Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 15
Found at i:2093629 original size:15 final size:16
Alignment explanation
Indices: 2093609--2093646 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2093599 TTAATTATGT
* *
2093609 ATATGAAA-GTTTGGA
1 ATATGAAAGGGTTGAA
2093624 ATATGAAAGGGTTGAA
1 ATATGAAAGGGTTGAA
2093640 ATATGAA
1 ATATGAA
2093647 GGATTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (16 bp):
ATATGAAAGGGTTGAA
Found at i:2093837 original size:64 final size:64
Alignment explanation
Indices: 2093769--2093989 Score: 234
Period size: 64 Copynumber: 3.5 Consensus size: 64
2093759 TTGAAGGTGT
** ** * *
2093769 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATTAGTG
2093832 C
64 C
* *
2093833 ATCGATGCATAAATAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
* * * * *
2093897 ATCGATGCATAAGTCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTA-TG
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATTAGTG
2093960 C
64 C
* * *
2093961 ACCGATGCATCAGTAGTGCATCAATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
2093990 ACCTTCATTA
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 124 0.93
65 9 0.07
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
Found at i:2094923 original size:103 final size:103
Alignment explanation
Indices: 2094739--2094964 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
2094729 GTCGAGGGTC
*
2094739 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
2094804 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATAA
2094842 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2094907 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATAA
2094945 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
2094965 TATTATATGG
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 116 0.99
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATAA
Found at i:2095006 original size:23 final size:23
Alignment explanation
Indices: 2094973--2095035 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2094963 ATTATTATAT
2094973 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * * *
2094996 GGCACTCCGGTGCAACTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
2095019 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
2095036 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2095040 original size:23 final size:23
Alignment explanation
Indices: 2094963--2095040 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
2094953 CCTTATGGAC
*
2094963 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2094987 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* * *
2095010 ACTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2095033 ATTATATG
1 ATTATATG
2095041 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2099553 original size:64 final size:64
Alignment explanation
Indices: 2099485--2099705 Score: 250
Period size: 64 Copynumber: 3.5 Consensus size: 64
2099475 TTGAAGGTGT
** **
2099485 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTTGTG
2099548 C
64 C
* ** * *
2099549 ATCGATGCATAAATAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGTAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
* * * * *
2099613 ATCGATGCATAAGTCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
* *
2099677 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
2099706 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 125 0.95
65 6 0.05
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
Found at i:2100682 original size:103 final size:103
Alignment explanation
Indices: 2100457--2100674 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
2100447 GTCGAGGGTC
*
2100457 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
2100522 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2100560 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2100625 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2100663 TATGTGGTCCTT
1 TATGTGGTCCTT
2100675 ATAGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2100724 original size:23 final size:23
Alignment explanation
Indices: 2100691--2100753 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2100681 ATTATTATAT
*
2100691 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * * *
2100714 GGCACTCCGGTGCAACTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
2100737 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
2100754 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2100758 original size:23 final size:23
Alignment explanation
Indices: 2100681--2100758 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
2100671 CCTTATAGAC
* *
2100681 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2100705 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* * *
2100728 ACTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2100751 ATTATATG
1 ATTATATG
2100759 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 39 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2101874 original size:23 final size:22
Alignment explanation
Indices: 2101826--2101874 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2101816 CTTGAATGTC
2101826 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
2101847 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
2101870 AAGGA
1 AAGGA
2101875 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:2102744 original size:47 final size:47
Alignment explanation
Indices: 2102690--2102809 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
2102680 CCTTATGGAC
2102690 ATTATTATATGGCACTACGGTGCAATTCTACGCAGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCAGCACTCCGGTGCA
* * *
2102737 ATTATTATATGGTACTAAGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCAGCACTCCGGTGCA
* *
2102784 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
2102810 ATATGAGCTG
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
46 18 0.27
47 48 0.73
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCAGCACTCCGGTGCA
Found at i:2102810 original size:23 final size:23
Alignment explanation
Indices: 2102690--2102814 Score: 106
Period size: 23 Copynumber: 5.3 Consensus size: 23
2102680 CCTTATGGAC
*
2102690 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * ** *
2102714 ATTCTACGCAGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* * *
2102737 ATTATTATATGGTACTAAGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2102761 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2102784 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2102807 ATTATATG
1 ATTATATG
2102815 AGCTGTGATG
Statistics
Matches: 75, Mismatches: 25, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
23 57 0.76
24 18 0.24
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2107601 original size:23 final size:22
Alignment explanation
Indices: 2107553--2107601 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2107543 CCAGAATGTC
2107553 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
2107574 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
2107597 AAGGA
1 AAGGA
2107602 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:2108493 original size:23 final size:23
Alignment explanation
Indices: 2108417--2108494 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
2108407 CCTTATGGAC
*
2108417 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2108441 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2108464 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2108487 ATTATATG
1 ATTATATG
2108495 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2110057 original size:8 final size:8
Alignment explanation
Indices: 2110041--2110120 Score: 57
Period size: 8 Copynumber: 10.8 Consensus size: 8
2110031 TATTATTAAA
*
2110041 ATAAAATT
1 ATAATATT
2110049 ATAATATT
1 ATAATATT
2110057 AT-ATATT
1 ATAATATT
* *
2110064 ATAACAAT
1 ATAATATT
2110072 AT-A-ATT
1 ATAATATT
2110078 ATAATATT
1 ATAATATT
*
2110086 A-AA-AAT
1 ATAATATT
2110092 ATAATATT
1 ATAATATT
*
2110100 ATACTATT
1 ATAATATT
2110108 A-AA-ATT
1 ATAATATT
2110114 ATCAATA
1 AT-AATA
2110121 AGCATCATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
6 11 0.20
7 14 0.25
8 30 0.54
9 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAATATT
Found at i:2110058 original size:29 final size:29
Alignment explanation
Indices: 2110024--2110086 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2110014 ATTAATAATT
2110024 TATTATATATTATTAA-AATAAAATTATAA
1 TATTATATATTA-TAACAATAAAATTATAA
*
2110053 TATTATATATTATAACAATATAATTATAA
1 TATTATATATTATAACAATAAAATTATAA
2110082 TATTA
1 TATTA
2110087 AAAATATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
TATTATATATTATAACAATAAAATTATAA
Found at i:2110100 original size:22 final size:22
Alignment explanation
Indices: 2110042--2110120 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
2110032 ATTATTAAAA
*
2110042 TAAAATTATAATATTAT-ATAT
1 TAAAAATATAATATTATAATAT
2110063 TATAACAATAT-A-ATTATAATAT
1 TA-AA-AATATAATATTATAATAT
*
2110085 TAAAAATATAATATTATACTAT
1 TAAAAATATAATATTATAATAT
*
2110107 TAAAATTATCAATA
1 TAAAAATAT-AATA
2110121 AGCATCATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.10
21 10 0.20
22 26 0.53
23 8 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAATATAATATTATAATAT
Found at i:2111547 original size:18 final size:17
Alignment explanation
Indices: 2111520--2111572 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
2111510 AGCAAAAACG
*
2111520 TTTTATTTAATTATTAAA
1 TTTTAATTAATT-TTAAA
2111538 TTTTAATTAATTTTAACTA
1 TTTTAATTAATTTTAA--A
* *
2111557 TATTAAATAATTTTAA
1 TTTTAATTAATTTTAA
2111573 TATAGATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 4 0.13
18 11 0.37
19 15 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAATTAATTTTAAA
Found at i:2111567 original size:19 final size:18
Alignment explanation
Indices: 2111527--2111576 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2111517 ACGTTTTATT
* *
2111527 TAATTATTAA-ATTTTAAT
1 TAATT-TTAATATATTAAA
2111545 TAATTTTAACTATATTAAA
1 TAATTTTAA-TATATTAAA
2111564 TAATTTTAATATA
1 TAATTTTAATATA
2111577 GATTAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 15 0.54
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTTTAATATATTAAA
Found at i:2111584 original size:20 final size:19
Alignment explanation
Indices: 2111540--2111576 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2111530 TTATTAAATT
*
2111540 TTAATTAATTTTAACTATA
1 TTAAATAATTTTAACTATA
2111559 TTAAATAATTTTAA-TATA
1 TTAAATAATTTTAACTATA
2111577 GATTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATAATTTTAACTATA
Found at i:2111961 original size:19 final size:20
Alignment explanation
Indices: 2111932--2111969 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2111922 TTAAAAATGA
2111932 TTTGATTTTGAAAACCAAAG
1 TTTGATTTTGAAAACCAAAG
*
2111952 TTTG-TTTTGAAAATCAAA
1 TTTGATTTTGAAAACCAAA
2111970 ATGAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (20 bp):
TTTGATTTTGAAAACCAAAG
Found at i:2112626 original size:96 final size:94
Alignment explanation
Indices: 2112503--2112693 Score: 355
Period size: 96 Copynumber: 2.0 Consensus size: 94
2112493 GAACATTTTA
2112503 AATTTTTAATATTTTTTCATAATTTTTAGTTCATCATAATAAATTTTGGTCAAAATTGATTTTCA
1 AATTTTTAATATTTTTTCATAATTTTTAGTTCATCATAATAAATTTTGGTCAAAATTGATTTTCA
*
2112568 ATGTAAATGATATCTCTCTAACAACTGAT
66 ATGCAAATGATATCTCTCTAACAACTGAT
2112597 AATTTTTAATATTTTTTTTCATAATTTTTAGTTCATCATAATAAATTTTGGTCAAAATTGATTTT
1 AATTTTTAATA--TTTTTTCATAATTTTTAGTTCATCATAATAAATTTTGGTCAAAATTGATTTT
2112662 CAATGCAAATGATATCTCTCTAACAACTGAT
64 CAATGCAAATGATATCTCTCTAACAACTGAT
2112693 A
1 A
2112694 CCAACTTTTC
Statistics
Matches: 94, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
94 11 0.12
96 83 0.88
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (94 bp):
AATTTTTAATATTTTTTCATAATTTTTAGTTCATCATAATAAATTTTGGTCAAAATTGATTTTCA
ATGCAAATGATATCTCTCTAACAACTGAT
Found at i:2115043 original size:27 final size:25
Alignment explanation
Indices: 2115013--2115074 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
2115003 CAAAAAAAGA
*
2115013 TAATTAGAAAACATAATAAGTTTCAAC
1 TAATT-GAAAA-ATAATAAGTCTCAAC
* * *
2115040 TAATTTAAAAATTATAAGTCTCGAC
1 TAATTGAAAAATAATAAGTCTCAAC
*
2115065 TAATTTAAAA
1 TAATTGAAAA
2115075 GATCCGTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 22 0.71
26 4 0.13
27 5 0.16
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (25 bp):
TAATTGAAAAATAATAAGTCTCAAC
Found at i:2115112 original size:23 final size:23
Alignment explanation
Indices: 2115082--2115125 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2115072 AAAGATCCGT
2115082 AATATTTTGGTCACAATATTTGA
1 AATATTTTGGTCACAATATTTGA
*
2115105 AATATTTTGGTCATAATATTT
1 AATATTTTGGTCACAATATTT
2115126 CATTTTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (23 bp):
AATATTTTGGTCACAATATTTGA
Found at i:2121817 original size:32 final size:32
Alignment explanation
Indices: 2121749--2121824 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
2121739 GGTTAGGCCC
* **
2121749 TAATAATAAATATTAGAAAAAATCTAAGCCCA
1 TAATAATAAATAGTAGAAAAAATCTAAAACCA
**
2121781 TAATAATAAATAGTAGGAAAAAAT-TAAAACTT
1 TAATAATAAATAGTA-GAAAAAATCTAAAACCA
*
2121813 TAATAAAAAATA
1 TAATAATAAATA
2121825 TTAAAGATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 29 0.78
33 8 0.22
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.26
Consensus pattern (32 bp):
TAATAATAAATAGTAGAAAAAATCTAAAACCA
Found at i:2122050 original size:24 final size:24
Alignment explanation
Indices: 2122017--2122083 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
2122007 TCATGAACAC
* *
2122017 TAAATAAACACATTCGTGAATATA
1 TAAATGAACACATTCGTGAACATA
* *
2122041 TAATTGAACACGTTCGTGAACATA
1 TAAATGAACACATTCGTGAACATA
* *
2122065 TAAATGTATACATTCGTGA
1 TAAATGAACACATTCGTGA
2122084 CCAATATATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (24 bp):
TAAATGAACACATTCGTGAACATA
Found at i:2123082 original size:25 final size:25
Alignment explanation
Indices: 2123035--2123082 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2123025 GTATTATTGT
* *
2123035 AATTATTTCTAAATATATAAGGTAA
1 AATTATTTCTAAAAAAATAAGGTAA
* *
2123060 AATTATTTTTAAAAAAATCAGGT
1 AATTATTTCTAAAAAAATAAGGT
2123083 CGGGTCGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (25 bp):
AATTATTTCTAAAAAAATAAGGTAA
Found at i:2127267 original size:18 final size:18
Alignment explanation
Indices: 2127232--2127266 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2127222 TTTTTATCCG
*
2127232 AAAAAATCCGGTTTTTTT
1 AAAAAAACCGGTTTTTTT
2127250 AAAAAAACC-GTTTTTTT
1 AAAAAAACCGGTTTTTTT
2127267 TGCAAACCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (18 bp):
AAAAAAACCGGTTTTTTT
Found at i:2127386 original size:21 final size:21
Alignment explanation
Indices: 2127362--2127433 Score: 144
Period size: 21 Copynumber: 3.4 Consensus size: 21
2127352 GGGGAAAAAA
2127362 CCGGATCGGTTTTTATCCGAT
1 CCGGATCGGTTTTTATCCGAT
2127383 CCGGATCGGTTTTTATCCGAT
1 CCGGATCGGTTTTTATCCGAT
2127404 CCGGATCGGTTTTTATCCGAT
1 CCGGATCGGTTTTTATCCGAT
2127425 CCGGATCGG
1 CCGGATCGG
2127434 ATTGAAATCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.14, C:0.25, G:0.26, T:0.35
Consensus pattern (21 bp):
CCGGATCGGTTTTTATCCGAT
Found at i:2127870 original size:16 final size:16
Alignment explanation
Indices: 2127851--2127881 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2127841 TATTATGCAT
2127851 AATATATCTTTTTAAA
1 AATATATCTTTTTAAA
*
2127867 AATATATTTTTTTAA
1 AATATATCTTTTTAA
2127882 TTTTTAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATATCTTTTTAAA
Found at i:2127902 original size:23 final size:23
Alignment explanation
Indices: 2127859--2127903 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2127849 ATAATATATC
*
2127859 TTTTTAAAAATATATTTTTTTAA
1 TTTTTAAAAATATATTATTTTAA
*
2127882 TTTTTAATAAGTA-ATTATTTTA
1 TTTTTAA-AAATATATTATTTTA
2127904 TAACATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTTAAAAATATATTATTTTAA
Found at i:2127919 original size:2 final size:2
Alignment explanation
Indices: 2127908--2127938 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2127898 ATTTTATAAC
2127908 AT AT -T 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
2127939 TCAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2129815 original size:39 final size:39
Alignment explanation
Indices: 2129761--2129836 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
2129751 TGAATATAAG
*
2129761 ATAATATATGTTCAAAGACTTTCAATCATCTCACAATGA
1 ATAATATATATTCAAAGACTTTCAATCATCTCACAATGA
*
2129800 ATAATATATATTCAAAGACTTTCAATTATCTCACAAT
1 ATAATATATATTCAAAGACTTTCAATCATCTCACAAT
2129837 AAAATGCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (39 bp):
ATAATATATATTCAAAGACTTTCAATCATCTCACAATGA
Found at i:2131638 original size:2 final size:2
Alignment explanation
Indices: 2131594--2131619 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2131584 AAAAAGTAAC
2131594 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2131620 CACAAACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2136729 original size:96 final size:96
Alignment explanation
Indices: 2136549--2136736 Score: 222
Period size: 96 Copynumber: 2.0 Consensus size: 96
2136539 ACTCTCATAA
* * * * * *
2136549 AAGTGGAAAATAACCCAAATTTGAATATAAATCCATAAATATCGCTAATGAATCCTCGAAAGATT
1 AAGTGGAAAATAACCCAAATTTGAATAGAAACCCAAAAACATCACTAATGAATCCTCGAAAGATC
* * *
2136614 ATCAAGTGAGAAAATCTAAATGAAGGCCTTC
66 ATCAAGAGAGAAAACCTAAACGAAGGCCTTC
*
2136645 AAGTGGAAAATAACCCCAACTTT-AATAGAAACCCAAAAACA-CAACTAATGAATCCTTC-AAAG
1 AAGTGGAAAATAA-CCCAAATTTGAATAGAAACCCAAAAACATC-ACTAATGAATCC-TCGAAAG
2136707 A-CATCAAGAGAGAAAAACCTAAACGAAGGC
63 ATCATCAAGAGAG-AAAACCTAAACGAAGGC
2136737 AATAAGACTT
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
95 10 0.13
96 58 0.74
97 10 0.13
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.20
Consensus pattern (96 bp):
AAGTGGAAAATAACCCAAATTTGAATAGAAACCCAAAAACATCACTAATGAATCCTCGAAAGATC
ATCAAGAGAGAAAACCTAAACGAAGGCCTTC
Found at i:2137044 original size:16 final size:18
Alignment explanation
Indices: 2137012--2137044 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2137002 TGGTAAGGTG
2137012 GAAAGAAATTGGAAAGAT
1 GAAAGAAATTGGAAAGAT
2137030 GAAA-AAATT-GAAAGA
1 GAAAGAAATTGGAAAGA
2137045 GACAGAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (18 bp):
GAAAGAAATTGGAAAGAT
Found at i:2137333 original size:19 final size:19
Alignment explanation
Indices: 2137285--2137336 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
2137275 TGTTGCTCAT
*
2137285 ACTCGAGTACAGGTGTCAG
1 ACTCGAGTACATGTGTCAG
2137304 ACTCGAGTACATGTGTCAG
1 ACTCGAGTACATGTGTCAG
2137323 ACTCG-GATACATGT
1 ACTCGAG-TACATGT
2137337 CTAGATGTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 1 0.03
19 30 0.97
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (19 bp):
ACTCGAGTACATGTGTCAG
Found at i:2138425 original size:10 final size:10
Alignment explanation
Indices: 2138410--2138436 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2138400 CTGCTACTAC
2138410 TTTCTTTTTT
1 TTTCTTTTTT
2138420 TTTCTTTTTT
1 TTTCTTTTTT
2138430 TTTCTTT
1 TTTCTTT
2138437 CCTTACGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:2142903 original size:12 final size:12
Alignment explanation
Indices: 2142886--2142921 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
2142876 AAAAACATCA
2142886 ACAGCTTGCTCC
1 ACAGCTTGCTCC
2142898 ACAGCTTGCTCC
1 ACAGCTTGCTCC
2142910 ACAGCTTGCTCC
1 ACAGCTTGCTCC
2142922 TGAAACTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.42, G:0.17, T:0.25
Consensus pattern (12 bp):
ACAGCTTGCTCC
Found at i:2157480 original size:32 final size:32
Alignment explanation
Indices: 2157439--2157501 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
2157429 AAAACTTGAT
2157439 AGAAACACCAAGCATCTGACAAGGTAAACAAC
1 AGAAACACCAAGCATCTGACAAGGTAAACAAC
2157471 AGAAACACCAAGCATCTGACAAGGTAAACAA
1 AGAAACACCAAGCATCTGACAAGGTAAACAA
2157502 GTGGTACCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.10
Consensus pattern (32 bp):
AGAAACACCAAGCATCTGACAAGGTAAACAAC
Found at i:2160705 original size:23 final size:23
Alignment explanation
Indices: 2160640--2160706 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
2160630 GTGCCATATA
*
2160640 TTTGTCCCGAAAGACCATATAGG
1 TTTGTCCCGAAAGACCACATAGG
* *
2160663 TTTGTCCC-AAATGACTACATAGT
1 TTTGTCCCGAAA-GACCACATAGG
*
2160686 TTTGTCCCGAAGGACCACATA
1 TTTGTCCCGAAAGACCACATA
2160707 AAACCCTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.08
23 32 0.86
24 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (23 bp):
TTTGTCCCGAAAGACCACATAGG
Found at i:2162273 original size:21 final size:21
Alignment explanation
Indices: 2162247--2162291 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2162237 GATTTCTGGG
* *
2162247 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2162268 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2162289 CAA
1 CAA
2162292 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:2163185 original size:31 final size:31
Alignment explanation
Indices: 2163147--2163271 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
2163137 AGGGTCGAGG
2163147 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
2163178 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
2163209 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* * *
2163240 GATTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
2163271 G
1 G
2163272 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:2163724 original size:21 final size:20
Alignment explanation
Indices: 2163676--2163726 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2163666 CTTATCCTTG
*
2163676 GTATCGATATCTTCACATCA
1 GTATCGATATCTTCACACCA
*
2163696 GTAACGATACTTCTTCA-ACCA
1 GTATCGATA--TCTTCACACCA
2163717 GTATCGATAT
1 GTATCGATAT
2163727 TGTTCATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 8 0.31
21 11 0.42
22 6 0.23
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (20 bp):
GTATCGATATCTTCACACCA
Found at i:2165975 original size:23 final size:22
Alignment explanation
Indices: 2165927--2165975 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2165917 CCATAATGTC
2165927 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
2165948 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
2165971 AAGGA
1 AAGGA
2165976 AAATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:2166854 original size:103 final size:103
Alignment explanation
Indices: 2166670--2166887 Score: 402
Period size: 103 Copynumber: 2.1 Consensus size: 103
2166660 GTCGAGGGTC
2166670 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2166735 TTGATCCTTATCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTATCATATGTATATGATTCTTAAGGAATGA
*
2166773 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2166838 TTGAT-CTCTATTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCT-TATCATATGTATATGATTCTTAAGGAATGA
2166876 TATGTGGTCCTT
1 TATGTGGTCCTT
2166888 ATGGACATTA
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
102 2 0.02
103 110 0.98
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTATCATATGTATATGATTCTTAAGGAATGA
Found at i:2166963 original size:47 final size:47
Alignment explanation
Indices: 2166894--2167013 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
2166884 CCTTATGGAC
*
2166894 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGTA
1 ATTATTATATGGCACTATGGTGCAATTCTACGCGGCACTCCGGTGTA
2166941 ATTATTATATGGCACTATGGTGCAATTCTACGCGGCACTCCGGTGTA
1 ATTATTATATGGCACTATGGTGCAATTCTACGCGGCACTCCGGTGTA
*
2166988 ATTA-TATGTGGCACT-TCGGTGCAATT
1 ATTATTATATGGCACTAT-GGTGCAATT
2167014 ATATGAGATG
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
45 1 0.01
46 19 0.27
47 50 0.71
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (47 bp):
ATTATTATATGGCACTATGGTGCAATTCTACGCGGCACTCCGGTGTA
Found at i:2167014 original size:23 final size:23
Alignment explanation
Indices: 2166894--2167018 Score: 106
Period size: 23 Copynumber: 5.3 Consensus size: 23
2166884 CCTTATGGAC
* *
2166894 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTCCGGTGCA
* * * *
2166918 ATTCTACGCGGCACTCCGGTGTA
1 ATTATATGTGGCACTCCGGTGCA
* **
2166941 ATTATTATATGGCACTATGGTGCA
1 ATTA-TATGTGGCACTCCGGTGCA
* * * *
2166965 ATTCTACGCGGCACTCCGGTGTA
1 ATTATATGTGGCACTCCGGTGCA
*
2166988 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
2167011 ATTATATG
1 ATTATATG
2167019 AGATGTGGTG
Statistics
Matches: 75, Mismatches: 25, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
23 56 0.75
24 19 0.25
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTCCGGTGCA
Found at i:2171801 original size:23 final size:22
Alignment explanation
Indices: 2171753--2171801 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2171743 CCAGAATGTC
2171753 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
2171774 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
2171797 AAGGA
1 AAGGA
2171802 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:2172155 original size:30 final size:30
Alignment explanation
Indices: 2172121--2172181 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2172111 ATGCATGAGT
* *
2172121 ATATGTGACA-TGATTTATATGATTCATATG
1 ATATGTGACACTGAATTATATGAAT-ATATG
*
2172151 ATATGTGATACTGAATTATATGAATATATG
1 ATATGTGACACTGAATTATATGAATATATG
2172181 A
1 A
2172182 GAATATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (30 bp):
ATATGTGACACTGAATTATATGAATATATG
Found at i:2172720 original size:103 final size:103
Alignment explanation
Indices: 2172495--2172712 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
2172485 GTCAAGGGTC
2172495 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
2172560 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2172598 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2172663 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2172701 TATGTGGTCCTT
1 TATGTGGTCCTT
2172713 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2172796 original size:23 final size:23
Alignment explanation
Indices: 2172722--2172796 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
2172712 TATGGACATT
*
2172722 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTCCGGTGCA
* *
2172743 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTCCGGTGCA
* * *
2172766 ATTATATGTGGTACTTCGGTGCA
1 ATTATATGCGGCACTCCGGTGCA
*
2172789 ATTGTATG
1 ATTATATG
2172797 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
21 5 0.12
23 38 0.88
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATTATATGCGGCACTCCGGTGCA
Found at i:2177127 original size:23 final size:22
Alignment explanation
Indices: 2177082--2177141 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
2177072 ATAATTTGCA
*
2177082 CCGAAGTACCACATA-TTTGTC
1 CCGAAGAACCACATAGTTTGTC
2177103 CCGAAGAACCACATAGTTTTGTC
1 CCGAAGAACCACATAG-TTTGTC
* *
2177126 CCAAAGGACCACATAG
1 CCGAAGAACCACATAG
2177142 AACCCTCGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 14 0.41
23 20 0.59
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (22 bp):
CCGAAGAACCACATAGTTTGTC
Found at i:2177323 original size:13 final size:14
Alignment explanation
Indices: 2177305--2177345 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2177295 TTGTTGAGCA
2177305 CATATAT-TATTTT
1 CATATATATATTTT
2177318 CATATATAATATTTT
1 CATATAT-ATATTTT
*
2177333 CATATACATATTT
1 CATATATATATTT
2177346 CACATATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 12 0.48
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (14 bp):
CATATATATATTTT
Found at i:2179751 original size:24 final size:24
Alignment explanation
Indices: 2179724--2179770 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2179714 CGAAGTGTCA
2179724 CGTAG-AGTTTGCCCCGAAGGACCG
1 CGTAGAAG-TTGCCCCGAAGGACCG
* *
2179748 CGTAGAAGTTGTCCCTAAGGACC
1 CGTAGAAGTTGCCCCGAAGGACC
2179771 ATGTAGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (24 bp):
CGTAGAAGTTGCCCCGAAGGACCG
Found at i:2182185 original size:29 final size:30
Alignment explanation
Indices: 2182141--2182199 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2182131 ATTTTAATAT
2182141 GAAGAACTAAAATAAATAAAATTA-AAATTC
1 GAAGAACTAAAATAAA-AAAATTATAAATTC
* *
2182171 GAAG-ACTAAATTAAAAATATTATAAATTC
1 GAAGAACTAAAATAAAAAAATTATAAATTC
2182200 AGTTTAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (30 bp):
GAAGAACTAAAATAAAAAAATTATAAATTC
Found at i:2183260 original size:20 final size:19
Alignment explanation
Indices: 2183237--2183281 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2183227 TTTTTTTTAT
* *
2183237 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
2183257 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
2183276 TATTTA
1 TATTTA
2183282 ATAATAATAG
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:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:2183271 original size:26 final size:30
Alignment explanation
Indices: 2183232--2183287 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2183222 TTATATTTTT
*
2183232 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
2183259 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
2183288 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:2183288 original size:3 final size:3
Alignment explanation
Indices: 2183280--2183353 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
2183270 TTAATATATT
* * *
2183280 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2183328 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2183354 TGGATAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2183923 original size:113 final size:113
Alignment explanation
Indices: 2183674--2184325 Score: 1128
Period size: 113 Copynumber: 5.9 Consensus size: 113
2183664 GAATTATGCC
* *
2183674 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
2183739 ATGAA-CTTCTCCGG-AA--AAGAT-AATCAAGTGATGAATTCAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
2183782 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
2183847 ATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
*
2183895 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
2183960 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
2184008 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
2184073 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
2184121 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
2184186 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTT-AACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
2184233 AAAAGTTGAAC-AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--ATGAGTTCTTC-CATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
2184294 ATGAA-CTTATCTGGCAATGAATGATCCATCAA
66 ATGAACCTTCTCTGGCAATG-ATGATCCATCAA
2184326 GTGGATTTGA
Statistics
Matches: 526, Mismatches: 12, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
107 13 0.02
108 89 0.17
109 19 0.04
110 2 0.00
111 35 0.07
112 18 0.03
113 350 0.67
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
Found at i:2183946 original size:24 final size:23
Alignment explanation
Indices: 2183911--2183955 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2183901 TGAACAAGTT
2183911 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
2183935 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
2183956 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:2185098 original size:83 final size:83
Alignment explanation
Indices: 2184954--2185195 Score: 400
Period size: 83 Copynumber: 3.0 Consensus size: 83
2184944 TTTACTATGA
* *
2184954 GCAAATTCATCTTCCAAATTCAATGATTG-TTCTGTCCAACCAAATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGCTTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
2185018 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
** *
2185036 GCAAATTCATCTTCCAAATTCAATGCTTGATTCTGTATAATCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGCTTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
2185101 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* *
2185119 GCAAATTCATCTTCC--ATTTAAGGCTTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGCTTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
2185182 TTCCAGAAGATGCT
66 TTCCAGAAGATGCT
2185196 TGATTCTGTC
Statistics
Matches: 149, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
81 57 0.38
82 28 0.19
83 64 0.43
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (83 bp):
GCAAATTCATCTTCCAAATTCAATGCTTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:2185197 original size:52 final size:52
Alignment explanation
Indices: 2185141--2185657 Score: 857
Period size: 52 Copynumber: 10.1 Consensus size: 52
2185131 TCCATTTAAG
*
2185141 GCTTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
*
2185193 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACATTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
2185245 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
* *
2185297 GC-T-ATTCTGTCTAATTAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
* *
2185347 GCTTGATTCTGTTCAATCAGATCAGATAACTCAAAGAACATTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
*
2185399 GCTTGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
* * *
2185451 GC-T-ATTCTGTCTAATTAGATCAGATAACTTAAAGAACACTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
* *
2185501 GCTTGATTCTGTTCAATCAGATCAGATAACTCAAAGAACATTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
*
2185553 GCTTGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
* *
2185605 G-TT-ATTCTGTCTAATTAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
2185655 GCT
1 GCT
2185658 ATTGGCAAAT
Statistics
Matches: 437, Mismatches: 23, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
50 141 0.32
51 7 0.02
52 289 0.66
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (52 bp):
GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
Found at i:2185364 original size:102 final size:104
Alignment explanation
Indices: 2185141--2185657 Score: 845
Period size: 102 Copynumber: 5.0 Consensus size: 104
2185131 TCCATTTAAG
* *
2185141 GCTTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTC
1 GCTTGATTCTGTTCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTC
* *
2185206 CAATCAGATCAGATAACTCAAAGAACATTTCCAGAAGAT
66 TAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
*
2185245 GCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC-T-ATTCTGTC
1 GCTTGATTCTGTTCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTC
*
2185308 TAATTAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
66 TAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
*
2185347 GCTTGATTCTGTTCAATCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTTGATTCTGTC
1 GCTTGATTCTGTTCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTC
2185412 TAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
66 TAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
* *
2185451 GC-T-ATTCTG-TCTAATTAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTTGATTCTGT
1 GCTTGATTCTGTTC-AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGT
*
2185513 -TCAATCAGATCAGATAACTCAAAGAACATTTCCAGAAGAT
65 CT-AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
2185553 GCTTGATTCTG-TCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG-TT-ATTCTGT
1 GCTTGATTCTGTTC-AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGT
*
2185615 CTAATTAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
65 CTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
2185655 GCT
1 GCT
2185658 ATTGGCAAAT
Statistics
Matches: 391, Mismatches: 15, Indels: 16
0.93 0.04 0.04
Matches are distributed among these distances:
101 3 0.01
102 234 0.60
103 7 0.02
104 147 0.38
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (104 bp):
GCTTGATTCTGTTCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTC
TAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
Found at i:2185426 original size:154 final size:154
Alignment explanation
Indices: 2185159--2185657 Score: 962
Period size: 154 Copynumber: 3.2 Consensus size: 154
2185149 CTGTCCAACC
*
2185159 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTCCAATCAGATCAGATAACT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTTCAATCAGATCAGATAACT
*
2185224 CAAAGAACATTTCCAGAAGATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
66 CAAAGAACATTTCCAGAAGATGCTTGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTC
2185289 CAGAAGATGCTATTCTGTCTAATT
131 CAGAAGATGCTATTCTGTCTAATT
2185313 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTTCAATCAGATCAGATAACT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTTCAATCAGATCAGATAACT
2185378 CAAAGAACATTTCCAGAAGATGCTTGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTC
66 CAAAGAACATTTCCAGAAGATGCTTGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTC
2185443 CAGAAGATGCTATTCTGTCTAATT
131 CAGAAGATGCTATTCTGTCTAATT
*
2185467 AGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTTGATTCTGTTCAATCAGATCAGATAACT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTTCAATCAGATCAGATAACT
2185532 CAAAGAACATTTCCAGAAGATGCTTGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTC
66 CAAAGAACATTTCCAGAAGATGCTTGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTC
*
2185597 CAGAAGATGTTATTCTGTCTAATT
131 CAGAAGATGCTATTCTGTCTAATT
2185621 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
2185658 ATTGGCAAAT
Statistics
Matches: 340, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 340 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (154 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTTCAATCAGATCAGATAACT
CAAAGAACATTTCCAGAAGATGCTTGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATTCTGTCTAATT
Found at i:2198594 original size:29 final size:30
Alignment explanation
Indices: 2198550--2198608 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2198540 ATTTTAATAT
2198550 GAAGAACTAAAATAAATAAAATTA-AAATTC
1 GAAGAACTAAAATAAA-AAAATTATAAATTC
* *
2198580 GAAG-ACTAAATTAAAAATATTATAAATTC
1 GAAGAACTAAAATAAAAAAATTATAAATTC
2198609 AGTTTAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (30 bp):
GAAGAACTAAAATAAAAAAATTATAAATTC
Found at i:2199692 original size:22 final size:21
Alignment explanation
Indices: 2199643--2199693 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2199633 CCTGTAATTA
* *
2199643 TATATT-TTTTTATTATTATT
1 TATATTATTTTTAATAATATT
2199663 TAT-TTATTTTTAATAATATT
1 TATATTATTTTTAATAATATT
2199683 TATATGTATTT
1 TATAT-TATTT
2199694 AATATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 18 0.69
21 1 0.04
22 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATATTATTTTTAATAATATT
Found at i:2199710 original size:3 final size:3
Alignment explanation
Indices: 2199702--2199793 Score: 157
Period size: 3 Copynumber: 30.7 Consensus size: 3
2199692 TTAATATATT
*
2199702 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2199750 TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2199794 TGGATAAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2205201 original size:18 final size:18
Alignment explanation
Indices: 2205178--2205221 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
2205168 GTTGAAGGCT
2205178 TAGTGTTGTTCGTTACGA
1 TAGTGTTGTTCGTTACGA
2205196 TAGTGTTGTTCGTTACGA
1 TAGTGTTGTTCGTTACGA
2205214 TAGTGTTG
1 TAGTGTTG
2205222 GTGTGGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.09, G:0.30, T:0.45
Consensus pattern (18 bp):
TAGTGTTGTTCGTTACGA
Found at i:2207948 original size:45 final size:45
Alignment explanation
Indices: 2207879--2207974 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
2207869 CGATGCCTTT
* * * * *
2207879 TTCTTTATCATATTACAAATTTATGGTAATTTCTATTATTATTCA
1 TTCTTCATCATATTACAAACTTATGATAATGTCTATTATCATTCA
2207924 TTCTTCATCATATTACAAACTTATGATAATGTCTATTATCATTCA
1 TTCTTCATCATATTACAAACTTATGATAATGTCTATTATCATTCA
2207969 TTCTTC
1 TTCTTC
2207975 TGTAGTTTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.50
Consensus pattern (45 bp):
TTCTTCATCATATTACAAACTTATGATAATGTCTATTATCATTCA
Found at i:2211106 original size:20 final size:21
Alignment explanation
Indices: 2211077--2211116 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2211067 CAACAGAATA
*
2211077 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
2211098 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
2211117 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:2211155 original size:20 final size:20
Alignment explanation
Indices: 2211130--2211168 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2211120 TAATAGAATA
*
2211130 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
2211150 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
2211169 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:2213971 original size:20 final size:21
Alignment explanation
Indices: 2213942--2213981 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2213932 CATCAGAATA
*
2213942 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
2213963 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
2213982 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:2214020 original size:20 final size:20
Alignment explanation
Indices: 2213995--2214033 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2213985 TAATAGAATA
**
2213995 AAAATTGATTTTATCTAATT
1 AAAATTGATCCTATCTAATT
2214015 AAAATTGATCCTATCTAAT
1 AAAATTGATCCTATCTAAT
2214034 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATTGATCCTATCTAATT
Found at i:2217043 original size:22 final size:23
Alignment explanation
Indices: 2217018--2217060 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2217008 ATATGGTTTT
2217018 GGAAAAAAAGT-AAAGTTTAAAC
1 GGAAAAAAAGTGAAAGTTTAAAC
* *
2217040 GGAACAAAAGTGACAGTTTAA
1 GGAAAAAAAGTGAAAGTTTAA
2217061 GTACTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (23 bp):
GGAAAAAAAGTGAAAGTTTAAAC
Found at i:2225985 original size:14 final size:14
Alignment explanation
Indices: 2225966--2225994 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2225956 ATCGATTGTA
2225966 GGTTGTAGCAATAC
1 GGTTGTAGCAATAC
2225980 GGTTGTAGCAATAC
1 GGTTGTAGCAATAC
2225994 G
1 G
2225995 AATACCACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (14 bp):
GGTTGTAGCAATAC
Found at i:2234897 original size:28 final size:28
Alignment explanation
Indices: 2234866--2234960 Score: 131
Period size: 28 Copynumber: 3.5 Consensus size: 28
2234856 TTTGACAAGG
*
2234866 ACATAATTTTAAATAAACGAACACAAAC
1 ACATAATTTTAAATAAACGAACACGAAC
* * *
2234894 ACATAATTTTAAATAAATGAACATGGAC
1 ACATAATTTTAAATAAACGAACACGAAC
*
2234922 ACATAATTTTAAATAAACGAGCACGAAC
1 ACATAATTTTAAATAAACGAACACGAAC
2234950 AC--AATTTTAAA
1 ACATAATTTTAAA
2234961 ATTCTCAAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 9 0.15
28 50 0.85
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (28 bp):
ACATAATTTTAAATAAACGAACACGAAC
Found at i:2241057 original size:2 final size:2
Alignment explanation
Indices: 2241050--2241087 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2241040 ATAATCAATA
2241050 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
2241088 TATTTAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2241422 original size:13 final size:13
Alignment explanation
Indices: 2241392--2241424 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
2241382 ATTATATATG
2241392 ATTTTAAAAAAAT
1 ATTTTAAAAAAAT
2241405 A-TTTAAAAAAAT
1 ATTTTAAAAAAAT
2241417 ATTTTAAA
1 ATTTTAAA
2241425 CATGTACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTTTAAAAAAAT
Found at i:2241573 original size:3 final size:3
Alignment explanation
Indices: 2241565--2241625 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
2241555 TTAATTGTTA
* * *
2241565 ATT ATT ATT ATT ATT ATT -TT AATT ATT ATC ACT ATT ATT AATA ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT -ATT ATT
2241611 -TT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
2241626 GGTTACAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.83
4 4 0.08
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2241586 original size:21 final size:22
Alignment explanation
Indices: 2241562--2241625 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 22
2241552 GTTTTAATTG
2241562 TTAATTATTATTATTATTATT-
1 TTAATTATTATTATTATTATTA
* *
2241583 TTAATTATTATCACTATTATTA
1 TTAATTATTATTATTATTATTA
*
2241605 ATAATT-TTATTATTATTATTA
1 TTAATTATTATTATTATTATTA
2241626 GGTTACAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAATTATTATTATTATTATTA
Found at i:2243052 original size:5 final size:5
Alignment explanation
Indices: 2243042--2243196 Score: 310
Period size: 5 Copynumber: 31.0 Consensus size: 5
2243032 TGTAAACTCG
2243042 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
2243092 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
2243142 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
2243192 CATAT
1 CATAT
2243197 AACATATATC
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 150 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
CATAT
Found at i:2247907 original size:20 final size:22
Alignment explanation
Indices: 2247882--2247924 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2247872 TACCATTACT
2247882 TAAACCAAC-TTATA-TCCATA
1 TAAACCAACTTTATATTCCATA
*
2247902 TAAACCATCTTTATATTCCATA
1 TAAACCAACTTTATATTCCATA
2247924 T
1 T
2247925 CTCATTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 5 0.25
22 7 0.35
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAACCAACTTTATATTCCATA
Found at i:2249837 original size:18 final size:18
Alignment explanation
Indices: 2249814--2249884 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
2249804 ACTGTATATT
2249814 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
2249832 TGTCCCGAAAGACCACTA
1 TGTCCCGAATGACCACTA
*
2249850 TGTCCCGAAGGACCACTA
1 TGTCCCGAATGACCACTA
2249868 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
2249885 CCTTAAGAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:2250705 original size:24 final size:24
Alignment explanation
Indices: 2250673--2250730 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
2250663 ACTCTACGGG
*
2250673 GTATCGATACATCCCTTAACGTGT
1 GTATCGATACATCCCTTAAAGTGT
2250697 GTATCGATACATCCCTTAAAGTGT
1 GTATCGATACATCCCTTAAAGTGT
2250721 GTATCGATAC
1 GTATCGATAC
2250731 GCTACCTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (24 bp):
GTATCGATACATCCCTTAAAGTGT
Found at i:2266678 original size:23 final size:20
Alignment explanation
Indices: 2266627--2266686 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
2266617 TTTTGGTGCA
*
2266627 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
2266646 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
2266667 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
2266687 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:2266708 original size:20 final size:21
Alignment explanation
Indices: 2266669--2266708 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2266659 CCCCCTTTGA
*
2266669 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
2266690 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
2266709 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:2269946 original size:35 final size:34
Alignment explanation
Indices: 2269907--2270003 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 34
2269897 AAAAGTTTAT
* *
2269907 AATATATAATATAAACATAAAATTTATAAAT-TCAA
1 AATATATAATATAAA-ATAAAATATAAAAATAT-AA
* *
2269942 AATATATAGTCTAAAAATAAAATATAAAAATATAA
1 AATATATAATAT-AAAATAAAATATAAAAATATAA
*
2269977 AA-A-ATAAAATAAAATAAAATAATAAAA
1 AATATATAATATAAAATAAAAT-ATAAAA
2270004 TTACAACTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
32 10 0.19
33 10 0.19
34 1 0.02
35 27 0.52
36 4 0.08
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (34 bp):
AATATATAATATAAAATAAAATATAAAAATATAA
Found at i:2269970 original size:7 final size:7
Alignment explanation
Indices: 2269907--2269987 Score: 51
Period size: 7 Copynumber: 11.6 Consensus size: 7
2269897 AAAAGTTTAT
*
2269907 AATATAT
1 AATATAA
2269914 AATAT-A
1 AATATAA
*
2269920 AACATAA
1 AATATAA
*
2269927 AATTTATA
1 AATATA-A
2269935 AAT-TCAA
1 AATAT-AA
*
2269942 AATATAT
1 AATATAA
* *
2269949 AGTCTAA
1 AATATAA
2269956 AA-ATAA
1 AATATAA
2269962 AATATAAA
1 AATAT-AA
2269970 AATATAA
1 AATATAA
*
2269977 AAAATAA
1 AATATAA
2269984 AATA
1 AATA
2269988 AAATAAAATA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
6 9 0.16
7 34 0.61
8 13 0.23
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (7 bp):
AATATAA
Found at i:2269976 original size:15 final size:14
Alignment explanation
Indices: 2269954--2270004 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
2269944 TATATAGTCT
*
2269954 AAAAATAAAATATA
1 AAAAATAAAAAATA
2269968 AAAATATAAAAAATA
1 AAAA-ATAAAAAATA
2269983 AAATAA-AATAAAATA
1 AAA-AATAA-AAAATA
2269998 ATAAAAT
1 A-AAAAT
2270005 TACAACTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 6 0.19
15 22 0.71
16 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:2269979 original size:22 final size:22
Alignment explanation
Indices: 2269954--2270004 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2269944 TATATAGTCT
*
2269954 AAAAATAAAATATAAA-AATATA
1 AAAAATAAAATA-AAATAAAATA
2269976 AAAAATAAAATAAAATAAAATA
1 AAAAATAAAATAAAATAAAATA
2269998 ATAAAAT
1 A-AAAAT
2270005 TACAACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.69
23 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAAATAAAATAAAATAAAATA
Found at i:2272048 original size:22 final size:22
Alignment explanation
Indices: 2272020--2272065 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2272010 TCGTTTAAAG
2272020 AAGTTGGCTTAATGATTTTCCT
1 AAGTTGGCTTAATGATTTTCCT
2272042 AAGTTGGCTTAATGATTTTCCT
1 AAGTTGGCTTAATGATTTTCCT
2272064 AA
1 AA
2272066 TTCGTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (22 bp):
AAGTTGGCTTAATGATTTTCCT
Found at i:2281740 original size:32 final size:32
Alignment explanation
Indices: 2281699--2281781 Score: 139
Period size: 32 Copynumber: 2.6 Consensus size: 32
2281689 AGTATACACG
*
2281699 AAAGACGCATTGCACTCCATGCATCTCCCCCT
1 AAAGACGCATTGCACTCCATGCATCTCCCCCC
*
2281731 AAAGACGCATTGCACTCCATGCGTCTCCCCCC
1 AAAGACGCATTGCACTCCATGCATCTCCCCCC
*
2281763 GAAGACGCATTGCACTCCA
1 AAAGACGCATTGCACTCCA
2281782 CGAGTCTCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (32 bp):
AAAGACGCATTGCACTCCATGCATCTCCCCCC
Found at i:2281789 original size:32 final size:32
Alignment explanation
Indices: 2281699--2281791 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 32
2281689 AGTATACACG
*
2281699 AAAGACGCATTGCACTCCATGCA-TCTCCCCCT
1 AAAGACGCATTGCACTCCATG-AGTCTCCCCCC
*
2281731 AAAGACGCATTGCACTCCATGCGTCTCCCCCC
1 AAAGACGCATTGCACTCCATGAGTCTCCCCCC
* *
2281763 GAAGACGCATTGCACTCCACGAGTCTCCC
1 AAAGACGCATTGCACTCCATGAGTCTCCC
2281792 ATTTCCCTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (32 bp):
AAAGACGCATTGCACTCCATGAGTCTCCCCCC
Found at i:2282003 original size:22 final size:21
Alignment explanation
Indices: 2281978--2282045 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
2281968 GAGGGGGCAC
2281978 AAGAAAAACAGGAGAAGGAAGG
1 AAGAAAAACAGGAGAA-GAAGG
*
2282000 AAG---AA-AGGAAGAAGAAGA
1 AAGAAAAACAGG-AGAAGAAGG
2282018 AAGAAAAACAGGAGAATGAAGG
1 AAGAAAAACAGGAGAA-GAAGG
2282040 AAGAAA
1 AAGAAA
2282046 GGAAGAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
18 10 0.26
19 6 0.16
21 6 0.16
22 16 0.42
ACGTcount: A:0.63, C:0.03, G:0.32, T:0.01
Consensus pattern (21 bp):
AAGAAAAACAGGAGAAGAAGG
Found at i:2282015 original size:3 final size:3
Alignment explanation
Indices: 2282007--2282143 Score: 71
Period size: 3 Copynumber: 46.0 Consensus size: 3
2281997 AGGAAGAAAG
* *
2282007 GAA GAA GAA GAAA GAA -AA -ACA GGA GAA TGAA GGAA GAA -AG GAA GAA
1 GAA GAA GAA G-AA GAA GAA GA-A GAA GAA -GAA -GAA GAA GAA GAA GAA
*
2282053 GAA GAAA GAA -AA GAA GGAA GAA GGAA GAA -AG GAA GAA G-A GAA -AA
1 GAA G-AA GAA GAA GAA -GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
*
2282097 GAG GAA GGAA GAA G-A GAA -AA GATA -AA GAAA GAA GAA GAA G-A GAA
1 GAA GAA -GAA GAA GAA GAA GAA GA-A GAA G-AA GAA GAA GAA GAA GAA
2282141 GAA
1 GAA
2282144 AGTTAGAGTC
Statistics
Matches: 106, Mismatches: 9, Indels: 38
0.69 0.06 0.25
Matches are distributed among these distances:
2 18 0.17
3 63 0.59
4 25 0.24
ACGTcount: A:0.64, C:0.01, G:0.34, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:2282023 original size:40 final size:39
Alignment explanation
Indices: 2281978--2282095 Score: 181
Period size: 40 Copynumber: 3.1 Consensus size: 39
2281968 GAGGGGGCAC
2281978 AAGAAAAACAGGAGAAGGAAGGAAGAAAGGAAGAAGAAGA
1 AAGAAAAACAGGAGAA-GAAGGAAGAAAGGAAGAAGAAGA
2282018 AAGAAAAACAGGAGAATGAAGGAAGAAAGGAAGAAGAAGA
1 AAGAAAAACAGGAGAA-GAAGGAAGAAAGGAAGAAGAAGA
2282058 AAGAAAAGA-A-G-GAAGAAGGAAGAAAGGAAGAAG-AGA
1 AAGAAAA-ACAGGAGAAGAAGGAAGAAAGGAAGAAGAAGA
2282094 AA
1 AA
2282096 AGAGGAAGGA
Statistics
Matches: 76, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
36 5 0.07
37 19 0.25
38 3 0.04
39 1 0.01
40 47 0.62
41 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.01
Consensus pattern (39 bp):
AAGAAAAACAGGAGAAGAAGGAAGAAAGGAAGAAGAAGA
Found at i:2282055 original size:22 final size:21
Alignment explanation
Indices: 2281990--2282145 Score: 106
Period size: 20 Copynumber: 7.8 Consensus size: 21
2281980 GAAAAACAGG
2281990 AGAAGGAAGGAAGAAAGGAAGA
1 AGAA-GAAGGAAGAAAGGAAGA
* *
2282012 AGAAGAAAGAAAAACAGG-AG-
1 AGAAGAAGGAAGAA-AGGAAGA
*
2282032 A-ATGAAGGAAGAAAGGAAGA
1 AGAAGAAGGAAGAAAGGAAGA
*
2282052 AGAAG-A--AAGAAAAGAAG-
1 AGAAGAAGGAAGAAAGGAAGA
2282069 -GAAGAAGGAAGAAAGGAAGA
1 AGAAGAAGGAAGAAAGGAAGA
2282089 AG-AGAA--AAGAGGAAGGAAGA
1 AGAAGAAGGAAGA--AAGGAAGA
*
2282109 AG-AGAA--AAGATAAAGAAAGA
1 AGAAGAAGGAAG--AAAGGAAGA
2282129 AGAAGAAGAGAAGAAAG
1 AGAAGAAG-GAAGAAAG
2282146 TTAGAGTCGG
Statistics
Matches: 108, Mismatches: 9, Indels: 34
0.72 0.06 0.23
Matches are distributed among these distances:
16 4 0.04
17 1 0.01
18 17 0.16
19 21 0.19
20 33 0.31
21 17 0.16
22 12 0.11
24 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.35, T:0.01
Consensus pattern (21 bp):
AGAAGAAGGAAGAAAGGAAGA
Found at i:2282076 original size:37 final size:37
Alignment explanation
Indices: 2281995--2282110 Score: 157
Period size: 40 Copynumber: 3.1 Consensus size: 37
2281985 ACAGGAGAAG
2281995 GAAGGAAGAAAGGAAGAAGAAGAAAGAAAA-ACAGGAGAA
1 GAAGGAAGAAAGGAAGAAGAAGAAAGAAAAGA-A-G-GAA
2282034 TGAAGGAAGAAAGGAAGAAGAAGAAAGAAAAGAAGGAA
1 -GAAGGAAGAAAGGAAGAAGAAGAAAGAAAAGAAGGAA
* *
2282072 GAAGGAAGAAAGGAAGAAG-AGAAA-AGAGGAAGGAA
1 GAAGGAAGAAAGGAAGAAGAAGAAAGAAAAGAAGGAA
2282107 GAAG
1 GAAG
2282111 AGAAAAGATA
Statistics
Matches: 73, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
35 13 0.18
36 5 0.07
37 19 0.26
38 3 0.04
39 1 0.01
40 31 0.42
41 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.36, T:0.01
Consensus pattern (37 bp):
GAAGGAAGAAAGGAAGAAGAAGAAAGAAAAGAAGGAA
Found at i:2284571 original size:33 final size:33
Alignment explanation
Indices: 2284531--2284593 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
2284521 ATATGGCTAC
2284531 TGTTGTTGACATTGTTGTTTAAGTTGTTGTTGT
1 TGTTGTTGACATTGTTGTTTAAGTTGTTGTTGT
*
2284564 TGTTGTTGACTTTGTTGTTTAAGTTGTTGT
1 TGTTGTTGACATTGTTGTTTAAGTTGTTGT
2284594 AGTACTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.11, C:0.03, G:0.27, T:0.59
Consensus pattern (33 bp):
TGTTGTTGACATTGTTGTTTAAGTTGTTGTTGT
Found at i:2285234 original size:15 final size:14
Alignment explanation
Indices: 2285210--2285248 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2285200 TAATATTTAT
2285210 TAATAAATAAAATG
1 TAATAAATAAAATG
*
2285224 TAATCAAATAACATG
1 TAAT-AAATAAAATG
2285239 TATATAAATA
1 TA-ATAAATA
2285249 CTAGTTGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 16 0.73
16 2 0.09
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (14 bp):
TAATAAATAAAATG
Found at i:2286935 original size:6 final size:6
Alignment explanation
Indices: 2286926--2286965 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
2286916 TCGAGGTGAT
* * *
2286926 GGTGGC GGTGGC GGTGGC GGTGGC GGCGGT GGTGGT GGTG
1 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTG
2286966 AAAAAGGGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.12, G:0.68, T:0.20
Consensus pattern (6 bp):
GGTGGC
Found at i:2290643 original size:36 final size:36
Alignment explanation
Indices: 2290603--2290676 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
2290593 TCAAATTAGC
* * ***
2290603 AATTCTATTTATTTTTTAACGACGTGTAACCAAAAT
1 AATTCTATTAATTTATTAACGACAAATAACCAAAAT
*
2290639 AATTCTGTTAATTTATTAACGACAAATAACCAAAAT
1 AATTCTATTAATTTATTAACGACAAATAACCAAAAT
2290675 AA
1 AA
2290677 AACTAAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (36 bp):
AATTCTATTAATTTATTAACGACAAATAACCAAAAT
Found at i:2296774 original size:55 final size:53
Alignment explanation
Indices: 2296715--2297131 Score: 446
Period size: 51 Copynumber: 8.0 Consensus size: 53
2296705 CAAATGGCGG
*
2296715 GTCTGCTCCCTATTCTTTCATG-GAGTATAAGACTCGAACAATCTTCAATAAACGT
1 GTCTGCTCCCTATTCCTTCA-GAGAGTATAAGACTCG--CAATCTTCAATAAACGT
* * * *
2296770 GTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCG--CAATCTTCAATAAACGT
* * * *
2296825 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAAAAAACGG
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCG--CAATCTTCAATAAACGT
* *
2296880 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCG--ATCTTCAAAAAACGG
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGCAATCTTCAATAAACGT
* *
2296931 GTATGCTCCCTATTCTTTCAGAGAGTATAAGACT----ATCTTCAATAAACGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGCAATCTTCAATAAACGT
* * ** *
2296980 GTCTGCTCTCTATTCCTTCAGAGAGTATAGGACT--CAATCTTCAACGAACTT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGCAATCTTCAATAAACGT
* * ** *
2297031 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT--CAATCTTCAACGAACTT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGCAATCTTCAATAAACGT
* * *
2297082 GGCTGCTCCCTATTCCTTCAGAGAGTATAGGACT--CAATCTTCAACAAACG
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGCAATCTTCAATAAACG
2297132 AGTTTGCTTC
Statistics
Matches: 332, Mismatches: 27, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
49 43 0.13
51 154 0.46
54 1 0.00
55 134 0.40
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (53 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGCAATCTTCAATAAACGT
Found at i:2296850 original size:110 final size:103
Alignment explanation
Indices: 2296715--2297131 Score: 468
Period size: 100 Copynumber: 4.0 Consensus size: 103
2296705 CAAATGGCGG
2296715 GTCTGCTCCCTATTCTTTCATG-GAGTATAAGACTCGAACAATCTTCAATAAACGTGTCTGCTCC
1 GTCTGCTCCCTATTCTTTCA-GAGAGTATAAGACT----CAATCTTCAATAAACGTGTCTGCTCC
* * **
2296779 CTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGT
61 CTATTCCTTCAGAGAGTATAAGACTCG---AATCTTCAAAAAACGT
* * * *
2296825 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAAAAAACGGGTCTGCTCCC
1 GTCTGCTCCCTATTCTTTCAGAGAGTATAAGACT----CAATCTTCAATAAACGTGTCTGCTCCC
*
2296890 TATTCCTTCAGAGAGTATAAGACTCG-ATCTTCAAAAAACGG
62 TATTCCTTCAGAGAGTATAAGACTCGAATCTTCAAAAAACGT
* *
2296931 GTATGCTCCCTATTCTTTCAGAGAGTATAAGACT--ATCTTCAATAAACGTGTCTGCTCTCTATT
1 GTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCAATCTTCAATAAACGTGTCTGCTCCCTATT
* ** *
2296994 CCTTCAGAGAGTATAGGACTC-AATCTTCAACGAACTT
66 CCTTCAGAGAGTATAAGACTCGAATCTTCAAAAAACGT
* * * ** * *
2297031 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGGCTGCTCCCTATT
1 GTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCAATCTTCAATAAACGTGTCTGCTCCCTATT
* *
2297096 CCTTCAGAGAGTATAGGACTC-AATCTTCAACAAACG
66 CCTTCAGAGAGTATAAGACTCGAATCTTCAAAAAACG
2297132 AGTTTGCTTC
Statistics
Matches: 273, Mismatches: 30, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
100 87 0.32
102 58 0.21
106 43 0.16
109 1 0.00
110 84 0.31
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (103 bp):
GTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCAATCTTCAATAAACGTGTCTGCTCCCTATT
CCTTCAGAGAGTATAAGACTCGAATCTTCAAAAAACGT
Found at i:2298507 original size:27 final size:27
Alignment explanation
Indices: 2298477--2298594 Score: 81
Period size: 27 Copynumber: 4.6 Consensus size: 27
2298467 TTGAACCCTC
*
2298477 CTTTTATTTCTCTTTTTTCA-TTTTTCT
1 CTTTT-TTTCTCTTTTTCCATTTTTTCT
*
2298504 CTTTTTCTTC-CATTTTCCATTTTTTCT
1 CTTTTT-TTCTCTTTTTCCATTTTTTCT
* *
2298531 CTTTTTTTTTC-TTTT-CGTTTTTTC-
1 CTTTTTTTCTCTTTTTCCATTTTTTCT
* **
2298555 CATCATTT-T-TTTTTCTCATTTTTT-T
1 CTTTTTTTCTCTTTTTC-CATTTTTTCT
*
2298580 CTTCTTTTCTCTTTT
1 CTTTTTTTCTCTTTT
2298595 ATTTCTTCTT
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
23 5 0.07
24 5 0.07
25 21 0.29
26 15 0.21
27 26 0.36
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (27 bp):
CTTTTTTTCTCTTTTTCCATTTTTTCT
Found at i:2298584 original size:14 final size:13
Alignment explanation
Indices: 2298523--2298584 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 13
2298513 CCATTTTCCA
2298523 TTTTTTCTC-TTT
1 TTTTTTCTCATTT
2298535 TTTTTTCT--TTT
1 TTTTTTCTCATTT
2298546 CGTTTTTTCCATCATTT
1 --TTTTTT-C-TCATTT
2298563 TTTTTTCTCATTT
1 TTTTTTCTCATTT
2298576 TTTTCTTCT
1 TTTT-TTCT
2298585 TTTCTCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.07
12 8 0.19
13 16 0.37
14 6 0.14
15 7 0.16
17 3 0.07
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTTCTCATTT
Found at i:2298589 original size:19 final size:19
Alignment explanation
Indices: 2298565--2298604 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
2298555 CATCATTTTT
2298565 TTTTCTCATTTT-TTTCTTC
1 TTTTCTC-TTTTATTTCTTC
2298584 TTTTCTCTTTTATTTCTTC
1 TTTTCTCTTTTATTTCTTC
2298603 TT
1 TT
2298605 CAAGCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCTCTTTTATTTCTTC
Found at i:2311881 original size:10 final size:11
Alignment explanation
Indices: 2311866--2311894 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2311856 TAATTATGAA
2311866 TTAAGTATG-T
1 TTAAGTATGTT
2311876 TTAAGTATGTT
1 TTAAGTATGTT
2311887 TTAAGTAT
1 TTAAGTAT
2311895 AAACATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (11 bp):
TTAAGTATGTT
Found at i:2318390 original size:2 final size:2
Alignment explanation
Indices: 2318385--2318427 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2318375 AATTAAATTT
2318385 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2318427 T
1 T
2318428 GAGATTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2319320 original size:21 final size:21
Alignment explanation
Indices: 2319257--2319313 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2319247 TATTTACAAT
** *
2319257 TGTACAATCACGAGCAATATTA
1 TGTACAA-CACGATAAATATCA
2319279 TGTACAACACGATAAATATCA
1 TGTACAACACGATAAATATCA
2319300 TGTACAACACGATA
1 TGTACAACACGATA
2319314 TTGATCACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (21 bp):
TGTACAACACGATAAATATCA
Found at i:2321411 original size:30 final size:30
Alignment explanation
Indices: 2321375--2321445 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
2321365 CATGTTCAAT
* *
2321375 GTCATCACTTTGGACACATGACAATATCAC
1 GTCATCACTTTGAACACATAACAATATCAC
* *
2321405 GTCATCACTTTGAACATATAATAATATCAC
1 GTCATCACTTTGAACACATAACAATATCAC
*
2321435 ATCATCACTTT
1 GTCATCACTTT
2321446 CGGTATGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (30 bp):
GTCATCACTTTGAACACATAACAATATCAC
Found at i:2322819 original size:32 final size:31
Alignment explanation
Indices: 2322737--2322834 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 31
2322727 TATCCTAAAT
* * *
2322737 TGATGATGTGACACA-CCACATGTACGTAAG
1 TGATAATGTGACGCAGCCACATGTACATAAG
* * *
2322767 TGATAACGT-AGTGCACGCCACATGTACATAAT
1 TGATAATGTGA-CGCA-GCCACATGTACATAAG
*
2322799 TGATAATGTGACGCATGCCACATTTACATAAG
1 TGATAATGTGACGCA-GCCACATGTACATAAG
2322831 TGAT
1 TGAT
2322835 GGGGTAGCAC
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
29 1 0.02
30 9 0.17
32 42 0.79
33 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (31 bp):
TGATAATGTGACGCAGCCACATGTACATAAG
Found at i:2327183 original size:134 final size:136
Alignment explanation
Indices: 2327035--2327306 Score: 494
Period size: 134 Copynumber: 2.0 Consensus size: 136
2327025 TTAACGGTGG
* * *
2327035 AGTGACTAAAAAAATTGAATGCATAAAGTTCAGTGAGTAAATTGAAATAATTGAAAGTACGATGG
1 AGTGACTAAAAAAATTGAATGCATAAAGTTCAGTGAGTAAATTGAAACAATTAAAAGTACGACGG
2327100 GTGAAATATGAGAGAGAGTAAAGTTTAGTGAGT-AGTG-TATAATTTATCATATTTGTAAACTTT
66 GTGAAATATGAGAGAGAGTAAAGTTTAGTGAGTAAGTGATATAATTTATCATATTTGTAAACTTT
2327163 TAAATA
131 TAAATA
2327169 AGTGACTAAAAAAATTGAATGCATAAAGTTCAGTGAGTAAATTGAAACAATTAAAAGTACGACGG
1 AGTGACTAAAAAAATTGAATGCATAAAGTTCAGTGAGTAAATTGAAACAATTAAAAGTACGACGG
2327234 GTGAAATATGAGAGAGAGTAAAGTTTAGTGAGTAAGTGTATATAATTTATCATATTTGTAAACTT
66 GTGAAATATGAGAGAGAGTAAAGTTTAGTGAGTAAGTG-ATATAATTTATCATATTTGTAAACTT
2327299 TTAAATA
130 TTAAATA
2327306 A
1 A
2327307 TATTTTAGTT
Statistics
Matches: 132, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
134 95 0.72
135 4 0.03
137 33 0.25
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.31
Consensus pattern (136 bp):
AGTGACTAAAAAAATTGAATGCATAAAGTTCAGTGAGTAAATTGAAACAATTAAAAGTACGACGG
GTGAAATATGAGAGAGAGTAAAGTTTAGTGAGTAAGTGATATAATTTATCATATTTGTAAACTTT
TAAATA
Found at i:2327505 original size:11 final size:11
Alignment explanation
Indices: 2327489--2327515 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2327479 TGTTATTCTG
2327489 TTTAAGATTTA
1 TTTAAGATTTA
2327500 TTTAAGATTTA
1 TTTAAGATTTA
2327511 TTTAA
1 TTTAA
2327516 TTCATTTATG
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:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (11 bp):
TTTAAGATTTA
Found at i:2330919 original size:22 final size:22
Alignment explanation
Indices: 2330878--2330945 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
2330868 CTCGTATAAA
2330878 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
2330901 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2330923 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2330945 T
1 T
2330946 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2331206 original size:30 final size:31
Alignment explanation
Indices: 2331165--2331224 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2331155 TAGACATAGT
*
2331165 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
2331195 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
2331225 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:2331281 original size:29 final size:28
Alignment explanation
Indices: 2331239--2331309 Score: 115
Period size: 29 Copynumber: 2.5 Consensus size: 28
2331229 TTTTCTGCAT
*
2331239 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATA-CA
*
2331268 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
2331296 ATTCATGTCATGTA
1 ATTCATGTCATGTA
2331310 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 15 0.38
29 25 0.62
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:2331648 original size:19 final size:20
Alignment explanation
Indices: 2331611--2331648 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2331601 CTTTTTCTCA
*
2331611 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
2331631 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2331649 TCAAGCAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:2331747 original size:67 final size:68
Alignment explanation
Indices: 2331612--2331761 Score: 225
Period size: 68 Copynumber: 2.2 Consensus size: 68
2331602 TTTTTCTCAT
* * *
2331612 GGGGGAATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
2331676 TGA
66 TGA
* * *
2331679 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCAATCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
2331743 TGA
66 TGA
2331746 -GGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
2331762 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
66 16 0.21
67 18 0.24
68 42 0.55
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
TGA
Done.