Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 95 of 221
Found at i:28942784 original size:24 final size:24
Alignment explanation
Indices: 28942683--28942785 Score: 86
Period size: 24 Copynumber: 4.2 Consensus size: 24
28942673 TAGATGGAAA
*
28942683 TTAAAATAATAATATATGATAAA-
1 TTAAAATAATAATACATGATAAAC
*
28942706 TTAAAAAAAGTAATTACACATGA-AAAC
1 TTAAAATAA-TAA-T--ACATGATAAAC
*
28942733 TTAGAATAATAATACAT-ATAAAAC
1 TTAAAATAATAATACATGAT-AAAC
* * *
28942757 TTAAAATGATAATATATGATAAAT
1 TTAAAATAATAATACATGATAAAC
28942781 TTAAA
1 TTAAA
28942786 CAATGTTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 12 0.19
24 29 0.45
25 4 0.06
26 6 0.09
27 12 0.19
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (24 bp):
TTAAAATAATAATACATGATAAAC
Found at i:28949434 original size:47 final size:47
Alignment explanation
Indices: 28949356--28949997 Score: 1015
Period size: 47 Copynumber: 13.6 Consensus size: 47
28949346 CCCTTCGGGA
* * * * * *
28949356 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28949403 CCTGTCACATATAGACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28949450 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28949497 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28949544 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28949591 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCA-GC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATT-AGGC
* *
28949640 CTTATCACATATATATACACTTT--CA--CATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28949685 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28949732 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28949781 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28949828 CTTATCACATATATACATTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28949875 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28949922 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28949971 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28949998 TATTCAAATA
Statistics
Matches: 557, Mismatches: 26, Indels: 24
0.92 0.04 0.04
Matches are distributed among these distances:
43 13 0.02
45 28 0.05
47 365 0.66
49 150 0.27
50 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28951348 original size:85 final size:85
Alignment explanation
Indices: 28951219--28951397 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
28951209 TATTTTATTG
*
28951219 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
28951284 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
28951304 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
28951369 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
28951389 CCCATGCTC
1 CCCATGCTC
28951398 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:28952872 original size:30 final size:30
Alignment explanation
Indices: 28952837--28952933 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
28952827 TAAGTCGATG
28952837 TTCAATTCAATTCCACACCTATATTCATTA
1 TTCAATTCAATTCCACACCTATATTCATTA
* *** * *
28952867 TTCAATTACACTTCCATTTCTA-AGTCGA-TG
1 TTCAATT-CAATTCCACACCTATATTC-ATTA
28952897 TTCAATTCAATTCCACACCTATATTCATTA
1 TTCAATTCAATTCCACACCTATATTCATTA
28952927 TTCAATT
1 TTCAATT
28952934 ACACTTAGTC
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
29 11 0.22
30 29 0.57
31 11 0.22
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (30 bp):
TTCAATTCAATTCCACACCTATATTCATTA
Found at i:28952892 original size:60 final size:60
Alignment explanation
Indices: 28952818--28952939 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
28952808 AAATTCACTT
28952818 TTCCATTTCTAAGTCGATGTTCAATTCAATTCCACACCTATATTCATTATTCAATTACAC
1 TTCCATTTCTAAGTCGATGTTCAATTCAATTCCACACCTATATTCATTATTCAATTACAC
28952878 TTCCATTTCTAAGTCGATGTTCAATTCAATTCCACACCTATATTCATTATTCAATTACAC
1 TTCCATTTCTAAGTCGATGTTCAATTCAATTCCACACCTATATTCATTATTCAATTACAC
28952938 TT
1 TT
28952940 AGTCAATTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (60 bp):
TTCCATTTCTAAGTCGATGTTCAATTCAATTCCACACCTATATTCATTATTCAATTACAC
Found at i:28953050 original size:45 final size:45
Alignment explanation
Indices: 28952983--28953070 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
28952973 ACATATACTC
* * *
28952983 GGTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTCT
1 GGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGTCT
*
28953028 GGTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGT
1 GGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGT
28953071 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
GGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGTCT
Found at i:28953550 original size:61 final size:61
Alignment explanation
Indices: 28953475--28953596 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
28953465 CTTTTTATTC
28953475 AATTTCCTTGCATTTTAGGCCTAGCTAAACCATTTTCATAACTATAGCAGTCCACAATACT
1 AATTTCCTTGCATTTTAGGCCTAGCTAAACCATTTTCATAACTATAGCAGTCCACAATACT
28953536 AATTTCCTTGCATTTTAGGCCTAGCTAAACCATTTTCATAACTATAGCAGTCCACAATACT
1 AATTTCCTTGCATTTTAGGCCTAGCTAAACCATTTTCATAACTATAGCAGTCCACAATACT
28953597 TACTTATCCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (61 bp):
AATTTCCTTGCATTTTAGGCCTAGCTAAACCATTTTCATAACTATAGCAGTCCACAATACT
Found at i:28956028 original size:17 final size:16
Alignment explanation
Indices: 28956006--28956049 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
28955996 GGTGTCACTT
*
28956006 GAATTAAATTAATTATA
1 GAATTAAATTAATT-CA
*
28956023 GAATTAATTTAATTCA
1 GAATTAAATTAATTCA
28956039 GTAATTAAATT
1 G-AATTAAATT
28956050 TCCAACACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (16 bp):
GAATTAAATTAATTCA
Found at i:28964751 original size:40 final size:40
Alignment explanation
Indices: 28964697--28964774 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
28964687 TTAATTTAAA
28964697 TAAACTCATCTTAGTTAATAAATAAGTTGCTGGACTTTAT
1 TAAACTCATCTTAGTTAATAAATAAGTTGCTGGACTTTAT
* * * * *
28964737 TAAACTCATTTTAGTTAGTAATTGAGTTGTTGGACTTT
1 TAAACTCATCTTAGTTAATAAATAAGTTGCTGGACTTT
28964775 CTTTTATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (40 bp):
TAAACTCATCTTAGTTAATAAATAAGTTGCTGGACTTTAT
Found at i:28970671 original size:40 final size:40
Alignment explanation
Indices: 28970605--28970682 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
28970595 TTAATTTAAA
28970605 TAAACTCATCTTAGGTAATAAATGAGTTGCTGGACTTTAT
1 TAAACTCATCTTAGGTAATAAATGAGTTGCTGGACTTTAT
* * * *
28970645 TAAACTCATCTTAGTTACTAATTGAGTTGTTGGACTTT
1 TAAACTCATCTTAGGTAATAAATGAGTTGCTGGACTTT
28970683 CTTTTATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (40 bp):
TAAACTCATCTTAGGTAATAAATGAGTTGCTGGACTTTAT
Found at i:28977579 original size:18 final size:18
Alignment explanation
Indices: 28977556--28977597 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28977546 CGGTTGGCTG
*
28977556 AAAATATGGTTTTTACTA
1 AAAATAAGGTTTTTACTA
* *
28977574 AAAATAAGTTTTTTTCTA
1 AAAATAAGGTTTTTACTA
28977592 AAAATA
1 AAAATA
28977598 CGAACGAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (18 bp):
AAAATAAGGTTTTTACTA
Found at i:28987013 original size:11 final size:11
Alignment explanation
Indices: 28986997--28987023 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28986987 GTCTGTGTCC
28986997 CATAACCAATT
1 CATAACCAATT
28987008 CATAACCAATT
1 CATAACCAATT
28987019 CATAA
1 CATAA
28987024 AATTTTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (11 bp):
CATAACCAATT
Found at i:28987742 original size:40 final size:40
Alignment explanation
Indices: 28987709--28987828 Score: 195
Period size: 40 Copynumber: 3.0 Consensus size: 40
28987699 TGTGTGTTCG
* *
28987709 GGGGTACTGAAGTACAAATAGGGGCACGCATGTGCATTCA
1 GGGGTACCGAAGTACAAATAGGGGCACGAATGTGCATTCA
* *
28987749 GGGGCACCGAAGTACAAATAGGGGCACAAATGTGCATTCA
1 GGGGTACCGAAGTACAAATAGGGGCACGAATGTGCATTCA
*
28987789 GGGGTACCGAAGTACAAATAGGGGTACGAATGTGCATTCA
1 GGGGTACCGAAGTACAAATAGGGGCACGAATGTGCATTCA
28987829 AACAACAAGT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (40 bp):
GGGGTACCGAAGTACAAATAGGGGCACGAATGTGCATTCA
Found at i:28987771 original size:20 final size:19
Alignment explanation
Indices: 28987717--28987818 Score: 64
Period size: 20 Copynumber: 5.2 Consensus size: 19
28987707 CGGGGGTACT
28987717 GAAGTACAAATAGGGGCAC
1 GAAGTACAAATAGGGGCAC
* * *
28987736 GCATGTGC-ATTCAGGGGCACC
1 G-AAGTACAAAT-AGGGGCA-C
28987757 GAAGTACAAATAGGGGCAC
1 GAAGTACAAATAGGGGCAC
* * * *
28987776 AAATGTGC-ATTCAGGGGTACC
1 GAA-GTACAAAT-AGGGGCA-C
*
28987797 GAAGTACAAATAGGGGTAC
1 GAAGTACAAATAGGGGCAC
28987816 GAA
1 GAA
28987819 TGTGCATTCA
Statistics
Matches: 62, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
19 12 0.19
20 41 0.66
21 9 0.15
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (19 bp):
GAAGTACAAATAGGGGCAC
Found at i:28990989 original size:136 final size:136
Alignment explanation
Indices: 28990745--28991295 Score: 935
Period size: 136 Copynumber: 4.1 Consensus size: 136
28990735 AACTAATTTG
*
28990745 TAAAACTGTCAAATGTTATGGATTATGTAATTGATGAGTTTAGTAT-TTTTTTAAGTTTTATGAT
1 TAAAA-TGTCAAATGTTATGGATTATGTAATTGATGAGTTTAGTATGTTTTTGAAGTTTTATGAT
* *
28990809 AAATTATTAAGCTTTATTATTAAATAAGACTATTTTGTAAAGTAATTTTTAGTAATTTTAATGTT
65 AAATTATTAAGCTTTATTGTTAAATAAGACTATTTTGTAAAGTAATTTTTAGCAATTTTAATGTT
*
28990874 AAAGGAT
130 AAAGGAC
*
28990881 TAAAATGTCAAATGTTATGGATTATGTAATTGATGAGTTTAGTGTGTTTTTGAAGTTTTATGATA
1 TAAAATGTCAAATGTTATGGATTATGTAATTGATGAGTTTAGTATGTTTTTGAAGTTTTATGATA
* * *
28990946 AATTAGTAAGCTTTATTGTTGAATAAGACTATTTTGCAAAGTAATTTTTAGCAATTTTAATGTTA
66 AATTATTAAGCTTTATTGTTAAATAAGACTATTTTGTAAAGTAATTTTTAGCAATTTTAATGTTA
28991011 AAGGAC
131 AAGGAC
* *
28991017 TAAAATGTCAAATGTTCTGGATTATGTAATTGATGAGTTTAGTATGTTTTTGAAGTTTTATTATA
1 TAAAATGTCAAATGTTATGGATTATGTAATTGATGAGTTTAGTATGTTTTTGAAGTTTTATGATA
*
28991082 AATTATTAAGCTTTATTGTTAAATAAGACTATTTAGTAAAGTAATTTTTAGCAATTTTAATGTTA
66 AATTATTAAGCTTTATTGTTAAATAAGACTATTTTGTAAAGTAATTTTTAGCAATTTTAATGTTA
*
28991147 AAGGAT
131 AAGGAC
*
28991153 TAAAATGTCAAATGTTATGGATTATGTAATTGATGATTTTAGTATGTTTTTGAAGTTTTATGATA
1 TAAAATGTCAAATGTTATGGATTATGTAATTGATGAGTTTAGTATGTTTTTGAAGTTTTATGATA
* *
28991218 AATTATTAAGTTTTATTGTTAAATAAGACTATTTTGT-AAGTAATTTTTAGTAATTTTAATGTTA
66 AATTATTAAGCTTTATTGTTAAATAAGACTATTTTGTAAAGTAATTTTTAGCAATTTTAATGTTA
*
28991282 AAAGAC
131 AAGGAC
28991288 TAAAATGT
1 TAAAATGT
28991296 TAAAGTGATA
Statistics
Matches: 390, Mismatches: 24, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
135 77 0.20
136 313 0.80
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (136 bp):
TAAAATGTCAAATGTTATGGATTATGTAATTGATGAGTTTAGTATGTTTTTGAAGTTTTATGATA
AATTATTAAGCTTTATTGTTAAATAAGACTATTTTGTAAAGTAATTTTTAGCAATTTTAATGTTA
AAGGAC
Found at i:29008022 original size:64 final size:64
Alignment explanation
Indices: 29007938--29008125 Score: 288
Period size: 64 Copynumber: 2.9 Consensus size: 64
29007928 AGGTAAGTTT
* *
29007938 GTCGATAGTTTTGGGAATTGACGATTGTAAGTAATTTAGATTAAGTGATTGAGATTGAGTTTTC
1 GTCGATAGTTTTGGGAATTGACGATTGTAAGTAATTCAGATTAAGTGACTGAGATTGAGTTTTC
* ** * *
29008002 GTTGATAGTTTCAGGAATTGACTATTGTAAGTAATTCAGATTAAGTGACTGAGATTGAGTTTTT
1 GTCGATAGTTTTGGGAATTGACGATTGTAAGTAATTCAGATTAAGTGACTGAGATTGAGTTTTC
*
29008066 GTCGATAGTTTTGGGAATTGACTG-TTGTAAGTAATTCAGATTAAGTGACTGGGATTGAGT
1 GTCGATAGTTTTGGGAATTGAC-GATTGTAAGTAATTCAGATTAAGTGACTGAGATTGAGT
29008126 CTCCAATTTT
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
64 111 1.00
ACGTcount: A:0.28, C:0.06, G:0.27, T:0.39
Consensus pattern (64 bp):
GTCGATAGTTTTGGGAATTGACGATTGTAAGTAATTCAGATTAAGTGACTGAGATTGAGTTTTC
Found at i:29010618 original size:125 final size:126
Alignment explanation
Indices: 29010396--29010653 Score: 464
Period size: 125 Copynumber: 2.1 Consensus size: 126
29010386 GAATTAGGAG
*
29010396 TTATTAATGTACATGGACTAAATCACGTAAGAGCTAAAAGTTGAATTATAGATTGAAATTAATTA
1 TTATTAATGTACATGGACTAAATCACGTAAGAGCTAAAAGTTAAATTATAGATTGAAATTAATTA
*
29010461 AAAGGAGTAAAGTAGTAATTACACCACTAATTAAATGTTGATGGGCGATGGTGGGTTGG-T
66 AAAGGACTAAAGTAGTAATTACACCACTAATTAAATGTTGATGGGCGATGGTGGGTTGGTT
* *
29010521 TTATTAATGTACATGGACTAAATCGCGTAAGTGCTAAAAGTTAAATTATAGATTGAAATTAATTA
1 TTATTAATGTACATGGACTAAATCACGTAAGAGCTAAAAGTTAAATTATAGATTGAAATTAATTA
*
29010586 AAAGGACTAAAGTAGTAATTACACCACTAATTAAATGTTGATGGGTGATGGTGGGTTGGTT
66 AAAGGACTAAAGTAGTAATTACACCACTAATTAAATGTTGATGGGCGATGGTGGGTTGGTT
29010647 TTATTAA
1 TTATTAA
29010654 AAATTTATTA
Statistics
Matches: 127, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
125 119 0.94
126 8 0.06
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (126 bp):
TTATTAATGTACATGGACTAAATCACGTAAGAGCTAAAAGTTAAATTATAGATTGAAATTAATTA
AAAGGACTAAAGTAGTAATTACACCACTAATTAAATGTTGATGGGCGATGGTGGGTTGGTT
Found at i:29013558 original size:11 final size:11
Alignment explanation
Indices: 29013542--29013571 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
29013532 TCAGATTACT
29013542 CGTTGCTGAGG
1 CGTTGCTGAGG
29013553 CGTTGCTGAGG
1 CGTTGCTGAGG
29013564 CGTTGCTG
1 CGTTGCTG
29013572 TCTACTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.20, G:0.43, T:0.30
Consensus pattern (11 bp):
CGTTGCTGAGG
Found at i:29015868 original size:26 final size:24
Alignment explanation
Indices: 29015839--29015894 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
29015829 ATTATTATAA
29015839 AATAATTAAATTGTAATTAAATTATT
1 AATAATTAAATT-TAATTAAATTA-T
* * *
29015865 AATATGTTGAATTTAATTAATTTAT
1 AATA-ATTAAATTTAATTAAATTAT
29015890 AATAA
1 AATAA
29015895 CTTTTTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
25 5 0.20
26 14 0.56
27 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (24 bp):
AATAATTAAATTTAATTAAATTAT
Found at i:29019128 original size:11 final size:11
Alignment explanation
Indices: 29019112--29019151 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
29019102 ACCATACCTT
29019112 GCAACATTAGA
1 GCAACATTAGA
29019123 GCAACATTAGA
1 GCAACATTAGA
29019134 GCAACATTAGA
1 GCAACATTAGA
29019145 GCAACAT
1 GCAACAT
29019152 ATTATTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.17
Consensus pattern (11 bp):
GCAACATTAGA
Found at i:29023846 original size:26 final size:26
Alignment explanation
Indices: 29023788--29023847 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
29023778 ATTCTTCTCC
*
29023788 TAAA-TTTCAATTTTATTTAATTATT
1 TAAATTTTCAATTTTATTAAATTATT
*
29023813 TAATTTTTCAA-TTTATTGAAATTA-T
1 TAAATTTTCAATTTTATT-AAATTATT
29023838 TAAGATTTTC
1 TAA-ATTTTC
29023848 TACTAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (26 bp):
TAAATTTTCAATTTTATTAAATTATT
Found at i:29035428 original size:61 final size:57
Alignment explanation
Indices: 29035333--29035460 Score: 175
Period size: 61 Copynumber: 2.2 Consensus size: 57
29035323 ATAATATTAT
* * *
29035333 TTTAATAGTTTTAATATTACATTTAATTTAATATTTATCTTATAGATAAGTATTCTATCAA
1 TTTAATA-TTTTAATATTAAATTTAATCTAATATTTATC-T-TA-ATAAGTATTATATCAA
*
29035394 TTTAATATATTTAATATTAAATTTAATCTAATATTTATCTTAATAAGTATTATATTAA
1 TTTAATAT-TTTAATATTAAATTTAATCTAATATTTATCTTAATAAGTATTATATCAA
29035452 TTTAATATT
1 TTTAATATT
29035461 AAAGTAATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
57 1 0.02
58 22 0.35
59 2 0.03
60 2 0.03
61 35 0.56
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (57 bp):
TTTAATATTTTAATATTAAATTTAATCTAATATTTATCTTAATAAGTATTATATCAA
Found at i:29041191 original size:47 final size:47
Alignment explanation
Indices: 29040908--29041402 Score: 570
Period size: 49 Copynumber: 10.6 Consensus size: 47
29040898 TTAAACCCAT
29040908 ATGTGAAAGTGTATATACATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCGATGTGATGA
29040957 ATGTGAAAGTGTATATACATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
29041006 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
29041055 ATGTGAAAGTGTATATACATGTGATAAGGCCTAATAGCCGCTGTGATGA
1 ATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCGATGTGATGA
29041104 ATGTGAAAGTGTATATACATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
29041153 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG-TGT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * **
29041199 ATAT--ATGTG-ATA-A-G-GCCTAATGG-CTGATGTGAGGAATGTGA--A
1 ATGTGAAAGTGTATATATGTG-ATAA-GGCCTAATG-GCCG-ATGTGATGA
* * *
29041241 A-GT----GTATACATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
29041283 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
29041330 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
29041377 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
29041403 TCCCGAAGGG
Statistics
Matches: 392, Mismatches: 33, Indels: 44
0.84 0.07 0.09
Matches are distributed among these distances:
39 2 0.01
40 9 0.02
41 15 0.04
42 16 0.04
43 11 0.03
44 4 0.01
46 5 0.01
47 131 0.33
49 194 0.49
51 5 0.01
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:29041200 original size:34 final size:34
Alignment explanation
Indices: 29041161--29041229 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
29041151 GAATGTGAAA
29041161 GTGTATATATGTGATAAGGCCTAATGGCCGATGT
1 GTGTATATATGTGATAAGGCCTAATGGCCGATGT
*
29041195 GTGTATATATGTGATAAGGCCTAATGGCTGATGT
1 GTGTATATATGTGATAAGGCCTAATGGCCGATGT
29041229 G
1 G
29041230 AGGAATGTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.33
Consensus pattern (34 bp):
GTGTATATATGTGATAAGGCCTAATGGCCGATGT
Found at i:29041211 original size:81 final size:82
Alignment explanation
Indices: 29041112--29041278 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 82
29041102 GAATGTGAAA
*
29041112 GTGTATATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-ATATGTGAT
1 GTGTATATACATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATAATATGTGAT
*
29041176 AAGGCCTAATGGCCGAT
66 AAGGCCTAATAGCCGAT
* * *
29041193 GTGTGTATATATGTGATAAGGCCTAATGGCTGATGTGAGGAATGTGAAAGTGTATACATATGTGA
1 GTGTATATACATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATA-ATATGTGA
29041258 TAAGGCCTAATAGCCGAT
65 TAAGGCCTAATAGCCGAT
29041276 GTG
1 GTG
29041279 ATGAATGTGA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
81 51 0.65
83 28 0.35
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.30
Consensus pattern (82 bp):
GTGTATATACATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATAATATGTGAT
AAGGCCTAATAGCCGAT
Found at i:29041230 original size:130 final size:130
Alignment explanation
Indices: 29041063--29041325 Score: 445
Period size: 130 Copynumber: 2.0 Consensus size: 130
29041053 GAATGTGAAA
* * *
29041063 GTGTATATACATGTGATAAGGCCTAATAGCCGCTGTGATGAATGTGAAAGTGTATATACATGTGA
1 GTGTATATACATGTGATAAGGCCTAATAGCCGATGTGAGGAATGTGAAAGTGTATACACATGTGA
*
29041128 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
66 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * * * *
29041193 GTGTGTATATATGTGATAAGGCCTAATGGCTGATGTGAGGAATGTGAAAGTGTATACATATGTGA
1 GTGTATATACATGTGATAAGGCCTAATAGCCGATGTGAGGAATGTGAAAGTGTATACACATGTGA
29041258 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
66 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
29041323 GTG
1 GTG
29041326 ATGAATGTGA
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 124 1.00
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.30
Consensus pattern (130 bp):
GTGTATATACATGTGATAAGGCCTAATAGCCGATGTGAGGAATGTGAAAGTGTATACACATGTGA
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
Found at i:29041256 original size:49 final size:47
Alignment explanation
Indices: 29041195--29041402 Score: 283
Period size: 47 Copynumber: 4.4 Consensus size: 47
29041185 TGGCCGATGT
*
29041195 GTGTATATATGTGATAAGGCCTAATGGCTGATGTGAGGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAA
* *
29041242 GTGTATACATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAA
1 GTGTAT--ATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAA
*
29041291 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAA
* * * * * *
29041338 GTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG-ATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGA-GGAATGTGAAA
*
29041385 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
29041403 TCCCGAAGGG
Statistics
Matches: 144, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
47 99 0.69
48 1 0.01
49 44 0.31
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAA
Found at i:29041302 original size:96 final size:94
Alignment explanation
Indices: 29041195--29041402 Score: 299
Period size: 96 Copynumber: 2.2 Consensus size: 94
29041185 TGGCCGATGT
* *
29041195 GTGTATATATGTGATAAGGCCTAATGGCTGATGTGAGGAATGTGAAAGTGTATACATATGTGATA
1 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTAT--ATATGTGACA
* * *
29041260 AGGCCTAATAGCCGATGTGATGAATGTGAAA
64 AGGCCGAATAGCCAACGTGATGAATGTGAAA
* *
29041291 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGG
1 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATATATGTGACAAG
* * *
29041356 GCCGAGTGGCCAACGTGATGGATGTGAAA
66 GCCGAATAGCCAACGTGATGAATGTGAAA
*
29041385 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
29041403 TCCCGAAGGG
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
94 50 0.50
96 51 0.50
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (94 bp):
GTGTATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATATATGTGACAAG
GCCGAATAGCCAACGTGATGAATGTGAAA
Found at i:29041577 original size:37 final size:37
Alignment explanation
Indices: 29041521--29041599 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
29041511 CCGAGCTCTA
* * * *
29041521 AAGACCCGATGACTACGTGTGGGGATTTTGTCTGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
29041558 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
29041595 AAGAC
1 AAGAC
29041600 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:29050299 original size:47 final size:47
Alignment explanation
Indices: 29050241--29050588 Score: 669
Period size: 47 Copynumber: 7.4 Consensus size: 47
29050231 CAGCCAAGAC
29050241 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
29050288 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
29050335 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
29050382 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATCTCAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
29050429 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
29050476 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
29050523 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
29050570 AGTGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
29050589 TCCCGAAGGG
Statistics
Matches: 296, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 296 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:29050763 original size:37 final size:37
Alignment explanation
Indices: 29050707--29050777 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
29050697 CTGAGCTCTA
* * *
29050707 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGAGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGAGT
*
29050744 AAGACCCGATAACTTCGTGTGGAGATTATGTCCG
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCG
29050778 GGTTAGACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGAGT
Found at i:29060122 original size:124 final size:124
Alignment explanation
Indices: 29059654--29060118 Score: 549
Period size: 126 Copynumber: 3.7 Consensus size: 124
29059644 TTGAAGTCGC
* * * * *
29059654 TTCTGAGCAACTAGTTTAAAAAATGCTTCAAGCAGGATGCTTTGTGAGAAGAATTTGTGAAATCG
1 TTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCG
* * *
29059719 CGCCCTCGTGGACGCGCTTTTACTACAGTTGATCCTGGAAGAAATAATTTCGAGTTGACGT
66 CGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCT-GAA-AAATAATTTCGAGTTGACGT
* * * * * *
29059780 TTTTGAGGAAATAGTTTAAAAAACGCTTCAAGAAATATGCTTTATAAGAAGAATTTGTG-AATCG
1 TTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCG
* * * *
29059844 CGCCCACATGGACGCACTTTTGCTACAGTAGGTCCTGAGAAAATAATTTTGAGTTGACGT
66 CGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGA-AAAATAATTTCGAGTTGACGT
* * *
29059904 TTCTGAGCAAATAGTATAAAACAACGCTACAAGCAACATGCTATT-TGAGAATAATTTGTGAAAT
1 TTCTGAGCAAATAGTATAAAA-AACGCTTCAAGCAAGATGCT-TTATGAGAAGAATTTGTGAAAT
* * * *
29059968 CGCGCCCTCGTGGACGCGCTTTTGCTATAGTTGGTCCTAGAAAAATAATTTCAACTTGACGT
64 CGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCT-GAAAAATAATTTCGAGTTGACGT
* ** ** * *
29060030 TTCTAAGCAAATAGTAT-AAAGTCGCTTCTTGCAGGATGCTTTATGAGAAGAATTTGTGAAATCA
1 TTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCG
* *
29060094 CACTCACGTGGACGCGCTTTTGCTA
66 CGCCCACGTGGACGCGCTTTTGCTA
29060119 TAGTAACATG
Statistics
Matches: 288, Mismatches: 45, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
123 2 0.01
124 93 0.32
125 69 0.24
126 122 0.42
127 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (124 bp):
TTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCG
CGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGAAAAATAATTTCGAGTTGACGT
Found at i:29063136 original size:22 final size:22
Alignment explanation
Indices: 29063095--29064184 Score: 1195
Period size: 22 Copynumber: 50.0 Consensus size: 22
29063085 TCAAATTATA
29063095 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
29063116 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063138 TTAAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063160 TTAAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
29063182 TTTAGGTTAAGGG-TTAGTATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063203 TTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
29063225 TTTAA-TTTAGGGGTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
29063246 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063268 TTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063290 TTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063311 TTTAGGTTAAAGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063332 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063354 TTTAATTTAAGGG-TTAGTG-T
1 TTTAAGTTAAGGGTTTAGGGTT
29063374 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063395 TTTAAGTTTAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063417 TTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063438 TTTAGGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063459 TTTAGGCTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063481 TTTAATTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063502 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063524 TTTAAGTTAAGGGTCTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063546 TTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063567 TTTAGGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063588 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063610 TTTAATTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063631 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
29063653 TTTAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
** * *
29063674 TTTATTTTAAGGG-TTATGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063695 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
29063717 TTTAATTTAAGGG-TTATGATT
1 TTTAAGTTAAGGGTTTAGGGTT
29063738 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
29063760 TTTAAGTTAAGAGCCT-GAGGTT
1 TTTAAGTTAAGGGTTTAG-GGTT
*
29063782 TTAAAGTT-AGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063803 TTCAAGTTAAGGG-TTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063824 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063846 TTTAATTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
29063867 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
29063889 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29063911 TTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063932 TTCAAGTTAATGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
29063953 TTTAATTTAAGGATTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
29063975 TTGAATTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
29063997 TTTAATTTAAGAGTTTAGGGTTT
1 TTTAAGTTAAGGGTTTAGGG-TT
* *
29064020 TTTAGGTTAAGGGTTTAGAG-T
1 TTTAAGTTAAGGGTTTAGGGTT
29064041 TTTAATGTTAAGGG-TTAGGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
* *
29064063 TTTAGGTTAAGTGTTTAGGGTTAGGGTT
1 TTTAAGTTAA--G----GGTTTAGGGTT
* *
29064091 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * *
29064113 TTAAAATTAAGGGGTTAGGGGT
1 TTTAAGTTAAGGGTTTAGGGTT
*
29064135 TTTAATTTAAGGGTTAGGGTTAGGGTT
1 TTTAAGTTAAGGG-T----TTAGGGTT
* *
29064162 TTTAGGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
29064184 T
1 T
29064185 GTCAATTAAA
Statistics
Matches: 919, Mismatches: 113, Indels: 73
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.01
21 393 0.43
22 454 0.49
23 19 0.02
26 2 0.00
27 20 0.02
28 18 0.02
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.46
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:29063162 original size:43 final size:43
Alignment explanation
Indices: 29063095--29064155 Score: 912
Period size: 43 Copynumber: 24.5 Consensus size: 43
29063085 TCAAATTATA
*
29063095 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* *
29063138 TTAAAGTTAAAGGTTTAGGGTTTTAAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * ** * *
29063182 TTTAGGTT-AAGGGTTAGTATTTTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAAGGTTTAG-GGTTTTAAGTTAAGGGTTTAGGGTT
* ** * *
29063225 TTTAATTTAGGGGTTAAGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
29063268 TTTAAGTT-AAGGTTTTAGGGTTTTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAAGG-TTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* *
29063311 TTTAGGTTAAAGG-TTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * *
29063354 TTTAA-TTTAAGGGTTAGTGTTTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAAGGTTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
* *
29063395 TTTAAGTTTAGGGTTTAGGGTTTTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * * *
29063438 TTTAGGTT-AAGGGTTAGGGTTTTTAGGCTAAGGGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * * * *
29063481 TTTAATTTAAGGGTTAAGGTTTTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAAGGTTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
* *
29063524 TTTAAGTTAAGGGTCTAGGGTTTTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * *
29063567 TTTAGGTT-AAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * * * *
29063610 TTTAATTTAAGGGTTAAGGTTTTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAAGGTTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
** * *
29063653 TTTAAGTT-AAGGTTTAGGGTTTTTATTTTAAGGG-TTATGATT
1 TTTAAGTTAAAGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * * * * *
29063695 TTTAGGTTAAGGGTTTATGGTTTTTAATTTAAGGG-TTATGATT
1 TTTAAGTTAAAGGTTTA-GGGTTTTAAGTTAAGGGTTTAGGGTT
* * **
29063738 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGAGCCT-GAGGTT
1 TTTAAGTTAAAGGTTTAGGG-TTTTAAGTTAAGGGTTTAG-GGTT
* * *
29063782 TTAAAGTT-AGGGTTTAGGGTTTTCAAGTTAAGGG-TTATGGTT
1 TTTAAGTTAAAGGTTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * * *
29063824 TTTAGGTTAAGGGTTTATGGTTTTTAATTTAAGGG-TTAGGGTT
1 TTTAAGTTAAAGGTTTA-GGGTTTTAAGTTAAGGGTTTAGGGTT
*
29063867 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * *
29063911 TTAAAGTT-AAGGGTTAGGGTTTTCAAGTTAATGG-TTAGGGTT
1 TTTAAGTTAAAGGTTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * * *
29063953 TTTAA-TTTAAGGATTTATGGTTTTGAATTTAAGGGTTTATGGTT
1 TTTAAGTTAAAGG-TTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * *
29063997 TTTAA-TTTAAGAGTTTAGGGTTTTTTAGGTTAAGGGTTTAGAG-T
1 TTTAAGTTAAAG-GTTTAGGG--TTTTAAGTTAAGGGTTTAGGGTT
* * *
29064041 TTTAATGTT-AAGGGTTAGGGTTTTTAGGTTAAGTGTTTAGGGTTAGGGTT
1 TTTAA-GTTAAAGGTTTAGGG-TTTTAAGTTAA--G----GGTTTAGGGTT
* * * * * *
29064091 TTTAGGTTAAGGGTTTATGGTTTTAAAATTAAGGGGTTAGGGGT
1 TTTAAGTTAAAGGTTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* *
29064135 TTTAA-TTTAAGGGTTAGGGTT
1 TTTAAGTTAAAGGTTTAGGGTT
29064156 AGGGTTTTTA
Statistics
Matches: 841, Mismatches: 127, Indels: 100
0.79 0.12 0.09
Matches are distributed among these distances:
41 8 0.01
42 153 0.18
43 463 0.55
44 160 0.19
45 18 0.02
46 6 0.01
48 1 0.00
49 14 0.02
50 18 0.02
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.46
Consensus pattern (43 bp):
TTTAAGTTAAAGGTTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
Found at i:29064063 original size:28 final size:28
Alignment explanation
Indices: 29064024--29064101 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
29064014 GGGTTTTTTA
*
29064024 GGTTAAGGGTTTAGAGTTTTAA-TGTTAAG
1 GGTT-AGGGTTTAGAG-GTTAAGTGTTAAG
** *
29064053 GGTTAGGGTTTTTAGGTTAAGTGTTTAG
1 GGTTAGGGTTTAGAGGTTAAGTGTTAAG
**
29064081 GGTTAGGGTTTTTAGGTTAAG
1 GGTTAGGGTTTAGAGGTTAAG
29064102 GGTTTATGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 4 0.09
28 36 0.82
29 4 0.09
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.44
Consensus pattern (28 bp):
GGTTAGGGTTTAGAGGTTAAGTGTTAAG
Found at i:29064094 original size:15 final size:14
Alignment explanation
Indices: 29064053--29064106 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
29064043 TAATGTTAAG
29064053 GGTTAGGGTTTTTA
1 GGTTAGGGTTTTTA
* *
29064067 GGTTA-AGTGTTTA
1 GGTTAGGGTTTTTA
29064080 GGGTTAGGGTTTTTA
1 -GGTTAGGGTTTTTA
29064095 GGTTAAGGGTTT
1 GGTT-AGGGTTT
29064107 ATGGTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 6 0.18
14 14 0.42
15 13 0.39
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (14 bp):
GGTTAGGGTTTTTA
Found at i:29064106 original size:28 final size:28
Alignment explanation
Indices: 29064051--29064112 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
29064041 TTTAATGTTA
*
29064051 AGGGTTAGGGTTTTTAGGTTAAGTGTTT
1 AGGGTTAGGGTTTTTAGGTTAAGGGTTT
29064079 AGGGTTAGGGTTTTTAGGTTAAGGGTTT
1 AGGGTTAGGGTTTTTAGGTTAAGGGTTT
*
29064107 ATGGTT
1 AGGGTT
29064113 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (28 bp):
AGGGTTAGGGTTTTTAGGTTAAGGGTTT
Found at i:29064159 original size:27 final size:27
Alignment explanation
Indices: 29064124--29064176 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
29064114 TAAAATTAAG
*
29064124 GGGTTAGGGGTTTTAATTTAAGGGTTA
1 GGGTTAGGGGTTTTAAGTTAAGGGTTA
* *
29064151 GGGTTAGGGTTTTTAGGTTAAGGGTT
1 GGGTTAGGGGTTTTAAGTTAAGGGTT
29064177 TAAGGTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.42
Consensus pattern (27 bp):
GGGTTAGGGGTTTTAAGTTAAGGGTTA
Found at i:29064193 original size:71 final size:70
Alignment explanation
Indices: 29063943--29064184 Score: 264
Period size: 71 Copynumber: 3.5 Consensus size: 70
29063933 TCAAGTTAAT
** * * * *
29063943 GGTTAGGGTTTTTAATTTAAGGATTTATGGTTTTGAATTTAAGGGTTTATGGTTTTTAATTTAA-
1 GGTTAGGGTTTTTAGGTTAAGGGTTTAAGGTTTT-AATTTAAGGGGTTAGGGTTTTTAATTTAAG
29064007 -G--A-
65 GGTTAG
* **
29064009 GTTTAGGGTTTTTTAGGTTAAGGGTTT-AGAGTTTTAATGTTAA-GGGTTAGGGTTTTTAGGTTA
1 GGTTAGGG-TTTTTAGGTTAAGGGTTTAAG-GTTTTAAT-TTAAGGGGTTAGGGTTTTTAATTTA
*
29064072 AGTGTTTAG
63 AG-GGTTAG
* * *
29064081 GGTTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTAAAATTAAGGGGTTAGGGGTTTTAATTTAAG
1 GGTTAGGGTTTTTAGGTTAAGGGTTTAAGGTTTT-AATTTAAGGGGTTAGGGTTTTTAATTTAAG
29064146 GGTTAG
65 GGTTAG
29064152 GGTTAGGGTTTTTAGGTTAAGGGTTTAAGGTTT
1 GGTTAGGGTTTTTAGGTTAAGGGTTTAAGGTTT
29064185 GTCAATTAAA
Statistics
Matches: 146, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
66 28 0.19
67 24 0.16
71 65 0.45
72 29 0.20
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (70 bp):
GGTTAGGGTTTTTAGGTTAAGGGTTTAAGGTTTTAATTTAAGGGGTTAGGGTTTTTAATTTAAGG
GTTAG
Found at i:29064732 original size:18 final size:18
Alignment explanation
Indices: 29064706--29064748 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29064696 GACTCGAAAA
* *
29064706 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
29064724 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
29064742 AGGAAAC
1 AGGAAAC
29064749 GCAGCTAGCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:29065357 original size:7 final size:7
Alignment explanation
Indices: 29065347--29065379 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
29065337 TTATATACAT
29065347 AATACTA
1 AATACTA
29065354 AATACTA
1 AATACTA
29065361 AATACTA
1 AATACTA
*
29065368 AATATTA
1 AATACTA
29065375 AATAC
1 AATAC
29065380 CAATCGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Found at i:29066499 original size:18 final size:17
Alignment explanation
Indices: 29066478--29066511 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
29066468 TTTTACGGTT
29066478 TAAAAAAATTTTTAAAAA
1 TAAAAAAA-TTTTAAAAA
29066496 TAAAAAAATTTTAAAA
1 TAAAAAAATTTTAAAA
29066512 TTATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAAAATTTTAAAAA
Found at i:29066603 original size:22 final size:25
Alignment explanation
Indices: 29066578--29066624 Score: 73
Period size: 22 Copynumber: 2.0 Consensus size: 25
29066568 ATAAATATGG
29066578 ATTTGAGA-GAAATTT-TGA-AGGA
1 ATTTGAGAGGAAATTTGTGAGAGGA
29066600 ATTTGAGAGGAAATTTGTGAGAGGA
1 ATTTGAGAGGAAATTTGTGAGAGGA
29066625 TTAGTTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 7 0.32
24 3 0.14
25 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (25 bp):
ATTTGAGAGGAAATTTGTGAGAGGA
Found at i:29067616 original size:18 final size:18
Alignment explanation
Indices: 29067571--29067608 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
29067561 GCAAAATTAT
*
29067571 AATTAT-GAATAAATGTG
1 AATTATGGATTAAATGTG
29067588 AATTATGGATTAAAT-TG
1 AATTATGGATTAAATGTG
29067605 AATT
1 AATT
29067609 TTGAGATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (18 bp):
AATTATGGATTAAATGTG
Found at i:29067894 original size:41 final size:41
Alignment explanation
Indices: 29067831--29068018 Score: 180
Period size: 41 Copynumber: 4.6 Consensus size: 41
29067821 GTTAGTTATT
* ** *
29067831 CCCTAAATTACACATACATGCCCCTATTTATACTTCGGTAC
1 CCCTGAATTACACATATGTGCCCCTATTTGTACTTCGGTAC
*
29067872 CCCTGAATTACACATATGTGCCCCTATTTGTACTTTGGTAC
1 CCCTGAATTACACATATGTGCCCCTATTTGTACTTCGGTAC
* * * * *
29067913 CCCTGAATTGCACATACGTGCCCCTGTTTGTACGTCAGTAC
1 CCCTGAATTACACATATGTGCCCCTATTTGTACTTCGGTAC
* * * * * * **
29067954 CCTTAAATTGCATAT-TCGTGCCCCTGTTCGTACTTCGAAAC
1 CCCTGAATTACACATAT-GTGCCCCTATTTGTACTTCGGTAC
* *
29067995 CCCCGAACTACACATATGTGCCCC
1 CCCTGAATTACACATATGTGCCCC
29068019 GGTTTACACT
Statistics
Matches: 119, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 118 0.99
42 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (41 bp):
CCCTGAATTACACATATGTGCCCCTATTTGTACTTCGGTAC
Found at i:29067938 original size:21 final size:21
Alignment explanation
Indices: 29067871--29067938 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
29067861 TACTTCGGTA
* *
29067871 CCCCTGAATTACACATATGTG
1 CCCCTGAATTGCACATACGTG
* * * ** *
29067892 CCCCT-ATTTGTACTTTGGTA
1 CCCCTGAATTGCACATACGTG
29067912 CCCCTGAATTGCACATACGTG
1 CCCCTGAATTGCACATACGTG
29067933 CCCCTG
1 CCCCTG
29067939 TTTGTACGTC
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.31
Consensus pattern (21 bp):
CCCCTGAATTGCACATACGTG
Found at i:29068983 original size:42 final size:42
Alignment explanation
Indices: 29068937--29069025 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
29068927 GTACACAGGC
**
29068937 GTGTGAGGCTATTACGAGAGTTACATGGCCTAGCACACGGAT
1 GTGTGAGGCTATTACGAGAGTTACACAGCCTAGCACACGGAT
* * * * *
29068979 GTGTGTGGCTATTTCGAGATTTACACAGCCTAGCATACGGGT
1 GTGTGAGGCTATTACGAGAGTTACACAGCCTAGCACACGGAT
29069021 GTGTG
1 GTGTG
29069026 GCTTAGCCGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (42 bp):
GTGTGAGGCTATTACGAGAGTTACACAGCCTAGCACACGGAT
Found at i:29070464 original size:35 final size:35
Alignment explanation
Indices: 29070418--29070486 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
29070408 ACAAAAATAT
*
29070418 GTTAAAAAGGCTGTGAAGCATATCTCGCTAACATA
1 GTTAAAAAGGCTGTGAACCATATCTCGCTAACATA
*
29070453 GTTAAAAAGGCTGTGAACCATATCTCGCTTACAT
1 GTTAAAAAGGCTGTGAACCATATCTCGCTAACAT
29070487 TGGGTGCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (35 bp):
GTTAAAAAGGCTGTGAACCATATCTCGCTAACATA
Found at i:29074248 original size:53 final size:53
Alignment explanation
Indices: 29074157--29074267 Score: 145
Period size: 53 Copynumber: 2.1 Consensus size: 53
29074147 TAAGAGGCAT
* * * *
29074157 TTACACAGTAATGCTTTGTAACTCTATTCCGACAATGGATATGGGTTAGGGGTG
1 TTACACAGTAATACTCTGTAACTCTATTCAGACAATGGAGATGGGTTA-GGGTG
*
29074211 TTACACA-TAATACTCTGTAACTCTAATTCAG-CGATGGAGATGGGTTAGGGTG
1 TTACACAGTAATACTCTGTAACTCT-ATTCAGACAATGGAGATGGGTTAGGGTG
29074263 TTACA
1 TTACA
29074268 TTTAGTGGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
52 10 0.20
53 29 0.57
54 12 0.24
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (53 bp):
TTACACAGTAATACTCTGTAACTCTATTCAGACAATGGAGATGGGTTAGGGTG
Found at i:29083377 original size:15 final size:15
Alignment explanation
Indices: 29083357--29083386 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29083347 CTATGCATGC
*
29083357 AAAATATAAAAGACA
1 AAAATACAAAAGACA
29083372 AAAATACAAAAGACA
1 AAAATACAAAAGACA
29083387 TAATAGTAAA
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:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:29090330 original size:37 final size:36
Alignment explanation
Indices: 29090268--29090343 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
29090258 GATAATCACT
*
29090268 TTAATATTAAATTAATAAAATACTATTAAGATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
29090305 TTAA-ATTAAATCTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAAT-TAATA-AAATACTATTAAAATAATA
29090341 TTA
1 TTA
29090344 TTTTTGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 12 0.34
37 21 0.60
38 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:29092516 original size:20 final size:20
Alignment explanation
Indices: 29092491--29092537 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29092481 AACTATTTCA
29092491 TTACTTA-TTTACCACTCCAT
1 TTACTTACTTT-CCACTCCAT
* *
29092511 TTACTTACTTTCTATTCCAT
1 TTACTTACTTTCCACTCCAT
29092531 TTACTTA
1 TTACTTA
29092538 GCATAAGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (20 bp):
TTACTTACTTTCCACTCCAT
Found at i:29093578 original size:48 final size:46
Alignment explanation
Indices: 29093451--29093571 Score: 154
Period size: 48 Copynumber: 2.6 Consensus size: 46
29093441 TGTGCCATGG
* * * *
29093451 TGTCTTTCAACTATGGTCTTATTT-ATTCTCGTCTTGATGCCATAA
1 TGTCTTTCAACTATGGTCTTATTTCTTTTTCATCTTCATGCCATAA
* * *
29093496 TGTCTTTCAACCATGGTCTTATTCTTTTTTTTCATCTTCTTGCCATAA
1 TGTCTTTCAACTATGGTCTTA-T-TTCTTTTTCATCTTCATGCCATAA
29093544 TGTCTTTCAACTATGGTCTTATTTCTTT
1 TGTCTTTCAACTATGGTCTTATTTCTTT
29093572 GATTCATGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
45 20 0.31
46 6 0.09
47 3 0.05
48 36 0.55
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.51
Consensus pattern (46 bp):
TGTCTTTCAACTATGGTCTTATTTCTTTTTCATCTTCATGCCATAA
Found at i:29093603 original size:45 final size:45
Alignment explanation
Indices: 29093536--29093733 Score: 154
Period size: 45 Copynumber: 4.4 Consensus size: 45
29093526 TTCATCTTCT
* * *
29093536 TGCCATAATGTCTTTCAACTATGGTCTTATTTCTTTGATTCATGA
1 TGCCATAACGTCTTTCAGCTATGGTCTTATTTCTTAGATTCATGA
* * * * *
29093581 TGCCATAGCGTCTTTCAGCTATGGTTTTA-CTCAATAGGATT-GTGA
1 TGCCATAACGTCTTTCAGCTATGGTCTTATTTC-TTA-GATTCATGA
* ** *
29093626 TGCCATAACGTCTTTCA-ATCATGGTCTTATTTGATAGAATCATGA
1 TGCCATAACGTCTTTCAGCT-ATGGTCTTATTTCTTAGATTCATGA
** * * *
29093671 TGCCATAACGTCTTTCAG-TCACAGTCTTA-CTCAATAGAATCATGA
1 TGCCATAACGTCTTTCAGCT-ATGGTCTTATTTC-TTAGATTCATGA
*
29093716 TGCCATAACATCTTTCAG
1 TGCCATAACGTCTTTCAG
29093734 TCATGGTTTT
Statistics
Matches: 126, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
44 7 0.06
45 114 0.90
46 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (45 bp):
TGCCATAACGTCTTTCAGCTATGGTCTTATTTCTTAGATTCATGA
Found at i:29093669 original size:90 final size:90
Alignment explanation
Indices: 29093536--29093790 Score: 255
Period size: 90 Copynumber: 2.8 Consensus size: 90
29093526 TTCATCTTCT
* ** * * *
29093536 TGCCATAATGTCTTTCAA-CTATGGTCTTATTTCTTTGATTCATGATGCCATAGCGTCTTTCAG-
1 TGCCATAACGTCTTTCAATC-ATGGTCTTATTTGATAGAATCATGATGCCATAACGTCTTTCAGT
** * * **
29093599 CTATGGTTTTACTCAATAGGATTGTGA
65 C-ACAGTCTTACTCAATAGAATCATGA
29093626 TGCCATAACGTCTTTCAATCATGGTCTTATTTGATAGAATCATGATGCCATAACGTCTTTCAGTC
1 TGCCATAACGTCTTTCAATCATGGTCTTATTTGATAGAATCATGATGCCATAACGTCTTTCAGTC
29093691 ACAGTCTTACTCAATAGAATCATGA
66 ACAGTCTTACTCAATAGAATCATGA
* * * * * ** * *
29093716 TGCCATAACATCTTTCAGTCATGGTTTTACTCGATAGAATTGTAATGACATAACGTCTCTT-AGT
1 TGCCATAACGTCTTTCAATCATGGTCTTATTTGATAGAATCATGATGCCATAACGTCT-TTCAGT
**
29093780 CATGGTCTTAC
65 CACAGTCTTAC
29093791 ACGTTTCCGG
Statistics
Matches: 139, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
90 135 0.97
91 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (90 bp):
TGCCATAACGTCTTTCAATCATGGTCTTATTTGATAGAATCATGATGCCATAACGTCTTTCAGTC
ACAGTCTTACTCAATAGAATCATGA
Found at i:29093734 original size:45 final size:45
Alignment explanation
Indices: 29093575--29093790 Score: 238
Period size: 45 Copynumber: 4.8 Consensus size: 45
29093565 TTTCTTTGAT
* * *
29093575 TCATGATGCCATAGCGTCTTTCAG-CTATGGTTTTACTCAATAGGA
1 TCATGATGCCATAACGTCTTTCAGTC-ATGGTCTTACTCAATAGAA
** * * **
29093620 TTGTGATGCCATAACGTCTTTCAATCATGGTCTTATTTGATAGAA
1 TCATGATGCCATAACGTCTTTCAGTCATGGTCTTACTCAATAGAA
**
29093665 TCATGATGCCATAACGTCTTTCAGTCACAGTCTTACTCAATAGAA
1 TCATGATGCCATAACGTCTTTCAGTCATGGTCTTACTCAATAGAA
* * *
29093710 TCATGATGCCATAACATCTTTCAGTCATGGTTTTACTCGATAGAA
1 TCATGATGCCATAACGTCTTTCAGTCATGGTCTTACTCAATAGAA
** * *
29093755 TTGTAATGACATAACGTCTCTT-AGTCATGGTCTTAC
1 TCATGATGCCATAACGTCT-TTCAGTCATGGTCTTAC
29093791 ACGTTTCCGG
Statistics
Matches: 141, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
45 138 0.98
46 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (45 bp):
TCATGATGCCATAACGTCTTTCAGTCATGGTCTTACTCAATAGAA
Found at i:29093833 original size:135 final size:135
Alignment explanation
Indices: 29093536--29093834 Score: 295
Period size: 135 Copynumber: 2.2 Consensus size: 135
29093526 TTCATCTTCT
* * * * * *
29093536 TGCCATAATGTCTTTCAACTATGGTCTTATTTCTTTGATTCATGATGCCATAGCGTCTTTCAGCT
1 TGCCATAATGTCTTTCAACTATGGTCTTATCTCATAGAATCATGATGCCATAACATCTTTCAGCT
* * * ***
29093601 ATGGTTTTACTCAATAGGATTGTGATGCCATAACGTCTTTCAATCATGGTCTTATTTGATAGAAT
66 ATGGTTTTACTCAATAGAATTGTAATGACATAACGTCTTTCAATCATGGTCTTACACGATAGAAT
29093666 CATGA
131 CATGA
* * **
29093671 TGCCATAACGTCTTTC-AGTCACAGTCTTA-CTCAATAGAATCATGATGCCATAACATCTTTCAG
1 TGCCATAATGTCTTTCAACT-ATGGTCTTATCTC-ATAGAATCATGATGCCATAACATCTTTCAG
* * *
29093734 -TCATGGTTTTACTCGATAGAATTGTAATGACATAACGTCTCTT-AGTCATGGTCTTACACGTTT
64 CT-ATGGTTTTACTCAATAGAATTGTAATGACATAACGTCT-TTCAATCATGGTCTTACACG-AT
* * *
29093797 CCG-GT-ATGG
126 -AGAATCATGA
*
29093806 TGCCATAGTGTCTTTCAACTATGGTCTTA
1 TGCCATAATGTCTTTCAACTATGGTCTTA
29093835 ATCATTTCCT
Statistics
Matches: 130, Mismatches: 27, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
134 5 0.04
135 118 0.91
136 6 0.05
137 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (135 bp):
TGCCATAATGTCTTTCAACTATGGTCTTATCTCATAGAATCATGATGCCATAACATCTTTCAGCT
ATGGTTTTACTCAATAGAATTGTAATGACATAACGTCTTTCAATCATGGTCTTACACGATAGAAT
CATGA
Found at i:29102542 original size:40 final size:40
Alignment explanation
Indices: 29102444--29102706 Score: 334
Period size: 40 Copynumber: 6.6 Consensus size: 40
29102434 TCCTCGTTCA
* * * * *
29102444 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
29102483 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29102523 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29102563 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
29102603 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
29102643 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
29102683 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29102707 CAGCATTCAA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 37 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:29110492 original size:40 final size:40
Alignment explanation
Indices: 29110394--29110656 Score: 334
Period size: 40 Copynumber: 6.6 Consensus size: 40
29110384 TCCTCGTTCA
* * * * *
29110394 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
29110433 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29110473 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29110513 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
29110553 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
29110593 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
29110633 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29110657 CAGCATTCAA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 37 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:29118813 original size:16 final size:18
Alignment explanation
Indices: 29118789--29118821 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29118779 AAAACAATAG
29118789 TAAATTTAAT-TTGTAAA
1 TAAATTTAATATTGTAAA
29118806 TAAA-TTAATATTGTAA
1 TAAATTTAATATTGTAA
29118822 CAAACGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
TAAATTTAATATTGTAAA
Found at i:29121161 original size:67 final size:66
Alignment explanation
Indices: 29121079--29121222 Score: 209
Period size: 67 Copynumber: 2.2 Consensus size: 66
29121069 TAGATACATG
* * *
29121079 TGTAAGACCACAGCTGGGCTATGACATTTTGATGATAAGACCATAA-TTGAGTTATGACAATACA
1 TGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACTAG-GTTATGACAATAC-
29121143 AAA
64 AAA
* * *
29121146 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTAGGTTATGGCACTACAA
1 TGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACTAGGTTATGACAATACAA
29121211 A
66 A
29121212 TGTAAGACCAT
1 TGTAAGACCAT
29121223 GGCAGGGCCA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
66 14 0.20
67 54 0.77
68 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (66 bp):
TGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACTAGGTTATGACAATACAA
A
Found at i:29121190 original size:33 final size:33
Alignment explanation
Indices: 29121081--29121193 Score: 102
Period size: 33 Copynumber: 3.4 Consensus size: 33
29121071 GATACATGTG
* * *
29121081 TAAGACCACAGCTGGGCTATGACATTTTGATGA
1 TAAGACCATAACTGGGCTATGACATTCTGATGA
* * * * **
29121114 TAAGACCATAATTGAGTTATGACAATACAAAATG-
1 TAAGACCATAACTGGGCTATGAC-ATTC-TGATGA
* *
29121148 TAAGACCATAGCTGGGCTATGGCATTCTGATGA
1 TAAGACCATAACTGGGCTATGACATTCTGATGA
29121181 TAAGACCATAACT
1 TAAGACCATAACT
29121194 AGGTTATGGC
Statistics
Matches: 59, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
32 3 0.05
33 33 0.56
34 20 0.34
35 3 0.05
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGACATTCTGATGA
Found at i:29121218 original size:33 final size:32
Alignment explanation
Indices: 29121114--29121222 Score: 94
Period size: 33 Copynumber: 3.3 Consensus size: 32
29121104 ATTTTGATGA
* *
29121114 TAAGACCATAA-TTGAGTTATGACAATACAAAATG
1 TAAGACCATAACTAG-GTTATGGC-ATAC-AAATG
* * * * **
29121148 TAAGACCATAGCTGGGCTATGGCATTCTGATG
1 TAAGACCATAACTAGGTTATGGCATACAAATG
29121180 ATAAGACCATAACTAGGTTATGGCACTACAAATG
1 -TAAGACCATAACTAGGTTATGGCA-TACAAATG
29121214 TAAGACCAT
1 TAAGACCAT
29121223 GGCAGGGCCA
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
32 3 0.05
33 33 0.56
34 21 0.36
35 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (32 bp):
TAAGACCATAACTAGGTTATGGCATACAAATG
Found at i:29121254 original size:66 final size:67
Alignment explanation
Indices: 29121108--29121256 Score: 171
Period size: 66 Copynumber: 2.2 Consensus size: 67
29121098 TATGACATTT
* * * *
29121108 TGATGATAAGACCATAATTGAGTTATGACAATACAAAATGTAAGACCATAGCTGGGCTATGGCAT
1 TGATGATAAGACCATAATAGAGTTATGACAATACAAAATGTAAGACCATAGCAGGGCCATGGAAT
*
29121173 TC
66 GC
* * *
29121175 TGATGATAAGACCATAACTAG-GTTATGGCACTAC-AAATGTAAGACCATGGCAGGGCCATGGTA
1 TGATGATAAGACCATAA-TAGAGTTATGACAATACAAAATGTAAGACCATAGCAGGGCCATGG-A
29121238 ATGC
64 ATGC
29121242 ATG-TG-TAAGACCATA
1 -TGATGATAAGACCATA
29121257 GTTGGACTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
66 34 0.48
67 33 0.46
68 4 0.06
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (67 bp):
TGATGATAAGACCATAATAGAGTTATGACAATACAAAATGTAAGACCATAGCAGGGCCATGGAAT
GC
Found at i:29125621 original size:13 final size:13
Alignment explanation
Indices: 29125602--29125654 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
29125592 AGTTCTTCAT
29125602 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
29125615 CGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
29125628 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
29125641 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
29125654 T
1 T
29125655 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 30 0.88
14 2 0.06
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:29129390 original size:5 final size:5
Alignment explanation
Indices: 29129380--29129404 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29129370 GCCAAAGATG
29129380 TGAAT TGAAT TGAAT TGAAT TGAAT
1 TGAAT TGAAT TGAAT TGAAT TGAAT
29129405 ATAAATTAAT
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TGAAT
Found at i:29129822 original size:24 final size:25
Alignment explanation
Indices: 29129775--29129833 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
29129765 TTGGCTCTCA
* *
29129775 CGAGCTTCCCGTTATATAGTTCTTG
1 CGAGCTTCCCATTATATAGCTCTTG
*
29129800 CGAGCTTCCCATTA-ATAGCTCTTT
1 CGAGCTTCCCATTATATAGCTCTTG
*
29129824 TGAGCTTCCC
1 CGAGCTTCCC
29129834 GATTGGTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (25 bp):
CGAGCTTCCCATTATATAGCTCTTG
Found at i:29129945 original size:27 final size:27
Alignment explanation
Indices: 29129906--29129996 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
29129896 TGGCTCTCTG
29129906 GAGCTTCCCGATTAAAGGCTATTTCAT
1 GAGCTTCCCGATTAAAGGCTATTTCAT
* * *
29129933 GAGCTTCCTGATTAAATGCTTTTTCAT
1 GAGCTTCCCGATTAAAGGCTATTTCAT
* * * * *
29129960 GAGCTTTCCAATTCATGGCT-CTTCA-
1 GAGCTTCCCGATTAAAGGCTATTTCAT
29129985 GAGCTTCCCGAT
1 GAGCTTCCCGAT
29129997 ATTGGATCGC
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 10 0.19
26 4 0.08
27 38 0.73
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (27 bp):
GAGCTTCCCGATTAAAGGCTATTTCAT
Found at i:29133176 original size:31 final size:30
Alignment explanation
Indices: 29133131--29133192 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
29133121 GATTCATCAA
*
29133131 TGGAAAATTAAATAA-AGAAA-ATGAATAAAT
1 TGGAAAATGAAATAATA-AAAGATG-ATAAAT
29133161 TGGAAAGATGAAATAATAAAAGATGATAAAT
1 TGGAAA-ATGAAATAATAAAAGATGATAAAT
29133192 T
1 T
29133193 AATTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 6 0.21
31 18 0.64
32 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (30 bp):
TGGAAAATGAAATAATAAAAGATGATAAAT
Found at i:29134279 original size:23 final size:25
Alignment explanation
Indices: 29134253--29134300 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
29134243 GAACTCCTTG
*
29134253 ATTACA-GCTCTCATGAG-TTTCCC
1 ATTACAGGCTCACATGAGCTTTCCC
29134276 ATTACATGGCTCACATGAGCTTTCC
1 ATTACA-GGCTCACATGAGCTTTCC
29134301 GTTATATGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
25 10 0.48
26 5 0.24
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (25 bp):
ATTACAGGCTCACATGAGCTTTCCC
Found at i:29135142 original size:20 final size:21
Alignment explanation
Indices: 29135117--29135160 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
29135107 ATTAATTTTG
*
29135117 TAAGTT-TGGAAATTTTAA-TA
1 TAAGTTAT-GAAATGTTAAGTA
29135137 TAAGTTATGAAATGTTAAGTA
1 TAAGTTATGAAATGTTAAGTA
29135158 TAA
1 TAA
29135161 AACTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (21 bp):
TAAGTTATGAAATGTTAAGTA
Found at i:29138780 original size:47 final size:47
Alignment explanation
Indices: 29138724--29139094 Score: 643
Period size: 47 Copynumber: 7.9 Consensus size: 47
29138714 ATTCAGCCAA
*
29138724 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
29138771 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
29138818 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
29138865 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
29138912 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
29138961 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
29139008 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
* *
29139055 GAAAGTGTATATGTGTGATAACGCCTAATAGCCGATGTGA
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGA
29139095 AAGTGTATAT
Statistics
Matches: 315, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
47 268 0.85
49 47 0.15
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
Found at i:29138829 original size:94 final size:94
Alignment explanation
Indices: 29138724--29139302 Score: 879
Period size: 94 Copynumber: 6.2 Consensus size: 94
29138714 ATTCAGCCAA
* *
29138724 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
29138789 TAAGGCCTAATAGCCGATGTGATGAATGT
66 TAAGGCCTAATGGCCGATGTGATGAATGT
*
29138818 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29138883 TAAGGCCTAATGGCCGATGTGATGAATGT
66 TAAGGCCTAATGGCCGATGTGATGAATGT
*
29138912 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
29138977 GATAAGGCCTAATGGCCGATGTGATGAATGT
64 GATAAGGCCTAATGGCCGATGTGATGAATGT
* *
29139008 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29139073 TAACGCCTAATAGCC--------G-ATGT
66 TAAGGCCTAATGGCCGATGTGATGAATGT
*
29139093 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
29139158 TAAGGCCTAATCGCCGATGTGATGAATGT
66 TAAGGCCTAATGGCCGATGTGATGAATGT
* *
29139187 GAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGA
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * *
29139252 CAGGGCCGAGTGGCCAACGTGATGGATGT
66 TAAGGCCTAATGGCCGATGTGATGAATGT
* *
29139281 GAAAGTGCATAAATGTGATAAG
1 GAAAGTGTATATATGTGATAAG
29139303 TCCCGAAGGG
Statistics
Matches: 447, Mismatches: 27, Indels: 22
0.90 0.05 0.04
Matches are distributed among these distances:
85 81 0.18
86 1 0.00
93 1 0.00
94 272 0.61
96 92 0.21
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (94 bp):
GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
TAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:29139102 original size:38 final size:38
Alignment explanation
Indices: 29139051--29139132 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
29139041 GATGTGATGA
29139051 ATGTGAAAGTGTATATGTGTGATAACGCCTAATAGCCG
1 ATGTGAAAGTGTATATGTGTGATAACGCCTAATAGCCG
*
29139089 ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCG
1 ATGTGAAAGTGTATATGTGTGATAACGCCTAATAGCCG
29139127 ATGTGA
1 ATGTGA
29139133 TGAATGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (38 bp):
ATGTGAAAGTGTATATGTGTGATAACGCCTAATAGCCG
Found at i:29139113 original size:85 final size:87
Alignment explanation
Indices: 29139002--29139251 Score: 369
Period size: 85 Copynumber: 2.8 Consensus size: 87
29138992 CCGATGTGAT
29139002 GAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
*
29139067 GTGTGATAACGCCTAATAGCC-
66 ATGTGATAACGCCTAATAGCCG
29139088 G-ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
* *
29139152 ATGTGATAAGGCCTAATCGCCGATGTG
66 ATGTGATAACGCCTAATAGCC-----G
* * *
29139179 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 --GAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
29139244 ATATGTGA
64 ATATGTGA
29139252 CAGGGCCGAG
Statistics
Matches: 149, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
85 81 0.54
86 1 0.01
93 1 0.01
94 66 0.44
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (87 bp):
GAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAACGCCTAATAGCCG
Found at i:29139118 original size:132 final size:132
Alignment explanation
Indices: 29138814--29139226 Score: 646
Period size: 132 Copynumber: 3.0 Consensus size: 132
29138804 GATGTGATGA
29138814 ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
*
29138879 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
66 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATG
29138944 GCCGATGTGATG
129 GCC--------G
* * *
29138956 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 -ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
* * *
29139021 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAACGCCTAATAG
65 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
29139086 CCG
130 CCG
29139089 ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
*
29139154 GTGATAAGGCCTAATCGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
66 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
*
29139219 CA
131 CG
29139221 ATGTGA
1 ATGTGA
29139227 TGAATGTGAA
Statistics
Matches: 255, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
132 130 0.51
133 1 0.00
141 23 0.09
143 101 0.40
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (132 bp):
ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
CG
Found at i:29139133 original size:22 final size:22
Alignment explanation
Indices: 29139068--29139133 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
29139058 AGTGTATATG
*
29139068 TGTGATAACGCCTAATAGCCGA
1 TGTGATAAGGCCTAATAGCCGA
*
29139090 TGTGA-AAGTG--T-ATA--TG-
1 TGTGATAAG-GCCTAATAGCCGA
29139106 TGTGATAAGGCCTAATAGCCGA
1 TGTGATAAGGCCTAATAGCCGA
29139128 TGTGAT
1 TGTGAT
29139134 GAATGTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 16
0.63 0.06 0.31
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 1 0.03
19 6 0.18
20 1 0.03
21 3 0.09
22 12 0.36
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (22 bp):
TGTGATAAGGCCTAATAGCCGA
Found at i:29139140 original size:47 final size:47
Alignment explanation
Indices: 29139089--29139302 Score: 311
Period size: 47 Copynumber: 4.6 Consensus size: 47
29139079 CTAATAGCCG
* * *
29139089 ATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGA
* *
29139136 ATGTGAAAGTGTATATATGTGATAAGGCCTAATCGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGA
29139183 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGA
* * * * * *
29139230 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGA
* *
29139277 ATGTGAAAGTGCATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
29139303 TCCCGAAGGG
Statistics
Matches: 153, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 153 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGA
Found at i:29146517 original size:2 final size:2
Alignment explanation
Indices: 29146510--29146545 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29146500 TCTCAAATAT
29146510 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29146546 CCTTCTACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:29150698 original size:72 final size:71
Alignment explanation
Indices: 29150616--29150758 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 71
29150606 TCTCGGATTT
* *
29150616 AAAAAAGGGATCATGCCCAGTAAGTTAGGACGCGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
29150681 CTTGAG
66 CTTGAG
29150687 AAAAAATGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAA
1 AAAAAA-GGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAA
29150752 ACTTGAG
65 ACTTGAG
29150759 TTTGAAAAGA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 6 0.09
72 63 0.91
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (71 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGAG
Found at i:29151292 original size:3 final size:3
Alignment explanation
Indices: 29151284--29151333 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
29151274 AAATAGAAAT
* *
29151284 ATA ATA ATA ATA ATA ATA ATA ATA ATG ATG ATA ATA ATA ATA ATCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
29151330 ATA A
1 ATA A
29151334 GATAACAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29151317 original size:24 final size:24
Alignment explanation
Indices: 29151287--29151350 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
29151277 TAGAAATATA
29151287 ATAATAATAATAATAAT-AATAATG
1 ATAATAATAATAATAATCAATAA-G
*
29151311 ATGATAATAATAATAATCAATAAG
1 ATAATAATAATAATAATCAATAAG
* *
29151335 ATAACAAGAATAATAA
1 ATAATAATAATAATAA
29151351 AAAAGGACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (24 bp):
ATAATAATAATAATAATCAATAAG
Found at i:29157243 original size:25 final size:26
Alignment explanation
Indices: 29157209--29157259 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
29157199 TAAGCTTTCA
29157209 TGTATTTTCCTTCATT-TTGTGGTTT
1 TGTATTTTCCTTCATTCTTGTGGTTT
29157234 TGTATTTTCCTTCATTCTTGTGGTTT
1 TGTATTTTCCTTCATTCTTGTGGTTT
29157260 AAGTTTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.08, C:0.14, G:0.16, T:0.63
Consensus pattern (26 bp):
TGTATTTTCCTTCATTCTTGTGGTTT
Found at i:29157854 original size:16 final size:16
Alignment explanation
Indices: 29157833--29157865 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29157823 TCTCATCCTC
29157833 TTTTCTTTTTCTAATT
1 TTTTCTTTTTCTAATT
*
29157849 TTTTCTTTTTTTAATT
1 TTTTCTTTTTCTAATT
29157865 T
1 T
29157866 CTATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTTCTAATT
Found at i:29157938 original size:66 final size:68
Alignment explanation
Indices: 29157851--29158003 Score: 199
Period size: 70 Copynumber: 2.2 Consensus size: 68
29157841 TTCTAATTTT
** *
29157851 TTCT-TTTTTT-AATTTCTATTTA-TTTAAATTAATTTATCCTTTAATTATTTC-TT-TTTTATT
1 TTCTATTTTTTAAATTTAAATTTACTTTAAATTAATTTACCCTTTAATTATTTCTTTCTTTTA-T
29157911 TAAA
65 TAAA
29157915 TTCTATTTTTTAAATTTAAATTTATTCCTTTAAATTAATTTACCCTTTAATTATTTCTTTCTTTT
1 TTCTATTTTTTAAATTTAAATTTA---CTTTAAATTAATTTACCCTTTAATTATTTCTTTCTTTT
29157980 ATTAAA
63 ATTAAA
29157986 TTCTATTTTTTTAAATTT
1 TTCTA-TTTTTTAAATTT
29158004 GTGTAACACC
Statistics
Matches: 77, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
64 4 0.05
65 6 0.08
66 10 0.13
70 28 0.36
71 12 0.16
72 17 0.22
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.63
Consensus pattern (68 bp):
TTCTATTTTTTAAATTTAAATTTACTTTAAATTAATTTACCCTTTAATTATTTCTTTCTTTTATT
AAA
Found at i:29157952 original size:19 final size:19
Alignment explanation
Indices: 29157908--29157950 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
29157898 TTTCTTTTTT
*
29157908 ATTTAAATTCTATTTTTTAA
1 ATTTAAATT-TATTCTTTAA
29157928 ATTTAAATTTATTCCTTTAA
1 ATTTAAATTTATT-CTTTAA
29157948 ATT
1 ATT
29157951 AATTTACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTAAATTTATTCTTTAA
Found at i:29159631 original size:47 final size:47
Alignment explanation
Indices: 29159553--29159879 Score: 492
Period size: 47 Copynumber: 6.9 Consensus size: 47
29159543 CCCTTCGGGA
* * * * * * *
29159553 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
29159600 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29159647 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29159696 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29159745 CTTATCATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29159792 CCTATTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTA-TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29159840 CTTATCACATATATACACTTTCACATTCATCACATCGGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCC
29159880 TCACATTCAT
Statistics
Matches: 258, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 119 0.46
48 44 0.17
49 95 0.37
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29159885 original size:20 final size:20
Alignment explanation
Indices: 29159860--29159899 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29159850 ATATACACTT
29159860 TCACATTCATCACATCGGCC
1 TCACATTCATCACATCGGCC
29159880 TCACATTCATCACATCGGCC
1 TCACATTCATCACATCGGCC
29159900 ATTAGGCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.40, G:0.10, T:0.25
Consensus pattern (20 bp):
TCACATTCATCACATCGGCC
Found at i:29159886 original size:67 final size:67
Alignment explanation
Indices: 29159813--29159946 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
29159803 ATATACACTT
29159813 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
29159878 CC
66 CC
29159880 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
29159945 CC
66 CC
29159947 ATTAGGCCTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (67 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
CC
Found at i:29162390 original size:20 final size:19
Alignment explanation
Indices: 29162293--29162423 Score: 75
Period size: 20 Copynumber: 7.2 Consensus size: 19
29162283 TATCCTTTAA
*
29162293 TTATTTTTTT-AGTTAAAT
1 TTATTTTTTTAAATTAAAT
*
29162311 TCTA-TTTTTAAAATTTAAAT
1 T-TATTTTTTTAAA-TTAAAT
** *
29162331 TTATTCCTTTAAA-TATAT
1 TTATTTTTTTAAATTAAAT
* *
29162349 TTA-TCTATT-AATT--AT
1 TTATTTTTTTAAATTAAAT
29162364 TTA-TTTTTT-AATTAAAT
1 TTATTTTTTTAAATTAAAT
*
29162381 TCTATTTTTTAAAATTTAAAT
1 T-TATTTTTTTAAA-TTAAAT
*
29162402 TTATTCTTTTAAATT-AAT
1 TTATTTTTTTAAATTAAAT
29162420 TTAT
1 TTAT
29162424 CCTTCAATAT
Statistics
Matches: 89, Mismatches: 13, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
15 13 0.15
16 2 0.02
17 8 0.09
18 22 0.25
19 12 0.13
20 25 0.28
21 7 0.08
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (19 bp):
TTATTTTTTTAAATTAAAT
Found at i:29162401 original size:21 final size:21
Alignment explanation
Indices: 29162375--29162414 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
29162365 TATTTTTTAA
29162375 TTAAATTCTATT-TTTTAAAAT
1 TTAAATT-TATTCTTTTAAAAT
29162396 TTAAATTTATTCTTTTAAA
1 TTAAATTTATTCTTTTAAA
29162415 TTAATTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAATTTATTCTTTTAAAAT
Found at i:29162413 original size:71 final size:70
Alignment explanation
Indices: 29162255--29162453 Score: 275
Period size: 70 Copynumber: 2.9 Consensus size: 70
29162245 GGGATGTCAC
* * *
29162255 AATTTGAATTTATTCCTTTAAATAGATTTATCCTTTAATTA--T-TTTTTTAGTTAAATTCTATT
1 AATTTAAATTTATTCCTTTAAATATATTTATCCTTTAATTATTTATTTTTTAATTAAATTCTATT
29162317 TTTAA
66 TTTAA
29162322 AATTTAAATTTATTCCTTTAAATATATTTAT-CTATTAATTATTTATTTTTTAATTAAATTCTAT
1 AATTTAAATTTATTCCTTTAAATATATTTATCCT-TTAATTATTTATTTTTTAATTAAATTCTA-
29162386 TTTTTAA
64 TTTTTAA
* * *
29162393 AATTTAAATTTATTCTTTTAAAT-TAATTTATCCTTCAA-TATTTACTTTTTAATTAAATTCT
1 AATTTAAATTTATTCCTTTAAATAT-ATTTATCCTTTAATTATTTATTTTTTAATTAAATTCT
29162454 GGTACTGAGG
Statistics
Matches: 119, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
66 2 0.02
67 36 0.30
69 1 0.01
70 40 0.34
71 38 0.32
72 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.57
Consensus pattern (70 bp):
AATTTAAATTTATTCCTTTAAATATATTTATCCTTTAATTATTTATTTTTTAATTAAATTCTATT
TTTAA
Found at i:29162527 original size:53 final size:55
Alignment explanation
Indices: 29162445--29162552 Score: 152
Period size: 53 Copynumber: 2.0 Consensus size: 55
29162435 TACTTTTTAA
*
29162445 TTAAATTCTGGTACTGAGGTGATGGCCATCAATGTCCCAACACCCAA-ATTTTTT
1 TTAAATTCTGGTACTGAGGTGATGACCATCAATGTCCCAACACCCAATATTTTTT
*
29162499 TTAAA-TCTGGTAC-GAGGGTG-TCGACCATCATTGTCCCAACACCCAATATTTTTT
1 TTAAATTCTGGTACTGA-GGTGAT-GACCATCAATGTCCCAACACCCAATATTTTTT
29162553 AAAAAAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
52 3 0.06
53 34 0.69
54 12 0.24
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (55 bp):
TTAAATTCTGGTACTGAGGTGATGACCATCAATGTCCCAACACCCAATATTTTTT
Found at i:29165373 original size:186 final size:187
Alignment explanation
Indices: 29165017--29165391 Score: 547
Period size: 186 Copynumber: 2.0 Consensus size: 187
29165007 ACCTCACCAT
* * * **
29165017 TGAGTCATTGCTTTGCTGCATCTTTCCTCTCTTGTTATCTCTGATCACCACCCCAAGCGCCGCCT
1 TGAGTCACTGCCTTGCAGCATCTTTCCTCTCTTGTTATCTCCAATCACCACCCCAAGCGCCGCCT
** *
29165082 CTCCCACCGTGACAACCACTGTGCATTTCTCTTTTTTTTCTTATTCTTCTATTCTATTCTCTTTT
66 CTCCCACCGTGACAACCACCATGCATTTCTCTCTTTTTTCTTATTCTTCTATTCTATTCTCTTTT
29165147 CCCCTCATTTAAAAGAAGTGATCGAACCCACCTCCTCTCTCTCCCCTCCACCAGAAC
131 CCCCTCATTTAAAAGAAGTGATCGAACCCACCTCCTCTCTCTCCCCTCCACCAGAAC
* * **
29165204 TGAGTCACTGCCTTGCAGCATCTTTCCTCTCATT-TTCTCTCCAATCACCGCCTTAAGCGCCGCC
1 TGAGTCACTGCCTTGCAGCATCTTTCCTCTC-TTGTTATCTCCAATCACCACCCCAAGCGCCGCC
* *
29165268 TCTTCCACCGTGACAACCACCATGCATTTCTC-CTTTTTTCTTATTCTTCTATTCTTTTCTCTTT
65 TCTCCCACCGTGACAACCACCATGCATTTCTCTCTTTTTTCTTATTCTTCTATTCTATTCTCTTT
* * * * * *
29165332 TCCCTTTATTTAAAATAAGTGGTTGAACCCACCTCCTCTCTCTCCCCTCCACTAGAAC
130 TCCCCTCATTTAAAAGAAGTGATCGAACCCACCTCCTCTCTCTCCCCTCCACCAGAAC
29165390 TG
1 TG
29165392 CGCCTCTGTC
Statistics
Matches: 167, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
186 84 0.50
187 81 0.49
188 2 0.01
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.37
Consensus pattern (187 bp):
TGAGTCACTGCCTTGCAGCATCTTTCCTCTCTTGTTATCTCCAATCACCACCCCAAGCGCCGCCT
CTCCCACCGTGACAACCACCATGCATTTCTCTCTTTTTTCTTATTCTTCTATTCTATTCTCTTTT
CCCCTCATTTAAAAGAAGTGATCGAACCCACCTCCTCTCTCTCCCCTCCACCAGAAC
Found at i:29166447 original size:48 final size:48
Alignment explanation
Indices: 29166375--29166488 Score: 156
Period size: 48 Copynumber: 2.4 Consensus size: 48
29166365 AAGGTGGAAG
** * *
29166375 TATATGGTAGTTTATCTGTGTTAATGTGACACTGTTCATGAATCTGAT
1 TATATGGTAGTTTATCTGCATTAATGTGACACTGTTCACGAATCTAAT
* ** *
29166423 TATATGGCAGTTTATCTGCATTAATGTGATGCTGTTCACGATTCTAAT
1 TATATGGTAGTTTATCTGCATTAATGTGACACTGTTCACGAATCTAAT
29166471 TATATGGTAGTTTATCTG
1 TATATGGTAGTTTATCTG
29166489 TGACCTTGGT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (48 bp):
TATATGGTAGTTTATCTGCATTAATGTGACACTGTTCACGAATCTAAT
Found at i:29176550 original size:50 final size:50
Alignment explanation
Indices: 29176492--29176615 Score: 149
Period size: 50 Copynumber: 2.5 Consensus size: 50
29176482 TATTAAGGTT
* * *
29176492 ATGAGAGGTCCCGTGTAAGACCATCTCTGGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATCTCTGGGACATGGCATGGGCACCAAG
*** * * *
29176542 ATGAGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATCTCTGGGACATGGCATGGGCACCAAG
**
29176592 ATGAGAATTCCCATGTAAGACCAT
1 ATGAGAGGTCCCATGTAAGACCAT
29176616 ATTTGGGATA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATCTCTGGGACATGGCATGGGCACCAAG
Found at i:29187079 original size:13 final size:14
Alignment explanation
Indices: 29187030--29187079 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
29187020 AGTTTTTCAC
*
29187030 TCACTTTTTCCTTT
1 TCACTCTTTCCTTT
29187044 TCA-TCTTTCCCTTT
1 TCACTCTTT-CCTTT
* *
29187058 TCTCACTTT-CTTT
1 TCACTCTTTCCTTT
29187071 TCACTCTTT
1 TCACTCTTT
29187080 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 15 0.52
14 10 0.34
15 4 0.14
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (14 bp):
TCACTCTTTCCTTT
Found at i:29187133 original size:24 final size:25
Alignment explanation
Indices: 29187087--29187141 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
29187077 TTTTTTTAAA
29187087 ATTTTCTTTCGTTTTCTCATTTT-T
1 ATTTTCTTTCGTTTTCTCATTTTCT
29187111 ATTTTCTTT-GTTTTCACTC-TTTTCT
1 ATTTTCTTTCGTTTT--CTCATTTTCT
29187136 -TTTTCT
1 ATTTTCT
29187142 CTCATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 5 0.18
24 19 0.68
25 4 0.14
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (25 bp):
ATTTTCTTTCGTTTTCTCATTTTCT
Found at i:29192600 original size:50 final size:50
Alignment explanation
Indices: 29192498--29192689 Score: 186
Period size: 50 Copynumber: 3.7 Consensus size: 50
29192488 GGAATGAGAC
* * *
29192498 CCCATGTAAGACCATGTCTGGGACATGGCATTGACATTATTGAGGTTATGAGAGGT
1 CCCATGTAAGACCATATCTGGGACATGGCATTGGC---ATCGA-G--ATGAGAGGT
* * * *
29192554 CCCATGTAAGATCATGTTTGGGACATGGCGTTGGCATCGAGATGAGAGGT
1 CCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGAGATGAGAGGT
** * * * **
29192604 CCCCCGTAAGACCATATCTGGGACATTGCATGGGCATCGATATGAGAACT
1 CCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGAGATGAGAGGT
* *
29192654 CCCTTGTAAGACCATATCTGGGATATGGCATTGGCA
1 CCCATGTAAGACCATATCTGGGACATGGCATTGGCA
29192690 GTATGGCTTT
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
50 79 0.69
52 1 0.01
53 4 0.03
56 31 0.27
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (50 bp):
CCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGAGATGAGAGGT
Found at i:29192930 original size:20 final size:20
Alignment explanation
Indices: 29192905--29192953 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
29192895 TGAGTTTTTT
29192905 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
29192925 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
29192945 AAG-AAGCAA
1 AAGTAAGCAA
29192954 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:29203544 original size:51 final size:51
Alignment explanation
Indices: 29203483--29203824 Score: 293
Period size: 51 Copynumber: 6.7 Consensus size: 51
29203473 AGTTTTACGG
* * *
29203483 TTCACGTAGTAGCCTTCACACAATACTACACACGTGACCAAAGCTTTTCGG
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGA
* *** * * * *
29203534 TACACATAGTAGCCTTCATTTAGTACTACAAATGTAACC--ATCATTTATCGA
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGC-TTT-TCGA
* * * *
29203585 TTCACATAGTAACCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGG
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGA
* * * ** * *
29203636 TACACATTGTAGCCTTCCCTTAGTACTACACATGTGACC--ATCATTTATCGA
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGC-TTT-TCGA
* * *
29203687 TTCACGTAGTAGCCTTCACACAGTGCTACACACGTGACCAAAGCTTCTCGA
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGA
* * * * * *
29203738 TACACATTGTAGCCTTCA-ATTAGAACTACACATGTGACC--ATCATTTATCGA
1 TTCACATAGTAGCCTTCACA-CAGTACTACACACGTGACCAAAGC-TTT-TCGA
29203789 TTCACATAGTAGCCTTCACACAGTACTACACACGTG
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTG
29203825 TTCATTGATA
Statistics
Matches: 223, Mismatches: 56, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
49 6 0.03
50 8 0.04
51 200 0.90
52 5 0.02
53 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.28
Consensus pattern (51 bp):
TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGA
Found at i:29203659 original size:102 final size:102
Alignment explanation
Indices: 29203483--29203824 Score: 549
Period size: 102 Copynumber: 3.4 Consensus size: 102
29203473 AGTTTTACGG
* * * *
29203483 TTCACGTAGTAGCCTTCACACAATACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCC
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCC
* * *
29203548 TTCATTTAGTACTACAAATGTAACCATCATTTATCGA
66 TTCAATTAGTACTACACATGTGACCATCATTTATCGA
* *
29203585 TTCACATAGTAACCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATTGTAGCC
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCC
**
29203650 TTCCCTTAGTACTACACATGTGACCATCATTTATCGA
66 TTCAATTAGTACTACACATGTGACCATCATTTATCGA
* * *
29203687 TTCACGTAGTAGCCTTCACACAGTGCTACACACGTGACCAAAGCTTCTCGATACACATTGTAGCC
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCC
*
29203752 TTCAATTAGAACTACACATGTGACCATCATTTATCGA
66 TTCAATTAGTACTACACATGTGACCATCATTTATCGA
29203789 TTCACATAGTAGCCTTCACACAGTACTACACACGTG
1 TTCACATAGTAGCCTTCACACAGTACTACACACGTG
29203825 TTCATTGATA
Statistics
Matches: 220, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 220 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.28
Consensus pattern (102 bp):
TTCACATAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCC
TTCAATTAGTACTACACATGTGACCATCATTTATCGA
Found at i:29207895 original size:23 final size:24
Alignment explanation
Indices: 29207859--29207912 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
29207849 CTCATGTAAC
* *
29207859 TCAATTCTTCATTT-TTAT-TTCA
1 TCAATTCATAATTTCTTATGTTCA
29207881 TTCAATTCATAATTTCTTATGTTCA
1 -TCAATTCATAATTTCTTATGTTCA
29207906 -CAATTCA
1 TCAATTCA
29207913 AATCAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 19 0.70
24 4 0.15
25 4 0.15
ACGTcount: A:0.28, C:0.19, G:0.02, T:0.52
Consensus pattern (24 bp):
TCAATTCATAATTTCTTATGTTCA
Found at i:29209512 original size:50 final size:50
Alignment explanation
Indices: 29209436--29209775 Score: 294
Period size: 51 Copynumber: 6.8 Consensus size: 50
29209426 TTTTATCATT
* *
29209436 CGATACACGTAGTACCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* * *
29209486 CGGTTCAGGTAGTAGCCTTCATATAGTACTACACACGTGATCAAGTTTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* * * * *
29209536 CGATTCACATAGTAGCCTTCACACAGTACTACACAGGTGACCAAAGCTTCT-
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTA
* * * * * * *
29209587 CGGTACACATTGTAGCCTTCACTTAGTACTACACAAGTGA-CCA--TTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* * * *
29209634 TCGATTCACGTAGTAGCCTTCACACAGTACTACACTCGTGACCAAAGCTTCT-
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTA
* * * * * * * * **
29209686 CGATACACATTGTAGCCTTCACTTAGAACTACACATGTCACCAACATTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* *
29209736 TCGATTCATGTAGTAGCCTTCACACAGTACTACACACGTG
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTG
29209776 TTCATCGATA
Statistics
Matches: 227, Mismatches: 52, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
46 2 0.01
48 32 0.14
49 4 0.02
50 84 0.37
51 100 0.44
52 3 0.01
53 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (50 bp):
CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
Found at i:29209657 original size:99 final size:100
Alignment explanation
Indices: 29209435--29209775 Score: 413
Period size: 99 Copynumber: 3.4 Consensus size: 100
29209425 CTTTTATCAT
* * * * * * ** *
29209435 TCGATACACGTAGTACCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGTTCAGGTAG
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATTG
* * *
29209498 TAGCCTTCA-TATAGTACTACACACGTGATCAAGTTT-
65 TAGCCTTCACT-TAGTACTACACAAGTGACCCA-TTTA
* *
29209534 TACGATTCACATAGTAGCCTTCACACAGTACTACACAGGTGACCAAAGCTTCTCGGTACACATTG
1 T-CGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTG
29209599 TAGCCTTCACTTAGTACTACACAAGTGA-CCATTTA
65 TAGCCTTCACTTAGTACTACACAAGTGACCCATTTA
* *
29209634 TCGATTCACGTAGTAGCCTTCACACAGTACTACACTCGTGACCAAAGCTTCTCGATACACATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
* * *
29209699 AGCCTTCACTTAGAACTACACATGTCACCAACATTTA
66 AGCCTTCACTTAGTACTACACAAGTGACC--CATTTA
*
29209736 TCGATTCATGTAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTG
29209776 TTCATCGATA
Statistics
Matches: 212, Mismatches: 22, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
99 88 0.42
100 40 0.19
101 36 0.17
102 48 0.23
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (100 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
AGCCTTCACTTAGTACTACACAAGTGACCCATTTA
Found at i:29211667 original size:68 final size:69
Alignment explanation
Indices: 29211528--29211709 Score: 323
Period size: 68 Copynumber: 2.7 Consensus size: 69
29211518 TAATAATTTA
*
29211528 TCACCATAAAATAAACGG-AAGTTATCATCGGTTAACAAATACTTAAGGCATAACCAAAAGCCAA
1 TCACCATAAAATAAA-GGAAAGTTATCATCGGTTAACAAATACTTAAGGCATAAACAAAAGCCAA
29211592 TCTTT
65 TCTTT
*
29211597 TCACCATAAAATAAAGGAAAGTTATCATCAGTTAAC-AATACTTAAGGCATAAACAAAAGCCAAT
1 TCACCATAAAATAAAGGAAAGTTATCATCGGTTAACAAATACTTAAGGCATAAACAAAAGCCAAT
29211661 CTTT
66 CTTT
29211665 TCACCATAAAATAAAGGAAAGTTATCATCGGTTAACAAATACTTA
1 TCACCATAAAATAAAGGAAAGTTATCATCGGTTAACAAATACTTA
29211710 TGTATTATCA
Statistics
Matches: 108, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
68 68 0.63
69 40 0.37
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (69 bp):
TCACCATAAAATAAAGGAAAGTTATCATCGGTTAACAAATACTTAAGGCATAAACAAAAGCCAAT
CTTT
Found at i:29220568 original size:17 final size:17
Alignment explanation
Indices: 29220548--29220580 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29220538 TATATTATGG
29220548 ATGATATCATATGTAAC
1 ATGATATCATATGTAAC
*
29220565 ATGATATTATATGTAA
1 ATGATATCATATGTAA
29220581 AAAGAGATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (17 bp):
ATGATATCATATGTAAC
Found at i:29220634 original size:39 final size:39
Alignment explanation
Indices: 29220589--29220667 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
29220579 AAAAAGAGAT
29220589 TGATAAAGTAAATGATATGTTTGTATGTGAGAAATTTAC
1 TGATAAAGTAAATGATATGTTTGTATGTGAGAAATTTAC
*
29220628 TGATAAATTAAATGATATGTTTGTATGTGAGAAATTTAC
1 TGATAAAGTAAATGATATGTTTGTATGTGAGAAATTTAC
29220667 T
1 T
29220668 TATTCTATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.41
Consensus pattern (39 bp):
TGATAAAGTAAATGATATGTTTGTATGTGAGAAATTTAC
Found at i:29222170 original size:18 final size:18
Alignment explanation
Indices: 29222149--29222186 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
29222139 GAGGTGATTA
29222149 AAAACTAGGATTTTAACT
1 AAAACTAGGATTTTAACT
29222167 AAAACTAGGATTTTAACT
1 AAAACTAGGATTTTAACT
29222185 AA
1 AA
29222187 GTAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (18 bp):
AAAACTAGGATTTTAACT
Found at i:29233609 original size:27 final size:27
Alignment explanation
Indices: 29233579--29233755 Score: 167
Period size: 27 Copynumber: 6.5 Consensus size: 27
29233569 AAATTGTACA
* *
29233579 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
** *
29233606 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
29233633 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * *
29233660 GCACTAAGAGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* *
29233688 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * * *
29233715 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTG
*
29233742 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
29233756 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 101 0.82
28 22 0.18
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:29233692 original size:82 final size:81
Alignment explanation
Indices: 29233579--29233734 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
29233569 AAATTGTACA
* * * *
29233579 GCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGAGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
29233643 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29233660 GCACTAAGAGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGAGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
29233725 TGCGAGTTGA
65 TGCGAATTGA
29233735 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGAGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29236747 original size:20 final size:20
Alignment explanation
Indices: 29236703--29236747 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
29236693 ACTTAAAATT
*
29236703 TTTAAATTTCATTTGTTTTA
1 TTTAAATTTCATATGTTTTA
*
29236723 TTTAAATTTTATAT-TTTTA
1 TTTAAATTTCATATGTTTTA
29236742 TGTTAA
1 T-TTAA
29236748 TAAAGGGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTAAATTTCATATGTTTTA
Found at i:29241191 original size:79 final size:82
Alignment explanation
Indices: 29241080--29241264 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
29241070 GCTACTCGTT
* * *
29241080 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
29241143 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
29241160 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
29241223 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
29241240 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29241265 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:29241264 original size:40 final size:40
Alignment explanation
Indices: 29241061--29241264 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
29241051 CGGAATTTAA
** *
29241061 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
29241101 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
29241141 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29241180 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
29241220 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29241260 CCGGA
1 CCGGA
29241265 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29247385 original size:18 final size:18
Alignment explanation
Indices: 29247364--29247400 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29247354 AATATAATGG
29247364 ATATAATTATATATTAAT
1 ATATAATTATATATTAAT
*
29247382 ATATAATTGTATATTAAT
1 ATATAATTATATATTAAT
29247400 A
1 A
29247401 ATTATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATATAATTATATATTAAT
Found at i:29249978 original size:40 final size:40
Alignment explanation
Indices: 29249878--29250049 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
29249868 GCTCCTCGTT
* * *
29249878 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
29249918 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
** * *
29249957 CGGATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
29249997 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
29250037 CAAATGCCTTCGG
1 CAAATGCCTTCGG
29250050 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 35 0.30
40 78 0.67
41 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:29250062 original size:80 final size:79
Alignment explanation
Indices: 29249878--29250102 Score: 231
Period size: 80 Copynumber: 2.8 Consensus size: 79
29249868 GCTCCTCGTT
* * * * *
29249878 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
29249942 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
** * *
29249957 CGGATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
29250022 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
29250037 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
29250101 GA
63 GA
29250103 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 38 0.32
80 68 0.57
81 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:29250111 original size:41 final size:41
Alignment explanation
Indices: 29250034--29250111 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
29250024 TTTGTATCTC
* * *
29250034 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
29250075 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
29250112 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:29258692 original size:12 final size:13
Alignment explanation
Indices: 29258668--29258696 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29258658 AGGCTATGAC
29258668 TATTGCATTTATT
1 TATTGCATTTATT
29258681 TATTGC-TTTATT
1 TATTGCATTTATT
29258693 TATT
1 TATT
29258697 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:29260620 original size:22 final size:22
Alignment explanation
Indices: 29260592--29260635 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29260582 AGCAATACAA
29260592 AGGACTTGCCCTCTTCAAAGCC
1 AGGACTTGCCCTCTTCAAAGCC
29260614 AGGACTTGCCCTCTTCAAAGCC
1 AGGACTTGCCCTCTTCAAAGCC
29260636 TACTCTTTCA
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:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (22 bp):
AGGACTTGCCCTCTTCAAAGCC
Done.