Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 26
Found at i:3123269 original size:43 final size:44
Alignment explanation
Indices: 3123217--3123326 Score: 132
Period size: 43 Copynumber: 2.5 Consensus size: 44
3123207 AAAAAAGTGT
* * *
3123217 CCCAACATTTATTATTTCTTGCTAATATGGGCCTTCTAAA-TGC
1 CCCAACATTTATTATTTCTTGCTAATACGGGCCTTCAAAACTAC
* * * *
3123260 CCTAACATTTATTATTTCTGGATGATACGGGCCTTCAAAACTAC
1 CCCAACATTTATTATTTCTTGCTAATACGGGCCTTCAAAACTAC
* *
3123304 CCCAACATTCATCATTTCTTGCT
1 CCCAACATTTATTATTTCTTGCT
3123327 CCAGCACTAA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 34 0.63
44 20 0.37
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.37
Consensus pattern (44 bp):
CCCAACATTTATTATTTCTTGCTAATACGGGCCTTCAAAACTAC
Found at i:3126720 original size:13 final size:13
Alignment explanation
Indices: 3126702--3126734 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3126692 AAAATAAATT
*
3126702 AATGCAAAACAAG
1 AATGCAAAACAAA
3126715 AATGC-AAACAAA
1 AATGCAAAACAAA
3126727 AATGCAAA
1 AATGCAAA
3126735 TGCACAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.64, C:0.15, G:0.12, T:0.09
Consensus pattern (13 bp):
AATGCAAAACAAA
Found at i:3128691 original size:16 final size:16
Alignment explanation
Indices: 3128667--3128709 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
3128657 TGCATATATT
3128667 AAATATATTAAAACA-A
1 AAATATATTAAAA-ATA
*
3128683 AAATTTATTTAAAAATA
1 AAATATA-TTAAAAATA
3128700 AAATATATTA
1 AAATATATTA
3128710 TTTTTGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATATTAAAAATA
Found at i:3134538 original size:66 final size:65
Alignment explanation
Indices: 3134424--3134588 Score: 176
Period size: 66 Copynumber: 2.5 Consensus size: 65
3134414 AAATTATCTC
* * ** * *
3134424 GAGCAATATTAAATTTTGATTT-AAGAGAAACGATTTTTTTGTTTTTGTTTTTA-GTAAAATTTT
1 GAGCAAGATAAAATTTT-ATTTCAAGAGAAACGATTTTTTTGTTTTTG-TTGGAGGGAAAATGTT
3134487 TT
64 TT
* *
3134489 GAGCGAGATAAAATTTTATTTCAAGA-AAA-GTATTTTTTTGCTTTTTTGTTGGAGGGAAACTGT
1 GAGCAAGATAAAATTTTATTTCAAGAGAAACG-ATTTTTTTG--TTTTTGTTGGAGGGAAAATGT
3134552 TTT
63 TTT
*
3134555 GAGCAAGATGAAATTTTATTTCAAGAGAAACGAT
1 GAGCAAGATAAAATTTTATTTCAAGAGAAACGAT
3134589 CTCAAGTGAG
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
63 1 0.01
64 16 0.19
65 21 0.25
66 39 0.47
67 5 0.06
68 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (65 bp):
GAGCAAGATAAAATTTTATTTCAAGAGAAACGATTTTTTTGTTTTTGTTGGAGGGAAAATGTTTT
Found at i:3135382 original size:2 final size:2
Alignment explanation
Indices: 3135375--3135438 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3135365 AAATAGAGTA
3135375 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
3135417 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3135439 CCTTTAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3138153 original size:12 final size:13
Alignment explanation
Indices: 3138120--3138155 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3138110 TGACTATGTC
3138120 TGAGTTGACTCAA
1 TGAGTTGACTCAA
*
3138133 TGGGTTGACTC-A
1 TGAGTTGACTCAA
3138145 TGAGTTGACTC
1 TGAGTTGACTC
3138156 GGCTGGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (13 bp):
TGAGTTGACTCAA
Found at i:3145863 original size:21 final size:19
Alignment explanation
Indices: 3145835--3145880 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
3145825 TCATTGAATC
3145835 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
3145855 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
3145874 ACTTAGT
1 A-TTAGT
3145881 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:3147971 original size:64 final size:66
Alignment explanation
Indices: 3147866--3148028 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 66
3147856 CGGTTCACCA
* *
3147866 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTG-GTGCATCGATGCATA
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCAGCGATGCATA
3147929 G
66 G
** * ** *
3147930 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCAGCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCAGCGATGCATA
3147994 G
66 G
* * *
3147995 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
3148029 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 37 0.45
65 46 0.55
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCAGCGATGCATA
G
Found at i:3148000 original size:19 final size:19
Alignment explanation
Indices: 3147976--3148014 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3147966 GAAAATATTC
3147976 AGAGTGCAGCGATGCATGG
1 AGAGTGCAGCGATGCATGG
* *
3147995 AGAGTGCATCGGTGCATGG
1 AGAGTGCAGCGATGCATGG
3148014 A
1 A
3148015 ATGCATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.41, T:0.18
Consensus pattern (19 bp):
AGAGTGCAGCGATGCATGG
Found at i:3156327 original size:64 final size:66
Alignment explanation
Indices: 3156222--3156384 Score: 208
Period size: 65 Copynumber: 2.5 Consensus size: 66
3156212 CGGTGCACCA
***
3156222 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATA-GCCTGGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATGCAAAGTGCATCGATGCATG
3156285 G
66 G
** * *
3156286 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAAAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATGCAAAGTGCATCGATGCATG
3156350 G
66 G
* *
3156351 AGAGTGCATC-AGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGA-TGCATGAAATGCATTCGATGTT
3156385 CAATTAATTC
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATGCAAAGTGCATCGATGCATG
G
Found at i:3156358 original size:19 final size:18
Alignment explanation
Indices: 3156333--3156382 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
3156323 AAAATATTCA
3156333 AAGTGCATCGATGCATGG
1 AAGTGCATCGATGCATGG
3156351 AGAGTGCATC-AGTGCATGG
1 A-AGTGCATCGA-TGCATGG
3156370 AA-TGCATTCGATG
1 AAGTGCA-TCGATG
3156383 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 4 0.14
18 7 0.25
19 17 0.61
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (18 bp):
AAGTGCATCGATGCATGG
Found at i:3157219 original size:19 final size:19
Alignment explanation
Indices: 3157182--3157219 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3157172 GGATGCAGTA
*
3157182 GCCTATTACTGATCAGAAT
1 GCCTATTACTCATCAGAAT
3157201 GCCTAATTACTCATC-GAAT
1 GCCT-ATTACTCATCAGAAT
3157220 ACGCATTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (19 bp):
GCCTATTACTCATCAGAAT
Found at i:3158646 original size:20 final size:20
Alignment explanation
Indices: 3158621--3158659 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3158611 GCTTAAATAA
3158621 ATGC-AATACATAATGCAAAT
1 ATGCAAATACA-AATGCAAAT
*
3158641 ATGCAAATGCAAATGCAAA
1 ATGCAAATACAAATGCAAA
3158660 AAATGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (20 bp):
ATGCAAATACAAATGCAAAT
Found at i:3162578 original size:30 final size:30
Alignment explanation
Indices: 3162544--3162612 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
3162534 AAAGTGTGAT
3162544 GGTTGAATTCAAATGGATTAGGAAATAAAG
1 GGTTGAATTCAAATGGATTAGGAAATAAAG
3162574 GGTTGAATTCAAATGGATTAGGAAATAAAG
1 GGTTGAATTCAAATGGATTAGGAAATAAAG
*
3162604 GATTGAATT
1 GGTTGAATT
3162613 ACAATTATGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.42, C:0.03, G:0.26, T:0.29
Consensus pattern (30 bp):
GGTTGAATTCAAATGGATTAGGAAATAAAG
Found at i:3168694 original size:21 final size:21
Alignment explanation
Indices: 3168669--3168721 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3168659 CAACAATTCT
*
3168669 TTTCATGAAAAGATTAAATCC
1 TTTCATGAAAAGATTAAACCC
*
3168690 TTTCATGAAAAGATTAAGCCC
1 TTTCATGAAAAGATTAAACCC
*
3168711 TTTCATCAAAA
1 TTTCATGAAAA
3168722 AGAGAAGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (21 bp):
TTTCATGAAAAGATTAAACCC
Found at i:3170385 original size:51 final size:50
Alignment explanation
Indices: 3170324--3170424 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 50
3170314 TGTTTTGAGT
* * *
3170324 TTTATTAAATTCTCACCGTTTAACAGAAGTTAGTTTTGTTTTGAGGTTTTA
1 TTTATTAAATTCTCACCGTTCAACAGAAATTAGTTATGTTTTG-GGTTTTA
* *
3170375 TTTATTAAATTCTCGCCGTTCAACAGAAATTGGTTATGTTTTGGGTTTTA
1 TTTATTAAATTCTCACCGTTCAACAGAAATTAGTTATGTTTTGGGTTTTA
3170425 ATATCGTTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 7 0.16
51 38 0.84
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.48
Consensus pattern (50 bp):
TTTATTAAATTCTCACCGTTCAACAGAAATTAGTTATGTTTTGGGTTTTA
Found at i:3172293 original size:21 final size:21
Alignment explanation
Indices: 3172268--3172361 Score: 91
Period size: 21 Copynumber: 4.4 Consensus size: 21
3172258 AACATTTCTC
*
3172268 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAGTCCT
* *
3172289 TTCATGAAAGGATTAAGCCCT
1 TTCATGAAAAGATTAAGTCCT
* *
3172310 TTCATCAAAAGGA-TAAGTCTT
1 TTCATGAAAA-GATTAAGTCCT
* * *
3172331 TTAATAAAAAGGTTAAGTCCT
1 TTCATGAAAAGATTAAGTCCT
3172352 TTCATCGAAA
1 TTCAT-GAAA
3172362 GGTCTTAAGC
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.02
21 51 0.89
22 5 0.09
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (21 bp):
TTCATGAAAAGATTAAGTCCT
Found at i:3175104 original size:14 final size:16
Alignment explanation
Indices: 3175076--3175107 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3175066 TATTTAATTA
3175076 TTCTCTTCTTCTTATT
1 TTCTCTTCTTCTTATT
3175092 TTCTCTT-TT-TTATT
1 TTCTCTTCTTCTTATT
3175106 TT
1 TT
3175108 TCACTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTCTTCTTCTTATT
Found at i:3175133 original size:14 final size:14
Alignment explanation
Indices: 3175081--3175134 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
3175071 AATTATTCTC
3175081 TTCTTCTTAT-TTT
1 TTCTTCTTATATTT
* *
3175094 CTCTT-TTTTATTT
1 TTCTTCTTATATTT
*
3175107 TTC-ACTT-TATTT
1 TTCTTCTTATATTT
3175119 TTCTTCTTATATTT
1 TTCTTCTTATATTT
3175133 TT
1 TT
3175135 TTATCAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
12 11 0.34
13 14 0.44
14 7 0.22
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTCTTATATTT
Found at i:3175652 original size:258 final size:258
Alignment explanation
Indices: 3175140--3178307 Score: 3720
Period size: 258 Copynumber: 12.2 Consensus size: 258
3175130 TTTTTTTATC
* * * * *
3175140 AAAA-ATTAAATGA-AAATTTTGAAAATCGCTTTCTCATTCTTTTACAGATACCATATGAAAACA
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCA-T-TTTT-CAAAAATCATATGAAAACA
* * * * * * * *
3175203 TCTTGCCCAAAGGTCTTATTGATGGCCCGAAGGACATATCATCTTGCTCGAAAGACTGACAAATT
63 TCCTACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATG
* * * * *
3175268 AACCAAAGGATTTAATCATCATGCTCGAAAGAGTTACTGATGGCCCGAAGGACTAACCAAATTTG
128 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
* * * * *
3175333 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACGTTCTTACATTTCAAAATTTTCATTTTCT
193 GAAATAGTTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCT
3175398 G
258 G
* * *
3175399 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATAC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * * * * *
3175464 TATCCGAAGGTCTTATAGATAGCCCAAACGACTTATCATCTTGCTCGAAAGATTGAAAGATGGCC
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
*
3175529 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAA
131 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
* *
3175594 ATAGTTTTA-TGGGTAAGAAACCTTGGAAACCACTTTTTTACTTTTCAAAAATTTCATTTTCTG
196 ATAG-TTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
* *
3175657 AAAACATTAAATAAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * * *
3175722 TACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAATGACAGATGACC
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
* * *
3175787 TC-AAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGATTTCCCAATTTTGGA
131 -CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGA
* * *** * **
3175851 AATAGTTTACTAGGTAAGAAACTTTGGAAATTGGTTTCTTACATTTCAAATTTTTCATTTTCTG
195 AATAGTTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
** *
3175915 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTTTAAAATCATGTGAAAACATCC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * * * * *
3175980 TATCCGAAGGTCTTATAGATGGCCCAAAAGACTTATTATCTTGTTCAAAAGACCGACAGATGACC
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
*
3176045 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACATACCAATTTTGGAA
131 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
*
3176110 ATAGCTTT-CTGGGTAAGAAACCTTGGAAATCACTTTTTTACTTTTCAAAAATTTCATTTTCTG
196 ATAG-TTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
* * * *
3176173 AAAACATTAAATAAGGAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATATGAAAACATCC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * * *
3176238 TACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAATGATAGATGACC
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
* * *
3176303 TC-AATGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCAAAGGAC-TACCCAATTTTGG
131 -CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-CCAATTTTGG
** * * * **
3176366 AAATAGTTTACTAAGTAAGAAACTTTGGAAATCGCTTTCTTACATTTCAAATTTTTCATTTTCTG
194 AAATAGTTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
** *
3176431 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTTGAAAATCATGTGAAAACATCC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * * *
3176496 TATCCGAAGGTCTTATAGATGGCCCAAAGGGCTTATCATCTTGCTCGAAAGACCGACAGATAACC
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
* *
3176561 CGAAGGATTTAATCATCATGCTTGAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTTGGAA
131 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
* *
3176626 ATAGTTTACTTGGTAAGAAACCGTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
196 ATAGTTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
*
3176689 AAAACATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * *
3176754 TACCTGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATTACC
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
* * * *
3176819 CAAAGGATTTAATCATCATGCTCGAAAGACATACTGATGGCCCAAAGGACATACCAATTTTGGAA
131 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
* ** * * ** * * *
3176884 ACAGTTTACTATGTAAGAAACTTTGGGAATCGGTTTCTTACGTTTCAAAAATTCCATTTTTTG
196 ATAGTTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
* * * * *
3176947 AAAATATCAATTGAGAAATTTTAAAAATCACTTTCTCATTTTTCAAAAATCATGTGAAAACATCC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * * * *
3177012 TACCCAAAGGTCTTACAGATGGCCCGAAGGACATATCATCTTGCTCGAAAGACTGACAGATGACT
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
* * *
3177077 CGAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACAAATTTTGGAA
131 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
* * * *
3177142 ATATTTTACTGCGTAAGAAACCTTGAAAATCACTTTCTTACTTTTCAGAAATTTCATTTTCTG
196 ATAGTTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
* * *
3177205 AAAA-ATTAAATGAGAAACATTGAAAATCATTTTCTCATTTTTCAAAAATCATATGAAAACATCA
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * * * *
3177269 TACCCGGAGGTCTTATGGATGGCCCAAAGGAGTTATCAACTTGCTCGAAAGACTGACAGATGACT
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
* *
3177334 CGAAGGATATAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
131 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
* * *
3177399 ATAGTTTACTGGGTAAGAAACCTTGAAAATCACTTTCTTACTCTTCATAAATTTCATTTTCTG
196 ATAGTTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
* *
3177462 AAAACATTAAATGAGAAACTTTGAAAATAACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* * * * *
3177527 TACCCGAAGGTCTTATGGATGGCCCAAAGTAGTTATCAACTTGCTCGAAAGACTGACAGATGACT
66 TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
* * * * * *
3177592 CGAAGGATATAATTATCATGATCAAAAGACTTACAGATGGCCTGAAGGACTTACCAATTTTGGAA
131 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
* * * *
3177657 ATAGTTTACTGGATAAGAGAA-TTTGGAAATCGC---C--A------AAAAA-ATCATTTTCTG
196 ATAGTTTACTGGGTAAGA-AACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
* *
3177708 AAAATATTAAATGAGAAACTTTGAAAATCTCTTTCTCTTTTTTCAAAAATCATATGAAAACATCC
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* ** * * * * *
3177773 TACCTGAAGGTCTTAT-GAATGGCCTGAAGGATTTATCATCTTGATTGAAACACTGACAAATGAC
66 TACCCGAAGGTCTTATAG-ATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGAC
* * * * ** * * * *
3177837 CCGAAGGATTT-ATCATCTTGATCGAAACACTGACAAATGACCCGAAGGATTTATTC-ATCGTGC
130 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-CCAAT--T-T
* * * * * *
3177900 TCGAAAGACTTACTAATGGCCCG-AAGGACTTACCAATTTTGGAAATAGTTTAATGGGTAAGAAA
191 TGGAAATAGTT--TACTGG---GTAA-GA--AACC----TTGG----A----AA----T----CA
*
3177964 CTTTTGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTCTG
228 C-TTT---CTTAC-TT-------TTCAAAAATTTCATTTTCTG
* * * * ** * *
3178007 AAAACATTAAATGAGAAACTTTGGAAATAACATTCTCATTTTTTGAAAATCATGTGAAAACATCT
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
* *
3178072 TGCCTGAAGGTCTTATAGATGG-CCATAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGAC
66 TACCCGAAGGTCTTATAGATGGCCCA-AAGGACTTATCATCTTGCTCGAAAGACTGACAGATGAC
* * * * ** *
3178136 CCAAAAGATTTAATCATCATGCTCGAAAGACTTATTGATGGCCCAAAAAACTT----ATCTTGGA
130 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGA
* * **
3178197 AATAGTTTACTGTGTAA-AAACCTTTGGAAATCGCTTTCTTACTGTTT-AAAAATTTTGTTTTCT
195 AATAGTTTACTGGGTAAGAAACC-TTGGAAATCACTTTCTTACT-TTTCAAAAATTTCATTTTCT
3178260 G
258 G
* * *
3178261 CAAATATTAAATGAGAAACTTTGGAAATCACTTTCTTA-TTTTCAAAA
1 AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAA
3178308 CAACTTAATG
Statistics
Matches: 2502, Mismatches: 331, Indels: 158
0.84 0.11 0.05
Matches are distributed among these distances:
245 36 0.01
246 133 0.05
247 5 0.00
248 8 0.00
250 5 0.00
252 2 0.00
253 10 0.00
254 49 0.02
255 3 0.00
257 243 0.10
258 1744 0.70
259 25 0.01
260 10 0.00
261 22 0.01
262 5 0.00
263 1 0.00
265 3 0.00
266 1 0.00
267 2 0.00
270 1 0.00
271 1 0.00
274 2 0.00
275 1 0.00
278 1 0.00
282 5 0.00
284 1 0.00
285 3 0.00
287 1 0.00
288 1 0.00
289 2 0.00
291 4 0.00
293 8 0.00
296 2 0.00
298 6 0.00
299 126 0.05
300 30 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (258 bp):
AAAATATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAAAATCATATGAAAACATCC
TACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACC
CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
ATAGTTTACTGGGTAAGAAACCTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTG
Found at i:3175835 original size:42 final size:41
Alignment explanation
Indices: 3175739--3175838 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
3175729 AGGTCTTATG
* *
3175739 GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAATGACA
1 GATGGCCCGAAGGATTTATCATCATGCTCAAAAGAATGACA
* * * *
3175780 GATGACCTC-AAGGATTTAATCATCATGCTCAAAAGACTTACT
1 GATGGCC-CGAAGGATTT-ATCATCATGCTCAAAAGAATGACA
3175822 GATGGCCCGAAGGATTT
1 GATGGCCCGAAGGATTT
3175839 CCCAATTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
41 14 0.29
42 35 0.71
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGATTTATCATCATGCTCAAAAGAATGACA
Found at i:3176863 original size:42 final size:41
Alignment explanation
Indices: 3176771--3176868 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 41
3176761 AGGTCTTATG
*
3176771 GATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACA
1 GATGGCCCAAAGGACTTATCATCATGCTCGAAAGACTGACA
** * *
3176812 GATTACCCAAAGGATTTAATCATCATGCTCGAAAGACAT-ACT
1 GATGGCCCAAAGGACTT-ATCATCATGCTCGAAAGAC-TGACA
3176854 GATGGCCCAAAGGAC
1 GATGGCCCAAAGGAC
3176869 ATACCAATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 14 0.30
42 32 0.68
43 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (41 bp):
GATGGCCCAAAGGACTTATCATCATGCTCGAAAGACTGACA
Found at i:3177083 original size:41 final size:42
Alignment explanation
Indices: 3177026--3177126 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
3177016 CAAAGGTCTT
* *
3177026 ACAGATGGCCCGAAGGACAT-ATCATCTTGCTCGAAAGACTG
1 ACAGATGACCCGAAGGACATAATCATCATGCTCGAAAGACTG
* ** * *
3177067 ACAGATGACTCGAAGGATTTAATTATCATGCTCGAAAGACTT
1 ACAGATGACCCGAAGGACATAATCATCATGCTCGAAAGACTG
* * *
3177109 ACTGATGGCCCAAAGGAC
1 ACAGATGACCCGAAGGAC
3177127 TTACAAATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
41 16 0.34
42 31 0.66
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (42 bp):
ACAGATGACCCGAAGGACATAATCATCATGCTCGAAAGACTG
Found at i:3177923 original size:42 final size:41
Alignment explanation
Indices: 3177798--3177927 Score: 188
Period size: 41 Copynumber: 3.1 Consensus size: 41
3177788 TGAATGGCCT
*
3177798 GAAGGATTTATCATCTTGATTGAAACACTGACAAATGACCC
1 GAAGGATTTATCATCTTGATCGAAACACTGACAAATGACCC
3177839 GAAGGATTTATCATCTTGATCGAAACACTGACAAATGACCC
1 GAAGGATTTATCATCTTGATCGAAACACTGACAAATGACCC
* * * * * *
3177880 GAAGGATTTATTCATCGTGCTCGAAAGACTTACTAATGGCCC
1 GAAGGATTTA-TCATCTTGATCGAAACACTGACAAATGACCC
3177922 GAAGGA
1 GAAGGA
3177928 CTTACCAATT
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 50 0.62
42 31 0.38
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (41 bp):
GAAGGATTTATCATCTTGATCGAAACACTGACAAATGACCC
Found at i:3186625 original size:22 final size:23
Alignment explanation
Indices: 3186600--3186643 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3186590 AATTAAGTTT
3186600 TAATCTTA-AAA-TAATTTCAAAA
1 TAATCTTACAAAGT-ATTTCAAAA
*
3186622 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAAGTATTTCAAA
3186644 CCATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATCTTACAAAGTATTTCAAAA
Found at i:3200977 original size:6 final size:6
Alignment explanation
Indices: 3200956--3200996 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
3200946 ACAAACGTAA
*
3200956 AAATGC AAAGATGC AAATGC AAATGC AAATAC AAATGC AAA
1 AAATGC -AA-ATGC AAATGC AAATGC AAATGC AAATGC AAA
3200997 AGGTGTCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 23 0.74
7 4 0.13
8 4 0.13
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AAATGC
Found at i:3205076 original size:3 final size:3
Alignment explanation
Indices: 3205068--3205118 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
3205058 ATGATATTAG
* * *
3205068 TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA TAC T-A TAG TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
3205113 TAA TAA
1 TAA TAA
3205119 ATATAATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 37 0.93
4 2 0.05
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3206246 original size:60 final size:60
Alignment explanation
Indices: 3206110--3206246 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 60
3206100 TTATTCTGGG
* * * * * *
3206110 GACCTTTTTGTTAA-TTTTAATAGTTAGGGGACTCAGCAAAACTATACTCTATTGTTGAGG
1 GACCATTTTG-TAACTTTGAATAGTTAGGGGACTCAACAAAACTATACTCTATGGTCGAGA
* *
3206170 GACTATTTTGTAACTTTGAATAGTT-GGGGAACTCAAC-AAAGTAATACTCTATGGTCGAGA
1 GACCATTTTGTAACTTTGAATAGTTAGGGG-ACTCAACAAAACT-ATACTCTATGGTCGAGA
3206230 GACCA-TTTGTATACTTT
1 GACCATTTTGTA-ACTTT
3206247 ACGGTAAGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
59 17 0.27
60 47 0.73
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (60 bp):
GACCATTTTGTAACTTTGAATAGTTAGGGGACTCAACAAAACTATACTCTATGGTCGAGA
Found at i:3209656 original size:138 final size:138
Alignment explanation
Indices: 3209491--3210500 Score: 1193
Period size: 138 Copynumber: 7.3 Consensus size: 138
3209481 TGAATATTCC
* * * * *
3209491 ATAATTAATTTAAATTGACTAGGTTAATAATTAAAGGCTCCACTTTAGGCTTAATTTTATACTTA
1 ATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCACTTTAGGCTTAATTTCATACTTA
* * *
3209556 GTCTTTTAATTTAGGAGAATTATTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATAAT
66 GTCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTAT
3209621 TCGAATCA
131 TCGAATCA
* * * * * *
3209629 ATAACTT-ATTAACATTGACCATGTTAATGATTAAAG-ATCCACTTTAGGCTTAATTTCATACTT
1 ATAA-TTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCACTTTAGGCTTAATTTCATACTT
* ** * *
3209692 AATCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTTACTTTTGCTCGAGATTCCAGTTTAATTA
65 AGTCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTA
*
3209757 TTCTAATCA
130 TTCGAATCA
* * * * * *
3209766 GTAATTAATTAAAATTGATTAGGTTAATTATTAGAGACTCCACTTTAGGCTTAATTCCATACTTA
1 ATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCACTTTAGGCTTAATTTCATACTTA
* * * * *
3209831 GTCTTCTAATTTAGGAGAACTTTTAATTTGGTCCTTGCTTTTTCTCGAGGTTCCATTTTAGTTAT
66 GTCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTAT
*
3209896 TTGAATCA
131 TCGAATCA
* *
3209904 ATAATTGATTAAAATTGACTAGGTTAATAATTAAAGCCTCCA-TTGTAGGCTTAATTTCAAACTT
1 ATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCACTT-TAGGCTTAATTTCATACTT
* * ** * *
3209968 AGTCATTTAATTTAGGGGAATTTTTAATTTGGTCCTAACTTTTACTCGATGTTCCATTTTAATTA
65 AGTCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTA
*
3210033 TTTGAATCA
130 TTCGAATCA
* *
3210042 ATAATTGATTAAAATTGACTAGGTTAACAATTAGAGCCTCCAATTTTAGGCTTAATTTCATACTT
1 ATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCC-ACTTTAGGCTTAATTTCATACTT
* * * * * *
3210107 TGTCATCTAATTTAGGGGAATTTTTAGTTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTA
65 AGTCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTA
*
3210172 TTTGAATCA
130 TTCGAATCA
* * **
3210181 ATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCAATTTCAGGCTTGTTTTTCATACT
1 ATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCACTTT-AGGCTT-AATTTCATACT
* * * *
3210246 TAGTCCTTTAATTTAGGGGAATTTTTTATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATT
64 TAGTCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATT
*
3210311 ATTCGAATAA
129 ATTCGAATCA
* * * * * ** * **
3210321 AAAACTGATTAAAATTGACCAGGTTATTTATTAGAGCCTCTTCTTTATGCTTAATTTCATAAATA
1 ATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCACTTTAGGCTTAATTTCATACTTA
* * * * * *
3210386 ATCCTTTAATTTAGGAGAATTTTTTATTTGGTCATCGCTTTTATGCTCGAGGTTCCATTTTGACT
66 GTCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGC-TTT-TGCTCGAGGTTCCATTTTAATT
3210451 ATTC-AACTCA
129 ATTCGAA-TCA
* * * *
3210461 ATAATTTATTAAAAATGATTTGGATTAAT-ATTAGAGCCTC
1 ATAATTGATTAAAATTGACTAGG-TTAATAATTAGAGCCTC
3210501 TAGGTTTAGT
Statistics
Matches: 754, Mismatches: 106, Indels: 22
0.85 0.12 0.02
Matches are distributed among these distances:
136 2 0.00
137 118 0.16
138 321 0.43
139 142 0.19
140 167 0.22
141 4 0.01
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (138 bp):
ATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCACTTTAGGCTTAATTTCATACTTA
GTCTTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTAT
TCGAATCA
Found at i:3215320 original size:19 final size:20
Alignment explanation
Indices: 3215274--3215320 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
3215264 AATATGGTTT
**
3215274 ATAAAATACATAAATTTTGTA
1 ATAAAA-ACATAAATTTTAAA
*
3215295 ATTAAAACA-AAATTTTAAA
1 ATAAAAACATAAATTTTAAA
3215314 ATAAAAA
1 ATAAAAA
3215321 TTTAACTACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 14 0.64
20 3 0.14
21 5 0.23
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAAAAACATAAATTTTAAA
Found at i:3216628 original size:3 final size:3
Alignment explanation
Indices: 3216620--3216711 Score: 184
Period size: 3 Copynumber: 30.7 Consensus size: 3
3216610 TTTCTACATA
3216620 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3216668 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3216712 AATTAAGGCC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3216780 original size:11 final size:11
Alignment explanation
Indices: 3216721--3216783 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
3216711 AAATTAAGGC
3216721 CCCAACCTAAAA
1 CCCAACC-AAAA
*
3216733 CCCAATCAAAA
1 CCCAACCAAAA
* *
3216744 CCCATCCATAA
1 CCCAACCAAAA
* **
3216755 CCCAAACAAGT
1 CCCAACCAAAA
*
3216766 CCCAACCAGAA
1 CCCAACCAAAA
3216777 CCCAACC
1 CCCAACC
3216784 TAAATACTCA
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
11 32 0.84
12 6 0.16
ACGTcount: A:0.44, C:0.44, G:0.03, T:0.08
Consensus pattern (11 bp):
CCCAACCAAAA
Found at i:3216819 original size:24 final size:24
Alignment explanation
Indices: 3216792--3216843 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3216782 CCTAAATACT
*
3216792 CAAAACAAAACCAGACCCGGAGCC
1 CAAAACAAAACCAGACCCAGAGCC
* ** *
3216816 CAAACCAGGACCCGACCCAGAGCC
1 CAAAACAAAACCAGACCCAGAGCC
3216840 CAAA
1 CAAA
3216844 TTAAACTTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.40, G:0.17, T:0.00
Consensus pattern (24 bp):
CAAAACAAAACCAGACCCAGAGCC
Found at i:3230192 original size:7 final size:7
Alignment explanation
Indices: 3230151--3230179 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3230141 AAAGAAGAAG
3230151 AAAAGGA
1 AAAAGGA
3230158 AAAAGGA
1 AAAAGGA
3230165 AAAAGGA
1 AAAAGGA
3230172 AAAAGGA
1 AAAAGGA
3230179 A
1 A
3230180 GAAAAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:3231565 original size:135 final size:134
Alignment explanation
Indices: 3231231--3231671 Score: 591
Period size: 135 Copynumber: 3.3 Consensus size: 134
3231221 AGATAAACCA
* *
3231231 ATTAACATTTCCAATGGAGAGTTCATA-TAAGAAGAACGT-ATCCGATAGAGGGAGAAGAAGTTT
1 ATTAACATTTCCAATGGAGAGTTCATATTGAGAAGAAC-TCATCCGATAGAGGGAGAAGAAGTTC
* * **
3231294 GTAATGAAAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGTGACTTCTCACT
65 ATAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGTGACGCCTCACT
3231359 TGAGG
130 TGAGG
* *
3231364 ATTAACATTTCCAATGGAGAGTTTATAATT-AGAAGAACTCATCCGATAGAGGGAGAAGAAATTC
1 ATTAACATTTCCAATGGAGAGTTCAT-ATTGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * * * * * * *
3231428 ATAAAGAGGAGAACTTGTTCAACCTTTGATCGATTTACGATATTTTGAATCAATAAAGCCTCACT
65 ATAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGTGACGCCTCACT
3231493 TGAGGG
130 TGA-GG
* * * *
3231499 ATTAACATTTCCAATGGACAGTTCATATTGAGAATAACTCTTCCGATAGAGGGAGAATAAGTTCA
1 ATTAACATTTCCAATGGAGAGTTCATATTGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
* * * *
3231564 TAATGAGAATAACTTGTTCAACCTTTGCTCGATTCACGACATTTCGAATTAGCGACGCCTCACTT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGTGACGCCTCACTT
3231629 GAAGG
131 G-AGG
* *
3231634 ATTAATATTTCCAATGGAGAGTTCATAATGAGAAGAAC
1 ATTAACATTTCCAATGGAGAGTTCATATTGAGAAGAAC
3231672 ATGTTCAACA
Statistics
Matches: 265, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
133 26 0.10
134 90 0.34
135 148 0.56
136 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (134 bp):
ATTAACATTTCCAATGGAGAGTTCATATTGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGTGACGCCTCACTT
GAGG
Found at i:3231694 original size:95 final size:95
Alignment explanation
Indices: 3231558--3231766 Score: 253
Period size: 95 Copynumber: 2.2 Consensus size: 95
3231548 AGGGAGAATA
* * *
3231558 AGTTCATAATGAGAATAACTTGTTCAACCTTTGCTCGATTCA-CGACATTTCGAATTAGCGACGC
1 AGTTCATAATGAGAAGAACATGTTCAACATTTGCTCGATTCACCG-CATTTCGAATTAGCGACGC
** * *
3231622 CTCACT-TGAAGGATTAATATTTCCAATGGAG
65 CTCACTAT-AAGGACAAACATTTCCAATAGAG
* * *
3231653 AGTTCATAATGAGAAGAACATGTTCAACATTTTCTAC-ATTCACCGCATTTCGAATTAGTGATGC
1 AGTTCATAATGAGAAGAACATGTTCAACATTTGCT-CGATTCACCGCATTTCGAATTAGCGACGC
* *
3231717 CTCACTATAGGGACAAACATTTCCAGTAGAG
65 CTCACTATAAGGACAAACATTTCCAATAGAG
*
3231748 AGTTCATGATGAGAAGAAC
1 AGTTCATAATGAGAAGAAC
3231767 TCGCATCTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
95 94 0.96
96 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (95 bp):
AGTTCATAATGAGAAGAACATGTTCAACATTTGCTCGATTCACCGCATTTCGAATTAGCGACGCC
TCACTATAAGGACAAACATTTCCAATAGAG
Found at i:3231981 original size:29 final size:29
Alignment explanation
Indices: 3231949--3232007 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3231939 CCCAAACAAG
3231949 CCCCAACCAAAACCCAACTTAAAACCCAA
1 CCCCAACCAAAACCCAACTTAAAACCCAA
3231978 CCCCAACCAAAACCCAACTTAAAACCCAA
1 CCCCAACCAAAACCCAACTTAAAACCCAA
3232007 C
1 C
3232008 TTTGTACTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.46, G:0.00, T:0.07
Consensus pattern (29 bp):
CCCCAACCAAAACCCAACTTAAAACCCAA
Found at i:3240653 original size:55 final size:55
Alignment explanation
Indices: 3240587--3241082 Score: 398
Period size: 55 Copynumber: 9.2 Consensus size: 55
3240577 GTGAAGCAAA
* *
3240587 TGAAGATTGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
* * * * * *
3240642 TGAAGATTGTTCAAGTCTCATACTCTCTTAAGCAATAGGGAGCAGACATGAATAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
* *
3240697 TGAAAATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
* * * *
3240752 TGAAAATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-ATGT
* * * **
3240807 TGAAGA---TT-GAGTCCTATACTTTCTGAAGGAATAGGGAG-AGGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCA-GACACGAATGT
* * * * **
3240858 TGAAGGTTGTTCAAGTCATATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATG-T
* * * * *
3240914 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-ATGT
* * * * * ** * *
3240965 TGAAGA-T-TT--AGTCCTATACTCTCTGAAGGAATAGAGAACGGACTTG-TTTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
* * * * *
3241015 ATGAAGATTGTTTGAGTTTTATACTCCCTGAAGCAAA-AGGGAGCAAAC-CCAATGGT
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCAGACACGAAT-GT
*
3241071 CGAAGATTGTTC
1 TGAAGATTGTTC
3241083 AAAGAAGAGG
Statistics
Matches: 366, Mismatches: 55, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
50 4 0.01
51 86 0.23
52 41 0.11
53 4 0.01
54 3 0.01
55 219 0.60
56 9 0.02
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
Found at i:3240958 original size:158 final size:160
Alignment explanation
Indices: 3240596--3240998 Score: 460
Period size: 161 Copynumber: 2.5 Consensus size: 160
3240586 ATGAAGATTG
* ** * *
3240596 TTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGA-ATGTTGAAGATTGTTCAAGT-C
1 TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACAC-ATTTGTTGAAGATTG----AGTCC
* * * ** * ** *
3240659 TCATACTCTCTTAAGCAATAGGGAGCA-GACATGAATATTGAAAATTGTTCGAGTCTAATACTCT
61 T-ATACTCTCTGAAGGAATAGGGAG-AGGACACGTTTGTTGAAGGTTGTTCAAGTCTAATACTCT
*
3240723 CTGAAGAAATAGGGAGCAGACACGAATGTTGAAAATTA
124 CTGAAGAAATAGGGAGCAGACACGAATGTTG-AAATGA
*
3240761 TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCTATAC
1 TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCTATAC
*
3240826 TTTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGGTTGTTCAAGTC-ATATACTCTCTGAAG
66 TCTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGGTTGTTCAAGTCTA-ATACTCTCTGAAG
* **
3240890 AAATAGGGAGCGGACACGTTTGATTG-AA-GA
130 AAATAGGGAGCAGACACGAATG-TTGAAATGA
* * *
3240920 TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACACATTTGTTGAAGATTTAGTCCTATAC
1 TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCTATAC
3240984 TCTCTGAAGGAATAG
66 TCTCTGAAGGAATAG
3240999 AGAACGGACT
Statistics
Matches: 210, Mismatches: 23, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
158 72 0.34
159 3 0.01
160 4 0.02
161 76 0.36
162 5 0.02
164 1 0.00
165 49 0.23
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (160 bp):
TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCTATAC
TCTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGGTTGTTCAAGTCTAATACTCTCTGAAGA
AATAGGGAGCAGACACGAATGTTGAAATGA
Found at i:3241020 original size:51 final size:51
Alignment explanation
Indices: 3240716--3241024 Score: 341
Period size: 51 Copynumber: 5.9 Consensus size: 51
3240706 TTCGAGTCTA
* * ** * *
3240716 ATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAAATTATTCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTG--AA-GATT-GAGTCCT
* *
3240771 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGAGTCCT
* * * *
3240822 ATACTTTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGGTTGTTCAAGTCAT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTG----AGTCCT
*
3240877 ATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGATTGAAGATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTG-TTGAAGATTGAGTCCT
* * *
3240929 ATACTCTCTGAAGGAATGGGGAGCGGACACATTTGTTGAAGATTTAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGAGTCCT
* * **
3240980 ATACTCTCTGAAGGAATAGAGAACGGACTTGTTT-TATGAAGATTG
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGT-TGAAGATTG
3241025 TTTGAGTTTT
Statistics
Matches: 220, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
50 1 0.00
51 97 0.44
52 40 0.18
53 2 0.01
55 71 0.32
56 9 0.04
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (51 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGAGTCCT
Found at i:3241020 original size:158 final size:159
Alignment explanation
Indices: 3240596--3241059 Score: 460
Period size: 158 Copynumber: 2.9 Consensus size: 159
3240586 ATGAAGATTG
* ** * *
3240596 TTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGA-ATGTTGAAGATTGTTCAAGT-C
1 TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACAC-ATTTGTTGAAGATTG----AGTCC
* * * * ** * *
3240659 TCATACTCTCTTAAGCAATAGGGAGCA-GACATGAATATTGAAAATTGTTCGAGTCTAATACTCT
61 T-ATACTCTCTGAAGGAATAGAGAG-AGGACACGTTTGTTGAAGATTGTTCGAGTCT-ATACTCT
*
3240723 CTGAAGAAATAGGGAGCAGACACGAATGTTGAAAATTA
123 CTGAAGAAATAGGGAGCAGACACGAATGTTG-AAATGA
*
3240761 TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCTATAC
1 TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCTATAC
* * * *
3240826 TTTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGGTTGTTCAAGTCATATACTCTCTGAAGA
66 TCTCTGAAGGAATAGAGAGAGGACACGTTTGTTGAAGATTGTTCGAGTC-TATACTCTCTGAAGA
* **
3240891 AATAGGGAGCGGACACGTTTGATTG-AA-GA
130 AATAGGGAGCAGACACGAATG-TTGAAATGA
* * *
3240920 TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACACATTTGTTGAAGATTTAGTCCTATAC
1 TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCTATAC
** * * *
3240984 TCTCTGAAGGAATAGAGA-ACGGACTTGTTT-TATGAAGATTGTTTGAGTTTTATACTCCCTGAA
66 TCTCTGAAGGAATAGAGAGA-GGACACGTTTGT-TGAAGATTGTTCGAG-TCTATACTCTCTGAA
3241047 GCAAA-AGGGAGCA
128 G-AAATAGGGAGCA
3241060 AACCCAATGG
Statistics
Matches: 258, Mismatches: 32, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
157 2 0.01
158 114 0.44
159 7 0.03
160 3 0.01
161 76 0.29
162 6 0.02
164 1 0.00
165 49 0.19
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (159 bp):
TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTGAGTCCTATAC
TCTCTGAAGGAATAGAGAGAGGACACGTTTGTTGAAGATTGTTCGAGTCTATACTCTCTGAAGAA
ATAGGGAGCAGACACGAATGTTGAAATGA
Found at i:3241271 original size:3 final size:3
Alignment explanation
Indices: 3241249--3241304 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
3241239 ATATTATAAA
* *
3241249 TAT TAAT TA- TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3241294 TATT TAT TAT T
1 TA-T TAT TAT T
3241305 TTACATTTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3242695 original size:22 final size:22
Alignment explanation
Indices: 3242667--3242712 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3242657 TGGATATATG
*
3242667 TTTTAGTCCATCATAGTTTAAC
1 TTTTAGTCCATCATAATTTAAC
3242689 TTTTAGTCCATCATAATTTAAC
1 TTTTAGTCCATCATAATTTAAC
3242711 TT
1 TT
3242713 AATGTGTACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTTAGTCCATCATAATTTAAC
Found at i:3242788 original size:12 final size:12
Alignment explanation
Indices: 3242771--3242800 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3242761 TTGTATTATC
3242771 ATATATACATAT
1 ATATATACATAT
3242783 ATATATACATAT
1 ATATATACATAT
3242795 ATATAT
1 ATATAT
3242801 TTCCTTAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATACATAT
Found at i:3243795 original size:31 final size:32
Alignment explanation
Indices: 3243757--3243845 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
3243747 AGTCGAGGGG
*
3243757 TACCTATGTCTTTC-GAGACATATGGACAGT-T
1 TACCTATGTCCTTCGGA-ACATATGGACAGTGT
*
3243788 TACCTATGTCCTTCGGAACATATGGACATTGT
1 TACCTATGTCCTTCGGAACATATGGACAGTGT
* * *
3243820 TACCTATGTTCATCAGAACATATGGA
1 TACCTATGTCCTTCGGAACATATGGA
3243846 TAGGTCTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
31 25 0.49
32 26 0.51
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (32 bp):
TACCTATGTCCTTCGGAACATATGGACAGTGT
Found at i:3245885 original size:20 final size:20
Alignment explanation
Indices: 3245860--3245926 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
3245850 GCAGCCCACA
3245860 CAGCAGCACCAAATCCGCGG
1 CAGCAGCACCAAATCCGCGG
3245880 CAGCAGCACCAAATCCGCGG
1 CAGCAGCACCAAATCCGCGG
3245900 CAGCAGCACCAAATCCGCGG
1 CAGCAGCACCAAATCCGCGG
*
3245920 TAGCAGC
1 CAGCAGC
3245927 TCTAGCACGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.30, C:0.39, G:0.25, T:0.06
Consensus pattern (20 bp):
CAGCAGCACCAAATCCGCGG
Found at i:3256464 original size:47 final size:47
Alignment explanation
Indices: 3256368--3256466 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
3256358 TTGAATAAAT
* * * **
3256368 GCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCTCGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAAGATTATTTGTCAAGAACAA
* * *
3256415 GCATGCGAATTAGATATCATGCGGTTAAGATT-TTTGTGAATAACAAA
1 GCATGCGAACTAGATATCATGCGGTTAAGATTATTTGTCAAGAAC-AA
3256462 GCATG
1 GCATG
3256467 GGGTAGATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 7 0.16
47 36 0.84
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAAGATTATTTGTCAAGAACAA
Found at i:3263238 original size:20 final size:19
Alignment explanation
Indices: 3263213--3263292 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 19
3263203 CATTTATCAA
3263213 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGG-CATC
* * *
3263233 AGTAAGTCTTTCGAGCATG
1 AGTAAGTCCTTCGGGCATC
3263252 ATGTTGAAGTCCTTCGGGTCATC
1 A-G-T-AAGTCCTTCGGG-CATC
* *
3263275 AGTAAGTCTTTCGAGCAT
1 AGTAAGTCCTTCGGGCAT
3263293 GATAATTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
19 7 0.15
20 24 0.50
21 2 0.04
22 11 0.23
23 4 0.08
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (19 bp):
AGTAAGTCCTTCGGGCATC
Found at i:3263275 original size:42 final size:42
Alignment explanation
Indices: 3263215--3263312 Score: 153
Period size: 42 Copynumber: 2.3 Consensus size: 42
3263205 TTTATCAAAG
* *
3263215 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT-GT
1 TAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATAAT
3263256 TGAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATAAT
1 T-AAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATAAT
*
3263299 TAAATCCTTCGGGT
1 TAAGTCCTTCGGGT
3263313 AATTTTTAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.02
42 49 0.94
43 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (42 bp):
TAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATAAT
Found at i:3263366 original size:80 final size:80
Alignment explanation
Indices: 3263271--3263681 Score: 660
Period size: 80 Copynumber: 5.1 Consensus size: 80
3263261 TCCTTCGGGT
*
3263271 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAATA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
*
3263336 GTAGTGAAGCAAACC
66 GTAGTGAAGCAAATC
* * * * * *
3263351 CATCAGTAACTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGTAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
*
3263416 GTAGTGAAACAAATC
66 GTAGTGAAGCAAATC
3263431 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
* *
3263496 TTAGTGAAGCAAACC
66 GTAGTGAAGCAAATC
* * * * * *
3263511 CATCAGTAAGTCTTTCGAGCATTATGATTAAATCATTCGGGTAATTTATAAGACTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
3263576 GTAGTGAAGCAAATC
66 GTAGTGAAGCAAATC
3263591 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
3263656 GTAGTGAAGCAAATC
66 GTAGTGAAGCAAATC
*
3263671 CGTCAGTAAGT
1 CATCAGTAAGT
3263682 GCCATCAGTA
Statistics
Matches: 298, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 298 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
GTAGTGAAGCAAATC
Found at i:3263540 original size:160 final size:160
Alignment explanation
Indices: 3263271--3263681 Score: 732
Period size: 160 Copynumber: 2.6 Consensus size: 160
3263261 TCCTTCGGGT
*
3263271 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAATA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
* *
3263336 GTAGTGAAGCAAACCCATCAGTAACTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTA
66 GTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTATA
* *
3263401 AGCCTTCACCGTAGAGTAGTGAAACAAATC
131 AGACTTCACCGAAGAGTAGTGAAACAAATC
3263431 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
* *
3263496 TTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATTATGATTAAATCATTCGGGTAATTTATA
66 GTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTATA
*
3263561 AGACTTCACCGAAGAGTAGTGAAGCAAATC
131 AGACTTCACCGAAGAGTAGTGAAACAAATC
3263591 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
* *
3263656 GTAGTGAAGCAAATCCGTCAGTAAGT
66 GTAGTGAAGCAAACCCATCAGTAAGT
3263682 GCCATCAGTA
Statistics
Matches: 240, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
160 240 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (160 bp):
CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
GTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTATA
AGACTTCACCGAAGAGTAGTGAAACAAATC
Found at i:3264371 original size:53 final size:53
Alignment explanation
Indices: 3264147--3264353 Score: 317
Period size: 53 Copynumber: 3.9 Consensus size: 53
3264137 AGAATCACAC
* * * * *
3264147 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGTAAGAAGGAGCGAACCTGTAGA
1 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
*
3264200 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCTTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
3264253 AAGAAGATAT-TTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGAT-TGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
3264306 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCC
1 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCC
3264354 ACTGGTTGAA
Statistics
Matches: 140, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
52 1 0.01
53 138 0.99
54 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:3271327 original size:3 final size:3
Alignment explanation
Indices: 3271319--3271359 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3271309 AGGTTAATAA
3271319 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3271360 AGATTATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3273858 original size:241 final size:236
Alignment explanation
Indices: 3273433--3273923 Score: 673
Period size: 241 Copynumber: 2.1 Consensus size: 236
3273423 TGGGCCATCT
* * * *
3273433 ATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCAATTTCCAAAGTT
1 ATAAGTCCTTCGGGAAGGATGATTTCACATGATTTTCGAAAAATGAGAAAGCAATGTCCAAAGTT
*
3273498 TCTCATTTAATGTTTTTAAAAAATGAAATTTTGAAAAGTAAGAAAGTATTTTCCAAAGTTTCTTA
66 TCTCATTTAATGTTTTCAAAAAATGAAATTTTGAAAAGTAAGAAAGTATTTTCCAAAGTTTCTTA
* * * *
3273563 CCCAGTAAACTATTTCCAAAAGGGGTAACCCCTTCGGCCCAGCATTAAGCCTTTCGAGTATGATG
131 CCCAGTAAACTATTTCCAAAAGGGGTAACCCATTCGGCCCACCAGTAAGCCTTTCGAGCATGATG
*
3273628 ATTAAATCCTTCGGGTCATATGTCAGTCTTTCGAGCAAGGCG
196 ATTAAATCCTTC-GGTCATATGTCAGTCTTTCGAGCAAGACG
* * * **
3273670 ATAAGTCCTTCGGGAATGATGATTTCACATGATTTTTGAAAAATTGAG-AAGCGATGTCCAATTT
1 ATAAGTCCTTCGGGAAGGATGATTTCACATGATTTTCGAAAAA-TGAGAAAGCAATGTCCAAAGT
3273734 TTCTCATTTAATTTTGTTTTCAAAAAATGAAACTTTTGAAAAGTAAGAAA-TCGA-TTTCCAAAG
65 TTCTCATTTAA---TGTTTTCAAAAAATGAAA-TTTTGAAAAGTAAGAAAGT--ATTTTCCAAAG
** ** * *
3273797 TTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCTACCAGTAAGCCTTTCGAG
124 TTTCTTACCCAGTAAACTATTTCCAAAAGGGGTAACCCATTCGGCCCACCAGTAAGCCTTTCGAG
* * *
3273862 CCTGATGATTAAATCCTTCGGTCATCTGTCAGTCTTTCGAGCAAGATG
189 CATGATGATTAAATCCTTCGGTCATATGTCAGTCTTTCGAGCAAGACG
3273910 ATAAGTCCTTCGGG
1 ATAAGTCCTTCGGG
3273924 CCATCTATAA
Statistics
Matches: 223, Mismatches: 24, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
237 61 0.27
238 4 0.02
240 58 0.26
241 99 0.44
242 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (236 bp):
ATAAGTCCTTCGGGAAGGATGATTTCACATGATTTTCGAAAAATGAGAAAGCAATGTCCAAAGTT
TCTCATTTAATGTTTTCAAAAAATGAAATTTTGAAAAGTAAGAAAGTATTTTCCAAAGTTTCTTA
CCCAGTAAACTATTTCCAAAAGGGGTAACCCATTCGGCCCACCAGTAAGCCTTTCGAGCATGATG
ATTAAATCCTTCGGTCATATGTCAGTCTTTCGAGCAAGACG
Found at i:3274147 original size:42 final size:41
Alignment explanation
Indices: 3274087--3274166 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
3274077 GCCATCAGTA
*
3274087 AGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTC
1 AGTCTTTCAAGCAAGATGA-TAAATCCTTCGGGTCATCTGTC
* * *
3274129 AGTCTTTCGAGCAAGATGATAAGTCGTTCGGGTCATCT
1 AGTCTTTCAAGCAAGATGATAAATCCTTCGGGTCATCT
3274167 ATAAGACCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 17 0.50
42 17 0.50
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (41 bp):
AGTCTTTCAAGCAAGATGATAAATCCTTCGGGTCATCTGTC
Found at i:3274278 original size:20 final size:19
Alignment explanation
Indices: 3274249--3274286 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3274239 CATTTAATTT
*
3274249 AAAAAAAGAAGAAGAAAAG
1 AAAAAAAGAAAAAGAAAAG
3274268 AAAAAAGAGAAAAAGAAAA
1 AAAAAA-AGAAAAAGAAAA
3274287 ATGAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAGAAAAG
Found at i:3274287 original size:32 final size:31
Alignment explanation
Indices: 3274250--3274312 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
3274240 ATTTAATTTA
*
3274250 AAAAAAGAAGAAGAAAAGAAAAAAGAGAAAAAG
1 AAAAATGAA-AAGAAAAG-AAAAAGAGAAAAAG
* * *
3274283 AAAAATGAAATGAAATGAAAAAGATAAAAA
1 AAAAATGAAAAGAAAAGAAAAAGAGAAAAA
3274313 TAAATATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 12 0.46
32 6 0.23
33 8 0.31
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAAATGAAAAGAAAAGAAAAAGAGAAAAAG
Found at i:3277403 original size:19 final size:19
Alignment explanation
Indices: 3277379--3277415 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3277369 TTTTGCCCCG
3277379 AACCCG-ACCCGATCCCAAA
1 AACCCGAACCCGA-CCCAAA
3277398 AACCCGAACCCGACCCAA
1 AACCCGAACCCGACCCAA
3277416 TCCTGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.38, C:0.49, G:0.11, T:0.03
Consensus pattern (19 bp):
AACCCGAACCCGACCCAAA
Found at i:3277945 original size:34 final size:35
Alignment explanation
Indices: 3277902--3277974 Score: 123
Period size: 34 Copynumber: 2.1 Consensus size: 35
3277892 TAGGGTCAGC
3277902 TAATTAATATAAAAAATA-TATA-ATATTATATATA
1 TAATTAATATAAAAAATATTATATATA-TATATATA
3277936 TAATTAATATAAAAAATATTATATATATATATATA
1 TAATTAATATAAAAAATATTATATATATATATATA
3277971 TAAT
1 TAAT
3277975 CGGGGAGGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
34 18 0.49
35 16 0.43
36 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
TAATTAATATAAAAAATATTATATATATATATATA
Found at i:3287202 original size:26 final size:26
Alignment explanation
Indices: 3287118--3287203 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 26
3287108 TTGAATTAAA
3287118 CAAAATGATCCAAATACCCCTG-AACTC
1 CAAAATGAT-CAAATACCCC-GAAACTC
*
3287145 CAAAATGATAAAAATACCCCGAAACTC
1 CAAAATGAT-CAAATACCCCGAAACTC
* *
3287172 TAAAATGATCAAAGTACCAC-AAACTC
1 CAAAATGATCAAA-TACCCCGAAACTC
3287198 CAAAAT
1 CAAAAT
3287204 AACTGAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
26 15 0.29
27 36 0.71
ACGTcount: A:0.49, C:0.27, G:0.07, T:0.17
Consensus pattern (26 bp):
CAAAATGATCAAATACCCCGAAACTC
Found at i:3288621 original size:14 final size:14
Alignment explanation
Indices: 3288602--3288648 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3288592 GCGAGAATAT
3288602 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
3288616 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
* *
3288630 CTGAGGTCATCCGA
1 CCGAGGCCATCCGA
*
3288644 GCGAG
1 CCGAG
3288649 CTATGCGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.34, G:0.34, T:0.11
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:3288773 original size:29 final size:29
Alignment explanation
Indices: 3288697--3288773 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
3288687 GGAGCAGGAG
*
3288697 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTATAAGGTCGCCC
3288726 GGAGTGCATGGCGACCTATAAGGTCGCCC
1 GGAGTGCATGGCGACCTATAAGGTCGCCC
*
3288755 GGAGGGCATGGCGACCTAT
1 GGAGTGCATGGCGACCTAT
3288774 GCTTGGGGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.16
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTATAAGGTCGCCC
Found at i:3289925 original size:22 final size:20
Alignment explanation
Indices: 3289899--3289940 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3289889 TGAGAATGTT
3289899 GTGGCAAATGAAATGGATGGTG
1 GTGGC-AATGAAAT-GATGGTG
*
3289921 GTGGCAATGGAATGATGGTG
1 GTGGCAATGAAATGATGGTG
3289941 TAATGTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.29, C:0.05, G:0.43, T:0.24
Consensus pattern (20 bp):
GTGGCAATGAAATGATGGTG
Found at i:3299418 original size:20 final size:20
Alignment explanation
Indices: 3299389--3299427 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3299379 TTTCCACTAC
*
3299389 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
3299409 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
3299428 TATGAGGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3300216 original size:19 final size:19
Alignment explanation
Indices: 3300171--3300217 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3300161 AAAATATAAT
3300171 TTAATATTA-TAATGTACA
1 TTAATATTATTAATGTACA
* *
3300189 TTTATATTATTTATAGTAC-
1 TTAATATTATTAAT-GTACA
3300208 TTAATATTAT
1 TTAATATTAT
3300218 CTATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.33
19 12 0.50
20 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (19 bp):
TTAATATTATTAATGTACA
Found at i:3300540 original size:18 final size:18
Alignment explanation
Indices: 3300517--3300560 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3300507 ATCATAGTAT
3300517 ATAAAATTATTA-AAAATA
1 ATAAAATT-TTATAAAATA
*
3300535 ATAAAATTTTATAACATA
1 ATAAAATTTTATAAAATA
3300553 A-AAAATTT
1 ATAAAATTT
3300561 CAAAGTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAAATTTTATAAAATA
Found at i:3305608 original size:17 final size:17
Alignment explanation
Indices: 3305586--3305618 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3305576 AACTTAACTC
3305586 TCTTTGAATTCTTAGTA
1 TCTTTGAATTCTTAGTA
3305603 TCTTTGAATTCTTAGT
1 TCTTTGAATTCTTAGT
3305619 GGACAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (17 bp):
TCTTTGAATTCTTAGTA
Found at i:3307849 original size:2 final size:2
Alignment explanation
Indices: 3307842--3307870 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3307832 TGGTGATCCC
3307842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3307871 CTATTATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3309194 original size:136 final size:137
Alignment explanation
Indices: 3309030--3309416 Score: 398
Period size: 137 Copynumber: 2.8 Consensus size: 137
3309020 GCTGTCACTC
* * * *
3309030 AGGGAATATCAAACCTTGGAAAAAAGAGATATGTTCC-GTTTCTTTTGAAGGGAATATCAAATCA
1 AGGGAATATCAAACCTTGGAAAAAAGAGACATGTTCCACTTAC-TCTGAAGGGAATATCAAATCA
*
3309094 TGGA-AAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCTGGCAGACTTGTTCCACT
65 TGGAGAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTGGCAGACTTGTTCCACT
3309158 TACTCTGA
130 TACTCTGA
* * * * * *
3309166 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCTT
1 AGGGAATATCAAACCTTGGAAAAAAGAGACATGTTCCACTTACTCTGAAGGGAATATCAAATCAT
* * * *
3309231 GGAGAATAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGT
66 GGAGAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAAATC--T--G--G-CAGACTTGT
* * *
3309296 TTCGCTTACTTTGA
124 TCCACTTACTCTGA
* * * *
3309310 AGGGAATATCAGA--TATGG------CAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
1 AGGGAATATCAAACCT-TGGAAAAAAGAGACATGTTCCACTTACTCTGAAGGGAATATCAAATCA
* * *
3309367 TGGATAAGAGAGACCTGTTTCACTTACTCTGAAGGGAATATCAAATCTGG
65 TGGAGAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTGG
3309417 GAGAGTTGAT
Statistics
Matches: 215, Mismatches: 26, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
131 1 0.00
133 1 0.00
135 1 0.00
136 54 0.25
137 121 0.56
139 1 0.00
141 1 0.00
142 1 0.00
143 4 0.02
144 30 0.14
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (137 bp):
AGGGAATATCAAACCTTGGAAAAAAGAGACATGTTCCACTTACTCTGAAGGGAATATCAAATCAT
GGAGAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTGGCAGACTTGTTCCACTT
ACTCTGA
Found at i:3309213 original size:89 final size:89
Alignment explanation
Indices: 3309075--3309416 Score: 515
Period size: 89 Copynumber: 3.8 Consensus size: 89
3309065 CCGTTTCTTT
* *
3309075 TGAAGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGAT
1 TGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGAT
3309139 CTGGCAGACTTGTTCCACTTACTC
66 CTGGCAGACTTGTTCCACTTACTC
3309163 TGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGAT
1 TGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGAT
*
3309228 CTTGGAGAATAGAGACTTGTTCCACTTACTC
66 C-T-G-G----CAGACTTGTTCCACTTACTC
* * * *
3309259 TGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTTCGCTTACTTTGAAGGGAATATCAGAT
1 TGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGAT
*
3309324 ATGGCAGACTTGTTCCACTTACTC
66 CTGGCAGACTTGTTCCACTTACTC
* * *
3309348 TGAAGGGAATATCAAATCTTGGATAAGAGAGACCTGTTTCACTTACTCTGAAGGGAATATCAAAT
1 TGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGAT
3309413 CTGG
66 CTGG
3309417 GAGAGTTGAT
Statistics
Matches: 231, Mismatches: 15, Indels: 15
0.89 0.06 0.06
Matches are distributed among these distances:
88 22 0.10
89 123 0.53
90 1 0.00
91 1 0.00
92 1 0.00
93 1 0.00
94 1 0.00
95 1 0.00
96 80 0.35
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (89 bp):
TGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGAT
CTGGCAGACTTGTTCCACTTACTC
Found at i:3309220 original size:48 final size:48
Alignment explanation
Indices: 3309144--3309420 Score: 370
Period size: 48 Copynumber: 5.9 Consensus size: 48
3309134 CAGATCTGGC
*
3309144 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAG
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAG
* *
3309192 AGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCTTGGAGAATAG
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAG
* *
3309240 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTTGAGAAGAG
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAG
* * * * * *
3309288 AGACCTGTTTCGCTTACTTTGAAGGGAATATCAGAT-AT---G--G-C
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAG
* *
3309329 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAG
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAG
* *
3309377 AGACCTGTTTCACTTACTCTGAAGGGAATATCAAATCTGGGAGA
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGA
3309421 GTTGATCCAT
Statistics
Matches: 196, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
41 31 0.16
42 2 0.01
44 1 0.01
47 2 0.01
48 160 0.82
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (48 bp):
AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAG
Found at i:3309341 original size:185 final size:184
Alignment explanation
Indices: 3309075--3309420 Score: 584
Period size: 185 Copynumber: 1.9 Consensus size: 184
3309065 CCGTTTCTTT
*
3309075 TGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATC
1 TGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATA
3309140 TGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCAC
66 TGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCAC
* *
3309205 TTACTCTGAAGGGAATATCAGATCTTGGAGAATAGAGACTTGTTCCACTTACTC
131 TTACTCTGAAGGGAATATCAAATCTGGGAGAATAGAGACTTGTTCCACTTACTC
* * * * * *
3309259 TGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTTCGCTTACTTTGAAGGGAATATCAGAT
1 TGAAGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGAT
* *
3309324 ATGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACCTGTTTCA
65 ATGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCA
3309389 CTTACTCTGAAGGGAATATCAAATCTGGGAGA
130 CTTACTCTGAAGGGAATATCAAATCTGGGAGA
3309421 GTTGATCCAT
Statistics
Matches: 150, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
184 21 0.14
185 129 0.86
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (184 bp):
TGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATA
TGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCAC
TTACTCTGAAGGGAATATCAAATCTGGGAGAATAGAGACTTGTTCCACTTACTC
Found at i:3310631 original size:21 final size:22
Alignment explanation
Indices: 3310607--3310659 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3310597 CCTTTTATTT
3310607 TTTTTCTTTTCTTTTT-TCTCA
1 TTTTTCTTTTCTTTTTCTCTCA
*
3310628 TTTTTC-TTTCTTTTTCTTTCA
1 TTTTTCTTTTCTTTTTCTCTCA
3310649 TTTTTCATTTT
1 TTTTTC-TTTT
3310660 TTTAGTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 9 0.32
21 16 0.57
23 3 0.11
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTCTTTTTCTCTCA
Found at i:3310641 original size:10 final size:11
Alignment explanation
Indices: 3310607--3310654 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
3310597 CCTTTTATTT
3310607 TTTTTCTTTTC-
1 TTTTTC-TTTCA
*
3310618 TTTTT-TCTCA
1 TTTTTCTTTCA
3310628 TTTTTCTTTC-
1 TTTTTCTTTCA
3310638 TTTTTCTTTCA
1 TTTTTCTTTCA
3310649 TTTTTC
1 TTTTTC
3310655 ATTTTTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 3 0.09
10 15 0.47
11 14 0.44
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTCA
Found at i:3310668 original size:29 final size:27
Alignment explanation
Indices: 3310599--3310682 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 27
3310589 TAAACCCTCC
3310599 TTTT-ATTTTT-TTTC-TTTTCTTT-T
1 TTTTCATTTTTCTTTCTTTTTCTTTAT
*
3310622 TTCTCATTTTTCTTTCTTTTTCTTTCAT
1 TTTTCATTTTTCTTTCTTTTTCTTT-AT
3310650 TTTTCATTTTT-TTAGTCTTTTTCATTTAT
1 TTTTCATTTTTCTT--TCTTTTTC-TTTAT
3310679 TTTT
1 TTTT
3310683 TTCAGGCGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.06
24 6 0.12
25 4 0.08
26 8 0.16
27 2 0.04
28 11 0.22
29 14 0.27
30 3 0.06
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.77
Consensus pattern (27 bp):
TTTTCATTTTTCTTTCTTTTTCTTTAT
Found at i:3310683 original size:30 final size:29
Alignment explanation
Indices: 3310599--3310683 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
3310589 TAAACCCTCC
* *
3310599 TTTTATTT-TTTTTCTTTTCTTTTTTCTCAT
1 TTTTCTTTCTTTTTC-TTTCATTTTT-TCAT
3310629 TTTTCTTTCTTTTTCTTTCA-TTTTTCAT
1 TTTTCTTTCTTTTTCTTTCATTTTTTCAT
3310657 TTTT-TTAGTCTTTTTCATTT-ATTTTTT
1 TTTTCTT--TCTTTTTC-TTTCATTTTTT
3310684 TCAGGCGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
27 2 0.04
28 8 0.17
29 13 0.27
30 19 0.40
31 6 0.12
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.78
Consensus pattern (29 bp):
TTTTCTTTCTTTTTCTTTCATTTTTTCAT
Found at i:3322728 original size:2 final size:2
Alignment explanation
Indices: 3322721--3322745 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3322711 TGGTGATCCC
3322721 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3322746 CTATTATAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3324532 original size:24 final size:25
Alignment explanation
Indices: 3324505--3324561 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
3324495 TAATAAAACC
**
3324505 AAATAATAACTATATAATCTTA-TA
1 AAATAATAACTATATAAAATTATTA
* *
3324529 AAATCAT-AGTATATAAAATTATTA
1 AAATAATAACTATATAAAATTATTA
3324553 AAATAATAA
1 AAATAATAA
3324562 AATTTTATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.42
24 14 0.54
25 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATAATAACTATATAAAATTATTA
Found at i:3326646 original size:20 final size:20
Alignment explanation
Indices: 3326621--3326662 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3326611 TTTTTTTTTT
3326621 TTTGTGCATAGGATAAGACC
1 TTTGTGCATAGGATAAGACC
3326641 TTTGTGCATAGGATAAGACC
1 TTTGTGCATAGGATAAGACC
3326661 TT
1 TT
3326663 ACCGCAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (20 bp):
TTTGTGCATAGGATAAGACC
Found at i:3326758 original size:39 final size:39
Alignment explanation
Indices: 3326640--3326760 Score: 197
Period size: 39 Copynumber: 3.1 Consensus size: 39
3326630 AGGATAAGAC
*
3326640 CTTTGTGCATAGGATAAGACCTTACCGCAAGCTCCTTTG
1 CTTTGTGCATAGGATAAGACCTTACCGCAAGCTCATTTG
* *
3326679 CATTGTGCATAGGATAAGACCTTGCCGCAAGCTCATTTG
1 CTTTGTGCATAGGATAAGACCTTACCGCAAGCTCATTTG
* *
3326718 CTTTGTGCATATGATAAGACCTTACCGCATGCTCATTTG
1 CTTTGTGCATAGGATAAGACCTTACCGCAAGCTCATTTG
3326757 CTTT
1 CTTT
3326761 ATGAATAAGG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (39 bp):
CTTTGTGCATAGGATAAGACCTTACCGCAAGCTCATTTG
Found at i:3329469 original size:2 final size:2
Alignment explanation
Indices: 3329462--3329496 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3329452 CCAACATACA
3329462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3329497 AACATATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3330634 original size:19 final size:20
Alignment explanation
Indices: 3330597--3330637 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3330587 GGGATTAGGT
3330597 AAGTTAAAAATCTGAAAAAA
1 AAGTTAAAAATCTGAAAAAA
3330617 AAGTTAAAAATCTGAAAAAA
1 AAGTTAAAAATCTGAAAAAA
3330637 A
1 A
3330638 TTGTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.20
Consensus pattern (20 bp):
AAGTTAAAAATCTGAAAAAA
Found at i:3334236 original size:21 final size:21
Alignment explanation
Indices: 3334210--3334249 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3334200 AGAGAAATGC
3334210 ACTTGAATTATCCTTGCTGCT
1 ACTTGAATTATCCTTGCTGCT
*
3334231 ACTTGAATTGTCCTTGCTG
1 ACTTGAATTATCCTTGCTG
3334250 TCACCCCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
ACTTGAATTATCCTTGCTGCT
Found at i:3335297 original size:12 final size:11
Alignment explanation
Indices: 3335274--3335311 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
3335264 GTCATTCTCA
3335274 AAAAAAAT-TT
1 AAAAAAATATT
3335284 AAAAAAATGATT
1 AAAAAAAT-ATT
3335296 AAAACAAATATT
1 AAAA-AAATATT
3335308 AAAA
1 AAAA
3335312 CCTAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.32
12 13 0.52
13 4 0.16
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (11 bp):
AAAAAAATATT
Found at i:3337419 original size:19 final size:19
Alignment explanation
Indices: 3337395--3337434 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3337385 CGAATAATTT
* *
3337395 AATCGAATATATAATTTTA
1 AATCGAATATAAAATCTTA
3337414 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
3337433 AA
1 AA
3337435 ATTCAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:3337554 original size:13 final size:13
Alignment explanation
Indices: 3337536--3337569 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3337526 TAATATTTTC
*
3337536 TTTGAAAATCATT
1 TTTGAAAATCAAT
3337549 TTTG-AAATCAAT
1 TTTGAAAATCAAT
3337561 TTTGAAAAT
1 TTTGAAAAT
3337570 TACTCCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:3339305 original size:13 final size:12
Alignment explanation
Indices: 3339272--3339307 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3339262 CTAATGGGCA
3339272 AATTTTGAAAAC
1 AATTTTGAAAAC
*
3339284 CATTTTGAAAAC
1 AATTTTGAAAAC
3339296 AATGTTTGAAAA
1 AAT-TTTGAAAA
3339308 ATTATAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (12 bp):
AATTTTGAAAAC
Found at i:3339841 original size:21 final size:20
Alignment explanation
Indices: 3339788--3339845 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
3339778 TACACCTGTG
*
3339788 AGTGTATCGATACAGATTCA
1 AGTGTATCGATACACATTCA
*
3339808 AGGAATATATCGATACACATTCA
1 A-G--TGTATCGATACACATTCA
3339831 TAGTGTATCGATACA
1 -AGTGTATCGATACA
3339846 TAGCAAGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
23 17 0.55
24 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (20 bp):
AGTGTATCGATACACATTCA
Found at i:3339873 original size:14 final size:14
Alignment explanation
Indices: 3339854--3339880 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3339844 CATAGCAAGG
3339854 AGGTATCGATACAT
1 AGGTATCGATACAT
3339868 AGGTATCGATACA
1 AGGTATCGATACA
3339881 CTGTGCACAA
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:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (14 bp):
AGGTATCGATACAT
Found at i:3343079 original size:20 final size:20
Alignment explanation
Indices: 3343054--3343096 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3343044 TCTAAGAGCC
*
3343054 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
3343074 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
3343094 CAT
1 CAT
3343097 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:3347430 original size:21 final size:21
Alignment explanation
Indices: 3347404--3347460 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
3347394 AGGAGCGTAG
3347404 GTGTATCGGTACACTATCAGA
1 GTGTATCGGTACACTATCAGA
3347425 GTGTATCGGTACACTATCAGA
1 GTGTATCGGTACACTATCAGA
3347446 GTGTATCGGTACACT
1 GTGTATCGGTACACT
3347461 CAATGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTATCGGTACACTATCAGA
Found at i:3347820 original size:19 final size:19
Alignment explanation
Indices: 3347793--3347832 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3347783 CAAATAATTT
* *
3347793 AATCAAATATATAATTTTA
1 AATCAAATATAAAATCTTA
*
3347812 AATCGAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
3347831 AA
1 AA
3347833 ATTCAATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Found at i:3349502 original size:2 final size:2
Alignment explanation
Indices: 3349495--3349587 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
3349485 TCTTATGTAA
3349495 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3349537 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3349579 AC AC AC AC A
1 AC AC AC AC A
3349588 TATATATATA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3350521 original size:2 final size:2
Alignment explanation
Indices: 3350514--3350541 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3350504 AATAAAAATA
3350514 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
3350542 GGGGATGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3351344 original size:15 final size:14
Alignment explanation
Indices: 3351324--3351353 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3351314 TAACTTTGAA
3351324 TTATGAACTATAAAC
1 TTATGAACTA-AAAC
3351339 TTATGAACTAAAAC
1 TTATGAACTAAAAC
3351353 T
1 T
3351354 CTAAACCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (14 bp):
TTATGAACTAAAAC
Found at i:3355394 original size:65 final size:65
Alignment explanation
Indices: 3355287--3355679 Score: 373
Period size: 58 Copynumber: 6.4 Consensus size: 65
3355277 TGGTTAAGTA
* * * * *
3355287 ATTTAATGGTTAGGGGTATGTTTTATGTTTTATCTTACTGATAAGTTAAGAATCTAATCCAAATG
1 ATTTAATGGTTAGGGATATGTTTTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATG
* * *
3355352 ATTTAATGGTTAGGGATATGTTTTGTGTTTTATTTTAATGATAAGTTAAAAATCCAATCTAAATG
1 ATTTAATGGTTAGGGATATGTTTTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATG
* * * * *
3355417 ATTT-A--GTT---GTTAAG-GTTATATTTTATGTTAATAATAAGTTAAGAATCCAATCTAAATG
1 ATTTAATGGTTAGGGATATGTTTTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATG
* * *
3355475 ATTTAATGGTTAGGGATATGTTTTATGTTTTATTTTAATGATAAGGTAA-AAGTCCAATTTAAAT
1 ATTTAATGGTTAGGGATATGTTTTATGTTTTATGTTAATGATAAGTTAAGAA-TCCAATCTAAAT
3355539 G
65 G
*
3355540 A-TTAAGTGGTTAGGG----G---TATGTTTTATGTTAATGATAAGATAAGAATCCAATCTAAAT
1 ATTTAA-TGGTTAGGGATATGTTTTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAAT
3355597 G
65 G
* * * * *
3355598 ATTCAGTGGTTAGGGCTATG--TT-TG----GTGTTAATGATAAGATAAGAATCCAATCTAAATG
1 ATTTAATGGTTAGGGATATGTTTTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATG
* * * *
3355656 ATTCAGTGGTTAGGGGTATTTTTT
1 ATTTAATGGTTAGGGATATGTTTT
3355680 TAATTAACAC
Statistics
Matches: 279, Mismatches: 31, Indels: 41
0.79 0.09 0.12
Matches are distributed among these distances:
58 139 0.50
59 9 0.03
60 2 0.01
61 4 0.01
62 6 0.02
63 1 0.00
64 11 0.04
65 107 0.38
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.42
Consensus pattern (65 bp):
ATTTAATGGTTAGGGATATGTTTTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATG
Found at i:3355513 original size:123 final size:123
Alignment explanation
Indices: 3355309--3355667 Score: 462
Period size: 123 Copynumber: 3.0 Consensus size: 123
3355299 GGGGTATGTT
* * * *
3355309 TTATGTTTTATCTTACTGATAAGTTAAGAATCTAATCCAAATGATTTAATGGTTAGGGATATGTT
1 TTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATGATTTAATGGTTAGGGATATGTT
* * * *
3355374 TTGTGTTTTATTTTAATGATAAGTTAAAAATCCAATCTAAATGATTTAGTTGTTAAGG
66 TTATGTTTTATTTTAATGATAAGGTAAAAATCCAATCTAAATGATTAAGTGGTTAAGG
* *
3355432 TTATATTTTATGTTAATAATAAGTTAAGAATCCAATCTAAATGATTTAATGGTTAGGGATATGTT
1 TTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATGATTTAATGGTTAGGGATATGTT
* * *
3355497 TTATGTTTTATTTTAATGATAAGGTAAAAGTCCAATTTAAATGATTAAGTGGTTAGGG
66 TTATGTTTTATTTTAATGATAAGGTAAAAATCCAATCTAAATGATTAAGTGGTTAAGG
* * * * *
3355555 GTATGTTTTATGTTAATGATAAGATAAGAATCCAATCTAAATGATTCAGTGGTTAGGGCTATG--
1 TTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATGATTTAATGGTTAGGGATATGTT
* * * * *
3355618 TT-TG----GTGTTAATGATAAGATAAGAATCCAATCTAAATGATTCAGTGGTTA
66 TTATGTTTTATTTTAATGATAAGGTAAAAATCCAATCTAAATGATTAAGTGGTTA
3355668 GGGGTATTTT
Statistics
Matches: 209, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
116 39 0.19
120 2 0.01
121 2 0.01
123 166 0.79
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (123 bp):
TTATGTTTTATGTTAATGATAAGTTAAGAATCCAATCTAAATGATTTAATGGTTAGGGATATGTT
TTATGTTTTATTTTAATGATAAGGTAAAAATCCAATCTAAATGATTAAGTGGTTAAGG
Found at i:3357299 original size:21 final size:22
Alignment explanation
Indices: 3357270--3357316 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
3357260 TAGGTTGGTC
3357270 TTAGAATTTA-GTGTTTAAA-GT
1 TTAGAATTTATGT-TTTAAAGGT
*
3357291 TTAGGATTTATGTTTTAAAGGT
1 TTAGAATTTATGTTTTAAAGGT
3357313 TTAG
1 TTAG
3357317 TGGTTATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (22 bp):
TTAGAATTTATGTTTTAAAGGT
Found at i:3357594 original size:2 final size:2
Alignment explanation
Indices: 3357587--3357614 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3357577 CCAATTTTTG
3357587 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
3357615 CTTTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3359796 original size:19 final size:19
Alignment explanation
Indices: 3359772--3359808 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3359762 GCATTACTCC
3359772 TAAAATATTTTAATTAGGT
1 TAAAATATTTTAATTAGGT
*
3359791 TAAAATATTTTAGTTAGG
1 TAAAATATTTTAATTAGG
3359809 GAATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (19 bp):
TAAAATATTTTAATTAGGT
Found at i:3362094 original size:20 final size:20
Alignment explanation
Indices: 3362058--3362096 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3362048 AACAACACAT
*
3362058 TTTGCATTTGTATTTGCATC
1 TTTGCATTTGTAATTGCATC
3362078 TTTGCATTATG-AATTGCAT
1 TTTGCATT-TGTAATTGCAT
3362097 ATTTTTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (20 bp):
TTTGCATTTGTAATTGCATC
Found at i:3366128 original size:55 final size:55
Alignment explanation
Indices: 3366056--3366775 Score: 758
Period size: 55 Copynumber: 13.0 Consensus size: 55
3366046 ACATGGTATG
* *
3366056 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * * * *
3366111 TTTTCAAATGAGTTTTTAAAGAAATTAAATCTGATTTTCGGAAATTTCTTGATTA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * * *
3366166 TTTTTAAAAGAGTTTTCAAAGAAACTAAG-CAAGATTTTCATAAGTTTCTTGATTA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGATGA
* * **
3366221 TTTTTAAATGAGTTTTTAAAGAAACTAAATCTAATTTGT-AGAAGTTTCTTGACAA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTT-TCAGAAGTTTCTTGATGA
* * * ** *
3366276 TTTTCAAATGAATTTTTAAAGGAACTAAGTCTGATTTTTTGAAAGTTTCTTGATTA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAG-AAGTTTCTTGATGA
* * *
3366332 TTTTTAAATGAGCTTTTAAAGAAACTAAATCTGATTTTCAGAAGTTTCTTGATTA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * *
3366387 TTTTTAAATAAGCTTTCAAAGAAACTATGT-TAGATTTTCAGAAGTTTCTTGATGA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCT-GATTTTCAGAAGTTTCTTGATGA
* * *
3366442 -TTTTAAATGAGTTTTTAAAGAAACGAAGTCTAATTTTCAGAAGTTTCTTGACGA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
*
3366496 TTTTCAAATGAGTTTTTAAAGAAACTAAGTCT-AGTTTTCAGAAGTTTCTTGATGA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGA-TTTTCAGAAGTTTCTTGATGA
*
3366551 TTTTCAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * * * ** *
3366606 TTTTTAAATGAGCTTTCAAAGAAATTAAGTATGATTTTCTGGGGGTTT-TTTATGA
1 TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTC-AGAAGTTTCTTGATGA
* * * * * *
3366661 CTATTTCAAATGAATTTTTAAAGAAGCTAAG-CATAATTTTTAGAGGTTTCTTGATGA
1 -T-TTTTAAATGAGTTTTTAAAGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGATGA
* ** *
3366718 TAATTGTAAACAAAAGTTTTT-AAGAAACTAAG-CTTGATTTTCA-AGGGTTTCTTGATGA
1 T--TT-TTAA-ATGAGTTTTTAAAGAAACTAAGTC-TGATTTTCAGA-AGTTTCTTGATGA
3366776 GTAAGTCCTT
Statistics
Matches: 562, Mismatches: 84, Indels: 35
0.83 0.12 0.05
Matches are distributed among these distances:
54 49 0.09
55 372 0.66
56 62 0.11
57 38 0.07
58 34 0.06
59 7 0.01
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (55 bp):
TTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
Found at i:3366840 original size:42 final size:42
Alignment explanation
Indices: 3366791--3366917 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 42
3366781 TCCTTTAGGC
*
3366791 CATCAGTAAGTCTTTCGAGCATGCTGCTTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
* * * **
3366833 CATCAGTATGTTTTTTGAGCATGATGCTTAAATCCTTCAAGT
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
* * * *
3366875 CACCTA-TAAGTGTTTCGAGCAAGATG---AAATCCTTCGGGC
1 CATC-AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
3366914 CATC
1 CATC
3366918 TATAAGACCT
Statistics
Matches: 69, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
39 13 0.19
42 55 0.80
43 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
Found at i:3367279 original size:20 final size:20
Alignment explanation
Indices: 3367254--3367307 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3367244 TCTTACTTAT
* *
3367254 TAAGTCATTCGGGCCATCAG
1 TAAGTCTTTCGAGCCATCAG
3367274 TAAGTCTTTCGAGCCATCAG
1 TAAGTCTTTCGAGCCATCAG
3367294 TAAGTCTTTCGAGC
1 TAAGTCTTTCGAGC
3367308 ATGATGCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (20 bp):
TAAGTCTTTCGAGCCATCAG
Found at i:3367348 original size:20 final size:20
Alignment explanation
Indices: 3367274--3367348 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
3367264 GGGCCATCAG
*
3367274 TAAGTCTTTCGAGCCATC-A
1 TAAGTCTTTCGAGTCATCTA
*
3367293 GTAAGTCTTTCGAGCATGATGCT-
1 -TAAGTCTTTCGAG--TCAT-CTA
*
3367316 TAAATGC-TTCGAGTCATCTA
1 TAAGT-CTTTCGAGTCATCTA
3367336 TAAGTCTTTCGAG
1 TAAGTCTTTCGAG
3367349 CAAGATGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
19 3 0.07
20 26 0.60
22 12 0.28
23 2 0.05
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (20 bp):
TAAGTCTTTCGAGTCATCTA
Found at i:3367440 original size:260 final size:262
Alignment explanation
Indices: 3367069--3367548 Score: 707
Period size: 261 Copynumber: 1.8 Consensus size: 262
3367059 TCCTTTGGAC
** * *
3367069 CATCTATAAGTCTTTCGAGCAAGATGATAAGTACTTCGGCTTGTCCATAAGACTTTTAGGCATGA
1 CATCTATAAGTCTTTCGAGCAAGATGATAAGTACTTCGGCTCATCCATAAGACTTTTAGGAAAGA
* * * *
3367134 TGTTTTCACACAATTTTTGAAAAATGAGAAAGCGATTTCGAAAGTTTATCGTTTAAATCTTTTCT
66 TGTTATCACACAATTTTGGAAAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAAATCTTTTCT
* * * * *
3367199 GAAATTTTA-TTTTTCTTGAAAAGTGAGAAAATGATTTCCAAAGTTTCTTACTTATTAAGTCATT
131 GAAAATTGATTTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCATT
*
3367263 CGGGCCATCAGTAAGTCTTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATGCTTCGA
196 CGAGCCATCAGTAAGTCTTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATGCTTCGA
3367328 GT
261 GT
*
3367330 CATCTATAAGTCTTTCGAGCAAGATGATAAGT-CATTCGGC-CATCCATAAGA-TCTTTGGGAAA
1 CATCTATAAGTCTTTCGAGCAAGATGATAAGTAC-TTCGGCTCATCCATAAGACT-TTTAGGAAA
** * *
3367392 GATGTTATCACATGATTTTGGAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTT
64 GATGTTATCACACAATTTTGGAAAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAAATCTTTT
* *
3367457 CTGAAAATTGATTTTTTCTTGAAAAGTAAGAAAACGATTTCCAATGTTTCTTACTTAGTAAGTCC
129 CTGAAAATTGATTTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCA
* *
3367522 TTCGAGCCGTCAGTAAGTCTTTTGAGC
194 TTCGAGCCATCAGTAAGTCTTTCGAGC
3367549 ATGATGCCCA
Statistics
Matches: 193, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
259 1 0.01
260 82 0.42
261 110 0.57
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (262 bp):
CATCTATAAGTCTTTCGAGCAAGATGATAAGTACTTCGGCTCATCCATAAGACTTTTAGGAAAGA
TGTTATCACACAATTTTGGAAAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAAATCTTTTCT
GAAAATTGATTTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCATT
CGAGCCATCAGTAAGTCTTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATGCTTCGA
GT
Found at i:3369423 original size:3 final size:3
Alignment explanation
Indices: 3369376--3369404 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3369366 ATTTATTTAT
3369376 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3369405 TAATTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3369809 original size:13 final size:14
Alignment explanation
Indices: 3369786--3369838 Score: 90
Period size: 14 Copynumber: 3.9 Consensus size: 14
3369776 TTTTCTGTCT
3369786 TTCATTTTTTTCCC
1 TTCATTTTTTTCCC
*
3369800 TTCATTTTTTTCCA
1 TTCATTTTTTTCCC
3369814 TTCA-TTTTTTCCC
1 TTCATTTTTTTCCC
3369827 TTCATTTTTTTC
1 TTCATTTTTTTC
3369839 AGTACTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.33
14 24 0.67
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCATTTTTTTCCC
Found at i:3369829 original size:27 final size:28
Alignment explanation
Indices: 3369786--3369838 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
3369776 TTTTCTGTCT
3369786 TTCATTTTTTTCCCTTCATTTTTTTCCA
1 TTCATTTTTTTCCCTTCATTTTTTTCCA
3369814 TTCA-TTTTTTCCCTTCATTTTTTTC
1 TTCATTTTTTTCCCTTCATTTTTTTC
3369839 AGTACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (28 bp):
TTCATTTTTTTCCCTTCATTTTTTTCCA
Found at i:3369909 original size:2 final size:2
Alignment explanation
Indices: 3369902--3369926 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3369892 TTTTAGTCCC
3369902 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3369927 CATGCATGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3373659 original size:9 final size:10
Alignment explanation
Indices: 3373645--3373714 Score: 63
Period size: 10 Copynumber: 6.9 Consensus size: 10
3373635 AAAACATAAA
3373645 AGAAAAG-AG
1 AGAAAAGAAG
3373654 AGAAAAGAAG
1 AGAAAAGAAG
*
3373664 AGAAAGAAAAG
1 AGAAA-AGAAG
3373675 AGTGAAAAGAAG
1 A--GAAAAGAAG
*
3373687 AG-AAAGAAA
1 AGAAAAGAAG
* *
3373696 AGAAAAAAAA
1 AGAAAAGAAG
3373706 AGAAAAGAA
1 AGAAAAGAA
3373715 AAAAGGAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 15 0.29
10 22 0.43
11 5 0.10
12 5 0.10
13 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (10 bp):
AGAAAAGAAG
Found at i:3373673 original size:23 final size:23
Alignment explanation
Indices: 3373643--3373724 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
3373633 GAAAAACATA
3373643 AAAGAAAAGAGAGAAAAGAAGAG
1 AAAGAAAAGAGAGAAAAGAAGAG
*
3373666 AAAGAAAAGAGTGAAAAGAAGAG
1 AAAGAAAAGAGAGAAAAGAAGAG
*
3373689 AAAGAAAAGA-A-AAAAAAAGA-
1 AAAGAAAAGAGAGAAAAGAAGAG
*
3373709 AAAGAAAAAAG-GAAAA
1 AAAGAAAAGAGAGAAAA
3373725 AATACTTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.17
21 12 0.23
23 32 0.60
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.01
Consensus pattern (23 bp):
AAAGAAAAGAGAGAAAAGAAGAG
Found at i:3373717 original size:14 final size:14
Alignment explanation
Indices: 3373642--3373718 Score: 64
Period size: 14 Copynumber: 5.1 Consensus size: 14
3373632 AGAAAAACAT
3373642 AAAAGAAAAGAGAGAA
1 AAAAGAAAAGA-A-AA
3373658 AAGAAGAGAAAGAAAA
1 AA-AAGA-AAAGAAAA
* ** *
3373674 GAGTGAAAAGAAGA
1 AAAAGAAAAGAAAA
*
3373688 GAAAGAAAAGAAAAA
1 AAAAGAAAAG-AAAA
3373703 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
3373717 AA
1 AA
3373719 GGAAAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
14 21 0.42
15 14 0.28
16 5 0.10
17 5 0.10
18 5 0.10
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.01
Consensus pattern (14 bp):
AAAAGAAAAGAAAA
Found at i:3373726 original size:15 final size:15
Alignment explanation
Indices: 3373622--3373718 Score: 63
Period size: 15 Copynumber: 6.1 Consensus size: 15
3373612 GATATATAAC
3373622 AAAAAGAAGAAGAAAAA
1 AAAAAGAA-AAG-AAAA
3373639 CATAAAAGAAAAGAGAGAA
1 -A-AAAAGAAAAGA-A-AA
*
3373658 AAGAAGAGAAAG-AAA
1 AAAAAGA-AAAGAAAA
* ** *
3373673 AGAGTGAAAAG-AAG
1 AAAAAGAAAAGAAAA
*
3373687 AGAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
3373702 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
3373717 AA
1 AA
3373719 GGAAAAAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 15 0.23
15 23 0.36
16 1 0.02
17 6 0.09
18 10 0.16
19 9 0.14
ACGTcount: A:0.75, C:0.01, G:0.22, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:3374495 original size:28 final size:28
Alignment explanation
Indices: 3374463--3374561 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
3374453 AACCCAGAAT
*
3374463 ACATTGCCTCCCCAAATTAACCTGAAAC
1 ACATTACCTCCCCAAATTAACCTGAAAC
**
3374491 ACATTAATTCCCCAAATTAACCTGAAAC
1 ACATTACCTCCCCAAATTAACCTGAAAC
*
3374519 ACATTACTTCCCCAAATTAACCTGAAAC
1 ACATTACCTCCCCAAATTAACCTGAAAC
* *
3374547 ACATTTCCTTCCCAA
1 ACATTACCTCCCCAA
3374562 GTTAGCATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.25
Consensus pattern (28 bp):
ACATTACCTCCCCAAATTAACCTGAAAC
Found at i:3376161 original size:12 final size:12
Alignment explanation
Indices: 3376144--3376174 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3376134 TTTTTTTTCA
3376144 AAAAAAAAAGGC
1 AAAAAAAAAGGC
3376156 AAAAAAAAAGGC
1 AAAAAAAAAGGC
3376168 AAAAAAA
1 AAAAAAA
3376175 CAAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGGC
Found at i:3376179 original size:19 final size:20
Alignment explanation
Indices: 3376155--3376194 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3376145 AAAAAAAAGG
* *
3376155 CAAAAAAAAAGGCAAAAAAA
1 CAAAAAAAGAGCCAAAAAAA
3376175 CAAAAAAAGAGCCAAAAAAA
1 CAAAAAAAGAGCCAAAAAAA
3376195 AGCCAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (20 bp):
CAAAAAAAGAGCCAAAAAAA
Found at i:3376190 original size:12 final size:11
Alignment explanation
Indices: 3376145--3376202 Score: 59
Period size: 12 Copynumber: 5.4 Consensus size: 11
3376135 TTTTTTTCAA
*
3376145 AAAAAAAAGGCA
1 AAAAAAAA-GCC
*
3376157 AAAAAAAAGGC
1 AAAAAAAAGCC
3376168 -AAAAAAA--C
1 AAAAAAAAGCC
3376176 AAAAAAAGAGCC
1 AAAAAAA-AGCC
3376188 AAAAAAAAGCC
1 AAAAAAAAGCC
3376199 AAAA
1 AAAA
3376203 TTTCAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 1 0.03
9 6 0.15
10 8 0.20
11 9 0.22
12 16 0.40
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGCC
Found at i:3381642 original size:55 final size:55
Alignment explanation
Indices: 3381550--3382271 Score: 669
Period size: 55 Copynumber: 13.2 Consensus size: 55
3381540 GACATGGTAT
* * * * *
3381550 TTTTTAAATGAGCTTTTAAATAAAATAAGTCTAATTTTCAAAAGTTTCTTGACGA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * * *
3381605 TTTTCAAATGAGTTTTTAAAGAAACTAAATCTGATTTTTCTGAAGTTTCTTGATTA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGA-TTTTCAGAAGTTTCTTGATGA
* ** * * *
3381661 TTTATAAATGAGCTTCCAAAGAAACTAAGTCTGATTTTTAAAAGTTTCTTAATGA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * * *
3381716 TTTTTAAGTGAGTTTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCATGACGA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * ** *
3381771 TTTTCAAATGAGCTTTTAAAGGAACTAAGTCTGATTTTTGGAAGTTTCTTGATTA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * *
3381826 TTTTTAAATGAACTTTTAAAGAAACTAAATAC-GATTTTCGGAAGTTTCTTGATTA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGT-CTGATTTTCAGAAGTTTCTTGATGA
* * *
3381881 TTTTTAAATGAGCTTTCAAAGAATCTAAGTCTGATTTTTAGAAGTTTCTTGATG-
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * *
3381935 GTTTTAAATGAGTTTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGA-CA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * *
3381989 TTTTCAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCATAAGTTTCTTGATGA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * * **
3382044 TTTTTAAATGAGCTTTCAAAGAAATTATGTTTGATTTTCAGGGGTTTCTTGATGA
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
** * * * * * **
3382099 TTATTTCAAATGAATTTTTGAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG-
1 TT-TTT-AAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
* * * * * * *
3382155 TTTTCAAATGA-ATTTGAAAGAAGCTAAG-CATAAATTTT-AG-GGATTTCTTTATG-
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTC-T-GATTTTCAGAAG-TTTCTTGATGA
* * * *
3382208 TTTTCAAATGAG-TTTGAAAGAAGCTAAG-CTTGATTTTCA-AGGGTTTCTTGATG-
1 TTTTTAAATGAGCTTTTAAAGAAACTAAGTC-TGATTTTCAGA-AGTTTCTTGATGA
*
3382261 TTTTCAAATGA
1 TTTTTAAATGA
3382272 ATTTGAAAAA
Statistics
Matches: 563, Mismatches: 90, Indels: 30
0.82 0.13 0.04
Matches are distributed among these distances:
52 8 0.01
53 76 0.13
54 109 0.19
55 281 0.50
56 51 0.09
57 38 0.07
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (55 bp):
TTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA
Found at i:3381963 original size:54 final size:55
Alignment explanation
Indices: 3381516--3382368 Score: 622
Period size: 55 Copynumber: 15.5 Consensus size: 55
3381506 TTTAGGAACA
* * * * * *
3381516 AAGTTTGATTTTTAGAGGTTTCTTGACATGGTATTTTTTAAATGAGCTTTTAAATAAAAT
1 AAGTCTGATTTTTAGAAGTTTCTTG--ATGG---TTTTCAAATGAGTTTTTAAAGAAACT
* * * * *
3381576 AAGTCTAATTTTCAAAAGTTTCTTGACGATTTTCAAATGAGTTTTTAAAGAAACT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* * ** * **
3381631 AAATCTGATTTTTCTGAAGTTTCTTGATTATTTAT-AAATGAGCTTCCAAAGAAACT
1 AAGTCTGATTTTT-AGAAGTTTCTTGATGGTTT-TCAAATGAGTTTTTAAAGAAACT
* * * * *
3381687 AAGTCTGATTTTTAAAAGTTTCTTAATGATTTTTAAGTGAGTTTTTAAAGAAACT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* * * * *
3381742 AAGTCTGATTTTTAGAAGTTTCATGACGATTTTCAAATGAGCTTTTAAAGGAACT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* ** * **
3381797 AAGTCTGATTTTTGGAAGTTTCTTGATTATTTTTAAATGAACTTTTAAAGAAACT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* ** ** * * * *
3381852 AAATAC-GATTTTCGGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAATCT
1 AAGT-CTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
3381907 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTT-AAATGAGTTTTTAAAGAAACT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* * **
3381961 AAGTTTGATTTTCAGAAGTTTCTTGA-CATTTTCAAATGAGTTTTTAAAGAAACT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* * * * * * *
3382015 AAGTCTGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* * * ** * * * *
3382070 ATGTTTGATTTTCAGGGGTTTCTTGATGATTATTTCAAATGAATTTTTGAAGAAGCT
1 AAGTCTGATTTTTAGAAGTTTCTTGATG-GT-TTTCAAATGAGTTTTTAAAGAAACT
* * ** * * *
3382127 AAGCCTAATTTTTAGGGGTTTCTTGAT-GTTTTCAAATGA-ATTTGAAAGAAGCT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* * * * * *
3382180 AAG-CATAAATTTTAG-GGATTTCTTTAT-GTTTTCAAATGAG-TTTGAAAGAAGCT
1 AAGTC-TGATTTTTAGAAG-TTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* * * ** *
3382233 AAG-CTTGATTTTCA-AGGGTTTCTTGAT-GTTTTCAAATGAATTTGAAAAAAAACT
1 AAGTC-TGATTTTTAGA-AGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
* * * * * * *
3382287 AAGCCTAATTTTTTG-GGTTTTATTGAT-GTTTTCAAATGAAGTTTTTAAA-ATATT
1 AAGTCTGATTTTTAGAAG-TTTCTTGATGGTTTTCAAATG-AGTTTTTAAAGAAACT
* * *
3382341 AAGCCTAATTTTTAGGAGTTTCTTGATG
1 AAGTCTGATTTTTAGAAGTTTCTTGATG
3382369 ATATCTGTAA
Statistics
Matches: 657, Mismatches: 115, Indels: 47
0.80 0.14 0.06
Matches are distributed among these distances:
52 3 0.00
53 92 0.14
54 163 0.25
55 289 0.44
56 47 0.07
57 41 0.06
58 2 0.00
60 20 0.03
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.43
Consensus pattern (55 bp):
AAGTCTGATTTTTAGAAGTTTCTTGATGGTTTTCAAATGAGTTTTTAAAGAAACT
Done.