Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 332 of 438
Found at i:104084518 original size:20 final size:19
Alignment explanation
Indices: 104084473--104084510 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
104084463 CATCCAAACA
104084473 CCAGAAAAGTAAACTATTT
1 CCAGAAAAGTAAACTATTT
*
104084492 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAACTATTT
104084511 TCTAGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (19 bp):
CCAGAAAAGTAAACTATTT
Found at i:104085072 original size:44 final size:43
Alignment explanation
Indices: 104085007--104085090 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 43
104084997 TTTTTAAAGG
*
104085007 TTAAACTTATCATTATCAA-TTTATATTTTTAACATTATTTTAAC
1 TTAAACTTATCATTATCAATTTTA-ATTTTTAA-ATAATTTTAAC
* *
104085051 TTAATCTTATACA-TATGAATTTTAATTTTTAAATAATTTT
1 TTAAACTTAT-CATTATCAATTTTAATTTTTAAATAATTTT
104085091 GTTATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
43 7 0.20
44 22 0.63
45 6 0.17
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (43 bp):
TTAAACTTATCATTATCAATTTTAATTTTTAAATAATTTTAAC
Found at i:104085432 original size:16 final size:16
Alignment explanation
Indices: 104085411--104085443 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
104085401 TATCATTATT
*
104085411 ATTTATTAGCTTTTAA
1 ATTTATTAGATTTTAA
104085427 ATTTATTAGATTTTAA
1 ATTTATTAGATTTTAA
104085443 A
1 A
104085444 AAATAAATTT
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:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTTATTAGATTTTAA
Found at i:104086563 original size:126 final size:126
Alignment explanation
Indices: 104086109--104086757 Score: 815
Period size: 126 Copynumber: 5.2 Consensus size: 126
104086099 GTTTTGTTTT
* * * * *
104086109 TTTTTCTATAGTAGTT-TCTGAAAAATTAATGTTGAGAAGACGGTTTTGAAAAGATAATGTCAAA
1 TTTTTCTACAGTAGTTCT-TGAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGTCAAA
* * * * * *
104086173 AACGCTTCAAACAAGATGCATTATCAGCAAAATTACTGAAAAAGGCTCCCACGTGGATGCTC
65 AACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTTAAAAAAGCTCCCACGTGGACGCTC
* * * *
104086235 TTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTGTAAAAAAATTAGTGTCAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAA-TAGTGTCAAA
* *
104086300 AACGCTTCAAGCATGATGCATTGTCAGCAAAATTA-TTGAAAAAAGCTCCCACGTGGACGCTC
65 AACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTT-AAAAAAGCTCCCACGTGGACGCTC
* * * *
104086362 TTTTTCTATAGTAGTTCCT-AAAAAATAATTTTAAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGTCAAAA
** * * *
104086426 ATACTTCAAGCAGGATGCACTGTCAGCAAAATTACTTAAAAAAGCTCCCATGTGGACGCTT
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTTAAAAAAGCTCCCACGTGGACGCTC
* *
104086487 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAGTGTTAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGTCAAAA
* *** * *
104086552 ACGCTTCAAGCAAGATGCACTGTCAGTAAAATTACAGGAAAAAGCTCCCACGTGGACACTT
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTTAAAAAAGCTCCCACGTGGACGCTC
* * *
104086613 TTTTTCTACTGTAGATCTTGAAAAAATAATTTTGAGAAGA--GTATTCTGAAAAAATAGTGTAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGT-TT-TGAAAAAATAGTGTCAA
* * * * * * *
104086676 AAACACTTCAAGCAAGATTCACTGTCAGCAAAATTAC-TAAAAAACCTTCCACATGGATGCAC
64 AAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTTAAAAAAGCTCCCACGTGGACGCTC
104086738 TTTTTCTACAGTAGTTCTTG
1 TTTTTCTACAGTAGTTCTTG
104086758 CTTGACCTTA
Statistics
Matches: 458, Mismatches: 58, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
124 2 0.00
125 116 0.25
126 260 0.57
127 80 0.17
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTTAAAAAAGCTCCCACGTGGACGCTC
Found at i:104092509 original size:18 final size:18
Alignment explanation
Indices: 104092468--104092510 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
104092458 GAATGGGAAA
* *
104092468 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
104092486 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
104092504 ATGATAC
1 AGGATAC
104092511 GAACCTGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.26, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:104106371 original size:40 final size:40
Alignment explanation
Indices: 104106293--104106516 Score: 310
Period size: 40 Copynumber: 5.5 Consensus size: 40
104106283 ACCCAAGTAT
* *
104106293 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
104106332 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
104106372 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
104106412 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
104106455 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
104106495 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
104106517 CATCCGAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 12 0.07
40 117 0.70
41 1 0.01
43 36 0.22
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:104106489 original size:83 final size:80
Alignment explanation
Indices: 104106293--104106516 Score: 317
Period size: 83 Copynumber: 2.8 Consensus size: 80
104106283 ACCCAAGTAT
* * * *
104106293 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
104106357 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
104106372 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
104106436 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
104106455 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
104106517 CATCCGAATA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 13 0.10
80 49 0.38
83 67 0.52
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:104114601 original size:40 final size:40
Alignment explanation
Indices: 104114523--104114746 Score: 310
Period size: 40 Copynumber: 5.5 Consensus size: 40
104114513 ACCCAAGTAT
* *
104114523 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
104114562 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
104114602 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
104114642 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
104114685 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
104114725 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
104114747 CATCCGAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 12 0.07
40 117 0.70
41 1 0.01
43 36 0.22
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:104114719 original size:83 final size:80
Alignment explanation
Indices: 104114523--104114746 Score: 317
Period size: 83 Copynumber: 2.8 Consensus size: 80
104114513 ACCCAAGTAT
* * * *
104114523 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
104114587 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
104114602 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
104114666 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
104114685 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
104114747 CATCCGAATA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 13 0.10
80 49 0.38
83 67 0.52
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:104117307 original size:80 final size:80
Alignment explanation
Indices: 104117174--104117335 Score: 254
Period size: 80 Copynumber: 2.0 Consensus size: 80
104117164 AAATAGATGG
*
104117174 AAAACTTGTTATTGTATGCTTAGATTTAATAAACGAGATTGGTAAATTGAGTTT-CTGTTATACG
1 AAAACTTGTTATTGTATGCTTAGATTTAATAAACGAGATTAGTAAATTGAGTTTCCT-TTATACG
*
104117238 AACTTACTAAGCATGT
65 AACTTACGAAGCATGT
* * *
104117254 AAAACTTGTTATTGTATGCTTAGATTTAATAATCGGGATTAGTAAATTTAGTTTCCTTTATACGA
1 AAAACTTGTTATTGTATGCTTAGATTTAATAAACGAGATTAGTAAATTGAGTTTCCTTTATACGA
*
104117319 ACTTACGAAGCTTGT
66 ACTTACGAAGCATGT
104117334 AA
1 AA
104117336 TTCCCACTCC
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
80 73 0.97
81 2 0.03
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (80 bp):
AAAACTTGTTATTGTATGCTTAGATTTAATAAACGAGATTAGTAAATTGAGTTTCCTTTATACGA
ACTTACGAAGCATGT
Found at i:104118583 original size:28 final size:29
Alignment explanation
Indices: 104118543--104118622 Score: 117
Period size: 28 Copynumber: 2.8 Consensus size: 29
104118533 GCCAGAAATG
* * *
104118543 TCCAACCAAAACACACCAGTATCATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
*
104118572 TCC-TCCCAAACACACCAGAATAATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
104118600 TCCATCCAAAACACACCAGAATA
1 TCCATCCAAAACACACCAGAATA
104118623 GCATAGAGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 24 0.53
29 21 0.47
ACGTcount: A:0.47, C:0.33, G:0.04, T:0.16
Consensus pattern (29 bp):
TCCATCCAAAACACACCAGAATAATATAA
Found at i:104118803 original size:17 final size:17
Alignment explanation
Indices: 104118781--104118813 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
104118771 TTTTTTTATT
*
104118781 TCAATTTCATTTCCATG
1 TCAATTTCAATTCCATG
104118798 TCAATTTCAATTCCAT
1 TCAATTTCAATTCCAT
104118814 TTCAGTATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.45
Consensus pattern (17 bp):
TCAATTTCAATTCCATG
Found at i:104119173 original size:14 final size:14
Alignment explanation
Indices: 104119154--104119180 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
104119144 CTCTGTTTCT
104119154 TTTTGTTTCTTTTG
1 TTTTGTTTCTTTTG
104119168 TTTTGTTTCTTTT
1 TTTTGTTTCTTTT
104119181 TATTTTCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.81
Consensus pattern (14 bp):
TTTTGTTTCTTTTG
Found at i:104139746 original size:40 final size:39
Alignment explanation
Indices: 104139619--104139748 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
104139609 ATGCTGGAAA
* *
104139619 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG
* * *
104139659 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG
*
104139699 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG
104139739 TTATATCCGG
1 TTATATCCGG
104139749 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG
Found at i:104144972 original size:12 final size:12
Alignment explanation
Indices: 104144955--104144984 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
104144945 CGTAACATGA
*
104144955 CCGTGTTGTAGG
1 CCGTGTAGTAGG
104144967 CCGTGTAGTAGG
1 CCGTGTAGTAGG
104144979 CCGTGT
1 CCGTGT
104144985 GCCATAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.20, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTAGTAGG
Found at i:104145238 original size:103 final size:103
Alignment explanation
Indices: 104145054--104145243 Score: 276
Period size: 103 Copynumber: 1.8 Consensus size: 103
104145044 GATGGCCAGG
* *
104145054 TAGGCCATGTGATCCACACGACCAAGGCCAATTTGGGCCGTGTGGGCCACACGGGCTTGTGAGCC
1 TAGGCCATGTGATCCACACGACCAAAGCCAATTTGGGCCGTGTGGGCCACACGGGCGTGTGAGCC
* *
104145119 CACACGGGTAGTCCACACGGGCGTATAGGATTCTGGGC
66 CACACGGGCAGGCCACACGGGCGTATAGGATTCTGGGC
* * *
104145157 TAGGCCGTGTGATCCATAC-AGCCAAAGCCAATTTGGGTCGTGTGGGCCACACGGGCGTGTG-GC
1 TAGGCCATGTGATCCACACGA-CCAAAGCCAATTTGGGCCGTGTGGGCCACACGGGCGTGTGAG-
*
104145220 CCCACACGGGCAGGCCACATGGGC
64 CCCACACGGGCAGGCCACACGGGC
104145244 ATGTGGGCCC
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
102 2 0.03
103 75 0.97
ACGTcount: A:0.20, C:0.29, G:0.34, T:0.17
Consensus pattern (103 bp):
TAGGCCATGTGATCCACACGACCAAAGCCAATTTGGGCCGTGTGGGCCACACGGGCGTGTGAGCC
CACACGGGCAGGCCACACGGGCGTATAGGATTCTGGGC
Found at i:104148089 original size:38 final size:38
Alignment explanation
Indices: 104148038--104148118 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
104148028 GACAAATATA
* * * *
104148038 AAAAACCATAATTAATCCTAGTGACAATGGGTCAAAAC
1 AAAAACCACAATTAACCCCAATGACAATGGGTCAAAAC
* * *
104148076 AAAAACCACAATTAACCCCAATGACAATTGGTTAGAAC
1 AAAAACCACAATTAACCCCAATGACAATGGGTCAAAAC
104148114 AAAAA
1 AAAAA
104148119 TATTAAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.51, C:0.20, G:0.11, T:0.19
Consensus pattern (38 bp):
AAAAACCACAATTAACCCCAATGACAATGGGTCAAAAC
Found at i:104148295 original size:343 final size:341
Alignment explanation
Indices: 104147429--104148407 Score: 1444
Period size: 341 Copynumber: 2.9 Consensus size: 341
104147419 CAAAACCTGT
* * * * *
104147429 AAAAATATTAAAAGATAGAGTAAGTTTAATTACATAGTAAGTAACTAGCATTTCCCTTGGTTGGG
1 AAAAATATTAAAAGATGGAGTGAGTTTAACTACACAGTAAGTAACTAGCATTTCCCTTGGTTGAG
* *
104147494 TTAAGCAAGCACAAAAGCATTTATGCTAAATATTTAGTAAAAAATCCATAATTTTAAAATTTATG
66 TTAAGCAAGCACAAAAGCATTTAAGCTAAATATTTAGTAAAAAATCCATAATTGTAAAATTTATG
* * *
104147559 GTTATACCACAATAAATAATTCAAAGCATATCCCGTGTTAAAACTGTGATAAAGACAAATCAAT-
131 ATTATACCACAATAAATAATTCAAAGCATATTCCGTGTCAAAACTGTGATAAAGACAAATCAATA
*
104147623 A-TTCTGAAATACTGATAGATAAAAAAAATAACAACT-CCATTTTTTATACCTTAACCTCGATGA
196 ATTTCTGAAATACTGATAGA-AAAAAAAATAACAACTCCCATTTTTTAT-CCTTAACCCCGATGA
* * *
104147686 CAAATGTCAAAAACCATAATTAACCCCAGTGGCAATGGGTCGAAACAAAAACCATAATTAACCCA
259 CAAATGT-AAAAACCATAATTAACCCCAGTGACAATGGGTCAAAACAAAAACCACAATTAACCCA
* ** *
104147751 AATGTCAATTTTTTGGAAC
323 AATGACAATTGGTTAGAAC
* * * *
104147770 AAAAGTATTAAAAGATGGAGTGAGGTTAACTACACAGTAAGTAACAAGCATTTCCCTTAGTTGAG
1 AAAAATATTAAAAGATGGAGTGAGTTTAACTACACAGTAAGTAACTAGCATTTCCCTTGGTTGAG
*
104147835 TTAAGTAAGCACAAAAGCATTTAAGCTAAATATTTAGTAAAAAATCCATAATTGTAAAATTTATG
66 TTAAGCAAGCACAAAAGCATTTAAGCTAAATATTTAGTAAAAAATCCATAATTGTAAAATTTATG
* * *
104147900 ATTATACCATAATAAGTAATTCAAAGCATATTCCGTGTCAAAACTGTGATAAAGATAAATCAATA
131 ATTATACCACAATAAATAATTCAAAGCATATTCCGTGTCAAAACTGTGATAAAGACAAATCAATA
* * * *
104147965 ATTTCTTAAATATTGATAGACAAAAAAAATAACGACTCCCTTTTTTTATCTCTTAACCCCGATGA
196 ATTTCTGAAATACTGATAGA-AAAAAAAATAACAACTCCCATTTTTTATC-CTTAACCCCGATGA
* * * *
104148030 CAAATATAAAAAACCATAATTAATCCTAGTGACAATGGGTCAAAACAAAAACCACAATTAACCCC
259 CAAATGT-AAAAACCATAATTAACCCCAGTGACAATGGGTCAAAACAAAAACCACAATTAACCCA
104148095 AATGACAATTGGTTAGAAC
323 AATGACAATTGGTTAGAAC
* **
104148114 AAAAATATTAAAAGATGGAGTGAGTTTAACTACACAGCAAGTAACTATAATTTCCCTTGGTTGAG
1 AAAAATATTAAAAGATGGAGTGAGTTTAACTACACAGTAAGTAACTAGCATTTCCCTTGGTTGAG
* *
104148179 TTAAGCAAGCAC-AAAGCATTTAGGCTAAATATTTAGTAAAAAATTCATAATTGTAAAATTTATG
66 TTAAGCAAGCACAAAAGCATTTAAGCTAAATATTTAGTAAAAAATCCATAATTGTAAAATTTATG
* *
104148243 ATTATACCACAATAAATAATTCAAACCATATTCTGTGTCAAAACTGTGATAAAGACAAATCAATA
131 ATTATACCACAATAAATAATTCAAAGCATATTCCGTGTCAAAACTGTGATAAAGACAAATCAATA
* * * *
104148308 ATTTCTGAAATACTGATAGATAAAAAAATAACAACACCCATTTTTTATCCCTTAGCCCCAATGAC
196 ATTTCTGAAATACTGATAGAAAAAAAAATAACAACTCCCATTTTTTAT-CCTTAACCCCGATGAC
* *
104148373 AAATGTCAAAACCACAATTAACCCCAGTGACAATG
260 AAATGTAAAAACCATAATTAACCCCAGTGACAATG
104148408 TAACACCCCT
Statistics
Matches: 569, Mismatches: 64, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
341 201 0.35
342 43 0.08
343 161 0.28
344 164 0.29
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (341 bp):
AAAAATATTAAAAGATGGAGTGAGTTTAACTACACAGTAAGTAACTAGCATTTCCCTTGGTTGAG
TTAAGCAAGCACAAAAGCATTTAAGCTAAATATTTAGTAAAAAATCCATAATTGTAAAATTTATG
ATTATACCACAATAAATAATTCAAAGCATATTCCGTGTCAAAACTGTGATAAAGACAAATCAATA
ATTTCTGAAATACTGATAGAAAAAAAAATAACAACTCCCATTTTTTATCCTTAACCCCGATGACA
AATGTAAAAACCATAATTAACCCCAGTGACAATGGGTCAAAACAAAAACCACAATTAACCCAAAT
GACAATTGGTTAGAAC
Found at i:104152088 original size:38 final size:38
Alignment explanation
Indices: 104152034--104152107 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
104152024 GGTTGTTACA
*
104152034 GACAATAGGTCGAAACATAAACCACAATTAACCCCAGT
1 GACAATAGGTCAAAACATAAACCACAATTAACCCCAGT
*
104152072 GACAATGGGTCAAAACATAAACCACAATTAACCCCA
1 GACAATAGGTCAAAACATAAACCACAATTAACCCCA
104152108 ATGATAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (38 bp):
GACAATAGGTCAAAACATAAACCACAATTAACCCCAGT
Found at i:104156567 original size:30 final size:30
Alignment explanation
Indices: 104156510--104156567 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
104156500 TATAATTTCA
*
104156510 TTTTATTTTTATTATAATTTGGCCCTAACC
1 TTTTATTTTTATTATAATTTAGCCCTAACC
* *
104156540 TTTTATTTTTGTT-TCAATTTAGTCCTAA
1 TTTTATTTTTATTAT-AATTTAGCCCTAA
104156568 TGATCATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.57
Consensus pattern (30 bp):
TTTTATTTTTATTATAATTTAGCCCTAACC
Found at i:104156751 original size:20 final size:21
Alignment explanation
Indices: 104156728--104156771 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
104156718 TTTTAATCCT
104156728 TTTTAAATT-TTTTATATA-TA
1 TTTT-AATTATTTTATATATTA
*
104156748 TTTTATTTATTTTATATATTA
1 TTTTAATTATTTTATATATTA
104156769 TTT
1 TTT
104156772 ATTTTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 13 0.62
21 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTAATTATTTTATATATTA
Found at i:104156765 original size:22 final size:22
Alignment explanation
Indices: 104156734--104156967 Score: 70
Period size: 24 Copynumber: 10.2 Consensus size: 22
104156724 TCCTTTTTAA
*
104156734 ATTTTTTATATATATTTTATTT
1 ATTTTATATATATATTTTATTT
104156756 ATTTTATATAT-TA-TTTATTT
1 ATTTTATATATATATTTTATTT
* * * *
104156776 -TTACTATAAACAT-TATTTATAT
1 ATT-TTATATATATAT-TTTATTT
* * * * *
104156798 ATGTAAAAAATTTATTATATATATT
1 ATTTTATATATATATT-T-TAT-TT
* * *
104156823 ATTTT-TATTTATGTATTATTT
1 ATTTTATATATATATTTTATTT
* *
104156844 ATTATATTATTTATATTTTATTAT
1 ATTTTA-TATATATATTTTATT-T
104156868 ATATTT-TATTATATATTTTATTAT
1 AT-TTTATA-TATATATTTTATT-T
* * * *
104156892 ATATTATATCATTTTATTATATAT
1 ATTTTATAT-A-TATATTTTATTT
104156916 ATTATTCAT-TATATTATTTTTATTT
1 ATT-TT-ATATATA-TA-TTTTATTT
*
104156941 ATTATATATTATATTATTTTA-TT
1 ATTTTATA-TATA-TATTTTATTT
104156964 ATTT
1 ATTT
104156968 ATTATTTATT
Statistics
Matches: 154, Mismatches: 35, Indels: 45
0.66 0.15 0.19
Matches are distributed among these distances:
19 2 0.01
20 12 0.08
21 9 0.06
22 25 0.16
23 30 0.19
24 41 0.27
25 33 0.21
26 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (22 bp):
ATTTTATATATATATTTTATTT
Found at i:104156772 original size:20 final size:20
Alignment explanation
Indices: 104156737--104156977 Score: 85
Period size: 20 Copynumber: 11.9 Consensus size: 20
104156727 TTTTTAAATT
104156737 TTTTATATA-TATTTTATTTA
1 TTTTATATATTA-TTTATTTA
104156757 TTTTATATATTATTTATTT-
1 TTTTATATATTATTTATTTA
* * *
104156776 TTACTATAAACATTATTTATATA
1 TT--T-TATATATTATTTATTTA
* * * * *
104156799 TGTAAAAAATT-TATTATATA
1 TTTTATATATTAT-TTATTTA
* * *
104156819 TATTAT-TTTTATTTATGTA
1 TTTTATATATTATTTATTTA
104156838 TTATTTATTATATTATTTATATT-
1 -T-TTTA-TATATTATTTAT-TTA
* *
104156861 TTATTATATATTTTATTATATA
1 TT-TTATATATTAT-TTATTTA
*
104156883 TTTTAT-TA-TATATTATATCA
1 TTTTATATATTAT-TTAT-TTA
*
104156903 TTTTAT-TATATATATTATTCA
1 TTTTATATAT-TAT-TTATTTA
*
104156924 TTATAT-TATT-TTTATTTA
1 TTTTATATATTATTTATTTA
104156942 --TTATATATTATATTATTT-
1 TTTTATATATTAT-TTATTTA
* *
104156960 TATTATTTATTATTTATT
1 TTTTATATATTATTTATT
104156978 ATTATGTATA
Statistics
Matches: 174, Mismatches: 24, Indels: 47
0.71 0.10 0.19
Matches are distributed among these distances:
16 3 0.02
17 4 0.02
18 7 0.04
19 30 0.17
20 56 0.32
21 31 0.18
22 32 0.18
23 10 0.06
24 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTTATATATTATTTATTTA
Found at i:104156846 original size:7 final size:7
Alignment explanation
Indices: 104156807--104156980 Score: 108
Period size: 7 Copynumber: 23.4 Consensus size: 7
104156797 TATGTAAAAA
104156807 ATTTATT
1 ATTTATT
104156814 ATATATATT
1 AT-T-TATT
104156823 ATTT-TT
1 ATTTATT
104156829 ATTTATGT
1 ATTTAT-T
104156837 A-TTATTT
1 ATTTA-TT
104156844 ATTATATT
1 ATT-TATT
104156852 ATTTA-T
1 ATTTATT
104156858 ATTTTATT
1 A-TTTATT
*
104156866 ATATATT
1 ATTTATT
*
104156873 TTATTATAT
1 AT-TTAT-T
104156882 ATTTTATT
1 A-TTTATT
*
104156890 ATATATT
1 ATTTATT
*
104156897 ATATCATT
1 AT-TTATT
*
104156905 TTATTATAT
1 AT-TTAT-T
104156914 ATATTATT
1 AT-TTATT
104156922 CATTATATT
1 -ATT-TATT
104156931 ATTT-TT
1 ATTTATT
104156937 ATTTATT
1 ATTTATT
*
104156944 ATATATT
1 ATTTATT
104156951 A--TATT
1 ATTTATT
104156956 ATTTTATT
1 A-TTTATT
104156964 ATTTATT
1 ATTTATT
104156971 ATTTATT
1 ATTTATT
104156978 ATT
1 ATT
104156981 ATGTATAATT
Statistics
Matches: 136, Mismatches: 11, Indels: 40
0.73 0.06 0.21
Matches are distributed among these distances:
5 5 0.04
6 14 0.10
7 54 0.40
8 36 0.26
9 26 0.19
10 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (7 bp):
ATTTATT
Found at i:104156853 original size:12 final size:12
Alignment explanation
Indices: 104156807--104156982 Score: 127
Period size: 12 Copynumber: 15.8 Consensus size: 12
104156797 TATGTAAAAA
104156807 ATTTATTATA-T
1 ATTTATTATATT
104156818 ATATTATT-T-TT
1 AT-TTATTATATT
*
104156829 ATTTA-TGTATT
1 ATTTATTATATT
104156840 ATTTATTATATT
1 ATTTATTATATT
*
104156852 ATTTA-TATTTT
1 ATTTATTATATT
104156863 A-TTA-TATA-T
1 ATTTATTATATT
104156872 -TTTATTATA-T
1 ATTTATTATATT
104156882 ATTTTATTATA-T
1 A-TTTATTATATT
* *
104156894 ATTATATCATTTT
1 ATT-TATTATATT
104156907 A-TTATATATATT
1 ATTTAT-TATATT
*
104156919 ATTCATTATATT
1 ATTTATTATATT
104156931 ATTT-TTAT-TT
1 ATTTATTATATT
104156941 A-TTA-TATATT
1 ATTTATTATATT
*
104156951 ATATTATTTTATT
1 AT-TTATTATATT
104156964 ATTTATTAT-TT
1 ATTTATTATATT
104156975 A-TTATTAT
1 ATTTATTAT
104156983 GTATAATTTT
Statistics
Matches: 136, Mismatches: 11, Indels: 37
0.74 0.06 0.20
Matches are distributed among these distances:
9 10 0.07
10 28 0.21
11 31 0.23
12 55 0.40
13 12 0.09
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:104156892 original size:34 final size:34
Alignment explanation
Indices: 104156808--104156993 Score: 129
Period size: 31 Copynumber: 5.8 Consensus size: 34
104156798 ATGTAAAAAA
*
104156808 TTTATTATATATATTATT-TTTATTTATGTAT-TA-
1 TTTATTATATATATTATTATAT-TTTAT-TATATAT
104156841 TTTATTATAT-TA-T-TTATATTTTATTATATAT
1 TTTATTATATATATTATTATATTTTATTATATAT
*
104156872 TTTATTATATATTTTATTATA---TATTATATCAT
1 TTTATTATATATATTATTATATTTTATTATAT-AT
* *
104156904 TTTATTATATATATTATT-CATTATA-T-TAT-T
1 TTTATTATATATATTATTATATTTTATTATATAT
104156934 TTTATT-TAT-TATATATTATATTATT-TTAT-TA-
1 TTTATTATATATAT-TATTATATT-TTATTATATAT
*
104156965 TTTATTATTTATTATTATGTATAATTTTA
1 TTTATTATATA-TATTAT-TAT-ATTTTA
104156994 AAAATTTGTA
Statistics
Matches: 124, Mismatches: 7, Indels: 42
0.72 0.04 0.24
Matches are distributed among these distances:
28 3 0.02
29 10 0.08
30 19 0.15
31 31 0.25
32 28 0.23
33 15 0.12
34 15 0.12
35 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (34 bp):
TTTATTATATATATTATTATATTTTATTATATAT
Found at i:104157377 original size:18 final size:18
Alignment explanation
Indices: 104157354--104157388 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
104157344 ATCTCATAAA
104157354 TTATTTATTATTTTTATG
1 TTATTTATTATTTTTATG
*
104157372 TTATTTATTGTTTTTAT
1 TTATTTATTATTTTTAT
104157389 ATATTTGCAT
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:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TTATTTATTATTTTTATG
Found at i:104157575 original size:119 final size:111
Alignment explanation
Indices: 104157430--104157642 Score: 257
Period size: 111 Copynumber: 1.8 Consensus size: 111
104157420 ATATTTTAAG
* * **
104157430 TTATATTTGCATGAAATATTATTGTATATATATTATGTAATTTATAT-TGTTATATTCATTGTTT
1 TTATATCTGCATGAAATATTA----ATGTATATTATGTAATTTATATCT-TT-T-TT-ATCATTT
* * *
104157494 TCTATGTTGTATTTTGCATGAAATGTTAATGTATGTATATTTATGTTATTTATGA
58 TCTATATTATA-TTTGCATGAAATGTTAAAGTATGTATATTTATGTTATTTATGA
* *
104157549 TTATATCTGCATGAAATGTTAATGTATATTATGTAATTTATGTCTTTTTTATCATTTTCTATATT
1 TTATATCTGCATGAAATATTAATGTATATTATGTAATTTATATCTTTTTTATCATTTTCTATATT
104157614 ATATTTGCATGAAATGTTAAAGTATGTAT
66 ATATTTGCATGAAATGTTAAAGTATGTAT
104157643 CATGTATTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
111 25 0.30
112 14 0.17
113 2 0.02
114 1 0.01
115 22 0.26
116 1 0.01
119 19 0.23
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (111 bp):
TTATATCTGCATGAAATATTAATGTATATTATGTAATTTATATCTTTTTTATCATTTTCTATATT
ATATTTGCATGAAATGTTAAAGTATGTATATTTATGTTATTTATGA
Found at i:104168808 original size:90 final size:90
Alignment explanation
Indices: 104168668--104169252 Score: 850
Period size: 90 Copynumber: 6.5 Consensus size: 90
104168658 TCACCGTTAG
* * * * *
104168668 CAGATTTGGCGTCTTTGTATTAGACGAGGAGCAGATCGAAGATAGCAGATCTGAAATTTGTGTTT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGT
104168733 TTACATCGAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* *
104168758 CAGATTTGGTGTCTCTGTATTAGACGGGGAGCAGATCGAAGGTAGCAGATCTGACATTCGTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGT
*
104168823 TTATATCGAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * *
104168848 CAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCGAAGATAGTAGATCTGACATTCATGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGT
104168913 TTACATCGAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * * * * *
104168938 CAGATTCGGGGTCTCTATATTAGACGAGGAGTAGATCGAAGATAACAGATCTGACATTCGTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGT
*
104169003 TTACATCGAGAAGCAGATCGAATATGA
66 TTACATC--GAAGCAGATCGAAGATGA
* * * *
104169030 TAGATTTGGCGTCTCTATATTAGATGGGGAGCAGATCGAAGATAGCAAATCTGACATT-GTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGT
*
104169094 TTACATCAAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
** *
104169119 CAGATTTGGATTCTCTGTATTAGACGAGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGT
*
104169184 TTACATCGAAGTAGATCGAAGATAGA
66 TTACATCGAAGCAGATCGAAGAT-GA
* * * *
104169210 -AGATTTGGCGTCTCTATATTTGAAGGGGAGCAGATCAAAGATA
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATA
104169253 TTAACATGGC
Statistics
Matches: 443, Mismatches: 48, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
89 67 0.15
90 294 0.66
91 15 0.03
92 67 0.15
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (90 bp):
CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGT
TTACATCGAAGCAGATCGAAGATGA
Found at i:104169245 original size:45 final size:46
Alignment explanation
Indices: 104168668--104169252 Score: 210
Period size: 45 Copynumber: 13.0 Consensus size: 46
104168658 TCACCGTTAG
* * * * *
104168668 CAGATTTGGCGTCTTTGTATTAGACGAGGAGCAGATCGAAGATAG-
1 CAGATTTGGCATCTCTGTATTTGAAGCGGAGCAGATCGAAGATAGA
* ** * * * * *
104168713 CAGATCTGAAATTTGTGT-TTTTACATCGAAGCAGATCGAAGAT-GA
1 CAGATTTGGCATCTCTGTATTTGA-AGCGGAGCAGATCGAAGATAGA
** * * * *
104168758 CAGATTTGGTGTCTCTGTATTAGACGGGGAGCAGATCGAAGGTAG-
1 CAGATTTGGCATCTCTGTATTTGAAGCGGAGCAGATCGAAGATAGA
* * * * *
104168803 CAGATCTGACAT-TCGTGTGTTT-ATATCGAAGCAGATCGAAGAT-GA
1 CAGATTTGGCATCTC-TGTATTTGA-AGCGGAGCAGATCGAAGATAGA
* * * * *
104168848 CAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCGAAGATAG-
1 CAGATTTGGCATCTCTGTATTTGAAGCGGAGCAGATCGAAGATAGA
* * * * * *
104168893 TAGATCTGACAT-TCATGTGTTT-ACATCGAAGCAGATCGAAGAT-GA
1 CAGATTTGGCATCTC-TGTATTTGA-AGCGGAGCAGATCGAAGATAGA
* ** * * * * *
104168938 CAGATTCGGGGTCTCTATATTAGACGAGGAGTAGATCGAAGATA-A
1 CAGATTTGGCATCTCTGTATTTGAAGCGGAGCAGATCGAAGATAGA
* * * * *
104168983 CAGATCTGACAT-TCGTGTGTTT-ACATCGAGAAGCAGATCGAATAT-GA
1 CAGATTTGGCATCTC-TGTATTTGA-AGCG-G-AGCAGATCGAAGATAGA
* * * * * *
104169030 TAGATTTGGCGTCTCTATATTAGATGGGGAGCAGATCGAAGATAG-
1 CAGATTTGGCATCTCTGTATTTGAAGCGGAGCAGATCGAAGATAGA
* * * * * * **
104169075 CAAATCTGACAT-TGTGTGTTT-ACATCAAAGCAGATCGAAGAT-GA
1 CAGATTTGGCATCTCTGTATTTGA-AGCGGAGCAGATCGAAGATAGA
* * *
104169119 CAGATTTGG-ATTCTCTGTATTAGACGAGGAGCAGATCGAAGATAG-
1 CAGATTTGGCA-TCTCTGTATTTGAAGCGGAGCAGATCGAAGATAGA
* * * * * *
104169164 CAGATCTGACAT-TCGTGTGTTT-ACATCGAAGTAGATCGAAGATAGA
1 CAGATTTGGCATCTC-TGTATTTGA-AGCGGAGCAGATCGAAGATAGA
* * * *
104169210 -AGATTTGGCGTCTCTATATTTGAAGGGGAGCAGATCAAAGATA
1 CAGATTTGGCATCTCTGTATTTGAAGCGGAGCAGATCGAAGATA
104169253 TTAACATGGC
Statistics
Matches: 365, Mismatches: 139, Indels: 72
0.63 0.24 0.12
Matches are distributed among these distances:
43 3 0.01
44 44 0.12
45 269 0.74
46 20 0.05
47 26 0.07
48 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (46 bp):
CAGATTTGGCATCTCTGTATTTGAAGCGGAGCAGATCGAAGATAGA
Found at i:104170729 original size:29 final size:29
Alignment explanation
Indices: 104170697--104170753 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
104170687 TTTTAATCCT
*
104170697 TTTTAAATTTTTTATATATAATTTATTTA
1 TTTTAAATATTTTATATATAATTTATTTA
*
104170726 TTTTAAATATTTTATATATTATTTATTT
1 TTTTAAATATTTTATATATAATTTATTT
104170754 TTACTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTTAAATATTTTATATATAATTTATTTA
Found at i:104170834 original size:23 final size:23
Alignment explanation
Indices: 104170804--104170959 Score: 125
Period size: 23 Copynumber: 7.0 Consensus size: 23
104170794 TATATTATTT
*
104170804 TTATTTATGTATTATTTATTATA
1 TTATTTATATATTATTTATTATA
* *
104170827 TTATTTATATTTTA-TTATATATT
1 TTATTTATATATTATTTAT-TATA
104170850 TTATTTATATATT-TTTA-TATA
1 TTATTTATATATTATTTATTATA
*
104170871 TTA--TATCATTTTA-TTATATATA
1 TTATTTAT-ATATTATTTAT-TATA
* *
104170893 TTATTCATTATATTATTT-TTATT
1 TTATTTA-TATATTATTTATTATA
*
104170916 TTA-TTATATATTATATTATTTTA
1 TTATTTATATATTAT-TTATTATA
104170939 TTATTTAT-TATT-TATTATTAT
1 TTATTTATATATTAT-TTATTAT
104170960 GTATAATTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
19 3 0.03
20 7 0.07
21 14 0.13
22 23 0.21
23 46 0.43
24 11 0.10
25 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATTTATATATTATTTATTATA
Found at i:104170923 original size:55 final size:56
Alignment explanation
Indices: 104170786--104170950 Score: 197
Period size: 55 Copynumber: 3.1 Consensus size: 56
104170776 ATGTAAAAAT
* *
104170786 TTATTC-TATATATTATTTTTA-TTTATGTAT-TATT-TATTATATTATT-TATATT
1 TTATTCATATATATTATTTTTATTTTAT-TATATATTATATTATTTTATTATATATA
* * *
104170838 TTATT-ATATATTTTATTTATATATTT-TTATATATTATATCATTTTATTATATATA
1 TTATTCATATATATTATTTTTAT-TTTATTATATATTATATTATTTTATTATATATA
104170893 TTATTCAT-TATATTATTTTTATTTTATTATATATTATATTATTTTATTAT-T-TA
1 TTATTCATATATATTATTTTTATTTTATTATATATTATATTATTTTATTATATATA
104170946 TTATT
1 TTATT
104170951 TATTATTATG
Statistics
Matches: 97, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
52 21 0.22
53 12 0.12
54 17 0.18
55 45 0.46
56 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.67
Consensus pattern (56 bp):
TTATTCATATATATTATTTTTATTTTATTATATATTATATTATTTTATTATATATA
Found at i:104171547 original size:119 final size:112
Alignment explanation
Indices: 104171402--104171615 Score: 275
Period size: 112 Copynumber: 1.8 Consensus size: 112
104171392 ATATTTTAAG
* * * **
104171402 TTATATTTGCATGAAATATTATTGTATATATATTATGTAATTTATATTGTTATATTCATTGTTTT
1 TTATATCTGCATGAAATATTA----ATGTATATTATGTAATTTATATCGTTAT-TT-ATCATTTT
* * *
104171467 CTATGTTGTATTTTGCATGAAATGTTAATGTATGTATATTTATGTTATTTATGA
60 CTATATTATA-TTTGCATGAAATGTTAAAGTATGTATATTTATGTTATTTATGA
* *
104171521 TTATATCTGCATGAAATGTTAATGTATATTATGTAATTTATGTCGTTATTTATCATTTTCTATAT
1 TTATATCTGCATGAAATATTAATGTATATTATGTAATTTATATCGTTATTTATCATTTTCTATAT
104171586 TATATTTGCATGAAATGTTAAAGTATGTAT
66 TATATTTGCATGAAATGTTAAAGTATGTAT
104171616 CATGTATTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
112 25 0.29
113 14 0.16
114 2 0.02
115 25 0.29
119 19 0.22
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.52
Consensus pattern (112 bp):
TTATATCTGCATGAAATATTAATGTATATTATGTAATTTATATCGTTATTTATCATTTTCTATAT
TATATTTGCATGAAATGTTAAAGTATGTATATTTATGTTATTTATGA
Found at i:104172530 original size:49 final size:49
Alignment explanation
Indices: 104172469--104172591 Score: 158
Period size: 49 Copynumber: 2.5 Consensus size: 49
104172459 TATTGTGTGT
* *
104172469 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACTGA-TAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCACTAGATGAAAGC
* * * *
104172518 CAGTGTAAGACCTGTCTAGGACATGGCATTGGCCTCACTATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCACTAGATGAAAGC
*
104172567 CAGTGTAAGGCCATGTCTGGGACAT
1 CAGTGTAAGACC-TGTCTGGGACAT
104172592 AGCGTCGGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 3 0.05
49 50 0.78
50 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCACTAGATGAAAGC
Found at i:104176048 original size:12 final size:12
Alignment explanation
Indices: 104176033--104176059 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
104176023 ACTATTTATT
104176033 TCACTTAGTTTC
1 TCACTTAGTTTC
104176045 TCACTTAGTTTC
1 TCACTTAGTTTC
104176057 TCA
1 TCA
104176060 AGTTCTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.48
Consensus pattern (12 bp):
TCACTTAGTTTC
Found at i:104176527 original size:18 final size:18
Alignment explanation
Indices: 104176504--104176539 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
104176494 GAGAGTTGTA
104176504 ACACACCGGATATACAAT
1 ACACACCGGATATACAAT
104176522 ACACACCGGATATACAAT
1 ACACACCGGATATACAAT
104176540 CAGTTGTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.17
Consensus pattern (18 bp):
ACACACCGGATATACAAT
Found at i:104176735 original size:17 final size:17
Alignment explanation
Indices: 104176713--104176746 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
104176703 ATTGTTTTTG
* *
104176713 TGATTTTTATAATGTGA
1 TGATTTATAAAATGTGA
104176730 TGATTTATAAAATGTGA
1 TGATTTATAAAATGTGA
104176747 AATATTGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
TGATTTATAAAATGTGA
Found at i:104176761 original size:2 final size:2
Alignment explanation
Indices: 104176754--104176778 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
104176744 TGAAATATTG
104176754 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
104176779 GTGTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104177056 original size:47 final size:47
Alignment explanation
Indices: 104176948--104177058 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
104176938 AAGGAGGAAG
* * * * *
104176948 AAGTGGCAATTTATATGTAAAAGTGGTGGCTTGTCCATAATTTTATT
1 AAGTGGCAGTTTATCTGGAAAAGTGGTGGCTTGTCCACAATATTATT
*
104176995 AAGTGGTAGTTTATCTGGAAAAGTGGTGGCTTGTCCACAATATTATT
1 AAGTGGCAGTTTATCTGGAAAAGTGGTGGCTTGTCCACAATATTATT
104177042 AAGTGGCAGTTTATCTG
1 AAGTGGCAGTTTATCTG
104177059 CATTACTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (47 bp):
AAGTGGCAGTTTATCTGGAAAAGTGGTGGCTTGTCCACAATATTATT
Found at i:104179672 original size:21 final size:21
Alignment explanation
Indices: 104179646--104179709 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
104179636 ACTTGTTAAG
104179646 AGAAGAATTGCTCATTTTACT
1 AGAAGAATTGCTCATTTTACT
104179667 AGAAGAATTGCTCATTTTACT
1 AGAAGAATTGCTCATTTTACT
*
104179688 AGAAGAATTGCTCATTTCACT
1 AGAAGAATTGCTCATTTTACT
104179709 A
1 A
104179710 TGTATTTGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (21 bp):
AGAAGAATTGCTCATTTTACT
Found at i:104183919 original size:28 final size:28
Alignment explanation
Indices: 104183887--104183959 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
104183877 GGGTTGTGTG
*
104183887 GGCCACACGGG-TGTATGTTAGGCCGTGA
1 GGCCACACGGGCT-TATGTTAGGCCATGA
* *
104183915 GGCCATACGGGCTTGTGTTAGGCCATGA
1 GGCCACACGGGCTTATGTTAGGCCATGA
* *
104183943 GGCTACACGGGCATATG
1 GGCCACACGGGCTTATG
104183960 GGCCCATTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 36 0.97
29 1 0.03
ACGTcount: A:0.19, C:0.22, G:0.37, T:0.22
Consensus pattern (28 bp):
GGCCACACGGGCTTATGTTAGGCCATGA
Found at i:104194713 original size:13 final size:14
Alignment explanation
Indices: 104194695--104194736 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
104194685 TTTTAATTTT
104194695 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
104194708 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
104194723 ATTTTAAATAATAT
1 ATTTT-AATAATAT
104194737 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:104194721 original size:16 final size:16
Alignment explanation
Indices: 104194699--104194735 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
104194689 AATTTTATTT
104194699 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
104194716 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
104194731 TAATA
1 TAATA
104194736 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:104195280 original size:14 final size:14
Alignment explanation
Indices: 104195260--104195302 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
104195250 TTTTCAGAAA
104195260 AATAAATCATTTTC
1 AATAAATCATTTTC
*
104195274 TATAAATCATTTTC
1 AATAAATCATTTTC
* *
104195288 AAGAAATAATTTTC
1 AATAAATCATTTTC
104195302 A
1 A
104195303 GTGAAACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (14 bp):
AATAAATCATTTTC
Found at i:104195396 original size:19 final size:19
Alignment explanation
Indices: 104195374--104195444 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 19
104195364 TTAAAATACA
104195374 ATTTTTAATATTTTTATTG
1 ATTTTTAATATTTTTATTG
* **
104195393 ATTTGTTGA-ATTTTTATAA
1 ATTT-TTAATATTTTTATTG
* *
104195412 ATTTTCATTATTTTT-TTG
1 ATTTTTAATATTTTTATTG
**
104195430 GGTTTTAATATTTTT
1 ATTTTTAATATTTTT
104195445 TACAATTTTT
Statistics
Matches: 38, Mismatches: 12, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
18 13 0.34
19 22 0.58
20 3 0.08
ACGTcount: A:0.24, C:0.01, G:0.08, T:0.66
Consensus pattern (19 bp):
ATTTTTAATATTTTTATTG
Found at i:104197672 original size:15 final size:15
Alignment explanation
Indices: 104197632--104197666 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
104197622 ATATTTTTAG
*
104197632 TTATTGTTATTAATT
1 TTATTATTATTAATT
*
104197647 TTATTATTATTACTT
1 TTATTATTATTAATT
104197662 TTATT
1 TTATT
104197667 TCTATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTATTATTAATT
Found at i:104199246 original size:17 final size:18
Alignment explanation
Indices: 104199225--104199264 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
104199215 GGAGTGTAGG
104199225 GTTGGACGGAGATAGTGT
1 GTTGGACGGAGATAGTGT
*
104199243 -TTGGACGGAGATGGTGT
1 GTTGGACGGAGATAGTGT
104199260 GTTGG
1 GTTGG
104199265 CTGGATGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.17, C:0.05, G:0.47, T:0.30
Consensus pattern (18 bp):
GTTGGACGGAGATAGTGT
Found at i:104202023 original size:17 final size:18
Alignment explanation
Indices: 104201998--104202034 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
104201988 CATTTTTTTC
104201998 AATTAAAAAAATAT-TAA
1 AATTAAAAAAATATATAA
*
104202015 AATTCAAAAAATATATAA
1 AATTAAAAAAATATATAA
104202033 AA
1 AA
104202035 AATTCAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
AATTAAAAAAATATATAA
Found at i:104202053 original size:22 final size:20
Alignment explanation
Indices: 104202013--104202051 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
104202003 AAAAAATATT
104202013 AAAATTCAAAAAATATATAA
1 AAAATTCAAAAAATATATAA
* *
104202033 AAAATTCAGAAATTATATA
1 AAAATTCAAAAAATATATA
104202052 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAATTCAAAAAATATATAA
Found at i:104202149 original size:12 final size:12
Alignment explanation
Indices: 104202132--104202157 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
104202122 TTAAAAACAC
104202132 ATGAAACATGAT
1 ATGAAACATGAT
104202144 ATGAAACATGAT
1 ATGAAACATGAT
104202156 AT
1 AT
104202158 ATTACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
ATGAAACATGAT
Found at i:104211007 original size:46 final size:47
Alignment explanation
Indices: 104210901--104211022 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
104210891 TGTCTTCGAC
** * *
104210901 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
104210951 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
104210997 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
104211023 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:104220039 original size:22 final size:23
Alignment explanation
Indices: 104220009--104220054 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
104219999 GAAAAACCAA
104220009 AAAGAAAAGAAGAAAAAAAAGAG
1 AAAGAAAAGAAGAAAAAAAAGAG
*
104220032 AAAG-AAAGAAGAAAGAAAAGAG
1 AAAGAAAAGAAGAAAAAAAAGAG
104220054 A
1 A
104220055 GGAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (23 bp):
AAAGAAAAGAAGAAAAAAAAGAG
Found at i:104220040 original size:19 final size:17
Alignment explanation
Indices: 104220007--104220064 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
104219997 AAGAAAAACC
104220007 AAAAAGAAAAGAAGAAA
1 AAAAAGAAAAGAAGAAA
*
104220024 AAAAAGAGAAAGAA-AGA
1 AAAAAGA-AAAGAAGAAA
*
104220041 AGAAAGAAAAGAGAGGAAA
1 AAAAAGAAAAGA-A-GAAA
104220060 AAAAA
1 AAAAA
104220065 TGATGGAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.15
17 16 0.48
18 6 0.18
19 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAGAAA
Found at i:104223339 original size:44 final size:45
Alignment explanation
Indices: 104223249--104223377 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
104223239 GACAGAACGA
*
104223249 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
104223295 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
104223339 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
104223378 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:104230728 original size:44 final size:45
Alignment explanation
Indices: 104230638--104230766 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
104230628 GACAGAACGA
*
104230638 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
104230684 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
104230728 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
104230767 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:104232516 original size:24 final size:25
Alignment explanation
Indices: 104232489--104232543 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
104232479 GAAAAGCCAA
104232489 AAAGAAAAGAAGAAA-AAAAAAGAG
1 AAAGAAAAGAAGAAAGAAAAAAGAG
*
104232513 AAAG-AAAGAAGAAAGAAAAGAGAG
1 AAAGAAAAGAAGAAAGAAAAAAGAG
104232537 AAA-AAAA
1 AAAGAAAA
104232544 TGATGGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (25 bp):
AAAGAAAAGAAGAAAGAAAAAAGAG
Found at i:104232521 original size:20 final size:20
Alignment explanation
Indices: 104232487--104232535 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
104232477 AAGAAAAGCC
104232487 AAAAAGA-AAAGAAGAA-AA
1 AAAAAGAGAAAGAAGAAGAA
104232505 AAAAAGAGAAAGAAAGAAGAA
1 AAAAAGAGAAAG-AAGAAGAA
104232526 AGAAAAGAGA
1 A-AAAAGAGA
104232536 GAAAAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
20 5 0.19
21 3 0.11
22 8 0.30
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAAAGAGAAAGAAGAAGAA
Found at i:104232539 original size:20 final size:22
Alignment explanation
Indices: 104232494--104232538 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
104232484 GCCAAAAAGA
104232494 AAAGAAGAAAAAAAAAGAGAAAG
1 AAAGAAGAAAAAAAAAGAG-AAG
*
104232517 AAAGAAGAAAGAAAAGAGAGAA
1 AAAGAAGAAA-AAAAAAGAGAA
104232539 AAAAATGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
AAAGAAGAAAAAAAAAGAGAAG
Found at i:104232542 original size:11 final size:11
Alignment explanation
Indices: 104232493--104232543 Score: 59
Period size: 12 Copynumber: 4.4 Consensus size: 11
104232483 AGCCAAAAAG
104232493 AAAAGAAGAAA
1 AAAAGAAGAAA
104232504 AAAA-AAGAGAA
1 AAAAGAAGA-AA
104232515 AGAAAGAAGAAA
1 A-AAAGAAGAAA
104232527 GAAAAGAGAGAAA
1 -AAAAGA-AGAAA
104232540 AAAA
1 AAAA
104232544 TGATGGAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.11
11 7 0.20
12 14 0.40
13 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:104232590 original size:4 final size:5
Alignment explanation
Indices: 104232560--104232601 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
104232550 AGAATGTGCC
* *
104232560 AAAAG AAAAG AAAAT AAAAT AAAAT -AAAT AAAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AA
104232602 TATGAACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
4 4 0.12
5 26 0.76
6 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:104233770 original size:20 final size:22
Alignment explanation
Indices: 104233716--104233771 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
104233706 TTAAGAATTA
* *
104233716 TTTTAGTAT-TATTTTTATTTG
1 TTTTAATATATATTTTTATGTG
*
104233737 TTTTAATATTTATTTTTATGT-
1 TTTTAATATATATTTTTATGTG
104233758 TTTTAA-ATATATTT
1 TTTTAATATATATTT
104233772 GATTTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 14 0.45
22 10 0.32
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTTAATATATATTTTTATGTG
Found at i:104233788 original size:26 final size:24
Alignment explanation
Indices: 104233742--104233800 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
104233732 ATTTGTTTTA
*
104233742 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
104233766 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
*
104233792 -TTTTTATTT
1 ATATTTATTT
104233801 AATAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.32
25 8 0.26
26 13 0.42
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:104234704 original size:19 final size:19
Alignment explanation
Indices: 104234650--104234704 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
104234640 TATGTCAAGT
*
104234650 TAAT-AAACAATTCAAAAA
1 TAATAAAACAAATCAAAAA
* *
104234668 TTATAAAA-ATAATAAAAAA
1 TAATAAAACA-AATCAAAAA
*
104234687 TAATAAAACAAGTCAAAA
1 TAATAAAACAAATCAAAA
104234705 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
18 4 0.14
19 23 0.82
20 1 0.04
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (19 bp):
TAATAAAACAAATCAAAAA
Found at i:104234722 original size:37 final size:38
Alignment explanation
Indices: 104234650--104234744 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 38
104234640 TATGTCAAGT
* *
104234650 TAAT-AAACAATTCAAAAATTATAAAAATAATAAAAAA
1 TAATAAAACAAGTCAAAAATTATAAAAATAAAAAAAAA
*
104234687 TAATAAAACAAGTC-AAAATT-TAAAAATATAAAAAAAC
1 TAATAAAACAAGTCAAAAATTATAAAAATA-AAAAAAAA
* * *
104234724 TCATAAAA-AATTTAAAAATTA
1 TAATAAAACAAGTCAAAAATTA
104234745 GTATGAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
36 11 0.23
37 29 0.60
38 8 0.17
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.25
Consensus pattern (38 bp):
TAATAAAACAAGTCAAAAATTATAAAAATAAAAAAAAA
Found at i:104235925 original size:2 final size:2
Alignment explanation
Indices: 104235918--104235944 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104235908 TAAATTACTA
104235918 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
104235945 ATGTTAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104238036 original size:3 final size:3
Alignment explanation
Indices: 104238021--104238063 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
104238011 TATTAGCCAA
*
104238021 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
104238064 CCATTATGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:104238223 original size:3 final size:3
Alignment explanation
Indices: 104238215--104238481 Score: 124
Period size: 3 Copynumber: 90.0 Consensus size: 3
104238205 ATTTTCTACT
104238215 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *** *
104238263 TTA ATA -CA TTA CTA GTA TT- TTA TTA TCA TTA CCC TTA TTA ATA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
104238308 TTA GTA TT- TTC TTA TTA GTAA TCTA TTA TTA TTC TTA TTA GTGTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA -T-TA TTA
* * * *
104238356 TTA TT- TCCTA TTTA TCA -TA TTA TTG TTG TTA TTA GTA TGTA -TA TTA
1 TTA TTA T--TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* * * * * * **
104238402 TT- TT- TTC CTA TTA TTA TTA TTA CTA ATA TCA CTA TTA GCA TT- TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
104238446 TTA TTA CTG TTA TTA TTA TTA TTT TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
104238482 ATTTTAATTC
Statistics
Matches: 198, Mismatches: 49, Indels: 34
0.70 0.17 0.12
Matches are distributed among these distances:
2 19 0.10
3 165 0.83
4 11 0.06
5 2 0.01
6 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:104238595 original size:15 final size:16
Alignment explanation
Indices: 104238561--104238595 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
104238551 TATTTAAACT
104238561 TTATTAGTTTTTATTA
1 TTATTAGTTTTTATTA
104238577 -TATTA-TTTTTATTA
1 TTATTAGTTTTTATTA
104238591 TTATT
1 TTATT
104238596 TGTTCACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTATTAGTTTTTATTA
Found at i:104242860 original size:25 final size:25
Alignment explanation
Indices: 104242832--104242884 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
104242822 ATTATAGGGT
*
104242832 TAGATAGCATTTATCGACCCTACGA
1 TAGATAGCATTTACCGACCCTACGA
104242857 TAGATAGCATTTACCGACCCTACGA
1 TAGATAGCATTTACCGACCCTACGA
104242882 TAG
1 TAG
104242885 GCCCACAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (25 bp):
TAGATAGCATTTACCGACCCTACGA
Found at i:104243051 original size:85 final size:85
Alignment explanation
Indices: 104242936--104243093 Score: 237
Period size: 85 Copynumber: 1.9 Consensus size: 85
104242926 TTTTTAGTAT
* * *
104242936 TATGGGCCCACACGCCCAGATTAGCCTTGCCCGTGTGGCCCACACGGT-CTGACCCAATAATCGA
1 TATGGGCCCACACACCCAGATTAGCATTGCCCGTATGGCCCACA-GGTCCTGACCCAATAATCGA
104243000 CACGCCCGTATGGGTTGCCCG
65 CACGCCCGTATGGGTTGCCCG
* * *
104243021 TATGGGCCCACACATCCAGATTGGCATTGCCCGTATGGCCCACATGTCCTGACCCAATAATCGAC
1 TATGGGCCCACACACCCAGATTAGCATTGCCCGTATGGCCCACAGGTCCTGACCCAATAATCGAC
*
104243086 ATGCCCGT
66 ACGCCCGT
104243094 GTAAGCCCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 2 0.03
85 63 0.97
ACGTcount: A:0.21, C:0.35, G:0.23, T:0.20
Consensus pattern (85 bp):
TATGGGCCCACACACCCAGATTAGCATTGCCCGTATGGCCCACAGGTCCTGACCCAATAATCGAC
ACGCCCGTATGGGTTGCCCG
Found at i:104243275 original size:82 final size:82
Alignment explanation
Indices: 104243172--104243340 Score: 239
Period size: 82 Copynumber: 2.1 Consensus size: 82
104243162 CTCTGGCCAT
* * * * * *
104243172 CACATGACCGTTTCTTACGCACAGCCTGGCCTTCATCGATCACACGGCCGTGTCATCACACACGG
1 CACACGACCGTGTCTTACGCACAACCTAGCCTTCATCGATCACACGACCGTGTCATCACACACAG
104243237 CCTAACACACGGCCCAC
66 CCTAACACACGGCCCAC
* * * *
104243254 CACACGACCGTGTCTTGCGCACAACCTAGCCTTCGTCGATCACACGATCGTGTCGTCACACACAG
1 CACACGACCGTGTCTTACGCACAACCTAGCCTTCATCGATCACACGACCGTGTCATCACACACAG
*
104243319 CCTACCACACGGCCCAC
66 CCTAACACACGGCCCAC
104243336 CACAC
1 CACAC
104243341 AGTAGTGTGA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.24, C:0.41, G:0.18, T:0.17
Consensus pattern (82 bp):
CACACGACCGTGTCTTACGCACAACCTAGCCTTCATCGATCACACGACCGTGTCATCACACACAG
CCTAACACACGGCCCAC
Found at i:104243807 original size:16 final size:16
Alignment explanation
Indices: 104243774--104243811 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
104243764 TAACGAGAAT
104243774 AAAAAATAGAAAGCTGA
1 AAAAAATAGAAA-CTGA
104243791 AAAAAATCAGAAA-TGA
1 AAAAAAT-AGAAACTGA
104243807 AAAAA
1 AAAAA
104243812 CAGAGGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.71, C:0.05, G:0.13, T:0.11
Consensus pattern (16 bp):
AAAAAATAGAAACTGA
Found at i:104245254 original size:47 final size:48
Alignment explanation
Indices: 104245155--104245426 Score: 215
Period size: 47 Copynumber: 5.7 Consensus size: 48
104245145 TAATTTGTGT
*
104245155 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGG-C-ATTGAGACGAGT-
1 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTAATGAG--GA-TA
**
104245203 GCCAGTGTAAGA-CATGTCCGGGACAT-GCATCGGCCTCAATGAGGATA
1 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCT-AATGAGGATA
* *
104245250 GCCAGTGTAA-AACATGTCTAGGACAT-GCATCGG-CT-ATGA-GACA
1 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTAATGAGGATA
* * * *** * * *
104245293 TGTCAGTGTAAGACCATGTCTGGGAAATGGCATTAACATAGAT-ATGCAAGA
1 -GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTA-ATGA-G-GATA
* * *
104245344 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATGAGGATA
1 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCC-TAATGAGGATA
* *
104245393 GCTAGTGTAAGACCATGTCTAGGACATGACATCG
1 GCCAGTGTAAGACCATGTCTAGGACATGGCATCG
104245427 ACAACTTAAC
Statistics
Matches: 180, Mismatches: 28, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
43 3 0.02
44 13 0.07
45 13 0.07
46 15 0.08
47 45 0.25
48 13 0.07
49 41 0.23
50 33 0.18
51 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.22
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTAATGAGGATA
Found at i:104247002 original size:28 final size:28
Alignment explanation
Indices: 104246951--104247029 Score: 124
Period size: 28 Copynumber: 2.9 Consensus size: 28
104246941 CGTTTTTGGT
*
104246951 AAAACGCCGCT-AAAAATAGAGCAATAG
1 AAAACGCCGCTAAAAAACAGAGCAATAG
*
104246978 AAAACGCAGCTAAAAAACAGAGCAATAG
1 AAAACGCCGCTAAAAAACAGAGCAATAG
*
104247006 AAAACGCCGCTAAAAACCAGAGCA
1 AAAACGCCGCTAAAAAACAGAGCA
104247030 TTAGCGGCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 10 0.21
28 37 0.79
ACGTcount: A:0.53, C:0.22, G:0.18, T:0.08
Consensus pattern (28 bp):
AAAACGCCGCTAAAAAACAGAGCAATAG
Found at i:104247056 original size:41 final size:41
Alignment explanation
Indices: 104247006--104247102 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
104246996 AGAGCAATAG
***
104247006 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCAAT
*
104247047 AAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCAAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCAAT
104247088 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
104247103 GTCATATAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.19
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCAAT
Found at i:104248563 original size:8 final size:8
Alignment explanation
Indices: 104248527--104248623 Score: 99
Period size: 8 Copynumber: 11.9 Consensus size: 8
104248517 TTTATATGAT
104248527 AATTTAAA
1 AATTTAAA
104248535 AATTATAAA
1 AATT-TAAA
104248544 AATCTTCAAAA
1 AAT-TT--AAA
104248555 AATTTAAA
1 AATTTAAA
104248563 AA-TTAAA
1 AATTTAAA
104248570 AA-TTAAA
1 AATTTAAA
*
104248577 AAATTAAA
1 AATTTAAA
*
104248585 AAATTAAA
1 AATTTAAA
*
104248593 AACTTAAA
1 AATTTAAA
*
104248601 AACTTAAA
1 AATTTAAA
*
104248609 AACTTAAA
1 AATTTAAA
104248617 AATTTAA
1 AATTTAA
104248624 TATTTAATAT
Statistics
Matches: 82, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
7 14 0.17
8 51 0.62
9 8 0.10
10 3 0.04
11 6 0.07
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (8 bp):
AATTTAAA
Found at i:104248623 original size:16 final size:16
Alignment explanation
Indices: 104248530--104248623 Score: 111
Period size: 16 Copynumber: 5.8 Consensus size: 16
104248520 ATATGATAAT
104248530 TTAAAAATTATAAAAATC
1 TTAAAAATT-TAAAAA-C
104248548 TTCAAAAAATTTAAAAA-
1 TT--AAAAATTTAAAAAC
*
104248565 TTAAAAA-TTAAAAAA
1 TTAAAAATTTAAAAAC
*
104248580 TTAAAAAATTAAAAAC
1 TTAAAAATTTAAAAAC
*
104248596 TTAAAAACTTAAAAAC
1 TTAAAAATTTAAAAAC
104248612 TTAAAAATTTAA
1 TTAAAAATTTAA
104248624 TATTTAATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.10
15 12 0.17
16 33 0.48
17 2 0.03
18 2 0.03
19 6 0.09
20 7 0.10
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATTTAAAAAC
Found at i:104254036 original size:23 final size:23
Alignment explanation
Indices: 104254009--104254093 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
104253999 AAAGTGCTGC
104254009 AAATTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTTAAATGTTGT
*
104254032 AAATTGAAGTGCTTAAATGTTGT
1 AAATTGAAGTGTTTAAATGTTGT
* ** *
104254055 AAATTGAAGTGCTTTAAGTACTGC
1 AAATTGAAGTG-TTTAAATGTTGT
104254079 AAATTGAAGTGTTTA
1 AAATTGAAGTGTTTA
104254094 GCTGCTGGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 37 0.67
24 18 0.33
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (23 bp):
AAATTGAAGTGTTTAAATGTTGT
Found at i:104264431 original size:13 final size:13
Alignment explanation
Indices: 104264413--104264437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104264403 TGGCCGTGTG
104264413 AAAGGACACGGGC
1 AAAGGACACGGGC
104264426 AAAGGACACGGG
1 AAAGGACACGGG
104264438 TGTGTGTCCA
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:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (13 bp):
AAAGGACACGGGC
Found at i:104270022 original size:35 final size:35
Alignment explanation
Indices: 104269983--104270049 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
104269973 TTCCCAATTG
* * *
104269983 GGCCTGGGCCTATGTCAGATATAGATACAGATTCA
1 GGCCTGAGCCCATGTCAGATACAGATACAGATTCA
* *
104270018 GGCCTGAGCCCATTTCAGATGCAGATACAGAT
1 GGCCTGAGCCCATGTCAGATACAGATACAGAT
104270050 ACAAATATGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (35 bp):
GGCCTGAGCCCATGTCAGATACAGATACAGATTCA
Found at i:104271766 original size:11 final size:11
Alignment explanation
Indices: 104271750--104271774 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
104271740 GTTAGCATAT
104271750 ACAAGCAAAAA
1 ACAAGCAAAAA
104271761 ACAAGCAAAAA
1 ACAAGCAAAAA
104271772 ACA
1 ACA
104271775 CTTTACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.20, G:0.08, T:0.00
Consensus pattern (11 bp):
ACAAGCAAAAA
Found at i:104277506 original size:49 final size:49
Alignment explanation
Indices: 104277366--104277507 Score: 185
Period size: 49 Copynumber: 2.9 Consensus size: 49
104277356 AACATCGGCT
** *
104277366 GCCAACCTAGTTAATAACTAACATGTCCTACCAGTGGCCCAACATACAC
1 GCCAACCTAGTTAGCAACTAACATGTCCTACCAGTGGCCCATCATACAC
* *
104277415 GCCAACCTAGTTAGCAACTAACATGTCCTACAAGTGGCCCATCATGCAC
1 GCCAACCTAGTTAGCAACTAACATGTCCTACCAGTGGCCCATCATACAC
* * * * * *
104277464 TCCCACCTGGTTAGCAGCTAAAATGTCCTACCAGTGGTCCATCA
1 GCCAACCTAGTTAGCAACTAACATGTCCTACCAGTGGCCCATCA
104277508 CATCTGTCAT
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 81 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.22
Consensus pattern (49 bp):
GCCAACCTAGTTAGCAACTAACATGTCCTACCAGTGGCCCATCATACAC
Found at i:104287440 original size:35 final size:35
Alignment explanation
Indices: 104287399--104287468 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
104287389 AGAAGATAAT
104287399 GCCCCCCAAAAAACCTCTTCCTTTTTTCCTTTCCA
1 GCCCCCCAAAAAACCTCTTCCTTTTTTCCTTTCCA
104287434 GCCCCCCAAAAAACCTCTTCCTTTTTTCCTTTCCA
1 GCCCCCCAAAAAACCTCTTCCTTTTTTCCTTTCCA
104287469 CGTGAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.43, G:0.03, T:0.34
Consensus pattern (35 bp):
GCCCCCCAAAAAACCTCTTCCTTTTTTCCTTTCCA
Found at i:104288662 original size:17 final size:17
Alignment explanation
Indices: 104288640--104288672 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
104288630 CACTAACATT
*
104288640 AAAATGCAATGACAATA
1 AAAATGCAACGACAATA
104288657 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
104288673 GTGCACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATA
Found at i:104301862 original size:6 final size:6
Alignment explanation
Indices: 104301837--104301906 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
104301827 TGAATCCTCC
* * *
104301837 TATTTT T-TATT TATTCT TATTTT TA-TTT TATTTT ATTTTTT TATTTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT -TATTTT TA-TTTT
*
104301885 TTTTTT TATTTT TA-TTT TATTT
1 TATTTT TATTTT TATTTT TATTT
104301907 CAATTTTATT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 14 0.27
6 27 0.53
7 10 0.20
ACGTcount: A:0.16, C:0.01, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:104301867 original size:5 final size:5
Alignment explanation
Indices: 104301841--104301926 Score: 78
Period size: 5 Copynumber: 17.8 Consensus size: 5
104301831 TCCTCCTATT
104301841 TTTTA -TTTA TTCTTA TTTTTA TTTTA TTTTA -TTT- TTTTA TTTT- TTTT-
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
104301888 TTTTA TTTTTA TTTTA TTTCAA TTTTA --TTA TTTTA TTTT
1 TTTTA -TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTT
104301927 GAAAGACATA
Statistics
Matches: 69, Mismatches: 2, Indels: 20
0.76 0.02 0.22
Matches are distributed among these distances:
3 3 0.04
4 18 0.26
5 31 0.45
6 15 0.22
7 2 0.03
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:104301899 original size:37 final size:38
Alignment explanation
Indices: 104301837--104301926 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
104301827 TGAATCCTCC
*
104301837 TATT-TTTTATTTATTCTTATTTTTATTTTATTT-TATTT
1 TATTATTTTATTT-TT-TTATTTTTATTTTATTTCAATTT
* *
104301875 TTTTATTTTTTTTTTTTATTTTTATTTTATTTCAATTT
1 TATTATTTTATTTTTTTATTTTTATTTTATTTCAATTT
104301913 TATTATTTTATTTT
1 TATTATTTTATTTT
104301927 GAAAGACATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
37 17 0.38
38 21 0.47
39 7 0.16
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (38 bp):
TATTATTTTATTTTTTTATTTTTATTTTATTTCAATTT
Found at i:104301900 original size:43 final size:43
Alignment explanation
Indices: 104301839--104301926 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
104301829 AATCCTCCTA
* *
104301839 TTTTTTATTTATTCTTATTTTTATTT-TATTTTATTTTTTTATT
1 TTTTTTATTTATTCTTA-TTTTATTTCAATTTTATTATTTTATT
* *
104301882 TTTTTTTTTTATTTTTATTTTATTTCAATTTTATTATTTTATT
1 TTTTTTATTTATTCTTATTTTATTTCAATTTTATTATTTTATT
104301925 TT
1 TT
104301927 GAAAGACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 8 0.20
43 32 0.80
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (43 bp):
TTTTTTATTTATTCTTATTTTATTTCAATTTTATTATTTTATT
Found at i:104304766 original size:13 final size:13
Alignment explanation
Indices: 104304750--104304782 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
104304740 TTTAATTAAA
*
104304750 TTAGTTAATTAGT
1 TTAGATAATTAGT
104304763 TTAGATAATTAGT
1 TTAGATAATTAGT
104304776 TTA-ATAA
1 TTAGATAA
104304783 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:104306077 original size:2 final size:2
Alignment explanation
Indices: 104306070--104306097 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
104306060 ATCATCTTAC
104306070 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
104306098 CACAATTAAA
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:104312394 original size:8 final size:8
Alignment explanation
Indices: 104312346--104312405 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
104312336 AGCCGACAGC
104312346 AAAGAAGAA
1 AAAG-AGAA
104312355 AAAGA-AA
1 AAAGAGAA
104312362 ATAAGAGAA
1 A-AAGAGAA
* *
104312371 GAAG-GAT
1 AAAGAGAA
*
104312378 AAAGCGAA
1 AAAGAGAA
104312386 AAAGAGAA
1 AAAGAGAA
104312394 AAAG-GAA
1 AAAGAGAA
104312401 AAAGA
1 AAAGA
104312406 AAGAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 15 0.36
8 21 0.50
9 6 0.14
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAGAGAA
Found at i:104312403 original size:15 final size:16
Alignment explanation
Indices: 104312346--104312405 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 16
104312336 AGCCGACAGC
104312346 AAAGAAGAAAAAGA-AA
1 AAAG-AGAAAAAGAGAA
* *
104312362 ATAAGAGAAGAAG-GAT
1 A-AAGAGAAAAAGAGAA
*
104312378 AAAGCGAAAAAGAGAA
1 AAAGAGAAAAAGAGAA
104312394 AAAG-GAAAAAGA
1 AAAGAGAAAAAGA
104312406 AAGAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 17 0.47
16 16 0.44
17 3 0.08
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.03
Consensus pattern (16 bp):
AAAGAGAAAAAGAGAA
Found at i:104314274 original size:2 final size:2
Alignment explanation
Indices: 104314267--104314292 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
104314257 GCTTACTTCA
104314267 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
104314293 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104315495 original size:2 final size:2
Alignment explanation
Indices: 104315482--104315532 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
104315472 TTTAACTAAA
*
104315482 AT AT AA 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
104315524 AT AT AT AT A
1 AT AT AT AT A
104315533 CCAACCCTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:104316878 original size:28 final size:28
Alignment explanation
Indices: 104316846--104316940 Score: 131
Period size: 28 Copynumber: 3.4 Consensus size: 28
104316836 TCGCCACAGG
104316846 CTATTCTTTTCAAAGTTTGCCACAAATG-
1 CTATTCTTTTCAAAGTTTGCCACAAA-GA
*
104316874 CTATTCTTTTCATAA-TTCGCCACAAAGA
1 CTATTCTTTTCA-AAGTTTGCCACAAAGA
* *
104316902 CTATTCTTTTTAGAGTTTGCCACAAAGA
1 CTATTCTTTTCAAAGTTTGCCACAAAGA
104316930 CTATTCTTTTC
1 CTATTCTTTTC
104316941 TGTCGTGTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.03
28 55 0.93
29 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.41
Consensus pattern (28 bp):
CTATTCTTTTCAAAGTTTGCCACAAAGA
Found at i:104316919 original size:56 final size:54
Alignment explanation
Indices: 104316833--104316940 Score: 155
Period size: 56 Copynumber: 2.0 Consensus size: 54
104316823 AATATCCTAA
*
104316833 AATTCGCCACAGGCTATTCTTTTCAAAGTTTGCCACAAATG-CTATTCTTTTCAT
1 AATTCGCCACAGACTATTCTTTTCAAAGTTTGCCACAAA-GACTATTCTTTTCAT
* *
104316887 AATTCGCCACAAAGACTATTCTTTTTAGAGTTTGCCACAAAGACTATTCTTTTC
1 AATTCGCCAC--AGACTATTCTTTTCAAAGTTTGCCACAAAGACTATTCTTTTC
104316941 TGTCGTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
54 10 0.21
55 1 0.02
56 37 0.77
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (54 bp):
AATTCGCCACAGACTATTCTTTTCAAAGTTTGCCACAAAGACTATTCTTTTCAT
Found at i:104324575 original size:2 final size:2
Alignment explanation
Indices: 104324530--104324556 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104324520 TATTTCTAAA
104324530 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
104324557 GTAGTAACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104330451 original size:22 final size:22
Alignment explanation
Indices: 104330415--104330459 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
104330405 CTCTGTTTCG
104330415 TTTCTTTCTTATGTTCT-TTATT
1 TTTCTTTCTTATGTT-TATTATT
* *
104330437 TTTCTTTTTTTTGTTTATTATT
1 TTTCTTTCTTATGTTTATTATT
104330459 T
1 T
104330460 AGTTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (22 bp):
TTTCTTTCTTATGTTTATTATT
Found at i:104330483 original size:10 final size:11
Alignment explanation
Indices: 104330464--104330496 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
104330454 TTATTTAGTT
104330464 TAATTATAATA
1 TAATTATAATA
104330475 TAA-TATAATA
1 TAATTATAATA
104330485 TAATTATAATA
1 TAATTATAATA
104330496 T
1 T
104330497 TTTCTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAATTATAATA
Found at i:104341727 original size:19 final size:20
Alignment explanation
Indices: 104341690--104341726 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
104341680 TGGTAATGTT
104341690 AATGTTTTAATTCAATTTTG
1 AATGTTTTAATTCAATTTTG
104341710 AATG-TTTAATT-AATTTT
1 AATGTTTTAATTCAATTTT
104341727 TATGTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (20 bp):
AATGTTTTAATTCAATTTTG
Found at i:104348621 original size:136 final size:136
Alignment explanation
Indices: 104348377--104348661 Score: 536
Period size: 136 Copynumber: 2.1 Consensus size: 136
104348367 TATTGGGCCT
**
104348377 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCTTTTCAGATTACAATAAACTGGGCCTTA
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCTTTTCAGATTACAATAAACTGGGCCTTA
104348442 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAAC
66 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAAC
104348507 ATATGC
131 ATATGC
104348513 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTT-AGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAG-CCTTTTCAGATTACAATAAACTGGGCCTT
104348577 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
65 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
104348642 CATATGC
130 CATATGC
104348649 AAGCCCATTTGGG
1 AAGCCCATTTGGG
104348662 GAGACTACTC
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
136 140 0.96
137 6 0.04
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCTTTTCAGATTACAATAAACTGGGCCTTA
GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAAC
ATATGC
Found at i:104350477 original size:26 final size:26
Alignment explanation
Indices: 104350441--104350576 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
104350431 ACATGAATTC
*
104350441 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
104350467 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
104350493 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
104350519 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
104350545 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
104350571 TTATCA
1 TTATCA
104350577 ATTTGTATCA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:104354421 original size:64 final size:64
Alignment explanation
Indices: 104354348--104354556 Score: 156
Period size: 64 Copynumber: 3.2 Consensus size: 64
104354338 CTGGGCCAGA
*
104354348 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * **** * ** *
104354412 GCCCATTTCAAAATAC-ATGCAACATCAAAACATATGCAAGCCC--ATTTGGGTAACAGTGGTAC
1 GCCCATTTCAGATTACAAT-AAAC-T-GGGCCTTA-GC---CCCTTATTCAGATAACA---GTA-
* *
104354474 TGGGCCAGA-
55 TGGCCCATAG
*
104354483 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
104354547 GCCCATTTCA
1 GCCCATTTCA
104354557 AAATACATGC
Statistics
Matches: 101, Mismatches: 29, Indels: 30
0.63 0.18 0.19
Matches are distributed among these distances:
63 9 0.09
64 28 0.28
65 4 0.04
66 3 0.03
67 11 0.11
68 11 0.11
69 3 0.03
70 4 0.04
71 19 0.19
72 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:104354556 original size:135 final size:136
Alignment explanation
Indices: 104354314--104354597 Score: 534
Period size: 135 Copynumber: 2.1 Consensus size: 136
104354304 TATTGGGCCT
**
104354314 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
104354379 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCA-AAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGAAAC
104354443 ATATGC
131 ATATGC
104354449 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
104354514 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGAAAC
104354579 ATATGC
131 ATATGC
104354585 AAGCCCATTTGGG
1 AAGCCCATTTGGG
104354598 GAGACTACTC
Statistics
Matches: 145, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
135 123 0.85
136 22 0.15
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGAAAC
ATATGC
Found at i:104354881 original size:25 final size:26
Alignment explanation
Indices: 104354844--104354895 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
104354834 TCAAACATGC
104354844 ATTTAGGTCAATTTA-ACCCTAGGGGT
1 ATTTAGGTCAATTTACA-CCTAGGGGT
* *
104354870 ATTTCGGT-AATTTTCACCTAGGGGT
1 ATTTAGGTCAATTTACACCTAGGGGT
104354895 A
1 A
104354896 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (26 bp):
ATTTAGGTCAATTTACACCTAGGGGT
Found at i:104356408 original size:26 final size:26
Alignment explanation
Indices: 104356372--104356507 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
104356362 ACATGAATTC
104356372 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
104356398 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
104356424 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
104356450 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
104356476 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
104356502 TTATCA
1 TTATCA
104356508 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:104359083 original size:20 final size:18
Alignment explanation
Indices: 104359036--104359084 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
104359026 TTCAATTATG
104359036 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
104359053 ATTAAGA-TAATTACTTTAAT
1 ATTAA-ATTAA-TA-TTTAAT
104359073 ATTAAATTAATA
1 ATTAAATTAATA
104359085 ATGTAACACC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 4 0.15
20 14 0.52
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:104366262 original size:46 final size:46
Alignment explanation
Indices: 104366195--104366369 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
104366185 TGTAACCCGC
*
104366195 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGGCATTTGCAT
* *
104366241 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTGCAT
* * * * *
104366291 -C-TCA-CGAACACGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
104366334 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
104366370 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 4 0.04
46 60 0.56
47 27 0.25
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
Found at i:104366315 original size:93 final size:93
Alignment explanation
Indices: 104366203--104366373 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
104366193 GCCCATAAGT
* * * *
104366203 GAACTCGGACTCAACTCAACGAGCTT-GGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACACGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
104366267 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
104366296 GAACACGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACACGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
104366361 CGAGTTCGGATGC
66 CGAGTTCGGATGC
104366374 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACACGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:104370068 original size:2 final size:2
Alignment explanation
Indices: 104370061--104370101 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
104370051 TCAAACCAAT
104370061 TA TA TA 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 TA TA TA T
104370102 TCATATTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:104370587 original size:56 final size:56
Alignment explanation
Indices: 104370484--104370590 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
104370474 TTACATGTAA
* * * *
104370484 TCACATATCGATGCCATTGTCCCAGACAGTGTCTTACTTACATACATATATTGGAG
1 TCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTCACACACATATATTGGAG
* *
104370540 TCACATATCGATGCCACTGTCCCTGACAGGGTCTTACTCGCACACATATAT
1 TCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTCACACACATATAT
104370591 CTATGCCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (56 bp):
TCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTCACACACATATATTGGAG
Found at i:104374053 original size:27 final size:28
Alignment explanation
Indices: 104374009--104374106 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
104373999 ATAGTGAGTC
104374009 CGCACAC-TAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
104374035 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
104374063 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
104374093 CGCACACTTAGTGC
1 CGCACACTTAGTGC
104374107 CATTCTCATG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 7 0.11
27 14 0.23
28 22 0.35
30 19 0.31
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:104381982 original size:27 final size:28
Alignment explanation
Indices: 104381938--104382035 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
104381928 ATAGTGAGTC
104381938 CGCACAC-TAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
104381964 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
104381992 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
104382022 CGCACACTTAGTGC
1 CGCACACTTAGTGC
104382036 CATTCTCATG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 7 0.11
27 14 0.23
28 22 0.35
30 19 0.31
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:104383929 original size:26 final size:26
Alignment explanation
Indices: 104383893--104383976 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
104383883 TGATACAAAT
104383893 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
104383919 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
104383945 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
104383971 TGATAA
1 TGATAA
104383977 GAATTTCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:104385636 original size:27 final size:27
Alignment explanation
Indices: 104385595--104385734 Score: 156
Period size: 27 Copynumber: 5.2 Consensus size: 27
104385585 GAGGAAGCGT
* *
104385595 TCTGGTGGCTATGCCACAAATATTTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
104385622 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
104385649 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
104385676 TCTAGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * * *
104385704 TCAGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
104385730 TCTGG
1 TCTGG
104385735 CAGCCATGCT
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
26 4 0.04
27 80 0.82
28 13 0.13
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:104385684 original size:54 final size:55
Alignment explanation
Indices: 104385595--104385732 Score: 172
Period size: 54 Copynumber: 2.5 Consensus size: 55
104385585 GAGGAAGCGT
* * * * *
104385595 TCTGGTGGCTATGCCACAAATATTTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCTCTGCCACAAATATCTGTA
* *
104385649 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCTCTGCCACAAATATCTGTA
* * *
104385704 TCAGGTGACTCTGTCACAT-TATCTGTTCT
1 TCTGGTGGCTCTGCCACATATATCTGTTCT
104385733 GGCAGCCATG
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 56 0.77
55 17 0.23
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCTCTGCCACAAATATCTGTA
Found at i:104386845 original size:19 final size:20
Alignment explanation
Indices: 104386821--104386862 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
104386811 TTTGACCAGT
* *
104386821 TTTTGGG-TCTTGGTCTCAA
1 TTTTGGGCTCTTAGCCTCAA
104386840 TTTTGGGCTCTTAGCCTCAA
1 TTTTGGGCTCTTAGCCTCAA
104386860 TTT
1 TTT
104386863 AAGATCTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (20 bp):
TTTTGGGCTCTTAGCCTCAA
Found at i:104388103 original size:36 final size:36
Alignment explanation
Indices: 104388056--104388127 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
104388046 TCTTCAGTTT
* * *
104388056 GAACTTAGGCAATCTATGAGCTAATATTTGCTTGTC
1 GAACTTAGGCAATCAATAACCTAATATTTGCTTGTC
104388092 GAACTTAGGCAATCAATAACCTAATATTTGCTTGTC
1 GAACTTAGGCAATCAATAACCTAATATTTGCTTGTC
104388128 ACAATTTCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (36 bp):
GAACTTAGGCAATCAATAACCTAATATTTGCTTGTC
Found at i:104390026 original size:29 final size:29
Alignment explanation
Indices: 104389994--104390128 Score: 155
Period size: 29 Copynumber: 4.7 Consensus size: 29
104389984 ATACCCTCCG
** * *
104389994 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
104390023 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
104390052 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
104390081 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
104390110 AGCACGCACACTTAGTGCC
1 AGCTCGCACACTTAGTGCC
104390129 GATCTCGTCA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 92 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Done.