Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 142 of 230
Found at i:41726184 original size:47 final size:47
Alignment explanation
Indices: 41726125--41726609 Score: 799
Period size: 47 Copynumber: 10.3 Consensus size: 47
41726115 CAACACAGTT
41726125 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
41726172 TATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
41726219 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
41726266 TATATATGTGATAATGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
41726313 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
41726360 TATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * *
41726407 CATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
41726454 TATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
41726501 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * * * * *
41726548 TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
41726595 CATAAATGTGATAAG
1 TATATATGTGATAAG
41726610 TCCCGAAGGG
Statistics
Matches: 411, Mismatches: 27, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 411 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:41726784 original size:37 final size:37
Alignment explanation
Indices: 41726732--41726806 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
41726722 GCTCTAAAGG
* *
41726732 CCCGATGACTACGTGTGG-GACTTTTGTCCGGGTAAGA
1 CCCGATAACTACGTGTGGAGA-TTATGTCCGGGTAAGA
*
41726769 CCCGATAACTTCGTGTGGAGATTATGTCCGGGTAAGA
1 CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAGA
41726806 C
1 C
41726807 TTCGTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 32 0.94
38 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (37 bp):
CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAGA
Found at i:41750439 original size:15 final size:16
Alignment explanation
Indices: 41750394--41750446 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
41750384 TCATTTCTCA
*
41750394 TCATC-CATTATCC-C
1 TCATCTCATCATCCTC
41750408 TCATCTCATCATCCCTC
1 TCATCTCATCAT-CCTC
*
41750425 TCATCT-TTCATCCTC
1 TCATCTCATCATCCTC
41750440 TC-TCTCA
1 TCATCTCA
41750447 ACTCTCTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
16 6 0.19
17 7 0.22
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (16 bp):
TCATCTCATCATCCTC
Found at i:41759632 original size:51 final size:51
Alignment explanation
Indices: 41759542--41759664 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 51
41759532 TGATAGGGCG
* * * * *
41759542 CATGTGTAGTGCTATGTGCAGGCTACTATGCGTACCGGATAGCTTC-GATAA
1 CATGTGTAGTACTATGTGCAGACTAATACGCGTACCGGATAG-TGCTGATAA
* * * * *
41759593 CGTGTGTAGTACTATGTGCAGACTAATACGTGTATCGGATAGTGCTGGTCA
1 CATGTGTAGTACTATGTGCAGACTAATACGCGTACCGGATAGTGCTGATAA
41759644 CATGTGTAGTACTATGTGCAG
1 CATGTGTAGTACTATGTGCAG
41759665 GCTACTATGT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 2 0.03
51 58 0.97
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
CATGTGTAGTACTATGTGCAGACTAATACGCGTACCGGATAGTGCTGATAA
Found at i:41759681 original size:102 final size:101
Alignment explanation
Indices: 41759494--41759681 Score: 252
Period size: 102 Copynumber: 1.9 Consensus size: 101
41759484 GATGGTCACA
* * * *
41759494 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAAATGATAGGGCGCATGTGTAGTGCTATGT
1 TGTGTAGTACTATGTGCAGACTAATACGTGTACCAAAATGATAGGGCACATGTGTAGTACTATGT
*
41759559 GCAGGCTACTATGCGTACCGGATAGCTTCGATAACG
66 GCAGGCTACTATGCGAACCGGATAGCTTCGATAACG
* * * * *
41759595 TGTGTAGTACTATGTGCAGACTAATACGTGTATCGGATAGTGCT-GGTCACATGTGTAGTACTAT
1 TGTGTAGTACTATGTGCAGACTAATACGTGTA-C-CAAAATGATAGGGCACATGTGTAGTACTAT
*
41759659 GTGCAGGCTACTATGTGAACCGG
64 GTGCAGGCTACTATGCGAACCGG
41759682 TATCATTAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
101 30 0.41
102 39 0.53
103 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (101 bp):
TGTGTAGTACTATGTGCAGACTAATACGTGTACCAAAATGATAGGGCACATGTGTAGTACTATGT
GCAGGCTACTATGCGAACCGGATAGCTTCGATAACG
Found at i:41759920 original size:16 final size:16
Alignment explanation
Indices: 41759899--41759930 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41759889 TGATTGAAAG
41759899 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
41759915 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
41759931 GCAACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:41760307 original size:11 final size:11
Alignment explanation
Indices: 41760291--41760315 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41760281 TTATGGTAAT
41760291 TGAAATAGGGG
1 TGAAATAGGGG
41760302 TGAAATAGGGG
1 TGAAATAGGGG
41760313 TGA
1 TGA
41760316 CTTTAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (11 bp):
TGAAATAGGGG
Found at i:41761559 original size:59 final size:60
Alignment explanation
Indices: 41761466--41761585 Score: 215
Period size: 59 Copynumber: 2.0 Consensus size: 60
41761456 ACTCGAAGAT
*
41761466 AATAATTTGAAAGTTTTTTAATTTGGATGAAATTTTATAACTTGATTTAATATGTTTATA
1 AATAATTTGAAAGTTTTTTAATTTGGATGAAATTTTATAACTCGATTTAATATGTTTATA
*
41761526 AATAATTTGGAAG-TTTTTAATTTGGATGAAATTTTATAACTCGATTTAATATGTTTATA
1 AATAATTTGAAAGTTTTTTAATTTGGATGAAATTTTATAACTCGATTTAATATGTTTATA
41761585 A
1 A
41761586 GTGTATTTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 46 0.79
60 12 0.21
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (60 bp):
AATAATTTGAAAGTTTTTTAATTTGGATGAAATTTTATAACTCGATTTAATATGTTTATA
Found at i:41761799 original size:22 final size:23
Alignment explanation
Indices: 41761774--41761818 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
41761764 CCTAATTCTA
*
41761774 ATATAAGTTGATAAA-AAT-TAAT
1 ATATAAATT-ATAAATAATATAAT
41761796 ATATAAATTATAAATAATATAAT
1 ATATAAATTATAAATAATATAAT
41761819 TTTATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
ATATAAATTATAAATAATATAAT
Found at i:41764674 original size:25 final size:25
Alignment explanation
Indices: 41764628--41764677 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41764618 CAATTAAAAA
* * *
41764628 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
41764653 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
41764678 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:41764717 original size:125 final size:125
Alignment explanation
Indices: 41764503--41766134 Score: 2834
Period size: 125 Copynumber: 13.1 Consensus size: 125
41764493 CAATTCAAAC
* * * *
41764503 GATTAAAGCCACCTCGGTAAATCTTGATTAAAGCTACAACAGCAAATCTTATGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
41764568 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAATTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
*
41764628 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATC
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
* * *
41764693 CAGTGTAATAGATTAAAGCGAAATTGGTGAATCTTGTTTCTCCGACATTGTAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* *
41764753 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAACGAATCTTACGCCCCAAGCAATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
41764818 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTTCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
*
41764878 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTATGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
41764943 CAGTGGAATACATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* * *
41765003 GATTAAAGTCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACACCCCAAGCAATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
41765068 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
41765128 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
* *
41765193 CAGTGGAATACATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGTAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
*
41765253 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAATAGCGAATCTTACGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
41765318 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* * *
41765378 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTAAAACAGCGAATCTTATGCCCCAAGCAATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
* * *
41765443 CAATGGAATAGATTAAAGCCAAATTTGTGAATCTTGTTTCTCCAACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* * *
41765503 GATTAAAGCCACATTGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCAAAG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
41765568 CAGTGGAATACATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* * *
41765628 GATGAAAGCCACATCGGTGAATCTTGA-TAACAACTACAACAGCGAATCTTACGCCCCAAGCAAT
1 GATTAAAGCCACATCGGTGAATCTTGATTAA-AGCTACAACAGCGAATCTTACGCCCCAAGCGAT
41765692 GCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
65 GCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* *
41765753 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAACGAATCTTACGCCCCAAGCGATT
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
* * *
41765818 CAGTGGAATACATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAATTAAATA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* *
41765878 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTAAAACAGCGAATCTTACGCCCCAAGCAATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
41765943 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* *
41766003 TATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCTAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
* * * *
41766068 CAGTGGAACAGATTAAAACCAAGTTGGTGAATCTTGTTTCTCCAACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
41766128 GATTAAA
1 GATTAAA
41766135 TGACAAATCT
Statistics
Matches: 1427, Mismatches: 78, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
124 3 0.00
125 1421 1.00
126 3 0.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (125 bp):
GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
Found at i:41764924 original size:25 final size:25
Alignment explanation
Indices: 41764878--41764927 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41764868 CAGTTAAAAA
* * *
41764878 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
41764903 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
41764928 ATGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:41765174 original size:25 final size:25
Alignment explanation
Indices: 41765128--41765177 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41765118 CAGTTAAAAA
* * *
41765128 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
41765153 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
41765178 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:41767746 original size:3 final size:3
Alignment explanation
Indices: 41767738--41767780 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
41767728 ATAAATTTCA
*
41767738 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41767781 GCTTTTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41768693 original size:110 final size:110
Alignment explanation
Indices: 41768414--41768809 Score: 638
Period size: 109 Copynumber: 3.6 Consensus size: 110
41768404 TCAAAAAAGA
* *
41768414 AAAATATTTCTAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCTTAAGGTGCT
1 AAAA-ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
*
41768479 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTCTT
* *
41768525 -AAAATTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
41768589 GGTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTCTT
66 GGTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTCTT
*
41768634 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
* * *
41768699 GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATA-CC-CCTT
66 GGTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTCTT
* * *
41768742 CAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACT
1 -AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
41768806 GGGT
65 GGGT
41768810 TTCAATTTCT
Statistics
Matches: 270, Mismatches: 13, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
108 23 0.09
109 146 0.54
110 101 0.37
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (110 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTCTT
Found at i:41769828 original size:24 final size:23
Alignment explanation
Indices: 41769779--41769836 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
41769769 CAATAATAGA
* *
41769779 AATATTAAAATATATTCAAAATT
1 AATATTAAAATATATTAAAAAAT
41769802 AATATTGAAAATAT-TTAATAAAAT
1 AATATT-AAAATATATTAA-AAAAT
41769826 AAT-TTATAAAT
1 AATATTA-AAAT
41769837 TTTTGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 15 0.50
24 14 0.47
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AATATTAAAATATATTAAAAAAT
Found at i:41771221 original size:32 final size:32
Alignment explanation
Indices: 41771127--41771224 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
41771117 AGCCTTTAAT
*
41771127 AATTTTTAAAAT--TTTTAATTAGAC-C-CCC
1 AATTTTTAAAATAATTTTAATTAGACTCTCCA
* * * * * *
41771155 AATTTTTTAGA-AATTCTCATTAGCCT-TCTAA
1 AATTTTTAAAATAATTTTAATTAGACTCTC-CA
41771186 AATTTTTAAAATAATTTTAATTAGACTCTCCA
1 AATTTTTAAAATAATTTTAATTAGACTCTCCA
41771218 AATTTTT
1 AATTTTT
41771225 TGGAGATCCT
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
28 9 0.18
29 9 0.18
30 1 0.02
31 9 0.18
32 20 0.40
33 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.46
Consensus pattern (32 bp):
AATTTTTAAAATAATTTTAATTAGACTCTCCA
Found at i:41771249 original size:63 final size:59
Alignment explanation
Indices: 41771111--41771250 Score: 165
Period size: 63 Copynumber: 2.3 Consensus size: 59
41771101 TGAAAAGTTA
* * *
41771111 TCATTAAGCCTTTAATAATTTTTAAAATTTTTAATTAGACCCCCAATTTTTTAGAAATTC
1 TCATTAAGCCTCTAA-AATTTTTAAAATTTTTAATTAGACCCCAAATTTTTTAGAAATCC
* *
41771171 TCATT-AGCCTTCTAAAATTTTTAAAATAATTTTAATTAGACTCTCCAAATTTTTTGGAGATCC
1 TCATTAAGCC-TCTAAAATTTTTAAAAT--TTTTAATTAGAC-C-CCAAATTTTTTAGAAATCC
*
41771234 TCATTAAGCCCCTAAAA
1 TCATTAAGCCTCTAAAA
41771251 GTTCTAAGGA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
59 16 0.24
60 9 0.13
61 12 0.18
62 1 0.01
63 26 0.38
64 4 0.06
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (59 bp):
TCATTAAGCCTCTAAAATTTTTAAAATTTTTAATTAGACCCCAAATTTTTTAGAAATCC
Found at i:41771777 original size:15 final size:16
Alignment explanation
Indices: 41771751--41771780 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41771741 ATATATATAT
41771751 ATATATTATTTTTAAG
1 ATATATTATTTTTAAG
41771767 ATATA-TATTTTTAA
1 ATATATTATTTTTAA
41771781 TTTATGGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATATATTATTTTTAAG
Found at i:41772531 original size:27 final size:27
Alignment explanation
Indices: 41772490--41772627 Score: 109
Period size: 27 Copynumber: 5.1 Consensus size: 27
41772480 AACACGTCAA
*
41772490 GAAAGGAAAGTCTTTGTGGTGAAATAT
1 GAAAGGAAAGCCTTTGTGGTGAAATAT
***
41772517 GAAAGGAAAGCCTTTGTGACAAAATA-
1 GAAAGGAAAGCCTTTGTGGTGAAATAT
* * * *
41772543 CAAGAGAAAAGCCTTTGTAGCGAAATAT
1 GAA-AGGAAAGCCTTTGTGGTGAAATAT
* * *
41772571 GAAAAGAAAGTCTTTGTAGTG-AATCAT
1 GAAAGGAAAGCCTTTGTGGTGAAAT-AT
* * * *
41772598 GAAAGAAAAGCTTTTATGGTGAATTAT
1 GAAAGGAAAGCCTTTGTGGTGAAATAT
41772625 GAA
1 GAA
41772628 TGGATAGTCT
Statistics
Matches: 86, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
26 5 0.06
27 77 0.90
28 4 0.05
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (27 bp):
GAAAGGAAAGCCTTTGTGGTGAAATAT
Found at i:41775240 original size:49 final size:48
Alignment explanation
Indices: 41775150--41775242 Score: 141
Period size: 49 Copynumber: 1.9 Consensus size: 48
41775140 AGTGTCGTCC
* * *
41775150 CATCTAGAGTTAATACTAAAAGTAATCCATTGAAAGTTGGTGCCCTCA
1 CATCTAGAATTAACACTAAAAATAATCCATTGAAAGTTGGTGCCCTCA
*
41775198 CATCTAGAATTAACACTAAAAAATAATTCATTGAAAGTTGGTGCC
1 CATCTAGAATTAACACT-AAAAATAATCCATTGAAAGTTGGTGCC
41775243 TCCAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 15 0.38
49 25 0.62
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (48 bp):
CATCTAGAATTAACACTAAAAATAATCCATTGAAAGTTGGTGCCCTCA
Found at i:41778949 original size:353 final size:353
Alignment explanation
Indices: 41778303--41779008 Score: 1385
Period size: 353 Copynumber: 2.0 Consensus size: 353
41778293 TTTGGAAGTT
41778303 GTAGATCCAATTCTGAGGGATGGCTCGAGAAGTGAAATAACGAGATGTATCCAGCTTGGGTTGCT
1 GTAGATCCAATTCTGAGGGATGGCTCGAGAAGTGAAATAACGAGATGTATCCAGCTTGGGTTGCT
*
41778368 TTGTGTTCAAGAAGATACTGCTTATAGACCTACCATGGCCTCTGCGGTTCTCATGCTTAGTAGCT
66 TTGTGTTCAAGAAGATACTGCTTATAGACCAACCATGGCCTCTGCGGTTCTCATGCTTAGTAGCT
41778433 ATTCCATCTCTCTTCCAATGCCATCGGCACCTCCATTGTCTATGCATTCCATCAGGGAGAGAGAA
131 ATTCCATCTCTCTTCCAATGCCATCGGCACCTCCATTGTCTATGCATTCCATCAGGGAGAGAGAA
41778498 ACGAAGTCGAAGTCATCATCCTTCTCTAATCAATCTAAAAGAGAAACCGTCCAAGTCTCTGTCAA
196 ACGAAGTCGAAGTCATCATCCTTCTCTAATCAATCTAAAAGAGAAACCGTCCAAGTCTCTGTCAA
41778563 TTAGGCTTTGGTTTCTGAACTAGATCGTCATTGAAGTTTGAAGATGGTACTTTGTACTTCCATAA
261 TTAGGCTTTGGTTTCTGAACTAGATCGTCATTGAAGTTTGAAGATGGTACTTTGTACTTCCATAA
*
41778628 CATATTTTCTCTTACATGGTAATCATAA
326 CATATTTTCTCTTACATAGTAATCATAA
*
41778656 GTAGATCCAATTCTGAGGGATGGCTTGAGAAGTGAAATAACGAGATGTATCCAGCTTGGGTTGCT
1 GTAGATCCAATTCTGAGGGATGGCTCGAGAAGTGAAATAACGAGATGTATCCAGCTTGGGTTGCT
41778721 TTGTGTTCAAGAAGATACTGCTTATAGACCAACCATGGCCTCTGCGGTTCTCATGCTTAGTAGCT
66 TTGTGTTCAAGAAGATACTGCTTATAGACCAACCATGGCCTCTGCGGTTCTCATGCTTAGTAGCT
41778786 ATTCCATCTCTCTTCCAATGCCATCGGCACCTCCATTGTCTATGCATTCCATCAGGGAGAGAGAA
131 ATTCCATCTCTCTTCCAATGCCATCGGCACCTCCATTGTCTATGCATTCCATCAGGGAGAGAGAA
41778851 ACGAAGTCGAAGTCATCATCCTTCTCTAATCAATCTAAAAGAGAAACCGTCCAAGTCTCTGTCAA
196 ACGAAGTCGAAGTCATCATCCTTCTCTAATCAATCTAAAAGAGAAACCGTCCAAGTCTCTGTCAA
41778916 TTAGGCTTTGGTTTCTGAACTAGATCGTCATTGAAGTTTGAAGATGGTACTTTGTACTTCCATAA
261 TTAGGCTTTGGTTTCTGAACTAGATCGTCATTGAAGTTTGAAGATGGTACTTTGTACTTCCATAA
41778981 CATATTTTCTCTTACATAGTAATCATAA
326 CATATTTTCTCTTACATAGTAATCATAA
41779009 AAAAGAAAAA
Statistics
Matches: 350, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
353 350 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (353 bp):
GTAGATCCAATTCTGAGGGATGGCTCGAGAAGTGAAATAACGAGATGTATCCAGCTTGGGTTGCT
TTGTGTTCAAGAAGATACTGCTTATAGACCAACCATGGCCTCTGCGGTTCTCATGCTTAGTAGCT
ATTCCATCTCTCTTCCAATGCCATCGGCACCTCCATTGTCTATGCATTCCATCAGGGAGAGAGAA
ACGAAGTCGAAGTCATCATCCTTCTCTAATCAATCTAAAAGAGAAACCGTCCAAGTCTCTGTCAA
TTAGGCTTTGGTTTCTGAACTAGATCGTCATTGAAGTTTGAAGATGGTACTTTGTACTTCCATAA
CATATTTTCTCTTACATAGTAATCATAA
Found at i:41780323 original size:45 final size:44
Alignment explanation
Indices: 41780255--41780345 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
41780245 AGTATAATAA
** * * **
41780255 CACATTTAGTCCTTCATACTTACACATTCTATCCGTTTGATCCTT
1 CACATTTAACCCTTCACACTTACAAATTCTATCAATTTGA-CCTT
*
41780300 CACATTTAACCCTTCACATTTACAAATTCTATCAATTTGACCTT
1 CACATTTAACCCTTCACACTTACAAATTCTATCAATTTGACCTT
41780344 CA
1 CA
41780346 AATACATACA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 6 0.15
45 33 0.85
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.40
Consensus pattern (44 bp):
CACATTTAACCCTTCACACTTACAAATTCTATCAATTTGACCTT
Found at i:41780442 original size:24 final size:26
Alignment explanation
Indices: 41780395--41780447 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
41780385 GGAAAAAAAT
41780395 ATAATATTATTTATATGTTTATA-TAA
1 ATAATATTA-TTATATGTTTATATTAA
*
41780421 ATAATATTA-TATGTGTTTATATTAA
1 ATAATATTATTATATGTTTATATTAA
41780446 AT
1 AT
41780448 TATAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 5 0.20
26 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (26 bp):
ATAATATTATTATATGTTTATATTAA
Found at i:41782687 original size:20 final size:21
Alignment explanation
Indices: 41782648--41782693 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
41782638 ATCTCATTCC
41782648 CATGCAACATATCAAACATG-
1 CATGCAACATATCAAACATGA
*
41782668 CATGCAACATAT-ATATCATGA
1 CATGCAACATATCA-AACATGA
41782689 CATGC
1 CATGC
41782694 CCATATACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 17 0.74
21 5 0.22
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (21 bp):
CATGCAACATATCAAACATGA
Found at i:41782761 original size:27 final size:27
Alignment explanation
Indices: 41782724--41782869 Score: 224
Period size: 27 Copynumber: 5.4 Consensus size: 27
41782714 CATAAATCAT
41782724 ACAGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
*
41782751 ACTGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
*
41782778 ACAGTCATTTTATAACATAGGGGCTTA
1 ACAGTCATTTTATAACATAGGGGCATA
*
41782805 ACAGTCATTTTATAGCATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
*
41782832 ATAGTCATTTTACT-ACAT-GAGGGCATA
1 ACAGTCATTTTA-TAACATAG-GGGCATA
41782859 ACAGTCATTTT
1 ACAGTCATTTT
41782870 TTAATAGTTT
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
26 1 0.01
27 107 0.98
28 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGGCATA
Found at i:41789960 original size:34 final size:32
Alignment explanation
Indices: 41789912--41789975 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 32
41789902 AATAACAGTC
41789912 CAGTTCAGTTGGGCCCTAGCCCATTATAGTAT
1 CAGTTCAGTTGGGCCCTAGCCCATTATAGTAT
*
41789944 CAGTATCAGTGTGGGCCTTAGCCCATTATAGT
1 CAGT-TCAGT-TGGGCCCTAGCCCATTATAGT
41789976 GATAGTAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 4 0.14
33 5 0.17
34 20 0.69
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (32 bp):
CAGTTCAGTTGGGCCCTAGCCCATTATAGTAT
Found at i:41790292 original size:27 final size:27
Alignment explanation
Indices: 41790256--41790321 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
41790246 CATAAATCAT
41790256 ACAGTCATTTTATAACATAGGGGAATA
1 ACAGTCATTTTATAACATAGGGGAATA
* * *
41790283 ATAGTCATTTTATAGCATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGAATA
41790310 ACAGTCATTTTA
1 ACAGTCATTTTA
41790322 CCACGTGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGGAATA
Found at i:41818872 original size:16 final size:17
Alignment explanation
Indices: 41818853--41818895 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
41818843 ATGTTTTATG
41818853 TTTTTTTTATTTG-TAC
1 TTTTTTTTATTTGTTAC
*
41818869 -TTTTTTTA-TTGTTAT
1 TTTTTTTTATTTGTTAC
41818884 TTTTTTTTATTT
1 TTTTTTTTATTT
41818896 TTCAGACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 8 0.35
17 2 0.09
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTTTTTTATTTGTTAC
Found at i:41820162 original size:14 final size:14
Alignment explanation
Indices: 41820143--41820173 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
41820133 TTGAATGCTT
41820143 TGAGTGAACCTTAG
1 TGAGTGAACCTTAG
41820157 TGAGTGAACCTTAG
1 TGAGTGAACCTTAG
41820171 TGA
1 TGA
41820174 CTGCTTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (14 bp):
TGAGTGAACCTTAG
Found at i:41825587 original size:43 final size:42
Alignment explanation
Indices: 41825515--41825891 Score: 506
Period size: 43 Copynumber: 8.8 Consensus size: 42
41825505 GCGTCGCAAA
* * *
41825515 CTTTAGCGGCG-TTTCCACAAAAAATGCCGCTAAAGATCAAGAC
1 CTTTAGCGGCGCTTTCC-C-ACAAACGCCGCTAAAGACCAAGAC
41825558 CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTCC-CACAAACGCCGCTAAAGACCAAGAC
*
41825601 CTTTAGCGGCGCTTTCCACACAAACGCTGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTCC-CACAAACGCCGCTAAAGACCAAGAC
41825644 CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTCC-CACAAACGCCGCTAAAGACCAAGAC
*
41825687 CTTTAGCGGTGCTAATT-CCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCT--TTCCCACAAACGCCGCTAAAGACCAAGAC
** *
41825730 CTTTAGCTACGCTTCTCCCACAAACGCTGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTT-TCCCACAAACGCCGCTAAAGACCAAGAC
*** *
41825773 CTTTAGCGGCGCTTCTTTTACAAACGCCGCTAAAAACCAAGAC
1 CTTTAGCGGCGCTT-TCCCACAAACGCCGCTAAAGACCAAGAC
* *
41825816 CTTTAGCGGCGCTTCTCCTACAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTT-TCCCACAAACGCCGCTAAAGACCAAGAC
*
41825859 CGTTAGCGGCGCTTCTCCCACAAACGCCGCTAA
1 CTTTAGCGGCGCTT-TCCCACAAACGCCGCTAA
41825892 TTTTGGCAAA
Statistics
Matches: 305, Mismatches: 24, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 293 0.96
44 8 0.03
45 2 0.01
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:41828771 original size:16 final size:16
Alignment explanation
Indices: 41828752--41828890 Score: 71
Period size: 16 Copynumber: 9.0 Consensus size: 16
41828742 TATTAAGTAA
41828752 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
41828768 ATTATATAAGTTATGT
1 ATTATGTAAGTTATGT
*
41828784 AAGTTACGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
* * *
41828800 GAGCTATGTAAGTTGTAT
1 -A-TTATGTAAGTTATGT
*
41828818 TTTATGTAAGTTA--T
1 ATTATGTAAGTTATGT
* *
41828832 -TTA-GTATG-TAAG-
1 ATTATGTAAGTTATGT
* *
41828844 -CTATGTAAGTTGTGT
1 ATTATGTAAGTTATGT
*
41828859 ATTATGTAAGCTATGT
1 ATTATGTAAGTTATGT
*
41828875 ATTATGTTAGTTATGT
1 ATTATGTAAGTTATGT
41828891 CGGTTATATA
Statistics
Matches: 92, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
11 2 0.02
12 6 0.07
13 7 0.08
14 3 0.03
16 63 0.68
17 3 0.03
18 8 0.09
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.47
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:41828781 original size:25 final size:25
Alignment explanation
Indices: 41828740--41828831 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 25
41828730 TATATATTTC
*
41828740 TGTATTA-AGTAAATTATGTAAGTTA
1 TGTATTATA-TAAGTTATGTAAGTTA
41828765 TGTATTATATAAGTTATGTAAGTTA
1 TGTATTATATAAGTTATGTAAGTTA
* * * * *
41828790 CGTATTATGTGAGCTATGTAAGTTG
1 TGTATTATATAAGTTATGTAAGTTA
* * *
41828815 TATTTTATGTAAGTTAT
1 TGTATTATATAAGTTAT
41828832 TTAGTATGTA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (25 bp):
TGTATTATATAAGTTATGTAAGTTA
Found at i:41828786 original size:9 final size:9
Alignment explanation
Indices: 41828748--41829111 Score: 141
Period size: 9 Copynumber: 43.3 Consensus size: 9
41828738 TCTGTATTAA
*
41828748 GTAAATTAT
1 GTAAGTTAT
41828757 GTAAGTTAT
1 GTAAGTTAT
41828766 GT-A-TTAT
1 GTAAGTTAT
*
41828773 ATAAGTTAT
1 GTAAGTTAT
*
41828782 GTAAGTTAC
1 GTAAGTTAT
41828791 GT-A-TTAT
1 GTAAGTTAT
* *
41828798 GTGAGCTAT
1 GTAAGTTAT
41828807 GTAAG-T-T
1 GTAAGTTAT
**
41828814 GTATTTTAT
1 GTAAGTTAT
41828823 GTAAGTTAT
1 GTAAGTTAT
*
41828832 -TTAG-TAT
1 GTAAGTTAT
*
41828839 GTAAGCTAT
1 GTAAGTTAT
*
41828848 GTAAGTTGT
1 GTAAGTTAT
41828857 GT-A-TTAT
1 GTAAGTTAT
*
41828864 GTAAGCTAT
1 GTAAGTTAT
41828873 GT-A-TTAT
1 GTAAGTTAT
*
41828880 GTTAGTTAT
1 GTAAGTTAT
**
41828889 GTCGGTTAT
1 GTAAGTTAT
*
41828898 AT-A-TTAT
1 GTAAGTTAT
*
41828905 GTATGTTAT
1 GTAAGTTAT
*
41828914 GTAAGTTGT
1 GTAAGTTAT
*
41828923 -TCAGTTA-
1 GTAAGTTAT
*
41828930 -TAAGCTAT
1 GTAAGTTAT
41828938 GTAAGTTAT
1 GTAAGTTAT
*
41828947 GTGAGTTA-
1 GTAAGTTAT
41828955 -T-A--TAT
1 GTAAGTTAT
41828960 GTAAGTTAT
1 GTAAGTTAT
41828969 GTATAAG-T-T
1 G--TAAGTTAT
*
41828978 -TAATTTGTAT
1 GTAA-GT-TAT
*
41828988 -TAAGCTAT
1 GTAAGTTAT
*
41828996 GTAAGTTGT
1 GTAAGTTAT
*
41829005 G-AA-TAAT
1 GTAAGTTAT
41829012 GTAAGTTAT
1 GTAAGTTAT
*
41829021 GAAAGTTAT
1 GTAAGTTAT
*
41829030 GTATTAAGTTGT
1 G---TAAGTTAT
41829042 GT-A-TTAT
1 GTAAGTTAT
*
41829049 GTAAGTTGT
1 GTAAGTTAT
*
41829058 G-AA-TAAT
1 GTAAGTTAT
41829065 GTAAGTTAT
1 GTAAGTTAT
41829074 G-AACGTTAT
1 GTAA-GTTAT
41829083 GT-A-TTAT
1 GTAAGTTAT
41829090 GTTAAGTTAT
1 G-TAAGTTAT
*
41829100 GAAAGTTAT
1 GTAAGTTAT
41829109 GTA
1 GTA
41829112 TTAAGTTGTG
Statistics
Matches: 263, Mismatches: 50, Indels: 84
0.66 0.13 0.21
Matches are distributed among these distances:
4 2 0.01
6 5 0.02
7 55 0.21
8 37 0.14
9 143 0.54
10 10 0.04
11 4 0.02
12 7 0.03
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:41828823 original size:41 final size:41
Alignment explanation
Indices: 41828752--41828916 Score: 163
Period size: 41 Copynumber: 4.0 Consensus size: 41
41828742 TATTAAGTAA
* * *
41828752 ATTATGTAAGTTATGT-A-TTATATAAGTTATGTAAGTTACGT
1 ATTATGTAAGCTATGTAAGTTGTAT-A-TTATGTAAGTTATGT
* * *
41828793 ATTATGTGAGCTATGTAAGTTGTATTTTATGTAAGTTATTT
1 ATTATGTAAGCTATGTAAGTTGTATATTATGTAAGTTATGT
* * *
41828834 AGTATGTAAGCTATGTAAGTTGTGTATTATGTAAGCTATGT
1 ATTATGTAAGCTATGTAAGTTGTATATTATGTAAGTTATGT
* * ** * *
41828875 ATTATGTTAGTTATGTCGGTTATATATTATGTATGTTATGT
1 ATTATGTAAGCTATGTAAGTTGTATATTATGTAAGTTATGT
41828916 A
1 A
41828917 AGTTGTTCAG
Statistics
Matches: 101, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 95 0.94
42 1 0.01
43 5 0.05
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.48
Consensus pattern (41 bp):
ATTATGTAAGCTATGTAAGTTGTATATTATGTAAGTTATGT
Found at i:41828848 original size:25 final size:25
Alignment explanation
Indices: 41828820--41828875 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
41828810 AGTTGTATTT
*
41828820 TATGTAAGTTATTTAGTATGTAAGC
1 TATGTAAGTTATGTAGTATGTAAGC
* *
41828845 TATGTAAGTTGTGTATTATGTAAGC
1 TATGTAAGTTATGTAGTATGTAAGC
41828870 TATGTA
1 TATGTA
41828876 TTATGTTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (25 bp):
TATGTAAGTTATGTAGTATGTAAGC
Found at i:41828888 original size:25 final size:25
Alignment explanation
Indices: 41828828--41828918 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 25
41828818 TTTATGTAAG
41828828 TTAT-TTAG-TATGTAAGCTATGTAA
1 TTATGTTAGTTATGTAAGCTATGT-A
*
41828852 GT-TGTGTA-TTATGTAAGCTATGTA
1 TTATGT-TAGTTATGTAAGCTATGTA
** * *
41828876 TTATGTTAGTTATGTCGGTTATATA
1 TTATGTTAGTTATGTAAGCTATGTA
41828901 TTATG-TATGTTATGTAAG
1 TTATGTTA-GTTATGTAAG
41828919 TTGTTCAGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
23 1 0.02
24 8 0.15
25 44 0.83
ACGTcount: A:0.27, C:0.03, G:0.21, T:0.48
Consensus pattern (25 bp):
TTATGTTAGTTATGTAAGCTATGTA
Found at i:41829015 original size:16 final size:16
Alignment explanation
Indices: 41828994--41829076 Score: 76
Period size: 16 Copynumber: 4.9 Consensus size: 16
41828984 GTATTAAGCT
41828994 ATGTAAGTTGTGAATA
1 ATGTAAGTTGTGAATA
* *
41829010 ATGTAAGTTATGAAAGTT
1 ATGTAAGTTGTG-AA-TA
* *
41829028 ATGTATTAAGTTGTGTATT
1 ATG---TAAGTTGTGAATA
41829047 ATGTAAGTTGTGAATA
1 ATGTAAGTTGTGAATA
*
41829063 ATGTAAGTTATGAA
1 ATGTAAGTTGTGAA
41829077 CGTTATGTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
16 35 0.64
17 2 0.04
18 4 0.07
19 5 0.09
20 1 0.02
21 8 0.15
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (16 bp):
ATGTAAGTTGTGAATA
Found at i:41829241 original size:37 final size:36
Alignment explanation
Indices: 41829200--41829324 Score: 127
Period size: 37 Copynumber: 3.5 Consensus size: 36
41829190 TAGAAACTGA
41829200 TATGTAATTAGAAATTGTATCTTAATATTATATAAGT
1 TATGTAATTAGAAATT-TATCTTAATATTATATAAGT
*
41829237 TATGTAATGAG-AA---A--TTAATATTATATAAGT
1 TATGTAATTAGAAATTTATCTTAATATTATATAAGT
* *
41829267 TATGTAATTCGAAATTTTATCTTAATATTGTATAAGT
1 TATGTAATTAGAAA-TTTATCTTAATATTATATAAGT
* *
41829304 TATCTAAATATATAAATTTAT
1 TATGT-AAT-TAGAAATTTAT
41829325 GTGTACTTAG
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
30 25 0.35
31 2 0.03
32 1 0.01
35 1 0.01
36 2 0.03
37 29 0.40
38 8 0.11
39 4 0.06
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (36 bp):
TATGTAATTAGAAATTTATCTTAATATTATATAAGT
Found at i:41829376 original size:94 final size:94
Alignment explanation
Indices: 41829251--41829457 Score: 258
Period size: 94 Copynumber: 2.2 Consensus size: 94
41829241 TAATGAGAAA
* * * ** *
41829251 TTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTATAAGTTATCTAAATA-T
1 TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATCTAAATATT
* *
41829315 ATA-AATTTATGTGTACTTAGAAATTACAAT-
66 ATAGAAGTTA--TGTAATTAGAAATT-CAATC
* *
41829345 TTAACATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATCTTAATATT
1 TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATCTAAATATT
**
41829410 ATAGAAGTTATGTAATTAGAAATTTTATC
66 ATAGAAGTTATGTAATTAGAAATTCAATC
41829439 TTAATATTATATAAGTTAT
1 TTAATATTATATAAGTTAT
41829458 CTTAATATTT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
93 2 0.02
94 86 0.89
95 4 0.04
96 5 0.05
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (94 bp):
TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATCTAAATATT
ATAGAAGTTATGTAATTAGAAATTCAATC
Found at i:41829420 original size:20 final size:20
Alignment explanation
Indices: 41829379--41829546 Score: 127
Period size: 20 Copynumber: 8.7 Consensus size: 20
41829369 TCCAAATTTA
* * *
41829379 ATCTTAAAATAATATAACTT
1 ATCTTAATATTATATAAGTT
*
41829399 ATCTTAATATTATAGAAGTT
1 ATCTTAATATTATATAAGTT
* * *
41829419 AT-GT-A-ATTAGA-AATTTT
1 ATCTTAATATTATATAA-GTT
41829436 ATCTTAATATTATATAAGTT
1 ATCTTAATATTATATAAGTT
41829456 ATCTTAATATTTATATAAGTT
1 ATCTTAATA-TTATATAAGTT
* * *
41829477 AT-AT-A-ATTAGA-AATTTT
1 ATCTTAATATTATATAA-GTT
* * *
41829494 GTCTTAATACTATATAAGTA
1 ATCTTAATATTATATAAGTT
41829514 ATCTTAATATTATATAAGTT
1 ATCTTAATATTATATAAGTT
*
41829534 ATCTTAATTTTAT
1 ATCTTAATATTAT
41829547 GTTATTTCCA
Statistics
Matches: 114, Mismatches: 23, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
16 4 0.04
17 16 0.14
18 4 0.04
19 4 0.04
20 69 0.61
21 17 0.15
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (20 bp):
ATCTTAATATTATATAAGTT
Found at i:41829493 original size:58 final size:57
Alignment explanation
Indices: 41829345--41829535 Score: 265
Period size: 57 Copynumber: 3.3 Consensus size: 57
41829335 AAATTACAAT
* ** * * * *
41829345 TTAACATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATC
1 TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
*
41829402 TTAATATTATAGAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
1 TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
* * * *
41829459 TTAATATTTATATAAGTTATATAATTAGAAATTTTGTCTTAATACTATATAAGTAATC
1 TTAATA-TTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
41829517 TTAATATTATATAAGTTAT
1 TTAATATTATATAAGTTAT
41829536 CTTAATTTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
57 68 0.57
58 52 0.43
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (57 bp):
TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
Found at i:41831421 original size:18 final size:18
Alignment explanation
Indices: 41831380--41831428 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
41831370 ATATAGTTAC
41831380 TGAAAAAT-TTAAATACT
1 TGAAAAATATTAAATACT
41831397 T-AGAAAATATTAAA-ACAT
1 TGA-AAAATATTAAATAC-T
41831415 TGAAAAAGTATTAA
1 TGAAAAA-TATTAA
41831429 CGAATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 8 0.30
18 11 0.41
19 7 0.26
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (18 bp):
TGAAAAATATTAAATACT
Found at i:41835020 original size:28 final size:28
Alignment explanation
Indices: 41834938--41835115 Score: 225
Period size: 28 Copynumber: 6.4 Consensus size: 28
41834928 GAGATTGGCG
* * * *
41834938 CTAAGTGTGCGGGTTTAAATTGTGCAGCA
1 CTAAGTGTGCGAGTTT-GATTATGTAGCA
* *
41834967 CTAAGTGTGCGA-ATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
41834994 CTAAGTGTGCGAGTTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
41835022 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
41835050 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
41835078 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
* *
41835105 CTGAGTCTGCG
1 CTAAGTGTGCG
41835116 GACTTATTAT
Statistics
Matches: 135, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
27 43 0.32
28 81 0.60
29 11 0.08
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:41837485 original size:228 final size:228
Alignment explanation
Indices: 41837092--41837509 Score: 504
Period size: 228 Copynumber: 1.8 Consensus size: 228
41837082 GTGAAGCCGA
* * * * *
41837092 AACGATTCGTTTTGGTCAAAATTTTTGCGGTGCTTAAGCAGAAGCGCCACTAAAAGCTAATATAT
1 AACGATGCGTTTTGGTCAAAATATTTGCGGCGATTAAGCAGAAGCGACACTAAAAGCTAATATAT
* * *
41837157 AGCGGTGTTTACGGGTACGCGCCACTAAAGGCACTATAGCTCAAGACGAAACGTTGCGTTTCGAT
66 AGCGGCGTTTACGGCTAAGCGCCACTAAAGGCACTATAGCTCAAGACGAAACGTTGCGTTTCGAT
* * ** * * *
41837222 TTAAAATTTTTCAGTGTTTTTTAGTTAAACGCCGCTATTTA-TGGGATATAGCGGCGTTTTTAGG
131 TTAAAATGTTCCAGCATTTTTCAGTTAAACGCCGCTA-ATAGCGGGATATAGCGGCGTTTTTAGG
41837286 TAAGCGCCACTAATGCCTTTATACGTCAAACCCG
195 TAAGCGCCACTAATGCCTTTATACGTCAAACCCG
* * * *
41837320 AACGATGCGTTTTGTTCAAAATATTTGCGGCGATTCAGGA-ATAGCGACACTAAAAGCTGATATA
1 AACGATGCGTTTTGGTCAAAATATTTGCGGCGATTAAGCAGA-AGCGACACTAAAAGCTAATATA
** * *
41837384 TAGCGGCGTTTTTGGCTAAGCGCCGCTAAAGGCTCTATAGCTCAAGACGAAAC-TCTGCGTTTCG
65 TAGCGGCGTTTACGGCTAAGCGCCACTAAAGGCACTATAGCTCAAGACGAAACGT-TGCGTTTCG
* * ** *
41837448 GTTTCAAAA-GTTCC-GACATTTTTCGGTTACGCGCCGCTAATAGCGGGCTATAGCGGCGTTTT
129 ATTT-AAAATGTTCCAG-CATTTTTCAGTTAAACGCCGCTAATAGCGGGATATAGCGGCGTTTT
41837510 CCACAAGCGC
Statistics
Matches: 157, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
227 5 0.03
228 148 0.94
229 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (228 bp):
AACGATGCGTTTTGGTCAAAATATTTGCGGCGATTAAGCAGAAGCGACACTAAAAGCTAATATAT
AGCGGCGTTTACGGCTAAGCGCCACTAAAGGCACTATAGCTCAAGACGAAACGTTGCGTTTCGAT
TTAAAATGTTCCAGCATTTTTCAGTTAAACGCCGCTAATAGCGGGATATAGCGGCGTTTTTAGGT
AAGCGCCACTAATGCCTTTATACGTCAAACCCG
Found at i:41839659 original size:38 final size:38
Alignment explanation
Indices: 41839592--41839690 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
41839582 CAAGTGTTTC
*
41839592 AAAATATTT--AATAAA-TTAGAAATATGATTAAAAAT
1 AAAATATTTACAATAAATTTAGAAAGATGATTAAAAAT
41839627 AAAATATTTACAATAAATTTAGAAACGA-GATTAAAAAT
1 AAAATATTTACAATAAATTTAGAAA-GATGATTAAAAAT
*
41839665 AAAATA-TCAGCAAATAAATTTAGAAA
1 AAAATATTTA-C-AATAAATTTAGAAA
41839691 TGATATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
35 9 0.16
37 8 0.14
38 24 0.43
39 15 0.27
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (38 bp):
AAAATATTTACAATAAATTTAGAAAGATGATTAAAAAT
Found at i:41842468 original size:15 final size:15
Alignment explanation
Indices: 41842448--41842477 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41842438 ATGTAGGAGG
*
41842448 GATAAATCATATCCT
1 GATAAATCAAATCCT
41842463 GATAAATCAAATCCT
1 GATAAATCAAATCCT
41842478 ACTACATGGA
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:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (15 bp):
GATAAATCAAATCCT
Found at i:41855771 original size:31 final size:29
Alignment explanation
Indices: 41855736--41855811 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
41855726 TAATGGCTCG
*
41855736 GTGACTAAAATGTTACAATACAATAACATAA
1 GTGACTAAAATGTAAC-ATACAA-AACATAA
* * * *
41855767 GTGACTAAAACGTAACATTCCAAATATAA
1 GTGACTAAAATGTAACATACAAAACATAA
41855796 GTGACTAAAATGTAAC
1 GTGACTAAAATGTAAC
41855812 CTGAGGTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.54
30 4 0.10
31 14 0.36
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (29 bp):
GTGACTAAAATGTAACATACAAAACATAA
Found at i:41858762 original size:14 final size:15
Alignment explanation
Indices: 41858739--41858771 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
41858729 ACTCTAGAAA
41858739 TTTT-AAAAAAT-AT
1 TTTTAAAAAAATCAT
41858752 TTTTAAAAAAATCAT
1 TTTTAAAAAAATCAT
41858767 TTTTA
1 TTTTA
41858772 GCCATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 7 0.39
15 7 0.39
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAAAAAATCAT
Found at i:41865878 original size:22 final size:22
Alignment explanation
Indices: 41865850--41865893 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41865840 CAGGTGACAT
41865850 GATATCCACTCCTTTGTGTCGC
1 GATATCCACTCCTTTGTGTCGC
41865872 GATATCCACTCCTTTGTGTCGC
1 GATATCCACTCCTTTGTGTCGC
41865894 AACACCCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.36
Consensus pattern (22 bp):
GATATCCACTCCTTTGTGTCGC
Found at i:41865902 original size:22 final size:22
Alignment explanation
Indices: 41865855--41865902 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
41865845 GACATGATAT
* * *
41865855 CCACTCCTTTGTGTCGCGATAT
1 CCACTCCTTTGTGTCGCAACAC
41865877 CCACTCCTTTGTGTCGCAACAC
1 CCACTCCTTTGTGTCGCAACAC
41865899 CCAC
1 CCAC
41865903 GACAATTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.40, G:0.15, T:0.29
Consensus pattern (22 bp):
CCACTCCTTTGTGTCGCAACAC
Found at i:41867122 original size:26 final size:26
Alignment explanation
Indices: 41867036--41867202 Score: 172
Period size: 26 Copynumber: 6.3 Consensus size: 26
41867026 TTATGGTTTT
* * *
41867036 CCACAAAGGCTTTCAATTCATTTTATG
1 CCACAAAGGCTTTC-TTTCATATTACG
* * *
41867063 CCACAAAGGCTACTCTTTCATATTGCA
1 CCACAAAGGCT-TTCTTTCATATTACG
* * *
41867090 CCTCAAAGGCATTCTTTCATGTTACG
1 CCACAAAGGCTTTCTTTCATATTACG
* *
41867116 CCACAAAGGCTTTGTTTCATATTACA
1 CCACAAAGGCTTTCTTTCATATTACG
*
41867142 CCACAAAGGCTTTCTTTCATACTACG
1 CCACAAAGGCTTTCTTTCATATTACG
* * *
41867168 CCACAAAGGCTTCCTTTCATACTACA
1 CCACAAAGGCTTTCTTTCATATTACG
*
41867194 CGACAAAGG
1 CCACAAAGG
41867203 TTTTTCCTTA
Statistics
Matches: 116, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
26 87 0.75
27 27 0.23
28 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (26 bp):
CCACAAAGGCTTTCTTTCATATTACG
Found at i:41867157 original size:52 final size:52
Alignment explanation
Indices: 41867036--41867202 Score: 199
Period size: 52 Copynumber: 3.2 Consensus size: 52
41867026 TTATGGTTTT
* * * * *
41867036 CCACAAAGGCTTTCAATTCATTTTATGCCACAAAGGCTACTCTTTCATATTGCA
1 CCACAAAGGCTTTC-TTTCATATTACGCCACAAAGGCT-TTCTTTCATATTACA
* * * *
41867090 CCTCAAAGGCATTCTTTCATGTTACGCCACAAAGGCTTTGTTTCATATTACA
1 CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCATATTACA
* * *
41867142 CCACAAAGGCTTTCTTTCATACTACGCCACAAAGGCTTCCTTTCATACTACA
1 CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCATATTACA
*
41867194 CGACAAAGG
1 CCACAAAGG
41867203 TTTTTCCTTA
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
52 65 0.67
53 20 0.21
54 12 0.12
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (52 bp):
CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCATATTACA
Found at i:41871575 original size:21 final size:21
Alignment explanation
Indices: 41871540--41871594 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
41871530 CATGGTTTGC
* *
41871540 TCACATGGTCATGTGACCC-A
1 TCACACGGCCATGTGACCCAA
41871560 TCTACACGGCCATGTGACCCAA
1 TC-ACACGGCCATGTGACCCAA
*
41871582 TCACATGGCCATG
1 TCACACGGCCATG
41871595 GGGCCTATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.83
22 3 0.10
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (21 bp):
TCACACGGCCATGTGACCCAA
Found at i:41874710 original size:57 final size:57
Alignment explanation
Indices: 41874628--41874761 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 57
41874618 ACAGAGTCTC
* * * * * * *
41874628 GCCACAAAAGC-ATCATTTAAGAGGTTTGCCACGAAGGCTTAGCC-TTCTAGAGTTTT
1 GCCACAAAGGCTATCATTTAACAGGTTCGCCACAAAGGCTT-GCCTTTATACAGTTCT
41874684 GCCACAAAGGCTATCATTTAACAGGTTCGCCACAAAGGCTTGCCTTTATACAGTTCT
1 GCCACAAAGGCTATCATTTAACAGGTTCGCCACAAAGGCTTGCCTTTATACAGTTCT
* * *
41874741 GGCACAAAGACTGTCATTTAA
1 GCCACAAAGGCTATCATTTAA
41874762 TAGTTGTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
56 13 0.20
57 53 0.80
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (57 bp):
GCCACAAAGGCTATCATTTAACAGGTTCGCCACAAAGGCTTGCCTTTATACAGTTCT
Found at i:41874717 original size:28 final size:28
Alignment explanation
Indices: 41874626--41874723 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
41874616 TTACAGAGTC
*
41874626 TCGCCACAAAAGC-ATCATTTAAGAGGT
1 TCGCCACAAAGGCTATCATTTAAGAGGT
* * * * *
41874653 TTGCCACGAAGGCTTAGCCTTCT-AGAGTT
1 TCGCCACAAAGGC-TATCATT-TAAGAGGT
* *
41874682 TTGCCACAAAGGCTATCATTTAACAGGT
1 TCGCCACAAAGGCTATCATTTAAGAGGT
41874710 TCGCCACAAAGGCT
1 TCGCCACAAAGGCT
41874724 TGCCTTTATA
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
27 11 0.20
28 22 0.40
29 21 0.38
30 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (28 bp):
TCGCCACAAAGGCTATCATTTAAGAGGT
Found at i:41874760 original size:29 final size:27
Alignment explanation
Indices: 41874626--41874761 Score: 78
Period size: 29 Copynumber: 4.8 Consensus size: 27
41874616 TTACAGAGTC
* * *
41874626 TCGCCACAAAAGCATCATTTAAGAGGT
1 TCGCCACAAAGGCTTCATTTAACAGGT
* * * * *
41874653 TTGCCACGAAGGCTTAGCCTTCT-AGAGTT
1 TCGCCACAAAGGCTT--CATT-TAACAGGT
*
41874682 TTGCCACAAAGGCTATCATTTAACAGGT
1 TCGCCACAAAGGCT-TCATTTAACAGGT
*
41874710 TCGCCACAAAGGCTTGCCTTTATACA-GT
1 TCGCCACAAAGGCTT-CATTTA-ACAGGT
* *
41874738 TCTGGCACAAAGACTGTCATTTAA
1 TC-GCCACAAAGGCT-TCATTTAA
41874762 TAGTTGTTTT
Statistics
Matches: 85, Mismatches: 15, Indels: 17
0.73 0.13 0.15
Matches are distributed among these distances:
27 13 0.15
28 30 0.35
29 39 0.46
30 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (27 bp):
TCGCCACAAAGGCTTCATTTAACAGGT
Found at i:41893157 original size:26 final size:26
Alignment explanation
Indices: 41893074--41893296 Score: 259
Period size: 26 Copynumber: 8.5 Consensus size: 26
41893064 TCATGGTTTT
* * *
41893074 CCACAAAGCCTTTCAATTCATTTTACG
1 CCACAAAGGCTTTC-TTTCATATTACG
* * * *
41893101 CCACAAACGTTGTTCTTTCATATTGCA
1 CCACAAAGGCT-TTCTTTCATATTACG
41893128 CCACAAAGGCTTTCATTT-ATATTACG
1 CCACAAAGGCTTTC-TTTCATATTACG
** *
41893154 CCACAAAGTTTTTCTTTCATACTACG
1 CCACAAAGGCTTTCTTTCATATTACG
* *
41893180 CCACAAAGGCTTTCTTCCATATTACA
1 CCACAAAGGCTTTCTTTCATATTACG
* *
41893206 CCACAAAGGCTTTTTTTCATACTACG
1 CCACAAAGGCTTTCTTTCATATTACG
* *
41893232 ACACAAAGGTTTTCTTTCATATTACG
1 CCACAAAGGCTTTCTTTCATATTACG
*
41893258 CCACAAAGGCTTCCTTTCATATTACG
1 CCACAAAGGCTTTCTTTCATATTACG
41893284 CCACAAAGGCTTT
1 CCACAAAGGCTTT
41893297 TCATTATTTT
Statistics
Matches: 162, Mismatches: 31, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
25 3 0.02
26 128 0.79
27 28 0.17
28 3 0.02
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (26 bp):
CCACAAAGGCTTTCTTTCATATTACG
Found at i:41893706 original size:26 final size:25
Alignment explanation
Indices: 41893655--41893923 Score: 252
Period size: 26 Copynumber: 10.3 Consensus size: 25
41893645 GTTTTCAACG
* *
41893655 AAGGCTTTCAATTCATTTTACTCCACA
1 AAGGCTTTC--TTCATATTACGCCACA
41893682 AAGGCTTTAGCTT-ATATTACGCCACA
1 AAGGCTTT--CTTCATATTACGCCACA
* *
41893708 AAGGCTTTCTTTCATACTATGCCACA
1 AAGGCTTTC-TTCATATTACGCCACA
*
41893734 AAAGCTTTCTTCCATATTACGCCACA
1 AAGGCTTTCTT-CATATTACGCCACA
* * *
41893760 AAGGCTTTCTTCCATACTACACCATA
1 AAGGCTTTCTT-CATATTACGCCACA
* * * *
41893786 AAGGCTTTTGTTCACACTACGCCATA
1 AAGGC-TTTCTTCATATTACGCCACA
* * *
41893812 AATGCTTTCTTCCATATTATGCCATA
1 AAGGCTTTCTT-CATATTACGCCACA
*
41893838 AAGGCTTTCTTCCATACTACGCCACA
1 AAGGCTTTCTT-CATATTACGCCACA
*
41893864 AAGGCTTTCTTTCATATTACGTCACA
1 AAGGCTTTC-TTCATATTACGCCACA
* *
41893890 AAGGTTTTCTTTCATATTACGCTACA
1 AAGGCTTTC-TTCATATTACGCCACA
41893916 AAGGCTTT
1 AAGGCTTT
41893924 TCATTATTTG
Statistics
Matches: 205, Mismatches: 29, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
24 1 0.00
25 9 0.04
26 177 0.86
27 17 0.08
29 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (25 bp):
AAGGCTTTCTTCATATTACGCCACA
Found at i:41893709 original size:575 final size:576
Alignment explanation
Indices: 41892765--41893871 Score: 1591
Period size: 575 Copynumber: 1.9 Consensus size: 576
41892755 AAAGGCTATT
* * *
41892765 CTTATGTGGGGTTTTCCCATCATCGTATGAGACACGCAAAAAAACCTCTTTAGGTAATAACCTTC
1 CTTATGTGAGGTTTTCCCATCATCGCATGAGACACACAAAAAAACCTCTTTAGGTAATAACCTTC
* * *
41892830 CTTTAAGTTCCTTTAAAGAGTTCCATGGCCATGGACTTTTCCTTTTAGAATTCATGTTTAAATTC
66 CTTTAAGTTCCTTTAAAGAGTGCCATGGCCATGGACTTTTCCTTTCAGAATTCATGTTTAAAGTC
** * *
41892895 CCGATCGACCTCTGTTGACAATACACCAAATAAATTGATATAGAATCCGCCACAAAGGATATCTT
131 CCGAAAGACCTCTGTTGACAATACACCAAATAAATTGATATAGAACCCGCCAAAAAGGATATCTT
* * * * *
41892960 TTACAGTACACCATTAAGATTCTTATCATTACACATCAAGAGCATCTCCTTTTAGAGATAGCCAT
196 TTACAATACACCATTAAGATTCTTATCATTACACACCAAGAACATCTCCTTTCAGAGATAGCCAC
* *
41893025 AAAAGCTTTCATCTTGTGATTTACTACAAAGACTTTTTTTCATGGTTTTCCACAAAGCCTTTCAA
261 AAAAGCTTTCATCTTGTGATTTACCACAAAGACTTTTTTTCATGGTTTTCAACAAAGCCTTTCAA
* * *
41893090 TTCATTTTACGCCACAAACGTTGTTCTTTCATATTGCACCACAAAGGCTTTCATTT-ATATTACG
326 TTCATTTTACGCCACAAACGTTGTGCTTTCATATTACACCACAAAGGCTTTC-TTTCATACTACG
* * *
41893154 CCAC-AAAGTTTTTCTTTCATACTACGCCACAAAGGCTTTCTTCCATATTACACCACAAAGGCTT
390 CCACAAAAG-CTTTCTTCCATACTACGCCACAAAGGCTTTCTTCCATACTACACCACAAAGGCTT
* * * * * *
41893218 TTTTTCATACTACGACACAAAGGTTTTCTTTCATATTACGCCACAAAGGCTTCCTTTCATATTAC
454 TTGTTCACACTACGACACAAAGGCTTTCTTCCATATTACGCCACAAAGGCTTCCTTCCATACTAC
41893283 GCCACAAAGGCTTTTCATTATTTTTCGTGTTTTTCTGATATTGATTTTCCTAAACTCA
519 GCCACAAAGGCTTTTCATTATTTTTCGTGTTTTTCTGATATTGATTTTCCTAAACTCA
* *
41893341 CTTATGTGAGGTTTTCCCATCATCGCATGGGACACACAAAAAAACC-CTTTGGGTAATAACCTTC
1 CTTATGTGAGGTTTTCCCATCATCGCATGAGACACACAAAAAAACCTCTTTAGGTAATAACCTTC
* * **
41893405 TTTTAAGTTGCTTTAAAGAGTGCCATGGCCATGGACTTTTCCTTTCAGAATTTGTGTTTAAAGTC
66 CTTTAAGTTCCTTTAAAGAGTGCCATGGCCATGGACTTTTCCTTTCAGAATTCATGTTTAAAGTC
* *
41893470 CCGAAAGACCTCTTTTGACAATGCACCAAA-AAATTTGATATAGAACCCGCCAAAAAGGATATCT
131 CCGAAAGACCTCTGTTGACAATACACCAAATAAA-TTGATATAGAACCCGCCAAAAAGGATATCT
* ** *
41893534 TTTATAATATGCCATTAAGATTCTTATCATTACACGCCAAGAACATCTCCTTTCAGAGACT-GCC
195 TTTACAATACACCATTAAGATTCTTATCATTACACACCAAGAACATCTCCTTTCAGAGA-TAGCC
* * *
41893598 ACAAAAGCTTTCATCTTGTGATTTACCACAAAGGCTTTTTTTTCATGGTTTTCAACGAAGGCTTT
259 ACAAAAGCTTTCATCTTGTGATTTACCACAAAGAC-TTTTTTTCATGGTTTTCAACAAAGCCTTT
* * *
41893663 CAATTCATTTTACTCCACAAAGGCTT-TAGC-TT-ATATTACGCCACAAAGGCTTTCTTTCATAC
323 CAATTCATTTTACGCCACAAACG-TTGT-GCTTTCATATTACACCACAAAGGCTTTCTTTCATAC
* * *
41893725 TATGCCACAAAAGCTTTCTTCCATATTACGCCACAAAGGCTTTCTTCCATACTACACCATAAAGG
386 TACGCCACAAAAGCTTTCTTCCATACTACGCCACAAAGGCTTTCTTCCATACTACACCACAAAGG
* * * * * *
41893790 CTTTTGTTCACACTACGCCATAAATGCTTTCTTCCATATTATGCCATAAAGGCTTTCTTCCATAC
451 CTTTTGTTCACACTACGACACAAAGGCTTTCTTCCATATTACGCCACAAAGGCTTCCTTCCATAC
41893855 TACGCCACAAAGGCTTT
516 TACGCCACAAAGGCTTT
41893872 CTTTCATATT
Statistics
Matches: 468, Mismatches: 56, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
574 6 0.01
575 362 0.77
576 97 0.21
577 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (576 bp):
CTTATGTGAGGTTTTCCCATCATCGCATGAGACACACAAAAAAACCTCTTTAGGTAATAACCTTC
CTTTAAGTTCCTTTAAAGAGTGCCATGGCCATGGACTTTTCCTTTCAGAATTCATGTTTAAAGTC
CCGAAAGACCTCTGTTGACAATACACCAAATAAATTGATATAGAACCCGCCAAAAAGGATATCTT
TTACAATACACCATTAAGATTCTTATCATTACACACCAAGAACATCTCCTTTCAGAGATAGCCAC
AAAAGCTTTCATCTTGTGATTTACCACAAAGACTTTTTTTCATGGTTTTCAACAAAGCCTTTCAA
TTCATTTTACGCCACAAACGTTGTGCTTTCATATTACACCACAAAGGCTTTCTTTCATACTACGC
CACAAAAGCTTTCTTCCATACTACGCCACAAAGGCTTTCTTCCATACTACACCACAAAGGCTTTT
GTTCACACTACGACACAAAGGCTTTCTTCCATATTACGCCACAAAGGCTTCCTTCCATACTACGC
CACAAAGGCTTTTCATTATTTTTCGTGTTTTTCTGATATTGATTTTCCTAAACTCA
Found at i:41893767 original size:78 final size:77
Alignment explanation
Indices: 41893672--41893923 Score: 301
Period size: 78 Copynumber: 3.2 Consensus size: 77
41893662 TCAATTCATT
* * *
41893672 TTACTCCACAAAGGCTTTAGCTT-ATATTACGCCACAAAGGCTTTCTTTCATACTATGCCACAAA
1 TTACGCCACAAAGGCTTT--CTTCATACTACGCCACAAAGGCTTTCTTTCATACTACGCCACAAA
41893736 AGCTTTCTTCCATA
64 AGCTTTCTTCCATA
* * * *
41893750 TTACGCCACAAAGGCTTTCTTCCATACTACACCATAAAGGCTTT-TGTTCACACTACGCCATAAA
1 TTACGCCACAAAGGCTTTCTT-CATACTACGCCACAAAGGCTTTCT-TTCATACTACGCCACAAA
*
41893814 TGCTTTCTTCCATA
64 AGCTTTCTTCCATA
* * * * *
41893828 TTATGCCATAAAGGCTTTCTTCCATACTACGCCACAAAGGCTTTCTTTCATATTACGTCACAAAG
1 TTACGCCACAAAGGCTTTCTT-CATACTACGCCACAAAGGCTTTCTTTCATACTACGCCACAAAA
* *
41893893 GTTTTCTTTCATA
65 GCTTTCTTCCATA
*
41893906 TTACGCTACAAAGGCTTT
1 TTACGCCACAAAGGCTTT
41893924 TCATTATTTG
Statistics
Matches: 148, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
76 3 0.02
77 1 0.01
78 143 0.97
79 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (77 bp):
TTACGCCACAAAGGCTTTCTTCATACTACGCCACAAAGGCTTTCTTTCATACTACGCCACAAAAG
CTTTCTTCCATA
Found at i:41900224 original size:21 final size:21
Alignment explanation
Indices: 41900195--41900234 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
41900185 AAATTAAGTA
41900195 TTTTCATTAAGATTTAGTTATG
1 TTTTCATTAAG-TTTAGTTATG
*
41900217 TTTT-ATTAAGTTTTGTTA
1 TTTTCATTAAGTTTAGTTA
41900235 AATCCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.60
Consensus pattern (21 bp):
TTTTCATTAAGTTTAGTTATG
Found at i:41903390 original size:27 final size:27
Alignment explanation
Indices: 41903360--41903537 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41903350 ATATTGAGTC
* * * *
41903360 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41903387 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41903414 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41903442 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41903469 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41903496 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41903523 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41903538 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41903499 original size:82 final size:81
Alignment explanation
Indices: 41903381--41903536 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41903371 TGCTATATAA
* *
41903381 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41903446 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41903463 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41903527 CACTTAGTGC
65 CACTTAGTGC
41903537 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41904032 original size:12 final size:12
Alignment explanation
Indices: 41904015--41904040 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41904005 ATGGCATACT
41904015 TATGTATATATA
1 TATGTATATATA
41904027 TATGTATATATA
1 TATGTATATATA
41904039 TA
1 TA
41904041 CTTCGGAATG
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:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:41911482 original size:27 final size:27
Alignment explanation
Indices: 41911452--41911629 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41911442 ATATTGAGTC
* * * *
41911452 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41911479 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41911506 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41911534 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41911561 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41911588 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41911615 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41911630 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41911591 original size:82 final size:81
Alignment explanation
Indices: 41911473--41911628 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41911463 TGCTATATAA
* *
41911473 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41911538 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41911555 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41911619 CACTTAGTGC
65 CACTTAGTGC
41911629 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41912122 original size:12 final size:12
Alignment explanation
Indices: 41912105--41912130 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41912095 ATGGCATACT
41912105 TATGTATATATA
1 TATGTATATATA
41912117 TATGTATATATA
1 TATGTATATATA
41912129 TA
1 TA
41912131 CTTCGGAATG
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:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:41914339 original size:26 final size:26
Alignment explanation
Indices: 41914289--41914344 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
41914279 ATATATGGTC
*
41914289 ACACGAGCTGTGAAATGAGTATGCTT
1 ACACGAGCTGTGAAATGAGCATGCTT
* *
41914315 ACACGAGCTGTGAAATGGGCCTGCTT
1 ACACGAGCTGTGAAATGAGCATGCTT
41914341 ACAC
1 ACAC
41914345 AAGCAGTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (26 bp):
ACACGAGCTGTGAAATGAGCATGCTT
Found at i:41921643 original size:21 final size:20
Alignment explanation
Indices: 41921614--41921654 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
41921604 ACACCAAAAC
*
41921614 AGGCTTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCG-TTTTT
41921635 AGGCCTTTAGCGGCGTTTTT
1 AGGCCTTTAGCGGCGTTTTT
41921655 CCCACGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.10, C:0.20, G:0.29, T:0.41
Consensus pattern (20 bp):
AGGCCTTTAGCGGCGTTTTT
Found at i:41921698 original size:43 final size:43
Alignment explanation
Indices: 41921638--41921791 Score: 229
Period size: 43 Copynumber: 3.6 Consensus size: 43
41921628 GCTTTTTAGG
* * * *
41921638 CCTTTAGCGGCGTTTTTCCCACGAATGCCGCTAAAGACCAAGG
1 CCTTTAGCGACGCTTTTCCCACAAATGCCGCTAAAGACCAAGA
41921681 CCTTTAGCGACGCTTTTCCCGA-AAATGCCGCTAAAGACCAAGA
1 CCTTTAGCGACGCTTTTCCC-ACAAATGCCGCTAAAGACCAAGA
* * *
41921724 CCTTTAGCGGCGCTTTTCCCAAAAATGCCGCTAAAGATCAAGA
1 CCTTTAGCGACGCTTTTCCCACAAATGCCGCTAAAGACCAAGA
41921767 CCTTTAGCGACGCTTTTCCCACAAA
1 CCTTTAGCGACGCTTTTCCCACAAA
41921792 CGCCACTGAA
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.01
43 99 0.98
44 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
CCTTTAGCGACGCTTTTCCCACAAATGCCGCTAAAGACCAAGA
Found at i:41922030 original size:35 final size:35
Alignment explanation
Indices: 41921994--41922061 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
41921984 CTATGAAAAT
41921994 TTTAACTTTA-AAACTAAATATAA-AAATTAATAAA
1 TTTAACTTTAGAAACTAAA-ATAATAAATTAATAAA
* **
41922028 TTTAATTTTAGAATTTAAAATAATAAATTAATAA
1 TTTAACTTTAGAAACTAAAATAATAAATTAATAA
41922062 CACAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (35 bp):
TTTAACTTTAGAAACTAAAATAATAAATTAATAAA
Found at i:41922205 original size:19 final size:19
Alignment explanation
Indices: 41922183--41922248 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
41922173 ACAGTAACGA
41922183 AAAATTAAACACCACACAT
1 AAAATTAAACACCACACAT
* *
41922202 AAAATTACATAGA-CAGTAACGA-
1 AAAATTA-A-ACACCA--CAC-AT
41922224 AAAATTAAACACCACACAT
1 AAAATTAAACACCACACAT
41922243 AAAATT
1 AAAATT
41922249 TATCAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
18 1 0.03
19 15 0.42
20 5 0.14
21 5 0.14
22 9 0.25
23 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAATTAAACACCACACAT
Found at i:41922218 original size:41 final size:41
Alignment explanation
Indices: 41922171--41922248 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
41922161 ATTAAAACAC
41922171 AGACAGTAACGAAAAATTAAACACCACACATAAAATTACAT
1 AGACAGTAACGAAAAATTAAACACCACACATAAAATTACAT
41922212 AGACAGTAACGAAAAATTAAACACCACACATAAAATT
1 AGACAGTAACGAAAAATTAAACACCACACATAAAATT
41922249 TATCAAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.56, C:0.19, G:0.08, T:0.17
Consensus pattern (41 bp):
AGACAGTAACGAAAAATTAAACACCACACATAAAATTACAT
Found at i:41923342 original size:68 final size:68
Alignment explanation
Indices: 41923268--41923507 Score: 462
Period size: 68 Copynumber: 3.5 Consensus size: 68
41923258 CAAGTGATTA
41923268 AAAAGTTGCACATTACCCACATCCAAGCCGATTAAAAGTTAAAAAGGATAAGCTATTAAAAGTTA
1 AAAAGTTGCACATTACCCACATCCAAGCCGATTAAAAGTTAAAAAGGATAAGCTATTAAAAGTTA
41923333 AAT
66 AAT
41923336 AAAAGTTGCACATTACCCACATCCAAGCCGATTAAAAGTTAAAAAGGATAAGCTATTAAAAGTTA
1 AAAAGTTGCACATTACCCACATCCAAGCCGATTAAAAGTTAAAAAGGATAAGCTATTAAAAGTTA
41923401 AAT
66 AAT
*
41923404 AAAAGTTGCACATTACCCACATCCAAGCCGATTAAAAGTTAAAAAGGATAAGCTCTTAAAAGTTA
1 AAAAGTTGCACATTACCCACATCCAAGCCGATTAAAAGTTAAAAAGGATAAGCTATTAAAAGTTA
41923469 AAT
66 AAT
*
41923472 AAAAGTTGCACATTACCCACATCCAAGCCAATTAAA
1 AAAAGTTGCACATTACCCACATCCAAGCCGATTAAA
41923508 TTATGCTTAA
Statistics
Matches: 170, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 170 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (68 bp):
AAAAGTTGCACATTACCCACATCCAAGCCGATTAAAAGTTAAAAAGGATAAGCTATTAAAAGTTA
AAT
Found at i:41925889 original size:21 final size:22
Alignment explanation
Indices: 41925851--41925892 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
41925841 ACCCCGAATC
*
41925851 TTTAAACCCTAAATCACTAACT
1 TTTAAACCCTAAACCACTAACT
*
41925873 TTTAACCCCT-AACCACTAAC
1 TTTAAACCCTAAACCACTAAC
41925893 CCATAAACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (22 bp):
TTTAAACCCTAAACCACTAACT
Found at i:41925981 original size:33 final size:33
Alignment explanation
Indices: 41925943--41926015 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
41925933 TAATCTAAAT
* *
41925943 CCTAAACCCTAA-CTCGACCCTGAATCCCTAATC
1 CCTAAACCCTAACCT-GACCCCGAATCCCTAACC
* **
41925976 CCTAAACTCTAACCTGACCCCGAATTTCTAACC
1 CCTAAACCCTAACCTGACCCCGAATCCCTAACC
41926009 CCTAAAC
1 CCTAAAC
41926016 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.32, C:0.41, G:0.05, T:0.22
Consensus pattern (33 bp):
CCTAAACCCTAACCTGACCCCGAATCCCTAACC
Found at i:41926088 original size:115 final size:116
Alignment explanation
Indices: 41925888--41926096 Score: 268
Period size: 115 Copynumber: 1.8 Consensus size: 116
41925878 CCCCTAACCA
* *
41925888 CTAACCCATAAACCTTATTTAATATATAAATTAAAAAATACTAATTAATCTAAATCCTAAACCCT
1 CTAACCCATAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCT
* **
41925953 AACTCGACCCTGAATCCCT-AATCCCTAAACTCTAACCTGACCCCGAATTT
66 AACTCGACCATGAAAACCTAAATCCCTAAACTCTAACCTGACCCCGAATTT
* *
41926003 CTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAA-CC-ATAA-CC
1 CTAACCCATAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTA-AACCC
41926065 TGACAC-CGAATCCAT-AAAACCTAAATCCCTAA
65 T-A-ACTCG-A-CCATGAAAACCTAAATCCCTAA
41926097 CTGATCTTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
113 4 0.05
114 7 0.09
115 58 0.72
116 12 0.15
ACGTcount: A:0.43, C:0.27, G:0.03, T:0.27
Consensus pattern (116 bp):
CTAACCCATAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCT
AACTCGACCATGAAAACCTAAATCCCTAAACTCTAACCTGACCCCGAATTT
Found at i:41927445 original size:41 final size:41
Alignment explanation
Indices: 41927388--41927623 Score: 357
Period size: 41 Copynumber: 5.8 Consensus size: 41
41927378 TTTTATTATT
41927388 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
*
41927429 ATTAGTGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
* * * * *
41927470 AGTAGCGGCGCTTCTCCAAAAACGCCACTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
* * * *
41927511 ATTAGCGGCGCTTCTCCAAAAATGCCGCTAAAGGCCGGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
* *
41927552 ATTAGCGGCGCTTTTTCATAAACGCCGCTAAAGGCCTGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
41927593 ATTAGCGGCGCTTTTTCAAAAA-GCCGCTAAA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
41927624 TGCCCCCAAA
Statistics
Matches: 178, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
40 9 0.05
41 169 0.95
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:41927787 original size:40 final size:38
Alignment explanation
Indices: 41927664--41927796 Score: 133
Period size: 40 Copynumber: 3.4 Consensus size: 38
41927654 GGGCTTAGGC
*
41927664 TTTT-GCGGCGCTTTTCAAAAAACGCCGCTAATGCTTAT
1 TTTTAGCGGCG-TTTTCAAAAAACGCCGCTAATGCTGAT
* *
41927702 TTTTAGCGGCGTTTTGCAAAAATCGCCGCTAATGCTCGAC
1 TTTTAGCGGCGTTTT-CAAAAAACGCCGCTAATGCT-GAT
* * * *
41927742 CTTTAGCGGCGTTTTTATAAAACCGCTGCTAATGCCTGAT
1 TTTTAGCGGCGTTTTCA-AAAAACGCCGCTAATG-CTGAT
* *
41927782 TTTTAGTGCCGTTTT
1 TTTTAGCGGCGTTTT
41927797 TTGTCCAAAC
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
38 8 0.10
39 26 0.33
40 43 0.54
41 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (38 bp):
TTTTAGCGGCGTTTTCAAAAAACGCCGCTAATGCTGAT
Found at i:41930312 original size:30 final size:30
Alignment explanation
Indices: 41930278--41930339 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
41930268 TTCTCAGCGG
*
41930278 ACACTTCTGACATATTAAATTAACTAACAC
1 ACACTTCCGACATATTAAATTAACTAACAC
41930308 ACACTTCCGACATATTAAATTAACTAACAC
1 ACACTTCCGACATATTAAATTAACTAACAC
41930338 AC
1 AC
41930340 TCTAACCCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.27
Consensus pattern (30 bp):
ACACTTCCGACATATTAAATTAACTAACAC
Found at i:41937244 original size:5 final size:5
Alignment explanation
Indices: 41937234--41937260 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41937224 GAGTCTGTAA
41937234 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
41937261 ATATGGACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:41938697 original size:20 final size:20
Alignment explanation
Indices: 41938672--41938732 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41938662 TTGTACGAGA
41938672 TTGCACTTCGATGCCTCTGT
1 TTGCACTTCGATGCCTCTGT
*
41938692 TTGCACTTC-AGTGCCTTTGT
1 TTGCACTTCGA-TGCCTCTGT
* *
41938712 TTGCACTTCGTTGTCTCTGT
1 TTGCACTTCGATGCCTCTGT
41938732 T
1 T
41938733 AGCATCCCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.08, C:0.26, G:0.20, T:0.46
Consensus pattern (20 bp):
TTGCACTTCGATGCCTCTGT
Found at i:41942484 original size:5 final size:5
Alignment explanation
Indices: 41942474--41942498 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41942464 CTATTTAATT
41942474 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
41942499 TCCCTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:41945560 original size:16 final size:16
Alignment explanation
Indices: 41945536--41945571 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41945526 GAAATATTTA
*
41945536 TTTTAATTTTTTATAT
1 TTTTAATTTATTATAT
*
41945552 TTTTGATTTATTATAT
1 TTTTAATTTATTATAT
41945568 TTTT
1 TTTT
41945572 TAAAAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTAATTTATTATAT
Found at i:41946118 original size:16 final size:17
Alignment explanation
Indices: 41946099--41946131 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41946089 GAAAAAAAGT
*
41946099 AAATTAATTAAA-ATAA
1 AAATTAAATAAACATAA
41946115 AAATTAAATAAACATAA
1 AAATTAAATAAACATAA
41946132 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATTAAATAAACATAA
Found at i:41960157 original size:16 final size:16
Alignment explanation
Indices: 41960136--41960166 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41960126 ATTGTGTTGA
*
41960136 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
41960152 GAAAATTAATTAATT
1 GAAAATTAATTAATT
41960167 TAAACTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:41969664 original size:19 final size:19
Alignment explanation
Indices: 41969631--41969670 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41969621 AAAATATCAT
*
41969631 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
41969650 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
41969669 AT
1 AT
41969671 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:41977799 original size:26 final size:26
Alignment explanation
Indices: 41977753--41977828 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
41977743 AAGAATTTTC
* **
41977753 TCAAAATTTTACTAGAAGTAAAATCG
1 TCAAAATTTTACTGGGGGTAAAATCG
* * *
41977779 TTAAAATTTTATTGGGGGTAAAGTCG
1 TCAAAATTTTACTGGGGGTAAAATCG
*
41977805 TCAAACTTTTACTGGGGGTAAAAT
1 TCAAAATTTTACTGGGGGTAAAAT
41977829 TGAGATAAGA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTACTGGGGGTAAAATCG
Found at i:41980426 original size:20 final size:19
Alignment explanation
Indices: 41980401--41980475 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
41980391 GAAATGTAAT
41980401 CAAAGACACCAATGTGCAAA
1 CAAAGACACCAA-GTGCAAA
* *
41980421 CAAAGACACTGAAGTGCATA
1 CAAAGACAC-CAAGTGCAAA
** *
41980441 CAGCGGCACCAAAGTGCAAA
1 CAAAGACACC-AAGTGCAAA
*
41980461 CAAAGGCACCGAAGT
1 CAAAGACACC-AAGT
41980476 ACATAACTAG
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.44, C:0.25, G:0.21, T:0.09
Consensus pattern (19 bp):
CAAAGACACCAAGTGCAAA
Found at i:41982818 original size:26 final size:27
Alignment explanation
Indices: 41982771--41982824 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
41982761 TCTCTCTCTC
**
41982771 TTAATTTCTTTTTTTATGTTTTCCTTT
1 TTAATTTCTTTTTCCATGTTTTCCTTT
* *
41982798 TTAATTT-TTTTTCCATTTTTTTCTTT
1 TTAATTTCTTTTTCCATGTTTTCCTTT
41982824 T
1 T
41982825 ATTCCTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.76
Consensus pattern (27 bp):
TTAATTTCTTTTTCCATGTTTTCCTTT
Found at i:41985199 original size:22 final size:24
Alignment explanation
Indices: 41985174--41985230 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
41985164 AATTAAATTT
**
41985174 TTAATGTA-TTTTTATAAT-ATAA
1 TTAATGTAGTTTAAATAATAATAA
41985196 TTAAT-TAGTTTAAATAATAAATAA
1 TTAATGTAGTTTAAATAAT-AATAA
41985220 TTAATGTAGTT
1 TTAATGTAGTT
41985231 AATAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 2 0.07
22 13 0.45
24 9 0.31
25 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (24 bp):
TTAATGTAGTTTAAATAATAATAA
Found at i:41985232 original size:24 final size:24
Alignment explanation
Indices: 41985187--41985236 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
41985177 ATGTATTTTT
41985187 ATAATATAATTAATTAGTTTAAATA
1 ATAATATAATTAATTAGTTT-AATA
41985212 ATAA-ATAATTAATGTAG-TTAATA
1 ATAATATAATTAAT-TAGTTTAATA
41985235 AT
1 AT
41985237 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 6 0.25
24 11 0.46
25 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
ATAATATAATTAATTAGTTTAATA
Found at i:41985488 original size:17 final size:18
Alignment explanation
Indices: 41985456--41985489 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41985446 ATGAATGTTT
41985456 ATAACCCCTAAATTCATC
1 ATAACCCCTAAATTCATC
41985474 ATAACCCCT-AATTCAT
1 ATAACCCCTAAATTCAT
41985490 TATCTTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAACCCCTAAATTCATC
Found at i:41993121 original size:46 final size:46
Alignment explanation
Indices: 41993006--41993213 Score: 177
Period size: 46 Copynumber: 4.5 Consensus size: 46
41992996 AGTTTTTGCC
* * * **
41993006 CAGGTTCTCAGCTCTTGCATATATTGCGGACTGGAGAATACATA-TT
1 CAGGTTCCCAGCTCCTGCATATGTTGCAAACTGGAGAATACA-AGTT
* * ** **
41993052 CAAGTTCCCAGTTCCTATATATGTTGCGGACTGGAGAATAC-AGATT
1 CAGGTTCCCAGCTCCTGCATATGTTGCAAACTGGAGAATACAAG-TT
* * * *
41993098 CAGGTTCCCAACTCCTGCGTATGTTGCAAATTGGAAAATACAAGTT
1 CAGGTTCCCAGCTCCTGCATATGTTGCAAACTGGAGAATACAAGTT
* * * * *
41993144 TAGGTTCCCAACTCTTGCATATGTTGCAAACTAGAGAATACAATTT
1 CAGGTTCCCAGCTCCTGCATATGTTGCAAACTGGAGAATACAAGTT
* * *
41993190 TAGGTTCCTAGCTCCTGCAGATGT
1 CAGGTTCCCAGCTCCTGCATATGT
41993214 GGAAACGCAG
Statistics
Matches: 131, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
44 1 0.01
46 128 0.98
47 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (46 bp):
CAGGTTCCCAGCTCCTGCATATGTTGCAAACTGGAGAATACAAGTT
Found at i:41997347 original size:26 final size:27
Alignment explanation
Indices: 41997316--41997385 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
41997306 ACAGAGATCA
41997316 CCACAAAGGCTTCCTTT-CAAAAATAG
1 CCACAAAGGCTTCCTTTACAAAAATAG
** *
41997342 CCACAAAGGCTTTTTTTAACAAAGATAG
1 CCACAAAGGCTTCCTTT-ACAAAAATAG
*
41997370 TCACAAAGGCTTCCTT
1 CCACAAAGGCTTCCTT
41997386 ATAGAAACTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 15 0.42
28 21 0.58
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (27 bp):
CCACAAAGGCTTCCTTTACAAAAATAG
Found at i:41997404 original size:54 final size:55
Alignment explanation
Indices: 41997278--41997414 Score: 156
Period size: 54 Copynumber: 2.5 Consensus size: 55
41997268 ATTCATTTAA
* * *
41997278 CAAAGATAGCCATAAAGGCATCTTTTTAACAGAGATCACCACAAAGGCTTCCTTT
1 CAAAAATAGCCATAAAGGCATTTTTTTAACAAAGATCACCACAAAGGCTTCCTTT
* *
41997333 CAAAAATAGCCACAAAGGC-TTTTTTTAACAAAGAT-AGTCACAAAGGCTTCCTTAT
1 CAAAAATAGCCATAAAGGCATTTTTTTAACAAAGATCA-CCACAAAGGCTTCCTT-T
* *
41997388 -AGAAACT-GCCATAAAGGCATTTCTTTA
1 CA-AAAATAGCCATAAAGGCATTTTTTTA
41997415 GGTTGCGCCA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
53 1 0.01
54 40 0.57
55 29 0.41
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (55 bp):
CAAAAATAGCCATAAAGGCATTTTTTTAACAAAGATCACCACAAAGGCTTCCTTT
Found at i:41999024 original size:20 final size:20
Alignment explanation
Indices: 41998978--41999038 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
41998968 GTATGATAAC
41998978 TTTAAATAATATAACTAATCA
1 TTTAAATAATATAACTAAT-A
41998999 TTTAAATAATA-ATACT-ATA
1 TTTAAATAATATA-ACTAATA
*
41999018 TTTTAAATTATACTAA-TAATA
1 -TTTAAATAATA-TAACTAATA
41999039 AACTTAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 1 0.03
20 14 0.41
21 18 0.53
22 1 0.03
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAATAATATAACTAATA
Found at i:42000512 original size:44 final size:45
Alignment explanation
Indices: 42000394--42000515 Score: 126
Period size: 45 Copynumber: 2.7 Consensus size: 45
42000384 ATCGGCTTCA
* ** *
42000394 ATCTACTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTCCG
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCCATCTCAG
* *
42000439 ATCTG-TCCCACTGCAACTTCAAGGG-GATAAGACCTG-CTTACTCAG
1 ATCTGCT-CCACTGCAACCTC-AGGGAGATAAGACCTGCCAT-CTCAG
*
42000484 -TCTGCTCCACTACAACCTCAGGGAGATAAGAC
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGAC
42000516 ATGATACTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
43 4 0.06
44 26 0.41
45 30 0.47
46 4 0.06
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCCATCTCAG
Found at i:42000658 original size:45 final size:45
Alignment explanation
Indices: 42000355--42000687 Score: 174
Period size: 44 Copynumber: 7.6 Consensus size: 45
42000345 CTTTAATCCA
* * * * ** *
42000355 CTCCACTACAATTTCAGGGAGATAGGA-TTATCGGCTTCAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAATCTG
* * * *
42000399 CTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTCCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAATCTG
** * *
42000444 -TCCCACTGCAACTTCAAGGG-GATAAGACCTG-CTTAC-TCAGTCTG
1 CT-CCACTGCAACTTC-AGGGAGATAAGATTTGTCAT-CTTCAATCTG
* * ** *
42000488 CTCCACTACAACCTCAGGGAGATAAGACATG--ATACTATCCA-CT-
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTCAT-CT-TCAATCTG
* * *** * * *
42000531 CT--ACTGTAACTTCAGAGAGATAAGATCCATTA-CTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAATCTG
* * * * * *
42000573 CTCCACTACAATTTCA-AGAGATAGGA-TTATCAGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAATCTG
*
42000616 CTCCACTGCAACCTCAGGGAGATAAGATTTGTCATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAATCTG
* *
42000661 -TCCCATTGCAACTTCAGGGGGATAAGA
1 CT-CCACTGCAACTTCAGGGAGATAAGA
42000688 CCTGTGATTT
Statistics
Matches: 217, Mismatches: 54, Indels: 35
0.71 0.18 0.11
Matches are distributed among these distances:
40 2 0.01
41 22 0.10
42 5 0.02
43 40 0.18
44 72 0.33
45 72 0.33
46 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAATCTG
Found at i:42000773 original size:217 final size:216
Alignment explanation
Indices: 42000241--42000713 Score: 606
Period size: 218 Copynumber: 2.2 Consensus size: 216
42000231 TGGGTACTTT
* * ** * * * * * * * *
42000241 AGGGGAATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGAAGATAAGACCTAATGCG
1 AGGGG-ATAAGACCTGATTACCCAACCTACTCCACTACAACCTCAGGGAGATAAGACATGATACT
* *
42000306 ATTCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCACTCCACTACAATTTCA
65 ATCCACTCTACTGTAACTT-AG-AAGATAAGATCCATTACTTTAATCCACTCCACTACAATTTCA
* *
42000371 GGGAGATAGGATTATCGGCTTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCT
128 GAGAGATAGGATTATCAGCTTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCT
*
42000436 CCGATCTGTCCCACTGCAACTTCA
193 CCAATCTGTCCCACTGCAACTTCA
* * ** *
42000460 AGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAGGGAGATAAGACATGATACTA
1 AGGGGATAAGACCTGATTACCCAACCTACTCCACTACAACCTCAGGGAGATAAGACATGATACTA
*
42000525 TCCACTCTACTGTAACTTCAGAGAGATAAGATCCATTACTTTAATCCGCTCCACTACAATTTCA-
66 TCCACTCTACTGTAACTT-AGA-AGATAAGATCCATTACTTTAATCCACTCCACTACAATTTCAG
* * *
42000589 AGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGTCATCTT
129 AGAGATAGGATTATCAGCTTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTC
*
42000654 CAATCTGTCCCATTGCAACTTCA
194 CAATCTGTCCCACTGCAACTTCA
* * *
42000677 GGGGGATAAGACCTGTGATTTCCCAACCTATTCCACT
1 AGGGGATAAGACC--TGATTACCCAACCTACTCCACT
42000714 GCTGACCAGG
Statistics
Matches: 226, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
217 94 0.42
218 112 0.50
219 20 0.09
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (216 bp):
AGGGGATAAGACCTGATTACCCAACCTACTCCACTACAACCTCAGGGAGATAAGACATGATACTA
TCCACTCTACTGTAACTTAGAAGATAAGATCCATTACTTTAATCCACTCCACTACAATTTCAGAG
AGATAGGATTATCAGCTTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTCCA
ATCTGTCCCACTGCAACTTCA
Found at i:42002194 original size:6 final size:6
Alignment explanation
Indices: 42002180--42002259 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
42002170 CTTCTCTCAT
* * * ** **
42002180 TTTTTA TTTTCA TTTTGA CTTTGA TTTTGA TTTTGA TTTTTCTC TTTCTTC
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA -TTTT-GA TTT-TGA
42002231 TTTTG- TTTCTGA TTTTGA TTTTGA TTTTG
1 TTTTGA TTT-TGA TTTTGA TTTTGA TTTTG
42002260 CTTGATTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
5 3 0.05
6 43 0.69
7 15 0.24
8 1 0.02
ACGTcount: A:0.11, C:0.09, G:0.11, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:42006082 original size:62 final size:63
Alignment explanation
Indices: 42005956--42006085 Score: 156
Period size: 62 Copynumber: 2.1 Consensus size: 63
42005946 CTTTAACCTA
* * * * * *
42005956 ATAATTTTAGATATTTCAATTGTATTACACAAATTGTTTCACTCACGTTGTTTGTATATTTTG
1 ATAATTTTACACATTTCAATTGTATTACACAAATTGTTTCACTCACATTATTTGCATATATTG
* * *
42006019 ATAATTTTACACATTTCAATT-TATTATACAAATTGTTTC-TTCCATATTATTTGCATATATTG
1 ATAATTTTACACATTTCAATTGTATTACACAAATTGTTTCACT-CACATTATTTGCATATATTG
42006081 ATAAT
1 ATAAT
42006086 GTCATTGATT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
61 1 0.02
62 37 0.65
63 19 0.33
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (63 bp):
ATAATTTTACACATTTCAATTGTATTACACAAATTGTTTCACTCACATTATTTGCATATATTG
Found at i:42007238 original size:15 final size:15
Alignment explanation
Indices: 42007210--42007269 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
42007200 ATATTATATG
*
42007210 AAAAATTAAATAAAAT
1 AAAAA-TAATTAAAAT
42007226 AAAAATAATT-AAAT
1 AAAAATAATTAAAAT
* *
42007240 TAAAATAAATTAAAAA
1 AAAAAT-AATTAAAAT
*
42007256 AACAAATAACTAAA
1 AA-AAATAATTAAA
42007270 TCTATTATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 9 0.25
15 8 0.22
16 15 0.42
17 4 0.11
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAATTAAAAT
Found at i:42010358 original size:18 final size:19
Alignment explanation
Indices: 42010335--42010372 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42010325 TTTGATATTT
* *
42010335 TATAAA-TTATTAGAAACA
1 TATAAACTTACTAAAAACA
42010353 TATAAACTTACTAAAAACA
1 TATAAACTTACTAAAAACA
42010372 T
1 T
42010373 CTAGAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (19 bp):
TATAAACTTACTAAAAACA
Found at i:42021266 original size:28 final size:28
Alignment explanation
Indices: 42021203--42021300 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 28
42021193 ATATTAAGTC
*
42021203 CGCACACTCAGTGCTATAAAATC-AACT
1 CGCACACTTAGTGCTATAAAATCAAACT
*
42021230 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
42021258 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATA-AAATCAAACT
42021287 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42021301 CAATCTCATG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 21 0.34
28 20 0.32
29 21 0.34
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:42021295 original size:29 final size:28
Alignment explanation
Indices: 42021202--42021300 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
42021192 TATATTAAGT
* *
42021202 CCGCACACTCAGTGCTATAAAATC-AAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* *
42021229 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* *
42021257 TCGCACACTTAGTGCTGA-ACAATTTAAAC
1 CCGCACACTTAGTGCT-ATACAA-TCAAAC
42021286 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
42021301 CAATCTCATG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
27 21 0.33
28 22 0.35
29 20 0.32
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.24
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:42029496 original size:28 final size:28
Alignment explanation
Indices: 42029433--42029530 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 28
42029423 ATATTAAGTC
*
42029433 CGCACACTCAGTGCTATAAAATC-AACT
1 CGCACACTTAGTGCTATAAAATCAAACT
*
42029460 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
42029488 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATA-AAATCAAACT
42029517 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42029531 CAATCTCATG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 21 0.34
28 20 0.32
29 21 0.34
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:42029525 original size:29 final size:28
Alignment explanation
Indices: 42029432--42029530 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
42029422 TATATTAAGT
* *
42029432 CCGCACACTCAGTGCTATAAAATC-AAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* *
42029459 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* *
42029487 TCGCACACTTAGTGCTGA-ACAATTTAAAC
1 CCGCACACTTAGTGCT-ATACAA-TCAAAC
42029516 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
42029531 CAATCTCATG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
27 21 0.33
28 22 0.35
29 20 0.32
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.24
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:42033255 original size:28 final size:29
Alignment explanation
Indices: 42033224--42033283 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
42033214 TTGCAATGAA
* * *
42033224 TTAGGACATATTA-AAACTCACAATTAAT
1 TTAGAACAAATTAGAAACACACAATTAAT
**
42033252 TTAGAACAAATTAGAAACACTTAATTAAT
1 TTAGAACAAATTAGAAACACACAATTAAT
42033281 TTA
1 TTA
42033284 TGTCTAGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (29 bp):
TTAGAACAAATTAGAAACACACAATTAAT
Found at i:42039427 original size:28 final size:29
Alignment explanation
Indices: 42039358--42039427 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 29
42039348 CCACCAGAAT
* *
42039358 AAGGAAAGTCCGCCAAGGACCTTCTTAAG
1 AAGGAAAGTCCACCAAGGACCATCTTAAG
* *
42039387 AAGG-GAGTTCACCAAGGACCATCTT-AG
1 AAGGAAAGTCCACCAAGGACCATCTTAAG
**
42039414 GTGGAAAGTCCACC
1 AAGGAAAGTCCACC
42039428 GGGAATTTAC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 4 0.12
28 24 0.75
29 4 0.12
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (29 bp):
AAGGAAAGTCCACCAAGGACCATCTTAAG
Found at i:42041821 original size:43 final size:43
Alignment explanation
Indices: 42041773--42041862 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
42041763 TCAAAAGTCC
42041773 ATGGTTAGCCAGGGCATGATCTAGTGGTGAACAAGTAAGCTTT
1 ATGGTTAGCCAGGGCATGATCTAGTGGTGAACAAGTAAGCTTT
*
42041816 ATGGTTAGCCATGGCATGATCTAGTGGTGAACAAGTAAGCTTT
1 ATGGTTAGCCAGGGCATGATCTAGTGGTGAACAAGTAAGCTTT
42041859 ATGG
1 ATGG
42041863 CATAAAAGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.29
Consensus pattern (43 bp):
ATGGTTAGCCAGGGCATGATCTAGTGGTGAACAAGTAAGCTTT
Found at i:42044861 original size:15 final size:15
Alignment explanation
Indices: 42044837--42044868 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42044827 TATGCATGCA
*
42044837 AAATATAAAAGACAT
1 AAATACAAAAGACAT
42044852 AAATACAAAAGACAT
1 AAATACAAAAGACAT
42044867 AA
1 AA
42044869 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:42046764 original size:27 final size:27
Alignment explanation
Indices: 42046730--42046844 Score: 117
Period size: 27 Copynumber: 4.3 Consensus size: 27
42046720 CGAAAAGGTT
*
42046730 GTAAAATTATCGAAATACCTTCGAAGG
1 GTAAAATTATCGAAATACCTCCGAAGG
* *
42046757 GTAAAATTACCGAAATACC-CTTGATA-G
1 GTAAAATTATCGAAATACCTC-CGA-AGG
* * *
42046784 ATAAAACTATCGAAATACCCCCGAAGG
1 GTAAAATTATCGAAATACCTCCGAAGG
* * *
42046811 GAAAAATTATCAAAATACCTCCGTAGG
1 GTAAAATTATCGAAATACCTCCGAAGG
42046838 GTAAAAT
1 GTAAAAT
42046845 GACTGTTATA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
26 1 0.01
27 67 0.96
28 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCTCCGAAGG
Found at i:42049819 original size:22 final size:22
Alignment explanation
Indices: 42049791--42049833 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42049781 TATGAGGAAT
* *
42049791 GGGAAATTAAAGGGAATCAACA
1 GGGAAATTAAAGAGAAACAACA
42049813 GGGAAATTAAAGAGAAACAAC
1 GGGAAATTAAAGAGAAACAAC
42049834 GCTACAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.26, T:0.12
Consensus pattern (22 bp):
GGGAAATTAAAGAGAAACAACA
Found at i:42061486 original size:23 final size:23
Alignment explanation
Indices: 42061415--42061521 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
42061405 CCTAATCAGT
42061415 ATACGACACAT-AAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
* * *
42061437 GT--GACACATGATGTGCCTG--
1 ATACGACACATAAAGTGCCTGAA
* *
42061456 ATACGACACATGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
42061479 ATACGACACATAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAA
42061502 ATACGACACATAAAGTGCCT
1 ATACGACACATAAAGTGCCT
42061522 TTATGGTGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.01
20 7 0.10
21 24 0.33
22 1 0.01
23 40 0.55
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:42063754 original size:32 final size:33
Alignment explanation
Indices: 42063716--42063812 Score: 99
Period size: 32 Copynumber: 2.9 Consensus size: 33
42063706 AAGAAAAATT
* *
42063716 CAGGAAAAAGAATCTTGAAGAAATTGAATCTGA
1 CAGGAAAAAAAAACTTGAAGAAATTGAATCTGA
* * *
42063749 C-GGAAAAAAAAACTAGGAGAAATTGAAAT-GGA
1 CAGGAAAAAAAAACTTGAAGAAATTG-AATCTGA
* *
42063781 CATGAAAATAAAACCTTGAAGAAATTGAATCT
1 CAGGAAAA-AAAAACTTGAAGAAATTGAATCT
42063813 TACTTGGAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
32 23 0.46
33 12 0.24
34 15 0.30
ACGTcount: A:0.52, C:0.09, G:0.20, T:0.20
Consensus pattern (33 bp):
CAGGAAAAAAAAACTTGAAGAAATTGAATCTGA
Found at i:42064298 original size:21 final size:21
Alignment explanation
Indices: 42064257--42064298 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42064247 ATAGATAATG
*
42064257 AAAAAATATATAAATTATTTT
1 AAAAAATATATAAAATATTTT
*
42064278 AAAAATTATAGTAAAAT-TTTT
1 AAAAAATATA-TAAAATATTTT
42064299 CTCTTGACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAAAATATATAAAATATTTT
Found at i:42066076 original size:25 final size:24
Alignment explanation
Indices: 42066029--42066078 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
42066019 TCTCTCTCTC
*
42066029 TGTTTTTTATTTTACTTTATTTCT
1 TGTTTTTTATTTTACATTATTTCT
42066053 TGTTTTTTAGTTTTTACATT-TTTCT
1 TGTTTTTTA--TTTTACATTATTTCT
42066078 T
1 T
42066079 ATCAGGTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 6 0.26
26 8 0.35
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.74
Consensus pattern (24 bp):
TGTTTTTTATTTTACATTATTTCT
Found at i:42071144 original size:9 final size:9
Alignment explanation
Indices: 42071130--42071164 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
42071120 TGATACTATA
42071130 AAAATAAGG
1 AAAATAAGG
42071139 AAAATAAGG
1 AAAATAAGG
*
42071148 AAAATAAAG
1 AAAATAAGG
*
42071157 AAAGTAAG
1 AAAATAAG
42071165 CATAAAGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (9 bp):
AAAATAAGG
Done.