Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 287 of 362
Found at i:96495777 original size:17 final size:18
Alignment explanation
Indices: 96495755--96495788 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96495745 TGAAGCATAC
96495755 AGAAAGA-CAGAATCGTG
1 AGAAAGATCAGAATCGTG
*
96495772 AGAAAGATCGGAATCGT
1 AGAAAGATCAGAATCGT
96495789 TTTAGCAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.12, G:0.29, T:0.15
Consensus pattern (18 bp):
AGAAAGATCAGAATCGTG
Found at i:96501233 original size:27 final size:26
Alignment explanation
Indices: 96501181--96501240 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
96501171 ACACATATAT
*
96501181 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
96501207 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
96501234 ATATCTG
1 ATATCTG
96501241 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:96505364 original size:37 final size:37
Alignment explanation
Indices: 96505305--96505413 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
96505295 AGCTCAGACG
* *
96505305 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
96505342 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
96505379 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
96505414 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:96505697 original size:47 final size:47
Alignment explanation
Indices: 96505618--96505809 Score: 271
Period size: 47 Copynumber: 4.1 Consensus size: 47
96505608 TATATATATT
* * * * *
96505618 TCACATTGACCATTCGACTTTA-C-CACATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* *
96505663 CCATATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* *
96505710 TCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTTA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* *
96505757 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
96505804 TCACAT
1 TCACAT
96505810 AAAATCCTAA
Statistics
Matches: 132, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 17 0.13
46 1 0.01
47 114 0.86
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
Found at i:96505736 original size:22 final size:22
Alignment explanation
Indices: 96505709--96505784 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
96505699 GCTCACATTC
96505709 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
96505731 ATCACATATATG-CATGCTC-ACATTT
1 ATCACAT-T-GGCCAT--TCGGC-CTT
96505756 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
96505778 ATCACAT
1 ATCACAT
96505785 ATATGCATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 18 0.44
23 6 0.15
24 6 0.15
25 11 0.27
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:96528295 original size:42 final size:42
Alignment explanation
Indices: 96528219--96528303 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
96528209 GGTTACTGAG
*
96528219 ATGAGATTCGTGTAAGACGATGTCTGGGACATTGGCATCGAT
1 ATGAGATTCGTGTAAGACGATGTCTAGGACATTGGCATCGAT
* *
96528261 ATGAGATTCGTGTAAGACTATAG-CTAGG-CTATTGGCATTGAT
1 ATGAGATTCGTGTAAGACGAT-GTCTAGGAC-ATTGGCATCGAT
96528303 A
1 A
96528304 GACTATAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 1 0.03
42 36 0.95
43 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (42 bp):
ATGAGATTCGTGTAAGACGATGTCTAGGACATTGGCATCGAT
Found at i:96534419 original size:28 final size:27
Alignment explanation
Indices: 96534363--96534420 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
96534353 AGATTTTTTA
*
96534363 TGAAAATTGAAATTAGGGATTAAATTG
1 TGAAAATTGAAATTAGGGATTAAAGTG
96534390 TGAAATATTGAAATT-GTGG-TTAAAAGTG
1 TGAAA-ATTGAAATTAG-GGATT-AAAGTG
96534418 TGA
1 TGA
96534421 TTATTTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34
Consensus pattern (27 bp):
TGAAAATTGAAATTAGGGATTAAAGTG
Found at i:96535931 original size:37 final size:37
Alignment explanation
Indices: 96535856--96535931 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 37
96535846 TTACGAAGTA
* * * *
96535856 TTACCCGGACATAATCTCCACACGAAGTTATCGAGTC
1 TTACCCGGACAAAATCCCCACACGAAGTCAACGAGTC
* *
96535893 TTACCCGGACAAAATCCCCACACGTAGTCAACGGGTC
1 TTACCCGGACAAAATCCCCACACGAAGTCAACGAGTC
96535930 TT
1 TT
96535932 TAGAGCTCGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (37 bp):
TTACCCGGACAAAATCCCCACACGAAGTCAACGAGTC
Found at i:96536128 original size:47 final size:47
Alignment explanation
Indices: 96536050--96536578 Score: 860
Period size: 47 Copynumber: 11.1 Consensus size: 47
96536040 CCCTTCGGGA
* * * * * *
96536050 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
96536097 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
96536144 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
96536191 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
96536240 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
96536287 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
96536336 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
96536385 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
96536432 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
96536479 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
96536528 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
96536575 CTTA
1 CTTA
96536579 CTATCATTTC
Statistics
Matches: 457, Mismatches: 19, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
47 272 0.60
49 185 0.40
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:96536251 original size:96 final size:96
Alignment explanation
Indices: 96536050--96536578 Score: 886
Period size: 96 Copynumber: 5.5 Consensus size: 96
96536040 CCCTTCGGGA
* * * * * * * *
96536050 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
96536113 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
96536144 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
96536209 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
96536240 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
96536305 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
96536336 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCAC--GTATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
96536399 ACACTTTCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
96536432 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
96536497 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
96536528 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
96536579 CTATCATTTC
Statistics
Matches: 412, Mismatches: 17, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
94 93 0.23
96 273 0.66
98 46 0.11
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:96536348 original size:143 final size:142
Alignment explanation
Indices: 96536050--96536578 Score: 880
Period size: 143 Copynumber: 3.7 Consensus size: 142
96536040 CCCTTCGGGA
* * * * * * * *
96536050 CTTATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
96536114 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
66 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
96536179 CGGCCATTAGGC
131 CGGCCATTAGGC
* *
96536191 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
96536256 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
65 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
96536321 CATCGGCCATTAGGC
128 CATCGGCCATTAGGC
* *
96536336 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACGTATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
96536401 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCACATTCATCACA
65 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
96536466 TCGGCCATTAGGC
130 TCGGCCATTAGGC
*
96536479 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
96536544 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
65 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
96536579 CTATCATTTC
Statistics
Matches: 366, Mismatches: 18, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
141 7 0.02
143 220 0.60
145 139 0.38
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (142 bp):
CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGC
Found at i:96540182 original size:40 final size:39
Alignment explanation
Indices: 96540031--96540220 Score: 271
Period size: 39 Copynumber: 4.9 Consensus size: 39
96540021 CGAATACACG
* * *
96540031 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGAT--A
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
* * * *
96540069 TAACCAGCACGAATGCTCTTCGGA-TTAG-CCGAATACA
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
96540106 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
96540145 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
96540185 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGAT
96540221 TTAGTAACTC
Statistics
Matches: 138, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
35 5 0.04
36 3 0.02
37 25 0.18
38 22 0.16
39 44 0.32
40 39 0.28
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
Found at i:96540245 original size:39 final size:40
Alignment explanation
Indices: 96540044--96540338 Score: 231
Period size: 39 Copynumber: 7.5 Consensus size: 40
96540034 CCAGCATGAT
* * *
96540044 TGCTCTTCGGGACCTAGCCCGGATATA---ACCAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATATAGTCACTAGCACCAA
* * **
96540082 TGCTCTTCGGA-TTAG-CCGAATACA-TCACTAGCATGAA
1 TGCTCTTCGGACTTAGCCCGGATATAGTCACTAGCACCAA
* **
96540119 TGCTCTTCGGACTTAGCCCGGATACA-TCACTAGCATGAA
1 TGCTCTTCGGACTTAGCCCGGATATAGTCACTAGCACCAA
* **
96540158 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATGAA
1 TGCTCTTC-GGACTTAGCCCGGATATAGTCACTAGCACCAA
* * *
96540198 TGCTCTTCGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGACTTAGCCCGGATATAGTCACTAGCACCAA
* * *
96540238 TGC-CTTCGGGCTTAGCCCGGA-ATTAGT-ATCTCGCACAAA
1 TGCTCTTCGGACTTAGCCCGGATA-TAGTCA-CTAGCACCAA
* *
96540277 TGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAGCA-CAA
1 TGCTCTTCGGA-CTTAGCCCGGATATAGTCAC-TAGCACCAA
*
96540317 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTC-GGACTTAGCCCGGA
96540339 CATCATTCGA
Statistics
Matches: 222, Mismatches: 22, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
35 7 0.03
36 3 0.01
37 23 0.10
38 13 0.06
39 84 0.38
40 83 0.37
41 9 0.04
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGACTTAGCCCGGATATAGTCACTAGCACCAA
Found at i:96540245 original size:79 final size:78
Alignment explanation
Indices: 96540031--96540258 Score: 281
Period size: 79 Copynumber: 2.9 Consensus size: 78
96540021 CGAATACACG
* * *
96540031 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGA-TATAAC-CAGCACGAATGCTCTTC-GGA
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATTATAACTC-GCACGAATGCTCTTCGGGA
*
96540093 -TTAG-CCGAATACA
64 CTTAGCCCGGATACA
* * * *
96540106 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGAC
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGAT-TATAACTCGCACGAATGCTCTTCGGGAC
96540171 TTAGCCCGGATACA
65 TTAGCCCGGATACA
*
96540185 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATTTAGTAACTCGCACCAATGC-CTTCGGG-
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGA-TTA-TAACTCGCACGAATGCTCTTCGGGA
96540248 CTTAGCCCGGA
64 CTTAGCCCGGA
96540259 ATTAGTATCT
Statistics
Matches: 132, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
74 13 0.10
75 19 0.14
76 18 0.14
77 3 0.02
78 15 0.11
79 51 0.39
80 13 0.10
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (78 bp):
TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATTATAACTCGCACGAATGCTCTTCGGGACT
TAGCCCGGATACA
Found at i:96540279 original size:79 final size:78
Alignment explanation
Indices: 96540044--96540338 Score: 254
Period size: 79 Copynumber: 3.8 Consensus size: 78
96540034 CCAGCATGAT
* *
96540044 TGCTCTTCGGGACCTAGCCCGGATATA---ACCAGCACGAATGCTCTTC-GGA-TTAG-CC-GAA
1 TGCTCTTC-GGACTTAGCCCGGATATAGTCACTAGCAC-AATGC-CTTCGGGACTTAGCCCGGAA
**
96540102 TACATCACTAGCATGAA
63 TACAT-ACTAGCACAAA
* *
96540119 TGCTCTTCGGACTTAGCCCGGATACA-TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG-AT
1 TGCTCTTCGGACTTAGCCCGGATATAGTCACTAGCA-CAATGC-CTTCGGGACTTAGCCCGGAAT
**
96540182 ACATCACTAGCATGAA
64 ACAT-ACTAGCACAAA
* * *
96540198 TGCTCTTCGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAATT
1 TGCTCTTCGGACTTAGCCCGGATATAGTCACTAGCA-CAATGCCTTCGGGACTTAGCCCGGAA-T
* *
96540262 A-GTATCTCGCACAAA
64 ACATA-CTAGCACAAA
* * *
96540277 TGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGA-CTTAGCCCGGATATAGTCAC-TAGCACAATGCCTTCGGGACTTAGCCCGGA
96540339 CATCATTCGA
Statistics
Matches: 186, Mismatches: 20, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
74 16 0.09
75 8 0.04
76 16 0.09
77 3 0.02
78 22 0.12
79 91 0.49
80 30 0.16
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
TGCTCTTCGGACTTAGCCCGGATATAGTCACTAGCACAATGCCTTCGGGACTTAGCCCGGAATAC
ATACTAGCACAAA
Found at i:96540684 original size:29 final size:29
Alignment explanation
Indices: 96540645--96540723 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
96540635 CTTAATAATC
*
96540645 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
96540675 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
96540704 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
96540724 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:96540766 original size:43 final size:43
Alignment explanation
Indices: 96540705--96540807 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
96540695 TGCATTTCAA
96540705 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
96540748 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
96540791 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
96540808 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:96544265 original size:27 final size:27
Alignment explanation
Indices: 96544234--96544411 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
96544224 TAAATTGTAC
96544234 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
96544261 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
96544287 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
96544315 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
96544343 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
96544370 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
96544397 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
96544412 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:96544348 original size:82 final size:81
Alignment explanation
Indices: 96544235--96544390 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
96544225 AAATTGTACA
* *
96544235 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
96544299 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
96544316 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
96544381 TGCGAGTTGA
65 TGCGAATTGA
96544391 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:96544402 original size:82 final size:81
Alignment explanation
Indices: 96544231--96544411 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
96544221 GATTAAATTG
* *
96544231 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
96544296 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
96544312 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
96544376 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
96544394 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
96544412 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:96553311 original size:28 final size:27
Alignment explanation
Indices: 96553219--96553342 Score: 187
Period size: 28 Copynumber: 4.6 Consensus size: 27
96553209 ATATTAAGTC
* *
96553219 CGCACACTCAGTGCTATATAA-CAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
96553245 CGCACACTTAGTGCTATATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
96553272 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAA-CT
96553300 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
96553328 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
96553343 GTACAATTTA
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.22
27 28 0.31
28 41 0.45
29 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:96553321 original size:55 final size:54
Alignment explanation
Indices: 96553219--96553342 Score: 196
Period size: 55 Copynumber: 2.3 Consensus size: 54
96553209 ATATTAAGTC
* * *
96553219 CGCACACTCAGTGCTATATAACAACTCGCACACTTAGTGCTATATAATCAAA-T
1 CGCACACTTAGTGCTACATAACAACTCGCACACTTAGTGCTACATAATCAAACT
96553272 CGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAA-CAA-CTCGCACACTTAGTGCTACATAATCAAACT
96553328 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
96553343 GTACAATTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
53 19 0.29
54 3 0.05
55 27 0.42
56 16 0.25
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAACAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:96558725 original size:19 final size:19
Alignment explanation
Indices: 96558701--96558785 Score: 57
Period size: 19 Copynumber: 4.5 Consensus size: 19
96558691 CTATGCGCTT
96558701 ATGTGCCAAGATGCACTTC
1 ATGTGCCAAGATGCACTTC
** *
96558720 ATGTGCCATTATGCGCTT-
1 ATGTGCCAAGATGCACTTC
* *
96558738 -TGAATGCCAGGATGCACCTC
1 ATG--TGCCAAGATGCACTTC
* * *
96558758 ATGTGTCAAGATACACTTT
1 ATGTGCCAAGATGCACTTC
*
96558777 GTGTGCCAA
1 ATGTGCCAA
96558786 TAATGCGTTT
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
17 2 0.04
19 44 0.92
21 2 0.04
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (19 bp):
ATGTGCCAAGATGCACTTC
Found at i:96561160 original size:12 final size:12
Alignment explanation
Indices: 96561143--96561167 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
96561133 TTTTCTGCAA
96561143 TTTAATTTTTAT
1 TTTAATTTTTAT
96561155 TTTAATTTTTAT
1 TTTAATTTTTAT
96561167 T
1 T
96561168 ACTAATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTAATTTTTAT
Found at i:96572504 original size:20 final size:19
Alignment explanation
Indices: 96572470--96572508 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
96572460 ATGACATACA
*
96572470 CATCTTGCTAACTTAATCAT
1 CATCTTGATAACTT-ATCAT
*
96572490 CATCTTGATATCTTATCAT
1 CATCTTGATAACTTATCAT
96572509 AAATTATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (19 bp):
CATCTTGATAACTTATCAT
Found at i:96578534 original size:13 final size:14
Alignment explanation
Indices: 96578516--96578545 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
96578506 ATGGGCATGT
96578516 GTGACCACACGG-C
1 GTGACCACACGGAC
96578529 GTGACCACACGGAC
1 GTGACCACACGGAC
96578543 GTG
1 GTG
96578546 TGACCCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.23, C:0.33, G:0.33, T:0.10
Consensus pattern (14 bp):
GTGACCACACGGAC
Found at i:96579938 original size:28 final size:28
Alignment explanation
Indices: 96579895--96580079 Score: 219
Period size: 28 Copynumber: 6.6 Consensus size: 28
96579885 TTTCAATGTC
* * * *
96579895 TCGCACACTAAATGCCGTACTCGATACC
1 TCGCACACTAAGTGCCATCCTCGATACT
* *
96579923 TCGCACACTAAGTGCCATTCTGGATGA-T
1 TCGCACACTAAGTGCCATCCTCGAT-ACT
* *
96579951 TTGCACACTAAGTTCCATCCTCGATACT
1 TCGCACACTAAGTGCCATCCTCGATACT
* * * * **
96579979 TAGCTCACTAAGTGCCATTCTGGATGTT
1 TCGCACACTAAGTGCCATCCTCGATACT
96580007 TCGCACACTAAGTGCCATCCTCGATACT
1 TCGCACACTAAGTGCCATCCTCGATACT
*
96580035 TCACACACTAAGTGCCATCCTCGATACT
1 TCGCACACTAAGTGCCATCCTCGATACT
96580063 TCGCACACTAAGTGCCA
1 TCGCACACTAAGTGCCA
96580080 CATTTAGCCG
Statistics
Matches: 131, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 1 0.01
28 129 0.98
29 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (28 bp):
TCGCACACTAAGTGCCATCCTCGATACT
Found at i:96584265 original size:26 final size:26
Alignment explanation
Indices: 96584234--96584428 Score: 129
Period size: 26 Copynumber: 7.5 Consensus size: 26
96584224 GTATATAGTA
** *
96584234 CCTGCTAAATAGCCACCGGCTCAAAG
1 CCTGCTAAATAAACACCAGCTCAAAG
* * *
96584260 CCTGCTAAATAAACACTAGCTAAAAA
1 CCTGCTAAATAAACACCAGCTCAAAG
* *
96584286 CCTACTAAATAAACATCAGCTCAAAG
1 CCTGCTAAATAAACACCAGCTCAAAG
* * * * *
96584312 CCTGCGAAATAAGCATCGGCTCATAG
1 CCTGCTAAATAAACACCAGCTCAAAG
* * * * *
96584338 CTTGCTTAGTAATCACCTGCTCAAAG
1 CCTGCTAAATAAACACCAGCTCAAAG
* **** * *
96584364 CTTGCTAAATAATTGTCAGCTTAAAA
1 CCTGCTAAATAAACACCAGCTCAAAG
* * **
96584390 CCTGCTAAACAATCACTGGCTCAAAG
1 CCTGCTAAATAAACACCAGCTCAAAG
96584416 CCTGCTAAATAAA
1 CCTGCTAAATAAA
96584429 TATCGGCTTA
Statistics
Matches: 126, Mismatches: 43, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 126 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (26 bp):
CCTGCTAAATAAACACCAGCTCAAAG
Found at i:96584436 original size:26 final size:26
Alignment explanation
Indices: 96584250--96584448 Score: 109
Period size: 26 Copynumber: 7.7 Consensus size: 26
96584240 AAATAGCCAC
*
96584250 CGGCTCAAAGCCTGCTAAATAAACA-
1 CGGCTCAAAGCCTGCTAAATAAATAT
* * * * *
96584275 CTAGCTAAAAACCTACTAAATAAACAT
1 C-GGCTCAAAGCCTGCTAAATAAATAT
* * **
96584302 CAGCTCAAAGCCTGCGAAATAAGCAT
1 CGGCTCAAAGCCTGCTAAATAAATAT
* * * * *
96584328 CGGCTCATAGCTTGCTTAGT-AATCAC
1 CGGCTCAAAGCCTGCTAAATAAAT-AT
* * * *
96584354 CTGCTCAAAGCTTGCTAAATAATTGT
1 CGGCTCAAAGCCTGCTAAATAAATAT
* * * *
96584380 CAGCTTAAAACCTGCTAAA-CAATCA-
1 CGGCTCAAAGCCTGCTAAATAAAT-AT
96584405 CTGGCTCAAAGCCTGCTAAATAAATAT
1 C-GGCTCAAAGCCTGCTAAATAAATAT
* *
96584432 CGGCTTAAGGCCTGCTA
1 CGGCTCAAAGCCTGCTA
96584449 TTCAGGTACA
Statistics
Matches: 128, Mismatches: 38, Indels: 15
0.71 0.21 0.08
Matches are distributed among these distances:
25 5 0.04
26 116 0.91
27 7 0.05
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (26 bp):
CGGCTCAAAGCCTGCTAAATAAATAT
Found at i:96584438 original size:52 final size:52
Alignment explanation
Indices: 96584233--96584448 Score: 159
Period size: 52 Copynumber: 4.2 Consensus size: 52
96584223 GGTATATAGT
** * *
96584233 ACCTGCTAAATAGCCACCGGCTCAAAGCCTGCTAAATAAACA-CTAGCTAAAA
1 ACCTGCTAAATAATCACTGGCTCAAAGCCTGCTAAATAAACATC-AGCTTAAA
* * * * * * * *
96584285 ACCTACTAAATAAACA-TCAGCTCAAAGCCTGCGAAATAAGCATCGGCTCATA
1 ACCTGCTAAATAATCACT-GGCTCAAAGCCTGCTAAATAAACATCAGCTTAAA
* * * * * ***
96584337 GCTTGCTTAGTAATCACCT-GCTCAAAGCTTGCTAAATAATTGTCAGCTTAAA
1 ACCTGCTAAATAATCA-CTGGCTCAAAGCCTGCTAAATAAACATCAGCTTAAA
* * * *
96584389 ACCTGCTAAACAATCACTGGCTCAAAGCCTGCTAAATAAATATCGGCTTAAG
1 ACCTGCTAAATAATCACTGGCTCAAAGCCTGCTAAATAAACATCAGCTTAAA
*
96584441 GCCTGCTA
1 ACCTGCTA
96584449 TTCAGGTACA
Statistics
Matches: 124, Mismatches: 35, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
51 2 0.02
52 120 0.97
53 1 0.01
54 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (52 bp):
ACCTGCTAAATAATCACTGGCTCAAAGCCTGCTAAATAAACATCAGCTTAAA
Found at i:96589279 original size:41 final size:41
Alignment explanation
Indices: 96589181--96589263 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
96589171 TAGCATAATA
96589181 AAGCAAACATCAAAATAGTGAGACTTTTGCTTTATAACCAT
1 AAGCAAACATCAAAATAGTGAGACTTTTGCTTTATAACCAT
96589222 AAGCAAACATCAAAATAGTGAGACTTTTGCTTTATAACCAT
1 AAGCAAACATCAAAATAGTGAGACTTTTGCTTTATAACCAT
96589263 A
1 A
96589264 CTTATAACCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (41 bp):
AAGCAAACATCAAAATAGTGAGACTTTTGCTTTATAACCAT
Found at i:96590577 original size:22 final size:21
Alignment explanation
Indices: 96590530--96590582 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
96590520 TGTTAGTTTC
*
96590530 TTAATGTTTTAACCTTTAATA
1 TTAATATTTTAACCTTTAATA
* * *
96590551 ATAATATTTTAACATTTTATTA
1 TTAATATTTTAAC-CTTTAATA
96590573 TTAATTATTT
1 TTAA-TATTT
96590583 AATTAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 11 0.44
22 9 0.36
23 5 0.20
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAATATTTTAACCTTTAATA
Found at i:96594996 original size:32 final size:32
Alignment explanation
Indices: 96594937--96595140 Score: 223
Period size: 32 Copynumber: 6.3 Consensus size: 32
96594927 ATGAACCTTT
* * * **
96594937 CCTTTTCTAGTTGTACACTCAAGGTGTACATTC
1 CCTTTTCAAG-TGTACACACAAAGTGTACATAA
* *
96594970 CCTTTTTAA-TGGTACACATAAAGTGTACA-AGA
1 CCTTTTCAAGT-GTACACACAAAGTGTACATA-A
*
96595002 CCTTTTCAAGTGTACACAAAAAGTGTACATAA
1 CCTTTTCAAGTGTACACACAAAGTGTACATAA
*
96595034 CCTTTTCAAGTGTACACACAAAGTGTATATAA
1 CCTTTTCAAGTGTACACACAAAGTGTACATAA
* * *
96595066 CCTTTTCAATTATACACACAAAGTGTACATAG
1 CCTTTTCAAGTGTACACACAAAGTGTACATAA
* * *
96595098 CCATTTCAGGAGTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGTACACACAAAGTGTACATAA
*
96595130 TCTTTTCAAGT
1 CCTTTTCAAGT
96595141 ATCATCCTTT
Statistics
Matches: 142, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
31 1 0.01
32 132 0.93
33 9 0.06
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (32 bp):
CCTTTTCAAGTGTACACACAAAGTGTACATAA
Found at i:96595060 original size:96 final size:96
Alignment explanation
Indices: 96594937--96595140 Score: 248
Period size: 96 Copynumber: 2.1 Consensus size: 96
96594927 ATGAACCTTT
* * * ** * * *
96594937 CCTTTTCTAGTTGTACACTCAAGGTGTACATTCCCTTTTTAATGGTACACATAAAGTGTACA-AG
1 CCTTTTCAAG-TGTACACACAAAGTGTACATAACCTTTTCAATGATACACACAAAGTGTACATAG
* *
96595001 ACCTTTTCAAGTGTACACAAAAAGTGTACATAA
65 -CCATTTCAAGAGTACACAAAAAGTGTACATAA
* *
96595034 CCTTTTCAAGTGTACACACAAAGTGTATATAACCTTTTCAATTATACACACAAAGTGTACATAGC
1 CCTTTTCAAGTGTACACACAAAGTGTACATAACCTTTTCAATGATACACACAAAGTGTACATAGC
* *
96595099 CATTTCAGGAGTACACACAAAGTGTACATAA
66 CATTTCAAGAGTACACAAAAAGTGTACATAA
*
96595130 TCTTTTCAAGT
1 CCTTTTCAAGT
96595141 ATCATCCTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
96 80 0.88
97 11 0.12
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (96 bp):
CCTTTTCAAGTGTACACACAAAGTGTACATAACCTTTTCAATGATACACACAAAGTGTACATAGC
CATTTCAAGAGTACACAAAAAGTGTACATAA
Found at i:96601830 original size:32 final size:32
Alignment explanation
Indices: 96601771--96601878 Score: 128
Period size: 32 Copynumber: 3.3 Consensus size: 32
96601761 GTGGACCTTT
* * * * **
96601771 CCTTTTCCAGTTGTACACCCGAGGTGTACATTC
1 CCTTTTCAAG-TGTACACACAAAGTGTACATAA
96601804 CCTTTTCAA-TGGTACACACAAAGTGTACATAA
1 CCTTTTCAAGT-GTACACACAAAGTGTACATAA
*
96601836 CCTTTTCAAGTGTACACACAAAGTGTATATAA
1 CCTTTTCAAGTGTACACACAAAGTGTACATAA
96601868 CCTTTTCAAGT
1 CCTTTTCAAGT
96601879 ACCACCCTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.02
32 56 0.85
33 9 0.14
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (32 bp):
CCTTTTCAAGTGTACACACAAAGTGTACATAA
Found at i:96603958 original size:19 final size:19
Alignment explanation
Indices: 96603934--96603976 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
96603924 GCAGATTGTA
*
96603934 CACACCGGTGTGGAAATCT
1 CACACCCGTGTGGAAATCT
96603953 CACACCCGTGTGGAAATCT
1 CACACCCGTGTGGAAATCT
96603972 CACAC
1 CACAC
96603977 GCTCGTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.19
Consensus pattern (19 bp):
CACACCCGTGTGGAAATCT
Found at i:96620909 original size:3 final size:3
Alignment explanation
Indices: 96620901--96620932 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
96620891 TAATTATGTA
96620901 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
96620933 CAATGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:96622209 original size:20 final size:20
Alignment explanation
Indices: 96622186--96622226 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
96622176 TTAATAAAAT
*
96622186 TTAAATATTTTAT-ATTTTTA
1 TTAAA-ATTTAATAATTTTTA
96622206 TTAAAATTTAATAATTTTTA
1 TTAAAATTTAATAATTTTTA
96622226 T
1 T
96622227 AACTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAAAATTTAATAATTTTTA
Found at i:96622225 original size:10 final size:9
Alignment explanation
Indices: 96622102--96622259 Score: 56
Period size: 9 Copynumber: 16.7 Consensus size: 9
96622092 CTTTTTATGC
96622102 ATTTTT-TA
1 ATTTTTATA
*
96622110 ATTTTTTATG
1 A-TTTTTATA
96622120 ATTTTTATAA
1 ATTTTTAT-A
* * *
96622130 AATTCTACA
1 ATTTTTATA
96622139 ATATTTTATA
1 AT-TTTTATA
*
96622149 ATTTTTTTACA
1 A--TTTTTATA
*
96622160 ATTTTCATTCTA
1 A-TTT--TTATA
96622172 ATTTTTAATA
1 ATTTTT-ATA
**
96622182 AAATTTA-A
1 ATTTTTATA
96622190 ATATTTTAT-
1 AT-TTTTATA
96622199 ATTTTTATTAA
1 ATTTTTA-T-A
* *
96622210 AATTTAATA
1 ATTTTTATA
96622219 ATTTTTATA
1 ATTTTTATA
* *
96622228 ACTTTTATTG
1 ATTTTTA-TA
96622238 ATTTTTAT-
1 ATTTTTATA
96622246 -TTTTTATA
1 ATTTTTATA
96622254 ATTTTT
1 ATTTTT
96622260 TGCCACATGT
Statistics
Matches: 110, Mismatches: 23, Indels: 33
0.66 0.14 0.20
Matches are distributed among these distances:
7 7 0.06
8 8 0.07
9 44 0.40
10 31 0.28
11 15 0.14
12 5 0.05
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:96622564 original size:80 final size:81
Alignment explanation
Indices: 96622363--96622578 Score: 231
Period size: 80 Copynumber: 2.6 Consensus size: 81
96622353 GCCAAAGAGC
* * *
96622363 CTTTTTGATGCATTTTACAGTTCAAGTATCTAATTGAGTGAAAAAAATTCAGTGGCTTAATTATT
1 CTTTTTGATGCATTTTAAAGTTCAAGTATCCAATTGAGTGCAAAAAA---AGTGGCTTAATTATT
96622428 TTTTTTCAAAAAGTTTGAGGGT
63 TTTTTT---AAAGTTTGAGGGT
* * * * * * *
96622450 CTTTCTAATGCGTTTTGAAAGTTTAAATACCCAATTGAGTGCAAAAAAA-TGGCTTAATTGTTTT
1 CTTTTTGATGCATTTT-AAAGTTCAAGTATCCAATTGAGTGCAAAAAAAGTGGCTTAATTATTTT
96622514 TTTT-AAGTTTGAGGG-
65 TTTTAAAGTTTGAGGGT
*
96622529 CATTTTTGATGCATTTTAAAAGTTCAAGTATCCAATTAAGTGCAAAAAAA
1 C-TTTTTGATGCATTTT-AAAGTTCAAGTATCCAATTGAGTGCAAAAAAA
96622579 AGAAGAAGAA
Statistics
Matches: 109, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
79 1 0.01
80 51 0.47
84 18 0.17
85 1 0.01
87 13 0.12
88 25 0.23
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (81 bp):
CTTTTTGATGCATTTTAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAGTGGCTTAATTATTTTT
TTTAAAGTTTGAGGGT
Found at i:96622584 original size:3 final size:3
Alignment explanation
Indices: 96622578--96622625 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
96622568 GTGCAAAAAA
96622578 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
96622626 CAAGGGCTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:96623327 original size:40 final size:40
Alignment explanation
Indices: 96623272--96623352 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
96623262 TATCAAATAA
96623272 AAGAGTTTGTGAGCTGCCTGTGGTGCTTGCATCTAGCATC
1 AAGAGTTTGTGAGCTGCCTGTGGTGCTTGCATCTAGCATC
96623312 AAGAGTTTGTGAGCTGCCTGTGGTGCTTGCATCTAGCATC
1 AAGAGTTTGTGAGCTGCCTGTGGTGCTTGCATCTAGCATC
96623352 A
1 A
96623353 TTCTCTCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.32
Consensus pattern (40 bp):
AAGAGTTTGTGAGCTGCCTGTGGTGCTTGCATCTAGCATC
Found at i:96623905 original size:11 final size:11
Alignment explanation
Indices: 96623889--96623913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
96623879 CTCATATTCA
96623889 CAAATTTCTCT
1 CAAATTTCTCT
96623900 CAAATTTCTCT
1 CAAATTTCTCT
96623911 CAA
1 CAA
96623914 TTCCTTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (11 bp):
CAAATTTCTCT
Found at i:96624090 original size:178 final size:175
Alignment explanation
Indices: 96623752--96624106 Score: 613
Period size: 178 Copynumber: 2.0 Consensus size: 175
96623742 CAGTTACCCG
96623752 TCCCAATAGCTACCCCACCCAATGATTATTTAAATAGCCATTGAAACCCCCACTAATAGCTCTTT
1 TCCCAATAGCTACCCCACCCAATGATTATTTAAATAGCCATTGAAACCCCCACTAATAGCTCTTT
*
96623817 TTATATATATAAAAACCCCTAATTCTTTTCTTTTTTTTCGATTCAATCTCAACTATCTATGTCTC
66 TTATATATATAAAAACCCCTAATTCTTTTCTTTTTTTTCAATTCAATCTCAACTATCTATGTCTC
*
96623882 ATATTCACAAATTTCTCTCAAATTTCTCTCAATTCCTTCTTAATT
131 ATATTCACAAATCTCTCTCAAATTTCTCTCAATTCCTTCTTAATT
*
96623927 TCCCAATAGCTACCCCACCCAATGGTTATTTAAATAGCCATTGAAACCTCCCACTAATAGCTCTT
1 TCCCAATAGCTACCCCACCCAATGATTATTTAAATAGCCATTGAAACC-CCCACTAATAGCTCTT
* * *
96623992 TTT-TTTCTATATAAACCCCTAATTCTTTTCTTCTTTTTTTTCAATTCAATCTCAACTATCTATG
65 TTTATATATATAAAAACCCCTAATTC--TT-TTCTTTTTTTTCAATTCAATCTCAACTATCTATG
96624056 TCTCATATTCACAAATCTCTCTCAAATTTCTCTCAATTCCTTCTTAATT
127 TCTCATATTCACAAATCTCTCTCAAATTTCTCTCAATTCCTTCTTAATT
96624105 TC
1 TC
96624107 TCACTCAATT
Statistics
Matches: 170, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
175 66 0.39
176 19 0.11
177 2 0.01
178 83 0.49
ACGTcount: A:0.28, C:0.27, G:0.04, T:0.41
Consensus pattern (175 bp):
TCCCAATAGCTACCCCACCCAATGATTATTTAAATAGCCATTGAAACCCCCACTAATAGCTCTTT
TTATATATATAAAAACCCCTAATTCTTTTCTTTTTTTTCAATTCAATCTCAACTATCTATGTCTC
ATATTCACAAATCTCTCTCAAATTTCTCTCAATTCCTTCTTAATT
Found at i:96624138 original size:20 final size:20
Alignment explanation
Indices: 96624083--96624139 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
96624073 TCTCTCAAAT
* * * *
96624083 TTCTCTCAATTCCTTCTTAA
1 TTCTCTCAACTCATTTTTTA
*
96624103 TT-TCTC-ACTCAATTTTTA
1 TTCTCTCAACTCATTTTTTA
96624121 TTCTCTCAACTCATTTTTT
1 TTCTCTCAACTCATTTTTT
96624140 TAATTAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
18 9 0.31
19 8 0.28
20 12 0.41
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.54
Consensus pattern (20 bp):
TTCTCTCAACTCATTTTTTA
Found at i:96625748 original size:26 final size:23
Alignment explanation
Indices: 96625706--96625765 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 23
96625696 TTTGGTTCTC
*
96625706 GATTTTTATATTGATTTTGGAATAT
1 GATTTTTAGATTGATTTT--AATAT
96625731 AGATTTTTAGACTT-ATTTTAATAT
1 -GATTTTTAGA-TTGATTTTAATAT
*
96625755 GACTTTTAGAT
1 GATTTTTAGAT
96625766 ATTATTTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 5 0.16
26 14 0.45
27 2 0.06
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (23 bp):
GATTTTTAGATTGATTTTAATAT
Found at i:96625770 original size:24 final size:24
Alignment explanation
Indices: 96625726--96625772 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
96625716 TTGATTTTGG
* *
96625726 AATATAGATTTTTAGACTTATTTT
1 AATATAGACTTTTAGAATTATTTT
96625750 AATAT-GACTTTTAGATATTATTT
1 AATATAGACTTTTAGA-ATTATTT
96625773 GGTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (24 bp):
AATATAGACTTTTAGAATTATTTT
Found at i:96626526 original size:29 final size:31
Alignment explanation
Indices: 96626490--96626551 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 31
96626480 AACTCTATTT
96626490 TTATATAATTTTTATAT-TTTT-TTTAAAAA
1 TTATATAATTTTTATATATTTTCTTTAAAAA
*
96626519 TTATATAATTTTTATATATTTTCTTTTAAAA
1 TTATATAATTTTTATATATTTTCTTTAAAAA
96626550 TT
1 TT
96626552 TTAAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 17 0.57
30 4 0.13
31 9 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (31 bp):
TTATATAATTTTTATATATTTTCTTTAAAAA
Found at i:96626559 original size:22 final size:22
Alignment explanation
Indices: 96626519--96626571 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
96626509 TTTTTAAAAA
* *
96626519 TTATATAATTTTTATATATTTTCT
1 TTATA-AAATTTTAAATATTTT-T
96626543 TT-TAAAATTTTAAATATTTTT
1 TTATAAAATTTTAAATATTTTT
96626564 TTATAAAA
1 TTATAAAA
96626572 AATAGATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.73
23 2 0.08
24 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATAAAATTTTAAATATTTTT
Found at i:96629225 original size:16 final size:16
Alignment explanation
Indices: 96629204--96629237 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
96629194 GGTTGGAGAT
96629204 CATTGGAGCATCATCA
1 CATTGGAGCATCATCA
96629220 CATTGGAGCATCATCA
1 CATTGGAGCATCATCA
96629236 CA
1 CA
96629238 CTATCCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (16 bp):
CATTGGAGCATCATCA
Found at i:96632403 original size:46 final size:46
Alignment explanation
Indices: 96632260--96632403 Score: 134
Period size: 46 Copynumber: 3.1 Consensus size: 46
96632250 CCCGCCCATA
* *
96632260 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CT
* * * * *
96632309 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCCT
* *
96632353 AGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
96632399 AGTGA
1 AGTGA
96632404 CATGTCACTT
Statistics
Matches: 75, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
44 8 0.11
46 32 0.43
47 31 0.41
49 4 0.05
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
Found at i:96634810 original size:30 final size:30
Alignment explanation
Indices: 96634766--96634854 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
96634756 CAAAGATAAC
96634766 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
96634795 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
96634825 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
96634855 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:96634814 original size:15 final size:15
Alignment explanation
Indices: 96634766--96634845 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
96634756 CAAAGATAAC
*
96634766 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
96634780 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
96634795 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
96634810 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
96634825 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
96634840 AAGAAA
1 AAGAAA
96634846 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:96634854 original size:15 final size:15
Alignment explanation
Indices: 96634777--96634854 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
96634767 AGAAAACCGA
96634777 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
96634792 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
96634806 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
96634821 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
96634837 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
96634852 ATA
1 ATA
96634855 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:96637905 original size:93 final size:93
Alignment explanation
Indices: 96637793--96637962 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
96637783 GCCCATAAGT
* *
96637793 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGAACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
96637857 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
* *
96637886 GAACTCGAACTCAACTCAACTAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
96637951 CGAGTTCGGATG
66 CGAGCTCGGATG
96637963 GCCAAACATC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:96637960 original size:46 final size:45
Alignment explanation
Indices: 96637785--96637959 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 45
96637775 TGTAACCCGC
*
96637785 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
*
96637831 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** * * *
96637877 ACATCTCTCGAACTCGAACTCAACTCAACTAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
*
96637924 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
96637960 ATGGCCAAAC
Statistics
Matches: 106, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 65 0.61
47 30 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:96637979 original size:46 final size:44
Alignment explanation
Indices: 96637790--96637979 Score: 113
Period size: 46 Copynumber: 4.1 Consensus size: 44
96637780 CCCGCCCATA
* * * *
96637790 AGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GGATG-CCAACATCC-T
*
96637835 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACATC-CT
* * * * *
96637885 --CGAACTCGAACTCAACTCAACTAGTTCGGACAT-TC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCAACATCC-T
96637928 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGGCCAAACATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGAT-GCC-AACATCCT
96637975 AGTGA
1 AGTGA
96637980 CATGTCACTT
Statistics
Matches: 113, Mismatches: 14, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
42 1 0.01
43 5 0.04
44 2 0.02
45 3 0.03
46 62 0.55
47 26 0.23
48 6 0.05
49 2 0.02
50 5 0.04
51 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACATCCT
Found at i:96640858 original size:44 final size:44
Alignment explanation
Indices: 96640808--96640892 Score: 145
Period size: 44 Copynumber: 1.9 Consensus size: 44
96640798 ACATGTAACA
96640808 CATCCATAATGAACTC-GAACCAACTCAACGAGCTCGGATGCTCG
1 CATCCATAATGAACTCAG-ACCAACTCAACGAGCTCGGATGCTCG
*
96640852 CATCCATAATGAACTCAGACCAACTCAATGAGCTCGGATGC
1 CATCCATAATGAACTCAGACCAACTCAACGAGCTCGGATGC
96640893 CTCATACATA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.19
Consensus pattern (44 bp):
CATCCATAATGAACTCAGACCAACTCAACGAGCTCGGATGCTCG
Found at i:96657285 original size:263 final size:255
Alignment explanation
Indices: 96656759--96657289 Score: 771
Period size: 263 Copynumber: 2.0 Consensus size: 255
96656749 CATCTTCAAC
*
96656759 CTAAAATACATGGAAAATAAGAGAGAGAGAAGAAACTTTCATGGCATAATTGGGTAAGTTTCCTT
1 CTAAAATACATGGAAAACAAGAGAGAGAGAAGAAACTTTCATGGCATAATTGGGTAAGTTTCCTT
**
96656824 GTCCTGTTTTTAGTAATTTTCATATTTTTGAAATAATCTATTTATTTGGGGGATCAATTTGAAAA
66 GTCCCATTTTTAGTAATTTTCATATTTTTGAAATAATCTATTTATTTGGGGGATCAATTTGAAAA
* * *
96656889 GTTATCAAAGTATAAAAATTGGGTCATGGATGAATATGCTGAAAATTTGAAATTTATGATAGAAA
131 GTTATCAAAGTATAAAAATTGAGTCATGGATGAATA--CTG---A-TTGAAAATTATGACAGAAA
*
96656954 ATGAAAGGTTGTTGATAGATAAACAACTTTTACGAAGTGATTTTTGATGAAAACATGATTTAGGG
190 ATGAAAGGTTGTTGATAGATAAACAACTTTTACGAAGTAATTTTTGATGAAAACATGATTTAGGG
96657019 A
255 A
* * * *
96657020 CTAAAATACATGGAAAACAGGAGAGAGAGAAGAAACTTTTATGGCTTAATTGGGTAAGTTTTCTT
1 CTAAAATACATGGAAAACAAGAGAGAGAGAAGAAACTTTCATGGCATAATTGGGTAAGTTTCCTT
*
96657085 GTCCCATTTTTAGTAATTTTGATATTTTTGAAACTGGGATAACTTAATCTATTTATTT-GGGGAT
66 GTCCCATTTTTAGTAATTTTCATA-TTTT-----T--GA-AA--TAATCTATTTATTTGGGGGAT
*
96657149 CAATTTGAAAAGTTATCAAAGTATAAAAATTGAGTCATGGATGAATA-TG-TTGAAAATTATGGC
120 CAATTTGAAAAGTTATCAAAGTATAAAAATTGAGTCATGGATGAATACTGATTGAAAATTATGAC
96657212 AGAAAATGAAAGGTTGTTGATAGATAAACAACTTTTACGAAGTAATTTTTGATGAAAACATGATT
185 AGAAAATGAAAGGTTGTTGATAGATAAACAACTTTTACGAAGTAATTTTTGATGAAAACATGATT
96657277 TAGGGA
250 TAGGGA
96657283 CTAAAAT
1 CTAAAAT
96657290 GTAAAATTGT
Statistics
Matches: 246, Mismatches: 13, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
261 81 0.33
262 4 0.02
263 88 0.36
267 1 0.00
268 2 0.01
269 2 0.01
270 2 0.01
271 52 0.21
272 14 0.06
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.35
Consensus pattern (255 bp):
CTAAAATACATGGAAAACAAGAGAGAGAGAAGAAACTTTCATGGCATAATTGGGTAAGTTTCCTT
GTCCCATTTTTAGTAATTTTCATATTTTTGAAATAATCTATTTATTTGGGGGATCAATTTGAAAA
GTTATCAAAGTATAAAAATTGAGTCATGGATGAATACTGATTGAAAATTATGACAGAAAATGAAA
GGTTGTTGATAGATAAACAACTTTTACGAAGTAATTTTTGATGAAAACATGATTTAGGGA
Found at i:96666848 original size:7 final size:7
Alignment explanation
Indices: 96666836--96666876 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
96666826 CACATTTCTA
96666836 CTCATCC
1 CTCATCC
96666843 CTCATCC
1 CTCATCC
96666850 CTCATCC
1 CTCATCC
96666857 CTCATCC
1 CTCATCC
*
96666864 TTCATCC
1 CTCATCC
*
96666871 TTCATC
1 CTCATC
96666877 ATTCTCTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.15, C:0.51, G:0.00, T:0.34
Consensus pattern (7 bp):
CTCATCC
Found at i:96685872 original size:49 final size:49
Alignment explanation
Indices: 96685771--96685864 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
96685761 TGTTATCAGA
* *
96685771 CAACCCAGGGGGGTAGAATGTACATATCCTAGTAGTCATCATTGTCGAG
1 CAACCCAGGGGGATAGAATCTACATATCCTAGTAGTCATCATTGTCGAG
* * * * *
96685820 CAACCCAGGGTGATAGTATCTACATGTTCTAGTAGTCATCGTTGT
1 CAACCCAGGGGGATAGAATCTACATATCCTAGTAGTCATCATTGT
96685865 TGGGCAACTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (49 bp):
CAACCCAGGGGGATAGAATCTACATATCCTAGTAGTCATCATTGTCGAG
Found at i:96692534 original size:40 final size:39
Alignment explanation
Indices: 96692417--96692546 Score: 152
Period size: 40 Copynumber: 3.3 Consensus size: 39
96692407 ATTTGATATG
* * * * **
96692417 ACACTAAGTGCCATACATATCCGAAGCTATCTCAAATCGC
1 ACACTAAGTGCCATATATA-GCAAAGCTATGTCGTATCGC
*
96692457 ACACTAAGTCCCATATATAGCAAAGCTATGTCGTATCGC
1 ACACTAAGTGCCATATATAGCAAAGCTATGTCGTATCGC
* * *
96692496 ACACTAAGTGTCATGTATAGCTGAAGCTATGTCGTATCGC
1 ACACTAAGTGCCATATATAGC-AAAGCTATGTCGTATCGC
96692536 ACACTAAGTGC
1 ACACTAAGTGC
96692547 TACAAATAAC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 33 0.43
40 44 0.57
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (39 bp):
ACACTAAGTGCCATATATAGCAAAGCTATGTCGTATCGC
Found at i:96694033 original size:43 final size:43
Alignment explanation
Indices: 96693985--96694140 Score: 170
Period size: 43 Copynumber: 3.6 Consensus size: 43
96693975 CCGAAAAAAA
** * *
96693985 TATACTGGTACACACAGTGCATCATCGGACAAGCTGAAATAAT
1 TATACTGACACACACAGTGCATCATCGAACAAGCTGAAGTAAT
* * * *
96694028 TATACTGACACATATAGTGCATCATCGAAAAAACTGAAGTAAT
1 TATACTGACACACACAGTGCATCATCGAACAAGCTGAAGTAAT
* * * *
96694071 TATATTGGCACCCACAGTGCATCATCAAACAAG-TCGAAGTAAT
1 TATACTGACACACACAGTGCATCATCGAACAAGCT-GAAGTAAT
* *
96694114 TATACTGACACACAGAGTACATCATCG
1 TATACTGACACACACAGTGCATCATCG
96694141 GATAAACCGA
Statistics
Matches: 90, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 1 0.01
43 89 0.99
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (43 bp):
TATACTGACACACACAGTGCATCATCGAACAAGCTGAAGTAAT
Found at i:96694046 original size:87 final size:87
Alignment explanation
Indices: 96693895--96694151 Score: 229
Period size: 86 Copynumber: 3.0 Consensus size: 87
96693885 AAATTGAAGG
* * * * * *
96693895 AAATATAATGGCATACACAGTTCATCATCGGACAAGCCGAAACAATTCTACT-AGCACGCT-TAG
1 AAATATAATGGCACACACAGTGCATCATCGGACAAGCTGAAATAATTATACTGA-CAC-ATATAG
96693958 TGAATCATTGGAATAAACCGAAAA
64 TGAATCATTGGAATAAACCGAAAA
* *
96693982 AAATATACTGGTACACACAGTGCATCATCGGACAAGCTGAAATAATTATACTGACACATATAGTG
1 AAATATAATGGCACACACAGTGCATCATCGGACAAGCTGAAATAATTATACTGACACATATAGTG
* * * * **
96694047 CATCA-TCGAAAAAACTGAAGT
66 AATCATTGGAATAAACCGAAAA
* * * ** * * *
96694068 AATTATATTGGCACCCACAGTGCATCATCAAACAAG-TCGAAGTAATTATACTGACACACAGAGT
1 AAATATAATGGCACACACAGTGCATCATCGGACAAGCT-GAAATAATTATACTGACACATATAGT
*
96694132 -ACATCATCGG-ATAAACCGAA
65 GA-ATCATTGGAATAAACCGAA
96694152 GTATAACATG
Statistics
Matches: 137, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
85 1 0.01
86 77 0.56
87 58 0.42
88 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (87 bp):
AAATATAATGGCACACACAGTGCATCATCGGACAAGCTGAAATAATTATACTGACACATATAGTG
AATCATTGGAATAAACCGAAAA
Found at i:96694152 original size:43 final size:43
Alignment explanation
Indices: 96693909--96694154 Score: 161
Period size: 43 Copynumber: 5.7 Consensus size: 43
96693899 ATAATGGCAT
* * ** *
96693909 ACACAGTTCATCATCGGACAAGCCGAAACAATTCTACT-AGCAC
1 ACACAGTGCATCATCGGACAAACCGAAGTAATTATACTGA-CAC
* ** * * * ** * **
96693952 GCTTAGTGAATCATTGGAATAAACCGAAAAAAATATACTGGTAC
1 ACACAGTGCATCATCGG-ACAAACCGAAGTAATTATACTGACAC
* * *
96693996 ACACAGTGCATCATCGGACAAGCTGAAATAATTATACTGACAC
1 ACACAGTGCATCATCGGACAAACCGAAGTAATTATACTGACAC
* * * * * * *
96694039 ATATAGTGCATCATCGAAAAAACTGAAGTAATTATATTGGCAC
1 ACACAGTGCATCATCGGACAAACCGAAGTAATTATACTGACAC
* ** **
96694082 CCACAGTGCATCATCAAACAAGTCGAAGTAATTATACTGACAC
1 ACACAGTGCATCATCGGACAAACCGAAGTAATTATACTGACAC
* * *
96694125 ACAGAGTACATCATCGGATAAACCGAAGTA
1 ACACAGTGCATCATCGGACAAACCGAAGTA
96694155 TAACATGTAA
Statistics
Matches: 150, Mismatches: 51, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
43 120 0.80
44 30 0.20
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (43 bp):
ACACAGTGCATCATCGGACAAACCGAAGTAATTATACTGACAC
Found at i:96697123 original size:93 final size:93
Alignment explanation
Indices: 96696964--96697149 Score: 293
Period size: 93 Copynumber: 2.0 Consensus size: 93
96696954 CGTTGTATCA
* *
96696964 AGTACTAACAAGCCCAAGGACTAATTTGCAAAACTACTTAATATTTTGAAAGTTTTCATTTATGA
1 AGTACTAACAAGCCCAAGGACTAATTTGCAAAACTACTTAATATTTTGAAACTTTTCATTAATGA
96697029 ATTCATGTGTTTTTTAAT-TATTGATGAT
66 ATTCATGTGTTTTTTAATGT-TTGATGAT
* * * * *
96697057 AGTACTAGCTAGCCCAGGGACTAATTTGCAAAATTGCTTAATATTTTGAAACTTTTCATTAATGA
1 AGTACTAACAAGCCCAAGGACTAATTTGCAAAACTACTTAATATTTTGAAACTTTTCATTAATGA
96697122 ATTCATGTGTTTTTTAATGTTTGATGAT
66 ATTCATGTGTTTTTTAATGTTTGATGAT
96697150 GAATTATGAT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
93 84 0.99
94 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (93 bp):
AGTACTAACAAGCCCAAGGACTAATTTGCAAAACTACTTAATATTTTGAAACTTTTCATTAATGA
ATTCATGTGTTTTTTAATGTTTGATGAT
Found at i:96703133 original size:34 final size:34
Alignment explanation
Indices: 96703090--96703158 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
96703080 AAATTTATCT
*
96703090 TGGTCTTGATGAACATCCACTTAATAATAAAATA
1 TGGTCTTGATGAACATCCACTTAACAATAAAATA
96703124 TGGTCTTGATGAACATCCACTTAACAATAAAATA
1 TGGTCTTGATGAACATCCACTTAACAATAAAATA
96703158 T
1 T
96703159 TCATAATACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (34 bp):
TGGTCTTGATGAACATCCACTTAACAATAAAATA
Found at i:96706568 original size:44 final size:43
Alignment explanation
Indices: 96706484--96706570 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
96706474 ATTTGAACTA
* *
96706484 GTAAACTTTTAGTTTACTATGCACGTGATTTAACATTACTAAT
1 GTAAACTTCTAGTTTACAATGCACGTGATTTAACATTACTAAT
* *
96706527 GTAAACTTCTGGTTTACAATCGCATGTGATTTAACCA-TACTAAT
1 GTAAACTTCTAGTTTACAAT-GCACGTGATTTAA-CATTACTAAT
96706571 ATATTGATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 17 0.45
44 19 0.50
45 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (43 bp):
GTAAACTTCTAGTTTACAATGCACGTGATTTAACATTACTAAT
Found at i:96707463 original size:21 final size:22
Alignment explanation
Indices: 96707427--96707470 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
96707417 AATAAATATT
*
96707427 AATTAATTAATTTAATTAGATA
1 AATTAATTAATTTAATTAAATA
*
96707449 AATTAATT-TTTTAATTAAATA
1 AATTAATTAATTTAATTAAATA
96707470 A
1 A
96707471 TTTTCTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTAATTAATTTAATTAAATA
Found at i:96707601 original size:24 final size:24
Alignment explanation
Indices: 96707574--96707622 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
96707564 ATTCACAATG
96707574 ACTAATTAATTTAATTCTATTTTC
1 ACTAATTAATTTAATTCTATTTTC
96707598 ACTAATTAATTTAATTCTATTTTC
1 ACTAATTAATTTAATTCTATTTTC
96707622 A
1 A
96707623 AACTTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (24 bp):
ACTAATTAATTTAATTCTATTTTC
Found at i:96708868 original size:22 final size:22
Alignment explanation
Indices: 96708840--96708893 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
96708830 TTTAGGGTCG
*
96708840 ACGTCGTGACATCACCTCCTTC
1 ACGTCGTGACATCACCTCCTCC
**
96708862 ACGTCGTGATGTCACCTCCTCC
1 ACGTCGTGACATCACCTCCTCC
*
96708884 ACATCGTGAC
1 ACGTCGTGAC
96708894 GCTGCCAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.39, G:0.17, T:0.26
Consensus pattern (22 bp):
ACGTCGTGACATCACCTCCTCC
Found at i:96716940 original size:20 final size:21
Alignment explanation
Indices: 96716897--96716941 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
96716887 ATATTCTGAT
* *
96716897 ACATATCAATCACATATAAGC
1 ACATATCAATCACATACAACC
*
96716918 ACATAT-AATTACATACAACC
1 ACATATCAATCACATACAACC
96716938 ACAT
1 ACAT
96716942 TTAGTCATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
ACATATCAATCACATACAACC
Found at i:96716974 original size:13 final size:13
Alignment explanation
Indices: 96716956--96716982 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
96716946 TCATAGTGTA
96716956 TGATAATTTGGCT
1 TGATAATTTGGCT
96716969 TGATAATTTGGCT
1 TGATAATTTGGCT
96716982 T
1 T
96716983 TTGAGTTTAT
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:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (13 bp):
TGATAATTTGGCT
Found at i:96720526 original size:27 final size:27
Alignment explanation
Indices: 96720478--96720636 Score: 173
Period size: 27 Copynumber: 5.9 Consensus size: 27
96720468 GCGAGGTTGC
* * *
96720478 CAGATATTGTGACGGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
*
96720505 CAGATATTGTAGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
96720531 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* * *
96720558 CAGATAATTGTGGCATAGCCACTAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
96720585 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
96720612 CAAATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
96720637 GACGCTTCCT
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
26 10 0.09
27 98 0.88
28 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:96720639 original size:54 final size:54
Alignment explanation
Indices: 96720478--96720639 Score: 229
Period size: 54 Copynumber: 3.0 Consensus size: 54
96720468 GCGAGGTTGC
* * * * * *
96720478 CAGATAT-TGTGACGGAGTCACCAGATACAGAT-ATTGTAGCAGAGCCACCAGAA
1 CAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAGGA
*
96720531 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACTAGGA
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGA
*
96720585 CAGATATATGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGCCACCAGGA
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGA
96720639 C
1 C
96720640 GCTTCCTCCA
Statistics
Matches: 98, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
53 12 0.12
54 86 0.88
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (54 bp):
CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGA
Found at i:96720756 original size:27 final size:26
Alignment explanation
Indices: 96720732--96720784 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
96720722 TTTTCAGTCA
96720732 AAATTAAC-CCTAGGGGTATAACAGT
1 AAATTAACACCTAGGGGTATAACAGT
* **
96720757 AATTTTGCACCTAGGGGTATAACAGT
1 AAATTAACACCTAGGGGTATAACAGT
96720783 AA
1 AA
96720785 TTTTCCATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (26 bp):
AAATTAACACCTAGGGGTATAACAGT
Found at i:96720769 original size:26 final size:27
Alignment explanation
Indices: 96720740--96720815 Score: 100
Period size: 26 Copynumber: 2.8 Consensus size: 27
96720730 CAAAATTAAC
*
96720740 CCTAGGGGTATAACAGTAATTTTGC-A
1 CCTAGGGGTATAACAGTAATTTTCCAA
96720766 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATAACAGTAATTTTCCA-A
* * *
96720794 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATAACAGTAATTT
96720816 AGCTGCTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 24 0.55
28 20 0.45
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (27 bp):
CCTAGGGGTATAACAGTAATTTTCCAA
Found at i:96722289 original size:26 final size:26
Alignment explanation
Indices: 96722258--96722365 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
96722248 TGAAATGCCC
*
96722258 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
96722284 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
96722310 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
96722336 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
96722362 ATCA
1 ATCA
96722366 ATTTATACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:96735451 original size:40 final size:40
Alignment explanation
Indices: 96735396--96735590 Score: 302
Period size: 40 Copynumber: 4.9 Consensus size: 40
96735386 AGATATAGCT
*
96735396 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
96735436 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * * *
96735476 ACTCGCACAATTGCCTTCAGGACTTGGCCCAGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
96735516 ACTCGCACAAATGCCTTCGGGACTTAGCCCAGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
96735556 ACTCGCACAAATGCCTTCGGG-CTTAGCCGGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
96735591 CAATCCGAAT
Statistics
Matches: 143, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 11 0.08
40 132 0.92
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:96735511 original size:80 final size:80
Alignment explanation
Indices: 96735370--96735583 Score: 299
Period size: 80 Copynumber: 2.7 Consensus size: 80
96735360 AAACCAAGTA
** * * *
96735370 CCTTCGGGGTTTAG-CCAGATATAGCT-ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATA
1 CCTTCGGGACTTAGCCCAGATATAG-TAACTCGCACAAATGCCTTCAGGACTTAGCCCAGTTATA
*
96735433 GTAACTCGCACAATTG
65 GTAACTCGCACAAATG
* * * *
96735449 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCAGGACTTGGCCCAGTTATAG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATGCCTTCAGGACTTAGCCCAGTTATAG
96735514 TAACTCGCACAAATG
66 TAACTCGCACAAATG
*
96735529 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATGCCTTC-GGGCTTAGCC
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATGCCTTCAGGACTTAGCC
96735584 GGGTTATCAA
Statistics
Matches: 118, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
79 21 0.18
80 97 0.82
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATGCCTTCAGGACTTAGCCCAGTTATAG
TAACTCGCACAAATG
Found at i:96753189 original size:23 final size:23
Alignment explanation
Indices: 96753163--96753207 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
96753153 TGGGTATGAG
*
96753163 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
96753186 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
96753208 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:96758833 original size:17 final size:17
Alignment explanation
Indices: 96758811--96758850 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
96758801 GTAATTTTTA
96758811 CTTACTAAGC-ATATGAG
1 CTTACTAAGCTATAT-AG
*
96758828 CTTACTAAGCTTTATAG
1 CTTACTAAGCTATATAG
96758845 CTTACT
1 CTTACT
96758851 CTGTTTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (17 bp):
CTTACTAAGCTATATAG
Found at i:96761433 original size:17 final size:17
Alignment explanation
Indices: 96761397--96761445 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
96761387 AAATAAGGAA
* * *
96761397 AAAATTAATAATGAATT
1 AAAATTAAAAATAAAGT
*
96761414 AAAATTAAAATTAAAGT
1 AAAATTAAAAATAAAGT
*
96761431 AAATTTAAAAATAAA
1 AAAATTAAAAATAAA
96761446 CAAATCTCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAATTAAAAATAAAGT
Found at i:96763331 original size:15 final size:15
Alignment explanation
Indices: 96763311--96763367 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
96763301 ATTCAATATT
96763311 AATATTTTAATAATA
1 AATATTTTAATAATA
*
96763326 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
96763345 AATATATTAATAATA
1 AATATTTTAATAATA
*
96763360 AATGTTTT
1 AATATTTT
96763368 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:96782644 original size:21 final size:20
Alignment explanation
Indices: 96782620--96782659 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
96782610 GTCAAAATCA
*
96782620 CCACACGGGTGTGTTGCCCTT
1 CCACACGGGCGTG-TGCCCTT
96782641 CCACACGGGCGTGTGCCCT
1 CCACACGGGCGTGTGCCCT
96782660 GTTTTAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.38, G:0.30, T:0.23
Consensus pattern (20 bp):
CCACACGGGCGTGTGCCCTT
Found at i:96791612 original size:113 final size:113
Alignment explanation
Indices: 96791429--96791640 Score: 354
Period size: 113 Copynumber: 1.9 Consensus size: 113
96791419 TATCCTTGCT
* *
96791429 AGGCAGTATGACACTATTTCAATATTTTTTATCTACTATTACGTATTATACTATGGAAACTATTT
1 AGGCAGTATGACACTAATTCAATATTTTTTATCTACTAGTACGTATTATACTATGGAAACTATTT
96791494 TGCTTCCTTTGAGTTGTTATAATCACATTAAAATTCTCTACCCTTTTC
66 TGCTTCCTTTGAGTTGTTATAATCACATTAAAATTCTCTACCCTTTTC
* * *
96791542 AGGCCGTATGACACTAATTCAATATTTTTTGT-TGACTAGTATGTATTATACTATGGAAACTATT
1 AGGCAGTATGACACTAATTCAATATTTTTTATCT-ACTAGTACGTATTATACTATGGAAACTATT
*
96791606 TTGCTTCCTTTGAGTTGTTGTAATCACATTAAAAT
65 TTGCTTCCTTTGAGTTGTTATAATCACATTAAAAT
96791641 GGTCTAACAT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
112 1 0.01
113 91 0.99
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (113 bp):
AGGCAGTATGACACTAATTCAATATTTTTTATCTACTAGTACGTATTATACTATGGAAACTATTT
TGCTTCCTTTGAGTTGTTATAATCACATTAAAATTCTCTACCCTTTTC
Found at i:96807199 original size:48 final size:48
Alignment explanation
Indices: 96807128--96807233 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
96807118 CAAGATAAAT
* * *
96807128 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
96807176 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
96807224 ATGTGTATAT
1 ATATGTATAT
96807234 ATTGTGGCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:96807417 original size:37 final size:37
Alignment explanation
Indices: 96807367--96807438 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
96807357 GAAATATATT
96807367 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
*
96807404 CCGGGTAAGACCCGATGACTACGTGTGGGGATTAT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
96807439 TCGAGCTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
Found at i:96810018 original size:53 final size:54
Alignment explanation
Indices: 96809933--96810139 Score: 218
Period size: 53 Copynumber: 3.8 Consensus size: 54
96809923 TTCCATTTTA
* *
96809933 AACTTACCATTGCCATGCCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * *
96809986 AACTCACCATTGCCGTGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * *
96810040 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
96810095 AACTTACCAATGCCATGCCTTGGCAAGGCCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
96810140 AAACCCTAAT
Statistics
Matches: 122, Mismatches: 30, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 46 0.38
54 36 0.30
55 40 0.33
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:96812928 original size:30 final size:30
Alignment explanation
Indices: 96812881--96812937 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
96812871 TTGTAGGAGC
*
96812881 CACATGGGCTAGGCACACGCCCATGTGAGA
1 CACATGAGCTAGGCACACGCCCATGTGAGA
96812911 CACATGAGCT-GGACACACGCCCATGTG
1 CACATGAGCTAGG-CACACGCCCATGTG
96812938 CCAACTCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (30 bp):
CACATGAGCTAGGCACACGCCCATGTGAGA
Found at i:96817122 original size:6 final size:6
Alignment explanation
Indices: 96817058--96817104 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
96817048 TTAATTTAAT
96817058 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
96817105 CTAGTCATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:96817330 original size:28 final size:28
Alignment explanation
Indices: 96817299--96817355 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
96817289 GTTGTTCGGT
96817299 ATTGTGGTTTAAGTTTTCACTTCGATTC
1 ATTGTGGTTTAAGTTTTCACTTCGATTC
96817327 ATTGTGGTTTAAGTTTTCACTTCGATTC
1 ATTGTGGTTTAAGTTTTCACTTCGATTC
96817355 A
1 A
96817356 GTCTCTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (28 bp):
ATTGTGGTTTAAGTTTTCACTTCGATTC
Found at i:96818719 original size:6 final size:6
Alignment explanation
Indices: 96818684--96818728 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
96818674 TGTCTTTTCT
* * *
96818684 TTTTTA GTTTTA GTTTTA TTTTTA TTTTTA TGTTTA -TTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
96818729 CTTAGACTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:96824503 original size:21 final size:21
Alignment explanation
Indices: 96824477--96824516 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
96824467 ACCTTTTCTA
96824477 AAGTTAAAA-GTCAAAACTATC
1 AAGTTAAAAGGT-AAAACTATC
96824498 AAGTTAAAAGGTAAAACTA
1 AAGTTAAAAGGTAAAACTA
96824517 CATTGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATC
Found at i:96827151 original size:31 final size:29
Alignment explanation
Indices: 96827116--96827190 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
96827106 ACGGCTCAAC
* *
96827116 GACTAAAATGTTACAATGCGATAACGTAAGT
1 GACTAAAATGTAACAATGC-A-AACATAAGT
* *
96827147 GACTAAAATGTAACATTTCAAACATAAGT
1 GACTAAAATGTAACAATGCAAACATAAGT
96827176 GACTAAAATGTAACA
1 GACTAAAATGTAACA
96827191 CTCCTAACCC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.57
30 1 0.03
31 16 0.40
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (29 bp):
GACTAAAATGTAACAATGCAAACATAAGT
Found at i:96828544 original size:33 final size:33
Alignment explanation
Indices: 96828507--96828584 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
96828497 TGGCTCTGTC
* * *
96828507 ATGGTCTTACATTC-GTAGTGTCATAACCTAGTT
1 ATGGTCTTACATTCAG-AATGTCATAACCCAGCT
96828540 ATGGTCTTATCA-TCAGAATGTCATAACCCAGCT
1 ATGGTCTTA-CATTCAGAATGTCATAACCCAGCT
*
96828573 ATAGTCTTACAT
1 ATGGTCTTACAT
96828585 ATAAATACTG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 2 0.05
33 33 0.87
34 3 0.08
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (33 bp):
ATGGTCTTACATTCAGAATGTCATAACCCAGCT
Found at i:96828929 original size:31 final size:31
Alignment explanation
Indices: 96828891--96828949 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
96828881 ATCTAAAATA
96828891 TAAAATTATTCATTCATTAGCATATATTATG
1 TAAAATTATTCATTCATTAGCATATATTATG
96828922 TAAAATTATTCATTCATTAGCATATATT
1 TAAAATTATTCATTCATTAGCATATATT
96828950 TCAATTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (31 bp):
TAAAATTATTCATTCATTAGCATATATTATG
Found at i:96830086 original size:39 final size:37
Alignment explanation
Indices: 96830043--96830140 Score: 99
Period size: 39 Copynumber: 2.6 Consensus size: 37
96830033 TTTTTTATAT
96830043 TTTTTAAATTTTAAATAATTTTTTAGAATTTTTACATGC
1 TTTTT-AATTTTAAATAATTTTTTAGAATTTTTA-ATGC
* ** * *
96830082 TTTTTGAATTTTAAAAAATGATTTATAATTTTTAATGG
1 TTTTT-AATTTTAAATAATTTTTTAGAATTTTTAATGC
* *
96830120 TTTTTCATTTT-CATAATTTTT
1 TTTTTAATTTTAAATAATTTTT
96830141 ATATTTTTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 6 0.12
37 5 0.10
38 8 0.17
39 29 0.60
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (37 bp):
TTTTTAATTTTAAATAATTTTTTAGAATTTTTAATGC
Found at i:96830140 original size:10 final size:9
Alignment explanation
Indices: 96830126--96830173 Score: 55
Period size: 8 Copynumber: 5.4 Consensus size: 9
96830116 ATGGTTTTTC
*
96830126 ATTTTCATA
1 ATTTTTATA
96830135 ATTTTTAT-
1 ATTTTTATA
96830143 ATTTTTAT-
1 ATTTTTATA
*
96830151 ATTTTTTTA
1 ATTTTTATA
96830160 TATTTTTATA
1 -ATTTTTATA
96830170 ATTT
1 ATTT
96830174 GTTTTTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 15 0.44
9 11 0.32
10 8 0.24
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTTTATA
Found at i:96830157 original size:18 final size:21
Alignment explanation
Indices: 96830136--96830188 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 21
96830126 ATTTTCATAA
96830136 TTTTTATATTTTTAT-A-TT-
1 TTTTTATATTTTTATAATTTG
96830154 TTTTTATATTTTTATAATTTG
1 TTTTTATATTTTTATAATTTG
96830175 TTTTTATATGTTTT
1 TTTTTATAT-TTTT
96830189 TACATTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.48
19 1 0.03
20 2 0.06
21 9 0.29
22 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTTATATTTTTATAATTTG
Found at i:96830188 original size:10 final size:9
Alignment explanation
Indices: 96830136--96830196 Score: 52
Period size: 10 Copynumber: 6.3 Consensus size: 9
96830126 ATTTTCATAA
96830136 TTTTTATA-
1 TTTTTATAT
96830144 TTTTTATATT
1 TTTTTATA-T
96830154 TTTTTATAT
1 TTTTTATAT
*
96830163 TTTTATAATTT
1 TTTT-T-ATAT
96830174 GTTTTTATAT
1 -TTTTTATAT
*
96830184 GTTTTTACAT
1 -TTTTTATAT
96830194 TTT
1 TTT
96830197 AAAAAATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.18
9 8 0.18
10 21 0.47
11 4 0.09
12 4 0.09
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTTTATAT
Found at i:96859003 original size:3 final size:3
Alignment explanation
Indices: 96858995--96859021 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
96858985 TGGGCTGTGA
96858995 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
96859022 AAATTAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:96861361 original size:35 final size:35
Alignment explanation
Indices: 96861321--96861388 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
96861311 ATTTTTTAAA
*
96861321 ATTATTTTTCAAGTAAACAAAATAATTAATCTTGT
1 ATTATTTTCCAAGTAAACAAAATAATTAATCTTGT
*
96861356 ATTATTTTCCAAGTAAATAAAATAATTAATCTT
1 ATTATTTTCCAAGTAAACAAAATAATTAATCTT
96861389 TTTTGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (35 bp):
ATTATTTTCCAAGTAAACAAAATAATTAATCTTGT
Found at i:96874913 original size:238 final size:238
Alignment explanation
Indices: 96874458--96874930 Score: 745
Period size: 237 Copynumber: 2.0 Consensus size: 238
96874448 AATTGTTAAA
* *
96874458 AATACAAAAAAATAAAAATCAATCTAGCCCATCTCAAGGAAGGCTATACACATGATGCTAAAAAT
1 AATACAAAAAAATAAAAATCAAACTAGCCCATCTCAAGGAAGGCTATACACATAATGCTAAAAAT
*
96874523 AAAAACAAACAATAATTGTGCACAGCACAGTAATTAGGTCCATGTTACACCAGAGCTAAATATTT
66 AAAAACAAACAATAATTGTGCACAGCACAGTAATTAGGCCCATGTTACACCAGAGCTAAATATTT
* *
96874588 TGCTAAATACCCAGGATACGTATTTGCTAGAGAAGTACATGTAATAATGAACAATATGTCATTTA
131 TGATAAATACCCAGGATACGTATTTGCTAGAGAAGTACATGTAATAATGAACAACATGTCATTTA
* * *
96874653 TGCCTACAAAAGGAATCCTAAAGAATACAAAAGAATCTGCTCT
196 TACCTACAAAAGGAACCCTAAAGAATACAAAAGAACCTGCTCT
* * * * * *
96874696 AATAC-AAATAATAAATATCAAACTAGCCTATCTTAAGGAA-GTTATACACATAATGGTTAAAAA
1 AATACAAAAAAATAAAAATCAAACTAGCCCATCTCAAGGAAGGCTATACACATAAT-GCTAAAAA
* *
96874759 -AACAAACAAACAATAATTGTTCACAGCACGGTAATTAGGCCCATGTTACACCAGAGCTAAATAT
65 TAA-AAACAAACAATAATTGTGCACAGCACAGTAATTAGGCCCATGTTACACCAGAGCTAAATAT
*
96874823 TTTGATAAATACCCAGGATATTGTATTTGCTAGAGAAGTACATGTAATAATGAACAACATGTCAT
129 TTTGATAAATACCCAGGATA-CGTATTTGCTAGAGAAGTACATGTAATAATGAACAACATGTCAT
96874888 TTATACCTACAAAAGGAACCCTAAAGAATACAAAAGAACCTGC
193 TTATACCTACAAAAGGAACCCTAAAGAATACAAAAGAACCTGC
96874931 ACTATTGTAG
Statistics
Matches: 215, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
236 14 0.07
237 114 0.53
238 87 0.40
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (238 bp):
AATACAAAAAAATAAAAATCAAACTAGCCCATCTCAAGGAAGGCTATACACATAATGCTAAAAAT
AAAAACAAACAATAATTGTGCACAGCACAGTAATTAGGCCCATGTTACACCAGAGCTAAATATTT
TGATAAATACCCAGGATACGTATTTGCTAGAGAAGTACATGTAATAATGAACAACATGTCATTTA
TACCTACAAAAGGAACCCTAAAGAATACAAAAGAACCTGCTCT
Found at i:96876929 original size:12 final size:12
Alignment explanation
Indices: 96876912--96876947 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
96876902 TCCGGTCCGC
96876912 TTATATTAATTT
1 TTATATTAATTT
*
96876924 TTATATTATTTT
1 TTATATTAATTT
96876936 TTATA-TAATTT
1 TTATATTAATTT
96876947 T
1 T
96876948 AAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTAATTT
Found at i:96877091 original size:30 final size:30
Alignment explanation
Indices: 96877048--96877106 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
96877038 CTTAACAAGC
*
96877048 AAATTTCTCTAAAATAATAACAAAATTAAA
1 AAATGTCTCTAAAATAATAACAAAATTAAA
*
96877078 AAATGTCTTTAAAATAATAACAAAATTAA
1 AAATGTCTCTAAAATAATAACAAAATTAA
96877107 CAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (30 bp):
AAATGTCTCTAAAATAATAACAAAATTAAA
Found at i:96877721 original size:27 final size:27
Alignment explanation
Indices: 96877658--96877721 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 27
96877648 CGTTTGAATC
*
96877658 AAAACTGAAATATCAAATTTTGAAAATA
1 AAAACT-AAATATCAAATTTGGAAAATA
*
96877686 ACGAA--AAATGATCAAA-TTGGAAAATA
1 A-AAACTAAAT-ATCAAATTTGGAAAATA
96877712 AAAACTAAAT
1 AAAACTAAAT
96877722 CCACAGCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
25 2 0.07
26 14 0.48
27 10 0.34
28 1 0.03
29 2 0.07
ACGTcount: A:0.59, C:0.08, G:0.09, T:0.23
Consensus pattern (27 bp):
AAAACTAAATATCAAATTTGGAAAATA
Found at i:96880298 original size:42 final size:42
Alignment explanation
Indices: 96880234--96880360 Score: 150
Period size: 42 Copynumber: 3.0 Consensus size: 42
96880224 CTTTGTTTTC
** * *
96880234 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
* * *
96880277 T-GATGCCATAGCCCAGTTATGGTCTTATACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
* *
96880318 TCGATGCCATAGCCTAGCTATGGTCTTACAC-TAATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
96880359 TC
1 TC
96880361 TCACTGATGC
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
41 12 0.17
42 58 0.82
43 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:96880502 original size:31 final size:31
Alignment explanation
Indices: 96880467--96880615 Score: 235
Period size: 31 Copynumber: 4.8 Consensus size: 31
96880457 CTTGTCACTT
*
96880467 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
96880498 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
96880529 GTAGCCGGAGCTACCACTTTTCACTGATCAC
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
**
96880560 GTAGCAAAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
96880591 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
96880616 TGTCATTTGT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:96880697 original size:50 final size:51
Alignment explanation
Indices: 96880591--96880719 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
96880581 CACTGATCAG
* * *
96880591 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
96880642 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
96880692 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
96880720 TGCCATGGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:96883578 original size:31 final size:32
Alignment explanation
Indices: 96883506--96883583 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
96883496 TCAAAATTAC
* *
96883506 ACATGAAA-TTTGGTTTTATGTCCAATTTTAT
1 ACATAAAATTTTGATTTTATGTCCAATTTTAT
*
96883537 ACA-AAAATTTTGATTTT-TGTGCAATTTTAT
1 ACATAAAATTTTGATTTTATGTCCAATTTTAT
96883567 ACATAAAATTTTGATTT
1 ACATAAAATTTTGATTT
96883584 GATTTAATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 18 0.43
31 24 0.57
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (32 bp):
ACATAAAATTTTGATTTTATGTCCAATTTTAT
Found at i:96884168 original size:20 final size:21
Alignment explanation
Indices: 96884122--96884168 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
96884112 ATAAAAGTTA
96884122 TAATTTTCTTTATATATTTTG
1 TAATTTTCTTTATATATTTTG
* * *
96884143 TGATTTTTTTTATA-ATTTTT
1 TAATTTTCTTTATATATTTTG
96884163 TAATTT
1 TAATTT
96884169 GTTAGTAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (21 bp):
TAATTTTCTTTATATATTTTG
Found at i:96884303 original size:2 final size:2
Alignment explanation
Indices: 96884291--96884327 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
96884281 ACTTTGCTAT
96884291 TA TA T- 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
96884328 ACACTAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:96888704 original size:27 final size:27
Alignment explanation
Indices: 96888674--96888727 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
96888664 ATATTATATT
96888674 GATTTAATCATAAATTTAAAAAATTAA
1 GATTTAATCATAAATTTAAAAAATTAA
96888701 GATTTAATCATAAATTTAAAAAATTAA
1 GATTTAATCATAAATTTAAAAAATTAA
96888728 CTCTGAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (27 bp):
GATTTAATCATAAATTTAAAAAATTAA
Found at i:96888870 original size:25 final size:24
Alignment explanation
Indices: 96888828--96888874 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
96888818 TTTTATTTTA
* *
96888828 ATATTAGTACTAATTAAATATAATT
1 ATATTAATACTAAATAAA-ATAATT
*
96888853 ATATTAATATTAAATAAAATAA
1 ATATTAATACTAAATAAAATAA
96888875 AAATCTCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATTAATACTAAATAAAATAATT
Found at i:96891399 original size:21 final size:21
Alignment explanation
Indices: 96891375--96891492 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
96891365 ACTCCTATGA
96891375 GTTTCAGTTTAGCCCTTCTGG
1 GTTTCAGTTTAGCCCTTCTGG
* * * **
96891396 GTTTTAATTTAGCTCTTCTTA
1 GTTTCAGTTTAGCCCTTCTGG
* * * *
96891417 GCTTCAATTTAACCCTTATGG
1 GTTTCAGTTTAGCCCTTCTGG
* * * * *
96891438 GTTTCCGTTCAGCTCTTATGA
1 GTTTCAGTTTAGCCCTTCTGG
* * *
96891459 GTTTCCGTTCAACCCTTAC-GG
1 GTTTCAGTTTAGCCCTT-CTGG
*
96891480 GTTTCTGTTTAGC
1 GTTTCAGTTTAGC
96891493 ACTTATGTGC
Statistics
Matches: 70, Mismatches: 26, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
GTTTCAGTTTAGCCCTTCTGG
Found at i:96904241 original size:48 final size:45
Alignment explanation
Indices: 96904165--96904516 Score: 160
Period size: 48 Copynumber: 7.6 Consensus size: 45
96904155 TGTCCGGGTA
* *
96904165 TAAGACCATAT-TAGGGATATAGCTTCGGCATCGTTAAGTGATTTCGTG
1 TAAGACCATATCT-GGGATATGGCATCGGCATC---AAGTGATTTCGTG
* ** *
96904213 TAAGACCATGTCTGGGATATGGCATCGGCATCAAGATGTGATCCCGTA
1 TAAGACCATATCTGGGATATGGCATCGGCATC-A-A-GTGATTTCGTG
* *
96904261 TAAGACCATATCAGGGATATGGCTTCGGCA--AAGTGATTTCGTG
1 TAAGACCATATCTGGGATATGGCATCGGCATCAAGTGATTTCGTG
* * * * ** *
96904304 TAAGACCATGTCTGGTACATGGCATC-G-AT-AAGAGATCCCGTA
1 TAAGACCATATCTGGGATATGGCATCGGCATCAAGTGATTTCGTG
* * * * * * * * ** *
96904346 TAAAACCATGTTTGGAACATGGCATCAGTATCAGTATGAGATCCCATG
1 TAAGACCATATCTGGGATATGGCATCGGCATCA--A-GTGATTTCGTG
* * *
96904394 TAAGACCATATCTGGGATATGGCATTGGCATCAATGTGAGGCCTT-GTA
1 TAAGACCATATCTGGGATATGGCATCGGCATCAA-GTGA---TTTCGTG
* * * * * * * *
96904442 TAAGACCATGTTTGGGGTATGGCATCGACACTGATATGAGACTTCGTA
1 TAAGACCATATCTGGGATATGGCATCGGCA-TCA-A-GTGATTTCGTG
*
96904490 TAAGACCATATCTGGAATATGGCATCG
1 TAAGACCATATCTGGGATATGGCATCG
96904517 ATATGTGGTC
Statistics
Matches: 236, Mismatches: 52, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
41 1 0.00
42 33 0.14
43 30 0.13
44 3 0.01
45 2 0.01
46 6 0.03
47 5 0.02
48 148 0.63
49 3 0.01
50 5 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (45 bp):
TAAGACCATATCTGGGATATGGCATCGGCATCAAGTGATTTCGTG
Found at i:96921501 original size:21 final size:23
Alignment explanation
Indices: 96921457--96921502 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
96921447 AAGTTAAATA
* *
96921457 AATATTCATATTTGTATAATTAT
1 AATACTCATATATGTATAATTAT
96921480 AATACTCATATAT-TAT-ATTAT
1 AATACTCATATATGTATAATTAT
96921501 AA
1 AA
96921503 AATATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (23 bp):
AATACTCATATATGTATAATTAT
Found at i:96922742 original size:17 final size:18
Alignment explanation
Indices: 96922720--96922753 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
96922710 TTCAATATGA
96922720 TATTTTAGT-TTTTTTCC
1 TATTTTAGTATTTTTTCC
*
96922737 TATTTTGGTATTTTTTC
1 TATTTTAGTATTTTTTC
96922754 AGTTTAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (18 bp):
TATTTTAGTATTTTTTCC
Found at i:96925691 original size:29 final size:29
Alignment explanation
Indices: 96925649--96925704 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
96925639 TTTAACTAAC
96925649 TTAAAATAAATATATTA-TAAATTATTTAT
1 TTAAAATAAATATATTATTAAA-TATTTAT
*
96925678 TTAAATTAAATATATTATTAAATATTT
1 TTAAAATAAATATATTATTAAATATTT
96925705 TAAAATAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAAAATAAATATATTATTAAATATTTAT
Done.