Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 65 of 79
Found at i:21414334 original size:35 final size:36
Alignment explanation
Indices: 21414293--21414365 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 36
21414283 TTAAATTAGG
*
21414293 TTAGGGTTTTTAATTAAATTAAATTA-GGTTGGGGT
1 TTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGT
21414328 TTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGT
21414364 TT
1 TT
21414366 TTAATCAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 26 0.72
36 10 0.28
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.47
Consensus pattern (36 bp):
TTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGT
Found at i:21414345 original size:30 final size:29
Alignment explanation
Indices: 21414267--21414375 Score: 139
Period size: 29 Copynumber: 3.6 Consensus size: 29
21414257 GTACAAGTTC
21414267 GGGTTTTTAATTAAAATTAAATTA-GGTTA
1 GGGTTTTTAATT-AAATTAAATTAGGGTTA
21414296 GGGTTTTTAATTAAATTAAATTAGGTTGGGGTTTA
1 GGGTTTTTAATTAAATTAAATTA-----GGG-TTA
21414331 GGGTTTTTAATTAAATTAAATTAGGGTTA
1 GGGTTTTTAATTAAATTAAATTAGGGTTA
*
21414360 GGGTTTTTAATCAAAT
1 GGGTTTTTAATTAAAT
21414376 AATATCAAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
28 11 0.15
29 30 0.42
30 3 0.04
34 2 0.03
35 26 0.36
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (29 bp):
GGGTTTTTAATTAAATTAAATTAGGGTTA
Found at i:21415537 original size:7 final size:7
Alignment explanation
Indices: 21415527--21415579 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
21415517 TTATATACAT
21415527 AATACTA
1 AATACTA
21415534 AATACTA
1 AATACTA
21415541 AATACTA
1 AATACTA
21415548 AATACTA
1 AATACTA
21415555 AATACTA
1 AATACTA
21415562 AATACTA
1 AATACTA
21415569 AATACTA
1 AATACTA
21415576 AATA
1 AATA
21415580 TCTATTTGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:21415758 original size:20 final size:20
Alignment explanation
Indices: 21415720--21415758 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21415710 CTTTTATTTT
*
21415720 TAAAATCTACATAATAATTG
1 TAAAATCTACATAAAAATTG
21415740 TAAAATCTA-ATATAAAATT
1 TAAAATCTACATA-AAAATT
21415759 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAATCTACATAAAAATTG
Found at i:21416360 original size:50 final size:51
Alignment explanation
Indices: 21416302--21416423 Score: 185
Period size: 50 Copynumber: 2.4 Consensus size: 51
21416292 TATTTTAAAA
* *
21416302 AAGGAAATTGAGAGCAAATTGAAATTAAATATGG-GTT-TGAGAGATTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGA-ATTTTGG
* *
21416352 AATGAAATTGAGAGGAAATTGAAATTAAATATGGATTTATGAGAATTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGG
21416403 AAGGAAATTGAGAGAAAATTG
1 AAGGAAATTGAGAGAAAATTG
21416424 GGAGGAAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 32 0.49
51 28 0.43
52 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.26, T:0.30
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGG
Found at i:21416418 original size:22 final size:22
Alignment explanation
Indices: 21416399--21416443 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
21416389 TATGAGAATT
21416399 TTGGAAGGAAATTGAGAGAAAA
1 TTGGAAGGAAATTGAGAGAAAA
* *
21416421 TTGGGAGGAAATTGAGAGGAAA
1 TTGGAAGGAAATTGAGAGAAAA
21416443 T
1 T
21416444 ATGAGGGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (22 bp):
TTGGAAGGAAATTGAGAGAAAA
Found at i:21416423 original size:11 final size:11
Alignment explanation
Indices: 21416404--21416448 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
21416394 GAATTTTGGA
21416404 AGGAAATTGAG
1 AGGAAATTGAG
* *
21416415 AGAAAATTGGG
1 AGGAAATTGAG
21416426 AGGAAATTGAG
1 AGGAAATTGAG
21416437 AGGAAATATGAG
1 AGGAAAT-TGAG
21416449 GGAGGATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 25 0.86
12 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:21417934 original size:25 final size:23
Alignment explanation
Indices: 21417901--21417946 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
21417891 ATCTTTCATA
21417901 TTTTATTAATGGAATATTTTAATTT
1 TTTTATTAA-GGAA-ATTTTAATTT
* *
21417926 TTTTCTTAAGGTAATTTTAAT
1 TTTTATTAAGGAAATTTTAAT
21417947 ATGTTGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 3 0.16
25 8 0.42
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (23 bp):
TTTTATTAAGGAAATTTTAATTT
Found at i:21419153 original size:27 final size:27
Alignment explanation
Indices: 21419118--21419169 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
21419108 AGTGAGGTGA
*
21419118 CACCAGTGGAGGGTGAGAAAGAGGCGG
1 CACCAGTGGAAGGTGAGAAAGAGGCGG
*
21419145 CACCGGTGGAAGGTGAGAAAGAGGC
1 CACCAGTGGAAGGTGAGAAAGAGGC
21419170 AACACCCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.46, T:0.08
Consensus pattern (27 bp):
CACCAGTGGAAGGTGAGAAAGAGGCGG
Found at i:21419175 original size:27 final size:27
Alignment explanation
Indices: 21419117--21419175 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
21419107 GAGTGAGGTG
* *
21419117 ACACCAGTGGAGGGTGAGAAAGAGGCG
1 ACACCAGTGGAAGGTGAGAAAGAGGCA
* *
21419144 GCACCGGTGGAAGGTGAGAAAGAGGCA
1 ACACCAGTGGAAGGTGAGAAAGAGGCA
21419171 ACACC
1 ACACC
21419176 CGTGCTGAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.41, T:0.07
Consensus pattern (27 bp):
ACACCAGTGGAAGGTGAGAAAGAGGCA
Found at i:21419332 original size:15 final size:16
Alignment explanation
Indices: 21419314--21419346 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21419304 CAGTATTTTT
21419314 TTAA-AAAATTAATTA
1 TTAAGAAAATTAATTA
*
21419329 TTAAGAAATTTAATTA
1 TTAAGAAAATTAATTA
21419345 TT
1 TT
21419347 TTTACAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAGAAAATTAATTA
Found at i:21434632 original size:14 final size:14
Alignment explanation
Indices: 21434613--21434640 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21434603 TCAATTTATT
21434613 AATGAAATATTAAA
1 AATGAAATATTAAA
21434627 AATGAAATATTAAA
1 AATGAAATATTAAA
21434641 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
AATGAAATATTAAA
Found at i:21436557 original size:11 final size:11
Alignment explanation
Indices: 21436541--21436565 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21436531 GAATTTACAG
21436541 TAGAAATTGAA
1 TAGAAATTGAA
21436552 TAGAAATTGAA
1 TAGAAATTGAA
21436563 TAG
1 TAG
21436566 GAAAATTTAA
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:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (11 bp):
TAGAAATTGAA
Found at i:21437548 original size:20 final size:21
Alignment explanation
Indices: 21437513--21437554 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
21437503 AACATAAACC
21437513 ATATTTCTTTAATTTTAAAAT
1 ATATTTCTTTAATTTTAAAAT
*
21437534 ATATTT-TTTATTTTTAAAAT
1 ATATTTCTTTAATTTTAAAAT
21437554 A
1 A
21437555 CACTGCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTTCTTTAATTTTAAAAT
Found at i:21442909 original size:3 final size:3
Alignment explanation
Indices: 21442901--21442977 Score: 82
Period size: 3 Copynumber: 25.7 Consensus size: 3
21442891 AATTTGTATC
* * ** *
21442901 ATT ATT ATT ATT ATT AGT ACT ATT ATT ATT ATT GGT ATT ATT ATT CTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
21442949 ATT ATT CTT ATT ATT TTT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21442978 CAACTTATTT
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:21443421 original size:28 final size:28
Alignment explanation
Indices: 21443338--21443429 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
21443328 CTCTTTTAAA
*
21443338 TATTTTAATATCTTTAATTTATTTCA-ACT
1 TATTTTAATAT-TTTAATTTATTT-ATATT
* *
21443367 TATTTCAATATTGTTAATTAATTTATATT
1 TATTTTAATATT-TTAATTTATTTATATT
* *
21443396 TATTTTAACATTTTAATTTATATATATT
1 TATTTTAATATTTTAATTTATTTATATT
21443424 ATATTT
1 -TATTT
21443430 ATTTCTTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
28 16 0.30
29 37 0.70
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (28 bp):
TATTTTAATATTTTAATTTATTTATATT
Found at i:21448161 original size:17 final size:16
Alignment explanation
Indices: 21448141--21448181 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
21448131 AAAAACAAAA
21448141 AAAAAAATAAAATGAA-G
1 AAAAAAATAAAA--AAGG
21448158 AAAAAAATAAAAAAGG
1 AAAAAAATAAAAAAGG
21448174 AAAAAAAT
1 AAAAAAAT
21448182 CAAAGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 9 0.39
17 12 0.52
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAAATAAAAAAGG
Found at i:21448171 original size:19 final size:19
Alignment explanation
Indices: 21448137--21448180 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
21448127 CAAAAAAAAC
*
21448137 AAAAAAAAAAATAAAATGA
1 AAAAAAAAAAATAAAAGGA
*
21448156 AGAAAAAAATAA-AAAAGGA
1 A-AAAAAAAAAATAAAAGGA
21448175 AAAAAA
1 AAAAAA
21448181 TCAAAGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAAAAAAAAATAAAAGGA
Found at i:21448176 original size:16 final size:16
Alignment explanation
Indices: 21448141--21448186 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
21448131 AAAAACAAAA
21448141 AAAAAAATAAAATGAAG
1 AAAAAAATAAAA-GAAG
21448158 AAAAAAATAAAA-AAGG
1 AAAAAAATAAAAGAA-G
*
21448174 AAAAAAATCAAAG
1 AAAAAAATAAAAG
21448187 TCAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 12 0.46
17 12 0.46
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (16 bp):
AAAAAAATAAAAGAAG
Found at i:21449147 original size:15 final size:16
Alignment explanation
Indices: 21449127--21449161 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
21449117 CACTTTGAGT
*
21449127 AAAAAATGAAAAA-TA
1 AAAAAACGAAAAAGTA
21449142 AAAAAACGAAAAAGTA
1 AAAAAACGAAAAAGTA
21449158 AAAA
1 AAAA
21449162 TAGAGAGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.80, C:0.03, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAACGAAAAAGTA
Found at i:21450498 original size:44 final size:44
Alignment explanation
Indices: 21450425--21450640 Score: 306
Period size: 44 Copynumber: 4.9 Consensus size: 44
21450415 GTGAAATCAC
* *
21450425 AAGCCATAGTTCCCTGACCAGCAGCGGAATAGGTGGAAGACTGT
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGT
* * *
21450469 AAGTCCTAGTTCCCTAACCAGCAGTGGAATAGGTCGAAGACTGT
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGT
* * *
21450513 AAGTCCTAGTTCTCTGACCAGTAGTGGAATAGGTGGAAGACTGT
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGT
* * * **
21450557 AAGCCCTAGTTCCCTGACCAACAATAGAATAAATGGAAGACTGT
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGT
*
21450601 GAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGA
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGA
21450641 TAAGTCCTAT
Statistics
Matches: 149, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 149 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (44 bp):
AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGT
Found at i:21450957 original size:44 final size:44
Alignment explanation
Indices: 21450860--21450972 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 44
21450850 GAAGATGGCA
* * *
21450860 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * *
21450904 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* *
21450947 AGATCTTATCTCTCTGAAGTTACAGT
1 A-ATCTTATCTCCCTGAAGTTGCAGT
21450973 ACAGTGGATC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 3 0.05
44 54 0.95
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:21451171 original size:50 final size:48
Alignment explanation
Indices: 21451033--21451687 Score: 481
Period size: 50 Copynumber: 13.1 Consensus size: 48
21451023 TGAGAATAGC
* * *
21451033 GAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTACT-CCCAGAC-ATGCAGTGGAACAGATTAAAGCTACATCAGT
* * ** * *
21451083 GAATCTTGCTTCCC-GACATTGCAATTAAAAAGATTAAAGCTACAACAGT
1 GAATCTTAC-TCCCAGACA-TGCAGTGGAACAGATTAAAGCTACATCAGT
* *
21451132 GAATCTTACTCCACAGGCGATGCAGTGGAACAGATTAAAGAC-ACATCGGT
1 GAATCTTACTCC-CAGAC-ATGCAGTGGAACAGATTAAAG-CTACATCAGT
* ** * * * *
21451182 GAATCTTACTTCCCCGACATTGCAGTTAAAAATATTAAAGCTACAACAGC
1 GAATCTTAC-TCCCAGACA-TGCAGTGGAACAGATTAAAGCTACATCAGT
* *
21451232 GAATCTTACTCCTCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTACTCC-CAGAC-ATGCAGTGGAACAGATTAAAGCTACATCAGT
* * ** * *
21451282 GAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAT-AGC
1 GAATCTTAC-TCCCAGACA-TGCAGTGGAACAGATTAAAGCTAC-ATCAGT
* * *
21451332 GAATCTTACTCCCCAGGAGATGTAGTGGAACAGATTAAAGCTACATCGGT
1 GAATCTTACT-CCCA-GACATGCAGTGGAACAGATTAAAGCTACATCAGT
* * ** * * *
21451382 GAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
1 GAATCTTAC-TCCCAGACA-TGCAGTGGAACAGATTAAAGCTACATCAGT
* * * *
21451432 GAATCTTACTCCCCAGGAGATGTAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTACT-CCCA-GACATGCAGTGGAACAGATTAAAGCTACATCAGT
* * ** * * *
21451482 GAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
1 GAATCTTAC-TCCCAGACA-TGCAGTGGAACAGATTAAAGCTACATCAGT
* * * * *
21451532 GAATCTTACTCTCTAGGCGATGCAGTGGAACATATTAAAGCCACATCGGT
1 GAATCTTACTC-CCAGAC-ATGCAGTGGAACAGATTAAAGCTACATCAGT
* * ** * *
21451582 GAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGT
1 GAATCTTAC-TCCCAGACA-TGCAGTGGAACAGATTAAAGCTACATCAGT
** *
21451632 GAATCTTACTCCCCAAGTTATGCAGTGGAACAGATT-AAGCCACATCAGT
1 GAATCTTACT-CCC-AGACATGCAGTGGAACAGATTAAAGCTACATCAGT
21451681 GAATCTT
1 GAATCTT
21451688 GCTTCCCCGA
Statistics
Matches: 460, Mismatches: 116, Indels: 59
0.72 0.18 0.09
Matches are distributed among these distances:
48 4 0.01
49 72 0.16
50 359 0.78
51 25 0.05
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (48 bp):
GAATCTTACTCCCAGACATGCAGTGGAACAGATTAAAGCTACATCAGT
Found at i:21451253 original size:100 final size:100
Alignment explanation
Indices: 21451030--21452013 Score: 1282
Period size: 100 Copynumber: 9.9 Consensus size: 100
21451020 GACTGAGAAT
*
21451030 AGCGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTT-
1 AGCGAATCTTACTCCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
*
21451094 CCCGACATTGCAATTAAAAAGATTAAAGCTACAAC
66 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* * * * *
21451129 AGTGAATCTTACTCCACAGGCGATGCAGTGGAACAGATTAAAGACACATCGGTGAATCTTACTTC
1 AGCGAATCTTACTCCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
*
21451194 CCCGACATTGCAGTTAAAAATATTAAAGCTACAAC
66 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
*
21451229 AGCGAATCTTACTCCTCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
1 AGCGAATCTTACTCCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
*
21451294 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAT
66 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* *
21451329 AGCGAATCTTACTCCCCAGGA-GATGTAGTGGAACAGATTAAAGCTACATCGGTGAATCTTGCTT
1 AGCGAATCTTACTCCCCA-GACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTT
21451393 CCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
65 CCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
*
21451429 AGCGAATCTTACTCCCCAGGA-GATGTAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTT
1 AGCGAATCTTACTCCCCA-GACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTT
21451493 CCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
65 CCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* * * *
21451529 AGCGAATCTTACTCTCTAGGCGATGCAGTGGAACATATTAAAGCCACATCGGTGAATCTTGCTTC
1 AGCGAATCTTACTCCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
21451594 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
66 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* *
21451629 AGTGAATCTTACTCCCCA-A-GTTATGCAGTGGAACAGATT-AAGCCACATCAGTGAATCTTGCT
1 AGCGAATCTTACTCCCCAGACG--ATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
* *
21451691 TCCCCGACATTGTAGTT----A-A--AAAGCTACCAC
64 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* ** * * *
21451721 AGCGAATCTTACTCCTCAGGTGACGCAGTGGAACAGATTAAAGCCACAAT-GGCGAACCTTGCTT
1 AGCGAATCTTACTCCCCAGACGATGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTT
* * *
21451785 CCCTGACATTGCAGTTAAAAATATTATAGCTACAAC
65 CCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* * * * * * * * ** *
21451821 AGTGAATCTTACTTCTCA-AGCGGTGTAGTGGAACAAATTAACGCCACAACGGCAAAACTTGCTT
1 AGCGAATCTTACTCCCCAGA-CGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTT
* *
21451885 CCCCGATATTGCAGTTAGAAAGATTAAAGCTACAAC
65 CCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* * * * ** * *
21451921 AGCGAATCTTACTTCCCAGGC-AGTGTAGTGGAACAGATTGAAGATACAAT-AGCGAATCTTGCT
1 AGCGAATCTTACTCCCCAGACGA-TGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCT
* ** *
21451984 TCCTCGACATCACAGTTAAACAGATTAAAG
64 TCCCCGACATTGCAGTTAAAAAGATTAAAG
21452014 TTACGAGTTA
Statistics
Matches: 786, Mismatches: 78, Indels: 41
0.87 0.09 0.05
Matches are distributed among these distances:
92 42 0.05
93 32 0.04
94 4 0.01
95 1 0.00
97 1 0.00
98 2 0.00
99 100 0.13
100 601 0.76
101 3 0.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (100 bp):
AGCGAATCTTACTCCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
Found at i:21451799 original size:50 final size:50
Alignment explanation
Indices: 21451745--21452013 Score: 157
Period size: 50 Copynumber: 5.4 Consensus size: 50
21451735 CTCAGGTGAC
* ** *
21451745 GCAGTGGAACAGATTAAAGCCACAATGGCGAACCTTGCTTCCCTGACATT
1 GCAGTGGAACAGATTAAAGCTACAACAGCGAATCTTGCTTCCCTGACATT
** * * * * * * * **
21451795 GCAGTTAAAAATATTATAGCTACAACAGTGAATCTTACTTCTC-AAGCGGT
1 GCAGTGGAACAGATTAAAGCTACAACAGCGAATCTTGCTTCCCTGA-CATT
* * * * * * * * *
21451845 GTAGTGGAACAAATTAACGCCACAACGGCAAAACTTGCTTCCCCGATATT
1 GCAGTGGAACAGATTAAAGCTACAACAGCGAATCTTGCTTCCCTGACATT
* * * * *
21451895 GCAGTTAGAA-AGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGT
1 GCAG-TGGAACAGATTAAAGCTACAACAGCGAATCTTGCTTCCCTGACATT
* * * * *
21451945 GTAGTGGAACAGATTGAAGATACAATAGCGAATCTTGCTT-CCTCGACATC
1 GCAGTGGAACAGATTAAAGCTACAACAGCGAATCTTGCTTCCCT-GACATT
* **
21451995 ACAGTTAAACAGATTAAAG
1 GCAGTGGAACAGATTAAAG
21452014 TTACGAGTTA
Statistics
Matches: 153, Mismatches: 61, Indels: 10
0.68 0.27 0.04
Matches are distributed among these distances:
49 7 0.05
50 141 0.92
51 5 0.03
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (50 bp):
GCAGTGGAACAGATTAAAGCTACAACAGCGAATCTTGCTTCCCTGACATT
Found at i:21455765 original size:50 final size:51
Alignment explanation
Indices: 21455632--21455818 Score: 198
Period size: 51 Copynumber: 3.6 Consensus size: 51
21455622 ACATGCAAAA
** * *
21455632 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGGTGTCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAAC
* ** *
21455683 GCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG-CCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAAC
* * *
21455733 GCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTTAATGATGT-CAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATC-----GGTGTCCAAC
*
21455789 GCCATGTCTCAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
21455819 TCTCATTCCC
Statistics
Matches: 112, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
50 37 0.33
51 41 0.37
56 34 0.30
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.28
Consensus pattern (51 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAAC
Found at i:21457086 original size:14 final size:15
Alignment explanation
Indices: 21457058--21457086 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21457048 GAGAAGCTAT
21457058 TTAAAATACATATTA
1 TTAAAATACATATTA
21457073 TTAAAATA-ATATTA
1 TTAAAATACATATTA
21457087 AATTTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATACATATTA
Found at i:21464436 original size:9 final size:9
Alignment explanation
Indices: 21464422--21464448 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
21464412 CAACTTATAG
21464422 CAAATCCAT
1 CAAATCCAT
21464431 CAAATCCAT
1 CAAATCCAT
21464440 CAAATCCAT
1 CAAATCCAT
21464449 TAAACAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (9 bp):
CAAATCCAT
Found at i:21473091 original size:28 final size:29
Alignment explanation
Indices: 21473050--21473118 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
21473040 AGGGTTTTAA
* * *
21473050 AAATATTTAATTTTATTTATAGTTAT-TT
1 AAATATATAATTTTAATTATAGATATGTT
* *
21473078 AAATATATATTTTTAATTGTAGATATGTT
1 AAATATATAATTTTAATTATAGATATGTT
*
21473107 TAATATATAATT
1 AAATATATAATT
21473119 ATATTAGAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (29 bp):
AAATATATAATTTTAATTATAGATATGTT
Found at i:21473359 original size:2 final size:2
Alignment explanation
Indices: 21473352--21473377 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21473342 GATACGTGTA
21473352 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
21473378 TTAAAAGAAA
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:21473450 original size:2 final size:2
Alignment explanation
Indices: 21473443--21473468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21473433 GATACGTGTA
21473443 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
21473469 TTAAAAGAAA
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:21473484 original size:91 final size:92
Alignment explanation
Indices: 21473329--21473510 Score: 357
Period size: 91 Copynumber: 2.0 Consensus size: 92
21473319 ATGTTAAATG
21473329 TTATTCTTAAAAAGATACGTGTAATATATATATATATATATATATATATTTAAAAGAAAAGGAAT
1 TTATTCTTAAAAAGATACGTGTAATATATATATATATATATATATATATTTAAAAGAAAAGGAAT
21473394 ACATTTAATAGATAA-GAATTTTGTTT
66 ACATTTAATAGATAATGAATTTTGTTT
21473420 TTATTCTTAAAAAGATACGTGTAATATATATATATATATATATATATATTTAAAAGAAAAGGAAT
1 TTATTCTTAAAAAGATACGTGTAATATATATATATATATATATATATATTTAAAAGAAAAGGAAT
21473485 ACATTTAATAGATAATGAATTTTGTT
66 ACATTTAATAGATAATGAATTTTGTT
21473511 GGTGAATGTA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 80 0.89
92 10 0.11
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (92 bp):
TTATTCTTAAAAAGATACGTGTAATATATATATATATATATATATATATTTAAAAGAAAAGGAAT
ACATTTAATAGATAATGAATTTTGTTT
Found at i:21474414 original size:18 final size:20
Alignment explanation
Indices: 21474388--21474424 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
21474378 GAAGATTTCT
21474388 TTGGAGGT-GTA-AAACGGG
1 TTGGAGGTGGTAGAAACGGG
*
21474406 TTGGCGGTGGTAGAAACGG
1 TTGGAGGTGGTAGAAACGG
21474425 CTCCTATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 3 0.19
20 6 0.38
ACGTcount: A:0.24, C:0.08, G:0.46, T:0.22
Consensus pattern (20 bp):
TTGGAGGTGGTAGAAACGGG
Found at i:21480550 original size:10 final size:10
Alignment explanation
Indices: 21480535--21480560 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
21480525 TTTAAATATT
21480535 AAAAATTAGA
1 AAAAATTAGA
21480545 AAAAATTAGA
1 AAAAATTAGA
21480555 AAAAAT
1 AAAAAT
21480561 ATATAAAAAN
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (10 bp):
AAAAATTAGA
Found at i:21480844 original size:85 final size:86
Alignment explanation
Indices: 21480711--21480869 Score: 248
Period size: 85 Copynumber: 1.8 Consensus size: 86
21480701 TAAGAGCAGT
* * *
21480711 GGCTTAATTGCTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCC
1 GGCTTAATT-CTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAGTACCC
21480776 AATTGAGTGAAAGAGAAGTAGG
65 AATTGAGTGAAAGAGAAGTAGG
* * *
21480798 GGCTTAATT-TTTTTTGAAGAAGTTTGAGGGCCTTTTTGATACATTTTGAAAGTTCAAGTACTCA
1 GGCTTAATTCTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAGTACCCA
21480862 ATTGAGTG
66 ATTGAGTG
21480870 CAAAAAAATG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
85 57 0.86
87 9 0.14
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (86 bp):
GGCTTAATTCTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAGTACCCA
ATTGAGTGAAAGAGAAGTAGG
Found at i:21480883 original size:14 final size:14
Alignment explanation
Indices: 21480864--21480895 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
21480854 AGTACTCAAT
21480864 TGAGTGCAAAAAAA
1 TGAGTGCAAAAAAA
21480878 TGAGTGCAAAAAAA
1 TGAGTGCAAAAAAA
21480892 TGAG
1 TGAG
21480896 GGACTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.25, T:0.16
Consensus pattern (14 bp):
TGAGTGCAAAAAAA
Found at i:21481267 original size:20 final size:22
Alignment explanation
Indices: 21481230--21481270 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
21481220 TCGAAAAAAC
21481230 CTAAAATATATCAAATATATAA
1 CTAAAATATATCAAATATATAA
21481252 CTAAAAT-TAT-AAATATATA
1 CTAAAATATATCAAATATATA
21481271 TAATTGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
CTAAAATATATCAAATATATAA
Found at i:21481332 original size:9 final size:9
Alignment explanation
Indices: 21481320--21481424 Score: 52
Period size: 10 Copynumber: 11.0 Consensus size: 9
21481310 AAATTGTAAA
21481320 AAAAATTAT
1 AAAAATTAT
21481329 AAAAAATCTAT
1 -AAAAAT-TAT
*
21481340 AAAAACTAT
1 AAAAATTAT
*
21481349 AAACATTATT
1 AAAAATTA-T
21481359 AGAAAATGTA-
1 A-AAAAT-TAT
* *
21481369 AAATATAAT
1 AAAAATTAT
21481378 AAAAA-TAT
1 AAAAATTAT
*
21481386 AAAAAATATT
1 AAAAATTA-T
** *
21481396 AGTAATCAT
1 AAAAATTAT
21481405 AAAAGATTAT
1 AAAA-ATTAT
21481415 AAAAAATTAT
1 -AAAAATTAT
21481425 TACATACTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 18
0.68 0.14 0.17
Matches are distributed among these distances:
8 8 0.11
9 22 0.31
10 28 0.39
11 11 0.15
12 2 0.03
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:21481388 original size:18 final size:17
Alignment explanation
Indices: 21481338--21481389 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
21481328 TAAAAAATCT
21481338 ATAAAAACTATAAACATTA
1 ATAAAAA-TATAAA-ATTA
* *
21481357 TTAGAAAATGTAAAATATA
1 ATA-AAAATATAAAAT-TA
21481376 ATAAAAATATAAAA
1 ATAAAAATATAAAA
21481390 AATATTAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 12 0.44
19 11 0.41
20 4 0.15
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (17 bp):
ATAAAAATATAAAATTA
Found at i:21482184 original size:17 final size:19
Alignment explanation
Indices: 21482164--21482200 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21482154 ATATATGAAA
21482164 TAATT-AAA-AATATAATT
1 TAATTGAAATAATATAATT
*
21482181 TAATTGAAATAATATTATT
1 TAATTGAAATAATATAATT
21482200 T
1 T
21482201 TTTATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TAATTGAAATAATATAATT
Found at i:21482613 original size:18 final size:20
Alignment explanation
Indices: 21482580--21482618 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
21482570 CATTAAGCCT
*
21482580 AATAAATTTAATTATTTTAA
1 AATAAATTTAATTATTGTAA
21482600 AATAAA-TT-ATTATTGTAA
1 AATAAATTTAATTATTGTAA
21482618 A
1 A
21482619 GTTAGAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
AATAAATTTAATTATTGTAA
Found at i:21494341 original size:76 final size:76
Alignment explanation
Indices: 21494249--21494399 Score: 302
Period size: 76 Copynumber: 2.0 Consensus size: 76
21494239 AATTGCTAAC
21494249 TAGTCCTTCCTTATTTTTCCACTACTTACATAAATTCTCATAACTTCCTAACAAGGCAAGATTCT
1 TAGTCCTTCCTTATTTTTCCACTACTTACATAAATTCTCATAACTTCCTAACAAGGCAAGATTCT
21494314 AGTTGGGAGGT
66 AGTTGGGAGGT
21494325 TAGTCCTTCCTTATTTTTCCACTACTTACATAAATTCTCATAACTTCCTAACAAGGCAAGATTCT
1 TAGTCCTTCCTTATTTTTCCACTACTTACATAAATTCTCATAACTTCCTAACAAGGCAAGATTCT
21494390 AGTTGGGAGG
66 AGTTGGGAGG
21494400 ATGGAAGAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (76 bp):
TAGTCCTTCCTTATTTTTCCACTACTTACATAAATTCTCATAACTTCCTAACAAGGCAAGATTCT
AGTTGGGAGGT
Found at i:21502564 original size:5 final size:5
Alignment explanation
Indices: 21502554--21502587 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
21502544 AACAAAGTGT
21502554 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
21502588 CTTTAACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:21513260 original size:18 final size:19
Alignment explanation
Indices: 21513227--21513262 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21513217 GTTTTCTCGT
21513227 TCTCTTATTAGGTTTTTTG
1 TCTCTTATTAGGTTTTTTG
*
21513246 TCTCTTCTT-GGTTTTTT
1 TCTCTTATTAGGTTTTTT
21513263 TTAAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.06, C:0.14, G:0.14, T:0.67
Consensus pattern (19 bp):
TCTCTTATTAGGTTTTTTG
Found at i:21518203 original size:22 final size:25
Alignment explanation
Indices: 21518157--21518205 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
21518147 TAGTTTATGC
21518157 AGGTTCATCTACAAGATCATCTCAA
1 AGGTTCATCTACAAGATCATCTCAA
*
21518182 AGGTTC-T-TACAA-ATCGTCTCAA
1 AGGTTCATCTACAAGATCATCTCAA
21518204 AG
1 AG
21518206 TCACATTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 5 0.22
24 1 0.04
25 6 0.26
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (25 bp):
AGGTTCATCTACAAGATCATCTCAA
Found at i:21523790 original size:24 final size:23
Alignment explanation
Indices: 21523741--21523790 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
21523731 ATAAAGTAGT
* *
21523741 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATCA
21523764 TATATTATGATTTTTATTAAT-TCA
1 TATA-TATGATTTTTA-TAATATCA
21523788 TAT
1 TAT
21523791 TTTAAATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTATAATATCA
Found at i:21523996 original size:16 final size:16
Alignment explanation
Indices: 21523977--21524020 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
21523967 CTGATTACCA
*
21523977 CTCTATTCTATTACAG
1 CTCTATTCCATTACAG
21523993 CTCTATTCCATTACAAG
1 CTCTATTCCATTAC-AG
*
21524010 -TCCATTCCATT
1 CTCTATTCCATT
21524021 CCCCCAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 23 0.92
17 2 0.08
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.41
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:21527145 original size:69 final size:69
Alignment explanation
Indices: 21526993--21527150 Score: 192
Period size: 69 Copynumber: 2.3 Consensus size: 69
21526983 ATCATTTTAT
* * * * *
21526993 CCGACCAGCGCTGGGCACAACCTTTGTTAGCTTGTCTGACTAGTGCTGGGCACACAATTATCGGT
1 CCGACTAGCGCTGGGCGCAACCTTTGTCAGCTTGTCTGACTAGTGCTAGGCACACAATCATCGGT
*
21527058 TCAT
66 TCAA
* * * * *
21527062 CCGATTAGCACTGGGCGCAACTTTTGTCAGCTTGTTTGACTAGTGCTAGGCACACAATCATTGG-
1 CCGACTAGCGCTGGGCGCAACCTTTGTCAGCTTGTCTGACTAGTGCTAGGCACACAATCATCGGT
21527126 TCAAA
66 TC-AA
*
21527131 CCGACTAGCGCTGGGTGCAA
1 CCGACTAGCGCTGGGCGCAA
21527151 ACATCGTTGG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
68 2 0.03
69 72 0.97
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (69 bp):
CCGACTAGCGCTGGGCGCAACCTTTGTCAGCTTGTCTGACTAGTGCTAGGCACACAATCATCGGT
TCAA
Found at i:21533239 original size:16 final size:15
Alignment explanation
Indices: 21533218--21533251 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
21533208 TATTTTATAA
21533218 TATTTTAATTATATTT
1 TATTTTAATTAT-TTT
21533234 TATTTTAATTATTTT
1 TATTTTAATTATTTT
21533249 TAT
1 TAT
21533252 ATGTGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTAATTATTTT
Found at i:21533269 original size:22 final size:22
Alignment explanation
Indices: 21533226--21533269 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
21533216 AATATTTTAA
* *
21533226 TTATATTTTATTTTAATTATTT
1 TTATATTGTATTTTAATAATTT
21533248 TTATATGTGTATTTT-ATAATTT
1 TTATAT-TGTATTTTAATAATTT
21533270 ATACTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
TTATATTGTATTTTAATAATTT
Found at i:21534322 original size:15 final size:17
Alignment explanation
Indices: 21534291--21534322 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21534281 TCACTTTTAA
21534291 AAATATATAACAATTTT
1 AAATATATAACAATTTT
21534308 AAAT-TATAA-AATTTT
1 AAATATATAACAATTTT
21534323 TATATTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATATAACAATTTT
Found at i:21535539 original size:11 final size:11
Alignment explanation
Indices: 21535513--21535548 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
21535503 TTTATGCCAA
*
21535513 AAGAAGCAACAA
1 AAGAA-CAACAG
21535525 AAGAACAACAG
1 AAGAACAACAG
21535536 AAGAACAACAG
1 AAGAACAACAG
21535547 AA
1 AA
21535549 AGATTGCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.67, C:0.17, G:0.17, T:0.00
Consensus pattern (11 bp):
AAGAACAACAG
Found at i:21543284 original size:23 final size:24
Alignment explanation
Indices: 21543256--21543301 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
21543246 TTTTGGTGCT
*
21543256 GTTATTTTT-CTGCTGTTTTTGTA
1 GTTATTTTTGCTACTGTTTTTGTA
*
21543279 GTTATTTTTGCTATTGTTTTTGT
1 GTTATTTTTGCTACTGTTTTTGT
21543302 TATTTGTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.09, C:0.07, G:0.17, T:0.67
Consensus pattern (24 bp):
GTTATTTTTGCTACTGTTTTTGTA
Found at i:21549821 original size:22 final size:22
Alignment explanation
Indices: 21549760--21549814 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
21549750 ATGCTCCCTA
* *
21549760 TGTTGCTACATCGAACCCTCCG
1 TGTTGCGACATCGAAACCTCCG
*
21549782 TGTTGCGACATCGAAACCTCTG
1 TGTTGCGACATCGAAACCTCCG
21549804 TGTTGCGACAT
1 TGTTGCGACAT
21549815 ACTAACCAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (22 bp):
TGTTGCGACATCGAAACCTCCG
Found at i:21556238 original size:13 final size:13
Alignment explanation
Indices: 21556219--21556249 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
21556209 AAATGATTAC
21556219 ATGAATTGGTTAT
1 ATGAATTGGTTAT
*
21556232 GTGAATTGGTTAT
1 ATGAATTGGTTAT
21556245 ATGAA
1 ATGAA
21556250 AATATATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (13 bp):
ATGAATTGGTTAT
Found at i:21556707 original size:2 final size:2
Alignment explanation
Indices: 21556700--21556732 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
21556690 AGGGTTTTGG
21556700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21556733 CGCATTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21557326 original size:8 final size:8
Alignment explanation
Indices: 21557313--21557338 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21557303 TTAGGGGCAT
21557313 TTTGGTAA
1 TTTGGTAA
21557321 TTTGGTAA
1 TTTGGTAA
21557329 TTTGGTAA
1 TTTGGTAA
21557337 TT
1 TT
21557339 AAAATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (8 bp):
TTTGGTAA
Found at i:21558487 original size:41 final size:42
Alignment explanation
Indices: 21558352--21558500 Score: 162
Period size: 41 Copynumber: 3.5 Consensus size: 42
21558342 TTTGAACATG
* * * * *
21558352 AGGTGGTTGCTAAGTGCTGATTCCACAGGGATCCTATGAACTT-G
1 AGGTGGTTGCTAAGTGCTGATTCCAC-CGTATCAT-TG-ATTTAA
*
21558396 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTTGAA
1 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTT-AA
*
21558439 AGG-GGTTGCTATGTGCTGATTCC-CCGTATCATTGA-TTATA
1 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTTA-A
21558479 AGGTGGTTGCTAAGTGCTGATT
1 AGGTGGTTGCTAAGTGCTGATT
21558501 GCATGGGGAT
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
39 1 0.01
40 6 0.06
41 31 0.33
42 21 0.22
43 9 0.10
44 26 0.28
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (42 bp):
AGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTTAA
Found at i:21558593 original size:44 final size:44
Alignment explanation
Indices: 21558338--21558594 Score: 303
Period size: 44 Copynumber: 6.0 Consensus size: 44
21558328 NNNNNNNNNN
*
21558338 ATCCTTTGAACATGAGGTGGTTGCTAAGTGCTGATTCCACAGGG
1 ATCCTTTGAACATGAGGTGGTTGCTAAGTGCTGATTCCACCGGG
* * *
21558382 ATCCTATGAACTTGAGGTGGTTGCTAAGTGCTGATTCCACC-GT
1 ATCCTTTGAACATGAGGTGGTTGCTAAGTGCTGATTCCACCGGG
** * *
21558425 ATCC-TTG-ATTTGAAAGG-GGTTGCTATGTGCTGATTCC-CC-GT
1 ATCCTTTGAACATG--AGGTGGTTGCTAAGTGCTGATTCCACCGGG
* ** * * **
21558466 AT-CATTGATTATAAGGTGGTTGCTAAGTGCTGATTGCATGGGG
1 ATCCTTTGAACATGAGGTGGTTGCTAAGTGCTGATTCCACCGGG
*
21558509 ATCCTTTGAACATGAGGTGGTTGCTAAGTGTTGATTCCACCGGG
1 ATCCTTTGAACATGAGGTGGTTGCTAAGTGCTGATTCCACCGGG
21558553 ATCCTTTGAACATGAGGTGGTTGCTAAGTGCTGATTCCACCG
1 ATCCTTTGAACATGAGGTGGTTGCTAAGTGCTGATTCCACCG
21558595 TGTAACAGTT
Statistics
Matches: 181, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
40 4 0.02
41 31 0.17
42 23 0.13
43 11 0.06
44 112 0.62
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (44 bp):
ATCCTTTGAACATGAGGTGGTTGCTAAGTGCTGATTCCACCGGG
Found at i:21563642 original size:7 final size:7
Alignment explanation
Indices: 21563625--21563668 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
21563615 TTAGCTTTAA
21563625 ATATT-T
1 ATATTAT
21563631 ATATTAT
1 ATATTAT
21563638 ATATTAT
1 ATATTAT
21563645 ATATTAT
1 ATATTAT
21563652 ATATTAT
1 ATATTAT
21563659 ATATTAT
1 ATATTAT
21563666 ATA
1 ATA
21563669 ATGGGTCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:21565687 original size:208 final size:208
Alignment explanation
Indices: 21565329--21565744 Score: 814
Period size: 208 Copynumber: 2.0 Consensus size: 208
21565319 ACAAAAAACT
21565329 CAAGCAGCTGAAATAAATCGTTTGGTATCCATTAATGAGTTAGCAACAAGAATAGGTATGAATCA
1 CAAGCAGCTGAAATAAATCGTTTGGTATCCATTAATGAGTTAGCAACAAGAATAGGTATGAATCA
21565394 GATTGGCACTTTACAACATCTTGGTGAGACTCGATAGAGTTCTCATTTAAATTCAATTACTATTT
66 GATTGGCACTTTACAACATCTTGGTGAGACTCGATAGAGTTCTCATTTAAATTCAATTACTATTT
21565459 TACTAACAATGTACAATGCTACTAGCACAATTCTTGAAAATCTAAAAAATATCGCTCCTAACCAT
131 TACTAACAATGTACAATGCTACTAGCACAATTCTTGAAAATCTAAAAAATATCGCTCCTAACCAT
21565524 TCTCAGCGAGGAG
196 TCTCAGCGAGGAG
*
21565537 CAAGCAGCTGAAATAACTCGTTTGGTATCCATTAATGAGTTAGCAACAAGAATAGGTATGAATCA
1 CAAGCAGCTGAAATAAATCGTTTGGTATCCATTAATGAGTTAGCAACAAGAATAGGTATGAATCA
*
21565602 GATTGGCACTTTACAACATCTTGGTGAGACTCGATGGAGTTCTCATTTAAATTCAATTACTATTT
66 GATTGGCACTTTACAACATCTTGGTGAGACTCGATAGAGTTCTCATTTAAATTCAATTACTATTT
21565667 TACTAACAATGTACAATGCTACTAGCACAATTCTTGAAAATCTAAAAAATATCGCTCCTAACCAT
131 TACTAACAATGTACAATGCTACTAGCACAATTCTTGAAAATCTAAAAAATATCGCTCCTAACCAT
21565732 TCTCAGCGAGGAG
196 TCTCAGCGAGGAG
21565745 ATGCTCATAA
Statistics
Matches: 206, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
208 206 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (208 bp):
CAAGCAGCTGAAATAAATCGTTTGGTATCCATTAATGAGTTAGCAACAAGAATAGGTATGAATCA
GATTGGCACTTTACAACATCTTGGTGAGACTCGATAGAGTTCTCATTTAAATTCAATTACTATTT
TACTAACAATGTACAATGCTACTAGCACAATTCTTGAAAATCTAAAAAATATCGCTCCTAACCAT
TCTCAGCGAGGAG
Found at i:21576669 original size:117 final size:117
Alignment explanation
Indices: 21576463--21576699 Score: 456
Period size: 117 Copynumber: 2.0 Consensus size: 117
21576453 ATTCTTTAAA
*
21576463 GACAGTTATTGCCTATGTTACTCAGACTAGGAATGAATATTGGATCAGATACAAATATTTTGGAT
1 GACAGTTATTGCCTATGTTACTCAGACTAGGAATGAATATCGGATCAGATACAAATATTTTGGAT
*
21576528 TTTTAATAACTTCTTTTATATCTTTAGAGAATCATACCTTAACATCTATCAT
66 TTTTAATAACTTCTTTTATATCTTTAGAGAATCATACCTTAACATCGATCAT
21576580 GACAGTTATTGCCTATGTTACTCAGACTAGGAATGAATATCGGATCAGATACAAATATTTTGGAT
1 GACAGTTATTGCCTATGTTACTCAGACTAGGAATGAATATCGGATCAGATACAAATATTTTGGAT
21576645 TTTTAATAACTTCTTTTATATCTTTAGAGAATCATACCTTAACATCGATCAT
66 TTTTAATAACTTCTTTTATATCTTTAGAGAATCATACCTTAACATCGATCAT
21576697 GAC
1 GAC
21576700 TATTGGATGA
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (117 bp):
GACAGTTATTGCCTATGTTACTCAGACTAGGAATGAATATCGGATCAGATACAAATATTTTGGAT
TTTTAATAACTTCTTTTATATCTTTAGAGAATCATACCTTAACATCGATCAT
Found at i:21585100 original size:13 final size:13
Alignment explanation
Indices: 21585058--21585103 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
21585048 TCAAATTTTC
*
21585058 AAAAGCACTCCTG
1 AAAAGCACTTCTG
*
21585071 AAAAGCATTTCTG
1 AAAAGCACTTCTG
21585084 AAAAGCACTTC-G
1 AAAAGCACTTCTG
21585096 CAAAAGCA
1 -AAAAGCA
21585104 ATAAAGAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 1 0.03
13 28 0.97
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.17
Consensus pattern (13 bp):
AAAAGCACTTCTG
Found at i:21592757 original size:19 final size:18
Alignment explanation
Indices: 21592709--21592758 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
21592699 AATAATTTTT
21592709 AAAATA-TAAAAAAACTC
1 AAAATATTAAAAAAACTC
**
21592726 AAAA-ATTATAAAAAGTTC
1 AAAATATTA-AAAAAACTC
21592744 ATAAATATTAAAAAA
1 A-AAATATTAAAAAA
21592759 TAGCATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 1 0.04
17 6 0.22
18 8 0.30
19 8 0.30
20 4 0.15
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATATTAAAAAAACTC
Found at i:21597045 original size:38 final size:38
Alignment explanation
Indices: 21596994--21597293 Score: 294
Period size: 38 Copynumber: 7.9 Consensus size: 38
21596984 AGAAATGTAA
** * *
21596994 TGTTATTTAGGCTATATGCTTAGCAGGCTGTGTGCCGG
1 TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGG
* * *
21597032 TGTTATTCGGGCTATGTGCCCAGCAAGCTGTGTGCCGA
1 TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGG
* * * * * * * *
21597070 TGTTATTTGGGATATGTTCCTTGTAGGATTTGTGCCGA
1 TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGG
* **
21597108 TTTTATTCGGGCTATGTGCCTAATAGGCTGTGTGCCGG
1 TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGG
* * * *
21597146 TGTTATTTGGGTTGTGTGCCTAGCAGGCTTTGTGCCGG
1 TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGG
* * *
21597184 TGATATTCGGGCTATGTACCTAGCAGGCTGTGTACCGG
1 TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGG
* * * * *
21597222 TGTTATTCGGGCTCTGTGCCTAGCAGCCTTTATGCCAG
1 TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGG
* * * *
21597260 TGTTATTTGGGCTCTGTGCCTAGCAAGCTTTGTG
1 TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTG
21597294 TCGATGTATT
Statistics
Matches: 211, Mismatches: 51, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 211 1.00
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (38 bp):
TGTTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGG
Found at i:21597200 original size:114 final size:114
Alignment explanation
Indices: 21596993--21597303 Score: 327
Period size: 114 Copynumber: 2.7 Consensus size: 114
21596983 TAGAAATGTA
** * * * * *
21596993 ATGTTATTTAGGCTATATGCTTAGCAGGCTGTGTGCCGGTGTTATTCGGGCTATGTGCCCAGCAA
1 ATGTTATTCGGGCTATGTGCCTAACAGGCTGTGTGCCGGTGTTATTTGGGCTATGTGCCTAGCAA
* * * * * * * *
21597058 GCTGTGTGCCGATGTTATTTGGGATATGTTCCTTGTAGGATTTGTGCCG
66 GCTTTGTGCCGATGATATTCGGGATATGTACCTAGCAGGATGTGTACCG
* * * * *
21597107 ATTTTATTCGGGCTATGTGCCTAATAGGCTGTGTGCCGGTGTTATTTGGGTTGTGTGCCTAGCAG
1 ATGTTATTCGGGCTATGTGCCTAACAGGCTGTGTGCCGGTGTTATTTGGGCTATGTGCCTAGCAA
* * *
21597172 GCTTTGTGCCGGTGATATTCGGGCTATGTACCTAGCAGGCTGTGTACCG
66 GCTTTGTGCCGATGATATTCGGGATATGTACCTAGCAGGATGTGTACCG
* * * * * * * *
21597221 GTGTTATTCGGGCTCTGTGCCTAGCAGCCTTTATGCCAGTGTTATTTGGGCTCTGTGCCTAGCAA
1 ATGTTATTCGGGCTATGTGCCTAACAGGCTGTGTGCCGGTGTTATTTGGGCTATGTGCCTAGCAA
*
21597286 GCTTTGTGTCGATG-TATT
66 GCTTTGTGCCGATGATATT
21597304 GAAAGTTTAT
Statistics
Matches: 160, Mismatches: 37, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
113 4 0.03
114 156 0.98
ACGTcount: A:0.14, C:0.18, G:0.31, T:0.37
Consensus pattern (114 bp):
ATGTTATTCGGGCTATGTGCCTAACAGGCTGTGTGCCGGTGTTATTTGGGCTATGTGCCTAGCAA
GCTTTGTGCCGATGATATTCGGGATATGTACCTAGCAGGATGTGTACCG
Found at i:21599139 original size:18 final size:19
Alignment explanation
Indices: 21599111--21599146 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21599101 GCAGGTTTCT
21599111 AAAACTGGAAATGAAAACG
1 AAAACTGGAAATGAAAACG
*
21599130 AAAA-TGGAAATGGAAAC
1 AAAACTGGAAATGAAAAC
21599147 TTGCAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.22, T:0.11
Consensus pattern (19 bp):
AAAACTGGAAATGAAAACG
Found at i:21599315 original size:26 final size:25
Alignment explanation
Indices: 21599284--21599332 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
21599274 ACGAATTTTG
*
21599284 TCAAAATTTTATTGAGTGTAAAATCA
1 TCAAAATTTTATT-AGGGTAAAATCA
21599310 TCAAAATTTTATTAGGGTAAAAT
1 TCAAAATTTTATTAGGGTAAAAT
21599333 TAGGGTGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (25 bp):
TCAAAATTTTATTAGGGTAAAATCA
Found at i:21609400 original size:14 final size:15
Alignment explanation
Indices: 21609378--21609454 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
21609368 CAATCAAACA
21609378 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
21609392 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
21609407 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
21609427 CCA-AAAATCATTTT
1 CCAGAAAATCATTTT
* *
21609441 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
21609455 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.40
15 16 0.32
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:21609438 original size:34 final size:35
Alignment explanation
Indices: 21609382--21609448 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
21609372 CAAACACCAG
* *
21609382 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
*
21609417 AAAACATTTTCCA-AAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
21609449 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
Found at i:21610121 original size:19 final size:18
Alignment explanation
Indices: 21610088--21610123 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21610078 AAACCGCCTA
*
21610088 TATAATAAAATTAAAATG
1 TATAAAAAAATTAAAATG
21610106 TATAAAAAATATTAAAAT
1 TATAAAAAA-ATTAAAAT
21610124 AAAACTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
TATAAAAAAATTAAAATG
Found at i:21616107 original size:179 final size:180
Alignment explanation
Indices: 21615798--21616157 Score: 508
Period size: 179 Copynumber: 2.0 Consensus size: 180
21615788 TTTTGAAGAG
* * * *
21615798 AAATTTGTGTGATTGTCAAATAAGATGCCCATGTGATTGTGGCATTATGTATTGTTCCCAGCTCG
1 AAATTTATGTGATTGTCAAATAAGATGCCCATATGATTGTAGCATTATGTATTATTCCCAGCTCG
* ** * * * *
21615863 CAATTTAAGCCTCTTCATATCTAAATGTCTTTTCTTAAATTATAGACATATTTCCTTACCAAACT
66 CAATTGAAGCCTCCCCATATCTAAAAGTATTTTCCTAAATTATAGACATACTTCCTTACCAAACT
**
21615928 CTGGAATCAAAAGGTCTTGTTTCTATGGTAGTAAGATCTTGATTCTTGCA
131 CTAAAATCAAAAGGTCTTGTTTCTATGGTAGTAAGATCTTGATTCTTGCA
** *
21615978 AAATTTATGTGATTGTCAAATAAGAT-TTCATATGATTGTAGCATTATGTATTATTTCCAGCTCG
1 AAATTTATGTGATTGTCAAATAAGATGCCCATATGATTGTAGCATTATGTATTATTCCCAGCTCG
* * **
21616042 CAATTCGAA-CCTCCCCATATCTAAAAGTATTTTCCTAAATTATAGGCATCCTTCCTTGTCAAAC
66 CAATT-GAAGCCTCCCCATATCTAAAAGTATTTTCCTAAATTATAGACATACTTCCTTACCAAAC
*
21616106 TCTAAAATCAAAAGGTCTTGTTTCTATGGTCGTAAGATCTTGATTCTTGCA
130 TCTAAAATCAAAAGGTCTTGTTTCTATGGTAGTAAGATCTTGATTCTTGCA
21616157 A
1 A
21616158 CACTTTGCCT
Statistics
Matches: 158, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
179 131 0.83
180 27 0.17
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (180 bp):
AAATTTATGTGATTGTCAAATAAGATGCCCATATGATTGTAGCATTATGTATTATTCCCAGCTCG
CAATTGAAGCCTCCCCATATCTAAAAGTATTTTCCTAAATTATAGACATACTTCCTTACCAAACT
CTAAAATCAAAAGGTCTTGTTTCTATGGTAGTAAGATCTTGATTCTTGCA
Found at i:21619893 original size:184 final size:185
Alignment explanation
Indices: 21619584--21619956 Score: 685
Period size: 184 Copynumber: 2.0 Consensus size: 185
21619574 GGAGAAGAAA
21619584 AAGACTTTTCTGATGAAATGATAGAAAAGATTAATAAAAATCATATTTCTAAAAAAGAAATATAT
1 AAGACTTTTCTGATGAAATGATAGAAAAGATTAATAAAAATCATATTTCTAAAAAAGAAATATAT
21619649 AAGATCTCTAAGTTTAAAATATGGACTCAGAGACATATAGAAAAAATTAACGGTAACACAGTCGC
66 AAGATCTCTAAGTTTAAAATATGGACTCAGAGACATATAGAAAAAATTAACGGTAACACAGTCGC
*
21619714 TAAGGATACAAAAGGAGGATTAACATAAATCACT-TTTTTACCAAAGATAAAATC
131 TAAGGATACAAAAGGAGGATTAACAGAAATCACTCTTTTTACCAAAGATAAAATC
*
21619768 AAGACTTTTCTGATGAAATGATAGAAAAGATTAATAAAAATCATATTTCTAAAGAAGAAATATAT
1 AAGACTTTTCTGATGAAATGATAGAAAAGATTAATAAAAATCATATTTCTAAAAAAGAAATATAT
*
21619833 AAGATCTCTAAGTTTAAAATATGGACTCAGAGACATATAGAAAAAATTAGCGGTAACACAGTCGC
66 AAGATCTCTAAGTTTAAAATATGGACTCAGAGACATATAGAAAAAATTAACGGTAACACAGTCGC
* * *
21619898 TAAGGATATAAGAGGAGGATTAACAGAAATCCCTCTTTTTACCAAAGATAAAATC
131 TAAGGATACAAAAGGAGGATTAACAGAAATCACTCTTTTTACCAAAGATAAAATC
21619953 AAGA
1 AAGA
21619957 GAAATAGACT
Statistics
Matches: 182, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
184 158 0.87
185 24 0.13
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (185 bp):
AAGACTTTTCTGATGAAATGATAGAAAAGATTAATAAAAATCATATTTCTAAAAAAGAAATATAT
AAGATCTCTAAGTTTAAAATATGGACTCAGAGACATATAGAAAAAATTAACGGTAACACAGTCGC
TAAGGATACAAAAGGAGGATTAACAGAAATCACTCTTTTTACCAAAGATAAAATC
Found at i:21620516 original size:17 final size:17
Alignment explanation
Indices: 21620496--21620528 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21620486 TAATTATCTT
*
21620496 AATTAAATTATTAAAAA
1 AATTAAAATATTAAAAA
21620513 AATTAAAATATTAAAA
1 AATTAAAATATTAAAA
21620529 TAAGAAGAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTAAAATATTAAAAA
Found at i:21633850 original size:3 final size:3
Alignment explanation
Indices: 21633844--21634384 Score: 1082
Period size: 3 Copynumber: 180.3 Consensus size: 3
21633834 ACTAGTTAGG
21633844 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21633892 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21633940 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21633988 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21634036 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21634084 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21634132 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21634180 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21634228 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21634276 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21634324 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21634372 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
21634385 NNNNNNNNNN
Statistics
Matches: 538, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 538 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21635051 original size:3 final size:3
Alignment explanation
Indices: 21635036--21635099 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
21635026 AAAAGGTATT
* * **
21635036 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAG TTT TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
21635082 TAA TAA TAA -AA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
21635100 GCACATATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:21636508 original size:2 final size:2
Alignment explanation
Indices: 21636498--21636532 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
21636488 TACAATTTTT
* *
21636498 TA TA CA TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21636533 CTTTTACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:21636575 original size:12 final size:12
Alignment explanation
Indices: 21636554--21636584 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21636544 TTTTATAATC
*
21636554 TTATTCATTTCT
1 TTATTTATTTCT
21636566 TTATTTATTTCT
1 TTATTTATTTCT
21636578 TTATTTA
1 TTATTTA
21636585 CATTTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTATTTCT
Found at i:21656426 original size:39 final size:39
Alignment explanation
Indices: 21656365--21656518 Score: 236
Period size: 39 Copynumber: 3.9 Consensus size: 39
21656355 TCAATACACT
*
21656365 GGCACACAGCCTGCTAGGCACATAGCCCGAATAATCACC
1 GGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCACC
* * *
21656404 GGTACAAAGCCTGCTAGGCACATAGCTCGAATAATCACT
1 GGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCACC
*
21656443 GGCACAAAGCCTGCTAGGCACATAGCCTGAATAATCACC
1 GGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCACC
* * *
21656482 AGCACAAAGCCAGCTAGGCACATAGCCTGAATAATCA
1 GGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCA
21656519 TCGGATTTCT
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 105 1.00
ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16
Consensus pattern (39 bp):
GGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCACC
Found at i:21656939 original size:43 final size:43
Alignment explanation
Indices: 21656891--21656979 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
21656881 TTTATCCAAA
*
21656891 TATTCTAGGCCCTCAAAAAACCCCTAATAAACCTAAAATTCAC
1 TATTCTAGGCCCTAAAAAAACCCCTAATAAACCTAAAATTCAC
21656934 TATTCTAGGCCCTAAAAAAACCCCTAATAAACCTAAAATTCAC
1 TATTCTAGGCCCTAAAAAAACCCCTAATAAACCTAAAATTCAC
21656977 TAT
1 TAT
21656980 CAAACCCTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.43, C:0.28, G:0.04, T:0.25
Consensus pattern (43 bp):
TATTCTAGGCCCTAAAAAAACCCCTAATAAACCTAAAATTCAC
Found at i:21658828 original size:23 final size:23
Alignment explanation
Indices: 21658791--21658836 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
21658781 AGGTTGTAGT
* *
21658791 TGTAATATCCTGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
21658814 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
21658837 AATAAGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:21666204 original size:39 final size:39
Alignment explanation
Indices: 21666150--21666346 Score: 295
Period size: 39 Copynumber: 5.1 Consensus size: 39
21666140 GTTTTCAATA
* * * *
21666150 CACCGGCATACAGCCTGTTAGGCACATACCCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
*
21666189 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATGAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
*
21666228 CACCGGCACAAAGCCTGGTAGGCACATAGCCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
* * *
21666267 TACCAGCACAAAGCCTGCTAGGCACATAGCCTGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
* *
21666306 CACCGGCATAAAGCCTGCTAGGCACATAGCCTGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
21666345 CA
1 CA
21666347 TCGGATTTCT
Statistics
Matches: 144, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 144 1.00
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (39 bp):
CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
Found at i:21667663 original size:39 final size:39
Alignment explanation
Indices: 21667582--21667785 Score: 284
Period size: 39 Copynumber: 5.2 Consensus size: 39
21667572 TGTAAGTTTT
* * ** * *
21667582 TAATACACCGGCACACAGCCTGCTAGGCGTATGGCCCAAA
1 TAAT-CACCAGCACAAAGCCTGCTAGGCACATAGCCCGAA
*
21667622 TAATCACCAGAACAAAGCCTGCTAGGCACATAGCCCGAA
1 TAATCACCAGCACAAAGCCTGCTAGGCACATAGCCCGAA
* **
21667661 TAATCACCAGCACAAAGCCTGCTAAGCACATAGATCGAA
1 TAATCACCAGCACAAAGCCTGCTAGGCACATAGCCCGAA
*
21667700 TAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCGAA
1 TAATCACCAGCACAAAGCCTGCTAGGCACATAGCCCGAA
21667739 TAATCACC-GCCACAAAGCCTGCTAGGCACATAGCCCGAA
1 TAATCACCAG-CACAAAGCCTGCTAGGCACATAGCCCGAA
21667778 TAATCACC
1 TAATCACC
21667786 GGATTTCTAT
Statistics
Matches: 148, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 143 0.97
40 4 0.03
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.14
Consensus pattern (39 bp):
TAATCACCAGCACAAAGCCTGCTAGGCACATAGCCCGAA
Found at i:21671684 original size:4 final size:4
Alignment explanation
Indices: 21671677--21671716 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
21671667 CAAAATAAAT
*
21671677 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ACTAA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A-TTA ATTA ATT
21671717 TCTCAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 30 0.91
5 3 0.09
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:21691563 original size:25 final size:25
Alignment explanation
Indices: 21691515--21691564 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
21691505 TTTCGAGCTA
*
21691515 TATAACGGGAAGCTCATGTAAGCCG
1 TATAACGGGAAGCTCATGAAAGCCG
*
21691540 TATATCGGGAAGCTCAT-AAGAGCCG
1 TATAACGGGAAGCTCATGAA-AGCCG
21691565 CAATTAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (25 bp):
TATAACGGGAAGCTCATGAAAGCCG
Found at i:21691609 original size:25 final size:25
Alignment explanation
Indices: 21691520--21691737 Score: 65
Period size: 25 Copynumber: 8.7 Consensus size: 25
21691510 AGCTATATAA
*
21691520 CGGGAAGCTCATGTA-AGCC-GTATAT
1 CGGGAAGCTCATG-AGAGCCATTA-AT
* **
21691545 CGGGAAGCTCATAAGAGCC-GCAAT
1 CGGGAAGCTCATGAGAGCCATTAAT
** *
21691569 TAGGTAGCTC-TAGAGAGCCATTAAT
1 CGGGAAGCTCAT-GAGAGCCATTAAT
*
21691594 CGGGAAGCTCATGAGAGAGCCTTTAAT
1 CGGGAAGCTCAT--GAGAGCCATTAAT
** * * **
21691621 CAAGAAGCTCGTAAGAGCCATATGTT
1 CGGGAAGCTCATGAGAGCCAT-TAAT
* * * * *
21691647 AGGG-TGCTCATAAGAGCTAAATAA-
1 CGGGAAGCTCATGAGAGC-CATTAAT
* *
21691671 CGGGAAGCTCGTGAGAGCCA-AATAT
1 CGGGAAGCTCATGAGAGCCATTA-AT
* * * *
21691696 CAGGAAGCTCAAGAGAGACAAT-AT
1 CGGGAAGCTCATGAGAGCCATTAAT
* *
21691720 TGGGATGCTCATGAGAGC
1 CGGGAAGCTCATGAGAGC
21691738 GAATAATGGG
Statistics
Matches: 138, Mismatches: 44, Indels: 23
0.67 0.21 0.11
Matches are distributed among these distances:
23 2 0.01
24 36 0.26
25 73 0.53
26 5 0.04
27 22 0.16
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.20
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCATTAAT
Found at i:21691637 original size:27 final size:27
Alignment explanation
Indices: 21691580--21691637 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
21691570 AGGTAGCTCT
** *
21691580 AGAGAGCCATTAATCGGGAAGCTCATG
1 AGAGAGCCATTAATCAAGAAGCTCATA
* *
21691607 AGAGAGCCTTTAATCAAGAAGCTCGTA
1 AGAGAGCCATTAATCAAGAAGCTCATA
21691634 AGAG
1 AGAG
21691638 CCATATGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (27 bp):
AGAGAGCCATTAATCAAGAAGCTCATA
Found at i:21691742 original size:24 final size:24
Alignment explanation
Indices: 21691702--21691748 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21691692 ATATCAGGAA
*
21691702 GCTCAAGAGAGACAATATTGGGAT
1 GCTCAAGAGAGACAATAATGGGAT
*
21691726 GCTCATGAGAG-CGAATAATGGGA
1 GCTCAAGAGAGAC-AATAATGGGA
21691749 CACTCTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (24 bp):
GCTCAAGAGAGACAATAATGGGAT
Found at i:21703047 original size:18 final size:19
Alignment explanation
Indices: 21703015--21703050 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21703005 ATTGAATATA
21703015 TTTTTAATATATTTTTTAG
1 TTTTTAATATATTTTTTAG
*
21703034 TTTTTATTAT-TTTTTTA
1 TTTTTAATATATTTTTTA
21703051 ATAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTTAATATATTTTTTAG
Found at i:21706808 original size:26 final size:26
Alignment explanation
Indices: 21706773--21706859 Score: 129
Period size: 26 Copynumber: 3.3 Consensus size: 26
21706763 TTTTACTCAA
* *
21706773 ATAAATTTTTGACAATTTTACCCCCG
1 ATAAAATTTTGACAATTTTACCCCTG
**
21706799 ATAAAATTTTGACAATTTTACCATTG
1 ATAAAATTTTGACAATTTTACCCCTG
*
21706825 GTAAAATTTTGACAATTTTACCCCTG
1 ATAAAATTTTGACAATTTTACCCCTG
21706851 ATAAAATTT
1 ATAAAATTT
21706860 ATTTTCATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (26 bp):
ATAAAATTTTGACAATTTTACCCCTG
Found at i:21711406 original size:25 final size:25
Alignment explanation
Indices: 21711359--21711424 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
21711349 CCTGTAAATG
**
21711359 TATGCTCATACAAGCTATGAATCTA
1 TATGCTCATACAAGCTACAAATCTA
**
21711384 TATGCTC-TCACAAGCTACAAATCGG
1 TATGCTCAT-ACAAGCTACAAATCTA
* *
21711409 TAAGCTCATACGAGCT
1 TATGCTCATACAAGCT
21711425 GTGATGTGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.03
25 31 0.94
26 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (25 bp):
TATGCTCATACAAGCTACAAATCTA
Found at i:21713337 original size:3 final size:3
Alignment explanation
Indices: 21713329--21713415 Score: 156
Period size: 3 Copynumber: 29.0 Consensus size: 3
21713319 TACTGTATTA
*
21713329 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
21713377 AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21713416 CCGGTAGTTA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21715194 original size:6 final size:6
Alignment explanation
Indices: 21715183--21715230 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
21715173 GGAAAATTTT
* * *
21715183 CCTTTC CCTTTC CCTTCC CCTTCC CCTTCC CTTTCC CCTTCC CCTTCC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC
21715231 TCTATCCTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CCTTCC
Found at i:21718004 original size:34 final size:35
Alignment explanation
Indices: 21717946--21718012 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
21717936 CAAACACCAA
21717946 AAAATATTTTCCAGTAAATCATTTTACAGAAAATT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAATT
*
21717981 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
21718013 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAATT
Found at i:21718551 original size:16 final size:15
Alignment explanation
Indices: 21718530--21718575 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
21718520 TAAAAATATT
21718530 TAAAATATATAAATTA
1 TAAAATATATAAA-TA
*
21718546 TAAAATATATATAATG
1 TAAAATATATA-AATA
21718562 TAAAATATTATAAA
1 TAAAATA-TATAAA
21718576 AAGGCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
TAAAATATATAAATA
Found at i:21721993 original size:10 final size:10
Alignment explanation
Indices: 21721950--21722082 Score: 55
Period size: 10 Copynumber: 13.7 Consensus size: 10
21721940 TTTTTGATGG
* *
21721950 ATTTTACAAT
1 ATTTTATAAA
21721960 ATTTTATAAA
1 ATTTTATAAA
* *
21721970 ATTTTACAAT
1 ATTTTATAAA
21721980 ATTTTATAAA
1 ATTTTATAAA
**
21721990 ATTTT-TCTA
1 ATTTTATAAA
*
21721999 TTTTTAT-AA
1 ATTTTATAAA
*
21722008 TTTTTA-ATAA
1 ATTTTATA-AA
*
21722018 ATTTT-TATA
1 ATTTTATAAA
*
21722027 ATTTT-TAATT
1 ATTTTATAA-A
*
21722037 TTTTTATTAAA
1 ATTTTA-TAAA
*
21722048 ATTTAAT-AA
1 ATTTTATAAA
*
21722057 TTTTTAT-AA
1 ATTTTATAAA
*
21722066 ATTTTATTAA
1 ATTTTATAAA
*
21722076 TTTTTAT
1 ATTTTAT
21722083 TTTTTAAAAT
Statistics
Matches: 93, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
9 36 0.39
10 50 0.54
11 4 0.04
12 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:21722005 original size:19 final size:20
Alignment explanation
Indices: 21721950--21722007 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
21721940 TTTTTGATGG
21721950 ATTTTACAATATTTTATAAA
1 ATTTTACAATATTTTATAAA
21721970 ATTTTACAATATTTTATAAA
1 ATTTTACAATATTTTATAAA
* *
21721990 ATTTTTCTAT-TTTTATAA
1 ATTTTACAATATTTTATAA
21722008 TTTTTAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 8 0.22
20 28 0.78
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTACAATATTTTATAAA
Found at i:21722017 original size:29 final size:27
Alignment explanation
Indices: 21721998--21722096 Score: 64
Period size: 29 Copynumber: 3.6 Consensus size: 27
21721988 AAATTTTTCT
21721998 ATTTTTAT-AATTTTTAATAAATTTTTATA
1 ATTTTTATAAATTTTT-AT-AA-TTTTATA
** *
21722027 ATTTTTA-ATTTTTTTATTAAAATTTAATA
1 ATTTTTATAAATTTTTA-T--AATTTTATA
21722056 ATTTTTATAAA-TTTTATTAATTTT-TA
1 ATTTTTATAAATTTTTA-TAATTTTATA
*
21722082 TTTTTTA-AAATTTTT
1 ATTTTTATAAATTTTT
21722097 GCCACATGTC
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
25 3 0.05
26 12 0.21
27 5 0.09
28 1 0.02
29 33 0.57
30 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
ATTTTTATAAATTTTTATAATTTTATA
Found at i:21722022 original size:19 final size:19
Alignment explanation
Indices: 21721961--21722082 Score: 106
Period size: 20 Copynumber: 6.3 Consensus size: 19
21721951 TTTTACAATA
*
21721961 TTTTATAAAATTTT-ACAAT
1 TTTTAT-AAATTTTAATAAT
**
21721980 ATTTTATAAAATTTTTCT-AT
1 -TTTTAT-AAATTTTAATAAT
*
21722000 TTTTATAATTTTTAATAAAT
1 TTTTATAAATTTTAAT-AAT
* *
21722020 TTTTATAATTTTTAAT-TT
1 TTTTATAAATTTTAATAAT
*
21722038 TTTTATTAAAATTTAATAAT
1 TTTTA-TAAATTTTAATAAT
*
21722058 TTTTATAAATTTTATTAAT
1 TTTTATAAATTTTAATAAT
21722077 TTTTAT
1 TTTTAT
21722083 TTTTTAAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
18 13 0.15
19 33 0.38
20 40 0.47
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATAAATTTTAATAAT
Found at i:21722083 original size:10 final size:10
Alignment explanation
Indices: 21721998--21722083 Score: 74
Period size: 9 Copynumber: 8.9 Consensus size: 10
21721988 AAATTTTTCT
21721998 ATTTTTA-TA
1 ATTTTTATTA
*
21722007 ATTTTTAATAA
1 ATTTTT-ATTA
21722018 ATTTTTA-TA
1 ATTTTTATTA
21722027 ATTTTTAATT-
1 ATTTTT-ATTA
21722037 -TTTTTATTA
1 ATTTTTATTA
** *
21722046 AAATTTAATA
1 ATTTTTATTA
21722056 ATTTTTA-TA
1 ATTTTTATTA
*
21722065 AATTTTATTA
1 ATTTTTATTA
21722075 ATTTTTATT
1 ATTTTTATT
21722084 TTTTAAAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
8 3 0.05
9 26 0.43
10 24 0.39
11 8 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:21722083 original size:39 final size:37
Alignment explanation
Indices: 21721961--21722082 Score: 122
Period size: 39 Copynumber: 3.2 Consensus size: 37
21721951 TTTTACAATA
* *
21721961 TTTTATAAAATTTTACAATATTTTATAAAATTTT-TCTAT
1 TTTTATAAAATTTAATAAT-TTTTAT-AAATTTTAT-TAT
** *
21722000 TTTTATAATTTTTAATAAATTTTTATAATTTTTAATT-T
1 TTTTATAAAATTTAAT-AATTTTTATAAATTTT-ATTAT
21722038 TTTTATTAAAATTTAATAATTTTTATAAATTTTATTAAT
1 TTTTA-TAAAATTTAATAATTTTTATAAATTTTATT-AT
21722077 TTTTAT
1 TTTTAT
21722083 TTTTTAAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
37 3 0.04
38 28 0.41
39 34 0.49
40 4 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (37 bp):
TTTTATAAAATTTAATAATTTTTATAAATTTTATTAT
Found at i:21722380 original size:88 final size:88
Alignment explanation
Indices: 21722201--21722380 Score: 204
Period size: 88 Copynumber: 2.0 Consensus size: 88
21722191 TAAAGAACCG
* * * * *
21722201 TTTTGATGCATTTTACAGTTCAAGTACCTAATTGAGTGAAAAAAATCAGGGACTTAATTGATTTT
1 TTTTAATGCATTTGAAAGTTCAAATACCTAATTGAGTGAAAAAAAACAGGGACTTAATTGATTTT
* *
21722266 CTTTAAAAAAGTTTGAGGGTTTT
66 CTTTAAAAAAGTTTGAAGGTTCT
* * * *
21722289 TTTTAATGCATTTGAAAGTTCAAATACCTAATTGCGTGCAAAAAAAAACAATGGTC-TAATTGCT
1 TTTTAATGCATTTGAAAGTTCAAATACCTAATTGAGTG--AAAAAAAAC-AGGGACTTAATTGAT
*
21722353 TTT-TTTGAAAAAGTTTGAAGG-TCT
63 TTTCTTTAAAAAAGTTTGAAGGTTCT
21722377 TTTT
1 TTTT
21722381 GATATATTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
88 39 0.51
89 16 0.21
90 18 0.23
91 4 0.05
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (88 bp):
TTTTAATGCATTTGAAAGTTCAAATACCTAATTGAGTGAAAAAAAACAGGGACTTAATTGATTTT
CTTTAAAAAAGTTTGAAGGTTCT
Found at i:21722396 original size:89 final size:87
Alignment explanation
Indices: 21722217--21722452 Score: 192
Period size: 89 Copynumber: 2.7 Consensus size: 87
21722207 TGCATTTTAC
* *
21722217 AGTTCAAGTACCTAATTGAGTGAAAAAAATCAGGGACTTAATTGATTTTCTTTAAAAAAGTTTGA
1 AGTTCAAATACCTAATTGAGTGAAAAAAAACAGGGACTTAATTGATTTTCTTTAAAAAAGTTTGA
* * * *
21722282 GGGTTTTTTTTAATGCATTTGAA
66 AGGTCTTTTTGAAT-CATTTAAA
* * * * *
21722305 AGTTCAAATACCTAATTGCGTGCAAAAAAAAACAATGGTC-TAATTGCTTTT-TTTGAAAAAGTT
1 AGTTCAAATACCTAATTGAGTG--AAAAAAAAC-AGGGACTTAATTGATTTTCTTTAAAAAAGTT
21722368 TGAAGGTCTTTTTGATAT-ATTTTAAA
63 TGAAGGTCTTTTTGA-ATCA-TTTAAA
* * * * * * * * *
21722394 AGTTTAAGTATCTTATTAAGTGAAAAAAGAAGTAGGGGCTTAGTTGCTTTT-TTTAAAAA
1 AGTTCAAATACCTAATTGAGTGAAAAAA-AA-CAGGGACTTAATTGATTTTCTTTAAAAA
21722453 CAAATTAAAA
Statistics
Matches: 118, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
87 6 0.05
88 27 0.23
89 61 0.52
90 20 0.17
91 4 0.03
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.38
Consensus pattern (87 bp):
AGTTCAAATACCTAATTGAGTGAAAAAAAACAGGGACTTAATTGATTTTCTTTAAAAAAGTTTGA
AGGTCTTTTTGAATCATTTAAA
Found at i:21723809 original size:42 final size:42
Alignment explanation
Indices: 21723756--21723976 Score: 298
Period size: 42 Copynumber: 5.2 Consensus size: 42
21723746 CACAAAAAAC
* *
21723756 GCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCACAATT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCACAAAT
* *
21723798 GCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTCCAAAAAT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCACAAAT
* ** * *
21723840 GCCGCTAAAGACCAAAACCTTTAGTAGCACTTTTCCACAATT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCACAAAT
*
21723882 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCCACAAAT
* * * *
21723925 GCCGCTAAAGACCATGACCTTTAGCGACGCTTTTCTCAAAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTC-CACAAAT
21723968 GCCGCTAAA
1 GCCGCTAAA
21723977 AACATAACCT
Statistics
Matches: 157, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 104 0.66
43 53 0.34
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (42 bp):
GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCACAAAT
Found at i:21723849 original size:84 final size:85
Alignment explanation
Indices: 21723750--21723959 Score: 332
Period size: 84 Copynumber: 2.5 Consensus size: 85
21723740 AAGCGCCACA
*
21723750 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCACAATTGCCGCTAAAGACTAAGA
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCACAATTGCCGCTAAAGACCAAGA
21723815 CCTTTAGCGGCGC-TTTTCC
66 CCTTTAGCGGCGCTTTTTCC
* * **
21723834 AAAAATGCCGCTAAAGACCAAAACCTTTAGTAGCACTTTTCCACAATTGCCGCTAAAGACCAAGA
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCACAATTGCCGCTAAAGACCAAGA
21723899 CCTTTAGCGGCGCTTTTTCC
66 CCTTTAGCGGCGCTTTTTCC
* * * *
21723919 ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTC
21723960 TCAAAAACGC
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 73 0.65
85 39 0.35
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCACAATTGCCGCTAAAGACCAAGA
CCTTTAGCGGCGCTTTTTCC
Found at i:21728263 original size:13 final size:13
Alignment explanation
Indices: 21728239--21728297 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
21728229 TTCTTCATTA
*
21728239 CTTTTGAAAAGTG
1 CTTTTGAGAAGTG
*
21728252 CTTTTCAGAAGTG
1 CTTTTGAGAAGTG
* * *
21728265 CTGTGGAAAAGTG
1 CTTTTGAGAAGTG
*
21728278 TTTTTGAGAAGTG
1 CTTTTGAGAAGTG
21728291 CTTTTGA
1 CTTTTGA
21728298 AAATTTTGAG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.39
Consensus pattern (13 bp):
CTTTTGAGAAGTG
Found at i:21728299 original size:26 final size:26
Alignment explanation
Indices: 21728239--21728300 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
21728229 TTCTTCATTA
21728239 CTTTTGAAAAGTGCTTTTCAGAAGTG
1 CTTTTGAAAAGTGCTTTTCAGAAGTG
* * * *
21728265 CTGTGGAAAAGTGTTTTTGAGAAGTG
1 CTTTTGAAAAGTGCTTTTCAGAAGTG
21728291 CTTTTGAAAA
1 CTTTTGAAAA
21728301 TTTTGAGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (26 bp):
CTTTTGAAAAGTGCTTTTCAGAAGTG
Found at i:21730239 original size:19 final size:19
Alignment explanation
Indices: 21730215--21730256 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
21730205 AAATTATAAA
*
21730215 TTTTATTTTTTTATTTCAT
1 TTTTATTTTTGTATTTCAT
*
21730234 TTTTATTTTTGTATTTTAT
1 TTTTATTTTTGTATTTCAT
21730253 TTTT
1 TTTT
21730257 TCTTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTGTATTTCAT
Found at i:21730623 original size:14 final size:14
Alignment explanation
Indices: 21730604--21730637 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
21730594 AACCCTAAAT
*
21730604 CCCTAACTCTTAAC
1 CCCTAACTCATAAC
21730618 CCCTAACTCATAAC
1 CCCTAACTCATAAC
21730632 CCCTAA
1 CCCTAA
21730638 ACCTTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAACTCATAAC
Found at i:21730653 original size:21 final size:20
Alignment explanation
Indices: 21730629--21730669 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
21730619 CCTAACTCAT
*
21730629 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
21730650 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
21730670 TAAATCTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:21730881 original size:25 final size:25
Alignment explanation
Indices: 21730835--21730882 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21730825 TATATGAAAT
* **
21730835 TATTTAATATATAAATTTAAAAACA
1 TATTTAAAATATAAATAAAAAAACA
21730860 TATTTAAAATATAAATAAAAAAA
1 TATTTAAAATATAAATAAAAAAA
21730883 TTAATCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
TATTTAAAATATAAATAAAAAAACA
Found at i:21730960 original size:21 final size:22
Alignment explanation
Indices: 21730929--21730971 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
21730919 ATCCTAAACT
*
21730929 CTAAATCCTTAACTATTAACCC
1 CTAAATCCTTAAATATTAACCC
*
21730951 CTAAA-CCTTAAATCTTAACCC
1 CTAAATCCTTAAATATTAACCC
21730972 AACCCTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (22 bp):
CTAAATCCTTAAATATTAACCC
Found at i:21731008 original size:33 final size:33
Alignment explanation
Indices: 21730966--21731029 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
21730956 CCTTAAATCT
* *
21730966 TAACCCAACCCTGAATCTC-TAATCCCTAAACCC
1 TAACCCAACCCAGAATC-CATAACCCCTAAACCC
21730999 TAACCCAACCCAGAATCCATAACCCCTAAAC
1 TAACCCAACCCAGAATCCATAACCCCTAAAC
21731030 ATTATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.38, C:0.42, G:0.03, T:0.17
Consensus pattern (33 bp):
TAACCCAACCCAGAATCCATAACCCCTAAACCC
Found at i:21731150 original size:14 final size:14
Alignment explanation
Indices: 21731127--21731159 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
21731117 TAACTGATCT
*
21731127 TAACCTCTAGCCCC
1 TAACCCCTAGCCCC
21731141 TAACCCCTAGCCCC
1 TAACCCCTAGCCCC
21731155 TAACC
1 TAACC
21731160 TATAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.52, G:0.06, T:0.18
Consensus pattern (14 bp):
TAACCCCTAGCCCC
Found at i:21731752 original size:47 final size:47
Alignment explanation
Indices: 21731687--21731777 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
21731677 GATTGAAAAA
21731687 AATAATAAATAGTTAGGAGGTAGGACTTCTCTTTAATAAAAACAAAT
1 AATAATAAATAGTTAGGAGGTAGGACTTCTCTTTAATAAAAACAAAT
*
21731734 AATAATAAATAGTTAGGAGTTAGGACTTCTCTTTAATAAAAACA
1 AATAATAAATAGTTAGGAGGTAGGACTTCTCTTTAATAAAAACA
21731778 TTTTGTATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (47 bp):
AATAATAAATAGTTAGGAGGTAGGACTTCTCTTTAATAAAAACAAAT
Found at i:21732020 original size:41 final size:41
Alignment explanation
Indices: 21731969--21732233 Score: 377
Period size: 41 Copynumber: 6.5 Consensus size: 41
21731959 GTTTTTTTTA
*
21731969 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTT
1 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTC
* ** *
21732010 AAAAATGCCGCTAAAGATCTGAGCATTAGCGGCGCTTCTTC
1 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTC
* **
21732051 AAAAACGCCGCTAAAGGCTAGAGCATTAGCAACGCTTCTTC
1 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTC
* * * *
21732092 AAAAACGCCGCTAAATGCCCGAACACTAGCGGCGCTTCTTC
1 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTC
* *
21732133 AAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTATTC
1 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTC
* *
21732174 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGTGCTTATTC
1 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTC
*
21732215 AAAAACGCCACTAAAGGCC
1 AAAAACGCCGCTAAAGGCC
21732234 CCAAAAACTC
Statistics
Matches: 198, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 198 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTC
Found at i:21732337 original size:39 final size:40
Alignment explanation
Indices: 21732294--21732404 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 40
21732284 TTCAGAAAAT
* *
21732294 GCCGCTAATGCT-TATTTTTAGCGGTGTTTTTGGAGAAGC
1 GCCGCTAATGCTCTATTTTTAGCGGCGTTTTTGGAAAAGC
* ** *
21732333 GCCGCTAATACTCTACCTTTAGCGGCGTTTTTGTAAAAGC
1 GCCGCTAATGCTCTATTTTTAGCGGCGTTTTTGGAAAAGC
* *
21732373 GCCGCTAATGCTCGATTTTTAGTGGCGTTTTT
1 GCCGCTAATGCTCTATTTTTAGCGGCGTTTTT
21732405 TTGTCCAAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 11 0.18
40 49 0.82
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (40 bp):
GCCGCTAATGCTCTATTTTTAGCGGCGTTTTTGGAAAAGC
Found at i:21733836 original size:2 final size:2
Alignment explanation
Indices: 21733831--21733872 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
21733821 CTTTTCTTTT
* *
21733831 TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG T- TG GG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
21733872 T
1 T
21733873 TGGGTGGGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:21737778 original size:24 final size:24
Alignment explanation
Indices: 21737728--21737781 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
21737718 TATTCTGTTA
* *
21737728 GCCTTTGTGGCGTATTCTAATTTG
1 GCCTTTATGGCGTATTCTAATTGG
21737752 GCCTTTATGGCGTATTCTAGA-TGG
1 GCCTTTATGGCGTATTCTA-ATTGG
21737776 GCCTTT
1 GCCTTT
21737782 GTAGCATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.43
Consensus pattern (24 bp):
GCCTTTATGGCGTATTCTAATTGG
Found at i:21744434 original size:17 final size:17
Alignment explanation
Indices: 21744412--21744456 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
21744402 CTTTATGAAC
21744412 TATTTTATTTATTTATT
1 TATTTTATTTATTTATT
*
21744429 TATTTTATTTATTTCTT
1 TATTTTATTTATTTATT
21744446 TACTTTT-TTTA
1 TA-TTTTATTTA
21744457 ATACTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTATTTATTTATT
Done.