Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 103 of 106
Found at i:39404959 original size:17 final size:17
Alignment explanation
Indices: 39404937--39404980 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
39404927 ATAAATTTTT
39404937 TATATTTATTTTTA-ATA
1 TATATTTATTTTTAGA-A
*
39404954 TATATTAATTTTTAGAA
1 TATATTTATTTTTAGAA
*
39404971 TATATGTATT
1 TATATTTATT
39404981 ACTTGTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TATATTTATTTTTAGAA
Found at i:39447081 original size:108 final size:108
Alignment explanation
Indices: 39446887--39447139 Score: 332
Period size: 108 Copynumber: 2.3 Consensus size: 108
39446877 ATTGTTTACC
* * * *
39446887 GCTTCCACTACCCTCACTTGAATGCTTACTGCTTCCAGTTTCATGATCAAGTTCTAGATGTCTTC
1 GCTTCCACTACCCTCACATGAACGATTACTGCTTCCAGTTTCATCATCAAGTTCTAGATGTCTTC
39446952 TTGAATGCCCACTGCTACCACTGC-CCTCACTTAAACGCTCACT
66 TTGAATGCCCACTGCTACCACT-CTCCTCACTTAAACGCTCACT
* *
39446995 GCTTCCACTACCCTCGCATGAACGATTAC-GTCTTTCAGTTTCATCATCAAGTTCTAGATGTCTT
1 GCTTCCACTACCCTCACATGAACGATTACTG-CTTCCAGTTTCATCATCAAGTTCTAGATGTCTT
* * * * *
39447059 CTTGAATGCTCACTGCTTCCACTCTCCTCACTTGAATGCTTACT
65 CTTGAATGCCCACTGCTACCACTCTCCTCACTTAAACGCTCACT
* * *
39447103 GCTTCCACT-CTCCTCACTTGAATGCTTACTGCTTCCA
1 GCTTCCACTAC-CCTCACATGAACGATTACTGCTTCCA
39447140 CTTCCCTCAC
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
107 3 0.02
108 121 0.97
109 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (108 bp):
GCTTCCACTACCCTCACATGAACGATTACTGCTTCCAGTTTCATCATCAAGTTCTAGATGTCTTC
TTGAATGCCCACTGCTACCACTCTCCTCACTTAAACGCTCACT
Found at i:39447174 original size:30 final size:30
Alignment explanation
Indices: 39447059--39447167 Score: 159
Period size: 30 Copynumber: 3.6 Consensus size: 30
39447049 TAGATGTCTT
*
39447059 CTTGAATGCTCACTGCTTCCAC-TCTCCTCA
1 CTTGAATGCTTACTGCTTCCACTTC-CCTCA
39447089 CTTGAATGCTTACTGCTTCCAC-TCTCCTCA
1 CTTGAATGCTTACTGCTTCCACTTC-CCTCA
39447119 CTTGAATGCTTACTGCTTCCACTTCCCTCA
1 CTTGAATGCTTACTGCTTCCACTTCCCTCA
* *
39447149 CTCGAATGCCTACTGCTTC
1 CTTGAATGCTTACTGCTTC
39447168 TGCTTCCAAC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
30 73 0.97
31 2 0.03
ACGTcount: A:0.17, C:0.38, G:0.11, T:0.35
Consensus pattern (30 bp):
CTTGAATGCTTACTGCTTCCACTTCCCTCA
Found at i:39447374 original size:22 final size:22
Alignment explanation
Indices: 39447346--39447389 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
39447336 TCCCTATAGG
39447346 TCTACCTGGAAAATGAAAACAA
1 TCTACCTGGAAAATGAAAACAA
39447368 TCTACCTGGAAAATGAAAACAA
1 TCTACCTGGAAAATGAAAACAA
39447390 AAGGAAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (22 bp):
TCTACCTGGAAAATGAAAACAA
Found at i:39452720 original size:9 final size:9
Alignment explanation
Indices: 39452676--39452725 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
39452666 GAATCAGAGA
39452676 CTCTCCTCTT
1 CTCTCCT-TT
39452686 CTC-CCTTT
1 CTCTCCTTT
*
39452694 C-CTCTTTT
1 CTCTCCTTT
39452702 CTCTCTCTTT
1 CTCTC-CTTT
39452712 CTCTCCTTT
1 CTCTCCTTT
39452721 CTCTC
1 CTCTC
39452726 TCTATAGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
7 1 0.03
8 8 0.23
9 15 0.43
10 11 0.31
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (9 bp):
CTCTCCTTT
Found at i:39452723 original size:19 final size:19
Alignment explanation
Indices: 39452676--39452728 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
39452666 GAATCAGAGA
39452676 CTCTCCTCTTCTC-C-CTTT
1 CTCTCCT-TTCTCTCTCTTT
*
39452694 C-CTCTTTTCTCTCTCTTT
1 CTCTCCTTTCTCTCTCTTT
39452712 CTCTCCTTTCTCTCTCT
1 CTCTCCTTTCTCTCTCT
39452729 ATAGAGTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 5 0.17
17 5 0.17
18 6 0.20
19 14 0.47
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (19 bp):
CTCTCCTTTCTCTCTCTTT
Found at i:39474684 original size:50 final size:50
Alignment explanation
Indices: 39474630--39474799 Score: 292
Period size: 50 Copynumber: 3.5 Consensus size: 50
39474620 GGGTTTACTA
* *
39474630 AATATTTTAATTTCTAAAAAGAAATATTTTTATATTTTTTAAAAAAATTT
1 AATATTTTAATTTCTAAAAAGAAATATTTTCATATTTTTTAAAAAATTTT
39474680 AATATTTTAATTTCTAAAAAGAAATATTTTCATA-TTTTT--AAAATTTT
1 AATATTTTAATTTCTAAAAAGAAATATTTTCATATTTTTTAAAAAATTTT
*
39474727 AATATTTTAATTTCTAAAAAGAAATATTTTCATATTTTTTAAAAATTTTT
1 AATATTTTAATTTCTAAAAAGAAATATTTTCATATTTTTTAAAAAATTTT
39474777 AATATTTTAATTTCTAAAAAGAA
1 AATATTTTAATTTCTAAAAAGAA
39474800 TACTAATTAT
Statistics
Matches: 114, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
47 41 0.36
48 5 0.04
49 5 0.04
50 63 0.55
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (50 bp):
AATATTTTAATTTCTAAAAAGAAATATTTTCATATTTTTTAAAAAATTTT
Found at i:39483362 original size:2 final size:2
Alignment explanation
Indices: 39483357--39483397 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39483347 TATATATGTT
39483357 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
39483398 TATGCAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39484471 original size:283 final size:282
Alignment explanation
Indices: 39484001--39484525 Score: 747
Period size: 283 Copynumber: 1.9 Consensus size: 282
39483991 ACATAACCTT
* *
39484001 TAAAATATCAATCAATTGAGAATTTAATTAACTATAAATGAGAAAAATAGATATTCAAGGTAAAT
1 TAAAATATCAATCAATCGAGAATTTAATTAACTATAAATGAAAAAAATAGATATTCAAGGTAAAT
* * * * * * *
39484066 AACCATATTATTATAGTAAGTGAGATATAAAAAGGAAAATTGTCTACCGAAGTTAAGCTGATCAT
66 AACCATATTATTACAATAAGTGAGATACAAAAAGAAAAATTATCTACCAAAGTTAAGCTGATCAG
* * *
39484131 ATACAATCTTTGGTGAAAATTTTTTTTGACTCTCAAGATTGTTGGTATCAGCACCTGCTCAAA-T
131 ATACAATCTTTGGTGAAAATTTTTTGTAACTCTCAAGATTGTTGGTATCAACACCTGCTCAAATT
*
39484195 GAAAGTAACATTTGCATTATGTTATC-AATATAATTTATCTACTACAGTTACAGTTTACTTAGAA
196 G-AAGTAACATTTGCATTAGGTTATCAAATATAATTTATCTACTACAGTTACAGTTTACTTAGAA
39484259 AGAGTAGATAAAAGTATAATTTC
260 AGAGTAGATAAAAGTATAATTTC
* *
39484282 TAAAATATCAATTAATCGAGAATTTAATTAACTATAAAT-AAAAAAATATTGATATTCTAGGTAA
1 TAAAATATCAATCAATCGAGAATTTAATTAACTATAAATGAAAAAAATA--GATATTCAAGGTAA
* *
39484346 ATAACCATATTATTACAATAAGTGAGATACCAAAAA-AAAAAGTTATGTACCAAAGTTAAGTTGA
64 ATAACCATATTATTACAATAAGTGAGATA-CAAAAAGAAAAA-TTATCTACCAAAGTTAAGCTGA
* * *
39484410 TCAGATACAATTTTTGGTGAAGATTTTTTGTAACTCT-TAGAATTGTTGAG-ATCAACACCTGCT
127 TCAGATACAATCTTTGGTGAAAATTTTTTGTAACTCTCAAG-ATTGTTG-GTATCAACACCTGCT
*
39484473 CAAATTGAATTAACATTTGCATTAGGTTATCAAAATATAATTTATCTACTACA
190 CAAATTGAAGTAACATTTGCATTAGGTTATC-AAATATAATTTATCTACTACA
39484526 TCACCAATTC
Statistics
Matches: 214, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
280 8 0.04
281 37 0.17
282 46 0.21
283 100 0.47
284 3 0.01
285 20 0.09
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (282 bp):
TAAAATATCAATCAATCGAGAATTTAATTAACTATAAATGAAAAAAATAGATATTCAAGGTAAAT
AACCATATTATTACAATAAGTGAGATACAAAAAGAAAAATTATCTACCAAAGTTAAGCTGATCAG
ATACAATCTTTGGTGAAAATTTTTTGTAACTCTCAAGATTGTTGGTATCAACACCTGCTCAAATT
GAAGTAACATTTGCATTAGGTTATCAAATATAATTTATCTACTACAGTTACAGTTTACTTAGAAA
GAGTAGATAAAAGTATAATTTC
Found at i:39484776 original size:286 final size:284
Alignment explanation
Indices: 39484001--39484812 Score: 756
Period size: 286 Copynumber: 2.9 Consensus size: 284
39483991 ACATAACCTT
* ** * *
39484001 TAAAATATCAATCAATTGAGAATTTAATTAACTATAAATGAGAAAAATA--GATATTC-AAGGTA
1 TAAAATATCAAACAATCAAGAATTTAATTAACTATAAAT-AAAAAAATATTGATATTCTAA-GCA
* * * * * * * * *
39484063 AATAACCATATTATTATAGTAAGTGAGATA-TAAAAAGGAAAA-TTGTCTACCGAAGTTAAGCTG
64 AATAACCATATTATTACAATAAGTGAGATACCAAAAA-AAAAAGTTATGTACCAAAATTAAGTTG
* * * * *
39484126 ATCATATACAATCTTTGGTGAAAATTTTTTTTGACTCTCAAGATTGTTGGTATCAGCACCTGCTC
128 ATCAAATACAATGTTTGGTGAAAATTTTTTATGACTCTTAAAATTGTTGGTATCAGCACCTGCTC
* * * * * *
39484191 AAATGAAAGTAACATTTGCATTATGTTATC--AATATAATTTATCTACTACAGTTACAGTTTACT
193 AAATGGAAGTAACATTTGCATTAAGTTATCAAAATATAATTTATCTACTACA-TCACAATTCACA
* * * ***
39484254 TAGAAAGAGTAGATAAAAGTATAATTTC
257 TAGAAAAAGCAGATAAAACTATAACACC
** * * *
39484282 TAAAATATCAATTAATCGAGAATTTAATTAACTATAAATAAAAAAATATTGATATTCTAGGTAAA
1 TAAAATATCAAACAATCAAGAATTTAATTAACTATAAATAAAAAAATATTGATATTCTAAGCAAA
*
39484347 TAACCATATTATTACAATAAGTGAGATACCAAAAAAAAAAGTTATGTACCAAAGTTAAGTTGATC
66 TAACCATATTATTACAATAAGTGAGATACCAAAAAAAAAAGTTATGTACCAAAATTAAGTTGATC
* * * * * * *
39484412 AGATACAATTTTTGGTGAAGATTTTTTGTAACTCTTAGAATTGTTGAG-ATCAACACCTGCTCAA
131 AAATACAATGTTTGGTGAAAATTTTTTATGACTCTTAAAATTGTTG-GTATCAGCACCTGCTCAA
* * *
39484476 ATTGAATTAACATTTGCATTAGGTTATCAAAATATAATTTATCTACTACATCACCAATTCACATA
195 ATGGAAGTAACATTTGCATTAAGTTATCAAAATATAATTTATCTACTACATCA-CAATTCACATA
39484541 GAAAAAGCAGATAAATATCTCCAAGATAACACC
259 GAAAAAGCAGATAAA-A-CT-----ATAACACC
* *
39484574 TAAAATATCAAACAATCAAGAATTTAATTAACTATAAAT-AGAATATATTGATATT-TCAAGCAA
1 TAAAATATCAAACAATCAAGAATTTAATTAACTATAAATAAAAAAATATTGATATTCT-AAGCAA
* * * * * * * * * *
39484637 ATAA-C-TATTGTTCCAGTAAGT-A-ATA-TAGAACAAGAAGTTGTGTATCAAAATTTAGTTGAT
65 ATAACCATATTATTACAATAAGTGAGATACCAAAAAAAAAAGTTATGTACCAAAATTAAGTTGAT
* * * *
39484697 TAAATATC-ATGTTTGGTGAAAATTTTTCATGACTCTTAAAATTGCTGGTATCAGCACATGCTCA
130 CAAATA-CAATGTTTGGTGAAAATTTTTTATGACTCTTAAAATTGTTGGTATCAGCACCTGCTCA
* * * * * *
39484761 AATGGAAGCAACATTTGCATTAAGTCATCAAAATGTTATTTATTTATTACAT
194 AATGGAAGTAACATTTGCATTAAGTTATCAAAATATAATTTATCTACTACAT
39484813 GACTAGTTTA
Statistics
Matches: 439, Mismatches: 73, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
280 8 0.02
281 37 0.08
282 42 0.10
283 103 0.23
284 3 0.01
285 42 0.10
286 120 0.27
287 5 0.01
288 1 0.00
289 13 0.03
290 2 0.00
291 22 0.05
292 41 0.09
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (284 bp):
TAAAATATCAAACAATCAAGAATTTAATTAACTATAAATAAAAAAATATTGATATTCTAAGCAAA
TAACCATATTATTACAATAAGTGAGATACCAAAAAAAAAAGTTATGTACCAAAATTAAGTTGATC
AAATACAATGTTTGGTGAAAATTTTTTATGACTCTTAAAATTGTTGGTATCAGCACCTGCTCAAA
TGGAAGTAACATTTGCATTAAGTTATCAAAATATAATTTATCTACTACATCACAATTCACATAGA
AAAAGCAGATAAAACTATAACACC
Found at i:39485298 original size:235 final size:234
Alignment explanation
Indices: 39484849--39485304 Score: 535
Period size: 235 Copynumber: 1.9 Consensus size: 234
39484839 AAAGACCTCT
* * * *
39484849 AAGATAATCTTTAAAATATTAATCAATTGAAAATTTAGTTAATTATAAATAAAAAATACTAATAT
1 AAGATAATCTTTAAAATATCAATCAATTCAAAATTTAATTAACTATAAATAAAAAATACTAATAT
** * * *
39484914 TTCAAAAAATAAACATTATTGTAGTGAGTGAAATATAAAAAAAAAAAATTTATACCGATGTTAAA
66 TTCAAAAAATAAACATTATTGTAGCAAGTGAAATATAAAAAAAAAAAATTCATACCCAAGTTAAA
* * * ** * *
39484979 TTGATCAGATACAATATTTGATGAAGATTTTTCTTGACTCTCAAAACTCTTAAGATCAGTATCTG
131 TTGATCAAATACAATATTTGATGAAGATTTTTCTTGACTCTCAAAACACCTAAGATCAACACCTA
*
39485044 CTCAAATGAAAACAACATTTGAATTAAAAAGAGGTTTTC
196 CTCAAATGAAAACAACATTTAAATTAAAAAGAGGTTTTC
* * *
39485083 AAGATAATCTTTAAAATATCAATCAA-TCAAGAATTTAATTAACTATAAATTAAAAATATTGATA
1 AAGATAATCTTTAAAATATCAATCAATTCAA-AATTTAATTAACTATAAATAAAAAATACTAATA
* * * *
39485147 TTTCAAGTAAAT-AACTATTATTGTTA-CAAGTGAGATAT-AATAAAGAAAATTGCATACCCAAG
65 TTTCAA-AAAATAAAC-ATTATTG-TAGCAAGTGAAATATAAAAAAAAAAAATT-CATACCCAAG
* * * * *
39485209 TTAAGTTGATCAAATACAATCTTTGATGAAGATTTTTCTTGACTCTCAGAACACCTGAGATTAAC
126 TTAAATTGATCAAATACAATATTTGATGAAGATTTTTCTTGACTCTCAAAACACCTAAGATCAAC
* **
39485274 ACCTATTCAAAT-ATAAGTAACATTTAAATTA
191 ACCTACTCAAATGA-AAACAACATTTAAATTA
39485305 GGTCATCAAA
Statistics
Matches: 184, Mismatches: 32, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
233 3 0.02
234 74 0.40
235 105 0.57
236 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.34
Consensus pattern (234 bp):
AAGATAATCTTTAAAATATCAATCAATTCAAAATTTAATTAACTATAAATAAAAAATACTAATAT
TTCAAAAAATAAACATTATTGTAGCAAGTGAAATATAAAAAAAAAAAATTCATACCCAAGTTAAA
TTGATCAAATACAATATTTGATGAAGATTTTTCTTGACTCTCAAAACACCTAAGATCAACACCTA
CTCAAATGAAAACAACATTTAAATTAAAAAGAGGTTTTC
Found at i:39488083 original size:135 final size:134
Alignment explanation
Indices: 39487810--39488135 Score: 391
Period size: 135 Copynumber: 2.4 Consensus size: 134
39487800 TTTAAAAATA
* * * * * *
39487810 TCAGGCAATACACTTAATCAGATAACGTTTAAGAAATATCTTAAGAATAAGACTAAGTTAGATAA
1 TCAGGCAACAAACTTAATCAAATAACGTTTAAGAAATATC-TCAG--T--GA-GAA-TCAGATAA
* * * * * * *
39487875 GCTTAAATATTATAACGTTTAAGAATAAGATTAAGTCAGATAAGCTTAAAGACTCAATCATTAAG
59 GCTTAAAGAGTATAACGTTTAAGAATAAAATTAAGTCAGATAAACGTAAAAACTCAATCATTAAA
39487940 ACTATTTCAAC
124 ACTATTTCAAC
* * *
39487951 TCAGGTAACAAACTTAGTCAGATAACGTTTAAGAAATATCTCAGTGAGAATCAGATAAGCTTAAA
1 TCAGGCAACAAACTTAATCAAATAACGTTTAAGAAATATCTCAGTGAGAATCAGATAAGCTTAAA
* *
39488016 GAGTCTAACGTTTAAGAATAAAATTTAAGTCAGATAAACGTAAAAACTCAGTCATTAAAACTATT
66 GAGTATAACGTTTAAGAATAAAA-TTAAGTCAGATAAACGTAAAAACTCAATCATTAAAACTATT
39488081 TCAAC
130 TCAAC
* * *
39488086 TCAGGCAACAGACTTAATCAAATAATGTTTAAGAAATATCTTAGTGAGAA
1 TCAGGCAACAAACTTAATCAAATAACGTTTAAGAAATATCTCAGTGAGAA
39488136 GAAACAGACT
Statistics
Matches: 162, Mismatches: 22, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
134 33 0.20
135 87 0.54
136 2 0.01
138 1 0.01
140 3 0.02
141 36 0.22
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (134 bp):
TCAGGCAACAAACTTAATCAAATAACGTTTAAGAAATATCTCAGTGAGAATCAGATAAGCTTAAA
GAGTATAACGTTTAAGAATAAAATTAAGTCAGATAAACGTAAAAACTCAATCATTAAAACTATTT
CAAC
Found at i:39488162 original size:46 final size:46
Alignment explanation
Indices: 39488092--39488318 Score: 293
Period size: 46 Copynumber: 5.0 Consensus size: 46
39488082 CAACTCAGGC
* * *
39488092 AACAGACTTAATCAAATAATGTTTAAGAAATATCTTAGTGAGAAGA
1 AACAGACTTAGTCAGATAACGTTTAAGAAATATCTTAGTGAGAAGA
* *
39488138 AACAGACTTAATCAGATAACGTTTAAGAAATATCTCAGTGAGAAG-
1 AACAGACTTAGTCAGATAACGTTTAAGAAATATCTTAGTGAGAAGA
* *
39488183 -AC--A-TTAGTCAGATAACATTTAAGAAATATGTTAGTGAGAAGA
1 AACAGACTTAGTCAGATAACGTTTAAGAAATATCTTAGTGAGAAGA
* * *
39488225 AATAAATTTAGTCAGATAACGTTTAAGAAATATCTTAGTGAGAAGA
1 AACAGACTTAGTCAGATAACGTTTAAGAAATATCTTAGTGAGAAGA
* * * *
39488271 AACAGACTTAGTTAGATAATGTTTAAAAAATATCTCAGTGAGAAGA
1 AACAGACTTAGTCAGATAACGTTTAAGAAATATCTTAGTGAGAAGA
39488317 AA
1 AA
39488319 AAAATTAAAT
Statistics
Matches: 159, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
41 34 0.21
42 1 0.01
43 1 0.01
44 2 0.01
45 1 0.01
46 120 0.75
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (46 bp):
AACAGACTTAGTCAGATAACGTTTAAGAAATATCTTAGTGAGAAGA
Found at i:39488259 original size:87 final size:90
Alignment explanation
Indices: 39488113--39488330 Score: 280
Period size: 87 Copynumber: 2.4 Consensus size: 90
39488103 TCAAATAATG
* * *
39488113 TTTAAGAAATATCTTAGTGAGAAGAAACAGACTTAATCAGATAACGTTTAAGAAATATCTCAGTG
1 TTTAAGAAATATCTTAGTGAGAAGAAAAAAATTTAATCAGATAACGTTTAAGAAATATCTCAGTG
39488178 AGAAG-AC-A-TTAGTCAGATAACA
66 AGAAGAACAACTTAGTCAGATAACA
* * * *
39488200 TTTAAGAAATATGTTAGTGAGAAGAAATAAATTTAGTCAGATAACGTTTAAGAAATATCTTAGTG
1 TTTAAGAAATATCTTAGTGAGAAGAAAAAAATTTAATCAGATAACGTTTAAGAAATATCTCAGTG
* **
39488265 AGAAGAAACAGACTTAGTTAGATAATG
66 AGAAG-AACA-ACTTAGTCAGATAACA
* * *
39488292 TTTAAAAAATATCTCAGTGAGAAGAAAAAAATTAAATCA
1 TTTAAGAAATATCTTAGTGAGAAGAAAAAAATTTAATCA
39488331 AGGTACAAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
87 64 0.58
89 2 0.02
91 1 0.01
92 44 0.40
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (90 bp):
TTTAAGAAATATCTTAGTGAGAAGAAAAAAATTTAATCAGATAACGTTTAAGAAATATCTCAGTG
AGAAGAACAACTTAGTCAGATAACA
Found at i:39490897 original size:604 final size:589
Alignment explanation
Indices: 39489627--39491393 Score: 2020
Period size: 604 Copynumber: 3.0 Consensus size: 589
39489617 CTCCAGGGCC
* * * ** * *
39489627 AGTAGAGTACCCAAGGAAAAAGGACCTTTTAGGAACATAGTTTCTTTCCCTGGCACAATAG--GA
1 AGTAGAGTACCCGAGGAAAAACGACCTTTCAGGCTCACAATTTCTTTCCCTGGCACAATAGCTGA
* * * * * ** *
39489690 GAGA-ATCGTAAGTT-ACAGCATATGAGC-GCAAAGGAGGAATTAT------AAAAAGATAGGAT
66 GATACATCGTAAGTTAACAGCATAAGAGCAACAAAGGAGAAATTATAAAAAAAAAAAGAAAACAC
* *
39489746 AC-AC--AACATTGCAGTGATACTCTCAGAGATGAGGTAAT-CGTACCT--TT-TGCCTGAGTGG
131 ACAACATAACATTGCAGTGATACTCTCAGAGATGAGG-CATCCGTACCTGCTTCTCCCTGAGTGG
* * * * *
39489804 ATCCCGAATTCGCTTCCTGCTTAGACCAACCATCACTTGTATTCATTTGTTCTAAATCTTTT-AG
195 ATCCCGAATTCCCTT-CTGCTTAGACCTACCATCACTTGTATTCTTTTGTTTTATATCTTTTGA-
** * * * * * **
39489868 GGAAATGCCATAGTCAGGGTTACTGACTTTCCTTTTTTTCCGAAGCAAAACCAATTTCGAACGAG
258 GGAAACCCCA-AGTCAGAGTTAC--ACTTTTC-TTTTTT-CGAGGCAAAACCAAGTTGGAACTTG
* * * * * ** **
39489933 ATGCAGCTTTCACAGCAAGAGCTGAATTACTTCCAGGGCCATCTCCTTTTGTAGTTGCTCTCCGG
318 ATGCAGCATTGACAGCAAGAGCTAAATTACTTCCAGGGCCATCTCCTTCT-CAGTTGAACTTTGG
* * * ** *
39489998 GTTTTTTTTAGAGACTGTATTTTAGAAGTCAAATGGAACTTCTTACTACCTTTTACGTGAACTGC
382 G-TTTTTTT----A----ATTTTAGAAGTCAAATGAAACTTCTCACTATCTGCTACATGAACTGC
* * *
39490063 CTGTTTTGGTGGAGCAGGAGAGGACGAATTTGCATTTTCTGTTG-GCGGCAGACACTTGGAACCG
438 CTG-TTTGGTGGAGCAGGAGAGGAAGAATTTGCATTTTCTGTTGTG-GGGAGACACTTGGAATCG
* * * *
39490127 ACAGGATTTGTCAGAGCTTGACTCTTCGTAGAACCCAGATTACCCCGTCTAATCTGTTTTGCTGT
501 GCAGG-TTTGTCAGAGCTTGACTCCTCTTAGAACCCAGATTACCCCGTCCAATCTGTTTTGCTGT
39490192 TTGAGTGCCAGAGTTTAGTTTGTTG
565 TTGAGTGCCAGAGTTTAGTTTGTTG
*
39490217 AGTAGAGTACCCGAGGAAAAACGACCTTTCAGGCTCACAATTTTTTTCCCTGGCACAATAGCTGA
1 AGTAGAGTACCCGAGGAAAAACGACCTTTCAGGCTCACAATTTCTTTCCCTGGCACAATAGCTGA
* ** *
39490282 GATATATCGTAAGTTAACAGCATAAGAGCAACAAAGGGAGAGCTTATAAAGAAGAAAAAATACAC
66 GATACATCGTAAGTTAACAGCATAAGAGCAACAAA-GGAGAAATTATAAA-AA-AAAAAAGA-A-
* *
39490347 AACACACAACATAACATTGCAATGATACTCTCAGAAATGAGGCATCCGTTACCTGCTTCTCCCTG
126 AACACACAACATAACATTGCAGTGATACTCTCAGAGATGAGGCATCCG-TACCTGCTTCTCCCTG
* * *
39490412 AGTGGATCCCGAATTCACCTTCTGCTTAGACTTGCAATCACTTGTATTCTTTTGTTTTATATCTT
190 AGTGGATCCCGAATTC-CCTTCTGCTTAGACCTACCATCACTTGTATTCTTTTGTTTTATATCTT
39490477 TTGAGGAAACCCCAAAGTCAGAGTTACAAACTTTGATCTTTTTTCGAGGCAAAACCAAGTTGGAA
254 TTGAGGAAACCCC-AAGTCAGAGTTAC--ACTTT--TCTTTTTTCGAGGCAAAACCAAGTTGGAA
* *
39490542 CTTGATGCAGCATTGACAGCAAGAGCTAAATTACTTTCAAGGCCATCTCCTTCCTCAGTTGAACT
314 CTTGATGCAGCATTGACAGCAAGAGCTAAATTACTTCCAGGGCCATCTCCTT-CTCAGTTGAACT
* * * *
39490607 TTGGGTTTTTTTAATTTTAGATGTCAAACGAAACTTCTCACTATCTGCAACATGAGCTGCCTGTT
378 TTGGGTTTTTTTAATTTTAGAAGTCAAATGAAACTTCTCACTATCTGCTACATGAACTGCCTGTT
*
39490672 CAGGTGGAGCAGGAGAGGAAGAATTTGCATTTTCTGTTGTGGGGAGACACTTGGAATCGGCAGGC
443 -TGGTGGAGCAGGAGAGGAAGAATTTGCATTTTCTGTTGTGGGGAGACACTTGGAATCGGCAGG-
*
39490737 TTTGTCAGAGTTTGACTCCTCTTAGAACCCAGATTACCCCGTCCAATCTGTTTTGCTGTTTGAGT
506 TTTGTCAGAGCTTGACTCCTCTTAGAACCCAGATTACCCCGTCCAATCTGTTTTGCTGTTTGAGT
39490802 GCC-GCAGTTTAGTTTGTTG
571 GCCAG-AGTTTAGTTTGTTG
*
39490821 AGTAGAGTACCCGAGGAAAAACGACCTTTTAGGCTCACAATTTCTTTCCCTGGCACAATAGCTGA
1 AGTAGAGTACCCGAGGAAAAACGACCTTTCAGGCTCACAATTTCTTTCCCTGGCACAATAGCTGA
* *
39490886 GATACATCGTAAGTTAACAGCATAAGAGCAACAAAGGAGAAATTATAAAAAAGAAAAGAAAATAC
66 GATACATCGTAAGTTAACAGCATAAGAGCAACAAAGGAGAAATTATAAAAAAAAAAAGAAAACAC
* *
39490951 ACAACATAACATTGTAGTGATACTCTCAGAGATGAGGCATCCGTACCTGCTTCTCCCTGAGTAGA
131 ACAACATAACATTGCAGTGATACTCTCAGAGATGAGGCATCCGTACCTGCTTCTCCCTGAGTGGA
* * *
39491016 TCCTGAATTCTCCTTCTGCTTAGACCTACCATCACTTGTATTCTTTTGTTTTATTTGTTTTGAGG
196 TCCCGAATTC-CCTTCTGCTTAGACCTACCATCACTTGTATTCTTTTGTTTTATATCTTTTGAGG
* *
39491081 AAACCCC-A---A-AG-T---C----CTTTTTTGGAGACAAAACCAAGTTGGAACTTGATGCAGC
260 AAACCCCAAGTCAGAGTTACACTTTTCTTTTTTCGAGGCAAAACCAAGTTGGAACTTGATGCAGC
* * *
39491133 ATTGACAGCAAGAGCAAAATTACTTCCAGGGCCATCTCCTTTCTCAGTTGTACTTTGGGTTTTTC
325 ATTGACAGCAAGAGCTAAATTACTTCCAGGGCCATCTCC-TTCTCAGTTGAACTTTGGGTTTTTT
* ** *
39491198 TAATTTTAGAAGTCAAATGCAACTTCTCACTATCTGCTACATGAACTGAGTGTGTTGGCGGAGCA
389 TAATTTTAGAAGTCAAATGAAACTTCTCACTATCTGCTACATGAACTGCCTGT-TTGGTGGAGCA
*
39491263 GGAGAGGAAGCATTTGCATTTTCTGTTGTGGGGAGACACTTGGAATCGGCAGGTTTAGTCAGAGC
453 GGAGAGGAAGAATTTGCATTTTCTGTTGTGGGGAGACACTTGGAATCGGCAGGTTT-GTCAGAGC
* * * ** * * * * *
39491328 TTGACTCCTGTTACAACACAGATTAATCCGTCCGA-CATATTTTGTTGTTGGAGTGCCAGAGCTT
517 TTGACTCCTCTTAGAACCCAGATTACCCCGTCCAATC-TGTTTTGCTGTTTGAGTGCCAGAGTTT
39491392 AG
581 AG
39491394 GGTCACGACT
Statistics
Matches: 1019, Mismatches: 120, Indels: 86
0.83 0.10 0.07
Matches are distributed among these distances:
579 4 0.00
580 259 0.25
581 4 0.00
586 1 0.00
590 53 0.05
591 1 0.00
592 7 0.01
593 11 0.01
594 12 0.01
595 4 0.00
596 9 0.01
598 86 0.08
599 44 0.04
600 1 0.00
601 6 0.01
602 2 0.00
603 15 0.01
604 277 0.27
605 1 0.00
606 4 0.00
607 2 0.00
608 3 0.00
609 30 0.03
610 5 0.00
612 9 0.01
613 156 0.15
614 12 0.01
615 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (589 bp):
AGTAGAGTACCCGAGGAAAAACGACCTTTCAGGCTCACAATTTCTTTCCCTGGCACAATAGCTGA
GATACATCGTAAGTTAACAGCATAAGAGCAACAAAGGAGAAATTATAAAAAAAAAAAGAAAACAC
ACAACATAACATTGCAGTGATACTCTCAGAGATGAGGCATCCGTACCTGCTTCTCCCTGAGTGGA
TCCCGAATTCCCTTCTGCTTAGACCTACCATCACTTGTATTCTTTTGTTTTATATCTTTTGAGGA
AACCCCAAGTCAGAGTTACACTTTTCTTTTTTCGAGGCAAAACCAAGTTGGAACTTGATGCAGCA
TTGACAGCAAGAGCTAAATTACTTCCAGGGCCATCTCCTTCTCAGTTGAACTTTGGGTTTTTTTA
ATTTTAGAAGTCAAATGAAACTTCTCACTATCTGCTACATGAACTGCCTGTTTGGTGGAGCAGGA
GAGGAAGAATTTGCATTTTCTGTTGTGGGGAGACACTTGGAATCGGCAGGTTTGTCAGAGCTTGA
CTCCTCTTAGAACCCAGATTACCCCGTCCAATCTGTTTTGCTGTTTGAGTGCCAGAGTTTAGTTT
GTTG
Found at i:39493877 original size:13 final size:13
Alignment explanation
Indices: 39493859--39493884 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39493849 AATCATTAAT
39493859 AATATATTTTTTA
1 AATATATTTTTTA
39493872 AATATATTTTTTA
1 AATATATTTTTTA
39493885 TAGAAAATAT
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:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATATTTTTTA
Found at i:39495543 original size:24 final size:24
Alignment explanation
Indices: 39495516--39495569 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
39495506 CTTCTTGGGT
39495516 TGTGAAGACCAAGTAAATTGGTGA
1 TGTGAAGACCAAGTAAATTGGTGA
39495540 TGTGAAGACCAAGTAAATTGGTGA
1 TGTGAAGACCAAGTAAATTGGTGA
*
39495564 AGTGAA
1 TGTGAA
39495570 AACTTCCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.30, T:0.24
Consensus pattern (24 bp):
TGTGAAGACCAAGTAAATTGGTGA
Found at i:39502877 original size:335 final size:335
Alignment explanation
Indices: 39502267--39502937 Score: 1333
Period size: 335 Copynumber: 2.0 Consensus size: 335
39502257 AATACAGAAG
39502267 CCAAACTGAAACTAACCTGTGAAAGTTGAGCAAAATTTGGGTCTTTCAGGCGTGTTCTCCCCTAT
1 CCAAACTGAAACTAACCTGTGAAAGTTGAGCAAAATTTGGGTCTTTCAGGCGTGTTCTCCCCTAT
39502332 CTGGTGTAATGCAGCCAAGTGATTTGTCATTATACCATCAAGGAAAGATTGTCAAGGAAGGCCAT
66 CTGGTGTAATGCAGCCAAGTGATTTGTCATTATACCATCAAGGAAAGATTGTCAAGGAAGGCCAT
39502397 GTGCCCAAGAAGAAATGACCAAGCATCATGCAAGCTATGACACCTCCTTTGCTCTCTACCAGATA
131 GTGCCCAAGAAGAAATGACCAAGCATCATGCAAGCTATGACACCTCCTTTGCTCTCTACCAGATA
39502462 CGTCTTCAATAAAGTAGAGATATAAGCCTCTAAGTTGGAAGGATAATGAAAGAAGGAATGCATGA
196 CGTCTTCAATAAAGTAGAGATATAAGCCTCTAAGTTGGAAGGATAATGAAAGAAGGAATGCATGA
39502527 ACATCCTGCAATTATAAAATGTTTTAGACCTTTAGTTTAAATTCTTGCATCTGGTATTGTCCATC
261 ACATCCTGCAATTATAAAATGTTTTAGACCTTTAGTTTAAATTCTTGCATCTGGTATTGTCCATC
39502592 ACCAATGTTA
326 ACCAATGTTA
*
39502602 CCAAACTGAACCTAACCTGTGAAAGTTGAGCAAAATTTGGGTCTTTCAGGCGTGTTCTCCCCTAT
1 CCAAACTGAAACTAACCTGTGAAAGTTGAGCAAAATTTGGGTCTTTCAGGCGTGTTCTCCCCTAT
39502667 CTGGTGTAATGCAGCCAAGTGATTTGTCATTATACCATCAAGGAAAGATTGTCAAGGAAGGCCAT
66 CTGGTGTAATGCAGCCAAGTGATTTGTCATTATACCATCAAGGAAAGATTGTCAAGGAAGGCCAT
39502732 GTGCCCAAGAAGAAATGACCAAGCATCATGCAAGCTATGACACCTCCTTTGCTCTCTACCAGATA
131 GTGCCCAAGAAGAAATGACCAAGCATCATGCAAGCTATGACACCTCCTTTGCTCTCTACCAGATA
39502797 CGTCTTCAATAAAGTAGAGATATAAGCCTCTAAGTTGGAAGGATAATGAAAGAAGGAATGCATGA
196 CGTCTTCAATAAAGTAGAGATATAAGCCTCTAAGTTGGAAGGATAATGAAAGAAGGAATGCATGA
39502862 ACATCCTGCAATTATAAAATGTTTTAGACCTTTAGTTTAAATTCTTGCATCTGGTATTGTCCATC
261 ACATCCTGCAATTATAAAATGTTTTAGACCTTTAGTTTAAATTCTTGCATCTGGTATTGTCCATC
39502927 ACCAATGTTA
326 ACCAATGTTA
39502937 C
1 C
39502938 TAAATCCCAC
Statistics
Matches: 335, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
335 335 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (335 bp):
CCAAACTGAAACTAACCTGTGAAAGTTGAGCAAAATTTGGGTCTTTCAGGCGTGTTCTCCCCTAT
CTGGTGTAATGCAGCCAAGTGATTTGTCATTATACCATCAAGGAAAGATTGTCAAGGAAGGCCAT
GTGCCCAAGAAGAAATGACCAAGCATCATGCAAGCTATGACACCTCCTTTGCTCTCTACCAGATA
CGTCTTCAATAAAGTAGAGATATAAGCCTCTAAGTTGGAAGGATAATGAAAGAAGGAATGCATGA
ACATCCTGCAATTATAAAATGTTTTAGACCTTTAGTTTAAATTCTTGCATCTGGTATTGTCCATC
ACCAATGTTA
Found at i:39511234 original size:2 final size:2
Alignment explanation
Indices: 39511227--39511255 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39511217 AGCTACTAAT
39511227 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39511256 AACTCAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39514122 original size:29 final size:29
Alignment explanation
Indices: 39514047--39514126 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
39514037 GAAGTTTATA
* * * *
39514047 AGAATAGGTATAAAAAAAGAAGCTGTACG
1 AGAATAAGTATACAAGAATAAGCTGTACG
39514076 AGAAT-AG-ATACAAGAGAATAAGCTGTAC-
1 AGAATAAGTATAC-A-AGAATAAGCTGTACG
39514104 ATGAATAAGTATACAAGAATAAG
1 A-GAATAAGTATACAAGAATAAG
39514127 GTAAGAGGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 3 0.07
28 3 0.07
29 29 0.69
30 3 0.07
31 4 0.10
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (29 bp):
AGAATAAGTATACAAGAATAAGCTGTACG
Found at i:39514648 original size:15 final size:15
Alignment explanation
Indices: 39514619--39514693 Score: 89
Period size: 15 Copynumber: 5.0 Consensus size: 15
39514609 ATCACTTTGA
*
39514619 ACAGTAATACCTTAG
1 ACAGTAATACTTTAG
* *
39514634 GCAGTACTACTTTAG
1 ACAGTAATACTTTAG
39514649 ACAGTAATACTTTAG
1 ACAGTAATACTTTAG
*
39514664 ACAGTAATACCTTA-
1 ACAGTAATACTTTAG
*
39514678 ATCAGTAATGCTTTAG
1 A-CAGTAATACTTTAG
39514694 GTAGTAACAC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
14 1 0.02
15 49 0.98
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (15 bp):
ACAGTAATACTTTAG
Found at i:39514807 original size:41 final size:41
Alignment explanation
Indices: 39514750--39514881 Score: 157
Period size: 41 Copynumber: 3.3 Consensus size: 41
39514740 TTTTGTAATG
*
39514750 TTAAAATCTTTTGTAATATTTGATTGATTATGCAATAATAT
1 TTAATATCTTTTGTAATATTTGATTGATTATGCAATAATAT
* **
39514791 TTAATATCTTTCGTAATATTTGATTGCATT-T----TTTTAT
1 TTAATATCTTTTGTAATATTTGATTG-ATTATGCAATAATAT
* *
39514828 GTCAATATCTTTTGTAATATTTTATTGATTATGCAATAATAT
1 -TTAATATCTTTTGTAATATTTGATTGATTATGCAATAATAT
39514870 TTAATATCTTTT
1 TTAATATCTTTT
39514882 TCATAAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
37 7 0.09
38 24 0.32
41 36 0.49
42 7 0.09
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (41 bp):
TTAATATCTTTTGTAATATTTGATTGATTATGCAATAATAT
Found at i:39514916 original size:65 final size:65
Alignment explanation
Indices: 39514838--39514968 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
39514828 GTCAATATCT
*
39514838 TTTGTAATATTTTATTGATTATGCAATAATATTTAATATCTTTTTCATAAAAAATATTGATTCTA
1 TTTGTAATATTTTATTGATTATGCAATAATATTGAATATCTTTTTCATAAAAAATATTGATTCTA
* *
39514903 TTTGTAATATTTTATTGATTATGTAATAATATTGAATATCTTTTTCATAAAAAATCTTGATTCTA
1 TTTGTAATATTTTATTGATTATGCAATAATATTGAATATCTTTTTCATAAAAAATATTGATTCTA
39514968 T
1 T
39514969 GTGACTTATA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (65 bp):
TTTGTAATATTTTATTGATTATGCAATAATATTGAATATCTTTTTCATAAAAAATATTGATTCTA
Found at i:39525797 original size:126 final size:124
Alignment explanation
Indices: 39525556--39525805 Score: 473
Period size: 126 Copynumber: 2.0 Consensus size: 124
39525546 AAAGCATGAT
39525556 AAGCCACATTTGCATAATAACATGGAAACATGTCTGATCTTGAATCGGCCCCATATTAAAATTCA
1 AAGCCACATTTGCATAATAACATGGAAACATGTCTGATCTTGAATCGGCCCCATATTAAAATTCA
39525621 CTGTCACATGCCCCAAAGTCATAATCTCCTTGTTATCAAAAGAAGTGATAGCCATAGGA
66 CTGTCACATGCCCCAAAGTCATAATCTCCTTGTTATCAAAAGAAGTGATAGCCATAGGA
*
39525680 NAAGCCACATTTGCATCTATAACATGGAAACATGTCTGATCTTGAATCGGCCCCATATTAAAATT
1 -AAGCCACATTTGCAT-AATAACATGGAAACATGTCTGATCTTGAATCGGCCCCATATTAAAATT
39525745 CACTGTCACATGCCCCAAAGTCATAATCTCCTTGTTATCAAAAGAAGTGATAGCCATAGGA
64 CACTGTCACATGCCCCAAAGTCATAATCTCCTTGTTATCAAAAGAAGTGATAGCCATAGGA
39525806 CGACGTAAAC
Statistics
Matches: 123, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
125 15 0.12
126 108 0.88
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (124 bp):
AAGCCACATTTGCATAATAACATGGAAACATGTCTGATCTTGAATCGGCCCCATATTAAAATTCA
CTGTCACATGCCCCAAAGTCATAATCTCCTTGTTATCAAAAGAAGTGATAGCCATAGGA
Found at i:39527925 original size:13 final size:13
Alignment explanation
Indices: 39527907--39527931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39527897 TACAAGATAA
39527907 TTAGAGAGAGAAT
1 TTAGAGAGAGAAT
39527920 TTAGAGAGAGAA
1 TTAGAGAGAGAA
39527932 GCTTTGAAGT
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:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
TTAGAGAGAGAAT
Found at i:39528233 original size:29 final size:28
Alignment explanation
Indices: 39528157--39528236 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 28
39528147 GAGGTTTACA
*
39528157 AGAATAGGTATAAGAGAAGAAGCTGTAC
1 AGAATAGGTATAAGAGAATAAGCTGTAC
*
39528185 GAGAATAGGTACAAGAGAATAAGCTGTAC
1 -AGAATAGGTATAAGAGAATAAGCTGTAC
* *
39528214 ATGAATAAGTATACGAGAATAAG
1 A-GAATAGGTATAAGAGAATAAG
39528237 GTAAGAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 1 0.02
29 44 0.98
ACGTcount: A:0.47, C:0.07, G:0.26, T:0.19
Consensus pattern (28 bp):
AGAATAGGTATAAGAGAATAAGCTGTAC
Found at i:39528235 original size:14 final size:14
Alignment explanation
Indices: 39528157--39528236 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
39528147 GAGGTTTACA
* *
39528157 AGAATAGGTATAAG
1 AGAATAAGTATACG
* *
39528171 AGAAGAAGCTGTACG
1 AGAATAAG-TATACG
* * *
39528186 AGAATAGGTACAAG
1 AGAATAAGTATACG
*
39528200 AGAATAAGCTGTAC-
1 AGAATAAG-TATACG
39528214 ATGAATAAGTATACG
1 A-GAATAAGTATACG
39528229 AGAATAAG
1 AGAATAAG
39528237 GTAAGAGGGT
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
14 28 0.58
15 20 0.42
ACGTcount: A:0.47, C:0.07, G:0.26, T:0.19
Consensus pattern (14 bp):
AGAATAAGTATACG
Found at i:39535367 original size:2 final size:2
Alignment explanation
Indices: 39535362--39535433 Score: 119
Period size: 2 Copynumber: 36.0 Consensus size: 2
39535352 TTATAGTGTG
*
39535362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA AA NTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
39535404 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39535434 AGAAAGACTG
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.02
2 64 0.97
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39541884 original size:12 final size:12
Alignment explanation
Indices: 39541863--39541908 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
39541853 TGTAGGAGTC
39541863 CCGGTGGTTGTG
1 CCGGTGGTTGTG
*
39541875 CCGGTTGTTGTG
1 CCGGTGGTTGTG
* *
39541887 CCTGTGGTTGTC
1 CCGGTGGTTGTG
*
39541899 CCTGTGGTTG
1 CCGGTGGTTG
39541909 GGGTCGTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.00, C:0.20, G:0.41, T:0.39
Consensus pattern (12 bp):
CCGGTGGTTGTG
Found at i:39554832 original size:2 final size:2
Alignment explanation
Indices: 39554825--39554854 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39554815 ATTTAATACA
39554825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39554855 TGTGAGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39555293 original size:3 final size:3
Alignment explanation
Indices: 39555278--39555308 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
39555268 CATAACTTTC
39555278 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
39555309 TTTTATACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:39566019 original size:2 final size:2
Alignment explanation
Indices: 39566012--39566041 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39566002 CGGAGAAAAC
*
39566012 AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39566042 GTTTCATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39566991 original size:2 final size:2
Alignment explanation
Indices: 39566980--39567019 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
39566970 TCATGTAACA
*
39566980 AT AT -T AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39567020 GAGATTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:39570261 original size:28 final size:28
Alignment explanation
Indices: 39570207--39570261 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
39570197 TTTATAAGTT
* * * * *
39570207 TTTAAATTAATTTTTATTTTTATTTAAA
1 TTTAAAATAAATTTTATATTAAATTAAA
39570235 TTTAAAATAAATTTTATATTAAATTAA
1 TTTAAAATAAATTTTATATTAAATTAA
39570262 TTAATTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTAAAATAAATTTTATATTAAATTAAA
Found at i:39570346 original size:18 final size:17
Alignment explanation
Indices: 39570317--39570354 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
39570307 TTTTTATTTT
39570317 ATTTTAAATTAAAATAA
1 ATTTTAAATTAAAATAA
*
39570334 ATTTTATAATTAAAATTA
1 ATTTTA-AATTAAAATAA
39570352 ATT
1 ATT
39570355 AATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTAAATTAAAATAA
Found at i:39589015 original size:2 final size:2
Alignment explanation
Indices: 39589008--39589032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39588998 GTCAAATCAC
39589008 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39589033 ATTGAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39606061 original size:2 final size:2
Alignment explanation
Indices: 39606054--39606085 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39606044 CTGCCATTTA
39606054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39606086 TGTTTTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39606502 original size:3 final size:3
Alignment explanation
Indices: 39606494--39606518 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39606484 TGTAAGGTAT
39606494 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
39606519 TGGCTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:39609687 original size:10 final size:10
Alignment explanation
Indices: 39609672--39609702 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
39609662 TTGATAATTC
39609672 AATTAATAAT
1 AATTAATAAT
39609682 AATTAATAAT
1 AATTAATAAT
39609692 -ATTAATAAT
1 AATTAATAAT
39609701 AA
1 AA
39609703 GAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTAATAAT
Found at i:39614456 original size:2 final size:2
Alignment explanation
Indices: 39614413--39614446 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
39614403 AAGGCAAAAT
39614413 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39614447 AATTTCTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39615758 original size:12 final size:12
Alignment explanation
Indices: 39615741--39615779 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39615731 GAGAGGAGAG
39615741 AGAGAGAGAGGA
1 AGAGAGAGAGGA
*
39615753 AGAGAGAGAGAA
1 AGAGAGAGAGGA
*
39615765 AGAGAAAGANGGA
1 AGAGAGAGA-GGA
39615778 AG
1 AG
39615780 GGGGGGGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGGA
Found at i:39616167 original size:452 final size:448
Alignment explanation
Indices: 39615300--39616216 Score: 1734
Period size: 452 Copynumber: 2.0 Consensus size: 448
39615290 AGAGAGAATG
*
39615300 GAGAAGAGAGA-ATAAAGA-AAAATGGAAGGGGGGGGAAGGGGGGGCCAGCCACAGTGTAACATC
1 GAGAAGAGAGAGAGAAAGAGAAAATGGAAGGGGGGGGAAGGGGGGGCCAGCCACAGTGTAACATC
39615363 TTTTGCATATACAATGATCCCTTTTAGTGGGGGCGAATGGAGGAAGCTGAAAGCCAAATAACGGT
66 TTTTGCATATACAATGATCCCTTTTAGTGGGGGCGAATGGAGGAAGCTGAAAGCCAAATAACGGT
39615428 TGGAGATTCTGACCTTTCACTTGTGTGAGCTTGCAAGCAAGACAAAGTAAGGCATAGTTTGGATG
131 TGGAGATTCTGACCTTTCACTTGTGTGAGCTTGCAAGCAAGACAAAGTAAGGCATAGTTTGGATG
39615493 TTGCAGCAGCAGCAGGTTCAGTTTTGGTTATGTTGCAATGTAATCAATTTATCTAGTACTCCTCA
196 TTGCAGCAGCAGCAGGTTCAGTTTTGGTTATGTTGCAATGTAATCAATTTATCTAGTACTCCTCA
39615558 GTCGTTGGGATCATAAAAAAAAAATAGAAAAGATACCCAGAAATCGTGACCGTCCAATCCATCAC
261 GTCGTTGGGATCATAAAAAAAAAATAGAAAAGATACCCAGAAATCGTGACCGTCCAATCCATCAC
39615623 CGAACGGTTCTCATTTGAGTACACGTGCTGCCTATCTTTTCTTCCCTTTTTAATCTTTTGCTTCC
326 CGAACGGTTCTCATTTGAGTACACGTGCTGCCTATCTTTTCTTCCCTTTTTAATCTTTTGCTTCC
*
39615688 ATGCATGGAATTCTCCTCCAACTACAACACAAAAACAAAGG-GGGAGAGGAGAGAGAGAGA
391 ATGCATGGAATTCTCCTCCAACTACAACACAAAAAC--AGGAAGGAGA-GAGAGAGAGAGA
*
39615748 GAGGAAGAGAGAGAGAAAGAGAAAGANGGAAGGGGGGGGAAGGGGGGGCCAGCCACAGTGTAACA
1 GA-GAAGAGAGAGAGAAAGAGAAA-ATGGAAGGGGGGGGAAGGGGGGGCCAGCCACAGTGTAACA
39615813 TCTTTTGCATATACAATGATCCCTTTTAGTGGGGGCGAATGGAGGAAGCTGAAAGCCAAATAACG
64 TCTTTTGCATATACAATGATCCCTTTTAGTGGGGGCGAATGGAGGAAGCTGAAAGCCAAATAACG
39615878 GTTGGAGATTCTGACCTTTCACTTGTGTGAGCTTGCAAGCAAGACAAAGTAAGGCATAGTTTGGA
129 GTTGGAGATTCTGACCTTTCACTTGTGTGAGCTTGCAAGCAAGACAAAGTAAGGCATAGTTTGGA
39615943 TGTTGCAGCAGCAGCAGGTTCAGTTTTGGTTATGTTGCAATGTAATCAATTTATCTAGTACTCCT
194 TGTTGCAGCAGCAGCAGGTTCAGTTTTGGTTATGTTGCAATGTAATCAATTTATCTAGTACTCCT
39616008 CAGTCGTTGGGATCATAAAAAAAAAATAGAAAAGATACCCAGAAATCGTGACCGTCCAATCCATC
259 CAGTCGTTGGGATCATAAAAAAAAAATAGAAAAGATACCCAGAAATCGTGACCGTCCAATCCATC
39616073 ACCGAACGGTTCTCATTTGAGTACACGTGCTGCCTATCTTTTCTTCCCTTTTTAATCTTTTGCTT
324 ACCGAACGGTTCTCATTTGAGTACACGTGCTGCCTATCTTTTCTTCCCTTTTTAATCTTTTGCTT
39616138 CCATGCATGGAATTCTCCTCCAACTACAACACAAAAACAGGAAGGAGAGAGAGAGAGAGA
389 CCATGCATGGAATTCTCCTCCAACTACAACACAAAAACAGGAAGGAGAGAGAGAGAGAGA
39616198 GAG-AGAGAGAGAGAAAGAG
1 GAGAAGAGAGAGAGAAAGAG
39616217 TCATGGTTTT
Statistics
Matches: 461, Mismatches: 3, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
448 18 0.04
449 10 0.02
450 23 0.05
451 8 0.02
452 402 0.87
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (448 bp):
GAGAAGAGAGAGAGAAAGAGAAAATGGAAGGGGGGGGAAGGGGGGGCCAGCCACAGTGTAACATC
TTTTGCATATACAATGATCCCTTTTAGTGGGGGCGAATGGAGGAAGCTGAAAGCCAAATAACGGT
TGGAGATTCTGACCTTTCACTTGTGTGAGCTTGCAAGCAAGACAAAGTAAGGCATAGTTTGGATG
TTGCAGCAGCAGCAGGTTCAGTTTTGGTTATGTTGCAATGTAATCAATTTATCTAGTACTCCTCA
GTCGTTGGGATCATAAAAAAAAAATAGAAAAGATACCCAGAAATCGTGACCGTCCAATCCATCAC
CGAACGGTTCTCATTTGAGTACACGTGCTGCCTATCTTTTCTTCCCTTTTTAATCTTTTGCTTCC
ATGCATGGAATTCTCCTCCAACTACAACACAAAAACAGGAAGGAGAGAGAGAGAGAGA
Found at i:39616189 original size:2 final size:2
Alignment explanation
Indices: 39616182--39616216 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
39616172 AAACAGGAAG
*
39616182 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
39616217 TCATGGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39621355 original size:35 final size:36
Alignment explanation
Indices: 39621307--39621383 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 36
39621297 TCATTAAATG
39621307 TTAATATTATCAACGAGTTAAAATGTTCCCACTTGA
1 TTAATATTATCAACGAGTTAAAATGTTCCCACTTGA
*
39621343 TTAATA-TATCAACGAGTTAAAATGTTGCCACTTGA
1 TTAATATTATCAACGAGTTAAAATGTTCCCACTTGA
39621378 TTAATA
1 TTAATA
39621384 AGTAAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 34 0.85
36 6 0.15
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (36 bp):
TTAATATTATCAACGAGTTAAAATGTTCCCACTTGA
Found at i:39621617 original size:13 final size:13
Alignment explanation
Indices: 39621579--39621623 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
39621569 TAATTGAGTG
*
39621579 AAATATTGGATATT
1 AAATATTTGATA-T
*
39621593 AAAAATTTTGATAT
1 AAATA-TTTGATAT
39621607 AAATATTTGATAT
1 AAATATTTGATAT
39621620 AAAT
1 AAAT
39621624 TATATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.44
14 9 0.33
15 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (13 bp):
AAATATTTGATAT
Found at i:39628988 original size:14 final size:15
Alignment explanation
Indices: 39628965--39629002 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
39628955 TATTTAAGCA
39628965 AGGG-GAGGGAAGGG
1 AGGGAGAGGGAAGGG
39628979 -GGGAGAGGGAAGGG
1 AGGGAGAGGGAAGGG
*
39628993 AGGGAAAGGG
1 AGGGAGAGGG
39629003 TATAGTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 10 0.48
15 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (15 bp):
AGGGAGAGGGAAGGG
Found at i:39632260 original size:127 final size:125
Alignment explanation
Indices: 39632030--39632281 Score: 468
Period size: 127 Copynumber: 2.0 Consensus size: 125
39632020 TCTAAAGTAG
*
39632030 AATGTGATTAGGATTCGATGTGGAATAAGAAGTTTAAACCATACAACTACTTAATATTGTATACA
1 AATGTGATTAGGATTCAATGTGGAATAAGAAGTTTAAACCATACAACTACTTAATATTGTATACA
39632095 AACAAAAATTCTAATCAAATAAGATCTAGAATTATAGTCAACCTAAAACTCAACAGATAA
66 AACAAAAATTCTAATCAAATAAGATCTAGAATTATAGTCAACCTAAAACTCAACAGATAA
39632155 NAATGTGATTAGGATTCAATGTGGAATAAGAAGTTTAAAACCATACAACTACTTAATATTGTATA
1 -AATGTGATTAGGATTCAATGTGGAATAAGAAGTTT-AAACCATACAACTACTTAATATTGTATA
*
39632220 CAAACAAAAATTCTAATCAAATAAGATCTAGAATTCTAGTCAACCTAAAACTCAACAGATAA
64 CAAACAAAAATTCTAATCAAATAAGATCTAGAATTATAGTCAACCTAAAACTCAACAGATAA
39632282 TGTGAAAAAC
Statistics
Matches: 123, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
126 34 0.28
127 89 0.72
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (125 bp):
AATGTGATTAGGATTCAATGTGGAATAAGAAGTTTAAACCATACAACTACTTAATATTGTATACA
AACAAAAATTCTAATCAAATAAGATCTAGAATTATAGTCAACCTAAAACTCAACAGATAA
Found at i:39632392 original size:2 final size:2
Alignment explanation
Indices: 39632337--39632379 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
39632327 TTATCAATAC
39632337 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39632376 AT AT
1 AT AT
39632380 TAAAGTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39632552 original size:15 final size:16
Alignment explanation
Indices: 39632521--39632558 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
39632511 AAAAATTTAT
39632521 ATTTTTTCTGACGAAA
1 ATTTTTTCTGACGAAA
*
39632537 ATTTTTTTTGAC-AAA
1 ATTTTTTCTGACGAAA
39632552 ATTTTTT
1 ATTTTTT
39632559 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (16 bp):
ATTTTTTCTGACGAAA
Found at i:39632591 original size:25 final size:25
Alignment explanation
Indices: 39632549--39632607 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
39632539 TTTTTTTGAC
*
39632549 AAAA-TTT-TTTATTTAAAAAAATT
1 AAAATTTTGTTTATTGAAAAAAATT
39632572 AAAATTTTGTTTATTGAAAAAAATT
1 AAAATTTTGTTTATTGAAAAAAATT
39632597 AAAATTTTGTT
1 AAAATTTTGTT
39632608 GAAAATTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 4 0.12
24 3 0.09
25 26 0.79
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (25 bp):
AAAATTTTGTTTATTGAAAAAAATT
Found at i:39656565 original size:11 final size:11
Alignment explanation
Indices: 39656549--39656576 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39656539 GGACTTTGAT
39656549 TCTTAAATAAG
1 TCTTAAATAAG
39656560 TCTTAAATAAG
1 TCTTAAATAAG
39656571 TCTTAA
1 TCTTAA
39656577 CAATCACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (11 bp):
TCTTAAATAAG
Found at i:39657487 original size:15 final size:15
Alignment explanation
Indices: 39657443--39657488 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
39657433 GTATAATTTT
39657443 ATTAATTAAAGAAAA
1 ATTAATTAAAGAAAA
*
39657458 ATCT-TTTCAAA-AAAA
1 AT-TAATT-AAAGAAAA
39657473 ATTAATTAAAGAAAA
1 ATTAATTAAAGAAAA
39657488 A
1 A
39657489 AAAACCTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (15 bp):
ATTAATTAAAGAAAA
Found at i:39657946 original size:2 final size:2
Alignment explanation
Indices: 39657939--39657968 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39657929 AGAATATAAT
*
39657939 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39657969 CACTTTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39658842 original size:20 final size:21
Alignment explanation
Indices: 39658801--39658840 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
39658791 TTAATTTTTT
*
39658801 TTTTAAAAATATAATAATAAA
1 TTTTAAAAATATAATAAAAAA
39658822 TTTT-AAAAT-TAATAAAAAA
1 TTTTAAAAATATAATAAAAAA
39658841 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTTAAAAATATAATAAAAAA
Found at i:39659639 original size:4 final size:5
Alignment explanation
Indices: 39659610--39659638 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
39659600 TTTGCCCCCA
39659610 CTCCC CTCCC CTCCC CTCCC CT-CC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC
39659639 TTATCTAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.79, G:0.00, T:0.21
Consensus pattern (5 bp):
CTCCC
Found at i:39669337 original size:2 final size:2
Alignment explanation
Indices: 39669330--39669376 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
39669320 TTCATGTTTC
*
39669330 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39669372 TA TA T
1 TA TA T
39669377 TTATGTATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39671217 original size:2 final size:2
Alignment explanation
Indices: 39671200--39671233 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
39671190 TTTCAGACTT
*
39671200 TA TA T- TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39671234 TTGAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39673110 original size:42 final size:41
Alignment explanation
Indices: 39673058--39673190 Score: 176
Period size: 42 Copynumber: 3.2 Consensus size: 41
39673048 AAGTAATCAG
* * *
39673058 AAACCAGAAAGTGCAGCACCAAAACCTGATCTCCCTACCAAA
1 AAACCTGAAAGCGCAGCACCAAAACCTGATCTCCC-ACCATA
*
39673100 AAACCTGAAAGGGCAGCACCAAAACCTGATCTCCCCACCATA
1 AAACCTGAAAGCGCAGCACCAAAACCTGATCT-CCCACCATA
* * *
39673142 AAACCTGTAAGCACAGCACCAAAACCCGATCGTCCCACCATA
1 AAACCTGAAAGCGCAGCACCAAAACCTGATC-TCCCACCATA
39673184 AAACCTG
1 AAACCTG
39673191 GAACTACAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 78 0.95
43 4 0.05
ACGTcount: A:0.40, C:0.35, G:0.13, T:0.12
Consensus pattern (41 bp):
AAACCTGAAAGCGCAGCACCAAAACCTGATCTCCCACCATA
Found at i:39679983 original size:4 final size:4
Alignment explanation
Indices: 39679974--39679998 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39679964 TAATACCAAA
39679974 AGCC AGCC AGCC AGCC AGCC AGCC A
1 AGCC AGCC AGCC AGCC AGCC AGCC A
39679999 ACCTGCCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.48, G:0.24, T:0.00
Consensus pattern (4 bp):
AGCC
Found at i:39687858 original size:23 final size:24
Alignment explanation
Indices: 39687817--39687861 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39687807 CAATCGTTAA
**
39687817 TTTTTATTTAATAGTAAATAAAAG
1 TTTTTATTTAATAAAAAATAAAAG
39687841 TTTTTATTTAA-AAAAAATAAA
1 TTTTTATTTAATAAAAAATAAA
39687862 TTATACAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
TTTTTATTTAATAAAAAATAAAAG
Found at i:39691930 original size:27 final size:26
Alignment explanation
Indices: 39691891--39691948 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
39691881 TTGATTATAT
39691891 TTTTAATTAAAAAAAAT-ATTAAAAAA
1 TTTTAATTAAAAAAAATAATT-AAAAA
* *
39691917 TTTTGATTATAAAAACATAATTAAAAA
1 TTTTAATTA-AAAAAAATAATTAAAAA
39691944 TTTTA
1 TTTTA
39691949 CATCTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.30
27 16 0.59
28 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (26 bp):
TTTTAATTAAAAAAAATAATTAAAAA
Found at i:39692464 original size:53 final size:53
Alignment explanation
Indices: 39692384--39692484 Score: 184
Period size: 53 Copynumber: 1.9 Consensus size: 53
39692374 AATTATTTGT
* *
39692384 ACCAAGATTTTCTTCCCCCAAAAGTTTTGAACCTCACAACATACCAAATTTAA
1 ACCAAGATTTTCTTCCCCCAAAAGTTTTAAACCCCACAACATACCAAATTTAA
39692437 ACCAAGATTTTCTTCCCCCAAAAGTTTTAAACCCCACAACATACCAAA
1 ACCAAGATTTTCTTCCCCCAAAAGTTTTAAACCCCACAACATACCAAA
39692485 AACAATCCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.39, C:0.31, G:0.05, T:0.26
Consensus pattern (53 bp):
ACCAAGATTTTCTTCCCCCAAAAGTTTTAAACCCCACAACATACCAAATTTAA
Found at i:39698243 original size:28 final size:28
Alignment explanation
Indices: 39698203--39698258 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
39698193 GAACTTTCTT
39698203 CTTTGTATATCTAACAATGTGGAAAAAG
1 CTTTGTATATCTAACAATGTGGAAAAAG
39698231 CTTTGTATATCTAACAATGTGGAAAAAG
1 CTTTGTATATCTAACAATGTGGAAAAAG
39698259 TTGTAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (28 bp):
CTTTGTATATCTAACAATGTGGAAAAAG
Found at i:39701221 original size:60 final size:61
Alignment explanation
Indices: 39701062--39701232 Score: 299
Period size: 61 Copynumber: 2.8 Consensus size: 61
39701052 TGTACTTGAA
*
39701062 CACATTTAAAAGCTATGCACTTTATGAAGGGTGGTTTTTAATGAAATATGCTTTGCCTGTC
1 CACATTTAAAAGCTATGCACCTTATGAAGGGTGGTTTTTAATGAAATATGCTTTGCCTGTC
* *
39701123 CATATTTAAAAGTTATGCACCTTATGAAGGGTGGTTTTTAATGAAATATGCTTTGCCTGTC
1 CACATTTAAAAGCTATGCACCTTATGAAGGGTGGTTTTTAATGAAATATGCTTTGCCTGTC
*
39701184 CACA-TTAAAAGCTATGCACCTTATAAAGGGTGGTTTTTAATGAAATATG
1 CACATTTAAAAGCTATGCACCTTATGAAGGGTGGTTTTTAATGAAATATG
39701233 AATTGCTTTC
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
60 43 0.41
61 61 0.59
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (61 bp):
CACATTTAAAAGCTATGCACCTTATGAAGGGTGGTTTTTAATGAAATATGCTTTGCCTGTC
Found at i:39709059 original size:2 final size:2
Alignment explanation
Indices: 39709052--39709078 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39709042 TAATAAAGTG
39709052 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
39709079 GTATGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39715716 original size:18 final size:18
Alignment explanation
Indices: 39715695--39715729 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39715685 TTTATTAACA
* *
39715695 AAATGATAATATTTAATT
1 AAATAATAATATATAATT
39715713 AAATAATAATATATAAT
1 AAATAATAATATATAAT
39715730 ATTTATCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAATAATAATATATAATT
Found at i:39725005 original size:2 final size:2
Alignment explanation
Indices: 39724998--39725049 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
39724988 GCCACTCTTT
* * * *
39724998 TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TT TC TA T- TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39725039 TC TC TC TC TC T
1 TC TC TC TC TC T
39725050 TAAACTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.02, C:0.44, G:0.02, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39736944 original size:11 final size:10
Alignment explanation
Indices: 39736923--39736956 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
39736913 AAGTAAATTT
*
39736923 TTATAATTAA
1 TTATTATTAA
39736933 TTATTGATTAA
1 TTATT-ATTAA
39736944 TTATTATTAA
1 TTATTATTAA
39736954 TTA
1 TTA
39736957 AAATATCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
TTATTATTAA
Found at i:39743068 original size:2 final size:2
Alignment explanation
Indices: 39743061--39743095 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
39743051 GGATTTTATC
*
39743061 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39743096 TCCAGGCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39745965 original size:3 final size:3
Alignment explanation
Indices: 39745957--39745984 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39745947 TGCAATAACT
39745957 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
39745985 TAAAGAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:39746527 original size:46 final size:44
Alignment explanation
Indices: 39746477--39746626 Score: 116
Period size: 46 Copynumber: 3.4 Consensus size: 44
39746467 AAATCTTATA
39746477 AATTTTCAATTTTCATAATTATAATAATAACACATCAAATCTTGTG
1 AATTTTCAATTTTCATAATTATAATAATAA-ACATCAAAT-TTGTG
* * ** *
39746523 AATTTTTC-ATTTTTAT-GTTAATTTTAATAAA-GTC--A-TT-TG
1 AA-TTTTCAATTTTCATAATT-ATAATAATAAACATCAAATTTGTG
* **
39746562 AATTATCAATTTTCATAATTATGGTAATAATACATCAAATTTGGTG
1 AATTTTCAATTTTCATAATTATAATAATAA-ACATCAAATTT-GTG
*
39746608 AATTTTCAACTTTCATAAT
1 AATTTTCAATTTTCATAAT
39746627 AATTACCATG
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
38 4 0.05
39 19 0.24
40 5 0.06
41 2 0.03
42 1 0.01
43 1 0.01
44 4 0.05
45 3 0.04
46 36 0.45
47 5 0.06
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (44 bp):
AATTTTCAATTTTCATAATTATAATAATAAACATCAAATTTGTG
Found at i:39746600 original size:85 final size:86
Alignment explanation
Indices: 39746404--39746613 Score: 237
Period size: 85 Copynumber: 2.4 Consensus size: 86
39746394 ATTTTTGTTG
* * * * *
39746404 TAATTTTGGTAATGAGACATAAAATCTTATGAATTTTTAATTTTTATGGCAATTTCAGTAATAAA
1 TAATTATGGTAATAACACATCAAATCTTGTGAATTTTTAATTTTTATGGCAATTT-A-TAATAAA
*
39746469 ATCTTATAAATTTTCAATTTTCA
64 ATCTTATAAATTATCAATTTTCA
** * ** *
39746492 TAATTATAATAATAACACATCAAATCTTGTGAATTTTTCATTTTTATGTTAATTT-TAATAAAGT
1 TAATTATGGTAATAACACATCAAATCTTGTGAATTTTTAATTTTTATGGCAATTTATAATAAAAT
*
39746556 CATT-TGAATTATCAATTTTCA
66 C-TTATAAATTATCAATTTTCA
*
39746577 TAATTATGGTAATAATACATCAAAT-TTGGTGAATTTT
1 TAATTATGGTAATAACACATCAAATCTT-GTGAATTTT
39746614 CAACTTTCAT
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
84 2 0.02
85 55 0.53
86 2 0.02
88 45 0.43
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.46
Consensus pattern (86 bp):
TAATTATGGTAATAACACATCAAATCTTGTGAATTTTTAATTTTTATGGCAATTTATAATAAAAT
CTTATAAATTATCAATTTTCA
Found at i:39747342 original size:158 final size:159
Alignment explanation
Indices: 39746995--39747493 Score: 573
Period size: 160 Copynumber: 3.2 Consensus size: 159
39746985 AGTAATTTGC
* * * * * **
39746995 AATTTTGGTAATATTTCGTCAAA-TCTGGTAAATTTTGTAATAATTTTGATAATGCCACCTCAAT
1 AATTTTGGTAATATCTCGTCAAATTC-GATACATATTGTAATAATTTTGATAATGTCATGTCAAT
* * * * *
39747059 TGTTATTCTTATATTTACAATAGTTAG-AAATATTTGTTCAATTACTTACCAAAATCATATAATA
65 TTTTATTCTTATCTTCACAATAGGTAGAAAATATTTGATCAATTACTTACC-AAATCATATAATA
* *
39747123 TATACTATTTATTATTATAAGTAATAAATTATT
129 TAT-CTATTTATTATTATAAATAATAATTTA-T
* * * ** * *
39747156 AA-TTTAGCAATATCTCGTCAAATTCGATAGATATTGTGGTAATTTTGGTAATGTTATGTCAATT
1 AATTTTGGTAATATCTCGTCAAATTCGATACATATTGTAATAATTTTGATAATGTCATGTCAATT
*
39747220 TTTATTCTTATCTTCACAATAGGTAGAAAAT-TTTGATCAATCACTTACGCAAATCATATAATAT
66 TTTATTCTTATCTTCACAATAGGTAGAAAATATTTGATCAATTACTTAC-CAAATCATATAATAT
39747284 ATC-ATTTATTATTATAAATAATAATTTAT
130 ATCTATTTATTATTATAAATAATAATTTAT
* * *
39747313 AATTTTGGTTATAACTCGTCAAATTCGATACATTTTGTAATAATTTTGATAATGTCATGTCAATT
1 AATTTTGGTAATATCTCGTCAAATTCGATACATATTGTAATAATTTTGATAATGTCATGTCAATT
* ** * * * *
39747378 TTCATTCAAATCTTCACAATA-GTA-AAAATCTTTTATCAATTACTTACTAGAATTATATAATAT
66 TTTATTCTTATCTTCACAATAGGTAGAAAATATTTGATCAATTACTTACCA-AATCATATAATAT
* *
39747441 A-CTAATTATTATTATAATTAATAATTTAT
130 ATCTATTTATTATTATAAATAATAATTTAT
*
39747470 AATTTTGGTAATATCTCTTCAAAT
1 AATTTTGGTAATATCTCGTCAAAT
39747494 CCAATAAATT
Statistics
Matches: 288, Mismatches: 43, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
156 7 0.02
157 79 0.27
158 93 0.32
159 1 0.00
160 99 0.34
161 9 0.03
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (159 bp):
AATTTTGGTAATATCTCGTCAAATTCGATACATATTGTAATAATTTTGATAATGTCATGTCAATT
TTTATTCTTATCTTCACAATAGGTAGAAAATATTTGATCAATTACTTACCAAATCATATAATATA
TCTATTTATTATTATAAATAATAATTTAT
Found at i:39747465 original size:19 final size:19
Alignment explanation
Indices: 39747429--39747466 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39747419 ACTTACTAGA
*
39747429 ATTATATAATATACTAATT
1 ATTATATAATATAATAATT
39747448 ATTATTATAAT-TAATAATT
1 ATTA-TATAATATAATAATT
39747467 TATAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATATAATATAATAATT
Found at i:39747472 original size:157 final size:154
Alignment explanation
Indices: 39746995--39747523 Score: 562
Period size: 157 Copynumber: 3.4 Consensus size: 154
39746985 AGTAATTTGC
* * * **
39746995 AATTTTGGTAATATTTCGTCAAA-TCTGGTAAATTTTGTAATAATTTTGATAATGCCACCTCAAT
1 AATTTTGGTAATATCTCGTCAAATTC-GATAAATTTTGTAATAATTTTGATAATGTCATGTCAAT
* * *
39747059 TGTTATTCTTATATTTACAATAGTTAGAAATATTTGT-TCAATTACTTACCAAAATCATATAATA
65 T-TTATTCTTATCTTCACAATAG-TA-AAA-ATTTTTATCAATTACTTACC-AAATCATAT-A-A
* *
39747123 TATACTATTTATTATTATAAGTAATAAATTATT
123 TATACTATTTATTATTATAAATAATAATTTA-T
* * * * ** * *
39747156 AA-TTTAGCAATATCTCGTCAAATTCGATAGATATTGTGGTAATTTTGGTAATGTTATGTCAATT
1 AATTTTGGTAATATCTCGTCAAATTCGATAAATTTTGTAATAATTTTGATAATGTCATGTCAA-T
* *
39747220 TTTATTCTTATCTTCACAATAGGTAGAAAATTTTGATCAATCACTTACGCAAATCATATAATATA
65 TTTATTCTTATCTTCACAATA-GTA-AAAATTTTTATCAATTACTTAC-CAAATCATATAATATA
39747285 -TCATTTATTATTATAAATAATAATTTAT
127 CT-ATTTATTATTATAAATAATAATTTAT
* * *
39747313 AATTTTGGTTATAACTCGTCAAATTCGATACATTTTGTAATAATTTTGATAATGTCATGTCAATT
1 AATTTTGGTAATATCTCGTCAAATTCGATAAATTTTGTAATAATTTTGATAATGTCATGTCAATT
** * *
39747378 TTCATTCAAATCTTCACAATAGTAAAAATCTTTTATCAATTACTTACTAGAATTATATAATATAC
66 TT-ATTCTTATCTTCACAATAGTAAAAAT-TTTTATCAATTACTTACCA-AATCATATAATATAC
* *
39747443 TAATTATTATTATAATTAATAATTTAT
128 TATTTATTATTATAAATAATAATTTAT
* * * * * *
39747470 AATTTTGGTAATATCTCTTCAAATCCAATAAATTCTATAATACTTTTGATAATG
1 AATTTTGGTAATATCTCGTCAAATTCGATAAATTTTGTAATAATTTTGATAATG
39747524 CCACACCAAG
Statistics
Matches: 310, Mismatches: 47, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
156 6 0.02
157 108 0.35
158 95 0.31
159 5 0.02
160 88 0.28
161 8 0.03
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (154 bp):
AATTTTGGTAATATCTCGTCAAATTCGATAAATTTTGTAATAATTTTGATAATGTCATGTCAATT
TTATTCTTATCTTCACAATAGTAAAAATTTTTATCAATTACTTACCAAATCATATAATATACTAT
TTATTATTATAAATAATAATTTAT
Found at i:39751224 original size:90 final size:89
Alignment explanation
Indices: 39751130--39751416 Score: 272
Period size: 90 Copynumber: 3.2 Consensus size: 89
39751120 TCGGTATGTA
* *
39751130 TTGTAATAATTTTGGTAATGCCATATCAATTTTTATTATTATAAGTAATAATTTATAATTGTGGT
1 TTGTAATAATTTTGGTAATGTCA-ATCAATTTTTATTATTATAAGTAATAATTTATAATTGTAGT
39751195 AATATCTCAAAAAAAT-TGATAAATG
65 AATATCT-AAAAAAATCTGATAAATG
* * ** * * *
39751220 TTGTAATAATTTTGGTAACGTTAAGTC-GGTTTTATTATTATAACTATTAATTTATAATTTTAGT
1 TTGTAATAATTTTGGTAATGTCAA-TCAATTTTTATTATTATAAGTAATAATTTATAATTGTAGT
***
39751284 AATATCTTGTAAAATCTGATAAATG
65 AATATCTAAAAAAATCTGATAAATG
** * * * * * * *
39751309 TTGTAATAATTTTAATAATATCACGTCAATTTTCATCATTCTAAGTAATAATTTATAATTTTAAT
1 TTGTAATAATTTTGGTAATGTCA-ATCAATTTTTATTATTATAAGTAATAATTTATAATTGTAGT
* *** * *
39751374 GATATCTTGTAAAATCTGGTAAATA
65 AATATCTAAAAAAATCTGATAAATG
*
39751399 TTGTAATTATTTTGGTAA
1 TTGTAATAATTTTGGTAA
39751417 CCATCATCAA
Statistics
Matches: 161, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
88 5 0.03
89 68 0.42
90 88 0.55
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (89 bp):
TTGTAATAATTTTGGTAATGTCAATCAATTTTTATTATTATAAGTAATAATTTATAATTGTAGTA
ATATCTAAAAAAATCTGATAAATG
Found at i:39761694 original size:81 final size:81
Alignment explanation
Indices: 39761608--39761760 Score: 252
Period size: 81 Copynumber: 1.9 Consensus size: 81
39761598 TTTTCCTTTT
*
39761608 AAAAGAAAAAAAAAATCTCATCTTGAATATCTATTAAACTAAAAACACAATACCCAGAAACACCC
1 AAAAGAAAAAAAAAATCTCATCTTGAATATCCATTAAACTAAAAACACAATACCCAGAAACACCC
39761673 AAGCTTCTTTTCTATC
66 AAGCTTCTTTTCTATC
** * * *
39761689 AAAAGATGAGACAAATCTCATCTTGAATATCCATTGAACTAAAAACACAATACCCAGAAACACCC
1 AAAAGAAAAAAAAAATCTCATCTTGAATATCCATTAAACTAAAAACACAATACCCAGAAACACCC
39761754 AAGCTTC
66 AAGCTTC
39761761 AAAACTGAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (81 bp):
AAAAGAAAAAAAAAATCTCATCTTGAATATCCATTAAACTAAAAACACAATACCCAGAAACACCC
AAGCTTCTTTTCTATC
Found at i:39763884 original size:16 final size:17
Alignment explanation
Indices: 39763808--39763887 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 17
39763798 TATATAACCA
*
39763808 TATTATATT-ATATATT
1 TATTATATTAATATATC
* *
39763824 TA-TAAATTAAAATATC
1 TATTATATTAATATATC
*
39763840 TATTATATTTAATATATG
1 TATTATA-TTAATATATC
* *
39763858 TATAATTTATTACTATAT-
1 TAT--TATATTAATATATC
39763876 TATTATATTAAT
1 TATTATATTAAT
39763888 TATAAAATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
15 5 0.10
16 16 0.33
17 3 0.06
18 14 0.29
19 8 0.16
20 3 0.06
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (17 bp):
TATTATATTAATATATC
Found at i:39764387 original size:53 final size:53
Alignment explanation
Indices: 39764307--39764438 Score: 237
Period size: 53 Copynumber: 2.5 Consensus size: 53
39764297 CCCTATAAAT
* *
39764307 CTAGTATTAGATTCAGCCTCCTCTCGCCTTCCCCAACTCTTCTCGCCTTCTCC
1 CTAGTATTAGCTTCAGTCTCCTCTCGCCTTCCCCAACTCTTCTCGCCTTCTCC
39764360 CTAGTATTAGCTTCAGTCTCCTCTCGCCTTCCCCAACTCTTCTCGCCTTCTCC
1 CTAGTATTAGCTTCAGTCTCCTCTCGCCTTCCCCAACTCTTCTCGCCTTCTCC
*
39764413 CTAGTATTAGCTTCAATCTCCTCTCG
1 CTAGTATTAGCTTCAGTCTCCTCTCG
39764439 TGGGATAACA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 76 1.00
ACGTcount: A:0.14, C:0.41, G:0.10, T:0.36
Consensus pattern (53 bp):
CTAGTATTAGCTTCAGTCTCCTCTCGCCTTCCCCAACTCTTCTCGCCTTCTCC
Found at i:39767284 original size:15 final size:15
Alignment explanation
Indices: 39767264--39767295 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39767254 TATATATATA
*
39767264 TTATAATTAATAATT
1 TTATAAGTAATAATT
39767279 TTATAAGTAATAATT
1 TTATAAGTAATAATT
39767294 TT
1 TT
39767296 TGTAATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATAAGTAATAATT
Found at i:39767888 original size:15 final size:16
Alignment explanation
Indices: 39767868--39767899 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39767858 TCCACGAAAA
39767868 TAAATATAT-TTATAT
1 TAAATATATATTATAT
39767883 TAAATATATATTATAT
1 TAAATATATATTATAT
39767899 T
1 T
39767900 TTGTGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATATATATTATAT
Found at i:39768613 original size:25 final size:25
Alignment explanation
Indices: 39768585--39768675 Score: 110
Period size: 25 Copynumber: 3.3 Consensus size: 25
39768575 ATCCTTTCCG
39768585 AAAAAATTCTTTAAACTTTAAATCC
1 AAAAAATTCTTTAAACTTTAAATCC
39768610 AAAAAATTCTTTAATTCTTTAAACTTTAAATCC
1 --AAAA------AATTCTTTAAACTTTAAATCC
39768643 AAAAAATTCTTTAAACTTTAAATCC
1 AAAAAATTCTTTAAACTTTAAATCC
39768668 AAAAAATT
1 AAAAAATT
39768676 ACCTCCTTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
25 29 0.50
27 4 0.07
31 4 0.07
33 21 0.36
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAAAATTCTTTAAACTTTAAATCC
Found at i:39768623 original size:18 final size:18
Alignment explanation
Indices: 39768600--39768657 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
39768590 ATTCTTTAAA
39768600 CTTTAAATCCAAAAAATT
1 CTTTAAATCCAAAAAATT
* ***
39768618 CTTT-AATTCTTTAAA--
1 CTTTAAATCCAAAAAATT
39768633 CTTTAAATCCAAAAAATT
1 CTTTAAATCCAAAAAATT
39768651 CTTTAAA
1 CTTTAAA
39768658 CTTTAAATCC
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
15 4 0.14
16 7 0.24
17 7 0.24
18 11 0.38
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.40
Consensus pattern (18 bp):
CTTTAAATCCAAAAAATT
Found at i:39768627 original size:33 final size:33
Alignment explanation
Indices: 39768589--39768664 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
39768579 TTTCCGAAAA
39768589 AATTCTTTAAACTTTAAATCCAAAAAATTCTTT
1 AATTCTTTAAACTTTAAATCCAAAAAATTCTTT
39768622 AATTCTTTAAACTTTAAATCCAAAAAATTCTTT
1 AATTCTTTAAACTTTAAATCCAAAAAATTCTTT
*
39768655 AA-ACTTTAAA
1 AATTCTTTAAA
39768665 TCCAAAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 7 0.17
33 35 0.83
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (33 bp):
AATTCTTTAAACTTTAAATCCAAAAAATTCTTT
Found at i:39768740 original size:25 final size:25
Alignment explanation
Indices: 39768712--39768761 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39768702 ATCCTTTCCG
*
39768712 AAAAAGTTCTTTAAACTTTAAATCC
1 AAAAAATTCTTTAAACTTTAAATCC
39768737 AAAAAATTCTTTAAACTTTAAATCC
1 AAAAAATTCTTTAAACTTTAAATCC
39768762 TTTAAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAAAATTCTTTAAACTTTAAATCC
Found at i:39768764 original size:16 final size:16
Alignment explanation
Indices: 39768740--39768774 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
39768730 TAAATCCAAA
*
39768740 AAATTCTTTAAACTTT
1 AAATCCTTTAAACTTT
39768756 AAATCCTTTAAACTTT
1 AAATCCTTTAAACTTT
39768772 AAA
1 AAA
39768775 AGTTGTACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATCCTTTAAACTTT
Found at i:39770822 original size:30 final size:30
Alignment explanation
Indices: 39770786--39770848 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
39770776 TGTGGGTCCC
*
39770786 ATTAAAAGCATATCATGTAAAAACACTCCT
1 ATTAAAAGCATATCATATAAAAACACTCCT
39770816 ATTAAAAGCATATCATATAAAAACACTCCT
1 ATTAAAAGCATATCATATAAAAACACTCCT
39770846 ATT
1 ATT
39770849 GCACGTTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (30 bp):
ATTAAAAGCATATCATATAAAAACACTCCT
Found at i:39770999 original size:25 final size:25
Alignment explanation
Indices: 39770971--39771049 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
39770961 ACAAACATCC
39770971 AACACTCACTCCAACACAAAATAAA
1 AACACTCACTCCAACACAAAATAAA
* *
39770996 AACACTC-CT--ATTCACAAAA-ACA
1 AACACTCACTCCA-ACACAAAATAAA
**
39771018 CCCACTCACTCCAACACAAAATAAA
1 AACACTCACTCCAACACAAAATAAA
39771043 AACACTC
1 AACACTC
39771050 CTATTCACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 9 0.22
25 15 0.37
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (25 bp):
AACACTCACTCCAACACAAAATAAA
Found at i:39771001 original size:21 final size:21
Alignment explanation
Indices: 39770977--39771050 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
39770967 ATCCAACACT
39770977 CACTCCAACACAAAATAAAAA
1 CACTCCAACACAAAATAAAAA
* **
39770998 CACTCCTATTCACAAAA-ACACCCACT
1 CACTCC-A-ACACAAAATA-A---AAA
39771024 CACTCCAACACAAAATAAAAA
1 CACTCCAACACAAAATAAAAA
39771045 CACTCC
1 CACTCC
39771051 TATTCACAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 13 0.32
22 2 0.05
23 8 0.20
24 8 0.20
25 2 0.05
26 7 0.17
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (21 bp):
CACTCCAACACAAAATAAAAA
Found at i:39771029 original size:47 final size:47
Alignment explanation
Indices: 39770973--39771068 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
39770963 AAACATCCAA
39770973 CACTCACTCCAACACAAAATAAAAACACTCCTATTCACAAAAACACC
1 CACTCACTCCAACACAAAATAAAAACACTCCTATTCACAAAAACACC
39771020 CACTCACTCCAACACAAAATAAAAACACTCCTATTCACAAAAACACC
1 CACTCACTCCAACACAAAATAAAAACACTCCTATTCACAAAAACACC
39771067 CA
1 CA
39771069 ACACTCACTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (47 bp):
CACTCACTCCAACACAAAATAAAAACACTCCTATTCACAAAAACACC
Found at i:39771058 original size:23 final size:23
Alignment explanation
Indices: 39770985--39771061 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
39770975 CTCACTCCAA
39770985 CACAAAATAAAAACACTCCTATT
1 CACAAAATAAAAACACTCCTATT
* ** *
39771008 CACAAAA-ACACCCACTCACTCCA-A
1 CACAAAATAAAAACACTC-CT--ATT
39771032 CACAAAATAAAAACACTCCTATT
1 CACAAAATAAAAACACTCCTATT
39771055 CACAAAA
1 CACAAAA
39771062 ACACCCAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 8 0.20
23 16 0.39
24 9 0.22
25 8 0.20
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (23 bp):
CACAAAATAAAAACACTCCTATT
Found at i:39771071 original size:25 final size:25
Alignment explanation
Indices: 39770996--39771074 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
39770986 ACAAAATAAA
39770996 AACACTCCTATTCACAAAAACACCC
1 AACACTCCTATTCACAAAAACACCC
* * *
39771021 ACTCACTCC-A-ACACAAAATA-A--A
1 A-ACACTCCTATTCACAAAA-ACACCC
39771043 AACACTCCTATTCACAAAAACACCC
1 AACACTCCTATTCACAAAAACACCC
39771068 AACACTC
1 AACACTC
39771075 ACTCCTACCT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 6 0.15
22 3 0.07
23 8 0.20
24 8 0.20
25 10 0.24
26 6 0.15
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (25 bp):
AACACTCCTATTCACAAAAACACCC
Found at i:39771201 original size:31 final size:31
Alignment explanation
Indices: 39771163--39771224 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
39771153 TTGAACACAA
39771163 CTTCACTCTCCTCTCGCCTCACAAAATGGAT
1 CTTCACTCTCCTCTCGCCTCACAAAATGGAT
39771194 CTTCACTCTCCTCTCGCCTCACAAAATGGAT
1 CTTCACTCTCCTCTCGCCTCACAAAATGGAT
39771225 TTGCGGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.39, G:0.10, T:0.29
Consensus pattern (31 bp):
CTTCACTCTCCTCTCGCCTCACAAAATGGAT
Found at i:39772389 original size:16 final size:16
Alignment explanation
Indices: 39772368--39772402 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
39772358 GATGATATTA
39772368 ATAGTTTATAATTGGT
1 ATAGTTTATAATTGGT
39772384 ATAGTTTATAATTGGT
1 ATAGTTTATAATTGGT
39772400 ATA
1 ATA
39772403 CTAATATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (16 bp):
ATAGTTTATAATTGGT
Found at i:39773729 original size:28 final size:29
Alignment explanation
Indices: 39773673--39773730 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
39773663 TGAGTCACTC
* *
39773673 TCTGAGAGAAAAAACTCCATGTGACTCCAT
1 TCTGAGAGAAAAAACTCCA-GTAAATCCAT
*
39773703 TCTGAGAGAAAAAATTCCA-TAAATCCAT
1 TCTGAGAGAAAAAACTCCAGTAAATCCAT
39773731 GTGACTCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
30 18 0.72
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (29 bp):
TCTGAGAGAAAAAACTCCAGTAAATCCAT
Found at i:39778553 original size:17 final size:18
Alignment explanation
Indices: 39778515--39778577 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 18
39778505 ATAATTAATA
39778515 ATATATATATTAAAATTATTT
1 ATAT-TATATTAAAA-T-TTT
*
39778536 ATATTATATT-ATATTTT
1 ATATTATATTAAAATTTT
*
39778553 ATA-TAAATTAAAATTTT
1 ATATTATATTAAAATTTT
39778570 AT-TTATAT
1 ATATTATAT
39778578 AACTAATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 5 0.14
17 18 0.50
18 1 0.03
19 2 0.06
20 6 0.17
21 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTATATTAAAATTTT
Found at i:39779040 original size:26 final size:26
Alignment explanation
Indices: 39779011--39779060 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
39779001 TTTCAATATA
*
39779011 TATTATT-ATTTTTAGTTTTATTTATT
1 TATTATTCATTTATA-TTTTATTTATT
*
39779037 TATTTTTCATTTATATTTTATTTA
1 TATTATTCATTTATATTTTATTTA
39779061 CTCATATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (26 bp):
TATTATTCATTTATATTTTATTTATT
Found at i:39779056 original size:22 final size:22
Alignment explanation
Indices: 39779007--39779060 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
39778997 TTTCTTTCAA
*
39779007 TATATATTA-TTATTTTTAGTT
1 TATATTTTATTTATTTTTAGTT
39779028 T-TA-TTTATTTATTTTTCA-TT
1 TATATTTTATTTATTTTT-AGTT
39779048 TATATTTTATTTA
1 TATATTTTATTTA
39779061 CTCATATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 4 0.14
22 8 0.29
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TATATTTTATTTATTTTTAGTT
Found at i:39780510 original size:65 final size:65
Alignment explanation
Indices: 39780406--39780548 Score: 268
Period size: 65 Copynumber: 2.2 Consensus size: 65
39780396 CTTAACGCCC
39780406 AAAGGCTTTGGATGATTCCATTTGGGGCGGGATCTGATGTCGTGGAGAAGCATCGAATTCAATGG
1 AAAGGCTTTGGATGATTCCATTTGGGGCGGGATCTGATGTCGTGGAGAAGCATCGAATTCAATGG
*
39780471 AAAGGTTTTGGATGATTCCATTTGGGGCGGGATCTGATGTCGTGGAGAAGCATCGAATTCAATGG
1 AAAGGCTTTGGATGATTCCATTTGGGGCGGGATCTGATGTCGTGGAGAAGCATCGAATTCAATGG
39780536 AAAGGCTCTTGGA
1 AAAGGCT-TTGGA
39780549 ACCATTCGGG
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 70 0.93
66 5 0.07
ACGTcount: A:0.25, C:0.13, G:0.34, T:0.28
Consensus pattern (65 bp):
AAAGGCTTTGGATGATTCCATTTGGGGCGGGATCTGATGTCGTGGAGAAGCATCGAATTCAATGG
Found at i:39786460 original size:48 final size:48
Alignment explanation
Indices: 39786396--39786540 Score: 274
Period size: 48 Copynumber: 3.0 Consensus size: 48
39786386 ATTTACATCC
*
39786396 TTAC-TTTCAAATTTATATTCAGCCTCAGCCTTTTCATAAATAAGCCT
1 TTACATTTCAAACTTATATTCAGCCTCAGCCTTTTCATAAATAAGCCT
39786443 TTACATTTCAAACTTATATTCAGCCTCAGCCTTTTCATAAATAAGCCT
1 TTACATTTCAAACTTATATTCAGCCTCAGCCTTTTCATAAATAAGCCT
39786491 TTACATTTCAAACTTATATTCAGCCTCAGCCTTTTCATAAATAAGCCT
1 TTACATTTCAAACTTATATTCAGCCTCAGCCTTTTCATAAATAAGCCT
39786539 TT
1 TT
39786541 CACTATGCGA
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
47 4 0.04
48 92 0.96
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.39
Consensus pattern (48 bp):
TTACATTTCAAACTTATATTCAGCCTCAGCCTTTTCATAAATAAGCCT
Found at i:39786479 original size:27 final size:27
Alignment explanation
Indices: 39786448--39786527 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
39786438 AGCCTTTACA
39786448 TTTCAAACTTATATTCAGCCTCAGCCT
1 TTTCAAACTTATATTCAGCCTCAGCCT
* *
39786475 TTTCATAA---ATA---AGCCTTTA--CA
1 TTTCA-AACTTATATTCAGCC-TCAGCCT
39786496 TTTCAAACTTATATTCAGCCTCAGCCT
1 TTTCAAACTTATATTCAGCCTCAGCCT
39786523 TTTCA
1 TTTCA
39786528 TAAATAAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 20
0.62 0.06 0.32
Matches are distributed among these distances:
20 2 0.05
21 6 0.15
22 4 0.10
23 5 0.13
25 5 0.13
26 4 0.10
27 11 0.28
28 2 0.05
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (27 bp):
TTTCAAACTTATATTCAGCCTCAGCCT
Found at i:39797844 original size:30 final size:27
Alignment explanation
Indices: 39797789--39797862 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
39797779 ATTCACAAAA
39797789 ATTTAAATAATTTTTATTTTTTATTAC
1 ATTTAAATAATTTTTATTTTTTATTAC
*
39797816 ATTTAATTAAATTTTTATATTTTATATTA-
1 ATTTAAAT-AATTTTTAT-TTTT-TATTAC
* *
39797845 AATCAAATAAGTTTTTAT
1 ATTTAAATAA-TTTTTAT
39797863 AATTAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 7 0.18
28 11 0.28
29 16 0.41
30 5 0.13
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTTAAATAATTTTTATTTTTTATTAC
Found at i:39811625 original size:26 final size:27
Alignment explanation
Indices: 39811578--39811642 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
39811568 TCAAATAGCT
* *
39811578 TGGCCCATATGATTGCCACTT-GGCCA
1 TGGCCTATATGATTGACACTTGGGCCA
**
39811604 TGGCCTATATGATTGATGCTTGGGCCA
1 TGGCCTATATGATTGACACTTGGGCCA
39811631 TGG-CTCATATGA
1 TGGCCT-ATATGA
39811643 GGGTAGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (27 bp):
TGGCCTATATGATTGACACTTGGGCCA
Found at i:39813795 original size:4 final size:4
Alignment explanation
Indices: 39813781--39813812 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
39813771 TTCTTATCTT
39813781 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
39813813 TGTGTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:39815210 original size:15 final size:14
Alignment explanation
Indices: 39815185--39815223 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
39815175 ACAAAAGAAG
39815185 GAAAAATGAAAAAA
1 GAAAAATGAAAAAA
*
39815199 GAAAAATGGAAAAA
1 GAAAAATGAAAAAA
* *
39815213 GGAAAAGGAAA
1 GAAAAATGAAA
39815224 GAGAGAAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (14 bp):
GAAAAATGAAAAAA
Found at i:39815395 original size:15 final size:14
Alignment explanation
Indices: 39815371--39815400 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
39815361 TGGTTATTGG
39815371 GTTTGTTTTGTTTT
1 GTTTGTTTTGTTTT
39815385 GTTTCGTTTTGTTTT
1 GTTT-GTTTTGTTTT
39815400 G
1 G
39815401 ATGTTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.03, G:0.23, T:0.73
Consensus pattern (14 bp):
GTTTGTTTTGTTTT
Found at i:39826158 original size:16 final size:16
Alignment explanation
Indices: 39826137--39826168 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39826127 ACTTCGAATT
39826137 CCCCTCTCTCCCTTTC
1 CCCCTCTCTCCCTTTC
*
39826153 CCCCTCTCTCTCTTTC
1 CCCCTCTCTCCCTTTC
39826169 TCTCTACCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (16 bp):
CCCCTCTCTCCCTTTC
Found at i:39830496 original size:76 final size:76
Alignment explanation
Indices: 39830359--39830503 Score: 220
Period size: 76 Copynumber: 1.9 Consensus size: 76
39830349 CAAATACGGC
* *
39830359 CACAAAAATGAACTAATTCAATACTTCGTATGATATGAAAATTTGAACATTAGAGTCACTTTAGC
1 CACAAAAATGAACTAATTCAATACATCATATGATATGAAAATTTGAACATTAGAGTCACTTTAGC
39830424 CCATAACATAT
66 CCATAACATAT
* * * *
39830435 CACAAAAATTAACTAATTCAATACATCATGTGATATGAAAATTTGGACA-TAGGAGTTACTTTAG
1 CACAAAAATGAACTAATTCAATACATCATATGATATGAAAATTTGAACATTA-GAGTCACTTTAG
39830499 CCCAT
65 CCCAT
39830504 TACCCAAAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
75 2 0.03
76 60 0.97
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (76 bp):
CACAAAAATGAACTAATTCAATACATCATATGATATGAAAATTTGAACATTAGAGTCACTTTAGC
CCATAACATAT
Found at i:39844769 original size:215 final size:212
Alignment explanation
Indices: 39844372--39845010 Score: 762
Period size: 215 Copynumber: 3.0 Consensus size: 212
39844362 TCCTAATTTC
* * * *
39844372 TTTAATTCAAGAATGAATAGCAAAATCC-AAGTGTAGCAGGATTTCAGAGGATGCTCATTGTTGG
1 TTTAATT-AAGAATGAACAGCAAAATCCAAAG-GAAGCAGGACTTCAGAGGATGCTC-TTGTTAG
** * *
39844436 TGACGCAAAGAAGCGTCTTATACACAAGATCCTGCATGAATGCATAATATCCATGGAAAGCGTAA
63 TGAAACAAAGAAGCTTCTTATACACAAGATCCTGCATGAATGCATAATATCCATGGAAGGC-TAA
*
39844501 ATGAGAGAAATCTAGTCATCTTCCCCATTTATTAATCTTGTAGCTCAAAACCTTCCCCTTTCACT
127 ATGA-AGAATTCTAGTCATCTTCCCCATTTATTAATCTTGTAGCTCAAAACCTTCCCCTTTCACT
*
39844566 TTGAATCAGCTCAATGTTTCAG
191 TTGAATCTGCTCAATGTTTCAG
* * * * *
39844588 TTTAATTAAAGGATGACCAG-AAAATCCCAGGGGAGCAGGACTTCAGAGGATGCTCTTTGTTAGT
1 TTTAATT-AAGAATGAACAGCAAAATCCAAAGGAAGCAGGACTTCAGAGGATGCTC-TTGTTAGT
* *
39844652 GAAACAAAGAAGCTTCTTATACACAAGATCCTGCATGAAAGCATAATATCTATGGAAGGCTTAAA
64 GAAACAAAGAAGCTTCTTATACACAAGATCCTGCATGAATGCATAATATCCATGGAAGGC-TAAA
* * *
39844717 TGACAGAATTCTAATCATCTTCCCCATTTATTAATCTTGCAGCTCTAAACCTTCCCCTTTCA-TT
128 TGA-AGAATTCTAGTCATCTTCCCCATTTATTAATCTTGTAGCTCAAAACCTTCCCCTTTCACTT
* *
39844781 TCGAAGCTGCTCCATGTTTCAG
192 T-GAATCTGCTCAATGTTTCAG
** * *
39844803 TTTAATTAAGAATGAATGGCAACATCCAAAGGAAGCAGG-GTTGCAGAGGATGCTACTTGTTAGT
1 TTTAATTAAGAATGAACAGCAAAATCCAAAGGAAGCAGGACTT-CAGAGGATGCT-CTTGTTAGT
* * * *
39844867 GAAACAAAGAAGCTTCTCATACACAAGATCATGCATGAATGCATGATAACCAT----GG--AAAT
64 GAAACAAAGAAGCTTCTTATACACAAGATCCTGCATGAATGCATAATATCCATGGAAGGCTAAAT
* * * *
39844926 G-AGAATTCTAGTAAGCTTCCCCATTTATTAAT-TTCGTAGCACAAAACCTTCCCCTTTCACTGT
129 GAAGAATTCTAGTCATCTTCCCCATTTATTAATCTT-GTAGCTCAAAACCTTCCCCTTTCACTTT
*
39844989 GAATCTGCTCAATTTTTCAG
193 GAATCTGCTCAATGTTTCAG
39845009 TT
1 TT
39845011 GCAAGATCTA
Statistics
Matches: 367, Mismatches: 49, Indels: 24
0.83 0.11 0.05
Matches are distributed among these distances:
205 2 0.01
206 68 0.19
207 2 0.01
208 5 0.01
211 2 0.01
214 13 0.04
215 256 0.70
216 19 0.05
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (212 bp):
TTTAATTAAGAATGAACAGCAAAATCCAAAGGAAGCAGGACTTCAGAGGATGCTCTTGTTAGTGA
AACAAAGAAGCTTCTTATACACAAGATCCTGCATGAATGCATAATATCCATGGAAGGCTAAATGA
AGAATTCTAGTCATCTTCCCCATTTATTAATCTTGTAGCTCAAAACCTTCCCCTTTCACTTTGAA
TCTGCTCAATGTTTCAG
Found at i:39853104 original size:11 final size:11
Alignment explanation
Indices: 39853088--39853112 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39853078 CCAATACCAA
39853088 AAAAAAAAAAG
1 AAAAAAAAAAG
39853099 AAAAAAAAAAG
1 AAAAAAAAAAG
39853110 AAA
1 AAA
39853113 TGGAGCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:39857018 original size:16 final size:16
Alignment explanation
Indices: 39856993--39857026 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39856983 AAAATAACAT
* *
39856993 ATTATTAATATTTTTA
1 ATTATAAATATTATTA
39857009 ATTATAAATATTATTA
1 ATTATAAATATTATTA
39857025 AT
1 AT
39857027 ATGTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATAAATATTATTA
Found at i:39857019 original size:25 final size:26
Alignment explanation
Indices: 39856986--39857034 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
39856976 CAATTGAAAA
*
39856986 ATAACATATTATTAATATTTTTAATT
1 ATAACATATTATTAATATGTTTAATT
39857012 ATAA-ATATTATTAATATGTTTAA
1 ATAACATATTATTAATATGTTTAA
39857035 AATGTACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
ATAACATATTATTAATATGTTTAATT
Found at i:39878999 original size:2 final size:2
Alignment explanation
Indices: 39878994--39879024 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39878984 TATACTTCAA
39878994 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39879025 GACACACAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39880949 original size:30 final size:30
Alignment explanation
Indices: 39880858--39880954 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 30
39880848 AAAATTAAAA
*
39880858 TTATTTTAAA--AAATAAATAAATTATTATTAT
1 TTATTTTAAATTAAATAAAT--ATTTTTATT-T
* * *
39880889 TTATTAT-ATTTAATTAAA-ATTTTATATTT
1 TTATTTTAAATTAAATAAATATTTT-TATTT
39880918 TTATTTTAAATTAAATAAATATTTTTATTT
1 TTATTTTAAATTAAATAAATATTTTTATTT
39880948 TTATTTT
1 TTATTTT
39880955 GATCTAAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
29 11 0.20
30 26 0.48
31 11 0.20
32 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTATTTTAAATTAAATAAATATTTTTATTT
Found at i:39880963 original size:30 final size:28
Alignment explanation
Indices: 39880858--39880965 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 28
39880848 AAAATTAAAA
** *
39880858 TTATTTTAAAAAATAAATAAATTATTATTAT
1 TTATTTTATTAAATAAAT--ATTTTTATT-T
* *
39880889 TTATTATATTTAATTAAA-ATTTTATATTT
1 TTATTTTA-TTAAATAAATATTTT-TATTT
39880918 TTATTTTAAATTAAATAAATATTTTTATTT
1 TTATTTT--ATTAAATAAATATTTTTATTT
39880948 TTATTTTGATCTAAATAA
1 TTATTTT-AT-TAAATAA
39880966 GCCTATATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
29 13 0.21
30 31 0.49
31 13 0.21
32 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
TTATTTTATTAAATAAATATTTTTATTT
Found at i:39884376 original size:2 final size:2
Alignment explanation
Indices: 39884369--39884412 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
39884359 ATCCATTTTA
39884369 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39884410 AT A
1 AT A
39884413 ATTTTTGGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39898142 original size:21 final size:21
Alignment explanation
Indices: 39898115--39898158 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
39898105 TTGCTTTTGC
*
39898115 TTTT-TTTTT-TTTTGGTTGT
1 TTTTGTTTTTATTTTAGTTGT
*
39898134 TTTTGTTTTTATTTTATTTGT
1 TTTTGTTTTTATTTTAGTTGT
39898155 TTTT
1 TTTT
39898159 TTGGTAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 12 0.57
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (21 bp):
TTTTGTTTTTATTTTAGTTGT
Found at i:39898143 original size:25 final size:23
Alignment explanation
Indices: 39898109--39898161 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
39898099 TGTTCTTTGC
* *
39898109 TTTTGCTTTTTTTTTTTTTGGTTGT
1 TTTTGCTTTTATTTTATTT-GTT-T
*
39898134 TTTTGTTTTTATTTTATTTGTTT
1 TTTTGCTTTTATTTTATTTGTTT
39898157 TTTTG
1 TTTTG
39898162 GTAGATTCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 3 0.12
25 16 0.64
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.81
Consensus pattern (23 bp):
TTTTGCTTTTATTTTATTTGTTT
Found at i:39900005 original size:26 final size:25
Alignment explanation
Indices: 39899976--39900057 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
39899966 ATTATTAAAA
39899976 AATTTAATTTTTTATTTTTTATAATT
1 AATTTAA-TTTTTATTTTTTATAATT
* *
39900002 AATTAAATTTTTACATTTTTATTAAGTT
1 AATTTAATTTTTA-TTTTTTA-TAA-TT
* **
39900030 AATAT-ATTTTTATAATTTATAATT
1 AATTTAATTTTTATTTTTTATAATT
39900054 AATT
1 AATT
39900058 ATTATTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
24 5 0.11
25 9 0.20
26 16 0.36
27 10 0.22
28 5 0.11
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (25 bp):
AATTTAATTTTTATTTTTTATAATT
Found at i:39900175 original size:25 final size:24
Alignment explanation
Indices: 39900147--39900230 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 24
39900137 AAAATAATAT
39900147 ATAATAAATGATATTTTAATTTAAA
1 ATAATAAAT-ATATTTTAATTTAAA
*
39900172 ATAATTAAA-ATTTATTTAATTTAAA
1 ATAA-TAAATATAT-TTTAATTTAAA
**
39900197 ATAA-AAATATAATAATTTGGTTTAAA
1 ATAATAAATAT-AT--TTTAATTTAAA
39900223 ATAATAAA
1 ATAATAAA
39900231 AAATAATTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.06
24 5 0.10
25 20 0.41
26 18 0.37
27 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
ATAATAAATATATTTTAATTTAAA
Done.