Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 25
Found at i:3936344 original size:12 final size:12
Alignment explanation
Indices: 3936325--3936367 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
3936315 ACATCAATTT
3936325 AGTTAGGTGAAG
1 AGTTAGGTGAAG
* *
3936337 AATTAGGTAAAG
1 AGTTAGGTGAAG
3936349 AGTTAGGTG-AG
1 AGTTAGGTGAAG
3936360 AGTTAGGT
1 AGTTAGGT
3936368 ATTTGTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:3940983 original size:12 final size:12
Alignment explanation
Indices: 3940966--3941020 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
3940956 ACATCAATTT
3940966 AGTTAGGTGAAG
1 AGTTAGGTGAAG
3940978 AGTTAGGTGAAG
1 AGTTAGGTGAAG
* * *
3940990 AATTAGGTAAAA
1 AGTTAGGTGAAG
*
3941002 AATTAGGTG-AG
1 AGTTAGGTGAAG
3941013 AGTTAGGT
1 AGTTAGGT
3941021 ATTTGTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
11 8 0.22
12 29 0.78
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.27
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:3978867 original size:18 final size:19
Alignment explanation
Indices: 3978830--3978866 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3978820 TCCACAGTGA
* *
3978830 AAAAAGTATGGACACTTTT
1 AAAAAGGATAGACACTTTT
3978849 AAAAAGGATAGACACTTT
1 AAAAAGGATAGACACTTT
3978867 ACAATATAAC
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:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (19 bp):
AAAAAGGATAGACACTTTT
Found at i:3978895 original size:21 final size:22
Alignment explanation
Indices: 3978870--3978921 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
3978860 ACACTTTACA
*
3978870 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
3978893 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
3978916 ATATAA
1 ATATAA
3978922 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:3978906 original size:23 final size:23
Alignment explanation
Indices: 3978880--3978942 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
3978870 ATATAACCAC
3978880 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
3978903 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
3978926 TACCTATTACATCATAT
1 TACCTATTACATTATAT
3978943 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:3979384 original size:38 final size:38
Alignment explanation
Indices: 3979333--3979413 Score: 128
Period size: 38 Copynumber: 2.1 Consensus size: 38
3979323 CTCAAGTTTA
*
3979333 GATTTTGATTTCC-TTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTT-GCACCATATGAGATTTG
*
3979371 GATTTTGATTTCCTTTTGCTTGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGCACCATATGAGATTTG
3979409 GATTT
1 GATTT
3979414 GATGAGCATC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 33 0.82
39 7 0.17
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (38 bp):
GATTTTGATTTCCTTTTGCTTGCACCATATGAGATTTG
Found at i:3979686 original size:18 final size:18
Alignment explanation
Indices: 3979663--3979699 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3979653 CCGAATATAT
3979663 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
3979681 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
3979699 A
1 A
3979700 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:3979971 original size:25 final size:25
Alignment explanation
Indices: 3979943--3979993 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
3979933 ATTATCCAAA
*
3979943 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
3979968 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
3979993 T
1 T
3979994 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:3980310 original size:23 final size:22
Alignment explanation
Indices: 3980253--3980322 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
3980243 GACACTTACA
*
3980253 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
3980276 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
* *
3980297 ATATAAGGGCTACCTA-TACATC
1 ATATAA-CGCTACCTATTACATT
3980319 ATAT
1 ATAT
3980323 GTTACCTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 17 0.43
22 13 0.32
23 10 0.25
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:3980727 original size:22 final size:22
Alignment explanation
Indices: 3980669--3980737 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
3980659 ACACTTTACA
*
3980669 ATATAACCACTACCTATTACA-T
1 ATATAA-CGCTACCTATTACATT
*
3980691 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
* *
3980712 ATATAAGGCTACCTATTACATC
1 ATATAACGCTACCTATTACATT
3980734 ATAT
1 ATAT
3980738 GTTTACCTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 12 0.30
21 6 0.15
22 22 0.55
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:3983325 original size:196 final size:198
Alignment explanation
Indices: 3982783--3984120 Score: 2313
Period size: 196 Copynumber: 6.9 Consensus size: 198
3982773 TTTAAATTAG
3982783 TATCGACACAAACTATATTAGTGTCGAC-CA-TATTTAGACATATTC-CTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
3982845 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
3982909 CGACACTTTTTATATATGGATCGAC-CTTTATGGGTGCA-CTTGTTTTCCATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAA
3982972 AAAA
195 AAAA
3982976 TATCGACAC-AA--ATATTAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
3983036 ATTGTA-CGGTTAAATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
3983098 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCA-CTTGTTTT-AATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3983161 AAA
196 AAA
3983164 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG-TAT
3983228 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
3983293 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
3983358 AAAA
195 AAAA
*
3983362 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
3983427 ATTGTACCGGTTAGATTG-AAAATTACATATTACATT-TACTTTTGGTTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
3983490 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTC-TTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3983554 AAA
196 AAA
3983557 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
3983622 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3983686 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3983750 AAA
196 AAA
*
3983753 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
3983818 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3983883 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3983947 AAA
196 AAA
*
3983950 TATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATCCTCTC--AAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
3984012 ATTGTA-CGGTTAGATTG-AAAATTACATA-TACATTATACTTTTGGTTTTCGATG-TTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
3984073 TTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
3984121 GGCCATATTG
Statistics
Matches: 1105, Mismatches: 18, Indels: 45
0.95 0.02 0.04
Matches are distributed among these distances:
188 20 0.02
189 81 0.07
190 70 0.06
191 53 0.05
192 93 0.08
193 30 0.03
194 28 0.03
195 171 0.15
196 327 0.30
197 84 0.08
198 98 0.09
199 50 0.05
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:3983737 original size:391 final size:394
Alignment explanation
Indices: 3982783--3984120 Score: 2348
Period size: 391 Copynumber: 3.4 Consensus size: 394
3982773 TTTAAATTAG
3982783 TATCGACACAAACTATATTAGTGTCGAC-CA-TATTTAGACATATTC-CTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
3982845 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
*
3982910 GACACTTTTTATATATGGATCGAC-CTTTATGGGTGCA-CTTGTTTTCCATTCATTCTGGGAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAA
*
3982973 AAATATCGACAC-AA--ATATTAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGT
*
3983033 ATAATTGTA-CGGTTAAATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGG
260 ATAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
3983096 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCA-CTTG-TTTTAATTCATTCTGGAA
325 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAA
3983159 AAAAA
390 AAAAA
3983164 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG-TAT
3983228 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGA
3983293 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
129 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
3983358 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
194 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
*
3983423 TATAATTGTACCGGTTAGATTGAAAATTACATATTACATT-TACTTTTGGTTTCGATGATTTTGG
259 TATAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
3983487 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTC-TTCTGGA
324 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGA
3983551 AAAAAA
389 AAAAAA
3983557 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
3983622 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
3983687 GACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
3983751 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTA
196 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTA
3983816 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
261 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* **
3983881 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-A
325 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAA
3983945 AAAAA
390 AAAAA
*
3983950 TATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATCCTCTC--AAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
3984012 ATTGTA-CGGTTAGATTG-AAAATTACATA-TACATTATACTTTTGGTTTTCGATGTTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTGGGAT
*
3984074 TGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
3984121 GGCCATATTG
Statistics
Matches: 922, Mismatches: 12, Indels: 37
0.95 0.01 0.04
Matches are distributed among these distances:
380 18 0.02
381 11 0.01
382 15 0.02
383 13 0.01
384 60 0.07
385 33 0.04
386 31 0.03
387 36 0.04
388 31 0.03
389 28 0.03
390 52 0.06
391 198 0.21
392 144 0.16
393 186 0.20
394 66 0.07
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (394 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
AAAA
Found at i:3984269 original size:17 final size:17
Alignment explanation
Indices: 3984239--3984283 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
3984229 TTATATTCAC
3984239 ATACAAAA-TAAATCGT
1 ATACAAAATTAAATCGT
*
3984255 ATACAAAATTAAATCTT
1 ATACAAAATTAAATCGT
3984272 ATACAAAATTAA
1 ATACAAAATTAA
3984284 CTCGACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (17 bp):
ATACAAAATTAAATCGT
Found at i:3986090 original size:33 final size:33
Alignment explanation
Indices: 3986044--3986109 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3986034 CCATCTTATA
*
3986044 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
3986077 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
3986110 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:3988429 original size:20 final size:20
Alignment explanation
Indices: 3988404--3988441 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3988394 GGTATCATTT
3988404 TACCGGTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
3988424 TACCGGTTTTATCATTTT
1 TACCGGTTTTATCATTTT
3988442 TACCTGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (20 bp):
TACCGGTTTTATCATTTTGA
Found at i:3989560 original size:2 final size:2
Alignment explanation
Indices: 3989553--3989643 Score: 83
Period size: 2 Copynumber: 45.5 Consensus size: 2
3989543 CAAGAAGACC
* * * * * * *
3989553 AG AG AG AG AA AG GG GG AG AG AG AG AA AG GG GG AG AG AG AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
3989595 AG GG AG AG AC AG AA AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3989637 AG AG AG A
1 AG AG AG A
3989644 ATGTTGGGTG
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.48, C:0.01, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3989571 original size:14 final size:14
Alignment explanation
Indices: 3989553--3989635 Score: 103
Period size: 14 Copynumber: 5.6 Consensus size: 14
3989543 CAAGAAGACC
3989553 AGAGAGAGAAAGGGGG
1 AGAGAGAGAAA--GGG
3989569 AGAGAGAGAAAGGGGG
1 AGAGAGAGAAA--GGG
3989585 AGAGAGAGAAAGGG
1 AGAGAGAGAAAGGG
*
3989599 AGAGACAGAAAGGG
1 AGAGAGAGAAAGGG
* *
3989613 AGAGAGAGAGAGAG
1 AGAGAGAGAAAGGG
3989627 AGAGAGAGA
1 AGAGAGAGA
3989636 GAGAGAGAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
14 36 0.57
16 27 0.43
ACGTcount: A:0.48, C:0.01, G:0.51, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAAAGGG
Found at i:3989643 original size:16 final size:16
Alignment explanation
Indices: 3989553--3989639 Score: 115
Period size: 16 Copynumber: 5.6 Consensus size: 16
3989543 CAAGAAGACC
*
3989553 AGAGAGAGAAAGGGGG
1 AGAGAGAGAAAGGGAG
*
3989569 AGAGAGAGAAAGGGGG
1 AGAGAGAGAAAGGGAG
3989585 AGAGAGAGAAA-GG-G
1 AGAGAGAGAAAGGGAG
*
3989599 AGAGACAGAAAGGGAG
1 AGAGAGAGAAAGGGAG
* *
3989615 AGAGAGAGAGAGAGAG
1 AGAGAGAGAAAGGGAG
3989631 AGAGAGAGA
1 AGAGAGAGA
3989640 GAGAATGTTG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.17
15 4 0.06
16 50 0.77
ACGTcount: A:0.48, C:0.01, G:0.51, T:0.00
Consensus pattern (16 bp):
AGAGAGAGAAAGGGAG
Found at i:3990883 original size:37 final size:37
Alignment explanation
Indices: 3990828--3990935 Score: 198
Period size: 37 Copynumber: 2.9 Consensus size: 37
3990818 AACATAACGT
*
3990828 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
3990865 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
3990902 TAGAATTTTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
3990936 GGATCCATAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
Found at i:3991398 original size:18 final size:18
Alignment explanation
Indices: 3991361--3991404 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3991351 TTATTTTGTT
* **
3991361 TTATCATTTTTTAATTTA
1 TTATTATTTTTTAAAATA
3991379 TTATTATTTTTTAAAATA
1 TTATTATTTTTTAAAATA
3991397 TT-TTATTT
1 TTATTATTT
3991405 ATATGTGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTATTTTTTAAAATA
Found at i:3999195 original size:21 final size:21
Alignment explanation
Indices: 3999153--3999196 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3999143 ACCCCGGGAG
*
3999153 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
3999174 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
3999195 CT
1 CT
3999197 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:3999853 original size:31 final size:31
Alignment explanation
Indices: 3999782--3999861 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
3999772 ATTTAACAAA
* * **
3999782 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
3999813 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
3999844 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
3999862 CAAAATCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:4001226 original size:3 final size:3
Alignment explanation
Indices: 4001213--4001243 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4001203 CTTTACCTAC
*
4001213 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4001244 CTATTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:4001258 original size:9 final size:10
Alignment explanation
Indices: 4001213--4001257 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
4001203 CTTTACCTAC
4001213 TATTT-TTAT
1 TATTTATTAT
4001222 TA-TTATTAT
1 TATTTATTAT
4001231 TA-TTATTAT
1 TATTTATTAT
4001240 TATTCTATT-T
1 TATT-TATTAT
4001250 TATTTATT
1 TATTTATT
4001258 TCTATTTACC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.06
9 21 0.64
10 6 0.18
11 4 0.12
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTTATTAT
Found at i:4001881 original size:5 final size:5
Alignment explanation
Indices: 4001871--4002108 Score: 412
Period size: 5 Copynumber: 47.6 Consensus size: 5
4001861 AATTAATCAA
4001871 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
4001921 ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
4001973 ATAAT ATAAT ATAAT ATAAT A-AAT ATAAT AT-AT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
4002021 ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
4002069 ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
4002109 CCAAACATTC
Statistics
Matches: 225, Mismatches: 0, Indels: 16
0.93 0.00 0.07
Matches are distributed among these distances:
3 2 0.01
4 10 0.04
5 201 0.89
6 4 0.02
7 8 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:4020379 original size:20 final size:20
Alignment explanation
Indices: 4020302--4020391 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
4020292 GAACTCCAAT
**
4020302 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-GAATTTTGAA
*
4020323 TTCGCAACTCG-ATTTCTGAA
1 TTCGCAACACGAATTT-TGAA
* *
4020343 TTCGCAACTCGATTTTTGAA
1 TTCGCAACACGAATTTTGAA
*
4020363 TTCGGAACACGAATTTT-AA
1 TTCGCAACACGAATTTTGAA
4020382 TTTCGCAACA
1 -TTCGCAACA
4020392 GGTTTTATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
19 6 0.10
20 40 0.69
21 12 0.21
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
TTCGCAACACGAATTTTGAA
Found at i:4020566 original size:14 final size:16
Alignment explanation
Indices: 4020547--4020583 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4020537 TTCCCATCTC
4020547 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
4020561 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
4020577 TAATTTT
1 TAATTTT
4020584 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:4021131 original size:379 final size:384
Alignment explanation
Indices: 4020397--4021166 Score: 1390
Period size: 379 Copynumber: 2.0 Consensus size: 384
4020387 CAACAGGTTT
4020397 TATTTTCGCAACACAAATGTTTTGGGTATATAACTACGCAGCAGCAACAACTCATAACCTAAATC
1 TATTTTCGCAACACAAATGTTTTGGGTATATAACTACGCAGCAGCAACAACTCATAACCTAAATC
*
4020462 CCTAAATCGCAACTCATTCCATCTCCATCTATCACTCTCTTCGGCGATATCCGTTTCTATATCCA
66 CCTAAATCGCAACTCATTCCATCTCCATCTATCACTCTCTCCGGCGATATCCGTTTCTATATCCA
4020527 ACAACATCCTTTCCCATCTCTAATTTTTTTTACATAATTTTATTTCTATATAATTTTCAATGATT
131 ACAACATCCTTTCCCATCTCTAATTTTTTTTACATAATTTTATTTCTATATAATTTTCAATGATT
4020592 TCTCTACCAAATTATCAACTATCAACTTAATAAAGGTATGTTTTTCTCTAAATTAGTGATGATAT
196 TCTCTACCAAA-TAT--A-TATCAACTTAATAAAGGTATGTTTTTCTCTAAATTAGTGATGATAT
4020657 GTAGTTTATAGCTCGTTTGTTTAGTAAATTAATTCACAATTTGTAGAATGAAATCATCTAATGTT
257 GTAGTTTATAGCTCGTTTGTTTAGTAAATTAATTCACAATTTGTAGAATGAAATCATCTAATGTT
*
4020722 GATCATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGGGAGAATGTTCATGGTGTTTTACAA
322 GATCATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGAGAGAATGTTCATGGTGTTTTACAA
* *
4020785 TATTTTCGCAACACAAATGTTTTGGGTATATAACTACGCAGTAGCAATAACTCATAACCTAAATC
1 TATTTTCGCAACACAAATGTTTTGGGTATATAACTACGCAGCAGCAACAACTCATAACCTAAATC
4020850 CCTAAATCGCAACTCATTCCATCTCCATCTATCACTCTCTCCGGCGATATCCGTTTCTATATCCA
66 CCTAAATCGCAACTCATTCCATCTCCATCTATCACTCTCTCCGGCGATATCCGTTTCTATATCCA
4020915 ACAACATCC-TTCCCTATCTCT-A-TTTTTTTACATAATTTTATTTCTATATAATTTTCAATGAT
131 ACAACATCCTTTCCC-ATCTCTAATTTTTTTTACATAATTTTATTTCTATATAATTTTCAATGAT
* *
4020977 TTCTCT-CCCAA-AT-TATCAACTTAATAAAGGTATGTTTTTCTCTAAGTTAGTGATGATATGTA
195 TTCTCTACCAAATATATATCAACTTAATAAAGGTATGTTTTTCTCTAAATTAGTGATGATATGTA
*
4021039 GTTTATAGCTCGTTTGTTTAGTAAATTAATTTACAATTTGTAGAATGAAATCATCTAATGTTGAT
260 GTTTATAGCTCGTTTGTTTAGTAAATTAATTCACAATTTGTAGAATGAAATCATCTAATGTTGAT
4021104 CATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGAGAGAATGTTCATGGTGTTTTACAA
325 CATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGAGAGAATGTTCATGGTGTTTTACAA
4021164 TAT
1 TAT
4021167 ATGCCTTTAC
Statistics
Matches: 374, Mismatches: 7, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
379 174 0.47
383 2 0.01
385 4 0.01
386 46 0.12
387 6 0.02
388 142 0.38
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.40
Consensus pattern (384 bp):
TATTTTCGCAACACAAATGTTTTGGGTATATAACTACGCAGCAGCAACAACTCATAACCTAAATC
CCTAAATCGCAACTCATTCCATCTCCATCTATCACTCTCTCCGGCGATATCCGTTTCTATATCCA
ACAACATCCTTTCCCATCTCTAATTTTTTTTACATAATTTTATTTCTATATAATTTTCAATGATT
TCTCTACCAAATATATATCAACTTAATAAAGGTATGTTTTTCTCTAAATTAGTGATGATATGTAG
TTTATAGCTCGTTTGTTTAGTAAATTAATTCACAATTTGTAGAATGAAATCATCTAATGTTGATC
ATGTTTGGATAGATTTGTGTTTTGGAGGGTCATGAGAGAATGTTCATGGTGTTTTACAA
Found at i:4021961 original size:12 final size:12
Alignment explanation
Indices: 4021944--4021968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4021934 ATATAACCCT
4021944 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4021956 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4021968 G
1 G
4021969 TCCCCAAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4021978 original size:15 final size:15
Alignment explanation
Indices: 4021960--4021995 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
4021950 GAAAAAGAAG
4021960 AAGAAAAAGTCCCCA
1 AAGAAAAAGTCCCCA
*
4021975 AAG-AAAAGTCCCCG
1 AAGAAAAAGTCCCCA
4021989 AAGAAAA
1 AAGAAAA
4021996 TGTCACGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.56, C:0.22, G:0.17, T:0.06
Consensus pattern (15 bp):
AAGAAAAAGTCCCCA
Found at i:4022314 original size:12 final size:12
Alignment explanation
Indices: 4022297--4022321 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4022287 ATATAACCCT
4022297 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4022309 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4022321 G
1 G
4022322 TCCCCAAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4022324 original size:353 final size:353
Alignment explanation
Indices: 4021678--4022384 Score: 1288
Period size: 353 Copynumber: 2.0 Consensus size: 353
4021668 GATTATGAGC
4021678 CAACAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTAGTCAATACCCAGACTTT
1 CAACAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTAGTCAATACCCAGACTTT
* * *
4021743 GATCTTGGTCAATACTCGGATTTTGATGATGTTTCAGAAGAAGAAACAGACCATGCGCGTAATGA
66 GATCTTGGTCAATACTCGGATTTTGATGATGTTTCAGAAAAAAAAACAGACCATGCACGTAATGA
*
4021808 TTTTGATATTGGTCAATACCCGAATTTTGATGATGAAACAGCCGCTGCCGATGAAGATGTTGTTG
131 TTTTGATATTGGTCAATACCCGAATTTTGATGATGAAACAGCCGCTGCCGAGGAAGATGTTGTTG
* *
4021873 ATAATAATGAGGAGGAAGTTATGATTGTGAATGAACATGTTGAACATCTATTCTTTAATTCATAT
196 ATAATAATGAGAAGGAAGTTATGACTGTGAATGAACATGTTGAACATCTATTCTTTAATTCATAT
* *
4021938 AACCCTGAAGAAGAAAAAGAAGAAGAAAAAGTCCCCAAAGAAAAGTCCCCGAAGAAAATGTCACG
261 AACCCTGAAGAAGAAAAAGAAGAAGAAAAAGTCCCCAAAGAAAAGTCCCCGAAAAAAATGCCACG
*
4022003 GGAGTATAACTGGAATATGCCATAATTA
326 GGAGTATAACTGGAATATGCCAGAATTA
**
4022031 CAACAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTAGTCAATACCTGGACTTT
1 CAACAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTAGTCAATACCCAGACTTT
*
4022096 GATCTTGGTCAATACTCGGATTTTGATGATGTTTCAGAAAAAAAAACAGACCCTGCACGTAATGA
66 GATCTTGGTCAATACTCGGATTTTGATGATGTTTCAGAAAAAAAAACAGACCATGCACGTAATGA
* *
4022161 TTTTGATATTGGTCAATACCCGAATTTTGATTATGAAATAGCCGCTGCCGAGGAAGATGTTGTTG
131 TTTTGATATTGGTCAATACCCGAATTTTGATGATGAAACAGCCGCTGCCGAGGAAGATGTTGTTG
4022226 ATAATAATGAGAAGGAAGTTATGACTGTGAATGAACATGTTGAACATCTATTCTTTAATTCATAT
196 ATAATAATGAGAAGGAAGTTATGACTGTGAATGAACATGTTGAACATCTATTCTTTAATTCATAT
4022291 AACCCTGAAGAAGAAAAAGAAGAAGAAAAAGTCCCCAAAGAAAAGTCCCCGAAAAAAATGCCACG
261 AACCCTGAAGAAGAAAAAGAAGAAGAAAAAGTCCCCAAAGAAAAGTCCCCGAAAAAAATGCCACG
4022356 GGAGTATAACTGGAATATGCCAGAATTA
326 GGAGTATAACTGGAATATGCCAGAATTA
4022384 C
1 C
4022385 TTCAGATATC
Statistics
Matches: 340, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
353 340 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (353 bp):
CAACAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTAGTCAATACCCAGACTTT
GATCTTGGTCAATACTCGGATTTTGATGATGTTTCAGAAAAAAAAACAGACCATGCACGTAATGA
TTTTGATATTGGTCAATACCCGAATTTTGATGATGAAACAGCCGCTGCCGAGGAAGATGTTGTTG
ATAATAATGAGAAGGAAGTTATGACTGTGAATGAACATGTTGAACATCTATTCTTTAATTCATAT
AACCCTGAAGAAGAAAAAGAAGAAGAAAAAGTCCCCAAAGAAAAGTCCCCGAAAAAAATGCCACG
GGAGTATAACTGGAATATGCCAGAATTA
Found at i:4024163 original size:20 final size:20
Alignment explanation
Indices: 4024111--4024177 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
4024101 GATTCTTTCG
**
4024111 TTGCGATAGTCAAATTCGT-A
1 TTGCGATAGTCATTTTC-TCA
4024131 TTGCGATAGTCATTTTCTCA
1 TTGCGATAGTCATTTTCTCA
* *
4024151 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCTCA
4024171 TTGCGAT
1 TTGCGAT
4024178 TTTGTTGTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.02
20 41 0.98
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCTCA
Found at i:4024189 original size:34 final size:34
Alignment explanation
Indices: 4024146--4024244 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 34
4024136 ATAGTCATTT
* *
4024146 TCTCATTGCGATAGTCATTTTCGCGTTGCGATTT
1 TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTC
* * ** *
4024180 TGTTGTTGCGATTTTCA-TTTCGCATTGCGATTC
1 TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTC
*
4024213 TCTCGTTGCGATAGTTATTTTCGCGTTGCGAT
1 TCTCGTTGCGATAGTCATTTTCGCGTTGCGAT
4024245 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 26 0.51
34 25 0.49
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.45
Consensus pattern (34 bp):
TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTC
Found at i:4024221 original size:33 final size:34
Alignment explanation
Indices: 4024100--4024244 Score: 112
Period size: 34 Copynumber: 4.1 Consensus size: 34
4024090 ATAGCGGACA
* ** *
4024100 CGATTCTTTCGTTGCGATAGTCAAATTCGTATTG
1 CGATTCTCTCGTTGCGATAGTCATTTTCGCATTG
* *
4024134 CGATAGTCATTTTCTCATTGCGATAGTCATTTTCGCGTTG
1 CGAT--TC----TCTCGTTGCGATAGTCATTTTCGCATTG
* * * **
4024174 CGATTTTGTTGTTGCGATTTTCA-TTTCGCATTG
1 CGATTCTCTCGTTGCGATAGTCATTTTCGCATTG
* *
4024207 CGATTCTCTCGTTGCGATAGTTATTTTCGCGTTG
1 CGATTCTCTCGTTGCGATAGTCATTTTCGCATTG
4024241 CGAT
1 CGAT
4024245 AGTCATTTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
33 26 0.31
34 29 0.35
36 2 0.02
38 1 0.01
40 26 0.31
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (34 bp):
CGATTCTCTCGTTGCGATAGTCATTTTCGCATTG
Found at i:4024241 original size:20 final size:20
Alignment explanation
Indices: 4024216--4024267 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
4024206 GCGATTCTCT
*
4024216 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
4024236 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
*
4024256 CATTGCGATAGT
1 CGTTGCGATAGT
4024268 AAACTATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:4026190 original size:20 final size:20
Alignment explanation
Indices: 4026167--4026255 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
4026157 CTGAAACTTT
* *
4026167 AAATCGTAACATGAAAATGA
1 AAATCGCAACACGAAAATGA
*
4026187 AAATCGCAACACGAAAATTA
1 AAATCGCAACACGAAAATGA
** * **
4026207 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
4026227 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
4026246 AAATCGCAAC
1 AAATCGCAAC
4026256 GACAGAATCG
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
19 12 0.21
20 44 0.79
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:4026653 original size:22 final size:22
Alignment explanation
Indices: 4026591--4026656 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
4026581 TGACCGTGAA
*
4026591 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
4026613 TGATATT-GTCGGAGATGGGGAC
1 TGAT-TTCGTCGGAGATGGGGAC
4026635 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
4026657 GGATGTCGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 2 0.05
22 37 0.90
23 2 0.05
ACGTcount: A:0.21, C:0.12, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:4026876 original size:20 final size:20
Alignment explanation
Indices: 4026853--4026905 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
4026843 CGATAGTCAG
*
4026853 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
4026873 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
4026893 ATTCGCATTGCGA
1 ATTCGCATTGCGA
4026906 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:4026926 original size:21 final size:21
Alignment explanation
Indices: 4026902--4026947 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
4026892 TATTCGCATT
4026902 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
4026923 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
4026944 GCGA
1 GCGA
4026948 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:4027249 original size:14 final size:14
Alignment explanation
Indices: 4027230--4027259 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4027220 TGTTTAATAA
4027230 TTGAAAAATATTTT
1 TTGAAAAATATTTT
4027244 TTGAAAAATATTTT
1 TTGAAAAATATTTT
4027258 TT
1 TT
4027260 ATAGTATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (14 bp):
TTGAAAAATATTTT
Found at i:4027323 original size:42 final size:44
Alignment explanation
Indices: 4027239--4027329 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 44
4027229 ATTGAAAAAT
* * ** *
4027239 ATTTTTTGAAAAATATTTTTTATAGTATTTGATATTTGTAATTG
1 ATTTTATGAAAAACATTTTTTATAGTATTTGATAGATATAATTG
*
4027283 GTTTTATGAAAAACA-TTTTT-TAGTATTTGATAGATATAATTG
1 ATTTTATGAAAAACATTTTTTATAGTATTTGATAGATATAATTG
4027325 ATTTT
1 ATTTT
4027330 TCTAATGTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 23 0.57
43 5 0.12
44 12 0.30
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (44 bp):
ATTTTATGAAAAACATTTTTTATAGTATTTGATAGATATAATTG
Found at i:4027463 original size:10 final size:10
Alignment explanation
Indices: 4027445--4027483 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
4027435 CACTCAAAAA
4027445 ATATTATTTT
1 ATATTATTTT
*
4027455 ATTTTATTTT
1 ATATTATTTT
4027465 ATATTATTTT
1 ATATTATTTT
4027475 A-A-TATTTT
1 ATATTATTTT
4027483 A
1 A
4027484 ATATCACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 7 0.26
9 1 0.04
10 19 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATATTATTTT
Found at i:4027664 original size:22 final size:21
Alignment explanation
Indices: 4027637--4027698 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
4027627 TATGTAATAA
4027637 ATTATTAATATAATTAATATT
1 ATTATTAATATAATTAATATT
* *
4027658 ATTTATTATTTTATAAAT-ATATT
1 A-TTATTA--ATATAATTAATATT
*
4027681 ATTATTAA-ATTATTAATA
1 ATTATTAATATAATTAATA
4027699 ATGAGTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 1 0.03
22 12 0.38
23 6 0.19
24 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTAATATAATTAATATT
Found at i:4027694 original size:30 final size:30
Alignment explanation
Indices: 4027638--4027695 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
4027628 ATGTAATAAA
* *
4027638 TTATTAATATAATTAATATTATTTATTATT
1 TTATAAATATAATTAATATTAATTATTATT
*
4027668 TTATAAATAT-ATTATTATTAAATTATTA
1 TTATAAATATAATTAATATT-AATTATTA
4027696 ATAATGAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATAAATATAATTAATATTAATTATTATT
Found at i:4027726 original size:19 final size:19
Alignment explanation
Indices: 4027704--4027749 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
4027694 TAATAATGAG
*
4027704 TAATATTAAT-TTATACATT
1 TAATATTAATATAATA-ATT
4027723 TAATATTAATATAATAATT
1 TAATATTAATATAATAATT
4027742 TAATATTA
1 TAATATTA
4027750 TATTATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATATTAATATAATAATT
Found at i:4027761 original size:35 final size:34
Alignment explanation
Indices: 4027675--4027776 Score: 84
Period size: 35 Copynumber: 2.9 Consensus size: 34
4027665 ATTTTATAAA
*
4027675 TATATTATTATTAAATTATTAATAATGAGTAATATTAATT
1 TATATTA-TATT-AA-TATTAAT-AT-AATAAT-TTAATT
*
4027715 TATA-CAT-TTAATATTAATATAATAATTTAATAT
1 TATATTATATTAATATTAATATAATAATTTAAT-T
*
4027748 TATATTATATTAATA-AAATACTAATAATT
1 TATATTATATTAATATTAATA-TAATAATT
4027777 AAAATTAAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
32 5 0.09
33 10 0.19
34 8 0.15
35 21 0.39
36 2 0.04
37 2 0.04
38 1 0.02
39 1 0.02
40 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (34 bp):
TATATTATATTAATATTAATATAATAATTTAATT
Found at i:4030670 original size:20 final size:20
Alignment explanation
Indices: 4030645--4030733 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 20
4030635 TATTTGCAAC
*
4030645 GCGATTTTTAGATTCGCGTT
1 GCGATTTTTAAATTCGCGTT
* ** *
4030665 GCGATTTTAAAAATTTACCTT
1 GCGATTTT-TAAATTCGCGTT
* **
4030686 GCGATTTTTAAATTTGTATT
1 GCGATTTTTAAATTCGCGTT
* * *
4030706 GTGATTTTTATATTCGTGTT
1 GCGATTTTTAAATTCGCGTT
4030726 GCGATTTT
1 GCGATTTT
4030734 AGAAACTGTG
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (20 bp):
GCGATTTTTAAATTCGCGTT
Found at i:4042991 original size:36 final size:36
Alignment explanation
Indices: 4042877--4042995 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
4042867 TGGTAACAAA
4042877 CTTTGAAAAA-ATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-G-TTTTCAAAGTTTGGTAAATGTTT
4042914 CTTTG-AAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
4042949 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
4042986 -GTTGAAAAAT
1 CTTTGAAAAAT
4042996 GATAATGGGA
Statistics
Matches: 77, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
35 28 0.36
36 21 0.27
37 28 0.36
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:4047666 original size:21 final size:20
Alignment explanation
Indices: 4047642--4047705 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
4047632 AACTTTGAAA
4047642 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
4047663 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
4047677 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
4047698 AAATGTTT
1 AAATGTTT
4047706 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:4047680 original size:35 final size:36
Alignment explanation
Indices: 4047634--4047755 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
4047624 TGGTAACCAA
4047634 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
4047671 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
4047706 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
4047743 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
4047756 AATTAGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:4056512 original size:8 final size:8
Alignment explanation
Indices: 4056499--4056539 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
4056489 CTCATTTTCA
4056499 GAGAATTT
1 GAGAATTT
4056507 GAGAATTT
1 GAGAATTT
*
4056515 -AGAGTTT
1 GAGAATTT
4056522 GAGAATTT
1 GAGAATTT
4056530 GAGAATTT
1 GAGAATTT
4056538 GA
1 GA
4056540 AAGATTGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:4056524 original size:15 final size:16
Alignment explanation
Indices: 4056499--4056539 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
4056489 CTCATTTTCA
4056499 GAGAATTTGAGAATTT
1 GAGAATTTGAGAATTT
*
4056515 -AGAGTTTGAGAATTT
1 GAGAATTTGAGAATTT
4056530 GAGAATTTGA
1 GAGAATTTGA
4056540 AAGATTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (16 bp):
GAGAATTTGAGAATTT
Found at i:4056833 original size:126 final size:128
Alignment explanation
Indices: 4056607--4056851 Score: 467
Period size: 126 Copynumber: 1.9 Consensus size: 128
4056597 CTATAATCGG
4056607 TTCACTATTCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
4056672 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACA-TAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
4056734 TTCACTATTCACATGAAGGCGCGTTCCCG-GGGGGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
4056798 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGT
66 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGT
4056852 TTGAATAACT
Statistics
Matches: 116, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
126 74 0.64
127 42 0.36
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:4057292 original size:30 final size:30
Alignment explanation
Indices: 4057231--4057329 Score: 110
Period size: 31 Copynumber: 3.1 Consensus size: 30
4057221 TTAAGTTGAA
*
4057231 ATTTAATGTTAAATTTCGAATACTATATTTT
1 ATTTAAT-TTAAATTTCGAATAATATATTTT
*
4057262 ATTTAAATTTAAATTT-GAATAATATTTTTT
1 ATTT-AATTTAAATTTCGAATAATATATTTT
*
4057292 ATTTTTATTTTAAATTTCGAATAATATAATTTGT
1 A--TTTAATTTAAATTTCGAATAATAT-ATTT-T
4057326 ATTT
1 ATTT
4057330 TAAAAACATT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
30 13 0.22
31 22 0.38
32 18 0.31
33 3 0.05
34 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (30 bp):
ATTTAATTTAAATTTCGAATAATATATTTT
Found at i:4059155 original size:16 final size:16
Alignment explanation
Indices: 4059136--4059210 Score: 75
Period size: 16 Copynumber: 4.8 Consensus size: 16
4059126 TTAATAATTC
4059136 TAAATAATAATATATA
1 TAAATAATAATATATA
*
4059152 TAAAT-ATTAT-TA-A
1 TAAATAATAATATATA
*
4059165 TAAAAAATAATATTATA
1 TAAATAATAATA-TATA
* *
4059182 TAAATATTAATATAAA
1 TAAATAATAATATATA
*
4059198 AAAATAATAATAT
1 TAAATAATAATAT
4059211 TTAAAAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
13 5 0.11
14 6 0.13
15 4 0.09
16 21 0.45
17 11 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATAATAATATATA
Found at i:4059184 original size:30 final size:28
Alignment explanation
Indices: 4059136--4059210 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 28
4059126 TTAATAATTC
* *
4059136 TAAATAATAATATATATAAATATTATTAA
1 TAAAAAATAATATATATAAATATTAAT-A
4059165 TAAAAAATAATATTATATAAATATTAATA
1 TAAAAAATAATA-TATATAAATATTAATA
4059194 TAAAAAAATAATA-ATAT
1 T-AAAAAATAATATATAT
4059211 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 4 0.10
29 13 0.31
30 25 0.60
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
TAAAAAATAATATATATAAATATTAATA
Found at i:4059231 original size:16 final size:16
Alignment explanation
Indices: 4059137--4059233 Score: 65
Period size: 16 Copynumber: 6.1 Consensus size: 16
4059127 TAATAATTCT
* *
4059137 AAATAATAATATATAT
1 AAATAATAATATAAAA
* *
4059153 AAAT-ATTAT-TAATA
1 AAATAATAATATAAAA
* *
4059167 AAA-AATAATATTATAT
1 AAATAATAATA-TAAAA
*
4059183 AAATATTAATATAAAA
1 AAATAATAATATAAAA
4059199 AAATAATAATATTTAAAA
1 AAATAATAATA--TAAAA
* *
4059217 AAATACTAACATAAAA
1 AAATAATAATATAAAA
4059233 A
1 A
4059234 TAAATTTTTA
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
14 9 0.15
15 4 0.07
16 28 0.46
17 6 0.10
18 14 0.23
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAATAATATAAAA
Found at i:4059231 original size:34 final size:32
Alignment explanation
Indices: 4059166--4059238 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 32
4059156 TATTATTAAT
* * * *
4059166 AAAAAATAATATTATATAAATATTAATATAAA
1 AAAAAATAATATTAAAAAAATACTAACATAAA
4059198 AAAATAATAATATTTAAAAAAATACTAACATAAA
1 AAAA-AATAATA-TTAAAAAAATACTAACATAAA
*
4059232 AATAAAT
1 AAAAAAT
4059239 TTTTACCACT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 4 0.12
33 10 0.29
34 20 0.59
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (32 bp):
AAAAAATAATATTAAAAAAATACTAACATAAA
Found at i:4082602 original size:56 final size:56
Alignment explanation
Indices: 4082513--4082618 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 56
4082503 ACTCTTCACT
* * * * *
4082513 ACTCTGATAACAATAATAAATTTTATCTTATATTTATAGATTTTAGTGTTTATTTC
1 ACTCTAATAACAATAATAAATCTCATCTCATATTTATAGATTTAAGTGTTTATTTC
* *
4082569 ACTCTAATAATAATGATAAATCTCATCTCATATTTATAGATTTAAGTGTT
1 ACTCTAATAACAATAATAAATCTCATCTCATATTTATAGATTTAAGTGTT
4082619 CATTAAATTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 43 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (56 bp):
ACTCTAATAACAATAATAAATCTCATCTCATATTTATAGATTTAAGTGTTTATTTC
Found at i:4084575 original size:28 final size:26
Alignment explanation
Indices: 4084542--4084597 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
4084532 AAATATTTAG
*
4084542 ATTATTTTACGAATATTTTTAGATATAT
1 ATTATTTTA-GAATATTCTTA-ATATAT
4084570 ATTATTTTAGAATATTCTTAATATAT
1 ATTATTTTAGAATATTCTTAATATAT
4084596 AT
1 AT
4084598 CTCGTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 8 0.30
27 10 0.37
28 9 0.33
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (26 bp):
ATTATTTTAGAATATTCTTAATATAT
Found at i:4085532 original size:2 final size:2
Alignment explanation
Indices: 4085525--4085594 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
4085515 CTTTGATTTC
4085525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4085567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4085595 TTTTAATATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4098372 original size:2 final size:2
Alignment explanation
Indices: 4098318--4098356 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4098308 ACATAGGACC
4098318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4098357 GGTGTGTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4098504 original size:27 final size:28
Alignment explanation
Indices: 4098447--4098504 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
4098437 AGAGGTGCAC
*
4098447 AAAAAATTCGAATATCCGATTTTGCGCAA
1 AAAAAATTCGAATATCCGAATTTGCG-AA
* *
4098476 AAAATATTCGAA-A-CCGAATTTGGGAA
1 AAAAAATTCGAATATCCGAATTTGCGAA
4098502 AAA
1 AAA
4098505 CTGGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 9 0.35
28 1 0.04
29 11 0.42
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (28 bp):
AAAAAATTCGAATATCCGAATTTGCGAA
Found at i:4098670 original size:20 final size:20
Alignment explanation
Indices: 4098645--4098689 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
4098635 TTATCCGGAA
*
4098645 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
4098665 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
4098685 AAAAA
1 AAAAA
4098690 ATTAGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:4098859 original size:172 final size:173
Alignment explanation
Indices: 4098673--4099017 Score: 649
Period size: 172 Copynumber: 2.0 Consensus size: 173
4098663 TTAAAAATCC
4098673 GGTCTGAGGTTTAAAAAATTAGATGACCGGATTTTTTACCGGATTAAAAACCGGTTTTTTTAAAA
1 GGTCTGAGGTTTAAAAAATTAGATGACCGGATTTTTTACCGGATTAAAAACCGGTTTTTTTAAAA
4098738 CCGAAACCGATTACACCGGTTACATCATCCGACCCTCTAAACCGGTTATGATCCGAACCGATTTT
66 CCGAAACCGATTACACCGGTTACATCATCCGACCCTCTAAACCGGTTATGATCCGAACCGATTTT
*
4098803 TTTATAAAACGA-TTTTGGCTTAG-GAAAAAACGGAGATCGGTT
131 TTTATAAAACGATTTTTGGCTTAGTGAAAAAACCG-GATCGGTT
4098845 GGTCTGAGGTTTAAAAAATTAGATGACCGGATTTTTTACCGGATTAAAAACCGGTTTTTTTAAAA
1 GGTCTGAGGTTTAAAAAATTAGATGACCGGATTTTTTACCGGATTAAAAACCGGTTTTTTTAAAA
4098910 CCGAAACCGATTACACCGGTTACATCATCCGACCCTCTAAACCGGTTATGATCCGAACCGATTTT
66 CCGAAACCGATTACACCGGTTACATCATCCGACCCTCTAAACCGGTTATGATCCGAACCGATTTT
*
4098975 TTTATAAACCGATTTTTGGCTTAGTGAAAAAACCGGATCGGTT
131 TTTATAAAACGATTTTTGGCTTAGTGAAAAAACCGGATCGGTT
4099018 TTTATCCGAT
Statistics
Matches: 169, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
172 141 0.83
173 19 0.11
174 9 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (173 bp):
GGTCTGAGGTTTAAAAAATTAGATGACCGGATTTTTTACCGGATTAAAAACCGGTTTTTTTAAAA
CCGAAACCGATTACACCGGTTACATCATCCGACCCTCTAAACCGGTTATGATCCGAACCGATTTT
TTTATAAAACGATTTTTGGCTTAGTGAAAAAACCGGATCGGTT
Found at i:4104970 original size:21 final size:21
Alignment explanation
Indices: 4104946--4104999 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
4104936 TTTGGGTTAG
*
4104946 GATTTAGGATTTATGGTTTAA
1 GATTTAGGATTTAAGGTTTAA
*
4104967 GATTTA-AATTTTAAGGTTTAA
1 GATTTAGGA-TTTAAGGTTTAA
*
4104988 GGTTTAGG-TTTA
1 GATTTAGGATTTA
4105000 GATTTTAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (21 bp):
GATTTAGGATTTAAGGTTTAA
Found at i:4104999 original size:27 final size:28
Alignment explanation
Indices: 4104955--4105013 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
4104945 GGATTTAGGA
*
4104955 TTTATGGTTTAAGATTTAAATTTTAAGG
1 TTTAAGGTTTAAGATTTAAATTTTAAGG
* *
4104983 TTTAAGGTTT-AGGTTTAGATTTTAAGG
1 TTTAAGGTTTAAGATTTAAATTTTAAGG
4105010 TTTA
1 TTTA
4105014 CCGTAGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (28 bp):
TTTAAGGTTTAAGATTTAAATTTTAAGG
Found at i:4105013 original size:7 final size:7
Alignment explanation
Indices: 4104955--4105013 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
4104945 GGATTTAGGA
*
4104955 TTTATGG
1 TTTAAGG
*
4104962 TTTAAGA
1 TTTAAGG
**
4104969 TTTAAAT
1 TTTAAGG
4104976 TTTAAGG
1 TTTAAGG
4104983 TTTAAGG
1 TTTAAGG
4104990 TTT-AGG
1 TTTAAGG
*
4104996 TTT-AGAT
1 TTTAAG-G
4105003 TTTAAGG
1 TTTAAGG
4105010 TTTA
1 TTTA
4105014 CCGTAGAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 8 0.19
7 32 0.76
8 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (7 bp):
TTTAAGG
Found at i:4109961 original size:2 final size:2
Alignment explanation
Indices: 4109954--4109999 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4109944 ATTGCATAAG
4109954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4109996 AT AT
1 AT AT
4110000 TCATATGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4119907 original size:23 final size:23
Alignment explanation
Indices: 4119839--4119907 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
4119829 ACATATTATA
4119839 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
4119862 CGGCTCTAT-GGTGTAATTCTACG
1 TGGCACT-TCGGTGCATTTCTACG
*
4119885 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
4119908 ATTTGTGATG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 1 0.03
23 33 0.94
24 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:4120094 original size:20 final size:20
Alignment explanation
Indices: 4120062--4120100 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4120052 TATGTAATGT
4120062 TGAATATATTAATTGTTAAA
1 TGAATATATTAATTGTTAAA
4120082 TGAATGATA-TAATTGTTAA
1 TGAAT-ATATTAATTGTTAA
4120101 GAAGTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (20 bp):
TGAATATATTAATTGTTAAA
Found at i:4122719 original size:35 final size:35
Alignment explanation
Indices: 4122677--4122752 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
4122667 AATATATGTC
* *
4122677 TGATAATTGTAAAA-CATCTTATAACTGTAAATATA
1 TGATAATT-AAAAATCATCTGATAACTGTAAATATA
* *
4122712 TGATAATTAAAAATCATCTGATAATTGTAAATATC
1 TGATAATTAAAAATCATCTGATAACTGTAAATATA
4122747 TGATAA
1 TGATAA
4122753 CCGTGAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 4 0.11
35 32 0.89
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (35 bp):
TGATAATTAAAAATCATCTGATAACTGTAAATATA
Found at i:4122735 original size:18 final size:17
Alignment explanation
Indices: 4122705--4122752 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
4122695 TTATAACTGT
*
4122705 AAATATATGATAATTAA
1 AAATATCTGATAATTAA
**
4122722 AAATCATCTGATAATTGT
1 AAAT-ATCTGATAATTAA
4122740 AAATATCTGATAA
1 AAATATCTGATAA
4122753 CCGTGAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (17 bp):
AAATATCTGATAATTAA
Found at i:4122761 original size:18 final size:17
Alignment explanation
Indices: 4122722--4122770 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
4122712 TGATAATTAA
**
4122722 AAATCATCTGATAATTGT
1 AAAT-ATCTGATAACCGT
4122740 AAATATCTGATAACCGT
1 AAATATCTGATAACCGT
*
4122757 GAAATGTCTGATAA
1 -AAATATCTGATAA
4122771 TTGTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (17 bp):
AAATATCTGATAACCGT
Found at i:4129702 original size:2 final size:2
Alignment explanation
Indices: 4129695--4129729 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4129685 CACCTAACCC
4129695 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
4129730 TATTTCAATT
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:4130950 original size:30 final size:30
Alignment explanation
Indices: 4130888--4130952 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
4130878 TATGACAATA
* * * *
4130888 AACCGGCTGAAAATCGGTAAAATCGGAGTG
1 AACCGGCTAAAAACCGGCAAAACCGGAGTG
**
4130918 AACCGGCTAAAAACCGGCAAAACCGGTTTG
1 AACCGGCTAAAAACCGGCAAAACCGGAGTG
4130948 AACCG
1 AACCG
4130953 CCGGTTCACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (30 bp):
AACCGGCTAAAAACCGGCAAAACCGGAGTG
Found at i:4132251 original size:25 final size:26
Alignment explanation
Indices: 4132193--4132251 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
4132183 TAAATTTCGG
4132193 TTAATTTTCGAATTAACTAAAATTTTTT
1 TTAATTTTCGAATT-A-TAAAATTTTTT
** *
4132221 AGAATTTTCGAATT-TAATATTTTTT
1 TTAATTTTCGAATTATAAAATTTTTT
4132246 TTAATT
1 TTAATT
4132252 AAAAACAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 14 0.54
28 12 0.46
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (26 bp):
TTAATTTTCGAATTATAAAATTTTTT
Found at i:4132421 original size:23 final size:23
Alignment explanation
Indices: 4132395--4132439 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4132385 GCAAAACTGG
* *
4132395 AAGCATAATTCAGTATACAAACC
1 AAGCATAATTAAGCATACAAACC
4132418 AAGCATAATTAAGCATACAAAC
1 AAGCATAATTAAGCATACAAAC
4132440 AGTTTACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.20, G:0.09, T:0.20
Consensus pattern (23 bp):
AAGCATAATTAAGCATACAAACC
Found at i:4132892 original size:19 final size:19
Alignment explanation
Indices: 4132868--4132907 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
4132858 AATCCTCCCA
4132868 AAAAGTTTCCATTTGCACC
1 AAAAGTTTCCATTTGCACC
*
4132887 AAAAGTTTCCTTTTGCACC
1 AAAAGTTTCCATTTGCACC
4132906 AA
1 AA
4132908 GCATTACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (19 bp):
AAAAGTTTCCATTTGCACC
Found at i:4137005 original size:11 final size:10
Alignment explanation
Indices: 4136984--4137041 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
4136974 ACTTTTTTTA
*
4136984 AAAAATAAAT
1 AAAAATGAAT
4136994 AAAAATGCAAT
1 AAAAATG-AAT
4137005 AAAAATGAATT
1 AAAAATGAA-T
*
4137016 GAAAATGAAT
1 AAAAATGAAT
* *
4137026 AAAATTCAAT
1 AAAAATGAAT
4137036 AAAAAT
1 AAAAAT
4137042 ATAATGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 21 0.52
11 19 0.47
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.22
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:4137009 original size:21 final size:20
Alignment explanation
Indices: 4136984--4137041 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
4136974 ACTTTTTTTA
4136984 AAAAATAAATAAAAATGCAAT
1 AAAAATAAATAAAAATG-AAT
* *
4137005 AAAAATGAATTGAAAATGAAT
1 AAAAAT-AAATAAAAATGAAT
* *
4137026 AAAATTCAATAAAAAT
1 AAAAATAAATAAAAAT
4137042 ATAATGTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 7 0.23
21 14 0.47
22 9 0.30
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.22
Consensus pattern (20 bp):
AAAAATAAATAAAAATGAAT
Found at i:4137532 original size:18 final size:18
Alignment explanation
Indices: 4137506--4137557 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
4137496 TAAAATTAAA
4137506 ATTTAATATTTAATATTT
1 ATTTAATATTTAATATTT
* *
4137524 ATTTTATATTTTATATTT
1 ATTTAATATTTAATATTT
* *
4137542 -TTTAAAAATTAATATT
1 ATTTAATATTTAATATT
4137558 AGAAAGAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTAATATTTAATATTT
Found at i:4137642 original size:21 final size:21
Alignment explanation
Indices: 4137605--4137663 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
4137595 CTTTACATTA
* *
4137605 TATTTTTATTGAATTTTATT-
1 TATTTTTATTCATTTTTATTG
4137625 TATTTTTAATTCATTTTTATTG
1 TATTTTT-ATTCATTTTTATTG
* *
4137647 CATTTTTATTTATTTTT
1 TATTTTTATTCATTTTT
4137664 TTAAAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (21 bp):
TATTTTTATTCATTTTTATTG
Found at i:4137661 original size:10 final size:10
Alignment explanation
Indices: 4137605--4137663 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
4137595 CTTTACATTA
4137605 TATTTTTATT
1 TATTTTTATT
* *
4137615 GAATTTTATT
1 TATTTTTATT
4137625 TATTTTTAATT
1 TATTTTT-ATT
*
4137636 CATTTTTATT
1 TATTTTTATT
*
4137646 GCATTTTTATT
1 -TATTTTTATT
4137657 TATTTTT
1 TATTTTT
4137664 TTAAAAAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 22 0.54
11 19 0.46
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (10 bp):
TATTTTTATT
Found at i:4140437 original size:6 final size:6
Alignment explanation
Indices: 4140426--4140452 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4140416 TTATTTGCGA
4140426 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
4140453 AAAACTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:4140601 original size:38 final size:36
Alignment explanation
Indices: 4140537--4140609 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 36
4140527 ATAAATATTA
*
4140537 AATAAATCAAAGAAAAAAACATAAAATAATAATAAC
1 AATAAATCAAAGAAAAAAACATAAAATAAAAATAAC
4140573 AATAAATCAAAAGGAAAAAAA-ATAAAAATAAAAATAA
1 AATAAATC-AAA-GAAAAAAACAT-AAAATAAAAATAA
4140610 ATTAATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 8 0.24
37 5 0.15
38 20 0.61
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.15
Consensus pattern (36 bp):
AATAAATCAAAGAAAAAAACATAAAATAAAAATAAC
Found at i:4144261 original size:23 final size:23
Alignment explanation
Indices: 4144220--4144286 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
4144210 AAACTAACGT
*
4144220 TAAACGAA-ATGTTTGCGAACAA
1 TAAACGAACATGTTCGCGAACAA
* *
4144242 TAAACGAACATGTTCACGAACAC
1 TAAACGAACATGTTCGCGAACAA
* *
4144265 TAAACAAACATATTCGCGAACA
1 TAAACGAACATGTTCGCGAACA
4144287 TTTAAATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
22 8 0.21
23 30 0.79
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.19
Consensus pattern (23 bp):
TAAACGAACATGTTCGCGAACAA
Found at i:4144342 original size:29 final size:28
Alignment explanation
Indices: 4144309--4144412 Score: 81
Period size: 28 Copynumber: 3.7 Consensus size: 28
4144299 CGCAAACATT
4144309 AAATAAACTAAAACGAACACCTTCGAAAA
1 AAATAAACTAAAACGAACACCTTC-AAAA
* * *
4144338 AAAT-AACCAAATACGAACACGATACTAAAA
1 AAATAAACTAAA-ACGAACAC-CTTC-AAAA
* * *
4144368 AAATTAAACTAATATGAATACCTTC-AAA
1 AAA-TAAACTAAAACGAACACCTTCAAAA
4144396 AAATAAA-T-AAACGAACA
1 AAATAAACTAAAACGAACA
4144413 TGAACAACCT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
25 6 0.10
26 1 0.02
27 4 0.07
28 12 0.21
29 12 0.21
30 11 0.19
31 7 0.12
32 5 0.09
ACGTcount: A:0.60, C:0.17, G:0.06, T:0.17
Consensus pattern (28 bp):
AAATAAACTAAAACGAACACCTTCAAAA
Found at i:4148269 original size:15 final size:17
Alignment explanation
Indices: 4148228--4148284 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
4148218 ATTTTATCTT
4148228 TAATTATTTATATTTATA
1 TAATTA-TTATATTTATA
*
4148246 TAATAATTAT-TTTATA
1 TAATTATTATATTTATA
* *
4148262 T-ATTATTAGTATATATT
1 TAATTATTA-TATTTATA
4148279 TAATTA
1 TAATTA
4148285 GTGTGAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 6 0.19
16 8 0.25
17 9 0.28
18 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TAATTATTATATTTATA
Found at i:4148520 original size:21 final size:21
Alignment explanation
Indices: 4148496--4148559 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
4148486 GCAAATTCGC
4148496 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
4148517 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
4148537 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
4148558 GT
1 GT
4148560 CAACAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:4148576 original size:22 final size:22
Alignment explanation
Indices: 4148548--4148663 Score: 68
Period size: 22 Copynumber: 5.5 Consensus size: 22
4148538 TTCCATTTCG
4148548 CGTTGCGATAGTCAACAGTTGT
1 CGTTGCGATAGTCAACAGTTGT
**
4148570 CGTTGCGATTTTCTAA-A--T-T
1 CGTTGCGATAGTC-AACAGTTGT
**
4148589 CGTTGCGATTTTTCAA-A--T-T
1 CGTTGCGA-TAGTCAACAGTTGT
* *
4148608 CATTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCAACAGTTGT
* *
4148630 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCAACAGTTGT
* *
4148652 CATTGTGATAGT
1 CGTTGCGATAGT
4148664 TAAAAAAAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
18 4 0.05
19 22 0.29
20 6 0.08
21 1 0.01
22 42 0.55
23 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (22 bp):
CGTTGCGATAGTCAACAGTTGT
Found at i:4148593 original size:19 final size:19
Alignment explanation
Indices: 4148569--4148616 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
4148559 TCAACAGTTG
4148569 TCGTTGCGA-TTTTCTAAAT
1 TCGTTGCGATTTTTC-AAAT
4148588 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTTCAAAT
*
4148607 TCATTGCGAT
1 TCGTTGCGAT
4148617 AGTCTACAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGTTGCGATTTTTCAAAT
Found at i:4148750 original size:6 final size:6
Alignment explanation
Indices: 4148739--4148790 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
4148729 AGACACGTAT
4148739 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
4148787 GACC
1 GACC
4148791 CGAGACGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:4149306 original size:6 final size:6
Alignment explanation
Indices: 4149282--4149321 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
4149272 GCCGTCCGTC
*
4149282 TCGT-G TCG-GG TCG-GG TCGTGG TCGTGG TTGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
4149322 AATACGTGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 12 0.39
6 19 0.61
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:4149444 original size:22 final size:21
Alignment explanation
Indices: 4149416--4149548 Score: 77
Period size: 22 Copynumber: 6.4 Consensus size: 21
4149406 CGACGAATTT
4149416 TCGCAACGAATTTGGTAGACTA
1 TCGCAACGAATTTGGTA-ACTA
*
4149438 TCGCAAC-AATAACT-GTATACTA
1 TCGCAACGAAT--TTGGTA-ACTA
*
4149460 TCGCAACGAATTTGG-AA-AA
1 TCGCAACGAATTTGGTAACTA
*
4149479 TCGCAACGAATTTGG-AA-AA
1 TCGCAACGAATTTGGTAACTA
**
4149498 TCGCAACGACAACT-GTAGACTA
1 TCGCAACGA-ATTTGGTA-ACTA
*
4149520 TCGCAACGCGATTT--TCAACTA
1 TCGCAACG-AATTTGGT-AACTA
4149541 TCGCAACG
1 TCGCAACG
4149549 CGAAATGGAA
Statistics
Matches: 91, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
19 30 0.33
20 4 0.04
21 19 0.21
22 34 0.37
23 4 0.04
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (21 bp):
TCGCAACGAATTTGGTAACTA
Found at i:4149483 original size:19 final size:19
Alignment explanation
Indices: 4149459--4149506 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
4149449 ACTGTATACT
4149459 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
4149478 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
4149497 ATCGCAACGA
1 ATCGCAACGA
4149507 CAACTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:4149542 original size:21 final size:21
Alignment explanation
Indices: 4149516--4149592 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
4149506 ACAACTGTAG
4149516 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
** **
4149537 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
*
4149558 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
4149578 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
4149593 AATGCAACGC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:4149613 original size:41 final size:41
Alignment explanation
Indices: 4149519--4149596 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
4149509 ACTGTAGACT
4149519 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
4149560 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
4149597 CAACGCGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:4152767 original size:18 final size:18
Alignment explanation
Indices: 4152746--4152780 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4152736 TGTCATCCGA
*
4152746 TCTTATTATTTAATTCAT
1 TCTTATCATTTAATTCAT
*
4152764 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4152781 GTCCTTTCGA
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:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTTATCATTTAATTCAT
Found at i:4154114 original size:8 final size:8
Alignment explanation
Indices: 4154074--4154128 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
4154064 TCAAAGTTTT
4154074 GGTCAACAG
1 GGTCAAC-G
4154083 TGGTCAACG
1 -GGTCAACG
4154092 CCGGTCAAC-
1 --GGTCAACG
*
4154101 GGTCAATG
1 GGTCAACG
4154109 GGTCAACG
1 GGTCAACG
4154117 GGTCAACG
1 GGTCAACG
4154125 GGTC
1 GGTC
4154129 GGGTCGGGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 19 0.47
9 1 0.03
10 14 0.35
ACGTcount: A:0.24, C:0.25, G:0.35, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:4155206 original size:15 final size:15
Alignment explanation
Indices: 4155186--4155226 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4155176 AAAAAAATAC
*
4155186 AAAATACAATACCAA
1 AAAATAAAATACCAA
* *
4155201 AAAATATAATACCAG
1 AAAATAAAATACCAA
4155216 AAAATAAAATA
1 AAAATAAAATA
4155227 TTATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.12, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAATAAAATACCAA
Found at i:4155224 original size:5 final size:5
Alignment explanation
Indices: 4155216--4155293 Score: 57
Period size: 5 Copynumber: 15.6 Consensus size: 5
4155206 ATAATACCAG
** * * ** * *
4155216 AAAAT AAAAT ATTAT AAAAT AATAT AAAAT ACAAT ACCAT ACATT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * *
4155266 AACAT AAAAT AAAAT ACAAG AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
4155294 TTTACATAAC
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.68, C:0.08, G:0.01, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:4155251 original size:55 final size:55
Alignment explanation
Indices: 4155176--4155281 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 55
4155166 TATTTATATG
* *
4155176 AAAAAAATACAAAATACAATACCAAAAAATATAATACCAGAAAATAAAATATTAT
1 AAAAAAATACAAAATACAATACCAAAAAATAAAATAACAGAAAATAAAATATTAT
* * * * * *
4155231 AAAATAATATAAAATACAATACCATACATTAAAATAACATAAAATAAAATA
1 AAAAAAATACAAAATACAATACCAAAAAATAAAATAACAGAAAATAAAATA
4155282 CAAGAAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.67, C:0.10, G:0.01, T:0.22
Consensus pattern (55 bp):
AAAAAAATACAAAATACAATACCAAAAAATAAAATAACAGAAAATAAAATATTAT
Found at i:4155290 original size:55 final size:55
Alignment explanation
Indices: 4155175--4155292 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 55
4155165 ATATTTATAT
* * * **
4155175 GAAAAAAATACAAAATACAATACCAAAAAATATAATACCAGAAAATAAAATATTA
1 GAAAATAATACAAAATACAATACCAAAAAATAAAATAACAGAAAATAAAATACAA
* * * * * *
4155230 TAAAATAATATAAAATACAATACCATACATTAAAATAACATAAAATAAAATACAA
1 GAAAATAATACAAAATACAATACCAAAAAATAAAATAACAGAAAATAAAATACAA
4155285 GAAAATAA
1 GAAAATAA
4155293 ATTTACATAA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20
Consensus pattern (55 bp):
GAAAATAATACAAAATACAATACCAAAAAATAAAATAACAGAAAATAAAATACAA
Found at i:4158397 original size:7 final size:7
Alignment explanation
Indices: 4158385--4158409 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4158375 ATATGTTATT
4158385 ATATGTG
1 ATATGTG
4158392 ATATGTG
1 ATATGTG
4158399 ATATGTG
1 ATATGTG
4158406 ATAT
1 ATAT
4158410 TAAACTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (7 bp):
ATATGTG
Found at i:4158750 original size:31 final size:31
Alignment explanation
Indices: 4158712--4158834 Score: 126
Period size: 31 Copynumber: 4.0 Consensus size: 31
4158702 GAGTTGAGGG
*
4158712 TTTACCTATATTCTTTGGGACATATGGACTA
1 TTTACCTATATTCTTCGGGACATATGGACTA
* * *
4158743 TTTACCTATGTTCTTCGGGATATATGGATTA
1 TTTACCTATATTCTTCGGGACATATGGACTA
* * *
4158774 TTTACCTATGTTCTTTGGAACATATGG--TA
1 TTTACCTATATTCTTCGGGACATATGGACTA
*
4158803 TGATTACCTAGATTCTTCGGGATC-TATGGACT
1 T--TTACCTATATTCTTCGGGA-CATATGGACT
4158835 GGTCCTTTGG
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
29 3 0.04
31 71 0.93
32 1 0.01
33 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (31 bp):
TTTACCTATATTCTTCGGGACATATGGACTA
Found at i:4158789 original size:62 final size:61
Alignment explanation
Indices: 4158712--4158832 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 61
4158702 GAGTTGAGGG
*
4158712 TTTACCTATATTCTTTGGGACATATGG-ACTATTTACCTATG-TTCTTCGGGATATATGGATTA
1 TTTACCTATATTCTTTGGAACATATGGTA-TA-TTACCTA-GATTCTTCGGGATATATGGATTA
* *
4158774 TTTACCTATGTTCTTTGGAACATATGGTATGATTACCTAGATTCTTCGGGATCTATGGA
1 TTTACCTATATTCTTTGGAACATATGGTAT-ATTACCTAGATTCTTCGGGATATATGGA
4158833 CTGGTCCTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 1 0.02
62 50 0.94
63 2 0.04
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (61 bp):
TTTACCTATATTCTTTGGAACATATGGTATATTACCTAGATTCTTCGGGATATATGGATTA
Found at i:4162196 original size:20 final size:21
Alignment explanation
Indices: 4162146--4162208 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
4162136 GATTCTCCTG
4162146 TGGGGGGAATCGGTTCCCATTCAA
1 TGGGGGG-ATCGGTTCCC--TCAA
*
4162170 AGGGGGGATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
* *
4162190 TGGGGGGATTGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
4162209 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
23 10 0.29
24 6 0.17
ACGTcount: A:0.16, C:0.22, G:0.37, T:0.25
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:4169067 original size:110 final size:110
Alignment explanation
Indices: 4168874--4169076 Score: 309
Period size: 110 Copynumber: 1.8 Consensus size: 110
4168864 GCGTAACTTT
* * * *
4168874 TCATCCCAACAACTTTCATGTATGGTGGGACGAGACACTATAACATAGTAGAGATTTTCTACAAA
1 TCATCCCAACAACTTCCATGTATGATGGGACGAGACACTATAACATAGTAGAGATTTCCAACAAA
* *
4168939 AGGTGAAAGTGTTTCTTATGAAAAGAGCCTTCATTTTTCTAAAGA
66 AGGTGAAAGCGCTTCTTATGAAAAGAGCCTTCATTTTTCTAAAGA
* *
4168984 TCATCCCAACAACTTCCATGTATGATGGGATGAGACACTATTACAT-GATAGAGATTTCCAACAA
1 TCATCCCAACAACTTCCATGTATGATGGGACGAGACACTATAACATAG-TAGAGATTTCCAACAA
*
4169048 AAGGTGAAAGCGCTTCTTATGAAACGAGC
65 AAGGTGAAAGCGCTTCTTATGAAAAGAGC
4169077 ATTCCCTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 1 0.01
110 82 0.99
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (110 bp):
TCATCCCAACAACTTCCATGTATGATGGGACGAGACACTATAACATAGTAGAGATTTCCAACAAA
AGGTGAAAGCGCTTCTTATGAAAAGAGCCTTCATTTTTCTAAAGA
Found at i:4173389 original size:54 final size:54
Alignment explanation
Indices: 4173307--4173414 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
4173297 CATAGCAACC
4173307 GAGTAGTTTTATCCCCAATACACAAATGGAAGTGATGGGTAATTATAACTCATT
1 GAGTAGTTTTATCCCCAATACACAAATGGAAGTGATGGGTAATTATAACTCATT
4173361 GAGTAGTTTTATCCCCAATACACAAATGGAAGTGATGGGTAATTATAACTCATT
1 GAGTAGTTTTATCCCCAATACACAAATGGAAGTGATGGGTAATTATAACTCATT
4173415 AAGTGATCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (54 bp):
GAGTAGTTTTATCCCCAATACACAAATGGAAGTGATGGGTAATTATAACTCATT
Found at i:4182346 original size:85 final size:85
Alignment explanation
Indices: 4182232--4182402 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
4182222 ATTTGATTTC
4182232 AATTTAAATGGCATTTTCTAATCATATACAATACATATATATTTTTTCGTATTTTTTTCATATGT
1 AATTTAAATGGCATTTTCTAATCATATACAATACATATATATTTTTTCGTATTTTTTTCATATGT
4182297 GATTTACATATTCCATACAA
66 GATTTACATATTCCATACAA
4182317 AATTTAAATGGCATTTTCTAATCATATACAATACATATATATTTTTTCGTATTTTTTTCATATGT
1 AATTTAAATGGCATTTTCTAATCATATACAATACATATATATTTTTTCGTATTTTTTTCATATGT
4182382 GATTTACATATTCCATACAA
66 GATTTACATATTCCATACAA
4182402 A
1 A
4182403 GTTGAAGGAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.47
Consensus pattern (85 bp):
AATTTAAATGGCATTTTCTAATCATATACAATACATATATATTTTTTCGTATTTTTTTCATATGT
GATTTACATATTCCATACAA
Found at i:4186303 original size:26 final size:26
Alignment explanation
Indices: 4186261--4186311 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
4186251 ATAAATGAAA
4186261 AGATTACAACTTCATTAGATCTATCG
1 AGATTACAACTTCATTAGATCTATCG
* *
4186287 AGATTACAATTTTATTAGATCTATC
1 AGATTACAACTTCATTAGATCTATC
4186312 TATGTCTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (26 bp):
AGATTACAACTTCATTAGATCTATCG
Found at i:4187162 original size:11 final size:11
Alignment explanation
Indices: 4187146--4187182 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4187136 CAACTAATTG
4187146 ACCTCTTTCTT
1 ACCTCTTTCTT
4187157 ACCTC-TTC-T
1 ACCTCTTTCTT
4187166 ATCCTCTTTCTT
1 A-CCTCTTTCTT
4187178 ACCTC
1 ACCTC
4187183 GTCTATCGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 12 0.52
12 2 0.09
ACGTcount: A:0.11, C:0.41, G:0.00, T:0.49
Consensus pattern (11 bp):
ACCTCTTTCTT
Found at i:4187172 original size:21 final size:21
Alignment explanation
Indices: 4187147--4187189 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4187137 AACTAATTGA
*
4187147 CCTCTTTCTTACCTCTTCTAT
1 CCTCTTTCTTACCTCGTCTAT
4187168 CCTCTTTCTTACCTCGTCTAT
1 CCTCTTTCTTACCTCGTCTAT
4187189 C
1 C
4187190 GACGTTATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.40, G:0.02, T:0.49
Consensus pattern (21 bp):
CCTCTTTCTTACCTCGTCTAT
Found at i:4187950 original size:20 final size:20
Alignment explanation
Indices: 4187927--4187968 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
4187917 TATCAGTACT
4187927 ATAGGCATATTATCGATACC
1 ATAGGCATATTATCGATACC
*
4187947 ATAGGCATATTATTGATACC
1 ATAGGCATATTATCGATACC
4187967 AT
1 AT
4187969 TAGACCCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (20 bp):
ATAGGCATATTATCGATACC
Found at i:4188618 original size:2 final size:2
Alignment explanation
Indices: 4188611--4188671 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
4188601 AATCCCAACA
4188611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4188653 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
4188672 ATAATAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4189677 original size:18 final size:18
Alignment explanation
Indices: 4189633--4189667 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4189623 AGTTTACAAT
*
4189633 TAAATAATAAAATAAAAA
1 TAAATATTAAAATAAAAA
4189651 TAAATATTAAAATAAAA
1 TAAATATTAAAATAAAA
4189668 TAATTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATATTAAAATAAAAA
Found at i:4189723 original size:12 final size:12
Alignment explanation
Indices: 4189706--4189730 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4189696 TAATGAATAA
4189706 AAAAACAATTAT
1 AAAAACAATTAT
4189718 AAAAACAATTAT
1 AAAAACAATTAT
4189730 A
1 A
4189731 CCTTACTAGA
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAACAATTAT
Found at i:4190454 original size:20 final size:20
Alignment explanation
Indices: 4190429--4190466 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4190419 TTTAGTTCAC
4190429 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
4190449 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
4190467 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Done.