Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 95 of 226
Found at i:29692098 original size:30 final size:28
Alignment explanation
Indices: 29692024--29692098 Score: 57
Period size: 30 Copynumber: 2.6 Consensus size: 28
29692014 TACATTTATA
29692024 TTTTATAATAT-C-TATACATTT-TCCAT
1 TTTTATAATATGCATATACATTTAT-CAT
* ** *
29692050 ATTTTATAATCTATATATAAATTTATACAT
1 -TTTTATAATATGCATATACATTTAT-CAT
29692080 TCTTTATAATATGCATATA
1 T-TTTATAATATGCATATA
29692099 TATATTCTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 10 0.27
29 9 0.24
30 18 0.49
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTTATAATATGCATATACATTTATCAT
Found at i:29692156 original size:158 final size:157
Alignment explanation
Indices: 29691844--29692172 Score: 396
Period size: 158 Copynumber: 2.1 Consensus size: 157
29691834 ATAGTTTTTA
* *
29691844 TATATATGTATATACATTTATATTTTATAATATTTATACATTTTCCATATTATATAATCTATATA
1 TATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATA
** * * * ** *
29691909 TATGTTTATACATTTTTTATAATATGTATATATATATACATATACATATTTTATTATTATTTTAT
66 TAAATTTATACATTCTTTATAATATGCATATATATATACATATACATATTTCAAAACTA-TTTAT
* * * **
29691974 TATTTTATTTTCATAGTTTTTATATATT
130 AAATATATTTTCATAGTTTTTATATACG
*
29692002 TATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTTTATAATCTATATA
1 TATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATA
*
29692067 TAAATTTATACATTCTTTATAATATGCATATATATATTC-T-TACACTA-TTCAAAACTA-TTAT
66 TAAATTTATACATTCTTTATAATATGCATATATATATACATATACA-TATTTCAAAACTATTTAT
**
29692128 AAATATATTTTCCACATTTTTTTATATATACG
130 AAATATATTTT---CATAGTTTT-TATATACG
*
29692160 TATATATCCATAT
1 TATATATGCATAT
29692173 TTTCATAATT
Statistics
Matches: 146, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
154 12 0.08
156 10 0.07
157 10 0.07
158 114 0.78
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (157 bp):
TATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATA
TAAATTTATACATTCTTTATAATATGCATATATATATACATATACATATTTCAAAACTATTTATA
AATATATTTTCATAGTTTTTATATACG
Found at i:29692198 original size:158 final size:155
Alignment explanation
Indices: 29691827--29692198 Score: 375
Period size: 158 Copynumber: 2.4 Consensus size: 155
29691817 ATTATTATTT
* * * *
29691827 TATTTTCATAGTTTTTATATA--TATGTAT--ATACATTTATATTTTATAATATTTATACATTTT
1 TATTTTCACAGTTTTTATATATGTATATATCCATATATTTATAATTTATAATATTTATACATTTT
** * *
29691888 CCATATTATATAATCTATATATATGTTTATACATTTTTTATAATATGTATATATATATACATATA
66 CCATATTATATAATCTATATATAAATTTATACATTCTTTATAATATGCATATATATATACATATA
* ** * * * *
29691953 CATATTTTATTATTATTTTATTATTT
131 CATATTTCAAAACTA-TTTATAAATA
* * * * *
29691979 TATTTTCATAGTTTTTATATATTTATATATGCATATACATTTATATTTTATAATATCTATACATT
1 TATTTTCACAGTTTTTATATATGTATATATCCATAT--ATTTATAATTTATAATATTTATACATT
* *
29692044 TTCCATATTTTATAATCTATATATAAATTTATACATTCTTTATAATATGCATATATATATTC-T-
64 TTCCATATTATATAATCTATATATAAATTTATACATTCTTTATAATATGCATATATATATACATA
29692107 TACACTA-TTCAAAACTA-TTATAAATA
129 TACA-TATTTCAAAACTATTTATAAATA
*
29692133 TATTTTCCACATTTTTTTATATATACGTATATATCCATAT-TTTCATAATTTACTAATATATTAT
1 TATTTT-CACA-GTTTTTATATAT--GTATATATCCATATATTT-ATAATTTA-TAATAT-TTAT
29692197 AC
59 AC
29692199 TTATATATAT
Statistics
Matches: 184, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
152 21 0.11
154 18 0.10
155 6 0.03
156 31 0.17
157 9 0.05
158 99 0.54
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (155 bp):
TATTTTCACAGTTTTTATATATGTATATATCCATATATTTATAATTTATAATATTTATACATTTT
CCATATTATATAATCTATATATAAATTTATACATTCTTTATAATATGCATATATATATACATATA
CATATTTCAAAACTATTTATAAATA
Found at i:29696315 original size:17 final size:17
Alignment explanation
Indices: 29696290--29696328 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
29696280 CAGAATTAAA
*
29696290 ATTTGATTGAGAAATTT
1 ATTTAATTGAGAAATTT
29696307 ATTTAATTGAGAAATTT
1 ATTTAATTGAGAAATTT
29696324 ATTTA
1 ATTTA
29696329 GTTAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
ATTTAATTGAGAAATTT
Found at i:29703564 original size:7 final size:7
Alignment explanation
Indices: 29703552--29703579 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29703542 AAGTCCATAT
29703552 ATATTTA
1 ATATTTA
29703559 ATATTTA
1 ATATTTA
29703566 ATATTTA
1 ATATTTA
29703573 ATATTTA
1 ATATTTA
29703580 CGAGTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTTA
Found at i:29705083 original size:76 final size:76
Alignment explanation
Indices: 29704939--29705085 Score: 181
Period size: 76 Copynumber: 1.9 Consensus size: 76
29704929 GCGCTGGGCA
* * * * *
29704939 CAACTCATTATTGGTACATCCAACTAGTGCTGAGCACACATTTGATATTGTCAATTTACTCGATT
1 CAACTCATTATTGGTACATCCAACTAATGCTGAGCACACATATGATATCGTCAATTTACTCAACT
29705004 AGCACTAGGCG
66 AGCACTAGGCG
* ** *
29705015 CAACTCATTGTTGGTACATTTAACTAATGCTCGA-CACACATATGATATCGTCGATTTA-TCTAA
1 CAACTCATTATTGGTACATCCAACTAATGCT-GAGCACACATATGATATCGTCAATTTACTC-AA
29705078 CTAGCACT
64 CTAGCACT
29705086 GGGGGCAAGC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
75 2 0.03
76 56 0.93
77 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (76 bp):
CAACTCATTATTGGTACATCCAACTAATGCTGAGCACACATATGATATCGTCAATTTACTCAACT
AGCACTAGGCG
Found at i:29715951 original size:76 final size:76
Alignment explanation
Indices: 29715808--29716013 Score: 169
Period size: 76 Copynumber: 2.7 Consensus size: 76
29715798 CCGCTAGGCG
* ** * *
29715808 CAACTCATTCTTGGTACATCAAACTAGTGTTGGGCACACATTTGGTATCATCAGTTTACCCGACT
1 CAACTCATTATTGGTACATCAAACTAGTGCAGGGCACACATTTGATATCATCAGGTTACCCGACT
29715873 AGCGTTGGGCA
66 AGCGTTGGGCA
* * * * * ** * *
29715884 CAACTCATTATTGGTACATCCAACTAGTGCAGTGCATATATTTGATATCGTTGGGTTACTCGTCT
1 CAACTCATTATTGGTACATCAAACTAGTGCAGGGCACACATTTGATATCATCAGGTTACCCGACT
** **
29715949 AGCACTGGGTG
66 AGCGTTGGGCA
* * * ** ** **
29715960 CAACTTATTGTTTGTTTATCTGACTAGTGTTGGGCACACATTTGATATCATCAG
1 CAACTCATTATTGGTACATCAAACTAGTGCAGGGCACACATTTGATATCATCAG
29716014 TTTATCTAAC
Statistics
Matches: 97, Mismatches: 33, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
76 97 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
CAACTCATTATTGGTACATCAAACTAGTGCAGGGCACACATTTGATATCATCAGGTTACCCGACT
AGCGTTGGGCA
Found at i:29719919 original size:14 final size:15
Alignment explanation
Indices: 29719893--29719922 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29719883 GTTGGGATAA
29719893 TATTTTATATTATTT
1 TATTTTATATTATTT
29719908 TATTTT-TATTATTT
1 TATTTTATATTATTT
29719922 T
1 T
29719923 TGTTTTCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTATATTATTT
Found at i:29727635 original size:17 final size:17
Alignment explanation
Indices: 29727613--29727647 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29727603 TAAGACAATT
29727613 CGGGCATATGGGCCACA
1 CGGGCATATGGGCCACA
* *
29727630 CGGGCATGTGGGCTACA
1 CGGGCATATGGGCCACA
29727647 C
1 C
29727648 AGGTAAGGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.29, G:0.37, T:0.14
Consensus pattern (17 bp):
CGGGCATATGGGCCACA
Found at i:29731173 original size:46 final size:46
Alignment explanation
Indices: 29731115--29731207 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
29731105 TTACCGAATT
*
29731115 TCATCTTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
1 TCATATTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
29731161 TCATATTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
1 TCATATTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
29731207 T
1 T
29731208 GATAGCAACA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (46 bp):
TCATATTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
Found at i:29731283 original size:9 final size:9
Alignment explanation
Indices: 29731250--29731362 Score: 52
Period size: 10 Copynumber: 12.1 Consensus size: 9
29731240 ATTCATTTTC
29731250 ATCATAAATA
1 ATCATAAA-A
*
29731260 TTCATAAAA
1 ATCATAAAA
*
29731269 CT-ATAAAA
1 ATCATAAAA
29731277 ATCATAAAA
1 ATCATAAAA
*
29731286 AT-AAAAAA
1 ATCATAAAA
29731294 ATCATTAAAAA
1 ATCA-T-AAAA
*
29731305 ACTTATAAAA
1 A-TCATAAAA
* *
29731315 CTTATAAAA
1 ATCATAAAA
*
29731324 ATATATAAAA
1 AT-CATAAAA
29731334 AT-ATATAAA
1 ATCATA-AAA
* *
29731343 AACTTATAAA
1 ATCATA-AAA
*
29731353 ATTATAAAA
1 ATCATAAAA
29731362 A
1 A
29731363 ATTATAAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
8 17 0.21
9 28 0.34
10 29 0.35
11 6 0.07
12 2 0.02
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (9 bp):
ATCATAAAA
Found at i:29731283 original size:17 final size:17
Alignment explanation
Indices: 29731261--29731304 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
29731251 TCATAAATAT
* *
29731261 TCATAAAACTATAAAAA
1 TCATAAAAATAAAAAAA
29731278 TCATAAAAATAAAAAAA
1 TCATAAAAATAAAAAAA
29731295 TCATTAAAAA
1 TCA-TAAAAA
29731305 ACTTATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (17 bp):
TCATAAAAATAAAAAAA
Found at i:29731313 original size:38 final size:39
Alignment explanation
Indices: 29731265--29731371 Score: 127
Period size: 38 Copynumber: 2.8 Consensus size: 39
29731255 AAATATTCAT
*
29731265 AAAAC-TATAAAAATCATAAAAATA-A-AAAAATCAT-TAA
1 AAAACTTATAAAAATTATAAAAATATATAAAAAT-ATAT-A
*
29731302 AAAACTTATAAAACTTATAAAAATATATAAAAATATATA
1 AAAACTTATAAAAATTATAAAAATATATAAAAATATATA
29731341 AAAACTTAT-AAAATTATAAAAA-ATTATAAAA
1 AAAACTTATAAAAATTATAAAAATA-TATAAAA
29731372 TTGTAATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
37 6 0.10
38 36 0.58
39 13 0.21
40 7 0.11
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (39 bp):
AAAACTTATAAAAATTATAAAAATATATAAAAATATATA
Found at i:29731314 original size:20 final size:20
Alignment explanation
Indices: 29731280--29731372 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 20
29731270 TATAAAAATC
* *
29731280 ATAAAAATAAAAAAATCATT
1 ATAAAAATTATAAAATCATT
29731300 A-AAAAACTTATAAAA-C-TT
1 ATAAAAA-TTATAAAATCATT
29731318 ATAAAAATATATAAAA--ATAT
1 ATAAAAAT-TATAAAATCAT-T
*
29731338 ATAAAAACTTATAAAATTA-T
1 ATAAAAA-TTATAAAATCATT
29731358 A-AAAAATTATAAAAT
1 ATAAAAATTATAAAAT
29731373 TGTAATATAT
Statistics
Matches: 63, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
18 13 0.21
19 24 0.38
20 24 0.38
21 1 0.02
22 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAATTATAAAATCATT
Found at i:29731333 original size:30 final size:29
Alignment explanation
Indices: 29731273--29731371 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 29
29731263 ATAAAACTAT
* * *
29731273 AAAAATCATAAAA-ATAAAAAAATCAT-TA
1 AAAAATTATAAAACTTATAAAAAT-ATATA
29731301 AAAAACTTATAAAACTTATAAAAATATAT-
1 AAAAA-TTATAAAACTTATAAAAATATATA
29731330 AAAAATATATAAAAACTTAT-AAAAT-TATA
1 AAAAAT-TAT-AAAACTTATAAAAATATATA
29731359 AAAAATTATAAAA
1 AAAAATTATAAAA
29731372 TTGTAATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
27 4 0.06
28 12 0.19
29 28 0.45
30 18 0.29
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAATTATAAAACTTATAAAAATATATA
Found at i:29731371 original size:9 final size:9
Alignment explanation
Indices: 29731265--29731371 Score: 92
Period size: 10 Copynumber: 11.3 Consensus size: 9
29731255 AAATATTCAT
*
29731265 AAAACTATA
1 AAAATTATA
*
29731274 AAAATCATA
1 AAAATTATA
*
29731283 AAAA-TAAA
1 AAAATTATA
*
29731291 AAAATCATTAA
1 AAAATTA-T-A
29731302 AAAACTTATA
1 AAAA-TTATA
*
29731312 AAACTTATA
1 AAAATTATA
29731321 AAAATATATA
1 AAAAT-TATA
29731331 AAAATATATA
1 AAAAT-TATA
29731341 AAAACTTAT-
1 AAAA-TTATA
29731350 AAAATTATAA
1 AAAATTAT-A
29731360 AAAATTATA
1 AAAATTATA
29731369 AAA
1 AAA
29731372 TTGTAATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
8 10 0.12
9 29 0.36
10 33 0.41
11 7 0.09
12 2 0.02
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAATTATA
Found at i:29731384 original size:18 final size:18
Alignment explanation
Indices: 29731299--29731373 Score: 89
Period size: 18 Copynumber: 3.9 Consensus size: 18
29731289 AAAAAATCAT
29731299 TAAAAAACTTATAAAACTTA
1 TAAAAAA-TTATAAAA-TTA
29731319 T-AAAAATATATAAAAATATA
1 TAAAAAAT-TAT-AAAAT-TA
*
29731339 TAAAAACTTATAAAATTA
1 TAAAAAATTATAAAATTA
29731357 TAAAAAATTATAAAATT
1 TAAAAAATTATAAAATT
29731374 GTAATATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
18 19 0.39
19 14 0.29
20 11 0.22
21 5 0.10
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAATTATAAAATTA
Found at i:29732107 original size:20 final size:19
Alignment explanation
Indices: 29732084--29732135 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
29732074 TTTTTTTTAC
*
29732084 ATTTTTATAGGTTTTTGTGA
1 ATTTTTATAGGTTTTTAT-A
*
29732104 ATTTTTATAAGTTTTTATA
1 ATTTTTATAGGTTTTTATA
*
29732123 AGTTTTATAGGTT
1 ATTTTTATAGGTT
29732136 CATATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (19 bp):
ATTTTTATAGGTTTTTATA
Found at i:29732131 original size:9 final size:10
Alignment explanation
Indices: 29732085--29732128 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
29732075 TTTTTTTACA
*
29732085 TTTTTATAGG
1 TTTTTATAAG
*
29732095 TTTTTGTGAA-
1 TTTTTAT-AAG
29732105 TTTTTATAAG
1 TTTTTATAAG
29732115 TTTTTATAAG
1 TTTTTATAAG
29732125 TTTT
1 TTTT
29732129 ATAGGTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.90
11 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.64
Consensus pattern (10 bp):
TTTTTATAAG
Found at i:29732179 original size:21 final size:20
Alignment explanation
Indices: 29732166--29732210 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
29732156 TTATGGTTTA
29732166 TTTATAAGCTTTTATGAATTT
1 TTTATAAG-TTTTATGAATTT
*
29732187 TTTATAAGTTTTAT-AATTA
1 TTTATAAGTTTTATGAATTT
29732206 TTTAT
1 TTTAT
29732211 TTATGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 6 0.26
21 8 0.35
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTATAAGTTTTATGAATTT
Found at i:29732209 original size:19 final size:21
Alignment explanation
Indices: 29732163--29732210 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
29732153 TATTTATGGT
29732163 TTATTTATAAGCTTTTATGAA
1 TTATTTATAAGCTTTTATGAA
*
29732184 TTTTTTATAAG-TTTTAT-AA
1 TTATTTATAAGCTTTTATGAA
29732203 TTATTTAT
1 TTATTTAT
29732211 TTATGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATTTATAAGCTTTTATGAA
Found at i:29734525 original size:26 final size:26
Alignment explanation
Indices: 29734477--29734531 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
29734467 TTTGAAATTT
* * *
29734477 ATTCGAATCGAATCAAGTGGAATGAA
1 ATTCGAATCGAATCAAATCGAATAAA
* *
29734503 ATTCGAGTCGAGTCAAATCGAATAAA
1 ATTCGAATCGAATCAAATCGAATAAA
29734529 ATT
1 ATT
29734532 GTTCAAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (26 bp):
ATTCGAATCGAATCAAATCGAATAAA
Found at i:29734782 original size:17 final size:18
Alignment explanation
Indices: 29734760--29734799 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
29734750 TTTTTTAGAT
*
29734760 TTTTTTAAAAATTAT-AA
1 TTTTTTAAAAAATATAAA
29734777 TTTTTTAAAAAATATAAA
1 TTTTTTAAAAAATATAAA
29734795 TTTTT
1 TTTTT
29734800 GAATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTTTAAAAAATATAAA
Found at i:29734818 original size:19 final size:19
Alignment explanation
Indices: 29734789--29734843 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
29734779 TTTTAAAAAA
29734789 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTGAATTTT
29734807 TATAAATATTTT-AATTTTT
1 TATAAATATTTTGAA-TTTT
*
29734826 TAAAAATTATTTTGAATT
1 TATAAA-TATTTTGAATT
29734844 ATTTTTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.28
19 13 0.41
20 8 0.25
21 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:29734826 original size:20 final size:22
Alignment explanation
Indices: 29734802--29734849 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 22
29734792 AAATTTTTGA
*
29734802 ATTTTTATAAA-TATTTT-AAT
1 ATTTTTAAAAATTATTTTGAAT
29734822 -TTTTTAAAAATTATTTTGAATT
1 ATTTTTAAAAATTATTTTGAA-T
29734844 ATTTTT
1 ATTTTT
29734850 TAATTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 9 0.39
20 6 0.26
21 2 0.09
22 1 0.04
23 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTTTAAAAATTATTTTGAAT
Found at i:29740964 original size:7 final size:7
Alignment explanation
Indices: 29740912--29740964 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
29740902 ACTAAAAAAC
29740912 AAAATCAA
1 AAAATC-A
29740920 AAAATCA
1 AAAATCA
29740927 AAAATCAA
1 AAAATC-A
29740935 CAAAATC-
1 -AAAATCA
29740942 AAAATC-
1 AAAATCA
*
29740948 AAAATAA
1 AAAATCA
29740955 AAAATCA
1 AAAATCA
29740962 AAA
1 AAA
29740965 TTGGAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 11 0.28
7 16 0.40
8 7 0.17
9 6 0.15
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATCA
Found at i:29740975 original size:21 final size:20
Alignment explanation
Indices: 29740920--29740965 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
29740910 ACAAAATCAA
*
29740920 AAAATCAAAAATCAACAAAATC
1 AAAATC-AAAATAAAC-AAATC
29740942 AAAATCAAAATAAA-AAATC
1 AAAATCAAAATAAACAAATC
29740961 AAAAT
1 AAAAT
29740966 TGGAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
21 7 0.30
22 6 0.26
ACGTcount: A:0.72, C:0.13, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAATCAAAATAAACAAATC
Found at i:29741004 original size:12 final size:12
Alignment explanation
Indices: 29740984--29741016 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29740974 AAGAATGATG
29740984 AAAAA-AAAAGA
1 AAAAAGAAAAGA
29740995 AAAAAGAAAAGA
1 AAAAAGAAAAGA
*
29741007 AAGAAGAAAA
1 AAAAAGAAAA
29741017 AGAGAGGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:29741015 original size:19 final size:17
Alignment explanation
Indices: 29740983--29741017 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
29740973 TAAGAATGAT
29740983 GAAAAAAAAAGAAAAAA
1 GAAAAAAAAAGAAAAAA
29741000 GAAAAGAAAGAAGAAAAA
1 GAAAA-AAA-AAGAAAAA
29741018 GAGAGGCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAAGAAAAAA
Found at i:29742446 original size:88 final size:88
Alignment explanation
Indices: 29742283--29742446 Score: 249
Period size: 88 Copynumber: 1.9 Consensus size: 88
29742273 CTCCCTGAGC
* * *
29742283 AGCAGTGGAATAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAG
1 AGCAGTGGAATAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCGAAG
*
29742348 ATACGAGTCTTTTCTTCCTGGGT
66 ATACCAGTCTTTTCTTCCTGGGT
* *
29742371 AGCAGTGGAATAGGTTAAAAAT-GACAGATCTTGCCTTCCTGTACTGGCGGCGAAGCAGATCGAA
1 AGCAGTGGAATAGGTTAAAAATAG-CAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCGAA
*
29742435 GATACCCGTCTT
65 GATACCAGTCTT
29742447 ATCGTCTTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 1 0.01
88 67 0.99
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (88 bp):
AGCAGTGGAATAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCGAAG
ATACCAGTCTTTTCTTCCTGGGT
Found at i:29742859 original size:50 final size:50
Alignment explanation
Indices: 29742796--29743181 Score: 225
Period size: 50 Copynumber: 7.7 Consensus size: 50
29742786 TTTAGCATTA
29742796 TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
1 TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
* * * * *** * **
29742846 TAGTGGAATAGATTGAAGCTACGACAGCGGATCTGGTTTCCCTGACATTG
1 TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
* * ** * * *
29742896 AAAATTAAAAAGATTTAAGCCACAATGGCGGATCTTACTTCCCTGGCGATG
1 -TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
* ** * * *** * * **
29742947 TAGTGGAACAGATTGAAGCTTCGACGGCAGATCTGGTTTCCCCGACATTG
1 TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
* * * * ** *
29742997 CAAT-TAAAAGGATTGAAGCCACAATGGTAGATCTTACTTCCCTAGCGGTG
1 TAGTGGAAAA-GATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
* * * * * * ** * * **
29743047 CAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCAGACATTG
1 TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
* * ** * *
29743097 CAATTAAAAAGATTGAAGCCACAACGGTGGATCTTACTTCCTTGGCGGTG
1 TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
* * * *
29743147 TAGTGGAATAGATTGAAGTCACGACGGCGAATCTT
1 TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTT
29743182 GTTTCCTCGA
Statistics
Matches: 230, Mismatches: 103, Indels: 6
0.68 0.30 0.02
Matches are distributed among these distances:
49 3 0.01
50 190 0.83
51 37 0.16
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (50 bp):
TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTG
Found at i:29742861 original size:167 final size:167
Alignment explanation
Indices: 29742462--29742879 Score: 561
Period size: 167 Copynumber: 2.5 Consensus size: 167
29742452 CTTAACGTTG
* * *
29742462 CAATGGAAAAGACTGAAGCCACAACGGCGGATCTTATTTTCCTGG-TGTCTTAGCGGAGTAGATT
1 CAATGGAAAAGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGCAGT-GTAGCGGAGTAGATT
* * *
29742526 GAAGCTACGACGGCGGATCTTATCTTCCTGGTGTTAAGACTTGGATTAGCTGAAGTGGAGCGGAT
65 GAAGCTACGACGACGGATCTTATCTCCCTGGTGTTAAGACTTAGATTAGCTGAAGTGGAGCGGAT
* * *
29742591 TAAAGCTGTGGGCAGCGAATCCTATCTCTTTTGCATTG
130 TAAAGCTGTGGGCAGCAAATCCTATCTCTTTAGCATTA
** * * * *
29742629 CAATTAAAAAGATTAAAGCCACAACGGCGGATCTTATTTTCCTGGCATTGCAGCGGAGCAGATTG
1 CAATGGAAAAGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGCAGTGTAGCGGAGTAGATTG
* * *
29742694 AAGCCACGACGACGGATCTTATCTCCCTGGTGTTAAGGCTTAGATTAGCTGAAGTGGAGTGGATT
66 AAGCTACGACGACGGATCTTATCTCCCTGGTGTTAAGACTTAGATTAGCTGAAGTGGAGCGGATT
* *
29742759 GAAGCTGTGGGCAGCAAATTCTATCTCTTTAGCATTA
131 AAAGCTGTGGGCAGCAAATCCTATCTCTTTAGCATTA
* * * * * * *
29742796 TAGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTG
1 CAATGGAAAAGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGCAGTGTAGCGGAGTAGATTG
29742861 AAGCTACGAC-AGCGGATCT
66 AAGCTACGACGA-CGGATCT
29742880 GGTTTCCCTG
Statistics
Matches: 215, Mismatches: 34, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
166 1 0.00
167 213 0.99
168 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (167 bp):
CAATGGAAAAGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGCAGTGTAGCGGAGTAGATTG
AAGCTACGACGACGGATCTTATCTCCCTGGTGTTAAGACTTAGATTAGCTGAAGTGGAGCGGATT
AAAGCTGTGGGCAGCAAATCCTATCTCTTTAGCATTA
Found at i:29743054 original size:100 final size:100
Alignment explanation
Indices: 29742802--29743204 Score: 549
Period size: 100 Copynumber: 4.0 Consensus size: 100
29742792 ATTATAGTGG
*
29742802 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* * * *
29742867 CGACAGCGGATCTGGTTTCCCTGACATTGAAAATTA
66 CGACGGCGAATCTGGTTTCCCCGACATTG-CAATTA
* * * *
29742903 AAAAGATTTAAGCCACAATGGCGGATCTTACTTCCCTGGCGATGTAGTGGAACAGATTGAAGCTT
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
29742968 CGACGGC-AGATCTGGTTTCCCCGACATTGCAATTA
66 CGACGGCGA-ATCTGGTTTCCCCGACATTGCAATTA
* * ** * *
29743003 AAAGGATTGAAGCCACAATGGTAGATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* * *
29743068 CGACGACGAATCTTGTTTCCCAGACATTGCAATTA
66 CGACGGCGAATCTGGTTTCCCCGACATTGCAATTA
* * *
29743103 AAAAGATTGAAGCCACAACGGTGGATCTTACTTCCTTGGCGGTGTAGTGGAATAGATTGAAG-TC
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCT-
* * *
29743167 ACGACGGCGAATCTTGTTTCCTCGACATTGCAGTTA
65 ACGACGGCGAATCTGGTTTCCCCGACATTGCAATTA
29743203 AA
1 AA
29743205 CAATTTGAAA
Statistics
Matches: 268, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
99 1 0.00
100 181 0.68
101 86 0.32
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
CGACGGCGAATCTGGTTTCCCCGACATTGCAATTA
Found at i:29744913 original size:10 final size:10
Alignment explanation
Indices: 29744891--29744936 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
29744881 TGTTTATATT
29744891 TTTATTT-TA
1 TTTATTTGTA
29744900 TTTATTTGTA
1 TTTATTTGTA
29744910 TTTATTTGTA
1 TTTATTTGTA
*
29744920 TTTATTTCTA
1 TTTATTTGTA
*
29744930 TATATTT
1 TTTATTT
29744937 TTTAGATACC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
9 7 0.21
10 27 0.79
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (10 bp):
TTTATTTGTA
Found at i:29765049 original size:40 final size:40
Alignment explanation
Indices: 29764992--29765077 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
29764982 CTCGAGGGAG
* *
29764992 TAAGGTTGTTTTCAAAAACTGACCTTCAATCGGGATATTA
1 TAAGGTTGTTTTAAAAAACTGACCTTCAATCGAGATATTA
* *
29765032 TAAGGTTGTTTTAAAAAATTGACCTTCGATCGAGATATTA
1 TAAGGTTGTTTTAAAAAACTGACCTTCAATCGAGATATTA
*
29765072 TCAGGT
1 TAAGGT
29765078 CAAAATTAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (40 bp):
TAAGGTTGTTTTAAAAAACTGACCTTCAATCGAGATATTA
Found at i:29769615 original size:27 final size:27
Alignment explanation
Indices: 29769577--29769676 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
29769567 AACATGTCAA
* * *
29769577 GAAATAGTAGCCTTTTTGGGGAAATAT
1 GAAAGAGTAGCCTTTGTGGAGAAATAT
*
29769604 GAAAGAGTAGCCTTTGTGGCGAAATAT
1 GAAAGAGTAGCCTTTGTGGAGAAATAT
* *
29769631 GAAAGAGTAGCCTTTGTGGAAAAATAA
1 GAAAGAGTAGCCTTTGTGGAGAAATAT
*
29769658 GAACGAGTAGCCTTTGTGG
1 GAAAGAGTAGCCTTTGTGG
29769677 TGAACCCTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (27 bp):
GAAAGAGTAGCCTTTGTGGAGAAATAT
Found at i:29771152 original size:30 final size:30
Alignment explanation
Indices: 29771116--29771177 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
29771106 GTTTCATTCA
**
29771116 AACTCTTTTGTCTTAGAAAGGATTTTAAAT
1 AACTCTTGGGTCTTAGAAAGGATTTTAAAT
29771146 AACTCTTGGGTCTTAGAAAGGATTTTAAAT
1 AACTCTTGGGTCTTAGAAAGGATTTTAAAT
29771176 AA
1 AA
29771178 ATAAGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (30 bp):
AACTCTTGGGTCTTAGAAAGGATTTTAAAT
Found at i:29780827 original size:29 final size:30
Alignment explanation
Indices: 29780786--29780842 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
29780776 CTGTCGATGT
29780786 CACACGGGCGTGTG-CTGGGT-TGTGTGTAA
1 CACACGGGCGTGTGAC-GGGTATGTGTGTAA
29780815 CACA-GGGCTGTGTGACGGGTATGTGTGT
1 CACACGGGC-GTGTGACGGGTATGTGTGT
29780843 GTGGCTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 4 0.16
29 13 0.52
30 8 0.32
ACGTcount: A:0.14, C:0.16, G:0.42, T:0.28
Consensus pattern (30 bp):
CACACGGGCGTGTGACGGGTATGTGTGTAA
Found at i:29786798 original size:16 final size:17
Alignment explanation
Indices: 29786777--29786811 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29786767 CGCTCAACAA
29786777 AACAATTTT-TGAAAAC
1 AACAATTTTATGAAAAC
*
29786793 AACAATTTTATGTAAAC
1 AACAATTTTATGAAAAC
29786810 AA
1 AA
29786812 ACATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
AACAATTTTATGAAAAC
Found at i:29786817 original size:17 final size:17
Alignment explanation
Indices: 29786776--29786819 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
29786766 ACGCTCAACA
29786776 AAACAATTTTTGAAAAC
1 AAACAATTTTTGAAAAC
*
29786793 -AACAATTTTATGTAAAC
1 AAACAATTTT-TGAAAAC
29786810 AAAC-ATTTTT
1 AAACAATTTTT
29786820 CAGGACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 10 0.42
17 11 0.46
18 3 0.12
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (17 bp):
AAACAATTTTTGAAAAC
Found at i:29798313 original size:37 final size:37
Alignment explanation
Indices: 29798256--29798407 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
29798246 TATGATCACT
*
29798256 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
29798291 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
29798328 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
29798373 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
29798408 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:29798391 original size:46 final size:46
Alignment explanation
Indices: 29798324--29798690 Score: 446
Period size: 46 Copynumber: 7.6 Consensus size: 46
29798314 TAAGTGTAGC
* **
29798324 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
29798370 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
29798416 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
29798468 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
29798520 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
29798566 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
29798612 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
29798664 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
29798691 AGTACTCAAA
Statistics
Matches: 291, Mismatches: 17, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
46 155 0.53
48 1 0.00
49 1 0.00
50 2 0.01
51 3 0.01
52 129 0.44
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:29798443 original size:52 final size:52
Alignment explanation
Indices: 29798367--29798684 Score: 426
Period size: 52 Copynumber: 6.3 Consensus size: 52
29798357 TAGCTAAAGC
* *
29798367 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
29798420 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
29798472 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
29798524 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
29798570 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
29798616 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
29798668 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
29798685 ATCAGAAGTA
Statistics
Matches: 239, Mismatches: 16, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
46 84 0.35
47 2 0.01
48 2 0.01
52 133 0.56
53 18 0.08
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:29798632 original size:196 final size:196
Alignment explanation
Indices: 29798324--29798676 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
29798314 TAAGTGTAGC
* * * * *
29798324 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACT
*
29798389 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
* *
29798454 GTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
131 GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
29798519 T
196 T
*
29798520 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACT
*
29798585 TGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
*
29798650 GTAGCTAAAGCTACCACTTATCACTTT
131 GTAGCCAAAGCTACCACTTATCACTTT
29798677 ATCACTTGAT
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (196 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACT
TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
T
Found at i:29798679 original size:98 final size:97
Alignment explanation
Indices: 29798324--29798690 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
29798314 TAAGTGTAGC
* * * *
29798324 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTT-TCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACT
29798389 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
64 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
29798423 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTG
1 CAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT--A----
* *
29798488 TCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
59 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
29798527 CAC--T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATCACTTG
1 CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
*
29798587 ATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 ATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
29798619 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTT
1 CACTTT-CACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTT
29798684 GATCAGA
65 GATCAGA
29798691 AGTACTCAAA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 39 0.16
94 1 0.00
96 1 0.00
98 150 0.62
99 7 0.03
100 2 0.01
101 1 0.00
104 39 0.16
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
ATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:29800849 original size:45 final size:44
Alignment explanation
Indices: 29800798--29800883 Score: 138
Period size: 44 Copynumber: 1.9 Consensus size: 44
29800788 CACTGTAATA
29800798 GAATAGAGCTGTAATAGTAATTCAAT-TGTTTGGTTGAATGGATTG
1 GAATAGAGCTGTAATAGT-ATT-AATATGTTTGGTTGAATGGATTG
*
29800843 GAATAGAGCTGTAATAGTATTATTATGTTTGGTTGAATGGA
1 GAATAGAGCTGTAATAGTATTAATATGTTTGGTTGAATGGA
29800884 ATGATGTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 2 0.05
44 19 0.49
45 18 0.46
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.38
Consensus pattern (44 bp):
GAATAGAGCTGTAATAGTATTAATATGTTTGGTTGAATGGATTG
Found at i:29801070 original size:20 final size:20
Alignment explanation
Indices: 29800994--29801081 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
29800984 AATAAGATTA
*
29800994 TTAATAAAAATAATAAATAAT
1 TTAAT-AAAATAATATATAAT
*
29801015 TTAAT--AAT-AT-TTTAAT
1 TTAATAAAATAATATATAAT
* *
29801031 TTAATTAGTATTAA-ATATAAT
1 TTAA-TA-AAATAATATATAAT
29801052 TTAATAAAATAATATATAAT
1 TTAATAAAATAATATATAAT
29801072 TTAATAAAAT
1 TTAATAAAAT
29801082 TCTTAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
16 8 0.15
17 3 0.06
18 3 0.06
19 4 0.07
20 21 0.39
21 15 0.28
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
TTAATAAAATAATATATAAT
Found at i:29801110 original size:57 final size:56
Alignment explanation
Indices: 29800994--29801127 Score: 153
Period size: 57 Copynumber: 2.3 Consensus size: 56
29800984 AATAAGATTA
* * *
29800994 TTAATAAAAATAATAAATAATTTAATAATATTTTAATTTAATTAGTATTAAATATAAT
1 TTAAT-AAAATAATATATAATTTAATAAAATTTTAATATAATTAGTATT-AATATAAT
* *
29801052 TTAATAAAATAATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATATATAATTTAATAAAATT-TTAATATAATTAGTATTAATAT-AAT
* *
29801109 TTACTAAAATCATAATATA
1 TTAATAAAATAAT-ATATA
29801128 TAATACTATA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
56 4 0.06
57 38 0.58
58 24 0.36
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (56 bp):
TTAATAAAATAATATATAATTTAATAAAATTTTAATATAATTAGTATTAATATAAT
Found at i:29801745 original size:47 final size:47
Alignment explanation
Indices: 29801694--29801789 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
29801684 TTTTGTAGTG
*
29801694 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAATATTTT
1 TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAATATTTT
*
29801741 TTAATTATAATTTTCAATCATACAATATAAGTAATATAAAATATTTT
1 TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAATATTTT
29801788 TT
1 TT
29801790 TGAAGATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (47 bp):
TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAATATTTT
Found at i:29802832 original size:13 final size:13
Alignment explanation
Indices: 29802814--29802839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29802804 ATAGCATAAC
29802814 ATTTTATCAGAAT
1 ATTTTATCAGAAT
29802827 ATTTTATCAGAAT
1 ATTTTATCAGAAT
29802840 CTGCTCACTG
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:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTTTATCAGAAT
Found at i:29815980 original size:3 final size:3
Alignment explanation
Indices: 29815972--29816008 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
29815962 GAGAGAAAGC
29815972 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
29816009 GACCTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29821516 original size:45 final size:45
Alignment explanation
Indices: 29821443--29821648 Score: 330
Period size: 45 Copynumber: 4.6 Consensus size: 45
29821433 TACGTATGAT
*
29821443 CACTTATCAC-TTGTTC-C-TGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTG-TCACTTGATCAGATAAGTGTAGCTAAGCTAC
29821486 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAG-CTAC
*
29821531 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTAC
*
29821577 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTAC
29821622 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
29821649 AGTACTCAAA
Statistics
Matches: 153, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
43 12 0.08
44 5 0.03
45 94 0.61
46 40 0.26
47 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTAC
Found at i:29821595 original size:91 final size:90
Alignment explanation
Indices: 29821443--29821648 Score: 337
Period size: 91 Copynumber: 2.3 Consensus size: 90
29821433 TACGTATGAT
* *
29821443 CACTTATCACTTGTTC-C-TGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTT
*
29821506 GATCAGATAAGTGTAGCT-AGACTAC
66 GATCAGATAAGAGTAGCTAAG-CTAC
29821531 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
29821596 TGATCAGATAAGAGTAGCTAAGCTAC
65 TGATCAGATAAGAGTAGCTAAGCTAC
*
29821622 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
29821649 AGTACTCAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
88 15 0.14
89 1 0.01
90 19 0.17
91 73 0.66
92 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (90 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTT
GATCAGATAAGAGTAGCTAAGCTAC
Found at i:29823518 original size:21 final size:21
Alignment explanation
Indices: 29823494--29823535 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29823484 CTTTTTGTTC
* *
29823494 AATTAATTATCGGAACTTTAA
1 AATTAATTAACGAAACTTTAA
*
29823515 AATTTATTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
29823536 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:29846364 original size:166 final size:168
Alignment explanation
Indices: 29846092--29846495 Score: 639
Period size: 166 Copynumber: 2.5 Consensus size: 168
29846082 GTTTCTTTCG
*
29846092 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGCGATCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTGATGCGATCTGCTCCACTACTACTTAGG
* *
29846153 GAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATA
66 GAGATAAGATCTGGTTTCTTTCATCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATA
29846218 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
131 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
** * *
29846256 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTTTTCG-TCTGTTCCACTACTACTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTGATGCGATCTGCTCCACTACTACTTAGG
*
29846320 GAGATAAGAT-TGGTTTCTTTCATCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATC
66 GAGATAAGATCTGGTTTCTTTCATCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATA
29846384 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
131 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
* * *
29846422 TTTGCTCCACTACTGCTTAGGGAGATAAGATCTGG-TG-T--GATCTGCTCCACTATTCCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTGATGCGATCTGCTCCACTACTACTTAGG
29846483 GAGATAAGATCTG
66 GAGATAAGATCTG
29846496 CAATCTTCAA
Statistics
Matches: 221, Mismatches: 13, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
162 1 0.00
163 28 0.13
164 33 0.15
165 2 0.01
166 123 0.56
167 29 0.13
168 5 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (168 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTGATGCGATCTGCTCCACTACTACTTAGG
GAGATAAGATCTGGTTTCTTTCATCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATA
TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
Found at i:29846442 original size:206 final size:206
Alignment explanation
Indices: 29846070--29846495 Score: 605
Period size: 206 Copynumber: 2.1 Consensus size: 206
29846060 CAACTTCAAT
* * *
29846070 GAGATAGGAT-TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATC
1 GAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCCATC
* ** *
29846134 TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGA
66 TACTCCACTACTGCTTAGGGAGATAAGATC--GTTGATGTCGTCTGCTCCACTACTGCTTAGGGA
29846199 GATAAGACTTGATGTGATATGCTCCACTACTGCTTAGGGAGATAAGA-CTTGATGTGATCTGCTC
129 GATAAGACTTGATGTGATATGCTCCACTACTGCTTAGGGAGATAAGATC-TGATGTGATCTGCTC
*
29846263 CACTACTGCTTAGG
193 CACTACTCCTTAGG
* * *
29846277 GAGATAAGATCTGGTTT-TTTCGTCTGTTCCACTACTACTTAGGGAGATAAGA-TTGGTTTCTTT
1 GAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTT-GATGC---
29846340 CATCTACTCCACTACTGCTTAGGGAGATAAGA-C-TTGATGT-GATCTGCTCCACTACTGCTTAG
62 CATCTACTCCACTACTGCTTAGGGAGATAAGATCGTTGATGTCG-TCTGCTCCACTACTGCTTAG
* *
29846402 GGAGATAAGACTTGATGTGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTGTGATCTGC
126 GGAGATAAGACTTGATGTGATATGCTCCACTACTGCTTAGGGAGATAAGATCTGATGTGATCTGC
*
29846467 TCCACTATTCCTTAGG
191 TCCACTACTCCTTAGG
29846483 GAGATAAGATCTG
1 GAGATAAGATCTG
29846496 CAATCTTCAA
Statistics
Matches: 198, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
205 1 0.01
206 114 0.58
207 46 0.23
208 6 0.03
209 1 0.01
210 30 0.15
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (206 bp):
GAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCCATC
TACTCCACTACTGCTTAGGGAGATAAGATCGTTGATGTCGTCTGCTCCACTACTGCTTAGGGAGA
TAAGACTTGATGTGATATGCTCCACTACTGCTTAGGGAGATAAGATCTGATGTGATCTGCTCCAC
TACTCCTTAGG
Found at i:29846495 original size:40 final size:40
Alignment explanation
Indices: 29846092--29846491 Score: 484
Period size: 40 Copynumber: 9.8 Consensus size: 40
29846082 GTTTCTTTCG
*
29846092 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
** *
29846132 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGT-GA
29846176 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
*
29846216 TATGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
** *
29846256 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT--TGATGT-GA
* * * * *
29846299 TCTGTTCCACTACTACTTAGGGAGATAAGA-TTGGTTTCTTTCA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTT-G---ATGTGA
*
29846342 TCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
29846382 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
* *
29846422 TTTGCTCCACTACTGCTTAGGGAGATAAGA-TCTGGTGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACT-TGATGTGA
* *
29846462 TCTGCTCCACTATTCCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
29846492 TCTGCAATCT
Statistics
Matches: 314, Mismatches: 29, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
39 3 0.01
40 207 0.66
41 4 0.01
43 63 0.20
44 36 0.11
45 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
Found at i:29846530 original size:44 final size:44
Alignment explanation
Indices: 29846480--29846664 Score: 131
Period size: 44 Copynumber: 4.2 Consensus size: 44
29846470 ACTATTCCTT
* *
29846480 AGGGAGATAAGATCTGCAATCTTCAATTTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCTGCCC
* * *** * * *
29846524 AGGGAGAT-AGAACTACTGGCTTCAATGTACTCCACTG-TAATCTC
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCT--GCCC
* * * * * * * * * **
29846568 AAGAAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCTGCCC
* *
29846612 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCTGCCC
29846656 AGGGAGATA
1 AGGGAGATA
29846665 GAACTACCGG
Statistics
Matches: 99, Mismatches: 38, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
42 1 0.01
43 22 0.22
44 57 0.58
45 18 0.18
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (44 bp):
AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTGCTGCCC
Found at i:29846622 original size:132 final size:132
Alignment explanation
Indices: 29846460--29846766 Score: 533
Period size: 132 Copynumber: 2.3 Consensus size: 132
29846450 GATCTGGTGT
* * * *
29846460 GATCTGCTCCACTATTCCTTAGGGAGATAAGATCTGCAATCTTCAATTTATTCCACTGCTGCCCA
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
* *
29846525 GGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAATCTCAAGAAGGTAAAATCCGCCATCT
66 GGGAGATAGAACTACCGGATTCAATGTACTCCACTGTAATCTCAAGAAGGTAAAATCCGCCATCT
29846590 TC
131 TC
29846592 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
* * *
29846657 GGGAGATAGAACTACCGGATTCAGTGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCT
66 GGGAGATAGAACTACCGGATTCAATGTACTCCACTGTAATCTCAAGAAGGTAAAATCCGCCATCT
29846722 TC
131 TC
29846724 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
29846767 AGATCTGCTT
Statistics
Matches: 166, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 166 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
GGGAGATAGAACTACCGGATTCAATGTACTCCACTGTAATCTCAAGAAGGTAAAATCCGCCATCT
TC
Found at i:29846748 original size:44 final size:44
Alignment explanation
Indices: 29846575--29846753 Score: 125
Period size: 44 Copynumber: 4.1 Consensus size: 44
29846565 CTCAAGAAGG
* *
29846575 TAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 TAAAATCCGCCATCTTCGATCTACTCCACTACTGCTCAGGGAGA
* * ** * * * *
29846619 TAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGA
1 TAAAATCCGCCATCTTCGATCTACTCCACTACTGCTCAGGGAGA
* * * * *
29846663 TAGAACTACCG-GA--TTC-AGTGTACTCCACTGTAAT-CTCAGGGAGG
1 TA-AAAT-CCGCCATCTTCGA-TCTACTCCAC--TACTGCTCAGGGAGA
* *
29846707 TAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 TAAAATCCGCCATCTTCGATCTACTCCACTACTGCTCAGGGAGA
29846751 TAA
1 TAA
29846754 GATCTGTAAT
Statistics
Matches: 98, Mismatches: 27, Indels: 20
0.68 0.19 0.14
Matches are distributed among these distances:
42 4 0.04
43 18 0.18
44 57 0.58
45 16 0.16
46 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (44 bp):
TAAAATCCGCCATCTTCGATCTACTCCACTACTGCTCAGGGAGA
Found at i:29846969 original size:88 final size:88
Alignment explanation
Indices: 29846763--29847788 Score: 1139
Period size: 88 Copynumber: 11.7 Consensus size: 88
29846753 AGATCTGTAA
* * * * ** * * *
29846763 TCTTAGATCTGCTTCGCTGTCAATGCAGGAAGGCAAAATCTGCTATCTTCAGTCTGCTCCGCTGT
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCT-A
* * *
29846828 CAGTA-C-ATGA-AGGCAAGACTGGTT
65 CA--ACCGA-GAGAGGCAAGGCTTGTG
* * * * * * ** *
29846852 TCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGCTATCTTTGACCAGCT-TCACTA
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCT-GCTA
* * *
29846916 CAAACGAGGGAGGCAAGACTTGTG
65 CAACCGAGAGAGGCAAGGCTTGTG
*
29846940 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAACTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
29847005 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGCTTGTG
* * * *
29847028 TCTTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAATATCTGCTGTCTTTAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
29847093 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGCTTGTG
* * * **
29847116 TCTTTGATCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTATTCAACCAGCTCCACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
29847181 AACCGAGAGAGGCAAGGCTTGTG
66 AACCGAGAGAGGCAAGGCTTGTG
** * * ** *
29847204 TCTTCGATCTGCTTCGCTGTCAGGGTAGGAAGGCAAGATCTGTTGTTTTCAAATAACTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
** *
29847269 AACCGAGAGATACAAGGTTTGTG
66 AACCGAGAGAGGCAAGGCTTGTG
* * * * **
29847292 TCTTTGATCTGCTTCGCTATCAATGCAGGAAGGCAAGATTTGTTGTATTCAACCAGCTCCACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
29847357 AACTGAGAGAGGCAAGGCTTGTG
66 AACCGAGAGAGGCAAGGCTTGTG
* ** * * *
29847380 TCTTCGATCTGCTTCGCTGTTAGGGTAGGAAGACAAGATCTGTTGTCTTCAAACAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*** *
29847445 AACCGAGAGATATAAGGTTTGTG
66 AACCGAGAGAGGCAAGGCTTGTG
* *
29847468 TCTTTGATCTGCTTCGCTATCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
29847533 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGCTTGTG
*
29847556 TCTTCGATCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
* *
29847621 AACCGAGAGAGGTAAGG-TTTTG
66 AACCGAGAGAGGCAAGGCTTGTG
* * * * * ** * ** *
29847643 TTTTCGATCTGCTTCGCTGTTAATGCAGAAAGGCAAGATCTGCTATCTTTGACTAGCTCCACTGC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
* *
29847708 AACCGATG-GAGGCAATGCTT-TA
66 AACCGA-GAGAGGCAAGGCTTGTG
* ** * * * * *
29847730 TTTTTAATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTGCTGTCCTCAACCGGCTC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTC
29847789 CACTGCAACT
Statistics
Matches: 798, Mismatches: 132, Indels: 16
0.84 0.14 0.02
Matches are distributed among these distances:
86 1 0.00
87 122 0.15
88 625 0.78
89 50 0.06
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (88 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
AACCGAGAGAGGCAAGGCTTGTG
Found at i:29846974 original size:44 final size:45
Alignment explanation
Indices: 29846763--29847605 Score: 219
Period size: 44 Copynumber: 19.1 Consensus size: 45
29846753 AGATCTGTAA
* * *
29846763 TCTTAGATCTGCTTCGCTGTCAATGCAGGAAGGCAAAATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * * * * *
29846808 TCTTC-AGTCTGCTCCGCTGTCAGTACATGAAGGCAAGA-CTGGTT
1 TCTTCGA-TCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * * * *
29846852 TCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * * * * * *
29846897 TCTTTGACCAGCTTCACT-ACAA-ACGAGGGAGGCAAGA-CTTG-TG
1 TCTTCGATCTGCTTCGCTGTCAATGC-AGGAAGGCAAGATC-TGCTG
*
29846940 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * ** * * * *
29846985 TCTTCAACCAAC-TCTGCT-ACAA--CCGAGAGAGGCAAGGTTTG-TG
1 TCTTCGATCTGCTTC-GCTGTCAATGCAG-GA-AGGCAAGATCTGCTG
* *
29847028 TCTTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAATATCTGCTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
** * * * * * *
29847073 TCTTTAACCAGC-TCTGCT-ACAA--CCGAGAGAGGCAAGGTTTG-TG
1 TCTTCGATCTGCTTC-GCTGTCAATGCAG-GA-AGGCAAGATCTGCTG
* * *
29847116 TCTTTGATCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * * * * * * * *
29847161 TATTCAACCAGCTCCACT-ACAA--CCGAGAGAGGCAAG-GCTTG-TG
1 TCTTCGATCTGCTTCGCTGTCAATGCAG-GA-AGGCAAGATC-TGCTG
** * *
29847204 TCTTCGATCTGCTTCGCTGTCAGGGTAGGAAGGCAAGATCTGTTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * * * * *
29847249 TTTTCAAATAACT-C-T-GCT-ACAA-CCGAGAGATA--CAAGGTTTG-TG
1 TCTTC-GAT--CTGCTTCGCTGTCAATGC-AG-GA-AGGCAAGATCTGCTG
* * * *
29847292 TCTTTGATCTGCTTCGCTATCAATGCAGGAAGGCAAGATTTGTTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * * * * * * *
29847337 TATTCAACCAGCTCCACT-ACAACTG-A-GAGAGGCAAG-GCTTG-TG
1 TCTTCGATCTGCTTCGCTGTCAA-TGCAGGA-AGGCAAGATC-TGCTG
* ** * * *
29847380 TCTTCGATCTGCTTCGCTGTTAGGGTAGGAAGACAAGATCTGTTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * * * * * * *
29847425 TCTTCAAACAGC-TCTGCT-ACAA-CCGAGAGATA--TAAGGTTTG-TG
1 TCTTCGATCTGCTTC-GCTGTCAATGC-AG-GA-AGGCAAGATCTGCTG
* * *
29847468 TCTTTGATCTGCTTCGCTATCAATGCAGGAAGGCAAGATCTGTTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
* * * * * * *
29847513 TCTTCAACCAGC-TCTGCT-ACAA--CCGAGAGAGGCAAGGTTTG-TG
1 TCTTCGATCTGCTTC-GCTGTCAATGCAG-GA-AGGCAAGATCTGCTG
* *
29847556 TCTTCGATCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
29847601 TCTTC
1 TCTTC
29847606 AACCAGCTCT
Statistics
Matches: 568, Mismatches: 157, Indels: 146
0.65 0.18 0.17
Matches are distributed among these distances:
40 2 0.00
41 1 0.00
42 12 0.02
43 123 0.22
44 250 0.44
45 167 0.29
46 10 0.02
47 1 0.00
48 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (45 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTG
Found at i:29848443 original size:108 final size:108
Alignment explanation
Indices: 29848254--29848449 Score: 286
Period size: 108 Copynumber: 1.8 Consensus size: 108
29848244 GAAAAATGCT
29848254 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTAAGAACAAAGCTCTAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTAAGAACAAAGCTCTAAACAAACAAAT
*
29848319 CAATCAAGACATCAAATTTTGCTGAGATACGAGATGTATAAGA
66 CAATCAAGACAGCAAATTTTGCTGAGATACGAGATGTATAAGA
* * * * * **
29848362 TGAAAAAGATTATCACAATGGATAAGATGGAAA-TTTGTTGAGAGCAAAGCTCTAAATGAACAAA
1 TGAAAAAGATTATCAAAATGGACAAAAT-GAAATTTTGTTAAGAACAAAGCTCTAAACAAACAAA
* *
29848426 TTAATCAAGATAGCAAATTTTGCT
65 TCAATCAAGACAGCAAATTTTGCT
29848450 AGAATACAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 73 0.95
109 4 0.05
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTAAGAACAAAGCTCTAAACAAACAAAT
CAATCAAGACAGCAAATTTTGCTGAGATACGAGATGTATAAGA
Found at i:29848513 original size:45 final size:43
Alignment explanation
Indices: 29848415--29848515 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 43
29848405 GCAAAGCTCT
* * *
29848415 AAATGAACAAATTAATCAAGATAGCAAATTTTGCTAGAATACA
1 AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
* **
29848458 AAATGAGAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACAA
1 AAAT--GAATAAATTAATCAAGATAGCAAATTTTG-CAAAAATAC-A
29848505 AAATGAATAAA
1 AAATGAATAAA
29848516 ATAGAAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.08
45 32 0.67
46 7 0.15
47 5 0.10
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (43 bp):
AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
Found at i:29848821 original size:19 final size:18
Alignment explanation
Indices: 29848786--29848827 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
29848776 TGGCCTCTCA
29848786 TTTTTCTCTTTTCTTTTC
1 TTTTTCTCTTTTCTTTTC
*
29848804 GTTTTTCT-TTTATTTTTTC
1 -TTTTTCTCTTT-TCTTTTC
29848823 TTTTT
1 TTTTT
29848828 GTTTGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTCTCTTTTCTTTTC
Found at i:29864575 original size:32 final size:32
Alignment explanation
Indices: 29864534--29864596 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
29864524 AATTAAACCA
29864534 CATAGTTAAAGAACATTATTTCACAAACTAAT
1 CATAGTTAAAGAACATTATTTCACAAACTAAT
29864566 CATAGTTAAAGAACATTATTTCACAAACTAA
1 CATAGTTAAAGAACATTATTTCACAAACTAA
29864597 CAACTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (32 bp):
CATAGTTAAAGAACATTATTTCACAAACTAAT
Found at i:29866080 original size:2 final size:2
Alignment explanation
Indices: 29866073--29866107 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29866063 TTTAGATAGT
29866073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29866108 TACCTTATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29866900 original size:18 final size:18
Alignment explanation
Indices: 29866866--29866900 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29866856 AAATTAATAA
*
29866866 TTATAATTATAATTTAAT
1 TTATAATTATAAGTTAAT
*
29866884 TTATAATTATTAGTTAA
1 TTATAATTATAAGTTAA
29866901 AATTTTGAAA
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATAATTATAAGTTAAT
Found at i:29867384 original size:19 final size:19
Alignment explanation
Indices: 29867348--29867384 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29867338 GCTCTTACAA
* *
29867348 CTATTTGTTTTTTTTTTGT
1 CTATTTGTTATTTATTTGT
29867367 CTATTTGTTATTTATTTG
1 CTATTTGTTATTTATTTG
29867385 GTGTGGATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.73
Consensus pattern (19 bp):
CTATTTGTTATTTATTTGT
Found at i:29867776 original size:23 final size:23
Alignment explanation
Indices: 29867722--29867778 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
29867712 AAAAACTGAA
* * *
29867722 ATACCAAAAATCGAACAAAACTT
1 ATACTAAAAATCCAACAAAACTC
*
29867745 GTA-TAAAAAATCCAACAAAACTC
1 ATACT-AAAAATCCAACAAAACTC
29867768 ATACTAAAAAT
1 ATACTAAAAAT
29867779 GCTGAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.58, C:0.19, G:0.04, T:0.19
Consensus pattern (23 bp):
ATACTAAAAATCCAACAAAACTC
Found at i:29871347 original size:21 final size:21
Alignment explanation
Indices: 29871302--29871360 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
29871292 TATACAAATG
**
29871302 AATGAACAAAATTTGTACAAAAA
1 AATGAAC-AAATTTGT-GTAAAA
*
29871325 AATGAATAAATTTGTGTAAAA
1 AATGAACAAATTTGTGTAAAA
29871346 AATGAACAAATTTGT
1 AATGAACAAATTTGT
29871361 TAACAAGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.56
22 8 0.25
23 6 0.19
ACGTcount: A:0.54, C:0.05, G:0.12, T:0.29
Consensus pattern (21 bp):
AATGAACAAATTTGTGTAAAA
Found at i:29878600 original size:211 final size:211
Alignment explanation
Indices: 29878236--29878659 Score: 803
Period size: 211 Copynumber: 2.0 Consensus size: 211
29878226 ATAAAAGTCT
* * *
29878236 AAAACTTGGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATGAGTAATGCATACA
1 AAAACTTAGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATAAGTAACGCATACA
* *
29878301 AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTTACGAAAATACA
66 AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTCACAAAAATACA
29878366 TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
131 TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
29878431 GAACAATTTTCTTCTC
196 GAACAATTTTCTTCTC
29878447 AAAACTTAGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATAAGTAACGCATACA
1 AAAACTTAGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATAAGTAACGCATACA
29878512 AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTCACAAAAATACA
66 AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTCACAAAAATACA
29878577 TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
131 TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
29878642 GAACAATTTTCTTCTC
196 GAACAATTTTCTTCTC
29878658 AA
1 AA
29878660 CCTGTGAGTG
Statistics
Matches: 208, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 208 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (211 bp):
AAAACTTAGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATAAGTAACGCATACA
AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTCACAAAAATACA
TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
GAACAATTTTCTTCTC
Found at i:29888333 original size:32 final size:32
Alignment explanation
Indices: 29888263--29888401 Score: 163
Period size: 32 Copynumber: 4.4 Consensus size: 32
29888253 TAATGGCTAC
* *
29888263 AAGCCATAAGT-ACAGTAATATGATTGACACA
1 AAGCCATCAGTAACAGTAATATGATCGACACA
* * * *
29888294 AACCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGACACA
* ** *
29888326 CAGCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGACACA
* *
29888358 AAGCCATCAGTAACGGTAATATGATCAACACA
1 AAGCCATCAGTAACAGTAATATGATCGACACA
29888390 AAGCCATCAGTA
1 AAGCCATCAGTA
29888402 GCATCGTAAC
Statistics
Matches: 91, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
31 9 0.10
32 82 0.90
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGACACA
Found at i:29888599 original size:11 final size:11
Alignment explanation
Indices: 29888583--29888625 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
29888573 AATCAGTCAT
29888583 ACAAATCACAG
1 ACAAATCACAG
*
29888594 ACAAATCAGTCAT
1 ACAAATCA--CAG
*
29888607 ACCAATCACAG
1 ACAAATCACAG
29888618 ACAAATCA
1 ACAAATCA
29888626 ATCATTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:29888600 original size:24 final size:24
Alignment explanation
Indices: 29888573--29888630 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
29888563 CCATGCTCAG
29888573 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
29888597 AATCAGTCATACCAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
29888621 AATCAATCAT
1 AATCAGTCAT
29888631 TTACACTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.26, G:0.07, T:0.19
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:29888721 original size:17 final size:17
Alignment explanation
Indices: 29888699--29888733 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29888689 TATAGGAGTA
29888699 TTTTGGTCATTTAACCC
1 TTTTGGTCATTTAACCC
29888716 TTTTGGTCATTTAACCC
1 TTTTGGTCATTTAACCC
29888733 T
1 T
29888734 ATGGGGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (17 bp):
TTTTGGTCATTTAACCC
Found at i:29888749 original size:43 final size:44
Alignment explanation
Indices: 29888676--29888759 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
29888666 GAGGCATTAC
* * *
29888676 GGTCATTTTACCTTATAGGAGTATTTTGGTCATTTAACCCTTTT
1 GGTCATTTAACCCTATAGGAGTATTATGGTCATTTAACCCTTTT
* *
29888720 GGTCATTTAACCCTAT-GGGGTATTATGGTCATTTTACCCT
1 GGTCATTTAACCCTATAGGAGTATTATGGTCATTTAACCCT
29888760 ACAGGGGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 21 0.60
44 14 0.40
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (44 bp):
GGTCATTTAACCCTATAGGAGTATTATGGTCATTTAACCCTTTT
Found at i:29888766 original size:27 final size:26
Alignment explanation
Indices: 29888722--29888866 Score: 141
Period size: 27 Copynumber: 5.4 Consensus size: 26
29888712 ACCCTTTTGG
* * **
29888722 TCATTTAACCCTATGGGGTATTATGG
1 TCATTTTACCCTACGGGGTATTATAA
* *
29888748 TCATTTTACCCTACAGGGGTATTACAG
1 TCATTTTACCCTAC-GGGGTATTATAA
*
29888775 TCATTTTACCCTACAGGGGTATTACAA
1 TCATTTTACCCTAC-GGGGTATTATAA
29888802 TCATTTTACCCTACGAGGGTATT-TCAA
1 TCATTTTACCCTACG-GGGTATTAT-AA
* *
29888829 TCATTTTACCC-ATCGAGGGTATTTTGA
1 TCATTTTACCCTA-CG-GGGTATTATAA
29888856 TCATTTTACCC
1 TCATTTTACCC
29888867 ATCGAGGGTA
Statistics
Matches: 107, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
26 14 0.13
27 92 0.86
28 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (26 bp):
TCATTTTACCCTACGGGGTATTATAA
Found at i:29888778 original size:70 final size:69
Alignment explanation
Indices: 29888650--29888786 Score: 159
Period size: 70 Copynumber: 2.0 Consensus size: 69
29888640 AGGGTCAAAA
* * ***
29888650 TGGTCATTTACCCTCAGAGGCATTACGGTCATTTTACCTTATAGGAGTATTTTGGTCATTTAACC
1 TGGTCATTTACCCTCAGAGGCATTACGGTCATTTTACCCTACAGGAGTATTACAGTCATTTAACC
29888715 CTTT
66 CTTT
* * * * *
29888719 TGGTCATTTAACCCT-ATGGGGTATTATGGTCATTTTACCCTACAGGGGTATTACAGTCATTTTA
1 TGGTCATTT-ACCCTCA-GAGGCATTACGGTCATTTTACCCTACAGGAGTATTACAGTCATTTAA
29888783 CCCT
64 CCCT
29888787 ACAGGGGTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
69 10 0.18
70 46 0.82
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (69 bp):
TGGTCATTTACCCTCAGAGGCATTACGGTCATTTTACCCTACAGGAGTATTACAGTCATTTAACC
CTTT
Found at i:29888860 original size:81 final size:81
Alignment explanation
Indices: 29888764--29889160 Score: 485
Period size: 81 Copynumber: 4.9 Consensus size: 81
29888754 TACCCTACAG
* * * *
29888764 GGGTATTACAGTCATTTTACCC-TAC-AGGGGTATTACAATCATTTTACCC-TACGAGGGTATTT
1 GGGTATTTCGGTCATTTTACCCAT-CGA-GGGTATTTCAATAATTTTACCCAT-CGAGGGTATTT
*
29888826 CAATCATTTTACCCATCGA
63 CAATAATTTTACCCATCGA
* * * * ** *
29888845 GGGTATTTTGATCATTTTACCCATCGAGGGTATTTCGATAATTTCACCCATTAAGGGTATTTCAG
1 GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
*
29888910 TTATTTTACCCATCGA
66 TAATTTTACCCATCGA
* * *
29888926 CGGTATTTCGGTAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCAA
1 GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
29888991 TAATTTTACCCATCGA
66 TAATTTTACCCATCGA
* * ** * *
29889007 GGGTATTTCGGTTATTTTACCCATTGAGGGTATTTTGATTATTTTACCCATCGAGGGTATTTCGA
1 GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
29889072 TAATTTTACCCATCGA
66 TAATTTTACCCATCGA
* * * * * *
29889088 GGGTATTACGGTTATTTTACCCATCGAAGGTGTTTCGATAATTTTACCCATCGAGGGTATTTCAG
1 GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
*
29889153 TTATTTTA
66 TAATTTTA
29889161 GAGGCCCATT
Statistics
Matches: 273, Mismatches: 40, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
81 270 0.99
82 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (81 bp):
GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
TAATTTTACCCATCGA
Found at i:29888867 original size:27 final size:27
Alignment explanation
Indices: 29888804--29889150 Score: 457
Period size: 27 Copynumber: 12.9 Consensus size: 27
29888794 TATTACAATC
* *
29888804 ATTTTACCC-TACGAGGGTATTTCAATC
1 ATTTTACCCAT-CGAGGGTATTTCGATA
* *
29888831 ATTTTACCCATCGAGGGTATTTTGATC
1 ATTTTACCCATCGAGGGTATTTCGATA
29888858 ATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* ** *
29888885 ATTTCACCCATTAAGGGTATTTC-AGTT
1 ATTTTACCCATCGAGGGTATTTCGA-TA
* *
29888912 ATTTTACCCATCGACGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGATA
29888939 ATTTTACCCATCGAGGGTATTTC-AGTA
1 ATTTTACCCATCGAGGGTATTTCGA-TA
*
29888966 ATTTTACCCATCGAGGGTATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
29888993 ATTTTACCCATCGAGGGTATTTCGGTT
1 ATTTTACCCATCGAGGGTATTTCGATA
* * *
29889020 ATTTTACCCATTGAGGGTATTTTGATT
1 ATTTTACCCATCGAGGGTATTTCGATA
29889047 ATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* * *
29889074 ATTTTACCCATCGAGGGTATTACGGTT
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
29889101 ATTTTACCCATCGAAGGTGTTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
29889128 ATTTTACCCATCGAGGGTATTTC
1 ATTTTACCCATCGAGGGTATTTC
29889151 AGTTATTTTA
Statistics
Matches: 280, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.00
27 277 0.99
28 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGATA
Found at i:29889158 original size:27 final size:27
Alignment explanation
Indices: 29888764--29889160 Score: 423
Period size: 27 Copynumber: 14.7 Consensus size: 27
29888754 TACCCTACAG
* *
29888764 GGGTATTACAGTCATTTTACCC-TAC-A
1 GGGTATTTCAGTAATTTTACCCAT-CGA
* * *
29888790 GGGGTATTACAATCATTTTACCC-TACGA
1 -GGGTATTTCAGTAATTTTACCCAT-CGA
* *
29888818 GGGTATTTCAATCATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* *
29888845 GGGTATTT-TGATCATTTTACCCATCGA
1 GGGTATTTCAG-TAATTTTACCCATCGA
* **
29888872 GGGTATTTC-GATAATTTCACCCATTAA
1 GGGTATTTCAG-TAATTTTACCCATCGA
*
29888899 GGGTATTTCAGTTATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* *
29888926 CGGTATTTCGGTAATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
29888953 GGGTATTTCAGTAATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
*
29888980 GGGTATTTCAATAATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* * *
29889007 GGGTATTTCGGTTATTTTACCCATTGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* *
29889034 GGGTATTT-TGATTATTTTACCCATCGA
1 GGGTATTTCAG-TAATTTTACCCATCGA
29889061 GGGTATTTC-GATAATTTTACCCATCGA
1 GGGTATTTCAG-TAATTTTACCCATCGA
* * *
29889088 GGGTATTACGGTTATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* *
29889115 AGGTGTTTC-GATAATTTTACCCATCGA
1 GGGTATTTCAG-TAATTTTACCCATCGA
*
29889142 GGGTATTTCAGTTATTTTA
1 GGGTATTTCAGTAATTTTA
29889161 GAGGCCCATT
Statistics
Matches: 326, Mismatches: 34, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
26 2 0.01
27 319 0.98
28 5 0.02
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACCCATCGA
Found at i:29892836 original size:43 final size:43
Alignment explanation
Indices: 29892787--29893109 Score: 423
Period size: 43 Copynumber: 7.5 Consensus size: 43
29892777 CAAATATACT
*
29892787 GACCACGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* *
29892830 GACCACGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTACA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* * *
29892873 AACCACGACCTTTAGCGACGCTTTTCCCACTAACGCCGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* * * *
29892916 GACTATGGCCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
** * *
29892959 GACCACGACCTTTAGCAACACTTTTCTCACAAACGCCGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* * *
29893002 GACTATGACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* ** *
29893045 GACCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
** *
29893088 GAATA-AACCTTTAGCGGCGCTT
1 GACCACGACCTTTAGCGGCGCTT
29893110 CTTGTAAAAA
Statistics
Matches: 244, Mismatches: 36, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
42 16 0.07
43 228 0.93
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (43 bp):
GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
Found at i:29893139 original size:42 final size:42
Alignment explanation
Indices: 29893052--29893142 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
29893042 ATAGACCATG
* * *
29893052 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAATAA
1 ACCTTTAGCGGCGCTTTTATCAAAAACACCGCTAAAAAATAA
* *
29893094 ACCTTTAGCGGCGCTTCTTGT-AAAAACACCGTTAAAAACAT-A
1 ACCTTTAGCGGCGCTT-TTATCAAAAACACCGCTAAAAA-ATAA
29893136 ACCTTTA
1 ACCTTTA
29893143 AAAAAATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 37 0.88
43 5 0.12
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (42 bp):
ACCTTTAGCGGCGCTTTTATCAAAAACACCGCTAAAAAATAA
Found at i:29896786 original size:2 final size:2
Alignment explanation
Indices: 29896779--29896809 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29896769 GCGGCATTCG
29896779 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
29896810 GATACTTGTT
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:29897378 original size:13 final size:13
Alignment explanation
Indices: 29897362--29897386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29897352 ACTAAAATCA
29897362 TAACATAAAGATT
1 TAACATAAAGATT
29897375 TAACATAAAGAT
1 TAACATAAAGAT
29897387 CTAAAACATC
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:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
TAACATAAAGATT
Found at i:29897402 original size:19 final size:19
Alignment explanation
Indices: 29897378--29897437 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
29897368 AAAGATTTAA
29897378 CATAAAGATCTAAAACATC
1 CATAAAGATCTAAAACATC
* *
29897397 CAT-AA-ATC-AAATCATAA
1 CATAAAGATCTAAAACAT-C
29897414 CATAAAGATCTAAAACATC
1 CATAAAGATCTAAAACATC
*
29897433 TATAA
1 CATAA
29897438 TGGATCCACT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 6 0.19
17 6 0.19
18 4 0.12
19 10 0.31
20 6 0.19
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.23
Consensus pattern (19 bp):
CATAAAGATCTAAAACATC
Found at i:29897806 original size:25 final size:25
Alignment explanation
Indices: 29897777--29897824 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
29897767 CGTTTTTCAT
29897777 AAAAACGCCACAAAAAATTATTTTG
1 AAAAACGCCACAAAAAATTATTTTG
*
29897802 AAAAACGCCGCAAAAAATTATTT
1 AAAAACGCCACAAAAAATTATTT
29897825 CATTTGGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.52, C:0.17, G:0.08, T:0.23
Consensus pattern (25 bp):
AAAAACGCCACAAAAAATTATTTTG
Found at i:29897872 original size:24 final size:22
Alignment explanation
Indices: 29897845--29897895 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 22
29897835 AAAAGGACAC
*
29897845 TATTTTG-CTATGCTAAAAATATTT
1 TATTTTGTCTAT--TAAAAAT-TAT
29897869 TATTTTGTCTATTAAAAATTAT
1 TATTTTGTCTATTAAAAATTAT
29897891 TATTT
1 TATTT
29897896 AAGTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 7 0.28
23 7 0.28
24 7 0.28
25 4 0.16
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (22 bp):
TATTTTGTCTATTAAAAATTAT
Found at i:29899087 original size:20 final size:21
Alignment explanation
Indices: 29899062--29899105 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
29899052 ATCCTAAATT
*
29899062 AACCATATATA-TATACCCTA
1 AACCATATATATTAAACCCTA
29899082 AACCATATATATTAAACCCTA
1 AACCATATATATTAAACCCTA
29899103 AAC
1 AAC
29899106 TATTATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
AACCATATATATTAAACCCTA
Found at i:29899493 original size:42 final size:41
Alignment explanation
Indices: 29899413--29899575 Score: 182
Period size: 41 Copynumber: 3.9 Consensus size: 41
29899403 TTAAAGCCCC
* * * **
29899413 GAGCATTAGCGGCTCTTTTCCTAAAACACCGCTAAAGATCT
1 GAGCATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGATCT
*
29899454 GAGCAATAGCGGCGCTTTTTCAAAAATGCCGCTAAAAGATCT
1 GAGCATTAGCGGCGCTTTTTCAAAAATGCCGCT-AAAGATCT
*
29899496 GAGCATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGATCT
1 GAGCATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGATCT
* * ** * *
29899537 AAGCGTTAGCAGTGCTTTTTTTTAAAAATGCCTCTAAAG
1 GAGCATTAGC-G-GCGCTTTTTCAAAAATGCCGCTAAAG
29899576 CCCCGAAAGG
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 43 0.41
42 40 0.38
43 21 0.20
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGATCT
Found at i:29899554 original size:83 final size:84
Alignment explanation
Indices: 29899413--29899574 Score: 193
Period size: 83 Copynumber: 1.9 Consensus size: 84
29899403 TTAAAGCCCC
* * * *
29899413 GAGCATTAGCGGCTCTTTTCCTAAAACACCGCTAAAGATCTGAGCAATAGCGGCGC-TTTTTCAA
1 GAGCATTAGCGGCGCTTTTCCAAAAACACCGCTAAAGATCTAAGCAATAGCAGCGCTTTTTTCAA
29899477 AAATGCCGCTAAAAGATCT
66 AAATGCCGCTAAAAGATCT
** ** * *
29899496 GAGCATTAGCGGCGCTTCTT-CAAAAATGCCGCTAAAGATCTAAGCGTTAGCAGTGCTTTTTTTT
1 GAGCATTAGCGGCGCTT-TTCCAAAAACACCGCTAAAGATCTAAGCAATAGCAGCGC-TTTTTTC
*
29899560 AAAAATGCCTCTAAA
64 AAAAATGCCGCTAAA
29899575 GCCCCGAAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
83 44 0.68
84 2 0.03
85 19 0.29
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (84 bp):
GAGCATTAGCGGCGCTTTTCCAAAAACACCGCTAAAGATCTAAGCAATAGCAGCGCTTTTTTCAA
AAATGCCGCTAAAAGATCT
Found at i:29905469 original size:25 final size:25
Alignment explanation
Indices: 29905435--29905492 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
29905425 GTGTGCCTAG
29905435 CAGGCTTTGTGCTAGTATATATAAT
1 CAGGCTTTGTGCTAGTATATATAAT
* * *
29905460 CAGGCTTTGTTCTGGTGTATATAAT
1 CAGGCTTTGTGCTAGTATATATAAT
*
29905485 TAGGCTTT
1 CAGGCTTT
29905493 ATGCCTATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (25 bp):
CAGGCTTTGTGCTAGTATATATAAT
Found at i:29906655 original size:18 final size:19
Alignment explanation
Indices: 29906619--29906655 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
29906609 TAAGTATTTA
29906619 TATCATAATTAAGTTATGT
1 TATCATAATTAAGTTATGT
29906638 TATCA-AATATAA-TTATGT
1 TATCATAAT-TAAGTTATGT
29906656 GAATTTCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (19 bp):
TATCATAATTAAGTTATGT
Found at i:29914615 original size:18 final size:18
Alignment explanation
Indices: 29914594--29914629 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29914584 TTTATTTTTA
*
29914594 ATCAAATATATATTATAT
1 ATCAAATATATATAATAT
29914612 ATCAAATATATATAATAT
1 ATCAAATATATATAATAT
29914630 GGGTTGGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
ATCAAATATATATAATAT
Found at i:29918514 original size:25 final size:25
Alignment explanation
Indices: 29918479--29918528 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
29918469 CCTAGTAGGA
*
29918479 TTTGTGTCGGTGTATATAATCAAGC
1 TTTGTGCCGGTGTATATAATCAAGC
*
29918504 TTTGTGCCGGTGTATATTATCAAGC
1 TTTGTGCCGGTGTATATAATCAAGC
29918529 CTTGAGCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (25 bp):
TTTGTGCCGGTGTATATAATCAAGC
Found at i:29927006 original size:29 final size:29
Alignment explanation
Indices: 29926959--29927281 Score: 199
Period size: 29 Copynumber: 11.1 Consensus size: 29
29926949 ATGTGCTAAA
* **
29926959 CGATGGTCGTAACTGTCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
29926988 TGATGGTCGAAACCATCCCATTTCATTAAT
1 CGATGGTCGAAACCATCCCTTTTCA-TATT
* ** *
29927018 CGATAGTCGTCACCATCCCTTTTGATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
** ** *
29927047 TTATGGTCGTTACCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
29927076 CGAT-ATCCGAAGCTATCCCTTTTCATAATT
1 CGATGGT-CGAAACCATCCCTTTTCAT-ATT
* * *
29927106 -GATAG-CTAAAGCTATCCCTTTTCATATT
1 CGATGGTCGAAA-CCATCCCTTTTCATATT
** *
29927134 CGATGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
29927163 CGATAG-CCAAAGCTATCCCTTTTCATATT
1 CGATGGTCGAAA-CCATCCCTTTTCATATT
* * **
29927192 CAATGGTTGCCACCATCCC-TTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* *
29927220 CTATGGTC-ATCACCATCCCTTTTCATATT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
* *** * *
29927249 TGATGGTCTTCATCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
29927278 CGAT
1 CGAT
29927282 ACCCGAAGCT
Statistics
Matches: 224, Mismatches: 58, Indels: 24
0.73 0.19 0.08
Matches are distributed among these distances:
28 33 0.15
29 164 0.73
30 27 0.12
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:29927123 original size:58 final size:58
Alignment explanation
Indices: 29927061--29927315 Score: 194
Period size: 58 Copynumber: 4.4 Consensus size: 58
29927051 GGTCGTTACC
* * *
29927061 ATCCCTTTTCATAATCGAT-ATCCG-AAGCTATCCCTTTTCATAATTGATAGCTAAAGCT
1 ATCCCTTTTCATAATCGATGAT-CGTAA-CCATCCCTTTTCATAATCGATAGCCAAAGCT
* * *
29927119 ATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCT
1 ATCCCTTTTCATAATCGATGATCGTAACCATCCCTTTTCATAATCGATAGCCAAAGCT
* * * * ** * * * * * *
29927177 ATCCCTTTTCATATTCAATGGTTGCCACCATCCC-TTTCATATTCTATGGTCATCA-CC
1 ATCCCTTTTCATAATCGATGATCGTAACCATCCCTTTTCATAATCGATAGCCA-AAGCT
* * * * * * * *
29927234 ATCCCTTTTCATATTTGATGGTCTTCATCATCCCTTTTCATAATCGATACCCGAAGCT
1 ATCCCTTTTCATAATCGATGATCGTAACCATCCCTTTTCATAATCGATAGCCAAAGCT
* *
29927292 ATCCCTTTTTATTAGTCGATGATC
1 ATCCCTTTTCA-TAATCGATGATC
29927316 CTCGATACGC
Statistics
Matches: 158, Mismatches: 33, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
57 44 0.28
58 103 0.65
59 11 0.07
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (58 bp):
ATCCCTTTTCATAATCGATGATCGTAACCATCCCTTTTCATAATCGATAGCCAAAGCT
Found at i:29927149 original size:87 final size:87
Alignment explanation
Indices: 29927029--29927246 Score: 280
Period size: 87 Copynumber: 2.5 Consensus size: 87
29927019 GATAGTCGTC
* * * * *
29927029 ACCATCCCTTTTGATATTTTATGGTCGTTACCATCCCTTTTCATAATCGATATCCGAAGCTATCC
1 ACCATCCCTTTTCATATTCTATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCC
*
29927094 CTTTTCATAATT-GATAGCT-AA
66 CTTTTCAT-ATTCAATAGCTGAA
* *
29927115 AGCTATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATC
1 A-CCATCCCTTTTCATATTCTATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATC
* * **
29927180 CCTTTTCATATTCAATGGTTGCC
65 CCTTTTCATATTCAATAGCTGAA
*
29927203 ACCATCCC-TTTCATATTCTATGGTCATCACCATCCCTTTTCATA
1 ACCATCCCTTTTCATATTCTATGGTCGTCACCATCCCTTTTCATA
29927247 TTTGATGGTC
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
86 38 0.33
87 75 0.66
88 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.38
Consensus pattern (87 bp):
ACCATCCCTTTTCATATTCTATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCC
CTTTTCATATTCAATAGCTGAA
Found at i:29928361 original size:12 final size:12
Alignment explanation
Indices: 29928344--29928368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29928334 ATGACACTCC
29928344 AAAAATATTTAT
1 AAAAATATTTAT
29928356 AAAAATATTTAT
1 AAAAATATTTAT
29928368 A
1 A
29928369 GCTCGATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATATTTAT
Found at i:29935243 original size:40 final size:40
Alignment explanation
Indices: 29935199--29935277 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
29935189 TACGTGGCAA
* * *
29935199 CAAAGCGCGCTTACGTAGACGCGCTTTGTTGCCACGTAGG
1 CAAAGCGCGCTGACGTAGACACGCTTTGCTGCCACGTAGG
* * *
29935239 CAAAGCGCGCTGACGTGGATACGTTTTGCTGCCACGTAG
1 CAAAGCGCGCTGACGTAGACACGCTTTGCTGCCACGTAG
29935278 CACGCCCCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (40 bp):
CAAAGCGCGCTGACGTAGACACGCTTTGCTGCCACGTAGG
Found at i:29935488 original size:51 final size:51
Alignment explanation
Indices: 29935421--29935518 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
29935411 AATTATTTTC
29935421 TCAAATTGCTCTCAATTTCCT-TCCAAATTTCTCTAAAATCCATATTTAATT
1 TCAAATTGCTCTCAATTTCCTCT-CAAATTTCTCTAAAATCCATATTTAATT
* * * *
29935472 TCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTAAAATCCATATTT
29935519 TTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.02, T:0.46
Consensus pattern (51 bp):
TCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTAAAATCCATATTTAATT
Found at i:29935560 original size:18 final size:17
Alignment explanation
Indices: 29935525--29935556 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29935515 ATTTTTAATT
29935525 ATTTTTTAAAAATTTTA
1 ATTTTTTAAAAATTTTA
29935542 ATTTTTT-AAAATTTT
1 ATTTTTTAAAAATTTT
29935557 TTAAATCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTTAAAAATTTTA
Found at i:29937798 original size:126 final size:126
Alignment explanation
Indices: 29937573--29937891 Score: 557
Period size: 126 Copynumber: 2.5 Consensus size: 126
29937563 CCCAAACATG
** * *
29937573 CTACTGTAGCAAAAGCGCGTCCACGAAGGCGTGATTTTAGAAATTTTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
*
29937638 TTGAAGCATTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCATTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* *
29937699 CTACTGTAGCAAAAGCGTGTCTACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
*
29937764 TTGAAGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCATTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
*
29937825 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATGAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
29937890 TT
66 TT
29937892 TGATTTTATC
Statistics
Matches: 182, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 182 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:29957324 original size:20 final size:20
Alignment explanation
Indices: 29957295--29957336 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29957285 TACCATTTCT
* *
29957295 AATGAGGTTGGAGGACAAGC
1 AATGAAGTTGGAAGACAAGC
*
29957315 AATGAAGTTGGAAGATAAGC
1 AATGAAGTTGGAAGACAAGC
29957335 AA
1 AA
29957337 CAAAGGGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.33, T:0.17
Consensus pattern (20 bp):
AATGAAGTTGGAAGACAAGC
Found at i:29966277 original size:12 final size:14
Alignment explanation
Indices: 29966250--29966278 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29966240 AAATCAAAGT
29966250 AAACACACAAACAA
1 AAACACACAAACAA
29966264 AAACACACAAA-AA
1 AAACACACAAACAA
29966277 AA
1 AA
29966279 TTAATCCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (14 bp):
AAACACACAAACAA
Found at i:29966748 original size:8 final size:8
Alignment explanation
Indices: 29966732--29966772 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
29966722 ATTAATAATA
29966732 AAAAAAAT
1 AAAAAAAT
*
29966740 AAGAAAAT
1 AAAAAAAT
29966748 AAAAAAAT
1 AAAAAAAT
29966756 AAAAAAACT
1 AAAAAAA-T
*
29966765 AACAAAAT
1 AAAAAAAT
29966773 TTAAAACAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 22 0.76
9 7 0.24
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:29966778 original size:25 final size:25
Alignment explanation
Indices: 29966715--29966778 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
29966705 AACTAAACAC
* *
29966715 AACAAAAATTAATAATAAAAAAAAT
1 AACAAAATTTAAAAATAAAAAAAAT
* ** *
29966740 AAGAAAATAAAAAAATAAAAAAACT
1 AACAAAATTTAAAAATAAAAAAAAT
29966765 AACAAAATTTAAAA
1 AACAAAATTTAAAA
29966779 CAGAAAATAG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.17
Consensus pattern (25 bp):
AACAAAATTTAAAAATAAAAAAAAT
Found at i:29972231 original size:70 final size:72
Alignment explanation
Indices: 29972117--29972267 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
29972107 CGGGAATCAT
* *
29972117 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
29972181 GATATCG
66 GATATCG
***
29972188 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
29972252 GATATCG
66 GATATCG
29972259 CACTTAGCA
1 CACTTAGCA
29972268 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:29972307 original size:103 final size:103
Alignment explanation
Indices: 29972187--29972406 Score: 363
Period size: 104 Copynumber: 2.1 Consensus size: 103
29972177 AATGGATATC
29972187 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
29972251 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACC-GGGAATCA
29972290 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
29972355 GGATCACGCACATAGCACCACCCATAAATCGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGAATCA
*
29972393 GCACATAGCAACCC
1 GCACTTAGCAACCC
29972407 TTTTATATAC
Statistics
Matches: 110, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
103 38 0.35
104 71 0.65
105 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGAATCA
Found at i:29973481 original size:14 final size:15
Alignment explanation
Indices: 29973462--29973490 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29973452 GCCCAAACGT
29973462 CGAAATTTT-CGAAA
1 CGAAATTTTACGAAA
29973476 CGAAATTTTACGAAA
1 CGAAATTTTACGAAA
29973491 ATTTTCCGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (15 bp):
CGAAATTTTACGAAA
Found at i:29979741 original size:70 final size:72
Alignment explanation
Indices: 29979627--29979777 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
29979617 GGGGAATCAT
* *
29979627 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
29979691 GATATCG
66 GATATCG
***
29979698 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
29979762 GATATCG
66 GATATCG
29979769 CACTTAGCA
1 CACTTAGCA
29979778 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:29979881 original size:104 final size:103
Alignment explanation
Indices: 29979697--29979919 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
29979687 AATGGATATC
29979697 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
29979762 GATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
29979800 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
29979865 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
65 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
29979904 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
29979920 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 17 0.15
104 94 0.84
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:29980281 original size:29 final size:29
Alignment explanation
Indices: 29980248--29980311 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29980238 TAATCCACCA
29980248 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
29980277 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
29980307 CCCAA
1 CCCAA
29980312 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:29980285 original size:30 final size:30
Alignment explanation
Indices: 29980255--29980311 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29980245 CCACCCAACT
29980255 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
29980284 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
29980312 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:29984369 original size:27 final size:27
Alignment explanation
Indices: 29984329--29984393 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
29984319 TTAGCCTTCT
* *
29984329 TGGCGTACTTTGAATGGATCACCTATG
1 TGGCATACTCTGAATGGATCACCTATG
* * *
29984356 TGGCATACTCTGAATGGATCGCTTTTG
1 TGGCATACTCTGAATGGATCACCTATG
*
29984383 TTGCATACTCT
1 TGGCATACTCT
29984394 AATTAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (27 bp):
TGGCATACTCTGAATGGATCACCTATG
Found at i:29991973 original size:23 final size:23
Alignment explanation
Indices: 29991925--29991970 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29991915 TAAATTATAT
*
29991925 ATTTTTTTATTTTAACTATTTTA
1 ATTTTTTTATTTTAACTATTTAA
29991948 ATTTTTTTATATTT-A-TATTTAA
1 ATTTTTTTAT-TTTAACTATTTAA
29991970 A
1 A
29991971 ATTAAAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTTTTTATTTTAACTATTTAA
Found at i:29993221 original size:24 final size:24
Alignment explanation
Indices: 29993181--29993244 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
29993171 TTTAAAAAGA
** *
29993181 TAATAATAAATTTAAAT-TTTATAT
1 TAATAATAAATAAAAATAGTTAT-T
29993205 TAATAATAAATAAAAATAGTTATT
1 TAATAATAAATAAAAATAGTTATT
*
29993229 TAAATATTAAATAAAA
1 T-AATAATAAATAAAA
29993245 TAAACTCTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.50
25 17 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TAATAATAAATAAAAATAGTTATT
Found at i:29993378 original size:17 final size:16
Alignment explanation
Indices: 29993356--29993394 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
29993346 TTTTAAAAAA
*
29993356 ATATTTAAGTATTTTAT
1 ATATTTAA-AATTTTAT
29993373 ATATTTTAAAATTTTAT
1 ATA-TTTAAAATTTTAT
29993390 ATATT
1 ATATT
29993395 ATTATTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATATTTAAAATTTTAT
Found at i:29993399 original size:27 final size:27
Alignment explanation
Indices: 29993303--29993399 Score: 69
Period size: 27 Copynumber: 3.6 Consensus size: 27
29993293 TTTATTTTTA
* *
29993303 TTTAA-TATTAATATAAATTTT-AAAT
1 TTTAACTATTATTATATATTTTAAAAT
*
29993328 TTATTACTATTATTATAT-TTTTAAAAAAAT
1 TT-TAACTATTATTATATATTTT---AAAAT
*
29993358 ATTTAAGTATT-TTATATATTTTAAAAT
1 -TTTAACTATTATTATATATTTTAAAAT
29993385 TTTATA-TATTATTAT
1 TTTA-ACTATTATTAT
29993400 TTCTGTTCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
25 2 0.04
26 14 0.25
27 19 0.33
29 6 0.11
30 14 0.25
31 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
TTTAACTATTATTATATATTTTAAAAT
Done.