Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 93 of 318
Found at i:28164707 original size:81 final size:81
Alignment explanation
Indices: 28164446--28164708 Score: 244
Period size: 81 Copynumber: 3.2 Consensus size: 81
28164436 ATTTTACCCC
* * * * * * ** *
28164446 ACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGTATTTCTACCCTACAAGGGTATT
1 ACAAGGGTATTTCGGTAATTCTACCCTACAAGGGCATTTCGGTAATTCCACCAAACAGGGGTATT
* * **
28164511 TCGGTCATTCTACCCT
66 TCAGTAATTCTACCAA
* **
28164527 AC-AGGGCTATTTCGGTAATTCTACCCTACAGGGGCATTTCGGTAATTCCACCCTACAGGGGTAT
1 ACAAGGG-TATTTCGGTAATTCTACCCTACAAGGGCATTTCGGTAATTCCACCAAACAGGGGTAT
**
28164591 TTCAGTAATTCTACCCT
65 TTCAGTAATTCTACCAA
* * *
28164608 ACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGGTAATTTCA-CAAAGCAGGGGTAT
1 ACAAGGGTATTTCGGTAATTCTACCCTACAAGGGCATTTCGGTAATTCCACCAAA-CAGGGGTAT
** *
28164672 TTTGGTAATTTTA-CAA
65 TTCAGTAATTCTACCAA
* *
28164688 ACTAATGGTATTTTGGTAATT
1 AC-AAGGGTATTTCGGTAATT
28164709 TTATTGATCG
Statistics
Matches: 156, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
80 9 0.06
81 143 0.92
82 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (81 bp):
ACAAGGGTATTTCGGTAATTCTACCCTACAAGGGCATTTCGGTAATTCCACCAAACAGGGGTATT
TCAGTAATTCTACCAA
Found at i:28164776 original size:54 final size:54
Alignment explanation
Indices: 28164666--28164805 Score: 138
Period size: 54 Copynumber: 2.6 Consensus size: 54
28164656 CACAAAGCAG
** * * ** *
28164666 GGGTATTTTGGTAATTTTACAAACTAATGGTATTTTGGTAATTTTATTGATCGA
1 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTATTCATCGA
*
28164720 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTT-TTACATTGA
1 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTATT-CATCGA
*** * * *
28164774 GGGTAAAATGGTAATTCTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTGTAAACCAAGGGTA
28164806 AGACGGTAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 2 0.03
54 69 0.97
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTATTCATCGA
Found at i:28164786 original size:81 final size:81
Alignment explanation
Indices: 28164729--28164955 Score: 260
Period size: 81 Copynumber: 2.8 Consensus size: 81
28164719 AGGGTATTTT
** * * * * *
28164729 GGTAATTTTGTAAACCAAGGGT-ATTTCAGTAATTTTTTACATTGAGGGTAAAATGGTAATTCTG
1 GGTAATTTTGTAAACCAAGGGTAAAAT-AGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTA
28164793 TAAATCGAGGGTAAGAC
65 TAAATCGAGGGTAAGAC
* * *
28164810 GGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGT
1 GGTAATTTTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTAT
* *
28164875 AAATCGAGGGTAAAAT
66 AAATCGAGGGTAAGAC
* * * * * *
28164891 AGTAATTCTATAAATCGAGGGTAAAAT-GATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTA
1 GGTAATTTTGTAAACCAAGGGTAAAATAG-TAATTCTATAAATCGAGGGTAAAATGGTAATTCTA
28164955 T
65 T
28164956 CTTACAGGAG
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.01
81 126 0.98
82 2 0.02
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (81 bp):
GGTAATTTTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTAT
AAATCGAGGGTAAGAC
Found at i:28164787 original size:27 final size:27
Alignment explanation
Indices: 28164772--28164953 Score: 292
Period size: 27 Copynumber: 6.7 Consensus size: 27
28164762 TTTTTACATT
28164772 GAGGGTAAAATGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* * *
28164799 GAGGGTAAGACGGTAATTTTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
28164826 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
28164853 GAGGGTAAAATGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
28164880 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
28164907 GAGGGTAAAATGATAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
28164934 GAGGGTAAAATGGTAATTCT
1 GAGGGTAAAATGGTAATTCT
28164954 ATCTTACAGG
Statistics
Matches: 139, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 139 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (27 bp):
GAGGGTAAAATGGTAATTCTGTAAATC
Found at i:28164995 original size:27 final size:27
Alignment explanation
Indices: 28164965--28165114 Score: 171
Period size: 27 Copynumber: 5.6 Consensus size: 27
28164955 TCTTACAGGA
28164965 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
*
28164992 GTATTTCAGTAATTTTGCAAA-CTGAGG
1 GTATTTCAGTAATTTTACAAATC-GAGG
*
28165019 GTATTTCTGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* ** *
28165046 ATATTTGGGTAATTTTATAAATC-AGGG
1 GTATTTCAGTAATTTTACAAATCGA-GG
* * *
28165073 GTACTTT-GGTAATTTTACAAGTTGAGG
1 GTA-TTTCAGTAATTTTACAAATCGAGG
28165100 GTATTTCAGTAATTT
1 GTATTTCAGTAATTT
28165115 GGTAAACTAA
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.05
27 95 0.90
28 5 0.05
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.41
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATCGAGG
Found at i:28165051 original size:81 final size:82
Alignment explanation
Indices: 28164961--28165114 Score: 197
Period size: 81 Copynumber: 1.9 Consensus size: 82
28164951 TCTATCTTAC
*
28164961 AGGAGTATTTCAGTAATTTTACAAATC-GAGGGTA-TTTCAGTAATTTTGCAAACTGAGGGTATT
1 AGGAGTATTTCAGTAATTTTACAAATCAG-GGGTACTTT-AGTAATTTTACAAACTGAGGGTATT
*
28165024 TCTGTAATTTTACAAATCG
64 TCAGTAATTTTACAAATCG
** * * **
28165043 AGGA-TATTTGGGTAATTTTATAAATCAGGGGTACTTTGGTAATTTTACAAGTTGAGGGTATTTC
1 AGGAGTATTTCAGTAATTTTACAAATCAGGGGTACTTTAGTAATTTTACAAACTGAGGGTATTTC
28165107 AGTAATTT
66 AGTAATTT
28165115 GGTAAACTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
81 54 0.87
82 8 0.13
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (82 bp):
AGGAGTATTTCAGTAATTTTACAAATCAGGGGTACTTTAGTAATTTTACAAACTGAGGGTATTTC
AGTAATTTTACAAATCG
Found at i:28169287 original size:48 final size:48
Alignment explanation
Indices: 28169221--28169707 Score: 866
Period size: 48 Copynumber: 10.1 Consensus size: 48
28169211 GCGGAAATTG
*
28169221 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28169269 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATTTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
28169317 ATGTATGAGATAGGTATATGTGGTAAAGCTGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28169365 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
28169413 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28169461 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28169509 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28169557 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-AT
*
28169607 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28169655 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
28169703 ATGTA
1 ATGTA
28169708 GGCGATGTGT
Statistics
Matches: 422, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
48 374 0.89
49 4 0.01
50 44 0.10
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:28175257 original size:20 final size:21
Alignment explanation
Indices: 28175214--28175259 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
28175204 ACTGTTTTGT
28175214 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
28175234 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
28175253 TATGGGC
1 TATGGGC
28175260 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:28175352 original size:60 final size:60
Alignment explanation
Indices: 28175252--28175388 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
28175242 AACTGTGTTA
* * *
28175252 ATATGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCTACGACCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATATCTCGAATTGTAATAGGGCTACGACCCAGATTAATACTG
* * * *
28175312 ATATGGGCTAGGCCCAATATA-CTCTGATATTGTAA-GGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATATCTC-GA-ATTGTAATAGGGCTACGACCCAGATTAATACTG
28175372 ATATGGGCTAAGGCCCA
1 ATATGGGCT-AGGCCCA
28175389 GCTAACTCTG
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 3 0.04
60 51 0.76
61 13 0.19
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (60 bp):
ATATGGGCTAGGCCCAATATATCTCGAATTGTAATAGGGCTACGACCCAGATTAATACTG
Found at i:28179269 original size:20 final size:21
Alignment explanation
Indices: 28179226--28179271 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
28179216 ACTGTTTTGT
28179226 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
28179246 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
28179265 TATGGGC
1 TATGGGC
28179272 AAGACCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:28179391 original size:28 final size:27
Alignment explanation
Indices: 28179308--28179405 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 27
28179298 TAGGGCTACA
* *
28179308 GCCCAGATTGATACTGATATGGGCTAG
1 GCCCAGATTAATATTGATATGGGCTAG
* *
28179335 GCCCAGTATACTCTGATATTG-TAAGGGGCTATG
1 GCCCAG---A-T-TAATATTGAT-ATGGGCTA-G
28179368 GCCCAGATTAATATTGATATGGGCTAAG
1 GCCCAGATTAATATTGATATGGGCT-AG
28179396 GCCCAG-TTAA
1 GCCCAGATTAA
28179406 CTCTGATTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
27 10 0.17
28 20 0.34
29 3 0.05
30 2 0.03
31 2 0.03
32 14 0.24
33 7 0.12
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (27 bp):
GCCCAGATTAATATTGATATGGGCTAG
Found at i:28187201 original size:2 final size:2
Alignment explanation
Indices: 28187194--28187229 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28187184 TAAACAATTC
28187194 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
28187230 TTGTTTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28190954 original size:6 final size:6
Alignment explanation
Indices: 28190944--28191052 Score: 132
Period size: 6 Copynumber: 18.3 Consensus size: 6
28190934 TTGTTTTATC
* * * * * *
28190944 TTATTT CTATTT CTATTT CTATTT CTATTT CTATTT CTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
28190992 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTA-TT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
*
28191039 AT-TTT TTATGTT TT
1 TTATTT TTAT-TT TT
28191053 TATTATCTTT
Statistics
Matches: 96, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
5 9 0.09
6 83 0.86
7 4 0.04
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:28197713 original size:40 final size:41
Alignment explanation
Indices: 28197680--28197880 Score: 203
Period size: 41 Copynumber: 4.9 Consensus size: 41
28197670 GCGTTTGAAA
* * *
28197680 CAAAACGCCACTAAAAGCTGAGCAATAGTGGCGTTTTCATT
1 CAAAACGCCGCAAAAAGCTGAGCAATAGTGGCGTTTTTATT
** * *
28197721 CAAAGTGCCGCTAAAAA-CTGAGTAATAGTGGCGTTTTTATG
1 CAAAACGCCGC-AAAAAGCTGAGCAATAGTGGCGTTTTTATT
* *
28197762 CAAAACGCCGCAAAAAACTGAGAAATAGTGGCG-TTTTATT
1 CAAAACGCCGCAAAAAGCTGAGCAATAGTGGCGTTTTTATT
* *
28197802 CAAAACGCCGCAAAAAGCTGAG-ATATAGTGGCG-CTTTAGGT
1 CAAAACGCCGCAAAAAGCTGAGCA-ATAGTGGCGTTTTTA-TT
* * * * *
28197843 CCAAACGCCACAAAAGGTTGAGCTATAGTGGCGTTTTT
1 CAAAACGCCGCAAAAAGCTGAGCAATAGTGGCGTTTTT
28197881 GTAAAAGCGC
Statistics
Matches: 134, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 45 0.34
41 81 0.60
42 7 0.05
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (41 bp):
CAAAACGCCGCAAAAAGCTGAGCAATAGTGGCGTTTTTATT
Found at i:28197871 original size:81 final size:81
Alignment explanation
Indices: 28197680--28197879 Score: 228
Period size: 81 Copynumber: 2.4 Consensus size: 81
28197670 GCGTTTGAAA
**
28197680 CAAAACGCCACTAAAAGCTGAGCAATAGTGGCGTTTTCATTCAAAGTGCCGCTAAAAACTGAGTA
1 CAAAACGCCAC-AAAAGCTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTA
* *
28197745 ATAGTGGCGTTTTTATG
65 ATAGTGGCGTCTTTAGG
* * *
28197762 CAAAACGCCGCAAAAAACTGAGAAATAGTGGCGTTTT-ATTCAAAACGCCGC-AAAAAGCTGAG-
1 CAAAACGCCAC-AAAAGCTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAA-CTGAGT
28197824 ATATAGTGGCG-CTTTAGG
64 A-ATAGTGGCGTCTTTAGG
* * *
28197842 TCCAAACGCCACAAAAGGTTGAGCTATAGTGGCGTTTT
1 -CAAAACGCCACAAAA-GCTGAGCAATAGTGGCGTTTT
28197880 TGTAAAAGCG
Statistics
Matches: 100, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
80 15 0.15
81 52 0.52
82 33 0.33
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAAACGCCACAAAAGCTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTAA
TAGTGGCGTCTTTAGG
Found at i:28198476 original size:29 final size:29
Alignment explanation
Indices: 28198421--28198476 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
28198411 AAAATATGAA
* *
28198421 GCCTAACCCTTAAATCATAATCGATGACC
1 GCCTAACCCTTAAATCATAACCCATGACC
28198450 GCCTAATCCC-TAAATCATAACCCATGA
1 GCCTAA-CCCTTAAATCATAACCCATGA
28198477 TCTAAACTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.23
Consensus pattern (29 bp):
GCCTAACCCTTAAATCATAACCCATGACC
Found at i:28198673 original size:14 final size:15
Alignment explanation
Indices: 28198647--28198690 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
28198637 CTTTAAACCC
28198647 TTATAATACCCTAAA-
1 TTATAA-ACCCTAAAT
28198662 TTATAAACCCTAAAT
1 TTATAAACCCTAAAT
*
28198677 TTGTAAACCCTAAA
1 TTATAAACCCTAAA
28198691 AATAAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (15 bp):
TTATAAACCCTAAAT
Found at i:28199692 original size:20 final size:20
Alignment explanation
Indices: 28199647--28199698 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
28199637 CTCCACCCAA
*
28199647 ATTTCCCCAAATCCCTAACT
1 ATTTCCCCAAATCCCTAAAT
*
28199667 -TTTCCCCTAATCCCTAAAT
1 ATTTCCCCAAATCCCTAAAT
*
28199686 ATTTCCCCGAATC
1 ATTTCCCCAAATC
28199699 AAAATCGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.27, C:0.38, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTTCCCCAAATCCCTAAAT
Found at i:28199740 original size:19 final size:19
Alignment explanation
Indices: 28199716--28199769 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
28199706 AAATATCCTT
28199716 CTGCCGTTGAAGACTCCGA
1 CTGCCGTTGAAGACTCCGA
*
28199735 CTGCCGTTGAAGAATCCGA
1 CTGCCGTTGAAGACTCCGA
*
28199754 CTGCCATTGAAGACTC
1 CTGCCGTTGAAGACTC
28199770 TGAGTGGACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (19 bp):
CTGCCGTTGAAGACTCCGA
Found at i:28201113 original size:26 final size:26
Alignment explanation
Indices: 28201073--28201182 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
28201063 TGATACAAAT
28201073 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
28201099 TGAGAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28201125 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28201151 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28201177 TGATAA
1 TGATAA
28201183 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:28202903 original size:27 final size:26
Alignment explanation
Indices: 28202799--28202913 Score: 142
Period size: 27 Copynumber: 4.3 Consensus size: 26
28202789 TGGAGGAAGC
* *
28202799 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
28202826 GATT-TGGTGGCTCTGCCACATATATCT
1 G-TTCTGGTGGCTCTGCCACAT-TATCT
28202853 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
28202880 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
28202907 GTTCTGG
1 GTTCTGG
28202914 CAGCCATGCT
Statistics
Matches: 79, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
26 8 0.10
27 52 0.66
28 19 0.24
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:28202906 original size:54 final size:54
Alignment explanation
Indices: 28202799--28202913 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
28202789 TGGAGGAAGC
* *
28202799 GTTCTGGTGGCTATGCCACAAATATCTGATTTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
28202853 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
28202907 GTTCTGG
1 GTTCTGG
28202914 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:28205152 original size:3 final size:3
Alignment explanation
Indices: 28205144--28205169 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28205134 ATTGAGGCTA
28205144 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
28205170 TTTTCTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:28206370 original size:23 final size:23
Alignment explanation
Indices: 28206340--28206388 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
28206330 ACATTAATCT
28206340 AATGTATGAA-TTGCAGCCCTTTA
1 AATGTATGAATTTG-AGCCCTTTA
28206363 AATGTATGAATTTGAGCCCTTTA
1 AATGTATGAATTTGAGCCCTTTA
28206386 AAT
1 AAT
28206389 AAACTTGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (23 bp):
AATGTATGAATTTGAGCCCTTTA
Found at i:28206447 original size:10 final size:10
Alignment explanation
Indices: 28206432--28206482 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
28206422 TTATTATTTG
28206432 AAGTATGAAT
1 AAGTATGAAT
28206442 AAGTATGAAT
1 AAGTATGAAT
* **
28206452 AAGTTTTTAT
1 AAGTATGAAT
28206462 -A--ATGAAT
1 AAGTATGAAT
28206469 AAGTATGAAT
1 AAGTATGAAT
28206479 AAGT
1 AAGT
28206483 TTTTATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
7 3 0.09
8 1 0.03
9 1 0.03
10 27 0.84
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (10 bp):
AAGTATGAAT
Found at i:28206474 original size:27 final size:27
Alignment explanation
Indices: 28206436--28206489 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
28206426 TATTTGAAGT
28206436 ATGAATAAGTATGAATAAGTTTTTATA
1 ATGAATAAGTATGAATAAGTTTTTATA
28206463 ATGAATAAGTATGAATAAGTTTTTATA
1 ATGAATAAGTATGAATAAGTTTTTATA
28206490 TTTGATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (27 bp):
ATGAATAAGTATGAATAAGTTTTTATA
Found at i:28207043 original size:9 final size:9
Alignment explanation
Indices: 28207020--28207132 Score: 118
Period size: 9 Copynumber: 12.2 Consensus size: 9
28207010 ATTGATCATT
*
28207020 ACTTAAATA
1 ACTTACATA
*
28207029 AATTACATA
1 ACTTACATA
28207038 ACTTACATA
1 ACTTACATA
* *
28207047 ACTCATATA
1 ACTTACATA
28207056 ACTTACATA
1 ACTTACATA
*
28207065 ATTTACATAACA
1 ACTTACAT---A
28207077 ACTTACATA
1 ACTTACATA
*
28207086 ACTCACATA
1 ACTTACATA
28207095 ACTTACATA
1 ACTTACATA
*
28207104 ATTTACATA
1 ACTTACATA
*
28207113 ACTCACATA
1 ACTTACATA
*
28207122 ACGTACATA
1 ACTTACATA
28207131 AC
1 AC
28207133 AACTTACATA
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
9 77 0.91
12 8 0.09
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:28207089 original size:39 final size:39
Alignment explanation
Indices: 28207037--28207114 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
28207027 TAAATTACAT
*
28207037 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
28207076 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
28207115 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:28207114 original size:57 final size:57
Alignment explanation
Indices: 28207033--28207144 Score: 170
Period size: 57 Copynumber: 2.0 Consensus size: 57
28207023 TAAATAAATT
* * **
28207033 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
28207090 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAAC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAAC
28207145 CTAACTAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.29
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:28211447 original size:42 final size:43
Alignment explanation
Indices: 28211385--28211529 Score: 193
Period size: 44 Copynumber: 3.3 Consensus size: 43
28211375 GTAGAAAAAG
*
28211385 CGCCGCTAAAAGCCTCGACCTTTAG-GGCGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
* * * *
28211427 CGCCGCTAAAAGTCTTGACCTTTCGCGGCGCTTTTCCAAAAAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCC-CACAAA
* *
28211471 CGACGCTAAAAGCCTTGACCTTTTAGCGGCGCTTCTCCCACAAA
1 CGCCGCTAAAAGCCTTGACC-TTTAGCGGCGCTTTTCCCACAAA
*
28211515 CGCCACTAAAAGCCT
1 CGCCGCTAAAAGCCT
28211530 AGAAGCGCCG
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 22 0.25
43 11 0.13
44 39 0.45
45 15 0.17
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22
Consensus pattern (43 bp):
CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
Found at i:28211543 original size:20 final size:20
Alignment explanation
Indices: 28211515--28211552 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28211505 CTCCCACAAA
28211515 CGCCACTAAAAGCCTAGAAG
1 CGCCACTAAAAGCCTAGAAG
*
28211535 CGCCGCTAAAAGCCTAGA
1 CGCCACTAAAAGCCTAGA
28211553 CCTTTAGCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.32, G:0.21, T:0.11
Consensus pattern (20 bp):
CGCCACTAAAAGCCTAGAAG
Found at i:28211598 original size:43 final size:43
Alignment explanation
Indices: 28211535--28211736 Score: 341
Period size: 43 Copynumber: 4.7 Consensus size: 43
28211525 AGCCTAGAAG
*
28211535 CGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTCTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAA
28211578 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAA
* * * *
28211621 CGCCGCTAAAAGCCTTGACCTTTCGCGGTGCTTTTCCAACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAA
* *
28211664 CGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAA
28211707 CGCCGCTAAAAGCCTTGACCTTTAGCGGCG
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCG
28211737 TTTTTTTCCA
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 149 1.00
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (43 bp):
CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTCTCCCACAAA
Found at i:28211630 original size:106 final size:108
Alignment explanation
Indices: 28211427--28211635 Score: 332
Period size: 106 Copynumber: 2.0 Consensus size: 108
28211417 TTCCCACAAA
* * * *
28211427 CGCCGCTAAAAGTCTTGACCTTTCGCGGCGCTTTTCCAAAAAAACGACGCTAAAAGCCTTGACCT
1 CGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTCTCCAAAAAAACGACGCTAAAAGCCTTGACCT
28211492 TTTAGCGGCGCTTCTCCCACAAACGCCACTAAAAGCCTAGAAG
66 TTTAGCGGCGCTTCTCCCACAAACGCCACTAAAAGCCTAGAAG
* * *
28211535 CGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTCTCC-CACAAACGCCGCTAAAAGCCTTGACC-
1 CGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTCTCCAAAAAAACGACGCTAAAAGCCTTGACCT
*
28211598 TTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAAGCCT
66 TTTAGCGGCGCTTCTCCCACAAACGCCACTAAAAGCCT
28211636 TGACCTTTCG
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
106 37 0.40
107 23 0.25
108 33 0.35
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.20
Consensus pattern (108 bp):
CGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTCTCCAAAAAAACGACGCTAAAAGCCTTGACCT
TTTAGCGGCGCTTCTCCCACAAACGCCACTAAAAGCCTAGAAG
Found at i:28214199 original size:29 final size:28
Alignment explanation
Indices: 28214122--28214214 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 28
28214112 CACTCTTTGC
** * *
28214122 TCTGATATGCACTACAGTGTTGTTCTGT
1 TCTGATAAACACTATAGTGTTGTTCTAT
*
28214150 TCTGATAAACACTATAATGTTGTTCTAT
1 TCTGATAAACACTATAGTGTTGTTCTAT
*
28214178 TCTGATTAAACAC-ATTGGTGTTGTTCTAT
1 TCTGA-TAAACACTA-TAGTGTTGTTCTAT
*
28214207 TCTAATAA
1 TCTGATAA
28214215 TGCACTTTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 32 0.58
29 23 0.42
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (28 bp):
TCTGATAAACACTATAGTGTTGTTCTAT
Found at i:28216875 original size:137 final size:138
Alignment explanation
Indices: 28216668--28216934 Score: 351
Period size: 137 Copynumber: 1.9 Consensus size: 138
28216658 ATGTCATTAG
* * * * *
28216668 GGTTACCATGTTTCGGGTGCTGGTCTTGAATGTCCTACCGATGTCTGAGTTATCGCATTTGTTGC
1 GGTTACCATGTTTCGGGTGCTGGTCTTGAATGTCCTACCGATGGCTGAGGTACCGCATTAGTTAC
* * * * * *
28216733 GGATACTCGTCAGCTTGTTTGAGCAA-CATCATGTAGC-TACATTCCGACCTTCAGCTTGTGTAA
66 AGATACTCATCAACTTGTGTGAG-AAGCACCATGTAGCTTACATTCCGACCGTCAGCTTGTGTAA
28216796 GCAGACCCA
130 GCAGACCCA
* *
28216805 GGTTACCATGTTTTGGGTGCTGGTCTTGAATTTCCTACCGATGGCTGAGGT-CCGACATTAGTTA
1 GGTTACCATGTTTCGGGTGCTGGTCTTGAATGTCCTACCGATGGCTGAGGTACCG-CATTAGTTA
* * *
28216869 CAGATACTCATCAACTTGTGTGAGAAGCACCATGTAGCTTGCATTTCGATCGTCAGCTTGTGTAA
65 CAGATACTCATCAACTTGTGTGAGAAGCACCATGTAGCTTACATTCCGACCGTCAGCTTGTGTAA
28216934 G
130 G
28216935 TAGGCCCATT
Statistics
Matches: 111, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
136 4 0.04
137 84 0.76
138 23 0.21
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.33
Consensus pattern (138 bp):
GGTTACCATGTTTCGGGTGCTGGTCTTGAATGTCCTACCGATGGCTGAGGTACCGCATTAGTTAC
AGATACTCATCAACTTGTGTGAGAAGCACCATGTAGCTTACATTCCGACCGTCAGCTTGTGTAAG
CAGACCCA
Found at i:28221791 original size:2 final size:2
Alignment explanation
Indices: 28221786--28221819 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28221776 ATAATAAGAA
*
28221786 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28221820 GTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28223045 original size:25 final size:25
Alignment explanation
Indices: 28222996--28223045 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28222986 TACGTGATTG
*
28222996 ATATTGAAATGGCAAAGATGAGAAA
1 ATATTGAAATGGCAAAGAAGAGAAA
* *
28223021 ATATTGAAATGGCAAATAAGTGAAA
1 ATATTGAAATGGCAAAGAAGAGAAA
28223046 TGGAAATGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (25 bp):
ATATTGAAATGGCAAAGAAGAGAAA
Found at i:28227343 original size:23 final size:24
Alignment explanation
Indices: 28227308--28227353 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
28227298 AATTTCAAAT
*
28227308 TTTTATTAATTTTTATTTAATTTG
1 TTTTATTAATTTTAATTTAATTTG
* *
28227332 TTTT-TTATTTTTAATTTGATTT
1 TTTTATTAATTTTAATTTAATTT
28227354 AATAATTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTATTAATTTTAATTTAATTTG
Found at i:28229054 original size:40 final size:40
Alignment explanation
Indices: 28229009--28229089 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
28228999 AAAATTTTGT
28229009 GCTAAAAAGGTATTGTTAAGAAAAAAAAATATATGTATGC
1 GCTAAAAAGGTATTGTTAAGAAAAAAAAATATATGTATGC
28229049 GCTAAAAAGGTATTGTTAAGAAAAAAAAATATATGTATGC
1 GCTAAAAAGGTATTGTTAAGAAAAAAAAATATATGTATGC
28229089 G
1 G
28229090 TGTATGTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (40 bp):
GCTAAAAAGGTATTGTTAAGAAAAAAAAATATATGTATGC
Found at i:28229074 original size:19 final size:19
Alignment explanation
Indices: 28229012--28229075 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
28229002 ATTTTGTGCT
28229012 AAAAAGGTATTGTTAAGAA
1 AAAAAGGTATTGTTAAGAA
** ** **
28229031 AAAAAAATATATGTATGCGCT
1 AAAAAGGTAT-TGT-TAAGAA
28229052 AAAAAGGTATTGTTAAGAA
1 AAAAAGGTATTGTTAAGAA
28229071 AAAAA
1 AAAAA
28229076 AATATATGTA
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 15 0.48
20 6 0.19
21 10 0.32
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.25
Consensus pattern (19 bp):
AAAAAGGTATTGTTAAGAA
Found at i:28230912 original size:4 final size:4
Alignment explanation
Indices: 28230903--28230953 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
28230893 CATAATATAA
* * *
28230903 ACAT ACAT ACAT ACGT AGAT ACAT ACAT ACGT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
28230951 ACA
1 ACA
28230954 ACTCTTGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:28230926 original size:16 final size:16
Alignment explanation
Indices: 28230903--28230953 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
28230893 CATAATATAA
28230903 ACATACATACATACGT
1 ACATACATACATACGT
*
28230919 AGATACATACATACGT
1 ACATACATACATACGT
*
28230935 ACATACATACATACAT
1 ACATACATACATACGT
28230951 ACA
1 ACA
28230954 ACTCTTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (16 bp):
ACATACATACATACGT
Found at i:28231563 original size:30 final size:31
Alignment explanation
Indices: 28231490--28231564 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
28231480 AAAATTTGTT
*
28231490 ATTTTAGTCACTCTTGTTAGATAGGTTGCCA
1 ATTTTAGTCACTCTTGTTAGATAAGTTGCCA
* **
28231521 ATTTTAGTCACTCTTGTTGGATAAGTTTTCA
1 ATTTTAGTCACTCTTGTTAGATAAGTTGCCA
*
28231552 GTTTT-GTCACTCT
1 ATTTTAGTCACTCT
28231565 ACCGTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 8 0.21
31 31 0.79
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (31 bp):
ATTTTAGTCACTCTTGTTAGATAAGTTGCCA
Found at i:28232125 original size:16 final size:16
Alignment explanation
Indices: 28232104--28232136 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28232094 ATTCGAAGTT
28232104 GATTTCTTCATTACGA
1 GATTTCTTCATTACGA
28232120 GATTTCTTCATTACGA
1 GATTTCTTCATTACGA
28232136 G
1 G
28232137 GGGAGTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (16 bp):
GATTTCTTCATTACGA
Found at i:28232332 original size:47 final size:46
Alignment explanation
Indices: 28232271--28232371 Score: 152
Period size: 47 Copynumber: 2.2 Consensus size: 46
28232261 CATATATTTA
28232271 GCAATTTTGTTTTAGGGTTCATATGAAATTAGG-GATTTTTTTAGTTT
1 GCAATTTTGTTTTAGGGTTCATATGAAATT-GGAGA-TTTTTTAGTTT
*
28232318 GCAATATTT-TTTTAGGGTTTATATGAAATTGGAGATTTTTTAGTTT
1 GCAAT-TTTGTTTTAGGGTTCATATGAAATTGGAGATTTTTTAGTTT
28232364 GCAATTTT
1 GCAATTTT
28232372 AGGGATCATA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
45 3 0.06
46 18 0.35
47 27 0.53
48 3 0.06
ACGTcount: A:0.25, C:0.04, G:0.20, T:0.51
Consensus pattern (46 bp):
GCAATTTTGTTTTAGGGTTCATATGAAATTGGAGATTTTTTAGTTT
Found at i:28234134 original size:13 final size:13
Alignment explanation
Indices: 28234116--28234164 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 13
28234106 CACACGCTCA
28234116 TGTGGACCACTCG
1 TGTGGACCACTCG
28234129 TGTGGACCTACACGCTCG
1 TGTGGA-C--CA--CTCG
28234147 TGTGGACCACTCG
1 TGTGGACCACTCG
28234160 TGTGG
1 TGTGG
28234165 GCTCACACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 15 0.48
14 1 0.03
15 2 0.06
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.14, C:0.29, G:0.33, T:0.24
Consensus pattern (13 bp):
TGTGGACCACTCG
Found at i:28234173 original size:31 final size:30
Alignment explanation
Indices: 28234106--28234179 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
28234096 CCTAGAATCA
*
28234106 CACACGCTCATGTGGACCACTCGTGTGGAC
1 CACACGCTCGTGTGGACCACTCGTGTGGAC
*
28234136 CTACACGCTCGTGTGGACCACTCGTGTGGGC
1 C-ACACGCTCGTGTGGACCACTCGTGTGGAC
*
28234167 TCACACGCCCGTG
1 -CACACGCTCGTG
28234180 AGGCCCATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.16, C:0.35, G:0.28, T:0.20
Consensus pattern (30 bp):
CACACGCTCGTGTGGACCACTCGTGTGGAC
Found at i:28240683 original size:33 final size:33
Alignment explanation
Indices: 28240634--28240749 Score: 128
Period size: 33 Copynumber: 3.5 Consensus size: 33
28240624 ATGGACTTTT
* * *
28240634 CTTTTTCTAGTTGTACACTCGAGGTGCACATTC
1 CTTTTTCAAGTTGTACACTCGAAGTGCACATAC
* * *
28240667 CTTTTTCAAGTGGTACACACGAAGTGTACATAC
1 CTTTTTCAAGTTGTACACTCGAAGTGCACATAC
* **
28240700 CTTTTTCAATTTGTACACTTAAAGTGCACATAAC
1 CTTTTTCAAGTTGTACACTCGAAGTGCACAT-AC
28240734 C-TTTTCAAG-TGTACAC
1 CTTTTTCAAGTTGTACAC
28240750 ATGTAGTGTA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
32 7 0.10
33 59 0.86
34 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (33 bp):
CTTTTTCAAGTTGTACACTCGAAGTGCACATAC
Found at i:28240769 original size:66 final size:66
Alignment explanation
Indices: 28240628--28240789 Score: 159
Period size: 66 Copynumber: 2.5 Consensus size: 66
28240618 TTTCCGATGG
* * * * *
28240628 ACTTTTCTTTTTCTAGTTGTACACTCGAGGTGCACATTCCTTTTTCAAGTGGTACACACGAAGTG
1 ACTTTCCTTTTTCAAGTTGTACACTCAAAGTGCACATACCTTTTTCAAGTGGTACACACGAAGTG
28240693 T
66 T
* * * * * *
28240694 ACATACCTTTTTCAATTTGTACACTTAAAGTGCACATAACC-TTTTCAAGT-GTACACATGTAGT
1 ACTTTCCTTTTTCAAGTTGTACACTCAAAGTGCACAT-ACCTTTTTCAAGTGGTACACACGAAGT
28240757 GT
65 GT
* * *
28240759 ACCTTTCC-TTTTCAAGTGGTATACACAAAGT
1 A-CTTTCCTTTTTCAAGTTGTACACTCAAAGT
28240790 ATACCTTTCT
Statistics
Matches: 76, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
65 32 0.42
66 42 0.55
67 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (66 bp):
ACTTTCCTTTTTCAAGTTGTACACTCAAAGTGCACATACCTTTTTCAAGTGGTACACACGAAGTG
T
Found at i:28240804 original size:33 final size:33
Alignment explanation
Indices: 28240758--28240887 Score: 185
Period size: 33 Copynumber: 4.0 Consensus size: 33
28240748 ACATGTAGTG
28240758 TACCTTTCCTTTTCA-AGTGGTATACACAAAGTA
1 TACCTTTCCTTTTCATA-TGGTATACACAAAGTA
* *
28240791 TACCTTTCTTTTTCATATGATATACACAAAGTA
1 TACCTTTCCTTTTCATATGGTATACACAAAGTA
*
28240824 TAACTTTCCTTTTCATATGGTATACACAAAGTA
1 TACCTTTCCTTTTCATATGGTATACACAAAGTA
*
28240857 TACCTTTCCTTTTCA-A-GTGTACACACAAAGT
1 TACCTTTCCTTTTCATATG-GTATACACAAAGT
28240888 GTACATAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
31 1 0.01
32 13 0.15
33 73 0.83
34 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (33 bp):
TACCTTTCCTTTTCATATGGTATACACAAAGTA
Found at i:28240838 original size:66 final size:65
Alignment explanation
Indices: 28240733--28240887 Score: 206
Period size: 66 Copynumber: 2.4 Consensus size: 65
28240723 GTGCACATAA
*** * *
28240733 CCTTTTCAAGTGTACACATGTAGTGTACCTTTCCTTTTCA-AGTGGTATACACAAAGTATACCTT
1 CCTTTTCAAGTGTACACACAAAGTATAACTTTCCTTTTCATA-TGGTATACACAAAGTATACCTT
28240797 T
65 T
* *
28240798 CTTTTTCATA-TGATATACACAAAGTATAACTTTCCTTTTCATATGGTATACACAAAGTATACCT
1 CCTTTTCA-AGTG-TACACACAAAGTATAACTTTCCTTTTCATATGGTATACACAAAGTATACCT
28240862 TT
64 TT
28240864 CCTTTTCAAGTGTACACACAAAGT
1 CCTTTTCAAGTGTACACACAAAGT
28240888 GTACATAAAC
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
65 21 0.27
66 55 0.71
67 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (65 bp):
CCTTTTCAAGTGTACACACAAAGTATAACTTTCCTTTTCATATGGTATACACAAAGTATACCTTT
Found at i:28241638 original size:21 final size:22
Alignment explanation
Indices: 28241592--28241639 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
28241582 TGTAAAAATG
**
28241592 ATTTATCTATCAATAATCTTTC
1 ATTTATCTATCAATAAAATTTC
28241614 ATTT-TCTATCAA-AAAATTTC
1 ATTTATCTATCAATAAAATTTC
28241634 AATTTA
1 -ATTTA
28241640 CAGCATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.27
21 12 0.55
22 4 0.18
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTATCTATCAATAAAATTTC
Found at i:28243437 original size:40 final size:40
Alignment explanation
Indices: 28243392--28243558 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
28243382 CGGAATATAA
28243392 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
28243432 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
28243472 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
28243512 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
28243551 CCGGATAT
1 CCGGATAT
28243559 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28243542 original size:80 final size:79
Alignment explanation
Indices: 28243392--28243558 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
28243382 CGGAATATAA
* *
28243392 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
28243457 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
28243472 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
28243534 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
28243551 CCGGATAT
1 CCGGATAT
28243559 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:28244409 original size:17 final size:19
Alignment explanation
Indices: 28244386--28244431 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28244376 AAGAAGCATG
28244386 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
28244404 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
28244422 AATCATGCTC
1 AATCATGCTC
28244432 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:28251419 original size:40 final size:40
Alignment explanation
Indices: 28251374--28251540 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
28251364 CGGAATATAA
28251374 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
28251414 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
28251454 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
28251494 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
28251533 CCGGATAT
1 CCGGATAT
28251541 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28251524 original size:80 final size:79
Alignment explanation
Indices: 28251374--28251540 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
28251364 CGGAATATAA
* *
28251374 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
28251439 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
28251454 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
28251516 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
28251533 CCGGATAT
1 CCGGATAT
28251541 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:28252388 original size:17 final size:19
Alignment explanation
Indices: 28252365--28252410 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28252355 AAGAAGCATG
28252365 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
28252383 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
28252401 AATCATGCTC
1 AATCATGCTC
28252411 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:28256618 original size:48 final size:48
Alignment explanation
Indices: 28256560--28257316 Score: 1192
Period size: 48 Copynumber: 15.8 Consensus size: 48
28256550 TATGTATGAA
28256560 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
* *
28256608 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
* * * * * *
28256656 ATATGTATATGAGGTAAGGCCGAATGGCGAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
* * *
28256704 ATATGTATATGTGGTAAAGCCGAATGG-TGAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCT-AATGTGAAATATATGTGTG
*
28256752 ATATGTATATATGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
28256800 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
* * * *
28256848 ATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
* * * *
28256896 ATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
*
28256944 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
28256992 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
* * * * *
28257040 ATATGTATATGTGGTAAAGCCAAATGGCGAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
*
28257088 ATATGTATACGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
*
28257136 ATATGTATACGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
*
28257184 ATATGTATACGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
* * * * *
28257232 ATATGTATATGTGGTAAAGCCAAATGGCGAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
28257280 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
28257317 TGTTGTAACA
Statistics
Matches: 664, Mismatches: 43, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
48 663 1.00
49 1 0.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
Found at i:28256874 original size:192 final size:192
Alignment explanation
Indices: 28256547--28257316 Score: 1380
Period size: 192 Copynumber: 4.0 Consensus size: 192
28256537 TGTACAAGAT
*
28256547 AAATATGTATGAAATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATAT
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATAT
* * * *
28256612 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGAGGTAAGGCC
66 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
*
28256677 GAATGGCGAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGG-TGAATGTG
131 AAATGGCGAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCT-AATGTG
*
28256739 AAATATGTATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATAT
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATAT
28256804 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
66 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
* *
28256869 GAATGGCGAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTG
131 AAATGGCGAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
28256931 AAATATGTATGAGATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATATGTGTGATAT
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATAT
28256996 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
66 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
*
28257061 AAATGGCGAATGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCGAATGGCTAATGTG
131 AAATGGCGAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * * *
28257123 AAATATATGTGTGATATGTATACGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATAT
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATAT
*
28257188 GTATACGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
66 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
28257253 AAATGGCGAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
131 AAATGGCGAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
28257315 AA
1 AA
28257317 TGTTGTAACA
Statistics
Matches: 558, Mismatches: 19, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
192 558 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (192 bp):
AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATAT
GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
AAATGGCGAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
Found at i:28257469 original size:37 final size:37
Alignment explanation
Indices: 28257361--28257469 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
28257351 GGAAATGTAC
*
28257361 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
28257398 TCCGGGTAAGACCCAATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
28257435 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
28257470 CGTCTGAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:28261028 original size:21 final size:22
Alignment explanation
Indices: 28260984--28261025 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28260974 CGATGGATGC
*
28260984 GCATTGAGTTATAATATGTAAT
1 GCATTGAGTTATAAAATGTAAT
28261006 GCATT-AGTTAGTAAAATGTA
1 GCATTGAGTTA-TAAAATGTA
28261026 TGCCATTTGT
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:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (22 bp):
GCATTGAGTTATAAAATGTAAT
Found at i:28261032 original size:22 final size:23
Alignment explanation
Indices: 28260980--28261032 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
28260970 TAAACGATGG
*
28260980 ATGCGCATTGAGTTATAATATGTA
1 ATGC-CATTGAGTTATAAAATGTA
28261004 ATG-CATT-AGTTAGTAAAATGT-
1 ATGCCATTGAGTTA-TAAAATGTA
28261025 ATGCCATT
1 ATGCCATT
28261033 TGTATGTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 8 0.31
22 15 0.58
24 3 0.12
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (23 bp):
ATGCCATTGAGTTATAAAATGTA
Found at i:28269308 original size:40 final size:40
Alignment explanation
Indices: 28269209--28269410 Score: 268
Period size: 40 Copynumber: 5.0 Consensus size: 40
28269199 TGGATGATAA
*
28269209 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* * *
28269250 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28269290 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28269330 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28269370 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
28269409 CC
1 CC
28269411 AGTTAAATCC
Statistics
Matches: 145, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 15 0.10
40 101 0.70
41 23 0.16
42 4 0.03
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28276814 original size:68 final size:67
Alignment explanation
Indices: 28276768--28276925 Score: 280
Period size: 68 Copynumber: 2.3 Consensus size: 67
28276758 ATACTATATA
28276768 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
28276833 AAT
65 AAT
28276836 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
28276901 AAT
65 AAT
* *
28276904 GTAGCTAGGTCGCATGAGTGAT
1 GTAGCTAGGTCACATGTGTGAT
28276926 TCCAAGTGAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 88 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (67 bp):
GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGGAGAGATAA
AT
Found at i:28283632 original size:18 final size:18
Alignment explanation
Indices: 28283611--28283645 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28283601 AAAATCCATC
28283611 TCATCATCTCCTTCCTCG
1 TCATCATCTCCTTCCTCG
*
28283629 TCATCATTTCCTTCCTC
1 TCATCATCTCCTTCCTC
28283646 TTCACTTTCA
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:0.11, C:0.43, G:0.03, T:0.43
Consensus pattern (18 bp):
TCATCATCTCCTTCCTCG
Found at i:28286668 original size:21 final size:20
Alignment explanation
Indices: 28286642--28286681 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28286632 TAGAACTTAT
28286642 ATTTTTTAAATTTTGAAAATA
1 ATTTTTT-AATTTTGAAAATA
*
28286663 ATTTTTTTATTTTGAAAAT
1 ATTTTTTAATTTTGAAAAT
28286682 TTAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTTTAATTTTGAAAATA
Found at i:28286690 original size:22 final size:21
Alignment explanation
Indices: 28286642--28286692 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 21
28286632 TAGAACTTAT
28286642 ATTTTTTAAATTTTGAAAAT-A
1 ATTTTTT-AATTTTGAAAATAA
*
28286663 ATTTTTTTATTTTGAAAATTTAA
1 ATTTTTTAATTTTGAAAA--TAA
28286686 ATTTTTT
1 ATTTTTT
28286693 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 10 0.38
21 7 0.27
22 1 0.04
23 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTTTTTAATTTTGAAAATAA
Found at i:28288617 original size:3 final size:3
Alignment explanation
Indices: 28288557--28288603 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
28288547 CATACATTTA
28288557 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28288604 GTTTTGATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28292636 original size:18 final size:18
Alignment explanation
Indices: 28292613--28292656 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
28292603 GCTAACTATT
28292613 GGAAAAGGGGCTCTACCA
1 GGAAAAGGGGCTCTACCA
*
28292631 GGAAAAGGGGCTCTACCC
1 GGAAAAGGGGCTCTACCA
28292649 GGAAAAGG
1 GGAAAAGG
28292657 ACTCGGGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.36, T:0.09
Consensus pattern (18 bp):
GGAAAAGGGGCTCTACCA
Found at i:28297691 original size:44 final size:44
Alignment explanation
Indices: 28297596--28297753 Score: 146
Period size: 44 Copynumber: 3.6 Consensus size: 44
28297586 CACAGATTTT
* **
28297596 ACCCCATAAGCAGTAGGG-AA-ATAGATCGAAGGCAATGAGCTTTA
1 ACCCC-TAAGCAGTAGGGTAACA-AGCTCGAAGATAATGAGCTTTA
* * *
28297640 ACCCCCTAAGCAGTAGGGTAACAAGCT-GAAGTTCAT-AGATCTTA
1 A-CCCCTAAGCAGTAGGGTAACAAGCTCGAAGATAATGAGCT-TTA
* * *
28297684 TCACCCTAAGCAGTAGGGAAAC-AGATCGAAGATAATGAGCTTTA
1 AC-CCCTAAGCAGTAGGGTAACAAGCTCGAAGATAATGAGCTTTA
28297728 ACCTCCTAAGCAGTAGGGTAACAAGC
1 ACC-CCTAAGCAGTAGGGTAACAAGC
28297754 CAAATTTACA
Statistics
Matches: 91, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
43 8 0.09
44 68 0.75
45 14 0.15
46 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (44 bp):
ACCCCTAAGCAGTAGGGTAACAAGCTCGAAGATAATGAGCTTTA
Found at i:28298132 original size:178 final size:177
Alignment explanation
Indices: 28297724--28298161 Score: 474
Period size: 178 Copynumber: 2.5 Consensus size: 177
28297714 GATAATGAGC
*
28297724 TTTAACCTCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTAGGG
1 TTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAA-TTACAGACCTTAACCCCCTAAGTAGTAGGG
* * * * ** **
28297789 TAATAGGCTGAAAATTATAGATCTTGTCTCCCTGAAGTTGTAGTGGAACAGATCGAATCCAGCGA
65 TAACAAGCTGAAAATTATAGATCTTATCACCCTGAAGCAGTAGTGGAACAGATCGAAGACAGCGA
* * * *
28297854 ATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAAAT
130 ATCTTGCCCTCCTGAAGTTGCAGTGAAGCAGATTCAAGATCTACAAAT
* * * * * ** * *
28297902 CTT-ACCCCCGAAGCAGTAGGGAAACAGATCGAAGGTA-ACGAGCTTCAACCCCCTGAGTAGTAG
1 TTTAACCCCCTAAGCAGTAGGGTAACA-AGCCAAATTACA-GACCTT-AACCCCCTAAGTAGTAG
* ** * *
28297965 GGTAACAAGCTGGAGTTTATAGATCTTATCACCCT-CAGCAGTAG-GGAAGCAGATCAGAAGACG
63 GGTAACAAGCTGAAAATTATAGATCTTATCACCCTGAAGCAGTAGTGGAA-CAGATC-GAAGACA
28298028 GCGAATCTTGCCCTCCTGAAGTTGCAGTGAAGCAGATTCAA-A-CTACCAAAT
126 GCGAATCTTGCCCTCCTGAAGTTGCAGTGAAGCAGATTCAAGATCTA-CAAAT
*
28298079 TTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTCACCAGACCTTAACCCCCTAAGCAGTAGG
1 TTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATT-A-CAGACCTTAACCCCCTAAGTAGTAGG
* * *
28298144 GTAATAGGCTAAAAATTA
64 GTAACAAGCTGAAAATTA
28298162 CAAATCTCGT
Statistics
Matches: 207, Mismatches: 43, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
176 7 0.03
177 52 0.25
178 142 0.69
179 5 0.02
180 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (177 bp):
TTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTACAGACCTTAACCCCCTAAGTAGTAGGGT
AACAAGCTGAAAATTATAGATCTTATCACCCTGAAGCAGTAGTGGAACAGATCGAAGACAGCGAA
TCTTGCCCTCCTGAAGTTGCAGTGAAGCAGATTCAAGATCTACAAAT
Found at i:28300205 original size:19 final size:21
Alignment explanation
Indices: 28300164--28300206 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
28300154 TATTTTCGTA
*
28300164 TTATTATTATTATTAACGTATT
1 TTATTATTATTATAAACG-ATT
28300186 TTATTATTATT-TAAAC-ATT
1 TTATTATTATTATAAACGATT
28300205 TT
1 TT
28300207 TAGTTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
21 4 0.20
22 11 0.55
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATTATTATTATAAACGATT
Found at i:28300494 original size:3 final size:3
Alignment explanation
Indices: 28300414--28300480 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
28300404 ATACGTATAC
28300414 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28300462 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
28300481 GTTTTGATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28303023 original size:25 final size:24
Alignment explanation
Indices: 28302966--28303026 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
28302956 ATTATATTCC
28302966 TATTTAATTTTAACTAATAAATTAA
1 TATTTAATTTTAACT-ATAAATTAA
* *
28302991 AATATAATTTATAACT-TAAATTCAA
1 TATTTAATTT-TAACTATAAATT-AA
28303016 TATTTAATTTT
1 TATTTAATTTT
28303027 TCAACCCCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
24 7 0.23
25 18 0.60
26 5 0.17
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTTAATTTTAACTATAAATTAA
Found at i:28306268 original size:43 final size:44
Alignment explanation
Indices: 28306166--28306269 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 44
28306156 GCCCCAGACT
* * *
28306166 TGGTCTTACATGT-AATCAAATATTGATGCCACTGTCCCAAACA
1 TGGTCTTACACGTAAATCAAATATCGATACCACTGTCCCAAACA
* * *
28306209 GGGTCTTACAC-AAAATCAAATA-CGATACCGA-TGTCCCATACA
1 TGGTCTTACACGTAAATCAAATATCGATACC-ACTGTCCCAAACA
28306251 TGGTCTTACACGTAAATCA
1 TGGTCTTACACGTAAATCA
28306270 TAAGTCGATG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
42 25 0.50
43 25 0.50
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (44 bp):
TGGTCTTACACGTAAATCAAATATCGATACCACTGTCCCAAACA
Found at i:28314642 original size:16 final size:16
Alignment explanation
Indices: 28314621--28314652 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28314611 TAGGACATGG
28314621 CGTCAGCTTGTTGTGT
1 CGTCAGCTTGTTGTGT
28314637 CGTCAGCTTGTTGTGT
1 CGTCAGCTTGTTGTGT
28314653 GTTAGTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.31, T:0.44
Consensus pattern (16 bp):
CGTCAGCTTGTTGTGT
Found at i:28316699 original size:24 final size:24
Alignment explanation
Indices: 28316672--28316732 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
28316662 TATTATGTTA
28316672 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCCATAGTAAATC
28316696 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCCATAGTAAATC
*
28316720 ACACACATAGTGC
1 GCACACATAGTGC
28316733 ATTTGAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAATC
Found at i:28320215 original size:43 final size:44
Alignment explanation
Indices: 28320095--28320251 Score: 119
Period size: 43 Copynumber: 3.6 Consensus size: 44
28320085 AGCTTGTACA
* * *
28320095 ATACCAGTGTCCCAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATACCACTATCCCAGACATGGTCTTACATGTAAATCAAATATCG
* * * **
28320138 ATGCCACTGTCCCAGACAGGGTCTTACA-CAAAATCAAATA-CG
1 ATACCACTATCCCAGACATGGTCTTACATGTAAATCAAATATCG
* * *
28320180 ATACTGA-TATTCCAGACATGGTCTTACATGTAAATCATAA-GTCG
1 ATAC-CACTATCCCAGACATGGTCTTACATGTAAATCA-AATATCG
* * *
28320224 TTGCCAAC-ATCCCAGACGTGGTCTTACA
1 ATACC-ACTATCCCAGACATGGTCTTACA
28320252 CGAAAACACA
Statistics
Matches: 88, Mismatches: 19, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
42 23 0.26
43 40 0.45
44 25 0.28
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (44 bp):
ATACCACTATCCCAGACATGGTCTTACATGTAAATCAAATATCG
Found at i:28321827 original size:19 final size:18
Alignment explanation
Indices: 28321803--28321864 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 18
28321793 GAGAAGTGGA
28321803 ATAATATTTATAATTTTTT
1 ATAATATTTAT-ATTTTTT
*
28321822 ATAATATTTATATCCTTTT
1 ATAATATTTATAT-TTTTT
*
28321841 A-AATATTT-TATATTTT
1 ATAATATTTATATTTTTT
28321857 AT-ATATTT
1 ATAATATTT
28321865 TTAATTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 11 0.28
17 3 0.08
18 9 0.23
19 16 0.41
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATAATATTTATATTTTTT
Found at i:28321871 original size:16 final size:16
Alignment explanation
Indices: 28321818--28321865 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
28321808 ATTTATAATT
*
28321818 TTTTATAATATTTATATCC
1 TTTTA-AATATTT-TAT-A
28321837 TTTTAAATATTTTATA
1 TTTTAAATATTTTATA
*
28321853 TTTTATATATTTT
1 TTTTAAATATTTT
28321866 TAATTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 7 0.26
19 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAATATTTTATA
Found at i:28322008 original size:18 final size:17
Alignment explanation
Indices: 28321967--28322010 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
28321957 AGAAGGGAAA
*
28321967 TAATTTTTATAAATTTT
1 TAATATTTATAAATTTT
*
28321984 TATATATTTATAAGTTTTT
1 TA-ATATTTATAA-ATTTT
28322003 TAATATTT
1 TAATATTT
28322011 TTATATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 15 0.65
19 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TAATATTTATAAATTTT
Found at i:28322025 original size:26 final size:28
Alignment explanation
Indices: 28321966--28322026 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
28321956 CAGAAGGGAA
*
28321966 ATAA-TTTTTATAAATTTTTATATATTT
1 ATAAGTTTTTATAAATTTTTATATATTC
28321993 ATAAGTTTTT-TAATATTTTTATAT-TTC
1 ATAAGTTTTTATAA-ATTTTTATATATTC
28322020 AT-AGTTT
1 ATAAGTTT
28322027 GTTTTCAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 5 0.16
27 11 0.35
28 15 0.48
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (28 bp):
ATAAGTTTTTATAAATTTTTATATATTC
Found at i:28322880 original size:13 final size:13
Alignment explanation
Indices: 28322862--28322886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28322852 TTTATTTTTT
28322862 TTATATTTTAAAA
1 TTATATTTTAAAA
28322875 TTATATTTTAAA
1 TTATATTTTAAA
28322887 GGGATTGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATTTTAAAA
Found at i:28325076 original size:140 final size:139
Alignment explanation
Indices: 28324768--28325332 Score: 757
Period size: 140 Copynumber: 4.1 Consensus size: 139
28324758 AATAGAAACC
* * * *
28324768 AAAG-ATATAATTAATATATGAATTTGATTCATAAAAAATATTTATAGTATATATTTTA-TCGAA
1 AAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACT-AAA
* *
28324831 TTTATTAATATAAACAATTATATTAATTAATTTCT-GTCAAAAT-ATAAAAGACATGGAAATTAA
65 TTTATTAATATAAACAATTATATTAATTAATTT-TGGTCAAAATAAAAAAAGACATGAAAATTAA
*
28324894 TATTCTTTTGA
129 TATTCTTTTGG
* *
28324905 AAAGAATATAATTAATATTTGAATTTGATTCATACAAAATATTAATTTTATATATTTTACTAAAT
1 AAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAAT
* * *
28324970 TTATTAATAGAAACAGTTATATGAATTAATTTTGGTCAAAATAAAAAAAAGACATGAAAATTAAT
66 TTATTAATATAAACAATTATATTAATTAATTTTGGTCAAAAT-AAAAAAAGACATGAAAATTAAT
28325035 ATTCTTTTGG
130 ATTCTTTTGG
* *
28325045 AAAGAATATAATTAGTATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACTAAAT
1 AAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAAT
* * * * *
28325110 TTATTAAAATAAACAATTATATTAATGAATTTCGGTTAAAATATAAAAA-A-ATGAAAATTAATA
66 TTATTAATATAAACAATTATATTAATTAATTTTGGTCAAAATAAAAAAAGACATGAAAATTAATA
* *
28325173 TTATTCTGG
131 TTCTTTTGG
* * **
28325182 AAAGAATATAATTAATATATGAATTTGATTCATACAAAACATTAATTGTGTATATTTTACCGAAT
1 AAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAAT
* * * * * * **
28325247 TTATTAATATAAACAGTTATATTAATTAATTTTAGTCAAAA-CATAAAAGATATGGAAATTTTTA
66 TTATTAATATAAACAATTATATTAATTAATTTTGGTCAAAATAAAAAAAGACATGAAAATTAATA
28325311 TTCTTTTGG
131 TTCTTTTGG
28325320 AAAGAATATAATT
1 AAAGAATATAATT
28325333 CTTTTTTCTA
Statistics
Matches: 376, Mismatches: 45, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
136 4 0.01
137 120 0.32
138 120 0.32
139 7 0.02
140 125 0.33
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (139 bp):
AAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAAT
TTATTAATATAAACAATTATATTAATTAATTTTGGTCAAAATAAAAAAAGACATGAAAATTAATA
TTCTTTTGG
Found at i:28325267 original size:277 final size:276
Alignment explanation
Indices: 28324768--28325332 Score: 814
Period size: 277 Copynumber: 2.0 Consensus size: 276
28324758 AATAGAAACC
* *
28324768 AAAG-ATATAATTAATATATGAATTTGATTCATAAAAAATATTTATAGTATATATTTTATCGAAT
1 AAAGAATATAATTAATATATGAATTTGATTCATAAAAAATATTAATAGTATATATTTTATCAAAT
* * * * *
28324832 TTATTAATATAAACAATTATATTAATTAATTTCTGTCAAAATATAAAAGACATGGAAATTAATAT
66 TTATTAAAATAAACAATTATATTAATGAATTTCGGTCAAAATATAAAAGAAATGAAAATTAATAT
* * * * *
28324897 TCTTTTGAAAAGAATATAATTAATATTTGAATTTGATTCATACAAAATATTAATTTTATATATTT
131 TATTCTGAAAAGAATATAATTAATATATGAATTTGATTCATACAAAACATTAATTGTATATATTT
* *
28324962 TACTAAATTTATTAATAGAAACAGTTATATGAATTAATTTTGGTCAAAATAAAAAAAAGACATGA
196 TACCAAATTTATTAATAGAAACAGTTATATGAATTAATTTTAGTC-AAA-AAAAAAAAGACATGA
28325027 AAATTAATATTCTTTTGG
259 AAATTAATATTCTTTTGG
* *
28325045 AAAGAATATAATTAGTATATGAATTTGATTCATACAAAATATTAATTA-TATATATTTTA-CTAA
1 AAAGAATATAATTAATATATGAATTTGATTCATAAAAAATATTAA-TAGTATATATTTTATC-AA
*
28325108 ATTTATTAAAATAAACAATTATATTAATGAATTTCGGTTAAAATATAAAA-AAATGAAAATTAAT
64 ATTTATTAAAATAAACAATTATATTAATGAATTTCGGTCAAAATATAAAAGAAATGAAAATTAAT
* *
28325172 ATTATTCTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAACATTAATTGTGTATAT
129 ATTATTCTGAAAAGAATATAATTAATATATGAATTTGATTCATACAAAACATTAATTGTATATAT
* * * * * * *
28325237 TTTACCGAATTTATTAATATAAACAGTTATATTAATTAATTTTAGTCAAAACATAAAAGATATGG
194 TTTACCAAATTTATTAATAGAAACAGTTATATGAATTAATTTTAGTCAAAAAAAAAAAGACATGA
**
28325302 AAATTTTTATTCTTTTGG
259 AAATTAATATTCTTTTGG
28325320 AAAGAATATAATT
1 AAAGAATATAATT
28325333 CTTTTTTCTA
Statistics
Matches: 257, Mismatches: 28, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
275 40 0.16
276 3 0.01
277 117 0.46
278 95 0.37
279 2 0.01
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (276 bp):
AAAGAATATAATTAATATATGAATTTGATTCATAAAAAATATTAATAGTATATATTTTATCAAAT
TTATTAAAATAAACAATTATATTAATGAATTTCGGTCAAAATATAAAAGAAATGAAAATTAATAT
TATTCTGAAAAGAATATAATTAATATATGAATTTGATTCATACAAAACATTAATTGTATATATTT
TACCAAATTTATTAATAGAAACAGTTATATGAATTAATTTTAGTCAAAAAAAAAAAGACATGAAA
ATTAATATTCTTTTGG
Found at i:28330985 original size:42 final size:41
Alignment explanation
Indices: 28330925--28331074 Score: 158
Period size: 42 Copynumber: 3.6 Consensus size: 41
28330915 TAAGACTATG
*
28330925 TGTAAGACTATATCTGGGATATGGCATCTATATGAGACTTCA
1 TGTAAGACCATATCTGGGATATGGCATCTATATGAGA-TTCA
* * *
28330967 TGTAAGACCATATTTGGGATATGGTAT-TGATATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCT-ATATGAGA-TTCA
* * * * *
28331009 TGTAATACCATAGCTGGGCTATTGGCATCGATACGAGATTACA
1 TGTAAGACCATATCTGGGATA-TGGCATCTATATGAGATT-CA
*
28331052 TGTAAGAGCATATCTGGGATATG
1 TGTAAGACCATATCTGGGATATG
28331075 TCATTGTTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.01
42 56 0.64
43 30 0.34
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.33
Consensus pattern (41 bp):
TGTAAGACCATATCTGGGATATGGCATCTATATGAGATTCA
Found at i:28332165 original size:16 final size:16
Alignment explanation
Indices: 28332144--28332174 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28332134 TTTGGAAATG
28332144 TGATTTATGACATGAA
1 TGATTTATGACATGAA
*
28332160 TGATTTATGGCATGA
1 TGATTTATGACATGA
28332175 TAAAGGTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (16 bp):
TGATTTATGACATGAA
Found at i:28332796 original size:31 final size:31
Alignment explanation
Indices: 28332776--28332834 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28332766 GGAGTTTGTG
28332776 ACCACACGGCCTCCCCACACGGGCATGTGTC
1 ACCACACGGCCTCCCCACACGGGCATGTGTC
* *
28332807 ACCACACGGCCTGCCCACACAGGCATGT
1 ACCACACGGCCTCCCCACACGGGCATGT
28332835 CCTAAGCCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.44, G:0.22, T:0.12
Consensus pattern (31 bp):
ACCACACGGCCTCCCCACACGGGCATGTGTC
Found at i:28334655 original size:33 final size:33
Alignment explanation
Indices: 28334608--28334674 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
28334598 AATTTAGTCC
*
28334608 TTCTTGTAATTAAACACTTAATCGATAAAATTT
1 TTCTCGTAATTAAACACTTAATCGATAAAATTT
*
28334641 TTCTCGTAATTAAACACTTAATCGATGAAATTT
1 TTCTCGTAATTAAACACTTAATCGATAAAATTT
28334674 T
1 T
28334675 CGTATCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.42
Consensus pattern (33 bp):
TTCTCGTAATTAAACACTTAATCGATAAAATTT
Found at i:28338375 original size:17 final size:18
Alignment explanation
Indices: 28338342--28338375 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28338332 CGTGTGGTTA
28338342 ACCCGTGTGGACCCACAT
1 ACCCGTGTGGACCCACAT
28338360 ACCCGTGTGG-CCCACA
1 ACCCGTGTGGACCCACA
28338376 CGACCCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.21, C:0.41, G:0.24, T:0.15
Consensus pattern (18 bp):
ACCCGTGTGGACCCACAT
Found at i:28338381 original size:18 final size:18
Alignment explanation
Indices: 28338342--28338381 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
28338332 CGTGTGGTTA
*
28338342 ACCCGTGTGGACCCACAT
1 ACCCGTGTGGACCCACAG
28338360 ACCCGTGTGG-CCCACACG
1 ACCCGTGTGGACCCACA-G
28338378 ACCC
1 ACCC
28338382 ATTTTCTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.20, C:0.45, G:0.23, T:0.12
Consensus pattern (18 bp):
ACCCGTGTGGACCCACAG
Found at i:28347027 original size:31 final size:29
Alignment explanation
Indices: 28346958--28347028 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
28346948 AAAAATGAAT
* * *
28346958 AAAATCATAA-TTATATATAAAATTATAC
1 AAAATCAAAATTTGTATATAAAATTACAC
* *
28346986 AAAATTAAAATTTGTATATATAATTACAC
1 AAAATCAAAATTTGTATATAAAATTACAC
28347015 ATTAAATCAAAATT
1 A--AAATCAAAATT
28347029 AATGTATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 8 0.24
29 16 0.47
31 10 0.29
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAATCAAAATTTGTATATAAAATTACAC
Found at i:28351630 original size:80 final size:80
Alignment explanation
Indices: 28351546--28351694 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
28351536 TATGGTAACC
* * * *
28351546 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
28351610 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
28351626 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
28351691 CCGG
66 CCGG
28351695 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:28351636 original size:40 final size:38
Alignment explanation
Indices: 28351587--28351694 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
28351577 ATCACGATTT
*
28351587 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
28351627 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
28351667 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
28351695 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:28353740 original size:28 final size:28
Alignment explanation
Indices: 28353700--28353771 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 28
28353690 AAAATTGTAC
* *
28353700 AGCACTAAGTGTGCGAGCTTG-ATTCTAT
1 AGCACTAAGTGTGCGAGC-TGAAATATAT
28353728 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTG-AAATATAT
28353757 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28353772 GATTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.05
28 18 0.45
29 20 0.50
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTGAAATATAT
Found at i:28361644 original size:28 final size:28
Alignment explanation
Indices: 28361604--28361675 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 28
28361594 AAAATTGTAC
* *
28361604 AGCACTAAGTGTGCGAGCTTG-ATTCTAT
1 AGCACTAAGTGTGCGAGC-TGAAATATAT
28361632 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTG-AAATATAT
28361661 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28361676 GATTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.05
28 18 0.45
29 20 0.50
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTGAAATATAT
Found at i:28363882 original size:39 final size:39
Alignment explanation
Indices: 28363827--28363903 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
28363817 ATCATGATTC
* * *
28363827 CATAGCTTCTTGCAGCTATGGTCTTACTCATCTTAACCG
1 CATAGCATCTTGCAGCTACGATCTTACTCATCTTAACCG
* * *
28363866 CATAGCATCTTTCAGCTGCGATCTTACTCATTTTAACC
1 CATAGCATCTTGCAGCTACGATCTTACTCATCTTAACC
28363904 ATGATGTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAGCATCTTGCAGCTACGATCTTACTCATCTTAACCG
Found at i:28367350 original size:29 final size:29
Alignment explanation
Indices: 28367317--28367374 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28367307 TCAACCGAAT
28367317 AACAAAGTAAAAAGGGAGAAACCATGGAA
1 AACAAAGTAAAAAGGGAGAAACCATGGAA
28367346 AACAAAGTAAAAAGGGAGAAACCATGGAA
1 AACAAAGTAAAAAGGGAGAAACCATGGAA
28367375 GCTTCATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.59, C:0.10, G:0.24, T:0.07
Consensus pattern (29 bp):
AACAAAGTAAAAAGGGAGAAACCATGGAA
Found at i:28368717 original size:13 final size:13
Alignment explanation
Indices: 28368699--28368725 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28368689 TTTCAAAAGC
28368699 TTAGTAAGTCATA
1 TTAGTAAGTCATA
28368712 TTAGTAAGTCATA
1 TTAGTAAGTCATA
28368725 T
1 T
28368726 ACAAATAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTAGTAAGTCATA
Found at i:28369139 original size:42 final size:43
Alignment explanation
Indices: 28369039--28369210 Score: 165
Period size: 43 Copynumber: 4.0 Consensus size: 43
28369029 AGTTCGTACA
* * *
28369039 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
28369082 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAATCAAATATCG
* * *
28369124 ATGCCAACGTCCCAGACGTGATCTTACAGGTACATCATAAGT-T-G
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AAATCA-AA-TATCG
* * * * *
28369168 ATGCTAACGTCCCAGATGTGGTCTTACATGAAAACACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
28369211 GATCCTATGT
Statistics
Matches: 106, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
41 2 0.02
42 29 0.27
43 44 0.42
44 30 0.28
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
Found at i:28373194 original size:2 final size:2
Alignment explanation
Indices: 28373187--28373217 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28373177 TTTAATAAAT
28373187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28373218 CGAAATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28374341 original size:3 final size:3
Alignment explanation
Indices: 28374333--28374400 Score: 102
Period size: 3 Copynumber: 22.0 Consensus size: 3
28374323 TTAATTTTTC
28374333 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
28374381 TTTA TGTA TATA TT- TTA TTA
1 -TTA T-TA T-TA TTA TTA TTA
28374401 CAAATTACAT
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
2 2 0.03
3 50 0.82
4 9 0.15
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28389425 original size:29 final size:29
Alignment explanation
Indices: 28389335--28389494 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
28389325 ACTCGATTTC
* * **
28389335 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
28389364 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
28389392 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
28389422 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
28389451 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
28389480 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
28389495 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:28391759 original size:58 final size:58
Alignment explanation
Indices: 28391688--28391806 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
28391678 ATATGTATAC
*
28391688 ATGTGTATATAGGTTGTGAAATGGATAGGAGGAGAAGGAAAATAGTATAAGAGTTGTA
1 ATGTGTATATAGGTTGTGAAATGGAGAGGAGGAGAAGGAAAATAGTATAAGAGTTGTA
28391746 ATGTGTATATAGGTTGTGAAATGGAGAGGAGGAGAAGGAAAATAGTATAAGAGTTGTA
1 ATGTGTATATAGGTTGTGAAATGGAGAGGAGGAGAAGGAAAATAGTATAAGAGTTGTA
28391804 ATG
1 ATG
28391807 CTAAGAAGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.27
Consensus pattern (58 bp):
ATGTGTATATAGGTTGTGAAATGGAGAGGAGGAGAAGGAAAATAGTATAAGAGTTGTA
Found at i:28392271 original size:5 final size:5
Alignment explanation
Indices: 28392261--28392292 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
28392251 AAGAAAATAT
28392261 TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TA
28392293 ATTAAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:28392449 original size:3 final size:3
Alignment explanation
Indices: 28392441--28392498 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
28392431 ATTATATTAT
28392441 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28392489 ATA ATA ATA A
1 ATA ATA ATA A
28392499 CAAAACATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28392583 original size:14 final size:13
Alignment explanation
Indices: 28392548--28392590 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
28392538 GAAACAGGGG
28392548 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
*
28392561 AAATAAAAGAAAGAA
1 AAA-GAAAG-AAGAA
*
28392576 AAAGAAAGGAGAA
1 AAAGAAAGAAGAA
28392589 AA
1 AA
28392591 TTTAGGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 9 0.36
14 8 0.32
15 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:28393341 original size:13 final size:14
Alignment explanation
Indices: 28393323--28393355 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
28393313 GATTTTAATT
28393323 GAAATTG-AATTGA
1 GAAATTGAAATTGA
28393336 GAAATTGAAATTGA
1 GAAATTGAAATTGA
28393350 -AAATTG
1 GAAATTG
28393356 TATTAACCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (14 bp):
GAAATTGAAATTGA
Found at i:28393758 original size:13 final size:13
Alignment explanation
Indices: 28393715--28393758 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
28393705 AATATATATT
*
28393715 AACCCAAGTACCC
1 AACCCAATTACCC
28393728 AACCC-A--ACCC
1 AACCCAATTACCC
28393738 AACCCAATTACCC
1 AACCCAATTACCC
28393751 AACCCAAT
1 AACCCAAT
28393759 CATAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.32
11 1 0.04
12 1 0.04
13 17 0.61
ACGTcount: A:0.41, C:0.48, G:0.02, T:0.09
Consensus pattern (13 bp):
AACCCAATTACCC
Found at i:28393824 original size:7 final size:6
Alignment explanation
Indices: 28393783--28393823 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
28393773 ATAATTTAAT
*
28393783 AAATAA AAATAA AAATGTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
28393824 ACATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:28393824 original size:20 final size:20
Alignment explanation
Indices: 28393786--28393825 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28393776 ATTTAATAAA
**
28393786 TAAAAATAAAAATGTAAAAC
1 TAAAAATAAAAATAAAAAAC
28393806 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
28393826 ATATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:28393857 original size:9 final size:9
Alignment explanation
Indices: 28393843--28393919 Score: 91
Period size: 9 Copynumber: 8.6 Consensus size: 9
28393833 TTTATACAAA
28393843 TAATTCGGT
1 TAATTCGGT
28393852 TAATTCGGT
1 TAATTCGGT
* *
28393861 TAATTTGGG
1 TAATTCGGT
*
28393870 TAATTCGGG
1 TAATTCGGT
* *
28393879 TAATCCGGG
1 TAATTCGGT
28393888 TAATTCGGT
1 TAATTCGGT
*
28393897 TAATTCGAT
1 TAATTCGGT
*
28393906 TAATCCGGT
1 TAATTCGGT
28393915 TAATT
1 TAATT
28393920 TTATACTTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (9 bp):
TAATTCGGT
Found at i:28393882 original size:27 final size:27
Alignment explanation
Indices: 28393843--28393920 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
28393833 TTTATACAAA
*
28393843 TAATTCGGTTAATTCGGTTAATTTGGG
1 TAATTCGGTTAATCCGGTTAATTTGGG
* * * *
28393870 TAATTCGGGTAATCCGGGTAATTCGGT
1 TAATTCGGTTAATCCGGTTAATTTGGG
*
28393897 TAATTCGATTAATCCGGTTAATTT
1 TAATTCGGTTAATCCGGTTAATTT
28393921 TATACTTATT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (27 bp):
TAATTCGGTTAATCCGGTTAATTTGGG
Found at i:28394377 original size:16 final size:15
Alignment explanation
Indices: 28394326--28394378 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
28394316 GTTATATACT
28394326 CATGAATTGAGTATGG
1 CATGAATTGAGTAT-G
* * *
28394342 TATGAAATGATGTATT
1 CATGAATTGA-GTATG
28394358 CATGAATTGAGTACTG
1 CATGAATTGAGTA-TG
28394374 CATGA
1 CATGA
28394379 CTGATGCCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 22 0.76
17 4 0.14
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (15 bp):
CATGAATTGAGTATG
Found at i:28396067 original size:67 final size:67
Alignment explanation
Indices: 28395956--28396148 Score: 228
Period size: 68 Copynumber: 2.9 Consensus size: 67
28395946 CACAATCCTC
* *
28395956 ACAATTCCCATGAAAAAATGGCACTCTTGTGAAGCTTGTGAATAAAAAGTTAATGGCAAAATTCT
1 ACAATTCCCATGAAAAAATGGCACTCTTGAGAGGCTTGTGAATAAAAAGTTAATGGCAAAATTCT
*
28396021 TA
66 CA
* * * * **
28396023 ATAATTCCCATGACAAAATGGCACTCTTGCAG-GGCTTGTCAATAAAACGTTAAATGGCATGATT
1 ACAATTCCCATGAAAAAATGGCACTCTTG-AGAGGCTTGTGAATAAAAAGTT-AATGGCAAAATT
28396087 CTCA
64 CTCA
** * *
28396091 ACAATTTTCATGAAAAAATGGCACTCTT-ATGAGACTTGTGAATAACAAGTTAATGGCA
1 ACAATTCCCATGAAAAAATGGCACTCTTGA-GAGGCTTGTGAATAAAAAGTTAATGGCA
28396149 CAGTTCCCAT
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
66 1 0.01
67 51 0.49
68 53 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (67 bp):
ACAATTCCCATGAAAAAATGGCACTCTTGAGAGGCTTGTGAATAAAAAGTTAATGGCAAAATTCT
CA
Found at i:28396116 original size:68 final size:67
Alignment explanation
Indices: 28395956--28396148 Score: 212
Period size: 67 Copynumber: 2.9 Consensus size: 67
28395946 CACAATCCTC
* *
28395956 ACAATTCCCATGAAAAAATGGCACTCTTGTGAAGCTTGTGAATAAAAAGTTAATGGCAAAATTCT
1 ACAATTCCCATGAAAAAATGGCACTCTTGAGAAGCTTGTCAATAAAAAGTTAATGGCAAAATTCT
*
28396021 TA
66 CA
* * * * **
28396023 ATAATTCCCATGACAAAATGGCACTCTTGCAG-GGCTTGTCAATAAAACGTTAAATGGCATGATT
1 ACAATTCCCATGAAAAAATGGCACTCTTG-AGAAGCTTGTCAATAAAAAGTT-AATGGCAAAATT
28396087 CTCA
64 CTCA
** * *
28396091 ACAATTTTCATGAAAAAATGGCACTCTT-ATG-AGACTTGTGAATAACAAGTTAATGGCA
1 ACAATTCCCATGAAAAAATGGCACTCTTGA-GAAG-CTTGTCAATAAAAAGTTAATGGCA
28396149 CAGTTCCCAT
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
66 1 0.01
67 52 0.50
68 52 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (67 bp):
ACAATTCCCATGAAAAAATGGCACTCTTGAGAAGCTTGTCAATAAAAAGTTAATGGCAAAATTCT
CA
Found at i:28405176 original size:25 final size:25
Alignment explanation
Indices: 28405148--28405197 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
28405138 CTAAAGTTAA
*
28405148 TTAGAAATGTAAGACGCATAAGCTC
1 TTAGAAATGTAAGAAGCATAAGCTC
28405173 TTAGAAATGTAAGAAGCATAAGCTC
1 TTAGAAATGTAAGAAGCATAAGCTC
28405198 CATGTATCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (25 bp):
TTAGAAATGTAAGAAGCATAAGCTC
Found at i:28405440 original size:27 final size:27
Alignment explanation
Indices: 28405402--28405457 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
28405392 CCCTCGGGCA
28405402 CAACTTGCTCCATAAAAGAAAGGTACC
1 CAACTTGCTCCATAAAAGAAAGGTACC
28405429 CAACTTGCTCCATAAAAGAAAGGTACC
1 CAACTTGCTCCATAAAAGAAAGGTACC
28405456 CA
1 CA
28405458 CCCTAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.18
Consensus pattern (27 bp):
CAACTTGCTCCATAAAAGAAAGGTACC
Found at i:28406085 original size:24 final size:24
Alignment explanation
Indices: 28406053--28406101 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28406043 ACCCAGAGTA
28406053 CGTTACAAAATTTTATTCTTTAAT
1 CGTTACAAAATTTTATTCTTTAAT
28406077 CGTTACAAAATTTTATTCTTTAAT
1 CGTTACAAAATTTTATTCTTTAAT
28406101 C
1 C
28406102 ATGATCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (24 bp):
CGTTACAAAATTTTATTCTTTAAT
Done.