Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 106 of 193
Found at i:34065906 original size:22 final size:20
Alignment explanation
Indices: 34065871--34065914 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
34065861 AAATGTAATG
* *
34065871 TTATGTTTTGTACTTGATCACA
1 TTATGTTATATACTT-AT-ACA
34065893 TTATGTTATATACTTATACA
1 TTATGTTATATACTTATACA
34065913 TT
1 TT
34065915 TGGCTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.52
Consensus pattern (20 bp):
TTATGTTATATACTTATACA
Found at i:34071982 original size:22 final size:20
Alignment explanation
Indices: 34071947--34071990 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
34071937 AAATGTAATG
* *
34071947 TTATGTTTTGTACTTGATCACA
1 TTATGTTATATACTT-AT-ACA
34071969 TTATGTTATATACTTATACA
1 TTATGTTATATACTTATACA
34071989 TT
1 TT
34071991 TGGTTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.52
Consensus pattern (20 bp):
TTATGTTATATACTTATACA
Found at i:34072713 original size:76 final size:76
Alignment explanation
Indices: 34072582--34072726 Score: 209
Period size: 76 Copynumber: 1.9 Consensus size: 76
34072572 TTACAGTATA
* *
34072582 CCCAACACTAGTAAGATAAACTGACAAGGATTTGCACCCAGCACTAGTCGAATAACCAACGAATA
1 CCCAACACTAGTAAGATAAACTGACAAGGATTTGCACCCAACACTAGTCGAATAACCAACAAATA
34072647 TATAGGGTGTG
66 TATAGGGTGTG
* * * ** * *
34072658 CCCAGCACTAGTCAGATAAATTGACAAGGATTTGTGCCCAACAGTAGTCGGATAACCAACAAATA
1 CCCAACACTAGTAAGATAAACTGACAAGGATTTGCACCCAACACTAGTCGAATAACCAACAAATA
34072723 TATA
66 TATA
34072727 TACGCATTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 60 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (76 bp):
CCCAACACTAGTAAGATAAACTGACAAGGATTTGCACCCAACACTAGTCGAATAACCAACAAATA
TATAGGGTGTG
Found at i:34082080 original size:23 final size:23
Alignment explanation
Indices: 34082028--34082080 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
34082018 TTAGTGATCG
* **
34082028 AAATT-AAATTATAATTTTTATG
1 AAATTAAAAATATAATTTTTAAA
* *
34082050 ATAGTAAAAATATAATTTTTAAA
1 AAATTAAAAATATAATTTTTAAA
34082073 AAATTAAA
1 AAATTAAA
34082081 TCAAAATTTT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
AAATTAAAAATATAATTTTTAAA
Found at i:34082144 original size:7 final size:7
Alignment explanation
Indices: 34082132--34082161 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
34082122 TAACTTTATT
34082132 AATTTAA
1 AATTTAA
34082139 AATTTAA
1 AATTTAA
34082146 AATTTAA
1 AATTTAA
34082153 AATTTAA
1 AATTTAA
34082160 AA
1 AA
34082162 AATATTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATTTAA
Found at i:34082144 original size:15 final size:14
Alignment explanation
Indices: 34082116--34082158 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
34082106 AGTCAAAATG
* *
34082116 TAATTTTAACTTTA
1 TAATTTAAAATTTA
34082130 TTAATTTAAAATTTA
1 -TAATTTAAAATTTA
*
34082145 AAATTTAAAATTTA
1 TAATTTAAAATTTA
34082159 AAAAATATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATTTAAAATTTA
Found at i:34084317 original size:18 final size:18
Alignment explanation
Indices: 34084294--34084341 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
34084284 AAGGAACTAT
34084294 CTTGGACTTTCTGATTAC
1 CTTGGACTTTCTGATTAC
*
34084312 CTTGGACTTTCTGATTAT
1 CTTGGACTTTCTGATTAC
*
34084330 CTTGGAGTTTCT
1 CTTGGACTTTCT
34084342 CACTAGCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (18 bp):
CTTGGACTTTCTGATTAC
Found at i:34088793 original size:32 final size:32
Alignment explanation
Indices: 34088757--34088820 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
34088747 AATCAATCAC
34088757 ACGTCATTTTATTTTAATATTTAATCTTTGAA
1 ACGTCATTTTATTTTAATATTTAATCTTTGAA
34088789 ACGTCATTTTATTTTAATATTTAATCTTTGAA
1 ACGTCATTTTATTTTAATATTTAATCTTTGAA
34088821 CATTCTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (32 bp):
ACGTCATTTTATTTTAATATTTAATCTTTGAA
Found at i:34090960 original size:86 final size:86
Alignment explanation
Indices: 34090815--34090987 Score: 328
Period size: 86 Copynumber: 2.0 Consensus size: 86
34090805 CTACTTGCGA
34090815 TTTCTCGACCTTTAAATCAGAAGATAATACGCGTTCTTTTAGTTGTTTAGTTTATCAAACACTAC
1 TTTCTCGACCTTTAAATCAGAAGATAATACGCGTTCTTTTAGTTGTTTAGTTTATCAAACACTAC
* *
34090880 TTAAGTGAAAAGCTATTAAGT
66 TTAAGGGAAAAGCTACTAAGT
34090901 TTTCTCGACCTTTAAATCAGAAGATAATACGCGTTCTTTTAGTTGTTTAGTTTATCAAACACTAC
1 TTTCTCGACCTTTAAATCAGAAGATAATACGCGTTCTTTTAGTTGTTTAGTTTATCAAACACTAC
34090966 TTAAGGGAAAAGCTACTAAGT
66 TTAAGGGAAAAGCTACTAAGT
34090987 T
1 T
34090988 GAAGTAAAAC
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (86 bp):
TTTCTCGACCTTTAAATCAGAAGATAATACGCGTTCTTTTAGTTGTTTAGTTTATCAAACACTAC
TTAAGGGAAAAGCTACTAAGT
Found at i:34091719 original size:29 final size:29
Alignment explanation
Indices: 34091677--34091735 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
34091667 AATGAATGTA
* *
34091677 AGTGATCGATTTGTCA-TTTTCTAAAGTTT
1 AGTGATCGAGTTGTAATTTTTC-AAAGTTT
*
34091706 AGTGATTGAGTTGTAATTTTTCAAAGTTT
1 AGTGATCGAGTTGTAATTTTTCAAAGTTT
34091735 A
1 A
34091736 ATGACTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.27, C:0.07, G:0.19, T:0.47
Consensus pattern (29 bp):
AGTGATCGAGTTGTAATTTTTCAAAGTTT
Found at i:34096762 original size:17 final size:17
Alignment explanation
Indices: 34096729--34096760 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
34096719 TAAACTCATG
34096729 TGTTTTATAAAATTTTA
1 TGTTTTATAAAATTTTA
34096746 TGTTTT-TAAAATTTT
1 TGTTTTATAAAATTTT
34096761 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TGTTTTATAAAATTTTA
Found at i:34097035 original size:16 final size:18
Alignment explanation
Indices: 34097014--34097046 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
34097004 ATTATTTTTG
34097014 AAATTA-TAAA-AAATAT
1 AAATTATTAAATAAATAT
34097030 AAATTATTAAATAAATA
1 AAATTATTAAATAAATA
34097047 CACGTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTATTAAATAAATAT
Found at i:34099933 original size:66 final size:66
Alignment explanation
Indices: 34099827--34100019 Score: 332
Period size: 66 Copynumber: 2.9 Consensus size: 66
34099817 CAAAGACTAC
* * * *
34099827 TCAAGTGTCACGGTTTGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGAAGGAACGGGCTA
1 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGATGGAACGGGCTA
34099892 T
66 T
*
34099893 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTGCAGGGAGCTGATGGAACGGGCTA
1 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGATGGAACGGGCTA
34099958 T
66 T
*
34099959 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTTCTTATTACAGGGAGCTGATGGAACGG
1 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGATGGAACGG
34100020 AACAAGACAT
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 120 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (66 bp):
TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGATGGAACGGGCTA
T
Found at i:34101544 original size:23 final size:23
Alignment explanation
Indices: 34101499--34101541 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
34101489 GTAAGAAACG
34101499 GTTTGTAACTGTTGGAAATAATT
1 GTTTGTAACTGTTGGAAATAATT
34101522 GTTTGTAACTGTT-GAAATAA
1 GTTTGTAACTGTTGGAAATAA
34101542 ATTTGCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.42
Consensus pattern (23 bp):
GTTTGTAACTGTTGGAAATAATT
Found at i:34102139 original size:87 final size:86
Alignment explanation
Indices: 34101988--34102149 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 86
34101978 TTTAAATTCT
* * * * * *
34101988 GTGAATTCATCAAGTCCATCTCACCAGGACCACCCAAACTTTGGGATATGAACTCCTTAGGAGTA
1 GTGAATTCATCAAGTCCATCTCAACAGGACCACCCAAACTCTAGGATATAAACTCATTAAGAGTA
34102053 ATAAACTCAACCTCATAAGTCG
66 A-AAACTCAACCTCATAAGTCG
* * *
34102075 GTGAATTCATCAAGTCCATCTCAATAGGAGCACCCAAACTCTAGGATATAAATTCATTAAGAGTA
1 GTGAATTCATCAAGTCCATCTCAACAGGACCACCCAAACTCTAGGATATAAACTCATTAAGAGTA
*
34102140 AGAACTCAAC
66 AAAACTCAAC
34102150 TGTAACACCT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
86 8 0.12
87 57 0.88
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (86 bp):
GTGAATTCATCAAGTCCATCTCAACAGGACCACCCAAACTCTAGGATATAAACTCATTAAGAGTA
AAAACTCAACCTCATAAGTCG
Found at i:34102228 original size:16 final size:16
Alignment explanation
Indices: 34102199--34102244 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
34102189 TCTGGTGTTT
34102199 ACTATTCA-TTTTAC-
1 ACTATTCACTTTTACA
34102213 ACTATTCATCTTTTACA
1 ACTATTCA-CTTTTACA
*
34102230 ATTATTCAACTTTTA
1 ACTATTC-ACTTTTA
34102245 GTATCTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.30
16 6 0.22
17 12 0.44
18 1 0.04
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (16 bp):
ACTATTCACTTTTACA
Found at i:34104958 original size:59 final size:58
Alignment explanation
Indices: 34104892--34105076 Score: 153
Period size: 59 Copynumber: 3.1 Consensus size: 58
34104882 CAAAATGGTA
*
34104892 ATTTTAGAATTTCTGGGGCAAAAATGGTAATTTTGGAAAAATTTAGGGTTAGAAATGAC
1 ATTTTAGAATTTCTGGGGC-AAAATGGTAATTTTGGAAAAATTTAGGGTTAAAAATGAC
* * * * * * * * *
34104951 ATTTTAG-ATGTTCAGGGGTAAAACGATAATTTAT-GAAAGAA-TCAGGATAAAAAACGAG
1 ATTTTAGAAT-TTCTGGGGCAAAATGGTAATTT-TGGAAA-AATTTAGGGTTAAAAATGAC
* * * *
34105009 ACTTTTTGGATGTCTGGGGGCAAAATGGTAATTTTGGAAAAATTTTA-GGTTAAAAATGAT
1 A-TTTTAGAATTTCT-GGGGCAAAATGGTAATTTTGGAAAAA-TTTAGGGTTAAAAATGAC
34105069 ATTTTAGA
1 ATTTTAGA
34105077 CACTTGAGCG
Statistics
Matches: 94, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
58 29 0.31
59 32 0.34
60 31 0.33
61 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (58 bp):
ATTTTAGAATTTCTGGGGCAAAATGGTAATTTTGGAAAAATTTAGGGTTAAAAATGAC
Found at i:34105121 original size:118 final size:115
Alignment explanation
Indices: 34104906--34105155 Score: 267
Period size: 118 Copynumber: 2.1 Consensus size: 115
34104896 TAGAATTTCT
* ** *
34104906 GGGGCAAAAATGGTAATTTTGGAAAAATTTAGGGTTAGAAATGACATTTTAGATGTTCAGGGGTA
1 GGGGC-AAAATGGTAATTTTGGAAAAATTTAGGGTTAAAAATGACATTTTAGAACTTCAGGCGTA
34104971 AAACGATAATTTATGAAAGAATCAGGATAAAAAACGAGACTTTTTGG-ATGTCTG
65 AAACGATAATTTATGAAAGAATCAGGAT-AAAAACGAGA-TTTTTGGAAT-TC-G
* *
34105025 GGGGCAAAATGGTAATTTTGGAAAAATTTTA-GGTTAAAAATGATATTTTAGACACTTGA-GCGT
1 GGGGCAAAATGGTAATTTTGGAAAAA-TTTAGGGTTAAAAATGACATTTTAGA-ACTTCAGGCGT
* * * * *
34105088 AAAACGGTAATTT-TTAGAA-AATTATGATCAAAAATGAGATTTTTGGACATTCG
64 AAAACGATAATTTATGA-AAGAATCAGGAT-AAAAACGAGATTTTTGGA-ATTCG
*
34105141 GGGGTAAAATGGTAA
1 GGGGCAAAATGGTAA
34105156 GTTCGAGAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
116 22 0.19
117 20 0.18
118 59 0.52
119 12 0.11
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (115 bp):
GGGGCAAAATGGTAATTTTGGAAAAATTTAGGGTTAAAAATGACATTTTAGAACTTCAGGCGTAA
AACGATAATTTATGAAAGAATCAGGATAAAAACGAGATTTTTGGAATTCG
Found at i:34105197 original size:30 final size:29
Alignment explanation
Indices: 34105163--34105274 Score: 111
Period size: 30 Copynumber: 3.8 Consensus size: 29
34105153 TAAGTTCGAG
*
34105163 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
1 AGTTT-GAGGTCAAAAATGTAATTTTTGGA
* *
34105193 AGTTTGGGGT-AAAAATGTAATTTTTAGA
1 AGTTTGAGGTCAAAAATGTAATTTTTGGA
* *
34105221 AGTTTTAAGGTCAAAAATGTAATTTTGGAGA
1 AG-TTTGAGGTCAAAAATGTAATTTTTG-GA
* *
34105252 AGTTTGGGGGT-TAAAATGTAATT
1 AGTTT-GAGGTCAAAAATGTAATT
34105275 CATGGATAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 18 0.26
29 10 0.15
30 33 0.49
31 7 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
AGTTTGAGGTCAAAAATGTAATTTTTGGA
Found at i:34105208 original size:58 final size:58
Alignment explanation
Indices: 34105115--34105269 Score: 147
Period size: 58 Copynumber: 2.6 Consensus size: 58
34105105 AAAATTATGA
* *
34105115 TCAAAAAT-GAGATTTTTGGACA-TTCGGGGGTAAAATGGTAAGTTCGAG-AGTTTCGAGG
1 TCAAAAATGGA-ATTTTTGGA-AGTT-TGGGGTAAAATGGTAAGTTCGAGAAGTTTCAAGG
* ** *
34105173 TCAAAAATGGAATTTTTGGAAGTTTGGGGTAAAAAT-GTAATTTTTAGAAGTTTTAAGG
1 TCAAAAATGGAATTTTTGGAAGTTTGGGGT-AAAATGGTAAGTTCGAGAAGTTTCAAGG
* *
34105231 TCAAAAATGTAATTTTGGAGAAGTTTGGGGGTTAAAATG
1 TCAAAAATGGAATTTTTG-GAAGTTT-GGGG-TAAAATG
34105270 TAATTCATGG
Statistics
Matches: 81, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
57 14 0.17
58 48 0.59
59 9 0.11
60 9 0.11
61 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.34
Consensus pattern (58 bp):
TCAAAAATGGAATTTTTGGAAGTTTGGGGTAAAATGGTAAGTTCGAGAAGTTTCAAGG
Found at i:34107251 original size:6 final size:6
Alignment explanation
Indices: 34107231--34107315 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
34107221 AGTATTATTG
* * *
34107231 TAAATT T-AA-T TAAATT TAAATG TAAA-G TAAATT TAAATT GGTGAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT --TAAATT
*
34107278 TAAATT TAAGA-- TAAATT TAAATT TAAA-A TAAATT TAAA
1 TAAATT TAA-ATT TAAATT TAAATT TAAATT TAAATT TAAA
34107316 ATTTTAACTT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
4 3 0.05
5 16 0.25
6 39 0.61
7 1 0.02
8 5 0.08
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:34107263 original size:17 final size:16
Alignment explanation
Indices: 34107231--34107315 Score: 75
Period size: 17 Copynumber: 5.2 Consensus size: 16
34107221 AGTATTATTG
* *
34107231 TAAATTTAATTAAATT
1 TAAATTAAAGTAAATT
34107247 TAAATGTAAAGTAAATT
1 TAAAT-TAAAGTAAATT
* *
34107264 TAAATT--GGTGAATT
1 TAAATTAAAGTAAATT
*
34107278 TAAATTTAAGATAAATT
1 TAAATTAAAG-TAAATT
*
34107295 TAAATTTAAAATAAATT
1 TAAA-TTAAAGTAAATT
34107312 TAAA
1 TAAA
34107316 ATTTTAACTT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
14 12 0.21
16 7 0.12
17 33 0.59
18 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (16 bp):
TAAATTAAAGTAAATT
Found at i:34108080 original size:205 final size:205
Alignment explanation
Indices: 34107675--34108557 Score: 1441
Period size: 205 Copynumber: 4.3 Consensus size: 205
34107665 GTTCCGTTGA
* * * *
34107675 CTTCGACCTGCTTCGCAATGTCTCATCAGGAAACTGGG-TTCGAA-AGTTTGCTCGCATTGAGCC
1 CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGA-TTTGCTCGCATTGAGCC
34107738 TGGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATT
65 TGGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATT
* **
34107803 CGCTCCTCAAGATCTCCTCAGGAAGACGAATTTGGTCCACTCTCTCAGTGTCTCATCAGGAAGCT
130 CGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACT-TCTCAGTGTCTCATCAGGAAGCT
34107868 AACCATTTATTG
194 AACCATTTATTG
* *
34107880 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGCTTCGAAGATTTGCTCGCATTGAGCCT
1 CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCATTGAGCCT
* * * *
34107945 GAGTTTGATTTGGTTTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCAACACTTGTTTTAATTT
66 GGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTC
34108010 GCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAA
131 GCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAA
34108075 CCATTTATTG
196 CCATTTATTG
*
34108085 CTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCATTGAGCCT
1 CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCATTGAGCCT
* *
34108150 GGGCTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCGCTTGTTTTAATTC
66 GGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTC
* * *
34108215 ACTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTACACTTCTCAGTGTCTCATCAGGAAGCTAC
131 GCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAA
34108280 CCATTTATTG
196 CCATTTATTG
* *
34108290 CTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGATTCAAAGATTTGCTCGCATTGAGCCT
1 CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCATTGAGCCT
* * * *
34108355 GGGTTTGATTTGGTCTTTTTCTCAATGTCTCATCAGGAAGATGACCGCATTAC-TATTTTAATTC
66 GGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTC
34108419 GCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAA
131 GCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAA
*
34108484 GCATTTATTG
196 CCATTTATTG
* * *
34108494 CTTCGACCTGCTTCTCAGTATCTCATC-GAGAAGTTGGGGTTCGAAGATTTGCTCGTATTTGAGC
1 CTTCGACCTGCTTCTCAGTATCTCATCAG-GAAGCTGGGATTCGAAGATTTGCTCGCA-TTGAGC
34108558 GTTGAGTACG
Statistics
Matches: 634, Mismatches: 40, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
203 1 0.00
204 131 0.21
205 379 0.60
206 122 0.19
207 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (205 bp):
CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCATTGAGCCT
GGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTC
GCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAA
CCATTTATTG
Found at i:34120581 original size:28 final size:29
Alignment explanation
Indices: 34120550--34120604 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
34120540 CTTGTAGATA
*
34120550 CTCG-GAGACAAAATGATAATTTTGGACT
1 CTCGAGAGAAAAAATGATAATTTTGGACT
* *
34120578 CTCGAGGGAAAAAATGGTAATTTTGGA
1 CTCGAGAGAAAAAATGATAATTTTGGA
34120605 ATAATTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (29 bp):
CTCGAGAGAAAAAATGATAATTTTGGACT
Found at i:34120718 original size:27 final size:28
Alignment explanation
Indices: 34120688--34120749 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
34120678 AAACGAGACT
*
34120688 TTTTGGA-TGCTAGGGGGCAAAAT-GTAA
1 TTTTGGACT-CTAGAGGGCAAAATGGTAA
* *
34120715 TTTTGGACTCTCGAGGGTAAAATGGTAA
1 TTTTGGACTCTAGAGGGCAAAATGGTAA
34120743 TTTTGGA
1 TTTTGGA
34120750 AAAATTTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.27, C:0.08, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTTGGACTCTAGAGGGCAAAATGGTAA
Found at i:34120985 original size:30 final size:30
Alignment explanation
Indices: 34120866--34120989 Score: 102
Period size: 29 Copynumber: 4.3 Consensus size: 30
34120856 TTTCGAGAGT
*
34120866 TTTGA-GGTCAAAATAGAATTTTTGG-AAG
1 TTTGAGGGTCAAAATATAATTTTTGGAAAG
* *
34120894 -TTCAGGGGTAAAAATATAATTTTT--AAAG
1 TTTGA-GGGTCAAAATATAATTTTTGGAAAG
*
34120922 TTTTG-GGCTCAAAAATATAA-TTTTGGAAAAG
1 -TTTGAGGGTC-AAAATATAATTTTTGG-AAAG
* *
34120953 TTTGAGGGTCAAAATGTAATTTTTGGATAG
1 TTTGAGGGTCAAAATATAATTTTTGGAAAG
34120983 TTT-AGGG
1 TTTGAGGG
34120990 ACCTATAGAG
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
27 3 0.04
28 10 0.13
29 29 0.38
30 20 0.26
31 14 0.18
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTGAGGGTCAAAATATAATTTTTGGAAAG
Found at i:34123615 original size:15 final size:15
Alignment explanation
Indices: 34123597--34123626 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34123587 TGGTTCATTT
34123597 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
34123612 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
34123627 AATGTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:34125716 original size:20 final size:20
Alignment explanation
Indices: 34125688--34125726 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34125678 CCATGACTTT
*
34125688 CATTATTAAGTTTAATTAAC
1 CATTATTAACTTTAATTAAC
*
34125708 CATTTTTAACTTTAATTAA
1 CATTATTAACTTTAATTAA
34125727 ACCTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (20 bp):
CATTATTAACTTTAATTAAC
Found at i:34125735 original size:20 final size:20
Alignment explanation
Indices: 34125693--34125736 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
34125683 ACTTTCATTA
* *
34125693 TTAAGTTTAATTAACCATTT
1 TTAACTTTAATTAACCATAT
34125713 TTAACTTTAATTAAACC-TAT
1 TTAACTTTAATT-AACCATAT
34125733 TTAA
1 TTAA
34125737 AAGTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAACTTTAATTAACCATAT
Found at i:34130534 original size:24 final size:24
Alignment explanation
Indices: 34130495--34130588 Score: 100
Period size: 24 Copynumber: 3.9 Consensus size: 24
34130485 CCAGACAAAA
* *
34130495 TTAGCTCATACTAGCCCAG-ATAGG
1 TTAGCTCTTACGAGCCCAGAAT-GG
* *
34130519 TTAGCTCTCACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
34130543 CTAGCTCTTACGAGCCTAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
34130567 TCAGCTCTTACGAGCCCGGAAT
1 TTAGCTCTTACGAGCCCAGAAT
34130589 CAGAATAACG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 55 0.96
25 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:34131055 original size:15 final size:15
Alignment explanation
Indices: 34131023--34131069 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
34131013 ATATTTCACC
34131023 TTAAGTCCTTATAA-AT
1 TTAA-TCCTT-TAACAT
*
34131039 TTATTCCTTTAACATT
1 TTAATCCTTTAACA-T
34131055 TTAATCCTTTAACAT
1 TTAATCCTTTAACAT
34131070 AAAAATTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.11
15 7 0.26
16 17 0.63
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (15 bp):
TTAATCCTTTAACAT
Found at i:34131062 original size:16 final size:16
Alignment explanation
Indices: 34131038--34131069 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34131028 TCCTTATAAA
*
34131038 TTTATTCCTTTAACAT
1 TTTAATCCTTTAACAT
34131054 TTTAATCCTTTAACAT
1 TTTAATCCTTTAACAT
34131070 AAAAATTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATCCTTTAACAT
Found at i:34133778 original size:34 final size:35
Alignment explanation
Indices: 34133724--34133812 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 35
34133714 TCCAATAGAT
34133724 CTCTTCAAG-TCTCCCAGTAATTTAAATCATACAAG
1 CTCTTCAAGAT-TCCCAGTAATTTAAATCATACAAG
* * *
34133759 TTCTTCAAGATT-CCAGTAATTTAACTCATACGAG
1 CTCTTCAAGATTCCCAGTAATTTAAATCATACAAG
*
34133793 CTCTTTAAGATTCCCAGTAA
1 CTCTTCAAGATTCCCAGTAA
34133813 ATTTTAGCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 30 0.64
35 16 0.34
36 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.34
Consensus pattern (35 bp):
CTCTTCAAGATTCCCAGTAATTTAAATCATACAAG
Found at i:34133876 original size:19 final size:19
Alignment explanation
Indices: 34133845--34133993 Score: 160
Period size: 19 Copynumber: 7.8 Consensus size: 19
34133835 TCAATAAATT
*
34133845 GCTCTTACGAGCCAGTATC
1 GCTCTTTCGAGCCAGTATC
* *
34133864 ACTCTTTCAAGCCAGTATC
1 GCTCTTTCGAGCCAGTATC
34133883 GCTCTTTCGAGCCAGTATC
1 GCTCTTTCGAGCCAGTATC
* *
34133902 TG-TCTTACGAGCCAGTATT
1 -GCTCTTTCGAGCCAGTATC
* *
34133921 GCTCTTTTGAGCCAATATC
1 GCTCTTTCGAGCCAGTATC
* *
34133940 GCT-TTTACAAGCCAGTATT
1 GCTCTTT-CGAGCCAGTATC
*
34133959 GCTCTTTCGAGCCAATATC
1 GCTCTTTCGAGCCAGTATC
34133978 GCT-TTTACGAGCCAGT
1 GCTCTTT-CGAGCCAGT
34133994 CTTCAGTAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.07
19 95 0.90
20 4 0.04
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (19 bp):
GCTCTTTCGAGCCAGTATC
Found at i:34133978 original size:38 final size:38
Alignment explanation
Indices: 34133842--34133993 Score: 191
Period size: 38 Copynumber: 4.0 Consensus size: 38
34133832 CAGTCAATAA
* * *
34133842 ATTGCTCTTACGAGCCAGTATCACTCTTT-CAAGCCAGT
1 ATTGCTCTTTCGAGCCAATATCGCT-TTTACAAGCCAGT
* * * *
34133880 ATCGCTCTTTCGAGCCAGTATCTG-TCTTACGAGCCAGT
1 ATTGCTCTTTCGAGCCAATATC-GCTTTTACAAGCCAGT
*
34133918 ATTGCTCTTTTGAGCCAATATCGCTTTTACAAGCCAGT
1 ATTGCTCTTTCGAGCCAATATCGCTTTTACAAGCCAGT
*
34133956 ATTGCTCTTTCGAGCCAATATCGCTTTTACGAGCCAGT
1 ATTGCTCTTTCGAGCCAATATCGCTTTTACAAGCCAGT
34133994 CTTCAGTAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
37 3 0.03
38 96 0.97
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.34
Consensus pattern (38 bp):
ATTGCTCTTTCGAGCCAATATCGCTTTTACAAGCCAGT
Found at i:34133990 original size:57 final size:57
Alignment explanation
Indices: 34133842--34133991 Score: 180
Period size: 57 Copynumber: 2.6 Consensus size: 57
34133832 CAGTCAATAA
* * * *
34133842 ATTGCTCTTACGAGCCAGTATCACTCTTTCAAGCCAGTATCGCTCTTTCGAGCCAGT
1 ATTGCTCTTACGAGCCAGTATCGCTCTTTCGAGCCAATATCGCTCTTTCAAGCCAGT
* *
34133899 ATCTG-TCTTACGAGCCAGTATTGCTCTTTTGAGCCAATATCGCT-TTTACAAGCCAGT
1 AT-TGCTCTTACGAGCCAGTATCGCTCTTTCGAGCCAATATCGCTCTTT-CAAGCCAGT
* *
34133956 ATTGCTCTTTCGAGCCAATATCGCT-TTTACGAGCCA
1 ATTGCTCTTACGAGCCAGTATCGCTCTTT-CGAGCCA
34133992 GTCTTCAGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
56 8 0.10
57 69 0.87
58 2 0.03
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.33
Consensus pattern (57 bp):
ATTGCTCTTACGAGCCAGTATCGCTCTTTCGAGCCAATATCGCTCTTTCAAGCCAGT
Found at i:34138226 original size:35 final size:35
Alignment explanation
Indices: 34138182--34138250 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
34138172 AATAATGGGA
*
34138182 AAATAAATAAGGTAAATCTCTCAACCTTAAAAAGG
1 AAATAAATAAAGTAAATCTCTCAACCTTAAAAAGG
* * *
34138217 AAATAAATAAAGTGAATCTCTTAACTTTAAAAAG
1 AAATAAATAAAGTAAATCTCTCAACCTTAAAAAG
34138251 AACTAAGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (35 bp):
AAATAAATAAAGTAAATCTCTCAACCTTAAAAAGG
Found at i:34146999 original size:3 final size:3
Alignment explanation
Indices: 34146991--34147020 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34146981 TATCACCATT
34146991 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34147021 TAGCTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:34154954 original size:22 final size:22
Alignment explanation
Indices: 34154926--34154977 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
34154916 CTCGTACTTT
*
34154926 ATTAAAACTAATCAAATTGTTG
1 ATTAAAACTAATCAAATTATTG
*
34154948 ATTAAAACTAATCCAATTATTG
1 ATTAAAACTAATCAAATTATTG
*
34154970 ATAAAAAC
1 ATTAAAAC
34154978 ACATTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.33
Consensus pattern (22 bp):
ATTAAAACTAATCAAATTATTG
Found at i:34172751 original size:21 final size:22
Alignment explanation
Indices: 34172711--34172755 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
34172701 TTTCACTTGA
34172711 TTCTACTCAATTCAAATTTAAT
1 TTCTACTCAATTCAAATTTAAT
* *
34172733 TTCTACTCGATT-TAATTTAAT
1 TTCTACTCAATTCAAATTTAAT
34172754 TT
1 TT
34172756 GACATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (22 bp):
TTCTACTCAATTCAAATTTAAT
Found at i:34176988 original size:43 final size:43
Alignment explanation
Indices: 34176849--34177142 Score: 355
Period size: 43 Copynumber: 6.9 Consensus size: 43
34176839 TCCTTTTTAA
* * * * *
34176849 ATAATCTTATGCTC-TACTGAGTCATAAGTCTTCC-TTTAAAC
1 ATAATCTCATGCTCATCCTGAGACATGAGTCTTCCATTTATAC
* ** * * *
34176890 ATAATCTCACGCTCATTTTGAGTCACGAGTCTTCC--TTAAAC
1 ATAATCTCATGCTCATCCTGAGACATGAGTCTTCCATTTATAC
* * * *
34176931 ATAATCTCATGCTCATTCTAAGTCACGAGTCTTCCATTTATAC
1 ATAATCTCATGCTCATCCTGAGACATGAGTCTTCCATTTATAC
* * *
34176974 ATAATTTCATGCTCATCTTGAGACATGAGTCTTCCATTTATTC
1 ATAATCTCATGCTCATCCTGAGACATGAGTCTTCCATTTATAC
**
34177017 ATAATCTCATGCTCATCCCCAGACATGAGTCTTCCATTTATAC
1 ATAATCTCATGCTCATCCTGAGACATGAGTCTTCCATTTATAC
34177060 ATAATCTCATGCTCATCCCT-AGACATGAGTCTTCCATTTATAC
1 ATAATCTCATGCTCAT-CCTGAGACATGAGTCTTCCATTTATAC
*
34177103 ATAATCTCATGCTCATCCCGAGACATGAGTCTTCCATTTA
1 ATAATCTCATGCTCATCCTGAGACATGAGTCTTCCATTTA
34177143 CGCCAAGTGT
Statistics
Matches: 224, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
41 50 0.22
42 18 0.08
43 154 0.69
44 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (43 bp):
ATAATCTCATGCTCATCCTGAGACATGAGTCTTCCATTTATAC
Found at i:34182994 original size:18 final size:15
Alignment explanation
Indices: 34182955--34182993 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
34182945 TCTTTTTTAG
34182955 CATCTTCTTTCTCAA
1 CATCTTCTTTCTCAA
34182970 CATCTTCTTTCTCAA
1 CATCTTCTTTCTCAA
34182985 CATCTTCTT
1 CATCTTCTT
34182994 CAAGGACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (15 bp):
CATCTTCTTTCTCAA
Found at i:34194721 original size:38 final size:38
Alignment explanation
Indices: 34194679--34194751 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
34194669 GTCTATTCAG
* * * * *
34194679 AATTGTGCCCAGATTTGTCACTGCATGATGATGTCAAA
1 AATTGCGCCCAAAATTGTCACTGCAGGACGATGTCAAA
*
34194717 AATTGCGCCCAAAATTGTCATTGCAGGACGATGTC
1 AATTGCGCCCAAAATTGTCACTGCAGGACGATGTC
34194752 CAGAAGTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (38 bp):
AATTGCGCCCAAAATTGTCACTGCAGGACGATGTCAAA
Found at i:34194787 original size:26 final size:26
Alignment explanation
Indices: 34194758--34194816 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
34194748 TGTCCAGAAG
* *
34194758 TATCGCTGCATGAGCAT-GCTCAAAAT
1 TATCGCTGCAGGAAC-TCGCTCAAAAT
* *
34194784 TATCGTTGCAGGAACTCGTTCAAAAT
1 TATCGCTGCAGGAACTCGCTCAAAAT
34194810 TATCGCT
1 TATCGCT
34194817 TTGTGAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (26 bp):
TATCGCTGCAGGAACTCGCTCAAAAT
Found at i:34205578 original size:18 final size:18
Alignment explanation
Indices: 34205557--34205591 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34205547 AGTTATTAGT
34205557 GCAGTTAATG-CTATTATG
1 GCAGTTAA-GACTATTATG
34205575 GCAGTTAAGACTATTAT
1 GCAGTTAAGACTATTAT
34205592 TATGGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (18 bp):
GCAGTTAAGACTATTATG
Found at i:34207551 original size:24 final size:24
Alignment explanation
Indices: 34207519--34207565 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
34207509 TGAACCGTTG
34207519 AAAGTTGGAAGAGTAAGATTGGAC
1 AAAGTTGGAAGAGTAAGATTGGAC
34207543 AAAGTTGGAAGAGTAAGATTGGA
1 AAAGTTGGAAGAGTAAGATTGGA
34207566 GTGATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.34, T:0.21
Consensus pattern (24 bp):
AAAGTTGGAAGAGTAAGATTGGAC
Found at i:34212390 original size:16 final size:17
Alignment explanation
Indices: 34212369--34212405 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
34212359 AATAGGATGA
34212369 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
34212385 AAATAAATTTAATTAATT
1 AAATAAATTT-ATTAATT
34212403 AAA
1 AAA
34212406 ATTTTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:34212411 original size:16 final size:16
Alignment explanation
Indices: 34212369--34212412 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
34212359 AATAGGATGA
*
34212369 AAATAAATTTTTAATT
1 AAATAAAATTTTAATT
34212385 AAAT-AAA-TTTAATT
1 AAATAAAATTTTAATT
*
34212399 AATTAAAATTTTAA
1 AAATAAAATTTTAA
34212413 AACCCTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 10 0.42
15 5 0.21
16 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAAAATTTTAATT
Found at i:34213618 original size:36 final size:36
Alignment explanation
Indices: 34213578--34213714 Score: 118
Period size: 36 Copynumber: 3.8 Consensus size: 36
34213568 GCTAAAATAG
34213578 CATTATGCTCTAACCGAGACATAAGCAATCAAATGA
1 CATTATGCTCTAACCGAGACATAAGCAATCAAATGA
** * *
34213614 CATTATGCTCTAACCGAGATGTAAGTAATCACATAGGA
1 CATTATGCTCTAACCGAGACATAAGCAATCA-A-ATGA
* ** * * * *
34213652 -A-TATGCTCTAACCAAGATGTATGCAA-CCACTTA
1 CATTATGCTCTAACCGAGACATAAGCAATCAAATGA
*
34213685 GCATTACGCTCTAACCGAGACATAAGCAAT
1 -CATTATGCTCTAACCGAGACATAAGCAAT
34213715 TACATATACG
Statistics
Matches: 79, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
33 1 0.01
34 1 0.01
35 2 0.03
36 70 0.89
37 2 0.03
38 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (36 bp):
CATTATGCTCTAACCGAGACATAAGCAATCAAATGA
Found at i:34217305 original size:13 final size:13
Alignment explanation
Indices: 34217283--34217312 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34217273 CCACATTGAC
34217283 ATCATAATACAAT
1 ATCATAATACAAT
*
34217296 ATCATCATACAAT
1 ATCATAATACAAT
34217309 ATCA
1 ATCA
34217313 CATCATAAAA
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:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (13 bp):
ATCATAATACAAT
Found at i:34217318 original size:15 final size:15
Alignment explanation
Indices: 34217289--34217328 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
34217279 TGACATCATA
34217289 ATACAATAT--CATC
1 ATACAATATCACATC
34217302 ATACAATATCACATC
1 ATACAATATCACATC
*
34217317 ATA-AAAATCACA
1 ATACAATATCACA
34217329 ATGTAAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 9 0.38
14 8 0.33
15 7 0.29
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (15 bp):
ATACAATATCACATC
Found at i:34217864 original size:26 final size:26
Alignment explanation
Indices: 34217827--34217877 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
34217817 TTCTCGGAAA
* *
34217827 AAGTCAATGGTCAACGTTCAACGGTC
1 AAGTCAAAGGTCAACGATCAACGGTC
*
34217853 AAGTCAAAGGTCAATGATCAACGGT
1 AAGTCAAAGGTCAACGATCAACGGT
34217878 GAATGGTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (26 bp):
AAGTCAAAGGTCAACGATCAACGGTC
Found at i:34229081 original size:2 final size:2
Alignment explanation
Indices: 34229076--34229101 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34229066 ATGAAATCGC
34229076 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
34229102 TTTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34230972 original size:21 final size:21
Alignment explanation
Indices: 34230948--34231003 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
34230938 TTCAAGAAAA
*
34230948 CATTACAGGGGCACTGAAGTG
1 CATTACAGGGGCACCGAAGTG
* *
34230969 CATTCACAAGGGCACCGTAGTG
1 CATT-ACAGGGGCACCGAAGTG
34230991 CAATT-CAGGGGCA
1 C-ATTACAGGGGCA
34231004 TCACATAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.38
22 15 0.52
23 3 0.10
ACGTcount: A:0.29, C:0.23, G:0.30, T:0.18
Consensus pattern (21 bp):
CATTACAGGGGCACCGAAGTG
Found at i:34238224 original size:22 final size:22
Alignment explanation
Indices: 34238190--34238256 Score: 84
Period size: 21 Copynumber: 3.1 Consensus size: 22
34238180 AACATTACAA
* *
34238190 GGGCACTGAAGTGC-ATTCATAG
1 GGGCACCGTAGTGCAATTCA-AG
34238212 GGGCACCGTAGTGCAATTC-AG
1 GGGCACCGTAGTGCAATTCAAG
*
34238233 GGGCACCGTACTGCAATTCAAG
1 GGGCACCGTAGTGCAATTCAAG
34238255 GG
1 GG
34238257 CATCACATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
21 20 0.50
22 16 0.40
23 4 0.10
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.19
Consensus pattern (22 bp):
GGGCACCGTAGTGCAATTCAAG
Found at i:34241466 original size:9 final size:9
Alignment explanation
Indices: 34241462--34241493 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
34241452 ATGATGATGG
34241462 CGATGAGGA
1 CGATGAGGA
34241471 CGATGAGGA
1 CGATGAGGA
*
34241480 TGATGAGGA
1 CGATGAGGA
34241489 CGATG
1 CGATG
34241494 TTTCTTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.31, C:0.09, G:0.44, T:0.16
Consensus pattern (9 bp):
CGATGAGGA
Found at i:34241684 original size:23 final size:23
Alignment explanation
Indices: 34241636--34241735 Score: 121
Period size: 23 Copynumber: 4.4 Consensus size: 23
34241626 TTGCAGGTTG
* * * *
34241636 TTTTTTGTGCAGATTTGATGCT-
1 TTTTTGGTGCAGCTTTGGTACTA
*
34241658 TTTTTGGTGCAGGTTTGGTACTA
1 TTTTTGGTGCAGCTTTGGTACTA
*
34241681 TTTTTGGTGTAGCTTTGGTACTA
1 TTTTTGGTGCAGCTTTGGTACTA
* *
34241704 TCTTTGGTGCAACTTTGGTACTA
1 TTTTTGGTGCAGCTTTGGTACTA
34241727 TTTTTGGTG
1 TTTTTGGTG
34241736 TTATTTTGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
22 18 0.27
23 49 0.73
ACGTcount: A:0.13, C:0.10, G:0.26, T:0.51
Consensus pattern (23 bp):
TTTTTGGTGCAGCTTTGGTACTA
Found at i:34241688 original size:12 final size:12
Alignment explanation
Indices: 34241671--34241734 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
34241661 TTGGTGCAGG
*
34241671 TTTGGTACTATT
1 TTTGGTACTATC
* *
34241683 TTTGGT-GTAGC
1 TTTGGTACTATC
34241694 TTTGGTACTATC
1 TTTGGTACTATC
* *
34241706 TTTGGTGC-AAC
1 TTTGGTACTATC
*
34241717 TTTGGTACTATT
1 TTTGGTACTATC
34241729 TTTGGT
1 TTTGGT
34241735 GTTATTTTGA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
11 17 0.43
12 23 0.57
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (12 bp):
TTTGGTACTATC
Found at i:34242468 original size:20 final size:20
Alignment explanation
Indices: 34242428--34242552 Score: 107
Period size: 20 Copynumber: 6.3 Consensus size: 20
34242418 CTATTTTCAA
*
34242428 GGGCACTGAAGTGCA-ACAG
1 GGGCACCGAAGTGCATACAG
34242447 GGGCACCGAAGTGCATACAG
1 GGGCACCGAAGTGCATACAG
* *
34242467 GGGCACC-AGATTGC-TAATAG
1 GGGCACCGA-AGTGCAT-ACAG
*
34242487 GGGCATCGAAGTGCATACAG
1 GGGCACCGAAGTGCATACAG
* *
34242507 GGGCA-CTAGAGTGC-TAACAA
1 GGGCACCGA-AGTGCAT-ACAG
* *
34242527 GGGCACCAAAGTGCATAGAG
1 GGGCACCGAAGTGCATACAG
34242547 GGGCAC
1 GGGCAC
34242553 TGGAGTGCTA
Statistics
Matches: 86, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
19 19 0.22
20 62 0.72
21 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.34, T:0.13
Consensus pattern (20 bp):
GGGCACCGAAGTGCATACAG
Found at i:34242490 original size:40 final size:40
Alignment explanation
Indices: 34242437--34242565 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
34242427 AGGGCACTGA
34242437 AGTGC-AACAGGGGCACCGAAGTGCATACAGGGGCACCAG
1 AGTGCTAACAGGGGCACCGAAGTGCATACAGGGGCACCAG
* * * *
34242476 ATTGCTAATAGGGGCATCGAAGTGCATACAGGGGCACTAG
1 AGTGCTAACAGGGGCACCGAAGTGCATACAGGGGCACCAG
* * * **
34242516 AGTGCTAACAAGGGCACCAAAGTGCATAGAGGGGCACTGG
1 AGTGCTAACAGGGGCACCGAAGTGCATACAGGGGCACCAG
34242556 AGTGCTAACA
1 AGTGCTAACA
34242566 TTCCATAACT
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.32, C:0.21, G:0.33, T:0.14
Consensus pattern (40 bp):
AGTGCTAACAGGGGCACCGAAGTGCATACAGGGGCACCAG
Found at i:34242560 original size:60 final size:59
Alignment explanation
Indices: 34242428--34242565 Score: 140
Period size: 60 Copynumber: 2.3 Consensus size: 59
34242418 CTATTTTCAA
* * * * *
34242428 GGGCACTGAAGTGCAACAGGGGCACCGAAGTGCATACAGGGGCACCAGATTGCTAATAG
1 GGGCACTGAAGTGCAACAGGGGCACAGAAGTGCATACAAGGGCACCAAAGTGCTAAGAG
34242487 GGGCA-TCGAAGTGCATACAGGGGCACTAG-AGTGC-TAACAAGGGCACCAAAGTGC-ATAGAG
1 GGGCACT-GAAGTGCA-ACAGGGGCAC-AGAAGTGCAT-ACAAGGGCACCAAAGTGCTA-AGAG
*
34242547 GGGCACTGGAGTGCTAACA
1 GGGCACTGAAGTGC-AACA
34242566 TTCCATAACT
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
58 1 0.02
59 15 0.23
60 47 0.71
61 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.34, T:0.14
Consensus pattern (59 bp):
GGGCACTGAAGTGCAACAGGGGCACAGAAGTGCATACAAGGGCACCAAAGTGCTAAGAG
Found at i:34246898 original size:18 final size:19
Alignment explanation
Indices: 34246864--34246900 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34246854 CATTATCACC
34246864 CACCATAATCAAATTTGTT
1 CACCATAATCAAATTTGTT
*
34246883 CACCGTAATC-AATTTGTT
1 CACCATAATCAAATTTGTT
34246901 ATTAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (19 bp):
CACCATAATCAAATTTGTT
Found at i:34247183 original size:17 final size:17
Alignment explanation
Indices: 34247163--34247223 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
34247153 TTAGTATGAT
34247163 TAAATAATTCAATAATA
1 TAAATAATTCAATAATA
* *
34247180 TAAATAGTACAA-AATA
1 TAAATAATTCAATAATA
* *
34247196 TGAATTTTAATTTAATAATA
1 T-AA--ATAATTCAATAATA
34247216 TAAATAAT
1 TAAATAAT
34247224 AGATATAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
16 5 0.15
17 16 0.48
19 7 0.21
20 5 0.15
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:34247481 original size:30 final size:28
Alignment explanation
Indices: 34247445--34247504 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
34247435 TGGGGGTGAG
* *
34247445 ATGGGAGGGGGTAAAAGTTTTAGAGGGAAA
1 ATGGGAGGGAGT-AAAGTTTT-GAGAGAAA
34247475 ATGGGAGGGAGTAAAGTTTTGAGAGAAA
1 ATGGGAGGGAGTAAAGTTTTGAGAGAAA
34247503 AT
1 AT
34247505 AAAAAGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.32
29 8 0.29
30 11 0.39
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (28 bp):
ATGGGAGGGAGTAAAGTTTTGAGAGAAA
Found at i:34247748 original size:9 final size:9
Alignment explanation
Indices: 34247734--34247797 Score: 101
Period size: 9 Copynumber: 7.1 Consensus size: 9
34247724 TATAGTTTGA
*
34247734 TATTCGATT
1 TATTCGAAT
34247743 TATTCGAAT
1 TATTCGAAT
*
34247752 TATTCGAGT
1 TATTCGAAT
34247761 TATTCGAAT
1 TATTCGAAT
34247770 TATTCGAAT
1 TATTCGAAT
*
34247779 TATTCGAGT
1 TATTCGAAT
34247788 TATTCGAAT
1 TATTCGAAT
34247797 T
1 T
34247798 CGAAAACTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:34247765 original size:27 final size:27
Alignment explanation
Indices: 34247734--34247797 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
34247724 TATAGTTTGA
*
34247734 TATTCGATTTATTCGAATTATTCGAGT
1 TATTCGAATTATTCGAATTATTCGAGT
34247761 TATTCGAATTATTCGAATTATTCGAGT
1 TATTCGAATTATTCGAATTATTCGAGT
34247788 TATTCGAATT
1 TATTCGAATT
34247798 CGAAAACTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (27 bp):
TATTCGAATTATTCGAATTATTCGAGT
Found at i:34260001 original size:27 final size:25
Alignment explanation
Indices: 34259946--34260006 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
34259936 GTTATTCTGT
*
34259946 TTCTGGCTCGTAAGAGTAAAATATG
1 TTCTGGCTCGTAAGAGTAAAATATA
* *
34259971 TTCTGGGCTCGTAAGAGCTAAACTCTA
1 TTCT-GGCTCGTAAGAG-TAAAATATA
34259998 TTCTAGGCT
1 TTCT-GGCT
34260007 TGAAGGAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.13
26 12 0.40
27 14 0.47
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (25 bp):
TTCTGGCTCGTAAGAGTAAAATATA
Found at i:34262700 original size:19 final size:19
Alignment explanation
Indices: 34262676--34262713 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
34262666 CTCTTAACCA
*
34262676 ATACATCATTTAT-TATTCT
1 ATACAT-ATATATATATTCT
34262695 ATACATATATATATATTCT
1 ATACATATATATATATTCT
34262714 TTTTATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (19 bp):
ATACATATATATATATTCT
Found at i:34268834 original size:60 final size:58
Alignment explanation
Indices: 34268770--34268901 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 58
34268760 GGTAAAACGA
* *
34268770 TAATTTTTAGAAA-AATCGAGATCAAAAATGGAGTTTTTTTGGACATCC-GGGGTAAATTGG
1 TAATTTTT-GAAAGAATCAAGATCAAAAATGGAG--TTTTTGGACATCCAGGGG-AAAATGG
**
34268830 TAATTTTTGAAAGTTTCAAGATCAAAAATGGAGTTTTTGGACATCCAAGGGGAAAATGG
1 TAATTTTTGAAAGAATCAAGATCAAAAATGGAGTTTTTGGACATCC-AGGGGAAAATGG
34268889 TAATTTTTGAAAG
1 TAATTTTTGAAAG
34268902 TTTTGGGGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
58 13 0.20
59 23 0.35
60 29 0.45
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (58 bp):
TAATTTTTGAAAGAATCAAGATCAAAAATGGAGTTTTTGGACATCCAGGGGAAAATGG
Found at i:34268916 original size:59 final size:59
Alignment explanation
Indices: 34268793--34269022 Score: 193
Period size: 59 Copynumber: 3.9 Consensus size: 59
34268783 AATCGAGATC
* * * *
34268793 AAAAATGGAGTTTTTTTGGACATCC--GGGGTAAATTGGTAATTTTTGAAAGTTTCAAGATC
1 AAAAATGGAG--TTTTTGGA-ATCCAAGGGGTAAAATGGTAATTTTTGAAAGTTTTAAGGTT
**
34268853 AAAAATGGAGTTTTTGGACATCCAAGGGG-AAAATGGTAATTTTTGAAAGTTTTGGGGTT
1 AAAAATGGAGTTTTTGGA-ATCCAAGGGGTAAAATGGTAATTTTTGAAAGTTTTAAGGTT
* * * ** * *
34268912 AAAAATTGAATTTTTGGGAGT--TTGGGAGTAAAATGGTAATTTTTGGAAGCTTTAAGGTT
1 AAAAATGGAGTTTTT-GGAATCCAAGGG-GTAAAATGGTAATTTTTGAAAGTTTTAAGGTT
* * * * *
34268971 AAAAATGAAGTTTTTGGAAGCTTAA-GGGTAAAATGGTAACTTTTAAAAGTTT
1 AAAAATGGAGTTTTTGGAATC-CAAGGGGTAAAATGGTAATTTTTGAAAGTTT
34269023 CAGGGTCAAA
Statistics
Matches: 136, Mismatches: 26, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
57 3 0.02
58 17 0.12
59 97 0.71
60 19 0.14
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (59 bp):
AAAAATGGAGTTTTTGGAATCCAAGGGGTAAAATGGTAATTTTTGAAAGTTTTAAGGTT
Found at i:34268926 original size:30 final size:29
Alignment explanation
Indices: 34268890--34269072 Score: 92
Period size: 30 Copynumber: 6.2 Consensus size: 29
34268880 GGAAAATGGT
*
34268890 AATTTTTGAAAGTTTTGGGGTTAAAAATTG
1 AATTTTTGGAAG-TTTGGGGTTAAAAATTG
* *
34268920 AATTTTTGGGAGTTTGGGAG-T-AAAATGG
1 AATTTTTGGAAGTTTGGG-GTTAAAAATTG
**
34268948 TAATTTTTGGAAGCTTTAAGGTTAAAAA-TG
1 -AATTTTTGGAAG-TTTGGGGTTAAAAATTG
** *
34268978 AAGTTTTTGGAAGCTTAAGGG-T-AAAATGG
1 AA-TTTTTGGAAG-TTTGGGGTTAAAAATTG
* ** * *
34269007 TAACTTTTAAAAGTTTCAGGG-TCAAAATTG
1 -AATTTTTGGAAGTTT-GGGGTTAAAAATTG
* *
34269037 AAATTTTTGGAAGTTCGGGGGTAAAAATAT-
1 -AATTTTTGGAAGTTTGGGGTTAAAAAT-TG
34269067 AATTTT
1 AATTTT
34269073 CAAAAAGTTT
Statistics
Matches: 119, Mismatches: 22, Indels: 25
0.72 0.13 0.15
Matches are distributed among these distances:
28 12 0.10
29 44 0.37
30 58 0.49
31 5 0.04
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (29 bp):
AATTTTTGGAAGTTTGGGGTTAAAAATTG
Found at i:34268943 original size:118 final size:118
Alignment explanation
Indices: 34268817--34269062 Score: 293
Period size: 118 Copynumber: 2.1 Consensus size: 118
34268807 TTTGGACATC
* * *
34268817 CGGG-GTAAATTGGTAATTTTTGAAAG-TTTCAAGATCAAAAATGGAGTTTTTGGACATC-CAAG
1 CGGGAGTAAAATGGTAATTTTTGAAAGCTTT-AAGATCAAAAATGAAGTTTTTGGA-AGCTCAAG
* * ** *
34268879 GGGAAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATTG-AATTTTTGGGAGTT
64 GGGAAAATGGTAACTTTTAAAAGTTTCAGGG-TAAAAATTGAAATTTTTGGAAGTT
* * * * *
34268934 TGGGAGTAAAATGGTAATTTTTGGAAGCTTTAAGGTTAAAAATGAAGTTTTTGGAAGCTTAAGGG
1 CGGGAGTAAAATGGTAATTTTTGAAAGCTTTAAGATCAAAAATGAAGTTTTTGGAAGCTCAAGGG
* *
34268999 TAAAATGGTAACTTTTAAAAGTTTCAGGGTCAAAATTGAAATTTTTGGAAGTT
66 GAAAATGGTAACTTTTAAAAGTTTCAGGGTAAAAATTGAAATTTTTGGAAGTT
*
34269052 CGGGGGTAAAA
1 CGGGAGTAAAA
34269063 ATATAATTTT
Statistics
Matches: 108, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
117 13 0.12
118 92 0.85
119 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (118 bp):
CGGGAGTAAAATGGTAATTTTTGAAAGCTTTAAGATCAAAAATGAAGTTTTTGGAAGCTCAAGGG
GAAAATGGTAACTTTTAAAAGTTTCAGGGTAAAAATTGAAATTTTTGGAAGTT
Found at i:34269014 original size:29 final size:30
Alignment explanation
Indices: 34268876--34269049 Score: 112
Period size: 30 Copynumber: 5.9 Consensus size: 30
34268866 TTGGACATCC
* *
34268876 AAGGGGAAAATGGTAATTTTTGAAAG-TTT
1 AAGGGTAAAATGGTAATTTTTGGAAGCTTT
** * *
34268905 TGGGGTTAAAAATTG-AATTTTTGGGAG-TTT
1 AAGGG-T-AAAATGGTAATTTTTGGAAGCTTT
*
34268935 -GGGAGTAAAATGGTAATTTTTGGAAGCTTT
1 AAGG-GTAAAATGGTAATTTTTGGAAGCTTT
*
34268965 AAGGTTAAAAAT-G-AAGTTTTTGGAAGC-TT
1 AAGGGT-AAAATGGTAA-TTTTTGGAAGCTTT
* **
34268994 AAGGGTAAAATGGTAACTTTTAAAAG-TTT
1 AAGGGTAAAATGGTAATTTTTGGAAGCTTT
* * *
34269023 CAGGGTCAAAATTGAAATTTTTGGAAG
1 AAGGGT-AAAATGGTAATTTTTGGAAG
34269050 TTCGGGGGTA
Statistics
Matches: 113, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
28 11 0.10
29 42 0.37
30 47 0.42
31 13 0.12
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
AAGGGTAAAATGGTAATTTTTGGAAGCTTT
Found at i:34269059 original size:59 final size:59
Alignment explanation
Indices: 34268818--34269101 Score: 217
Period size: 59 Copynumber: 4.8 Consensus size: 59
34268808 TTGGACATCC
* * * * *
34268818 GGGGTAAATTGGTAATTTTTGAAAGTTTCAAGATCAAAAATGGAGTTTTTGGACA-TCCAA
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATGAAATTTTTGGA-AGTTC-A
*** * * *
34268878 GGGG-AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATTG-AATTTTTGGGAGTT-T
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAA-TGAAATTTTTGGAAGTTCA
* * *
34268935 GGGAGTAAAATGGTAATTTTTGGAAGCTTT-AAGGTTAAAAATGAAGTTTTTGGAAGCTT-A
1 GGG-GTAAAATGGTAATTTTTGAAAG-TTTCAAGGTCAAAAATGAAATTTTTGGAAG-TTCA
* * * * * *
34268995 AGGGTAAAATGGTAACTTTTAAAAGTTTCAGGGTCAAAATTGAAATTTTTGGAAGTTCG
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATGAAATTTTTGGAAGTTCA
* ** *
34269054 GGGGTAAAAAT-ATAATTTTCAAAAAGTTT-AAGGTC-AAAATGGAATTTT
1 GGGGT-AAAATGGTAATTTT-TGAAAGTTTCAAGGTCAAAAATGAAATTTT
34269102 GAAGAAGTTT
Statistics
Matches: 181, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
57 3 0.02
58 20 0.11
59 132 0.73
60 26 0.14
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.35
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATGAAATTTTTGGAAGTTCA
Found at i:34269084 original size:118 final size:117
Alignment explanation
Indices: 34268817--34269092 Score: 272
Period size: 118 Copynumber: 2.3 Consensus size: 117
34268807 TTTGGACATC
* * ** * * *
34268817 CGGG-GTAAATTGGTAATTTTTGAAAGTTTCAAGATCAAAAATGGAGTTTTTGGACATCCAAGGG
1 CGGGAGTAAAATGATAATTTTAAAAAGTTT-AAGGTCAAAAATGAAGTTTTTGGACAGCCAAGGG
* * ** *
34268881 GAAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATTGAATTTTTGGGAGTT
65 GAAAATGGTAACTTTTAAAAGTTTCAGGGTTAAAAATTGAATTTTTGGAAGTT
* * *** * *
34268934 TGGGAGTAAAATGGTAATTTTTGGAAGCTTTAAGGTTAAAAATGAAGTTTTTGGA-AGCTTAAGG
1 CGGGAGTAAAATGATAATTTTAAAAAG-TTTAAGGTCAAAAATGAAGTTTTTGGACAGC-CAAGG
* *
34268998 GTAAAATGGTAACTTTTAAAAGTTTCAGGG-TCAAAATTGAAATTTTTGGAAGTT
64 GGAAAATGGTAACTTTTAAAAGTTTCAGGGTTAAAAATTG-AATTTTTGGAAGTT
*
34269052 CGGGGGTAAAAAT-ATAATTTTCAAAAAGTTTAAGGTCAAAA
1 CGGGAGT-AAAATGATAATTTT-AAAAAGTTTAAGGTCAAAA
34269093 TGGAATTTTG
Statistics
Matches: 131, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
117 13 0.10
118 107 0.82
119 11 0.08
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (117 bp):
CGGGAGTAAAATGATAATTTTAAAAAGTTTAAGGTCAAAAATGAAGTTTTTGGACAGCCAAGGGG
AAAATGGTAACTTTTAAAAGTTTCAGGGTTAAAAATTGAATTTTTGGAAGTT
Found at i:34269628 original size:13 final size:12
Alignment explanation
Indices: 34269607--34269638 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
34269597 GTTTAAGTCA
34269607 TTTTTTCTTCAT
1 TTTTTTCTTCAT
34269619 TTTCTTTCTTCAT
1 TTT-TTTCTTCAT
34269632 TTTTTTC
1 TTTTTTC
34269639 AAAAATACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTTCTTCAT
Found at i:34271797 original size:8 final size:8
Alignment explanation
Indices: 34271784--34271808 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
34271774 CACCTTCTGA
34271784 TTAAAATT
1 TTAAAATT
34271792 TTAAAATT
1 TTAAAATT
34271800 TTAAAATT
1 TTAAAATT
34271808 T
1 T
34271809 AACAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAAAATT
Found at i:34273861 original size:14 final size:16
Alignment explanation
Indices: 34273837--34273875 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
34273827 GTGTCAGCCT
34273837 TTTTTTAATTATT-TA
1 TTTTTTAATTATTATA
34273852 TTTTTT-ATTATTATA
1 TTTTTTAATTATTATA
*
34273867 TTTTATAAT
1 TTTTTTAAT
34273876 AAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 13 0.62
16 2 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTAATTATTATA
Found at i:34274061 original size:9 final size:9
Alignment explanation
Indices: 34274047--34274094 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
34274037 GTGAAGTCGA
34274047 CGATGATGC
1 CGATGATGC
34274056 CGATGATGC
1 CGATGATGC
* *
34274065 CGAAG-TCGA
1 CGATGAT-GC
34274074 CGATGATGC
1 CGATGATGC
34274083 CGATGATGC
1 CGATGATGC
34274092 CGA
1 CGA
34274095 AGCCGACGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 1 0.03
9 31 0.94
10 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.19
Consensus pattern (9 bp):
CGATGATGC
Found at i:34274077 original size:27 final size:27
Alignment explanation
Indices: 34274039--34274102 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
34274029 GAAGACAAGT
34274039 GAAGTCGACGATGATGCCGATGATGCC
1 GAAGTCGACGATGATGCCGATGATGCC
34274066 GAAGTCGACGATGATGCCGATGATGCC
1 GAAGTCGACGATGATGCCGATGATGCC
*
34274093 GAAGCCGACG
1 GAAGTCGACG
34274103 CTAGTGACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.27, C:0.23, G:0.34, T:0.16
Consensus pattern (27 bp):
GAAGTCGACGATGATGCCGATGATGCC
Found at i:34274781 original size:24 final size:23
Alignment explanation
Indices: 34274733--34274782 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
34274723 CCATTATTTA
*
34274733 TTTTTTTATAATATTCCTTTCAT
1 TTTTTTTATAATATTCCTTTAAT
*
34274756 TTTTTATTTTAAT-TTCCTTCTAAT
1 TTTTT-TTATAATATTCCTT-TAAT
34274780 TTT
1 TTT
34274783 GATTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTTTATAATATTCCTTTAAT
Found at i:34276802 original size:20 final size:21
Alignment explanation
Indices: 34276768--34276807 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
34276758 CTAAAATAAA
34276768 AATTTGAATGTTTTA-TATTT
1 AATTTGAATGTTTTACTATTT
34276788 AATTTGAATAG-TTTACTATT
1 AATTTGAAT-GTTTTACTATT
34276808 GAAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (21 bp):
AATTTGAATGTTTTACTATTT
Found at i:34277341 original size:17 final size:17
Alignment explanation
Indices: 34277321--34277359 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
34277311 TGTTGTTGAC
34277321 AAAAAAT-AACAATATAT
1 AAAAAATGAA-AATATAT
*
34277338 AAAAATTGAAAATATAT
1 AAAAAATGAAAATATAT
34277355 AAAAA
1 AAAAA
34277360 TAAATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAAATGAAAATATAT
Found at i:34278722 original size:6 final size:6
Alignment explanation
Indices: 34278680--34278720 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
34278670 TTACACCTAT
*
34278680 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCT CCCTC
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTC
34278721 TCTCCTGCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.12, C:0.68, G:0.00, T:0.20
Consensus pattern (6 bp):
CCCTCA
Found at i:34279920 original size:16 final size:16
Alignment explanation
Indices: 34279896--34279930 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34279886 ATTTCTCAAA
34279896 TTTATTATTATGTA-T
1 TTTATTATTATGTAGT
34279911 TTTATCTATTATGTAGT
1 TTTAT-TATTATGTAGT
34279928 TTT
1 TTT
34279931 TCAAAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 9 0.50
17 4 0.22
ACGTcount: A:0.23, C:0.03, G:0.09, T:0.66
Consensus pattern (16 bp):
TTTATTATTATGTAGT
Found at i:34280862 original size:20 final size:20
Alignment explanation
Indices: 34280837--34280906 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
34280827 CTAATGATTT
34280837 TAAAATTATTTTTTAAAATA
1 TAAAATTATTTTTTAAAATA
** *
34280857 TAAAATTA--TTAAAATCAATT
1 TAAAATTATTTTTTAA--AATA
34280877 TAAAATTATTTTTTAAAATA
1 TAAAATTATTTTTTAAAATA
*
34280897 TATAATTATT
1 TAAAATTATT
34280907 AAAATTATCA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.10
20 31 0.79
22 4 0.10
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTATTTTTTAAAATA
Found at i:34280880 original size:40 final size:40
Alignment explanation
Indices: 34280835--34280911 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
34280825 AGCTAATGAT
34280835 TTTAAAATTATTTTTTAAAATATAAAATTATTAAAATCAA
1 TTTAAAATTATTTTTTAAAATATAAAATTATTAAAATCAA
*
34280875 TTTAAAATTATTTTTTAAAATATATAATTATTAAAAT
1 TTTAAAATTATTTTTTAAAATATAAAATTATTAAAAT
34280912 TATCATCTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (40 bp):
TTTAAAATTATTTTTTAAAATATAAAATTATTAAAATCAA
Found at i:34280941 original size:23 final size:20
Alignment explanation
Indices: 34280899--34280938 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
34280889 TTAAAATATA
34280899 TAATTATTAAAATTATCATC
1 TAATTATTAAAATTATCATC
34280919 TAATTATTAAAATTATCATC
1 TAATTATTAAAATTATCATC
34280939 ATCCTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATTATTAAAATTATCATC
Found at i:34286600 original size:22 final size:22
Alignment explanation
Indices: 34286564--34286620 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
34286554 AAATTTAGAA
*
34286564 TTTAATTTTTA-TATTTTTATTT
1 TTTAAATTTTATTA-TTTTATTT
34286586 TTTGGAAATTTTATTATTTTATTT
1 TTT--AAATTTTATTATTTTATTT
34286610 TTTAAATTTTA
1 TTTAAATTTTA
34286621 AAGTTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 11 0.35
24 18 0.58
25 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTAAATTTTATTATTTTATTT
Found at i:34287846 original size:22 final size:21
Alignment explanation
Indices: 34287820--34287861 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34287810 TATAATATTG
*
34287820 TAATAAAAATTTAAATAAACAA
1 TAAT-AAAATTGAAATAAACAA
*
34287842 TAATAGAATTGAAATAAACA
1 TAATAAAATTGAAATAAACA
34287862 CAAATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (21 bp):
TAATAAAATTGAAATAAACAA
Found at i:34288292 original size:13 final size:13
Alignment explanation
Indices: 34288274--34288298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34288264 AGATTAAATT
34288274 TTATTACTCAATA
1 TTATTACTCAATA
34288287 TTATTACTCAAT
1 TTATTACTCAAT
34288299 TAGAATCCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATTACTCAATA
Found at i:34298440 original size:21 final size:21
Alignment explanation
Indices: 34298414--34298465 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
34298404 GTGTTTAGAA
34298414 GTATCGGTAGTTTGTATACTT
1 GTATCGGTAGTTTGTATACTT
34298435 GTATCGGTAGTTTGTATACTT
1 GTATCGGTAGTTTGTATACTT
34298456 GTATCGGTAG
1 GTATCGGTAG
34298466 AAGTAGCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.44
Consensus pattern (21 bp):
GTATCGGTAGTTTGTATACTT
Found at i:34298546 original size:21 final size:21
Alignment explanation
Indices: 34298522--34298567 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
34298512 TAGAAGTAAG
*
34298522 ACTTGT-TTCAGTAGAAGAGTC
1 ACTTGTATT-AGTAGAACAGTC
*
34298543 ACTTGTATTAGTAGAACTGTC
1 ACTTGTATTAGTAGAACAGTC
34298564 ACTT
1 ACTT
34298568 ATGTCGGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (21 bp):
ACTTGTATTAGTAGAACAGTC
Found at i:34299832 original size:22 final size:23
Alignment explanation
Indices: 34299805--34299849 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
34299795 ATAAAATTAT
34299805 TAAATA-TTAAAATAAAAC-AATA
1 TAAATATTTAAAA-AAAACTAATA
34299827 TAAATATTTAAAAAAAACTAATA
1 TAAATATTTAAAAAAAACTAATA
34299850 AGGGCGGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAATATTTAAAAAAAACTAATA
Found at i:34300784 original size:15 final size:14
Alignment explanation
Indices: 34300757--34300783 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34300747 ATCATAAACC
34300757 AAATTTAAAAAAAG
1 AAATTTAAAAAAAG
34300771 AAATTTAAAAAAA
1 AAATTTAAAAAAA
34300784 AATTAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATTTAAAAAAAG
Found at i:34308158 original size:27 final size:27
Alignment explanation
Indices: 34308128--34308181 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
34308118 AGAGCGATAC
34308128 TCTAATATAGCTCAAGTAGAGCTTTGA
1 TCTAATATAGCTCAAGTAGAGCTTTGA
*
34308155 TCTATTATAGCTCAAGTAGAGCTTTGA
1 TCTAATATAGCTCAAGTAGAGCTTTGA
34308182 AGAGCTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (27 bp):
TCTAATATAGCTCAAGTAGAGCTTTGA
Found at i:34309412 original size:28 final size:27
Alignment explanation
Indices: 34309379--34309675 Score: 122
Period size: 28 Copynumber: 11.3 Consensus size: 27
34309369 ATATATAAAC
34309379 ATGCGTTTACACTCGTCAGCTTATACTT
1 ATGCGTTTACACTCGTCAGCTTATAC-T
* **
34309407 ATGCGTTTACACTCGACAGCTTGCAC-
1 ATGCGTTTACACTCGTCAGCTTATACT
*
34309433 A--CGTTTACACTCGTCAACTTATACAT
1 ATGCGTTTACACTCGTCAGCTTATAC-T
* * * **
34309459 ATGCATTTACGCTCGCCAGCTTGCAC-
1 ATGCGTTTACACTCGTCAGCTTATACT
* *
34309485 A--CGTTTACAATCATCAGCTTATACAT
1 ATGCGTTTACACTCGTCAGCTTATAC-T
* ** ** **
34309511 ATGCGCTTATGCTCACCAGCTTGCAC-
1 ATGCGTTTACACTCGTCAGCTTATACT
* *
34309537 A--CGTTTACGCTCGTCAGCTTATATAT
1 ATGCGTTTACACTCGTCAGCTTATA-CT
* **
34309563 ATGCGTTTACGCTCG-CTAGCTTGCAC-
1 ATGCGTTTACACTCGTC-AGCTTATACT
* * * *
34309589 A--CATTTACGCTCATCAACTTATACAT
1 ATGCGTTTACACTCGTCAGCTTATAC-T
* * * *
34309615 ATGCGTTTACGCTTGCCAGCTTACAC-
1 ATGCGTTTACACTCGTCAGCTTATACT
*
34309641 A--CGTTTACGCTCGTCAGCTTATACAT
1 ATGCGTTTACACTCGTCAGCTTATAC-T
*
34309667 ATGTGTTTA
1 ATGCGTTTA
34309676 GGCTATTTAA
Statistics
Matches: 195, Mismatches: 52, Indels: 44
0.67 0.18 0.15
Matches are distributed among these distances:
24 87 0.45
25 1 0.01
26 10 0.05
27 1 0.01
28 96 0.49
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (27 bp):
ATGCGTTTACACTCGTCAGCTTATACT
Found at i:34309443 original size:52 final size:52
Alignment explanation
Indices: 34309382--34309675 Score: 376
Period size: 52 Copynumber: 5.7 Consensus size: 52
34309372 TATAAACATG
* *
34309382 CGTTTACACTCGTCAGCTTATACTTATGCGTTTACACTCGACAGCTTGCACA
1 CGTTTACACTCGTCAGCTTATACATATGCGTTTACGCTCGACAGCTTGCACA
* * *
34309434 CGTTTACACTCGTCAACTTATACATATGCATTTACGCTCGCCAGCTTGCACA
1 CGTTTACACTCGTCAGCTTATACATATGCGTTTACGCTCGACAGCTTGCACA
* * * *
34309486 CGTTTACAATCATCAGCTTATACATATGCGCTTATGCTC-ACCAGCTTGCACA
1 CGTTTACACTCGTCAGCTTATACATATGCGTTTACGCTCGA-CAGCTTGCACA
* *
34309538 CGTTTACGCTCGTCAGCTTATATATATGCGTTTACGCTCG-CTAGCTTGCACA
1 CGTTTACACTCGTCAGCTTATACATATGCGTTTACGCTCGAC-AGCTTGCACA
* * * * * * *
34309590 CATTTACGCTCATCAACTTATACATATGCGTTTACGCTTGCCAGCTTACACA
1 CGTTTACACTCGTCAGCTTATACATATGCGTTTACGCTCGACAGCTTGCACA
* *
34309642 CGTTTACGCTCGTCAGCTTATACATATGTGTTTA
1 CGTTTACACTCGTCAGCTTATACATATGCGTTTA
34309676 GGCTATTTAA
Statistics
Matches: 210, Mismatches: 28, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
51 1 0.00
52 208 0.99
53 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (52 bp):
CGTTTACACTCGTCAGCTTATACATATGCGTTTACGCTCGACAGCTTGCACA
Found at i:34309666 original size:156 final size:156
Alignment explanation
Indices: 34309382--34309669 Score: 445
Period size: 156 Copynumber: 1.8 Consensus size: 156
34309372 TATAAACATG
* *
34309382 CGTTTACACTCGTCAGCTTATACTTATGCGTTTACACTCGACAGCTTGCACACGTTTACACTCGT
1 CGTTTACACTCGTCAGCTTATACTTATGCGTTTACACTCGACAGCTTGCACACATTTACACTCAT
*
34309447 CAACTTATACATATGCATTTACGCTCGCCAGCTTGCACACGTTTACAATCATCAGCTTATACATA
66 CAACTTATACATATGCATTTACGCTCGCCAGCTTACACACGTTTACAATCATCAGCTTATACATA
34309512 TGCGCTTATGCTCACCAGCTTGCACA
131 TGCGCTTATGCTCACCAGCTTGCACA
* * *
34309538 CGTTTACGCTCGTCAGCTTATA-TATATGCGTTTACGCTCG-CTAGCTTGCACACATTTACGCTC
1 CGTTTACACTCGTCAGCTTATACT-TATGCGTTTACACTCGAC-AGCTTGCACACATTTACACTC
* * ** *
34309601 ATCAACTTATACATATGCGTTTACGCTTGCCAGCTTACACACGTTTACGCTCGTCAGCTTATACA
64 ATCAACTTATACATATGCATTTACGCTCGCCAGCTTACACACGTTTACAATCATCAGCTTATACA
34309666 TATG
129 TATG
34309670 TGTTTAGGCT
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
155 2 0.02
156 117 0.98
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (156 bp):
CGTTTACACTCGTCAGCTTATACTTATGCGTTTACACTCGACAGCTTGCACACATTTACACTCAT
CAACTTATACATATGCATTTACGCTCGCCAGCTTACACACGTTTACAATCATCAGCTTATACATA
TGCGCTTATGCTCACCAGCTTGCACA
Found at i:34310741 original size:3 final size:3
Alignment explanation
Indices: 34310733--34310757 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34310723 TTTATGACCC
34310733 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
34310758 TGTAGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:34311771 original size:20 final size:20
Alignment explanation
Indices: 34311746--34311784 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
34311736 CATGTTAATT
34311746 TGAAATAATGTAAA-TGAGTA
1 TGAAATAAT-TAAATTGAGTA
34311766 TGAAATAATTAAATTGAGT
1 TGAAATAATTAAATTGAGT
34311785 TGTAATCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (20 bp):
TGAAATAATTAAATTGAGTA
Found at i:34314381 original size:22 final size:22
Alignment explanation
Indices: 34314322--34314384 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
34314312 TTGACCTAGA
* *
34314322 CCCGTTGATCGAACCCGACCCG
1 CCCGTTGACCGAACCTGACCCG
*
34314344 TCCGTTGACCGAACCTGACCCG
1 CCCGTTGACCGAACCTGACCCG
34314366 CCCGTTGACCGAACCTGAC
1 CCCGTTGACCGAACCTGAC
34314385 TTGACTCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.19, C:0.43, G:0.22, T:0.16
Consensus pattern (22 bp):
CCCGTTGACCGAACCTGACCCG
Found at i:34319875 original size:21 final size:21
Alignment explanation
Indices: 34319851--34319907 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
34319841 GAAGTAAGAT
*
34319851 TTGTTTTAGTAGAAGAGTCAC
1 TTGTATTAGTAGAAGAGTCAC
* **
34319872 TTGTATCAGTAGAATTGTCAC
1 TTGTATTAGTAGAAGAGTCAC
*
34319893 TTGTATTGGTAGAAG
1 TTGTATTAGTAGAAG
34319908 TCTACACTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.39
Consensus pattern (21 bp):
TTGTATTAGTAGAAGAGTCAC
Found at i:34320576 original size:18 final size:18
Alignment explanation
Indices: 34320548--34320590 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
34320538 GACCAATGGT
*
34320548 ACCTCCGGTAA-AGCCTCC
1 ACCTCCTGTAAGA-CCTCC
*
34320566 GCCTCCTGTAAGACCTCC
1 ACCTCCTGTAAGACCTCC
34320584 ACCTCCT
1 ACCTCCT
34320591 CTTGTGATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.19, C:0.47, G:0.14, T:0.21
Consensus pattern (18 bp):
ACCTCCTGTAAGACCTCC
Found at i:34327848 original size:19 final size:19
Alignment explanation
Indices: 34327824--34327863 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
34327814 CCCAAACCCG
34327824 TTAACCGTTGACAGTTGAC
1 TTAACCGTTGACAGTTGAC
* *
34327843 TTAACCGTTGGCCGTTGAC
1 TTAACCGTTGACAGTTGAC
34327862 TT
1 TT
34327864 TTTCCAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (19 bp):
TTAACCGTTGACAGTTGAC
Found at i:34334228 original size:20 final size:20
Alignment explanation
Indices: 34334203--34334262 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
34334193 TTGGTTTGAG
34334203 TAAATTGATGGCATGAGGAT
1 TAAATTGATGGCATGAGGAT
* *
34334223 TAAATTTAT---A-AAGG--
1 TAAATTGATGGCATGAGGAT
34334237 TAAATTGATGGCATGAGGAT
1 TAAATTGATGGCATGAGGAT
34334257 TAAATT
1 TAAATT
34334263 TATACTCCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
14 8 0.27
16 3 0.10
17 2 0.07
18 3 0.10
20 14 0.47
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (20 bp):
TAAATTGATGGCATGAGGAT
Found at i:34334245 original size:34 final size:34
Alignment explanation
Indices: 34334202--34334266 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
34334192 ATTGGTTTGA
34334202 GTAAATTGATGGCATGAGGATTAAATTTATAAAG
1 GTAAATTGATGGCATGAGGATTAAATTTATAAAG
34334236 GTAAATTGATGGCATGAGGATTAAATTTATA
1 GTAAATTGATGGCATGAGGATTAAATTTATA
34334267 CTCCTTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (34 bp):
GTAAATTGATGGCATGAGGATTAAATTTATAAAG
Found at i:34335988 original size:42 final size:42
Alignment explanation
Indices: 34335927--34336006 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
34335917 TGTCCCAACG
* * *
34335927 TCTTGACTAATCAAGTGACTCATTAGACATCGAGTCTTCAAT
1 TCTTGACTAATCAAGTGACTAATCAAACATCGAGTCTTCAAT
*
34335969 TCTTGACTAATC-AGATGACTAATCAAATATCGAGTCTT
1 TCTTGACTAATCAAG-TGACTAATCAAACATCGAGTCTT
34336007 TAATGTTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 31 0.94
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (42 bp):
TCTTGACTAATCAAGTGACTAATCAAACATCGAGTCTTCAAT
Found at i:34340438 original size:27 final size:27
Alignment explanation
Indices: 34340403--34340463 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
34340393 CAACAGCCTA
*
34340403 CCCGCTTTTAATGTCTCGA-TGGACTAT
1 CCCGCTTTTAATGTC-CCATTGGACTAT
*
34340430 CCTGCTTTTAATGTCCCATTGGACTAT
1 CCCGCTTTTAATGTCCCATTGGACTAT
34340457 CCCGCTT
1 CCCGCTT
34340464 ACCAAAGTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.38
Consensus pattern (27 bp):
CCCGCTTTTAATGTCCCATTGGACTAT
Found at i:34343007 original size:20 final size:20
Alignment explanation
Indices: 34342984--34343041 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
34342974 AAATGCTAGT
34342984 AGAGGCATCGAAGCT-CAAAC
1 AGAGGCATCGAAG-TGCAAAC
*
34343004 AGAGAC-TCTGAAGTGCAAAC
1 AGAGGCATC-GAAGTGCAAAC
34343024 AGAGGCATCGAAGTGCAA
1 AGAGGCATCGAAGTGCAA
34343042 TCCCGTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 28 0.85
21 2 0.06
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.12
Consensus pattern (20 bp):
AGAGGCATCGAAGTGCAAAC
Found at i:34343822 original size:22 final size:22
Alignment explanation
Indices: 34343797--34343839 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
34343787 AAATAGGGAG
* * *
34343797 AAAATAACAAGAAAATAGCATT
1 AAAACAACAAAAAAAGAGCATT
34343819 AAAACAACAAAAAAAGAGCAT
1 AAAACAACAAAAAAAGAGCAT
34343840 ATTTTTTGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.12, G:0.09, T:0.12
Consensus pattern (22 bp):
AAAACAACAAAAAAAGAGCATT
Found at i:34348807 original size:2 final size:2
Alignment explanation
Indices: 34348800--34348840 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
34348790 GTTTCTCAAA
34348800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34348841 AAATGAACGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34351675 original size:13 final size:13
Alignment explanation
Indices: 34351657--34351681 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34351647 AAGATATAAG
34351657 TTATTTAAATATC
1 TTATTTAAATATC
34351670 TTATTTAAATAT
1 TTATTTAAATAT
34351682 TATCTCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTTAAATATC
Found at i:34355248 original size:58 final size:58
Alignment explanation
Indices: 34355179--34355296 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
34355169 ATTTAAATAT
34355179 ATACAATTGAATCAGAATAAAAGCTTCATGTATATATAAGAACCGCAATTCAAGTTTC
1 ATACAATTGAATCAGAATAAAAGCTTCATGTATATATAAGAACCGCAATTCAAGTTTC
*
34355237 ATACAATTGAATCAGAATAAAAGCTTCATGTATATATAAGAATCGCAATTCAAGTTTC
1 ATACAATTGAATCAGAATAAAAGCTTCATGTATATATAAGAACCGCAATTCAAGTTTC
34355295 AT
1 AT
34355297 GTGTATAATT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (58 bp):
ATACAATTGAATCAGAATAAAAGCTTCATGTATATATAAGAACCGCAATTCAAGTTTC
Found at i:34355296 original size:31 final size:31
Alignment explanation
Indices: 34355203--34355303 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
34355193 GAATAAAAGC
*
34355203 TTCATGTATATATAAGAACCGCAATTCAAGT
1 TTCATGTATATATAAGAATCGCAATTCAAGT
* * ** *
34355234 TTCA--TACA-AT-TGAATCAG-AATAAAAGC
1 TTCATGTATATATAAGAATC-GCAATTCAAGT
34355261 TTCATGTATATATAAGAATCGCAATTCAAGT
1 TTCATGTATATATAAGAATCGCAATTCAAGT
*
34355292 TTCATGTGTATA
1 TTCATGTATATA
34355304 ATTGTACAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
27 14 0.27
28 3 0.06
29 6 0.12
30 3 0.06
31 26 0.50
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (31 bp):
TTCATGTATATATAAGAATCGCAATTCAAGT
Found at i:34355699 original size:20 final size:22
Alignment explanation
Indices: 34355674--34355715 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
34355664 TTTTAATATT
34355674 TATCCTAAACC-T-TTTTAAAA
1 TATCCTAAACCGTATTTTAAAA
34355694 TATCCTAAACCGTATTTTAAAA
1 TATCCTAAACCGTATTTTAAAA
34355716 AGGACTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (22 bp):
TATCCTAAACCGTATTTTAAAA
Found at i:34364506 original size:25 final size:25
Alignment explanation
Indices: 34364434--34364508 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
34364424 GGCGATGAGA
34364434 AAATTATGGAATAGTCCTTGTACTT
1 AAATTATGGAATAGTCCTTGTACTT
* *
34364459 AAATT-T--AAGTA-T-GTTGTATTT
1 AAATTATGGAA-TAGTCCTTGTACTT
34364480 AAATTATGGAATAGTCCTTGTACTT
1 AAATTATGGAATAGTCCTTGTACTT
34364505 AAAT
1 AAAT
34364509 GTGAATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
21 12 0.30
22 4 0.10
23 4 0.10
24 4 0.10
25 16 0.40
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.43
Consensus pattern (25 bp):
AAATTATGGAATAGTCCTTGTACTT
Found at i:34365189 original size:43 final size:43
Alignment explanation
Indices: 34365125--34365239 Score: 178
Period size: 43 Copynumber: 2.7 Consensus size: 43
34365115 TATATAAGTA
*
34365125 GAAG-ACTTATGTCTCGATAAGAGTATAAGATTATTGTAAATG
1 GAAGAACTTATGTCTCGATAAGAGCATAAGATTATTGTAAATG
* *
34365167 GAAGAACTTATGTCTCGGTAAGAGCATAAGATTATTTTAAATG
1 GAAGAACTTATGTCTCGATAAGAGCATAAGATTATTGTAAATG
* *
34365210 GAAGAACTTATGACTCGATGAGAGCATAAG
1 GAAGAACTTATGTCTCGATAAGAGCATAAG
34365240 GTTAATTCAG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
42 4 0.06
43 62 0.94
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (43 bp):
GAAGAACTTATGTCTCGATAAGAGCATAAGATTATTGTAAATG
Found at i:34368877 original size:56 final size:56
Alignment explanation
Indices: 34368804--34368921 Score: 229
Period size: 56 Copynumber: 2.1 Consensus size: 56
34368794 TTTGGTTTAA
34368804 AACATTTATTTACTTAATTTACCAATATACCCTTTGTTCACACTTTAATTTTAACC
1 AACATTTATTTACTTAATTTACCAATATACCCTTTGTTCACACTTTAATTTTAACC
34368860 AACATTTATTTACTTAATTTACCAATATACCCTTTGTTCACACTTTAATTTTAACC
1 AACATTTATTTACTTAATTTACCAATATACCCTTTGTTCACACTTTAATTTTAACC
34368916 AA-ATTT
1 AACATTT
34368922 TAGTCAAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 4 0.06
56 58 0.94
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (56 bp):
AACATTTATTTACTTAATTTACCAATATACCCTTTGTTCACACTTTAATTTTAACC
Found at i:34372003 original size:15 final size:15
Alignment explanation
Indices: 34371985--34372058 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
34371975 TCAAAATATA
*
34371985 AAATAACATAAGAAT
1 AAATAACATAAAAAT
34372000 AAATAACA-AATAAAT
1 AAATAACATAA-AAAT
*
34372015 AAATAA-A-AACAAT
1 AAATAACATAAAAAT
34372028 AAATAA-ATAAAAATT
1 AAATAACATAAAAA-T
34372043 AAAT-AC-T-AAAAT
1 AAATAACATAAAAAT
34372055 AAAT
1 AAAT
34372059 GAATAAATAC
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
12 5 0.10
13 14 0.27
14 11 0.21
15 22 0.42
ACGTcount: A:0.72, C:0.05, G:0.01, T:0.22
Consensus pattern (15 bp):
AAATAACATAAAAAT
Done.