Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 23
Found at i:3321096 original size:23 final size:22
Alignment explanation
Indices: 3321048--3321096 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3321038 CCATAATGTC
3321048 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
3321069 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
3321092 AAGGA
1 AAGGA
3321097 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:3321912 original size:103 final size:103
Alignment explanation
Indices: 3321584--3321904 Score: 615
Period size: 103 Copynumber: 3.1 Consensus size: 103
3321574 GTCGAGGGTC
3321584 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
3321649 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
3321687 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3321752 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
3321790 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
3321855 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
3321893 TATGTGGTCCTT
1 TATGTGGTCCTT
3321905 ATGGACATTA
Statistics
Matches: 215, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 215 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:3321965 original size:47 final size:47
Alignment explanation
Indices: 3321911--3322030 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
3321901 CCTTATGGAC
* *
3321911 ATTATTATATGGCACTACGGTGCAATTCTACGCGGTACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCCACGCGGCACTCCGGTGCA
*
3321958 ATTATTATATGGCACTACGGTGCAATTCCACGCGGCACTCTGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCCACGCGGCACTCCGGTGCA
* *
3322005 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
3322031 ATATGAGCTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 20 0.29
47 48 0.71
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCCACGCGGCACTCCGGTGCA
Found at i:3322031 original size:23 final size:23
Alignment explanation
Indices: 3321911--3322035 Score: 108
Period size: 23 Copynumber: 5.3 Consensus size: 23
3321901 CCTTATGGAC
*
3321911 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
3321935 ATTCTACGCGGTACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
3321958 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
** * *
3321982 ATTCCACGCGGCACT-CTGGTGCA
1 ATTATATGTGGCACTAC-GGTGCA
*
3322005 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
3322028 ATTATATG
1 ATTATATG
3322036 AGCTGTGGTG
Statistics
Matches: 77, Mismatches: 21, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
22 1 0.01
23 55 0.71
24 21 0.27
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:3326826 original size:23 final size:22
Alignment explanation
Indices: 3326778--3326826 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3326768 CCAAAATGTC
3326778 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
3326799 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
3326822 AAGGA
1 AAGGA
3326827 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:3327588 original size:103 final size:103
Alignment explanation
Indices: 3327363--3327579 Score: 398
Period size: 103 Copynumber: 2.1 Consensus size: 103
3327353 GTCGAGGGTC
*
3327363 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
3327428 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
3327466 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
3327531 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
3327569 TATGTGGTCCT
1 TATGTGGTCCT
3327580 CATGGACATT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:3327641 original size:47 final size:47
Alignment explanation
Indices: 3327587--3327706 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
3327577 CCTCATGGAC
*
3327587 ATTATTATATGGCACTACGGTGTAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
*
3327634 ATTATTATATGGCACTATGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
3327681 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
3327707 ATATGAGTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 19 0.28
47 49 0.72
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:3327707 original size:23 final size:23
Alignment explanation
Indices: 3327587--3327711 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
3327577 CCTCATGGAC
* * *
3327587 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTCCGGTGCA
* * *
3327611 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
* **
3327634 ATTATTATATGGCACTATGGTGCA
1 ATTA-TATGTGGCACTCCGGTGCA
* * *
3327658 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
*
3327681 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
3327704 ATTATATG
1 ATTATATG
3327712 AGTTGTGGTG
Statistics
Matches: 78, Mismatches: 22, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
23 58 0.74
24 20 0.26
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTCCGGTGCA
Found at i:3334360 original size:9 final size:9
Alignment explanation
Indices: 3334346--3334385 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
3334336 CTGCTGGAAA
3334346 ACCGGTTTG
1 ACCGGTTTG
3334355 ACCGGTTTG
1 ACCGGTTTG
*
3334364 ACCGGTCTG
1 ACCGGTTTG
*
3334373 AACCGGGTTG
1 -ACCGGTTTG
3334383 ACC
1 ACC
3334386 CGACCCGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3334383 original size:19 final size:18
Alignment explanation
Indices: 3334346--3334385 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3334336 CTGCTGGAAA
* *
3334346 ACCGGTTTGACCGGTTTG
1 ACCGGTCTGACCGGGTTG
3334364 ACCGGTCTGAACCGGGTTG
1 ACCGGTCTG-ACCGGGTTG
3334383 ACC
1 ACC
3334386 CGACCCGACT
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:0.15, C:0.28, G:0.33, T:0.25
Consensus pattern (18 bp):
ACCGGTCTGACCGGGTTG
Found at i:3334401 original size:17 final size:17
Alignment explanation
Indices: 3334379--3334435 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
3334369 TCTGAACCGG
3334379 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
3334396 GTTGACCCGACCCGAAT
1 GTTGACCCGACCCGACT
* *
3334413 GTTGACCCGACCTGACC
1 GTTGACCCGACCCGACT
3334430 GTTGAC
1 GTTGAC
3334436 TGTGACCGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:3335400 original size:64 final size:63
Alignment explanation
Indices: 3335325--3335449 Score: 146
Period size: 64 Copynumber: 2.0 Consensus size: 63
3335315 CTAATGTGAC
* ** * *
3335325 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
3335388 TCTTAGGATAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGG-TAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
3335450 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
63 8 0.15
64 43 0.83
65 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:3341679 original size:9 final size:9
Alignment explanation
Indices: 3341647--3341716 Score: 59
Period size: 10 Copynumber: 7.3 Consensus size: 9
3341637 CTGATGGAAA
3341647 ACCGGTTTG
1 ACCGGTTTG
*
3341656 ACCAGTTTTG
1 ACC-GGTTTG
3341666 AACCGGTTTG
1 -ACCGGTTTG
* *
3341676 ACCGATCTTA
1 ACCGGT-TTG
3341686 ACCGGTTTG
1 ACCGGTTTG
*
3341695 ACCGGTCTG
1 ACCGGTTTG
*
3341704 AACCGGATTG
1 -ACCGGTTTG
3341714 ACC
1 ACC
3341717 CGACCCGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 21 0.44
10 24 0.50
11 3 0.06
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3341690 original size:19 final size:19
Alignment explanation
Indices: 3341646--3341716 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
3341636 GCTGATGGAA
*
3341646 AACCGGTTTGACC-AGTTTT
1 AACCGGTTTGACCGA-TCTT
3341665 GAACCGGTTTGACCGATCTT
1 -AACCGGTTTGACCGATCTT
* *
3341685 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGATCTT
*
3341704 AACCGGATTGACC
1 AACCGGTTTGACC
3341717 CGACCCGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 29 0.63
20 16 0.35
21 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGATCTT
Found at i:3341733 original size:17 final size:17
Alignment explanation
Indices: 3341711--3341767 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
3341701 CTGAACCGGA
3341711 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACTG
*
3341728 TTGACCCGACCCGAATG
1 TTGACCCGACCCGACTG
* * *
3341745 TTGACCTGACCTGACCG
1 TTGACCCGACCCGACTG
3341762 TTGACC
1 TTGACC
3341768 GTTGACTGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.19, C:0.37, G:0.23, T:0.21
Consensus pattern (17 bp):
TTGACCCGACCCGACTG
Found at i:3341768 original size:7 final size:7
Alignment explanation
Indices: 3341756--3341793 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
3341746 TGACCTGACC
3341756 TGACCGT
1 TGACCGT
3341763 TGACCGT
1 TGACCGT
*
3341770 TGACTG-
1 TGACCGT
3341776 TGACCGT
1 TGACCGT
3341783 TGACCGT
1 TGACCGT
3341790 TGAC
1 TGAC
3341794 TTTCTTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
TGACCGT
Found at i:3341781 original size:20 final size:20
Alignment explanation
Indices: 3341756--3341794 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3341746 TGACCTGACC
3341756 TGACCGTTGACCGTTGACTG
1 TGACCGTTGACCGTTGACTG
3341776 TGACCGTTGACCGTTGACT
1 TGACCGTTGACCGTTGACT
3341795 TTCTTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (20 bp):
TGACCGTTGACCGTTGACTG
Found at i:3342731 original size:63 final size:63
Alignment explanation
Indices: 3342663--3342786 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
3342653 CTAATGTGAC
* ** * *
3342663 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
3342726 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
3342787 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:3346995 original size:2 final size:2
Alignment explanation
Indices: 3346988--3347074 Score: 129
Period size: 2 Copynumber: 43.5 Consensus size: 2
3346978 TATGAAAGTT
*
3346988 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
3347030 CC TT TC TC TC TC TC CC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3347072 TC T
1 TC T
3347075 ATATATATAT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3347079 original size:2 final size:2
Alignment explanation
Indices: 3347074--3347136 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
3347064 TCTCTCTCTC
3347074 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
3347116 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
3347137 GCACCTTGGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3353680 original size:2 final size:2
Alignment explanation
Indices: 3353669--3353701 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3353659 CTTCTCTAGG
3353669 GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3353702 AAGGGGGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3356607 original size:31 final size:31
Alignment explanation
Indices: 3356567--3356633 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
3356557 AGTTACGTCG
*
3356567 GGGAACATATTGAAAACAGACTAAATGTTGA
1 GGGATCATATTGAAAACAGACTAAATGTTGA
* * *
3356598 GGGATCATATTGCAAACGGACTAAATGTTGG
1 GGGATCATATTGAAAACAGACTAAATGTTGA
3356629 GGGAT
1 GGGAT
3356634 TATTTTGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.28, T:0.24
Consensus pattern (31 bp):
GGGATCATATTGAAAACAGACTAAATGTTGA
Found at i:3358628 original size:31 final size:31
Alignment explanation
Indices: 3358590--3358655 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
3358580 AGTTACGTCG
* *
3358590 GGGACCATATTGCAAACGGACTAACTGTTTA
1 GGGACCATATTGCAAACCGACTAAATGTTTA
*
3358621 GGGACCATATTGCAAACCGACTAAATGTTTG
1 GGGACCATATTGCAAACCGACTAAATGTTTA
3358652 GGGA
1 GGGA
3358656 TTGTATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (31 bp):
GGGACCATATTGCAAACCGACTAAATGTTTA
Found at i:3363889 original size:20 final size:21
Alignment explanation
Indices: 3363864--3363956 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
3363854 TTTTCCCAAT
*
3363864 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3363884 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
3363905 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3363925 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3363946 TCGCAATGCGA
1 TCGCAATGCGA
3363957 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3363910 original size:41 final size:41
Alignment explanation
Indices: 3363864--3363956 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3363854 TTTTCCCAAT
3363864 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3363905 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3363946 TCGCAATGCGA
1 TCGCAATGCGA
3363957 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:3364019 original size:41 final size:41
Alignment explanation
Indices: 3363942--3364019 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 41
3363932 GCGAATTGGG
* * **
3363942 AAAATCGCAATGCGATACTGACTATCACAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCACAACACGATAATAA
* * *
3363983 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCACAACACGATA
3364020 CTGACTTTCG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 30 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCACAACACGATAATAA
Found at i:3364038 original size:20 final size:20
Alignment explanation
Indices: 3363945--3364038 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
3363935 AATTGGGAAA
3363945 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * **
3363965 ATCACAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* * *
3363986 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* **
3364006 TTCGCAACACGATACTGACT
1 ATCGCAATGCGATACTGACT
*
3364026 TTCGCAATGCGAT
1 ATCGCAATGCGAT
3364039 TTACATAGCG
Statistics
Matches: 55, Mismatches: 18, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
20 42 0.76
21 13 0.24
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3364634 original size:19 final size:19
Alignment explanation
Indices: 3364612--3364776 Score: 143
Period size: 19 Copynumber: 9.1 Consensus size: 19
3364602 GAAACCAAAA
*
3364612 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3364631 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3364650 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
3364669 TCGCGGTTGTGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
3364689 TCGCGTTGCAATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
3364705 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
3364722 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
3364736 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
3364755 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3364775 TC
1 TC
3364777 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
14 19 0.16
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 57 0.48
20 35 0.29
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3364694 original size:39 final size:38
Alignment explanation
Indices: 3364612--3364776 Score: 143
Period size: 33 Copynumber: 4.6 Consensus size: 38
3364602 GAAACCAAAA
*
3364612 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
3364650 TCGCGTTGCGATTTTTATTTCGCGGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * * **
3364689 TCGCGTTGCAATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
3364722 TCGCGTTGCGA--TTC---TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
3364755 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTCATTTC
3364777 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 17, Indels: 17
0.75 0.13 0.13
Matches are distributed among these distances:
31 3 0.03
33 33 0.33
34 10 0.10
35 1 0.01
36 4 0.04
38 21 0.21
39 29 0.29
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:3364742 original size:14 final size:14
Alignment explanation
Indices: 3364725--3364751 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3364715 AGTCATTTCG
3364725 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3364739 CGTTGCGATTCTC
1 CGTTGCGATTCTC
3364752 ATTATCTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.22, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3364761 original size:20 final size:20
Alignment explanation
Indices: 3364736--3364774 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3364726 GTTGCGATTC
3364736 TCTCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
3364756 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
3364775 TCAACCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:3366852 original size:21 final size:21
Alignment explanation
Indices: 3366828--3366894 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3366818 TCATTCCTCG
3366828 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
3366849 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
3366870 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
3366891 AGAG
1 AGAG
3366895 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:3366852 original size:42 final size:42
Alignment explanation
Indices: 3366772--3366894 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
3366762 GCTCGAATCG
* * * * * * *
3366772 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
3366814 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
3366856 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
3366895 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 62 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:3368269 original size:14 final size:14
Alignment explanation
Indices: 3368250--3368285 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3368240 ATTGTTTAAT
3368250 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3368264 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3368278 TGATTTGT
1 TGATTTGT
3368286 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3368428 original size:20 final size:20
Alignment explanation
Indices: 3368392--3368444 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3368382 AAAAAGTACT
*
3368392 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGAAA
3368411 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCGAAAATGAAA
*
3368431 ATGGCAACGCGAAA
1 ATCGCAACGCGAAA
3368445 TTAAATTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGAAA
Found at i:3368472 original size:19 final size:19
Alignment explanation
Indices: 3368450--3368637 Score: 199
Period size: 19 Copynumber: 10.7 Consensus size: 19
3368440 CGAAATTAAA
*
3368450 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3368469 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3368488 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3368507 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
3368526 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
3368542 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
3368559 TTCACATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
3368573 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3368592 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
3368608 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3368625 TTCGCATTGCGAT
1 TTCGCATTGCGAT
3368638 AGTAATTTCC
Statistics
Matches: 139, Mismatches: 15, Indels: 30
0.76 0.08 0.16
Matches are distributed among these distances:
14 22 0.16
16 13 0.09
17 12 0.09
19 92 0.66
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3368501 original size:38 final size:35
Alignment explanation
Indices: 3368450--3368637 Score: 201
Period size: 33 Copynumber: 5.4 Consensus size: 35
3368440 CGAAATTAAA
*
3368450 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTCGCATTGCGA--TTCATTTCGC-TTGCGATTTTCAT
3368488 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTCGCATTGCGA--TTCATTTCGC-TTGCGATTTTCAT
**
3368526 TTCGCATTGCGATTC-CCTCG-TTGCGATTTTCAT
1 TTCGCATTGCGATTCATTTCGCTTGCGATTTTCAT
* * *
3368559 TTCACATTGCGA---AATTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTCATTTCGC-TTGCGATTTTCAT
*
3368592 TTCGCATTGCGATTC-TCTCG-TTGCGATTTTCAT
1 TTCGCATTGCGATTCATTTCGCTTGCGATTTTCAT
3368625 TTCGCATTGCGAT
1 TTCGCATTGCGAT
3368638 AGTAATTTCC
Statistics
Matches: 133, Mismatches: 11, Indels: 17
0.83 0.07 0.11
Matches are distributed among these distances:
31 2 0.02
33 74 0.56
35 5 0.04
36 3 0.02
38 49 0.37
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (35 bp):
TTCGCATTGCGATTCATTTCGCTTGCGATTTTCAT
Found at i:3368555 original size:33 final size:33
Alignment explanation
Indices: 3368475--3368637 Score: 211
Period size: 33 Copynumber: 4.8 Consensus size: 33
3368465 TCATTTCGCA
*
3368475 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
3368511 CATTGCGATTTTCATTTCGCATTGCGATTCCCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* * **
3368546 TTGCGATTTTCATTTCACATTGCGAAAT-TAGCG
1 TTGCGATTTTCATTTCGCATTGCG-ATTCTCTCG
3368579 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
3368612 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
3368638 AGTAATTTCC
Statistics
Matches: 112, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
32 2 0.02
33 77 0.69
34 2 0.02
35 3 0.03
36 3 0.03
38 25 0.22
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:3370960 original size:24 final size:24
Alignment explanation
Indices: 3370926--3370979 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3370916 CTGAAACATC
* *
3370926 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
3370950 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
3370974 ATCAAA
1 ATCAAA
3370980 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:3372060 original size:19 final size:19
Alignment explanation
Indices: 3372036--3372092 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
3372026 GACATTCATT
3372036 TGACTATCGCAACGCGAAA
1 TGACTATCGCAACGCGAAA
3372055 TGACTATCGCAACGCGAAA
1 TGACTATCGCAACGCGAAA
*
3372074 TGGCTATCGCAACGCGAAA
1 TGACTATCGCAACGCGAAA
3372093 ATGGTTATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (19 bp):
TGACTATCGCAACGCGAAA
Found at i:3372096 original size:20 final size:19
Alignment explanation
Indices: 3372039--3372112 Score: 103
Period size: 19 Copynumber: 3.8 Consensus size: 19
3372029 ATTCATTTGA
*
3372039 CTATCGCAACGCGAAATGA
1 CTATCGCAACGCGAAATGG
3372058 CTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGG
3372077 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCG-AAATGG
* * *
3372097 TTATCACAACGAGAAA
1 CTATCGCAACGCGAAA
3372113 ATCGCAATGC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 34 0.68
20 16 0.32
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (19 bp):
CTATCGCAACGCGAAATGG
Found at i:3372157 original size:14 final size:16
Alignment explanation
Indices: 3372137--3372210 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
3372127 TGAAAATCGC
3372137 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
3372152 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
3372169 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
3372188 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
3372204 -TTGCGAT
1 ATTGCGAT
3372211 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:3372174 original size:19 final size:19
Alignment explanation
Indices: 3372133--3372200 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
3372123 GAAATGAAAA
3372133 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
3372149 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3372166 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3372185 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
3372201 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3374256 original size:20 final size:19
Alignment explanation
Indices: 3374221--3374287 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
3374211 GAAACTTAAA
3374221 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3374240 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
3374260 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3374279 ATCGCAACG
1 ATCGCAACG
3374288 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3374295 original size:14 final size:14
Alignment explanation
Indices: 3374276--3374333 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3374266 ATGCGAAATG
3374276 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3374290 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3374306 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3374322 AAAATCGCAACG
1 AAAATCGCAACG
3374334 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3374318 original size:32 final size:33
Alignment explanation
Indices: 3374260--3374338 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
3374250 GGAAATGGCT
*
3374260 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3374293 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3374325 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3374339 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:3374367 original size:19 final size:18
Alignment explanation
Indices: 3374345--3374409 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
3374335 GAAACACAAA
3374345 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
3374364 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
3374380 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
3374396 TCGCATTGCGATTT
1 TCGCATTGCGATTT
3374410 TGTCGTTGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.23
16 8 0.21
18 12 0.31
19 10 0.26
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:3374386 original size:14 final size:14
Alignment explanation
Indices: 3374367--3374424 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
3374357 TTTCATTTCG
3374367 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3374381 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3374397 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
3374413 CGTTGCAATTTT
1 CGTTGCGATTTT
3374425 CATTTAGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3374435 original size:33 final size:33
Alignment explanation
Indices: 3374350--3374440 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
3374340 ACAAATCGCA
*
3374350 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3374383 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
3374415 TTGCAATTTTCATTTAGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
3374441 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:3374459 original size:20 final size:20
Alignment explanation
Indices: 3374434--3374479 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3374424 TCATTTAGCA
3374434 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
3374454 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
3374474 TTGCGA
1 TTGCGA
3374480 AAGTAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:3374971 original size:18 final size:18
Alignment explanation
Indices: 3374945--3374989 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3374935 GTCGATCAAA
*
3374945 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
3374963 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
3374981 TGATGGCTC
1 TGATGGCTC
3374990 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:3376332 original size:20 final size:20
Alignment explanation
Indices: 3376307--3376344 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3376297 AATAGTTTCT
3376307 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
3376327 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
3376345 GAGAGAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3376633 original size:22 final size:22
Alignment explanation
Indices: 3376608--3376651 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3376598 GATTTAGATA
3376608 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3376630 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3376652 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.45, T:0.18
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3376864 original size:20 final size:20
Alignment explanation
Indices: 3376839--3376891 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3376829 GATTATGTAT
*
3376839 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
3376859 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
3376879 TATCTCGTTGCGA
1 TATCGCGTTGCGA
3376892 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:3376904 original size:41 final size:41
Alignment explanation
Indices: 3376859--3376936 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
3376849 CGAAAGTCAG
* * *
3376859 TATCGCGTTGCGA-AAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGATAA-TAAGTATCACATTGCGATTTTTTAT
*
3376900 TATCGCATTGCGATAATCAGTATCACATTGCGATTTT
1 TATCGCATTGCGATAATAAGTATCACATTGCGATTTT
3376937 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGATAATAAGTATCACATTGCGATTTTTTAT
Found at i:3376952 original size:41 final size:41
Alignment explanation
Indices: 3376922--3377014 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
3376912 ATAATCAGTA
* *
3376922 TCACATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
3376963 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
3377004 TCACATTGCGA
1 TCACATTGCGA
3377015 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (41 bp):
TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:3376953 original size:21 final size:21
Alignment explanation
Indices: 3376927--3376997 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
3376917 CAGTATCACA
3376927 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
3376948 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
3376968 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
3376989 TTGCGATTT
1 TTGCGATTT
3376998 ACTTATTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:3377012 original size:20 final size:20
Alignment explanation
Indices: 3376941--3377014 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
3376931 GATTTTCCCA
*
3376941 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
3376961 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
3376982 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
*
3377002 ATTCACATTGCGA
1 ATTCGCATTGCGA
3377015 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:3382839 original size:97 final size:97
Alignment explanation
Indices: 3382660--3382857 Score: 335
Period size: 97 Copynumber: 2.0 Consensus size: 97
3382650 ATTGTCCTTT
3382660 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTTGCCATTAAAAACTAGTA
1 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTTGCCATTAAAAACTAGTA
*
3382725 GTTTATCGACTCCTTTTTTTGTAAGAATTGTA
66 GTTTATCGACTCCTTTTTTTGTAAGAAGTGTA
**
3382757 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAG-TTTTTTGCTGTTAAAAACTAGTA
1 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTTGCCATTAAAAACTAGTA
* *
3382821 GTTTATTGACTACTTTTTTTTGTAAGAAGTGTA
66 GTTTATCGACT-CCTTTTTTTGTAAGAAGTGTA
3382854 TAAC
1 TAAC
3382858 CTACTCTTAA
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 31 0.33
97 64 0.67
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (97 bp):
TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTTGCCATTAAAAACTAGTA
GTTTATCGACTCCTTTTTTTGTAAGAAGTGTA
Found at i:3386732 original size:8 final size:9
Alignment explanation
Indices: 3386715--3386744 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
3386705 AAAGAAAGGG
3386715 AATAAAAAA
1 AATAAAAAA
3386724 AATAAAAAA
1 AATAAAAAA
3386733 AATAAAAAA
1 AATAAAAAA
3386742 AAT
1 AAT
3386745 TAAACAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AATAAAAAA
Found at i:3396473 original size:23 final size:23
Alignment explanation
Indices: 3396447--3396549 Score: 197
Period size: 23 Copynumber: 4.5 Consensus size: 23
3396437 ATTTTCATTT
3396447 GTTAAAGCCAATGAGATTGGAGC
1 GTTAAAGCCAATGAGATTGGAGC
3396470 GTTAAAGCCAATGAGATTGGAGC
1 GTTAAAGCCAATGAGATTGGAGC
3396493 GTTAAAGCCAATGAGATTGGAGC
1 GTTAAAGCCAATGAGATTGGAGC
*
3396516 GTTAAAGCTAATGAGATTGGAGC
1 GTTAAAGCCAATGAGATTGGAGC
3396539 GTTAAAGCCAA
1 GTTAAAGCCAA
3396550 CACCTTTCAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (23 bp):
GTTAAAGCCAATGAGATTGGAGC
Found at i:3397724 original size:24 final size:24
Alignment explanation
Indices: 3397681--3397746 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
3397671 TGTTCGGTTA
*
3397681 TATGTTCGTTCAT-TTATGTTC-ATT
1 TATGTTCGTTTATGTT-TGTTCGA-T
*
3397705 TATTTTCGTTTATGTTTGTTCGAT
1 TATGTTCGTTTATGTTTGTTCGAT
3397729 TATGTTCGTTTATGTTTG
1 TATGTTCGTTTATGTTTG
3397747 AACAGATGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 34 0.92
25 3 0.08
ACGTcount: A:0.14, C:0.09, G:0.17, T:0.61
Consensus pattern (24 bp):
TATGTTCGTTTATGTTTGTTCGAT
Found at i:3401391 original size:24 final size:24
Alignment explanation
Indices: 3401333--3401385 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3401323 TAATCACCAA
3401333 AATAACTTTTTACCTCTCATTTTT
1 AATAACTTTTTACCTCTCATTTTT
3401357 AATAACTTTTTACCTCTCATTTTT
1 AATAACTTTTTACCTCTCATTTTT
3401381 AATAA
1 AATAA
3401386 TGTTTTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (24 bp):
AATAACTTTTTACCTCTCATTTTT
Found at i:3407172 original size:22 final size:21
Alignment explanation
Indices: 3407145--3407187 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
3407135 CCTAATATTG
3407145 CAATGTCAAAATTAGGTTGCAA
1 CAATGTCAAAATTAGG-TGCAA
3407167 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
3407188 TATTGTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:3412941 original size:16 final size:16
Alignment explanation
Indices: 3412922--3412952 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3412912 TTATTAGCAT
3412922 ATAAATTATAATAAAA
1 ATAAATTATAATAAAA
*
3412938 ATAAGTTATAATAAA
1 ATAAATTATAATAAA
3412953 TCATAGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAATTATAATAAAA
Found at i:3413174 original size:2 final size:2
Alignment explanation
Indices: 3413167--3413242 Score: 83
Period size: 2 Copynumber: 40.0 Consensus size: 2
3413157 CATTTGTGTT
3413167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA GTGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA
*
3413210 TA T- TA -A TA T- TA T- TA T- TA TA AA 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
3413243 AGCTGAAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
1 6 0.09
2 55 0.86
3 2 0.03
4 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3416214 original size:154 final size:154
Alignment explanation
Indices: 3415934--3416241 Score: 553
Period size: 154 Copynumber: 2.0 Consensus size: 154
3415924 TATTCACTCT
*
3415934 TTAATACCAACAATTCTTGTCCATAGATCATCTTCAGAATCATCACTGAATAGATCTTAAGAATA
1 TTAATACCAACAATTCTTGTCCATAGATCATCTTCAGAATCATCACTGAATAGATCTTAAGAAGA
*
3415999 TGAACAAATATTCTGATGGTCTTTATTTCATTTCCACATTTCAACAATATCATGAATTGTCCATG
66 TGAACAAATATTCTGATGGTCTTTATTTCATTTCCACATTTCAACAATATCAGGAATTGTCCATG
*
3416064 TACTTAATTTGTGGTTCATTACCC
131 TACTTAATTCGTGGTTCATTACCC
**
3416088 TTAATACCAACAATTCTTGTCCATAGATCATCTTCAGAATCATTGCTGAATAGATCTTAAGAAGA
1 TTAATACCAACAATTCTTGTCCATAGATCATCTTCAGAATCATCACTGAATAGATCTTAAGAAGA
*
3416153 TGAACAAATATTCTGATGGTCTTTATTTCATTTCCACATTTCAATAATATCAGGAATTGTCCATG
66 TGAACAAATATTCTGATGGTCTTTATTTCATTTCCACATTTCAACAATATCAGGAATTGTCCATG
*
3416218 TACTTCATTCGTGGTTCATTACCC
131 TACTTAATTCGTGGTTCATTACCC
3416242 ATAGGGATAA
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 147 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (154 bp):
TTAATACCAACAATTCTTGTCCATAGATCATCTTCAGAATCATCACTGAATAGATCTTAAGAAGA
TGAACAAATATTCTGATGGTCTTTATTTCATTTCCACATTTCAACAATATCAGGAATTGTCCATG
TACTTAATTCGTGGTTCATTACCC
Found at i:3418400 original size:31 final size:31
Alignment explanation
Indices: 3418362--3418521 Score: 91
Period size: 32 Copynumber: 5.1 Consensus size: 31
3418352 GAACCTCGGC
*
3418362 AACTGTCCATA-GGTCCTGAAGAACCTAGGTA
1 AACTGTCCATATGGTCCT-AAGAACATAGGTA
* *
3418393 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGGTCCTAAGAACATAGGTA
* * * *
3418424 TATTGTCCATAT-GT-CTCAAAATACCTAGGTA
1 AACTGTCCATATGGTCCT-AAGA-ACATAGGTA
* * *
3418455 ATTCTGTCTATAT-GTCCCGAA-ATACATAGGTA
1 A-ACTGTCCATATGGT-CCTAAGA-ACATAGGTA
*
3418487 ATTA-TGTCCATATGTTCCGT-AGAACATAGGTA
1 A--ACTGTCCATATGGTCC-TAAGAACATAGGTA
3418519 AAC
1 AAC
3418522 CCTCGACTCT
Statistics
Matches: 99, Mismatches: 19, Indels: 22
0.71 0.14 0.16
Matches are distributed among these distances:
29 2 0.02
30 4 0.04
31 40 0.40
32 47 0.47
33 5 0.05
34 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGGTCCTAAGAACATAGGTA
Found at i:3418514 original size:32 final size:33
Alignment explanation
Indices: 3418396--3418519 Score: 109
Period size: 32 Copynumber: 3.9 Consensus size: 33
3418386 CTAGGTAAAC
* *
3418396 TGTCCATATGTTCCTTAGA-ACATAGGT-A-TA
1 TGTCCATATGTTCCGTAAATACATAGGTAATTA
* * *
3418426 TTGTCCATATG-TCTC-AAAATACCTAGGTAATTC
1 -TGTCCATATGTTC-CGTAAATACATAGGTAATTA
* *
3418459 TGTCTATATGTCCCG-AAATACATAGGTAATTA
1 TGTCCATATGTTCCGTAAATACATAGGTAATTA
*
3418491 TGTCCATATGTTCCGTAGA-ACATAGGTAA
1 TGTCCATATGTTCCGTAAATACATAGGTAA
3418520 ACCCTCGACT
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
30 4 0.05
31 18 0.24
32 49 0.65
33 4 0.05
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (33 bp):
TGTCCATATGTTCCGTAAATACATAGGTAATTA
Found at i:3422608 original size:32 final size:31
Alignment explanation
Indices: 3422472--3422611 Score: 106
Period size: 32 Copynumber: 4.5 Consensus size: 31
3422462 ATAGGTCCCA
* *
3422472 AAGAACCTAGGTAA-ATTGTCCATATGTTCCT
1 AAGAACATAGGTAATATTGTCCATAT-TTCCG
* * * *
3422503 TAGAACATAGGT-ATACTGTCCATATGTCTG
1 AAGAACATAGGTAATATTGTCCATATTTCCG
* *
3422533 AAAAGACATAGGTAAT-TATGTCCATATTTCCC
1 AAGA-ACATAGGTAATAT-TGTCCATATTTCCG
* * *
3422565 AAAAGATATAGGTAATTTTGTCCATATATTCCG
1 AAGA-ACATAGGTAATATTGTCCATAT-TTCCG
*
3422598 TAGAACATAGGTAA
1 AAGAACATAGGTAA
3422612 ACCCTCGACT
Statistics
Matches: 86, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
30 5 0.06
31 28 0.33
32 46 0.53
33 7 0.08
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (31 bp):
AAGAACATAGGTAATATTGTCCATATTTCCG
Found at i:3423153 original size:18 final size:18
Alignment explanation
Indices: 3423129--3423172 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3423119 TCATATCAAT
*
3423129 AACATATATACTCAT-GCA
1 AACATATA-AATCATAGCA
*
3423147 CACATATAAATCATAGCA
1 AACATATAAATCATAGCA
3423165 AACATATA
1 AACATATA
3423173 GTTATATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (18 bp):
AACATATAAATCATAGCA
Found at i:3423514 original size:24 final size:20
Alignment explanation
Indices: 3423461--3423518 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
3423451 TTCCCCTTGA
*
3423461 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
3423481 AGTGCATCGATGCATTCCTTAAC
1 AGTGCATCGATGCATT-C-T-AC
3423504 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3423519 CTATCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 15 0.45
21 1 0.03
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:3429055 original size:15 final size:15
Alignment explanation
Indices: 3429035--3429067 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3429025 GTCAACGGGG
3429035 TGACTCAGACCGAGT
1 TGACTCAGACCGAGT
3429050 TGACTCAGACCGAGT
1 TGACTCAGACCGAGT
3429065 TGA
1 TGA
3429068 ATCATATATT
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:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (15 bp):
TGACTCAGACCGAGT
Found at i:3429389 original size:22 final size:23
Alignment explanation
Indices: 3429348--3429391 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3429338 TTTAAATTTT
*
3429348 AAATATAAAAATATTCAAAAATC
1 AAATATAAAAATACTCAAAAATC
*
3429371 AAATATAAAAGTACT-AAAAAT
1 AAATATAAAAATACTCAAAAAT
3429392 AAAAGTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATATAAAAATACTCAAAAATC
Found at i:3429494 original size:21 final size:21
Alignment explanation
Indices: 3429452--3429500 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3429442 TATCGAAAAA
*
3429452 ATAAAATATATATCATAGATT
1 ATAAAATATATATCATAAATT
*
3429473 ATAAAATATA-ACTTATAAATT
1 ATAAAATATATA-TCATAAATT
3429494 ATTAAAA
1 A-TAAAA
3429501 AATTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAAATATATATCATAAATT
Found at i:3436081 original size:4 final size:4
Alignment explanation
Indices: 3436072--3436098 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3436062 AATAATTGCA
3436072 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
3436099 CCCAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3437084 original size:21 final size:21
Alignment explanation
Indices: 3437058--3437097 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3437048 GACTATCGCA
3437058 TTGCGATTTCCCAAATTCGTG
1 TTGCGATTTCCCAAATTCGTG
* *
3437079 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
3437098 CAATGCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGTG
Found at i:3437104 original size:21 final size:21
Alignment explanation
Indices: 3437031--3437105 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
3437021 CAGTTTCCAG
**
3437031 ATTCGCAATGCGATTCTGACT-
1 ATTCGCAATGCGATT-TCCCTA
* *
3437052 A-TCGCATTGCGATTTCCCAA
1 ATTCGCAATGCGATTTCCCTA
*** *
3437072 ATTCGTGTTGCGATTTTCCTA
1 ATTCGCAATGCGATTTCCCTA
3437093 ATTCGCAATGCGA
1 ATTCGCAATGCGA
3437106 ATACGTAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 26 0.63
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (21 bp):
ATTCGCAATGCGATTTCCCTA
Found at i:3437120 original size:20 final size:20
Alignment explanation
Indices: 3437095--3437186 Score: 130
Period size: 20 Copynumber: 4.5 Consensus size: 20
3437085 TTTTCCTAAT
3437095 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
3437115 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
3437136 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
3437156 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3437176 TCGCAATGCGA
1 TCGCAATGCGA
3437187 TTTACATAGC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 46 0.75
21 15 0.25
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3437141 original size:41 final size:40
Alignment explanation
Indices: 3437095--3437186 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
3437085 TTTTCCTAAT
**
3437095 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAA
* * *
3437136 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
3437176 TCGCAATGCGA
1 TCGCAATGCGA
3437187 TTTACATAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 16 0.35
41 30 0.65
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
Found at i:3437388 original size:22 final size:22
Alignment explanation
Indices: 3437363--3437424 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 22
3437353 GGTGACATCC
3437363 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
3437385 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
3437403 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3437425 TTCACAGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.50
22 16 0.50
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:3437797 original size:33 final size:33
Alignment explanation
Indices: 3437749--3437862 Score: 95
Period size: 40 Copynumber: 3.2 Consensus size: 33
3437739 ACTATCGAAA
3437749 TGCGATTC-TGTCGTTGCGATTTTCATTTCGCGT
1 TGCGATTCTTG-CGTTGCGATTTTCATTTCGCGT
** *
3437782 TGCGATTCTTGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTTGCGTTGCGATTTTC-ATTTCGCGT
* *
3437816 TGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGT
1 TGCGAT--TC---TT-GCGTTGCGATTTTCA-TTTCGCGT
3437856 TGCGATT
1 TGCGATT
3437863 TAAAGTTTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
33 19 0.30
34 16 0.25
36 2 0.03
38 1 0.02
39 3 0.05
40 23 0.36
ACGTcount: A:0.13, C:0.18, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTCTTGCGTTGCGATTTTCATTTCGCGT
Found at i:3437817 original size:20 final size:20
Alignment explanation
Indices: 3437792--3437841 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3437782 TGCGATTCTT
3437792 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
3437812 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
3437832 GTGTTGCGAT
1 GCGTTGCGAT
3437842 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:3437818 original size:34 final size:33
Alignment explanation
Indices: 3437749--3437821 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
3437739 ACTATCGAAA
** *
3437749 TGCGATTCTGTCGTTGCGATTTTCATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAATTCGCGT
3437782 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTC-AATTCGCGT
3437816 TGCGAT
1 TGCGAT
3437822 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40
Consensus pattern (33 bp):
TGCGATTCTGTCGTTGCGATAGTCAATTCGCGT
Found at i:3437847 original size:20 final size:20
Alignment explanation
Indices: 3437809--3437863 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3437799 GATAGTCAAA
* **
3437809 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
3437829 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
3437849 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
3437864 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:3437871 original size:20 final size:20
Alignment explanation
Indices: 3437828--3437871 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3437818 CGATAGTCAT
** *
3437828 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
3437848 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
3437868 TTTC
1 TTTC
3437872 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:3439611 original size:22 final size:21
Alignment explanation
Indices: 3439581--3439621 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3439571 GAATTTACTC
*
3439581 GTAATTTCACTTAGATTGCTTA
1 GTAAATTCA-TTAGATTGCTTA
*
3439603 GTAAATTCATTCGATTGCT
1 GTAAATTCATTAGATTGCT
3439622 GACAATACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (21 bp):
GTAAATTCATTAGATTGCTTA
Found at i:3439766 original size:20 final size:20
Alignment explanation
Indices: 3439741--3439884 Score: 174
Period size: 20 Copynumber: 7.5 Consensus size: 20
3439731 AGAATATTTT
3439741 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
3439761 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
3439781 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
3439797 A--ATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
3439815 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
3439835 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* * **
3439855 ACTATCACAATACGAATTTG
1 ACTATCGCAATGCGAAAATG
*
3439875 AATATCGCAA
1 ACTATCGCAA
3439885 CGAAAGAATC
Statistics
Matches: 107, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
14 7 0.07
16 3 0.03
17 4 0.04
18 4 0.04
20 89 0.83
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:3440028 original size:19 final size:20
Alignment explanation
Indices: 3439931--3440056 Score: 130
Period size: 20 Copynumber: 6.4 Consensus size: 20
3439921 GATTCTCTCG
* **
3439931 TTGCGATAGTCAAATTCGCA
1 TTGCGATTGTCATTTTCGCA
* **
3439951 TTGCGATAGTCAAATTCGCA
1 TTGCGATTGTCATTTTCGCA
*
3439971 TTGCGATAGTCATTTTCGCA
1 TTGCGATTGTCATTTTCGCA
* *
3439991 TTGCGATAGTCATTTTCGCG
1 TTGCGATTGTCATTTTCGCA
* *
3440011 TTGCGATTTTCA-TTTCGCG
1 TTGCGATTGTCATTTTCGCA
*
3440030 TTGCGATTTTCATTTT-GCA
1 TTGCGATTGTCATTTTCGCA
3440049 TTGCGATT
1 TTGCGATT
3440057 CTCTCGTTGC
Statistics
Matches: 99, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
19 29 0.29
20 70 0.71
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATTGTCATTTTCGCA
Found at i:3440663 original size:21 final size:21
Alignment explanation
Indices: 3440572--3440668 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
3440562 GACTCATCTG
*
3440572 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
3440594 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
3440614 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
3440635 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
3440656 TCATCGTTGAAGA
1 TCATCGTTCAAGA
3440669 AGTCCCTCCC
Statistics
Matches: 58, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.05
21 54 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:3442054 original size:14 final size:14
Alignment explanation
Indices: 3442035--3442070 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3442025 ATTGTTTAAT
3442035 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3442049 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3442063 TGATTTGT
1 TGATTTGT
3442071 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3442306 original size:19 final size:19
Alignment explanation
Indices: 3442284--3442386 Score: 172
Period size: 19 Copynumber: 5.4 Consensus size: 19
3442274 TAATTTCCCG
3442284 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3442303 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
3442322 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3442341 TTGCGATTTTCATTTTG-A
1 TTGCGATTTTCATTTCGCA
3442359 TTTGCGATTTTCATTTCGCA
1 -TTGCGATTTTCATTTCGCA
3442379 TTGCGATT
1 TTGCGATT
3442387 CTCTCGTTGC
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
18 1 0.01
19 76 0.97
20 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.16, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3442416 original size:20 final size:20
Alignment explanation
Indices: 3442391--3442479 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
3442381 GCGATTCTCT
3442391 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
3442411 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
3442431 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
3442451 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
3442471 CGTTGCGAT
1 CGTTGCGAT
3442480 TTCCGCGTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:3444948 original size:24 final size:24
Alignment explanation
Indices: 3444914--3444967 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3444904 CTAAAAAATC
3444914 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3444938 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3444962 ATCAAA
1 ATCAAA
3444968 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3444981 original size:24 final size:24
Alignment explanation
Indices: 3444914--3444981 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3444904 CTAAAAAATC
* * *
3444914 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
3444938 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3444962 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
3444982 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3447959 original size:20 final size:20
Alignment explanation
Indices: 3447936--3448102 Score: 169
Period size: 20 Copynumber: 8.3 Consensus size: 20
3447926 TAGAAACTCG
3447936 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
3447956 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
3447976 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
* *
3447996 TTGAGATTTACGTATTCGTA
1 TTGCGATTTACGTATTCGCA
* *
3448016 TTGCTATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* *
3448036 TTGCGATTTACGTAATCGAA
1 TTGCGATTTACGTATTCGCA
* * ** *
3448056 TTGCAATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
*
3448077 TTGTGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
3448097 TTGCGA
1 TTGCGA
3448103 ATTAGGAAAA
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
19 1 0.01
20 110 0.89
21 12 0.10
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:3447962 original size:40 final size:39
Alignment explanation
Indices: 3447915--3448046 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 39
3447905 GAAATTCAGT
*
3447915 ATTGCGATAGTTAGAAACTCG-TTGCGATTTACAGATTCGC
1 ATTGCGAT--TTACAAACTCGATTGCGATTTACAGATTCGC
* *
3447955 ATTGCGATTTACAGATTCGCATTGCGATTTACAGATTCGC
1 ATTGCGATTTACAAACTCG-ATTGCGATTTACAGATTCGC
* ** * * *
3447995 ATTGAGATTTACGTATTCGTATTGCTATTTAC-GTAATCGC
1 ATTGCGATTTACAAACTCG-ATTGCGATTTACAG-ATTCGC
3448035 ATTGCGATTTAC
1 ATTGCGATTTAC
3448047 GTAATCGAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
38 8 0.10
39 1 0.01
40 70 0.89
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (39 bp):
ATTGCGATTTACAAACTCGATTGCGATTTACAGATTCGC
Found at i:3448702 original size:2 final size:2
Alignment explanation
Indices: 3448695--3448738 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3448685 TACGATAAAC
3448695 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
3448737 AT
1 AT
3448739 CATAAAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3450045 original size:21 final size:21
Alignment explanation
Indices: 3449994--3450047 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
3449984 ATACCCGGGT
*
3449994 GTACATATACCCCCTGTAAGG
1 GTACCTATACCCCCTGTAAGG
*
3450015 GTACCTATACCCCCTGTAGGG
1 GTACCTATACCCCCTGTAAGG
3450036 GTATCC-ATACCC
1 GTA-CCTATACCC
3450048 ATATGATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (21 bp):
GTACCTATACCCCCTGTAAGG
Found at i:3450550 original size:34 final size:34
Alignment explanation
Indices: 3450492--3450556 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
3450482 CCTTTTGTAA
*
3450492 AGGGAAAGGTTCTAGCTAAGCTCATGTAAAAGCT
1 AGGGAAAGGTTCTAGCTAAGCTCATGAAAAAGCT
* * *
3450526 AGGGAAAGGTTCTAGTTTATCTCATGAAAAA
1 AGGGAAAGGTTCTAGCTAAGCTCATGAAAAA
3450557 CTATGGAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (34 bp):
AGGGAAAGGTTCTAGCTAAGCTCATGAAAAAGCT
Found at i:3453246 original size:18 final size:18
Alignment explanation
Indices: 3453223--3453279 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
3453213 TATATTTTCC
*
3453223 AACAATTGGTATCTTTTT
1 AACAATTGATATCTTTTT
3453241 AACAATTGATATCCTTTTGTT
1 AACAATTGATAT-C-TTT-TT
*
3453262 AACAAATGATATCTTTTT
1 AACAATTGATATCTTTTT
3453280 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 4 0.12
21 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (18 bp):
AACAATTGATATCTTTTT
Found at i:3453265 original size:21 final size:20
Alignment explanation
Indices: 3453223--3453279 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
3453213 TATATTTTCC
*
3453223 AACAATTGGTAT-C-TTTTT
1 AACAATTGATATCCTTTTTT
3453241 AACAATTGATATCCTTTTGTT
1 AACAATTGATATCCTTTT-TT
*
3453262 AACAAATGATAT-CTTTTT
1 AACAATTGATATCCTTTTT
3453280 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 11 0.32
19 2 0.06
20 8 0.24
21 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (20 bp):
AACAATTGATATCCTTTTTT
Found at i:3472573 original size:18 final size:19
Alignment explanation
Indices: 3472552--3472589 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3472542 TTGGGGAAGA
3472552 AAAAATGTTA-ATTTTATT
1 AAAAATGTTATATTTTATT
*
3472570 AAAAATGTTATTTTTTATT
1 AAAAATGTTATATTTTATT
3472589 A
1 A
3472590 GTTTACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
AAAAATGTTATATTTTATT
Found at i:3474209 original size:386 final size:386
Alignment explanation
Indices: 3472905--3474449 Score: 3003
Period size: 386 Copynumber: 4.0 Consensus size: 386
3472895 AACATCAATT
*
3472905 GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTAGAGTAGTTTACCCTTAATTATTTTGAG
1 GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTGGAGTAGTTTACCCTTAATTATTTTGAG
*
3472970 CTATTCTCGACAAAATGTCAAATCGTATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
66 CTATTCTCGACAAAATGTCAAATCGCATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
3473035 TATAATCCCTGAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
131 TATAATCCCTGAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
3473100 ATTATAAAATAATATTTATTTGAAA-TTTTTTAATTATTTGATAATAATTA-TTATATATAAATG
196 ATTATAAAATAATATTTATTTGAAATTTTTTTAATTATTTGATAATAATTATTTATATATAAATG
3473163 CACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGATTTATATTATT
261 CACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGATTTATATTATT
3473228 ATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
326 ATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
3473289 GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTGGAGTAGTTTACCCTTAATTATTTTGAG
1 GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTGGAGTAGTTTACCCTTAATTATTTTGAG
3473354 CTATTCTCGACAAAATGTCAAATCGCATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
66 CTATTCTCGACAAAATGTCAAATCGCATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
3473419 TATAATCCCTGAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
131 TATAATCCCTGAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
3473484 ATTATAAAATAATATTTATTTGAAATTTTTTTAATTATTTGATAATAATTATTTTATATATAAAT
196 ATTATAAAATAATATTTATTTGAAATTTTTTTAATTATTTGATAATAATTA-TTTATATATAAAT
3473549 GCACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGATTTATATTAT
260 GCACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGATTTATATTAT
3473614 TATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
325 TATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
3473676 GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTGGAGTAGTTTACCCTTAATTATTTTGAG
1 GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTGGAGTAGTTTACCCTTAATTATTTTGAG
3473741 CTATTCTCGACAAAATGTCAAATCGCATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
66 CTATTCTCGACAAAATGTCAAATCGCATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
*
3473806 TATAATCCCTAAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
131 TATAATCCCTGAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
*
3473871 ATTATAAAATAATATTTATTTGAAATATTTTTAATTATTTGATAATAATTATTTATATATAAATG
196 ATTATAAAATAATATTTATTTGAAATTTTTTTAATTATTTGATAATAATTATTTATATATAAATG
3473936 CACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGATTTATATTATT
261 CACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGATTTATATTATT
3474001 ATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
326 ATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
3474062 GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTGGAGTAGTTTACCCTTAATTATTTTGAG
1 GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTGGAGTAGTTTACCCTTAATTATTTTGAG
3474127 CTATTCTCGACAAAATGTCAAATCGCATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
66 CTATTCTCGACAAAATGTCAAATCGCATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
3474192 TATAATCCCTGAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
131 TATAATCCCTGAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
3474257 ATTATAAAATAATATTTATTTGAAATTTTTTTAATTATTTGATAATAATTATTTATATATAAATG
196 ATTATAAAATAATATTTATTTGAAATTTTTTTAATTATTTGATAATAATTATTTATATATAAATG
3474322 CACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGA-TT-TA-TATT
261 CACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGATTTATATTATT
3474384 ATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
326 ATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
3474445 G-GAAA
1 GTGAAA
3474450 CATTTTTAGG
Statistics
Matches: 1152, Mismatches: 6, Indels: 8
0.99 0.01 0.01
Matches are distributed among these distances:
382 4 0.00
383 66 0.06
384 220 0.19
385 27 0.02
386 452 0.39
387 383 0.33
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (386 bp):
GTGAAAACAAAAACTTATCCAAACATTAGTGACTATTGGAGTAGTTTACCCTTAATTATTTTGAG
CTATTCTCGACAAAATGTCAAATCGCATTTTCGATTTATCCTTTTTGCTTGGTCATCCCAAGGTA
TATAATCCCTGAACGAATCTAATAATTTTAAGCCATTGTTGTGTGAATTATTTTTATATATAACG
ATTATAAAATAATATTTATTTGAAATTTTTTTAATTATTTGATAATAATTATTTATATATAAATG
CACTTGGTATTTTAAGGAATAACAAATATTTCTTAGACTGTTAAAATCGTTTGATTTATATTATT
ATTATTATAAATTATTTGAGACATAAGATTAGGTTTTAATATATGATAAAAAATTAGAATA
Found at i:3483077 original size:23 final size:23
Alignment explanation
Indices: 3483051--3483118 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
3483041 TTAACGGACG
**
3483051 TTAAATGAACATGTTCACAAACA
1 TTAAATGAACATGAACACAAACA
* * *
3483074 TTAAACGAATATGAACACGAACA
1 TTAAATGAACATGAACACAAACA
*
3483097 CTAAATG-A-ATGAACACAAACA
1 TTAAATGAACATGAACACAAACA
3483118 T
1 T
3483119 ATATAAAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 12 0.33
22 1 0.03
23 23 0.64
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (23 bp):
TTAAATGAACATGAACACAAACA
Found at i:3483880 original size:35 final size:35
Alignment explanation
Indices: 3483782--3483882 Score: 123
Period size: 35 Copynumber: 2.9 Consensus size: 35
3483772 CTTGCAACAC
* *
3483782 ATTCATCAATTACATTCTAAACCCCAAAATCCAAA
1 ATTCTTCAATTACATTCTAAACCCCAAATTCCAAA
* *
3483817 ATTCTTCAATTACATTCTAAACCTCAAATTCTAAA
1 ATTCTTCAATTACATTCTAAACCCCAAATTCCAAA
* **
3483852 ATAT-TTCAATTACATGCCCAACCCCAAATTC
1 AT-TCTTCAATTACATTCTAAACCCCAAATTC
3483883 ACAATCCAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 56 0.98
36 1 0.02
ACGTcount: A:0.41, C:0.28, G:0.01, T:0.31
Consensus pattern (35 bp):
ATTCTTCAATTACATTCTAAACCCCAAATTCCAAA
Found at i:3484242 original size:149 final size:148
Alignment explanation
Indices: 3484044--3484337 Score: 489
Period size: 149 Copynumber: 2.0 Consensus size: 148
3484034 AAATATGCAA
*
3484044 TTCAATTTATAAAATAGTTAACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
1 TTCAATTTATAAAATAGTTAACTCAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
* * *
3484109 GAATTGAATTGAATTTTCAAGTTTTTGTTTAAATTTAATTATAAATATTTATCATATTATAATAT
66 GAATTGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
3484174 TATTTGATTCTAATTCAG
131 TATTTGATTCTAATTCAG
* * * *
3484192 TTCAGTTTATAAAATAGTTGACTACAAAATTTTTTCTATTTGAGTTTATAAAATTTAAATCAAGT
1 TTCAATTTATAAAATAGTTAACT-CAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATAAAGT
**
3484257 CGAATTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATA
65 CGAATTGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATA
3484322 TTATTTGATTCTAATT
130 TTATTTGATTCTAATT
3484338 TAAATAGTTT
Statistics
Matches: 135, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
148 21 0.16
149 114 0.84
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (148 bp):
TTCAATTTATAAAATAGTTAACTCAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
GAATTGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
TATTTGATTCTAATTCAG
Found at i:3494376 original size:25 final size:22
Alignment explanation
Indices: 3494326--3494369 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3494316 TTAATGGACA
3494326 TAGTGCATCATCCCACTAGACC
1 TAGTGCATCATCCCACTAGACC
*
3494348 TAGTGCCTCATCCCACTAGACC
1 TAGTGCATCATCCCACTAGACC
3494370 AACTAGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.23
Consensus pattern (22 bp):
TAGTGCATCATCCCACTAGACC
Found at i:3498281 original size:20 final size:19
Alignment explanation
Indices: 3498258--3498330 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
3498248 AAGAAATAGA
3498258 AGAAAGCAAAAGAGAGAGAG
1 AGAAAGCAAAAGA-AGAGAG
* *
3498278 AGAAA-TAAAGTAAAAGAGAG
1 AGAAAGCAAA--AGAAGAGAG
**
3498298 AGAAAATAAAAGAA-AGCAG
1 AGAAAGCAAAAGAAGAG-AG
3498317 AGAAAGCAAAAGAA
1 AGAAAGCAAAAGAA
3498331 AAAAAATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 2 0.05
19 20 0.45
20 16 0.36
21 6 0.14
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.04
Consensus pattern (19 bp):
AGAAAGCAAAAGAAGAGAG
Found at i:3498307 original size:16 final size:18
Alignment explanation
Indices: 3498274--3498310 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3498264 CAAAAGAGAG
3498274 AGAGAGAAATAAAGTAAA
1 AGAGAGAAATAAAGTAAA
*
3498292 AGAGAGAGA-AAA-TAAA
1 AGAGAGAAATAAAGTAAA
3498308 AGA
1 AGA
3498311 AAGCAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (18 bp):
AGAGAGAAATAAAGTAAA
Found at i:3500509 original size:58 final size:57
Alignment explanation
Indices: 3500428--3500713 Score: 232
Period size: 58 Copynumber: 5.1 Consensus size: 57
3500418 CCCAAACAAC
*
3500428 ATGATG-TTTTCAAAAGAATTTTTAAAGAAACTAAGCCTGATATTCAGGGGTTTCTTG
1 ATGATGATTTTCAAATGAATTTTTAAAGAAACTAAGCCTGAT-TTCAGGGGTTTCTTG
* * * *
3500485 ATGATGATTTTCAAATGAACTTTTAAAAGAAGCTAAGCCTAATTTTAGGGGTTTC-T-
1 ATGATGATTTTCAAATGAA-TTTTTAAAGAAACTAAGCCTGATTTCAGGGGTTTCTTG
* * * *
3500541 -TGATG-TTTTCAAAATGAGTTTTT--AGAAACTAAACCTGATTTCAGGGATTTTTTG
1 ATGATGATTTTC-AAATGAATTTTTAAAGAAACTAAGCCTGATTTCAGGGGTTTCTTG
* * ** * *
3500595 ATGATTA-TTTCAAAAGAATTTTTAAAGAGGCTAAGCCTAATTTTTAGGGGTTTCTTG
1 ATGATGATTTTCAAATGAATTTTTAAAGAAACTAAGCCTGA-TTTCAGGGGTTTCTTG
* * * * * ** *
3500652 ATGATAATTAT-AAATGACAGATTTT-AATAAATTAAGATTGATTTTCAAGGGTTTCTTG
1 ATGATGATTTTCAAATGA-A-TTTTTAAAGAAACTAAGCCTGA-TTTCAGGGGTTTCTTG
3500710 ATGA
1 ATGA
3500714 GTAAGTCATT
Statistics
Matches: 180, Mismatches: 36, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
52 22 0.12
53 1 0.01
54 19 0.11
55 19 0.11
56 11 0.06
57 31 0.17
58 53 0.29
59 24 0.13
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (57 bp):
ATGATGATTTTCAAATGAATTTTTAAAGAAACTAAGCCTGATTTCAGGGGTTTCTTG
Found at i:3500606 original size:55 final size:54
Alignment explanation
Indices: 3500435--3500656 Score: 200
Period size: 52 Copynumber: 4.0 Consensus size: 54
3500425 AACATGATGT
*
3500435 TTTCAAAAGAATTTTTAAAGAAACTAAGCCTGATATTCAGGGGTTTCTTGATGATGA
1 TTTCAAAAGAATTTTT--AGAAACTAAGCCTGAT-TTCAGGGGTTTCTTGATGATTA
* * * * *
3500492 TTTTCAAATGAACTTTTAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCTTGATG--T-
1 -TTTCAAAAGAA-TTTT--TAGAAACTAAGCCTGATTTCAGGGGTTTCTTGATGATTA
* * * *
3500547 TTTCAAAATGAGTTTTTAGAAACTAAACCTGATTTCAGGGATTTTTTGATGATTA
1 TTTCAAAA-GAATTTTTAGAAACTAAGCCTGATTTCAGGGGTTTCTTGATGATTA
* *
3500602 TTTCAAAAGAATTTTTA-AAGAGGCTAAGCCTAATTTTTAGGGGTTTCTTGATGAT
1 TTTCAAAAGAATTTTTAGAA-A--CTAAGCCTGA-TTTCAGGGGTTTCTTGATGAT
3500657 AATTATAAAT
Statistics
Matches: 132, Mismatches: 21, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
52 28 0.21
53 2 0.02
54 21 0.16
55 10 0.08
56 8 0.06
57 18 0.14
58 27 0.20
59 18 0.14
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (54 bp):
TTTCAAAAGAATTTTTAGAAACTAAGCCTGATTTCAGGGGTTTCTTGATGATTA
Found at i:3500641 original size:109 final size:111
Alignment explanation
Indices: 3500429--3500654 Score: 325
Period size: 109 Copynumber: 2.0 Consensus size: 111
3500419 CCAAACAACA
* *
3500429 TGATGTTTTCAAAAGAATTTTTAAAGAAACTAAGCCTGATATTCAGGGGTTTCTTGATGATGATT
1 TGATGTTTTCAAAAGAATTTTT-AAGAAACTAAACCTGATATTCAGGGATTTCTTGATGATGATT
*
3500494 TTCAAATGAACTTTTAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCT
65 TTCAAAAGAACTTTTAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCT
* * *
3500541 TGATGTTTTCAAAATGAGTTTTT-AGAAACTAAACCTGAT-TTCAGGGATTTTTTGATGATTA-T
1 TGATGTTTTCAAAA-GAATTTTTAAGAAACTAAACCTGATATTCAGGGATTTCTTGATGATGATT
* *
3500603 TTCAAAAGAA-TTTTTAAAGAGGCTAAGCCTAATTTTTAGGGGTTTCT
65 TTCAAAAGAACTTTTAAAAGAAGCTAAGCCTAA-TTTTAGGGGTTTCT
3500650 TGATG
1 TGATG
3500655 ATAATTATAA
Statistics
Matches: 104, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
108 20 0.19
109 29 0.28
110 19 0.18
111 15 0.14
112 14 0.13
113 7 0.07
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (111 bp):
TGATGTTTTCAAAAGAATTTTTAAGAAACTAAACCTGATATTCAGGGATTTCTTGATGATGATTT
TCAAAAGAACTTTTAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCT
Found at i:3501107 original size:41 final size:42
Alignment explanation
Indices: 3501008--3501107 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
3500998 ACAAAAGTTT
* * *
3501008 TTCGGGCCATC-AGTAAGTCTTTCAAGCATGATGCTTAAATCC
1 TTCGGGCCATCTA-TAAGTCTTTCAAGCAAGATGCATAAATCA
* * * * *
3501050 TTTGGGTCATCTATAAGTCTTTCGAGCAAGATG-ATGAGTCA
1 TTCGGGCCATCTATAAGTCTTTCAAGCAAGATGCATAAATCA
3501091 TTCGGGCCATCTATAAG
1 TTCGGGCCATCTATAAG
3501108 ACCTTCAGGC
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 19 0.40
42 27 0.57
43 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (42 bp):
TTCGGGCCATCTATAAGTCTTTCAAGCAAGATGCATAAATCA
Found at i:3501334 original size:41 final size:42
Alignment explanation
Indices: 3501230--3501334 Score: 101
Period size: 41 Copynumber: 2.5 Consensus size: 42
3501220 GAATCAGCAA
* * *
3501230 AAGTCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCATGATGCTT
1 AAGTCTTTCGGGCCATCCA-TAAGTCTTTCGAGCAAGATGCAT
* * * *
3501272 AAATCCTTT--GGTCATCTATAAGTGTTTCGAGCAAGATG-AT
1 AAGT-CTTTCGGGCCATCCATAAGTCTTTCGAGCAAGATGCAT
3501312 AAGTCTTTCGGGCCATCCATAAG
1 AAGTCTTTCGGGCCATCCATAAG
3501335 ACCTTCGATC
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
39 4 0.08
40 4 0.08
41 34 0.69
42 4 0.08
43 3 0.06
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
AAGTCTTTCGGGCCATCCATAAGTCTTTCGAGCAAGATGCAT
Found at i:3502875 original size:20 final size:20
Alignment explanation
Indices: 3502836--3502886 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3502826 AAAATGTGTT
*
3502836 TATGAATAGTA-CGGTATTG
1 TATGAATAGTATCGATATTG
3502855 TATGAATAGTATCGATATTG
1 TATGAATAGTATCGATATTG
*
3502875 TATAAATAGTAT
1 TATGAATAGTAT
3502887 TAATACTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (20 bp):
TATGAATAGTATCGATATTG
Found at i:3502973 original size:19 final size:19
Alignment explanation
Indices: 3502945--3503006 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
3502935 AATGCAAAAT
*
3502945 GTATATCGATACTGCTACA
1 GTATACCGATACTGCTACA
*
3502964 GTATACCGATACTACTACA
1 GTATACCGATACTGCTACA
3502983 GTATACCGATACATTGCTACA
1 GTATACCGATAC--TGCTACA
3503004 GTA
1 GTA
3503007 ATTTCAACCC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 29 0.76
21 9 0.24
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (19 bp):
GTATACCGATACTGCTACA
Found at i:3504974 original size:29 final size:29
Alignment explanation
Indices: 3504938--3505012 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
3504928 TTTCAATTTA
3504938 TCTT-ATTTGGTCACTGAATTTTAAAATC
1 TCTTAATTTGGTCACTGAATTTTAAAATC
3504966 TCTTAATTTGGTCACTGAATTTTAAAATC
1 TCTTAATTTGGTCACTGAATTTTAAAATC
3504995 TCTTAATTTGGTCACTGA
1 TCTTAATTTGGTCACTGA
3505013 CCCAATATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 4 0.09
29 42 0.91
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (29 bp):
TCTTAATTTGGTCACTGAATTTTAAAATC
Found at i:3508832 original size:14 final size:14
Alignment explanation
Indices: 3508813--3508841 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3508803 TATATAAATC
3508813 TTATTTTATTTTAG
1 TTATTTTATTTTAG
3508827 TTATTTTATTTTAG
1 TTATTTTATTTTAG
3508841 T
1 T
3508842 ATTATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTATTTTATTTTAG
Found at i:3513670 original size:2 final size:2
Alignment explanation
Indices: 3513663--3513694 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3513653 GAATTTAATA
3513663 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
3513695 GGGAGAGCAT
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
Done.