Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 23 of 29
Found at i:3613744 original size:143 final size:144
Alignment explanation
Indices: 3613563--3613822 Score: 325
Period size: 143 Copynumber: 1.8 Consensus size: 144
3613553 ATTAGGTCAT
*
3613563 TTTTATGCCAAAGGTGTGTATTTATGATAGGTTCATC-TTTTACTTATC-TTTTCATATCTTTTA
1 TTTTATGCCAAAGGTATGTATTTATGATAGGTTCATCTTTTTA--TATCATTTTCATATCTTTTA
** * * *
3613626 GGGTTACCGTGATACTTTTACATTGAAAGTATAC-CTAGAAGCATTTTGGTAATTTCTTAGAACC
64 GGGTTACCGAAATACTTTCACATCGAAAGAATACTCTAGAAGCATTTTGGTAATTTCTTAGAACC
3613690 AAGTCACTGAGTCAGG
129 AAGTCACTGAGTCAGG
* *
3613706 TTTTATGCCAAAGGTATGCT-TTTGA-GATAGG-TCTATCTTTTTATATCATTTTCGTGTCTTTT
1 TTTTATGCCAAAGGTATG-TATTT-ATGATAGGTTC-ATCTTTTTATATCATTTTCATATCTTTT
* * **
3613768 AGGGTTACCGAAATACTTTCACGTCGAAAGAATACTTTAGGGGCATTTTGGTAAT
63 AGGGTTACCGAAATACTTTCACATCGAAAGAATACTCTAGAAGCATTTTGGTAAT
3613823 CTGAGTCCTA
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
142 6 0.06
143 70 0.71
144 23 0.23
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (144 bp):
TTTTATGCCAAAGGTATGTATTTATGATAGGTTCATCTTTTTATATCATTTTCATATCTTTTAGG
GTTACCGAAATACTTTCACATCGAAAGAATACTCTAGAAGCATTTTGGTAATTTCTTAGAACCAA
GTCACTGAGTCAGG
Found at i:3615688 original size:27 final size:28
Alignment explanation
Indices: 3615650--3615703 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
3615640 TTTAAAAATG
3615650 GGGTTGGAGTATCTCCTAA-G-AAGAATA
1 GGGTTGGAGTATC-CCTAATGAAAGAATA
3615677 GGGTTGGAGTATCCCTAATGAAAGAAT
1 GGGTTGGAGTATCCCTAATGAAAGAAT
3615704 TTTGACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.20
27 14 0.56
28 6 0.24
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (28 bp):
GGGTTGGAGTATCCCTAATGAAAGAATA
Found at i:3619835 original size:6 final size:6
Alignment explanation
Indices: 3619824--3619860 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
3619814 TTATGATTAC
3619824 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T
3619861 CTTTTAGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:3625200 original size:159 final size:159
Alignment explanation
Indices: 3624922--3625314 Score: 465
Period size: 158 Copynumber: 2.4 Consensus size: 159
3624912 ATTAAACATC
* * * *
3624922 AAAATTCTTTAAATATTATCATCT-AATCACATTAAATTAGTTTTGAAAAAAATTCATTCATTTT
1 AAAATTCATCAAATATTATCATTTGATTCACATTAAATTAGTTTT-AAAAAAATTCATTCA--TT
* *
3624986 TATGAGTTTTTCATTTTTCCTTAAAATTCCTTATGTTTTTAAAATACAAAATTTTCTTCTTCGTA
63 T-TCA---TTTCATTTTTCCTTAAAATTCCTTA-GTTTTTAAAATACAAAATTTTCTTCTCCGT-
* * *
3625051 AATT-TTTTTGAGAAGATTTTTATCAATTTTAAATTTTT
122 AATTAGTTTTGAGAAGA-TTTCATCAATTTAAAATTTTT
3625089 AAAATTCATCAAATATTATCATTTGATTCACATTAAATTA-TTTTAAAAAAATTCATTCATTTTC
1 AAAATTCATCAAATATTATCATTTGATTCACATTAAATTAGTTTTAAAAAAATTCATTCATTTTC
* * *
3625153 A-TTCATTTTTCCTTATAATTTCTCTTA-TTTTTAAAATATAAAGTTTTCTTCTCCGTAATTAGT
66 ATTTCATTTTTCCTTA-AAATTC-CTTAGTTTTTAAAATACAAAATTTTCTTCTCCGTAATTAGT
* * *
3625216 TTTGGGAGGATTTCATCGATTTAAAATTTTT
129 TTTGAGAAGATTTCATCAATTTAAAATTTTT
* * * *
3625247 AAAATTTATCAAATATTATTATTTGATTCACATTAAATTAGTTTT-GAAAAATTCATTCATTTTT
1 AAAATTCATCAAATATTATCATTTGATTCACATTAAATTAGTTTTAAAAAAATTCATTCATTTTC
3625311 ATTT
66 ATTT
3625315 TTATTTAAAA
Statistics
Matches: 201, Mismatches: 19, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
158 78 0.39
159 55 0.27
160 5 0.02
161 4 0.02
163 2 0.01
164 3 0.01
166 15 0.07
167 25 0.12
168 14 0.07
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (159 bp):
AAAATTCATCAAATATTATCATTTGATTCACATTAAATTAGTTTTAAAAAAATTCATTCATTTTC
ATTTCATTTTTCCTTAAAATTCCTTAGTTTTTAAAATACAAAATTTTCTTCTCCGTAATTAGTTT
TGAGAAGATTTCATCAATTTAAAATTTTT
Found at i:3629858 original size:21 final size:20
Alignment explanation
Indices: 3629834--3629892 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
3629824 TTTATTAGTT
*
3629834 AACTCATTATTTTCATCTTGC
1 AACTCATTATTTTC-TCTTCC
* *
3629855 AACTCATTTCTTTTCTTTTCC
1 AACTCA-TTATTTTCTCTTCC
3629876 AACTCATTCATTTTCTC
1 AACTCATT-ATTTTCTC
3629893 CTCTAGTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 2 0.06
21 22 0.71
22 7 0.23
ACGTcount: A:0.20, C:0.27, G:0.02, T:0.51
Consensus pattern (20 bp):
AACTCATTATTTTCTCTTCC
Found at i:3632221 original size:70 final size:70
Alignment explanation
Indices: 3632108--3632247 Score: 255
Period size: 70 Copynumber: 2.0 Consensus size: 70
3632098 GTAAGGTGTT
*
3632108 CGGGATGCAAAAAGTATGGAAAAATCACATTTTTGTCTAGATGTATCGATACATTCAAGAAGTGT
1 CGGGATGCAAAAAGTATGGAAAAATCACATTTTTATCTAGATGTATCGATACATTCAAGAAGTGT
3632173 ATCGA
66 ATCGA
3632178 CGGGATGCAAAAAGTAT-GAAAAAGTCACATTTTTATCTAGATGTATCGATACATTCAAGAAGTG
1 CGGGATGCAAAAAGTATGGAAAAA-TCACATTTTTATCTAGATGTATCGATACATTCAAGAAGTG
3632242 TATCGA
65 TATCGA
3632248 TACAAGGTCC
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 6 0.09
70 62 0.91
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (70 bp):
CGGGATGCAAAAAGTATGGAAAAATCACATTTTTATCTAGATGTATCGATACATTCAAGAAGTGT
ATCGA
Found at i:3632363 original size:20 final size:20
Alignment explanation
Indices: 3632338--3632412 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
3632328 TATTTACCTA
3632338 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
3632358 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
3632378 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
*
3632398 AATATATCGATACAT
1 AATGTATCGATACAT
3632413 CTAGTTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:3637397 original size:21 final size:21
Alignment explanation
Indices: 3637350--3637407 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3637340 AAAAATTATC
*
3637350 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
3637371 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
3637392 CAAATGTATCGATACA
1 CAAATGTATCGATACA
3637408 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:3637467 original size:19 final size:19
Alignment explanation
Indices: 3637443--3637510 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
3637433 AATTCAACAA
3637443 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3637462 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
3637477 --TGTTTCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3637494 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3637511 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3637568 original size:13 final size:13
Alignment explanation
Indices: 3637550--3637575 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3637540 CATTTTTTTG
3637550 TGTATCGATACAT
1 TGTATCGATACAT
3637563 TGTATCGATACAT
1 TGTATCGATACAT
3637576 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3640015 original size:79 final size:79
Alignment explanation
Indices: 3639931--3640114 Score: 314
Period size: 79 Copynumber: 2.3 Consensus size: 79
3639921 ATTAAGTTTC
* *
3639931 TCAATTTTTCACAATCGGGGATACTCCAATCCCGTTATTTCCGAGGGAATACTCAAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGAATACTCAAACCCCGATT
3639996 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* * *
3640010 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCTAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGAATACTCAAACCCCGATT
*
3640075 TTATTTCTAAAACA
66 TTATCTCTAAAACA
3640089 TCAATTTTTCATAATCGGGGATACTC
1 TCAATTTTTCATAATCGGGGATACTC
3640115 TAACTCCGAT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 99 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGAATACTCAAACCCCGATT
TTATCTCTAAAACA
Found at i:3640130 original size:51 final size:53
Alignment explanation
Indices: 3640054--3640176 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 53
3640044 TTATTTCCGA
* * * *
3640054 GGGGATACTCTAACCCCGGTTTTATTTCTAAAACAT-CAATTT-TTCATAATC
1 GGGGATACTCTAACCCCGATTTTATTTCCAAAAAATACAATTTCTTCACAATC
*
3640105 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATC
1 GGGGATACTCTAACCCCGATTTTATTTCCAAAAAATA-CAATTTCTTCACAATC
*
3640159 GGGGATACTCCAACCCCG
1 GGGGATACTCTAACCCCG
3640177 TTAATCATCG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 32 0.52
53 6 0.10
54 24 0.39
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (53 bp):
GGGGATACTCTAACCCCGATTTTATTTCCAAAAAATACAATTTCTTCACAATC
Found at i:3640190 original size:27 final size:28
Alignment explanation
Indices: 3640156--3640231 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
3640146 TTTCTTCACA
3640156 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
3640183 ATCGGGGATACTCCAACCCTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
3640211 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
3640232 GTTTTATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:3640209 original size:160 final size:159
Alignment explanation
Indices: 3640023--3640331 Score: 439
Period size: 160 Copynumber: 1.9 Consensus size: 159
3640013 ATTTTTCATA
* **
3640023 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCTAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCGCTAAAAC
* *
3640088 A-TCAATTTTT-CATAATCGGGGATACTCTAA-CTCCGATTTTATTTCCAAAAAATACCAA-TTT
66 ACT-AATTTTTCCACAATCGGGGATACTCCAATC-CCGATTTTATTTCC--AAAATACCAATTTT
3640149 -CTTCACAATCGGGGATACTCCAACCCCGTTAATC
127 CCTT--CAATCGGGGATACTCCAACCCCGTTAATC
*
3640183 ATCGGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCGCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCGCTAAAAC
* * *
3640248 ACTAATTTTTCCACAATTGGGGATACTCCAATCCCGATTTTATTTTCAAAATGCCAATTTTCCTT
66 ACTAATTTTTCCACAATCGGGGATACTCCAATCCCGATTTTATTTCCAAAATACCAATTTTCCTT
*
3640313 TAATCGGGGATACTCCAAC
131 CAATCGGGGATACTCCAAC
3640332 TCCGATTTTA
Statistics
Matches: 134, Mismatches: 10, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
159 27 0.20
160 72 0.54
161 34 0.25
162 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (159 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCGCTAAAAC
ACTAATTTTTCCACAATCGGGGATACTCCAATCCCGATTTTATTTCCAAAATACCAATTTTCCTT
CAATCGGGGATACTCCAACCCCGTTAATC
Found at i:3640307 original size:52 final size:53
Alignment explanation
Indices: 3640214--3640380 Score: 166
Period size: 52 Copynumber: 3.2 Consensus size: 53
3640204 TTATTTCCGA
* * * * * *
3640214 GGGGATACTCCAACCCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATT
1 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAATACCAATTTTTCCACAATC
* * **
3640266 GGGGATACTCCAA-TCCCGATTTTATTTTC-AAAATGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACT-CCGATTTTATTTCCAAAAATACCAATTTTTCC-ACAATC
3640318 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCCACAATC
*
3640370 GAGGATACTCC
1 GGGGATACTCC
3640381 GACCTCGTTA
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
51 6 0.06
52 71 0.76
53 12 0.13
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (53 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCCACAATC
Found at i:3640403 original size:28 final size:28
Alignment explanation
Indices: 3640367--3640443 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
3640357 ATTTTTCACA
* * * *
3640367 ATCGAGGATACTCCGACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
3640395 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*** *
3640423 CGAGGGGATACTCCAATCCCG
1 ATCGGGGATACTCCAACCCCG
3640444 ATTTTTTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:3642502 original size:49 final size:51
Alignment explanation
Indices: 3642378--3642511 Score: 202
Period size: 49 Copynumber: 2.7 Consensus size: 51
3642368 AAAATGCCTG
* *
3642378 AATGTATTGATACATTG-AGAAATGTATCGATACATCTAGGTTAAAACCCAA
1 AATGTATCGATACAATGAAG-AATGTATCGATACATCTAGGTTAAAACCCAA
* *
3642429 AATATATCGATACAATGAAGAATGTATCGATACATCTAGG-TAAAA-CCAT
1 AATGTATCGATACAATGAAGAATGTATCGATACATCTAGGTTAAAACCCAA
3642478 AATGTATCGATACAATGAAGAATGTATCGATACA
1 AATGTATCGATACAATGAAGAATGTATCGATACA
3642512 AATTGTGAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
49 36 0.47
50 5 0.06
51 34 0.44
52 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (51 bp):
AATGTATCGATACAATGAAGAATGTATCGATACATCTAGGTTAAAACCCAA
Found at i:3643172 original size:42 final size:41
Alignment explanation
Indices: 3643126--3643230 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 41
3643116 CTTGCTCTGC
* * * *
3643126 GAGGACAAAGGAAAAAGGAGAATGAAATGGGTCTTGCTCCTT
1 GAGGACAAAGGAAAAAGAAAAAGGAAA-GAGTCTTGCTCCTT
3643168 GAGGACAAAGGAAAAAAAAGAAAAAGGAAAGAGTCTTGCTCCTT
1 GAGGACAAAGG---AAAAAGAAAAAGGAAAGAGTCTTGCTCCTT
3643212 GAGGACAAAGGGAAAAAGA
1 GAGGACAAA-GGAAAAAGA
3643231 GTACGTCCTG
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
42 18 0.33
44 22 0.40
45 15 0.27
ACGTcount: A:0.47, C:0.10, G:0.30, T:0.13
Consensus pattern (41 bp):
GAGGACAAAGGAAAAAGAAAAAGGAAAGAGTCTTGCTCCTT
Found at i:3643316 original size:42 final size:41
Alignment explanation
Indices: 3643234--3643348 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 41
3643224 AAAAAGAGTA
*
3643234 CGTCCTGCTTTTCAAGGACAAAGG-GAAAAGAAAATGAAGTG
1 CGTCCTGCTTTT-AAGGACAAAGGAGAAAAGAAAATAAAGTG
*
3643275 CG-CCTTGCTCTTTAAGGACAAAGGAGAAAAGGAAATAAAGTG
1 CGTCC-TGCT-TTTAAGGACAAAGGAGAAAAGAAAATAAAGTG
* *
3643317 CGTCCTACTTTTTGAGGACAAAGGA-AAAAGAA
1 CGTCCTGC-TTTTAAGGACAAAGGAGAAAAGAA
3643349 GGAAATGAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
40 2 0.03
41 23 0.36
42 36 0.56
43 3 0.05
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (41 bp):
CGTCCTGCTTTTAAGGACAAAGGAGAAAAGAAAATAAAGTG
Found at i:3643341 original size:49 final size:44
Alignment explanation
Indices: 3643234--3643382 Score: 132
Period size: 44 Copynumber: 3.5 Consensus size: 44
3643224 AAAAAGAGTA
* ** * *
3643234 CGTCCTGCTTTTCAAGGACAAAGGGAAAAG-A--AAATGAAGTG
1 CGTCCTACTTTTTGAGGACAAAGGAAAAAGAAGGAAATGAAATG
* * * *
3643275 CG-CCTTGCTCTTTAAGGACAAAGG-AGAA-AAGGAAAT-AAAGTG
1 CGTCC-TACTTTTTGAGGACAAAGGAAAAAGAAGGAAATGAAA-TG
3643317 CGTCCTACTTTTTGAGGACAAAGGAAAAAGAAGGAAATGAAATG
1 CGTCCTACTTTTTGAGGACAAAGGAAAAAGAAGGAAATGAAATG
* *
3643361 TGTCCTGCTTTTTGAGGACAAA
1 CGTCCTACTTTTTGAGGACAAA
3643383 AAGGTGCCAC
Statistics
Matches: 89, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
40 6 0.07
41 21 0.24
42 24 0.27
43 5 0.06
44 30 0.34
45 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (44 bp):
CGTCCTACTTTTTGAGGACAAAGGAAAAAGAAGGAAATGAAATG
Found at i:3643366 original size:44 final size:42
Alignment explanation
Indices: 3643234--3643382 Score: 133
Period size: 42 Copynumber: 3.5 Consensus size: 42
3643224 AAAAAGAGTA
* ** * * *
3643234 CGTCCTGCTTTTCAAGGACAAAGG-GAAAAGAAAATGAAGTG
1 CGTCCTACTTTTTGAGGACAAAGGAAAAAAGGAAATAAAGTG
* * * *
3643275 CG-CCTTGCTCTTTAAGGACAAAGGAGAAAAGGAAATAAAGTG
1 CGTCC-TACTTTTTGAGGACAAAGGAAAAAAGGAAATAAAGTG
3643317 CGTCCTACTTTTTGAGGACAAAGGAAAAAGAAGGAAATGAAA-TG
1 CGTCCTACTTTTTGAGGACAAAGG-AAAA-AAGGAAAT-AAAGTG
* *
3643361 TGTCCTGCTTTTTGAGGACAAA
1 CGTCCTACTTTTTGAGGACAAA
3643383 AAGGTGCCAC
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
40 2 0.02
41 19 0.21
42 33 0.36
43 5 0.05
44 30 0.33
45 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (42 bp):
CGTCCTACTTTTTGAGGACAAAGGAAAAAAGGAAATAAAGTG
Found at i:3643468 original size:62 final size:61
Alignment explanation
Indices: 3643371--3643942 Score: 672
Period size: 62 Copynumber: 9.2 Consensus size: 61
3643361 TGTCCTGCTT
* * *
3643371 TTTGAGGACAAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTTTTC
1 TTTGAGGAC-TAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTTCTC
* **
3643433 TTTGAGGACTAAAGGATGCCACCAATTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTGGTC
1 TTTGAGGACTAAAGG-TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTTCTC
* * *
3643495 TTTGAGGACGAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTC
1 TTTGAGGAC-TAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTTCTC
* *
3643557 TTTGAGGACTAAAGGGTGCTACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTGCTC
1 TTTGAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTTCTC
* ** * ** * *
3643619 TTTAAGGAAAAAAAGGTGCCACCAACTCGTGCGAACTTTAAAAAGAAAAAGGCACCCCATT-T-
1 TTTGAGG-ACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA-TCC-TTCTC
* * *
3643681 TTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA--AATGTCTTGTTC
1 TTTGAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCAT-CCTT-CTC
* *
3643743 TTTGAGGACTAAAAGGTGCCACCAACTCGTGTCGGCTTTGAAAAAGAAAAAGGCGT-CTTGCTC
1 TTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTG-AAAAGAAAAAGGCATCCTT-CTC
* * * * *
3643806 TTTGAGGACTTAAGGGTGCCAACAACTCTTGTAGGCTTTGTAAAGAAAAAGGCA-CCTTGCTC
1 TTTGAGGAC-TAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTT-CTC
3643868 TTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCAT-CTTGCTC
1 TTTGAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTT-CTC
*
3643930 TTTAAGGACTAAA
1 TTTGAGGACTAAA
3643943 AGGCTAAAAA
Statistics
Matches: 441, Mismatches: 50, Indels: 38
0.83 0.09 0.07
Matches are distributed among these distances:
59 2 0.00
60 2 0.00
61 16 0.04
62 353 0.80
63 65 0.15
64 2 0.00
65 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (61 bp):
TTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTTCTC
Found at i:3643514 original size:124 final size:124
Alignment explanation
Indices: 3643363--3643942 Score: 765
Period size: 124 Copynumber: 4.7 Consensus size: 124
3643353 ATGAAATGTG
* *
3643363 TCCTGCTTTTTGAGGACAAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCC
1 TCCTGCTCTTTGAGGACAAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCC
* * *
3643428 TTTTCTTTGAGGACTAAAGGATGCCACCAATTCGTGTGGGCTTTGAAAAGAAAAAGGCA
66 TTCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
* * *
3643487 TCCTGGTCTTTGAGGACGAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCC
1 TCCTGCTCTTTGAGGACAAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCC
* *
3643552 TACTCTTTGAGGACTAAAGGGTGCTACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
66 TTCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
* * * ** * *
3643611 TCCTGCTCTTTAAGGAAAAAAAGGTGCCACCAACTCGTGCGAACTTTAAAAAGAAAAAGGCACCC
1 TCCTGCTCTTTGAGGACAAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA-TC
****
3643676 CATT-T-TTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAAATG
65 C-TTCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
* * * * *
3643735 TCTTGTTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTCGGCTTTGAAAAAGAAAAAGGCGT-
1 TCCTGCTCTTTGAGGACAAAAAGGTGCCACCAACTCGTGTGGGCTTTG-AAAAGAAAAAGGCATC
* * * * *
3643799 CTTGCTCTTTGAGGACTTAAGGGTGCCAACAACTCTTGTAGGCTTTGTAAAGAAAAAGGCA
65 CTT-CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
* *
3643860 -CCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCAT-
1 TCC-TGCTCTTTGAGGACAAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATC
*
3643923 CTTGCTCTTTAAGGACTAAA
65 CTT-CTCTTTGAGGACTAAA
3643943 AGGCTAAAAA
Statistics
Matches: 395, Mismatches: 54, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
122 2 0.01
123 1 0.00
124 288 0.73
125 103 0.26
126 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (124 bp):
TCCTGCTCTTTGAGGACAAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCC
TTCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
Found at i:3644984 original size:13 final size:13
Alignment explanation
Indices: 3644966--3645001 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
3644956 TCTCACCAAG
3644966 GTTTTTTGTTTTT
1 GTTTTTTGTTTTT
*
3644979 GTTTTTTTTTTTT
1 GTTTTTTGTTTTT
3644992 GCTTTTTTGT
1 G-TTTTTTGT
3645002 AGAAGAGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (13 bp):
GTTTTTTGTTTTT
Found at i:3645280 original size:35 final size:36
Alignment explanation
Indices: 3645233--3645301 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
3645223 TATTCATTCT
* *
3645233 ATTTGTTTTTTCTCTTGT-TTTTTGATTTTTTTTCA
1 ATTTGTTTTTTCTCTTGTGTTTCTCATTTTTTTTCA
* *
3645268 ATTTTTTTTTTCTTTTGTGTTTCTCATTTTTTTT
1 ATTTGTTTTTTCTCTTGTGTTTCTCATTTTTTTT
3645302 TGCTTTTACC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 16 0.55
36 13 0.45
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (36 bp):
ATTTGTTTTTTCTCTTGTGTTTCTCATTTTTTTTCA
Found at i:3648198 original size:21 final size:19
Alignment explanation
Indices: 3648174--3648227 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
3648164 TTTCAACAAT
3648174 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAA-AGT-A
* * *
3648195 TTGTATCAATACATAAGTG
1 TTGTATCGATACAAAAGTA
3648214 TTGTATCGATACAA
1 TTGTATCGATACAA
3648228 TGTATCGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACAAAAGTA
Found at i:3648233 original size:13 final size:13
Alignment explanation
Indices: 3648215--3648239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3648205 ACATAAGTGT
3648215 TGTATCGATACAA
1 TGTATCGATACAA
3648228 TGTATCGATACA
1 TGTATCGATACA
3648240 TAAGTGGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3648239 original size:32 final size:32
Alignment explanation
Indices: 3648196--3648266 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
3648186 AAACAGTAAT
* *
3648196 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGGTGTATCGATAAAA
*
3648228 TGTATCGATACATAAGTGGTGTATCGATAAAA
1 TGTATCAATACATAAGTGGTGTATCGATAAAA
3648260 TGTATCA
1 TGTATCA
3648267 CTACGAAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCAATACATAAGTGGTGTATCGATAAAA
Found at i:3648252 original size:19 final size:18
Alignment explanation
Indices: 3648196--3648256 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
3648186 AAACAGTAAT
*
3648196 TGTATCAATACATAAGTG
1 TGTATCGATACATAAGTG
3648214 TTGTATCGATAC--AA---
1 -TGTATCGATACATAAGTG
3648228 TGTATCGATACATAAGTGG
1 TGTATCGATACATAAGT-G
3648247 TGTATCGATA
1 TGTATCGATA
3648257 AAATGTATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.31
15 2 0.06
17 2 0.06
19 20 0.57
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (18 bp):
TGTATCGATACATAAGTG
Found at i:3648387 original size:52 final size:53
Alignment explanation
Indices: 3648302--3648408 Score: 155
Period size: 52 Copynumber: 2.0 Consensus size: 53
3648292 TATCGATACA
* ** *
3648302 TTACTCAGATGTATCGATACATTGATCTTTGTATCGATACAT-CTGGGAAATT
1 TTACCCAGATGTATCGATACATTGATCAATGTATCGATACATGCAGGGAAATT
3648354 TTACCCAGATGTATCGATACATT-ATTCAATGTATCGATACATGCAGGGAAATT
1 TTACCCAGATGTATCGATACATTGA-TCAATGTATCGATACATGCAGGGAAATT
3648407 TT
1 TT
3648409 CATATTTTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
51 1 0.02
52 37 0.76
53 11 0.22
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (53 bp):
TTACCCAGATGTATCGATACATTGATCAATGTATCGATACATGCAGGGAAATT
Found at i:3656502 original size:43 final size:43
Alignment explanation
Indices: 3656425--3656526 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
3656415 CCTGCTTTGC
* *
3656425 GAGGACAAAGGA-AAAAAGAGAACGAAATGGGTCTTGCTCCTT
1 GAGGACAAAGGAGAAAAAGAAAAAGAAATGGGTCTTGCTCCTT
*
3656467 GAGGACAAAGGAGAAAAAGAAAAAAGAAA-GTGTCTTGCTCCTT
1 GAGGACAAAGGAGAAAAAG-AAAAAGAAATGGGTCTTGCTCCTT
3656510 GAGGACAAAAGGAGAAA
1 GAGGAC-AAAGGAGAAA
3656527 GAGTACGTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
42 12 0.22
43 25 0.46
44 17 0.31
ACGTcount: A:0.46, C:0.12, G:0.28, T:0.14
Consensus pattern (43 bp):
GAGGACAAAGGAGAAAAAGAAAAAGAAATGGGTCTTGCTCCTT
Found at i:3656573 original size:41 final size:42
Alignment explanation
Indices: 3656511--3656623 Score: 104
Period size: 41 Copynumber: 2.7 Consensus size: 42
3656501 TTGCTCCTTG
* * *
3656511 AGGACAAAAGGAGAAAG-AGTACGTCCTGCTCTTCGAGGATAA-
1 AGGA-AAAAGGA-AATGAAGTACGTCCTGCTCTTCAAGGACAAT
* * *
3656553 AGGAAAAAGGAAATGAAGTACGCCCTACTCTTTAAGGACAAT
1 AGGAAAAAGGAAATGAAGTACGTCCTGCTCTTCAAGGACAAT
* * * *
3656595 GGGGAAAAGGAAATTAAATACGTCCTGCT
1 AGGAAAAAGGAAATGAAGTACGTCCTGCT
3656624 TTTTGAGAAC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.05
41 27 0.47
42 27 0.47
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.19
Consensus pattern (42 bp):
AGGAAAAAGGAAATGAAGTACGTCCTGCTCTTCAAGGACAAT
Found at i:3658382 original size:164 final size:165
Alignment explanation
Indices: 3658060--3658442 Score: 522
Period size: 164 Copynumber: 2.3 Consensus size: 165
3658050 TCTATTCTGT
* *
3658060 AATTTTTTTCGAGGGGATTTTTCTGGGTTTTCAATTTTTAAAATTCATCAAATATTAACATTTAT
1 AATTTTTTT-GAGGGGATTTTTCTCGGTTTTTAATTTTTAAAATTCATCAAATATTAACATTTAT
* *
3658125 TTCATATTAATCCAGTTTTCAAAAATTCATACATTTTCATGAGTTTTTGATTTTTTTCCTTGAAA
65 TTCATATCAA--CAGTTTTCAAAAATTCATACATTTTCATCAGTTTTTGATTTTTTTCCTTGAAA
*
3658190 CTCCCCTTTTTTTGAAATACAATATTTTTTACTCCATAA
128 CTCCCATTTTTTTGAAATACAATATTTTTTACTCCAT-A
* * * *
3658229 AATTTTTTTGAGAGGATTTTTCTCGGTTTTTAATTTTTAAAATTCTTGAAATATTATCATTTATT
1 AATTTTTTTGAGGGGATTTTTCTCGGTTTTTAATTTTTAAAATTCATCAAATATTAACATTTATT
* * *
3658294 TCATA-CAA-AGTTTTGAAAACTTCA-ATCATTTTCATTCATTTTTTGA-TTTTTTCCTTGAAAC
66 TCATATCAACAGTTTTCAAAAATTCATA-CATTTTCA-TCAGTTTTTGATTTTTTTCCTTGAAAC
* ** *
3658355 TCTCATTTTTTTGAAATACGGTATTTTTTACTCCGTA
129 TCCCATTTTTTTGAAATACAATATTTTTTACTCCATA
* *
3658392 AATTTTTTGGAGGGGATTTTTCTCGATTTTTAATTTTTAAAATTCATCAAA
1 AATTTTTTTGAGGGGATTTTTCTCGGTTTTTAATTTTTAAAATTCATCAAA
3658443 GATAATTTTT
Statistics
Matches: 191, Mismatches: 21, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
163 48 0.25
164 68 0.36
165 9 0.05
167 2 0.01
168 55 0.29
169 9 0.05
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (165 bp):
AATTTTTTTGAGGGGATTTTTCTCGGTTTTTAATTTTTAAAATTCATCAAATATTAACATTTATT
TCATATCAACAGTTTTCAAAAATTCATACATTTTCATCAGTTTTTGATTTTTTTCCTTGAAACTC
CCATTTTTTTGAAATACAATATTTTTTACTCCATA
Found at i:3658676 original size:8 final size:7
Alignment explanation
Indices: 3658654--3658685 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
3658644 CAAAGATCAA
3658654 TTTATTT
1 TTTATTT
3658661 TTTATTT
1 TTTATTT
3658668 TTTATTT
1 TTTATTT
3658675 TTTGATTT
1 TTT-ATTT
3658683 TTT
1 TTT
3658686 TTACTTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:3661378 original size:156 final size:153
Alignment explanation
Indices: 3660655--3661766 Score: 801
Period size: 155 Copynumber: 7.1 Consensus size: 153
3660645 GTTACCGAGA
** * * *
3660655 TACTTTCACGTCGAAGGTATCTTTTAAGGCCATTTTCA-TAATTTTTTTCAGAACTGAGTCTTAG
1 TACTTT-ACGTCGAAGGTATC-CCTAAGGGCATTTTTAGTAA-TTTTTT-AGAACTGAGTCCTAG
* * * * *
3660719 GTTATCACCAAGTCTGCTTTTATGCCAAAGGT-GAGTATTTAGGATAGGTTTA-CCCTTTTTCTA
62 GTTGTCACTAGGTCTGCTTTTATGCCAAAGGTAGA-TATTTAGGATAGGTTCACCCCATTTTCTA
*
3660782 TCCTTTTTAAGTCCTTTAAGGGG-ATTGGG
126 TCCTTTTTAAGTCC-TT-AGGGGTATTAGG
* * *
3660811 ATACTTTCATGTCGAAGGTATCCCCT-AGCGGTATTTTT-GTAATTTTTTA-AAATCGAGTCCTA
1 -TACTTT-ACGTCGAAGGTAT-CCCTAAG-GGCATTTTTAGTAATTTTTTAGAACT-GAGTCCTA
* * * * * * * *
3660873 GTTTATCACCAGGTCCGTTTTTATGCCAAATGTGGGTATTTAGGATAGGTTCACCCC-TTTTCTA
61 GGTTGTCACTAGGTCTGCTTTTATGCCAAAGGTAGATATTTAGGATAGGTTCACCCCATTTTCTA
***
3660937 TCCTTTTTAAGTCCTTCAGGGGTACCGGG
126 TCCTTTTTAAGTCCTT-AGGGGTATTAGG
* * * * * * ** *
3660966 ATATTTTCACATTGAAGGTATCCCCTAGGGGCATTTTCATTTTTTTTTTAGAA-TCGAGTCTTAG
1 -TACTTT-ACGTCGAAGGTAT-CCCTAAGGGCATTTTTAGTAATTTTTTAGAACT-GAGTCCTAG
* * * * * * * *
3661030 GTTATCACTAGATCTGCTTTTATACCGAAGGTGGGTATTTAGGATAGGTTCA-CTCATTTTTTAA
62 GTTGTCACTAGGTCTGCTTTTATGCCAAAGGTAGATATTTAGGATAGGTTCACCCCATTTTCT-A
* * ** * * *
3661094 TCCTTTTTAAGTCTTTTACGTTTGCTGAGA
126 TCCTTTTTAAGTC-CTTAGGGGT-ATTAGG
* * ** * *
3661124 CACTTTTACGTTGAAGGTATACCCATGGGGGCATTTTCA-T-ATTTTCTTAGAACTGAGTCCTAA
1 TAC-TTTACGTCGAAGGTAT-CCC-TAAGGGCATTTTTAGTAATTTT-TTAGAACTGAGTCCTAG
* * *
3661187 GTTGTCACTGGGTCTGCTTTTATGCCAAAGATAGATATTTAGGATAGGTTCACCCCATCTGT-TA
62 GTTGTCACTAGGTCTGCTTTTATGCCAAAGGTAGATATTTAGGATAGGTTCACCCCAT-TTTCTA
*
3661251 TCCTTTTTAAGTCTCATAGGGGTATTAGG
126 TCCTTTTTAAGTC-CTTAGGGGTATTAGG
* *
3661280 TACCTTTACGTCGAAAGTATCCTCTAAGGGGATTTTTAGTAATTTTTTAGAACTGAGTCCTAGGT
1 TA-CTTTACGTCGAAGGTATCC-CTAAGGGCATTTTTAGTAATTTTTTAGAACTGAGTCCTAGGT
* * ** * * * *
3661345 TGTCACTAGGTCCGCTTATATGCTGAAGGTAGATATTTAGGATAGGATCATCCCA-TTTCAAACC
64 TGTCACTAGGTCTGCTTTTATGCCAAAGGTAGATATTTAGGATAGGTTCACCCCATTTTCTATCC
* ***
3661409 TTTTTAAGTCCTTTAGAGGTACCGGG
129 TTTTTAAGTCC-TTAGGGGTATTAGG
* * * *
3661435 TACTTGTACGTCAAAGGTATCCCTTAGGAGCATTTTT-GTAATTTTTTAGAA-TCGAGTCTTAAG
1 TACTT-TACGTCGAAGGTATCCCTAAGG-GCATTTTTAGTAATTTTTTAGAACT-GAGTCCTAGG
* * * *
3661498 TTGTCACTAGGTCTGCTTTTAAGCAAAAGGTAGATATCTAGGATAGGTTCACCCCATATGT-TAT
63 TTGTCACTAGGTCTGCTTTTATGCCAAAGGTAGATATTTAGGATAGGTTCACCCCAT-TTTCTAT
* * *
3661562 CCTTTTTAAATCTTATAAGGGTATTAGG
127 CCTTTTTAAGTCCT-TAGGGGTATTAGG
* * * * *
3661590 TACTTTTACGTCGAAGGTATCCCTTAAGTGCATTTTT-GTAATTTTTCAAAACCGAATCCTAGGT
1 TAC-TTTACGTCGAAGGTATCCC-TAAGGGCATTTTTAGTAATTTTTTAGAACTGAGTCCTAGGT
* * * * * * **
3661654 TGTCAC-CGGGCTTGCTTTTATGTCGAAGGTAGGTA-TTAGGATAGGTTCATCTTATTTT-TAAT
64 TGTCACTAGGTC-TGCTTTTATGCCAAAGGTAGATATTTAGGATAGGTTCACCCCATTTTCT-AT
* *
3661716 CTTTTTTAAGTCCTTTAGGGGTA-TCGAG
127 CCTTTTTAAGTCC-TTAGGGGTATTAG-G
*
3661744 TACTATTATGTCGAAGGTATCCC
1 TACT-TTACGTCGAAGGTATCCC
3661767 CTAGATTCGA
Statistics
Matches: 766, Mismatches: 149, Indels: 83
0.77 0.15 0.08
Matches are distributed among these distances:
153 7 0.01
154 151 0.20
155 257 0.34
156 176 0.23
157 147 0.19
158 26 0.03
159 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (153 bp):
TACTTTACGTCGAAGGTATCCCTAAGGGCATTTTTAGTAATTTTTTAGAACTGAGTCCTAGGTTG
TCACTAGGTCTGCTTTTATGCCAAAGGTAGATATTTAGGATAGGTTCACCCCATTTTCTATCCTT
TTTAAGTCCTTAGGGGTATTAGG
Found at i:3669498 original size:22 final size:21
Alignment explanation
Indices: 3669449--3669500 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3669439 ATCATGCAAG
* *
3669449 TTTTTATTTTTCTTAGCTAAT
1 TTTTTATTTTTATTAGCAAAT
**
3669470 TCATTATTTTTATTAGCCAAAT
1 TTTTTATTTTTATTAG-CAAAT
3669492 TTTTTATTT
1 TTTTTATTT
3669501 CAACTTGCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTTATTTTTATTAGCAAAT
Found at i:3675025 original size:17 final size:17
Alignment explanation
Indices: 3674987--3675019 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3674977 GGAAAGGTTG
*
3674987 TGAAAGAGAAGAAAAAA
1 TGAAAAAGAAGAAAAAA
3675004 TGAAAAAGAAGAAAAA
1 TGAAAAAGAAGAAAAA
3675020 GAGAAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (17 bp):
TGAAAAAGAAGAAAAAA
Found at i:3675516 original size:112 final size:111
Alignment explanation
Indices: 3675302--3675555 Score: 285
Period size: 112 Copynumber: 2.3 Consensus size: 111
3675292 AACTTGGAAG
* *** * *
3675302 AACATCAAATTTGTTTAATTTTAAAAGAAATTCATGTTTTATACATCTTGATCCATTTGTGCCTA
1 AACATCAAATTTG-TTGATTTTAAAAGAAATTCACAATTTATACATCTTGATCCATTCGTACCTA
* **
3675367 CGAAACTAGGCACATATCTTGTCAATTTCGATTTTTTTAAGCCCTGC
65 CGAAACTAGGCACATATCTTATCAATTTCGAAATTTTTAAGCCCTGC
* * *
3675414 AACATCAAATTTGCTTGATTTTCAAAGAAATTCACAATTTATTCATTTTGATCCATTCGTACCTA
1 AACATCAAATTTG-TTGATTTTAAAAGAAATTCACAATTTATACATCTTGATCCATTCGTACCTA
* * * * * * *
3675479 GGAAA-TAGAGCACGTATCTTATCAGTTTTGAAATTTTTGAGCCTTGT
65 CGAAACTAG-GCACATATCTTATCAATTTCGAAATTTTTAAGCCCTGC
*
3675526 AACAGCAAATTTGTTGGATTTTAAAAGAAA
1 AACATCAAATTTGTT-GATTTTAAAAGAAA
3675556 CTTATATTTC
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
111 5 0.04
112 113 0.96
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (111 bp):
AACATCAAATTTGTTGATTTTAAAAGAAATTCACAATTTATACATCTTGATCCATTCGTACCTAC
GAAACTAGGCACATATCTTATCAATTTCGAAATTTTTAAGCCCTGC
Found at i:3676045 original size:44 final size:45
Alignment explanation
Indices: 3675995--3676104 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 45
3675985 CATTGATATC
* *
3675995 TGCATTATTCCATATGCATTTGCTCTTCTATA-GATGTTT-GCATT
1 TGCATTATTCCATATGCATTTGCTCTT-TAGATGACGTTTGGCATT
* * * * *
3676039 TGCATTATTTCACATACATCTGCTCTTTAGATGACGTTTGGTATT
1 TGCATTATTCCATATGCATTTGCTCTTTAGATGACGTTTGGCATT
*
3676084 TGCATCA-TCTCATATGCATTT
1 TGCATTATTC-CATATGCATTT
3676105 TCCATTTTAC
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
43 3 0.06
44 30 0.59
45 18 0.35
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.45
Consensus pattern (45 bp):
TGCATTATTCCATATGCATTTGCTCTTTAGATGACGTTTGGCATT
Found at i:3676876 original size:35 final size:36
Alignment explanation
Indices: 3676837--3676924 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
3676827 TGTTCGACTA
3676837 TATCTGGTCAAACTCTTCCCACCACT-ATTTGATTG
1 TATCTGGTCAAACTCTTCCCACCACTCATTTGATTG
** * * *
3676872 TATCTGGTCAAACTCTTTTCATCTCTCGTTTGATTG
1 TATCTGGTCAAACTCTTCCCACCACTCATTTGATTG
* *
3676908 TACCTGGCCAAACTCTT
1 TATCTGGTCAAACTCTT
3676925 TTCTTCCCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 22 0.49
36 23 0.51
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.40
Consensus pattern (36 bp):
TATCTGGTCAAACTCTTCCCACCACTCATTTGATTG
Found at i:3676995 original size:48 final size:48
Alignment explanation
Indices: 3676916--3677028 Score: 147
Period size: 48 Copynumber: 2.4 Consensus size: 48
3676906 TGTACCTGGC
* * *
3676916 CAAACTCTTTTC-TTCCCTCATTTAACCGTATTGGTGTTAGGGCCTAGT
1 CAAACTCTTTTCATT-TCTCATTTAACCGTATTAGTGTTAAGGCCTAGT
* * * *
3676964 CAAACTCTTTTCATTTCTCGTTTGACTGTATTAGTGTTAAGGCCTTGT
1 CAAACTCTTTTCATTTCTCATTTAACCGTATTAGTGTTAAGGCCTAGT
3677012 CAAACTCTTTTCATTTC
1 CAAACTCTTTTCATTTC
3677029 GATTTGACGT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
48 55 0.96
49 2 0.04
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.43
Consensus pattern (48 bp):
CAAACTCTTTTCATTTCTCATTTAACCGTATTAGTGTTAAGGCCTAGT
Found at i:3677079 original size:44 final size:43
Alignment explanation
Indices: 3677010--3677494 Score: 337
Period size: 44 Copynumber: 11.1 Consensus size: 43
3677000 TTAAGGCCTT
*
3677010 GTCAAACTCTTTTCATT--TCGATTTGACGTATGGTTACCACCTTG
1 GTCAAA-TCTTTTCATTCAT-G-TTTGACGTATGGTTACCACCCTG
* ** *
3677054 GTCAAATCTTTCTCATTCACGTTTGACACATGGTTACCACCCTA
1 GTCAAATCTTT-TCATTCATGTTTGACGTATGGTTACCACCCTG
* * *
3677098 GTCAGATTCTTTTCATCTCA--CTT-ACGTATGGTTACCACCTTG
1 GTCA-AATCTTTTCAT-TCATGTTTGACGTATGGTTACCACCCTG
* * * * * *
3677140 GTCAGATTCTTTTCA-TCTTGCTTGACATAAGGTTACCACCTTG
1 GTCA-AATCTTTTCATTCATGTTTGACGTATGGTTACCACCCTG
* * ** *
3677183 GTCAATTTTTTTTGTTCATGTTTGACATATGGTTACCACCCTG
1 GTCAAATCTTTTCATTCATGTTTGACGTATGGTTACCACCCTG
* *
3677226 GTCAAACTTTTTTCAATTC--GATTTGACGTAT-GTTACTACCCTG
1 GTCAAA-TCTTTTC-ATTCATG-TTTGACGTATGGTTACCACCCTG
* * * * *
3677269 GTAAAATCTTCCTCATTCATGTTTGATGTATGGTTATCACCCTA
1 GTCAAATCTT-TTCATTCATGTTTGACGTATGGTTACCACCCTG
* * * * * *
3677313 GTCAAACTCTTCTCATT-TTAGTCTGATGTATGGTTACTACCTTG
1 GTCAAA-TCTTTTCATTCAT-GTTTGACGTATGGTTACCACCCTG
* * * *
3677357 GTCAGATTCTTTTCA-TCTTGCTTGATGTATGGTTACCACCCTG
1 GTCA-AATCTTTTCATTCATGTTTGACGTATGGTTACCACCCTG
* * * * *
3677400 GTCAAGTTCTTTTCATTTATGATTTGATGTTTGGTTACCACCCTA
1 GTCAA-ATCTTTTCATTCATG-TTTGACGTATGGTTACCACCCTG
* *
3677445 GTCAAATCTTCTTCCTTTC-TGTTTGACGTATGGTTACCACCCTA
1 GTCAAATCTT-TT-CATTCATGTTTGACGTATGGTTACCACCCTG
3677489 GTCAAA
1 GTCAAA
3677495 CCATTCTAAC
Statistics
Matches: 360, Mismatches: 56, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.01
42 48 0.13
43 120 0.33
44 140 0.39
45 47 0.13
46 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (43 bp):
GTCAAATCTTTTCATTCATGTTTGACGTATGGTTACCACCCTG
Found at i:3677136 original size:42 final size:43
Alignment explanation
Indices: 3677017--3677415 Score: 226
Period size: 43 Copynumber: 9.2 Consensus size: 43
3677007 CTTGTCAAAC
* * *
3677017 TCTTTTCATTTCGATTTGACGTATGGTTACCACCTTGGTCA-AA
1 TCTTTTCATCTC-ACTTGACGTATGGTTACCACCTTGGTCAGAT
** * *
3677060 TCTTTCTCAT-TCACGTTTGACACATGGTTACCACCCTAGTCAGAT
1 TCTTT-TCATCTCAC--TTGACGTATGGTTACCACCTTGGTCAGAT
3677105 TCTTTTCATCTCACTT-ACGTATGGTTACCACCTTGGTCAGAT
1 TCTTTTCATCTCACTTGACGTATGGTTACCACCTTGGTCAGAT
** * *
3677147 TCTTTTCATCTTGCTTGACATAAGGTTACCACCTTGGTCA-AT
1 TCTTTTCATCTCACTTGACGTATGGTTACCACCTTGGTCAGAT
* ** * * * *
3677189 TTTTTTTGT-TCATGTTTGACATATGGTTACCACCCTGGTCAAACT
1 TCTTTTCATCTCA--CTTGACGTATGGTTACCACCTTGGTCAGA-T
* * * * *
3677234 T-TTTTCAAT-TCGATTTGACGTAT-GTTACTACCCTGGT-AAAA
1 TCTTTTC-ATCTC-ACTTGACGTATGGTTACCACCTTGGTCAGAT
* * * * * * * *
3677275 TCTTCCTCAT-TCATGTTTGATGTATGGTTATCACCCTAGTCAAAC
1 TCTT-TTCATCTCA--CTTGACGTATGGTTACCACCTTGGTCAGAT
* * * * * *
3677320 TCTTCTCATTTTAGTCTGATGTATGGTTACTACCTTGGTCAGAT
1 TCTTTTCATCTCACT-TGACGTATGGTTACCACCTTGGTCAGAT
** * *
3677364 TCTTTTCATCTTGCTTGATGTATGGTTACCACCCTGGTCA-AGT
1 TCTTTTCATCTCACTTGACGTATGGTTACCACCTTGGTCAGA-T
3677407 TCTTTTCAT
1 TCTTTTCAT
3677416 TTATGATTTG
Statistics
Matches: 288, Mismatches: 47, Indels: 42
0.76 0.12 0.11
Matches are distributed among these distances:
41 3 0.01
42 55 0.19
43 112 0.39
44 93 0.32
45 24 0.08
46 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (43 bp):
TCTTTTCATCTCACTTGACGTATGGTTACCACCTTGGTCAGAT
Found at i:3677310 original size:87 final size:88
Alignment explanation
Indices: 3677197--3677495 Score: 286
Period size: 87 Copynumber: 3.4 Consensus size: 88
3677187 ATTTTTTTTG
* * * *
3677197 TTCATGTTTGACATATGGTTACCACCCTGGTCAAACTTTTTTCAATTCGATTTGACGTAT-GTTA
1 TTCATGTTTGACGTATGGTTACCACCCTAGTCAAACTTTTTTCAATTTGATTTGATGTATGGTTA
*
3677261 CTACCCTGGTAAAATCTTCCTCA
66 CTACCCTGGTAAAATCTTCTTCA
* * * * * *
3677284 TTCATGTTTGATGTATGGTTATCACCCTAGTCAAACTCTTCTC-ATTTTAGTCTGATGTATGGTT
1 TTCATGTTTGACGTATGGTTACCACCCTAGTCAAACTTTTTTCAATTTGA-TTTGATGTATGGTT
* * *
3677348 ACTACCTTGGTCAGATTCTT-TTCA
65 ACTACCCTGGT-AAAATCTTCTTCA
* * * * * * *
3677372 -TCTTGCTTGATGTATGGTTACCACCCTGGTC-AAGTTCTTTTCATTTATGATTTGATGTTTGGT
1 TTCATGTTTGACGTATGGTTACCACCCTAGTCAAACTT-TTTTCAATT-TGATTTGATGTATGGT
* * * *
3677435 TACCACCCTAGTCAAATCTTCTTCCT
64 TACTACCCTGGTAAAATCTTCTT-CA
3677461 TTC-TGTTTGACGTATGGTTACCACCCTAGTCAAAC
1 TTCATGTTTGACGTATGGTTACCACCCTAGTCAAAC
3677496 CATTCTAACC
Statistics
Matches: 166, Mismatches: 36, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
86 7 0.04
87 81 0.49
88 40 0.24
89 34 0.20
90 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (88 bp):
TTCATGTTTGACGTATGGTTACCACCCTAGTCAAACTTTTTTCAATTTGATTTGATGTATGGTTA
CTACCCTGGTAAAATCTTCTTCA
Found at i:3677651 original size:43 final size:43
Alignment explanation
Indices: 3677621--3678723 Score: 865
Period size: 43 Copynumber: 25.7 Consensus size: 43
3677611 CTGCATATTA
* * * *
3677621 GCTTTAACCTTGGAAACTTCTTCACCCTTAAGTCTGCCTATTG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* ** *
3677664 GCTTTGACCCTAAAGACTTCTTTACCCTTAAGTCTGCCTGTCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
** * *
3677707 GCTTTGACCTTAAAGACTTCTTCA-CTTATAAGTCTGCTTGTCG
1 GCTTTGACCTTGGAGACTTCTTCACCCT-TAAGTCTGCCTGTCG
* *
3677750 GCTTTGACCCTAGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * * * * *
3677793 GCTTTGACCCTGGAGACTTCCTCACCCATAAGTTTGCTTGTCA
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* ** * ** * *
3677836 GCTTTAACCTTAAAGACTTCCTCACTTTTAAGTTTGCCTATCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * *
3677879 GCTTTGACCCTGGAGGCTT-TCTCACCCTTAAGTCTACCTGTCG
1 GCTTTGACCTTGGAGACTTCT-TCACCCTTAAGTCTGCCTGTCG
* * * * * * * *
3677922 GCTTTAACCCTAGAGGCTT-TGTCACCCATCAGTCTGCTTGTCA
1 GCTTTGACCTTGGAGACTTCT-TCACCCTTAAGTCTGCCTGTCG
* * * * ** *
3677965 GCTTTGACCTTGGAGACTACCTCA-TCTAAAGTCTGTTTATCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * * * *
3678007 GCTTTGACCTTGAAAACTTCCTCACCCTTAAGTCTACC-GCTCA
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTG-TCG
* * * *
3678050 GCTTTGACCATGGAGACTTCTTCACCCTTAAGTCTGCTTATCA
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* *
3678093 ACTTTAACCCTT-GAGACTTCTTCACCC-T---TCTGCCTGTCG
1 GCTTTGA-CCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * * * ** ***
3678132 GCTTTGACCATAGAAACTTCCTCACTGTTAAGTCTATTTGTCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
3678175 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * * * * *
3678218 GCTTTGACCCTAGAGACTTCCTCAGCCATAAGTCTGCCTAGTCA
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCT-GTCG
* * * * * * *
3678262 ACTTTGACCCTAGAGACTTCCTCACCCTAAAGTCTGCTTGTTG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
*
3678305 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTACCTGTCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * ** * * *
3678348 ACTTTGACCCTAAAGACTTCCTT-ACCCTTTAGTCTGCCTATCA
1 GCTTTGACCTTGGAGACTT-CTTCACCCTTAAGTCTGCCTGTCG
* * * * *
3678391 GCTTTGACCTTGGAGACTACCTCA-TCTCAAGTCTGCCTTGTCA
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCC-TGTCG
* * * * *
3678434 GCTTTGACCTTGAAGACTTCCTCACCCTTAAGTTTTCCTGTCA
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * * *
3678477 GCTTTGACCCTAGAGAATTCCTT-ACCCTTAAG-CTTGCCTCTCG
1 GCTTTGACCTTGGAGACTT-CTTCACCCTTAAGTC-TGCCTGTCG
* * * * *
3678520 GCTTTGACCCTAGAGACTTCTTCACCCTTAAGTTTGTCTATCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* *
3678563 GCTTTAACCCTT-GAGACTTCTTCATCCTTAAGTCTGCCTGTCG
1 GCTTTGA-CCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * * *
3678606 GCTTTGA-CTTAGGA-AGCTTTTTTACCTTTAAGTCTGCCAGTCG
1 GCTTTGACCTT-GGAGA-CTTCTTCACCCTTAAGTCTGCCTGTCG
* * * * * *
3678649 ACTTTGACCCTAGAGACTTCCTCACCCTTAAGTCTACCTATCG
1 GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
* * *
3678692 GCTTTGACCCTAGAGATTTTCTT-ACCCTTAAG
1 GCTTTGACCTTGGAGA-CTTCTTCACCCTTAAG
3678724 ACTACTTGTT
Statistics
Matches: 842, Mismatches: 189, Indels: 58
0.77 0.17 0.05
Matches are distributed among these distances:
38 3 0.00
39 24 0.03
40 1 0.00
41 3 0.00
42 51 0.06
43 694 0.82
44 66 0.08
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.35
Consensus pattern (43 bp):
GCTTTGACCTTGGAGACTTCTTCACCCTTAAGTCTGCCTGTCG
Found at i:3678744 original size:22 final size:22
Alignment explanation
Indices: 3678716--3678759 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3678706 GATTTTCTTA
*
3678716 CCCTTAAGACTACTTGTTGGCT
1 CCCTTAAGACTACTTGTCGGCT
*
3678738 CCCTTAAGTCTACTTGTCGGCT
1 CCCTTAAGACTACTTGTCGGCT
3678760 TTGACCCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.36
Consensus pattern (22 bp):
CCCTTAAGACTACTTGTCGGCT
Found at i:3678970 original size:128 final size:128
Alignment explanation
Indices: 3678738--3679063 Score: 327
Period size: 128 Copynumber: 2.6 Consensus size: 128
3678728 CTTGTTGGCT
* * * *
3678738 CCCTTAAGTCTACTTGTCGGCTTTGACCCTAGAGAC--T-TCACCCCTAAGTCTACCTGTCAGCT
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTTCTCACCCTTAAGTCTACCTGTCAGCT
* * * * ** * * *
3678800 TTAACCCTAAAGATTCCTCACCCTTAAGTTTGCCTGTAGGCTTTGACGTTGGAGACTTCTTCA
66 TTAACCCTAAAGATACCTCACCCTTAAGTCTGCATATAGGCTTTGACCCTAGAAACTTCCTCA
* *
3678863 CCCTTAAGTCTACCTGTCAGCGTTGACCTTAGAGACTTTCTCACCCTTAAGTCTGCCTGTCAGCT
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTTCTCACCCTTAAGTCTACCTGTCAGCT
* * * * * *
3678928 TTGACCTTGACGACTACCTCA-TCTTAAGTCTGCATATTGGCTTTGACCCTAGAAACTTCCTCA
66 TTAACCCTAAAGA-TACCTCACCCTTAAGTCTGCATATAGGCTTTGACCCTAGAAACTTCCTCA
* * * * ** * * * * *
3678991 CCCTGAAGTTTGCCTATTTGCTTTGACATTAGAGACTTCCTTACCCTTAAGTCTATCGGTCAGCT
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTTCTCACCCTTAAGTCTACCTGTCAGCT
3679056 TTAACCCT
66 TTAACCCT
3679064 GGAGATTTCC
Statistics
Matches: 161, Mismatches: 36, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
125 32 0.20
127 1 0.01
128 122 0.76
129 6 0.04
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (128 bp):
CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTTCTCACCCTTAAGTCTACCTGTCAGCT
TTAACCCTAAAGATACCTCACCCTTAAGTCTGCATATAGGCTTTGACCCTAGAAACTTCCTCA
Found at i:3679005 original size:85 final size:86
Alignment explanation
Indices: 3678775--3679045 Score: 246
Period size: 85 Copynumber: 3.2 Consensus size: 86
3678765 CCTAGAGACT
* * * *
3678775 TCACCCCTAAGTCTACCTGTCAGCTTTAACCCTA-AAGA-TTCCTCACCCTTAAGTTTGCCTGTA
1 TCACCCTTAAGTCTACATATCAGCTTTGACCCTAGAA-ACTTCCTCACCCTTAAGTTTGCCTGTA
* * *
3678838 GGCTTTGACGTTGGAGACTTCT
65 GGCTTTGACCTTGGAGACTACC
* * * * * * *
3678860 TCACCCTTAAGTCTACCTGTCAGCGTTGACCTTAGAGACTTTCTCACCCTTAAGTCTGCCTGTCA
1 TCACCCTTAAGTCTACATATCAGCTTTGACCCTAGAAACTTCCTCACCCTTAAGTTTGCCTGT-A
3678925 -GCTTTGACCTT-GACGACTACC
65 GGCTTTGACCTTGGA-GACTACC
* * ** * * **
3678946 TCA-TCTTAAGTCTGCATATTGGCTTTGACCCTAGAAACTTCCTCACCCTGAAGTTTGCCTATTT
1 TCACCCTTAAGTCTACATATCAGCTTTGACCCTAGAAACTTCCTCACCCTTAAGTTTGCCTGTAG
* * *
3679010 GCTTTGACATTAGAGACTTCC
66 GCTTTGACCTTGGAGACTACC
*
3679031 TTACCCTTAAGTCTA
1 TCACCCTTAAGTCTA
3679046 TCGGTCAGCT
Statistics
Matches: 150, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
85 97 0.65
86 52 0.35
87 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.34
Consensus pattern (86 bp):
TCACCCTTAAGTCTACATATCAGCTTTGACCCTAGAAACTTCCTCACCCTTAAGTTTGCCTGTAG
GCTTTGACCTTGGAGACTACC
Found at i:3679057 original size:43 final size:43
Alignment explanation
Indices: 3678738--3679057 Score: 267
Period size: 43 Copynumber: 7.6 Consensus size: 43
3678728 CTTGTTGGCT
* * *
3678738 CCCTTAAGTCTACTTGTCGGCTTTGACCCTAGAGAC-T--TCA
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTCCTCA
* * * *
3678778 CCCCTAAGTCTACCTGTCAGCTTTAACCCTAAAGA-TTCCTCA
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTCCTCA
* * * * *
3678820 CCCTTAAGTTTGCCTGT-AGGCTTTGACGTTGGAGACTTCTTCA
1 CCCTTAAGTCTACCTGTCA-GCTTTGACCTTAGAGACTTCCTCA
* *
3678863 CCCTTAAGTCTACCTGTCAGCGTTGACCTTAGAGACTTTCTCA
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTCCTCA
* *
3678906 CCCTTAAGTCTGCCTGTCAGCTTTGACCTT-GACGACTACCTCA
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGA-GACTTCCTCA
* * * * ** * *
3678949 -TCTTAAGTCTGCATATTGGCTTTGACCCTAGAAACTTCCTCA
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTCCTCA
* * * * ** * *
3678991 CCCTGAAGTTTGCCTATTTGCTTTGACATTAGAGACTTCCTTA
1 CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTCCTCA
* *
3679034 CCCTTAAGTCTATCGGTCAGCTTT
1 CCCTTAAGTCTACCTGTCAGCTTT
3679058 AACCCTGGAG
Statistics
Matches: 221, Mismatches: 50, Indels: 15
0.77 0.17 0.05
Matches are distributed among these distances:
40 31 0.14
41 1 0.00
42 61 0.28
43 127 0.57
44 1 0.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (43 bp):
CCCTTAAGTCTACCTGTCAGCTTTGACCTTAGAGACTTCCTCA
Found at i:3679559 original size:167 final size:165
Alignment explanation
Indices: 3679361--3679675 Score: 407
Period size: 167 Copynumber: 1.9 Consensus size: 165
3679351 TAGACCCAAA
* * *
3679361 AGACTCCTTTGTCATTCGTCTACCTGTCGGCTTAGAATTGAGAGACTTCTTTATCCATCATTTGC
1 AGACTCCTTTGTCATTCGTCTACCCGTCGGCTTAGAATCGAGAGACTTCTTTATCCATCATGTG-
* * * ** *
3679426 CCATCGGCTTAAACCCGTGAGATTTTTTTATCTTTCGTAT-CTTGTTAACTTAGACCTAGGGAGA
65 CCATCGACTTAAACCCGGGAGACTTTTTTATCTTTCGTATGCCCGTCAACTTAGACCTA--GAGA
3679490 CTTTTTCATCTTTCATCTACCATCAGCTTGTACCCAGG
128 CTTTTTCATCTTTCATCTACCATCAGCTTGTACCCAGG
* * * **
3679528 AGACTTCTTTGTCATTCGTCTGCCCGTCGGCTTAGACTCGAGAGACTTCTTTATCCATTGTGTGC
1 AGACTCCTTTGTCATTCGTCTACCCGTCGGCTTAGAATCGAGAGACTTCTTTATCCATCATGTGC
* * * * ** *
3679593 CATCGACTTAGACCTGGGAGACTTTTTTATCTTTTGTTTGCCCGTCGGCTTAGACTTAGAGACTT
66 CATCGACTTAAACCCGGGAGACTTTTTTATCTTTCGTATGCCCGTCAACTTAGACCTAGAGACTT
3679658 TTTCATCTTTCATCTACC
131 TTTCATCTTTCATCTACC
3679676 GTTGGCTTAG
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
165 25 0.20
166 33 0.26
167 68 0.54
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (165 bp):
AGACTCCTTTGTCATTCGTCTACCCGTCGGCTTAGAATCGAGAGACTTCTTTATCCATCATGTGC
CATCGACTTAAACCCGGGAGACTTTTTTATCTTTCGTATGCCCGTCAACTTAGACCTAGAGACTT
TTTCATCTTTCATCTACCATCAGCTTGTACCCAGG
Found at i:3679574 original size:83 final size:82
Alignment explanation
Indices: 3679486--3679754 Score: 199
Period size: 83 Copynumber: 3.3 Consensus size: 82
3679476 TAGACCTAGG
*
3679486 GAGACTTTTTCATCTTTCATCTACCATC-AGCTT-GTACCCAGGAGACTTCTTTGTCATTCGTCT
1 GAGACTTTTTCATCTTTCATCTACCATCGA-CTTAG-ACCCAGGAGACTTCTTTATCATTCGTCT
3679549 GCCCGTCGGCTTAGACTCGA
64 GCCCGTCGGCTTAGACT-GA
* * * * ** * * * *
3679569 GAGACTTCTTT-ATCCATT-GTGTGCCATCGACTTAGACCTGGGAGACTTTTTTATCTTTTGTTT
1 GAGACTT-TTTCAT-CTTTCATCTACCATCGACTTAGACCCAGGAGACTTCTTTATCATTCGTCT
*
3679632 GCCCGTCGGCTTAGACTTA
64 GCCCGTCGGCTTAGACTGA
* * * * * * * *
3679651 GAGACTTTTTCATCTTTCATCTACCGTTGGCTTAGA-TCTGGTAGACTT-TTCATCAATCGTCTA
1 GAGACTTTTTCATCTTTCATCTACCATCGACTTAGACCCAGG-AGACTTCTTTATCATTCGTCTG
** * * *
3679714 CCTATCGACTTAGACCCGG
65 CCCGTCGGCTTAGA-CTGA
*
3679733 GAGACCTTTTCATCTTTCATCT
1 GAGACTTTTTCATCTTTCATCT
3679755 GCCCGTCGGC
Statistics
Matches: 143, Mismatches: 35, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
81 28 0.20
82 50 0.35
83 57 0.40
84 8 0.06
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.38
Consensus pattern (82 bp):
GAGACTTTTTCATCTTTCATCTACCATCGACTTAGACCCAGGAGACTTCTTTATCATTCGTCTGC
CCGTCGGCTTAGACTGA
Found at i:3679614 original size:41 final size:43
Alignment explanation
Indices: 3679526--3679623 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 43
3679516 CTTGTACCCA
* * *
3679526 GGAGACTTCTTTGT-CATTCGTCTGCCCGTCGGCTTAGACTCG
1 GGAGACTTCTTTATCCATTCGTCTGCCCATCGACTTAGACTCG
* *
3679568 AGAGACTTCTTTATCCATT-GTGTG-CCATCGACTTAGAC-CTG
1 GGAGACTTCTTTATCCATTCGTCTGCCCATCGACTTAGACTC-G
*
3679609 GGAGACTTTTTTATC
1 GGAGACTTCTTTATC
3679624 TTTTGTTTGC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 1 0.02
41 26 0.55
42 16 0.34
43 4 0.09
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.36
Consensus pattern (43 bp):
GGAGACTTCTTTATCCATTCGTCTGCCCATCGACTTAGACTCG
Found at i:3679697 original size:41 final size:41
Alignment explanation
Indices: 3679651--3679754 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 41
3679641 CTTAGACTTA
* * *
3679651 GAGACTTTTTCATCTTTCATCTACCGT-T-GGCTTAGATCTGG
1 GAGAC-TTTTCATCTTTCATCTACC-TATCGACTTAGACCCGG
* ** *
3679692 TAGACTTTTCATCAATCGTCTACCTATCGACTTAGACCCGG
1 GAGACTTTTCATCTTTCATCTACCTATCGACTTAGACCCGG
3679733 GAGACCTTTTCATCTTTCATCT
1 GAGA-CTTTTCATCTTTCATCT
3679755 GCCCGTCGGC
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
39 1 0.02
40 17 0.35
41 17 0.35
42 14 0.29
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.38
Consensus pattern (41 bp):
GAGACTTTTCATCTTTCATCTACCTATCGACTTAGACCCGG
Found at i:3679776 original size:42 final size:42
Alignment explanation
Indices: 3679546--3679781 Score: 137
Period size: 41 Copynumber: 5.7 Consensus size: 42
3679536 TTGTCATTCG
* * * *
3679546 TCTGCCCGTCGGCTTAGACTCGAGAGA-CTTCTTTATCCATT-G
1 TCTGCCCGTCGGCTTAGACTCGGGAGACCTT-TTCAT-CTTTCA
* * * * * **
3679588 TGTG-CCATCGACTTAGAC-CTGGGAGACTTTTTTATCTTTTG
1 TCTGCCCGTCGGCTTAGACTC-GGGAGACCTTTTCATCTTTCA
* ** *
3679629 TTTGCCCGTCGGCTTAGACT-TAGAGACTTTTTCATCTTTCA
1 TCTGCCCGTCGGCTTAGACTCGGGAGACCTTTTCATCTTTCA
* * * ** *
3679670 TCT-ACCGTTGGCTTAGA-TCTGGTAGA-CTTTTCATCAATCG
1 TCTGCCCGTCGGCTTAGACTC-GGGAGACCTTTTCATCTTTCA
* ** * *
3679710 TCTACCTATCGACTTAGACCCGGGAGACCTTTTCATCTTTCA
1 TCTGCCCGTCGGCTTAGACTCGGGAGACCTTTTCATCTTTCA
*
3679752 TCTGCCCGTCGGCTTAAACTCGGGAGACCT
1 TCTGCCCGTCGGCTTAGACTCGGGAGACCT
3679782 CTTTATTATT
Statistics
Matches: 144, Mismatches: 40, Indels: 20
0.71 0.20 0.10
Matches are distributed among these distances:
39 1 0.01
40 29 0.20
41 61 0.42
42 53 0.37
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (42 bp):
TCTGCCCGTCGGCTTAGACTCGGGAGACCTTTTCATCTTTCA
Found at i:3681434 original size:164 final size:166
Alignment explanation
Indices: 3681084--3681824 Score: 779
Period size: 165 Copynumber: 4.5 Consensus size: 166
3681074 TTCAAACATC
* ** ** * * * * * * *
3681084 AAAATTCTTCAAATATTATCATTTA-ACCCCATCAAATCAGTTTTAAAAAATTAATTTACTTGCA
1 AAAATTCATCAAATATTATCATTTATTTCATATTAATTCATTTTTAAAAAATTCATTCATTTTCA
* * * * * * * **
3681148 TGAGTTTTTGAATTTTTTTCTTGAAATTCT-TTTTTTTCGAAATACGATATTTTCTACTTTGTAA
66 TGAGTTTTTG-ATTTTTTCCTTAAAACTCTCATTTTTTCAAAATACAATATTTTTTACTCCGTAA
* ** *
3681212 ATTTTTTTAG-GAGATTTTTCTTAATTTTGAATTTTT
130 ATTTTTTTCGAGAGATTTTTCTCGATTTTCAATTTTT
* *
3681248 -AAATTCATCAAATATTATCATTTATTTCGTATTAATTCA-TTTTAAAAAAATCATTCATTTTCA
1 AAAATTCATCAAATATTATCATTTATTTCATATTAATTCATTTTTAAAAAATTCATTCATTTTCA
* * * ***
3681311 TTCA-TTTTTTA-TTTTTCCTTAAAACTCTCATTTTTT-GAAATATGGTATTTTTTACTCCGTAA
66 -TGAGTTTTTGATTTTTTCCTTAAAACTCTCATTTTTTCAAAATACAATATTTTTTACTCCGTAA
3681373 ATTTTTTTCGAGAGAATTTTTCTCGATTTTCAATTTTT
130 ATTTTTTTCGAGAG-ATTTTTCTCGATTTTCAATTTTT
* * *
3681411 AAAATTCATCAAATATCATCATTTATTTCATATTAATTCATTTTTCAAAAATTCAATCATTTTCA
1 AAAATTCATCAAATATTATCATTTATTTCATATTAATTCATTTTTAAAAAATTCATTCATTTTCA
* * * * * * *
3681476 TGAGTTTTTGATTTTTTCCTTTAAACTCTCATTTTTTAAAAATATAGTGTTTTTTA-TTCGTATA
66 TGAGTTTTTGATTTTTTCCTTAAAACTCTCATTTTTTCAAAATACAATATTTTTTACTCCGTAAA
*
3681540 -TTTTTTCGAGGGGATTTTTCTCGATTTTCAATTTTT
131 TTTTTTTCGA-GAGATTTTTCTCGATTTTCAATTTTT
* * *
3681576 AAAAGTCATTAAATATTATCATTTATTTCATATTAATTCATTTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATCATTTATTTCATATTAATTCATTTTTAAAAAATTCATTCATTTTCA
* * * *
3681641 GGAGTTTTTGATTTTTCTCCTTGAAACTCTCCTTTTTTCAAAATACAATATTTTTTACTCCGTAT
66 TGAGTTTTTGATTTTT-TCCTTAAAACTCTCATTTTTTCAAAATACAATATTTTTTACTCCGTAA
* *
3681706 ATTTTTTTCGAGTTGATTTTTCTCGGTTTTCAATTTTT
130 ATTTTTTTCGAG-AGATTTTTCTCGATTTTCAATTTTT
* * * * *
3681744 AAAATTCATCAAACATTATTATGTGA-TTCATATTAAATCA-TTTTAAAATAATTAATTCA-TTT
1 AAAATTCATCAAATATTATCAT-TTATTTCATATTAATTCATTTTTAAAA-AATTCATTCATTTT
* *
3681806 CATGAATTTTAGATTTTTT
64 CATGAGTTTTTGATTTTTT
3681825 TGCTGAAATT
Statistics
Matches: 494, Mismatches: 66, Indels: 32
0.83 0.11 0.05
Matches are distributed among these distances:
161 44 0.09
162 10 0.02
163 67 0.14
164 49 0.10
165 135 0.27
166 67 0.14
167 48 0.10
168 72 0.15
169 2 0.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (166 bp):
AAAATTCATCAAATATTATCATTTATTTCATATTAATTCATTTTTAAAAAATTCATTCATTTTCA
TGAGTTTTTGATTTTTTCCTTAAAACTCTCATTTTTTCAAAATACAATATTTTTTACTCCGTAAA
TTTTTTTCGAGAGATTTTTCTCGATTTTCAATTTTT
Found at i:3681738 original size:333 final size:327
Alignment explanation
Indices: 3681224--3681824 Score: 816
Period size: 333 Copynumber: 1.8 Consensus size: 327
3681214 TTTTTTAGGA
* * * *
3681224 GATTTTTCTTAATTTTGAATTTTTAAATTCATCAAATATTATCATTTATTTCGTATTAATTCATT
1 GATTTTTCTCAATTTTCAATTTTTAAAGTCATCAAATATTATCATTTATTTCATATTAATTCATT
* * * *
3681289 TTAAAAAAATCATTCATTTTCATTCATTTTTTATTTTTCCTTAAAACTCTCATTTTTTGAAATAT
66 TTAAAAAAATCATTCATTTTCATGCATTTTTGATTTTTCCTTAAAACTCTCATTTTTTAAAATAC
**
3681354 GGTATTTTTTACTCCGTAAATTTTTTTCGAGAGAATTTTTCTCGATTTTCAATTTTTAAAATTCA
131 AATATTTTTTACTCCGTAAATTTTTTTCGAGAGAATTTTTCTCGATTTTCAATTTTTAAAATTCA
* * * * *
3681419 TCAAATATCATCAT-TTATTTCATATTAATTCATTTTTCAAA-AATTCAA-TCATTTTCATGAGT
196 TCAAACATCATCATGTGA-TTCATATTAAATCA-TTTTAAAATAATT-AATTCA-TTTCATGAAT
*
3681481 TTTTGATTTTTTCCTTTAAACTCTCATTTTTTAAAAATATAGTGTTTTTTATTCGTATATTTTTT
257 TTTAGATTTTTTCCTTTAAACTCTCATTTTTTAAAAATATAGTGTTTTTTATTCGTATATTTTTT
3681546 CGAGGG
322 CGAGGG
* *
3681552 GATTTTTCTCGATTTTCAATTTTTAAAAGTCATTAAATATTATCATTTATTTCATATTAATTCAT
1 GATTTTTCTCAATTTTCAATTTTT-AAAGTCATCAAATATTATCATTTATTTCATATTAATTCA-
* * * * *
3681617 TTTTCAAAAATTCATTCATTTTCA-GGAGTTTTTGATTTTTCTCCTTGAAACTCTCCTTTTTTCA
64 TTTTAAAAAAATCATTCATTTTCATGCA-TTTTTGA-TTTT-TCCTTAAAACTCTCATTTTTT-A
* * *
3681681 AAATACAATATTTTTTACTCCGTATATTTTTTTCGAGTTG-ATTTTTCTCGGTTTTCAATTTTTA
125 AAATACAATATTTTTTACTCCGTAAATTTTTTTCGAG-AGAATTTTTCTCGATTTTCAATTTTTA
* *
3681745 AAATTCATCAAACATTATTATGTGATTCATATTAAATCATTTTAAAATAATTAATTCATTTCATG
189 AAATTCATCAAACATCATCATGTGATTCATATTAAATCATTTTAAAATAATTAATTCATTTCATG
3681810 AATTTTAGATTTTTT
254 AATTTTAGATTTTTT
3681825 TGCTGAAATT
Statistics
Matches: 235, Mismatches: 28, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
328 21 0.09
329 37 0.16
330 28 0.12
331 4 0.02
332 48 0.20
333 94 0.40
334 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (327 bp):
GATTTTTCTCAATTTTCAATTTTTAAAGTCATCAAATATTATCATTTATTTCATATTAATTCATT
TTAAAAAAATCATTCATTTTCATGCATTTTTGATTTTTCCTTAAAACTCTCATTTTTTAAAATAC
AATATTTTTTACTCCGTAAATTTTTTTCGAGAGAATTTTTCTCGATTTTCAATTTTTAAAATTCA
TCAAACATCATCATGTGATTCATATTAAATCATTTTAAAATAATTAATTCATTTCATGAATTTTA
GATTTTTTCCTTTAAACTCTCATTTTTTAAAAATATAGTGTTTTTTATTCGTATATTTTTTCGAG
GG
Found at i:3681908 original size:333 final size:329
Alignment explanation
Indices: 3681241--3681909 Score: 752
Period size: 333 Copynumber: 2.0 Consensus size: 329
3681231 CTTAATTTTG
* *
3681241 AATTTTT-AAATTCATCAAATATTATCATTTATTTCGTATTAATTCATTTTAAAAAAATCATTCA
1 AATTTTTAAAAGTCATCAAATATTATCATTTATTTCATATTAATTCATTTTAAAAAAATCATTCA
* * * ***
3681305 TTTTCATTCATTTTTTATTTTTCCTTAAAACTCTCATTTTTTGAAATATGGTATTTTTTACTCCG
66 TTTTCATGCATTTTTGATTTTTCCTTAAAACTCTCATTTTTTAAAATACAATATTTTTTACTCCG
* *
3681370 TAAATTTTTTTCGAGAGAATTTTTCTCGATTTTCAATTTTTAAAATTCATCAAATATCATCATTT
131 TAAATTTTTTTCGAGAGAATTTTTCTCGATTTTCAATTTTTAAAATTCATCAAACATCATCATTG
* * * * *
3681435 ATTTCATATTAATTCATTTTTCAAAAATTCAATCATTTTCATGAGTTTTTGATTTTTTCCTTTAA
196 ATTTCATATTAAATCATTTTTAAAAAATTCAATCATTTTCATGAATTTTAGATTTTTTCCTTGAA
* * * *
3681500 ACTCTCATTTTTTAAAAATATAGTGTTTTTTATTCGTATATTTTTTCGAGGGGATTTTTCTCGAT
261 ACTCTCATTTTTTAAAAATATAGTGTTTCTTATCCGTAAATATTTTCGAGGGGATTTTTCTCGAT
* **
3681565 TTTC
326 CTAA
* * *
3681569 AATTTTTAAAAGTCATTAAATATTATCATTTATTTCATATTAATTCATTTTTCAAAAATTCATTC
1 AATTTTTAAAAGTCATCAAATATTATCATTTATTTCATATTAATTCA-TTTTAAAAAAATCATTC
* * *
3681634 ATTTTCA-GGAGTTTTTGATTTTTCTCCTTGAAACTCTCCTTTTTTCAAAATACAATATTTTTTA
65 ATTTTCATGCA-TTTTTGA-TTTT-TCCTTAAAACTCTCATTTTTT-AAAATACAATATTTTTTA
* * * *
3681698 CTCCGTATATTTTTTTCGAGTTG-ATTTTTCTCGGTTTTCAATTTTTAAAATTCATCAAACATTA
126 CTCCGTAAATTTTTTTCGAG-AGAATTTTTCTCGATTTTCAATTTTTAAAATTCATCAAACATCA
*
3681762 TTATGTGA-TTCATATTAAATCA-TTTTAAAATAATT-AATTCA-TTTCATGAATTTTAGATTTT
190 TCAT-TGATTTCATATTAAATCATTTTTAAAA-AATTCAA-TCATTTTCATGAATTTTAGA-TTT
* * * *
3681823 TTTGC-TGAAATTTCTC-TTTTTTCGAGAAAT-TGAGT-TTTCTTCTCCGTAAATATTTTCGGAG
251 TTTCCTTGAAA-CTCTCATTTTTT--AAAAATAT-AGTGTTTCTTATCCGTAAATATTTTC-GAG
* *
3681884 GGG--TTTTCTTTGGTCTAA
311 GGGATTTTTC-TCGATCTAA
3681902 AATTTTTA
1 AATTTTTA
3681910 TAATTCTTCT
Statistics
Matches: 285, Mismatches: 39, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
328 7 0.02
329 37 0.13
330 28 0.10
331 4 0.01
332 57 0.20
333 135 0.47
334 17 0.06
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (329 bp):
AATTTTTAAAAGTCATCAAATATTATCATTTATTTCATATTAATTCATTTTAAAAAAATCATTCA
TTTTCATGCATTTTTGATTTTTCCTTAAAACTCTCATTTTTTAAAATACAATATTTTTTACTCCG
TAAATTTTTTTCGAGAGAATTTTTCTCGATTTTCAATTTTTAAAATTCATCAAACATCATCATTG
ATTTCATATTAAATCATTTTTAAAAAATTCAATCATTTTCATGAATTTTAGATTTTTTCCTTGAA
ACTCTCATTTTTTAAAAATATAGTGTTTCTTATCCGTAAATATTTTCGAGGGGATTTTTCTCGAT
CTAA
Found at i:3687227 original size:13 final size:13
Alignment explanation
Indices: 3687209--3687234 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3687199 CAAGGTAGCT
3687209 TTGTATCGATACA
1 TTGTATCGATACA
3687222 TTGTATCGATACA
1 TTGTATCGATACA
3687235 ACGCTTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3687270 original size:19 final size:17
Alignment explanation
Indices: 3687222--3687257 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3687212 TATCGATACA
*
3687222 TTGTATCGATACAACGC
1 TTGTATCGATACAACAC
3687239 TTGTATCGATACAACAC
1 TTGTATCGATACAACAC
3687256 TT
1 TT
3687258 ATGTATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (17 bp):
TTGTATCGATACAACAC
Found at i:3688486 original size:155 final size:154
Alignment explanation
Indices: 3687590--3688513 Score: 705
Period size: 156 Copynumber: 6.0 Consensus size: 154
3687580 TTTCTCAATT
* * * * * *
3687590 GAGTCCTAGGTTATCACCAGATCCGCTTTTATG-CTGAAGGTA-AGTATTTAGGATATG-TC-CA
1 GAGTCCTAAGTTATCACCGGGTCTGCTTTTATGTC-GAAGGTAGA-TATTTAGGATAGGTTCACC
* *
3687651 CCATTTTCTATCCCTTTTAAGTCCTTTAAAGGTA-CTAGGATACTTTTACGTCGAAGGTATCCCC
64 CCATTGT-TATCCTTTTTAAGTCCTTTAAAGGTATC-AGG-TACTTTTACGTCGAAGGTAT-CCC
* *
3687715 CTAGGGGCATTTTTTTAATTTTTCAGAACCA
125 CTAGGGGCATTTTTGTAATTTTTTAGAA-CA
* * * * * *
3687746 -AGT-CTTAGATTATCACCAGGTCCGTTTTTATGTCGAAGGTAGGTATTTAGGATAAGTTCACCC
1 GAGTCCTAAG-TTATCACCGGGTCTGCTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCACCC
* * * * * * *
3687809 TATTTTTTATCCTTTTTAAGTCCTTTAAGGGTACCGAGATACTTTCACGTCGAAGGTATCCCCTT
65 CA-TTGTTATCCTTTTTAAGTCCTTTAAAGGTATC-AGGTACTTTTACGTCGAAGGTATCCCCTA
*
3687874 GGGGCATTTTTGTATTTTTTTAGAATC-
128 GGGGCATTTTTGTAATTTTTTAGAA-CA
* ** ** * ** ** * *
3687901 GAGTCCTAGGTTATCACCAAGTCCACTTTTTTACCGAAGGCGGGTATTTAGGATAGGTTCACCTC
1 GAGTCCTAAGTTATCACCGGGTCTGCTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCACCCC
* * * * * * * * ** **
3687966 -TTTTCTATCCTTCTAAAGT-CTTTTAGGGTTACTGAGATACTTTTACATTAAAGGTATACCTGT
66 ATTGT-TATCCTTTTTAAGTCCTTTAAAGG-TA-TCAGGTACTTTTACGTCGAAGGTAT-CCCCT
** * *
3688029 AGGGGCATTTTCAT-ATTTTCTTAAAACC
127 AGGGGCATTTTTGTAATTTT-TTAGAACA
* *
3688057 GAGTCCTAAGTTGTCACCGAGTCTGCTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCACCCC
1 GAGTCCTAAGTTATCACCGGGTCTGCTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCACCCC
* * * ** *
3688122 ATCTGTTATGCTTCTTAAGT-C-TTATAGGAGTATCAGGTACTTTTAAATCGAAGGTATCCTCTA
66 AT-TGTTATCCTTTTTAAGTCCTTTA-AAG-GTATCAGGTACTTTTACGTCGAAGGTATCCCCTA
* * * *
3688185 GGGGGATTTTTTGAAAATTTTCAGAACTA
128 GGGGCA-TTTTTGTAATTTTTTAGAAC-A
* ** * * * *
3688214 -AGTCCTAGGTTGCCACCGGGTCTCCTTTAATGTCGAAGGTAGATATTTAGGATAGGTTCATCCT
1 GAGTCCTAAGTTATCACCGGGTCTGCTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCACCCC
* ** * * * *
3688278 ATT-TCAAAACTTTTTAAGTCCTTTAGAGGTA-CCGAGTACTTGTACGTCGAAGGTATCCCCTAA
66 ATTGT-TATCCTTTTTAAGTCCTTTAAAGGTATCAG-GTACTTTTACGTCGAAGGTATCCCCTAG
*
3688341 AGGCATTTTTGTAATTTTTTAGAACA
129 GGGCATTTTTGTAATTTTTTAGAACA
** * *
3688367 GAGTATTAAGTTATCACCGGGTTTGCTTTTATTTCGAAGGTAGATATTTAGGATAGGTTCACCCC
1 GAGTCCTAAGTTATCACCGGGTCTGCTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCACCCC
* *
3688432 ATCTGTTATCCTTTTTAAGT-CTTATAAAGGTATCAGGTACTTTTACGTCAAAGGTAT-CCTTAG
66 AT-TGTTATCCTTTTTAAGTCCTT-TAAAGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAG
* **
3688495 GGACATTTTCATAATTTTT
129 GGGCATTTTTGTAATTTTT
3688514 GTCCCCACAT
Statistics
Matches: 612, Mismatches: 125, Indels: 64
0.76 0.16 0.08
Matches are distributed among these distances:
153 1 0.00
154 112 0.18
155 169 0.28
156 245 0.40
157 75 0.12
158 10 0.02
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (154 bp):
GAGTCCTAAGTTATCACCGGGTCTGCTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCACCCC
ATTGTTATCCTTTTTAAGTCCTTTAAAGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAGGG
GCATTTTTGTAATTTTTTAGAACA
Found at i:3689046 original size:52 final size:51
Alignment explanation
Indices: 3688967--3689258 Score: 202
Period size: 52 Copynumber: 5.7 Consensus size: 51
3688957 AAAGAATGTT
* * *
3688967 AATGTGCTGATTCACGG-TCAGCGACATTAGACTTGAAGATGAGAAGGATGCC
1 AATGTGCTGATTCAAGGCT-AGCGACATTGGACTTAAAGATGAGAA-GATGCC
* * * * **
3689019 AATGTGCTGATTCAAGGCTAGCTACATTGG-GTTTAGGAATGTTACAGATGCC
1 AATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAG-ATGAGA-AGATGCC
* * * ** ** * * *
3689071 AATATGCTGATTGAAGGCCATTGATTTTGTACTTAAAG--GTGAAGATGCT
1 AATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAGAAGATGCC
* * * *
3689120 AATGTGTTGATTCAAGGCCAGCAACATTGGACTTAAAGATGACAA-AGTCGCC
1 AATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAGAAGA-T-GCC
* * * *
3689172 AATATGCTGATTCAAAGCTAGCGATATTGGACTTAAAGAT--GAAGGTGCC
1 AATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAGAAGATGCC
* * * *
3689221 AATGTGATGATTCAAGGCCAACAACATTGGACTTAAAG
1 AATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAG
3689259 GTGCCAATAT
Statistics
Matches: 182, Mismatches: 49, Indels: 21
0.72 0.19 0.08
Matches are distributed among these distances:
49 69 0.38
50 7 0.04
51 8 0.04
52 92 0.51
53 6 0.03
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (51 bp):
AATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAGAAGATGCC
Found at i:3689147 original size:101 final size:101
Alignment explanation
Indices: 3688971--3689258 Score: 276
Period size: 101 Copynumber: 2.8 Consensus size: 101
3688961 AATGTTAATG
** * * * * *
3688971 TGCTGATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAGGATGCCAATGTGCTGATTCAAGG
1 TGCTGATTCAAAGCCAGCGATATTGGACTTAAAGAT--GAA-GATGCCAATGTGATGATTCAAGG
* * ** * *
3689036 CTAGCTACATTGGGTTTAGGAATG-TTACAGA-T-GCCAATA
63 CCAGCAACATTGGACTTA--AA-GATGACAAAGTCGCCAATA
* * ** * * * * *
3689075 TGCTGATTGAAGGCCATTGATTTTGTACTTAAAGGTGAAGATGCTAATGTGTTGATTCAAGGCCA
1 TGCTGATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGATGATTCAAGGCCA
3689140 GCAACATTGGACTTAAAGATGACAAAGTCGCCAATA
66 GCAACATTGGACTTAAAGATGACAAAGTCGCCAATA
* *
3689176 TGCTGATTCAAAGCTAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGATGATTCAAGGCCA
1 TGCTGATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGATGATTCAAGGCCA
*
3689241 ACAACATTGGACTTAAAG
66 GCAACATTGGACTTAAAG
3689259 GTGCCAATAT
Statistics
Matches: 150, Mismatches: 31, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
98 1 0.01
99 7 0.05
100 1 0.01
101 113 0.75
102 3 0.02
104 25 0.17
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (101 bp):
TGCTGATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGATGATTCAAGGCCA
GCAACATTGGACTTAAAGATGACAAAGTCGCCAATA
Found at i:3689275 original size:43 final size:43
Alignment explanation
Indices: 3689213--3689298 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
3689203 CTTAAAGATG
*
3689213 AAGGTGCCAATGTGATGATTCAAGGCCAACAACATTGGACTTA
1 AAGGTGCCAATATGATGATTCAAGGCCAACAACATTGGACTTA
* ** *
3689256 AAGGTGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTA
1 AAGGTGCCAATATGATGATTCAAGGCCAACAACATTGGACTTA
3689299 GAAGAAGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (43 bp):
AAGGTGCCAATATGATGATTCAAGGCCAACAACATTGGACTTA
Found at i:3689348 original size:31 final size:27
Alignment explanation
Indices: 3689310--3689537 Score: 84
Period size: 28 Copynumber: 8.0 Consensus size: 27
3689300 AAGAAGATGC
3689310 CACCAACTTGTGTGGGCTTTTGAAAGGGTTG
1 CACCAACTTGTGT--GCTTTT-AAA-GGTTG
3689341 CACCAACTTGTGTGCTTTTAAAGGTTG
1 CACCAACTTGTGTGCTTTTAAAGGTTG
*** * *
3689368 CCACTGCCTTGTGAGC-TTTGAAGGTTG
1 -CACCAACTTGTGTGCTTTTAAAGGTTG
** * *
3689395 CCACTGACTTGTGGGCTTTGAAAAGG-TG
1 -CACCAACTTGTGTGCTTT-TAAAGGTTG
* * **
3689423 CCACTAACTTGTGGGCTTTTGCAAA-AATG
1 -CACCAACTTGTGTGCTTTT--AAAGGTTG
** * * *
3689452 CCACTGACTTATGGGCTTTTGAAGGTTG
1 -CACCAACTTGTGTGCTTTTAAAGGTTG
* * * *
3689480 CCACTAACTTGTGGGCTTTAAAAGGGGTG
1 -CACCAACTTGTGTGCTTTTAAA-GGTTG
* * *
3689509 CCACCGACTTGTGGGCTTTTGAAGGTTG
1 -CACCAACTTGTGTGCTTTTAAAGGTTG
3689537 C
1 C
3689538 CATTGACTTG
Statistics
Matches: 162, Mismatches: 27, Indels: 20
0.78 0.13 0.10
Matches are distributed among these distances:
27 32 0.20
28 61 0.38
29 56 0.35
31 13 0.08
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (27 bp):
CACCAACTTGTGTGCTTTTAAAGGTTG
Found at i:3689443 original size:29 final size:29
Alignment explanation
Indices: 3689320--3689730 Score: 401
Period size: 29 Copynumber: 14.5 Consensus size: 29
3689310 CACCAACTTG
* **
3689320 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
* *
3689349 TGTGTGCTTTT--AAAGGTTGCCACTGCCT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
*
3689377 TGTGAGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
*
3689404 TGTGGGC-TTTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
*
3689432 TGTGGGCTTTTGCAAAA-ATGCCACTGACT
1 TGTGGGCTTTTG-AAAAGGTGCCACTGACT
* *
3689461 TATGGGCTTTTG--AAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
*
3689489 TGTGGGC-TTT-AAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTGAAAA--GGTGCCACTGACT
*
3689518 TGTGGGCTTTTG--AAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
*
3689546 TGTGGGC-TTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
* * *
3689574 TATGGACTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
* *
3689603 TGTGGGCTTTTGATAAGATGCCACTGAC-
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
* **
3689631 TGTGGAC-TTTGAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
* *
3689659 TGTGGGCTTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
3689688 TGTGGGC-TTTGAAAAGGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
3689717 TGTGGGC-TTTGAAA
1 TGTGGGCTTTTGAAA
3689731 GGCGAGGAAT
Statistics
Matches: 327, Mismatches: 34, Indels: 42
0.81 0.08 0.10
Matches are distributed among these distances:
26 2 0.01
27 62 0.19
28 98 0.30
29 156 0.48
30 9 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAAGGTGCCACTGACT
Found at i:3689468 original size:57 final size:59
Alignment explanation
Indices: 3689320--3689730 Score: 425
Period size: 57 Copynumber: 7.3 Consensus size: 59
3689310 CACCAACTTG
* * ** * *
3689320 TGTGGGCTTTTGAAAGGGTTG-CACCAACTTGTGTGCTTTT--AAAGGTTGCCACTGCCT
1 TGTGGGCTTTTGAAA-AGATGCCACTGACTTGTGGGCTTTTGAAAAGGTTGCCACTGACT
* * * *
3689377 TGTGAGC-TTTG-AAGGTTGCCACTGACTTGTGGGC-TTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTGAAAAGGTTGCCACTGACT
* *
3689432 TGTGGGCTTTTGCAAAA-ATGCCACTGACTTATGGGCTTTTG--AAGGTTGCCACTAACT
1 TGTGGGCTTTTG-AAAAGATGCCACTGACTTGTGGGCTTTTGAAAAGGTTGCCACTGACT
* * *
3689489 TGTGGGC-TTT-AAAAGGGGTGCCACCGACTTGTGGGCTTTTG--AAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAAA--GATGCCACTGACTTGTGGGCTTTTGAAAAGGTTGCCACTGACT
* * *
3689546 TGTGGGC-TTTGAAAAGATGCCACTGACTTATGGACTTTTGAAAA-GATGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTGAAAAGGTTGCCACTGACT
* *
3689603 TGTGGGCTTTTGATAAGATGCCACTGAC-TGTGGAC-TTTGAAAA--TATGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTGAAAAGGT-TGCCACTGACT
* *
3689659 TGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGC-TTTGAAAAGGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTGAAAAGGTTGCCACTGACT
3689717 TGTGGGC-TTTGAAA
1 TGTGGGCTTTTGAAA
3689731 GGCGAGGAAT
Statistics
Matches: 307, Mismatches: 28, Indels: 38
0.82 0.08 0.10
Matches are distributed among these distances:
54 12 0.04
55 29 0.09
56 86 0.28
57 131 0.43
58 49 0.16
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (59 bp):
TGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTGAAAAGGTTGCCACTGACT
Found at i:3689497 original size:85 final size:84
Alignment explanation
Indices: 3689320--3689731 Score: 433
Period size: 85 Copynumber: 4.9 Consensus size: 84
3689310 CACCAACTTG
* * * * ** * *
3689320 TGTGGGCTTTTGAAAGGGTTG-CACCAACTTGTGTGCTTTT-AAAGGTTGCCACTGCCTTGTGAG
1 TGTGGGCTTTTGAAA-AGATGCCACTAACTTGTGGGCTTTTGAAA-AATGCCACTGACTTGTGGG
*
3689383 CTTTGAAGGTTGCCACTGACT
64 CTTTGAAAGTTGCCACTGACT
* *
3689404 TGTGGGC-TTTGAAAAGGTGCCACTAACTTGTGGGCTTTTGCAAAAATGCCACTGACTTATGGGC
1 TGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTTG-AAAAATGCCACTGACTTGTGGGC
* *
3689468 TTTTGAAGGTTGCCACTAACT
65 -TTTGAAAGTTGCCACTGACT
* ** *** *
3689489 TGTGGGC-TTT-AAAAGGGGTGCCACCGACTTGTGGGCTTTTGAAGGTTGCCATTGACTTGTGGG
1 TGTGGGCTTTTGAAAA--GATGCCACTAACTTGTGGGCTTTTGAAAAATGCCACTGACTTGTGGG
*
3689552 CTTTGAAAAGATGCCACTGACT
64 CTTTG-AAAGTTGCCACTGACT
* * * * *
3689574 TATGGACTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTGATAAGATGCCACTGAC-TGTGGAC
1 TGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTTGA-AAAATGCCACTGACTTGTGGGC
*
3689638 TTTGAAAATATGCCACTGACT
65 TTTGAAAGT-TGCCACTGACT
3689659 TGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGC-TTTGAAAAGGATGCCACTGACTTGTGGG
1 TGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTTGAAAA--ATGCCACTGACTTGTGGG
3689723 CTTTGAAAG
64 CTTTGAAAG
3689732 GCGAGGAATG
Statistics
Matches: 278, Mismatches: 36, Indels: 26
0.82 0.11 0.08
Matches are distributed among these distances:
82 3 0.01
83 26 0.09
84 38 0.14
85 157 0.56
86 50 0.18
87 4 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (84 bp):
TGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTTGAAAAATGCCACTGACTTGTGGGCT
TTGAAAGTTGCCACTGACT
Found at i:3691212 original size:18 final size:16
Alignment explanation
Indices: 3691160--3691213 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 16
3691150 CATCCGGACC
3691160 TTTTTGTTATTTTTTTT
1 TTTTTGTT-TTTTTTTT
*
3691177 CTTTTTGTTTTTTGTTT
1 -TTTTTGTTTTTTTTTT
3691194 TTTTTGTCTCTTTTTTTT
1 TTTTTGT-T-TTTTTTTT
3691212 TT
1 TT
3691214 GCGGAGAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 7 0.22
17 8 0.25
18 17 0.53
ACGTcount: A:0.02, C:0.06, G:0.07, T:0.85
Consensus pattern (16 bp):
TTTTTGTTTTTTTTTT
Found at i:3691214 original size:24 final size:25
Alignment explanation
Indices: 3691160--3691214 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
3691150 CATCCGGACC
*
3691160 TTTTTGTTATTTTTTTTCTTTTTGT
1 TTTTTGTTATTTTTTGTCTTTTTGT
3691185 TTTTTGTT-TTTTTTGTCTCTTTT-T
1 TTTTTGTTATTTTTTGTCT-TTTTGT
3691209 TTTTTG
1 TTTTTG
3691215 CGGAGAATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (25 bp):
TTTTTGTTATTTTTTGTCTTTTTGT
Found at i:3696011 original size:21 final size:21
Alignment explanation
Indices: 3695982--3696031 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3695972 AGTTGTTATG
* * *
3695982 TTGTTCACTAGACGCTGCAAT
1 TTGTCCACTAGACACTCCAAT
*
3696003 TTGTCCACTAGCCACTCCAAT
1 TTGTCCACTAGACACTCCAAT
3696024 TTGTCCAC
1 TTGTCCAC
3696032 AGAGACATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (21 bp):
TTGTCCACTAGACACTCCAAT
Found at i:3697620 original size:13 final size:13
Alignment explanation
Indices: 3697602--3697626 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3697592 TACCAAGAAC
3697602 ATGTATCGATACA
1 ATGTATCGATACA
3697615 ATGTATCGATAC
1 ATGTATCGATAC
3697627 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3697625 original size:32 final size:33
Alignment explanation
Indices: 3697584--3697647 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
3697574 CAATTCAGTG
3697584 TGTATCGATACCAAG-AACATGTATCGATACAA
1 TGTATCGATACCAAGCAACATGTATCGATACAA
* *
3697616 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACCAAGCAACATGTATCGATACA
3697648 TTTAGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACCAAGCAACATGTATCGATACAA
Found at i:3699749 original size:155 final size:154
Alignment explanation
Indices: 3699542--3699863 Score: 486
Period size: 155 Copynumber: 2.1 Consensus size: 154
3699532 TCATAGGGGT
*
3699542 ATTTTCATAATTTCTTAGAATCGAGTCTTAGGTTGTCACTAGGTTCGCTTTTATGCCAAAGATGG
1 ATTTTCATAATTTCTTAGAATCGAGTCTTAGGTTGTCACTAGGTCCGCTTTTATGCCAAAGATGG
*
3699607 GTATTT-AGAATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTTAAGGGTATTAGGTACTT
66 GTATTTAAG-ATAGGTTCATCCCATCTATAAT-CTTTTTAAGTCCTTTAAGGGTACTAGGTACTT
3699671 CTACGTCGAAGATATCCCCTATAGGC
129 CTACGTCGAAGATATCCCCTATAGGC
* * *
3699697 ATTTTTATAATTTTTTAGAATCGAGTCTTAGGTTGTCACTAGGTCCGCTTTTATGCCAAAGGTGG
1 ATTTTCATAATTTCTTAGAATCGAGTCTTAGGTTGTCACTAGGTCCGCTTTTATGCCAAAGATGG
* * *
3699762 GTATTTAAGATAGGTTTATCTCATCTATAATCTTTTTAAGTCCTTTAGGGGTACTAGGTACTTCT
66 GTATTTAAGATAGGTTCATCCCATCTATAATCTTTTTAAGTCCTTTAAGGGTACTAGGTACTTCT
* * * *
3699827 ATGTCGAAGGTATTCCCT-TCGGGC
131 ACGTCGAAGATATCCCCTAT-AGGC
*
3699851 ATTTTCGTAATTT
1 ATTTTCATAATTT
3699864 ATCAAATCCA
Statistics
Matches: 151, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
153 1 0.01
154 61 0.40
155 87 0.58
156 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (154 bp):
ATTTTCATAATTTCTTAGAATCGAGTCTTAGGTTGTCACTAGGTCCGCTTTTATGCCAAAGATGG
GTATTTAAGATAGGTTCATCCCATCTATAATCTTTTTAAGTCCTTTAAGGGTACTAGGTACTTCT
ACGTCGAAGATATCCCCTATAGGC
Found at i:3701491 original size:12 final size:13
Alignment explanation
Indices: 3701474--3701502 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3701464 ATACATTGTT
3701474 CATTGTATC-ATA
1 CATTGTATCGATA
3701486 CATTGTATCGATA
1 CATTGTATCGATA
3701499 CATT
1 CATT
3701503 CAGGCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3703954 original size:79 final size:79
Alignment explanation
Indices: 3703806--3704028 Score: 257
Period size: 79 Copynumber: 2.8 Consensus size: 79
3703796 TCTTCATCTC
* * * * * *
3703806 GGGGATGCTCCAACCCTGATTTTATTTCAAAAACATCAATTTTTCATAATCGGGGATGCTCTAAT
1 GGGGATACTCCAACCCTAATTTTATTTCAAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
*
3703871 CCCGTTATTTCCGA
66 CCCGTCATTTCCGA
* * * * * * *
3703885 GGGGATACTCCAACCCCAATTTTATTCCCAAAACACCAGTTTTTCACAATTGGGCATACTCCAAC
1 GGGGATACTCCAACCCTAATTTTATTTCAAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
*
3703950 CCCGTCATTTTCGA
66 CCCGTCATTTCCGA
** * ** *
3703964 GGGGATACTCTGACCCTAGTTTTATTTTTAAAACACCAATTTTTCATAATCGGGGATACTTCAAC
1 GGGGATACTCCAACCCTAATTTTATTTCAAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
3704029 TCCGATTTTA
Statistics
Matches: 117, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
79 117 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCTAATTTTATTTCAAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
CCCGTCATTTCCGA
Found at i:3704038 original size:51 final size:51
Alignment explanation
Indices: 3703983--3704079 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
3703973 CTGACCCTAG
** * *
3703983 TTTTATTTTTAAAACACCAATTTTTCATAATCGGGGATACTTCAACTCCGA
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACTCCGA
*
3704034 TTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
3704080 CCCGTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (51 bp):
TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACTCCGA
Found at i:3704062 original size:130 final size:128
Alignment explanation
Indices: 3703885--3704291 Score: 424
Period size: 130 Copynumber: 3.1 Consensus size: 128
3703875 TTATTTCCGA
* * * * * *
3703885 GGGGATACTCCAACCCCAATTTTATTCCCAAAACACCAGTTTTTCACAATTGGGCATACTCCAAC
1 GGGGATACTCCAA-CCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
* *
3703950 CCCGTCATTTTCGAGGGGATACTCTGACCCTAGTTTTATTTTTAAAACACCAATTTTTCATAATC
65 CCCGTTATTTTCGAGGGGATACTCT-ACCCTAGTTTTATTTTTAAAATACCAATTTTTCATAATC
*
3704015 GGGGATACTTCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAAC-CCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
* * * * *** * *
3704080 CCCGTTA-TTTCTGAGGGGATACTCTAACCCCAGCTTTATTTCTAATATTATTGATTTCTCACAA
65 CCCGTTATTTTC-GAGGGGATACTCT-ACCCTAGTTTTATTTTTAA-AATACCAATTTTTCATAA
3704144 TC
127 TC
* ** * * *
3704146 GGGGATACTTCAACCTCGGCTTTATTTCTAAATCA-TCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACC-CGATTTTATTTCCAAAACACT-AATTTTTCACAATCGGGGATACTCCAA
* * * * *
3704210 GCCCGTTATTTTAGAGGGGATACTCTAACCTCGATTTTATTTTCAAAATACCAA-TTTTCTATAA
64 CCCCGTTATTTTCGAGGGGATACTCTACCCTAG-TTTTATTTTTAAAATACCAATTTTTC-ATAA
3704274 TC
127 TC
**
3704276 AAGGATACTCCAACCC
1 GGGGATACTCCAACCC
3704292 TGTTATTTTC
Statistics
Matches: 228, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
129 10 0.04
130 118 0.52
131 97 0.43
132 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (128 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGAGGGGATACTCTACCCTAGTTTTATTTTTAAAATACCAATTTTTCATAATC
Found at i:3704205 original size:51 final size:53
Alignment explanation
Indices: 3704094--3704205 Score: 158
Period size: 51 Copynumber: 2.2 Consensus size: 53
3704084 TTATTTCTGA
* *
3704094 GGGGATAC-TCTAACCCCAGCTTTATTTCTAATATTATTGATTTCTCACAATC
1 GGGGATACTTCTAACCCCAGCTTTATTTCTAATATCATCGATTTCTCACAATC
* * *
3704146 GGGGATACTTC-AACCTCGGCTTTATTTCTAA-ATCATCGATTTTTCACAATC
1 GGGGATACTTCTAACCCCAGCTTTATTTCTAATATCATCGATTTCTCACAATC
3704197 GGGGATACT
1 GGGGATACT
3704206 CCAAGCCCGT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
51 26 0.48
52 26 0.48
53 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (53 bp):
GGGGATACTTCTAACCCCAGCTTTATTTCTAATATCATCGATTTCTCACAATC
Found at i:3704249 original size:79 final size:78
Alignment explanation
Indices: 3704146--3704365 Score: 216
Period size: 79 Copynumber: 2.8 Consensus size: 78
3704136 TCTCACAATC
** * *
3704146 GGGGATACT-TCAACCTCGGCTTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCT-AACCTCGATTTTATTTCTAAATCA-CAATTTTTCATAATCGGGGATACTCCAA
3704210 GCCC-GTTATTTTAGA
64 -CCCTGTTATTTTAGA
* **
3704225 GGGGATACTCTAACCTCGATTTTATTTTCAAAAT-ACCAA-TTTTCTATAATCAAGGATACTCCA
1 GGGGATACTCTAACCTCGATTTTA-TTTCTAAATCA-CAATTTTTC-ATAATCGGGGATACTCCA
*
3704288 ACCCTGTTATTTTCGA
63 ACCCTGTTATTTTAGA
* * * *
3704304 GCGGATACTCCAACCCCGATTTTTATTTCTAGAA-CACCAATTTTCCATAATCGGGGATACTC
1 GGGGATACTCTAACCTCGA-TTTTATTTCTA-AATCA-CAATTTTTCATAATCGGGGATACTC
3704366 TAGCCCCGTT
Statistics
Matches: 117, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
78 8 0.07
79 70 0.60
80 35 0.30
81 4 0.03
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (78 bp):
GGGGATACTCTAACCTCGATTTTATTTCTAAATCACAATTTTTCATAATCGGGGATACTCCAACC
CTGTTATTTTAGA
Found at i:3704269 original size:131 final size:130
Alignment explanation
Indices: 3703885--3704269 Score: 413
Period size: 131 Copynumber: 2.9 Consensus size: 130
3703875 TTATTTCCGA
* * * * * * * * *
3703885 GGGGATACTCCAACCCCAATTTTATTCCCAAAACACCAGTTTTTCACAATTGGGCATACTCCAAC
1 GGGGATACTTCAACTCCGACTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
* * * * * *
3703950 CCCGTCATTTTCGAGGGGATACTCTGACCCTAGTTTTATTTTTAAAACACCAATTTT-TCATAAT
66 CCCGTTATTTT-GAGGGGATACTCTAACCCCAGTTTTATTTTCAAAATACCAATTTTCTCACAAT
3704014 C
130 C
*
3704015 GGGGATACTTCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTTCAACTCCGACTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
* * ** *
3704080 CCCGTTATTTCTGAGGGGATACTCTAACCCCAGCTTTA-TTTC-TAATATTATTGATTTCTCACA
66 CCCGTTATTT-TGAGGGGATACTCTAACCCCAGTTTTATTTTCAAAATACCAAT--TTTCTCACA
3704143 ATC
128 ATC
* * * *
3704146 GGGGATACTTCAAC-CTCGGCTTTATTTCTAAATCA-TCGATTTTTCACAATCGGGGATACTCCA
1 GGGGATACTTCAACTC-CGACTTTATTTCCAAAACACT-AATTTTTCACAATCGGGGATACTCCA
* *
3704209 AGCCCGTTATTTTAGAGGGGATACTCTAACCTC-GATTTTATTTTCAAAATACCAATTTTCT
64 ACCCCGTTATTTT-GAGGGGATACTCTAACCCCAG-TTTTATTTTCAAAATACCAATTTTCT
3704270 ATAATCAAGG
Statistics
Matches: 214, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
128 5 0.02
129 3 0.01
130 96 0.45
131 100 0.47
132 4 0.02
133 6 0.03
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (130 bp):
GGGGATACTTCAACTCCGACTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTGAGGGGATACTCTAACCCCAGTTTTATTTTCAAAATACCAATTTTCTCACAATC
Found at i:3716772 original size:8 final size:8
Alignment explanation
Indices: 3716753--3716797 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
3716743 TCTTTTTAAA
3716753 AAAAAACT
1 AAAAAACT
3716761 -AAAAACT
1 AAAAAACT
3716768 AAAAAAACT
1 -AAAAAACT
**
3716777 AAAAATTT
1 AAAAAACT
3716785 AAAAAACT
1 AAAAAACT
3716793 AAAAA
1 AAAAA
3716798 CAAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 7 0.23
8 17 0.55
9 7 0.23
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAAACT
Found at i:3716773 original size:16 final size:16
Alignment explanation
Indices: 3716752--3716805 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
3716742 TTCTTTTTAA
3716752 AAAAAAACTAAAAACT
1 AAAAAAACTAAAAACT
*
3716768 AAAAAAACTAAAAATT
1 AAAAAAACTAAAAACT
*
3716784 TAAAAAACTAAAAAC-
1 AAAAAAACTAAAAACT
3716799 AAAAAAA
1 AAAAAAA
3716806 AAACAAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 6 0.18
16 28 0.82
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAACTAAAAACT
Found at i:3716809 original size:11 final size:11
Alignment explanation
Indices: 3716793--3716843 Score: 50
Period size: 10 Copynumber: 4.5 Consensus size: 11
3716783 TTAAAAAACT
3716793 AAAAACAAAAA
1 AAAAACAAAAA
3716804 AAAAAC-AAAA
1 AAAAACAAAAA
*
3716814 CAAAACAAAGAA
1 AAAAACAAA-AA
*
3716826 AAAAGAGAGAAAA
1 AAAA-ACA-AAAA
3716839 AAAAA
1 AAAAA
3716844 GAACCTGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 9 0.27
11 8 0.24
12 6 0.18
13 8 0.24
14 2 0.06
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:3717980 original size:55 final size:54
Alignment explanation
Indices: 3717914--3718159 Score: 332
Period size: 55 Copynumber: 4.5 Consensus size: 54
3717904 CTCCTTTCAC
* *
3717914 CTTTTAGTCCTCAAAGAGCAGAACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
3717968 CCTTTCAATCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTAGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
3718023 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * **
3718078 TTTTCCAGTCCTCAAAGAGTAGGATACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
3718133 CTTCCCAGTCCTCAAAGAGCAGGACGC
1 CTT-TCAGTCCTCAAAGAGCAGGACGC
3718160 TCTCTCCTTT
Statistics
Matches: 171, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
54 3 0.02
55 166 0.97
56 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (54 bp):
CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:3717980 original size:94 final size:97
Alignment explanation
Indices: 3717803--3717994 Score: 268
Period size: 94 Copynumber: 2.0 Consensus size: 97
3717793 ATCTAAACTT
* * *
3717803 TCTCCTTTCACTTTTTAGTCCTCAAAGAGCACGATGCCTTTTCCTTTTAAAGCCCACACTAGTTG
1 TCTCCTTTCACCTTTTAGTCCTCAAAGAGCACGACGCCTTTTCC---TAAAGCCCACACAAGTTG
*
3717868 GTGGCACCTTCTAGTCCTCAAAGAGTAGGACGCTC
63 GTGGCACCTTCTAATCCTCAAAGAGTAGGACGCTC
3717903 TCTCCTTTCACCTTTTAGTCCTCAAAGAGCA-GAACGCC-TTT-C-AAAGCCCACACAAGTTGGT
1 TCTCCTTTCACCTTTTAGTCCTCAAAGAGCACG-ACGCCTTTTCCTAAAGCCCACACAAGTTGGT
3717964 GGCACCTT-TCAATCCTCAAAGAGTAGGACGC
65 GGCACCTTCT-AATCCTCAAAGAGTAGGACGC
3717995 CTTTCAAAGC
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
93 1 0.01
94 46 0.53
98 1 0.01
99 4 0.05
100 34 0.40
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (97 bp):
TCTCCTTTCACCTTTTAGTCCTCAAAGAGCACGACGCCTTTTCCTAAAGCCCACACAAGTTGGTG
GCACCTTCTAATCCTCAAAGAGTAGGACGCTC
Found at i:3718299 original size:211 final size:204
Alignment explanation
Indices: 3717976--3718367 Score: 520
Period size: 211 Copynumber: 1.9 Consensus size: 204
3717966 CACCTTTCAA
* *
3717976 TCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGA
1 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGA
*
3718041 GCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGATAC-
66 GCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGG--ACG
*
3718105 CTCTT-AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
129 CTCTTCAAAACCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
3718169 TCGCCCTTTAG
194 TCGCCCTTTAG
* * *
3718180 TCCTCATAGAGCAGGACACCATTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAA
1 TCCTCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTAGTGGCA-TTTTCCAGTCCTCAAA
* * * *
3718244 GAGTAGAATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
64 GAGCAG---GAC---ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
* * * * * *
3718309 AGGACGTTTTTCAAAACTCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGA
123 AGGACGCTCTTCAAAACCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGA
3718368 TGTTTTCTCC
Statistics
Matches: 161, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
204 39 0.24
205 23 0.14
208 2 0.01
209 2 0.01
210 3 0.02
211 92 0.57
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (204 bp):
TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGA
GCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCT
CTTCAAAACCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTC
GCCCTTTAG
Found at i:3718518 original size:122 final size:115
Alignment explanation
Indices: 3718173--3718552 Score: 388
Period size: 122 Copynumber: 3.2 Consensus size: 115
3718163 CTCCTTTCGC
* ***
3718173 CCTT-TAGTCCTCATAGAGCAGGACACCATTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAG
1 CCTTCTAGTCCTCAAAGAGCAGGAC-GTTTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCTAG
* *
3718236 TCCTCAAAGAGTAGAATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
64 TCCTCAAAGAGTAGGATGCCTTTT-CTTTTAAAGCCCACACGAGTTGGTGGCA
** * * * *
3718289 TTTTCCAGTCCTCAAAGAGCAGGACGTTTTTCAAAACTCACACAAGTTGGTGGCATTTTCTAGTC
1 CCTTCTAGTCCTCAAAGAGCAGGACGTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTC
* * * **
3718354 CTCAAAGAGCAGGATG-TTTTCTCCTTTTAAAGACCATTCGAGTTGGTGGCA
66 CTCAAAGAGTAGGATGCCTTT-T-CTTTTAAAGCCCACACGAGTTGGTGGCA
* * * *
3718405 CCTTCTAGTCTTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGTACCTT
1 CCTTCTAGTCCTCAAAGAGCAGGA--C-GT-T-TTT-CAAAGCCCACACAAGTTGGTGGCACTTT
* * *
3718470 CCAGTCCTCAAAAAGTAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
60 CTAGTCCTCAAAGAGTAGGATGCCTTTTCTTTT-AAAGCCCACACGAGTTGGTGGCA
* * *
3718527 CGTTTTAGTCCTCAAAGAACAGGACG
1 CCTTCTAGTCCTCAAAGAGCAGGACG
3718553 CCTTTTCCTT
Statistics
Matches: 213, Mismatches: 40, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
115 3 0.01
116 74 0.35
117 39 0.18
118 1 0.00
119 1 0.00
120 2 0.01
121 8 0.04
122 82 0.38
123 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (115 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTC
CTCAAAGAGTAGGATGCCTTTTCTTTTAAAGCCCACACGAGTTGGTGGCA
Found at i:3718551 original size:61 final size:60
Alignment explanation
Indices: 3718204--3718565 Score: 321
Period size: 61 Copynumber: 6.0 Consensus size: 60
3718194 GACACCATTT
* * * *
3718204 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGAATGCCTTTTCCTTTT-
1 AAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGACG-CTTTT-CTTTTC
3718266 AAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACG----T-TTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTT--AGTCCTCAAAGAGCAGGACGCTTTTCTTTTC
* * * * *
3718321 AAAACTCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGATG-TTTTCTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGACGCTTTTCT--TTTC
* ** * * * * *
3718382 AAAGACCATTCGAGTTGGTGGCACCTTCTAGTCTTCAAAGAGCAGGATGCTTTCTCTTTGC
1 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCTTT-TCTTTTC
* ** * *
3718443 AAAGCCCACACAAGTTGGTGGTACCTTCCAGTCCTCAAAAAGTAGGACGCCTTTTCTTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG-CTTTTCTTTTC
* * *
3718504 AAAGCCCACACGAGTTGGTGGCACGTTTTAGTCCTCAAAGAACAGGACGCCTTTTCCTTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG-CTTTT-CTTTTC
3718566 TCCTTTGTCC
Statistics
Matches: 247, Mismatches: 37, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
54 4 0.02
55 40 0.16
56 4 0.02
57 1 0.00
58 1 0.00
59 2 0.01
60 3 0.01
61 151 0.61
62 38 0.15
63 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (60 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCTTTTCTTTTC
Found at i:3718656 original size:40 final size:40
Alignment explanation
Indices: 3718529--3718673 Score: 154
Period size: 45 Copynumber: 3.5 Consensus size: 40
3718519 TGGTGGCACG
*
3718529 TTTTAGTCCTCAAAGAACAGGACGC-CTTT-TCCTTTTCTCC
1 TTTT-GTCCTCAAAGAGCAGGACGCACTTTAT-CTTTTCTCC
* * *
3718569 -TTTGTCCTCAAAGAGCAGGACACACTTCATTCCCTTCTTTTCCC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTA-T--CTT-TTCT-CC
3718613 TTTTGTCCTCAAAGAGCAGGACGCACTTTAT-TTTTCTCTC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTATCTTTTCTC-C
3718653 TTTTGTCCTCAAAGAGCAGGA
1 TTTTGTCCTCAAAGAGCAGGA
3718674 TGCATTTCGT
Statistics
Matches: 90, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
38 18 0.20
39 7 0.08
40 25 0.28
41 3 0.03
42 4 0.04
43 3 0.03
44 3 0.03
45 27 0.30
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.36
Consensus pattern (40 bp):
TTTTGTCCTCAAAGAGCAGGACGCACTTTATCTTTTCTCC
Found at i:3719158 original size:13 final size:13
Alignment explanation
Indices: 3719140--3719169 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3719130 ATACATTGTT
3719140 CATTGTATCGATA
1 CATTGTATCGATA
*
3719153 CATTGTATTGATA
1 CATTGTATCGATA
3719166 CATT
1 CATT
3719170 ATGAGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3721651 original size:79 final size:80
Alignment explanation
Indices: 3721517--3721738 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 80
3721507 TCTTCATCTC
* * *
3721517 GGGGATACTGCAACCTCGATTTTATTTCCAAAACA-TCAATTTTTCATAATCAGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACT-AATTTTTCATAATCAGGGATACTCCAA
* *
3721581 TCCC-GTTATTT-TCGA
65 ACCCTGTCATTTCT-GA
* * * * *
3721596 GGGGATACTTCAACCCCGACTTTA-TTCTTAAAACACTAGTTTTTCACAATTAGGGATACT-CAA
1 GGGGATACTCCAACCCCGATTTTATTTC-TAAAACACTAATTTTTCATAATCAGGGATACTCCAA
3721659 ACCCTGTCATTTCTGA
65 ACCCTGTCATTTCTGA
* * *
3721675 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCATAATCAGGGATACTCCAA
3721739 CTCCGATTTT
Statistics
Matches: 120, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
78 9 0.08
79 103 0.86
80 8 0.07
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCATAATCAGGGATACTCCAAA
CCCTGTCATTTCTGA
Found at i:3721751 original size:51 final size:51
Alignment explanation
Indices: 3721675--3721794 Score: 195
Period size: 51 Copynumber: 2.4 Consensus size: 51
3721665 TCATTTCTGA
* *
3721675 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
* *
3721726 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
*
3721777 AGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3721795 TTATTTCATC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:3721810 original size:28 final size:28
Alignment explanation
Indices: 3721778--3721850 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
3721768 TTCACAATCA
*
3721778 GGGATACTCCAACCCCGTTATTT-CATCG
1 GGGATACTCCAACCCCGTTATTTCCA-AG
*
3721806 GGGATACTCTAACCCCGTTATTTCCAAG
1 GGGATACTCCAACCCCGTTATTTCCAAG
3721834 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
3721851 GCTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 39 0.95
29 2 0.05
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCCAAG
Found at i:3721810 original size:158 final size:158
Alignment explanation
Indices: 3721648--3721958 Score: 376
Period size: 158 Copynumber: 2.0 Consensus size: 158
3721638 TTCACAATTA
* ** * *
3721648 GGGATACTCAAACCCTGTCATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCA
1 GGGATACTCAAACCCCGTCATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACCA
* *
3721713 ATTT-TCCATAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTTTTCACAAT
66 ATTTCT-CACAATCGGGGATACTCCAAC-CCTGACTTTATTTCCAAAACACCAATTTTTCACAAT
3721776 C-AGGGATACTCCAACCCCGTTATTTCATCG
129 CGA-GGATACTCCAACCCCGTTATTTCATCG
* * * * ***
3721806 GGGATACTCTAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTG
1 GGGATACTCAAACCCCGTCATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACCA
* * * * ***
3721871 ATTTCTCACAATCGGGGATACTTCAACCCTGGCTTTATTTCTAAATCATTGATTTTTCACAATCG
66 ATTTCTCACAATCGGGGATACTCCAACCCTGACTTTATTTCCAAAACACCAATTTTTCACAATCG
*
3721936 AGGATACTCCAACCCTGTTATTT
131 AGGATACTCCAACCCCGTTATTT
3721959 TCGATGGGAT
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
157 2 0.02
158 124 0.97
159 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (158 bp):
GGGATACTCAAACCCCGTCATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACCA
ATTTCTCACAATCGGGGATACTCCAACCCTGACTTTATTTCCAAAACACCAATTTTTCACAATCG
AGGATACTCCAACCCCGTTATTTCATCG
Found at i:3721905 original size:51 final size:51
Alignment explanation
Indices: 3721833--3721952 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
3721823 TTATTTCCAA
*
3721833 GGGGATACTCCAACCCCGGCTTTATTTCCAAAAT-ATTGATTTCTCACAATC
1 GGGGATACTCCAACCCTGGCTTTATTT-CAAAATCATTGATTTCTCACAATC
* * *
3721884 GGGGATACTTCAACCCTGGCTTTATTTCTAAATCATTGATTTTTCACAATC
1 GGGGATACTCCAACCCTGGCTTTATTTCAAAATCATTGATTTCTCACAATC
*
3721935 GAGGATACTCCAACCCTG
1 GGGGATACTCCAACCCTG
3721953 TTATTTTCGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 5 0.08
51 57 0.92
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGGCTTTATTTCAAAATCATTGATTTCTCACAATC
Found at i:3721968 original size:79 final size:78
Alignment explanation
Indices: 3721885--3722103 Score: 257
Period size: 79 Copynumber: 2.8 Consensus size: 78
3721875 CTCACAATCG
* ** * *
3721885 GGGATACTTCAACCCTGGCTTTATTTCTAAATCATTGATTTTTCACAATCGAGGATACTCCAACC
1 GGGATACTTCAACCCCGATTTTATTTCTAAATCACTGATTTTTCATAATCGAGGATACTCCAACC
3721950 CTGTTATTTTCGA
66 CTGTTATTTTCGA
* * *
3721963 TGGGATATTTCAACCCCGATTTTATTTTCAAAAT-ACT-AATTTTCTATAATC-AGGGATACTCC
1 -GGGATACTTCAACCCCGATTTTA-TTTCTAAATCACTGATTTTTC-ATAATCGA-GGATACTCC
3722025 AACCCTGTTATTTTCGA
62 AACCCTGTTATTTTCGA
* *
3722042 GCGGATACTCCAACCCCGATTTTTATTTCTAGAA-CACCGATTTTTCATAATCGAGGATACTC
1 G-GGATACTTCAACCCCGA-TTTTATTTCTA-AATCACTGATTTTTCATAATCGAGGATACTC
3722104 TAGCCCCGTT
Statistics
Matches: 118, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
78 8 0.07
79 72 0.61
80 31 0.26
81 7 0.06
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (78 bp):
GGGATACTTCAACCCCGATTTTATTTCTAAATCACTGATTTTTCATAATCGAGGATACTCCAACC
CTGTTATTTTCGA
Found at i:3727336 original size:20 final size:21
Alignment explanation
Indices: 3727297--3727337 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3727287 ACAGCCCATG
3727297 TTCATGCATTTTGAGCTATGT
1 TTCATGCATTTTGAGCTATGT
*
3727318 TTCATGCATTTTTAG-TATGT
1 TTCATGCATTTTGAGCTATGT
3727338 AGTTATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (21 bp):
TTCATGCATTTTGAGCTATGT
Found at i:3728588 original size:24 final size:26
Alignment explanation
Indices: 3728561--3728611 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
3728551 ATCAAATTTT
3728561 TATTCAT-CG-GGGATACTCCAACCC
1 TATTCATCCGAGGGATACTCCAACCC
*
3728585 TATTCTTCCGAAGGGATACTCCAACCC
1 TATTCATCCG-AGGGATACTCCAACCC
3728612 CGTCTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
27 15 0.65
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.25
Consensus pattern (26 bp):
TATTCATCCGAGGGATACTCCAACCC
Found at i:3736815 original size:20 final size:19
Alignment explanation
Indices: 3736781--3736886 Score: 84
Period size: 19 Copynumber: 5.8 Consensus size: 19
3736771 ACTGTCAGTT
*
3736781 TCATGTATTGATACAATTG
1 TCATGTATCGATACAATTG
*
3736800 TCCATATATCGATACAA-TG
1 T-CATGTATCGATACAATTG
*
3736819 ATCATGTATCCATAC-A---
1 -TCATGTATCGATACAATTG
3736835 --ATGTATCGATACAATTG
1 TCATGTATCGATACAATTG
3736852 TCCATGTATCGATACAA-TG
1 T-CATGTATCGATACAATTG
*
3736871 ATCGTGTATCGATACA
1 -TCATGTATCGATACA
3736887 TATCGATACT
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
13 11 0.15
14 1 0.01
18 1 0.01
19 29 0.41
20 29 0.41
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (19 bp):
TCATGTATCGATACAATTG
Found at i:3736862 original size:52 final size:52
Alignment explanation
Indices: 3736783--3736886 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
3736773 TGTCAGTTTC
*
3736783 ATGTATTGATACAATTGTCCATATATCGATACAATGATCATGTATCCATACA
1 ATGTATCGATACAATTGTCCATATATCGATACAATGATCATGTATCCATACA
* * *
3736835 ATGTATCGATACAATTGTCCATGTATCGATACAATGATCGTGTATCGATACA
1 ATGTATCGATACAATTGTCCATATATCGATACAATGATCATGTATCCATACA
3736887 TATCGATACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (52 bp):
ATGTATCGATACAATTGTCCATATATCGATACAATGATCATGTATCCATACA
Found at i:3736867 original size:33 final size:32
Alignment explanation
Indices: 3736806--3736874 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
3736796 ATTGTCCATA
3736806 TATCGATACAATGATCATGTATCCATACAATG
1 TATCGATACAATGATCATGTATCCATACAATG
*
3736838 TATCGATACAATTG-TCCATGTATCGATACAATG
1 TATCGATACAA-TGAT-CATGTATCCATACAATG
3736871 -ATCG
1 TATCG
3736875 TGTATCGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 16 0.47
33 18 0.53
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (32 bp):
TATCGATACAATGATCATGTATCCATACAATG
Found at i:3736880 original size:19 final size:20
Alignment explanation
Indices: 3736782--3736886 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
3736772 CTGTCAGTTT
*
3736782 CATGTATTGATACAATTGTC
1 CATGTATCGATACAATTGTC
*
3736802 CATATATCGATACAA-TGAT-
1 CATGTATCGATACAATTG-TC
*
3736821 CATGTATCCATAC-A-----
1 CATGTATCGATACAATTGTC
3736835 -ATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
3736854 CATGTATCGATACAA-TGAT-
1 CATGTATCGATACAATTG-TC
*
3736873 CGTGTATCGATACA
1 CATGTATCGATACA
3736887 TATCGATACT
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
13 11 0.16
14 1 0.01
18 1 0.01
19 28 0.40
20 29 0.41
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:3744378 original size:40 final size:40
Alignment explanation
Indices: 3744333--3744449 Score: 234
Period size: 40 Copynumber: 2.9 Consensus size: 40
3744323 CAATTCGAAG
3744333 ATGTCTTGATAAAAGTTCAAAAATCAATGTGAGAAAAGAA
1 ATGTCTTGATAAAAGTTCAAAAATCAATGTGAGAAAAGAA
3744373 ATGTCTTGATAAAAGTTCAAAAATCAATGTGAGAAAAGAA
1 ATGTCTTGATAAAAGTTCAAAAATCAATGTGAGAAAAGAA
3744413 ATGTCTTGATAAAAGTTCAAAAATCAATGTGAGAAAA
1 ATGTCTTGATAAAAGTTCAAAAATCAATGTGAGAAAA
3744450 TAAAGTAGTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.26
Consensus pattern (40 bp):
ATGTCTTGATAAAAGTTCAAAAATCAATGTGAGAAAAGAA
Found at i:3749481 original size:16 final size:15
Alignment explanation
Indices: 3749457--3749503 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
3749447 AAATAGTGCC
3749457 AAAAAACAAAAAAAT
1 AAAAAACAAAAAAAT
3749472 AAACAAACAAAAATAAT
1 AAA-AAACAAAAA-AAT
*
3749489 AAAAAACAATAAAAT
1 AAAAAACAAAAAAAT
3749504 CATATGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.21
16 17 0.59
17 6 0.21
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAACAAAAAAAT
Found at i:3757008 original size:20 final size:20
Alignment explanation
Indices: 3756932--3757010 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
3756922 AAAAAGCCAG
* *
3756932 AATGTATCGATACAATGAGA
1 AATGTATCGATACATTTAGA
3756952 AATGTATCGATACAATTGTA-A
1 AATGTATCGATAC-ATT-TAGA
* *
3756973 ACATGTATTGATACATTTAGT
1 A-ATGTATCGATACATTTAGA
3756994 AATGTATCGATACATTT
1 AATGTATCGATACATTT
3757011 CCTTAGTAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 30 0.60
21 8 0.16
22 12 0.24
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTTAGA
Found at i:3758133 original size:70 final size:70
Alignment explanation
Indices: 3757996--3758139 Score: 200
Period size: 70 Copynumber: 2.1 Consensus size: 70
3757986 AAAATATCAT
* * * * *
3757996 AGTAACCCTAAAATACTTGATAATATCATGAAATGACTAACCTATTCCTCAAGCACACCTTTGAC
1 AGTAACCCTAAAAGACTCGATAATATCATGAAATCACTAACCTATTCCTCAAGAACACCTTTAAC
3758061 ATGAA
66 ATGAA
* **
3758066 AGTAATCCTAAAAGACTCGATAATATCATGAAATCACTAACCTATTCCT-AAGGAACATGTTTAA
1 AGTAACCCTAAAAGACTCGATAATATCATGAAATCACTAACCTATTCCTCAA-GAACACCTTTAA
3758130 CATGAA
65 CATGAA
3758136 AGTA
1 AGTA
3758140 TCCCGATGAC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
69 2 0.03
70 63 0.97
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (70 bp):
AGTAACCCTAAAAGACTCGATAATATCATGAAATCACTAACCTATTCCTCAAGAACACCTTTAAC
ATGAA
Found at i:3759301 original size:11 final size:12
Alignment explanation
Indices: 3759282--3759319 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
3759272 TACCAAGGAA
3759282 ATGTATCGATAC
1 ATGTATCGATAC
3759294 AT-TATCGATAC
1 ATGTATCGATAC
3759305 ATTGTATCGATAC
1 A-TGTATCGATAC
3759318 AT
1 AT
3759320 CGATCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.42
12 4 0.17
13 10 0.42
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:3759314 original size:13 final size:13
Alignment explanation
Indices: 3759283--3759319 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3759273 ACCAAGGAAA
3759283 TGTATCGATACA-
1 TGTATCGATACAT
3759295 T-TATCGATACAT
1 TGTATCGATACAT
3759307 TGTATCGATACAT
1 TGTATCGATACAT
3759320 CGATCTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3759331 original size:20 final size:21
Alignment explanation
Indices: 3759283--3759340 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
3759273 ACCAAGGAAA
3759283 TGTATCGATACATTATCGATACAT
1 TGTATCGATAC---ATCGATACAT
*
3759307 TGTATCGATACATCGAT-CTT
1 TGTATCGATACATCGATACAT
3759327 TGTATCGATACATC
1 TGTATCGATACATC
3759341 TAGGAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 6 0.18
24 11 0.33
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATCGATACAT
Found at i:3760969 original size:69 final size:70
Alignment explanation
Indices: 3760874--3761012 Score: 244
Period size: 69 Copynumber: 2.0 Consensus size: 70
3760864 AGAATATCAT
**
3760874 CGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTT-AAAAACGGGGTTGGAGT
1 CGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTTGAAAAACAAGGTTGGAGT
3760938 ATCCC
66 ATCCC
*
3760943 CGACAATGATAATTTGGACAAAATAAGATTTAAATTTTGATGAGTTTGAAAAACAAGGTTGGAGT
1 CGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTTGAAAAACAAGGTTGGAGT
3761008 ATCCC
66 ATCCC
3761013 TTTGAAAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
69 46 0.70
70 20 0.30
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (70 bp):
CGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTTGAAAAACAAGGTTGGAGT
ATCCC
Found at i:3762188 original size:21 final size:21
Alignment explanation
Indices: 3762162--3762203 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3762152 TTGAACTCTT
3762162 TTAATCAAGAATCTAGATCTG
1 TTAATCAAGAATCTAGATCTG
3762183 TTAATCAAGAATCTAGATCTG
1 TTAATCAAGAATCTAGATCTG
3762204 AAAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
TTAATCAAGAATCTAGATCTG
Found at i:3762873 original size:14 final size:14
Alignment explanation
Indices: 3762848--3762885 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
3762838 AATACCTTAG
3762848 TGTTTCTTTTGCTGT
1 TGTTTCTTTTGCT-T
3762863 TGTTT-TTTTGCTT
1 TGTTTCTTTTGCTT
3762876 TGTTTGCTTT
1 TGTTT-CTTT
3762886 CAACTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 7 0.33
15 8 0.38
ACGTcount: A:0.00, C:0.11, G:0.18, T:0.71
Consensus pattern (14 bp):
TGTTTCTTTTGCTT
Found at i:3763642 original size:20 final size:20
Alignment explanation
Indices: 3763619--3763672 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3763609 CTCCTTGTTG
3763619 GGTTGCTGATCGTCTTGCTT
1 GGTTGCTGATCGTCTTGCTT
* *
3763639 GGTTGCTGAACATCTTGCTT
1 GGTTGCTGATCGTCTTGCTT
*
3763659 GGTTGCTGGTCGTC
1 GGTTGCTGATCGTC
3763673 CTTTGCTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.07, C:0.20, G:0.31, T:0.41
Consensus pattern (20 bp):
GGTTGCTGATCGTCTTGCTT
Found at i:3764014 original size:20 final size:20
Alignment explanation
Indices: 3763989--3764028 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3763979 CATATTCCAT
*
3763989 TTGCTTTTGTCTCCTATTGC
1 TTGCTTTTGTCTCCCATTGC
3764009 TTGCTTTTGTCTCCCATTGC
1 TTGCTTTTGTCTCCCATTGC
3764029 AAGCATGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.28, G:0.15, T:0.53
Consensus pattern (20 bp):
TTGCTTTTGTCTCCCATTGC
Found at i:3764196 original size:16 final size:16
Alignment explanation
Indices: 3764149--3764203 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
3764139 TTTCATTATC
*
3764149 ATTTTTTTATT-TTTT
1 ATTTTATTATTATTTT
*
3764164 ATTTTTTTGATTA-TTT
1 ATTTTATT-ATTATTTT
3764180 ATTTTATTATTATTTT
1 ATTTTATTATTATTTT
3764196 AATTTTAT
1 -ATTTTAT
3764204 ATAAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
15 12 0.34
16 16 0.46
17 7 0.20
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
ATTTTATTATTATTTT
Found at i:3772822 original size:13 final size:13
Alignment explanation
Indices: 3772804--3772829 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3772794 TACAGCAAGT
3772804 ATGTATCGATACA
1 ATGTATCGATACA
3772817 ATGTATCGATACA
1 ATGTATCGATACA
3772830 CAAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3772827 original size:32 final size:32
Alignment explanation
Indices: 3772786--3772848 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3772776 TAGCCAAACT
**
3772786 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAATTGTATCGATACAA
3772818 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
3772849 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:3775054 original size:21 final size:21
Alignment explanation
Indices: 3775021--3775065 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3775011 TTGCAAGTTG
*
3775021 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3775043 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3775063 AAA
1 AAA
3775066 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3776888 original size:15 final size:15
Alignment explanation
Indices: 3776868--3776898 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3776858 TAAAAATGTC
*
3776868 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3776883 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3776898 C
1 C
3776899 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3778995 original size:13 final size:13
Alignment explanation
Indices: 3778977--3779028 Score: 104
Period size: 13 Copynumber: 4.0 Consensus size: 13
3778967 ACATTTTTCT
3778977 TTGTATCGATACA
1 TTGTATCGATACA
3778990 TTGTATCGATACA
1 TTGTATCGATACA
3779003 TTGTATCGATACA
1 TTGTATCGATACA
3779016 TTGTATCGATACA
1 TTGTATCGATACA
3779029 GGGTGATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Done.