Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 10 of 120
Found at i:2977328 original size:93 final size:92
Alignment explanation
Indices: 2977166--2977443 Score: 337
Period size: 93 Copynumber: 3.0 Consensus size: 92
2977156 TGATGCCAAT
* * * *
2977166 TTATGGTTTTGGTGCTTTTATTATATCTAGATTTGGGATTTAGTCCTTATAATTTAATTTGACAT
1 TTATGGTTTTGGT-CTTTTATTATA-CCAGATTTGAGATTTAGTCCCTATAATTTAATTTAACAT
2977231 AATTTTTCTAT-TACTTTTATAATATCAAA
64 AATTTTTC-ATCTACTTTTATAATATCAAA
*
2977260 TTATGGTTTTGGTCATTTTATTATACCGGGATTTGAGA-TTAGTCCCTATAATTTAATTTAACAT
1 TTATGGTTTTGGTC-TTTTATTATACC-AGATTTGAGATTTAGTCCCTATAATTTAATTTAACAT
*
2977324 AATTTTTCATCAACTTTTATAATATCAAA
64 AATTTTTCATCTACTTTTATAATATCAAA
* * * ** *
2977353 TTGTGATTTTGGTCCTTTTATTATACTCATATAGGAGATTTAGTCCCTATCATTTAATTTGACAC
1 TTATGGTTTTGGT-CTTTTATTATAC-CAGATTTGAGATTTAGTCCCTATAATTTAATTT-A-AC
*
2977418 A-AAATTTTCATCTACTTTTATAATAT
62 ATAATTTTTCATCTACTTTTATAATAT
2977444 AATTAGTTGC
Statistics
Matches: 161, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
92 2 0.01
93 79 0.49
94 53 0.33
95 24 0.15
96 3 0.02
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.49
Consensus pattern (92 bp):
TTATGGTTTTGGTCTTTTATTATACCAGATTTGAGATTTAGTCCCTATAATTTAATTTAACATAA
TTTTTCATCTACTTTTATAATATCAAA
Found at i:2977722 original size:90 final size:90
Alignment explanation
Indices: 2977565--2977733 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 90
2977555 CGATTAAACC
*
2977565 ATGATTTAGTTAGTCCAAATAATTACCATGGTTAATAATTTCGATTAAAGCGTTGAAGTGGAATT
1 ATGATTTAGTTAGTCCAAATAATTACCATGATTAATAATTTCGATTAAAGCGTTGAAGTGGAATT
*
2977630 TTCCTTAAACATACACGGTTAAGCA
66 TTCCGTAAACATACACGGTTAAGCA
* ** *
2977655 ATGATTTAGTTAGTCCAAATAATTATCATGATTAATAATTTC-AGTTAAATTGTTGAGGT-GAAT
1 ATGATTTAGTTAGTCCAAATAATTACCATGATTAATAATTTCGA-TTAAAGCGTTGAAGTGGAA-
2977718 TTTTCCGTAAACATAC
64 TTTTCCGTAAACATAC
2977734 TTATTCTGAT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
89 4 0.06
90 67 0.94
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (90 bp):
ATGATTTAGTTAGTCCAAATAATTACCATGATTAATAATTTCGATTAAAGCGTTGAAGTGGAATT
TTCCGTAAACATACACGGTTAAGCA
Found at i:2981603 original size:16 final size:16
Alignment explanation
Indices: 2981574--2981681 Score: 65
Period size: 16 Copynumber: 6.1 Consensus size: 16
2981564 CCGATATAAT
*
2981574 AAATATATTT-ATTTTT
1 AAATAT-TTTAATTTTA
*
2981590 AAATTTTTTAATTTTA
1 AAATATTTTAATTTTA
*
2981606 AAATATTTTAAAATACTTTT
1 AAATATTTT--AAT--TTTA
* *
2981626 TATTATTTTAATTTTA
1 AAATATTTTAATTTTA
2981642 AAATATTTTAAAATATTTTA
1 AAATATTTT---A-ATTTTA
2981662 AAATATTTTTTAATTTTA
1 AAATA--TTTTAATTTTA
2981680 AA
1 AA
2981682 TAATTTTAGT
Statistics
Matches: 72, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
15 3 0.04
16 28 0.39
18 14 0.19
19 2 0.03
20 21 0.29
22 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTTAATTTTA
Found at i:2981658 original size:26 final size:26
Alignment explanation
Indices: 2981610--2981662 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2981600 ATTTTAAAAT
* *
2981610 ATTTTAAAATACTTTTTATTATTTTA
1 ATTTTAAAATACTTTTAAATATTTTA
2981636 ATTTTAAAATA-TTTTAAAATATTTTA
1 ATTTTAAAATACTTTT-AAATATTTTA
2981662 A
1 A
2981663 AATATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAAAATACTTTTAAATATTTTA
Found at i:2981689 original size:10 final size:10
Alignment explanation
Indices: 2981600--2981670 Score: 80
Period size: 10 Copynumber: 7.5 Consensus size: 10
2981590 AAATTTTTTA
2981600 ATTTTAAAAT
1 ATTTTAAAAT
2981610 ATTTTAAAAT
1 ATTTTAAAAT
* *
2981620 ACTTTT-TATT
1 A-TTTTAAAAT
2981630 ATTTT---A-
1 ATTTTAAAAT
2981636 ATTTTAAAAT
1 ATTTTAAAAT
2981646 ATTTTAAAAT
1 ATTTTAAAAT
2981656 ATTTTAAAAT
1 ATTTTAAAAT
2981666 ATTTT
1 ATTTT
2981671 TTAATTTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
6 5 0.09
9 5 0.09
10 39 0.74
11 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:2981702 original size:38 final size:39
Alignment explanation
Indices: 2981595--2981689 Score: 130
Period size: 36 Copynumber: 2.5 Consensus size: 39
2981585 TTTTTAAATT
2981595 TTTTAATTTTAAAATATTTTAAAATACTTTT----TATTA
1 TTTTAATTTTAAAATATTTTAAAATA-TTTTAAAATATTA
2981631 TTTTAATTTTAAAATATTTTAAAATATTTTAAAATATT-
1 TTTTAATTTTAAAATATTTTAAAATATTTTAAAATATTA
2981669 TTTTAATTTT-AAATAATTTTA
1 TTTTAATTTTAAAAT-ATTTTA
2981690 GTATTTATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
35 4 0.07
36 26 0.48
37 4 0.07
38 16 0.30
39 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (39 bp):
TTTTAATTTTAAAATATTTTAAAATATTTTAAAATATTA
Found at i:2982956 original size:21 final size:22
Alignment explanation
Indices: 2982918--2982971 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2982908 ATTCATACAG
*
2982918 AAAATAAAACGTAATAATAA-T
1 AAAATAAAAGGTAATAATAACT
*
2982939 AAAAATAAAAGGT-GTAATAAGCT
1 -AAAATAAAAGGTAATAATAA-CT
2982962 AAAATAAAAG
1 AAAATAAAAG
2982972 TTGGTCCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 6 0.21
22 21 0.75
23 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAATAAAAGGTAATAATAACT
Found at i:2984031 original size:66 final size:66
Alignment explanation
Indices: 2983949--2984082 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
2983939 GGCATAGCCA
2983949 ATACACCTCTAATCAGTGGGTCTTACTTAATACCCCTTTAATACTTTGTTTGGTTGAGGTATTCT
1 ATACACCTCTAATCAGTGGGTCTTACTTAATACCCCTTTAATACTTTGTTTGGTTGAGGTATTCT
2984014 T
66 T
2984015 ATACACCTCTAATCAGTGGGTCTTACTTAATACCCCTTTAATACTTTGTTTGGTTGAGGTATTCT
1 ATACACCTCTAATCAGTGGGTCTTACTTAATACCCCTTTAATACTTTGTTTGGTTGAGGTATTCT
2984080 T
66 T
2984081 AT
1 AT
2984083 TACAGGTCTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (66 bp):
ATACACCTCTAATCAGTGGGTCTTACTTAATACCCCTTTAATACTTTGTTTGGTTGAGGTATTCT
T
Found at i:2984297 original size:36 final size:36
Alignment explanation
Indices: 2984251--2984329 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
2984241 ACTTCACAAC
* *
2984251 TTAGCCGTTCCTTCTATTTCTTCTTTCTGTTTCAGT
1 TTAGCTGTTCCTTCTATTTCTTCCTTCTGTTTCAGT
*
2984287 TTAGCTGTTCCTTCTGTTTCTTCCTTCTGTTTCAGT
1 TTAGCTGTTCCTTCTATTTCTTCCTTCTGTTTCAGT
2984323 TTAGCTG
1 TTAGCTG
2984330 CTTCACAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (36 bp):
TTAGCTGTTCCTTCTATTTCTTCCTTCTGTTTCAGT
Found at i:2984312 original size:13 final size:13
Alignment explanation
Indices: 2984294--2984319 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2984284 AGTTTAGCTG
2984294 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
2984307 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
2984320 AGTTTAGCTG
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:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
TTCCTTCTGTTTC
Found at i:2993025 original size:138 final size:138
Alignment explanation
Indices: 2992777--2993054 Score: 511
Period size: 138 Copynumber: 2.0 Consensus size: 138
2992767 GAGGCTTAAA
* *
2992777 AACGTATGGATGCTTTGAGGAGTCCCTGTTTTGAATTTTAGAATCATATGTAATTTCTTTAAAAA
1 AACGTATGGATGCTTTCAGGAGTCCCTGTTTTGAATTTTAGAACCATATGTAATTTCTTTAAAAA
2992842 TTGGCATTAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTA
66 TTGGCATTAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTA
2992907 TTTGATTT
131 TTTGATTT
* *
2992915 AACGTCTGGATGCTTTCAGGAGTCCCTGTTTTGAATTTTAGAACCATATGTAATTTCTTTAGAAA
1 AACGTATGGATGCTTTCAGGAGTCCCTGTTTTGAATTTTAGAACCATATGTAATTTCTTTAAAAA
*
2992980 TTGGCATTAAATTGTTTTTAGGTTTTATATTAACATTTCTCTTTGTTATGTTATTATGCAACTTA
66 TTGGCATTAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTA
2993045 TTTGATTT
131 TTTGATTT
2993053 AA
1 AA
2993055 AATTTTACAA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (138 bp):
AACGTATGGATGCTTTCAGGAGTCCCTGTTTTGAATTTTAGAACCATATGTAATTTCTTTAAAAA
TTGGCATTAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTA
TTTGATTT
Found at i:3001473 original size:18 final size:18
Alignment explanation
Indices: 3001440--3001474 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3001430 TTGCAATTTG
*
3001440 TCAAAATGTTCACAATAT
1 TCAAAATGGTCACAATAT
*
3001458 TCAAAATGGTCTCAATA
1 TCAAAATGGTCACAATA
3001475 CTAACACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (18 bp):
TCAAAATGGTCACAATAT
Found at i:3004122 original size:26 final size:26
Alignment explanation
Indices: 3004073--3004122 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3004063 TGGTTTCCTT
*
3004073 AACTATAGTTTCTTATTCTTCAAGTA
1 AACTATAGTTTCTTATTCTACAAGTA
*
3004099 AACTTTAGTTTCTTAGTT-TACAAG
1 AACTATAGTTTCTTA-TTCTACAAG
3004123 AATAAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (26 bp):
AACTATAGTTTCTTATTCTACAAGTA
Found at i:3004285 original size:29 final size:29
Alignment explanation
Indices: 3004227--3004286 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
3004217 TTCTAATGAG
** *
3004227 TCTAAGGTTAGGAGCTCCATTTGACTAGT
1 TCTAAGGTTAGGAGCTCCATTCAACGAGT
*
3004256 TCTAAGGTTAGGAGCTCCCTTCAACGAGT
1 TCTAAGGTTAGGAGCTCCATTCAACGAGT
3004285 TC
1 TC
3004287 CATACGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (29 bp):
TCTAAGGTTAGGAGCTCCATTCAACGAGT
Found at i:3033402 original size:11 final size:12
Alignment explanation
Indices: 3033385--3033413 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3033375 ATCATTAATA
3033385 AATAAATGAGTC
1 AATAAATGAGTC
3033397 -ATAAATGAGTC
1 AATAAATGAGTC
3033408 AATAAA
1 AATAAA
3033414 CAAGCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (12 bp):
AATAAATGAGTC
Found at i:3037641 original size:2 final size:2
Alignment explanation
Indices: 3037634--3037664 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3037624 TATTTTGAAT
3037634 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3037665 TTTATTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3038708 original size:110 final size:108
Alignment explanation
Indices: 3038513--3038822 Score: 442
Period size: 110 Copynumber: 2.8 Consensus size: 108
3038503 AAAATTCAAG
* * *
3038513 AGGATATTTAGCAATTTGG-CTAAACGTGAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGA
1 AGGATATTTAGCTATTTGGTC-GAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGA
*
3038577 ATTTCCAAACGCAAAACATTGCCTTATTTTTTAAAAAGTTTTTAAA
65 ATTTCCAAACGCAAAATATTGCCTTA--TTTTAAAAAGTTTTTAAA
* * * *
3038623 AGGATTTTTAGCTATTTGGTCGAACGAGAAATCGAAACTCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGAA
* *
3038688 TTTCCAAACGCCAAATATTGCCTTATTTTGAAAAGTTTTTAAA
66 TTTCCAAACGCAAAATATTGCCTTATTTTAAAAAGTTTTTAAA
* *
3038731 AGGATATTTAGCTATTTGGTCGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTC
1 AGGATATTTAGCTATTTGGTCGAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTTCTC
3038796 GAATTTCCCAAACGCAAAATATTGCCT
63 GAATTT-CCAAACGCAAAATATTGCCT
3038823 CAATTTGAAA
Statistics
Matches: 178, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
108 44 0.25
110 103 0.58
111 12 0.07
112 19 0.11
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (108 bp):
AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGAA
TTTCCAAACGCAAAATATTGCCTTATTTTAAAAAGTTTTTAAA
Found at i:3039031 original size:18 final size:17
Alignment explanation
Indices: 3039010--3039058 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
3039000 ACATAAATGA
3039010 ACATAAAAAAATGAAAAT
1 ACATAAAAAAAT-AAAAT
**
3039028 ACATGAAAATTATAAAAT
1 ACAT-AAAAAAATAAAAT
*
3039046 ATATAAAAAAATA
1 ACATAAAAAAATA
3039059 TGTATGTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 7 0.28
18 12 0.48
19 6 0.24
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (17 bp):
ACATAAAAAAATAAAAT
Found at i:3039727 original size:3 final size:3
Alignment explanation
Indices: 3039678--3039756 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
3039668 AAATAAAAAC
* * * * * *
3039678 ATA ACA ATA ATA ACA ATA AGA TTA ATA A-A TATA CTA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
3039723 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3039757 AATTACTAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
2 1 0.02
3 60 0.97
4 1 0.02
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3042744 original size:15 final size:16
Alignment explanation
Indices: 3042724--3042753 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3042714 TTTCAAAATT
3042724 TTAAAAATA-TAAAAG
1 TTAAAAATAGTAAAAG
3042739 TTAAAAATAGTAAAA
1 TTAAAAATAGTAAAA
3042754 TTAGAGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
TTAAAAATAGTAAAAG
Found at i:3043816 original size:19 final size:17
Alignment explanation
Indices: 3043783--3043818 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
3043773 CCTAAATTCA
3043783 ATTAATAAAAACTTAAT
1 ATTAATAAAAACTTAAT
3043800 ATTATATAAAAATCTTAAT
1 ATTA-ATAAAAA-CTTAAT
3043819 CTAACACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAATAAAAACTTAAT
Found at i:3048520 original size:43 final size:46
Alignment explanation
Indices: 3048448--3048571 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 46
3048438 AATGTCATAT
* **
3048448 CCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG-C-CCATG
1 CCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGACGCCATG
* * *
3048492 -CCAGACATGGTGTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 CCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG---ACGCCATG
3048540 TCCCAGACATGGTCTTACATGGGACCTCTCAT
1 -CCCAGACATGGTCTTACATGGGACCTCTCAT
3048572 GATCTCAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 31 0.48
47 1 0.02
48 5 0.08
50 28 0.43
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (46 bp):
CCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGACGCCATG
Found at i:3048564 original size:50 final size:53
Alignment explanation
Indices: 3048492--3048616 Score: 175
Period size: 56 Copynumber: 2.4 Consensus size: 53
3048482 GGTGCCCATG
* *
3048492 CCAGACATGGTGTTACAGGGGACCTCTC-ATCTC-GG-TGCCAACGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCAATCTCAGGATGCCAACGCCATGTC
*
3048542 CCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAATGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCA--ATCTC-AGGATGCCAACGCCATGTC
3048598 CCAGACATGGTCTTACATG
1 CCAGACATGGTCTTACATG
3048617 AGATCTCTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
50 26 0.39
53 5 0.08
55 2 0.03
56 33 0.50
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.24
Consensus pattern (53 bp):
CCAGACATGGTCTTACATGGGACCTCTCAATCTCAGGATGCCAACGCCATGTC
Found at i:3048988 original size:30 final size:30
Alignment explanation
Indices: 3048954--3049011 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3048944 CTTCGACTCT
*
3048954 AACTTTGGCAAAATTACAATTTTGCCCCTA
1 AACTTTGACAAAATTACAATTTTGCCCCTA
* * *
3048984 AACTTTTACATAATTACGATTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
3049012 AAAGTTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:3050980 original size:18 final size:20
Alignment explanation
Indices: 3050961--3050999 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3050951 GAGCAGACCA
3050961 TGCAGCTAGAGCC-ATGCATGT
1 TGCAGCTAGAGCCTATGCA--T
3050982 TGCAGCTAGAGCCTATGC
1 TGCAGCTAGAGCCTATGC
3051000 TACTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (20 bp):
TGCAGCTAGAGCCTATGCAT
Found at i:3056619 original size:14 final size:14
Alignment explanation
Indices: 3056576--3056669 Score: 55
Period size: 14 Copynumber: 6.4 Consensus size: 14
3056566 AATTTGAATC
3056576 ATGTGAACCCCCTGT
1 ATGTGAA-CCCCTGT
* ** *
3056591 ACGTGAGTCCATGT
1 ATGTGAACCCCTGT
3056605 ATGTGAACCCCTGT
1 ATGTGAACCCCTGT
* *
3056619 ATGCGAACCAC-GAT
1 ATGTGAACCCCTG-T
* *
3056633 AGGCGAACCTCCTGT
1 ATGTGAACC-CCTGT
*
3056648 ATGTGAACTCCCATAT
1 ATGTGAAC-CCC-TGT
3056664 ATGTGA
1 ATGTGA
3056670 TCCCTTAGTG
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
13 1 0.02
14 33 0.56
15 15 0.25
16 10 0.17
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (14 bp):
ATGTGAACCCCTGT
Found at i:3056808 original size:15 final size:15
Alignment explanation
Indices: 3056766--3056831 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 15
3056756 ATGTGATTTA
*
3056766 ATATGTGAGAACCC-
1 ATATGTGCGAACCCT
**
3056780 ATACATGCGAACCCT
1 ATATGTGCGAACCCT
*
3056795 ATATGTGTGAACCCT
1 ATATGTGCGAACCCT
*
3056810 ATATGTGCGAACCTT
1 ATATGTGCGAACCCT
3056825 ATATGTG
1 ATATGTG
3056832 AACCTGTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
14 11 0.26
15 32 0.74
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (15 bp):
ATATGTGCGAACCCT
Found at i:3056808 original size:29 final size:30
Alignment explanation
Indices: 3056766--3056832 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
3056756 ATGTGATTTA
3056766 ATATGTGAGAACCC-ATACATGCGAACCCT
1 ATATGTGAGAACCCTATACATGCGAACCCT
* ** *
3056795 ATATGTGTGAACCCTATATGTGCGAACCTT
1 ATATGTGAGAACCCTATACATGCGAACCCT
3056825 ATATGTGA
1 ATATGTGA
3056833 ACCTGTTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (30 bp):
ATATGTGAGAACCCTATACATGCGAACCCT
Found at i:3059470 original size:15 final size:16
Alignment explanation
Indices: 3059445--3059474 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3059435 ACATGCTATA
3059445 AAAATAATATTTTAAT
1 AAAATAATATTTTAAT
3059461 AAAA-AATATTTTAA
1 AAAATAATATTTTAA
3059475 AATTATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATAATATTTTAAT
Found at i:3059567 original size:16 final size:16
Alignment explanation
Indices: 3059546--3059576 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3059536 AAACTTTTTT
3059546 TTATAAATGTTATATC
1 TTATAAATGTTATATC
*
3059562 TTATAAATTTTATAT
1 TTATAAATGTTATAT
3059577 TATTATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
TTATAAATGTTATATC
Found at i:3065604 original size:2 final size:2
Alignment explanation
Indices: 3065592--3065632 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3065582 CTCAATTTTC
3065592 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3065633 ACTNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3065745 original size:2 final size:2
Alignment explanation
Indices: 3065738--3065777 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3065728 NNNNNNNNCT
3065738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3065778 AATAACATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3066232 original size:24 final size:23
Alignment explanation
Indices: 3066188--3066234 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3066178 AGATAATTTA
** *
3066188 ATTAAAAAAATGTAAATTTAAAT
1 ATTAAAAAAATCAAAAATTAAAT
3066211 ATTAAAAAAGATCAAAAATTAAAT
1 ATTAAAAAA-ATCAAAAATTAAAT
3066235 GAATGACGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
ATTAAAAAAATCAAAAATTAAAT
Found at i:3081071 original size:3 final size:3
Alignment explanation
Indices: 3081065--3081123 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
3081055 TATGTTGCTC
3081065 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
3081113 ACT ATC ATT AT
1 ATT ATT ATT AT
3081124 ATTTATACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3081271 original size:6 final size:6
Alignment explanation
Indices: 3081254--3081296 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
3081244 AAATACTCAT
* *
3081254 TTTATA TCTATA TTTATA --TATA TGTATA TTTATA TTTATA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTT
3081297 TTCTCACGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 4 0.12
6 28 0.88
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (6 bp):
TTTATA
Found at i:3081281 original size:16 final size:16
Alignment explanation
Indices: 3081256--3081288 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3081246 ATACTCATTT
3081256 TATATCTATATTTATA
1 TATATCTATATTTATA
*
3081272 TATATGTATATTTATA
1 TATATCTATATTTATA
3081288 T
1 T
3081289 TTATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TATATCTATATTTATA
Found at i:3089818 original size:24 final size:24
Alignment explanation
Indices: 3089791--3089836 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3089781 ACATTTAACT
* *
3089791 TAATCGAATATGTTCATGAACATA
1 TAATCGAAAATGTTCACGAACATA
*
3089815 TAATTGAAAATGTTCACGAACA
1 TAATCGAAAATGTTCACGAACA
3089837 ATGTTCATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (24 bp):
TAATCGAAAATGTTCACGAACATA
Found at i:3093157 original size:3 final size:3
Alignment explanation
Indices: 3093142--3093226 Score: 73
Period size: 3 Copynumber: 28.0 Consensus size: 3
3093132 AAAAGGTATT
* *** * *
3093142 TAA TAA TAT TAA TAA TAA TAA GGC TAA TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3093190 TAGC T-T TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
3093227 ATAGTAGCAC
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 61 0.92
4 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3095876 original size:11 final size:11
Alignment explanation
Indices: 3095862--3095887 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3095852 TTTTAAATGA
3095862 TATTATTATTT
1 TATTATTATTT
3095873 TATTATTATTT
1 TATTATTATTT
3095884 TATT
1 TATT
3095888 TAGTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTATTT
Found at i:3097741 original size:45 final size:45
Alignment explanation
Indices: 3097668--3097908 Score: 351
Period size: 45 Copynumber: 5.4 Consensus size: 45
3097658 ATGTGCCGAC
** *
3097668 TACTGTTACTG-TACTGATTCGATACTTTGTGTGTCGAATACGGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
*
3097712 TACTGTTACTGTTA-TCGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACTGTTACT-GATTCGGCACTTTGTGTGTCGAATACTGT
* *
3097757 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTAT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
3097802 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
* * ** * *
3097847 TACCGTTACTGTTACAGATTCAACTCTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
3097892 TACTGTTACTGTTACTG
1 TACTGTTACTGTTACTG
3097909 CTACCATTAC
Statistics
Matches: 177, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
44 12 0.07
45 165 0.93
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:3101997 original size:15 final size:15
Alignment explanation
Indices: 3101964--3101996 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3101954 GATTGACTTG
3101964 TTTTATATTTTAATA
1 TTTTATATTTTAATA
3101979 TTTTATATTTTAAT-
1 TTTTATATTTTAATA
3101993 TTTT
1 TTTT
3101997 TTCTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATATTTTAATA
Found at i:3102689 original size:12 final size:11
Alignment explanation
Indices: 3102672--3102705 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
3102662 TCAAGAAATG
3102672 AGAAAAAGAACA
1 AGAAAAAGAA-A
3102684 AGAAAAAGAAA
1 AGAAAAAGAAA
3102695 AG-AAAAGAAA
1 AGAAAAAGAAA
3102705 A
1 A
3102706 TTTCTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 3 0.14
12 10 0.45
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:3104171 original size:24 final size:25
Alignment explanation
Indices: 3104130--3104181 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
3104120 TTTCGAGCAA
* * *
3104130 TTTAATTTTTCTTCTTTTATGTTCT
1 TTTAACTTTCCTTCTTTTATCTTCT
*
3104155 TTTAACTTTCCTT-TTTTTTCTTCT
1 TTTAACTTTCCTTCTTTTATCTTCT
3104179 TTT
1 TTT
3104182 TATTCAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTAACTTTCCTTCTTTTATCTTCT
Found at i:3106336 original size:13 final size:13
Alignment explanation
Indices: 3106318--3106344 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3106308 CTTATGTAAC
3106318 GAAGAAAGGTGCT
1 GAAGAAAGGTGCT
3106331 GAAGAAAGGTGCT
1 GAAGAAAGGTGCT
3106344 G
1 G
3106345 CTGAAGTGCT
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:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (13 bp):
GAAGAAAGGTGCT
Found at i:3115937 original size:3 final size:3
Alignment explanation
Indices: 3115929--3115966 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3115919 CAATTTCTAG
*
3115929 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3115967 CCCATAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3117776 original size:39 final size:39
Alignment explanation
Indices: 3117733--3117811 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
3117723 ATTATCGAGT
3117733 TAATACCATTTTACGTTGATGTATTGCATATACAAACAA
1 TAATACCATTTTACGTTGATGTATTGCATATACAAACAA
*
3117772 TAATACCATTTTACGTTGATTTATTGCATATACAAACAA
1 TAATACCATTTTACGTTGATGTATTGCATATACAAACAA
3117811 T
1 T
3117812 TATATTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (39 bp):
TAATACCATTTTACGTTGATGTATTGCATATACAAACAA
Found at i:3118578 original size:19 final size:19
Alignment explanation
Indices: 3118554--3118591 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3118544 CAAGTGTGTA
3118554 TCTACTTTAGTGGTTAAGT
1 TCTACTTTAGTGGTTAAGT
3118573 TCTACTTTAGTGGTTAAGT
1 TCTACTTTAGTGGTTAAGT
3118592 GTTTTTGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (19 bp):
TCTACTTTAGTGGTTAAGT
Found at i:3130443 original size:2 final size:2
Alignment explanation
Indices: 3130426--3130460 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3130416 GCTACTTTAT
3130426 TA TA T- TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3130461 GAGAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3133461 original size:45 final size:45
Alignment explanation
Indices: 3133410--3133498 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
3133400 TTTCCTATAG
3133410 ATTTTGATTTTCGGAACATGCCAATCAGATCTTCTAGAAGCTTAA
1 ATTTTGATTTTCGGAACATGCCAATCAGATCTTCTAGAAGCTTAA
3133455 ATTTTGATTTTCGGAACATGCCAATCAGATCTTCTAGAAGCTTA
1 ATTTTGATTTTCGGAACATGCCAATCAGATCTTCTAGAAGCTTA
3133499 CACTATTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (45 bp):
ATTTTGATTTTCGGAACATGCCAATCAGATCTTCTAGAAGCTTAA
Found at i:3138946 original size:18 final size:18
Alignment explanation
Indices: 3138923--3138960 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3138913 TTTTTAGTTA
*
3138923 TTTTATAAATTTATATAT
1 TTTTATAAATTTATAAAT
3138941 TTTTATAAATTTATAAAT
1 TTTTATAAATTTATAAAT
3138959 TT
1 TT
3138961 AGATTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATAAATTTATAAAT
Found at i:3144024 original size:27 final size:26
Alignment explanation
Indices: 3143923--3144075 Score: 171
Period size: 26 Copynumber: 5.7 Consensus size: 26
3143913 TACGAAGTTT
* *
3143923 GCCACAAAGGCATTCTTTCATATTAT
1 GCCACAAAGGCTTTCTTTCATATTAC
*
3143949 GCCACAAAGACTTTCTTTCATATTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
** *
3143975 ATCACAAAGGCTTTCTTTCATATTAT
1 GCCACAAAGGCTTTCTTTCATATTAC
*
3144001 GCCTCAAAGGCTTTTCTTTCATATTAC
1 GCCACAAAGGC-TTTCTTTCATATTAC
* * *
3144028 GTCATAAAGGCTTTTTTCTTCATATTAC
1 GCCACAAAGGC-TTTCT-TTCATATTAC
*
3144056 ACCACAAAGGCTTTTCTTTC
1 GCCACAAAGGC-TTTCTTTC
3144076 CTAACGTGTT
Statistics
Matches: 106, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
26 53 0.50
27 30 0.28
28 23 0.22
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (26 bp):
GCCACAAAGGCTTTCTTTCATATTAC
Found at i:3144074 original size:55 final size:53
Alignment explanation
Indices: 3143925--3144075 Score: 205
Period size: 52 Copynumber: 2.8 Consensus size: 53
3143915 CGAAGTTTGC
* *
3143925 CACAAAGGCATTCTTTCATATTATGCCACAAAGAC-TTTCTTTCATATTACAT
1 CACAAAGGCTTTCTTTCATATTATGCCACAAAGGCTTTTCTTTCATATTACAT
* *
3143977 CACAAAGGCTTTCTTTCATATTATGCCTCAAAGGCTTTTCTTTCATATTACGT
1 CACAAAGGCTTTCTTTCATATTATGCCACAAAGGCTTTTCTTTCATATTACAT
* * **
3144030 CATAAAGGCTTTTTTCTTCATATTACACCACAAAGGCTTTTCTTTC
1 CACAAAGGC-TTTCT-TTCATATTATGCCACAAAGGCTTTTCTTTC
3144076 CTAACGTGTT
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
52 32 0.37
53 24 0.28
54 4 0.05
55 27 0.31
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (53 bp):
CACAAAGGCTTTCTTTCATATTATGCCACAAAGGCTTTTCTTTCATATTACAT
Found at i:3144705 original size:20 final size:20
Alignment explanation
Indices: 3144661--3144705 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3144651 TTGTCACATC
* *
3144661 AAAATTTAATTAATTTTTTT
1 AAAATTTAATAAATATTTTT
3144681 AAAATTTAA-AAATATTTTT
1 AAAATTTAATAAATATTTTT
3144700 ATAAAT
1 A-AAAT
3144706 GTTACGCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATTTAATAAATATTTTT
Found at i:3144916 original size:9 final size:9
Alignment explanation
Indices: 3144865--3144898 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3144855 CAAAAAATAC
3144865 AAATT-AAA
1 AAATTAAAA
3144873 AAATTAAAA
1 AAATTAAAA
*
3144882 AAAGTAAAA
1 AAATTAAAA
3144891 AAATTAAA
1 AAATTAAA
3144899 TGAAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATTAAAA
Found at i:3150960 original size:23 final size:23
Alignment explanation
Indices: 3150921--3150976 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
3150911 GACTTGGGAG
3150921 TGAGTATTGGGTATGGGTATGGGCA
1 TGAGTA-T-GGTATGGGTATGGGCA
* *
3150946 TGGGTATGGTATGGGTATGGGTA
1 TGAGTATGGTATGGGTATGGGCA
3150969 TGAGTATG
1 TGAGTATG
3150977 AGTACGAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 22 0.79
24 1 0.04
25 5 0.18
ACGTcount: A:0.20, C:0.02, G:0.45, T:0.34
Consensus pattern (23 bp):
TGAGTATGGTATGGGTATGGGCA
Found at i:3150980 original size:6 final size:6
Alignment explanation
Indices: 3150928--3150976 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
3150918 GAGTGAGTAT
* *
3150928 TGGGTA TGGGTA TGGGCA TGGGTA T-GGTA TGGGTA TGGGTA TGAGTA
1 TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA
3150975 TG
1 TG
3150977 AGTACGAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (6 bp):
TGGGTA
Found at i:3151754 original size:27 final size:28
Alignment explanation
Indices: 3151712--3151767 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
3151702 GTTCTGAGTG
3151712 AAAAGAAATATGTTTT-GTTGAAATAGTA
1 AAAAGAAATATGTTTTAGTTG-AATAGTA
3151740 AAAAGAAATAT-TTTTAGTTGAATAGTA
1 AAAAGAAATATGTTTTAGTTGAATAGTA
3151767 A
1 A
3151768 GATTGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (28 bp):
AAAAGAAATATGTTTTAGTTGAATAGTA
Found at i:3154932 original size:3 final size:3
Alignment explanation
Indices: 3154924--3155125 Score: 120
Period size: 3 Copynumber: 67.3 Consensus size: 3
3154914 TAAATAAGTA
* * * * *
3154924 AAT AAT AAT AGT AAT ATT AAT AGT AGT AA- AAT AAAT AAAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT
* ** * *
3154970 AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TCT AAT GAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * ** * * * *
3155018 ACT AAT AAT AAT AGT AAG GGT AAT AAT AAT AAT ATT GAT AAT ACT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * ** *
3155066 AAT AAT AAT AAT CGT AAT AAT AA- ACT AAT TAG CTT AAT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3155113 AAT AAC AAT AAT A
1 AAT AAT AAT AAT A
3155126 GGACTAAATT
Statistics
Matches: 147, Mismatches: 49, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
2 3 0.02
3 137 0.93
4 7 0.05
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3158995 original size:57 final size:58
Alignment explanation
Indices: 3158826--3158998 Score: 147
Period size: 63 Copynumber: 2.9 Consensus size: 58
3158816 ATTGAATCTA
* * * * *
3158826 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAAATTTGCC--ATGTCTAGGTATCAAATTAGGCCC
1 AAAAAAAGCTTAGGTACCAAATTA-G-AAAAAA--TACCAAAT-TC-AAGTACCAAATT-GGGCT
* ** *
3158889 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAATTGGGCT
1 AAAAAAAGCTTAGGTACCAAATTA-GAAAAAATACCAAATTCAAGTACCAAATTGGGCT
*
3158948 AAAAAAA-CTTAGGTACCAAATTA-AAAAAACTACCAAATTTAAGTACCAAAT
1 AAAAAAAGCTTAGGTACCAAATTAGAAAAAA-TACCAAATTCAAGTACCAAAT
3158999 GTTATATTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
56 6 0.06
57 17 0.18
58 15 0.16
59 10 0.11
60 13 0.14
61 2 0.02
62 7 0.07
63 25 0.26
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (58 bp):
AAAAAAAGCTTAGGTACCAAATTAGAAAAAATACCAAATTCAAGTACCAAATTGGGCT
Found at i:3169345 original size:19 final size:18
Alignment explanation
Indices: 3169305--3169400 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 18
3169295 ATTTGAATTT
3169305 TTTTTTATAAATTCTTTACGA
1 TTTTTTAT-AATT-TTT-CGA
3169326 TTTTTTATAATTTTTGCGA
1 TTTTTTATAATTTTT-CGA
* * *
3169345 TTTCTATAAAATTTTTCTA
1 TTT-TTTATAATTTTTCGA
**
3169364 TTTTTATTATAATTTTTAAA
1 -TTTT-TTATAATTTTTCGA
3169384 TATTTTCTATAATTTTT
1 T-TTTT-TATAATTTTT
3169401 TATAAAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
19 14 0.23
20 40 0.65
21 8 0.13
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTTATAATTTTTCGA
Found at i:3169421 original size:31 final size:31
Alignment explanation
Indices: 3169351--3169431 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
3169341 GCGATTTCTA
**
3169351 TAAA-ATTTTTCTAT--TTTTATTATAATTTT
1 TAAATATTTTTCTATAATTTT-TTATAAAATT
3169380 TAAATAT-TTTCTATAATTTTTTATAAAATT
1 TAAATATTTTTCTATAATTTTTTATAAAATT
* *
3169410 TTAATATTTTTCTATAACTTTT
1 TAAATATTTTTCTATAATTTTT
3169432 ATCGATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 11 0.25
30 16 0.36
31 17 0.39
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (31 bp):
TAAATATTTTTCTATAATTTTTTATAAAATT
Found at i:3174036 original size:32 final size:31
Alignment explanation
Indices: 3173994--3174056 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
3173984 TTGAATTTAA
* *
3173994 TAAAATAAAACAAA-ACATTAAATTAAATATT
1 TAAAATAAAACAAATA-ATAAAATCAAATATT
3174025 TAAAAGTAAAACAAATAATAAAATCAAATATT
1 TAAAA-TAAAACAAATAATAAAATCAAATATT
3174057 CATATCCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.18
32 22 0.79
33 1 0.04
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (31 bp):
TAAAATAAAACAAATAATAAAATCAAATATT
Found at i:3183054 original size:29 final size:29
Alignment explanation
Indices: 3182925--3183090 Score: 154
Period size: 29 Copynumber: 5.6 Consensus size: 29
3182915 GTCATTAGGG
* *
3182925 TTTATCAGACACTATGTACAGGTGATTATA
1 TTTATCAGGCACTATGTACCGGTG-TTATA
* * **
3182955 TTTATCAGGTACTATGAACCGGTGGCCATA
1 TTTATCAGGCACTATGTACCGGT-GTTATA
* * * *
3182985 -TTATCAGGTACTTTGTATCGGTGTTCATG
1 TTTATCAGGCACTATGTACCGGTGTT-ATA
*
3183014 TTGTATCAGGCACTATGTGCCGGTGTTATA
1 TT-TATCAGGCACTATGTACCGGTGTTATA
* *
3183044 TTTATCAGGCACTATGTGCCAGTGTTATA
1 TTTATCAGGCACTATGTACCGGTGTTATA
**
3183073 TTTATCAGATACTATGTA
1 TTTATCAGGCACTATGTA
3183091 TAGGTGGTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
28 1 0.01
29 62 0.56
30 27 0.24
31 21 0.19
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (29 bp):
TTTATCAGGCACTATGTACCGGTGTTATA
Found at i:3183079 original size:89 final size:90
Alignment explanation
Indices: 3182927--3183096 Score: 209
Period size: 89 Copynumber: 1.9 Consensus size: 90
3182917 CATTAGGGTT
* *
3182927 TATCAGACACTATGTACAGGTGATTATATTTATCAGGTACTATGAACCGGTGGCCATATTATCAG
1 TATCAGACACTATGTACAGGTGATTATATTTATCAGGCACTATGAACCAGTGGCCATATTATCAG
* * *
3182992 GTACTTTGTATCGGTGTTCATGTTG
66 ATACTATGTATAGGTGTTCATGTTG
* * * ** **
3183017 TATCAGGCACTATGTGCCGGTG-TTATATTTATCAGGCACTATGTGCCAGT-GTTATATTTATCA
1 TATCAGACACTATGTACAGGTGATTATATTTATCAGGCACTATGAACCAGTGGCCATA-TTATCA
3183080 GATACTATGTATAGGTG
65 GATACTATGTATAGGTG
3183097 GTGGATATAA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
88 4 0.06
89 44 0.66
90 19 0.28
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (90 bp):
TATCAGACACTATGTACAGGTGATTATATTTATCAGGCACTATGAACCAGTGGCCATATTATCAG
ATACTATGTATAGGTGTTCATGTTG
Found at i:3185166 original size:51 final size:49
Alignment explanation
Indices: 3185036--3185219 Score: 176
Period size: 51 Copynumber: 3.7 Consensus size: 49
3185026 GAAAGTGATG
*
3185036 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTT
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCG----GATAGTTT
* * * *
3185089 G-CA--TGTCTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGTTT
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTT
* * * *
3185135 CGATCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGGATGGTAATG
1 -G-TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT--TT
* *
3185188 GTCACATGTGTAGTACTATGTGCAGGGTACTA
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTA
3185220 TATGAACTGA
Statistics
Matches: 108, Mismatches: 16, Indels: 16
0.77 0.11 0.11
Matches are distributed among these distances:
46 7 0.06
47 1 0.01
49 2 0.02
50 31 0.29
51 62 0.57
52 3 0.03
53 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (49 bp):
GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTT
Found at i:3185281 original size:45 final size:45
Alignment explanation
Indices: 3185230--3185318 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
3185220 TATGAACTGA
* *
3185230 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
*
3185275 ACATCATTGATTAATGAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
3185319 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:3188779 original size:6 final size:6
Alignment explanation
Indices: 3188755--3188835 Score: 72
Period size: 6 Copynumber: 13.0 Consensus size: 6
3188745 AGAGCCGTTG
* * * * * *
3188755 CCTCCA CTTCCA CCACCT CCTCCT CCTCCA CCACCA CCTCCT CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA
*
3188803 CCTCCA CCTCCA CCACTACCA CCTCCA CTTCCA
1 CCTCCA CCTCCA -C-CT-CCA CCTCCA CCTCCA
3188836 TATCCGAACC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
6 52 0.85
7 3 0.05
8 3 0.05
9 3 0.05
ACGTcount: A:0.17, C:0.63, G:0.00, T:0.20
Consensus pattern (6 bp):
CCTCCA
Found at i:3188784 original size:18 final size:18
Alignment explanation
Indices: 3188763--3188813 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
3188753 TGCCTCCACT
*
3188763 TCCACCACCTCCTCCTCC
1 TCCACCACCACCTCCTCC
3188781 TCCACCACCACCTCCTCC
1 TCCACCACCACCTCCTCC
*
3188799 TCCACCTCCACCTCC
1 TCCACCACCACCTCC
3188814 ACCACTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.14, C:0.67, G:0.00, T:0.20
Consensus pattern (18 bp):
TCCACCACCACCTCCTCC
Found at i:3188824 original size:15 final size:15
Alignment explanation
Indices: 3188779--3188830 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
3188769 ACCTCCTCCT
* *
3188779 CCTCCACCACCACCT
1 CCTCCACCACTACCA
*
3188794 CCTCCTCCACCT-CCA
1 CCTCCACCA-CTACCA
3188809 CCTCCACCACTACCA
1 CCTCCACCACTACCA
3188824 CCTCCAC
1 CCTCCAC
3188831 TTCCATATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.06
15 28 0.90
16 1 0.03
ACGTcount: A:0.19, C:0.65, G:0.00, T:0.15
Consensus pattern (15 bp):
CCTCCACCACTACCA
Found at i:3190174 original size:12 final size:12
Alignment explanation
Indices: 3190157--3190219 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
3190147 TCCTCCATTG
*
3190157 CCACCACCGCCT
1 CCACCACCACCT
* *
3190169 CCACCACCTCCA
1 CCACCACCACCT
3190181 CCACCACCACCT
1 CCACCACCACCT
*
3190193 CCTCCACCACCT
1 CCACCACCACCT
* *
3190205 CCACCTCCACTT
1 CCACCACCACCT
3190217 CCA
1 CCA
3190220 TATCCAGATC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.21, C:0.65, G:0.02, T:0.13
Consensus pattern (12 bp):
CCACCACCACCT
Found at i:3190178 original size:9 final size:9
Alignment explanation
Indices: 3190160--3190209 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
3190150 TCCATTGCCA
*
3190160 CCACCGCCT
1 CCACCACCT
3190169 CCACCACCT
1 CCACCACCT
*
3190178 CCACCACCA
1 CCACCACCT
*
3190187 CCACCTCCT
1 CCACCACCT
3190196 CCACCACCT
1 CCACCACCT
3190205 CCACC
1 CCACC
3190210 TCCACTTCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.20, C:0.68, G:0.02, T:0.10
Consensus pattern (9 bp):
CCACCACCT
Found at i:3190187 original size:15 final size:15
Alignment explanation
Indices: 3190157--3190214 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
3190147 TCCTCCATTG
* *
3190157 CCACCACCGCCTCCA
1 CCACCACCTCCACCA
* *
3190172 CCACCTCCACCACCA
1 CCACCACCTCCACCA
*
3190187 CCACCTCCTCCACCA
1 CCACCACCTCCACCA
*
3190202 CCTCCACCTCCAC
1 CCACCACCTCCAC
3190215 TTCCATATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.21, C:0.67, G:0.02, T:0.10
Consensus pattern (15 bp):
CCACCACCTCCACCA
Found at i:3190323 original size:18 final size:18
Alignment explanation
Indices: 3190300--3190335 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3190290 CGCCACTGCC
3190300 TCCACTTCCATATCCAAA
1 TCCACTTCCATATCCAAA
3190318 TCCACTTCCATATCCAAA
1 TCCACTTCCATATCCAAA
3190336 CCCTCCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.28
Consensus pattern (18 bp):
TCCACTTCCATATCCAAA
Found at i:3190345 original size:18 final size:18
Alignment explanation
Indices: 3190301--3190345 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3190291 GCCACTGCCT
* *
3190301 CCACTTCCATATCCAAAT
1 CCACCTCCATATCCAAAC
*
3190319 CCACTTCCATATCCAAAC
1 CCACCTCCATATCCAAAC
*
3190337 CCTCCTCCA
1 CCACCTCCA
3190346 CTGCCACCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.47, G:0.00, T:0.24
Consensus pattern (18 bp):
CCACCTCCATATCCAAAC
Found at i:3190355 original size:3 final size:3
Alignment explanation
Indices: 3190349--3190397 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
3190339 TCCTCCACTG
* * * * *
3190349 CCA CCA CCT CCA CGA CTA CCT CCT CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
3190397 C
1 C
3190398 TAGCACTACC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.27, C:0.63, G:0.02, T:0.08
Consensus pattern (3 bp):
CCA
Found at i:3190432 original size:18 final size:18
Alignment explanation
Indices: 3190411--3190446 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3190401 CACTACCACC
3190411 TCCACTTCCATATCCAGA
1 TCCACTTCCATATCCAGA
*
3190429 TCCACTTCCGTATCCAGA
1 TCCACTTCCATATCCAGA
3190447 CCCTTCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.39, G:0.08, T:0.28
Consensus pattern (18 bp):
TCCACTTCCATATCCAGA
Found at i:3190569 original size:99 final size:99
Alignment explanation
Indices: 3190366--3190555 Score: 236
Period size: 99 Copynumber: 1.9 Consensus size: 99
3190356 CTCCACGACT
* * * *
3190366 ACCTCCTCCACCACCACCACCACCACCACCACTAGCACTACCACCTCCACTTCCATATCCAGATC
1 ACCTCCACCACCACCACCACCACCACCACCACTAGAAATACCACCTCCACTTCCATATCCAGACC
* ****
3190431 CACTTCCGTATCCAGACCCTTCTCCACTGCCACC
66 CACTTCCATATCCAGACCCGAAACCACTGCCACC
* * * * *
3190465 ACCTCCACCACCACCTCCTCCTCCACCACCACTAGAAATACGACCTTCACTTCCATATCCAGACC
1 ACCTCCACCACCACCACCACCACCACCACCACTAGAAATACCACCTCCACTTCCATATCCAGACC
* *
3190530 CACTTCCATATCCGGATCCGAAACCA
66 CACTTCCATATCCAGACCCGAAACCA
3190556 TATCCCGATC
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
99 75 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.18
Consensus pattern (99 bp):
ACCTCCACCACCACCACCACCACCACCACCACTAGAAATACCACCTCCACTTCCATATCCAGACC
CACTTCCATATCCAGACCCGAAACCACTGCCACC
Found at i:3190586 original size:3 final size:3
Alignment explanation
Indices: 3190580--3190614 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3190570 TCCATTGCCG
*
3190580 CCA CCA CCA CCA CCT CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
3190615 TCCTCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.69, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:3192214 original size:9 final size:9
Alignment explanation
Indices: 3192200--3192241 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3192190 ATATTAATTT
3192200 TTTTTATAA
1 TTTTTATAA
3192209 TTTTTAT-A
1 TTTTTATAA
3192217 TTTTTAATAA
1 TTTTT-ATAA
* *
3192227 TTTTAATGA
1 TTTTTATAA
3192236 TTTTTA
1 TTTTTA
3192242 ATTCTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.21
9 17 0.61
10 5 0.18
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3192226 original size:18 final size:19
Alignment explanation
Indices: 3192199--3192243 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3192189 AATATTAATT
* *
3192199 TTTTTTATAATTTTTAT-A
1 TTTTTAATAATTTTAATGA
3192217 TTTTTAATAATTTTAATGA
1 TTTTTAATAATTTTAATGA
3192236 TTTTTAAT
1 TTTTTAAT
3192244 TCTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTAATAATTTTAATGA
Found at i:3192229 original size:10 final size:10
Alignment explanation
Indices: 3192199--3192243 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
3192189 AATATTAATT
*
3192199 TTTTTTATAA
1 TTTTTAATAA
3192209 TTTTT-AT-A
1 TTTTTAATAA
3192217 TTTTTAATAA
1 TTTTTAATAA
*
3192227 -TTTTAATGA
1 TTTTTAATAA
3192236 TTTTTAAT
1 TTTTTAAT
3192244 TCTATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 6 0.19
9 12 0.39
10 13 0.42
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:3193094 original size:19 final size:18
Alignment explanation
Indices: 3193052--3193096 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
3193042 CTACAATTGA
3193052 TTTTTTAATGATTTTTTT
1 TTTTTTAATGATTTTTTT
3193070 TATTTTTAA-GATTTTTAATT
1 T-TTTTTAATGATTTTT--TT
3193090 TTTTTTA
1 TTTTTTA
3193097 CAATTATTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.33
19 13 0.54
20 3 0.12
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTTTAATGATTTTTTT
Found at i:3196355 original size:21 final size:21
Alignment explanation
Indices: 3196314--3196378 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
3196304 CCATTGCCTT
* *
3196314 CACCTCCGCCTCCTCCACCTC
1 CACCTCCACCACCTCCACCTC
*
3196335 CA-CTGCCACCACCTCCTCCTC
1 CACCT-CCACCACCTCCACCTC
* *
3196356 CACCTCTACCACCTCCACTTC
1 CACCTCCACCACCTCCACCTC
3196377 CA
1 CA
3196379 TTCCCACTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.15, C:0.62, G:0.03, T:0.20
Consensus pattern (21 bp):
CACCTCCACCACCTCCACCTC
Found at i:3196466 original size:21 final size:20
Alignment explanation
Indices: 3196442--3196500 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
3196432 ACCACCTCTG
*
3196442 CCACCGCCACCTCCACTGCCA
1 CCACCACCACCTCCACT-CCA
* * *
3196463 CCACCTCCTCCTCCACCTCTA
1 CCACCACCACCTCCA-CTCCA
*
3196484 CCACTACCACCTCCACT
1 CCACCACCACCTCCACT
3196501 TCCAGATCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.19, C:0.61, G:0.03, T:0.17
Consensus pattern (20 bp):
CCACCACCACCTCCACTCCA
Found at i:3196472 original size:18 final size:18
Alignment explanation
Indices: 3196429--3196473 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3196419 CTCCTCCATG
* *
3196429 ACCACCACCTCTGCCACC
1 ACCACCTCCACTGCCACC
*
3196447 GCCACCTCCACTGCCACC
1 ACCACCTCCACTGCCACC
*
3196465 ACCTCCTCC
1 ACCACCTCC
3196474 TCCACCTCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.62, G:0.07, T:0.13
Consensus pattern (18 bp):
ACCACCTCCACTGCCACC
Found at i:3196517 original size:24 final size:24
Alignment explanation
Indices: 3196490--3196540 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
3196480 TCTACCACTA
3196490 CCACCTCCACT-TCCAGATCCAGAC
1 CCACCTCCA-TATCCAGATCCAGAC
*
3196514 CCACTTCCATATCCAGATCCAGAC
1 CCACCTCCATATCCAGATCCAGAC
3196538 CCA
1 CCA
3196541 TATCCCGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.27, C:0.47, G:0.08, T:0.18
Consensus pattern (24 bp):
CCACCTCCATATCCAGATCCAGAC
Found at i:3196519 original size:18 final size:18
Alignment explanation
Indices: 3196496--3196530 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3196486 ACTACCACCT
3196496 CCACTTCCAGATCCAGAC
1 CCACTTCCAGATCCAGAC
*
3196514 CCACTTCCATATCCAGA
1 CCACTTCCAGATCCAGA
3196531 TCCAGACCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.43, G:0.09, T:0.20
Consensus pattern (18 bp):
CCACTTCCAGATCCAGAC
Found at i:3196598 original size:15 final size:15
Alignment explanation
Indices: 3196563--3196613 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
3196553 CCTCCGTTGT
3196563 CACCACCTCCACCAC
1 CACCACCTCCACCAC
*
3196578 CGCCACCTCCACTGCCAC
1 CACCACCTCCA---CCAC
*
3196596 CACCACCTCCTCCAC
1 CACCACCTCCACCAC
3196611 CAC
1 CAC
3196614 TTCCTATCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.22, C:0.65, G:0.04, T:0.10
Consensus pattern (15 bp):
CACCACCTCCACCAC
Found at i:3199186 original size:3 final size:3
Alignment explanation
Indices: 3199178--3199207 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3199168 TAAATGAGTA
*
3199178 AAT AAT AAT AAG AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3199208 TTGAAGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3200160 original size:19 final size:19
Alignment explanation
Indices: 3200145--3200183 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3200135 TTAAAAAGAA
* *
3200145 AAAATTATATATAAAAAAT
1 AAAATAATAAATAAAAAAT
3200164 AAAATAATAAATAAAAAAT
1 AAAATAATAAATAAAAAAT
3200183 A
1 A
3200184 GTGACCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAATAATAAATAAAAAAT
Found at i:3201074 original size:131 final size:130
Alignment explanation
Indices: 3200916--3201342 Score: 588
Period size: 131 Copynumber: 3.3 Consensus size: 130
3200906 CACTGCAACT
* * * * **
3200916 TCAGGGAAATAAGACTGGTGGCTTAAATCTACTTCCTACTATCTCGGAAAGATAAGATTCATCGT
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATCTAGG-AAGATAAGATTCGCCGT
* * * *
3200981 CTTTGATTTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGTTG
65 CTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTG
3201046 C
130 C
* * * *
3201047 TCAGGGAGATAGGACTGATGGCTTAAATTTGCTTCCTACTATCTTGGGAAGATACGATTCGCCGT
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATC-TAGGAAGATAAGATTCGCCGT
* * *
3201112 CTTCGACCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTG
65 CTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTG
3201177 C
130 C
* * * *
3201178 TCAGAGAGATAAGG-CTGGT-GCCTAAATCTGCTTCATACTACCTTAGGAAGATAAGATTCGCCG
1 TCAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCTACTATC-TAGGAAGATAAGATTCGCCG
*
3201241 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAATCTTCAACCTACTCCACTGCT
64 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCT
3201306 GC
129 GC
**
3201308 TCAGGGAGATAGGACTGGTGGCTTCGATCTGCTTC
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTC
3201343 ACTGCCAGTA
Statistics
Matches: 260, Mismatches: 32, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
129 3 0.01
130 115 0.44
131 136 0.52
132 6 0.02
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (130 bp):
TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTATCTAGGAAGATAAGATTCGCCGTC
TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGC
Found at i:3201159 original size:44 final size:44
Alignment explanation
Indices: 3200989--3201670 Score: 224
Period size: 44 Copynumber: 15.6 Consensus size: 44
3200979 GTCTTTGATT
* * *
3200989 TGCTCTACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
* ** * * * *
3201033 TACTCCACTGTTGCTCAGGGAGATAGGA-CTG--ATGGCTTAAATT
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAT--CTTCAATC
* ** * *
3201076 TGCTTCCTACTA-T-CTT-GGGAAGATACGAT-TCGCCGTCTTCGACC
1 TGC-TCC-ACTACTGCTTAGGG-AGATAAGATCT-GCAATCTTCAATC
* *
3201120 TGCTCCACTACTACTTAGGGAGATAAGATCTGCAATCTTCAACC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
* * * * * * * *
3201164 TACTCCACTGCTGCTCAGAGAGATAAG-GCTG--GTGCCTAAATC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAT-CTTCAATC
* * * ** **
3201206 TGCTTCA-TACTACCTTAGGAAGATAAGAT-TCGCCGTCTTTGATC
1 TGCTCCACTACT-GCTTAGGGAGATAAGATCT-GCAATCTTCAATC
* *
3201250 TGCTCCACTACTGCTTAGGGAGATAAGATTTGCAATCTTCAACC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
* * * * **** *
3201294 TACTCCACTGCTGCTCAGGGAGATAGGA-CTGGTGGCTTCGATC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
* * * * * * * * *
3201337 TGCTTCACTGCCAG-TACAGGAAGACAAGATCTACAATCTTCGACC
1 TGCTCCACT-ACTGCT-TAGGGAGATAAGATCTGCAATCTTCAATC
* * * * * * *
3201382 TACTCCACTGCTGCTCAGGGAGATAGGA-CT--AGTGGCTTAAATT
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAT--CTTCAATC
* * *
3201425 TGCTTCC-CTACTACCTT-GAGAAGATAAGAT-TCGTC-ATCTTCGATC
1 TGC-TCCACTACT-GCTTAG-GGAGATAAGATCT-G-CAATCTTCAATC
* *
3201470 TGCTCCACTACTGCTTAGGGATATAAGATCTGCAATCTTCAACC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
* * * * * **** *
3201514 TACTCCGCTGCTGCTCAGGGAGATAAG-GCTGGTGGCTTAAATC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
* * ** *
3201557 TGCTTCCTACTAC--CTTAGGAAGATAAGATTTGCCGTCTTCGATC
1 TGC-TCC-ACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
* * * *
3201601 TGCTCCACTACTGCTTAGGAAGATAAGATTTACAATCTTCAACC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
* ** * *
3201645 TACTCCACCGCTGGTCAGGGAGATAA
1 TGCTCCACTACTGCTTAGGGAGATAA
3201671 AGCTTGATAT
Statistics
Matches: 456, Mismatches: 138, Indels: 88
0.67 0.20 0.13
Matches are distributed among these distances:
41 8 0.02
42 34 0.07
43 83 0.18
44 280 0.61
45 49 0.11
46 1 0.00
47 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATC
Found at i:3201527 original size:220 final size:218
Alignment explanation
Indices: 3201144--3201562 Score: 637
Period size: 220 Copynumber: 1.9 Consensus size: 218
3201134 TTAGGGAGAT
* *
3201144 AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGGCTGGTGCCTAAATCTGC
1 AAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGGCTAGTGCCTAAATCTGC
* *
3201209 TTCATACTACCTTAGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGAT
66 TTCATACTACCTTAGGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
* **
3201274 AAGATTTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGAT-AGGACTGGTGGCTTCGATCT
131 AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG-CTGGTGGCTTAAATCT
3201338 GCTTCACTGCCAGTACAGGAAGAC
195 GCTTCACTGCCAGTACAGGAAGAC
* * * *
3201362 AAGATCTACAATCTTCGACCTACTCCACTGCTGCTCAGGGAGAT-AGGACTAGTGGCTTAAATTT
1 AAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGG-CTAGT-GCCTAAATCT
* *
3201426 GCTTCCCTACTACCTT-GAGAAGATAAGATTCGTCATCTTCGATCTGCTCCACTACTGCTTAGGG
64 GCTT-CATACTACCTTAG-GAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
* *
3201490 ATATAAGATCTGCAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAA
127 AGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAA
3201555 TCTGCTTC
192 TCTGCTTC
3201563 CTACTACCTT
Statistics
Matches: 181, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
217 3 0.02
218 45 0.25
219 13 0.07
220 117 0.65
221 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (218 bp):
AAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGGCTAGTGCCTAAATCTGC
TTCATACTACCTTAGGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTG
CTTCACTGCCAGTACAGGAAGAC
Found at i:3201637 original size:131 final size:133
Alignment explanation
Indices: 3201354--3201670 Score: 471
Period size: 131 Copynumber: 2.4 Consensus size: 133
3201344 CTGCCAGTAC
* *
3201354 AGGAAGACAAGATCTACAATCTTCGACCTACTCCACTGCTGCTCAGGGAGAT-AGGACTAGTGGC
1 AGGAAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGACTAGTGGC
* *
3201418 TTAAATTTGCTTCCCTACTACCTTGAGAAGATAAGATTCGTCATCTTCGATCTGCTCCACTACTG
66 TTAAATCTGCTTCCCTACTACCTTGAGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTG
3201483 CTT
131 CTT
* * * * *
3201486 AGGGATATAAGATCTGCAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGATAAGG-CTGGTGGC
1 AGGAAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGACTAGTGGC
* *
3201550 TTAAATCTGCTT-CCTACTACCTT-AGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACT
66 TTAAATCTGCTTCCCTACTACCTTGA-GAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACT
3201613 GCTT
130 GCTT
* * *
3201617 AGGAAGATAAGATTTACAATCTTCAACCTACTCCACCGCTGGTCAGGGAGATAA
1 AGGAAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAA
3201671 AGCTTGATAT
Statistics
Matches: 165, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
130 1 0.01
131 97 0.59
132 64 0.39
133 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (133 bp):
AGGAAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGACTAGTGGC
TTAAATCTGCTTCCCTACTACCTTGAGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTG
CTT
Found at i:3207786 original size:110 final size:110
Alignment explanation
Indices: 3207585--3208127 Score: 792
Period size: 110 Copynumber: 5.0 Consensus size: 110
3207575 AAGGAAAATT
* *
3207585 TTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
3207650 CGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAAA
66 CGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAAA
* * * * * *
3207695 TTTCGAAGTAAGGCAATATTTTGCGTTTGGAAATTTGAGAAAACGTGCCTTAATTTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* ***
3207760 CGATTTTTCTCGTTCGACCAAATAGCCAAATATCTTTTTTTTTAAA
66 CGATTTTTCTCGTTCGACCAAATAGCCAAATATC-CTTTTAAAAAA
** * *
3207806 --TCAAAATAAGGCAATGTTTTTTGTTTGGAAATTCGAGAAAACGTGCTCTAGTGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* * *
3207869 CGATTTTTTTCTCATTCAACCAAATAGCCAAATATCCTTTCAAAAAA
66 CGA--TTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAAA
3207916 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCT-GGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
3207980 CGATTTTTTCTCGTTCAACCAAATAGCCAAATATCC-TTTCAAAAA
66 CGA-TTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAAA
* *
3208025 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAACTCGAGAAAACGTGCCCTAATGTGTTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
3208090 CGA--TTTCTCGTTGGACCAAATAGCCAAATATCCTTTTA
66 CGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTA
3208128 TATCTTAATC
Statistics
Matches: 388, Mismatches: 38, Indels: 16
0.88 0.09 0.04
Matches are distributed among these distances:
107 28 0.07
108 3 0.01
109 120 0.31
110 140 0.36
111 44 0.11
112 53 0.14
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (110 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAAA
Found at i:3207990 original size:221 final size:218
Alignment explanation
Indices: 3207590--3208125 Score: 792
Period size: 221 Copynumber: 2.4 Consensus size: 218
3207580 AAATTTTTCT
*
3207590 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
* * *
3207655 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAAATTTCGAAGTAAGGCAATATTTTGCG
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAAAAAATTTCAAAATAAGGCAATATTTTGCG
* * * *
3207720 TTTGGAAATTTGAGAAAACGTGCCTTAATTTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAG
131 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
* ***
3207785 CCAAATATCTTTTTTTTTAAA-TCA
196 CCAAATATC--CTTTCAAAAATTCA
** * *
3207809 AAATAAGGCAATGTTTTTTGTTTGGAAATTCGAGAAAACGTGCTCTAGTGTGCTGGGTTTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA--
* * *
3207874 TTTTTCTCATTCAACCAAATAGCCAAATATCCTTTCAAAAAATTTCAAAATAAGGCAATGTTTTG
64 TTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAAAAAATTTCAAAATAAGGCAATATTTTG
3207939 CGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCT-GGTTTCGATTTTTTCTCGTTCAACCAAA
129 CGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTTTCTCGTTCAACCAAA
3208003 TAGCCAAATATCCTTTCAAAAATTTCA
193 TAGCCAAATATCCTTTCAAAAA-TTCA
* *
3208030 AAATAAGGCAATGTTTTGCGTTTGGAAACTCGAGAAAACGTGCCCTAATGTGTTGGGTTTCGA--
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
*
3208093 TTTCTCGTTGGACCAAATAGCCAAATATCCTTT
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTT
3208126 TATATCTTAA
Statistics
Matches: 284, Mismatches: 28, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
217 30 0.11
219 64 0.23
220 8 0.03
221 182 0.64
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (218 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
TTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAAAAAATTTCAAAATAAGGCAATATTTTGCG
TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
CCAAATATCCTTTCAAAAATTCA
Found at i:3209332 original size:9 final size:9
Alignment explanation
Indices: 3209318--3209349 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
3209308 TAACAGCCTC
3209318 AAAATAAAA
1 AAAATAAAA
3209327 AAAATAAAAA
1 AAAAT-AAAA
3209337 AAAATAAAA
1 AAAATAAAA
3209346 AAAA
1 AAAA
3209350 GCCTCAACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAATAAAA
Found at i:3209338 original size:10 final size:10
Alignment explanation
Indices: 3209318--3209349 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3209308 TAACAGCCTC
3209318 AAAAT-AAAA
1 AAAATAAAAA
3209327 AAAATAAAAA
1 AAAATAAAAA
3209337 AAAATAAAAA
1 AAAATAAAAA
3209347 AAA
1 AAA
3209350 GCCTCAACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:3211412 original size:32 final size:32
Alignment explanation
Indices: 3211354--3211414 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
3211344 AGAGGTGGGA
*
3211354 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAAG
* * *
3211386 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
3211415 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.20
Consensus pattern (32 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAAG
Found at i:3211612 original size:9 final size:9
Alignment explanation
Indices: 3211595--3211631 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3211585 TATAGTTTGA
3211595 TATTCGAAT
1 TATTCGAAT
*
3211604 TATTTGAAT
1 TATTCGAAT
*
3211613 TATTCGAGT
1 TATTCGAAT
3211622 TATTCGAAT
1 TATTCGAAT
3211631 T
1 T
3211632 TAAAAGCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3213282 original size:21 final size:21
Alignment explanation
Indices: 3213241--3213312 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
3213231 CCATTGCCTT
* *
3213241 CACCTCCACCTCCGCCTCCTC
1 CACCTCCACCTCCACCACCTC
3213262 CACCTCCA-CTACCACCACCTC
1 CACCTCCACCT-CCACCACCTC
** *
3213283 TTCCTCCACCTCTACCACCTC
1 CACCTCCACCTCCACCACCTC
*
3213304 CACTTCCAC
1 CACCTCCAC
3213313 TCCCACTTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.17, C:0.61, G:0.01, T:0.21
Consensus pattern (21 bp):
CACCTCCACCTCCACCACCTC
Found at i:3213303 original size:15 final size:15
Alignment explanation
Indices: 3213241--3213312 Score: 51
Period size: 15 Copynumber: 5.0 Consensus size: 15
3213231 CCATTGCCTT
*
3213241 CACCTCCACCTCCGC
1 CACCTCCACCTCCAC
*
3213256 CTCCTCCACCTCCAC
1 CACCTCCACCTCCAC
* *
3213271 TACCACCACCT---C
1 CACCTCCACCTCCAC
** *
3213283 TTCCTCCACCTCTAC
1 CACCTCCACCTCCAC
*
3213298 CACCTCCACTTCCAC
1 CACCTCCACCTCCAC
3213313 TCCCACTTCC
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
12 10 0.23
15 33 0.77
ACGTcount: A:0.17, C:0.61, G:0.01, T:0.21
Consensus pattern (15 bp):
CACCTCCACCTCCAC
Found at i:3219780 original size:2 final size:2
Alignment explanation
Indices: 3219767--3219796 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
3219757 TTTAGGAAAG
3219767 TA TA TA TCA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
3219797 GATAATGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3222836 original size:21 final size:21
Alignment explanation
Indices: 3222812--3222883 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
3222802 CCATTGCCTT
* *
3222812 CACCTCCACCTCCGCCTCCTC
1 CACCTCCACCTCCACCACCTC
3222833 CACCTCCA-CTGCCACCACCTC
1 CACCTCCACCT-CCACCACCTC
* * * *
3222854 CTCCTCCACCTCTACCGCTTC
1 CACCTCCACCTCCACCACCTC
*
3222875 CACTTCCAC
1 CACCTCCAC
3222884 TCCCACTCCC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.14, C:0.61, G:0.04, T:0.21
Consensus pattern (21 bp):
CACCTCCACCTCCACCACCTC
Found at i:3222877 original size:27 final size:27
Alignment explanation
Indices: 3222812--3222871 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
3222802 CCATTGCCTT
* * *
3222812 CACCTCCACCTCCGCCTCCTCCACCTC
1 CACCGCCACCACCTCCTCCTCCACCTC
*
3222839 CACTGCCACCACCTCCTCCTCCACCTC
1 CACCGCCACCACCTCCTCCTCCACCTC
*
3222866 TACCGC
1 CACCGC
3222872 TTCCACTTCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.13, C:0.63, G:0.05, T:0.18
Consensus pattern (27 bp):
CACCGCCACCACCTCCTCCTCCACCTC
Found at i:3222949 original size:18 final size:17
Alignment explanation
Indices: 3222928--3222984 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 17
3222918 ATATCCTGAC
3222928 CCTCCTCCATGACCACCA
1 CCTCCTCC-TGACCACCA
*
3222946 CCTCCGCC--ACCACCA
1 CCTCCTCCTGACCACCA
*
3222961 CCTCC-ACTG-CCACCA
1 CCTCCTCCTGACCACCA
3222976 CCTCCTCCT
1 CCTCCTCCT
3222985 CCACCTCTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 23 0.70
16 2 0.06
18 7 0.21
ACGTcount: A:0.18, C:0.61, G:0.05, T:0.16
Consensus pattern (17 bp):
CCTCCTCCTGACCACCA
Found at i:3223027 original size:24 final size:24
Alignment explanation
Indices: 3223000--3223050 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3222990 TCTACCTCTA
*
3223000 CCACCTCCACT-TCCATATCCAGAC
1 CCACCTCCA-TATCCAGATCCAGAC
*
3223024 CCACTTCCATATCCAGATCCAGAC
1 CCACCTCCATATCCAGATCCAGAC
3223048 CCA
1 CCA
3223051 TATCCCGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.27, C:0.47, G:0.06, T:0.20
Consensus pattern (24 bp):
CCACCTCCATATCCAGATCCAGAC
Found at i:3223029 original size:18 final size:18
Alignment explanation
Indices: 3223006--3223063 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
3222996 TCTACCACCT
3223006 CCACTTCCATATCCAGAC
1 CCACTTCCATATCCAGAC
*
3223024 CCACTTCCATATCCAGAT
1 CCACTTCCATATCCAGAC
*** *
3223042 CCAGACCCATATCCCGAC
1 CCACTTCCATATCCAGAC
3223060 CCAC
1 CCAC
3223064 CTCCGTTGCC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.28, C:0.47, G:0.07, T:0.19
Consensus pattern (18 bp):
CCACTTCCATATCCAGAC
Found at i:3223052 original size:132 final size:126
Alignment explanation
Indices: 3222817--3223121 Score: 378
Period size: 132 Copynumber: 2.4 Consensus size: 126
3222807 GCCTTCACCT
* * * *
3222817 CCACCTCCGCCTCCTCCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCGCTTCCACTTCC
1 CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCGCTACCACCTCC
* * * * * * *
3222882 ACTCCCACTCCCACTTCCGTATCCGGACCCTGATCCATATCCTGACCCTCCTCC-ATGACCA
66 ACTCCCACACCCACTTCCATATCCAGACCCAGACCCATATCCCGACCCACCTCCGATG-CCA
*
3222943 CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCTCTACCACCTCC
1 CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCGCTACCACCTCC
* * *
3223008 ACTTCCATATCCAGACCCACTTCCATATCCAGATCCAGACCCATATCCCGACCCACCTCCGTTGC
66 AC-T-C----CCACACCCACTTCCATATCCAGACCCAGACCCATATCCCGACCCACCTCCGATGC
3223073 CA
125 CA
* * *
3223075 CCACCTCCACCACCACCACCTCCGCTGCCACCACCACCTCCTCCACC
1 CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACC
3223122 ACTTCCTATC
Statistics
Matches: 154, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
126 62 0.40
127 1 0.01
128 1 0.01
132 88 0.57
133 2 0.01
ACGTcount: A:0.19, C:0.56, G:0.06, T:0.19
Consensus pattern (126 bp):
CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCGCTACCACCTCC
ACTCCCACACCCACTTCCATATCCAGACCCAGACCCATATCCCGACCCACCTCCGATGCCA
Found at i:3223080 original size:15 final size:15
Alignment explanation
Indices: 3223060--3223109 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
3223050 ATATCCCGAC
*
3223060 CCACCTCCGTTGCCA
1 CCACCTCCGCTGCCA
* **
3223075 CCACCTCCACCACCA
1 CCACCTCCGCTGCCA
3223090 CCACCTCCGCTGCCA
1 CCACCTCCGCTGCCA
3223105 CCACC
1 CCACC
3223110 ACCTCCTCCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.18, C:0.62, G:0.08, T:0.12
Consensus pattern (15 bp):
CCACCTCCGCTGCCA
Found at i:3223094 original size:30 final size:30
Alignment explanation
Indices: 3223060--3223123 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
3223050 ATATCCCGAC
* *
3223060 CCACCTCCGTTGCCACCACCTCCACCACCA
1 CCACCTCCGCTGCCACCACCACCACCACCA
* *
3223090 CCACCTCCGCTGCCACCACCACCTCCTCCA
1 CCACCTCCGCTGCCACCACCACCACCACCA
3223120 CCAC
1 CCAC
3223124 TTCCTATCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.19, C:0.62, G:0.06, T:0.12
Consensus pattern (30 bp):
CCACCTCCGCTGCCACCACCACCACCACCA
Found at i:3223120 original size:15 final size:15
Alignment explanation
Indices: 3223072--3223123 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
3223062 ACCTCCGTTG
*
3223072 CCACCACCTCCACCA
1 CCACCACCTCCTCCA
3223087 CCACCACCTCCGCTGCCA
1 CCACCACCT-C-CT-CCA
3223105 CCACCACCTCCTCCA
1 CCACCACCTCCTCCA
3223120 CCAC
1 CCAC
3223124 TTCCTATCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 16 0.48
16 3 0.09
17 2 0.06
18 12 0.36
ACGTcount: A:0.21, C:0.65, G:0.04, T:0.10
Consensus pattern (15 bp):
CCACCACCTCCTCCA
Found at i:3223123 original size:18 final size:18
Alignment explanation
Indices: 3223072--3223123 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
3223062 ACCTCCGTTG
*
3223072 CCACCACCTCCACCACCA
1 CCACCTCCTCCACCACCA
* **
3223090 CCACCTCCGCTGCCACCA
1 CCACCTCCTCCACCACCA
3223108 CCACCTCCTCCACCAC
1 CCACCTCCTCCACCAC
3223124 TTCCTATCCC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.21, C:0.65, G:0.04, T:0.10
Consensus pattern (18 bp):
CCACCTCCTCCACCACCA
Found at i:3227751 original size:18 final size:18
Alignment explanation
Indices: 3227724--3227774 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
3227714 TCCACTACTA
*
3227724 CCATAACCTGACCCACTT
1 CCATAACCTGAACCACTT
*
3227742 CCATATCCTGAACCACTT
1 CCATAACCTGAACCACTT
3227760 CCATAACCTGAACCA
1 CCATAACCTGAACCA
3227775 TTGCCTCCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.41, G:0.06, T:0.22
Consensus pattern (18 bp):
CCATAACCTGAACCACTT
Found at i:3227798 original size:15 final size:15
Alignment explanation
Indices: 3227778--3227812 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3227768 TGAACCATTG
*
3227778 CCTCCACCACCTCCA
1 CCTCCACCACCACCA
*
3227793 CCTCCACCGCCACCA
1 CCTCCACCACCACCA
3227808 CCTCC
1 CCTCC
3227813 TCCTCCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.69, G:0.03, T:0.11
Consensus pattern (15 bp):
CCTCCACCACCACCA
Found at i:3227805 original size:21 final size:21
Alignment explanation
Indices: 3227781--3227827 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3227771 ACCATTGCCT
3227781 CCACCACCTCCACCTCCACCG
1 CCACCACCTCCACCTCCACCG
* * *
3227802 CCACCACCTCCTCCTCCTCCT
1 CCACCACCTCCACCTCCACCG
3227823 CCACC
1 CCACC
3227828 TCTACCGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.68, G:0.02, T:0.15
Consensus pattern (21 bp):
CCACCACCTCCACCTCCACCG
Found at i:3227957 original size:24 final size:24
Alignment explanation
Indices: 3227907--3227957 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3227897 TCCAGAGCTG
*
3227907 CCACCACCTCCACCTCCGCCCCCA
1 CCACCACCTCCACCTCCGCCACCA
* * *
3227931 CCACCCCCTCCACCTCCTCCACTA
1 CCACCACCTCCACCTCCGCCACCA
3227955 CCA
1 CCA
3227958 TAAGCTCCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.69, G:0.02, T:0.12
Consensus pattern (24 bp):
CCACCACCTCCACCTCCGCCACCA
Found at i:3228018 original size:12 final size:12
Alignment explanation
Indices: 3227967--3228019 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
3227957 ATAAGCTCCC
3227967 GAACCATATCCT
1 GAACCATATCCT
* *
3227979 GAGCCACT-TCCG
1 GAACCA-TATCCT
*
3227991 GAACCATACCCT
1 GAACCATATCCT
*
3228003 GAACCATATCCA
1 GAACCATATCCT
3228015 GAACC
1 GAACC
3228020 TGAGCCTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 1 0.03
12 30 0.94
13 1 0.03
ACGTcount: A:0.32, C:0.38, G:0.13, T:0.17
Consensus pattern (12 bp):
GAACCATATCCT
Found at i:3228018 original size:24 final size:24
Alignment explanation
Indices: 3227967--3228019 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3227957 ATAAGCTCCC
* * *
3227967 GAACCATATCCTGAGCCACTTCCG
1 GAACCATACCCTGAACCACTTCCA
3227991 GAACCATACCCTGAACCA-TATCCA
1 GAACCATACCCTGAACCACT-TCCA
3228015 GAACC
1 GAACC
3228020 TGAGCCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.32, C:0.38, G:0.13, T:0.17
Consensus pattern (24 bp):
GAACCATACCCTGAACCACTTCCA
Found at i:3232111 original size:28 final size:29
Alignment explanation
Indices: 3232074--3232141 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 29
3232064 ATAAAAAATA
3232074 ACCAAAATATTATAA-ATTTTTATTATTT
1 ACCAAAATATTATAATATTTTTATTATTT
3232102 ACCAAAATATTATAATTATTTTTATTATTT
1 ACCAAAATATTATAA-TATTTTTATTATTT
3232132 ACCAAAATAT
1 ACCAAAATAT
3232142 ATCAAAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 15 0.39
30 23 0.61
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (29 bp):
ACCAAAATATTATAATATTTTTATTATTT
Done.