Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 54
Found at i:3145380 original size:65 final size:63
Alignment explanation
Indices: 3145195--3145383 Score: 163
Period size: 65 Copynumber: 2.9 Consensus size: 63
3145185 GTTGGGAGCG
* * * *
3145195 TCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATTGCTGGTGCATCGATGC
1 TCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTTGGTGCATCGATGC
3145258 A
63 A
* * *
3145259 TCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATTGGTGTATGGTAT-GTGCATCGATGC
1 TCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGTGCATCGATGC
3145323 A
63 A
* **
3145324 TGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGTGCATCG
1 TCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGTGCATCG
3145384 GTACATCACT
Statistics
Matches: 102, Mismatches: 13, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 34 0.33
65 56 0.55
66 5 0.05
67 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (63 bp):
TCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGCATCGATGCA
Found at i:3146550 original size:9 final size:9
Alignment explanation
Indices: 3146536--3146595 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
3146526 ACCGTGTCTA
3146536 GACCGAGCT
1 GACCGAGCT
*
3146545 GACCGAGCC
1 GACCGAGCT
*
3146554 GACCAAGCT
1 GACCGAGCT
* *
3146563 GATCAAG-T
1 GACCGAGCT
3146571 CGACCGAGCT
1 -GACCGAGCT
*
3146581 GACTGAGCT
1 GACCGAGCT
3146590 GACCGA
1 GACCGA
3146596 TCGAGCCGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 1 0.02
9 39 0.95
10 1 0.02
ACGTcount: A:0.27, C:0.32, G:0.30, T:0.12
Consensus pattern (9 bp):
GACCGAGCT
Found at i:3146562 original size:18 final size:18
Alignment explanation
Indices: 3146536--3146595 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
3146526 ACCGTGTCTA
3146536 GACCGAGCTGACCGAGCC
1 GACCGAGCTGACCGAGCC
* * * *
3146554 GACCAAGCTGATCAAGTC
1 GACCGAGCTGACCGAGCC
* *
3146572 GACCGAGCTGACTGAGCT
1 GACCGAGCTGACCGAGCC
3146590 GACCGA
1 GACCGA
3146596 TCGAGCCGAC
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.27, C:0.32, G:0.30, T:0.12
Consensus pattern (18 bp):
GACCGAGCTGACCGAGCC
Found at i:3146600 original size:22 final size:21
Alignment explanation
Indices: 3146575--3146632 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
3146565 TCAAGTCGAC
3146575 CGAGCTGACTGAGCTGA-CCGAT
1 CGAGCTGACTGAGCT-ACCCG-T
*
3146597 CGAGCCGACTGAGCTACCCGT
1 CGAGCTGACTGAGCTACCCGT
*
3146618 CTGAGCTGACCGAGC
1 C-GAGCTGACTGAGC
3146633 CGCCTGACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.16
Consensus pattern (21 bp):
CGAGCTGACTGAGCTACCCGT
Found at i:3149013 original size:10 final size:11
Alignment explanation
Indices: 3148984--3149014 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
3148974 CATGATGTTT
3148984 AAGAAAAAAGA
1 AAGAAAAAAGA
3148995 AAGAAAAAAGA
1 AAGAAAAAAGA
3149006 AAGTAAAAA
1 AAG-AAAAA
3149015 CCTATTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:3149165 original size:2 final size:2
Alignment explanation
Indices: 3149158--3149203 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3149148 TTTGTATACA
3149158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3149200 AT AT
1 AT AT
3149204 GAGTCTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3150283 original size:12 final size:12
Alignment explanation
Indices: 3150266--3150290 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3150256 ATTTACATAA
3150266 ATAAATATATAT
1 ATAAATATATAT
3150278 ATAAATATATAT
1 ATAAATATATAT
3150290 A
1 A
3150291 ATTTATGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:3151022 original size:26 final size:26
Alignment explanation
Indices: 3150986--3151037 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3150976 AAAATTATCG
3150986 AAAGAAATTTTCTAATACGTGAATAT
1 AAAGAAATTTTCTAATACGTGAATAT
3151012 AAAGAAATTTTCTAATACGTGAATAT
1 AAAGAAATTTTCTAATACGTGAATAT
3151038 TTAATCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (26 bp):
AAAGAAATTTTCTAATACGTGAATAT
Found at i:3155089 original size:21 final size:21
Alignment explanation
Indices: 3155056--3155097 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3155046 ATCGTGGAAA
* *
3155056 AGCTTCAAATATTGGTGTTAC
1 AGCTCCAAATATTGGTATTAC
*
3155077 AGCTCCAACTATTGGTATTAC
1 AGCTCCAAATATTGGTATTAC
3155098 CTCTGAAGAA
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:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (21 bp):
AGCTCCAAATATTGGTATTAC
Found at i:3162124 original size:11 final size:12
Alignment explanation
Indices: 3162106--3162138 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3162096 AAAAGGAAAA
3162106 AGGAAAAAAATG
1 AGGAAAAAAATG
3162118 AGGAAAAAAATG
1 AGGAAAAAAATG
3162130 AGGAAAAAA
1 AGGAAAAAA
3162139 GAAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (12 bp):
AGGAAAAAAATG
Found at i:3163692 original size:110 final size:111
Alignment explanation
Indices: 3163390--3163808 Score: 592
Period size: 111 Copynumber: 3.8 Consensus size: 111
3163380 ACAGTGGAAA
* *
3163390 GGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCATATTCCAAAAT
1 GGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCCTATTCCAAGAT
* * * *
3163455 TTGATATTCCCTGAGTAACATCGGAACAAGTCTACCACGATTTAAT
66 TTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTCAAT
* * * * *
3163501 AGATTAACTCCTCCAGATCTGATATTCTCTTAGAAGAAGTGGAACATATCACTCTATTCCAAGAT
1 GGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCCTATTCCAAGAT
*
3163566 TTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCGATTCAAT
66 TTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTCAAT
*
3163612 GGATCAACTCCTCCAGATCTGATATT-CCTTAGAAGAAGTGGAACAGATCACCCTATTCCAACAT
1 GGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCCTATTCCAAGAT
* *
3163676 TTGATATTCCCTGAGTGACAGCGGAATAAGTCTACCCCAATTCAAT
66 TTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTCAAT
* * * * * *
3163722 GGATCAACTCCCCCATATCTGATATTCCCTTTAGAAGAAGCGGAATAGATC-CCTCTCATCCCCA
1 GGATCAACTCCTCCAGATCTGATATTCCC-TTAGAAGAAGTGGAACAGATCACC-CT-ATTCCAA
3163786 GATTTGATA-TCCCTTGAGTGACA
63 GATTTGATATTCCC-TGAGTGACA
3163809 TTGGAACTGA
Statistics
Matches: 275, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
110 101 0.37
111 127 0.46
112 25 0.09
113 22 0.08
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (111 bp):
GGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACCCTATTCCAAGAT
TTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCCGATTCAAT
Found at i:3163948 original size:3 final size:3
Alignment explanation
Indices: 3163940--3163979 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
3163930 TTTGGTCCCG
*
3163940 TTA TTA TTAA GTTA TGA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3163980 TAAGATTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.88
4 2 0.06
5 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3165477 original size:2 final size:2
Alignment explanation
Indices: 3165470--3165531 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3165460 TTTTGTAAGG
3165470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3165512 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3165532 TCATAGATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3165711 original size:2 final size:2
Alignment explanation
Indices: 3165694--3165731 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3165684 ATTTTTATTA
* *
3165694 AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3165732 TTAGTTGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3169616 original size:30 final size:30
Alignment explanation
Indices: 3169582--3169648 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3169572 ACCGGTTTAG
*
3169582 CCGAGCCACCTAGACCGAACCGTTCCTAAA
1 CCGAGCCACCTAGACCGAACCGTACCTAAA
** * * *
3169612 CCGAGCTGCCTGGACTGAACCGTACCTAGA
1 CCGAGCCACCTAGACCGAACCGTACCTAAA
3169642 CCGAGCC
1 CCGAGCC
3169649 GACTGAGTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.39, G:0.22, T:0.13
Consensus pattern (30 bp):
CCGAGCCACCTAGACCGAACCGTACCTAAA
Found at i:3180772 original size:21 final size:21
Alignment explanation
Indices: 3180742--3180785 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3180732 AGACGAGCTC
* *
3180742 TGGCTTTGAAGTAAGGCACCT
1 TGGCTATGAAGTAAAGCACCT
*
3180763 TGGCTATGAAGTAAAGCTCCT
1 TGGCTATGAAGTAAAGCACCT
3180784 TG
1 TG
3180786 ATTCTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (21 bp):
TGGCTATGAAGTAAAGCACCT
Found at i:3180863 original size:25 final size:25
Alignment explanation
Indices: 3180835--3180892 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
3180825 CGTAGTGGAT
3180835 ATGAACTCTTGAATTGTAGCTTCCA
1 ATGAACTCTTGAATTGTAGCTTCCA
3180860 ATGAACTCTTGAATTGTAGCTTCCA
1 ATGAACTCTTGAATTGTAGCTTCCA
3180885 ATGAACTC
1 ATGAACTC
3180893 ATGCTTGCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (25 bp):
ATGAACTCTTGAATTGTAGCTTCCA
Found at i:3183136 original size:24 final size:24
Alignment explanation
Indices: 3183092--3183141 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3183082 ATAAAGAACC
*
3183092 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
3183116 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
3183140 AA
1 AA
3183142 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:3191234 original size:210 final size:211
Alignment explanation
Indices: 3190984--3191423 Score: 668
Period size: 210 Copynumber: 2.1 Consensus size: 211
3190974 CAGAGCCAAT
*
3190984 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
* * * ** * *
3191049 AACAAATAATTTCCCAATTTTAGGCTTAATTTTAACTTCACATCGAAGGATATTGGACTCGAGAC
66 AACAAATAATTTCCCAATTTCAGGCTCAATTTCAACTTCACATCGAAGGATATTAAACTCAAAAC
* * * * *
3191114 -CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCTGAG
131 ACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGAG
3191178 CCAATTTCAACTTCAC
196 CCAATTTCAACTTCAC
3191194 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
*
3191259 AACAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAAACTCAAAAC
66 AACAAATAATTTCCCAATTTCAGGCTCAATTTCAACTTCACATCGAAGGATATTAAACTCAAAAC
* * * * *
3191324 AGCACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCTGTCAACAAACAATTTTCCAGTTCCAGA
131 A-CACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGA
3191389 GCCAATTTCAACTTCAC
195 GCCAATTTCAACTTCAC
*
3191406 -GACGGAGGATATTGGACT
1 AG-CGAAGGATATTGGACT
3191424 TGGAACAATA
Statistics
Matches: 207, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
210 121 0.58
211 1 0.00
212 85 0.41
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (211 bp):
AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
AACAAATAATTTCCCAATTTCAGGCTCAATTTCAACTTCACATCGAAGGATATTAAACTCAAAAC
ACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGAG
CCAATTTCAACTTCAC
Found at i:3191276 original size:106 final size:105
Alignment explanation
Indices: 3190984--3191423 Score: 607
Period size: 106 Copynumber: 4.2 Consensus size: 105
3190974 CAGAGCCAAT
*
3190984 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
* * *
3191049 AACAAATAATTTCCCAATTTTAG-GCTTAATTTTAACTTCAC
65 AACAAATAATTTCCCAATTTCAGAGC-CAATTTCAACTTCAC
*
3191090 ATCGAAGGATATTGGACTCGAGAC-CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCA
1 AGCGAAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCA
*
3191154 ACAAATAATTTCCCAATTTCTGAGCCAATTTCAACTTCAC
66 ACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC
3191194 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
* *
3191259 AACAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCAC
65 AACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC
* ** * * * * * * *
3191300 ATCGAAGGATATTAAACTCAAAACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCTGTC
1 AGCGAAGGATATTGGACTCGAGACA-CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
* * * *
3191365 AACAAACAATTTTCCAGTTCCAGAGCCAATTTCAACTTCAC
65 AACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC
*
3191406 -GACGGAGGATATTGGACT
1 AG-CGAAGGATATTGGACT
3191424 TGGAACAATA
Statistics
Matches: 299, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
104 95 0.32
105 3 0.01
106 201 0.67
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (105 bp):
AGCGAAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCA
ACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC
Found at i:3191955 original size:35 final size:35
Alignment explanation
Indices: 3191909--3191980 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3191899 CCAAAAAAGA
3191909 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
3191944 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
3191979 AG
1 AG
3191981 TGTTTTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:3192379 original size:17 final size:18
Alignment explanation
Indices: 3192353--3192392 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3192343 ATTATATGGA
3192353 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
3192369 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
3192387 TATTAT
1 TATTAT
3192393 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:3192455 original size:2 final size:2
Alignment explanation
Indices: 3192450--3192474 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3192440 TACTATATTT
3192450 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
3192475 TTCTTTAATA
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:3192844 original size:41 final size:39
Alignment explanation
Indices: 3192799--3192875 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
3192789 AGGACTCATT
* *
3192799 TTTTTGTTTTATTTCTAACTAAAGTCTCTCTCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CTCCCACTTTCCTC
*
3192840 TTTTTGTCTTATTTCTGACTAAAGCCTCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCTCCCACTTTC
3192876 GGTAAAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 10 0.30
40 1 0.03
41 22 0.67
ACGTcount: A:0.17, C:0.26, G:0.06, T:0.51
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCTCCCACTTTCCTC
Found at i:3193047 original size:9 final size:9
Alignment explanation
Indices: 3193043--3193084 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
3193033 CCTTATCTTA
3193043 TTTATTTAT
1 TTTATTTAT
3193052 TTTATTTAT
1 TTTATTTAT
3193061 TTTATTT-T
1 TTTATTTAT
3193069 TTCCT-TTTAT
1 TT--TATTTAT
3193079 TTTATT
1 TTTATT
3193085 CTCTTTATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 4 0.14
9 21 0.72
10 4 0.14
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:3193056 original size:18 final size:17
Alignment explanation
Indices: 3193011--3193119 Score: 73
Period size: 18 Copynumber: 6.2 Consensus size: 17
3193001 CTATATATAA
3193011 TTATTTTTTTA-C-TAT
1 TTATTTTTTTATCTTAT
3193026 TT-TTTTTCCTTATCTTAT
1 TTATTTTT--TTATCTTAT
3193044 TTATTTATTTTAT-TTATT
1 TTATTT-TTTTATCTTA-T
** *
3193062 TTATTTTTTCCTTTTATT
1 TTATTTTTTTATCTTA-T
*
3193080 TTATTCTCTTTATCTTAT
1 TTATT-TTTTTATCTTAT
* *
3193098 TTGTTTTCTTTACCTTAT
1 TTATTTT-TTTATCTTAT
3193116 TTAT
1 TTAT
3193120 CTAACACATT
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
14 5 0.07
15 2 0.03
16 3 0.04
17 9 0.12
18 43 0.58
19 10 0.14
20 2 0.03
ACGTcount: A:0.16, C:0.11, G:0.01, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTATCTTAT
Found at i:3193060 original size:22 final size:22
Alignment explanation
Indices: 3193035--3193080 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3193025 TTTTTTTTCC
3193035 TTATCTTATTTATTT-ATTTTAT
1 TTATCTTATTT-TTTCATTTTAT
* *
3193057 TTATTTTATTTTTTCCTTTTAT
1 TTATCTTATTTTTTCATTTTAT
3193079 TT
1 TT
3193081 TATTCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATCTTATTTTTTCATTTTAT
Found at i:3194492 original size:44 final size:42
Alignment explanation
Indices: 3194444--3194561 Score: 103
Period size: 44 Copynumber: 2.8 Consensus size: 42
3194434 CGTTTACATT
3194444 AAAAACACCAATAAAGTACATCATTATTGCGGCATTTATTACGA
1 AAAAACACCAATAAAGTACATCATTATTGCGGCATTTATTA--A
** * * * * * *
3194488 AAAAATGCCACTAAATTACATTATTATTGCCGCGTTTATTAT
1 AAAAACACCAATAAAGTACATCATTATTGCGGCATTTATTAA
* * *
3194530 AAAAACA-CAATTAAAGTATATGACTATTGCGG
1 AAAAACACCAA-TAAAGTACATCATTATTGCGG
3194562 TGTTTGAACA
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
41 2 0.04
42 21 0.37
44 34 0.60
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (42 bp):
AAAAACACCAATAAAGTACATCATTATTGCGGCATTTATTAA
Found at i:3194813 original size:83 final size:81
Alignment explanation
Indices: 3194721--3194887 Score: 289
Period size: 83 Copynumber: 2.0 Consensus size: 81
3194711 TACTACTCTG
* *
3194721 TTGCGGCATTTGTATACAAATGTCGCTAAAGTACTTCTTTGTTGTGGCGTTTGTTGTAAAAATGC
1 TTGCGGCATTTCTATACAAATGCCGCTAAAGTAC-TCTTTGTTGTGGCGTTTGTTG-AAAAATGC
3194786 CACTATATATGAACCCTA
64 CACTATATATGAACCCTA
*
3194804 TTGCGGCATTTCTATACAAATGCCTCTAAAGTACTCTTTGTTGTGGCGTTTGTTGAAAAATGCCA
1 TTGCGGCATTTCTATACAAATGCCGCTAAAGTACTCTTTGTTGTGGCGTTTGTTGAAAAATGCCA
3194869 CTATATATGAACCCTA
66 CTATATATGAACCCTA
3194885 TTG
1 TTG
3194888 TGGCGTTTAT
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
81 29 0.36
82 21 0.26
83 31 0.38
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (81 bp):
TTGCGGCATTTCTATACAAATGCCGCTAAAGTACTCTTTGTTGTGGCGTTTGTTGAAAAATGCCA
CTATATATGAACCCTA
Found at i:3194891 original size:41 final size:41
Alignment explanation
Indices: 3194762--3194895 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
3194752 TACTTCTTTG
3194762 TTGTGGCGTTTGTTGTAAAAATGCCACTATATATGAACCCTA
1 TTGTGGCGTTTGTTG-AAAAATGCCACTATATATGAACCCTA
* * * * * * * *
3194804 TTGCGGCATTTCTAT-ACAAATGCCTCTA-A-A-GTACTCTTTG
1 TTGTGGCGTTTGT-TGAAAAATGCCACTATATATGAAC-C-CTA
3194844 TTGTGGCGTTTGTTGAAAAATGCCACTATATATGAACCCTA
1 TTGTGGCGTTTGTTGAAAAATGCCACTATATATGAACCCTA
3194885 TTGTGGCGTTT
1 TTGTGGCGTTT
3194896 ATATAAAAAC
Statistics
Matches: 69, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 23 0.33
41 24 0.35
42 12 0.17
43 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (41 bp):
TTGTGGCGTTTGTTGAAAAATGCCACTATATATGAACCCTA
Found at i:3197014 original size:29 final size:29
Alignment explanation
Indices: 3196972--3197030 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3196962 AAAGAGATAG
3196972 TCTATTTCAGGAGTTGTGTTGAAATCTCT
1 TCTATTTCAGGAGTTGTGTTGAAATCTCT
*
3197001 TCTATTTCAGGAGTTTTGTTGAAATCTCT
1 TCTATTTCAGGAGTTGTGTTGAAATCTCT
3197030 T
1 T
3197031 GTAATAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (29 bp):
TCTATTTCAGGAGTTGTGTTGAAATCTCT
Found at i:3201931 original size:17 final size:17
Alignment explanation
Indices: 3201909--3201950 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3201899 ATATATACAT
*
3201909 ATAATAATAATACATGA
1 ATAATAATAATAAATGA
*
3201926 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
3201943 ATAA-AATA
1 ATAATAATA
3201951 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:3203237 original size:105 final size:103
Alignment explanation
Indices: 3202939--3203525 Score: 802
Period size: 105 Copynumber: 5.7 Consensus size: 103
3202929 CATTGTTCCA
* * * * ** *
3202939 AGTCCAATATCCTCCATCGTTAAGTTGAAATTGGCTCTGGAACCAGGAAATTGTTTGTTGAC-AC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG-A-TTGGAAATTG-TTGTTGACAAG
* * *
3203003 CAGCCGTCCCTTCGT-GTGAAGTTGAACTTGTGTTGTCTCG
63 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
3203043 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCT-GAAT-GAAATT-TTGTTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGAAATTGTTGTTGACAAGCAG
*
3203105 CGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3203143 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAATTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGATT-GGAAATTGTTGTTGACAAGC
*
3203208 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3203248 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT-GAAATT-TTGTTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGAAATTGTTGTTGACAAGCAG
3203310 CGGTCCCTTCG-CGTGAAGTTGAACTTGCGTTGTCTGG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3203347 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGAAA-TTGTTGTTGACAAGC
*
3203412 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3203452 A-TCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAGTTGTTGTTGACAACCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGAAATTGTTGTTGACAAGCA
3203515 GC-GTCCCTTCG
65 GCGGTCCCTTCG
3203526 GCTGTCTGGA
Statistics
Matches: 436, Mismatches: 34, Indels: 29
0.87 0.07 0.06
Matches are distributed among these distances:
98 8 0.02
99 75 0.17
100 88 0.20
101 17 0.04
102 25 0.06
103 47 0.11
104 65 0.15
105 111 0.25
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (103 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGAAATTGTTGTTGACAAGCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:3203339 original size:204 final size:205
Alignment explanation
Indices: 3202939--3203525 Score: 864
Period size: 204 Copynumber: 2.9 Consensus size: 205
3202929 CATTGTTCCA
* * * * *** *
3202939 AGTCCAATATCCTCCATCGTTAAGTTGAAATTGGCTCTGGAACCAGGAAATTGTTTGTTGAC-AC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTG-TTGTTGACAAA
* ** *
3203003 CAGCCGTCCCTTCGT-GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
** *
3203067 TTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCATTCGTCGTGAAGTTGAACTT
130 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
3203132 GCGTTGTCTGG
195 GCGTTGTCTGG
* * *
3203143 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAATTTGTTGTTGACAAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTGTTGTTGACAAAC
*
3203208 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
3203273 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCG-CGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
3203337 CGTTGTCTGG
196 CGTTGTCTGG
* *
3203347 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAA-TTGTTGTTGACAAA
3203411 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGA-TCC-ATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
3203474 TTGAAATTGGCTCTGAGATTGGAAGTTGTTGTTGACAACCAGC-GTCCCTTCG
130 TTGAAATTGGCTCTGA-A-T-GAAATT-TTGTTGACAAGCAGCGGTCCCTTCG
3203526 GCTGTCTGGA
Statistics
Matches: 349, Mismatches: 27, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
202 33 0.09
203 16 0.05
204 181 0.52
205 105 0.30
206 14 0.04
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (205 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTGTTGTTGACAAAC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGG
Found at i:3203660 original size:293 final size:302
Alignment explanation
Indices: 3202939--3203991 Score: 1193
Period size: 293 Copynumber: 3.4 Consensus size: 302
3202929 CATTGTTCCA
* * * * **
3202939 AGTCCAATATCCTCCATCGTTAAGTTGAAATTGGCTCTGGAACCAGGAAA-TTGTTTGTTGAC-A
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA--TTGAAAGTTG-TTGTTGACAA
* * ** * *
3203002 CCAGCCGTCCCTTCGT-GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
62 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTCCGTTGTGAA
** * *
3203066 GTTGAAATTGAATCTGA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCATTCGTCGTGAAGTT
127 GTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * **
3203126 GAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGG-
192 GAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
3203190 AATTTG-TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
257 AAATTGTTTATTGACAACCAGCGGTCCCTTC-TCG-G-A---G--C--G---TGTCTGG
*
3203248 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-TT-TTGTTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAAGTTGTTGTTGACAAGCAG
*
3203310 CGGTCCCTTCG-CGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTG
*
3203374 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* * *
3203439 TTGCATTGTCTGGA-TCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GG-AAGT
196 TTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAAT
*
3203500 TG-TTGTTGACAACCAGC-GTCCC-T-TC-G-GC-TGTCTGG
261 TGTTTATTGACAACCAGCGGTCCCTTCTCGGAGCGTGTCTGG
*
3203535 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATT-GAAAGTTGTTGTTGACAAGC
*
3203600 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTCCGTTGTGAAGT
*
3203665 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
129 TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
*
3203730 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
194 ACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
3203795 ATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
259 ATTGTTTATTGACAACCAGCGGTCCCTTC-TC-----G--G-A---GCG-TGTCTGG
*
3203852 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGA-AAGTTG-TTGTTGACAAG
* * ** * * *
3203917 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATTCTCCGTCGTG
63 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT-CCA--ATATCCTCCGTTGTG
*
3203982 GAGTTGAAAT
125 AAGTTGAAAT
3203992 CGCGGATGGC
Statistics
Matches: 660, Mismatches: 41, Indels: 74
0.85 0.05 0.10
Matches are distributed among these distances:
287 45 0.07
288 1 0.00
289 1 0.00
290 4 0.01
291 2 0.00
292 25 0.04
293 128 0.19
294 3 0.00
295 37 0.06
296 2 0.00
297 5 0.01
298 14 0.02
299 5 0.01
300 2 0.00
302 4 0.01
303 8 0.01
304 75 0.11
305 12 0.02
306 22 0.03
307 40 0.06
308 8 0.01
309 84 0.13
310 1 0.00
315 2 0.00
316 2 0.00
317 54 0.08
318 50 0.08
319 3 0.00
321 21 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (302 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAAGTTGTTGTTGACAAGCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTG
AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAAT
TGTTTATTGACAACCAGCGGTCCCTTCTCGGAGCGTGTCTGG
Found at i:3203695 original size:188 final size:191
Alignment explanation
Indices: 3203136--3203930 Score: 976
Period size: 188 Copynumber: 4.0 Consensus size: 191
3203126 GAACTTGCGT
* * * * *
3203136 TGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAATTTGTTGTT
1 TGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTT
* *
3203201 GACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCT
66 GACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTT
* * *
3203266 GTGAAGTTGAAATTGGCTCTGA-A-T-GAAATTTTGTTGACAAGCAGCGGTCCCTTCGCGTGAAG
131 GTGAAGTTGAAATTGGCTCTGAGATTGGGAATGTTGTTGACAACCAGC-GTCCCTT--C------
3203328 TTGAACTTGCG
187 --G-A---GCG
3203339 TTGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGT
1 -TGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGT
3203404 TGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGA-TCC-ATATCCTTCGT
65 TGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGT
3203467 TGTGAAGTTGAAATTGGCTCTGAGATT-GGAAGTTGTTGTTGACAACCAGCGTCCCTTCG-GC-
130 TGTGAAGTTGAAATTGGCTCTGAGATTGGGAA--TGTTGTTGACAACCAGCGTCCCTTCGAGCG
3203528 TGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTT
1 TGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTT
3203593 GACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTT
66 GACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTT
3203658 GTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTG
131 GTGAAGTTGAAATTGGCTCTGAGATTGGGAA--TGTTGTTGACAACCAGC-GTCCC-T--TC---
3203723 AAGTTGAACTTGCG
187 -----G-A---GCG
* * * *
3203737 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTT
1 -TGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTG-TT
* * *
3203802 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
63 GTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTC
* *
3203867 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCG
128 GTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAA--TG-TTGTTGACAACCAG-CGTCCCTTCG
3203931 TTGTGAAGTT
Statistics
Matches: 542, Mismatches: 19, Indels: 62
0.87 0.03 0.10
Matches are distributed among these distances:
188 113 0.21
189 3 0.01
190 40 0.07
191 23 0.04
192 5 0.01
193 1 0.00
195 3 0.01
202 34 0.06
203 6 0.01
204 111 0.20
205 7 0.01
206 15 0.03
208 2 0.00
210 50 0.09
211 8 0.01
212 101 0.19
213 19 0.04
214 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (191 bp):
TGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTT
GACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTT
GTGAAGTTGAAATTGGCTCTGAGATTGGGAATGTTGTTGACAACCAGCGTCCCTTCGAGCG
Found at i:3203710 original size:105 final size:106
Alignment explanation
Indices: 3203528--3203960 Score: 717
Period size: 105 Copynumber: 4.1 Consensus size: 106
3203518 TCCCTTCGGC
* * *
3203528 TGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTG-TTGT
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGT
* *
3203592 TGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCAT
66 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
3203633 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGT
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGT
3203697 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
66 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
* * *
3203738 TGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTA
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAGTTGTTTG
3203803 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
65 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
3203845 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGT
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGT
* * *
3203910 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
66 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
3203951 TGTCTCGAGT
1 TGTCTGGAGT
3203961 GCCACGATAT
Statistics
Matches: 310, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
105 153 0.49
106 61 0.20
107 96 0.31
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (106 bp):
TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGT
TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
Found at i:3203904 original size:212 final size:211
Alignment explanation
Indices: 3203528--3203991 Score: 725
Period size: 212 Copynumber: 2.2 Consensus size: 211
3203518 TCCCTTCGGC
* * * *
3203528 TGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTT
1 TGTCTGGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTATT
*
3203593 GACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTT
66 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTT
* * *
3203658 GTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGT
131 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGT
3203722 GAAGTTGAACTTGCGT
196 GAAGTTGAACTTGCGT
*
3203738 TGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTA
1 TGTCTGGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAATTG-TTA
*
3203803 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
64 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCG
*
3203868 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTT
129 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTC
*
3203933 GTGAAGTTGAACTTGTGT
194 GTGAAGTTGAACTTGCGT
* * *
3203951 TGTCTCGAGTGCCACGATATTCTCCG-TCGTGGAGTTGAAAT
1 TGTCTGGAGT-CCA--ATATCCTCCGCT-GTGAAGTTGAAAT
3203992 CGCGGATGGC
Statistics
Matches: 231, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
210 48 0.21
211 8 0.03
212 100 0.43
213 51 0.22
214 3 0.01
215 1 0.00
216 20 0.09
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (211 bp):
TGTCTGGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTATT
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTT
GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGT
GAAGTTGAACTTGCGT
Found at i:3204771 original size:67 final size:67
Alignment explanation
Indices: 3204700--3204858 Score: 241
Period size: 67 Copynumber: 2.4 Consensus size: 67
3204690 AGAACGAAAT
* *
3204700 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATAGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGAC
3204763 AAAA
64 AAAA
*
3204767 TTTGTTTCGAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
3204832 AA
66 AA
**
3204834 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
3204859 GAGAGACGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 79 0.94
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
AA
Found at i:3204783 original size:36 final size:35
Alignment explanation
Indices: 3204733--3205005 Score: 196
Period size: 36 Copynumber: 7.9 Consensus size: 35
3204723 AAAGATTTTG
*
3204733 TGTTTCAAGAGAAACTGTCTCATAGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCA-AGGAGACAAAATT
* ** **
3204769 TGTTTCGAGGGAAACAATCTCAA--AG---ATTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
*
3204799 GTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTC-AAGGAGACAAAATT
* * *
3204836 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
** * * *
3204872 CATTTCAAGGGAAA-TGTTTTCAA--TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGAGACAAAATT
3204900 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAA-GGAGACAAAA-TT
* *
3204938 TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
3204974 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAA
3205006 TGGTGAGCAC
Statistics
Matches: 184, Mismatches: 30, Indels: 46
0.71 0.12 0.18
Matches are distributed among these distances:
28 5 0.03
29 13 0.07
30 5 0.03
31 17 0.09
32 3 0.02
33 3 0.02
34 2 0.01
35 5 0.03
36 97 0.53
37 30 0.16
38 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
Found at i:3204883 original size:103 final size:101
Alignment explanation
Indices: 3204733--3204988 Score: 309
Period size: 103 Copynumber: 2.5 Consensus size: 101
3204723 AAAGATTTTG
* *
3204733 TGTTTCAAGAGAAACTGTCTCATAG-GAGACAAAATTTGTTTCGAGGGAAACAATCTCAAAGATT
1 TGTTTCAAGGGAAACTGTCTCA-AGAGAGAC-AAATTTGTTTCAAGGGAAACAATCTCAAAG--T
*
3204797 TTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAA-TT
62 TTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
* * ** *** * *
3204836 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGGGAAACAATCTCAAAGTTTA
* *
3204901 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTT
65 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
*
3204938 TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA-TTTGTTTCAAGGGAAAC
3204989 TGTCTCAAGA
Statistics
Matches: 129, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
101 38 0.29
102 45 0.35
103 46 0.36
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (101 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTGTTTCAAGGGAAACAATCTCAAAGTTTAT
GTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
Found at i:3205470 original size:18 final size:18
Alignment explanation
Indices: 3205443--3205478 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3205433 TGATGAATCC
* *
3205443 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
3205461 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
3205479 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:3205917 original size:22 final size:22
Alignment explanation
Indices: 3205892--3205961 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
3205882 TTGTGTTTGG
*
3205892 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
3205914 TC-AAGGTTTAACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
* *
3205935 TTAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
3205957 TCAAA
1 TCAAA
3205962 AGATTGATGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 18 0.44
22 23 0.56
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:3205919 original size:21 final size:21
Alignment explanation
Indices: 3205895--3205960 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
3205885 TGTTTGGTCA
*
3205895 AAGGTTTGGCATTTGATGCTC
1 AAGGTTTGACATTTGATGCTC
* *
3205916 AAGGTTTAACATTTGATGCTTA
1 AAGGTTTGACATTTGATGC-TC
*
3205938 AAGGTTTGACATTGGATGCTC
1 AAGGTTTGACATTTGATGCTC
3205959 AA
1 AA
3205961 AAGATTGATG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (21 bp):
AAGGTTTGACATTTGATGCTC
Found at i:3205968 original size:22 final size:22
Alignment explanation
Indices: 3205924--3205968 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3205914 TCAAGGTTTA
* * * *
3205924 ACATTTGATGCTTAAAGGTTTG
1 ACATTGGATGCTCAAAAGATTG
3205946 ACATTGGATGCTCAAAAGATTG
1 ACATTGGATGCTCAAAAGATTG
3205968 A
1 A
3205969 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (22 bp):
ACATTGGATGCTCAAAAGATTG
Found at i:3206622 original size:23 final size:22
Alignment explanation
Indices: 3206595--3206668 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
3206585 TTTTTGTCCC
3206595 TTTTTCTTTTTGATTTTTGCTCT
1 TTTTTCTTTTTG-TTTTTGCTCT
* * *
3206618 TTTTTCCTTTTGTTCTTGTTTCT
1 TTTTTCTTTTTGTTTTTG-CTCT
*
3206641 CTTTTTCTTTGTTTTTTTTTGCT-T
1 -TTTTTC-TT-TTTGTTTTTGCTCT
3206665 TTTT
1 TTTT
3206669 GCTTCTTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
22 5 0.12
23 18 0.45
24 7 0.17
25 2 0.05
26 8 0.20
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTTGTTTTTGCTCT
Found at i:3206627 original size:8 final size:7
Alignment explanation
Indices: 3206615--3206684 Score: 61
Period size: 8 Copynumber: 9.1 Consensus size: 7
3206605 TGATTTTTGC
3206615 TCTTTTT
1 TCTTTTT
3206622 TCCTTTTGT
1 T-CTTTT-T
*
3206631 TCTTGTT
1 TCTTTTT
3206638 TCTCTTTT
1 TCT-TTTT
3206646 TCTTTGTT
1 TCTTT-TT
3206654 T-TTTTT
1 TCTTTTT
3206660 TGCTTTTT
1 T-CTTTTT
3206668 TGCTTCTTT
1 T-CTT-TTT
3206677 TCTTTTT
1 TCTTTTT
3206684 T
1 T
3206685 GTTCTTGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
6 3 0.06
7 14 0.26
8 31 0.57
9 6 0.11
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:3206628 original size:16 final size:17
Alignment explanation
Indices: 3206609--3206663 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
3206599 TCTTTTTGAT
*
3206609 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
3206625 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* *
3206642 TTTTTCT-TTGTTT-TT
1 TTTTGCTCTTGTTTCTC
3206657 TTTTGCT
1 TTTTGCT
3206664 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 7 0.22
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:3206683 original size:16 final size:16
Alignment explanation
Indices: 3206640--3206690 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
3206630 TTCTTGTTTC
*
3206640 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
3206656 T-TTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
3206672 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
3206687 TCTT
1 TCTT
3206691 GATTAGATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 11 0.35
17 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:3208688 original size:16 final size:17
Alignment explanation
Indices: 3208667--3208705 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
3208657 CAAATCCTAA
3208667 TCGCATATTTGTCTAG-
1 TCGCATATTTGTCTAGT
3208683 TCGCATATTTGTCTAGT
1 TCGCATATTTGTCTAGT
3208700 TCGCAT
1 TCGCAT
3208706 GCTTTGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (17 bp):
TCGCATATTTGTCTAGT
Found at i:3210247 original size:15 final size:16
Alignment explanation
Indices: 3210214--3210265 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
3210204 ATATATACAT
3210214 ATAAAATAATACAATA
1 ATAAAATAATACAATA
3210230 ATAAAA-AATA-AATGA
1 ATAAAATAATACAAT-A
*
3210245 ATAAAAT-ATCCATATA
1 ATAAAATAATACA-ATA
3210261 ATAAA
1 ATAAA
3210266 TAAAGGGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 13 0.42
17 2 0.06
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (16 bp):
ATAAAATAATACAATA
Found at i:3216092 original size:14 final size:15
Alignment explanation
Indices: 3216062--3216098 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3216052 ATAAGTTAGT
3216062 TAAAA-ATTTAAATA
1 TAAAATATTTAAATA
*
3216076 TAAATTATTTAAA-A
1 TAAAATATTTAAATA
3216090 TAAAATATT
1 TAAAATATT
3216099 AATTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAATATTTAAATA
Found at i:3216226 original size:123 final size:123
Alignment explanation
Indices: 3216086--3216324 Score: 326
Period size: 123 Copynumber: 1.9 Consensus size: 123
3216076 TAAATTATTT
*
3216086 AAAATAAAATATTAATTATATTA-TTTTTATAATATTATTTTAAATAATAATTAGATGCAATATT
1 AAAATAAAATATTAATTATATTATTTTTTATAATATTATTTTAAATAATAATTAGA-CCAA-A-T
* *
3216150 ATTTTAACCT-T-ATTAAAA-ACCCTAAA-TTTTTCTTGCTTTGAAGCCGTCGTGGCCGTTTA
63 A--GTAACCTCTAATTAAAACACCCTAAATTTTTTCTTGCTTTGAAGCCATCGTGGCCGTTTA
* * *
3216209 AAAATAAAATGTTAATTATATTATTTTTTATAATCTTGTTTTAAATAATAATTAGACCAAATAGT
1 AAAATAAAATATTAATTATATTATTTTTTATAATATTATTTTAAATAATAATTAGACCAAATAGT
3216274 AACCTCTAAATTAAAACACCCTAAATTTTTTTCTTGCTTTGAAGCCATCGT
66 AACCTCT-AATTAAAACACCCTAAA-TTTTTTCTTGCTTTGAAGCCATCGT
3216325 TGTTGTTGCC
Statistics
Matches: 103, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
119 6 0.06
120 1 0.01
121 2 0.02
122 8 0.08
123 33 0.32
124 30 0.29
125 23 0.22
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.43
Consensus pattern (123 bp):
AAAATAAAATATTAATTATATTATTTTTTATAATATTATTTTAAATAATAATTAGACCAAATAGT
AACCTCTAATTAAAACACCCTAAATTTTTTCTTGCTTTGAAGCCATCGTGGCCGTTTA
Found at i:3217067 original size:13 final size:14
Alignment explanation
Indices: 3217049--3217077 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3217039 TTAGTGATGA
3217049 TTGAAATT-AAGAT
1 TTGAAATTAAAGAT
3217062 TTGAAATTAAAGAT
1 TTGAAATTAAAGAT
3217076 TT
1 TT
3217078 TGAGAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (14 bp):
TTGAAATTAAAGAT
Found at i:3222936 original size:201 final size:203
Alignment explanation
Indices: 3222591--3222995 Score: 787
Period size: 201 Copynumber: 2.0 Consensus size: 203
3222581 TACCTCAACC
3222591 ACCAAAAAGCAAAACCGTAGAATAACACTTTTAACCGCCCTTGAATTTGGATTCGGTGCTAACTG
1 ACCAAAAAGCAAAACCGTAGAATAACACTTTTAACCGCCCTTGAATTTGGATTCGGTGCTAACTG
3222656 ATGAAACAAATGGCATATACATTGTAACCTGGATCCACAGTACATCAACAAATAACCTGAGCTTC
66 ATGAAACAAATGGCATATACATTGTAACCTGGATCCACAGTACATCAACAAATAACCTGAGCTTC
3222721 GGACTGCAGTTCTATGTGTCACTTCCATCTTGTTTGAAGTTGTCTCAATGTGTC-T-TTGTTCTT
131 GGACTGCAGTTCTATGTGTCACTTCCATCTTGTTTGAAGTTGTCTCAATGTGTCTTGTTGTTCTT
3222784 ACATATCG
196 ACATATCG
3222792 ACCAAAAAGCAAAACCGTAGAATAACACTTTTAACCGCCCTTGAATTTGGATTCGGTGCTAACTG
1 ACCAAAAAGCAAAACCGTAGAATAACACTTTTAACCGCCCTTGAATTTGGATTCGGTGCTAACTG
3222857 ATGAAACAAATGGCATATACATTGTAACCTGGATCCACAGTACATCAACAAATAACCTGAGCTTC
66 ATGAAACAAATGGCATATACATTGTAACCTGGATCCACAGTACATCAACAAATAACCTGAGCTTC
3222922 GGACTGCAGTTCTATGTGTCACTTCCATCTTGTTTGAAGTTGTCTCAATGTGTCTTTGTTGTTCT
131 GGACTGCAGTTCTATGTGTCACTTCCATCTTGTTTGAAGTTGTCTCAATGTGTC-TTGTTGTTCT
3222987 TACATATCG
195 TACATATCG
3222996 GCCAGCACTT
Statistics
Matches: 201, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
201 184 0.92
203 1 0.00
204 16 0.08
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (203 bp):
ACCAAAAAGCAAAACCGTAGAATAACACTTTTAACCGCCCTTGAATTTGGATTCGGTGCTAACTG
ATGAAACAAATGGCATATACATTGTAACCTGGATCCACAGTACATCAACAAATAACCTGAGCTTC
GGACTGCAGTTCTATGTGTCACTTCCATCTTGTTTGAAGTTGTCTCAATGTGTCTTGTTGTTCTT
ACATATCG
Found at i:3223788 original size:2 final size:2
Alignment explanation
Indices: 3223781--3223805 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3223771 CTGATTGAGG
3223781 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 T
3223806 TTTCCCCGTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3229051 original size:16 final size:16
Alignment explanation
Indices: 3229030--3229065 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3229020 AAATTAAAAC
*
3229030 AAAATAAATAATAAAT
1 AAAATAAAAAATAAAT
3229046 AAAATAAAAAATAAAT
1 AAAATAAAAAATAAAT
3229062 AAAA
1 AAAA
3229066 ATGTCGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAAAAAATAAAT
Found at i:3229488 original size:18 final size:18
Alignment explanation
Indices: 3229465--3229503 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3229455 CATACTCGGT
3229465 TGGACTTCCTCCGAGTAA
1 TGGACTTCCTCCGAGTAA
3229483 TGGACTTCCTCCGAGTAA
1 TGGACTTCCTCCGAGTAA
3229501 TGG
1 TGG
3229504 CCATATTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (18 bp):
TGGACTTCCTCCGAGTAA
Found at i:3231106 original size:41 final size:41
Alignment explanation
Indices: 3231061--3231142 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
3231051 CCGTCATATA
3231061 CTATTTGCTAGTAGAACCTATGCAACAAAATAAGATGAAGC
1 CTATTTGCTAGTAGAACCTATGCAACAAAATAAGATGAAGC
*
3231102 CTATTTGTTAGTAGAACCTATGCAACAAAATAAGATGAAGC
1 CTATTTGCTAGTAGAACCTATGCAACAAAATAAGATGAAGC
3231143 ATTTTGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (41 bp):
CTATTTGCTAGTAGAACCTATGCAACAAAATAAGATGAAGC
Found at i:3231285 original size:2 final size:2
Alignment explanation
Indices: 3231278--3231364 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
3231268 AGTAAATGCT
3231278 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3231320 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3231362 TC T
1 TC T
3231365 ATATATATAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3231369 original size:2 final size:2
Alignment explanation
Indices: 3231364--3231390 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3231354 TCTCTCTCTC
3231364 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 T
3231391 GTAATAACAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3233562 original size:41 final size:41
Alignment explanation
Indices: 3233505--3233640 Score: 236
Period size: 41 Copynumber: 3.3 Consensus size: 41
3233495 CTATCGCAAA
* *
3233505 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCTAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
*
3233546 TTCGCGATGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
*
3233587 TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
3233628 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3233641 TTTCCATTTC
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 90 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:3233638 original size:61 final size:61
Alignment explanation
Indices: 3233568--3233701 Score: 259
Period size: 61 Copynumber: 2.2 Consensus size: 61
3233558 TAGTTGAAAA
3233568 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATT
*
3233629 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATT
3233690 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3233702 AGTCTACAGT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATT
Found at i:3233674 original size:82 final size:82
Alignment explanation
Indices: 3233501--3233681 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 82
3233491 TCCACTATCG
* * * *
3233501 CAAATTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCTATTTCGCGATGCGATAGTTGAA
1 CAAAATCGCGTTGCGATAGTTGAAAATCGCATTACGATTTTCCATTTCGCGATGCGATAGTTCAA
*
3233566 AATCGCGTTGCGATTTT
66 AATCGCGTTGCGATGTT
* ** * * * *
3233583 CCATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGAT-TTTCCA
1 CAAAATCGCGTTGCGATAGTTGAAAATCGCATTACGATTTTCCATTTCGCGATGCGATAGTTCAA
**
3233647 TTTCGCGTTGCGATAGTT
66 AATCGCGTTGCGAT-GTT
*
3233665 GAAAATCGCGTTGCGAT
1 CAAAATCGCGTTGCGAT
3233682 TTTCCATTTC
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 15 0.18
82 67 0.82
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (82 bp):
CAAAATCGCGTTGCGATAGTTGAAAATCGCATTACGATTTTCCATTTCGCGATGCGATAGTTCAA
AATCGCGTTGCGATGTT
Found at i:3233738 original size:19 final size:19
Alignment explanation
Indices: 3233714--3233761 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
3233704 TCTACAGTTG
*
3233714 TCGTTGTGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
3233733 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
*
3233752 TCGTTACGAT
1 TCGTTGCGAT
3233762 AGTCTACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:3233786 original size:22 final size:22
Alignment explanation
Indices: 3233752--3233825 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
3233742 TTTTTCAAAT
*
3233752 TCGTTACGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
* * **
3233774 TTGTTGCGATAGTTTACAAAT-
1 TCGTTGCGATAGTCTACAGTTG
* *
3233795 TCGTTGCAATTGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
3233817 TCGTTGCGA
1 TCGTTGCGA
3233826 AAATTCGTTG
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
21 15 0.38
22 24 0.62
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:3233797 original size:43 final size:41
Alignment explanation
Indices: 3233733--3233825 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 41
3233723 TTTTCCAAAT
* *
3233733 TCGTTGCGATTTTTCAAATTCGTTACGATAGTCTACAGTTG
1 TCGTTGCGATTTTACAAATTCGTTACAATAGTCTACAGTTG
* * *
3233774 TTGTTGCGATAGTTTACAAATTCGTTGCAATTGTCTACAGTTG
1 TCGTTGCGAT--TTTACAAATTCGTTACAATAGTCTACAGTTG
3233817 TCGTTGCGA
1 TCGTTGCGA
3233826 AAATTCGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 9 0.20
43 35 0.80
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (41 bp):
TCGTTGCGATTTTACAAATTCGTTACAATAGTCTACAGTTG
Found at i:3234877 original size:6 final size:6
Alignment explanation
Indices: 3234866--3234892 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3234856 TCTCGTCTCG
3234866 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
3234893 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:3235036 original size:20 final size:20
Alignment explanation
Indices: 3235013--3235065 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3235003 ACTGTAGACT
3235013 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
*
3235033 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
*
3235053 ATTGCAACGCGAA
1 ATCGCAACGCGAA
3235066 TTTGCGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:3241280 original size:93 final size:94
Alignment explanation
Indices: 3241159--3241332 Score: 314
Period size: 93 Copynumber: 1.9 Consensus size: 94
3241149 GAGCAAAGCC
*
3241159 TTAACCACTTAACCAAACACCTCATTTCGTTTAATCCTTATATCAACA-TTTTTTTAATATTATT
1 TTAACCACTGAACCAAACACCTCATTTCGTTTAATCCTTATATCAACATTTTTTTTAATATTATT
3241223 AATGATAGAAAAACAAAGAAACAAAGACA
66 AATGATAGAAAAACAAAGAAACAAAGACA
*
3241252 TTAACCACTGAACCAAACACCTCGTTTCGTTTAATCCTTATATCAACATTTTTTTTAATATTATT
1 TTAACCACTGAACCAAACACCTCATTTCGTTTAATCCTTATATCAACATTTTTTTTAATATTATT
*
3241317 AATGATAGAAAGACAA
66 AATGATAGAAAAACAA
3241333 TCAAAGACAT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
93 46 0.60
94 31 0.40
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.34
Consensus pattern (94 bp):
TTAACCACTGAACCAAACACCTCATTTCGTTTAATCCTTATATCAACATTTTTTTTAATATTATT
AATGATAGAAAAACAAAGAAACAAAGACA
Found at i:3242038 original size:5 final size:5
Alignment explanation
Indices: 3242030--3242059 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3242020 AATTGATTTG
3242030 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
3242060 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:3246124 original size:46 final size:48
Alignment explanation
Indices: 3246033--3246125 Score: 147
Period size: 46 Copynumber: 2.0 Consensus size: 48
3246023 ATACTTTGTG
3246033 TATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTCC
1 TATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTCC
*
3246081 TATGATGGTTATCGATC-ATTTT-TTTAATGCCTATA-TTGCATTTTC
1 TATGATGGTTATCGATCGATTTTGTTTAATGCATA-AGTTGCATTTTC
3246126 GTATCAATAC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
46 20 0.47
47 6 0.14
48 17 0.40
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (48 bp):
TATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTCC
Found at i:3246295 original size:53 final size:54
Alignment explanation
Indices: 3246152--3246330 Score: 200
Period size: 54 Copynumber: 3.4 Consensus size: 54
3246142 TACTTTCGAC
* * * * * * *
3246152 ACTATGTGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTACCGTATCAGA
1 ACTATATGTGCAACCCATGGAATTCATAATGAGTTTATGAATTACCATTTCGGA
* * * *
3246206 ACTATGTGTGCAACCCATGGTATTCATAATGAGTTTATGAATGACCATTTCGGC
1 ACTATATGTGCAACCCATGGAATTCATAATGAGTTTATGAATTACCATTTCGGA
** *
3246260 ACTATATGTGC-ATTCATGGAATTCATAATGAGTTTATGGATTACCATTTCGGA
1 ACTATATGTGCAACCCATGGAATTCATAATGAGTTTATGAATTACCATTTCGGA
* *
3246313 ACT-TAGGTGCAACTCATG
1 ACTATATGTGCAACCCATG
3246331 TACCTTGTAT
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
52 6 0.06
53 45 0.42
54 55 0.52
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (54 bp):
ACTATATGTGCAACCCATGGAATTCATAATGAGTTTATGAATTACCATTTCGGA
Found at i:3252977 original size:48 final size:48
Alignment explanation
Indices: 3252921--3253015 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
3252911 ATACTTTGTG
*
3252921 TATGATGGTTATCGATT-GATTTTGTTCAATGCAGAAGTTGCATTTTCA
1 TATGATGGTTATC-ATTCAATTTTGTTCAATGCAGAAGTTGCATTTTCA
* ** *
3252969 TATGATGGTTATCATTCAATTTTGTTTAATGCCTATGTTGCATTTTC
1 TATGATGGTTATCATTCAATTTTGTTCAATGCAGAAGTTGCATTTTC
3253016 GTATCAGTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 3 0.07
48 38 0.93
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (48 bp):
TATGATGGTTATCATTCAATTTTGTTCAATGCAGAAGTTGCATTTTCA
Found at i:3253185 original size:53 final size:54
Alignment explanation
Indices: 3253037--3253187 Score: 164
Period size: 54 Copynumber: 2.8 Consensus size: 54
3253027 ACATGTACTT
* * * * *
3253037 TCGACACTATTTGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTCCTATA
1 TCGACACTATATGTGCAACCCATGGAATTCATAATGAGTTTATGAATACCTATA
* * * *
3253091 TCGACACTATGTGTGCAACCCATGGTATTCATATTGAGTTTATGAATGACC-ATT
1 TCGACACTATATGTGCAACCCATGGAATTCATAATGAGTTTATGAAT-ACCTATA
**
3253145 TC-AGCACTATATGTGC-ATTCATGGAATTCATAATGAGTTTATG
1 TCGA-CACTATATGTGCAACCCATGGAATTCATAATGAGTTTATG
3253188 GGTTACCATT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
53 24 0.29
54 56 0.68
55 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (54 bp):
TCGACACTATATGTGCAACCCATGGAATTCATAATGAGTTTATGAATACCTATA
Found at i:3253220 original size:53 final size:53
Alignment explanation
Indices: 3253035--3253220 Score: 146
Period size: 54 Copynumber: 3.5 Consensus size: 53
3253025 CTACATGTAC
** * * * *
3253035 TTTCGACACTATTTGTGCAACCCACGAAATTCATAATGAGTTTGTGAATT-CCTA
1 TTTCGACACT-TAGGTGCAACTCATGGAATTCATAATGAGTTTATGAATTACC-A
* * * * *
3253089 TATCGACAC-TATGTGTGCAACCCATGGTATTCATATTGAGTTTATGAATGACCA
1 TTTCGACACTTA-G-GTGCAACTCATGGAATTCATAATGAGTTTATGAATTACCA
* * **
3253143 TTTC-AGCACTATATGTGC-ATTCATGGAATTCATAATGAGTTTATGGGTTACCA
1 TTTCGA-CACT-TAGGTGCAACTCATGGAATTCATAATGAGTTTATGAATTACCA
*
3253196 TTTCGACACTTAGGTACAACTCATG
1 TTTCGACACTTAGGTGCAACTCATG
3253221 TTCCTTGTAT
Statistics
Matches: 103, Mismatches: 21, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
52 6 0.06
53 43 0.42
54 50 0.49
55 2 0.02
56 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (53 bp):
TTTCGACACTTAGGTGCAACTCATGGAATTCATAATGAGTTTATGAATTACCA
Found at i:3260087 original size:81 final size:81
Alignment explanation
Indices: 3259389--3260067 Score: 905
Period size: 81 Copynumber: 8.4 Consensus size: 81
3259379 CATTTAACTT
** * * **
3259389 TTCATCTAACTTCCATGATTGACA-CTTTCTAGCCAAATACACAATTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTCTA-CCAAATGCACAGCTAGGCCATTTATCTTTTAC
**
3259453 TCAACGGTCTTTAATTG
65 TCAACGGTCTTTAACCG
* * * *
3259470 TTCATCTAACTGGCATAATAGGCACCTTCCTACCAAATGCACAACTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT
** *
3259535 CAACAATCTTTAATCG
66 CAACGGTCTTTAACCG
* *
3259551 TTCATCTAACTGGCATAATTGACACCTTCCTACCAAATGTACAGCTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT
3259616 CAACGGTCTTTAACCG
66 CAACGGTCTTTAACCG
* * * * * * * *
3259632 TTCATCGAACTGGCATAATTGACACATTTCTATCGAATACACAACTAGTCTATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT
3259697 CAACGGTCTTTAACCG
66 CAACGGTCTTTAACCG
* * * *
3259713 TTCATCTAACTGGCATAATTGACACATTTATACCAAATGCACAGCTAGACCATTTATATTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
3259778 TAACGGTCTTTAACCG
66 CAACGGTCTTTAACCG
* * * *
3259794 TTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACTGGTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT
* *
3259859 CAATGGTCTTTAACCT
66 CAACGGTCTTTAACCG
* *
3259875 TTCATCTAACTAGG-GTAATTGACACCTTTCTACTAAATGCACAGCTAGGCCATTTATCTTTTAC
1 TTCATCTAACT-GGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTAC
* *
3259939 TCAATGGTCTTTAACCA
65 TCAACGGTCTTTAACCG
**
3259956 TTCATCTAACTGGCATAATTGACACCTTT-TAGCCAAATATACAGCTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTCTA-CCAAATGCACAGCTAGGCCATTTATCTTTTAC
*
3260020 TCAACGGTCTTTAATCG
65 TCAACGGTCTTTAACCG
* *
3260037 TTCATCTAACTAGCATAATTGACATCTTTCT
1 TTCATCTAACTGGCATAATTGACACCTTTCT
3260068 GTAAAATGCT
Statistics
Matches: 530, Mismatches: 63, Indels: 9
0.88 0.10 0.01
Matches are distributed among these distances:
80 4 0.01
81 517 0.98
82 9 0.02
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACGGTCTTTAACCG
Found at i:3260151 original size:68 final size:68
Alignment explanation
Indices: 3260037--3260629 Score: 936
Period size: 68 Copynumber: 8.7 Consensus size: 68
3260027 TCTTTAATCG
* * * * *
3260037 TTCATCTAACTAGCATAATTGACATCTTTCTGTAAAATGCTCAGTTAGGCCTCAAAGGCATTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3260102 CCT
66 CCT
* * * * * *
3260105 TTCATCTAACTGACATAATTAACACCTTTTTGTCATATTCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3260170 CCT
66 CCT
*
3260173 TTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3260238 CCT
66 CCT
* * * *
3260241 TTCAACTAACTGGCATAATTGACACCTTTCTATCAAGTTCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3260306 CCT
66 CCT
* * * *
3260309 TTCATCTAACTGGCATAATTGACACATTTCTTTGAAATGCACAGTTATGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3260374 CCT
66 CCT
* *
3260377 TTCATCTAACTGACATAATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3260442 CCT
66 CCT
*
3260445 TTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
3260510 CGT
66 CCT
* *
3260513 TTCATCTAACTGACATAATTGA-ACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3260577 CCT
66 CCT
*
3260580 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
3260630 TTATTAATCT
Statistics
Matches: 479, Mismatches: 45, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
67 64 0.13
68 415 0.87
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:3260954 original size:55 final size:55
Alignment explanation
Indices: 3260833--3260990 Score: 207
Period size: 55 Copynumber: 2.9 Consensus size: 55
3260823 CATATATTTT
* *
3260833 CCATACGGAAATTCATACACTTAGTATGGATTTCTTAG-TTTGCACATATAGTTC
1 CCATACGAAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACATAAAGTTC
* *
3260887 CCATACGAAAATTCTTACACTT-GATATGAATTTCTTAGTTTTGCAC-TCAAAGTTC
1 CCATACGAAAATTCATACACTTAG-TATGGATTTCTTAGTTTTGCACAT-AAAGTTC
3260942 CCATAC-ATAAATTCATACACTTAGTATGGATTTCTTAAGTTTTTGCACA
1 CCATACGA-AAATTCATACACTTAGTATGGATTTCTT-AG-TTTTGCACA
3260991 CTTAATGTCA
Statistics
Matches: 90, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
53 1 0.01
54 35 0.39
55 43 0.48
56 3 0.03
57 8 0.09
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (55 bp):
CCATACGAAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACATAAAGTTC
Found at i:3261387 original size:19 final size:21
Alignment explanation
Indices: 3261343--3261392 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
3261333 CCCACCATGA
*
3261343 TATCGATACTACTATACTATGG
1 TATCGATACTACTATA-TACGG
3261365 TATCGATAC-ACTAT-TACGG
1 TATCGATACTACTATATACGG
3261384 TATCGATAC
1 TATCGATAC
3261393 CATTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.48
21 5 0.19
22 9 0.33
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (21 bp):
TATCGATACTACTATATACGG
Found at i:3265936 original size:243 final size:242
Alignment explanation
Indices: 3265524--3266090 Score: 825
Period size: 243 Copynumber: 2.3 Consensus size: 242
3265514 TTATAATTTT
* * * * * *
3265524 TTTAGTCTTTTACCCAAAGGCATTTAACTTTTCATCTAACTTGCATGATTAACA-CTTTCCT-TC
1 TTTA-TCTTTTACTCAAAGTC-TTTAACTGTTCATCTAACTGGCATAATTGACACCTTT-CTGTC
* * * *
3265587 AAAATACACAGTTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCATTTATCTAACTGGCATA
63 -AAATGCACAGTTAGGCCATTTATCTTTCACTCAACGGACTTTAACCATTCATCTAACTGGCATA
* * *
3265652 ATTGACACCTTTCTACCAAATGCACAACTAGGCCTTTTATCTTTTACTCAACGATCTTTAACCAT
127 ATTGACACCTTTCTACAAAATGCACAACTAGGACATTTATCTTTTACTCAACGATCTTTAACCAT
*
3265717 TCATCTAACTGGTATAATTGACACCTTTCTACCAAATGCACAACTAGG-CA
192 TCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACTAGGCCA
3265767 TTTGATCTTTTACTCAACAGTCTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGTCA
1 TTT-ATCTTTTACTCAA-AGTCTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGTCA
* * *
3265832 AATGCACAGCTAGGCCATTTATCTTTCACTCAATGGACTTTAACCGTTCATCTAACTGGCATAAT
64 AATGCACAGTTAGGCCATTTATCTTTCACTCAACGGACTTTAACCATTCATCTAACTGGCATAAT
* * *
3265897 TGACACCTTTCTACAAAATGCACAGCTAGGACATTTATCTTTTATTCAACGATCTTTAACCGTTC
129 TGACACCTTTCTACAAAATGCACAACTAGGACATTTATCTTTTACTCAACGATCTTTAACCATTC
* *
3265962 ATCTAACTGGCATAATTGCCACCTTTCTGCCAAATGCACAACTAGGCCA
194 ATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACTAGGCCA
* * *
3266011 TTTATCTTTTACTCAATGGTCTTTAACCGTTCATCCAACTGGCATAATTGACACCTTTCTGTCAA
1 TTTATCTTTTACTCAA-AGTCTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA
3266076 ATGCACAGTTAGGCC
65 ATGCACAGTTAGGCC
3266091 TCAAAGGCAC
Statistics
Matches: 292, Mismatches: 27, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
243 277 0.95
244 15 0.05
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (242 bp):
TTTATCTTTTACTCAAAGTCTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAA
TGCACAGTTAGGCCATTTATCTTTCACTCAACGGACTTTAACCATTCATCTAACTGGCATAATTG
ACACCTTTCTACAAAATGCACAACTAGGACATTTATCTTTTACTCAACGATCTTTAACCATTCAT
CTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACTAGGCCA
Found at i:3266089 original size:81 final size:81
Alignment explanation
Indices: 3265554--3266090 Score: 736
Period size: 81 Copynumber: 6.6 Consensus size: 81
3265544 CATTTAACTT
* * * * * * *
3265554 TTCATCTAACTTGCATGATTAACA-CTTTCCTTCAAAATACACAGTTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTT-CTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
*
3265618 TCAACGGTCTTTAACCA
65 TCAACGGTCTTTAACCG
* * * *
3265635 TTTATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACTAGGCCTTTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* *
3265700 CAACGATCTTTAACCA
66 CAACGGTCTTTAACCG
* * *
3265716 TTCATCTAACTGGTATAATTGACACCTTTCTACCAAATGCACAACTAGG-CATTTGATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTT-ATCTTTTAC
* *
3265780 TCAACAGTCTTTAACTG
65 TCAACGGTCTTTAACCG
* *
3265797 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCATTTATCTTTCACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* *
3265862 CAATGGACTTTAACCG
66 CAACGGTCTTTAACCG
* * * *
3265878 TTCATCTAACTGGCATAATTGACACCTTTCTACAAAATGCACAGCTAGGACATTTATCTTTTATT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
3265943 CAACGATCTTTAACCG
66 CAACGGTCTTTAACCG
* *
3265959 TTCATCTAACTGGCATAATTGCCACCTTTCTGCCAAATGCACAACTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
3266024 CAATGGTCTTTAACCG
66 CAACGGTCTTTAACCG
* * *
3266040 TTCATCCAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCC
3266091 TCAAAGGCAC
Statistics
Matches: 404, Mismatches: 49, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
80 4 0.01
81 391 0.97
82 9 0.02
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACGGTCTTTAACCG
Found at i:3266558 original size:68 final size:68
Alignment explanation
Indices: 3266040--3266554 Score: 656
Period size: 68 Copynumber: 7.6 Consensus size: 68
3266030 TCTTTAACCG
*
3266040 TTCATCCAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3266105 CCT
66 CCT
* * *
3266108 TTCATCTAACTAGAATAATTGACACCTTTCTGTCAAATGCACAGTTAGGACTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3266173 CCT
66 CCT
* * * ** * * *
3266176 TTTATCTAATTGCCATAATTGACATTTTTCTGTCAAATGTACAGTTAGGCCTAAAAGGCACTAAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3266241 CCT
66 CCT
* * ** *
3266244 TTCATATAA-TTGCATAATTGACATATTTCTGTCAAATGAACAGTTAGGCCTCAAAGGCACTTTA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCAC-TTA
3266308 -CCT
65 GCCT
* * * * *
3266311 TTCATCTAACTGGAATAATTGACACTTTTTTTGTGAAATGCACAGTTAGGCCTCAAAGGAACTTA
1 TTCATCTAACTGGCATAATTGACAC-CTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
3266376 GACT
65 GCCT
*
3266380 TTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
3266445 ACT
66 CCT
* * * * * * * * **
3266448 TTCATCTAACTTGTATAATTGATACCTTTCTATCAAATGTACAGTTGGGCCTTAAAAGTTCTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3266513 CCT
66 CCT
* * *
3266516 TTCATCTAACTGGCATAATTGATACATTTATGTCAAATG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATG
3266555 TACAATTATT
Statistics
Matches: 388, Mismatches: 55, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
67 57 0.15
68 274 0.71
69 57 0.15
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:3266866 original size:55 final size:55
Alignment explanation
Indices: 3266732--3266891 Score: 232
Period size: 55 Copynumber: 2.9 Consensus size: 55
3266722 ACATATATTT
* * *
3266732 CCCATACGGAAATTCATACACTTAGTATGGATTTCTTA-ATTTGTACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTG
* * *
3266786 CTCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACTCAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTG
*
3266841 CCCATACAGAAATTCATACACTTAGTATGGATTTCTTAAGTTTTTGCACAC
1 CCCATACGGAAATTCATACACTTAGTATGGATTTCTT-AG-TTTTGCACAC
3266892 TTAGTGCCAT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
54 36 0.39
55 46 0.49
56 2 0.02
57 9 0.10
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (55 bp):
CCCATACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTG
Found at i:3274148 original size:54 final size:53
Alignment explanation
Indices: 3274073--3274224 Score: 148
Period size: 53 Copynumber: 2.9 Consensus size: 53
3274063 CAACCCACAT
* * *
3274073 AATTCATAATGAGTTTGTGAATTACCGTATC-GACACTATGTGTGCAACGCAT-G
1 AATTCATAATGAGTTTATGAATTACCATATCAGA-ACTATATGTGC-ACGCATAG
* * * **
3274126 ATATTCATAATGAGTTTATGAATGACCATTTCAGAACTATATGTTCATTCATAG
1 A-ATTCATAATGAGTTTATGAATTACCATATCAGAACTATATGTGCACGCATAG
* * * *
3274180 AATTCATAATGAGTTTATGGATTACCATTTCGGAACT-TAAGTGCA
1 AATTCATAATGAGTTTATGAATTACCATATCAGAACTATATGTGCA
3274225 ACTCATGTAC
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
52 6 0.07
53 38 0.46
54 37 0.45
55 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (53 bp):
AATTCATAATGAGTTTATGAATTACCATATCAGAACTATATGTGCACGCATAG
Found at i:3278420 original size:17 final size:17
Alignment explanation
Indices: 3278398--3278432 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3278388 GTCTCCTTAA
3278398 GAATGAAAAATAGTCTG
1 GAATGAAAAATAGTCTG
3278415 GAATGAAAAATAGTCTG
1 GAATGAAAAATAGTCTG
3278432 G
1 G
3278433 CTTGATCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.23
Consensus pattern (17 bp):
GAATGAAAAATAGTCTG
Found at i:3279471 original size:21 final size:21
Alignment explanation
Indices: 3279447--3279490 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3279437 AAATATTAAA
3279447 AATTTATAGTTAAATTT-ATTT
1 AATTTATA-TTAAATTTAATTT
* *
3279468 AATTTTTATTTAATTTAATTT
1 AATTTATATTAAATTTAATTT
3279489 AA
1 AA
3279491 AAAATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTTATATTAAATTTAATTT
Found at i:3279506 original size:20 final size:22
Alignment explanation
Indices: 3279481--3279525 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 22
3279471 TTTTATTTAA
3279481 TTTAATT-TAAA-AA-ATTATAT
1 TTTAATTCTAAACAATATTAT-T
3279501 TTTAATTCTAAACAATATTATT
1 TTTAATTCTAAACAATATTATT
3279523 TTT
1 TTT
3279526 TTAATCATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 6 0.27
23 5 0.23
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATTCTAAACAATATTATT
Found at i:3280670 original size:13 final size:13
Alignment explanation
Indices: 3280652--3280678 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3280642 TTTTTCAAAA
3280652 TCAAACTTAATGT
1 TCAAACTTAATGT
3280665 TCAAACTTAATGT
1 TCAAACTTAATGT
3280678 T
1 T
3280679 TAGTTTAGAT
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TCAAACTTAATGT
Found at i:3284741 original size:81 final size:81
Alignment explanation
Indices: 3284606--3284767 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
3284596 TTTTTGAAAA
3284606 TTTTCCTAATCATTTAAGACCAAGACCGAATGGTTTATATACTCAAGACTAGGTTTTCATGATTT
1 TTTTCCTAATCATTTAAGACCAAGACCGAATGGTTTATATACTCAAGACTAGGTTTTCATGATTT
3284671 TATTCGATTTCGAATC
66 TATTCGATTTCGAATC
3284687 TTTTCCTAATCATTTAAGACCAAGACCGAATGGTTTATATACTCAAGACTAGGTTTTCATGATTT
1 TTTTCCTAATCATTTAAGACCAAGACCGAATGGTTTATATACTCAAGACTAGGTTTTCATGATTT
3284752 TATTCGATTTCGAATC
66 TATTCGATTTCGAATC
3284768 GATTCAAGCA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (81 bp):
TTTTCCTAATCATTTAAGACCAAGACCGAATGGTTTATATACTCAAGACTAGGTTTTCATGATTT
TATTCGATTTCGAATC
Found at i:3285866 original size:48 final size:48
Alignment explanation
Indices: 3285814--3285909 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
3285804 ATTTTGTAAC
*
3285814 TGAATCTAACTTCTTATGGGAGATTTTCATTGTTCATGTGATAACTCA
1 TGAATCTAACTTCTTATGGGAGAGTTTCATTGTTCATGTGATAACTCA
3285862 TGAATCTAACTTCTTATGGGAGAGTTTCATTGTTCATGTGATAACTCA
1 TGAATCTAACTTCTTATGGGAGAGTTTCATTGTTCATGTGATAACTCA
3285910 AGAAAATGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.41
Consensus pattern (48 bp):
TGAATCTAACTTCTTATGGGAGAGTTTCATTGTTCATGTGATAACTCA
Found at i:3294748 original size:22 final size:22
Alignment explanation
Indices: 3294704--3294748 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3294694 AAAGAAAAAA
* *
3294704 ATAAAATAAAATTAAGCATATG
1 ATAAAATAAAATAAAGCAAATG
3294726 ATAAAATAAAATAAATG-AAATG
1 ATAAAATAAAATAAA-GCAAATG
3294748 A
1 A
3294749 AATAAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (22 bp):
ATAAAATAAAATAAAGCAAATG
Found at i:3294787 original size:11 final size:11
Alignment explanation
Indices: 3294773--3294810 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3294763 AAAATAAAGT
3294773 GAAATTAAAAC
1 GAAATTAAAAC
*
3294784 GAAATTAAAAT
1 GAAATTAAAAC
*
3294795 GAAAATAAAAC
1 GAAATTAAAAC
3294806 GAAAT
1 GAAAT
3294811 GGGTTGCCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (11 bp):
GAAATTAAAAC
Found at i:3294792 original size:22 final size:22
Alignment explanation
Indices: 3294767--3294810 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3294757 TTGCTAAAAA
* *
3294767 TAAAGTGAAATTAAAACGAAAT
1 TAAAATGAAAATAAAACGAAAT
3294789 TAAAATGAAAATAAAACGAAAT
1 TAAAATGAAAATAAAACGAAAT
3294811 GGGTTGCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (22 bp):
TAAAATGAAAATAAAACGAAAT
Found at i:3300485 original size:4 final size:4
Alignment explanation
Indices: 3300476--3300505 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
3300466 AGATAAAAAT
3300476 TAAA TAAA TAAA TAAA TAAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA T
3300506 TGGGAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:3300497 original size:17 final size:17
Alignment explanation
Indices: 3300472--3300505 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3300462 AATGAGATAA
*
3300472 AAATTAAATAAATAAAT
1 AAATAAAATAAATAAAT
3300489 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
3300506 TGGGAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Found at i:3301242 original size:85 final size:85
Alignment explanation
Indices: 3301114--3301273 Score: 268
Period size: 85 Copynumber: 1.9 Consensus size: 85
3301104 AGATAATTCC
*
3301114 TAAAATAATATCTTAAATCCTAATTAAAACACGTAAAACTATTTAAACTAAAATACCTAAAACAA
1 TAAAATAATATCCTAAATCCTAATTAAAACACGTAAAACTATTTAAACTAAAATACCTAAAACAA
3301179 AGATAAAATAAAATAATATT
66 AGATAAAATAAAATAATATT
* * *
3301199 TAAAATAATATCCTAAATCCTAATTGAAATAC-TAAAACTTATTTAAACTAAAATACTTAAAACA
1 TAAAATAATATCCTAAATCCTAATTAAAACACGTAAAAC-TATTTAAACTAAAATACCTAAAACA
3301263 AAGATAAAATA
65 AAGATAAAATA
3301274 TTATCCTAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
84 6 0.09
85 64 0.91
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.29
Consensus pattern (85 bp):
TAAAATAATATCCTAAATCCTAATTAAAACACGTAAAACTATTTAAACTAAAATACCTAAAACAA
AGATAAAATAAAATAATATT
Found at i:3317720 original size:2 final size:2
Alignment explanation
Indices: 3317707--3317804 Score: 146
Period size: 2 Copynumber: 50.0 Consensus size: 2
3317697 GTACCTTATC
* *
3317707 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3317749 AT -T AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3317789 TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3317805 CTATTCATTT
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
1 2 0.02
2 85 0.98
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3318123 original size:81 final size:80
Alignment explanation
Indices: 3317981--3318360 Score: 483
Period size: 81 Copynumber: 4.7 Consensus size: 80
3317971 TCTTAGTGTT
* * * * * * *
3317981 TAACCGTTCATATAACTAGCATAATTGGCACCTTTCTACCAATTGCACAATTAGGCCATTATTCC
1 TAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTTCACAGTTAGGCTATTATTCT
* *
3318046 CTTACTCAACGGTAT
66 TTTACTCAACGGTAC
* *
3318061 TAAACTGTTCATCTAACTGGCATAATTGACACATTTCTACCAATTTCACAGTTAGGCTATTATTC
1 T-AACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTTCACAGTTAGGCTATTATTC
3318126 TTTTACTCAACGGTAC
65 TTTTACTCAACGGTAC
* * *
3318142 TAACCGTTCATCTAATTGGCATAATTGATACCTTTGTACCAATTTCACAGTTAGGCTATTATTCT
1 TAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTTCACAGTTAGGCTATTATTCT
3318207 TTTACTCAACGGTAC
66 TTTACTCAACGGTAC
* ** * *
3318222 TAAAGCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCTATTATTA
1 T-AACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTTCACAGTTAGGCTATTATTC
* *
3318287 TATTACTTAACGGTAC
65 TTTTACTCAACGGTAC
* ** * *
3318303 TTAACCGTTCATCTAACTGACATAATTGGTACCATTCTACCAATTGT-ACAATTAGGCT
1 -TAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATT-TCACAGTTAGGCT
3318361 TCAAAGGCAC
Statistics
Matches: 267, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
80 76 0.28
81 190 0.71
82 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (80 bp):
TAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTTCACAGTTAGGCTATTATTCT
TTTACTCAACGGTAC
Found at i:3318234 original size:161 final size:162
Alignment explanation
Indices: 3317980--3318360 Score: 534
Period size: 161 Copynumber: 2.4 Consensus size: 162
3317970 CTCTTAGTGT
* * * * *
3317980 TTAACCGTTCATATAACTAGCATAATTGGCACCTTTCTACCAATTGCACAATTAGGCCATTATTC
1 TTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTTCACAATTAGGCTATTATTC
* *
3318045 CCTTACTCAACGGTATTAAACTGTTCATCTAACTGGCATAATTGACACATTTCTACCAATTTCAC
66 CCTTACTCAACGGTACTAAACTGTTCATCTAACTGGCATAATTGACACATTTCTACCAATTGCAC
* *
3318110 AGTTAGGCTATTATTCTTTTACTCAACGGTAC
131 AGTTAGGCTATTATTATATTACTCAACGGTAC
* * * *
3318142 -TAACCGTTCATCTAATTGGCATAATTGATACCTTTGTACCAATTTCACAGTTAGGCTATTATTC
1 TTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTTCACAATTAGGCTATTATTC
** ** *
3318206 TTTTACTCAACGGTACTAAAGC-GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCA
66 CCTTACTCAACGGTACTAAA-CTGTTCATCTAACTGGCATAATTGACACATTTCTACCAATTGCA
*
3318270 CAGTTAGGCTATTATTATATTACTTAACGGTAC
130 CAGTTAGGCTATTATTATATTACTCAACGGTAC
* *
3318303 TTAACCGTTCATCTAACTGACATAATTGGTACCATTCTACCAATTGT-ACAATTAGGCT
1 TTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATT-TCACAATTAGGCT
3318361 TCAAAGGCAC
Statistics
Matches: 191, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
161 140 0.73
162 50 0.26
163 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (162 bp):
TTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTTCACAATTAGGCTATTATTC
CCTTACTCAACGGTACTAAACTGTTCATCTAACTGGCATAATTGACACATTTCTACCAATTGCAC
AGTTAGGCTATTATTATATTACTCAACGGTAC
Found at i:3318426 original size:68 final size:68
Alignment explanation
Indices: 3318354--3318701 Score: 527
Period size: 68 Copynumber: 5.1 Consensus size: 68
3318344 AATTGTACAA
* *
3318354 TTAGGCTTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGAAACATTTCTGTCAAATGCA
1 TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCA
*
3318419 CAT
66 CAG
* ** * *
3318422 TTAGGCCTCAAAGGCACTTATCCTTTCATCTAACTGGCATAAATGATTCCTCTCTGTCAAAGGCA
1 TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCA
3318487 CAG
66 CAG
* * *
3318490 TTAGGCCTCAAAGGCACTTAGCCTTTCACCTAACTGGCATAAATGACACCTTTCTGTCAAGTGCA
1 TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCA
3318555 CAG
66 CAG
*
3318558 TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGAAACCTTTTTGTCAAATGCA
1 TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCA
3318623 CAG
66 CAG
* * * * *
3318626 GTAGGCCTCAAAGGCACTTAG-CTATTCATCTAACTGGCATAAATGACACATTTCTTTCAAATGA
1 TTAGGCCTCAAAGGCACTTAGCCT-TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGC
3318690 ACAG
65 ACAG
3318694 TTAGGCCT
1 TTAGGCCT
3318702 ATTAAACTTT
Statistics
Matches: 253, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
67 2 0.01
68 251 0.99
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (68 bp):
TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCA
CAG
Found at i:3321189 original size:54 final size:54
Alignment explanation
Indices: 3321125--3321233 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
3321115 AATCTTTATT
3321125 AATTGCCTACTACCTTTCCACTCATACTTTTACCATGACCCATTAAGGTTTACG
1 AATTGCCTACTACCTTTCCACTCATACTTTTACCATGACCCATTAAGGTTTACG
3321179 AATTGCCTACTACCTTTCCACTCATACTTTTACCATGACCCATTAAGGTTTACG
1 AATTGCCTACTACCTTTCCACTCATACTTTTACCATGACCCATTAAGGTTTACG
3321233 A
1 A
3321234 CTATCATTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.27, C:0.29, G:0.09, T:0.35
Consensus pattern (54 bp):
AATTGCCTACTACCTTTCCACTCATACTTTTACCATGACCCATTAAGGTTTACG
Found at i:3322823 original size:42 final size:42
Alignment explanation
Indices: 3322764--3322847 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
3322754 GCTCTGATAT
3322764 CAATAAATGTAACACCCATATCACATATACCTTTCCGTATAC
1 CAATAAATGTAACACCCATATCACATATACCTTTCCGTATAC
*
3322806 CAATAAATGTAACACCCATATCACGTATACCTTTCCGTATAC
1 CAATAAATGTAACACCCATATCACATATACCTTTCCGTATAC
3322848 AAGATACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (42 bp):
CAATAAATGTAACACCCATATCACATATACCTTTCCGTATAC
Found at i:3323872 original size:81 final size:81
Alignment explanation
Indices: 3323735--3324104 Score: 478
Period size: 81 Copynumber: 4.6 Consensus size: 81
3323725 ATGTTTAATT
* * * *
3323735 GTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGTACAGTTA-GACCATTATTCCTTAA
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGA-TATTATTCCTTTA
* * *
3323799 CTTAACGATATTAAACC
65 CTCAACGGTACTAAACC
* * *
3323816 GTTCATCTAACTGGCATAATTGATACCTTTCTAGCAATTGCACAGTTA-GACTATTATTCTTTTA
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGA-TATTATTCCTTTA
*
3323880 CTCAACGGTACTAAACT
65 CTCAACGGTACTAAACC
* *
3323897 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGATAGTATTCTTTTAC
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGATATTATTCCTTTAC
* * *
3323962 TTAACGGTAATCAACC
66 TCAACGGTACTAAACC
*
3323978 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGC-CTAATTAGGATATTATT-CTATT
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC-AGTTAGGATATTATTCCT-TT
*
3324041 ACTCAACGGTACTAAATC
64 ACTCAACGGTACTAAACC
* * * *
3324059 ATTCATCTAACTAGCATAATTGGTATCTTTCTACGAATTGCACAGT
1 GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGT
3324105 AAGGCCTCAA
Statistics
Matches: 255, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
80 2 0.01
81 250 0.98
82 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (81 bp):
GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGATATTATTCCTTTAC
TCAACGGTACTAAACC
Found at i:3324158 original size:68 final size:68
Alignment explanation
Indices: 3324097--3324377 Score: 398
Period size: 68 Copynumber: 4.2 Consensus size: 68
3324087 TTCTACGAAT
* * *
3324097 TGCACAGTAAGGCCTCAAAGGCACTTAGCTTTTCATCTAACTGGCATAAATGACACATTTCTGTC
1 TGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTC
3324162 AAA
66 AAA
3324165 TGCACAGTTAGG---C-----CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTC
1 TGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTC
3324222 AAA
66 AAA
* * *
3324225 TGCACAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAATTGGCATAATTGACACCTTTCTGTC
1 TGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTC
3324290 AAA
66 AAA
* *
3324293 TGCACAGTTAGGCCTCAAAGGCACACTTAGCCTTTCATCTAACTGGCATAAATAACACCTTTTTG
1 TGCACAGTTAGGCCTCAAAGG--CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTG
3324358 TCAAA
64 TCAAA
**
3324363 TGCACTTTTAGGCCT
1 TGCACAGTTAGGCCT
3324378 ATTAATATTT
Statistics
Matches: 191, Mismatches: 12, Indels: 18
0.86 0.05 0.08
Matches are distributed among these distances:
60 57 0.30
63 1 0.01
65 1 0.01
68 76 0.40
70 56 0.29
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (68 bp):
TGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTC
AAA
Found at i:3324211 original size:60 final size:61
Alignment explanation
Indices: 3324118--3324367 Score: 295
Period size: 60 Copynumber: 3.9 Consensus size: 61
3324108 GCCTCAAAGG
* *
3324118 CACTTAGCTTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGC-
1 CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCA
3324178 CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAA
1 CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGG---C--
3324243 AGA
61 --A
* *
3324246 CACTTAGCCTTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAA
1 CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAG-T-----T---
3324311 AGGCA
57 AGGCA
* *
3324316 CACTTAGCCTTTCATCTAACTGGCATAAATAACACCTTTTTGTCAAATGCAC
1 CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCAC
3324368 TTTTAGGCCT
Statistics
Matches: 165, Mismatches: 8, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
60 57 0.35
63 1 0.01
68 52 0.32
69 1 0.01
70 49 0.30
74 2 0.01
77 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (61 bp):
CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCA
Found at i:3324288 original size:128 final size:132
Alignment explanation
Indices: 3324097--3324377 Score: 390
Period size: 128 Copynumber: 2.1 Consensus size: 132
3324087 TTCTACGAAT
* * *
3324097 TGCACAGTAAGGCCTCAAAGGCACTTAGCTTTTCATCTAACTGGCATAAATGACACATTTCTGTC
1 TGCACAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTC
*
3324162 AAATGCACAG-T-T-AGGC-CACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCA
66 AAATGCACAGTTCTAAGGCACACTTAGCCTTTCATCTAACTGGCATAAATAACACCTTTCTGTCA
3324223 AA
131 AA
* * *
3324225 TGCACAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAATTGGCATAATTGACACCTTTCTGTC
1 TGCACAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTC
3324290 AAATGCACAGTTAGGCCTCAAAGGCACACTTAGCCTTTCATCTAACTGGCATAAATAACACCTTT
66 AAATGCACAGTT----CT--AAGGCACACTTAGCCTTTCATCTAACTGGCATAAATAACACCTTT
*
3324355 TTGTCAAA
125 CTGTCAAA
**
3324363 TGCACTTTTAGGCCT
1 TGCACAGTTAGGCCT
3324378 ATTAATATTT
Statistics
Matches: 133, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
128 69 0.52
129 1 0.01
134 1 0.01
137 4 0.03
138 58 0.44
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (132 bp):
TGCACAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTC
AAATGCACAGTTCTAAGGCACACTTAGCCTTTCATCTAACTGGCATAAATAACACCTTTCTGTCA
AA
Found at i:3324709 original size:59 final size:57
Alignment explanation
Indices: 3324627--3324740 Score: 174
Period size: 59 Copynumber: 2.0 Consensus size: 57
3324617 TTTAACATAT
* *
3324627 AGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAATATTTTAGCACACAA
1 AGTGCCCATACGAAAATTCATACACTTAGTATGAATTTCTTAAGATTTT-GCACACAA
* *
3324685 AGTGCCCAATATGAAAATTTATACACTTAGTATGAATTTCTTAAGATTTTGCACAC
1 AGTGCCC-ATACGAAAATTCATACACTTAGTATGAATTTCTTAAGATTTTGCACAC
3324741 TTAGTTCCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 13 0.25
59 38 0.75
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (57 bp):
AGTGCCCATACGAAAATTCATACACTTAGTATGAATTTCTTAAGATTTTGCACACAA
Found at i:3325246 original size:95 final size:96
Alignment explanation
Indices: 3325064--3325287 Score: 231
Period size: 95 Copynumber: 2.4 Consensus size: 96
3325054 TGGCTCTATA
** * * ** * *
3325064 GTATCGATACTAC-TACC-TAGTACCGATACTTCTATACTATGGTACCGATATTTCCTTCGGGTA
1 GTATCGATACCCCTTACCATAGTATCGATACTACCCTACTATGGTACCGATATCTCCTACGGGTA
* *
3325127 TCGATACCAAAAATAGGTTCGATGTTGCTTG
66 TCGATACCAAAAATAGATTCGATGTTGCATG
* * *
3325158 GTATCGATA-CCCTTACCATGGTTTCGATACTACCCTACTATGGTACCGATA-CTCTCTACTGGT
1 GTATCGATACCCCTTACCATAGTATCGATACTACCCTACTATGGTACCGATATCTC-CTACGGGT
* * * * * *
3325221 ATTGATACTAAAATTATATTTGATGTTTCATG
65 ATCGATACCAAAAATAGATTCGATGTTGCATG
*
3325253 GTATCGATACCCCTTATCATAGTATCGATACTACC
1 GTATCGATACCCCTTACCATAGTATCGATACTACC
3325288 TCCTCGGTAT
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
93 1 0.01
94 15 0.14
95 66 0.63
96 22 0.21
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (96 bp):
GTATCGATACCCCTTACCATAGTATCGATACTACCCTACTATGGTACCGATATCTCCTACGGGTA
TCGATACCAAAAATAGATTCGATGTTGCATG
Found at i:3327626 original size:18 final size:18
Alignment explanation
Indices: 3327603--3327645 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3327593 CACATATACC
3327603 ATCATTAACAACATCAAT
1 ATCATTAACAACATCAAT
* **
3327621 ATCATTACCAACATCTCT
1 ATCATTAACAACATCAAT
3327639 ATCATTA
1 ATCATTA
3327646 TCATTATCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.33
Consensus pattern (18 bp):
ATCATTAACAACATCAAT
Found at i:3327880 original size:31 final size:31
Alignment explanation
Indices: 3327841--3327963 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
3327831 CTCGAAGGAC
3327841 CAGTCCATATGTTCCGAAGAACATAGGTAATA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA-A
* *
3327873 -AGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
3327903 CAGTCCATATATTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
3327934 CAGTCCATTTGTTCTGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
3327964 CCCTCGACTC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
30 1 0.01
31 81 0.99
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:3336169 original size:10 final size:10
Alignment explanation
Indices: 3336156--3336261 Score: 81
Period size: 10 Copynumber: 10.6 Consensus size: 10
3336146 AAAGAGGTAA
3336156 AAAAAAAAAG
1 AAAAAAAAAG
*
3336166 AAAAAATATAG
1 AAAAAA-AAAG
* * *
3336177 AGAAATAACG
1 AAAAAAAAAG
*
3336187 AAAAGAAAAG
1 AAAAAAAAAG
*
3336197 AAAAAAGAAG
1 AAAAAAAAAG
* *
3336207 AGAAAAGAAG
1 AAAAAAAAAG
3336217 AAAAAAAAA-
1 AAAAAAAAAG
*
3336226 AAGAAAAGAAG
1 AA-AAAAAAAG
*
3336237 -AAAAAGAAG
1 AAAAAAAAAG
*
3336246 AAAAAAAAAT
1 AAAAAAAAAG
3336256 AAAAAA
1 AAAAAA
3336262 TAGAACAAAT
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
9 10 0.13
10 58 0.77
11 7 0.09
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3336196 original size:5 final size:5
Alignment explanation
Indices: 3336186--3336259 Score: 51
Period size: 5 Copynumber: 14.0 Consensus size: 5
3336176 GAGAAATAAC
* *
3336186 GAAAA GAAAA GAAAAAA GAAGA GAAAA GAAGAA -AAAA AAAAA GAAAA
1 GAAAA GAAAA G--AAAA GAAAA GAAAA GAA-AA GAAAA GAAAA GAAAA
* * *
3336233 GAAGAA AAAGAA GAAAA AAAAA TAAAA
1 GAA-AA GAA-AA GAAAA GAAAA GAAAA
3336260 AATAGAACAA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
4 2 0.04
5 39 0.68
6 11 0.19
7 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (5 bp):
GAAAA
Found at i:3336205 original size:25 final size:24
Alignment explanation
Indices: 3336177--3336261 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 24
3336167 AAAAATATAG
3336177 AGAAATAACGAAAAGAAAAGAAAAA
1 AGAAATAA-GAAAAGAAAAGAAAAA
* *
3336202 AGAAGAGAA-AAGAAGAAAAAAAAAA
1 AGAA-ATAAGAA-AAGAAAAGAAAAA
* *
3336227 AGAAAAGAAGAAAA-AGAAGAAAAA
1 AG-AAATAAGAAAAGAAAAGAAAAA
3336251 A-AAATAA-AAAA
1 AGAAATAAGAAAA
3336262 TAGAACAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
21 4 0.08
22 5 0.10
24 11 0.22
25 24 0.47
26 7 0.14
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.02
Consensus pattern (24 bp):
AGAAATAAGAAAAGAAAAGAAAAA
Found at i:3336209 original size:30 final size:28
Alignment explanation
Indices: 3336156--3336261 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 28
3336146 AAAGAGGTAA
*
3336156 AAAAAAAAAGAAAAAATATAGAGAAATAACG
1 AAAAAAAAAGAAAAAAGA-AGAGAAA-AA-G
*
3336187 AAAAGAAAAGAAAAAAGAAGAGAAAAGAAG
1 AAAAAAAAAGAAAAAAGAAGAG-AAA-AAG
*
3336217 AAAAAAAAA-AAGAAAAGAAGAAAAAGAAG
1 AAAAAAAAAGAA-AAAAGAAGAGAAA-AAG
*
3336246 AAAAAAAAATAAAAAA
1 AAAAAAAAAGAAAAAA
3336262 TAGAACAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
29 22 0.33
30 24 0.36
31 21 0.31
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (28 bp):
AAAAAAAAAGAAAAAAGAAGAGAAAAAG
Found at i:3336212 original size:17 final size:15
Alignment explanation
Indices: 3336192--3336251 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 15
3336182 TAACGAAAAG
3336192 AAAAGAAAAAAGAAGA
1 AAAAGAAAAAAGAA-A
3336208 GAAAAGAAGAAAA-AAA
1 -AAAAGAA-AAAAGAAA
3336224 AAAAGAAAAGAAGAAA
1 AAAAGAAAA-AAGAAA
3336240 AAGAAGAAAAAA
1 AA-AAGAAAAAA
3336252 AAATAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.05
15 9 0.23
16 8 0.21
17 16 0.41
18 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAGAAA
Found at i:3336228 original size:37 final size:39
Alignment explanation
Indices: 3336187--3336261 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
3336177 AGAAATAACG
* *
3336187 AAAAGAAAAG-A-AAAAAGAAGAGAAAAGAAGAAAAAAA
1 AAAAGAAAAGAAGAAAAAGAAGAAAAAAAAAGAAAAAAA
*
3336224 AAAAGAAAAGAAGAAAAAGAAGAAAAAAAAATAAAAAA
1 AAAAGAAAAGAAGAAAAAGAAGAAAAAAAAAGAAAAAA
3336262 TAGAACAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 10 0.30
38 1 0.03
39 22 0.67
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (39 bp):
AAAAGAAAAGAAGAAAAAGAAGAAAAAAAAAGAAAAAAA
Found at i:3336266 original size:22 final size:23
Alignment explanation
Indices: 3336187--3336250 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 23
3336177 AGAAATAACG
3336187 AAAAGAAAAG-A-AAAAAGAAGA
1 AAAAGAAAAGAAGAAAAAGAAGA
* *
3336208 GAAAAGAAGAAAAAAAAAAAGAA-A
1 -AAAAGAA-AAGAAGAAAAAGAAGA
*
3336232 AGAAGAAAAAGAAGAAAAA
1 AAAAG-AAAAGAAGAAAAA
3336251 AAAATAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
22 7 0.21
23 15 0.44
24 4 0.12
25 8 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAGAAGAAAAAGAAGA
Found at i:3342809 original size:17 final size:18
Alignment explanation
Indices: 3342774--3342809 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3342764 TGATTCAATC
3342774 AGTATCGATACCAATGAT
1 AGTATCGATACCAATGAT
3342792 AGTATCGATACC-ATGAT
1 AGTATCGATACCAATGAT
3342809 A
1 A
3342810 AGGGGTATCG
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:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (18 bp):
AGTATCGATACCAATGAT
Found at i:3343528 original size:31 final size:31
Alignment explanation
Indices: 3343490--3343591 Score: 96
Period size: 31 Copynumber: 3.1 Consensus size: 31
3343480 TGTTGCTCCT
3343490 TTCTGACGCCATCTGAGCTCCAATCGTAAAA
1 TTCTGACGCCATCTGAGCTCCAATCGTAAAA
* * ** *
3343521 TTCTGACGCCATCTGAAAACCCCTTTCTTCAAGCTCAA
1 TTCTGACGCCATCTG--AGCTCCAATCGT-AA----AA
3343559 TTCTGACGCCATCTGAGCTCCAATCGTAAAA
1 TTCTGACGCCATCTGAGCTCCAATCGTAAAA
3343590 TT
1 TT
3343592 AAAATCACCA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
31 19 0.35
33 7 0.13
34 2 0.04
35 2 0.04
36 7 0.13
38 17 0.31
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.28
Consensus pattern (31 bp):
TTCTGACGCCATCTGAGCTCCAATCGTAAAA
Done.