Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 103 of 144
Found at i:24153657 original size:29 final size:30
Alignment explanation
Indices: 24153574--24153658 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 30
24153564 GAGATTTTGG
**
24153574 AAAGTTTAAGGGTAAAATGGTAATTTTGGTG
1 AAAGTTTAAGGGTAAAATGGTAATTTT-GAA
* *
24153605 AAA--TTAAGGTTAAAAATGG-GATTTT-AA
1 AAAGTTTAAGGGT-AAAATGGTAATTTTGAA
*
24153632 AAAGTTTAGGGGTAAAATGGTAATTTT
1 AAAGTTTAAGGGTAAAATGGTAATTTT
24153659 TTGTGAAATC
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
27 3 0.07
28 7 0.16
29 23 0.53
30 7 0.16
31 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAGTTTAAGGGTAAAATGGTAATTTTGAA
Found at i:24153672 original size:29 final size:28
Alignment explanation
Indices: 24153640--24153954 Score: 188
Period size: 29 Copynumber: 10.8 Consensus size: 28
24153630 AAAAAGTTTA
24153640 GGGGTAAAATGGTAATTTTTTGTGAAATC
1 GGGGTAAAATGGTAA-TTTTTGTGAAATC
* * *
24153669 GGGGTTAAAATGG-AA-TTTTGGGAAGTTTA
1 GGGG-TAAAATGGTAATTTTTGTGAA--ATC
* *
24153698 GAGGTGAAATGGTAATTTTTGGTGAAATC
1 GGGGTAAAATGGTAATTTTT-GTGAAATC
* *
24153727 GGGGTTAAAAATGG-AATTTTAG-GAAATTTA
1 GGGG-T-AAAATGGTAATTTTTGTGAAA--TC
24153757 GGGGTAAAATGGTAATTTTTGATGAAATC
1 GGGGTAAAATGGTAATTTTTG-TGAAATC
* *
24153786 GGGGTTAAAAATGG-AATTTTAG-GAAGTTC
1 GGGG-T-AAAATGGTAATTTTTGTGAA-ATC
24153815 GGGGGTAAAATGGTAATTTTTGATGAAATC
1 -GGGGTAAAATGGTAATTTTTG-TGAAATC
*
24153845 GGGGTTATAAATGG-GA-TTTTG-GAAAGTTC
1 GGGG-TA-AAATGGTAATTTTTGTGAAA--TC
24153874 GAGGGTAAAATGGTAATTTTTGATGAAATC
1 G-GGGTAAAATGGTAATTTTTG-TGAAATC
* *
24153904 GAGGTTATAAAT-G-AGA-TTTTG-GAAAGTTT
1 G-GGGTA-AAATGGTA-ATTTTTGTGAAA--TC
24153933 GAGGGTAAAATGGTAATTTTTG
1 G-GGGTAAAATGGTAATTTTTG
24153955 AATAGTCCAG
Statistics
Matches: 227, Mismatches: 23, Indels: 71
0.71 0.07 0.22
Matches are distributed among these distances:
27 16 0.07
28 38 0.17
29 70 0.31
30 65 0.29
31 34 0.15
32 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTTGTGAAATC
Found at i:24155797 original size:6 final size:6
Alignment explanation
Indices: 24155786--24155861 Score: 68
Period size: 6 Copynumber: 12.8 Consensus size: 6
24155776 TTAAATTTGA
* * *
24155786 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT AAGTAAAG TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
* *
24155834 GTAAAT TTAAAT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
24155862 ATCTATTTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
5 12 0.22
6 39 0.71
8 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:24155807 original size:17 final size:17
Alignment explanation
Indices: 24155787--24155861 Score: 111
Period size: 17 Copynumber: 4.6 Consensus size: 17
24155777 TAAATTTGAT
24155787 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
24155804 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAG
*
24155818 TAAAGTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
*
24155835 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAG
24155852 TAAATTTAAA
1 TAAATTTAAA
24155862 ATCTATTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
14 12 0.23
15 1 0.02
16 1 0.02
17 38 0.73
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:24155809 original size:11 final size:11
Alignment explanation
Indices: 24155793--24155844 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
24155783 TGATTAAATT
24155793 TAAATTTAAAG
1 TAAATTTAAAG
24155804 TAAATTTAAA-
1 TAAATTTAAAG
*
24155814 T-AA-GTAAAG
1 TAAATTTAAAG
24155823 TTAAATTTAAAG
1 -TAAATTTAAAG
24155835 TAAATTTAAA
1 TAAATTTAAA
24155845 TTTAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 4 0.11
9 2 0.06
10 2 0.06
11 22 0.63
12 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (11 bp):
TAAATTTAAAG
Found at i:24155829 original size:31 final size:31
Alignment explanation
Indices: 24155787--24155845 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
24155777 TAAATTTGAT
*
24155787 TAAATTTAAATTTAAAGTAAATTTAAATAAG
1 TAAAGTTAAATTTAAAGTAAATTTAAATAAG
24155818 TAAAGTTAAATTTAAAGTAAATTTAAAT
1 TAAAGTTAAATTTAAAGTAAATTTAAAT
24155846 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (31 bp):
TAAAGTTAAATTTAAAGTAAATTTAAATAAG
Found at i:24155883 original size:28 final size:28
Alignment explanation
Indices: 24155786--24155883 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 28
24155776 TTAAATTTGA
*
24155786 TTAAATTTAAATTTAAAGTAAATTTAAAT
1 TTAAA-TTAAATTTAAAATAAATTTAAAT
* *
24155815 AAGTAAAGTTAAATTTAAAGTAAATTTAAAT
1 --TTAAA-TTAAATTTAAAATAAATTTAAAT
* **
24155846 TTAAAATAAATTTAAAATCTATTTAAACT
1 TTAAATTAAATTTAAAATAAATTTAAA-T
24155875 TT-AATTAAA
1 TTAAATTAAA
24155884 ACCAAAGGCC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 24 0.41
29 7 0.12
31 27 0.47
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (28 bp):
TTAAATTAAATTTAAAATAAATTTAAAT
Found at i:24156500 original size:6 final size:6
Alignment explanation
Indices: 24156489--24156513 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24156479 TGACTAGAAA
24156489 AAAACT AAAACT AAAACT AAAACT A
1 AAAACT AAAACT AAAACT AAAACT A
24156514 CTATTGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAACT
Found at i:24169258 original size:3 final size:3
Alignment explanation
Indices: 24169250--24169285 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
24169240 GGACTGTAAA
*
24169250 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24169286 TAAGAAGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24169634 original size:11 final size:11
Alignment explanation
Indices: 24169618--24169661 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
24169608 AATATTGATG
24169618 ATATTTTATTA
1 ATATTTTATTA
24169629 ATATTTTACTTA
1 ATATTTTA-TTA
24169641 GATA-TTTATTA
1 -ATATTTTATTA
*
24169652 TTATTTTATT
1 ATATTTTATT
24169662 TAGAAAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 17 0.59
12 7 0.24
13 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (11 bp):
ATATTTTATTA
Found at i:24169651 original size:23 final size:24
Alignment explanation
Indices: 24169617--24169665 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
24169607 TAATATTGAT
24169617 GATATTTTATTAATATTTTACTTA
1 GATATTTTATTAATATTTTACTTA
* *
24169641 GATA-TTTATTATTATTTTATTTA
1 GATATTTTATTAATATTTTACTTA
24169664 GA
1 GA
24169666 AAATGGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (24 bp):
GATATTTTATTAATATTTTACTTA
Found at i:24171211 original size:73 final size:71
Alignment explanation
Indices: 24171131--24171376 Score: 255
Period size: 73 Copynumber: 3.4 Consensus size: 71
24171121 TTACACGGAT
*
24171131 TGGACACACAGGCGTGTGGCCAGACCGTGTGCCCATATTATTTGAAAGTTCAGAAACAGTGAGTT
1 TGGACACACGGGCGTGT-GCCAGACCGTGTGCCCATATTATTTGAAAG-TCAGAAACAGTGAGTT
24171196 ACACAGCC
64 ACACAGCC
* * * * * * *
24171204 TAGACACATGGGCGTGTGTCAAACCGTGTG--GATATTCTGTCTGTGAAA-TAAGAAACAGTGAG
1 TGGACACACGGGCGTGTGCCAGACCGTGTGCCCATA-T-TAT-T-TGAAAGTCAGAAACAGTGAG
*
24171266 TTACACAGAC
62 TTACACAGCC
** * ** *
24171276 TGGACACACGGGCGTGTGCCAGACCGTGTGCCCATACAATTTTACGCGAACAGAAACAGTGAGTT
1 TGGACACACGGGCGTGTGCCAGACCGTGTGCCCATATTATTTGA-AAG-TCAGAAACAGTGAGTT
*
24171341 ACACGGCC
64 ACACAGCC
24171349 TGGACACACGGGCGTGTGCCAGACCGTG
1 TGGACACACGGGCGTGTGCCAGACCGTG
24171377 ACACACACGG
Statistics
Matches: 140, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
70 5 0.04
71 2 0.01
72 62 0.44
73 63 0.45
74 8 0.06
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (71 bp):
TGGACACACGGGCGTGTGCCAGACCGTGTGCCCATATTATTTGAAAGTCAGAAACAGTGAGTTAC
ACAGCC
Found at i:24171529 original size:38 final size:37
Alignment explanation
Indices: 24171463--24171576 Score: 129
Period size: 38 Copynumber: 3.0 Consensus size: 37
24171453 AAAGTTATCA
* *
24171463 AATTACTGAACTGACAGTGACACTGTAAACATTGCAAT
1 AATTACTGAACTG-CAATGACACTGTAAACACTGCAAT
* *
24171501 ATATTACTGAACTGCATTGACACTGTAAACACTACAAT
1 A-ATTACTGAACTGCAATGACACTGTAAACACTGCAAT
* * *
24171539 AATATATTGACCAGCAATGACACTGTAAAACACTGCAA
1 AAT-TACTGAACTGCAATGACACTGT-AAACACTGCAA
24171577 AACAATACTG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
37 2 0.03
38 41 0.63
39 22 0.34
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.25
Consensus pattern (37 bp):
AATTACTGAACTGCAATGACACTGTAAACACTGCAAT
Found at i:24176557 original size:38 final size:39
Alignment explanation
Indices: 24176454--24176601 Score: 176
Period size: 39 Copynumber: 3.8 Consensus size: 39
24176444 GAAAGTTATC
24176454 AAATTACTGAACTGGCAGTGACACTGTAAACACTGCAAT
1 AAATTACTGAACTGGCAGTGACACTGTAAACACTGCAAT
*
24176493 AAATTACTGAACTGGCAGTGATACTGTAAACACTGCAAT
1 AAATTACTGAACTGGCAGTGACACTGTAAACACTGCAAT
* * *
24176532 -ACTATATTGATC-GGCAGTGACACTGTAAACACTGCAA-
1 AAAT-TACTGAACTGGCAGTGACACTGTAAACACTGCAAT
* * * * *
24176569 AACAATACTGAATTGACGGTGAAACTGTAAACA
1 AA-ATTACTGAACTGGCAGTGACACTGTAAACA
24176602 TCGTAGTACT
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
38 32 0.35
39 60 0.65
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (39 bp):
AAATTACTGAACTGGCAGTGACACTGTAAACACTGCAAT
Found at i:24176612 original size:77 final size:77
Alignment explanation
Indices: 24176466--24176642 Score: 207
Period size: 77 Copynumber: 2.3 Consensus size: 77
24176456 ATTACTGAAC
* * *
24176466 TGGCAGTGACACTGTAAACACTGCAATAAATTACTGAACTGGCAGTGATACTGTAAACACTGCAA
1 TGGCAGTGACACTGTAAACACTGCAATAAAATACTGAACTGACAGTGAAACTGTAAACACTGCAA
*
24176531 TACTATATTGA-
66 TACTATACTGAG
* *
24176542 TCGGCAGTGACACTGTAAACACTGCAA-AACAATACTGAATTGACGGTGAAACTGTAAACA-TCG
1 T-GGCAGTGACACTGTAAACACTGCAATAA-AATACTGAACTGACAGTGAAACTGTAAACACT-G
* *
24176605 TAGTACTATACTGAG
63 CAATACTATACTGAG
* *
24176620 TAGCTAGTGAAACTGTAAACACT
1 TGGC-AGTGACACTGTAAACACT
24176643 ACTAGACTGG
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
76 4 0.05
77 64 0.74
78 18 0.21
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (77 bp):
TGGCAGTGACACTGTAAACACTGCAATAAAATACTGAACTGACAGTGAAACTGTAAACACTGCAA
TACTATACTGAG
Found at i:24186039 original size:2 final size:2
Alignment explanation
Indices: 24186034--24186069 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24186024 AAAACGTTTG
24186034 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
24186070 TAATTTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24186678 original size:41 final size:41
Alignment explanation
Indices: 24186633--24186725 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
24186623 ACCTCGCGTT
*
24186633 TTGGTTCAAATTAGTACCGAAACTTGGTTTCATAGTTCAAA
1 TTGGTTCAAATTAGTACCAAAACTTGGTTTCATAGTTCAAA
24186674 TTGGTTCAAATTAGTACCAAAACTTGGTTTCATAGTTCAAA
1 TTGGTTCAAATTAGTACCAAAACTTGGTTTCATAGTTCAAA
24186715 TTGGTTCAAAT
1 TTGGTTCAAAT
24186726 AAGTCATTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (41 bp):
TTGGTTCAAATTAGTACCAAAACTTGGTTTCATAGTTCAAA
Found at i:24186679 original size:18 final size:18
Alignment explanation
Indices: 24186656--24186720 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 18
24186646 GTACCGAAAC
24186656 TTGGTTTCATAGTTCAAA
1 TTGGTTTCATAGTTCAAA
*
24186674 TTGG-TTCAAATTAGTACCAAAA
1 TTGGTTTC--A-TAGT-TC-AAA
24186696 CTTGGTTTCATAGTTCAAA
1 -TTGGTTTCATAGTTCAAA
24186715 TTGGTT
1 TTGGTT
24186721 CAAATAAGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 3 0.08
18 10 0.26
19 4 0.11
20 5 0.13
21 5 0.13
22 4 0.11
23 4 0.11
24 3 0.08
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (18 bp):
TTGGTTTCATAGTTCAAA
Found at i:24186700 original size:23 final size:22
Alignment explanation
Indices: 24186633--24186702 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
24186623 ACCTCGCGTT
24186633 TTGGTTCAAATTAGTACCGAAAC
1 TTGGTTCAAATTAGTACC-AAAC
*
24186656 TTGGTTTC--A-TAGT-TCAAA-
1 TTGG-TTCAAATTAGTACCAAAC
24186674 TTGGTTCAAATTAGTACCAAAAC
1 TTGGTTCAAATTAGTACC-AAAC
24186697 TTGGTT
1 TTGGTT
24186703 TCATAGTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 4 0.11
20 5 0.13
21 5 0.13
22 4 0.11
23 10 0.26
24 3 0.08
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (22 bp):
TTGGTTCAAATTAGTACCAAAC
Found at i:24186709 original size:21 final size:20
Alignment explanation
Indices: 24186644--24186709 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
24186634 TGGTTCAAAT
24186644 TAGTACCGAAACTTGGTTTCA
1 TAGTACC-AAACTTGGTTTCA
*
24186665 TAGT-TCAAA-TTGG-TTCAAA
1 TAGTACCAAACTTGGTTTC--A
24186684 TTAGTACCAAAACTTGGTTTCA
1 -TAGTACC-AAACTTGGTTTCA
24186706 TAGT
1 TAGT
24186710 TCAAATTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 4 0.11
20 5 0.14
21 9 0.25
22 4 0.11
23 4 0.11
24 3 0.08
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (20 bp):
TAGTACCAAACTTGGTTTCA
Found at i:24192866 original size:96 final size:96
Alignment explanation
Indices: 24192729--24192969 Score: 270
Period size: 96 Copynumber: 2.5 Consensus size: 96
24192719 GCAGAGTTCA
* * * *
24192729 GTTGGTTGTTTGGTAGGGATGCCGGAGAGTTCCCAGTATTGTTCACGGAACTAGTACTGAACTG-
1 GTTGGCTGTTTGGTAGGGATGCAGGAGGGTTCCCAGTATTGTTCACGGAACTAGAACTG-ACTGC
** **
24192793 GGTTGGGCTGTTAAAACTGG-AAGAGGAGTTAG
65 ACTCAGGCTGTTAAAACTGGCAA-AGGAGTTAG
* * * * * *
24192825 GTTGGCTGTTCGGTAGGGATGCAGGAGGGTTCCCAGAATTGTTCACAGAATTAGAAGTGATTGCA
1 GTTGGCTGTTTGGTAGGGATGCAGGAGGGTTCCCAGTATTGTTCACGGAACTAGAACTGACTGCA
* * *
24192890 CTCAGGCTGTTAAAGCTGGCAATGGAGTTCG
66 CTCAGGCTGTTAAAACTGGCAAAGGAGTTAG
* * *
24192921 GTTGGCTGTTTGGTAGGGATGCAGGACGATTCCCGGTATTGTTCACGGA
1 GTTGGCTGTTTGGTAGGGATGCAGGAGGGTTCCCAGTATTGTTCACGGA
24192970 GCTATCAGAA
Statistics
Matches: 120, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
95 3 0.03
96 115 0.96
97 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.29
Consensus pattern (96 bp):
GTTGGCTGTTTGGTAGGGATGCAGGAGGGTTCCCAGTATTGTTCACGGAACTAGAACTGACTGCA
CTCAGGCTGTTAAAACTGGCAAAGGAGTTAG
Found at i:24194979 original size:237 final size:235
Alignment explanation
Indices: 24194372--24195086 Score: 910
Period size: 237 Copynumber: 3.0 Consensus size: 235
24194362 CTTATACAAT
* * * *
24194372 GGCACCAATTGGTAGATCATAAATAAACCAGTAACTTATTACCAGACA-CAAATATGCAGAAAGA
1 GGCACCAATCGGTAGATCATAAATAAACAAATAACTTATTACCAGACATCAAATATCCAGAAAGA
* * **
24194436 CATTCAGTAACTTCGACACCTTAATAAATTATATTTCATTGTTCAACTTCATTCACTTTCACAAT
66 CATTCAGTAACTTCAACACCTTAATAAATCATATCCCATTGTTC-A-TT-A---ACTTTCACAAT
*
24194501 CAAATAAATGGGAAAGATGTAAATTTTTTTCCTATGTTGCTCCGACTATTCATTTTTCTTTTTAA
125 CAAATAAATGGG-AAGATGTAAA-TTTTTTCCTATGTTGTTCCGACTATTCATTTTTCTTTTTAA
* *
24194566 GTAACCCTATCCAACACATTTTCTAAGGAGATATGATCCTCTAACAAAT
188 GT-ACCCTATCCAACACATTTTCAAAGGAGATATGATCCTCTAACAAAG
* * * * * * *
24194615 AGCACCAACCGGTAGATCATAAATAAACAAATAGCTTATTACCAGCCATTAAATATTCAAAAAGA
1 GGCACCAATCGGTAGATCATAAATAAACAAATAACTTATTACCAGACATCAAATATCCAGAAAGA
* * * *
24194680 CATTCAATAACTTCAACACCTTAATAGATCATATCCCATTGTTCCTTTACTTTCACAATCAAATA
66 CATTCAGTAACTTCAACACCTTAATAAATCATATCCCATTGTTCATTAACTTTCACAATCAAATA
* * ** *
24194745 AATGGGAAGATGTAACTTTTTTCCTGTGTTGTTTTGACTATTCGTTTTTCTTTTTAAGTATCCCT
131 AATGGGAAGATGTAAATTTTTTCCTATGTTGTTCCGACTATTCATTTTTCTTTTTAAGTA-CCCT
*
24194810 ATCCAACACATTTCCAAAGGAGATATGATCCTCTAACAAAG
195 ATCCAACACATTTTCAAAGGAGATATGATCCTCTAACAAAG
* * * * *
24194851 GGCACCTATCGGTAGATCATAAATAAATAAAAAAACTTATTACCAAACATCGAATATCCAGAAAG
1 GGCACCAATCGGTAGATCATAAATAAA-CAAATAACTTATTACCAGACATCAAATATCCAGAAAG
** *
24194916 ACATTCAGTAACTTCAACGTCTTAATAAATCATATCCCATTGTTCATTAACTTTCTCAATCAAAT
65 ACATTCAGTAACTTCAACACCTTAATAAATCATATCCCATTGTTCATTAACTTTCACAATCAAAT
* * * *
24194981 AAATGAGAAGATGTAAATATTTTTCCTATGTTGTTCCAACTATACAATTTTTTTCCTTTTAAGTA
130 AAATGGGAAGATGTAAAT-TTTTTCCTATGTTGTTCCGACTATTC-A--TTTTTCTTTTTAAGTA
*
24195046 CCATTATCCAACACATTTTCAAAGGAGATATGATCCTCTAA
191 CC-CTATCCAACACATTTTCAAAGGAGATATGATCCTCTAA
24195087 GAACCTTCCA
Statistics
Matches: 407, Mismatches: 57, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
235 1 0.00
236 104 0.26
237 111 0.27
238 44 0.11
240 2 0.00
241 51 0.13
242 2 0.00
243 41 0.10
244 51 0.13
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (235 bp):
GGCACCAATCGGTAGATCATAAATAAACAAATAACTTATTACCAGACATCAAATATCCAGAAAGA
CATTCAGTAACTTCAACACCTTAATAAATCATATCCCATTGTTCATTAACTTTCACAATCAAATA
AATGGGAAGATGTAAATTTTTTCCTATGTTGTTCCGACTATTCATTTTTCTTTTTAAGTACCCTA
TCCAACACATTTTCAAAGGAGATATGATCCTCTAACAAAG
Found at i:24195960 original size:29 final size:28
Alignment explanation
Indices: 24195926--24196006 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
24195916 CTTATAATTG
* *
24195926 AAATTAAATTTTAAAATCTAAAAATACAT
1 AAATTAAATTTTAAAATATAAAAATA-AA
*
24195955 AAATTAAATTCTAGAAA-ATAAAAATAAA
1 AAATTAAATTTTA-AAATATAAAAATAAA
*
24195983 AAGATTAAATTTT-AAATTTAAAAA
1 AA-ATTAAATTTTAAAATATAAAAA
24196007 GAGTACATAG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 3 0.07
28 9 0.20
29 29 0.66
30 3 0.07
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (28 bp):
AAATTAAATTTTAAAATATAAAAATAAA
Found at i:24198443 original size:17 final size:18
Alignment explanation
Indices: 24198393--24198443 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
24198383 ATTACATATA
*
24198393 TAATATATTATACTAGAGT
1 TAATATATTATA-TAAAGT
* *
24198412 TTATATATAATATAAAGT
1 TAATATATTATATAAAGT
24198430 TAAT-TATTATATAA
1 TAATATATTATATAA
24198444 TAATTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 9 0.33
18 8 0.30
19 10 0.37
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (18 bp):
TAATATATTATATAAAGT
Found at i:24204922 original size:24 final size:22
Alignment explanation
Indices: 24204884--24205013 Score: 79
Period size: 21 Copynumber: 5.9 Consensus size: 22
24204874 TTTTTTGCTA
* *
24204884 TTTTGGTGTTGTTTTTTATTGT
1 TTTTGCTGTTATTTTTTATTGT
*
24204906 TTTGGTGCTGTTATTTTTGTTGTTGT
1 TTT--TGCTGTTA-TTTT-TTATTGT
*
24204932 TTTTGCTGCTA-TTTTTATTGT
1 TTTTGCTGTTATTTTTTATTGT
** * *
24204953 TTTTATTGTTATTTTGCTATTAT
1 TTTTGCTGTTATTTT-TTATTGT
* *
24204976 TTTT-CTGTT-GTTTTTGTTG-
1 TTTTGCTGTTATTTTTTATTGT
* *
24204995 TTTGGATGTTATTTTTTAT
1 TTTTGCTGTTATTTTTTAT
24205014 GCATTTTTCC
Statistics
Matches: 81, Mismatches: 19, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
19 3 0.04
20 7 0.09
21 23 0.28
22 13 0.16
23 9 0.11
24 13 0.16
25 4 0.05
26 9 0.11
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.69
Consensus pattern (22 bp):
TTTTGCTGTTATTTTTTATTGT
Found at i:24204946 original size:12 final size:12
Alignment explanation
Indices: 24204911--24204996 Score: 56
Period size: 12 Copynumber: 7.6 Consensus size: 12
24204901 ATTGTTTTGG
24204911 TGCTGTTATTTT
1 TGCTGTTATTTT
* *
24204923 TGTTGTTGTTTT
1 TGCTGTTATTTT
*
24204935 TGCTGCTATTTT
1 TGCTGTTATTTT
** *
24204947 TATTGTT-TTTA
1 TGCTGTTATTTT
24204958 T--TGTTA-TTT
1 TGCTGTTATTTT
*
24204967 TGCTATTATTTT
1 TGCTGTTATTTT
*
24204979 T-CTGTTGTTTT
1 TGCTGTTATTTT
*
24204990 TGTTGTT
1 TGCTGTT
24204997 TGGATGTTAT
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
9 7 0.13
11 17 0.31
12 31 0.56
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.70
Consensus pattern (12 bp):
TGCTGTTATTTT
Found at i:24205814 original size:2 final size:2
Alignment explanation
Indices: 24205807--24205848 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
24205797 TCTATTTTAT
24205807 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
24205849 AATAAAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24206010 original size:33 final size:34
Alignment explanation
Indices: 24205972--24206035 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
24205962 AAAAGTGATA
*
24205972 TATATAATATGGT-AATTAAATTAAATTAATTAT
1 TATATAATATGCTCAATTAAATTAAATTAATTAT
*
24206005 TATATAATATGCTCAATTAAATTAAGTTAAT
1 TATATAATATGCTCAATTAAATTAAATTAAT
24206036 AGTGGAGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (34 bp):
TATATAATATGCTCAATTAAATTAAATTAATTAT
Found at i:24209658 original size:28 final size:30
Alignment explanation
Indices: 24209616--24209679 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
24209606 AAATCATAGT
* *
24209616 AAAATTTAATTAAAAATAAAAAATAGTGG-
1 AAAATTCAATTAAAAATAAAAAATAATGGC
* *
24209645 AAAATTCAA-TAAAATTAAAAATTAATGGC
1 AAAATTCAATTAAAAATAAAAAATAATGGC
24209674 AAAATT
1 AAAATT
24209680 AAGCACATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (30 bp):
AAAATTCAATTAAAAATAAAAAATAATGGC
Found at i:24210196 original size:12 final size:12
Alignment explanation
Indices: 24210179--24210209 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
24210169 ACATGTATGT
24210179 ATACACACACAC
1 ATACACACACAC
24210191 ATACACACACAC
1 ATACACACACAC
*
24210203 ACACACA
1 ATACACA
24210210 TATATATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.42, G:0.00, T:0.06
Consensus pattern (12 bp):
ATACACACACAC
Found at i:24212509 original size:144 final size:145
Alignment explanation
Indices: 24212243--24212534 Score: 523
Period size: 144 Copynumber: 2.0 Consensus size: 145
24212233 AAAAGTTTGG
*
24212243 TGATAAGGTTAGCATGTGTTTAATGTTGGGATTTTTTTTTTCTTGCAAAACAAGCTATTTGAGAT
1 TGATAAGGTTAGCATGTGTTTAATGTTGGGATTTTTTTTTTCTTGCAAAACAAGCTACTTGAGAT
*
24212308 ATGCAATTAACATTATAAAAGAAAAATATTAAGTTTTAATTCGATTAGCATTAACGTTGTTGTCG
66 ATACAATTAACATTATAAAAGAAAAATATTAAGTTTTAATTCGATTAGCATTAACGTTGTTGTCG
*
24212373 TGGTAGCTGACCATA
131 TGGTAGCCGACCATA
*
24212388 TGATAAGGTTAGCATGTGTTTAATGTTGGGA-TTTTTTTTTCTTGCAAAACAAGTTACTTGAGAT
1 TGATAAGGTTAGCATGTGTTTAATGTTGGGATTTTTTTTTTCTTGCAAAACAAGCTACTTGAGAT
* *
24212452 ATACAATTAACATTATAAAAGAAAAATATTAAGTTTTAATTCGATTGGCATTGACGTTGTTGTCG
66 ATACAATTAACATTATAAAAGAAAAATATTAAGTTTTAATTCGATTAGCATTAACGTTGTTGTCG
24212517 TGGTAGCCGACCATA
131 TGGTAGCCGACCATA
24212532 TGA
1 TGA
24212535 GGGTTAATGG
Statistics
Matches: 141, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
144 110 0.78
145 31 0.22
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (145 bp):
TGATAAGGTTAGCATGTGTTTAATGTTGGGATTTTTTTTTTCTTGCAAAACAAGCTACTTGAGAT
ATACAATTAACATTATAAAAGAAAAATATTAAGTTTTAATTCGATTAGCATTAACGTTGTTGTCG
TGGTAGCCGACCATA
Found at i:24214261 original size:23 final size:23
Alignment explanation
Indices: 24214235--24214305 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
24214225 ACACTAGTGC
24214235 GCTTACCG-TTCAGCACTGTGTGT
1 GCTTACCGTTTC-GCACTGTGTGT
* *
24214258 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACCGTTTCGCACTGTGTGT
* *
24214281 GCCTACTGTTTCGCACT-TCGTGT
1 GCTTACCGTTTCGCACTGT-GTGT
24214304 GC
1 GC
24214306 CTACTGATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 1 0.02
23 39 0.91
24 3 0.07
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (23 bp):
GCTTACCGTTTCGCACTGTGTGT
Found at i:24214279 original size:25 final size:24
Alignment explanation
Indices: 24214247--24214360 Score: 98
Period size: 23 Copynumber: 5.0 Consensus size: 24
24214237 TTACCGTTCA
*
24214247 GCAC-TGTGTGTGCTTACTGTTTC
1 GCACTTGTGTGTGCCTACTGTTTC
24214270 GCACTT-TGTGTGCCTACTGTTTC
1 GCACTTGTGTGTGCCTACTGTTTC
*
24214293 GCACTT-CGTGTGCCTACTGATTT-
1 GCACTTGTGTGTGCCTACTG-TTTC
* * * * *
24214316 GCGC-TATGTGCGCCTATTGATT-
1 GCACTTGTGTGTGCCTACTGTTTC
*
24214338 GCAC-TGTGTGTGCTTACTGTTTC
1 GCACTTGTGTGTGCCTACTGTTTC
24214361 CCCAGCACAT
Statistics
Matches: 74, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
22 19 0.26
23 51 0.69
24 4 0.05
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.41
Consensus pattern (24 bp):
GCACTTGTGTGTGCCTACTGTTTC
Found at i:24214331 original size:46 final size:45
Alignment explanation
Indices: 24214247--24214360 Score: 133
Period size: 46 Copynumber: 2.5 Consensus size: 45
24214237 TTACCGTTCA
* * *
24214247 GCACTGTGTGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGTTT
1 GCACTGTGTGTGCTTACTGTTTCGCACTATGTGCGCCTACTGATT
* * *
24214292 CGCACT-TCGTGTGCCTACTGATTT-GCGCTATGTGCGCCTATTGATT
1 -GCACTGT-GTGTGCTTACTG-TTTCGCACTATGTGCGCCTACTGATT
24214338 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCTTACTGTTTC
24214361 CCCAGCACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
44 3 0.05
45 17 0.30
46 34 0.60
47 3 0.05
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.41
Consensus pattern (45 bp):
GCACTGTGTGTGCTTACTGTTTCGCACTATGTGCGCCTACTGATT
Found at i:24216135 original size:12 final size:12
Alignment explanation
Indices: 24216102--24216136 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
24216092 AATTTTTATT
*
24216102 TTTTTAGTTAAA
1 TTTTTAGTTTAA
*
24216114 TTGTTAGTTTAA
1 TTTTTAGTTTAA
24216126 TTTTTAGTTTA
1 TTTTTAGTTTA
24216137 TTAAATCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (12 bp):
TTTTTAGTTTAA
Found at i:24217500 original size:6 final size:6
Alignment explanation
Indices: 24217489--24217535 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
24217479 AAAATGGCAG
* *
24217489 TATTCC TATTCC TATTCG TATTCC TATTCC TATTCC TGTTCC -ATTCC
1 TATTCC TATTCC TATTCC TATTCC TATTCC TATTCC TATTCC TATTCC
24217536 ACAAGTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.15, C:0.32, G:0.04, T:0.49
Consensus pattern (6 bp):
TATTCC
Found at i:24221788 original size:61 final size:61
Alignment explanation
Indices: 24221714--24221834 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 61
24221704 AACCCCTCCA
** * * *
24221714 TTTTTTTTACACTCATTTAGG-TACTTT-AACTTTCGAAATGTATCAAAAAGGCCCTCAAACC
1 TTTTTTTTACACTCAAAT-GGATA-TTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACC
* *
24221775 TTTTTTTTGCACTCAAATGGATATTTGAACTTTCAAAATGCATCATAAAGACCCTCAAAC
1 TTTTTTTTACACTCAAATGGATATTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAC
24221835 TTAAAAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
60 5 0.10
61 46 0.90
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (61 bp):
TTTTTTTTACACTCAAATGGATATTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACC
Found at i:24222064 original size:46 final size:46
Alignment explanation
Indices: 24221997--24222123 Score: 143
Period size: 46 Copynumber: 2.7 Consensus size: 46
24221987 TAAATCATGA
* *
24221997 AAAAATATAAAAAATATAAAATTTTACAAAAATCGTAA-ACAATTAT
1 AAAAATATAAGAAATATAAAATTTTA-AAAAATCGTAAGAAAATTAT
*
24222043 -AAAATATATAGAAATATAAAATTTTATAAAATCGTAAGAAAATTAT
1 AAAAATATA-AGAAATATAAAATTTTAAAAAATCGTAAGAAAATTAT
*
24222089 ACAAAATGTAAAGAAATAT-AAATTTCGTAAAAAAT
1 A-AAAATAT-AAGAAATATAAAATTT--TAAAAAAT
24222124 TATAAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
45 18 0.26
46 23 0.33
47 6 0.09
48 14 0.20
49 8 0.12
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.29
Consensus pattern (46 bp):
AAAAATATAAGAAATATAAAATTTTAAAAAATCGTAAGAAAATTAT
Found at i:24222084 original size:21 final size:21
Alignment explanation
Indices: 24222060--24222104 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24222050 ATAGAAATAT
* *
24222060 AAAATTTTATAAAATCGT-AAG
1 AAAATTATACAAAAT-GTAAAG
24222081 AAAATTATACAAAATGTAAAG
1 AAAATTATACAAAATGTAAAG
24222102 AAA
1 AAA
24222105 TATAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATTATACAAAATGTAAAG
Found at i:24222338 original size:37 final size:37
Alignment explanation
Indices: 24222266--24222338 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
24222256 GGGGTCGTTA
* **
24222266 ATTTTTTATGATTTTTATAAAATTTTATAATTTTTTT
1 ATTTTTTACGATTTTTATAAAAAATTATAATTTTTTT
*
24222303 ATTTTTTACGATTTTTATAAAAAAATTCTAATTTTT
1 ATTTTTTACGATTTTTAT-AAAAAATTATAATTTTT
24222339 AATAAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (37 bp):
ATTTTTTACGATTTTTATAAAAAATTATAATTTTTTT
Found at i:24243300 original size:2 final size:2
Alignment explanation
Indices: 24243293--24243358 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
24243283 TGGCAAAATA
24243293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24243335 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
24243359 TAAGAGTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24251924 original size:17 final size:17
Alignment explanation
Indices: 24251902--24251935 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
24251892 AGAAATCAGA
24251902 ATATATGATAATATAAT
1 ATATATGATAATATAAT
24251919 ATATATGATAATATAAT
1 ATATATGATAATATAAT
24251936 TACAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATATATGATAATATAAT
Found at i:24260795 original size:2 final size:2
Alignment explanation
Indices: 24260788--24260815 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24260778 GGTTATTATG
24260788 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
24260816 GCTCTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24261436 original size:30 final size:29
Alignment explanation
Indices: 24261377--24261445 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
24261367 TTTAATAGTT
*
24261377 TATATATTTATAATTTTAAAAGGATTAAA
1 TATATTTTTATAATTTTAAAAGGATTAAA
* *
24261406 TCATATTTTTATCATTTTAAAGAGTA-TAAA
1 T-ATATTTTTATAATTTTAAA-AGGATTAAA
*
24261436 TATAATTTTA
1 TATATTTTTA
24261446 CCTCTATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 9 0.26
30 22 0.65
31 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (29 bp):
TATATTTTTATAATTTTAAAAGGATTAAA
Found at i:24263610 original size:16 final size:16
Alignment explanation
Indices: 24263589--24263631 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
24263579 ATTGTGTAAT
24263589 AAATATATTTATAAAA
1 AAATATATTTATAAAA
* **
24263605 AAATATA-TTAGAAGT
1 AAATATATTTATAAAA
24263620 AAATATATTTAT
1 AAATATATTTAT
24263632 GTTTGTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
AAATATATTTATAAAA
Found at i:24263883 original size:22 final size:22
Alignment explanation
Indices: 24263858--24263900 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24263848 TTATTGAATT
24263858 TCAAAACATT-TTAATTATATCC
1 TCAAAACATTATT-ATTATATCC
*
24263880 TCAAAATATTATTATTATATC
1 TCAAAACATTATTATTATATC
24263901 AATTAGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (22 bp):
TCAAAACATTATTATTATATCC
Found at i:24267470 original size:24 final size:24
Alignment explanation
Indices: 24267443--24267546 Score: 163
Period size: 24 Copynumber: 4.3 Consensus size: 24
24267433 AGCCCACACG
24267443 AGCCCAGAATGATTAGCTCTTACA
1 AGCCCAGAATGATTAGCTCTTACA
* *
24267467 AGCCCAGAATGGTTAGCTCTTACG
1 AGCCCAGAATGATTAGCTCTTACA
24267491 AGCCCAGAATGATTAGCTCTTACA
1 AGCCCAGAATGATTAGCTCTTACA
* * *
24267515 AGCCCAAAATGGTTAGCTCTTACG
1 AGCCCAGAATGATTAGCTCTTACA
24267539 AGCCCAGA
1 AGCCCAGA
24267547 CAGAGTTTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (24 bp):
AGCCCAGAATGATTAGCTCTTACA
Found at i:24267492 original size:48 final size:48
Alignment explanation
Indices: 24267440--24267546 Score: 205
Period size: 48 Copynumber: 2.2 Consensus size: 48
24267430 TTTAGCCCAC
*
24267440 ACGAGCCCAGAATGATTAGCTCTTACAAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTTACAAGCCCAAAATGGTTAGCTCTT
24267488 ACGAGCCCAGAATGATTAGCTCTTACAAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTTACAAGCCCAAAATGGTTAGCTCTT
24267536 ACGAGCCCAGA
1 ACGAGCCCAGA
24267547 CAGAGTTTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (48 bp):
ACGAGCCCAGAATGATTAGCTCTTACAAGCCCAAAATGGTTAGCTCTT
Found at i:24270905 original size:2 final size:2
Alignment explanation
Indices: 24270898--24270929 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24270888 GTGAATTTTA
24270898 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
24270930 TAGGGTACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24276594 original size:16 final size:17
Alignment explanation
Indices: 24276562--24276594 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24276552 TTAAAATGAT
*
24276562 AATTTTATAATTTATAA
1 AATTTTATAATTAATAA
24276579 AATTTTA-AATTAATAA
1 AATTTTATAATTAATAA
24276595 CAGTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTTATAATTAATAA
Found at i:24277099 original size:27 final size:27
Alignment explanation
Indices: 24277068--24277135 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 27
24277058 ATTCAATTTG
*
24277068 GTACTTAAGTTTTTGTTTTATCC-ATT-
1 GTACTTAAGTTTTT-TTTAATCCAATTA
*
24277094 GCTACTTTTAGTTTTTTTTAATCCAATTAA
1 G-TAC-TTAAGTTTTTTTTAATCCAATT-A
24277124 GTACTTAAGTTT
1 GTACTTAAGTTT
24277136 GACTTCACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
26 1 0.03
27 10 0.29
28 19 0.56
29 3 0.09
30 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (27 bp):
GTACTTAAGTTTTTTTTAATCCAATTA
Found at i:24278308 original size:12 final size:12
Alignment explanation
Indices: 24278291--24278317 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24278281 AAATTAAAAA
24278291 AAATGAAAAATT
1 AAATGAAAAATT
24278303 AAATGAAAAATT
1 AAATGAAAAATT
24278315 AAA
1 AAA
24278318 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (12 bp):
AAATGAAAAATT
Found at i:24279215 original size:19 final size:20
Alignment explanation
Indices: 24279193--24279234 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
24279183 TAGAAGTTAG
*
24279193 AAAAAAT-ATTAAAAATTAT
1 AAAAAATCATAAAAAATTAT
24279212 -AAAAATCATAAAAAATTAT
1 AAAAAATCATAAAAAATTAT
24279231 AAAA
1 AAAA
24279235 TTTTCTGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 6 0.30
19 11 0.55
20 3 0.15
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATCATAAAAAATTAT
Found at i:24279216 original size:10 final size:10
Alignment explanation
Indices: 24279193--24279306 Score: 53
Period size: 9 Copynumber: 12.0 Consensus size: 10
24279183 TAGAAGTTAG
24279193 AAAAAA-TAT
1 AAAAAATTAT
*
24279202 TAAAAATTAT
1 AAAAAATTAT
*
24279212 -AAAAATCAT
1 AAAAAATTAT
24279221 AAAAAATTAT
1 AAAAAATTAT
** *
24279231 AAAATTTTCT
1 AAAAAATTAT
* ** *
24279241 GAAGTAGTA-
1 AAAAAATTAT
*
24279250 AGAAAATTAT
1 AAAAAATTAT
*
24279260 -AAAAATTGT
1 AAAAAATTAT
*
24279269 AAAGGAA-TAT
1 AAA-AAATTAT
*
24279279 -AAAATTTAT
1 AAAAAATTAT
24279288 AAAAAATTAT
1 AAAAAATTAT
24279298 -AAAAATTAT
1 AAAAAATTAT
24279307 CGTACCAAAA
Statistics
Matches: 75, Mismatches: 23, Indels: 14
0.67 0.21 0.12
Matches are distributed among these distances:
8 1 0.01
9 38 0.51
10 34 0.45
11 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:24279266 original size:9 final size:9
Alignment explanation
Indices: 24279252--24279306 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
24279242 AAGTAGTAAG
24279252 AAAATTATA
1 AAAATTATA
*
24279261 AAAATTGTA
1 AAAATTATA
24279270 AAGGAA-TATA
1 AA--AATTATA
*
24279280 AAATTTATAA
1 AAAATTAT-A
24279290 AAAATTATA
1 AAAATTATA
24279299 AAAATTAT
1 AAAATTAT
24279307 CGTACCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 22 0.58
10 13 0.34
11 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:24279281 original size:19 final size:19
Alignment explanation
Indices: 24279252--24279306 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
24279242 AAGTAGTAAG
*
24279252 AAAATTATAAAAATTGTAA
1 AAAATTATAAAAATTATAA
* *
24279271 AGGAA-TATAAAATTTATAA
1 A-AAATTATAAAAATTATAA
24279290 AAAATTATAAAAATTAT
1 AAAATTATAAAAATTAT
24279307 CGTACCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.07
19 25 0.86
20 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAATTATAAAAATTATAA
Found at i:24279530 original size:28 final size:29
Alignment explanation
Indices: 24279493--24279553 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
24279483 TTTATCTTTT
*
24279493 TTTTATGATTTTTATAAAATTTTATAT-A
1 TTTTACGATTTTTATAAAATTTTATATAA
* *
24279521 TTTTACGATTTTTATAAATTTTTTTATAA
1 TTTTACGATTTTTATAAAATTTTATATAA
24279550 TTTT
1 TTTT
24279554 TAATATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTTACGATTTTTATAAAATTTTATATAA
Found at i:24279578 original size:25 final size:24
Alignment explanation
Indices: 24279540--24279595 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
24279530 TTTTATAAAT
24279540 TTTTTTATAATTTTTAATATTTTA
1 TTTTTTATAATTTTTAATATTTTA
* * *
24279564 TTTTTTATAGGTTTTTATTTTTTTA
1 TTTTTTATA-ATTTTTAATATTTTA
24279589 TATTTTT
1 T-TTTTT
24279596 TTGCTACATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 9 0.33
25 13 0.48
26 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTTATAATTTTTAATATTTTA
Found at i:24279595 original size:17 final size:17
Alignment explanation
Indices: 24279540--24279596 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
24279530 TTTTATAAAT
*
24279540 TTTTTTATAATTTTTA-A
1 TTTTTTAT-TTTTTTATA
*
24279557 TATTTTA-TTTTTTATA
1 TTTTTTATTTTTTTATA
*
24279573 GGTTTTTATTTTTTTATA
1 -TTTTTTATTTTTTTATA
24279591 TTTTTT
1 TTTTTT
24279597 TGCTACATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.19
16 1 0.03
17 16 0.50
18 9 0.28
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTTTTATA
Found at i:24284855 original size:16 final size:16
Alignment explanation
Indices: 24284834--24284886 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
24284824 TGAGTGAAAA
24284834 GAAAATTAGAAGGATG
1 GAAAATTAGAAGGATG
* *
24284850 GAAAATT-GAAGGGTA
1 GAAAATTAGAAGGATG
* *
24284865 GAAAACTAAAAGGATG
1 GAAAATTAGAAGGATG
*
24284881 AAAAAT
1 GAAAAT
24284887 ATAATTTATC
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (16 bp):
GAAAATTAGAAGGATG
Found at i:24284868 original size:15 final size:16
Alignment explanation
Indices: 24284833--24284884 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
24284823 TTGAGTGAAA
24284833 AGAAAATTAGAAGGAT
1 AGAAAATTAGAAGGAT
* *
24284849 GGAAAATT-GAAGGGT
1 AGAAAATTAGAAGGAT
* *
24284864 AGAAAACTAAAAGGAT
1 AGAAAATTAGAAGGAT
24284880 -GAAAA
1 AGAAAA
24284885 ATATAATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.56, C:0.02, G:0.27, T:0.15
Consensus pattern (16 bp):
AGAAAATTAGAAGGAT
Found at i:24285252 original size:6 final size:6
Alignment explanation
Indices: 24285243--24285291 Score: 53
Period size: 7 Copynumber: 7.5 Consensus size: 6
24285233 AATTTGCTTT
*
24285243 AAATTA AAATTA AAATTA AAATTTA AACACTA AACATTA AGAATTA AAA
1 AAATTA AAATTA AAATTA AAA-TTA AA-ATTA AA-ATTA A-AATTA AAA
24285292 GTCTAATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 17 0.45
7 19 0.50
8 2 0.05
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (6 bp):
AAATTA
Found at i:24287256 original size:24 final size:24
Alignment explanation
Indices: 24287224--24287271 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
24287214 TTTTAACCCC
24287224 GATTTCACCGAAAATTACCATTTT
1 GATTTCACCGAAAATTACCATTTT
24287248 GATTTCACCGAAAATTACCATTTT
1 GATTTCACCGAAAATTACCATTTT
24287272 ACCCTCCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (24 bp):
GATTTCACCGAAAATTACCATTTT
Found at i:24287325 original size:83 final size:82
Alignment explanation
Indices: 24287175--24287330 Score: 233
Period size: 83 Copynumber: 1.9 Consensus size: 82
24287165 AAACAACCCA
* * * * *
24287175 AAAATTACCATTTTACCCCTGAATCTTTTAGAATTCCATTTTTAACCCCGATTTCACCGAAAATT
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGACTT-ACCAAAAATT
24287240 ACCATTTTGATTTCACCG
65 ACCATTTTGATTTCACCG
24287258 AAAATTACCATTTTACCCTCCGAATCTTCTAAAATTCCATTTTTAACCCCGAACTT-CCAAAAAT
1 AAAATTACCATTTTACCC-CCGAATCTTCTAAAATTCCATTTTTAACCCCG-ACTTACCAAAAAT
24287322 TACCATTTT
64 TACCATTTT
24287331 ACCCCCGAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 34 0.52
84 29 0.44
85 3 0.05
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (82 bp):
AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGACTTACCAAAAATTA
CCATTTTGATTTCACCG
Found at i:24287329 original size:59 final size:58
Alignment explanation
Indices: 24287258--24287751 Score: 568
Period size: 59 Copynumber: 8.4 Consensus size: 58
24287248 GATTTCACCG
*
24287258 AAAATTACCATTTTACCCTCCGAATCTTCTAAAATTCCATTTTTAACCCCGAACTT-CCA
1 AAAATTACCATTTTACCC-CCGAATCTTTTAAAATTCCATTTTTAACCCCG-ACTTACCA
** *
24287317 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCAAATTTCACCA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGACTT-ACCA
* * * * **
24287376 AAAATTACCATTGTACCCTCCGAATATTCTAAAATTCCATTTTTAACCCTGAACTT-CTG
1 AAAATTACCATTTTACCC-CCGAATCTTTTAAAATTCCATTTTTAACCCCG-ACTTACCA
* * * * *
24287435 AAAATTACTATTTTACCCTCGACTCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGACTT-ACCA
**
24287494 AAAATTACCATTTTACCCCCGAATCTTCCAAAATTCCATTTTTAACCCCGACTTCACCAA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGACTT-ACC-A
* * *
24287554 AAAATTACCATTTTACCCCCGTATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGACTT-ACCA
* * * * *
24287613 AAAATAACCATTTTACCCTCGTATCTTTTAAAATCCCATTTTT-ATCCCGACTTCACCAAA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGACTT-ACC--A
* *
24287673 AAAATTATCATTTTACCCCC-ATATCTTTTAAAATTCCA-TTTTAACCCCGATTTTACC-
1 AAAATTACCATTTTACCCCCGA-ATCTTTTAAAATTCCATTTTTAACCCCGA-CTTACCA
*
24287730 AAAATTACCATTTTGCCCCCGA
1 AAAATTACCATTTTACCCCCGA
24287752 GTATCCAAAA
Statistics
Matches: 374, Mismatches: 48, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
57 24 0.06
58 69 0.18
59 153 0.41
60 123 0.33
61 5 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGACTTACCA
Found at i:24287393 original size:118 final size:119
Alignment explanation
Indices: 24287248--24287751 Score: 688
Period size: 118 Copynumber: 4.3 Consensus size: 119
24287238 TTACCATTTT
24287248 GATTTCACCGAAAATTACCATTTTACCCTCCGAATCTTCTAAAATTCCATTTTTAACCCCGAACT
1 GATTTCACCGAAAATTACCATTTTACCCTCCGAATCTTCTAAAATTCCATTTTTAACCCCG-ACT
*
24287313 T-CC-AAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCA
65 TACCAAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCC
* * * * *
24287366 AATTTCACCAAAAATTACCATTGTACCCTCCGAATATTCTAAAATTCCATTTTTAACCCTGAACT
1 GATTTCACCGAAAATTACCATTTTACCCTCCGAATCTTCTAAAATTCCATTTTTAACCCCG-ACT
** * * *
24287431 T--CTGAAAATTACTATTTTACCCTCGACTCTTTTAAAATTCCATTTTTAACCCC
65 TACCAAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCC
*
24287484 GATTTCACCGAAAATTACCATTTTACCC-CCGAATCTTCCAAAATTCCATTTTTAACCCCGACTT
1 GATTTCACCGAAAATTACCATTTTACCCTCCGAATCTTCTAAAATTCCATTTTTAACCCCGACTT
*
24287548 CACCAAAAAATTACCATTTTACCCCCGTATCTTTTAAAATTCCATTTTTAACCCC
66 -ACCAAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCC
* * * * *
24287603 GATTTCACCGAAAATAACCATTTTACCCT-CGTATCTTTTAAAATCCCATTTTT-ATCCCGACTT
1 GATTTCACCGAAAATTACCATTTTACCCTCCGAATCTTCTAAAATTCCATTTTTAACCCCGACTT
*
24287666 CACCAAAAAAATTATCATTTTACCCCC-ATATCTTTTAAAATTCCA-TTTTAACCCC
66 -ACC-AAAAAATTACCATTTTACCCCCGA-ATCTTTTAAAATTCCATTTTTAACCCC
* *
24287721 GATTTTACC-AAAATTACCATTTTGCCC-CCGA
1 GATTTCACCGAAAATTACCATTTTACCCTCCGA
24287752 GTATCCAAAA
Statistics
Matches: 344, Mismatches: 34, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
116 4 0.01
117 48 0.14
118 162 0.47
119 130 0.38
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (119 bp):
GATTTCACCGAAAATTACCATTTTACCCTCCGAATCTTCTAAAATTCCATTTTTAACCCCGACTT
ACCAAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCC
Found at i:24287617 original size:30 final size:30
Alignment explanation
Indices: 24287464--24287626 Score: 140
Period size: 29 Copynumber: 5.4 Consensus size: 30
24287454 CGACTCTTTT
24287464 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCATTTTTAACCCCGATTTCACCG
*
24287494 AAAATTACCA-TTTTACCCCCGAATCTT--CC-
1 AAAATT-CCATTTTTAACCCCG-AT-TTCACCG
* *
24287523 AAAATTCCATTTTTAACCCCGACTTCACCAA
1 AAAATTCCATTTTTAACCCCGATTTCACC-G
* * ****
24287554 AAAATTACCA-TTTTACCCCCG-TATCTTTT
1 AAAATT-CCATTTTTAACCCCGATTTCACCG
24287583 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCATTTTTAACCCCGATTTCACCG
*
24287613 AAAATAACCATTTT
1 AAAAT-TCCATTTT
24287627 ACCCTCGTAT
Statistics
Matches: 104, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
27 2 0.02
28 7 0.07
29 34 0.33
30 28 0.27
31 28 0.27
32 5 0.05
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:24287627 original size:30 final size:29
Alignment explanation
Indices: 24287464--24287627 Score: 111
Period size: 30 Copynumber: 5.5 Consensus size: 29
24287454 CGACTCTTTT
*
24287464 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATACCA-TTTTAACCCCGATTTCACCG
*
24287494 AAAATTACCATTTTACCCCCGAATCTT--CC-
1 AAAA-TACCATTTTAACCCCG-AT-TTCACCG
* * *
24287523 AAAATTCCATTTTTAACCCCGACTTCACCAA
1 AAAATACCA-TTTTAACCCCGATTTCACC-G
* * ****
24287554 AAAATTACCATTTTACCCCCG-TATCTTTT
1 AAAA-TACCATTTTAACCCCGATTTCACCG
*
24287583 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATACCA-TTTTAACCCCGATTTCACCG
24287613 AAAATAACCATTTTA
1 AAAAT-ACCATTTTA
24287628 CCCTCGTATC
Statistics
Matches: 101, Mismatches: 21, Indels: 24
0.69 0.14 0.16
Matches are distributed among these distances:
27 2 0.02
28 9 0.09
29 30 0.30
30 31 0.31
31 23 0.23
32 6 0.06
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATACCATTTTAACCCCGATTTCACCG
Found at i:24287759 original size:28 final size:28
Alignment explanation
Indices: 24287702--24287761 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
24287692 CATATCTTTT
* *
24287702 AAAATTCCATTTTAACCCCGATTTTACC
1 AAAATTCCATTTTAACCCCGAGTATACC
**
24287730 AAAATTACCATTTTGCCCCCGAGTAT-CC
1 AAAATT-CCATTTTAACCCCGAGTATACC
24287758 AAAA
1 AAAA
24287762 GTCTCGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCGAGTATACC
Found at i:24289040 original size:10 final size:11
Alignment explanation
Indices: 24289017--24289042 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
24289007 GTTCTTTTAA
24289017 TTTTATTCATT
1 TTTTATTCATT
24289028 TTTTATTCATT
1 TTTTATTCATT
24289039 TTTT
1 TTTT
24289043 TTATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTCATT
Found at i:24289044 original size:13 final size:13
Alignment explanation
Indices: 24289017--24289053 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
24289007 GTTCTTTTAA
24289017 TTTTATTCA--TT
1 TTTTATTCATTTT
24289028 TTTTATTCATTTT
1 TTTTATTCATTTT
*
24289041 TTTTATTTATTTT
1 TTTTATTCATTTT
24289054 GAACTTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTCATTTT
Found at i:24295183 original size:53 final size:51
Alignment explanation
Indices: 24295053--24295195 Score: 151
Period size: 51 Copynumber: 2.8 Consensus size: 51
24295043 ATTGATATAA
* * * * *
24295053 TAACAATTTTAACCTTCAAAGTTTACACATTTTGTCAATTTGATCTTGACT
1 TAACAAATTTAACCTACAAAATTTACACATTCTGTCAACTTGATCTTGACT
* * * *
24295104 TAACAAATTTAGCCTACAACATTTACACATTCTGTCAGCTTGATCCTCTGATT
1 TAACAAATTTAACCTACAAAATTTACACATTCTGTCAACTTGAT-CT-TGACT
* * * *
24295157 TAACAAATTTAACCTGCAAAACTTACATACTCTGTCAAC
1 TAACAAATTTAACCTACAAAATTTACACATTCTGTCAAC
24295196 ATTTATGTAA
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
51 36 0.49
52 2 0.03
53 36 0.49
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (51 bp):
TAACAAATTTAACCTACAAAATTTACACATTCTGTCAACTTGATCTTGACT
Found at i:24306350 original size:18 final size:16
Alignment explanation
Indices: 24306318--24306361 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
24306308 ATGGAATGAG
24306318 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
24306334 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
24306348 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
24306362 ACCCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:24306624 original size:31 final size:31
Alignment explanation
Indices: 24306589--24306676 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 31
24306579 GTGATCACTT
*
24306589 CGTAACATAATACTAACATAAGTGACTAAAA
1 CGTAACATAATACAAACATAAGTGACTAAAA
* *
24306620 CGTAACAT--TTCAAACATAAGTGACTACAA
1 CGTAACATAATACAAACATAAGTGACTAAAA
* * * *
24306649 TGTAATATAAGACAAACAAAAGTGACTA
1 CGTAACATAATACAAACATAAGTGACTA
24306677 TTTTTATAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 24 0.51
31 23 0.49
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (31 bp):
CGTAACATAATACAAACATAAGTGACTAAAA
Found at i:24307095 original size:25 final size:26
Alignment explanation
Indices: 24307059--24307122 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 26
24307049 AAGTTCACAC
*
24307059 ATATTATTTTTTAA-ATTTAAAAAAT
1 ATATTATATTTTAATATTTAAAAAAT
*
24307084 ATATTATATTTTTTAATATTTAATAAAT
1 ATATTATA--TTTTAATATTTAAAAAAT
*
24307112 TTA-TATATTTT
1 ATATTATATTTT
24307123 TTATTTATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 11 0.33
27 10 0.30
28 12 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATTATATTTTAATATTTAAAAAAT
Found at i:24307131 original size:28 final size:28
Alignment explanation
Indices: 24307063--24307125 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
24307053 TCACACATAT
24307063 TATTTTTTAA-ATTTAAAAAATATATTA
1 TATTTTTTAATATTTAAAAAATATATTA
* *
24307090 TATTTTTTAATATTTAATAAATTTA-TA
1 TATTTTTTAATATTTAAAAAATATATTA
24307117 TATTTTTTA
1 TATTTTTTA
24307126 TTTATTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATTTTTTAATATTTAAAAAATATATTA
Found at i:24307758 original size:15 final size:16
Alignment explanation
Indices: 24307727--24307762 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
24307717 CATTTGTTTT
*
24307727 AAATATTAAATTTAAA
1 AAATATTAAACTTAAA
24307743 AAATATT-AACTTAAA
1 AAATATTAAACTTAAA
24307758 AAATA
1 AAATA
24307763 GTTATAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATTAAACTTAAA
Found at i:24307850 original size:24 final size:25
Alignment explanation
Indices: 24307818--24307865 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
24307808 ACTAATTTAT
24307818 AATATAAATAGTATATAACTTAATA
1 AATATAAATAGTATATAACTTAATA
* * *
24307843 AATA-AAATATTATTTAATTTAAT
1 AATATAAATAGTATATAACTTAAT
24307866 TTAAATGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AATATAAATAGTATATAACTTAATA
Found at i:24307924 original size:24 final size:22
Alignment explanation
Indices: 24307884--24307931 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
24307874 AAAAATAATT
*
24307884 TTTTTAATTTCTATTTATTTAA
1 TTTTTAATTTCTATTTATCTAA
*
24307906 TTTTTAATTTTTATGTTTATCTAA
1 TTTTTAATTTCTA--TTTATCTAA
24307930 TT
1 TT
24307932 AAATATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
24 10 0.45
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTAATTTCTATTTATCTAA
Found at i:24309529 original size:16 final size:16
Alignment explanation
Indices: 24309506--24309561 Score: 103
Period size: 16 Copynumber: 3.5 Consensus size: 16
24309496 CGTTTGGTTC
24309506 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
24309522 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
24309538 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
24309554 GCTGTAAT
1 GCTGTAAT
24309562 CAGTAATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.32, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:24309596 original size:46 final size:44
Alignment explanation
Indices: 24309543--24309636 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
24309533 ATAGAGCTGT
* *
24309543 AATGGAATAGAGCTGTAATCAGTAATTCAGT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-GTGTGTTTGGTTGAATGG
*
24309589 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCGTGTGTTTGGTTGAATGG
24309633 AATG
1 AATG
24309637 ATACTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCGTGTGTTTGGTTGAATGG
Found at i:24309776 original size:17 final size:16
Alignment explanation
Indices: 24309743--24309836 Score: 59
Period size: 16 Copynumber: 6.0 Consensus size: 16
24309733 GATTATTATT
24309743 AAATATAATTTAATAA
1 AAATATAATTTAATAA
*
24309759 AAATATTAA-TTAATTA
1 AAATA-TAATTTAATAA
* * *
24309775 AATTATATTTTAATAT
1 AAATATAATTTAATAA
* * *
24309791 AATTATTATTAAAT-A
1 AAATATAATTTAATAA
* **
24309806 AAATTTAATAAAAT-A
1 AAATATAATTTAATAA
*
24309821 ATATATAATTTAATAA
1 AAATATAATTTAATAA
24309837 TATTTTTAAC
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
15 23 0.40
16 32 0.55
17 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATAATTTAATAA
Found at i:24309789 original size:32 final size:30
Alignment explanation
Indices: 24309734--24309835 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
24309724 TTTCAATAAG
24309734 ATTATT-ATTAAATATAATTTAATAAAAAT
1 ATTATTAATTAAATATAATTTAATAAAAAT
* *
24309763 ATTAATTAATTAAATTATATTTTAAT--ATA-
1 ATT-ATTAATTAAA-TATAATTTAATAAAAAT
*
24309792 ATTATT-ATTAAATAAAATTTAAT-AAAAT
1 ATTATTAATTAAATATAATTTAATAAAAAT
* *
24309820 AATATATAATTTAATA
1 ATTAT-TAATTAAATA
24309836 ATATTTTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
26 9 0.15
27 8 0.14
28 7 0.12
29 7 0.12
30 12 0.20
31 6 0.10
32 10 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTATTAATTAAATATAATTTAATAAAAAT
Found at i:24309796 original size:58 final size:59
Alignment explanation
Indices: 24309734--24309888 Score: 183
Period size: 58 Copynumber: 2.6 Consensus size: 59
24309724 TTTCAATAAG
* * *
24309734 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTAAATTATA-TTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTAAATAATATTTTTAACATA
* *
24309792 ATTATTATTAAATAAAATTTAAT-AAAATAATATATAATTTAATAATATTTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTAAATAATATTTTTAACATA
* *
24309850 ATTATTATTAAAATATGAA-TTAGTAAAAATTATAATATA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
24309889 TAATATTAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
57 19 0.23
58 41 0.49
59 9 0.11
60 9 0.11
61 5 0.06
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTAAATAATATTTTTAACATA
Found at i:24309882 original size:25 final size:24
Alignment explanation
Indices: 24309853--24309903 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
24309843 TAACATAATT
*
24309853 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
24309878 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
24309902 AT
1 AT
24309904 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:24317200 original size:21 final size:20
Alignment explanation
Indices: 24317159--24317211 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
24317149 TTCAAATTCA
* *
24317159 TATTATATTATTTATGTTATT
1 TATTATTTTATTTATGATA-T
24317180 TATTATTTTATTTCAT-ATAT
1 TATTATTTTATTT-ATGATAT
24317200 TATGTATTTTAT
1 TAT-TATTTTAT
24317212 ATAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.14
21 22 0.79
22 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (20 bp):
TATTATTTTATTTATGATAT
Found at i:24330307 original size:9 final size:9
Alignment explanation
Indices: 24330293--24330338 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
24330283 TTTAAAATTA
24330293 TATTATTTT
1 TATTATTTT
24330302 TATTATTTT
1 TATTATTTT
* *
24330311 AAATATTTT
1 TATTATTTT
24330320 TATAATATTTT
1 TAT--TATTTT
24330331 TATTATTT
1 TATTATTT
24330339 ATTAACGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 22 0.71
11 9 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TATTATTTT
Found at i:24330328 original size:11 final size:11
Alignment explanation
Indices: 24330290--24330333 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
24330280 TTTTTTAAAA
*
24330290 TTATATTATTT
1 TTATAATATTT
24330301 TTAT--TA-TT
1 TTATAATATTT
24330309 TTA-AATATTT
1 TTATAATATTT
24330319 TTATAATATTT
1 TTATAATATTT
24330330 TTAT
1 TTAT
24330334 TATTTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 5 0.17
9 4 0.14
10 5 0.17
11 15 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATAATATTT
Found at i:24330337 original size:20 final size:18
Alignment explanation
Indices: 24330293--24330338 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
24330283 TTTAAAATTA
24330293 TATTATTTTTATTATTTT
1 TATTATTTTTATTATTTT
* *
24330311 AAATATTTTTATAATATTTT
1 TATTATTTTTAT--TATTTT
24330331 TATTATTT
1 TATTATTT
24330339 ATTAACGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTATTTTTATTATTTT
Found at i:24332339 original size:17 final size:18
Alignment explanation
Indices: 24332317--24332357 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
24332307 TTGGATATTG
24332317 TATAAAATTTATT-TTAT
1 TATAAAATTTATTATTAT
*
24332334 TATAAATTTTATTATTAT
1 TATAAAATTTATTATTAT
*
24332352 TTTAAA
1 TATAAA
24332358 GGCATTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATAAAATTTATTATTAT
Found at i:24335120 original size:26 final size:26
Alignment explanation
Indices: 24335091--24335143 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
24335081 TCTTATATAT
24335091 AACATTACACAAATTGATCGGTCGAA
1 AACATTACACAAATTGATCGGTCGAA
*
24335117 AACATTGCACAAATTGATCGGTCGAA
1 AACATTACACAAATTGATCGGTCGAA
24335143 A
1 A
24335144 CTGACCCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (26 bp):
AACATTACACAAATTGATCGGTCGAA
Found at i:24337972 original size:11 final size:11
Alignment explanation
Indices: 24337952--24337985 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
24337942 AATGCATTAT
*
24337952 ATTATTTAAAA
1 ATTATATAAAA
24337963 ATTATATAAAA
1 ATTATATAAAA
*
24337974 ATAATATAAAA
1 ATTATATAAAA
24337985 A
1 A
24337986 ATTAATATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTATATAAAA
Found at i:24338466 original size:7 final size:7
Alignment explanation
Indices: 24338450--24338510 Score: 106
Period size: 7 Copynumber: 8.9 Consensus size: 7
24338440 TAAAATTATA
24338450 AAATTT-
1 AAATTTC
24338456 AAATTTC
1 AAATTTC
24338463 AAATTTC
1 AAATTTC
24338470 AAATTTC
1 AAATTTC
24338477 AAATTTC
1 AAATTTC
24338484 AAATTTC
1 AAATTTC
24338491 AAATTTC
1 AAATTTC
*
24338498 AAATTTT
1 AAATTTC
24338505 AAATTT
1 AAATTT
24338511 ATAAAAAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
6 6 0.11
7 47 0.89
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (7 bp):
AAATTTC
Found at i:24340377 original size:15 final size:16
Alignment explanation
Indices: 24340359--24340393 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
24340349 TTATCTCGAT
*
24340359 TATATTTATAA-TAAA
1 TATATTTACAAGTAAA
24340374 TATATTTACAAGTAAA
1 TATATTTACAAGTAAA
24340390 TATA
1 TATA
24340394 AATTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (16 bp):
TATATTTACAAGTAAA
Found at i:24345528 original size:29 final size:29
Alignment explanation
Indices: 24345496--24345581 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
24345486 CCAAATATAG
**
24345496 ATATAATATGGATACAGTTACAGATGCAA
1 ATATAATACAGATACAGTTACAGATGCAA
*
24345525 ATATAATACAGATACAGTTACAAATGCAA
1 ATATAATACAGATACAGTTACAGATGCAA
*
24345554 ATATAATACAGATATAGTTACAGATGCA
1 ATATAATACAGATACAGTTACAGATGCA
24345582 GATTCCTACC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.27
Consensus pattern (29 bp):
ATATAATACAGATACAGTTACAGATGCAA
Found at i:24346532 original size:21 final size:21
Alignment explanation
Indices: 24346484--24346534 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
24346474 GTAGTAGTTT
**
24346484 TACCGATACAAGTATGGTTTC
1 TACCGATACAAGTATGGTAAC
*
24346505 TATCGATACAAGTCAT-GTAAC
1 TACCGATACAAGT-ATGGTAAC
24346526 TACCGATAC
1 TACCGATAC
24346535 CAAAAACTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (21 bp):
TACCGATACAAGTATGGTAAC
Found at i:24353591 original size:30 final size:30
Alignment explanation
Indices: 24353557--24353646 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
24353547 GCTGCTAAAG
* *
24353557 TTTAATTTACACCCAAAT-ACGCCGTTACCC
1 TTTAATTTACA-CCAAATAAAGCCGTTAACC
**
24353587 TTTAATTGGCACCAAATAAAGCCGTTAACC
1 TTTAATTTACACCAAATAAAGCCGTTAACC
* * * *
24353617 ATTAATATACACCAAATTAAGCCATTAACC
1 TTTAATTTACACCAAATAAAGCCGTTAACC
24353647 ATAAATTTGT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
29 6 0.12
30 43 0.88
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.28
Consensus pattern (30 bp):
TTTAATTTACACCAAATAAAGCCGTTAACC
Found at i:24354194 original size:15 final size:15
Alignment explanation
Indices: 24354174--24354206 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
24354164 CGACAATCAT
24354174 ACAGGAGTCCAAATA
1 ACAGGAGTCCAAATA
24354189 ACAGGAGTCCAAATA
1 ACAGGAGTCCAAATA
24354204 ACA
1 ACA
24354207 TAAGATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (15 bp):
ACAGGAGTCCAAATA
Found at i:24362241 original size:29 final size:29
Alignment explanation
Indices: 24362200--24362255 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
24362190 TAGCATAATT
*
24362200 ATTGATATAACAT-TATTTTATATTTATAC
1 ATTGATATAACATATA-ATTATATTTATAC
24362229 ATTGCATAT-ACATATAATTATATTTAT
1 ATTG-ATATAACATATAATTATATTTAT
24362256 CCAATATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (29 bp):
ATTGATATAACATATAATTATATTTATAC
Found at i:24364986 original size:13 final size:15
Alignment explanation
Indices: 24364954--24364988 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
24364944 ACTCATGTAT
24364954 AAAAATATATCAAAC
1 AAAAATATATCAAAC
*
24364969 AAAAATATTTC-AAC
1 AAAAATATATCAAAC
24364983 AAAAAT
1 AAAAAT
24364989 GAAAAATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATATATCAAAC
Found at i:24368545 original size:55 final size:54
Alignment explanation
Indices: 24368322--24368545 Score: 189
Period size: 55 Copynumber: 4.0 Consensus size: 54
24368312 AAAAATTTGC
* * * * * *
24368322 ATGGCCGACACCCCTTTTTTGTCAGAAAAAATATAATTTTTTGGTGTTGGCCATTAA
1 ATGGTCGACACCCC-CTTTTCTCA-AAAAAAT-TCATTTTTGGGTGTTGGCCATCAA
* * * ***
24368379 ATGG-CTGACACCCCATTTTCTCGAAAAAATTGCATTTTTGGGTGTTGACCATTGC
1 ATGGTC-GACACCCCCTTTTCTCAAAAAAATT-CATTTTTGGGTGTTGGCCATCAA
*** *
24368434 ATGGTCGACACCCCCTGTTTGAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
1 ATGGTCGACACCCCCT-TTT-CTCAAAAAAATTC---ATTTTTGGGTGTTGGCCATCAA
*
24368493 ATGGTCGACACCCCCTTTTCTCAAAAAAATTGCATTTTTGGGTGTCGGCCATC
1 ATGGTCGACACCCCCTTTTCTCAAAAAAATT-CATTTTTGGGTGTTGGCCATC
24368546 CTATTCTCGA
Statistics
Matches: 135, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
54 1 0.01
55 56 0.41
56 12 0.09
57 29 0.21
58 4 0.03
59 33 0.24
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (54 bp):
ATGGTCGACACCCCCTTTTCTCAAAAAAATTCATTTTTGGGTGTTGGCCATCAA
Found at i:24368647 original size:61 final size:62
Alignment explanation
Indices: 24368549--24368725 Score: 229
Period size: 61 Copynumber: 2.9 Consensus size: 62
24368539 GGCCATCCTA
* * *
24368549 TTCTCGAGAAAAAAATTTAAAATTTTTTTGGTGTTGGCCATCAAATGGT-CGACACTCCCTTT
1 TTCTCGAGAAAAAAAATTCAAATTTTTTTCGTGTTGGCCATCAAATGGTCCGACAC-CCCTTT
*
24368611 TT-TCGAGAAAAAAAATTCAAATTTTTTTCATGTTGGCCATCAAAT-GTCCGACACCCCTTT
1 TTCTCGAGAAAAAAAATTCAAATTTTTTTCGTGTTGGCCATCAAATGGTCCGACACCCCTTT
*
24368671 TTCTCGA-ATAAAAAAATTCTAAATTTTTTTTTTGTGTTGGCCATCAAATGG-CCGA
1 TTCTCGAGA-AAAAAAATTC-AAA--TTTTTTTCGTGTTGGCCATCAAATGGTCCGA
24368726 TACCAACTTC
Statistics
Matches: 102, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
60 11 0.11
61 59 0.58
62 5 0.05
64 26 0.25
65 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (62 bp):
TTCTCGAGAAAAAAAATTCAAATTTTTTTCGTGTTGGCCATCAAATGGTCCGACACCCCTTT
Found at i:24369562 original size:17 final size:17
Alignment explanation
Indices: 24369542--24369592 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
24369532 AAAAAATAAT
24369542 AATTAGAATATACAAGA
1 AATTAGAATATACAAGA
*
24369559 AATTAG-A-A-AGAA-A
1 AATTAGAATATACAAGA
*
24369572 AATTAAAATATACAAGA
1 AATTAGAATATACAAGA
24369589 AATT
1 AATT
24369593 TGAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 2 0.07
16 4 0.15
17 11 0.41
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.24
Consensus pattern (17 bp):
AATTAGAATATACAAGA
Found at i:24369608 original size:30 final size:30
Alignment explanation
Indices: 24369548--24369639 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
24369538 TAATAATTAG
** *
24369548 AATATACAAGAAATTAGAAAGAAAAATTAA
1 AATATACAAGAAATTAGAAATTAAATTTAA
*
24369578 AATATACAAGAAATTTGAAATTAAATTTAA
1 AATATACAAGAAATTAGAAATTAAATTTAA
* * *
24369608 ACTA-AAAACGAAATTACAAATTAAATTTAA
1 AATATACAA-GAAATTAGAAATTAAATTTAA
24369638 AA
1 AA
24369640 AGTAAAGGGA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 3 0.06
30 49 0.94
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (30 bp):
AATATACAAGAAATTAGAAATTAAATTTAA
Found at i:24371888 original size:10 final size:10
Alignment explanation
Indices: 24371856--24371907 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
24371846 TGAAACTTGA
24371856 TCAACGGCGG
1 TCAACGGCGG
* * *
24371866 ACAAAGTCGG
1 TCAACGGCGG
24371876 TCAACGGCGG
1 TCAACGGCGG
**
24371886 TCAACGATGG
1 TCAACGGCGG
*
24371896 TCAATGGCGG
1 TCAACGGCGG
24371906 TC
1 TC
24371908 TCAGGACGTT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (10 bp):
TCAACGGCGG
Found at i:24371897 original size:20 final size:20
Alignment explanation
Indices: 24371856--24371907 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
24371846 TGAAACTTGA
*
24371856 TCAACGGCGGACAAAGTCGG
1 TCAACGGCGGTCAAAGTCGG
*
24371876 TCAACGGCGGTCAACGAT-GG
1 TCAACGGCGGTCAAAG-TCGG
*
24371896 TCAATGGCGGTC
1 TCAACGGCGGTC
24371908 TCAGGACGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (20 bp):
TCAACGGCGGTCAAAGTCGG
Found at i:24371967 original size:22 final size:22
Alignment explanation
Indices: 24371919--24371973 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
24371909 CAGGACGTTG
* **
24371919 GTGAGCTGGAATTTTGGTTTTT
1 GTGAGCTGGAATATTGGTTTAA
*
24371941 CTGAGCTGGAATATTGGTTTAA
1 GTGAGCTGGAATATTGGTTTAA
*
24371963 GTGAGGTGGAA
1 GTGAGCTGGAA
24371974 AGTGGGTGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38
Consensus pattern (22 bp):
GTGAGCTGGAATATTGGTTTAA
Found at i:24372388 original size:175 final size:175
Alignment explanation
Indices: 24372084--24372441 Score: 648
Period size: 175 Copynumber: 2.0 Consensus size: 175
24372074 ATAAAAATTG
24372084 TAAT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACA
1 TAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACA
*
24372148 TTTAAAATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATA
66 ATT--AATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATA
*
24372213 AATAATGTATTGTCAAATCAACATATTATATGATAAAAATTATAATA
129 AATAATGTATTGTCAAATCAACACATTATATGATAAAAATTATAATA
24372260 TAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACA
1 TAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACA
24372325 CATT-ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAA
66 -ATTAATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAA
*
24372389 ATAATGTATTGTCGAATCAACACATTATATGATAAAAATTATAATA
130 ATAATGTATTGTCAAATCAACACATTATATGATAAAAATTATAATA
24372435 TAATAAT
1 TAATAAT
24372442 TGTTGAAACC
Statistics
Matches: 177, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
175 111 0.63
176 4 0.02
177 60 0.34
178 2 0.01
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (175 bp):
TAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACA
ATTAATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAA
TAATGTATTGTCAAATCAACACATTATATGATAAAAATTATAATA
Found at i:24372407 original size:86 final size:86
Alignment explanation
Indices: 24372069--24372441 Score: 619
Period size: 86 Copynumber: 4.3 Consensus size: 86
24372059 TAAATTTAAA
24372069 ATATGATAAAAATTGT-A-AT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
*
24372131 GTATTGTCAAATCAACA-TTT
66 GTATTGTCAAATCAACACATT
24372151 AAAATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
1 ---ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
*
24372216 AATGTATTGTCAAATCAACATATT
63 AATGTATTGTCAAATCAACACATT
*
24372240 ATATGATAAAAATTATAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
1 ATATGATAAAAATTGT-A-AT-ATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
24372305 AATGTATTGTCAAATCAACACATT
63 AATGTATTGTCAAATCAACACATT
24372329 ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
*
24372394 GTATTGTCGAATCAACACATT
66 GTATTGTCAAATCAACACATT
*
24372415 ATATGATAAAAATTATAATATAATAAT
1 ATATGATAAAAATTGTAATATAATAAT
24372442 TGTTGAAACC
Statistics
Matches: 275, Mismatches: 6, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
85 16 0.06
86 108 0.39
87 5 0.02
88 63 0.23
89 83 0.30
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.39
Consensus pattern (86 bp):
ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
GTATTGTCAAATCAACACATT
Found at i:24373710 original size:29 final size:30
Alignment explanation
Indices: 24373678--24373953 Score: 107
Period size: 30 Copynumber: 9.4 Consensus size: 30
24373668 TTGACTTTTT
*
24373678 GGGGTAAAAATGTAATTTTTGGTGAAA-TC
1 GGGGTAAAAATGTAATTTTTGGTAAAATTC
* *
24373707 GGGGTCAAAAATG-AAATTTTGG-AAAATTT
1 GGGGT-AAAAATGTAATTTTTGGTAAAATTC
*
24373736 GAGGGT-AAAATGGTAATTTTTGGTAAAAAT-
1 G-GGGTAAAAAT-GTAATTTTTGGTAAAATTC
* * ** * *
24373766 AGGGT-CAAATGGGA-TTTTGG-AAAGTTTA
1 GGGGTAAAAATGTAATTTTTGGTAAA-ATTC
* *
24373794 GGGGT-AAAATGATAATTTTTGGTGAAATTA
1 GGGGTAAAAATG-TAATTTTTGGTAAAATTC
* * ** **
24373824 GGGTTAAAAGTGGGA-TTTTGG-AAGGTTTC
1 GGGGTAAAAATGTAATTTTTGGTAA-AATTC
* *
24373853 GGGGT-AAAATAGTAATTTTTGGTGAAA-CC
1 GGGGTAAAAAT-GTAATTTTTGGTAAAATTC
** *
24373882 GAGGGTAAAAATGGGA-TTTTGG-AAAGTTC
1 G-GGGTAAAAATGTAATTTTTGGTAAAATTC
* * *
24373911 GGGGGT-AAAATGGTAATTTTGGGTGAAATTA
1 -GGGGTAAAAAT-GTAATTTTTGGTAAAATTC
*
24373942 GGGTTAAAAATG
1 GGGGTAAAAATG
24373954 GAATCTTGGA
Statistics
Matches: 178, Mismatches: 45, Indels: 47
0.66 0.17 0.17
Matches are distributed among these distances:
26 3 0.02
27 7 0.04
28 31 0.17
29 54 0.30
30 56 0.31
31 27 0.15
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (30 bp):
GGGGTAAAAATGTAATTTTTGGTAAAATTC
Found at i:24373743 original size:59 final size:58
Alignment explanation
Indices: 24373675--24374107 Score: 398
Period size: 59 Copynumber: 7.4 Consensus size: 58
24373665 TTTTTGACTT
* * *
24373675 TTTGGGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTTGGAAAA
1 TTTGGGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAG
* *
24373733 TTTGAGGGTAAAATGGTAATTTTTGGTAAAAAT-AGGGTC--AAATGGGATTTTGGAAAG
1 TTTG-GGGTAAAATGGTAATTTTTGGT-GAAATCAGGGTCAAAAATGGAATTTTGGAAAG
* * * * * *
24373790 TTTAGGGGTAAAATGATAATTTTTGGTGAAATTAGGGTTAAAAGTGGGATTTTGGAAGG
1 TTT-GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAG
* * *
24373849 TTTCGGGGTAAAATAGTAATTTTTGGTGAAACCGAGGGT-AAAAATGGGATTTTGGAAAG
1 TTT-GGGGTAAAATGGTAATTTTTGGTGAAATC-AGGGTCAAAAATGGAATTTTGGAAAG
* * * * * *
24373908 TTCGGGGGTAAAATGGTAATTTTGGGTGAAATTAGGGTTAAAAATGGAATCTTGGAAGG
1 TT-TGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAG
* *
24373967 TTAGGGGGTAAAATGGTAATTTTGGGTGAAATC-GAGGTCAAAAATGGAATTTTGGAAAG
1 TT-TGGGGTAAAATGGTAATTTTTGGTGAAATCAG-GGTCAAAAATGGAATTTTGGAAAG
* *** * * * *
24374026 TTTGGGGGAAAAACAATAATTTTT-G-GAAGTTTTAAGGTTAAAAATGGAATTTTGGAAAG
1 TTT-GGGGTAAAATGGTAATTTTTGGTGAA--ATCAGGGTCAAAAATGGAATTTTGGAAAG
24374085 TTTCGGGGTTAAAAATGG-AATTT
1 TTT-GGGG-T-AAAATGGTAATTT
24374108 GGGAAAGTTT
Statistics
Matches: 313, Mismatches: 45, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
56 4 0.01
57 47 0.15
58 17 0.05
59 227 0.73
60 14 0.04
61 4 0.01
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.33
Consensus pattern (58 bp):
TTTGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAG
Found at i:24373825 original size:30 final size:29
Alignment explanation
Indices: 24373678--24373998 Score: 109
Period size: 29 Copynumber: 10.9 Consensus size: 29
24373668 TTGACTTTTT
*
24373678 GGGGTAAAAATGTAATTTTTGGTGAAA-TC
1 GGGGT-AAAATGTAATTTTTGGTGAAATTA
* * *
24373707 GGGGTCAAAAATG-AAATTTTGG-AAAATTT
1 GGGGT--AAAATGTAATTTTTGGTGAAATTA
* *
24373736 GAGGGTAAAATGGTAATTTTTGGTAAAAATA
1 G-GGGTAAAAT-GTAATTTTTGGTGAAATTA
* **
24373767 -GGGTCAAATGGGA-TTTT-G-GAAAGTTTA
1 GGGGTAAAATGTAATTTTTGGTGAAA--TTA
24373794 GGGGTAAAATGATAATTTTTGGTGAAATTA
1 GGGGTAAAATG-TAATTTTTGGTGAAATTA
* ** * *
24373824 GGGTTAAAAGTGGGA-TTTT-G-GAAGGTTTC
1 GGGGTAAAA-TGTAATTTTTGGTGAA--ATTA
**
24373853 GGGGTAAAATAGTAATTTTTGGTGAAA-CC
1 GGGGTAAAAT-GTAATTTTTGGTGAAATTA
** *
24373882 GAGGGTAAAAATGGGA-TTTT-G-GAAAGTTCG
1 G-GGGT-AAAATGTAATTTTTGGTGAAA-TT-A
*
24373912 GGGGTAAAATGGTAATTTTGGGTGAAATTA
1 GGGGTAAAAT-GTAATTTTTGGTGAAATTA
* * * *
24373942 GGGTTAAAAATGGAA-TCTT-G-GAAGGTTA
1 GGGGT-AAAATGTAATTTTTGGTGAA-ATTA
*
24373970 GGGGGTAAAATGGTAATTTTGGGTGAAAT
1 -GGGGTAAAAT-GTAATTTTTGGTGAAAT
24373999 CGAGGTCAAA
Statistics
Matches: 214, Mismatches: 42, Indels: 70
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.01
26 1 0.00
27 16 0.07
28 36 0.17
29 62 0.29
30 58 0.27
31 24 0.11
32 14 0.07
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.32
Consensus pattern (29 bp):
GGGGTAAAATGTAATTTTTGGTGAAATTA
Found at i:24373937 original size:118 final size:117
Alignment explanation
Indices: 24373678--24374107 Score: 460
Period size: 118 Copynumber: 3.6 Consensus size: 117
24373668 TTGACTTTTT
** * * **
24373678 GGGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTTGGAAAATTTGAGGGT
1 GGGGT-AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGGTTTG-GGGT
** * *
24373742 AAAATGGTAATTTTTGGT-AAAAATAGGGT-CAAATGGGATTTTGGAAAGTTTA
64 AAAATGGTAATTTTTGGTGAAAACGAGGGTAAAAATGGGATTTTGGAAAGTTTG
* * *
24373794 GGGGTAAAATGATAATTTTTGGTGAAATTAGGGTTAAAAGTGGGATTTTGGAAGGTTTCGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGGTTT-GGGGTA
* * *
24373859 AAATAGTAATTTTTGGTGAAACCGAGGGTAAAAATGGGATTTTGGAAAGTTCG
65 AAATGGTAATTTTTGGTGAAAACGAGGGTAAAAATGGGATTTTGGAAAGTTTG
* * *
24373912 GGGGTAAAATGGTAATTTTGGGTGAAATTAGGGTTAAAAATGGAATCTTGGAAGGTTAGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGGTT-TGGGGTA
* * *
24373977 AAATGGTAATTTTGGGTGAAATCGA-GGTCAAAAATGGAATTTTGGAAAGTTTG
65 AAATGGTAATTTTTGGTGAAAACGAGGGT-AAAAATGGGATTTTGGAAAGTTTG
* *** * * *
24374030 GGGGAAAAACAATAATTTTT-G-GAAGTTTTAAGGTTAAAAATGGAATTTTGGAAAGTTTCGGGG
1 GGGGTAAAATGGTAATTTTTGGTGAA--ATTAGGGTTAAAAATGGAATTTTGGAAGGTTT-GGGG
24374093 TTAAAAATGG-AATTT
63 -T-AAAATGGTAATTT
24374108 GGGAAAGTTT
Statistics
Matches: 266, Mismatches: 37, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
115 5 0.02
116 67 0.25
117 13 0.05
118 168 0.63
119 6 0.02
120 7 0.03
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGGTTTGGGGTAA
AATGGTAATTTTTGGTGAAAACGAGGGTAAAAATGGGATTTTGGAAAGTTTG
Found at i:24373991 original size:29 final size:28
Alignment explanation
Indices: 24373884--24374121 Score: 101
Period size: 30 Copynumber: 8.1 Consensus size: 28
24373874 GTGAAACCGA
* *
24373884 GGGTAAAAATGGGATTTTGGAAAGTTCGG
1 GGGTAAAAATGGAATTTTGG-AAGTTAGG
*
24373913 GGGT-AAAATGGTAATTTTGGGTGAAATTA-G
1 GGGTAAAAATGG-AATTTT--G-GAAGTTAGG
* *
24373943 GGTTAAAAATGGAATCTTGGAAGGTTAGG
1 GGGTAAAAATGGAATTTTGGAA-GTTAGG
** ** *
24373972 GGGT-AAAATGGTAATTTTGGGTGAAATCG
1 GGGTAAAAATGG-AATTTTGGAAGTTA-GG
* *
24374001 AGGTCAAAAATGGAATTTTGGAAAGTTTGG
1 GGGT-AAAAATGGAATTTTGG-AAGTTAGG
* *
24374031 GGGAAAAACAAT--AATTTTTGGAAGTTTTA-A
1 GGG-TAAA-AATGGAA-TTTTGGAAG--TTAGG
* *
24374061 GGTTAAAAATGGAATTTTGGAAAGTTTCGG
1 GGGTAAAAATGGAATTTTGG-AAG-TTAGG
* * *
24374091 GGTTAAAAATGGAATTTGGGAAAGTTTGG
1 GGGTAAAAATGGAATTTTGG-AAGTTAGG
24374120 GG
1 GG
24374122 ACTAGAGAGC
Statistics
Matches: 158, Mismatches: 30, Indels: 42
0.69 0.13 0.18
Matches are distributed among these distances:
27 3 0.02
28 23 0.15
29 47 0.30
30 59 0.37
31 25 0.16
32 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.31
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTGGAAGTTAGG
Found at i:24374054 original size:89 final size:87
Alignment explanation
Indices: 24373959--24374121 Score: 188
Period size: 89 Copynumber: 1.8 Consensus size: 87
24373949 AAATGGAATC
* *
24373959 TTGGAAG-GTTAGGGGGT-AAAATGGTAATTTTGGGTGAAA-TCGAGGTCAAAAATGGAATTTTG
1 TTGGAAGTGTTA-AGGGTAAAAATGG-AATTTT--G-GAAATTCGAGGTCAAAAATGGAATTTGG
24374021 GAAAGTTTGGGGGAAAAACAATAATTT
61 GAAAGTTTGGGGGAAAAACAATAATTT
* * * *
24374048 TTGGAAGTTTTAAGGTTAAAAATGGAATTTTGGAAAGTTTCGGGGTTAAAAATGGAATTTGGGAA
1 TTGGAAGTGTTAAGGGTAAAAATGGAATTTTGGAAA--TTCGAGGTCAAAAATGGAATTTGGGAA
24374113 AGTTTGGGG
64 AGTTTGGGG
24374122 ACTAGAGAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
86 4 0.06
87 1 0.02
89 48 0.76
90 10 0.16
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.31
Consensus pattern (87 bp):
TTGGAAGTGTTAAGGGTAAAAATGGAATTTTGGAAATTCGAGGTCAAAAATGGAATTTGGGAAAG
TTTGGGGGAAAAACAATAATTT
Found at i:24375092 original size:12 final size:12
Alignment explanation
Indices: 24375077--24375106 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24375067 TTTCTTTTTT
24375077 TTATTATTAAAA
1 TTATTATTAAAA
24375089 TTATTATTAAAA
1 TTATTATTAAAA
*
24375101 ATATTA
1 TTATTA
24375107 ATATTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTATTATTAAAA
Found at i:24375118 original size:15 final size:15
Alignment explanation
Indices: 24375078--24375125 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
24375068 TTCTTTTTTT
*
24375078 TATTATTAAA-ATTAT
1 TATTA-TAAATATTAA
*
24375093 TATTAAAAATATTAA
1 TATTATAAATATTAA
24375108 TATTATAAATATTTAA
1 TATTATAAATA-TTAA
24375124 TA
1 TA
24375126 ATATTATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 3 0.11
15 19 0.68
16 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTATAAATATTAA
Found at i:24375882 original size:17 final size:17
Alignment explanation
Indices: 24375856--24375892 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
24375846 ACATTTAATT
*
24375856 TTTATTTTAAATTTAAA
1 TTTATATTAAATTTAAA
*
24375873 TTTATATTAAGTTTAAA
1 TTTATATTAAATTTAAA
24375890 TTT
1 TTT
24375893 TAGAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATATTAAATTTAAA
Found at i:24376085 original size:11 final size:11
Alignment explanation
Indices: 24376073--24376112 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
24376063 CTATATATAT
24376073 TTTTAAATA-A
1 TTTTAAATACA
24376083 TTTTAAATACA
1 TTTTAAATACA
**
24376094 TTTTAAATTTA
1 TTTTAAATACA
24376105 TTTTAAAT
1 TTTTAAAT
24376113 TTCAACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAATACA
Found at i:24376113 original size:11 final size:11
Alignment explanation
Indices: 24376073--24376128 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
24376063 CTATATATAT
*
24376073 TTTTAAA-TAA
1 TTTTAAATTTA
**
24376083 TTTTAAATACA
1 TTTTAAATTTA
24376094 TTTTAAATTTA
1 TTTTAAATTTA
24376105 TTTTAAATTTCAA
1 TTTTAAATTT--A
*
24376118 CTTTAAATTTA
1 TTTTAAATTTA
24376129 AAGTAGAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
10 7 0.18
11 21 0.55
13 10 0.26
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAATTTA
Done.