Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 336 of 410
Found at i:104087621 original size:14 final size:14
Alignment explanation
Indices: 104087602--104087631 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
104087592 CATTTCACAA
104087602 TTTGTTGTTACTAT
1 TTTGTTGTTACTAT
*
104087616 TTTGTTGTTATTAT
1 TTTGTTGTTACTAT
104087630 TT
1 TT
104087632 GAATATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.13, T:0.70
Consensus pattern (14 bp):
TTTGTTGTTACTAT
Found at i:104088444 original size:39 final size:40
Alignment explanation
Indices: 104088401--104088481 Score: 139
Period size: 39 Copynumber: 2.0 Consensus size: 40
104088391 TATTTAATGC
104088401 AATAAAATATTTATTATATTTATTTGTA-T-TTTTTAATAT
1 AATAAAATATTTATTATATTTATTT-TAGTGTTTTTAATAT
104088440 AATAAAATATTTATTATATTTATTTTAGTGTTTTTAATAT
1 AATAAAATATTTATTATATTTATTTTAGTGTTTTTAATAT
104088480 AA
1 AA
104088482 ATACTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
38 2 0.05
39 26 0.65
40 12 0.30
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (40 bp):
AATAAAATATTTATTATATTTATTTTAGTGTTTTTAATAT
Found at i:104088893 original size:21 final size:21
Alignment explanation
Indices: 104088867--104088908 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
104088857 CCCTTTAAAT
104088867 TTTTTTATGTATTAATCATAA
1 TTTTTTATGTATTAATCATAA
104088888 TTTTTTATGTATTAATCATAA
1 TTTTTTATGTATTAATCATAA
104088909 ATCAACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTTTATGTATTAATCATAA
Found at i:104093278 original size:22 final size:23
Alignment explanation
Indices: 104093251--104093295 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
104093241 AGGTATCTAC
104093251 AAATCAAAT-CTCTAAGATTACA
1 AAATCAAATCCTCTAAGATTACA
*
104093273 AAATCATATCCTCTAAGATTACA
1 AAATCAAATCCTCTAAGATTACA
104093296 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (23 bp):
AAATCAAATCCTCTAAGATTACA
Found at i:104093288 original size:23 final size:22
Alignment explanation
Indices: 104093248--104093304 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
104093238 AAAAGGTATC
*
104093248 TACAAATCAAAT-CTCTAAGAT
1 TACAAATCATATCCTCTAAGAT
104093269 TACAAAATCATATCCTCTAAGAT
1 TAC-AAATCATATCCTCTAAGAT
*
104093292 TACATATCATATC
1 TACAAATCATATC
104093305 TAAGATTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 17 0.53
23 12 0.38
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.32
Consensus pattern (22 bp):
TACAAATCATATCCTCTAAGAT
Found at i:104093308 original size:19 final size:20
Alignment explanation
Indices: 104093260--104093317 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 20
104093250 CAAATCAAAT
*
104093260 CTCTAAGATTACAAAATCATA
1 CTCTAAGATTAC-ATATCATA
104093281 TCCTCTAAGATTACATATCATA
1 --CTCTAAGATTACATATCATA
104093303 -TCTAAGATTACATAT
1 CTCTAAGATTACATAT
104093318 ATTTGAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
22 7 0.21
23 12 0.35
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (20 bp):
CTCTAAGATTACATATCATA
Found at i:104095335 original size:30 final size:29
Alignment explanation
Indices: 104095299--104095358 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
104095289 CAAATTTCAG
104095299 GAGCCACAAGGGTCGGA-CACACGGCCATGT
1 GAGCCACAAGGG-C-GACCACACGGCCATGT
* *
104095329 GAGCCACACGGGCTACCACACGGCCATGT
1 GAGCCACAAGGGCGACCACACGGCCATGT
104095358 G
1 G
104095359 CCAAACCGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 15 0.56
30 11 0.41
ACGTcount: A:0.25, C:0.33, G:0.32, T:0.10
Consensus pattern (29 bp):
GAGCCACAAGGGCGACCACACGGCCATGT
Found at i:104096045 original size:26 final size:26
Alignment explanation
Indices: 104096016--104096066 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
104096006 TAAAAAAAAC
104096016 ACAAAAATAAATACCAAAATGGGTTT
1 ACAAAAATAAATACCAAAATGGGTTT
*
104096042 ACAAAAATAAATACTAAAATGGGTT
1 ACAAAAATAAATACCAAAATGGGTT
104096067 ATTTGCTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (26 bp):
ACAAAAATAAATACCAAAATGGGTTT
Found at i:104099834 original size:3 final size:3
Alignment explanation
Indices: 104099826--104099889 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
104099816 TAAATTCCTA
* * *
104099826 TCT TCT TCT TCT TCT TCT TTT TAT TCT TTT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
104099874 TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT T
104099890 TGTTAGGAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:104105948 original size:21 final size:18
Alignment explanation
Indices: 104105922--104105962 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 18
104105912 ATAGAACATA
104105922 AAGAATTATTTAAAATTTATT
1 AAGAATTA--TAAAATTT-TT
104105943 AAGAATTATAAAATTTTT
1 AAGAATTATAAAATTTTT
104105961 AA
1 AA
104105963 AATAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
21 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
AAGAATTATAAAATTTTT
Found at i:104106079 original size:10 final size:9
Alignment explanation
Indices: 104106051--104106107 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
104106041 TAAAAAATAT
*
104106051 TTATAAATA
1 TTATAAAAA
*
104106060 TT-TATAAA
1 TTATAAAAA
104106068 TTATAAATAA
1 TTATAAA-AA
*
104106078 TTATTAAAA
1 TTATAAAAA
*
104106087 TTTTCAAAAA
1 TTAT-AAAAA
104106097 TTATAAAAA
1 TTATAAAAA
104106106 TT
1 TT
104106108 GTATATACTC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
8 6 0.16
9 17 0.45
10 15 0.39
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
TTATAAAAA
Found at i:104106089 original size:27 final size:29
Alignment explanation
Indices: 104106045--104106107 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
104106035 AAAATATAAA
* *
104106045 AAATATTTATAAATA-TTT-ATAAATTAT
1 AAATAATTATAAATATTTTCAAAAATTAT
104106072 AAATAATTATTAAA-ATTTTCAAAAATTAT
1 AAATAATTA-TAAATATTTTCAAAAATTAT
104106101 AAA-AATT
1 AAATAATT
104106108 GTATATACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 9 0.29
28 11 0.35
29 11 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATAATTATAAATATTTTCAAAAATTAT
Found at i:104106518 original size:11 final size:11
Alignment explanation
Indices: 104106504--104106528 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
104106494 TTTTAAATAA
104106504 TTATTAATTTT
1 TTATTAATTTT
104106515 TTATTAATTTT
1 TTATTAATTTT
104106526 TTA
1 TTA
104106529 GATTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTAATTTT
Found at i:104108848 original size:2 final size:2
Alignment explanation
Indices: 104108841--104108869 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
104108831 CACAAATTAT
104108841 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 T
104108870 GGAGCATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104109432 original size:26 final size:26
Alignment explanation
Indices: 104109403--104109510 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
104109393 TGGTACAAAT
*
104109403 TGATAATGGGTTAGGTAAATGGTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
104109429 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104109455 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
104109481 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104109507 TGAT
1 TGAT
104109511 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:104111028 original size:26 final size:26
Alignment explanation
Indices: 104110999--104111051 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
104110989 TTTACAGTTT
104110999 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
104111025 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
104111051 T
1 T
104111052 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:104111478 original size:16 final size:16
Alignment explanation
Indices: 104111457--104111495 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
104111447 TTAGGCCCAA
104111457 TGGGCTTGAGCTGACT
1 TGGGCTTGAGCTGACT
104111473 TGGGCTTGAGCTGACT
1 TGGGCTTGAGCTGACT
104111489 TGGGCTT
1 TGGGCTT
104111496 TGAATGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.10, C:0.18, G:0.38, T:0.33
Consensus pattern (16 bp):
TGGGCTTGAGCTGACT
Found at i:104118226 original size:46 final size:45
Alignment explanation
Indices: 104118164--104118480 Score: 377
Period size: 46 Copynumber: 6.9 Consensus size: 45
104118154 TTATCTTTGA
* * * *
104118164 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCTGT
* * *
104118210 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTATTCATTTTATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCTGT
*** * *
104118256 CACACTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTT-CTGT
*
104118302 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTC-TGT
** * * *
104118347 CACATTGCCATGGTATCTTTCAACCATGGTTTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTC-TGT
* *
104118393 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTAAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCT-GT
104118439 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA-TACATTTC
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACT-CATTTC
104118481 ATTTCAGAGA
Statistics
Matches: 241, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.00
45 41 0.17
46 199 0.83
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (45 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCTGT
Found at i:104118402 original size:137 final size:138
Alignment explanation
Indices: 104118164--104118482 Score: 417
Period size: 137 Copynumber: 2.3 Consensus size: 138
104118154 TTATCTTTGA
* * * * * ** *
104118164 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTGTCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGTCACATTGCCATGGTATCT
** * * **
104118228 TTCAACCATGGTCTTATTCATTTTATGTCACACTGCCATGGTATCTTTCAACCATGGTCTTATTC
65 TTCAACCATGGTCTTACACATTTCATATCACACTGCCATGGTATCTTTCAACCATGGTCTTACAC
**
104118293 ATTTCCCGT
130 ATTTCCAAT
104118302 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCACATTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACATTGCCATGGTATCTT
* ***
104118366 TCAACCATGGTTTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
66 TCAACCATGGTCTTACACATTTCATATCACACTGCCATGGTATCTTTCAACCATGGTCTTACACA
*
104118431 TTTCTAAT
131 TTTCCAAT
*
104118439 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
104118483 TTCAGAGAGC
Statistics
Matches: 157, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
136 4 0.03
137 115 0.73
138 38 0.24
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (138 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACATTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCATATCACACTGCCATGGTATCTTTCAACCATGGTCTTACACA
TTTCCAAT
Found at i:104118482 original size:92 final size:93
Alignment explanation
Indices: 104118169--104118482 Score: 424
Period size: 92 Copynumber: 3.4 Consensus size: 93
104118159 TTTGACATGA
* * * *
104118169 TGCCATAGTGTCTTTCAACTATGGTCTTACT-CATTTTC-TGTCATGTTGCCATGGTGTCTTTCA
1 TGCCATGGTATCTTTCAACCATGGTCTTA-TACA-TTTCATGTCATGTTGCCATGGTATCTTTCA
*
104118232 ACCATGGTCTTATTCATTT-TATGTCACAC
64 ACCATGGTCTTATTCATTTCTATGTCACAT
* **
104118261 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGTCATGTTGCCATGGTATCTTTCAAC
104118326 CATGGTCTTATTC-TTTC-ATGTCACAT
66 CATGGTCTTATTCATTTCTATGTCACAT
* * *
104118352 TGCCATGGTATCTTTCAACCATGGTTTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGTCATGTTGCCATGGTATCTTTCAAC
** * **
104118417 CATGGTCTTACACATTTCTA-ATCATGT
66 CATGGTCTTATTCATTTCTATGTCACAT
104118444 TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCAT
104118483 TTCAGAGAGC
Statistics
Matches: 198, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
91 86 0.43
92 111 0.56
93 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.42
Consensus pattern (93 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTATTCATTTCTATGTCACAT
Found at i:104122015 original size:29 final size:29
Alignment explanation
Indices: 104121954--104122043 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
104121944 CACATACCTG
* *
104121954 TATATGGCCCACTAGG-CCTAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* *
104121982 TATATGACCCATTAGGCCCAAATCATATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* * *
104122011 TATATGGCCCATCAAGCCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
104122040 TATA
1 TATA
104122044 GTCATGCTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
28 14 0.27
29 38 0.73
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:104123048 original size:4 final size:4
Alignment explanation
Indices: 104123039--104123068 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
104123029 TTTATACTAA
*
104123039 AAAT AAAT AAAT AAAT AGAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
104123069 TACACCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:104126374 original size:19 final size:19
Alignment explanation
Indices: 104126350--104126388 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
104126340 CAGTTTTTGT
*
104126350 TTACAATCC-AAATAACAAA
1 TTACAAGCCTAAAT-ACAAA
104126369 TTACAAGCCTAAATACAAA
1 TTACAAGCCTAAATACAAA
104126388 T
1 T
104126389 AAAAAGAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.21, G:0.03, T:0.23
Consensus pattern (19 bp):
TTACAAGCCTAAATACAAA
Found at i:104128029 original size:16 final size:16
Alignment explanation
Indices: 104127997--104128026 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104127987 TTCTCTTGTG
104127997 TTTGTTATGTTTATTA
1 TTTGTTATGTTTATTA
104128013 TTTGTTAT-TTTATT
1 TTTGTTATGTTTATT
104128027 TATGGTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (16 bp):
TTTGTTATGTTTATTA
Found at i:104128029 original size:25 final size:25
Alignment explanation
Indices: 104128001--104128051 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
104127991 CTTGTGTTTG
104128001 TTAT-GTTTA-TTATTTGTTATTTTAT
1 TTATGGTTTATTTA-TT-TTATTTTAT
*
104128026 TTATGGTTTGTTTATTTTATTTTAT
1 TTATGGTTTATTTATTTTATTTTAT
104128051 T
1 T
104128052 CTTGTGCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.61
26 6 0.26
27 3 0.13
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.73
Consensus pattern (25 bp):
TTATGGTTTATTTATTTTATTTTAT
Found at i:104132823 original size:21 final size:21
Alignment explanation
Indices: 104132799--104132867 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
104132789 AGGCTATGAC
*
104132799 CCATATTCGGGAGATGATCGA
1 CCATCTTCGGGAGATGATCGA
104132820 CCATCTTCGGGAGATGATCGA
1 CCATCTTCGGGAGATGATCGA
104132841 CCATCTTCGGGAGATGATCGA
1 CCATCTTCGGGAGATGATCGA
104132862 CCATCT
1 CCATCT
104132868 ACAGACTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (21 bp):
CCATCTTCGGGAGATGATCGA
Found at i:104141447 original size:44 final size:44
Alignment explanation
Indices: 104141350--104141591 Score: 127
Period size: 44 Copynumber: 5.5 Consensus size: 44
104141340 AGCCACCAGC
* * **
104141350 CTTATCT-CTCTGAAATTGCAGCGGAGTAGA-CTGAAGAAAGCAAAT
1 CTTATCTCCT-TGAAGTTACAGCGGAGTAGATC-GAAGCTA-CAAAT
*
104141395 CTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAAT
1 CTTATCTCCTTGAAGTTACAGCGGAGTAGATCGAAGCTACAAAT
* * ** * * * * *
104141439 CTCT-TCTCCCTGAAATTACATTGGAGTAAATTGAAGCCACCAAC
1 CT-TATCTCCTTGAAGTTACAGCGGAGTAGATCGAAGCTACAAAT
** * * * *
104141483 CTTATCTCCTTGAAGTTTTACCGAAATAGATCGAAGTTACAAAT
1 CTTATCTCCTTGAAGTTACAGCGGAGTAGATCGAAGCTACAAAT
* * * ** * *
104141527 CTCT-TCTCCCTAAAATTACATTGGAGCAGATCGAAGCCAC-AAT
1 CT-TATCTCCTTGAAGTTACAGCGGAGTAGATCGAAGCTACAAAT
*
104141570 CCTTAT-TTCTCTGAAGTTACAG
1 -CTTATCTCCT-TGAAGTTACAG
104141592 TAGACAGGAT
Statistics
Matches: 144, Mismatches: 45, Indels: 17
0.70 0.22 0.08
Matches are distributed among these distances:
43 7 0.05
44 102 0.71
45 32 0.22
46 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (44 bp):
CTTATCTCCTTGAAGTTACAGCGGAGTAGATCGAAGCTACAAAT
Found at i:104141587 original size:88 final size:88
Alignment explanation
Indices: 104141395--104141575 Score: 256
Period size: 88 Copynumber: 2.1 Consensus size: 88
104141385 GAAAGCAAAT
** * * * *
104141395 CTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACAT
1 CTTATCTCCTTGAAGTTTTACCGAAATAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTACAT
* *
104141460 TGGAGTAAATTGAAGCCACCAAC
66 TGGAGCAAATCGAAGCCACCAAC
*
104141483 CTTATCTCCTTGAAGTTTTACCGAAATAGATCGAAGTTACAAATCTCTTCTCCCTAAAATTACAT
1 CTTATCTCCTTGAAGTTTTACCGAAATAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTACAT
*
104141548 TGGAGCAGATCGAAGCCA-CAATC
66 TGGAGCAAATCGAAGCCACCAA-C
104141571 CTTAT
1 CTTAT
104141576 TTCTCTGAAG
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 3 0.04
88 79 0.96
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (88 bp):
CTTATCTCCTTGAAGTTTTACCGAAATAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTACAT
TGGAGCAAATCGAAGCCACCAAC
Found at i:104143436 original size:16 final size:17
Alignment explanation
Indices: 104143417--104143460 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
104143407 TTACCTTAAA
104143417 ATTTTTATATA-CATTT
1 ATTTTTATATACCATTT
*
104143433 A-TTTTATCTTACCATTT
1 ATTTTTAT-ATACCATTT
104143450 ATTTTTATATA
1 ATTTTTATATA
104143461 TATCCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 6 0.26
16 3 0.13
17 8 0.35
18 6 0.26
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTATATACCATTT
Found at i:104143667 original size:16 final size:16
Alignment explanation
Indices: 104143635--104143664 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104143625 TTCTCTTGTG
104143635 TTTGTTATGTTTATTA
1 TTTGTTATGTTTATTA
104143651 TTTGTTAT-TTTATT
1 TTTGTTATGTTTATT
104143665 TATGGTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (16 bp):
TTTGTTATGTTTATTA
Found at i:104143667 original size:25 final size:25
Alignment explanation
Indices: 104143639--104143689 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
104143629 CTTGTGTTTG
104143639 TTAT-GTTTA-TTATTTGTTATTTTAT
1 TTATGGTTTATTTA-TT-TTATTTTAT
*
104143664 TTATGGTTTGTTTATTTTATTTTAT
1 TTATGGTTTATTTATTTTATTTTAT
104143689 T
1 T
104143690 CTTGTGCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.61
26 6 0.26
27 3 0.13
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.73
Consensus pattern (25 bp):
TTATGGTTTATTTATTTTATTTTAT
Found at i:104145156 original size:4 final size:4
Alignment explanation
Indices: 104145147--104145173 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
104145137 GATTCATCAT
104145147 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
104145174 TCTAAAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:104146778 original size:22 final size:22
Alignment explanation
Indices: 104146727--104146787 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
104146717 AAAGAGTCGA
* **
104146727 ATTAAATTGTAATTTTTATTAT
1 ATTAAATTATAATTTTTAAAAT
*
104146749 AGTAAAATTATAATTTTTAAAAT
1 A-TTAAATTATAATTTTTAAAAT
*
104146772 ATTAAATTAAAATTTT
1 ATTAAATTATAATTTT
104146788 ATCATTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
ATTAAATTATAATTTTTAAAAT
Found at i:104147749 original size:2 final size:2
Alignment explanation
Indices: 104147742--104147768 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104147732 GAGTTTTCAA
104147742 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
104147769 GTATTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104148839 original size:23 final size:23
Alignment explanation
Indices: 104148796--104148884 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 23
104148786 AACTCTCAAT
104148796 AAAATTATAAAAATA-ATACTTTA
1 AAAATTATAAAAATATA-ACTTTA
*
104148819 AAAATTATAAAAATATAACTTAAAAA
1 AAAATTATAAAAATATAACTT---TA
104148845 AAAATT-TAAAAATATAAACTATT-
1 AAAATTATAAAAATAT-AACT-TTA
*
104148868 AAAATTATAAAATTATA
1 AAAATTATAAAAATATA
104148885 TTATTACTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
23 26 0.46
24 9 0.16
25 9 0.16
26 11 0.20
27 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATTATAAAAATATAACTTTA
Found at i:104159618 original size:14 final size:14
Alignment explanation
Indices: 104159599--104159625 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
104159589 AGATATTGTT
104159599 AATGCTGTCAAGTC
1 AATGCTGTCAAGTC
104159613 AATGCTGTCAAGT
1 AATGCTGTCAAGT
104159626 TTGAAAGCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (14 bp):
AATGCTGTCAAGTC
Found at i:104164131 original size:31 final size:33
Alignment explanation
Indices: 104164093--104164159 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
104164083 TTTAGCTAAA
*
104164093 TGGGCCCACAG-GCCCA-TGTGGT-TTGCTCGTG
1 TGGGCCCAC-GCGCCCAGTGTGGTCTTGCCCGTG
*
104164124 TGGGCCCACGCGCCCAGTTTGGTCTTGCCCGTG
1 TGGGCCCACGCGCCCAGTGTGGTCTTGCCCGTG
104164157 TGG
1 TGG
104164160 ATCACACGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 1 0.03
31 14 0.45
32 5 0.16
33 11 0.35
ACGTcount: A:0.07, C:0.31, G:0.36, T:0.25
Consensus pattern (33 bp):
TGGGCCCACGCGCCCAGTGTGGTCTTGCCCGTG
Found at i:104164328 original size:12 final size:12
Alignment explanation
Indices: 104164311--104164343 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
104164301 CGTGTTGTCG
104164311 CACACGGCCTAC
1 CACACGGCCTAC
*
104164323 CACACGGTCTAC
1 CACACGGCCTAC
104164335 CACACGGCC
1 CACACGGCC
104164344 GTGTGGCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.48, G:0.18, T:0.09
Consensus pattern (12 bp):
CACACGGCCTAC
Found at i:104167302 original size:47 final size:49
Alignment explanation
Indices: 104167184--104167361 Score: 182
Period size: 44 Copynumber: 3.8 Consensus size: 49
104167174 TGTAACCCGC
* * *
104167184 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC----G-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
* *
104167228 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
104167278 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
104167321 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC
104167362 CAAACATCCT
Statistics
Matches: 110, Mismatches: 10, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 33 0.30
45 2 0.02
46 29 0.26
47 29 0.26
48 3 0.03
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:104167348 original size:93 final size:91
Alignment explanation
Indices: 104167191--104167361 Score: 297
Period size: 93 Copynumber: 1.9 Consensus size: 91
104167181 CGCCCATAAG
* *
104167191 CGAACTCGGACTCAACTCAACGAGCTCGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCAAC
1 CGAACTCGGACTCAACTCAACGAGCTCGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
104167256 GAGTTCGGATGCCTAGTTACATCTCA
66 GAGTTCGGATGCCTAGTTACATCTCA
*
104167282 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTC-G-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
104167347 ACGAGTTCGGATGCC
64 ACGAGTTCGGATGCC
104167362 CAAACATCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 26 0.35
92 1 0.01
93 48 0.64
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (91 bp):
CGAACTCGGACTCAACTCAACGAGCTCGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCA
Found at i:104169765 original size:15 final size:15
Alignment explanation
Indices: 104169743--104169819 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
104169733 AAGAAACCGA
104169743 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
104169758 ATAGAGAAATCC-AG
1 ATAAAGAAATCCAAG
*
104169772 A-ATAGAGAATCC-AG
1 ATAAAGA-AATCCAAG
* *
104169786 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
104169802 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
104169817 ATA
1 ATA
104169820 TGATACTATG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.08
14 10 0.20
15 31 0.62
16 5 0.10
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:104169784 original size:14 final size:14
Alignment explanation
Indices: 104169758--104169800 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
104169748 GAAATCCAAG
104169758 ATAGAGAAATCCAGA
1 ATAGAG-AATCCAGA
104169773 ATAGAGAATCCAGA
1 ATAGAGAATCCAGA
*
104169787 ATAAAGAGATCCAG
1 ATAGAGA-ATCCAG
104169801 GATAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
ATAGAGAATCCAGA
Found at i:104172767 original size:46 final size:46
Alignment explanation
Indices: 104172692--104172865 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
104172682 TGTAACCCGC
* *
104172692 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
104172738 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
104172788 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
104172830 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
104172866 ATGTCCAAAC
Statistics
Matches: 107, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 2 0.02
44 2 0.02
45 26 0.24
46 35 0.33
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:104172857 original size:92 final size:93
Alignment explanation
Indices: 104172699--104172868 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 93
104172689 CGCCCATAAG
* * *
104172699 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
104172764 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
104172792 CGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
104172856 ACGAGTTCGGATG
66 ACGAGTTCGGATG
104172869 TCCAAACATC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 47 0.64
93 26 0.36
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:104176291 original size:14 final size:14
Alignment explanation
Indices: 104176272--104176350 Score: 83
Period size: 14 Copynumber: 5.6 Consensus size: 14
104176262 TTATTTATAA
*
104176272 TATTATTTACATTT
1 TATTATATACATTT
104176286 TATTATAT--ATTT
1 TATTATATACATTT
104176298 TGATT-TATACATTT
1 T-ATTATATACATTT
104176312 TATTATATATCATTT
1 TATTATATA-CATTT
*
104176327 TATTATATATATTAT
1 TATTATATACATT-T
104176342 TCATTATAT
1 T-ATTATAT
104176351 TATTTTTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
12 8 0.14
13 6 0.11
14 19 0.34
15 16 0.29
16 7 0.12
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (14 bp):
TATTATATACATTT
Found at i:104176293 original size:19 final size:19
Alignment explanation
Indices: 104176265--104176369 Score: 58
Period size: 19 Copynumber: 5.5 Consensus size: 19
104176255 TTGTGTATTA
*
104176265 TTTATAATATTATTTACAT
1 TTTATTATATTATTTACAT
**
104176284 TTTATTATA-TATTTTGAT
1 TTTATTATATTATTTACAT
* *
104176302 TTATACATTTTATTATATATCAT
1 TT-T--ATTATATTATTTA-CAT
104176325 TTTATTATA-TATATT--A-
1 TTTATTATATTAT-TTACAT
* **
104176341 TTCATTATATTATTTTTAT
1 TTTATTATATTATTTACAT
104176360 TTTATTATAT
1 TTTATTATAT
104176370 ATTATATAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
16 10 0.15
17 4 0.06
18 10 0.15
19 21 0.32
20 6 0.09
21 5 0.08
22 5 0.08
23 4 0.06
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTATTATATTATTTACAT
Found at i:104176332 original size:3 final size:3
Alignment explanation
Indices: 104176311--104176399 Score: 62
Period size: 3 Copynumber: 29.3 Consensus size: 3
104176301 TTTATACATT
* *
104176311 TTA TTA TATA TCA TT- TTA TTA -TA TATA TTA TTCA TTA -TA TTA TTT
1 TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TT-A TTA TTA TTA TTA
*
104176356 TTA TT- TTA TTA TATA TTA -TA TAA TTA TTTA TTA TTTA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA T
104176400 GTATAATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
2 10 0.14
3 41 0.59
4 18 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:104176355 original size:29 final size:28
Alignment explanation
Indices: 104176227--104176404 Score: 101
Period size: 26 Copynumber: 6.4 Consensus size: 28
104176217 TGTAAAAAAG
*
104176227 TTATTATATATATTATTTTTATT-TTTAT-
1 TTATTAT-TATATTA-TTTTATTATATATA
* ** * *
104176255 TTGTGTATTAT-TTATAATATTATTTACA
1 TTAT-TATTATATTATTTTATTATATATA
*
104176283 TT-TTATTATA-TATTTTGATT-TATACA
1 TTATTATTATATTATTTT-ATTATATATA
104176309 TT-TTATTATATATCATTTTATTATATATA
1 TTATTATTATAT-T-ATTTTATTATATATA
*
104176338 TTATTCATTATATTATTTTTATTTTAT-TA
1 TTATT-ATTATATTA-TTTTATTATATATA
104176367 TATATTA-TATAATTA-TTTATTAT-T-TA
1 T-TATTATTAT-ATTATTTTATTATATATA
104176393 TTATTATGTATA
1 TTATTAT-TATA
104176405 ATTTTAAAAA
Statistics
Matches: 124, Mismatches: 10, Indels: 34
0.74 0.06 0.20
Matches are distributed among these distances:
25 5 0.04
26 35 0.28
27 21 0.17
28 15 0.12
29 24 0.19
30 17 0.14
31 7 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTATTATTATATTATTTTATTATATATA
Found at i:104176397 original size:7 final size:7
Alignment explanation
Indices: 104176310--104176397 Score: 65
Period size: 7 Copynumber: 12.3 Consensus size: 7
104176300 ATTTATACAT
104176310 TTTATTA
1 TTTATTA
* *
104176317 TATATCA
1 TTTATTA
104176324 TTTTATTA
1 -TTTATTA
*
104176332 TATA-TA
1 TTTATTA
104176338 -TTATTCA
1 TTTATT-A
104176345 TTATATTA
1 TT-TATTA
104176353 TTT-TTA
1 TTTATTA
104176359 TTTTATTA
1 -TTTATTA
*
104176367 TATATTA
1 TTTATTA
*
104176374 TATAATTA
1 T-TTATTA
104176382 TTTATTA
1 TTTATTA
104176389 TTTATTA
1 TTTATTA
104176396 TT
1 TT
104176398 ATGTATAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 2 0.03
6 6 0.10
7 34 0.54
8 17 0.27
9 4 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTATTA
Found at i:104188033 original size:44 final size:44
Alignment explanation
Indices: 104187918--104188062 Score: 202
Period size: 44 Copynumber: 3.3 Consensus size: 44
104187908 TATATCTTCT
* *
104187918 AGAAAGCAGATTTGGTGTCTCTGTATTGACAGGGAGCAGATCGA
1 AGAAAGCAGATCTGGTGTCTCTGTATTGACAGAGAGCAGATCGA
* *
104187962 AG-AAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGA
1 AGAAAGCAGATCTGGTGTCTCTGTATTGACAGAGAGCAGATCGA
* * * *
104188005 AGAAAGCACATCTGGTATCTCTGCATTGACAGAGAGCAGATTGA
1 AGAAAGCAGATCTGGTGTCTCTGTATTGACAGAGAGCAGATCGA
*
104188049 AGATAGCAGATCTG
1 AGAAAGCAGATCTG
104188063 ACATTCGTGT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 41 0.46
44 49 0.54
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (44 bp):
AGAAAGCAGATCTGGTGTCTCTGTATTGACAGAGAGCAGATCGA
Found at i:104188096 original size:45 final size:44
Alignment explanation
Indices: 104188039--104188277 Score: 146
Period size: 45 Copynumber: 5.3 Consensus size: 44
104188029 ATTGACAGAG
* *
104188039 AGCAGATTGAAGATAGCAGATCTGACATTCGTGTATTTACATCGA
1 AGCAGATCGAAGATAGCAGATTTGACATTCGTGTA-TTACATCGA
* * * * *
104188084 AGCAGATCGAAGAT-GACAGATTTGGCGTCTC-TGTATTAGATGGGG
1 AGCAGATCGAAGATAG-CAGATTTGACAT-TCGTGTATTACAT-CGA
* * * * * * *
104188129 AGTAGATCAAAGGTAGCAGATCTGACATTTGTGTGTTTGCATCGA
1 AGCAGATCGAAGATAGCAGATTTGACATTCGTGT-ATTACATCGA
* * * * *
104188174 AGCAGATCGAAGAT-GACAGATTTGGCGTCTC-TGTATCAGA-CGGGG
1 AGCAGATCGAAGATAG-CAGATTTGACAT-TCGTGTATTACATC--GA
* * * *
104188219 AGCAGATCAAAGATAGCAGATTTGACATTCGTGTGGTTAAATTGA
1 AGCAGATCGAAGATAGCAGATTTGACATTCGTGT-ATTACATCGA
104188264 AGCAGATCGAAGAT
1 AGCAGATCGAAGAT
104188278 GACAAATTTG
Statistics
Matches: 140, Mismatches: 40, Indels: 28
0.67 0.19 0.13
Matches are distributed among these distances:
43 1 0.01
44 12 0.09
45 115 0.82
46 12 0.09
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (44 bp):
AGCAGATCGAAGATAGCAGATTTGACATTCGTGTATTACATCGA
Found at i:104188172 original size:90 final size:90
Alignment explanation
Indices: 104187924--104188589 Score: 506
Period size: 90 Copynumber: 7.5 Consensus size: 90
104187914 TTCTAGAAAG
* * * * * *
104187924 CAGATTTGGTGTCTCTGTATT-GACAGGGAGCAGATCGAAGA-AGCAGATTTGGCGTCTC-TGT-
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACAT-TCGTGTG
* *
104187985 ATTGACA--GAGAGCAGATCGAAGA-AA
65 GTT-ACATCGA-AGCAGATCGAAGATGA
* * ** * * * ** *
104188010 GCACATCTGGTATCTCTGCATT-GACAGAGAGCAGATTGAAGATAGCAGATCTGACATTCGTGTA
1 -CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTG
*
104188074 TTTACATCGAAGCAGATCGAAGATGA
65 GTTACATCGAAGCAGATCGAAGATGA
* * * * *
104188100 CAGATTTGGCGTCTCTGTATTAGATGGGGAGTAGATCAAAGGTAGCAGATCTGACATTTGTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTGG
*
104188165 TTGCATCGAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* *
104188190 CAGATTTGGCGTCTCTGTATCAGACGGGGAGCAGATCAAAGATAGCAGATTTGACATTCGTGTGG
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTGG
* *
104188255 TTAAATTGAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * * * *
104188280 CAAATTTGGTGCCTCTGTATTAGACGGGGAGCAAATTAAAGATAGCAGATCTGACATTCGTGTGG
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTGG
* * * *
104188345 TTATATCGAAACAGATCAAAAATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * * * * * *
104188370 TAGATTTGGCATCTCTGTATTAGACGGGGAGTAGATCGAATA-AGCAGATTTGGCATCTC-TGT-
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACAT-TCGTGTG
* * * *
104188432 ATTGACA--GAGAGTAGATCAGAAAAAG-
65 GTT-ACATCGA-AGCAGATC-GAAGATGA
* * * * * * * * *
104188458 CACATCTGGCATTTCTGTATT-GACAGAGAGCAGATCGAAGATAGCAGATTTGACGTCTC-TGT-
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACAT-TCGTGTG
* ** *
104188520 ATTGAC-GGGGAGCAGATCGAAGAT-A
65 GTT-ACATCGAAGCAGATCGAAGATGA
* * * *
104188545 GCAAATTTGGCATCTCTGTATTAGACGGGGTGCAAATCAAAGATA
1 -CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATA
104188590 TCAACATGGC
Statistics
Matches: 474, Mismatches: 88, Indels: 32
0.80 0.15 0.05
Matches are distributed among these distances:
87 59 0.12
88 91 0.19
89 71 0.15
90 253 0.53
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (90 bp):
CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTGG
TTACATCGAAGCAGATCGAAGATGA
Found at i:104188419 original size:44 final size:44
Alignment explanation
Indices: 104188371--104188606 Score: 244
Period size: 44 Copynumber: 5.4 Consensus size: 44
104188361 CAAAAATGAT
* *
104188371 AGATTTGGCATCTCTGTATTAGACGGGGAGTAGATCGAATA-AGC
1 AGATTTGGCATCTCTGTATT-GACGGGGAGCAGATCGAAGATAGC
* * * *
104188415 AGATTTGGCATCTCTGTATTGACAGAGAGTAGATCAGAA-AAAGC
1 AGATTTGGCATCTCTGTATTGACGGGGAGCAGATC-GAAGATAGC
* * * * *
104188459 ACATCTGGCATTTCTGTATTGACAGAGAGCAGATCGAAGATAGC
1 AGATTTGGCATCTCTGTATTGACGGGGAGCAGATCGAAGATAGC
* *
104188503 AGATTTGACGTCTCTGTATTGACGGGGAGCAGATCGAAGATAGC
1 AGATTTGGCATCTCTGTATTGACGGGGAGCAGATCGAAGATAGC
* * * * *
104188547 AAATTTGGCATCTCTGTATTAGACGGGGTGCAAATCAAAGATATC
1 AGATTTGGCATCTCTGTATT-GACGGGGAGCAGATCGAAGATAGC
**
104188592 A-ACATGGCATCTCTG
1 AGATTTGGCATCTCTG
104188607 AGTTTGTGGA
Statistics
Matches: 165, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
43 17 0.10
44 127 0.77
45 21 0.13
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (44 bp):
AGATTTGGCATCTCTGTATTGACGGGGAGCAGATCGAAGATAGC
Found at i:104189255 original size:51 final size:51
Alignment explanation
Indices: 104189179--104189288 Score: 177
Period size: 51 Copynumber: 2.2 Consensus size: 51
104189169 GAAAACATGG
*
104189179 GCTATAAAAGCTGAATATCTTCACTGTAAT-AGGGACCTATTTTTTTACAGA
1 GCTATAAAAGCTGAATATCTTCACTGTAATAAGGG-CCTATTTTTTTACACA
*
104189230 GCTATAAAAGCTGAATATCTTCACTGTAATAAGGGCCTTTTTTTTTACACA
1 GCTATAAAAGCTGAATATCTTCACTGTAATAAGGGCCTATTTTTTTACACA
*
104189281 GATATAAA
1 GCTATAAA
104189289 GAGATATACA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 51 0.93
52 4 0.07
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (51 bp):
GCTATAAAAGCTGAATATCTTCACTGTAATAAGGGCCTATTTTTTTACACA
Found at i:104190041 original size:25 final size:26
Alignment explanation
Indices: 104189994--104190048 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
104189984 TTTTAGTCCT
*
104189994 TTTTAAATTTTTATATAATTTATTTA
1 TTTTAAATTTATATATAATTTATTTA
104190020 TTTTAAATATTATATAT-A-TTATTTA
1 TTTTAAAT-TTATATATAATTTATTTA
104190045 TTTT
1 TTTT
104190049 TACTCTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.41
26 9 0.33
27 7 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTAAATTTATATATAATTTATTTA
Found at i:104190049 original size:26 final size:27
Alignment explanation
Indices: 104189993--104190050 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
104189983 ATTTTAGTCC
*
104189993 TTTTTAAATTTTTATATAATTTATTTA
1 TTTTTAAATTTATATATAATTTATTTA
104190020 -TTTTAAATATTATATAT-A-TTATTTA
1 TTTTTAAAT-TTATATATAATTTATTTA
104190045 TTTTTA
1 TTTTTA
104190051 CTCTAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 7 0.25
26 14 0.50
27 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTTAAATTTATATATAATTTATTTA
Found at i:104190124 original size:7 final size:7
Alignment explanation
Indices: 104190079--104190251 Score: 63
Period size: 7 Copynumber: 23.4 Consensus size: 7
104190069 TATGTAAAGA
104190079 ATTTATT
1 ATTTATT
104190086 ATATATATT
1 AT-T-TATT
104190095 ATTT-TT
1 ATTTATT
104190101 ATTT-TT
1 ATTTATT
*
104190107 ATTTGTGT
1 ATTTAT-T
104190115 A-TTATTT
1 ATTTA-TT
104190122 ATTATATT
1 ATT-TATT
104190130 ATTTACATT
1 ATTT--ATT
*
104190139 TTATTATAT
1 AT-TTAT-T
*
104190148 ATTT-TG
1 ATTTATT
*
104190154 ATTTATAC
1 ATTTAT-T
104190162 ATTTTATT
1 A-TTTATT
* *
104190170 ATATATC
1 ATTTATT
104190177 ATTTTATT
1 A-TTTATT
*
104190185 ATATA-T
1 ATTTATT
104190191 A-TTATT
1 ATTTATT
104190197 CATTATATT
1 -ATT-TATT
*
104190206 AATT-TT
1 ATTTATT
104190212 ATTTTATT
1 A-TTTATT
*
104190220 ATATATT
1 ATTTATT
*
104190227 ATATAATT
1 AT-TTATT
104190235 ATTTATT
1 ATTTATT
104190242 ATTTATT
1 ATTTATT
104190249 ATT
1 ATT
104190252 ATGTATAATT
Statistics
Matches: 126, Mismatches: 18, Indels: 44
0.67 0.10 0.23
Matches are distributed among these distances:
5 2 0.02
6 22 0.17
7 44 0.35
8 33 0.26
9 23 0.18
10 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (7 bp):
ATTTATT
Found at i:104190143 original size:19 final size:19
Alignment explanation
Indices: 104190119--104190193 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 19
104190109 TTGTGTATTA
104190119 TTTATTATATTATTTACAT
1 TTTATTATATTATTTACAT
**
104190138 TTTATTATA-TATTTTGAT
1 TTTATTATATTATTTACAT
* *
104190156 TTATACATTTTATTATATATCAT
1 TT-T--ATTATATTATTTA-CAT
104190179 TTTATTATATATATT
1 TTTATTATAT-TATT
104190194 ATTCATTATA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
18 9 0.21
19 10 0.24
20 6 0.14
21 8 0.19
22 5 0.12
23 4 0.10
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTATTATATTATTTACAT
Found at i:104190143 original size:26 final size:26
Alignment explanation
Indices: 104190114--104190230 Score: 100
Period size: 26 Copynumber: 4.6 Consensus size: 26
104190104 TTTATTTGTG
*
104190114 TATTATTTATTATATTATTTACATTT
1 TATTATATATTATATTATTTACATTT
* *
104190140 TATTATATATTTTGATT-TATACATTT
1 TATTATATATTAT-ATTATTTACATTT
* * * *
104190166 TATTATATATCATTTTA-TTATA-TA
1 TATTATATATTATATTATTTACATTT
*
104190190 TATTAT-TCATTATATTAATTT-TATTT
1 TATTATAT-ATTATATT-ATTTACATTT
104190216 TATTATATATTATAT
1 TATTATATATTATAT
104190231 AATTATTTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
23 1 0.01
24 13 0.18
25 8 0.11
26 46 0.64
27 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (26 bp):
TATTATATATTATATTATTTACATTT
Found at i:104190211 original size:45 final size:44
Alignment explanation
Indices: 104190117--104190243 Score: 110
Period size: 41 Copynumber: 3.0 Consensus size: 44
104190107 ATTTGTGTAT
* * *
104190117 TATTTATTATATTATT-TACATTTTA-T-TATATATT-TTGATT-
1 TATTAATTTTATTATTAT-CATTTTATTATATATATTATTCATTA
104190157 TA-TACATTTTATTATATATCATTTTATTATATATATTATTCATTA
1 TATTA-ATTTTATTAT-TATCATTTTATTATATATATTATTCATTA
* * *
104190202 TATTAATTTTATT-TTATTA-TATATTATATA-ATTATTTATTA
1 TATTAATTTTATTATTATCATTTTATTATATATATTATTCATTA
104190243 T
1 T
104190244 TTATTATTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
39 1 0.01
40 11 0.15
41 19 0.26
42 12 0.16
43 12 0.16
44 6 0.08
45 10 0.14
46 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (44 bp):
TATTAATTTTATTATTATCATTTTATTATATATATTATTCATTA
Found at i:104190647 original size:18 final size:18
Alignment explanation
Indices: 104190624--104190658 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
104190614 ATCTCATAAA
*
104190624 TTATTTGTTATTTTTATG
1 TTATTTATTATTTTTATG
*
104190642 TTATTTATTGTTTTTAT
1 TTATTTATTATTTTTAT
104190659 ATATTTGCAT
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:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
TTATTTATTATTTTTATG
Found at i:104192150 original size:18 final size:17
Alignment explanation
Indices: 104192127--104192170 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
104192117 CGCCCGTGTA
104192127 ACATGCCCATGTAGGCCC
1 ACATGCCCATGT-GGCCC
**
104192145 ACATGCCTGTGTGGCCC
1 ACATGCCCATGTGGCCC
*
104192162 ACACGCCCA
1 ACATGCCCA
104192171 GTTCAGTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.20, C:0.41, G:0.23, T:0.16
Consensus pattern (17 bp):
ACATGCCCATGTGGCCC
Found at i:104193743 original size:24 final size:25
Alignment explanation
Indices: 104193701--104193750 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
104193691 ATTTATTTTG
104193701 TTTTATTATTTAATAATTTTATATA
1 TTTTATTATTTAATAATTTTATATA
* * *
104193726 TTTT-TTATTTATTGATTTTTTATA
1 TTTTATTATTTAATAATTTTATATA
104193750 T
1 T
104193751 AGTTATCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTTATTATTTAATAATTTTATATA
Found at i:104204162 original size:2 final size:2
Alignment explanation
Indices: 104204155--104204189 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
104204145 ACATAACCGA
104204155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
104204190 ATCAAATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:104207419 original size:20 final size:20
Alignment explanation
Indices: 104207394--104207439 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
104207384 ATTGGGCCTT
104207394 TCCCATATTAACACAGTTGG
1 TCCCATATTAACACAGTTGG
* *
104207414 TCCCATTTTAATACAGTTGG
1 TCCCATATTAACACAGTTGG
104207434 -CCCATA
1 TCCCATA
104207440 ACAAAACAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
TCCCATATTAACACAGTTGG
Found at i:104210274 original size:18 final size:20
Alignment explanation
Indices: 104210232--104210272 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
104210222 TATAATTTTT
* *
104210232 AAATATATATAATACATCAA
1 AAATATATAAAATAAATCAA
104210252 AAATAT-TAAAATAAATCAA
1 AAATATATAAAATAAATCAA
104210271 AA
1 AA
104210273 TAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATATATAAAATAAATCAA
Found at i:104210389 original size:30 final size:30
Alignment explanation
Indices: 104210355--104210414 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
104210345 ACTTAACAAG
104210355 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAATAAAATTAA
* *
104210385 CAAATGCCTTTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAATAAAATTAA
104210415 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAATAAAATTAA
Found at i:104210417 original size:12 final size:12
Alignment explanation
Indices: 104210395--104210423 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
104210385 CAAATGCCTT
104210395 TAAAA-TAATAA
1 TAAAATTAATAA
104210406 TAAAATTAATAA
1 TAAAATTAATAA
104210418 TAAAAT
1 TAAAAT
104210424 AAATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:104212832 original size:23 final size:24
Alignment explanation
Indices: 104212795--104212845 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
104212785 TAGTTGAACC
*
104212795 GATTTTTATAATTTTTAATATTTT
1 GATTTTTATAATTTTTAATAATTT
*
104212819 GATTTTT-TATTTTTTAATAATTT
1 GATTTTTATAATTTTTAATAATTT
104212842 -ATTT
1 GATTT
104212846 GCTATGAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.16
23 14 0.56
24 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
GATTTTTATAATTTTTAATAATTT
Found at i:104213158 original size:26 final size:25
Alignment explanation
Indices: 104213129--104213177 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
104213119 ATTTAAAATA
104213129 TGAAAAATAAAATATTAAATTTTATT
1 TGAAAAATAAAA-ATTAAATTTTATT
* *
104213155 TGAAATATAATAATTAAATTTTA
1 TGAAAAATAAAAATTAAATTTTA
104213178 AATTTTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
TGAAAAATAAAAATTAAATTTTATT
Found at i:104213184 original size:32 final size:33
Alignment explanation
Indices: 104213107--104213184 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 33
104213097 AAAAGTACAT
104213107 TTTTAAATTTTTATTTAAAATATGAAAAATAAAA
1 TTTTAAA-TTTTATTTAAAATATGAAAAATAAAA
* * * *
104213141 TATTAAATTTTATTTGAAATAT-AATAATTAAA
1 TTTTAAATTTTATTTAAAATATGAAAAATAAAA
104213173 TTTTAAATTTTA
1 TTTTAAATTTTA
104213185 AGAGTGCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 19 0.49
33 14 0.36
34 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTTAAATTTTATTTAAAATATGAAAAATAAAA
Found at i:104237015 original size:44 final size:44
Alignment explanation
Indices: 104236845--104237050 Score: 194
Period size: 42 Copynumber: 4.7 Consensus size: 44
104236835 GCTGATAAAA
* *
104236845 TTAGCGGCG-TTTGTTT-GAAAAAAGCGCGGCTAAAGACCAGGACTT
1 TTAGCGGCGCTTT-TTTAG-AAAAA-CGCCGCTAAAGACGAGGACTT
* * * *
104236890 CTAGCAGCGC--TTTTAGAAAAACACCGCTGAAGACGAGGACTT
1 TTAGCGGCGCTTTTTTAGAAAAACGCCGCTAAAGACGAGGACTT
* * *
104236932 TTAACGGCAC--TTTTAGAAAAACGCCGCTGAAGACGAGGACTT
1 TTAGCGGCGCTTTTTTAGAAAAACGCCGCTAAAGACGAGGACTT
*
104236974 TTAGCGGCGCTTTCTTTA-AAAAACGCCGCTAAAGAAC-AGGACCT
1 TTAGCGGCGCTTT-TTTAGAAAAACGCCGCTAAAG-ACGAGGACTT
* *
104237018 TTAGCAGCGCTTGTTTTATAAAAACGCCGCTAA
1 TTAGCGGCGCTT-TTTTAGAAAAACGCCGCTAA
104237051 TTTGCCCAGT
Statistics
Matches: 137, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
42 62 0.45
43 8 0.06
44 39 0.28
45 28 0.20
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (44 bp):
TTAGCGGCGCTTTTTTAGAAAAACGCCGCTAAAGACGAGGACTT
Found at i:104237367 original size:21 final size:21
Alignment explanation
Indices: 104237343--104237387 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
104237333 TTCTGTTCTG
*
104237343 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCGCGCTGCTGC
104237364 CTCCGCCTCCCGCGCTGCTGC
1 CTCCGCCTCCCGCGCTGCTGC
104237385 CTC
1 CTC
104237388 TGCTCTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.58, G:0.20, T:0.22
Consensus pattern (21 bp):
CTCCGCCTCCCGCGCTGCTGC
Found at i:104239291 original size:12 final size:12
Alignment explanation
Indices: 104239274--104239312 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
104239264 CGGGGAGAGA
104239274 GCCGTGGTCGAG
1 GCCGTGGTCGAG
104239286 GCCGTGGTCGAG
1 GCCGTGGTCGAG
104239298 G-CGTGGTCGAG
1 GCCGTGGTCGAG
104239309 GCCG
1 GCCG
104239313 AGGTAGTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.08, C:0.26, G:0.51, T:0.15
Consensus pattern (12 bp):
GCCGTGGTCGAG
Found at i:104239304 original size:11 final size:11
Alignment explanation
Indices: 104239276--104239310 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
104239266 GGGAGAGAGC
104239276 CGTGGTCGAGG
1 CGTGGTCGAGG
104239287 CCGTGGTCGAGG
1 -CGTGGTCGAGG
104239299 CGTGGTCGAGG
1 CGTGGTCGAGG
104239310 C
1 C
104239311 CGAGGTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.09, C:0.23, G:0.51, T:0.17
Consensus pattern (11 bp):
CGTGGTCGAGG
Found at i:104245667 original size:26 final size:26
Alignment explanation
Indices: 104245638--104245690 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
104245628 TTTACAGTTT
104245638 TACCCCTAGGAGATAAATT-ACCAAAA
1 TACCCCTAGG-GATAAATTGACCAAAA
* *
104245664 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCAAAA
104245690 T
1 T
104245691 GCATGCTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCAAAA
Found at i:104268923 original size:33 final size:33
Alignment explanation
Indices: 104268886--104269018 Score: 180
Period size: 33 Copynumber: 4.0 Consensus size: 33
104268876 TTGAACAGAA
*
104268886 TGATGAAGCTGTCCC-GATAGATATTCCAATCAC
1 TGATGAAGCTG-CCCTGATAGATGTTCCAATCAC
* * *
104268919 TGATGAAGCTACCCTAATAGATGTTCCAATCAA
1 TGATGAAGCTGCCCTGATAGATGTTCCAATCAC
* *
104268952 TGATGAAGCTGCCCCTG-TAGATGGTCCAATCAT
1 TGATGAAGCTG-CCCTGATAGATGTTCCAATCAC
104268985 TGATGAAGCTGCCCTGATAGATGTTCCAATCAC
1 TGATGAAGCTGCCCTGATAGATGTTCCAATCAC
104269018 T
1 T
104269019 TATGTTGAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
32 8 0.09
33 75 0.86
34 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (33 bp):
TGATGAAGCTGCCCTGATAGATGTTCCAATCAC
Found at i:104273145 original size:18 final size:18
Alignment explanation
Indices: 104273106--104273203 Score: 146
Period size: 18 Copynumber: 5.5 Consensus size: 18
104273096 AATGATATGT
104273106 AATCTTAGATATGA-TAC
1 AATCTTAGATATGATTAC
* *
104273123 AATCTTAAATATGATTGC
1 AATCTTAGATATGATTAC
104273141 AATCTTAGATATGA-TAC
1 AATCTTAGATATGATTAC
*
104273158 AATCTTAGATATGATTGC
1 AATCTTAGATATGATTAC
104273176 AATCTTAGATATGATATAC
1 AATCTTAGATATGAT-TAC
104273195 AATCTTAGA
1 AATCTTAGA
104273204 AGATATGATT
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
17 29 0.40
18 32 0.44
19 11 0.15
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (18 bp):
AATCTTAGATATGATTAC
Found at i:104273145 original size:35 final size:35
Alignment explanation
Indices: 104273097--104273201 Score: 165
Period size: 35 Copynumber: 2.9 Consensus size: 35
104273087 ATATTCTTCA
*
104273097 ATGATATGTAATCTTAGATATGATACAATCTTAAAT
1 ATGAT-TGCAATCTTAGATATGATACAATCTTAAAT
*
104273133 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAAAT
104273168 ATGATTGCAATCTTAGATATGATATACAATCTTA
1 ATGATTGCAATCTTAGATATG--ATACAATCTTA
104273202 GAAGATATGA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 49 0.75
36 5 0.08
37 11 0.17
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (35 bp):
ATGATTGCAATCTTAGATATGATACAATCTTAAAT
Found at i:104273523 original size:12 final size:11
Alignment explanation
Indices: 104273512--104273541 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
104273502 TTTAATTTAT
104273512 TTTATATATTA
1 TTTATATATTA
104273523 TTTATTATATTA
1 TTTA-TATATTA
104273535 TTTATAT
1 TTTATAT
104273542 TTTCAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATATATTA
Found at i:104273533 original size:21 final size:21
Alignment explanation
Indices: 104273509--104273625 Score: 63
Period size: 21 Copynumber: 5.8 Consensus size: 21
104273499 ATTTTTAATT
104273509 TATTTTATATATTATTTATTA
1 TATTTTATATATTATTTATTA
*
104273530 TATTATT-TATATT-TTCA--A
1 TATT-TTATATATTATTTATTA
*
104273548 AATTTGTA-A-ATTA-TTATTA
1 TATTT-TATATATTATTTATTA
* * *
104273567 TATATTATATTTTAACTTA-TA
1 TATTTTATATATT-ATTTATTA
*
104273588 TATCTTATATATTTATTTATT-
1 TATTTTATATA-TTATTTATTA
* *
104273609 TATATTATACATTATTT
1 TATTTTATATATTATTT
104273626 TAAAAACTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 25
0.67 0.10 0.23
Matches are distributed among these distances:
17 6 0.08
18 8 0.11
19 5 0.07
20 11 0.15
21 35 0.48
22 8 0.11
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (21 bp):
TATTTTATATATTATTTATTA
Found at i:104274006 original size:3 final size:3
Alignment explanation
Indices: 104273998--104274064 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
104273988 TATGTTACTA
104273998 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
104274046 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
104274065 GTCTTGTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:104274251 original size:2 final size:2
Alignment explanation
Indices: 104274244--104274274 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
104274234 TTATATTTCT
104274244 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 T
104274275 TAATTAATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104279567 original size:1 final size:1
Alignment explanation
Indices: 104279561--104279599 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
104279551 CTTCTATTTC
* * *
104279561 AAAAAAAAAAAAAAAAAAAGAAAAAGAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
104279600 TGGAGAGGCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:104280618 original size:44 final size:44
Alignment explanation
Indices: 104280474--104280653 Score: 186
Period size: 44 Copynumber: 4.1 Consensus size: 44
104280464 CAAAGAAACA
* *
104280474 AGATTTGGCATCTCTATGTTTATAGGGAACAGATCGAAGATAGT
1 AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGC
* * * * * * * * **
104280518 AGATCTGACATTCCTGTGCTTACAGTGAAGCAGATTGAAGATTTC
1 AGATTTGGCATCCCTATGTTTATAGGGAA-CAGATCGAAGATAGC
*
104280563 AGCA--TGGCATCCCTATGTTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTATGTTTATAGGGAACAGA-TCGAAGATAGC
*
104280606 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGC
104280650 AGAT
1 AGAT
104280654 CTAACCTTCA
Statistics
Matches: 108, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
42 2 0.02
43 13 0.12
44 78 0.72
45 14 0.13
46 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (44 bp):
AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGC
Found at i:104281233 original size:119 final size:119
Alignment explanation
Indices: 104280645--104281236 Score: 981
Period size: 119 Copynumber: 5.0 Consensus size: 119
104280635 CAGATCGAAG
104280645 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
*
104280710 TTACAAGGAACAAATCGAGGACATAGTAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
***
104280764 ATAGCAGATCTAACCTTCAGATGTTTATACTGCTTC--ATCCAAGATGATTTGGCATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
*
104280827 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACATTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* *
104280881 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTATGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
104280946 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* * * * *
104281000 ATAGTAGATCTAACCTTTAGATGTTTATACTGAAGTAGATCGAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
* *
104281065 TTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACATTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* * *
104281119 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGC
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
* * * *
104281184 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAA
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAA
104281237 CAACTCAAGA
Statistics
Matches: 439, Mismatches: 32, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
117 112 0.26
119 327 0.74
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (119 bp):
ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
Found at i:104281384 original size:83 final size:83
Alignment explanation
Indices: 104281160--104281511 Score: 598
Period size: 83 Copynumber: 4.2 Consensus size: 83
104281150 GAAGCAGATC
104281160 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
104281225 AATGTTCTCAAACA-ACT
66 AATGTTCTCAAACAGACT
*
104281242 CAAGATGGTTTGGCATCCTTGTGCATACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
104281307 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* * *
104281325 GAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACCTTGCAGACATGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
104281390 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* * *
104281408 CAAGATGGTTTAGGCATCCTTGTGCTTACAAGGAACAAGTCGAGGACCTTGCAGATATGATTCTC
1 CAAGATGGTTT-GGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTC
*
104281473 AAATGTTCTCAAATAGACT
65 AAATGTTCTCAAACAGACT
* *
104281492 CAAGATGATTTGACATCCTT
1 CAAGATGGTTTGGCATCCTT
104281512 ACAAATCAAA
Statistics
Matches: 256, Mismatches: 12, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
82 78 0.30
83 100 0.39
84 78 0.30
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (83 bp):
CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
AATGTTCTCAAACAGACT
Found at i:104281981 original size:35 final size:35
Alignment explanation
Indices: 104281904--104282069 Score: 273
Period size: 34 Copynumber: 4.7 Consensus size: 35
104281894 AATGCTATGT
* *
104281904 AATCTTAGATATGATACAATCTTA-AAATGACTGC
1 AATCTTAGATATGATACAATCTTAGATATGATTGC
104281938 AATCTTAGATATGATACAATCTTAGATATGATTGC
1 AATCTTAGATATGATACAATCTTAGATATGATTGC
104281973 AATCTTAGATATGATACAATCTT-GATATGATTGC
1 AATCTTAGATATGATACAATCTTAGATATGATTGC
*
104282007 AATTTTAGATATGATACAATCTTAGATATGATTGC
1 AATCTTAGATATGATACAATCTTAGATATGATTGC
104282042 AATCTTAGATATGATATACAATCTTAGA
1 AATCTTAGATATG--ATACAATCTTAGA
104282070 AGATATGATT
Statistics
Matches: 124, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
34 57 0.46
35 54 0.44
37 13 0.10
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (35 bp):
AATCTTAGATATGATACAATCTTAGATATGATTGC
Found at i:104281988 original size:69 final size:69
Alignment explanation
Indices: 104281904--104282067 Score: 274
Period size: 69 Copynumber: 2.3 Consensus size: 69
104281894 AATGCTATGT
104281904 AATCTTAGATATGATACAATCTTAAAATGACTGCAATCTTAGATATGATACAATCTTAGATATGA
1 AATCTTAGATATGATACAATCTTAAAATGACTGCAATCTTAGATATGATACAATCTTAGATATGA
104281969 TTGC
66 TTGC
* * * *
104281973 AATCTTAGATATGATACAATCTTGATATGATTGCAATTTTAGATATGATACAATCTTAGATATGA
1 AATCTTAGATATGATACAATCTTAAAATGACTGCAATCTTAGATATGATACAATCTTAGATATGA
104282038 TTGC
66 TTGC
104282042 AATCTTAGATATGATATACAATCTTA
1 AATCTTAGATATG--ATACAATCTTA
104282068 GAAGATATGA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
69 78 0.89
71 10 0.11
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (69 bp):
AATCTTAGATATGATACAATCTTAAAATGACTGCAATCTTAGATATGATACAATCTTAGATATGA
TTGC
Found at i:104282389 original size:12 final size:11
Alignment explanation
Indices: 104282378--104282407 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
104282368 TTTAATTTAT
104282378 TTTATATATTA
1 TTTATATATTA
104282389 TTTATTATATTA
1 TTTA-TATATTA
104282401 TTTATAT
1 TTTATAT
104282408 TTCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATATATTA
Found at i:104282399 original size:21 final size:21
Alignment explanation
Indices: 104282375--104282490 Score: 54
Period size: 21 Copynumber: 5.8 Consensus size: 21
104282365 ATTTTTAATT
104282375 TATTTTATATATTATTTATTA
1 TATTTTATATATTATTTATTA
*
104282396 TATTATT-TATA-T-TTCA--A
1 TATT-TTATATATTATTTATTA
*
104282413 AATTTGTA-A-ATTA-TTATTA
1 TATTT-TATATATTATTTATTA
* * *
104282432 TATATTATATTTTAACTTA-TA
1 TATTTTATATATT-ATTTATTA
*
104282453 TATCTTATATATTTATTTATT-
1 TATTTTATATA-TTATTTATTA
* *
104282474 TATATTATACATTATTT
1 TATTTTATATATTATTT
104282491 TAAAAACTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 27
0.65 0.10 0.25
Matches are distributed among these distances:
16 2 0.03
17 9 0.13
18 2 0.03
19 8 0.11
20 9 0.13
21 33 0.46
22 8 0.11
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TATTTTATATATTATTTATTA
Found at i:104282867 original size:3 final size:3
Alignment explanation
Indices: 104282859--104282935 Score: 129
Period size: 3 Copynumber: 25.3 Consensus size: 3
104282849 TATGTTACTA
104282859 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
104282907 TAT TAT TAT TAT TAT GT-T TAT ATAT TAT T
1 TAT TAT TAT TAT TAT -TAT TAT -TAT TAT T
104282936 GTATTTGCTT
Statistics
Matches: 71, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.01
3 66 0.93
4 4 0.06
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:104284745 original size:40 final size:40
Alignment explanation
Indices: 104284700--104284867 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
104284690 CGGAATACAA
104284700 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
104284740 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * * *
104284780 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
104284820 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
104284860 CCGGATAT
1 CCGGATAT
104284868 CATTCAATTG
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
39 3 0.03
40 101 0.95
41 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:104292676 original size:40 final size:40
Alignment explanation
Indices: 104292631--104292760 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
104292621 CGGAATACAA
104292631 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
104292671 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * * *
104292711 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
104292751 CCGGATATAA
1 CCGGATATAA
104292761 TTTCCAGCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:104303567 original size:46 final size:46
Alignment explanation
Indices: 104303509--104303730 Score: 225
Period size: 46 Copynumber: 4.7 Consensus size: 46
104303499 ATTCGTGTGT
* * *
104303509 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-GATGA
* *
104303555 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CGAGATGA
* * * *
104303603 GGGCTAGTGTAAGACATGTCTGGGACATGCAACGGCCTCGAGATGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATG-A
* * *
104303650 -AGGCTGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGA
* * *
104303695 TAGTCAATGTAAGACCATGTCTGGGACATGGCATCG
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
104303731 ACTTGAGATA
Statistics
Matches: 146, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
45 1 0.01
46 71 0.49
47 46 0.32
48 27 0.18
49 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.22
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGA
Found at i:104303739 original size:93 final size:94
Alignment explanation
Indices: 104303561--104303780 Score: 227
Period size: 93 Copynumber: 2.4 Consensus size: 94
104303551 ATGAGAGCCA
* * *
104303561 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGG
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGACGAAGGCTAATGTAAGACATGTCTGG
*
104303626 GACATGCAACGGCCTCGAGATGTAAGGCT
66 GACATGCAACGGACTCGAGATGTAAGGCT
* *
104303655 GTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACGAGATGATAGTC-AATGTAAGACCATGTC
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCAT-CGAGACGA-AGGCTAATGTAAGA-CATGTC
* * * *
104303716 TGGGACATGGCATC-GACTTGAGATATGA-GCT
63 TGGGACAT-GCAACGGACTCGAGATGTAAGGCT
* * **
104303747 AGTATAAGACCGTGTCTAAGACATGGCATCGGCA
1 -GTGTAAGACCATGTCTGGGACATGGCATCGGCA
104303781 CCTTACCCTA
Statistics
Matches: 104, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
91 1 0.01
92 25 0.24
93 47 0.45
94 23 0.22
95 8 0.08
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (94 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGACGAAGGCTAATGTAAGACATGTCTGG
GACATGCAACGGACTCGAGATGTAAGGCT
Found at i:104303755 original size:47 final size:47
Alignment explanation
Indices: 104303508--104303779 Score: 226
Period size: 47 Copynumber: 5.8 Consensus size: 47
104303498 CATTCGTGTG
* *
104303508 TGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGC-C-ACATTA
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGA-TA
* * *
104303552 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA
1 T--GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAGA-TA
* * *
104303603 -GGGCTAGTGTAAGA-CATGTCTGGGACAT-GCAACGGCCTCGAGATG
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTCGAGATA
*
104303648 TAAGGCT-GTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATGA
1 TGA-GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCT-CGAGAT-A
* * *
104303695 T-AG-TCAATGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATA
1 TGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATA
* * **
104303741 TGAGCTAGTATAAGACCGTGTCTAAGACATGGCATCGGC
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
104303780 ACCTTACCCT
Statistics
Matches: 185, Mismatches: 25, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
44 2 0.01
45 3 0.02
46 68 0.37
47 81 0.44
48 28 0.15
51 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATA
Found at i:104303770 original size:140 final size:140
Alignment explanation
Indices: 104303515--104303771 Score: 349
Period size: 140 Copynumber: 1.8 Consensus size: 140
104303505 GTGTGAGCTA
* *
104303515 GTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGG
1 GTGTAAGACATGTCTGGGACATGCATCAGCCACATGATGAGAGCCAATGTAAGACCATGTCTGGG
* * * **
104303580 ACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCAACGGCCTCGAG
66 ACATGGCATCGACATTGAGACGAGAGCTAGTATAAGACATGTCTAAGACATGCAACGGCCTCGAG
104303645 ATGTAAGGCT
131 ATGTAAGGCT
* * * *
104303655 GTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGATAGTCAATGTAAGACCATGTCTGG
1 GTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATGATGAGAGCCAATGTAAGACCATGTCTGG
* *
104303719 GACATGGCATCGAC-TTGAGA-TATGAGCTAGTATAAGACCGTGTCTAAGACATG
65 GACATGGCATCGACATTGAGACGA-GAGCTAGTATAAGA-CATGTCTAAGACATG
104303772 GCATCGGCAC
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
138 1 0.01
139 18 0.18
140 81 0.80
141 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (140 bp):
GTGTAAGACATGTCTGGGACATGCATCAGCCACATGATGAGAGCCAATGTAAGACCATGTCTGGG
ACATGGCATCGACATTGAGACGAGAGCTAGTATAAGACATGTCTAAGACATGCAACGGCCTCGAG
ATGTAAGGCT
Found at i:104304837 original size:5 final size:5
Alignment explanation
Indices: 104304829--104304867 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
104304819 CCTCTTATCT
*
104304829 TTTTA TTTTA TTTTA TTTT- TTTTA TTATTA TTTTC TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTT
104304868 GAAAGACATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:104304856 original size:17 final size:18
Alignment explanation
Indices: 104304823--104304862 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
104304813 TTGAATCCTC
104304823 TTATCTTTTTATTTTATT
1 TTATCTTTTTATTTTATT
*
104304841 TTATTTTTTTTATTATTATT
1 TTA-TCTTTTTATT-TTATT
104304861 TT
1 TT
104304863 CTTTTGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 9 0.47
20 7 0.37
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (18 bp):
TTATCTTTTTATTTTATT
Found at i:104304859 original size:20 final size:19
Alignment explanation
Indices: 104304828--104304867 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
104304818 TCCTCTTATC
104304828 TTTTTATTTTATTTTATTT
1 TTTTTATTTTATTTTATTT
*
104304847 TTTTTATTATTATTTTCTTT
1 TTTTTATT-TTATTTTATTT
104304867 T
1 T
104304868 GAAAGACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTATTTTATTTTATTT
Found at i:104305975 original size:21 final size:20
Alignment explanation
Indices: 104305951--104306016 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 20
104305941 TATTTAGGTT
104305951 TTATATATTAAATTATATATA
1 TTATATATTAAATTAT-TATA
104305972 TTATAATGATT--ATTATTATA
1 TTAT-AT-ATTAAATTATTATA
*
104305992 GTTTTATATTAAATTATTATGA
1 -TTATATATTAAATTATTAT-A
104306014 TTA
1 TTA
104306017 CTTAATTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
19 3 0.08
20 6 0.16
21 22 0.59
22 3 0.08
23 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTATATATTAAATTATTATA
Found at i:104308810 original size:14 final size:14
Alignment explanation
Indices: 104308791--104308817 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
104308781 TAAATACTTG
104308791 ATTTGTTCTTAATT
1 ATTTGTTCTTAATT
104308805 ATTTGTTCTTAAT
1 ATTTGTTCTTAAT
104308818 GCTTGAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (14 bp):
ATTTGTTCTTAATT
Found at i:104309853 original size:26 final size:27
Alignment explanation
Indices: 104309824--104309964 Score: 180
Period size: 27 Copynumber: 5.3 Consensus size: 27
104309814 AGCATGGCTG
* *
104309824 CCAGAACAGATA-ATGTGACAGAGTCA
1 CCAGAACAGATATATGTGGCAGAGCCA
104309850 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGA-ACAGATATAT-GTGGCAGAGCCA
104309878 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* *
104309905 CCAGATCAGATATTTGTGGCA-AGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * *
104309931 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
104309958 CCAGAAC
1 CCAGAAC
104309965 GCTTCCTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
26 31 0.29
27 58 0.55
28 17 0.16
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:104309949 original size:53 final size:55
Alignment explanation
Indices: 104309824--104309962 Score: 194
Period size: 53 Copynumber: 2.6 Consensus size: 55
104309814 AGCATGGCTG
* *
104309824 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* *
104309878 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATATTTGTGGCA-AGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
104309931 CCAGATCAGATATTTGTGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGA
104309963 ACGCTTCCTC
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
53 34 0.44
54 25 0.32
55 18 0.23
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (55 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:104311616 original size:26 final size:26
Alignment explanation
Indices: 104311580--104311714 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
104311570 CATGAAATTC
*
104311580 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
104311606 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
104311632 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
104311658 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
104311684 TTATCATG-GACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
104311709 TTATCA
1 TTATCA
104311715 ATTTGTATCA
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
25 22 0.21
26 84 0.79
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:104315620 original size:27 final size:26
Alignment explanation
Indices: 104315583--104315696 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
104315573 AGCATGGCTG
** *
104315583 CCAGAACAGATAATGTGATAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
104315609 CCAGATACAGATAATCGTGGCAG-GCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
104315636 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
104315663 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
104315690 CCAGAAC
1 CCAGAAC
104315697 GCTTCCTCCA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.25
27 53 0.69
28 5 0.06
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:104315641 original size:53 final size:54
Alignment explanation
Indices: 104315583--104315696 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
104315573 AGCATGGCTG
* * *
104315583 CCAGAACAGATA-ATGTGATAGAGTCACCAGATACAGATAATCGTGGCA-GGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCATAGCCA
* * *
104315636 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
104315690 CCAGAAC
1 CCAGAAC
104315697 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
53 25 0.47
54 28 0.53
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
Found at i:104317346 original size:26 final size:26
Alignment explanation
Indices: 104317310--104317445 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
104317300 CATGAAATTC
* *
104317310 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
* * *
104317336 TTATCATGAAACATTTACGTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
104317362 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
104317388 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
104317414 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
104317440 TTATCA
1 TTATCA
104317446 ATTTGTATCA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:104320387 original size:21 final size:20
Alignment explanation
Indices: 104320341--104320393 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
104320331 AATTTCTCCC
** *
104320341 TTTTCTTTCTTTCCCTTTTT
1 TTTTCTTTCTTTCCCCCTGT
104320361 TCTTTCTTTCTTTCCCCCCTGT
1 T-TTTCTTTCTTT-CCCCCTGT
104320383 TTTTCGTTTCT
1 TTTTC-TTTCT
104320394 ATTTTGTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 15 0.56
22 11 0.41
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (20 bp):
TTTTCTTTCTTTCCCCCTGT
Found at i:104320638 original size:5 final size:5
Alignment explanation
Indices: 104320610--104320638 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
104320600 TTACTTTATT
104320610 TAAT- TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA
104320639 ATATTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:104323421 original size:13 final size:13
Alignment explanation
Indices: 104323386--104323421 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
104323376 TGCCGTACAG
104323386 TGCAAAAAAATGT
1 TGCAAAAAAATGT
*
104323399 TGTAAAAAAATGT
1 TGCAAAAAAATGT
104323412 TGCAATAAAA
1 TGCAA-AAAA
104323422 CTACTAGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.25
Consensus pattern (13 bp):
TGCAAAAAAATGT
Found at i:104324885 original size:21 final size:20
Alignment explanation
Indices: 104324847--104324885 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
104324837 ACCAAATCAA
* *
104324847 ACCTAAGACCTTATACACAT
1 ACCTAAAACCTTAAACACAT
104324867 ACCTAAAACACTTAAACAC
1 ACCTAAAAC-CTTAAACAC
104324886 TAACGCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.21
Consensus pattern (20 bp):
ACCTAAAACCTTAAACACAT
Found at i:104330440 original size:23 final size:23
Alignment explanation
Indices: 104330407--104330508 Score: 62
Period size: 23 Copynumber: 4.2 Consensus size: 23
104330397 GGATAGCCAT
* *
104330407 ATATCGAGAAGTTCAAGCGAGCC
1 ATATCGAGAAGCTCAAGAGAGCC
* *
104330430 ATATCGGGAAGCTCTAGAGAGCC
1 ATATCGAGAAGCTCAAGAGAGCC
* *
104330453 ATTAATC-AGGAAGCTCATGAAAGAGCTT
1 A-T-ATCGA-GAAGCTCA--AGAGAGC-C
* *
104330481 TTATCGAGAAGCTCACGAAGAGCC
1 ATATCGAGAAGCTCAAG-AGAGCC
104330505 ATAT
1 ATAT
104330509 AACGAGACGC
Statistics
Matches: 58, Mismatches: 13, Indels: 15
0.67 0.15 0.17
Matches are distributed among these distances:
23 20 0.34
24 4 0.07
25 15 0.26
26 11 0.19
27 8 0.14
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.21
Consensus pattern (23 bp):
ATATCGAGAAGCTCAAGAGAGCC
Found at i:104330467 original size:25 final size:24
Alignment explanation
Indices: 104330315--104330468 Score: 86
Period size: 25 Copynumber: 6.3 Consensus size: 24
104330305 CTATATAAAG
*
104330315 GGAAGCTCATA-AGAGCTATAATCA
1 GGAAGCTC-TAGAGAGCCATAATCA
* *
104330339 GGAAGCTC-ATGCGAGCCAATAA-CG
1 GGAAGCTCTA-GAGAGCC-ATAATCA
* * *
104330363 GGTAA-CTCCAAAAAGCCATTAATCA
1 GG-AAGCTCTAGAGAGCCA-TAATCA
* *
104330388 GGAAGCTCTGGATAGCCATATATC-
1 GGAAGCTCTAGAGAGCCATA-ATCA
* * * *
104330412 GAGAAGTTCAAGCGAGCCAT-ATCG
1 G-GAAGCTCTAGAGAGCCATAATCA
104330436 GGAAGCTCTAGAGAGCCATTAATCA
1 GGAAGCTCTAGAGAGCCA-TAATCA
104330461 GGAAGCTC
1 GGAAGCTC
104330469 ATGAAAGAGC
Statistics
Matches: 97, Mismatches: 20, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
22 1 0.01
23 18 0.19
24 32 0.33
25 46 0.47
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (24 bp):
GGAAGCTCTAGAGAGCCATAATCA
Found at i:104333402 original size:14 final size:15
Alignment explanation
Indices: 104333377--104333405 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
104333367 AAATTTGAAC
104333377 TTGATCATAAACTAT
1 TTGATCATAAACTAT
104333392 TTGAT-ATAAACTAT
1 TTGATCATAAACTAT
104333406 ATTGGATGGA
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:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (15 bp):
TTGATCATAAACTAT
Found at i:104338876 original size:143 final size:142
Alignment explanation
Indices: 104338594--104338880 Score: 556
Period size: 143 Copynumber: 2.0 Consensus size: 142
104338584 TTAATCTTCA
*
104338594 ACTTGGTCATCGGTGAGTTTTTCCAACATAACCTCAAAAACAATCTACTTATTGATATACACCGA
1 ACTTGGTCATCGGTGAGTTTTTCCAACATAACCTCAAAAACAATCTACTTATTGATATACACAGA
104338659 AGAAAAAAACAAGAAAAGCTGACCAAATATCCCAAAGATCCCTCTGACTACCCCCATTCCAAACC
66 AGAAAAAAACAAGAAAAGCTGACCAAATATCCCAAAGATCCCTCTGACTACCCCCATTCCAAACC
104338724 CCGTCACCATTC
131 CCGTCACCATTC
104338736 ACTTGGTCATCGGTGAGTTTTTCCAACATAACCTCAAAAACAATCTACTTATTGATATACACAGA
1 ACTTGGTCATCGGTGAGTTTTTCCAACATAACCTCAAAAACAATCTACTTATTGATATACACAGA
104338801 AGAAAAAAAACAAGAAAAGCTGACCAAATATCCCAAAGATCCCTCTGACTACCCCCATTCCAAAC
66 AG-AAAAAAACAAGAAAAGCTGACCAAATATCCCAAAGATCCCTCTGACTACCCCCATTCCAAAC
104338866 CCCGTCACCATTC
130 CCCGTCACCATTC
104338879 AC
1 AC
104338881 CGTTTGATGA
Statistics
Matches: 143, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
142 66 0.46
143 77 0.54
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.22
Consensus pattern (142 bp):
ACTTGGTCATCGGTGAGTTTTTCCAACATAACCTCAAAAACAATCTACTTATTGATATACACAGA
AGAAAAAAACAAGAAAAGCTGACCAAATATCCCAAAGATCCCTCTGACTACCCCCATTCCAAACC
CCGTCACCATTC
Found at i:104339031 original size:19 final size:20
Alignment explanation
Indices: 104338983--104339031 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
104338973 GGTGATTAGA
*
104338983 TGTTTTAACAATATTCTTAAT
1 TGTTTTAAAAATATTCTT-AT
*
104339004 TG-TTT-AAAATATTGTT-T
1 TGTTTTAAAAATATTCTTAT
104339021 TGTTTTAAAAA
1 TGTTTTAAAAA
104339032 AATTAGCGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 13 0.54
20 3 0.12
21 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (20 bp):
TGTTTTAAAAATATTCTTAT
Found at i:104340673 original size:27 final size:26
Alignment explanation
Indices: 104340601--104340657 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
104340591 TCAAACAAGA
*
104340601 CTTTAGTAAAAAATAGTTTAAGTTTT
1 CTTTTGTAAAAAATAGTTTAAGTTTT
104340627 CTTTTGTAAAAAATAGTTTAAGTTTT
1 CTTTTGTAAAAAATAGTTTAAGTTTT
104340653 CTTTT
1 CTTTT
104340658 TTGATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (26 bp):
CTTTTGTAAAAAATAGTTTAAGTTTT
Found at i:104341900 original size:50 final size:50
Alignment explanation
Indices: 104341836--104341937 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
104341826 TTAAAGTGAT
104341836 TTGTAGTGTAATTTATTTTAAATTCTATCTTTTATAAATCTATTAAAGAC
1 TTGTAGTGTAATTTATTTTAAATTCTATCTTTTATAAATCTATTAAAGAC
104341886 TTGTAGTGTAATTTATTTTAAATTCTATCTTTTATAAATCTATTAAAGAC
1 TTGTAGTGTAATTTATTTTAAATTCTATCTTTTATAAATCTATTAAAGAC
104341936 TT
1 TT
104341938 AATTTATGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (50 bp):
TTGTAGTGTAATTTATTTTAAATTCTATCTTTTATAAATCTATTAAAGAC
Done.