Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007777.1 Hibiscus syriacus cultivar Beakdansim tig00110059_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1720799
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1549564 original size:13 final size:12
Alignment explanation
Indices: 1549543--1549591 Score: 80
Period size: 13 Copynumber: 3.9 Consensus size: 12
1549533 GTAGGTAATA
1549543 ATTATTATTATT
1 ATTATTATTATT
1549555 ATTAATTATTATT
1 ATT-ATTATTATT
1549568 ATTATTAATTATT
1 ATTATT-ATTATT
1549581 ATTATTATTAT
1 ATTATTATTAT
1549592 ATTTTTTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.31
13 24 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTATTATTATT
Found at i:1549565 original size:19 final size:20
Alignment explanation
Indices: 1549538--1549591 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1549528 AGTGGGTAGG
*
1549538 TAATAATTATTATTATT-AT
1 TAATTATTATTATTATTAAT
1549557 TAATTATTATTATTATTAAT
1 TAATTATTATTATTATTAAT
1549577 T-ATTATTATTATTAT
1 TAATTATTATTATTAT
1549592 ATTTTTTCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 30 0.91
20 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATTATTATTATTATTAAT
Found at i:1550002 original size:46 final size:47
Alignment explanation
Indices: 1549908--1550000 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
1549898 AGAATTTTAG
* ****
1549908 TAAATTC-AATTTTTTTAATTCAAATATTTGTCATATAATAAAATTT
1 TAAATTCAAATTTTTATAATTCAAATATCCAACATATAATAAAATTT
* *
1549954 TAAATTCAAATTTTTATAATTCAGATATCCAACATATAATAATATTT
1 TAAATTCAAATTTTTATAATTCAAATATCCAACATATAATAAAATTT
1550001 AATTTAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 7 0.18
47 32 0.82
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (47 bp):
TAAATTCAAATTTTTATAATTCAAATATCCAACATATAATAAAATTT
Found at i:1550620 original size:13 final size:13
Alignment explanation
Indices: 1550580--1550621 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
1550570 TAGTTTGACC
1550580 AACTGATTTGATT
1 AACTGATTTGATT
*
1550593 AATTGATTTGA--
1 AACTGATTTGATT
1550604 AACTGATTTGATT
1 AACTGATTTGATT
1550617 AACTG
1 AACTG
1550622 TTTATATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 10 0.40
13 15 0.60
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (13 bp):
AACTGATTTGATT
Found at i:1552430 original size:21 final size:21
Alignment explanation
Indices: 1552404--1552443 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1552394 ACTTAACAAT
1552404 GATAATGA-CATATCATCATAA
1 GATAAT-ACCATATCATCATAA
1552425 GATAATACCATATCATCAT
1 GATAATACCATATCATCAT
1552444 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (21 bp):
GATAATACCATATCATCATAA
Found at i:1553046 original size:14 final size:14
Alignment explanation
Indices: 1553027--1553056 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1553017 TTTAGATTTT
*
1553027 TTAAAATTACATTA
1 TTAAAAATACATTA
1553041 TTAAAAATACATTA
1 TTAAAAATACATTA
1553055 TT
1 TT
1553057 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:1553149 original size:7 final size:7
Alignment explanation
Indices: 1553137--1553303 Score: 108
Period size: 7 Copynumber: 23.9 Consensus size: 7
1553127 TATGTCATAG
1553137 GGTTTAT
1 GGTTTAT
1553144 GGTTTA-
1 GGTTTAT
*
1553150 GGTTTTAA
1 GG-TTTAT
1553158 GGTTTAT
1 GGTTTAT
*
1553165 GATTTAT
1 GGTTTAT
*
1553172 GATTTAT
1 GGTTTAT
*
1553179 GATTTAT
1 GGTTTAT
* *
1553186 GATTTAG
1 GGTTTAT
1553193 GGTTTAT
1 GGTTTAT
*
1553200 GATTTA-
1 GGTTTAT
*
1553206 GGATTCAT
1 GG-TTTAT
1553214 GGTTTAT
1 GGTTTAT
** *
1553221 AATTTAG
1 GGTTTAT
*
1553228 GGTTTAG
1 GGTTTAT
1553235 GGTTTAT
1 GGTTTAT
1553242 GGTTTA-
1 GGTTTAT
*
1553248 GGATTCAT
1 GG-TTTAT
* *
1553256 GATTTAG
1 GGTTTAT
1553263 GGTTTAT
1 GGTTTAT
1553270 GGTTTA-
1 GGTTTAT
1553276 GAGTTTAT
1 G-GTTTAT
** *
1553284 AATTTAG
1 GGTTTAT
1553291 GGTTTAT
1 GGTTTAT
1553298 GGTTTA
1 GGTTTA
1553304 ATTTATACAC
Statistics
Matches: 125, Mismatches: 27, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
6 6 0.05
7 114 0.91
8 5 0.04
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.50
Consensus pattern (7 bp):
GGTTTAT
Found at i:1553151 original size:14 final size:14
Alignment explanation
Indices: 1553134--1553303 Score: 151
Period size: 14 Copynumber: 12.1 Consensus size: 14
1553124 AATTATGTCA
1553134 TAGGGTTTATGGTT
1 TAGGGTTTATGGTT
* *
1553148 TAGGTTTTAAGGTT
1 TAGGGTTTATGGTT
* * *
1553162 TATGATTTATGATT
1 TAGGGTTTATGGTT
* * *
1553176 TATGATTTATGATT
1 TAGGGTTTATGGTT
*
1553190 TAGGGTTTATGATT
1 TAGGGTTTATGGTT
* *
1553204 TAGGATTCATGGTT
1 TAGGGTTTATGGTT
*** *
1553218 TATAATTTAGGGTT
1 TAGGGTTTATGGTT
1553232 TAGGGTTTATGGTT
1 TAGGGTTTATGGTT
* * *
1553246 TAGGATTCATGATT
1 TAGGGTTTATGGTT
1553260 TAGGGTTTATGGTT
1 TAGGGTTTATGGTT
* **
1553274 TAGAGTTTATAATT
1 TAGGGTTTATGGTT
1553288 TAGGGTTTATGGTT
1 TAGGGTTTATGGTT
1553302 TA
1 TA
1553304 ATTTATACAC
Statistics
Matches: 125, Mismatches: 31, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 125 1.00
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.50
Consensus pattern (14 bp):
TAGGGTTTATGGTT
Found at i:1553186 original size:42 final size:42
Alignment explanation
Indices: 1553139--1553283 Score: 182
Period size: 42 Copynumber: 3.5 Consensus size: 42
1553129 TGTCATAGGG
* * * *
1553139 TTTATGGTTTAGGTTTTAAGGTTTATGATTTATGATTTATGA
1 TTTATGGTTTAGGGTTTATGGTTTAGGATTCATGATTTATGA
* * * *
1553181 TTTATGATTTAGGGTTTATGATTTAGGATTCATGGTTTATAA
1 TTTATGGTTTAGGGTTTATGGTTTAGGATTCATGATTTATGA
* * *
1553223 TTTAGGGTTTAGGGTTTATGGTTTAGGATTCATGATTTAGGG
1 TTTATGGTTTAGGGTTTATGGTTTAGGATTCATGATTTATGA
*
1553265 TTTATGGTTTAGAGTTTAT
1 TTTATGGTTTAGGGTTTAT
1553284 AATTTAGGGT
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (42 bp):
TTTATGGTTTAGGGTTTATGGTTTAGGATTCATGATTTATGA
Found at i:1553622 original size:17 final size:18
Alignment explanation
Indices: 1553583--1553619 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1553573 AATGTCAAAT
1553583 AATTAAAATTACAAGACAC
1 AATTAAAA-TACAAGACAC
1553602 AATTAAAA-ACAAG-CAC
1 AATTAAAATACAAGACAC
1553618 AA
1 AA
1553620 ATTGAAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
19 8 0.44
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AATTAAAATACAAGACAC
Found at i:1555882 original size:17 final size:17
Alignment explanation
Indices: 1555862--1555900 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1555852 GAGTTTGAGT
1555862 TTGAATCGATCTCGAGC
1 TTGAATCGATCTCGAGC
1555879 TTGAATCGATCTCGAGC
1 TTGAATCGATCTCGAGC
1555896 TTGAA
1 TTGAA
1555901 CCGAGCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (17 bp):
TTGAATCGATCTCGAGC
Found at i:1556081 original size:31 final size:31
Alignment explanation
Indices: 1556046--1556118 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
1556036 GAGTCTTTTT
1556046 GAGTTCGAGTCGAGTTTCAATATTTTCTTTC
1 GAGTTCGAGTCGAGTTTCAATATTTTCTTTC
1556077 GAGTTCGAGTCGAGTTTCAATATTTTCTTTC
1 GAGTTCGAGTCGAGTTTCAATATTTTCTTTC
1556108 GAGTTCGAGTC
1 GAGTTCGAGTC
1556119 AACTTGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.42
Consensus pattern (31 bp):
GAGTTCGAGTCGAGTTTCAATATTTTCTTTC
Found at i:1574224 original size:15 final size:15
Alignment explanation
Indices: 1574204--1574243 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
1574194 ATAAACAAAA
1574204 CATTCCTTCCATCTC
1 CATTCCTTCCATCTC
1574219 CATTCCTTCCATCTC
1 CATTCCTTCCATCTC
1574234 CATTCCTTCC
1 CATTCCTTCC
1574244 TTCACCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.47, G:0.00, T:0.40
Consensus pattern (15 bp):
CATTCCTTCCATCTC
Found at i:1575928 original size:20 final size:20
Alignment explanation
Indices: 1575893--1575944 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 20
1575883 CCTGTCCGGT
1575893 TGCAATTGCAAAAACTAATGC
1 TGCAATTGC-AAAACTAATGC
1575914 TGCAATTGCAAAACTAATGC
1 TGCAATTGCAAAACTAATGC
1575934 TGCAATTGCAA
1 TGCAATTGCAA
1575945 CCTATTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (20 bp):
TGCAATTGCAAAACTAATGC
Found at i:1580643 original size:13 final size:14
Alignment explanation
Indices: 1580625--1580657 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
1580615 TGTCACGTTC
1580625 ATATTTTTTAAA-A
1 ATATTTTTTAAATA
1580638 ATA-TTTTTAAATA
1 ATATTTTTTAAATA
1580651 ATATTTT
1 ATATTTT
1580658 ACTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 7 0.39
14 3 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTTTTTAAATA
Found at i:1582042 original size:21 final size:21
Alignment explanation
Indices: 1582016--1582057 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1582006 CCAGAATGGG
*
1582016 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1582037 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1582058 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1582216 original size:19 final size:19
Alignment explanation
Indices: 1582164--1582229 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1582154 GGCCTCGGGG
* *
1582164 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAATAGTAAT
* * *
1582183 TCATTTTTC-AATAGTAAT
1 TTACTGTTCAAATAGTAAT
*
1582201 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAATAGTAAT
*
1582220 TTACTATTCA
1 TTACTGTTCA
1582230 TAAAAATATT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
18 13 0.36
19 23 0.64
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAT
Found at i:1582326 original size:29 final size:31
Alignment explanation
Indices: 1582294--1582352 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
1582284 AAATTTTGAA
*
1582294 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1582323 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
1582353 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1583662 original size:19 final size:20
Alignment explanation
Indices: 1583619--1583666 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1583609 TCTAAATCCT
*
1583619 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1583639 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1583658 TTTTCAAAA
1 TTTTCAAAA
1583667 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1584579 original size:34 final size:32
Alignment explanation
Indices: 1584526--1584595 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1584516 CCTTACAAAC
*
1584526 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
* *
1584558 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
1584592 TCCC
1 TCCC
1584596 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:1584905 original size:21 final size:21
Alignment explanation
Indices: 1584879--1584920 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1584869 CCAGAATGGG
*
1584879 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1584900 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1584921 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1585078 original size:19 final size:19
Alignment explanation
Indices: 1585026--1585080 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1585016 GAGCCTCGGG
* *
1585026 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAATAGTAAT
* * *
1585045 TCATTTTTC-AATAGTAAT
1 TTACTGTTCAAATAGTAAT
1585063 TTACTGTTCAAATAGTAA
1 TTACTGTTCAAATAGTAA
1585081 AGTACTATTC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAT
Found at i:1585188 original size:29 final size:31
Alignment explanation
Indices: 1585156--1585215 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1585146 AAATTTTGAA
*
1585156 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1585185 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1585216 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1593371 original size:60 final size:60
Alignment explanation
Indices: 1593258--1593373 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
1593248 TAGTCGGGGT
* * * *
1593258 GATCATTTTATAACTTTTAATAGTTATAGGACTCAACAAAGTAGTGCCATATAATTTGAG
1 GATCATTTTATAACTTTTAATAGTAAGAGGACTCAACAAAGTACTACCATATAATTTGAG
* * * ** *
1593318 GATCATTTTGTAATTTTTAATAGTAAGGGGACTTGACAAAGTACTACCCTATAATT
1 GATCATTTTATAACTTTTAATAGTAAGAGGACTCAACAAAGTACTACCATATAATT
1593374 GGGGGATAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTAAGAGGACTCAACAAAGTACTACCATATAATTTGAG
Found at i:1598480 original size:57 final size:56
Alignment explanation
Indices: 1598288--1598548 Score: 181
Period size: 57 Copynumber: 4.5 Consensus size: 56
1598278 GATTTTCAAG
* * * ** *
1598288 AAATAAATCCAACGATTTAATTCCTTTTAAAAAATAGAATCATACAAAATTCTATA-A
1 AAATAAATTCAACAATTTATTTCCTTTTATCAAATAGAATCA-ACAAGATTCTA-AGA
* * * * *
1598345 AAATAAATTTAACAATTTATTTTCTTCTA-C-AATATGAAATCAATCTAGATTTTCAAGA
1 AAATAAATTCAACAATTTATTTCCTTTTATCAAATA-G-AATCAA-CAAGATTCT-AAGA
** ** * * * *
1598403 AAATAAATTTGACGTTTTATTTCCTTTTATCAAACAGAATCATATAAGATTATAGGA
1 AAATAAATTCAACAATTTATTTCCTTTTATCAAATAGAATCA-ACAAGATTCTAAGA
*
1598460 AAATAAATTCAACAATTTATTT-CGTTT-TCAAAGTTAGAATCAACGCAAGATTCTAAGA
1 AAATAAATTCAACAATTTATTTCCTTTTATCAAA--TAGAATCAA--CAAGATTCTAAGA
1598518 TGAAATAAATTCAACAATTTATTTCTCTTTT
1 --AAATAAATTCAACAATTTATTTC-CTTTT
1598549 TCCAGTGTTA
Statistics
Matches: 158, Mismatches: 30, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
55 9 0.06
56 7 0.04
57 63 0.40
58 47 0.30
59 3 0.02
60 25 0.16
62 4 0.03
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (56 bp):
AAATAAATTCAACAATTTATTTCCTTTTATCAAATAGAATCAACAAGATTCTAAGA
Found at i:1599478 original size:14 final size:14
Alignment explanation
Indices: 1599458--1599498 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1599448 TAAGATTGTT
1599458 ATCCGAGAGTAAAA
1 ATCCGAGAGTAAAA
*
1599472 TTCCGAGAGTAAAA
1 ATCCGAGAGTAAAA
*
1599486 ATCCGAGACTAAA
1 ATCCGAGAGTAAA
1599499 TTGGAATCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (14 bp):
ATCCGAGAGTAAAA
Found at i:1601940 original size:22 final size:23
Alignment explanation
Indices: 1601915--1601957 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1601905 TTTTAGGATT
1601915 TTTATATTTAAT-TTTTAAATAG
1 TTTATATTTAATATTTTAAATAG
*
1601937 TTTATATTTTATATTTTAAAT
1 TTTATATTTAATATTTTAAAT
1601958 TACTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTATATTTAATATTTTAAATAG
Found at i:1601947 original size:23 final size:22
Alignment explanation
Indices: 1601915--1601957 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1601905 TTTTAGGATT
1601915 TTTATATTTA-ATTTTTAAATAG
1 TTTATATTTATA-TTTTAAATAG
1601937 TTTATATTTTATATTTTAAAT
1 TTTATA-TTTATATTTTAAAT
1601958 TACTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 12 0.63
24 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTATATTTATATTTTAAATAG
Found at i:1602083 original size:23 final size:23
Alignment explanation
Indices: 1602053--1602102 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1602043 TAATTTAGCC
1602053 CATTTGCATGTCATATGCCATGT
1 CATTTGCATGTCATATGCCATGT
*
1602076 CATTTGCATGTCATCTGCCATGT
1 CATTTGCATGTCATATGCCATGT
1602099 CATT
1 CATT
1602103 AGCTACTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (23 bp):
CATTTGCATGTCATATGCCATGT
Found at i:1602087 original size:11 final size:12
Alignment explanation
Indices: 1602053--1602102 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
1602043 TAATTTAGCC
1602053 CATTTG-CATGT
1 CATTTGCCATGT
*
1602064 CATATGCCATGT
1 CATTTGCCATGT
1602076 CATTTG-CATGT
1 CATTTGCCATGT
*
1602087 CATCTGCCATGT
1 CATTTGCCATGT
1602099 CATT
1 CATT
1602103 AGCTACTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 15 0.45
12 18 0.55
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (12 bp):
CATTTGCCATGT
Found at i:1602703 original size:24 final size:23
Alignment explanation
Indices: 1602670--1602727 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
1602660 AAATACTATC
* *
1602670 ATTATATTTATTTTTATTCTTTTA
1 ATTATTTTTATTTTGATT-TTTTA
*
1602694 ATTATTTTTAATTTGATTTTTTA
1 ATTATTTTTATTTTGATTTTTTA
*
1602717 ATT-TTATTATT
1 ATTATTTTTATT
1602728 AATTTTGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 6 0.21
23 8 0.28
24 15 0.52
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (23 bp):
ATTATTTTTATTTTGATTTTTTA
Found at i:1602729 original size:12 final size:12
Alignment explanation
Indices: 1602695--1602733 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1602685 ATTCTTTTAA
1602695 TTATTTTTAATT
1 TTATTTTTAATT
*
1602707 TGATTTTTTAATT
1 TTA-TTTTTAATT
*
1602720 TTATTATTAATT
1 TTATTTTTAATT
1602732 TT
1 TT
1602734 GCAATCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (12 bp):
TTATTTTTAATT
Found at i:1602866 original size:14 final size:15
Alignment explanation
Indices: 1602839--1602868 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1602829 TAATTTATAT
1602839 TTAAAATATAAAAAA
1 TTAAAATATAAAAAA
1602854 TTAAAAT-TAAAAAA
1 TTAAAATATAAAAAA
1602868 T
1 T
1602869 GTAAGGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAATATAAAAAA
Found at i:1605209 original size:20 final size:21
Alignment explanation
Indices: 1605159--1605209 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
1605149 TATGAATGGA
1605159 GTATCGATA-CTACATGGTTG
1 GTATCGATACCTACATGGTTG
1605179 GTATCGATACCTACGA-GG-TG
1 GTATCGATACCTAC-ATGGTTG
1605199 GTATCGATACC
1 GTATCGATACC
1605210 GGGATTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 22 0.76
21 6 0.21
22 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (21 bp):
GTATCGATACCTACATGGTTG
Found at i:1613749 original size:20 final size:20
Alignment explanation
Indices: 1613724--1613761 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1613714 ATCAACTTAT
1613724 GAGTATCGATACCCTAGGTA
1 GAGTATCGATACCCTAGGTA
*
1613744 GAGTATCGATACTCTAGG
1 GAGTATCGATACCCTAGG
1613762 GCCAATATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (20 bp):
GAGTATCGATACCCTAGGTA
Found at i:1615055 original size:27 final size:27
Alignment explanation
Indices: 1615017--1615070 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1615007 AAACCAAGAG
*
1615017 ATGTCCATGATTACATTAACATAATCA
1 ATGTCCATGATTACATGAACATAATCA
1615044 ATGTCCATGATTACATGAACATAATCA
1 ATGTCCATGATTACATGAACATAATCA
1615071 TGAGAACCAA
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:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
ATGTCCATGATTACATGAACATAATCA
Found at i:1615319 original size:36 final size:36
Alignment explanation
Indices: 1615279--1615382 Score: 118
Period size: 36 Copynumber: 2.9 Consensus size: 36
1615269 ATGATATTGG
* * *
1615279 TACTAGTAATAAGTTATATCACTTGGTGAATATACA
1 TACTAATAATAAGTCATATCACTTGGTGAATAAACA
* * * *
1615315 TACTAACAATAAGTCATGTCACTTGATGAACAAACA
1 TACTAATAATAAGTCATATCACTTGGTGAATAAACA
* * *
1615351 TGCTAATAATAAATCATTTCACTTGGTGAATA
1 TACTAATAATAAGTCATATCACTTGGTGAATA
1615383 CACTTATTAA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (36 bp):
TACTAATAATAAGTCATATCACTTGGTGAATAAACA
Found at i:1619089 original size:2 final size:2
Alignment explanation
Indices: 1619084--1619286 Score: 76
Period size: 2 Copynumber: 104.0 Consensus size: 2
1619074 AATTGAAAAA
* *
1619084 AT AT AT A- AT AT AT AT AT AT AT A- AGT TT AT AT AT AA AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
1619124 AT AT AT A- ACT AT AT TT AT AT -T AT AA ACT AT AT A- AT -T AT -T
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * *
1619163 AT A- AG CT AT AT AT AT AT AT -T AT GT TT AT AT GA- ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT
* * * * * *
1619204 AT A- AT AA ACT AT AT AT GT AT AA ACT AT AA AA AGT AT AT AGT TT
1 AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT A-T AT
*
1619247 AT AA ACT AT A- AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1619287 TATTCAAAAG
Statistics
Matches: 150, Mismatches: 26, Indels: 50
0.66 0.12 0.22
Matches are distributed among these distances:
1 15 0.10
2 126 0.84
3 9 0.06
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1619126 original size:29 final size:29
Alignment explanation
Indices: 1619084--1619184 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 29
1619074 AATTGAAAAA
1619084 ATATAT-AA-TATATATATATATAAGTTT
1 ATATATAAATTATATATATATATAAGTTT
1619111 ATATATAAATTATATATATA-ACTATA-TTT
1 ATATATAAATTATATATATATA-TA-AGTTT
* *
1619140 ATATTATAAACTATATA-ATTATTATAAGCTAT
1 ATA-TATAAATTATATATA-TA-TATAAG-TTT
*
1619172 ATATATATATTAT
1 ATATATAAATTAT
1619185 GTTTATATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
27 6 0.10
28 3 0.05
29 19 0.32
30 16 0.27
31 10 0.17
32 6 0.10
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (29 bp):
ATATATAAATTATATATATATATAAGTTT
Found at i:1619231 original size:25 final size:26
Alignment explanation
Indices: 1619203--1619259 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
1619193 GAACTATATA
1619203 TATAATAAACTATATA-TGTATAAAC
1 TATAATAAACTATATAGTGTATAAAC
* *
1619228 TATAA-AAAGTATATAGTTTATAAAC
1 TATAATAAACTATATAGTGTATAAAC
1619253 TATAATA
1 TATAATA
1619260 TATTAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 9 0.32
25 18 0.64
26 1 0.04
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (26 bp):
TATAATAAACTATATAGTGTATAAAC
Found at i:1619650 original size:17 final size:17
Alignment explanation
Indices: 1619614--1619661 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
1619604 TCTATAAATA
* *
1619614 TATATAAATGTATGTATG
1 TATATAAA-CTATATATG
1619632 TATATAAACTATATATG
1 TATATAAACTATATATG
1619649 --TATAAACTATATA
1 TATATAAACTATATA
1619662 AAATATATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 13 0.46
17 7 0.25
18 8 0.29
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (17 bp):
TATATAAACTATATATG
Found at i:1619824 original size:7 final size:7
Alignment explanation
Indices: 1619814--1619872 Score: 57
Period size: 7 Copynumber: 8.6 Consensus size: 7
1619804 AAAAAAAAAA
1619814 CTAAACC
1 CTAAACC
*
1619821 CTAAACT
1 CTAAACC
*
1619828 TTAAACC
1 CTAAACC
* * *
1619835 ATACACA
1 CTAAACC
*
1619842 CTAAACA
1 CTAAACC
1619849 CTAAACC
1 CTAAACC
1619856 CTAAA-C
1 CTAAACC
1619862 CTAAACC
1 CTAAACC
1619869 CTAA
1 CTAA
1619873 TATAAATGGA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 6 0.14
7 36 0.86
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:1620196 original size:13 final size:13
Alignment explanation
Indices: 1620164--1620190 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1620154 TAATTTACAT
1620164 TTAAATAATTTTA
1 TTAAATAATTTTA
1620177 TTAAATAATTTTA
1 TTAAATAATTTTA
1620190 T
1 T
1620191 ATAATATGTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:1620540 original size:21 final size:21
Alignment explanation
Indices: 1620516--1620557 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1620506 AAAAATGCAC
1620516 TTAAGTGGGAAAAAAGCAAAA
1 TTAAGTGGGAAAAAAGCAAAA
* * *
1620537 TTAATTGGGGAAAAAGTAAAA
1 TTAAGTGGGAAAAAAGCAAAA
1620558 CCATTCAAAA
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:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (21 bp):
TTAAGTGGGAAAAAAGCAAAA
Found at i:1620903 original size:2 final size:2
Alignment explanation
Indices: 1620853--1620892 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1620843 CATGTATAAA
* *
1620853 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AC CT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1620893 AAAACTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1621004 original size:13 final size:13
Alignment explanation
Indices: 1620986--1621054 Score: 75
Period size: 13 Copynumber: 5.2 Consensus size: 13
1620976 AGAAACCTTA
*
1620986 AATCATAAACCCT
1 AATCATAAACACT
*
1620999 AATCATAAACTCT
1 AATCATAAACACT
*
1621012 AATCATAAACTCT
1 AATCATAAACACT
*
1621025 AAACCATAAACACT
1 -AATCATAAACACT
*
1621039 AAACCATAAACACT
1 -AATCATAAACACT
1621053 AA
1 AA
1621055 ACCCTAAACC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
13 27 0.52
14 25 0.48
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (13 bp):
AATCATAAACACT
Found at i:1621034 original size:14 final size:14
Alignment explanation
Indices: 1620984--1621063 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
1620974 ATAGAAACCT
* *
1620984 TAAATCATAAACCC
1 TAAACCATAAACAC
* *
1620998 T-AATCATAAACTC
1 TAAACCATAAACAC
* *
1621011 T-AATCATAAACTC
1 TAAACCATAAACAC
1621024 TAAACCATAAACAC
1 TAAACCATAAACAC
1621038 TAAACCATAAACAC
1 TAAACCATAAACAC
*
1621052 TAAACCCTAAAC
1 TAAACCATAAAC
1621064 CTTAATATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
13 25 0.41
14 36 0.59
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACAC
Found at i:1621042 original size:21 final size:21
Alignment explanation
Indices: 1621002--1621064 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1620992 AAACCCTAAT
* *
1621002 CATAAACTCTAATCA-TAAAC
1 CATAAACACTAAACACTAAAC
1621022 TC-TAAACCA-TAAACACTAAAC
1 -CATAAA-CACTAAACACTAAAC
*
1621043 CATAAACACTAAACCCTAAAC
1 CATAAACACTAAACACTAAAC
1621064 C
1 C
1621065 TTAATATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 12 0.34
21 23 0.66
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (21 bp):
CATAAACACTAAACACTAAAC
Found at i:1621253 original size:14 final size:14
Alignment explanation
Indices: 1621234--1621280 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1621224 ATTTTTTCTT
1621234 TATATAAATTAAAC
1 TATATAAATTAAAC
1621248 TATAT-AATT----
1 TATATAAATTAAAC
1621257 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1621271 TATATTAATT
1 TATATAAATT
1621281 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1621258 original size:23 final size:24
Alignment explanation
Indices: 1621232--1621281 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1621222 TTATTTTTTC
1621232 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1621255 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1621279 TTT
1 TTT
1621282 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1621352 original size:13 final size:13
Alignment explanation
Indices: 1621320--1621346 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1621310 TATTATACAT
1621320 TTAAATAATTTTA
1 TTAAATAATTTTA
1621333 TTAAATAATTTTA
1 TTAAATAATTTTA
1621346 T
1 T
1621347 ATAATAGGTC
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:1621533 original size:16 final size:16
Alignment explanation
Indices: 1621514--1621589 Score: 98
Period size: 16 Copynumber: 4.7 Consensus size: 16
1621504 AAATATCAGA
*
1621514 TCAGGTTAAAAACATG
1 TCAGGTTAAAAACAGG
1621530 TCAGGTTAAAAACAGG
1 TCAGGTTAAAAACAGG
* *
1621546 TCAGGTTGAAAACATG
1 TCAGGTTAAAAACAGG
* *
1621562 TCAGTTTGAAAACAGG
1 TCAGGTTAAAAACAGG
1621578 TCAGGTTGAAAA
1 TCAGGTT-AAAA
1621590 TAAGTCGGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
16 49 0.94
17 3 0.06
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (16 bp):
TCAGGTTAAAAACAGG
Found at i:1621550 original size:32 final size:32
Alignment explanation
Indices: 1621497--1621589 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 32
1621487 TAATATATGA
* * *
1621497 GTCAGG-TAAATATCAGATCAGGTTAAAAACAT
1 GTCAGGTTAAA-AACAGGTCAGGTTGAAAACAT
1621529 GTCAGGTTAAAAACAGGTCAGGTTGAAAACAT
1 GTCAGGTTAAAAACAGGTCAGGTTGAAAACAT
* *
1621561 GTCAGTTTGAAAACAGGTCAGGTTGAAAA
1 GTCAGGTTAAAAACAGGTCAGGTTGAAAA
1621590 TAAGTCGGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 51 0.93
33 4 0.07
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (32 bp):
GTCAGGTTAAAAACAGGTCAGGTTGAAAACAT
Found at i:1624715 original size:18 final size:19
Alignment explanation
Indices: 1624679--1624715 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1624669 CACGGAATGT
1624679 AAGATTACCAATGAGAATAA
1 AAGATTACCAA-GAGAATAA
1624699 AAGATTACCAA-AGAATA
1 AAGATTACCAAGAGAATA
1624716 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.19
Consensus pattern (19 bp):
AAGATTACCAAGAGAATAA
Found at i:1626298 original size:262 final size:262
Alignment explanation
Indices: 1625832--1626355 Score: 940
Period size: 262 Copynumber: 2.0 Consensus size: 262
1625822 TTTATTTCGA
*
1625832 GCTTGAGCTGTCAATGAGAGAGTAAAGTTTAGTAAGTAAGCGTGTAATTTCCCTTTAACCATTGA
1 GCTTGAGCTGTCAATGAGAGAGTAAAGTTTAGTAAGTAAGCATGTAATTTCCCTTTAACCATTGA
*
1625897 AGTCGCTTAGTTCATGTTTCATTTAATATCACAATACAATTAGAGAAATTGTAATCATCGAAGTC
66 AGTCGCTTAGTTCATGTTTCATTTAATATCACAATACAATTAGAGAAATTGTAATAATCGAAGTC
* *
1625962 AATTAATTTATGTTAGTTTGGTATTTCGCTACAATTAGAGCTGTTAATTAAGATATATGGTAAAT
131 AATTAATTTATGTTAGTTTGGTATTTCACTACAATTAGAGCGGTTAATTAAGATATATGGTAAAT
** *
1626027 TACACGCTTACTTACTAAACTTTGTTCTCTCCTATTTTACCTACTATACTTTCAATTTTTTTCAA
196 TACACGCTTACTTACTAAACTTTACTCTCTCCTATTTCACCTACTATACTTTCAATTTTTTTCAA
1626092 TT
261 TT
* *
1626094 GCTTGAGCTGTCAATGAGAGAGTAAAGTTTAGTAAGTAAGCATGTAATTTCTCTTTAACTATTGA
1 GCTTGAGCTGTCAATGAGAGAGTAAAGTTTAGTAAGTAAGCATGTAATTTCCCTTTAACCATTGA
1626159 AGTCGCTTAGTTCATGTTTCATTTAATATCACAATACAATTAGAGAAATTGTAATAATCGAAGTC
66 AGTCGCTTAGTTCATGTTTCATTTAATATCACAATACAATTAGAGAAATTGTAATAATCGAAGTC
1626224 AATTAATTTATGTTAGTTTGGTATTTCACTACAATTAGAGCGGTTAATTAAGATATATGGTAAAT
131 AATTAATTTATGTTAGTTTGGTATTTCACTACAATTAGAGCGGTTAATTAAGATATATGGTAAAT
* * *
1626289 TATACGCTTACTTACTAAATTTTACTCTCTCCTATTTCACTTACTATACTTTCAATTTTTTTCAA
196 TACACGCTTACTTACTAAACTTTACTCTCTCCTATTTCACCTACTATACTTTCAATTTTTTTCAA
1626354 TT
261 TT
1626356 TGACCTCTGA
Statistics
Matches: 250, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
262 250 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (262 bp):
GCTTGAGCTGTCAATGAGAGAGTAAAGTTTAGTAAGTAAGCATGTAATTTCCCTTTAACCATTGA
AGTCGCTTAGTTCATGTTTCATTTAATATCACAATACAATTAGAGAAATTGTAATAATCGAAGTC
AATTAATTTATGTTAGTTTGGTATTTCACTACAATTAGAGCGGTTAATTAAGATATATGGTAAAT
TACACGCTTACTTACTAAACTTTACTCTCTCCTATTTCACCTACTATACTTTCAATTTTTTTCAA
TT
Found at i:1626653 original size:21 final size:21
Alignment explanation
Indices: 1626629--1626784 Score: 138
Period size: 21 Copynumber: 7.6 Consensus size: 21
1626619 ACGTTGCATT
*
1626629 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
** ** **
1626650 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
1626670 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
** **
1626691 TCGCGTTGCGATA-TTCCATT
1 TCGCGTTGCGATAGTTGAAAA
1626711 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
1626732 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
1626752 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
1626773 TCGTGTTGCGAT
1 TCGCGTTGCGAT
1626785 TTTCCATTTC
Statistics
Matches: 100, Mismatches: 32, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
20 45 0.45
21 55 0.55
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1626670 original size:41 final size:41
Alignment explanation
Indices: 1626625--1626807 Score: 330
Period size: 41 Copynumber: 4.5 Consensus size: 41
1626615 ATTCACGTTG
* *
1626625 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
1626666 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATATTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1626707 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
1626748 CATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1626789 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
1626808 CTGCAGTTGT
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 137 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1626803 original size:20 final size:20
Alignment explanation
Indices: 1626650--1626804 Score: 121
Period size: 20 Copynumber: 7.6 Consensus size: 20
1626640 TAGTTGAAAA
* *
1626650 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATGTTCCATT
** **
1626670 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-GTTCCATT
*
1626691 TCGCGTTGCGATATTCCATT
1 TCGCGTTGCGATGTTCCATT
** **
1626711 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-GTTCCATT
*
1626732 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATGTTCCATT
** **
1626752 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-GTTCCATT
* *
1626773 TCGTGTTGCGATTTTCCATT
1 TCGCGTTGCGATGTTCCATT
1626793 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1626805 AGTCTGCAGT
Statistics
Matches: 99, Mismatches: 33, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
20 55 0.56
21 44 0.44
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATGTTCCATT
Found at i:1626824 original size:22 final size:22
Alignment explanation
Indices: 1626796--1626867 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1626786 TTCCATTTCG
*
1626796 CGTTGCGATAGTCTGCAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
1626818 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
1626837 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1626859 CGTTGCGAT
1 CGTTGCGAT
1626868 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1626841 original size:19 final size:19
Alignment explanation
Indices: 1626817--1626882 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1626807 TCTGCAGTTG
1626817 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
1626836 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1626857 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1626877 TCGTTG
1 TCGTTG
1626883 AAAAAAAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1626841 original size:41 final size:41
Alignment explanation
Indices: 1626653--1626882 Score: 179
Period size: 41 Copynumber: 5.6 Consensus size: 41
1626643 TTGAAAATCG
* * * * *
1626653 CGTTGCGTTTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTG-CAGTTGT
* * * * *
1626694 CGTTGCGATATTCCATTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTG-CAGTTGT
* * * *
1626735 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCGT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTG-CAGTTGT
*
1626777 -GTTGCGATTTTCCATTTCGCGTTGCGATAGTCTGCAGTTGT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTGCAGTTGT
*
1626818 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTGCAGTTGT
1626859 CGTTGCGATTTTCCAAATT-CGTTG
1 CGTTGCGATTTTCC-AATTCCGTTG
1626883 AAAAAAAAGA
Statistics
Matches: 177, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
41 159 0.90
42 15 0.08
43 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTCTGCAGTTGT
Found at i:1626841 original size:82 final size:81
Alignment explanation
Indices: 1626625--1626848 Score: 308
Period size: 82 Copynumber: 2.7 Consensus size: 81
1626615 ATTCACGTTG
* * *
1626625 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAA
1626690 ATCGCGTTGCGATATTC
65 ATCGCGTTGCGATATTC
*
1626707 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAA
* *
1626772 ATCGTGTTGCGATTTTC
65 ATCGCGTTGCGATATTC
* * *
1626789 CATTTCGCGTTGCGATAGTCTG-CAGTTGTCGTTGCGATTTTCCAAATT-CGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGT
1626849 CTACAGTTGT
Statistics
Matches: 131, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
82 112 0.85
83 16 0.12
84 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (81 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTTGAAAA
TCGCGTTGCGATATTC
Found at i:1626841 original size:123 final size:122
Alignment explanation
Indices: 1626625--1626848 Score: 326
Period size: 123 Copynumber: 1.8 Consensus size: 122
1626615 ATTCACGTTG
*
1626625 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
*
1626690 ATCGCGTTGCGATATTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
66 ATCGCGTTGCGATATTCCAATTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
1626748 CATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTG-C
1 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAA
* * *
1626812 AGTTGTCGTTGCGATTTTCCAAATT-CGTTGCGATAGT
65 AATCG-CGTTGCGATATTCC-AATTCCGTTGCGATAGT
1626849 CTACAGTTGT
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
123 72 0.80
124 15 0.17
125 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (122 bp):
CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
ATCGCGTTGCGATATTCCAATTCCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1626882 original size:123 final size:121
Alignment explanation
Indices: 1626634--1626882 Score: 299
Period size: 123 Copynumber: 2.0 Consensus size: 121
1626624 GCATTTCGCA
*
1626634 TTGCGATAGTTGAAAATCGCGTTGCGTTTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTG
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTG
* *
1626699 CGATATTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCG
66 CGATATTCCAATTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CG
* * * *
1626757 TTGCGATAGTTGAAAATCGTGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTG-CAGTTGTCGT
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGT
* * * *
1626821 TGCGATTTTCCAAATT-CGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CG
64 TGCGATATTCC-AATTCCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCG
1626880 TTG
1 TTG
1626883 AAAAAAAAGA
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
123 73 0.67
124 30 0.28
125 6 0.06
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (121 bp):
TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTG
CGATATTCCAATTCCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCG
Found at i:1626968 original size:6 final size:6
Alignment explanation
Indices: 1626958--1626996 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1626948 GACACGTATT
*
1626958 ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1626997 CGAGACGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.33, C:0.51, G:0.13, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:1627007 original size:5 final size:5
Alignment explanation
Indices: 1626997--1627027 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1626987 GACCACGACC
1626997 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1627028 GCGGCGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:1627528 original size:6 final size:6
Alignment explanation
Indices: 1627512--1627549 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1627502 TCTCGTCTCG
1627512 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1627550 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1627696 original size:20 final size:21
Alignment explanation
Indices: 1627671--1627793 Score: 88
Period size: 21 Copynumber: 6.0 Consensus size: 21
1627661 ACTGTAGACT
*
1627671 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAAATGCAACA
** * *
1627691 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACA
** * *
1627712 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACA
*
1627733 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAAATGCAACA
*** * **
1627753 ATCGCAACGCGGTTTTCAATT
1 ATCGCAACGCGAAATGCAACA
1627774 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1627794 GCGAATTTAC
Statistics
Matches: 80, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
20 29 0.36
21 51 0.64
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACA
Found at i:1627713 original size:41 final size:42
Alignment explanation
Indices: 1627621--1627723 Score: 124
Period size: 41 Copynumber: 2.5 Consensus size: 42
1627611 AAAATCTTTT
*
1627621 ATTTTAACTATCGCAA--CGAATTTGGAAAATCGCAACGACA
1 ATTTTAACTATCGCAACGCGAATATGGAAAATCGCAACGACA
* * *
1627661 ACTGTAGACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CG
1 ATTTTA-ACTATCGCAACGCGAATATGGAAAATCGCAACGACA
1627702 ATTTTCAACTATCGCAACGCGA
1 ATTTT-AACTATCGCAACGCGA
1627724 TTTTCAACTA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 4 0.08
41 29 0.55
42 16 0.30
43 4 0.08
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
ATTTTAACTATCGCAACGCGAATATGGAAAATCGCAACGACA
Found at i:1627717 original size:21 final size:21
Alignment explanation
Indices: 1627691--1627785 Score: 120
Period size: 21 Copynumber: 4.6 Consensus size: 21
1627681 GAAATGGAAA
1627691 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1627712 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
1627733 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
* *
1627753 ATCGCAACGCGGTTTTCAATT
1 ATCGCAACGCGATTTTCAACT
1627774 ATCGCAACGCGA
1 ATCGCAACGCGA
1627786 AATGCAACGC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.23
21 47 0.77
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1627738 original size:62 final size:62
Alignment explanation
Indices: 1627668--1627785 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
1627658 ACAACTGTAG
1627668 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
* *
1627730 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGGTTTTCAATTATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGA
1627786 AATGCAACGC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
Found at i:1627757 original size:41 final size:41
Alignment explanation
Indices: 1627712--1627789 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1627702 ATTTTCAACT
1627712 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
* *
1627753 ATCGCAACGCGGTTTTCAATTATCGCAACGCGAAATG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1627790 CAACGCGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:1631818 original size:12 final size:12
Alignment explanation
Indices: 1631797--1631855 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
1631787 GAATGTTTTA
*
1631797 TCTGACTTCTGC
1 TCTGAATTCTGC
*
1631809 TCTGAATTCTGT
1 TCTGAATTCTGC
* *
1631821 TATGATTTCTGC
1 TCTGAATTCTGC
*
1631833 TCTGAATTCTGT
1 TCTGAATTCTGC
*
1631845 TCTGATTTCTG
1 TCTGAATTCTG
1631856 ATATCTCTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (12 bp):
TCTGAATTCTGC
Found at i:1631831 original size:24 final size:24
Alignment explanation
Indices: 1631803--1631855 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1631793 TTTATCTGAC
1631803 TTCTGCTCTGAATTCTGTTATGAT
1 TTCTGCTCTGAATTCTGTTATGAT
*
1631827 TTCTGCTCTGAATTCTGTTCTGAT
1 TTCTGCTCTGAATTCTGTTATGAT
1631851 TTCTG
1 TTCTG
1631856 ATATCTCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.51
Consensus pattern (24 bp):
TTCTGCTCTGAATTCTGTTATGAT
Found at i:1635273 original size:24 final size:24
Alignment explanation
Indices: 1635246--1635297 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1635236 ATGTTTTATT
* *
1635246 TGATTTCTTCTATAAATTTTGTTC
1 TGATTTCTACTATAAATTCTGTTC
* *
1635270 TGATTTCTACTCTAAATTCTGTTT
1 TGATTTCTACTATAAATTCTGTTC
1635294 TGAT
1 TGAT
1635298 ATCTCCGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.56
Consensus pattern (24 bp):
TGATTTCTACTATAAATTCTGTTC
Found at i:1635485 original size:32 final size:32
Alignment explanation
Indices: 1635449--1635511 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1635439 TTGGGTAGGT
1635449 TCTGTGGCCCTGAG-ATTTTTCTTGAGTAGGCC
1 TCTGTGGCCCTGAGAATTTTT-TTGAGTAGGCC
*
1635481 TCTGTGGCCCTGAGAATTTTTTTGGGTAGGC
1 TCTGTGGCCCTGAGAATTTTTTTGAGTAGGC
1635512 TCGTAGGCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.13, C:0.19, G:0.30, T:0.38
Consensus pattern (32 bp):
TCTGTGGCCCTGAGAATTTTTTTGAGTAGGCC
Found at i:1636277 original size:2 final size:2
Alignment explanation
Indices: 1636270--1636295 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1636260 TATCATTGTG
1636270 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
1636296 TAACAAGTAA
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:1637990 original size:185 final size:186
Alignment explanation
Indices: 1637678--1638068 Score: 687
Period size: 185 Copynumber: 2.1 Consensus size: 186
1637668 TTTTCTAATT
* * *
1637678 TATATAA-AAATTAAATATTTTATAATTAAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
1637742 ATTATAGAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
1637807 TTGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGAGCCTATATGTTA
131 TTGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* * *
1637863 TATATAATATATTTAATATTTTTTAATT-CAAAAAATAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
1637927 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
1637992 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 TTGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
1638048 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1638069 AAAATTTTAT
Statistics
Matches: 196, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
185 179 0.91
186 17 0.09
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:1639404 original size:3 final size:3
Alignment explanation
Indices: 1639396--1639436 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1639386 GCCCTTGGTT
1639396 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1639437 GTTGTTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1641443 original size:16 final size:17
Alignment explanation
Indices: 1641422--1641456 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1641412 TCGAAAACTC
1641422 AACTG-AAAATCGATTA
1 AACTGAAAAATCGATTA
*
1641438 AACTGAAAAATTGATTA
1 AACTGAAAAATCGATTA
1641455 AA
1 AA
1641457 TTTGGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (17 bp):
AACTGAAAAATCGATTA
Found at i:1643644 original size:14 final size:16
Alignment explanation
Indices: 1643613--1643644 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1643603 CTATCAAACG
1643613 TAAAATATTATCATTT
1 TAAAATATTATCATTT
1643629 TAAAAT-TTAT-ATTT
1 TAAAATATTATCATTT
1643643 TA
1 TA
1643645 TTAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 4 0.25
16 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAATATTATCATTT
Found at i:1644292 original size:127 final size:127
Alignment explanation
Indices: 1644147--1644398 Score: 504
Period size: 127 Copynumber: 2.0 Consensus size: 127
1644137 AAATTGATGC
1644147 TATATATATTTGAGAATGGTCTAAACCGATATAAAATCCCATTGACATAAAAGAAAGCAGTTGGA
1 TATATATATTTGAGAATGGTCTAAACCGATATAAAATCCCATTGACATAAAAGAAAGCAGTTGGA
1644212 GCATTGTTAATTGTTGCCATCAAAGACAGTTTATATTGACGTGCTTCCTTTAACCTAAATTG
66 GCATTGTTAATTGTTGCCATCAAAGACAGTTTATATTGACGTGCTTCCTTTAACCTAAATTG
1644274 TATATATATTTGAGAATGGTCTAAACCGATATAAAATCCCATTGACATAAAAGAAAGCAGTTGGA
1 TATATATATTTGAGAATGGTCTAAACCGATATAAAATCCCATTGACATAAAAGAAAGCAGTTGGA
1644339 GCATTGTTAATTGTTGCCATCAAAGACAGTTTATATTGACGTGCTTCCTTTAACCTAAAT
66 GCATTGTTAATTGTTGCCATCAAAGACAGTTTATATTGACGTGCTTCCTTTAACCTAAAT
1644399 CGTAGTTGTT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 125 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (127 bp):
TATATATATTTGAGAATGGTCTAAACCGATATAAAATCCCATTGACATAAAAGAAAGCAGTTGGA
GCATTGTTAATTGTTGCCATCAAAGACAGTTTATATTGACGTGCTTCCTTTAACCTAAATTG
Found at i:1645399 original size:20 final size:20
Alignment explanation
Indices: 1645365--1645402 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1645355 ACATTTTCGA
1645365 GAATGAATATCATATTGTAG
1 GAATGAATATCATATTGTAG
1645385 GAAT-AATATCAATATTGT
1 GAATGAATATC-ATATTGT
1645403 TATTATGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (20 bp):
GAATGAATATCATATTGTAG
Found at i:1645702 original size:86 final size:85
Alignment explanation
Indices: 1645557--1645719 Score: 254
Period size: 86 Copynumber: 1.9 Consensus size: 85
1645547 TCTAAAGGAG
* * * *
1645557 TATCGATATCGAGGGTTAAGTATCAATATTGACCCGAGAGTATTGATACAACCCGTTATTTTTCT
1 TATCGATACCGAGGGTTAAGTATCAATACTAACCCGAGAGTATTGATACAACCAGTTA-TTTTCT
1645622 TAATTAAAATTTACTATAGAA
65 TAATTAAAATTTACTATAGAA
* * *
1645643 TATCGGTACCGAGGGTTGAGTATCAATACTAACTCGAGAGTATTGATACAACCAGTTATTTTCTT
1 TATCGATACCGAGGGTTAAGTATCAATACTAACCCGAGAGTATTGATACAACCAGTTATTTTCTT
1645708 AATTAAAATTTA
66 AATTAAAATTTA
1645720 TCGTGGAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 19 0.27
86 51 0.73
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (85 bp):
TATCGATACCGAGGGTTAAGTATCAATACTAACCCGAGAGTATTGATACAACCAGTTATTTTCTT
AATTAAAATTTACTATAGAA
Found at i:1652545 original size:20 final size:22
Alignment explanation
Indices: 1652515--1652554 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1652505 TATTGATACT
1652515 AGGGTCTTGGT-TCGAGACCCA
1 AGGGTCTTGGTATCGAGACCCA
1652536 AGGG-CTTGGTATCGAGACC
1 AGGGTCTTGGTATCGAGACC
1652555 AATTTTCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.23, G:0.35, T:0.23
Consensus pattern (22 bp):
AGGGTCTTGGTATCGAGACCCA
Found at i:1662953 original size:15 final size:15
Alignment explanation
Indices: 1662933--1662962 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1662923 GTGGCATACT
1662933 TCCTCCACCTCCTTC
1 TCCTCCACCTCCTTC
*
1662948 TCCTCCTCCTCCTTC
1 TCCTCCACCTCCTTC
1662963 AACACCTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.60, G:0.00, T:0.37
Consensus pattern (15 bp):
TCCTCCACCTCCTTC
Found at i:1665516 original size:27 final size:27
Alignment explanation
Indices: 1665477--1665530 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1665467 TGTGAAAAAA
1665477 TATTTTTAATAAAAGTA-TAAAAATATT
1 TATTTTTAAT-AAAGTATTAAAAATATT
** *
1665504 TATTTTTTTTAAATTATTAAAAATATT
1 TATTTTTAATAAAGTATTAAAAATATT
1665531 AAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TATTTTTAATAAAGTATTAAAAATATT
Found at i:1665556 original size:8 final size:9
Alignment explanation
Indices: 1665518--1665554 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
1665508 TTTTTTAAAT
1665518 TATTAAAAA
1 TATTAAAAA
1665527 TATTAAAAA
1 TATTAAAAA
1665536 TATATAAAAA
1 TAT-TAAAAA
1665546 T-TTAAAAA
1 TATTAAAAA
1665554 T
1 T
1665555 TTCAAGGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 7 0.26
9 13 0.48
10 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TATTAAAAA
Found at i:1666454 original size:22 final size:23
Alignment explanation
Indices: 1666381--1666462 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 23
1666371 AGTTTGTCTA
* *
1666381 TATGACATTTTTTCTTCTGTCTT
1 TATGACACTTTTTCTTCTATCTT
* *
1666404 TATGACACGTTTTCTTTTATCTT
1 TATGACACTTTTTCTTCTATCTT
*
1666427 TATGACACATTTTCTTCTATC-T
1 TATGACACTTTTTCTTCTATCTT
1666449 TATGACACTTTTTC
1 TATGACACTTTTTC
1666463 AGTAGTTTCG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
22 14 0.27
23 38 0.73
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (23 bp):
TATGACACTTTTTCTTCTATCTT
Found at i:1670658 original size:20 final size:18
Alignment explanation
Indices: 1670609--1670661 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
1670599 ATGAATAAAA
1670609 ATATGAAA-TAAAATTTT
1 ATATGAAAGTAAAATTTT
*
1670626 ATATTGAATGTAATAATTTT
1 ATA-TGAAAGTAA-AATTTT
1670646 ATATGAGAAGTAAAAT
1 ATATGA-AAGTAAAAT
1670662 AGATCTCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 3 0.10
18 4 0.13
19 9 0.30
20 14 0.47
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (18 bp):
ATATGAAAGTAAAATTTT
Found at i:1671125 original size:15 final size:15
Alignment explanation
Indices: 1671105--1671154 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1671095 CGATCCGATT
1671105 CGAATAACACATATC
1 CGAATAACACATATC
1671120 CGAATAACACATA-C
1 CGAATAACACATATC
* * *
1671134 TTGAATACCATATATC
1 -CGAATAACACATATC
1671150 CGAAT
1 CGAAT
1671155 TTTGATCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (15 bp):
CGAATAACACATATC
Found at i:1671597 original size:20 final size:20
Alignment explanation
Indices: 1671560--1671595 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
1671550 GTTTCCCATT
1671560 TTCCTCTCCATTTTCTCTTC
1 TTCCTCTCCATTTTCTCTTC
1671580 TTCCTCT-C-TTTTCTCT
1 TTCCTCTCCATTTTCTCT
1671596 CTAAATTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (20 bp):
TTCCTCTCCATTTTCTCTTC
Found at i:1675176 original size:51 final size:53
Alignment explanation
Indices: 1675062--1675176 Score: 121
Period size: 57 Copynumber: 2.2 Consensus size: 53
1675052 GTTATGAATG
* *
1675062 AAATTT-AATTTTGGTCTGACTCGAAGTTAAAAGTACTCTATTTTATCTGGATATT
1 AAATTTAAATTTTGGTCTGACTAGAAGTTAAAAGTACTCTATTTTATCT-G-CA-T
* *
1675117 ATAATTTAAATTTTGGTCTTACTAGAAGTTAAAAGTACT-TTTATTTATCT-CA-
1 A-AATTTAAATTTTGGTCTGACTAGAAGTTAAAAGTACTCTAT-TTTATCTGCAT
1675169 AAATTTAA
1 AAATTTAA
1675177 TTAAAAAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
51 7 0.13
52 1 0.02
54 1 0.02
55 1 0.02
56 7 0.13
57 36 0.68
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (53 bp):
AAATTTAAATTTTGGTCTGACTAGAAGTTAAAAGTACTCTATTTTATCTGCAT
Found at i:1681182 original size:60 final size:59
Alignment explanation
Indices: 1681086--1681231 Score: 186
Period size: 60 Copynumber: 2.4 Consensus size: 59
1681076 TTTATAGGAT
* * **
1681086 AAAG-TACACAAATGATCCCCAACTATAGTACGTTGCTTTATTGAATCATTTGACTATTA
1 AAAGTTACA-AAATGATCCCTAACTATAGGACGTTGCTTTATTGAATCATCCGACTATTA
** * *
1681145 AAAGTTACAAAATGATCCTCTAACTATAGGGTGTTGCTTTGTTGATTCATCCGACTATTA
1 AAAGTTACAAAATGATCC-CTAACTATAGGACGTTGCTTTATTGAATCATCCGACTATTA
1681205 AAAGTTACAAAATGATCACCTAACTAT
1 AAAGTTACAAAATGATC-CCTAACTAT
1681232 TCATATGTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 13 0.17
60 62 0.82
61 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (59 bp):
AAAGTTACAAAATGATCCCTAACTATAGGACGTTGCTTTATTGAATCATCCGACTATTA
Found at i:1681810 original size:15 final size:14
Alignment explanation
Indices: 1681792--1681825 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1681782 AAAAAAATCA
1681792 TTTTTAGCCTTTAAT
1 TTTTTA-CCTTTAAT
*
1681807 TTTTTACTTTTAAT
1 TTTTTACCTTTAAT
1681821 TTTTT
1 TTTTT
1681826 TAATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTTACCTTTAAT
Found at i:1682401 original size:139 final size:141
Alignment explanation
Indices: 1682190--1682449 Score: 443
Period size: 139 Copynumber: 1.9 Consensus size: 141
1682180 TTTTTACTGG
*
1682190 TATGAAAATTATTATTAATTAAATAGTACCCACAATAAGGTTATAAATATTTTGGCTAATCCGAG
1 TATGAAAATTATTATTAATTAAATAGTACCCACAATAAGGTTAT-AATATTTTGGCTAATCCAAG
* * *
1682255 GCAAATTATTCTATTTGATTGTTAGCATTTGATGATATTAAAATTTTATTGATATGAAAATTATT
65 GCAAATTATTCTATCTGATTGTTAGCATTTGATGATAATAAAAGTTTATTGATATGAAAATTATT
1682320 TCATTATCTAGA
130 TCATTATCTAGA
* *
1682332 TATGAGAATTATTATTAATT-AATAGTACCCACAATAAGGTTAT-ATATTTTGGCTAATCCAAGT
1 TATGAAAATTATTATTAATTAAATAGTACCCACAATAAGGTTATAATATTTTGGCTAATCCAAGG
1682395 CAAATTATTCTATCTGATTGTTAGCATTTGATGATAATAAAAGTTTATTGATATG
66 CAAATTATTCTATCTGATTGTTAGCATTTGATGATAATAAAAGTTTATTGATATG
1682450 TACCATTTAA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
139 70 0.62
141 23 0.21
142 19 0.17
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (141 bp):
TATGAAAATTATTATTAATTAAATAGTACCCACAATAAGGTTATAATATTTTGGCTAATCCAAGG
CAAATTATTCTATCTGATTGTTAGCATTTGATGATAATAAAAGTTTATTGATATGAAAATTATTT
CATTATCTAGA
Found at i:1685119 original size:17 final size:18
Alignment explanation
Indices: 1685099--1685134 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1685089 ATAATTTAAG
1685099 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
1685116 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
1685134 T
1 T
1685135 ATGCATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:1685215 original size:2 final size:2
Alignment explanation
Indices: 1685177--1685201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1685167 AACTATAATT
1685177 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
1685202 GCATAAACTA
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:1685276 original size:65 final size:66
Alignment explanation
Indices: 1685112--1685286 Score: 209
Period size: 65 Copynumber: 2.7 Consensus size: 66
1685102 ATATATAAAC
* * *
1685112 TATATTTATAT-TATAAACTATATATGCATAAACTATA-AAAAGTATATAGTTTATAAACTATAA
1 TATATATATATATATATA-TATATATGCATAAACTATATAAAAGTAAATAGTTTATAAACTATAA
1685175 TT
65 TT
*
1685177 TATATATATATATATATATATATATGCATAAACTATATAAAA-TAAATAGTTTATAAATTATAAT
1 TATATATATATATATATATATATATGCATAAACTATATAAAAGTAAATAGTTTATAAACTATAAT
1685241 T
66 T
* * * *
1685242 TATAT-TAATATGGTATATATATGTATGTAT-AACTA-ATATAAGTAA
1 TATATAT-ATAT-ATATATATATATATGCATAAACTATATAAAAGTAA
1685287 TCTATATTAT
Statistics
Matches: 97, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
64 6 0.06
65 67 0.69
66 24 0.25
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (66 bp):
TATATATATATATATATATATATATGCATAAACTATATAAAAGTAAATAGTTTATAAACTATAAT
T
Found at i:1685444 original size:21 final size:21
Alignment explanation
Indices: 1685420--1685465 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1685410 CATTAAACAT
1685420 TAAACCAT-AACCCTTAAACCC
1 TAAACCATAAACCC-TAAACCC
* *
1685441 TAAACCTTAAACCCTAAGCCC
1 TAAACCATAAACCCTAAACCC
1685462 TAAA
1 TAAA
1685466 TTATATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (21 bp):
TAAACCATAAACCCTAAACCC
Found at i:1685454 original size:14 final size:14
Alignment explanation
Indices: 1685413--1685457 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1685403 TCCTAAACAT
* *
1685413 TAAACATTAAACCA
1 TAAACCTTAAACCC
*
1685427 TAACCCTTAAACCC
1 TAAACCTTAAACCC
1685441 TAAACCTTAAACCC
1 TAAACCTTAAACCC
1685455 TAA
1 TAA
1685458 GCCCTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:1685557 original size:2 final size:2
Alignment explanation
Indices: 1685509--1685539 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1685499 AAATATGCAC
1685509 TA TA -A 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
1685540 AAGTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1685805 original size:11 final size:11
Alignment explanation
Indices: 1685793--1685851 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
1685783 TACATGTATG
*
1685793 TATAAACTATG
1 TATAAACTATA
1685804 TAT-AA-TATA
1 TATAAACTATA
1685813 TATAAACTATA
1 TATAAACTATA
1685824 TATATATA-TATA
1 TATA-A-ACTATA
*
1685836 TATAACCTATA
1 TATAAACTATA
1685847 GTATA
1 -TATA
1685852 TGTATATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 6 0.15
10 4 0.10
11 16 0.40
12 13 0.32
13 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (11 bp):
TATAAACTATA
Found at i:1685818 original size:20 final size:21
Alignment explanation
Indices: 1685793--1685887 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 21
1685783 TACATGTATG
1685793 TATAAACTATGTATA-ATATA
1 TATAAACTATGTATATATATA
*
1685813 TATAAACTATATATATATATA
1 TATAAACTATGTATATATATA
*
1685834 TATATAACCTATAGTATATGTATA
1 TATA-AA-CTAT-GTATATATATA
* * * * *
1685858 TACAATCTATTTATATGT-TT
1 TATAAACTATGTATATATATA
1685878 TATAAACTAT
1 TATAAACTAT
1685888 ATATGTAACC
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
20 23 0.37
21 16 0.26
22 6 0.10
23 5 0.08
24 12 0.19
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (21 bp):
TATAAACTATGTATATATATA
Found at i:1685836 original size:65 final size:65
Alignment explanation
Indices: 1685765--1685891 Score: 157
Period size: 65 Copynumber: 2.0 Consensus size: 65
1685755 ACATGTAAAC
* * * *
1685765 TATATATGTAACTTATAGTACATGTATGTATAAACTATGTATAAT-ATATATAAACTATATATAT
1 TATATATATAACCTATAGTACATGTATATACAAACTATGTAT-ATGATATATAAACTATATATAT
1685829 A
65 A
* * * * *
1685830 TATATATATAACCTATAGTATATGTATATACAATCTATTTATATGTTTTATAAACTATATAT
1 TATATATATAACCTATAGTACATGTATATACAAACTATGTATATGATATATAAACTATATAT
1685892 GTAACCTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 2 0.04
65 50 0.96
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (65 bp):
TATATATATAACCTATAGTACATGTATATACAAACTATGTATATGATATATAAACTATATATATA
Found at i:1685922 original size:21 final size:20
Alignment explanation
Indices: 1685898--1685986 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 20
1685888 ATATGTAACC
*
1685898 TATAGTTTATAAACAATAGTT
1 TATA-TTTATAAACTATAGTT
**
1685919 TATA-TTAGTGTACTATAAGTT
1 TATATTTA-TAAACTAT-AGTT
* *
1685940 TATACTTTATAACCTATAGTA
1 TATA-TTTATAAACTATAGTT
1685961 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAAACTATAGTT
1685982 TATAT
1 TATAT
1685987 AATGTTAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.06
20 7 0.13
21 35 0.65
22 6 0.11
23 3 0.06
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (20 bp):
TATATTTATAAACTATAGTT
Found at i:1686130 original size:11 final size:11
Alignment explanation
Indices: 1686116--1686162 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
1686106 TATATTATTT
1686116 ATAATAATATA
1 ATAATAATATA
1686127 ATAATAATATA
1 ATAATAATATA
*
1686138 TTAATAATA-A
1 ATAATAATATA
1686148 TATAATATATATA
1 -ATAATA-ATATA
1686161 AT
1 AT
1686163 TTATATTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 1 0.03
11 24 0.77
12 5 0.16
13 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATAATATA
Found at i:1686161 original size:14 final size:15
Alignment explanation
Indices: 1686116--1686162 Score: 62
Period size: 14 Copynumber: 3.1 Consensus size: 15
1686106 TATATTATTT
1686116 ATAATA-ATATAATA
1 ATAATATATATAATA
1686130 ATAATATAT-TAATA
1 ATAATATATATAATA
1686144 ATAATATAATATATATA
1 ATAATAT-ATATA-ATA
1686161 AT
1 AT
1686163 TTATATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 18 0.62
15 4 0.14
16 2 0.07
17 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATATATATAATA
Found at i:1686631 original size:24 final size:24
Alignment explanation
Indices: 1686603--1686658 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1686593 TGTGAACGTG
* * *
1686603 TTATGTTTGTTTGGTTATGTTCGT
1 TTATGTTCGTTCGATTATGTTCGT
1686627 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTCGT
1686651 TTATGTTC
1 TTATGTTC
1686659 ATTCATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.11, C:0.09, G:0.21, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTCGT
Found at i:1688600 original size:40 final size:40
Alignment explanation
Indices: 1688549--1688660 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 40
1688539 AAGTTACATT
*
1688549 GAATCACTTAACATCATATAACCATTAATATTAGTATCT-A
1 GAATCAGTTAACATCATATAACCATTAATATTAGTAT-TGA
* * *
1688589 GTATCAGTTAACATCATATAACAATTAACATTAGTATTGA
1 GAATCAGTTAACATCATATAACCATTAATATTAGTATTGA
*
1688629 GAATCACG-TAACATCAGATAATCCATATAATA
1 GAATCA-GTTAACATCATATAA-CCAT-TAATA
1688661 AAGATAATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.02
40 51 0.85
41 4 0.07
42 4 0.07
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (40 bp):
GAATCAGTTAACATCATATAACCATTAATATTAGTATTGA
Found at i:1692682 original size:5 final size:5
Alignment explanation
Indices: 1692660--1693157 Score: 726
Period size: 5 Copynumber: 100.4 Consensus size: 5
1692650 ATAATTTCAT
1692660 ATATA ATATA TATAATA ATATA ATAT- ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA -AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1692711 ATATA ATATA ATAT- ATATA ATATA ATAT- A-ATA ATATA ATATA A-ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1692757 TATATA ATATA ATAT- ATATAA ATATA ATAT- AT-TA ATATA ATATAA
1 -ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA ATATA ATAT-A
1692802 ATATA ATATA ATATA ATAT- ATA-A TATATA ATATA ATATA ATATA A-ATA
1 ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATATA ATATA ATATA
1692850 ATATA ATATA ATATA ATATA ATATA ATATA ATAT- A-ATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* *
1692897 ATATA AAAT- ATATT ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1692946 ATATA ATAT- ATATA ATATA ATATAA TATATA ATATA ATATA ATAT- ATAATAA
1 ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA AT-AT-A
1692998 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAATA TATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA -ATATA ATATA
1693050 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1693100 TATATA ATATA ATATA ATATA ATATA ATATA ATA-A TATATA ATATA ATATA
1 -ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATATA
1693151 ATATA AT
1 ATATA AT
1693158 TTTAAATACT
Statistics
Matches: 458, Mismatches: 3, Indels: 64
0.87 0.01 0.12
Matches are distributed among these distances:
3 5 0.01
4 44 0.10
5 365 0.80
6 33 0.07
7 11 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:1699451 original size:64 final size:65
Alignment explanation
Indices: 1699377--1699533 Score: 205
Period size: 65 Copynumber: 2.4 Consensus size: 65
1699367 ACACCCTAAT
* * *
1699377 TCGAATGCATTTTGTGTACCGATTCACA-ACCATGCATCGATGCACTCCT-GATTTTATTGAAAC
1 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTT-TTGAAAC
1699440 A
65 A
* *
1699441 TCGAATGCATTTTATGTATCGATGCACAGATCATGCATCGATGCACTCCTGGATCTTTTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
*
1699506 TCGAAT--ATAATTAGTGTACCGATGCACA
1 TCGAATGCAT-TTTA-TGTACCGATGCACA
1699534 CCAATTGTAC
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
63 2 0.02
64 28 0.34
65 47 0.57
66 5 0.06
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
Found at i:1703052 original size:301 final size:301
Alignment explanation
Indices: 1702505--1703106 Score: 1042
Period size: 301 Copynumber: 2.0 Consensus size: 301
1702495 CGAGTAATTA
1702505 TTAGGCTAATTTTAAAGAAAACTCCATATGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTAT
1 TTAGGCTAATTTTAAAGAAAACTCCATATGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTAT
* * *
1702570 TTTCATCCTTTTGGATGTAAATGTTTTGTTTTAAACATTGGTAAAGAAAATCTTGGCAAATTTGA
66 TTTCATCCTTTTAGATGTAAATGTTTTGTTTTAAACATCGGTAAAGAAAATCTTGGAAAATTTGA
* *
1702635 TGCTAAAAGTGATGAAGGAATTTTTCTGGGTTATTCCTTAAATTCTAAAGCTTATCGAGTATTTA
131 TGCTAAAAGTGATGAAGGAATTTTTCTGAGTTATTCCTTAAATTATAAAGCTTATCGAGTATTTA
* * *
1702700 CTAAAAGAACTTTAGTGGTAGAAGAGTCTATACTTGTTGTTTTTTATGATAATCCCCTTCCGAGG
196 ATAAAAGAACTTTAGTGGTAGAAGAGTCTATACATGTTGTTTTTGATGATAATCCCCTTCCGAGG
*
1702765 AAGGATTCTTGTATGAGTGATGATGTAGGTATTGTAAAAGC
261 AAGGATTCTTGTATGAGTGACGATGTAGGTATTGTAAAAGC
1702806 TTAGGCTAATTTTAAAGAAAACTCCATATGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTAT
1 TTAGGCTAATTTTAAAGAAAACTCCATATGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTAT
* *
1702871 TTTCATCCTTTTAGATGTCAATGTTTTGTTTTAAACATCGGTAAATAAAATCTTGGAAAATTTGA
66 TTTCATCCTTTTAGATGTAAATGTTTTGTTTTAAACATCGGTAAAGAAAATCTTGGAAAATTTGA
*
1702936 TGCTAAAAGTGATGAAGGAATTTTTCTGATTTATTCCTTAAATTATAAAGCTTATCGAGTATTTA
131 TGCTAAAAGTGATGAAGGAATTTTTCTGAGTTATTCCTTAAATTATAAAGCTTATCGAGTATTTA
* * *
1703001 ATTAAAGAACTTTAGTGGTAGAATAGTCTATACATGTTGTTTTTGATGATAATCCCCTTCCGATG
196 ATAAAAGAACTTTAGTGGTAGAAGAGTCTATACATGTTGTTTTTGATGATAATCCCCTTCCGAGG
* **
1703066 AAGGATTCTTGTGTGAGTGACGATGTATTTATTGTAAAAGC
261 AAGGATTCTTGTATGAGTGACGATGTAGGTATTGTAAAAGC
1703107 AAATGACTTT
Statistics
Matches: 283, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
301 283 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (301 bp):
TTAGGCTAATTTTAAAGAAAACTCCATATGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTAT
TTTCATCCTTTTAGATGTAAATGTTTTGTTTTAAACATCGGTAAAGAAAATCTTGGAAAATTTGA
TGCTAAAAGTGATGAAGGAATTTTTCTGAGTTATTCCTTAAATTATAAAGCTTATCGAGTATTTA
ATAAAAGAACTTTAGTGGTAGAAGAGTCTATACATGTTGTTTTTGATGATAATCCCCTTCCGAGG
AAGGATTCTTGTATGAGTGACGATGTAGGTATTGTAAAAGC
Found at i:1705171 original size:44 final size:44
Alignment explanation
Indices: 1705108--1705210 Score: 145
Period size: 44 Copynumber: 2.3 Consensus size: 44
1705098 TTTGTGCACA
*
1705108 ATGCATCGATACACTATGAAAGTATA-CTGATGCATCCCTTGAAT
1 ATGCATCGATACACTATGAAAGTACACCT-ATGCATCCCTTGAAT
* * *
1705152 ATGCATCGATACACTATGAAGGTGCACCTATGCATGCCTTGAAT
1 ATGCATCGATACACTATGAAAGTACACCTATGCATCCCTTGAAT
*
1705196 GTGCATCGATACACT
1 ATGCATCGATACACT
1705211 TGTCGGGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
44 51 0.96
45 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (44 bp):
ATGCATCGATACACTATGAAAGTACACCTATGCATCCCTTGAAT
Found at i:1705698 original size:13 final size:13
Alignment explanation
Indices: 1705673--1705717 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1705663 AAAATTACAT
1705673 ATTGTTATTCAAAC
1 ATTGTT-TTCAAAC
*
1705687 ATTGTTTTCAAAA
1 ATTGTTTTCAAAC
**
1705700 ATAATTTTCAAAC
1 ATTGTTTTCAAAC
1705713 ATTGT
1 ATTGT
1705718 CCTTTAGGAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:1707170 original size:27 final size:27
Alignment explanation
Indices: 1707128--1707179 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1707118 TGTTTTATTT
*
1707128 TGGATGTTTGAATGTTTGAATTTGATA
1 TGGATGTTTGAATGTTTGAACTTGATA
**
1707155 TGGATGTTTGGGTGTTTGAACTTGA
1 TGGATGTTTGAATGTTTGAACTTGA
1707180 ATGCTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (27 bp):
TGGATGTTTGAATGTTTGAACTTGATA
Found at i:1707461 original size:12 final size:14
Alignment explanation
Indices: 1707434--1707468 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1707424 AGGGGGAGTA
1707434 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
1707448 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
1707460 ATTTTCAAA
1 ATTTTCAAA
1707469 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:1707706 original size:18 final size:18
Alignment explanation
Indices: 1707671--1707720 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1707661 ACTAAAGTGT
* *
1707671 AAAT-TTTTTTAAATTTA
1 AAATATTTTTGAAACTTA
1707688 AAATATTTTTGAAACTTA
1 AAATATTTTTGAAACTTA
1707706 AAATATTTTTGAAAC
1 AAATATTTTTGAAAC
1707721 AATTTTGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 4 0.13
18 26 0.87
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (18 bp):
AAATATTTTTGAAACTTA
Found at i:1707893 original size:64 final size:65
Alignment explanation
Indices: 1707819--1707975 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 65
1707809 ACACCCTAAT
* * *
1707819 TCGAATGCATTTTGTGTACCAATGCACA-ACCATGCATCAATGCACTCCT-GATTTTATTGAAAC
1 TCGAATGCATTTAGTGTACCGATGCACATACCATGCATCAATGCACTCCTGGATCTT-TTGAAAC
1707882 A
65 A
* ** *
1707883 TCGAATGCATTTAATGTACCGATGCACATACCATGCATTGATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTAGTGTACCGATGCACATACCATGCATCAATGCACTCCTGGATCTTTTGAAACA
* * *
1707948 TCAAATGTAATTAGTGTACCGATGCACA
1 TCGAATGCATTTAGTGTACCGATGCACA
1707976 CCAAGTGTAC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 25 0.31
65 51 0.64
66 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTAGTGTACCGATGCACATACCATGCATCAATGCACTCCTGGATCTTTTGAAACA
Found at i:1707990 original size:65 final size:64
Alignment explanation
Indices: 1707833--1707994 Score: 168
Period size: 65 Copynumber: 2.5 Consensus size: 64
1707823 ATGCATTTTG
* * * * *
1707833 TGTACCAATGCACAACCATGCA-TCAATGCACTCCTGATTTTATTGAAACATCGAATGCATTTAA
1 TGTACCGATGCACAACCATGCACT-GATGCACTCCTGATCTTATTGAAACATCAAATGCAATTAA
* * *
1707897 TGTACCGATGCACATACCATGCATTGATGCACTCCTGGCTCTT-TTGAAACATCAAATGTAATTA
1 TGTACCGATGCACA-ACCATGCACTGATGCACTCCT-GATCTTATTGAAACATCAAATGCAATTA
*
1707961 G
64 A
*
1707962 TGTACCGATGCAC-ACCAAGTGTACTGATGCACT
1 TGTACCGATGCACAACC-A-TGCACTGATGCACT
1707995 AGGTCTTATA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 3 0.04
64 14 0.17
65 61 0.73
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
TGTACCGATGCACAACCATGCACTGATGCACTCCTGATCTTATTGAAACATCAAATGCAATTAA
Done.