATTTAAAAAATTGAAAATCAT
3194962 AAAATATATATATATATATATTTAAAAAATTGAAAAT-AT
1 AAAATATATATATAT-TATATTTAAAAAATTGAAAATCAT
3195001 AAAA
1 AAAA
3195005 ATGTTTAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 20 0.53
40 18 0.47
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (39 bp):
AAAATATATATATATTATATTTAAAAAATTGAAAATCAT
Found at i:3195869 original size:17 final size:18
Alignment explanation
Indices: 3195847--3195880 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3195837 CCAACACTAT
3195847 CTCTACATTA-TCACAAA
1 CTCTACATTATTCACAAA
*
3195864 CTCTACTTTATTCACAA
1 CTCTACATTATTCACAA
3195881 TATTTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (18 bp):
CTCTACATTATTCACAAA
Found at i:3196666 original size:95 final size:95
Alignment explanation
Indices: 3196503--3196692 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
3196493 ATAGTGTCAA
3196503 AAAATCTAAAGCAAAAAGGAAGCAAATCGAAGAAGCCTCTATTCTTTCAAATTCCTTCAATGAAT
1 AAAATCTAAAGCAAAAAGGAAGCAAATCGAAGAAGCCTCTATTCTTTCAAATTCCTTCAATGAAT
3196568 CAACTGAAAAGTTTCGGGAATCATTATCTT
66 CAACTGAAAAGTTTCGGGAATCATTATCTT
3196598 AAAATCTAAAGCAAAAAGGAAGCAAATCGAAGAAGCCTCTATTCTTTCAAATTCCTTCAATGAAT
1 AAAATCTAAAGCAAAAAGGAAGCAAATCGAAGAAGCCTCTATTCTTTCAAATTCCTTCAATGAAT
3196663 CAACTGAAAAGTTTCGGGAATCATTATCTT
66 CAACTGAAAAGTTTCGGGAATCATTATCTT
3196693 TAACATGAGC
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (95 bp):
AAAATCTAAAGCAAAAAGGAAGCAAATCGAAGAAGCCTCTATTCTTTCAAATTCCTTCAATGAAT
CAACTGAAAAGTTTCGGGAATCATTATCTT
Found at i:3197257 original size:20 final size:20
Alignment explanation
Indices: 3197232--3197275 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3197222 TCTATCTTGC
3197232 AATCTACTTCAATCTAATTT
1 AATCTACTTCAATCTAATTT
*
3197252 AATCTACTTTAATCTAATTT
1 AATCTACTTCAATCTAATTT
3197272 AATC
1 AATC
3197276 ATTAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (20 bp):
AATCTACTTCAATCTAATTT
Found at i:3197272 original size:10 final size:10
Alignment explanation
Indices: 3197232--3197275 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
3197222 TCTATCTTGC
* *
3197232 AATCTACTTC
1 AATCTAATTT
3197242 AATCTAATTT
1 AATCTAATTT
*
3197252 AATCTACTTT
1 AATCTAATTT
3197262 AATCTAATTT
1 AATCTAATTT
3197272 AATC
1 AATC
3197276 ATTAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (10 bp):
AATCTAATTT
Found at i:3198795 original size:12 final size:12
Alignment explanation
Indices: 3198778--3198804 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3198768 TTCGTTTTGT
3198778 GAATGTGTTCAC
1 GAATGTGTTCAC
3198790 GAATGTGTTCAC
1 GAATGTGTTCAC
3198802 GAA
1 GAA
3198805 CGTGCTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (12 bp):
GAATGTGTTCAC
Found at i:3199117 original size:12 final size:12
Alignment explanation
Indices: 3199100--3199158 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
3199090 GAATGAGTCG
3199100 ATAAACGAGCTC
1 ATAAACGAGCTC
*
3199112 ATAAACAAGGC-C
1 ATAAACGA-GCTC
* *
3199124 ATAAACGAACTT
1 ATAAACGAGCTC
*
3199136 ATAAACGAGTTC
1 ATAAACGAGCTC
*
3199148 ATAAATGAGCT
1 ATAAACGAGCT
3199159 TGTTCGTGAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
11 1 0.03
12 33 0.92
13 2 0.06
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (12 bp):
ATAAACGAGCTC
Found at i:3199619 original size:37 final size:38
Alignment explanation
Indices: 3199559--3199642 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
3199549 TGGTAACCAA
3199559 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
3199596 CTTTGAAAAATA-GTTTTTTAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
3199633 -GTTGAAAAAT
1 CTTTGAAAAAT
3199643 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:3204023 original size:34 final size:34
Alignment explanation
Indices: 3203968--3204130 Score: 141
Period size: 35 Copynumber: 4.7 Consensus size: 34
3203958 TGAAAGTATT
*
3203968 AAAATGGTTTTC-AAGTTTGGTAACCA-ACTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAACATACTTTG
* *
3204000 AAAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTG
1 -AAAATGGTTTTCAAAGTTTGGTAAACA-TACTTTG
* ** * *
3204036 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTT
1 AAAATGGTTTTCAAAGTTTGGTAAA-CATACTTTG
* ** *
3204071 AACATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAA-CATACTTTG
*
3204106 AAAAATAGTTTTTCAAAGTTTGGTA
1 -AAAAT-GGTTTTCAAAGTTTGGTA
3204131 GATGTTTGTT
Statistics
Matches: 112, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
33 12 0.11
34 12 0.11
35 62 0.55
36 9 0.08
37 17 0.15
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAAACATACTTTG
Found at i:3204143 original size:36 final size:36
Alignment explanation
Indices: 3203995--3204148 Score: 215
Period size: 35 Copynumber: 4.3 Consensus size: 36
3203985 TGGTAACCAA
*
3203995 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
3204031 CTTTG-AAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
3204066 CTTT-TAACATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
3204101 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
3204138 -GTTGAAAAATG
1 CTTTGAAAAATG
3204149 ATAATGGGAT
Statistics
Matches: 106, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
35 65 0.61
36 18 0.17
37 23 0.22
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:3208515 original size:21 final size:21
Alignment explanation
Indices: 3208489--3208544 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
3208479 TTTTTGAGGG
3208489 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
3208510 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
*
3208531 TTATATAAGTTTAA
1 TTATATAAGCTTAA
3208545 AACACCAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATATAAGCTTAAGGAAAGC
Found at i:3209245 original size:7 final size:7
Alignment explanation
Indices: 3209233--3209257 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3209223 TGATTACATG
3209233 TATGTGA
1 TATGTGA
3209240 TATGTGA
1 TATGTGA
3209247 TATGTGA
1 TATGTGA
3209254 TATG
1 TATG
3209258 AACTATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (7 bp):
TATGTGA
Found at i:3209582 original size:31 final size:30
Alignment explanation
Indices: 3209499--3209619 Score: 120
Period size: 31 Copynumber: 3.9 Consensus size: 30
3209489 ATCGAGGGTT
3209499 TACCTATGTTCTACGGAACATATGGACATAA
1 TACCTATGTTCTACGGAACATATGGACAT-A
* *
3209530 TTACCTATG-TCTTTCGG-ACATATGGATAGTA
1 -TACCTATGTTC-TACGGAACATATGGACA-TA
*
3209561 TACCTATGTTCTAAGGAACATATGGACAATA
1 TACCTATGTTCTACGGAACATATGGAC-ATA
* * * *
3209592 TACCTAGGTTCTTCGGGACCTATGGACA
1 TACCTATGTTCTACGGAACATATGGACA
3209620 GTTGTCGAGG
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
30 12 0.16
31 48 0.65
32 14 0.19
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
TACCTATGTTCTACGGAACATATGGACATA
Found at i:3209616 original size:62 final size:62
Alignment explanation
Indices: 3209499--3209617 Score: 163
Period size: 62 Copynumber: 1.9 Consensus size: 62
3209489 ATCGAGGGTT
* *
3209499 TACCTATGTTCTACGGAACATATGGACATAATTACCTATGTCTTTCGGACATATGGATAGTA
1 TACCTATGTTCTAAGGAACATATGGACATAATTACCTAGGTCTTTCGGACATATGGATAGTA
*
3209561 TACCTATGTTCTAAGGAACATATGGAC--AATATACCTAGGT-TCTTCGGGACCTATGGA
1 TACCTATGTTCTAAGGAACATATGGACATAAT-TACCTAGGTCT-TTC-GGACATATGGA
3209618 CAGTTGTCGA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
60 4 0.08
61 11 0.22
62 36 0.71
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATGGACATAATTACCTAGGTCTTTCGGACATATGGATAGTA
Found at i:3215211 original size:31 final size:31
Alignment explanation
Indices: 3215133--3215213 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
3215123 ACCTATATCT
* * *
3215133 TTCGGGATATATGGATAGTATACCTATGTTC
1 TTCGGGACATATGGACAGTATACCTAGGTTC
** * *
3215164 TAAGGAACATAGGGACAGTATACCTAGGTTC
1 TTCGGGACATATGGACAGTATACCTAGGTTC
*
3215195 TTCGGGACCTATGGACAGT
1 TTCGGGACATATGGACAGT
3215214 TGCCGAGGAT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (31 bp):
TTCGGGACATATGGACAGTATACCTAGGTTC
Found at i:3215255 original size:30 final size:30
Alignment explanation
Indices: 3215200--3215302 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
3215190 GGTTCTTCGG
* * *
3215200 GACCTATGGACAGTTGCCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
3215230 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3215260 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3215290 GACCTCTGGATAG
1 GACCTCTGGATAG
3215303 GTCCTTCGGG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:3222437 original size:24 final size:25
Alignment explanation
Indices: 3222410--3222496 Score: 83
Period size: 24 Copynumber: 3.6 Consensus size: 25
3222400 AAATTGAACG
*
3222410 ACCGGTTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
3222434 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT--AACCGGATAAAAA
* *
3222461 ACTGG-TTTTTTATCCGGA-AAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
* *
3222484 TCC-ATTTTTTTAA
1 ACCGGTTTTTTTAA
3222497 AAAAAACTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
23 13 0.25
24 18 0.35
26 6 0.12
27 15 0.29
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:3222521 original size:40 final size:42
Alignment explanation
Indices: 3222456--3222540 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 42
3222446 CAAACCGGAT
**
3222456 AAAAAACTGGTTTTTTATCCGGAAAAAATCC-ATTTTTTTAA
1 AAAAAACTGAATTTTTATCCGGAAAAAATCCGATTTTTTTAA
*
3222497 AAAAAACTGAATTTTTATCC-GAAAAAATCCGGTTTTTTTAA
1 AAAAAACTGAATTTTTATCCGGAAAAAATCCGATTTTTTTAA
3222538 AAA
1 AAA
3222541 CCGAAACCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 10 0.25
41 30 0.75
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (42 bp):
AAAAAACTGAATTTTTATCCGGAAAAAATCCGATTTTTTTAA
Found at i:3223023 original size:51 final size:52
Alignment explanation
Indices: 3222983--3223082 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 52
3222973 GATGTGAGAT
*
3222983 AATAAAATAAAAAAGTATAACACTTAACGCATACTTACACC-AGTGTAAGTG
1 AATAAAATAAAAAAGTATAACACTTAACACATACTTACACCGAGTGTAAGTG
* * * *
3223034 AATAAAATAAAAAAGTGTAGCACTTAATACGTACTTACACC--GTGTAAGT
1 AATAAAATAAAAAAGTATAACACTTAACACATACTTACACCGAGTGTAAGT
3223083 ATGTACATCT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 8 0.18
51 36 0.82
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (52 bp):
AATAAAATAAAAAAGTATAACACTTAACACATACTTACACCGAGTGTAAGTG
Found at i:3223378 original size:10 final size:11
Alignment explanation
Indices: 3223354--3223379 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3223344 TTATGACACA
3223354 TTTTCTTATGT
1 TTTTCTTATGT
3223365 TTTTCTTATGT
1 TTTTCTTATGT
3223376 TTTT
1 TTTT
3223380 TTGTTCTTTG
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:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTCTTATGT
Found at i:3224070 original size:39 final size:39
Alignment explanation
Indices: 3223937--3224070 Score: 94
Period size: 40 Copynumber: 3.4 Consensus size: 39
3223927 TAAAAGGATT
*
3223937 TTTTAAG-TGAATTATTGAAATAGAAGGAGTTAATGGAT
1 TTTTAAGTTGAATTATTGAAATAGAAGGAGTTAATGGAA
** * ** *
3223975 TTTTAAGTTGAATTTGACTTGTCATA-AGATGAAATAA-GAAA
1 TTTTAAGTTGAA-TT-A-TTGAAATAGA-AGGAGTTAATGGAA
** * *
3224016 TTCAAAAAATCGAATTATTGAAATAGAAGGAGTTAATGGAA
1 TT--TTAAGTTGAATTATTGAAATAGAAGGAGTTAATGGAA
3224057 TTTTAAGTTGAATT
1 TTTTAAGTTGAATT
3224071 TGACTTGTCA
Statistics
Matches: 66, Mismatches: 21, Indels: 17
0.63 0.20 0.16
Matches are distributed among these distances:
38 7 0.11
39 12 0.18
40 14 0.21
41 13 0.20
42 14 0.21
43 6 0.09
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (39 bp):
TTTTAAGTTGAATTATTGAAATAGAAGGAGTTAATGGAA
Found at i:3224082 original size:82 final size:82
Alignment explanation
Indices: 3223945--3224103 Score: 309
Period size: 82 Copynumber: 1.9 Consensus size: 82
3223935 TTTTTTAAGT
*
3223945 GAATTATTGAAATAGAAGGAGTTAATGGATTTTTAAGTTGAATTTGACTTGTCATAAGATGAAAT
1 GAATTATTGAAATAGAAGGAGTTAATGGAATTTTAAGTTGAATTTGACTTGTCATAAGATGAAAT
3224010 AAGAAATTCAAAAAATC
66 AAGAAATTCAAAAAATC
3224027 GAATTATTGAAATAGAAGGAGTTAATGGAATTTTAAGTTGAATTTGACTTGTCATAAGATGAAAT
1 GAATTATTGAAATAGAAGGAGTTAATGGAATTTTAAGTTGAATTTGACTTGTCATAAGATGAAAT
3224092 AAGAAATTCAAA
66 AAGAAATTCAAA
3224104 GCGTTAGAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (82 bp):
GAATTATTGAAATAGAAGGAGTTAATGGAATTTTAAGTTGAATTTGACTTGTCATAAGATGAAAT
AAGAAATTCAAAAAATC
Found at i:3227277 original size:55 final size:55
Alignment explanation
Indices: 3227215--3227573 Score: 438
Period size: 55 Copynumber: 6.5 Consensus size: 55
3227205 GATTGAGTCA
* ** ** *
3227215 TATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGCTCGAGTTC
1 TATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTC
* * *
3227270 TATACTCTCTGAAGGAATAGAGAGCGGACTCGTTT-TATGAAGATTGTTCGAGTTC
1 TATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTAT-TGAAGATTGTTCGAGTTC
* * * *
3227325 TATACTACCTGAACGAATAGGGAGTGGGCCCGTTTATTGAAGATTGTTCGAGTTC
1 TATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTC
* * *
3227380 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATAAAGATTGTTCGAGTTC
1 TATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTAT-TGAAGATTGTTCGAGTTC
* * *
3227435 TATACTCCCTGAACGAATAAGGAGCAGACCCGTTTATTGAAGATTGTTCGAG-TC
1 TATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTC
* * * *
3227489 TTATACTCCCTGAATGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAG-TC
1 -TATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTC
*
3227544 TTATACTCCCTGAAGGAATAGGGAGAGGAC
1 -TATACTCCCTGAAGGAATAGGGAGCGGAC
3227574 TCATCATTCG
Statistics
Matches: 267, Mismatches: 32, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
54 4 0.01
55 261 0.98
56 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (55 bp):
TATACTCCCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTC
Found at i:3251413 original size:22 final size:25
Alignment explanation
Indices: 3251367--3251424 Score: 88
Period size: 22 Copynumber: 2.5 Consensus size: 25
3251357 AATTGAAGTG
3251367 AAAATAGTTAT-ATGTATATTCAAA
1 AAAATAGTTATAATGTATATTCAAA
3251391 AAAATAGTTATAAT-T-TATT-AAA
1 AAAATAGTTATAATGTATATTCAAA
3251413 AAAATAGTTATA
1 AAAATAGTTATA
3251425 TAATGCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 15 0.45
23 4 0.12
24 12 0.36
25 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (25 bp):
AAAATAGTTATAATGTATATTCAAA
Found at i:3251436 original size:22 final size:23
Alignment explanation
Indices: 3251367--3251448 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 23
3251357 AATTGAAGTG
*
3251367 AAAATAGTTATATGTAT-ATTCAAA
1 AAAATAGTTATAT-AATGATT-AAA
* *
3251391 AAAATAGTTATA-ATTTATTAAA
1 AAAATAGTTATATAATGATTAAA
*
3251413 AAAATAGTTATATAATGCTT--A
1 AAAATAGTTATATAATGATTAAA
3251434 AAAATAGTTATATAA
1 AAAATAGTTATATAA
3251449 AATTAATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
21 16 0.31
22 16 0.31
23 7 0.14
24 12 0.24
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
AAAATAGTTATATAATGATTAAA
Found at i:3255397 original size:22 final size:21
Alignment explanation
Indices: 3255354--3255398 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
3255344 GTACTTTTTT
* *
3255354 AAAATTATTTAAAAAAATAGA
1 AAAATTATATAAAAAAACAGA
*
3255375 AAAATATATATAAAATAACAGA
1 AAAAT-TATATAAAAAAACAGA
3255397 AA
1 AA
3255399 GAAAAAGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAATTATATAAAAAAACAGA
Found at i:3257489 original size:26 final size:25
Alignment explanation
Indices: 3257460--3257511 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
3257450 ATATATTAAG
*
3257460 ATTTGATAAAATTATTAATTTTTATT
1 ATTTGATAAAATTATT-ATTTATATT
*
3257486 ATTTTATAAAATTATTATTTATATT
1 ATTTGATAAAATTATTATTTATATT
3257511 A
1 A
3257512 AAAATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTGATAAAATTATTATTTATATT
Found at i:3271342 original size:31 final size:31
Alignment explanation
Indices: 3271304--3271381 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
3271294 CAACAGTTAC
* *
3271304 TTGGGGGACCATATTACAAATAGACTAAATG
1 TTGGGGGACCATATTACAAACAAACTAAATG
3271335 TTGGGGGACCATATTACAAACAAACTAAATG
1 TTGGGGGACCATATTACAAACAAACTAAATG
* *
3271366 TTAGGGGACTATATTA
1 TTGGGGGACCATATTA
3271382 TAAGTTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (31 bp):
TTGGGGGACCATATTACAAACAAACTAAATG
Found at i:3272660 original size:31 final size:31
Alignment explanation
Indices: 3272623--3272695 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
3272613 TTGCAATACA
3272623 GTCCCCCAATATTTAGTTCATTTATAATATG
1 GTCCCCCAATATTTAGTTCATTTATAATATG
3272654 GTCCCCCAATATTTAGTTCATTTATAATATG
1 GTCCCCCAATATTTAGTTCATTTATAATATG
3272685 GTCCCCCAATA
1 GTCCCCCAATA
3272696 GTTACTTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (31 bp):
GTCCCCCAATATTTAGTTCATTTATAATATG
Found at i:3272740 original size:31 final size:31
Alignment explanation
Indices: 3272704--3272770 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
3272694 TAGTTACTTT
* *
3272704 GGGGACCATATTATAAACAGACTAAATGTTG
1 GGGGACCATATTACAAACACACTAAATGTTG
* *
3272735 GGGGACTATATTGCAAACACACTAAATGTTG
1 GGGGACCATATTACAAACACACTAAATGTTG
3272766 GGGGA
1 GGGGA
3272771 TTGTATAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTACAAACACACTAAATGTTG
Found at i:3273609 original size:23 final size:22
Alignment explanation
Indices: 3273576--3273638 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
3273566 AACCGTAAGT
3273576 TGCCAAAAGGCATAGAAAAACA
1 TGCCAAAAGGCATAGAAAAACA
*
3273598 TGCCACAAAGGCATAGATAAACA
1 TGCCA-AAAGGCATAGAAAAACA
* *
3273621 TGGCATAAAGACATAGAA
1 TGCCA-AAAGGCATAGAA
3273639 CATGTCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.51, C:0.17, G:0.19, T:0.13
Consensus pattern (22 bp):
TGCCAAAAGGCATAGAAAAACA
Found at i:3273642 original size:20 final size:20
Alignment explanation
Indices: 3273617--3273655 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3273607 GGCATAGATA
*
3273617 AACATGGCATAAAGACATAG
1 AACATGGCAAAAAGACATAG
*
3273637 AACATGTCAAAAAGACATA
1 AACATGGCAAAAAGACATA
3273656 ATTTGTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
AACATGGCAAAAAGACATAG
Found at i:3275837 original size:26 final size:26
Alignment explanation
Indices: 3275801--3275870 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
3275791 AAGTTAAGAT
3275801 GGAAATGAGAAGAGAGAAGCGAAAAA
1 GGAAATGAGAAGAGAGAAGCGAAAAA
*
3275827 GGAAATGAGAAGAGATAAGCGAAAAA
1 GGAAATGAGAAGAGAGAAGCGAAAAA
3275853 GGAAATGAGAAGAGAGAA
1 GGAAATGAGAAGAGAGAA
3275871 AAAGAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.57, C:0.03, G:0.34, T:0.06
Consensus pattern (26 bp):
GGAAATGAGAAGAGAGAAGCGAAAAA
Found at i:3277742 original size:97 final size:97
Alignment explanation
Indices: 3277576--3277779 Score: 354
Period size: 97 Copynumber: 2.1 Consensus size: 97
3277566 TTGCTTAGTA
* * * *
3277576 AATTCATTCGGTTGCTGCTAATAATGCTAAATTGTTTAGTCTTTAACCCTGTGAAGTTAGTATTT
1 AATTCATTCAGTTGCTGCCAATAATGCTAAACTATTTAGTCTTTAACCCTGTGAAGTTAGTATTT
3277641 GTCTTTGTTTTGTCTTTTGGTTGAAGTAATAC
66 GTCTTTGTTTTGTCTTTTGGTTGAAGTAATAC
*
3277673 AATTCATTCAGTTGCTGCCAATAATGCTGAACTATTTAGTCTTTAACCCTGTGAAGTTAGTATTT
1 AATTCATTCAGTTGCTGCCAATAATGCTAAACTATTTAGTCTTTAACCCTGTGAAGTTAGTATTT
*
3277738 GTCTTTGTTTTGTCTTTTGGTTGAAGTAATGC
66 GTCTTTGTTTTGTCTTTTGGTTGAAGTAATAC
3277770 AATTCATTCA
1 AATTCATTCA
3277780 AGTTTCAAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 101 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.45
Consensus pattern (97 bp):
AATTCATTCAGTTGCTGCCAATAATGCTAAACTATTTAGTCTTTAACCCTGTGAAGTTAGTATTT
GTCTTTGTTTTGTCTTTTGGTTGAAGTAATAC
Found at i:3279427 original size:21 final size:22
Alignment explanation
Indices: 3279376--3279438 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
3279366 GATTCACCTG
* *
3279376 TCATCATTCAAAAGGCCTCTCA
1 TCATCATTCAAGAGGCCCCTCA
*
3279398 T-ATCGTTCAAGAGGCCCCT-A
1 TCATCATTCAAGAGGCCCCTCA
*
3279418 TCATCCTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTC
3279439 CCACCGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.25, C:0.35, G:0.14, T:0.25
Consensus pattern (22 bp):
TCATCATTCAAGAGGCCCCTCA
Found at i:3279451 original size:21 final size:22
Alignment explanation
Indices: 3279401--3279454 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
3279391 CCTCTCATAT
*
3279401 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGCCCCTACCATC
*
3279423 C-TTCAAGAGGCCCCTCCCA-C
1 CGTTCAAGAGGCCCCTACCATC
*
3279443 CGTTTAAGAGGC
1 CGTTCAAGAGGC
3279455 TCATGTCATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.20
Consensus pattern (22 bp):
CGTTCAAGAGGCCCCTACCATC
Found at i:3279452 original size:42 final size:42
Alignment explanation
Indices: 3279401--3279494 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
3279391 CCTCTCATAT
*
3279401 CGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
* * * * * * *
3279443 CGTTTAAGAGGCTCATGTCATCGTTCAGGAGGTCCCTCTCAC
1 CGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
*
3279485 CGTTCGAGAG
1 CGTTCAAGAG
3279495 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.20, C:0.34, G:0.22, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
Found at i:3280947 original size:64 final size:64
Alignment explanation
Indices: 3280841--3281167 Score: 274
Period size: 64 Copynumber: 5.3 Consensus size: 64
3280831 TGATGTATTC
* *
3280841 GTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCGTGTTTAATTGATTT
1 GTAAAAGTTGATTTGTTTAATTGATGTGGAAATAAGACTTATTTTTTGCGTGTTTAATTGATTT
* ** * *
3280905 GTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGTCCTG---AAGTGAGCT
1 GTAAAAGTTGATTTGTTTAATTGATGTGGAAATAAGACTTATTTTTTG-CGTGTTTAATTGA--T
**
3280967 GC
63 TT
* * * * * *
3280969 GTGAAA-TTGA--TG--T-ATT--TGT-G-CATAA-AC-AATTGTCTGCGTG-A-AATTGATGTA
1 GTAAAAGTTGATTTGTTTAATTGATGTGGAAATAAGACTTATTTTTTGCGTGTTTAATTGA--T-
3281020 TT
63 TT
* *
3281022 CGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCGTGTTTAATTGATTT
1 -GTAAAAGTTGATTTGTTTAATTGATGTGGAAATAAGACTTATTTTTTGCGTGTTTAATTGATTT
* ** **
3281087 GTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGTTTGTTTAATTGATTT
1 GTAAAAGTTGATTTGTTTAATTGATGTGGAAATAAGACTTATTTTTTGCGTGTTTAATTGATTT
3281151 GTAAAAGTTGATTTGTT
1 GTAAAAGTTGATTTGTT
3281168 GTTTTAAATT
Statistics
Matches: 206, Mismatches: 37, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
51 3 0.01
52 12 0.06
53 1 0.00
54 9 0.04
55 4 0.02
56 3 0.01
57 2 0.01
58 3 0.01
59 2 0.01
60 3 0.01
61 2 0.01
62 7 0.03
63 5 0.02
64 127 0.62
65 6 0.03
66 11 0.05
68 6 0.03
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (64 bp):
GTAAAAGTTGATTTGTTTAATTGATGTGGAAATAAGACTTATTTTTTGCGTGTTTAATTGATTT
Found at i:3281078 original size:182 final size:182
Alignment explanation
Indices: 3280771--3281135 Score: 721
Period size: 182 Copynumber: 2.0 Consensus size: 182
3280761 TGCAGGTTAA
3280771 TCCTGAAGTGAGCTGCGTGAAATTGATGTATTTGTGCATAAACAACTGTCTGCGTGAAATTGATG
1 TCCTGAAGTGAGCTGCGTGAAATTGATGTATTTGTGCATAAACAACTGTCTGCGTGAAATTGATG
3280836 TATTCGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCGTGTTTAATTG
66 TATTCGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCGTGTTTAATTG
3280901 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTG
131 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTG
*
3280953 TCCTGAAGTGAGCTGCGTGAAATTGATGTATTTGTGCATAAACAATTGTCTGCGTGAAATTGATG
1 TCCTGAAGTGAGCTGCGTGAAATTGATGTATTTGTGCATAAACAACTGTCTGCGTGAAATTGATG
3281018 TATTCGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCGTGTTTAATTG
66 TATTCGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCGTGTTTAATTG
3281083 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTG
131 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTG
3281135 T
1 T
3281136 TTGTTTAATT
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 182 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (182 bp):
TCCTGAAGTGAGCTGCGTGAAATTGATGTATTTGTGCATAAACAACTGTCTGCGTGAAATTGATG
TATTCGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCGTGTTTAATTG
ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTG
Found at i:3281298 original size:20 final size:19
Alignment explanation
Indices: 3281271--3281344 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
3281261 TTGCGTTACG
*
3281271 AAAGTCAAATTCGCGCTGC
1 AAAGTCAAATTCGCACTGC
3281290 AATAGTCAAATTCGCAACGTG-
1 AA-AGTCAAATTCGC-AC-TGC
* *
3281311 AAAGTCAAATTCGCAATGTG
1 AAAGTCAAATTCGCACTG-C
3281331 AAAGTCAAATTCGC
1 AAAGTCAAATTCGC
3281345 GTTGCAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
18 2 0.04
19 3 0.06
20 38 0.79
21 3 0.06
22 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (19 bp):
AAAGTCAAATTCGCACTGC
Found at i:3281583 original size:18 final size:18
Alignment explanation
Indices: 3281560--3281595 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3281550 AAGTCGGTTG
* *
3281560 TGATTGGGATTTTGATTT
1 TGATTGCGATCTTGATTT
3281578 TGATTGCGATCTTGATTT
1 TGATTGCGATCTTGATTT
3281596 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.25, T:0.53
Consensus pattern (18 bp):
TGATTGCGATCTTGATTT
Found at i:3283671 original size:21 final size:22
Alignment explanation
Indices: 3283633--3283675 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3283623 GTAGCATTTT
3283633 CTTCTTTTTCTTTTCTTCAGGGA
1 CTTCTTTTTC-TTTCTTCAGGGA
3283656 CTTCTTTTTC-TTCTTCAGGG
1 CTTCTTTTTCTTTCTTCAGGG
3283676 TTATATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.07, C:0.23, G:0.14, T:0.56
Consensus pattern (22 bp):
CTTCTTTTTCTTTCTTCAGGGA
Found at i:3284857 original size:20 final size:20
Alignment explanation
Indices: 3284832--3284941 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
3284822 AACTAAAACC
3284832 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
3284852 TGTTGCG-AATTCGAAAATT-G
1 TGTTGCGAAATT--AAAATTCG
* *
3284872 AGTTGCGAAAATAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
3284892 CGTTGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATT-A-AAATTCG
* * * *
3284912 AGTTACGAATTTGAAATTCAG
1 TGTTGCGAAATTAAAATTC-G
3284933 TGTTGCGAA
1 TGTTGCGAA
3284942 TTTGGAAATC
Statistics
Matches: 71, Mismatches: 10, Indels: 17
0.72 0.10 0.17
Matches are distributed among these distances:
19 16 0.23
20 32 0.45
21 23 0.32
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:3284877 original size:40 final size:40
Alignment explanation
Indices: 3284833--3284961 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
3284823 ACTAAAACCT
*
3284833 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATTGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
* *
3284873 GTTGCGAAAATAAAATTCGCGTTGCGAATTC-AGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGA-AAATCGA
* * * * * *
3284913 GTTACGAATTTGAAATTCAGTGTTGCGAATTTGGAAATCGC
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCGAAAATCGA
3284954 GTTGCGAA
1 GTTGCGAA
3284962 TTTAGAAACT
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 49 0.66
41 24 0.32
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
Found at i:3284955 original size:61 final size:60
Alignment explanation
Indices: 3284889--3285005 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
3284879 AAAATAAAAT
* *
3284889 TCGCGTTGCGAATTCAGAAA-TCGAGTTACGAATTTGAAATTCAGTGTTGCGAATTTGGAAA
1 TCGCGTTGCGAATTCAGAAACT-GAGTTACGAAATTGAAATTC-GCGTTGCGAATTTGGAAA
* * * *
3284950 TCGCGTTGCGAATTTAGAAACTGAGTTGCGAAATTGGAGTTCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTCAGAAACTGAGTTACGAAATTGAAATTCGCGTTGCGAATTTG
3285006 TTGGTCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 13 0.27
61 35 0.71
62 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (60 bp):
TCGCGTTGCGAATTCAGAAACTGAGTTACGAAATTGAAATTCGCGTTGCGAATTTGGAAA
Found at i:3284959 original size:20 final size:20
Alignment explanation
Indices: 3284889--3285005 Score: 103
Period size: 20 Copynumber: 5.8 Consensus size: 20
3284879 AAAATAAAAT
**
3284889 TCGCGTTGCGAATTCAGAAA
1 TCGCGTTGCGAATTTGGAAA
* *
3284909 TCGAGTTACGAATTT-GAAA
1 TCGCGTTGCGAATTTGGAAA
*
3284928 TTCAGTGTTGCGAATTTGGAAA
1 -TC-GCGTTGCGAATTTGGAAA
*
3284950 TCGCGTTGCGAATTTAGAAA
1 TCGCGTTGCGAATTTGGAAA
* * **
3284970 -CTGAGTTGCGAAATTGGAGT
1 TC-GCGTTGCGAATTTGGAAA
3284990 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
3285006 TTGGTCATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.06
20 55 0.71
21 14 0.18
22 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGGAAA
Found at i:3287625 original size:17 final size:16
Alignment explanation
Indices: 3287603--3287636 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3287593 TAAAAACAAT
3287603 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3287620 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3287636 A
1 A
3287637 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3288155 original size:24 final size:24
Alignment explanation
Indices: 3288111--3288157 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3288101 ATAAAGAACC
*
3288111 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3288135 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
3288158 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3291466 original size:19 final size:20
Alignment explanation
Indices: 3291444--3291487 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3291434 GAGAAAAGGT
3291444 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
3291463 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
3291483 AAAAG
1 AAAAG
3291488 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:3297782 original size:17 final size:16
Alignment explanation
Indices: 3297760--3297793 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3297750 TAAAAACAGT
3297760 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3297777 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3297793 A
1 A
3297794 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3298312 original size:24 final size:24
Alignment explanation
Indices: 3298268--3298314 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3298258 ATAAAGAACC
*
3298268 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3298292 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
3298315 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3300064 original size:19 final size:19
Alignment explanation
Indices: 3300040--3300078 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3300030 ACCTTCTAAA
3300040 TTATTTAATTTCATTATAC
1 TTATTTAATTTCATTATAC
*
3300059 TTATTTAATTTTATTATAC
1 TTATTTAATTTCATTATAC
3300078 T
1 T
3300079 AAATGCACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTAATTTCATTATAC
Found at i:3301578 original size:32 final size:32
Alignment explanation
Indices: 3301537--3301601 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3301527 GCAATGATGT
3301537 TCGATAATAAAGGGCTGAATTCCTATCCTTGA
1 TCGATAATAAAGGGCTGAATTCCTATCCTTGA
3301569 TCGATAATAAAGGGCTGAATTCCTATCCTTGA
1 TCGATAATAAAGGGCTGAATTCCTATCCTTGA
3301601 T
1 T
3301602 GCCACTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (32 bp):
TCGATAATAAAGGGCTGAATTCCTATCCTTGA
Found at i:3304713 original size:20 final size:22
Alignment explanation
Indices: 3304683--3304732 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
3304673 ATATTTTTTG
3304683 TATTT-TATATTATTA-AAAT-
1 TATTTATATATTATTACAAATC
*
3304702 TATTTATATATTTTTACAAATC
1 TATTTATATATTATTACAAATC
*
3304724 TAATTATAT
1 TATTTATAT
3304733 CCATATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 9 0.35
21 4 0.15
22 8 0.31
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTATATATTATTACAAATC
Found at i:3324864 original size:10 final size:10
Alignment explanation
Indices: 3324849--3324889 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
3324839 TGTACGAACG
3324849 AACGAACATA
1 AACGAACATA
3324859 AACGAACACAATA
1 AACG-A-AC-ATA
3324872 AACGAACATA
1 AACGAACATA
3324882 AACGAACA
1 AACGAACA
3324890 ATATTAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 15 0.54
11 3 0.11
12 3 0.11
13 7 0.25
ACGTcount: A:0.61, C:0.22, G:0.10, T:0.07
Consensus pattern (10 bp):
AACGAACATA
Found at i:3336594 original size:30 final size:30
Alignment explanation
Indices: 3336523--3336582 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3336513 ACAATTTAAG
3336523 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
3336553 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
3336583 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:3336692 original size:13 final size:13
Alignment explanation
Indices: 3336674--3336711 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3336664 AGTGCATCCA
3336674 TGCATCCCTGCAG
1 TGCATCCCTGCAG
3336687 TGCATCCCTGCAG
1 TGCATCCCTGCAG
*
3336700 TGCATCCATGCA
1 TGCATCCCTGCA
3336712 TCTGCACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.18, C:0.37, G:0.21, T:0.24
Consensus pattern (13 bp):
TGCATCCCTGCAG
Found at i:3336727 original size:22 final size:20
Alignment explanation
Indices: 3336700--3336751 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
3336690 ATCCCTGCAG
*
3336700 TGCATCCATGCATCTGCACTAA
1 TGCATCCATGCATCAG-AC-AA
* *
3336722 TGCATCGATGCATCAGGCAA
1 TGCATCCATGCATCAGACAA
3336742 TGCATCCATG
1 TGCATCCATG
3336752 TACCCAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 11 0.42
21 1 0.04
22 14 0.54
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TGCATCCATGCATCAGACAA
Found at i:3336817 original size:20 final size:21
Alignment explanation
Indices: 3336776--3336830 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
3336766 ATGCAATTAG
3336776 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
3336797 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
3336817 TGCATCCATGCATC
1 TGCATCGATGCATC
3336831 AAGGCTGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:3337235 original size:34 final size:32
Alignment explanation
Indices: 3337196--3337265 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
3337186 TTTTGTAAAG
*
3337196 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3337230 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3337262 GGGA
1 GGGA
3337266 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3339140 original size:2 final size:2
Alignment explanation
Indices: 3339128--3339169 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3339118 TTATAAATTT
* *
3339128 TA TA AA TA TA TA TA TA CA 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
3339170 AATTTTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3339434 original size:20 final size:20
Alignment explanation
Indices: 3339409--3339446 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3339399 ATTCTATTCC
*
3339409 CTGGTAATCTTATATTCTCA
1 CTGGTAATCTTACATTCTCA
*
3339429 CTGGTAATTTTACATTCT
1 CTGGTAATCTTACATTCT
3339447 GTGCACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTACATTCTCA
Found at i:3346070 original size:21 final size:21
Alignment explanation
Indices: 3346046--3346108 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 21
3346036 AATTTCGATA
3346046 AGTTTAATGATCGTTTATAAC
1 AGTTTAATGATCGTTTATAAC
* *
3346067 AG-TTAAT-AT-ATTCGAT-A-
1 AGTTTAATGATCGTT-TATAAC
3346084 AGTTTAATGATCGTTTATAAC
1 AGTTTAATGATCGTTTATAAC
3346105 AGTT
1 AGTT
3346109 AATATAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 2 0.06
18 8 0.25
19 8 0.25
20 8 0.25
21 6 0.19
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (21 bp):
AGTTTAATGATCGTTTATAAC
Found at i:3346081 original size:38 final size:38
Alignment explanation
Indices: 3346039--3346114 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3346029 CCATAATAAT
3346039 TTCGATAAGTTTAATGATCGTTTATAACAGTTAATATA
1 TTCGATAAGTTTAATGATCGTTTATAACAGTTAATATA
3346077 TTCGATAAGTTTAATGATCGTTTATAACAGTTAATATA
1 TTCGATAAGTTTAATGATCGTTTATAACAGTTAATATA
3346115 GTAAGTACAT
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:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (38 bp):
TTCGATAAGTTTAATGATCGTTTATAACAGTTAATATA
Found at i:3346103 original size:19 final size:19
Alignment explanation
Indices: 3346043--3346103 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
3346033 AATAATTTCG
3346043 ATAAGTTTAATGATCGTTT
1 ATAAGTTTAATGATCGTTT
* *
3346062 ATAACAG-TTAAT-AT-ATTCG
1 AT-A-AGTTTAATGATCGTT-T
3346081 ATAAGTTTAATGATCGTTT
1 ATAAGTTTAATGATCGTTT
3346100 ATAA
1 ATAA
3346104 CAGTTAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 2 0.06
18 8 0.25
19 12 0.38
20 8 0.25
21 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.43
Consensus pattern (19 bp):
ATAAGTTTAATGATCGTTT
Found at i:3348950 original size:8 final size:8
Alignment explanation
Indices: 3348939--3348967 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3348929 CCTCTTGTCC
3348939 TCTCTCTA
1 TCTCTCTA
3348947 TCTCTCTA
1 TCTCTCTA
3348955 TCTCTCTA
1 TCTCTCTA
3348963 TCTCT
1 TCTCT
3348968 TAGGTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.38, G:0.00, T:0.52
Consensus pattern (8 bp):
TCTCTCTA
Found at i:3351415 original size:14 final size:15
Alignment explanation
Indices: 3351396--3351428 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3351386 ATAATAAACG
*
3351396 AACATAAACGAAC-T
1 AACATAAACAAACAT
3351410 AACATAAACAAACAT
1 AACATAAACAAACAT
3351425 AACA
1 AACA
3351429 AATGAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.64, C:0.21, G:0.03, T:0.12
Consensus pattern (15 bp):
AACATAAACAAACAT
Found at i:3351789 original size:14 final size:14
Alignment explanation
Indices: 3351770--3351799 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3351760 TTAAATGTTT
3351770 ACGAACGTAAATGA
1 ACGAACGTAAATGA
3351784 ACGAACGTAAATGA
1 ACGAACGTAAATGA
3351798 AC
1 AC
3351800 ATAAATGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (14 bp):
ACGAACGTAAATGA
Found at i:3352289 original size:15 final size:15
Alignment explanation
Indices: 3352269--3352302 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3352259 TATTATTCTC
3352269 TTAAAAATCCTGAAT
1 TTAAAAATCCTGAAT
*
3352284 TTAAAAATCTTGAAT
1 TTAAAAATCCTGAAT
3352299 TTAA
1 TTAA
3352303 GCACCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (15 bp):
TTAAAAATCCTGAAT
Found at i:3353173 original size:19 final size:19
Alignment explanation
Indices: 3353149--3353185 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3353139 AATTGTGTTA
3353149 TTTAAATTATTGTGGATTT
1 TTTAAATTATTGTGGATTT
* *
3353168 TTTAAATTTTTTTGGATT
1 TTTAAATTATTGTGGATT
3353186 AGTTTATATT
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:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (19 bp):
TTTAAATTATTGTGGATTT
Found at i:3356538 original size:24 final size:24
Alignment explanation
Indices: 3356511--3356568 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
3356501 ATTTTGTTTC
*
3356511 GTTTTAATATCTAAAATTTCATTT
1 GTTTTAAAATCTAAAATTTCATTT
*
3356535 GTTTTAAAATCTAAACTTTCATTT
1 GTTTTAAAATCTAAAATTTCATTT
3356559 GTTTTAAAAT
1 GTTTTAAAAT
3356569 AATACTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (24 bp):
GTTTTAAAATCTAAAATTTCATTT
Found at i:3357162 original size:2 final size:2
Alignment explanation
Indices: 3357157--3357197 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3357147 TTTTATGTCA
3357157 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
3357198 ATGGGCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3357426 original size:18 final size:18
Alignment explanation
Indices: 3357392--3357430 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3357382 ACAAAGTTAG
*
3357392 TAAAACGACTAATAATAA
1 TAAAACGACTAAAAATAA
3357410 TAAAATCGA-TAAAAATAA
1 TAAAA-CGACTAAAAATAA
3357428 TAA
1 TAA
3357431 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (18 bp):
TAAAACGACTAAAAATAA
Found at i:3357797 original size:21 final size:22
Alignment explanation
Indices: 3357773--3357819 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
3357763 GTTGATATTT
3357773 TATTTT-ATGTTTTTTT-TTCTA
1 TATTTTAAT-TTTTTTTATTCTA
*
3357794 TATTTTAATTTTTTTTATTTTA
1 TATTTTAATTTTTTTTATTCTA
3357816 TATT
1 TATT
3357820 CAATAAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
TATTTTAATTTTTTTTATTCTA
Found at i:3375967 original size:17 final size:19
Alignment explanation
Indices: 3375937--3375975 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
3375927 AATATTTTAA
3375937 ATTATATGTAATTTAAAAT
1 ATTATATGTAATTTAAAAT
*
3375956 ATTATAT-T-ATTTATAAT
1 ATTATATGTAATTTAAAAT
3375973 ATT
1 ATT
3375976 TTAGATCGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTATATGTAATTTAAAAT
Found at i:3376515 original size:56 final size:56
Alignment explanation
Indices: 3376444--3376605 Score: 189
Period size: 56 Copynumber: 2.9 Consensus size: 56
3376434 AAAAATAAGA
* * ** * * *
3376444 GTTTTGAAATTGAGTATATCTATCTGTTATTGTTATTAATAATCATAAAAGTAGGG
1 GTTTCGAAATCGAGTATATCTATCAATTATTGTCATTAAGAAGCATAAAAGTAGGG
* **
3376500 GTTTCGAAATCGAGTATATCTATCAATTATTGTCATTAAGAAGCATAAAAATAAAG
1 GTTTCGAAATCGAGTATATCTATCAATTATTGTCATTAAGAAGCATAAAAGTAGGG
** * * *
3376556 ACTCCGAAATCGAGTATATATATCAATTGTTGTCATTAAGAAGCATAAAA
1 GTTTCGAAATCGAGTATATCTATCAATTATTGTCATTAAGAAGCATAAAA
3376606 ATAAAGACCT
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 91 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (56 bp):
GTTTCGAAATCGAGTATATCTATCAATTATTGTCATTAAGAAGCATAAAAGTAGGG
Found at i:3376606 original size:56 final size:56
Alignment explanation
Indices: 3376503--3376630 Score: 213
Period size: 56 Copynumber: 2.3 Consensus size: 56
3376493 AGTAGGGGTT
*
3376503 TCGAAATCGAGTATATCTATCAATTATTGTCATTAAGAAGCATAAAAATAAAGA-C
1 TCGAAATCGAGTATATATATCAATTATTGTCATTAAGAAGCATAAAAATAAAGACC
*
3376558 TCCGAAATCGAGTATATATATCAATTGTTGTCATTAAGAAGCATAAAAATAAAGACC
1 T-CGAAATCGAGTATATATATCAATTATTGTCATTAAGAAGCATAAAAATAAAGACC
*
3376615 TCGAAATCGAATATAT
1 TCGAAATCGAGTATAT
3376631 CTAGAAAATA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
55 1 0.01
56 65 0.96
57 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (56 bp):
TCGAAATCGAGTATATATATCAATTATTGTCATTAAGAAGCATAAAAATAAAGACC
Found at i:3382259 original size:166 final size:168
Alignment explanation
Indices: 3381985--3382318 Score: 654
Period size: 166 Copynumber: 2.0 Consensus size: 168
3381975 TTAACTACTC
3381985 AACTTTCAAATTGCTCCTATTTAATCACTCTAATTTATTTTATTAACAAATTTTGTGACATGACA
1 AACTTTCAAATTGCTCCTATTTAATCACTCTAATTTATTTTATTAACAAATTTTGTGACATGACA
3382050 TTTTTATTATTATTTTAGTAAGAATAGAAAAATAAGGATTTAAATATACAAAA-GTGTCCAATAT
66 TTTTTATTATTATTTTAGTAAGAATAGAAAAATAAGGATTTAAATATACAAAAGGTGTCCAATAT
3382114 ATGC-TTTGGTTCCAGTTTAGTACCTAATGTTTACTTT
131 ATGCTTTTGGTTCCAGTTTAGTACCTAATGTTTACTTT
3382151 AACTTTCAAATTGCTCCTATTTAATCACTCTAATTTATTTTATTAACAAATTTTGTGACATGACA
1 AACTTTCAAATTGCTCCTATTTAATCACTCTAATTTATTTTATTAACAAATTTTGTGACATGACA
3382216 TTTTTATTATTATTTTAGTAAGAATAGAAAAATAAGGATTTAAATATACAAAAGGTGTCCAATAT
66 TTTTTATTATTATTTTAGTAAGAATAGAAAAATAAGGATTTAAATATACAAAAGGTGTCCAATAT
3382281 ATGCTTTTGGTTCCAGTTTAGTACCTAATGTTTACTTT
131 ATGCTTTTGGTTCCAGTTTAGTACCTAATGTTTACTTT
3382319 GTTCCAGTTT
Statistics
Matches: 166, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
166 118 0.71
167 15 0.09
168 33 0.20
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (168 bp):
AACTTTCAAATTGCTCCTATTTAATCACTCTAATTTATTTTATTAACAAATTTTGTGACATGACA
TTTTTATTATTATTTTAGTAAGAATAGAAAAATAAGGATTTAAATATACAAAAGGTGTCCAATAT
ATGCTTTTGGTTCCAGTTTAGTACCTAATGTTTACTTT
Found at i:3383087 original size:32 final size:31
Alignment explanation
Indices: 3383046--3383105 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
3383036 AGCTAAAAAT
*
3383046 TAATTTGAAAGTTAGAGTGATCAAATTAAGAG
1 TAATTTGAAAGTTA-AGTAATCAAATTAAGAG
*
3383078 TAATTTGAAAGTTAAGTAATTAAATTAA
1 TAATTTGAAAGTTAAGTAATCAAATTAA
3383106 AAAATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.47, C:0.02, G:0.17, T:0.35
Consensus pattern (31 bp):
TAATTTGAAAGTTAAGTAATCAAATTAAGAG
Found at i:3385842 original size:12 final size:12
Alignment explanation
Indices: 3385812--3385845 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3385802 TAAAAGTCTG
3385812 GCCTGTTTAAAA
1 GCCTGTTTAAAA
**
3385824 GTATGTTTAAAA
1 GCCTGTTTAAAA
3385836 GCCTGTTTAA
1 GCCTGTTTAA
3385846 CAATAAACAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (12 bp):
GCCTGTTTAAAA
Found at i:3386046 original size:41 final size:40
Alignment explanation
Indices: 3385973--3386052 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 40
3385963 CTTATAAAGC
*
3385973 TTTTTAATAAGCCTAAGCCTGATATGTCTAGTTAAATAAG
1 TTTTTAAAAAGCCTAAGCCTGATATGTCTAGTTAAATAAG
* * * *
3386013 TTTTTAAAAAGGCCTGAGTCTGATCTGTTTAGTTAAATAA
1 TTTTTAAAAA-GCCTAAGCCTGATATGTCTAGTTAAATAA
3386053 ATCAAGCTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 9 0.26
41 25 0.74
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (40 bp):
TTTTTAAAAAGCCTAAGCCTGATATGTCTAGTTAAATAAG
Done.