Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_pilon, whole genome shotgun sequence
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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:131 original size:16 final size:16
Alignment explanation
Indices: 110--143 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
100 TTACTATTCA
*
110 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
126 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
142 CG
1 CG
144 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:890 original size:15 final size:16
Alignment explanation
Indices: 872--902 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
862 TGGCAGATCC
872 AATCCAG-ACGGGAAA
1 AATCCAGAACGGGAAA
887 AATCCAGAACGGGAAA
1 AATCCAGAACGGGAAA
903 GAAGATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.19, G:0.26, T:0.06
Consensus pattern (16 bp):
AATCCAGAACGGGAAA
Found at i:8642 original size:24 final size:24
Alignment explanation
Indices: 8590--8650 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
8580 ATATCAAAGA
*
8590 ACACATCATTTGGAACTTCAAGTG
1 ACACATCTTTTGGAACTTCAAGTG
*
8614 ACACATCTTTTGGAACTTTAAGT-
1 ACACATCTTTTGGAACTTCAAGTG
*
8637 ATCACATATTTTGG
1 A-CACATCTTTTGG
8651 TCCTCCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (24 bp):
ACACATCTTTTGGAACTTCAAGTG
Found at i:9233 original size:14 final size:15
Alignment explanation
Indices: 9210--9238 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9200 ATTTTTTTCC
9210 TTCATCTTTTCCACT
1 TTCATCTTTTCCACT
9225 TTCAT-TTTTCCACT
1 TTCATCTTTTCCACT
9239 CATTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCATCTTTTCCACT
Found at i:14892 original size:21 final size:21
Alignment explanation
Indices: 14867--14910 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
14857 AATTTAGTTA
14867 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
14888 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
14909 AT
1 AT
14911 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:14920 original size:28 final size:30
Alignment explanation
Indices: 14887--14949 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
14877 TAGTATAAAT
14887 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
14915 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
14945 TATTA
1 TATTA
14950 TATAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 20 0.61
29 1 0.03
30 12 0.36
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (30 bp):
TATTAGTTTGTTAGTTTAAGTTATATATTA
Found at i:16101 original size:16 final size:16
Alignment explanation
Indices: 16080--16110 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16070 CATCGAAGCG
16080 AACTCCCACCAAATAT
1 AACTCCCACCAAATAT
16096 AACTCCCACCAAATA
1 AACTCCCACCAAATA
16111 GGATTAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (16 bp):
AACTCCCACCAAATAT
Found at i:30886 original size:15 final size:15
Alignment explanation
Indices: 30866--30904 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
30856 AATGATTTAA
*
30866 TAATGATTTTATTTT
1 TAATGATTTTATATT
30881 TAATGATTTTATATT
1 TAATGATTTTATATT
30896 TAATGATTT
1 TAATGATTT
30905 AGTAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (15 bp):
TAATGATTTTATATT
Found at i:30974 original size:21 final size:22
Alignment explanation
Indices: 30936--30980 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
30926 TGAATATTAA
*
30936 TAATGATTTATTATTAAT-ATT
1 TAATGATTTATTACTAATGATT
30957 TAATGATTTGA-TACTAATGATT
1 TAATGATTT-ATTACTAATGATT
30979 TA
1 TA
30981 GTAATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
TAATGATTTATTACTAATGATT
Found at i:31076 original size:21 final size:22
Alignment explanation
Indices: 31050--31090 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31040 ATAATAATGA
31050 TTATAATA-GTCGAATTTATCT
1 TTATAATATGTCGAATTTATCT
31071 TTATAATATGTCGAATTTAT
1 TTATAATATGTCGAATTTAT
31091 TTTTTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (22 bp):
TTATAATATGTCGAATTTATCT
Found at i:31255 original size:14 final size:14
Alignment explanation
Indices: 31233--31280 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
31223 TGTTAATATT
*
31233 TAATTATTTGATAG
1 TAATGATTTGATAG
31247 TAATGA-TT--TAG
1 TAATGATTTGATAG
31258 TAATGATTTGATAG
1 TAATGATTTGATAG
31272 TAATGATTT
1 TAATGATTT
31281 ATTATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 2 0.07
13 2 0.07
14 17 0.57
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:31301 original size:21 final size:22
Alignment explanation
Indices: 31272--31434 Score: 73
Period size: 21 Copynumber: 7.1 Consensus size: 22
31262 GATTTGATAG
* *
31272 TAATGATTTATTATTAAT-ATT
1 TAATGATTTAATAGTAATGATT
*
31293 TAATTATTTAATAGTAATGATT
1 TAATGATTTAATAGTAATGATT
* * *
31315 TAATAATGGTTACTAATAATGATT
1 TAATGAT--TTAATAGTAATGATT
* *
31339 T-ATTA-TTAATATTTAATGATT
1 TAATGATTTAATA-GTAATGATT
* * * *
31360 TGATAGTAATGATTTAGTAATGATTAGT
1 TAAT-G-ATTTA-ATAGTAATGA-T--T
* *
31388 AATAATGATTTATTATTAAT-ATT
1 --TAATGATTTAATAGTAATGATT
31411 TAATGATTTAATAGTAATGATT
1 TAATGATTTAATAGTAATGATT
31433 TA
1 TA
31435 GTAATGATTA
Statistics
Matches: 108, Mismatches: 19, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
20 5 0.05
21 40 0.37
22 16 0.15
23 4 0.04
24 15 0.14
25 9 0.08
26 4 0.04
27 7 0.06
28 4 0.04
29 1 0.01
30 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (22 bp):
TAATGATTTAATAGTAATGATT
Found at i:31366 original size:59 final size:58
Alignment explanation
Indices: 31225--31536 Score: 410
Period size: 59 Copynumber: 5.2 Consensus size: 58
31215 AATTAGTTTG
* *
31225 TTAATATTTAATTATTTGATAGTAATGATTTAGTAATGATTTGATAGTAATGATTTATTA
1 TTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA-TT-ATAATAATGATTTATTA
* * * *
31285 TTAATATTTAATTATTTAATAGTAATGATTTAATAATGGTTACTAATAATGATTTATTA
1 TTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTA-TAATAATGATTTATTA
31344 TTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGATTTATTA
1 TTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTA-TAATAATGATTTATTA
* * * *
31403 TTAATATTTAATGATTTAATAGTAATGATTTAGTAATGATTAGAATAATGAAATTATCA
1 TTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTATAATAATG-ATTTATTA
* *
31462 TTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATAATAATAATTTGA-TA
1 TTAATATTTAATGATTTGATAGTAATGATT--TAGTAATG--ATTATAATAATGATTT-ATTA
31524 TTAATGATTTAAT
1 TTAAT-ATTTAAT
31537 AATTATTACT
Statistics
Matches: 225, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
58 8 0.04
59 147 0.65
60 36 0.16
61 7 0.03
62 9 0.04
63 18 0.08
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.47
Consensus pattern (58 bp):
TTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTATAATAATGATTTATTA
Found at i:31371 original size:14 final size:13
Alignment explanation
Indices: 31352--31398 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
31342 TATTAATATT
31352 TAATGATTTGATAG
1 TAATGATTTG-TAG
31366 TAATGA-TT-TAG
1 TAATGATTTGTAG
* *
31377 TAATGATTAGTAA
1 TAATGATTTGTAG
31390 TAATGATTT
1 TAATGATTT
31399 ATTATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.32
12 1 0.04
13 12 0.43
14 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (13 bp):
TAATGATTTGTAG
Found at i:31388 original size:10 final size:11
Alignment explanation
Indices: 31363--31443 Score: 58
Period size: 11 Copynumber: 7.0 Consensus size: 11
31353 AATGATTTGA
31363 TAGTAATGATT
1 TAGTAATGATT
31374 TAGTAATGATT
1 TAGTAATGATT
*
31385 AGTAATAATGATT
1 --TAGTAATGATT
* * *
31398 TATTATTAATAT
1 TAGTAATGAT-T
31410 T--TAATGATTT
1 TAGTAATGA-TT
31420 AATAGTAATGATT
1 --TAGTAATGATT
31433 TAGTAATGATT
1 TAGTAATGATT
31444 AGAATAATGA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
10 5 0.09
11 30 0.54
12 3 0.05
13 12 0.21
14 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:31396 original size:24 final size:25
Alignment explanation
Indices: 31352--31399 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
31342 TATTAATATT
* *
31352 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTAGATAATAATGATTTAG
31377 TAATGATTAG-TAATAATGATTTA
1 TAATGATTAGATAATAATGATTTA
31400 TTATTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.44
Consensus pattern (25 bp):
TAATGATTAGATAATAATGATTTAG
Found at i:31489 original size:14 final size:14
Alignment explanation
Indices: 31470--31539 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
31460 CATTAATATT
*
31470 TAATGATTTGATAG
1 TAATGATTTGATAA
*
31484 TAATGATTAG-TAA
1 TAATGATTTGATAA
*
31497 TAATGAAATT-ATAA
1 TAATG-ATTTGATAA
* *
31511 TAATAATTTGATAT
1 TAATGATTTGATAA
*
31525 TAATGATTTAATAA
1 TAATGATTTGATAA
31539 T
1 T
31540 TATTACTAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
13 10 0.23
14 33 0.77
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:32129 original size:13 final size:12
Alignment explanation
Indices: 32022--32208 Score: 58
Period size: 11 Copynumber: 15.6 Consensus size: 12
32012 CTGGTTTGGT
32022 TTATAATAATGA
1 TTATAATAATGA
* *
32034 -TATGAT-TTGA
1 TTATAATAATGA
32044 TTTAGTAATAAT--
1 -TTA-TAATAATGA
32056 TTGATAATAATGA
1 TT-ATAATAATGA
*
32069 TTTAATAATAAT-T
1 -TT-ATAATAATGA
* *
32082 TTATATTTAA-AA
1 TTATA-ATAATGA
32094 TTATAATAATGA
1 TTATAATAATGA
*
32106 TT-TAGTAATGA
1 TTATAATAATGA
32117 TTACTAATAATGA
1 TTA-TAATAATGA
*
32130 TTTATTATTAAT-A
1 -TTA-TAATAATGA
*
32143 TT-TAATGAT--
1 TTATAATAATGA
*
32152 TTGATATTAATGA
1 TT-ATAATAATGA
*
32165 TTA-AGTAATGA
1 TTATAATAATGA
* *
32176 CTAATAATAATAAAA
1 -TTATAATAAT--GA
32191 TTATAATAATGA
1 TTATAATAATGA
32203 TT-TAAT
1 TTATAAT
32209 CATTAATAAT
Statistics
Matches: 129, Mismatches: 24, Indels: 45
0.65 0.12 0.23
Matches are distributed among these distances:
9 2 0.02
10 8 0.06
11 46 0.36
12 24 0.19
13 19 0.15
14 29 0.22
15 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (12 bp):
TTATAATAATGA
Found at i:32243 original size:18 final size:18
Alignment explanation
Indices: 32194--32231 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
32184 AATAAAATTA
*
32194 TAATAATGATTTAATCAT
1 TAATAATGATTTAATAAT
32212 TAATAATGATTTAATAAT
1 TAATAATGATTTAATAAT
32230 TA
1 TA
32232 TTAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (18 bp):
TAATAATGATTTAATAAT
Found at i:39686 original size:22 final size:22
Alignment explanation
Indices: 39648--39711 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 22
39638 TTTCTGGCAG
* *
39648 GAGGAATCGATACCCCCTTAAA
1 GAGGAACCGATTCCCCCTTAAA
* * *
39670 GGGGAACCGATTTCCCCTTTGAA
1 GAGGAACCGA-TTCCCCCTTAAA
*
39693 TAGGAACCGATTCCCCCTT
1 GAGGAACCGATTCCCCCTT
39712 TGGAGGGAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (22 bp):
GAGGAACCGATTCCCCCTTAAA
Found at i:42598 original size:10 final size:10
Alignment explanation
Indices: 42566--42600 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
42556 GAAGCCATTG
42566 ATCAACAACA
1 ATCAACAACA
*
42576 ATAAACAACA
1 ATCAACAACA
*
42586 ATCAACAAGA
1 ATCAACAACA
42596 ATCAA
1 ATCAA
42601 GAGAGAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.63, C:0.23, G:0.03, T:0.11
Consensus pattern (10 bp):
ATCAACAACA
Found at i:44413 original size:44 final size:41
Alignment explanation
Indices: 44357--44473 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 41
44347 TTAACTATTT
*
44357 AACTAAC-TACAAACTAATTAAAT-ATTTTTTATATATAACTAAC
1 AACTAACAAACAAACTAATTAAATAATTTTTTATA-AT-A-T-AC
* * *
44400 AACTAACAAACAAATTAATTAATTAATTTTTT-TAATATAT
1 AACTAACAAACAAACTAATTAAATAATTTTTTATAATATAC
*
44440 AACTATCAAACAAACTAATTAAATAATTTTTTAT
1 AACTAACAAACAAACTAATTAAATAATTTTTTAT
44474 TTATGTATGA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
40 30 0.47
41 2 0.03
42 1 0.02
43 9 0.14
44 15 0.23
45 7 0.11
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (41 bp):
AACTAACAAACAAACTAATTAAATAATTTTTTATAATATAC
Found at i:44792 original size:22 final size:21
Alignment explanation
Indices: 44765--44824 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
44755 ATCATTCAAC
44765 GCAGCAATAATTGATGCATGAA
1 GCAGCAATAA-TGATGCATGAA
* *
44787 GCAGCAAATGATGCTGCATGAA
1 GCAGC-AATAATGATGCATGAA
* *
44809 GCAACAAAAATGATGC
1 GCAGCAATAATGATGC
44825 TGCAATAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 8 0.26
22 19 0.61
23 4 0.13
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (21 bp):
GCAGCAATAATGATGCATGAA
Found at i:44824 original size:24 final size:22
Alignment explanation
Indices: 44779--44828 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
44769 CAATAATTGA
*
44779 TGCATGAAGCAGCAAATGATGC
1 TGCATGAAGCAACAAATGATGC
44801 TGCATGAAGCAACAAAAATGATGC
1 TGCATGAAGCAAC--AAATGATGC
44825 TGCA
1 TGCA
44829 ATAATGCAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 12 0.48
24 13 0.52
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (22 bp):
TGCATGAAGCAACAAATGATGC
Found at i:44893 original size:19 final size:19
Alignment explanation
Indices: 44871--44907 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44861 CGGGGAACAG
*
44871 GCGAGCATGAGGGGAGCAT
1 GCGAGCATGAGAGGAGCAT
44890 GCGAGCATGAGAGGAGCA
1 GCGAGCATGAGAGGAGCA
44908 GGCGGTAGGA
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:0.30, C:0.16, G:0.46, T:0.08
Consensus pattern (19 bp):
GCGAGCATGAGAGGAGCAT
Found at i:52239 original size:20 final size:20
Alignment explanation
Indices: 52211--52261 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
52201 AGGTAAGGAA
*
52211 AGTATCGATACCCTCATAGC
1 AGTAGCGATACCCTCATAGC
52231 AGTAGCGATACCCTCATAGC
1 AGTAGCGATACCCTCATAGC
52251 AGTAGCGATAC
1 AGTAGCGATAC
52262 TGCTTATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTAGCGATACCCTCATAGC
Found at i:53734 original size:36 final size:36
Alignment explanation
Indices: 53694--53832 Score: 244
Period size: 36 Copynumber: 3.9 Consensus size: 36
53684 ATGGTGCTGG
53694 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
53730 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
53766 ACATTGATA-AGCGAATGTACTAAAGCTGATATGATA
1 ACATTGATACA-CGAATGTACCAAAGCTGATATGATA
*
53802 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
53833 ATACTCAACT
Statistics
Matches: 98, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
35 1 0.01
36 96 0.98
37 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:57327 original size:18 final size:19
Alignment explanation
Indices: 57286--57328 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
57276 TTGGTTCACG
57286 GAATATAAGATTATCAGTGA
1 GAATATAAGATTATCAG-GA
*
57306 GAATGTAAGATTATCA-GA
1 GAATATAAGATTATCAGGA
57324 GAATA
1 GAATA
57329 GGATTACTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.28
Consensus pattern (19 bp):
GAATATAAGATTATCAGGA
Found at i:57552 original size:37 final size:36
Alignment explanation
Indices: 57479--57552 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
57469 GTTGGAAAAT
* * *
57479 ATTTATATATTTTCTTTAAAATTTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
*
57515 ATTTATATATTTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTA-AAAATTAAAAATCATAAA
57552 A
1 A
57553 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 9 0.28
37 14 0.44
38 9 0.28
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:58114 original size:17 final size:18
Alignment explanation
Indices: 58092--58125 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
58082 TTTTTAATTT
58092 ATATATTAATT-TTTTGC
1 ATATATTAATTATTTTGC
58109 ATATATTAATTATTTTG
1 ATATATTAATTATTTTG
58126 AAATTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (18 bp):
ATATATTAATTATTTTGC
Found at i:59101 original size:23 final size:23
Alignment explanation
Indices: 59072--59157 Score: 136
Period size: 23 Copynumber: 3.7 Consensus size: 23
59062 TTGAATGATT
59072 CAGTGTTGACTGATTCAGCAAAA
1 CAGTGTTGACTGATTCAGCAAAA
*
59095 CATTGTTGACTGATTCAGCAAAA
1 CAGTGTTGACTGATTCAGCAAAA
**
59118 CAGTGTTGACTGATTCAATAAAA
1 CAGTGTTGACTGATTCAGCAAAA
*
59141 CAGTGTTGAATGATTCA
1 CAGTGTTGACTGATTCA
59158 ACACAGAAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (23 bp):
CAGTGTTGACTGATTCAGCAAAA
Found at i:59275 original size:15 final size:16
Alignment explanation
Indices: 59237--59277 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
59227 ACAGAGCCTC
*
59237 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
59253 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
59269 T-AATCATTC
1 TGAATCATTC
59278 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:60251 original size:15 final size:15
Alignment explanation
Indices: 60230--60271 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
60220 TCCGTCCCGT
*
60230 ATCCGCCTGCCCCGC
1 ATCCGCCTGCCCCAC
*
60245 ATTCGCCTGCCCCAC
1 ATCCGCCTGCCCCAC
*
60260 ATCCGCCCGCCC
1 ATCCGCCTGCCC
60272 ACTAAATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.10, C:0.60, G:0.17, T:0.14
Consensus pattern (15 bp):
ATCCGCCTGCCCCAC
Found at i:67991 original size:22 final size:22
Alignment explanation
Indices: 67966--68013 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
67956 TGTCCATAAA
*
67966 GACCTATGTATTTGTCCCGAAG
1 GACCTATGTATATGTCCCGAAG
*
67988 GACCTTTGTATATGTCCCGAAG
1 GACCTATGTATATGTCCCGAAG
68010 GACC
1 GACC
68014 GCATAGACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (22 bp):
GACCTATGTATATGTCCCGAAG
Found at i:69349 original size:23 final size:22
Alignment explanation
Indices: 69319--69367 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 22
69309 TCTCCTTCAT
69319 TCCCACGTGTAACCCATATATA
1 TCCCACGTGTAACCCATATATA
69341 TCCCTACGTGTAACCCATATATA
1 TCCC-ACGTGTAACCCATATATA
69364 TCCC
1 TCCC
69368 CACTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.29, C:0.35, G:0.08, T:0.29
Consensus pattern (22 bp):
TCCCACGTGTAACCCATATATA
Found at i:78405 original size:17 final size:18
Alignment explanation
Indices: 78383--78416 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
78373 GAGGTAATTT
78383 TTTATTA-TTTAAATTAG
1 TTTATTATTTTAAATTAG
78400 TTTATTATTTTAAATTA
1 TTTATTATTTTAAATTA
78417 TTAGTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATTATTTTAAATTAG
Found at i:78492 original size:21 final size:21
Alignment explanation
Indices: 78468--78507 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
78458 GTTAATTAGT
78468 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
78489 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
78508 CATACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:78564 original size:38 final size:41
Alignment explanation
Indices: 78520--78620 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 41
78510 TACATAAATA
* *
78520 AAAAAATATTTAGTTAATTTGTTTGATAGTTA-TGTAT-T-T
1 AAAAAATATTTAATTAGTTTGTTTGATAGTTAGT-TATATAT
* *
78559 -AAAAATAATTAATTAGTTTGTTTGTTAGTTAGTTATATAT
1 AAAAAATATTTAATTAGTTTGTTTGATAGTTAGTTATATAT
78599 AAAAAATATTTAATTAGTTTGT
1 AAAAAATATTTAATTAGTTTGT
78621 GTTAGTTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
38 30 0.57
39 2 0.04
40 1 0.02
41 20 0.38
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.50
Consensus pattern (41 bp):
AAAAAATATTTAATTAGTTTGTTTGATAGTTAGTTATATAT
Found at i:78710 original size:44 final size:48
Alignment explanation
Indices: 78631--78721 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 48
78621 GTTAGTTAAA
* * *
78631 TAGTTAAGTTATATTTGTTTGTTGAATTTATATTAT-A-TAAAAAATT
1 TAGTTAAGTTATATTTATTAGTTGAAGTTATATTATAATTAAAAAATT
*
78677 TAGTTAAG-TA-ATTTATTAGTTTAAGTTATATTATAATTAAAAAAT
1 TAGTTAAGTTATATTTATTAGTTGAAGTTATATTATAATTAAAAAAT
78722 AGTTTATTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 20 0.51
45 3 0.08
46 16 0.41
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (48 bp):
TAGTTAAGTTATATTTATTAGTTGAAGTTATATTATAATTAAAAAATT
Found at i:81124 original size:17 final size:15
Alignment explanation
Indices: 81102--81141 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
81092 GTTGGATATG
81102 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
81118 TTTAAATATTATAATA
1 -TTAAATATTATAAAA
81134 TTAAATAT
1 TTAAATAT
81142 GCATATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:81196 original size:22 final size:22
Alignment explanation
Indices: 81171--81214 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
81161 GTAAAAAAGA
*
81171 ATAAATTCGACTATTTATAAAT
1 ATAAATTCGACTAGTTATAAAT
81193 ATAAATTCGACTAGTTATAAAT
1 ATAAATTCGACTAGTTATAAAT
81215 TCAACTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (22 bp):
ATAAATTCGACTAGTTATAAAT
Found at i:81275 original size:11 final size:11
Alignment explanation
Indices: 81261--81417 Score: 84
Period size: 11 Copynumber: 13.0 Consensus size: 11
81251 TCTATTTAAA
*
81261 TATTTAATCAT
1 TATTAAATCAT
*
81272 TATTAAATAAT
1 TATTAAATCAT
81283 TATTAGTAATCAT
1 TATTA--AATCAT
81296 TATTAAATCAT
1 TATTAAATCAT
81307 TAATATCAAATCAT
1 T-AT-T-AAATCAT
*
81321 TATTATAATTTTAT
1 TATTA-AA--TCAT
81335 TATTACTAATCAT
1 TATTA--AATCAT
*
81348 TACTAAATCAT
1 TATTAAATCAT
81359 TAGTATCAAATCAT
1 TA-T-T-AAATCAT
* *
81373 TA--AATATTAA
1 TATTAA-ATCAT
*
81383 TAATAAATCAT
1 TATTAAATCAT
81394 TATTAGTAATCAT
1 TATTA--AATCAT
*
81407 TACTAAATCAT
1 TATTAAATCAT
81418 ATCATTAATA
Statistics
Matches: 116, Mismatches: 13, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
9 2 0.02
10 5 0.04
11 43 0.37
12 7 0.06
13 31 0.27
14 25 0.22
15 3 0.03
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (11 bp):
TATTAAATCAT
Found at i:81292 original size:24 final size:23
Alignment explanation
Indices: 81261--81465 Score: 105
Period size: 24 Copynumber: 8.3 Consensus size: 23
81251 TCTATTTAAA
*
81261 TATT-TAATCATTATTAAATAAT
1 TATTATAATCATTATTAAATCAT
81283 TATTAGTAATCATTATTAAATCAT
1 TATTA-TAATCATTATTAAATCAT
* *
81307 TAATATCAAATCATTATTATAATTTTAT
1 TATTAT--AATCATTATTA-AA--TCAT
*
81335 TATTACTAATCATTACTAAATCAT
1 TATTA-TAATCATTATTAAATCAT
* *
81359 TAGTATCAA--ATCATTAAAT-AT
1 TATTAT-AATCATTATTAAATCAT
*
81380 TAATAATAAATCATTATTAGTAATCAT
1 T-ATTAT-AATCATTATTA--AATCAT
* *
81407 TACTAAATCATATCATTAATAAATCAT
1 TA-T-TAT-A-ATCATTATTAAATCAT
*
81434 TAAATATAAAATCATTATTAAAAT-AT
1 T--AT-TATAATCATTATT-AAATCAT
81460 TATTAT
1 TATTAT
81466 CAAATCATAA
Statistics
Matches: 143, Mismatches: 19, Indels: 41
0.70 0.09 0.20
Matches are distributed among these distances:
21 3 0.02
22 17 0.12
23 4 0.03
24 38 0.27
25 11 0.08
26 19 0.13
27 26 0.18
28 14 0.10
29 11 0.08
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.43
Consensus pattern (23 bp):
TATTATAATCATTATTAAATCAT
Found at i:81348 original size:52 final size:49
Alignment explanation
Indices: 81266--81374 Score: 155
Period size: 52 Copynumber: 2.2 Consensus size: 49
81256 TTAAATATTT
* *
81266 AATCATTATTAAATAATTATTAGTAATCATTATTAAATCATTAATATCA
1 AATCATTATTAAATAATTATTACTAATCATTACTAAATCATTAATATCA
* *
81315 AATCATTATTATAATTTTATTATTACTAATCATTACTAAATCATTAGTATCA
1 AATCATTATTA-AA--TAATTATTACTAATCATTACTAAATCATTAATATCA
81367 AATCATTA
1 AATCATTA
81375 AATATTAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 11 0.21
50 2 0.04
52 40 0.75
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (49 bp):
AATCATTATTAAATAATTATTACTAATCATTACTAAATCATTAATATCA
Found at i:81423 original size:16 final size:16
Alignment explanation
Indices: 81402--81433 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
81392 ATTATTAGTA
*
81402 ATCATTACTAAATCAT
1 ATCATTAATAAATCAT
81418 ATCATTAATAAATCAT
1 ATCATTAATAAATCAT
81434 TAAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTAATAAATCAT
Found at i:81463 original size:11 final size:12
Alignment explanation
Indices: 81266--81464 Score: 72
Period size: 11 Copynumber: 15.9 Consensus size: 12
81256 TTAAATATTT
81266 AATCATTATT-A
1 AATCATTATTAA
* *
81277 AATAATTATTAGT
1 AATCATTATTA-A
81290 AATCATTATT-A
1 AATCATTATTAA
*
81301 AATCATTAATATCA
1 AATCATT-AT-TAA
81315 AATCATTATTATA
1 AATCATTATTA-A
* * *
81328 ATTTTATTATTACT
1 A-ATCATTATTA-A
*
81342 AATCATTACT-A
1 AATCATTATTAA
*
81353 AATCATTAGTATCA
1 AATCATTA-T-TAA
81367 AATCATTA--AA
1 AATCATTATTAA
* * * *
81377 TATTAATAAT-A
1 AATCATTATTAA
*
81388 AATCATTATTAGT
1 AATCATTATTA-A
*
81401 AATCATTACT-A
1 AATCATTATTAA
81412 AATCATATCATTAATA
1 AATCAT-T-ATT-A-A
81428 AATCATTAAATATAA
1 AATCATT--AT-TAA
81443 AATCATTATTAA
1 AATCATTATTAA
81455 AAT-ATTATTA
1 AATCATTATTA
81465 TCAAATCATA
Statistics
Matches: 140, Mismatches: 27, Indels: 42
0.67 0.13 0.20
Matches are distributed among these distances:
10 6 0.04
11 44 0.31
12 10 0.07
13 34 0.24
14 26 0.19
15 9 0.06
16 10 0.07
17 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (12 bp):
AATCATTATTAA
Found at i:82929 original size:16 final size:16
Alignment explanation
Indices: 82910--82966 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 16
82900 CTAATATAAA
82910 TTAAACAAAATATTTT
1 TTAAACAAAATATTTT
82926 TTAAACAACAATAAATATTT
1 TTAAACAA-AAT--AT-TTT
*
82946 TTAAACTAAATATTTT
1 TTAAACAAAATATTTT
82962 TTAAA
1 TTAAA
82967 GGGAATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 16 0.44
17 5 0.14
19 5 0.14
20 10 0.28
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAACAAAATATTTT
Found at i:83092 original size:15 final size:16
Alignment explanation
Indices: 83067--83103 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
83057 TGTATTTATG
83067 TCTTCTTCCTTTC-TTT
1 TCTT-TTCCTTTCTTTT
83083 TCTTTTCCTTTCTTTT
1 TCTTTTCCTTTCTTTT
83099 TCTTT
1 TCTTT
83104 CTTCGAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
TCTTTTCCTTTCTTTT
Found at i:83481 original size:28 final size:30
Alignment explanation
Indices: 83433--83495 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
83423 AATTTTTATA
83433 TAATATAATATATAACTTAAACGAACAAAC
1 TAATATAATATATAACTTAAACGAACAAAC
* *
83463 TAATAT-A-ATATAACTTAAACTAGCAAAC
1 TAATATAATATATAACTTAAACGAACAAAC
83491 TAATA
1 TAATA
83496 ATTTCATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 24 0.77
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.29
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACGAACAAAC
Found at i:83611 original size:19 final size:20
Alignment explanation
Indices: 83562--83611 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
83552 AACTTATCTC
83562 CCTTTC-TTCTTCTTCCTTT
1 CCTTTCTTTCTTCTTCCTTT
*
83581 CCTTTCTCTCTTC-TCCATTT
1 CCTTTCTTTCTTCTTCC-TTT
83601 -CTTTCTTTCTT
1 CCTTTCTTTCTT
83612 TTGCTTCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (20 bp):
CCTTTCTTTCTTCTTCCTTT
Found at i:86594 original size:68 final size:64
Alignment explanation
Indices: 86474--86599 Score: 157
Period size: 68 Copynumber: 1.9 Consensus size: 64
86464 AAGATAATTA
*
86474 TATATACTTTTGAACATTTCAAATTAAAATAATATCTATTTAATTTTGAATAGTAAAATGTGAT
1 TATATACTTTTGAACATTTCAAATTAAAATAATATCTATTTAATTCTGAATAGTAAAATGTGAT
* *
86538 TATAT-CTTTTGAATATTTTAAATTAAAAGATATTATTATCTATTTACA-TCTGAATAGTAAAA
1 TATATACTTTTGAACATTTCAAATT-AAA-ATA--A-TATCTATTTA-ATTCTGAATAGTAAAA
86600 GATGTCTAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
63 17 0.32
64 8 0.15
65 3 0.06
67 1 0.02
68 23 0.43
69 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (64 bp):
TATATACTTTTGAACATTTCAAATTAAAATAATATCTATTTAATTCTGAATAGTAAAATGTGAT
Found at i:88242 original size:72 final size:67
Alignment explanation
Indices: 88146--88340 Score: 177
Period size: 65 Copynumber: 2.9 Consensus size: 67
88136 GTATGATAAT
* * *
88146 TACTCTTTGAATATGTCAATTTAAAAATATATTTATTATATTTTTAACTTTGAATATTAAAGATA
1 TACT-TTTGAATATTTCAAATTAAAAATA-A-TTATTATA-TTTTAA-TTTGAATATTAAAAATA
88211 ATTATACA
61 ATT-TACA
* * *
88219 TACTTTTGAATATTTCAAATT-AAAATAA-TA-TCTA-TTTAATTTTGAATAGTAAAAATTATTT
1 TACTTTTGAATATTTCAAATTAAAAATAATTATTATATTTTAA-TTTGAATATTAAAAATAATTT
*
88280 ATA
65 ACA
* *
88283 T-CTTTTGAATATTTTAAATTTAAAAATAATT-TTATATGCTTATATTTGAATATTAAAA
1 TACTTTTGAATATTTCAAA-TTAAAAATAATTATTATAT-TTTA-ATTTGAATATTAAAA
88341 TATATCTGTT
Statistics
Matches: 103, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
63 16 0.16
64 6 0.06
65 29 0.28
66 4 0.04
67 3 0.03
68 18 0.17
69 1 0.01
70 1 0.01
71 6 0.06
72 15 0.15
73 4 0.04
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (67 bp):
TACTTTTGAATATTTCAAATTAAAAATAATTATTATATTTTAATTTGAATATTAAAAATAATTTA
CA
Found at i:90019 original size:15 final size:16
Alignment explanation
Indices: 89989--90019 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
89979 GTGAGAATAA
89989 AAGATTACTAGGGAAT
1 AAGATTACTAGGGAAT
90005 AAGATTACT-GGGAAT
1 AAGATTACTAGGGAAT
90020 GTTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGATTACTAGGGAAT
Found at i:103488 original size:22 final size:21
Alignment explanation
Indices: 103438--103496 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
103428 ATATGGAAAA
103438 GAAAAGT-AATT-AAAAATAT
1 GAAAAGTAAATTCAAAAATAT
*
103457 -AAATAATAAATTCAAAAGATAT
1 GAAA-AGTAAATTCAAAA-ATAT
*
103479 GAAAAGTAAATCCAAAAA
1 GAAAAGTAAATTCAAAAA
103497 ACAATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 4 0.12
21 5 0.16
22 15 0.47
23 3 0.09
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.22
Consensus pattern (21 bp):
GAAAAGTAAATTCAAAAATAT
Found at i:104795 original size:29 final size:31
Alignment explanation
Indices: 104761--104836 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
104751 GTGTGAGCAC
*
104761 ATCTTAATTAAATAAAA-T-AGAGTGATCAT
1 ATCTTAATTAAATAAAATTAAAAGTGATCAT
104790 ATCTTAATTAAATAAAATTAAAAGTGATCAT
1 ATCTTAATTAAATAAAATTAAAAGTGATCAT
104821 ATCTTAATTAAATAAA
1 ATCTTAATTAAATAAA
104837 GTAAAAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 17 0.39
30 1 0.02
31 26 0.59
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (31 bp):
ATCTTAATTAAATAAAATTAAAAGTGATCAT
Found at i:106228 original size:180 final size:180
Alignment explanation
Indices: 105902--106745 Score: 1120
Period size: 180 Copynumber: 4.7 Consensus size: 180
105892 TGTCGGTTTA
* * * * **
105902 TGTCGATACTTTATAAAATATATCGATCCACATCAATATACCAGAAAAAAATATGACAAAACCGG
1 TGTCGATACTTTATAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGG
* *
105967 T-TACGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
66 TAT-CGAAAGGACAAAACCGGT-AAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
* * * *
106031 A-TATCTACACATTGTGAATTTAAAGGAGAAACAATTTTAGCGCCTATAAAG
129 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * * *
106082 TATCGATTCTTTATAAATATGTATCGATCCACAA-GATATAACAGGTAAATCA-ATGATAAAACC
1 TGTCGATACTTTATAAA-ATGTATCGATCCACAACGATATAACAGGTAAA-AATATGACAAAACC
* * * *
106145 GGTCTCGAGAA-GACAAAACCGGGTAAGGGCTA-CGGATATATTGAAAGTGTCAATACTGTAATA
64 GGTATCGA-AAGGACAAAACC-GGTAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
*
106208 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAATAGTTTTAGCGCCTAT-AAG
127 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * *
106261 TGTCGATATTTTATAACAATGTATCGATCTACAATGATATAACAGGTAAAAATATGACAAAA-CG
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * *
106325 GTATCTAAAGGACAAAACCGTTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
65 GTATCGAAAGGACAAAACCGGTA-AGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
106390 AGTATCGACACTTTGTGAATTTAAAAGAG-AACAGTTTTAGCGCCTATAAAG
129 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * *
106441 TGTCGATACTTTATAAAAATGTATCGATCAATAACGATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTAT-AAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * *
106506 GTATCTAAAGGACAAAA-CGGTATAGAGCGACCGAATATATTTAAAGTGTCGATACTTTAATATA
65 GTATCGAAAGGACAAAACCGGTA-AGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
106570 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
129 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* *
106622 TGTCGATACTTTATACAATGTATCGGTCCACAACG-TATAACA-GT-AAAATATGACAAAACCGG
1 TGTCGATACTTTATAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGG
* * * * *
106684 TCTCGAAATGACAAAATCGGTAAAGCGCTACCGGATATAATGAAAGTGTCGATACTTTAATA
66 TATCGAAAGGACAAAACCGGT-AAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
106746 AGTACGCGTA
Statistics
Matches: 593, Mismatches: 53, Indels: 38
0.87 0.08 0.06
Matches are distributed among these distances:
177 30 0.05
178 45 0.08
179 110 0.19
180 331 0.56
181 77 0.13
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (180 bp):
TGTCGATACTTTATAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGG
TATCGAAAGGACAAAACCGGTAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAG
TATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
Found at i:109079 original size:21 final size:21
Alignment explanation
Indices: 109049--109092 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
109039 AAGACAATCA
*
109049 AGAGTGGAAGAGACACTTGAG
1 AGAGTCGAAGAGACACTTGAG
109070 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGACACTTGAG
109091 AG
1 AG
109093 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.36, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGACACTTGAG
Found at i:109214 original size:32 final size:32
Alignment explanation
Indices: 109124--109216 Score: 161
Period size: 32 Copynumber: 2.9 Consensus size: 32
109114 AAATAGATGG
109124 AGTGGTGAAAGAA-TTGAGGTGTTGAAGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTG-AGGGTGA
109156 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGTGA
*
109188 AGTGGTGAAAGAAGTTGATGTGTTGAGGG
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGG
109217 GAACTTAAGA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 48 0.81
33 11 0.19
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGTGA
Found at i:113018 original size:23 final size:22
Alignment explanation
Indices: 112991--113033 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
112981 CAAAGAGGAC
112991 AAATCAAAGAAGATGGAGGAGAA
1 AAATC-AAGAAGATGGAGGAGAA
* *
113014 AAATCAAGCAGTTGGAGGAG
1 AAATCAAGAAGATGGAGGAG
113034 CAAATGAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.07, G:0.33, T:0.12
Consensus pattern (22 bp):
AAATCAAGAAGATGGAGGAGAA
Found at i:113737 original size:3 final size:3
Alignment explanation
Indices: 113729--113811 Score: 91
Period size: 3 Copynumber: 28.3 Consensus size: 3
113719 CATTTATATC
* * * *
113729 ATT ATT ATT AAT ATT ATT ATT ATC ATT ATT AAT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
113777 ATT ATT ATT A-T ATT ATT -TT TTT ATTT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT A
113812 AAATATTAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
2 6 0.09
3 58 0.87
4 3 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:115584 original size:12 final size:12
Alignment explanation
Indices: 115567--115605 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
115557 GGCGACTCAC
115567 AAATTATT-TTCA
1 AAATTATTATT-A
115579 AAATTATTATTA
1 AAATTATTATTA
*
115591 AAATTATAATTA
1 AAATTATTATTA
115603 AAA
1 AAA
115606 AGTACCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 23 0.92
13 2 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATTATTATTA
Found at i:116016 original size:17 final size:17
Alignment explanation
Indices: 115996--116041 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
115986 TCAAATTTTT
115996 TTATTTTTATTTATTTA
1 TTATTTTTATTTATTTA
*
116013 TTATTTTTATAATATTTA
1 TTATTTTTAT-TTATTTA
*
116031 -TATGTTTATTT
1 TTATTTTTATTT
116042 GCAAGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 18 0.72
18 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TTATTTTTATTTATTTA
Found at i:116060 original size:12 final size:14
Alignment explanation
Indices: 116035--116067 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
116025 TATTTATATG
116035 TTTATTTGCAAGTA
1 TTTATTTGCAAGTA
116049 TTTATTT-C-AGTA
1 TTTATTTGCAAGTA
116061 TTTATTT
1 TTTATTT
116068 ATGTCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 1 0.05
14 7 0.37
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (14 bp):
TTTATTTGCAAGTA
Found at i:126435 original size:30 final size:30
Alignment explanation
Indices: 126400--126465 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
126390 ATTATGCTTG
126400 AAGAAAAA-AGAAGAAAAAAAAAAA-AGAAAA
1 AAGAAAAATAGAA-AAAAAAAAAAAGA-AAAA
* *
126430 AAGAAAAATAGAAATAGAAAAAAAGAAAAA
1 AAGAAAAATAGAAAAAAAAAAAAAGAAAAA
126460 AAGAAA
1 AAGAAA
126466 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (30 bp):
AAGAAAAATAGAAAAAAAAAAAAAGAAAAA
Found at i:126462 original size:8 final size:8
Alignment explanation
Indices: 126403--126465 Score: 71
Period size: 8 Copynumber: 8.2 Consensus size: 8
126393 ATGCTTGAAG
126403 AAAAAAGA
1 AAAAAAGA
126411 AGAAAAA-A
1 A-AAAAAGA
126419 AAAAAAG-
1 AAAAAAGA
126426 AAAAAAGA
1 AAAAAAGA
*
126434 AAAATAG-
1 AAAAAAGA
*
126441 -AAATAGA
1 AAAAAAGA
126448 AAAAAAGA
1 AAAAAAGA
126456 AAAAAAGA
1 AAAAAAGA
126464 AA
1 AA
126466 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
6 6 0.12
7 12 0.25
8 25 0.52
9 5 0.10
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:127673 original size:50 final size:50
Alignment explanation
Indices: 127593--127795 Score: 343
Period size: 50 Copynumber: 4.1 Consensus size: 50
127583 GAAAGAGACT
127593 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
* *
127643 AATAACATCTTCTGGAAGTGCTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
*
127693 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
* * * *
127743 AATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
127793 AAT
1 AAT
127796 CAATCATTGA
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 145 1.00
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
Found at i:128874 original size:118 final size:119
Alignment explanation
Indices: 128509--129079 Score: 980
Period size: 119 Copynumber: 4.9 Consensus size: 119
128499 TAGCAAAGAT
128509 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
*
128574 ATCTGCAGAAGGAAGAAGAAGTTCATAATGAGAA-AAC-TGTTCAATCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
128626 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
*
128691 ATCTGCAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
*
128745 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAG-ACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
128809 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
128863 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
* *
128928 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
* * * * *
128982 TTGAATTCATC-AGTTGAGGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAA--C-TC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
*
129041 ATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
129080 CATCAAGAGC
Statistics
Matches: 439, Mismatches: 12, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
113 39 0.09
114 1 0.00
116 18 0.04
117 102 0.23
118 138 0.31
119 141 0.32
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (119 bp):
TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
Found at i:128923 original size:237 final size:237
Alignment explanation
Indices: 128509--129079 Score: 976
Period size: 237 Copynumber: 2.4 Consensus size: 237
128499 TAGCAAAGAT
*
128509 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAG-ACTCGTC
*
128574 ATCTGCAGAAGGAAGAAGAAGTTCATAATGAGAA-AAC-TGTTCAATCTTTTGCTTGAATTCATC
65 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATC
*
128637 AAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGCAGAAG
130 AAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
*
128702 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
195 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
128745 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGACTCGTCA
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGACTCGTCA
128810 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCA
66 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCA
128875 AATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
131 AATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
*
128940 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
196 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
128982 TTGAATTCATC-AGTTGAGGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGA-AC-TCA
1 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGACTCGTCA
*
129042 TCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
66 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
129080 CATCAAGAGC
Statistics
Matches: 321, Mismatches: 12, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
232 40 0.12
233 1 0.00
234 17 0.05
235 43 0.13
236 78 0.24
237 142 0.44
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (237 bp):
TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGACTCGTCA
TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCA
AATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:129335 original size:3 final size:3
Alignment explanation
Indices: 129329--129417 Score: 101
Period size: 3 Copynumber: 30.0 Consensus size: 3
129319 TTTATCCATT
* * * *
129329 TTA TTA TCA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
129377 TCA TTA TTA TT- TT- TTA TTA TTA TTT TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
129418 AATATATAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
2 4 0.06
3 65 0.90
4 3 0.04
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:129335 original size:12 final size:11
Alignment explanation
Indices: 129314--129387 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 11
129304 TGAAGATACT
*
129314 ATTTTTTTATCC
1 ATTTTATTAT-C
129326 ATTTTATTATC
1 ATTTTATTATC
129337 ATTATTATTAAT-
1 ATT-TTATT-ATC
129349 ATTATTATTATC
1 ATT-TTATTATC
129361 A--TTATTA--
1 ATTTTATTATC
*
129368 ATATTATTATC
1 ATTTTATTATC
129379 ATTATTATT
1 ATT-TTATT
129388 TTTTATTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
7 1 0.02
9 12 0.23
11 8 0.15
12 29 0.56
13 2 0.04
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTATTATC
Found at i:129397 original size:13 final size:13
Alignment explanation
Indices: 129379--129413 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
129369 TATTATTATC
129379 ATTATTATTTTTT
1 ATTATTATTTTTT
129392 ATTATTA-TTTTT
1 ATTATTATTTTTT
129404 ATTTATTATT
1 A-TTATTATT
129414 ATTAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 13 0.65
14 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTATTATTTTTT
Found at i:133734 original size:36 final size:37
Alignment explanation
Indices: 133689--133845 Score: 99
Period size: 36 Copynumber: 4.3 Consensus size: 37
133679 AGATGATTTG
133689 TCTCACTTGAGACTATTTTACTTAAAAGAAGA-TTTA
1 TCTCACTTGAGACTATTTTACTTAAAAGAAGACTTTA
* * * * * * * *
133725 TTTCCCTTGAGATTGTCATT-CTTAAAA-CAGACATTG
1 TCTCACTTGAGACTAT-TTTACTTAAAAGAAGACTTTA
* *
133761 TCTCACTTGAGACTGTTTTACTTGAAAGAAGA-TTTA
1 TCTCACTTGAGACTATTTTACTTAAAAGAAGACTTTA
* * ** * * *
133797 TTTCTCTCAAGA-TAATTTTTCTTAAAACAAGATTTTA
1 TCTCACTTGAGACT-ATTTTACTTAAAAGAAGACTTTA
*
133834 TCTCGCTTGAGA
1 TCTCACTTGAGA
133846 TAGTTTCCCT
Statistics
Matches: 87, Mismatches: 28, Indels: 11
0.69 0.22 0.09
Matches are distributed among these distances:
35 6 0.07
36 64 0.74
37 17 0.20
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (37 bp):
TCTCACTTGAGACTATTTTACTTAAAAGAAGACTTTA
Found at i:133819 original size:72 final size:72
Alignment explanation
Indices: 133686--133825 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 72
133676 TGCAGATGAT
** **
133686 TTGTCTCACTTGAGACTATTTTACTTAAAAGAAGATTTATTTCCCTTGAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTATTTTACTTAAAAGAAGATTTATTTCCCTCAAGATAATCATTCTTAAA
133751 ACAGACA
66 ACAGACA
* * * **
133758 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCTCTCAAGATAATTTTTCTTAAA
1 TTGTCTCACTTGAGACTATTTTACTTAAAAGAAGATTTATTTCCCTCAAGATAATCATTCTTAAA
133823 ACA
66 ACA
133826 AGATTTTATC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (72 bp):
TTGTCTCACTTGAGACTATTTTACTTAAAAGAAGATTTATTTCCCTCAAGATAATCATTCTTAAA
ACAGACA
Found at i:133967 original size:36 final size:36
Alignment explanation
Indices: 133927--133998 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
133917 ATTTGAAATG
* *
133927 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
*
133963 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
133999 TAAACATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
Found at i:134043 original size:101 final size:101
Alignment explanation
Indices: 133828--134268 Score: 660
Period size: 101 Copynumber: 4.4 Consensus size: 101
133818 TTAAAACAAG
* * * * *
133828 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAGAAAATTTTGTCTCCCTTGAGATAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTG-AA-A-CAAATTTTGTCTCCCTTGAGACAGTTTCT
**
133893 CTTGAAACAT----ATTGAAAACATTTCATTTGAAATGA
63 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
133928 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
133993 GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
134029 ATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC---AAATTTTGTCTCCCTTGAGACAGTTTCT
*
134094 TTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
63 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
134133 A--TTGTCTCTCTTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTATCTT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
* *
134196 GAAACATAAACGTTGAAAACATTTCCCTTGAAATGT
66 GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
134232 ATTTTGTCTCTCTTGAGATAATTTCCCTTGAAACAAA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
134269 ACCTTTGAAA
Statistics
Matches: 317, Mismatches: 15, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
97 37 0.12
98 1 0.00
99 66 0.21
100 27 0.09
101 90 0.28
102 29 0.09
104 67 0.21
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (101 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:134182 original size:36 final size:34
Alignment explanation
Indices: 134117--134184 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
134107 CATTGAAAAC
** *
134117 ATTTCCCTTGAAATGAATTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTGTCTCCCTTGAGATA
134151 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 ATTTCCCTTGAAACAAA--TTGTCTCCCTTGAGA
134185 CAGTTTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 15 0.52
36 14 0.48
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (34 bp):
ATTTCCCTTGAAACAAATTGTCTCCCTTGAGATA
Found at i:134198 original size:203 final size:200
Alignment explanation
Indices: 133828--134266 Score: 709
Period size: 203 Copynumber: 2.2 Consensus size: 200
133818 TTAAAACAAG
* * * *
133828 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAGAAAATTTTGTCTCCCTTGAGATAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
133893 CTTGAAACATATTGAAAACATTTCATTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
66 CTTGAAACATATTGAAAACATTTCACTTGAAATGAA-TTTGTCTCTCTTGAGATAATTTCCCTTG
*
133958 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
130 AAACAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAACATTTCCCTTG
134023 AAATGA
195 AAATGA
134029 ATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
134094 TTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA-TTGTCTCTCTTGAGATAATTTCCC
66 CTTGAAACAT----ATTGAAAACATTTCACTTGAAATGAATTTGTCTCTCTTGAGATAATTTCCC
*
134158 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACGTTGAAAACATTTCCC
127 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAACATTTCCC
*
134223 TTGAAATGT
192 TTGAAATGA
* *
134232 ATTTTGTCTCTCTTGAGATAATTTCCCTTGAAACA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACA
134267 AAACCTTTGA
Statistics
Matches: 221, Mismatches: 13, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
201 70 0.32
203 127 0.57
205 24 0.11
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (200 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
CTTGAAACATATTGAAAACATTTCACTTGAAATGAATTTGTCTCTCTTGAGATAATTTCCCTTGA
AACAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAACATTTCCCTTGA
AATGA
Found at i:134565 original size:2 final size:2
Alignment explanation
Indices: 134558--134597 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
134548 TATACGTTAC
134558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
134598 ATAAACACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:135883 original size:2 final size:2
Alignment explanation
Indices: 135876--135900 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
135866 TAATGTTGTT
135876 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 T
135901 TTATTCCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:136720 original size:22 final size:24
Alignment explanation
Indices: 136669--136720 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
136659 CTTTGTGAGT
136669 GATATTTAAAATATTTCATGATAA
1 GATATTTAAAATATTTCATGATAA
*
136693 GATATTT-AAATATTTCATGA-CA
1 GATATTTAAAATATTTCATGATAA
136715 GATATT
1 GATATT
136721 CTGATAAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 7 0.26
23 13 0.48
24 7 0.26
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (24 bp):
GATATTTAAAATATTTCATGATAA
Found at i:137702 original size:199 final size:199
Alignment explanation
Indices: 137286--137970 Score: 745
Period size: 199 Copynumber: 3.4 Consensus size: 199
137276 ATATTTTTTC
* * * *
137286 TAAAAGTATCGA-CACAAAAAACATTGAAACCAATAATTATAAAT-TAATAGGTAAATTAACAAT
1 TAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTAT-AATGTAATAGGTAAATTTACAAT
* * * * * **
137349 GTAACCGGTATAAATATATCGG--TTAATTAGAAAACATGTCAACATAATGTATC-GACACTTGT
65 GTAACCGGTATAAATATACCGGTTTTAA--AGAAAATAGGTCATCATAAAGTATCAG-CACTAAT
137411 GT-AATTTGTGTCGATACTTATTTTCCAGAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTC
127 -TAAATTTGTGTCGATACTTA-TTTCCAGAATGAATG-CCAAACGAGGTGCACGCATAAAGTGTC
* *
137475 GATACAATTAT
189 AATACATTTAT
* *
137486 TAAAAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAATATGTAAATTTACAATG
1 TAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG
*
137550 TAACCGGTATAAATATACTGGTTTTAAGAGAAAATAGGTCATCATAAAGTATCAGCACTAATTAA
66 TAACCGGTATAAATATACCGGTTTTAA-AGAAAATAGGTCATCATAAAGTATCAGCACTAATTAA
* * * *
137615 ATTTATGTCGATACATT-TTATCCATAATGAATGCCAAATG-GGTGCACACATAAAGTGTCAATA
130 ATTTGTGTCGATAC-TTATT-TCCAGAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCAATA
137678 CATTTAT
193 CATTTAT
* *
137685 TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTACAATGTGATAGGTAAATTTACAATG
1 TAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG
* * * * * ** **
137749 TAATCGATAGAAATATACCGGTTTTATAAAAAAATAGGTC-TAAATAATA-TATCAATACTCTTT
66 TAACCGGTATAAATATACCGGTTTTA-AAGAAAATAGGTCAT-CATAA-AGTATCAGCACTAATT
* * * * *
137812 AAGTTTGTGCCGATACTTGTTTCCAGAATGAATACCCAACGAGGTGCACGCATAAAGTGT-ATAT
128 AAATTTGTGTCGATACTTATTTCCAGAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCA-AT
137876 ACATTTA-
192 ACATTTAT
* * *
137883 -AAATTGTATCCAT-CCAAAAAACATGGAAACCGATAATTATAATGTAATAGGTAAATTTACAAT
1 TAAA-AGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAAT
* * *
137946 ATTACTGGTATAAATATACCGGTTT
65 GTAACCGGTATAAATATACCGGTTT
137971 ACTTATAAAA
Statistics
Matches: 414, Mismatches: 54, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
197 5 0.01
198 94 0.23
199 173 0.42
200 76 0.18
201 59 0.14
202 7 0.02
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (199 bp):
TAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG
TAACCGGTATAAATATACCGGTTTTAAAGAAAATAGGTCATCATAAAGTATCAGCACTAATTAAA
TTTGTGTCGATACTTATTTCCAGAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCAATACAT
TTAT
Found at i:138017 original size:23 final size:23
Alignment explanation
Indices: 137988--138040 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
137978 AAATAAGTCA
137988 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
138011 ATATAAGCGCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
138034 ATATAAG
1 ATATAAG
138041 TGATACCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:138047 original size:23 final size:23
Alignment explanation
Indices: 137988--138049 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
137978 AAATAAGTCA
137988 ATATAAGC-ACTACCTATTACATT
1 ATATAAGCGA-TACCTATTACATT
*
138011 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGATACCTATTACATT
*
138034 ATATAAGTGATACCTA
1 ATATAAGCGATACCTA
138050 ATATGTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (23 bp):
ATATAAGCGATACCTATTACATT
Found at i:138109 original size:87 final size:87
Alignment explanation
Indices: 138008--138173 Score: 287
Period size: 87 Copynumber: 1.9 Consensus size: 87
137998 TACCTATTAC
*
138008 ATTATATAAGCGCTACCTATTACATTATATAAGTGATACCTAATATGTTATTATACTTGATAATA
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTATACTTGATAATA
138073 TTTCCGGTTAAATGCTTATTTT
66 TTTCCGGTTAAATGCTTATTTT
* * * *
138095 ATTATATAATCGCTACCTATTATATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATA
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTATACTTGATAATA
138160 TTTCCGGTTAAATG
66 TTTCCGGTTAAATG
138174 ATATAATATA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (87 bp):
ATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTATACTTGATAATA
TTTCCGGTTAAATGCTTATTTT
Found at i:138115 original size:23 final size:23
Alignment explanation
Indices: 138089--138145 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
138079 GTTAAATGCT
* *
138089 TATTTTATTATATAATCGCTACC
1 TATTATATTATATAAGCGCTACC
138112 TATTATATTATATAAGCGCTACC
1 TATTATATTATATAAGCGCTACC
* *
138135 TAATATGTTAT
1 TATTATATTAT
138146 TGTACTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (23 bp):
TATTATATTATATAAGCGCTACC
Found at i:142880 original size:22 final size:22
Alignment explanation
Indices: 142863--142929 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
142853 CTCGTATAAA
142863 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
142885 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
142907 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
142929 T
1 T
142930 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:143868 original size:18 final size:18
Alignment explanation
Indices: 143847--143881 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
143837 TCCCCTCTAG
143847 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
143865 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
143882 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:144496 original size:20 final size:20
Alignment explanation
Indices: 144468--144507 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
144458 CATATTCGCT
* *
144468 TGAAGGGGTATCGGTTCCCC
1 TGAAGGGGTACCGATTCCCC
*
144488 TGAATGGGTACCGATTCCCC
1 TGAAGGGGTACCGATTCCCC
144508 CTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (20 bp):
TGAAGGGGTACCGATTCCCC
Found at i:147633 original size:22 final size:22
Alignment explanation
Indices: 147616--147681 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
147606 CTCGTATAAA
147616 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
147638 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
147660 TGCACTGAAGTG-CCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
147681 T
1 T
147682 ATGTCCATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 10 0.23
22 33 0.77
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:148616 original size:18 final size:18
Alignment explanation
Indices: 148595--148629 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
148585 TCCCCTCTAG
148595 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
148613 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
148630 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:149258 original size:22 final size:21
Alignment explanation
Indices: 149212--149254 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
149202 TTCATATTCG
* *
149212 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
149233 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
149254 C
1 C
149255 CTTGCCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:150728 original size:35 final size:35
Alignment explanation
Indices: 150677--150752 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
150667 TTTCGATGTA
*
150677 TTGATTGAAATTACATGAAAGAAGTTTCCTCCTTC
1 TTGACTGAAATTACATGAAAGAAGTTTCCTCCTTC
*
150712 TTGACTGAAATTACATGAAAGAAGTTTCCTCTTTC
1 TTGACTGAAATTACATGAAAGAAGTTTCCTCCTTC
150747 TTGACT
1 TTGACT
150753 TTAATATGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (35 bp):
TTGACTGAAATTACATGAAAGAAGTTTCCTCCTTC
Found at i:151865 original size:13 final size:13
Alignment explanation
Indices: 151847--151873 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
151837 TTACAGACAC
151847 GCATATGAAGACT
1 GCATATGAAGACT
151860 GCATATGAAGACT
1 GCATATGAAGACT
151873 G
1 G
151874 TTTAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:157533 original size:15 final size:16
Alignment explanation
Indices: 157513--157543 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
157503 TATGAGTAGG
157513 CACAAGT-AAATTTCA
1 CACAAGTAAAATTTCA
157528 CACAAGTAAAATTTCA
1 CACAAGTAAAATTTCA
157544 GGTGGACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (16 bp):
CACAAGTAAAATTTCA
Found at i:158342 original size:36 final size:35
Alignment explanation
Indices: 158302--158383 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 35
158292 CAATTTCAAA
* *
158302 CATTAGTCAATGATTTATAAAG-TACTTATTATTAGT
1 CATTAGTCAATG-GTTATAAAGTTA-GTATTATTAGT
*
158338 CATTAGCCAATGGTTATAAAGTTTAGTATTATTAGT
1 CATTAGTCAATGGTTATAAAG-TTAGTATTATTAGT
158374 CATTA-TCAAT
1 CATTAGTCAAT
158384 CCCTGATTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 12 0.30
36 26 0.65
37 2 0.05
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (35 bp):
CATTAGTCAATGGTTATAAAGTTAGTATTATTAGT
Found at i:159992 original size:42 final size:41
Alignment explanation
Indices: 159887--159994 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
159877 GTAATAAAGT
* * **
159887 TCAATGCACCAACCTTATCC-CGTATACTTCTCGAGTAAAGT
1 TCAATGCACCAACCTTA-CCTCGTATACTTATCGAGCAAAAC
* * *
159928 TTAACGCACCAACCTTATCTCGTATACTTATCGGAGCAAAAC
1 TCAATGCACCAACCTTACCTCGTATACTTATC-GAGCAAAAC
*
159970 TCAATGTACCAACCTTACCTCGTAT
1 TCAATGCACCAACCTTACCTCGTAT
159995 CTCTTATAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
40 1 0.02
41 26 0.48
42 27 0.50
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.29
Consensus pattern (41 bp):
TCAATGCACCAACCTTACCTCGTATACTTATCGAGCAAAAC
Found at i:171114 original size:19 final size:18
Alignment explanation
Indices: 171090--171129 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
171080 AAATGGGGGA
171090 AATGAGGAACGAATTTGGG
1 AATGAGGAACGAA-TTGGG
*
171109 AATGAGGAATGAATTGGG
1 AATGAGGAACGAATTGGG
171127 AAT
1 AAT
171130 TTAGAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.40, C:0.03, G:0.35, T:0.23
Consensus pattern (18 bp):
AATGAGGAACGAATTGGG
Found at i:173421 original size:10 final size:10
Alignment explanation
Indices: 173406--173434 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
173396 GATACTTTAC
173406 CAAAAATATT
1 CAAAAATATT
173416 CAAAAATATT
1 CAAAAATATT
173426 -AAAAATATT
1 CAAAAATATT
173435 AATATTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (10 bp):
CAAAAATATT
Found at i:173429 original size:9 final size:9
Alignment explanation
Indices: 173407--173436 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
173397 ATACTTTACC
173407 AAAAATATT
1 AAAAATATT
173416 CAAAAATATT
1 -AAAAATATT
173426 AAAAATATT
1 AAAAATATT
173435 AA
1 AA
173437 TATTTTACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATATT
Found at i:173451 original size:21 final size:21
Alignment explanation
Indices: 173425--173464 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
173415 TCAAAAATAT
*
173425 TAAAAATATTAATATTTTACG
1 TAAAAATAATAATATTTTACG
173446 TAAAAATAATAATATTTTA
1 TAAAAATAATAATATTTTA
173465 GATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAAATAATAATATTTTACG
Found at i:183490 original size:36 final size:36
Alignment explanation
Indices: 183450--183518 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
183440 GATGTTTGGG
* * *
183450 AATCATCGATATCGGTATCACTGAACGACCCTTCGA
1 AATCAACGACATCAGTATCACTGAACGACCCTTCGA
*
183486 AATCAACGGCATCAGTATCACTGAACGACCCTT
1 AATCAACGACATCAGTATCACTGAACGACCCTT
183519 TGATTGTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (36 bp):
AATCAACGACATCAGTATCACTGAACGACCCTTCGA
Found at i:189159 original size:18 final size:21
Alignment explanation
Indices: 189109--189161 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
189099 GTGACGTTTA
189109 TATTATAATAATATTATATAT
1 TATTATAATAATATTATATAT
*
189130 TATATATCATAATATTAT-T-T
1 TAT-TATAATAATATTATATAT
189150 TATTA-AATAATA
1 TATTATAATAATA
189162 CAAATGGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 4 0.14
21 4 0.14
22 13 0.45
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTATAATAATATTATATAT
Found at i:190378 original size:7 final size:8
Alignment explanation
Indices: 190348--190375 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
190338 GGATTAATTA
190348 ATTTTAAT
1 ATTTTAAT
190356 ATTTTAAT
1 ATTTTAAT
190364 ATTTTAAT
1 ATTTTAAT
190372 ATTT
1 ATTT
190376 AATTACACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
ATTTTAAT
Found at i:196638 original size:65 final size:65
Alignment explanation
Indices: 196567--196692 Score: 243
Period size: 65 Copynumber: 1.9 Consensus size: 65
196557 GAAAAACCTG
196567 ATTAGATATGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGATCTA
1 ATTAGATATGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGATCTA
*
196632 ATTAGATATGGAGACATGAAATGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGA
1 ATTAGATATGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGA
196693 GATGATTTGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (65 bp):
ATTAGATATGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGATCTA
Found at i:196710 original size:65 final size:65
Alignment explanation
Indices: 196567--196756 Score: 224
Period size: 65 Copynumber: 2.9 Consensus size: 65
196557 GAAAAACCTG
* * **
196567 ATTAGATATGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGATCTA
1 ATTAGATAGGGAGACATGAAAAGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGAGATA
* * *
196632 ATTAGATATGGAGACATGAAATGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGAGATG
1 ATTAGATAGGGAGACATGAAAAGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGAGATA
* * * * *
196697 ATTTGA-AGGGGAGATAT-AAAAGAAATTAGAATAAATCATTCTTGTGA-TGTGTTTCAAGAG
1 ATTAGATA-GGGAGACATGAAAAG-AATTAGGATAAATCCTTCTTGTGAGT-TATTTCAAGAG
196757 TCAAATCAGA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
64 6 0.05
65 105 0.95
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (65 bp):
ATTAGATAGGGAGACATGAAAAGAATTAGGATAAATCCTTCTTGTGAGTTATTTCAAGAGAGATA
Found at i:198234 original size:16 final size:16
Alignment explanation
Indices: 198215--198265 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 16
198205 CGAGTGATGT
198215 TTATATTATAATAATA
1 TTATATTATAATAATA
198231 TTATATATATATCATAATA
1 TTATAT-TATA--ATAATA
198250 TTATTATTA-AATAATA
1 TTA-TATTATAATAATA
198266 CAAATGGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 12 0.39
17 4 0.13
18 1 0.03
19 11 0.35
20 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATATTATAATAATA
Found at i:198249 original size:19 final size:18
Alignment explanation
Indices: 198216--198265 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
198206 GAGTGATGTT
198216 TATATTATAATAATATTA
1 TATATTATAATAATATTA
*
198234 TATATATATCATAATATTA
1 TATAT-TATAATAATATTA
198253 T-TATTA-AATAATA
1 TATATTATAATAATA
198266 CAAATGGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 6 0.21
17 2 0.07
18 8 0.28
19 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTATAATAATATTA
Found at i:199373 original size:2 final size:2
Alignment explanation
Indices: 199366--199400 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
199356 TAGTCCTTAA
199366 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 A
199401 GGTTAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:200952 original size:5 final size:5
Alignment explanation
Indices: 200942--200966 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
200932 TTAGTTGGTT
200942 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
200967 GGGTACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:203295 original size:22 final size:22
Alignment explanation
Indices: 203251--203297 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
203241 ACTAATACTC
* *
203251 AGGGAAGTATCGATATCATAGG
1 AGGGAAGTATAGATACCATAGG
203273 AGGGAAGTATAGATACC-TAAGG
1 AGGGAAGTATAGATACCAT-AGG
203295 AGG
1 AGG
203298 AGTATCGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.19
Consensus pattern (22 bp):
AGGGAAGTATAGATACCATAGG
Found at i:209019 original size:42 final size:42
Alignment explanation
Indices: 208931--209069 Score: 102
Period size: 42 Copynumber: 3.3 Consensus size: 42
208921 AATAGCGACG
* * * * * *
208931 TTTGTGGTAAAAATGTCACAAAAAATAATA-TA-TAGCGGCGT
1 TTTGTAGTAAAAATATCACTAAAAACAATAGAATTAGCGGC-A
* *
208972 TTTGTATTAAAAATATCACTAAAAACAATAGCATTAGCGGCA
1 TTTGTAGTAAAAATATCACTAAAAACAATAGAATTAGCGGCA
* * * * * * *
209014 TTTGTAGCAAAAACACCACTAAAGACAAGAGAATTACCGGCG
1 TTTGTAGTAAAAATATCACTAAAAACAATAGAATTAGCGGCA
* *
209056 TTTGTGGCAAAAAT
1 TTTGTAGTAAAAAT
209070 GCCATTAAAG
Statistics
Matches: 78, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
41 25 0.32
42 46 0.59
43 7 0.09
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (42 bp):
TTTGTAGTAAAAATATCACTAAAAACAATAGAATTAGCGGCA
Found at i:209091 original size:42 final size:42
Alignment explanation
Indices: 208988--209084 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
208978 TTAAAAATAT
* * * *
208988 CACTAAAAACAATAGCATTAGCGGCATTTGTAGCAAAAACAC
1 CACTAAAGACAAGAGAATTACCGGCATTTGTAGCAAAAACAC
* * **
209030 CACTAAAGACAAGAGAATTACCGGCGTTTGTGGCAAAAATGC
1 CACTAAAGACAAGAGAATTACCGGCATTTGTAGCAAAAACAC
*
209072 CATTAAAGACAAG
1 CACTAAAGACAAG
209085 CAAATTAGCG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (42 bp):
CACTAAAGACAAGAGAATTACCGGCATTTGTAGCAAAAACAC
Found at i:214020 original size:29 final size:30
Alignment explanation
Indices: 213988--214049 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
213978 ATAAATGAAT
*
213988 AAAATTT-ATTGTTCTTGTTCGTTCATTAA
1 AAAATTTAATTGTTCGTGTTCGTTCATTAA
214017 AAAATTTAGATTGTTCGTGTTCGTTCATTAA
1 AAAATTTA-ATTGTTCGTGTTCGTTCATTAA
214048 AA
1 AA
214050 TGATAAACGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 7 0.23
31 23 0.77
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (30 bp):
AAAATTTAATTGTTCGTGTTCGTTCATTAA
Found at i:214080 original size:24 final size:24
Alignment explanation
Indices: 214052--214098 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
214042 CATTAAAATG
* * *
214052 ATAAACGAAGACAAATGAATGAAT
1 ATAAACAAACACAAACGAATGAAT
214076 ATAAACAAACACAAACGAATGAA
1 ATAAACAAACACAAACGAATGAA
214099 CGTAAAATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (24 bp):
ATAAACAAACACAAACGAATGAAT
Found at i:214104 original size:24 final size:24
Alignment explanation
Indices: 214052--214104 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
214042 CATTAAAATG
* * * *
214052 ATAAACGAAGACAAATGAATGAAT
1 ATAAACAAACACAAACGAATGAAC
214076 ATAAACAAACACAAACGAATGAAC
1 ATAAACAAACACAAACGAATGAAC
*
214100 GTAAA
1 ATAAA
214105 ATGAATTGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (24 bp):
ATAAACAAACACAAACGAATGAAC
Found at i:219894 original size:36 final size:36
Alignment explanation
Indices: 219854--219962 Score: 155
Period size: 36 Copynumber: 3.0 Consensus size: 36
219844 TATTTTAAGG
219854 ATGAGGTTGGATTAAATTTGGATTTATGATGAAGAA
1 ATGAGGTTGGATTAAATTTGGATTTATGATGAAGAA
219890 ATGAGGTTGGATTAAATTTGGATTTATGATGAAGAA
1 ATGAGGTTGGATTAAATTTGGATTTATGATGAAGAA
* *** * * *
219926 AAGAGGTCATATCAATTTTGAATTTATGATGAAGAA
1 ATGAGGTTGGATTAAATTTGGATTTATGATGAAGAA
219962 A
1 A
219963 AACTAACTCG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (36 bp):
ATGAGGTTGGATTAAATTTGGATTTATGATGAAGAA
Found at i:225272 original size:2 final size:2
Alignment explanation
Indices: 225265--225293 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
225255 AAACTCCATA
225265 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
225294 ACTAGGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:227836 original size:16 final size:16
Alignment explanation
Indices: 227795--227836 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
227785 AATATGATAT
*
227795 TAATTTAATTGGATTA
1 TAATTGAATTGGATTA
*
227811 -ATTTGTAATTGGATTA
1 TAATTG-AATTGGATTA
227827 TAATTGAATT
1 TAATTGAATT
227837 AAGTTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (16 bp):
TAATTGAATTGGATTA
Found at i:229229 original size:36 final size:37
Alignment explanation
Indices: 229115--229237 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 37
229105 ATTAAACCCT
* *
229115 AAACCATAAAACATTACATTAAAGAGATAAAAACAAC
1 AAACCATAACACATTACATTAAGGAGATAAAAACAAC
*
229152 AAACCATAA-ACATTACATTAAGAAGATAAAAACAAC
1 AAACCATAACACATTACATTAAGGAGATAAAAACAAC
* * * *
229188 AAACC-TAACACATTACGTTAAGGACATAAATACAAT
1 AAACCATAACACATTACATTAAGGAGATAAAAACAAC
*
229224 AAACCTTACACACA
1 AAACCATA-ACACA
229238 CACCTTAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 3 0.04
36 57 0.75
37 11 0.14
38 5 0.07
ACGTcount: A:0.57, C:0.20, G:0.06, T:0.18
Consensus pattern (37 bp):
AAACCATAACACATTACATTAAGGAGATAAAAACAAC
Found at i:232320 original size:3 final size:3
Alignment explanation
Indices: 232306--232365 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
232296 CTTATCATTC
* *
232306 TCT TCT TAT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCCT ACT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT
*
232352 TAT TCAT TCT TCT T
1 TCT TC-T TCT TCT T
232366 TTGGAGTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 44 0.90
4 5 0.10
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Done.