Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 197 of 378
Found at i:58047484 original size:40 final size:40
Alignment explanation
Indices: 58047338--58047542 Score: 209
Period size: 39 Copynumber: 5.2 Consensus size: 40
58047328 AGGAGCACGA
* * * *
58047338 ATGTGCGATT-AGGGGCACCGAAGTGCAAACAAGGGCACAA
1 ATGTGC-ATTCAGGGGTACCGAAGTACAAACAGGGGCACAG
* * * * * *
58047378 ATGTACATTTAGGGGCACCAAAGTGCAATCAGGGGCACAG
1 ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACAG
* *
58047418 ATGTGCATTCA-GGGTACTGAAGTACAAACAAGGGCACAG
1 ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACAG
* *
58047457 ATGTGCATTCAGGGGTATCGAAGTACAAATAGGGGCAC-G
1 ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACAG
* * * * *
58047496 ATGTGCATTCAAGAGTATCGAAATACAAACAGGGGCACTG
1 ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACAG
58047536 ATGTGCA
1 ATGTGCA
58047543 AGTAGGGGCA
Statistics
Matches: 141, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
39 71 0.50
40 70 0.50
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (40 bp):
ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACAG
Found at i:58047491 original size:79 final size:79
Alignment explanation
Indices: 58047308--58047542 Score: 235
Period size: 79 Copynumber: 3.0 Consensus size: 79
58047298 ATTGCATAAT
* * * * * * *
58047308 AGGGGCACCAAAGTGCAATCAGGAGCACGAATGTGCGATT-AGGGGCACCGAAGTGCAAACAAGG
1 AGGGGCACCAAAGTACAATCAGGGGCACG-ATGTGC-ATTCAAGAGTATCGAAGTACAAACAAGG
* * *
58047372 GCACAAATGTACATTT
64 GCACAGATGTGCATTC
* *
58047388 AGGGGCACCAAAGTGCAATCAGGGGCACAGATGTGCATTC-AGGGTA-CTGAAGTACAAACAAGG
1 AGGGGCACCAAAGTACAATCAGGGGCAC-GATGTGCATTCAAGAGTATC-GAAGTACAAACAAGG
58047451 GCACAGATGTGCATTC
64 GCACAGATGTGCATTC
* * * * *
58047467 AGGGGTATCGAAGTACAAAT-AGGGGCACGATGTGCATTCAAGAGTATCGAAATACAAACAGGGG
1 AGGGGCACCAAAGTAC-AATCAGGGGCACGATGTGCATTCAAGAGTATCGAAGTACAAACAAGGG
*
58047531 CACTGATGTGCA
65 CACAGATGTGCA
58047543 AGTAGGGGCA
Statistics
Matches: 134, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
78 12 0.09
79 84 0.63
80 37 0.28
81 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (79 bp):
AGGGGCACCAAAGTACAATCAGGGGCACGATGTGCATTCAAGAGTATCGAAGTACAAACAAGGGC
ACAGATGTGCATTC
Found at i:58056721 original size:42 final size:43
Alignment explanation
Indices: 58056621--58056733 Score: 106
Period size: 42 Copynumber: 2.7 Consensus size: 43
58056611 CAATGCCGAC
* * * *
58056621 GTCCCAGACGTGGTCTTACATATAATTCAATATCGATGCCTCT
1 GTCCCAGACATGGTCTTACACATAAATCAATATCGATGCCTAT
* *
58056664 GTCCCAAACAGGGTCTTACACA-AAATCAGATA-CGATG-CTAAT
1 GTCCCAGACATGGTCTTACACATAAATCA-ATATCGATGCCT-AT
* * *
58056706 TTCCCAGACATGGTCTTATACGTAAATC
1 GTCCCAGACATGGTCTTACACATAAATC
58056734 TCAAATGAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.04
42 28 0.50
43 26 0.46
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACATAAATCAATATCGATGCCTAT
Found at i:58062394 original size:10 final size:10
Alignment explanation
Indices: 58062356--58062394 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
58062346 GAATATGTTG
*
58062356 AATTTTAATT
1 AATTTTGATT
58062366 AATTTTATGATT
1 AA-TTT-TGATT
58062378 AATTTTGATT
1 AATTTTGATT
58062388 AATTTTG
1 AATTTTG
58062395 GTTATTTTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 14 0.54
11 6 0.23
12 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (10 bp):
AATTTTGATT
Found at i:58071016 original size:52 final size:52
Alignment explanation
Indices: 58070937--58071037 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
58070927 GAATTAAGAA
58070937 ATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGTGGC
1 ATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGTGGC
* *
58070989 ATCCGAGCTCGTTGAGTTGGTCTGAGTTCATAATGGATGTGATACATGT
1 ATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
58071038 AATTGGGTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.32
Consensus pattern (52 bp):
ATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGTGGC
Found at i:58071487 original size:6 final size:6
Alignment explanation
Indices: 58071476--58071509 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
58071466 AAGAATAAAC
* *
58071476 TTATGT TTATGT TTATGA TTATGA TTATGT TTAT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTAT
58071510 TATGTCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (6 bp):
TTATGT
Found at i:58077232 original size:16 final size:16
Alignment explanation
Indices: 58077213--58077260 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
58077203 TTTATGTTTT
58077213 CTTATTTTTAACTTTA
1 CTTATTTTTAACTTTA
*
58077229 CTTATTTTATTTACTTTA
1 CTTA-TTT-TTAACTTTA
58077247 -TTATTATTTAACTT
1 CTTATT-TTTAACTT
58077261 ATAATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 12 0.44
17 7 0.26
18 8 0.30
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTATTTTTAACTTTA
Found at i:58079622 original size:20 final size:20
Alignment explanation
Indices: 58079597--58079637 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58079587 TGAATATTTG
* *
58079597 TAATATTGATTTAATTTAAT
1 TAATATGGATTAAATTTAAT
*
58079617 TAATATGGCTTAAATTTAAT
1 TAATATGGATTAAATTTAAT
58079637 T
1 T
58079638 CATGTTAGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (20 bp):
TAATATGGATTAAATTTAAT
Found at i:58095356 original size:19 final size:19
Alignment explanation
Indices: 58095327--58095395 Score: 113
Period size: 19 Copynumber: 3.7 Consensus size: 19
58095317 GAACTTTTTG
58095327 TTTTA-GAAAACTGTTCGT
1 TTTTAGGAAAACTGTTCGT
58095345 TTTTAGGAAAACTGTTCGT
1 TTTTAGGAAAACTGTTCGT
* *
58095364 TTTTAGGAAAGCTGTTCAT
1 TTTTAGGAAAACTGTTCGT
58095383 TTTTAGGAAAACT
1 TTTTAGGAAAACT
58095396 TTAATCTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
18 5 0.11
19 42 0.89
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (19 bp):
TTTTAGGAAAACTGTTCGT
Found at i:58097340 original size:16 final size:15
Alignment explanation
Indices: 58097321--58097361 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
58097311 TTCTTGTGAA
58097321 AAAAAAGAAGAAAAAG
1 AAAAAA-AAGAAAAAG
58097337 AAAAGAAAAGAAAAAG
1 AAAA-AAAAGAAAAAG
58097353 AACAAAAAA
1 AA-AAAAAA
58097362 AGAGAGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:58097342 original size:11 final size:10
Alignment explanation
Indices: 58097320--58097364 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 10
58097310 ATTCTTGTGA
58097320 AAAAAAAGAAG
1 AAAAAAA-AAG
58097331 AAAAAGAAAAG
1 AAAAA-AAAAG
58097342 AAAAGAAAAAG
1 AAAA-AAAAAG
58097353 AACAAAAAAAG
1 AA-AAAAAAAG
58097364 A
1 A
58097365 GAGCATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 26 0.84
12 5 0.16
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:58098699 original size:24 final size:25
Alignment explanation
Indices: 58098650--58098699 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
58098640 ACCCTTCTCA
* *
58098650 TCTCTTCACTTCTTTCTCATTTTTC
1 TCTCTTCACTTCCTTCTCATTGTTC
58098675 TCTCTTCA-TTCCCTTC-CATTGTTC
1 TCTCTTCACTT-CCTTCTCATTGTTC
58098699 T
1 T
58098700 TCATTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.08, C:0.34, G:0.02, T:0.56
Consensus pattern (25 bp):
TCTCTTCACTTCCTTCTCATTGTTC
Found at i:58098996 original size:24 final size:24
Alignment explanation
Indices: 58098964--58099011 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
58098954 AATACGGCTA
58098964 AAATTTAATTCGTGTTAGGTTGAT
1 AAATTTAATTCGTGTTAGGTTGAT
58098988 AAATTTAATTCGTGTTAGGTTGAT
1 AAATTTAATTCGTGTTAGGTTGAT
58099012 TGCATTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (24 bp):
AAATTTAATTCGTGTTAGGTTGAT
Found at i:58111512 original size:28 final size:29
Alignment explanation
Indices: 58111445--58111545 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
58111435 ATAGTGAATC
*
58111445 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
58111474 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
58111502 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
58111532 CGCACACTTAGTGC
1 CGCACACTTAGTGC
58111546 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:58119026 original size:28 final size:29
Alignment explanation
Indices: 58118959--58119059 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
58118949 ATAGTGAATC
*
58118959 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
58118988 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
58119016 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
58119046 CGCACACTTAGTGC
1 CGCACACTTAGTGC
58119060 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:58122455 original size:34 final size:34
Alignment explanation
Indices: 58122321--58122461 Score: 165
Period size: 34 Copynumber: 4.1 Consensus size: 34
58122311 ATTGATTTGG
* *
58122321 TATAAGCATATGAAGTGCTACCGTATTGATCTAT
1 TATAAGCATATTAATTGCTACCGTATTGATCTAT
* *
58122355 TATAAGCTTATTAATTGGTACCGTATTGATCTAT
1 TATAAGCATATTAATTGCTACCGTATTGATCTAT
* * * * *
58122389 TATGAGTATATTAATTGCTATCATATTGATCTGT
1 TATAAGCATATTAATTGCTACCGTATTGATCTAT
* * * *
58122423 TATAAGAATATTAATTGCTACCTTAATGATCTGT
1 TATAAGCATATTAATTGCTACCGTATTGATCTAT
58122457 TATAA
1 TATAA
58122462 ACATGTCATA
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 91 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (34 bp):
TATAAGCATATTAATTGCTACCGTATTGATCTAT
Found at i:58124165 original size:45 final size:45
Alignment explanation
Indices: 58124101--58124190 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
58124091 ATCAGTTCAA
58124101 GCTTTACTGGGCCTAAGCCCTATTCAGAAATCAGTGTTAACTGGG
1 GCTTTACTGGGCCTAAGCCCTATTCAGAAATCAGTGTTAACTGGG
58124146 GCTTTACTGGGCCTAAGCCCTATTCAGAAATCAGTGTTAACTGGG
1 GCTTTACTGGGCCTAAGCCCTATTCAGAAATCAGTGTTAACTGGG
58124191 CCTTAGCCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (45 bp):
GCTTTACTGGGCCTAAGCCCTATTCAGAAATCAGTGTTAACTGGG
Found at i:58126684 original size:15 final size:15
Alignment explanation
Indices: 58126647--58126675 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58126637 TTTCCCTATC
58126647 TAATAATAATAATTA
1 TAATAATAATAATTA
58126662 TAATAATAATAATT
1 TAATAATAATAATT
58126676 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:58126804 original size:19 final size:18
Alignment explanation
Indices: 58126767--58126810 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
58126757 ATACATACAG
58126767 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
58126784 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
58126803 TACTAATT
1 TAATAATT
58126811 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:58128854 original size:28 final size:27
Alignment explanation
Indices: 58128753--58128854 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
58128743 TCAGTGTTAA
* *
58128753 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
58128781 CTGGGCCATAGCCCCT-TACAGTATCAGAGT
1 CTGGGCC-TAGCCCATAT-CAGTATCA-A-T
*
58128811 AAATTGGGCCTAGCCCATATCAGTATCAAT
1 ---CTGGGCCTAGCCCATATCAGTATCAAT
58128841 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
58128855 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 26 0.44
29 1 0.02
30 2 0.03
31 1 0.02
32 15 0.25
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:58128889 original size:60 final size:59
Alignment explanation
Indices: 58128754--58128890 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
58128744 CAGTGTTAAC
* *
58128754 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTAAAT
1 TGGGCCTT-GCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTAAAT
* * * *
58128815 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATAT
1 TGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TAAAT
*
58128875 TGGGCCTTGGCCATAT
1 TGGGCCTTGCCCATAT
58128891 TAACACAGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 4 0.06
60 49 0.75
61 12 0.18
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (59 bp):
TGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTAAAT
Found at i:58128937 original size:19 final size:20
Alignment explanation
Indices: 58128895--58128937 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
58128885 CCATATTAAC
** *
58128895 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
58128915 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
58128934 ACAG
1 ACAG
58128938 CCTCATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:58129276 original size:26 final size:26
Alignment explanation
Indices: 58129227--58129276 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
58129217 GTCAAAATTA
* * **
58129227 ACCTAGGGGTATAACGGTCTTTTTGC
1 ACCTAGGGGTAAAACGATAATTTTGC
58129253 ACCTAGGGGTAAAACGATAATTTT
1 ACCTAGGGGTAAAACGATAATTTT
58129277 CATACTTAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (26 bp):
ACCTAGGGGTAAAACGATAATTTTGC
Found at i:58129550 original size:8 final size:8
Alignment explanation
Indices: 58129537--58129569 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
58129527 TTTACAAATG
58129537 TCGGCTTT
1 TCGGCTTT
58129545 TCGGCTTT
1 TCGGCTTT
58129553 TCGGCTTT
1 TCGGCTTT
*
58129561 TCGACTTT
1 TCGGCTTT
58129569 T
1 T
58129570 GCCGATCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.03, C:0.24, G:0.21, T:0.52
Consensus pattern (8 bp):
TCGGCTTT
Found at i:58134344 original size:37 final size:37
Alignment explanation
Indices: 58134285--58134393 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
58134275 AGCTCAGACG
* *
58134285 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
58134322 AAATCTCCACACGTAGTCATCGGGTCTTACCTGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
58134359 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
58134394 ATACATTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:58134509 original size:48 final size:48
Alignment explanation
Indices: 58134438--58135159 Score: 1210
Period size: 48 Copynumber: 15.0 Consensus size: 48
58134428 TGTTACAACA
* * *
58134438 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
58134486 TTCACATTTGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58134534 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
58134582 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAGACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
58134630 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58134678 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
58134726 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
58134774 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
58134822 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATACAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
58134870 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
58134918 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
58134966 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
58135014 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
58135062 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
58135110 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58135158 TT
1 TT
58135160 ATCTTGTACA
Statistics
Matches: 633, Mismatches: 41, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 633 1.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:58134606 original size:144 final size:144
Alignment explanation
Indices: 58134438--58135159 Score: 1372
Period size: 144 Copynumber: 5.0 Consensus size: 144
58134428 TGTTACAACA
*
58134438 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTTGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
58134503 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
58134568 TATCACACATATAT
131 TATCACACATATAT
*
58134582 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAGACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
58134647 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
58134712 TATCACACATATAT
131 TATCACACATATAT
58134726 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
58134791 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
*
58134856 TATCACACATACAT
131 TATCACACATATAT
58134870 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
*
58134935 GCTTTACCACATATACATATCTCACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
* *
58135000 TATCACATACATAT
131 TATCACACATATAT
58135014 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
58135079 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
* *
58135144 TATCTCATATATAT
131 TATCACACATATAT
58135158 TT
1 TT
58135160 ATCTTGTACA
Statistics
Matches: 567, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 567 1.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (144 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
TATCACACATATAT
Found at i:58138572 original size:19 final size:19
Alignment explanation
Indices: 58138548--58138584 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
58138538 TGTGAATTTC
58138548 CTGATGTGTTTCCAAAAGT
1 CTGATGTGTTTCCAAAAGT
*
58138567 CTGATGTGTTTCCTAAAG
1 CTGATGTGTTTCCAAAAG
58138585 AACTTCCGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (19 bp):
CTGATGTGTTTCCAAAAGT
Found at i:58140166 original size:25 final size:25
Alignment explanation
Indices: 58140138--58140191 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
58140128 CGCCTTATAG
*
58140138 GCTTTCCAGATAACTCACCACAAAA
1 GCTTTACAGATAACTCACCACAAAA
* *
58140163 GCTTTATAGATAACTCACCACAAAG
1 GCTTTACAGATAACTCACCACAAAA
58140188 GCTT
1 GCTT
58140192 GGTTTGGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (25 bp):
GCTTTACAGATAACTCACCACAAAA
Found at i:58149083 original size:43 final size:42
Alignment explanation
Indices: 58149035--58149203 Score: 130
Period size: 43 Copynumber: 4.0 Consensus size: 42
58149025 GTTAATGAGA
* *
58149035 TGTGATTACATGTAAGACCATGTCTGGAAAATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATATCTGG-ACATTGGCATTGTAT
** * * *
58149078 TGTGATTATTTTTAAGACCATGTTTGGTACATTGGCATTGTTAT
1 TGTGATTACATGTAAGACCATATCTGG-ACATTGGCATTG-TAT
* * * * *
58149122 T-TGATTCCGTGTAAGACCCTATCTAGGACAGT-GCATCG-AT
1 TGTGATTACATGTAAGACCATATCT-GGACATTGGCATTGTAT
* *
58149162 ATGTGATAACATGTAAGACCATATCTGG-GATATGGCATTGTA
1 -TGTGATTACATGTAAGACCATATCTGGACAT-TGGCATTGTA
58149204 CGAGCTTTAT
Statistics
Matches: 97, Mismatches: 22, Indels: 14
0.73 0.17 0.11
Matches are distributed among these distances:
40 3 0.03
41 4 0.04
42 29 0.30
43 55 0.57
44 6 0.06
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (42 bp):
TGTGATTACATGTAAGACCATATCTGGACATTGGCATTGTAT
Found at i:58153884 original size:93 final size:93
Alignment explanation
Indices: 58153774--58153944 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
58153764 CGCCCTAAGT
* * * * *
58153774 GAACTCGGACTCTACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
58153839 CGAGTTCGGATGCCTAGTTATATCTCAC
66 CGAGTTCGGATGCCTAGTTATATCTCAC
* * *
58153867 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
58153932 CGAGTTCGGATGC
66 CGAGTTCGGATGC
58153945 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTATATCTCAC
Found at i:58153941 original size:46 final size:46
Alignment explanation
Indices: 58153769--58153941 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 46
58153759 TAACCCGCCC
* * * * * *
58153769 TAAGTGAACTCGGACTCTACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
**
58153815 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ATAT-C-
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
58153863 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
58153908 TAGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
58153942 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 57 0.56
47 29 0.28
48 2 0.02
49 2 0.02
50 2 0.02
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:58154396 original size:30 final size:30
Alignment explanation
Indices: 58154362--58154421 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
58154352 ATTTAATACT
58154362 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * * *
58154392 AACTTTTGCATAATTACACTTTTGCTCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
58154422 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:58156363 original size:28 final size:28
Alignment explanation
Indices: 58156327--58156398 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
58156317 TCAAATATGG
* *
58156327 CACTCAGTGTACGAAATATTGAGAATGA
1 CACTAAGTGTGCGAAATATTGAGAATGA
* *
58156355 CACTAAGTGTGCGAGATATTGAGAATGG
1 CACTAAGTGTGCGAAATATTGAGAATGA
*
58156383 CACTTAGTGTGCGAAA
1 CACTAAGTGTGCGAAA
58156399 CATCAATGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (28 bp):
CACTAAGTGTGCGAAATATTGAGAATGA
Found at i:58158553 original size:46 final size:45
Alignment explanation
Indices: 58158486--58158702 Score: 208
Period size: 46 Copynumber: 4.7 Consensus size: 45
58158476 TGTAACCCGC
* * *
58158486 CCATAAGCGAACTCGGACTCAACTCAATGAGCTTGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTGGACATTCGCAT
* *
58158532 CCATAAGTAAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT-GGA---C-A-TTCGCAT
* * * * *
58158582 --TTCA-CGAACTCGGACTCAACTCAACAAGTTTGGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTGGACATTCGCAT
* * **
58158625 CCATAAGTGAACTTGGACTCAACTCAACGAGTCGGATGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTGGACATTCGCAT
58158670 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
58158703 CAGATGCTTA
Statistics
Matches: 139, Mismatches: 21, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 1 0.01
45 47 0.34
46 51 0.37
47 24 0.17
48 4 0.03
49 1 0.01
50 4 0.03
51 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTGGACATTCGCAT
Found at i:58158622 original size:93 final size:92
Alignment explanation
Indices: 58158493--58158662 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 92
58158483 CGCCCATAAG
** *
58158493 CGAACTCGGACTCAACTCAATGAGCTTGGGCATTCGCATCCATAAGTAAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTTGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
58158558 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAG-TCGGATGCCTAGTTACATTTCA
* * * *
58158586 CGAACTCGGACTCAACTCAACAAGTTTGGACGTTCGCATCCATAAGTGAACTTGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTTGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
58158651 ACGAGTCGGATG
66 ACGAGTCGGATG
58158663 TTCGCATCCA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 7 0.10
93 63 0.90
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACAAGCTTGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
ACGAGTCGGATGCCTAGTTACATTTCA
Found at i:58164601 original size:37 final size:37
Alignment explanation
Indices: 58164495--58164603 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
58164485 AGCTCAGATG
* * *
58164495 AAATCTCCACACGAAGTTATCGGGTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
58164532 AAATCTCCATACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
58164569 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
58164604 ATATATTTCC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:58164858 original size:48 final size:48
Alignment explanation
Indices: 58164750--58165124 Score: 536
Period size: 48 Copynumber: 7.6 Consensus size: 48
58164740 ACACATCGCC
*
58164750 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
58164800 TATATATTTCACATT-GACCATTCGGCTTTACCATATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
*
58164848 TACATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC----A
* * *
58164900 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
58164948 TACATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
58164996 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC----A
* * *
58165048 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
58165096 TACATATTTCACATTAGCCATTCGGCTTT
1 TACATATTTCACATTAGCCATTCGGCTTT
58165125 TGTGACACCC
Statistics
Matches: 296, Mismatches: 19, Indels: 22
0.88 0.06 0.07
Matches are distributed among these distances:
48 163 0.55
49 1 0.00
50 41 0.14
52 91 0.31
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:58164957 original size:100 final size:98
Alignment explanation
Indices: 58164750--58165124 Score: 542
Period size: 100 Copynumber: 3.8 Consensus size: 98
58164740 ACACATCGCC
* * *
58164750 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATATATATATTTCACATT
* * *
58164815 GACCATTCGGCTTTACCATATATGCATATCTCA
66 AACCATTCGGCTTTACCACATATACATATCTCA
*
58164848 TACATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTCATATATATATATTTCACA
1 TACATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTC--ATATATATATTTCACA
*
58164913 TTAACCATTCAGCTTTACCACATATACATATCTCA
64 TTAACCATTCGGCTTTACCACATATACATATCTCA
* *
58164948 TACATATTTCACATTAGCCATTCAGCTTTACCACATATACATATCTC--ATACATATTTCACATT
1 TACATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATATATATATTTCACATT
*
58165011 AGCCATTCGGCTTTACCACATATACATATCTCATATA
66 AACCATTCGGCTTTACCACATATACATATCTC----A
* *
58165048 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTC--ATACATATTTCACATT
1 TACATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATATATATATTTCACATT
*
58165111 AGCCATTCGGCTTT
66 AACCATTCGGCTTT
58165125 TGTGACACCC
Statistics
Matches: 258, Mismatches: 13, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
96 45 0.17
98 45 0.17
100 168 0.65
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (98 bp):
TACATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATATATATATTTCACATT
AACCATTCGGCTTTACCACATATACATATCTCA
Found at i:58165002 original size:148 final size:148
Alignment explanation
Indices: 58164753--58165124 Score: 638
Period size: 148 Copynumber: 2.5 Consensus size: 148
58164743 CATCGCCTAC
* * * *
58164753 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT-GA
1 ATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTC--ATACATATTTCACATTAG-
* *
58164817 CCATTCGGCTTTACCATATATGCATATCTCATACATATTTCACATTAACCATTCGGCTTTACCAC
63 CCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAACCATTCGGCTTTACCAC
58164882 ATATACATATCTCATATATAT
128 ATATACATATCTCATATATAT
58164903 ATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
* *
58164968 TTCAGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
66 TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAACCATTCGGCTTTACCACATA
58165033 TACATATCTCATATATAT
131 TACATATCTCATATATAT
58165051 ATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
58165116 TTCGGCTTT
66 TTCGGCTTT
58165125 TGTGACACCC
Statistics
Matches: 212, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
148 170 0.80
149 1 0.00
150 41 0.19
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (148 bp):
ATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAACCATTCGGCTTTACCACATA
TACATATCTCATATATAT
Found at i:58166897 original size:40 final size:39
Alignment explanation
Indices: 58166831--58166981 Score: 153
Period size: 40 Copynumber: 3.8 Consensus size: 39
58166821 AAATTGAATG
* * *
58166831 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GGTAATT
* * ***
58166870 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCAAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GGTAATT
*
58166910 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCG-GTAATT
* *
58166950 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
58166982 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
39 16 0.17
40 74 0.80
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGGTAATT
Found at i:58166995 original size:40 final size:39
Alignment explanation
Indices: 58166868--58166997 Score: 161
Period size: 40 Copynumber: 3.3 Consensus size: 39
58166858 ATGCTGGAAA
* *
58166868 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCAAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-TGG
* * * **
58166908 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATGG
*
58166948 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA-ATGG
58166988 TTATATCCGG
1 TTATATCCGG
58166998 TTATATTCCG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 72 0.97
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATGG
Found at i:58179974 original size:41 final size:41
Alignment explanation
Indices: 58179929--58180046 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
58179919 TGAAAGATAA
58179929 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
58179970 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
58180000 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
58180041 ATGTAG
1 ATGTAG
58180047 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:58179985 original size:71 final size:71
Alignment explanation
Indices: 58179897--58180060 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
58179887 GAGATGTATC
58179897 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
58179962 AGGACA
66 AGGACA
58179968 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
58180033 AGGACA
66 AGGACA
58180039 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
58180061 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:58183757 original size:46 final size:46
Alignment explanation
Indices: 58183704--58183879 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
58183694 TATTTGGGCA
58183704 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
58183750 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
58183797 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
58183843 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58183880 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:58183859 original size:93 final size:93
Alignment explanation
Indices: 58183700--58183871 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
58183690 GGGATATTTG
* *
58183700 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
58183765 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
58183793 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
58183858 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
58183872 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:58185781 original size:40 final size:40
Alignment explanation
Indices: 58185744--58185929 Score: 245
Period size: 40 Copynumber: 4.7 Consensus size: 40
58185734 GCTACTCGTT
*
58185744 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
58185784 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
58185824 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
58185864 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
58185905 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58185930 CATCATTCGA
Statistics
Matches: 134, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
39 3 0.02
40 118 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:58193746 original size:40 final size:40
Alignment explanation
Indices: 58193709--58193894 Score: 245
Period size: 40 Copynumber: 4.7 Consensus size: 40
58193699 GCTACTCGTT
*
58193709 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
58193749 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
58193789 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
58193829 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
58193870 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58193895 CATCATTCGA
Statistics
Matches: 134, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
39 3 0.02
40 118 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:58202055 original size:9 final size:9
Alignment explanation
Indices: 58202041--58202121 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 9
58202031 ATTTGAATCA
58202041 AAATAAAAT
1 AAATAAAAT
58202050 AAAT-AAAT
1 AAATAAAAT
** *
58202058 AAGGAAGA-
1 AAATAAAAT
*
58202066 AAAT-CAAT
1 AAATAAAAT
*
58202074 CAAATAAATT
1 -AAATAAAAT
*
58202084 AAATAAAAG
1 AAATAAAAT
*
58202093 AAACAAAAT
1 AAATAAAAT
58202102 AAGATAAAAT
1 AA-ATAAAAT
58202112 AAAATAAAAT
1 -AAATAAAAT
58202122 TGTGAAAAAT
Statistics
Matches: 52, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
7 1 0.02
8 8 0.15
9 26 0.50
10 15 0.29
11 2 0.04
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:58203525 original size:25 final size:23
Alignment explanation
Indices: 58203485--58203532 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
58203475 TGCATTATGG
58203485 AAGGAAAATAAAGAAATGAAAAAAA
1 AAGGAAAATAAAGAAA--AAAAAAA
* *
58203510 AAGGAAAATGATGAAAAAAAAAA
1 AAGGAAAATAAAGAAAAAAAAAA
58203533 GTGTGGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (23 bp):
AAGGAAAATAAAGAAAAAAAAAA
Found at i:58204849 original size:29 final size:29
Alignment explanation
Indices: 58204816--58204975 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
58204806 GTGACGAGAT
58204816 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
58204845 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
58204874 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
58204903 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
58204932 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
58204961 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
58204976 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:58210050 original size:40 final size:39
Alignment explanation
Indices: 58209885--58210068 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
58209875 AAATTGAATG
* * *
58209885 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
58209925 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
58209965 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
58210005 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
58210044 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
58210069 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:58210093 original size:80 final size:81
Alignment explanation
Indices: 58209925--58210113 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
58209915 GCTGGAAATT
* * * *
58209925 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
58209990 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
58210006 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
58210069 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
58210085 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
58210114 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:58216239 original size:29 final size:29
Alignment explanation
Indices: 58216206--58216365 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
58216196 GTGACGAGAT
58216206 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
58216235 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
58216264 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
58216293 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
58216322 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
58216351 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
58216366 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:58221656 original size:24 final size:25
Alignment explanation
Indices: 58221620--58221672 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
58221610 AATCAAAACC
58221620 TAAAAAAACTAAAA-AAAAATCTAAT
1 TAAAAAAACTAAAACAAAAAT-TAAT
58221645 TAAAAAAA-TAAAACAAAAATTAAT
1 TAAAAAAACTAAAACAAAAATTAAT
58221669 TAAA
1 TAAA
58221673 GGGGAGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (25 bp):
TAAAAAAACTAAAACAAAAATTAAT
Found at i:58223885 original size:2 final size:2
Alignment explanation
Indices: 58223878--58223918 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
58223868 AAAATGTGGT
58223878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58223919 TAATGAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58232306 original size:13 final size:14
Alignment explanation
Indices: 58232288--58232320 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
58232278 ATTTTTTAAA
*
58232288 TTTAAAACAAT-AT
1 TTTAAAAAAATAAT
58232301 TTTAAAAAAATAAT
1 TTTAAAAAAATAAT
58232315 TTTAAA
1 TTTAAA
58232321 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTAAAAAAATAAT
Found at i:58233741 original size:30 final size:30
Alignment explanation
Indices: 58233707--58233766 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
58233697 TATTTTATTA
*
58233707 TTAATTTTGTTATTGTTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
58233737 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
58233767 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.02, G:0.17, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:58236097 original size:20 final size:20
Alignment explanation
Indices: 58236069--58236115 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
58236059 TTTTCAAGGC
*
58236069 AAATGCCTTTTGAC-TTAGGA
1 AAATTCCTTTTG-CTTTAGGA
58236089 AAATTCC--TTGCTTTAGGA
1 AAATTCCTTTTGCTTTAGGA
58236107 AAATTCCTT
1 AAATTCCTT
58236116 GCTGAGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
20 6 0.26
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
AAATTCCTTTTGCTTTAGGA
Found at i:58236106 original size:18 final size:18
Alignment explanation
Indices: 58236083--58236118 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
58236073 GCCTTTTGAC
58236083 TTAGGAAAATTCCTTGCT
1 TTAGGAAAATTCCTTGCT
58236101 TTAGGAAAATTCCTTGCT
1 TTAGGAAAATTCCTTGCT
58236119 GAGTTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
TTAGGAAAATTCCTTGCT
Found at i:58241915 original size:21 final size:21
Alignment explanation
Indices: 58241891--58241933 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
58241881 GATACCCTTG
* * *
58241891 TAAAATATTGGTACTTTAATA
1 TAAAATATAGATAATTTAATA
*
58241912 TAAAGTATAGATAATTTAATA
1 TAAAATATAGATAATTTAATA
58241933 T
1 T
58241934 GCTATCAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (21 bp):
TAAAATATAGATAATTTAATA
Found at i:58244754 original size:33 final size:33
Alignment explanation
Indices: 58244712--58244777 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
58244702 ATATTGTTGA
58244712 TCGATTTGTTCTATAAGTCCATTTGGCTCATAC
1 TCGATTTGTTCTATAAGTCCATTTGGCTCATAC
58244745 TCGATTTGTTCTATAAGTCCATTTGGCTCATAC
1 TCGATTTGTTCTATAAGTCCATTTGGCTCATAC
58244778 CCTAGATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (33 bp):
TCGATTTGTTCTATAAGTCCATTTGGCTCATAC
Found at i:58247707 original size:93 final size:93
Alignment explanation
Indices: 58247548--58247719 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
58247538 CGCCCATAAG
* * * *
58247548 CGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
58247613 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * *
58247641 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
58247706 ACGAGCTCGGATGC
66 ACGAGCTCGGATGC
58247720 TCAACCATCC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:58247716 original size:46 final size:46
Alignment explanation
Indices: 58247541--58247716 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
58247531 TGTAACCCGC
* * * *
58247541 CCATAAGCGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * * * * *
58247587 CCATGAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* *
58247637 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
*
58247680 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
58247717 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 28 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:58249521 original size:17 final size:17
Alignment explanation
Indices: 58249499--58249531 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58249489 GATGATTGAG
*
58249499 TTAATAAATATTATTTC
1 TTAATAAATAATATTTC
58249516 TTAATAAATAATATTT
1 TTAATAAATAATATTT
58249532 ACAAGGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATAAATAATATTTC
Found at i:58254178 original size:24 final size:24
Alignment explanation
Indices: 58254149--58254194 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
58254139 CAAAAATGAC
58254149 AATAATGATGAAAACGATAATAAT
1 AATAATGATGAAAACGATAATAAT
* * *
58254173 AATAATGTTGATAATGATAATA
1 AATAATGATGAAAACGATAATA
58254195 GTGGTGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.30
Consensus pattern (24 bp):
AATAATGATGAAAACGATAATAAT
Found at i:58254185 original size:18 final size:18
Alignment explanation
Indices: 58254164--58254230 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
58254154 TGATGAAAAC
58254164 GATAATAATAATAATGTT
1 GATAATAATAATAATGTT
* * *
58254182 GATAATGATAATAGTGGT
1 GATAATAATAATAATGTT
* *
58254200 GGTAA-AACT-ATAATATT
1 GATAATAA-TAATAATGTT
*
58254217 GATGATAATAATAA
1 GATAATAATAATAA
58254231 AAATAATAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
17 10 0.28
18 26 0.72
ACGTcount: A:0.48, C:0.01, G:0.16, T:0.34
Consensus pattern (18 bp):
GATAATAATAATAATGTT
Found at i:58254578 original size:23 final size:23
Alignment explanation
Indices: 58254552--58254600 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
58254542 ATAAAAGAGG
*
58254552 AAAATATAATAACAATAATAGTA
1 AAAATACAATAACAATAATAGTA
**
58254575 AAAATACAATAGTAATAATAGTA
1 AAAATACAATAACAATAATAGTA
58254598 AAA
1 AAA
58254601 GGTGTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAATACAATAACAATAATAGTA
Found at i:58254760 original size:14 final size:14
Alignment explanation
Indices: 58254737--58254772 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
58254727 TAAAAATTAC
58254737 TATATATATATACA
1 TATATATATATACA
*
58254751 TATATCTATATACA
1 TATATATATATACA
58254765 TATATATA
1 TATATATA
58254773 AAAACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATATATATACA
Found at i:58256293 original size:18 final size:18
Alignment explanation
Indices: 58256270--58256311 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
58256260 TTGGGAGTTA
58256270 TTTGGGTAGGTTATTTGT
1 TTTGGGTAGGTTATTTGT
58256288 TTTGGGTAGGTTATTTGT
1 TTTGGGTAGGTTATTTGT
58256306 TTTGGG
1 TTTGGG
58256312 CCCAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.00, G:0.36, T:0.55
Consensus pattern (18 bp):
TTTGGGTAGGTTATTTGT
Found at i:58256304 original size:13 final size:12
Alignment explanation
Indices: 58256254--58256286 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
58256244 TTGGGTCTGG
58256254 GGTTATTTGGGA
1 GGTTATTTGGGA
58256266 -GTTATTTGGGTA
1 GGTTATTTGGG-A
58256278 GGTTATTTG
1 GGTTATTTG
58256287 TTTTGGGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.48
Consensus pattern (12 bp):
GGTTATTTGGGA
Found at i:58259438 original size:40 final size:40
Alignment explanation
Indices: 58259389--58259575 Score: 173
Period size: 39 Copynumber: 4.8 Consensus size: 40
58259379 TACTCGTTCA
* * * **
58259389 AAACACCTTCGGGACATAGCCCGGTTATGGTAACCCGCAC
1 AAACGCCTTCGGGACTTAGCCCGGATATCATAACCCGCAC
* *
58259429 AAACGCCTTCGGGACTTAACCCGGATATCATAACTCGCAC
1 AAACGCCTTCGGGACTTAGCCCGGATATCATAACCCGCAC
** * * *
58259469 AATTGCCTTCGGG-CTTAGCCCGGATATCATAGCTCTCAC
1 AAACGCCTTCGGGACTTAGCCCGGATATCATAACCCGCAC
** * ***
58259508 AATTGCCTTCGGG-CTTAGCCCGGATATCACAATTTGCAC
1 AAACGCCTTCGGGACTTAGCCCGGATATCATAACCCGCAC
**
58259547 AATTGCCTTCGGG-CTTAGCCCGGATATCA
1 AAACGCCTTCGGGACTTAGCCCGGATATCA
58259576 CAATTCGCAC
Statistics
Matches: 130, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 86 0.66
40 44 0.34
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
AAACGCCTTCGGGACTTAGCCCGGATATCATAACCCGCAC
Found at i:58259576 original size:39 final size:39
Alignment explanation
Indices: 58259424--58259586 Score: 227
Period size: 39 Copynumber: 4.2 Consensus size: 39
58259414 TATGGTAACC
** * * *
58259424 CGCACAAACGCCTTCGGGACTTAACCCGGATATCATAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATT
* **
58259464 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
58259503 CTCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
58259542 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
58259581 CGCACA
1 CGCACA
58259587 TTCATTCACA
Statistics
Matches: 112, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 96 0.86
40 16 0.14
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
Found at i:58270511 original size:24 final size:24
Alignment explanation
Indices: 58270482--58270527 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
58270472 CAAAAATGAC
58270482 AATAATGATGAAAACGATAATAAT
1 AATAATGATGAAAACGATAATAAT
* * *
58270506 AATAATGTTGATAATGATAATA
1 AATAATGATGAAAACGATAATA
58270528 GTGGTGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.30
Consensus pattern (24 bp):
AATAATGATGAAAACGATAATAAT
Found at i:58270518 original size:18 final size:18
Alignment explanation
Indices: 58270497--58270563 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
58270487 TGATGAAAAC
58270497 GATAATAATAATAATGTT
1 GATAATAATAATAATGTT
* * *
58270515 GATAATGATAATAGTGGT
1 GATAATAATAATAATGTT
* *
58270533 GGTAA-AACT-ATAATATT
1 GATAATAA-TAATAATGTT
*
58270550 GATGATAATAATAA
1 GATAATAATAATAA
58270564 AAATAATAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
17 10 0.28
18 26 0.72
ACGTcount: A:0.48, C:0.01, G:0.16, T:0.34
Consensus pattern (18 bp):
GATAATAATAATAATGTT
Found at i:58270912 original size:23 final size:23
Alignment explanation
Indices: 58270886--58270934 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
58270876 ATAAAAGAGG
*
58270886 AAAATATAATAACAATAATAGTA
1 AAAATACAATAACAATAATAGTA
**
58270909 AAAATACAATAGTAATAATAGTA
1 AAAATACAATAACAATAATAGTA
58270932 AAA
1 AAA
58270935 GGTGTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAATACAATAACAATAATAGTA
Found at i:58271094 original size:14 final size:14
Alignment explanation
Indices: 58271071--58271106 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
58271061 TAAAAATTAC
58271071 TATATATATATACA
1 TATATATATATACA
*
58271085 TATATCTATATACA
1 TATATATATATACA
58271099 TATATATA
1 TATATATA
58271107 AAAACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATATATATACA
Found at i:58272027 original size:2 final size:2
Alignment explanation
Indices: 58272020--58272062 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
58272010 TTGTTTACAC
58272020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58272062 T
1 T
58272063 GCGAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58272653 original size:11 final size:13
Alignment explanation
Indices: 58272636--58272668 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
58272626 TTGGGTCTGG
58272636 GGTTATTTGGA-A
1 GGTTATTTGGATA
58272648 -GTTATTTGGATA
1 GGTTATTTGGATA
58272660 GGTTATTTG
1 GGTTATTTG
58272669 TTTTGGGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (13 bp):
GGTTATTTGGATA
Found at i:58272679 original size:18 final size:18
Alignment explanation
Indices: 58272652--58272693 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
58272642 TTGGAAGTTA
*
58272652 TTTGGATAGGTTATTTGT
1 TTTGGGTAGGTTATTTGT
58272670 TTTGGGTAGGTTATTTGT
1 TTTGGGTAGGTTATTTGT
58272688 TTTGGG
1 TTTGGG
58272694 CCCAAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (18 bp):
TTTGGGTAGGTTATTTGT
Found at i:58275515 original size:52 final size:51
Alignment explanation
Indices: 58275386--58275516 Score: 144
Period size: 52 Copynumber: 2.6 Consensus size: 51
58275376 ATGTGTTCTG
* * * *
58275386 CATTTAATGAAGTCATGCATTATGTAAC-CTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTAAGTAACTCCCATGTTAGTTAAGTTTGCAT
* * *
58275436 CA-TAAATTATGAT-ATTCATTATA-TAACTCCCCTGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAG-TCATGCATTA-AGTAACTCCCATGTTAGTT-AAGTTTGCAT
58275487 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTAAGTAACTC
58275517 ATTTGTTTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
49 17 0.26
50 13 0.20
51 14 0.22
52 21 0.32
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTAAGTAACTCCCATGTTAGTTAAGTTTGCAT
Found at i:58294005 original size:28 final size:28
Alignment explanation
Indices: 58293954--58294028 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
58293944 CTTTTCAAAG
*
58293954 CTCAATTGATTGCTAACTTTCAATTAAAAA
1 CTCAATTAATTG-TAA-TTTCAATTAAAAA
58293984 CTCAATTAATTGTAATTTCAATTAAAAA
1 CTCAATTAATTGTAATTTCAATTAAAAA
*
58294012 CTTAATTAAATT-TAATT
1 CTCAATT-AATTGTAATT
58294029 ATTTTCTAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 24 0.57
29 7 0.17
30 11 0.26
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (28 bp):
CTCAATTAATTGTAATTTCAATTAAAAA
Found at i:58296044 original size:3 final size:3
Alignment explanation
Indices: 58295733--58296031 Score: 266
Period size: 3 Copynumber: 98.0 Consensus size: 3
58295723 ACGTAACAAC
* * *
58295733 ATA ATA ATA GATA CGATA ATA CTA ATA ACA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA -ATA --ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
58295781 ATA TTA ATA A-A ATA AAA ATA ATT GTA ATA A-A ATA A-A ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
58295826 ATA ATA ATG ATA ATA ATG ATA ATAA ATA ATA ATA GTAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA ATA ATA
* * * *
58295873 ATA ATA GTA ATA ATA ATG ATA ATAA ATA ATA GTA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
* * *
58295919 ATG ATA ATAA ATA ATA ATA ATA ATA GTA GTA ATA ATA ATA ATGA AT-
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * *
58295965 ATAA ATA ATA GTA A-A ATA ATA ATA ATA ATA ATG ACA ATAA ATA ATA
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
* *
58296011 GTA AAA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
58296032 GTAGGAATAA
Statistics
Matches: 238, Mismatches: 44, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
2 10 0.04
3 202 0.85
4 22 0.09
5 4 0.02
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:58297418 original size:45 final size:45
Alignment explanation
Indices: 58297232--58297534 Score: 202
Period size: 45 Copynumber: 6.5 Consensus size: 45
58297222 TCCACTCCGT
* * * * *
58297232 TGCAACTTCAAGGATATCAGATTT-TTGGT-TTTAGTCTGCTCTAC
1 TGCAACTTCAGGGAAATAAGATTTGTT-GTCTTTAATTTGCTCTAC
* * *
58297276 TGCGACTTCAGGGAAATAAGACTTGCTGTGGTAAATTTAATTTGAC-CTAC
1 TGCAACTTCAGGGAAATAAGA-TT--TGTTGT--CTTTAATTTG-CTCTAC
* * * * *
58297326 TGCAACTTCTGAGG-TATAGGATTTGTAG-CTTTAATTTACTCTAC
1 TGCAACTTCAG-GGAAATAAGATTTGTTGTCTTTAATTTGCTCTAC
* *
58297370 TGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTGCTCTAC
1 TGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAATTTGCTCTAC
* * *
58297415 TGCAACTTCAGGGAGATAAGATTTGTAATTTGTAGCTTCAATTTGCTCCAC
1 TGCAACTTCAGGGAAATAAGATTTG----TTGT--CTTTAATTTGCTCTAC
* * * * * * * *
58297466 TGTAATTTCAGGGAAATGAGATTTGGTATCTTTAGTATGCTCCAC
1 TGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAATTTGCTCTAC
*
58297511 TGCAACTTCAGGGAGATAAGATTT
1 TGCAACTTCAGGGAAATAAGATTT
58297535 ATGACTCTTA
Statistics
Matches: 202, Mismatches: 39, Indels: 35
0.73 0.14 0.13
Matches are distributed among these distances:
43 3 0.01
44 50 0.25
45 72 0.36
47 9 0.04
48 1 0.00
49 6 0.03
50 25 0.12
51 36 0.18
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (45 bp):
TGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAATTTGCTCTAC
Found at i:58297476 original size:96 final size:96
Alignment explanation
Indices: 58297346--58297626 Score: 323
Period size: 96 Copynumber: 2.9 Consensus size: 96
58297336 GAGGTATAGG
* * * *
58297346 ATTTGTAGCTTTAATTTACTCTACTGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTGCT
1 ATTTGTAGCTTTAATTTGCTCCACTGCAATTTCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCT
*
58297411 CTACTGCAACTTCAGGGAGATAAGATTTGT-A
66 C-ACTGCAACTTCAGGGAGATAAGATTTATGA
* * * * * *
58297442 ATTTGTAGCTTCAATTTGCTCCACTGTAATTTCAGGGAAATGAGATTTGGTATCTTTAGTATGCT
1 ATTTGTAGCTTTAATTTGCTCCACTGCAATTTCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCT
58297507 CCACTGCAACTTCAGGGAGATAAGATTTATGA
66 -CACTGCAACTTCAGGGAGATAAGATTTATGA
* * * * * * * * * *
58297539 CTCT-TAGTTTTGATCTGTTCCACTACAATGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCT
1 ATTTGTAGCTTTAATTTGCTCCACTGCAATTTCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCT
*
58297603 ACACTGCAACTTTAGGGAGATAAG
66 -CACTGCAACTTCAGGGAGATAAG
58297627 GCTAGTGGCT
Statistics
Matches: 155, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
96 151 0.97
97 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (96 bp):
ATTTGTAGCTTTAATTTGCTCCACTGCAATTTCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCT
CACTGCAACTTCAGGGAGATAAGATTTATGA
Found at i:58297728 original size:143 final size:143
Alignment explanation
Indices: 58297551--58297886 Score: 476
Period size: 143 Copynumber: 2.3 Consensus size: 143
58297541 CTTAGTTTTG
* ** * *
58297551 ATCTGTTCCACTACAATGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTACACTGCAACTTT
1 ATCTGTTCCACTGCAACATCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTACACTGCAACTTC
*
58297616 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAGGAAGATAAGATTCACCATA
66 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAGGAAGATAAGATCCACCATA
58297681 ATTTGTAGCT-TCA
131 ATTTGTAGCTGT-A
* * * *
58297694 ATCTGTTCCAATGCAACATCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCGCTGTAACTTC
1 ATCTGTTCCACTGCAACATCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTACACTGCAACTTC
* * * * *
58297759 AGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCTCCATA
66 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAGGAAGATAAGATCCACCATA
58297824 ATTTGTAGCTGTA
131 ATTTGTAGCTGTA
* * * * *
58297837 ATTTGTTCCACTGTAACTTTAAGGAAATAAGATTCGTTGTCTTCAGTCTG
1 ATCTGTTCCACTGCAACATCAGGGAAATAAGATTCGTTGTCTTCAGTCTG
58297887 ATCTGCTGTA
Statistics
Matches: 171, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
143 170 0.99
144 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (143 bp):
ATCTGTTCCACTGCAACATCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTACACTGCAACTTC
AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAGGAAGATAAGATCCACCATA
ATTTGTAGCTGTA
Found at i:58297895 original size:143 final size:142
Alignment explanation
Indices: 58297573--58297956 Score: 475
Period size: 143 Copynumber: 2.7 Consensus size: 142
58297563 ACAATGTCAG
* * * *
58297573 GGAAATAAGATTCGCTGTCTTCAGTCTGCTACACTGCAACTTTAGGGAGATAAGGCTAGTGGCTT
1 GGAAATAAGATTCGTTGTCTTCAGTCTGCT-CGCTGTAACTTCAGGGAGATAAGGCTAGTGGCTT
* * * *
58297638 CAATCTACTCCACTACAACTTCAGGAAGATAAGATTCACCATAATTTGTAGCTTCAATCTGTTCC
65 CAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCACCATAATTTGTAGCTTCAATCTGTTCC
*
58297703 AATGCAACATCAG
130 AATGCAACATCAA
*
58297716 GGAAATAAGATTCGTTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGCTGGTGGCTT
1 GGAAATAAGATTCGTTGTCTTCAGTCTGCT-CGCTGTAACTTCAGGGAGATAAGGCTAGTGGCTT
* *
58297781 CAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCTCCATAATTTGTAGCTGT-AATTTGTTC
65 CAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCACCATAATTTGTAGCT-TCAATCTGTTC
* * * *
58297845 CACTGTAACTTTAA
129 CAATGCAACATCAA
* ** * * ***
58297859 GGAAATAAGATTCGTTGTCTTCAGTCTGATCTGCTGTAACTTCAGAAAGATAAGACTTGTAATTT
1 GGAAATAAGATTCGTTGTCTTCAGTCTGCTC-GCTGTAACTTCAGGGAGATAAGGCTAGTGGCTT
* *
58297924 CAACCTGCTCTACTGCAACTTTA-GAGAGATAAG
65 CAATCTGCTCCACTGCAACTTTAGGA-AGATAAG
58297957 GTTAGTGGCT
Statistics
Matches: 211, Mismatches: 27, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
142 3 0.01
143 207 0.98
144 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (142 bp):
GGAAATAAGATTCGTTGTCTTCAGTCTGCTCGCTGTAACTTCAGGGAGATAAGGCTAGTGGCTTC
AATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCACCATAATTTGTAGCTTCAATCTGTTCCA
ATGCAACATCAA
Found at i:58306093 original size:19 final size:19
Alignment explanation
Indices: 58306056--58306098 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
58306046 TCGTGAAATT
*
58306056 TAATGCATATGATGCAATG
1 TAATGCAAATGATGCAATG
58306075 TAATGCAAATGCATG-AATG
1 TAATGCAAATG-ATGCAATG
*
58306094 CAATG
1 TAATG
58306099 AATGCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (19 bp):
TAATGCAAATGATGCAATG
Found at i:58309714 original size:5 final size:6
Alignment explanation
Indices: 58309697--58309721 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58309687 GAGCAAAGAT
58309697 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
58309722 CAAGGCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:58310250 original size:3 final size:3
Alignment explanation
Indices: 58309839--58310237 Score: 374
Period size: 3 Copynumber: 132.0 Consensus size: 3
58309829 ATAAGAAATG
*
58309839 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* *
58309885 ATA GTA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
58309934 AT- ATAA ATA ATA GTA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * * * * *
58309978 ATA ATA ATA ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
58310026 ATG ATA ATG ATA ATAA ATT ATA ATA AAA ATA ATT ACA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
58310072 GTA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
58310121 AT- ATAA ATA ATA GTA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * *
58310165 ATA ATA ATG ATG ATG ATG ATG ATG ATG ATG ATA ATA ATG ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * *
58310211 ATT ATA ATA AAA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
58310238 GTAGGAATAA
Statistics
Matches: 347, Mismatches: 38, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
2 8 0.02
3 320 0.92
4 19 0.05
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:58313243 original size:90 final size:90
Alignment explanation
Indices: 58313149--58313333 Score: 230
Period size: 90 Copynumber: 2.1 Consensus size: 90
58313139 TTTTACATTC
* * * ** *
58313149 AATTGAGTATTTGAACTTTCAAAATGCATCAAAAAA-ACCCTTTAACTTTTTCA-AAATAAAGCA
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAATACCCTCAAAATTTTTCATAAA-AAA-CA
* * *
58313212 ATTAAGCTACTGCTTTTTTTTTCACTT
64 ATTAAGCCACTACTTTTTTTTGCACTT
* *
58313239 AATTGGGTACTTGAACTGTCAAAATGTATAAAAAAATACCCTCAAAATTTTTCATAAAAAACAAT
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAATACCCTCAAAATTTTTCATAAAAAACAAT
*
58313304 TAAGCCCCTACTTTTTTTTGCACTT
66 TAAGCCACTACTTTTTTTTGCACTT
58313329 AATTG
1 AATTG
58313334 TCAAAATGCA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
90 61 0.75
91 17 0.21
92 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (90 bp):
AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAATACCCTCAAAATTTTTCATAAAAAACAAT
TAAGCCACTACTTTTTTTTGCACTT
Found at i:58313486 original size:10 final size:9
Alignment explanation
Indices: 58313458--58313543 Score: 61
Period size: 10 Copynumber: 9.4 Consensus size: 9
58313448 CCTATGACAA
58313458 AAAAATTAT
1 AAAAATTAT
58313467 AAAAA--AT
1 AAAAATTAT
58313474 AAAAATTATT
1 AAAAATTA-T
**
58313484 AAATTTTAAT
1 AAAAATT-AT
58313494 AAAAA-TAT
1 AAAAATTAT
*
58313502 AAAAATATTT
1 AAAAAT-TAT
*
58313512 AAAATTTACT
1 AAAAATTA-T
*
58313522 AAAAATTAG
1 AAAAATTAT
*
58313531 AAAAATTGT
1 AAAAATTAT
58313540 AAAA
1 AAAA
58313544 TTGTAAAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
7 7 0.12
8 7 0.12
9 19 0.32
10 25 0.42
11 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:58313504 original size:28 final size:29
Alignment explanation
Indices: 58313465--58313537 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
58313455 CAAAAAAATT
*
58313465 ATAAAAA-ATAAAAATTA-TTAAATTTTA
1 ATAAAAATATAAAAATTATTTAAAATTTA
58313492 ATAAAAATATAAAAA-TATTTAAAATTTA
1 ATAAAAATATAAAAATTATTTAAAATTTA
* *
58313520 CTAAAAATTAGAAAAATT
1 ATAAAAA-TATAAAAATT
58313538 GTAAAATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.23
28 22 0.56
29 7 0.18
30 1 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
ATAAAAATATAAAAATTATTTAAAATTTA
Found at i:58313846 original size:10 final size:10
Alignment explanation
Indices: 58313833--58313888 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
58313823 GATTATAAAA
58313833 TTTTATATATT
1 TTTTATATA-T
*
58313844 TTTTCTATAT
1 TTTTATATAT
*
58313854 TTCTATATA-
1 TTTTATATAT
58313863 TTTTATA-AT
1 TTTTATATAT
58313872 TTTTA-ATGAT
1 TTTTATAT-AT
58313882 TTTTATA
1 TTTTATA
58313889 ATCTTTTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 2 0.05
9 11 0.30
10 15 0.41
11 9 0.24
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTATATAT
Found at i:58318420 original size:28 final size:28
Alignment explanation
Indices: 58318359--58318456 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
58318349 TCACAAATTG
** * *
58318359 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
58318388 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
58318416 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
58318444 GCACTAAGTGTGC
1 GCACTAAGTGTGC
58318457 GGGCTTATGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:58323944 original size:13 final size:14
Alignment explanation
Indices: 58323920--58323953 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
58323910 TTGGATAAAA
58323920 AAATTATTTTTAAG
1 AAATTATTTTTAAG
58323934 AAATT-TTTTTAAG
1 AAATTATTTTTAAG
*
58323947 AATTTAT
1 AAATTAT
58323954 GAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
AAATTATTTTTAAG
Found at i:58324369 original size:2 final size:2
Alignment explanation
Indices: 58324362--58324402 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
58324352 TTTTAATTTA
58324362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58324403 CATGTAGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58334071 original size:90 final size:90
Alignment explanation
Indices: 58333952--58334118 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 90
58333942 AAGTGATTTT
* * * *
58333952 GTATAAGACCATGTTTGAGACATGGCATCGATATG-AGGTCTCGTATAAGACCATGTCT-GAGAC
1 GTATAAGACCATATCTGAGACATGACATCGATATGTAGGTC-CATATAAGACCATGTCTGGA-AC
58334015 ATGGCGTCGGCACCGATTCAAGACTTC
64 ATGGCGTCGGCACCGATTCAAGACTTC
* * * * *
58334042 GTATAAGACCATATCTGGGATATGACATCGATGTGTAGTTCCATGTAAGACCATGTCTGGAACAT
1 GTATAAGACCATATCTGAGACATGACATCGATATGTAGGTCCATATAAGACCATGTCTGGAACAT
* *
58334107 GGCTTTGGCACC
66 GGCGTCGGCACC
58334119 CTATTTGGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
90 58 0.91
91 6 0.09
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (90 bp):
GTATAAGACCATATCTGAGACATGACATCGATATGTAGGTCCATATAAGACCATGTCTGGAACAT
GGCGTCGGCACCGATTCAAGACTTC
Found at i:58338311 original size:23 final size:23
Alignment explanation
Indices: 58338282--58338335 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
58338272 ATTTTTAGAT
58338282 TTTAATTATGTAAATATA-TA-TAA
1 TTTAATTA--TAAATATATTATTAA
58338305 TTTAATTATAAATATATTATTAA
1 TTTAATTATAAATATATTATTAA
*
58338328 ATTAATTA
1 TTTAATTA
58338336 ATTATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 8 0.29
22 2 0.07
23 18 0.64
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAATTATAAATATATTATTAA
Found at i:58338359 original size:25 final size:26
Alignment explanation
Indices: 58338306--58338361 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
58338296 TATATATAAT
*
58338306 TTAATTATAAATATATTATTAAATTAA
1 TTAATTATAAATATATTATT-AATGAA
58338333 TTAATTATAAATATCA-TATT-ATGAA
1 TTAATTATAAATAT-ATTATTAATGAA
58338358 TTAA
1 TTAA
58338362 ATTAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 8 0.30
27 18 0.67
28 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TTAATTATAAATATATTATTAATGAA
Found at i:58338541 original size:20 final size:20
Alignment explanation
Indices: 58338476--58338542 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
58338466 AAATAGATAT
58338476 TTATTATTTATC--ATTATTA
1 TTATTA-TTATCAAATTATTA
* *
58338495 TTATT-CTATCAAATTATAA
1 TTATTATTATCAAATTATTA
*
58338514 TT-TATATTATTAAATTATTA
1 TTAT-TATTATCAAATTATTA
58338534 TTATTATTA
1 TTATTATTA
58338543 AAAATAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.11
18 1 0.03
19 14 0.37
20 18 0.47
21 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTATCAAATTATTA
Found at i:58338658 original size:20 final size:20
Alignment explanation
Indices: 58338633--58338670 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58338623 TAGTTAATTA
58338633 ATTTTTATT-TAATTAAAAAG
1 ATTTTTATTAT-ATTAAAAAG
58338653 ATTTTTATTATATTAAAA
1 ATTTTTATTATATTAAAA
58338671 TATTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTTTATTATATTAAAAAG
Found at i:58338836 original size:13 final size:14
Alignment explanation
Indices: 58338818--58338864 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
58338808 TTATTAAGTT
58338818 AATAAAATAAAAG-
1 AATAAAATAAAAGA
*
58338831 AATAAAATAAATGA
1 AATAAAATAAAAGA
58338845 AATAAAAT-AAAGA
1 AATAAAATAAAAGA
*
58338858 AACAAAA
1 AATAAAA
58338865 CAAAGTAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 22 0.73
14 8 0.27
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:58339687 original size:21 final size:21
Alignment explanation
Indices: 58339661--58339728 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
58339651 TTGTTTTGAG
58339661 TACTGAATTGAATTGTGAAGT
1 TACTGAATTGAATTGTGAAGT
* *
58339682 TACTGAA-T--ATTGTTATGT
1 TACTGAATTGAATTGTGAAGT
* * *
58339700 GTACTGCATTGAACTGTGAAAT
1 -TACTGAATTGAATTGTGAAGT
58339722 TACTGAA
1 TACTGAA
58339729 GTAATGAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 2 0.06
21 13 0.37
22 6 0.17
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
TACTGAATTGAATTGTGAAGT
Found at i:58339694 original size:40 final size:40
Alignment explanation
Indices: 58339642--58339728 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
58339632 AATTATGGAA
* * *
58339642 TACTGAATATTGTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTATGAGTACTGAATTGAACTGTGAAAT
* *
58339682 TACTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGAGTACTGAATTGAACTGTGAAAT
58339722 TACTGAA
1 TACTGAA
58339729 GTAATGAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (40 bp):
TACTGAATATTGTTATGAGTACTGAATTGAACTGTGAAAT
Found at i:58339949 original size:12 final size:12
Alignment explanation
Indices: 58339932--58339956 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58339922 GCCGACTATT
58339932 GTTACTGTTACC
1 GTTACTGTTACC
58339944 GTTACTGTTACC
1 GTTACTGTTACC
58339956 G
1 G
58339957 ATTCGACACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:58339982 original size:43 final size:45
Alignment explanation
Indices: 58339934--58340042 Score: 143
Period size: 43 Copynumber: 2.5 Consensus size: 45
58339924 CGACTATTGT
*
58339934 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTG-CAT-AA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTCATGAA
* **
58339977 TACTGTTACCGTTATTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTCATGAA
*
58340022 TACTGTTACTGTTACTGTTAC
1 TACTGTTACCGTTACTGTTAC
58340043 TATTGTCGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 34 0.60
44 2 0.04
45 21 0.37
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTCATGAA
Found at i:58341353 original size:18 final size:18
Alignment explanation
Indices: 58341326--58341369 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
58341316 AGGGGAATTG
*
58341326 TACCTGCTACTAAATCAA
1 TACCTACTACTAAATCAA
* *
58341344 TACCTACTACTACATCAG
1 TACCTACTACTAAATCAA
58341362 TACCTACT
1 TACCTACT
58341370 GTCAGACGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.30
Consensus pattern (18 bp):
TACCTACTACTAAATCAA
Found at i:58346112 original size:20 final size:22
Alignment explanation
Indices: 58346072--58346122 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
58346062 ATTTTTAGAT
58346072 TTTAATTATGTAAATATATATAA
1 TTTAATTA-GTAAATATATATAA
*
58346095 TTTAATTA-TAAA-ATATATTA
1 TTTAATTAGTAAATATATATAA
*
58346115 TTAAATTA
1 TTTAATTA
58346123 ATTAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
23 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAATTAGTAAATATATATAA
Found at i:58346112 original size:24 final size:23
Alignment explanation
Indices: 58346072--58346126 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
58346062 ATTTTTAGAT
**
58346072 TTTAATTATGTAAATA-TATATAA
1 TTTAATTATAAAAATATTAT-TAA
58346095 TTTAATTATAAAATATATTATTAA
1 TTTAATTATAAAA-ATATTATTAA
*
58346119 ATTAATTA
1 TTTAATTA
58346127 ATTATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.41
24 13 0.48
25 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAATTATAAAAATATTATTAA
Found at i:58346150 original size:25 final size:27
Alignment explanation
Indices: 58346096--58346152 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
58346086 TATATATAAT
*
58346096 TTAATTATAAAATATATTATTAAATTAA
1 TTAATTATAAAATATATTATT-AATGAA
58346124 TTAATTAT-AAATATCA-TATT-ATGAA
1 TTAATTATAAAATAT-ATTATTAATGAA
58346149 TTAA
1 TTAA
58346153 ATTAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.30
27 10 0.37
28 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TTAATTATAAAATATATTATTAATGAA
Found at i:58346347 original size:20 final size:20
Alignment explanation
Indices: 58346282--58346348 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
58346272 TATTTATGAT
58346282 TTATTATTTATC--ATTATTA
1 TTATTA-TTATCAAATTATTA
* *
58346301 TTATT-CTATCAAATTATAA
1 TTATTATTATCAAATTATTA
*
58346320 TT-TATATTATTAAATTATTA
1 TTAT-TATTATCAAATTATTA
58346340 TTATTATTA
1 TTATTATTA
58346349 AAAATAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.11
18 1 0.03
19 14 0.37
20 18 0.47
21 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTATCAAATTATTA
Found at i:58346618 original size:18 final size:17
Alignment explanation
Indices: 58346578--58346619 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
58346568 ATATATATTT
*
58346578 ATTATTA-AATAAGATA
1 ATTATTATAATAAAATA
*
58346594 TTTATTATAATAATAATA
1 ATTATTATAATAA-AATA
58346612 ATTATTAT
1 ATTATTAT
58346620 TATTAAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 6 0.29
17 5 0.24
18 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTATTATAATAAAATA
Found at i:58346647 original size:13 final size:14
Alignment explanation
Indices: 58346629--58346667 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
58346619 TTATTAAGTT
58346629 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
58346642 AATAAAAGAAATGA
1 AATAAAATAAAAGA
58346656 AATAAAATAAAA
1 AATAAAATAAAA
58346668 TAAAGAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:58346680 original size:18 final size:18
Alignment explanation
Indices: 58346642--58346692 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
58346632 AAAATAAAAG
* *
58346642 AATAAAAGAAATGAAATAA
1 AATAAAATAAA-GAAACAA
58346661 AATAAAATAAAGAAACAA
1 AATAAAATAAAGAAACAA
* *
58346679 AACAAAGTAAAGAA
1 AATAAAATAAAGAA
58346693 GAAACAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.12
Consensus pattern (18 bp):
AATAAAATAAAGAAACAA
Found at i:58346743 original size:14 final size:15
Alignment explanation
Indices: 58346726--58346758 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
58346716 CAGAGCAGGG
58346726 AAAG-AAGAAAAAGA
1 AAAGAAAGAAAAAGA
*
58346740 AAAGAAAGAAAAATA
1 AAAGAAAGAAAAAGA
58346755 AAAG
1 AAAG
58346759 GAAAAACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (15 bp):
AAAGAAAGAAAAAGA
Found at i:58347530 original size:40 final size:40
Alignment explanation
Indices: 58347468--58347554 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
58347458 AATTATGGAA
* * *
58347468 TACTGAATATTGTTTTGAGTACTAAATTGAATTGTGAAGT
1 TACTGAATATTGTTATGAGTACTAAATTGAACTGTGAAAT
* * **
58347508 TACTTAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGAGTACTAAATTGAACTGTGAAAT
58347548 TACTGAA
1 TACTGAA
58347555 GTAATGAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41
Consensus pattern (40 bp):
TACTGAATATTGTTATGAGTACTAAATTGAACTGTGAAAT
Found at i:58353957 original size:19 final size:19
Alignment explanation
Indices: 58353935--58353980 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
58353925 CGTGTCCTAA
* *
58353935 CCACATGGGTGTGTAAAAT
1 CCACACGGGCGTGTAAAAT
*
58353954 CCACACGGGCGTGTGAAAT
1 CCACACGGGCGTGTAAAAT
58353973 CCACACGG
1 CCACACGG
58353981 CCTACCCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.17
Consensus pattern (19 bp):
CCACACGGGCGTGTAAAAT
Found at i:58358350 original size:2 final size:2
Alignment explanation
Indices: 58358343--58358368 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58358333 TTTTTGTTTC
58358343 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
58358369 CATTATGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58365440 original size:105 final size:106
Alignment explanation
Indices: 58365287--58365478 Score: 244
Period size: 105 Copynumber: 1.8 Consensus size: 106
58365277 ACTCAATAAT
* * * *
58365287 AGCAGCTAATTTTAAATATTAATAGAAATTCAGCTTTTACAATCAAAAACAAAATAAT-CAATGA
1 AGCAGCTAATTTTAAATATTAATAGAAACTCAGCATTTAAAATAAAAAACAAAAT-ATCCAATGA
* * *
58365351 AAATTAACGATCCTTATACCAATAATATTGCAATCACTAGAC
65 AAATTAACAATCCTCACACCAATAATATTGCAATCACTAGAC
* * * ** *
58365393 AGCAGCTAATTTTAGA-CTTATTAGAAACTCAGCATTTAAAATAAAAAACCCACTATCCAATGAA
1 AGCAGCTAATTTTAAATATTAATAGAAACTCAGCATTTAAAATAAAAAACAAAATATCCAATGAA
58365457 AATTAACAATCCTCACACCAAT
66 AATTAACAATCCTCACACCAAT
58365479 TAAAATTTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
104 2 0.03
105 55 0.76
106 15 0.21
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (106 bp):
AGCAGCTAATTTTAAATATTAATAGAAACTCAGCATTTAAAATAAAAAACAAAATATCCAATGAA
AATTAACAATCCTCACACCAATAATATTGCAATCACTAGAC
Done.