Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 29 of 82
Found at i:10226496 original size:34 final size:32
Alignment explanation
Indices: 10226425--10226493 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
10226415 GAAAGAGTTT
* **
10226425 TGCTGCAAATTTTGAGAGAGAAAAGAAAGTTT
1 TGCTGCAAATTTTGAGAGAGAAAACAAAGTGC
* *
10226457 TGCTGCAAATTTTGATAGAGAAAAC-AAGGGC
1 TGCTGCAAATTTTGAGAGAGAAAACAAAGTGC
10226488 TGCTGC
1 TGCTGC
10226494 TGCTGGGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (32 bp):
TGCTGCAAATTTTGAGAGAGAAAACAAAGTGC
Found at i:10227667 original size:43 final size:43
Alignment explanation
Indices: 10227607--10227772 Score: 187
Period size: 43 Copynumber: 3.9 Consensus size: 43
10227597 TTGTGTGATA
* *
10227607 ATGATGACCTAGCTATGTGCGATGT-GGGAGTGCACATGAGCCG
1 ATGATGACC-GGCTATGTGCGATGTAGGGAGTGCACATAAGCCG
* *
10227650 ATGATGACTCGGCTATGTGCGA-GTAGGTAGTGCACATAAGCGG
1 ATGATGAC-CGGCTATGTGCGATGTAGGGAGTGCACATAAGCCG
* *
10227693 ATGATGACCCGACTATGTGCG-TGTAGGGAGTGCGCATAAGCCG
1 ATGATGA-CCGGCTATGTGCGATGTAGGGAGTGCACATAAGCCG
* * *
10227736 ATGATGACCTAGCTATGTGC-AAGTAGAGAGTGCACAT
1 ATGATGACC-GGCTATGTGCGATGTAGGGAGTGCACAT
10227773 GACGATGAAT
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
42 4 0.04
43 98 0.94
44 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (43 bp):
ATGATGACCGGCTATGTGCGATGTAGGGAGTGCACATAAGCCG
Found at i:10228507 original size:19 final size:20
Alignment explanation
Indices: 10228480--10228525 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
10228470 AAGAGGCAAG
*
10228480 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
10228499 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
10228518 ATAATATT
1 ATAATATT
10228526 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:10228971 original size:20 final size:20
Alignment explanation
Indices: 10228926--10228963 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10228916 TTTTGGCCCC
10228926 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
10228946 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
10228964 AGATTTGAGG
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:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:10230214 original size:13 final size:13
Alignment explanation
Indices: 10230196--10230220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10230186 TGAATAAATG
10230196 TGATTTTATAAAA
1 TGATTTTATAAAA
10230209 TGATTTTATAAA
1 TGATTTTATAAA
10230221 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:10233495 original size:21 final size:22
Alignment explanation
Indices: 10233470--10233518 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
10233460 AAAAATCTCA
*
10233470 TTCTTCCAGCAGCTTCTTCAT-
1 TTCTTCCAGCAACTTCTTCATC
* *
10233491 TTCTT-CAGCAACTTTTTCTTC
1 TTCTTCCAGCAACTTCTTCATC
10233512 TTCTTCC
1 TTCTTCC
10233519 TCCCATCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.52
21 10 0.43
22 1 0.04
ACGTcount: A:0.12, C:0.33, G:0.06, T:0.49
Consensus pattern (22 bp):
TTCTTCCAGCAACTTCTTCATC
Found at i:10234772 original size:15 final size:16
Alignment explanation
Indices: 10234744--10234785 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
10234734 AGAAATGAAG
10234744 AAAGACAAAAAAAAAA
1 AAAGACAAAAAAAAAA
* *
10234760 AAAG-CAAAGAAAACA
1 AAAGACAAAAAAAAAA
*
10234775 AAAGAGAAAAA
1 AAAGACAAAAA
10234786 TGTAGAAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAGACAAAAAAAAAA
Found at i:10235431 original size:16 final size:17
Alignment explanation
Indices: 10235406--10235449 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
10235396 AAAAAACGTG
10235406 GAAAAGAGAAAAAG-AAA
1 GAAAA-AGAAAAAGAAAA
10235423 GAAAAAG-AAAAGAAAA
1 GAAAAAGAAAAAGAAAA
*
10235439 GAAATAGAAAA
1 GAAAAAGAAAA
10235450 TAAGTGGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAA
Found at i:10235502 original size:32 final size:32
Alignment explanation
Indices: 10235439--10235506 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
10235429 GAAAAGAAAA
* * *
10235439 GAAATAGAAAATAAGTGGGCATGGCCTAATAG
1 GAAATAGAAAATAAATGGGCATGCCCAAATAG
*
10235471 GAAATA-AAAATAAATGGGCTTAGCCCAAATAG
1 GAAATAGAAAATAAATGGGCAT-GCCCAAATAG
10235503 GAAA
1 GAAA
10235507 AATGGAGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.18
Consensus pattern (32 bp):
GAAATAGAAAATAAATGGGCATGCCCAAATAG
Found at i:10242568 original size:55 final size:55
Alignment explanation
Indices: 10242392--10242599 Score: 337
Period size: 55 Copynumber: 3.8 Consensus size: 55
10242382 AAGCATCGGC
* *
10242392 TCATTAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCACCCACCGG
*
10242447 TCATCAGCTCATGTGCATTCCCACACCGCACATA-CTAGAATCATCACCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCACCCACCGG
* * *
10242501 TCATCAGCTCATGTGCACTCCCACACCACACATAGTTGGAATCATCACCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCACCCACCGG
* *
10242556 TCATCAGCTCATGTGCACTCCCACACCGCACATAACTGGAATCA
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCA
10242600 CCTATCATCA
Statistics
Matches: 142, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
54 51 0.36
55 91 0.64
ACGTcount: A:0.28, C:0.38, G:0.14, T:0.21
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCACCCACCGG
Found at i:10242588 original size:109 final size:110
Alignment explanation
Indices: 10242392--10242599 Score: 346
Period size: 109 Copynumber: 1.9 Consensus size: 110
10242382 AAGCATCGGC
* * *
10242392 TCATTAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCACCGGTCATCAGCTC
1 TCATCAGCTCATGTGCACTCCCACACCACACATAGCTAGAATCATCACCCACCGGTCATCAGCTC
*
10242457 ATGTGCATTCCCACACCGCACAT-ACTAGAATCATCACCCACCGG
66 ATGTGCACTCCCACACCGCACATAACTAGAATCATCACCCACCGG
* *
10242501 TCATCAGCTCATGTGCACTCCCACACCACACATAGTTGGAATCATCACCCACCGGTCATCAGCTC
1 TCATCAGCTCATGTGCACTCCCACACCACACATAGCTAGAATCATCACCCACCGGTCATCAGCTC
*
10242566 ATGTGCACTCCCACACCGCACATAACTGGAATCA
66 ATGTGCACTCCCACACCGCACATAACTAGAATCA
10242600 CCTATCATCA
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
109 82 0.90
110 9 0.10
ACGTcount: A:0.28, C:0.38, G:0.14, T:0.21
Consensus pattern (110 bp):
TCATCAGCTCATGTGCACTCCCACACCACACATAGCTAGAATCATCACCCACCGGTCATCAGCTC
ATGTGCACTCCCACACCGCACATAACTAGAATCATCACCCACCGG
Found at i:10243920 original size:14 final size:15
Alignment explanation
Indices: 10243901--10243942 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
10243891 CATTGAATAA
10243901 AATATTAATATT-TT
1 AATATTAATATTATT
*
10243915 AATATT-ATTTTATT
1 AATATTAATATTATT
10243929 AATA-TAATATTATT
1 AATATTAATATTATT
10243943 TTATTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATATTAATATTATT
Found at i:10244580 original size:80 final size:80
Alignment explanation
Indices: 10244352--10244611 Score: 326
Period size: 80 Copynumber: 3.2 Consensus size: 80
10244342 TATGAGCTCC
* * * * *
10244352 ATTTATGAGATTGT-AACATGCATGTCATGAGATGTATGTGTTAGGATAGTCATAAACACTATCG
1 ATTTATGAGATTATGAA-ATGCATGCCATGAGATGTATGTGTCAGGATAGTCATATACACTATGG
* *
10244416 GCTAAGCATGTGAGTT
65 GCTATGCATGTGAATT
* * *
10244432 ATTTATGAGATTATTAAATGCATGCCATGAGATGTATGTGTCAAGATAGTCATATGCACTATGGG
1 ATTTATGAGATTATGAAATGCATGCCATGAGATGTATGTGTCAGGATAGTCATATACACTATGGG
10244497 CTATGCATGTGAATT
66 CTATGCATGTGAATT
* * * *
10244512 ATTTATGAGGTTATGAAATGCATGCCATAAGATGTATGTGTCGGGATAGTCATATACACCATGGG
1 ATTTATGAGATTATGAAATGCATGCCATGAGATGTATGTGTCAGGATAGTCATATACACTATGGG
* *
10244577 CTATGTATGT-AACTG
66 CTATGCATGTGAA-TT
* *
10244592 ATTTATGAGGTCATGAAATG
1 ATTTATGAGATTATGAAATG
10244612 TAACGAGCTC
Statistics
Matches: 159, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
79 2 0.01
80 155 0.97
81 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (80 bp):
ATTTATGAGATTATGAAATGCATGCCATGAGATGTATGTGTCAGGATAGTCATATACACTATGGG
CTATGCATGTGAATT
Found at i:10249231 original size:43 final size:43
Alignment explanation
Indices: 10249183--10249288 Score: 149
Period size: 43 Copynumber: 2.5 Consensus size: 43
10249173 CAGCTCATGT
** * *
10249183 GCACTCCCTACTCGCACATGGCTGGGTCATTACCGGTTTATGC
1 GCACTCCCTACTCGCACATAACTGGGTCATCACCGGCTTATGC
* * *
10249226 GCACTCCTTACTTGCACATAACTGGGTCATCATCGGCTTATGC
1 GCACTCCCTACTCGCACATAACTGGGTCATCACCGGCTTATGC
10249269 GCACTCCCTACTCGCACATA
1 GCACTCCCTACTCGCACATA
10249289 GCCAAGTCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.27
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAACTGGGTCATCACCGGCTTATGC
Found at i:10255213 original size:43 final size:43
Alignment explanation
Indices: 10255166--10255280 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
10255156 CAGCTCATGT
**** * *
10255166 GCACTCCTTACTCGCACATGGTTGGGTCATCACCGGTTTATGC
1 GCACTCCTTACTCGCACATAACCGAGTCATCACCGGCTTATGC
* *
10255209 GCACTCCTTACTCGCAGATAACCGAGTCATCATCGGCTTATGC
1 GCACTCCTTACTCGCACATAACCGAGTCATCACCGGCTTATGC
* * * *
10255252 GCACTCCCTACTCACACATAGCCTAGTCA
1 GCACTCCTTACTCGCACATAACCGAGTCA
10255281 ATATCATTAC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (43 bp):
GCACTCCTTACTCGCACATAACCGAGTCATCACCGGCTTATGC
Found at i:10259183 original size:37 final size:37
Alignment explanation
Indices: 10259131--10259225 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 37
10259121 CTTCAACTCT
* *
10259131 TGTGCACTCCTTACTCGCACAAGGCAATACCACCATA
1 TGTGCACTCCCTACTCGCACAACGCAATACCACCATA
* * ** ** *
10259168 TGTGCACTCCCTACTCGCACATCTCAATGTCATTATG
1 TGTGCACTCCCTACTCGCACAACGCAATACCACCATA
10259205 TGTGCACTCCCTACTCGCACA
1 TGTGCACTCCCTACTCGCACA
10259226 CCTCATTATC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.24, C:0.36, G:0.14, T:0.26
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACAACGCAATACCACCATA
Found at i:10261804 original size:54 final size:54
Alignment explanation
Indices: 10261737--10261888 Score: 250
Period size: 54 Copynumber: 2.8 Consensus size: 54
10261727 ATACTGTCTA
* * * *
10261737 GCTATGTGCACGATGTGGTGGGATGGACATGAGCTAGGTGAGATGGGCTATCTG
1 GCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATATCCG
* *
10261791 GTTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTCCG
1 GCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATATCCG
10261845 GCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGAT
1 GCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGAT
10261889 TGAATGATTG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.20, C:0.13, G:0.41, T:0.26
Consensus pattern (54 bp):
GCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATATCCG
Found at i:10266022 original size:2 final size:2
Alignment explanation
Indices: 10266017--10266054 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
10266007 ACTATATACC
* *
10266017 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10266055 CAATCACCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10266147 original size:42 final size:42
Alignment explanation
Indices: 10266101--10266219 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
10266091 ATATGCAATG
*
10266101 GCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCAACA
1 GCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAACA
* * *
10266143 GCTTATGTGCGCTCCCACTCGCACATAGCCTGGTCAGCAACG
1 GCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAACA
* * *
10266185 GCTTATGTGCACTCCTACTCGTACATAGTCGGGTC
1 GCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
10266220 CACATCAACA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (42 bp):
GCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAACA
Found at i:10268888 original size:35 final size:35
Alignment explanation
Indices: 10268859--10268973 Score: 128
Period size: 35 Copynumber: 3.4 Consensus size: 35
10268849 GGTTGATCTC
10268859 GTGAAAAACCATTGTTTTAGGTTGTGGTTGAGCCT
1 GTGAAAAACCATTGTTTTAGGTTGTGGTTGAGCCT
* * * * *
10268894 TTGAAAAACCA---CTTTGGGTTTTGGTTGAGCCC
1 GTGAAAAACCATTGTTTTAGGTTGTGGTTGAGCCT
***
10268926 GTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCT
1 GTGAAAAACCATTGTTTTAGGTTGTGGTTGAGCCT
*
10268961 TTGAAAAACCATT
1 GTGAAAAACCATT
10268974 TTGGATTATA
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
32 27 0.43
35 36 0.57
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (35 bp):
GTGAAAAACCATTGTTTTAGGTTGTGGTTGAGCCT
Found at i:10268918 original size:67 final size:67
Alignment explanation
Indices: 10268840--10269033 Score: 228
Period size: 67 Copynumber: 2.9 Consensus size: 67
10268830 AAGTTAATTG
* * ***
10268840 TTGGGTTTTGGTTGATCTCGTGAAAAACCATTGTTTTAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
10268905 CT
66 CT
10268907 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
*
10268972 TT
66 CT
* * * * ** * * * * *
10268974 TTGGATTATAGTTAAGCCCGAAAAAAACTACTGTAAAAGGTTTTGGCTGAGCC-TTGAAAA
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAA
10269034 GCCATTGTAA
Statistics
Matches: 110, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
66 7 0.06
67 103 0.94
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (67 bp):
TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
CT
Found at i:10268924 original size:32 final size:31
Alignment explanation
Indices: 10268878--10268974 Score: 122
Period size: 32 Copynumber: 3.0 Consensus size: 31
10268868 CATTGTTTTA
10268878 GGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
1 GGTTGTGGTTGAGCCTTTGAAAAACCA-TTTG
* **
10268910 GGTTTTGGTTGAGCCCGTGAAAAACCATTGTG
1 GGTTGTGGTTGAGCCTTTGAAAAACCATT-TG
10268942 AAAGGTTGTGGTTGAGCCTTTGAAAAACCATTT
1 ---GGTTGTGGTTGAGCCTTTGAAAAACCATTT
10268975 TGGATTATAG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
31 2 0.04
32 26 0.47
34 1 0.02
35 26 0.47
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (31 bp):
GGTTGTGGTTGAGCCTTTGAAAAACCATTTG
Found at i:10284097 original size:45 final size:43
Alignment explanation
Indices: 10283982--10284164 Score: 249
Period size: 43 Copynumber: 4.2 Consensus size: 43
10283972 TCTCCCTCAA
* * **
10283982 CTGGGTCATCATCAGCTCATGTGCACTCCTAAACCACACACGG
1 CTGGGTCATCATCAGCTCATGTGCACTCCTACACCGCACATAG
* *
10284025 TTGGGTCATCATCAGCTCATGTGCACTCCTACACCGCACATGG
1 CTGGGTCATCATCAGCTCATGTGCACTCCTACACCGCACATAG
*
10284068 CTGGGTCATCTCATCAGCTCATATGCACTCCTACACCGCACATAG
1 CTGGGTCA--TCATCAGCTCATGTGCACTCCTACACCGCACATAG
* * *
10284113 CTAGGTCATCATTAGCTCATGTGCACTCCTACACTGCACATAG
1 CTGGGTCATCATCAGCTCATGTGCACTCCTACACCGCACATAG
*
10284156 CTAGGTCAT
1 CTGGGTCAT
10284165 AATTATCACA
Statistics
Matches: 127, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
43 87 0.69
45 40 0.31
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (43 bp):
CTGGGTCATCATCAGCTCATGTGCACTCCTACACCGCACATAG
Found at i:10284139 original size:88 final size:87
Alignment explanation
Indices: 10283982--10284164 Score: 251
Period size: 88 Copynumber: 2.1 Consensus size: 87
10283972 TCTCCCTCAA
* * * *
10283982 CTGGGTCA-TCATCAGCTCATGTGCACTCCTAAACCACACACGGTTGGGTCATCATCAGCTCATG
1 CTGGGTCATTCATCAGCTCATATGCACTCCTAAACCACACACAGCTAGGTCATCATCAGCTCATG
*
10284046 TGCACTCCTACACCGCACATGG
66 TGCACTCCTACACCGCACATAG
* * * *
10284068 CTGGGTCATCTCATCAGCTCATATGCACTCCTACACCGCACATAGCTAGGTCATCATTAGCTCAT
1 CTGGGTCAT-TCATCAGCTCATATGCACTCCTAAACCACACACAGCTAGGTCATCATCAGCTCAT
*
10284133 GTGCACTCCTACACTGCACATAG
65 GTGCACTCCTACACCGCACATAG
*
10284156 CTAGGTCAT
1 CTGGGTCAT
10284165 AATTATCACA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 8 0.10
88 76 0.90
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (87 bp):
CTGGGTCATTCATCAGCTCATATGCACTCCTAAACCACACACAGCTAGGTCATCATCAGCTCATG
TGCACTCCTACACCGCACATAG
Found at i:10290709 original size:17 final size:19
Alignment explanation
Indices: 10290668--10290709 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
10290658 TTGTATATAT
10290668 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
10290689 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
10290706 ATGA
1 ATGA
10290710 TGTTGAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:10290763 original size:37 final size:37
Alignment explanation
Indices: 10290704--10290822 Score: 157
Period size: 37 Copynumber: 3.2 Consensus size: 37
10290694 TAATGTTGTG
* * *
10290704 TGATGATGTTGAAGTTTACGAGTAGGGAGTGCACACA
1 TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACA
* * * *
10290741 TAATGATGTTAGAGTGTGCGAGTCGGGAGTGCACCCA
1 TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACA
* *
10290778 TGATGTTGTTAAAGTGTGCAAGTAGGGAGTGCACACA
1 TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACA
10290815 TGATGATG
1 TGATGATG
10290823 ATATTGCATT
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.28, C:0.12, G:0.34, T:0.27
Consensus pattern (37 bp):
TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:10294032 original size:2 final size:2
Alignment explanation
Indices: 10294027--10294057 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10294017 TATATATATA
10294027 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
10294058 TATAGAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:10305786 original size:43 final size:43
Alignment explanation
Indices: 10305729--10305847 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
10305719 GTAATTATAT
* **
10305729 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGTCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
10305772 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
10305815 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
10305848 GAGCTGGTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.20
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:10305857 original size:43 final size:43
Alignment explanation
Indices: 10305739--10305860 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 43
10305729 TGACTCGGCT
* **
10305739 ATGTGCGAGTAGGGAGTGCGCATAAG-TCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCT-G-GTGATGACCCAGCC
* *
10305782 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAGCC
*
10305825 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGA
10305861 TGATGATGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.23, C:0.18, G:0.39, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAGCC
Found at i:10305908 original size:2 final size:2
Alignment explanation
Indices: 10305901--10305925 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10305891 GGTATGTATG
10305901 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 T
10305926 GTAAATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10308625 original size:35 final size:35
Alignment explanation
Indices: 10308583--10308690 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 35
10308573 GGAGTGCGTG
10308583 TGATGATATTGAAATGTAG-GTGAAGGGAGTACACA
1 TGATGATATTGAAATGT-GCGTGAAGGGAGTACACA
* * * *
10308618 TGGTGATATTAAAATGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGAAGGGAGTACACA
*** * * *
10308653 TGATGATATTGCCTTGTACGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGAAGGGAGTACACA
10308688 TGA
1 TGA
10308691 GCTGAGTAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
34 1 0.02
35 61 0.98
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCGTGAAGGGAGTACACA
Found at i:10325932 original size:36 final size:35
Alignment explanation
Indices: 10325884--10325955 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 35
10325874 TGTTGAATTT
*
10325884 AATTTCTATACACATTTAACTAATTAAAACTACCA
1 AATTTCTATACACATTTAACTAACTAAAACTACCA
10325919 ANATTTCTATACACATTTAACTAACTAAAACTACCA
1 A-ATTTCTATACACATTTAACTAACTAAAACTACCA
10325955 A
1 A
10325956 TTTAACTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (35 bp):
AATTTCTATACACATTTAACTAACTAAAACTACCA
Found at i:10339698 original size:35 final size:35
Alignment explanation
Indices: 10339659--10339735 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
10339649 GTAGGCAATA
10339659 CACATGATGATATTGAAATGCGCATGGAGAGAGTG
1 CACATGATGATATTGAAATGCGCATGGAGAGAGTG
*** * * *
10339694 CACATGATGATATTGCCTTGTGCATGTAGGGAGTG
1 CACATGATGATATTGAAATGCGCATGGAGAGAGTG
10339729 CACATGA
1 CACATGA
10339736 GCTGAGTAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (35 bp):
CACATGATGATATTGAAATGCGCATGGAGAGAGTG
Found at i:10339768 original size:2 final size:2
Alignment explanation
Indices: 10339761--10339788 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10339751 GGTGGTGTAC
10339761 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
10339789 GCTATAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10341500 original size:35 final size:34
Alignment explanation
Indices: 10341456--10341563 Score: 117
Period size: 35 Copynumber: 3.1 Consensus size: 34
10341446 GGAGTGTGTG
*
10341456 TGATGATATTGAAATGTGCATGTAGGTAGTACACA
1 TGATGATATTGAAATGTGCATGTAGG-AGTGCACA
* * *
10341491 TGATGATATTGAAATGTACGTATAGAGAGTGCACA
1 TGATGATATTGAAATGTGCATGTAG-GAGTGCACA
*** *
10341526 TGATGATATTGCCTTGTGCATGCAGGGAGTGCACA
1 TGATGATATTGAAATGTGCATGTA-GGAGTGCACA
10341561 TGA
1 TGA
10341564 GTTAAGTAAG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 58 0.97
36 2 0.03
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (34 bp):
TGATGATATTGAAATGTGCATGTAGGAGTGCACA
Found at i:10343327 original size:35 final size:35
Alignment explanation
Indices: 10343296--10343403 Score: 171
Period size: 35 Copynumber: 3.1 Consensus size: 35
10343286 GCAGTGCGTG
10343296 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
*
10343331 TGATGATATTGAAATGTGCGCGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
*** *
10343366 TGATGATATTGCCTTGTGCGTATAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
10343401 TGA
1 TGA
10343404 GCTGAGTAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.29
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
Found at i:10348442 original size:73 final size:72
Alignment explanation
Indices: 10348268--10348429 Score: 202
Period size: 73 Copynumber: 2.2 Consensus size: 72
10348258 TAAGTGTGCA
* * * * *
10348268 TCTTAGTCGATTAAGTTAGTTATATCTTCT-AATCCTATTTCTAGTAGTGAGCTCTTAGTCGACT
1 TCTTAGTCAATTAAGTTAATTCTGTC-TCTGAA-CCTATTTCTAGTAGTGAGCTCTTAGTCGACC
10348332 AACAAAACC
64 AACAAAACC
*
10348341 TCTTAGTCGATTAAGTTAATTCTGTCTCTGAACCTAGTTTCTAGTAGT-ATGCTCTTAGTCGACC
1 TCTTAGTCAATTAAGTTAATTCTGTCTCTGAACCTA-TTTCTAGTAGTGA-GCTCTTAGTCGACC
**
10348405 AACAATTCC
64 AACAAAACC
10348414 TCTTAGTCAATTAAGT
1 TCTTAGTCAATTAAGT
10348430 CGTCTTTGTC
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
72 8 0.10
73 71 0.90
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (72 bp):
TCTTAGTCAATTAAGTTAATTCTGTCTCTGAACCTATTTCTAGTAGTGAGCTCTTAGTCGACCAA
CAAAACC
Found at i:10350602 original size:39 final size:40
Alignment explanation
Indices: 10350518--10350622 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 40
10350508 GTGCCCTGTT
* *
10350518 TCTCGCTGCAGTGAGAAACATTCTATTTTTGCTGCTTGCAA
1 TCTCGTTGCAGTGAGAAACATTCT-GTTTTGCTGCTTGCAA
10350559 -CTCGTTGCAGTGAGAAACATTCTGTTTTGCCT-CTTG-AA
1 TCTCGTTGCAGTGAGAAACATTCTGTTTTG-CTGCTTGCAA
** *
10350597 TCTCGTTGCAACGAGAAACTTTCTGT
1 TCTCGTTGCAGTGAGAAACATTCTGT
10350623 CCTGCATGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.04
39 31 0.54
40 24 0.42
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (40 bp):
TCTCGTTGCAGTGAGAAACATTCTGTTTTGCTGCTTGCAA
Found at i:10353279 original size:21 final size:22
Alignment explanation
Indices: 10353255--10353350 Score: 94
Period size: 21 Copynumber: 4.6 Consensus size: 22
10353245 ATTCTGCCTG
*
10353255 ACTTTG-AATGATGGCATCAGT
1 ACTTTGTAATGAAGGCATCAGT
*
10353276 AC-TTGTAATGAAGGCATCTGT
1 ACTTTGTAATGAAGGCATCAGT
* *
10353297 -CTTTGTCATGAAGGCACCAGT
1 ACTTTGTAATGAAGGCATCAGT
* *
10353318 -CTTTGTCATGAAGGCACCAGT
1 ACTTTGTAATGAAGGCATCAGT
*
10353339 -CTTTGTCATGAA
1 ACTTTGTAATGAA
10353351 TTACATGAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
20 4 0.06
21 64 0.94
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (22 bp):
ACTTTGTAATGAAGGCATCAGT
Found at i:10358137 original size:20 final size:20
Alignment explanation
Indices: 10358101--10358138 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10358091 TCAATCATTA
*
10358101 GTTTCTTTCTCTATCTTTAT
1 GTTTCTTTCTATATCTTTAT
10358121 GTTTCTTT-TATATTCTTT
1 GTTTCTTTCTATA-TCTTT
10358139 GCCTTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (20 bp):
GTTTCTTTCTATATCTTTAT
Found at i:10359536 original size:55 final size:55
Alignment explanation
Indices: 10359451--10359600 Score: 237
Period size: 55 Copynumber: 2.7 Consensus size: 55
10359441 ATGTATACAA
* * * *
10359451 CCACCGGGTCATCAGCTCATGTACACTCCCACATCGCACATAGCTGGGATCATCAT
1 CCACC-GGTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAC
* *
10359507 CCACCGGTCATCAGCTCATGTGCACTCCCACACCTCACATAGTTGGAATCATCAC
1 CCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAC
10359562 CCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACA
1 CCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACA
10359601 CACACGATTA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 82 0.94
56 5 0.06
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (55 bp):
CCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAC
Found at i:10361594 original size:43 final size:43
Alignment explanation
Indices: 10361546--10361632 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
10361536 CCCACCACAC
*
10361546 TCAGCTCATGTGCACTCCCTAC-TCGCACATACCTAGGTCATCA
1 TCAGCTCATGTGCACTCCC-ACACCGCACATACCTAGGTCATCA
* *
10361589 TCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCCACACCGCACATACCTAGGTCATCA
10361632 T
1 T
10361633 TATCACACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 2 0.05
43 38 0.95
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCACACCGCACATACCTAGGTCATCA
Found at i:10362464 original size:21 final size:21
Alignment explanation
Indices: 10362431--10362482 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
10362421 TGAGATGGGA
*
10362431 GGAAGAATAAGAAAAAGCTACT
1 GGAA-AATGAGAAAAAGCTACT
* * **
10362453 GGAAAATGAGAAGATGCTGTT
1 GGAAAATGAGAAAAAGCTACT
10362474 GGAAAATGA
1 GGAAAATGA
10362483 TATTTATAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.48, C:0.06, G:0.29, T:0.17
Consensus pattern (21 bp):
GGAAAATGAGAAAAAGCTACT
Found at i:10368737 original size:43 final size:43
Alignment explanation
Indices: 10368689--10368771 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 43
10368679 CCACACTCAG
10368689 CTCATGTGCACTCCC-TACTCGCACATACCC-AGGTCATCATCAA
1 CTCATGTGCACTCCCATAC-CGCACATACCCGA-GTCATCATCAA
*
10368732 CTCATGTGCACTCCCATACCGCACATAGCCGAGTCATCAT
1 CTCATGTGCACTCCCATACCGCACATACCCGAGTCATCAT
10368772 TATCACACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
43 33 0.89
44 4 0.11
ACGTcount: A:0.25, C:0.39, G:0.13, T:0.23
Consensus pattern (43 bp):
CTCATGTGCACTCCCATACCGCACATACCCGAGTCATCATCAA
Found at i:10377091 original size:60 final size:60
Alignment explanation
Indices: 10376991--10377138 Score: 183
Period size: 60 Copynumber: 2.5 Consensus size: 60
10376981 CGAAATACAT
* *
10376991 TCTCGCTGCAGCGAGAAACTTTCTATTTCTAGGTAGCAATTTCACTACA-ACGAGATTGAA
1 TCTCGTTGCAGCGAGAAACTTTCTGTTTCTAGGTAGCAATTTCACTACAGA-GAGATTGAA
* * * ** *
10377051 TTTCGTTGCAGCGAGAAACATTCTGTTTCTGGGTTA-CAATTTTGCTGCAGAGAGATTGAA
1 TCTCGTTGCAGCGAGAAACTTTCTGTTTCTAGG-TAGCAATTTCACTACAGAGAGATTGAA
*
10377111 TCTCGTTGCAGCGAAAAACTTTCTGTTT
1 TCTCGTTGCAGCGAGAAACTTTCTGTTT
10377139 TGGTCTCCTA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
60 72 0.96
61 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (60 bp):
TCTCGTTGCAGCGAGAAACTTTCTGTTTCTAGGTAGCAATTTCACTACAGAGAGATTGAA
Found at i:10380410 original size:29 final size:28
Alignment explanation
Indices: 10380363--10380536 Score: 168
Period size: 29 Copynumber: 5.9 Consensus size: 28
10380353 GGCAGCTTTG
*
10380363 ACATGTTTGTCTTAATTTAGATAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
10380391 ACATGTTTGTTCTTAATTTAGACAAGAAA
1 ACATGTTTG-TCTTAATTTAGACAAGAAA
* *
10380420 ATATGTTTGCCTTAATTTAAGACAAGAAAA
1 ACATGTTTGTCTTAATTT-AGACAAG-AAA
* * *
10380450 ATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* * *
10380479 ACATATTTCTCTCAATTTAGACAAGATAAA
1 ACATGTTTGTCTTAATTTAGACAAG--AAA
* * *
10380509 ATATTTTTTGTCTTAATTACAGACAAGA
1 ACA-TGTTTGTCTTAATT-TAGACAAGA
10380537 GTTGTCTTAA
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
28 35 0.29
29 38 0.31
30 18 0.15
31 24 0.20
32 7 0.06
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:10380476 original size:59 final size:58
Alignment explanation
Indices: 10380363--10380536 Score: 201
Period size: 59 Copynumber: 3.0 Consensus size: 58
10380353 GGCAGCTTTG
* * * *
10380363 ACATGTTTGTCTTAATTTAGATAAG-AAAACA-TGTTTGTTCTTAATTTAGACAAGAAA
1 ACATGTTTGCCTTAATTTAGACAAGAAAAATATTTTTTG-TCTTAATTTAGACAAGAAA
* *
10380420 ATATGTTTGCCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATGTTTGCCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
10380479 ACATATTT-CTCTCAATTTAGACAAGATAAAATATTTTTTGTCTTAATTACAGACAAGA
1 ACATGTTTGC-CTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAATT-TAGACAAGA
10380537 GTTGTCTTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
57 16 0.16
58 15 0.15
59 57 0.57
60 12 0.12
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (58 bp):
ACATGTTTGCCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:10385421 original size:43 final size:43
Alignment explanation
Indices: 10385364--10385477 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
10385354 GTAATGATAT
* *
10385364 TGACTCGACTATGTGCGAGTAGGGAGTGCACATAAGCCGATGA
1 TGACTCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGATGA
* ** ** *
10385407 TGACTCGGTTATGTGCGAGTAAAGAGTGTGCATAACCCGGTGA
1 TGACTCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGATGA
* *
10385450 TGAC-CTAGCCATGTGCGAGTAGGGAGTG
1 TGACTC-GGCTATGTGCGAGTAGGGAGTG
10385478 TGCATGAGCT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 1 0.02
43 56 0.98
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (43 bp):
TGACTCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGATGA
Found at i:10385520 original size:23 final size:23
Alignment explanation
Indices: 10385491--10385545 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
10385481 ATGAGCTGGG
*
10385491 GATGATGGGATGGTTTGCATGAT
1 GATGATGGGATGGTGTGCATGAT
*
10385514 GATGATGGGATGGTGTGTATGAT
1 GATGATGGGATGGTGTGCATGAT
*
10385537 GATGTTGGG
1 GATGATGGG
10385546 TATATGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.02, G:0.44, T:0.35
Consensus pattern (23 bp):
GATGATGGGATGGTGTGCATGAT
Found at i:10393787 original size:37 final size:37
Alignment explanation
Indices: 10393746--10393851 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 37
10393736 TGGTGATGTT
* **
10393746 GAGTGTACGAGTAAGGAGTGCACACATGATGATGATG
1 GAGTGTGCGAGTAAGGAGTGCACACATGATGATGACA
*
10393783 GAGTGTGCGAGTAGGGAGTGCACACATGATGATGACA
1 GAGTGTGCGAGTAAGGAGTGCACACATGATGATGACA
* *
10393820 AAGTGTGCGAGTAAAGAGTGCACACATGATGA
1 GAGTGTGCGAGTAAGGAGTGCACACATGATGA
10393852 CAATATATGT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (37 bp):
GAGTGTGCGAGTAAGGAGTGCACACATGATGATGACA
Found at i:10398929 original size:17 final size:17
Alignment explanation
Indices: 10398907--10398939 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10398897 ATAATAATAA
10398907 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
10398924 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
10398940 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:10400295 original size:12 final size:12
Alignment explanation
Indices: 10400280--10400318 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
10400270 ATTTTTTAAA
10400280 ATATTATTATAT
1 ATATTATTATAT
*
10400292 ATATTCTTA-A-
1 ATATTATTATAT
10400302 ATATTATTATAT
1 ATATTATTATAT
10400314 ATATT
1 ATATT
10400319 CTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 13 0.57
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTATTATAT
Found at i:10400295 original size:24 final size:23
Alignment explanation
Indices: 10400263--10400326 Score: 103
Period size: 22 Copynumber: 2.8 Consensus size: 23
10400253 TATTTTAAAA
*
10400263 TATATATATTTTTTAAAATATTAT
1 TATATATA-TTCTTAAAATATTAT
10400287 TATATATATTCTT-AAATATTAT
1 TATATATATTCTTAAAATATTAT
10400309 TATATATATTCTTAAAAT
1 TATATATATTCTTAAAAT
10400327 TTTTTCAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
22 22 0.58
23 8 0.21
24 8 0.21
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATATATTCTTAAAATATTAT
Found at i:10401675 original size:71 final size:70
Alignment explanation
Indices: 10401559--10401699 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 70
10401549 GAACAAATGC
10401559 ACTCTAAATGGTGATAACTACATTGAATGGAAAAACAACCTTAATATCATCCTTAATTATGACAA
1 ACTCTAAATGGTGATAACTACATTGAATGGAAAAACAACCTTAATATCATCCTTAATTATGACAA
10401624 GATCA
66 GATCA
**
10401629 NACTCTAAATGGTGATAACTAC-TCTGAATGGAAAAGA-AACCTTAATATTGTCCTTAATTATGA
1 -ACTCTAAATGGTGATAACTACAT-TGAATGGAAAA-ACAACCTTAATATCATCCTTAATTATGA
10401692 CAAGATCA
63 CAAGATCA
10401700 CATGGGTTCT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
70 1 0.02
71 64 0.97
72 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.29
Consensus pattern (70 bp):
ACTCTAAATGGTGATAACTACATTGAATGGAAAAACAACCTTAATATCATCCTTAATTATGACAA
GATCA
Found at i:10402838 original size:20 final size:20
Alignment explanation
Indices: 10402813--10402850 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10402803 CTGTAGAAGC
10402813 AATACGATTTGAAATTGTAA
1 AATACGATTTGAAATTGTAA
10402833 AATACGATTTGAAATTGT
1 AATACGATTTGAAATTGT
10402851 CTAATTTTTA
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:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (20 bp):
AATACGATTTGAAATTGTAA
Found at i:10413298 original size:17 final size:17
Alignment explanation
Indices: 10413276--10413308 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10413266 ATAATAATAA
10413276 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
10413293 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
10413309 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:10417473 original size:60 final size:61
Alignment explanation
Indices: 10417399--10417579 Score: 208
Period size: 60 Copynumber: 3.0 Consensus size: 61
10417389 ACATCATCAA
* * * * * *
10417399 CTACTCATGGGAACTGCCCATGGCA-ACAGATGAATCGGGGCTTCAGGTCCCCCTTTTTAC
1 CTACTCGTGGGAACTACCCACGCCACACATATAAATCGGGGCTTCAGGTCCCCCTTTTTAC
* * *
10417459 CTACTCGTGGGAACTACCCACACCACCATATATAAATCGGGGCTTCAGGTCTCCC--TTTAC
1 CTACTCGTGGGAACTACCCACGCCA-CACATATAAATCGGGGCTTCAGGTCCCCCTTTTTAC
* *
10417519 CTACTCGTGGGAACTACCCACGCCATC-CAATATAAATCGAGGCTTCAGGTCCCCTTTTTTA
1 CTACTCGTGGGAACTACCCACGCCA-CAC-ATATAAATCGGGGCTTCAGGTCCCCCTTTTTA
10417580 AATCAAATAT
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
60 73 0.72
62 28 0.28
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (61 bp):
CTACTCGTGGGAACTACCCACGCCACACATATAAATCGGGGCTTCAGGTCCCCCTTTTTAC
Found at i:10417506 original size:62 final size:62
Alignment explanation
Indices: 10417431--10417579 Score: 232
Period size: 60 Copynumber: 2.4 Consensus size: 62
10417421 GCAACAGATG
10417431 AATCGGGGCTTCAGGTCCCCCTTTTTACCTACTCGTGGGAACTACCCACACCA-CCATATATA
1 AATCGGGGCTTCAGGTCCCCCTTTTTACCTACTCGTGGGAACTACCCACACCATCCA-ATATA
* *
10417493 AATCGGGGCTTCAGGTCTCCC--TTTACCTACTCGTGGGAACTACCCACGCCATCCAATATA
1 AATCGGGGCTTCAGGTCCCCCTTTTTACCTACTCGTGGGAACTACCCACACCATCCAATATA
* *
10417553 AATCGAGGCTTCAGGTCCCCTTTTTTA
1 AATCGGGGCTTCAGGTCCCCCTTTTTA
10417580 AATCAAATAT
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
60 52 0.66
61 3 0.04
62 24 0.30
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (62 bp):
AATCGGGGCTTCAGGTCCCCCTTTTTACCTACTCGTGGGAACTACCCACACCATCCAATATA
Found at i:10417950 original size:2 final size:2
Alignment explanation
Indices: 10417943--10417974 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
10417933 AAGCCTGTAG
10417943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10417975 AAGAAAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10419399 original size:20 final size:20
Alignment explanation
Indices: 10419374--10419420 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
10419364 AGAAAGAAGT
* * *
10419374 AAGAAAAGAAGGGAAATGAA
1 AAGAAAACAAGGAAAATCAA
10419394 AAGAAAACAAGGAAAATCAA
1 AAGAAAACAAGGAAAATCAA
*
10419414 ATGAAAA
1 AAGAAAA
10419421 AAAATTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.68, C:0.04, G:0.21, T:0.06
Consensus pattern (20 bp):
AAGAAAACAAGGAAAATCAA
Found at i:10428934 original size:33 final size:36
Alignment explanation
Indices: 10428851--10428979 Score: 140
Period size: 36 Copynumber: 3.7 Consensus size: 36
10428841 TCAACTCAAC
* * * *
10428851 TCATATGCACTCCCACACTGCACATCG-TTAATATCC
1 TCATGTGCACTCCCACACTGCACATGGCAT-ATATCA
* * *
10428887 TCATGTGCAGTCCCACATTGCACATGGCA-A-GT-A
1 TCATGTGCACTCCCACACTGCACATGGCATATATCA
*
10428920 TCATGTGCACTCCCACACCGCACATGGCATATATCA
1 TCATGTGCACTCCCACACTGCACATGGCATATATCA
*
10428956 TCATGCGCACTCCCACACTGCACA
1 TCATGTGCACTCCCACACTGCACA
10428980 CCACCATCAC
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
33 26 0.34
34 2 0.03
35 2 0.03
36 46 0.61
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (36 bp):
TCATGTGCACTCCCACACTGCACATGGCATATATCA
Found at i:10428970 original size:69 final size:69
Alignment explanation
Indices: 10428851--10428979 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 69
10428841 TCAACTCAAC
* * * * * *
10428851 TCATATGCACTCCCACACTGCACATCGTTAATATCCTCATGTGCAGTCCCACATTGCACATGGCA
1 TCATATGCACTCCCACACCGCACATCGATAATATCATCATGCGCACTCCCACACTGCACATGGCA
10428916 AGTA
66 AGTA
* *
10428920 TCATGTGCACTCCCACACCGCACATGGCAT-ATATCATCATGCGCACTCCCACACTGCACA
1 TCATATGCACTCCCACACCGCACATCG-ATAATATCATCATGCGCACTCCCACACTGCACA
10428980 CCACCATCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 50 0.98
70 1 0.02
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (69 bp):
TCATATGCACTCCCACACCGCACATCGATAATATCATCATGCGCACTCCCACACTGCACATGGCA
AGTA
Found at i:10429954 original size:60 final size:60
Alignment explanation
Indices: 10429890--10430005 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
10429880 AGATTGAATC
*
10429890 TCACTACAGTGAAATTTTAACCCA-GAAACAGA-AGGTTTCTCGCTGTAGCGAGATTCTTTA
1 TCACTACAGTGAAA-TTCAACCCATGAAACAGAGA-GTTTCTCGCTGTAGCGAGATTCTTTA
* ****
10429950 TCACTGCAGTGAAATTCAGTTGATGAAACAGAGAGTTTCTCGCTGTAGCGAGATTC
1 TCACTACAGTGAAATTCAACCCATGAAACAGAGAGTTTCTCGCTGTAGCGAGATTC
10430006 CTTTTTGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 4 0.08
60 43 0.90
61 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (60 bp):
TCACTACAGTGAAATTCAACCCATGAAACAGAGAGTTTCTCGCTGTAGCGAGATTCTTTA
Found at i:10430475 original size:43 final size:44
Alignment explanation
Indices: 10430374--10430476 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 44
10430364 CCCATCATCA
* ***
10430374 TCATCAC-CAGCTCATGCGCACTCCCTACTCGCACATAGTTGGG
1 TCATCACTCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
* *
10430417 TCATCACT-GGGTTATGCGCACTCCCTACTCGCACATAACCGGG
1 TCATCACTCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
10430460 TCATC-CTCAGCTTATGC
1 TCATCACTCAGCTTATGC
10430477 TGTAACGACC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.04
43 48 0.96
ACGTcount: A:0.20, C:0.36, G:0.18, T:0.25
Consensus pattern (44 bp):
TCATCACTCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
Found at i:10444042 original size:16 final size:16
Alignment explanation
Indices: 10444015--10444047 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10444005 ACACAACACT
10444015 ATATCAAACATATATGC
1 ATATCAAACATA-ATGC
10444032 ATATC-AACATAATGC
1 ATATCAAACATAATGC
10444047 A
1 A
10444048 GCCGCATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (16 bp):
ATATCAAACATAATGC
Found at i:10446259 original size:15 final size:14
Alignment explanation
Indices: 10446230--10446260 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
10446220 AAAAAAAGGA
10446230 AAGGAAAAGAAATG
1 AAGGAAAAGAAATG
10446244 AAGGAAAAGAAAATG
1 AAGGAAAAG-AAATG
10446259 AA
1 AA
10446261 AAAAAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (14 bp):
AAGGAAAAGAAATG
Found at i:10460241 original size:27 final size:27
Alignment explanation
Indices: 10460203--10460270 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
10460193 TTTGGTGGTG
10460203 AAAATTACGGTTTTACCTCAGG-GCGAC
1 AAAATTACGGTTTTACCTC-GGAGCGAC
* *
10460230 AAAATTATGGTTTTACCTCGGAGTGAC
1 AAAATTACGGTTTTACCTCGGAGCGAC
*
10460257 AAAATTACCGTTTT
1 AAAATTACGGTTTT
10460271 GCCCCTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (27 bp):
AAAATTACGGTTTTACCTCGGAGCGAC
Found at i:10462780 original size:14 final size:14
Alignment explanation
Indices: 10462763--10462792 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10462753 TTTTGCTTAA
*
10462763 AACGATTTGGAAAC
1 AACGACTTGGAAAC
10462777 AACGACTTGGAAAC
1 AACGACTTGGAAAC
10462791 AA
1 AA
10462793 GGTTCAATAA
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:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (14 bp):
AACGACTTGGAAAC
Found at i:10469703 original size:19 final size:19
Alignment explanation
Indices: 10469679--10469716 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
10469669 ACTTCTAAAC
10469679 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
10469698 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
10469717 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:10470884 original size:27 final size:27
Alignment explanation
Indices: 10470846--10470901 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
10470836 ACTTTTCCTT
* *
10470846 ATAATTTTTTTTATCACATTGAGGACA
1 ATAAATTTTTTTATCACATTAAGGACA
10470873 ATAAATTTTTTTATCACATTAAGGACA
1 ATAAATTTTTTTATCACATTAAGGACA
10470900 AT
1 AT
10470902 GTTTTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (27 bp):
ATAAATTTTTTTATCACATTAAGGACA
Found at i:10479316 original size:21 final size:20
Alignment explanation
Indices: 10479292--10479339 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
10479282 AATCTTACCT
10479292 TTTTTCACTTGTTTTCTTGAA
1 TTTTTCACTT-TTTTCTTGAA
*
10479313 TTTTCACACTTTTTTCTTGAA
1 TTTT-TCACTTTTTTCTTGAA
10479334 TTTTTC
1 TTTTTC
10479340 CACCTAGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.15, C:0.17, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTTTCACTTTTTTCTTGAA
Found at i:10479339 original size:22 final size:22
Alignment explanation
Indices: 10479297--10479337 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
10479287 TACCTTTTTT
10479297 CACTTGTTTTCTTGAATTTTCA
1 CACTTGTTTTCTTGAATTTTCA
10479319 CACTT-TTTTCTTGAATTTT
1 CACTTGTTTTCTTGAATTTT
10479338 TCCACCTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (22 bp):
CACTTGTTTTCTTGAATTTTCA
Found at i:10485532 original size:19 final size:19
Alignment explanation
Indices: 10485508--10485544 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
10485498 CCATTTGACT
10485508 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
10485527 TATTGGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
10485545 AGTTTAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:10496129 original size:28 final size:28
Alignment explanation
Indices: 10496098--10496157 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
10496088 TTTTAGAGCA
**
10496098 TAGGGGCAAAATGGTAATTTTGCCACC-C
1 TAGGGGCAAAACAGTAATTTT-CCACCAC
10496126 TAGGGGCAAAACAGTAATTTTCCACCAC
1 TAGGGGCAAAACAGTAATTTTCCACCAC
10496154 TAGG
1 TAGG
10496158 ACACTTATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (28 bp):
TAGGGGCAAAACAGTAATTTTCCACCAC
Found at i:10497839 original size:13 final size:13
Alignment explanation
Indices: 10497821--10497845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10497811 TTTCAGAAAA
10497821 TTTATAAAATCAT
1 TTTATAAAATCAT
10497834 TTTATAAAATCA
1 TTTATAAAATCA
10497846 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:10501159 original size:15 final size:14
Alignment explanation
Indices: 10501139--10501184 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
10501129 TTCTTAAAAC
10501139 AACTTTAAAATCGAA
1 AACTTTAAAATC-AA
10501154 AACTTTAAAATCCAA
1 AACTTTAAAAT-CAA
*
10501169 AGCTTTAAAATCAA
1 AACTTTAAAATCAA
10501183 AA
1 AA
10501185 TCTCTGATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 23 0.82
16 1 0.04
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (14 bp):
AACTTTAAAATCAA
Found at i:10503643 original size:19 final size:19
Alignment explanation
Indices: 10503619--10503655 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10503609 CTTCTAAACT
10503619 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
*
10503638 TCAAATCATATTCCAATA
1 TCAAATCATACTCCAATA
10503656 AGTCAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:10518322 original size:28 final size:28
Alignment explanation
Indices: 10518273--10518543 Score: 312
Period size: 29 Copynumber: 9.6 Consensus size: 28
10518263 TTGTCTTTAG
* * *
10518273 TTAAGACAAAACATGCTATCTTGTCTATA
1 TTAAGA-AAAACATGTTTTCTTGTCTAAA
* * *
10518302 TTGAGAGAAACATGTTTTCTTGTCTAGA
1 TTAAGAAAAACATGTTTTCTTGTCTAAA
* *
10518330 TTAAGATAAAATATATTTTCTTGTCTAAA
1 TTAAGA-AAAACATGTTTTCTTGTCTAAA
* *
10518359 TTTAGACAAAACATATTTTCTTGTCTAAA
1 TTAAGA-AAAACATGTTTTCTTGTCTAAA
*
10518388 TTAAGACAAACATGTTTTCTTGTCTAAA
1 TTAAGAAAAACATGTTTTCTTGTCTAAA
* *
10518416 TTAAG-ACAATATGTTTTCTTGTCTAAA
1 TTAAGAAAAACATGTTTTCTTGTCTAAA
10518443 TTAAGACAAAACATGTTTTCTTGTCTAAA
1 TTAAGA-AAAACATGTTTTCTTGTCTAAA
* *
10518472 TTAAG-ACAATATGTTTTCTTGTCTAAA
1 TTAAGAAAAACATGTTTTCTTGTCTAAA
* * *
10518499 TTAAGACAAACATTTTTTCTTGTTTAAA
1 TTAAGAAAAACATGTTTTCTTGTCTAAA
*
10518527 TTATGACAAAACATGTT
1 TTAAGA-AAAACATGTT
10518544 AAAGCTACTA
Statistics
Matches: 206, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
27 49 0.24
28 70 0.34
29 87 0.42
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (28 bp):
TTAAGAAAAACATGTTTTCTTGTCTAAA
Found at i:10518462 original size:84 final size:84
Alignment explanation
Indices: 10518273--10518543 Score: 373
Period size: 84 Copynumber: 3.2 Consensus size: 84
10518263 TTGTCTTTAG
* * * * * *
10518273 TTAAGACAAAACATGCTATCTTGTCTATATTGAGAGAAACATGTTTTCTTGTCTAGATTAAGATA
1 TTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAG--A
*
10518338 AAATATATTTTCTTGTCTAAA
64 CAATATATTTTCTTGTCTAAA
* *
10518359 TTTAGACAAAACATATTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACA
1 TTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACA
*
10518424 ATATGTTTTCTTGTCTAAA
66 ATATATTTTCTTGTCTAAA
*
10518443 TTAAGACAAAACATGTTTTCTTGTCTAAATTAAGAC-AATATGTTTTCTTGTCTAAATTAAGACA
1 TTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGAC-
* * *
10518507 AACATTTTTTCTTGTTTAAA
65 AATATATTTTCTTGTCTAAA
*
10518527 TTATGACAAAACATGTT
1 TTAAGACAAAACATGTT
10518544 AAAGCTACTA
Statistics
Matches: 167, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
83 26 0.16
84 87 0.52
86 54 0.32
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (84 bp):
TTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACA
ATATATTTTCTTGTCTAAA
Found at i:10523963 original size:37 final size:36
Alignment explanation
Indices: 10523906--10523975 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
10523896 CTTCCCTCAT
*
10523906 TTTTTTAATAAAAAATATTTTAATAG-AAGAAAAATA
1 TTTTTTAATAAAAAAAATTTTAAT-GTAAGAAAAATA
10523942 TTTTTT-ATAAAAATAGAATTTTAATGTAAGAAAA
1 TTTTTTAATAAAAA-A-AATTTTAATGTAAGAAAA
10523976 GCTTTTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 7 0.23
36 8 0.27
37 15 0.50
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (36 bp):
TTTTTTAATAAAAAAAATTTTAATGTAAGAAAAATA
Found at i:10523983 original size:37 final size:35
Alignment explanation
Indices: 10523904--10523984 Score: 85
Period size: 37 Copynumber: 2.2 Consensus size: 35
10523894 CCCTTCCCTC
*
10523904 ATTTTTTTAATAAAAAATATTTTAATAGAAGAAAA
1 ATTTTTTTAATAAAAAAAATTTTAATAGAAGAAAA
10523939 ATATTTTTT-ATAAAAATAGAATTTTAAT-GTAAGAAAA
1 AT-TTTTTTAATAAAAA-A-AATTTTAATAG-AAGAAAA
*
10523976 GCTTTTTTT
1 -ATTTTTTT
10523985 CTTTAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
35 9 0.23
36 8 0.21
37 21 0.54
38 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (35 bp):
ATTTTTTTAATAAAAAAAATTTTAATAGAAGAAAA
Found at i:10525361 original size:30 final size:30
Alignment explanation
Indices: 10525325--10525525 Score: 249
Period size: 30 Copynumber: 6.9 Consensus size: 30
10525315 AGACAACATG
* *
10525325 TTTTCTTGTCTAGATTATGACAAAACATAT
1 TTTTCTTGTCTAAATTAAGACAAAACATAT
*
10525355 TTTTCTTGTCTATATTAAGACAAAACATGA-
1 TTTTCTTGTCTAAATTAAGACAAAACAT-AT
*
10525385 -TTTCTTGTCTAAATTGAGAC---A-ATAT
1 TTTTCTTGTCTAAATTAAGACAAAACATAT
*
10525410 GTTTTCTTGTCTAGATTAAGACAAAACATAT
1 -TTTTCTTGTCTAAATTAAGACAAAACATAT
* *
10525441 TTTTCTTGTCTATATTAAGACAAAACAT-G
1 TTTTCTTGTCTAAATTAAGACAAAACATAT
10525470 TTTTCTTGTCTAAATTAAGAC-AAACATA-
1 TTTTCTTGTCTAAATTAAGACAAAACATAT
*
10525498 TTTTCTTGTATAAATTAAGACAAAACAT
1 TTTTCTTGTCTAAATTAAGACAAAACAT
10525526 GTTAAAGCTG
Statistics
Matches: 151, Mismatches: 10, Indels: 21
0.83 0.05 0.12
Matches are distributed among these distances:
24 1 0.01
25 2 0.01
26 1 0.01
27 18 0.12
28 26 0.17
29 44 0.29
30 54 0.36
31 5 0.03
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (30 bp):
TTTTCTTGTCTAAATTAAGACAAAACATAT
Found at i:10525404 original size:29 final size:29
Alignment explanation
Indices: 10525271--10525526 Score: 242
Period size: 29 Copynumber: 8.9 Consensus size: 29
10525261 TTAAGATGGC
* *
10525271 TCTTGTCTTTAATTAAGCCAAAACATG-TT
1 TCTTGTC-TAAATTAAGACAAAACATGATT
* ** *
10525300 ATCTTCTCTAAATCGAGAC--AACATGTTT
1 -TCTTGTCTAAATTAAGACAAAACATGATT
* *
10525328 TCTTGTCTAGATTATGACAAAACAT-ATTTT
1 TCTTGTCTAAATTAAGACAAAACATGA--TT
*
10525358 TCTTGTCTATATTAAGACAAAACATGATT
1 TCTTGTCTAAATTAAGACAAAACATGATT
* * *
10525387 TCTTGTCTAAATTGAGAC--AATATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGATT
*
10525414 TCTTGTCTAGATTAAGACAAAACAT-ATTTT
1 TCTTGTCTAAATTAAGACAAAACATGA--TT
* *
10525444 TCTTGTCTATATTAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGATT
10525473 TCTTGTCTAAATTAAGAC-AAACAT-ATTT
1 TCTTGTCTAAATTAAGACAAAACATGA-TT
*
10525501 TCTTGTATAAATTAAGACAAAACATG
1 TCTTGTCTAAATTAAGACAAAACATG
10525527 TTAAAGCTGC
Statistics
Matches: 186, Mismatches: 26, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
27 42 0.23
28 27 0.15
29 59 0.32
30 57 0.31
31 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAACATGATT
Found at i:10525427 original size:86 final size:85
Alignment explanation
Indices: 10525271--10525525 Score: 375
Period size: 86 Copynumber: 2.9 Consensus size: 85
10525261 TTAAGATGGC
* * * *
10525271 TCTTGTCTTTAATTAAGCCAAAACATGTTATCTTCTCTAAATCGAGACAACATGTTTTCTTGTCT
1 TCTTGTCTAT-ATTAAGACAAAACATGTT-TCTTGTCTAAATTGAGACAACATGTTTTCTTGTCT
*
10525336 AGATTATGACAAAACATATTTT
64 AGATTAAGACAAAACATATTTT
*
10525358 TCTTGTCTATATTAAGACAAAACATGATTTCTTGTCTAAATTGAGACAATATGTTTTCTTGTCTA
1 TCTTGTCTATATTAAGACAAAACATG-TTTCTTGTCTAAATTGAGACAACATGTTTTCTTGTCTA
10525423 GATTAAGACAAAACATATTTT
65 GATTAAGACAAAACATATTTT
* * *
10525444 TCTTGTCTATATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATATTTTCTTGTAT
1 TCTTGTCTATATTAAGACAAAACATG-TTTCTTGTCTAAATTGAGAC-AACATGTTTTCTTGTCT
*
10525509 AAATTAAGACAAAACAT
64 AGATTAAGACAAAACAT
10525526 GTTAAAGCTG
Statistics
Matches: 154, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
86 113 0.73
87 41 0.27
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (85 bp):
TCTTGTCTATATTAAGACAAAACATGTTTCTTGTCTAAATTGAGACAACATGTTTTCTTGTCTAG
ATTAAGACAAAACATATTTT
Found at i:10525527 original size:57 final size:58
Alignment explanation
Indices: 10525271--10525528 Score: 294
Period size: 57 Copynumber: 4.5 Consensus size: 58
10525261 TTAAGATGGC
* * * * ** *
10525271 TCTTGTCTTTAATTAAGCCAAAACATGTTATCTTCTCTAAATCGAGAC--AACATGTTT
1 TCTTGTC-TAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAACATATTT
* * * *
10525328 TCTTGTCTAGATTATGACAAAACATATTTTTCTTGTCTATATTAAGACAAAACATGA-TT
1 TCTTGTCTAAATTAAGACAAAACAT-GTTTTCTTGTCTAAATTAAGACAAAACAT-ATTT
* * *
10525387 TCTTGTCTAAATTGAGAC--AATATGTTTTCTTGTCTAGATTAAGACAAAACATATTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAACATA-TTT
*
10525444 TCTTGTCTATATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGAC-AAACATATTT
1 TCTTGTCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAACATATTT
*
10525501 TCTTGTATAAATTAAGACAAAACATGTT
1 TCTTGTCTAAATTAAGACAAAACATGTT
10525529 AAAGCTGCCA
Statistics
Matches: 170, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
55 1 0.01
56 41 0.24
57 74 0.44
58 7 0.04
59 47 0.28
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (58 bp):
TCTTGTCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAACATATTT
Found at i:10534628 original size:12 final size:12
Alignment explanation
Indices: 10534611--10534635 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10534601 AAGAAAATGG
10534611 AATATTTTATTT
1 AATATTTTATTT
10534623 AATATTTTATTT
1 AATATTTTATTT
10534635 A
1 A
10534636 GTTTGATTAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATATTTTATTT
Found at i:10535486 original size:21 final size:21
Alignment explanation
Indices: 10535407--10535495 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 21
10535397 TTGAATGGAG
*
10535407 GCATCAGTCCTTATCATAAAT
1 GCATCAGTCTTTATCATAAAT
* * * *
10535428 GAATTAGTC-TTAGTTATGAAT
1 GCATCAGTCTTTA-TCATAAAT
* *
10535449 GCATTAGTTTTTATCATAAAT
1 GCATCAGTCTTTATCATAAAT
* *
10535470 GCATCAGTCTTTGTCATGAATT
1 GCATCAGTCTTTATCAT-AAAT
10535492 GCAT
1 GCAT
10535496 GAACATATCT
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.06
21 40 0.75
22 10 0.19
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
GCATCAGTCTTTATCATAAAT
Found at i:10538854 original size:43 final size:43
Alignment explanation
Indices: 10538784--10538902 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
10538774 GTAATTATGT
* *
10538784 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
10538827 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
10538870 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
10538903 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:10538912 original size:43 final size:43
Alignment explanation
Indices: 10538794--10538915 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
10538784 TGACTCGGCT
* **
10538794 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
10538837 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
10538880 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
10538916 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:10538926 original size:20 final size:20
Alignment explanation
Indices: 10538901--10538963 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
10538891 GGGAGTGCGC
10538901 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
10538921 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
10538941 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
10538960 ATGA
1 ATGA
10538964 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:10544526 original size:17 final size:18
Alignment explanation
Indices: 10544497--10544535 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
10544487 AGATTTGGCT
10544497 ATTTTTTGAAAAGCTAAC
1 ATTTTTTGAAAAGCTAAC
*
10544515 ATTTTTTG-AAAGCTAAG
1 ATTTTTTGAAAAGCTAAC
10544532 ATTT
1 ATTT
10544536 AAGTAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (18 bp):
ATTTTTTGAAAAGCTAAC
Found at i:10555367 original size:43 final size:43
Alignment explanation
Indices: 10555306--10555393 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
10555296 TGCAATATCA
* *
10555306 TCATCATCAGCTCATGTGCATTCCCACACCCCACATAGCTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACCCCACATAGCTAGG
*
10555349 TCATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGG
1 TCATCATCAGCTCATGTGCACTCCCACACCCCACATAGCTAGG
10555392 TC
1 TC
10555394 CTCAGTGTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.23
Consensus pattern (43 bp):
TCATCATCAGCTCATGTGCACTCCCACACCCCACATAGCTAGG
Found at i:10560561 original size:42 final size:42
Alignment explanation
Indices: 10560474--10560648 Score: 255
Period size: 42 Copynumber: 4.1 Consensus size: 42
10560464 ACCATCCCAC
** *
10560474 CATCATCAGCTCATGTGCACTCCCTAGTCGCACATAAC-AGGGT
1 CATCATCAGCTCATGTGCACTCCC-ACACGCACATAGCTA-GGT
*
10560517 CATCATCAGGTCATGTGCACT-CCACACCGCACATAGCTAGGT
1 CATCATCAGCTCATGTGCACTCCCACA-CGCACATAGCTAGGT
*
10560559 CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGGT
*
10560601 CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGGT
10560643 CATCAT
1 CATCAT
10560649 TATCACAAAA
Statistics
Matches: 123, Mismatches: 6, Indels: 7
0.90 0.04 0.05
Matches are distributed among these distances:
41 1 0.01
42 96 0.78
43 26 0.21
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.22
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGGT
Found at i:10577598 original size:16 final size:16
Alignment explanation
Indices: 10577573--10577605 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10577563 GGGGAGGAGT
10577573 ATGGTAGAACCTTAGG
1 ATGGTAGAACCTTAGG
*
10577589 ATGGTTGAACCTTAGG
1 ATGGTAGAACCTTAGG
10577605 A
1 A
10577606 AACTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (16 bp):
ATGGTAGAACCTTAGG
Found at i:10577821 original size:21 final size:21
Alignment explanation
Indices: 10577792--10577840 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
10577782 GAAAAATGGA
10577792 TGCTGATATGTTTATGGTATTT
1 TGCT-ATATGTTTATGGTATTT
10577814 TGCTATATGTTTATGGTATTT
1 TGCTATATGTTTATGGTATTT
*
10577835 TACTAT
1 TGCTAT
10577841 TGAAAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.20, C:0.06, G:0.18, T:0.55
Consensus pattern (21 bp):
TGCTATATGTTTATGGTATTT
Found at i:10591757 original size:2 final size:2
Alignment explanation
Indices: 10591750--10591793 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
10591740 TTGGGAACGT
10591750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10591792 TA
1 TA
10591794 CTTGGTTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10596210 original size:21 final size:21
Alignment explanation
Indices: 10596186--10596229 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
10596176 AGATTAACTT
10596186 ATCTATCGATAAATGAATAAC
1 ATCTATCGATAAATGAATAAC
* * *
10596207 ATCTATTGATAGATTAATAAC
1 ATCTATCGATAAATGAATAAC
10596228 AT
1 AT
10596230 TTTTCAAATT
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:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTATCGATAAATGAATAAC
Found at i:10598539 original size:22 final size:23
Alignment explanation
Indices: 10598509--10598563 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
10598499 TGCTTCTTAA
* *
10598509 AAACTAGTCACGCAATGCCTATC
1 AAACTAGTCACACAATGCCCATC
10598532 AAAC-AGTCACACAATGCCCATC
1 AAACTAGTCACACAATGCCCATC
*
10598554 -AACTGGTCAC
1 AAACTAGTCAC
10598564 GTAATCACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 21 0.75
23 4 0.14
ACGTcount: A:0.36, C:0.33, G:0.13, T:0.18
Consensus pattern (23 bp):
AAACTAGTCACACAATGCCCATC
Found at i:10598675 original size:23 final size:23
Alignment explanation
Indices: 10598625--10598675 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
10598615 CTAAGTCTTG
10598625 CAATG-CCTACCAACCAGTCACA
1 CAATGCCCTACCAACCAGTCACA
* *
10598647 -ATATGCCCTATCAACTAGTCACA
1 CA-ATGCCCTACCAACCAGTCACA
10598670 CAATGC
1 CAATGC
10598676 ATAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 3 0.12
23 19 0.79
24 1 0.04
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.20
Consensus pattern (23 bp):
CAATGCCCTACCAACCAGTCACA
Found at i:10599598 original size:304 final size:304
Alignment explanation
Indices: 10599046--10599651 Score: 738
Period size: 304 Copynumber: 2.0 Consensus size: 304
10599036 ATAATATAAT
*
10599046 TAGTAACTGGTTGTCTGAATCGAAAACATAAAAAAAGTTACAAACATTAGTCTCAACACTATTAG
1 TAGTAACTAGTTGTCTGAATCGAAAACATAAAAAAAGTTACAAACATTAGTCTCAACACTATTAG
* * * * *
10599111 CAATACTCTTTAGTGCATAACTTTTCTTCGGCCCTTCAATGGCGTCCTTCCTCAAGGTCTAGTTA
66 CAAAACTCTCTAGTGCATAACTTTTCCTCAGCCCTTCAATAGCGTCCTTCCTCAAGGTCTAGTTA
* * * ** ** * *
10599176 TCGGCACCAATCAACCACTTTATAGTAGTGATTACACAATCCCCGTAAGTGTTTCCATCCTCTTG
131 CCGACACCAATCAACCACTCTATACCAACGATTACACAATCCCCGCAAGTGTTTCCATCCTCCTG
** * * ** *
10599241 TACTGGTGTTTCATGATTTAATTGCCTGCTCATCGGCTTCCAAGGTAATTTTTTATGATGCGCCT
196 TACAAGTGTTTCATGATTAAATTGCCTACTCATCCACGTCCAAGGTAATTTTTTATGATGCGCCT
*
10599306 AGTCAAAGTACTTGGACT-GGTGGCATATATTGGGAAACAATGCG
261 AGTCAAAGTACTTGGACTAGG-GGCATATAATGGGAAACAATGCG
* * * * * *
10599350 TAGTAACTAGTTGTGTGAATTGAAAACATAAACAAAGTTATAAAC-TTAAGTCTTAACCCTATTA
1 TAGTAACTAGTTGTCTGAATCGAAAACATAAAAAAAGTTACAAACATT-AGTCTCAACACTATTA
* * * * *
10599414 GCAAAAGTCTCTAGTGCATAACTTTTCCTCAGCCTTTTACTAGCGTCCTTCCTTAAGGTCTAG-T
65 GCAAAACTCTCTAGTGCATAACTTTTCCTCAGCCCTTCAATAGCGTCCTTCCTCAAGGTCTAGTT
* ** * * * *
10599478 AGCCTACACTGATCAGCCACTCTATACCAACGATTAC-CTAATCCTCGCAAGTG-TTCTAGTTCT
130 A-CCGACACCAATCAACCACTCTATACCAACGATTACAC-AATCCCCGCAAGTGTTTCCA-TCCT
*
10599541 CCTGTACCAAG-GTTTCATGATTAAATTGCCTACTCATCCACGTCCAAGGTCATTTTTTATGATG
192 CCTGTA-CAAGTGTTTCATGATTAAATTGCCTACTCATCCACGTCCAAGGTAATTTTTTATGATG
10599605 CGCCTAGTCAAAGTACTTGGACTAGGGGCATATAATGGGAAACAATG
256 CGCCTAGTCAAAGTACTTGGACTAGGGGCATATAATGGGAAACAATG
10599652 TGATTCGGGG
Statistics
Matches: 254, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
303 9 0.04
304 241 0.95
305 4 0.02
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (304 bp):
TAGTAACTAGTTGTCTGAATCGAAAACATAAAAAAAGTTACAAACATTAGTCTCAACACTATTAG
CAAAACTCTCTAGTGCATAACTTTTCCTCAGCCCTTCAATAGCGTCCTTCCTCAAGGTCTAGTTA
CCGACACCAATCAACCACTCTATACCAACGATTACACAATCCCCGCAAGTGTTTCCATCCTCCTG
TACAAGTGTTTCATGATTAAATTGCCTACTCATCCACGTCCAAGGTAATTTTTTATGATGCGCCT
AGTCAAAGTACTTGGACTAGGGGCATATAATGGGAAACAATGCG
Found at i:10600723 original size:57 final size:57
Alignment explanation
Indices: 10600617--10600724 Score: 126
Period size: 57 Copynumber: 1.9 Consensus size: 57
10600607 TCTCCCACTA
* * ** * * *
10600617 GATCTCTAGCTGCATTGACTTTATCTACAGTTGCATATCTTGCTGGATCTCATGTTG
1 GATCTCAAACTGCATTGACTGCATCTACAGTTGCATATCCTACTAGATCTCATGTTG
* * *
10600674 GATCTCAAACTGCATTGACTGCATTTATAGTTGCATATCCTATTAGATCTC
1 GATCTCAAACTGCATTGACTGCATCTACAGTTGCATATCCTACTAGATCTC
10600725 CAATTATAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
57 41 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (57 bp):
GATCTCAAACTGCATTGACTGCATCTACAGTTGCATATCCTACTAGATCTCATGTTG
Found at i:10604019 original size:60 final size:60
Alignment explanation
Indices: 10603932--10604085 Score: 175
Period size: 60 Copynumber: 2.6 Consensus size: 60
10603922 ACCAAAACAA
* * ** * * *
10603932 AAAGTTTTTCGCTGCAGGGAGATTGAATCTCACTGTAGCGAAATTGTGACCCA-AAAACAG
1 AAAGTTTCTCGCTACAGCAAGAATGAATTTCACTGTAGCGAAATTGTAACCCAGAAAA-AG
* **
10603992 AATGTTTCTCGCTACAGCAAGAATGAATTTTGCTGTAGCGAAATTGTAACCCAGAAAAAG
1 AAAGTTTCTCGCTACAGCAAGAATGAATTTCACTGTAGCGAAATTGTAACCCAGAAAAAG
* * *
10604052 AAAGTTTCTCGCTGCAGCGAGACTGAATTTCACT
1 AAAGTTTCTCGCTACAGCAAGAATGAATTTCACT
10604086 ACAGCAAGAA
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 73 0.95
61 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (60 bp):
AAAGTTTCTCGCTACAGCAAGAATGAATTTCACTGTAGCGAAATTGTAACCCAGAAAAAG
Found at i:10604354 original size:2 final size:2
Alignment explanation
Indices: 10604342--10604375 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
10604332 ACCATATACC
* *
10604342 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10604376 CAATCATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10609167 original size:37 final size:37
Alignment explanation
Indices: 10609126--10609272 Score: 285
Period size: 37 Copynumber: 4.0 Consensus size: 37
10609116 ATGATGTTGA
10609126 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
10609163 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
*
10609200 AGTGTGCAAGTAGGGAGTGCACACATGATGATGATAG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
10609237 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
10609273 TTGCATTGAG
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 108 1.00
ACGTcount: A:0.31, C:0.11, G:0.37, T:0.22
Consensus pattern (37 bp):
AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
Found at i:10619788 original size:42 final size:42
Alignment explanation
Indices: 10619739--10619854 Score: 142
Period size: 42 Copynumber: 2.8 Consensus size: 42
10619729 TGTTGATGTG
* * **
10619739 GACCCGGCTATGTGCGAGTAGGAGTGCACATGAGCTGTTGAT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTGAT
* *
10619781 GACCCGGCTATGTGCAAGTGGGAGTGCACATAAGCCATTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTGAT
* ** *
10619823 AACCCCACTATGTGCGAGTGGGAATGCACATA
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATA
10619855 TGCCGTTGCA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTGAT
Found at i:10619911 original size:2 final size:2
Alignment explanation
Indices: 10619904--10619956 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
10619894 ATGATGATTG
10619904 AT AT AT AT NAT 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
*
10619947 AT AC AT AT AT
1 AT AT AT AT AT
10619957 GGTATATGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10631283 original size:20 final size:20
Alignment explanation
Indices: 10631260--10631313 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 20
10631250 ATATAAATGA
10631260 AAAATATACATTTCA-TATCT
1 AAAATATACATTT-AGTATCT
*
10631280 AAAA-ATAAATTTAGGTATCT
1 AAAATATACATTTA-GTATCT
10631300 -AAATCATACATTTA
1 AAAAT-ATACATTTA
10631314 AATTGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.04
19 10 0.36
20 9 0.32
21 8 0.29
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (20 bp):
AAAATATACATTTAGTATCT
Found at i:10642208 original size:13 final size:13
Alignment explanation
Indices: 10642190--10642215 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10642180 GAAGCTACTC
10642190 TTCCCAAACTTCT
1 TTCCCAAACTTCT
10642203 TTCCCAAACTTCT
1 TTCCCAAACTTCT
10642216 AAACATGCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
TTCCCAAACTTCT
Found at i:10650730 original size:26 final size:26
Alignment explanation
Indices: 10650670--10650731 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
10650660 ACCATATACC
*
10650670 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
10650696 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
10650722 CATCATCATC
1 CATCATCATC
10650732 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:10651024 original size:42 final size:42
Alignment explanation
Indices: 10650966--10651089 Score: 212
Period size: 42 Copynumber: 3.0 Consensus size: 42
10650956 ATGGGGGCAA
* *
10650966 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
10651008 CAACGGCTTATATGCACTCCTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
10651050 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
10651090 CAAATCAACA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.22
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:10653781 original size:37 final size:37
Alignment explanation
Indices: 10653731--10653923 Score: 250
Period size: 37 Copynumber: 5.2 Consensus size: 37
10653721 AATGCAATAT
* *
10653731 CATCATCTTGTGTGCACTCCCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
* *
10653768 TATCATCATGTGTGCACTTCCC-ACACGCACAC-TCTAA
1 CATCATCATGTGTGCAC-TCCCTACTCGCACACTTC-AA
10653805 CATCATCATGTGTGCACTTCCC-ACTCGCACAC-TCTAA
1 CATCATCATGTGTGCAC-TCCCTACTCGCACACTTC-AA
* *
10653842 CATCATCATGTGTGCACTCCTTACTCGTACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
* *
10653879 CATCATCATGTGTGCATTCCCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
10653916 CATCATCA
1 CATCATCA
10653924 CACAACATTA
Statistics
Matches: 140, Mismatches: 12, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
36 5 0.04
37 129 0.92
38 6 0.04
ACGTcount: A:0.26, C:0.36, G:0.09, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:10655264 original size:29 final size:32
Alignment explanation
Indices: 10655208--10655296 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 32
10655198 CTCTATGGAA
*
10655208 TTGGGATTCGATATTTGTTTTGACTTTGGACT
1 TTGGAATTCGATATTTGTTTTGACTTTGGACT
* *
10655240 TTGGAATT-GATA-TTG-TTTGATTTTGGATT
1 TTGGAATTCGATATTTGTTTTGACTTTGGACT
* * * *
10655269 TTGG-TTTTGGTATTTGTTTAGACTTTGG
1 TTGGAATTCGATATTTGTTTTGACTTTGG
10655297 TTTTTGAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 2 0.04
29 19 0.40
30 6 0.13
31 13 0.28
32 7 0.15
ACGTcount: A:0.16, C:0.04, G:0.26, T:0.54
Consensus pattern (32 bp):
TTGGAATTCGATATTTGTTTTGACTTTGGACT
Found at i:10655812 original size:24 final size:22
Alignment explanation
Indices: 10655760--10655808 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
10655750 ATAAATATCA
10655760 TTTTCCAGCAGCTTTTTCTCAT
1 TTTTCCAGCAGCTTTTTCTCAT
10655782 TTTTCCAGCAGCTTCTTT-TC-T
1 TTTTCCAGCAGCTT-TTTCTCAT
10655803 TTTTCC
1 TTTTCC
10655809 TCCAATCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.27
22 16 0.62
23 3 0.12
ACGTcount: A:0.10, C:0.29, G:0.08, T:0.53
Consensus pattern (22 bp):
TTTTCCAGCAGCTTTTTCTCAT
Found at i:10656672 original size:54 final size:54
Alignment explanation
Indices: 10656591--10656769 Score: 295
Period size: 54 Copynumber: 3.3 Consensus size: 54
10656581 AAAACATTTT
*
10656591 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAT
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
10656645 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
** * * * *
10656699 ATCTCACTTAACTCATGTGCATCCCACCATATCGTGCACATAGTCAGACACCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
10656753 ATCTCACCCAGCTCATG
1 ATCTCACCCAGCTCATG
10656770 CACGGTTACA
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 115 1.00
ACGTcount: A:0.27, C:0.40, G:0.13, T:0.20
Consensus pattern (54 bp):
ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
Found at i:10663351 original size:29 final size:28
Alignment explanation
Indices: 10663310--10663461 Score: 173
Period size: 28 Copynumber: 5.3 Consensus size: 28
10663300 GACAGCTTTG
*
10663310 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAA
*
10663338 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATATTT-GTCTTAATTTAGACAAGAAA
* *
10663367 ATATATTTGCCTTAATTTAAGACAAGAAA
1 ACATATTTGTCTTAATTT-AGACAAGAAA
* *
10663396 A-ATATTTTTTGTCTTAATGTAGTCAAGAAA
1 ACATA---TTTGTCTTAATTTAGACAAGAAA
*
10663426 ACATATTTGTCTCAATTTAGACAAGATAA
1 ACATATTTGTCTTAATTTAGACAAGA-AA
10663455 A-ATATTT
1 ACATATTT
10663462 TTTGTCTTAA
Statistics
Matches: 108, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
28 44 0.41
29 40 0.37
30 10 0.09
31 14 0.13
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
ACATATTTGTCTTAATTTAGACAAGAAA
Found at i:10663423 original size:59 final size:58
Alignment explanation
Indices: 10663310--10663472 Score: 220
Period size: 59 Copynumber: 2.8 Consensus size: 58
10663300 GACAGCTTTG
* * * * *
10663310 ACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATGTAGACAAGAAA
* * *
10663367 ATATATTTGCCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATGTAGTCAAGAAA
1 ACATATTTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATGTAGACAAGAAA
*
10663426 ACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTTGTCTTAAT
1 ACATATTTGTCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAAT
10663473 TACAGACAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 15 0.16
58 15 0.16
59 62 0.67
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (58 bp):
ACATATTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATGTAGACAAGAAA
Found at i:10663647 original size:17 final size:17
Alignment explanation
Indices: 10663625--10663657 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10663615 ATAATAATAA
10663625 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
10663642 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
10663658 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:10664684 original size:33 final size:33
Alignment explanation
Indices: 10664647--10664713 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
10664637 TTTTTATGAC
* *
10664647 TATTTTTTT-GGAAAAATGAGTTTTTCTTGTATT
1 TATTTTTTTAAGAAAAA-GAGTTTTTCTTATATT
10664680 TATTTTTTTAAAGAAAAAGAGTTTTTCTTATATT
1 TATTTTTTT-AAGAAAAAGAGTTTTTCTTATATT
10664714 AAAATTCTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 9 0.30
34 15 0.50
35 6 0.20
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (33 bp):
TATTTTTTTAAGAAAAAGAGTTTTTCTTATATT
Found at i:10665369 original size:2 final size:2
Alignment explanation
Indices: 10665362--10665394 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
10665352 TGTGGCTTAT
*
10665362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10665395 TTTATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:10686468 original size:25 final size:25
Alignment explanation
Indices: 10686439--10686494 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
10686429 TCACAACCAC
**
10686439 GTATATCAACTTGTGGCCTAGCCAA
1 GTATATCAACCCGTGGCCTAGCCAA
* * *
10686464 GTATATCATCCCGTGGCCTTGCCAC
1 GTATATCAACCCGTGGCCTAGCCAA
10686489 GTATAT
1 GTATAT
10686495 ATATCACAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (25 bp):
GTATATCAACCCGTGGCCTAGCCAA
Done.