Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 12 of 318
Found at i:3041607 original size:32 final size:31
Alignment explanation
Indices: 3041556--3041630 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
3041546 TTTTTTTTGG
*
3041556 TTTTTTTTTGCTGGAAATTTTTTTCTGGAAA
1 TTTTTTTTTGCTGGAAATTTTTTGCTGGAAA
**
3041587 TTTTTTTTGGTGCTGG-AATTTTTTGCTGGATT
1 TTTTTTTT--TGCTGGAAATTTTTTGCTGGAAA
3041619 TTTTTTTTTGCT
1 TTTTTTTTTGCT
3041631 TCCCCTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.10
31 8 0.21
32 21 0.54
33 6 0.15
ACGTcount: A:0.12, C:0.07, G:0.19, T:0.63
Consensus pattern (31 bp):
TTTTTTTTTGCTGGAAATTTTTTGCTGGAAA
Found at i:3041622 original size:14 final size:14
Alignment explanation
Indices: 3041545--3041624 Score: 51
Period size: 15 Copynumber: 5.6 Consensus size: 14
3041535 CGTTCTATTG
*
3041545 TTTTTTTT--TGGT
1 TTTTTTTTGCTGGA
3041557 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGG-A
*
3041572 ATTTTTTT-CTGGAAA
1 TTTTTTTTGCTGG--A
3041587 TTTTTTTTGGTGCTGGA
1 -TTTTTTT--TGCTGGA
*
3041604 -ATTTTTTGCTGGA
1 TTTTTTTTGCTGGA
3041617 TTTTTTTT
1 TTTTTTTT
3041625 TTTGCTTCCC
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
12 8 0.15
13 7 0.13
14 13 0.24
15 14 0.26
16 6 0.11
17 1 0.02
18 1 0.02
19 4 0.07
ACGTcount: A:0.11, C:0.05, G:0.19, T:0.65
Consensus pattern (14 bp):
TTTTTTTTGCTGGA
Found at i:3041627 original size:33 final size:32
Alignment explanation
Indices: 3041556--3041630 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
3041546 TTTTTTTTGG
*
3041556 TTTTTTTT-TGCTGGAAATTTTTTTCTGGAAA
1 TTTTTTTTGTGCTGGAAATTTTTTGCTGGAAA
*
3041587 TTTTTTTTGGTGCTGG-AATTTTTTGCTGG-AT
1 TTTTTTTT-GTGCTGGAAATTTTTTGCTGGAAA
*
3041618 TTTTTTTTTTGCT
1 TTTTTTTTGTGCT
3041631 TCCCCTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.10
31 17 0.44
32 12 0.31
33 6 0.15
ACGTcount: A:0.12, C:0.07, G:0.19, T:0.63
Consensus pattern (32 bp):
TTTTTTTTGTGCTGGAAATTTTTTGCTGGAAA
Found at i:3042072 original size:35 final size:35
Alignment explanation
Indices: 3042032--3042137 Score: 194
Period size: 35 Copynumber: 3.0 Consensus size: 35
3042022 GGGGTGTGTG
*
3042032 ATGGTGCTGGCGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
*
3042067 GTGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
3042102 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
3042137 A
1 A
3042138 AAGGCAAGTG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.23, C:0.12, G:0.49, T:0.16
Consensus pattern (35 bp):
ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
Found at i:3042798 original size:2 final size:2
Alignment explanation
Indices: 3042793--3042823 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3042783 ATAAAATGAT
3042793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3042824 TCCTTTGCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3042951 original size:16 final size:17
Alignment explanation
Indices: 3042916--3042953 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3042906 ACCGATATAA
* *
3042916 ATTTTTTAGTTCAAATT
1 ATTTTTTAGTTAAAAAT
3042933 ATTTTTTA-TTAAAAAT
1 ATTTTTTAGTTAAAAAT
3042949 ATTTT
1 ATTTT
3042954 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTTTTAGTTAAAAAT
Found at i:3054106 original size:30 final size:30
Alignment explanation
Indices: 3054041--3054116 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
3054031 AAAGAGAACT
*
3054041 GTGCTACGAGGCAGACAAAAACCCTAAACA
1 GTGCTACAAGGCAGACAAAAACCCTAAACA
* *
3054071 ATGCTACAAGGCAGACAAAAACCCTAGAGC-
1 GTGCTACAAGGCAGACAAAAACCCTA-AACA
3054101 GTGCTACAAGGCAGAC
1 GTGCTACAAGGCAGAC
3054117 TATATACTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 39 0.95
31 2 0.05
ACGTcount: A:0.41, C:0.26, G:0.22, T:0.11
Consensus pattern (30 bp):
GTGCTACAAGGCAGACAAAAACCCTAAACA
Found at i:3054422 original size:22 final size:23
Alignment explanation
Indices: 3054397--3054446 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
3054387 ATAACTTAAT
*
3054397 TAAATAT-ATATATA-TATATATG
1 TAAATATAATAAATATTA-ATATG
3054419 TAAA-ATAATAAATATTAATATG
1 TAAATATAATAAATATTAATATG
3054441 -AAATAT
1 TAAATAT
3054447 TTTATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 5 0.21
22 17 0.71
23 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAATATAATAAATATTAATATG
Found at i:3057998 original size:21 final size:20
Alignment explanation
Indices: 3057968--3058007 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3057958 TAAAACTTGT
*
3057968 ATAACTATCATCAAACATTC
1 ATAACTATCACCAAACATTC
*
3057988 ATAATCTATCACCAATCATT
1 ATAA-CTATCACCAAACATT
3058008 AAAAATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCACCAAACATTC
Found at i:3058014 original size:21 final size:21
Alignment explanation
Indices: 3057972--3058014 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3057962 ACTTGTATAA
* * *
3057972 CTATCATCAAACATTCATAAT
1 CTATCACCAAACATTAAAAAT
*
3057993 CTATCACCAATCATTAAAAAT
1 CTATCACCAAACATTAAAAAT
3058014 C
1 C
3058015 ATACATATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (21 bp):
CTATCACCAAACATTAAAAAT
Found at i:3058413 original size:208 final size:211
Alignment explanation
Indices: 3058052--3058466 Score: 674
Period size: 208 Copynumber: 2.0 Consensus size: 211
3058042 AAACCTTTAA
*
3058052 AAGTTTTGCAAATTAGTCCCTGGGATAGCTAGACTAAGCTGCAACGATCTAAAAAAACATAGAAA
1 AAGTTTTGCAAATTAGTCCCTGAGATAGCTAGACTAAGCTGCAACGATCTAAAAAAACATAGAAA
*
3058117 TCACTAAAAATCGAGTCAAAAGTAACTTACATGCACCTAGGATAGTTTCCAAACCTTGAAGCTCT
66 TCACTAAAAACCGAGTCAAAAGTAACTTACATGCACCTAGGATAGTTTCCAAACCTTGAAGCTCT
* **
3058182 TTTGATGGAGCTTTTCTTAGCTTAATTTCGGTTAGGTGAAGAAGAAACAAGATGATACCTTGTTT
131 TTTAATAAAGCTTTTCTTAGCTTAATTTCGGTTAGGTGAAGAAGAAACAAGATGATACCTTGTTT
3058247 TTCTTTAATTTAGTTT
196 TTCTTTAATTTAGTTT
* * * *
3058263 AAGTTTTTCAAATTAGTCCCT-AGTTAGCTCGACTAAGCTGTAACGATCT-AAAAAACATAGAAA
1 AAGTTTTGCAAATTAGTCCCTGAGATAGCTAGACTAAGCTGCAACGATCTAAAAAAACATAGAAA
* * * *
3058326 TCATTAAATACCGAGTCAAAA-TCACTTACATGCACTTAGGATAGTTTCCAAACCTTGAAGCTCT
66 TCACTAAAAACCGAGTCAAAAGTAACTTACATGCACCTAGGATAGTTTCCAAACCTTGAAGCTCT
* *
3058390 TTTAATAAAGTTTTTCTTAGCTTAATTTTGGTTAGGTGAAGAAGAAACAAGATGATACCTTGTTT
131 TTTAATAAAGCTTTTCTTAGCTTAATTTCGGTTAGGTGAAGAAGAAACAAGATGATACCTTGTTT
3058455 TTCTTTAATTTA
196 TTCTTTAATTTA
3058467 ATTAACTTCA
Statistics
Matches: 189, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
208 113 0.60
209 32 0.17
210 24 0.13
211 20 0.11
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (211 bp):
AAGTTTTGCAAATTAGTCCCTGAGATAGCTAGACTAAGCTGCAACGATCTAAAAAAACATAGAAA
TCACTAAAAACCGAGTCAAAAGTAACTTACATGCACCTAGGATAGTTTCCAAACCTTGAAGCTCT
TTTAATAAAGCTTTTCTTAGCTTAATTTCGGTTAGGTGAAGAAGAAACAAGATGATACCTTGTTT
TTCTTTAATTTAGTTT
Found at i:3059218 original size:9 final size:9
Alignment explanation
Indices: 3059204--3059236 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3059194 TTTCGGGGAA
3059204 TCGAGTTAT
1 TCGAGTTAT
*
3059213 TCGAGTTAA
1 TCGAGTTAT
3059222 TCGAGTTAT
1 TCGAGTTAT
3059231 TCGAGT
1 TCGAGT
3059237 CAACTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:3059225 original size:18 final size:18
Alignment explanation
Indices: 3059202--3059236 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3059192 AATTTCGGGG
3059202 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
3059220 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
3059237 CAACTAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:3060651 original size:26 final size:26
Alignment explanation
Indices: 3060575--3060651 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 26
3060565 ACACTAATAT
* * * *
3060575 CGCAGTAAAGCTGCCGGTAATAATAT
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* * * *
3060601 GGCAGCGAAGCTACCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
*
3060627 CGCAGCAAAGCTGCCAGTATTAGTA
1 CGCAGCAAAGCTGCCAGTAATAGTA
3060652 TATGTGGCAA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:3069172 original size:15 final size:16
Alignment explanation
Indices: 3069139--3069178 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3069129 TATTTTTTTG
3069139 TTAATT-TTTAATCAA
1 TTAATTATTTAATCAA
*
3069154 TTAATTATTTAAT-AT
1 TTAATTATTTAATCAA
3069169 TTAA-TATTTA
1 TTAATTATTTA
3069179 TGTTCAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 11 0.48
16 6 0.26
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATTATTTAATCAA
Found at i:3071049 original size:22 final size:23
Alignment explanation
Indices: 3071015--3071058 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3071005 TGATAGTTAT
*
3071015 ATCTCTATGAAT-AGACATGAAAA
1 ATCTCTATAAATAAGA-ATGAAAA
3071038 ATCT-TATAAATAAGAATGAAA
1 ATCTCTATAAATAAGAATGAAA
3071059 TTTCATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.27
Consensus pattern (23 bp):
ATCTCTATAAATAAGAATGAAAA
Found at i:3071826 original size:3 final size:3
Alignment explanation
Indices: 3071814--3071843 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3071804 TCTTGTGGAG
3071814 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3071844 CATTAAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3073492 original size:15 final size:15
Alignment explanation
Indices: 3073472--3073536 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
3073462 GTATCTTAGG
3073472 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
3073487 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
3073502 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
3073517 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
3073531 TTTCTT
1 TTTCTT
3073537 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
14 10 0.23
15 31 0.72
16 2 0.05
ACGTcount: A:0.09, C:0.15, G:0.14, T:0.62
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:3073506 original size:30 final size:29
Alignment explanation
Indices: 3073470--3073536 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
3073460 TCGTATCTTA
3073470 GGTTTCTTTAT-TCTGGATTTCTTTATTCTG
1 GGTTTCTTTATCT-TGGATTTCTTTATTC-G
*
3073500 GGTTTCTCTATCTTGGATTTCTTTATTCG
1 GGTTTCTTTATCTTGGATTTCTTTATTCG
*
3073529 GTTTTCTT
1 GGTTTCTT
3073537 GTTATCTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 7 0.21
30 25 0.76
31 1 0.03
ACGTcount: A:0.09, C:0.15, G:0.16, T:0.60
Consensus pattern (29 bp):
GGTTTCTTTATCTTGGATTTCTTTATTCG
Found at i:3076947 original size:2 final size:2
Alignment explanation
Indices: 3076893--3076928 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
3076883 TATTACATAA
3076893 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3076929 TAAAGATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3077364 original size:3 final size:3
Alignment explanation
Indices: 3077350--3077384 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3077340 AGAAATATAC
*
3077350 AAT AAT ATAT AAT AAT AAT TAT AAT AAT AAT AAT A
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
3077385 TGAAAATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:3081106 original size:5 final size:6
Alignment explanation
Indices: 3081086--3081115 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3081076 AGTTTATAAA
3081086 TTTATTT TTTATT TTTATT TTTATT TTTAT
1 TTTA-TT TTTATT TTTATT TTTATT TTTAT
3081116 GAAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:3083599 original size:48 final size:48
Alignment explanation
Indices: 3083544--3083640 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
3083534 TGATTCGTTA
3083544 AATATCTGATTACGTTCTATAATAGGATTAAGGGAAGAATGTGAGACT
1 AATATCTGATTACGTTCTATAATAGGATTAAGGGAAGAATGTGAGACT
*
3083592 AATATCTGATTACGTTCTATAATAGGATTAAGGGTAGAATGTGAGACT
1 AATATCTGATTACGTTCTATAATAGGATTAAGGGAAGAATGTGAGACT
3083640 A
1 A
3083641 TCTTATCTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (48 bp):
AATATCTGATTACGTTCTATAATAGGATTAAGGGAAGAATGTGAGACT
Found at i:3083942 original size:18 final size:18
Alignment explanation
Indices: 3083905--3083942 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3083895 TTGCAACCCC
*
3083905 AACCATAATTATAGTTTT
1 AACCATAATTATAGTATT
3083923 AACCATAATTCATA-TATT
1 AACCATAATT-ATAGTATT
3083941 AA
1 AA
3083943 TAAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (18 bp):
AACCATAATTATAGTATT
Found at i:3091479 original size:132 final size:133
Alignment explanation
Indices: 3091196--3091543 Score: 388
Period size: 132 Copynumber: 2.6 Consensus size: 133
3091186 AAAACCAAAA
* * * * *
3091196 CCCAGCAC-AGTAGGGCACGATT-CCTCGAATTTCTAAACATCGAGCATTGCCTTAGTTTT--AG
1 CCCAGCACGA-TAGGGCACGATTCCCT-GAATTGCCAAACATCGAACATTACCTTCGTTTTAAAG
* * * * * * * *
3091257 AATTTTTAAGAAATATGAGTGAAATTCTAAAGGGGATATTCGATTATTTTAAACCAACAGGAAAT
64 AGTTTTTAGGAAACATGAATGAAATTCCAAAGGGGACATTCGATTATTTTAAACAAACAAGAAAT
3091322 CGAAG
129 CGAAG
3091327 CCCAGCACGATAGGGCACGATTCCCTGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAGAG
1 CCCAGCACGATAGGGCACGATTCCCTGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAGAG
* * *
3091392 TTTTTAGGAAACATGAATGAAATTCCAAA-GGGACATTCGATTATTTTGAGCAAACAAGAAATTG
66 TTTTTAGGAAACATGAATGAAATTCCAAAGGGGACATTCGATTATTTTAAACAAACAAGAAATCG
3091456 CAA-
131 -AAG
* * * * * *
3091459 CCCGGCACGTTAGGGCACGATTCCGC-GAATTGCCAAATATCAAACATCACCTTCATTTTAAAG-
1 CCCAGCACGATAGGGCACGATTCC-CTGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAGA
*
3091522 GATTTTTAGAAAACATGAATGA
65 G-TTTTTAGGAAACATGAATGA
3091544 TTATAAAACT
Statistics
Matches: 187, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
131 49 0.26
132 107 0.57
133 31 0.17
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (133 bp):
CCCAGCACGATAGGGCACGATTCCCTGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAGAG
TTTTTAGGAAACATGAATGAAATTCCAAAGGGGACATTCGATTATTTTAAACAAACAAGAAATCG
AAG
Found at i:3094338 original size:45 final size:43
Alignment explanation
Indices: 3094221--3094344 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 43
3094211 TGTTATTATC
*
3094221 CTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGACTTCGAT
1 CTGCTCCACTGCAACTTCAGAGAGATAA-GATTGTGACTTCGAT
* * *
3094265 CTACTCCACTGCAACTTCAGGGGGATAAGATCTGAT-ATCTTC-AGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGAT-TG-TGA-CTTCGA-T
* *
3094310 CTGCTCCACTGCAACTTCTGAGAAATAAGACTTGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGT
3094345 AATTTTCAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
43 3 0.05
44 29 0.44
45 33 0.50
46 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGATTGTGACTTCGAT
Found at i:3106515 original size:132 final size:132
Alignment explanation
Indices: 3106230--3106579 Score: 420
Period size: 132 Copynumber: 2.7 Consensus size: 132
3106220 GTAAAACCGA
* * * *
3106230 AACCCAGCAC-AGTAGGGCACGATTCCTCGAATTTCTAAACATCGAGCATTGCCTT-ATTTT-TA
1 AACCCAGCACGA-TAGGGCACGATTCCACGAATTTCTAAACATCGAACATTACCTTCATTTTAAA
* * * * * * *
3106292 GAATTTTTAAGAAACATGAGTGAAATTCTAAGGGGGATATTCGATTATTTTGAACCAACAGGAAA
65 G-ATTTTTAGGAAACATGAATGAAATTCCAAGAGGGACATTCGATTATTTTGAACAAACAAGAAA
3106357 TCGC
129 TCGC
* *
3106361 AACCCAGCACGATAGGGCACGATTCCCCGAATTTCTAAACATCGAACATTACCTTCGTTTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCACGAATTTCTAAACATCGAACATTACCTTCATTTTAAAG
* *
3106426 ACTTTTTAGGAAACATGAATGAAATTCCAA-AGGGACATTTGATTATTTTGAGCAAACAAGAAAT
66 A-TTTTTAGGAAACATGAATGAAATTCCAAGAGGGACATTCGATTATTTTGAACAAACAAGAAAT
* *
3106490 TGT
130 CGC
* * * * * *
3106493 AACCCGGCACGTTAGGGCACGATTCCACGAATTGCCAAATATCGAACATCACCTTCATTTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCACGAATTTCTAAACATCGAACATTACCTTCATTTTAAA-
*
3106558 GATTTTTAGAAAACATGAATGA
65 GATTTTTAGGAAACATGAATGA
3106580 TTATAAAACT
Statistics
Matches: 189, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
131 50 0.26
132 110 0.58
133 29 0.15
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (132 bp):
AACCCAGCACGATAGGGCACGATTCCACGAATTTCTAAACATCGAACATTACCTTCATTTTAAAG
ATTTTTAGGAAACATGAATGAAATTCCAAGAGGGACATTCGATTATTTTGAACAAACAAGAAATC
GC
Found at i:3109698 original size:6 final size:6
Alignment explanation
Indices: 3109687--3109734 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
3109677 AGGCAACCTA
*
3109687 ATTTTT ATTTTT ATTTTT A-TTTT ATTTTAT CTTTTT ATTTATT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT-T ATTTTT ATTT-TT ATTTT
3109735 CAGATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 5 0.14
6 21 0.57
7 11 0.30
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:3109704 original size:12 final size:12
Alignment explanation
Indices: 3109687--3109734 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
3109677 AGGCAACCTA
3109687 ATTTTTATTTTT
1 ATTTTTATTTTT
3109699 ATTTTTA-TTTT
1 ATTTTTATTTTT
*
3109710 ATTTTATCTTTTT
1 ATTTT-TATTTTT
3109723 ATTTATTATTTT
1 ATTT-TTATTTT
3109735 CAGATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 9 0.29
12 8 0.26
13 13 0.42
14 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:3120231 original size:33 final size:33
Alignment explanation
Indices: 3120193--3120294 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 33
3120183 ACTTACAAAA
3120193 TGATAATTTAAGTTGATTGAACTACAAATGTAG
1 TGATAATTTAAGTTGATTGAACTACAAATGTAG
* *
3120226 TGATAA---AATTTTATTAGCATACTTACAAA---A-
1 TGATAATTTAAGTTGATT-G-A-AC-TACAAATGTAG
3120256 TGATAATTTAAGTTGATTGAACTACAAATGTAG
1 TGATAATTTAAGTTGATTGAACTACAAATGTAG
3120289 TGATAA
1 TGATAA
3120295 AGTTAACATC
Statistics
Matches: 54, Mismatches: 4, Indels: 22
0.68 0.05 0.28
Matches are distributed among these distances:
29 6 0.11
30 15 0.28
31 3 0.06
32 3 0.06
33 21 0.39
34 6 0.11
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (33 bp):
TGATAATTTAAGTTGATTGAACTACAAATGTAG
Found at i:3120248 original size:63 final size:63
Alignment explanation
Indices: 3120176--3120295 Score: 231
Period size: 63 Copynumber: 1.9 Consensus size: 63
3120166 AGGTTTATTT
*
3120176 TTAGTATACTTACAAAATGATAATTTAAGTTGATTGAACTACAAATGTAGTGATAAAATTTTA
1 TTAGCATACTTACAAAATGATAATTTAAGTTGATTGAACTACAAATGTAGTGATAAAATTTTA
3120239 TTAGCATACTTACAAAATGATAATTTAAGTTGATTGAACTACAAATGTAGTGATAAA
1 TTAGCATACTTACAAAATGATAATTTAAGTTGATTGAACTACAAATGTAGTGATAAA
3120296 GTTAACATCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (63 bp):
TTAGCATACTTACAAAATGATAATTTAAGTTGATTGAACTACAAATGTAGTGATAAAATTTTA
Found at i:3124214 original size:35 final size:36
Alignment explanation
Indices: 3124114--3124242 Score: 147
Period size: 35 Copynumber: 3.5 Consensus size: 36
3124104 GGCAAAGTGT
* **
3124114 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATTATCCCATACTGAGTTAA
3124149 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATTATC----CCATACTGAGTTAA
* *
3124189 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTGAA
1 GAAATGTAGGTATGGTATTATCCCATACTGAGTT-AA
3124225 -AAATGTAGGTATGGTATT
1 GAAATGTAGGTATGGTATT
3124243 TCAATGAGGA
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
35 49 0.60
36 2 0.02
39 2 0.02
40 29 0.35
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (36 bp):
GAAATGTAGGTATGGTATTATCCCATACTGAGTTAA
Found at i:3131596 original size:35 final size:35
Alignment explanation
Indices: 3131569--3131734 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
3131559 CATGGCAAAG
*
3131569 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
3131604 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
3131639 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
3131679 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
3131714 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
3131735 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:3131688 original size:75 final size:75
Alignment explanation
Indices: 3131569--3131739 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
3131559 CATGGCAAAG
** *
3131569 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
3131628 CCATACTGAGC
65 CCATACCGAGC
3131639 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
3131704 CATACCGAGT
66 CATACCGAGC
**
3131714 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
3131740 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:3148330 original size:3 final size:3
Alignment explanation
Indices: 3148322--3148349 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3148312 GAACTCATTT
3148322 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
3148350 CAAGTTAGAG
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3149062 original size:10 final size:10
Alignment explanation
Indices: 3149047--3149071 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3149037 CTCATAAGAT
3149047 TTTTTTTTTG
1 TTTTTTTTTG
3149057 TTTTTTTTTG
1 TTTTTTTTTG
3149067 TTTTT
1 TTTTT
3149072 ATCTTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3151762 original size:31 final size:31
Alignment explanation
Indices: 3151724--3151785 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
3151714 ATGCTCACTG
*
3151724 AACTATTTGAAAGCTTTCATTTAAGTCATTA
1 AACTATTTGAAAGCTTTCATTTAAATCATTA
* *
3151755 AACTATTTGAAAGTTTTTATTTAAATCATTA
1 AACTATTTGAAAGCTTTCATTTAAATCATTA
3151786 GGATGTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (31 bp):
AACTATTTGAAAGCTTTCATTTAAATCATTA
Found at i:3168433 original size:48 final size:48
Alignment explanation
Indices: 3168362--3168458 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
3168352 ATGGGTGCAT
3168362 CTAACATTTATAGAAGTGATTCTGATTTTTTAGATTACACATTCAAAA
1 CTAACATTTATAGAAGTGATTCTGATTTTTTAGATTACACATTCAAAA
3168410 CTAACATTTATAGAAGTGATTCTGATTTTTTAGATTACACATTCAAAA
1 CTAACATTTATAGAAGTGATTCTGATTTTTTAGATTACACATTCAAAA
3168458 C
1 C
3168459 AAAGCAGTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (48 bp):
CTAACATTTATAGAAGTGATTCTGATTTTTTAGATTACACATTCAAAA
Found at i:3176408 original size:15 final size:16
Alignment explanation
Indices: 3176388--3176418 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3176378 TTTTCAACCC
3176388 CTGGT-AGATATCGAT
1 CTGGTAAGATATCGAT
3176403 CTGGTAAGATATCGAT
1 CTGGTAAGATATCGAT
3176419 ATTCCTGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (16 bp):
CTGGTAAGATATCGAT
Found at i:3177027 original size:47 final size:47
Alignment explanation
Indices: 3176958--3177050 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
3176948 TGCTTCCACC
3176958 ACAATTTCTAAAATGTCAATTCAACCTCCCTATCGATGAGTTCAAGG
1 ACAATTTCTAAAATGTCAATTCAACCTCCCTATCGATGAGTTCAAGG
3177005 ACAATTTCTAAAATGTCAATTCAACCTCCCTATCGATGAGTTCAAG
1 ACAATTTCTAAAATGTCAATTCAACCTCCCTATCGATGAGTTCAAG
3177051 TTGATCCTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (47 bp):
ACAATTTCTAAAATGTCAATTCAACCTCCCTATCGATGAGTTCAAGG
Found at i:3191411 original size:10 final size:11
Alignment explanation
Indices: 3191387--3191411 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3191377 ATTGACTATC
3191387 TTTTCAAACAT
1 TTTTCAAACAT
3191398 TTTTCAAACAT
1 TTTTCAAACAT
3191409 TTT
1 TTT
3191412 GGGGTACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTCAAACAT
Found at i:3199670 original size:18 final size:18
Alignment explanation
Indices: 3199641--3199684 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3199631 GATGACCAAG
3199641 AAACCA-AAGTTCTCTAA
1 AAACCACAAGTTCTCTAA
3199658 AAACCACAAGTTCTCTAA
1 AAACCACAAGTTCTCTAA
3199676 AAACCACAA
1 AAACCACAA
3199685 CACAACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.50, C:0.27, G:0.05, T:0.18
Consensus pattern (18 bp):
AAACCACAAGTTCTCTAA
Found at i:3200869 original size:2 final size:2
Alignment explanation
Indices: 3200862--3200887 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3200852 GATTGTTTTC
3200862 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
3200888 TTGGGCAATT
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:3201393 original size:2 final size:2
Alignment explanation
Indices: 3201386--3201410 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3201376 TATCAAGTAT
3201386 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3201411 CTTTGCCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3202857 original size:16 final size:16
Alignment explanation
Indices: 3202836--3202872 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
3202826 TCAGAATAAA
3202836 GAATTTTACAATTATT
1 GAATTTTACAATTATT
3202852 GAATTTTACAATTATT
1 GAATTTTACAATTATT
3202868 GAATT
1 GAATT
3202873 GAATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (16 bp):
GAATTTTACAATTATT
Found at i:3202880 original size:16 final size:16
Alignment explanation
Indices: 3202843--3202881 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3202833 AAAGAATTTT
**
3202843 ACAATTATTGAATTTT
1 ACAATTATTGAATTGA
3202859 ACAATTATTGAATTGA
1 ACAATTATTGAATTGA
*
3202875 ATAATTA
1 ACAATTA
3202882 ATTTAACAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (16 bp):
ACAATTATTGAATTGA
Found at i:3207476 original size:46 final size:46
Alignment explanation
Indices: 3207423--3207598 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
3207413 TATTTGGGCA
3207423 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
3207469 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
3207516 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
3207562 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3207599 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:3207578 original size:93 final size:93
Alignment explanation
Indices: 3207419--3207590 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
3207409 GGGATATTTG
* *
3207419 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3207484 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
3207512 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3207577 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
3207591 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:3215114 original size:28 final size:31
Alignment explanation
Indices: 3215060--3215117 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 31
3215050 TCTTCTTATA
*
3215060 AAATCTAGGAAAATCAATCTAAATCTAAAAT
1 AAATCTAGGAAAATAAATCTAAATCTAAAAT
3215091 AAATCTA-GAAAA-AAAT-TAAATCTAAAA
1 AAATCTAGGAAAATAAATCTAAATCTAAAA
3215118 CACTAAAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.42
29 3 0.12
30 5 0.19
31 7 0.27
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.24
Consensus pattern (31 bp):
AAATCTAGGAAAATAAATCTAAATCTAAAAT
Found at i:3224731 original size:21 final size:21
Alignment explanation
Indices: 3224705--3224746 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3224695 ATCGGGAAGC
3224705 TAACATAAG-GGTAGATGGAGA
1 TAACATAAGAGG-AGATGGAGA
3224726 TAACATAAGAGGAGATGGAGA
1 TAACATAAGAGGAGATGGAGA
3224747 GCTGGCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.45, C:0.05, G:0.33, T:0.17
Consensus pattern (21 bp):
TAACATAAGAGGAGATGGAGA
Found at i:3225035 original size:27 final size:27
Alignment explanation
Indices: 3224997--3225138 Score: 185
Period size: 27 Copynumber: 5.3 Consensus size: 27
3224987 TAAGTTGTAT
3224997 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
3225024 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
3225051 AATTACCGAAATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
3225078 AAATATCGAAATACCCATGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
3225105 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
3225132 AATTACC
1 AATTACC
3225139 ATTTTGCCCC
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:3225079 original size:54 final size:54
Alignment explanation
Indices: 3224997--3225136 Score: 208
Period size: 54 Copynumber: 2.6 Consensus size: 54
3224987 TAAGTTGTAT
* * *
3224997 AATTACCGAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTATCGAAATACCCATGTAAGGTAG
* *
3225051 AATTACCGAAATACCCTTATAGGGTAGAAATATCGAAATACCCATGTAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTATCGAAATACCCATGTAAGGTAG
* * *
3225105 AATTACCGAGATACCCTTGTGGGGTAAAATTA
1 AATTACCGAAATACCCTTGTAGGGTAGAATTA
3225137 CCATTTTGCC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (54 bp):
AATTACCGAAATACCCTTGTAGGGTAGAATTATCGAAATACCCATGTAAGGTAG
Found at i:3225183 original size:27 final size:26
Alignment explanation
Indices: 3225139--3225192 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
3225129 TAAAATTACC
3225139 ATTTTGCCCCTAGGGTGTTAAATGACT
1 ATTTTGCCCCTAGGGTG-TAAATGACT
* * *
3225166 ATTTTGCTCCTCGTGTGTAAATGACT
1 ATTTTGCCCCTAGGGTGTAAATGACT
3225192 A
1 A
3225193 ACTTGTGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (26 bp):
ATTTTGCCCCTAGGGTGTAAATGACT
Found at i:3225836 original size:27 final size:26
Alignment explanation
Indices: 3225792--3225843 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
3225782 CTCGCTGCAA
*
3225792 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
3225819 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
3225844 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:3226130 original size:42 final size:43
Alignment explanation
Indices: 3226071--3226158 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
3226061 ATGATATATT
3226071 TGTTCTGTATCTGCTAT-GGCCTATAGGTTTCATTCTGATTTC
1 TGTTCTGTATCTGCTATGGGCCTATAGGTTTCATTCTGATTTC
* *
3226113 TGTTCTGTATTTGCTATGGGCCTATGGGTTTCATTCTGATTTC
1 TGTTCTGTATCTGCTATGGGCCTATAGGTTTCATTCTGATTTC
3226156 TGT
1 TGT
3226159 ACTGGGCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 16 0.37
43 27 0.63
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (43 bp):
TGTTCTGTATCTGCTATGGGCCTATAGGTTTCATTCTGATTTC
Found at i:3232590 original size:27 final size:27
Alignment explanation
Indices: 3232552--3232720 Score: 239
Period size: 27 Copynumber: 6.3 Consensus size: 27
3232542 TAAGTTGTAT
* * *
3232552 AATTACCGAAATACCTCTATAGAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
3232579 AATTACCGAAATACCCCTGTAAGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
3232606 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
3232633 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
3232660 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
3232687 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
3232714 AATTACC
1 AATTACC
3232721 ATTTTGCCCC
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 127 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:3233416 original size:27 final size:26
Alignment explanation
Indices: 3233372--3233423 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
3233362 CTCGCTGCAA
*
3233372 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
3233399 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
3233424 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:3237439 original size:2 final size:2
Alignment explanation
Indices: 3237432--3237464 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3237422 TCAATACAAA
3237432 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 A
3237465 AAAGAAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3240672 original size:14 final size:15
Alignment explanation
Indices: 3240646--3240678 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3240636 GAATTAAATT
3240646 TTAAAACCAATTGAC
1 TTAAAACCAATTGAC
*
3240661 TTAAAA-CAATTGAT
1 TTAAAACCAATTGAC
3240675 TTAA
1 TTAA
3240679 TTTCTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (15 bp):
TTAAAACCAATTGAC
Found at i:3240824 original size:13 final size:13
Alignment explanation
Indices: 3240806--3240831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3240796 TGTAAAAATA
3240806 TATACTATATTTG
1 TATACTATATTTG
3240819 TATACTATATTTG
1 TATACTATATTTG
3240832 AAACACATAA
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:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TATACTATATTTG
Found at i:3247873 original size:15 final size:17
Alignment explanation
Indices: 3247850--3247883 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3247840 CTTTTTTGAA
3247850 TTTATTAAAAT-ATTAT
1 TTTATTAAAATAATTAT
3247866 TTTA-TAAAATAATTAT
1 TTTATTAAAATAATTAT
3247882 TT
1 TT
3247884 CCATGCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATTAAAATAATTAT
Found at i:3248172 original size:38 final size:38
Alignment explanation
Indices: 3248090--3248181 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
3248080 CCCTTAGTTT
*
3248090 CATTAGCGGCGTTTCCAAAAAACGCCACTAAAGGATGAG
1 CATTAGCGGCGTTT-TAAAAAACGCCACTAAAGGATGAG
* * * *
3248129 TATTAGCGGCGTTTTATAAAACGCCACTATAGGTTGAG
1 CATTAGCGGCGTTTTAAAAAACGCCACTAAAGGATGAG
*
3248167 CATTAGCAGCGTTTT
1 CATTAGCGGCGTTTT
3248182 TCGAAAAACG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 33 0.72
39 13 0.28
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (38 bp):
CATTAGCGGCGTTTTAAAAAACGCCACTAAAGGATGAG
Found at i:3248314 original size:28 final size:29
Alignment explanation
Indices: 3248269--3248323 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
3248259 CAAAAAATAT
*
3248269 TTTATGTATATATTTATT-ATTTAAATGC
1 TTTATGTATATATTTATTGATTAAAATGC
*
3248297 TTTATTTATAT-TTATATTGATTAAAAT
1 TTTATGTATATATT-TATTGATTAAAAT
3248324 ACAATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 14 0.61
29 7 0.30
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTATGTATATATTTATTGATTAAAATGC
Found at i:3248697 original size:7 final size:7
Alignment explanation
Indices: 3248679--3248753 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
3248669 AGGGATTAGT
*
3248679 GGGTAAA
1 GGGTTAA
3248686 GGGTTAA
1 GGGTTAA
*
3248693 GGGTTAT
1 GGGTTAA
* *
3248700 GGATTAT
1 GGGTTAA
*
3248707 GGGTTAT
1 GGGTTAA
3248714 GGGTTTAA
1 GGG-TTAA
*
3248722 TGGTTAAA
1 GGGTT-AA
*
3248730 GGGAT-A
1 GGGTTAA
3248736 GGGTTAA
1 GGGTTAA
3248743 GGGGTTAA
1 -GGGTTAA
3248751 GGG
1 GGG
3248754 GTTTAATTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
6 5 0.09
7 33 0.60
8 17 0.31
ACGTcount: A:0.27, C:0.00, G:0.43, T:0.31
Consensus pattern (7 bp):
GGGTTAA
Found at i:3248721 original size:29 final size:30
Alignment explanation
Indices: 3248657--3248727 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
3248647 TAAGGGTTGT
*
3248657 GGTTTAAAGTTTAGGGATTAGTGGGTAAAG
1 GGTTTAAAGGTTAGGGATTAGTGGGTAAAG
* * * *
3248687 GG-TTAAGGGTTATGGATTA-TGGGTTATG
1 GGTTTAAAGGTTAGGGATTAGTGGGTAAAG
*
3248715 GGTTTAATGGTTA
1 GGTTTAAAGGTTA
3248728 AAGGGATAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (30 bp):
GGTTTAAAGGTTAGGGATTAGTGGGTAAAG
Found at i:3248898 original size:15 final size:16
Alignment explanation
Indices: 3248878--3248917 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3248868 TTAGTGGTTA
3248878 TTCATGGTTTA-AGGT
1 TTCATGGTTTAGAGGT
*
3248893 TTCATGGTTTAGGGGT
1 TTCATGGTTTAGAGGT
3248909 TT-ATGGTTT
1 TTCATGGTTT
3248918 GGGGTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.15, C:0.05, G:0.30, T:0.50
Consensus pattern (16 bp):
TTCATGGTTTAGAGGT
Found at i:3249234 original size:26 final size:27
Alignment explanation
Indices: 3249168--3249235 Score: 113
Period size: 26 Copynumber: 2.6 Consensus size: 27
3249158 TCAAAATTTG
3249168 AAGATTTCAAA-TTTAGAATAATTTTC
1 AAGATTTCAAATTTTAGAATAATTTTC
3249194 AAGATTTCAAATTTTA-AATAATTTTC
1 AAGATTTCAAATTTTAGAATAATTTTC
*
3249220 AATATTTCAAATTTTA
1 AAGATTTCAAATTTTA
3249236 TCTAATTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 36 0.90
27 4 0.10
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (27 bp):
AAGATTTCAAATTTTAGAATAATTTTC
Found at i:3249379 original size:18 final size:17
Alignment explanation
Indices: 3249348--3249382 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3249338 TAGTTGATTG
*
3249348 TTTTTTAATTTATATTA
1 TTTTTAAATTTATATTA
3249365 TTTTTAAATTATATATTA
1 TTTTTAAATT-TATATTA
3249383 AATAAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTAAATTTATATTA
Found at i:3251781 original size:19 final size:19
Alignment explanation
Indices: 3251730--3251789 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
3251720 ATTCTTATGA
3251730 TTTTAATA-TTTTTATACT
1 TTTTAATACTTTTTATACT
*
3251748 TTTTAATAGC-ATTTATA-T
1 TTTTAATA-CTTTTTATACT
*
3251766 TGTTTAATACTTTTTATGCT
1 T-TTTAATACTTTTTATACT
3251786 TTTT
1 TTTT
3251790 TTTTTACATT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 11 0.32
19 21 0.62
20 2 0.06
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTAATACTTTTTATACT
Found at i:3253692 original size:33 final size:33
Alignment explanation
Indices: 3253655--3253718 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
3253645 AAACTTACAA
*
3253655 AACTTACAAAACTTACATAATATATAAATATAT
1 AACTTACAAAACTTACATAATAAATAAATATAT
* *
3253688 AACTTACATAACTTACGTAATAAATAAATAT
1 AACTTACAAAACTTACATAATAAATAAATAT
3253719 TTTATATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (33 bp):
AACTTACAAAACTTACATAATAAATAAATATAT
Found at i:3253700 original size:9 final size:9
Alignment explanation
Indices: 3253634--3254077 Score: 92
Period size: 9 Copynumber: 49.1 Consensus size: 9
3253624 TATATCATAT
3253634 CATAACTTA
1 CATAACTTA
*
3253643 CAAAACTTA
1 CATAACTTA
*
3253652 CAAAACTTA
1 CATAACTTA
*
3253661 CAAAACTTA
1 CATAACTTA
3253670 CATAA--TA
1 CATAACTTA
* *
3253677 TATAA-ATA
1 CATAACTTA
*
3253685 TATAACTTA
1 CATAACTTA
3253694 CATAACTTA
1 CATAACTTA
*
3253703 CGTAATAA-ATA
1 C---ATAACTTA
* **
3253714 AATATTTTATA
1 CATA-ACT-TA
*
3253725 TCATAATTTA
1 -CATAACTTA
3253735 CATAACTTA
1 CATAACTTA
**
3253744 CATTCCTTA
1 CATAACTTA
*
3253753 CATAAATT-
1 CATAACTTA
* * *
3253761 TATATCATA
1 CATAACTTA
*
3253770 TCATAACTCA
1 -CATAACTTA
3253780 CATAACTTA
1 CATAACTTA
* *
3253789 TAAAACTTA
1 CATAACTTA
3253798 CATAATCTATAAA
1 CATAA-CT-T--A
*
3253811 TATATAGCTTA
1 CATA-A-CTTA
3253822 CATAACTTA
1 CATAACTTA
*
3253831 CGTAA--TA
1 CATAACTTA
* *
3253838 AATAA-ATA
1 CATAACTTA
* ** *
3253846 AATTTCATA
1 CATAACTTA
* *
3253855 TCATAATTTG
1 -CATAACTTA
3253865 CATAACTTA
1 CATAACTTA
**
3253874 CATTCCTTA
1 CATAACTTA
*
3253883 CATAAATT-
1 CATAACTTA
* * *
3253891 TATATCATA
1 CATAACTTA
3253900 TCATAACTTA
1 -CATAACTTA
3253910 CATAACTTA
1 CATAACTTA
*
3253919 CAAAACTTA
1 CATAACTTA
3253928 CATAA--TA
1 CATAACTTA
*
3253935 CATAA-ATA
1 CATAACTTA
*
3253943 TATAACTTA
1 CATAACTTA
3253952 CATAACTTA
1 CATAACTTA
*
3253961 CGTAA--TA
1 CATAACTTA
* *
3253968 AATAA-ATA
1 CATAACTTA
* ** *
3253976 TATTTCATA
1 CATAACTTA
*
3253985 TCATAATTTA
1 -CATAACTTA
3253995 CATAACTTA
1 CATAACTTA
* *
3254004 CACACCTTA
1 CATAACTTA
*
3254013 CATAAGTT-
1 CATAACTTA
* * *
3254021 TATAGTCATA
1 CATA-ACTTA
*
3254031 TTATAACTTA
1 -CATAACTTA
3254041 CATAACTTA
1 CATAACTTA
* *
3254050 CAAAAGTTA
1 CATAACTTA
*
3254059 CAAAACTTA
1 CATAACTTA
*
3254068 CTTAACTTA
1 CATAACTTA
3254077 C
1 C
3254078 GTAATACATA
Statistics
Matches: 314, Mismatches: 92, Indels: 58
0.68 0.20 0.12
Matches are distributed among these distances:
7 23 0.07
8 36 0.11
9 199 0.63
10 26 0.08
11 15 0.05
12 7 0.02
13 5 0.02
14 3 0.01
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:3253907 original size:130 final size:129
Alignment explanation
Indices: 3253646--3254060 Score: 672
Period size: 130 Copynumber: 3.2 Consensus size: 129
3253636 TAACTTACAA
* *
3253646 AACTTACAAAACTTACAAAACTTACATAATATATAAATATATAACTTACATAACTTACGTAATAA
1 AACTTACATAACTTACAAAACTTACATAATCTATAAATATATAACTTACATAACTTACGTAATAA
*
3253711 ATAAAT-ATTTTATATCATAATTTACATAACTTACATTCCTTACATAAATTTATATCATATCAT
66 ATAAATAATTTCATATCATAATTTACATAACTTACATTCCTTACATAAATTTATATCATATCAT
* * *
3253774 AACTCACATAACTTATAAAACTTACATAATCTATAAATATATAGCTTACATAACTTACGTAATAA
1 AACTTACATAACTTACAAAACTTACATAATCTATAAATATATAACTTACATAACTTACGTAATAA
*
3253839 ATAAATAAATTTCATATCATAATTTGCATAACTTACATTCCTTACATAAATTTATATCATATCAT
66 ATAAAT-AATTTCATATCATAATTTACATAACTTACATTCCTTACATAAATTTATATCATATCAT
3253904 AACTTACATAACTTACAAAACTTACATAATAC-ATAAATATATAACTTACATAACTTACGTAATA
1 AACTTACATAACTTACAAAACTTACATAAT-CTATAAATATATAACTTACATAACTTACGTAATA
** * *
3253968 AATAAATATATTTCATATCATAATTTACATAACTTACACACCTTACATAAGTTTATAGTCATATT
65 AATAAATA-ATTTCATATCATAATTTACATAACTTACATTCCTTACATAAATTTATA-TCATATC
3254033 AT
128 AT
*
3254035 AACTTACATAACTTACAAAAGTTACA
1 AACTTACATAACTTACAAAACTTACA
3254061 AAACTTACTT
Statistics
Matches: 266, Mismatches: 16, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
128 66 0.25
129 1 0.00
130 165 0.62
131 34 0.13
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (129 bp):
AACTTACATAACTTACAAAACTTACATAATCTATAAATATATAACTTACATAACTTACGTAATAA
ATAAATAATTTCATATCATAATTTACATAACTTACATTCCTTACATAAATTTATATCATATCAT
Found at i:3253949 original size:33 final size:33
Alignment explanation
Indices: 3253911--3253978 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
3253901 CATAACTTAC
*
3253911 ATAACTTACAAAACTTACATAATACATAAATAT
1 ATAACTTACAAAACTTACATAATAAATAAATAT
* *
3253944 ATAACTTACATAACTTACGTAATAAATAAATAT
1 ATAACTTACAAAACTTACATAATAAATAAATAT
3253977 AT
1 AT
3253979 TTCATATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.32
Consensus pattern (33 bp):
ATAACTTACAAAACTTACATAATAAATAAATAT
Found at i:3255869 original size:12 final size:12
Alignment explanation
Indices: 3255852--3255876 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3255842 AAGATCGAGG
3255852 GATGAATCTGAT
1 GATGAATCTGAT
3255864 GATGAATCTGAT
1 GATGAATCTGAT
3255876 G
1 G
3255877 GAGAGGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:3259181 original size:13 final size:14
Alignment explanation
Indices: 3259165--3259193 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3259155 TTCTAAATAT
3259165 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
3259178 TTATAATTGTTTAA
1 TTATAATTGTTTAA
3259192 TT
1 TT
3259194 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:3259629 original size:21 final size:21
Alignment explanation
Indices: 3259605--3259675 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
3259595 CTTAAGCGGA
*
3259605 GGCAGCAGAGAGGGAGGCAGC
1 GGCAGCAGCGAGGGAGGCAGC
*
3259626 GGCAGCAGCGAGAGAGGCAGC
1 GGCAGCAGCGAGGGAGGCAGC
* * *
3259647 GGCAGTAGCGATGGAGGCAGA
1 GGCAGCAGCGAGGGAGGCAGC
3259668 GGCAGCAG
1 GGCAGCAG
3259676 TAATGGCAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.28, C:0.20, G:0.49, T:0.03
Consensus pattern (21 bp):
GGCAGCAGCGAGGGAGGCAGC
Found at i:3259681 original size:21 final size:21
Alignment explanation
Indices: 3259603--3259697 Score: 65
Period size: 21 Copynumber: 4.6 Consensus size: 21
3259593 AACTTAAGCG
*
3259603 GAGGCAGCAG-AGAGGGAGGCA
1 GAGGCAGCAGCA-ATGGAGGCA
* *
3259624 GCGGCAGCAGCGA-GAGAGGCA
1 GAGGCAGCAGCAATG-GAGGCA
* * *
3259645 GCGGCAGTAGCGATGGAGGCA
1 GAGGCAGCAGCAATGGAGGCA
*
3259666 GAGGCAGCAGTAATGGCA-GCA
1 GAGGCAGCAGCAATGG-AGGCA
3259687 GA-GCAG-AGCAA
1 GAGGCAGCAGCAA
3259698 AAAGTACGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
19 4 0.06
20 5 0.08
21 51 0.82
22 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.45, T:0.04
Consensus pattern (21 bp):
GAGGCAGCAGCAATGGAGGCA
Found at i:3259966 original size:30 final size:30
Alignment explanation
Indices: 3259907--3259984 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
3259897 TTAGAATTAA
** *
3259907 TGTTTTTGGTTGTTTTTTATGCTAAATTTGC
1 TGTTTTTGGTTG-CATTTATACTAAATTTGC
* *
3259938 TGTTTTTGGTTGCATTTATACTATATTTGT
1 TGTTTTTGGTTGCATTTATACTAAATTTGC
* *
3259968 TGTATTTGGTTGGATTT
1 TGTTTTTGGTTGCATTT
3259985 TAATGCAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 28 0.70
31 12 0.30
ACGTcount: A:0.14, C:0.05, G:0.21, T:0.60
Consensus pattern (30 bp):
TGTTTTTGGTTGCATTTATACTAAATTTGC
Found at i:3260088 original size:40 final size:42
Alignment explanation
Indices: 3260044--3260151 Score: 148
Period size: 43 Copynumber: 2.6 Consensus size: 42
3260034 CAAAATTGGA
*
3260044 AAACGCCGCTAAAAGTCAT-A-TTTAGCGGCGCATTCCCCAC
1 AAACGCCGCTAAAAGTCATGACTTTAGCGGCGCATTCCACAC
* *
3260084 AAACGCCGCTAAAAGTTATGACTTTTAGCGGCGCTTTCCACAC
1 AAACGCCGCTAAAAGTCATGAC-TTTAGCGGCGCATTCCACAC
* *
3260127 AAACGCCGCTAAAAGCCATGGCTTT
1 AAACGCCGCTAAAAGTCATGACTTT
3260152 TAACAGCGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
40 18 0.31
41 1 0.02
42 3 0.05
43 37 0.63
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (42 bp):
AAACGCCGCTAAAAGTCATGACTTTAGCGGCGCATTCCACAC
Found at i:3261206 original size:20 final size:19
Alignment explanation
Indices: 3261163--3261206 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3261153 TGCACAAAAA
*
3261163 TAAAAAATATTAACTTATG
1 TAAAAAATATTAAATTATG
* *
3261182 GAAAAAATGATTAAATTTTG
1 TAAAAAAT-ATTAAATTATG
3261202 TAAAA
1 TAAAA
3261207 GAAAAAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (19 bp):
TAAAAAATATTAAATTATG
Found at i:3268933 original size:16 final size:16
Alignment explanation
Indices: 3268914--3268974 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
3268904 ATAATGTGAA
* *
3268914 AAAAATAAATTTAAAG
1 AAAAATAAAATAAAAG
*
3268930 AAAATTAAAATAAAAG
1 AAAAATAAAATAAAAG
* *
3268946 AAAATTAAGATAAAA-
1 AAAAATAAAATAAAAG
*
3268961 AAGAAATTAAATAA
1 AA-AAATAAAATAA
3268975 TATATATAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
15 2 0.05
16 35 0.95
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (16 bp):
AAAAATAAAATAAAAG
Found at i:3268982 original size:163 final size:163
Alignment explanation
Indices: 3268802--3269121 Score: 590
Period size: 164 Copynumber: 2.0 Consensus size: 163
3268792 AAGACCAATT
3268802 AATTAAATAATATATATAACAATTTAAAAAAAT-TATAAAGAAAATTAAAATAAATAAAATGTAA
1 AATTAAATAATATATATAACAATTTAAAAAAATATATAAAGAAAATTAAAATAAATAAAATGTAA
3268866 AACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAATGTGAAAAAAATAAATTTAAAGA
66 AACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAATGTG-AAAAAATAAATTTAAAGA
*
3268931 AAATTAAAATAAAAGA-AAATTAAGATAAAAAAGA
130 AAATTAAAATAAAAAAGAAATTAA-ATAAAAAAGA
*
3268965 AATTAAATAATATATATAACAATTTTAAAAAATATATAAAGAAAATTAAAATAAATAAAATGTAA
1 AATTAAATAATATATATAACAATTTAAAAAAATATATAAAGAAAATTAAAATAAATAAAATGTAA
3269030 AACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAATGTGAAAAAATAAATTTAAAGAA
66 AACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAATGTGAAAAAATAAATTTAAAGAA
3269095 AATTAAAATAAAAAAGAAATTAAATAA
131 AATTAAAATAAAAAAGAAATTAAATAA
3269122 TATATATAAC
Statistics
Matches: 153, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
163 69 0.45
164 84 0.55
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (163 bp):
AATTAAATAATATATATAACAATTTAAAAAAATATATAAAGAAAATTAAAATAAATAAAATGTAA
AACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAATGTGAAAAAATAAATTTAAAGAA
AATTAAAATAAAAAAGAAATTAAATAAAAAAGA
Found at i:3269053 original size:49 final size:49
Alignment explanation
Indices: 3268968--3269216 Score: 187
Period size: 49 Copynumber: 5.1 Consensus size: 49
3268958 AAAAAGAAAT
* * * *
3268968 TAAATAATATATATAAC-AATTTTAAAA-AATATATAAAGAAAATTAAAA
1 TAAATAAAATGTAAAACAAATTTTAAAATAAT-GATAAAGAAAATTAAAA
* *
3269016 TAAATAAAATGTAAAACAAATTTTAAAATGATGATAAATG-AATTTAAAA
1 TAAATAAAATGTAAAACAAATTTTAAAATAATGATAAA-GAAAATTAAAA
* * * * * *
3269065 TAAAT--AATGTGAAAAAATAAATTTAAAGAAAATTA-AAATAAAA-AAGAAA
1 TAAATAAAATGT-AAAACA-AATTTTAAA-ATAATGATAAAGAAAATTA-AAA
* * * *
3269114 TTAAATAATATATATAAC-AA-TTTAAAA-AATTATAAAGAAAATTAAAA
1 -TAAATAAAATGTAAAACAAATTTTAAAATAATGATAAAGAAAATTAAAA
* *
3269161 TAAATAAAATGTAAAACAAATTTTAAAATGATGATAAATG-AATTTAAAA
1 TAAATAAAATGTAAAACAAATTTTAAAATAATGATAAA-GAAAATTAAAA
3269210 TAAATAA
1 TAAATAA
3269217 TGTGAAAAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 33
0.73 0.12 0.15
Matches are distributed among these distances:
46 19 0.12
47 18 0.11
48 34 0.22
49 68 0.43
50 13 0.08
51 3 0.02
52 3 0.02
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (49 bp):
TAAATAAAATGTAAAACAAATTTTAAAATAATGATAAAGAAAATTAAAA
Found at i:3269102 original size:21 final size:21
Alignment explanation
Indices: 3269078--3269165 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
3269068 ATAATGTGAA
3269078 AAAATAAATTTAAAGAAAATT
1 AAAATAAATTTAAAGAAAATT
3269099 AAAATAAA---AAAG-AAATT
1 AAAATAAATTTAAAGAAAATT
* * *
3269116 -AAATAATATATATA-ACAATT
1 AAAATAA-ATTTAAAGAAAATT
*
3269136 TAAA-AAATTATAAAGAAAATT
1 AAAATAAATT-TAAAGAAAATT
3269157 AAAATAAAT
1 AAAATAAAT
3269166 AAAATGTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
16 6 0.12
17 6 0.12
18 4 0.08
19 2 0.04
20 11 0.21
21 19 0.37
22 4 0.08
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.27
Consensus pattern (21 bp):
AAAATAAATTTAAAGAAAATT
Found at i:3269183 original size:145 final size:147
Alignment explanation
Indices: 3268942--3269235 Score: 556
Period size: 145 Copynumber: 2.0 Consensus size: 147
3268932 AATTAAAATA
*
3268942 AAAGAAAATTAAGATAAAAAAGAAATTAAATAATATATATAACAATTTTAAAAAATATATAAAGA
1 AAAGAAAATTAAAATAAAAAAGAAATTAAATAATATATATAACAATTTTAAAAAATATATAAAGA
3269007 AAATTAAAATAAATAAAATGTAAAACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAA
66 AAATTAAAATAAATAAAATGTAAAACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAA
*
3269072 TGTGAAAAAATAAATTT
131 TGTGAAAAAAGAAATTT
3269089 AAAGAAAATTAAAATAAAAAAGAAATTAAATAATATATATAACAA-TTTAAAAAAT-TATAAAGA
1 AAAGAAAATTAAAATAAAAAAGAAATTAAATAATATATATAACAATTTTAAAAAATATATAAAGA
3269152 AAATTAAAATAAATAAAATGTAAAACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAA
66 AAATTAAAATAAATAAAATGTAAAACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAA
3269217 TGTGAAAAAAGAAATTT
131 TGTGAAAAAAGAAATTT
3269234 AA
1 AA
3269236 TATCAATAAT
Statistics
Matches: 145, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
145 91 0.63
146 10 0.07
147 44 0.30
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (147 bp):
AAAGAAAATTAAAATAAAAAAGAAATTAAATAATATATATAACAATTTTAAAAAATATATAAAGA
AAATTAAAATAAATAAAATGTAAAACAAATTTTAAAATGATGATAAATGAATTTAAAATAAATAA
TGTGAAAAAAGAAATTT
Found at i:3269352 original size:30 final size:26
Alignment explanation
Indices: 3269316--3269688 Score: 131
Period size: 26 Copynumber: 14.7 Consensus size: 26
3269306 CGAAAGTTTG
3269316 AAATAAATAATATATGAGGGAAAAAATTTA
1 AAATAAATAATATAT-A---AAAAAATTTA
* *
3269346 AAATAAATAATATGTAAAATAATTTA
1 AAATAAATAATATATAAAAAAATTTA
* ** *
3269372 AGATAAATAATATATAAATGAGTTT-
1 AAATAAATAATATATAAAAAAATTTA
* * *
3269397 AAATAAATATTATGTAAAAAGAAATATA
1 AAATAAATAATATAT-AAAA-AAATTTA
* * *
3269425 AAATAAGTAATATA-CAAAACATCTTAA
1 AAATAAATAATATATAAAAAAAT-TT-A
**
3269452 AAATAAATGGTATAT-AAAAAA--T-
1 AAATAAATAATATATAAAAAAATTTA
* * *
3269474 AGAT-AAT-ACATAT--AAAAATTTG
1 AAATAAATAATATATAAAAAAATTTA
***
3269496 AAATTGGTAATATATGAAAAAAATTTA
1 AAATAAATAATATAT-AAAAAAATTTA
* **
3269523 AAGT--A-AATA-ATAAAACTATTTA
1 AAATAAATAATATATAAAAAAATTTA
* * *
3269545 AAATGAATAATACATAAAACAAGTTTA
1 AAATAAATAATATATAAAA-AAATTTA
* * **
3269572 AAGTAAATAATGTATAAAGCAATTTA
1 AAATAAATAATATATAAAAAAATTTA
* * * * * *
3269598 GAGTATATAGTATATGAAATAATTTA
1 AAATAAATAATATATAAAAAAATTTA
* * *
3269624 AGAT-AAT-ATATCTAAAACAATTTA
1 AAATAAATAATATATAAAAAAATTTA
**
3269648 AAATAGTTTAATATAT---AAAATTTA
1 AAATA-AATAATATATAAAAAAATTTA
3269672 AAATAAATAA-ATA-AAAA
1 AAATAAATAATATATAAAA
3269689 TCAAAGAGTC
Statistics
Matches: 249, Mismatches: 69, Indels: 56
0.67 0.18 0.15
Matches are distributed among these distances:
19 5 0.02
20 4 0.02
21 4 0.02
22 21 0.08
23 6 0.02
24 40 0.16
25 21 0.08
26 68 0.27
27 54 0.22
28 11 0.04
29 1 0.00
30 14 0.06
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (26 bp):
AAATAAATAATATATAAAAAAATTTA
Found at i:3273057 original size:20 final size:18
Alignment explanation
Indices: 3273006--3273060 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
3272996 TATCATAAAA
* *
3273006 ATAAAAAGTATTAAAATG
1 ATAAAAATTATAAAAATG
*
3273024 ATATAAACTTATAAAAATTG
1 ATA-AAAATTATAAAAA-TG
3273044 TATAAAAATTATAAAAA
1 -ATAAAAATTATAAAAA
3273061 ATTGAATTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 14 0.47
21 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (18 bp):
ATAAAAATTATAAAAATG
Found at i:3277132 original size:54 final size:54
Alignment explanation
Indices: 3277068--3277441 Score: 466
Period size: 54 Copynumber: 6.9 Consensus size: 54
3277058 TGAAAACAAT
* * * * ** *
3277068 AACAATGAAAATGCGGGTCAGGACGGGAAGAATGCCACTCAGAGTAACACTGAC
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
* * * *
3277122 AACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGAG
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
* * * ** *
3277176 AACAATGAAAATGCGGGTCAGAATGAGAGCAATGCAACTCAGAGCAACACTGAG
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
* *
3277230 AACAATGAGAATGCGGGTCAGAACGAGAAAAATGCTGCTCCA-AGTAACGCTGAG
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCT-CAGAGTAACACTGAG
* *
3277284 AACAATGAGAATGTGGGTCAGAACGAGAACAATGCCGCTCCA-AGTAACACTGAG
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCT-CAGAGTAACACTGAG
* * *
3277338 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGAC
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
* *
3277392 AACAATGAGAATGCAGGTCAGAACGAGAACAATGC-GACTCAGAGCAACAC
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTG-CTCAGAGTAACAC
3277442 CGACGAAAAC
Statistics
Matches: 284, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
53 2 0.01
54 280 0.99
55 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (54 bp):
AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
Found at i:3277182 original size:108 final size:108
Alignment explanation
Indices: 3277068--3277512 Score: 482
Period size: 108 Copynumber: 4.0 Consensus size: 108
3277058 TGAAAACAAT
* * * *
3277068 AACAATGAAAATGCGGGTCAGGACGGGAAGAATGCCACTCAGAGTAACACTGACAACAATGAAAA
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACTCAGAGCAACACTGACAACAATGAAAA
* * *
3277133 TGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGAG
66 TGCGGGTCAGAACGAGAACAATGCTGCTCAGAGCAACACTGAC
* * * * *
3277176 AACAATGAAAATGCGGGTCAGAATGAGAGCAATGCAACTCAGAGCAACACTGAGAACAATGAGAA
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACTCAGAGCAACACTGACAACAATGAAAA
* * * *
3277241 TGCGGGTCAGAACGAGAAAAATGCTGCTCCA-AGTAACGCTGAG
66 TGCGGGTCAGAACGAGAACAATGCTGCT-CAGAGCAACACTGAC
* * * * * *
3277284 AACAATGAGAATGTGGGTCAGAACGAGAACAATGCCGCTCCA-AGTAACACTGAGAACAATGAGA
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT-CAGAGCAACACTGACAACAATGAAA
* * *
3277348 ATGCGGGTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGAC
65 ATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGCAACACTGAC
* * * *
3277392 AACAATGAGAATGCAGGTCAGAACGAGAACAATGCGACTCAGAGCAACACCGACGAAAACAACAA
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACTCAGAGCAACA-C--TG------ACAA
* *
3277457 CAATGAAAATGCAGGTCAGAATGAGAACAATG-TGACTCAGAGCAACACTGAC
57 CAATGAAAATGCGGGTCAGAACGAGAACAATGCTG-CTCAGAGCAACACTGAC
3277509 AACA
1 AACA
3277513 GCAGCAACAA
Statistics
Matches: 284, Mismatches: 39, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
107 3 0.01
108 223 0.79
109 5 0.02
111 1 0.00
116 2 0.01
117 50 0.18
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.13
Consensus pattern (108 bp):
AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACTCAGAGCAACACTGACAACAATGAAAA
TGCGGGTCAGAACGAGAACAATGCTGCTCAGAGCAACACTGAC
Found at i:3277202 original size:27 final size:27
Alignment explanation
Indices: 3277172--3277263 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
3277162 AGAGCAACAC
3277172 TGAGAACAATGAAAATGCGGGTCAGAA
1 TGAGAACAATGAAAATGCGGGTCAGAA
* * * *
3277199 TGAGAGCAATGCAACT-CAGAG-CA-ACA
1 TGAGAACAATGAAAATGC-GGGTCAGA-A
*
3277225 CTGAGAACAATGAGAATGCGGGTCAGAA
1 -TGAGAACAATGAAAATGCGGGTCAGAA
* *
3277253 CGAGAAAAATG
1 TGAGAACAATG
3277264 CTGCTCCAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 38 0.79
28 4 0.08
29 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.28, T:0.13
Consensus pattern (27 bp):
TGAGAACAATGAAAATGCGGGTCAGAA
Found at i:3277365 original size:27 final size:27
Alignment explanation
Indices: 3277281--3277425 Score: 91
Period size: 27 Copynumber: 5.4 Consensus size: 27
3277271 AAGTAACGCT
*
3277281 GAGAACAATGAGAATGTGGGTCAGAAC
1 GAGAACAATGAGAATGCGGGTCAGAAC
* * * **
3277308 GAGAACAATGCCG-CTCCAAGT-A-ACAC
1 GAGAACAATG-AGAATGCGGGTCAGA-AC
3277334 TGAGAACAATGAGAATGCGGGTCAGAAC
1 -GAGAACAATGAGAATGCGGGTCAGAAC
* * * * * * *
3277362 GAGAACAATGCTG-CTCCGAGTAACACC
1 GAGAACAATG-AGAATGCGGGTCAGAAC
* *
3277389 GACAACAATGAGAATGCAGGTCAGAAC
1 GAGAACAATGAGAATGCGGGTCAGAAC
3277416 GAGAACAATG
1 GAGAACAATG
3277426 CGACTCAGAG
Statistics
Matches: 82, Mismatches: 28, Indels: 16
0.65 0.22 0.13
Matches are distributed among these distances:
25 1 0.01
26 5 0.06
27 70 0.85
28 5 0.06
29 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (27 bp):
GAGAACAATGAGAATGCGGGTCAGAAC
Found at i:3277442 original size:54 final size:53
Alignment explanation
Indices: 3277068--3277512 Score: 426
Period size: 54 Copynumber: 8.1 Consensus size: 53
3277058 TGAAAACAAT
* * * * *
3277068 AACAATGAAAATGCGGGTCAGGACGGGAAGAATGCCACTCAGAGTAACACTGAC
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATG-CGCTCAGAGCAACACTGAC
* * *
3277122 AACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGAG
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGC-GCTCAGAGCAACACTGAC
* * * *
3277176 AACAATGAAAATGCGGGTCAGAATGAGAGCAATGCAACTCAGAGCAACACTGAG
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGC-GCTCAGAGCAACACTGAC
* * * * *
3277230 AACAATGAGAATGCGGGTCAGAACGAGAAAAATGCTGCTCCA-AGTAACGCTGAG
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGC-GCT-CAGAGCAACACTGAC
* * * *
3277284 AACAATGAGAATGTGGGTCAGAACGAGAACAATGCCGCTCCA-AGTAACACTGAG
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATG-CGCT-CAGAGCAACACTGAC
* * * *
3277338 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGAC
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGC-GCTCAGAGCAACACTGAC
* * *
3277392 AACAATGAGAATGCAGGTCAGAACGAGAACAATGCGACTCAGAGCAACACCGACGAAAACAAC
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCG-CTCAGAGCAACA-C--TG------AC
* * *
3277455 AACAATGAAAATGCAGGTCAGAATGAGAACAATGTGACTCAGAGCAACACTGAC
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCG-CTCAGAGCAACACTGAC
3277509 AACA
1 AACA
3277513 GCAGCAACAA
Statistics
Matches: 342, Mismatches: 34, Indels: 30
0.84 0.08 0.07
Matches are distributed among these distances:
53 4 0.01
54 282 0.82
55 4 0.01
57 2 0.01
60 1 0.00
62 1 0.00
63 48 0.14
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.13
Consensus pattern (53 bp):
AACAATGAAAATGCGGGTCAGAACGAGAACAATGCGCTCAGAGCAACACTGAC
Found at i:3277606 original size:51 final size:51
Alignment explanation
Indices: 3277524--3277622 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
3277514 CAGCAACAAC
*
3277524 AACAACAACGAAAATGCTAGTCAAAACGAGAACAATGC-TGCTCAGAGCAGT
1 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCAT-CTCAGAGCAGT
* ** *
3277575 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGC
1 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCATCTCAGAGC
3277623 TTCACCGACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (51 bp):
AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCATCTCAGAGCAGT
Found at i:3277674 original size:63 final size:63
Alignment explanation
Indices: 3277575--3277769 Score: 309
Period size: 63 Copynumber: 3.1 Consensus size: 63
3277565 TCAGAGCAGT
3277575 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
* *
3277638 AACAACAATGAAAATGCAAGTCAGGATGGGAACAATGCATCTCAAAGCTTCACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
* * * * * *
3277701 AACAACAACGAAAATGCAAGTCAGAACGAAAACAATGCTTCTCAGAGCTACACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
*
3277764 ACCAAC
1 AACAAC
3277770 GAGAGCAACG
Statistics
Matches: 121, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 121 1.00
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.13
Consensus pattern (63 bp):
AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
Found at i:3277709 original size:186 final size:189
Alignment explanation
Indices: 3277354--3277709 Score: 427
Period size: 186 Copynumber: 1.9 Consensus size: 189
3277344 GAGAATGCGG
* * * *
3277354 GTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGACAACAATGAGAATGCAGGTCAGAACGAG
1 GTCAAAACGAGAACAATGCTGCTCCGAGTAACACCAACAACAATGAAAATGCAAGTCAGAACGAG
*
3277419 AACAATGCGACTCAGAGCAACACCGACGAAAACAACAACAATGAAAATGCAGGTCAGAATGAGAA
66 AACAATGCGACTCAGAGCAACACCGACGAAAACAACAACAATGAAAATGCAAGTCAGAATGAGAA
* * * * *
3277484 CAATGTGACTCAGAGCAACACTGACAACAGCAGCAACAACAACAACAACGAAAATGCTA
131 CAATGTCACTCAAAGCAACACCGACAACACCAACAACAACAACAACAACGAAAATGCTA
* ** * *
3277543 GTCAAAACGAGAACAATGCTGCT-C-AG-AGCAGTAACAACAATGAAAATGCAAGTCAGGATGAG
1 GTCAAAACGAGAACAATGCTGCTCCGAGTAACACCAACAACAATGAAAATGCAAGTCAGAACGAG
** * * * *
3277605 AACAATGC-ATCTCAGAGCTTCACCGAC-ACCACCAACAACAATGAAAATGCAAGTCAGGATGGG
66 AACAATGCGA-CTCAGAGCAACACCGACGA-AAACAACAACAATGAAAATGCAAGTCAGAATGAG
** *
3277668 AACAATG-CATCTCAAAGCTTCACCGACACCACCAACAACAAC
129 AACAATGTCA-CTCAAAGCAACACCGACAACACCAACAACAAC
3277710 GAAAATGCAA
Statistics
Matches: 140, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
185 3 0.02
186 112 0.80
187 2 0.01
188 1 0.01
189 22 0.16
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (189 bp):
GTCAAAACGAGAACAATGCTGCTCCGAGTAACACCAACAACAATGAAAATGCAAGTCAGAACGAG
AACAATGCGACTCAGAGCAACACCGACGAAAACAACAACAATGAAAATGCAAGTCAGAATGAGAA
CAATGTCACTCAAAGCAACACCGACAACACCAACAACAACAACAACAACGAAAATGCTA
Found at i:3279469 original size:31 final size:31
Alignment explanation
Indices: 3279431--3279491 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3279421 CCTGACCTTA
* *
3279431 GCAACTAGGTCCGCTTTAGTAC-TTGAACTTG
1 GCAACTAGATCCACTTTAGT-CTTTGAACTTG
*
3279462 GCAACTAGATCCATTTTAGTCTTTGAACTT
1 GCAACTAGATCCACTTTAGTCTTTGAACTT
3279492 AGGTTCTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (31 bp):
GCAACTAGATCCACTTTAGTCTTTGAACTTG
Found at i:3291501 original size:15 final size:16
Alignment explanation
Indices: 3291483--3291516 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3291473 TTAGACCACG
3291483 AATTATTGACAA-AAA
1 AATTATTGACAATAAA
*
3291498 AATTATTTACAATAAA
1 AATTATTGACAATAAA
3291514 AAT
1 AAT
3291517 GTTAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
AATTATTGACAATAAA
Found at i:3294526 original size:16 final size:16
Alignment explanation
Indices: 3294505--3294538 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3294495 TACACGTAGG
3294505 ATTAATTTTAAT-TAAA
1 ATTAA-TTTAATATAAA
3294521 ATTAATTTAATATAAA
1 ATTAATTTAATATAAA
3294537 AT
1 AT
3294539 AGTTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAATTTAATATAAA
Found at i:3294776 original size:25 final size:25
Alignment explanation
Indices: 3294726--3294794 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 25
3294716 TTAAAAATAA
* * *
3294726 AAATATATATAATAATT-TTATATT
1 AAATATATATATTTATTATTAAATT
3294750 -AATATATATATTTATTATTAAATTT
1 AAATATATATATTTATTATTAAA-TT
* *
3294775 AAATAAAAATATTT-TTATTA
1 AAATATATATATTTATTATTA
3294795 TTTTCAAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
23 14 0.38
24 4 0.11
25 8 0.22
26 11 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATATATATATTTATTATTAAATT
Found at i:3295194 original size:21 final size:21
Alignment explanation
Indices: 3295168--3295209 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3295158 TTTAAAAAAT
* *
3295168 AAAAAAATTATATTTTGATTC
1 AAAAAAATTATAATTTAATTC
*
3295189 AAAAAATTTATAATTTAATTC
1 AAAAAAATTATAATTTAATTC
3295210 TTTCTTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAAAAATTATAATTTAATTC
Found at i:3296683 original size:13 final size:13
Alignment explanation
Indices: 3296665--3296689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3296655 TTTTTTTTAA
3296665 TTTTTAATTAATG
1 TTTTTAATTAATG
3296678 TTTTTAATTAAT
1 TTTTTAATTAAT
3296690 AAATATATTA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:3303229 original size:5 final size:5
Alignment explanation
Indices: 3303214--3303254 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
3303204 TGTTGGTTAA
*
3303214 ATATT AAATT ATATT ATATT A-ATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
3303255 TATAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:3303243 original size:19 final size:18
Alignment explanation
Indices: 3303215--3303258 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
3303205 GTTGGTTAAA
*
3303215 TATTAAATTATATTATAT
1 TATTATATTATATTATAT
3303233 TAATTATATTATATTATAT
1 T-ATTATATTATATTATAT
3303252 TATTATA
1 TATTATA
3303259 AATAAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATATTATATTATAT
Found at i:3303798 original size:3 final size:3
Alignment explanation
Indices: 3303784--3303823 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
3303774 AAATAGATAT
* *
3303784 TTA TTA TAA TTA TTA TTA TAA TGTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
3303824 ACTAATACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3304289 original size:22 final size:24
Alignment explanation
Indices: 3304261--3304304 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3304251 TATGGCAAGA
3304261 AATTAAG-CAGAAAAG-AAGTATG
1 AATTAAGTCAGAAAAGTAAGTATG
*
3304283 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTCAGAAAAGTAAGTA
3304305 AACTTAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
AATTAAGTCAGAAAAGTAAGTATG
Found at i:3304956 original size:41 final size:37
Alignment explanation
Indices: 3304908--3305018 Score: 105
Period size: 38 Copynumber: 2.9 Consensus size: 37
3304898 TCGACCTCGA
3304908 GTCGATGAGACACTGGGTGTCACTATTGTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCAC--TT-TACTTCGGATAG
* ** ** *
3304948 ATTCGATGAGGTACTGGGTACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACTTTACTTCGGATAG
* *
3304986 GCCGATGAGACACTGGGTGTCAACTTTGCTTCG
1 GTCGATGAGACACTGGGTGTC-ACTTTACTTCG
3305019 ATCTATCCGA
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
37 15 0.27
38 21 0.38
39 2 0.04
41 18 0.32
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCACTTTACTTCGGATAG
Found at i:3305001 original size:37 final size:40
Alignment explanation
Indices: 3304910--3305003 Score: 95
Period size: 41 Copynumber: 2.4 Consensus size: 40
3304900 GACCTCGAGT
** **
3304910 CGATGAGACACTGGGTGTCACTATTGTACTTCGGATAGATT
1 CGATGAGACACTGGGTACCAC-ATTGTACTTCGGATAGAGC
** *
3304951 CGATGAGGTACTGGGTACCAC-TT-TACTTCGGCTAG-GC
1 CGATGAGACACTGGGTACCACATTGTACTTCGGATAGAGC
3304988 CGATGAGACACTGGGT
1 CGATGAGACACTGGGT
3305004 GTCAACTTTG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
37 14 0.32
38 11 0.25
39 2 0.05
41 17 0.39
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (40 bp):
CGATGAGACACTGGGTACCACATTGTACTTCGGATAGAGC
Found at i:3306022 original size:45 final size:45
Alignment explanation
Indices: 3305971--3306066 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
3305961 TTCTCAGACC
3305971 ATAATTCAAATTATAGAAAATATAAAATATTATAAACATGCATAG
1 ATAATTCAAATTATAGAAAATATAAAATATTATAAACATGCATAG
*
3306016 ATAATTCAAATTATAGCAAATATAAAATATTATAAACATGCATAG
1 ATAATTCAAATTATAGAAAATATAAAATATTATAAACATGCATAG
3306061 ATAATT
1 ATAATT
3306067 AACAAATCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.32
Consensus pattern (45 bp):
ATAATTCAAATTATAGAAAATATAAAATATTATAAACATGCATAG
Found at i:3326931 original size:27 final size:27
Alignment explanation
Indices: 3326901--3326954 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
3326891 CGTAAACACG
*
3326901 TCATGAAATGAAAGCTTTTGTGGCGAA
1 TCATGAAATGAAAGCTTTTGTAGCGAA
3326928 TCATGAAATGAAAGCTTTTGTAGCGAA
1 TCATGAAATGAAAGCTTTTGTAGCGAA
3326955 GTATTAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (27 bp):
TCATGAAATGAAAGCTTTTGTAGCGAA
Found at i:3329011 original size:19 final size:19
Alignment explanation
Indices: 3328987--3329028 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3328977 AATCTAATAT
* *
3328987 TTTAAAGTTTAAAACTTAA
1 TTTAAAATTTAAAACATAA
*
3329006 TTTAAAATTTAAACCATAA
1 TTTAAAATTTAAAACATAA
3329025 TTTA
1 TTTA
3329029 GGGAGGCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTAAAATTTAAAACATAA
Found at i:3329094 original size:13 final size:13
Alignment explanation
Indices: 3329076--3329102 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3329066 AACAATGAAA
3329076 AAATTAGATTATC
1 AAATTAGATTATC
3329089 AAATTAGATTATC
1 AAATTAGATTATC
3329102 A
1 A
3329103 CACATTCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATTAGATTATC
Found at i:3335283 original size:17 final size:17
Alignment explanation
Indices: 3335263--3335296 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3335253 AAATAAATTT
3335263 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
3335280 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
3335297 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:3336014 original size:17 final size:17
Alignment explanation
Indices: 3335994--3336027 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3335984 AGGTTTAGGT
3335994 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
3336011 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
3336028 AAAATCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:3336177 original size:31 final size:29
Alignment explanation
Indices: 3336142--3336201 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3336132 GTGATCACTT
3336142 CGTAACAAAATAATAATATAAGTGACTAAAA
1 CGTAAC-AAATAA-AATATAAGTGACTAAAA
** *
3336173 CGTAACATTTTAAATATAAGTGACTAAAA
1 CGTAACAAATAAAATATAAGTGACTAAAA
3336202 TATAACCTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
30 3 0.12
31 6 0.23
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (29 bp):
CGTAACAAATAAAATATAAGTGACTAAAA
Found at i:3339092 original size:16 final size:16
Alignment explanation
Indices: 3339072--3339112 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3339062 AATCATTTCA
* *
3339072 AGTTTATATTATTTTG
1 AGTTTAAATTATATTG
*
3339088 TGTTTAAATTATATTG
1 AGTTTAAATTATATTG
3339104 AGTTTAAAT
1 AGTTTAAAT
3339113 GATTTCGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
AGTTTAAATTATATTG
Found at i:3340165 original size:30 final size:30
Alignment explanation
Indices: 3340131--3340193 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
3340121 ACTTATTTTA
3340131 TTGTTAATTTTAG-TATTATTTTAAAGGCAT
1 TTGTTAATTTT-GTTATTATTTTAAAGGCAT
*
3340161 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
3340191 TTG
1 TTG
3340194 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:3342391 original size:46 final size:46
Alignment explanation
Indices: 3342339--3342653 Score: 463
Period size: 46 Copynumber: 6.8 Consensus size: 46
3342329 GCTCTCTGAT
* *
3342339 ATGAAATGTGTAAGACCATGGTTGAAAAATACCATCGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
3342385 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
3342431 ATGAAATGTGTAAGACCAT-GTTGAAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTG-AAAGATACCATGGCAACGTGAC
*
3342477 ATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
**
3342523 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
*** * * *
3342569 ATGAAATGAACAATACCATGATTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * *
3342615 A-GAAAATGAGTGAGACCATAGTTGAAAGATACTATGGCA
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
3342654 TCATGTCGAA
Statistics
Matches: 249, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
45 5 0.02
46 240 0.96
47 4 0.02
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:3342799 original size:26 final size:26
Alignment explanation
Indices: 3342742--3342836 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 26
3342732 TCAAATGATG
* *
3342742 AATGGTTTTATGAATTGGTTATACAA
1 AATGGTTGTATGAAATGGTTATACAA
3342768 AATGGTTGTATGAAAT-GTT-TACAA
1 AATGGTTGTATGAAATGGTTATACAA
** * *
3342792 GAATTGGTCATATGGAAAT-ATATGTACAA
1 -AA-TGGTTGTAT-GAAATGGT-TATACAA
*
3342821 AATAGTTGTATGAAAT
1 AATGGTTGTATGAAAT
3342837 AATTAAGAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
24 5 0.09
25 5 0.09
26 26 0.46
27 12 0.21
28 3 0.05
29 5 0.09
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (26 bp):
AATGGTTGTATGAAATGGTTATACAA
Found at i:3343681 original size:26 final size:24
Alignment explanation
Indices: 3343647--3343699 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
3343637 CTTAAAACTT
*
3343647 AAAAATTAATGACTAAAATGATAAA
1 AAAAATTAA-AACTAAAATGATAAA
* *
3343672 AAAAGATTAAAATTAAAGTGATAAA
1 AAAA-ATTAAAACTAAAATGATAAA
3343697 AAA
1 AAA
3343700 TTTAAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (24 bp):
AAAAATTAAAACTAAAATGATAAA
Found at i:3343697 original size:24 final size:25
Alignment explanation
Indices: 3343660--3343713 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
3343650 AATTAATGAC
3343660 TAAAATGATAAAAAAAGATTAAA-AT
1 TAAAATGATAAAAAAA-ATTAAACAT
* *
3343685 TAAAGTGAT-AAAAAATTTAAACAT
1 TAAAATGATAAAAAAAATTAAACAT
3343709 TAAAA
1 TAAAA
3343714 ACTAAATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 5 0.20
24 12 0.48
25 8 0.32
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (25 bp):
TAAAATGATAAAAAAAATTAAACAT
Done.