Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_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: 2268343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:2129939 original size:255 final size:254
Alignment explanation
Indices: 2129462--2129939 Score: 610
Period size: 255 Copynumber: 1.9 Consensus size: 254
2129452 ATAAATTTTT
* **
2129462 TTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTTTTTTTGAAAAATCT
1 TTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTCTCTTGAGAAAGTTTTTTTAAGAAAAATCT
* * * *
2129527 TTGAGTTTGTTTCTTTGGAAACAACATTTACCATCTGTGAGCCTGTTTCCCTTGAAACAAAACTC
66 TTGAGTCTGTTTCTTTAGAAACAAAATTAACCATCTGTGAGCCTGTTTCCCTTGAAACAAAACTC
* * ** * *
2129592 ATCTTTGATTATTTTTCTTTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAAAAC
131 ATCTTTGATGATATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTAATCAAAAAC
* **
2129657 CAACATTTGAGATTGTTTCTTTTGAAACAAATTTGGTCTCACTTAAGACGTAACCTATC
196 CAACATTTGAGATAGTTTCCCTTGAAACAAATTTGGTCTCACTTAAGACGTAACCTATC
* *
2129716 TTTGAGTCTGTTTCTTTGGA-AACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAAGAAAAAT
1 TTTGAGTATGTTTCTTT-GATAACAAAATTTTGTCTCTCTTGAGAAAGTTT-TTTTAAGAAAAAT
* * **
2129780 CTTTGAGTCTGTTTCTTTAGAAACAAAATTAATCATCTTTGAGTTTGTTTCCCTTGAAACAAAAC
64 CTTTGAGTCTGTTTCTTTAGAAACAAAATTAACCATCTGTGAGCCTGTTTCCCTTGAAACAAAAC
*
2129845 AAAT-ATCTTTGA-GATCATTTCCCTTGAAAC-GAATTTTGTCTCCCTTGAGACAGTTTCT-ATC
129 ---TCATCTTTGATGAT-ATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTAATC
* *
2129906 AAAATCCTATC-TTTGAG-TCAGTTTCCCTTGAAAC
190 AAAAACC-AACATTTGAGAT-AGTTTCCCTTGAAAC
2129940 CATTATCCCT
Statistics
Matches: 191, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
254 45 0.24
255 96 0.50
256 30 0.16
257 19 0.10
258 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (254 bp):
TTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTCTCTTGAGAAAGTTTTTTTAAGAAAAATCT
TTGAGTCTGTTTCTTTAGAAACAAAATTAACCATCTGTGAGCCTGTTTCCCTTGAAACAAAACTC
ATCTTTGATGATATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTAATCAAAAAC
CAACATTTGAGATAGTTTCCCTTGAAACAAATTTGGTCTCACTTAAGACGTAACCTATC
Found at i:2130060 original size:43 final size:44
Alignment explanation
Indices: 2129997--2130199 Score: 168
Period size: 43 Copynumber: 4.7 Consensus size: 44
2129987 TCATCCCCTG
2129997 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC-CTTAGATA
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACACTTAGATA
* * * * *
2130040 ACCA-ATCGTCCTCATCACGTAGCAACCGTGTTATCACATTTAGATG
1 ACCAGATC-TCCTCATCACGTAGGAGCCGTGTCA--ACACTTAGATA
* * * * * * *
2130086 GCCAGAACTCTTCATCACGTATGAGCCGTCTCATCAC-TCG---
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACACTTAGATA
* * *
2130126 ACCTGATCTCCTCATCACGTGGGAGCCGTGTCAAC-CTTTGATA
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACACTTAGATA
* * *
2130169 ACCAGAACTCTTCATCACGTATGAGCCGTGT
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGT
2130200 TATCACCTTC
Statistics
Matches: 121, Mismatches: 30, Indels: 18
0.72 0.18 0.11
Matches are distributed among these distances:
39 1 0.01
40 29 0.24
42 3 0.02
43 54 0.45
44 2 0.02
45 2 0.02
46 28 0.23
47 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (44 bp):
ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACACTTAGATA
Found at i:2130184 original size:129 final size:131
Alignment explanation
Indices: 2129987--2130325 Score: 411
Period size: 129 Copynumber: 2.6 Consensus size: 131
2129977 AGGAACTGTG
* *
2129987 TCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCA-ATCGTCC
1 TCATCCCC-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGAAC-TCT
2130051 TCATCACGTA-GCAACCGTGTTATCACATT-T-AGATGGCC-AGAACTCTTCATCACGTATGAGC
64 TCATCACGTATG-AACCGTGTTATCACATTCTAAGATGGCCAAGAACTCTTCATCACGTATGAGC
*
2130112 CGTC
128 AGTC
* * * *
2130116 TCATCACTCGACCTGATCTCCTCATCACGTGGGAGCCGTGTCAACCTTTGATAACCAGAACTCTT
1 TCATC-CCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGAACTCTT
* * * *
2130181 CATCACGTATGAGCCGTGTTATCACCTTCGTAAAGATGGCCAATAACTCTTCATCACGTATGAGT
65 CATCACGTATGAACCGTGTTATCACATTC-T-AAGATGGCCAAGAACTCTTCATCACGTATGAGC
*
2130246 AGTG
128 AGTC
* * ** * *
2130250 TCATCCCCGACCAAATCTCCTCATCACGTAGGAACCAAGTCACCCTTAGA-AGACCCGAACTCTT
1 TCATCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATA-ACCAGAACTCTT
2130314 CATCACGTATGA
65 CATCACGTATGA
2130326 GCAGTGTCGT
Statistics
Matches: 179, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
129 77 0.43
130 5 0.03
131 1 0.01
132 1 0.01
133 67 0.37
134 28 0.16
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (131 bp):
TCATCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGAACTCTTC
ATCACGTATGAACCGTGTTATCACATTCTAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGT
C
Found at i:2130357 original size:133 final size:133
Alignment explanation
Indices: 2130091--2130342 Score: 283
Period size: 133 Copynumber: 1.9 Consensus size: 133
2130081 AGATGGCCAG
* * ** * * **
2130091 AACTCTTCATCACGTATGAGCCGTCTCATCACTCGACCTGATCTCCTCATCACGTGGGAGCCGTG
1 AACTCTTCATCACGTATGAGCAGTCTCATCACCCGACCAAATCTCCTCATCACGTAGGAACCAAG
* * * ** * *
2130156 TCAACCTTTGATAACCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTCGTAAAGATGGC
66 TCAACCTTAGATAACCAGAACTCTTCATCACGTATGAGCAGTGTCATCACCAACG-AAACATAGC
2130221 CAAT
130 CAAT
* *
2130225 AACTCTTCATCACGTATGAGTAGTGTCATC-CCCGACCAAATCTCCTCATCACGTAGGAACCAAG
1 AACTCTTCATCACGTATGAGCAGTCTCATCACCCGACCAAATCTCCTCATCACGTAGGAACCAAG
* * * *
2130289 TCACCCTTAGA-AGACCCGAACTCTTCATCACGTATGAGCAGTGTCGTCCCCAAC
66 TCAACCTTAGATA-ACCAGAACTCTTCATCACGTATGAGCAGTGTCATCACCAAC
2130343 AACCACATAT
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
132 1 0.01
133 70 0.71
134 27 0.28
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (133 bp):
AACTCTTCATCACGTATGAGCAGTCTCATCACCCGACCAAATCTCCTCATCACGTAGGAACCAAG
TCAACCTTAGATAACCAGAACTCTTCATCACGTATGAGCAGTGTCATCACCAACGAAACATAGCC
AAT
Found at i:2130513 original size:3 final size:3
Alignment explanation
Indices: 2130498--2130573 Score: 98
Period size: 3 Copynumber: 25.0 Consensus size: 3
2130488 AATTTTAATT
* * * *
2130498 TTA TTA TTG TTA TTA TTA TTA TTA TTA ATG TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2130546 TTA TTT TTA TTAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA
2130574 ATTACATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 61 0.95
4 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2133929 original size:34 final size:34
Alignment explanation
Indices: 2133890--2133960 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
2133880 TATTTTTTTT
2133890 ATAAAAGAATAGGCATATATATAGTACCAACTTA
1 ATAAAAGAATAGGCATATATATAGTACCAACTTA
2133924 ATAAAAGAATAGGCATATATATAGTACCAACTTA
1 ATAAAAGAATAGGCATATATATAGTACCAACTTA
2133958 ATA
1 ATA
2133961 GTCAAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (34 bp):
ATAAAAGAATAGGCATATATATAGTACCAACTTA
Found at i:2138096 original size:21 final size:21
Alignment explanation
Indices: 2138072--2138111 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2138062 ATTTTATAAC
*
2138072 TTATATAAT-AATTAATATTTT
1 TTATAAAATAAATT-ATATTTT
2138093 TTATAAAATAAATTATATT
1 TTATAAAATAAATTATATT
2138112 AATTTCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATAAAATAAATTATATTTT
Found at i:2138972 original size:32 final size:31
Alignment explanation
Indices: 2138931--2139006 Score: 118
Period size: 32 Copynumber: 2.5 Consensus size: 31
2138921 TTTTAGTTGG
*
2138931 ACAGAAAGCAATCCGAATCGAAATCGACCCAA
1 ACAGAAAGCAACCCGAATCGAAATCGA-CCAA
2138963 ACAGAAAGCAACCCGAATCGAAATCGACCAA
1 ACAGAAAGCAACCCGAATCGAAATCGACCAA
*
2138994 ACCG-AAGCAACCC
1 ACAGAAAGCAACCC
2139007 ATATCAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 9 0.21
31 7 0.17
32 26 0.62
ACGTcount: A:0.46, C:0.32, G:0.16, T:0.07
Consensus pattern (31 bp):
ACAGAAAGCAACCCGAATCGAAATCGACCAA
Found at i:2140266 original size:17 final size:17
Alignment explanation
Indices: 2140244--2140287 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
2140234 TTAAGCGCTG
2140244 AATGATTCAATGACCTA
1 AATGATTCAATGACCTA
2140261 AATGATTCAATGACCTA
1 AATGATTCAATGACCTA
2140278 AATGATTCAA
1 AATGATTCAA
2140288 AAGCTCTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (17 bp):
AATGATTCAATGACCTA
Found at i:2141629 original size:21 final size:22
Alignment explanation
Indices: 2141603--2141643 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2141593 TTATTTTATG
*
2141603 TTTTAATATATCT-TTTAATTT
1 TTTTAAAATATCTATTTAATTT
*
2141624 TTTTAAAATATTTATTTAAT
1 TTTTAAAATATCTATTTAAT
2141644 CCACATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTAAAATATCTATTTAATTT
Found at i:2175678 original size:34 final size:34
Alignment explanation
Indices: 2175639--2175711 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
2175629 TTAAGTTGAA
2175639 TTTAATGTTAAATTTCAAATACCATAATTTGTAT
1 TTTAATGTTAAATTTCAAATACCATAATTTGTAT
* * *
2175673 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCAAATACCATAATTTGTAT
*
2175707 ATTAA
1 TTTAA
2175712 AAACATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.49
Consensus pattern (34 bp):
TTTAATGTTAAATTTCAAATACCATAATTTGTAT
Found at i:2177906 original size:17 final size:16
Alignment explanation
Indices: 2177884--2177956 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 16
2177874 TGCATTATAA
2177884 AAATTTATAATTAATAT
1 AAATTTA-AATTAATAT
* * *
2177901 AAATTTATTATAAATTT
1 AAATTTA-AATTAATAT
*
2177918 AAATTTAAAATAATAAT
1 AAATTTAAATTAAT-AT
2177935 AAATATTAACATTAATTAT
1 AAAT-TTAA-ATTAA-TAT
2177954 AAA
1 AAA
2177957 AAAATATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 4 0.09
17 26 0.59
18 4 0.09
19 9 0.20
20 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTTAAATTAATAT
Found at i:2178054 original size:19 final size:17
Alignment explanation
Indices: 2178030--2178070 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
2178020 CACTTTCCAT
2178030 TATAATTGTAGACAAAAAA
1 TATAATT-TAG-CAAAAAA
2178049 TATAA-TTAGCAAAAAA
1 TATAATTTAGCAAAAAA
2178065 -ATAATT
1 TATAATT
2178071 AATAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 3 0.14
18 1 0.05
19 5 0.24
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (17 bp):
TATAATTTAGCAAAAAA
Found at i:2178068 original size:15 final size:16
Alignment explanation
Indices: 2178042--2178071 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2178032 TAATTGTAGA
2178042 CAAAAAATATAATTAG
1 CAAAAAATATAATTAG
2178058 CAAAAAA-ATAATTA
1 CAAAAAATATAATTA
2178072 ATAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (16 bp):
CAAAAAATATAATTAG
Found at i:2178099 original size:15 final size:15
Alignment explanation
Indices: 2178079--2178126 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2178069 TTAATAAATT
2178079 TAAATAATAATTATA
1 TAAATAATAATTATA
* *
2178094 TAAAT-ATTATTTTAA
1 TAAATAATAATTAT-A
*
2178109 TAAATAATATTTATA
1 TAAATAATAATTATA
2178124 TAA
1 TAA
2178127 TTATTTTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 6 0.23
15 15 0.58
16 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAATAATAATTATA
Found at i:2178107 original size:27 final size:28
Alignment explanation
Indices: 2178077--2178134 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
2178067 AATTAATAAA
2178077 TTTAAAT-AATAATTATATAAAT-ATTAT
1 TTTAAATAAATAA-TATATAAATAATTAT
* *
2178104 TTT-AATAAATAATATTTATATAATTAT
1 TTTAAATAAATAATATATAAATAATTAT
2178131 TTTA
1 TTTA
2178135 CTATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTAAATAAATAATATATAAATAATTAT
Found at i:2178617 original size:131 final size:131
Alignment explanation
Indices: 2178376--2178635 Score: 421
Period size: 131 Copynumber: 2.0 Consensus size: 131
2178366 ACCCACGTGT
* *
2178376 CATCCGACTCAGCAGAACCCCGTGAAAGCGCATCCCCGGAGATGCACCTTACACGCGTGGCATCC
1 CATCCGACTCAGCAGAACCCCGTGAAAACGCATCCCCGGAGATGCACCTTACACGCGTGACATCC
* * * *
2178441 CAGTCAACAAAAACCCAGATAAAGTGCATTCCTAGGATGCGCCTTTGTGCCACCTCAGTCGAATG
66 CAGTCAACAAAAACCCAGATAAAGTGCATTCCTAAGATACACCTTTATGCCACCTCAGTCGAATG
2178506 G
131 G
* * *
2178507 CATCCGACTCAGCATAACCTCGTGAAAACGCATCCCCGGATATGCACCTTACACGCGTGACATCC
1 CATCCGACTCAGCAGAACCCCGTGAAAACGCATCCCCGGAGATGCACCTTACACGCGTGACATCC
* *
2178572 CAGTCAACAAAAACTCAGATAAAGTGTATTCCTAAGATACACCTTTATGCCACCTCAGTCGAAT
66 CAGTCAACAAAAACCCAGATAAAGTGCATTCCTAAGATACACCTTTATGCCACCTCAGTCGAAT
2178636 AAATATTACT
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 118 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (131 bp):
CATCCGACTCAGCAGAACCCCGTGAAAACGCATCCCCGGAGATGCACCTTACACGCGTGACATCC
CAGTCAACAAAAACCCAGATAAAGTGCATTCCTAAGATACACCTTTATGCCACCTCAGTCGAATG
G
Found at i:2182432 original size:26 final size:27
Alignment explanation
Indices: 2182401--2182457 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
2182391 CTTGAGAAAT
*
2182401 TTATTAATTTAGAGAGTTGTTAA-TAA
1 TTATTAATTTAAAGAGTTGTTAAGTAA
*
2182427 TTATTAATTTAAAGAGTTTTTAAGTAA
1 TTATTAATTTAAAGAGTTGTTAAGTAA
2182454 TTAT
1 TTAT
2182458 ATTGTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (27 bp):
TTATTAATTTAAAGAGTTGTTAAGTAA
Found at i:2183049 original size:24 final size:24
Alignment explanation
Indices: 2183022--2183071 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2183012 CGAGTAGAGA
2183022 TGGAATTGCATAAAGTTGAGACGG
1 TGGAATTGCATAAAGTTGAGACGG
2183046 TGGAATTGCATAAAGTTGAGACGG
1 TGGAATTGCATAAAGTTGAGACGG
2183070 TG
1 TG
2183072 ATTGAGTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.34, T:0.26
Consensus pattern (24 bp):
TGGAATTGCATAAAGTTGAGACGG
Found at i:2186347 original size:19 final size:19
Alignment explanation
Indices: 2186323--2186364 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2186313 TCTAGAGATA
2186323 CACAGCTTTATAATCAAAG
1 CACAGCTTTATAATCAAAG
2186342 CACAGCTTTATAATCAAAG
1 CACAGCTTTATAATCAAAG
2186361 CACA
1 CACA
2186365 ATGTCTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (19 bp):
CACAGCTTTATAATCAAAG
Found at i:2196621 original size:18 final size:18
Alignment explanation
Indices: 2196598--2196632 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2196588 TTAAGTTTAC
2196598 AATATTAAAAGGTATAAA
1 AATATTAAAAGGTATAAA
* *
2196616 AATATTACAAGTTATAA
1 AATATTAAAAGGTATAA
2196633 CTTATATAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (18 bp):
AATATTAAAAGGTATAAA
Found at i:2197401 original size:11 final size:11
Alignment explanation
Indices: 2197385--2197410 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2197375 TATCTAAAAT
2197385 AAATTTATCTA
1 AAATTTATCTA
2197396 AAATTTATCTA
1 AAATTTATCTA
2197407 AAAT
1 AAAT
2197411 AATAAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTTATCTA
Found at i:2197418 original size:19 final size:19
Alignment explanation
Indices: 2197394--2197459 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
2197384 TAAATTTATC
2197394 TAAAATTTATCTAAAATAA
1 TAAAATTTATCTAAAATAA
*
2197413 TAAAATTCTAT-AAAAATAAA
1 TAAAATT-TATCTAAAAT-AA
*
2197433 CTTCAAATTTATCTAAAA-AA
1 --TAAAATTTATCTAAAATAA
2197453 TCAAAAT
1 T-AAAAT
2197460 CCATAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 1 0.03
19 16 0.43
20 7 0.19
21 3 0.08
22 10 0.27
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTTATCTAAAATAA
Found at i:2202651 original size:96 final size:96
Alignment explanation
Indices: 2202487--2202681 Score: 261
Period size: 96 Copynumber: 2.0 Consensus size: 96
2202477 CGAAATTTAC
* * *
2202487 CTCCAAATACAAAGATGGAACCAAGACATCTGTCTTCAACATAGATTCCAGAAATTTAAAACACA
1 CTCCAAATACAAAGAAGGAACCAAGACATCTGTCTTCAACATAGAGTCCAGAAATTAAAAACACA
2202552 AACCCCAAACATTCAACTGGATTCCAGGACG
66 AACCCCAAACATTCAACTGGATTCCAGGACG
* * **
2202583 CTCCAAATACAAAGAAGGATCCATGACATC-GATCTTCAACATAGAAGT-C-GGCATTAAAAAAC
1 CTCCAAATACAAAGAAGGAACCAAGACATCTG-TCTTCAACATAG-AGTCCAGAAATT-AAAAAC
* *
2202645 ACAAACCCCAAACATTCAGCTGGATTCCATGACG
63 ACAAACCCCAAACATTCAACTGGATTCCAGGACG
2202679 CTC
1 CTC
2202682 TACCAACAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 5 0.06
96 80 0.92
97 2 0.02
ACGTcount: A:0.41, C:0.27, G:0.13, T:0.19
Consensus pattern (96 bp):
CTCCAAATACAAAGAAGGAACCAAGACATCTGTCTTCAACATAGAGTCCAGAAATTAAAAACACA
AACCCCAAACATTCAACTGGATTCCAGGACG
Found at i:2209600 original size:38 final size:37
Alignment explanation
Indices: 2209494--2209601 Score: 93
Period size: 38 Copynumber: 2.9 Consensus size: 37
2209484 CAAGAACAAT
* *
2209494 ATGTTCAAAGTTTGGCCACCTACCAAA-GAATTTTCCA
1 ATGTTCAAAGTTTGGCCACC-ACCAAATGAAATTTACA
*
2209531 ATGTGT-ACAAG-TTAGCCACCA--AATATGAAATTTAC-
1 ATGT-TCA-AAGTTTGGCCACCACCAA-ATGAAATTTACA
2209566 ATGTTCAAAGTTTGGCCACCAACCAAGATGAAATTT
1 ATGTTCAAAGTTTGGCCACC-ACCAA-ATGAAATTT
2209602 TCAACTTGTC
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
34 6 0.11
35 14 0.25
36 9 0.16
37 13 0.23
38 15 0.26
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (37 bp):
ATGTTCAAAGTTTGGCCACCACCAAATGAAATTTACA
Found at i:2210896 original size:31 final size:31
Alignment explanation
Indices: 2210843--2210903 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2210833 TACAAATGTT
*
2210843 AAAAATAAATTAAAATTTTGAAAA-AATATA
1 AAAAATAAATTAAAATTATGAAAAGAATATA
2210873 AAAAAGTATAATT-AAATTATGAAAAGAATAT
1 AAAAA-TA-AATTAAAATTATGAAAAGAATAT
2210904 TGATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 5 0.19
31 13 0.48
32 9 0.33
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (31 bp):
AAAAATAAATTAAAATTATGAAAAGAATATA
Found at i:2211926 original size:34 final size:34
Alignment explanation
Indices: 2211880--2211948 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2211870 AAAAAAACTG
* * *
2211880 TAAATTAAATATATTCATATCCGACATTCGTATT
1 TAAATTAAATATACTCAAATCCGACACTCGTATT
* *
2211914 TAAATTATATATACTCAAATTCGACACTCGTATT
1 TAAATTAAATATACTCAAATCCGACACTCGTATT
2211948 T
1 T
2211949 GAGTTCAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (34 bp):
TAAATTAAATATACTCAAATCCGACACTCGTATT
Found at i:2216791 original size:224 final size:228
Alignment explanation
Indices: 2216518--2216939 Score: 699
Period size: 226 Copynumber: 1.9 Consensus size: 228
2216508 AGTGAAAAAT
* * *
2216518 ACCCGACCTGAAAATATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTC
1 ACCCGACCTCAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTA
* * *
2216583 TATATATA-AT-TTTTTTCAATTAAGTCGCTATTTTTATTAAATAAAAATATTTTTTTTATTATT
66 TATATATATATATTTTTCCAATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTTATTATT
*
2216646 TCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTC-GGTGAAACTTTATTTTGGTCGGGTCG
131 TCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTAGTCGGGTCG
2216710 GGTTCGGGTTTAGGGTGAAAAATACTCGACCTG
196 GGTTCGGGTTTAGGGTGAAAAATACTCGACCTG
*
2216743 ACCCGACC-CAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTA
1 ACCCGACCTCAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTA
* *
2216807 TATATATATATATTTTTCCAATTAAGTCACTTTTTTTATTGAATAAAAATAATTTTTTTATTATT
66 TATATATATATATTTTTCCAATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTTATTATT
* * *
2216872 TCGGGTCGGGTTTTTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTAGTCGGGTCG
131 TCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTAGTCGGGTCG
2216937 GGT
196 GGT
2216940 CTAGGATGAA
Statistics
Matches: 181, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
224 60 0.33
225 10 0.06
226 83 0.46
227 28 0.15
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (228 bp):
ACCCGACCTCAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTA
TATATATATATATTTTTCCAATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTTATTATT
TCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTAGTCGGGTCG
GGTTCGGGTTTAGGGTGAAAAATACTCGACCTG
Found at i:2217330 original size:18 final size:17
Alignment explanation
Indices: 2217292--2217343 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
2217282 ATATGAAATT
* *
2217292 AGATTTCAATTCCTGAC
1 AGATTCCAATTCCTCAC
2217309 AGATTCCAATTCCTTCAC
1 AGATTCCAATTCC-TCAC
2217327 AGATTCCAATTTCCTCA
1 AGATTCCAA-TTCCTCA
2217344 GAAACATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 12 0.39
18 15 0.48
19 4 0.13
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (17 bp):
AGATTCCAATTCCTCAC
Found at i:2223798 original size:37 final size:36
Alignment explanation
Indices: 2223724--2223798 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 36
2223714 CAAAAAACTA
* * *
2223724 AATAAAATCGAGCTAAATAAAATAGCATATGAAAAT
1 AATAAAATCAAGCTAAATAAAATAGCAAATAAAAAT
*
2223760 AATAGAAATCAAGCTAAATAAAA-AGTAAATAAACAAT
1 AATA-AAATCAAGCTAAATAAAATAGCAAATAAA-AAT
2223797 AA
1 AA
2223799 ATTTTGAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 11 0.33
37 22 0.67
ACGTcount: A:0.63, C:0.08, G:0.09, T:0.20
Consensus pattern (36 bp):
AATAAAATCAAGCTAAATAAAATAGCAAATAAAAAT
Found at i:2228240 original size:17 final size:17
Alignment explanation
Indices: 2228199--2228233 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2228189 TTTGAGTAGT
2228199 CACTTAAGAATTTTTAC
1 CACTTAAGAATTTTTAC
2228216 CACTTAAGAATTTTTAC
1 CACTTAAGAATTTTTAC
2228233 C
1 C
2228234 CTGTAAGTTG
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:0.20, G:0.06, T:0.40
Consensus pattern (17 bp):
CACTTAAGAATTTTTAC
Found at i:2228497 original size:16 final size:16
Alignment explanation
Indices: 2228467--2228515 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
2228457 TTTTCATATG
*
2228467 TAAA-ATAATTAAATA
1 TAAATATAAATAAATA
*
2228482 TAAATATTAATAAATA
1 TAAATATAAATAAATA
*
2228498 -AATTATAAATAAA-A
1 TAAATATAAATAAATA
2228512 TAAA
1 TAAA
2228516 CTAAAAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 1 0.04
15 17 0.63
16 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATATAAATAAATA
Found at i:2228520 original size:21 final size:19
Alignment explanation
Indices: 2228467--2228520 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2228457 TTTTCATATG
*
2228467 TAAAATAATTAAATATAAA
1 TAAAATAAATAAATATAAA
*
2228486 TATTAATAAATAAATTATAAA
1 TA-AAATAAATAAA-TATAAA
2228507 TAAAATAAACTAAA
1 TAAAATAAA-TAAA
2228521 AATTATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.52
21 12 0.41
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATAAATAAATATAAA
Found at i:2229774 original size:6 final size:6
Alignment explanation
Indices: 2229763--2229787 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2229753 TCCAACCAAC
2229763 CCCCTT CCCCTT CCCCTT CCCCTT C
1 CCCCTT CCCCTT CCCCTT CCCCTT C
2229788 AAAAAGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCCTT
Found at i:2230452 original size:16 final size:16
Alignment explanation
Indices: 2230427--2230469 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
2230417 AACGTCTTTT
2230427 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
2230443 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
2230460 ACAAAAATTT
1 AAAAAAATTT
2230470 GCGTTTACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:2232548 original size:25 final size:25
Alignment explanation
Indices: 2232520--2232687 Score: 300
Period size: 25 Copynumber: 6.7 Consensus size: 25
2232510 GGGATTAGTG
*
2232520 TTGAAACCCTAAATTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
* *
2232545 TTGAAACCCTAAATTAATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
2232570 TTGAAACCCTAAACTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
2232595 TTGAAACCCTAAACTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
2232620 TTGAAACCCTAAACTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
2232645 TTGAAACCCTAAACTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
*
2232670 TTGAAACCCTAATCTGAT
1 TTGAAACCCTAAACTGAT
2232688 GGGTTGTTGG
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 139 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (25 bp):
TTGAAACCCTAAACTGATTTAGGGT
Found at i:2232825 original size:3 final size:3
Alignment explanation
Indices: 2232817--2232872 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
2232807 GCAAAAATTG
*
2232817 TAA TAA TAAA TAA TAA TAA -AA TAA T-A TAA TGA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2232861 TAA TAA TAA TAA
1 TAA TAA TAA TAA
2232873 AACGGAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2233235 original size:87 final size:87
Alignment explanation
Indices: 2233076--2233417 Score: 567
Period size: 87 Copynumber: 3.9 Consensus size: 87
2233066 CGTCTAAGGG
* * * * * * * * *
2233076 TGACATGGCTCCTACGTGATGAGGAAATCTGGTCATTTTTAGGGATGATAACTCGGTTCCTACGT
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCA-TCTAAAGG-TGATAACACGGTTCCTACGT
* *
2233141 AATGAGGACGACTGGTTATCAGGT
64 GATGAGGACGGCTGGTTATCAGGT
2233165 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
2233230 TGAGGACGGCTGGTTATCAGGT
66 TGAGGACGGCTGGTTATCAGGT
2233252 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
2233317 TGAGGACGGCTGGTTATCAGGT
66 TGAGGACGGCTGGTTATCAGGT
2233339 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
2233404 TGAGGACGGCTGGT
66 TGAGGACGGCTGGT
2233418 CAGTTGATGT
Statistics
Matches: 242, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
87 207 0.86
88 5 0.02
89 30 0.12
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (87 bp):
TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
TGAGGACGGCTGGTTATCAGGT
Found at i:2233270 original size:41 final size:41
Alignment explanation
Indices: 2233136--2233360 Score: 184
Period size: 41 Copynumber: 5.2 Consensus size: 41
2233126 ACTCGGTTCC
* *
2233136 TACGTAATGAGGACGACTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
* * ** * * *
2233177 TACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATC---AGGT--TGACACGGCTCT
2233223 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
* * ** * * *
2233264 TACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATC---AGGT--TGACACGGCTCT
2233310 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
2233351 TACGTGATGA
1 TACGTGATGA
2233361 AGAGATCTGG
Statistics
Matches: 141, Mismatches: 29, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
40 2 0.01
41 65 0.46
43 8 0.06
44 8 0.06
46 56 0.40
47 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (41 bp):
TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
Found at i:2234393 original size:1 final size:1
Alignment explanation
Indices: 2234389--2234416 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2234379 TTTCATTTCC
2234389 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2234417 AGGTGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2245368 original size:16 final size:16
Alignment explanation
Indices: 2245343--2245385 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
2245333 AACGTCTTTT
2245343 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
2245359 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
2245376 ACAAAAATTT
1 AAAAAAATTT
2245386 GCGTTTACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:2247468 original size:25 final size:25
Alignment explanation
Indices: 2247440--2247582 Score: 259
Period size: 25 Copynumber: 5.7 Consensus size: 25
2247430 GGGATTAGTG
*
2247440 TTGAAACCCTAAATTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
*
2247465 TTGAAACCCTAAATTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
2247490 TTGAAACCCTAAACTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
2247515 TTGAAACCCTAAACTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
2247540 TTGAAACCCTAAACTGATTTAGGGT
1 TTGAAACCCTAAACTGATTTAGGGT
*
2247565 TTGAAACCCTAATCTGAT
1 TTGAAACCCTAAACTGAT
2247583 GGGTTGTTGG
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 116 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (25 bp):
TTGAAACCCTAAACTGATTTAGGGT
Found at i:2247720 original size:3 final size:3
Alignment explanation
Indices: 2247712--2247772 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
2247702 GCAAAAATTG
*
2247712 TAA TAA TAAA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2247756 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
2247773 CGGAAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 43 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2249331 original size:14 final size:15
Alignment explanation
Indices: 2249302--2249334 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2249292 GACAAAACAC
2249302 TATAATAAACACTAA
1 TATAATAAACACTAA
*
2249317 TATAA-AAATACTAA
1 TATAATAAACACTAA
2249331 TATA
1 TATA
2249335 CTCTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAATAAACACTAA
Found at i:2253311 original size:13 final size:15
Alignment explanation
Indices: 2253275--2253313 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2253265 TATAAAGCTT
*
2253275 CATTTAAAATTGTCG
1 CATTTAAACTTGTCG
2253290 CATTTAAACTTGTC-
1 CATTTAAACTTGTCG
2253304 CA-TTAAACTT
1 CATTTAAACTT
2253314 TAGGTACCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
14 2 0.09
15 13 0.57
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (15 bp):
CATTTAAACTTGTCG
Found at i:2261615 original size:23 final size:23
Alignment explanation
Indices: 2261589--2261636 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2261579 ATAAAGTACA
*
2261589 ATAACATACTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
2261612 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
2261635 AT
1 AT
2261637 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:2261894 original size:29 final size:29
Alignment explanation
Indices: 2261840--2261905 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
2261830 TCATTTGCAC
* *
2261840 AAAAAATTATTTGATTTTTGATATTTTAT
1 AAAATATTATTTGATTTTTGATATTTAAT
2261869 AAAATATTATTTAGAATTTTT-A-ATTTAAT
1 AAAATATTATTT-G-ATTTTTGATATTTAAT
2261898 AATAATAT
1 AA-AATAT
2261906 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 19 0.59
30 7 0.22
31 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTGATTTTTGATATTTAAT
Found at i:2262087 original size:23 final size:23
Alignment explanation
Indices: 2262061--2262123 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2262051 ATATAACCAC
2262061 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2262084 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2262107 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2262124 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2262583 original size:34 final size:34
Alignment explanation
Indices: 2262543--2262608 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
2262533 AAGTTGTAGA
*
2262543 TTTTGATTTCCTTTTGCTTGGCATCATATGAGAT
1 TTTTGATTTCCTTTTGCTTGGCACCATATGAGAT
2262577 TTTTGATTTCCTTTTGCTTGGCACCATATGAG
1 TTTTGATTTCCTTTTGCTTGGCACCATATGAG
2262609 CTTTGGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (34 bp):
TTTTGATTTCCTTTTGCTTGGCACCATATGAGAT
Found at i:2262904 original size:18 final size:18
Alignment explanation
Indices: 2262881--2262917 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2262871 CGAAATATAT
2262881 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2262899 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2262917 A
1 A
2262918 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2263380 original size:23 final size:23
Alignment explanation
Indices: 2263354--2263412 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
2263344 AACCACTACC
2263354 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
2263377 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
2263400 TATTACATCATAT
1 TATTACATTATAT
2263413 GTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:2263453 original size:21 final size:22
Alignment explanation
Indices: 2263428--2263476 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2263418 CCTATTATAT
2263428 TAAAAGTG-TCCATACTTTTTA
1 TAAAAGTGATCCATACTTTTTA
* *
2263449 TAAAAG-GATCGATACTTTTTT
1 TAAAAGTGATCCATACTTTTTA
2263470 TAAAAGT
1 TAAAAGT
2263477 TATGTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
TAAAAGTGATCCATACTTTTTA
Found at i:2266901 original size:181 final size:182
Alignment explanation
Indices: 2266273--2266936 Score: 1083
Period size: 181 Copynumber: 3.7 Consensus size: 182
2266263 TTAAAATTAC
* *
2266273 CGACACTTTTT-AAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTAAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
* * *
2266337 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAAACCGGTATATTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT-AAAACCGGTATATTATACCGATT
* * *
2266402 ATATTAAAAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
130 ATATT-ACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* * * *
2266456 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTAAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
*
2266521 ATTAAAAAGTGTCGATATAGGTTGTAGACCTA-TCGCGCATAAAACCGGTATATTTATACCGTTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATA-TTATACCGATT
2266585 ATATTACAAAATTATCTATTACATT-TAATTAT-GGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
2266636 CGACACTTTTTAACAAT-GTATCGACACA-TTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
2266699 GATTAAAAAGTGTCGGATATAGGTTGTAGACCTATTCGCGCATAAAACC-GTATATTATACCGAT
65 GATTAAAAAGTGTC-GATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTATACCGAT
2266763 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
129 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
2266817 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTCCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
2266881 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAAAAAACCGGTATATT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATT
2266937 TATAATAGTT
Statistics
Matches: 456, Mismatches: 16, Indels: 19
0.93 0.03 0.04
Matches are distributed among these distances:
179 82 0.18
180 72 0.16
181 102 0.22
182 86 0.19
183 32 0.07
184 82 0.18
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (182 bp):
CGACACTTTTTAAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTATACCGATTA
TATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Done.