Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009159.1 Corchorus capsularis cultivar CVL-1 contig09180, 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: 46488
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:262 original size:20 final size:20
Alignment explanation
Indices: 224--261 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
214 GAATTTATAA
224 ATAACCTTATAATTGTTTTG
1 ATAACCTTATAATTGTTTTG
244 ATAACC-TATAATTGTTTT
1 ATAACCTTATAATTGTTTT
262 TTAGTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (20 bp):
ATAACCTTATAATTGTTTTG
Found at i:3209 original size:74 final size:74
Alignment explanation
Indices: 3118--3274 Score: 260
Period size: 74 Copynumber: 2.1 Consensus size: 74
3108 TTAAGGAAGG
* * * *
3118 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATTGGGGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATCACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCAAAGAGGGGCTTTT
**
3183 TAGTCATTC
66 TAGTCACCC
3192 GAAAAGTGTAATCACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCAAAGAGGGGCTTTT
1 GAAAAGTGTAATCACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCAAAGAGGGGCTTTT
3257 TAGTCACCC
66 TAGTCACCC
3266 GAAAAGTGT
1 GAAAAGTGT
3275 GAAAAGACCA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (74 bp):
GAAAAGTGTAATCACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCAAAGAGGGGCTTTT
TAGTCACCC
Found at i:11178 original size:39 final size:39
Alignment explanation
Indices: 11124--11199 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
11114 AGTCAAGATA
11124 ATTGAATACCGATTCCCAGCAATCTGAGGGCAGATTTAT
1 ATTGAATACCGATTCCCAGCAATCTGAGGGCAGATTTAT
11163 ATTGAATACCGATTCCCAGCAATCTGAGGGCAGATTT
1 ATTGAATACCGATTCCCAGCAATCTGAGGGCAGATTT
11200 CTAGCACCGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (39 bp):
ATTGAATACCGATTCCCAGCAATCTGAGGGCAGATTTAT
Found at i:26095 original size:20 final size:21
Alignment explanation
Indices: 26059--26106 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
26049 TAGATTTAGA
* *
26059 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTACATTGCTTTCTT
26080 TTTAATTTA-ATTGCTTTCTT
1 TTTAATTTACATTGCTTTCTT
26100 TTTAATT
1 TTTAATT
26107 GATAATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTAATTTACATTGCTTTCTT
Found at i:32490 original size:30 final size:30
Alignment explanation
Indices: 32411--32471 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
32401 TAAAGGATCA
32411 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
32441 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
32471 A
1 A
32472 TTGATGTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.33
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCATCC
Found at i:38798 original size:16 final size:16
Alignment explanation
Indices: 38779--38821 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
38769 CCGAACCCGA
*
38779 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
38795 ACCCAAACCCGAAAAT
1 ACCCGAACCCGAAAAT
38811 ACCCGAACCCG
1 ACCCGAACCCG
38822 CCTGAACCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.42, G:0.12, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:39627 original size:23 final size:23
Alignment explanation
Indices: 39597--39651 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
39587 TACCGTAAGT
*
39597 GAACCCGAACCCGACCCGGGCCC
1 GAACCCGAACCCGACCCGAGCCC
*
39620 GAACCCGAACCCGATCCGAGCCC
1 GAACCCGAACCCGACCCGAGCCC
39643 GAACCCGAA
1 GAACCCGAA
39652 ATACCCGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.47, G:0.24, T:0.02
Consensus pattern (23 bp):
GAACCCGAACCCGACCCGAGCCC
Found at i:39638 original size:17 final size:17
Alignment explanation
Indices: 39618--39650 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39608 CGACCCGGGC
39618 CCGAACCCGAACCCGAT
1 CCGAACCCGAACCCGAT
*
39635 CCGAGCCCGAACCCGA
1 CCGAACCCGAACCCGA
39651 AATACCCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.48, G:0.21, T:0.03
Consensus pattern (17 bp):
CCGAACCCGAACCCGAT
Found at i:39663 original size:32 final size:32
Alignment explanation
Indices: 39622--39698 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
39612 CCGGGCCCGA
***
39622 ACCCGAACCCGATCCGAGCCCGAACCCG-AAAT
1 ACCCGAACCCGAAAAGA-CCCGAACCCGAAAAT
*
39654 ACCCGAACCCGAAAATACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAGACCCGAACCCGAAAAT
39686 ACCCGAACCCGAA
1 ACCCGAACCCGAA
39699 GTACCCAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 10 0.25
32 30 0.75
ACGTcount: A:0.38, C:0.42, G:0.16, T:0.05
Consensus pattern (32 bp):
ACCCGAACCCGAAAAGACCCGAACCCGAAAAT
Found at i:39671 original size:16 final size:16
Alignment explanation
Indices: 39640--39713 Score: 116
Period size: 16 Copynumber: 4.8 Consensus size: 16
39630 CCGATCCGAG
39640 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
39655 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
39671 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
39687 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
*
39702 CCCAAACCCGAA
1 CCCGAACCCGAA
39714 CCCGCCCGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
15 23 0.42
16 32 0.58
ACGTcount: A:0.41, C:0.41, G:0.14, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:39678 original size:31 final size:30
Alignment explanation
Indices: 39640--39713 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 30
39630 CCGATCCGAG
39640 CCCGAACCCGAAATACCCGAACCCGAAAATA
1 CCCGAACCCGAAATACCCGAACCCG-AAATA
*
39671 CCCGAACCCGAAAATACCCGAACCCGAAGTA
1 CCCGAACCCG-AAATACCCGAACCCGAAATA
*
39702 CCCAAACCCGAA
1 CCCGAACCCGAA
39714 CCCGCCCGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 2 0.05
31 23 0.57
32 15 0.38
ACGTcount: A:0.41, C:0.41, G:0.14, T:0.05
Consensus pattern (30 bp):
CCCGAACCCGAAATACCCGAACCCGAAATA
Found at i:39682 original size:6 final size:6
Alignment explanation
Indices: 39597--39666 Score: 63
Period size: 6 Copynumber: 11.5 Consensus size: 6
39587 TACCGTAAGT
** * *
39597 GAACCC GAACCC G-ACCC GGGCCC GAACCC GAACCC G-ATCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
39643 GAACCC GAAATACCC GAACCC GAA
1 GAACCC G--A-ACCC GAACCC GAA
39667 AATACCCGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
5 9 0.17
6 36 0.69
7 1 0.02
8 1 0.02
9 5 0.10
ACGTcount: A:0.30, C:0.46, G:0.21, T:0.03
Consensus pattern (6 bp):
GAACCC
Found at i:40920 original size:21 final size:20
Alignment explanation
Indices: 40874--40920 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
40864 TAAAATTATC
* *
40874 AATT-AAAAGAAAGCAATTA
1 AATTAAAAACAAAGCAAGTA
*
40893 AACTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGC-AAGTA
40914 AATTAAA
1 AATTAAA
40921 TCTAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (20 bp):
AATTAAAAACAAAGCAAGTA
Found at i:42280 original size:19 final size:18
Alignment explanation
Indices: 42243--42282 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
42233 TTCTTGAAAT
*
42243 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
42261 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
42280 AAT
1 AAT
42283 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:44044 original size:50 final size:50
Alignment explanation
Indices: 43964--44785 Score: 693
Period size: 48 Copynumber: 16.9 Consensus size: 50
43954 TCAAATGTGA
* * *
43964 AAAGAAAACTG-AACCTTCCGACCGGAAAGGGGCATTTTGGGAAACAAAC
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* * * * *
44013 AAAGAAAACAAG-GATCTTCCGACCAGGAAGGGGCA-TTTTGGTGAGCAAAC
1 AAAGAAAAC-TGTGACCTTCCGACCGGGAAGGGGCATTTTTGG-AAACAAAC
* * * *
44063 AAAGAAAAC-GAGGACCTTCCGACCAGGAAGGGGTATTTTTGGAAACAAAT
1 AAAGAAAACTG-TGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* * * * *
44113 AAAGAAAACAAG-GACCTTCCGACTGCGAAGGGGCATTTTGGGAAGCAAAC
1 AAAGAAAAC-TGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
*
44163 AAAGAAAACAAG-GACCTTCCGACCGGGAAGGGGCA-TTTTGGAAA-AAGA-
1 AAAGAAAAC-TGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAA-AC
** *
44211 TGAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTT-GAAATAAGA-
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAA-AC
* *
44260 ATAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGG--A-ATA-
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* * * * *
44306 GAAGGAAACTGTGACCTTCCAACCGGGAATGGGCATTTTTGG-AA-TAAC
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* * *
44354 AGAAGAAAACTGTGACATTCCGACCGAGAAGGGGCATTTTTGGAATA-AGAC
1 A-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAA-ACAAAC
* * *
44405 -AAGAAAATTGTGACCTTCAGACCGGGAAGGGGCATTTTTGGAAACAAAT
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* * * * * * *
44454 AAAGAAAACAGAGACCTTCCAACCAGGAAGGAGCATTTTTTGTAAACAAAT
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCA-TTTTTGGAAACAAAC
* * *
44505 AAAGAAAACTGTGACCTTCCGACCAGGAAGGGGC-TTTTTGG-AATAAAT
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* * * *
44553 AAAG-AGACTATGACCTTCCGACCGGGAA-GGGC-TTTTTGG-AATAAAT
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* * * * *
44599 AAAGAAGACTATGACCTTCCGACCGGGAAGGGGC-TTTTTTG-AATAAAT
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* ** * * **
44647 AAA-AAAGACTATGACCTTTAGACCGGGAAAGGGC-TTTTTGG-AATAAGT
1 AAAGAAA-ACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* ** * **
44695 AAAGACAACTGTGACCTTCCGACCAAGAAGGGGC-TTTTTGG-AATAAGT
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
* * *
44743 AAAGACAATTGTGACCTTCCGATCGGGAAGGGGC-TTTTTGGAA
1 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAA
44786 TAAGAAAAGT
Statistics
Matches: 662, Mismatches: 86, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
46 60 0.09
47 51 0.08
48 180 0.27
49 154 0.23
50 163 0.25
51 53 0.08
52 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (50 bp):
AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAC
Found at i:44270 original size:49 final size:47
Alignment explanation
Indices: 43963--44788 Score: 615
Period size: 50 Copynumber: 17.0 Consensus size: 47
43953 CTCAAATGTG
* * * *
43963 AAAAGAAAACTG-AACCTTCCGACCGGAAAGGGGCATTTTGGGAAACAA
1 AAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTT-TGAAA-TA
* * *
44011 ACAAAGAAAACAAG-GATCTTCCGACCAGGAAGGGGCATTTTGGTGAGCAA-A
1 A-AAAGAAAAC-TGTGACCTTCCGACCGGGAAGGGGCATTTT--TGA--AATA
* * * * *
44062 CAAAGAAAAC-GAGGACCTTCCGACCAGGAAGGGGTATTTTTGGAAACAA
1 AAAAGAAAACTG-TGACCTTCCGACCGGGAAGGGGCATTTTT-GAAA-TA
* * * *
44111 ATAAAGAAAACAAG-GACCTTCCGACTGCGAAGGGGCATTTTGGGAAGCA-A
1 A-AAAGAAAAC-TGTGACCTTCCGACCGGGAAGGGGCATTTT-TGAA--ATA
* *
44161 ACAAAGAAAACAAG-GACCTTCCGACCGGGAAGGGGCATTTTGGAAA-A
1 A-AAAGAAAAC-TGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
*
44208 AGATGAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
1 A-A-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
*
44257 AGAATAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAT-
1 A-AA-AGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
* * * * *
44305 AGAAGGAAACTGTGACCTTCCAACCGGGAATGGGCATTTTTGGAATA
1 AAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
* * *
44352 ACAGAAGAAAACTGTGACATTCCGACCGAGAAGGGGCATTTTTGGAATA
1 A-A-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
* * *
44401 AGACAAGAAAATTGTGACCTTCAGACCGGGAAGGGGCATTTTTGGAAACAA
1 A-A-AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTT-GAAA-TA
* * * * * *
44452 ATAAAGAAAACAGAGACCTTCCAACCAGGAAGGAGCATTTTTTGTAAACAA
1 A-AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCA-TTTTTG-AAA-TA
* *
44503 ATAAAGAAAACTGTGACCTTCCGACCAGGAAGGGGC-TTTTTGGAATA
1 A-AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
* * *
44550 AATAA-AGAGACTATGACCTTCCGACCGGGAA-GGGC-TTTTTGGAATAA
1 AA-AAGA-AAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAAT-A
* * *
44597 ATAAAGAAGACTATGACCTTCCGACCGGGAAGGGGCTTTTTTG-AATA
1 A-AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
* * ** * *
44644 AATAAAAAAGACTATGACCTTTAGACCGGGAAAGGGC-TTTTTGGAATA
1 AA-AAGAAA-ACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
* ** *
44692 AGTAAAGACAACTGTGACCTTCCGACCAAGAAGGGGC-TTTTTGGAATA
1 A--AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
* * * *
44740 AGTAAAGACAATTGTGACCTTCCGATCGGGAAGGGGC-TTTTTGGAATA
1 A--AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
44788 A
1 A
44789 GAAAAGTAAA
Statistics
Matches: 663, Mismatches: 76, Indels: 78
0.81 0.09 0.10
Matches are distributed among these distances:
46 57 0.09
47 74 0.11
48 159 0.24
49 155 0.23
50 164 0.25
51 50 0.08
52 2 0.00
53 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (47 bp):
AAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGAAATA
Found at i:44846 original size:41 final size:41
Alignment explanation
Indices: 44789--45530 Score: 463
Period size: 47 Copynumber: 17.1 Consensus size: 41
44779 TTTGGAATAA
* * *
44789 GAAAAGTAAACAACACCTTCCGATGAGGAAGGGTAGACTGG
1 GAAAACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
44830 GAAAACTAAACAACACCTTCCGATG-GAGAA-GGCAAACTGG
1 GAAAACTAAACAACACCTTCCGATGAG-GAAGGGCAAACTGG
* * * *
44870 GAAATCTAACCAACACCTTCCGGTGGGGAAGGGCAAACTGG
1 GAAAACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
** *
44911 G-AATTTAAACAACACCTTCCAATGAGGAAGGGCAAACTGG
1 GAAAACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
44951 AATAGTAAACAACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
1 ----G--AA-AACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
* * * *
44999 GAATTGGCAACTAGACAACATCTTCCGGT-AGGAAGGAG-AAATTGG
1 GAA-----AACTAAACAACACCTTCCGATGAGGAAGG-GCAAACTGG
*
45044 GAATTTGATAACTAAACAACACCTTCCGACT-AGGAAGGGCAAACTAG
1 G-A----A-AACTAAACAACACCTTCCGA-TGAGGAAGGGCAAACTGG
* * * * * * * *
45091 GAAAAGTAAACAATACCTTCTGACGGGGAAGGACAAATTAGAAATTT
1 GAAAACTAAACAACACCTTCCGATGAGGAAGGGCAAACT-G-----G
* *
45138 GACAACTAAACAACACATTCCGACTG-GGAAGGGCAAACTGG
1 GAAAACTAAACAACACCTTCCGA-TGAGGAAGGGCAAACTGG
* *
45179 GAAAAGTAAACAACACCTTCCGATGAGGAAGGGCAAGCTGG
1 GAAAACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
45220 GAAATGTAGACTTAAACAACACCTTCCGAT-AGGGAAGGGCAAACTGG
1 G-AA---A-AC-TAAACAACACCTTCCGATGA-GGAAGGGCAAACTGG
*
45267 GAAAACTAAACAACACCTTCCGACCG-GGAAGGGCAAACTGAG
1 GAAAACTAAACAACACCTTCCGA-TGAGGAAGGGCAAACTG-G
* * *
45309 AATGAGACAACTAAGCAACACCTTCCGACCG-GGAAGGGCTAAAC-AG
1 ---GA-A-AACTAAACAACACCTTCCGA-TGAGGAAGGGC-AAACTGG
* *
45355 G--AA-TAAGACAACACCTTCCGACGGGGAAGGGCAAACTGG
1 GAAAACTAA-ACAACACCTTCCGATGAGGAAGGGCAAACTGG
* * * *
45394 G-AAGCTAAATAACACCTTCCGGTGGGGAAGGGCAAACTTGG
1 GAAAACTAAACAACACCTTCCGATGAGGAAGGGCAAAC-TGG
* *
45435 GATAAAGCAACTAGACAACACCTTCCGATTG-GGAAGGGCGAACTGG
1 G---AA--AACTAAACAACACCTTCCGA-TGAGGAAGGGCAAACTGG
* * * *
45481 AATAAGACAAACTATACAACATCTTCCGGTGGGGAAGGGCAAACTGG
1 -----GA-AAACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
45528 GAA
1 GAA
45531 TAAGCGGATT
Statistics
Matches: 567, Mismatches: 66, Indels: 136
0.74 0.09 0.18
Matches are distributed among these distances:
38 9 0.02
39 25 0.04
40 97 0.17
41 141 0.25
42 10 0.02
43 2 0.00
44 2 0.00
45 18 0.03
46 52 0.09
47 165 0.29
48 43 0.08
49 1 0.00
50 1 0.00
51 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.15
Consensus pattern (41 bp):
GAAAACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
Found at i:45047 original size:45 final size:46
Alignment explanation
Indices: 44916--45336 Score: 285
Period size: 41 Copynumber: 9.4 Consensus size: 46
44906 ACTGGGAATT
* **
44916 TAAACAACACCTTCCAATGAGGAAGGGCAAACT-GGAATAGTAAACAAC
1 TAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGAAT--TTGACAAC
*
44964 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-TTGGCAAC
1 TAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGAATTTGACAAC
* * * * *
45010 TAGACAACATCTTCCGGTAGGAAGGAG-AAATTGGGAATTTGATAAC
1 TAAACAACACCTTCCGATAGGAAGG-GCAAACTGGGAATTTGACAAC
* *
45056 TAAACAACACCTTCCGACTAGGAAGGGCAAACTAGG-A----A-AAG
1 TAAACAACACCTTCCGA-TAGGAAGGGCAAACTGGGAATTTGACAAC
* * ** * * * *
45097 TAAACAATACCTTCTGACGGGGAAGGACAAATTAGAAATTTGACAAC
1 TAAACAACACCTTCCGA-TAGGAAGGGCAAACTGGGAATTTGACAAC
* * *
45144 TAAACAACACATTCCGACTGGGAAGGGCAAACTGGG-A----A-AAG
1 TAAACAACACCTTCCGA-TAGGAAGGGCAAACTGGGAATTTGACAAC
* * *
45185 TAAACAACACCTTCCGATGAGGAAGGGCAAGCTGGGAAATGTAGAC--T
1 TAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGG-AAT-TTGACAAC
45232 TAAACAACACCTTCCGATAGGGAAGGGCAAACTGGG-A----A-AAC
1 TAAACAACACCTTCCGATA-GGAAGGGCAAACTGGGAATTTGACAAC
** * **
45273 TAAACAACACCTTCCGACCGGGAAGGGCAAACTGAGAATGAGACAAC
1 TAAACAACACCTTCCGA-TAGGAAGGGCAAACTGGGAATTTGACAAC
*
45320 TAAGCAACACCTTCCGA
1 TAAACAACACCTTCCGA
45337 CCGGGAAGGG
Statistics
Matches: 300, Mismatches: 43, Indels: 61
0.74 0.11 0.15
Matches are distributed among these distances:
40 2 0.01
41 96 0.32
42 4 0.01
43 1 0.00
45 17 0.06
46 47 0.16
47 96 0.32
48 33 0.11
49 4 0.01
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (46 bp):
TAAACAACACCTTCCGATAGGAAGGGCAAACTGGGAATTTGACAAC
Found at i:45159 original size:88 final size:88
Alignment explanation
Indices: 44896--45389 Score: 420
Period size: 88 Copynumber: 5.6 Consensus size: 88
44886 CTTCCGGTGG
* ** * * * * * *
44896 GGAAGGGCAAACT-GGGAATTTAAACAACACCTTCCAATGAGGAAGGGCAAACTGGAATAGTAAA
1 GGAAGGGCAAACTAGGAAAAGTAAACAACACCTTCCGACGGGGAAGGGCAAATTGGAA-ATTAGA
44960 CAACTAAACAACACCTTCCGA-TGA
65 CAACTAAACAACACCTTCCGACT-A
* * * * * *
44984 GGAAGGGCAAACTGGGAATTGGCAACTAGACAACATCTTCCG--GTAGGAAGGAG-AAATTGGGA
1 GGAAGGGCAAACTAGGAA-----AAGTAAACAACACCTTCCGACG-GGGAAGG-GCAAATTGGAA
* *
45046 ATTTGATAACTAAACAACACCTTCCGACTA
59 ATTAGACAACTAAACAACACCTTCCGACTA
* * * * *
45076 GGAAGGGCAAACTAGGAAAAGTAAACAATACCTTCTGACGGGGAAGGACAAATTAGAAATTTGAC
1 GGAAGGGCAAACTAGGAAAAGTAAACAACACCTTCCGACGGGGAAGGGCAAATTGGAAATTAGAC
* *
45141 AACTAAACAACACATTCCGACTG
66 AACTAAACAACACCTTCCGACTA
* * * * *
45164 GGAAGGGCAAACTGGGAAAAGTAAACAACACCTTCCGATGAGGAAGGGCAAGCTGGGAAATGTAG
1 GGAAGGGCAAACTAGGAAAAGTAAACAACACCTTCCGACGGGGAAGGGCAA-ATTGGAAAT-TAG
*
45229 AC--TTAAACAACACCTTCCGA-TA
64 ACAACTAAACAACACCTTCCGACTA
* * * * *
45251 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACCGGGAAGGGCAAACT-GAGAATGAG
1 -GGAAGGGCAAACTAGGAAAAGTAAACAACACCTTCCGACGGGGAAGGGCAAATTGGA-AATTAG
* **
45315 ACAACTAAGCAACACCTTCCGACCG
64 ACAACTAAACAACACCTTCCGACTA
45340 GGAAGGGCTAAAC-AGG--AA-TAAGACAACACCTTCCGACGGGGAAGGGCAAA
1 GGAAGGGC-AAACTAGGAAAAGTAA-ACAACACCTTCCGACGGGGAAGGGCAAA
45390 CTGGGAAGCT
Statistics
Matches: 333, Mismatches: 52, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
85 3 0.01
86 35 0.11
87 18 0.05
88 187 0.56
89 14 0.04
90 4 0.01
92 42 0.13
93 15 0.05
94 15 0.05
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (88 bp):
GGAAGGGCAAACTAGGAAAAGTAAACAACACCTTCCGACGGGGAAGGGCAAATTGGAAATTAGAC
AACTAAACAACACCTTCCGACTA
Found at i:45274 original size:129 final size:122
Alignment explanation
Indices: 44789--45530 Score: 470
Period size: 129 Copynumber: 5.7 Consensus size: 122
44779 TTTGGAATAA
* *
44789 GAAAAGTAAACAACACCTTCCGATGAGGAAGGGTAGACTGGGAAA-ACTAAACAACACCTTCCGA
1 GAAAAGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAGACTAAACAACACCTTCCGA
* * *
44853 TGGAGAA-GGCAAACTGGGAAATCTAACCAACACCTTCCGGTGGGGAAGGGCAAACTGG
66 TGG-GAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGCT-GGGAAGGGCAAACTGG
** * *
44911 G-AATTTAAACAACACCTTCCAATGAGGAAGGGCAAACTGGAATAGTAAACAACTAAACAACACC
1 GAAAAGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGG----G-AAA-GACTAAACAACACC
* * * *
44975 TTCCGATGAGGAAGGGCAAACTGGGAATTGGCAACTAGACAACATCTTCCGGTAGGAAGGAG-AA
60 TTCCGATG-GGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGCTGGGAAGG-GCAA
*
45039 ATTGG
118 ACTGG
* * * *
45044 GAATTTGATAACTAAACAACACCTTCCGACT-AGGAAGGGCAAACTAGGAAA-AGTAAACAATAC
1 G-A----A-AAGTAAACAACACCTTCCGA-TGAGGAAGGGCAAACTGGGAAAGACTAAACAACAC
* * * * * * *
45107 CTTCTGACGGGGAAGGACAAATTAGAAATTTGACAACTAAACAACACATTCCGACTGGGAAGGGC
59 CTTCCGA-TGGGAAGGGCAAACT-G-----GGAAAACTAAACAACACCTTCCG-CTGGGAAGGGC
45172 AAACTGG
116 AAACTGG
*
45179 GAAAAGTAAACAACACCTTCCGATGAGGAAGGGCAAGCTGGGAAATGTAGACTTAAACAACACCT
1 GAAAAGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGG-AA---AGAC-TAAACAACACCT
*
45244 TCCGATAGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACCGGGAAGGGCAAACTGAG
61 TCCGAT-GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCG-CTGGGAAGGGCAAACTG-G
* * * *
45309 AATGAGACAACTAAGCAACACCTTCCGACCG-GGAAGGGCTAAAC-AGG--A-A-TAAGACAACA
1 ---GA-A-AAGTAAACAACACCTTCCGA-TGAGGAAGGGC-AAACTGGGAAAGACTAA-ACAACA
* * * *
45368 CCTTCCGACGGGGAAGGGCAAACTGGG-AAGCTAAATAACACCTTCCGGTGGGGAAGGGCAAACT
58 CCTTCCGA-TGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGCT-GGGAAGGGCAAAC-
45432 TGG
120 TGG
* * *
45435 GATAAAGCAACTAGACAACACCTTCCGATTG-GGAAGGGCGAACTGGAATAAGAC-AAACTATAC
1 GA-AAAG----TAAACAACACCTTCCGA-TGAGGAAGGGCAAACTGGGA-AAGACTAAAC-A-AC
*
45498 AACATCTTCCGGTGGGGAAGGGCAAACTGGGAA
57 -AC--CTTCCGAT-GGGAAGGGCAAACTGGGAA
45531 TAAGCGGATT
Statistics
Matches: 488, Mismatches: 63, Indels: 125
0.72 0.09 0.18
Matches are distributed among these distances:
121 34 0.07
122 3 0.01
123 3 0.01
125 4 0.01
126 63 0.13
127 33 0.07
128 26 0.05
129 89 0.18
130 8 0.02
131 2 0.00
132 2 0.00
133 43 0.09
134 64 0.13
135 73 0.15
136 5 0.01
139 3 0.01
140 32 0.07
141 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.15
Consensus pattern (122 bp):
GAAAAGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAGACTAAACAACACCTTCCGA
TGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGCTGGGAAGGGCAAACTGG
Found at i:45279 original size:176 final size:173
Alignment explanation
Indices: 44795--45530 Score: 659
Period size: 176 Copynumber: 4.2 Consensus size: 173
44785 ATAAGAAAAG
* *
44795 TAAACAACACCTTCCGATGAGGAAGGGTAGACTGGGAAAACTAAACAACACCTTCCGATG-GAGA
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAG-GA
* * * **
44859 A-GGCAAACTGGGAAA--T--CTAACCAACACCTTCCGGTGGGGAAGGGCAAACTGGG-AATTTA
65 AGGGCAAACTGGGAAATGTAACTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAAAACTA
* * * * *
44918 AACAACACCTTCCAATGAGGAAGGGCAAACTGGAATAGTAAACAAC
130 AACAACACCTTCCGACGGGGAAGGGCAAACT-GAA-ATTAGACAAC
* * *
44964 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTGGCAACTAGACAACATCTTCCGGT-
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGATG
* * *
45028 AGGAAGGAG-AAATTGGGAATTTGATAACTAAACAACACCTTCCGACTA-GGAAGGGCAAACTAG
61 AGGAAGG-GCAAACTGGGAA-ATG-TAACTAAACAACACCTTCCGA-TAGGGAAGGGCAAACTGG
* * * * * *
45091 GAAAAGTAAACAATACCTTCTGACGGGGAAGGACAAATTAGAAATTTGACAAC
122 GAAAACTAAACAACACCTTCCGACGGGGAAGGGCAAACT-GAAATTAGACAAC
* *
45144 TAAACAACACATTCCGACTG-GGAAGGGCAAACTGGGAAAAGTAAACAACACCTTCCGATGAGGA
1 TAAACAACACCTTCCGA-TGAGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGGA
*
45208 AGGGCAAGCTGGGAAATGTAGACTTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAAAAC
65 AGGGCAAACTGGGAAATGTA-AC-TAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAAAAC
* *
45273 TAAACAACACCTTCCGACCGGGAAGGGCAAACTGAGAATGAGACAAC
128 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGA-AATTAGACAAC
* * * * *
45320 TAAGCAACACCTTCCGACCG-GGAAGGGCTAAAC-AGG--AA-TAAGACAACACCTTCCGACGGG
1 TAAACAACACCTTCCGA-TGAGGAAGGGC-AAACTGGGAAAACTAA-ACAACACCTTCCGATGAG
* * *
45380 GAAGGGCAAACTGGG-AA-G---CTAAATAACACCTTCCGGTGGGGAAGGGCAAACTTGGGATAA
63 GAAGGGCAAACTGGGAAATGTAACTAAACAACACCTTCCGATAGGGAAGGGCAAAC-TGGG---A
* ** * * *
45440 AGCAACTAGACAACACCTTCCGATTGGGAAGGGCGAACTGGAATAAGACAAAC
124 A--AACTAAACAACACCTTCCGACGGGGAAGGGCAAACTGAAATTAGAC-AAC
* * * *
45493 TATACAACATCTTCCGGTGGGGAAGGGCAAACTGGGAA
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA
45531 TAAGCGGATT
Statistics
Matches: 468, Mismatches: 63, Indels: 66
0.78 0.11 0.11
Matches are distributed among these distances:
167 29 0.06
168 5 0.01
169 36 0.08
171 2 0.00
172 13 0.03
173 67 0.14
174 63 0.13
175 27 0.06
176 115 0.25
177 4 0.01
178 1 0.00
180 72 0.15
181 34 0.07
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (173 bp):
TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGGAA
GGGCAAACTGGGAAATGTAACTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAAAACTAA
ACAACACCTTCCGACGGGGAAGGGCAAACTGAAATTAGACAAC
Found at i:45382 original size:39 final size:40
Alignment explanation
Indices: 45317--45431 Score: 139
Period size: 39 Copynumber: 2.9 Consensus size: 40
45307 AGAATGAGAC
*
45317 AACTAAG-CAACACCTTCCGACCGGGAAGGGCTAAAC-AGG
1 AACTAAGACAACACCTTCCGACGGGGAAGGGC-AAACTAGG
*
45356 AA-TAAGACAACACCTTCCGACGGGGAAGGGCAAACTGGG
1 AACTAAGACAACACCTTCCGACGGGGAAGGGCAAACTAGG
* **
45395 AAGCTAA-ATAACACCTTCCGGTGGGGAAGGGCAAACT
1 AA-CTAAGACAACACCTTCCGACGGGGAAGGGCAAACT
45432 TGGGATAAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
38 8 0.12
39 29 0.43
40 27 0.40
41 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.28, T:0.12
Consensus pattern (40 bp):
AACTAAGACAACACCTTCCGACGGGGAAGGGCAAACTAGG
Found at i:45461 original size:126 final size:126
Alignment explanation
Indices: 45235--45490 Score: 331
Period size: 126 Copynumber: 2.0 Consensus size: 126
45225 GTAGACTTAA
*
45235 ACAACACCTTCCGATAGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACCGGGAAGGG
1 ACAACACCTTCCGACAGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACCGGGAAGGG
*
45300 CAAACTGAGAATGAGACAACTAAGCAACACCTTCCGACCGGGAAGGGCTAAACAGGAATAAG
66 CAAACTGAGAATAAGACAACTAAGCAACACCTTCCGACCGGGAAGGGC-AAACAGGAATAAG
* * * ***
45362 ACAACACCTTCCGACGGGGAAGGGCAAACTGGG-AAGCTAAATAACACCTTCCGGTGGGGAAGGG
1 ACAACACCTTCCGACAGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACCGGGAAGGG
* ** * *
45426 CAAACTTG-GGATAA-AGCAACT-AGACAACACCTTCCGATTGGGAAGGGCGAACTGGAATAAG
66 CAAAC-TGAGAATAAGA-CAACTAAG-CAACACCTTCCGACCGGGAAGGGCAAACAGGAATAAG
45487 ACAA
1 ACAA
45491 ACTATACAAC
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
125 18 0.16
126 62 0.55
127 33 0.29
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (126 bp):
ACAACACCTTCCGACAGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACCGGGAAGGG
CAAACTGAGAATAAGACAACTAAGCAACACCTTCCGACCGGGAAGGGCAAACAGGAATAAG
Found at i:46150 original size:49 final size:50
Alignment explanation
Indices: 46031--46150 Score: 111
Period size: 49 Copynumber: 2.4 Consensus size: 50
46021 TCTTATTAAC
* * ** * **
46031 TAATCACAAA-TTCCATCATTTAGTTCAAAGATTTTATTTTTATTTCACCT
1 TAATCA-AAAGTTTCATCTTTTAGTTCAAAGATTCCACTTTTATTTCAAAT
* *
46081 TAATCAAAAGTTTAACCTTTTA-TTCAAAGATTCCACTTTTATTTCAAAT
1 TAATCAAAAGTTTCATCTTTTAGTTCAAAGATTCCACTTTTATTTCAAAT
*
46130 TATTC-AAAGATTTCATCTTTT
1 TAATCAAAAG-TTTCATCTTTT
46151 GCGTAAGGAT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
48 4 0.07
49 38 0.68
50 14 0.25
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (50 bp):
TAATCAAAAGTTTCATCTTTTAGTTCAAAGATTCCACTTTTATTTCAAAT
Found at i:46208 original size:20 final size:20
Alignment explanation
Indices: 46180--46221 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
46170 ATTTACAAAA
* *
46180 TTTACTTAAAAGTTCAATCT
1 TTTAATTAAAAATTCAATCT
*
46200 TTTAATTAAAAATTCCATCT
1 TTTAATTAAAAATTCAATCT
46220 TT
1 TT
46222 ATTCACAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAATTAAAAATTCAATCT
Found at i:46220 original size:52 final size:51
Alignment explanation
Indices: 46158--46438 Score: 258
Period size: 51 Copynumber: 5.6 Consensus size: 51
46148 TTTGCGTAAG
*
46158 GATTCAATCTTTATTTACAAAATTTACTTAAAAG-TTCAATCTTTTAATTAAA
1 GATTCAATCTTTATTTAC-AAA-TTACTTAAAAGATTCAATCTTTCAATTAAA
* * * * * *
46210 AATTCCATCTTTATTCACAAATTATTTAAAAGATTTAATCTTTCACTTAAA
1 GATTCAATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCAATTAAA
* * * * *
46261 GATCCAATATTCATTTACAAATCACTTAAAAGCTTC-A-C---C-A-TAAA
1 GATTCAATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCAATTAAA
* * * * *
46305 GATTCAATCCTTATTTACAAACTACTTAAAAGATTCAATTTTTTTACTT-AA
1 GATTCAATCTTTATTTACAAATTACTTAAAAGATTCAA-TCTTTCAATTAAA
* * * *
46356 GAATTCAATCTTTATTAACAAATCACTTAAAAGCTTC-ATCTTTCAACATAAA
1 G-ATTCAATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCAA-TTAAA
46408 GATTCAATCTTTATTTACAAATTACTTAAAA
1 GATTCAATCTTTATTTACAAATTACTTAAAA
46439 ATCCAAATCT
Statistics
Matches: 178, Mismatches: 39, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
44 33 0.19
45 1 0.01
46 1 0.01
49 1 0.01
50 16 0.09
51 77 0.43
52 49 0.28
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.40
Consensus pattern (51 bp):
GATTCAATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCAATTAAA
Found at i:46260 original size:51 final size:50
Alignment explanation
Indices: 46086--46438 Score: 251
Period size: 51 Copynumber: 7.1 Consensus size: 50
46076 CACCTTAATC
* * *
46086 AAAAGTTTAACCTTTTA-TTCAAAGATTCCA-CTTTTATTT-CAAATTA-TT
1 AAAAGTTTAATCTTTCACTT-AAAGATTCAATC-TTTATTTACAAATTACTT
* * ** * *
46134 CAAAGATTTCATCTTTTGCGTAAGGATTCAATCTTTATTTACAAAATTTACTT
1 AAAAG-TTTAATCTTTCACTTAAAGATTCAATCTTTATTTAC-AAA-TTACTT
* * * * * * *
46187 AAAAGTTCAATCTTTTAATTAAAAATTCCATCTTTATTCACAAATTATTT
1 AAAAGTTTAATCTTTCACTTAAAGATTCAATCTTTATTTACAAATTACTT
* * * *
46237 AAAAGATTTAATCTTTCACTTAAAGATCCAATATTCATTTACAAATCACTT
1 AAAAG-TTTAATCTTTCACTTAAAGATTCAATCTTTATTTACAAATTACTT
* * * *
46288 AAAAGCTTCA-C---CA--TAAAGATTCAATCCTTATTTACAAACTACTT
1 AAAAGTTTAATCTTTCACTTAAAGATTCAATCTTTATTTACAAATTACTT
* * * * *
46332 AAAAGATTCAATTTTTTTACTT-AAGAATTCAATCTTTATTAACAAATCACTT
1 AAAAG-TTTAA-TCTTTCACTTAAAG-ATTCAATCTTTATTTACAAATTACTT
* * *
46384 AAAAGCTTCATCTTTCAACATAAAGATTCAATCTTTATTTACAAATTACTT
1 AAAAGTTTAATCTTTC-ACTTAAAGATTCAATCTTTATTTACAAATTACTT
46435 AAAA
1 AAAA
46439 ATCCAAATCT
Statistics
Matches: 232, Mismatches: 54, Indels: 35
0.72 0.17 0.11
Matches are distributed among these distances:
44 30 0.13
45 2 0.01
46 2 0.01
48 4 0.02
49 25 0.11
50 21 0.09
51 81 0.35
52 61 0.26
53 6 0.03
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (50 bp):
AAAAGTTTAATCTTTCACTTAAAGATTCAATCTTTATTTACAAATTACTT
Found at i:46306 original size:44 final size:44
Alignment explanation
Indices: 46257--46341 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
46247 ATCTTTCACT
*
46257 TAAAGATCCAAT-ATTCATTTACAAA-TCACTTAAAAGCTTCACCA
1 TAAAGATCCAATCATT-ATTTACAAACT-ACTTAAAAGATTCACCA
* *
46301 TAAAGATTCAATCCTTATTTACAAACTACTTAAAAGATTCA
1 TAAAGATCCAATCATTATTTACAAACTACTTAAAAGATTCA
46342 ATTTTTTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 33 0.92
45 3 0.08
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (44 bp):
TAAAGATCCAATCATTATTTACAAACTACTTAAAAGATTCACCA
Found at i:46425 original size:147 final size:147
Alignment explanation
Indices: 46158--46438 Score: 370
Period size: 147 Copynumber: 1.9 Consensus size: 147
46148 TTTGCGTAAG
* * *
46158 GATTCAATCTTTATTTACAAAATTTACTTAAAAGTTCAATCTTTTAATTAAAAATTCCATCTTTA
1 GATTCAATCCTTATTTACAAAATCTACTTAAAAGTTCAATCTTTTAATTAAAAATTCAATCTTTA
* * * * *
46223 TTCACAAATTATTTAAAAGATTTAATCTTTCACTTAAAGATCCAATATTCATTTACAAATCACTT
66 TTAACAAATCACTTAAAAGACTTAATCTTTCACATAAAGATCCAATATTCATTTACAAATCACTT
46288 AAAAGCTTCACCATAAA
131 AAAAGCTTCACCATAAA
* * *
46305 GATTCAATCCTTATTTAC-AAA-CTACTTAAAAGATTCAATTTTTTTACTTAAGAATTCAATCTT
1 GATTCAATCCTTATTTACAAAATCTACTTAAAAG-TTCAA-TCTTTTAATTAAAAATTCAATCTT
* * * * *
46368 TATTAACAAATCACTTAAAAG-CTTCATCTTTCAACATAAAGATTCAATCTTTATTTACAAATTA
64 TATTAACAAATCACTTAAAAGACTTAATCTTTC-ACATAAAGATCCAATATTCATTTACAAATCA
46432 CTTAAAA
128 CTTAAAA
46439 ATCCAAATCT
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
145 10 0.09
146 17 0.15
147 88 0.77
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.40
Consensus pattern (147 bp):
GATTCAATCCTTATTTACAAAATCTACTTAAAAGTTCAATCTTTTAATTAAAAATTCAATCTTTA
TTAACAAATCACTTAAAAGACTTAATCTTTCACATAAAGATCCAATATTCATTTACAAATCACTT
AAAAGCTTCACCATAAA
Done.