Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 188 of 226
Found at i:59718137 original size:18 final size:19
Alignment explanation
Indices: 59718114--59718157 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
59718104 TTTGCAACCC
*
59718114 AAGGGGAAGGGGAA-AGGG
1 AAGGGGAAGGGGAAGAGGA
59718132 AAGGGGAAGGGGAAGAGGA
1 AAGGGGAAGGGGAAGAGGA
59718151 AAGGGGA
1 AAGGGGA
59718158 GAAGAAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (19 bp):
AAGGGGAAGGGGAAGAGGA
Found at i:59718164 original size:24 final size:24
Alignment explanation
Indices: 59718114--59718166 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
59718104 TTTGCAACCC
* **
59718114 AAGGGGAAGGGGAAAGGGAAGGGG
1 AAGGGGAAGAGGAAAGGGAAGAAG
*
59718138 AAGGGGAAGAGGAAAGGGGAGAAG
1 AAGGGGAAGAGGAAAGGGAAGAAG
59718162 AAGGG
1 AAGGG
59718167 TAACCAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (24 bp):
AAGGGGAAGAGGAAAGGGAAGAAG
Found at i:59718503 original size:21 final size:21
Alignment explanation
Indices: 59718477--59718532 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
59718467 AACAGCGGTG
*
59718477 GCGGTGAAATTAGATACTATA
1 GCGGTGAGATTAGATACTATA
* *
59718498 GCGGTGAGATTAGATATTGTA
1 GCGGTGAGATTAGATACTATA
*
59718519 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
59718533 AATAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:59719488 original size:11 final size:11
Alignment explanation
Indices: 59719450--59719517 Score: 86
Period size: 11 Copynumber: 6.2 Consensus size: 11
59719440 TAAATCCTTT
59719450 CTCTCAATTT-
1 CTCTCAATTTC
59719460 CTCTCTAATATT-
1 CTCTC-AAT-TTC
59719472 CTCTCAATTTC
1 CTCTCAATTTC
59719483 CTCTCAATTTC
1 CTCTCAATTTC
*
59719494 CTCTCAAATTC
1 CTCTCAATTTC
*
59719505 CTCTCAAATTC
1 CTCTCAATTTC
59719516 CT
1 CT
59719518 ATTTAAAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
10 7 0.13
11 40 0.74
12 7 0.13
ACGTcount: A:0.22, C:0.34, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:59719492 original size:33 final size:33
Alignment explanation
Indices: 59719450--59719517 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
59719440 TAAATCCTTT
*
59719450 CTCTCAATTT-CTCTCTAATATT-CTCTCAATTTC
1 CTCTCAATTTCCTCTC-AA-ATTCCTCTCAAATTC
59719483 CTCTCAATTTCCTCTCAAATTCCTCTCAAATTC
1 CTCTCAATTTCCTCTCAAATTCCTCTCAAATTC
59719516 CT
1 CT
59719518 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 3 0.09
33 24 0.75
34 5 0.16
ACGTcount: A:0.22, C:0.34, G:0.00, T:0.44
Consensus pattern (33 bp):
CTCTCAATTTCCTCTCAAATTCCTCTCAAATTC
Found at i:59719570 original size:28 final size:27
Alignment explanation
Indices: 59719523--59719582 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
59719513 TTCCTATTTA
*
59719523 AAAAAAGTTTTAATTTTTTAATTATTTTT
1 AAAAAAGTTTTAATATTTT-ATT-TTTTT
59719552 AAAAAAGTTTTAA-ATTTTATTTTTTT
1 AAAAAAGTTTTAATATTTTATTTTTTT
*
59719578 GAAAA
1 AAAAA
59719583 TTTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.31
27 3 0.10
28 4 0.14
29 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (27 bp):
AAAAAAGTTTTAATATTTTATTTTTTT
Found at i:59720701 original size:7 final size:7
Alignment explanation
Indices: 59720689--59720714 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59720679 TAGTCGATTG
59720689 GTATTTA
1 GTATTTA
59720696 GTATTTA
1 GTATTTA
59720703 GTATTTA
1 GTATTTA
59720710 GTATT
1 GTATT
59720715 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:59721300 original size:30 final size:30
Alignment explanation
Indices: 59721227--59721308 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
59721217 ATCAACGAGG
* * * *
59721227 CCCAGACAATCACCCGGCCCATCATCAGCA
1 CCCACACAATCACCCGACCCAGCAACAGCA
*
59721257 CCCATACAATCACCAC-ACCCAGCAACAGCA
1 CCCACACAATCACC-CGACCCAGCAACAGCA
* *
59721287 CCGACACAGTCACCCGACCCAG
1 CCCACACAATCACCCGACCCAG
59721309 TAGTTCAACC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.33, C:0.48, G:0.12, T:0.07
Consensus pattern (30 bp):
CCCACACAATCACCCGACCCAGCAACAGCA
Found at i:59721384 original size:18 final size:18
Alignment explanation
Indices: 59721361--59721403 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
59721351 TGCCAGGTGC
*
59721361 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTTTAT
59721379 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTTTAT
*
59721397 GTTTCCT
1 GTATCCT
59721404 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTTTAT
Found at i:59721685 original size:21 final size:21
Alignment explanation
Indices: 59721661--59721701 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
59721651 ATCCCCTACC
* *
59721661 GGAGGAACCAGAATCCTCGCT
1 GGAGCAACCAGAACCCTCGCT
*
59721682 GGAGCAACCATAACCCTCGC
1 GGAGCAACCAGAACCCTCGC
59721702 CAGAAGCTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.24, T:0.12
Consensus pattern (21 bp):
GGAGCAACCAGAACCCTCGCT
Found at i:59725462 original size:20 final size:20
Alignment explanation
Indices: 59725413--59725464 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
59725403 GTATATAAAG
*
59725413 TATCGATACAACAAATTAAT
1 TATCGATACCACAAATTAAT
*
59725433 TATCAATACCACAAATTAAT
1 TATCGATACCACAAATTAAT
59725453 TATCGATACCAC
1 TATCGATACCAC
59725465 TATTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (20 bp):
TATCGATACCACAAATTAAT
Found at i:59726750 original size:19 final size:19
Alignment explanation
Indices: 59726697--59726744 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
59726687 ATATGAGTTT
59726697 ATGCACTT-ATGTGCTAGG
1 ATGCACTTCATGTGCTAGG
*
59726715 ATGCACTTCGTGTGCTAGG
1 ATGCACTTCATGTGCTAGG
59726734 ATGCACTTCAT
1 ATGCACTTCAT
59726745 TCGCTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (19 bp):
ATGCACTTCATGTGCTAGG
Found at i:59728428 original size:13 final size:13
Alignment explanation
Indices: 59728392--59728428 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
59728382 AAACCTAAGA
59728392 AAAGAGAAAATCT
1 AAAGAGAAAATCT
**
59728405 AAAGACTAAATCT
1 AAAGAGAAAATCT
59728418 AAAGAGAAAAT
1 AAAGAGAAAAT
59728429 TATACAAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.62, C:0.08, G:0.14, T:0.16
Consensus pattern (13 bp):
AAAGAGAAAATCT
Found at i:59747820 original size:46 final size:46
Alignment explanation
Indices: 59747729--59747821 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 46
59747719 TCGCATTAAG
* * *
59747729 TGGTTATAAATCTCTAAGACATTGATTCTGACAGACATTTGCAAAC
1 TGGTAATAAATCTCTAAGACATTGATTCTGACAGAAATTTACAAAC
* * **
59747775 TGGTAATAAATCT-TGAAGACATTTATTTTGATGGAAATTTACAAAC
1 TGGTAATAAATCTCT-AAGACATTGATTCTGACAGAAATTTACAAAC
59747821 T
1 T
59747822 TTAGATAGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (46 bp):
TGGTAATAAATCTCTAAGACATTGATTCTGACAGAAATTTACAAAC
Found at i:59749074 original size:45 final size:45
Alignment explanation
Indices: 59748938--59749107 Score: 180
Period size: 45 Copynumber: 3.8 Consensus size: 45
59748928 TCTAGCGTGC
*** * *
59748938 TTTCACATGATGCCATAGTGTCTTTTAGCTATGGTCTTACTTATTT
1 TTTC-CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATTT
* * * * *
59748984 CTACCATGATGCCATAGCGTCTTTCGGCTATGGTCTTACTCATTT
1 TTTCCATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATTT
* *
59749029 TTTTCATGATGCCATAACATCTTTCAACTATGGTCTTACTCA-TT
1 TTTCCATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATTT
* **
59749073 TTTGCAGTGACACCATAACATCTTTCAGCTATGGT
1 TTTCCA-TGATGCCATAACATCTTTCAGCTATGGT
59749108 ATTTGTAAGA
Statistics
Matches: 106, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
44 7 0.07
45 97 0.92
46 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (45 bp):
TTTCCATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATTT
Found at i:59749626 original size:22 final size:22
Alignment explanation
Indices: 59749586--59749627 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
59749576 TTATTTTTTT
*
59749586 TATTAAAATGTTAAAATAATAA
1 TATTAAAATGTAAAAATAATAA
59749608 TATTAAAA-GTAAAACATAAT
1 TATTAAAATGTAAAA-ATAAT
59749628 TTAAGGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
TATTAAAATGTAAAAATAATAA
Found at i:59750477 original size:12 final size:13
Alignment explanation
Indices: 59750460--59750523 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
59750450 TGGTTATTTG
59750460 AAATGATTATAT-
1 AAATGATTATATA
* *
59750472 AAATGAATAAATA
1 AAATGATTATATA
*
59750485 AAATGATTATATG
1 AAATGATTATATA
* *
59750498 AATTGGTTATATA
1 AAATGATTATATA
*
59750511 GAAATAATTATAT
1 -AAATGATTATAT
59750524 TAAGTGTTTA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
12 10 0.26
13 20 0.51
14 9 0.23
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.38
Consensus pattern (13 bp):
AAATGATTATATA
Found at i:59752288 original size:25 final size:26
Alignment explanation
Indices: 59752229--59752292 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 26
59752219 GTACATTTTT
59752229 GCTCATACGAGC-G-ATAAATGGTAA
1 GCTCATACGAGCTGAATAAATGGTAA
* * *
59752253 GCTCCTCCGAGCTGAAT-AATGGTTA
1 GCTCATACGAGCTGAATAAATGGTAA
*
59752278 TCTCATACGAGCTGA
1 GCTCATACGAGCTGA
59752293 GTATCAGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 10 0.31
25 20 0.62
26 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (26 bp):
GCTCATACGAGCTGAATAAATGGTAA
Found at i:59763478 original size:15 final size:15
Alignment explanation
Indices: 59763455--59763484 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59763445 GCATAACTGT
*
59763455 TCCTGAGGTAAAGAA
1 TCCTCAGGTAAAGAA
59763470 TCCTCAGGTAAAGAA
1 TCCTCAGGTAAAGAA
59763485 CATTTACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (15 bp):
TCCTCAGGTAAAGAA
Found at i:59768321 original size:396 final size:396
Alignment explanation
Indices: 59767589--59768365 Score: 1482
Period size: 396 Copynumber: 2.0 Consensus size: 396
59767579 TCCGCGAATA
59767589 TGCTTTTTGTTTCTTGTATTTTGGTATTCTCCATGTCCATTTTATGGTCCATGTTCAGGATTCGC
1 TGCTTTTTGTTTCTTGTATTTTGGTATTCTCCATGTCCATTTTATGGTCCATGTTCAGGATTCGC
59767654 GATTGTCCCTCCCAACAATTTTGTCTCCAAGGTTCAACCTTGTGTCTTCTTTTTGAGCTTTTGAT
66 GATTGTCCCTCCCAACAATTTTGTCTCCAAGGTTCAACCTTGTGTCTTCTTTTTGAGCTTTTGAT
59767719 TTTTTAAAAGGCTGCTGGAAAGTGGGAAGGGAGAAAGCAAAGTCATAATTGATTGAAAATATATG
131 TTTTTAAAAGGCTGCTGGAAAGTGGGAAGGGAGAAAGCAAAGTCATAATTGATTGAAAATATATG
* *
59767784 ACTAAACTGTAACGAAATTTCTAGTATAACTGTTCTATTAAAAGAAAAATCAAATTATTTTGTTC
196 ACTAAAATGTAACGAAATTTCTAGAATAACTGTTCTATTAAAAGAAAAATCAAATTATTTTGTTC
* *
59767849 TAAAATAAATGATATATATAAGTACTTTTAATTATTTTATTTTCTTTCCTATCCAAGTGTACTTT
261 TAAAATAAATGATATATATAAATACTTTTAATTATTTTATTTTCTTTCCTATCCAAATGTACTTT
59767914 TTGCTTGTGGAAGCAAAAAACTGGCAGCAAAAACAGTAACCAAATGACAAACGGTATTCTCCATG
326 TTGCTTGTGGAAGCAAAAAACTGGCAGCAAAAACAGTAACCAAATGACAAACGGTATTCTCCATG
59767979 TATTTT
391 TATTTT
**
59767985 TGCTTTTTGTTTCTTGTATTTTGGTATTCTCCATGTCCATTTTATGGTCTGTGTTCAGGATTCGC
1 TGCTTTTTGTTTCTTGTATTTTGGTATTCTCCATGTCCATTTTATGGTCCATGTTCAGGATTCGC
59768050 GATTGTCCCTCCCAACAATTTTGTCTCCAAGGTTCAACCTTGTGTCTTCTTTTTGAGCTTTTGAT
66 GATTGTCCCTCCCAACAATTTTGTCTCCAAGGTTCAACCTTGTGTCTTCTTTTTGAGCTTTTGAT
59768115 TTTTTAAAAGGCTGCTGGAAAGTGGGAAGGGAGAAAGCAAAGTCATAATTGATTGAAAATATATG
131 TTTTTAAAAGGCTGCTGGAAAGTGGGAAGGGAGAAAGCAAAGTCATAATTGATTGAAAATATATG
59768180 ACTAAAATGTAACGAAATTTCTAGAATAACTGTTCTATTAAAAGAAAAATCAAATTATTTTGTTC
196 ACTAAAATGTAACGAAATTTCTAGAATAACTGTTCTATTAAAAGAAAAATCAAATTATTTTGTTC
59768245 TAAAATAAATGATATATATAAATACTTTTAATTATTTTATTTTCTTTCCTATCCAAATGTACTTT
261 TAAAATAAATGATATATATAAATACTTTTAATTATTTTATTTTCTTTCCTATCCAAATGTACTTT
* *
59768310 TTGCTTGTGGAAGCAAAAAACTGGCGGCAAAAACAGTAACCAAATGACAAATGGTA
326 TTGCTTGTGGAAGCAAAAAACTGGCAGCAAAAACAGTAACCAAATGACAAACGGTA
59768366 CCTTAGCATA
Statistics
Matches: 373, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
396 373 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (396 bp):
TGCTTTTTGTTTCTTGTATTTTGGTATTCTCCATGTCCATTTTATGGTCCATGTTCAGGATTCGC
GATTGTCCCTCCCAACAATTTTGTCTCCAAGGTTCAACCTTGTGTCTTCTTTTTGAGCTTTTGAT
TTTTTAAAAGGCTGCTGGAAAGTGGGAAGGGAGAAAGCAAAGTCATAATTGATTGAAAATATATG
ACTAAAATGTAACGAAATTTCTAGAATAACTGTTCTATTAAAAGAAAAATCAAATTATTTTGTTC
TAAAATAAATGATATATATAAATACTTTTAATTATTTTATTTTCTTTCCTATCCAAATGTACTTT
TTGCTTGTGGAAGCAAAAAACTGGCAGCAAAAACAGTAACCAAATGACAAACGGTATTCTCCATG
TATTTT
Found at i:59768441 original size:23 final size:24
Alignment explanation
Indices: 59768414--59768458 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
59768404 GAGTCATTAA
*
59768414 TTAAGTTACTAAT-AAAATTTTAC
1 TTAAGTTACAAATAAAAATTTTAC
59768437 TTAAGTTACAAATAAAAATTTT
1 TTAAGTTACAAATAAAAATTTT
59768459 TCGTCCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (24 bp):
TTAAGTTACAAATAAAAATTTTAC
Found at i:59770147 original size:38 final size:38
Alignment explanation
Indices: 59770096--59770171 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
59770086 ATGAAGCAAC
59770096 ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
1 ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
59770134 ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
1 ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
59770172 TTCTCACATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (38 bp):
ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
Found at i:59775997 original size:2 final size:2
Alignment explanation
Indices: 59775990--59776030 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
59775980 GACCGTGTAG
59775990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59776031 ATACTATAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59782838 original size:30 final size:30
Alignment explanation
Indices: 59782802--59782864 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
59782792 AGAAGTTAGG
59782802 AAGAATTTAGTGTCTAGAAGTCTCTTGAAT
1 AAGAATTTAGTGTCTAGAAGTCTCTTGAAT
*
59782832 AAGAATTTAGTGTCTGGAAGTCTCTTGAAT
1 AAGAATTTAGTGTCTAGAAGTCTCTTGAAT
59782862 AAG
1 AAG
59782865 TTTGGTTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (30 bp):
AAGAATTTAGTGTCTAGAAGTCTCTTGAAT
Found at i:59802505 original size:137 final size:138
Alignment explanation
Indices: 59802048--59802599 Score: 887
Period size: 138 Copynumber: 4.0 Consensus size: 138
59802038 AATATAGATA
* * *
59802048 AATTAATATATCAATTTGATTCATA-AAAATATTAATTGCATATATTTTA-C-CATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATA
* * * * *
59802110 TAAACGATTATATTAATTAATTTAAGTCAAAATGTAAAAGATATAAAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
59802175 AAGAATAT
131 AAGAATAT
*
59802183 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAGTTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATA
* * *
59802248 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
59802313 AAGAATAT
131 AAGAATAT
* *
59802321 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATGTATTTTATTGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATA
*
59802386 TAAACAATTATATTAATTAA-TTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
59802450 AAGAATAT
131 AAGAATAT
* * *
59802458 AATTAATATATGAATTTGATTCATACAAAATATTAAATGTATATATTTTAACGAATTTATTAATG
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATA
* * *
59802523 TAAAAAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATCCTTTTGGA
66 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
59802588 AAGAATAT
131 AAGAATAT
59802596 AATT
1 AATT
59802600 CATTTTTCAA
Statistics
Matches: 389, Mismatches: 24, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
135 24 0.06
136 23 0.06
137 131 0.34
138 211 0.54
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATA
TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:59802591 original size:275 final size:273
Alignment explanation
Indices: 59802048--59802599 Score: 881
Period size: 275 Copynumber: 2.0 Consensus size: 273
59802038 AATATAGATA
*
59802048 AATTAATATATCAATTTGATTCATAAAAATATTAATTGCATATATTTTACCATTTATTAATATAA
1 AATTAATATATCAATTTGATTCATAAAAATATTAATTGCATATATTTTACAATTTATTAATATAA
* * *
59802113 ACGATTATATTAATTAATTTAAGTCAAAATGTAAAAGATATAAAAATTAATATTCTTTTGGAAAG
66 ACAATTATATTAATTAATTTAAGTCAAAATATAAAAGACATAAAAATTAATATTCTTTTGGAAAG
* * *
59802178 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAGTTTAT
131 AATATAATTAATATATGAATTTGATTCATACAAAATATTAAATGTATATATTTTAACGAATTTAT
* * * * *
59802243 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATTCTT
196 TAATATAAAAAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATCCTT
59802308 TTGGAAAGAATAT
261 TTGGAAAGAATAT
* * * *
59802321 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATGTATTTTATTGAATTTATTAATA
1 AATTAATATATCAATTTGATTCATA-AAAATATTAATTGCATATATTTTA--CAATTTATTAATA
** *
59802386 TAAACAATTATATTAATTAA-TTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
63 TAAACAATTATATTAATTAATTTAAGTCAAAATATAAAAGACATAAAAATTAATATTCTTTTGGA
59802450 AAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAAATGTATATATTTTAACGAATT
128 AAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAAATGTATATATTTTAACGAATT
* *
59802515 TATTAATGTAAAAAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATC
193 TATTAATATAAAAAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATC
59802580 CTTTTGGAAAGAATAT
258 CTTTTGGAAAGAATAT
59802596 AATT
1 AATT
59802600 CATTTTTCAA
Statistics
Matches: 255, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
273 24 0.09
274 22 0.09
275 179 0.70
276 30 0.12
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (273 bp):
AATTAATATATCAATTTGATTCATAAAAATATTAATTGCATATATTTTACAATTTATTAATATAA
ACAATTATATTAATTAATTTAAGTCAAAATATAAAAGACATAAAAATTAATATTCTTTTGGAAAG
AATATAATTAATATATGAATTTGATTCATACAAAATATTAAATGTATATATTTTAACGAATTTAT
TAATATAAAAAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATCCTT
TTGGAAAGAATAT
Found at i:59802706 original size:75 final size:75
Alignment explanation
Indices: 59802580--59802722 Score: 234
Period size: 75 Copynumber: 1.9 Consensus size: 75
59802570 AATTAATATC
* * *
59802580 CTTTTGGAAAGAATATAATTCATTTTTCAAAGTTTCCATTTGCCTTCTCTATTAATAAGGGAATA
1 CTTTTGAAAAGAATATAATTCATTTTTCAAACTTTCCATTTGCCTTATCTATTAATAAGGGAATA
59802645 ATCCTATGCT
66 ATCCTATGCT
*
59802655 CTTTTGAAAAGAATATAATTTC-TTTTTCTAACTTTCCATTTGCCTTATCTATTAATAAGGGAAT
1 CTTTTGAAAAGAATATAA-TTCATTTTTCAAACTTTCCATTTGCCTTATCTATTAATAAGGGAAT
59802719 AATC
65 AATC
59802723 TTGGTTTTCC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 60 0.95
76 3 0.05
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.43
Consensus pattern (75 bp):
CTTTTGAAAAGAATATAATTCATTTTTCAAACTTTCCATTTGCCTTATCTATTAATAAGGGAATA
ATCCTATGCT
Found at i:59804088 original size:20 final size:21
Alignment explanation
Indices: 59804056--59804100 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
59804046 TTCAACTATC
59804056 ATTAAACTTAATCACTTTAAT
1 ATTAAACTTAATCACTTTAAT
59804077 ATTAAA-TTAATCACTTTAAT
1 ATTAAACTTAATCACTTTAAT
59804097 -TTAA
1 ATTAA
59804101 TATATAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAAACTTAATCACTTTAAT
Found at i:59804169 original size:66 final size:71
Alignment explanation
Indices: 59804025--59804161 Score: 229
Period size: 75 Copynumber: 1.9 Consensus size: 71
59804015 TGCTCTTTTT
59804025 ATATATAGAGAGTTTAGAGAGTTCAACTATCATTAAACTTAATCACTTTAATATTAAATTAATCA
1 ATATATAGAGAGTTTAGAGAGTTCAACTATCATTAAACTTAATCACTTTAATATTAAATTAA-CA
59804090 CTTTAATTTA
65 --TTAA-TTA
*
59804100 ATATATAGAGAGTTTAGAGAGTTCAACTATGATTAAACTTAATCACTTTAATATTAAATTAA
1 ATATATAGAGAGTTTAGAGAGTTCAACTATCATTAAACTTAATCACTTTAATATTAAATTAA
59804162 TATAATATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (71 bp):
ATATATAGAGAGTTTAGAGAGTTCAACTATCATTAAACTTAATCACTTTAATATTAAATTAACAT
TAATTA
Found at i:59807497 original size:25 final size:25
Alignment explanation
Indices: 59807468--59807517 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
59807458 ACTACTGAGT
* *
59807468 TTATTGTCCGGTAAGCCTGCCCGAG
1 TTATTATCCGGTAAGCCTCCCCGAG
59807493 TTATTATCCGGTAAGCCTCCCCGAG
1 TTATTATCCGGTAAGCCTCCCCGAG
59807518 GGAGGTACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.28
Consensus pattern (25 bp):
TTATTATCCGGTAAGCCTCCCCGAG
Found at i:59814698 original size:27 final size:27
Alignment explanation
Indices: 59814653--59814811 Score: 153
Period size: 27 Copynumber: 6.0 Consensus size: 27
59814643 TATCTGGACC
* *
59814653 AAAATATCCTCAAATGGTAAAATGACT
1 AAAATACCCTCAAAGGGTAAAATGACT
* *
59814680 GAAATACCCTAAAAGGGTAAAATGACT
1 AAAATACCCTCAAAGGGTAAAATGACT
* *
59814707 AAAATACCCTC-GATGGTAAAATGA-T
1 AAAATACCCTCAAAGGGTAAAATGACT
* * *
59814732 CGAAATACCCTCGATGGGTAAAATGACT
1 -AAAATACCCTCAAAGGGTAAAATGACT
* ** *
59814760 AAAATACCCCCATGGGGTAGAAT-ACT
1 AAAATACCCTCAAAGGGTAAAATGACT
* *
59814786 AAAATACCCCCATAGGGTAAAATGAC
1 AAAATACCCTCAAAGGGTAAAATGAC
59814812 CGTAAAACCC
Statistics
Matches: 108, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
25 1 0.01
26 45 0.42
27 61 0.56
28 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (27 bp):
AAAATACCCTCAAAGGGTAAAATGACT
Found at i:59814724 original size:53 final size:52
Alignment explanation
Indices: 59814666--59814811 Score: 170
Period size: 53 Copynumber: 2.8 Consensus size: 52
59814656 ATATCCTCAA
* *
59814666 ATGGTAAAATGACTGAAATACCCTAAAAGGGTAAAATGACTAAAATACCCTCG
1 ATGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGACTAAAATACCC-CC
* *
59814719 ATGGTAAAATGA-TCGAAATACCCTCGATGGGTAAAATGACTAAAATACCCCC
1 ATGGTAAAATGACT-GAAATACCCTCAAAGGGTAAAATGACTAAAATACCCCC
* * * *
59814771 ATGGGGTAGAAT-ACTAAAATACCCCCATAGGGTAAAATGAC
1 AT--GGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGAC
59814812 CGTAAAACCC
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
52 4 0.05
53 67 0.85
54 8 0.10
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (52 bp):
ATGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGACTAAAATACCCCC
Found at i:59814786 original size:26 final size:26
Alignment explanation
Indices: 59814668--59814811 Score: 141
Period size: 26 Copynumber: 5.4 Consensus size: 26
59814658 ATCCTCAAAT
* ** *
59814668 GGTAAAATGACTGAAATACCCTAAAAG
1 GGTAAAATGACTAAAATACCC-CCATG
*
59814695 GGTAAAATGACTAAAATACCCTCGAT-
1 GGTAAAATGACTAAAATACCC-CCATG
* *
59814721 GGTAAAATGA-TCGAAATACCCTCGATG
1 GGTAAAATGACT-AAAATACCC-CCATG
59814748 GGTAAAATGACTAAAATACCCCCATGG
1 GGTAAAATGACTAAAATACCCCCAT-G
*
59814775 GGTAGAAT-ACTAAAATACCCCCATAG
1 GGTAAAATGACTAAAATACCCCCAT-G
59814801 GGTAAAATGAC
1 GGTAAAATGAC
59814812 CGTAAAACCC
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.01
26 50 0.49
27 50 0.49
28 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (26 bp):
GGTAAAATGACTAAAATACCCCCATG
Found at i:59814924 original size:27 final size:27
Alignment explanation
Indices: 59814788--59814924 Score: 150
Period size: 27 Copynumber: 5.1 Consensus size: 27
59814778 AGAATACTAA
**
59814788 AATACCCCCATAGGGTAAAATGACCGT
1 AATACCCCTGTAGGGTAAAATGACCGT
* *
59814815 AAAACCCTTGTAGGGTAAAATGACCGT
1 AATACCCCTGTAGGGTAAAATGACCGT
* * *
59814842 AATGCCCCTGTAGGGTAAAATGATCAT
1 AATACCCCTGTAGGGTAAAATGACCGT
* * * **
59814869 AA-GCCCTTATAGGGTAAAATGAGAGT
1 AATACCCCTGTAGGGTAAAATGACCGT
*
59814895 AATACCCCTGTAGGGTAAAATAACCGT
1 AATACCCCTGTAGGGTAAAATGACCGT
59814922 AAT
1 AAT
59814925 TCCCTGGTGT
Statistics
Matches: 89, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
26 21 0.24
27 68 0.76
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAATGACCGT
Found at i:59814939 original size:53 final size:53
Alignment explanation
Indices: 59814788--59814923 Score: 173
Period size: 53 Copynumber: 2.5 Consensus size: 53
59814778 AGAATACTAA
** *
59814788 AATACCCCCATAGGGTAAAATGACCGTAAAACCCTTGTAGGGTAAAATGACCGT
1 AATACCCCTGTAGGGTAAAATGACCGT-AAACCCTTGTAGGGTAAAATGACAGT
* * * * * *
59814842 AATGCCCCTGTAGGGTAAAATGATCATAAGCCCTTATAGGGTAAAATGAGAGT
1 AATACCCCTGTAGGGTAAAATGACCGTAAACCCTTGTAGGGTAAAATGACAGT
*
59814895 AATACCCCTGTAGGGTAAAATAACCGTAA
1 AATACCCCTGTAGGGTAAAATGACCGTAA
59814924 TTCCCTGGTG
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 47 0.68
54 22 0.32
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (53 bp):
AATACCCCTGTAGGGTAAAATGACCGTAAACCCTTGTAGGGTAAAATGACAGT
Found at i:59815021 original size:24 final size:24
Alignment explanation
Indices: 59814988--59815046 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
59814978 TCTGTGGTTA
59814988 AATGACTGATTTATCTGTG-TTTGG
1 AATGACTGATTTATCTGTGATTT-G
* * *
59815012 TATGACTGATTTGTTTGTGATTTG
1 AATGACTGATTTATCTGTGATTTG
59815036 AATGACTGATT
1 AATGACTGATT
59815047 CTAAGCATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTATCTGTGATTTG
Found at i:59815140 original size:21 final size:20
Alignment explanation
Indices: 59815111--59815153 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
59815101 TGGAGGAAGT
*
59815111 ACTGTACTGGTGGCTTTGCC
1 ACTGTACTGGTGGCTTGGCC
59815131 ACTGTTACTGGTGGCTTGGCC
1 ACTG-TACTGGTGGCTTGGCC
59815152 AC
1 AC
59815154 ATATACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.12, C:0.26, G:0.30, T:0.33
Consensus pattern (20 bp):
ACTGTACTGGTGGCTTGGCC
Found at i:59815323 original size:32 final size:32
Alignment explanation
Indices: 59815211--59815395 Score: 149
Period size: 32 Copynumber: 5.8 Consensus size: 32
59815201 GCTGCGATGC
* *
59815211 TACTGATGGCTTTGTACCGATCATAGTACCGC
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* * *
59815243 TACTGATGGCTTTGTCCCGATTATAGTACCAT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* *
59815275 TACTGATGGCTTTGTGCCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* * * * * **
59815307 TACCGATGGCTGTGTGCTGGTCAT-TTCACTAT
1 TACTGATGGCTTTGTGCCGATCATAGT-ACCGT
** * * ***
59815339 TACTGATGGCTGCGTGCTGGTCATA-TGACTAC
1 TACTGATGGCTTTGTGCCGATCATAGT-ACCGT
59815371 TACTGATGGCTTTGTGCCGATCATA
1 TACTGATGGCTTTGTGCCGATCATA
59815396 TCATTGCTAC
Statistics
Matches: 127, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
31 2 0.02
32 125 0.98
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACCGT
Found at i:59815396 original size:32 final size:32
Alignment explanation
Indices: 59815210--59815424 Score: 143
Period size: 32 Copynumber: 6.8 Consensus size: 32
59815200 TGCTGCGATG
* **
59815210 CTACTGATGGCTTTGTACCGATCATA-GTACCG
1 CTACTGATGGCTTTGTGCCGATCATATG-ACTA
* * *
59815242 CTACTGATGGCTTTGTCCCGATTATA-GTACCA
1 CTACTGATGGCTTTGTGCCGATCATATG-ACTA
* *
59815274 TTACTGATGGCTTTGTGCCGATCATATTA-T-
1 CTACTGATGGCTTTGTGCCGATCATATGACTA
* * * * * *
59815304 CGTTACCGATGGCTGTGTGCTGGTCATTTCACTA
1 C--TACTGATGGCTTTGTGCCGATCATATGACTA
* ** * *
59815338 TTACTGATGGCTGCGTGCTGGTCATATGACTA
1 CTACTGATGGCTTTGTGCCGATCATATGACTA
* * *
59815370 CTACTGATGGCTTTGTGCCGATCATATCATTG
1 CTACTGATGGCTTTGTGCCGATCATATGACTA
* *
59815402 CTACT-ATGGCTTTTTGCCAATCA
1 CTACTGATGGCTTTGTGCCGATCA
59815425 CATTACTGTA
Statistics
Matches: 148, Mismatches: 30, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
31 16 0.11
32 131 0.89
33 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (32 bp):
CTACTGATGGCTTTGTGCCGATCATATGACTA
Found at i:59818574 original size:41 final size:42
Alignment explanation
Indices: 59818516--59818594 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 42
59818506 AAAAAATAAT
* *
59818516 TTAAAAAGAATAGAAGATAATC-TAGGGTTGTT-GAAAAGAAC
1 TTAAAAAGAATACAAGATAAACAT-GGGTTGTTGGAAAAGAAC
59818557 TTAAAAAG-ATGACAAGATAAACATGGGTTGTTGGAAAA
1 TTAAAAAGAAT-ACAAGATAAACATGGGTTGTTGGAAAA
59818595 AGAAAGCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
40 2 0.06
41 25 0.76
42 6 0.18
ACGTcount: A:0.48, C:0.05, G:0.23, T:0.24
Consensus pattern (42 bp):
TTAAAAAGAATACAAGATAAACATGGGTTGTTGGAAAAGAAC
Found at i:59824262 original size:27 final size:25
Alignment explanation
Indices: 59824230--59824280 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
59824220 TATATTGATT
59824230 CATTTACATTAAAAATAACATAATAAA
1 CATTTA-ATT-AAAATAACATAATAAA
* *
59824257 CATTTAATTTAAATAACATTATAA
1 CATTTAATTAAAATAACATAATAA
59824281 TGATTACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 3 0.14
27 6 0.27
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (25 bp):
CATTTAATTAAAATAACATAATAAA
Found at i:59829457 original size:42 final size:42
Alignment explanation
Indices: 59829397--59829477 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
59829387 CTAGAAAAAC
* *
59829397 ATTTAAAAAAGGAGAAGATAATCTTGCGTTGTT-GAAAATGA
1 ATTTAAAAAAGGAGAAGATAAACATGCGTTGTTGGAAAATGA
*
59829438 ATTTAAAAATAGGAGAAGATAAACATGGGTTGTTGGAAAA
1 ATTTAAAAA-AGGAGAAGATAAACATGCGTTGTTGGAAAA
59829478 AAGCTATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 9 0.26
42 21 0.60
43 5 0.14
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (42 bp):
ATTTAAAAAAGGAGAAGATAAACATGCGTTGTTGGAAAATGA
Found at i:59834125 original size:16 final size:17
Alignment explanation
Indices: 59834104--59834143 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
59834094 CGTTTGGTTT
*
59834104 GCTGTAATTGAATA-AA
1 GCTGTAATGGAATAGAA
59834120 GCTGTAATGGAATAGAA
1 GCTGTAATGGAATAGAA
59834137 -CTGTAAT
1 GCTGTAAT
59834144 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (17 bp):
GCTGTAATGGAATAGAA
Found at i:59834176 original size:45 final size:44
Alignment explanation
Indices: 59834125--59834217 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
59834115 ATAAAGCTGT
* *
59834125 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTATAATAGT-ATTC-ATGTGTTTGGTTGAATGA
*
59834170 AATGGAATAGAACTATAATAGTATTCTTGTGTTTGGTTGAATGA
1 AATGGAATAGAACTATAATAGTATTCATGTGTTTGGTTGAATGA
59834214 AATG
1 AATG
59834218 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTATAATAGTATTCATGTGTTTGGTTGAATGA
Found at i:59834438 original size:55 final size:54
Alignment explanation
Indices: 59834329--59834445 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 54
59834319 TATTATTAAT
* * *
59834329 ATAAATAATAAATAATTTAATCATATTTTAACATAATTATTTTTAAATATAATTTA
1 ATAAA-AATAAATAATTTAATAAAATTTTAACATAATTATTCTT-AATATAATTTA
* **
59834385 ATAAAAATATATAATTTAATAAAATTCTTATTATAATTATTCTT-ATATGAATTTA
1 ATAAAAATAAATAATTTAATAAAATT-TTAACATAATTATTCTTAATAT-AATTTA
*
59834440 CTAAAA
1 ATAAAA
59834446 TCATAATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 4 0.08
55 29 0.56
56 19 0.37
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (54 bp):
ATAAAAATAAATAATTTAATAAAATTTTAACATAATTATTCTTAATATAATTTA
Found at i:59834695 original size:23 final size:24
Alignment explanation
Indices: 59834684--59834729 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
59834674 TCATAATATC
59834684 CAAACATAATATTCAT-ATATTAA
1 CAAACATAATATTCATAATATTAA
59834707 CAAACATAATATTCAT-ATATTAA
1 CAAACATAATATTCATAATATTAA
59834730 TAAAAAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (24 bp):
CAAACATAATATTCATAATATTAA
Found at i:59840350 original size:23 final size:23
Alignment explanation
Indices: 59840321--59840441 Score: 145
Period size: 23 Copynumber: 5.3 Consensus size: 23
59840311 GTGTTATTGA
*
59840321 TCAGTGGTAACTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* * *
59840344 TCGGTGGTAGCTACGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
*
59840367 TCAGTGGTAGCTTTGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* * *
59840390 TCAGTGCTAGCTACGGCTACGTAT
1 TCAGTGGTAGCTTCGGCTACAT-T
*
59840414 T-AGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
59840436 TCAGTG
1 TCAGTG
59840442 TGGCACTTAT
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
22 1 0.01
23 77 0.96
24 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:59840387 original size:46 final size:46
Alignment explanation
Indices: 59840320--59840441 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
59840310 AGTGTTATTG
* * *
59840320 ATCAGTGGTAACTTCGGCTACATTTCGGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGGCTACAT
* *
59840366 ATCAGTGGTAGCTTTGGCTACATTTCAGTGCTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGGCTACAT
* *
59840412 ATTAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
59840442 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGGCTACAT
Found at i:59840594 original size:13 final size:13
Alignment explanation
Indices: 59840555--59840607 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
59840545 AATTCTTCAT
59840555 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
** *
59840568 TGCAGTGGAAAAG
1 TGCTTTTGAAAAG
*
59840581 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
59840594 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
59840607 T
1 T
59840608 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:59844558 original size:18 final size:18
Alignment explanation
Indices: 59844537--59844578 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
59844527 AATGATTTTT
59844537 ATTTTAATATTT-TTAAAA
1 ATTTTAA-ATTTGTTAAAA
*
59844555 ATTTCAAATTTGTTAAAA
1 ATTTTAAATTTGTTAAAA
*
59844573 TTTTTA
1 ATTTTA
59844579 TATAATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTAAATTTGTTAAAA
Found at i:59844558 original size:24 final size:25
Alignment explanation
Indices: 59844502--59844558 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
59844492 AAACACTTAT
* *
59844502 AATATTTTTTATTTTTTATTTTTTA
1 AATAATTTTTATTTTATATTTTTTA
*
59844527 AATGATTTTTATTTTA-ATATTTTTA
1 AATAATTTTTATTTTATAT-TTTTTA
59844552 AA-AATTT
1 AATAATTT
59844559 CAAATTTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
AATAATTTTTATTTTATATTTTTTA
Found at i:59847577 original size:14 final size:15
Alignment explanation
Indices: 59847555--59847584 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
59847545 AAAGAAGAAG
59847555 TGGTGAAGAAAATGA
1 TGGTGAAGAAAATGA
59847570 TGGT-AAGAAAATGA
1 TGGTGAAGAAAATGA
59847584 T
1 T
59847585 TAGTGGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (15 bp):
TGGTGAAGAAAATGA
Found at i:59852292 original size:30 final size:30
Alignment explanation
Indices: 59852258--59852315 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
59852248 TTCGAGCTTT
59852258 GGGGCAAAAGTGTAATTATGTAAAAGTTTA
1 GGGGCAAAAGTGTAATTATGTAAAAGTTTA
* * *
59852288 GGGGCAAAATTGTAATTTTGTCAAAGTT
1 GGGGCAAAAGTGTAATTATGTAAAAGTT
59852316 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAGTGTAATTATGTAAAAGTTTA
Found at i:59852724 original size:56 final size:51
Alignment explanation
Indices: 59852652--59852901 Score: 213
Period size: 50 Copynumber: 4.9 Consensus size: 51
59852642 ACATTAAGAG
**
59852652 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--ACCGA
* * *
59852703 GATTATGAGAGGTCCCATGTAAAACCATGTCTGAGACATGGCGTTGGC-ACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAACCGA
* *
59852756 GATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGC-AGCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAACCGA
* * * ** * * * **
59852806 TATGTGACGTCCCCCGTAAGACCATATCTGGGACATCGCATGGGC-ACTTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAACCGA
* ** * **
59852856 TATGAGAACTCCCATGTAAGACCATATCTGGGATGTGGCATTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
59852902 GTACAAGAAA
Statistics
Matches: 162, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
50 118 0.73
51 1 0.01
53 4 0.02
54 6 0.04
56 33 0.20
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (51 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAACCGA
Found at i:59852869 original size:100 final size:101
Alignment explanation
Indices: 59852652--59852902 Score: 256
Period size: 100 Copynumber: 2.5 Consensus size: 101
59852642 ACATTAAGAG
*
59852652 GATGAG-A-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATTATGAGAGG
1 GATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---A--GAGATTATGAGACG
* * * * *
59852715 TCCCATGTAAAACCATGTCTGAGACATGGCGTTGGCACCGA
61 TCCCACGTAAAACCATATCTGAGACATCGCATGGGCACCGA
** * * * *
59852756 GATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCAGCGA-TATGTGACGTCCCC
1 GATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAGAGATTATGAGACGTCCCA
* * **
59852820 CGTAAGACCATATCTGGGACATCGCATGGGCACTTA
66 CGTAAAACCATATCTGAGACATCGCATGGGCACCGA
* * **
59852856 TATGAGAACTCCCATGTAAGACCATATCTGGGATGTGGCATTGGCAG
1 GATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAG
59852903 TACAAGAAAC
Statistics
Matches: 123, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
100 78 0.63
101 3 0.02
103 1 0.01
104 6 0.05
106 35 0.28
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (101 bp):
GATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAGAGATTATGAGACGTCCCA
CGTAAAACCATATCTGAGACATCGCATGGGCACCGA
Found at i:59859775 original size:50 final size:50
Alignment explanation
Indices: 59859665--59859893 Score: 194
Period size: 50 Copynumber: 4.5 Consensus size: 50
59859655 ACATTAAGAG
* * * *
59859665 GATGAGA--TCCCATGTAAGACCATGCCTGGGACATGGCATTGCCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCA---A
* * * *
59859716 GATAATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGACGTTTGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCAA
* *
59859769 GATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCAA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCAA
* * ** * * *
59859819 TATGTGAGGTCCCCCGTAAGACCATATCTGGGACATCG-CATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACAT-GACATTGGCACCAA
* **
59859869 TATGAGAACTCCCATGTAAGACCAT
1 GATGAGAGGTCCCATGTAAGACCAT
59859894 ATCTAGGATG
Statistics
Matches: 145, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
50 103 0.71
51 2 0.01
53 2 0.01
54 6 0.04
56 32 0.22
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCAA
Found at i:59859866 original size:100 final size:102
Alignment explanation
Indices: 59859665--59859912 Score: 245
Period size: 100 Copynumber: 2.4 Consensus size: 102
59859655 ACATTAAGAG
* * * *
59859665 GATGAGATCCCATGTAAGACCATGCCTGGGACATGGCATTGCCATCATTGAGATAATGAGAGGTC
1 GATGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATC--TCAGATAATGAGAGGTC
* * * * **
59859730 CCATGTAAGACCATGTTTGGGACATGACGTTTGCACCGA
64 CCACGTAAGACCATATCTGGGACATGACATGGGCACCGA
*
59859769 GATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-C-CA-AT-ATGTGAGGTC
1 GATGAGA--TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCTCAGATAATGAGAGGTC
* *
59859830 CCCCGTAAGACCATATCTGGGACATCG-CATGGGCACCTA
64 CCACGTAAGACCATATCTGGGACAT-GACATGGGCACCGA
* * **
59859869 TATGAGAACTCCCATGTAAGACCATATCTAGGATGTGGCATTGG
1 GATGAG-A-TCCCATGTAAGACCATGTCTAGGACATGGCATTGG
59859913 AAGTACAAGA
Statistics
Matches: 122, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
100 75 0.61
101 4 0.03
102 1 0.01
104 7 0.06
105 1 0.01
106 34 0.28
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (102 bp):
GATGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCTCAGATAATGAGAGGTCCC
ACGTAAGACCATATCTGGGACATGACATGGGCACCGA
Found at i:59870465 original size:15 final size:14
Alignment explanation
Indices: 59870445--59870474 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59870435 CACATACCTC
*
59870445 TTTTTTAAAATATT
1 TTTTTTTAAATATT
59870459 TTTTTTTAAATATT
1 TTTTTTTAAATATT
59870473 TT
1 TT
59870475 ACTTTGCCTC
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTTAAATATT
Found at i:59870757 original size:3 final size:3
Alignment explanation
Indices: 59870742--59870779 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
59870732 ATTCAAAAAG
* *
59870742 CAT CAT TAT CAT CAT CAT CAT CAT TAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
59870780 CTATAGTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (3 bp):
CAT
Found at i:59882072 original size:210 final size:210
Alignment explanation
Indices: 59881710--59882134 Score: 787
Period size: 210 Copynumber: 2.0 Consensus size: 210
59881700 TCGATATCAG
* *
59881710 AGATGTTCCCTACACTAACTCAATAGCAAACTCAACCTCTCTGATTAGCTGTAACCTAGGTAATT
1 AGATGTTCCCTACACTAACTCAATAGCAAACTCAACCTCTCTGATTAACTGTAACCCAGGTAATT
*
59881775 CTTCTAGAAATAGTCCAGTATACTCGCATACCACAAGAACCAATTCTAGCTTTAGTTTAGAAACT
66 CTACTAGAAATAGTCCAGTATACTCGCATACCACAAGAACCAATTCTAGCTTTAGTTTAGAAACT
* * *
59881840 CTAGAATCAAATATATAAGCAAGATACTTTTCACTGCCTTTTCTACCATATTTCTGTGTTGGCAT
131 CTAGAATCAAATATATAAGCAAGATACGTTTCACTACCTTTTCTACCATATTTCTGTCTTGGCAT
*
59881905 AGCCGAAATAACATT
196 AGACGAAATAACATT
59881920 AGATGTTCCCTACACTAACTCAATAGCAAACTCAACCTCTCTGATTAACTGTAACCCAGGTAATT
1 AGATGTTCCCTACACTAACTCAATAGCAAACTCAACCTCTCTGATTAACTGTAACCCAGGTAATT
59881985 CTACTAGAAATAGTCCAGTATACTCGCATACCACAAGAACCAATTCTAGCTTTAGTTTAGAAACT
66 CTACTAGAAATAGTCCAGTATACTCGCATACCACAAGAACCAATTCTAGCTTTAGTTTAGAAACT
59882050 CTAGAATCAAATATATAAGCAAGATACGTTTCACTACCTTTTCTACCATATTTCTGTCTTGGCAT
131 CTAGAATCAAATATATAAGCAAGATACGTTTCACTACCTTTTCTACCATATTTCTGTCTTGGCAT
59882115 AGACGAAATAACATT
196 AGACGAAATAACATT
59882130 AGATG
1 AGATG
59882135 CACTATCCAA
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
210 208 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (210 bp):
AGATGTTCCCTACACTAACTCAATAGCAAACTCAACCTCTCTGATTAACTGTAACCCAGGTAATT
CTACTAGAAATAGTCCAGTATACTCGCATACCACAAGAACCAATTCTAGCTTTAGTTTAGAAACT
CTAGAATCAAATATATAAGCAAGATACGTTTCACTACCTTTTCTACCATATTTCTGTCTTGGCAT
AGACGAAATAACATT
Found at i:59885548 original size:50 final size:50
Alignment explanation
Indices: 59885493--59885637 Score: 173
Period size: 50 Copynumber: 2.9 Consensus size: 50
59885483 CGTTGAGATT
* *
59885493 ATGAGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * *
59885543 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* ** * * * *
59885593 ATGATAACTCCCTTGTAAGACTATATCTGGGATATGGCATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
59885638 AAAACATCCC
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:59905724 original size:31 final size:31
Alignment explanation
Indices: 59905684--59905753 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
59905674 GTTACATGTT
59905684 ACACA-TAAGCATCTTGTCACATTAAATTGA
1 ACACACTAAGCATCTTGTCACATTAAATTGA
59905714 ACACACTAAGCATCTTGTCACATTAAATTGA
1 ACACACTAAGCATCTTGTCACATTAAATTGA
*
59905745 ACACGCTAA
1 ACACACTAA
59905754 TAATTGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 5 0.13
31 33 0.87
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (31 bp):
ACACACTAAGCATCTTGTCACATTAAATTGA
Found at i:59906561 original size:15 final size:15
Alignment explanation
Indices: 59906541--59906569 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59906531 GTATTGTTGC
59906541 TTGATAACACGGTGA
1 TTGATAACACGGTGA
59906556 TTGATAACACGGTG
1 TTGATAACACGGTG
59906570 TGTCAAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:59912589 original size:49 final size:49
Alignment explanation
Indices: 59912498--59912594 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
59912488 ATTTATTTAT
* * * * *
59912498 AGGTTGAAAAACTTTATTCTAATCAATGTCAAATAGATGAAGTGTAGTA
1 AGGTTGAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTA
59912547 AGGTTGAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
1 AGGTTGAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
59912595 TCTATATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (49 bp):
AGGTTGAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTA
Found at i:59915493 original size:2 final size:2
Alignment explanation
Indices: 59915486--59915526 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
59915476 TAGTAAAAAG
59915486 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
59915527 GCCTTACAAG
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:59919038 original size:22 final size:22
Alignment explanation
Indices: 59919008--59919050 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
59918998 CCCAACACTT
59919008 GTTAGTAAAA-TATTATAAAAAA
1 GTTAGTAAAATTATT-TAAAAAA
*
59919030 GTTATTAAAATTATTTAAAAA
1 GTTAGTAAAATTATTTAAAAA
59919051 TATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
GTTAGTAAAATTATTTAAAAAA
Found at i:59919059 original size:10 final size:11
Alignment explanation
Indices: 59919014--59919062 Score: 50
Period size: 10 Copynumber: 4.5 Consensus size: 11
59919004 ACTTGTTAGT
59919014 AAAATATTATA
1 AAAATATTATA
59919025 AAAA-AGTTATTA
1 AAAATA-TTA-TA
*
59919037 AAATTATT-TA
1 AAAATATTATA
59919047 AAAATATTA-A
1 AAAATATTATA
59919057 AAAATA
1 AAAATA
59919063 GGTTTAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 17 0.53
11 7 0.22
12 7 0.22
13 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AAAATATTATA
Found at i:59919299 original size:13 final size:13
Alignment explanation
Indices: 59919273--59919307 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
59919263 AAAAATACAT
59919273 AAATAATTTTAAA
1 AAATAATTTTAAA
59919286 AAAT-ATTTTAAA
1 AAATAATTTTAAA
*
59919298 AATTAATTTT
1 AAATAATTTT
59919308 TTTTTGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATAATTTTAAA
Found at i:59919611 original size:22 final size:21
Alignment explanation
Indices: 59919574--59919614 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
59919564 ATATTTTATG
*
59919574 TAAAATTTATTATAAAATATA
1 TAAAATTTAGTATAAAATATA
59919595 TAAAATATTAGTATAAAATA
1 TAAAAT-TTAGTATAAAATA
59919615 ATTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAATTTAGTATAAAATATA
Found at i:59922528 original size:30 final size:30
Alignment explanation
Indices: 59922492--59922548 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
59922482 GCATAGAAAT
*
59922492 TAGTACATTAAGTATG-AGTAAATTTTTATA
1 TAGTACATTAAATATGTA-TAAATTTTTATA
59922522 TAGTACATTAAATATGTATAAATTTTT
1 TAGTACATTAAATATGTATAAATTTTT
59922549 CCTCATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.46
Consensus pattern (30 bp):
TAGTACATTAAATATGTATAAATTTTTATA
Found at i:59923328 original size:22 final size:22
Alignment explanation
Indices: 59923289--59923330 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
59923279 TTAAAATCAA
*
59923289 AACAAAAACAAAGAAAGAAAGT
1 AACAAAAAAAAAGAAAGAAAGT
59923311 AACAAAAAAAGAAG-AAGAAA
1 AACAAAAAAA-AAGAAAGAAA
59923331 AAAGACAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.02
Consensus pattern (22 bp):
AACAAAAAAAAAGAAAGAAAGT
Found at i:59925564 original size:27 final size:22
Alignment explanation
Indices: 59925511--59925556 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
59925501 CCAGCTCAAT
59925511 AGCTCGAGATTCCCAGTCACTA
1 AGCTCGAGATTCCCAGTCACTA
*
59925533 AGCTCGGGATTCCCAGTCACTA
1 AGCTCGAGATTCCCAGTCACTA
59925555 AG
1 AG
59925557 AGGAGCTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (22 bp):
AGCTCGAGATTCCCAGTCACTA
Found at i:59928234 original size:16 final size:16
Alignment explanation
Indices: 59928210--59928248 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
59928200 CAGTTGATTA
* *
59928210 GACAATATTTTGCTAT
1 GACATTATTTTGATAT
59928226 GACATTATTTTGATAT
1 GACATTATTTTGATAT
59928242 GAGCATT
1 GA-CATT
59928249 TCACCTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (16 bp):
GACATTATTTTGATAT
Found at i:59936972 original size:32 final size:32
Alignment explanation
Indices: 59936915--59937106 Score: 233
Period size: 32 Copynumber: 6.0 Consensus size: 32
59936905 AGCTATAACT
*
59936915 ACAGTAATATGATTGGCACAAAGCCATCAGTA
1 ACAGTAATATGATCGGCACAAAGCCATCAGTA
* * * *
59936947 GCAGTGATATGATCGACACACAGCCATCAGTA
1 ACAGTAATATGATCGGCACAAAGCCATCAGTA
** * *
59936979 ATGGTAATATGATCGGCACAAAGCTATTAGTA
1 ACAGTAATATGATCGGCACAAAGCCATCAGTA
* * *
59937011 ACGGTAATATAATCGGTACAAAGCCATCAGTA
1 ACAGTAATATGATCGGCACAAAGCCATCAGTA
*
59937043 AC-GATAATATGATCGGCACAAAGCCACCAGTA
1 ACAG-TAATATGATCGGCACAAAGCCATCAGTA
* *
59937075 ACGGTAATATGACCGGCACAAAGCCATCAGTA
1 ACAGTAATATGATCGGCACAAAGCCATCAGTA
59937107 GCATCGCAAC
Statistics
Matches: 135, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
31 1 0.01
32 133 0.99
33 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (32 bp):
ACAGTAATATGATCGGCACAAAGCCATCAGTA
Found at i:59937310 original size:24 final size:24
Alignment explanation
Indices: 59937278--59937383 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
59937268 CCATGCGCAG
*
59937278 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATACAAATCACAGACA
* *
59937302 AATCAGTCATACCAATCACTGACA
1 AATCAGTCATACAAATCACAGACA
* **
59937326 AATCAGTTATTTAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
** * *
59937350 AATCAGTCATTTACATCACGGACA
1 AATCAGTCATACAAATCACAGACA
*
59937374 AATCAATCAT
1 AATCAGTCAT
59937384 TTACACTCGA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.24
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:59937386 original size:48 final size:48
Alignment explanation
Indices: 59937290--59937386 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 48
59937280 TCAGTCATAC
* * *
59937290 AAATCACAAACAAATCAGTCATACCAATCACTGACAAATCAGTTATTT
1 AAATCACAAACAAATCAGTCATACCAATCACGGACAAATCAATCATTT
*
59937338 AAATCACAGACAAATCAGTCATTTA-C-ATCACGGACAAATCAATCATTT
1 AAATCACAAACAAATCAGTCA--TACCAATCACGGACAAATCAATCATTT
59937386 A
1 A
59937387 CACTCGAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 40 0.93
49 1 0.02
50 2 0.05
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (48 bp):
AAATCACAAACAAATCAGTCATACCAATCACGGACAAATCAATCATTT
Found at i:59937458 original size:27 final size:27
Alignment explanation
Indices: 59937407--59937547 Score: 115
Period size: 27 Copynumber: 5.2 Consensus size: 27
59937397 GCAAAATAGT
* * *
59937407 TTTTAACCTCCAAGGGCATTACGATCA
1 TTTTACCCTACAAGGGTATTACGATCA
* * *
59937434 TTTTACCTTACAGGGGTATTTCGATCA
1 TTTTACCCTACAAGGGTATTACGATCA
* *
59937461 TTTAACCCTATGAA-GGTATTACTG-TCA
1 TTTTACCCTA-CAAGGGTATTAC-GATCA
* * * * *
59937488 TTTTACCCTATAAGGGTTTTTCGGTTA
1 TTTTACCCTACAAGGGTATTACGATCA
*
59937515 TTTTACCTTACAAGGGTATTACGATCA
1 TTTTACCCTACAAGGGTATTACGATCA
*
59937542 TGTTAC
1 TTTTAC
59937548 AAATATTGGG
Statistics
Matches: 87, Mismatches: 23, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
26 3 0.03
27 82 0.94
28 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (27 bp):
TTTTACCCTACAAGGGTATTACGATCA
Found at i:59938637 original size:41 final size:41
Alignment explanation
Indices: 59938574--59938660 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
59938564 CCTAACAGAG
*
59938574 AAAGGAAAAATGGAATTGGAAAAGAAGTACAGATGAAAGCA
1 AAAGAAAAAATGGAATTGGAAAAGAAGTACAGATGAAAGCA
* * * *
59938615 AAAGAAAAAATTGAATTTGAAAATAAGTACAGATGAAAGTA
1 AAAGAAAAAATGGAATTGGAAAAGAAGTACAGATGAAAGCA
59938656 AAAGA
1 AAAGA
59938661 GAGGATCAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.16
Consensus pattern (41 bp):
AAAGAAAAAATGGAATTGGAAAAGAAGTACAGATGAAAGCA
Found at i:59938950 original size:24 final size:24
Alignment explanation
Indices: 59938912--59938977 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
59938902 AGCCTTGAAA
* * *
59938912 CTCCTTGAAAATCTCCAC-CCCCC
1 CTCCTTGATATTCTCCACTCACCC
* *
59938935 TCTCCTTGATTTTCTCCGCTCACCC
1 -CTCCTTGATATTCTCCACTCACCC
*
59938960 CTCCTTGATATCCTCCAC
1 CTCCTTGATATTCTCCAC
59938978 AACCAACTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
24 29 0.88
25 4 0.12
ACGTcount: A:0.15, C:0.47, G:0.06, T:0.32
Consensus pattern (24 bp):
CTCCTTGATATTCTCCACTCACCC
Found at i:59940456 original size:24 final size:24
Alignment explanation
Indices: 59940429--59940479 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
59940419 ACCATTCCAT
59940429 TTACTTACTTTCCACTT-CATTTAC
1 TTACTTACTTTCCA-TTCCATTTAC
59940453 TTACTTACTTTCCATTCCATTTAC
1 TTACTTACTTTCCATTCCATTTAC
59940477 TTA
1 TTA
59940480 GCATAAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (24 bp):
TTACTTACTTTCCATTCCATTTAC
Found at i:59940476 original size:20 final size:20
Alignment explanation
Indices: 59940420--59940479 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 20
59940410 AGACGATGAA
59940420 CCATTCCATTTACTTACTTT
1 CCATTCCATTTACTTACTTT
59940440 CCACTT-CATTTACTTACTTACTTT
1 CCA-TTCCA--T--TTACTTACTTT
59940464 CCATTCCATTTACTTA
1 CCATTCCATTTACTTA
59940480 GCATAAGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
20 12 0.35
21 2 0.06
22 2 0.06
23 2 0.06
24 16 0.47
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (20 bp):
CCATTCCATTTACTTACTTT
Found at i:59945472 original size:32 final size:33
Alignment explanation
Indices: 59945427--59945511 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
59945417 TAAATTGTGA
* *
59945427 AGGGTGAGAGAGAGGCGGCATTGG-GTAAGTGG
1 AGGGTGAGAGAGAGGCGACATTGGTGGAAGTGG
* *
59945459 AGGGTGAGGGAGAGGCGACATTGGTGGCAGTGG
1 AGGGTGAGAGAGAGGCGACATTGGTGGAAGTGG
59945492 AGGGTGAGAGAGAGGCGACA
1 AGGGTGAGAGAGAGGCGACA
59945512 ACGGATTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 22 0.47
33 25 0.53
ACGTcount: A:0.26, C:0.08, G:0.53, T:0.13
Consensus pattern (33 bp):
AGGGTGAGAGAGAGGCGACATTGGTGGAAGTGG
Found at i:59948638 original size:3 final size:3
Alignment explanation
Indices: 59948632--59948665 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
59948622 ATTATTTCTT
59948632 TTA TTA TTA TTA CTT- TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T
59948666 AATCTTCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:59948638 original size:15 final size:15
Alignment explanation
Indices: 59948620--59948658 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
59948610 ATTCTTTTCT
*
59948620 TTATTATTTCTTTTA
1 TTATTATTACTTTTA
59948635 TTATTATTACTTTTA
1 TTATTATTACTTTTA
59948650 TTATTATTA
1 TTATTATTA
59948659 TTATTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATTACTTTTA
Found at i:59959357 original size:21 final size:21
Alignment explanation
Indices: 59959331--59959373 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
59959321 AAATGTGGAC
59959331 TTAATTGAATGCTAGAGGTAT
1 TTAATTGAATGCTAGAGGTAT
59959352 TTAATTGAATGCTAGAGGTAT
1 TTAATTGAATGCTAGAGGTAT
59959373 T
1 T
59959374 AAATGGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.40
Consensus pattern (21 bp):
TTAATTGAATGCTAGAGGTAT
Found at i:59959646 original size:41 final size:41
Alignment explanation
Indices: 59959577--59959746 Score: 189
Period size: 41 Copynumber: 4.1 Consensus size: 41
59959567 AAGATTACTT
*
59959577 CTGAATTGCACATACA-TGCCACTATTTGTACTTCGGTACCC
1 CTGAATTGCACATA-AGTGCCCCTATTTGTACTTCGGTACCC
* * *
59959618 CTGAATTGCACATAAGTGCCTCTGTTTGTACTTTGGTACCC
1 CTGAATTGCACATAAGTGCCCCTATTTGTACTTCGGTACCC
* * * * *
59959659 CTAAATTGCACATACGTGCCCCTGTCTGTACTTTGGTACCC
1 CTGAATTGCACATAAGTGCCCCTATTTGTACTTCGGTACCC
* * * * *
59959700 TTGAATTGCACATATGTGCCCCTATTTATAATTCAGTACCC
1 CTGAATTGCACATAAGTGCCCCTATTTGTACTTCGGTACCC
*
59959741 TTGAAT
1 CTGAAT
59959747 GTATTTCTGT
Statistics
Matches: 112, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 1 0.01
41 111 0.99
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (41 bp):
CTGAATTGCACATAAGTGCCCCTATTTGTACTTCGGTACCC
Found at i:59974316 original size:23 final size:23
Alignment explanation
Indices: 59974271--59974316 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
59974261 ACAGCCGTAT
**
59974271 TTTAGTCTTAAACAGATTTTTAG
1 TTTAGTCTTAAACAGATAGTTAG
59974294 TTTAGTCTTAAACATGA-AGTTAG
1 TTTAGTCTTAAACA-GATAGTTAG
59974317 ATCTCCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (23 bp):
TTTAGTCTTAAACAGATAGTTAG
Found at i:59976271 original size:26 final size:23
Alignment explanation
Indices: 59976222--59976278 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
59976212 TATAATTCTA
59976222 TATCATCAATTCATTCCATATAT
1 TATCATCAATTCATTCCATATAT
59976245 TATCATCAATTCATTCCATATAT
1 TATCATCAATTCATTCCATATAT
*
59976268 TATTATCAATT
1 TATCATCAATT
59976279 AAAAAATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (23 bp):
TATCATCAATTCATTCCATATAT
Found at i:59981233 original size:40 final size:40
Alignment explanation
Indices: 59981196--59981459 Score: 298
Period size: 40 Copynumber: 6.6 Consensus size: 40
59981186 CATATGCCTT
**
59981196 TGTTTGTACTTCGGTACCCCTGAACACACATACATGCCCC
1 TGTTTGTACTTCGGTACCCCTGAATGCACATACATGCCCC
** *
59981236 -GATTTGTACTTTTGTACCCCTGAATGCACATACGTGCCCC
1 TG-TTTGTACTTCGGTACCCCTGAATGCACATACATGCCCC
* * * * **
59981276 TGTTTGTGCTTCGATACCCTTAAATGCACATAGGTGCCCC
1 TGTTTGTACTTCGGTACCCCTGAATGCACATACATGCCCC
* *
59981316 TGTTTGTACTTCGATACCCCTGAATGCACATACTTGCCCC
1 TGTTTGTACTTCGGTACCCCTGAATGCACATACATGCCCC
*
59981356 TGTTTATACTTCGGTACCCCTGAATGCACATACATGCCCC
1 TGTTTGTACTTCGGTACCCCTGAATGCACATACATGCCCC
* ** * *
59981396 TATTTGTACTTTAGTTCCCTTGAATGCACATACATG-CCC
1 TGTTTGTACTTCGGTACCCCTGAATGCACATACATGCCCC
* * * *
59981435 TATTTATACTTTGGTAGCCCTGAAT
1 TGTTTGTACTTCGGTACCCCTGAAT
59981460 CAAATAGTAT
Statistics
Matches: 191, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
39 24 0.13
40 166 0.87
41 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (40 bp):
TGTTTGTACTTCGGTACCCCTGAATGCACATACATGCCCC
Found at i:59981354 original size:120 final size:119
Alignment explanation
Indices: 59981138--59981406 Score: 335
Period size: 120 Copynumber: 2.2 Consensus size: 119
59981128 ATTATTATAT
* * * * **
59981138 AATGCATATACGTGCCCCTACTCGTACTTCGATACCCGTAAATGTATACATATGCCTTTGTTTGT
1 AATGCACATACGTGCCCCTATTTGTACTTCGATACCCGTAAATG-ACACATATGCCCCTGTTTGT
* * **
59981203 ACTTCGGTACCCCTGAACACACATACATGCCCC-GATTTGTACTTTTGTACCCCTG
65 ACTTCGATACCCCTGAACACACATACATGCCCCTG-TTTATACTTCGGTACCCCTG
* * *
59981258 AATGCACATACGTGCCCCTGTTTGTGCTTCGATACCCTTAAATG-CACATAGGTGCCCCTGTTTG
1 AATGCACATACGTGCCCCTATTTGTACTTCGATACCCGTAAATGACACATA--TGCCCCTGTTTG
** *
59981322 TACTTCGATACCCCTGAATGCACATACTTGCCCCTGTTTATACTTCGGTACCCCTG
64 TACTTCGATACCCCTGAACACACATACATGCCCCTGTTTATACTTCGGTACCCCTG
*
59981378 AATGCACATACATGCCCCTATTTGTACTT
1 AATGCACATACGTGCCCCTATTTGTACTT
59981407 TAGTTCCCTT
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
118 5 0.04
120 121 0.95
121 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (119 bp):
AATGCACATACGTGCCCCTATTTGTACTTCGATACCCGTAAATGACACATATGCCCCTGTTTGTA
CTTCGATACCCCTGAACACACATACATGCCCCTGTTTATACTTCGGTACCCCTG
Found at i:59988406 original size:26 final size:26
Alignment explanation
Indices: 59988370--59988431 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
59988360 CTTGTAAGTG
59988370 TTCTGAAACTGATA-CATGCTATAATA
1 TTCTGAAACTGATATC-TGCTATAATA
* *
59988396 TTCTGAAACTGATATCTGTTATGATA
1 TTCTGAAACTGATATCTGCTATAATA
59988422 TTCTGAAACT
1 TTCTGAAACT
59988432 ACTGTAGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (26 bp):
TTCTGAAACTGATATCTGCTATAATA
Found at i:60004254 original size:29 final size:30
Alignment explanation
Indices: 60004220--60004292 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
60004210 CCTTGTTATA
*
60004220 ATTATTATAATTATAA-TTTAC-GATCAAAT
1 ATTATTATAATTATAATTTTACAG-TCAAAC
*
60004249 ATTATTATAATTATAATTTTTCAGTCAAAC
1 ATTATTATAATTATAATTTTACAGTCAAAC
60004279 ATTATTATAATTAT
1 ATTATTATAATTAT
60004293 GGTAATTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 16 0.40
30 23 0.57
31 1 0.03
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (30 bp):
ATTATTATAATTATAATTTTACAGTCAAAC
Found at i:60009523 original size:171 final size:171
Alignment explanation
Indices: 60009232--60009564 Score: 531
Period size: 171 Copynumber: 1.9 Consensus size: 171
60009222 GCAACAAGAG
* * * * * * *
60009232 AGCTTTAGACTGTACTAACTGAGGCTCATGTTTTGGTACAGCCTGAACCTGGAAAAGATTTTACG
1 AGCTTAAGACTGTACTAACTGAGGCTCATGTTTTCGTAAAGCCTAAACCTGAAAAAGAGTTCACG
* * *
60009297 GTTTACAATGATGCATCACATGTCAGTTTAGGATGTGTGTTGATGCATGATGGAAAGGTGGTTGT
66 GTTTACAATGATGCATCACATGTCAGTTTAGGATATGTGTTGATGCAGGATGGAAAGGTGGTTGC
* *
60009362 ATATGTGTCTCGCTAGTTTAAGACACACGAGGGCTTTGAGA
131 ATATGTGTCTCACTAGCTTAAGACACACGAGGGCTTTGAGA
*
60009403 AGCTTAAGACTGTACTGACTGAGGCTCATGTTTTCGTAAAGCCTAAACCTGAAAAAGAGTTCACG
1 AGCTTAAGACTGTACTAACTGAGGCTCATGTTTTCGTAAAGCCTAAACCTGAAAAAGAGTTCACG
* *
60009468 GTTTACAATGATGCATCACATGTCAGTTTGGGATATGTTTTGATGCAGGATGGAAAGGTGGTTGC
66 GTTTACAATGATGCATCACATGTCAGTTTAGGATATGTGTTGATGCAGGATGGAAAGGTGGTTGC
60009533 ATATGTGTCTCACTAGCTTAAGACACACGAGG
131 ATATGTGTCTCACTAGCTTAAGACACACGAGG
60009565 TGAAATATCT
Statistics
Matches: 147, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
171 147 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (171 bp):
AGCTTAAGACTGTACTAACTGAGGCTCATGTTTTCGTAAAGCCTAAACCTGAAAAAGAGTTCACG
GTTTACAATGATGCATCACATGTCAGTTTAGGATATGTGTTGATGCAGGATGGAAAGGTGGTTGC
ATATGTGTCTCACTAGCTTAAGACACACGAGGGCTTTGAGA
Found at i:60029672 original size:20 final size:22
Alignment explanation
Indices: 60029641--60029680 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
60029631 ATAATTCAAT
60029641 AAATTGAAAATTTA-GATAATC
1 AAATTGAAAATTTAGGATAATC
60029662 AAATT-AAAATTTAGGATAA
1 AAATTGAAAATTTAGGATAA
60029681 AAATTGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATTGAAAATTTAGGATAATC
Found at i:60030378 original size:30 final size:30
Alignment explanation
Indices: 60030321--60030382 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
60030311 GCTTTTTGAA
* *
60030321 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
60030351 AATATTTACAAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
60030381 AA
1 AA
60030383 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:60041072 original size:38 final size:38
Alignment explanation
Indices: 60041015--60041164 Score: 174
Period size: 38 Copynumber: 3.9 Consensus size: 38
60041005 AAGCCTATTA
* * *
60041015 GGCACAAAGCCTGCTAGGCATAAAGCCCGAATAACACT
1 GGCACTAAGCCTACTAGGCACAAAGCCCGAATAACACT
* * *
60041053 GGTATTAAGCCTACTAGGCACAAAGCCTGAATAACACT
1 GGCACTAAGCCTACTAGGCACAAAGCCCGAATAACACT
* * * * * *
60041091 AGCACTAAGCCTGCTAGACACAAAGTCCGAATATCACC
1 GGCACTAAGCCTACTAGGCACAAAGCCCGAATAACACT
* *
60041129 GACACTAAGCCTACTAGGCACAAAGCCCAAATAACA
1 GGCACTAAGCCTACTAGGCACAAAGCCCGAATAACA
60041165 ATATAATTCA
Statistics
Matches: 90, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 90 1.00
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.15
Consensus pattern (38 bp):
GGCACTAAGCCTACTAGGCACAAAGCCCGAATAACACT
Found at i:60041147 original size:76 final size:76
Alignment explanation
Indices: 60041016--60041164 Score: 199
Period size: 76 Copynumber: 2.0 Consensus size: 76
60041006 AGCCTATTAG
* * * ** * *
60041016 GCACAAAGCCTGCTAGGCATAAAGCCCGAATAACACTGGTATTAAGCCTACTAGGCACAAAGCCT
1 GCACAAAGCCTGCTAGACACAAAGCCCGAATAACACCGACACTAAGCCTACTAGGCACAAAGCCC
*
60041081 GAATAACACTA
66 AAATAACACTA
* * *
60041092 GCACTAAGCCTGCTAGACACAAAGTCCGAATATCACCGACACTAAGCCTACTAGGCACAAAGCCC
1 GCACAAAGCCTGCTAGACACAAAGCCCGAATAACACCGACACTAAGCCTACTAGGCACAAAGCCC
60041157 AAATAACA
66 AAATAACA
60041165 ATATAATTCA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.15
Consensus pattern (76 bp):
GCACAAAGCCTGCTAGACACAAAGCCCGAATAACACCGACACTAAGCCTACTAGGCACAAAGCCC
AAATAACACTA
Found at i:60054973 original size:40 final size:40
Alignment explanation
Indices: 60054918--60055082 Score: 224
Period size: 40 Copynumber: 4.1 Consensus size: 40
60054908 GTTTGGATAA
* * *
60054918 AAAAAAGCCGCTATAGATCGAGCATTAGCGGCGATTTTTG
1 AAAAATGCCACTATAGATCGAGCATTAGCGGCGCTTTTTG
*
60054958 AAAAATGCTACTATAGATCGAGCATTAGCGGCGCTTTTTG
1 AAAAATGCCACTATAGATCGAGCATTAGCGGCGCTTTTTG
* * *
60054998 AGAAACGCCACTATTGATCGAGCATTAGCGGCGCTTTTTG
1 AAAAATGCCACTATAGATCGAGCATTAGCGGCGCTTTTTG
* * *
60055038 AGAAACT-CCGCTATTGATCGAGCATTAGCGGCGCTTTTTG
1 A-AAAATGCCACTATAGATCGAGCATTAGCGGCGCTTTTTG
60055078 AAAAA
1 AAAAA
60055083 CCGCAAAAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
39 3 0.03
40 106 0.95
41 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (40 bp):
AAAAATGCCACTATAGATCGAGCATTAGCGGCGCTTTTTG
Found at i:60066234 original size:7 final size:7
Alignment explanation
Indices: 60066134--60066408 Score: 60
Period size: 7 Copynumber: 38.6 Consensus size: 7
60066124 ATTAGTTATC
*
60066134 TTTATAG
1 TTTATGG
*
60066141 TTTAGGG
1 TTTATGG
*
60066148 TGTATGG
1 TTTATGG
*
60066155 TTTAGGG
1 TTTATGG
*
60066162 TTTAAGG
1 TTTATGG
*
60066169 TTTAGGAG
1 TTTATG-G
60066177 TTACTAT--
1 TT--TATGG
*
60066184 TTTAAGG
1 TTTATGG
60066191 TTTATGG
1 TTTATGG
*
60066198 ATTATGAG
1 TTTATG-G
60066206 TTTA-GAG
1 TTTATG-G
* *
60066213 ATTATGA
1 TTTATGG
60066220 TTTATGG
1 TTTATGG
60066227 TTTATGG
1 TTTATGG
*
60066234 TTTAAGG
1 TTTATGG
* **
60066241 GTTGGGG
1 TTTATGG
*
60066248 TTTGA-AG
1 TTT-ATGG
*
60066255 TTTAGGAG
1 TTTATG-G
60066263 TTACTAT--
1 TT--TATGG
*
60066270 TTTAAGG
1 TTTATGG
60066277 TTTATGG
1 TTTATGG
*
60066284 ATTATGGG
1 TTTAT-GG
60066292 TTTA-GAG
1 TTTATG-G
* *
60066299 ATTATGA
1 TTTATGG
60066306 TTTATGG
1 TTTATGG
60066313 TTTATGG
1 TTTATGG
*
60066320 TTTAAGG
1 TTTATGG
* **
60066327 GTTGGGG
1 TTTATGG
**
60066334 TTTAAAG
1 TTTATGG
*
60066341 TTTAGGG
1 TTTATGG
*
60066348 GTTATGG
1 TTTATGG
* *
60066355 GTTAAGG
1 TTTATGG
* *
60066362 GTTAGGGG
1 TTTA-TGG
*
60066370 TTTAGGG
1 TTTATGG
60066377 TTTATGG
1 TTTATGG
* *
60066384 TTCATGT
1 TTTATGG
*
60066391 TTTATGA
1 TTTATGG
*
60066398 TTTAGGG
1 TTTATGG
60066405 TTTA
1 TTTA
60066409 GGGGATAGAG
Statistics
Matches: 194, Mismatches: 56, Indels: 36
0.68 0.20 0.13
Matches are distributed among these distances:
5 4 0.02
6 2 0.01
7 162 0.84
8 22 0.11
10 4 0.02
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.45
Consensus pattern (7 bp):
TTTATGG
Found at i:60066279 original size:86 final size:85
Alignment explanation
Indices: 60066159--60066351 Score: 341
Period size: 86 Copynumber: 2.2 Consensus size: 85
60066149 GTATGGTTTA
60066159 GGGTTTAAGGTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGAGTTTAGAGATTATGATTTA
1 GGGTTTAA-GTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGAGTTTAGAGATTATGATTTA
60066224 TGGTTTATGGTTTAAGGGTTG
65 TGGTTTATGGTTTAAGGGTTG
*
60066245 GGGTTTGAAGTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATGATTTA
1 GGGTTT-AAGTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGAGTTTAGAGATTATGATTTA
60066310 TGGTTTATGGTTTAAGGGTTG
65 TGGTTTATGGTTTAAGGGTTG
*
60066331 GGGTTTAAAGTTTAGGGGTTA
1 GGGTTT-AAGTTTAGGAGTTA
60066352 TGGGTTAAGG
Statistics
Matches: 103, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
86 101 0.98
87 2 0.02
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.45
Consensus pattern (85 bp):
GGGTTTAAGTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGAGTTTAGAGATTATGATTTAT
GGTTTATGGTTTAAGGGTTG
Found at i:60066385 original size:14 final size:14
Alignment explanation
Indices: 60066134--60066408 Score: 89
Period size: 14 Copynumber: 19.3 Consensus size: 14
60066124 ATTAGTTATC
*
60066134 TTTATAGTTTAGGG
1 TTTATGGTTTAGGG
*
60066148 TGTATGGTTTAGGG
1 TTTATGGTTTAGGG
*
60066162 TTTAAGGTTTAGGAG
1 TTTATGGTTTAGG-G
*
60066177 TTACTAT--TTTAAGG
1 TT--TATGGTTTAGGG
* *
60066191 TTTATGGATTATGAG
1 TTTATGGTTTA-GGG
* * *
60066206 TTTA-GAGATTATGA
1 TTTATG-GTTTAGGG
*
60066220 TTTATGGTTTATGG
1 TTTATGGTTTAGGG
* * *
60066234 TTTAAGGGTTGGGG
1 TTTATGGTTTAGGG
*
60066248 TTTGA-AGTTTAGGAG
1 TTT-ATGGTTTAGG-G
*
60066263 TTACTAT--TTTAAGG
1 TT--TATGGTTTAGGG
*
60066277 TTTATGGATTATGGG
1 TTTATGGTTTA-GGG
* * *
60066292 TTTA-GAGATTATGA
1 TTTATG-GTTTAGGG
*
60066306 TTTATGGTTTATGG
1 TTTATGGTTTAGGG
* * *
60066320 TTTAAGGGTTGGGG
1 TTTATGGTTTAGGG
**
60066334 TTTAAAGTTTAGGG
1 TTTATGGTTTAGGG
* *
60066348 GTTATGGGTTAAGGG
1 TTTAT-GGTTTAGGG
*
60066363 -TTAGGGGTTTAGGG
1 TTTA-TGGTTTAGGG
* * *
60066377 TTTATGGTTCATGT
1 TTTATGGTTTAGGG
*
60066391 TTTATGATTTAGGG
1 TTTATGGTTTAGGG
60066405 TTTA
1 TTTA
60066409 GGGGATAGAG
Statistics
Matches: 191, Mismatches: 49, Indels: 42
0.68 0.17 0.15
Matches are distributed among these distances:
12 6 0.03
14 131 0.69
15 50 0.26
16 1 0.01
17 3 0.02
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.45
Consensus pattern (14 bp):
TTTATGGTTTAGGG
Found at i:60066409 original size:7 final size:7
Alignment explanation
Indices: 60066306--60066438 Score: 63
Period size: 7 Copynumber: 18.7 Consensus size: 7
60066296 GAGATTATGA
*
60066306 TTTATGG
1 TTTAGGG
*
60066313 TTTATGG
1 TTTAGGG
60066320 TTTAAGGG
1 TTT-AGGG
*
60066328 -TTGGGG
1 TTTAGGG
**
60066334 TTTAAAG
1 TTTAGGG
60066341 TTTAGGG
1 TTTAGGG
*
60066348 GTTATGGG
1 TTTA-GGG
*
60066356 TTAAGGG
1 TTTAGGG
60066363 -TTAGGGG
1 TTTA-GGG
60066370 TTTAGGG
1 TTTAGGG
*
60066377 TTTATGG
1 TTTAGGG
* * *
60066384 TTCATGT
1 TTTAGGG
* *
60066391 TTTATGA
1 TTTAGGG
60066398 TTTAGGG
1 TTTAGGG
60066405 TTTAGGG
1 TTTAGGG
** *
60066412 GATAGAG
1 TTTAGGG
*
60066419 ATTAGGGG
1 TTTA-GGG
60066427 TTTAGGG
1 TTTAGGG
60066434 TTTAG
1 TTTAG
60066439 ATTAATTAAT
Statistics
Matches: 95, Mismatches: 25, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
6 5 0.05
7 74 0.78
8 16 0.17
ACGTcount: A:0.20, C:0.01, G:0.38, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:60071713 original size:43 final size:43
Alignment explanation
Indices: 60071666--60071764 Score: 162
Period size: 43 Copynumber: 2.3 Consensus size: 43
60071656 GTACGGTACT
* *
60071666 TTTAGTGGCGTTTGTGATAAAAATGCCGCTAAAGGTCATGTTC
1 TTTAGTGGCATTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
* *
60071709 TTTAGTGGCATTTGTGATAAAAGCGCCGCTAATGGTCATGTTC
1 TTTAGTGGCATTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
60071752 TTTAGTGGCATTT
1 TTTAGTGGCATTT
60071765 TTTCACATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.37
Consensus pattern (43 bp):
TTTAGTGGCATTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
Found at i:60073660 original size:52 final size:49
Alignment explanation
Indices: 60073604--60073780 Score: 130
Period size: 50 Copynumber: 3.5 Consensus size: 49
60073594 TTCGGGAATA
* *
60073604 CTCATTAGAGCACATAATCAGAAAGCTTTCTCTTGAGCCATATAACTGGAAG
1 CTCATTAGAGC-CATAATCAGAAAGC-TTATC-TGAGCCATATAACGGGAAG
* **
60073656 CTCA-TATGAGCCATTTAA-CAGGAAGCTTATCTGAGCTGTATAACGGGAAG
1 CTCATTA-GAGCCA--TAATCAGAAAGCTTATCTGAGCCATATAACGGGAAG
* * * *
60073706 CTCATAAGAGCCATAATCA-AGAAGCTCATGC-AAGCCA-ATAACGGGTAG
1 CTCATTAGAGCCATAATCAGA-AAGCTTAT-CTGAGCCATATAACGGGAAG
***
60073754 CTCCGAAGAGCCATTAATCAGAAAGCT
1 CTCATTAGAGCCA-TAATCAGAAAGCT
60073781 CCGGATAGCC
Statistics
Matches: 102, Mismatches: 14, Indels: 21
0.74 0.10 0.15
Matches are distributed among these distances:
48 24 0.24
49 23 0.23
50 28 0.27
51 9 0.09
52 15 0.15
53 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (49 bp):
CTCATTAGAGCCATAATCAGAAAGCTTATCTGAGCCATATAACGGGAAG
Found at i:60073668 original size:25 final size:25
Alignment explanation
Indices: 60073637--60073734 Score: 99
Period size: 25 Copynumber: 4.0 Consensus size: 25
60073627 AGCTTTCTCT
*
60073637 TGAGCCATATAACTGGAAGCTCATA
1 TGAGCCATATAACAGGAAGCTCATA
* * *
60073662 TGAGCCATTTAACAGGAAGCTTATC
1 TGAGCCATATAACAGGAAGCTCATA
** *
60073687 TGAGCTGTATAACGGGAAGCTCATA
1 TGAGCCATATAACAGGAAGCTCATA
* * *
60073712 AGAGCCATA-ATCAAGAAGCTCAT
1 TGAGCCATATAACAGGAAGCTCAT
60073735 GCAAGCCAAT
Statistics
Matches: 57, Mismatches: 16, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
24 11 0.19
25 46 0.81
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTCATA
Found at i:60074407 original size:5 final size:5
Alignment explanation
Indices: 60074378--60074416 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
60074368 TAAATTTAGC
* *
60074378 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
60074417 CATCTTAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:60081569 original size:25 final size:25
Alignment explanation
Indices: 60081538--60081658 Score: 115
Period size: 25 Copynumber: 4.9 Consensus size: 25
60081528 GCTCTCTCTC
* *
60081538 GAGCCATATAATGGGAAGCACATAT
1 GAGCCATATAATGGGAAGCTCATAA
* * **
60081563 GAGCCATGTAATGGGAAGCTTATCC
1 GAGCCATATAATGGGAAGCTCATAA
* **
60081588 GGGCTGTATAATGGGAAGCTCATAA
1 GAGCCATATAATGGGAAGCTCATAA
60081613 GAGCC--ATAATGAGGAAGCTCATAA
1 GAGCCATATAATG-GGAAGCTCATAA
60081637 GAGCC--ATAATGAGGAAGCTCAT
1 GAGCCATATAATG-GGAAGCTCAT
60081659 GTGAACCAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
23 6 0.07
24 34 0.42
25 41 0.51
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (25 bp):
GAGCCATATAATGGGAAGCTCATAA
Found at i:60081632 original size:24 final size:24
Alignment explanation
Indices: 60081595--60081658 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
60081585 TCCGGGCTGT
60081595 ATAATG-GGAAGCTCATAAGAGCC
1 ATAATGAGGAAGCTCATAAGAGCC
60081618 ATAATGAGGAAGCTCATAAGAGCC
1 ATAATGAGGAAGCTCATAAGAGCC
60081642 ATAATGAGGAAGCTCAT
1 ATAATGAGGAAGCTCAT
60081659 GTGAACCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 6 0.15
24 34 0.85
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.19
Consensus pattern (24 bp):
ATAATGAGGAAGCTCATAAGAGCC
Found at i:60081776 original size:25 final size:25
Alignment explanation
Indices: 60081745--60081812 Score: 91
Period size: 26 Copynumber: 2.7 Consensus size: 25
60081735 GAGCCATATT
*
60081745 AGGAAGCTCCGGAGAGCCATTAATC
1 AGGAAGCTCCGAAGAGCCATTAATC
* *
60081770 AGGAAGCTCACAAAGAGCCTTTAATC
1 AGGAAGCTC-CGAAGAGCCATTAATC
*
60081796 TGGAAGCTCCGAAGAGC
1 AGGAAGCTCCGAAGAGC
60081813 TATATATCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (25 bp):
AGGAAGCTCCGAAGAGCCATTAATC
Found at i:60101622 original size:107 final size:107
Alignment explanation
Indices: 60101436--60101650 Score: 430
Period size: 107 Copynumber: 2.0 Consensus size: 107
60101426 ATTTAGGTTA
60101436 GCCTCAGGAACATGAAGAATATTAGACAATTTGAAAGGATGAGAATTAAGAGTTAAGACAGACGA
1 GCCTCAGGAACATGAAGAATATTAGACAATTTGAAAGGATGAGAATTAAGAGTTAAGACAGACGA
60101501 GCCAACACGAAAGATAGGTAAGGTTTTACCATTGGTGAGAGT
66 GCCAACACGAAAGATAGGTAAGGTTTTACCATTGGTGAGAGT
60101543 GCCTCAGGAACATGAAGAATATTAGACAATTTGAAAGGATGAGAATTAAGAGTTAAGACAGACGA
1 GCCTCAGGAACATGAAGAATATTAGACAATTTGAAAGGATGAGAATTAAGAGTTAAGACAGACGA
60101608 GCCAACACGAAAGATAGGTAAGGTTTTACCATTGGTGAGAGT
66 GCCAACACGAAAGATAGGTAAGGTTTTACCATTGGTGAGAGT
60101650 G
1 G
60101651 ACTTCATCAG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (107 bp):
GCCTCAGGAACATGAAGAATATTAGACAATTTGAAAGGATGAGAATTAAGAGTTAAGACAGACGA
GCCAACACGAAAGATAGGTAAGGTTTTACCATTGGTGAGAGT
Found at i:60104979 original size:27 final size:25
Alignment explanation
Indices: 60104949--60104998 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
60104939 AATAACTTAA
* *
60104949 TAAGTTGTAGTGATTGAGAAGAAGAAC
1 TAAGTTGCAATGA-TGAGAA-AAGAAC
60104976 TAAGTTGCAATGATGAGAAAAGA
1 TAAGTTGCAATGATGAGAAAAGA
60104999 GAAATTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 6 0.29
27 11 0.52
ACGTcount: A:0.44, C:0.04, G:0.28, T:0.24
Consensus pattern (25 bp):
TAAGTTGCAATGATGAGAAAAGAAC
Found at i:60109048 original size:27 final size:26
Alignment explanation
Indices: 60108985--60109065 Score: 81
Period size: 28 Copynumber: 3.0 Consensus size: 26
60108975 AAAAATATAT
* *
60108985 AAATATATAAATATAAAATTATTAAA
1 AAATATTTAAATATAAAATTATAAAA
* * *
60109011 AATTACATTAACATTTAAAATTATAAAA
1 AAATA-TTTAA-ATATAAAATTATAAAA
*
60109039 AAATATTTAAAATATAAAAATATAAAA
1 AAATATTT-AAATATAAAATTATAAAA
60109066 TATTGTAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
26 4 0.09
27 19 0.44
28 20 0.47
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATATTTAAATATAAAATTATAAAA
Found at i:60109084 original size:8 final size:7
Alignment explanation
Indices: 60108976--60109068 Score: 50
Period size: 8 Copynumber: 13.0 Consensus size: 7
60108966 AAATTATAAA
60108976 AAAATAT
1 AAAATAT
60108983 ATAAATAT
1 A-AAATAT
60108991 ATAAATAT
1 A-AAATAT
60108999 AAAATTATT
1 AAAA-TA-T
60109008 AAAA-AT
1 AAAATAT
* *
60109014 TACAT-T
1 AAAATAT
* *
60109020 AACATTT
1 AAAATAT
60109027 AAAATTAT
1 AAAA-TAT
60109035 AAAA-A-
1 AAAATAT
* *
60109040 AATATTT
1 AAAATAT
60109047 AAAATAT
1 AAAATAT
60109054 AAAAATAT
1 -AAAATAT
60109062 AAAATAT
1 AAAATAT
60109069 TGTAAAAAGT
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
5 3 0.04
6 9 0.13
7 21 0.31
8 30 0.44
9 5 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (7 bp):
AAAATAT
Found at i:60109093 original size:62 final size:61
Alignment explanation
Indices: 60108965--60109093 Score: 145
Period size: 62 Copynumber: 2.1 Consensus size: 61
60108955 AGAATTTTCA
* * ** *
60108965 AAAATTATAAAAAAATATATAAATATATAAATATAAAATTATTAAAAATTACATTAACATTT
1 AAAATTATAAAAAAATATATAAATATAAAAATATAAAATTATTAAAAAGTACAAAAACA-TG
* *
60109027 AAAATTATAAAAAAATATTTAAAATATAAAAATATAAAA-TATTGTAAAAAGTATAAAAACA-G
1 AAAATTATAAAAAAATATAT-AAATATAAAAATATAAAATTA-T-TAAAAAGTACAAAAACATG
60109089 AAAAT
1 AAAAT
60109094 AAATTGAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
62 26 0.46
63 18 0.32
64 13 0.23
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (61 bp):
AAAATTATAAAAAAATATATAAATATAAAAATATAAAATTATTAAAAAGTACAAAAACATG
Found at i:60109613 original size:21 final size:19
Alignment explanation
Indices: 60109576--60109627 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
60109566 TAAATATTTC
60109576 TTTATAA-TTTT-ATAATT
1 TTTATAATTTTTAATAATT
60109593 TTCTATTAATTTTTAATAATT
1 TT-TA-TAATTTTTAATAATT
*
60109614 TTTATGATTTTTAA
1 TTTATAATTTTTAA
60109628 ACATTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 12 0.40
20 6 0.20
21 8 0.27
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATAATTTTTAATAATT
Found at i:60109614 original size:10 final size:10
Alignment explanation
Indices: 60109579--60109627 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
60109569 ATATTTCTTT
60109579 ATAA-TTTT-
1 ATAATTTTTA
60109587 ATAATTTTCTA
1 ATAATTTT-TA
*
60109598 TTAATTTTTA
1 ATAATTTTTA
60109608 ATAATTTTT-
1 ATAATTTTTA
*
60109617 ATGATTTTTA
1 ATAATTTTTA
60109627 A
1 A
60109628 ACATTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 4 0.12
9 11 0.32
10 12 0.35
11 7 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:60109623 original size:9 final size:9
Alignment explanation
Indices: 60109576--60109626 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
60109566 TAAATATTTC
60109576 TTTATAA-T
1 TTTATAATT
60109584 TTTATAATT
1 TTTATAATT
60109593 TTCTATTAATT
1 TT-TA-TAATT
60109604 TTTAATAATT
1 TTT-ATAATT
*
60109614 TTTATGATT
1 TTTATAATT
60109623 TTTA
1 TTTA
60109627 AACATTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 7 0.18
9 12 0.32
10 11 0.29
11 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:60109633 original size:29 final size:27
Alignment explanation
Indices: 60109512--60109634 Score: 78
Period size: 29 Copynumber: 4.5 Consensus size: 27
60109502 ATTTTAGTTT
* *
60109512 TTTTTATACTTTTTTAATAA---TAT-
1 TTTTTAAACATTTTTAATAATTTTATA
*
60109535 TTTTTAAACATTTTCAAT-ATTTTATA
1 TTTTTAAACATTTTTAATAATTTTATA
* * *
60109561 GGTTTTAAATATTTCTTTATAATTTTATAA
1 -TTTTTAAACATTT-TTAATAATTTTAT-A
*
60109591 TTTTCTATTA-ATTTTTAATAATTTTTATGA
1 TTTT-TA-AACATTTTTAATAA-TTTTAT-A
60109621 TTTTTAAACATTTT
1 TTTTTAAACATTTT
60109635 AAAAAGATTG
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
22 1 0.01
23 15 0.20
25 3 0.04
27 11 0.14
28 4 0.05
29 23 0.30
30 18 0.24
31 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTTAAACATTTTTAATAATTTTATA
Found at i:60113962 original size:29 final size:29
Alignment explanation
Indices: 60113919--60114088 Score: 191
Period size: 29 Copynumber: 5.8 Consensus size: 29
60113909 GTATCGACGC
*
60113919 CCATCGAATATGAAAAGGGATGGTGGTGA
1 CCATCGAATATGAAAAGGGATGGTGGCGA
* * * *
60113948 TCATCGAGTATGAAAAGAGATGGTAGCGA
1 CCATCGAATATGAAAAGGGATGGTGGCGA
**
60113977 CCATCGAATATGAAAAGGGATGGCT-TTGA
1 CCATCGAATATGAAAAGGGATGG-TGGCGA
* *
60114006 CCATCGAATATGAAAAAGGGTTGGTGACGA
1 CCATCGAATATG-AAAAGGGATGGTGGCGA
*
60114036 CCATCGAATATGAAAAGGGATGGCT-TCGA
1 CCATCGAATATGAAAAGGGATGG-TGGCGA
* *
60114065 CCATCGAATATAAAAATGGATGGT
1 CCATCGAATATGAAAAGGGATGGT
60114089 TCTGACAATC
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 93 0.77
30 26 0.22
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTGGCGA
Found at i:60114052 original size:59 final size:59
Alignment explanation
Indices: 60113914--60114088 Score: 225
Period size: 59 Copynumber: 3.0 Consensus size: 59
60113904 ACGAAGTATC
* * * *
60113914 GACGCCCATCGAATATGAAAAGGGATGG-TGGTGATCATCGAGTATG-AAAAGAGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGCT-TTGACCATCGAATATGAAAAAGAGATGGT
* *
60113972 -AGCGACCATCGAATATGAAAAGGGATGGCTTTGACCATCGAATATGAAAAAGGGTTGGT
1 GA-CGACCATCGAATATGAAAAGGGATGGCTTTGACCATCGAATATGAAAAAGAGATGGT
*
60114031 GACGACCATCGAATATGAAAAGGGATGGCTTCGACCATCGAATAT-AAAAATG-GATGGT
1 GACGACCATCGAATATGAAAAGGGATGGCTTTGACCATCGAATATGAAAAA-GAGATGGT
60114089 TCTGACAATC
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
57 1 0.01
58 48 0.46
59 54 0.52
60 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (59 bp):
GACGACCATCGAATATGAAAAGGGATGGCTTTGACCATCGAATATGAAAAAGAGATGGT
Done.