Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 40 of 128
Found at i:12514976 original size:18 final size:17
Alignment explanation
Indices: 12514940--12514987 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
12514930 TTTATTTTTC
*
12514940 TTATTTATTTCTTTTTCA
1 TTATTTATTT-TTTCTCA
12514958 TTATTTATTTTTATCTCA
1 TTATTTATTTTT-TCTCA
*
12514976 TCAATTTATTTT
1 T-TATTTATTTT
12514988 ATGGTTCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.08
18 15 0.58
19 9 0.35
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTATTTTTTCTCA
Found at i:12518051 original size:31 final size:31
Alignment explanation
Indices: 12518016--12518078 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
12518006 AATCCCATGG
12518016 TGAGACACAACCCCTGTAAACCCAAGAATGT
1 TGAGACACAACCCCTGTAAACCCAAGAATGT
12518047 TGAGACACAACCCCTGTAAACCCAAGAATGT
1 TGAGACACAACCCCTGTAAACCCAAGAATGT
12518078 T
1 T
12518079 TAATTCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.17
Consensus pattern (31 bp):
TGAGACACAACCCCTGTAAACCCAAGAATGT
Found at i:12525937 original size:28 final size:28
Alignment explanation
Indices: 12525873--12525939 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
12525863 GCCTTATTCA
12525873 ATAACAGT-ACATTGTGGGCCTTAGCCC
1 ATAACAGTAACATTGTGGGCCTTAGCCC
* *
12525900 A-ATATAGTAACGA-TGTGGGCCTTGGCCC
1 ATA-ACAGTAAC-ATTGTGGGCCTTAGCCC
12525928 ATAACAGTAACA
1 ATAACAGTAACA
12525940 GATATCAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
26 1 0.03
27 6 0.18
28 24 0.73
29 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (28 bp):
ATAACAGTAACATTGTGGGCCTTAGCCC
Found at i:12526003 original size:29 final size:31
Alignment explanation
Indices: 12525950--12526016 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
12525940 GATATCAGTC
*
12525950 ATGCAGTGAACAGTATGTAATATCATTAATCA
1 ATGCAGTGAACAGTA-GCAATATCATTAATCA
12525982 ATGCAGT-AACAGTA-CAATATCATTAATCA
1 ATGCAGTGAACAGTAGCAATATCATTAATCA
*
12526011 GTGCAG
1 ATGCAG
12526017 ATATGCAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 19 0.58
31 7 0.21
32 7 0.21
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (31 bp):
ATGCAGTGAACAGTAGCAATATCATTAATCA
Found at i:12526465 original size:27 final size:27
Alignment explanation
Indices: 12526410--12526608 Score: 247
Period size: 27 Copynumber: 7.4 Consensus size: 27
12526400 GGGTATAATA
* * *
12526410 GTCATTTTACGCTA-CGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
12526436 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
12526463 GTCATTCTACCCTATCGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
12526490 GTCATTCTACCCTATCGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
12526517 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
12526544 ATTATTTTACCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * **
12526571 ATTATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
12526598 GTCATTTTACC
1 GTCATTTTACC
12526609 TATTTTGAGG
Statistics
Matches: 155, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
26 13 0.08
27 142 0.92
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:12526528 original size:81 final size:81
Alignment explanation
Indices: 12526410--12526608 Score: 285
Period size: 81 Copynumber: 2.5 Consensus size: 81
12526400 GGGTATAATA
* *
12526410 GTCATTTTACGCTA-CGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTCTACC
1 GTCATTTTACCCTATCGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACC
12526474 CTATCGG-GGTATTTCG
66 CTAT-GGAGGTATTTCG
* * * *
12526490 GTCATTCTACCCTATCGGGGTATTTTGGTCATTCTACCCTATGGGGGTATTTCGATTATTTTACC
1 GTCATTTTACCCTATCGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACC
12526555 CTATGGAGGTATTTCG
66 CTATGGAGGTATTTCG
* * * *
12526571 ATTATTTTACCCTATGGGGGTATTTTAGTCATTTTACC
1 GTCATTTTACCCTATCGGGGTATTTTGGTCATTTTACC
12526609 TATTTTGAGG
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
80 14 0.13
81 91 0.87
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (81 bp):
GTCATTTTACCCTATCGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACC
CTATGGAGGTATTTCG
Found at i:12528731 original size:33 final size:33
Alignment explanation
Indices: 12528689--12528770 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
12528679 GGCCCATATG
* *
12528689 CCCGTGTGGCCTCACCCACCCAAATTCACCTTA
1 CCCGTGTGGCCCCACACACCCAAATTCACCTTA
* * *
12528722 CCCGTGTGGCCCCACACGCCCAAATTGACCTTG
1 CCCGTGTGGCCCCACACACCCAAATTCACCTTA
* *
12528755 CTCGTGT-GACCCACAC
1 CCCGTGTGGCCCCACAC
12528771 GGCCTTGCCC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 8 0.19
33 34 0.81
ACGTcount: A:0.20, C:0.44, G:0.17, T:0.20
Consensus pattern (33 bp):
CCCGTGTGGCCCCACACACCCAAATTCACCTTA
Found at i:12532577 original size:29 final size:29
Alignment explanation
Indices: 12532544--12532601 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
12532534 TCGTCGCGAA
12532544 GCAAAGAAACTACACCCTTCAGATTCTGC
1 GCAAAGAAACTACACCCTTCAGATTCTGC
*
12532573 GCAAAGAAACTACACCCTTCAGTTTCTGC
1 GCAAAGAAACTACACCCTTCAGATTCTGC
12532602 TTAGGTGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (29 bp):
GCAAAGAAACTACACCCTTCAGATTCTGC
Found at i:12536883 original size:57 final size:57
Alignment explanation
Indices: 12536799--12536974 Score: 271
Period size: 57 Copynumber: 3.1 Consensus size: 57
12536789 AATTTTCAGA
* *
12536799 TCATTTTCATTTTTGAGAAAACTACATTCATTTCCAAATGTTTTCATTTCTCCATTT
1 TCATTTTCATTTTGGAGAAAACAACATTCATTTCCAAATGTTTTCATTTCTCCATTT
* * *
12536856 TCATTTTTATTTTGGAGTAAACCACATTCATTTCCAAATGTTTTCATTTCTCCATTT
1 TCATTTTCATTTTGGAGAAAACAACATTCATTTCCAAATGTTTTCATTTCTCCATTT
* *
12536913 TCATTTTCATTTTGGAGAAAACAACAGTTCATTTCCAAATGTTTCCCATTTCTTCATTT
1 TCATTTTCATTTTGGAGAAAACAACA-TTCATTTCCAAATGTTT-TCATTTCTCCATTT
12536972 TCA
1 TCA
12536975 CTATTTCTAT
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
57 76 0.70
58 17 0.16
59 15 0.14
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (57 bp):
TCATTTTCATTTTGGAGAAAACAACATTCATTTCCAAATGTTTTCATTTCTCCATTT
Found at i:12538104 original size:37 final size:37
Alignment explanation
Indices: 12538063--12538135 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
12538053 GTGTTGTGGC
* * * *
12538063 GTGTTATTGGTTGGATTAGATCTTATGAGAGTTTGGT
1 GTGTTATCGATTGGATCAGATCTTATAAGAGTTTGGT
* *
12538100 GTGTTATCGATTGGATCAGCTCTTATAAGTGTTTGG
1 GTGTTATCGATTGGATCAGATCTTATAAGAGTTTGG
12538136 CACGTTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.19, C:0.07, G:0.30, T:0.44
Consensus pattern (37 bp):
GTGTTATCGATTGGATCAGATCTTATAAGAGTTTGGT
Found at i:12542510 original size:26 final size:27
Alignment explanation
Indices: 12542472--12542524 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
12542462 ACTATAGCAC
*
12542472 AAATCAGTTATTTACCCTCGAGGGGCA
1 AAATCAGTCATTTACCCTCGAGGGGCA
*
12542499 AAAT-AGTCATTTACCCTCTAGGGGCA
1 AAATCAGTCATTTACCCTCGAGGGGCA
12542525 TTATGGTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (27 bp):
AAATCAGTCATTTACCCTCGAGGGGCA
Found at i:12546576 original size:43 final size:43
Alignment explanation
Indices: 12546529--12546611 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
12546519 AGGGTAAATC
** * *
12546529 CAACAACCCAAGTTTATCTTCT-CTTTTTCTTAATTTCTTTATG
1 CAACAACCCAAGACTATCTTCTCCTCTTT-TTAAATTCTTTATG
*
12546572 CAACAACCCGAGACTATCTTCTCCTCTTTTTAAATTCTTT
1 CAACAACCCAAGACTATCTTCTCCTCTTTTTAAATTCTTT
12546612 TTTCAAGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 29 0.85
44 5 0.15
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.45
Consensus pattern (43 bp):
CAACAACCCAAGACTATCTTCTCCTCTTTTTAAATTCTTTATG
Found at i:12547868 original size:16 final size:16
Alignment explanation
Indices: 12547847--12547879 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12547837 TTTAGGGATC
12547847 AATTTACAAGTAAACT
1 AATTTACAAGTAAACT
12547863 AATTTACAAGTAAACT
1 AATTTACAAGTAAACT
12547879 A
1 A
12547880 TCTTAAGCTA
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:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (16 bp):
AATTTACAAGTAAACT
Found at i:12551196 original size:15 final size:15
Alignment explanation
Indices: 12551176--12551205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12551166 TTTGTAAAAA
*
12551176 TTAAATATAACTAAG
1 TTAAATACAACTAAG
12551191 TTAAATACAACTAAG
1 TTAAATACAACTAAG
12551206 AAAACTAAGT
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:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (15 bp):
TTAAATACAACTAAG
Found at i:12552436 original size:42 final size:43
Alignment explanation
Indices: 12552389--12552476 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 43
12552379 AGGGTAAATC
*
12552389 CAACAACCCAAG-TATATCTTCTCCT-TTTTTAACTTCTTTTTT
1 CAACAACCCAAGAT-TATCTTCTCCTCTTTTTAAATTCTTTTTT
12552431 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
12552474 CAA
1 CAA
12552477 GGATAAAAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
42 23 0.53
43 20 0.47
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.45
Consensus pattern (43 bp):
CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
Found at i:12557162 original size:21 final size:21
Alignment explanation
Indices: 12557138--12557184 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
12557128 TTTTTTATAA
12557138 ATTTATGATCATGGGAGCTTG
1 ATTTATGATCATGGGAGCTTG
12557159 ATTTATGATCATGGGAGCTTG
1 ATTTATGATCATGGGAGCTTG
12557180 ATTTA
1 ATTTA
12557185 GCTTGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (21 bp):
ATTTATGATCATGGGAGCTTG
Found at i:12561017 original size:3 final size:3
Alignment explanation
Indices: 12561009--12561043 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
12560999 TCAGAAGCAG
*
12561009 AGA AGA AGA AGA ATA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
12561044 GCCTACTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:12561722 original size:103 final size:104
Alignment explanation
Indices: 12561615--12561839 Score: 269
Period size: 105 Copynumber: 2.2 Consensus size: 104
12561605 TTTAATCGTT
* * * * *
12561615 AGCTAGGAATGTAGGTCCGCTTA-T-TTTCAGAGTTGTGAGCTTAACTTAGCTAACTTAAATATC
1 AGCTAGGAACGTAGGTCCGC-AACTGTTTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATC
* *
12561678 TAGAGGCTGCAATTTTAAACTGGAAAGCC-TTTATAATATC
65 TAGAGGCTGCAATTTTAAA-TCGAAAACCTTTTATAATATC
* **
12561718 AGCTAGGAGCGTAGGTTTGCAAGCTGTTTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATC
1 AGCTAGGAACGTAGGTCCGCAA-CTGTTTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATC
**
12561783 TAGAGGCTGTGATTTTAAATCGAAAACCTTTTATAATATC
65 TAGAGGCTGCAATTTTAAATCGAAAACCTTTTATAATATC
*
12561823 AG-TTGGAAGCGTAGGTC
1 AGCTAGGAA-CGTAGGTC
12561840 TGTGAGCTAT
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
102 1 0.01
103 16 0.16
104 12 0.12
105 73 0.72
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (104 bp):
AGCTAGGAACGTAGGTCCGCAACTGTTTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCT
AGAGGCTGCAATTTTAAATCGAAAACCTTTTATAATATC
Found at i:12561766 original size:105 final size:105
Alignment explanation
Indices: 12561639--12561838 Score: 296
Period size: 105 Copynumber: 1.9 Consensus size: 105
12561629 GTCCGCTTAT
* * * *
12561639 TTTCAGAGTTGTGAGCTTAACTTAGCTAACTTAAATATCTAGAGGCTGCAATTTTAAACTGGAAA
1 TTTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCTAGAGGCTGCAATTTTAAA-TCGAAA
*
12561704 GCC-TTTATAATATCAGCTAGG-AGCGTAGGTTTGCAAGCTG
65 ACCTTTTATAATATCAG-TAGGAAGCGTAGGTTTGCAAGCTG
**
12561744 TTTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCTAGAGGCTGTGATTTTAAATCGAAAA
1 TTTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCTAGAGGCTGCAATTTTAAATCGAAAA
*
12561809 CCTTTTATAATATCAGTTGGAAGCGTAGGT
66 CCTTTTATAATATCAGTAGGAAGCGTAGGT
12561839 CTGTGAGCTA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
104 10 0.12
105 75 0.88
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (105 bp):
TTTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCTAGAGGCTGCAATTTTAAATCGAAAA
CCTTTTATAATATCAGTAGGAAGCGTAGGTTTGCAAGCTG
Found at i:12561917 original size:69 final size:69
Alignment explanation
Indices: 12561816--12562629 Score: 536
Period size: 69 Copynumber: 11.8 Consensus size: 69
12561806 AAACCTTTTA
* * * *
12561816 TAATATCAG-TTGGAAGCGTAGGTCTG-TGAGCTATTTTGGAGGCTACGATCTTAAACTGGCAAG
1 TAATATCAGCTGGGAA-CGTAGGTCCGCT-AGCTATGTTGGAGGCTACGATCATAAACTGGCAAG
*
12561879 CTTTTG
64 CCTTTG
* * ** * **
12561885 TAATATCAGCTGGGAACGTAAGTCCGCTAGCTATGCTGGAGGCTGTGATCAT-AATTCGGTGAGC
1 TAATATCAGCTGGGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACT-GGCAAGC
12561949 CTTTG
65 CTTTG
* * * * * * *
12561954 TAATATCAGCTGGGAACATAGGTCC-ATGAGCGATGTTGAAGGCTACAATCATAAACTGGAAAAC
1 TAATATCAGCTGGGAACGTAGGTCCGCT-AGCTATGTTGGAGGCTACGATCATAAACTGGCAAGC
12562018 CTTTG
65 CTTTG
* * * * * * * **
12562023 TAATATTAACTGGGAACGTAGGTCCACTAGATATGTTGGAGGCTGCAATCATAAACTAGTGAGCC
1 TAATATCAGCTGGGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCC
*
12562088 TTTA
66 TTTG
** *
12562092 TAATATCAATTGGGAACGTAGGTCCG-TGAGC-A-GCTTCGGAGGCTACGATCATAAA-TCGACA
1 TAATATCAGCTGGGAACGTAGGTCCGCT-AGCTATG-TT-GGAGGCTACGATCATAAACT-GGCA
*
12562153 AGCCTTTA
62 AGCCTTTG
* * * * * * * * * *
12562161 TAATATCAACTGGGAACTTAGGTCCGCTAGTTGTGTTAGAGGCTATGATCATAAACCGACCAGCT
1 TAATATCAGCTGGGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCC
*
12562226 TTTA
66 TTTG
** * * * * * * ** *
12562230 TAATATCAATTAGGAACGTAGGTCCGCAAGTTGTGTTGGATGCTACAATCATAAACCAGCAAGCT
1 TAATATCAGCTGGGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCC
12562295 TTTG
66 TTTG
* * * * * * * *
12562299 TAATGTCAGCTAGGAACATTGGTCCGCTAGCTGTGTTGGAGGTTGCGATCATAAA-TAGGCGAGC
1 TAATATCAGCTGGGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACT-GGCAAGC
12562363 CTTTG
65 CTTTG
* * * * * * * * * * *
12562368 GAATACCAGCTAGGAACGTAGGTTCGCTAGCTATGTTGGATGTTGCAATCATAAACTAGTACGCC
1 TAATATCAGCTGGGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCC
12562433 TTTG
66 TTTG
* * * * * * * * *
12562437 TATTACCAGTTGGGAACATAGGTCCG-TGAGTTGTGTTAGAGGCTACGATCATAAACCGGTAAGC
1 TAATATCAGCTGGGAACGTAGGTCCGCT-AGCTATGTTGGAGGCTACGATCATAAACTGGCAAGC
*
12562501 CTTTT
65 CTTTG
* * * * * * ** * * *
12562506 TAATATCAGCTAGGAACATAGGTATC-TTAGCTTTGTTGGAAGCTGTGATCATAAACCGTCGAGC
1 TAATATCAGCTGGGAACGTAGGT-CCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGC
12562570 CTTTG
65 CTTTG
** * * *
12562575 TAATATCAATTGGGAACGTAGGTCCG-TGAGCTGTGTTGGAGGCTGCAATCATAAA
1 TAATATCAGCTGGGAACGTAGGTCCGCT-AGCTATGTTGGAGGCTACGATCATAAA
12562630 TCAACAAGCC
Statistics
Matches: 586, Mismatches: 138, Indels: 42
0.77 0.18 0.05
Matches are distributed among these distances:
67 1 0.00
68 12 0.02
69 556 0.95
70 16 0.03
71 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (69 bp):
TAATATCAGCTGGGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCC
TTTG
Found at i:12562012 original size:138 final size:138
Alignment explanation
Indices: 12561812--12562629 Score: 619
Period size: 138 Copynumber: 5.9 Consensus size: 138
12561802 TCGAAAACCT
* * * * * *
12561812 TTTATAATATCAG-TTGGAAGCGTAGGTCTGTGAGCTATTTTGGAGGCTACGATCTTAAACTGGC
1 TTTATAATATCAGCTAGGAA-CGTAGGTCCGTGAGCGATGTTGGAGGCTACAATCATAAACTGGC
* * * * * * **
12561876 AAGCTTTTGTAATATCAGCTGGGAACGTAAGTCCGCTAGCTATGCTGGAGGCTGTGATCATAATT
65 AAGCCTTTGTAATATCAGCTGGGAACATAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAAC
12561941 CGGTGAGCC
130 CGGTGAGCC
* * * * * *
12561950 TTTGTAATATCAGCTGGGAACATAGGTCCATGAGCGATGTTGAAGGCTACAATCATAAACTGGAA
1 TTTATAATATCAGCTAGGAACGTAGGTCCGTGAGCGATGTTGGAGGCTACAATCATAAACTGGCA
* * * * * * * * *
12562015 AACCTTTGTAATATTAACTGGGAACGTAGGTCCACTAGATATGTTGGAGGCTGCAATCATAAACT
66 AGCCTTTGTAATATCAGCTGGGAACATAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAACC
*
12562080 AGTGAGCC
131 GGTGAGCC
** * *
12562088 TTTATAATATCAATTGGGAACGTAGGTCCGTGAGC-A-GCTTCGGAGGCTACGATCATAAA-TCG
1 TTTATAATATCAGCTAGGAACGTAGGTCCGTGAGCGATG-TT-GGAGGCTACAATCATAAACT-G
* * * * * * **
12562150 ACAAGCCTTTATAATATCAACTGGGAACTTAGGTCCGCTAGTTGTGTTAGAGGCTATGATCATAA
63 GCAAGCCTTTGTAATATCAGCTGGGAACATAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAA
*** *
12562215 ACCGACCAGCT
128 ACCGGTGAGCC
** ** * * **
12562226 TTTATAATATCAATTAGGAACGTAGGTCCGCAAGTTG-TGTTGGATGCTACAATCATAAACCAGC
1 TTTATAATATCAGCTAGGAACGTAGGTCCGTGAG-CGATGTTGGAGGCTACAATCATAAACTGGC
* * * * * *
12562290 AAGCTTTTGTAATGTCAGCTAGGAACATTGGTCCGCTAGCTGTGTTGGAGGTTGCGATCATAAAT
65 AAGCCTTTGTAATATCAGCTGGGAACATAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAAC
* *
12562355 AGGCGAGCC
130 CGGTGAGCC
** * * * * * * * *
12562364 TTTGGAATACCAGCTAGGAACGTAGGTTCGCT-AGCTATGTTGGATGTTGCAATCATAAACTAGT
1 TTTATAATATCAGCTAGGAACGTAGGTCCG-TGAGCGATGTTGGAGGCTACAATCATAAACTGGC
* * * * * * *
12562428 ACGCCTTTGTATTACCAGTTGGGAACATAGGTCCG-TGAGTTGTGTTAGAGGCTACGATCATAAA
65 AAGCCTTTGTAATATCAGCTGGGAACATAGGTCCGCT-AGCTGTGTTGGAGGCTGCGATCATAAA
*
12562492 CCGGTAAGCC
129 CCGGTGAGCC
* * * * ** * *** * *
12562502 TTTTTAATATCAGCTAGGAACATAGGTATC-TTAGCTTTGTTGGAAGCTGTGATCATAAACCGTC
1 TTTATAATATCAGCTAGGAACGTAGGT-CCGTGAGCGATGTTGGAGGCTACAATCATAAACTGGC
* ** * *
12562566 GAGCCTTTGTAATATCAATTGGGAACGTAGGTCCG-TGAGCTGTGTTGGAGGCTGCAATCATAAA
65 AAGCCTTTGTAATATCAGCTGGGAACATAGGTCCGCT-AGCTGTGTTGGAGGCTGCGATCATAAA
12562630 TCAACAAGCC
Statistics
Matches: 538, Mismatches: 129, Indels: 26
0.78 0.19 0.04
Matches are distributed among these distances:
136 1 0.00
137 6 0.01
138 521 0.97
139 9 0.02
140 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (138 bp):
TTTATAATATCAGCTAGGAACGTAGGTCCGTGAGCGATGTTGGAGGCTACAATCATAAACTGGCA
AGCCTTTGTAATATCAGCTGGGAACATAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAACC
GGTGAGCC
Found at i:12563102 original size:13 final size:13
Alignment explanation
Indices: 12563084--12563116 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
12563074 ACACTGTATA
12563084 TGTACAACTTCGT
1 TGTACAACTTCGT
12563097 TGTACAACTTCGT
1 TGTACAACTTCGT
12563110 TGTACAA
1 TGTACAA
12563117 GAATAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTACAACTTCGT
Found at i:12573328 original size:48 final size:48
Alignment explanation
Indices: 12573257--12573352 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
12573247 TTATACGATA
12573257 TATTTTTTGCATTTATGATATACAATGGTTTTTACCACATCGAACTTT
1 TATTTTTTGCATTTATGATATACAATGGTTTTTACCACATCGAACTTT
12573305 TATTTTTTGCATTTATGATATACAATGGTTTTTACCACATCGAACTTT
1 TATTTTTTGCATTTATGATATACAATGGTTTTTACCACATCGAACTTT
12573353 GCTCAGATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (48 bp):
TATTTTTTGCATTTATGATATACAATGGTTTTTACCACATCGAACTTT
Found at i:12574669 original size:48 final size:48
Alignment explanation
Indices: 12574616--12574712 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
12574606 GTGGTGTATT
* * **
12574616 TATGTTGCTTTAAGGACTGTTGTTTGGTGTATTAATTTAGCAGAAAAA
1 TATGTTACTTTAAGGACTATTGTTTGGTGTATTAATGCAGCAGAAAAA
*
12574664 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAATGCAGCAGAAAAA
1 TATGTTACTTTAAGGACTATTGTTTGGTGTATTAATGCAGCAGAAAAA
12574712 T
1 T
12574713 TCTTGTTTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (48 bp):
TATGTTACTTTAAGGACTATTGTTTGGTGTATTAATGCAGCAGAAAAA
Found at i:12574849 original size:91 final size:91
Alignment explanation
Indices: 12574664--12574852 Score: 240
Period size: 91 Copynumber: 2.1 Consensus size: 91
12574654 AGCAGAAAAA
*
12574664 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAATGCAGCAGAAAAATTCTTGTTTAGTCGTCA
1 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGTCGTCA
* ** *
12574729 ATTAATGTTGTCTAAGTGACTGTATT
66 ATAAATGAGGTCTAAGTGACTGTAAT
* * *
12574755 TATGTTGTTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAG-TAAATTGTTGTTTAGAT-GTC
1 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAG-TCGTC
* *
12574818 AATAAATGAGGTTTGAA-TGACTTTAAAT
65 AATAAATGAGGTCT-AAGTGACTGT-AAT
12574846 TATGTTA
1 TATGTTA
12574853 ATAATGGTCG
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
90 32 0.38
91 52 0.62
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (91 bp):
TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGTCGTCA
ATAAATGAGGTCTAAGTGACTGTAAT
Found at i:12575674 original size:43 final size:43
Alignment explanation
Indices: 12575620--12575783 Score: 240
Period size: 43 Copynumber: 3.8 Consensus size: 43
12575610 TTTTATAAAT
*
12575620 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCTAC
* * *
12575663 AAACGCAGCTATAGATCAGGATCTTTAGCGGCGCTTTTT-TAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCTAC
* * *
12575705 AAACGCCGCTATAGATCAATACCTTTAGCGGCGCTTATACTAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCTAC
* *
12575748 AAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
12575784 CTCGCTTTAG
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
42 35 0.33
43 72 0.67
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCTAC
Found at i:12575774 original size:85 final size:85
Alignment explanation
Indices: 12575620--12575783 Score: 247
Period size: 85 Copynumber: 1.9 Consensus size: 85
12575610 TTTTATAAAT
* * * *
12575620 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAACAAACGCAGCTATAGATCAGGAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATACAACAAACGCAGCTATAGATCAAGAC
*
12575685 CTTTAGCGGCGCTTTTTTAC
66 CTTTAGCGACGCTTTTTTAC
* * * *
12575705 AAACGCCGCTATAGATCAATACCTTTAGCGGCGCTTATACTACAAACGCCGCTATAGCTCAAGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATACAACAAACGCAGCTATAGATCAAGAC
12575770 CTTTAGCGACGCTT
66 CTTTAGCGACGCTT
12575784 CTCGCTTTAG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (85 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATACAACAAACGCAGCTATAGATCAAGAC
CTTTAGCGACGCTTTTTTAC
Found at i:12575821 original size:59 final size:61
Alignment explanation
Indices: 12575727--12575847 Score: 228
Period size: 59 Copynumber: 2.0 Consensus size: 61
12575717 AGATCAATAC
12575727 CTTTAGCGGCGCTTATACTACAAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTTCTCG
1 CTTTAGCGGCGCTTATACTACAAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTTCTCG
12575788 CTTTAGC-G-GCTTATACTACAAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTTCTCG
1 CTTTAGCGGCGCTTATACTACAAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTTCTCG
12575847 C
1 C
12575848 AAAAACGCCA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 52 0.87
60 1 0.02
61 7 0.12
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (61 bp):
CTTTAGCGGCGCTTATACTACAAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTTCTCG
Found at i:12578528 original size:13 final size:13
Alignment explanation
Indices: 12578510--12578539 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
12578500 TAAACAATGC
12578510 ATAAACAAGGCAT
1 ATAAACAAGGCAT
12578523 ATAAACAAGGCAT
1 ATAAACAAGGCAT
12578536 ATAA
1 ATAA
12578540 TTAAGCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (13 bp):
ATAAACAAGGCAT
Found at i:12578573 original size:20 final size:20
Alignment explanation
Indices: 12578548--12578590 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12578538 AATTAAGCCT
12578548 CAATAATTTATACTTGAACC
1 CAATAATTTATACTTGAACC
12578568 CAATAATTTATACTTGAACC
1 CAATAATTTATACTTGAACC
12578588 CAA
1 CAA
12578591 ACTTTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.33
Consensus pattern (20 bp):
CAATAATTTATACTTGAACC
Found at i:12579469 original size:10 final size:9
Alignment explanation
Indices: 12579456--12579504 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
12579446 ATAATTTTAT
*
12579456 TTTTTATAA
1 TTTTTACAA
12579465 TTTTTACAA
1 TTTTTACAA
12579474 TTTTTTACAA
1 -TTTTTACAA
12579484 -TTTTACAA
1 TTTTTACAA
*
12579492 TTTTTATAA
1 TTTTTACAA
12579501 TTTT
1 TTTT
12579505 AAATTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 8 0.22
9 19 0.53
10 9 0.25
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTACAA
Found at i:12579470 original size:9 final size:9
Alignment explanation
Indices: 12579444--12579504 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
12579434 TATATTCAAA
12579444 TTATAA-TT
1 TTATAATTT
12579452 TTAT--TTT
1 TTATAATTT
12579459 TTATAATTT
1 TTATAATTT
*
12579468 TTACAATTT
1 TTATAATTT
*
12579477 TT-TACAATT
1 TTATA-ATTT
*
12579486 TTACAATTT
1 TTATAATTT
12579495 TTATAATTT
1 TTATAATTT
12579504 T
1 T
12579505 AAATTATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
7 6 0.14
8 5 0.12
9 30 0.71
10 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (9 bp):
TTATAATTT
Found at i:12579706 original size:89 final size:89
Alignment explanation
Indices: 12579601--12579771 Score: 238
Period size: 89 Copynumber: 1.9 Consensus size: 89
12579591 TATAAATAAC
** * * * *
12579601 TTATTTAATATATAAATTAAAAAGTACTAATTAAT-TCAAATCTTAAACCCTAACCCA-ACCCCA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCT-AAACCCTAAACCCTAAACCATAACCC-
*
12579664 AATCCCTAATCCCTAACCCCTAAACT
64 AATCCCTAACCCCTAACCCCTAAACT
*
12579690 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAAACCATAACCCGA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAAACCATAACCCAA
12579755 TCCCTAACCCCTAACCC
66 TCCCTAACCCCTAACCC
12579772 TTAACCCTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
89 67 0.93
90 5 0.07
ACGTcount: A:0.43, C:0.28, G:0.01, T:0.27
Consensus pattern (89 bp):
TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAAACCATAACCCAA
TCCCTAACCCCTAACCCCTAAACT
Found at i:12579737 original size:7 final size:7
Alignment explanation
Indices: 12579725--12579799 Score: 57
Period size: 7 Copynumber: 11.0 Consensus size: 7
12579715 ACTAATTAAT
12579725 CTAAACC
1 CTAAACC
12579732 CTAAACC
1 CTAAACC
12579739 CTAAACC
1 CTAAACC
*
12579746 AT-AACC
1 CTAAACC
* *
12579752 C-GATCC
1 CTAAACC
*
12579758 CTAACCC
1 CTAAACC
12579765 CT-AACC
1 CTAAACC
*
12579771 CTTAACC
1 CTAAACC
*
12579778 CTTAACCC
1 C-TAAACC
*
12579786 CTAACCC
1 CTAAACC
12579793 CTAAACC
1 CTAAACC
12579800 TTATTTAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
6 13 0.24
7 37 0.67
8 5 0.09
ACGTcount: A:0.35, C:0.47, G:0.01, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:12579742 original size:14 final size:14
Alignment explanation
Indices: 12579725--12579799 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 14
12579715 ACTAATTAAT
12579725 CTAAACCCTAAACC
1 CTAAACCCTAAACC
*
12579739 CTAAACCAT-AACC
1 CTAAACCCTAAACC
* * *
12579752 C-GATCCCTAACCC
1 CTAAACCCTAAACC
*
12579765 CT-AACCCTTAACC
1 CTAAACCCTAAACC
* *
12579778 CTTAACCCCTAACCC
1 C-TAAACCCTAAACC
12579793 CTAAACC
1 CTAAACC
12579800 TTATTTAATA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
12 4 0.09
13 18 0.40
14 14 0.31
15 9 0.20
ACGTcount: A:0.35, C:0.47, G:0.01, T:0.17
Consensus pattern (14 bp):
CTAAACCCTAAACC
Found at i:12579785 original size:21 final size:21
Alignment explanation
Indices: 12579759--12579802 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12579749 ACCCGATCCC
* *
12579759 TAACCCCTAACCCTTAACCCT
1 TAACCCCTAACCCCTAAACCT
12579780 TAACCCCTAACCCCTAAACCT
1 TAACCCCTAACCCCTAAACCT
12579801 TA
1 TA
12579803 TTTAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (21 bp):
TAACCCCTAACCCCTAAACCT
Found at i:12579874 original size:110 final size:110
Alignment explanation
Indices: 12579674--12579906 Score: 296
Period size: 110 Copynumber: 2.1 Consensus size: 110
12579664 AATCCCTAAT
* *
12579674 CCCTAACCCCTAAACTTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACC
1 CCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCGAAACC
*
12579739 CTAAACCATAACCCGATCCCTAACCCCT-AA-CCCTTAACCCTTAAC
66 CTAAACCATAACCCGATCCATAA-CCCTAAATCCC-TAACCCTTAAC
* *
12579784 CCCTAACCCCTAAACCTTATTTAATATAT-AATTAAAACACACTAATTAATCTAAACCCGAAACT
1 CCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCGAAACC
** *
12579848 CT-AACC-TAACACCGATTTTATAAACCCTAAATCCCTAACTCTTAAC
66 CTAAACCATAAC-CCGA-TCCAT-AACCCTAAATCCCTAACCCTTAAC
**
12579894 ATCTAACCCCTAA
1 CCCTAACCCCTAA
12579907 CCTAACCCCT
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
107 4 0.04
108 8 0.07
109 40 0.37
110 53 0.49
111 3 0.03
ACGTcount: A:0.41, C:0.31, G:0.01, T:0.27
Consensus pattern (110 bp):
CCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCGAAACC
CTAAACCATAACCCGATCCATAACCCTAAATCCCTAACCCTTAAC
Found at i:12579906 original size:7 final size:7
Alignment explanation
Indices: 12579896--12579932 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
12579886 CTCTTAACAT
12579896 CTAACCC
1 CTAACCC
12579903 CTAA--C
1 CTAACCC
12579908 CTAACCC
1 CTAACCC
12579915 CTAACCC
1 CTAACCC
12579922 CTAACCC
1 CTAACCC
12579929 CTAA
1 CTAA
12579933 TCTATAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.18
7 23 0.82
ACGTcount: A:0.32, C:0.51, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:12579919 original size:26 final size:26
Alignment explanation
Indices: 12579881--12579932 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
12579871 ACCCTAAATC
* * *
12579881 CCTAACTCTTAACATCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
*
12579907 CCTAACCCCTAACCCCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
12579933 TCTATAAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (26 bp):
CCTAACCCCTAACACCTAACCCCTAA
Found at i:12579991 original size:14 final size:15
Alignment explanation
Indices: 12579969--12580002 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12579959 CTTAAACAAA
*
12579969 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
12579983 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
12579998 AATCT
1 AATCT
12580003 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:12582102 original size:146 final size:148
Alignment explanation
Indices: 12581675--12582169 Score: 834
Period size: 148 Copynumber: 3.4 Consensus size: 148
12581665 NNNNNNNNNN
12581675 TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTT
1 TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTT
*
12581740 AGCGGCGCTTCTTATAAAGCACCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
** *
12581805 TTCT-AAAATTTTTTTTAT
131 TTCTAAAAAAATTTTAT-T
* * *
12581823 TTTTTTTATAAATTGATTTATTTTTTGCGACATTTTTATAGGAAACGCCGCTATTGCTTACCTTT
1 TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTT
* *
12581888 AGCGGTGCTTCTTATAAAGCGCCACAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
12581953 TTCTAAAAAAATTTTATT
131 TTCTAAAAAAATTTTATT
12581971 TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTT
1 TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTT
* * *
12582036 AGC-G-GCTTCTTATAAAGCGCCGCAAATTTTTTTCATTTTTAACAAAAAGACGCCGTTTTGCTA
66 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
12582099 TTCTAAAAAAATTTTATT
131 TTCTAAAAAAATTTTATT
* *
12582117 TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATATGAAACACCGCTA
1 TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTA
12582170 AAGCCCTGGG
Statistics
Matches: 328, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
146 124 0.38
147 1 0.00
148 194 0.59
149 9 0.03
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (148 bp):
TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTT
AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
TTCTAAAAAAATTTTATT
Found at i:12582282 original size:114 final size:113
Alignment explanation
Indices: 12582137--12582625 Score: 655
Period size: 114 Copynumber: 4.3 Consensus size: 113
12582127 AGTTGATTTA
* * * * *
12582137 TTTTTTGCGGCGTTTTTAT-ATGAAACACCGCTAAAGCCCTGGGCATTAGCGGCGC-TTTACCAA
1 TTTTTTGCGGCG-CTTTATCA-AAAACGCCGCTAAAGCCCTAGGCATTAGCGGCGCATCT--CAA
* * *
12582200 AAACGCCGCTAAATCCCTGAAAG-TTCAGAAAACGGCGTCGTTGGGCTTAGGT
62 AAACGCCGCTAAATCCCCGAAAGCTT-AAAAAACGGCATCGTTGGGCTTAGGT
*
12582252 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTAGGCATTAGCGGCGCATCCTTAAAAA
1 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTAGGCATTAGCGGCGCAT-CTCAAAAA
*
12582317 CGCCGCTAAATCCCCGAAAGCTTAAAAAACGGCGTCGTTGGGCTTAGGT
65 CGCCGCTAAATCCCCGAAAGCTTAAAAAACGGCATCGTTGGGCTTAGGT
*
12582366 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTAGGCATTAGCGGCGCATACTTAAAAA
1 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTAGGCATTAGCGGCGCAT-CTCAAAAA
*
12582431 CGCCGCTAAATCCCCGAAAGCTTAAAAAACAGCATCGTTGGGCTTAGGT
65 CGCCGCTAAATCCCCGAAAGCTTAAAAAACGGCATCGTTGGGCTTAGGT
** * * * * *
12582480 TTTTTTGCGGCGCTTTCCCAAAAATGCCGCTAAAACCCT-GAACATTAGCGGCGCTTTCTTAAAA
1 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTAG-GCATTAGCGGCGC-ATCTCAAAA
* * *
12582544 ACGCCGCTAAATCCCCGAAGGCTCAGAAAACGGCATCGTTGGGCTTAGG-
64 ACGCCGCTAAATCCCCGAAAGCTTAAAAAACGGCATCGTTGGGCTTAGGT
*
12582593 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
1 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAA
12582626 TGCTTTTTTT
Statistics
Matches: 345, Mismatches: 23, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
113 32 0.09
114 295 0.86
115 17 0.05
116 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (113 bp):
TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTAGGCATTAGCGGCGCATCTCAAAAAC
GCCGCTAAATCCCCGAAAGCTTAAAAAACGGCATCGTTGGGCTTAGGT
Found at i:12582710 original size:12 final size:12
Alignment explanation
Indices: 12582693--12582718 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12582683 TTTTTTATCC
12582693 AAACGCCGCTAA
1 AAACGCCGCTAA
12582705 AAACGCCGCTAA
1 AAACGCCGCTAA
12582717 AA
1 AA
12582719 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:12588759 original size:7 final size:7
Alignment explanation
Indices: 12588744--12588777 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
12588734 TCAAGTAATT
*
12588744 CATTAAA
1 CATTTAA
12588751 CATTTAA
1 CATTTAA
12588758 CATTTAA
1 CATTTAA
12588765 CATTTAA
1 CATTTAA
12588772 CATTTA
1 CATTTA
12588778 CTAATGTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
CATTTAA
Found at i:12589307 original size:2 final size:2
Alignment explanation
Indices: 12589302--12589330 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12589292 ATTAAACATC
12589302 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 A
12589331 CATTAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12591690 original size:26 final size:25
Alignment explanation
Indices: 12591640--12591715 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 25
12591630 ACACCAATAT
* * *
12591640 CGCAGTAAAGTTGCCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGT-ACAGTAA
* *
12591666 CGCAGCAAAGCTGCCATTATCAGTAT
1 CGCAGCAAAGCTGCCAGTA-CAGTAA
*
12591692 CGCATCAAAGCTGCCAGTACAGTA
1 CGCAGCAAAGCTGCCAGTACAGTA
12591716 TACTTCCTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 6 0.14
26 36 0.86
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (25 bp):
CGCAGCAAAGCTGCCAGTACAGTAA
Found at i:12595299 original size:14 final size:14
Alignment explanation
Indices: 12595280--12595309 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12595270 ACTTGTGAGT
12595280 TATTAAAGCACGTA
1 TATTAAAGCACGTA
12595294 TATTAAAGCACGTA
1 TATTAAAGCACGTA
12595308 TA
1 TA
12595310 CGATGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
TATTAAAGCACGTA
Found at i:12598477 original size:9 final size:9
Alignment explanation
Indices: 12598463--12598493 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12598453 GTCAAACGAA
12598463 TCGAGTTAT
1 TCGAGTTAT
*
12598472 TCGAGTTAA
1 TCGAGTTAT
12598481 TCGAGTTAT
1 TCGAGTTAT
12598490 TCGA
1 TCGA
12598494 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12600625 original size:9 final size:9
Alignment explanation
Indices: 12600611--12600653 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
12600601 CCTTTCTAAC
12600611 CTCTCAATT
1 CTCTCAATT
*
12600620 CTCTCAACT
1 CTCTCAATT
*
12600629 CTCTTAATT
1 CTCTCAATT
*
12600638 TTCTCAATT
1 CTCTCAATT
*
12600647 TTCTCAA
1 CTCTCAA
12600654 GTTTTGTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (9 bp):
CTCTCAATT
Found at i:12600632 original size:18 final size:18
Alignment explanation
Indices: 12600588--12600644 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
12600578 TACTCAAGTC
* *
12600588 CAACTCTCTCAATCCTTT
1 CAACTCTCTCAATTCTCT
12600606 CTAAC-CTCTCAATTCTCT
1 C-AACTCTCTCAATTCTCT
* *
12600624 CAACTCTCTTAATTTTCT
1 CAACTCTCTCAATTCTCT
12600642 CAA
1 CAA
12600645 TTTTCTCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.09
18 27 0.82
19 3 0.09
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (18 bp):
CAACTCTCTCAATTCTCT
Found at i:12603432 original size:43 final size:43
Alignment explanation
Indices: 12603384--12603508 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 43
12603374 AGCTTGTACA
* * *
12603384 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
12603427 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
* *
12603470 ATGCCAATGTCCCAGACGTGGTCTTACACGAAAAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-TAAACACA
12603509 TATCAGAGGT
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
42 4 0.06
43 58 0.82
44 9 0.13
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:12612732 original size:19 final size:20
Alignment explanation
Indices: 12612704--12612750 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
12612694 TGATTATTGG
* *
12612704 TTTTGATTATGTGATGG-CT
1 TTTTGTTTATGTGATGGCCA
12612723 TTTTGTTTATGTGATGGCCA
1 TTTTGTTTATGTGATGGCCA
12612743 TTTTGTTT
1 TTTTGTTT
12612751 GTATCTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.13, C:0.06, G:0.23, T:0.57
Consensus pattern (20 bp):
TTTTGTTTATGTGATGGCCA
Found at i:12616837 original size:185 final size:184
Alignment explanation
Indices: 12616521--12616869 Score: 556
Period size: 185 Copynumber: 1.9 Consensus size: 184
12616511 ATGCCATAGC
12616521 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
1 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
* * *
12616586 GTTCAACTTAATTCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATTACTGCAGTCCTTTTG
66 GTTCAACTAAATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTTG
12616651 TCTTGTGTAATATTTGCACTCAAACTCTTATTGTGTAATATTTTTCTGTTTTAGT
131 TCTTGTGTAATATTTGCACTCAAACT-TTATTGTGTAATATTTTTCTGTTTTAGT
* * * * **
12616706 ACATGAGAACACTAAAAAACTTTGTAGCTGGTGTTGGTATGGCTTTTCTGAAAATGTAGCTTAAT
1 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
* * *
12616771 GTTCAAC-AACATGCATGTTTATCTCAGGAAGGCAGTGTGCGGTTTGCATGACTGCAGTCTTTTT
66 GTTCAACTAA-ATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTT
*
12616835 GTCTTGTGTGATATTTGCACTCAAACTTTATTGTG
130 GTCTTGTGTAATATTTGCACTCAAACTTTATTGTG
12616870 AAATTAATAT
Statistics
Matches: 150, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
184 9 0.06
185 141 0.94
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (184 bp):
ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
GTTCAACTAAATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTTG
TCTTGTGTAATATTTGCACTCAAACTTTATTGTGTAATATTTTTCTGTTTTAGT
Found at i:12629919 original size:148 final size:148
Alignment explanation
Indices: 12629591--12629905 Score: 630
Period size: 148 Copynumber: 2.1 Consensus size: 148
12629581 CCCTTAGGCT
12629591 TTGCTTGGTAGAGTTGAAAGAAGATTGGAAAGATGGAAAATTGAAGGGGTAGAAAAATAGAAAGA
1 TTGCTTGGTAGAGTTGAAAGAAGATTGGAAAGATGGAAAATTGAAGGGGTAGAAAAATAGAAAGA
12629656 TAGAAAATAAATTTTTTTTCCCTAGACGTGCTTGATAGGGAAGATGGAAATTTTGAAAGAAAAAG
66 TAGAAAATAAATTTTTTTTCCCTAGACGTGCTTGATAGGGAAGATGGAAATTTTGAAAGAAAAAG
12629721 TAGTTTTCTGTCCATCCG
131 TAGTTTTCTGTCCATCCG
12629739 TTGCTTGGTAGAGTTGAAAGAAGATTGGAAAGATGGAAAATTGAAGGGGTAGAAAAATAGAAAGA
1 TTGCTTGGTAGAGTTGAAAGAAGATTGGAAAGATGGAAAATTGAAGGGGTAGAAAAATAGAAAGA
12629804 TAGAAAATAAATTTTTTTTCCCTAGACGTGCTTGATAGGGAAGATGGAAATTTTGAAAGAAAAAG
66 TAGAAAATAAATTTTTTTTCCCTAGACGTGCTTGATAGGGAAGATGGAAATTTTGAAAGAAAAAG
12629869 TAGTTTTCTGTCCATCCG
131 TAGTTTTCTGTCCATCCG
12629887 TTGCTTGGTAGAGTTGAAA
1 TTGCTTGGTAGAGTTGAAA
12629906 AATAAAAGGA
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 167 1.00
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (148 bp):
TTGCTTGGTAGAGTTGAAAGAAGATTGGAAAGATGGAAAATTGAAGGGGTAGAAAAATAGAAAGA
TAGAAAATAAATTTTTTTTCCCTAGACGTGCTTGATAGGGAAGATGGAAATTTTGAAAGAAAAAG
TAGTTTTCTGTCCATCCG
Found at i:12644833 original size:20 final size:21
Alignment explanation
Indices: 12644796--12644852 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
12644786 TTTTTTATAA
*
12644796 TTTAAAAAAA-AATTTGAAAT
1 TTTAAAAAAATATTTTGAAAT
* *
12644816 TTT-TATAAATATTTTG-AAT
1 TTTAAAAAAATATTTTGAAAT
12644835 TTTAAAAAAATATTTTGA
1 TTTAAAAAAATATTTTGA
12644853 TTTTTTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTAAAAAAATATTTTGAAAT
Found at i:12648018 original size:2 final size:2
Alignment explanation
Indices: 12648013--12648057 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12648003 TTGGTGTGTT
12648013 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12648055 TC T
1 TC T
12648058 TATGAGTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12653190 original size:2 final size:2
Alignment explanation
Indices: 12653177--12653207 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12653167 AGCCAGGCTT
*
12653177 TA TA TG 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
12653208 TGAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12659332 original size:9 final size:9
Alignment explanation
Indices: 12659318--12659358 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
12659308 TTTCGAATTT
12659318 GAATAACTC
1 GAATAACTC
*
12659327 GAATAATTC
1 GAATAACTC
12659336 GAATAACTC
1 GAATAACTC
*
12659345 GAATAATTC
1 GAATAACTC
12659354 GAATA
1 GAATA
12659359 TCAAACTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (9 bp):
GAATAACTC
Found at i:12659334 original size:18 final size:18
Alignment explanation
Indices: 12659313--12659358 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
12659303 TGAGTTTTCG
*
12659313 AATTTGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
12659331 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
12659349 AATTCGAATA
1 AATTCGAATA
12659359 TCAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:12659435 original size:21 final size:20
Alignment explanation
Indices: 12659397--12659436 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12659387 CCAAACCTCC
* *
12659397 CAAACCTTTTACTTTTCCCT
1 CAAAACTTTTACTCTTCCCT
12659417 CAAAACTTTTACTCCTTCCC
1 CAAAACTTTTACT-CTTCCC
12659437 ACTTTCCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.40
Consensus pattern (20 bp):
CAAAACTTTTACTCTTCCCT
Found at i:12659651 original size:9 final size:9
Alignment explanation
Indices: 12659637--12659739 Score: 134
Period size: 9 Copynumber: 11.4 Consensus size: 9
12659627 TTTGGTTAAA
*
12659637 AATTAACTG
1 AATTAACCG
12659646 AATTAACCG
1 AATTAACCG
*
12659655 AATTACCCG
1 AATTAACCG
* *
12659664 AATTAATCA
1 AATTAACCG
*
12659673 AATTAATCG
1 AATTAACCG
* *
12659682 GATTACCCG
1 AATTAACCG
12659691 AATTAACCG
1 AATTAACCG
*
12659700 AATTACCCG
1 AATTAACCG
12659709 AATTAACCG
1 AATTAACCG
12659718 AATTAACCG
1 AATTAACCG
12659727 AATTAACCG
1 AATTAACCG
12659736 AATT
1 AATT
12659740 GAATCACTAC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 81 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:12660190 original size:30 final size:30
Alignment explanation
Indices: 12660137--12660195 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12660127 AACCTTTTAT
*
12660137 TTTTCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCCAC
*
12660166 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCC-AAAACTTTTACTCCCTTCCCA
12660196 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.20, C:0.39, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:12665387 original size:23 final size:23
Alignment explanation
Indices: 12665360--12665411 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
12665350 ACTAAATATT
12665360 AAATAAAAATAATTACATTTTCA
1 AAATAAAAATAATTACATTTTCA
12665383 AAATAAAAATAATTACATTTTCA
1 AAATAAAAATAATTACATTTTCA
12665406 AAATAA
1 AAATAA
12665412 TAATTTGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAAAAATAATTACATTTTCA
Found at i:12677187 original size:34 final size:34
Alignment explanation
Indices: 12677149--12677219 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
12677139 TTTATGTTTC
12677149 CAAATCAAAATCAACTCAAATAAATAATCTTTAA
1 CAAATCAAAATCAACTCAAATAAATAATCTTTAA
*
12677183 CAAATCAAAATCAACTCAAATAAGTAATCTTTAA
1 CAAATCAAAATCAACTCAAATAAATAATCTTTAA
12677217 CAA
1 CAA
12677220 TTATACATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.55, C:0.18, G:0.01, T:0.25
Consensus pattern (34 bp):
CAAATCAAAATCAACTCAAATAAATAATCTTTAA
Found at i:12679986 original size:2 final size:2
Alignment explanation
Indices: 12679968--12680014 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
12679958 CAAATCTAAA
12679968 AT AT AT -T AT -T AT CAT AT AT AT AT AT AT AT AT AT AT -T A- AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12680007 -T AT AT AT A
1 AT AT AT AT A
12680015 ATTATAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
1 5 0.13
2 32 0.82
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12681456 original size:102 final size:103
Alignment explanation
Indices: 12681269--12681474 Score: 405
Period size: 102 Copynumber: 2.0 Consensus size: 103
12681259 GATCCCTAAA
12681269 CCCAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAACTAGGATGATAAA
1 CCCAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAACTAGGATGATAAA
12681334 ATAGGATCCATCCCTCCAAAGTTTAGAAGGACGTTGTT
66 ATAGGATCCATCCCTCCAAAGTTTAGAAGGACGTTGTT
12681372 CCCAAATAGT-ATAATTTTATTTATATCTACTATTTATATTATTAAATTAAACTAGGATGATAAA
1 CCCAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAACTAGGATGATAAA
12681436 ATAGGATCCATCCCTCCAAAGTTTAGAAGGACGTTGTT
66 ATAGGATCCATCCCTCCAAAGTTTAGAAGGACGTTGTT
12681474 C
1 C
12681475 TGTCATTGCT
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 93 0.90
103 10 0.10
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (103 bp):
CCCAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAACTAGGATGATAAA
ATAGGATCCATCCCTCCAAAGTTTAGAAGGACGTTGTT
Found at i:12685478 original size:45 final size:44
Alignment explanation
Indices: 12685428--12685520 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
12685418 GGTTCGCTGT
*
12685428 AATGGAATAGAGAC-GTAATAGTAATT-TAAT-TGTTTGGTTGAATGG
1 AATGGAATAGA-ACTGTAATAGT-ATTCT--TGTGTTTGGTTGAATGA
12685473 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGA
1 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGA
12685517 AATG
1 AATG
12685521 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGA
Found at i:12686741 original size:30 final size:30
Alignment explanation
Indices: 12686707--12686766 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
12686697 TTCAGTTTTA
12686707 AGCCAAGATAAAGTAGGCAATACCAGAATT
1 AGCCAAGATAAAGTAGGCAATACCAGAATT
12686737 AGCCAAGATAAAGTAGGCAATACCAGAATT
1 AGCCAAGATAAAGTAGGCAATACCAGAATT
12686767 GTGATGAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (30 bp):
AGCCAAGATAAAGTAGGCAATACCAGAATT
Found at i:12688573 original size:29 final size:29
Alignment explanation
Indices: 12688540--12688627 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 29
12688530 AAAGAAACAG
12688540 AAGTTAAATAGCAGACGATGAAGATTAGA
1 AAGTTAAATAGCAGACGATGAAGATTAGA
12688569 AAG-T---TAG-A-A--ATGAAGATTAGA
1 AAGTTAAATAGCAGACGATGAAGATTAGA
* * *
12688590 AAGTTGAATAGCAGACGATGGAGATTAAA
1 AAGTTAAATAGCAGACGATGAAGATTAGA
*
12688619 AAGTAAAAT
1 AAGTTAAAT
12688628 GAACGCTGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
21 15 0.32
22 1 0.02
23 1 0.02
24 1 0.02
25 6 0.13
26 1 0.02
27 1 0.02
28 1 0.02
29 20 0.43
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.22
Consensus pattern (29 bp):
AAGTTAAATAGCAGACGATGAAGATTAGA
Found at i:12688832 original size:18 final size:18
Alignment explanation
Indices: 12688809--12688848 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
12688799 AGATTTGGAA
*
12688809 AAGAAGGAAATGTAGGAG
1 AAGAAGGAAACGTAGGAG
12688827 AAGAAGGAAACGTAGGAG
1 AAGAAGGAAACGTAGGAG
12688845 AAGA
1 AAGA
12688849 TGCTGAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.38, T:0.07
Consensus pattern (18 bp):
AAGAAGGAAACGTAGGAG
Found at i:12696613 original size:13 final size:13
Alignment explanation
Indices: 12696595--12696621 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12696585 AAGTCTCTGC
12696595 AGTTAATAAAAAA
1 AGTTAATAAAAAA
12696608 AGTTAATAAAAAA
1 AGTTAATAAAAAA
12696621 A
1 A
12696622 TTTATTAAGC
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:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
AGTTAATAAAAAA
Found at i:12696772 original size:10 final size:10
Alignment explanation
Indices: 12696739--12696797 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
12696729 ATATTTTCTC
12696739 ATAAAAAA-T
1 ATAAAAAATT
*
12696748 ATTAAAATATT
1 A-TAAAAAATT
12696759 -TAAAAAATT
1 ATAAAAAATT
12696768 ATAAATAAACTT
1 ATAAA-AAA-TT
*
12696780 ATAAAAAAATC
1 AT-AAAAAATT
12696791 ATAAAAA
1 ATAAAAA
12696798 CATGAACTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.22
10 15 0.37
11 7 0.17
12 7 0.17
13 3 0.07
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:12697333 original size:10 final size:10
Alignment explanation
Indices: 12697318--12697422 Score: 74
Period size: 10 Copynumber: 10.7 Consensus size: 10
12697308 TAATTCAAGG
*
12697318 TTTTATGATT
1 TTTTATAATT
12697328 TTTTATAA-T
1 TTTTATAATT
*
12697337 TTTTATAAGT
1 TTTTATAATT
* *
12697347 ATATATCAA-T
1 TTTTAT-AATT
* *
12697357 TTTAAT-ATA
1 TTTTATAATT
*
12697366 TTTAATAATT
1 TTTTATAATT
12697376 TTTT-TAATT
1 TTTTATAATT
12697385 TTTTATAATT
1 TTTTATAATT
*
12697395 TTTCATAAGTT
1 TTTTATAA-TT
* *
12697406 TTTAAGAATT
1 TTTTATAATT
12697416 TTTTATA
1 TTTTATA
12697423 TGTTTTTCCT
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
8 1 0.01
9 24 0.32
10 40 0.53
11 10 0.13
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTATAATT
Found at i:12697339 original size:9 final size:9
Alignment explanation
Indices: 12697327--12697409 Score: 60
Period size: 9 Copynumber: 8.7 Consensus size: 9
12697317 GTTTTATGAT
12697327 TTTTTATAA
1 TTTTTATAA
12697336 TTTTTATAA
1 TTTTTATAA
* *
12697345 GTATATATCAA
1 -TTTTTAT-AA
*
12697356 TTTTAAT-A
1 TTTTTATAA
*
12697364 TATTTAATAA
1 T-TTTTATAA
*
12697374 TTTTTTTAA
1 TTTTTATAA
12697383 TTTTTTATAA
1 -TTTTTATAA
12697393 TTTTTCATAA
1 TTTTT-ATAA
12697403 GTTTTTA
1 -TTTTTA
12697410 AGAATTTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
8 2 0.03
9 26 0.44
10 24 0.41
11 7 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12697415 original size:21 final size:20
Alignment explanation
Indices: 12697326--12697429 Score: 72
Period size: 19 Copynumber: 5.2 Consensus size: 20
12697316 GGTTTTATGA
*
12697326 TTTTTTATAATTTTTATAAG
1 TTTTTAATAATTTTTATAAG
* * *
12697346 TATAT-ATCAATTTTAAT-A-
1 TTTTTAAT-AATTTTTATAAG
* *
12697364 TATTTAATAATTTTTTTAA-
1 TTTTTAATAATTTTTATAAG
*
12697383 TTTTTTATAATTTTTCATAAG
1 TTTTTAATAATTTTT-ATAAG
* *
12697404 TTTTTAAGAATTTTTTATATG
1 TTTTTAATAA-TTTTTATAAG
12697425 TTTTT
1 TTTTT
12697430 CCTAAAATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
18 11 0.17
19 19 0.29
20 14 0.21
21 17 0.26
22 5 0.08
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTAATAATTTTTATAAG
Found at i:12697553 original size:30 final size:31
Alignment explanation
Indices: 12697493--12697566 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
12697483 ACTATTAGAA
*
12697493 TTTATTAGATTTTTTGATGATATTTATAAGTT
1 TTTATTA-ATTTTTTGATAATATTTATAAGTT
*
12697525 TTTATTAATTTTTT-ATAA-ATTTTGTAAGTT
1 TTTATTAATTTTTTGATAATA-TTTATAAGTT
*
12697555 TATATTAATTTT
1 TTTATTAATTTT
12697567 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 1 0.03
30 23 0.61
31 7 0.18
32 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (31 bp):
TTTATTAATTTTTTGATAATATTTATAAGTT
Found at i:12697602 original size:20 final size:19
Alignment explanation
Indices: 12697577--12697623 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
12697567 AATAAAAAAT
12697577 TAATTTCTTTCCTATTTTTA
1 TAATTT-TTTCCTATTTTTA
*
12697597 TAATTTTTTTCTATTTTT-
1 TAATTTTTTCCTATTTTTA
*
12697615 TTATTTTTT
1 TAATTTTTT
12697624 ATCATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TAATTTTTTCCTATTTTTA
Found at i:12697612 original size:19 final size:19
Alignment explanation
Indices: 12697577--12697634 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
12697567 AATAAAAAAT
*
12697577 TAATTTCTTTCCTATTTTTA
1 TAATTT-TTTTCTATTTTTA
12697597 TAATTTTTTTCTATTTTT-
1 TAATTTTTTTCTATTTTTA
*
12697615 TTATTTTTTATC-ATTTTTA
1 TAATTTTTT-TCTATTTTTA
12697634 T
1 T
12697635 GGGAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 14 0.41
19 14 0.41
20 6 0.18
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (19 bp):
TAATTTTTTTCTATTTTTA
Found at i:12710318 original size:17 final size:17
Alignment explanation
Indices: 12710275--12710318 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
12710265 AAAATTGTCA
*
12710275 AATAAATAAAATTACATT
1 AATAAA-AAATTTACATT
12710293 -ATAAAAAATTTACATT
1 AATAAAAAATTTACATT
12710309 AATAAAAAAT
1 AATAAAAAAT
12710319 CACAAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAAAAAATTTACATT
Found at i:12710634 original size:98 final size:98
Alignment explanation
Indices: 12710280--12710673 Score: 448
Period size: 98 Copynumber: 4.0 Consensus size: 98
12710270 TGTCAAATAA
** * * *
12710280 ATAAAATTACATTATAAAAAATTTACATTAATAAAAAATCACAAAATACTAAACTGAACACTAAC
1 ATAAAATTATTTTA-AAAAAAATTACATTACTAAAAAATCACAAAACACT-AA---AACACTAAC
12710345 AATTTATATAACCTAATCATAAATTACT-A-AAAA-AACT
61 AA-TT-TATAACCTAATCATAAATTACTAACAAAATAACT
* *
12710382 ATAAAATTATCTTTAAAAAAAATTACATTACTAAAAAATCACAAAACCCTAAACTAAACGGTAAC
1 ATAAAATTAT-TTTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAA--ACAC--TAAC
* * *
12710447 AAATTATAAACTAATCACAAATTACTAACAAAATAACT
61 AATTTATAACCTAATCATAAATTACTAACAAAATAACT
* * *
12710485 ATAACATTA----AAAAAAATTTACATTACTAATAAAA-CACAAAATAC-AAAACACTAACAATT
1 ATAAAATTATTTTAAAAAAAATTACATTACTAA-AAAATCACAAAACACTAAAACACTAACAATT
* *
12710544 TACAACCTAATCATAAATTACTAATAAAATAACT
65 TATAACCTAATCATAAATTACTAACAAAATAACT
*
12710578 ATAAAATTATTTTTAAAAAAAATTACATTACTAAAATATCACAAAACAC-AAAACACTAACAATT
1 ATAAAATTA-TTTTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAAACACTAACAATT
12710642 TATAACCTAATCATAAATTACTAACAAAATAA
65 TATAACCTAATCATAAATTACTAACAAAATAA
12710674 TTCACAAAAT
Statistics
Matches: 251, Mismatches: 26, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
93 45 0.18
95 3 0.01
97 6 0.02
98 101 0.40
99 4 0.02
100 23 0.09
101 4 0.02
102 50 0.20
103 15 0.06
ACGTcount: A:0.57, C:0.15, G:0.01, T:0.27
Consensus pattern (98 bp):
ATAAAATTATTTTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAAACACTAACAATTT
ATAACCTAATCATAAATTACTAACAAAATAACT
Found at i:12710692 original size:88 final size:90
Alignment explanation
Indices: 12710600--12710767 Score: 236
Period size: 92 Copynumber: 1.9 Consensus size: 90
12710590 TTAAAAAAAA
* *
12710600 TTACATTACTAA-AATATCAC-AAA-AC-ACAAAACACTAACAATTTATAACCTAATCATAAATT
1 TTACATTAATAAGAA-ATCACAAAATACAACAAAACAC-AACAATTTATAACATAATCATAAATT
12710661 ACTAACAAAATAATTCACAAAATAATT
64 ACTAACAAAATAATTCACAAAATAATT
* *
12710688 TTACATTAATAAGAAATCACAAAATACTAAACTAAACACAACAATTTATAACATAATCCTAAATT
1 TTACATTAATAAGAAATCACAAAATAC--AACAAAACACAACAATTTATAACATAATCATAAATT
12710753 ACTAACAAAATAATT
64 ACTAACAAAATAATT
12710768 ATAAAAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
88 16 0.23
89 5 0.07
90 2 0.03
92 39 0.56
93 8 0.11
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.27
Consensus pattern (90 bp):
TTACATTAATAAGAAATCACAAAATACAACAAAACACAACAATTTATAACATAATCATAAATTAC
TAACAAAATAATTCACAAAATAATT
Found at i:12710712 original size:98 final size:95
Alignment explanation
Indices: 12710514--12710773 Score: 273
Period size: 98 Copynumber: 2.7 Consensus size: 95
12710504 ACATTACTAA
* * *
12710514 TAAAA-CACAAAATACAAAACACTAACAATTTACAACCTAATCATAAATTACTAATAAAATAACT
1 TAAAATCACAAAA-ACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAATT
* * * * *
12710578 ATAAAATTATTTTTAAAAAAAATTACATTAC
65 ACAAAATTAATTTTAAAAAAAATGAAATCAC
12710609 TAAAATATCACAAAACACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAA
1 T-AAA-ATCACAAAA-ACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAA
* *
12710674 TTCACAAAA-TAATTTTACATTAATAA-GAAATCAC
63 TT-ACAAAATTAATTTTA-A-AAAAAATGAAATCAC
* * * *
12710708 -AAAAT-AC-TAAACTAAACAC-AACAATTTATAACATAATCCTAAATTACTAACAAAATAATTA
1 TAAAATCACAAAAACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAATTA
*
12710769 TAAAA
66 CAAAA
12710774 AAAACTGCAT
Statistics
Matches: 143, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
91 5 0.03
92 39 0.27
93 8 0.06
94 2 0.01
95 3 0.02
96 5 0.03
97 4 0.03
98 62 0.43
99 11 0.08
100 4 0.03
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (95 bp):
TAAAATCACAAAAACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAATTA
CAAAATTAATTTTAAAAAAAATGAAATCAC
Found at i:12711185 original size:28 final size:28
Alignment explanation
Indices: 12711143--12711218 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
12711133 ATGGGACTAG
* *
12711143 TGTAATTTTATAAAATTAAATTCTTTGA
1 TGTAATTTAATAAAATTAAATGCTTTGA
*
12711171 TGTAATTTAACAAAATTAAATGCTTTGA
1 TGTAATTTAATAAAATTAAATGCTTTGA
12711199 TGTAATTTAATAAAATTAAA
1 TGTAATTTAATAAAATTAAA
12711219 AGCATGGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (28 bp):
TGTAATTTAATAAAATTAAATGCTTTGA
Found at i:12717172 original size:48 final size:48
Alignment explanation
Indices: 12717081--12717172 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
12717071 GTGAAAAATC
* * * ** *
12717081 TTTGAGTTAGTTAAGTTGATAAGTTTTATTTTATTGTCTTAACTTAGT
1 TTTGAGTTAGTCAAGTTGACAAGTCTTATTTTATCATCCTAACTTAGT
12717129 TTTGAGTTAGTCAAGTTGACAAGTCTTATTTTATCATCCTAACT
1 TTTGAGTTAGTCAAGTTGACAAGTCTTATTTTATCATCCTAACT
12717173 CGATGTGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (48 bp):
TTTGAGTTAGTCAAGTTGACAAGTCTTATTTTATCATCCTAACTTAGT
Found at i:12720218 original size:44 final size:44
Alignment explanation
Indices: 12720148--12720266 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 44
12720138 CTGCAAACCA
*
12720148 CTGTGAATCCACAACCAGAAGCAGATTCCATCTACAGGGTA-TTG
1 CTGTGAATCCACAGCCAGAAGCAGATTCCATCTAC-GGGTACTTG
* * * *
12720192 CTGTGAATCCACAGCCA-ATGGTAGATTCCATTTGCGGGTACTTG
1 CTGTGAATCCACAGCCAGA-AGCAGATTCCATCTACGGGTACTTG
* * *
12720236 TTGTGTATCCACAGCC-GAAAGCAAATTCCAT
1 CTGTGAATCCACAGCCAG-AAGCAGATTCCAT
12720267 TTGCAAGATT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.10
44 54 0.89
45 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (44 bp):
CTGTGAATCCACAGCCAGAAGCAGATTCCATCTACGGGTACTTG
Found at i:12724125 original size:60 final size:60
Alignment explanation
Indices: 12724053--12724235 Score: 167
Period size: 60 Copynumber: 3.1 Consensus size: 60
12724043 AGATAAGCCC
* ** * *
12724053 TGAACTTGGCAATTGTTTTCACATTGAGG-CTTGAACTTTTTTTTGGTCTAAGTTAGGTCT
1 TGAACTTAGCAATTGTTCCCACACTG-GGTCTTGAACTTTTTTTTGGTCCAAGTTAGGTCT
* **
12724113 TGAACTTAGCAATTGTTCCCACACTGGGTCTTGAACTTTTTTTTTGTCCAAGTTAGACCT
1 TGAACTTAGCAATTGTTCCCACACTGGGTCTTGAACTTTTTTTTGGTCCAAGTTAGGTCT
* * * * * ** *
12724173 TGAA-TTTGACAATTCTTCACGCATTATGACTTGAACTTTTTTTT-GTCCAAGTTA-GTCAT
1 TGAACTTAG-CAATTGTTCCCACACTGGGTCTTGAACTTTTTTTTGGTCCAAGTTAGGTC-T
12724232 TGAA
1 TGAA
12724236 AACCTGAAAG
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
58 1 0.01
59 20 0.20
60 81 0.79
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (60 bp):
TGAACTTAGCAATTGTTCCCACACTGGGTCTTGAACTTTTTTTTGGTCCAAGTTAGGTCT
Found at i:12724863 original size:6 final size:6
Alignment explanation
Indices: 12724847--12724877 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12724837 GGAGAGAAAT
*
12724847 GAGAAG AAGAAG GAGAAG GAGAAG GAGAAG G
1 GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG G
12724878 TATGTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAGAAG
Found at i:12725329 original size:189 final size:196
Alignment explanation
Indices: 12725123--12725498 Score: 527
Period size: 189 Copynumber: 1.9 Consensus size: 196
12725113 TAATGTAAAA
* * * *
12725123 TTATTTTGTTTGTAATTTATGATTAGGTTATAAATTGTTAGTGTTCAG-T-G-TTTTGTGATTTT
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTACTGTTCAGTTAGATTCTGTGAGTTT
12725185 TTAGTAATGTAAATTTTTTTTAAAA-AATTATAGTTATTTTGTTAGTAATTTATGATTAGG-T-T
66 TTAGTAATGT-AA-TTTTTTTAAAATAATTATAGTTATTTTGTTAGTAATTTATGATTAGGTTAT
* *
12725247 ATAAATTATTA-G-T-GTTTTATATTTTGTGATTTATTAGTAATGTAATTTTTTTTAAAATGTTA
129 ATAAATTATTATGTTAGTTTAATATTTTGTGATTTATTAGTAATGTAAATTTTTTTAAAATGTTA
12725309 TAT
194 TAT
* *
12725312 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTACTGTTTAGTTTAGGATTCTGTGAGT
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTACTGTTCAG-TTA-GATTCTGTGAGT
*
12725377 TTTTAGTAATGTAATTTTTTTAAAATATTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTAT
64 TTTTAGTAATGTAATTTTTTTAAAATAATTATAGTTATTTTGTTAGTAATTTATGATTAGGTTAT
* * *
12725442 ATAAATTGTTATTGTTTAGTTTAATATTTTGTGATTTTTTATTAATGTAAATTTTTT
129 ATAAATTATTA-TG-TTAGTTTAATATTTTGTGATTTATTAGTAATGTAAATTTTTT
12725499 ATAATGTAAT
Statistics
Matches: 162, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
189 44 0.27
191 1 0.01
192 11 0.07
193 37 0.23
194 21 0.13
195 11 0.07
197 1 0.01
199 1 0.01
200 35 0.22
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (196 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTACTGTTCAGTTAGATTCTGTGAGTTT
TTAGTAATGTAATTTTTTTAAAATAATTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAT
AAATTATTATGTTAGTTTAATATTTTGTGATTTATTAGTAATGTAAATTTTTTTAAAATGTTATA
T
Found at i:12725426 original size:99 final size:98
Alignment explanation
Indices: 12725123--12725498 Score: 475
Period size: 95 Copynumber: 3.9 Consensus size: 98
12725113 TAATGTAAAA
* *
12725123 TTATTTTGTTTGTAATTTATGATTAGGTTATAAATTGTTAGTGTTCAG--T-G-TTTTGTGATTT
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTA-TGTTTAGTTTAGATTTTGTGATTT
12725184 TTTAGTAATGTAAATTTTTTTTAAAA-AATTATAG
65 TTTAGTAATGT-AATTTTTTTTAAAATAATTATAG
* * * *
12725218 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTA-GTGT--TTTATATTTTGTGATTTA
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTATGTTTAGTTTAGATTTTGTGATTTT
* *
12725280 TTAGTAATGTAATTTTTTTTAAAAT-GTTATAT
66 TTAGTAATGTAATTTTTTTTAAAATAATTATAG
* * *
12725312 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTACTGTTTAGTTTAGGATTCTGTGAGT
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTA-TGTTTAGTTTA-GATTTTGTGATT
*
12725377 TTTTAGTAATGTAA-TTTTTTTAAAATATTTATAG
64 TTTTAGTAATGTAATTTTTTTTAAAATAATTATAG
*
12725411 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTATTGTTTAGTTTAATATTTTGTGA
1 TTATTTTGTTAGTAATTTATGATTAGG-T-TATAAATTGTTA-TGTTTAGTTT-AGATTTTGTGA
* *
12725476 TTTTTTATTAATGTAAATTTTTT
62 TTTTTTAGTAATGTAATTTTTTT
12725499 ATAATGTAAT
Statistics
Matches: 243, Mismatches: 23, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
93 3 0.01
94 57 0.23
95 59 0.24
96 3 0.01
98 16 0.07
99 53 0.22
100 1 0.00
101 44 0.18
102 7 0.03
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (98 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTATGTTTAGTTTAGATTTTGTGATTTT
TTAGTAATGTAATTTTTTTTAAAATAATTATAG
Found at i:12725503 original size:16 final size:17
Alignment explanation
Indices: 12725475--12725507 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12725465 ATATTTTGTG
12725475 ATTTTTTATTAATGTAA
1 ATTTTTTATTAATGTAA
12725492 ATTTTTTA-TAATGTAA
1 ATTTTTTATTAATGTAA
12725508 TTTCATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTTTATTAATGTAA
Found at i:12727915 original size:75 final size:76
Alignment explanation
Indices: 12727823--12727985 Score: 247
Period size: 75 Copynumber: 2.2 Consensus size: 76
12727813 GTAATTTAAA
* * * * *
12727823 TAACTTTATATTTATGTAATGACTTTTTTGCCATTTTAGTTATTAATTTTAGGG-GTTTTTTGCA
1 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGTGTTTTTTACA
*
12727887 ATTTAAATAGT
66 ATTTAAATAAT
*
12727898 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGTTTTTTTTACA
1 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGTGTTTTTTACA
12727963 ATTTAAATAAT
66 ATTTAAATAAT
*
12727974 AAACTTTGTATT
1 TAACTTTGTATT
12727986 ATTTAATTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 50 0.63
76 29 0.37
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (76 bp):
TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGTGTTTTTTACA
ATTTAAATAAT
Found at i:12729667 original size:23 final size:23
Alignment explanation
Indices: 12729641--12729694 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
12729631 TACTAAATAA
* *
12729641 ATTAATAACAAT-AAAATAATAT
1 ATTAATAAAAATCAAAATAAAAT
*
12729663 CATTAA-AAAAATCAAATTAAAAT
1 -ATTAATAAAAATCAAAATAAAAT
12729686 ATTAATAAA
1 ATTAATAAA
12729695 CTAATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTAATAAAAATCAAAATAAAAT
Found at i:12733295 original size:27 final size:27
Alignment explanation
Indices: 12733209--12733296 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 27
12733199 GCCGCTTATG
* * *
12733209 AGATAGGTGTCACCAGTGGTGCCTACT
1 AGATAGGAGTCACCAGTGGCGCCTACC
* * *
12733236 AGATAAGAGTCACCAGTGGCACCTAGC
1 AGATAGGAGTCACCAGTGGCGCCTACC
*
12733263 AGATAGGAGTCACCAGTGACGCCTACC
1 AGATAGGAGTCACCAGTGGCGCCTACC
12733290 AGATAGG
1 AGATAGG
12733297 CACCACCTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (27 bp):
AGATAGGAGTCACCAGTGGCGCCTACC
Found at i:12736520 original size:9 final size:9
Alignment explanation
Indices: 12736506--12736563 Score: 62
Period size: 9 Copynumber: 6.0 Consensus size: 9
12736496 TTGTAAATAT
12736506 ATATTAAAA
1 ATATTAAAA
12736515 ATATTAAAA
1 ATATTAAAA
12736524 ATATTAAAA
1 ATATTAAAA
*
12736533 ATTACTAAAAA
1 A-TA-TTAAAA
*
12736544 ATCTTTAAAA
1 AT-ATTAAAA
12736554 ATATATAAAA
1 ATAT-TAAAA
12736564 TGCTAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 20 0.49
10 15 0.37
11 6 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATTAAAA
Found at i:12736533 original size:10 final size:10
Alignment explanation
Indices: 12736506--12736563 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
12736496 TTGTAAATAT
12736506 ATATT-AAAA
1 ATATTAAAAA
12736515 ATATT-AAAA
1 ATATTAAAAA
12736524 ATATTAAAAA
1 ATATTAAAAA
* *
12736534 TTACTAAAAA
1 ATATTAAAAA
* *
12736544 ATCTTTAAAA
1 ATATTAAAAA
12736554 ATATATAAAA
1 ATAT-TAAAA
12736564 TGCTAAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
9 14 0.36
10 21 0.54
11 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
ATATTAAAAA
Found at i:12738629 original size:14 final size:15
Alignment explanation
Indices: 12738605--12738633 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12738595 TTTTTCTATG
12738605 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
12738620 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
12738634 AGTTTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:12738966 original size:14 final size:15
Alignment explanation
Indices: 12738936--12738968 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
12738926 CATCTTGGTT
12738936 AAATACAAAGAAAAA
1 AAATACAAAGAAAAA
12738951 AAATACAAAGAAAAA
1 AAATACAAAGAAAAA
12738966 AAA
1 AAA
12738969 GAGAAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (15 bp):
AAATACAAAGAAAAA
Found at i:12739826 original size:43 final size:43
Alignment explanation
Indices: 12739776--12739891 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
12739766 TATGTGTTTT
*
12739776 CATGTAAGACCACATCTGGGA-TGTCGGCATCGATATCTGATTA
1 CATGTAAGACCACATCTGGGACAGT-GGCATCGATATCTGATTA
* *** *
12739819 CGTGTAAGACCTTGTCTGGGACAGTGGCATCGATATGTGATTA
1 CATGTAAGACCACATCTGGGACAGTGGCATCGATATCTGATTA
* *
12739862 CATGTAAGACCACGTTTGGGAC-GATGGCAT
1 CATGTAAGACCACATCTGGGACAG-TGGCAT
12739892 TGTACGAGCT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
42 1 0.02
43 58 0.95
44 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCACATCTGGGACAGTGGCATCGATATCTGATTA
Found at i:12754370 original size:34 final size:34
Alignment explanation
Indices: 12754332--12754405 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
12754322 TTTAGTGCTC
* *
12754332 TTTGGTTGTGTGGGATGGATACACTTATGTGCAA
1 TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
* *
12754366 TTTGGTTGTGAGGGATGAATGCACTTATGTTCAA
1 TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
12754400 TTTGGT
1 TTTGGT
12754406 GTATTTAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.08, G:0.31, T:0.41
Consensus pattern (34 bp):
TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
Found at i:12756353 original size:41 final size:41
Alignment explanation
Indices: 12756283--12756411 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 41
12756273 GCACATATCT
* * * * *
12756283 TGAAATGATACACCGGCACAAAGCTTGCTAGGCTTAAAGCC
1 TGAAATAATACACCGGCATAAAGCCTGCTAGACATAAAGCC
** * *
12756324 TGATTTAATACACCGGCATGAAGCCTGCTAGACATAAAGTC
1 TGAAATAATACACCGGCATAAAGCCTGCTAGACATAAAGCC
* * * *
12756365 TGAAATATTTCACCGGCATCAAGCCTGCTAGTCACATAGAGCC
1 TGAAATAATACACCGGCATAAAGCCTGCTAG--ACATAAAGCC
12756408 TGAA
1 TGAA
12756412 TATCTTGGAT
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 58 0.83
43 12 0.17
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (41 bp):
TGAAATAATACACCGGCATAAAGCCTGCTAGACATAAAGCC
Found at i:12758242 original size:13 final size:13
Alignment explanation
Indices: 12758224--12758249 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12758214 CATTTCCAGG
12758224 TCATTTTCATTTT
1 TCATTTTCATTTT
12758237 TCATTTTCATTTT
1 TCATTTTCATTTT
12758250 GAAGAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:12758301 original size:57 final size:58
Alignment explanation
Indices: 12758234--12758354 Score: 192
Period size: 57 Copynumber: 2.1 Consensus size: 58
12758224 TCATTTTCAT
*
12758234 TTTTCATTTTCATTTTGAAGAAAA-CTACATTCATTTCCAAATATTTCCC-TTTCTCCC
1 TTTTCATTTTCATTTTGAAGAAAACCT-CATTCATTTCCAAATATTTCCCATTTCTCCA
* *
12758291 TTTTCATTTTCATTTTGGAGAAAACCTCATTCATTTCCAAATGTTTCCCATTTCTCCA
1 TTTTCATTTTCATTTTGAAGAAAACCTCATTCATTTCCAAATATTTCCCATTTCTCCA
12758349 TTTTCA
1 TTTTCA
12758355 CCATTTCTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
57 44 0.75
58 15 0.25
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (58 bp):
TTTTCATTTTCATTTTGAAGAAAACCTCATTCATTTCCAAATATTTCCCATTTCTCCA
Found at i:12759769 original size:14 final size:14
Alignment explanation
Indices: 12759723--12759769 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
12759713 TGTATTATTT
*
12759723 TTATAATCTTAAATA
1 TTAT-ATCTAAAATA
*
12759738 TTAAATCTAAAA-A
1 TTATATCTAAAATA
*
12759751 TTATATGTAAAATA
1 TTATATCTAAAATA
12759765 TTATA
1 TTATA
12759770 ATATACAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 11 0.41
14 13 0.48
15 3 0.11
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (14 bp):
TTATATCTAAAATA
Found at i:12768399 original size:59 final size:59
Alignment explanation
Indices: 12768317--12768542 Score: 254
Period size: 59 Copynumber: 3.7 Consensus size: 59
12768307 AATTAGGTTG
*
12768317 CGATCTTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTA
1 CGATATTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTA
* * * * *
12768376 CGATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGTCATCGAGTTGTTTTATGA
1 CGATATTAAATAAACTAACCTTTATAATATCA-----G-A--T--GTGATCGAGTAGTTTTAGGA
*
12768441 GTTG
56 GTTA
* *
12768445 CAATCTTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTA
1 CGATATTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTA
* * *
12768504 CGATATTAAATCAGCTAACCTTTATAATATCAGCTGTGA
1 CGATATTAAATAAACTAACCTTTATAATATCAGATGTGA
12768543 ACGTAGGTCA
Statistics
Matches: 137, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
59 83 0.61
61 1 0.01
63 1 0.01
64 2 0.01
65 1 0.01
67 1 0.01
69 48 0.35
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (59 bp):
CGATATTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTA
Found at i:12768466 original size:69 final size:69
Alignment explanation
Indices: 12768355--12768652 Score: 364
Period size: 69 Copynumber: 4.5 Consensus size: 69
12768345 ATCAGATGTG
* * * *
12768355 ATCGAGTAGTTTTAGGAGTTACGATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTA
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAGCTGTGAACGTA
12768420 GGTC
66 GGTC
* * *
12768424 ATCGAGTTGTTTTATGAGTTGCAATCTTAAATAAACTAACCTTTATAATATCA-----G-A--T-
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAGCTGTGAACGTA
*
12768480 -GTG
66 GGTC
* * * *
12768483 ATCGAGTAGTTTTAGGAGTTACGATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTA
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAGCTGTGAACGTA
12768548 GGTC
66 GGTC
* * *
12768552 ATCGAGTTGTTTTATGAGTTGCAATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAGCTGTGAACGTA
12768617 GGTC
66 GGTC
** *
12768621 ATCGAACTATTTTAGGAGTTGCGATCTTAAAT
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAAT
12768653 TACCTAACTC
Statistics
Matches: 191, Mismatches: 28, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
59 48 0.25
61 1 0.01
63 1 0.01
64 2 0.01
65 1 0.01
67 1 0.01
69 137 0.72
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (69 bp):
ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAGCTGTGAACGTA
GGTC
Found at i:12768611 original size:128 final size:128
Alignment explanation
Indices: 12768313--12768604 Score: 566
Period size: 128 Copynumber: 2.3 Consensus size: 128
12768303 ATAAAATTAG
*
12768313 GTTGCGATCTTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTACG
1 GTTGCAATCTTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTACG
12768378 ATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGTCATCGAGTTGTTTTATGA
66 ATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGTCATCGAGTTGTTTTATGA
12768441 GTTGCAATCTTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTACG
1 GTTGCAATCTTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTACG
12768506 ATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGTCATCGAGTTGTTTTATGA
66 ATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGTCATCGAGTTGTTTTATGA
*
12768569 GTTGCAATCTTAAATCAACTAACCTTTATAATATCA
1 GTTGCAATCTTAAATAAACTAACCTTTATAATATCA
12768605 ACTGTGAACG
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 162 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (128 bp):
GTTGCAATCTTAAATAAACTAACCTTTATAATATCAGATGTGATCGAGTAGTTTTAGGAGTTACG
ATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGTCATCGAGTTGTTTTATGA
Found at i:12768757 original size:106 final size:106
Alignment explanation
Indices: 12768569--12768818 Score: 383
Period size: 106 Copynumber: 2.4 Consensus size: 106
12768559 TGTTTTATGA
* * ** * *
12768569 GTTGCAATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTAGGTCATCGAACTATTTT
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
* * *
12768634 AGGAGTTGCGATCTTAAATTACCTAACTCAAAGAAACTTAG
66 AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
* *
12768675 GTTGCGATCTTAAATCGGCTAACCTTTATAATACCAGTTGTGAACGTAGGTCATCAAACTATTTC
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
* *
12768740 AAGAGTTGCGATATTAAATCAGCTAACTCAAAGAAACTTCG
66 AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
12768781 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGT
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGT
12768819 ACTTGTATAG
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 129 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (106 bp):
GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
Found at i:12780983 original size:15 final size:15
Alignment explanation
Indices: 12780925--12781000 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
12780915 CCGAATAAGC
*
12780925 TTGAACTCAAAAATAC
1 TTGAACTCAAAAA-AT
* *
12780941 TTGAACATGATAAAAT
1 TTGAAC-TCAAAAAAT
**
12780957 TTGAACAAAAAAAAT
1 TTGAACTCAAAAAAT
12780972 TTGAACTCAAAAAAT
1 TTGAACTCAAAAAAT
* * *
12780987 CTGCACTTAAAAAA
1 TTGAACTCAAAAAA
12781001 ATCCAAACCC
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
15 30 0.62
16 13 0.27
17 5 0.10
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.25
Consensus pattern (15 bp):
TTGAACTCAAAAAAT
Found at i:12780985 original size:16 final size:16
Alignment explanation
Indices: 12780925--12780985 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
12780915 CCGAATAAGC
* *
12780925 TTGAACTCAAAAATAC
1 TTGAACTCAAAAAAAT
* *
12780941 TTGAACAT-GATAAAAT
1 TTGAAC-TCAAAAAAAT
*
12780957 TTGAAC-AAAAAAAAT
1 TTGAACTCAAAAAAAT
12780972 TTGAACTCAAAAAA
1 TTGAACTCAAAAAA
12780986 TCTGCACTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 12 0.34
16 22 0.63
17 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (16 bp):
TTGAACTCAAAAAAAT
Found at i:12782625 original size:26 final size:26
Alignment explanation
Indices: 12782593--12782646 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
12782583 CCTCCTCTAC
12782593 CACTAGTTTTTAACAATGAAAACTAT
1 CACTAGTTTTTAACAATGAAAACTAT
12782619 CACTAGTTTTTAACAATGAAAACTAT
1 CACTAGTTTTTAACAATGAAAACTAT
12782645 CA
1 CA
12782647 TATTTGGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (26 bp):
CACTAGTTTTTAACAATGAAAACTAT
Found at i:12785623 original size:26 final size:26
Alignment explanation
Indices: 12785552--12785626 Score: 93
Period size: 25 Copynumber: 2.9 Consensus size: 26
12785542 AAATATTTTC
12785552 TCAAAATTTTACTAGAG-GTAAAATCA
1 TCAAAATTTTACTAG-GTGTAAAATCA
* *
12785578 TCAAAA-TTTACT-GATGGTAAAATCG
1 TCAAAATTTTACTAGGT-GTAAAATCA
12785603 TCAAAATTTTACTAGGTGTAAAAT
1 TCAAAATTTTACTAGGTGTAAAAT
12785627 AGGGTTGAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.02
25 20 0.48
26 19 0.45
27 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACTAGGTGTAAAATCA
Found at i:12787804 original size:25 final size:25
Alignment explanation
Indices: 12787770--12787910 Score: 116
Period size: 25 Copynumber: 5.6 Consensus size: 25
12787760 GTACATGTAT
*
12787770 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTATGAATCGGTAA
* *
12787795 GCTC-TCACGAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
12787820 GCTCATA-GAAGCTGA-GAATCGGTAA
1 GCTCATACG-AGCT-ATGAATCGGTAA
*
12787845 GCTC-TCATGAG-T-TGCAAATCGGTAA
1 GCTCAT-ACGAGCTATG--AATCGGTAA
* *
12787870 GCTC-TCACGAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
12787895 GCTCATACGAGCTATG
1 GCTCATACGAGCTATG
12787911 GTGTGTCCGC
Statistics
Matches: 95, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
23 1 0.01
24 4 0.04
25 85 0.89
26 4 0.04
27 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCGGTAA
Found at i:12787883 original size:50 final size:50
Alignment explanation
Indices: 12787770--12787907 Score: 160
Period size: 50 Copynumber: 2.8 Consensus size: 50
12787760 GTACATGTAT
* *
12787770 GCTCATACGAGCT-ATGAATCGGTATGCTCTCACGAGCTGTAAATCGGTAA
1 GCTCATACGAGCTGA-GAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAA
* *
12787820 GCTCATA-GAAGCTGAGAATCGGTAAGCTCTCATGAGTTGCAAATCGGTAA
1 GCTCATACG-AGCTGAGAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAA
12787870 GCTC-TCACGAGCTGTA-AATCGGTAAGCTCAT-ACGAGCT
1 GCTCAT-ACGAGCTG-AGAATCGGTAAGCTC-TCACGAGCT
12787908 ATGGTGTGTC
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
49 2 0.03
50 70 0.92
51 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (50 bp):
GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAA
Found at i:12792220 original size:25 final size:25
Alignment explanation
Indices: 12792167--12792279 Score: 99
Period size: 25 Copynumber: 4.5 Consensus size: 25
12792157 GTACATGTAT
* *
12792167 GCTCATACGAGCTATGAATTCG-TAT
1 GCTCATACGAGCTAT-AAATCGATAA
12792192 GCTC-TCACGAGCTATAAATCGATAA
1 GCTCAT-ACGAGCTATAAATCGATAA
* * * *
12792217 GCTCATACAAGTCGA-GAATCGGTAA
1 GCTCATACGAG-CTATAAATCGATAA
*
12792242 GCTC-TAGCGAGCTACAAATCGATAA
1 GCTCATA-CGAGCTATAAATCGATAA
12792267 GCTCATACGAGCT
1 GCTCATACGAGCT
12792280 GTGGTGTGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
24 10 0.14
25 56 0.79
26 5 0.07
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTATAAATCGATAA
Found at i:12798640 original size:20 final size:19
Alignment explanation
Indices: 12798614--12798702 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 19
12798604 ATAGATGCGT
12798614 AACAGAGGCACCGAAGTGC
1 AACAGAGGCACCGAAGTGC
12798633 AGACAGAGGCA-CGATTA-TGC
1 A-ACAGAGGCACCGA--AGTGC
* *
12798653 AATCAAAGGCACCAAAGTGC
1 AA-CAGAGGCACCGAAGTGC
* * *
12798673 AAATAGAGACACCGAAGTGT
1 -AACAGAGGCACCGAAGTGC
12798693 AACAGAGGCA
1 AACAGAGGCA
12798703 TTGAACTGCA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
19 14 0.26
20 35 0.65
21 5 0.09
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.10
Consensus pattern (19 bp):
AACAGAGGCACCGAAGTGC
Found at i:12812690 original size:16 final size:16
Alignment explanation
Indices: 12812671--12812703 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12812661 TCACCTCAAT
12812671 AAATTTTATAAAATTA
1 AAATTTTATAAAATTA
*
12812687 AAATTTTATAATATTA
1 AAATTTTATAAAATTA
12812703 A
1 A
12812704 CTGAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTTATAAAATTA
Found at i:12813609 original size:19 final size:18
Alignment explanation
Indices: 12813587--12813628 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
12813577 AATTCAAAAA
12813587 TAAAAATA-AAAATATTTTT
1 TAAAAATATAAAA-A-TTTT
12813606 TAAAAATATAAAAATTTT
1 TAAAAATATAAAAATTTT
12813624 TAAAA
1 TAAAA
12813629 TTCAATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATATAAAAATTTT
Found at i:12816986 original size:16 final size:16
Alignment explanation
Indices: 12816950--12816996 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
12816940 CTCATCACTT
* *
12816950 TATGGTGTGTTGGGGG
1 TATGGTGTGTTTGGAG
12816966 T-TGGTGTGTTTGGAG
1 TATGGTGTGTTTGGAG
*
12816981 TATGGTTTGTTTGGAG
1 TATGGTGTGTTTGGAG
12816997 GACATGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.45
Consensus pattern (16 bp):
TATGGTGTGTTTGGAG
Found at i:12818652 original size:13 final size:14
Alignment explanation
Indices: 12818618--12818707 Score: 66
Period size: 13 Copynumber: 6.7 Consensus size: 14
12818608 CCAATGTTTC
* *
12818618 ATTTCATAT-ATCT
1 ATTTCATATAACCG
12818631 ATTTCCATATAACCG
1 ATTT-CATATAACCG
**
12818646 A-TTCATATAA-AT
1 ATTTCATATAACCG
* *
12818658 ATTTCATAT-ATCT
1 ATTTCATATAACCG
12818671 ATTTTCATATAACCG
1 A-TTTCATATAACCG
12818686 A-TTCATATAACC-
1 ATTTCATATAACCG
12818698 ATTTCATATA
1 ATTTCATATA
12818708 TCTATATTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
12 3 0.05
13 39 0.62
14 15 0.24
15 6 0.10
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTTCATATAACCG
Found at i:12818663 original size:40 final size:39
Alignment explanation
Indices: 12818617--12818721 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 39
12818607 TCCAATGTTT
12818617 CATTTCATATATCTATTTCCATATAACCGATTCATATAAA
1 CATTTCATATATCTATTT-CATATAACCGATTCATATAAA
* *
12818657 TATTTCATATATCTATTTTCATATAACCGATTCATATAAC
1 CATTTCATATATCTA-TTTCATATAACCGATTCATATAAA
12818697 CATTTCATATATCTATATTCATATA
1 CATTTCATATATCTAT-TTCATATA
12818722 TTCATTTTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
39 1 0.02
40 56 0.93
41 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (39 bp):
CATTTCATATATCTATTTCATATAACCGATTCATATAAA
Done.