Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 40
Found at i:2600839 original size:20 final size:20
Alignment explanation
Indices: 2600816--2600859 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2600806 GAAACTTTAA
2600816 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
2600836 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
2600856 ATCG
1 ATCG
2600860 TAACGCAAGA
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:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:2601295 original size:22 final size:22
Alignment explanation
Indices: 2601233--2601298 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
2601223 TGACCGTGAA
* *
2601233 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
2601255 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2601277 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2601299 GGATGTTGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:2601518 original size:20 final size:20
Alignment explanation
Indices: 2601502--2601608 Score: 160
Period size: 20 Copynumber: 5.3 Consensus size: 20
2601492 CAGATTCACG
2601502 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2601522 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
2601542 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* * **
2601562 TTGCAATTTTCCAAATTCGCA
1 TTGCGA-TTTACGTATTCGCA
2601583 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2601603 TTGCGA
1 TTGCGA
2601609 ATTAGGAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
20 61 0.80
21 15 0.20
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2601592 original size:41 final size:41
Alignment explanation
Indices: 2601502--2601611 Score: 159
Period size: 41 Copynumber: 2.7 Consensus size: 41
2601492 CAGATTCACG
* **
2601502 TTGCGATTTACGTATTCGCATTGCGA-TTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCAATTTTACAAATTCGCA
* *
2601542 TTGCGATTTACGTAATCGCATTGCAATTTTCCAAATTCGCA
1 TTGCGATTTACGTATTCGCATTGCAATTTTACAAATTCGCA
2601583 TTGCGATTTACGTATTCGCATTGCGAATT
1 TTGCGATTTACGTATTCGCATTGC-AATT
2601612 AGGAAAATCG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
40 24 0.39
41 34 0.55
42 4 0.06
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (41 bp):
TTGCGATTTACGTATTCGCATTGCAATTTTACAAATTCGCA
Found at i:2601629 original size:21 final size:21
Alignment explanation
Indices: 2601605--2601645 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2601595 TATTCGCATT
2601605 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
2601626 GCGAATTTGGAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
2601646 TGCAATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2612162 original size:20 final size:18
Alignment explanation
Indices: 2612133--2612173 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2612123 AAAACCAGAA
*
2612133 CCCCAGGGGGGTATCGATT
1 CCCCA-GGGGGAATCGATT
2612152 CCCCTAGGGGGAATCGATT
1 CCCC-AGGGGGAATCGATT
2612171 CCC
1 CCC
2612174 ATTCAAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.17, C:0.32, G:0.32, T:0.20
Consensus pattern (18 bp):
CCCCAGGGGGAATCGATT
Found at i:2612204 original size:22 final size:23
Alignment explanation
Indices: 2612157--2612218 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2612147 CGATTCCCCT
2612157 AGGGGGAATCGATTCCCATTCAA
1 AGGGGGAATCGATTCCCATTCAA
* *
2612180 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGATTCCCATTCAA
*
2612202 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
2612219 TCTGCCCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGATTCCCATTCAA
Found at i:2618016 original size:18 final size:19
Alignment explanation
Indices: 2617981--2618017 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2617971 CCGTTGAACA
2617981 GGGGGGAATCGGTATCCCT
1 GGGGGGAATCGGTATCCCT
2618000 GGGGGGAATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
2618018 CCGAGCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.14, C:0.22, G:0.43, T:0.22
Consensus pattern (19 bp):
GGGGGGAATCGGTATCCCT
Found at i:2621461 original size:22 final size:23
Alignment explanation
Indices: 2621435--2621488 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
2621425 TTTATGAATT
*
2621435 TAAATTTTTTTTAA-AAAATATA
1 TAAATTTTTTTAAAGAAAATATA
*
2621457 TAAA-TATTTTAAAGAAAATATA
1 TAAATTTTTTTAAAGAAAATATA
*
2621479 TAAATATTTT
1 TAAATTTTTT
2621489 ATAACTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.27
22 16 0.62
23 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAATTTTTTTAAAGAAAATATA
Found at i:2621468 original size:20 final size:21
Alignment explanation
Indices: 2621443--2621489 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
2621433 TTTAAATTTT
2621443 TTTTAA-AAAATATATAAATA
1 TTTTAAGAAAATATATAAATA
2621463 TTTTAAAGAAAATATATAAATA
1 TTTT-AAGAAAATATATAAATA
2621485 TTTTA
1 TTTTA
2621490 TAACTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 4 0.16
21 3 0.12
22 18 0.72
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTAAGAAAATATATAAATA
Found at i:2624792 original size:15 final size:15
Alignment explanation
Indices: 2624774--2624829 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2624764 TAACCGGTTT
2624774 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2624789 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
2624806 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2624821 CGATTTTAA
1 CGGTTTTAA
2624830 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:2624802 original size:17 final size:17
Alignment explanation
Indices: 2624777--2624827 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2624767 CCGGTTTCGG
2624777 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
2624794 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
2624809 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
2624826 TT
1 TT
2624828 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:2625246 original size:13 final size:13
Alignment explanation
Indices: 2625225--2625279 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2625215 AAGTTCGATA
*
2625225 AATTTAAATACTT
1 AATTGAAATACTT
2625238 AATTGAAATACTT
1 AATTGAAATACTT
* *
2625251 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
2625265 AATTGAAATACTT
1 AATTGAAATACTT
2625278 AA
1 AA
2625280 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2625325 original size:34 final size:33
Alignment explanation
Indices: 2625265--2625364 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 33
2625255 AACTCAACAT
* * *
2625265 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2625298 AATTCAAATACTTAAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTT-AAAAACTTCCAAGTTCGATA
2625332 AATTCAAATACTTAAAAACTTCC-AGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2625364 A
1 A
2625365 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 10 0.16
33 22 0.35
34 31 0.49
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2627693 original size:12 final size:12
Alignment explanation
Indices: 2627676--2627721 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2627666 TTCGGATAAA
2627676 AACCGGTTTTTT
1 AACCGGTTTTTT
2627688 AACCGGTTTTTTT
1 AACCGG-TTTTTT
2627701 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
2627715 ATCCGGT
1 AACCGGT
2627722 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:2627706 original size:15 final size:14
Alignment explanation
Indices: 2627675--2627714 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2627665 TTTCGGATAA
2627675 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
2627688 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
2627701 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
2627715 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:2627922 original size:36 final size:36
Alignment explanation
Indices: 2627850--2627922 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
2627840 CCTCCCTTTG
**
2627850 TTTTCACCTTGAGCGCGACACATGTAACCATTTGGT
1 TTTTCACCTTGAGCGCGACACATGTAACCACCTGGT
* *
2627886 TTTTCACTTTGAGCGTGACACATGTAACCACCTGGT
1 TTTTCACCTTGAGCGCGACACATGTAACCACCTGGT
2627922 T
1 T
2627923 GACGATAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (36 bp):
TTTTCACCTTGAGCGCGACACATGTAACCACCTGGT
Found at i:2636599 original size:14 final size:14
Alignment explanation
Indices: 2636576--2636609 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2636566 TTATTTCACT
*
2636576 GAAAACGTTTTCCG
1 GAAAATGTTTTCCG
2636590 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
*
2636604 TAAAAT
1 GAAAAT
2636610 AAATTACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (14 bp):
GAAAATGTTTTCCG
Found at i:2636957 original size:23 final size:23
Alignment explanation
Indices: 2636908--2636958 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2636898 GTGATATATT
**
2636908 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
2636931 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
2636954 ATATT
1 ATATT
2636959 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:2637159 original size:22 final size:23
Alignment explanation
Indices: 2637131--2637177 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2637121 TTGGTTATTT
2637131 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
2637153 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
2637176 TA
1 TA
2637178 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:2637182 original size:22 final size:22
Alignment explanation
Indices: 2637139--2637182 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2637129 TTTATTATAA
*
2637139 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
2637161 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
2637183 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:2639892 original size:2 final size:2
Alignment explanation
Indices: 2639885--2639917 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2639875 ATCCACATAC
2639885 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2639918 TAAAAAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2640911 original size:2 final size:2
Alignment explanation
Indices: 2640904--2640946 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2640894 GGGTTTAGAA
2640904 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
2640946 A
1 A
2640947 AGGGGCCCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2649171 original size:12 final size:13
Alignment explanation
Indices: 2649154--2649182 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2649144 TAATATATAA
2649154 AAAAATT-ATTTT
1 AAAAATTAATTTT
2649166 AAAAATTAATTTT
1 AAAAATTAATTTT
2649179 AAAA
1 AAAA
2649183 GACAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAAATTAATTTT
Found at i:2649759 original size:27 final size:26
Alignment explanation
Indices: 2649696--2649759 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 26
2649686 TTAACTCAAT
* *
2649696 CTGACTAGAAAATTATACATCCTTCA
1 CTGACTCGAAAAATATACATCCTTCA
2649722 CTCGA-TCCGAAAAATATACA-CCTTCCA
1 CT-GACT-CGAAAAATATACATCCTT-CA
2649749 CCTGACTCGAA
1 -CTGACTCGAA
2649760 TCCGATCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
26 7 0.23
27 21 0.68
28 3 0.10
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (26 bp):
CTGACTCGAAAAATATACATCCTTCA
Found at i:2650515 original size:11 final size:11
Alignment explanation
Indices: 2650501--2650530 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2650491 TATTCTTATT
2650501 TTATTAATATA
1 TTATTAATATA
*
2650512 TTATTAAAATA
1 TTATTAATATA
2650523 TTATTAAT
1 TTATTAAT
2650531 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTATTAATATA
Found at i:2650552 original size:19 final size:20
Alignment explanation
Indices: 2650514--2650580 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
2650504 TTAATATATT
*
2650514 ATTAAAATATTATTAATTAA
1 ATTAAAATATTATAAATTAA
*
2650534 ATTAAAATTTTA-AAATTAAA
1 ATTAAAATATTATAAATT-AA
*
2650554 ATTCCCAAA-ATTAT-AATTAA
1 ATT--AAAATATTATAAATTAA
2650574 ATTAAAA
1 ATTAAAA
2650581 AATATTCCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 21 0.55
21 7 0.18
22 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAAAATATTATAAATTAA
Found at i:2653020 original size:29 final size:29
Alignment explanation
Indices: 2652986--2653042 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
2652976 TCGTTCTAGT
*
2652986 TTGGTGATTAGCGTTTCATTTCGTAACTC
1 TTGGTGATTAACGTTTCATTTCGTAACTC
*
2653015 TTGGTGATTAATGTTTCATTTCGTAACT
1 TTGGTGATTAACGTTTCATTTCGTAACT
2653043 TAATTTGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.47
Consensus pattern (29 bp):
TTGGTGATTAACGTTTCATTTCGTAACTC
Found at i:2657973 original size:32 final size:32
Alignment explanation
Indices: 2657928--2657991 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2657918 GGACGTTAGA
2657928 TTCATTTACAGGCTTAAGAAAAGCCCCAAAAG
1 TTCATTTACAGGCTTAAGAAAAGCCCCAAAAG
* *
2657960 TTCATTTATAGGCTTAAGAATAGCCCCAAAAG
1 TTCATTTACAGGCTTAAGAAAAGCCCCAAAAG
2657992 ACCCCTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (32 bp):
TTCATTTACAGGCTTAAGAAAAGCCCCAAAAG
Found at i:2660786 original size:16 final size:16
Alignment explanation
Indices: 2660765--2660795 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2660755 TATTTTAATT
2660765 CTTTAAATTTCTGTTA
1 CTTTAAATTTCTGTTA
2660781 CTTTAAATTTCTGTT
1 CTTTAAATTTCTGTT
2660796 TTTTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (16 bp):
CTTTAAATTTCTGTTA
Found at i:2661801 original size:98 final size:103
Alignment explanation
Indices: 2661687--2661896 Score: 317
Period size: 103 Copynumber: 2.1 Consensus size: 103
2661677 ACATTTATCT
2661687 AAAAAT-AAT-TTAAAATATATATAATTT-AAA-A-TT-TTTA-TTTAAAAATATCAGAAAATGA
1 AAAAATAAATATTAAAATATATATAATTTAAAATATTTATTTATTTTAAAAATATCAGAAAATGA
* * *
2661745 ACATACAGTTGCTTTAAGATTATCCTTTCTTAATATTG
66 ACATACAGTTGCTTTAAAACTATCATTTCTTAATATTG
* *
2661783 AAAAATAAATATTAAAATATGTATAATTTAAAATATTTATTTATTTTAAAAATATCAGAAAATGG
1 AAAAATAAATATTAAAATATATATAATTTAAAATATTTATTTATTTTAAAAATATCAGAAAATGA
*
2661848 ACATCCAGTTGCTTTAAAACTATCATTTCTTAATATTG
66 ACATACAGTTGCTTTAAAACTATCATTTCTTAATATTG
2661886 AAAAATAAATA
1 AAAAATAAATA
2661897 AATGTTATTT
Statistics
Matches: 101, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
96 6 0.06
97 3 0.03
98 17 0.17
99 3 0.03
100 1 0.01
101 2 0.02
102 4 0.04
103 65 0.64
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (103 bp):
AAAAATAAATATTAAAATATATATAATTTAAAATATTTATTTATTTTAAAAATATCAGAAAATGA
ACATACAGTTGCTTTAAAACTATCATTTCTTAATATTG
Found at i:2662003 original size:20 final size:20
Alignment explanation
Indices: 2661957--2661996 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2661947 TTAAAGAAAT
*
2661957 ATAAAATGAAGAAAAATATA
1 ATAATATGAAGAAAAATATA
* *
2661977 ATAATATGAATAAAACTATA
1 ATAATATGAAGAAAAATATA
2661997 TATATATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (20 bp):
ATAATATGAAGAAAAATATA
Found at i:2663811 original size:45 final size:45
Alignment explanation
Indices: 2663744--2664454 Score: 1129
Period size: 45 Copynumber: 16.0 Consensus size: 45
2663734 TAAGTCTTAT
* *
2663744 CATCTTGCACT-ATAGGGATTACAGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGA-AGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* * *
2663789 CATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
2663834 CATCCTGCACTGAAGGGCTTACGGATGACTCGAAGGTTTTG-AAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
2663878 -A-----CA-T--AGGGCTTACGGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
2663914 CATCCTGCACTGAAGGGCTTACGGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
2663959 CATCCTGCACTGAAGGGCTTACAGATGACCCCGAAGGTTTTGATAA
1 CATCCTGCACTGAAGGGCTTACAGATGA-CCCGAAGGTTTTGAAAA
* *
2664005 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
2664050 CATCCTGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
2664095 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAAGTTTTAAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
2664140 CATCCTGCACTGAAGGGCTTACGGATGGCCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
2664185 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
2664230 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
2664275 CATCCTGCACTGAAGGGCTTACGGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
2664320 CATCCTGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
2664365 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* * *
2664410 CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
2664455 TATCAAAAAC
Statistics
Matches: 620, Mismatches: 34, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
35 27 0.04
36 3 0.00
37 2 0.00
38 2 0.00
42 2 0.00
43 2 0.00
44 3 0.00
45 536 0.86
46 43 0.07
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (45 bp):
CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:2664536 original size:76 final size:76
Alignment explanation
Indices: 2664393--2664658 Score: 421
Period size: 76 Copynumber: 3.5 Consensus size: 76
2664383 TTACAGATGA
* ** * * *
2664393 CCCGAAGG--TTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGGCTTATGGATGACCCGGAGGCTTTAAAAAC
2664456 ATCAAAAA-CT
66 ATCAAAAAGCT
2664466 CCCGAAGGCTTTTTTGAAAACATCCTGCACTGTAGGGCTTATGGATGACCCGGAGGCTTTAAAAA
1 CCCGAAGGC-TTTTTGAAAACATCCTGCACTGTAGGGCTTATGGATGACCCGGAGGCTTTAAAAA
2664531 CATCAAAAAGCT
65 CATCAAAAAGCT
*
2664543 CCCAAAGGCTTTTTGAAAACATCCTGCACTGTAGGGCTTATGGATGACCCGGAGGCTTTAAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGGCTTATGGATGACCCGGAGGCTTTAAAAAC
2664608 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
2664619 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTA
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGGCTTA
2664659 CAGATATGGG
Statistics
Matches: 179, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
73 8 0.04
76 161 0.90
77 10 0.06
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGGCTTATGGATGACCCGGAGGCTTTAAAAAC
ATCAAAAAGCT
Found at i:2675015 original size:2 final size:2
Alignment explanation
Indices: 2675010--2675035 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2675000 TATATTAATT
2675010 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
2675036 AAGATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2675332 original size:103 final size:99
Alignment explanation
Indices: 2675144--2675351 Score: 310
Period size: 103 Copynumber: 2.1 Consensus size: 99
2675134 ATTTATCTAA
* *
2675144 AAATAATTAAAAATATATATAATTTAAATTTTTTATTTAAAAATATCATAAAATGGACATCCAGT
1 AAAT-ATTAAAAATATATATAATTTAAATTTTTTATTTAAAAATATCAAAAAATGGACATCCAAT
2675209 TGCTTTAAGACTGCCCTTTCTAAATATTGAAAAAT
65 TGCTTTAAGACTGCCCTTTCTAAATATTGAAAAAT
*
2675244 AAATATT-AAAATATGTATAATTTAAAATATTTATTTATTTTAAAAATATCAAAAAATGGACATC
1 AAATATTAAAAATATATATAATTT--AA-ATTT-TTTA-TTTAAAAATATCAAAAAATGGACATC
* *
2675308 CAATTGCTTTAAGACTGCCTTTTCTTAATATTGAAAAAT
61 CAATTGCTTTAAGACTGCCCTTTCTAAATATTGAAAAAT
2675347 AAATA
1 AAATA
2675352 AATATTATTT
Statistics
Matches: 98, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
98 15 0.15
99 3 0.03
100 6 0.06
101 4 0.04
102 4 0.04
103 66 0.67
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (99 bp):
AAATATTAAAAATATATATAATTTAAATTTTTTATTTAAAAATATCAAAAAATGGACATCCAATT
GCTTTAAGACTGCCCTTTCTAAATATTGAAAAAT
Found at i:2675455 original size:2 final size:2
Alignment explanation
Indices: 2675448--2675474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2675438 TGAATAAAAC
2675448 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2675475 TTGTTATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2675458 original size:20 final size:20
Alignment explanation
Indices: 2675412--2675451 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2675402 TTAAAGAAAT
*
2675412 ATAAAATGAAGAAAAATATA
1 ATAATATGAAGAAAAATATA
* *
2675432 ATAATATGAATAAAACTATA
1 ATAATATGAAGAAAAATATA
2675452 TATATATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (20 bp):
ATAATATGAAGAAAAATATA
Found at i:2681013 original size:2 final size:2
Alignment explanation
Indices: 2681006--2681036 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2680996 TACCCAACAA
2681006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2681037 CAATAAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2682445 original size:69 final size:69
Alignment explanation
Indices: 2682323--2682578 Score: 341
Period size: 69 Copynumber: 3.7 Consensus size: 69
2682313 GACGTAACTT
* * *
2682323 ACACAAGATTGGATTTTAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGGTGAAGCAA
1 ACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGTAA
*
2682388 TGCA
66 TACA
* * * * * *
2682392 ACAAAATATTTGATTTCAACTTCACAACGAATGATATCCAACTCAAAGCCAATTTAGTAAAGTAA
1 ACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGTAA
2682457 TACA
66 TACA
* * * *
2682461 ACACAAGATTGGATTTCAACTTCACAATGAAGGATATTCAACCCAAAGCCAATTTGGTGAAGTAC
1 ACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGTAA
2682526 TACA
66 TACA
* * * * *
2682530 ACTCGAGATTGGATTTCAACTTCACAACGGAGGATATCTAACTCGAAGC
1 ACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
2682579 TTAAACTTCA
Statistics
Matches: 160, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 160 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (69 bp):
ACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGTAA
TACA
Found at i:2683007 original size:230 final size:231
Alignment explanation
Indices: 2682535--2683097 Score: 736
Period size: 230 Copynumber: 2.4 Consensus size: 231
2682525 CTACAACTCG
* * * * * * * * * *
2682535 AGATTGGATTTCAACTTCACAACGGAGGATATCTAACTCGAAGCTTAAACTTCACAACGAAGGAT
1 AGATTGGATTTAAACTTCATAACGAAGGACATCTAATTCAAAGC-TCAACTTCACAGCGAATGAG
* * *
2682600 CCATCCATGATTTCAACTTCACGATGAAGGATATCGTGCCCAAAAGATTGACCCAACTTCACGAT
65 CCATCCATGATTTCAACTTCACAAAGAAGGATATCGTACCCAAAAGATTGACCCAACTTCACGAT
* * * * * * *
2682665 GAATGAGTCATCTGTGACACAGCAATGAAAATCCAATTTCATTCAGAGTTAATTTTAACTTCACA
130 GAAGGAGTCATCTGTGACACAACAATAAAAAACCAATGTCATTCAGAGTCAATTTCAACTTCACA
* **
2682730 ATGAAAGATATTGAACTCGAAAGTGATGTAATTTACA
195 ATGAAAGATATTGAACTCGAAAGAGATACAATTTACA
2682767 AGATTGGATTTAAACTTCATAACGAAGGA-ATCTAATTCAAAGCTCAACTTCACAGCGAATGAGC
1 AGATTGGATTTAAACTTCATAACGAAGGACATCTAATTCAAAGCTCAACTTCACAGCGAATGAGC
* * * *
2682831 CATTCGTGATTTCAACTTCACAACGAAGGATATCGTACCCAAAAGATTGGCCCAACTTCACGATG
66 CATCCATGATTTCAACTTCACAAAGAAGGATATCGTACCCAAAAGATTGACCCAACTTCACGATG
*
2682896 AAGGAGTCATCTGTGACACAACAATAAAAAACCAGTGTCATTCAGAGTCAATTTCAACTTCAC-A
131 AAGGAGTCATCTGTGACACAACAATAAAAAACCAATGTCATTCAGAGTCAATTTCAACTTCACAA
*
2682960 TCGAAAGATATTGAACTCGAAAGAGATACAATTTATA
196 T-GAAAGATATTGAACTCGAAAGAGATACAATTTACA
* * * * * *
2682997 A-TTATGGATTTTAACTTCATAACGAATGACATCCAATTAAAAGCTCAATTTCACAGCGAATGAG
1 AGAT-TGGATTTAAACTTCATAACGAAGGACATCTAATTCAAAGCTCAACTTCACAGCGAATGAG
* * *
2683061 CTATCCACGATTTCAACTTCACAAAAAAGGATATCGT
65 CCATCCATGATTTCAACTTCACAAAGAAGGATATCGT
2683098 GCCTAATGAA
Statistics
Matches: 289, Mismatches: 39, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
229 3 0.01
230 186 0.64
231 74 0.26
232 26 0.09
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (231 bp):
AGATTGGATTTAAACTTCATAACGAAGGACATCTAATTCAAAGCTCAACTTCACAGCGAATGAGC
CATCCATGATTTCAACTTCACAAAGAAGGATATCGTACCCAAAAGATTGACCCAACTTCACGATG
AAGGAGTCATCTGTGACACAACAATAAAAAACCAATGTCATTCAGAGTCAATTTCAACTTCACAA
TGAAAGATATTGAACTCGAAAGAGATACAATTTACA
Found at i:2685492 original size:11 final size:11
Alignment explanation
Indices: 2685461--2685494 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2685451 TGATGTTTAA
2685461 ATTTATAATTT
1 ATTTATAATTT
2685472 -TTTATAATTT
1 ATTTATAATTT
*
2685482 ATTTTTAATTT
1 ATTTATAATTT
2685493 AT
1 AT
2685495 CATTAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTATAATTT
Found at i:2685986 original size:106 final size:104
Alignment explanation
Indices: 2685772--2686000 Score: 246
Period size: 106 Copynumber: 2.2 Consensus size: 104
2685762 ACAATTGTTC
* * * * * * *
2685772 TTTTTTA-TGACATATATTCGATACAATTATCAATATAAATTGTGGTGAATTTTTTTGACACTAA
1 TTTTTTAGTGACAAATGTTCGATACAATTATCAATAGAAATTGCGATAAATTTATTTGACACTAA
* * * **
2685836 AAATATATTTTTGTGACCATCAATATTATCACGCTAATTA
66 AAATATAGTTTTGGGACCACCAATATTATCACAATAA-TA
**
2685876 TTTTTTAGTGACCAAATGTTCGATATTATTATCAATAGAAATTGCGATAAATTTATTTGACACTA
1 TTTTTTAGTGA-CAAATGTTCGATACAATTATCAATAGAAATTGCGATAAATTTATTTGACACTA
* * * *
2685941 AAAGTAT-GTTTTGGGACCACCAATGTTGTCACAATAAATG
65 AAAATATAGTTTTGGGACCACCAATATTATCACAAT-AATA
2685981 TTTTTTAGTGATCAAATGTT
1 TTTTTTAGTGA-CAAATGTT
2686001 TGCCACTATT
Statistics
Matches: 103, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
104 7 0.07
105 44 0.43
106 52 0.50
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (104 bp):
TTTTTTAGTGACAAATGTTCGATACAATTATCAATAGAAATTGCGATAAATTTATTTGACACTAA
AAATATAGTTTTGGGACCACCAATATTATCACAATAATA
Found at i:2686017 original size:105 final size:106
Alignment explanation
Indices: 2685819--2686017 Score: 238
Period size: 105 Copynumber: 1.9 Consensus size: 106
2685809 AATTGTGGTG
* * * * ** *
2685819 AATTTTTTTGACACTAAAAATATATTTTTGTGACCATCAATATTATCACGCTAATTATTTTTTAG
1 AATTTATTTGACACTAAAAATATAGTTTTGGGACCACCAATATTATCACAATAAATATTTTTTAG
* * *
2685884 TGACCAAATGTTCGATATTATTATCAATAGAAATTGCGATA
66 TGACCAAATGTTCGACACTATTAACAATAGAAATTGCGATA
* * * *
2685925 AATTTATTTGACACTAAAAGTAT-GTTTTGGGACCACCAATGTTGTCACAATAAATGTTTTTTAG
1 AATTTATTTGACACTAAAAATATAGTTTTGGGACCACCAATATTATCACAATAAATATTTTTTAG
* * *
2685989 TGATCAAATGTTTGCCACTATTAACAATA
66 TGACCAAATGTTCGACACTATTAACAATA
2686018 ACTATGTCAC
Statistics
Matches: 76, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
105 55 0.72
106 21 0.28
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (106 bp):
AATTTATTTGACACTAAAAATATAGTTTTGGGACCACCAATATTATCACAATAAATATTTTTTAG
TGACCAAATGTTCGACACTATTAACAATAGAAATTGCGATA
Found at i:2687179 original size:22 final size:22
Alignment explanation
Indices: 2687154--2687198 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2687144 TTTTTTTATA
* *
2687154 AAAACGCCGGTATTGATTATGT
1 AAAACACCAGTATTGATTATGT
2687176 AAAACACCAGTATTGATTATGT
1 AAAACACCAGTATTGATTATGT
2687198 A
1 A
2687199 TTTAGTGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (22 bp):
AAAACACCAGTATTGATTATGT
Found at i:2687343 original size:21 final size:21
Alignment explanation
Indices: 2687319--2687359 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2687309 TAAACATGAA
*
2687319 TCCATAATAACAAACTTTAAT
1 TCCATAACAACAAACTTTAAT
*
2687340 TCCATAACAACCAACTTTAA
1 TCCATAACAACAAACTTTAA
2687360 ATGGATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (21 bp):
TCCATAACAACAAACTTTAAT
Found at i:2695517 original size:43 final size:43
Alignment explanation
Indices: 2695398--2695533 Score: 152
Period size: 42 Copynumber: 3.2 Consensus size: 43
2695388 TTGCACAATC
* * * * *
2695398 GCGGCGTTTA-TAATAAAAATGCCACTAAGGTATATCACTATT
1 GCGGCGTTTATTAAAAAAAATGTCACTAAAGTACATGACTATT
* * *
2695440 GCGGCATTTATTACAAAAAAA--TCACTAAATTACATGATTATT
1 GCGGCGTTTATTA-AAAAAAATGTCACTAAAGTACATGACTATT
*
2695482 GTGGCGTTTATTAAAAAAAATGTCACTAAAGTACATGACTATT
1 GCGGCGTTTATTAAAAAAAATGTCACTAAAGTACATGACTATT
*
2695525 GCGGTGTTT
1 GCGGCGTTT
2695534 GAACAAAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
41 7 0.09
42 35 0.46
43 28 0.37
44 6 0.08
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTATTAAAAAAAATGTCACTAAAGTACATGACTATT
Found at i:2695542 original size:43 final size:43
Alignment explanation
Indices: 2695398--2695574 Score: 143
Period size: 42 Copynumber: 4.2 Consensus size: 43
2695388 TTGCACAATC
* * * * *
2695398 GCGGCGTTTATA-ATAAAAATGCCACTAAGGTATATCACTATT
1 GCGGCGTTTATACAAAAAAATGTCACTAAAGTACATGACTATT
* * *
2695440 GCGGCATTTATTACAAAAAAA--TCACTAAATTACATGATTATT
1 GCGGCGTTTA-TACAAAAAAATGTCACTAAAGTACATGACTATT
*
2695482 GTGGCGTTTATTA-AAAAAAATGTCACTAAAGTACATGACTATT
1 GCGGCGTTTA-TACAAAAAAATGTCACTAAAGTACATGACTATT
* * * * * *
2695525 GCGGTGTTTGA-AC-AAAAAA-GCCGCTAAAGTACAAGTCTATA
1 GCGGCGTTT-ATACAAAAAAATGTCACTAAAGTACATGACTATT
2695566 GCGGCGTTT
1 GCGGCGTTT
2695575 GTTTACAAAC
Statistics
Matches: 109, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
41 32 0.29
42 42 0.39
43 28 0.26
44 7 0.06
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTATACAAAAAAATGTCACTAAAGTACATGACTATT
Found at i:2695883 original size:41 final size:41
Alignment explanation
Indices: 2695833--2696001 Score: 182
Period size: 41 Copynumber: 4.1 Consensus size: 41
2695823 AGATTAACCC
*
2695833 TATTGCGGCGTTTGTATAAAAACACTACTAAAGTACTACTT
1 TATTGCGGCGTTTGTATAAAAACACCACTAAAGTACTACTT
* * * *
2695874 TATTACGGCGTTTGTATAAAAACGCCGCTAACGTACTACTT
1 TATTGCGGCGTTTGTATAAAAACACCACTAAAGTACTACTT
* * * *
2695915 TATTGCGACATTTGT-TGCAAAAATGA-CACTAAAGTACTACTA
1 TATTGCGGCGTTTGTAT--AAAAA-CACCACTAAAGTACTACTT
* *
2695957 TGTTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTTA-TT
1 TATTGCGGCGTTTGTATAAAAACACCACTAAAGTAC-TACTT
2695998 TATT
1 TATT
2696002 ACATCATTTG
Statistics
Matches: 102, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
40 1 0.01
41 68 0.67
42 32 0.31
43 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (41 bp):
TATTGCGGCGTTTGTATAAAAACACCACTAAAGTACTACTT
Found at i:2695937 original size:83 final size:83
Alignment explanation
Indices: 2695850--2696029 Score: 224
Period size: 83 Copynumber: 2.2 Consensus size: 83
2695840 GCGTTTGTAT
* * *
2695850 AAAAA-CACTACTAAAGTACTACTTTATTACGGCGTTTGTATAAAAACGCCGCTAACGTAC-TAC
1 AAAAATCAC-ACTAAAGTACTACTATATTACGGCGTTTGTATAAAAACGCCACTAAAGTACTTA-
*
2695913 TTTATTGCGA-CATTTGTTGC
64 TTTATTAC-ATCATTTGTTGC
* * *
2695933 AAAAATGACACTAAAGTACTACTATGTTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTTATT
1 AAAAATCACACTAAAGTACTACTATATTACGGCGTTTGTATAAAAACGCCACTAAAGTACTTATT
*
2695998 TATTACATCATTTGTTGT
66 TATTACATCATTTGTTGC
2696016 AAAAATGC-CACTAA
1 AAAAAT-CACACTAA
2696030 TATGAACCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
82 1 0.01
83 79 0.94
84 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (83 bp):
AAAAATCACACTAAAGTACTACTATATTACGGCGTTTGTATAAAAACGCCACTAAAGTACTTATT
TATTACATCATTTGTTGC
Found at i:2695953 original size:42 final size:41
Alignment explanation
Indices: 2695843--2696029 Score: 164
Period size: 41 Copynumber: 4.5 Consensus size: 41
2695833 TATTGCGGCG
* * * *
2695843 TTTGTATAAAAACACTACTAAAGTACTACTTTATTACGGCG
1 TTTGTATAAAAACGCCACTAAAGTACTACTTTATTACGACA
* * *
2695884 TTTGTATAAAAACGCCGCTAACGTACTACTTTATTGCGACA
1 TTTGTATAAAAACGCCACTAAAGTACTACTTTATTACGACA
* * * * * * *
2695925 TTTGT-TGCAAAAATGACACTAAAGTACTACTATGTTGCGGCG
1 TTTGTAT--AAAAACGCCACTAAAGTACTACTTTATTACGACA
2695967 TTTGTATAAAAACGCCACTAAAGTACTTA-TTTATTAC-ATCA
1 TTTGTATAAAAACGCCACTAAAGTAC-TACTTTATTACGA-CA
* *
2696008 TTTGTTGTAAAAATGCCACTAA
1 TTTG-TATAAAAACGCCACTAA
2696030 TATGAACCCT
Statistics
Matches: 116, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
40 1 0.01
41 66 0.57
42 48 0.41
43 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (41 bp):
TTTGTATAAAAACGCCACTAAAGTACTACTTTATTACGACA
Found at i:2700928 original size:22 final size:22
Alignment explanation
Indices: 2700903--2700983 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
2700893 TCCAGTAGTT
2700903 CTAAGACACTTTAGTATCAGTG
1 CTAAGACACTTTAGTATCAGTG
* *
2700925 CTAATG-CACTTTTGTATCAGTA
1 CTAA-GACACTTTAGTATCAGTG
*
2700947 CTAAGACACTTTAATA-CTAGTG
1 CTAAGACACTTTAGTATC-AGTG
*
2700969 CTAAGACAGTTTAGT
1 CTAAGACACTTTAGT
2700984 TATGTGATGG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
21 2 0.04
22 46 0.94
23 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (22 bp):
CTAAGACACTTTAGTATCAGTG
Found at i:2701584 original size:56 final size:56
Alignment explanation
Indices: 2701498--2701650 Score: 270
Period size: 56 Copynumber: 2.7 Consensus size: 56
2701488 TCAAATCTTC
2701498 TGGATTTCGGGTTGGATCAGATTTGAGTGTTACATGGTGATGTGACAGTTAAAAAA
1 TGGATTTCGGGTTGGATCAGATTTGAGTGTTACATGGTGATGTGACAGTTAAAAAA
2701554 TGGATTTCGGGTTGGATCAGATTTGAGTGTTACATGGTGATGTGACAGTTAAAAAA
1 TGGATTTCGGGTTGGATCAGATTTGAGTGTTACATGGTGATGTGACAGTTAAAAAA
* ** *
2701610 TGAATTTCAAGTTGGATCAAATTTGAGTGTTACATGGTGAT
1 TGGATTTCGGGTTGGATCAGATTTGAGTGTTACATGGTGAT
2701651 ATATGTCACT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 93 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.35
Consensus pattern (56 bp):
TGGATTTCGGGTTGGATCAGATTTGAGTGTTACATGGTGATGTGACAGTTAAAAAA
Found at i:2702219 original size:20 final size:20
Alignment explanation
Indices: 2702156--2702219 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
2702146 TATAGAATTT
*
2702156 ATTTTTATTTATTAACTACA
1 ATTTTTATTTATTAACTATA
* * * * * * *
2702176 GTGTATAATAATTTACTTTA
1 ATTTTTATTTATTAACTATA
2702196 ATTTTTATTTATTAACTATA
1 ATTTTTATTTATTAACTATA
2702216 ATTT
1 ATTT
2702220 ATAATAATTT
Statistics
Matches: 29, Mismatches: 15, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTTATTTATTAACTATA
Found at i:2702228 original size:10 final size:10
Alignment explanation
Indices: 2702213--2702244 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2702203 TTTATTAACT
2702213 ATAATTTATA
1 ATAATTTATA
2702223 ATAATTTATA
1 ATAATTTATA
*
2702233 ATAATTTTTA
1 ATAATTTATA
2702243 AT
1 AT
2702245 TTTTATTAAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATAATTTATA
Found at i:2702238 original size:40 final size:38
Alignment explanation
Indices: 2702156--2702293 Score: 133
Period size: 40 Copynumber: 3.6 Consensus size: 38
2702146 TATAGAATTT
* *
2702156 ATTTTTATTTATTAACTACAGTGTATAATAATTTACTTTA
1 ATTTTTATTTATTAACTATAATGTATAATAATTTA--TTA
*
2702196 ATTTTTATTTATTAACTATAATTTATAATAATTTATAATA
1 ATTTTTATTTATTAACTATAATGTATAATAATTTAT--TA
* *
2702236 ATTTTTAATTT-TT-A-T-TAATGGAAGAAATAATTT-TTA
1 ATTTTT-ATTTATTAACTATAAT-GTA-TAATAATTTATTA
2702272 ATTTTTATTTATTAACTATAAT
1 ATTTTTATTTATTAACTATAAT
2702294 TTACGATATA
Statistics
Matches: 83, Mismatches: 6, Indels: 19
0.77 0.06 0.18
Matches are distributed among these distances:
35 4 0.05
36 10 0.12
37 5 0.06
38 5 0.06
39 13 0.16
40 42 0.51
41 4 0.05
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (38 bp):
ATTTTTATTTATTAACTATAATGTATAATAATTTATTA
Found at i:2702336 original size:136 final size:130
Alignment explanation
Indices: 2702192--2702432 Score: 349
Period size: 136 Copynumber: 1.8 Consensus size: 130
2702182 AATAATTTAC
* * * *
2702192 TTTAATTTTTATTTATTAACTATAATTTATAATAA-TTTATAATAATTTTTAATTTTTATTAATG
1 TTTAATTTTAATTTATTAACTATAATTTATAAAAATTTTAT-AT-ATTTTTAATTTTCACTAATG
* *
2702256 GAAGAAATAATTTTTAATTTTTATTTATTAACTATAATTTACGATATATTTTTTAAACTTTTTAA
64 AAAGAAATAA-TTTT-A--TTT-TTTATTAACTATAATTTACAATATATTTTTTAAACTTTTTAA
2702321 TGATAGA
124 TGATAGA
2702328 TTTAATTTTAATTTATTAACTATAATTTATAAAAATTTTATATATTTTTAATTTTCACTAATGAA
1 TTTAATTTTAATTTATTAACTATAATTTATAAAAATTTTATATATTTTTAATTTTCACTAATGAA
*
2702393 ATAAATAATTTTATTTTTTATTAACTATAATTTACAATAT
66 AGAAATAATTTTATTTTTTATTAACTATAATTTACAATAT
2702433 TAACTTAAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
130 23 0.24
131 3 0.03
133 1 0.01
134 4 0.04
135 26 0.27
136 35 0.36
137 5 0.05
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (130 bp):
TTTAATTTTAATTTATTAACTATAATTTATAAAAATTTTATATATTTTTAATTTTCACTAATGAA
AGAAATAATTTTATTTTTTATTAACTATAATTTACAATATATTTTTTAAACTTTTTAATGATAGA
Found at i:2702463 original size:136 final size:135
Alignment explanation
Indices: 2702192--2702463 Score: 286
Period size: 136 Copynumber: 2.0 Consensus size: 135
2702182 AATAATTTAC
* * * * *
2702192 TTTAATTTTTATTTATTAACTATAATTTATAATAATTTATAATAATTTTTAATTTTTATTAATGG
1 TTTAATTTTAATTTATTAACTATAATTTATAAAAATTTATAATAATTTTTAATTTTCACTAATGA
* ** * *****
2702257 AAGAAATAATTTTTAATTTTTATTTATTAACTATAATTTACGATATATTTTTTAAACTTTTTAAT
66 AAGAAATAATTTTTAA-TTTTATTTATTAACTATAATTTACAATATATTAATAAAAAAAAATAAT
*
2702322 GATAGA
130 CATAGA
2702328 TTTAATTTTAATTTATTAACTATAATTTATAAAAATTT-T-ATATATTTTTAATTTTCACTAATG
1 TTTAATTTTAATTTATTAACTATAATTTATAAAAATTTATAATA-ATTTTTAATTTTCACTAATG
*
2702391 AAATAAATAA-TTTT-A-TTT-TTTATTAACTATAATTTACAATATTAACTTAAAAATAAAAAAA
65 AAAGAAATAATTTTTAATTTTATTTATTAACTATAATTTACAATA-T-A-TT---AATAAAAAAA
2702452 AATAATCATAGA
124 AATAATCATAGA
2702464 GTAGTAGTTA
Statistics
Matches: 113, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
130 22 0.19
131 4 0.04
132 1 0.01
133 3 0.03
134 7 0.06
135 27 0.24
136 49 0.43
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (135 bp):
TTTAATTTTAATTTATTAACTATAATTTATAAAAATTTATAATAATTTTTAATTTTCACTAATGA
AAGAAATAATTTTTAATTTTATTTATTAACTATAATTTACAATATATTAATAAAAAAAAATAATC
ATAGA
Found at i:2711765 original size:20 final size:20
Alignment explanation
Indices: 2711723--2711767 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2711713 GTTTGCTAGC
*
2711723 AGTTAAGGTTGTTAATATTT
1 AGTTAAGGTTGTTAATATGT
* *
2711743 AGTTGAGGTTGTTAATGTGT
1 AGTTAAGGTTGTTAATATGT
2711763 AGTTA
1 AGTTA
2711768 CAAAGTCTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (20 bp):
AGTTAAGGTTGTTAATATGT
Found at i:2713147 original size:36 final size:36
Alignment explanation
Indices: 2713107--2713247 Score: 203
Period size: 36 Copynumber: 3.9 Consensus size: 36
2713097 GATTCAAGAA
*
2713107 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
* * *
2713143 GAACGGAAGAAAGCATCGACACTTTCGATTC-AAGAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAG-T
*
2713179 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
* *
2713215 GAACGGAAGGAAACATCGACACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAA
2713248 TTGTTCATCT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
35 3 0.03
36 86 0.93
37 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.18
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
Found at i:2713193 original size:72 final size:72
Alignment explanation
Indices: 2713097--2713247 Score: 286
Period size: 72 Copynumber: 2.1 Consensus size: 72
2713087 AAATGAAGGT
2713097 GATTCAAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAA-GAAAGCATCG
1 GATTCAAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAA-CATCG
2713161 ACACTTTC
65 ACACTTTC
2713169 GATTCAAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAACATCGA
1 GATTCAAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAACATCGA
2713234 CACTTTC
66 CACTTTC
2713241 GATTCAA
1 GATTCAA
2713248 TTGTTCATCT
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
72 74 0.95
73 4 0.05
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (72 bp):
GATTCAAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAACATCGA
CACTTTC
Found at i:2713471 original size:20 final size:20
Alignment explanation
Indices: 2713443--2713506 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
2713433 GTTTGCTAGC
*
2713443 AGTTAAGGTTGTTAATGTTT
1 AGTTGAGGTTGTTAATGTTT
2713463 AGTTGAGGTTGTTAATGTTT
1 AGTTGAGGTTGTTAATGTTT
*
2713483 AGTTGAGGTTGTTAATGTGT
1 AGTTGAGGTTGTTAATGTTT
2713503 AGTT
1 AGTT
2713507 ACAAAGTCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (20 bp):
AGTTGAGGTTGTTAATGTTT
Found at i:2716281 original size:28 final size:28
Alignment explanation
Indices: 2716241--2716298 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2716231 CCAAATCGAG
2716241 TCAATGTTTCCTAAATCACATTATCTAA
1 TCAATGTTTCCTAAATCACATTATCTAA
2716269 TCAATGTTTCCTAAATCACATTATCTAA
1 TCAATGTTTCCTAAATCACATTATCTAA
2716297 TC
1 TC
2716299 GAAGTCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (28 bp):
TCAATGTTTCCTAAATCACATTATCTAA
Found at i:2716296 original size:14 final size:14
Alignment explanation
Indices: 2716251--2716296 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2716241 TCAATGTTTC
2716251 CTAAATCACATTAT
1 CTAAATCACATTAT
*
2716265 CT-AATCA-ATGTTT
1 CTAAATCACAT-TAT
2716278 CCTAAATCACATTAT
1 -CTAAATCACATTAT
2716293 CTAA
1 CTAA
2716297 TCGAAGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 2 0.08
13 7 0.27
14 8 0.31
15 7 0.27
16 2 0.08
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (14 bp):
CTAAATCACATTAT
Found at i:2716948 original size:2 final size:2
Alignment explanation
Indices: 2716936--2717007 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
2716926 CCATTTGTTT
*
2716936 TA TA TA CA 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
2716978 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2717008 TTTAAATAGT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2717053 original size:36 final size:35
Alignment explanation
Indices: 2717013--2717223 Score: 162
Period size: 35 Copynumber: 5.9 Consensus size: 35
2717003 TATATTTTAA
2717013 ATAGTTTTTAAAACATTTTGAAAATTAATATAATAT
1 ATAGTTTTTAAAACATTTTGAAAATT-ATATAATAT
* * *
2717049 ATAGTTTTTAAAACATTTTTAAAAATATATATTAT
1 ATAGTTTTTAAAACATTTTGAAAATTATATAATAT
* * *
2717084 ATAGTTTTTAAAATATTTTGAAAATGTGTATAGT-T
1 ATAGTTTTTAAAACATTTTGAAAAT-TATATAATAT
*** *
2717119 -T--TTAAAAAAACATTTTGAAAACATATATATATTAT
1 ATAGTTTTTAAAACATTTTG-AAA-AT-TATATAATAT
* * *
2717154 ATAGTTTTGAAAATCATTTCGAAAA-CATATAATAT
1 ATAGTTTTTAAAA-CATTTTGAAAATTATATAATAT
** * *
2717189 ATAGTTTAAAAAAATATTTTTGAAAACTATATAAT
1 ATAGTTT-TTAAAACA-TTTTGAAAATTATATAAT
2717224 TTTAAAAACA
Statistics
Matches: 138, Mismatches: 26, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
32 12 0.09
33 3 0.02
34 9 0.07
35 48 0.35
36 43 0.31
37 8 0.06
38 9 0.07
39 6 0.04
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (35 bp):
ATAGTTTTTAAAACATTTTGAAAATTATATAATAT
Found at i:2717086 original size:35 final size:35
Alignment explanation
Indices: 2717002--2717296 Score: 179
Period size: 34 Copynumber: 8.6 Consensus size: 35
2716992 TATAATATAT
* * *
2717002 ATATATTTTAAATAGTTTTTAAAACATTTTGAAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTAAAA
* *
2717037 TTAATATAATATATAGTTTTTAAAACATTTTTAAAA
1 AT-ATATATTATATAGTTTTTAAAACATTTTTAAAA
* *
2717073 ATATATATTATATAGTTTTTAAAATA-TTTT--GA
1 ATATATATTATATAGTTTTTAAAACATTTTTAAAA
* * *
2717105 A-A-AT-GTGTATAGTTTTTAAAAAAACATTTTGAAAACA
1 ATATATATTATATAGTTTTT---AAAACATTTT-TAAA-A
* **
2717142 TATATATATTATATAGTTTTGAAAATCATTTCGAAAA
1 -ATATATATTATATAGTTTTTAAAA-CATTTTTAAAA
* * **
2717179 CATATA-A-TATATAG-TTTAAAAAAATATTTTTGAA
1 -ATATATATTATATAGTTTTTAAAACAT-TTTTAAAA
* * *
2717213 A-A-CTA-TATA-A-TTTTAAAAACATTTTAAAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTAAAA
* * *
2717243 ATATATATAATATA-ATTTTAAAATATTTTTAAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTAAAA
*
2717277 ATATATATTATATAGGTTTT
1 ATATATATTATATAGTTTTT
2717297 GGAAAATATT
Statistics
Matches: 199, Mismatches: 39, Indels: 44
0.71 0.14 0.16
Matches are distributed among these distances:
29 11 0.06
30 8 0.04
31 13 0.07
32 15 0.08
33 9 0.05
34 45 0.23
35 34 0.17
36 31 0.16
37 7 0.04
38 8 0.04
39 6 0.03
40 2 0.01
41 10 0.05
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (35 bp):
ATATATATTATATAGTTTTTAAAACATTTTTAAAA
Found at i:2717256 original size:65 final size:62
Alignment explanation
Indices: 2717151--2717283 Score: 144
Period size: 63 Copynumber: 2.1 Consensus size: 62
2717141 ATATATATAT
* * * * *
2717151 TATATAGTTTTGAAAATCATTTCGAAAACATATAATATATAGTTTAAAAAAATATTTTTGAAAAC
1 TATATAATTTTGAAAAACATTTCGAAAAAATATAATATATAATTT--AAAAATATTTTT-AAAAA
* *
2717216 TATATAATTTT-AAAAACATTT-TAAAAAATATATATAATATAATTTTAAAATATTTTTAAAAA
1 TATATAATTTTGAAAAACATTTCGAAAAAATATA-AT-ATATAATTTAAAAATATTTTTAAAAA
2717278 TATATA
1 TATATA
2717284 TTATATAGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
62 10 0.17
63 20 0.34
64 11 0.19
65 18 0.31
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (62 bp):
TATATAATTTTGAAAAACATTTCGAAAAAATATAATATATAATTTAAAAATATTTTTAAAAA
Found at i:2717296 original size:25 final size:23
Alignment explanation
Indices: 2717268--2717313 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
2717258 TTTTAAAATA
*
2717268 TTTTTAAAAATATATATTATATAGG
1 TTTTGAAAAATAT-T-TTATATAGG
*
2717293 TTTTGGAAAATATTTTATATA
1 TTTTGAAAAATATTTTATATA
2717314 TATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 1 0.05
25 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTTGAAAAATATTTTATATAGG
Found at i:2717309 original size:36 final size:33
Alignment explanation
Indices: 2717217--2717325 Score: 119
Period size: 34 Copynumber: 3.1 Consensus size: 33
2717207 TTTGAAAACT
*
2717217 ATATAATTTTAAAAACATTTTAAAAAATATATATA
1 ATATAATTTT-AAAATATTTT-AAAAATATATATA
*
2717252 ATATAATTTTAAAATATTTTTAAAAATATATATT
1 ATATAATTTTAAAATA-TTTTAAAAATATATATA
* * *
2717286 ATATAGGTTTTGGAAAATATTTTATATATATATATA
1 ATATA-ATTTT--AAAATATTTTAAAAATATATATA
2717322 ATAT
1 ATAT
2717326 TATTATTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
34 22 0.34
35 18 0.28
36 18 0.28
37 6 0.09
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.46
Consensus pattern (33 bp):
ATATAATTTTAAAATATTTTAAAAATATATATA
Found at i:2720362 original size:164 final size:164
Alignment explanation
Indices: 2720114--2721120 Score: 1305
Period size: 164 Copynumber: 6.1 Consensus size: 164
2720104 AGCATAACTT
* * * * **
2720114 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCAACTACACTCAGCTTCGAGGGCGCATCATTT
1 AAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTT
* * * *
2720179 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGCTCAGCTT
64 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
* * * *
2720244 CAAGGGCACAGCATTTGCAACATAACTCAAGGCTAG
129 CGAGGGCACATCATTTACAGCATAACTCAAGGCTAG
* * *
2720280 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTATGCTCAGCTTCAAGGCACATCATTTGC
1 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGC
*
2720345 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAGAGACCCTCGAGTTCGATTACACTCAGCTTCG
66 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCG
* * *
2720410 AGGACACATCATTTACGGCATAACTCAAGACTAG
131 AGGGCACATCATTTACAGCATAACTCAAGGCTAG
* * * * *
2720444 AAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACACTCAGCTCCCAGGCATATCATTTG
1 AAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTG
* * *
2720509 CAGCATAGCTTAAGTCGAGAAGAGCTATTTGCCAAAGACCCTCGAGTTCGATTATACTCAGCTTC
65 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTC
* *
2720574 GAGGGCATATCATTTGCAGCATAACTCAAGGCTAG
130 GAGGGCACATCATTTACAGCATAACTCAAGGCTAG
* * * * * *
2720609 AAGGGTTATCTCCCAACAAAGACCTTTGAGTTTGAGTACGCTCAGCTCCTAGGTATATCATTTGC
1 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGC
* * * *
2720674 AGCATAGCTTAAGTTGAGAAGGGATATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGTTTCG
66 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCG
* *
2720739 AGGGCACATCATTTATAGCATAACTCAAGGTTAG
131 AGGGCACATCATTTACAGCATAACTCAAGGCTAG
** * * * *
2720773 AAGGGTTATCTATCACCTAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGT
1 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGC
* *
2720838 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAATTACAATCAGCTTCG
66 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCG
*
2720903 AGGGCACATCTTTTACAGCATAACTCAAGGCTAG
131 AGGGCACATCATTTACAGCATAACTCAAGGCTAG
* * * *
2720937 AAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTG
1 AAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTG
* * * * **
2721002 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAGGCTCAG
65 CAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCAG
* * * * * * *
2721067 C-TCCAAGGCACATCATTTACAACATAGCTTAAGTCCAG
126 CTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAG
*
2721105 AAGGGCTATCTGCCAA
1 AAGGGTTATCTGCCAA
2721121 AGACCCTTCC
Statistics
Matches: 736, Mismatches: 99, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
164 409 0.56
165 245 0.33
166 16 0.02
168 41 0.06
169 25 0.03
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (164 bp):
AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGC
AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCG
AGGGCACATCATTTACAGCATAACTCAAGGCTAG
Found at i:2720776 original size:329 final size:328
Alignment explanation
Indices: 2720114--2721116 Score: 1342
Period size: 329 Copynumber: 3.0 Consensus size: 328
2720104 AGCATAACTT
* * * * * **
2720114 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCAACTACACTCAGCTTCGAGGGCGCATCATTT
1 AAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTACACTCAGC-TCCAAGGCATATCATTT
* * * *
2720179 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGCTCAGCTT
64 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
* * *
2720244 CAAGGGCACAGCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGA
129 CGAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGA
* * * *
2720309 GTTCGACTATGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
194 GTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCT
* * *
2720374 GCCAGAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACGGCATAACTCAAG
259 GCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACAGCATAACTCAAG
2720439 ACTAG
324 ACTAG
*
2720444 AAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACACTCAGCTCCCAGGCATATCATTTG
1 AAGGGTTATCTGTCACC-AAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTG
* * *
2720509 CAGCATAGCTTAAGTCGAGAAGAGCTATTTGCCAAAGACCCTCGAGTTCGATTATACTCAGCTTC
65 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTC
* * *
2720574 GAGGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTCCCAACAAAGACCTTTGAG
130 GAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAG
* * * * *
2720639 TTTGAGTACGCTCAGCTCCTAGGTATATCATTTGCAGCATAGCTTAAGTTGAGAAGGGATATCTG
195 TTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG
* * * *
2720704 CCAAAGACCCCCGAGTTCGATTACACTCAGTTTCGAGGGCACATCATTTATAGCATAACTCAAGG
260 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACAGCATAACTCAAGA
*
2720769 TTAG
325 CTAG
* * * *
2720773 AAGGGTTATCTATCACCTAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGT
1 AAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGC
* *
2720838 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAATTACAATCAGCTTCG
66 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCG
* * * * *
2720903 AGGGCACATCTTTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAG
131 AGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAG
* * *
2720968 TTCGACTACGCTCAACTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
195 TTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG
** * ** * * * * *
2721033 CCAACCAAAGACCTTCGAGTTCGACTAGGCTCAGCTCCAAGG-CACATCATTTACAACATAGCTT
260 ----CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACAGCATAACTC
* *
2721097 AAGTCCAG
321 AAGACTAG
*
2721105 AAGGGCTATCTG
1 AAGGGTTATCTG
2721117 CCAAAGACCC
Statistics
Matches: 586, Mismatches: 81, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
328 148 0.25
329 335 0.57
330 40 0.07
332 33 0.06
333 30 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (328 bp):
AAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGC
AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCG
AGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGT
TCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGC
CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACAGCATAACTCAAGAC
TAG
Found at i:2721125 original size:493 final size:492
Alignment explanation
Indices: 2720172--2721115 Score: 1359
Period size: 493 Copynumber: 1.9 Consensus size: 492
2720162 TCGAGGGCGC
* *** *
2720172 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGACCCCCGAGTTCGACTACAC
* *
2720237 TCAGCTTCAAGGGCACAGCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGA
66 TCAGCTTCAAGGGCACAGCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGA
* *
2720302 CCTTCGAGTTCGACTATGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
131 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
* * * *
2720367 GCTATCTGCCAGAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTACGGCATA
196 GCTATCTGCCAAAGACCCTCGAGTTCAATTACAATCAGCTTCGAGGACACATCATTTACAGCATA
* * * *
2720432 ACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACACTCAGCTCCCAG
261 ACTCAAGACTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTACACTCAACTCCAAG
* * *
2720497 GCATATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATTTGCCAAAGACCCTCGAGTTCGATT
326 GCATATCATTTGCAGCATAACTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGAGTTCGACT
* * * * * * * *
2720562 ATACTCAGCTTCGAGGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTCCCAACA
391 AGACTCAGCTTCCAAGGCACATCATTTACAACATAACTCAAGGCCAGAAGGGCTATCTCCC-ACA
2720627 AAGACCTTTGAGTTTGAGTACGCTCAGCTCCTAGGTAT
455 AAGACCTTTGAGTTTGAGTACGCTCAGCTCCTAGGTAT
* *
2720665 ATCATTTGCAGCATAGCTTAAGTTGAGAAGGGATATCTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGACCCCCGAGTTCGACTACAC
* * * * * * * * *
2720730 TCAGTTTCGAGGGCACATCATTTATAGCATAACTCAAGGTTAGAAGGGTTATCTATCACCTAAGA
66 TCAGCTTCAAGGGCACAGCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGA
* * *
2720795 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGCTTAAGTCGAGAAGG
131 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
* *
2720860 GCTATCTGCCAAAGACCCTCGAGTTCAATTACAATCAGCTTCGAGGGCACATCTTTTACAGCATA
196 GCTATCTGCCAAAGACCCTCGAGTTCAATTACAATCAGCTTCGAGGACACATCATTTACAGCATA
* *
2720925 ACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAG
261 ACTCAAGACTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTACACTCAACTCCAAG
* * *
2720990 GCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTC
326 GCATATCATTTGCAGCATAACTTAAGTCGAGAAGAGCTATCTG----CCAAAGACCCTCGAGTTC
* * * *
2721055 GACTAGGCTCAGC-TCCAAGGCACATCATTTACAACATAGCTTAAGTCCAGAAGGGCTATCT
387 GACTAGACTCAGCTTCCAAGGCACATCATTTACAACATAACTCAAGGCCAGAAGGGCTATCT
2721116 GCCAAAGACC
Statistics
Matches: 394, Mismatches: 53, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
493 329 0.84
496 38 0.10
497 27 0.07
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (492 bp):
ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGACCCCCGAGTTCGACTACAC
TCAGCTTCAAGGGCACAGCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGA
CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
GCTATCTGCCAAAGACCCTCGAGTTCAATTACAATCAGCTTCGAGGACACATCATTTACAGCATA
ACTCAAGACTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTACACTCAACTCCAAG
GCATATCATTTGCAGCATAACTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGAGTTCGACT
AGACTCAGCTTCCAAGGCACATCATTTACAACATAACTCAAGGCCAGAAGGGCTATCTCCCACAA
AGACCTTTGAGTTTGAGTACGCTCAGCTCCTAGGTAT
Found at i:2721484 original size:9 final size:8
Alignment explanation
Indices: 2721469--2721494 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2721459 TTTTCGTCCC
2721469 ATTTTTTT
1 ATTTTTTT
2721477 ATTTTTTT
1 ATTTTTTT
2721485 ATTTTTTT
1 ATTTTTTT
2721493 AT
1 AT
2721495 ATACATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2721563 original size:37 final size:37
Alignment explanation
Indices: 2721507--2721773 Score: 278
Period size: 37 Copynumber: 7.2 Consensus size: 37
2721497 ACATATATAT
* *
2721507 ATATATAGTAGTATATAG-TTTGAAAACATTTTTAAAAA
1 ATATATA-TAATATATAGTTTTTAAAACATTTTT-AAAA
* *
2721545 ATATATATAATATATAGTTTTGAAAAACATGTTTGAAAA
1 ATATATATAATATATAGTTTT-TAAAACAT-TTTTAAAA
* * * * *
2721584 CATTTATATATTATATAGGTTTTAAAACATCTTGAAAA
1 -ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
* *
2721622 TTA-ATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
*
2721658 ATATATATATTATATAGTTTTTAAAAACA-TTTTAAAA
1 ATATATATAATATATAGTTTTT-AAAACATTTTTAAAA
* *
2721695 ATAAATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
* *
2721732 ATATATAT--TATATAG-TTTTAAAATA-TTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
*
2721765 ATGTATATA
1 ATATATATA
2721774 GTTTTTTAAA
Statistics
Matches: 197, Mismatches: 24, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
33 15 0.08
34 9 0.05
35 7 0.04
36 36 0.18
37 68 0.35
38 23 0.12
39 18 0.09
40 21 0.11
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTAAAA
Found at i:2721702 original size:74 final size:73
Alignment explanation
Indices: 2721507--2721754 Score: 315
Period size: 74 Copynumber: 3.3 Consensus size: 73
2721497 ACATATATAT
* * * *
2721507 ATATATAGTAGTATATAG-TTTGAAAACATTTTTAAAAAATATATATAATATATAGTTTTGAAAA
1 ATATATA-TATTATATAGTTTTAAAAACA-TTTT-AAAAATAAATATAATATATAGTTTT-TAAA
*
2721571 ACATGTTTGAAAA
62 ACATTTTTG-AAA
* * * *
2721584 CATTTATATATTATATAGGTTTT-AAAACATCTTGAAAATTAATATAATATATAGTTTTTAAAAC
1 -ATATATATATTATATA-GTTTTAAAAACATTTTAAAAATAAATATAATATATAGTTTTTAAAAC
2721648 ATTTTTGAAA
64 ATTTTTGAAA
2721658 ATATATATATTATATAGTTTTTAAAAACATTTTAAAAATAAATATAATATATAGTTTTTAAAACA
1 ATATATATATTATATAG-TTTTAAAAACATTTTAAAAATAAATATAATATATAGTTTTTAAAACA
2721723 TTTTTG-AA
65 TTTTTGAAA
2721731 A-ATATATATTATATAGTTTTAAAA
1 ATATATATATTATATAGTTTTAAAA
2721755 TATTTTGAAA
Statistics
Matches: 154, Mismatches: 12, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
71 8 0.05
72 16 0.10
73 22 0.14
74 48 0.31
75 11 0.07
76 22 0.14
77 11 0.07
78 13 0.08
79 3 0.02
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (73 bp):
ATATATATATTATATAGTTTTAAAAACATTTTAAAAATAAATATAATATATAGTTTTTAAAACAT
TTTTGAAA
Found at i:2721806 original size:2 final size:2
Alignment explanation
Indices: 2721801--2721836 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2721791 TTTTGAAAAC
2721801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2721837 GTTTTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2721939 original size:38 final size:36
Alignment explanation
Indices: 2721895--2721972 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
2721885 TTTTGAAAAC
2721895 TATATAATTTTAAAAACATTTTTTAAAAATATATATAA
1 TATATAATTTT-AAAACA-TTTTTAAAAATATATATAA
* ** *
2721933 TATATAATTTTAAAATATTTTTAAATGTATATATTA
1 TATATAATTTTAAAACATTTTTAAAAATATATATAA
2721969 TATA
1 TATA
2721973 GGTTTTGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 20 0.56
37 5 0.14
38 11 0.31
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (36 bp):
TATATAATTTTAAAACATTTTTAAAAATATATATAA
Found at i:2723089 original size:4 final size:4
Alignment explanation
Indices: 2723080--2723310 Score: 363
Period size: 4 Copynumber: 57.8 Consensus size: 4
2723070 CGCTAGTTTA
2723080 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
2723128 ATAT ATAT ATAT ATAT ATAT ATGT ATAT ATGT ATAT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
2723176 ATAT ATGT ATAT ATGT ATAT ATAT ATAT ATGT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
2723224 ATAT ATAT ATAT ATAT ATAT GTAT ATAT ATAT ATAT ATAT ACAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
2723272 ACAT ATAT ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
2723311 ATAATTATTA
Statistics
Matches: 207, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 207 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:2723565 original size:22 final size:22
Alignment explanation
Indices: 2723528--2723588 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
2723518 TTTTTACTAA
*
2723528 ATTTTATTTTTA-TTTATTTATC
1 ATTTT-TTTTTATTTTATTTAAC
*
2723550 ATTTTTTTTTATTTTA-CTAAC
1 ATTTTTTTTTATTTTATTTAAC
* *
2723571 ATTTTTTTCTCTTTTATT
1 ATTTTTTTTTATTTTATT
2723589 ATTATTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 23 0.72
22 9 0.28
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (22 bp):
ATTTTTTTTTATTTTATTTAAC
Found at i:2723573 original size:21 final size:21
Alignment explanation
Indices: 2723519--2723578 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
2723509 TTCCTTCGTT
2723519 TTTTACTAA-ATTTTATTTTTA
1 TTTTACTAACATTTT-TTTTTA
* *
2723540 -TTTATTTATCATTTTTTTTTA
1 TTTTA-CTAACATTTTTTTTTA
2723561 TTTTACTAACATTTTTTT
1 TTTTACTAACATTTTTTT
2723579 CTCTTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 4 0.12
21 19 0.59
22 9 0.28
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTACTAACATTTTTTTTTA
Found at i:2727387 original size:14 final size:14
Alignment explanation
Indices: 2727369--2727407 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2727359 ATAATTTTAC
*
2727369 AATAATAAAATTAA
1 AATAATAAAAATAA
*
2727383 CATAATAAAAATAA
1 AATAATAAAAATAA
*
2727397 AAAAATAAAAA
1 AATAATAAAAA
2727408 ATTATAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAATAAAAATAA
Found at i:2739524 original size:19 final size:19
Alignment explanation
Indices: 2739474--2739528 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2739464 AAACAGACAG
*
2739474 TAAGTATCGATACTCTTGTA
1 TAAGTATCGATACT-TTATA
* * *
2739494 AAAGTTTTGATACTTTATA
1 TAAGTATCGATACTTTATA
2739513 TAAGTATCGATACTTT
1 TAAGTATCGATACTTT
2739529 TAAACATTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.44
Consensus pattern (19 bp):
TAAGTATCGATACTTTATA
Found at i:2750824 original size:4 final size:4
Alignment explanation
Indices: 2750815--2750849 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2750805 AATCTGCTGT
2750815 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
2750850 TGAGCTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:2752018 original size:43 final size:43
Alignment explanation
Indices: 2751882--2752096 Score: 232
Period size: 42 Copynumber: 5.2 Consensus size: 43
2751872 AGGTAATTAA
* *
2751882 CGGCGTTTGTACCCAAAAATGCCGCTATAGATCT-GACCTTTTG
1 CGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCGACCTTTTG
* * *
2751925 CGACGTTTGTTCCAAGAACGCCGTTATAGATC-CGACCTTTTG
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
* * *
2751967 CGGCGTTTGTGCCAAAAATGCCGCTATAGATCTCGACTTTTTG
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
* * *
2752010 CGGCGTTTGTTTC-AAAA---CG--ATAGATCTCGATCTTTTA
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
* * *
2752047 CGGTGTTTATTCC-AAAACGCCGCTATAGATATCGACCTTTTG
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
2752089 CGGCGTTT
1 CGGCGTTT
2752097 TTTTCTCAAA
Statistics
Matches: 142, Mismatches: 23, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
37 29 0.20
39 2 0.01
40 2 0.01
42 80 0.56
43 29 0.20
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (43 bp):
CGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
Found at i:2752063 original size:37 final size:37
Alignment explanation
Indices: 2751992--2752065 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
2751982 AAATGCCGCT
* * *
2751992 ATAGATCTCGACTTTTTGCGGCGTTTGTTTCAAAACG
1 ATAGATCTCGACTTTTTACGGCGTTTATTCCAAAACG
*
2752029 ATAGATCTCGA-TCTTTTACGGTGTTTATTCCAAAACG
1 ATAGATCTCGACT-TTTTACGGCGTTTATTCCAAAACG
2752066 CCGCTATAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (37 bp):
ATAGATCTCGACTTTTTACGGCGTTTATTCCAAAACG
Found at i:2752088 original size:79 final size:82
Alignment explanation
Indices: 2751894--2752101 Score: 246
Period size: 79 Copynumber: 2.5 Consensus size: 82
2751884 GCGTTTGTAC
* *
2751894 CCAAAAATGCCGCTATAGATCT-GACCTTTTGCGACGTTTGTTCCAAGAACGCCGTTATAGATCC
1 CCAAAAATGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTTCAAGAA--CCG-TATAGATCC
* *
2751958 GACCTTTTGCGGCGTTTGTG
63 GACCTTTTACGGCGTTTATG
*
2751978 CCAAAAATGCCGCTATAGATCTCGACTTTTTGCGGCGTTTGTTTCAA-AA-CG-ATAGATCTCGA
1 CCAAAAATGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTTCAAGAACCGTATAGATC-CGA
* * *
2752040 TCTTTTACGGTGTTTATT
65 CCTTTTACGGCGTTTATG
* * *
2752058 CC-AAAACGCCGCTATAGATATCGACCTTTTGCGGCGTTTTTTTC
1 CCAAAAATGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTTC
2752102 TCAAACGTTG
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
79 45 0.41
80 18 0.16
81 2 0.02
84 24 0.22
85 21 0.19
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (82 bp):
CCAAAAATGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTTCAAGAACCGTATAGATCCGAC
CTTTTACGGCGTTTATG
Found at i:2754082 original size:73 final size:71
Alignment explanation
Indices: 2753963--2754103 Score: 212
Period size: 73 Copynumber: 2.0 Consensus size: 71
2753953 ATTCTCTTTG
* * * *
2753963 ATTGGATAAGGCTAATTTGAATTACTTAAATTAACGAAATTTGTAGATATACTTCATTAAGTGTT
1 ATTGGATAAGGATAATTTCAATTACTTAAATTAAAGAAATTTGTAGATAAACTTCATTAA-T-TT
2754028 TTTTTTTT
64 TTTTTTTT
2754036 ATTGGATAAGGATAATTTCAATTACTTAAATTAAA-AGAATTTGTAGATAAACTTCATTAATTTT
1 ATTGGATAAGGATAATTTCAATTACTTAAATTAAAGA-AATTTGTAGATAAACTTCATTAATTTT
2754100 TTTT
65 TTTT
2754104 CTTTGTTTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
71 7 0.11
72 2 0.03
73 54 0.86
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (71 bp):
ATTGGATAAGGATAATTTCAATTACTTAAATTAAAGAAATTTGTAGATAAACTTCATTAATTTTT
TTTTTT
Found at i:2762603 original size:20 final size:20
Alignment explanation
Indices: 2762578--2762626 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2762568 CTTAGGGAAT
*
2762578 CGATTCCCCATGAGTGGTAC
1 CGATTCCCCATGAGGGGTAC
2762598 CGATTCCCCATGAGGGGTAC
1 CGATTCCCCATGAGGGGTAC
2762618 CGATTCCCC
1 CGATTCCCC
2762627 CCACGCTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.22
Consensus pattern (20 bp):
CGATTCCCCATGAGGGGTAC
Found at i:2768352 original size:22 final size:22
Alignment explanation
Indices: 2768322--2768407 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 22
2768312 TAATTATAGG
2768322 GAAGAGGGAATCGATACCCCCTT
1 GAAG-GGGAATCGATACCCCCTT
*
2768345 GAAGGGGAA-CTGATTCCCCCTTT
1 GAAGGGGAATC-GATACCCCC-TT
* * * *
2768368 GAATGGGAACCGAT-TCCCCAT
1 GAAGGGGAATCGATACCCCCTT
*
2768389 --ATGGGAATCGATACCCCCT
1 GAAGGGGAATCGATACCCCCT
2768408 GGGGTTCTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
19 11 0.21
20 4 0.08
21 2 0.04
22 17 0.33
23 17 0.33
24 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (22 bp):
GAAGGGGAATCGATACCCCCTT
Found at i:2768364 original size:23 final size:23
Alignment explanation
Indices: 2768338--2768386 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2768328 GGAATCGATA
*
2768338 CCCCCTTGAAGGGGAACTGATTC
1 CCCCCTTGAAGGGGAACCGATTC
* *
2768361 CCCCTTTGAATGGGAACCGATTC
1 CCCCCTTGAAGGGGAACCGATTC
2768384 CCC
1 CCC
2768387 ATATGGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.22
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Found at i:2770695 original size:16 final size:16
Alignment explanation
Indices: 2770674--2770705 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2770664 TAAAGTAAGG
2770674 GGGAGTAGTATTTTTC
1 GGGAGTAGTATTTTTC
2770690 GGGAGTAGTATTTTTC
1 GGGAGTAGTATTTTTC
2770706 AAAATCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (16 bp):
GGGAGTAGTATTTTTC
Found at i:2780587 original size:123 final size:127
Alignment explanation
Indices: 2780383--2780768 Score: 460
Period size: 135 Copynumber: 3.0 Consensus size: 127
2780373 TCTTTTGAGT
* ** *
2780383 ATGATGATTAAGTCCTTCCAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTA
1 ATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTA
* *
2780448 ATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGT-C-TT-TCAAG-C-G
66 AATTGTAAGCCTTCACCAAAGAGTAGTGAAGAAAATCCATCAGTAAGTCCATTAT-AAGTCTG
* * * *
2780506 -TGATGATGAAGTCATTCGGGCCATCAGCAAGTCTTTTCGAGCATGATGATTAAATCCTTCAGGT
1 ATGATGATGAAGTCCTTCGGGCCATCAGTAAGTC-TTTCGAGCATGATGATTAAATCATTCGGGT
*
2780570 AAATTGTAAGCCTTCACCAATGAGTAGTGAAGAAAATCCATCAGTAAGTGCCATTAGTAAGTCTT
65 AAATTGTAAGCCTTCACCAAAGAGTAGTGAAGAAAATCCATCAGTAAGT-CCATTA-TAAGTC--
2780635 TTGAG
126 -T--G
* * *
2780640 CATGATGATGAAGTCCTTCGGGGCATCAGTAAGTCGTTCGAGCATGATGGTTAAATCATTCGGGT
1 -ATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGT
* * **
2780705 AAGTTGTAAGCATTCACTGAAGAGTAGTGAAGAAAATCCATCAGTAAGTGCCATTAATAAGTCT
65 AAATTGTAAGCCTTCACCAAAGAGTAGTGAAGAAAATCCATCAGTAAGT-CCATT-ATAAGTCT
2780769 TTCGAGCATG
Statistics
Matches: 224, Mismatches: 23, Indels: 23
0.83 0.09 0.09
Matches are distributed among these distances:
122 28 0.12
123 73 0.33
125 1 0.00
126 2 0.01
127 3 0.01
128 2 0.01
132 1 0.00
134 1 0.00
135 82 0.37
136 31 0.14
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (127 bp):
ATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTA
AATTGTAAGCCTTCACCAAAGAGTAGTGAAGAAAATCCATCAGTAAGTCCATTATAAGTCTG
Found at i:2780828 original size:93 final size:93
Alignment explanation
Indices: 2780669--2780876 Score: 317
Period size: 93 Copynumber: 2.2 Consensus size: 93
2780659 GGGGCATCAG
* * **
2780669 TAAGTCGTTCGAGCATGATGGTTAAATCATTCGGGTAAGTTGTAAGCATTCACTGAAGAGTAGTG
1 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAAGTTGTAAGCATTCACCAAAGAGTAGTG
2780734 AAGAAAATCCATCAGTAAGTGCCATTAA
66 AAGAAAATCCATCAGTAAGTGCCATTAA
* * * *
2780762 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCAAATAGTAGTG
1 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAAGTTGTAAGCATTCACCAAAGAGTAGTG
* *
2780827 AAGCAAATCCATCAGTAAGTGCCATTAG
66 AAGAAAATCCATCAGTAAGTGCCATTAA
*
2780855 TAAGTCTTTCGAGCGTGATGAT
1 TAAGTCTTTCGAGCATGATGAT
2780877 GAAGTTCTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 104 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (93 bp):
TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAAGTTGTAAGCATTCACCAAAGAGTAGTG
AAGAAAATCCATCAGTAAGTGCCATTAA
Found at i:2780893 original size:135 final size:133
Alignment explanation
Indices: 2780762--2781175 Score: 526
Period size: 135 Copynumber: 3.2 Consensus size: 133
2780752 GTGCCATTAA
* *
2780762 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCAAATAGTAGTG
1 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCAAAGAGTAGTG
*
2780827 AAGCAAATCCATCAGTAAGTGCCATTAGTAAGTCTTTCGAGCGTGATGATGAAGTTCTTCGGGCC
66 AAGCAAATCCATCAGTAAGTGCCATTAGTAA-TCTTTCGAGC-TGATGATGAAGTCCTTCGGGCC
2780892 ATCAG
129 ATCAG
* * * *
2780897 TAAGTCTTTTGAGCATGATGATTAAATCATTTGGGTAATTTGTAAGCCTTCACCGAGGAGTAGTG
1 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCAAAGAGTAGTG
* *
2780962 AAGAAAATCCATCAGTAAGT--CATTCG-AA-----C-A--TGATGATGAAGTCCTTCGGGCCAT
66 AAGCAAATCCATCAGTAAGTGCCATTAGTAATCTTTCGAGCTGATGATGAAGTCCTTCGGGCCAT
2781016 CAG
131 CAG
* *
2781019 TAAGTCTTTCGAGCGTGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCTAAGAGTAGTG
1 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCAAAGAGTAGTG
* * * * * * * *
2781084 AAGCAATTTCATTAGTAAGTGCCATCAATAAATCTTTCGAGCATGATGATGAAATCCTTCGAGTC
66 AAGCAAATCCATCAGTAAGTGCCATTAGT-AATCTTTCGAGC-TGATGATGAAGTCCTTCGGGCC
*
2781149 ATCAT
129 ATCAG
*
2781154 TAAGTCTTTCGAGTATGATGAT
1 TAAGTCTTTCGAGCATGATGAT
2781176 GAAGTCCTTC
Statistics
Matches: 239, Mismatches: 27, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
122 102 0.43
124 3 0.01
125 1 0.00
126 3 0.01
131 1 0.00
132 3 0.01
133 5 0.02
135 121 0.51
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (133 bp):
TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCAAAGAGTAGTG
AAGCAAATCCATCAGTAAGTGCCATTAGTAATCTTTCGAGCTGATGATGAAGTCCTTCGGGCCAT
CAG
Found at i:2780900 original size:93 final size:93
Alignment explanation
Indices: 2780669--2780900 Score: 268
Period size: 93 Copynumber: 2.5 Consensus size: 93
2780659 GGGGCATCAG
* * * * * * * ** *
2780669 TAAGTCGTTCGAGCATGATGGTTAAATCATTCGGGTAAGT-TGTAAGCATTCACTGAAGAGTAGT
1 TAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCAA-TCAGTAAGCCTTCACCAAATAGTAGT
2780733 GAAGAAAATCCATCAGTAAGTGCCATTAA
65 GAAGAAAATCCATCAGTAAGTGCCATTAA
* * **
2780762 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCAAATAGTAGTG
1 TAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCAATCAGTAAGCCTTCACCAAATAGTAGTG
* *
2780827 AAGCAAATCCATCAGTAAGTGCCATTAG
66 AAGAAAATCCATCAGTAAGTGCCATTAA
* * * *
2780855 TAAGTCTTTCGAGCGTGATGATGAAGTTCTTCGGGCCATCAGTAAG
1 TAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCAATCAGTAAG
2780901 TCTTTTGAGC
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
92 1 0.01
93 120 0.99
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (93 bp):
TAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCAATCAGTAAGCCTTCACCAAATAGTAGTG
AAGAAAATCCATCAGTAAGTGCCATTAA
Found at i:2780942 original size:228 final size:229
Alignment explanation
Indices: 2780534--2780981 Score: 738
Period size: 228 Copynumber: 2.0 Consensus size: 229
2780524 GGCCATCAGC
2780534 AAGTCTTTTCGAGCATGATGATTAAATCCTTCAGGTAAATTGTAAGCCTTCACCAATGAGTAGTG
1 AAGTCTTTTCGAGCATGATGATTAAATCCTTCAGGTAAATTGTAAGCCTTCACCAATGAGTAGTG
* *
2780599 AAGAAAATCCATCAGTAAGTGCCATTAGTAAGTCTTTTGAGCATGATGATGAAGTCCTTCGGGGC
66 AAGAAAATCCATCAGTAAGTGCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCC
* *
2780664 ATCAGTAAGTCGTTCGAGCATGATGGTTAAATCATTCGGGTAAGTTGTAAGCATTCACTGAAGAG
131 ATCAGTAAGTCGTTCGAGCATGATGATTAAATCATTCGGGTAAGTTGTAAGCATTCACCGAAGAG
2780729 TAGTGAAGAAAATCCATCAGTAAGTGCCATTAAT
196 TAGTGAAGAAAATCCATCAGTAAGTGCCATTAAT
* *
2780763 AAGTC-TTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCAAAT-AGTAGT
1 AAGTCTTTTCGAGCATGATGATTAAATCCTTCAGGTAAATTGTAAGCCTTCACC-AATGAGTAGT
* * *
2780826 GAAGCAAATCCATCAGTAAGTGCCATTAGTAAGTCTTTCGAGCGTGATGATGAAGTTCTTCGGGC
65 GAAGAAAATCCATCAGTAAGTGCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGC
* * * * * *
2780891 CATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTTGGGTAATTTGTAAGCCTTCACCGAGGA
130 CATCAGTAAGTCGTTCGAGCATGATGATTAAATCATTCGGGTAAGTTGTAAGCATTCACCGAAGA
2780956 GTAGTGAAGAAAATCCATCAGTAAGT
195 GTAGTGAAGAAAATCCATCAGTAAGT
2780982 CATTCGAACA
Statistics
Matches: 203, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
228 195 0.96
229 8 0.04
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (229 bp):
AAGTCTTTTCGAGCATGATGATTAAATCCTTCAGGTAAATTGTAAGCCTTCACCAATGAGTAGTG
AAGAAAATCCATCAGTAAGTGCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCC
ATCAGTAAGTCGTTCGAGCATGATGATTAAATCATTCGGGTAAGTTGTAAGCATTCACCGAAGAG
TAGTGAAGAAAATCCATCAGTAAGTGCCATTAAT
Found at i:2781052 original size:42 final size:42
Alignment explanation
Indices: 2780970--2781053 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
2780960 TGAAGAAAAT
* * *
2780970 CCATCAGTAAGTCATTCGAACATGATGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * *
2781012 CCATCAGTAAGTCTTTCGAGCGTGATGATTAAATCATTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
2781054 TAATTTGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
Found at i:2781101 original size:122 final size:122
Alignment explanation
Indices: 2780848--2781103 Score: 395
Period size: 122 Copynumber: 2.1 Consensus size: 122
2780838 TCAGTAAGTG
* * * * *
2780848 CCATTAGTAAGTCTTTCGAGCGTGATGATGAAGTTCTTCGGGCCATCAGTAAGTCTTTTGAGCAT
1 CCATTAGTAAGTCATTCGAACATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
2780913 GATGATTAAATCATTTGGGTAATTTGTAAGCCTTCACCGAGGAGTAGTGAAGAAAAT
66 GATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGAAAAT
* *
2780970 CCATCAGTAAGTCATTCGAACATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCGT
1 CCATTAGTAAGTCATTCGAACATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
2781035 GATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCTAAGAGTAGTGAAGCAATT
66 GATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGAAAAT
*
2781092 TCATTAGTAAGT
1 CCATTAGTAAGT
2781104 GCCATCAATA
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (122 bp):
CCATTAGTAAGTCATTCGAACATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGAAAAT
Found at i:2781144 original size:22 final size:21
Alignment explanation
Indices: 2781111--2781228 Score: 91
Period size: 22 Copynumber: 5.6 Consensus size: 21
2781101 AGTGCCATCA
2781111 ATAAATCTTTCGAGCATGATG
1 ATAAATCTTTCGAGCATGATG
* *
2781132 ATGAAATCCTTCGAGTCATCAT-
1 AT-AAATCTTTCGAG-CATGATG
* *
2781154 -TAAGTCTTTCGAGTATGATG
1 ATAAATCTTTCGAGCATGATG
* * * *
2781174 ATGAAGTCCTTCGGGCCATCA-G
1 AT-AAATCTTTCGAG-CATGATG
2781196 -TAAATCTTTCGAGCATGATG
1 ATAAATCTTTCGAGCATGATG
2781216 ATTAAATCTTTCG
1 A-TAAATCTTTCG
2781229 GGTAATTTGT
Statistics
Matches: 74, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
19 8 0.11
20 20 0.27
21 5 0.07
22 33 0.45
23 8 0.11
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (21 bp):
ATAAATCTTTCGAGCATGATG
Found at i:2781190 original size:177 final size:177
Alignment explanation
Indices: 2780970--2781352 Score: 586
Period size: 177 Copynumber: 2.2 Consensus size: 177
2780960 TGAAGAAAAT
* * * * *
2780970 CCATCAGTAAGTCATTCGAACATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCGT
1 CCATCATTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAATCTTTCGAGCAT
* * * *
2781035 GATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCTAAGAGTAGTGAAGCAATTTCATTAGT
66 GATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGT
* * *
2781100 AAGTGCCATCAATAAATCTTTCGAGCATGATGATGAAATCCTTCGAG
131 AAGTGCCATCAATAAATCTTTCAAGCATGATAATGAAATCATTCGAG
* *
2781147 TCATCATTAAGTCTTTCGAGTATGATGATGAAGTCCTTCGGGCCATCAGTAAATCTTTCGAGCAT
1 CCATCATTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAATCTTTCGAGCAT
*
2781212 GATGATTAAATCTTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGT
66 GATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGT
* * * * *
2781277 AAGTGCCATTAGTAAGTCTTTCAAGCATGATAATGAAGTCATTCGGG
131 AAGTGCCATCAATAAATCTTTCAAGCATGATAATGAAATCATTCGAG
2781324 CCATCATTAAGTCTTTCGAGCATGATGAT
1 CCATCATTAAGTCTTTCGAGCATGATGAT
2781353 TAAATCTTTC
Statistics
Matches: 184, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
177 184 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (177 bp):
CCATCATTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAATCTTTCGAGCAT
GATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGT
AAGTGCCATCAATAAATCTTTCAAGCATGATAATGAAATCATTCGAG
Found at i:2781296 original size:135 final size:135
Alignment explanation
Indices: 2781146--2781642 Score: 791
Period size: 135 Copynumber: 3.7 Consensus size: 135
2781136 AATCCTTCGA
* * *
2781146 GTCATCATTAAGTCTTTCGAGTATGATGATGAAGTCCTTCGGGCCATCAGTAAATCTTTCGAGCA
1 GTCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGGGCCATCAGTAAATCTTTCGAGCA
*
2781211 TGATGATTAAATCTTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
66 TGATGATTAAATCTTTCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
2781276 TAAGT
131 TAAGT
* * * * * *
2781281 GCCATTAGTAAGTCTTTCAAGCATGATAATGAAGTCATTCGGGCCATCATTAAGTCTTTCGAGCA
1 GTCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGGGCCATCAGTAAATCTTTCGAGCA
*
2781346 TGATGATTAAATCTTTCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATAAG
66 TGATGATTAAATCTTTCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
2781411 TAAGT
131 TAAGT
* * *
2781416 GTCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTAGGGCCGTCAGTAAGTCTTTCGAGCA
1 GTCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGGGCCATCAGTAAATCTTTCGAGCA
* *
2781481 TGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAG-AAATCCATCAG
66 TGATGATTAAATCTTTCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
2781545 TAAGT
131 TAAGT
* *
2781550 GTTATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGCCATCAGTAAGA-CTTTCGAGC
1 GTCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGGGCCATCAGTAA-ATCTTTCGAGC
* *
2781614 ATGATGATTAAATCCTTCAGGTCATTTGT
65 ATGATGATTAAATCTTTCAGGTAATTTGT
2781643 GAGTCTTTCG
Statistics
Matches: 332, Mismatches: 29, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
134 99 0.30
135 233 0.70
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (135 bp):
GTCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCATTCGGGCCATCAGTAAATCTTTCGAGCA
TGATGATTAAATCTTTCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
TAAGT
Found at i:2781511 original size:42 final size:42
Alignment explanation
Indices: 2781116--2781687 Score: 187
Period size: 42 Copynumber: 13.0 Consensus size: 42
2781106 CATCAATAAA
* * * *
2781116 TCTTTCGAGCATGATGATGAAATCCTTCGAGTCATCAT-TAAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAAT-TTGTAAG
* * * ** ** *
2781158 TCTTTCGAGTATGATGATGAAGTCCTTCGGGCCATCAGTAAA
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
* *
2781200 TCTTTCGAGCATGATGATTAAATCTTTCGGGTAATTTGTAAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
* * * *
2781242 CCTTCACCGAAG-A-GTAGTGAAGCAAATCCA-TC-AGTAAGTGCCATTAGTAAG
1 TCTT--TCG-AGCATG-A-TGATG-AAAT-CATTCGGGTAA-T----TT-GTAAG
* * * ** *
2781293 TCTTTCAAGCATGATAATGAAGTCATTCGGGCCATCAT-TAAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAAT-TTGTAAG
* * *
2781335 TCTTTCGAGCATGATGATTAAATCTTTCAGGTAATTTGTAAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
* * * * * * **
2781377 CCTTCACCGAAG-A-GTAGTGAAGCAAATCCATAAGTAAGTGTCATCAGTAAG
1 TCTT--TCG-AGCATG-A-TGATG-AAAT-CAT---T-CGGGTAATTTGTAAG
* * *** **
2781428 TCTTTCGAGCATGATGATGAAGTCATTAGGGCCGTCAGTAAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
*
2781470 TCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
* * * *
2781512 CCTTCACCGAAG-A-GTAGTGAAGAAATCCA-TC-AGTAAGTGTTATCAGTAAG
1 TCTT--TCG-AGCATG-A-TGATGAAAT-CATTCGGGTAA---TT-T--GTAAG
** **
2781562 TCTTTCGAGCATGATGATGAAATCATTCGGGCCATCAGTAAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
* * * * * *
2781604 ACTTTCGAGCATGATGATTAAATCCTTCAGGTCATTTGTGAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
* *
2781646 TCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
1 TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
2781688 CATTCACCGA
Statistics
Matches: 389, Mismatches: 93, Indels: 96
0.67 0.16 0.17
Matches are distributed among these distances:
41 1 0.00
42 234 0.60
43 4 0.01
44 17 0.04
45 26 0.07
46 20 0.05
47 26 0.07
48 20 0.05
49 8 0.02
50 13 0.03
51 20 0.05
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (42 bp):
TCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTGTAAG
Found at i:2781578 original size:92 final size:92
Alignment explanation
Indices: 2781462--2781736 Score: 295
Period size: 92 Copynumber: 3.1 Consensus size: 92
2781452 ATTAGGGCCG
2781462 TCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGT
1 TCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGT
*
2781527 AGTGAAGAAATCCATCAGTAAGT-GTT
66 AGTGAAGAAATCCATCAGTAAGTCATT
* ** ** * *
2781553 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGCCATCAGTAAGACTT--TCG-AGCA
1 -TCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAG-A
** *
2781615 -T-GATGATTAAATCCTTCAG---GTCATT
64 GTAG-TGAAGAAATCCATCAGTAAGTCATT
* * *
2781640 T--GTGAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCATTCACCGAAGAGT
1 TCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGT
2781703 AGTGAAGCAAATCCATCAGTAAGTC-TT
66 AGTGAAG-AAATCCATCAGTAAGTCATT
2781730 TCGAGTA
1 TC-AGTA
2781737 TGATGATGAA
Statistics
Matches: 143, Mismatches: 25, Indels: 29
0.73 0.13 0.15
Matches are distributed among these distances:
84 42 0.29
86 6 0.04
87 8 0.06
88 12 0.08
89 16 0.11
90 6 0.04
91 3 0.02
92 48 0.34
93 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (92 bp):
TCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGT
AGTGAAGAAATCCATCAGTAAGTCATT
Found at i:2781762 original size:42 final size:42
Alignment explanation
Indices: 2781715--2781844 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 42
2781705 TGAAGCAAAT
* *
2781715 CCATCAGTAAGTCTTTCGAGTATGATGATGAAATCTTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * *
2781757 CCATCAATAAGTCTTTCAAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* ** * * * *
2781799 TCATTTGTGAGTCTTTCGAACAAGATGAT-AAATCCTTTGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
*
2781840 TCATC
1 CCATC
2781845 TGCAAGACCT
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
41 15 0.21
42 58 0.79
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
Found at i:2786068 original size:12 final size:12
Alignment explanation
Indices: 2786051--2786079 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2786041 GAGACATAGA
2786051 GAGTTTTCTTAT
1 GAGTTTTCTTAT
2786063 GAGTTTTCTTAT
1 GAGTTTTCTTAT
2786075 GAGTT
1 GAGTT
2786080 GTGAGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (12 bp):
GAGTTTTCTTAT
Found at i:2788540 original size:28 final size:27
Alignment explanation
Indices: 2788509--2788563 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
2788499 TTATCTTCAC
*
2788509 TTAACATATATTTTATTCTTATTTTAAA
1 TTAA-ATATATTTTATTATTATTTTAAA
*
2788537 TTAAAAAATATTTTATTATTATTTTAA
1 TT-AAATATATTTTATTATTATTTTAA
2788564 CTTTTAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TTAAATATATTTTATTATTATTTTAAA
Found at i:2788689 original size:29 final size:29
Alignment explanation
Indices: 2788638--2788806 Score: 166
Period size: 29 Copynumber: 5.8 Consensus size: 29
2788628 TATTTTAAGT
* *
2788638 AAATATA-TTTTAAATTAAGATAAGAATA
1 AAATATATTTTTAATTTAAAATAAGAATA
2788666 AAATATATTTTTAATTTAAAATAAGAATA
1 AAATATATTTTTAATTTAAAATAAGAATA
* * *
2788695 AAATATACTTTTAATTTAAAATAATATTA
1 AAATATATTTTTAATTTAAAATAAGAATA
* *
2788724 AAACATATATTTTAATATTAAAATAAAAATA
1 AAATATAT-TTTTAAT-TTAAAATAAGAATA
* * * *
2788755 AAATAT-TTTAATAAATT-AGACAA-AATA
1 AAATATATTT-TTAATTTAAAATAAGAATA
2788782 AAATATATTTTTAAAATTTAAAATA
1 AAATATATTTTT--AATTTAAAATA
2788807 TATAATATAT
Statistics
Matches: 115, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
27 11 0.10
28 14 0.12
29 59 0.51
30 14 0.12
31 17 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
AAATATATTTTTAATTTAAAATAAGAATA
Found at i:2788804 original size:89 final size:88
Alignment explanation
Indices: 2788640--2788806 Score: 214
Period size: 89 Copynumber: 1.9 Consensus size: 88
2788630 TTTTAAGTAA
* * * * *
2788640 ATATATTTTAAATTAAGATAAGAATAAAATATATTTTTAATTTAAAATAAGAATAAAATATACTT
1 ATATATTTTAAATTAAAATAAAAATAAAATATATTTATAAATTAAAACAAGAATAAAATATACTT
2788705 TTAATTTAAAATAATATTAAAAC
66 TTAATTTAAAATAATATTAAAAC
* *
2788728 ATATATTTTAATATTAAAATAAAAATAAAATAT-TTTAATAAATT-AGACAA-AATAAAATATAT
1 ATATATTTTAA-ATTAAAATAAAAATAAAATATATTT-ATAAATTAAAACAAGAATAAAATATAC
2788790 TTTTAAAATTTAAAATA
64 TTTT--AATTTAAAATA
2788807 TATAATATAT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
87 15 0.22
88 18 0.26
89 35 0.51
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (88 bp):
ATATATTTTAAATTAAAATAAAAATAAAATATATTTATAAATTAAAACAAGAATAAAATATACTT
TTAATTTAAAATAATATTAAAAC
Found at i:2790090 original size:13 final size:13
Alignment explanation
Indices: 2790064--2790098 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2790054 CAATCCAGGC
2790064 GACATACG-GGGT
1 GACATACGAGGGT
2790076 GACATACGAGGGT
1 GACATACGAGGGT
2790089 GACATACGAG
1 GACATACGAG
2790099 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:2790279 original size:93 final size:91
Alignment explanation
Indices: 2790112--2790307 Score: 365
Period size: 93 Copynumber: 2.1 Consensus size: 91
2790102 TATACGAGTC
2790112 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
1 ATACGAGCC-ATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
2790177 GCCAATGGGGAGCATGCAACGAGCCAT
65 GCCAATGGGGAGCATGCAACGAGCCAT
2790204 ATACGAGCCATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGAG
1 ATACGAGCCATGGGGAGCATGCAACGAGCC--ATACGAGCCAATGGGGAGCATGCAGGAATAGAG
2790269 AGCCAATGGGGAGCATGCAACGAGCCAT
64 AGCCAATGGGGAGCATGCAACGAGCCAT
2790297 ATACGAGCCAT
1 ATACGAGCCAT
2790308 ACGAGCCAAT
Statistics
Matches: 102, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 21 0.21
92 9 0.09
93 72 0.71
ACGTcount: A:0.34, C:0.22, G:0.33, T:0.12
Consensus pattern (91 bp):
ATACGAGCCATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGAG
CCAATGGGGAGCATGCAACGAGCCAT
Found at i:2790293 original size:61 final size:64
Alignment explanation
Indices: 2790112--2790306 Score: 257
Period size: 61 Copynumber: 3.2 Consensus size: 64
2790102 TATACGAGTC
* *
2790112 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGC-A-G-G-AAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
*
2790172 AGA-GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCC-ATGGGGAGCATGCAACGAGCCA
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-A-GAGCCAATGGGGAGCATGCAACGAGCCA
2790235 T
64 T
*
2790236 ATACGAGCCAATGGGGAGCATGC-A-G-G-AATAGAGAGCCAATGGGGAGCATGCAACGAGCCAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-AGAGCCAATGGGGAGCATGCAACGAGCCAT
2790297 ATACGAGCCA
1 ATACGAGCCA
2790307 TACGAGCCAA
Statistics
Matches: 121, Mismatches: 6, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
59 30 0.25
60 20 0.17
61 43 0.36
62 2 0.02
63 2 0.02
64 5 0.04
65 19 0.16
ACGTcount: A:0.34, C:0.22, G:0.33, T:0.11
Consensus pattern (64 bp):
ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
Found at i:2790388 original size:29 final size:29
Alignment explanation
Indices: 2790338--2790446 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
2790328 AGGAATAGAG
* *
2790338 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
2790367 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2790396 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
2790425 AAGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
2790447 CCATTCCCAT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 74 0.97
30 2 0.03
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:2790552 original size:54 final size:54
Alignment explanation
Indices: 2790480--2790587 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
2790470 GCACAGCCAC
2790480 ATAGATTCCTTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAATGCATGCAT
1 ATAGATTCCTTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAATGCATGCAT
*
2790534 ATAGATTCCTTCGCGTGCTCCCCGCTGCATGCCTACACCTCCCAATGCATGCAT
1 ATAGATTCCTTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAATGCATGCAT
2790588 GTGAACCATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.19, C:0.39, G:0.16, T:0.26
Consensus pattern (54 bp):
ATAGATTCCTTCACGTGCTCCCCGCTGCATGCCTACACCTCCCAATGCATGCAT
Found at i:2790607 original size:18 final size:18
Alignment explanation
Indices: 2790584--2790618 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2790574 CCCAATGCAT
2790584 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
2790602 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
2790619 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:2790755 original size:4 final size:4
Alignment explanation
Indices: 2790746--2790811 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
2790736 ATTGCAGCCG
** **
2790746 AGAA AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA
*
2790796 AGTA AG-A AG-A AGAA AG
1 AGAA AGAA AGAA AGAA AG
2790812 GGAGATAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 6 0.12
4 36 0.72
5 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:2790777 original size:21 final size:21
Alignment explanation
Indices: 2790745--2790803 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
2790735 GATTGCAGCC
2790745 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
2790765 GAGAAAGGAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
2790786 GAGAAAGGAAAGTAAGAA
1 GAGAAAGGAAAGAAAGAA
2790804 GAAGAAAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 6 0.16
21 31 0.84
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAGAAAGGAAAGAAAGAAAGG
Found at i:2790983 original size:41 final size:41
Alignment explanation
Indices: 2790938--2791026 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
2790928 TATATGATTG
* *
2790938 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
2790979 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
2791020 TTAGTTT
1 TTAGTTT
2791027 GTATTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:2791070 original size:46 final size:48
Alignment explanation
Indices: 2791007--2791098 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
2790997 TTATATAGTT
2791007 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
2791052 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
2791099 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 17 0.41
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:2791175 original size:32 final size:33
Alignment explanation
Indices: 2791139--2791215 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
2791129 TTAGTTAGTA
2791139 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
2791171 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
2791205 ATTTTATTAGT
1 AGTTTATTAGT
2791216 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Done.