Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008722.1 Hibiscus syriacus cultivar Beakdansim tig00111780_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: 447499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:2106 original size:10 final size:10
Alignment explanation
Indices: 2091--2116 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2081 TTAAAGAAAA
2091 AAACGGTCAC
1 AAACGGTCAC
2101 AAACGGTCAC
1 AAACGGTCAC
2111 AAACGG
1 AAACGG
2117 CTATATTAAC
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:0.42, C:0.27, G:0.23, T:0.08
Consensus pattern (10 bp):
AAACGGTCAC
Found at i:2191 original size:23 final size:24
Alignment explanation
Indices: 2147--2199 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
2137 TTAAACCCAG
***
2147 ACCGGTTTTTTTTTCGGAT-AAAA
1 ACCGGTTTTTTAACCGGATAAAAA
*
2170 ACCGGTTTTTTAACCGGTTAAAAA
1 ACCGGTTTTTTAACCGGATAAAAA
2194 ACCGGT
1 ACCGGT
2200 CTGGGTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
ACCGGTTTTTTAACCGGATAAAAA
Found at i:12176 original size:44 final size:44
Alignment explanation
Indices: 12113--12206 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
12103 TACACCAATA
* *
12113 ACAGTACATAAAACTTAAAAACATCCCCTGCCATAAAAGCCTTT
1 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAGCCTTC
12157 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAGCCTTC
1 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAGCCTTC
12201 ACAGTA
1 ACAGTA
12207 GACCAGAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (44 bp):
ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAGCCTTC
Found at i:16938 original size:30 final size:31
Alignment explanation
Indices: 16875--16935 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
16865 ACAGTCTTCT
* * *
16875 AACATTTATTCTGTTTGCAATATTGTCCCCC
1 AACATTTATTCCGTTTGAAATATGGTCCCCC
16906 AACATTTATTCCGTTTGAAATATGGTCCCC
1 AACATTTATTCCGTTTGAAATATGGTCCCC
16936 AACTTAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (31 bp):
AACATTTATTCCGTTTGAAATATGGTCCCCC
Found at i:18487 original size:37 final size:37
Alignment explanation
Indices: 18418--18488 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
18408 AATATTTATG
**
18418 ATGTTTTGATTGAGTTGTATTCGGTGAGTTTTTTTTT
1 ATGTTTTGATTGAGTTGTATTCAATGAGTTTTTTTTT
18455 ATGTTTTGATTGAGTTGTATTCAATGA-TTTTTTT
1 ATGTTTTGATTGAGTTGTATTCAATGAGTTTTTTT
18489 GATTGAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.17, C:0.03, G:0.21, T:0.59
Consensus pattern (37 bp):
ATGTTTTGATTGAGTTGTATTCAATGAGTTTTTTTTT
Found at i:22568 original size:29 final size:29
Alignment explanation
Indices: 22531--22600 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
22521 TTCAATATGT
22531 GTTGATAGATGTTA-ACT-TCCATTTTTTGA
1 GTTGATAGATGTTACA-TAT-CATTTTTTGA
*
22560 GTTGATAGATGTTACATATCATTTTTTGT
1 GTTGATAGATGTTACATATCATTTTTTGA
*
22589 GTTGATAAATGT
1 GTTGATAGATGT
22601 AAAGTGCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.49
Consensus pattern (29 bp):
GTTGATAGATGTTACATATCATTTTTTGA
Found at i:22735 original size:71 final size:72
Alignment explanation
Indices: 22618--22762 Score: 229
Period size: 71 Copynumber: 2.0 Consensus size: 72
22608 CATCTTTAGT
*
22618 GTCATTTTTTGTATATGGCATAGTGACTTAGGCAATATGGTATGGTTGCCAAAACATATACCACG
1 GTCATTTTTTGTATATGGCATAGTGACTTAGGCAATATGGTATGGTTGCCAAAACATATACAACG
22683 ATATATG
66 ATATATG
* * * * *
22690 GTCATTTTTTGTATAT-GCATAGTGGCTTAGTCAATATGGTATGGTTGTCAAACCATATACAATG
1 GTCATTTTTTGTATATGGCATAGTGACTTAGGCAATATGGTATGGTTGCCAAAACATATACAACG
22754 ATATATG
66 ATATATG
22761 GT
1 GT
22763 AACATTTGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
71 51 0.76
72 16 0.24
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (72 bp):
GTCATTTTTTGTATATGGCATAGTGACTTAGGCAATATGGTATGGTTGCCAAAACATATACAACG
ATATATG
Found at i:25597 original size:35 final size:35
Alignment explanation
Indices: 25547--25621 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
25537 TTCATGCTCA
* *
25547 AAATTCCAAAGTAATTCAATTTCATTCTAAACCTT
1 AAATTCCAAAATAATTCAATTACATTCTAAACCTT
*
25582 AAATTTCAAAATAATTCAATTACATTCTAAACCTT
1 AAATTCCAAAATAATTCAATTACATTCTAAACCTT
25617 AAATT
1 AAATT
25622 GAAGTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.37
Consensus pattern (35 bp):
AAATTCCAAAATAATTCAATTACATTCTAAACCTT
Found at i:25698 original size:35 final size:35
Alignment explanation
Indices: 25617--25729 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
25607 TCTAAACCTT
* *
25617 AAATTGAAGTATTTTAGAATTTGGGGGTTTAGAATT
1 AAATTGAATTATTTTAGAATTT-GGGGTTTAGAATA
* * * *
25653 TAATTAAATTATTTTAGAATTTAGGATTTAGAATA
1 AAATTGAATTATTTTAGAATTTGGGGTTTAGAATA
* *
25688 AAATTGAATTACTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAGAATA
25723 AAATTGA
1 AAATTGA
25730 GGACTATTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
35 46 0.71
36 19 0.29
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGGGGTTTAGAATA
Found at i:27175 original size:23 final size:21
Alignment explanation
Indices: 27149--27190 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
27139 TATAAAAAAT
27149 TATTTTTGATTAAATATTTTTGG
1 TATTTTT-ATTAAAT-TTTTTGG
*
27172 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
27191 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:27622 original size:45 final size:45
Alignment explanation
Indices: 27541--27698 Score: 271
Period size: 45 Copynumber: 3.5 Consensus size: 45
27531 TAGATGGGCA
* * * *
27541 ACGTTACATGGATAATATCAACATTTGAATAGTTTAAAGACAGCC
1 ACGTTACATGGATAATATCCACACTTGGATACTTTAAAGACAGCC
27586 ACGTTACATGGATAATATCCACACTTGGATACTTTAAAGACAGCC
1 ACGTTACATGGATAATATCCACACTTGGATACTTTAAAGACAGCC
27631 ACGTTACATGGATAATATCCACACTTGGATACTTTAAAGACAGCC
1 ACGTTACATGGATAATATCCACACTTGGATACTTTAAAGACAGCC
*
27676 ACGTGACATGGATAATATCCACA
1 ACGTTACATGGATAATATCCACA
27699 TTTGAATTGG
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 108 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (45 bp):
ACGTTACATGGATAATATCCACACTTGGATACTTTAAAGACAGCC
Found at i:30613 original size:2 final size:2
Alignment explanation
Indices: 30606--30634 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30596 ATCAAGCCAC
30606 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30635 TTCTCATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33002 original size:19 final size:18
Alignment explanation
Indices: 32962--33011 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
32952 TATAAATTCT
*
32962 AATATTTTAAAAGTTATAA
1 AATATTTT-AAATTTATAA
* *
32981 AATTTTGTTAAATTTATTA
1 AATATT-TTAAATTTATAA
33000 AATATTTTAAAT
1 AATATTTTAAAT
33012 AATTTTAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.23
19 18 0.69
20 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
AATATTTTAAATTTATAA
Found at i:33113 original size:19 final size:18
Alignment explanation
Indices: 33067--33114 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
33057 TAATTTTTTG
*
33067 GTTATTAACTTTTTAAAA
1 GTTATTAAATTTTTAAAA
* *
33085 GTTATAAAATTTTGTTAAA
1 GTTATTAAATTTT-TAAAA
*
33104 TTTATTAAATT
1 GTTATTAAATT
33115 ATTATAAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (18 bp):
GTTATTAAATTTTTAAAA
Found at i:33443 original size:15 final size:15
Alignment explanation
Indices: 33419--33454 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
33409 ACACCATTAA
*
33419 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
33434 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
*
33449 ACTAAA
1 ATTAAA
33455 CATATGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:36371 original size:3 final size:3
Alignment explanation
Indices: 36363--36443 Score: 135
Period size: 3 Copynumber: 27.0 Consensus size: 3
36353 ATTGATTTAT
* * *
36363 TTA TTA TTA TTA TAA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36411 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36444 AATATATATA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:36578 original size:16 final size:16
Alignment explanation
Indices: 36557--36600 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
36547 TAGCCCCATG
36557 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
*
36573 TCCAGCTGCCTCTGCC
1 TCCAGCCGCCTCTGCC
36589 TCCAGCCGCCTC
1 TCCAGCCGCCTC
36601 AGCCAACGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.07, C:0.55, G:0.18, T:0.20
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:38039 original size:12 final size:12
Alignment explanation
Indices: 38022--38058 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
38012 AAATTAAATA
38022 TATTTTGAATTT
1 TATTTTGAATTT
38034 TATTTTGAATTT
1 TATTTTGAATTT
38046 TATTTTGAATTT
1 TATTTTGAATTT
38058 T
1 T
38059 TAATAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTTGAATTT
Found at i:49209 original size:34 final size:34
Alignment explanation
Indices: 49166--49239 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
49156 AGATTCTGTC
*
49166 AAGAAATATTATGCTTG-AAGAAAAAGAAAAAAAA
1 AAGAAATATTATGCTTGAAAAAAAAAG-AAAAAAA
49200 AAGAAATATTATGCTTGAAAAAAAAAGAAAAAAA
1 AAGAAATATTATGCTTGAAAAAAAAAGAAAAAAA
49234 AAGAAA
1 AAGAAA
49240 AAATGGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 30 0.79
35 8 0.21
ACGTcount: A:0.68, C:0.03, G:0.14, T:0.16
Consensus pattern (34 bp):
AAGAAATATTATGCTTGAAAAAAAAAGAAAAAAA
Found at i:49242 original size:19 final size:19
Alignment explanation
Indices: 49218--49259 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
49208 TTATGCTTGA
49218 AAAAAAAAGAAAAAAAAAG
1 AAAAAAAAGAAAAAAAAAG
** *
49237 AAAAAATGGAAAAAAGAAG
1 AAAAAAAAGAAAAAAAAAG
49256 AAAA
1 AAAA
49260 GGGGGGGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAAG
Found at i:49259 original size:10 final size:10
Alignment explanation
Indices: 49216--49242 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49206 TATTATGCTT
49216 GAAAAAAAAA
1 GAAAAAAAAA
49226 GAAAAAAAAA
1 GAAAAAAAAA
49236 GAAAAAA
1 GAAAAAA
49243 TGGAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:50547 original size:83 final size:83
Alignment explanation
Indices: 50408--50835 Score: 793
Period size: 83 Copynumber: 5.2 Consensus size: 83
50398 GAATAAATGC
*
50408 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
50473 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
50491 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
50556 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
50574 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
50639 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
50657 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
*
50722 CATTAAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
50740 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
50805 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
50823 AATTTGCTCATAG
1 AATGTGCTCATAG
50836 TAGAAATAAG
Statistics
Matches: 335, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 335 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
CATTGAATTTGGAAGATG
Found at i:51822 original size:113 final size:113
Alignment explanation
Indices: 51627--52294 Score: 947
Period size: 113 Copynumber: 6.0 Consensus size: 113
51617 GCAAAGATTT
* * * * * *
51627 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAAAGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTAGATTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
51692 AAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
** * ****
51740 AAAT-TCATCA-TATGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 AAATCT-ATCACT-TGATGGATTAGATTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
51803 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
**
51853 AAATCTATCACTTGATGGATTATCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTAGATTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
51918 AATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
*
51966 AAATCTATCACTTGATGGATTAGATTTGCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTAGATTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
52031 AAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
* *
52079 AAATCCATCACTTGATGGATTAGATTTGCCAGAGAAAGTTCATAAGGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTAGATTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
52144 -AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
* *
52191 AAATCTATCACTTGATGGATTAAAATTT-CCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA
1 AAATCTATCACTTGATGGATT-AGATTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* ** *
52255 GAA-G-AG--GAAGTTCATAATAAGAAGAGCTTATTCAACCTTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
52295 TGACTCTGTC
Statistics
Matches: 510, Mismatches: 39, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
109 30 0.06
111 2 0.00
112 102 0.20
113 374 0.73
114 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AAATCTATCACTTGATGGATTAGATTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
Found at i:52344 original size:339 final size:338
Alignment explanation
Indices: 51655--52381 Score: 914
Period size: 339 Copynumber: 2.1 Consensus size: 338
51645 ATCAGCTTTT
* *
51655 CCAGAGAAAGTTCATAAAGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGA
* * * * ** * ****
51720 ATTTGTTCAACCTTTTGTTTAAATTCATCATATGATGGATTATCTTTTCCAGTTCGAGTTCATAA
66 ATTTGTTCAACCTTTCGCTCAAATCCATCATATGATGGATTAGATTTGCCAGAGAAAGTTCATAA
* * *
51785 TGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
131 GGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCG
** *
51850 CTCAAATCTATCACTTGATGGATTATCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
196 CTCAAATCTATCACTTGATGGATTAAATTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
* * * ***
51915 AAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGCTCAAATCTATCACTTG
261 AAGAATGAAG-AGAAATTCATAATAAGAAGAACTTATTCAACCTTTCGCTCAAATCTATCAAAGG
* * * **
51980 ATGGATTAGATTTG
325 AAGGATAACATTCC
*
51994 CTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGA
52059 ATTTGTTCAACCTTTCGCTCAAATCCATCACT-TGATGGATTAGATTTGCCAGAGAAAGTTCATA
66 ATTTGTTCAACCTTTCGCTCAAATCCATCA-TATGATGGATTAGATTTGCCAGAGAAAGTTCATA
52123 AGGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTC
130 AGGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTC
52187 GCTCAAATCTATCACTTGATGGATTAAAATTT-CCAGAGAAAGTTCATAATAAGAAGAACTCATC
195 GCTCAAATCTATCACTTGATGGATT-AAATTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATC
* * * **
52251 TGAAGAA-G-AG-GAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGACTC-TGTC-A-CAGA
259 TGAAGAATGAAGAGAAATTCATAATAAGAAGAACTTATTCAACCTTTCG-CTCAAATCTATCA-A
*
52310 AGGAAAGAGGTCAACATCATCC
322 AGG-AAG-GAT-AACAT--TCC
* * *
52332 CCAGTGGAAAGTTCATAATAAGAAGAACTCATATGAAGAAAGAGAAGAAT
1 CCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAG-GAAGAAT
52382 TTATTCAACA
Statistics
Matches: 335, Mismatches: 41, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
332 2 0.01
333 2 0.01
334 34 0.10
335 5 0.01
336 5 0.01
337 1 0.00
338 108 0.32
339 167 0.50
340 4 0.01
341 7 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (338 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGA
ATTTGTTCAACCTTTCGCTCAAATCCATCATATGATGGATTAGATTTGCCAGAGAAAGTTCATAA
GGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCG
CTCAAATCTATCACTTGATGGATTAAATTTGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
AAGAATGAAGAGAAATTCATAATAAGAAGAACTTATTCAACCTTTCGCTCAAATCTATCAAAGGA
AGGATAACATTCC
Found at i:52539 original size:3 final size:3
Alignment explanation
Indices: 52531--52629 Score: 108
Period size: 3 Copynumber: 33.0 Consensus size: 3
52521 ATTGATTTAT
* * * * *
52531 TTA TTA TTA TTA TAA TTA TAA TAA TTA TTA TTA TTA TTA TAA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
52579 TAA TAA TTA TTA TTA TTA TAA TTA TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52627 TTA
1 TTA
52630 AATATATATA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:52569 original size:27 final size:27
Alignment explanation
Indices: 52531--52633 Score: 163
Period size: 27 Copynumber: 3.9 Consensus size: 27
52521 ATTGATTTAT
52531 TTATTATTATTATAATTATAATAATTA
1 TTATTATTATTATAATTATAATAATTA
*
52558 TTATTATTATTATAATTATAATAATAA
1 TTATTATTATTATAATTATAATAATTA
* *
52585 TTATTATTATTATAATTATTATAAATA
1 TTATTATTATTATAATTATAATAATTA
*
52612 TTATTATTATTATTATTA-AATA
1 TTATTATTATTATAATTATAATA
52634 TATATATAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
26 3 0.04
27 67 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTATTATTATTATAATTATAATAATTA
Found at i:52764 original size:16 final size:16
Alignment explanation
Indices: 52743--52786 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
52733 TAGCCCCATG
52743 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
52759 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
52775 TCCAGCCGCCTC
1 TCCAGCCGCCTC
52787 AGCCAACGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.07, C:0.57, G:0.18, T:0.18
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:54220 original size:12 final size:12
Alignment explanation
Indices: 54203--54227 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54193 AAATTAAATA
54203 TATTTTGAATTT
1 TATTTTGAATTT
54215 TATTTTGAATTT
1 TATTTTGAATTT
54227 T
1 T
54228 TAATAATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTTGAATTT
Found at i:55210 original size:2 final size:2
Alignment explanation
Indices: 55203--55233 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
55193 TAATATTCAA
*
55203 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55234 CAGAAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:65237 original size:16 final size:16
Alignment explanation
Indices: 65205--65238 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
65195 TCTGTAATAG
**
65205 TAATTTTGGATTGTTT
1 TAATTTTGGATAATTT
65221 TAATTTTGGATAATTT
1 TAATTTTGGATAATTT
65237 TA
1 TA
65239 GCTATACTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (16 bp):
TAATTTTGGATAATTT
Found at i:65411 original size:24 final size:23
Alignment explanation
Indices: 65392--65437 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
65382 TAAAGAAATT
65392 ACAAT-TTTTAAATTGTAAGAAA
1 ACAATATTTTAAATTGTAAGAAA
**
65414 AGGATATTTTAAATTGTAAGAAA
1 ACAATATTTTAAATTGTAAGAAA
65437 A
1 A
65438 GGGTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (23 bp):
ACAATATTTTAAATTGTAAGAAA
Found at i:65427 original size:23 final size:23
Alignment explanation
Indices: 65397--65449 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
65387 AAATTACAAT
65397 TTTTAAATTGTAAGAAAAGGATA
1 TTTTAAATTGTAAGAAAAGGATA
*
65420 TTTTAAATTGTAAGAAAAGGGTA
1 TTTTAAATTGTAAGAAAAGGATA
65443 TTTTAAA
1 TTTTAAA
65450 CCTCAACACA
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:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (23 bp):
TTTTAAATTGTAAGAAAAGGATA
Found at i:67361 original size:35 final size:35
Alignment explanation
Indices: 67322--67390 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
67312 GGTGAAAGAA
67322 GGATGACGGGTCAATAAAATGTCTTCTCCTAACAG
1 GGATGACGGGTCAATAAAATGTCTTCTCCTAACAG
67357 GGATGACGGGTCAATAAAATGTCTTCTCCTAACA
1 GGATGACGGGTCAATAAAATGTCTTCTCCTAACA
67391 TTCTCATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (35 bp):
GGATGACGGGTCAATAAAATGTCTTCTCCTAACAG
Found at i:74250 original size:39 final size:39
Alignment explanation
Indices: 74194--74280 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
74184 CATGGGAGGA
*
74194 GGTGGTGCTGGCACTCCACAAAGAGGTGGAGGTCGTGGG
1 GGTGGTCCTGGCACTCCACAAAGAGGTGGAGGTCGTGGG
* * *
74233 GGTGGTCCTGG-AGCTCCACGAATAGGTGGAGGTGGTGGG
1 GGTGGTCCTGGCA-CTCCACAAAGAGGTGGAGGTCGTGGG
74272 GGTGGTCCT
1 GGTGGTCCT
74281 CCATGTCGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.02
39 42 0.98
ACGTcount: A:0.15, C:0.17, G:0.47, T:0.21
Consensus pattern (39 bp):
GGTGGTCCTGGCACTCCACAAAGAGGTGGAGGTCGTGGG
Found at i:74446 original size:6 final size:6
Alignment explanation
Indices: 74435--74485 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
74425 CCTCGTAAAA
* * * * *
74435 GAGGTG GAGGTG GAGGTG GAGGTG GTGGTG GTGGTG GTGGAG GAGGAG
1 GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG
74483 GAG
1 GAG
74486 AAGCTCCGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.16, C:0.00, G:0.67, T:0.18
Consensus pattern (6 bp):
GAGGTG
Found at i:77918 original size:5 final size:5
Alignment explanation
Indices: 77904--77935 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
77894 ATTAGAAACC
77904 AAAAG AAAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG A
77936 GAAATTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:79322 original size:2 final size:2
Alignment explanation
Indices: 79315--79343 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
79305 ATTTTATGAT
79315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
79344 TGATTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81891 original size:24 final size:25
Alignment explanation
Indices: 81863--81928 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 25
81853 CGATATTTTT
81863 ATTAAATAATAATTTTCTTGAT-TA
1 ATTAAATAATAATTTTCTTGATATA
* *
81887 ATTAAATAATATTTTTTTTGATAATA
1 ATTAAATAATAATTTTCTTGAT-ATA
*
81913 ATTAAATACTAATTTT
1 ATTAAATAATAATTTT
81929 ATTTGACGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 20 0.56
26 16 0.44
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (25 bp):
ATTAAATAATAATTTTCTTGATATA
Found at i:112157 original size:60 final size:60
Alignment explanation
Indices: 112064--112192 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
112054 AAAAATATTC
* * * * * *
112064 AAAGATTTGGGGACCAATATAGAATGAGGGTCATAGTTTGAGGGTGAAATTATAATGTTCA
1 AAAG-TTTAGGGACCAATATAGAATGAGAGTCATAGTTTAAGGATGAAACTAGAATGTTCA
* * * *
112125 AAAGTTTAGGGACCATTTTAGAATGAGAGTCATAGTTTAAGGATGTAACTGGAATGTTCA
1 AAAGTTTAGGGACCAATATAGAATGAGAGTCATAGTTTAAGGATGAAACTAGAATGTTCA
112185 AAAGTTTA
1 AAAGTTTA
112193 AAGACAAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
60 54 0.93
61 4 0.07
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (60 bp):
AAAGTTTAGGGACCAATATAGAATGAGAGTCATAGTTTAAGGATGAAACTAGAATGTTCA
Found at i:112206 original size:60 final size:60
Alignment explanation
Indices: 112083--112218 Score: 155
Period size: 60 Copynumber: 2.3 Consensus size: 60
112073 GGGACCAATA
* * * * ** * **
112083 TAGAATGAGGGTCATAGTTTGAGGGTGAAATTATAATGTTCAAAAGTTTAGGGACCATTT
1 TAGAATGAGGGTCATAGTTTAAGGATGAAACTAGAATGTTCAAAAGTTTAAAGACAAAAT
* * *
112143 TAGAATGAGAGTCATAGTTTAAGGATGTAACTGGAATGTTCAAAAGTTTAAAGACAAAAT
1 TAGAATGAGGGTCATAGTTTAAGGATGAAACTAGAATGTTCAAAAGTTTAAAGACAAAAT
*
112203 TAGAATAAGGGTCATA
1 TAGAATGAGGGTCATA
112219 AATTGTGAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (60 bp):
TAGAATGAGGGTCATAGTTTAAGGATGAAACTAGAATGTTCAAAAGTTTAAAGACAAAAT
Found at i:120704 original size:23 final size:23
Alignment explanation
Indices: 120678--120725 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
120668 ATAAAGTACA
*
120678 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
120701 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
120724 AT
1 AT
120726 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:121171 original size:23 final size:23
Alignment explanation
Indices: 121143--121202 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
121133 ATAACCACTA
121143 CTATTACATTATATAAACGATAC
1 CTATTACATTATATAAACGATAC
* *
121166 CTATTACATTATATAAGCGCTAC
1 CTATTACATTATATAAACGATAC
*
121189 CTATTACATCATAT
1 CTATTACATTATAT
121203 TTACCTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (23 bp):
CTATTACATTATATAAACGATAC
Found at i:121578 original size:22 final size:22
Alignment explanation
Indices: 121547--121622 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
121537 GATAGACACT
121547 TTACA-ATATAACAACTACCTA
1 TTACATATATAACAACTACCTA
121568 TTACATATAT-ACAACCTACCTA
1 TTACATATATAACAA-CTACCTA
*
121590 -TACATTATATAAGC-GCTACCTA
1 TTACA-TATATAA-CAACTACCTA
121612 TTACATCATAT
1 TTACAT-ATAT
121623 GTTTACCTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
21 13 0.28
22 24 0.51
23 9 0.19
24 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.33
Consensus pattern (22 bp):
TTACATATATAACAACTACCTA
Found at i:121803 original size:417 final size:416
Alignment explanation
Indices: 120792--121817 Score: 1668
Period size: 417 Copynumber: 2.5 Consensus size: 416
120782 TATTACATTA
* * *
120792 TATTATATTGAAATTGTTCATACTTTTTATAAAAAGGATCGATATTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTT-TTTTAAAGTTATGTAAT
120857 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
65 TTATGTTTCAATTTTTTTTAATAGTGTTTCAT-TTTTCCACCTACAATATTAATTTAATAATTTC
*
120921 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAA-TTA
129 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
120985 ATATATAAATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTA
194 ATATATAAATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTA
* *
121050 AAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAAAAAAAGTATTGACACTTTTATAAA
259 AAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAAAAAAAATATGGACACTTTTATAAA
*
121115 AAGGAGACACTTTACAATATAACCACTACTATTACATTATATAAACGATACCTATTACATTATAT
324 AAGGAGACACTTTACAATATAACAACTACTATTACATTATATAAACGATACCTATTACATTATAT
121180 AAGCGCTACCTATTACATCATATTTACC
389 AAGCGCTACCTATTACATCATATTTACC
*
121208 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTAAAGTTATGTAATT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATT
*
121273 TATGTTTC-ATTTTTTTTAATA-TGTTTCATGTTTCCACCTACAATATTAATTTAATAATTTCAT
66 TATGTTTCAATTTTTTTTAATAGTGTTTCATTTTTCCACCTACAATATTAATTTAATAATTTCAT
* * *
121336 TTGCACCAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTGTAATTTAA
131 TTGCACAAAAAATTATTTGATT-TTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
*
121401 TAATAATATATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACT-AATTAATATCTT
195 T-AT-ATAAATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT
*
121465 AAAACTCACTCAAAAGATAACCTTAAATTAATG-TTTCCACAGTGAAAAAAATATGGACATTTTT
258 AAAACTCACTC-AAAGATAACCTTAAATTAATGTTTTCCACA---AAAAAAATATGGACACTTTT
*
121529 ATAAAAAGGATAGACACTTTACAATATAACAACTACCTATTACA-TATATACAAC-CTACCTA-T
319 ATAAAAAGG--AGACACTTTACAATATAACAACTA-CTATTACATTATATA-AACGATACCTATT
121591 ACATTATATAAGCGCTACCTATTACATCATATGTTTACC
380 ACATTATATAAGCGCTACCTATTACATCATA--TTTACC
121630 TATTATATTG-AAGTGTCCATACTTTTT-T-AAAAGGATCGATACTTTTTTAAAGTTATGTAA-T
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATT
*
121691 TATGTTTCAATTTTTTTTAATAGTGTTCCATTTTTCCACCTACAATATT-ATTTAATAATTTCAT
66 TATGTTTCAATTTTTTTTAATAGTGTTTCATTTTTCCACCTACAATATTAATTTAATAATTTCAT
121755 TTGCACAAAAAATTA-TTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
121818 CAACATTAAC
Statistics
Matches: 572, Mismatches: 21, Indels: 33
0.91 0.03 0.05
Matches are distributed among these distances:
413 54 0.09
414 43 0.08
415 41 0.07
416 77 0.13
417 107 0.19
418 15 0.03
419 99 0.17
420 57 0.10
421 52 0.09
422 27 0.05
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (416 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATT
TATGTTTCAATTTTTTTTAATAGTGTTTCATTTTTCCACCTACAATATTAATTTAATAATTTCAT
TTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAAT
ATATAAATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAA
ACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAAAAAAAATATGGACACTTTTATAAAAA
GGAGACACTTTACAATATAACAACTACTATTACATTATATAAACGATACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTACC
Found at i:122148 original size:18 final size:18
Alignment explanation
Indices: 122125--122161 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
122115 CGAAATATAT
122125 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
122143 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
122161 A
1 A
122162 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:122620 original size:23 final size:23
Alignment explanation
Indices: 122591--122653 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
122581 ATATAACCAC
122591 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
122614 TATCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
122637 TACCTATTACATCATAT
1 TACCTATTACATTATAT
122654 GTTTACGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:123912 original size:20 final size:21
Alignment explanation
Indices: 123873--123919 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
123863 AGTGTATCTT
* *
123873 CGACTCTATCGAGTTTCTCTA
1 CGACTCGATCAAGTTTCTCTA
*
123894 CGACTCGATCAAG-TTCTCTT
1 CGACTCGATCAAGTTTCTCTA
123914 CGACTC
1 CGACTC
123920 TTGATTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.34
Consensus pattern (21 bp):
CGACTCGATCAAGTTTCTCTA
Found at i:126150 original size:17 final size:18
Alignment explanation
Indices: 126128--126170 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
126118 ATATATCCGG
126128 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
126145 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
126165 TATCAT
1 TATCAT
126171 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:126188 original size:20 final size:19
Alignment explanation
Indices: 126133--126179 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
126123 TCCGGTATCA
126133 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
126152 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
126173 TTTTACC
1 TTTTACC
126180 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:126326 original size:20 final size:20
Alignment explanation
Indices: 126300--126345 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
126290 CACTTTTAAA
*
126300 TTTACCGGTTTTATCAT-TT
1 TTTACCGATTTTATCATATT
126319 TGTTACCGATTTTATCATATT
1 T-TTACCGATTTTATCATATT
126340 TTTACC
1 TTTACC
126346 TGGTATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (20 bp):
TTTACCGATTTTATCATATT
Found at i:126446 original size:20 final size:20
Alignment explanation
Indices: 126418--126455 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
126408 TGCTTTTAAG
126418 TTATGTAATTA-TGTTTCAAT
1 TTATGTAA-TAGTGTTTCAAT
*
126438 TTATTTAATAGTGTTTCA
1 TTATGTAATAGTGTTTCA
126456 TTTTTCCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (20 bp):
TTATGTAATAGTGTTTCAAT
Found at i:127496 original size:21 final size:21
Alignment explanation
Indices: 127472--127516 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
127462 ATTTGCAACT
127472 CGAACTTGGACTATCGCAATG
1 CGAACTTGGACTATCGCAATG
127493 CGAACTTGGACTATCGCAATG
1 CGAACTTGGACTATCGCAATG
127514 CGA
1 CGA
127517 TTTACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
CGAACTTGGACTATCGCAATG
Found at i:127557 original size:41 final size:40
Alignment explanation
Indices: 127512--127657 Score: 159
Period size: 40 Copynumber: 3.5 Consensus size: 40
127502 ACTATCGCAA
* *
127512 TGCGA-TTTACATATTCGCATTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTACAAATTCG--TTGCGATAGTCGAAGTTCGCGT
* * *
127553 TGCGACTTTTTCAAATTCGTTGCGATAGTTGAAGTTCGCAT
1 TGCGA-TTTTACAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * *
127594 TGCGATTTTCCAAAATCGTTGTGATAGTCGAAGTTCGCGT
1 TGCGATTTTACAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
127634 TGCGATTTATTCCAAATTCGTTGC
1 TGCGA-TT-TTACAAATTCGTTGC
127658 AATCCCACAT
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
40 35 0.39
41 31 0.35
42 13 0.15
43 10 0.11
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (40 bp):
TGCGATTTTACAAATTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:127627 original size:40 final size:41
Alignment explanation
Indices: 127531--127657 Score: 175
Period size: 40 Copynumber: 3.1 Consensus size: 41
127521 CATATTCGCA
* *
127531 TTGCGATAGTCCAAGTTCGCGTTGCGACTTTTTCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGACTTTTCCAAATTCG
* * *
127572 TTGCGATAGTTGAAGTTCGCATTGCGA-TTTTCCAAAATCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGACTTTTCCAAATTCG
* *
127612 TTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGACTT-TTCCAAATTCG
127654 TTGC
1 TTGC
127658 AATCCCACAT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
40 35 0.47
41 26 0.35
42 13 0.18
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (41 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGACTTTTCCAAATTCG
Found at i:127931 original size:21 final size:21
Alignment explanation
Indices: 127907--128001 Score: 113
Period size: 21 Copynumber: 4.6 Consensus size: 21
127897 TTTGGAATAA
*
127907 ATCGTAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
127928 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
127947 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
127968 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
127989 ATCGCAATGCGAA
1 ATCGCAACGCGAA
128002 TATGTAAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
19 15 0.25
21 46 0.75
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:127960 original size:40 final size:42
Alignment explanation
Indices: 127882--127976 Score: 167
Period size: 40 Copynumber: 2.3 Consensus size: 42
127872 TGCGATTTTG
*
127882 GACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
127924 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
127964 GACTATCGCAACG
1 GACTATCGCAACG
127977 CGAACTTGGA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
40 31 0.60
41 1 0.02
42 20 0.38
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:142770 original size:2 final size:2
Alignment explanation
Indices: 142763--142792 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
142753 ACATACATGC
142763 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
142793 ACAAAAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:144510 original size:13 final size:13
Alignment explanation
Indices: 144492--144539 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
144482 TATTCTTAAC
144492 TTTTAAAAATATA
1 TTTTAAAAATATA
144505 TTTTAAAAATATA
1 TTTTAAAAATATA
*
144518 TTAATTTCAAAATATA
1 -T--TTTAAAAATATA
144534 TTTTAA
1 TTTTAA
144540 CTTAAGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 17 0.57
14 1 0.03
15 1 0.03
16 11 0.37
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAAAATATA
Found at i:144570 original size:21 final size:22
Alignment explanation
Indices: 144526--144570 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
144516 TATTAATTTC
*
144526 AAAATATATTTTAACTTAAGAAT
1 AAAATATATTTTAAC-TAAAAAT
144549 AAAATATATTTTAA-TAAAAAT
1 AAAATATATTTTAACTAAAAAT
144570 A
1 A
144571 TTTTAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
23 14 0.67
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATATATTTTAACTAAAAAT
Found at i:144573 original size:14 final size:15
Alignment explanation
Indices: 144546--144576 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
144536 TTAACTTAAG
144546 AATAAAATATATTTT
1 AATAAAATATATTTT
144561 AATAAAA-ATATTTT
1 AATAAAATATATTTT
144575 AA
1 AA
144577 AAACATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAAATATATTTT
Found at i:147381 original size:12 final size:11
Alignment explanation
Indices: 147366--147428 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
147356 TATTCATTAT
147366 TTATTTGTAATA
1 TTATTT-TAATA
*
147378 TTATTTTATTA
1 TTATTTTAATA
147389 TTACTTTTAATA
1 TTA-TTTTAATA
147401 -TATTTTAATTA
1 TTATTTTAA-TA
*
147412 TTACTTTAATTA
1 TTATTTTAA-TA
147424 TTATT
1 TTATT
147429 ATTTTCTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
10 6 0.14
11 11 0.25
12 27 0.61
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:147399 original size:23 final size:23
Alignment explanation
Indices: 147339--147428 Score: 82
Period size: 23 Copynumber: 4.0 Consensus size: 23
147329 AGTGTGTTTA
* *
147339 TATTA-TAATTTTAATTTTA-TT
1 TATTATTACTTTTAATATTATTT
*
147360 CATTATTTA-TTTGTAATATTATTT
1 TATTA-TTACTTT-TAATATTATTT
147384 TATTATTACTTTTAATA-TATTT
1 TATTATTACTTTTAATATTATTT
147406 TAATTATTAC-TTTAATTATTATT
1 T-ATTATTACTTTTAA-TATTATT
147429 ATTTTCTTAG
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
21 4 0.07
22 14 0.24
23 27 0.47
24 13 0.22
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (23 bp):
TATTATTACTTTTAATATTATTT
Found at i:148275 original size:25 final size:28
Alignment explanation
Indices: 148247--148298 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
148237 AATTATTTCT
148247 TTTCA-AA-ATTTATATATAT-TTATTA
1 TTTCATAATATTTATATATATATTATTA
*
148272 TTTCATAATATTTATATGTATATTATT
1 TTTCATAATATTTATATATATATTATT
148299 TTTTATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 2 0.09
27 11 0.48
28 5 0.22
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTCATAATATTTATATATATATTATTA
Found at i:150736 original size:20 final size:20
Alignment explanation
Indices: 150703--150741 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
150693 ATTTTCCCCC
* *
150703 CATTTTTATGTTTGTATTTA
1 CATTTTCATGTTTGCATTTA
*
150723 CATTTTCATTTTTGCATTT
1 CATTTTCATGTTTGCATTT
150742 GCATCTTTGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (20 bp):
CATTTTCATGTTTGCATTTA
Found at i:156764 original size:54 final size:54
Alignment explanation
Indices: 156651--156782 Score: 135
Period size: 54 Copynumber: 2.4 Consensus size: 54
156641 AACATTTGTG
* * * * * *
156651 CAGAAACCACAAGGAAA-AATGAATGTGTTGTCAAATGCTTTATGAACATCTGTA
1 CAGAAGCCACAA-GAAATGATGAATGTGTTATCAAAAGCTTTATGAAAATCCGTA
* *
156705 CAGAAGTCAC-AGGAATGGATGAATGTGTTATCAAAAGCTTTATGAAAATCCG-A
1 CAGAAGCCACAAGAAAT-GATGAATGTGTTATCAAAAGCTTTATGAAAATCCGTA
*
156758 GTAGAAGCCACAAGAAATGATGAAT
1 -CAGAAGCCACAAGAAATGATGAAT
156783 ATATGGTTAC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
52 3 0.05
53 2 0.03
54 53 0.84
55 5 0.08
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (54 bp):
CAGAAGCCACAAGAAATGATGAATGTGTTATCAAAAGCTTTATGAAAATCCGTA
Found at i:158025 original size:47 final size:46
Alignment explanation
Indices: 157834--158142 Score: 498
Period size: 45 Copynumber: 6.7 Consensus size: 46
157824 CTATTTCCTA
157834 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
157879 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
157924 CATTTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* **
157969 CATATGTAAGTATTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
* *
158016 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAACATTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
* *
158063 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
158109 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAA
158143 CATTTCCATC
Statistics
Matches: 249, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
45 118 0.47
46 46 0.18
47 85 0.34
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (46 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:158279 original size:3 final size:3
Alignment explanation
Indices: 158271--158316 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
158261 TTTCGTTTTG
158271 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
158317 ATAAAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:158294 original size:17 final size:17
Alignment explanation
Indices: 158272--158316 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
158262 TTCGTTTTGT
158272 TATTATTATTATTATTA
1 TATTATTATTATTATTA
158289 TATTATTATTATTATTA
1 TATTATTATTATTATTA
158306 T-TATATTATTA
1 TAT-TATTATTA
158317 ATAAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 1 0.04
17 26 0.96
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:158296 original size:20 final size:20
Alignment explanation
Indices: 158271--158316 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
158261 TTTCGTTTTG
158271 TTATTATTATTATTATTATA
1 TTATTATTATTATTATTATA
158291 TTATTATTATTATTATTATA
1 TTATTATTATTATTATTATA
158311 TTATTA
1 TTATTA
158317 ATAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATTATTATTATTATA
Found at i:159975 original size:12 final size:11
Alignment explanation
Indices: 159960--160025 Score: 71
Period size: 12 Copynumber: 5.7 Consensus size: 11
159950 TATTCATTAT
159960 TTATTTGTAATA
1 TTATTT-TAATA
*
159972 TTATTTTATTA
1 TTATTTTAATA
159983 TTACTTTTAATA
1 TTA-TTTTAATA
159995 -TATTTTAATTA
1 TTATTTTAA-TA
*
160006 TTACTTTAATTA
1 TTATTTTAA-TA
160018 TTATTTTA
1 TTATTTTA
160026 TCAATCTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
10 6 0.13
11 11 0.23
12 30 0.64
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:159993 original size:23 final size:23
Alignment explanation
Indices: 159941--160026 Score: 90
Period size: 23 Copynumber: 3.7 Consensus size: 23
159931 TATGTTATAA
* *
159941 TTTTAATTTTA-TTCATTATTTA-
1 TTTTAATATTATTTTATTA-TTAC
159963 TTTGTAATATTATTTTATTATTAC
1 TTT-TAATATTATTTTATTATTAC
159987 TTTTAATA-TATTTTAATTATTAC
1 TTTTAATATTATTTT-ATTATTAC
160010 -TTTAATTATTATTTTAT
1 TTTTAA-TATTATTTTAT
160027 CAATCTTATA
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
22 14 0.25
23 27 0.48
24 15 0.27
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (23 bp):
TTTTAATATTATTTTATTATTAC
Found at i:164189 original size:30 final size:31
Alignment explanation
Indices: 164149--164222 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
164139 AATTTCATGG
* * *
164149 ATTT-AATATTAAAA-TCAAATATATGTTTC
1 ATTTAAATATTAAAATTAAAAGATATGTTTA
* *
164178 TTTTAAATATTATAAATTAAAAGATATTTTTA
1 ATTTAAATATTA-AAATTAAAAGATATGTTTA
164210 ATTTAAATATTAA
1 ATTTAAATATTAA
164223 TAGGATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 3 0.08
30 7 0.19
31 4 0.11
32 22 0.61
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTTAAATATTAAAATTAAAAGATATGTTTA
Found at i:165700 original size:20 final size:20
Alignment explanation
Indices: 165675--165744 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
165665 TCACAATTCT
165675 CAATGCGAATAAGTAAATCG
1 CAATGCGAATAAGTAAATCG
165695 CAATGCGAATAAGTAAATCG
1 CAATGCGAATAAGTAAATCG
*
165715 CAATGCAAATAAGTAAATCG
1 CAATGCGAATAAGTAAATCG
165735 CAATGCGAAT
1 CAATGCGAAT
165745 CTGACTATCG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.20
Consensus pattern (20 bp):
CAATGCGAATAAGTAAATCG
Found at i:166329 original size:19 final size:19
Alignment explanation
Indices: 166287--166357 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
166277 TAGTTTCGAG
166287 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
166307 AATGACTATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
166326 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
166345 AACCAAAATCGCA
1 AATGAAAATCGCA
166358 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:166398 original size:14 final size:14
Alignment explanation
Indices: 166375--166463 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
166365 TTTCATTTCG
*
166375 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
166389 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
166408 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
166422 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
166441 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
166455 CGTTGCGAT
1 CGTTGCGAT
166464 AGTCATTTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 29 0.48
16 5 0.08
17 5 0.08
19 21 0.35
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:166400 original size:33 final size:33
Alignment explanation
Indices: 166358--166512 Score: 202
Period size: 33 Copynumber: 4.5 Consensus size: 33
166348 CAAAATCGCA
*
166358 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
166391 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
166424 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
166457 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTATCTCG
1 TTGCGATTTTCATTT-CGCGTTGCGA--TTC----TCTCG
166497 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
166513 AACCAAAAGA
Statistics
Matches: 110, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
33 78 0.71
34 10 0.09
36 3 0.03
39 1 0.01
40 18 0.16
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:166489 original size:20 final size:20
Alignment explanation
Indices: 166455--166512 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
166445 GCGATTCTCT
**
166455 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
166475 CGTTGCGATTTTCATTAT-CT
1 CGTTGCGATTTTCATT-TCCG
166495 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
166513 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:168337 original size:94 final size:94
Alignment explanation
Indices: 168176--168430 Score: 476
Period size: 94 Copynumber: 2.7 Consensus size: 94
168166 TCACTTAGAT
168176 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
1 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
168241 TAAATTTGTTCGGTTGCTGCCAATTCTGC
66 TAAATTTGTTCGGTTGCTGCCAATTCTGC
168270 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
1 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
*
168335 TAAATTTGTTCGTTTGCTGCCAATTCTGC
66 TAAATTTGTTCGGTTGCTGCCAATTCTGC
* *
168364 TAAACTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-AAG
1 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
168428 TAA
66 TAA
168431 TGCAATCCAT
Statistics
Matches: 158, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
93 6 0.04
94 152 0.96
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
TAAATTTGTTCGGTTGCTGCCAATTCTGC
Found at i:168519 original size:12 final size:12
Alignment explanation
Indices: 168502--168527 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
168492 TTAGTAACAC
168502 TGTTTTGTCTTT
1 TGTTTTGTCTTT
168514 TGTTTTGTCTTT
1 TGTTTTGTCTTT
168526 TG
1 TG
168528 GTTTCGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.19, T:0.73
Consensus pattern (12 bp):
TGTTTTGTCTTT
Found at i:168567 original size:19 final size:19
Alignment explanation
Indices: 168529--168569 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
168519 TGTCTTTTGG
**
168529 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
168548 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
168567 TTT
1 TTT
168570 TTCACATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:169062 original size:42 final size:42
Alignment explanation
Indices: 169011--169104 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
169001 CCACTCCTAT
* * *
169011 CGTTGAAGAGGCCCCTATCATTCATTGAA-A-GTCCCCTTCCAC
1 CGTTCAAGAGGCCACTATCA-TCATTGAAGAGGT-CCCTCCCAC
* *
169053 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCATTGAAGAGGTCCCTCCCAC
*
169095 CATTCAAGAG
1 CGTTCAAGAG
169105 CTCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 7 0.16
42 35 0.80
43 2 0.05
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCATTGAAGAGGTCCCTCCCAC
Found at i:170472 original size:14 final size:14
Alignment explanation
Indices: 170453--170488 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
170443 ATTGTTTAAT
170453 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
170467 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
170481 TGATTTGT
1 TGATTTGT
170489 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:170610 original size:19 final size:19
Alignment explanation
Indices: 170594--170671 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
170584 AAAAATGACT
170594 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
170613 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
170632 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
170646 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
170665 ATCGCAA
1 ATCGCAA
170672 CGACAAAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 35 0.69
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:170703 original size:33 final size:33
Alignment explanation
Indices: 170610--170692 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
170600 ATGCGAAATG
*
170610 AAAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
* *
170643 AGAATCGCAATGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
170676 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
170693 CTAAATTCGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:170720 original size:19 final size:18
Alignment explanation
Indices: 170698--170848 Score: 101
Period size: 19 Copynumber: 8.7 Consensus size: 18
170688 CGAAACTAAA
170698 TTCGCATTGCGATTTTCAT
1 TTCGC-TTGCGATTTTCAT
*
170717 TTCGCTTTGCGA--TTC-C
1 TTCGC-TTGCGATTTTCAT
*
170733 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
170750 TTCGCGTTGCGA--TTC-T
1 TTCGC-TTGCGATTTTCAT
*
170766 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
170783 TTCGCATTGCGA--TTC-T
1 TTCGC-TTGCGATTTTCAT
*
170799 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
**
170816 TTCGCATTGCGATAGTCAT
1 TTCGC-TTGCGATTTTCAT
170835 TTCCGCGTTGCGAT
1 TT-CGC-TTGCGAT
170849 AGACATTAAG
Statistics
Matches: 104, Mismatches: 12, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
14 18 0.17
16 20 0.19
17 20 0.19
19 36 0.35
20 10 0.10
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.44
Consensus pattern (18 bp):
TTCGCTTGCGATTTTCAT
Found at i:170746 original size:33 final size:33
Alignment explanation
Indices: 170704--170828 Score: 223
Period size: 33 Copynumber: 3.8 Consensus size: 33
170694 TAAATTCGCA
* *
170704 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
170737 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
170770 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
170803 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
170829 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:170773 original size:14 final size:14
Alignment explanation
Indices: 170754--170810 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
170744 TTTCATTTCG
170754 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
170768 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
170785 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
170801 CGTTGCGATT
1 CGTTGCGATT
170811 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:170847 original size:20 final size:20
Alignment explanation
Indices: 170801--170894 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
170791 GCGATTCTCT
**
170801 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
170820 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
170840 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
170859 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
170881 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
170895 AATGATTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:173170 original size:12 final size:12
Alignment explanation
Indices: 173153--173177 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
173143 TCTTGGGGGA
173153 CTTTTTCTTCTT
1 CTTTTTCTTCTT
173165 CTTTTTCTTCTT
1 CTTTTTCTTCTT
173177 C
1 C
173178 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:173379 original size:24 final size:24
Alignment explanation
Indices: 173352--173405 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
173342 TTGAAACATC
*
173352 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
173376 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
173400 ATCAAA
1 ATCAAA
173406 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:174199 original size:20 final size:20
Alignment explanation
Indices: 174135--174249 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
174125 GATTCTGTAT
*
174135 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
174155 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
174175 AATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGATAGTCAG
* * *
174195 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
174216 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
174236 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
174250 TTTCCAAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.77
21 13 0.16
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:174227 original size:41 final size:41
Alignment explanation
Indices: 174115--174252 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
174105 AACTTTGAAA
* * *
174115 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
* * ** ** * *
174156 ATCTCGTTGCGA--AAGTCAGAATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGT
174196 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
174237 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
174253 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
39 2 0.03
40 27 0.36
41 45 0.59
42 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
Found at i:174268 original size:41 final size:40
Alignment explanation
Indices: 174177--174330 Score: 116
Period size: 41 Copynumber: 3.8 Consensus size: 40
174167 AAAGTCAGAA
* * * * *
174177 TCGCGTTGCGAAAGTTAGTATCGCATTGCGATTTTGTATT
1 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGAAAT
* *
174217 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 -TCGCATTGCGATAGTCAGTATCGCATTGCGATTTT-GAAAT
* * ** *
174259 TCGCATTGCGAT--TTACTTATTCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGATAGTCA-GTA-TCGCATTGCG-ATTTTGAAAT
*
174300 TCGCATTGCGATAGTCA-TAATCGCGTTGCGA
1 TCGCATTGCGATAGTCAGT-ATCGCATTGCGA
174331 ATCTGGAAAC
Statistics
Matches: 92, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 79 0.86
42 6 0.07
43 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGAAAT
Found at i:174323 original size:20 final size:20
Alignment explanation
Indices: 174142--174330 Score: 82
Period size: 20 Copynumber: 9.3 Consensus size: 20
174132 TATTATCTCG
* * *
174142 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCATAATCGCA
* * *
174162 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
* *
174182 TTGCGAAAGTTAGT-ATCGCA
1 TTGCGATAGTCA-TAATCGCA
* * *
174202 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--TAGTCATAATCGCA
174223 TTGCGATAGTCAGT-ATCGCA
1 TTGCGATAGTCA-TAATCGCA
**
174243 TTGCGATTTTCCA-AATTCGCA
1 TTGCGATAGT-CATAA-TCGCA
* * *
174264 TTGCGAT-TTACTTATTCGCA
1 TTGCGATAGT-CATAATCGCA
* ** *
174284 TTGCGAATTGGGAAAATCGCA
1 TTGCG-ATAGTCATAATCGCA
*
174305 TTGCGATAGTCATAATCGCG
1 TTGCGATAGTCATAATCGCA
174325 TTGCGA
1 TTGCGA
174331 ATCTGGAAAC
Statistics
Matches: 131, Mismatches: 26, Indels: 24
0.72 0.14 0.13
Matches are distributed among these distances:
19 3 0.02
20 85 0.65
21 41 0.31
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:177565 original size:28 final size:28
Alignment explanation
Indices: 177509--177567 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
177499 GTATGTGGGG
* * *
177509 AAAATATAAAAATAATTAATTTAGTTTT
1 AAAATATAAAAATAAATAATTAAGATTT
177537 AAAATATAAAATATAAAT-ATTAAGATTT
1 AAAATATAAAA-ATAAATAATTAAGATTT
177565 AAA
1 AAA
177568 TCTAAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAATATAAAAATAAATAATTAAGATTT
Found at i:179566 original size:2 final size:2
Alignment explanation
Indices: 179559--179611 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
179549 TAAGAAAATA
179559 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
179601 AT AT AT AT AT A
1 AT AT AT AT AT A
179612 AAGTTAATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:182498 original size:6 final size:5
Alignment explanation
Indices: 182460--182583 Score: 65
Period size: 5 Copynumber: 23.8 Consensus size: 5
182450 ATATTATACT
* *
182460 TTTTC TTTTA TTTTA TTTTA TTTTCA TTTTTA TTCTTA -TTTA TTTATT
1 TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTTA TT-TTA TTTTA TTT-TA
** * ** * *
182508 TTTTA ACTAA CATT- TTTTA TATTA TTTTTA TTTTA CTTTA TTTTA TTATTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TT-TTA
*
182559 TTTTA TTATT- TTCTA TTATTA TTTT
1 TTTTA TT-TTA TTTTA TT-TTA TTTT
182584 TAGTAACTTT
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
4 6 0.07
5 57 0.63
6 24 0.26
7 4 0.04
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:182537 original size:11 final size:11
Alignment explanation
Indices: 182521--182585 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 11
182511 TAACTAACAT
182521 TTTTTATATTA
1 TTTTTATATTA
*
182532 TTTTTATTTTA
1 TTTTTATATTA
*
182543 CTTTATTTTATTA
1 -TTT-TTATATTA
182556 TTATTT-TATTA
1 TT-TTTATATTA
182567 TTTTCTATTATTA
1 TTTT-TA-TATTA
182580 TTTTTA
1 TTTTTA
182586 GTAACTTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
10 2 0.04
11 18 0.40
12 9 0.20
13 16 0.36
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:182575 original size:21 final size:21
Alignment explanation
Indices: 182523--182583 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
182513 ACTAACATTT
* *
182523 TTTATATTATTTTTATTTTAC
1 TTTATTTTATTATTATTTTAC
182544 TTTATTTTATTATTATTTTA-
1 TTTATTTTATTATTATTTTAC
182564 -TTATTTTCTATTATTATTTT
1 TTTA-TTT-TATTATTATTTT
182584 TAGTAACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 30 0.83
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATTTTATTATTATTTTAC
Found at i:182580 original size:16 final size:16
Alignment explanation
Indices: 182522--182581 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
182512 AACTAACATT
* *
182522 TTTTATATTATTTTTA
1 TTTTCTATTATTATTA
182538 TTTTACT-TTATT-TTA
1 TTTT-CTATTATTATTA
*
182553 TTAT-TATT-TTATTA
1 TTTTCTATTATTATTA
182567 TTTTCTATTATTATT
1 TTTTCTATTATTATT
182582 TTTAGTAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
13 3 0.08
14 8 0.22
15 10 0.28
16 14 0.39
17 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCTATTATTATTA
Found at i:182769 original size:13 final size:13
Alignment explanation
Indices: 182751--182780 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
182741 CGAACCGAAT
182751 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
182764 TTTTAATTTTTAA
1 TTTTAAATTTTAA
182777 TTTT
1 TTTT
182781 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:184553 original size:16 final size:15
Alignment explanation
Indices: 184532--184561 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
184522 AACACCCGCT
184532 TTAAAAATAATAAAAG
1 TTAAAAATAA-AAAAG
184548 TTAAAAATAAAAAA
1 TTAAAAATAAAAAA
184562 CTTCTTGCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
TTAAAAATAAAAAAG
Found at i:184677 original size:19 final size:17
Alignment explanation
Indices: 184628--184671 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
184618 TGATATAATG
184628 TCTCTATTACTTAAACC
1 TCTCTATTACTTAAACC
184645 TCTCTATTACTTAAACC
1 TCTCTATTACTTAAACC
184662 TCTCT-TTACT
1 TCTCTATTACT
184672 AATTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (17 bp):
TCTCTATTACTTAAACC
Found at i:185943 original size:73 final size:72
Alignment explanation
Indices: 185813--185985 Score: 220
Period size: 73 Copynumber: 2.3 Consensus size: 72
185803 TAAATAAGGA
* *
185813 GGTACCGATACCCCTCCTAGAGGTACCGTACCCATATGCCAATTTTGGCTCCAAGAAAAATAGAA
1 GGTACCGATA-CCC-CCTAGAGGTACCGTACCCATATGCCAATTTTAGCTCCAAGAAAAACAGAA
185878 TGCCCAATG
64 TGCCCAATG
* * * * ** *
185887 GGTACCGATACCCCCTAGAGGTACTGATTCCCTTGTGTTAATTTTAGCTCCGAGAAAAACAGAAT
1 GGTACCGATACCCCCTAGAGGTACCG-TACCCATATGCCAATTTTAGCTCCAAGAAAAACAGAAT
*
185952 GTCCAATG
65 GCCCAATG
185960 GGTACCGATACCCCCATAGAGGTACC
1 GGTACCGATACCCCC-TAGAGGTACC
185986 AATACCCGTA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 12 0.14
73 55 0.64
74 19 0.22
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (72 bp):
GGTACCGATACCCCCTAGAGGTACCGTACCCATATGCCAATTTTAGCTCCAAGAAAAACAGAATG
CCCAATG
Found at i:193468 original size:46 final size:46
Alignment explanation
Indices: 193396--193504 Score: 148
Period size: 46 Copynumber: 2.4 Consensus size: 46
193386 GGTACACTGA
* *
193396 GGGTGCATCGATGTATAAAATACATTCGATGTTTCAAACA-AGCCT
1 GGGTGCATCGATGCATAAAATACATTCGATGTTTCAAAAATAGCCT
* * *
193441 GGAGTGCATCGATGCATAAAATGCATTCGATGTTTTAAAAATAGCTT
1 GG-GTGCATCGATGCATAAAATACATTCGATGTTTCAAAAATAGCCT
*
193488 GGGTGCATTGATGCATA
1 GGGTGCATCGATGCATA
193505 GCTTATGCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.04
46 48 0.86
47 6 0.11
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (46 bp):
GGGTGCATCGATGCATAAAATACATTCGATGTTTCAAAAATAGCCT
Found at i:193910 original size:13 final size:13
Alignment explanation
Indices: 193889--193921 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
193879 TAAGATTTTC
193889 TTTGAAAACAATT
1 TTTGAAAACAATT
*
193902 TTTGTAAACAA-T
1 TTTGAAAACAATT
193914 TTTGAAAA
1 TTTGAAAA
193922 TTTACTCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (13 bp):
TTTGAAAACAATT
Found at i:194618 original size:27 final size:27
Alignment explanation
Indices: 194579--194633 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
194569 TGTGGGTGCC
* * *
194579 GGTGGAGGTGGAGCACGAGAGGAGCTA
1 GGTGCAGGAGGAGCACGAGAAGAGCTA
* *
194606 GGTGCAGGAGGAGCTCGTGAAGAGCTA
1 GGTGCAGGAGGAGCACGAGAAGAGCTA
194633 G
1 G
194634 CTCCCGGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.13, G:0.49, T:0.13
Consensus pattern (27 bp):
GGTGCAGGAGGAGCACGAGAAGAGCTA
Found at i:196173 original size:23 final size:23
Alignment explanation
Indices: 196145--196228 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
196135 ATGCATTGTT
*
196145 GAGTGCATCGATGCACATTCAAA
1 GAGTGCATCGATGCACATTCATA
* *
196168 GAGTGCATCGGTGTATC-TTCATA
1 GAGTGCATCGATGCA-CATTCATA
*
196191 -A-TGTATCGATGCACATTCATA
1 GAGTGCATCGATGCACATTCATA
* *
196212 GGGATGGATCGATGCAC
1 GAG-TGCATCGATGCAC
196229 TGGATAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 15 0.31
22 1 0.02
23 18 0.38
24 13 0.27
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCATA
Found at i:200097 original size:22 final size:21
Alignment explanation
Indices: 200055--200094 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
200045 AAGACTATTT
200055 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
200076 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
200095 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:202138 original size:65 final size:65
Alignment explanation
Indices: 202019--202145 Score: 161
Period size: 65 Copynumber: 2.0 Consensus size: 65
202009 TACACTGAGG
* * *
202019 GTGCATCGATGCATAAAATTCATTTGATGTTTCAAACACTCCTGGAGTGTATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATTCATTCGATGTTTCAAACAATCCTGGAGTGCATCGATGCATGGTAT
* *
202084 GTGCATCGATGCATAAAATGT-ATTCGATGTTTTAAA-AATAGCTTGG-GTGCATCGATGCATGG
1 GTGCATCGATGCATAAAAT-TCATTCGATGTTTCAAACAAT--CCTGGAGTGCATCGATGCATGG
202146 CTTATGCATC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
64 2 0.04
65 47 0.87
66 5 0.09
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATTCATTCGATGTTTCAAACAATCCTGGAGTGCATCGATGCATGGTAT
Found at i:204728 original size:117 final size:117
Alignment explanation
Indices: 204589--205020 Score: 550
Period size: 117 Copynumber: 3.7 Consensus size: 117
204579 TGATACTAAG
* * *
204589 TGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTGAGTGTGCT
*
204653 AAATGATAAGGAAATCATATTGAGTATATAGATTTCCAAATAGGGCACTTTA
66 AAATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTA
* * *
204705 TGTACTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAATGTGCT
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTGAGTGTGCT
204770 AAATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTA
66 AAATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTA
*
204822 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCACT-ACGGGTGC
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTGA-GTGTGC
* * * ** * * * **
204886 TACAAGGATAAGGAAATCATACTAAGGGTATGGATTTTCACATAGGGTACTTCG
65 TA-AATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTA
* * * * * *
204940 TGTGCTAAAAT-G-AGGGGGAAATCAAACTAAGTGTAT-GATCTTCCATATAGAGCACTAAGAGT
1 TGTGCTAAAATGGTA-AGGG-AATCATACTGAGTGTATGGAT-TTCCAGATAGAGCACTGAGTGT
*
205002 GCTAATATTATAAGGAAAT
63 GCTAA-ATGATAAGGAAAT
205021 TATACGAATT
Statistics
Matches: 282, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
116 7 0.02
117 174 0.62
118 100 0.35
119 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTGAGTGTGCT
AAATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTA
Found at i:204736 original size:59 final size:58
Alignment explanation
Indices: 204589--205043 Score: 400
Period size: 59 Copynumber: 7.8 Consensus size: 58
204579 TGATACTAAG
*
204589 TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAT-GGAGCAC-TGA
1 TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGG-GCACTTTA
* * * *
204646 GTGTGCTAAATGATAAGGAAATCATATTGAGTATATAGATTTCCAAATAGGGCACTTTA
1 -TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCACTTTA
* * * **
204705 TGTACTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGAT-GGAGCACTGAA
1 TGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGG-GCACTTTA
* * *
204764 TGTGCTAAATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTA
1 TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCACTTTA
* * * ***
204822 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTACG
1 TGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCACTTTA
* * * * * * * **
204881 GGTGCTACAAGGATAAGGAAATCATACTAAGGGTATGGATTTTCACATAGGGTACTTCG
1 TGTGCTA-AATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCACTTTA
*** * * * * *
204940 TGTGCTAAAATGAGGGGGAAATCAAACTAAGTGTAT-GATCTTCCATATAGAGCAC-TAA
1 TGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGAT-TTCCAGATAGGGCACTTTA
* * * * *
204998 GAGTGCTAATATTATAAGGAAATTATAC-GAATTGTATGAATTTCCA
1 -TGTGCTAA-ATGATAAGGAAATCATACTG-AGTGTATGGATTTCCA
205044 ATGGAATGTA
Statistics
Matches: 319, Mismatches: 65, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
58 109 0.34
59 207 0.65
60 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (58 bp):
TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCACTTTA
Found at i:212309 original size:23 final size:23
Alignment explanation
Indices: 212283--212349 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
212273 CACCACAACT
* *
212283 CGTATAAATGCACTGAAGTTCCA
1 CGTAGAAATGCACTGAAGTGCCA
* * * *
212306 CGTAGAATTGCACTTAAGGGCCG
1 CGTAGAAATGCACTGAAGTGCCA
212329 CGTAGAAATGCACTGAAGTGC
1 CGTAGAAATGCACTGAAGTGC
212350 AATATAAGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACTGAAGTGCCA
Found at i:214759 original size:58 final size:58
Alignment explanation
Indices: 214688--215155 Score: 335
Period size: 59 Copynumber: 8.0 Consensus size: 58
214678 TTACCAAATG
* *
214688 GCACTAAGTGTGCTAAATGATAAGGAAATCATAATGAGTGTATGGATTTCCAGATGGA
1 GCACTGAGTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
* * * *
214746 GCACTGAGTGTGCTAAATGATAAGGAAATCATATTGAGTATATGAATTTCCAAATAGG-
1 GCACTGAGTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAT-GGA
* * *
214804 GCACCTTA-TATGCTAAAATGGTAA-GAGAATCATACTGAGTGTATGGATTTCCAGATGGA
1 GCA-CTGAGTGTGCT-AAATGATAAGGA-AATCATACTGAGTGTATGGATTTCCAGATGGA
* * * *
214863 GCACTGAATGTGCTAAATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGG-
1 GCACTGAGTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAT-GGA
* * * * * * *
214921 GCACTTTA-TGTACTAAAATGATAAGGGAATTATACTGAGTGTATGAATTTTCAGATAGA
1 GCAC-TGAGTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
* * * * * * * *
214980 GCACT-ACGGGTGCTACAAGGATAACGAAATCATACTAAGGGTATGGTTTTTCACATAGG-
1 GCACTGA-GTGTGCTA-AATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAT-GGA
** *** * * * *
215039 GCACTTCGTGTGCTAAAATGAGGGGGAAATCAAACTAAGTGTAT-GATCTTCCATATAGA
1 GCACTGAGTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGAT-TTCCAGATGGA
* * * * * * * *
215098 GCACTAAGAGTCCTAATATTATAAGTAAATTATAC-GAATTGTATGAATTTCCA-ATGGA
1 GCACTGAGTGTGCTAA-ATGATAAGGAAATCATACTG-AGTGTATGGATTTCCAGATGGA
215156 ATGTATGGAT
Statistics
Matches: 320, Mismatches: 68, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
57 1 0.00
58 120 0.38
59 195 0.61
60 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (58 bp):
GCACTGAGTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
Found at i:214837 original size:117 final size:116
Alignment explanation
Indices: 214698--215013 Score: 447
Period size: 117 Copynumber: 2.7 Consensus size: 116
214688 GCACTAAGTG
*
214698 TGCT-AAATGATAAGGAAATCATAATGAGTGTATGGATTTCCAGATGGAGCACTGAGTGTGCTAA
1 TGCTAAAATGATAAGG-AATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAGTGTGCTAA
214762 ATGATAAGGAAATCATATTGAGTATATGAATTTCCAAATAGGGCACCTTATA
65 ATGATAAGGAAATCATATTGAGTATATGAATTTCCAAATAGGGCACCTTATA
* *
214814 TGCTAAAATGGTAAGAGAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAATGTGCTAA
1 TGCTAAAATGATAAG-GAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAGTGTGCTAA
* * *
214879 ATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTATG
65 ATGATAAGGAAATCATATTGAGTATATGAATTTCCAAATAGGGCACCTTATA
* * * * * *
214931 TACTAAAATGATAAGGGAATTATACTGAGTGTATGAATTTTCAGATAGAGCACT-ACGGGTGCTA
1 TGCTAAAATGATAA-GGAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGA-GTGTGCTA
* *
214995 CAAGGATAACGAAATCATA
64 -AATGATAAGGAAATCATA
215014 CTAAGGGTAT
Statistics
Matches: 179, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
116 5 0.03
117 156 0.87
118 18 0.10
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (116 bp):
TGCTAAAATGATAAGGAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAGTGTGCTAAA
TGATAAGGAAATCATATTGAGTATATGAATTTCCAAATAGGGCACCTTATA
Found at i:214843 original size:59 final size:58
Alignment explanation
Indices: 214696--214970 Score: 281
Period size: 58 Copynumber: 4.7 Consensus size: 58
214686 TGGCACTAAG
* * * * *
214696 TGTGCTAAATGATAAGGAAATCATAATGAGTGTATGGATTTCCAGAT-GGAGCA-CTGA
1 TGTGCTAAATGATAAGGAAATCATACTGAGTATATGAATTTCCAAATAGG-GCACCTTA
*
214753 GTGTGCTAAATGATAAGGAAATCATATTGAGTATATGAATTTCCAAATAGGGCACCTTA
1 -TGTGCTAAATGATAAGGAAATCATACTGAGTATATGAATTTCCAAATAGGGCACCTTA
* * * * * *
214812 TATGCTAAAATGGTAA-GAGAATCATACTGAGTGTATGGATTTCCAGAT-GGAGCA-CTGAA
1 TGTGCT-AAATGATAAGGA-AATCATACTGAGTATATGAATTTCCAAATAGG-GCACCT-TA
* * *
214871 TGTGCTAAATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTA
1 TGTGCTAAATGATAAGGAAATCATACTGAGTATATGAATTTCCAAATAGGGCACCTTA
* * * *
214929 TGTACTAAAATGATAAGGGAATTATACTGAGTGTATGAATTT
1 TGTGCT-AAATGATAAGGAAATCATACTGAGTATATGAATTT
214971 TCAGATAGAG
Statistics
Matches: 182, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
58 100 0.55
59 82 0.45
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (58 bp):
TGTGCTAAATGATAAGGAAATCATACTGAGTATATGAATTTCCAAATAGGGCACCTTA
Found at i:214984 original size:59 final size:58
Alignment explanation
Indices: 214696--215102 Score: 343
Period size: 59 Copynumber: 6.9 Consensus size: 58
214686 TGGCACTAAG
* * *
214696 TGTGCTAAATGATAAGGAAATCATAATGAGTGTATGGATTTCCAGATGGAGCAC-TGA
1 TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTTTA
* * * * * *
214753 GTGTGCTAAATGATAAGGAAATCATATTGAGTATATGAATTTCCAAATAGGGCACCTTA
1 -TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTTTA
* * * **
214812 TATGCTAAAATGGTAA-GAGAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAA
1 TGTGCT-AAATGATAAGGA-AATCATACTGAGTGTATGGATTTCCAGATAGAGCACTTTA
* * * *
214871 TGTGCTAAATGATAAGGAAATCATATTGAGTATATGGATTTCCAAATAGGGCACTTTA
1 TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTTTA
* * * * * ***
214929 TGTACTAAAATGATAAGGGAATTATACTGAGTGTATGAATTTTCAGATAGAGCACTACG
1 TGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTTTA
* * * * * * * * * **
214988 GGTGCTACAAGGATAACGAAATCATACTAAGGGTATGGTTTTTCACATAGGGCACTTCG
1 TGTGCTA-AATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTTTA
*** * * *
215047 TGTGCTAAAATGAGGGGGAAATCAAACTAAGTGTAT-GATCTTCCATATAGAGCACT
1 TGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGAT-TTCCAGATAGAGCACT
215103 AAGAGTCCTA
Statistics
Matches: 277, Mismatches: 64, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
58 104 0.38
59 172 0.62
60 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (58 bp):
TGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCACTTTA
Found at i:216490 original size:23 final size:20
Alignment explanation
Indices: 216460--216517 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
216450 CCCATTCAAC
*
216460 GTGTATCGATACCCTCTTTGAAT
1 GTGTATCGATACCC-CTAT--AT
216483 GTGTATCGATACCCCTATAT
1 GTGTATCGATACCCCTATAT
*
216503 GGGTATCGATACCCC
1 GTGTATCGATACCCC
216518 CTGTCAGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 16 0.48
22 3 0.09
23 14 0.42
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (20 bp):
GTGTATCGATACCCCTATAT
Found at i:216510 original size:20 final size:21
Alignment explanation
Indices: 216440--216517 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 21
216430 TTGTGCACCA
* *
216440 GGTATCGATACCCAT-TCAACG
1 GGTATCGATACCCCTAT-AATG
* *
216461 TGTATCGATACCCTCTTTGAATG
1 GGTATCGATACCC-CTAT-AATG
*
216484 TGTATCGATACCCCTAT-ATG
1 GGTATCGATACCCCTATAATG
216504 GGTATCGATACCCC
1 GGTATCGATACCCC
216518 CTGTCAGGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.33
21 12 0.24
22 4 0.08
23 17 0.35
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCCCTATAATG
Found at i:218762 original size:13 final size:14
Alignment explanation
Indices: 218731--218764 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
218721 AGGGGCAGTA
218731 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
218745 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
218757 ATTTTCAA
1 ATTTTCAA
218765 TAAGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 15 0.79
14 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Done.