Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002856.1 Hibiscus syriacus cultivar Beakdansim tig00005882_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: 208120
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3250 original size:38 final size:38
Alignment explanation
Indices: 3199--3276 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
3189 CGCGATTCTC
3199 TGGTGATGCATGTAATGTTCTCCATTTTCAATCTTCAT
1 TGGTGATGCATGTAATGTTCTCCATTTTCAATCTTCAT
*
3237 TGGTGATGCATGTAATGTTCTCCCTTTTCAATCTTCAT
1 TGGTGATGCATGTAATGTTCTCCATTTTCAATCTTCAT
3275 TG
1 TG
3277 TTTTCCATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (38 bp):
TGGTGATGCATGTAATGTTCTCCATTTTCAATCTTCAT
Found at i:8406 original size:21 final size:21
Alignment explanation
Indices: 8381--8422 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
8371 CATACAGGCA
8381 TGCAAATCTAAACAACCGAAC
1 TGCAAATCTAAACAACCGAAC
8402 TGCAAATCTAAACAACCGAAC
1 TGCAAATCTAAACAACCGAAC
8423 GCGGAGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.29, G:0.10, T:0.14
Consensus pattern (21 bp):
TGCAAATCTAAACAACCGAAC
Found at i:11474 original size:135 final size:136
Alignment explanation
Indices: 11213--11529 Score: 338
Period size: 135 Copynumber: 2.3 Consensus size: 136
11203 GATTAATTCG
* ** * * *
11213 AACTAAAAACAAGTCCTAATTCGATTTGATCATAAAAA-AAACCAATAACCTGAACTCTAATCGA
1 AACTAAAAACAAGTCCTGATTCGATTTGATCATAAAAAGTCACC----A--TGGATTCTAATTGA
* * * * * * *
11277 TCA-AAATCCAAACTAATTGTACTCAAAACGATTCGGACCCGGATATAATCGAGATAATCCT-AA
60 T-ATAAATCAAAACCAACTGTACTCAAAACGATTCGGAACCGGATACAATCGAAATAACCCTAAA
* *
11340 ACTCTG-GAAATGG
124 AATCTGAG-AATGA
*
11353 AGCTAAAAACAAGTCCTGATTCGATTTGATCATAAAAAGTCACCATGGATTCTAATTGATATAAA
1 AACTAAAAACAAGTCCTGATTCGATTTGATCATAAAAAGTCACCATGGATTCTAATTGATATAAA
* *
11418 TCAAAACCAACTGTACTCAAAACGATT-TGAACCGGAATACAATCGAAATTACCCTAAAAATCTG
66 TCAAAACCAACTGTACTCAAAACGATTCGGAACCGG-ATACAATCGAAATAACCCTAAAAATCTG
11482 AGAATGA
130 AGAATGA
* *
11489 AACTAAAAACAAGTCTTGATTTGATTTGATCATAAAAAGTC
1 AACTAAAAACAAGTCCTGATTCGATTTGATCATAAAAAGTC
11530 GACAACTTGA
Statistics
Matches: 151, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
134 7 0.05
135 54 0.36
136 49 0.32
137 2 0.01
140 36 0.24
141 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.25
Consensus pattern (136 bp):
AACTAAAAACAAGTCCTGATTCGATTTGATCATAAAAAGTCACCATGGATTCTAATTGATATAAA
TCAAAACCAACTGTACTCAAAACGATTCGGAACCGGATACAATCGAAATAACCCTAAAAATCTGA
GAATGA
Found at i:11619 original size:125 final size:125
Alignment explanation
Indices: 11302--11796 Score: 430
Period size: 125 Copynumber: 3.8 Consensus size: 125
11292 ATTGTACTCA
* * * *
11302 AAACGATTCGGACCCGGA-TATAATCGAGATAATCCTAAACTCTG-GAAATGGAGCTAAAAACAA
1 AAACGATTCGAACCC-GATTACAAT-GAGAT-ATCCTAAAATCTGAG-AATGGAACTAAAAACAA
* * * * * **
11365 GTCCTGATTCGATTTGATCATAAAAAGTC-AC--CATGGATTCTAATTGATATAAATCAAAACCA
62 GTCTTAATTAGATTTGATCATAAAAAGTCGACAACTTGGATTCTAA-TCA-AT---TCAATTCCA
11427 ACTGTACT
122 A----ACT
* * * * * *
11435 CAAAACGATTTGAACCGGAATACAATCGAAATTACCCTAAAAATCTGAGAATGAAACTAAAAACA
1 --AAACGATTCGAACCCGATTACAAT-GAGA-TATCCT-AAAATCTGAGAATGGAACTAAAAACA
* * * * *
11500 AGTCTTGATTTGATTTGATCATAAAAAGTCGACAACTTGAATTCTAATCGATTCAATTCCAAATT
61 AGTCTTAATTAGATTTGATCATAAAAAGTCGACAACTTGGATTCTAATCAATTCAATTCCAAACT
* * *
11565 AAATGATTCGAACCCGATTACAATGAGATATCCTAAAATCTGAGAATGGAACTAAAAACAAGCCC
1 AAACGATTCGAACCCGATTACAATGAGATATCCTAAAATCTGAGAATGGAACTAAAAACAAGTCT
* * *
11630 TAATTAGATTTGATCATAAAATGTCGACAACATGGATTCTAATCAATTCAATTCCAAGCT
66 TAATTAGATTTGATCATAAAAAGTCGACAACTTGGATTCTAATCAATTCAATTCCAAACT
* ** *
11690 AAACGATTCGAACCCGATTGCAATGAGATATCCTAAAATCTGA-AAACGAATCTAAAAGCAAGT-
1 AAACGATTCGAACCCGATTACAATGAGATATCCTAAAATCTGAGAATGGAA-CTAAAAACAAGTC
*
11753 TCTAATTCA-ATTTGATCATAGAAAAGGTCAACAACTTGGATTCT
65 T-TAATT-AGATTTGATCATA-AAAA-GTCGACAACTTGGATTCT
11797 CATTGATCTG
Statistics
Matches: 303, Mismatches: 45, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
124 5 0.02
125 147 0.49
126 9 0.03
127 19 0.06
128 20 0.07
130 2 0.01
134 10 0.03
135 25 0.08
136 50 0.17
137 5 0.02
138 1 0.00
139 10 0.03
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (125 bp):
AAACGATTCGAACCCGATTACAATGAGATATCCTAAAATCTGAGAATGGAACTAAAAACAAGTCT
TAATTAGATTTGATCATAAAAAGTCGACAACTTGGATTCTAATCAATTCAATTCCAAACT
Found at i:13855 original size:16 final size:16
Alignment explanation
Indices: 13820--13860 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
13810 GTTTACTTCA
*
13820 GAATGATT-AAACGTT
1 GAATGATTCAAACGCT
*
13835 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
13851 GAATGATTCA
1 GAATGATTCA
13861 GAGGCTCTGT
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:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:13944 original size:27 final size:27
Alignment explanation
Indices: 13912--13978 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
13902 GATAATGGAT
*
13912 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTATG
*
13939 CTGAATCATTCAGAATGTGCTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
13966 CTGAATCATTCAG
1 CTGAATCATTCAG
13979 CACTGTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTATG
Found at i:14245 original size:2 final size:2
Alignment explanation
Indices: 14238--14263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14228 AATGTTGCTT
14238 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
14264 CCATGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16382 original size:6 final size:6
Alignment explanation
Indices: 16371--16423 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
16361 GTGACAGTGG
* * *
16371 TGGTGA TGGTGA TGGAGA TGGAGA TGGTAGAA GTGGTGA TGGTGA TGGAGA
1 TGGTGA TGGTGA TGGTGA TGGTGA TGGT-G-A -TGGTGA TGGTGA TGGTGA
16422 TG
1 TG
16424 AAGATGATGG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 33 0.80
7 2 0.05
8 2 0.05
9 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.49, T:0.26
Consensus pattern (6 bp):
TGGTGA
Found at i:16434 original size:27 final size:28
Alignment explanation
Indices: 16374--16434 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
16364 ACAGTGGTGG
*
16374 TGATGGTGATGGAGATGGAGATGGTAGA
1 TGATGGTGATGGAGATGGAGATGGAAGA
* *
16402 AG-TGGTGATGGTGATGGAGAT-GAAGA
1 TGATGGTGATGGAGATGGAGATGGAAGA
16428 TGATGGT
1 TGATGGT
16435 AGTGATGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 5 0.18
27 22 0.79
28 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.46, T:0.26
Consensus pattern (28 bp):
TGATGGTGATGGAGATGGAGATGGAAGA
Found at i:16446 original size:24 final size:25
Alignment explanation
Indices: 16412--16471 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
16402 AGTGGTGATG
*
16412 GTGATGGAGATGA-AGATGATGGTA
1 GTGATGTAGATGATAGATGATGGTA
*
16436 GTGATGTAGATGATTGAGATGGTGGTA
1 GTGATGTAGATGA-T-AGATGATGGTA
16463 GTGATGTAG
1 GTGATGTAG
16472 TAGTTGTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 12 0.39
27 19 0.61
ACGTcount: A:0.28, C:0.00, G:0.42, T:0.30
Consensus pattern (25 bp):
GTGATGTAGATGATAGATGATGGTA
Found at i:18346 original size:24 final size:24
Alignment explanation
Indices: 18319--18376 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
18309 AGGAAATGAC
*
18319 TGTGGGGCTGGAAAAACAGCACCT
1 TGTGGGGCTGGAAAAACAGAACCT
18343 TGTGGGGCTGGAAAAACAGAACCT
1 TGTGGGGCTGGAAAAACAGAACCT
18367 TGTGGGGCTG
1 TGTGGGGCTG
18377 TTATAAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.38, T:0.19
Consensus pattern (24 bp):
TGTGGGGCTGGAAAAACAGAACCT
Found at i:21691 original size:25 final size:25
Alignment explanation
Indices: 21663--21710 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
21653 ACAAGTCATA
*
21663 TTCACAATCTGAATTAATA-ATAGTG
1 TTCACAATC-CAATTAATATATAGTG
*
21688 TTCACAGTCCAATTAATATATAG
1 TTCACAATCCAATTAATATATAG
21711 ATGAAAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (25 bp):
TTCACAATCCAATTAATATATAGTG
Found at i:41231 original size:19 final size:18
Alignment explanation
Indices: 41195--41229 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41185 AGTATGTTCA
41195 GGGGGTATCGATTCCCCT
1 GGGGGTATCGATTCCCCT
41213 GGGGGTATCGATTCCCC
1 GGGGGTATCGATTCCCC
41230 CTAAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.29, G:0.34, T:0.26
Consensus pattern (18 bp):
GGGGGTATCGATTCCCCT
Found at i:42626 original size:34 final size:32
Alignment explanation
Indices: 42564--42633 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
42554 ACCTTACAAC
* *
42564 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
42596 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
42630 TCCC
1 TCCC
42634 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:42873 original size:20 final size:22
Alignment explanation
Indices: 42848--42887 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
42838 AGTCGTATAT
42848 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
42868 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
42888 AATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:42939 original size:21 final size:21
Alignment explanation
Indices: 42915--42957 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
42905 CCCAGAATAG
*
42915 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
42936 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
42957 A
1 A
42958 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:43017 original size:21 final size:21
Alignment explanation
Indices: 42993--43036 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
42983 CTGTTGAACA
* *
42993 GGGGGGCAATTGGTACCCCCT
1 GGGGGGCAATCGATACCCCCT
*
43014 GGGGGGGAATCGATACCCCCT
1 GGGGGGCAATCGATACCCCCT
43035 GG
1 GG
43037 ACATTCTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (21 bp):
GGGGGGCAATCGATACCCCCT
Found at i:43099 original size:21 final size:20
Alignment explanation
Indices: 43070--43148 Score: 87
Period size: 21 Copynumber: 4.1 Consensus size: 20
43060 AAAACCTGCA
43070 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
43090 GGGGAGTATCTGTA--CCC--
1 GGGG-GTATCTGTACCCCCTG
43107 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCT-G
* *
43127 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTACCCCCTG
43147 GG
1 GG
43149 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
15 9 0.18
16 3 0.06
17 3 0.06
19 3 0.06
20 7 0.14
21 25 0.50
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.23
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:43142 original size:36 final size:36
Alignment explanation
Indices: 43071--43142 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
43061 AAACCTGCAG
* *
43071 GGGGTATCTGTACCCCCTGGGGGAGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGAGAATCTATACCC
*
43107 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGAGAATCTATACCC
43143 CCTGGGCAAT
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:0.15, C:0.28, G:0.33, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGAGAATCTATACCC
Found at i:43270 original size:29 final size:31
Alignment explanation
Indices: 43238--43297 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
43228 AAACTTTGAA
*
43238 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCAAAAAACCATTTTG
43267 TAAATTCAATTCAAGTCAAAAAACCATTTTG
1 TAAATTCAATTCAAGTCAAAAAACCATTTTG
43298 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCAAAAAACCATTTTG
Found at i:45952 original size:34 final size:32
Alignment explanation
Indices: 45899--45968 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
45889 ACCTTACAAC
*
45899 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
* *
45931 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
45965 TCCC
1 TCCC
45969 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:46208 original size:20 final size:22
Alignment explanation
Indices: 46183--46222 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
46173 AGTCGTATAT
46183 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
46203 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
46223 AATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:46289 original size:21 final size:22
Alignment explanation
Indices: 46250--46293 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
46240 CCCAGAATAG
*
46250 AGGGAATCGGTACCCCCTTCAT
1 AGGGAATCGATACCCCCTTCAT
46272 AGGGAATCGATA-CCCCTTCAT
1 AGGGAATCGATACCCCCTTCAT
46293 A
1 A
46294 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (22 bp):
AGGGAATCGATACCCCCTTCAT
Found at i:46432 original size:21 final size:21
Alignment explanation
Indices: 46406--46470 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
46396 AAAACCTGCA
46406 GGGGGGTATCTGTACCCCCTG
1 GGGGGGTATCTGTACCCCCTG
*
46427 GGGGGGTATCTGTACCCCCTA
1 GGGGGGTATCTGTACCCCCTG
* *
46448 GGGGGGAATCTATACCCCCTG
1 GGGGGGTATCTGTACCCCCTG
46469 GG
1 GG
46471 CAATCTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGTATCTGTACCCCCTG
Found at i:46592 original size:29 final size:31
Alignment explanation
Indices: 46560--46618 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 31
46550 AAACTTTGAA
46560 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
46589 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
46619 TGCCTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:48735 original size:13 final size:13
Alignment explanation
Indices: 48698--48737 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
48688 TCAATATTGA
48698 AAAATAAATA-TT
1 AAAATAAATATTT
*
48710 AAAATAATTTATTT
1 AAAATAA-ATATTT
48724 AAAATAAATATTT
1 AAAATAAATATTT
48737 A
1 A
48738 TTTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:48752 original size:16 final size:17
Alignment explanation
Indices: 48711--48754 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
48701 ATAAATATTA
48711 AAATAATTTATTTAAAAT
1 AAAT-ATTTATTTAAAAT
*
48729 AAATATTTATTT-ATAT
1 AAATATTTATTTAAAAT
*
48745 ATATATTTAT
1 AAATATTTAT
48755 GACTATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.50
17 8 0.33
18 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATATTTATTTAAAAT
Found at i:49737 original size:17 final size:16
Alignment explanation
Indices: 49715--49747 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
49705 TCCCTCCGTT
49715 TTTTTCTGTTTTTTTTC
1 TTTTTCT-TTTTTTTTC
49732 TTTTTCTTTTTTTTTC
1 TTTTTCTTTTTTTTTC
49748 AGGTTGGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:50182 original size:11 final size:11
Alignment explanation
Indices: 50159--50190 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
50149 TGTAATTAAT
50159 TATTTATATATA
1 TATTTA-ATATA
50171 TATTTAATATA
1 TATTTAATATA
50182 TATTTAATA
1 TATTTAATA
50191 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:50194 original size:3 final size:3
Alignment explanation
Indices: 50186--50235 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
50176 AATATATATT
50186 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50234 TA
1 TA
50236 TGGATAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:51033 original size:339 final size:340
Alignment explanation
Indices: 50553--51202 Score: 958
Period size: 339 Copynumber: 1.9 Consensus size: 340
50543 AGAATTATGC
* * *
50553 AAAAAGTTGAACAAGTTCTTCTTATTACGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ***
50618 TATGAACTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATTC
66 TATGAACTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAACCAAAAGGTTGAACAAATTC
*
50683 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAA
** *
50748 AAGCTGATCCATCAA-TTGATGAATTCAAACCAAAAGGTTGAACAAATTC-T-TC-TTATGAACT
196 AAAATAATCCATCAATTTGATGAATT-AAACCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
50809 TCTTCTTCCTTCTTCAGATGAGTT-TTCTCATTATGAA-CTTTCTCTGGAAAAAATAATCCATCA
260 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTT-TCTGGAAAAAATAATCCATCA
50872 ATTTGATGAATTTAGGT
324 ATTTGATGAATTTAGGT
* *
50889 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTC-T-TTCCTTCTTCAGATGACGAGTTCTTCT
1 AAAAAGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * *
50952 CATTATGAAC-TCTTCCTGGCAATGTTGATCCCTCAAATGATGAATTCAAACCAAAAGGTTGAAC
63 CATTATGAACTTC-T-CTGGAAAAGATAATCCATCAAATGATGAATTC-AACCAAAAGGTTGAAC
*
51016 AAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
125 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
* ***
51081 CTGAAAAAAATAATCCATCAATTTGATGAATTTAGGTAAAAGGTTGAACAAATTCTTCTCATTAT
190 CTGAAAAAAATAATCCATCAATTTGATGAATTAAACCAAAAGGTTGAACAAATTCTTCTCATTAT
51146 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTTCTGGAAAA
255 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTTCTGGAAAA
51203 GCTAATCTAT
Statistics
Matches: 279, Mismatches: 23, Indels: 17
0.87 0.07 0.05
Matches are distributed among these distances:
334 13 0.05
335 1 0.00
336 33 0.12
337 21 0.08
338 26 0.09
339 113 0.41
340 11 0.04
341 2 0.01
342 33 0.12
343 22 0.08
344 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (340 bp):
AAAAAGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAACCAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAA
AAAATAATCCATCAATTTGATGAATTAAACCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTTCTGGAAAAAATAATCCATCAAT
TTGATGAATTTAGGT
Found at i:51145 original size:114 final size:113
Alignment explanation
Indices: 50553--51220 Score: 931
Period size: 114 Copynumber: 5.9 Consensus size: 113
50543 AGAATTATGC
* * * * *
50553 AAAAAGTTGAACAAGTTCTTCTTATTACGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
50618 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTAAGGT
50665 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * ***
50730 TATGAACTTTCTCTGGAAAAGCTGATCCATCAATTGATGAATTCAAACC
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATT-AAGGT
50779 AAAAGGTTGAACAAATTC-T-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTT-TTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
50840 TATGAACTTTCTCTGGAAAAAATAATCCATCAATTTGATGAATTTAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAA-TTGATGAATTAAGGT
50889 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTC-T-TTCCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * * * ***
50952 CATTATGAACTCTTC-CTGGCAATGTTGATCCCTCAAATGATGAATTCAAACC
63 CATTATGAACT-TTCTCTGGAAAAGATAATCCATCAATTGATGAATT-AAGGT
*
51004 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
51069 TATGAACTTTCTCTGAAAAAAATAATCCATCAATTTGATGAATTTAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAA-TTGATGAATTAAGGT
51118 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
51183 TATGAACCTTT-TCTGGAAAAGCTAATCTATCAAATGAT
66 TATGAA-CTTTCTCTGGAAAAGATAATCCATCAATTGAT
51221 AGATTTGAAT
Statistics
Matches: 491, Mismatches: 48, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
110 56 0.11
111 58 0.12
112 72 0.15
113 52 0.11
114 157 0.32
115 78 0.16
116 4 0.01
117 14 0.03
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTAAGGT
Found at i:52120 original size:83 final size:83
Alignment explanation
Indices: 51928--52319 Score: 550
Period size: 83 Copynumber: 4.7 Consensus size: 83
51918 CCTACTGAAT
* * *
51928 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTCATCTTTCTAAATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATC-TTCTAAATT
*
51993 CAATAACTAGTTTTACCAAAC
63 CAATAACTAGTTCTACCAAAC
52014 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
* * * ** *
52079 TGATTGGTTCTGTCTAAC
66 TAACTAGTTCTACCAAAC
52097 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
* * * ** *
52162 TGATTGGTTCTGTCTAAC
66 TAACTAGTTCTACCAAAC
* * *
52180 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTCATCTTTCTAAATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATC-TTCTAAATT
*
52245 CAATAACTAGTTTTACCAAAC
63 CAATAACTAGTTCTACCAAAC
52266 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCT
52320 GTTCCAGTTA
Statistics
Matches: 280, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
83 146 0.52
84 19 0.07
85 14 0.05
86 101 0.36
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
TAACTAGTTCTACCAAAC
Found at i:52242 original size:169 final size:166
Alignment explanation
Indices: 51928--52319 Score: 550
Period size: 169 Copynumber: 2.3 Consensus size: 166
51918 CCTACTGAAT
* * *
51928 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTCATCTTTCTAAATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATC-TTCTAAATT
*
51993 CAATAACTAGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
63 CAATAACTAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
* * * ** *
52058 ACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAAC
128 ACATTCATCTTCTAAATTCAATAACTAGTTCTACCAAAC
52097 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
* * * ** * * *
52162 TGATTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCT
66 TAACTAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CA
* *
52227 CCTTCATCTTTCTAAATTCAATAACTAGTTTTACCAAAC
129 CATTCATC-TTCTAAATTCAATAACTAGTTCTACCAAAC
52266 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCT
52320 GTTCCAGTTA
Statistics
Matches: 200, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
166 62 0.31
167 11 0.05
168 11 0.05
169 116 0.58
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (166 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
TAACTAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
TTCATCTTCTAAATTCAATAACTAGTTCTACCAAAC
Found at i:53476 original size:8 final size:8
Alignment explanation
Indices: 53463--53552 Score: 70
Period size: 8 Copynumber: 12.1 Consensus size: 8
53453 TGACCCCCTT
53463 TCTTTTTC
1 TCTTTTTC
53471 TCTTTTTC
1 TCTTTTTC
53479 TCTTTTT-
1 TCTTTTTC
53486 T-TTTTTC
1 TCTTTTTC
* *
53493 TATTTTTT
1 TCTTTTTC
*
53501 TATTTATT-
1 TCTTT-TTC
*
53509 TTTTTTTC
1 TCTTTTTC
*
53517 T-TTTTTT
1 TCTTTTTC
53524 TC-TTTTC
1 TCTTTTTC
53531 TCTTTTT-
1 TCTTTTTC
53538 T-TTTTTC
1 TCTTTTTC
53545 T-TTTTTC
1 TCTTTTTC
53552 T
1 T
53553 TCAAGCATAA
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
6 10 0.14
7 25 0.35
8 34 0.48
9 2 0.03
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (8 bp):
TCTTTTTC
Found at i:53485 original size:1 final size:1
Alignment explanation
Indices: 53481--53550 Score: 59
Period size: 1 Copynumber: 70.0 Consensus size: 1
53471 TCTTTTTCTC
* * * * * * * * *
53481 TTTTTTTTTTTCTATTTTTTTATTTATTTTTTTTTCTTTTTTTTCTTTTCTCTTTTTTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53546 TTTTT
1 TTTTT
53551 CTTCAAGCAT
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:53490 original size:14 final size:14
Alignment explanation
Indices: 53463--53550 Score: 80
Period size: 13 Copynumber: 6.5 Consensus size: 14
53453 TGACCCCCTT
53463 TCTTTTTCTCTTTTTC
1 TCTTTTT-T-TTTTTC
53479 TC-TTTTTTTTTT-
1 TCTTTTTTTTTTTC
* *
53491 TCTATTTTTTTAT-
1 TCTTTTTTTTTTTC
*
53504 T-TATTTTTTTTTC
1 TCTTTTTTTTTTTC
53517 T-TTTTTTTCTTTTC
1 TCTTTTTTT-TTTTC
53531 TCTTTTTTTTTTTC
1 TCTTTTTTTTTTTC
53545 T-TTTTT
1 TCTTTTT
53551 CTTCAAGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
12 12 0.19
13 26 0.41
14 13 0.20
15 11 0.17
16 2 0.03
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (14 bp):
TCTTTTTTTTTTTC
Found at i:53524 original size:38 final size:38
Alignment explanation
Indices: 53473--53550 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
53463 TCTTTTTCTC
*
53473 TTTTTCTCTTTTTTTTTTTCTATTTTTTTATTTATTTT
1 TTTTTCTCTTTTTTCTTTTCTATTTTTTTATTTATTTT
* * * *
53511 TTTTTCTTTTTTTTCTTTTCTCTTTTTTTTTTTCTTTT
1 TTTTTCTCTTTTTTCTTTTCTATTTTTTTATTTATTTT
53549 TT
1 TT
53551 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (38 bp):
TTTTTCTCTTTTTTCTTTTCTATTTTTTTATTTATTTT
Found at i:64136 original size:27 final size:28
Alignment explanation
Indices: 64105--64182 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
64095 CTTTGACAGT
64105 AAAATAAATAATAAAATAAAATAAT-TG
1 AAAATAAATAATAAAATAAAATAATATG
* * *
64132 CAAATAAAATAA-AACATATAAATATTATG
1 AAAAT-AAATAATAAAATA-AAATAATATG
64161 AAAAT-AATAAGTAAATATAAAA
1 AAAATAAATAA-TAAA-ATAAAA
64183 ATTTTGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
27 14 0.35
28 12 0.30
29 11 0.28
30 3 0.08
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.26
Consensus pattern (28 bp):
AAAATAAATAATAAAATAAAATAATATG
Found at i:65885 original size:17 final size:16
Alignment explanation
Indices: 65863--65895 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
65853 CCCTCCGTTT
65863 TTTTTCTGTTTTTTTTC
1 TTTTTCT-TTTTTTTTC
65880 TTTTTCTTTTTTTTTC
1 TTTTTCTTTTTTTTTC
65896 AGGTTGGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:66333 original size:11 final size:11
Alignment explanation
Indices: 66317--66341 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
66307 TTATTTATAT
66317 ATATATATTTA
1 ATATATATTTA
66328 ATATATATTTA
1 ATATATATTTA
66339 ATA
1 ATA
66342 ATAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATATTTA
Found at i:66345 original size:3 final size:3
Alignment explanation
Indices: 66337--66377 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
66327 AATATATATT
66337 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
66378 TGGATAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:74276 original size:268 final size:264
Alignment explanation
Indices: 73624--74435 Score: 910
Period size: 261 Copynumber: 3.0 Consensus size: 264
73614 ACCTGCAGGT
* *
73624 GATAAATC-AATAGGTGATGATACCTGGTTTGATAAAGTTAACTTTTCAAAGCGAGACAAAGACC
1 GATAAATCAAATAGGTGATGATACCTGGTTTGATAAAGTTAAATTTTCATAGCGAGACAAAGACC
* ** * * *
73688 ACAAGACGCGATAAGCATTGTCTAC-CATC-TAAGTAATTTCAAGACATCATATGCTTGGTCGGC
66 ACAAGACACGATAAGCATTGTCT-CGCATCTTAA-TCCTTTCAAGACATCATATGTTTGGTCAGA
* * * * * *
73751 AATGATTGGAACTAATGTTAAACCCCATATAAATGCA-AGGCATTAACAGCAATTGTAATAGCAC
129 AATGATCGGAACTAATGTTAAAACCTATATAAAGGCATAAG-ATTAACAGCAACTGTAATAGCAC
* * * *
73815 ATGCAGAAGACGAAACACTATGCATGGT--GGCTGTGACAAAGT---ACTATTCGTATTAGCCAC
193 ATGCAAAAG-CGAAACAATATGCATGGTACGGCTGTGATAAAGTAACACTATT-GTATTAG-CAT
73875 GAAGCACAGA
255 GAAGCACAGA
* * *
73885 GATAAATCCAATAGGTGATTATACCTGGTTTGATAAAGTT-AACTTTCATAGCGAGACAAAGACC
1 GATAAATCAAATAGGTGATGATACCTGGTTTGATAAAGTTAAATTTTCATAGCGAGACAAAGACC
* * * * *
73949 GCAAGAAACAATAAGCATTGTCTCGCATCTAAATCCTTTCAAGGCATCATATGTTTGGTCAGAAA
66 ACAAGACACGATAAGCATTGTCTCGCATCTTAATCCTTTCAAGACATCATATGTTTGGTCAGAAA
* *
74014 TGATCGGAACTAATGTTAAAACCTATATAAAGGCATAAGATTAACAACAACTATAATAGCACATG
131 TGATCGGAACTAATGTTAAAACCTATATAAAGGCATAAGATTAACAGCAACTGTAATAGCACATG
*
74079 CACAAAGCGAAACAATCTGCATGGTACGGCTGTGATAAAGTACACACTATTTGTATTAGCAGTGA
196 CA-AAAGCGAAACAATATGCATGGTACGGCTGTGATAAAGTA-ACACTA-TTGTATTAGCA-TGA
74144 AGCACAGA
257 AGCACAGA
* * *
74152 GATAAATCAAATAGGTGATGATATCTGGTTCGATAAAGTTAAATTTTCATAGCAAGACAAAGACC
1 GATAAATCAAATAGGTGATGATACCTGGTTTGATAAAGTTAAATTTTCATAGCGAGACAAAGACC
* **
74217 ACAAGACACGATAAGCATTGGCTCGTTTCTTAATCCTTTCAAGACATCATATGTTTGGTCAGAAA
66 ACAAGACACGATAAGCATTGTCTCGCATCTTAATCCTTTCAAGACATCATATGTTTGGTCAG-AA
* * * *
74282 TGATAGGAAGTTCAGAACTAAAGTTAAAACCTATATAAAGGCATAAGATTAACAGCTACTGCAAT
130 --AT--G-A--TCGGAACTAATGTTAAAACCTATATAAAGGCATAAGATTAACAGCAACTGTAAT
* * * * * * *
74347 AACACATGCAGAAAACAAAACAATGTGCATGGTACAGCTGTGATGAAGTATACTACGA--GTATT
188 AGCACATGCA-AAAGCGAAACAATATGCATGGTACGGCTGTGATAAAGTA-AC-ACTATTGTATT
* *
74410 AGCAATGAAGCATAAA
250 AGC-ATGAAGCACAGA
74426 GATAAATCAA
1 GATAAATCAA
74436 TACATGATAA
Statistics
Matches: 468, Mismatches: 59, Indels: 35
0.83 0.10 0.06
Matches are distributed among these distances:
260 1 0.00
261 150 0.32
262 37 0.08
263 13 0.03
266 2 0.00
267 57 0.12
268 78 0.17
269 2 0.00
271 2 0.00
273 1 0.00
274 28 0.06
275 1 0.00
276 93 0.20
277 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (264 bp):
GATAAATCAAATAGGTGATGATACCTGGTTTGATAAAGTTAAATTTTCATAGCGAGACAAAGACC
ACAAGACACGATAAGCATTGTCTCGCATCTTAATCCTTTCAAGACATCATATGTTTGGTCAGAAA
TGATCGGAACTAATGTTAAAACCTATATAAAGGCATAAGATTAACAGCAACTGTAATAGCACATG
CAAAAGCGAAACAATATGCATGGTACGGCTGTGATAAAGTAACACTATTGTATTAGCATGAAGCA
CAGA
Found at i:80920 original size:21 final size:22
Alignment explanation
Indices: 80868--80923 Score: 80
Period size: 23 Copynumber: 2.6 Consensus size: 22
80858 TAAATTAATA
*
80868 ATATATAT-AAATGTTTCGATT
1 ATATATGTAAAATGTTTCGATT
80889 ATATTATGTAAAATGTTTCGATT
1 ATA-TATGTAAAATGTTTCGATT
80912 ATA-ATGTAAAAT
1 ATATATGTAAAAT
80924 ATTAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.38
22 4 0.12
23 16 0.50
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.45
Consensus pattern (22 bp):
ATATATGTAAAATGTTTCGATT
Found at i:84502 original size:126 final size:126
Alignment explanation
Indices: 84171--84766 Score: 1048
Period size: 123 Copynumber: 4.8 Consensus size: 126
84161 CTATAATCGG
84171 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
84236 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAG--ATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
84294 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
84359 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
*
84420 TTCACTATTCACGCGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
84485 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGTCACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
84545 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAG-A-A-TA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* * *
84606 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGTCACTAGATATCTCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
*
84667 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTA-TTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
84731 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
84767 ATAACTTAAA
Statistics
Matches: 453, Mismatches: 12, Indels: 14
0.95 0.03 0.03
Matches are distributed among these distances:
121 33 0.07
122 66 0.15
123 115 0.25
124 40 0.09
125 89 0.20
126 110 0.24
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
Found at i:85096 original size:34 final size:32
Alignment explanation
Indices: 85058--85152 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 32
85048 AAATTTAATG
85058 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATA-TATAATTT-TATTTTAAAT
* *
85092 TTAAATTT-GAATA-AT-ATTTT-TTTTTATT
1 TTAAATTTCGAATATATAATTTTATTTTAAAT
85120 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAAT-ATATAATTT-TATTTTAAA
85153 AACATTTATC
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
28 14 0.27
29 5 0.10
30 5 0.10
31 4 0.08
32 4 0.08
33 6 0.12
34 13 0.25
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (32 bp):
TTAAATTTCGAATATATAATTTTATTTTAAAT
Found at i:85747 original size:20 final size:21
Alignment explanation
Indices: 85665--85757 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
85655 ATATGGTATA
*
85665 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
85686 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
85707 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
85728 AACCCTGCGGGCT-CGAATGT
1 AACCCTGCGGGCTAGGAATGT
85748 AACCCTGCGG
1 AACCCTGCGG
85758 AGATGGCATA
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
20 19 0.28
21 46 0.68
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:85786 original size:20 final size:21
Alignment explanation
Indices: 85761--85807 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
85751 CCTGCGGAGA
*
85761 TGGCATAT-AACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
85781 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
85802 GGGCAT
1 TGGCAT
85808 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.21, C:0.13, G:0.40, T:0.26
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:87563 original size:34 final size:31
Alignment explanation
Indices: 87523--87605 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
87513 AATTCTAAAT
87523 AAATAATAATTATATAAATATTATTTTAATA-ATA
1 AAATAATAATTATATAAATA-TA--TTAATATA-A
* *
87557 AAATAATATTTACATAAATATATTAATATAA
1 AAATAATAATTATATAAATATATTAATATAA
* *
87588 AAATAATAACTATTTAAA
1 AAATAATAATTATATAAA
87606 AAAATACTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
31 21 0.50
32 1 0.02
33 2 0.05
34 18 0.43
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
AAATAATAATTATATAAATATATTAATATAA
Found at i:87583 original size:31 final size:33
Alignment explanation
Indices: 87523--87596 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 33
87513 AATTCTAAAT
*
87523 AAATAATAATTATATAAATATTATTTTAATA-ATA
1 AAATAATAATTACATAAATATTA-TTTAATATA-A
*
87557 AAATAATATTTACATAAATA-TA-TTAATATAA
1 AAATAATAATTACATAAATATTATTTAATATAA
87588 AAATAATAA
1 AAATAATAA
87597 CTATTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 15 0.42
32 1 0.03
33 2 0.06
34 18 0.50
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
AAATAATAATTACATAAATATTATTTAATATAA
Found at i:87587 original size:14 final size:15
Alignment explanation
Indices: 87521--87592 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 15
87511 ATAATTCTAA
87521 ATAAATAATAATT-AT
1 ATAAATAAT-ATTAAT
*
87536 ATAAATATTATTTTAAT
1 ATAAATA--ATATTAAT
* *
87553 AATAAAATAATATTTAC
1 -AT-AAATAATATTAAT
87570 ATAAAT-ATATTAAT
1 ATAAATAATATTAAT
87584 ATAAA-AATA
1 ATAAATAATA
87593 ATAACTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
14 14 0.31
15 11 0.24
16 4 0.09
17 9 0.20
18 2 0.04
19 5 0.11
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATAATATTAAT
Found at i:87626 original size:33 final size:34
Alignment explanation
Indices: 87558--87626 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
87548 TTAATAATAA
* * *
87558 AATAATATTTACATAAATATATTAATATAAAAAT
1 AATAATATTTACATAAAAATACTAACATAAAAAT
87592 AATAACTATTTA-A-AAAAATACTAACATAAAAAT
1 AATAA-TATTTACATAAAAATACTAACATAAAAAT
87625 AA
1 AA
87627 ATTTCTTACC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 19 0.61
34 6 0.19
35 6 0.19
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (34 bp):
AATAATATTTACATAAAAATACTAACATAAAAAT
Found at i:99553 original size:2 final size:2
Alignment explanation
Indices: 99548--99572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
99538 AAAATAAAAT
99548 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
99573 TAAAGAAAAA
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:104697 original size:17 final size:17
Alignment explanation
Indices: 104675--104707 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
104665 TCAAATTTTG
104675 AATTAAT-TAACAAAATA
1 AATTAATATAA-AAAATA
104692 AATTAATATAAAAAAT
1 AATTAATATAAAAAAT
104708 TATCTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AATTAATATAAAAAATA
Found at i:109827 original size:20 final size:20
Alignment explanation
Indices: 109789--109827 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
109779 CTAATGACAA
*
109789 TAAAACATATAATATTAAAT
1 TAAAACATATAATAGTAAAT
109809 TAAAA-ATATAAGTAGTAAA
1 TAAAACATATAA-TAGTAAA
109828 AGTAAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (20 bp):
TAAAACATATAATAGTAAAT
Found at i:110310 original size:3 final size:3
Alignment explanation
Indices: 110302--110334 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
110292 CCTTGCTTTC
110302 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
110335 TTTTGTCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:113290 original size:24 final size:24
Alignment explanation
Indices: 113257--113307 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
113247 TCAAGTCACT
*
113257 TTATTGTATCAATAATAAATAACC
1 TTATTATATCAATAATAAATAACC
* *
113281 TTATTATATCAATGATAAATAATC
1 TTATTATATCAATAATAAATAACC
113305 TTA
1 TTA
113308 AAATGATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (24 bp):
TTATTATATCAATAATAAATAACC
Found at i:118548 original size:20 final size:21
Alignment explanation
Indices: 118523--118567 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
118513 TTGTAAATCG
118523 CAACACAGAA-GTCAAATTCA
1 CAACACAGAATGTCAAATTCA
* * *
118543 CAACACTGAATTTCAAATTCG
1 CAACACAGAATGTCAAATTCA
118564 CAAC
1 CAAC
118568 TGAATTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.44, C:0.27, G:0.09, T:0.20
Consensus pattern (21 bp):
CAACACAGAATGTCAAATTCA
Found at i:118560 original size:21 final size:21
Alignment explanation
Indices: 118495--118614 Score: 92
Period size: 20 Copynumber: 6.0 Consensus size: 21
118485 ACCCAGTTTC
* *
118495 CAAAATCGCAACGC-GAATTT
1 CAAATTCGCAACACTGAATTT
* * *
118515 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAACACTGAATTT
*
118535 CAAATTCACAACACTGAATTT
1 CAAATTCGCAACACTGAATTT
118556 CAAATTCGC-A-ACTGAATTT
1 CAAATTCGCAACACTGAATTT
* *
118575 CAAATTCGCAACTC-GATTTT
1 CAAATTCGCAACACTGAATTT
* *
118595 CGAATTCGCAATAC-GAATTT
1 CAAATTCGCAACACTGAATTT
118615 AATTTTGCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
19 21 0.26
20 43 0.54
21 16 0.20
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (21 bp):
CAAATTCGCAACACTGAATTT
Found at i:118600 original size:20 final size:19
Alignment explanation
Indices: 118547--118605 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
118537 AATTCACAAC
118547 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCGCA
118566 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCGCA
* *
118585 ACTCGATTTTCGAATTCGCA
1 ACT-GAATTTCAAATTCGCA
118605 A
1 A
118606 TACGAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (19 bp):
ACTGAATTTCAAATTCGCA
Found at i:118801 original size:14 final size:16
Alignment explanation
Indices: 118782--118818 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
118772 TCCCCATCTC
118782 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
118796 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
118812 TAATTTT
1 TAATTTT
118819 GCAATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:119430 original size:12 final size:12
Alignment explanation
Indices: 119409--119442 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
119399 ACCACATTTC
*
119409 CAATACCAAACA
1 CAATATCAAACA
119421 CAATATCAAACA
1 CAATATCAAACA
*
119433 CAATCTCAAA
1 CAATATCAAA
119443 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:119492 original size:24 final size:24
Alignment explanation
Indices: 119463--119519 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
119453 TTTTCCTAAT
119463 CCAAA-TCTCAATCAACTTTCAGCA
1 CCAAATTC-CAATCAACTTTCAGCA
119487 CCAAATTCCAATCAACTTTCAGCA
1 CCAAATTCCAATCAACTTTCAGCA
119511 CCAAATTCC
1 CCAAATTCC
119520 GGTTTTCGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.37, C:0.35, G:0.04, T:0.25
Consensus pattern (24 bp):
CCAAATTCCAATCAACTTTCAGCA
Found at i:119606 original size:24 final size:24
Alignment explanation
Indices: 119578--119633 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
119568 GTGAGTACTA
**
119578 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACCCGAAATTTGATCTTG
* *
119602 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACCCGAAATTTGATCTTG
119626 GTCAATAC
1 GTCAATAC
119634 TTGGATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (24 bp):
GTCAATACCCGAAATTTGATCTTG
Found at i:121942 original size:18 final size:18
Alignment explanation
Indices: 121919--121954 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
121909 AAGCAAAAGG
121919 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
121937 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
121955 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:122287 original size:63 final size:63
Alignment explanation
Indices: 122188--122355 Score: 248
Period size: 63 Copynumber: 2.7 Consensus size: 63
122178 TCAAATTCTT
* * * *
122188 AACGCAAAAATCGCAATGCGAATTTGACTTTCGCGTTACGAATTTGACTTTCGCAACAATC-A
1 AACGCGAAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCAACAATCGA
* *
122250 CAACGCGAAAATCGCAACGCGAATTTTACTTTCGCGTTGCGATTTTGACTATCGCAACAATCGA
1 -AACGCGAAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCAACAATCGA
**
122314 AACAAGAAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAA
1 AACGCGAAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAA
122356 ATTGTACCTT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
63 93 0.99
64 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (63 bp):
AACGCGAAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCAACAATCGA
Found at i:122464 original size:25 final size:25
Alignment explanation
Indices: 122426--122475 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
122416 AAATCAATTA
*
122426 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
122451 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
122476 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:122883 original size:18 final size:18
Alignment explanation
Indices: 122862--122898 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
122852 GTAATTGGTG
122862 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
122880 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
122898 T
1 T
122899 ATATATAAAA
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:124063 original size:20 final size:20
Alignment explanation
Indices: 124016--124071 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
124006 TGTTGCGATT
124016 GTTGCGAAAGTCAAATTCGC
1 GTTGCGAAAGTCAAATTCGC
**** *
124036 AACACGAAAGTCAAATTTGC
1 GTTGCGAAAGTCAAATTCGC
124056 GTTGCGAAAGTCAAAT
1 GTTGCGAAAGTCAAAT
124072 AAGAAACGCG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
GTTGCGAAAGTCAAATTCGC
Found at i:124132 original size:20 final size:20
Alignment explanation
Indices: 124109--124190 Score: 92
Period size: 20 Copynumber: 4.1 Consensus size: 20
124099 TCGCAACGCC
* **
124109 AATTTGACTTTCGCGTTTTG
1 AATTTGACTTTCGCATTGCG
124129 AATTTGACTTTCGCATTGCG
1 AATTTGACTTTCGCATTGCG
* **
124149 AATTTGACTATCGCAACGCG
1 AATTTGACTTTCGCATTGCG
* *
124169 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCGCATTGCG
124189 AA
1 AA
124191 AGTGTACATT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
AATTTGACTTTCGCATTGCG
Found at i:124351 original size:64 final size:64
Alignment explanation
Indices: 124249--124406 Score: 262
Period size: 64 Copynumber: 2.5 Consensus size: 64
124239 AATTTAAAAC
*
124249 AACAAATCAACTTTTACAAATCAATTAAACAAGTAAAAAATAAGTATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGTATTATTTACACATCAATTA
* * * *
124313 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTTTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGTATTATTTACACATCAATTA
124377 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
124407 ATTCAACAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 84 0.95
65 4 0.05
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGTATTATTTACACATCAATTA
Found at i:125770 original size:21 final size:21
Alignment explanation
Indices: 125744--125903 Score: 194
Period size: 21 Copynumber: 7.6 Consensus size: 21
125734 GTGAATCGGG
* *
125744 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGGC
* **
125765 CTCTTGAATGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
125786 CTCTTGAACGGTGGTAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
125807 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* **
125828 CTCTTGAACGATAGGAGACGC
1 CTCTTGAACGATGGGAGGGGC
*
125849 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
125870 CTCTTGAACGATAGGAGGCGC
1 CTCTTGAACGATGGGAGGGGC
125891 CTCTTGAACGATG
1 CTCTTGAACGATG
125904 ACATGTGAAT
Statistics
Matches: 115, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 115 1.00
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:125810 original size:42 final size:42
Alignment explanation
Indices: 125744--125906 Score: 222
Period size: 42 Copynumber: 3.9 Consensus size: 42
125734 GTGAATCGGG
* * *
125744 CTCTTGAACGGTGGGAGG-GACCTCTTGAATGATGACAGGGGC
1 CTCTTGAACGATAGGAGGCG-CCTCTTGAACGATGACAGGGGC
* * *
125786 CTCTTGAACGGT-GGTAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATAGG-AGGCGCCTCTTGAACGATGACAGGGGC
* *
125828 CTCTTGAACGATAGGAGACGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATAGGAGGCGCCTCTTGAACGATGACAGGGGC
125870 CTCTTGAACGATAGGAGGCGCCTCTTGAACGATGACA
1 CTCTTGAACGATAGGAGGCGCCTCTTGAACGATGACA
125907 TGTGAATCAG
Statistics
Matches: 111, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
41 2 0.02
42 106 0.95
43 3 0.03
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGATAGGAGGCGCCTCTTGAACGATGACAGGGGC
Found at i:127985 original size:20 final size:20
Alignment explanation
Indices: 127960--128025 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
127950 AAACTTAAAT
*
127960 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
127980 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
128000 TCGCAACGCAAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
128020 TCGCAA
1 TCGCAA
128026 TGCGGAACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:128017 original size:40 final size:39
Alignment explanation
Indices: 127955--128042 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
127945 TTCTGAAACT
* * *
127955 TAAATTCGCAACGCGAACATGAAAATCGCAATGCGAAAA
1 TAAAATCGCAACGCAAAAATGAAAATCGCAATGCGAAAA
* *
127994 TGAAAATCGCAACGCAAAAATGAAAATCGCAATGCGGAAC
1 T-AAAATCGCAACGCAAAAATGAAAATCGCAATGCGAAAA
128034 TAAAATCGC
1 TAAAATCGC
128043 GTTGCGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 9 0.21
40 34 0.79
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.15
Consensus pattern (39 bp):
TAAAATCGCAACGCAAAAATGAAAATCGCAATGCGAAAA
Found at i:128078 original size:20 final size:21
Alignment explanation
Indices: 128049--128087 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
128039 TCGCGTTGCG
*
128049 ATTTTGGTGTTGC-AATTTTC
1 ATTTTCGTGTTGCGAATTTTC
128069 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
128088 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (21 bp):
ATTTTCGTGTTGCGAATTTTC
Found at i:128126 original size:17 final size:17
Alignment explanation
Indices: 128106--128140 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
128096 AAAACTATTC
128106 TTCTGCAAATTGAAACT
1 TTCTGCAAATTGAAACT
128123 TTCTGCAAATTGAAACT
1 TTCTGCAAATTGAAACT
128140 T
1 T
128141 GAATGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (17 bp):
TTCTGCAAATTGAAACT
Found at i:128475 original size:22 final size:22
Alignment explanation
Indices: 128445--128501 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
128435 GATGGAGATA
*
128445 GACGGATTTCGCCAGAGATGTG
1 GACGGATTTCGCCAGAGATGGG
* * *
128467 GACGAATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
128489 GACGGATGTCGCC
1 GACGGATTTCGCC
128502 GTAGAGAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:128676 original size:20 final size:19
Alignment explanation
Indices: 128651--128703 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
128641 TAAACGCGCT
* *
128651 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTAAATTC-GTG
*
128671 TTGCGATTTATAAATTCGTG
1 TTGCGAATT-TAAATTCGTG
128691 TTGCGAATTTAAA
1 TTGCGAATTTAAA
128704 AATTGGGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 19 0.68
21 5 0.18
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (19 bp):
TTGCGAATTTAAATTCGTG
Found at i:128706 original size:21 final size:20
Alignment explanation
Indices: 128668--128707 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
128658 TTTGACTTCT
*
128668 GTGTTGCGATTTATAAATTC
1 GTGTTGCGATTTAAAAATTC
128688 GTGTTGCGAATTTAAAAATT
1 GTGTTGCG-ATTTAAAAATT
128708 GGGTTACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (20 bp):
GTGTTGCGATTTAAAAATTC
Found at i:145802 original size:22 final size:22
Alignment explanation
Indices: 145776--145821 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
145766 ATATATATAT
* *
145776 TTAAATTTTTAATTTTAAAATA
1 TTAAATATATAATTTTAAAATA
145798 TTAAATATATAATTTTAAAATA
1 TTAAATATATAATTTTAAAATA
145820 TT
1 TT
145822 GCTTAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATATATAATTTTAAAATA
Found at i:153766 original size:3 final size:3
Alignment explanation
Indices: 153758--153796 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
153748 ACATATAAAT
153758 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
153797 AAACTACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:166331 original size:23 final size:23
Alignment explanation
Indices: 166300--166346 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
166290 CGATCTAAAA
166300 ATATATAGAACTTAACGGATCTT
1 ATATATAGAACTTAACGGATCTT
*
166323 ATATGTAGAACTTAACGGATCTT
1 ATATATAGAACTTAACGGATCTT
166346 A
1 A
166347 CCTCTCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (23 bp):
ATATATAGAACTTAACGGATCTT
Found at i:168852 original size:33 final size:33
Alignment explanation
Indices: 168810--168891 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
168800 TTTATTTTGA
*
168810 CCTTTGAGATCCCCATTTGCATGCACTTTAAAC
1 CCTTTGAGATCACCATTTGCATGCACTTTAAAC
* * * *
168843 CCTTTGAGATCACCATTTGGATGTATTTTGAAC
1 CCTTTGAGATCACCATTTGCATGCACTTTAAAC
* *
168876 CCTTTGAAATCTCCAT
1 CCTTTGAGATCACCAT
168892 GGTCTCCGGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (33 bp):
CCTTTGAGATCACCATTTGCATGCACTTTAAAC
Found at i:171450 original size:2 final size:2
Alignment explanation
Indices: 171437--171501 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
171427 TTATTTTACT
*
171437 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
171479 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
171502 GTGTGTGTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:171740 original size:137 final size:134
Alignment explanation
Indices: 171574--171853 Score: 418
Period size: 133 Copynumber: 2.1 Consensus size: 134
171564 TATTTATCTT
* * * * *
171574 CATTATTTAGTTTTTCTATTACTATTATATAGATTTTTTTTCCTCCCTCTCATATTTAGTTATTA
1 CATTTTTTAATTTTTCCATTACTATTATAT--A--TTTTTTCCTCCCTCTCATATTTAGCTATCA
* *
171639 TATATATATGGTATTAATATTATTATATG-TTTTATTAGCTTTATTTATTTTACTTTATACGCTA
62 TATATATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATACGCTA
*
171703 TTGTTTTA
127 TTATTTTA
*
171711 CATTTTTTAATTTTTCCATTATTATTATATATTTTTTCCTCCCTCTCATATTTAGCTATCATATA
1 CATTTTTTAATTTTTCCATTACTATTATATATTTTTTCCTCCCTCTCATATTTAGCTATCATATA
* *
171776 TATATGGTATTGATATTATTATATGTTTTTATTAATTTTATTTATTCTACTTTATACGCTATTAT
66 TATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATACGCTATTAT
171841 TTTA
131 TTTA
171845 CATTTTTTA
1 CATTTTTTA
171854 TATATACATA
Statistics
Matches: 131, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
133 56 0.43
134 48 0.37
135 1 0.01
137 26 0.20
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (134 bp):
CATTTTTTAATTTTTCCATTACTATTATATATTTTTTCCTCCCTCTCATATTTAGCTATCATATA
TATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATACGCTATTAT
TTTA
Found at i:171756 original size:133 final size:134
Alignment explanation
Indices: 171609--171853 Score: 420
Period size: 133 Copynumber: 1.8 Consensus size: 134
171599 TATATAGATT
* *
171609 TTTTTTCCTCCCTCTCATATTTAGTTATTATATATATATGGTATTAATATTATTATATG-TTTTA
1 TTTTTTCCTCCCTCTCATATTTAGCTATCATATATATATGGTATTAATATTATTATATGTTTTTA
* * *
171673 TTAGCTTTATTTATTTTACTTTATACGCTATTGTTTTACATTTTTTAATTTTTCCATTATTATTA
66 TTAACTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTTAATTTTTCCATTATTATTA
171738 TATA
131 TATA
*
171742 TTTTTTCCTCCCTCTCATATTTAGCTATCATATATATATGGTATTGATATTATTATATGTTTTTA
1 TTTTTTCCTCCCTCTCATATTTAGCTATCATATATATATGGTATTAATATTATTATATGTTTTTA
*
171807 TTAATTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTTA
66 TTAACTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTTA
171854 TATATACATA
Statistics
Matches: 104, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
133 56 0.54
134 48 0.46
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.58
Consensus pattern (134 bp):
TTTTTTCCTCCCTCTCATATTTAGCTATCATATATATATGGTATTAATATTATTATATGTTTTTA
TTAACTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTTAATTTTTCCATTATTATTA
TATA
Found at i:183581 original size:105 final size:105
Alignment explanation
Indices: 183401--184071 Score: 1126
Period size: 105 Copynumber: 6.4 Consensus size: 105
183391 AGGTTTTACC
*
183401 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
183466 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATCC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
183506 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
183571 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
183611 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
183676 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
183716 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
183781 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
183821 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGTACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
183886 ACGAAGGGACCACTAGTTGTCAACAAACATCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * * *
183926 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTACAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
183991 ACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* ** *
184032 CAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
184072 GGAACAATAC
Statistics
Matches: 536, Mismatches: 29, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 494 0.92
106 42 0.08
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:185902 original size:142 final size:139
Alignment explanation
Indices: 185740--186026 Score: 429
Period size: 142 Copynumber: 2.1 Consensus size: 139
185730 TATTTATCTT
* * * * *
185740 CATTATTTAGTTTTTCTATTACTATTATATAGATTTTTTTCCTCCCTCTCATATTTAG-T-TAT-
1 CATTTTTTAATTTTTCCATTATTATTATATATA-TTTTTTCCTCCCTCTCATATTTAGATATATA
* *
185802 TATATATATATGGTATTAATATTATTATATG-TTTTATTAGCTTTATTTATTTTACTTTATACGC
65 TATATATATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATACGC
185866 TATTATTTTA
130 TATTATTTTA
185876 CATTTTTTAATTTTTCCATTATTATTATATATATTTTTTCCTCCCTCTCATATTTAGCTATCATA
1 CATTTTTTAATTTTTCCATTATTATTATATATATTTTTTCCTCCCTCTCATATTTAG--AT-ATA
* *
185941 TATATATATATATGGTATTGATATTATTATATGTTTTTATTAATTTTATTTATTCTACTTTATAC
63 TATATATATATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATAC
186006 GCTATTATTTTA
128 GCTATTATTTTA
186018 CATTTTTTA
1 CATTTTTTA
186027 TATATACATA
Statistics
Matches: 135, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
135 24 0.18
136 28 0.21
138 1 0.01
140 3 0.02
141 30 0.22
142 49 0.36
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (139 bp):
CATTTTTTAATTTTTCCATTATTATTATATATATTTTTTCCTCCCTCTCATATTTAGATATATAT
ATATATATATGGTATTAATATTATTATATGTTTTTATTAACTTTATTTATTCTACTTTATACGCT
ATTATTTTA
Found at i:186785 original size:13 final size:13
Alignment explanation
Indices: 186763--186808 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
186753 TATACGATAG
186763 ATTATTAATTTTT
1 ATTATTAATTTTT
* *
186776 GTTATGAATTTTTT
1 ATTATTAA-TTTTT
186790 ATTATTAATTTTT
1 ATTATTAATTTTT
186803 A-TATTA
1 ATTATTA
186809 TATGTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 5 0.18
13 12 0.43
14 11 0.39
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (13 bp):
ATTATTAATTTTT
Found at i:186794 original size:14 final size:14
Alignment explanation
Indices: 186771--186809 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
186761 AGATTATTAA
*
186771 TTTTTGTTATGAAT
1 TTTTTATTATGAAT
*
186785 TTTTTATTATTAAT
1 TTTTTATTATGAAT
186799 TTTTATATTAT
1 TTTT-TATTAT
186810 ATGTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (14 bp):
TTTTTATTATGAAT
Found at i:187135 original size:17 final size:16
Alignment explanation
Indices: 187093--187146 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 16
187083 CTTATATTGG
187093 TTTTAGTTATAATTTGA
1 TTTTA-TTATAATTTGA
187110 --TTATTAT--TTT-A
1 TTTTATTATAATTTGA
187121 TTTTAGTTATAATTTGA
1 TTTTA-TTATAATTTGA
187138 TTTTATTAT
1 TTTTATTAT
187147 TCAGGGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
11 1 0.03
12 3 0.10
13 3 0.10
14 8 0.26
15 3 0.10
16 7 0.23
17 6 0.19
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (16 bp):
TTTTATTATAATTTGA
Found at i:195788 original size:15 final size:16
Alignment explanation
Indices: 195763--195792 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
195753 CATTATTTTA
195763 TTTTACTTTTCTTTCC
1 TTTTACTTTTCTTTCC
195779 TTTT-CTTTTCTTTC
1 TTTTACTTTTCTTTC
195793 TATATGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTACTTTTCTTTCC
Found at i:197032 original size:27 final size:27
Alignment explanation
Indices: 196994--197050 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
196984 CGATATAATG
*
196994 ATATAATTATCCTAA-ATAATTGTTATA
1 ATATAATAATCC-AAGATAATTGTTATA
*
197021 ATATAATAATCCAAGCTAATTGTTATA
1 ATATAATAATCCAAGATAATTGTTATA
197048 ATA
1 ATA
197051 CTCTCTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (27 bp):
ATATAATAATCCAAGATAATTGTTATA
Found at i:197158 original size:12 final size:12
Alignment explanation
Indices: 197143--197173 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
197133 TACTCTCAAG
197143 TTTAATTTAAAT
1 TTTAATTTAAAT
197155 TTTAATTTAAAT
1 TTTAATTTAAAT
197167 TTTAATT
1 TTTAATT
197174 GAGTGAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTAATTTAAAT
Found at i:198314 original size:21 final size:21
Alignment explanation
Indices: 198290--198362 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
198280 GGAATAAATT
198290 GCAACGCGAACTTTGACTATC
1 GCAACGCGAACTTTGACTATC
* *
198311 GCAA--CGAA-TTTGTAATAAAGC
1 GCAACGCGAACTTTG-ACT--ATC
198332 GCAACGCGAACTTTGACTATC
1 GCAACGCGAACTTTGACTATC
*
198353 GCAATGCGAA
1 GCAACGCGAA
198363 TATGTAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
18 4 0.10
19 6 0.15
21 21 0.51
23 6 0.15
24 4 0.10
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (21 bp):
GCAACGCGAACTTTGACTATC
Found at i:198329 original size:42 final size:42
Alignment explanation
Indices: 198270--198356 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
198260 TGGACAATCA
**
198270 CAACGAATTTGGAATAAATTGCAACGCGAACTTTGACTATCG
1 CAACGAATTTGGAATAAAGCGCAACGCGAACTTTGACTATCG
*
198312 CAACGAATTTGTAATAAAGCGCAACGCGAACTTTGACTATCG
1 CAACGAATTTGGAATAAAGCGCAACGCGAACTTTGACTATCG
198354 CAA
1 CAA
198357 TGCGAATATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (42 bp):
CAACGAATTTGGAATAAAGCGCAACGCGAACTTTGACTATCG
Found at i:200300 original size:10 final size:10
Alignment explanation
Indices: 200282--200317 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
200272 AAAATTTCTT
200282 GTTCATGTTC
1 GTTCATGTTC
*
200292 GTTCGTGTTC
1 GTTCATGTTC
200302 GTTCATGTTC
1 GTTCATGTTC
200312 GTTCAT
1 GTTCAT
200318 TTAAATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.08, C:0.19, G:0.22, T:0.50
Consensus pattern (10 bp):
GTTCATGTTC
Found at i:200613 original size:24 final size:24
Alignment explanation
Indices: 200581--200628 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
200571 GAGATTGAGC
* *
200581 TAAACATAAATAAACGCACATAAA
1 TAAACATAAACAAACGAACATAAA
*
200605 TAAACATAAACGAACGAACATAAA
1 TAAACATAAACAAACGAACATAAA
200629 CGAATGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.62, C:0.17, G:0.06, T:0.15
Consensus pattern (24 bp):
TAAACATAAACAAACGAACATAAA
Found at i:200624 original size:14 final size:14
Alignment explanation
Indices: 200607--200642 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
200597 CACATAAATA
200607 AACATAAACGAACG
1 AACATAAACGAACG
*
200621 AACATAAACGAATG
1 AACATAAACGAACG
*
200635 AATATAAA
1 AACATAAA
200643 TTACTGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.61, C:0.14, G:0.11, T:0.14
Consensus pattern (14 bp):
AACATAAACGAACG
Done.