Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 11 of 82
Found at i:3485062 original size:45 final size:46
Alignment explanation
Indices: 3485007--3485117 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 46
3484997 AGTAATTGCA
**
3485007 TGACTAGTTAATAAGGCATTACATGACTAATTTTTA-AGCATTGTG
1 TGACTAGTTAATAAGGCATTACATGACTAATTAATAGAGCATTGTG
* * * * *
3485052 TGATTGGTTAAT-AGGCGTTGCGTGACTAATTAATAGAGCATTGTG
1 TGACTAGTTAATAAGGCATTACATGACTAATTAATAGAGCATTGTG
**
3485097 TGACTAGTTTGTAAGGCATTA
1 TGACTAGTTAATAAGGCATTA
3485118 TGTGATTGGT
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
44 18 0.35
45 27 0.53
46 6 0.12
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (46 bp):
TGACTAGTTAATAAGGCATTACATGACTAATTAATAGAGCATTGTG
Found at i:3485078 original size:67 final size:66
Alignment explanation
Indices: 3484877--3485146 Score: 225
Period size: 67 Copynumber: 4.0 Consensus size: 66
3484867 GCATTTCATC
** * * * * * *
3484877 ACTAGTTTTTAGGCATTGCGTTATTAATTTTTAGGCATTGTGTGATTGGTTGATAGGTATTGCGT
1 ACTAGTTAATAGGCATTACGTGACTAATTTTTAAGCATTGTGTGATTGGTTTATAGGCATTGCGT
3484942 G
66 G
* * ** * * ** * * * ** *
3484943 ATTGGTTTTTAGTCATTACGTGATTGGTTTTTAGGCATTGTGTGATTGATTTTTAGTAATTGCAT
1 ACTAGTTAATAGGCATTACGTGACTAATTTTTAAGCATTGTGTGATTGGTTTATAGGCATTGCGT
3485008 G
66 G
* * *
3485009 ACTAGTTAATAAGGCATTACATGACTAATTTTTAAGCATTGTGTGATTGGTTAATAGGCGTTGCG
1 ACTAGTTAAT-AGGCATTACGTGACTAATTTTTAAGCATTGTGTGATTGGTTTATAGGCATTGCG
3485074 TG
65 TG
* ** * * * *
3485076 ACTAATTAATAGAGCATTGTGTGACTAGTTTGTAAGGCATTATGTGATTGGTTTTTAGGCATTGC
1 ACTAGTTAATAG-GCATTACGTGACTAATTTTTAA-GCATTGTGTGATTGGTTTATAGGCATTGC
3485141 GTG
64 GTG
3485144 ACT
1 ACT
3485147 CAGGCATTGC
Statistics
Matches: 161, Mismatches: 40, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
66 61 0.38
67 69 0.43
68 31 0.19
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (66 bp):
ACTAGTTAATAGGCATTACGTGACTAATTTTTAAGCATTGTGTGATTGGTTTATAGGCATTGCGT
G
Found at i:3485115 original size:23 final size:22
Alignment explanation
Indices: 3485089--3485146 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
3485079 AATTAATAGA
3485089 GCATTGTGTGACTAGTTTGTAAG
1 GCATTGTGTGACTAGTTT-TAAG
* * * *
3485112 GCATTATGTGATTGGTTTTTAG
1 GCATTGTGTGACTAGTTTTAAG
*
3485134 GCATTGCGTGACT
1 GCATTGTGTGACT
3485147 CAGGCATTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.41
Consensus pattern (22 bp):
GCATTGTGTGACTAGTTTTAAG
Found at i:3485153 original size:16 final size:16
Alignment explanation
Indices: 3485132--3485162 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3485122 ATTGGTTTTT
*
3485132 AGGCATTGCGTGACTC
1 AGGCATTGCATGACTC
3485148 AGGCATTGCATGACT
1 AGGCATTGCATGACT
3485163 ACTTGATAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (16 bp):
AGGCATTGCATGACTC
Found at i:3485191 original size:151 final size:152
Alignment explanation
Indices: 3485001--3485296 Score: 328
Period size: 151 Copynumber: 2.0 Consensus size: 152
3484991 ATTTTTAGTA
* * * *
3485001 ATTGCATGACTAGTTAATAAGGCATTACATGACTAATTTTTAAGCATTGTGTGATTGGTTAATA-
1 ATTGCATGACTACTTAATAAGGCATTACATGAATAATTTTTAAGCATTGCGTGACTGGTTAATAG
* * * *
3485065 GGCGTTGCGTGACTAATTAATAGAGCATTGTGTGACTAGTTTG-TAAGGCATTATGTGATTGGTT
66 GGCATTACGTGACTAATTAATA-AGCATTGTGTGACT-GATTGATAAGGCATTATGTGAATGGTT
*
3485129 TTTA-GGCATTGCGTGACTCAGGC
129 TGTAGGGCATTGCGTGACTCAGGC
* *** * *** *
3485152 ATTGCATGACTACTTGATAAGGCATTTTGTGAATGATTTTTATTTATTGCGTGACTGGTTGATAG
1 ATTGCATGACTACTTAATAAGGCATTACATGAATAATTTTTAAGCATTGCGTGACTGGTTAATAG
* * ** * * *
3485217 GGCATTATGTGATTGGTTGATAAGTATTGTGTGACTGATTGATAAGGCATTGTGTGAATGGTTTG
66 GGCATTACGTGACTAATTAATAAGCATTGTGTGACTGATTGATAAGGCATTATGTGAATGGTTTG
3485282 TAGGGCATTGCGTGA
131 TAGGGCATTGCGTGA
3485297 TTGGTTTTTA
Statistics
Matches: 117, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
150 4 0.03
151 86 0.74
152 27 0.23
ACGTcount: A:0.25, C:0.09, G:0.27, T:0.39
Consensus pattern (152 bp):
ATTGCATGACTACTTAATAAGGCATTACATGAATAATTTTTAAGCATTGCGTGACTGGTTAATAG
GGCATTACGTGACTAATTAATAAGCATTGTGTGACTGATTGATAAGGCATTATGTGAATGGTTTG
TAGGGCATTGCGTGACTCAGGC
Found at i:3485233 original size:23 final size:23
Alignment explanation
Indices: 3485197--3485302 Score: 99
Period size: 23 Copynumber: 4.7 Consensus size: 23
3485187 ATTTTTATTT
*
3485197 ATTGCGTGACTGGTTGATAGGGC
1 ATTGTGTGACTGGTTGATAGGGC
* * * *
3485220 ATTATGTGATTGGTTGATA-AGT
1 ATTGTGTGACTGGTTGATAGGGC
* *
3485242 ATTGTGTGACTGATTGATAAGGC
1 ATTGTGTGACTGGTTGATAGGGC
*
3485265 ATTGTGTGAATGGTTTG-TAGGGC
1 ATTGTGTGACTGG-TTGATAGGGC
* *
3485288 ATTGCGTGATTGGTT
1 ATTGTGTGACTGGTT
3485303 TTTAGAGTAT
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
22 19 0.29
23 44 0.67
24 3 0.05
ACGTcount: A:0.21, C:0.07, G:0.34, T:0.39
Consensus pattern (23 bp):
ATTGTGTGACTGGTTGATAGGGC
Found at i:3485279 original size:45 final size:45
Alignment explanation
Indices: 3485152--3485279 Score: 132
Period size: 45 Copynumber: 2.8 Consensus size: 45
3485142 TGACTCAGGC
* * * ** **
3485152 ATTGCATGACT-ACTTGATAAGGCATTTTGTGAATGATTTTTATTT
1 ATTGCGTGACTGA-TTGATAAGGCATTATGTGAATGGTTGATAAGT
* * *
3485197 ATTGCGTGACTGGTTGATAGGGCATTATGTGATTGGTTGATAAGT
1 ATTGCGTGACTGATTGATAAGGCATTATGTGAATGGTTGATAAGT
* *
3485242 ATTGTGTGACTGATTGATAAGGCATTGTGTGAATGGTT
1 ATTGCGTGACTGATTGATAAGGCATTATGTGAATGGTT
3485280 TGTAGGGCAT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.41
Consensus pattern (45 bp):
ATTGCGTGACTGATTGATAAGGCATTATGTGAATGGTTGATAAGT
Found at i:3485314 original size:23 final size:23
Alignment explanation
Indices: 3485263--3485337 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
3485253 GATTGATAAG
* *
3485263 GCATTGTGTGAATGGTTTGTAGG
1 GCATTGCGTGAATGGTTTGTAGA
* *
3485286 GCATTGCGTGATTGGTTTTTAGA
1 GCATTGCGTGAATGGTTTGTAGA
* * * * *
3485309 GTATTGCATGACTGTTTTCTA-A
1 GCATTGCGTGAATGGTTTGTAGA
3485331 GCATTGC
1 GCATTGC
3485338 TTGGATATTA
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 7 0.17
23 35 0.83
ACGTcount: A:0.19, C:0.11, G:0.29, T:0.41
Consensus pattern (23 bp):
GCATTGCGTGAATGGTTTGTAGA
Found at i:3490066 original size:30 final size:29
Alignment explanation
Indices: 3490027--3490152 Score: 141
Period size: 28 Copynumber: 4.3 Consensus size: 29
3490017 TCTTTTCTTT
3490027 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAAAATATTTT-TCTTGTCTA
*
3490057 AATTCAGAC--AAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATAT-TTTTCTTGTCTA
*
3490085 GATTAAGACAAAAAATATTTTTCTTGTCTTA
1 AATTAAGAC-AAAAATATTTTTCTTGTC-TA
* * * *
3490116 AATTAAAACAAATATA-TTTTCTTATTTA
1 AATTAAGACAAAAATATTTTTCTTGTCTA
3490144 AATTAAGAC
1 AATTAAGAC
3490153 TAAGCATGTT
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
28 32 0.39
29 11 0.13
30 24 0.29
31 15 0.18
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (29 bp):
AATTAAGACAAAAATATTTTTCTTGTCTA
Found at i:3490079 original size:28 final size:27
Alignment explanation
Indices: 3490027--3490184 Score: 127
Period size: 28 Copynumber: 5.4 Consensus size: 27
3490017 TCTTTTCTTT
3490027 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGAC--AAATATTTT-TCTTGTCTA
*
3490057 AATTCAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAATAT-TTTTCTTGTCTA
*
3490085 GATTAAGACAAAAAATATTTTTCTTGTCTTA
1 AATTAAGAC---AAATATTTTTCTTGTC-TA
* * *
3490116 AATTAAAACAAATATATTTTCTTATTTA
1 AATTAAGACAAATAT-TTTTCTTGTCTA
** * *
3490144 AATTAAGACTAAGCATGTTTTCATGTTTA
1 AATTAAGAC-AAATAT-TTTTCTTGTCTA
*
3490173 GATTAAGACAAA
1 AATTAAGACAAA
3490185 CACGTTAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
28 40 0.38
29 33 0.31
30 18 0.17
31 15 0.14
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (27 bp):
AATTAAGACAAATATTTTTCTTGTCTA
Found at i:3490118 original size:59 final size:58
Alignment explanation
Indices: 3490027--3490152 Score: 173
Period size: 59 Copynumber: 2.2 Consensus size: 58
3490017 TCTTTTCTTT
* * * *
3490027 AATTAAGACAAAAATATTTTATCTTGTCTAAATTCAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTTATCTTGTCTAAATTAAAACAAATATATTTTCTTATCTA
* *
3490085 GATTAAGACAAAAAATATTTT-TCTTGTCTTAAATTAAAACAAATATATTTTCTTATTTA
1 AATTAAGAC-AAAAATATTTTATCTTGTC-TAAATTAAAACAAATATATTTTCTTATCTA
3490144 AATTAAGAC
1 AATTAAGAC
3490153 TAAGCATGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 15 0.25
59 44 0.75
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (58 bp):
AATTAAGACAAAAATATTTTATCTTGTCTAAATTAAAACAAATATATTTTCTTATCTA
Found at i:3493159 original size:20 final size:20
Alignment explanation
Indices: 3493114--3493151 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3493104 TTTTGGCCCC
3493114 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
3493134 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
3493152 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:3513921 original size:18 final size:18
Alignment explanation
Indices: 3513885--3513936 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
3513875 TTTGAAAAAA
*
3513885 TTTTAAAAATATATATAATTT
1 TTTTAAAAA-A-AT-TAATTG
3513906 TTTTAAAAAAATTAATTG
1 TTTTAAAAAAATTAATTG
* *
3513924 ATTAAAAAAAATT
1 TTTTAAAAAAATT
3513937 TGAGAAGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 16 0.57
19 2 0.07
20 1 0.04
21 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTTAAAAAAATTAATTG
Found at i:3522541 original size:22 final size:22
Alignment explanation
Indices: 3522505--3522560 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
3522495 TATTATTTTC
**
3522505 ATTTTATTTCATATTATCATAT
1 ATTTTATTTTTTATTATCATAT
* *
3522527 -TTTCTATTTTTTATTCTCCTAT
1 ATTT-TATTTTTTATTATCATAT
3522549 ATTTTATTTTTT
1 ATTTTATTTTTT
3522561 TTTTATATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.11
22 22 0.79
23 3 0.11
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTTTATTTTTTATTATCATAT
Found at i:3523215 original size:23 final size:23
Alignment explanation
Indices: 3523172--3523215 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3523162 TATAAAGCTA
* *
3523172 TATTATTATTTTTGTTCATTTAT
1 TATTATTATTATTATTCATTTAT
*
3523195 TATTATTATTATTATTTATTT
1 TATTATTATTATTATTCATTT
3523216 CTCGTTTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
TATTATTATTATTATTCATTTAT
Found at i:3524190 original size:85 final size:85
Alignment explanation
Indices: 3524095--3524277 Score: 271
Period size: 85 Copynumber: 2.2 Consensus size: 85
3524085 CCATCGCTCT
* *
3524095 CTCCTCTCTCTTCTCTCCCTTCTTTCCTTTCGCCGGTCACCTAAAGGCTTTCCCTTTCCCGGC-T
1 CTCCTCTCTCTTCCCTCCCTTCTTTCCTTTCGCCGGTCACCCAAAGGCTTTCCCTTTCCCGGCGT
3524159 CCGGTCAGCTATTTCTCACTA
66 -CGGTCAGCTATTTCTCACTA
* * * *
3524180 CTCCTCTCTCTTCCCTCTCTTCTTTCCTTTTGTCGGTCACCCAAAGGCTTTTCCTTTCCCGGCGT
1 CTCCTCTCTCTTCCCTCCCTTCTTTCCTTTCGCCGGTCACCCAAAGGCTTTCCCTTTCCCGGCGT
* *
3524245 CGGTCTGCTCTTTCTCACTA
66 CGGTCAGCTATTTCTCACTA
3524265 CTCCTCTCT-TTCC
1 CTCCTCTCTCTTCC
3524278 TACCGTCGAC
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
84 4 0.04
85 84 0.94
86 1 0.01
ACGTcount: A:0.08, C:0.41, G:0.11, T:0.40
Consensus pattern (85 bp):
CTCCTCTCTCTTCCCTCCCTTCTTTCCTTTCGCCGGTCACCCAAAGGCTTTCCCTTTCCCGGCGT
CGGTCAGCTATTTCTCACTA
Found at i:3524414 original size:12 final size:13
Alignment explanation
Indices: 3524391--3524419 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3524381 GTATTTTTTA
3524391 ATTTTTTGGGTAT
1 ATTTTTTGGGTAT
3524404 ATTTTTT-GGTAT
1 ATTTTTTGGGTAT
3524416 ATTT
1 ATTT
3524420 CTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (13 bp):
ATTTTTTGGGTAT
Found at i:3525673 original size:54 final size:54
Alignment explanation
Indices: 3525610--3525788 Score: 313
Period size: 54 Copynumber: 3.3 Consensus size: 54
3525600 GGTAACCGTG
*
3525610 CATGAGCTGGGTGAGATGTGGTGTCTGACTATGTGCACGATGTGGTGGGATGCA
1 CATGAGCTGGGTGAGATGTGGTGTCTGGCTATGTGCACGATGTGGTGGGATGCA
* *
3525664 CATGAGCTGGGTGAGGTATGGTGTCTGGCTATGTGCACGATGTGGTGGGATGCA
1 CATGAGCTGGGTGAGATGTGGTGTCTGGCTATGTGCACGATGTGGTGGGATGCA
* *
3525718 CATGAGCTGGATGAGATGTGGTGTCCGGCTATGTGCACGATGTGGTGGGATGCA
1 CATGAGCTGGGTGAGATGTGGTGTCTGGCTATGTGCACGATGTGGTGGGATGCA
3525772 CATGAGCTGGGTGAGAT
1 CATGAGCTGGGTGAGAT
3525789 AAAATGTTTT
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 117 1.00
ACGTcount: A:0.18, C:0.13, G:0.41, T:0.27
Consensus pattern (54 bp):
CATGAGCTGGGTGAGATGTGGTGTCTGGCTATGTGCACGATGTGGTGGGATGCA
Found at i:3531996 original size:20 final size:20
Alignment explanation
Indices: 3531971--3532011 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3531961 TTCTATTGAA
3531971 TTGTGAATGGAATTTTGTTG
1 TTGTGAATGGAATTTTGTTG
3531991 TTGTGAATGGAATTTTGTTG
1 TTGTGAATGGAATTTTGTTG
3532011 T
1 T
3532012 GAACAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (20 bp):
TTGTGAATGGAATTTTGTTG
Found at i:3532647 original size:72 final size:73
Alignment explanation
Indices: 3532566--3532702 Score: 188
Period size: 72 Copynumber: 1.9 Consensus size: 73
3532556 GAAGATGGCC
* * * *
3532566 AGTTTAGAAACAAAACCAACTTAATCAACTAAGA-GATATTGTTAG-CGACTAAGTGTTTACTGC
1 AGTTCAGAAACAAAACCAACTTAATCAACTAAGAGGA-ATAGTTAGTCGACTAAGAGCTTACTGC
3532629 CAGAAGCCG
65 CAGAAGCCG
* **
3532638 AGTTCAGAAACAAAACCGACTTAATTGACTAAGAGGAATAGTTAGTCGACTAAGAGCTTACTGCC
1 AGTTCAGAAACAAAACCAACTTAATCAACTAAGAGGAATAGTTAGTCGACTAAGAGCTTACTGCC
3532703 TAAAACTGGG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
72 37 0.66
73 19 0.34
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (73 bp):
AGTTCAGAAACAAAACCAACTTAATCAACTAAGAGGAATAGTTAGTCGACTAAGAGCTTACTGCC
AGAAGCCG
Found at i:3535097 original size:33 final size:33
Alignment explanation
Indices: 3535050--3535145 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
3535040 GACCAACTTC
*
3535050 AGTAATGGCATTCACATCATCACCACTAACTCT
1 AGTAGTGGCATTCACATCATCACCACTAACTCT
*
3535083 AGTAGTGGCATTCACATTATCACCA-TAGACTCT
1 AGTAGTGGCATTCACATCATCACCACTA-ACTCT
*
3535116 AGTAGTGACATTCACATCATCACCACTAAC
1 AGTAGTGGCATTCACATCATCACCACTAAC
3535146 ATTTTGCATA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.27
Consensus pattern (33 bp):
AGTAGTGGCATTCACATCATCACCACTAACTCT
Found at i:3539582 original size:27 final size:27
Alignment explanation
Indices: 3539545--3539609 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
3539535 TAAGGCATGC
* *
3539545 ACAACACACAGTCTCACAGCGTTATGA
1 ACAACACACAGCCTCACAACGTTATGA
*
3539572 ACAACACACAGCCTCACAACGTTATGC
1 ACAACACACAGCCTCACAACGTTATGA
*
3539599 ACAACATACAG
1 ACAACACACAG
3539610 ATTATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.15
Consensus pattern (27 bp):
ACAACACACAGCCTCACAACGTTATGA
Found at i:3547038 original size:29 final size:29
Alignment explanation
Indices: 3546996--3547056 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
3546986 TTTCTTTTCC
3546996 AGGTAGATGCAACTATGCTAGCATATCTT
1 AGGTAGATGCAACTATGCTAGCATATCTT
*
3547025 AGGTAGATGCAACTATGCTAGCGTATCTT
1 AGGTAGATGCAACTATGCTAGCATATCTT
3547054 AGG
1 AGG
3547057 ATTTGCATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (29 bp):
AGGTAGATGCAACTATGCTAGCATATCTT
Found at i:3554106 original size:15 final size:14
Alignment explanation
Indices: 3554062--3554106 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 14
3554052 AGAATTAATG
3554062 TATTACATCTGTACA
1 TATTACA-CTGTACA
3554077 TATTACACATGTACA
1 TATTACAC-TGTACA
3554092 TATTACACTGATACA
1 TATTACACTG-TACA
3554107 ATGTCAAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.11
15 25 0.89
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (14 bp):
TATTACACTGTACA
Found at i:3564011 original size:73 final size:73
Alignment explanation
Indices: 3563802--3564002 Score: 258
Period size: 73 Copynumber: 2.8 Consensus size: 73
3563792 AGACAGAATG
* * * *
3563802 CTCTTAGTCAACTAACTATGCTTCTTAGTCGATTAAGTCGTCTTTGTCTTTGAACCCACTTTTTG
1 CTCTTAGTCAACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACCCAATTTCTG
* *
3563867 GCAATAAG
66 ACAATAAA
* * * * * *
3563875 CTTTTAGTCAACTAACTGTGCTTCTTAGTCAATTAAGTCGTTTCTATTTCTGAACCCAATTTCTG
1 CTCTTAGTCAACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACCCAATTTCTG
* *
3563940 ATAGTAAA
66 ACAATAAA
* *
3563948 CTCTTAGTCAACTAACTAAGCTTCTTAGTCGATTAAGTCATCTCTGTCTCTGAAC
1 CTCTTAGTCAACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAAC
3564003 TCGGTTTCTT
Statistics
Matches: 106, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
73 106 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (73 bp):
CTCTTAGTCAACTAACTATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACCCAATTTCTG
ACAATAAA
Found at i:3565749 original size:33 final size:32
Alignment explanation
Indices: 3565673--3565773 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
3565663 TATGTTGTCT
* *
3565673 AACAATAATATTTTTTCAACATGGCATGTAAC
1 AACAATATTTTTTTTTCAACATGGCATGTAAC
3565705 AACAATATTTTTTTTTCAACATGGCATGTAAC
1 AACAATATTTTTTTTTCAACATGGCATGTAAC
3565737 AACAATATTTTTTTTTTCAACATGGCATGTAAC
1 AACAATA-TTTTTTTTTCAACATGGCATGTAAC
3565770 AACA
1 AACA
3565774 TTTTTTAACC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 37 0.56
33 29 0.44
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (32 bp):
AACAATATTTTTTTTTCAACATGGCATGTAAC
Found at i:3565802 original size:25 final size:26
Alignment explanation
Indices: 3565682--3565796 Score: 88
Period size: 32 Copynumber: 3.9 Consensus size: 26
3565672 TAACAATAAT
3565682 ATTTTTTCAACATGGCATGTAACAAC
1 ATTTTTTCAACATGGCATGTAACAAC
3565708 AATATTTTTTTTTCAACATGGCATGTAACAAC
1 ---A---TTTTTTCAACATGGCATGTAACAAC
3565740 AATATTTTTTTTTTCAACATGGCATGTAACAAC
1 ---A----TTTTTTCAACATGGCATGTAACAAC
*
3565773 ATTTTTT-AACCATGGCTTGTAACA
1 ATTTTTTCAA-CATGGCATGTAACA
3565797 TGTTTTTGTA
Statistics
Matches: 80, Mismatches: 1, Indels: 13
0.85 0.01 0.14
Matches are distributed among these distances:
25 2 0.03
26 19 0.24
29 1 0.01
30 1 0.01
32 29 0.36
33 28 0.35
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (26 bp):
ATTTTTTCAACATGGCATGTAACAAC
Found at i:3565803 original size:26 final size:26
Alignment explanation
Indices: 3565747--3565796 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3565737 AACAATATTT
3565747 TTTTTTTCAACATGGCATGTAACAAC
1 TTTTTTTCAACATGGCATGTAACAAC
* *
3565773 ATTTTTT-AACCATGGCTTGTAACA
1 TTTTTTTCAA-CATGGCATGTAACA
3565797 TGTTTTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (26 bp):
TTTTTTTCAACATGGCATGTAACAAC
Found at i:3565967 original size:21 final size:21
Alignment explanation
Indices: 3565937--3565977 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3565927 TTTTGTACAT
3565937 GACGTATAACAACCTAACCAC
1 GACGTATAACAACCTAACCAC
*
3565958 GACGTGTAACAACCTAACCA
1 GACGTATAACAACCTAACCA
3565978 TGGCTTGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.32, G:0.12, T:0.15
Consensus pattern (21 bp):
GACGTATAACAACCTAACCAC
Found at i:3566002 original size:66 final size:66
Alignment explanation
Indices: 3565896--3566032 Score: 211
Period size: 66 Copynumber: 2.1 Consensus size: 66
3565886 CAATATGGCA
*
3565896 TGTAACAACCTAACCATGTCTTGTCACATATTTTTGTACATGACGTATAACAACCTAACCACGAC
1 TGTAACAACCTAACCATGGCTTGTCACATATTTTTGTACATGACGTATAACAACCTAACCACGAC
3565961 G
66 G
* ** * * *
3565962 TGTAACAACCTAACCATGGCTTGTCACATGTTTTTGTACATGGTGTTTAACAACCTAACCATGGC
1 TGTAACAACCTAACCATGGCTTGTCACATATTTTTGTACATGACGTATAACAACCTAACCACGAC
3566027 G
66 G
3566028 TGTAA
1 TGTAA
3566033 TATGTTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (66 bp):
TGTAACAACCTAACCATGGCTTGTCACATATTTTTGTACATGACGTATAACAACCTAACCACGAC
G
Found at i:3566058 original size:45 final size:45
Alignment explanation
Indices: 3565960--3566058 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
3565950 CTAACCACGA
* * *
3565960 CGTGTAACAACCTAACCATGGCTTGTCACATGTTTTTGTACATGG
1 CGTGTAACAACCTAACCATGGCGTGTAACATGTTTTTATACATGG
* * * *
3566005 TGTTTAACAACCTAACCATGGCGTGTAATATGTTTTTATATATGG
1 CGTGTAACAACCTAACCATGGCGTGTAACATGTTTTTATACATGG
3566050 CGTGTAACA
1 CGTGTAACA
3566059 TCATAGCGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (45 bp):
CGTGTAACAACCTAACCATGGCGTGTAACATGTTTTTATACATGG
Found at i:3579632 original size:26 final size:26
Alignment explanation
Indices: 3579603--3579657 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
3579593 ACTAAAACCG
*
3579603 AAACATAAATAATA-ATCAAACCGATC
1 AAACATAAA-AAAAGATCAAACCGATC
*
3579629 AAACATAAAAAAAGATCAAACTGATC
1 AAACATAAAAAAAGATCAAACCGATC
3579655 AAA
1 AAA
3579658 TATAGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (26 bp):
AAACATAAAAAAAGATCAAACCGATC
Found at i:3580157 original size:212 final size:215
Alignment explanation
Indices: 3579790--3580254 Score: 557
Period size: 212 Copynumber: 2.1 Consensus size: 215
3579780 TATAAATTAA
*
3579790 ATATATATAATATATTAATTTATTGTATATATAAAATTAATAACACAACTTATATGTTATAATAT
1 ATATATATAATATATT-ATTTA-T-TATATATATAATTAATAACACAACTTATATGTTATAATA-
* * * * *
3579855 TTTGATTTTTATATCAAAGTTTATATATATAATAACTAATTATAAACAATATGTTATAAAAATTA
62 -TTGA-TTTTATACCAAAATTTATATAAATAATAACTAAGTATAAACAATATGTTATAAAAACTA
* *
3579920 AGATGATAACTAATAAAATTATTAAGTGTAATAATATAAATAAAATCTATTATAAGTTACAGTAA
125 AGATGATAACTAATAAAATTATTAAGTGTAATAATATAAATAAAATCTATTATAAGTCACAATAA
* *
3579985 TGCTTATAG-ATAAATTAAATATATGT
190 TACTTAT-GTATAAATTAAATATATAT
* *
3580011 ATATATATAATATATTACTTTATTATATATATAATTAATTACACAACTTATATGTTGT-A-A-TG
1 ATATATATAATATATTA-TTTATTATATATATAATTAATAACACAACTTATATGTTATAATATTG
* * * *
3580073 -TTTTATACCAAAATTTGTTTAAATAATAACTAAGTATAAATAATATGTTATAAAGACT-AGAGT
65 ATTTTATACCAAAATTTATATAAATAATAACTAAGTATAAACAATATGTTATAAAAACTAAGA-T
* ** * * * *
3580136 GATAATTAATAAGGTTATTAAGTGTAATCATATAAATAAAGTTTATTATAAGTCATAATAATACT
129 GATAACTAATAAAATTATTAAGTGTAATAATATAAATAAAATCTATTATAAGTCACAATAATACT
*
3580201 TATGTATAAATTATATATATAT
194 TATGTATAAATTAAATATATAT
* *
3580223 ATATATATGATAT-TTATATAATTATATATATA
1 ATATATATAATATATTAT-TTATTATATATATA
3580255 CTCATAACAT
Statistics
Matches: 214, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
210 1 0.00
211 20 0.09
212 135 0.63
214 2 0.01
217 1 0.00
218 1 0.00
219 32 0.15
220 2 0.01
221 20 0.09
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (215 bp):
ATATATATAATATATTATTTATTATATATATAATTAATAACACAACTTATATGTTATAATATTGA
TTTTATACCAAAATTTATATAAATAATAACTAAGTATAAACAATATGTTATAAAAACTAAGATGA
TAACTAATAAAATTATTAAGTGTAATAATATAAATAAAATCTATTATAAGTCACAATAATACTTA
TGTATAAATTAAATATATAT
Found at i:3580219 original size:2 final size:2
Alignment explanation
Indices: 3580212--3580254 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
3580202 ATGTATAAAT
*
3580212 TA TA TA TA TA TA TA TA TA TGA TA TT TA TA TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
3580253 TA
1 TA
3580255 CTCATAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 32 0.89
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3584593 original size:22 final size:22
Alignment explanation
Indices: 3584565--3584610 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3584555 TATAAAGAAG
3584565 TTTTTTTA-ATTTTTAATTTATA
1 TTTTTTTATATTTTTAATTT-TA
*
3584587 TTTTTTTATTTTTTTAATTTTA
1 TTTTTTTATATTTTTAATTTTA
3584609 TT
1 TT
3584611 CTATTTGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTATATTTTTAATTTTA
Found at i:3585437 original size:36 final size:36
Alignment explanation
Indices: 3585397--3585468 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
3585387 ATTATGTTAG
3585397 GATTTGTAAACAGCCCATTTTTCTAAAGATATGTAA
1 GATTTGTAAACAGCCCATTTTTCTAAAGATATGTAA
*
3585433 GATTTGTAAACAGTCCATTTTTCTAAAGATATGTAA
1 GATTTGTAAACAGCCCATTTTTCTAAAGATATGTAA
3585469 TTTTTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (36 bp):
GATTTGTAAACAGCCCATTTTTCTAAAGATATGTAA
Found at i:3587720 original size:40 final size:40
Alignment explanation
Indices: 3587676--3587808 Score: 196
Period size: 40 Copynumber: 3.3 Consensus size: 40
3587666 GCTTTAACCA
* ** *
3587676 TGAAAAGGTAGTGATGTTGTGAGGTTGTGCTTGCTCTTCT
1 TGAAAAGGTAATGACATTGTGAGGTTGTGCTTGCTCCTCT
*
3587716 TGAAAAGGCAATGACATTGTGAGGTTGTGCTTGCTCCTCT
1 TGAAAAGGTAATGACATTGTGAGGTTGTGCTTGCTCCTCT
3587756 TGAAAAGGTAATGACATTGTGAGGTTGTGCTTGCTCCT-T
1 TGAAAAGGTAATGACATTGTGAGGTTGTGCTTGCTCCTCT
*
3587795 TCGAAAAGGCAATG
1 T-GAAAAGGTAATG
3587809 TTTGTGTAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
39 2 0.02
40 83 0.98
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (40 bp):
TGAAAAGGTAATGACATTGTGAGGTTGTGCTTGCTCCTCT
Found at i:3591978 original size:22 final size:22
Alignment explanation
Indices: 3591953--3592008 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
3591943 CTTCCTTTAA
* *
3591953 CCAGTGCTGCAGCCTTGTTCTC
1 CCAGCGCTGCAACCTTGTTCTC
3591975 CCAGCGCTGCAACCTTGTTCTC
1 CCAGCGCTGCAACCTTGTTCTC
*
3591997 CTAGCGCTGCAA
1 CCAGCGCTGCAA
3592009 TGGTCTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.14, C:0.38, G:0.21, T:0.27
Consensus pattern (22 bp):
CCAGCGCTGCAACCTTGTTCTC
Found at i:3603194 original size:2 final size:2
Alignment explanation
Indices: 3603189--3603217 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3603179 CGGAATCTTG
3603189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3603218 CCTCGGTCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3611707 original size:20 final size:20
Alignment explanation
Indices: 3611684--3611724 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3611674 GAAGGAGAGG
3611684 GAAGGAAAAAGAAAGAAAAA
1 GAAGGAAAAAGAAAGAAAAA
* * *
3611704 GAAGTAGAAAGAAAGAGAAA
1 GAAGGAAAAAGAAAGAAAAA
3611724 G
1 G
3611725 CAACGACGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (20 bp):
GAAGGAAAAAGAAAGAAAAA
Found at i:3627663 original size:28 final size:28
Alignment explanation
Indices: 3627632--3627689 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
3627622 TCTACTTCTG
*
3627632 GTAGATTGA-AAGTATTCATCCACTTTTA
1 GTAGATT-ACAAGTATCCATCCACTTTTA
*
3627660 GTAGGTTACAAGTATCCATCCACTTTTA
1 GTAGATTACAAGTATCCATCCACTTTTA
3627688 GT
1 GT
3627690 GAGTGATCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (28 bp):
GTAGATTACAAGTATCCATCCACTTTTA
Found at i:3627856 original size:26 final size:25
Alignment explanation
Indices: 3627747--3627856 Score: 94
Period size: 26 Copynumber: 4.2 Consensus size: 25
3627737 TTTTTAGTAG
3627747 GTTAGTCCATCCACTTTTGATGGTGAA
1 GTTA-TCCATCCACTTTTGATGGT-AA
* * * ** *
3627774 ATTATCAATTCACTCATGGTGGTAA
1 GTTATCCATCCACTTTTGATGGTAA
* * *
3627799 GATTATCCATCCACTTCTGGTGATAA
1 G-TTATCCATCCACTTTTGATGGTAA
3627825 GTTTATCCATCCACTTTTGATGGTAAA
1 G-TTATCCATCCACTTTTGATGGT-AA
3627852 GTTAT
1 GTTAT
3627857 TTTTAGAATA
Statistics
Matches: 65, Mismatches: 16, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
25 2 0.03
26 57 0.88
27 6 0.09
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (25 bp):
GTTATCCATCCACTTTTGATGGTAA
Found at i:3628749 original size:25 final size:26
Alignment explanation
Indices: 3628715--3628764 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
3628705 TTCAACTTTT
3628715 AATAAAATATTAATA-TTAAATTATA
1 AATAAAATATTAATATTTAAATTATA
3628740 AATAAAATATTAATATTTAAATTAT
1 AATAAAATATTAATATTTAAATTAT
3628765 CAATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAAAATATTAATATTTAAATTATA
Found at i:3631220 original size:133 final size:134
Alignment explanation
Indices: 3631068--3631336 Score: 434
Period size: 133 Copynumber: 2.0 Consensus size: 134
3631058 ATAAAATAAA
* * * *
3631068 ATAATTATTGCAAAATTTGATTAATTAGAATGAAATACATTTAAAAATATT-TTAATATATTTAA
1 ATAATTATTACAAAATTTGATTAACTAGAACGAAATACA-TTAAAAATATTATTAATATATCTAA
* *
3631132 CTAGTTTAAAAA-CATAGTATTAGAATAAACATAAAAGATTGATTTATCTTTTGATAAAAATAAT
65 CTAATTTAAAAATAATAGTATTAGAATAAACATAAAAGATTGATTTATCTTTTGATAAAAATAAT
3631196 CAATG
130 CAATG
* *
3631201 ATAATTATTACAAAGTTTGATTAACTAGAACGAAATACATTAAAAATATTATTAATATATCTAAT
1 ATAATTATTACAAAATTTGATTAACTAGAACGAAATACATTAAAAATATTATTAATATATCTAAC
*
3631266 TAATTTAAAAATAATATTATTAGAATAAACATAAAAGATTGATTTATCTTTTGATAAAAATAATC
66 TAATTTAAAAATAATAGTATTAGAATAAACATAAAAGATTGATTTATCTTTTGATAAAAATAATC
3631331 AATG
131 AATG
3631335 AT
1 AT
3631337 TAAATCAAAC
Statistics
Matches: 125, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
132 11 0.09
133 57 0.46
134 57 0.46
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (134 bp):
ATAATTATTACAAAATTTGATTAACTAGAACGAAATACATTAAAAATATTATTAATATATCTAAC
TAATTTAAAAATAATAGTATTAGAATAAACATAAAAGATTGATTTATCTTTTGATAAAAATAATC
AATG
Found at i:3644405 original size:2 final size:2
Alignment explanation
Indices: 3644398--3644434 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3644388 TTTTCTTCTG
3644398 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 A
3644435 GACAGTCACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3645744 original size:11 final size:11
Alignment explanation
Indices: 3645723--3645751 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3645713 TAATGTTTTG
3645723 ATTAA-TAATA
1 ATTAATTAATA
3645733 ATTAATTAATA
1 ATTAATTAATA
3645744 ATTAATTA
1 ATTAATTA
3645752 TAAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTAATTAATA
Found at i:3649869 original size:88 final size:89
Alignment explanation
Indices: 3649741--3649920 Score: 326
Period size: 88 Copynumber: 2.0 Consensus size: 89
3649731 TACGAATCAT
* *
3649741 TCTCTTTTATATGTAAAAGAACAGATACAACAATGATAAGATAAATTTTAAGTTTATAAATAAGA
1 TCTCTTCTATATGTAAAAGAACAAATACAACAATGATAAGATAAATTTTAAGTTTATAAATAAGA
*
3649806 GTTTTATTCCACTTGATAAATGTA
66 GTTTTATTCCACTTCATAAATGTA
3649830 TCTCTTCTATATGTAAAA-AACAAATACAACAATGATAAGATAAATTTTAAGTTTATAAATAAGA
1 TCTCTTCTATATGTAAAAGAACAAATACAACAATGATAAGATAAATTTTAAGTTTATAAATAAGA
3649894 GTTTTATTCCACTTCATAAATGTA
66 GTTTTATTCCACTTCATAAATGTA
3649918 TCT
1 TCT
3649921 TTTGAATTAA
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
88 71 0.81
89 17 0.19
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (89 bp):
TCTCTTCTATATGTAAAAGAACAAATACAACAATGATAAGATAAATTTTAAGTTTATAAATAAGA
GTTTTATTCCACTTCATAAATGTA
Found at i:3657082 original size:17 final size:17
Alignment explanation
Indices: 3657062--3657095 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3657052 AGAATAAATT
3657062 AATTA-TTAATTATAAAA
1 AATTATTTAATTA-AAAA
3657079 AATTATTTAATTAAAAA
1 AATTATTTAATTAAAAA
3657096 TAAAAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTATTTAATTAAAAA
Found at i:3657083 original size:21 final size:22
Alignment explanation
Indices: 3657057--3657101 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3657047 TTATAAGAAT
**
3657057 AAATTAATT-ATTAATTATAAA
1 AAATTAATTAATTAAAAATAAA
*
3657078 AAATTATTTAATTAAAAATAAA
1 AAATTAATTAATTAAAAATAAA
3657100 AA
1 AA
3657102 TATCAAATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTAATTAATTAAAAATAAA
Found at i:3657893 original size:28 final size:28
Alignment explanation
Indices: 3657862--3658080 Score: 120
Period size: 27 Copynumber: 8.2 Consensus size: 28
3657852 TAATAAATAT
* *
3657862 ATTTTTTAATATGACCTGTAACAACTAA
1 ATTTTTCAATATGACATGTAACAACTAA
* * *
3657890 A-TTTTCAATAT-A-ATGGATAATAATTAC
1 ATTTTTCAATATGACAT-G-TAACAACTAA
* ** * *
3657917 ATTTTTCAACATGATGTGCAATAACTAA
1 ATTTTTCAATATGACATGTAACAACTAA
* * * *
3657945 A-TTTTCAACATGACATCTAACAATTAC
1 ATTTTTCAATATGACATGTAACAACTAA
*
3657972 ATTTTTCAATATGACGTGTAACAACTAA
1 ATTTTTCAATATGACATGTAACAACTAA
* * * *
3658000 ATTTTT-AACATAACATATAACAA-T-T
1 ATTTTTCAATATGACATGTAACAACTAA
* * * *
3658025 A-TATT-AACATGGCATGTAACAA-T-T
1 ATTTTTCAATATGACATGTAACAACTAA
*
3658049 A-TTTTCAATATGACGTGTAACAACTAA
1 ATTTTTCAATATGACATGTAACAACTAA
3658076 ATTTT
1 ATTTT
3658081 AAAACATGAC
Statistics
Matches: 145, Mismatches: 36, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
24 23 0.16
25 16 0.11
26 4 0.03
27 51 0.35
28 48 0.33
29 2 0.01
30 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (28 bp):
ATTTTTCAATATGACATGTAACAACTAA
Found at i:3657911 original size:55 final size:55
Alignment explanation
Indices: 3657852--3658025 Score: 190
Period size: 55 Copynumber: 3.2 Consensus size: 55
3657842 TCATTACGTG
* * * * *
3657852 TAATAAATATATTTTTTAATATGACCTGTAACAACTAAATTTTCAATAT-A-ATGGA
1 TAATAATTACATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATGACAT--A
* * * * *
3657907 TAATAATTACATTTTTCAACATGATGTGCAATAACTAAATTTTCAACATGACATC
1 TAATAATTACATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATGACATA
* * *
3657962 TAACAATTACATTTTTCAATATGACGTGTAACAACTAAATTTTTAACATAACATA
1 TAATAATTACATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATGACATA
*
3658017 TAACAATTA
1 TAATAATTA
3658026 TATTAACATG
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
55 96 0.97
56 1 0.01
57 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.37
Consensus pattern (55 bp):
TAATAATTACATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATGACATA
Found at i:3657955 original size:27 final size:27
Alignment explanation
Indices: 3657884--3657957 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
3657874 GACCTGTAAC
* * *
3657884 AACTAAATTTTCAATATAATGGATAAT
1 AACTAAATTTTCAACATGATGGACAAT
* *
3657911 AATTACATTTTTCAACATGATGTG-CAAT
1 AACTA-AATTTTCAACATGATG-GACAAT
3657939 AACTAAATTTTCAACATGA
1 AACTAAATTTTCAACATGA
3657958 CATCTAACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 17 0.45
28 20 0.53
29 1 0.03
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (27 bp):
AACTAAATTTTCAACATGATGGACAAT
Found at i:3658033 original size:24 final size:24
Alignment explanation
Indices: 3658004--3658050 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3657994 AACTAAATTT
3658004 TTAACATAACATATAACAATTATA
1 TTAACATAACATATAACAATTATA
** *
3658028 TTAACATGGCATGTAACAATTAT
1 TTAACATAACATATAACAATTAT
3658051 TTTCAATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (24 bp):
TTAACATAACATATAACAATTATA
Found at i:3658069 original size:76 final size:78
Alignment explanation
Indices: 3657951--3658102 Score: 220
Period size: 76 Copynumber: 2.0 Consensus size: 78
3657941 CTAAATTTTC
*
3657951 AACATGACATCTAACAATTACATTTTTCAATATGACGTGTAACAACTAAATTTT-TAACATAACA
1 AACATGACATCTAACAATTA-ATTTTTCAATATGACGTGTAACAACTAAATTTTAAAACATAACA
3658015 TATAACAATTATATT
65 TATAAC-ATTATATT
* * * *
3658030 AACATGGCATGTAACAATT-A-TTTTCAATATGACGTGTAACAACTAAATTTTAAAACATGACGT
1 AACATGACATCTAACAATTAATTTTTCAATATGACGTGTAACAACTAAATTTTAAAACATAACAT
3658093 ATAACATTAT
66 ATAACATTAT
3658103 GATAACTTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
76 36 0.54
77 14 0.21
79 17 0.25
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.34
Consensus pattern (78 bp):
AACATGACATCTAACAATTAATTTTTCAATATGACGTGTAACAACTAAATTTTAAAACATAACAT
ATAACATTATATT
Found at i:3660715 original size:31 final size:31
Alignment explanation
Indices: 3660674--3660757 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
3660664 GACTGACAGA
*
3660674 ATGATGTGGTAGTGCCATGTCACCCGACATG
1 ATGACGTGGTAGTGCCATGTCACCCGACATG
*
3660705 ATGACGTGGTAGTACCATGTCACCCGACATG
1 ATGACGTGGTAGTGCCATGTCACCCGACATG
* *
3660736 ATGGCGTGGCAGTGCCATGTCA
1 ATGACGTGGTAGTGCCATGTCA
3660758 TTTTGCCATG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.24
Consensus pattern (31 bp):
ATGACGTGGTAGTGCCATGTCACCCGACATG
Found at i:3661156 original size:6 final size:6
Alignment explanation
Indices: 3661145--3661174 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3661135 AAGGAAACTA
*
3661145 TATAAT TATAAT TATAAT TGTAAT TATAAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT
3661175 ATGAAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
TATAAT
Found at i:3662073 original size:21 final size:21
Alignment explanation
Indices: 3662049--3662102 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
3662039 CTACCAGCAT
*
3662049 CTTCACTTGCACTAGCAACAG
1 CTTCACTTGCACCAGCAACAG
*
3662070 CTTCACTTGGTGCACCAGCAGCAG
1 CTTCAC-T--TGCACCAGCAACAG
3662094 CTTCACTTG
1 CTTCACTTG
3662103 GTGCACCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 8 0.29
22 1 0.04
23 1 0.04
24 18 0.64
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (21 bp):
CTTCACTTGCACCAGCAACAG
Found at i:3662083 original size:24 final size:24
Alignment explanation
Indices: 3662056--3662126 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
3662046 CATCTTCACT
* *
3662056 TGCACTAGCAACAGCTTCACTTGG
1 TGCACCAGCAGCAGCTTCACTTGG
3662080 TGCACCAGCAGCAGCTTCACTTGG
1 TGCACCAGCAGCAGCTTCACTTGG
* *
3662104 TGCACCAGTAGTAGCTTCACTTG
1 TGCACCAGCAGCAGCTTCACTTG
3662127 CTCTACTAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (24 bp):
TGCACCAGCAGCAGCTTCACTTGG
Found at i:3663769 original size:43 final size:43
Alignment explanation
Indices: 3663710--3663840 Score: 174
Period size: 43 Copynumber: 3.0 Consensus size: 43
3663700 TTGTGTGATA
3663710 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
* ** *
3663753 ATGATGACTCAGCTATGTGCACTGTGGGAGTGCACATGAGCAG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
* * **
3663796 ATGATGACCCAGTTATATGCGAGT-AAGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCG-GTGTGGGAGTGCACATGAGCTG
3663839 AT
1 AT
3663841 ATGGTGAGAT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
43 74 0.99
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.24
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
Found at i:3663884 original size:2 final size:2
Alignment explanation
Indices: 3663879--3663905 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3663869 TGTATATATA
3663879 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3663906 TATAGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3668927 original size:63 final size:63
Alignment explanation
Indices: 3668828--3669068 Score: 326
Period size: 63 Copynumber: 3.9 Consensus size: 63
3668818 ACACGATCAT
*
3668828 GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAATTTAGAGAGCTAAGAGAGTTGATGAC
1 GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAATTTAGAGAGCTAAGAGAGCTGATGAC
* *
3668891 GATGGTGCTCAATAGAAAGTTGACAGAGCTGATACAA---AGAGCGCTAAGAGAGCTGATGAC
1 GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAATTTAGAGAGCTAAGAGAGCTGATGAC
* * * * * *
3668951 GATGGTGCTCAATAGAGAGTTGATAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAAT
1 GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAATTTAGAGAGCTAAGAGAGCTGATGAC
* * * * * *
3669014 AATGGTGCTTAACAGAGAGTTGACAGAGCTGATACAGTTTAGAGAGTTGAGAGAG
1 GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAATTTAGAGAGCTAAGAGAG
3669069 TTAAGCAAGC
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
60 56 0.36
63 100 0.64
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.22
Consensus pattern (63 bp):
GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAATTTAGAGAGCTAAGAGAGCTGATGAC
Found at i:3669047 original size:123 final size:123
Alignment explanation
Indices: 3668828--3669049 Score: 345
Period size: 123 Copynumber: 1.8 Consensus size: 123
3668818 ACACGATCAT
* * * * * *
3668828 GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAATTTAGAGAGCTAAGAGAGTTGATGACGA
1 GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAACAA
*
3668893 TGGTGCTCAATAGAAAGTTGACAGAGCTGATACAAAGAGCGCTAAGAGAGCTGATGAC
66 TGGTGCTCAACAGAAAGTTGACAGAGCTGATACAAAGAGCGCTAAGAGAGCTGATGAC
* *
3668951 GATGGTGCTCAATAGAGAGTTGATAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAATAA
1 GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAACAA
* *
3669016 TGGTGCTTAACAGAGAGTTGACAGAGCTGATACA
66 TGGTGCTCAACAGAAAGTTGACAGAGCTGATACA
3669050 GTTTAGAGAG
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
123 88 1.00
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.22
Consensus pattern (123 bp):
GATGGTGCTCAATAGAGAGTTGACAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAACAA
TGGTGCTCAACAGAAAGTTGACAGAGCTGATACAAAGAGCGCTAAGAGAGCTGATGAC
Found at i:3669234 original size:27 final size:27
Alignment explanation
Indices: 3669204--3669303 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 27
3669194 GAGAGTTGAC
3669204 AGAGTTGATACAGTTCAAAGAGCTAAG
1 AGAGTTGATACAGTTCAAAGAGCTAAG
* * * *
3669231 AGAGCTGATAACAATGGTGCTCAACAAAGAGTTGAT
1 AGAGTTGAT-AC-A--GT--T---CAAAGAGCTAAG
3669267 AGAGTTGATACAGTTCAAAGAGCTAAG
1 AGAGTTGATACAGTTCAAAGAGCTAAG
3669294 AGAGTTGATA
1 AGAGTTGATA
3669304 ACAATGGTGC
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
27 27 0.48
28 2 0.04
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 1 0.02
34 1 0.02
35 2 0.04
36 17 0.30
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (27 bp):
AGAGTTGATACAGTTCAAAGAGCTAAG
Found at i:3669259 original size:36 final size:36
Alignment explanation
Indices: 3669219--3669319 Score: 103
Period size: 36 Copynumber: 3.1 Consensus size: 36
3669209 TGATACAGTT
*
3669219 CAAAGAGCTAAGAGAGCTGATAACAATGGTGCTCAA
1 CAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAA
* * *
3669255 CAAAGAGTTGATAGAGTTGAT-AC-A--GT--T---
1 CAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAA
3669282 CAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAA
1 CAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAA
3669318 CA
1 CA
3669320 TAATGTTGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 18
0.66 0.09 0.24
Matches are distributed among these distances:
27 18 0.37
28 2 0.04
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 1 0.02
34 1 0.02
35 2 0.04
36 19 0.39
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.21
Consensus pattern (36 bp):
CAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAA
Found at i:3669361 original size:63 final size:63
Alignment explanation
Indices: 3669195--3669364 Score: 270
Period size: 63 Copynumber: 2.7 Consensus size: 63
3669185 GTATAAATAG
*
3669195 AGAGTTGACAGAGTTGATACAGTTCAAAGAGCTAAGAGAGCTGATAACAATGGTGCTCAACAA
1 AGAGTTGACAGAGTTGATACAGTTCAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAACAA
*
3669258 AGAGTTGATAGAGTTGATACAGTTCAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAACATA
1 AGAGTTGACAGAGTTGATACAGTTCAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAACA-A
* * * *
3669322 A-TGTTGACAAAGTTGATACAGTTCAGAGAGCTGAGAGAGTTGA
1 AGAGTTGACAGAGTTGATACAGTTCAAAGAGCTAAGAGAGTTGA
3669365 GCAAACTAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
63 97 0.98
64 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (63 bp):
AGAGTTGACAGAGTTGATACAGTTCAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAACAA
Found at i:3669457 original size:292 final size:289
Alignment explanation
Indices: 3668901--3669483 Score: 873
Period size: 292 Copynumber: 2.0 Consensus size: 289
3668891 GATGGTGCTC
* * * * *
3668901 AATAGAAAGTTGACAGAGCTGATACAAAGAGCGCTAAGAGAGCTGATGACGATGGTGCTCAATAG
1 AATAGAAAGTTGACAGAGCTGATACAAAGAGAGCTAAGAGAGCTGATAACAATGGTGCTCAACAA
* *
3668966 AGAGTTGATAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAATAATGGTGCTTAACAGAG
66 AGAGTTGATAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAACAATGGTGCTCAACAGAG
* * * * * *
3669031 AGTTGACAGAGCTGATACAGTTTAGAGAGTTGAGAGAGTTAAGCAAGCTGAGTAGCTGAGCATTT
131 AGTTGACAAAGCTGATACAGTTCAGAGAGCTGAGAGAGTTAAGCAAACTAAATAGCTGAGCATTT
* *
3669096 ATTTTCTCTATGACGGGAGGGAGATATCAAGAGATTAATTTGTCAAGATGTTTTTAAAAGTATTT
196 ATTTTCTCTATGACGGGAGAGAGATATCAAGAGATTAATTTGTCAAGATATTTTTAAAAGTATTT
3669161 TGATCTACTCATGTTTGTTTTTGGGTATA
261 TGATCTACTCATGTTTGTTTTTGGGTATA
* *
3669190 AATAGAGAGTTGACAGAGTTGATACAGTTCAA-AGAGCTAAGAGAGCTGATAACAATGGTGCTCA
1 AATAGAAAGTTGACAGAGCTGATACA----AAGAGAGCTAAGAGAGCTGATAACAATGGTGCTCA
* ** *
3669254 ACAAAGAGTTGATAGAGTTGATACAGTTCAAAGAGCTAAGAGAGTTGATAACAATGGTGCTCAAC
62 ACAAAGAGTTGATAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAACAATGGTGCTCAAC
* * *
3669319 ATA-ATGTTGACAAAGTTGATACAGTTCAGAGAGCTGAGAGAGTTGAGCAAACTAAATAGCTGAG
127 AGAGA-GTTGACAAAGCTGATACAGTTCAGAGAGCTGAGAGAGTTAAGCAAACTAAATAGCTGAG
* *
3669383 CATTTATTTTCTTTATGACGGTAGAGAGATATCAAGAGATTAATTTGTCAAGATATTTTTAAAAG
191 CATTTATTTTCTCTATGACGGGAGAGAGATATCAAGAGATTAATTTGTCAAGATATTTTTAAAAG
3669448 TATTTTGATCTACTCATGTTTGTTTTTGGGTATA
256 TATTTTGATCTACTCATGTTTGTTTTTGGGTATA
3669482 AA
1 AA
3669484 CAAATAATTT
Statistics
Matches: 263, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
289 24 0.09
291 1 0.00
292 236 0.90
293 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.30
Consensus pattern (289 bp):
AATAGAAAGTTGACAGAGCTGATACAAAGAGAGCTAAGAGAGCTGATAACAATGGTGCTCAACAA
AGAGTTGATAGAGCTGATACAAATCAAAGAGCTAAGAGAGCTGATAACAATGGTGCTCAACAGAG
AGTTGACAAAGCTGATACAGTTCAGAGAGCTGAGAGAGTTAAGCAAACTAAATAGCTGAGCATTT
ATTTTCTCTATGACGGGAGAGAGATATCAAGAGATTAATTTGTCAAGATATTTTTAAAAGTATTT
TGATCTACTCATGTTTGTTTTTGGGTATA
Found at i:3670150 original size:38 final size:39
Alignment explanation
Indices: 3670081--3670158 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
3670071 TTGGACACGA
3670081 TAAACTTTTTACAGTAGGGTTGGATAAGCATTACAGACTC
1 TAAACTTTTTACAGTA-GGTTGGATAAGCATTACAGACTC
*
3670121 TAAACTTTTTACAGTA-GTTGGATAAGCATTATAGACTC
1 TAAACTTTTTACAGTAGGTTGGATAAGCATTACAGACTC
3670159 CAATAATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 21 0.57
40 16 0.43
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (39 bp):
TAAACTTTTTACAGTAGGTTGGATAAGCATTACAGACTC
Found at i:3674294 original size:7 final size:7
Alignment explanation
Indices: 3674282--3674312 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
3674272 TTTTGTCAAG
3674282 GAAAGAA
1 GAAAGAA
3674289 GAAAGAA
1 GAAAGAA
3674296 GAAAGAA
1 GAAAGAA
3674303 GAAAGGAA
1 GAAA-GAA
3674311 GA
1 GA
3674313 TTCGAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.78
8 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:3679352 original size:207 final size:205
Alignment explanation
Indices: 3678977--3679447 Score: 545
Period size: 207 Copynumber: 2.3 Consensus size: 205
3678967 TTTGTTAGAA
* * * *
3678977 TTTTCAACAAAATTTCATCAAAATATTTTGTTAGAAATTTGTCAAAATTTTGAATAATAAAAATT
1 TTTTGAACGAAATTTCATCAAAATATTTTATTAGAAATTTGTCAAAATTTTGAATATTAAAAATT
* * * * * * * *
3679042 TGTCAGAATTTTGTTAGACAATTGTGGTGCCAATTCCGTTAAACTAGCTTCGTCATCATTTTCAA
66 AGTCAGAATTTTGTCAAAAAATTGCGGTGCCAATTCCATTAAACCAGCTTCATCATCATTTTCAA
* * * * **
3679107 CTAATTTTCAGTTAAAGAATATTTCATTGGAAGATTTTATTAAAAATTCAACAAAATTTCGTTTG
131 CTAATTTTCAATTAAAAAATATTGCATTGGAAGATTTTATTAAAAATACAACAAAATTTCGTTCA
*
3679172 AATT-TTCA-T
196 AATTGCT-ATT
* * * *
3679181 TTTTGGATGAAATTTTATAAAAATATTTTATTAGAAATTTGTCAAAATTTTGAATATTAAAAATT
1 TTTTGAACGAAATTTCATCAAAATATTTTATTAGAAATTTGTCAAAATTTTGAATATTAAAAATT
* *
3679246 CCAGCTCAGAATTTTGTCAAAAAATTGCGGTGCCAATTCCATTAAACCGGCTTTATCATCA-TTT
66 --AG-TCAGAATTTTGTCAAAAAATTGCGGTGCCAATTCCATTAAACCAGCTTCATCATCATTTT
* * *** *
3679310 CTGA-TGAATTTTCAATTAAAAAATATTGCATTGGAGGATTTTATTAAAAATACATTGAAATTTT
128 C-AACT-AATTTTCAATTAAAAAATATTGCATTGGAAGATTTTATTAAAAATACAACAAAATTTC
3679374 GTTCAAATTGCTATT
191 GTTCAAATTGCTATT
* * * *
3679389 TTTTTAACGAAATTTCATCAACATGTTTTATTAGAAATTTGTCAAAATTTCGAATATTA
1 TTTTGAACGAAATTTCATCAAAATATTTTATTAGAAATTTGTCAAAATTTTGAATATTA
3679448 CGAATGTAGA
Statistics
Matches: 221, Mismatches: 39, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
204 57 0.26
206 6 0.03
207 105 0.48
208 53 0.24
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (205 bp):
TTTTGAACGAAATTTCATCAAAATATTTTATTAGAAATTTGTCAAAATTTTGAATATTAAAAATT
AGTCAGAATTTTGTCAAAAAATTGCGGTGCCAATTCCATTAAACCAGCTTCATCATCATTTTCAA
CTAATTTTCAATTAAAAAATATTGCATTGGAAGATTTTATTAAAAATACAACAAAATTTCGTTCA
AATTGCTATT
Found at i:3683809 original size:29 final size:30
Alignment explanation
Indices: 3683777--3683845 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
3683767 TTAAAAAAAT
3683777 TTTAAATAAATTTT-TATTTTTATATTACA
1 TTTAAATAAATTTTGTATTTTTATATTACA
* * *
3683806 TTTAATTAATTTTTTGTATTTTTATTTTACA
1 TTTAAATAA-ATTTTGTATTTTTATATTACA
3683837 -TTAAATAAA
1 TTTAAATAAA
3683846 CTCCTATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 8 0.24
30 11 0.33
31 14 0.42
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTAAATAAATTTTGTATTTTTATATTACA
Found at i:3689409 original size:12 final size:12
Alignment explanation
Indices: 3689394--3689425 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3689384 CGACCTTTTC
*
3689394 TACGACCATGAT
1 TACGACCACGAT
3689406 TACGACCACGAT
1 TACGACCACGAT
3689418 TACGACCA
1 TACGACCA
3689426 AGACCACGGC
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:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (12 bp):
TACGACCACGAT
Found at i:3691113 original size:24 final size:23
Alignment explanation
Indices: 3691069--3691114 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3691059 ATATATTGAA
* * *
3691069 ATATTTTTTCTAATTTTTTTAAG
1 ATATGTTTTCTAATCTCTTTAAG
3691092 ATATGTTTTCTCAATCTCTTTAA
1 ATATGTTTTCT-AATCTCTTTAA
3691115 TAAAGAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (23 bp):
ATATGTTTTCTAATCTCTTTAAG
Found at i:3691239 original size:41 final size:41
Alignment explanation
Indices: 3691179--3691260 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
3691169 AACTTACTTT
3691179 TAATGGAAGAAGAAAAGAAGAAGATGATGGAGTTGGAGAGA
1 TAATGGAAGAAGAAAAGAAGAAGATGATGGAGTTGGAGAGA
**
3691220 TAATGGAAGAAGAGGAGAAGAAGATGATGGAGTTGGAGAGA
1 TAATGGAAGAAGAAAAGAAGAAGATGATGGAGTTGGAGAGA
3691261 GATAAACGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.46, C:0.00, G:0.39, T:0.15
Consensus pattern (41 bp):
TAATGGAAGAAGAAAAGAAGAAGATGATGGAGTTGGAGAGA
Found at i:3695803 original size:2 final size:2
Alignment explanation
Indices: 3695796--3695848 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
3695786 TATCCAAATC
3695796 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3695837 TA TA TA TA TA TA
1 TA TA TA TA TA TA
3695849 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3695896 original size:2 final size:2
Alignment explanation
Indices: 3695889--3695940 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3695879 NNNNNNNNNN
3695889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3695931 TA TA TA TA TA
1 TA TA TA TA TA
3695941 ATCAAATCTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3698574 original size:7 final size:6
Alignment explanation
Indices: 3698538--3698573 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
3698528 AAAATCAACC
3698538 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAA
3698574 AGAGGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:3699161 original size:11 final size:12
Alignment explanation
Indices: 3699132--3699175 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
3699122 GAGTGGCTAG
* *
3699132 GAAAGAGAAGAA
1 GAAAGAAAAAAA
3699144 GAAAGAAAAAAA
1 GAAAGAAAAAAA
3699156 -AAAGAAAAAAA
1 GAAAGAAAAAAA
3699167 GAAAGAAAA
1 GAAAGAAAA
3699176 GGATTTGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
GAAAGAAAAAAA
Found at i:3699483 original size:21 final size:20
Alignment explanation
Indices: 3699456--3699591 Score: 77
Period size: 20 Copynumber: 6.7 Consensus size: 20
3699446 ATGGAAAATG
3699456 AAAATAAATAATAATAATAA
1 AAAATAAATAATAATAATAA
* *
3699476 ATAAATAAATGATAATATTAA
1 A-AAATAAATAATAATAATAA
*
3699497 AAAAT-CATAATACA-AATATA
1 AAAATAAATAATA-ATAATA-A
* *
3699517 AAAAT-TATAAAAAGTAA-AA
1 AAAATAAATAATAA-TAATAA
* *
3699536 ATAAAT-TATGAAGAATAATAA
1 A-AAATAAAT-AATAATAATAA
* *
3699557 AGAAATAAA-AAAAATAAGAA
1 A-AAATAAATAATAATAATAA
3699577 AAAATATAATAATAA
1 AAAATA-AATAATAA
3699592 ATATAATAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
19 16 0.17
20 40 0.43
21 35 0.38
22 1 0.01
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAATAAATAATAATAATAA
Found at i:3699593 original size:12 final size:12
Alignment explanation
Indices: 3699549--3699604 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
3699539 AATTATGAAG
*
3699549 AATAATAAAGA-
1 AATAATAAATAT
* *
3699560 AATAAAAAAAAT
1 AATAATAAATAT
* *
3699572 AAGAAAAAATAT
1 AATAATAAATAT
3699584 AATAATAAATAT
1 AATAATAAATAT
3699596 AATAATAAA
1 AATAATAAA
3699605 AAGAAGTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:3699603 original size:39 final size:41
Alignment explanation
Indices: 3699560--3699638 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 41
3699550 ATAATAAAGA
*
3699560 AATAAAAA-AA-ATAAG-AAAAAATATAATAATAAATATAAT
1 AATAAAAAGAAGAGAAGTAAAAAATA-AATAATAAATATAAT
*
3699599 AATAAAAAGAAGTAGAAGTAATAAATAAATAATAAATATA
1 AATAAAAAGAAG-AGAAGTAAAAAATAAATAATAAATATA
3699639 CATTTTTGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 8 0.24
40 2 0.06
42 17 0.50
43 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (41 bp):
AATAAAAAGAAGAGAAGTAAAAAATAAATAATAAATATAAT
Found at i:3702967 original size:14 final size:14
Alignment explanation
Indices: 3702930--3702967 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3702920 TTAAGAACAT
*
3702930 ACTTTTTTTTATTC
1 ACTTTTTTCTATTC
3702944 -CTTTTATTCTATTC
1 ACTTTT-TTCTATTC
3702958 ACTTTTTTCT
1 ACTTTTTTCT
3702968 TTTTCTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 5 0.24
14 11 0.52
15 5 0.24
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.68
Consensus pattern (14 bp):
ACTTTTTTCTATTC
Found at i:3703021 original size:28 final size:28
Alignment explanation
Indices: 3702988--3703047 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
3702978 TCTCTTTATT
* * **
3702988 ATTCATCCATTCTTAATGGGTTAAAAGC
1 ATTCATCCACTCCTAATAAGTTAAAAGC
*
3703016 ATTCATCCACTCCTAATAAGTTAAAAGT
1 ATTCATCCACTCCTAATAAGTTAAAAGC
3703044 ATTC
1 ATTC
3703048 TTATTATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (28 bp):
ATTCATCCACTCCTAATAAGTTAAAAGC
Found at i:3704265 original size:25 final size:23
Alignment explanation
Indices: 3704211--3704253 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3704201 CTATAAATAT
*
3704211 CATCTTCCAGCAGCTTCTTCTCA
1 CATCTTTCAGCAGCTTCTTCTCA
3704234 CAT-TTTCAGCAGCTTCTTCT
1 CATCTTTCAGCAGCTTCTTCT
3704254 TCTTCTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.16, C:0.35, G:0.09, T:0.40
Consensus pattern (23 bp):
CATCTTTCAGCAGCTTCTTCTCA
Found at i:3705024 original size:2 final size:2
Alignment explanation
Indices: 3705017--3705065 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3705007 CATGATGATG
3705017 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3705059 TA TA TA T
1 TA TA TA T
3705066 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3705676 original size:19 final size:19
Alignment explanation
Indices: 3705640--3705676 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3705630 TTTTAGAGAA
*
3705640 AAACCCTCGGCCAGTTGAG
1 AAACCCTCGGCCAATTGAG
*
3705659 AAACCCTCGTCCAATTGA
1 AAACCCTCGGCCAATTGA
3705677 TAATTTGAGC
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:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (19 bp):
AAACCCTCGGCCAATTGAG
Found at i:3706596 original size:17 final size:17
Alignment explanation
Indices: 3706558--3706598 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
3706548 TGGATAGATT
3706558 AAATCTTAATCTTAATCC
1 AAATC-TAATCTTAATCC
3706576 -AATCTAATC-TATATCC
1 AAATCTAATCTTA-ATCC
3706592 AAATCTA
1 AAATCTA
3706599 GTTATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 9 0.43
17 10 0.48
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATCTAATCTTAATCC
Found at i:3706596 original size:118 final size:118
Alignment explanation
Indices: 3706388--3706615 Score: 339
Period size: 118 Copynumber: 1.9 Consensus size: 118
3706378 CTTTATCTTG
* * * * *
3706388 ATAGAATTTACAAGATAAAGATAACATTTAGGGGATTTGATTTGGATGGATTAAATTTTGATATT
1 ATAGAATTTACAAGATAAAGATAACACTTAAGGGATTTGATTTGGATAGATTAAATCTTAATATT
* *
3706453 AATCCAATTTAATTTATATCCAAATCTAGATATATATAATAAAATCTATCAAA
66 AATCCAATCTAATCTATATCCAAATCTAGATATATATAATAAAATCTATCAAA
* * *
3706506 ATAGAATTTGCAAGATAAAGATAATACTTAAGGGATTTGATTTGGATAGATTAAATCTTAATCTT
1 ATAGAATTTACAAGATAAAGATAACACTTAAGGGATTTGATTTGGATAGATTAAATCTTAATATT
* * *
3706571 AATCCAATCTAATCTATATCCAAATCTAGTTATTTATAATTAAAT
66 AATCCAATCTAATCTATATCCAAATCTAGATATATATAATAAAAT
3706616 GTAAGAGTTC
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
118 97 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (118 bp):
ATAGAATTTACAAGATAAAGATAACACTTAAGGGATTTGATTTGGATAGATTAAATCTTAATATT
AATCCAATCTAATCTATATCCAAATCTAGATATATATAATAAAATCTATCAAA
Found at i:3708653 original size:28 final size:28
Alignment explanation
Indices: 3708574--3708655 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 28
3708564 CTGATAATGA
3708574 ATTTTA-TATATATTATTTATATTAAATTTT
1 ATTTTATTATA-ATTATTTATA-T-AATTTT
* *
3708604 ATTGTATT-TAA-TA-TTCT-T-ATTTT
1 ATTTTATTATAATTATTTATATAATTTT
*
3708627 ATTTTATTATAATTATTTTTATAATTTT
1 ATTTTATTATAATTATTTATATAATTTT
3708655 A
1 A
3708656 AATTTTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
23 12 0.29
24 3 0.07
25 3 0.07
26 3 0.07
27 4 0.10
28 8 0.19
29 1 0.02
30 7 0.17
31 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (28 bp):
ATTTTATTATAATTATTTATATAATTTT
Found at i:3708705 original size:20 final size:20
Alignment explanation
Indices: 3708623--3708712 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 20
3708613 AATATTCTTA
* *
3708623 TTTTATTTTATTATAATTAT
1 TTTTATTTAATTATAAATAT
*
3708643 TTTTA--TAATTTTAAAT-T
1 TTTTATTTAATTATAAATAT
**
3708660 TTAAATTTAA--A-AAATAAAT
1 TTTTATTTAATTATAAAT--AT
*
3708679 TTATATTTAATTATAAATAT
1 TTTTATTTAATTATAAATAT
3708699 TTTTATTTAATTAT
1 TTTTATTTAATTAT
3708713 TAATCGTATC
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
16 4 0.07
17 4 0.07
18 8 0.15
19 13 0.24
20 20 0.37
21 1 0.02
22 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATTTAATTATAAATAT
Found at i:3713519 original size:14 final size:14
Alignment explanation
Indices: 3713481--3713520 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3713471 GTTTATAACC
3713481 AAAGCCCAAAGCAT
1 AAAGCCCAAAGCAT
**
3713495 AAAGCATAAAGCAT
1 AAAGCCCAAAGCAT
*
3713509 AGAGCCCAAAGC
1 AAAGCCCAAAGC
3713521 CCAAGCCCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.25, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAGCCCAAAGCAT
Found at i:3717077 original size:25 final size:27
Alignment explanation
Indices: 3717036--3717103 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
3717026 TTATAACGGT
* *
3717036 AAAATGGT-CATTTGACC-AAAA-GGC
1 AAAATGGTAAATTTGACCAAAAATGGA
3717060 AAAATGGTAAATTTGACCAAAAATGGA
1 AAAATGGTAAATTTGACCAAAAATGGA
3717087 AAAATGGTAAATTTGAC
1 AAAATGGTAAATTTGAC
3717104 TATATTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
24 8 0.21
25 8 0.21
26 4 0.10
27 19 0.49
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (27 bp):
AAAATGGTAAATTTGACCAAAAATGGA
Found at i:3721011 original size:15 final size:15
Alignment explanation
Indices: 3720970--3721013 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
3720960 ACTGTACAAT
**
3720970 GTAATGTGATTATAG
1 GTAATGTGATTGCAG
3720985 GTAATGTGATTGCAG
1 GTAATGTGATTGCAG
3721000 GTAATGTGATTGCA
1 GTAATGTGATTGCA
3721014 AACAATGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.36
Consensus pattern (15 bp):
GTAATGTGATTGCAG
Found at i:3721020 original size:15 final size:15
Alignment explanation
Indices: 3720987--3721025 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3720977 GATTATAGGT
***
3720987 AATGTGATTGCAGGT
1 AATGTGATTGCAAAC
3721002 AATGTGATTGCAAAC
1 AATGTGATTGCAAAC
3721017 AATGTGATT
1 AATGTGATT
3721026 ATAGGGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAAAC
Found at i:3725178 original size:26 final size:26
Alignment explanation
Indices: 3725098--3725350 Score: 108
Period size: 26 Copynumber: 10.6 Consensus size: 26
3725088 ATTCTTTACT
3725098 AACTAGTCACGCAATGGC--TATC---
1 AACTAGTCACGCAAT-GCTTTATCAAA
*
3725120 AACTAGTCACGCAATGCTTTATCAGA
1 AACTAGTCACGCAATGCTTTATCAAA
* * *
3725146 AATTAGTTACGCAATGCTTTATTAAA
1 AACTAGTCACGCAATGCTTTATCAAA
*
3725172 AACTAGTCACGTAATG---T-TCAAA
1 AACTAGTCACGCAATGCTTTATCAAA
** * *
3725194 GTC-AGTCACGTAATGC-CTATC---
1 AACTAGTCACGCAATGCTTTATCAAA
* * * *
3725215 AACTATTCACGTAATAAC-TTATCAGA
1 AACTAGTCACGCAAT-GCTTTATCAAA
* *
3725241 AACTAATCACGTAATG-TCTTATCAAA
1 AACTAGTCACGCAATGCT-TTATCAAA
*
3725267 AACTAGTCACGCAATGC----CCAAA
1 AACTAGTCACGCAATGCTTTATCAAA
** *
3725289 GTC-AGTCACGCAATGC-CTATC---
1 AACTAGTCACGCAATGCTTTATCAAA
3725310 AACTAGTCACGCAATGAC-TTATCAAA
1 AACTAGTCACGCAATG-CTTTATCAAA
*
3725336 AACTAGTCACACAAT
1 AACTAGTCACGCAAT
3725351 ATTCAAAGTC
Statistics
Matches: 179, Mismatches: 28, Indels: 44
0.71 0.11 0.18
Matches are distributed among these distances:
21 29 0.16
22 47 0.26
23 16 0.09
24 3 0.02
26 84 0.47
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (26 bp):
AACTAGTCACGCAATGCTTTATCAAA
Found at i:3725268 original size:95 final size:94
Alignment explanation
Indices: 3725102--3725350 Score: 320
Period size: 95 Copynumber: 2.6 Consensus size: 94
3725092 TTTACTAACT
* * * *
3725102 AGTCACGCAATGGCTATCAACTAGTCACGCAATGCTTTATCAGAAATTAGTTACGCAATGCTTTA
1 AGTCACGCAATGCCTATCAACTAGTCACGCAATAC-TTATCAGAAACTAGTCACGCAATGCTTTA
* * **
3725167 TTAAAAACTAGTCACGTAATGTTCAAAGTC
65 TCAAAAACTAGTCACGCAATGCCCAAAGTC
* * * * *
3725197 AGTCACGTAATGCCTATCAACTATTCACGTAATAACTTATCAGAAACTAATCACGTAATG-TCTT
1 AGTCACGCAATGCCTATCAACTAGTCACGCAAT-ACTTATCAGAAACTAGTCACGCAATGCT-TT
3725261 ATCAAAAACTAGTCACGCAATGCCCAAAGTC
64 ATCAAAAACTAGTCACGCAATGCCCAAAGTC
* *
3725292 AGTCACGCAATGCCTATCAACTAGTCACGCAATGACTTATCAAAAACTAGTCACACAAT
1 AGTCACGCAATGCCTATCAACTAGTCACGCAAT-ACTTATCAGAAACTAGTCACGCAAT
3725351 ATTCAAAGTC
Statistics
Matches: 131, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
94 1 0.01
95 129 0.98
96 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (94 bp):
AGTCACGCAATGCCTATCAACTAGTCACGCAATACTTATCAGAAACTAGTCACGCAATGCTTTAT
CAAAAACTAGTCACGCAATGCCCAAAGTC
Found at i:3725314 original size:69 final size:70
Alignment explanation
Indices: 3725241--3725381 Score: 212
Period size: 69 Copynumber: 2.0 Consensus size: 70
3725231 ACTTATCAGA
* * * *
3725241 AACTAATCACGTAATGTCTTATCAAAAACTAGTCACGCAATGCCCAAAGTCAGTCACGCAATGCC
1 AACTAATCACGCAATGACTTATCAAAAACTAGTCACACAATACCCAAAGTCAGTCACGCAATGCC
3725306 -TATC
66 TTATC
* **
3725310 AACTAGTCACGCAATGACTTATCAAAAACTAGTCACACAATATTCAAAGTCAGTCACGCAATGCC
1 AACTAATCACGCAATGACTTATCAAAAACTAGTCACACAATACCCAAAGTCAGTCACGCAATGCC
3725375 TTATC
66 TTATC
3725380 AA
1 AA
3725382 AAACCAAGCA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 58 0.91
70 6 0.09
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.23
Consensus pattern (70 bp):
AACTAATCACGCAATGACTTATCAAAAACTAGTCACACAATACCCAAAGTCAGTCACGCAATGCC
TTATC
Found at i:3725546 original size:15 final size:15
Alignment explanation
Indices: 3725526--3725554 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3725516 GGGAATAAAA
3725526 ACCAAAAATTGCAAT
1 ACCAAAAATTGCAAT
3725541 ACCAAAAATTGCAA
1 ACCAAAAATTGCAA
3725555 CCAAACACGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (15 bp):
ACCAAAAATTGCAAT
Found at i:3725559 original size:13 final size:14
Alignment explanation
Indices: 3725524--3725559 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
3725514 GAGGGAATAA
3725524 AAACCAAAAATTGC
1 AAACCAAAAATTGC
3725538 AATACCAAAAATTGC
1 AA-ACCAAAAATTGC
3725553 -AACCAAA
1 AAACCAAA
3725560 CACGCAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 3 0.14
15 12 0.57
ACGTcount: A:0.58, C:0.22, G:0.06, T:0.14
Consensus pattern (14 bp):
AAACCAAAAATTGC
Found at i:3734055 original size:70 final size:72
Alignment explanation
Indices: 3733939--3734078 Score: 205
Period size: 70 Copynumber: 2.0 Consensus size: 72
3733929 ATGTGCCATA
* **
3733939 TAGGCTAAAGTCTCCCATTAGAAAGAGTAGTACTTTTTAGTTATGCATTG-CCTTAACAAATCTC
1 TAGGCTAAAGTCTCCCATCAG-AAGAGTAGTACTTTACAGTTATGCATTGTCC-TAACAAATCTC
3734003 AAACTTATT
64 AAACTTATT
*
3734012 TAGGCTGAAGTCTCCCATCAG-A-AGTAGTACTTTACAGTTATGCATTGTCCTAACAAATCTCAA
1 TAGGCTAAAGTCTCCCATCAGAAGAGTAGTACTTTACAGTTATGCATTGTCCTAACAAATCTCAA
3734075 ACTT
66 ACTT
3734079 TTATCAATTG
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
70 40 0.65
71 3 0.05
73 19 0.31
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (72 bp):
TAGGCTAAAGTCTCCCATCAGAAGAGTAGTACTTTACAGTTATGCATTGTCCTAACAAATCTCAA
ACTTATT
Found at i:3744906 original size:2 final size:2
Alignment explanation
Indices: 3744899--3744935 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3744889 CAGTCAGGTT
3744899 TA TA TA 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 TA TA TA T
3744936 NGATTCATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3744979 original size:69 final size:68
Alignment explanation
Indices: 3744868--3745005 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 68
3744858 AATAGTTTAA
3744868 GATTCATGCAAGTTCTTGCTTCAGTCAGGTTTATATATATATATATATATATATATATATATATA
1 GATTCATGCAAGTTCTTGCTTCAGTCAGGTTTATATATATATATATATATATATATATATATATA
3744933 TAT
66 TAT
3744936 NGATTCATGCAAGTTCTTGCTTCAGTCAGG-TTAGTATATATATATATATATATATATATATATA
1 -GATTCATGCAAGTTCTTGCTTCAGTCAGGTTTA-TATATATATATATATATATATATATATATA
3745000 TATAT
64 TATAT
3745005 G
1 G
3745006 CTCAGCTACA
Statistics
Matches: 68, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
68 4 0.06
69 64 0.94
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (68 bp):
GATTCATGCAAGTTCTTGCTTCAGTCAGGTTTATATATATATATATATATATATATATATATATA
TAT
Found at i:3745020 original size:2 final size:2
Alignment explanation
Indices: 3744970--3745004 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3744960 GTCAGGTTAG
3744970 TA TA 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 TA TA T
3745005 GCTCAGCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3745805 original size:2 final size:2
Alignment explanation
Indices: 3745798--3745838 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3745788 TTATTTTATT
3745798 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3745839 ATCATATATA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3760357 original size:19 final size:20
Alignment explanation
Indices: 3760330--3760375 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3760320 AGGAGACAAG
*
3760330 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
3760349 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
3760368 ATAATATT
1 ATAATATT
3760376 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:3760822 original size:20 final size:20
Alignment explanation
Indices: 3760777--3760814 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3760767 TTTTGGCCCC
3760777 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
3760797 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
3760815 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:3760898 original size:27 final size:27
Alignment explanation
Indices: 3760868--3760924 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
3760858 TTGGAGTAAA
*
3760868 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGGTAATTTT-CCACCACC
*
3760895 AGGGGCAAAATTGTAATTTTCCACCACC
1 A-GGGCAAAATGGTAATTTTCCACCACC
3760923 AG
1 AG
3760925 AACATTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACC
Found at i:3766873 original size:15 final size:14
Alignment explanation
Indices: 3766851--3766888 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
3766841 CCAGCTGTTG
3766851 CCTTCTTTGATTTT
1 CCTTCTTTGATTTT
*
3766865 CCTTTCTTTAATTTT
1 CC-TTCTTTGATTTT
3766880 CCTTCTTTG
1 CCTTCTTTG
3766889 TTCGCTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.08, C:0.24, G:0.05, T:0.63
Consensus pattern (14 bp):
CCTTCTTTGATTTT
Found at i:3773134 original size:27 final size:27
Alignment explanation
Indices: 3773104--3773164 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
3773094 TAAAAAATTG
* *
3773104 ATAATATCTTAAAATAATACTTTATTA
1 ATAAAATCTTAAAATAATACTTTATCA
* *
3773131 ATAAAATTTTAAAATAATATTTTATCA
1 ATAAAATCTTAAAATAATACTTTATCA
3773158 ATAAAAT
1 ATAAAAT
3773165 ATCAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (27 bp):
ATAAAATCTTAAAATAATACTTTATCA
Found at i:3773152 original size:13 final size:13
Alignment explanation
Indices: 3773104--3773154 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
3773094 TAAAAAATTG
*
3773104 ATAATATCTTAAA
1 ATAATATTTTAAA
* *
3773117 ATAATACTTTATTA
1 ATAATATTTTA-AA
*
3773131 ATAAAATTTTAAA
1 ATAATATTTTAAA
3773144 ATAATATTTTA
1 ATAATATTTTA
3773155 TCAATAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAATATTTTAAA
Found at i:3773171 original size:27 final size:27
Alignment explanation
Indices: 3773114--3773172 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
3773104 ATAATATCTT
* * *
3773114 AAAATAATACTTTATTAATAAAATTTT
1 AAAATAATACTTTATCAATAAAATATC
*
3773141 AAAATAATATTTTATCAATAAAATATC
1 AAAATAATACTTTATCAATAAAATATC
3773168 AAAAT
1 AAAAT
3773173 TTGATGACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
AAAATAATACTTTATCAATAAAATATC
Found at i:3779415 original size:23 final size:23
Alignment explanation
Indices: 3779389--3779434 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3779379 ATACAATAAC
3779389 CTTATCATAATATAATTAGGAAT
1 CTTATCATAATATAATTAGGAAT
*
3779412 CTTATCTTAATATAATTAGGAAT
1 CTTATCATAATATAATTAGGAAT
3779435 TGTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
CTTATCATAATATAATTAGGAAT
Found at i:3783224 original size:23 final size:24
Alignment explanation
Indices: 3783197--3783253 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
3783187 TACAATGATC
* *
3783197 TTATCCTAATATAATTAGGAA-TA
1 TTATCCTAATAGAATTAAGAATTA
3783220 TTATCCTAATAGAATTAAGAATTA
1 TTATCCTAATAGAATTAAGAATTA
*
3783244 TTATTCTAAT
1 TTATCCTAAT
3783254 CTAACTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (24 bp):
TTATCCTAATAGAATTAAGAATTA
Found at i:3786636 original size:27 final size:29
Alignment explanation
Indices: 3786599--3786664 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 29
3786589 ATTAATATTT
*
3786599 AAATGATAAATTATTAATA-TT-ATAAATA
1 AAAT-ATAAATTATTAATATTTAAAAAATA
3786627 AAATATAAATTATTAATATTTAAAAAATA
1 AAATATAAATTATTAATATTTAAAAAATA
3786656 AAATA-AAAT
1 AAATATAAAT
3786665 AAAAATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 14 0.40
28 10 0.29
29 11 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATATAAATTATTAATATTTAAAAAATA
Found at i:3786720 original size:131 final size:129
Alignment explanation
Indices: 3786497--3786826 Score: 379
Period size: 131 Copynumber: 2.7 Consensus size: 129
3786487 TAATCAATTA
*
3786497 TTAATATT-T-AA-AAAATATAAATTATTAATATTTAAAAGATAAAATTAAATAAAAATAAATAA
1 TTAATATTATAAATAAAATATAAATTATTAATATTTAAAA-ATAAAATAAAATAAAAATAAATAA
* *
3786559 TC---AT-A-A--T--A--AA-GTTTAAATTATAAATAAAATATTAATATTTAAA-TGATAAAT-
65 TCAGAATAACATTTAAATTAATGATTAAAGTATAAATAAAATATTAATATTTAAACT-ATAAATG
3786610 T
129 T
3786611 ATTAATATTATAAATAAAATATAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAATA
1 -TTAATATTATAAATAAAATATAAATTATTAATATTT-AAAAATAAAATAAAATAAAAATAAATA
* *
3786676 ATCATAATAACATTTAATATTAATGATTAAAGTATAAATAAAATATTAATATTTAAACTATCAAT
64 ATCAGAATAACATTTAA-ATTAATGATTAAAGTATAAATAAAATATTAATATTTAAACTATAAAT
3786741 GT
128 GT
* * * * * **
3786743 TTAGTATTTTAAATAAATTATACATTATTAATGTTTAAAAATAAAATAATTTAAAAATAAATAAT
1 TTAATATTATAAATAAAATATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAATAAT
*
3786808 CAGACTAACATTTAAATTA
66 CAGAATAACATTTAAATTA
3786827 TAAATAAAAT
Statistics
Matches: 183, Mismatches: 13, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
115 8 0.04
116 1 0.01
117 2 0.01
118 47 0.26
119 4 0.02
121 2 0.01
122 1 0.01
123 1 0.01
125 1 0.01
128 1 0.01
129 4 0.02
130 42 0.23
131 67 0.37
132 2 0.01
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (129 bp):
TTAATATTATAAATAAAATATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAATAAT
CAGAATAACATTTAAATTAATGATTAAAGTATAAATAAAATATTAATATTTAAACTATAAATGT
Found at i:3786804 original size:15 final size:16
Alignment explanation
Indices: 3786776--3786807 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3786766 ATTATTAATG
3786776 TTTAAAAATAAAATAA
1 TTTAAAAATAAAATAA
3786792 TTTAAAAAT-AAATAA
1 TTTAAAAATAAAATAA
3786807 T
1 T
3786808 CAGACTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTAAAAATAAAATAA
Found at i:3786849 original size:22 final size:22
Alignment explanation
Indices: 3786824--3786901 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
3786814 AACATTTAAA
3786824 TTATAAATAAAATATTAGTATT
1 TTATAAATAAAATATTAGTATT
**
3786846 TTAT-AATGTTAATGATTAG-A--
1 TTATAAAT-AAAAT-ATTAGTATT
*
3786866 TTATAAATAAAATATTAATATT
1 TTATAAATAAAATATTAGTATT
* *
3786888 TAAAAAATAAAATA
1 TTATAAATAAAATA
3786902 AAATAATCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
19 4 0.09
20 8 0.19
21 6 0.14
22 20 0.47
23 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
TTATAAATAAAATATTAGTATT
Found at i:3787395 original size:25 final size:25
Alignment explanation
Indices: 3787331--3787395 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
3787321 AGGATTTTAG
* * *
3787331 TGTTTATATAATATTTCAGCTATAA
1 TGTTTATATAATGTTTCAGATACAA
*
3787356 TGTTTATATAGTGTTTCA-ATAGCAA
1 TGTTTATATAATGTTTCAGATA-CAA
3787381 TGTTTATATAATGTT
1 TGTTTATATAATGTT
3787396 GATAATAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 2 0.06
25 32 0.94
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.49
Consensus pattern (25 bp):
TGTTTATATAATGTTTCAGATACAA
Found at i:3790625 original size:21 final size:22
Alignment explanation
Indices: 3790596--3790644 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
3790586 AGAAACTTTT
*
3790596 GTTTGAAT-CTTCTAATGTAAA
1 GTTTAAATCCTTCTAATGTAAA
* *
3790617 GTTTAAATCCTTTTAATTTAAA
1 GTTTAAATCCTTCTAATGTAAA
3790639 GTTTAA
1 GTTTAA
3790645 CAAATTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (22 bp):
GTTTAAATCCTTCTAATGTAAA
Found at i:3791538 original size:108 final size:111
Alignment explanation
Indices: 3791414--3791668 Score: 356
Period size: 113 Copynumber: 2.3 Consensus size: 111
3791404 CTTTTTCGAG
* ** *
3791414 GATGAGTAAATACAAATTTTAACTCTTTCTCTCCC-AGATTTCATTTAAAAATTT-GTTTTTGTT
1 GATGAGAAAATACAAATTTTAACTAATTCTC-CCCTAGATTTCATTCAAAAATTTGGTTTTTGTT
* *
3791477 TCTTTAAATTTAACACCCTTTGCA-TT-ACTTTGCATTTTGTAAAGT
65 TCTTTAAATCTAACACCCCTTGCATTTAACTTTGCATTTTGTAAAGT
* *
3791522 GATGAGAAAATTCAAATTTTAACTAATTCTCCCCTTGATTTCATTCAAAAATTTGGTTTTTGTTT
1 GATGAGAAAATACAAATTTTAACTAATTCTCCCCTAGATTTCATTCAAAAATTTGGTTTTTGTTT
*
3791587 CTTTAAATCTAACACCCCTTGCATTTAAAACTTTGCTTTTTGTAAAGT
66 CTTTAAATCTAACACCCCTTGCATTT--AACTTTGCATTTTGTAAAGT
* *
3791635 GACGAGCAAATACAAATTTTAACTAATTCTCCCC
1 GATGAGAAAATACAAATTTTAACTAATTCTCCCC
3791669 CATTTTGTCA
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
107 3 0.02
108 44 0.34
109 31 0.24
110 2 0.02
113 49 0.38
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (111 bp):
GATGAGAAAATACAAATTTTAACTAATTCTCCCCTAGATTTCATTCAAAAATTTGGTTTTTGTTT
CTTTAAATCTAACACCCCTTGCATTTAACTTTGCATTTTGTAAAGT
Found at i:3802046 original size:11 final size:11
Alignment explanation
Indices: 3802027--3802058 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
3802017 TAAAAAAATC
3802027 AAAATAAAAAAG
1 AAAA-AAAAAAG
3802039 AAAAAAAAAAG
1 AAAAAAAAAAG
3802050 AAAAAAAAA
1 AAAAAAAAA
3802059 GAGTCAGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Done.