Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008460.1 Hibiscus syriacus cultivar Beakdansim tig00111273_pilon, whole genome shotgun sequence
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: 2854393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 15
Found at i:704929 original size:20 final size:20
Alignment explanation
Indices: 704906--704950 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
704896 TTAGTAAATC
704906 GCAACACAGA-AGTCAAATTT
1 GCAACAC-GATAGTCAAATTT
* *
704926 GCAACGCGATAGTTAAATTT
1 GCAACACGATAGTCAAATTT
704946 GCAAC
1 GCAAC
704951 GCGGAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (20 bp):
GCAACACGATAGTCAAATTT
Found at i:704979 original size:19 final size:19
Alignment explanation
Indices: 704955--705009 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
704945 TGCAACGCGG
*
704955 AATTTCAAATTCACAACTA
1 AATTTCAAATTCGCAACTA
* *
704974 AATTTCAAATTTGCAACTG
1 AATTTCAAATTCGCAACTA
704993 AATTTCAAATTCGCAAC
1 AATTTCAAATTCGCAAC
705010 AAGTTTTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (19 bp):
AATTTCAAATTCGCAACTA
Found at i:705941 original size:24 final size:24
Alignment explanation
Indices: 705914--705967 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
705904 GTATTCGAAA
*
705914 TTTGATCTTGGTCAATACCCGGAT
1 TTTGATCTTGGGCAATACCCGGAT
* *
705938 TTTGATCTTGGGGAATACTCGGAT
1 TTTGATCTTGGGCAATACCCGGAT
705962 TTTGAT
1 TTTGAT
705968 GATGTTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGGCAATACCCGGAT
Found at i:708568 original size:19 final size:20
Alignment explanation
Indices: 708541--708582 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
708531 ATGTAGCCAT
708541 CAACACGAAAGTC-AATTCG
1 CAACACGAAAGTCAAATTCG
*
708560 CAACGCGAAAGTCAAATTCG
1 CAACACGAAAGTCAAATTCG
708580 CAA
1 CAA
708583 ACCGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (20 bp):
CAACACGAAAGTCAAATTCG
Found at i:709103 original size:24 final size:24
Alignment explanation
Indices: 709052--709104 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
709042 TTTCATATGT
* * *
709052 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
* *
709076 AATTTGAGTTTGTATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
709100 AATTT
1 AATTT
709105 CGGCTCCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:709837 original size:28 final size:28
Alignment explanation
Indices: 709805--709858 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
709795 ATAATTCTTA
*
709805 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
709833 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
709859 TTAATCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:709839 original size:14 final size:14
Alignment explanation
Indices: 709822--709858 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
709812 ATCAAATTAA
709822 ACAAATCAACTTTT
1 ACAAATCAACTTTT
709836 ACAAATCAACTTTT
1 ACAAATCAACTTTT
709850 ACAAATCAA
1 ACAAATCAA
709859 TTAATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:711256 original size:21 final size:22
Alignment explanation
Indices: 711230--711282 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
711220 GTGAATCGGG
711230 CTCTTGAACGGCA-GACA-GGAC
1 CTCTTGAACGG-ATGACAGGGAC
*
711251 CTCTTGAAC-GATGACAGGGGC
1 CTCTTGAACGGATGACAGGGAC
711272 CTCTTGAACGG
1 CTCTTGAACGG
711283 TGGGAGGGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 5 0.18
21 21 0.75
22 1 0.04
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.19
Consensus pattern (22 bp):
CTCTTGAACGGATGACAGGGAC
Found at i:711290 original size:21 final size:21
Alignment explanation
Indices: 711250--711348 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
711240 GCAGACAGGA
*
711250 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
711271 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
711292 CTTCTTCG-ATGATGAGAAGGG
1 CCTCTT-GAACGATGAGAGGGG
*
711313 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
711334 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
711349 TAGGTGCATC
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:711331 original size:42 final size:42
Alignment explanation
Indices: 711250--711348 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
711240 GCAGACAGGA
* * * * * *
711250 CCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAGAAGGGCCTCTTGAACGATAGGAGGCG
*
711292 CTTCTTCG-ATGATGAGAAGGGCCTCTTGAACGATAGGAGGCG
1 CCTCTT-GAATGATGAGAAGGGCCTCTTGAACGATAGGAGGCG
711334 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
711349 TAGGTGCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 45 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (42 bp):
CCTCTTGAATGATGAGAAGGGCCTCTTGAACGATAGGAGGCG
Found at i:711628 original size:20 final size:20
Alignment explanation
Indices: 711599--711645 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
711589 TGCATAGAGT
* *
711599 ATGAACCTCATTCTACAACA
1 ATGAAACTCATTATACAACA
*
711619 ATGAAACTCATTATGCAACA
1 ATGAAACTCATTATACAACA
711639 ATGAAAC
1 ATGAAAC
711646 AATCTCGCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (20 bp):
ATGAAACTCATTATACAACA
Found at i:714041 original size:20 final size:20
Alignment explanation
Indices: 714016--714144 Score: 129
Period size: 20 Copynumber: 6.5 Consensus size: 20
714006 GCGTAAAAAC
* *
714016 ATTTGACTTTTGCGTTGTGA
1 ATTTGACTTTCGCGTTGCGA
*
714036 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
714056 ATTTGACTTAT-GTGTTGCG-
1 ATTTGACTT-TCGCGTTGCGA
*
714075 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
***
714096 ATTTGACTTTTTTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
714116 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
714136 ATTTGACTT
1 ATTTGACTT
714145 CTGTATTGCG
Statistics
Matches: 87, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.02
19 5 0.06
20 73 0.84
21 5 0.06
22 2 0.02
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:714061 original size:40 final size:40
Alignment explanation
Indices: 714016--714176 Score: 195
Period size: 40 Copynumber: 4.0 Consensus size: 40
714006 GCGTAAAAAC
* *
714016 ATTTGACTTTTGCGTTGTGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
* *
714056 ATTTGACTTATGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTTTTGTGTTGCGAATTTGAC-TA-TCGCGTTGCGA
*
714096 ATTTGACTTTTTTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
* *
714136 ATTTGACTTCTGTATTGCG-ATTT-ACATATTCGCGTTGCGA
1 ATTTGACTTTTGTGTTGCGAATTTGAC-TA-TCGCGTTGCGA
714176 A
1 A
714177 ATTGGAAACT
Statistics
Matches: 105, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
38 4 0.04
39 11 0.10
40 83 0.79
41 5 0.05
42 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (40 bp):
ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:714118 original size:80 final size:80
Alignment explanation
Indices: 714016--714176 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 80
714006 GCGTAAAAAC
* *
714016 ATTTGACTTTTGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTAC
1 ATTTGACTTTTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTATTGCGATTTAC
714081 AAATTCGCGTTGCGA
66 AAATTCGCGTTGCGA
** *
714096 ATTTGACTTTTTTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGATTTAC
1 ATTTGACTTTTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTATTGCGATTTAC
*
714161 ATATTCGCGTTGCGA
66 AAATTCGCGTTGCGA
714176 A
1 A
714177 ATTGGAAACT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (80 bp):
ATTTGACTTTTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTATTGCGATTTAC
AAATTCGCGTTGCGA
Found at i:714209 original size:80 final size:80
Alignment explanation
Indices: 714035--714220 Score: 216
Period size: 80 Copynumber: 2.3 Consensus size: 80
714025 TTGCGTTGTG
* * *
714035 AATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGCGAATTT
1 AATTGGACTATCGCGTTGCGAATTTGACTTATGTATTGCGATTTACAAATTCGCGTTGCGAATTG
*** *
714100 GACTTTTTTGTTGCG
66 GACTGGGTTGTTGCA
* * *
714115 AATTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGATTTACATATTCGCGTTGCGAAATT
1 AATTGGACTATCGCGTTGCGAATTTGACTTATGTATTGCGATTTACAAATTCGCGTTGCG-AATT
714180 GGAAACTGGGTTG-TG-A
65 GG--ACTGGGTTGTTGCA
* *
714196 AATTGGAGT-TCGCGTTGCAAATTTG
1 AATTGGACTATCGCGTTGCGAATTTG
714221 TTGGTTATTT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
80 72 0.78
81 12 0.13
82 2 0.02
83 6 0.07
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (80 bp):
AATTGGACTATCGCGTTGCGAATTTGACTTATGTATTGCGATTTACAAATTCGCGTTGCGAATTG
GACTGGGTTGTTGCA
Found at i:714901 original size:14 final size:15
Alignment explanation
Indices: 714882--714912 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
714872 ATGTGACGAG
714882 TTTTATT-AAATTTT
1 TTTTATTCAAATTTT
714896 TTTTATTCAAATTTT
1 TTTTATTCAAATTTT
714911 TT
1 TT
714913 ACATCGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTCAAATTTT
Found at i:726098 original size:19 final size:20
Alignment explanation
Indices: 726076--726117 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
726066 ACTAACAGAG
*
726076 TAATTTAT-AATTATTTTTT
1 TAATTTATGAATCATTTTTT
*
726095 TAATTTCTGAATCATTTTTT
1 TAATTTATGAATCATTTTTT
726115 TAA
1 TAA
726118 AATCATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (20 bp):
TAATTTATGAATCATTTTTT
Found at i:732294 original size:14 final size:14
Alignment explanation
Indices: 732275--732313 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
732265 TAATGGGGAG
732275 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
732289 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
732303 GAATCTCTGCA
1 TAATCCCTGCA
732314 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:735017 original size:46 final size:48
Alignment explanation
Indices: 734895--735023 Score: 140
Period size: 46 Copynumber: 2.8 Consensus size: 48
734885 ATATAAATTT
* *
734895 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA-TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
* ** *
734941 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
* * *
734990 TTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
735024 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
46 29 0.41
47 3 0.04
48 22 0.31
49 16 0.23
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (48 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
Found at i:741817 original size:45 final size:47
Alignment explanation
Indices: 741695--741822 Score: 154
Period size: 48 Copynumber: 2.8 Consensus size: 47
741685 ATATAAATTT
* *
741695 CTTACC-TTTTATCCCATAAGCTCATAAGCTTATTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* ** *
741741 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* *
741789 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
741823 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
45 23 0.32
46 6 0.08
47 5 0.07
48 37 0.52
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (47 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
Found at i:749717 original size:65 final size:65
Alignment explanation
Indices: 749590--749749 Score: 173
Period size: 65 Copynumber: 2.4 Consensus size: 65
749580 CATGTTTATT
** * * *
749590 GATACACTACCTATGTATCGATACACAAATTACATTCTATGTTTTTAATTTTAAGGGGGTGTATC
1 GATACACTACCTATGTATCGATACACTTATTACATTCGATGTTTTTAATTTTAAGAGAGTGTATC
* *
749655 GATACACTACCTATGTATCGATACACTTATTGCATTCGATGTTTTT-ATTCGTT-TGAGAGTGTA
1 GATACACTACCTATGTATCGATACACTTATTACATTCGATGTTTTTAATT--TTAAGAGAGTGTA
749718 TC
64 TC
* *
749720 GGTAC-CTAACCAATATGTACCGATACACTT
1 GATACACT-ACC--TATGTATCGATACACTT
749750 TGCCCATAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
64 5 0.06
65 58 0.72
66 2 0.02
67 16 0.20
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (65 bp):
GATACACTACCTATGTATCGATACACTTATTACATTCGATGTTTTTAATTTTAAGAGAGTGTATC
Found at i:755849 original size:31 final size:29
Alignment explanation
Indices: 755797--755884 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
755787 GAGTCGAGGG
* *
755797 TTACATATGTCTTTCGAGACATATGGACAGT
1 TTACATATGTCTTT-GGGACATATGGACA-C
* *
755828 TTACCTATGTCATTTGGGACATATGGATAC
1 TTACATATGTC-TTTGGGACATATGGACAC
* *
755858 TTACTTATGTTCTTTGGAACATATGGA
1 TTACATATG-TCTTTGGGACATATGGA
755885 TAGGTTATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
30 22 0.45
31 24 0.49
32 3 0.06
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (29 bp):
TTACATATGTCTTTGGGACATATGGACAC
Found at i:755874 original size:30 final size:30
Alignment explanation
Indices: 755797--755887 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
755787 GAGTCGAGGG
* * *
755797 TTACATATGTCTTTCGAGACATATGGACAGT
1 TTACATATGTCTTT-GGGACATATGGATAGC
*
755828 TTACCTATGTCATTTGGGACATATGGATA-C
1 TTACATATGTC-TTTGGGACATATGGATAGC
* *
755858 TTACTTATGTTCTTTGGAACATATGGATAG
1 TTACATATG-TCTTTGGGACATATGGATAG
755888 GTTATTCGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
30 24 0.47
31 24 0.47
32 3 0.06
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.38
Consensus pattern (30 bp):
TTACATATGTCTTTGGGACATATGGATAGC
Found at i:760869 original size:30 final size:30
Alignment explanation
Indices: 760801--760889 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 30
760791 AGAGTCGAGG
* *
760801 GTTACCTATGTCTTTCGAGACATATGGATA
1 GTTACCTATGTCCTTCGAGACATATGGACA
760831 GTTTACCTATGTCCTTC-AGGACATATGGACA
1 G-TTACCTATGTCCTTCGA-GACATATGGACA
* *
760862 GTTACCTATGTTCTTCGAAACATATGGA
1 GTTACCTATGTCCTTCGAGACATATGGA
760890 TAGGTCCTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
30 25 0.48
31 27 0.52
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGAGACATATGGACA
Found at i:762472 original size:29 final size:29
Alignment explanation
Indices: 762438--762527 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 29
762428 CAAATTTTGG
762438 TTAGTGACCAAAATGTAAAATTTAAAAGT
1 TTAGTGACCAAAATGTAAAATTTAAAAGT
** * * *
762467 TTAGTGGTCAAAATATAAACTTAGAAAAGT
1 TTAGTGACCAAAATGTAAAATT-TAAAAGT
* **
762497 TCA-TGGACCAAAATTGTAATTTTTAAAAGT
1 TTAGT-GACCAAAA-TGTAAAATTTAAAAGT
762527 T
1 T
762528 GTGTATTTTG
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
29 19 0.41
30 21 0.46
31 6 0.13
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (29 bp):
TTAGTGACCAAAATGTAAAATTTAAAAGT
Found at i:774094 original size:2 final size:2
Alignment explanation
Indices: 774087--774122 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
774077 CTATTAAGTA
774087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
774123 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:774192 original size:15 final size:16
Alignment explanation
Indices: 774172--774202 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
774162 AAAACAAAGG
774172 TAAAAT-AAAATAAAA
1 TAAAATAAAAATAAAA
774187 TAAAATAAAAATAAAA
1 TAAAATAAAAATAAAA
774203 CACAACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAAATAAAA
Found at i:774199 original size:6 final size:5
Alignment explanation
Indices: 774172--774202 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
774162 AAAACAAAGG
774172 TAAAA TAAAA TAAAA TAAAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
774203 CACAACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:775621 original size:3 final size:3
Alignment explanation
Indices: 775604--775652 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
775594 CCTGCAAATG
775604 TAA TAA -AA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
775648 TAA TA
1 TAA TA
775653 TTTGTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:779322 original size:13 final size:13
Alignment explanation
Indices: 779304--779338 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
779294 TTGATCGGTG
779304 TAATTTTACATAA
1 TAATTTTACATAA
779317 TAA-TTT-CATAA
1 TAATTTTACATAA
779328 TAATTTTACAT
1 TAATTTTACAT
779339 GTATAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.40
12 6 0.30
13 6 0.30
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATTTTACATAA
Found at i:779465 original size:14 final size:15
Alignment explanation
Indices: 779444--779485 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 15
779434 CAAATTGATC
779444 TTATAATATAATTTT
1 TTATAATATAATTTT
*
779459 TTA-AATAT--TTTC
1 TTATAATATAATTTT
779471 TTATAATATAATTTT
1 TTATAATATAATTTT
779486 ACATGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.27
13 5 0.23
14 5 0.23
15 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATAATATAATTTT
Found at i:788288 original size:22 final size:22
Alignment explanation
Indices: 788260--788314 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
788250 TGTTCTTATT
788260 ATGAACTCTTCACTCTCATGGG
1 ATGAACTCTTCACTCTCATGGG
788282 ATGAACTCTTCACTCTCATGGG
1 ATGAACTCTTCACTCTCATGGG
*
788304 GTGAACTCTTC
1 ATGAACTCTTC
788315 TTTGGGAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (22 bp):
ATGAACTCTTCACTCTCATGGG
Found at i:789546 original size:37 final size:37
Alignment explanation
Indices: 789467--789552 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 37
789457 GGGAGACAAT
*
789467 CCTAAGAATGACTCAAATGACATTCTAGACAAACAGT
1 CCTAAGAATGACTCAAATGACATTCTAGACAAACAGC
* * *
789504 TCTAAGAATGACTCAAATGA-ATTTCTAGAGAAA-TGAC
1 CCTAAGAATGACTCAAATGACA-TTCTAGACAAACAG-C
789541 CCTAAGAATGAC
1 CCTAAGAATGAC
789553 AAAATAGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 2 0.05
37 40 0.95
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (37 bp):
CCTAAGAATGACTCAAATGACATTCTAGACAAACAGC
Found at i:791855 original size:27 final size:24
Alignment explanation
Indices: 791809--791862 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 24
791799 CTTAGCATAA
791809 AAATAAAACTTGAAAAATAAAGAAG
1 AAATAAAACTTGAAAAATAAA-AAG
791834 AAATAAAAACTTTGAAAAATAAAAAG
1 AAAT-AAAAC-TTGAAAAATAAAAAG
791860 AAA
1 AAA
791863 AAACTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 4 0.15
26 11 0.41
27 12 0.44
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (24 bp):
AAATAAAACTTGAAAAATAAAAAG
Found at i:793640 original size:14 final size:15
Alignment explanation
Indices: 793621--793650 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
793611 AGTACATTGC
793621 ATAAGCTTATC-GGT
1 ATAAGCTTATCAGGT
793635 ATAAGCTTATCAGGT
1 ATAAGCTTATCAGGT
793650 A
1 A
793651 CACTACCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
ATAAGCTTATCAGGT
Found at i:808226 original size:24 final size:24
Alignment explanation
Indices: 808182--808227 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
808172 ATAATAAACA
** *
808182 AACACAAACAAATGAACGTAAATG
1 AACACAAACAAACAAAAGTAAATG
808206 AACACAAACAAACAAAAGTAAA
1 AACACAAACAAACAAAAGTAAA
808228 CGAAAGTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.65, C:0.17, G:0.09, T:0.09
Consensus pattern (24 bp):
AACACAAACAAACAAAAGTAAATG
Found at i:808391 original size:15 final size:16
Alignment explanation
Indices: 808330--808390 Score: 70
Period size: 16 Copynumber: 3.7 Consensus size: 16
808320 TACTTTTTAT
808330 TTGAGTTTAAAATTAA
1 TTGAGTTTAAAATTAA
808346 TTGAGTTTAAAAATATTAA
1 TTGAGTTT--AAA-ATTAA
* *
808365 TGGA-CTTAAAATTAA
1 TTGAGTTTAAAATTAA
808380 TTGAGTTTAAA
1 TTGAGTTTAAA
808391 TATATTAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 8 0.22
16 16 0.43
18 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.41
Consensus pattern (16 bp):
TTGAGTTTAAAATTAA
Found at i:815038 original size:33 final size:33
Alignment explanation
Indices: 814996--815065 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
814986 ATCAAAGCAC
*
814996 AAACATGAAATCTACAAGTTAAGTATAATGCAA
1 AAACATGAAATCTACAAGTTAAGCATAATGCAA
815029 AAACATGAAATCTACAAGTTAAGCATAATGCAA
1 AAACATGAAATCTACAAGTTAAGCATAATGCAA
815062 AAAC
1 AAAC
815066 TAATTGACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.21
Consensus pattern (33 bp):
AAACATGAAATCTACAAGTTAAGCATAATGCAA
Found at i:816368 original size:19 final size:20
Alignment explanation
Indices: 816328--816369 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
816318 AATTCTAATG
*
816328 TTTTTATTTATATCATTTAA
1 TTTTTATTTATATCATTCAA
816348 TTTTT-TTTATAT-ATATCAA
1 TTTTTATTTATATCAT-TCAA
816367 TTT
1 TTT
816370 CCCTATTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 13 0.65
20 5 0.25
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTATTTATATCATTCAA
Found at i:818600 original size:16 final size:16
Alignment explanation
Indices: 818579--818611 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
818569 TAACCTACGT
818579 ATGAAAATCATCACGC
1 ATGAAAATCATCACGC
818595 ATGAAAATCATCACGC
1 ATGAAAATCATCACGC
818611 A
1 A
818612 CTAAGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (16 bp):
ATGAAAATCATCACGC
Found at i:822671 original size:21 final size:21
Alignment explanation
Indices: 822647--822686 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
822637 TTAGGAGATG
*
822647 AACTTAAACTTAAAGAGGATT
1 AACTAAAACTTAAAGAGGATT
* *
822668 AACTAAAATTTCAAGAGGA
1 AACTAAAACTTAAAGAGGA
822687 ACGAACTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (21 bp):
AACTAAAACTTAAAGAGGATT
Found at i:823118 original size:2 final size:2
Alignment explanation
Indices: 823111--823154 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
823101 TGCCTAGTTG
823111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
823153 AT
1 AT
823155 TTGTTCCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:823694 original size:6 final size:6
Alignment explanation
Indices: 823683--823744 Score: 110
Period size: 6 Copynumber: 10.7 Consensus size: 6
823673 GGGAACGAGA
823683 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
823731 GAGA-- GAGAGG GAGA
1 GAGAGG GAGAGG GAGA
823745 TCTGGAGCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.07
6 50 0.93
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:825863 original size:19 final size:18
Alignment explanation
Indices: 825806--825870 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
825796 GATAAATTAT
825806 TTATTTTTCAATTTAGTCC
1 TTATTTTTCAATTTA-TCC
**
825825 TTAATTTTTCATAAGT-TCC
1 TT-ATTTTTCA-ATTTATCC
825844 TTATTTCTTCAATTTATCC
1 TTATTT-TTCAATTTATCC
825863 TTTATTTT
1 -TTATTTT
825871 AAGTCATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
18 6 0.16
19 15 0.41
20 14 0.38
21 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.03, T:0.60
Consensus pattern (18 bp):
TTATTTTTCAATTTATCC
Found at i:825946 original size:155 final size:154
Alignment explanation
Indices: 825710--826247 Score: 699
Period size: 155 Copynumber: 3.5 Consensus size: 154
825700 TTTCTCCATC
* * * * **
825710 ATTTTAAGTTCACTTTTACCAAATTTTAACTACATGCTCATAAACCATC-ATAGAATAAATATGT
1 ATTTTAAG-TCATTTTTACCAAATTTGAACCACATGCTCATATACCA-CAATAGAATACCTATGT
** * * * * * *
825774 ATTTTTAATTCCACTTTTTGATGATAAATTATTTATTTTTCAATTTAGT-CCTTAATTTTTCATA
64 AACTTCAATTCCTCTTTTTGAT-A-ATATTTTTTATTTTTCAATTAAGTCCCTCAATTTTTCATA
* *
825838 AGTTCCTTATTTCTTCAATTTATCCTTT
127 ATTTCCTTATTTCTTCAATTCATCCTTT
* * *
825866 ATTTTAAGTCATTTTTACCAAATTTGAACTACATACTCATATACCACAATAAAATACCTATGTAA
1 ATTTTAAGTCATTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGAATACCTATGTAA
*
825931 CTTCATTTCCTCTTTTTGATAATATTTTTTATTTTTCAATTGAA-TCCCTCAATTTTTCATAATT
66 CTTCAATTCCTCTTTTTGATAATATTTTTTATTTTTCAATT-AAGTCCCTCAATTTTTCATAATT
*
825995 TTCTTATTTCTTCAATTCATCCTTT
130 TCCTTATTTCTTCAATTCATCCTTT
* * *
826020 ATTTTATGTCCATTTTTACCAAATTTGAACCACATGCTCATATACCAAAATAGAATACCTATGAA
1 ATTTTAAGT-CATTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGAATACCTATGTA
* * *
826085 ACTTCAATTCCTCTTTTTGACAATTTTTTTTATTTTTTAATTAAGTCCCTCAATTTTTCATAATT
65 ACTTCAATTCCTCTTTTTGATAATATTTTTTATTTTTCAATTAAGTCCCTCAATTTTTCATAATT
826150 TCCTTATTTCTTCAATTCATCCTTT
130 TCCTTATTTCTTCAATTCATCCTTT
* * *
826175 ATTTTAAGT-ATGTTTTCACCAAATTTGAACCACATGCTCATATACTACAATATAATA-TTATGT
1 ATTTTAAGTCAT-TTTT-ACCAAATTTGAACCACATGCTCATATACCACAATAGAATACCTATGT
826238 AACTTCAATT
64 AACTTCAATT
826248 TCTACCTTTT
Statistics
Matches: 339, Mismatches: 36, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
153 21 0.06
154 70 0.21
155 240 0.71
156 8 0.02
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.47
Consensus pattern (154 bp):
ATTTTAAGTCATTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGAATACCTATGTAA
CTTCAATTCCTCTTTTTGATAATATTTTTTATTTTTCAATTAAGTCCCTCAATTTTTCATAATTT
CCTTATTTCTTCAATTCATCCTTT
Found at i:830123 original size:31 final size:31
Alignment explanation
Indices: 830087--830146 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
830077 AACTTAAAAG
* *
830087 AGTTTTGTAATACTGAAATTTAAATAATTTT
1 AGTTTTATAATACTAAAATTTAAATAATTTT
830118 AGTTTTATAATACTAAAATTTAAATAATT
1 AGTTTTATAATACTAAAATTTAAATAATT
830147 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (31 bp):
AGTTTTATAATACTAAAATTTAAATAATTTT
Found at i:830645 original size:19 final size:20
Alignment explanation
Indices: 830610--830650 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
830600 TATTTAAACT
830610 TAAATAAAAATAATTAA-AA
1 TAAATAAAAATAATTAATAA
*
830629 TAAATATAAAAT-TTTAATAA
1 TAAATA-AAAATAATTAATAA
830649 TA
1 TA
830651 TATGAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATAAAAATAATTAATAA
Found at i:830748 original size:64 final size:64
Alignment explanation
Indices: 830672--830828 Score: 275
Period size: 64 Copynumber: 2.5 Consensus size: 64
830662 TTATATGATA
830672 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
830737 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
830801 TAAAATTAAAAT-TA-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
830829 TTAAATATAA
Statistics
Matches: 91, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
61 5 0.05
62 9 0.10
63 2 0.02
64 68 0.75
65 7 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (64 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:830772 original size:40 final size:37
Alignment explanation
Indices: 830693--830777 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 37
830683 ATCTATAATA
*
830693 TAATATTAAAAAATTAATATTTAATTTATTTAAAAAAT
1 TAATATT-AAAAATTAATATTTAATTAATTTAAAAAAT
830731 TAATATT-AAAATTAATATCTATAATATAATATTAAAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-TAAT-TTAAAAAAT
830771 TAATATT
1 TAATATT
830778 TAATTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.26
37 1 0.02
38 11 0.26
39 3 0.07
40 16 0.38
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (37 bp):
TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
Found at i:830781 original size:26 final size:26
Alignment explanation
Indices: 830728--830816 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 26
830718 TTATTTAAAA
830728 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
830753 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
* *
830779 AATTTAT-TTAAAAAATTAATATTAA
1 AATTAATATTAAAAAATTAATATTAT
*
830804 AATTAAAATTAAA
1 AATTAATATTAAA
830817 TATAATATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 16 0.29
25 11 0.20
26 16 0.29
27 1 0.02
28 11 0.20
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:830794 original size:24 final size:27
Alignment explanation
Indices: 830731--830838 Score: 95
Period size: 28 Copynumber: 4.1 Consensus size: 27
830721 TTTAAAAAAT
830731 TAATATT--AAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATAT-TATAATA
830757 TAATATTAAAAAATTAATATT-TAAT-
1 TAATATTAAAAAATTAATATTATAATA
* *
830782 TTAT-TTAAAAAATTAATATTAAAAT-
1 TAATATTAAAAAATTAATATTATAATA
* *
830807 TAAAATTAAATATAATATAAAATTA-AATA
1 TAATATTAAA-A-AAT-TAATATTATAATA
830836 TAA
1 TAA
830839 AACCTCTTTG
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
24 16 0.23
25 8 0.12
26 16 0.23
27 2 0.03
28 17 0.25
29 10 0.14
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
TAATATTAAAAAATTAATATTATAATA
Found at i:830835 original size:12 final size:12
Alignment explanation
Indices: 830790--830840 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
830780 ATTTATTTAA
830790 AAAATT-AATATT
1 AAAATTAAATA-T
830802 AAAATTAAA-AT
1 AAAATTAAATAT
*
830813 TAAA-TATAATAT
1 AAAATTA-AATAT
830825 AAAATTAAATAT
1 AAAATTAAATAT
830837 AAAA
1 AAAA
830841 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:846041 original size:20 final size:21
Alignment explanation
Indices: 846016--846077 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
846006 TTTTGGTGCA
846016 GAGGGAATCGATACCCCC-AT
1 GAGGGAATCGATACCCCCTAT
* * *
846036 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATACCCCCTAT
*
846057 GAAGGGGAATCAATACCCCCT
1 G-A-GGGAATCGATACCCCCT
846078 GGGGTTCTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
22 1 0.03
23 14 0.42
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (21 bp):
GAGGGAATCGATACCCCCTAT
Found at i:863121 original size:51 final size:51
Alignment explanation
Indices: 862994--863187 Score: 311
Period size: 51 Copynumber: 3.8 Consensus size: 51
862984 AGATGTATAT
* *
862994 ACTTACAACAGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* *
863045 ACTTACACCGGTATAA-TATGTGTTAAGTGCTACACTTTTTTGTTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
863095 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACA-TTTGTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTT-TTTATTTTATTC
* *
863146 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTT
863188 GTAGTATGAA
Statistics
Matches: 133, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
50 51 0.38
51 79 0.59
52 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
Found at i:863185 original size:101 final size:101
Alignment explanation
Indices: 862994--863189 Score: 322
Period size: 101 Copynumber: 1.9 Consensus size: 101
862984 AGATGTATAT
862994 ACTTACAACAGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACCGGTAT
1 ACTTACAACAGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACCGGTAT
863059 AATATGTGTTAAGTGCTACACTTTTTTGTTTTATTC
66 AATATGTGTTAAGTGCTACACTTTTTTGTTTTATTC
* * * *
863095 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACA-TTTGTTTATTTTATTCACTTACATCGGTG
1 ACTTACAACAGTGTAAGTATGTGTTAAGTGCTACACTTT-TTTATTTTATTCACTTACACCGGTA
*
863159 TAAGTATGTGTTAAGTGCTACATTTTTTTGT
65 TAA-TATGTGTTAAGTGCTACACTTTTTTGT
863190 AGTATGAATT
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
100 3 0.03
101 59 0.67
102 26 0.30
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.45
Consensus pattern (101 bp):
ACTTACAACAGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACCGGTAT
AATATGTGTTAAGTGCTACACTTTTTTGTTTTATTC
Found at i:872461 original size:16 final size:16
Alignment explanation
Indices: 872420--872462 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
872410 GTCGTCGGTG
*
872420 GAAGCTGCTAGAATGT
1 GAAGCTGCTGGAATGT
872436 GAAGCTGCTGGAATGT
1 GAAGCTGCTGGAATGT
872452 GAAGCTGCTGG
1 GAAGCTGCTGG
872463 TAGGTGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.14, G:0.37, T:0.23
Consensus pattern (16 bp):
GAAGCTGCTGGAATGT
Found at i:872627 original size:16 final size:16
Alignment explanation
Indices: 872602--872635 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
872592 TTCTAAAAAA
872602 TGATGACCCTACATGC
1 TGATGACCCTACATGC
*
872618 TGATGTCCCTACATGC
1 TGATGACCCTACATGC
872634 TG
1 TG
872636 CCTTGGATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (16 bp):
TGATGACCCTACATGC
Found at i:875014 original size:18 final size:18
Alignment explanation
Indices: 874975--875022 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
874965 AATATATTTA
*
874975 AAAACAATAAAAAAAATG
1 AAAACAATAAAATAAATG
*
874993 AAAACATATAAAATAACT-
1 AAAACA-ATAAAATAAATG
875011 AAAA-AATAAAAT
1 AAAACAATAAAAT
875023 TAAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.26
17 1 0.04
18 10 0.37
19 9 0.33
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAACAATAAAATAAATG
Found at i:875015 original size:19 final size:18
Alignment explanation
Indices: 874973--875015 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
874963 ACAATATATT
874973 TAAAAACAATAAAAAAAA
1 TAAAAACAATAAAAAAAA
* * *
874991 TGAAAACATATAAAATAAC
1 TAAAAACA-ATAAAAAAAA
875010 TAAAAA
1 TAAAAA
875016 ATAAAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (18 bp):
TAAAAACAATAAAAAAAA
Found at i:876334 original size:3 final size:3
Alignment explanation
Indices: 876326--876410 Score: 124
Period size: 3 Copynumber: 29.7 Consensus size: 3
876316 TTTAATATAT
876326 TAA TAA TAA -AA TAA TAA T-A TAA TAA TAA -AA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
876370 TAA TAA TAA TGA TAA TAA TAT TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
876411 TATGGATAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
2 8 0.11
3 66 0.89
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:876878 original size:114 final size:113
Alignment explanation
Indices: 876546--877083 Score: 782
Period size: 114 Copynumber: 4.7 Consensus size: 113
876536 ATTGAATAAA
* * ** *
876546 TTCTTCTT-TTTCTCCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGTTCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAATGATGATCCATC
* * *
876610 AAATGAAGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AATTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
876659 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTTTCATTATGAACTCTTTCTCTGGAAATGATGATC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAA--CTTTCTCTGGAAATGATGATC
*
876724 CATCAATTTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
61 CATCAA-TTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
876778 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-ATGATCCATC
*
876843 AAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA-
65 AATTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
876891 TTCTTCTTTCCTTCTTCAGATGAGTTC-TCTCATTATGAACTTTCTCTGGAAAAGAATGATCCAT
1 TTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-ATGATCCAT
876955 CAA-TGATGAATTCAAGCAAAAGG-TGAACAAGTTCTTCTCATTATG-AC
64 CAATTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
877002 TTCTTCTTCCTTTTTCAGATGACGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCA
1 TTCTTCTTCCTTCTTCAGATGA-GTTCTTCTCATTATGAACT-TT-CTCTGGAAATGATGATCCA
877067 TCAATTTGATGAATTCA
63 TCAA-TTGATGAATTCA
877084 TGATGATCCA
Statistics
Matches: 393, Mismatches: 16, Indels: 30
0.90 0.04 0.07
Matches are distributed among these distances:
110 16 0.04
111 32 0.08
112 34 0.09
113 68 0.17
114 97 0.25
115 23 0.06
116 18 0.05
117 18 0.05
118 18 0.05
119 69 0.18
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCA
ATTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:877094 original size:27 final size:27
Alignment explanation
Indices: 877056--877110 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
877046 TCCTCTGGAA
877056 ATGATGATCCATCAATTTGATGAATTC
1 ATGATGATCCATCAATTTGATGAATTC
*
877083 ATGATGATCCATCAGTTTGATGAATTC
1 ATGATGATCCATCAATTTGATGAATTC
877110 A
1 A
877111 AGTCTTTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (27 bp):
ATGATGATCCATCAATTTGATGAATTC
Found at i:877809 original size:83 final size:83
Alignment explanation
Indices: 877670--877865 Score: 374
Period size: 83 Copynumber: 2.4 Consensus size: 83
877660 TTCTAGTAAA
* *
877670 AGATAACTCAAAGAACACTTCCATAAGATGTTATTGGCGAATTTATCTTTTAAATTCAATACTTG
1 AGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTTATCTTTTAAATTCAATACTTG
877735 ATTTTGTCCAATCAGATC
66 ATTTTGTCCAATCAGATC
877753 AGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTTATCTTTTAAATTCAATACTTG
1 AGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTTATCTTTTAAATTCAATACTTG
877818 ATTTTGTCCAATCAGATC
66 ATTTTGTCCAATCAGATC
877836 AGATAACTCAAAGAACACTTCCAGAAGATG
1 AGATAACTCAAAGAACACTTCCAGAAGATG
877866 CTATGTTCTG
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 111 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (83 bp):
AGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTTATCTTTTAAATTCAATACTTG
ATTTTGTCCAATCAGATC
Found at i:877900 original size:52 final size:52
Alignment explanation
Indices: 877822--878279 Score: 756
Period size: 52 Copynumber: 8.9 Consensus size: 52
877812 TACTTGATTT
*
877822 TGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
*
877874 TGTCCAACCAGATCAGATGACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
* *
877926 TGTCCAACCAGATCAGATGACTTAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
877978 TGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
*
878030 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATG-TC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
*
878081 TGAT-CAACC-GATCAGATAACTCAAAG-A-ACTTCCAGAAGATGCTATGTTT
1 TG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
*
878130 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAG-AGATGTTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
878181 TGTCCAACCAGATCAGATAACTCAAAG-A-ACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
878231 TGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
878280 AGCACATTCA
Statistics
Matches: 383, Mismatches: 11, Indels: 24
0.92 0.03 0.06
Matches are distributed among these distances:
48 19 0.05
49 17 0.04
50 72 0.19
51 51 0.13
52 223 0.58
53 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (52 bp):
TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
Found at i:890114 original size:18 final size:18
Alignment explanation
Indices: 890091--890133 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
890081 AAAATGCTTG
890091 TAAATAAAATAAAACAT-A
1 TAAATAAAATAAAA-ATAA
**
890109 TAAATATTATAAAAATAA
1 TAAATAAAATAAAAATAA
890127 TAAATAA
1 TAAATAA
890134 TTTGAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAATAAAATAAAAATAA
Found at i:892148 original size:3 final size:3
Alignment explanation
Indices: 892140--892237 Score: 126
Period size: 3 Copynumber: 33.0 Consensus size: 3
892130 ATTTAATATT
* * *
892140 ATA ATA ATA A-A AAA ATA ATA ATA AAA ATA AAA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
892187 TTA TTA ATA ATG ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
892235 ATA
1 ATA
892238 TGGATAAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:894760 original size:159 final size:156
Alignment explanation
Indices: 894476--894803 Score: 471
Period size: 159 Copynumber: 2.1 Consensus size: 156
894466 TTTAATTCCA
* * *
894476 TTTTTACCAAATTTGAACAACATACTCCTAAACCATGGTAGAATACATGTTTACTTTCGATTACA
1 TTTTTACCAAATTTGAACAACATACTCCTAAACCATAGTAGAATACATGTCTACTTTCAATTACA
*
894541 CTTTTTGATAAATTTTTTTATTTTTCAATTTAGTCCTTTAATTTTTCATAATCTCCTTATTTATT
66 CTTTTTGATAAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATTTATT
* * *
894606 TAATTTGTCGTTTATTTTAAGTCAAT
131 TAATTCGACATTTATTTTAAGTCAAT
* * * * *
894632 TTTTTGCCAAATTTGAGTC-ACATGCTCCTAAACGATAGTAGAATACATGTCTACTTTCAATTCC
1 TTTTTACCAAATTTGA-ACAACATACTCCTAAACCATAGTAGAATACATGTCTACTTTCAATTAC
894696 TA-TTTTTGATAATAAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTAT
65 -ACTTTTTG---ATAAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTAT
* *
894760 TTCTTTAATTCGACATTTATTTTAAGTCAGT
126 TTATTTAATTCGACATTTATTTTAAGTCAAT
894791 TTTTTACCAAATT
1 TTTTTACCAAATT
894804 GATAAACATA
Statistics
Matches: 152, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
156 60 0.39
157 2 0.01
159 90 0.59
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (156 bp):
TTTTTACCAAATTTGAACAACATACTCCTAAACCATAGTAGAATACATGTCTACTTTCAATTACA
CTTTTTGATAAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATTTATT
TAATTCGACATTTATTTTAAGTCAAT
Found at i:897689 original size:15 final size:15
Alignment explanation
Indices: 897669--897699 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
897659 ATAATCTCAC
897669 ATAGCTAATAAACAT
1 ATAGCTAATAAACAT
897684 ATAGCTAATAAACAT
1 ATAGCTAATAAACAT
897699 A
1 A
897700 GAATAGCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (15 bp):
ATAGCTAATAAACAT
Found at i:897827 original size:24 final size:24
Alignment explanation
Indices: 897795--897850 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
897785 CTATTCTTTC
897795 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
897819 GCTTCAATTGAGTTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
897843 GCTTCAAT
1 GCTTCAAT
897851 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:898110 original size:30 final size:30
Alignment explanation
Indices: 898075--898140 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
898065 AGTGAACCGG
* *
898075 CGGTTCAAACCGGTTTTGCCGGTTTTCAAC
1 CGGTTCAAACCGGTTTTCCCAGTTTTCAAC
** *
898105 CGGTTCACTCCGGTTTTCCCAGTTTTCAGC
1 CGGTTCAAACCGGTTTTCCCAGTTTTCAAC
898135 CGGTTC
1 CGGTTC
898141 TTCCGGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.12, C:0.30, G:0.23, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTCCCAGTTTTCAAC
Found at i:898522 original size:13 final size:13
Alignment explanation
Indices: 898504--898530 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
898494 TTTTAGATGC
898504 AATAAGAAAAGTT
1 AATAAGAAAAGTT
898517 AATAAGAAAAGTT
1 AATAAGAAAAGTT
898530 A
1 A
898531 GAGATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (13 bp):
AATAAGAAAAGTT
Found at i:899175 original size:5 final size:5
Alignment explanation
Indices: 899165--899189 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
899155 GTTACGGTGT
899165 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
899190 GTACAATCTC
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:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:899904 original size:53 final size:53
Alignment explanation
Indices: 899843--900002 Score: 187
Period size: 53 Copynumber: 3.0 Consensus size: 53
899833 TTATATGCGC
* * * *
899843 TAAGATATTGAGATATTTACATACTTACATTGGTATAAATATATGTTAATTGT
1 TAAGATATTGAAAAATGTACATACTTACATTGGTATAAATATGTGTTAATTGT
* * * * * *
899896 TAAGATATTGATAAATGTACATACTTACGTCGGTGTAAGTATGTGTTAATTGC
1 TAAGATATTGAAAAATGTACATACTTACATTGGTATAAATATGTGTTAATTGT
* * * *
899949 TAAGATATTGAAAGATGTACATATTTACACTCGTA-AAATATGTGTTAATTGT
1 TAAGATATTGAAAAATGTACATACTTACATTGGTATAAATATGTGTTAATTGT
900001 TA
1 TA
900003 CACTTTCTTA
Statistics
Matches: 88, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
52 17 0.19
53 71 0.81
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (53 bp):
TAAGATATTGAAAAATGTACATACTTACATTGGTATAAATATGTGTTAATTGT
Found at i:905620 original size:3 final size:3
Alignment explanation
Indices: 905614--905663 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
905604 ATCATATGAG
*
905614 ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT A-T ATT ACT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT AT-T ATT
905660 ATT A
1 ATT A
905664 AATTCTAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:906048 original size:2 final size:2
Alignment explanation
Indices: 906043--906077 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
906033 AAAGTAAATT
906043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
906078 TGATTTTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:909047 original size:12 final size:13
Alignment explanation
Indices: 909023--909055 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
909013 CAGTTTTTGG
909023 GGCTTCTAAATCA
1 GGCTTCTAAATCA
909036 GGCTTC-AAATCA
1 GGCTTCTAAATCA
*
909048 GACTTCTA
1 GGCTTCTA
909056 GTTCAGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (13 bp):
GGCTTCTAAATCA
Found at i:917580 original size:394 final size:388
Alignment explanation
Indices: 916815--917599 Score: 1336
Period size: 394 Copynumber: 2.0 Consensus size: 388
916805 TTATCTCAAG
*
916815 AAACTTTTATTTGTTCCTGGTATAATTAAAAACTTGTTTGTTTCAAAATTTACTCAGGACAATCA
1 AAACTTTTATTTGTTCCTGGTATAACTAAAAACTTGTTTGTTTCAAAATTTACTCAGGACAATCA
* *
916880 GATTCTTCTTGAGTTTTATACGAACTTCTGCTAAGTTCGTGATCTTCGTACCTATAAAGTGTTAT
66 GATTCTTCTTGAGTTTTATACGAACTTCTCCTAAGTTCGTGATCTTCGTACCCATAAAGTGTTAT
* * *
916945 TAAAGGGAAGTGAAACCGATGGTATGTACATGCTATATCTACAAATAATATTGTTCAAACTACTG
131 TAAAGGGAAGTGAAACCGATGGCATATACATGCTATATCTACAAATAATATTGTTCAAACTACTA
* * * *
917010 GTAATAAAAATGTTGTTAATACGTCTGTTGTGAGTTGTAATTTGGTTAGTGCTTTAAAGGTCTCT
196 GTAATAAAAATGCTGTTAATAAGTCTGTTGTGAGTTGTAATTTGGTTAGTGCTCTAAAAGTCTCT
917075 CTTGAAACCTGGCACAAGAGGCTGAGACACCCCTCGAAAGAGGTTTTGCATACTGCTCTAAAACG
261 CTTGAAACCTGGCACAAGAGGCTGAGACACCCCTCGAAAGAGGTTTTGCATACTGCTCTAAAACG
*
917140 TTGTAATATAACATCTTTATGCATCAATAAAGATAAAATTTTGTGTGAAGCATGTCAATTAGA
326 TTGTAATATAACATCTTTATGCATCAATAAAGAGAAAATTTTGTGTGAAGCATGTCAATTAGA
*
917203 AAACTTTTATTTGTTCTTGGTATAACTAAAAACTTGTTGTCTGTTTCAAAATTTACTCAGGACAA
1 AAACTTTTATTTGTTCCTGGTATAACTAAAAACTTG-T-T-TGTTTCAAAATTTACTCAGGACAA
* *
917268 TCAGGTTCTTCTTGAGTTTTATTCGAACTTCTCCTAAGTTCGTGATCTTCGTACCCATAAAGTGT
63 TCAGATTCTTCTTGAGTTTTATACGAACTTCTCCTAAGTTCGTGATCTTCGTACCCATAAAGTGT
* * *
917333 TTTTAAAGGGAAGTGAAACTGATGGCCTATACATGCTATATCTACAAATAATATTGTTCAAACTA
128 TATTAAAGGGAAGTGAAACCGATGGCATATACATGCTATATCTACAAATAATATTGTTCAAACTA
917398 CTAGTAATAAAAATATTGCTGTTAATAAGTCTGTTGTGAGTTGTAATTTGGTTAGTGCTCTAAAA
193 CTAGTAAT-AAAA-A-TGCTGTTAATAAGTCTGTTGTGAGTTGTAATTTGGTTAGTGCTCTAAAA
* *
917463 GTCTCTCTTGAAACCTGGCACAAGAGGCTGGGATACCCCTCGAAAGAGGTTTTGCATACTGCTCT
255 GTCTCTCTTGAAACCTGGCACAAGAGGCTGAGACACCCCTCGAAAGAGGTTTTGCATACTGCTCT
*
917528 AAAACGTTGTAATATAACATCTTTATGCATCAATAAAGAGAAAATTTTGTGTGAAGCATGTCAGT
320 AAAACGTTGTAATATAACATCTTTATGCATCAATAAAGAGAAAATTTTGTGTGAAGCATGTCAAT
917593 TAGA
385 TAGA
917597 AAA
1 AAA
917600 ATCTCATAAA
Statistics
Matches: 371, Mismatches: 20, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
388 34 0.09
389 1 0.00
390 1 0.00
391 152 0.41
392 4 0.01
393 1 0.00
394 178 0.48
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (388 bp):
AAACTTTTATTTGTTCCTGGTATAACTAAAAACTTGTTTGTTTCAAAATTTACTCAGGACAATCA
GATTCTTCTTGAGTTTTATACGAACTTCTCCTAAGTTCGTGATCTTCGTACCCATAAAGTGTTAT
TAAAGGGAAGTGAAACCGATGGCATATACATGCTATATCTACAAATAATATTGTTCAAACTACTA
GTAATAAAAATGCTGTTAATAAGTCTGTTGTGAGTTGTAATTTGGTTAGTGCTCTAAAAGTCTCT
CTTGAAACCTGGCACAAGAGGCTGAGACACCCCTCGAAAGAGGTTTTGCATACTGCTCTAAAACG
TTGTAATATAACATCTTTATGCATCAATAAAGAGAAAATTTTGTGTGAAGCATGTCAATTAGA
Found at i:919039 original size:48 final size:49
Alignment explanation
Indices: 918986--919080 Score: 111
Period size: 49 Copynumber: 1.9 Consensus size: 49
918976 TTTGCATATA
* * *
918986 TTTTTCATTCAGACACATTTTAGAACTTTCATT-TTTCATATTCATATTC
1 TTTTCCATTCAGACAC-TTTAAGAACTTCCATTATTTCATATTCATATTC
* * * *
919035 TTTTCCTTTCAGTCACTTTAAGAACTTCCCTTATTTCATTTTCATA
1 TTTTCCATTCAGACACTTTAAGAACTTCCATTATTTCATATTCATA
919081 GCCCAATGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
48 13 0.34
49 25 0.66
ACGTcount: A:0.24, C:0.21, G:0.04, T:0.51
Consensus pattern (49 bp):
TTTTCCATTCAGACACTTTAAGAACTTCCATTATTTCATATTCATATTC
Found at i:919254 original size:35 final size:35
Alignment explanation
Indices: 919169--919376 Score: 227
Period size: 35 Copynumber: 5.9 Consensus size: 35
919159 GAACATATAA
* * *
919169 GCACACACAGTGCTATCACATCGGAAACATAATTAT
1 GCACACAAAGTGCAATCACATCGGAATCAT-ATTAT
* * *
919205 GCACGCAAAGTGCAATCACATTGGAATCATATCAT
1 GCACACAAAGTGCAATCACATCGGAATCATATTAT
* * * * * *
919240 GCACACAAAATGCAATAACGTCGGTATCGTATCAT
1 GCACACAAAGTGCAATCACATCGGAATCATATTAT
* *
919275 ACGCACAAAGTGCAATCACATCGGAATCATATTAT
1 GCACACAAAGTGCAATCACATCGGAATCATATTAT
* ** *
919310 ACACACAAAGTGCAATCACATCGGAATTGTATTGT
1 GCACACAAAGTGCAATCACATCGGAATCATATTAT
* *
919345 GCACACAAAGTGCAATCACGTCGAAATCATAT
1 GCACACAAAGTGCAATCACATCGGAATCATAT
919377 ACTAGTGTAC
Statistics
Matches: 142, Mismatches: 30, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 117 0.82
36 25 0.18
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (35 bp):
GCACACAAAGTGCAATCACATCGGAATCATATTAT
Found at i:919360 original size:105 final size:106
Alignment explanation
Indices: 919172--919367 Score: 277
Period size: 105 Copynumber: 1.9 Consensus size: 106
919162 CATATAAGCA
* * * * *
919172 CACACAGTGCTATCACATCGGAAACATAATTATGCACGCAAAGTGCAATCACATTGGAATCATAT
1 CACAAAGTGCAATCACATCGGAAACATAATTATACACACAAAGTGCAATCACATCGGAATCATAT
919237 CATGCACACAAAATGCAATAACGTCGGTATCGTATCATACG
66 CATGCACACAAAATGCAATAACGTCGGTATCGTATCATACG
* **
919278 CACAAAGTGCAATCACATCGGAATCAT-ATTATACACACAAAGTGCAATCACATCGGAATTGTAT
1 CACAAAGTGCAATCACATCGGAAACATAATTATACACACAAAGTGCAATCACATCGGAATCATAT
** * *
919342 TGTGCACACAAAGTGCAATCACGTCG
66 CATGCACACAAAATGCAATAACGTCG
919368 AAATCATATA
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
105 54 0.69
106 24 0.31
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (106 bp):
CACAAAGTGCAATCACATCGGAAACATAATTATACACACAAAGTGCAATCACATCGGAATCATAT
CATGCACACAAAATGCAATAACGTCGGTATCGTATCATACG
Found at i:920759 original size:20 final size:19
Alignment explanation
Indices: 920716--920760 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
920706 CAAAATAATC
* *
920716 CAATTTCACATTCTAACAT
1 CAATTTCACACTCAAACAT
920735 CAATTTCAACACTCAAACAT
1 CAATTTC-ACACTCAAACAT
*
920755 TAATTT
1 CAATTT
920761 AAAGAATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTTCACACTCAAACAT
Found at i:924833 original size:60 final size:60
Alignment explanation
Indices: 924701--924833 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 60
924691 TCGGGTGATC
* * *
924701 ATTT-TGTAACTTTTAATGGTCAAAAGACTTAATAAAGCAACATTCTATAGTTAGAGGATT
1 ATTTATGT-ACTTTTAATAGTCAAAAGACTTAATAAAGCAACATCCTATAGTTAGAGGAAT
* ** * * *
924761 ATTTTAT-AACTTTTAATAGTTGAAAGACTTAATAAAGCAATATCCTATA-TTCGGGGGAAT
1 A-TTTATGTACTTTTAATAGTCAAAAGACTTAATAAAGCAACATCCTATAGTT-AGAGGAAT
924821 ATTTATGTACTTT
1 ATTTATGTACTTT
924834 ATCCATACAA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
59 7 0.12
60 48 0.81
61 3 0.05
62 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (60 bp):
ATTTATGTACTTTTAATAGTCAAAAGACTTAATAAAGCAACATCCTATAGTTAGAGGAAT
Found at i:929766 original size:25 final size:26
Alignment explanation
Indices: 929713--929775 Score: 119
Period size: 25 Copynumber: 2.5 Consensus size: 26
929703 ATCAATCATA
929713 ATAAACATTTCAAATTCCTTTTTCTC
1 ATAAACATTTCAAATTCCTTTTTCTC
929739 ATAAACATTTCAAATTCC-TTTTCTC
1 ATAAACATTTCAAATTCCTTTTTCTC
929764 ATAAACATTTCA
1 ATAAACATTTCA
929776 GAAACTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 19 0.51
26 18 0.49
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAACATTTCAAATTCCTTTTTCTC
Found at i:949238 original size:27 final size:27
Alignment explanation
Indices: 949187--949238 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
949177 TTAATAAAAT
* * **
949187 ATATATTTAAAAATTATTTTTTTAATA
1 ATATATTTAAAAACTACTTGATTAATA
949214 ATATATTTAAAAACTACTTGATTAA
1 ATATATTTAAAAACTACTTGATTAA
949239 AAGTTTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATATTTAAAAACTACTTGATTAATA
Found at i:951076 original size:96 final size:94
Alignment explanation
Indices: 950960--951631 Score: 663
Period size: 96 Copynumber: 7.1 Consensus size: 94
950950 TTCTAGTAGG
* *
950960 ATACATACATAATTACAAAAGCTATGGTTGTTTAGATGGAAGAAAATTGAAAAAAAAAAACTCGT
1 ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAATTG--AAAAAAAAACTCGT
*
951025 CTCCACATACTTTGTGGTAGGATACATATAT
64 CTCCACATACTTTCTGGTAGGATACATATAT
*
951056 ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAACTGAAAAAAAAACTCCGTC
1 ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAATTGAAAAAAAAACT-CGTC
951121 TCCACATACTTTCTGGTAGGATACATATAT
65 TCCACATACTTTCTGGTAGGATACATATAT
* * *
951151 ATACATACATATTTACAGAAGTTGTGGTTGTTTAAATGGAAGAAAATTG--AAAAAAACTCGTCT
1 ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAATTGAAAAAAAAACTCGTCT
* *
951214 CCAAATACTTTCTGGTAGGATATATATAT
66 CCACATACTTTCTGGTAGGATACATATAT
* * * * * * ** *
951243 ATATATATATATTTATAAAAGTTGTGGTTGTTTATATGGAAGAAAACTGGGAAAAAAACTTGTCT
1 ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAATTGAAAAAAAAACTCGTCT
* * * *
951308 CCACGTACTTTTTAGTAGGATATATATATATATATATATAT
66 CCACATACTTTCTGGTAGG------------ATACATATAT
* * * * *
951349 ATATATATATATTTACAAAAGTTGTGGTTGTTTAGAGGGAA-AAAATTG--AAAAATA-TCGTCT
1 ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAATTGAAAAAAAAACTCGTCT
* * **
951410 CCACTTACTCTCTAATAGGATAC--ATAT
66 CCACATACTTTCTGGTAGGATACATATAT
* * *
951437 AT--ATAC--A--TAC-AAAGCCGTGGCTGTTTAGATGGAAGAAAACTGAAAGAAAAAAAGAACT
1 ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAA-T---TGAAAAAAA-AACT
* * * *
951495 CGTCTCCACAAAATTTCTAGTAGGATACACATAT
61 CGTCTCCACATACTTTCTGGTAGGATACATATAT
*
951529 ATACATACATATTTACAAAAGCTGTAGTTGTTTAGATGGAAGAAAATTGAAAAAAAAAAACTCGT
1 ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAATTG--AAAAAAAAACTCGT
* * *
951594 CTCCCCATACTTTCTAGTATGATACATATAT
64 CTCCACATACTTTCTGGTAGGATACATATAT
951625 ATACATA
1 ATACATA
951632 AATGCCATGC
Statistics
Matches: 488, Mismatches: 53, Indels: 70
0.80 0.09 0.11
Matches are distributed among these distances:
81 20 0.04
82 7 0.01
83 1 0.00
84 1 0.00
86 4 0.01
88 11 0.02
89 1 0.00
90 27 0.06
92 81 0.17
93 9 0.02
94 43 0.09
95 79 0.16
96 87 0.18
97 7 0.01
98 4 0.01
99 26 0.05
102 20 0.04
103 6 0.01
105 6 0.01
106 48 0.10
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (94 bp):
ATACATACATATTTACAAAAGCTGTGGTTGTTTAGATGGAAGAAAATTGAAAAAAAAACTCGTCT
CCACATACTTTCTGGTAGGATACATATAT
Found at i:951334 original size:2 final size:2
Alignment explanation
Indices: 951327--951360 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
951317 TTTTAGTAGG
951327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
951361 TTACAAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:951437 original size:106 final size:106
Alignment explanation
Indices: 951233--951441 Score: 291
Period size: 106 Copynumber: 2.0 Consensus size: 106
951223 TTCTGGTAGG
* * *
951233 ATATATATATATATATATATATTTATAAAAGTTGTGGTTGTTTATATGGAAGAAAACTGGGAAAA
1 ATATATATATATATATATATATTTACAAAAGTTGTGGTTGTTTAGAGGGAAGAAAACTGGGAAAA
* * * *
951298 AAACTTGTCTCCACGTACTTTTTAGTAGGATATATATATAT
66 AAACTCGTCTCCACGTACTCTCTAATAGGATATATATATAT
*
951339 ATATATATATATATATATATATTTACAAAAGTTGTGGTTGTTTAGAGGGAA-AAAA-T-TGAAAA
1 ATATATATATATATATATATATTTACAAAAGTTGTGGTTGTTTAGAGGGAAGAAAACTGGGAAAA
* * *
951401 ATA-TCGTCTCCACTTACTCTCTAATAGGATACATATATAT
66 AAACTCGTCTCCACGTACTCTCTAATAGGATATATATATAT
951441 A
1 A
951442 CATACAAAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
102 32 0.35
103 7 0.08
104 1 0.01
105 4 0.04
106 48 0.52
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (106 bp):
ATATATATATATATATATATATTTACAAAAGTTGTGGTTGTTTAGAGGGAAGAAAACTGGGAAAA
AAACTCGTCTCCACGTACTCTCTAATAGGATATATATATAT
Found at i:951499 original size:90 final size:88
Alignment explanation
Indices: 951404--951631 Score: 251
Period size: 99 Copynumber: 2.5 Consensus size: 88
951394 TTGAAAAATA
* * * *
951404 TCGTCTCCACTTACTCTCTAATAGGATACATATATATACATAC-AAAGCCGTGGCTGTTTAGATG
1 TCGTCTCCACATACTTTCTAGTAGGATACATATATATACATACAAAAGCCGTAGCTGTTTAGATG
951468 GAAGAAAACTGAAAGAAAAAAAGAAC
66 GAAGAAAACTG-AA-AAAAAAA-AAC
* * * *
951494 TCGTCTCCACAAAATTTCTAGTAGGATACACATATATACATACATATTTACAAAAGCTGTAGTTG
1 TCGTCTCCACATACTTTCTAGTAGGAT--ACATATAT--ATAC--A--TACAAAAGCCGTAGCTG
*
951559 TTTAGATGGAAGAAAATTGAAAAAAAAAAAC
58 TTTAGATGGAAGAAAACTGAAAAAAAAAAAC
* *
951590 TCGTCTCCCCATACTTTCTAGTATGATACATATATATACATA
1 TCGTCTCCACATACTTTCTAGTAGGATACATATATATACATA
951632 AATGCCATGC
Statistics
Matches: 116, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
88 2 0.02
90 23 0.20
92 12 0.10
94 12 0.10
96 27 0.23
97 7 0.06
98 5 0.04
99 28 0.24
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.29
Consensus pattern (88 bp):
TCGTCTCCACATACTTTCTAGTAGGATACATATATATACATACAAAAGCCGTAGCTGTTTAGATG
GAAGAAAACTGAAAAAAAAAAAC
Found at i:954558 original size:16 final size:16
Alignment explanation
Indices: 954498--954559 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
954488 TAATAATATT
954498 TATTATATT-T-TTAA
1 TATTATATTATATTAA
* * *
954512 AAATATATATATAATAA
1 TATTATAT-TATATTAA
954529 TATTATATTATATTAA
1 TATTATATTATATTAA
954545 TATTA-ATTATTATTA
1 TATTATATTA-TATTA
954560 TTTATTGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.16
15 5 0.13
16 18 0.47
17 9 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATATTATATTAA
Found at i:962308 original size:46 final size:46
Alignment explanation
Indices: 962241--962333 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
962231 TGATCTCTCG
*
962241 ACCGTTAACTCCTGTTGAAGTATGAGTTTA-CAATTAAAAAATTAAA
1 ACCGTTAACTCCTGTTAAAGTATGAG-TTAGCAATTAAAAAATTAAA
* *
962287 ACCGTTAACTCTTGTTAAAGTATGAGTTAGCAATTTAAAAATTAAA
1 ACCGTTAACTCCTGTTAAAGTATGAGTTAGCAATTAAAAAATTAAA
962333 A
1 A
962334 AAAATCTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 3 0.07
46 40 0.93
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (46 bp):
ACCGTTAACTCCTGTTAAAGTATGAGTTAGCAATTAAAAAATTAAA
Found at i:976384 original size:33 final size:32
Alignment explanation
Indices: 976347--976417 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
976337 TTCACTTTTT
*
976347 TTAAAAATTAATAAAAATGT-AATAAAAAAAGAA
1 TTAAAAATGAAT-AAAAT-TCAATAAAAAAAGAA
*
976380 TTAAAAGTGAATAAAATTCAATAAAAAAAGAA
1 TTAAAAATGAATAAAATTCAATAAAAAAAGAA
976412 TGTAAA
1 T-TAAA
976418 GCTAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 1 0.03
32 19 0.56
33 14 0.41
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.24
Consensus pattern (32 bp):
TTAAAAATGAATAAAATTCAATAAAAAAAGAA
Found at i:977115 original size:326 final size:334
Alignment explanation
Indices: 976498--977162 Score: 1053
Period size: 326 Copynumber: 2.0 Consensus size: 334
976488 TATTAAATTC
* *
976498 TAATTTTATTAAAAATGAATAAATATTATTAATTGTTGTTAAAAAATAATAATTAATGAATAATA
1 TAATTTTATTAAAAATGAATAAACATTATTAATTATTGTT--AAAATAATAATTAA-GAATAATA
* *
976563 ATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTAATATTTTTAAACAATTA
63 ATTCATTTGATCCCTCAATTATAATTAAAAATTTATTTTAATATTTTAATATTTTTAAACAATTA
*
976628 ATTTTAAAAGTCAATAAATTTATCAAAAATATATGAAATTTGTAATTTTTTAAATTATAAAATAT
128 ATTTTAAAAGTCAATAAATTTATCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATA-
976693 TTATTATTATTATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATT
192 TTATTATTATTATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATT
* * * *
976758 AATATTTTAAAGTATTTACCCTCAAAGTTTTCCTATACTAGATTACACGTATTGTGTAATTTCAT
257 AATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTACACATATCGTGTAATTTCAT
976823 GCAAAAATCAAAA
322 GCAAAAATCAAAA
976836 TAATTTTATTAAAAATGAATAAACATTATTAATTATTGTT-AAA-AATAA-T-A-AATAATAATT
1 TAATTTTATTAAAAATGAATAAACATTATTAATTATTGTTAAAATAATAATTAAGAATAATAATT
* *
976896 CATTTGATCCCTCAATTATAATTAAAAATTTATTTTAATATTTTTTTATATTTTTAAACTATTAA
66 CATTTGATCCCTCAATTATAATTAAAAATTTATTTTAATA--TTTTAATATTTTTAAACAATTAA
* *
976961 TTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATTATTTTTTAAATTAT-AAA-A-T
129 TTTTAAAAGTCAATAAATTTATCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATT
* * *
977023 A-T-TTATTATCATCATTATTTTGTAAAAGAAATATTAGTTATAAAACTTTTATAAAATTATTCA
194 ATTATTATTATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTAA
*
977086 TATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACATATCGTGTAATTTCATGC
259 TATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTACACATATCGTGTAATTTCATGC
977151 AAAAATCAAAA
324 AAAAATCAAAA
977162 T
1 T
977163 TTATCGAGTT
Statistics
Matches: 308, Mismatches: 17, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
326 130 0.42
327 1 0.00
328 2 0.01
330 49 0.16
331 3 0.01
332 76 0.25
333 1 0.00
334 5 0.02
335 3 0.01
338 38 0.12
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (334 bp):
TAATTTTATTAAAAATGAATAAACATTATTAATTATTGTTAAAATAATAATTAAGAATAATAATT
CATTTGATCCCTCAATTATAATTAAAAATTTATTTTAATATTTTAATATTTTTAAACAATTAATT
TTAAAAGTCAATAAATTTATCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTAT
TATTATTATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTAATA
TTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTACACATATCGTGTAATTTCATGCAA
AAATCAAAA
Found at i:977857 original size:18 final size:18
Alignment explanation
Indices: 977831--977877 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
977821 TTTATATATC
*
977831 TTAACTTAAATTTACATA
1 TTAAATTAAATTTACATA
* *
977849 TTAAATTAATTTTACATC
1 TTAAATTAAATTTACATA
977867 TTAATATTAAA
1 TTAA-ATTAAA
977878 AAATATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTAAATTTACATA
Found at i:977891 original size:24 final size:24
Alignment explanation
Indices: 977864--977911 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
977854 TTAATTTTAC
977864 ATCTTAA-TATTAAAAAATATTTTT
1 ATCTTAACTATT-AAAAATATTTTT
*
977888 ATCTTAACTTATTAAATATATTTT
1 ATCTTAAC-TATTAAAAATATTTT
977912 ATTATTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 10 0.48
26 4 0.19
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (24 bp):
ATCTTAACTATTAAAAATATTTTT
Found at i:977959 original size:29 final size:30
Alignment explanation
Indices: 977902--978002 Score: 102
Period size: 29 Copynumber: 3.4 Consensus size: 30
977892 TAACTTATTA
* *
977902 AATATATTTTATTATT-TTTGTAACCTAAA-
1 AATATATTTTATTCTTATTT-TAACTTAAAC
*
977931 AATATATTTTATTCTTATTTTAATTTAAAC
1 AATATATTTTATTCTTATTTTAACTTAAAC
* *
977961 AATA-A-TTTATTCTTATATTAACTTAAAT
1 AATATATTTTATTCTTATTTTAACTTAAAC
*
977989 ATTTATATTTTATT
1 A-ATATATTTTATT
978003 ATAATAATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 21 0.35
29 25 0.42
30 8 0.13
31 6 0.10
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (30 bp):
AATATATTTTATTCTTATTTTAACTTAAAC
Found at i:978243 original size:30 final size:30
Alignment explanation
Indices: 978009--978307 Score: 169
Period size: 30 Copynumber: 10.2 Consensus size: 30
977999 TATTATAATA
* * * *
978009 ATATTTTAAATTTAAGATAAAAAATATAAT
1 ATATTTTTAAGTTAAGATAAAGAATAAAAT
* *
978039 ATATTTTTTGTAGTTAAGATAAA-AGTAAAAT
1 ATA-TTTTT-AAGTTAAGATAAAGAATAAAAT
*
978070 ATATTTTT--G-T-AG-TTAA-AATAGAAAT
1 ATATTTTTAAGTTAAGATAAAGAATA-AAAT
* * * *
978095 ATATTTTTAAGTTACGAT-AATAATGAAAG
1 ATATTTTTAAGTTAAGATAAAGAATAAAAT
* **
978124 ATATGTTTTAAGTTAA-AT-AAGAATTAGTT
1 ATAT-TTTTAAGTTAAGATAAAGAATAAAAT
* ** * *
978153 ATATTTAATACTTTAAGGT-AAGAATATAAT
1 ATATTT-TTAAGTTAAGATAAAGAATAAAAT
* **
978183 TTATGTAATAAGTTAAGATAAA-AATAAAAT
1 ATAT-TTTTAAGTTAAGATAAAGAATAAAAT
**
978213 ATATTTTTATA-TTAAGATAAAGTTTAAAAT
1 ATATTTTTA-AGTTAAGATAAAGAATAAAAT
* * *
978243 ATGTTTTTAATTTAAAATTAAA-AATAAAAT
1 ATATTTTTAAGTTAAGA-TAAAGAATAAAAT
*
978273 ATATTTTTAAGTTAAGA-CAAGAATAAAAT
1 ATATTTTTAAGTTAAGATAAAGAATAAAAT
978302 ATATTT
1 ATATTT
978308 AATAAGATAA
Statistics
Matches: 207, Mismatches: 43, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
24 6 0.03
25 14 0.07
26 1 0.00
27 2 0.01
28 5 0.02
29 56 0.27
30 92 0.44
31 20 0.10
32 11 0.05
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.41
Consensus pattern (30 bp):
ATATTTTTAAGTTAAGATAAAGAATAAAAT
Found at i:978342 original size:23 final size:24
Alignment explanation
Indices: 978295--978344 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
978285 TAAGACAAGA
*
978295 ATAAAATATATTTAATAAGATAAT
1 ATAAAATATAATTAATAAGATAAT
978319 ATAAAA-ATAATTAATAA-ATAAAT
1 ATAAAATATAATTAATAAGAT-AAT
978342 ATA
1 ATA
978345 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 2 0.08
23 16 0.67
24 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAAAATATAATTAATAAGATAAT
Found at i:978347 original size:2 final size:2
Alignment explanation
Indices: 978340--978379 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
978330 TAATAAATAA
*
978340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
978380 TATTAAGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:978919 original size:10 final size:10
Alignment explanation
Indices: 978901--978930 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
978891 GAGTGTATTC
978901 GGTTCGGTTT
1 GGTTCGGTTT
*
978911 GGTTTGGTTT
1 GGTTCGGTTT
978921 GGTTCGGTTT
1 GGTTCGGTTT
978931 TTTACTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.40, T:0.53
Consensus pattern (10 bp):
GGTTCGGTTT
Found at i:980052 original size:19 final size:19
Alignment explanation
Indices: 980016--980057 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
980006 TTTAATATAT
980016 TATCAAAAAAATATTTTAA
1 TATCAAAAAAATATTTTAA
* *
980035 TATCACAAACAATATTTAAA
1 TATCA-AAAAAATATTTTAA
980055 TAT
1 TAT
980058 TATCATGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (19 bp):
TATCAAAAAAATATTTTAA
Found at i:982434 original size:21 final size:21
Alignment explanation
Indices: 982408--982452 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
982398 GATTTCTGGG
* *
982408 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
982429 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
982450 CAA
1 CAA
982453 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:983318 original size:31 final size:31
Alignment explanation
Indices: 983280--983433 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
983270 GGGTCGAGGG
983280 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
983311 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
983342 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
983373 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
983404 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
983434 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:986413 original size:21 final size:21
Alignment explanation
Indices: 986387--986431 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
986377 GATTTCTGGG
* *
986387 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
986408 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
986429 CAA
1 CAA
986432 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:987332 original size:31 final size:31
Alignment explanation
Indices: 987294--987447 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
987284 GGGTCGAGGG
987294 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
987325 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
987356 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
987387 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
987418 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
987448 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:994313 original size:21 final size:22
Alignment explanation
Indices: 994275--994318 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
994265 AATGTTGGAT
*
994275 GGGAACTGATTCCCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
994297 GGGAACCGATT-CCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
994318 G
1 G
994319 TACTTCGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCTGCTACA
Found at i:995240 original size:21 final size:21
Alignment explanation
Indices: 995216--995261 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
995206 TGTCCTGAAT
995216 GACCACTGTATTATCCCGAAG
1 GACCACTGTATTATCCCGAAG
* *
995237 GACCACTGTATTGTTCCGAAG
1 GACCACTGTATTATCCCGAAG
995258 GACC
1 GACC
995262 TATGAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (21 bp):
GACCACTGTATTATCCCGAAG
Found at i:995355 original size:18 final size:17
Alignment explanation
Indices: 995328--995361 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
995318 ATATGGGCAT
*
995328 TATCATTTGTTCATTTCA
1 TATCACTTGTTC-TTTCA
995346 TATCACTTGTTCTTTC
1 TATCACTTGTTCTTTC
995362 TCTTCTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (17 bp):
TATCACTTGTTCTTTCA
Found at i:996346 original size:15 final size:15
Alignment explanation
Indices: 996322--996355 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
996312 CCGTAGGACC
*
996322 ACTACATCCCGAAGG
1 ACTACATCCCGAACG
*
996337 ACTACGTCCCGAACG
1 ACTACATCCCGAACG
996352 ACTA
1 ACTA
996356 TTATACCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAACG
Found at i:996482 original size:29 final size:28
Alignment explanation
Indices: 996440--996522 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 28
996430 TTTTATATGT
996440 TCATGTACTCATGTCATTTCTCTTGTGA
1 TCATGTACTCATGTCATTTCTCTTGTGA
996468 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTA-CTCATGTCATTTCTCTTGTGA
*
996497 TCATGTATTTCATGTCATTTTCTCTT
1 TCATGTA-CTCATGTCA-TTTCTCTT
996523 ATCACATATC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 36 0.71
30 8 0.16
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.49
Consensus pattern (28 bp):
TCATGTACTCATGTCATTTCTCTTGTGA
Found at i:1000802 original size:221 final size:223
Alignment explanation
Indices: 1000417--1000860 Score: 874
Period size: 221 Copynumber: 2.0 Consensus size: 223
1000407 ATTTTACATA
1000417 AACCACATAGCACATGCAAAACAAAACCTATCAATTCATATAATCCAACATACATACACTTCATA
1 AACCACATAGCACATGCAAAACAAAACCTATCAATTCATATAATCCAACATACATACACTTCATA
1000482 TCGTTAACATACTTATAATCAAGACTTAATGAGCTATTACTATAGGAATAGACTTATCACAAGTC
66 TCGTTAACATACTTATAATCAAGACTTAATGAGCTATTACTATAGGAATAGACTTATCACAAGTC
1000547 CAATTTCCATATAATCTTATACGATAAGATGCACTCACCTGGGCCTCGTTGTTTGAATCAATCCT
131 CAATTTCCATATAATCTTATACGATAAGATGCACTCACCTGGGCCTCGTTGTTTGAATCAATCCT
1000612 AATCCTTAGTTTGTTCCGGAACAAGCTT
196 AATCCTTAGTTTGTTCCGGAACAAGCTT
1000640 AACCACATAGCACATGCAAAACAAAACCTATCAATTCATATAATCCAACATACATACACTTCATA
1 AACCACATAGCACATGCAAAACAAAACCTATCAATTCATATAATCCAACATACATACACTTCATA
1000705 TCGTTAACATAC-T-TAATCAAGACTTAATGAGCTATTACTATAGGAATAGACTTATCACAAGTC
66 TCGTTAACATACTTATAATCAAGACTTAATGAGCTATTACTATAGGAATAGACTTATCACAAGTC
1000768 CAATTTCCATATAATCTTATACGATAAGATGCACTCACCTGGGCCTCGTTGTTTGAATCAATCCT
131 CAATTTCCATATAATCTTATACGATAAGATGCACTCACCTGGGCCTCGTTGTTTGAATCAATCCT
1000833 AATCCTTAGTTTGTTCCGGAACAAGCTT
196 AATCCTTAGTTTGTTCCGGAACAAGCTT
1000861 TCATTCTATA
Statistics
Matches: 221, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
221 143 0.65
222 1 0.00
223 77 0.35
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (223 bp):
AACCACATAGCACATGCAAAACAAAACCTATCAATTCATATAATCCAACATACATACACTTCATA
TCGTTAACATACTTATAATCAAGACTTAATGAGCTATTACTATAGGAATAGACTTATCACAAGTC
CAATTTCCATATAATCTTATACGATAAGATGCACTCACCTGGGCCTCGTTGTTTGAATCAATCCT
AATCCTTAGTTTGTTCCGGAACAAGCTT
Found at i:1001070 original size:64 final size:63
Alignment explanation
Indices: 1000980--1001135 Score: 181
Period size: 63 Copynumber: 2.4 Consensus size: 63
1000970 GAAGGTATGC
* * * *
1000980 ATCGATGCACTACACCATGCATCGATGCATAAATC-CTATTCGATG-TTTGTATTTAATGGGGAT
1 ATCGATGCACTCCA-TATGCATCGATGCATAAATCTC-ATTCGATGTTTTCTATTTAAT--GCAT
1001043 GA
62 GA
* * *
1001045 ATCGATGCACTCCTTATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTTAATTCATGC
1 ATCGATGCACTCCATATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTTAATGCATGA
* *
1001108 ATCGATGCACTGCATGTGCATCGATGCA
1 ATCGATGCACTCCATATGCATCGATGCA
1001136 CCTTAAACAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 28 0.35
64 27 0.34
65 24 0.30
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATCGATGCACTCCATATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTTAATGCATGA
Found at i:1004159 original size:79 final size:78
Alignment explanation
Indices: 1004002--1004153 Score: 268
Period size: 79 Copynumber: 1.9 Consensus size: 78
1003992 ATGTTCTGTT
1004002 CTATCATGTTATACCAATTCCATGCATTCTTCGTATCATATAAAATATCAGATTAATTACAGTAA
1 CTATCATGTTATACCAATTCCATGCATTCTTCGTATCATATAAAATATCAGATTAATTACAGTAA
1004067 ATACATACTACACA
66 ATACA-ACTACACA
1004081 CTATCATGTTATACCAATTCCATGCATTCTTCGTATCATATAAAATCATATCAGATTAATTACAG
1 CTATCATGTTATACCAATTCCATGCATTCTTCGTATCATAT-AAA--ATATCAGATTAATTACAG
1004146 TAAATACA
63 TAAATACA
1004154 TACACATAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
79 41 0.59
80 3 0.04
82 26 0.37
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.35
Consensus pattern (78 bp):
CTATCATGTTATACCAATTCCATGCATTCTTCGTATCATATAAAATATCAGATTAATTACAGTAA
ATACAACTACACA
Found at i:1004402 original size:23 final size:23
Alignment explanation
Indices: 1004376--1004421 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1004366 CACCACAGCT
*
1004376 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1004399 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
1004422 TAGTGCCGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1004424 original size:8 final size:8
Alignment explanation
Indices: 1004411--1004444 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1004401 TAGAATTGCA
1004411 CCGTAGTG
1 CCGTAGTG
1004419 CCGTAGTG
1 CCGTAGTG
* *
1004427 CCGCATTG
1 CCGTAGTG
1004435 CCGTAGTG
1 CCGTAGTG
1004443 CC
1 CC
1004445 ATATAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.24
Consensus pattern (8 bp):
CCGTAGTG
Found at i:1005755 original size:64 final size:66
Alignment explanation
Indices: 1005657--1005781 Score: 186
Period size: 64 Copynumber: 1.9 Consensus size: 66
1005647 TAATGAAGGT
*
1005657 ATGCATCGATGCACTACACCATGCATCGATGCATAAATC-CTATTCGATG-TTTGTATTTAATGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCTC-ATTCGATGTTTTCTATTTAATGG
1005720 TG
65 TG
*
1005722 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTTAA
1005782 ATTCGATGCA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
63 1 0.02
64 28 0.51
65 26 0.47
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTTAATGGT
G
Found at i:1009857 original size:21 final size:22
Alignment explanation
Indices: 1009819--1009862 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1009809 AATATTAGAG
*
1009819 GGGAATCGATTCCCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
1009841 GGGAACCGATT-CCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
1009862 G
1 G
1009863 TACTTCAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCTGCTACA
Found at i:1010795 original size:20 final size:20
Alignment explanation
Indices: 1010748--1010804 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1010738 GCATATGAAA
* *
1010748 TTTGTCCCGAATA-ACCATTG
1 TTTGTCTCGAA-AGACCACTG
1010768 TATTGTCTCGAAAGACCACTG
1 T-TTGTCTCGAAAGACCACTG
1010789 TTTGTCTCGAAAGACC
1 TTTGTCTCGAAAGACC
1010805 TATGAAACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (20 bp):
TTTGTCTCGAAAGACCACTG
Found at i:1015476 original size:17 final size:17
Alignment explanation
Indices: 1015454--1015490 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1015444 CAATTTTGAG
*
1015454 CTCGATTGAAGCTCAAA
1 CTCGATTCAAGCTCAAA
*
1015471 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCAAA
1015488 CTC
1 CTC
1015491 AAAGTCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCAAA
Found at i:1015581 original size:14 final size:14
Alignment explanation
Indices: 1015528--1015594 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
1015518 TTATATTACA
*
1015528 TTTAAAAATATATT
1 TTTAAAAATGTATT
1015542 TTTAAAAATGTATAAT
1 TTTAAAAATGTAT--T
* *
1015558 TATCAATAATGTATT
1 T-TTAAAAATGTATT
* *
1015573 TTTAATAATGTAAT
1 TTTAAAAATGTATT
1015587 TTTAAAAA
1 TTTAAAAA
1015595 ATCTAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
14 30 0.68
15 2 0.05
16 2 0.05
17 10 0.23
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (14 bp):
TTTAAAAATGTATT
Found at i:1016777 original size:2 final size:2
Alignment explanation
Indices: 1016770--1016797 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1016760 CCACGTTTTA
1016770 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1016798 TTAACCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.