Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 12 of 120
Found at i:3301887 original size:17 final size:15
Alignment explanation
Indices: 3301848--3301891 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
3301838 ATTTAATCTT
3301848 AAATTTAAATTTATA
1 AAATTTAAATTTATA
3301863 ATAGATTTAAATTGTATA
1 A-A-ATTTAAATT-TATA
3301881 CAAATTTAAAT
1 -AAATTTAAAT
3301892 CCAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 17 0.68
18 5 0.20
19 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATTTAAATTTATA
Found at i:3313144 original size:201 final size:200
Alignment explanation
Indices: 3312799--3313649 Score: 1145
Period size: 201 Copynumber: 4.2 Consensus size: 200
3312789 GAAGTAGTTC
3312799 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAACTC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTC-AACTC
* * * * * * *
3312864 GAGCAAATCTTCGAACACGGTTTCCTGATAAGACAC-AGAGAAGCAAGTCGAAGCAATGAAAAGG
65 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTA-AGAAGCAGGACGAAGCAATAAAAAGG
* * *
3312928 TCATCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCATCTTCCTGAAGAGATCCAGAAAAGC
129 TTAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAAGAGATCCAGAAAAGC
3312993 GAATCAA
194 GAATCAA
* * *
3313000 AACAAGCGATGCGGTCATCTTCCTGATGAGATACAGAGAAGAGTACCAACTTAACGCTCAA-TGC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACT-C
* *
3313064 GAGCAAACCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGTAGGACGAAGCAATAAAAAGGG
65 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGACGAAGCAATAAAAA-GG
* * *
3313129 TTAGCATCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAAGAGATCCAGAGAAGC
129 TTAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAAGAGATCCAGAAAAGC
3313194 GAATCAA
194 GAATCAA
* * * * * *
3313201 AACAAGCGAGGAGGTCATCTTCCTGATGAGATACAGAGAGGAACACCAACTTAGCGCTCAAGCAC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAA-CTC
* *
3313266 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGACGAAGCAATAAAAAGGT
65 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGACGAAGCAATAAAAAGGT
* *
3313331 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAAGAGATCCAGAGAAGCG
130 TAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAAGAGATCCAGAAAAGCG
3313396 AATCAA
195 AATCAA
* * * * *
3313402 AACAAACGAGGAGGTCATCTTCCTGATGAGATATAGAGAAGAATACTAACTCGACGCTCAGACTC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCA-ACTC
* * * *
3313467 GAGCAAATCTTCAAACCAAGCTTCTTGATGAGACACTGAGAAGCAGGACGAAGCAATAAAAAGGT
65 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGACGAAGCAATAAAAAGGT
* * * * *
3313532 TAGCTTCTTGATGAGACATAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCA-AAGAAGC
130 TAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAAGAGATCCAGAA-AAGC
*
3313596 GAATTAA
194 GAATCAA
* * ** * * *
3313603 AA-TAG-AATTACGGTCATCTTCCTGACGAGACACAGAGAAGAAGACCA
1 AACAAGCGA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCA
3313650 GATCAATGAA
Statistics
Matches: 580, Mismatches: 62, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
199 2 0.00
200 87 0.15
201 431 0.74
202 60 0.10
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (200 bp):
AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACTCG
AGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGACGAAGCAATAAAAAGGTT
AGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAAGAGATCCAGAAAAGCGA
ATCAA
Found at i:3316602 original size:17 final size:15
Alignment explanation
Indices: 3316582--3316625 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
3316572 TTTATTTTGG
3316582 ATTTAAATTTGTATACA
1 ATTTAAATTT-TATA-A
3316599 ATTTAAATCTATTATAA
1 ATTTAAAT-T-TTATAA
3316616 ATTTAAATTT
1 ATTTAAATTT
3316626 AAGATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 17 0.68
18 5 0.20
19 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTAAATTTTATAA
Found at i:3318550 original size:58 final size:59
Alignment explanation
Indices: 3318455--3318793 Score: 420
Period size: 58 Copynumber: 5.8 Consensus size: 59
3318445 TGGACTGTCT
* * ** * *
3318455 AAAAATTATCATTTTATCCTTAAATTTTCCAAAATCCCATTTTTAACCCCGATTTTACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
*
3318514 AAAAATTACCA-TTTACCCCCAAACTTTCCAAAATCCCATTTTTAATCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * *
3318572 AAAACTTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTTACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* *
3318631 -AAAATTACCATTTTACCCCCAAA-TCTTCCAAAGTTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACT-TTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * * * * * *
3318689 -AAAATTACTATTTTACCCCCAAACTCTCCAAAA-CCTC-GTTTTAACCTCAATTTTACT
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCC-CATTTTTAACCCCGATTTCACC
* * *
3318746 AAAAATTACCATTTTACCCTCAAACCTTCTAAAATCCCATTTTTAACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACC
3318794 TCGAATTTTC
Statistics
Matches: 242, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
57 17 0.07
58 160 0.66
59 65 0.27
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
Found at i:3318670 original size:117 final size:115
Alignment explanation
Indices: 3318480--3318824 Score: 416
Period size: 117 Copynumber: 3.0 Consensus size: 115
3318470 ATCCTTAAAT
3318480 TTTCCAAAATCCCATTTTTAACCCCGATTTTACCAAAAATTACCA-TTTACCCCCAAACTTTCCA
1 TTTCCAAAATCCCATTTTTAACCCCGATTTTACC-AAAATTACCATTTTACCCCCAAAC-TTCCA
*
3318544 AAATCCCATTTTTAATCCCGATTTCACCAAAACTTACCATTTTACCCCCGAAC
64 AAATCCCATTTTTAA-CCCGATTTCACCAAAACTTACCATTTTACCCCCAAAC
* *
3318597 TTTCCAAAATCCCATTTTTTACCCCGATTTCACCAAAATTACCATTTTACCCCCAAATCTTCCAA
1 TTTCCAAAATCCCATTTTTAACCCCGATTTTACCAAAATTACCATTTTACCCCCAAA-CTTCCAA
* * *
3318662 AGTTCCATTTTTAACCCCGATTTCACCAAAA-TTACTATTTTACCCCCAAAC
65 AATCCCATTTTTAA-CCCGATTTCACCAAAACTTACCATTTTACCCCCAAAC
* * * * * * *
3318713 TCTCCAAAA-CCTC-GTTTTAACCTCAATTTTACTAAAAATTACCATTTTACCCTCAAACCTTCT
1 TTTCCAAAATCC-CATTTTTAACCCCGATTTTAC-CAAAATTACCATTTTACCCCCAAA-CTTCC
3318776 AAAATCCCATTTTTAACCTCGAATTTTC-CCAAAAC-TA-CATTTTTACCCC
63 AAAATCCCATTTTTAACC-CG-A-TTTCACCAAAACTTACCA-TTTTACCCC
3318825 TCGAGAGTCA
Statistics
Matches: 199, Mismatches: 20, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
115 18 0.09
116 80 0.40
117 96 0.48
118 5 0.03
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (115 bp):
TTTCCAAAATCCCATTTTTAACCCCGATTTTACCAAAATTACCATTTTACCCCCAAACTTCCAAA
ATCCCATTTTTAACCCGATTTCACCAAAACTTACCATTTTACCCCCAAAC
Found at i:3318702 original size:29 final size:29
Alignment explanation
Indices: 3318495--3318708 Score: 142
Period size: 29 Copynumber: 7.3 Consensus size: 29
3318485 AAAATCCCAT
*
3318495 TTTTAACCCCGATTTTACCAAAAATTACCA
1 TTTTAACCCCGATTTCACC-AAAATTACCA
* * *
3318525 -TTTACCCCCAAACTTT--CCAAAA-TCCCA
1 TTTTAACCCC-GA-TTTCACCAAAATTACCA
*
3318552 TTTTTAATCCCGATTTCACCAAAACTTACCA
1 -TTTTAACCCCGATTTCACCAAAA-TTACCA
* *
3318583 TTTTACCCCCGAACTTT--CCAAAA-TCCCA
1 TTTTAACCCCG-A-TTTCACCAAAATTACCA
*
3318611 TTTTTTACCCCGATTTCACCAAAATTACCA
1 -TTTTAACCCCGATTTCACCAAAATTACCA
* * *
3318641 TTTTACCCCCAAATCTT--CCAAAGTT-CCA
1 TTTTAACCCC-GAT-TTCACCAAAATTACCA
*
3318669 TTTTTAACCCCGATTTCACCAAAATTACTA
1 -TTTTAACCCCGATTTCACCAAAATTACCA
*
3318699 TTTTACCCCC
1 TTTTAACCCC
3318709 AAACTCTCCA
Statistics
Matches: 142, Mismatches: 22, Indels: 41
0.69 0.11 0.20
Matches are distributed among these distances:
27 12 0.08
28 15 0.11
29 78 0.55
30 24 0.17
31 10 0.07
32 3 0.02
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (29 bp):
TTTTAACCCCGATTTCACCAAAATTACCA
Found at i:3319570 original size:28 final size:29
Alignment explanation
Indices: 3319522--3319601 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 29
3319512 TAAACTATCA
* *
3319522 AAAAATTATATTTTTGACCCC-AATTTTC
1 AAAAATTACATTTTTGACCCCAAATTTCC
3319550 AAAAATTACATTTTT-ACCCCCAAAATTTCC
1 AAAAATTACATTTTTGA-CCCC-AAATTTCC
3319580 AAAAATT---TTATTTGACCCCAAA
1 AAAAATTACATT-TTTGACCCCAAA
3319602 ACTTTCACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
27 6 0.13
28 25 0.56
29 1 0.02
30 13 0.29
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAATTACATTTTTGACCCCAAATTTCC
Found at i:3319622 original size:29 final size:28
Alignment explanation
Indices: 3319590--3319653 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
3319580 AAAAATTTTA
* * *
3319590 TTTGACCCCAAAACTTTCACAATTACCAT
1 TTTGACCCCAAAA-GTCCAAAATTACCAT
* *
3319619 TTTGCCCCCGAAAGTCCAAAATTACCAT
1 TTTGACCCCAAAAGTCCAAAATTACCAT
3319647 TTTGACC
1 TTTGACC
3319654 TCGAGTATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.30
Consensus pattern (28 bp):
TTTGACCCCAAAAGTCCAAAATTACCAT
Found at i:3320888 original size:22 final size:22
Alignment explanation
Indices: 3320863--3320930 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
3320853 ACGAATTTAT
3320863 ACTTCGGTTTAGCCTATGATGC
1 ACTTCGGTTTAGCCTATGATGC
** **
3320885 ACTTATGTGTTAG--TAT-ATTT
1 ACTTCGGT-TTAGCCTATGATGC
* *
3320905 ACTTCGGTTTAACCGATGATGC
1 ACTTCGGTTTAGCCTATGATGC
3320927 ACTT
1 ACTT
3320931 ATGTGCTAGT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 3 0.09
20 8 0.25
21 5 0.16
22 12 0.38
23 4 0.12
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (22 bp):
ACTTCGGTTTAGCCTATGATGC
Found at i:3320924 original size:42 final size:42
Alignment explanation
Indices: 3320862--3320966 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
3320852 AACGAATTTA
* *
3320862 TACTTCGGTTTAGCCTATGATGCACTTATGTGTTAGTATATT
1 TACTTCGGTTTAGCCGATGATGCACTTATGTGCTAGTATATT
*
3320904 TACTTCGGTTTAACCGATGATGCACTTATGTGCTAGTATATT
1 TACTTCGGTTTAGCCGATGATGCACTTATGTGCTAGTATATT
* * *
3320946 AACTTCAGTTTAGTCGATGAT
1 TACTTCGGTTTAGCCGATGAT
3320967 ATCTTAAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (42 bp):
TACTTCGGTTTAGCCGATGATGCACTTATGTGCTAGTATATT
Found at i:3329233 original size:15 final size:15
Alignment explanation
Indices: 3329213--3329245 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3329203 ATTAATTGTA
3329213 ATATTTTTTTATAAT
1 ATATTTTTTTATAAT
*
3329228 ATATTTTTTTATATT
1 ATATTTTTTTATAAT
3329243 ATA
1 ATA
3329246 CATATCCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTTTTTTATAAT
Found at i:3330456 original size:8 final size:8
Alignment explanation
Indices: 3330443--3330486 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
3330433 GGAGTTGCAA
3330443 TTTTTTCT
1 TTTTTTCT
3330451 TTTTTTC-
1 TTTTTTCT
3330458 TTTTTTCT
1 TTTTTTCT
*
3330466 GTTTTTCTT
1 TTTTTTC-T
3330475 TTATTTTCT
1 TT-TTTTCT
3330484 TTT
1 TTT
3330487 ACAAAACACT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 7 0.23
8 14 0.45
9 5 0.16
10 5 0.16
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.84
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3330463 original size:15 final size:15
Alignment explanation
Indices: 3330443--3330476 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3330433 GGAGTTGCAA
*
3330443 TTTTTTCTTTTTTTC
1 TTTTTTCTGTTTTTC
3330458 TTTTTTCTGTTTTTC
1 TTTTTTCTGTTTTTC
3330473 TTTT
1 TTTT
3330477 ATTTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (15 bp):
TTTTTTCTGTTTTTC
Found at i:3330508 original size:145 final size:145
Alignment explanation
Indices: 3330333--3330601 Score: 493
Period size: 145 Copynumber: 1.9 Consensus size: 145
3330323 CTTTTTCTGT
*
3330333 TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAGCAACACGATGGAGCAAACA
1 TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
* * *
3330398 AAGTGCTGCTGACGTACTCAGTAATTCCAAGCAGTGGAGTTGCAATTTTTTCTTTTTTTCTTTTT
66 AAGTGCTGCTGACATACTCAGTAATTCCAAGCAGTGGAGTGGCAATTTTTTCTTCTTTTCTTTTT
3330463 TCTGTTTTTCTTTTA
131 TCTGTTTTTCTTTTA
3330478 TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
1 TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
*
3330543 AAGTGTTGCTGACATACTCAGTAATTCCAAGCAGTGGAGTGGCAATTTTTTCTTCTTTT
66 AAGTGCTGCTGACATACTCAGTAATTCCAAGCAGTGGAGTGGCAATTTTTTCTTCTTTT
3330602 ATTTGTATTT
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
145 119 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (145 bp):
TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
AAGTGCTGCTGACATACTCAGTAATTCCAAGCAGTGGAGTGGCAATTTTTTCTTCTTTTCTTTTT
TCTGTTTTTCTTTTA
Found at i:3340496 original size:30 final size:30
Alignment explanation
Indices: 3340462--3340518 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3340452 TATTTTTTTA
3340462 TTTATTTC-AATATGTCACACTAACAAATAT
1 TTTATTTCGAA-ATGTCACACTAACAAATAT
3340492 TTTATTTCGAAATGTCACACTAACAAA
1 TTTATTTCGAAATGTCACACTAACAAA
3340519 CTTCCATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (30 bp):
TTTATTTCGAAATGTCACACTAACAAATAT
Found at i:3344686 original size:3 final size:3
Alignment explanation
Indices: 3344680--3344710 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3344670 ATAATAATAA
3344680 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3344711 TTAGACAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3345463 original size:14 final size:14
Alignment explanation
Indices: 3345421--3345465 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3345411 AAATTATTTT
3345421 TTTGAAATATAAAA
1 TTTGAAATATAAAA
* * *
3345435 TTATTAAAAAAAAAA
1 TT-TGAAATATAAAA
3345450 TTTGAAATATAAAA
1 TTTGAAATATAAAA
3345464 TT
1 TT
3345466 ATTATATGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TTTGAAATATAAAA
Found at i:3346579 original size:35 final size:38
Alignment explanation
Indices: 3346540--3346616 Score: 106
Period size: 35 Copynumber: 2.1 Consensus size: 38
3346530 TAAAATCATA
3346540 TAATAATTTTATA-TT-AAAAAATAA-TATAATAATTT
1 TAATAATTTTATATTTAAAAAAATAATTATAATAATTT
* *
3346575 TAATAATTTTATATTTCAAAAAAATAATTTTAATAGTTT
1 TAATAATTTTATATTT-AAAAAAATAATTATAATAATTT
3346614 TAA
1 TAA
3346617 AATCATTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
35 13 0.36
36 2 0.06
38 9 0.25
39 12 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (38 bp):
TAATAATTTTATATTTAAAAAAATAATTATAATAATTT
Found at i:3347111 original size:18 final size:17
Alignment explanation
Indices: 3347075--3347114 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3347065 TAATAAAAAT
3347075 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
3347092 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
3347107 ATAATTTT
1 ATAATTTT
3347115 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:3347817 original size:29 final size:30
Alignment explanation
Indices: 3347751--3347823 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 30
3347741 ATTTTTTACC
3347751 TAAATAATATAAAAAAAAAATTATACACTA
1 TAAATAATATAAAAAAAAAATTATACACTA
* *
3347781 GAATATAATATAAAAATAAAATTAATA-ACT-
1 TAA-ATAATATAAAAAAAAAATT-ATACACTA
3347811 TAAATAATATAAA
1 TAAATAATATAAA
3347824 TATATATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 10 0.26
30 4 0.11
31 21 0.55
32 3 0.08
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (30 bp):
TAAATAATATAAAAAAAAAATTATACACTA
Found at i:3353967 original size:8 final size:8
Alignment explanation
Indices: 3353946--3353978 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
3353936 TCATGTTTTT
3353946 TTTTAATA
1 TTTTAATA
3353954 -TTTAATA
1 TTTTAATA
3353961 TTTTAATA
1 TTTTAATA
3353969 TTTTAATA
1 TTTTAATA
3353977 TT
1 TT
3353979 CTTACAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTAATA
Found at i:3362986 original size:30 final size:30
Alignment explanation
Indices: 3362938--3362998 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
3362928 GAGTCCAAAT
*
3362938 TTTAAAATTTGATATTTTATATATTTCTTC
1 TTTAAAATATGATATTTTATATATTTCTTC
* *
3362968 TTTAGAAATATGAT-TTTTATTTATTTTTTC
1 TTTA-AAATATGATATTTTATATATTTCTTC
3362998 T
1 T
3362999 ATCATTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTAAAATATGATATTTTATATATTTCTTC
Found at i:3366210 original size:21 final size:21
Alignment explanation
Indices: 3366180--3366223 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3366170 AAAATTTTGA
*
3366180 TATATATTT-ATGTAAAATAAT
1 TATATATTTAATATAAAA-AAT
*
3366201 TATATCTTTAATATAAAAAAT
1 TATATATTTAATATAAAAAAT
3366222 TA
1 TA
3366224 ATACTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TATATATTTAATATAAAAAAT
Found at i:3370599 original size:18 final size:17
Alignment explanation
Indices: 3370576--3370633 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
3370566 TCAACAAAAA
3370576 ATTATAAATATATTTATT
1 ATTATAAATATATTT-TT
3370594 ATTATATAATTATATATTTT
1 ATTATA-AA-TATAT-TTTT
* * *
3370614 TTTAAAAATATATTTGT
1 ATTATAAATATATTTTT
3370631 ATT
1 ATT
3370634 GCATTTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 5 0.15
18 11 0.33
19 4 0.12
20 11 0.33
21 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTATAAATATATTTTT
Found at i:3372446 original size:33 final size:32
Alignment explanation
Indices: 3372409--3372495 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 32
3372399 ATATTAAGAT
3372409 TTTTTTATTTAATTTGGTACTT-GAACTTGACAC
1 TTTTTT-TTTAATTTGGTACTTAG-ACTTGACAC
* * * *
3372442 -TTTTTCTTAATTCGATACATAGACTTGACAC
1 TTTTTTTTTAATTTGGTACTTAGACTTGACAC
3372473 TTTTTTTTTTAATTTGGTACTTA
1 -TTTTTTTTTAATTTGGTACTTA
3372496 ATAATTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
31 20 0.47
32 6 0.14
33 17 0.40
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (32 bp):
TTTTTTTTTAATTTGGTACTTAGACTTGACAC
Found at i:3374649 original size:25 final size:25
Alignment explanation
Indices: 3374621--3374689 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
3374611 AAATATAAAT
*
3374621 TTAAAATATTTAATTTTAATTGAAA
1 TTAAAATATTTAATTTTAAATGAAA
* * *
3374646 TT-AAATATATATTTTATAAATGAAG
1 TTAAAATATTTAATTT-TAAATGAAA
*
3374671 TCAAATATATTTAATTTTA
1 TTAAA-ATATTTAATTTTA
3374690 TAGCTTTTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
24 11 0.32
25 10 0.29
26 4 0.12
27 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (25 bp):
TTAAAATATTTAATTTTAAATGAAA
Found at i:3374712 original size:7 final size:7
Alignment explanation
Indices: 3374700--3374726 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3374690 TAGCTTTTTC
3374700 AATTTAA
1 AATTTAA
3374707 AATTTAA
1 AATTTAA
3374714 AATTTAA
1 AATTTAA
3374721 AATTTA
1 AATTTA
3374727 CTTAGGTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:3375546 original size:19 final size:19
Alignment explanation
Indices: 3375522--3375559 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3375512 TAAAAATAAT
3375522 TAAATCCATATATTTCTAC
1 TAAATCCATATATTTCTAC
3375541 TAAATCCATATATTTCTAC
1 TAAATCCATATATTTCTAC
3375560 ATTACCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATCCATATATTTCTAC
Found at i:3378360 original size:29 final size:27
Alignment explanation
Indices: 3378327--3378383 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
3378317 CAAGAACATT
3378327 TTTATTTAATTATAATATATATTT-TAAAA
1 TTTATTTAATTA-AA-AT-TATTTATAAAA
*
3378356 TTTATTTTATTAAAATTATTTATAAAA
1 TTTATTTAATTAAAATTATTTATAAAA
3378383 T
1 T
3378384 ATTACAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 5 0.19
27 8 0.31
28 2 0.08
29 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATTTAATTAAAATTATTTATAAAA
Found at i:3379716 original size:13 final size:14
Alignment explanation
Indices: 3379689--3379717 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3379679 AATTTTTTTT
3379689 ACCTTGAATCTCGA
1 ACCTTGAATCTCGA
3379703 ACCTTGAA-CTCGA
1 ACCTTGAATCTCGA
3379716 AC
1 AC
3379718 TCTAACCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (14 bp):
ACCTTGAATCTCGA
Found at i:3390637 original size:26 final size:26
Alignment explanation
Indices: 3390604--3390653 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3390594 CAATAAAACT
3390604 AAAATCT-AACTTAAAAAAGAAAAGGG
1 AAAATCTAAAC-TAAAAAAGAAAAGGG
*
3390630 AAAATCTAAACTAAAAATGAAAAG
1 AAAATCTAAACTAAAAAAGAAAAG
3390654 AAAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (26 bp):
AAAATCTAAACTAAAAAAGAAAAGGG
Found at i:3395602 original size:1 final size:1
Alignment explanation
Indices: 3395596--3395623 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3395586 CCTCCCCTCA
3395596 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
3395624 GCGGAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3400667 original size:22 final size:21
Alignment explanation
Indices: 3400623--3400669 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
3400613 CGATCTAAGG
*
3400623 AAAAATAAAAGAAACAGATTT
1 AAAAATAAAAGAAACAGAATT
* *
3400644 AAAAATTAAAGAAAATAGAATT
1 AAAAATAAAAG-AAACAGAATT
3400666 AAAA
1 AAAA
3400670 GAAATAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (21 bp):
AAAAATAAAAGAAACAGAATT
Found at i:3405920 original size:22 final size:22
Alignment explanation
Indices: 3405892--3405947 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
3405882 AACCAAGTCA
3405892 AACCGTTGACCGACTGTTGACC
1 AACCGTTGACCGACTGTTGACC
3405914 AACCGTTGACCGACTGTTGACC
1 AACCGTTGACCGACTGTTGACC
* *
3405936 GACCATTGACCG
1 AACCGTTGACCG
3405948 TTGACCGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.21
Consensus pattern (22 bp):
AACCGTTGACCGACTGTTGACC
Found at i:3405944 original size:11 final size:11
Alignment explanation
Indices: 3405893--3405947 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
3405883 ACCAAGTCAA
3405893 ACCGTTGACCG
1 ACCGTTGACCG
* *
3405904 ACTGTTGACCA
1 ACCGTTGACCG
3405915 ACCGTTGACCG
1 ACCGTTGACCG
*
3405926 ACTGTTGACCG
1 ACCGTTGACCG
*
3405937 ACCATTGACCG
1 ACCGTTGACCG
3405948 TTGACCGTCG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.22
Consensus pattern (11 bp):
ACCGTTGACCG
Found at i:3407026 original size:23 final size:23
Alignment explanation
Indices: 3406995--3407261 Score: 273
Period size: 24 Copynumber: 11.4 Consensus size: 23
3406985 GTTCGTGATC
3406995 GTTCGTTTAACGTTCGTGAACAT
1 GTTCGTTTAACGTTCGTGAACAT
* *
3407018 GTTCATTTAACGTTTGTGAACAT
1 GTTCGTTTAACGTTCGTGAACAT
*
3407041 GTTCGTTTATATGTTCGTGAACAT
1 GTTCGTTTA-ACGTTCGTGAACAT
* * ** *
3407065 TTTAGTTTAACGTTCGTTTATAT
1 GTTCGTTTAACGTTCGTGAACAT
3407088 GTTCGTTTAACGTTCGTGAACAT
1 GTTCGTTTAACGTTCGTGAACAT
*
3407111 GTTCGTTTATATGTTCGTGAACAT
1 GTTCGTTTA-ACGTTCGTGAACAT
* ** *
3407135 TTTCGTTTAACGTTCGTTTATAT
1 GTTCGTTTAACGTTCGTGAACAT
*
3407158 GTTCGTTTAACGTTCGCGAACAT
1 GTTCGTTTAACGTTCGTGAACAT
* **
3407181 GTTCGTTTATGCGTTCGCAAACAT
1 GTTCGTTTA-ACGTTCGTGAACAT
* **
3407205 GTTCGTTTATGCGTTCGCAAACAT
1 GTTCGTTTA-ACGTTCGTGAACAT
** *
3407229 GTTCGTTTATGTGTTCGCGAACAT
1 GTTCGTTTA-ACGTTCGTGAACAT
*
3407253 GTTCATTTA
1 GTTCGTTTA
3407262 TGTTAACTAT
Statistics
Matches: 209, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
23 103 0.49
24 106 0.51
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (23 bp):
GTTCGTTTAACGTTCGTGAACAT
Found at i:3407197 original size:35 final size:35
Alignment explanation
Indices: 3407016--3407190 Score: 164
Period size: 35 Copynumber: 5.0 Consensus size: 35
3407006 GTTCGTGAAC
* *
3407016 ATGTTCATTTAACGTTTGTGAACATGTTCGTTTAT
1 ATGTTCGTTTAACGTTCGTGAACATGTTCGTTTAT
* * * *
3407051 ATGTTCG-TGAACATTTTAGTTTAAC--GTTCGTTTAT
1 ATGTTCGTTTAAC--GTTCG-TGAACATGTTCGTTTAT
3407086 ATGTTCGTTTAACGTTCGTGAACATGTTCGTTTAT
1 ATGTTCGTTTAACGTTCGTGAACATGTTCGTTTAT
* * *
3407121 ATGTTCG-TGAACATTTTCGTTTAAC--GTTCGTTTAT
1 ATGTTCGTTTAAC--GTTCG-TGAACATGTTCGTTTAT
*
3407156 ATGTTCGTTTAACGTTCGCGAACATGTTCGTTTAT
1 ATGTTCGTTTAACGTTCGTGAACATGTTCGTTTAT
3407191 GCGTTCGCAA
Statistics
Matches: 112, Mismatches: 16, Indels: 24
0.74 0.11 0.16
Matches are distributed among these distances:
33 7 0.06
34 15 0.13
35 67 0.60
36 15 0.13
37 8 0.07
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (35 bp):
ATGTTCGTTTAACGTTCGTGAACATGTTCGTTTAT
Found at i:3407197 original size:70 final size:70
Alignment explanation
Indices: 3406996--3407262 Score: 327
Period size: 70 Copynumber: 3.8 Consensus size: 70
3406986 TTCGTGATCG
* * * *
3406996 TTCGTTTAACGTTCGTGAACATGTTCATTTAACGTTTGTGAACATGTTCGTTTATATGTTCGTGA
1 TTCGTTTAACGTTCGTTAACATGTTCGTTTAACGTTCGCGAACATGTTCGTTTATATGTTCGTGA
3407061 ACATT
66 ACATT
* * * *
3407066 TTAGTTTAACGTTCGTTTATATGTTCGTTTAACGTTCGTGAACATGTTCGTTTATATGTTCGTGA
1 TTCGTTTAACGTTCGTTAACATGTTCGTTTAACGTTCGCGAACATGTTCGTTTATATGTTCGTGA
3407131 ACATT
66 ACATT
* * ** **
3407136 TTCGTTTAACGTTCGTTTATATGTTCGTTTAACGTTCGCGAACATGTTCGTTTATGCGTTCGCAA
1 TTCGTTTAACGTTCGTTAACATGTTCGTTTAACGTTCGCGAACATGTTCGTTTATATGTTCGTGA
*
3407201 ACATG
66 ACATT
* ** ** *
3407206 TTCGTTTATGCGTTCGCAAACATGTTCGTTTATGTGTTCGCGAACATGTTCATTTAT
1 TTCGTTTA-ACGTTCGTTAACATGTTCGTTTA-ACGTTCGCGAACATGTTCGTTTAT
3407263 GTTAACTATC
Statistics
Matches: 174, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
70 135 0.78
71 18 0.10
72 21 0.12
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (70 bp):
TTCGTTTAACGTTCGTTAACATGTTCGTTTAACGTTCGCGAACATGTTCGTTTATATGTTCGTGA
ACATT
Found at i:3407633 original size:10 final size:10
Alignment explanation
Indices: 3407615--3407646 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3407605 GATTAAGTAC
*
3407615 CTTCGAAATT
1 CTTCAAAATT
3407625 CTTCAAAATT
1 CTTCAAAATT
3407635 CTTCAAAATT
1 CTTCAAAATT
3407645 CT
1 CT
3407647 AACTTCAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (10 bp):
CTTCAAAATT
Found at i:3410189 original size:32 final size:33
Alignment explanation
Indices: 3410148--3410213 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3410138 GAGAGAGAGA
3410148 GAGAGTTT-AAAAACCAGGAGTCCCAAAAGCTT
1 GAGAGTTTAAAAAACCAGGAGTCCCAAAAGCTT
*
3410180 GAGAGTTTAAAAAACCAGTAGTCCCAAAAGCTT
1 GAGAGTTTAAAAAACCAGGAGTCCCAAAAGCTT
3410213 G
1 G
3410214 GGGTTCTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 8 0.25
33 24 0.75
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (33 bp):
GAGAGTTTAAAAAACCAGGAGTCCCAAAAGCTT
Found at i:3410909 original size:26 final size:26
Alignment explanation
Indices: 3410880--3410930 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
3410870 GAGTGAAATT
3410880 GTTTTCAATATCAATAATGGCTAGAG
1 GTTTTCAATATCAATAATGGCTAGAG
3410906 GTTTTCAATATCAATAATGGCTAGA
1 GTTTTCAATATCAATAATGGCTAGA
3410931 AATTATGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (26 bp):
GTTTTCAATATCAATAATGGCTAGAG
Found at i:3411874 original size:12 final size:12
Alignment explanation
Indices: 3411857--3411963 Score: 121
Period size: 12 Copynumber: 9.2 Consensus size: 12
3411847 TCTGATGGGT
3411857 CTAATAAACGAG
1 CTAATAAACGAG
*
3411869 CTAATAAACGAA
1 CTAATAAACGAG
* *
3411881 C-CATAAACGAA
1 CTAATAAACGAG
*
3411892 C-CATAAACGAG
1 CTAATAAACGAG
*
3411903 CTTATAAACGAG
1 CTAATAAACGAG
*
3411915 CTATTAAACGAG
1 CTAATAAACGAG
3411927 CTAATAAACGAG
1 CTAATAAACGAG
*
3411939 CTAATAAACGAA
1 CTAATAAACGAG
*
3411951 C-CATAAACGAG
1 CTAATAAACGAG
3411962 CT
1 CT
3411964 TGTTCGTAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
11 29 0.35
12 54 0.65
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.17
Consensus pattern (12 bp):
CTAATAAACGAG
Found at i:3412305 original size:3 final size:3
Alignment explanation
Indices: 3412297--3412336 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
3412287 TTACATCATT
*
3412297 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTC TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3412337 TTGGTTTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3418067 original size:29 final size:28
Alignment explanation
Indices: 3418035--3418188 Score: 80
Period size: 29 Copynumber: 5.2 Consensus size: 28
3418025 TTTGATGAAA
*
3418035 TTGGGGTTAAAAATGGGATTTTGGAAAGT
1 TTGGGG-TAAAAATGGAATTTTGGAAAGT
**** *
3418064 TTGGGGGTAAAAGGTATTTTTTTTTGGTAAA-A
1 TT-GGGGTAAAA---ATGGAATTTTGG-AAAGT
* * **
3418096 TCGGGGTTAAAAATGGGATTTTGGGGAGT
1 TTGGGG-TAAAAATGGAATTTTGGAAAGT
3418125 TTGAGGGT-AAAATGGTAATTTTTGG-AAGT
1 TTG-GGGTAAAAATGG-AA-TTTTGGAAAGT
* *
3418154 TTCGGGGTCAAAATGGAATTTTGGGAAGT
1 TT-GGGGTAAAAATGGAATTTTGGAAAGT
3418183 TTGGGG
1 TTGGGG
3418189 ACTAAAGAGT
Statistics
Matches: 96, Mismatches: 16, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
28 18 0.19
29 36 0.38
30 21 0.22
31 4 0.04
32 14 0.15
33 3 0.03
ACGTcount: A:0.27, C:0.02, G:0.35, T:0.36
Consensus pattern (28 bp):
TTGGGGTAAAAATGGAATTTTGGAAAGT
Found at i:3418102 original size:61 final size:62
Alignment explanation
Indices: 3418007--3418147 Score: 182
Period size: 61 Copynumber: 2.3 Consensus size: 62
3417997 TTGGATGCCC
* * *
3418007 GAGGGTGAAATGGTAA---TTTTTGATGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTT
1 GAGGGTAAAATGGTAATTTTTTTTGATAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
* * * **
3418066 GGGGGTAAAA-GGTATTTTTTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGGGAGTTT
1 GAGGGTAAAATGGTAATTTTTTTTGATAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
3418127 GAGGGTAAAATGGTAATTTTT
1 GAGGGTAAAATGGTAATTTTT
3418148 GGAAGTTTCG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 4 0.06
59 8 0.12
61 47 0.69
62 9 0.13
ACGTcount: A:0.30, C:0.01, G:0.33, T:0.37
Consensus pattern (62 bp):
GAGGGTAAAATGGTAATTTTTTTTGATAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
Found at i:3418188 original size:28 final size:27
Alignment explanation
Indices: 3418105--3418188 Score: 105
Period size: 29 Copynumber: 3.0 Consensus size: 27
3418095 ATCGGGGTTA
* *
3418105 AAAATGGGATTTTGGGGAGTTTGAGGGT
1 AAAATGGAATTTTGGGAAGTTTG-GGGT
*
3418133 AAAATGGTAATTTTTGGAAGTTTCGGGGT
1 AAAATGG-AATTTTGGGAAGTTT-GGGGT
3418162 CAAAATGGAATTTTGGGAAGTTTGGGG
1 -AAAATGGAATTTTGGGAAGTTTGGGG
3418189 ACTAAAGAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.22
29 30 0.61
30 8 0.16
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.33
Consensus pattern (27 bp):
AAAATGGAATTTTGGGAAGTTTGGGGT
Found at i:3418969 original size:26 final size:26
Alignment explanation
Indices: 3418923--3418974 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
3418913 TTCTTTTTCG
*
3418923 TTTTTTAAAAAACTTTCTTTGATTTTT
1 TTTTTTAAAAAACTCTCTTTG-TTTTT
3418950 TTTTTTAAAAAAAC-CT-TTTGTTTTT
1 TTTTTT-AAAAAACTCTCTTTGTTTTT
3418975 CATTCAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.22
26 4 0.17
27 7 0.30
28 7 0.30
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTTTTAAAAAACTCTCTTTGTTTTT
Found at i:3419283 original size:16 final size:16
Alignment explanation
Indices: 3419262--3419294 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3419252 TATTTAAAAT
*
3419262 TATTAATTATTATTAA
1 TATTAATTACTATTAA
3419278 TATTAATTACTATTAA
1 TATTAATTACTATTAA
3419294 T
1 T
3419295 GCCAACACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATTACTATTAA
Found at i:3421066 original size:201 final size:199
Alignment explanation
Indices: 3420419--3421069 Score: 982
Period size: 201 Copynumber: 3.2 Consensus size: 199
3420409 TTCATTGACC
* * * * * *
3420419 TGGTCTTCTTCCCTGTGTCTCAACAGGAAGATGACCGCAATC-ATCTGTTTTAATTCGCTTCTCT
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGC-CTCGCT-TGTTTTAATTCGCTTCTCT
** * *
3420483 GGATCTCCTCAGGAAGATAAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA
64 GGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTA
* *
3420548 TTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCAAAGATTTACTCGTATTGAGC
129 TTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGT-TTGAGC
*
3420613 GTTAAGT
193 GTTGAGT
* * *
3420620 TGGTGTTTTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTCGTTTTAATTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGG
* *
3420685 ATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTGTCTTATCAGGAAGCTAACCATTTTATT
66 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATT
* *
3420750 GCTTCGACCTGCTTCTCAGCGTCTCATCAGGAAG-TCGGGCTCGAAGATTTACTCGCATTTGAGC
131 GCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCT-GGGTTCGAAGATTTACTCG--TTTGAGC
3420814 GTTGAGT
193 GTTGAGT
3420821 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGG
*
3420886 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATT
66 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATT
* * * *
3420951 GCTTCGACTTGCTTCTCAATGTCTCATCTGGAAGCTGGGTTCGAAGATTTGCTCGTGTTGAGCGT
131 GCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGT-TTGAGCGT
3421016 TGAGT
195 TGAGT
*
3421021 TGGTATTCTTCTCTGTATTTCATCAGGAAGATGACCCGCCTCGCTTGTT
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGA-CCGCCTCGCTTGTT
3421070 GAACTACTCC
Statistics
Matches: 411, Mismatches: 32, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
199 2 0.00
200 176 0.43
201 231 0.56
202 2 0.00
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (199 bp):
TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGG
ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATT
GCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGTTTGAGCGTT
GAGT
Found at i:3433321 original size:57 final size:58
Alignment explanation
Indices: 3433169--3433421 Score: 375
Period size: 58 Copynumber: 4.4 Consensus size: 58
3433159 TTGACTTTCG
*
3433169 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGGATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAGTTCA
* * *
3433227 AGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAGTTCA
*
3433285 GGGGT-AAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTAGG-GAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTT-GGAAAGTTCA
* * * * ** *
3433342 GGGGTAAAATGGTATTTTTTGGTGAAATCGAGGTTAAAATAGAATTTTGGGGAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAGTTCA
3433400 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
3433422 AAGTTTCGGG
Statistics
Matches: 178, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
57 53 0.30
58 125 0.70
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAGTTCA
Found at i:3433361 original size:115 final size:116
Alignment explanation
Indices: 3433169--3433421 Score: 393
Period size: 115 Copynumber: 2.2 Consensus size: 116
3433159 TTGACTTTCG
3433169 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGGATTTTGGAAAGTTCAAGGGTAA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGGATTTTGGAAAGTTCAAGGGTAA
* * *
3433234 AATGGTAATTTTTGGTAAAATCGGGGTTAAAATGGGATTTTGGAAAGTTTA
66 AATGGTAATTTTTGGTAAAATCGAGGTTAAAATAGAATTTTGGAAAGTTTA
* * *
3433285 GGGGT-AAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTAGG-GAGTTCAGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGGATTTT-GGAAAGTTCAAGGGTA
* * **
3433348 AAATGGTATTTTTTGGTGAAATCGAGGTTAAAATAGAATTTTGGGGAGTTTA
65 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAATAGAATTTTGGAAAGTTTA
3433400 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
3433422 AAGTTTCGGG
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
115 102 0.82
116 23 0.18
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.34
Consensus pattern (116 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGGATTTTGGAAAGTTCAAGGGTAA
AATGGTAATTTTTGGTAAAATCGAGGTTAAAATAGAATTTTGGAAAGTTTA
Found at i:3433447 original size:30 final size:28
Alignment explanation
Indices: 3433169--3433461 Score: 141
Period size: 30 Copynumber: 10.1 Consensus size: 28
3433159 TTGACTTTCG
* *
3433169 GGGGTAAAATGGTAATTTTTGGTGAA-ATCA
1 GGGGTAAAATGG-AA-TTTTGG-GAAGTTTA
* * * *
3433199 GGGTTAAAATGGGATTTTGGAAAGTTCA
1 GGGGTAAAATGGAATTTTGGGAAGTTTA
* * ** *
3433227 AGGGTAAAATGGTAATTTTTGGTAA-AATC
1 GGGGTAAAATGG-AA-TTTTGGGAAGTTTA
* *
3433256 GGGGTTAAAATGGGATTTTGGAAAGTTTA
1 GGGG-TAAAATGGAATTTTGGGAAGTTTA
* *
3433285 GGGGT-AAATGGTAATTTTTGGTGAA--ATC
1 GGGGTAAAATGG-AA-TTTTGG-GAAGTTTA
* *
3433313 GGGGTTAAAATGGGATTTTAGGG-AGTTCA
1 GGGG-TAAAATGGAATTTT-GGGAAGTTTA
* * **
3433342 GGGGTAAAATGGTATTTTTTGGTGAAATCGA
1 GGGGTAAAATGG-A-ATTTTGG-GAAGTTTA
* * *
3433373 -GGTTAAAATAGAATTTTGGGGAGTTTA
1 GGGGTAAAATGGAATTTTGGGAAGTTTA
* *
3433400 GGGGTAAAATGGTAATTTTTGGAAGTTTC
1 GGGGTAAAATGG-AATTTTGGGAAGTTTA
*
3433429 GGGGTCAAAAATGGAATTTTGGGAAGTTGA
1 GGGGT--AAAATGGAATTTTGGGAAGTTTA
3433459 GGG
1 GGG
3433462 ACTAGAGAGC
Statistics
Matches: 196, Mismatches: 46, Indels: 42
0.69 0.16 0.15
Matches are distributed among these distances:
27 13 0.07
28 62 0.32
29 46 0.23
30 65 0.33
31 10 0.05
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (28 bp):
GGGGTAAAATGGAATTTTGGGAAGTTTA
Found at i:3433787 original size:32 final size:33
Alignment explanation
Indices: 3433726--3433789 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
3433716 TTATTGGGCC
*
3433726 AAATTAAGAATAATTAAAAGTATGAAAAGGACT
1 AAATTAAGAATAATTAAAAGAATGAAAAGGACT
*
3433759 AAATTAA-AATAATTAAAA-AATGCGAAAGGAC
1 AAATTAAGAATAATTAAAAGAATG-AAAAGGAC
3433790 CAAACGTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 3 0.11
32 18 0.64
33 7 0.25
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (33 bp):
AAATTAAGAATAATTAAAAGAATGAAAAGGACT
Found at i:3434192 original size:24 final size:25
Alignment explanation
Indices: 3434165--3434213 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
3434155 TATTTCTTTT
3434165 TTTCTTT-TTCGTTTTTTAAAAAAC
1 TTTCTTTATTCGTTTTTTAAAAAAC
**
3434189 TTTCTTTGATTTTTTTTTTAAAAAA
1 TTTCTTT-ATTCGTTTTTTAAAAAA
3434214 ACCTTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTCTTTATTCGTTTTTTAAAAAAC
Found at i:3434221 original size:25 final size:25
Alignment explanation
Indices: 3434176--3434226 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
3434166 TTCTTTTTCG
*
3434176 TTTTTTAAAAAACTTTCTTTGATTTT
1 TTTTTTAAAAAACTCTCTTTG-TTTT
3434202 TTTTTTAAAAAAAC-CT-TTTGTTTT
1 TTTTTT-AAAAAACTCTCTTTGTTTT
3434226 T
1 T
3434227 CATTCAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.22
25 4 0.17
26 7 0.30
27 7 0.30
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTTTTAAAAAACTCTCTTTGTTTT
Found at i:3434533 original size:16 final size:16
Alignment explanation
Indices: 3434512--3434544 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3434502 TATTTAAAAT
*
3434512 TATTAATTATTATTAA
1 TATTAATTACTATTAA
3434528 TATTAATTACTATTAA
1 TATTAATTACTATTAA
3434544 T
1 T
3434545 GCCAACACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATTACTATTAA
Found at i:3434985 original size:17 final size:18
Alignment explanation
Indices: 3434963--3435008 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
3434953 TTATTTGGAC
*
3434963 ATTT-AATTTTATTTTAA
1 ATTTAAATTTTATATTAA
3434980 ATTTAAATTTT-TATTAA
1 ATTTAAATTTTATATTAA
*
3434997 GTTTAAATTTTA
1 ATTTAAATTTTA
3435009 GAAAAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTAAATTTTATATTAA
Found at i:3437120 original size:15 final size:15
Alignment explanation
Indices: 3437100--3437131 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3437090 AGCTAAACCT
3437100 TTTTTGTCTTCTTTG
1 TTTTTGTCTTCTTTG
3437115 TTTTTGTCTTCTTTG
1 TTTTTGTCTTCTTTG
3437130 TT
1 TT
3437132 AGTTTGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.75
Consensus pattern (15 bp):
TTTTTGTCTTCTTTG
Found at i:3451473 original size:29 final size:30
Alignment explanation
Indices: 3451441--3451510 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
3451431 ATTAGTAAAA
*
3451441 ATAAAATTATATTTTAACTCCTT-AAAAGT
1 ATAAAATTATAATTTAACTCCTTAAAAAGT
* * *
3451470 ATAAAAATT-TAATTTAATTCTTTAAAAATT
1 AT-AAAATTATAATTTAACTCCTTAAAAAGT
*
3451500 ATAAAAATATA
1 ATAAAATTATA
3451511 GGCTATTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.41
Consensus pattern (30 bp):
ATAAAATTATAATTTAACTCCTTAAAAAGT
Found at i:3456085 original size:29 final size:30
Alignment explanation
Indices: 3456020--3456085 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
3456010 ATTTATCCCA
* * *
3456020 AGATTCTCAGGTTTTAGAAACATTATCTTG
1 AGATTCTCAGGTTTCAAAAACATTATCTCG
* * *
3456050 GGGTTCTCGGGTTTCAAAAAC-TTATCTCG
1 AGATTCTCAGGTTTCAAAAACATTATCTCG
3456079 AGATTCT
1 AGATTCT
3456086 TGATTTTTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (30 bp):
AGATTCTCAGGTTTCAAAAACATTATCTCG
Found at i:3457056 original size:29 final size:28
Alignment explanation
Indices: 3457009--3457087 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
3456999 ATAATTGTAT
* *
3457009 CTAAATTTTAAAATCTAAAAATAGAAAGA
1 CTAAATTTTAAAA-ATAAAAATAGAAAAA
*
3457038 CTAAATTTTTAAAAATAAAAATATAAAAA
1 CTAAA-TTTTAAAAATAAAAATAGAAAAA
* *
3457067 TTAAATTCTAAATAATAAAAA
1 CTAAATTTTAAA-AATAAAAA
3457088 AAACATATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 6 0.14
29 29 0.67
30 8 0.19
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (28 bp):
CTAAATTTTAAAAATAAAAATAGAAAAA
Found at i:3485072 original size:18 final size:18
Alignment explanation
Indices: 3485049--3485086 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3485039 ATTATTTAAA
*
3485049 AATTATTAAT-TTACTTAT
1 AATTATAAATGTTA-TTAT
3485067 AATTATAAATGTTATTAT
1 AATTATAAATGTTATTAT
3485085 AA
1 AA
3485087 AATTCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTATAAATGTTATTAT
Found at i:3506946 original size:193 final size:193
Alignment explanation
Indices: 3506570--3506948 Score: 496
Period size: 193 Copynumber: 2.0 Consensus size: 193
3506560 CCAGTACTCA
* * * *
3506570 ATGCTGCTCACACGAGTTATCGAGGATCGCAACGTATGCGGTACCCCAGCTATCGGTACGGTTCT
1 ATGCTGCTCACACGAGTTACCGAGGATCGCAACATATGCGGTACCCCAGCCATCGATACGGTTCT
* *
3506635 TGCCTGTACTATAAACTGTTCCCTAACGATACTGCTCACACGAGCTGTCGAGAGTATGCATAAAG
66 TG-CTGTACTATAAACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCATAAAG
* * *
3506700 CATAGTCCCAGCCATCGTAAGGCCTGTAATCCATTTAGGATCCATATTTCTTTTCTGAGTCACG
130 CATAATCCCAACCATCGTAAGGCCTCTAATCCATTTAGGATCCATATTTCTTTTCTGAGTCACG
* * * **
3506764 ATGCTGCTCACATGAGTTGCCGAGGACTTGCAACATATGCGGTACCTTAGCCATCGATACGGTAT
1 ATGCTGCTCACACGAGTTACCGAGGA-TCGCAACATATGCGGTACCCCAGCCATCGATACGGT-T
* * *
3506829 C-TG-TGT-GTAT-AACTGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCACTTA
64 CTTGCTGTACTATAAACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCA-TAA
* * * *
3506890 TGCATAAATCTCAACCATCGTAGGGCTTCTAATCCATTTAGGATCCATATTTCTTTTCT
128 AGCAT-AATCCCAACCATCGTAAGGCCTCTAATCCATTTAGGATCCATATTTCTTTTCT
3506949 CATTTCCCGA
Statistics
Matches: 160, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
191 44 0.28
192 9 0.06
193 50 0.31
194 23 0.14
195 32 0.20
196 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (193 bp):
ATGCTGCTCACACGAGTTACCGAGGATCGCAACATATGCGGTACCCCAGCCATCGATACGGTTCT
TGCTGTACTATAAACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCATAAAGC
ATAATCCCAACCATCGTAAGGCCTCTAATCCATTTAGGATCCATATTTCTTTTCTGAGTCACG
Found at i:3507020 original size:201 final size:191
Alignment explanation
Indices: 3506648--3507020 Score: 449
Period size: 201 Copynumber: 1.9 Consensus size: 191
3506638 CTGTACTATA
* * * *
3506648 AACTGTTCCCTAACGATACTGCTCACACGAGCTGTCGAGAGTATGCATAAAGCATAGTCCCAGCC
1 AACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCATAAAGCATAATCCCAACC
* * *
3506713 ATCGTAAGGCCTGTAATCCATTTAGGATCCATATTTCTTTTCTGAGTCACGATGCTGCTCACATG
66 ATCGTAAGGCCTCTAATCCATTTAGGATCCATATTTCTTTTCTGACTCACGATGCTGCTCACACG
** ** * * *
3506778 AGTTGCCGAGGACTTGCAACATATGCGGTACCTTAGCCATCGATACGGTATCTGTGTGTAT
131 AACTGCCGAGGACTCACAACATATGAGATACCTCAGCCATCGATACGGTATCTGTGTGTAT
* * * *
3506839 AACTGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAATCTCAA
1 AACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCA-TAAAGCAT-AATCCCAA
* *
3506904 CCATCGTAGGGCTTCTAATCCATTTAGGATCCATATTTCTTTTCTCATTTCCCGACTCACGATGC
64 CCATCGTAAGGCCTCTAATCCATTTAGGATCCATATTTC-TTT-TC---T---GACTCACGATGC
* * *
3506969 TGCTCGCACGAACTGTCGAGGACTCATAACATATGAGATACCTCAGCCATCG
121 TGCTCACACGAACTGCCGAGGACTCACAACATATGAGATACCTCAGCCATCG
3507021 CGTCGATTTC
Statistics
Matches: 149, Mismatches: 23, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
191 44 0.30
192 6 0.04
193 41 0.28
194 3 0.02
195 2 0.01
198 1 0.01
201 52 0.35
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (191 bp):
AACTGTTCCCTAACAATACTGCTCACACGAGCTGTCGAGAATATGCATAAAGCATAATCCCAACC
ATCGTAAGGCCTCTAATCCATTTAGGATCCATATTTCTTTTCTGACTCACGATGCTGCTCACACG
AACTGCCGAGGACTCACAACATATGAGATACCTCAGCCATCGATACGGTATCTGTGTGTAT
Found at i:3509706 original size:19 final size:20
Alignment explanation
Indices: 3509679--3509732 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3509669 AGCCCAATTA
* *
3509679 CAAACCCCAAA-ATTTAACC
1 CAAAACCCAAACATTAAACC
*
3509698 CAAAACCCAAACATTAAAGC
1 CAAAACCCAAACATTAAACC
*
3509718 TAAAACCCAATACAT
1 CAAAACCCAA-ACAT
3509733 GACCTAACAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 10 0.34
20 15 0.52
21 4 0.14
ACGTcount: A:0.52, C:0.31, G:0.02, T:0.15
Consensus pattern (20 bp):
CAAAACCCAAACATTAAACC
Found at i:3511308 original size:29 final size:29
Alignment explanation
Indices: 3511233--3511539 Score: 256
Period size: 29 Copynumber: 10.5 Consensus size: 29
3511223 CTGAATTATC
* * * *
3511233 CAAAAATCATATTTTAACCATCAAACTTTT
1 CAAAAATTACATTTT-ACCCTCAAACTTCT
*
3511263 CAAAAATTATATTTTTACCCTCAAACTTCT
1 CAAAAATTACA-TTTTACCCTCAAACTTCT
*
3511293 CAAAAATTACATTTTACCCTTAAACTTCT
1 CAAAAATTACATTTTACCCTCAAACTTCT
*
3511322 CAAAAATTACATTTTACCCTCGAACTT-T
1 CAAAAATTACATTTTACCCTCAAACTTCT
* *
3511350 TAAAAATCACATTTTTA-CCTCTAAACTT-T
1 CAAAAATTACA-TTTTACCCTC-AAACTTCT
3511379 CCAAAAATTACATTTTGACCC-CTAAACTTCT
1 -CAAAAATTACATTTT-ACCCTC-AAACTTCT
* * *
3511410 CAAAAATTATATTTTACCCCCAAACTT-A
1 CAAAAATTACATTTTACCCTCAAACTTCT
* *
3511438 CAAAAATCATATTTTTACCCTCAAACTTC-
1 CAAAAATTACA-TTTTACCCTCAAACTTCT
* * *
3511467 CCAAAATGACATTTTTACCCCTAAAACTT-T
1 CAAAAATTACA-TTTTA-CCCTCAAACTTCT
* *
3511497 CCAAAATTATATTTTAACCC-CAAAC-TCTT
1 CAAAAATTACATTTT-ACCCTCAAACTTC-T
*
3511526 CAAAACTT-CATTTT
1 CAAAAATTACATTTT
3511540 CGACCCTTTT
Statistics
Matches: 236, Mismatches: 26, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.00
28 33 0.14
29 110 0.47
30 85 0.36
31 7 0.03
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (29 bp):
CAAAAATTACATTTTACCCTCAAACTTCT
Found at i:3511454 original size:117 final size:117
Alignment explanation
Indices: 3511231--3511539 Score: 353
Period size: 117 Copynumber: 2.7 Consensus size: 117
3511221 CCCTGAATTA
* * * *
3511231 TCCAAAAATCATATTTTAACCATC-AAACTTTTCAAAAATTATATTTTTA-CCCTCAAACTTCTC
1 TCCAAAAATCACATTTTTACC-TCTAAACTTTCCAAAAATTATATTTTAACCCCT-AAACTTCTC
** * * *
3511294 AAAAATTACATTTTACCCTTAAACTTCTCAAAAATTACATTTTACCCTCGAACT
64 AAAAATTACATTTTACCCCCAAACTTCACAAAAATCACATTTTACCCTCAAACT
** * *
3511348 TTTAAAAATCACATTTTTACCTCTAAACTTTCCAAAAATTACATTTTGACCCCTAAACTTCTCAA
1 TCCAAAAATCACATTTTTACCTCTAAACTTTCCAAAAATTATATTTTAACCCCTAAACTTCTCAA
* *
3511413 AAATTATATTTTACCCCCAAACTT-ACAAAAATCATATTTTTACCCTCAAACT
66 AAATTACATTTTACCCCCAAACTTCACAAAAATCACA-TTTTACCCTCAAACT
* * *
3511465 TCCCAAAATGACATTTTTACCCCTAAAACTTTCC-AAAATTATATTTTAACCCC-AAAC-TCTTC
1 TCCAAAAATCACATTTTTACCTCT-AAACTTTCCAAAAATTATATTTTAACCCCTAAACTTC-TC
*
3511527 AAAACTT-CATTTT
64 AAAAATTACATTTT
3511540 CGACCCTTTT
Statistics
Matches: 164, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
115 7 0.04
116 23 0.14
117 121 0.74
118 13 0.08
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (117 bp):
TCCAAAAATCACATTTTTACCTCTAAACTTTCCAAAAATTATATTTTAACCCCTAAACTTCTCAA
AAATTACATTTTACCCCCAAACTTCACAAAAATCACATTTTACCCTCAAACT
Found at i:3513266 original size:21 final size:21
Alignment explanation
Indices: 3513242--3513293 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3513232 TGAGACAATA
*
3513242 CTACCGATTCAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
3513263 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
3513284 CTACCGATAC
1 CTACCGATAC
3513294 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:3516917 original size:18 final size:17
Alignment explanation
Indices: 3516880--3516913 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3516870 CATGTTTGCT
3516880 AAAAAAAACAATACATG
1 AAAAAAAACAATACATG
3516897 AAAAAAAACAATACATG
1 AAAAAAAACAATACATG
3516914 GAAAGTATAT
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:0.71, C:0.12, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAAAACAATACATG
Found at i:3527972 original size:22 final size:23
Alignment explanation
Indices: 3527942--3527993 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
3527932 ACGCTAGTGC
3527942 GCTTACTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
3527965 GCTT-CTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
*
3527987 GCCTACT
1 GCTTACT
3527994 ATTTCCCAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (23 bp):
GCTTACTGTTCAGCACTGTGTGT
Found at i:3535116 original size:21 final size:20
Alignment explanation
Indices: 3535091--3535132 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3535081 TACTTAGTCT
3535091 TTCATACTTAA-CTTAATCTAA
1 TTCAT-CTTAACCTTAAT-TAA
*
3535112 TTCATTTTAACCTTAATTAA
1 TTCATCTTAACCTTAATTAA
3535132 T
1 T
3535133 CACACCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.48
Consensus pattern (20 bp):
TTCATCTTAACCTTAATTAA
Found at i:3544738 original size:190 final size:190
Alignment explanation
Indices: 3544414--3544791 Score: 677
Period size: 190 Copynumber: 2.0 Consensus size: 190
3544404 TCCAACTTCC
* * * *
3544414 AGTGAGCGAACTTTAGGTAAGCTTCAGATCTGGGTTACTATGTAGATATTCCAACTTTCTGTCTT
1 AGTGAGCGAACTTTAGGTAAGCTTCAGATCAGGGTTACTAAGCAGATATTCCAACCTTCTGTCTT
3544479 AACAATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGGATGGCAACAATCCCAGCATG
66 AACAATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGGATGGCAACAATCCCAGCATG
3544544 GAATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAG
131 GAATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAG
*
3544604 AGTGAGCGAACTTTAGGTAAGCTTCAGAAT-AGGGTTACTAAGCAGATATTCCAACCTTCTTTCT
1 AGTGAGCGAACTTTAGGTAAGCTTCAG-ATCAGGGTTACTAAGCAGATATTCCAACCTTCTGTCT
* *
3544668 TAACAATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGGATGGCAACGATCCCAGCGT
65 TAACAATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGGATGGCAACAATCCCAGCAT
3544733 GGAATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTA
130 GGAATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTA
3544792 TAAGTGACAG
Statistics
Matches: 180, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
190 178 0.99
191 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (190 bp):
AGTGAGCGAACTTTAGGTAAGCTTCAGATCAGGGTTACTAAGCAGATATTCCAACCTTCTGTCTT
AACAATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGGATGGCAACAATCCCAGCATG
GAATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAG
Found at i:3545575 original size:33 final size:33
Alignment explanation
Indices: 3545538--3545604 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
3545528 CCGATTCAAT
3545538 TTTGAAAGTCTTGTTTAAAAGACAAGTATGTTA
1 TTTGAAAGTCTTGTTTAAAAGACAAGTATGTTA
*
3545571 TTTGAAGGTCTTGTTTAAAAGACAAGTATGTTA
1 TTTGAAAGTCTTGTTTAAAAGACAAGTATGTTA
3545604 T
1 T
3545605 ATACGAGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (33 bp):
TTTGAAAGTCTTGTTTAAAAGACAAGTATGTTA
Found at i:3547737 original size:11 final size:11
Alignment explanation
Indices: 3547723--3547792 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
3547713 AAAAAAATTT
*
3547723 AAAAATTGTTA
1 AAAAATTATTA
3547734 AAAAATTATTA
1 AAAAATTATTA
3547745 AAAAA-TATCTA
1 AAAAATTAT-TA
*
3547756 TAAAAATT-GT-
1 -AAAAATTATTA
3547766 AAAAA-TATT-
1 AAAAATTATTA
* *
3547775 TAAAATTATAA
1 AAAAATTATTA
3547786 AAAAATT
1 AAAAATT
3547793 TAAATAACTG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
8 1 0.02
9 10 0.21
10 6 0.13
11 24 0.51
12 5 0.11
13 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (11 bp):
AAAAATTATTA
Found at i:3547778 original size:10 final size:10
Alignment explanation
Indices: 3547713--3547796 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 10
3547703 ACCACGGACC
*
3547713 AAAAAAATTT
1 AAAAATATTT
3547723 AAAAAT-TGTT
1 AAAAATAT-TT
*
3547733 AAAAAATTATTA
1 -AAAAA-TATTT
3547745 AAAAATATCTAT
1 AAAAATAT-T-T
*
3547757 AAAAAT-TGT
1 AAAAATATTT
3547766 AAAAATATTT
1 AAAAATATTT
*
3547776 -AAAAT-TAT
1 AAAAATATTT
*
3547784 AAAAAAATTT
1 AAAAATATTT
3547794 AAA
1 AAA
3547797 TAACTGAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
8 2 0.04
9 17 0.30
10 17 0.30
11 12 0.21
12 8 0.14
13 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAAATATTT
Found at i:3547781 original size:18 final size:19
Alignment explanation
Indices: 3547715--3547845 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
3547705 CACGGACCAA
3547715 AAAAATT-TAAAAAT-TGTT
1 AAAAATTGTAAAAATAT-TT
*
3547733 AAAAAATTATTAAAAAATATCTAT
1 -AAAAATT-GT-AAAAATAT-T-T
3547757 AAAAATTGTAAAAATATTT
1 AAAAATTGTAAAAATATTT
* *
3547776 -AAAATTATAAAAAAATTT
1 AAAAATTGTAAAAATATTT
*
3547794 AAATAACTG-AAAAA-A-TT
1 AAA-AATTGTAAAAATATTT
*
3547811 AAAAAATGTAAACAAATATTT
1 AAAAATTGT-AA-AAATATTT
*
3547832 AAAAATTATAAAAA
1 AAAAATTGTAAAAA
3547846 AAATCCAAGA
Statistics
Matches: 91, Mismatches: 9, Indels: 24
0.73 0.07 0.19
Matches are distributed among these distances:
16 4 0.04
17 5 0.05
18 19 0.21
19 21 0.23
20 7 0.08
21 18 0.20
22 7 0.08
23 9 0.10
24 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAAATTGTAAAAATATTT
Found at i:3547845 original size:10 final size:9
Alignment explanation
Indices: 3547714--3547846 Score: 74
Period size: 10 Copynumber: 13.7 Consensus size: 9
3547704 CCACGGACCA
3547714 AAAAAATTT
1 AAAAAATTT
*
3547723 AAAAATTGTT
1 AAAAAAT-TT
3547733 AAAAAATTATT
1 AAAAAA-T-TT
3547744 AAAAAATATCT
1 AAAAAAT-T-T
3547755 ATAAAAATTGT
1 A-AAAAATT-T
3547766 AAAAATATTT
1 AAAAA-ATTT
3547776 --AAAATTAT
1 AAAAAATT-T
3547784 AAAAAAATTT
1 -AAAAAATTT
* * *
3547794 AAATAACTG
1 AAAAAATTT
3547803 AAAAAA-TT
1 AAAAAATTT
*
3547811 AAAAAATGT
1 AAAAAATTT
3547820 AAACAAATATT
1 AAA-AAAT-TT
*
3547831 TAAAAATTAT
1 AAAAAATT-T
3547841 AAAAAA
1 AAAAAA
3547847 AATCCAAGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
7 3 0.03
8 11 0.11
9 22 0.22
10 30 0.31
11 26 0.27
12 6 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAAATTT
Found at i:3547845 original size:38 final size:36
Alignment explanation
Indices: 3547715--3547846 Score: 104
Period size: 38 Copynumber: 3.4 Consensus size: 36
3547705 CACGGACCAA
*
3547715 AAAAATTTAAAAATTGTTAAAAAATTATTAAAAAATATCTAT
1 AAAAATTTAAAAA--ATTAAAAAA-TA-TAAAAAATAT-T-T
* *
3547757 AAAAATTGTAAAAATATTTAAAATTATAAAAAA-ATTT
1 AAAAATT-TAAAAA-ATTAAAAAATATAAAAAATATTT
* * *
3547794 AAATAACTGAAAAAATTAAAAAATGTAAACAAATATTT
1 AAA-AATTTAAAAAATTAAAAAATATAAA-AAATATTT
3547832 AAAAATTATAAAAAA
1 AAAAATT-TAAAAAA
3547847 AATCCAAGAT
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
36 12 0.16
37 15 0.20
38 17 0.23
39 2 0.03
40 7 0.09
41 2 0.03
42 14 0.19
43 6 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (36 bp):
AAAAATTTAAAAAATTAAAAAATATAAAAAATATTT
Found at i:3556857 original size:5 final size:5
Alignment explanation
Indices: 3556840--3556873 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3556830 GCTGGAATCT
*
3556840 CTCTA CTCCA CTCTA CTCTA CTCTA CTCTA CTCT
1 CTCTA CTCTA CTCTA CTCTA CTCTA CTCTA CTCT
3556874 TGGCCTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.18, C:0.44, G:0.00, T:0.38
Consensus pattern (5 bp):
CTCTA
Found at i:3560584 original size:20 final size:20
Alignment explanation
Indices: 3560559--3560627 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 20
3560549 TTTTTTTTTG
3560559 TTTTAAATATTATTAATATA
1 TTTTAAATATTATTAATATA
3560579 TTTTAAAT-TTA--AATATA
1 TTTTAAATATTATTAATATA
* *
3560596 TTTTTTAA-GTT-TT-ATATA
1 -TTTTAAATATTATTAATATA
3560614 TTTTAAATATTATT
1 TTTTAAATATTATT
3560628 TCATTAGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
17 12 0.30
18 15 0.38
19 5 0.12
20 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
TTTTAAATATTATTAATATA
Found at i:3560601 original size:19 final size:18
Alignment explanation
Indices: 3560559--3560617 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
3560549 TTTTTTTTTG
* *
3560559 TTTTAAATATTATTAATATA
1 TTTTAAAT-TTAAT-ATATT
3560579 TTTTAAATTTAAATATATT
1 TTTTAAATTT-AATATATT
* *
3560598 TTTTAAGTTTTATATATT
1 TTTTAAATTTAATATATT
3560616 TT
1 TT
3560618 AAATATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 9 0.26
19 15 0.44
20 10 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTAAATTTAATATATT
Found at i:3560626 original size:16 final size:17
Alignment explanation
Indices: 3560569--3560625 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 17
3560559 TTTTAAATAT
3560569 TATTAATATATTTTAAA
1 TATTAATATATTTTAAA
*
3560586 T-TTAAATATATTTTTTAAG
1 TATT-AATATA--TTTTAAA
*
3560605 T-TTTATATATTTTAAA
1 TATTAATATATTTTAAA
3560621 TATTA
1 TATTA
3560626 TTTCATTAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 9 0.28
17 9 0.28
18 5 0.16
19 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTAATATATTTTAAA
Found at i:3564430 original size:17 final size:18
Alignment explanation
Indices: 3564410--3564462 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
3564400 AGATAACAAC
*
3564410 ATATAAATTATAAAAA-A
1 ATATAAATTACAAAAATA
3564427 ATATAAATTACAAAAATA
1 ATATAAATTACAAAAATA
* * *
3564445 AGATAAATGAAAAAAATA
1 ATATAAATTACAAAAATA
3564463 GTTGAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (18 bp):
ATATAAATTACAAAAATA
Found at i:3564536 original size:19 final size:18
Alignment explanation
Indices: 3564509--3564595 Score: 63
Period size: 19 Copynumber: 4.8 Consensus size: 18
3564499 AAAAACTTAC
3564509 AAAAA-TTAAAAAATATAT
1 AAAAATTTAAAAAATAT-T
* *
3564527 AATAATTTAAAAATTATT
1 AAAAATTTAAAAAATATT
* *
3564545 AAAAATTTGTGAAAATTATT
1 AAAAA-TT-TAAAAAATATT
* *
3564565 --AATTTTTAAAAATATT
1 AAAAATTTAAAAAATATT
3564581 AAAAATTGTAAAAAA
1 AAAAATT-TAAAAAA
3564596 ATTTAGAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.17
17 2 0.04
18 15 0.28
19 18 0.33
20 10 0.19
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAAATTTAAAAAATATT
Found at i:3564551 original size:18 final size:18
Alignment explanation
Indices: 3564509--3564594 Score: 70
Period size: 18 Copynumber: 4.7 Consensus size: 18
3564499 AAAAACTTAC
*
3564509 AAAAA-TTAAAAAATATAT
1 AAAAATTTAAAAATTAT-T
*
3564527 AATAATTTAAAAATTATT
1 AAAAATTTAAAAATTATT
*
3564545 AAAAATTTGTGAAAATTATT
1 AAAAA-TT-TAAAAATTATT
**
3564565 -AATTTTTAAAAA-TATT
1 AAAAATTTAAAAATTATT
3564581 AAAAATTGTAAAAA
1 AAAAATT-TAAAAA
3564595 AATTTAGAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
16 4 0.07
17 9 0.17
18 17 0.31
19 14 0.26
20 10 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAAATTTAAAAATTATT
Found at i:3564608 original size:19 final size:21
Alignment explanation
Indices: 3564572--3564614 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3564562 ATTAATTTTT
3564572 AAAAATATTAAAAATTGT-AA
1 AAAAATATTAAAAATTGTGAA
* *
3564592 AAAAAT-TTAGAATTTGTGAA
1 AAAAATATTAAAAATTGTGAA
3564612 AAA
1 AAA
3564615 TATAAGAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAAATATTAAAAATTGTGAA
Found at i:3565756 original size:19 final size:20
Alignment explanation
Indices: 3565722--3565768 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3565712 ATATAATTTT
3565722 TATGATTTTCTAGA-TTTCA
1 TATGATTTTCTAGATTTTCA
3565741 TATGTATTTTCT-GATTTTCA
1 TATG-ATTTTCTAGATTTTCA
3565761 TAT-ATTTT
1 TATGATTTT
3565769 TCAATGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 6 0.23
20 15 0.58
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (20 bp):
TATGATTTTCTAGATTTTCA
Found at i:3565769 original size:19 final size:19
Alignment explanation
Indices: 3565727--3565788 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
3565717 ATTTTTATGA
*
3565727 TTTTCTAGA-TTTCATATGT
1 TTTTCT-GATTTTCATATAT
3565746 ATTTTCTGATTTTCATATAT
1 -TTTTCTGATTTTCATATAT
3565766 TTTTCAATG-TTTT-ATATAT
1 TTTTC--TGATTTTCATATAT
3565785 TTTT
1 TTTT
3565789 TAAATGTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 17 0.45
20 19 0.50
21 2 0.05
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.63
Consensus pattern (19 bp):
TTTTCTGATTTTCATATAT
Found at i:3565789 original size:21 final size:19
Alignment explanation
Indices: 3565760--3565807 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3565750 TCTGATTTTC
*
3565760 ATAT-ATTTTTCAATGTTTT
1 ATATAATTTTTAAATG-TTT
*
3565779 ATATATTTTTTAAATGTTT
1 ATATAATTTTTAAATGTTT
3565798 ATATACATTT
1 ATATA-ATTT
3565808 GGTAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (19 bp):
ATATAATTTTTAAATGTTT
Found at i:3565798 original size:19 final size:19
Alignment explanation
Indices: 3565755--3565802 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3565745 TATTTTCTGA
*
3565755 TTTTCATATATTTTTCAATG
1 TTTT-ATATATTTTTAAATG
3565775 TTTTATATATTTTTTAAATG
1 TTTTATATA-TTTTTAAATG
3565795 -TTTATATA
1 TTTTATATA
3565803 CATTTGGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTATATATTTTTAAATG
Found at i:3565813 original size:21 final size:20
Alignment explanation
Indices: 3565771--3565813 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3565761 TATATTTTTC
* **
3565771 AATGTTTTATATATTTTTTA
1 AATGTTTTATACATTTGGTA
3565791 AATGTTTATATACATTTGGTA
1 AATGTTT-TATACATTTGGTA
3565812 AA
1 AA
3565814 AAAATATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (20 bp):
AATGTTTTATACATTTGGTA
Found at i:3585339 original size:6 final size:6
Alignment explanation
Indices: 3585323--3585354 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3585313 AGATAAATTG
3585323 AAAAT- AAAATC AAAATC AAAATC AAAATC AAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAA
3585355 CAAGCCAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:3585664 original size:19 final size:19
Alignment explanation
Indices: 3585642--3585703 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
3585632 GATTTAGTTT
3585642 AAATTATTTAATTTTAAAA
1 AAATTATTTAATTTTAAAA
* * * **
3585661 AAATTATTAAAATATAGGA
1 AAATTATTTAATTTTAAAA
*
3585680 AATTTA-TT-ATTTTAAAA
1 AAATTATTTAATTTTAAAA
3585697 AAATTAT
1 AAATTAT
3585704 ACTTTTCGCT
Statistics
Matches: 30, Mismatches: 12, Indels: 3
0.67 0.27 0.07
Matches are distributed among these distances:
17 10 0.33
18 1 0.03
19 19 0.63
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AAATTATTTAATTTTAAAA
Found at i:3586535 original size:21 final size:20
Alignment explanation
Indices: 3586495--3586536 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3586485 AATATTTATA
*
3586495 TTTTTATTAATTTAATTCAT
1 TTTTTATTAATTTAACTCAT
3586515 TTTTTAGTTAAATTT-ACTCAT
1 TTTTTA-TT-AATTTAACTCAT
3586536 T
1 T
3586537 AATTTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTATTAATTTAACTCAT
Found at i:3586925 original size:18 final size:19
Alignment explanation
Indices: 3586886--3586925 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3586876 TAAAAAAATT
**
3586886 AAAAATCAAATTTAACTTA
1 AAAAATCAAATTTAACAAA
3586905 AAAAATCAAA-TTAACAAA
1 AAAAATCAAATTTAACAAA
3586923 AAA
1 AAA
3586926 TAAAAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATCAAATTTAACAAA
Found at i:3590751 original size:6 final size:6
Alignment explanation
Indices: 3590740--3590774 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3590730 AATCAAACCC
3590740 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTC
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTC
3590775 TTAACTCTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.51, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCA
Found at i:3592093 original size:17 final size:16
Alignment explanation
Indices: 3592068--3592113 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
3592058 TTTTTAATTT
*
3592068 TTTTAAATATTTATATTA
1 TTTT-AATATTTA-ATAA
3592086 TTTTAATATTTAATAA
1 TTTTAATATTTAATAA
3592102 TTTTATATATTT
1 TTTTA-ATATTT
3592114 TTTGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.31
17 14 0.54
18 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTAATATTTAATAA
Found at i:3598257 original size:17 final size:16
Alignment explanation
Indices: 3598234--3598272 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3598224 TTTAAATTAT
3598234 TTAATTTATTATATAAAA
1 TTAATTTA-TA-ATAAAA
3598252 -TAATTTATAATAAAA
1 TTAATTTATAATAAAA
3598267 TTAATT
1 TTAATT
3598273 ACTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.30
16 7 0.35
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATTTATAATAAAA
Found at i:3599403 original size:14 final size:13
Alignment explanation
Indices: 3599382--3599420 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
3599372 TTTTCAGAAT
3599382 TTTTTTTAAAATA
1 TTTTTTTAAAATA
3599395 TTTTGTTT-AAATA
1 TTTT-TTTAAAATA
3599408 TTATTTTTAAAAT
1 TT-TTTTTAAAAT
3599421 CTAGAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTTTTTAAAATA
Found at i:3599860 original size:23 final size:23
Alignment explanation
Indices: 3599814--3599865 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3599804 AACATGTTTA
*
3599814 ATTATATGTTCATGAACAGGTTCG
1 ATTA-ATGTTCATGAACAGATTCG
* * *
3599838 TTTAATGTTCGTGAACATATTCG
1 ATTAATGTTCATGAACAGATTCG
3599861 ATTAA
1 ATTAA
3599866 ATTAAATGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (23 bp):
ATTAATGTTCATGAACAGATTCG
Found at i:3599892 original size:23 final size:23
Alignment explanation
Indices: 3599849--3599894 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3599839 TTAATGTTCG
*
3599849 TGAACATATTCGATTAAATTAAA
1 TGAACATATTCGATGAAATTAAA
3599872 TGAACATATTCG-TGAACATTAAA
1 TGAACATATTCGATGAA-ATTAAA
3599895 CAAACGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (23 bp):
TGAACATATTCGATGAAATTAAA
Found at i:3600511 original size:158 final size:159
Alignment explanation
Indices: 3600339--3600661 Score: 639
Period size: 158 Copynumber: 2.0 Consensus size: 159
3600329 TAATGCCTAA
3600339 TTTTTTAAGTCGATAAAAATGAAACCAAGAATGATAAAATAAATAAATAAATAGAAGTAAGCATA
1 TTTTTTAAGTCGATAAAAATGAAACCAAGAATGATAAAATAAATAAATAAATAGAAGTAAGCATA
3600404 TTTGTAAAAATAGACTAATTTTTCTTTCCAAAAAATAGACTATTTTTTTAAAAAAATACATAAAA
66 TTTGTAAAAATAGACTAATTTTTCTTTCCAAAAAATAGACTATTTTTTTAAAAAAATACATAAAA
3600469 AATAAAACAAATTCTTTTAGAATATAAT-
131 AATAAAACAAATTCTTTTAGAATATAATC
3600497 TTTTTTAAGTCGATAAAAATGAAACCAAGAATGATAAAATAAATAAATAAATAGAAGTAAGCATA
1 TTTTTTAAGTCGATAAAAATGAAACCAAGAATGATAAAATAAATAAATAAATAGAAGTAAGCATA
3600562 TTTGTAAAAATAGACTAATTTTTCTTTCCAAAAAATAGACTATTTTTTTAAAAAAATACATAAAA
66 TTTGTAAAAATAGACTAATTTTTCTTTCCAAAAAATAGACTATTTTTTTAAAAAAATACATAAAA
3600627 AATAAAACAAATTCTTTTAGAATATAATC
131 AATAAAACAAATTCTTTTAGAATATAATC
3600656 TTTTTT
1 TTTTTT
3600662 GCAAACACAT
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 158 0.96
159 6 0.04
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (159 bp):
TTTTTTAAGTCGATAAAAATGAAACCAAGAATGATAAAATAAATAAATAAATAGAAGTAAGCATA
TTTGTAAAAATAGACTAATTTTTCTTTCCAAAAAATAGACTATTTTTTTAAAAAAATACATAAAA
AATAAAACAAATTCTTTTAGAATATAATC
Found at i:3611376 original size:18 final size:18
Alignment explanation
Indices: 3611334--3611387 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
3611324 AAAATAAAAA
* *
3611334 AAAAATCAAAATAATTTTT
1 AAAAATCCAAAT-ATTTAT
*
3611353 ACAAATCCAAATATTTAT
1 AAAAATCCAAATATTTAT
3611371 AAAAATTCCAAAT-TTTA
1 AAAAA-TCCAAATATTTA
3611388 ATTTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATCCAAATATTTAT
Found at i:3620367 original size:20 final size:19
Alignment explanation
Indices: 3620342--3620391 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
3620332 CTGATTTAAT
3620342 TGTAAAAGAAATTTAAAAAA
1 TGTAAAA-AAATTTAAAAAA
* *
3620362 TGTAAAAAGATTTTAAAAA
1 TGTAAAAAAATTTAAAAAA
3620381 --TAAAAAAATTT
1 TGTAAAAAAATTT
3620392 CATTTTATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 10 0.37
19 10 0.37
20 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (19 bp):
TGTAAAAAAATTTAAAAAA
Found at i:3620379 original size:19 final size:20
Alignment explanation
Indices: 3620342--3620381 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3620332 CTGATTTAAT
3620342 TGTAAAAGAAATTTAAAAAA
1 TGTAAAAGAAATTTAAAAAA
* *
3620362 TGTAAAA-AGATTTTAAAAA
1 TGTAAAAGAAATTTAAAAAA
3620381 T
1 T
3620382 AAAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (20 bp):
TGTAAAAGAAATTTAAAAAA
Found at i:3622019 original size:2 final size:2
Alignment explanation
Indices: 3622012--3622042 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3622002 CACATCAAAG
*
3622012 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3622043 GCAAAGAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3629834 original size:60 final size:60
Alignment explanation
Indices: 3629765--3629881 Score: 200
Period size: 60 Copynumber: 1.9 Consensus size: 60
3629755 ATATCGTCGA
*
3629765 TATTAGAGGAAAT-TCGTGTTAAAAAGTTATGCATTGAGCTCTACTTAACGAATTAATCAG
1 TATTAGAGGAAATCT-GTGTTAAAAAGTTATGCATTGAGCTATACTTAACGAATTAATCAG
*
3629825 TATTAGAGGAAATCTGTGTTAAAAAGTTATGCATTGAGCTATACTTAACTAATTAAT
1 TATTAGAGGAAATCTGTGTTAAAAAGTTATGCATTGAGCTATACTTAACGAATTAAT
3629882 ATTAAATAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 53 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (60 bp):
TATTAGAGGAAATCTGTGTTAAAAAGTTATGCATTGAGCTATACTTAACGAATTAATCAG
Found at i:3630236 original size:29 final size:30
Alignment explanation
Indices: 3630177--3630237 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
3630167 AAGTACCAAT
* ** *
3630177 TTAAAGAAAATGTCAAATTTATTTATTAAA
1 TTAAAGAAAATATCAAATTTAAATATGAAA
3630207 TTAAA-AAAATATCAAATTTAAATATGAAA
1 TTAAAGAAAATATCAAATTTAAATATGAAA
3630236 TT
1 TT
3630238 GAACTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (30 bp):
TTAAAGAAAATATCAAATTTAAATATGAAA
Found at i:3630493 original size:16 final size:16
Alignment explanation
Indices: 3630467--3630499 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3630457 GGCAAATTAA
3630467 AAAATATAAATTATATC
1 AAAATATAAATT-TATC
3630484 AAAA-ATAAATTTATC
1 AAAATATAAATTTATC
3630499 A
1 A
3630500 TTCCATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATAAATTTATC
Found at i:3630715 original size:30 final size:31
Alignment explanation
Indices: 3630679--3630738 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
3630669 TGTCATACGT
*
3630679 AAATTTTGATTTTA-TACAA-TTTTATATATG
1 AAATTTTGATTTGATTA-AATTTTTATATATG
3630709 AAATTTTGATTTGATTAAATTTTTATATAT
1 AAATTTTGATTTGATTAAATTTTTATATAT
3630739 AAAGTAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.55
Consensus pattern (31 bp):
AAATTTTGATTTGATTAAATTTTTATATATG
Found at i:3631724 original size:31 final size:32
Alignment explanation
Indices: 3631663--3631730 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 32
3631653 TTCAATTTAT
*
3631663 TCACTAACGTTTTAGATTTTTTTCTATTTTGG
1 TCACTAACGTTTTAGATTTATTTCTATTTTGG
* * *
3631695 TCACTCACGTTTTGGA-TTATTTCTGTTTTGG
1 TCACTAACGTTTTAGATTTATTTCTATTTTGG
3631726 TCACT
1 TCACT
3631731 TTTTGTTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 18 0.56
32 14 0.44
ACGTcount: A:0.16, C:0.16, G:0.15, T:0.53
Consensus pattern (32 bp):
TCACTAACGTTTTAGATTTATTTCTATTTTGG
Found at i:3636680 original size:21 final size:21
Alignment explanation
Indices: 3636655--3636717 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
3636645 ATTCTTGAAA
3636655 TTAAAAGAAGATAACTAAATT
1 TTAAAAGAAGATAACTAAATT
* *
3636676 TT-AAAG-TG-T-A-GAAA--
1 TTAAAAGAAGATAACTAAATT
3636690 TTAAAAGAAGATAACTAAATT
1 TTAAAAGAAGATAACTAAATT
3636711 TTAAAAG
1 TTAAAAG
3636718 TGTAGTGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 14
0.63 0.08 0.29
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 4 0.13
17 2 0.06
18 2 0.06
19 4 0.13
20 4 0.13
21 9 0.29
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.29
Consensus pattern (21 bp):
TTAAAAGAAGATAACTAAATT
Found at i:3636690 original size:35 final size:36
Alignment explanation
Indices: 3636651--3636722 Score: 137
Period size: 35 Copynumber: 2.0 Consensus size: 36
3636641 TTAAATTCTT
3636651 GAAATTAAAAGAAGATAACTAAATTTT-AAAGTGTA
1 GAAATTAAAAGAAGATAACTAAATTTTAAAAGTGTA
3636686 GAAATTAAAAGAAGATAACTAAATTTTAAAAGTGTA
1 GAAATTAAAAGAAGATAACTAAATTTTAAAAGTGTA
3636722 G
1 G
3636723 TGTACTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 27 0.75
36 9 0.25
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.28
Consensus pattern (36 bp):
GAAATTAAAAGAAGATAACTAAATTTTAAAAGTGTA
Found at i:3636991 original size:31 final size:31
Alignment explanation
Indices: 3636953--3637012 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3636943 TAAATTTTTG
* * *
3636953 AAAATAAAAATACAATGACTATATTTTAATC
1 AAAATAAAAATAAAAGGACTAAATTTTAATC
*
3636984 AAAATAAAAGTAAAAGGACTAAATTTTAA
1 AAAATAAAAATAAAAGGACTAAATTTTAA
3637013 ATTTGCGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (31 bp):
AAAATAAAAATAAAAGGACTAAATTTTAATC
Found at i:3638354 original size:11 final size:11
Alignment explanation
Indices: 3638335--3638374 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
3638325 ACCAAAACAG
3638335 CAGCAAAAATAA
1 CAGC-AAAATAA
3638347 CAGCAAAATAA
1 CAGCAAAATAA
3638358 CA--AAAATAA
1 CAGCAAAATAA
3638367 CAGCAAAA
1 CAGCAAAA
3638375 ATAGCAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.35
11 13 0.50
12 4 0.15
ACGTcount: A:0.68, C:0.17, G:0.07, T:0.07
Consensus pattern (11 bp):
CAGCAAAATAA
Found at i:3638371 original size:32 final size:32
Alignment explanation
Indices: 3638321--3638386 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
3638311 CAACCAAAAT
* * *
3638321 AATAACCAAAACAGCAGCAAAAATAACAGCAA
1 AATAACAAAAACAACAGCAAAAATAACAACAA
* *
3638353 AATAACAAAAATAACAGCAAAAATAGCAACAA
1 AATAACAAAAACAACAGCAAAAATAACAACAA
3638385 AA
1 AA
3638387 ACAACAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.67, C:0.18, G:0.08, T:0.08
Consensus pattern (32 bp):
AATAACAAAAACAACAGCAAAAATAACAACAA
Found at i:3638375 original size:21 final size:21
Alignment explanation
Indices: 3638338--3638405 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 21
3638328 AAAACAGCAG
3638338 CAAAAATAACAGC-AAAATAA
1 CAAAAATAACAGCAAAAATAA
3638358 CAAAAATAACAGCAAAAATAGCAA
1 CAAAAATAACAGCAAAAAT---AA
* **
3638382 CAAAAACAACAATAAAAATAA
1 CAAAAATAACAGCAAAAATAA
3638403 CAA
1 CAA
3638406 CATCAAAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 13 0.32
21 10 0.24
24 18 0.44
ACGTcount: A:0.71, C:0.16, G:0.04, T:0.09
Consensus pattern (21 bp):
CAAAAATAACAGCAAAAATAA
Found at i:3638433 original size:19 final size:19
Alignment explanation
Indices: 3638409--3638491 Score: 89
Period size: 21 Copynumber: 4.3 Consensus size: 19
3638399 ATAACAACAT
3638409 CAAAACAGTAAAAAAGCAC
1 CAAAACAGTAAAAAAGCAC
3638428 CAAAACAGTAAAAAA--AC
1 CAAAACAGTAAAAAAGCAC
*
3638445 CAAAACAGCAAAAAAAGCAAC
1 CAAAACAG-TAAAAAAGC-AC
* *
3638466 CAAAATAATAAAAAATAGCAC
1 CAAAACAGT-AAAAA-AGCAC
3638487 CAAAA
1 CAAAA
3638492 TAACAATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
17 10 0.19
18 6 0.11
19 15 0.28
21 20 0.37
22 3 0.06
ACGTcount: A:0.67, C:0.19, G:0.07, T:0.06
Consensus pattern (19 bp):
CAAAACAGTAAAAAAGCAC
Found at i:3638446 original size:17 final size:17
Alignment explanation
Indices: 3638409--3638460 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 17
3638399 ATAACAACAT
3638409 CAAAACAGTAAAAAAGCAC
1 CAAAACAGTAAAAAA--AC
3638428 CAAAACAGTAAAAAAAC
1 CAAAACAGTAAAAAAAC
*
3638445 CAAAACAGCAAAAAAA
1 CAAAACAGTAAAAAAA
3638461 GCAACCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 17 0.53
19 15 0.47
ACGTcount: A:0.69, C:0.19, G:0.08, T:0.04
Consensus pattern (17 bp):
CAAAACAGTAAAAAAAC
Found at i:3639274 original size:25 final size:26
Alignment explanation
Indices: 3639229--3639292 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
3639219 AAATATTAGA
**
3639229 AATTAAATTAGAAATAAAATTAATTTGT
1 AATTAAATT-G-AATAAAATTAATTACT
*
3639257 AATT-AATTGAATATAATTAATTACT
1 AATTAAATTGAATAAAATTAATTACT
3639282 AATTAAATTGA
1 AATTAAATTGA
3639293 TAAGTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 17 0.53
26 7 0.22
27 4 0.12
28 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (26 bp):
AATTAAATTGAATAAAATTAATTACT
Done.