Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 32 of 52
Found at i:5508522 original size:20 final size:21
Alignment explanation
Indices: 5508475--5508548 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
5508465 TTCTATAATT
*
5508475 TGTATCGATACAAACAGTAAA
1 TGTATCGATACATACAGTAAA
* *
5508496 GGTATCGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
* *
5508516 TGTATCGATACATGC-CTAAAA
1 TGTATCGATACATACAGT-AAA
5508537 TGTATCGATACA
1 TGTATCGATACA
5508549 AAACCACCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:5511776 original size:21 final size:21
Alignment explanation
Indices: 5511752--5511794 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5511742 TTTTGCCGAC
5511752 TATTTTGTGCATTCATGTTTT
1 TATTTTGTGCATTCATGTTTT
5511773 TATTTTGTGCATTCATGTTTT
1 TATTTTGTGCATTCATGTTTT
5511794 T
1 T
5511795 CCAAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (21 bp):
TATTTTGTGCATTCATGTTTT
Found at i:5513695 original size:14 final size:15
Alignment explanation
Indices: 5513671--5513699 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5513661 ACTAAACCAT
5513671 TAAAGTAAAAATAAA
1 TAAAGTAAAAATAAA
5513686 TAAA-TAAAAATAAA
1 TAAAGTAAAAATAAA
5513700 AATTCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
TAAAGTAAAAATAAA
Found at i:5516371 original size:25 final size:25
Alignment explanation
Indices: 5516322--5516372 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5516312 TATCATTACA
*
5516322 ATTTTATAAAAATTAATAGATAATT
1 ATTTTATAAAAATTAATAGAAAATT
* **
5516347 ATTTTATAAAATTTAATTTAAAATT
1 ATTTTATAAAAATTAATAGAAAATT
5516372 A
1 A
5516373 ATCTACTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
ATTTTATAAAAATTAATAGAAAATT
Found at i:5516715 original size:16 final size:16
Alignment explanation
Indices: 5516652--5516715 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
5516642 TGAAAATGTT
* *
5516652 AATAATTTAAATTTAA
1 AATAATCTAAACTTAA
* * *
5516668 AAAAATTTAAACTCAA
1 AATAATCTAAACTTAA
5516684 AACTAATAC-AAA-TTAA
1 AA-TAAT-CTAAACTTAA
5516700 AATAATCTAAACTTAA
1 AATAATCTAAACTTAA
5516716 TGATCGAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
14 1 0.03
15 7 0.18
16 24 0.63
17 6 0.16
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATCTAAACTTAA
Found at i:5519442 original size:2 final size:2
Alignment explanation
Indices: 5519435--5519464 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5519425 ATCACTACAT
5519435 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
5519465 AAAGTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5520818 original size:12 final size:12
Alignment explanation
Indices: 5520801--5520830 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5520791 ATTGTGGATA
5520801 TCATAGCCATAG
1 TCATAGCCATAG
5520813 TCATAGCCATAG
1 TCATAGCCATAG
*
5520825 CCATAG
1 TCATAG
5520831 ATAGATAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (12 bp):
TCATAGCCATAG
Found at i:5521696 original size:2 final size:2
Alignment explanation
Indices: 5521689--5521714 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5521679 CATTAGTTCA
5521689 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
5521715 TCTAGAGATT
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):
AT
Found at i:5529626 original size:27 final size:27
Alignment explanation
Indices: 5529596--5529647 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
5529586 TTGCATTGCT
5529596 TGAGCTCTTGCCACAATACCATTAAGG
1 TGAGCTCTTGCCACAATACCATTAAGG
*
5529623 TGAGCTCTTGCCACAATATCATTAA
1 TGAGCTCTTGCCACAATACCATTAA
5529648 TCTACAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (27 bp):
TGAGCTCTTGCCACAATACCATTAAGG
Found at i:5531343 original size:158 final size:151
Alignment explanation
Indices: 5531012--5531564 Score: 508
Period size: 158 Copynumber: 3.6 Consensus size: 151
5531002 ATTTTTTTAG
** * * * *
5531012 AATCGAGTCCTAACTTGTCACCGGGTCCGCTTCTATGCTGAAGGTGTACATTTAGGATAGGTTCA
1 AATCGAGTCCTAGGTTATCACCGAGTCTGCTTCTATGCCGAAGGTGTACATTTAGGATAGGTTCA
** * * * * *
5531077 TC-CCTGTACCTCTTTTAGTCCTTTAAGGTTACCGGGATA-TTTTCATGTCGAAGGTATACCCTT
66 TCTTTTTTTCCT-TTTAAGTCCTTTAAGGTTACCGGGATACTTTT-ATGTCGAAAGTATACCCAT
5531140 AGGGGCATTCTTATAATTTTCTAA
129 AGGGGCATT-TTATAATTTTCTAA
* * * * * *
5531164 AATTGAGTCTTGGGTTGTCACCGAGTCTGCTTCTATGCCAAAGGTAG-GCATTTAGGACT-GGTT
1 AATCGAGTCCTAGGTTATCACCGAGTCTGCTTCTATGCCGAAGGT-GTACATTTAGGA-TAGGTT
* * *
5531227 CATCTCATTTTCAAAATTCCTTTTAAGTCCATTAGGGGTACCGGGATACTTTTATGTCGAAAGTA
64 CATCT--TTTT-----TTCCTTTTAAGTCCTTTAAGGTTACCGGGATACTTTTATGTCGAAAGTA
**
5531292 T-CCCCCAGGGGCATTTTCATAATTTTCTAA
122 TACCCATAGGGGCATTTT-ATAATTTTCTAA
* * * *
5531322 AATCGAGTCCTAGGTTATCACCGGGTCTACTTCTATACCGAAGGTGTACATTTATGATAGGTTCA
1 AATCGAGTCCTAGGTTATCACCGAGTCTGCTTCTATGCCGAAGGTGTACATTTAGGATAGGTTCA
* * *
5531387 TCTTTTTTTCGTTTTAAG-CCTTTTAAGGTTACCAGGATACTTTCATGTCGAAAGTATACCCATA
66 TCTTTTTTTCCTTTTAAGTCC-TTTAAGGTTACCGGGATACTTTTATGTCGAAAGTATACCCATA
* *
5531451 GGGGCATTTTAATAATTTTTTCAG
130 GGGGCATTTT-ATAATTTTCT-AA
* * * * * *
5531475 AATCAAATCCTAGGTCATCA-CTAGGTCCGCTTCTATGCCGAAGGTGTAAATTTAGGATAGGTTC
1 AATCGAGTCCTAGGTTATCACCGA-GTCTGCTTCTATGCCGAAGGTGTACATTTAGGATAGGTTC
** * * *
5531539 ATCCATTTATCGTTTTACGTCCTTTA
65 ATCTTTTTTTCCTTTTAAGTCCTTTA
5531565 GACGTATTGG
Statistics
Matches: 326, Mismatches: 56, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
150 2 0.01
151 41 0.13
152 77 0.24
153 74 0.23
154 2 0.01
155 1 0.00
156 4 0.01
157 4 0.01
158 78 0.24
159 35 0.11
160 8 0.02
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (151 bp):
AATCGAGTCCTAGGTTATCACCGAGTCTGCTTCTATGCCGAAGGTGTACATTTAGGATAGGTTCA
TCTTTTTTTCCTTTTAAGTCCTTTAAGGTTACCGGGATACTTTTATGTCGAAAGTATACCCATAG
GGGCATTTTATAATTTTCTAA
Found at i:5532206 original size:15 final size:15
Alignment explanation
Indices: 5532183--5532218 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5532173 CGGGGCATGA
5532183 AAAAGAATAAACTTC
1 AAAAGAATAAACTTC
*
5532198 AAAATAATAAACTTC
1 AAAAGAATAAACTTC
5532213 AAAAGA
1 AAAAGA
5532219 TATTTCAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.64, C:0.11, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAGAATAAACTTC
Found at i:5535135 original size:12 final size:12
Alignment explanation
Indices: 5535120--5535167 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
5535110 GAAAACCAAA
5535120 AGAAAAAGAAAG
1 AGAAAAAGAAAG
*
5535132 AGAAAGAGAAAG
1 AGAAAAAGAAAG
*
5535144 AGAAAGAAAAAAG
1 AGAAA-AAGAAAG
5535157 -GAAAAAAGAAA
1 AG-AAAAAGAAA
5535168 AAAGTATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 22 0.73
13 8 0.27
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAAG
Found at i:5535160 original size:18 final size:17
Alignment explanation
Indices: 5535117--5535171 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 17
5535107 TAAGAAAACC
*
5535117 AAAAGAAAAAGAAAG-A
1 AAAAGGAAAAGAAAGAA
*
5535133 GAAAGAGAAAGAGAAAGAA
1 AAAAG-GAAA-AGAAAGAA
5535152 AAAAGG-AAA-AAAGAA
1 AAAAGGAAAAGAAAGAA
5535167 AAAAG
1 AAAAG
5535172 TATGAAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 11 0.33
16 5 0.15
17 5 0.15
18 7 0.21
19 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAGGAAAAGAAAGAA
Found at i:5537366 original size:35 final size:35
Alignment explanation
Indices: 5537327--5537455 Score: 125
Period size: 36 Copynumber: 3.6 Consensus size: 35
5537317 GATCAAATTG
* *
5537327 TTCCATCATTGTTTGACTGTATCTGGTCAAACTCT
1 TTCCATCATCGTTTGACTATATCTGGTCAAACTCT
* ** * * *
5537362 TTCCACCATCGTTTGGTTATGTCTGGTCAAAATTTT
1 TTCCATCATCGTTTGACTATATCTGGTC-AAACTCT
*
5537398 TTCCATAATCGTTTGACTATATCTGGTCAAACTCCT
1 TTCCATCATCGTTTGACTATATCTGGTCAAACT-CT
* *
5537434 TT-CATCCCTCATTTGACTATAT
1 TTCCAT-CATCGTTTGACTATAT
5537456 TAGTGTTAGG
Statistics
Matches: 73, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
35 29 0.40
36 44 0.60
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (35 bp):
TTCCATCATCGTTTGACTATATCTGGTCAAACTCT
Found at i:5537547 original size:48 final size:48
Alignment explanation
Indices: 5537420--5537745 Score: 307
Period size: 48 Copynumber: 6.6 Consensus size: 48
5537410 TTGACTATAT
* * * * *
5537420 CTGGTCAAACTCCTTTCATCCCTCATTTGACTATATTAGTGTTAGGGC
1 CTGGTCAAACTCTTTTCTTCCCTCGTTTGACTGTATTGGTGTTAGGGC
* *** * *
5537468 CTGGTCACACT-AAATCTTCCCTTGTTTGACTGTATTGGTATTAGGGC
1 CTGGTCAAACTCTTTTCTTCCCTCGTTTGACTGTATTGGTGTTAGGGC
* * *
5537515 CTGGTCAAACTCTTTTCATCCCTGGTTTGACTGTATTGGTGTTAGGAC
1 CTGGTCAAACTCTTTTCTTCCCTCGTTTGACTGTATTGGTGTTAGGGC
* *
5537563 CTAGTTAAACTCTTATT-TTCCCCTCGTTTGACTGTATTGGTGTTAGGGC
1 CTGGTCAAACTCTT-TTCTT-CCCTCGTTTGACTGTATTGGTGTTAGGGC
* * * *
5537612 CTAGTCAAACTTTTTTCTTCCCTCATTTGACATTTGATTATATTAGTGTTAGGGC
1 CTGGTCAAACTCTTTTCTTCCCTCGTTTGAC---TG----TATTGGTGTTAGGGC
* * * *
5537667 CTAGTTAAACTCTTTTTCTT-CCTCGTTTTGATTGTATTGGTGTTACGGC
1 CTGGTCAAACTC-TTTTCTTCCCTCG-TTTGACTGTATTGGTGTTAGGGC
*
5537716 CTGGTCAAACTCTTTTCTTCCCTCATTTGA
1 CTGGTCAAACTCTTTTCTTCCCTCGTTTGA
5537746 TTATATTAGT
Statistics
Matches: 228, Mismatches: 36, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
47 37 0.16
48 77 0.34
49 70 0.31
51 2 0.01
53 2 0.01
55 28 0.12
56 12 0.05
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (48 bp):
CTGGTCAAACTCTTTTCTTCCCTCGTTTGACTGTATTGGTGTTAGGGC
Found at i:5537602 original size:49 final size:47
Alignment explanation
Indices: 5537423--5537745 Score: 268
Period size: 49 Copynumber: 6.6 Consensus size: 47
5537413 ACTATATCTG
** * * * *
5537423 GTCAAACTCCTTTCATCCCTCATTTGACTATATTAGTGTTAGGGCCTG
1 GTCAAACT-CTTTTTTCCCTCGTTTGACTGTATTGGTGTTAGGGCCTA
* *** * * * *
5537471 GTCACACTAAATCTTCCCTTGTTTGACTGTATTGGTATTAGGGCCTG
1 GTCAAACTCTTTTTTCCCTCGTTTGACTGTATTGGTGTTAGGGCCTA
* * *
5537518 GTCAAACTCTTTTCATCCCTGGTTTGACTGTATTGGTGTTAGGACCTA
1 GTCAAACTCTTTT-TTCCCTCGTTTGACTGTATTGGTGTTAGGGCCTA
*
5537566 GTTAAACTCTTATTTTCCCCTCGTTTGACTGTATTGGTGTTAGGGCCTA
1 GTCAAACTCTT-TTTT-CCCTCGTTTGACTGTATTGGTGTTAGGGCCTA
* * *
5537615 GTCAAACTTTTTTCTTCCCTCATTTGACATTTGATTATATTAGTGTTAGGGCCTA
1 GTCAAACTCTTTT-TTCCCTCGTTTGAC---TG----TATTGGTGTTAGGGCCTA
* * * * *
5537670 GTTAAACTCTTTTTCTTCCTCGTTTTGATTGTATTGGTGTTACGGCCTG
1 GTCAAACTCTTTTT-TCCCTCG-TTTGACTGTATTGGTGTTAGGGCCTA
*
5537719 GTCAAACTCTTTTCTTCCCTCATTTGA
1 GTCAAACTCTTTT-TTCCCTCGTTTGA
5537746 TTATATTAGT
Statistics
Matches: 222, Mismatches: 39, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
47 38 0.17
48 65 0.29
49 75 0.34
50 1 0.00
51 2 0.01
53 2 0.01
54 1 0.00
55 33 0.15
56 5 0.02
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (47 bp):
GTCAAACTCTTTTTTCCCTCGTTTGACTGTATTGGTGTTAGGGCCTA
Found at i:5537703 original size:104 final size:97
Alignment explanation
Indices: 5537420--5537755 Score: 347
Period size: 104 Copynumber: 3.4 Consensus size: 97
5537410 TTGACTATAT
* * * * * * * ** *
5537420 CTGGTCAAACTCCTTTCATCCCTCATTTGACTATATTAGTGTTAGGGCCTGGTCACACT-AAATC
1 CTGGTCAAACTCTTTTCTTCCCTCATTTGACTGTATTAGTGTTAGGACCTAGTTAAACTCTTATT
* *
5537484 TT-CCCTTGTTTGACTGTATTGGTATTAGGGC
66 TTCCCCTCGTTTGACTGTATTGGTGTTAGGGC
* ** *
5537515 CTGGTCAAACTCTTTTCATCCCTGGTTTGACTGTATTGGTGTTAGGACCTAGTTAAACTCTTATT
1 CTGGTCAAACTCTTTTCTTCCCTCATTTGACTGTATTAGTGTTAGGACCTAGTTAAACTCTTATT
5537580 TTCCCCTCGTTTGACTGTATTGGTGTTAGGGC
66 TTCCCCTCGTTTGACTGTATTGGTGTTAGGGC
* * *
5537612 CTAGTCAAACTTTTTTCTTCCCTCATTTGACATTTGATTATATTAGTGTTAGGGCCTAGTTAAAC
1 CTGGTCAAACTCTTTTCTTCCCTCATTTGAC---TG----TATTAGTGTTAGGACCTAGTTAAAC
* * *
5537677 TC-T-TTTTCTTCCTCGTTTTGATTGTATTGGTGTTACGGC
59 TCTTATTTTC-CCCTCG-TTTGACTGTATTGGTGTTAGGGC
* *
5537716 CTGGTCAAACTCTTTTCTTCCCTCATTTGATTATATTAGT
1 CTGGTCAAACTCTTTTCTTCCCTCATTTGACTGTATTAGT
5537756 TACCACCCTG
Statistics
Matches: 202, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
95 50 0.25
96 4 0.02
97 60 0.30
100 2 0.01
101 1 0.00
102 5 0.02
103 6 0.03
104 74 0.37
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (97 bp):
CTGGTCAAACTCTTTTCTTCCCTCATTTGACTGTATTAGTGTTAGGACCTAGTTAAACTCTTATT
TTCCCCTCGTTTGACTGTATTGGTGTTAGGGC
Found at i:5537976 original size:44 final size:44
Alignment explanation
Indices: 5537754--5538171 Score: 190
Period size: 44 Copynumber: 9.4 Consensus size: 44
5537744 GATTATATTA
* * *
5537754 GTTACCACCCTGGTCAAACTTTTTTTTTTCATT-TCGATCTAACATATG
1 GTTACCACCCTGGTCAAA----TTTTTTTCATTCT-GATTTGACGTATG
* * * *
5537802 GTTACCACCTTGATCAGATTCTTTTCATTCTGA-TTGACGTATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGACGTATG
* * * * **** * * *
5537845 GTTACCGCTCTAGTCAAATCTGCCCCTATCCTG-TCTGATGTATG
1 GTTACCACCCTGGTCAAATTTTTTTC-ATTCTGATTTGACGTATG
* * * ** * *
5537889 GTTACCATCTTGGACAAATTCGCTTTC-TTCCT-ATATGATGTATG
1 GTTACCACCCTGGTCAAATT-TTTTTCATT-CTGATTTGACGTATG
* *
5537933 GTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGACGTATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGACGTATG
* * *** * *
5537977 GTTACCACCCTAGTCAAATCTGCCTCTGTTCTG-TTTGATGTATG
1 GTTACCACCCTGGTCAAATTTTTTTC-ATTCTGATTTGACGTATG
* * * *
5538021 GTTACCACCCTGGTCAAACTTTTCTCATT-TCAGTCTGACGTATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGA-TTTGACGTATG
* * * * * * *
5538065 GATACCACCCTAGTTAAATTTGCCTTT--TTCT-TTTCTGACATATA
1 GTTACCACCCTGGTCAAATTT--TTTTCATTCTGATT-TGACGTATG
* * * * * *
5538109 GTTACCACTCTGGCCAGATTCTTTTCATTCTGATTTGACATATA
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGACGTATG
5538153 GTTACCACCCTGGTCAAAT
1 GTTACCACCCTGGTCAAAT
5538172 CCTTCTAACC
Statistics
Matches: 267, Mismatches: 85, Indels: 40
0.68 0.22 0.10
Matches are distributed among these distances:
42 4 0.01
43 31 0.12
44 205 0.77
45 10 0.04
46 2 0.01
48 15 0.06
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (44 bp):
GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGACGTATG
Found at i:5537995 original size:88 final size:88
Alignment explanation
Indices: 5537884--5538171 Score: 251
Period size: 88 Copynumber: 3.3 Consensus size: 88
5537874 CCTGTCTGAT
* * * * *
5537884 GTATGGTTACCATCTTGGACAAATTCGCTTTCTTCCTATATGATGTATGGTTACCACCCTGGTTA
1 GTATGGTTACCACCCTAGTCAAATTCGCTTTCTTCCTATATGATGTATGGTTACCACCCTGGTCA
5537949 GATTTTTTTCATTCTGATTTGAC
66 GATTTTTTTCATTCTGATTTGAC
* * * *
5537972 GTATGGTTACCACCCTAGTCAAA-TCTGC-CTCTGTTCTGTTTGATGTATGGTTACCACCCTGGT
1 GTATGGTTACCACCCTAGTCAAATTC-GCTTTCT-TCCTATATGATGTATGGTTACCACCCTGGT
* * * * *
5538035 CAAACTTTTCTCATT-TCAGTCTGAC
64 CAGATTTTTTTCATTCTGA-TTTGAC
* * * * * * ** * * *
5538060 GTATGGATACCACCCTAGTTAAATTTGCCTTT-TTCTTTTCTGACATATAGTTACCACTCTGGCC
1 GTATGGTTACCACCCTAGTCAAATTCG-CTTTCTTCCTATATGATGTATGGTTACCACCCTGGTC
*
5538124 AGATTCTTTTCATTCTGATTTGAC
65 AGATTTTTTTCATTCTGATTTGAC
* * *
5538148 ATATAGTTACCACCCTGGTCAAAT
1 GTATGGTTACCACCCTAGTCAAAT
5538172 CCTTCTAACC
Statistics
Matches: 155, Mismatches: 38, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
87 7 0.05
88 142 0.92
89 5 0.03
90 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.40
Consensus pattern (88 bp):
GTATGGTTACCACCCTAGTCAAATTCGCTTTCTTCCTATATGATGTATGGTTACCACCCTGGTCA
GATTTTTTTCATTCTGATTTGAC
Found at i:5538064 original size:132 final size:130
Alignment explanation
Indices: 5537754--5538085 Score: 339
Period size: 132 Copynumber: 2.5 Consensus size: 130
5537744 GATTATATTA
* * * * *
5537754 GTTACCACCCTGGTCAAACTTTTTTTTTTCATTTC-GATCTAACATATGGTTACCACCTTGATCA
1 GTTACCACCCTGGTCAAAC-----TTTTTCATTTCAG-TCTGACGTATGGTTACCACCCTGGTTA
* * *
5537818 GATTCTTTTCATTCTGATTGACGTATGGTTACCGCTCTAGTCAAATCTGCCCCTATCCTGTCTGA
60 GATTTTTTTCATTCTGATTGACGTATGGTTACCACCCTAGTCAAATCTGCCCCTATCCTGTCTGA
5537883 TGTATG
125 TGTATG
* * * * * *
5537889 GTTACCATCTTGGACAAA-TTCGCTTTC-TTCCTA-TATGATGTATGGTTACCACCCTGGTTAGA
1 GTTACCACCCTGGTCAAACTT---TTTCATTTC-AGTCTGACGTATGGTTACCACCCTGGTTAGA
* * * *
5537951 TTTTTTTCATTCTGATTTGACGTATGGTTACCACCCTAGTCAAATCTGCCTCTGTTCTGTTTGAT
62 TTTTTTTCATTCTGA-TTGACGTATGGTTACCACCCTAGTCAAATCTGCCCCTATCCTGTCTGAT
5538016 GTATG
126 GTATG
* * *
5538021 GTTACCACCCTGGTCAAACTTTTCTCATTTCAGTCTGACGTATGGATACCACCCTAGTTAAATTT
1 GTTACCACCCTGGTCAAACTTTT-TCATTTCAGTCTGACGTATGGTTACCACCCTGGTTAGATTT
5538086 GCCTTTTTCT
Statistics
Matches: 160, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
129 2 0.01
130 2 0.01
131 42 0.26
132 97 0.61
133 2 0.01
135 15 0.09
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (130 bp):
GTTACCACCCTGGTCAAACTTTTTCATTTCAGTCTGACGTATGGTTACCACCCTGGTTAGATTTT
TTTCATTCTGATTGACGTATGGTTACCACCCTAGTCAAATCTGCCCCTATCCTGTCTGATGTATG
Found at i:5538298 original size:100 final size:101
Alignment explanation
Indices: 5538123--5538320 Score: 326
Period size: 100 Copynumber: 2.0 Consensus size: 101
5538113 CCACTCTGGC
* *
5538123 CAGATTCTTTTCATTCTGATTTGACATATAGTTACCACCCTGGTCAAATCCTTCTAACCCTTTGA
1 CAGATTCTTTTCATTCTGATTTGACATATAGTTACCACCCTAGTCAAACCCTTCTAACCCTTTGA
* *
5538188 CTAGCTTTTTAACTGATTGACTTCATCG-TTTTGCT
66 CTAACCTTTTAACTGATTGACTTCATCGATTTTGCT
* * *
5538223 CAGATTCTTTTCATTCTGATTTGACGTATGGTTACCACCCTAGTCAAACCCTTCTAACCTTTTGA
1 CAGATTCTTTTCATTCTGATTTGACATATAGTTACCACCCTAGTCAAACCCTTCTAACCCTTTGA
5538288 CTAACCTTTTAACTGATTGACTTCATCGATTTT
66 CTAACCTTTTAACTGATTGACTTCATCGATTTT
5538321 TCCTTGGTCA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
100 86 0.96
101 4 0.04
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (101 bp):
CAGATTCTTTTCATTCTGATTTGACATATAGTTACCACCCTAGTCAAACCCTTCTAACCCTTTGA
CTAACCTTTTAACTGATTGACTTCATCGATTTTGCT
Found at i:5538702 original size:84 final size:84
Alignment explanation
Indices: 5538380--5538709 Score: 331
Period size: 84 Copynumber: 3.9 Consensus size: 84
5538370 AACCCTTCTA
* * * * * * *
5538380 ACTTCCTTACCTTTAGTTTGCCCGTTGGTTTTGACCCTAGAGACTTCTTTACCTTTAGTCTGCTT
1 ACTTCTTTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTTACCCTTAGTCTGC-T
*
5538445 C-TCGGCTTTGACCTTGAAG
65 CGTCGGCTTTGACCTTGGAG
* * *
5538464 ACTTCTTTACCCTTAGTCTGCTTATCGACTTTGACCCTAGAGACTT-TCTTACCCTTAGTCTGCT
1 ACTTCTTTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCT-TTACCCTTAGTCTGCT
* * *
5538528 TGTCGGCTTTGACCCTAGAG
65 CGTCGGCTTTGACCTTGGAG
* * * ** * * * *
5538548 ATTTCTTTACCCTTAGTCTGCTTGTTGGCTTTGACTTTGGAGACTTCTTTACCGTTAGACTGCTT
1 ACTTCTTTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTTACCCTTAGTCTGCTC
5538613 GTCGGCTTTGACCTTGGAG
66 GTCGGCTTTGACCTTGGAG
* ** ** * * *
5538632 ACTGCTTTACTTTTAGTCTGCCTGTCGGCTTTGACCCGGGAGACTTTTTTACCCTTTGTCTGCCC
1 ACTTCTTTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTTACCCTTAGTCTGCTC
* *
5538697 ATCGGCTTCGACC
66 GTCGGCTTTGACC
5538710 CGAAAGACTC
Statistics
Matches: 201, Mismatches: 42, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
83 2 0.01
84 198 0.99
85 1 0.00
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (84 bp):
ACTTCTTTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTTACCCTTAGTCTGCTC
GTCGGCTTTGACCTTGGAG
Found at i:5538704 original size:42 final size:42
Alignment explanation
Indices: 5538409--5538694 Score: 349
Period size: 42 Copynumber: 6.8 Consensus size: 42
5538399 GCCCGTTGGT
* * *
5538409 TTTGACCCTAGAGACTTCTTTACCTTTAGTCTGCTTCTCGGC
1 TTTGACCCTGGAGACTTCTTTACCCTTAGTCTGCTTGTCGGC
* * * *
5538451 TTTGACCTTGAAGACTTCTTTACCCTTAGTCTGCTTATCGAC
1 TTTGACCCTGGAGACTTCTTTACCCTTAGTCTGCTTGTCGGC
*
5538493 TTTGACCCTAGAGACTT-TCTTACCCTTAGTCTGCTTGTCGGC
1 TTTGACCCTGGAGACTTCT-TTACCCTTAGTCTGCTTGTCGGC
* * *
5538535 TTTGACCCTAGAGATTTCTTTACCCTTAGTCTGCTTGTTGGC
1 TTTGACCCTGGAGACTTCTTTACCCTTAGTCTGCTTGTCGGC
** * *
5538577 TTTGACTTTGGAGACTTCTTTACCGTTAGACTGCTTGTCGGC
1 TTTGACCCTGGAGACTTCTTTACCCTTAGTCTGCTTGTCGGC
* * ** *
5538619 TTTGACCTTGGAGACTGCTTTACTTTTAGTCTGCCTGTCGGC
1 TTTGACCCTGGAGACTTCTTTACCCTTAGTCTGCTTGTCGGC
* * *
5538661 TTTGACCCGGGAGACTTTTTTACCCTTTGTCTGC
1 TTTGACCCTGGAGACTTCTTTACCCTTAGTCTGC
5538695 CCATCGGCTT
Statistics
Matches: 209, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
41 1 0.00
42 207 0.99
43 1 0.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.41
Consensus pattern (42 bp):
TTTGACCCTGGAGACTTCTTTACCCTTAGTCTGCTTGTCGGC
Found at i:5539599 original size:82 final size:82
Alignment explanation
Indices: 5539459--5539645 Score: 306
Period size: 82 Copynumber: 2.3 Consensus size: 82
5539449 TTGCACGATC
*
5539459 AAATGGACATTAAGATGATGGGAATTGGATTGCTTAATTTCTTGCCACATGATCATGCATGGACA
1 AAATGGACATTAAGATGATGGAAATTGGATTGCTTAATTTCTTGCCACATGATCATGCATGGACA
* *
5539524 CATGGCTAAGGGATGGA
66 CATGGCTAAGGGACGAA
* *
5539541 AATTGGACATTAAGATAATGGAAATTGGATTGCTTAATTTCTTGCCACATGATCATGCATGGACA
1 AAATGGACATTAAGATGATGGAAATTGGATTGCTTAATTTCTTGCCACATGATCATGCATGGACA
*
5539606 TATGGCTAAGGGACGAA
66 CATGGCTAAGGGACGAA
5539623 AAATGG-CATTAA-ATGATGGAAAT
1 AAATGGACATTAAGATGATGGAAAT
5539646 CAGCAGCTGA
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
80 10 0.10
81 6 0.06
82 81 0.84
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (82 bp):
AAATGGACATTAAGATGATGGAAATTGGATTGCTTAATTTCTTGCCACATGATCATGCATGGACA
CATGGCTAAGGGACGAA
Found at i:5540096 original size:24 final size:24
Alignment explanation
Indices: 5540069--5540115 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5540059 GAAAATAATC
*
5540069 AAAAATAGCAAATAAAAAAGGAAA
1 AAAAACAGCAAATAAAAAAGGAAA
* * *
5540093 AAAAGCAGCAAATGAAACAGGAA
1 AAAAACAGCAAATAAAAAAGGAA
5540116 GCAAATGAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.68, C:0.09, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAAACAGCAAATAAAAAAGGAAA
Found at i:5541140 original size:19 final size:20
Alignment explanation
Indices: 5541116--5541167 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
5541106 CAATTTGTCA
*
5541116 ATGTATCGATACAATG-AAC
1 ATGTATCGATACAAAGTAAC
*
5541135 ATGTATCGATACAAAGTAGC
1 ATGTATCGATACAAAGTAAC
5541155 ATGTATCGATACA
1 ATGTATCGATACA
5541168 TCTAGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACAAAGTAAC
Found at i:5548790 original size:18 final size:19
Alignment explanation
Indices: 5548758--5548797 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5548748 CAATGAAAAC
5548758 AAAAGCTCTTGGAAATGTG
1 AAAAGCTCTTGGAAATGTG
* *
5548777 AAAA-CTCTTTGAAATTTG
1 AAAAGCTCTTGGAAATGTG
5548795 AAA
1 AAA
5548798 GCTTCGATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (19 bp):
AAAAGCTCTTGGAAATGTG
Found at i:5549083 original size:20 final size:21
Alignment explanation
Indices: 5549055--5549095 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5549045 TTTCTTTATG
5549055 TATTGATACAATGTATCGATA
1 TATTGATACAATGTATCGATA
*
5549076 TATT-ATACCATGTATCGATA
1 TATTGATACAATGTATCGATA
5549096 CAAATAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
TATTGATACAATGTATCGATA
Found at i:5549177 original size:19 final size:20
Alignment explanation
Indices: 5549153--5549200 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5549143 ATGTCCATTA
*
5549153 ATCGATACAATG-AACATGT
1 ATCGATACAAAGCAACATGT
*
5549172 ATCGATACAAAGCAGCATGT
1 ATCGATACAAAGCAACATGT
*
5549192 ATCAATACA
1 ATCGATACA
5549201 TCTGGGTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (20 bp):
ATCGATACAAAGCAACATGT
Found at i:5550146 original size:13 final size:13
Alignment explanation
Indices: 5550128--5550154 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5550118 ACATTATGCT
5550128 TTGTATCGATACA
1 TTGTATCGATACA
5550141 TTGTATCGATACA
1 TTGTATCGATACA
5550154 T
1 T
5550155 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5550151 original size:33 final size:32
Alignment explanation
Indices: 5550109--5550170 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
5550099 CACACCCAGA
*
5550109 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
5550142 TGTATCGATACATGTTCATTGTATCGATA
1 TGTATCGATACATGTTCATTGTATCGATA
5550171 TATGGATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:5550163 original size:19 final size:19
Alignment explanation
Indices: 5550139--5550195 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
5550129 TGTATCGATA
*
5550139 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGAT
*
5550158 CATTGTATCGATATATGGAT
1 CATTGTATCGATACAT-GAT
*
5550178 AATTGTATCGATACATGA
1 CATTGTATCGATACATGA
5550196 AACTGGCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:5550184 original size:20 final size:19
Alignment explanation
Indices: 5550135--5550195 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
5550125 GCTTTGTATC
5550135 GATACATTGTATCGATACAT
1 GATA-ATTGTATCGATACAT
* * *
5550155 GTTCATTGTATCGATATAT
1 GATAATTGTATCGATACAT
5550174 GGATAATTGTATCGATACAT
1 -GATAATTGTATCGATACAT
5550194 GA
1 GA
5550196 AACTGGCAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (19 bp):
GATAATTGTATCGATACAT
Found at i:5550261 original size:33 final size:32
Alignment explanation
Indices: 5550224--5550286 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
5550214 TACCACTGTT
5550224 TGTATCGATACATG-GCACATTGTATCGATATAA
1 TGTATCGATACATGAG-A-ATTGTATCGATATAA
5550257 TGTATCGATACATGATGAATTGTATCGATA
1 TGTATCGATACATGA-GAATTGTATCGATA
5550287 CATTGCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATATAA
Found at i:5551905 original size:3 final size:3
Alignment explanation
Indices: 5551884--5551917 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5551874 CATTAAAGAC
* *
5551884 GAT GAA GAT GAT AAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
5551918 GTGACTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:5559095 original size:22 final size:23
Alignment explanation
Indices: 5559026--5559096 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 23
5559016 AAAATGACAA
*
5559026 AAAAAAAGT-CAAAAGCAAAAGT
1 AAAAAAAGTGCAAAAGCAAAACT
* * *
5559048 ACAAAATA-TG-AAAAGAAAAACA
1 A-AAAAAAGTGCAAAAGCAAAACT
5559070 AAAAAAAGTGCAAAAGCAAAA-T
1 AAAAAAAGTGCAAAAGCAAAACT
5559092 AAAAA
1 AAAAA
5559097 GGGAACAACA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 5 0.13
22 19 0.50
23 14 0.37
ACGTcount: A:0.72, C:0.08, G:0.11, T:0.08
Consensus pattern (23 bp):
AAAAAAAGTGCAAAAGCAAAACT
Found at i:5559117 original size:45 final size:44
Alignment explanation
Indices: 5559025--5559121 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 44
5559015 CAAAATGACA
* *
5559025 AAAAAAAAGTCAAAAGCAAAAGTACAAAATATGAAAAGAAAAAC
1 AAAAAAAAGTCAAAAGCAAAAGTACAAAATAGGAAAACAAAAAC
*
5559069 AAAAAAAAGTGCAAAAGCAAAA-TA-AAAA-GGGAACAACAAAAATCC
1 AAAAAAAAGT-CAAAAGCAAAAGTACAAAATAGGAA-AACAAAAA--C
5559114 AAAAAAAA
1 AAAAAAAA
5559122 CGGACATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
42 3 0.07
43 11 0.24
44 12 0.26
45 20 0.43
ACGTcount: A:0.71, C:0.10, G:0.11, T:0.07
Consensus pattern (44 bp):
AAAAAAAAGTCAAAAGCAAAAGTACAAAATAGGAAAACAAAAAC
Found at i:5560431 original size:27 final size:27
Alignment explanation
Indices: 5560386--5560626 Score: 243
Period size: 27 Copynumber: 8.8 Consensus size: 27
5560376 TTTCTTTTCA
* * * *
5560386 AAGTCCATAACTCCATGGCGTCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * * *
5560413 AAGTTCACAATTCTGTGGCATTCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
5560440 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
5560467 AAGTCCACAACTCCGTGGCATCCGTTTC
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* *
5560495 AAGTCCACAACTCCATGGCATTCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
5560522 AAAGTCCACAACTTCATGGCA-CTCTTCT
1 -AAGTCCACAACTCCGTGGCATC-CTTTT
5560550 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* **
5560577 AAGTCTACAACTTTGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* *
5560605 AAG-CTCACAAGTCAGTGGCATC
1 AAGTC-CACAACTCCGTGGCATC
5560627 ATCTCAAAGC
Statistics
Matches: 177, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
27 109 0.62
28 68 0.38
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:5560614 original size:55 final size:55
Alignment explanation
Indices: 5560386--5560626 Score: 249
Period size: 55 Copynumber: 4.4 Consensus size: 55
5560376 TTTCTTTTCA
* * * * * *
5560386 AAGTCCATAACTCCATGGCGTCCTTTAAAGTTCACAA-TTCTGTGGCATTC-TTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTC-GTGGCATCCTTTTT
* * * *
5560440 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCGTTTC
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTT
* * * *
5560495 AAGTCCACAACTCCATGGCATTCTTTTAAAGTCCACAACTTCATGGCA--CTCTTCT
1 AAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTTCGTGGCATCCT-TTTT
* *
5560550 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCTACAACTTTGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTT
* *
5560605 AAG-CTCACAAGTCAGTGGCATC
1 AAGTC-CACAACTCCGTGGCATC
5560627 ATCTCAAAGC
Statistics
Matches: 155, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
54 58 0.37
55 77 0.50
56 20 0.13
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (55 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTT
Found at i:5560625 original size:110 final size:110
Alignment explanation
Indices: 5560381--5560599 Score: 307
Period size: 110 Copynumber: 2.0 Consensus size: 110
5560371 TGGCATTTCT
* * * * * * *
5560381 TTTCAAAGTCCATAACTCCATGGC-GTCCTTTAAAGTTCACAATTCTGTGGCATTCTTTTAAGTC
1 TTTC-AAGTCCACAACTCCATGGCATTCTTTTAAAGTCCACAATTCTATGGCACTCTTCTAAGTC
5560445 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCG
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCG
5560491 TTTCAAGTCCACAACTCCATGGCATTCTTTTAAAGTCCACAACTTC-ATGGCACTCTTCTAAGTC
1 TTTCAAGTCCACAACTCCATGGCATTCTTTTAAAGTCCACAA-TTCTATGGCACTCTTCTAAGTC
* * **
5560555 CACAACTCCGTGGCATCCTTTTAAGTCTACAACTTTGTGGCATCC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
5560600 TTTTTAAGCT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
109 18 0.19
110 75 0.78
111 3 0.03
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (110 bp):
TTTCAAGTCCACAACTCCATGGCATTCTTTTAAAGTCCACAATTCTATGGCACTCTTCTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCG
Found at i:5560737 original size:32 final size:32
Alignment explanation
Indices: 5560630--5562923 Score: 973
Period size: 32 Copynumber: 74.4 Consensus size: 32
5560620 TGGCATCATC
*
5560630 TCAAAGCCCACATAAGTCGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* **
5560662 TCAAAG--CTCACAAGTCAATGGCATA---ATT
1 TCAAAGCCCACACAAGTCGGTGGCA-ACCCATT
* *
5560690 TCAAAGCTCACACAAGTCGGTGGCAACTCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * * *
5560722 TGAAAGCCCAGACAAGTTGGCGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
*
5560754 TCAAAGCCCAAACAAGTCGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
*
5560786 TCAAAGCCCACACAAGTCGGTGGTAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5560818 TCAAAGCCCACACAAGTCGGTGACAACCTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * *
5560850 TCAAAG-CC-CATAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5560878 CTCAAAGCCTACACAAGTCGGTGGCAACCCACT
1 -TCAAAGCCCACACAAGTCGGTGGCAACCCATT
** *
5560911 TCAAAG-CC-CACAAGTTAGTGGC-A-TCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * * *
5560939 TTAAAGCCCATACAAGTTGGTGGCAACTCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * * * *
5560971 TGAAAGCCCATACAAGTTGGTGACAACTCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561003 TCAAAGCCCACACAAGTTGGTAGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
**
5561035 TCAAAGCCCACACAAGTTAGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561067 TCAAAGCCCATACAAGTTGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561099 TCAAA-CCC-CACAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561127 TCAAAG-CC-CACAACTCAGTGGC-ACCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561155 TCAAAGCCCACACAAGTTGGTGGCAACCTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* ** *
5561187 TCAAAGCCCA-A-AACTTAGTGGC-A-TCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
**
5561215 TCAAAGCCCACACAAGT-TTTGG-AAGCCCA-T
1 TCAAAGCCCACACAAGTCGGTGGCAA-CCCATT
* * *** * ** * * * *
5561245 ACAAGTTGGTGGAAACCCATTTCAAAGTAG--ACACAAGT
1 TCAA-----AGCCCACACAAGTC--GGTGGCAAC-CCATT
*** * * * *** * * *
5561283 T-GGTGGCAAC-CAATTTCAAAGCCTACACAAGTCGGT
1 TCAAAGCCCACACAA-GTCGGTGGCAAC-CCA-T---T
* ** * *
5561319 GGC-AA-CCCATTTCAAAGTCCACAAGTCAGTGG-TATCC-TT
1 -TCAAAGCCCA-CAC-AAGTC-----G---GTGGCAACCCATT
*
5561358 TCAAAG-CC-CACAAGTCAGTGGCAA-CC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* ** *
5561386 CTCAAAGCCTACACAAGTCGGTGGCAACTAACT
1 -TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * * *
5561419 TCAACG-TC-CACAAG-CTAGTGGC-A-TCATT
1 TCAAAGCCCACACAAGTC-GGTGGCAACCCATT
* *
5561447 TCAAAGCCCACATAAGTCGGTGGCAACTCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * *
5561479 TGAAAGCCTATACAAGTCGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561511 TCAAAGTCCACACAAGTCAGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561543 TCAAAGCCCACACAAGTCAGG-GCCAACCTATT
1 TCAAAGCCCACACAAGTC-GGTGGCAACCCATT
* *
5561575 TCAAAG-CC-CACAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561603 TCAAAG-CCA-ACAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
*
5561631 CTCAAAGCCCACACAAGTCGGTGGCAACTCATT
1 -TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* **
5561664 TCAAAGCCCATACAAGTTTGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
*
5561696 TCAAAGCCCACACAAGTTGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
**
5561728 TCAAAGCCCACACAAGTTAGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
*
5561760 TCAAAGCCCATACAAGTCGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561792 TCAAAG-CC-CACAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * *
5561820 TCAAAG-CC-CACAACTCAGTCGC-ACCC--T
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5561847 TCAAAGCCCACACAAGTTGGTGGCAACCTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * *
5561879 TCAAAG-CC-CACAACTCAGTGGC-A-TCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
**
5561907 TCAAAGCCCACACAAGT-TTTGG-AAGCCCA-T
1 TCAAAGCCCACACAAGTCGGTGGCAA-CCCATT
* * *** * ** *** * * *
5561937 ACAAGTTGGTGGAAACCCATTTCAAAGCCCACACAAGTT
1 TCAA-----AGCCCACACAAGTCGGTGGCAAC-CCA-TT
** * ** * ** *
5561976 GGTGGC-AA-CCCATTTCAAAG-C-CTACACAAGTCGGTG
1 --T--CAAAGCCCA-CAC-AAGTCGGT-GGCAA-CCCATT
* ** * *
5562012 GC-AA-CCCATTTCAAAGTCCACAAGTCAGTGG-TATCC-TT
1 TCAAAGCCCA-CAC-AAGTC-----G---GTGGCAACCCATT
*
5562050 TCAAAG-CC-CACAAGTCAGTGGCAA-CC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
** *
5562078 CTCAAAGCCCACACAAGTCGGTGGCAACTAACT
1 -TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * * *
5562111 TCAACG-TC-CACAAGTCAGTGGC-A-TCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562139 TCAAAGCCCACATAAGTCGGTGGCAACTCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562171 TGAAAGCCCATACAAGTCGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
*
5562203 TCAAAGCCCACACAAGTCAGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
*
5562235 TCAAAGCCCACACAAGTCAGG-GCCAACCCATT
1 TCAAAGCCCACACAAGTC-GGTGGCAACCCATT
* *
5562267 TCAAAG-CC-CACAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
** *
5562295 TCAAAG-CCA-ACAAGTTAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
5562323 CTCAAAGCCCACACAAGTCGGTGGCAACCCATT
1 -TCAAAGCCCACACAAGTCGGTGGCAACCCATT
** *
5562356 TCAAAG-CC-CACAAGTTAGTGGC-A-TCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562384 TCAAAACCCACACAAGTCGGTGGCAACTCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * * *
5562416 TGAAAGCCCATAAAAGTTGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562448 TCAAAGCCCACACAAGTTGGTGGAAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562480 TCAAAGCCCACACAAGTCGATGGCATCCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * *
5562512 TCAAAGCTCACA-AA-TCAGTGGC-A-CCGTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * **
5562540 TCAAAG--CGCACAAGTCAGTGGC--TTC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562567 TCAAAG-TC-CACAAGTCAGTGGC-ACCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562595 TCAAAG-CC-TACAAGTCAGTGGC-ACCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
** * *
5562623 TCAAAG-CC-CACAAGTTAGTGGC-ACTCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * *
5562652 TCAAAG-CC-CATAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
*
5562680 TCAAAG-CC-CACAAGTCAGTGGC-ACCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * * * *
5562708 TCAAAGCCCAAAACACGAGTCGGTTGTAACTCTTT
1 TCAAAGCCC---ACACAAGTCGGTGGCAACCCATT
* * *
5562743 TCAAAG-CC-CATAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * * * *
5562771 TCAAAG-CC-CACGAGTCAGTGGTAACTCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562801 TCAAAG-CC-CACAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* * *
5562829 TCAAAG-CC-CATAAGTCAGTGGC-A-CCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562857 TCAAAG-CC-CACAAGTCAGTGGC-A-CCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
* *
5562885 TC-AAG-CC-CATAAGTCAGTGGC-ACCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
5562912 TCAAAGCCCACA
1 TCAAAGCCCACA
5562924 AGTTAATGGC
Statistics
Matches: 1791, Mismatches: 312, Indels: 320
0.74 0.13 0.13
Matches are distributed among these distances:
26 3 0.00
27 56 0.03
28 386 0.22
29 118 0.07
30 276 0.15
31 100 0.06
32 743 0.41
33 20 0.01
34 5 0.00
35 20 0.01
36 18 0.01
37 13 0.01
38 10 0.01
39 14 0.01
40 1 0.00
42 3 0.00
43 1 0.00
44 1 0.00
45 2 0.00
46 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (32 bp):
TCAAAGCCCACACAAGTCGGTGGCAACCCATT
Found at i:5561263 original size:20 final size:19
Alignment explanation
Indices: 5561221--5561264 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5561211 CATTTCAAAG
* * *
5561221 CCCACACAAGTTTTGGAAG
1 CCCATACAAGTTGTGGAAA
5561240 CCCATACAAGTTGGTGGAAA
1 CCCATACAAGTT-GTGGAAA
5561260 CCCAT
1 CCCAT
5561265 TTCAAAGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (19 bp):
CCCATACAAGTTGTGGAAA
Found at i:5561824 original size:245 final size:241
Alignment explanation
Indices: 5560605--5563077 Score: 1975
Period size: 245 Copynumber: 10.3 Consensus size: 241
5560595 CATCCTTTTT
* * * * *
5560605 AAGCTCACAAGTCAGTGGCATCATCTCAAAGCCCACATAAGTCGGTGGCAACCCATTTCAAAG-C
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC--AAGTCAGTGGC-ATCC-TTTCAAAGCC
* * * *
5560669 TCACAAGTCAATGGCATA--ATTTCAAAGCTCACACAAGTCGGTGGCAACTCATTTGAAAGCCCA
62 ACACAAGTCAGTGGCA-ACCATTTCAAAGC-C-CACAAGTCAGTGGC-A-TCATTTCAAAGCCCA
* * * * * *
5560732 GACAAGTTGGCGGCAACCCATTTCAAAGCCCAAACAAGTCGGTGGCAACCCATTTCAAAGCCCAC
122 CACAAGTTAGTGGC-ACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC
* * * *
5560797 ACAAGTCGGTGGTAACCCATTTCAAAGCCCACACAAGTCGGTGACAACCTATTTCA
186 ACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * *
5560853 AAGCCCATAAGTCAGTGGCATCCTTCTCAAAGCCTACACAAGTCGGTGGCAACCCACTTCAAAGC
1 AAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCC--CACAAGTCAGTGGC-ATCC-TTTCAAAGC
* * * ** *
5560918 C-CACAAGTTAGTGGC-ATCATTTTAAAGCCCATACAAGTTGGTGGCAACTCATTTGAAAGCCCA
61 CACACAAGTCAGTGGCAACCATTTCAAAGCCC--ACAAGTCAGTGGC-A-TCATTTCAAAGCCCA
* * * *
5560981 TACAAGTTGGTGACAACTCATTTCAAAGCCCACACAAGTTGGTAGCAACCCATTTCAAAGCCCAC
122 CACAAGTTAGTGGC-ACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC
* * *
5561046 ACAAGTTAGTGGCAACCCATTTCAAAGCCCATACAAGTTGGTGGCAACCCATTTCA
186 ACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * *
5561102 AACCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACA
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCACA
** * * *
5561167 CAAGTTGGTGGCAACCTATTTCAAAGCCCAAAACTTAGTGGCATCATTTCAAAGCCCACACAAGT
65 CAAGTCAGTGGCAACC-ATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGT
* * * ***
5561232 T-TTGG-----------AAGCCCATACAAGTTGGTGGAAACCCATTTCAAAGTAGACACAAGTTG
129 TAGTGGCACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTG
* *
5561285 GTGGCAACCAATTTCAAAGCCTACACAAGTCGGTGGCAACCCATTTCA
194 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * *
5561333 AAGTCCACAAGTCAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTCTCAAAGCCTAC
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCC-AC
* * * * * *
5561398 ACAAGTCGGTGGCAACTAACTTCAACGTCCACAAG-CTAGTGGCATCATTTCAAAGCCCACATAA
64 ACAAGTCAGTGGCAAC-CATTTCAAAGCCCACAAGTC-AGTGGCATCATTTCAAAGCCCACACAA
** * * * * *
5561462 GTCGGTGGCAACTCATTTGAAAGCCTATACAAGTCGGTGGCAACCCATTTCAAAGTCCACACAAG
127 GTTAGTGGC-ACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAG
** * *
5561527 TCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAGG-GCCAACCTATTTCA
191 TTGGTGGCAACCCATTTCAAAGCCCACACAAGTC-GGTGGCAACCCATTTCA
*
5561578 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCAACAAGTCAGTGGCATCCTTCTCAAAGCCCAC
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAG-CCAC
* ** *
5561643 ACAAGTCGGTGGCAACTCATTTCAAAGCCCATACAAGTTTGTGGCAACCCATTTCAAAGCCCACA
64 ACAAGTCAGTGGCAAC-CATTTCAAAGCCC--ACAAGTCAGTGGC-A-TCATTTCAAAGCCCACA
* * * *
5561708 CAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCATAC
124 CAAGTTAGTGGC-ACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * *
5561773 AAGTCGGTGGCAACCCATTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCA
188 AAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * ** *
5561823 AAGCCCACAACTCAGTCGCA-CCCTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCC
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CACAAGTCAGTGGCATCC--TTTCAAAGCC
* * * ** *
5561887 -CACAACTCAGTGGC-ATCATTTCAAAGCCCAC-A--CA--AG--T--TTTGGAAGCCCATACAA
62 ACACAAGTCAGTGGCAACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAA
* * * *
5561941 GTTGGTGGAAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCTACACAAG
127 GTTAGTGG-CACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAG
* * * * *
5562006 TCGGTGGCAACCCATTTCAAAG-TC-CACAAGTCAGTGG-TATCC-TTTCA
191 TTGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * *
5562053 AAGCCCACAAGTCAGTGGCAACCTTCTCAAAGCCCACACAAGTCGGTGGCA-ACTAACTTCAACG
1 AAGCCCACAAGTCAGTGGCATCCTT-TCAAAG-CC-CACAAGTCAGTGGCATCCT---TTCAAAG
* * * *
5562117 TC-CACAAGTCAGTGGC-ATCATTTCAAAGCCCACATAAGTCGGTGGCAACTCATTTGAAAGCCC
60 CCACACAAGTCAGTGGCAACCATTTCAAAGCCCAC--AAGTCAGTGGC-A-TCATTTCAAAGCCC
* ** * **
5562180 ATACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCA
121 ACACAAGTTAGTGGC-ACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCA
* * * *
5562245 CACAAGTCAGG-GCCAACCCATTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCA
185 CACAAGT-TGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * *
5562298 AAGCCAACAAGTTAGTGGCATCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
1 AAGCCCACAAGTCAGTGGCATCCTT-TCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAGC
* * * * *
5562363 C-CACAAGTTAGTGGC-ATCATTTCAAAACCCACACAAGTCGGTGGCAACTCATTTGAAAGCCCA
61 CACACAAGTCAGTGGCAACCATTTC-AAAGCC-CACAAGTCAGTGGC-A-TCATTTCAAAGCCCA
* * * * *
5562426 TAAAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGAAACCCATTTCAAAGCCCAC
122 CACAAGTTAGTGGC-ACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC
* * * * * *
5562491 ACAAGTCGATGGCATCCCATTTCAAAGCTCACA-AA-TCAGTGGC-A-CCGTTTCA
186 ACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * * *
5562543 AAGCGCACAAGTCAGTGGC-TTCTTTCAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCC-TAC
1 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACAC
* * * * *
5562606 AAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAG-CC-CATAAGTC
66 AAGTCAGTGGCAACCATTTCAAAGCCCACAAGTCAGTGGCA-TCATTTCAAAGCCCACACAAGTT
* ** *
5562668 AGTGGCA-TCCTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAGCCCAAAACACGAGT
130 AGTGGCACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCC---ACACAAGT
* * * * * * * *
5562728 CGGTTGTAACTCTTTTCAAAG-CC-CATAAGTCAGTGGC-ATCC-TTTCA
192 TGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * *
5562774 AAGCCCACGAGTCAGTGGTAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC-C
1 AAGCCCACAAGTCAGTGG-CA-TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCAC
* * * * *
5562838 ATAAGTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTC-AAG-CC-CATAAGT
64 ACAAGTCAGTGGCAACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGT
* * ** * **
5562899 CAGTGGCAC-CCTTTCAAAG-CC-CACAAGTTAATGGC-A-CCTTTTCAAAG-CC-CACAAGTCA
129 TAGTGGCACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTG
* * * ** * *
5562957 GTGG-TACTCTTTTCAAAG-CC-CACAAGTTAGTGGC-ATCC-TTTTA
194 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * * *
5563000 AAGCCCATAAGTCAGTGGCA-CCTTTTCAAAGTCCACAAGTTAGTAGCACCCTTTCAAAGCCCAC
1 AAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCAC
*
5563064 ACAAGTTAGTGGCA
64 ACAAGTCAGTGGCA
5563078 CCTTTTTTTA
Statistics
Matches: 1913, Mismatches: 224, Indels: 197
0.82 0.10 0.08
Matches are distributed among these distances:
223 1 0.00
224 32 0.02
225 3 0.00
226 63 0.03
227 10 0.01
228 11 0.01
229 7 0.00
230 151 0.08
231 197 0.10
232 188 0.10
233 10 0.01
234 86 0.04
235 3 0.00
236 12 0.01
237 13 0.01
238 5 0.00
239 29 0.02
240 5 0.00
241 15 0.01
242 1 0.00
243 22 0.01
244 45 0.02
245 540 0.28
246 69 0.04
247 36 0.02
248 47 0.02
249 308 0.16
250 1 0.00
251 3 0.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (241 bp):
AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACAC
AAGTCAGTGGCAACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTTA
GTGGCACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGT
GGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
Found at i:5561857 original size:27 final size:28
Alignment explanation
Indices: 5561791--5561918 Score: 105
Period size: 28 Copynumber: 4.5 Consensus size: 28
5561781 GGCAACCCAT
* * *
5561791 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAACTCAGTCGCATCCC
5561819 TTCAAAGCCCACAACTCAGTCGCA-CCC
1 TTCAAAGCCCACAACTCAGTCGCATCCC
* ** * * *
5561846 TTCAAAGCCCACACAAGTTGGTGGCAACCTAT
1 TTCAAAG-CC-CACAACTCAGTCGCATCC--C
* **
5561878 TTCAAAGCCCACAACTCAGTGGCATCAT
1 TTCAAAGCCCACAACTCAGTCGCATCCC
5561906 TTCAAAGCCCACA
1 TTCAAAGCCCACA
5561919 CAAGTTTTGG
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
27 9 0.11
28 38 0.46
29 11 0.13
30 15 0.18
31 2 0.02
32 7 0.09
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (28 bp):
TTCAAAGCCCACAACTCAGTCGCATCCC
Found at i:5561955 original size:20 final size:19
Alignment explanation
Indices: 5561913--5561956 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5561903 CATTTCAAAG
* * *
5561913 CCCACACAAGTTTTGGAAG
1 CCCATACAAGTTGTGGAAA
5561932 CCCATACAAGTTGGTGGAAA
1 CCCATACAAGTT-GTGGAAA
5561952 CCCAT
1 CCCAT
5561957 TTCAAAGCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (19 bp):
CCCATACAAGTTGTGGAAA
Found at i:5562107 original size:692 final size:682
Alignment explanation
Indices: 5560660--5563077 Score: 2947
Period size: 692 Copynumber: 3.5 Consensus size: 682
5560650 TGGCAACCCA
* * * * * * *
5560660 TTTCAAAGCTCACAAGTCAATGGCATA-ATTTCAAAGCTCACACAAGTCGGTGGCAACTCATTTG
1 TTTCAAAGCCCACAAGTCAGTGGCA-ACCTTTCAAAGCCCACACAAGTCGGTGGCAACTAACTTC
** * * * * *
5560724 AAAGCCCAGACAAGTTGGCGGCAACCCATTTCAAAGCCCAAACAAGTCGGTGGCAACCCATTTCA
65 AAAGCCC--ACAAGTCAGTGGC-A-TCATTTCAAAGCCCACATAAGTCGGTGGCAACTCATTTCA
* * * *
5560789 AAGCCCACACAAGTCGGTGGTAACCCATTTCAAAGCCCACACAAGTCGGTGACAACCTATTTCAA
126 AAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAA
* * * * * *
5560854 AGCCCATAAGTCAGTGGCATCCTTCTCAAAGCCTACACAAGTCGGTGGCAACCCACTTCAAAGCC
191 AGCCCACAAGTCAG-GGCAACCTTTTCAAAGCC--CACAAGTCAGTGGC-ATCC-TTTCAAAGCC
* * * * * *
5560919 CACAAGTTAGTGGCATCATTTTAAAGCCCATACAAGTTGGTGGCAACTCATTTGAAAGCCCATAC
251 AACAAGTTAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCC--AC
* * * *
5560984 AAGTTGGTGACAACTCATTTCAAAGCCCACACAAGTTGGTAGCAACCCATTTCAAAGCCCACACA
314 AAGTTAGTGGC-ACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACA
*
5561049 AGTTAGTGGCAACCCATTTCAAAGCCCATACAAGTTGGTGGCAACCCATTTCAAACCCCACAAGT
378 AGTTAGTGGCAACCCATTTCAAAGCCCATACAAGTTGGTGGCAACCCATTTCAAAGCCCACAAGT
5561114 CAGTGGCATCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACACAAGTTGGTGGC
443 CAGTGGCATCCTTTCAAAGCCCACAACTCAGTGGCACCC-TTCAAAGCCCACACAAGTTGGTGGC
* *
5561179 AACCTATTTCAAAGCCCAAAACTTAGTGGCATCATTTCAAAGCCCACACAAGTTTTGGAAGCCCA
507 AACCTATTTCAAAGCCCACAACTCAGTGGCATCATTTCAAAGCCCACACAAGTTTTGGAAGCCCA
** *
5561244 TACAAGTTGGTGGAAACCCATTTCAAAGTAGACACAAGTTGGTGGCAACCAATTTCAAAGCCTAC
572 TACAAGTTGGTGGAAACCCATTTCAAAG-CCACACAAGTTGGTGGCAACCCATTTCAAAGCCTAC
5561309 ACAAGTCGGTGGCAACCCATTTCAAAGTCCACAAGTCAGTGGTATCC
636 ACAAGTCGGTGGCAACCCATTTCAAAGTCCACAAGTCAGTGGTATCC
*
5561356 TTTCAAAGCCCACAAGTCAGTGGCAACCTTCTCAAAGCCTACACAAGTCGGTGGCAACTAACTTC
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT-TCAAAGCCCACACAAGTCGGTGGCAACTAACTTC
* * *
5561421 AACGTCCACAAG-CTAGTGGCATCATTTCAAAGCCCACATAAGTCGGTGGCAACTCATTTGAAAG
65 AAAGCCCACAAGTC-AGTGGCATCATTTCAAAGCCCACATAAGTCGGTGGCAACTCATTTCAAAG
* * *
5561485 CCTATACAAGTCGGTGGCAACCCATTTCAAAGTCCACACAAGTCAGTGGCAACCCATTTCAAAGC
129 CCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAG-
5561550 CCACACAAGTCAGGGCCAACCTATTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCAACA
193 CC-CACAAGTCAGGG-CAACCT-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCAACA
*
5561615 AGTCAGTGGCATCCTTCTCAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCCATACAAG
255 AGTTAGTGGCATCCTT-TCAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCC--ACAAG
*
5561680 TTTGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGT
317 TTAGTGGC-ACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGT
*
5561745 TAGTGGCAACCCATTTCAAAGCCCATACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAG
381 TAGTGGCAACCCATTTCAAAGCCCATACAAGTTGGTGGCAACCCATTTCAAAGCCCACAAGTCAG
*
5561810 TGGCATCCTTTCAAAGCCCACAACTCAGTCGCACCCTTCAAAGCCCACACAAGTTGGTGGCAACC
446 TGGCATCCTTTCAAAGCCCACAACTCAGTGGCACCCTTCAAAGCCCACACAAGTTGGTGGCAACC
5561875 TATTTCAAAGCCCACAACTCAGTGGCATCATTTCAAAGCCCACACAAGTTTTGGAAGCCCATACA
511 TATTTCAAAGCCCACAACTCAGTGGCATCATTTCAAAGCCCACACAAGTTTTGGAAGCCCATACA
5561940 AGTTGGTGGAAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCTACACAA
576 AGTTGGTGGAAACCCATTTCAAAG-CCACACAAGTTGGTGGCAACCCATTTCAAAGCCTACACAA
5562005 GTCGGTGGCAACCCATTTCAAAGTCCACAAGTCAGTGGTATCC
640 GTCGGTGGCAACCCATTTCAAAGTCCACAAGTCAGTGGTATCC
5562048 TTTCAAAGCCCACAAGTCAGTGGCAACCTTCTCAAAGCCCACACAAGTCGGTGGCAACTAACTTC
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT-TCAAAGCCCACACAAGTCGGTGGCAACTAACTTC
* * *
5562113 AACGTCCACAAGTCAGTGGCATCATTTCAAAGCCCACATAAGTCGGTGGCAACTCATTTGAAAGC
65 AAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACATAAGTCGGTGGCAACTCATTTCAAAGC
*
5562178 CCATACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCC
130 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAG-C
*
5562243 CACACAAGTCAGGGCCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCAACAA
194 C-CACAAGTCAGGG-CAA-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCAACAA
*
5562308 GTTAGTGGCATCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTTA
256 GTTAGTGGCATCCTT-TCAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCCACAAGTTA
* * * * * * * *
5562373 GTGGCA-TCATTTCAAAACCCACACAAGTCGGTGGCAACTCATTTGAAAGCCCATAAAAGTTGGT
320 GTGGCACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGT
* *
5562437 GGCAACCCATTTCAAAGCCCACACAAGTTGGTGGAAACCCATTTCAAAGCCCACACAAGTC-GAT
385 GGCAACCCATTTCAAAGCCCATACAAGTTGGTGGCAACCCATTTCAAAG-CC-CACAAGTCAG-T
* * * * **
5562501 GGCATCCCATTTCAAAGCTCACAAATCAGTGGCACCGTTTCAAAG--CGCACAAGTCAGTGG---
447 GGCAT-CC-TTTCAAAGCCCACAACTCAGTGGCACC-CTTCAAAGCCCACACAAGTTGGTGGCAA
* * * * * * * *
5562561 CTTCTTTCAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCCTACA-AGTCAGTGGCACCCTTTC
509 CCTATTTCAAAGCCCACAACTCAGTGGCATCATTTCAAAGCCCACACA---AGT-------TTTG
* * * * * * ** *
5562625 AAAGCCC--ACAAGTTAGTGG-CACTCTTTTCAAAGCC-CATAAGTCAGTGGC-ATCC-TTTCAA
564 GAAGCCCATACAAGTTGGTGGAAACCCATTTCAAAGCCACACAAGTTGGTGGCAACCCATTTCAA
* * * * *
5562684 AGCC--CACAAGTCAGTGGC-ACCC-TTTCAAAGCCCAAAACACGAGTCGGTTGTAACTCT
629 AGCCTACACAAGTCGGTGGCAACCCATTTCAAAGTCC---ACA--AGTCAGTGGT-A-TCC
* * * * * ***
5562741 TTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAG-CC-CACGAGTCAGTGGTAACTCTTTTCA
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCACACAAGTCGGTGGCAACTAACTTCA
* * *
5562804 AAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CATAAGTCAGTGGC-AC-CTTTTCAAAG-C
66 AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACATAAGTCGGTGGCAACTCATTTCAAAGCC
* * *
5562864 C-CACAAGTCAGTGGC-A-CCTTTTC-AAG-CC-CATAAGTCAGTGGC-ACCC-TTTCAAAGCCC
131 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCC
* * * * *
5562921 ACAAGTTAATGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGTACTCTTTTCAAAGCCCACAAGTT
196 ACAAG-TCAGGGCAACCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCAACAAGTT
* * * * * *
5562985 AGTGGCATCCTTTTAAAG-CC-CATAAGTCAGTGGC-AC-CTTTTCAAAGTCCACAAGTTAGTAG
259 AGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCCACAAGTTAGTGG
*
5563046 CACCC-TTTCAAAGCCCACACAAGTTAGTGGCA
324 CACCCATTTCAAAGCCCACACAAGTTGGTGGCA
5563078 CCTTTTTTTA
Statistics
Matches: 1554, Mismatches: 132, Indels: 99
0.87 0.07 0.06
Matches are distributed among these distances:
669 48 0.03
670 3 0.00
671 12 0.01
672 2 0.00
673 31 0.02
674 32 0.02
675 7 0.00
676 6 0.00
677 8 0.01
678 4 0.00
679 13 0.01
680 2 0.00
681 3 0.00
682 6 0.00
683 1 0.00
684 12 0.01
685 2 0.00
686 18 0.01
687 7 0.00
688 161 0.10
689 9 0.01
690 86 0.06
691 27 0.02
692 570 0.37
693 343 0.22
694 29 0.02
695 35 0.02
696 34 0.02
697 43 0.03
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (682 bp):
TTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCACACAAGTCGGTGGCAACTAACTTCA
AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACATAAGTCGGTGGCAACTCATTTCAAAGCC
CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCC
ACAAGTCAGGGCAACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCAACAAGTTAG
TGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCCACAAGTTAGTGGCA
CCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAAC
CCATTTCAAAGCCCATACAAGTTGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCCTT
TCAAAGCCCACAACTCAGTGGCACCCTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAG
CCCACAACTCAGTGGCATCATTTCAAAGCCCACACAAGTTTTGGAAGCCCATACAAGTTGGTGGA
AACCCATTTCAAAGCCACACAAGTTGGTGGCAACCCATTTCAAAGCCTACACAAGTCGGTGGCAA
CCCATTTCAAAGTCCACAAGTCAGTGGTATCC
Found at i:5564026 original size:20 final size:19
Alignment explanation
Indices: 5563980--5564033 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
5563970 TTTTTCCTAG
5563980 ATGTATCGATACA-TTGAA
1 ATGTATCGATACATTTGAA
*
5563998 ATTTATCGATACATGTATG-A
1 ATGTATCGATACAT-T-TGAA
5564018 ATGTATCGATACATTT
1 ATGTATCGATACATTT
5564034 TGTCATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 13 0.42
19 1 0.03
20 15 0.48
21 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTTGAA
Found at i:5564091 original size:20 final size:20
Alignment explanation
Indices: 5564049--5564099 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5564039 TTTTACCCAG
* * * *
5564049 ATGTATCAATACATTTTTTA
1 ATGTATCGATACATGTATGA
5564069 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATGA
5564089 ATGTATCGATA
1 ATGTATCGATA
5564100 TATTCTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTATGA
Found at i:5564115 original size:20 final size:20
Alignment explanation
Indices: 5564052--5564130 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 20
5564042 TACCCAGATG
* * * *
5564052 TATCAATACATTTTTTAATG
1 TATCGATACATTCTTCAATA
* * *
5564072 TATCGATACATGT-ATGAATG
1 TATCGATACAT-TCTTCAATA
*
5564092 TATCGATATATTCTTCAATA
1 TATCGATACATTCTTCAATA
*
5564112 TATCGATGCATTCTTCAAT
1 TATCGATACATTCTTCAAT
5564131 GCATCAATGC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (20 bp):
TATCGATACATTCTTCAATA
Found at i:5564140 original size:20 final size:20
Alignment explanation
Indices: 5564101--5564145 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5564091 GTATCGATAT
* *
5564101 ATTCTTCAATATATCGATGC
1 ATTCTTCAATACATCAATGC
*
5564121 ATTCTTCAATGCATCAATGC
1 ATTCTTCAATACATCAATGC
5564141 ATTCT
1 ATTCT
5564146 GTCTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (20 bp):
ATTCTTCAATACATCAATGC
Found at i:5570741 original size:20 final size:22
Alignment explanation
Indices: 5570701--5570743 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5570691 TTTTTAACCA
*
5570701 TTTATCAAGGGGGAGAAATTTT
1 TTTATCAAGAGGGAGAAATTTT
5570723 TTTATCAA-AGGGA-AAATTTT
1 TTTATCAAGAGGGAGAAATTTT
5570743 T
1 T
5570744 CTAACGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (22 bp):
TTTATCAAGAGGGAGAAATTTT
Found at i:5575524 original size:20 final size:21
Alignment explanation
Indices: 5575479--5575552 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 21
5575469 AAAAACTCAG
**
5575479 AATGTATCGATACA-AAGCGA
1 AATGTATCGATACATTTGCGA
*
5575499 ATTGTATCGATACATTTG-GA
1 AATGTATCGATACATTTGCGA
* * *
5575519 AATGTATCGCTACATTTAC-T
1 AATGTATCGATACATTTGCGA
*
5575539 TATGTATCGATACA
1 AATGTATCGATACA
5575553 AATTTTTGAC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 42 0.98
21 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTTGCGA
Found at i:5575605 original size:21 final size:21
Alignment explanation
Indices: 5575581--5575656 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
5575571 GACATGGTTT
*
5575581 TGTATCGATACATTTGAGACA
1 TGTATCAATACATTTGAGACA
* * ***
5575602 TGTATCGATACA-TTCACTTA
1 TGTATCAATACATTTGAGACA
5575622 TGTATCAATACATTTGAGACA
1 TGTATCAATACATTTGAGACA
5575643 TGTATCAATACATT
1 TGTATCAATACATT
5575657 CACTAATTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (21 bp):
TGTATCAATACATTTGAGACA
Found at i:5575638 original size:41 final size:42
Alignment explanation
Indices: 5575580--5575675 Score: 149
Period size: 41 Copynumber: 2.3 Consensus size: 42
5575570 CGACATGGTT
* * *
5575580 TTGTATCGATACATTTGAGACATGTATCGATACATTCACTTA
1 TTGTATCAATACATTTGAGACATGTATCAATACATTCACTAA
5575622 -TGTATCAATACATTTGAGACATGTATCAATACATTCACTAA
1 TTGTATCAATACATTTGAGACATGTATCAATACATTCACTAA
*
5575663 TTATATCAATACA
1 TTGTATCAATACA
5575676 AATCATAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 38 0.78
42 11 0.22
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (42 bp):
TTGTATCAATACATTTGAGACATGTATCAATACATTCACTAA
Found at i:5578198 original size:36 final size:34
Alignment explanation
Indices: 5578116--5578210 Score: 108
Period size: 36 Copynumber: 2.9 Consensus size: 34
5578106 CTTACAACAT
* *
5578116 TATC-TTTC-AAGGCTAAGATAGAA--ACTTCCT
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTTCCC
**
5578146 TATCTTTTCACGGGCTAAGATAGAACCTCTTTCCC
1 TATCTTTTCAAAGGCTAAGATAGAACCTC-TTCCC
5578181 TATCTTTTTCAAAGGCTAAGATAGAACCTC
1 TATC-TTTTCAAAGGCTAAGATAGAACCTC
5578211 CCAATCACTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
30 4 0.08
31 4 0.08
32 13 0.25
34 1 0.02
35 8 0.15
36 23 0.43
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (34 bp):
TATCTTTTCAAAGGCTAAGATAGAACCTCTTCCC
Found at i:5578690 original size:19 final size:20
Alignment explanation
Indices: 5578647--5578690 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5578637 CCGTTGGGCT
**
5578647 CAATGTATCGATACTATTCA
1 CAATGTATCGATACTATGAA
5578667 CAATGTATCGATAC-ATGAA
1 CAATGTATCGATACTATGAA
5578686 CAATG
1 CAATG
5578691 ACGAACATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (20 bp):
CAATGTATCGATACTATGAA
Found at i:5578803 original size:13 final size:13
Alignment explanation
Indices: 5578785--5578809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5578775 ACAATTCATG
5578785 ATGTATCGATACA
1 ATGTATCGATACA
5578798 ATGTATCGATAC
1 ATGTATCGATAC
5578810 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5581651 original size:93 final size:93
Alignment explanation
Indices: 5581468--5581713 Score: 282
Period size: 93 Copynumber: 2.6 Consensus size: 93
5581458 TTTTTAATTG
* * *
5581468 AAAAACGGGGTTGGAGTATCCTCTCGGAAGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTG
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAA-AAT-GGGTTGGAGTGTCCCCGATGA--ACAATTTA
* * *
5581533 AGTGAGAATAAAATTTGAATCTTGATAAGTAT-
62 AATCAGAATAAAATTTAAATCTTGATAAGT-TC
*
5581565 AAAAGCGGGGTTGGAGTATCCCCTCGGAAAATGGAGTTGGAGTATCCCCGATGAA-AATTTAAAT
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAAAATGG-GTTGGAGTGTCCCCGATGAACAATTTAAAT
**
5581629 CAGAATAAAATTTAAA-CTTTGATGCGTTC
65 CAGAATAAAATTTAAATC-TTGATAAGTTC
* * *
5581658 AAAAGTGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTGGAAGTGTCCCCGATGAA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGA-AAATGGGTTGG-AGTGTCCCCGATGAA
5581714 TAAAAATTTT
Statistics
Matches: 131, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
92 2 0.02
93 59 0.45
94 20 0.15
95 2 0.02
96 21 0.16
97 27 0.21
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (93 bp):
AAAAGCGGGGTTGGAGTATCCCCTCGGAAAATGGGTTGGAGTGTCCCCGATGAACAATTTAAATC
AGAATAAAATTTAAATCTTGATAAGTTC
Found at i:5583961 original size:20 final size:19
Alignment explanation
Indices: 5583911--5583988 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
5583901 GGTAAAAAGA
5583911 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
5583930 GCAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
*
5583950 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* *
5583970 AAAAAATGTATCGATACAT
1 -CATAATGTATCGATACAT
5583989 CAGGGTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.06
20 43 0.90
21 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:5583982 original size:40 final size:39
Alignment explanation
Indices: 5583911--5583988 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
5583901 GGTAAAAAGA
** *
5583911 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTAAAAAATATATCGATACATT
* *
5583950 CATACATGTATCGATATATTAAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTAAAAAATATATCGATACAT
5583989 CAGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTAAAAAATATATCGATACATT
Found at i:5584666 original size:28 final size:28
Alignment explanation
Indices: 5584605--5585919 Score: 1277
Period size: 28 Copynumber: 45.8 Consensus size: 28
5584595 CACCGACTCG
* * *
5584605 TGTGGGCTTTGAAAAGAGTTACCACTGGCT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT
*
5584635 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5584663 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
5584692 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5584720 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5584748 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5584776 TGTGGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
5584805 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5584833 TGTGGGCTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
**
5584862 TGTGGGCTTTGAAAATAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
5584891 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5584919 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5584947 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** *
5584975 TGTGGGCTTTGAAAATAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
5585004 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
5585033 TGTGGGCTTTGAAATGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5585061 TGTGGGCTTTGAAAAGAGTCCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
5585090 TGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
5585118 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5585146 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
5585175 TGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * **
5585203 TGTGGGCTTTAAAAAGGGTTGCCACCGAAAG
1 TGTGGGCTTT-GAAA-GGATGCCACTG-ACT
* * * *
5585234 TGTGGACTTTTGAAAGAGGTTCC-CATCAACTT
1 TGTGGGC-TTTGAAAG-GATGCCAC-T-GAC-T
* * *
5585266 GTGTGGGCTTTGAAAAAGGTTGTCACCGACTT
1 -TGTGGGCTTTG--AAAGGATGCCACTGAC-T
* * *
5585298 GTGTGGGCTTTGAAATGGGTTACCACCGACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* *
5585330 GTGTGGGCTTTGAAAAGGGTTGCCACCGACTT
1 -TGTGGGCTTTG-AAA-GGATGCCACTGAC-T
* *
5585362 GTGTGGGCTTTGAAATAGGTTGCCACCGACTT
1 -TGTGGGCTTTG-AA-AGGATGCCACTGAC-T
* *
5585394 GTGTGGGCTTCGAAATGG-TGCCACCGACTT
1 -TGTGGGCTTTGAAA-GGATGCCACTGAC-T
*
5585424 GTGTGGGCTTCGAAATGG-TGCCACTGACT
1 -TGTGGGCTTTGAAA-GGATGCCACTGACT
*
5585453 TATGGGCTTTGAAATGG-TGCCACTGACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
5585481 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5585509 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5585537 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
5585566 TGTGGGCTTTGAAA-GATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5585593 TATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5585621 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5585649 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5585677 TGTGGGCTTTGAAAAGGGTGCCACTGAGT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * * * *
5585706 TGTGGACTTTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
5585734 TGTGGAC-TTAAAAGAGATGCCACGGAGT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
* * * * *
5585762 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
5585790 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
5585817 TGTGGACTTT-AAAGGGTACCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
5585844 TGT--GCATTTAAAACGATGCCAC-GAAAT
1 TGTGGGC-TTTGAAAGGATGCCACTG-ACT
* * * * *
5585871 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5585899 TGTGGAC-TTAAAAGGATGCCA
1 TGTGGGCTTTGAAAGGATGCCA
5585920 TAGAGTTGTG
Statistics
Matches: 1157, Mismatches: 91, Indels: 77
0.87 0.07 0.06
Matches are distributed among these distances:
25 1 0.00
26 4 0.00
27 105 0.09
28 565 0.49
29 276 0.24
30 65 0.06
31 19 0.02
32 104 0.09
33 13 0.01
34 5 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:5584702 original size:57 final size:57
Alignment explanation
Indices: 5584528--5585940 Score: 1393
Period size: 57 Copynumber: 24.5 Consensus size: 57
5584518 TGAAAAGGGT
* * ** * *
5584528 TGCCACTAACTTACGTGGGCTTTTAAAAGGGTTGCCACTGAAAGTGTGGACTTTTGAAAAGAGT
1 TGCCACTGACTT--GTGGGCTTTGAAAAGGG-TGCCACTG-ACTTGTGGGC-TTTG-AAAG-GA
* * * *
5584592 TGCCACCGACTCGTGTGGGCTTTGAAAAGAGTTACCACTGGCTTGTGGGCTTTGAAAGGA
1 TGCCACTGACT--TGTGGGCTTTGAAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
5584652 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
5584709 TGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
5584765 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* **
5584822 TGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAATA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
*
5584879 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* **
5584936 TGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAATA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
5584992 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAATGA
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
5585050 TGCCACTGACTTGTGGGCTTTGAAAAGAGTCCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
5585107 TGCCACTGATTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * *
5585163 GTGCCACTAACTTGTGGGCTTTG-AAAGGATGCCACTGATTTGTGGGCTTTAAAAAGGGT
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT-GAAA-GGA
* ** * * * * *
5585222 TGCCACCGAAAGTGTGGACTTTTGAAAGAGGTTCCCA-TCAACTTGTGTGGGCTTTGAAAAAGGT
1 TGCCACTG-ACTTGTGGGC-TTTGAAA-AGGGTGCCACT-GAC-T-TGTGGGCTTTG--AAAGGA
* * * * * *
5585286 TGTCACCGACTTGTGTGGGCTTTGAAATGGGTTACCACCGACTTGTGTGGGCTTTGAAAAGGGT
1 TGCCACTGAC-T-TGTGGGCTTTGAAAAGGG-TGCCACTGAC-T-TGTGGGCTTTG-AAA-GGA
* * * *
5585350 TGCCACCGACTTGTGTGGGCTTTGAAATAGGTTGCCACCGACTTGTGTGGGCTTCGAAATGG-
1 TGCCACTGAC-T-TGTGGGCTTTGAAA-AGGGTGCCACTGAC-T-TGTGGGCTTTGAAA-GGA
* * * *
5585412 TGCCACCGACTTGTGTGGGCTTCG-AAATGGTGCCACTGACTTATGGGCTTTGAAATGG-
1 TGCCACTGAC-T-TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GGA
*
5585470 TGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
5585526 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
5585582 TGCCACTAACTTATGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
*
5585638 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGA
* * * * * *
5585695 TGCCACTGAGTTGTGGACTTT-AAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG-GA
* * * * * * * *
5585751 TGCCACGGAGTTGTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * * * * *
5585806 TGCCACGGAGTTGTGGACTTT--AAAGGGTACCACGGAGTTGT--GCATTTAAAACGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGC-TTTGAAAGGA
* * * * * *
5585860 TGCCAC-GAAATTGTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
1 TGCCACTG-ACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
5585915 TGCCA-TAGAGTTGTGGACTTT-AAAAG
1 TGCCACT-GACTTGTGGGCTTTGAAAAG
5585941 AAAATGCCAC
Statistics
Matches: 1197, Mismatches: 113, Indels: 87
0.86 0.08 0.06
Matches are distributed among these distances:
52 1 0.00
53 1 0.00
54 44 0.04
55 107 0.09
56 321 0.27
57 384 0.32
58 101 0.08
59 9 0.01
60 25 0.02
61 9 0.01
62 35 0.03
63 19 0.02
64 128 0.11
65 12 0.01
66 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (57 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:5584726 original size:85 final size:85
Alignment explanation
Indices: 5584528--5585919 Score: 1357
Period size: 85 Copynumber: 16.1 Consensus size: 85
5584518 TGAAAAGGGT
* * ** *
5584528 TGCCACTAACTTACGTGGGCTTTTAAAAGGGTTGCCACTGAAAGTGTGGACTTTTGAAAAGAGTT
1 TGCCACTGACTT--GTGGGC-TTTGAAAGGG-TGCCACT-AACTTGTGGGC-TTTGAAAAGAG-T
* *
5584593 GCCACCGACTCGTGTGGGCTTTGAAAAGAGT
59 GCCACTGACT--TGTGGGCTTTG-AAAG-GA
* * *
5584624 TACCACTGGCTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
5584689 ACTTGTGGGCTTTGAAAGGA
66 ACTTGTGGGCTTTGAAAGGA
* * *
5584709 TGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
*
5584773 ACTTGTGGGCTTTGAAAAGGG
66 ACTTGTGGGCTTTG-AAAGGA
* *
5584794 TGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
**
5584859 ACTTGTGGGCTTTGAAAATA
66 ACTTGTGGGCTTTGAAAGGA
* *
5584879 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACT
1 -TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
* *
5584943 AACTTGTGGGCTTTGAAAGGG
65 GACTTGTGGGCTTTGAAAGGA
**
5584964 TGCCACTGACTTGTGGGCTTTGAAAATAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
*
5585029 GACTTGTGGGCTTTGAAATGA
65 GACTTGTGGGCTTTGAAAGGA
* * * *
5585050 TGCCACTGACTTGTGGGCTTTGAAAAGAGTCCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACT
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
*
5585114 GATTTGTGGGCTTTGAAAGGA
65 GACTTGTGGGCTTTGAAAGGA
* *
5585135 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGA-TGCCACT
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
* * *
5585199 GATTTGTGGGCTTTAAAAAGGGT
65 GACTTGTGGGCTTT-GAAA-GGA
* ** * *
5585222 TGCCACCGAAAGTGTGGACTTTTGAAAGAGGTTCC-CATCAACTTGTGTGGGCTTTGAAAA-AGG
1 TGCCACTG-ACTTGTGGGC-TTTGAAAG-GGTGCCAC-T-AAC-T-TGTGGGCTTTGAAAAGA-G
* * *
5585285 TTGTCACCGACTTGTGTGGGCTTTGAAATGGGT
58 -TGCCACTGAC-T-TGTGGGCTTTGAAA--GGA
* * **
5585318 TACCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATAG-GT
1 TGCCACTGAC-T-TGTGGGCTTTG-AAAGGG-TGCCACTAAC-T-TGTGGGCTTTGAAA-AGAG-
* *
5585382 TGCCACCGACTTGTGTGGGCTTCGAAATGG-
58 TGCCACTGAC-T-TGTGGGCTTTGAAA-GGA
* * * * * *
5585412 TGCCACCGACTTGTGTGGGCTTCGAAATGGTGCCACTGACTTATGGGCTTTGAAATG-GTGCCAC
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCAC
5585476 TGACTTGTGGGCTTTGAAAGGA
64 TGACTTGTGGGCTTTGAAAGGA
*
5585498 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
5585563 ACTTGTGGGCTTTGAAA-GA
66 ACTTGTGGGCTTTGAAAGGA
* * * *
5585582 TGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
*
5585646 ACTTGTGGGCTTTGAAAGGG
66 ACTTGTGGGCTTTGAAAGGA
* * * * *
5585666 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGAGTTGTGGACTTT-AAAAGGGTGCCACA
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
* * *
5585730 GAGTTGTGGAC-TTAAAAGAGA
65 GACTTGTGGGCTTTGAAAG-GA
* * * * ** * * * *
5585751 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
* * *
5585814 AGTTGTGGACTTT-AAAGGG
66 ACTTGTGGGCTTTGAAAGGA
* * * * * * * * * * *
5585833 TACCACGGAGTTGT--GCATTTAAAACGATGCCACGAAATTGTGGACTTT-AAAAGGGTGCCACG
1 TGCCACTGACTTGTGGGC-TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
* * *
5585895 GAGTTGTGGAC-TTAAAAGGA
65 GACTTGTGGGCTTTGAAAGGA
5585915 TGCCA
1 TGCCA
5585920 TAGAGTTGTG
Statistics
Matches: 1149, Mismatches: 110, Indels: 88
0.85 0.08 0.07
Matches are distributed among these distances:
80 1 0.00
81 26 0.02
82 50 0.04
83 60 0.05
84 187 0.16
85 354 0.31
86 188 0.16
87 21 0.02
88 21 0.02
89 21 0.02
90 27 0.02
91 11 0.01
92 30 0.03
93 13 0.01
94 35 0.03
95 7 0.01
96 82 0.07
97 14 0.01
98 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (85 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
ACTTGTGGGCTTTGAAAGGA
Found at i:5585307 original size:96 final size:96
Alignment explanation
Indices: 5585146--5585403 Score: 282
Period size: 96 Copynumber: 2.8 Consensus size: 96
5585136 GCCACTGACT
* * * * * *
5585146 TGTGGGCTTTGAAAAGAG-TGCCACTAAC-T-TGTGGGCTTTG--AAAGGATGCCACTGA-TT-T
1 TGTGGACTTTGAAAAGGGTTCCCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGT
*
5585204 GTGGGCTTTAAAAAGGGTTGCCACCGA-AAG
66 GTGGGCTTTAAAAAGGGTTACCACCGACAAG
* *
5585234 TGTGGACTTTTG-AAAGAGGTTCCCATCAACTTGTGTGGGCTTTGAAAAAGGTTGTCACCGACTT
1 TGTGGAC-TTTGAAAAG-GGTTCCCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTT
* * **
5585298 GTGTGGGCTTTGAAATGGGTTACCACCGACTTG
64 GTGTGGGCTTTAAAAAGGGTTACCACCGACAAG
* * * *
5585331 TGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATAGGTTGCCACCGACTTGT
1 TGTGGACTTTGAAAAGGGTTCCCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGT
5585396 GTGGGCTT
66 GTGGGCTT
5585404 CGAAATGGTG
Statistics
Matches: 140, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
88 10 0.07
89 5 0.04
90 7 0.05
91 1 0.01
92 11 0.08
94 12 0.09
95 2 0.01
96 81 0.58
97 11 0.08
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (96 bp):
TGTGGACTTTGAAAAGGGTTCCCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGT
GTGGGCTTTAAAAAGGGTTACCACCGACAAG
Found at i:5585890 original size:109 final size:110
Alignment explanation
Indices: 5585648--5585938 Score: 404
Period size: 109 Copynumber: 2.6 Consensus size: 110
5585638 TGCCACTGAC
* * * * * *
5585648 TTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGAGTTGTGGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACAGAGTTGTGGAC
* * * *
5585713 TTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAG
64 TTT-AAAGGGTACCACAGAGTTGTGCACTTAAAAGAGATGCCACGAAA
*
5585761 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT
* * *
5585826 TAAAGGGTACCACGGAGTTGTGCATTTAAAA-CGATGCCACGAAA
66 TAAAGGGTACCACAGAGTTGTGCACTTAAAAGAGATGCCACGAAA
* *
5585870 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCATAGAGTTGTGGACTT
1 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT
5585935 TAAA
66 TAAA
5585939 AGAAAATGCC
Statistics
Matches: 162, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
109 76 0.47
110 26 0.16
111 27 0.17
112 2 0.01
113 31 0.19
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.26
Consensus pattern (110 bp):
TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT
TAAAGGGTACCACAGAGTTGTGCACTTAAAAGAGATGCCACGAAA
Found at i:5587008 original size:13 final size:13
Alignment explanation
Indices: 5586986--5587015 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5586976 GGTGAAAAGG
*
5586986 TTTTTCTTTTTTT
1 TTTTTATTTTTTT
5586999 TTTTTATTTTTTT
1 TTTTTATTTTTTT
5587012 TTTT
1 TTTT
5587016 AGGATTGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.03, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTATTTTTTT
Found at i:5592164 original size:97 final size:94
Alignment explanation
Indices: 5592041--5592287 Score: 311
Period size: 94 Copynumber: 2.6 Consensus size: 94
5592031 TTTTTAATTG
* *
5592041 AAAAACGGGGTTGGAGTATCCCCTCGGAAGAATGGGGTTGGAATGTCCCCGATGATGACAATTTG
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAAGAATGGGGTTGGAATGTCCCCGATGA--A-AATTTA
* *
5592106 AGTGAGAATAAGATTTGAA-TCTTGATAAGTAT-
63 AGTGAGAATAAAATTTAAACT-TTGATAAGT-TC
* * * *
5592138 AAAAGCGGGGTTGGAGTATCCCCTCGGAAAAATGGAGTTGGAGTATCCCCGATGAAAATTTAAGT
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAAGAATGGGGTTGGAATGTCCCCGATGAAAATTTAAGT
**
5592203 GAGAATAAAATTTAAACTTTGATGCGTTC
66 GAGAATAAAATTTAAACTTTGATAAGTTC
* *
5592232 AAAAGCGAGGTTGGAGTATCCCCTCGGAGGAATGGGG-TGGAAGTGTCCCCGATGAA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAAGAATGGGGTTGGAA-TGTCCCCGATGAA
5592288 TAAAAATTTT
Statistics
Matches: 131, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
93 5 0.04
94 74 0.56
95 2 0.02
97 50 0.38
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (94 bp):
AAAAGCGGGGTTGGAGTATCCCCTCGGAAGAATGGGGTTGGAATGTCCCCGATGAAAATTTAAGT
GAGAATAAAATTTAAACTTTGATAAGTTC
Found at i:5594524 original size:20 final size:20
Alignment explanation
Indices: 5594491--5594565 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
5594481 AAAAAGACAT
* *
5594491 AATGTATTGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
5594511 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
5594531 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
5594551 AATGTATCGATACAT
1 AATGTATCGATACAT
5594566 CAGGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.05
20 41 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:5594559 original size:40 final size:39
Alignment explanation
Indices: 5594488--5594565 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
5594478 GGTAAAAAGA
* * *
5594488 CATAATGTATTGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
5594527 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
5594566 CAGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:5596682 original size:21 final size:21
Alignment explanation
Indices: 5596641--5596684 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5596631 CTCTCTTTTA
* *
5596641 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
5596662 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
5596683 TC
1 TC
5596685 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:5598348 original size:21 final size:21
Alignment explanation
Indices: 5598324--5598370 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5598314 TTTGATGCTG
5598324 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
5598344 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
5598365 ATTTTG
1 ATTTTG
5598371 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:5598509 original size:13 final size:13
Alignment explanation
Indices: 5598491--5598529 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
5598481 ATAATCACCC
*
5598491 TGTATCGATACAG
1 TGTATCGATACAA
5598504 TGTATCGATACAA
1 TGTATCGATACAA
5598517 TGTATCGATACAA
1 TGTATCGATACAA
5598530 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5598540 original size:20 final size:20
Alignment explanation
Indices: 5598515--5598593 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
5598505 GTATCGATAC
5598515 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
* *
5598535 AATGTATCAATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
5598560 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
5598580 CATGTATCGATACA
1 AATGTATCGATACA
5598594 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
25 17 0.35
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:5600630 original size:15 final size:15
Alignment explanation
Indices: 5600610--5600640 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5600600 ATTTCGTTTG
*
5600610 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5600625 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5600640 G
1 G
5600641 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:5601975 original size:13 final size:13
Alignment explanation
Indices: 5601957--5601982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5601947 TACAGCAAGT
5601957 ATGTATCGATACA
1 ATGTATCGATACA
5601970 ATGTATCGATACA
1 ATGTATCGATACA
5601983 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5602505 original size:34 final size:35
Alignment explanation
Indices: 5602442--5602508 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
5602432 CTAAGTGATT
5602442 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
5602478 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
5602509 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:5605702 original size:13 final size:13
Alignment explanation
Indices: 5605684--5605708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5605674 TTTTCCAGAT
5605684 TGTATCGATACAA
1 TGTATCGATACAA
5605697 TGTATCGATACA
1 TGTATCGATACA
5605709 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5607636 original size:13 final size:13
Alignment explanation
Indices: 5607618--5607643 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5607608 TACAGCAAGT
5607618 ATGTATCGATACA
1 ATGTATCGATACA
5607631 ATGTATCGATACA
1 ATGTATCGATACA
5607644 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5608166 original size:34 final size:35
Alignment explanation
Indices: 5608103--5608169 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
5608093 CTAAGTGATT
5608103 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
5608139 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
5608170 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:5609324 original size:21 final size:21
Alignment explanation
Indices: 5609295--5609339 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5609285 AAGTTTTCAT
*
5609295 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
5609315 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
5609337 TTT
1 TTT
5609340 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:5611576 original size:13 final size:13
Alignment explanation
Indices: 5611558--5611583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5611548 CAATTTTTTG
5611558 TGTATCGATACAT
1 TGTATCGATACAT
5611571 TGTATCGATACAT
1 TGTATCGATACAT
5611584 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5613071 original size:21 final size:21
Alignment explanation
Indices: 5613014--5613073 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
5613004 TTTTTATTAG
5613014 CCAACTCA-TCATTTTCATTTT
1 CCAACTCATTCATTTTC-TTTT
*
5613035 GCAACTCATTTC-TTTTCTTTT
1 CCAACTCA-TTCATTTTCTTTT
*
5613056 CCAACTTATTCATTTTCT
1 CCAACTCATTCATTTTCT
5613074 CCTCTAGTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.09
21 23 0.70
22 5 0.15
23 2 0.06
ACGTcount: A:0.20, C:0.27, G:0.02, T:0.52
Consensus pattern (21 bp):
CCAACTCATTCATTTTCTTTT
Found at i:5618546 original size:13 final size:13
Alignment explanation
Indices: 5618528--5618555 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5618518 ATACAAAGAT
5618528 CAATGTATCGATA
1 CAATGTATCGATA
5618541 CAATGTATCGATA
1 CAATGTATCGATA
5618554 CA
1 CA
5618556 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:5618552 original size:33 final size:33
Alignment explanation
Indices: 5618510--5618575 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5618500 AAATTCCTAG
5618510 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
5618543 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
5618576 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:5626814 original size:25 final size:25
Alignment explanation
Indices: 5626786--5626855 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
5626776 ATATATATTT
5626786 TATATCAAAATGATTAAATGATTAA
1 TATATCAAAATGATTAAATGATTAA
** **
5626811 TATAT-AAAAAAATATAAAAAATTAA
1 TATATCAAAATGAT-TAAATGATTAA
5626836 TATATCAAAATGATTAAATG
1 TATATCAAAATGATTAAATG
5626856 GGGTAAAGCT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
24 6 0.17
25 23 0.66
26 6 0.17
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.33
Consensus pattern (25 bp):
TATATCAAAATGATTAAATGATTAA
Found at i:5627652 original size:11 final size:11
Alignment explanation
Indices: 5627616--5627669 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
5627606 AAATTTATTT
5627616 TATTATTTATTA
1 TATTATTT-TTA
***
5627628 TATTATTAAAA
1 TATTATTTTTA
5627639 TATTATTTTTA
1 TATTATTTTTA
5627650 TATTATTATTTA
1 TATTATT-TTTA
5627662 TA-TATTTT
1 TATTATTTT
5627670 ATAACTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 2 0.06
11 20 0.57
12 13 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:5627656 original size:14 final size:14
Alignment explanation
Indices: 5627615--5627671 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
5627605 AAAATTTATT
5627615 TTATTATTTAT-TA
1 TTATTATTTATATA
5627628 -TATTA-TTA-A-A
1 TTATTATTTATATA
* *
5627638 ATATTATTTTTATA
1 TTATTATTTATATA
5627652 TTATTATTTATATA
1 TTATTATTTATATA
5627666 TT-TTAT
1 TTATTAT
5627672 AACTAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
10 1 0.03
11 8 0.22
12 7 0.19
13 5 0.14
14 15 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTATTTATATA
Found at i:5628096 original size:22 final size:22
Alignment explanation
Indices: 5628071--5628114 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5628061 AATTTTTATC
*
5628071 TTATAAT-GTAATTATATATTTT
1 TTATAATAATAATTATA-ATTTT
5628093 TTATAATAATAATTATAATTTT
1 TTATAATAATAATTATAATTTT
5628115 ATTTTATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATAATAATAATTATAATTTT
Found at i:5628119 original size:25 final size:23
Alignment explanation
Indices: 5628064--5628121 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
5628054 ATTATAAAAT
* *
5628064 TTTTATCTTATAATGTAATTATA
1 TTTTATTTTATAATATAATTATA
*
5628087 TATT-TTTTATAATAATAATTATAA
1 TTTTATTTTATAAT-ATAATTAT-A
5628111 TTTTATTTTAT
1 TTTTATTTTAT
5628122 TAGTTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 8 0.29
23 10 0.36
24 4 0.14
25 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTATTTTATAATATAATTATA
Found at i:5629282 original size:14 final size:15
Alignment explanation
Indices: 5629263--5629293 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5629253 ATTTTAAGAG
5629263 TTTAAAATTTA-AAT
1 TTTAAAATTTATAAT
5629277 TTTAAAATTTATAAT
1 TTTAAAATTTATAAT
5629292 TT
1 TT
5629294 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAAATTTATAAT
Found at i:5631161 original size:12 final size:12
Alignment explanation
Indices: 5631133--5631166 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5631123 TGAATACGTG
5631133 TATTTATA-TAA
1 TATTTATATTAA
5631144 TATTTATATTAA
1 TATTTATATTAA
*
5631156 TTTTTATATTA
1 TATTTATATTA
5631167 TAATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTATATTAA
Found at i:5631167 original size:17 final size:17
Alignment explanation
Indices: 5631147--5631251 Score: 50
Period size: 17 Copynumber: 6.4 Consensus size: 17
5631137 TATATAATAT
5631147 TTATATTAATTTTTATA
1 TTATATTAATTTTTATA
*
5631164 -T-TA-TAA-TTAT-TA
1 TTATATTAATTTTTATA
*
5631176 TTATA-TAAATTTTA-A
1 TTATATTAATTTTTATA
* *
5631191 -TATATTTATTTGTGTCATG
1 TTATATTAATTT-T-T-ATA
5631210 TTTATATTTAA-TTTTATA
1 T-TATA-TTAATTTTTATA
5631228 TTATTATT-ATTTTTATA
1 TTA-TATTAATTTTTATA
5631245 TTATATT
1 TTATATT
5631252 CATATTACGA
Statistics
Matches: 67, Mismatches: 7, Indels: 29
0.65 0.07 0.28
Matches are distributed among these distances:
12 2 0.03
13 4 0.06
14 12 0.18
15 10 0.15
16 7 0.10
17 15 0.22
18 6 0.09
19 1 0.01
20 1 0.01
21 6 0.09
22 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (17 bp):
TTATATTAATTTTTATA
Found at i:5632105 original size:3 final size:3
Alignment explanation
Indices: 5632097--5632129 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5632087 TGTTGTATAA
5632097 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5632130 TATTGAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5633510 original size:17 final size:16
Alignment explanation
Indices: 5633469--5633550 Score: 71
Period size: 17 Copynumber: 5.0 Consensus size: 16
5633459 TGATAATACA
5633469 TATATTTATATATTAT
1 TATATTTATATATTAT
*
5633485 ATAAAATTTAATATATTAT
1 -T-ATATTT-ATATATTAT
*
5633504 TATATTTTTATTATTAT
1 TATATTTATA-TATTAT
*
5633521 TATA-TTATATTTTAAT
1 TATATTTATATATT-AT
5633537 TAT-TTT-TATATTAT
1 TATATTTATATATTAT
5633551 ATTTAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.04
15 8 0.15
16 13 0.24
17 16 0.30
18 6 0.11
19 9 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTTATATATTAT
Found at i:5633526 original size:22 final size:22
Alignment explanation
Indices: 5633501--5633554 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5633491 TTTAATATAT
*
5633501 TATTATATTTTTATTATTATTA
1 TATTATATTTTAATTATTATTA
*
5633523 TATTATATTTTAATTATTTTTA
1 TATTATATTTTAATTATTATTA
5633545 TATTATATTT
1 TATTATATTT
5633555 AAAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTATATTTTAATTATTATTA
Found at i:5633555 original size:11 final size:11
Alignment explanation
Indices: 5633501--5633555 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
5633491 TTTAATATAT
*
5633501 TATTATATTTT
1 TATTATATTTA
5633512 TATTAT-TATTA
1 TATTATAT-TTA
5633523 TATTATATTT-
1 TATTATATTTA
*
5633533 TAATTATTTTTA
1 T-ATTATATTTA
5633545 TATTATATTTA
1 TATTATATTTA
5633556 AAATTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 2 0.05
11 33 0.89
12 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATATTTA
Found at i:5633563 original size:20 final size:22
Alignment explanation
Indices: 5633501--5633564 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
5633491 TTTAATATAT
* * *
5633501 TATTATATTTTTATTATTATTA
1 TATTATATTTTAATAATTTTTA
*
5633523 TATTATATTTTAATTATTTTTA
1 TATTATATTTTAATAATTTTTA
5633545 TATTATA-TTTAA-AATTTTTA
1 TATTATATTTTAATAATTTTTA
5633565 AATGCAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 7 0.18
21 5 0.13
22 27 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTATATTTTAATAATTTTTA
Found at i:5638515 original size:16 final size:17
Alignment explanation
Indices: 5638477--5638516 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
5638467 CATGTACTGC
5638477 AAGAAGAAAGTAGGTTG
1 AAGAAGAAAGTAGGTTG
* *
5638494 AGGAAGAAAG-AGTTTG
1 AAGAAGAAAGTAGGTTG
5638510 AAGAAGA
1 AAGAAGA
5638517 GATGGACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (17 bp):
AAGAAGAAAGTAGGTTG
Found at i:5644752 original size:18 final size:18
Alignment explanation
Indices: 5644725--5644764 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5644715 TTAATTATAA
*
5644725 ATAAATATAAATATTAAT
1 ATAAAAATAAATATTAAT
* *
5644743 ATAAAAATAATTTTTAAT
1 ATAAAAATAAATATTAAT
5644761 ATAA
1 ATAA
5644765 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAAATAAATATTAAT
Found at i:5645104 original size:2 final size:2
Alignment explanation
Indices: 5645097--5645130 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5645087 ATTTGAATGA
5645097 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
5645131 TCAAATGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5645650 original size:2 final size:2
Alignment explanation
Indices: 5645645--5645699 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
5645635 ATATATATAT
5645645 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5645686 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
5645700 GTTGGTAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5646382 original size:24 final size:24
Alignment explanation
Indices: 5646327--5646375 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5646317 AAATTACTAA
* **
5646327 AAATTTAAAATTATTTTATTCATC
1 AAATTAAAAATTATTTTACCCATC
5646351 AAATTAAAAATTATTTTACCCATC
1 AAATTAAAAATTATTTTACCCATC
5646375 A
1 A
5646376 TTTTAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATTAAAAATTATTTTACCCATC
Found at i:5646622 original size:31 final size:31
Alignment explanation
Indices: 5646565--5646645 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
5646555 ATTAGCATAT
* *
5646565 ATAT-TATTTTATAACTTTATACTATTATATA
1 ATATGTATTATATAATTTTATACTATTA-ATA
*
5646596 ATATGTA-TATATAATTTTA-ACATATTAATC
1 ATATGTATTATATAATTTTATAC-TATTAATA
*
5646626 ATTTGTATTATATAAATTTT
1 ATATGTATTATAT-AATTTT
5646646 TACACGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
30 10 0.24
31 24 0.57
32 8 0.19
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (31 bp):
ATATGTATTATATAATTTTATACTATTAATA
Found at i:5649025 original size:3 final size:3
Alignment explanation
Indices: 5649019--5649197 Score: 214
Period size: 3 Copynumber: 59.7 Consensus size: 3
5649009 TGGTGGTGAT
*
5649019 GGA GGA GGA GGA GGA GGA GGA GGA GGG GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
* * * * * * * * * *
5649067 GGA GGG GGA GGA GGG GGA GGT GGT GGT GGT GGT GGT GGG GGA GGA GGG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
*
5649115 GGA GGA GGA GGA GGA GGA GGA GGA GGG GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
* * * *
5649163 GGT GGT GGT GGA GGA GGA GGA GGA GGG GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
5649198 TGGTGGTGGT
Statistics
Matches: 159, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 159 1.00
ACGTcount: A:0.24, C:0.00, G:0.71, T:0.05
Consensus pattern (3 bp):
GGA
Found at i:5650582 original size:6 final size:6
Alignment explanation
Indices: 5650571--5650596 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5650561 CCAGAAGGGA
5650571 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
5650597 AATTTTGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:5651650 original size:2 final size:2
Alignment explanation
Indices: 5651643--5651676 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5651633 TTTGTTTATA
5651643 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5651677 CACCAAAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5654172 original size:15 final size:16
Alignment explanation
Indices: 5654142--5654176 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5654132 TTTTAATATT
5654142 TAAAATTTAATAAAAA
1 TAAAATTTAATAAAAA
*
5654158 TAAAA-TTATTAAAAA
1 TAAAATTTAATAAAAA
5654173 TAAA
1 TAAA
5654177 TAAAAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAATTTAATAAAAA
Found at i:5655629 original size:16 final size:17
Alignment explanation
Indices: 5655608--5655672 Score: 50
Period size: 16 Copynumber: 4.0 Consensus size: 17
5655598 GTCATAATCG
*
5655608 TATTTA-ATATATTTTA
1 TATTTATATAAATTTTA
5655624 TATTTATATAAATTTTGA
1 TATTTATATAAATTTT-A
* *
5655642 TACGTTA-AT-AA-TTTG
1 TA-TTTATATAAATTTTA
5655657 TA-TTATATAAATTTTA
1 TATTTATATAAATTTTA
5655673 AGATATTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 4 0.10
16 12 0.31
17 10 0.26
18 5 0.13
19 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (17 bp):
TATTTATATAAATTTTA
Found at i:5662029 original size:27 final size:27
Alignment explanation
Indices: 5661999--5662051 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5661989 ATTAGTACTT
5661999 AATATTAATATTTAATG-TAT-ATATTTA
1 AATA-TAA-ATTTAATGATATAATATTTA
5662026 AATATAAATTTAATGATATAATATTT
1 AATATAAATTTAATGATATAATATTT
5662052 TAAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 8 0.33
26 6 0.25
27 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
AATATAAATTTAATGATATAATATTTA
Found at i:5662065 original size:27 final size:23
Alignment explanation
Indices: 5662005--5662062 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
5661995 ACTTAATATT
5662005 AATATTTAATGTATATATTTAAA
1 AATATTTAATGTATATATTTAAA
*
5662028 TATAAATTTAATGATATAATATTTTAAA
1 -A-ATATTTAATG-TAT-ATA-TTTAAA
5662056 AATATTT
1 AATATTT
5662063 TAAATACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
24 1 0.04
25 9 0.32
26 8 0.29
27 4 0.14
28 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
AATATTTAATGTATATATTTAAA
Found at i:5662219 original size:2 final size:2
Alignment explanation
Indices: 5662212--5662243 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5662202 TTAATATTCC
5662212 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5662244 GGGTTGGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5663980 original size:3 final size:3
Alignment explanation
Indices: 5663972--5664020 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5663962 TTTCTACTGG
5663972 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5664020 A
1 A
5664021 AAACATGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5664765 original size:31 final size:31
Alignment explanation
Indices: 5664729--5664787 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5664719 ATATTAATAA
5664729 TTTATATTAT-ATAAATTTTAAAATATTTTAC
1 TTTATATTATAATAAA-TTTAAAATATTTTAC
* *
5664760 TTTATATTTTAATAAATTTACAATATTT
1 TTTATATTATAATAAATTTAAAATATTT
5664788 ATGTAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
TTTATATTATAATAAATTTAAAATATTTTAC
Found at i:5665858 original size:15 final size:15
Alignment explanation
Indices: 5665838--5665879 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
5665828 AATAAAATAT
5665838 ATAAATATTAATAAA
1 ATAAATATTAATAAA
* *
5665853 ATAAATTTTAATAGA
1 ATAAATATTAATAAA
*
5665868 ATAAATAATAAT
1 ATAAATATTAAT
5665880 TCGAGCCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAATATTAATAAA
Found at i:5679353 original size:16 final size:16
Alignment explanation
Indices: 5679332--5679390 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
5679322 TAATCTAAAC
*
5679332 TTAAAATGATTCGAAT
1 TTAAAATAATTCGAAT
*
5679348 TTAAAATAACTCGAAT
1 TTAAAATAATTCGAAT
*
5679364 TTAAAATAATTCAAAT
1 TTAAAATAATTCGAAT
*
5679380 CTAAAATAATT
1 TTAAAATAATT
5679391 TAAATCTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (16 bp):
TTAAAATAATTCGAAT
Found at i:5679401 original size:32 final size:32
Alignment explanation
Indices: 5679333--5679407 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
5679323 AATCTAAACT
* * * * *
5679333 TAAAATGATTCGAATTTAAAATAACTCGAATT
1 TAAAATAATTCAAATCTAAAATAACTCAAATC
* *
5679365 TAAAATAATTCAAATCTAAAATAATTTAAATC
1 TAAAATAATTCAAATCTAAAATAACTCAAATC
5679397 TAAAAATAATT
1 T-AAAATAATT
5679408 TAAAAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (32 bp):
TAAAATAATTCAAATCTAAAATAACTCAAATC
Found at i:5679404 original size:17 final size:16
Alignment explanation
Indices: 5679365--5679411 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
5679355 AACTCGAATT
*
5679365 TAAAATAATTCAAATC
1 TAAAATAATTTAAATC
5679381 TAAAATAATTTAAATC
1 TAAAATAATTTAAATC
5679397 TAAAAATAATTTAAA
1 T-AAAATAATTTAAA
5679412 AATTTTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATAATTTAAATC
Found at i:5679444 original size:14 final size:15
Alignment explanation
Indices: 5679420--5679460 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
5679410 AAAATTTTAT
5679420 AATTCAAAATAACTT-
1 AATT-AAAATAACTTA
*
5679435 ATTTAAAATAACTTA
1 AATTAAAATAACTTA
5679450 AATTAAAATAA
1 AATTAAAATAA
5679461 ACTCAACCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTAAAATAACTTA
Found at i:5680064 original size:32 final size:33
Alignment explanation
Indices: 5680001--5680066 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
5679991 AATTTAACTC
* * *
5680001 AAAATCAATTTAAATTTAAAAATTTTTAAATTT
1 AAAATCAACTTAAATTTAAAAATATTCAAATTT
*
5680034 AAAAT-AACTTAATTTTAAAAATATTCAAATTT
1 AAAATCAACTTAAATTTAAAAATATTCAAATTT
5680066 A
1 A
5680067 TCTAATCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (33 bp):
AAAATCAACTTAAATTTAAAAATATTCAAATTT
Found at i:5680066 original size:16 final size:15
Alignment explanation
Indices: 5680010--5680066 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
5680000 CAAAATCAAT
*
5680010 TTAAATTTAAAAATTT
1 TTAAATTTAAAAA-TA
5680026 TTAAATTT-AAAATAA
1 TTAAATTTAAAAAT-A
*
5680041 CTTAATTTTAAAAATA
1 -TTAAATTTAAAAATA
5680057 TTCAAATTTA
1 TT-AAATTTA
5680067 TCTAATCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 6 0.18
16 22 0.65
17 5 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAAATTTAAAAATA
Done.