Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007849.1 Hibiscus syriacus cultivar Beakdansim tig00110206_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: 3141433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:2586596 original size:132 final size:128
Alignment explanation
Indices: 2586491--2587179 Score: 694
Period size: 129 Copynumber: 5.3 Consensus size: 128
2586481 CTAGTGCAGC
2586491 TGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAG
1 TGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAG
* *
2586556 CAGGTGGATATGGAGGTGGCGGCGGCAAAGGTGGTGGTGGAGGT-GCTGCAGGTGGATATGGAGG
66 CAGGTGGACATGGAGGTGGCGGTGG-AAAGGTGGTGGTGGAGGTAG-TGCAGGTGGATATGGAGG
* *
2586620 AGGAGCTTCTGGATATGGCAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAG
1 TGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAG
* * * *
2586685 CAGGTGGACATGGAGGTGGCGGTGGAAGTGGTGGTGGAGGAGCTAGTGCAGGTGGATATGGTGG
66 CAGGTGGACATGGAGGTGGCGGTGGAA-AGGTGGTGGTGGAGGTAGTGCAGGTGGATATGGAGG
* * *
2586749 TGGAGCTTCTGGATATGGCAGTGGAGGTGGCGAAGGAGGTGGAGCCGGAGCTGGTGGGTATGGAG
1 TGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAG-CTG-G-TGGTGGGTATGGAG
* * **** *
2586814 AAGCTGGTGCTGGTGGAGGTGGTGGTGGTAAAGGTGGTGGTGGAGGTAGTGCAGGTGGATATGGA
63 GAGCAGGTGGACATGGAGGTGGCGGTGG-AAAGGTGGTGGTGGAGGTAGTGCAGGTGGATATGGA
2586879 GG
127 GG
* * * * * * **
2586881 TGGAGCTTCCGGATATGGGAGCGGGGGTGGAGAAGGAGCTGGTAG-TGCAGGTGGGTATGGAGGA
1 TGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGG-AGCTGGTGGTGGGTATGGAGGA
* * * * * * *** * * *
2586945 GCCGGCGGACATGGAGGAGGAGGCGG--TGGTGGAAATGGTGGT-G-GC-GG-AGCTAGTGCG-G
65 GCAGGTGGACATGGAGGTGGCGGTGGAAAGGTGGTGGTGGAGGTAGTGCAGGTGGATA-TG-GAG
2587003 G
128 G
* * ** *
2587004 TGGGGCTTCTGGATATGGAAATGGAGGTGGCCAAGGAGGTGGAGCTGGTGCTGGCGGTTATGGAG
1 TGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGT-G-GG-TATGGAG
* * ** * * ** *
2587069 GAGCCGGTGGACATGGAGGTGGTGGTGGCAGTGGTGGAGGAGGAGCAAGTGCAGGTGGATATGGT
63 GAGCAGGTGGACATGGAGGTGGCGGTGG-AAAGGTGGTGGTGGAGGTAGTGCAGGTGGATATGGA
2587134 GG
127 GG
* * *
2587136 TGGAGCTTCTGGATACGGAAGTGGAGGCGGTGAAGGTGGTGGAG
1 TGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAG
2587180 GAGGAGCAAG
Statistics
Matches: 460, Mismatches: 79, Indels: 39
0.80 0.14 0.07
Matches are distributed among these distances:
122 5 0.01
123 43 0.09
124 4 0.01
125 3 0.01
126 42 0.09
128 2 0.00
129 199 0.43
130 4 0.01
131 5 0.01
132 146 0.32
133 7 0.02
ACGTcount: A:0.19, C:0.09, G:0.52, T:0.20
Consensus pattern (128 bp):
TGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAG
CAGGTGGACATGGAGGTGGCGGTGGAAAGGTGGTGGTGGAGGTAGTGCAGGTGGATATGGAGG
Found at i:2586778 original size:60 final size:61
Alignment explanation
Indices: 2586492--2586788 Score: 184
Period size: 66 Copynumber: 4.6 Consensus size: 61
2586482 TAGTGCAGCT
* * ** *
2586492 GGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGA
1 GGAGCTTCTGGATATGGCAGTGGAGGTGGTGGAGGAGGT--AGCTGCAGGTGGATATGGAGGA
* * * ** * * *
2586555 GCAGGTGGATATGGAGGTGGCGGCGGCAAAGGTGGTGGTGGAGGT-GCTGCAGGTGGATATGGAG
1 GGAGCT---TCTGGATATGGCAGTGG---AGGTGGTGGAGGAGGTAGCTGCAGGTGGATATGGAG
2586619 GA
60 GA
* ** *
2586621 GGAGCTTCTGGATATGGCAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGA
1 GGAGCTTCTGGATATGGCAGTGGAGGTGGTGGAGGAGGT--AGCTGCAGGTGGATATGGAGGA
* * * ** * * *
2586684 GCAGGTGGACATGGAGGTGGCGGTGGAAGTGGTGGTGGAGGAGCTAG-TGCAGGTGGATATGGTG
1 GGAGCT--TC-TGGATATGGCAGTGG-A--GGTGGTGGAGGAGGTAGCTGCAGGTGGATATGGAG
*
2586748 GT
60 GA
* *
2586750 GGAGCTTCTGGATATGGCAGTGGAGGTGGCGAAGGAGGT
1 GGAGCTTCTGGATATGGCAGTGGAGGTGGTGGAGGAGGT
2586789 GGAGCCGGAG
Statistics
Matches: 172, Mismatches: 47, Indels: 33
0.68 0.19 0.13
Matches are distributed among these distances:
60 26 0.15
62 1 0.01
63 50 0.29
64 1 0.01
65 1 0.01
66 63 0.37
67 3 0.02
69 27 0.16
ACGTcount: A:0.20, C:0.07, G:0.52, T:0.21
Consensus pattern (61 bp):
GGAGCTTCTGGATATGGCAGTGGAGGTGGTGGAGGAGGTAGCTGCAGGTGGATATGGAGGA
Found at i:2587230 original size:12 final size:12
Alignment explanation
Indices: 2587209--2587238 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2587199 ATACGGAGGA
2587209 GGTGGAAGCGGC
1 GGTGGAAGCGGC
*
2587221 GGTGGGAGCGGC
1 GGTGGAAGCGGC
2587233 GGTGGA
1 GGTGGA
2587239 GGAGCATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.63, T:0.10
Consensus pattern (12 bp):
GGTGGAAGCGGC
Found at i:2601688 original size:22 final size:22
Alignment explanation
Indices: 2601663--2601709 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2601653 AATCAATTGG
*
2601663 ATAAATATGTAAAATT-AAAAAT
1 ATAAA-ATATAAAATTAAAAAAT
2601685 ATAAAATATAAAATTAAAAAAT
1 ATAAAATATAAAATTAAAAAAT
2601707 ATA
1 ATA
2601710 GATTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAAAATATAAAATTAAAAAAT
Found at i:2601999 original size:16 final size:17
Alignment explanation
Indices: 2601972--2602009 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2601962 TCCCTACAAT
2601972 TTTTAGATTTTTATAGA
1 TTTTAGATTTTTATAGA
* *
2601989 TTTTA-ATTTTTTTATA
1 TTTTAGATTTTTATAGA
2602005 TTTTA
1 TTTTA
2602010 TGTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTAGATTTTTATAGA
Found at i:2605161 original size:14 final size:14
Alignment explanation
Indices: 2605142--2605174 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2605132 GGAAGGTTTA
2605142 CCATTCACAATCTG
1 CCATTCACAATCTG
2605156 CCATTCACAATCTG
1 CCATTCACAATCTG
2605170 CCATT
1 CCATT
2605175 GCTTCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.36, G:0.06, T:0.30
Consensus pattern (14 bp):
CCATTCACAATCTG
Found at i:2606286 original size:19 final size:20
Alignment explanation
Indices: 2606249--2606286 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2606239 TTACATTTTT
2606249 AAAATAAACATAAAGCTCAA
1 AAAATAAACATAAAGCTCAA
* *
2606269 AAAATTAACTTAAA-CTCA
1 AAAATAAACATAAAGCTCA
2606287 TGTATAGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAATAAACATAAAGCTCAA
Found at i:2615560 original size:25 final size:25
Alignment explanation
Indices: 2615506--2615604 Score: 191
Period size: 25 Copynumber: 4.0 Consensus size: 25
2615496 ATTTAGGGGA
2615506 TTAGGGTTTGAAACCCTAAT-TGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2615530 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2615555 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2615580 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2615605 GGGTTGATTG
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
24 20 0.27
25 54 0.73
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:2615680 original size:3 final size:3
Alignment explanation
Indices: 2615672--2615714 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
2615662 ATTAATAAAC
2615672 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2615715 CGATAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2615687 original size:19 final size:19
Alignment explanation
Indices: 2615672--2615714 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2615662 ATTAATAAAC
2615672 ATAATAATAATAAATAATA
1 ATAATAATAATAAATAATA
2615691 ATAATAATAAT-AATAATA
1 ATAATAATAATAAATAATA
2615709 A-AATAA
1 ATAATAA
2615715 CGATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.21
18 8 0.33
19 11 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAATAATAATAAATAATA
Found at i:2615970 original size:40 final size:40
Alignment explanation
Indices: 2615926--2616154 Score: 176
Period size: 40 Copynumber: 5.5 Consensus size: 40
2615916 ACATGGTTCC
*
2615926 TACGTGATGAGGACATCTGGTCGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
* * * * * *
2615966 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTG-ATAACACGGTTCC
1 TACGTGATGAGGAGATCTGG---TC----GGGGAATGACACGGCTCA
* ** * * *
2616012 TACGTGATGAGGACG-GCTGGTTATCTATGG-TTGACATGGCTCC
1 TACGTGATGAGGA-GATCTGG---TC-GGGGAATGACACGGCTCA
2616055 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
* *
2616095 TACGTGATGAAGAGATCTGGTTGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
* *
2616135 TACGTGATGAAGAGTTCTGG
1 TACGTGATGAGGAGATCTGG
2616155 CCATCTAAAG
Statistics
Matches: 151, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
39 2 0.01
40 86 0.57
42 1 0.01
43 29 0.19
46 29 0.19
47 4 0.03
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.24
Consensus pattern (40 bp):
TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
Found at i:2616016 original size:46 final size:42
Alignment explanation
Indices: 2615872--2616187 Score: 149
Period size: 40 Copynumber: 7.4 Consensus size: 42
2615862 TGTTGGGGAC
* *
2615872 GACACTGCTCATACGTGATGAAGAGTTCTTGTCG-TCTAAGG-G-T
1 GACACGGCTCATACGTGATGAAGAGATC-TG--GATCT-AGGTGAT
* * * * * *
2615915 GACATGGTTCCTACGTGATGAGGACATCTGG-TC--GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGATCTAGGTG-AT
*
2615955 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGATCTGG--ATCT--AGGTGAT
* * * * *
2616001 AACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--T
1 GACACGGCTCATACGTGATGAAGA-GATCTGG--ATCTA-GGTGAT
* * * *
2616044 GACATGGCTCCTACGTGATGAGGAGATCTGG-TC--GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGATCTAGGTG-AT
*
2616084 GACACGGCTCATACGTGATGAAGAGATCTGG-T-T-GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGATCTAGGTG-AT
*
2616124 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGATCTGG--ATCT--AGGTGAT
* * *
2616170 AACACGGTTCCTACGTGA
1 GACACGGCTCATACGTGA
2616188 CGAGGACGGC
Statistics
Matches: 215, Mismatches: 34, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
37 4 0.02
38 1 0.00
40 98 0.46
42 3 0.01
43 50 0.23
44 2 0.01
45 3 0.01
46 47 0.22
47 7 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (42 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGATCTAGGTGAT
Found at i:2616783 original size:15 final size:15
Alignment explanation
Indices: 2616740--2616783 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2616730 AAGATGATCT
*
2616740 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
2616755 TGTTTCAAAAGAAAA
1 TGTTTCAAGAGAAAA
*
2616770 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
2616784 CGACTCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:2617327 original size:66 final size:67
Alignment explanation
Indices: 2617239--2617436 Score: 229
Period size: 67 Copynumber: 3.0 Consensus size: 67
2617229 AAAGATTTAC
* ** * * * * *
2617239 TTCAAGAGAAACGGTCTCAAGAGATACAAAATTCAATTT-AAGAGAAACAGATTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
2617303 GT
66 GT
* ***
2617305 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
2617370 GT
66 GT
*** *
2617372 TTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAA-AATTCAATTTCAAAAGAAACAAACTCAAAGATTTT
2617436 T
65 T
2617437 TTCGCAAAAT
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
66 32 0.28
67 84 0.72
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (67 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
GT
Found at i:2617340 original size:37 final size:36
Alignment explanation
Indices: 2617299--2617420 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
2617289 ATTCAAAGAT
*
2617299 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAA
* * * *
2617336 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG---AT
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
2617366 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAGAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAA-AA
*
2617403 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCAAAAGAAAC
2617421 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 21 0.31
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 37 0.54
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
Found at i:2617445 original size:67 final size:67
Alignment explanation
Indices: 2617281--2617436 Score: 260
Period size: 67 Copynumber: 2.3 Consensus size: 67
2617271 TCAATTTAAG
* * *
2617281 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCA
2617346 AA
66 AA
2617348 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTTTC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAA-AATTTTGTTTC
*
2617412 CAA
65 AAA
2617415 AGAAACAAACTCAAAGATTTTT
1 AGAAACAAACTCAAAGATTTTT
2617437 TTCGCAAAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
66 2 0.02
67 82 0.98
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCA
AA
Found at i:2617503 original size:52 final size:53
Alignment explanation
Indices: 2617423--2617527 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 53
2617413 AAAGAAACAA
* *
2617423 ACTCAAAGATTTTTTTCGCAAAATTGTCTCAAGAGATACAAAACTTTGTTTCAG
1 ACTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
*
2617477 ACTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
2617528 AAATAAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 39 0.81
54 9 0.19
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
Found at i:2617607 original size:29 final size:29
Alignment explanation
Indices: 2617538--2617635 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 29
2617528 AAATAAATAG
* *
2617538 ACTCAAAG--TTTT-TTCAAAA-GAAACG
1 ACTCAAAGATTTTTATTCAAAAGGAACCA
2617563 ACTCAAAGATTATTTATTCAAAAGGAACCA
1 ACTCAAAGATT-TTTATTCAAAAGGAACCA
* *
2617593 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACCA
2617622 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
2617636 TTAAGAGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
25 8 0.13
27 1 0.02
28 3 0.05
29 37 0.59
30 14 0.22
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACCA
Found at i:2617967 original size:36 final size:36
Alignment explanation
Indices: 2617883--2617986 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
2617873 GAGAAAATGA
* * *
2617883 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
2617917 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
2617953 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
2617987 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:2618014 original size:36 final size:36
Alignment explanation
Indices: 2617884--2618002 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
2617874 AGAAAATGAT
* * * *
2617884 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
2617918 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
2617954 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
2617989 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
2618003 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:2618134 original size:105 final size:101
Alignment explanation
Indices: 2617954--2618190 Score: 273
Period size: 105 Copynumber: 2.3 Consensus size: 101
2617944 TAGAGAAATT
* *
2617954 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
2618019 TGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
2618056 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTGTTT
* * * * *
2618120 -TTAGTGAATCAAATTTAAAATTTGTATCTCAAAGGAAAAAT
61 AAT-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
2618161 GTCTCAAGCGAGACGCAATTTGTTTT-AGAA
1 GTCTCAAGCGAGACAAAATTTGTTTTGAGAA
2618191 TTCTCAAAAT
Statistics
Matches: 116, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
101 7 0.06
102 23 0.20
103 2 0.02
104 5 0.04
105 79 0.68
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:2618663 original size:14 final size:14
Alignment explanation
Indices: 2618644--2618670 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2618634 TTATATATCA
2618644 TGTATGTATGTGTG
1 TGTATGTATGTGTG
2618658 TGTATGTATGTGT
1 TGTATGTATGTGT
2618671 ATACTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
TGTATGTATGTGTG
Found at i:2622003 original size:31 final size:32
Alignment explanation
Indices: 2621947--2622008 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2621937 TGACAAAATG
2621947 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
2621979 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
2622009 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:2625677 original size:25 final size:25
Alignment explanation
Indices: 2625646--2625745 Score: 200
Period size: 25 Copynumber: 4.0 Consensus size: 25
2625636 ATTTAGGGGA
2625646 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2625671 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2625696 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2625721 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2625746 GGGTTGATTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:2625821 original size:3 final size:3
Alignment explanation
Indices: 2625813--2625858 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
2625803 ATTAATAAAC
2625813 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2625858 A
1 A
2625859 CGATAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2630038 original size:40 final size:40
Alignment explanation
Indices: 2629983--2630062 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
2629973 GATCCTATAC
2629983 GATCTGGATACAACTTAGGTATGATGGAAAGCATTTCTCA
1 GATCTGGATACAACTTAGGTATGATGGAAAGCATTTCTCA
2630023 GATCTGGATACAACTTAGGTATGATGGAAAGCATTTCTCA
1 GATCTGGATACAACTTAGGTATGATGGAAAGCATTTCTCA
2630063 CTTCTTACCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (40 bp):
GATCTGGATACAACTTAGGTATGATGGAAAGCATTTCTCA
Found at i:2631967 original size:41 final size:40
Alignment explanation
Indices: 2631913--2631991 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
2631903 GATTTGGCGT
* * *
2631913 CACGTGGGGTATAGCGC-GTCCCCTGATCTGCGCTATACGC
1 CACGTGGGATATAGCACTG-CCCCTGATCAGCGCTATACGC
*
2631953 CACGTAGGGATATAGCACTGCCCCTGCTCAGCGCTATAC
1 CACGT-GGGATATAGCACTGCCCCTGATCAGCGCTATAC
2631992 CTGGGTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 5 0.15
41 27 0.82
42 1 0.03
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.22
Consensus pattern (40 bp):
CACGTGGGATATAGCACTGCCCCTGATCAGCGCTATACGC
Found at i:2633630 original size:50 final size:51
Alignment explanation
Indices: 2633474--2633630 Score: 133
Period size: 50 Copynumber: 3.1 Consensus size: 51
2633464 CCCCCTGTAC
* ** * * *
2633474 CGCGCTATACCTCACGTGTTAGATAAA-CAG-TTATAGCGC-GGATCAGGAAC
1 CGCGCTATACC-CACGTGTAAGCCAAATCAGCATATAGCGCGGGA-CAGGGAG
* * * * * *
2633524 CGCACTATACCCACGTGTAAGTCATATCAGCGTATAGCGCGGTACAGGGGG
1 CGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGCGCGGGACAGGGAG
* *
2633575 CGCGCTATACCCACGTG-ACGCCAAATCAGCATATAGCTCGGGACAGGGAG
1 CGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGCGCGGGACAGGGAG
*
2633625 TGCGCT
1 CGCGCT
2633631 TTACTGCTAC
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
49 11 0.13
50 44 0.52
51 28 0.33
52 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (51 bp):
CGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGCGCGGGACAGGGAG
Found at i:2634441 original size:12 final size:11
Alignment explanation
Indices: 2634424--2634460 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
2634414 TCTTCTTCTA
2634424 CCTCCGATCTCT
1 CCTCCGATC-CT
2634436 CCTCCGATCCCT
1 CCTCCGAT-CCT
2634448 CCTCCGATCCT
1 CCTCCGATCCT
2634459 CC
1 CC
2634461 CCTTCCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 5 0.21
12 18 0.75
13 1 0.04
ACGTcount: A:0.08, C:0.57, G:0.08, T:0.27
Consensus pattern (11 bp):
CCTCCGATCCT
Found at i:2634876 original size:31 final size:31
Alignment explanation
Indices: 2634841--2634972 Score: 149
Period size: 31 Copynumber: 4.3 Consensus size: 31
2634831 CCAAAAATAG
* **
2634841 TTTAGACATATAAATGAGAAAAACGATATAA
1 TTTAGACACATAAATGAGAAAAATAATATAA
* * * *
2634872 TTTAGGCACGTAAAT-AAAAAGAATAATATAG
1 TTTAGACACATAAATGAGAAA-AATAATATAA
* *
2634903 TTTAGACACCTACATGAGAAAAATAATATAA
1 TTTAGACACATAAATGAGAAAAATAATATAA
* *
2634934 TTTAGACACATAAATGAGAAAAATATTATAG
1 TTTAGACACATAAATGAGAAAAATAATATAA
2634965 TTTAGACA
1 TTTAGACA
2634973 TTTTTTTATA
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
30 4 0.05
31 75 0.90
32 4 0.05
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (31 bp):
TTTAGACACATAAATGAGAAAAATAATATAA
Found at i:2634934 original size:62 final size:62
Alignment explanation
Indices: 2634837--2634972 Score: 175
Period size: 62 Copynumber: 2.2 Consensus size: 62
2634827 TTGACCAAAA
* * * *
2634837 ATAGTTTAGACATATAAATGAGAAAAACGATATAATTTAGGCACGTAAAT-AAAAAGAATAAT
1 ATAGTTTAGACACATAAATGAGAAAAACAATATAATTTAGACACATAAATGAAAAA-AATAAT
* * * * *
2634899 ATAGTTTAGACACCTACATGAGAAAAATAATATAATTTAGACACATAAATGAGAAAAATATT
1 ATAGTTTAGACACATAAATGAGAAAAACAATATAATTTAGACACATAAATGAAAAAAATAAT
2634961 ATAGTTTAGACA
1 ATAGTTTAGACA
2634973 TTTTTTTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 60 0.94
63 4 0.06
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.27
Consensus pattern (62 bp):
ATAGTTTAGACACATAAATGAGAAAAACAATATAATTTAGACACATAAATGAAAAAAATAAT
Found at i:2635069 original size:20 final size:20
Alignment explanation
Indices: 2635033--2635070 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2635023 ATAAGGCTTA
* *
2635033 TAAAAGTTATAATTTAAAGT
1 TAAAAGTTACAAGTTAAAGT
2635053 TAAAAGTTACAAGTTAAA
1 TAAAAGTTACAAGTTAAA
2635071 TTATATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (20 bp):
TAAAAGTTACAAGTTAAAGT
Found at i:2635148 original size:26 final size:27
Alignment explanation
Indices: 2635119--2635188 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
2635109 TCCTCACTGA
2635119 ATTTTATTTTATTTTC-TATTTCATTC
1 ATTTTATTTTATTTTCTTATTTCATTC
*
2635145 ATTTTTACTTTA-TTTCTTATTTCATTC
1 A-TTTTATTTTATTTTCTTATTTCATTC
*
2635172 ATTGTACTTTTAATTTT
1 ATTTTA-TTTT-ATTTT
2635189 TTTTAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 9 0.25
27 23 0.64
28 1 0.03
29 3 0.08
ACGTcount: A:0.20, C:0.11, G:0.01, T:0.67
Consensus pattern (27 bp):
ATTTTATTTTATTTTCTTATTTCATTC
Found at i:2635158 original size:27 final size:27
Alignment explanation
Indices: 2635120--2635174 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
2635110 CCTCACTGAA
*
2635120 TTTTATTTTATTT-TCTATTTCATTCAT
1 TTTTACTTTATTTCT-TATTTCATTCAT
2635147 TTTTACTTTATTTCTTATTTCATTCAT
1 TTTTACTTTATTTCTTATTTCATTCAT
2635174 T
1 T
2635175 GTACTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTACTTTATTTCTTATTTCATTCAT
Found at i:2637121 original size:33 final size:33
Alignment explanation
Indices: 2637078--2637157 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
2637068 AGTACTGTTA
*
2637078 CCTTAGCTTAGCTTTTAACCATTTGACTTTATT
1 CCTTATCTTAGCTTTTAACCATTTGACTTTATT
2637111 CCTTATCTTAGCTTTTAACCATTTGACTTTATT
1 CCTTATCTTAGCTTTTAACCATTTGACTTTATT
2637144 CCTTATCTTAGCTT
1 CCTTATCTTAGCTT
2637158 GCTATCGTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.50
Consensus pattern (33 bp):
CCTTATCTTAGCTTTTAACCATTTGACTTTATT
Found at i:2642883 original size:16 final size:17
Alignment explanation
Indices: 2642850--2642883 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2642840 CTTTTTGTTT
*
2642850 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
2642867 TTATTTTA-ATATTAAA
1 TTATTTTATATATTAAA
2642883 T
1 T
2642884 AATAGTGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:2643065 original size:61 final size:61
Alignment explanation
Indices: 2642967--2643089 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 61
2642957 GTCATACAAA
*
2642967 AATAATAATAAAATAAAATAATTTAAAACGACAAAAATAAG-AGCAATTAGAAAATTTAATG
1 AATAATAATAAAATAAAATAATTTAAAACGACAAAAATAAGAAG-AATTAGAAAAATTAATG
* ** *
2643028 AATAATAATAAAATAAAATAATTTAGAGGGA-ACAAAATATGAAGAATTAGAAAAATTAATG
1 AATAATAATAAAATAAAATAATTTAAAACGACA-AAAATAAGAAGAATTAGAAAAATTAATG
2643089 A
1 A
2643090 GTAAATTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 1 0.02
61 52 0.95
62 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.24
Consensus pattern (61 bp):
AATAATAATAAAATAAAATAATTTAAAACGACAAAAATAAGAAGAATTAGAAAAATTAATG
Found at i:2646361 original size:232 final size:227
Alignment explanation
Indices: 2645955--2646426 Score: 668
Period size: 232 Copynumber: 2.0 Consensus size: 227
2645945 ATTCATATAT
2645955 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
1 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTC-GTTTTTTTAAGTGTGATATTCGGGTC
* *
2646020 GGGTCGAGGTCGGGTTTAGGGTGAAAAATACCCAACCCGAAAATATATATAATTTTACATTATAT
65 GGGT----GTCGAGTTTAGGGTGAAAAATACCCAACCCGAAAAAATATATAATTTTACATTATAT
*
2646085 ATTTAGGAATAATTACAATAATACCCCTCTATATATAA-TTTTTTTCAATTAAGTCATTGTTTTT
126 ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCAATGTTTTT
* *
2646149 ATTGAATAAAAATAATTTTTTTATTATTTCGGGTTGGG
191 ATTGAATAAAAAT-ATTTTTTTATTATTTCGGATCGGG
2646187 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCA-G-C-TTTTTTTAAGTGTGATATTCGGGTCG
1 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGTTTTTTTAAGTGTGATATTCGGGTCG
* *
2646249 GGT-TTGAGTTTAGGGTGAAAAATAACCAACCCGACCCGACCCAAAAAATATATAATTTTATC-T
66 GGTGTCGAGTTTAGGGTGAAAAAT-----ACCCAACCCG----AAAAAATATATAATTTTA-CAT
*
2646312 TATATATTTAGGAATTATTACAATAATACCCCTCTATATATAATTTTTTTTTTCAATTAAGTCAA
121 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAA--TTTTTTTTCAATTAAGTCAA
2646377 TGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGATCGGG
184 TGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGATCGGG
2646421 TCGGGT
1 TCGGGT
2646427 TTCTAATTCA
Statistics
Matches: 219, Mismatches: 8, Indels: 24
0.87 0.03 0.10
Matches are distributed among these distances:
223 18 0.08
228 38 0.17
230 1 0.00
231 1 0.00
232 94 0.43
233 1 0.00
234 28 0.13
235 38 0.17
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (227 bp):
TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGTTTTTTTAAGTGTGATATTCGGGTCG
GGTGTCGAGTTTAGGGTGAAAAATACCCAACCCGAAAAAATATATAATTTTACATTATATATTTA
GGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCAATGTTTTTATTGA
ATAAAAATATTTTTTTATTATTTCGGATCGGG
Found at i:2649513 original size:66 final size:66
Alignment explanation
Indices: 2649431--2649558 Score: 231
Period size: 66 Copynumber: 1.9 Consensus size: 66
2649421 TTGAATGGCT
2649431 TGATGTTACATATTTTATGGATATGA-TTTATGATGTGATTATAAGCATGAATGAATGATAAAAA
1 TGATGTTACATATTTTATGGATAT-ACTTTATGATGTGATTATAAGCATGAATGAATGATAAAAA
2649495 TA
65 TA
*
2649497 TGATGTTACATATTTTATGGATATACTTTATGATGTGCTTATAAGCATGAATGAATGATAAA
1 TGATGTTACATATTTTATGGATATACTTTATGATGTGATTATAAGCATGAATGAATGATAAA
2649559 GTATGATATT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 1 0.02
66 59 0.98
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.40
Consensus pattern (66 bp):
TGATGTTACATATTTTATGGATATACTTTATGATGTGATTATAAGCATGAATGAATGATAAAAAT
A
Found at i:2650920 original size:31 final size:33
Alignment explanation
Indices: 2650876--2650959 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
2650866 TTGACGAGAG
* *
2650876 TTAAGGGTTAAATTAATATTTTAT-T-TAAAAT
1 TTAAAGGTAAAATTAATATTTTATCTCTAAAAT
2650907 TTAAAGGTAAAATTAATA-TTTATCTCTAAAAT
1 TTAAAGGTAAAATTAATATTTTATCTCTAAAAT
* * *
2650939 TTGAAGGTCAAATTGATATTT
1 TTAAAGGTAAAATTAATATTT
2650960 CATCAAAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
30 5 0.11
31 17 0.38
32 21 0.47
33 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (33 bp):
TTAAAGGTAAAATTAATATTTTATCTCTAAAAT
Found at i:2664799 original size:46 final size:47
Alignment explanation
Indices: 2664730--2664820 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 47
2664720 CTATAATTTG
* * *
2664730 ATTATTGAAATTTATCATCCGATAATGATATACCAATCTATTATTCA
1 ATTATTGAAATTTACCATCCGATAAAGATACACCAATCTATTATTCA
* * * *
2664777 ATTA-TGAATTTTACCATTCGATAAAGATACATCAGTCTATTATT
1 ATTATTGAAATTTACCATCCGATAAAGATACACCAATCTATTATT
2664821 TGATGATTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 33 0.89
47 4 0.11
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (47 bp):
ATTATTGAAATTTACCATCCGATAAAGATACACCAATCTATTATTCA
Found at i:2669009 original size:30 final size:30
Alignment explanation
Indices: 2668941--2669029 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 30
2668931 TCAAATTCAG
* * *
2668941 GGGTTAAATTGATATTTTATCTAAAGTTTA
1 GGGTCAAAATGATATTATATCTAAAGTTTA
*
2668971 GTGGTCAAAATGATATTCTATCTAAAGTTTA
1 G-GGTCAAAATGATATTATATCTAAAGTTTA
* *
2669002 GGGTCAAAATAAAATTATATCTAAAGTT
1 GGGTCAAAATGATATTATATCTAAAGTT
2669030 CAAGGGCCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 25 0.48
31 27 0.52
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (30 bp):
GGGTCAAAATGATATTATATCTAAAGTTTA
Found at i:2673139 original size:18 final size:19
Alignment explanation
Indices: 2673099--2673139 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2673089 AATAACTTAA
2673099 ATAATAATTAATATTATTC
1 ATAATAATTAATATTATTC
2673118 -TAATAA-TATATATT-TTC
1 ATAATAATTA-ATATTATTC
2673135 ATAAT
1 ATAAT
2673140 TTTTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAATAATTAATATTATTC
Found at i:2673824 original size:10 final size:11
Alignment explanation
Indices: 2673804--2673828 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2673794 GAGTAAACCC
2673804 AAAAAGAAAAA
1 AAAAAGAAAAA
2673815 AAAAAGAAAAA
1 AAAAAGAAAAA
2673826 AAA
1 AAA
2673829 GACAGCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:2676934 original size:20 final size:20
Alignment explanation
Indices: 2676892--2676936 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2676882 GTCATCCAAT
* *
2676892 TTTTTAAACCTCAGACCTAA
1 TTTTTAAACCCCAGACCGAA
* *
2676912 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCAGACCGAA
2676932 TTTTT
1 TTTTT
2676937 TCCCGAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGAA
Found at i:2678407 original size:3 final size:3
Alignment explanation
Indices: 2678399--2678433 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2678389 TAATTTCCTT
2678399 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2678434 TCGTTTGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2680682 original size:51 final size:51
Alignment explanation
Indices: 2680626--2680765 Score: 244
Period size: 51 Copynumber: 2.7 Consensus size: 51
2680616 GGATATACAA
*
2680626 TTAGCTAGCTTCTACATACGAGTATATGTCTTTCATTATAGGTCCATATCC
1 TTAGCTAGCTTCTACATACGAGTATATGCCTTTCATTATAGGTCCATATCC
2680677 TTAGCTAGCTTCTACATACGAGTATATGCCTTTCATTATAGGTCCATATCC
1 TTAGCTAGCTTCTACATACGAGTATATGCCTTTCATTATAGGTCCATATCC
* * *
2680728 TTAGCTAGCTGCGACATACGAGTATATGCCTTCCATTA
1 TTAGCTAGCTTCTACATACGAGTATATGCCTTTCATTA
2680766 CAAAAACTGG
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 85 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (51 bp):
TTAGCTAGCTTCTACATACGAGTATATGCCTTTCATTATAGGTCCATATCC
Found at i:2680844 original size:48 final size:49
Alignment explanation
Indices: 2680792--2680888 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
2680782 GTATCGATCA
2680792 AAACAAGTGATTTCC-AAAAAAAAGTTACTAGTTTAAAGACACTCAGTT
1 AAACAAGTGATTTCCAAAAAAAAAGTTACTAGTTTAAAGACACTCAGTT
*
2680840 AAACAAGTGATTTCCAAAAAAAAAGTTATTAGTTTAAAGACACTCAGTT
1 AAACAAGTGATTTCCAAAAAAAAAGTTACTAGTTTAAAGACACTCAGTT
2680889 CTTTTCTCAG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 15 0.32
49 32 0.68
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.28
Consensus pattern (49 bp):
AAACAAGTGATTTCCAAAAAAAAAGTTACTAGTTTAAAGACACTCAGTT
Found at i:2682818 original size:291 final size:291
Alignment explanation
Indices: 2682294--2682830 Score: 734
Period size: 291 Copynumber: 1.8 Consensus size: 291
2682284 TAGGCTGTCA
* * * * * *
2682294 ATTTGTGGGTTTTCACCCTAGAGGTGATTTCCTTTTTAATGCCTTTGGCATTTCATAACCTTCAC
1 ATTTGTGAGTTTTCACCCTAAAGATCATTTCCTTTTAAATGCCTTTGACATTTCATAACCTTCAC
* * * *
2682359 ATAGATTGAATATGAAACCTAAAACTAATTGTACTTGATCTACCCTGTGATTCGAAAAGTCATTT
66 AGAGATTGAATATGAAACCTAAAACTAATTGTACTTGATCCACCCTGCGATTAGAAAAGTCATTT
* * **
2682424 TTCATGAAAGACTTATCACATGTGCTTATTGTCTTCTCTTTTGATGAATTCAAGATTTCAATTTA
131 TTCATGAAAAACTCATCACATGTGCGCATTGTCTTCTCTTTTGATGAATTCAAGATTTCAATTTA
* * *
2682489 GTTCTTGCATTTGAAACATCAATGCTTTTGTTCTCGATCCTGAATATATTTTCATATGCTTCTTC
196 GTTCTTGCATCTGAAACATCAATACTTTCGTTCTCGATCCTGAATATATTTTCATATGCTTCTTC
2682554 TCTTTTATTTTTGGATCCTTCTAGACTACTC
261 TCTTTTATTTTTGGATCCTTCTAGACTACTC
* * * *
2682585 ATTTGTGAGTTTTCACTCTAAAGATCATTTCCTTTTAAATGCCTTTGACGTTTCATAATCTTCAT
1 ATTTGTGAGTTTTCACCCTAAAGATCATTTCCTTTTAAATGCCTTTGACATTTCATAACCTTCAC
* * ** * * *
2682650 AGAGATTGAATATGAAACCTGAAGCTAATTGTACTTGATCCA-TTTCGCGGTTAGATAAGTTATT
66 AGAGATTGAATATGAAACCTAAAACTAATTGTACTTGATCCACCCT-GCGATTAGAAAAGTCATT
* * * *
2682714 TTTCATGAAAAACTCATCACATGTGCGCCTTGTCTTCTCTTTTTATGACTTCAATATTTCAATTT
130 TTTCATGAAAAACTCATCACATGTGCGCATTGTCTTCTCTTTTGATGAATTCAAGATTTCAATTT
* * * *
2682779 GGTTCTTGCATCTGAAACGTCAATACTTTCGTTCTCGATCTTGAATCTATTT
195 AGTTCTTGCATCTGAAACATCAATACTTTCGTTCTCGATCCTGAATATATTT
2682831 CTGCATACTT
Statistics
Matches: 209, Mismatches: 36, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
290 1 0.00
291 208 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (291 bp):
ATTTGTGAGTTTTCACCCTAAAGATCATTTCCTTTTAAATGCCTTTGACATTTCATAACCTTCAC
AGAGATTGAATATGAAACCTAAAACTAATTGTACTTGATCCACCCTGCGATTAGAAAAGTCATTT
TTCATGAAAAACTCATCACATGTGCGCATTGTCTTCTCTTTTGATGAATTCAAGATTTCAATTTA
GTTCTTGCATCTGAAACATCAATACTTTCGTTCTCGATCCTGAATATATTTTCATATGCTTCTTC
TCTTTTATTTTTGGATCCTTCTAGACTACTC
Found at i:2688786 original size:31 final size:31
Alignment explanation
Indices: 2688749--2688808 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2688739 TAGTTGTATG
* *
2688749 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
2688780 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
2688809 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:2692082 original size:2 final size:2
Alignment explanation
Indices: 2692075--2692100 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2692065 ATAATAAATA
2692075 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
2692101 TAATTTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2703811 original size:5 final size:5
Alignment explanation
Indices: 2703801--2703829 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2703791 ACCCCACCAG
2703801 CTCAA CTCAA CTCAA CTCAA CTCAA CTCA
1 CTCAA CTCAA CTCAA CTCAA CTCAA CTCA
2703830 TAGGTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (5 bp):
CTCAA
Found at i:2704550 original size:20 final size:21
Alignment explanation
Indices: 2704511--2704550 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2704501 TATATAGCAA
2704511 AATATGAGATGTTAATGACTC
1 AATATGAGATGTTAATGACTC
2704532 AATATGATG-TGTT-ATGACT
1 AATATGA-GATGTTAATGACT
2704551 AGATGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 11 0.61
22 1 0.06
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (21 bp):
AATATGAGATGTTAATGACTC
Found at i:2707851 original size:2 final size:2
Alignment explanation
Indices: 2707844--2707873 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2707834 AGGAAACATT
2707844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2707874 AGTTGCACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2709714 original size:16 final size:16
Alignment explanation
Indices: 2709693--2709726 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2709683 TTACTATTCA
*
2709693 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
2709709 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
2709725 CG
1 CG
2709727 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:2715030 original size:188 final size:187
Alignment explanation
Indices: 2714421--2715186 Score: 636
Period size: 188 Copynumber: 4.1 Consensus size: 187
2714411 AAAGTAGGTG
* * *** * * * *
2714421 AACAAAATAAGTTGAAAGTTGAAAATGTTATCATTCATACCATGAAATTTGGTTGCGCCCATTAT
1 AACAAAATAAGTTGAAAGCTGAAAATGTTATCAATCATGGTAAGAAATCTGGATGCGCCCATGAT
* * * *
2714486 TGTTAGCGTTCGATAAGAAAATAAGTTGAGATT-GAGTTTGTTATAAGCTGCTTTAACATATTTG
66 TGTTAGCGTTCGATAAGAAAGTAAGTTGAGATTAG-GTTTGTTATAAGTTGCTTTAACAAATTCG
* * * * ** * * * *
2714550 ATTTTTGAACGAAGATGTTA-TTGGAGCTTAACAAATGAGTTTATCAAAATAAGGGCGGT
130 -GTTTCGACCGAAAATGTTACCAGGAGTTTAGCAAATG-GTTCATCAAAATAAGGACGGT
* * * ** * * * * *
2714609 AAGAAAATAAATTGAAAACCAAAAATATTATCCATCATGGGAAGAAATCTGGATACGCCTATGAT
1 AACAAAATAAGTTGAAAGCTGAAAATGTTATCAATCATGGTAAGAAATCTGGATGCGCCCATGAT
* * * * * *
2714674 TGTTAGTGTTCGATAAGAAAGTAAGTTGATATAAGGTTTGTTGTAAGGTACTTTAACAAATAT-G
66 TGTTAGCGTTCGATAAGAAAGTAAGTTGAGATTAGGTTTGTTATAAGTTGCTTTAACAAAT-TCG
* * * * * * **
2714738 GTTTTGACTGAAAATCTTATC-GGGGTTTAGCAAATTGATTCATCAAAATAAGGACGAC
130 GTTTCGACCGAAAATGTTACCAGGAGTTTAGCAAA-TGGTTCATCAAAATAAGGACGGT
* * ** * * * *
2714796 AACAAAATAAGTTGGAAGATGAAAAACTTATCAACCGTGGTAAGAAAT-TTGAGTGTGCCCATGA
1 AACAAAATAAGTTGAAAGCTGAAAATGTTATCAATCATGGTAAGAAATCTGGA-TGCGCCCATGA
* * * *
2714860 TTGTTAGCGTTTGATACGAAAGTAAGTTAAGATTAGGTTTGTTATAAGTTGTTTTAACAAATTCG
65 TTGTTAGCGTTCGATAAGAAAGTAAGTTGAGATTAGGTTTGTTATAAGTTGCTTTAACAAATTCG
* * * *
2714925 GCTTCGACCAAAAATGTTA-CAGAGAGTTTAGTAAATTGGTTCATCAAAATAAGGGCGGT
130 GTTTCGACCGAAAATGTTACCAG-GAGTTTAGCAAA-TGGTTCATCAAAATAAGGACGGT
*
2714984 AACAAAATAAGTTGAAAGCTGAAAATGTTATCAATCATGGTAAGAAATC-GGATTGTGCCCATGA
1 AACAAAATAAGTTGAAAGCTGAAAATGTTATCAATCATGGTAAGAAATCTGGA-TGCGCCCATGA
* * * * * * * *
2715048 ATATTAGTG-GCTGATAAGAAACT-AGATTGAGATCAGGTTTGTTATAAGTTGCTTTAATAAATC
65 TTGTTAGCGTTC-GATAAGAAAGTAAG-TTGAGATTAGGTTTGTTATAAGTTGCTTTAACAAATT
* * * * *
2715111 CGATTTCGACCGAAAATGTAACCA-AAGTTTAGCAAATGGATCTAGCAAAATAACAGGACGGT
128 CGGTTTCGACCGAAAATGTTACCAGGAGTTTAGCAAATGGTTC-ATCAAAAT-A-AGGACGGT
2715173 AA-AAAATAAGTTGA
1 AACAAAATAAGTTGA
2715187 TAGGCGAAAA
Statistics
Matches: 456, Mismatches: 107, Indels: 30
0.77 0.18 0.05
Matches are distributed among these distances:
186 10 0.02
187 170 0.37
188 263 0.58
189 13 0.03
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (187 bp):
AACAAAATAAGTTGAAAGCTGAAAATGTTATCAATCATGGTAAGAAATCTGGATGCGCCCATGAT
TGTTAGCGTTCGATAAGAAAGTAAGTTGAGATTAGGTTTGTTATAAGTTGCTTTAACAAATTCGG
TTTCGACCGAAAATGTTACCAGGAGTTTAGCAAATGGTTCATCAAAATAAGGACGGT
Found at i:2715979 original size:31 final size:31
Alignment explanation
Indices: 2715941--2716006 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
2715931 CTTTCATTTA
*
2715941 GGTCCCCCAACATTTAGTCCGTTTGTAATAT
1 GGTCCCCCAACATTTAGTCCGTTTGCAATAT
2715972 GGTCCCCCAACATTTAGTCCGTTTGCAATAT
1 GGTCCCCCAACATTTAGTCCGTTTGCAATAT
2716003 GGTC
1 GGTC
2716007 ACCAACGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (31 bp):
GGTCCCCCAACATTTAGTCCGTTTGCAATAT
Found at i:2717013 original size:30 final size:30
Alignment explanation
Indices: 2716964--2717043 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 30
2716954 CTTTTAAAAC
*
2716964 TTACAATAT-AGTCCCCCAACATTTAGTCTGT
1 TTACAATATGA-T-CCCCAACATTTAGTATGT
2716995 TTACAATATGATCCCCAACATTTAGTATGT
1 TTACAATATGATCCCCAACATTTAGTATGT
* *
2717025 TTGCAATATGGTCCCCAAC
1 TTACAATATGATCCCCAAC
2717044 GTAACTGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 34 0.76
31 10 0.22
32 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (30 bp):
TTACAATATGATCCCCAACATTTAGTATGT
Found at i:2723232 original size:2 final size:2
Alignment explanation
Indices: 2723225--2723256 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2723215 TTTTACTTAT
2723225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2723257 CAATAAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2723877 original size:11 final size:11
Alignment explanation
Indices: 2723857--2723891 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
2723847 AGTAACCAAC
2723857 AACT-ATAACA
1 AACTAATAACA
2723867 AACTAATAAC-
1 AACTAATAACA
2723877 AACTAATAACA
1 AACTAATAACA
2723888 AACT
1 AACT
2723892 CTAACATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (11 bp):
AACTAATAACA
Found at i:2728008 original size:29 final size:28
Alignment explanation
Indices: 2727964--2728023 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
2727954 TGAATAGTAA
2727964 AAAGGTGGGGCACGCCTAAATGGAAATT
1 AAAGGTGGGGCACGCCTAAATGGAAATT
2727992 AAAGGTGGGGGCACGCCTAAATGGAAATT
1 AAAGGT-GGGGCACGCCTAAATGGAAATT
2728021 AAA
1 AAA
2728024 TGGGTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.38, C:0.13, G:0.32, T:0.17
Consensus pattern (28 bp):
AAAGGTGGGGCACGCCTAAATGGAAATT
Found at i:2728452 original size:16 final size:16
Alignment explanation
Indices: 2728431--2728475 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
2728421 TTACTACTTA
*
2728431 CGTGAATAGTGAATTT
1 CGTGAATAGTAAATTT
*
2728447 CGTGAATATTAAATTT
1 CGTGAATAGTAAATTT
2728463 CGTGAATAGTAAA
1 CGTGAATAGTAAA
2728476 ATTTTGTCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (16 bp):
CGTGAATAGTAAATTT
Found at i:2734062 original size:12 final size:12
Alignment explanation
Indices: 2734045--2734076 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2734035 TTCCACACAT
2734045 ACGTACACGCAC
1 ACGTACACGCAC
2734057 ACGTACACGCAC
1 ACGTACACGCAC
*
2734069 ACGCACAC
1 ACGTACAC
2734077 ATGTGTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.44, G:0.16, T:0.06
Consensus pattern (12 bp):
ACGTACACGCAC
Found at i:2736915 original size:15 final size:15
Alignment explanation
Indices: 2736895--2736926 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2736885 TGTCTGTTTC
2736895 AAATCTCTATAATAA
1 AAATCTCTATAATAA
2736910 AAATCTCTATAATAA
1 AAATCTCTATAATAA
2736925 AA
1 AA
2736927 TTGTTTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATCTCTATAATAA
Found at i:2739474 original size:31 final size:31
Alignment explanation
Indices: 2739439--2739498 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
2739429 TGATAATAGT
2739439 TGATTTAA-TATCACGAGTTACATGATTTACA
1 TGATTTAATTA-CACGAGTTACATGATTTACA
*
2739470 TGATTTAATTACATGAGTTACATGATTTA
1 TGATTTAATTACACGAGTTACATGATTTA
2739499 AAAAATGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (31 bp):
TGATTTAATTACACGAGTTACATGATTTACA
Found at i:2739481 original size:22 final size:22
Alignment explanation
Indices: 2739456--2739499 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2739446 ATATCACGAG
*
2739456 TTACATGATTTACATGATTTAA
1 TTACATGAGTTACATGATTTAA
2739478 TTACATGAGTTACATGATTTAA
1 TTACATGAGTTACATGATTTAA
2739500 AAAATGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (22 bp):
TTACATGAGTTACATGATTTAA
Found at i:2743695 original size:26 final size:28
Alignment explanation
Indices: 2743665--2743716 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2743655 AACTATATAT
2743665 TATATATT-TA-AAATATTTTCAAAAGC
1 TATATATTATATAAATATTTTCAAAAGC
* *
2743691 TATATATTATATATATGTTTTCAAAA
1 TATATATTATATAAATATTTTCAAAA
2743717 TGTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 2 0.09
28 12 0.55
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (28 bp):
TATATATTATATAAATATTTTCAAAAGC
Found at i:2743732 original size:38 final size:38
Alignment explanation
Indices: 2743674--2743782 Score: 173
Period size: 38 Copynumber: 2.8 Consensus size: 38
2743664 TTATATATTT
* * *
2743674 AAAATATTTTCAAAAGCTATATATTATATATATGTTTTC
1 AAAATGTTTT-AAAAACTATATAATATATATATGTTTTC
*
2743713 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTTC
2743751 AAAATGTTTTAAAAACTATATAATATATATAT
1 AAAATGTTTTAAAAACTATATAATATATATAT
2743783 ATATATATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
38 56 0.86
39 9 0.14
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (38 bp):
AAAATGTTTTAAAAACTATATAATATATATATGTTTTC
Found at i:2743758 original size:49 final size:47
Alignment explanation
Indices: 2743705--2743950 Score: 135
Period size: 47 Copynumber: 5.2 Consensus size: 47
2743695 TATTATATAT
2743705 ATGTTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAA
1 ATGTTTT-AAAATGTTTTAAAAACTATATAATATATAAAT-TTTTCAAA
** * * * * * *
2743754 ATGTTTTAAAA-ACTAT-ATAA-TATAT-ATATATATATATAT--AT
1 ATGTTTTAAAATGTTTTAAAAACTATATAATATATAAATTTTTCAAA
*
2743795 ATATTTTAAAATGTTTTAAAAAAACTATATAATATATATATATATATATTCAAAA
1 ATGTTTTAAAATGTTTT--AAAAACTATATAATATATA-A-AT-T-T-TTC-AAA
2743850 ATG-TTT----T-TTTTAAAAACTATATAATATAT--ATGTTTTCAAAA
1 ATGTTTTAAAATGTTTTAAAAACTATATAATATATAAAT-TTTTC-AAA
* * * *
2743891 ATGTTTTTAAAAATGTTTTCAAAACTATATAATACATATATTTTT-GAA
1 ATG-TTTT-AAAATGTTTTAAAAACTATATAATATATAAATTTTTCAAA
2743939 ATGTTTTCAAAA
1 ATGTTTT-AAAA
2743951 CTATATAATA
Statistics
Matches: 150, Mismatches: 23, Indels: 50
0.67 0.10 0.22
Matches are distributed among these distances:
41 21 0.14
42 3 0.02
43 8 0.05
44 9 0.06
45 8 0.05
46 8 0.05
47 35 0.23
48 10 0.07
49 33 0.22
50 5 0.03
51 3 0.02
52 1 0.01
54 3 0.02
55 3 0.02
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (47 bp):
ATGTTTTAAAATGTTTTAAAAACTATATAATATATAAATTTTTCAAA
Found at i:2743778 original size:2 final size:2
Alignment explanation
Indices: 2743767--2743798 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2743757 TTTTAAAAAC
2743767 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2743799 TTTAAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2743823 original size:53 final size:52
Alignment explanation
Indices: 2743729--2743931 Score: 182
Period size: 53 Copynumber: 4.1 Consensus size: 52
2743719 TTTTAAAAAC
*
2743729 TATATA-ATATATAAATGTTTTCAAAATGTTTTAAAAACTATATAATATATA
1 TATATATATATATAAATATTTTCAAAATGTTTTAAAAACTATATAATATATA
*
2743780 TATATATATATATATATATTTT-AAAATGTTTTAAAAAAACTATATAATATATA
1 TATATATATATATAAATATTTTCAAAATGTTTT--AAAAACTATATAATATATA
*
2743833 TATATATATAT-TCAAAAATGTTT-----T-TTTTAAAAACTATATAATATATA
1 TATATATATATAT-AAATAT-TTTCAAAATGTTTTAAAAACTATATAATATATA
* * * * *
2743880 TGT-T-T-TCA-A-AAATGTTTTTAAAAATGTTTTCAAAACTATATAATACATA
1 TATATATAT-ATATAAAT-ATTTTCAAAATGTTTTAAAAACTATATAATATATA
2743929 TAT
1 TAT
2743932 TTTTGAAATG
Statistics
Matches: 128, Mismatches: 10, Indels: 30
0.76 0.06 0.18
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 2 0.02
46 1 0.01
47 21 0.16
48 1 0.01
49 27 0.21
50 1 0.01
51 16 0.12
52 14 0.11
53 34 0.27
54 3 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (52 bp):
TATATATATATATAAATATTTTCAAAATGTTTTAAAAACTATATAATATATA
Found at i:2743865 original size:47 final size:45
Alignment explanation
Indices: 2743658--2743880 Score: 170
Period size: 45 Copynumber: 5.1 Consensus size: 45
2743648 TTTTTGAAAC
* * * *
2743658 TATATAT-TATATATT-TAAAATATTTT-CAAAAGCTATAT-AT-
1 TATATATATATATATTCAAAAATGTTTTAAAAAAACTATATAATA
*
2743698 TATATATATGT-T-TTC-AAAATGTTTT--AAAAACTATATAATA
1 TATATATATATATATTCAAAAATGTTTTAAAAAAACTATATAATA
* *
2743738 TATA-A-ATGT-T-TTC-AAAATGTTTTAAAAACTATATAATATATATATA
1 TATATATATATATATTCAAAAATGTTTT-AAAA--A-A-ACTATATA-ATA
**
2743784 TATATATATATATATTTTAAAATGTTTTAAAAAAACTATATAATA
1 TATATATATATATATTCAAAAATGTTTTAAAAAAACTATATAATA
**
2743829 TATATATATATATATTCAAAAATGTTTTTTTTAAAAACTATATAATA
1 TATATATATATATATTCAAAAATG--TTTTAAAAAAACTATATAATA
2743876 TATAT
1 TATAT
2743881 GTTTTCAAAA
Statistics
Matches: 153, Mismatches: 11, Indels: 31
0.78 0.06 0.16
Matches are distributed among these distances:
38 28 0.18
39 14 0.09
40 12 0.08
41 4 0.03
43 1 0.01
44 1 0.01
45 32 0.21
46 14 0.09
47 26 0.17
48 4 0.03
49 1 0.01
50 6 0.04
51 10 0.07
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (45 bp):
TATATATATATATATTCAAAAATGTTTTAAAAAAACTATATAATA
Found at i:2743896 original size:12 final size:12
Alignment explanation
Indices: 2743879--2743914 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2743869 TATAATATAT
2743879 ATGTTTTCAAAA
1 ATGTTTTCAAAA
*
2743891 ATGTTTTTAAAA
1 ATGTTTTCAAAA
2743903 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2743915 CTATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:2743898 original size:39 final size:40
Alignment explanation
Indices: 2743780--2743903 Score: 117
Period size: 45 Copynumber: 3.0 Consensus size: 40
2743770 ATAATATATA
** **
2743780 TATATATATATATATATATTTTAAAATGTTTTAAAAAAAC
1 TATATATATATATATATATTCAAAAATGTTTTTTAAAAAC
2743820 TATATAATATATATATATATATATTCAAAAATGTTTTTTTTAAAAAC
1 ----T-ATATATATATATATATATTCAAAAATG--TTTTTTAAAAAC
* *
2743867 TATATA-ATATATATGTTTTCAAAAATG-TTTTTAAAAA
1 TATATATATATATATATATTCAAAAATGTTTTTTAAAAA
2743904 TGTTTTCAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
38 10 0.14
41 19 0.27
42 5 0.07
43 1 0.01
44 1 0.01
45 25 0.35
47 10 0.14
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (40 bp):
TATATATATATATATATATTCAAAAATGTTTTTTAAAAAC
Found at i:2743985 original size:40 final size:36
Alignment explanation
Indices: 2743905--2744008 Score: 106
Period size: 36 Copynumber: 2.8 Consensus size: 36
2743895 TTTTAAAAAT
* * *
2743905 GTTTTCAAAACTATATAATACATATATTTTTGAAAT
1 GTTTTCAAAACTATATAATATATATATTTTCGAAAC
2743941 GTTTTCAAAACTATATAATATATATATATATTCGAAAACC
1 GTTTTCAAAACTATATAATATATATAT-T-TTCG-AAA-C
*
2743981 GTTTTCTAAAAAT-TAT-ATAT-TATATTTT
1 GTTTTC-AAAACTATATAATATATATATTTT
2744009 TTTTCAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
36 28 0.47
37 2 0.03
38 8 0.14
39 7 0.12
40 9 0.15
41 5 0.08
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (36 bp):
GTTTTCAAAACTATATAATATATATATTTTCGAAAC
Found at i:2744063 original size:10 final size:9
Alignment explanation
Indices: 2744033--2744069 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
2744023 TTTCAACAAT
2744033 TATACTATA
1 TATACTATA
2744042 T-TACTATA
1 TATACTATA
2744050 TATAC-ATA
1 TATACTATA
2744058 TATA-TATA
1 TATACTATA
2744066 TATA
1 TATA
2744070 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 22 0.85
9 4 0.15
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (9 bp):
TATACTATA
Found at i:2744083 original size:19 final size:19
Alignment explanation
Indices: 2744059--2744096 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2744049 ATATACATAT
* *
2744059 ATATATATATAAAATAAAA
1 ATATATATAAAAAACAAAA
2744078 ATATATATAAAAAACAAAA
1 ATATATATAAAAAACAAAA
2744097 CAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
ATATATATAAAAAACAAAA
Found at i:2747398 original size:14 final size:14
Alignment explanation
Indices: 2747358--2747401 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
2747348 TATACAAAAA
2747358 TAAAATATCAAA-T
1 TAAAATATCAAATT
2747371 TAAAATAT-AAATT
1 TAAAATATCAAATT
* *
2747384 TTATATATCAAATT
1 TAAAATATCAAATT
2747398 TAAA
1 TAAA
2747402 CACAGTAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 3 0.12
13 15 0.60
14 7 0.28
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATATCAAATT
Found at i:2747718 original size:18 final size:18
Alignment explanation
Indices: 2747695--2747758 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
2747685 TTTATGAGGA
2747695 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
2747713 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
* * *
2747731 AATTAGAATATGTGAATG
1 AATTGGAATCTGTGAAGG
2747749 AATTGGAATC
1 AATTGGAATC
2747759 CAATTCCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.30
Consensus pattern (18 bp):
AATTGGAATCTGTGAAGG
Found at i:2748404 original size:37 final size:38
Alignment explanation
Indices: 2748325--2748411 Score: 140
Period size: 37 Copynumber: 2.3 Consensus size: 38
2748315 TTCACCCTAA
*
2748325 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCG
1 ACCCG-ACCCGACCCAAATATCACACTTAAAAAAACCCG
*
2748364 ACCCGACTCGACCCAAATATCACACTT-AAAAAACCCG
1 ACCCGACCCGACCCAAATATCACACTTAAAAAAACCCG
2748401 ACCCGACCCGA
1 ACCCGACCCGA
2748412 ACAAAATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 20 0.44
38 20 0.44
39 5 0.11
ACGTcount: A:0.39, C:0.40, G:0.10, T:0.10
Consensus pattern (38 bp):
ACCCGACCCGACCCAAATATCACACTTAAAAAAACCCG
Found at i:2748419 original size:37 final size:38
Alignment explanation
Indices: 2748341--2748419 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
2748331 ACCCGACCCG
* * *
2748341 AATATCACACTTAAAAAAACCCGACCCGACTCGACCCA
1 AATATCACACTTAAAAAAACCCGACCCGACCCGAACAA
2748379 AATATCACACTT-AAAAAACCCGACCCGACCCGAACAA
1 AATATCACACTTAAAAAAACCCGACCCGACCCGAACAA
2748416 AATA
1 AATA
2748420 AAGTTTCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 26 0.68
38 12 0.32
ACGTcount: A:0.46, C:0.34, G:0.08, T:0.13
Consensus pattern (38 bp):
AATATCACACTTAAAAAAACCCGACCCGACCCGAACAA
Found at i:2748644 original size:253 final size:256
Alignment explanation
Indices: 2748325--2748877 Score: 833
Period size: 264 Copynumber: 2.1 Consensus size: 256
2748315 TTCACCCTAA
* *
2748325 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCAAATATCACACT
1 ACCCG-ACCCGACCCGAATATCACACTTAAAAAAACCCAACCCAACTCGACCCAAATATCACACT
*
2748390 TAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGA-CCGACCCGAATATATGAATTA
65 TAAAAAACCCGACCCGACCCAAACAAAATAAAGTTTCATCCGATCCGACCCGAATATATGAATTA
* *
2748454 TAAAT-CC-GACCCGAAATAATAAAAAAATATTTTTATTTAGTAAAAACAGTGACTTAATCCGAC
130 GAAATCCCTGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGAC
*
2748517 CTGACCCGAATTATATATATTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCCGAACCCG
195 CCGACCCGAATTATATATATTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCCGAACCCG
* * * *
2748579 ACCCGACCTGACCCGAATATCACACTTAAAAAAACCTAACCTAACTCGACCCGAATATCACACTT
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCAACCCAACTCGACCCAAATATCACACTT
2748644 AAAAAACCCGACCCGACCCAAACAAAATAAAGTTTCATCCGATCCGACCCGAATATATGAATTAG
66 AAAAAACCCGACCCGACCCAAACAAAATAAAGTTTCATCCGATCCGACCCGAATATATGAATTAG
* *
2748709 AAATCCAACCCGACCTGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAATAGTGACTTA
131 AAAT------C--CCTGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTA
* * * *
2748774 ATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTCTGGTTTTTTTCACCCTAAACCCGAC
188 ATCCGACCCGACCCGAATTATATATATTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCCGAA
2748839 CCCG
253 CCCG
* * *
2748843 CCCCGCCCCGCCCCGAATATCACACTTAAAAAAAC
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAAC
2748878 TCGATCCGAC
Statistics
Matches: 268, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
253 95 0.35
254 30 0.11
263 2 0.01
264 141 0.53
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (256 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCAACCCAACTCGACCCAAATATCACACTT
AAAAAACCCGACCCGACCCAAACAAAATAAAGTTTCATCCGATCCGACCCGAATATATGAATTAG
AAATCCCTGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACC
CGACCCGAATTATATATATTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCCGAACCCG
Found at i:2751833 original size:18 final size:17
Alignment explanation
Indices: 2751801--2751834 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2751791 TCAGCCGGTC
2751801 CGGTTTGAACGGTTCAG
1 CGGTTTGAACGGTTCAG
*
2751818 CGGTTCTGACCGGTTCA
1 CGGTT-TGAACGGTTCA
2751835 CTAGTAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAG
Found at i:2753420 original size:32 final size:32
Alignment explanation
Indices: 2753379--2753443 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2753369 CAATAGAAAG
2753379 ATTCTCCACACCGATGAATTCAAGTAAATATC
1 ATTCTCCACACCGATGAATTCAAGTAAATATC
2753411 ATTCTCCACACCGATGAATTCAAGTAAATATC
1 ATTCTCCACACCGATGAATTCAAGTAAATATC
2753443 A
1 A
2753444 AACCATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (32 bp):
ATTCTCCACACCGATGAATTCAAGTAAATATC
Found at i:2755800 original size:3 final size:3
Alignment explanation
Indices: 2755792--2755848 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
2755782 CCACATCACT
*
2755792 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2755840 ATA ATA ATA
1 ATA ATA ATA
2755849 TATGGGGGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2765363 original size:30 final size:30
Alignment explanation
Indices: 2765301--2765366 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
2765291 AGAACTGGTA
* * * *
2765301 GAACCGGCTGAGAACTGGCAAAACCGGGGT
1 GAACCGGCTGAAAACCGGCAAAACAGAGGT
*
2765331 GAACCGGCTGAAAACCGGCAAAACAGATGT
1 GAACCGGCTGAAAACCGGCAAAACAGAGGT
2765361 GAACCG
1 GAACCG
2765367 CCGGCTCTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.32, T:0.09
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGCAAAACAGAGGT
Found at i:2767306 original size:103 final size:103
Alignment explanation
Indices: 2767081--2767298 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
2767071 GTCGAGGGTC
2767081 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
2767146 TTGATCCTTGGCATATGTATATGATTTTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
* * *
2767184 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2767249 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
*
2767287 TATGCGGTCCTT
1 TATGTGGTCCTT
2767299 ATGGACATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:2767364 original size:23 final size:23
Alignment explanation
Indices: 2767338--2767382 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2767328 AATTGTACGC
2767338 GGCACTCCGGTGCAATTATATGT
1 GGCACTCCGGTGCAATTATATGT
*
2767361 GGCACTTCGGTGCAATTATATG
1 GGCACTCCGGTGCAATTATATG
2767383 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATATGT
Found at i:2780109 original size:20 final size:20
Alignment explanation
Indices: 2780086--2780159 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
2780076 GAATATGTAA
* * *
2780086 ATCGCAATGCGATTATAACT
1 ATCGCAACGCGATTCTGACT
2780106 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2780126 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
2780146 ATCGCAATGCGATT
1 ATCGCAACGCGATT
2780160 TTCAAAGCGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2780361 original size:22 final size:22
Alignment explanation
Indices: 2780335--2780377 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2780325 GGCGACATCT
2780335 GTCCCCATCTCCGACAAAATCA
1 GTCCCCATCTCCGACAAAATCA
*
2780357 GTCCCCATCTCCGACGAAATC
1 GTCCCCATCTCCGACAAAATC
2780378 CGTATATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.42, G:0.12, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCA
Found at i:2780786 original size:19 final size:19
Alignment explanation
Indices: 2780764--2780807 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2780754 AGAATCGCAA
*
2780764 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTCCGCGT
2780783 TGCGATTTTCATTCCGCGT
1 TGCGATTTTCATTCCGCGT
2780802 TGCGAT
1 TGCGAT
2780808 AGTCAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.43
Consensus pattern (19 bp):
TGCGATTTTCATTCCGCGT
Found at i:2780857 original size:20 final size:20
Alignment explanation
Indices: 2780764--2780857 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 20
2780754 AGAATCGCAA
2780764 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTAAGTTTCGCGT
* *
2780783 TGCGATTTTCA-TTCCGCGT
1 TGCGATTTTAAGTTTCGCGT
* * *
2780802 TGCGATAGTCAAATTT-GCGT
1 TGCGAT-TTTAAGTTTCGCGT
** * * *
2780822 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTAAGTTTCGCGT
2780842 TGCGATTTTAAGTTTC
1 TGCGATTTTAAGTTTC
2780858 AGAAACTATT
Statistics
Matches: 56, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
19 26 0.46
20 28 0.50
21 2 0.04
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.44
Consensus pattern (20 bp):
TGCGATTTTAAGTTTCGCGT
Found at i:2782787 original size:20 final size:20
Alignment explanation
Indices: 2782762--2782809 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2782752 TAGTTTACTT
2782762 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
2782782 TCGCAATGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
2782802 TTGCAACG
1 TCGCAACG
2782810 AAAGAATCGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:2782877 original size:20 final size:19
Alignment explanation
Indices: 2782852--2782918 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
2782842 GCGATTCTCT
2782852 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
* *
2782872 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCA-ATTCG
2782892 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
2782910 TGTTGCGAT
1 CGTTGCGAT
2782919 TTTAAGTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 12 0.29
19 1 0.02
20 28 0.68
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:2784998 original size:20 final size:20
Alignment explanation
Indices: 2784973--2785026 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2784963 ATGTACACTT
*
2784973 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
2784993 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
2785013 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
2785027 TCAATTCACG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:2785123 original size:20 final size:20
Alignment explanation
Indices: 2785069--2785353 Score: 227
Period size: 20 Copynumber: 14.8 Consensus size: 20
2785059 GCGATTTTCT
** *
2785069 CGTTGCGATAGTCAAACACC
1 CGTTGCGATAGTCAAATTCG
* *
2785089 CGTTACGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2785109 AGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2785129 CGTTGTGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
2785143 CGTTGCGATAGTCAAATAC-
1 CGTTGCGATAGTCAAATTCG
*
2785162 CTGTTGCGATAATCAAATTCG
1 C-GTTGCGATAGTCAAATTCG
** *
2785183 TATTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
* *
2785203 CATTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2785223 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2785243 TGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2785263 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
2785277 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2785297 CGTTGTGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2785317 CGTTGAGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2785337 CGTTACGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2785354 GAATGTGTAA
Statistics
Matches: 207, Mismatches: 44, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
14 22 0.11
16 2 0.01
18 2 0.01
19 1 0.00
20 180 0.87
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2785150 original size:74 final size:74
Alignment explanation
Indices: 2785061--2785200 Score: 228
Period size: 74 Copynumber: 1.9 Consensus size: 74
2785051 TATGCTTTGC
2785061 GATTTTCTCGTTGCGATAGTCAAACACCCGTTACGATAATCAAATTCG-AGTTGCAATAGTCAAA
1 GATTTTCTCGTTGCGATAGTCAAACACCCGTTACGATAATCAAATTCGTA-TTGCAATAGTCAAA
2785125 TTCGCGTTGT
65 TTCGCGTTGT
* * * *
2785135 GATTTTCTCGTTGCGATAGTCAAATACCTGTTGCGATAATCAAATTCGTATTGCGATAGTCAAAT
1 GATTTTCTCGTTGCGATAGTCAAACACCCGTTACGATAATCAAATTCGTATTGCAATAGTCAAAT
2785200 T
66 T
2785201 TGCATTGCGA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 60 0.98
75 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (74 bp):
GATTTTCTCGTTGCGATAGTCAAACACCCGTTACGATAATCAAATTCGTATTGCAATAGTCAAAT
TCGCGTTGT
Found at i:2785316 original size:74 final size:74
Alignment explanation
Indices: 2785205--2785345 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
2785195 CAAATTTGCA
* * * *
2785205 TTGCGATAGACAAATTCGCGTTGCGATAGTCATATTCGTGTTGTGATAGTCAAATTCGCGTTGCG
1 TTGCGATAGACAAATTCGCGTTGCGATAGTCAAATTCGCGTTGAGATAGTCAAATTCGCGTTACG
2785270 ATTTTTGAG
66 ATTTTTGAG
* *
2785279 TTGCGATA-ATCAAATTCGCGTTGTGATAGTTAAATTCGCGTTGAGATAGTCAAATTCGCGTTAC
1 TTGCGATAGA-CAAATTCGCGTTGCGATAGTCAAATTCGCGTTGAGATAGTCAAATTCGCGTTAC
2785343 GAT
65 GAT
2785346 ATTCAAATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 1 0.02
74 59 0.98
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (74 bp):
TTGCGATAGACAAATTCGCGTTGCGATAGTCAAATTCGCGTTGAGATAGTCAAATTCGCGTTACG
ATTTTTGAG
Found at i:2785580 original size:140 final size:140
Alignment explanation
Indices: 2785324--2785593 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
2785314 TCGCGTTGAG
*
2785324 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
2785389 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAA
2785454 AATACACATA
131 AATACACATA
*
2785464 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
2785529 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAA
2785594 TACAACGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAA
AATACACATA
Found at i:2785676 original size:18 final size:18
Alignment explanation
Indices: 2785653--2785688 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2785643 AAGCTGGTTA
*
2785653 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2785671 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2785689 CTTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2787984 original size:24 final size:24
Alignment explanation
Indices: 2787950--2788003 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2787940 CTGAAACATC
2787950 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2787974 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2787998 ATCAAA
1 ATCAAA
2788004 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2788487 original size:16 final size:16
Alignment explanation
Indices: 2788453--2788486 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2788443 AACATTAGAG
2788453 TTTCATAAATTAACTT
1 TTTCATAAATTAACTT
*
2788469 TTTCATAAGTTAA-TT
1 TTTCATAAATTAACTT
2788484 TTT
1 TTT
2788487 TTAATAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTCATAAATTAACTT
Found at i:2788535 original size:47 final size:47
Alignment explanation
Indices: 2788466--2788560 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
2788456 CATAAATTAA
*
2788466 CTTTTTCATAAGTTAATTTTTTTAATAAACTTAAGGACTCTCTCTGT
1 CTTTTTCATAAGTTAACTTTTTTAATAAACTTAAGGACTCTCTCTGT
2788513 CTTTTTCATAAGTTAACTTTTTTAATAAACTTAAGGACTCTCTCTGT
1 CTTTTTCATAAGTTAACTTTTTTAATAAACTTAAGGACTCTCTCTGT
2788560 C
1 C
2788561 CTGCACCAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.47
Consensus pattern (47 bp):
CTTTTTCATAAGTTAACTTTTTTAATAAACTTAAGGACTCTCTCTGT
Found at i:2794647 original size:20 final size:20
Alignment explanation
Indices: 2794600--2794894 Score: 291
Period size: 20 Copynumber: 14.6 Consensus size: 20
2794590 AATGACCAAC
2794600 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
2794619 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
2794639 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
2794659 AAGATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
2794679 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
2794701 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
2794721 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
2794741 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
2794761 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
2794781 AGAATCGCAACGCGATCCAG
1 AAAATCGCAACGCGATTCAG
2794801 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
2794821 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
2794841 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
2794863 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
2794883 AAAATCGCAACG
1 AAAATCGCAACG
2794895 AAAATGAGTA
Statistics
Matches: 229, Mismatches: 29, Indels: 35
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.00
19 24 0.10
20 162 0.71
21 6 0.03
22 32 0.14
23 4 0.02
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:2794751 original size:40 final size:40
Alignment explanation
Indices: 2794600--2794894 Score: 407
Period size: 40 Copynumber: 7.3 Consensus size: 40
2794590 AATGACCAAC
* *
2794600 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTCAG
* * ****
2794639 AAAAGCGCAACGTTGAAAAGAAG-ATCGCAACGCGATTCAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGATTCAG
*
2794679 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAG
*
2794721 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
*
2794761 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
2794801 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
*
2794841 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAG
2794883 AAAATCGCAACG
1 AAAATCGCAACG
2794895 AAAATGAGTA
Statistics
Matches: 229, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
39 13 0.06
40 146 0.64
41 3 0.01
42 67 0.29
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
Found at i:2794812 original size:162 final size:161
Alignment explanation
Indices: 2794600--2794894 Score: 468
Period size: 162 Copynumber: 1.8 Consensus size: 161
2794590 AATGACCAAC
** * *
2794600 AAAATCGCAACGCGATATCAAAACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAG-AT
1 AAAATCGCAACGCGATATCAAAACCGCAACGCGATCCAGAAAAGCGCAACG-CGAAAACAAGAAT
2794664 CGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGC
65 CGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGC
2794729 AACGCGATTCCAAGAATCGCAACGCGATTTAG
130 AACGCGATTCCAAGAATCGCAACGCGATTTAG
* * ***
2794761 AAAATCGCAACGCGAT-TCCAAGAATCGCAACGCGATCCAGAAAATCGCAACGCGATTCCAAGAA
1 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATCCAGAAAAGCGCAACGCGAAAACAAGAA
2794825 TCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCG
64 TCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCG
2794890 CAACG
129 CAACG
2794895 AAAATGAGTA
Statistics
Matches: 122, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
160 1 0.01
161 24 0.20
162 97 0.80
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (161 bp):
AAAATCGCAACGCGATATCAAAACCGCAACGCGATCCAGAAAAGCGCAACGCGAAAACAAGAATC
GCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCA
ACGCGATTCCAAGAATCGCAACGCGATTTAG
Found at i:2795005 original size:6 final size:6
Alignment explanation
Indices: 2794995--2795134 Score: 210
Period size: 6 Copynumber: 23.5 Consensus size: 6
2794985 GACACGTATT
* * * * * * *
2794995 ACCACT ACCACT ACCACT ACCACT ACCACT ACCACG ACCACT ACCACT
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2795043 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2795091 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2795135 CGAGACGAGA
Statistics
Matches: 131, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
5 5 0.04
6 126 0.96
ACGTcount: A:0.33, C:0.51, G:0.11, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:2795642 original size:6 final size:6
Alignment explanation
Indices: 2795631--2795770 Score: 273
Period size: 6 Copynumber: 23.5 Consensus size: 6
2795621 TCTCGTCTCG
2795631 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2795679 GGTCGT GG-CGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2795726 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2795771 AATACGTGTC
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.04
6 128 0.96
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2795881 original size:20 final size:20
Alignment explanation
Indices: 2795856--2796014 Score: 124
Period size: 20 Copynumber: 7.8 Consensus size: 20
2795846 ACCTTGGAAG
*
2795856 ATCGCGTTGCGATTTTCTTA
1 ATCGCGTTGCGATTTTCTAA
**
2795876 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
* *
2795897 GATCGCGTTGCGATTTTATGA
1 -ATCGCGTTGCGATTTTCTAA
* **
2795918 ATCGCATTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
*
2795939 GATCGCGTTGCGATTTTCT-T
1 -ATCGCGTTGCGATTTTCTAA
* * *
2795959 TTCAACGTTGCGCTTTTCTAA
1 ATC-GCGTTGCGATTTTCTAA
* * *
2795980 ATCGCGTTGCGGTTTT-GAT
1 ATCGCGTTGCGATTTTCTAA
2795999 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
2796015 GTTGGTCATT
Statistics
Matches: 109, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
19 18 0.17
20 51 0.47
21 13 0.12
22 27 0.25
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTCTAA
Found at i:2795907 original size:42 final size:42
Alignment explanation
Indices: 2795848--2795958 Score: 195
Period size: 42 Copynumber: 2.6 Consensus size: 42
2795838 ATGCAACAAC
*
2795848 CTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT
1 CTTGGAAGATCGCGTTGCGATTTTCTTAATCGCATTGCGATT
* *
2795890 CTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATT
1 CTTGGAAGATCGCGTTGCGATTTTCTTAATCGCATTGCGATT
2795932 CTTGGAAGATCGCGTTGCGATTTTCTT
1 CTTGGAAGATCGCGTTGCGATTTTCTT
2795959 TTCAACGTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (42 bp):
CTTGGAAGATCGCGTTGCGATTTTCTTAATCGCATTGCGATT
Found at i:2795970 original size:42 final size:41
Alignment explanation
Indices: 2795848--2796012 Score: 190
Period size: 42 Copynumber: 4.0 Consensus size: 41
2795838 ATGCAACAAC
2795848 CTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT
1 CTTGGAAGATCGCGTTGCGATTTTCTT-ATCGCGTTGCGATT
* * *
2795890 CTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATT
1 CTTGGAAGATCGCGTTGCGATTTTCT-TATCGCGTTGCGATT
* * *
2795932 CTTGGAAGATCGCGTTGCGATTTTCTTTTCAACGTTGCGCTT
1 CTTGGAAGATCGCGTTGCGATTTTCTTATC-GCGTTGCGATT
** * **
2795974 -TTCTAA-ATCGCGTTGCGGTTTTGATATCGCGTTGCGATT
1 CTTGGAAGATCGCGTTGCGATTTTCTTATCGCGTTGCGATT
2796013 TTGTTGGTCA
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
39 9 0.09
40 18 0.17
41 6 0.06
42 71 0.68
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (41 bp):
CTTGGAAGATCGCGTTGCGATTTTCTTATCGCGTTGCGATT
Found at i:2796441 original size:16 final size:15
Alignment explanation
Indices: 2796416--2796445 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2796406 ATTTAAAAAT
2796416 AAATTATATTTTATC
1 AAATTATATTTTATC
2796431 AAATATATATTTTAT
1 AAAT-TATATTTTAT
2796446 TTTTAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATTATATTTTATC
Found at i:2802488 original size:10 final size:8
Alignment explanation
Indices: 2802455--2802493 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
2802445 ATGAAAAATA
*
2802455 TTTATTTT
1 TTTATATT
2802463 TTTATATT
1 TTTATATT
2802471 TTTATATT
1 TTTATATT
2802479 TTTACTTATT
1 TTTA--TATT
2802489 TTTAT
1 TTTAT
2802494 TTTCAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 20 0.71
10 8 0.29
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTATATT
Found at i:2805041 original size:14 final size:15
Alignment explanation
Indices: 2805022--2805050 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2805012 GATGCATAAA
2805022 TGAAAAG-AATGGTG
1 TGAAAAGAAATGGTG
2805036 TGAAAAGAAATGGTG
1 TGAAAAGAAATGGTG
2805051 AGAAGAGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (15 bp):
TGAAAAGAAATGGTG
Found at i:2805437 original size:17 final size:18
Alignment explanation
Indices: 2805412--2805445 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2805402 TGGGCCTTGT
2805412 TATCAATATTA-ATTTTG
1 TATCAATATTAGATTTTG
*
2805429 TATCGATATTAGATTTT
1 TATCAATATTAGATTTT
2805446 ATCTCAAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (18 bp):
TATCAATATTAGATTTTG
Found at i:2814974 original size:23 final size:24
Alignment explanation
Indices: 2814928--2814996 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
2814918 AGATAGAAAT
* *
2814928 AATAAACAAAACACAAAA-AGATCA
1 AATAAATAAAAAACAAAATA-ATCA
*
2814952 AATAAGT-AAAAACAAAATAATCA
1 AATAAATAAAAAACAAAATAATCA
2814975 AATAAATAAGAAAACAAAATAA
1 AATAAATAA-AAAACAAAATAA
2814997 AATAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 19 0.50
24 7 0.18
25 12 0.32
ACGTcount: A:0.72, C:0.10, G:0.04, T:0.13
Consensus pattern (24 bp):
AATAAATAAAAAACAAAATAATCA
Found at i:2815008 original size:27 final size:26
Alignment explanation
Indices: 2814951--2815010 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
2814941 CAAAAAGATC
* *
2814951 AAATAAGTAAAAACAAAATAATCAAAT
1 AAATAAG-AAAAACAAAATAATAAAAA
2814978 AAATAAG-AAAACAAAATAAAATAAAAA
1 AAATAAGAAAAACAAAAT--AATAAAAA
2815005 AAATAA
1 AAATAA
2815011 AATTATAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 10 0.34
27 19 0.66
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (26 bp):
AAATAAGAAAAACAAAATAATAAAAA
Found at i:2815093 original size:24 final size:25
Alignment explanation
Indices: 2815056--2815102 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
2815046 AAACGGAATG
*
2815056 AAATAGAAACATGA-ATAAAAGAAGA
1 AAATAGAAAAATGAGA-AAAAGAAGA
2815081 AAATA-AAAAATGAGAAAAAGAA
1 AAATAGAAAAATGAGAAAAAGAA
2815103 TAAAGTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (25 bp):
AAATAGAAAAATGAGAAAAAGAAGA
Found at i:2815131 original size:3 final size:3
Alignment explanation
Indices: 2815112--2815158 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
2815102 ATAAAGTGAA
* *
2815112 AAT AAT AAG AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2815159 AAAAAAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2815286 original size:17 final size:18
Alignment explanation
Indices: 2815264--2815319 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
2815254 TAATAAAAAA
2815264 ATAAAA-AAAAT-GTATAT
1 ATAAAACAAAATAGTA-AT
2815281 ATAAAACAAAATAAGTAAT
1 ATAAAACAAAAT-AGTAAT
* *
2815300 ATAAAATAATAATAATAAT
1 ATAAAACAA-AATAGTAAT
2815319 A
1 A
2815320 ATAATAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 16 0.48
20 6 0.18
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
ATAAAACAAAATAGTAAT
Done.