Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 19
Found at i:365368 original size:18 final size:18
Alignment explanation
Indices: 365345--365385 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
365335 AGCAAAAGGA
*
365345 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
365363 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
365381 AATCA
1 AATCA
365386 GAACCGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:365732 original size:54 final size:54
Alignment explanation
Indices: 365589--365733 Score: 184
Period size: 54 Copynumber: 2.7 Consensus size: 54
365579 TTTCTTTGAA
* *
365589 TTCGCAACGCGAATTTGACTTACGCGTTG-TGAATTTGACTATCGCGATGCTTAT
1 TTCGCAACGCGAATTTGACTTTCGCGTTGCT-AATTTGACTATCGCGACGCTTAT
*** * * * * *
365643 TTCGCGTTGCAAATTTGACATTCGCATTTCGAATTTGACTATCGCGACGCTTAT
1 TTCGCAACGCGAATTTGACTTTCGCGTTGCTAATTTGACTATCGCGACGCTTAT
365697 TTCGCAACGCGAATTTGACTTTCGCGTTGCTAATTTG
1 TTCGCAACGCGAATTTGACTTTCGCGTTGCTAATTTG
365734 TACATTCAAC
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (54 bp):
TTCGCAACGCGAATTTGACTTTCGCGTTGCTAATTTGACTATCGCGACGCTTAT
Found at i:365868 original size:66 final size:65
Alignment explanation
Indices: 365788--365962 Score: 228
Period size: 66 Copynumber: 2.6 Consensus size: 65
365778 ATTTTAAAAC
365788 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCATATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCATATTTACACATC-AATT
365853 A
65 A
* * * *
365854 AACAAATCAACTTTTACAAATCAATTAAAAAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCATATTTACACATCAATTA
*
365918 AACAAAACAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAA
365963 GTGTACCCCA
Statistics
Matches: 96, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
64 15 0.16
65 24 0.25
66 33 0.34
68 4 0.04
69 15 0.16
70 5 0.05
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCATATTTACACATCAATTA
Found at i:367337 original size:21 final size:20
Alignment explanation
Indices: 367313--367406 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 20
367303 GAGGGACCCA
367313 TTGAACGATGGCAGGGGCCTC
1 TTGAACGATGG-AGGGGCCTC
* *
367334 TTGAATGGTGGGAGGGGCCTC
1 TTGAACGAT-GGAGGGGCCTC
* *
367355 TTGAACGATTAGAGGAGCCTC
1 TTGAACGA-TGGAGGGGCCTC
* *
367376 TTGAATGATAGGAGGTGCCTC
1 TTGAACGAT-GGAGGGGCCTC
367397 TTGAACGATG
1 TTGAACGATG
367407 ACAGGTGAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.03
21 55 0.92
22 3 0.05
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.24
Consensus pattern (20 bp):
TTGAACGATGGAGGGGCCTC
Found at i:367348 original size:42 final size:42
Alignment explanation
Indices: 367289--367405 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
367279 GTGAATCGGG
* *
367289 CTCTTGAATGGTGGGAGGGACC-CATTGAACGA-TGGCAGGGGC
1 CTCTTGAATGGTGGGAGGGACCTC-TTGAACGATTAG-AGGAGC
*
367331 CTCTTGAATGGTGGGAGGGGCCTCTTGAACGATTAGAGGAGC
1 CTCTTGAATGGTGGGAGGGACCTCTTGAACGATTAGAGGAGC
* *
367373 CTCTTGAATGATAGGAGGTG-CCTCTTGAACGAT
1 CTCTTGAATGGTGGGAGG-GACCTCTTGAACGAT
367406 GACAGGTGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
42 63 0.94
43 4 0.06
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTGAACGATTAGAGGAGC
Found at i:367708 original size:21 final size:21
Alignment explanation
Indices: 367684--367772 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 21
367674 TGAAACAATC
* * *
367684 TCACGTAGAGCGGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
* *
367705 TCACATAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
* ***
367726 TCACGTAAAACATCCACCTCA
1 TCACGTAAAGCAGATACCTCA
* *
367747 CCACGTAAAGACCG-TACCTCA
1 TCACGTAAAG-CAGATACCTCA
367768 TCACG
1 TCACG
367773 CCATGCACCA
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
21 49 0.98
22 1 0.02
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.19
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:370093 original size:20 final size:20
Alignment explanation
Indices: 370068--370270 Score: 127
Period size: 20 Copynumber: 10.1 Consensus size: 20
370058 CGGGCTTTGT
*
370068 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGTGTTGC
* *
370088 GAATTTGAATTTTGTGTTGC
1 GAATTTGACTTTCGTGTTGC
** *
370108 GAATTTGAAATTCAGTGTTGT
1 GAATTTGACTTTC-GTGTTGC
* ***
370129 GAATTTGACTATCACATTGC
1 GAATTTGACTTTCGTGTTGC
370149 GAATTTGAC-TTCTGTGTTGC
1 GAATTTGACTTTC-GTGTTGC
* *
370169 G-ATTT-ACAAATTCGCGTTGC
1 GAATTTGAC--TTTCGTGTTGC
*
370189 G-ATTT-ACAGATTT-GCGTTGC
1 GAATTTGAC---TTTCGTGTTGC
*
370209 GAATTTGAC-TTCAGTGTTGT
1 GAATTTGACTTTC-GTGTTGC
370229 GAATTTGACTTAT-GTGTTGC
1 GAATTTGACTT-TCGTGTTGC
370249 GAATTTGAC-TTCTGTGTTGC
1 GAATTTGACTTTC-GTGTTGC
370269 GA
1 GA
370271 TTTACAAATT
Statistics
Matches: 146, Mismatches: 23, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
18 5 0.03
19 7 0.05
20 104 0.71
21 27 0.18
22 3 0.02
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (20 bp):
GAATTTGACTTTCGTGTTGC
Found at i:370114 original size:40 final size:40
Alignment explanation
Indices: 370068--370295 Score: 127
Period size: 40 Copynumber: 5.7 Consensus size: 40
370058 CGGGCTTTGT
* *
370068 GAATTTGACTTTCGCGTTGCGAATTTGAATTTTGTGTTGC
1 GAATTTGACTTTCGCGTTGCGAATTTGACTTTCGTGTTGC
** * * * ***
370108 GAATTTGAAATTCAGTGTTGTGAATTTGACTATCACATTGC
1 GAATTTGACTTTC-GCGTTGCGAATTTGACTTTCGTGTTGC
* * *
370149 GAATTTGAC-TTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGC
1 GAATTTGACTTTC-GCGTTGCGAATTTGAC--TTTCGTGTTGC
*
370189 G-ATTT-ACAGATTT-GCGTTGCGAATTTGAC-TTCAGTGTTGT
1 GAATTTGAC---TTTCGCGTTGCGAATTTGACTTTC-GTGTTGC
*
370229 GAATTTGACTTAT-GTGTTGCGAATTTGAC-TTCTGTGTTGC
1 GAATTTGACTT-TCGCGTTGCGAATTTGACTTTC-GTGTTGC
*
370269 G-ATTT-ACAAATTCGCGTTGCGAATTTG
1 GAATTTGAC--TTTCGCGTTGCGAATTTG
370296 GAAACTGGGT
Statistics
Matches: 147, Mismatches: 25, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
38 6 0.04
39 18 0.12
40 82 0.56
41 35 0.24
42 6 0.04
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (40 bp):
GAATTTGACTTTCGCGTTGCGAATTTGACTTTCGTGTTGC
Found at i:370132 original size:61 final size:61
Alignment explanation
Indices: 370068--370259 Score: 191
Period size: 61 Copynumber: 3.2 Consensus size: 61
370058 CGGGCTTTGT
* * *
370068 GAATTTGACTTTCGCGTTGCGAATTTGAATTTTGTGTTGCGAATTTGAAATTCAGTGTTGT
1 GAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAAATTCAGTGTTGC
* * * * *
370129 GAATTTGACTATCACATTGCGAATTTGACTTCTGTGTTGCG-ATTTACAAATTC-GCGTTGC
1 GAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTT-GAAATTCAGTGTTGC
* * *
370189 G-ATTT-ACAGATTT-GCGTTGCGAATTTGACTTCAGTGTTGTGAATTTG-ACTT-ATGTGTTGC
1 GAATTTGAC---TTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAAATTCA-GTGTTGC
370249 GAATTTGACTT
1 GAATTTGACTT
370260 CTGTGTTGCG
Statistics
Matches: 106, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
58 2 0.02
59 9 0.08
60 41 0.39
61 52 0.49
62 2 0.02
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (61 bp):
GAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAAATTCAGTGTTGC
Found at i:370308 original size:100 final size:99
Alignment explanation
Indices: 370078--370335 Score: 324
Period size: 100 Copynumber: 2.6 Consensus size: 99
370068 GAATTTGACT
*
370078 TTCGCGTTGCGAATTTGAATTTTGTGTTGCGAATTTGAAATTCAGTGTTGTGAATTTGACTATCA
1 TTCGCGTTGCGAATTTGAA-TTTGCGTTGCGAATTTG-AATTCAGTGTTGTGAATTTGACTATCA
370143 CATTGCGAATTTGACTTCTGTGTTGCGATTTACAAA
64 CATTGCGAATTTGACTTCTGTGTTGCGATTTACAAA
* *
370179 TTCGCGTTGCG-ATTTACAGATTTGCGTTGCGAATTTGACTTCAGTGTTGTGAATTTGACTTAT-
1 TTCGCGTTGCGAATTT-GA-ATTTGCGTTGCGAATTTGAATTCAGTGTTGTGAATTTGAC-TATC
***
370242 GTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAA
63 ACATTGCGAATTTGACTTCTGTGTTGCGATTTACAAA
** * * * *
370279 TTCGCGTTGCGAATTTGGAAACTGGGTTGCGAAATTGGAGTTCA-TATTGTGAATTTG
1 TTCGCGTTGCGAATTT-GAATTTGCGTTGCG-AATTTGAATTCAGTGTTGTGAATTTG
370336 TTGGTCATTT
Statistics
Matches: 138, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
100 91 0.66
101 46 0.33
102 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.41
Consensus pattern (99 bp):
TTCGCGTTGCGAATTTGAATTTGCGTTGCGAATTTGAATTCAGTGTTGTGAATTTGACTATCACA
TTGCGAATTTGACTTCTGTGTTGCGATTTACAAA
Found at i:388066 original size:21 final size:21
Alignment explanation
Indices: 388042--388105 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
388032 CCAACGGTTA
388042 AGATGACATCGTAACCATTTC
1 AGATGACATCGTAACCATTTC
* *
388063 AGATGACACCGTAGCCATTTC
1 AGATGACATCGTAACCATTTC
* **
388084 AGATGGCATCACAACCATTTC
1 AGATGACATCGTAACCATTTC
388105 A
1 A
388106 AATGGCACCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (21 bp):
AGATGACATCGTAACCATTTC
Found at i:388110 original size:21 final size:21
Alignment explanation
Indices: 388054--388120 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
388044 ATGACATCGT
* * **
388054 AACCATTTCAGATGACACCGT
1 AACCATTTCAAATGGCACCAC
* * *
388075 AGCCATTTCAGATGGCATCAC
1 AACCATTTCAAATGGCACCAC
388096 AACCATTTCAAATGGCACCAC
1 AACCATTTCAAATGGCACCAC
388117 AACC
1 AACC
388121 GTTTTATATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.21
Consensus pattern (21 bp):
AACCATTTCAAATGGCACCAC
Found at i:395089 original size:16 final size:16
Alignment explanation
Indices: 395068--395098 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
395058 AATATTGAAA
395068 CTTGAACTCGAAAAAG
1 CTTGAACTCGAAAAAG
395084 CTTGAACTCGAAAAA
1 CTTGAACTCGAAAAA
395099 AATTTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (16 bp):
CTTGAACTCGAAAAAG
Found at i:400449 original size:2 final size:2
Alignment explanation
Indices: 400442--400487 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
400432 TTATCCTTTC
400442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400484 AT AT
1 AT AT
400488 TATTAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:401852 original size:3 final size:3
Alignment explanation
Indices: 401830--401878 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
401820 CGGGCCGATC
* * *
401830 ATA ATA ATT ATA ACA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
401878 A
1 A
401879 AATGGGGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:402228 original size:123 final size:123
Alignment explanation
Indices: 402004--402975 Score: 1442
Period size: 123 Copynumber: 8.0 Consensus size: 123
401994 AAGATGGAGT
* * *
402004 TGTTGATGTTGTTTTATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCAGAT
1 TGTTGATGTTGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGTTGAATAAGTTCTTCAGAT
* *
402069 TATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCTTATTACGAACTCTTTCTGGAAA
66 TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAA
* * * *
402127 CGTTGATGCTGCTCTATCGCCTTCTGCGATAGAATCGAGAAAAAAGTTGAATAAGTTCTTCAGAT
1 TGTTGATGTTGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGTTGAATAAGTTCTTCAGAT
* * * * **
402192 TATGAACTTCTTCTTCATCTTCAGATTAGTTATTCTTATTAAGAACTCCTTCCAGAAA
66 TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAA
* * *
402250 TATTGATGCTT-CTTTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAGA
1 TGTTGATG-TTGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGTTGAATAAGTTCTTCAGA
* * * *
402314 TTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTTATCACAAACTCCTTCTGGAAA
65 TTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAA
* *
402373 TGTTGATGTTGCTATATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAGAT
1 TGTTGATGTTGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGTTGAATAAGTTCTTCAGAT
* * *
402438 TATGAACTTCTTCTTCCTTTTTAGATGAGTTCTTCTTATTACGAACTCCTTCTAGAAA
66 TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAA
** * *
402496 CATTGATGCTGCTCTATCTCCTTCT-CTGATAGAATCGAGCAAAAAATTGAATAAGTTCTTCAGA
1 TGTTGATGTTGCTCTATCTCCTTCTGC-GATAGAATCGAGCAAAAAGTTGAATAAGTTCTTCAGA
* * * *
402560 TTATGAACTTTTTCTTCCTCTTCAGATTAGTTCTTCTTATCACGAACTCTTTCTGGAAA
65 TTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAA
* * *
402619 TGTAGATGTTGCTCTATCTCCTTTTGCGATAGAATCAAGCAAAAAGTT---TAA----TTCAGAT
1 TGTTGATGTTGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGTTGAATAAGTTCTTCAGAT
*
402677 TATGAACTTCTTCTTCCTCTTCAGATTAGTTCTTCTTATTACGAACTCCTTCTGGAAA
66 TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAA
* *
402735 TGTTGATGTTGCTTTATCTCCTTCTGCGATAGAATCGAG-TAAAAGATTGAATAAGTTCTTCAGA
1 TGTTGATGTTGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAG-TTGAATAAGTTCTTCAGA
*
402799 TTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTTTGGAAA
65 TTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAA
* * *
402858 TGTTGATGTTTCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTCAATAAGTTCTTCAGAT
1 TGTTGATGTTGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGTTGAATAAGTTCTTCAGAT
402923 TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
66 TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
402976 TTCCTGAAAT
Statistics
Matches: 760, Mismatches: 76, Indels: 26
0.88 0.09 0.03
Matches are distributed among these distances:
115 5 0.01
116 99 0.13
119 3 0.00
120 3 0.00
122 3 0.00
123 641 0.84
124 6 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (123 bp):
TGTTGATGTTGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGTTGAATAAGTTCTTCAGAT
TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAA
Found at i:402934 original size:485 final size:487
Alignment explanation
Indices: 402018--402975 Score: 1546
Period size: 485 Copynumber: 2.0 Consensus size: 487
402008 GATGTTGTTT
* *
402018 TATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
1 TATCTCCTTCTGCGATAGAATCGAGCAAAAAATTGAATAAGTTCTTCAGATTATGAACTTCTTCT
* * *
402083 TCCTCTTCATATGAGTTCTTCTTATTACGAACTCTTTCTGGAAACGTTGATGCTGCTCTATCGCC
66 TCCTCTTCAGATGAGTTCTTCTTATCACGAACTCTTTCTGGAAACGTAGATGCTGCTCTATCGCC
*
402148 TTCTGCGATAGAATCGAGAAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCATCTT
131 TTCTGCGATAGAATCAAGAAAAAAGTT--ATAA--T-TTCAGATTATGAACTTCTTCTTCATCTT
402213 CAGATTAGTTATTCTTATTAAGAACTCCTTCCAGAAATATTGATGCTTCTTTATCTCCTTCTGCG
191 CAGATTAGTTATTCTTATTAAGAACTCCTTCCAGAAATATTGATGCTTCTTTATCTCCTTCTGCG
* *
402278 ATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAATTTCTTCTTCCTCTTCAGATAA
256 ATAGAATCGAGCAAAAGATTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATAA
402343 GTTCTTCTTATCACAAACTCCTTCTGGAAATGTTGATGTTGCTATATCTCCTTCTGCGATAGAAT
321 GTTCTTCTTATCACAAACTCCTTCTGGAAATGTTGATGTTGCTATATCTCCTTCTGCGATAGAAT
* * *
402408 CGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTTTTTAGATGAGTTCTTC
386 CGAGCAAAAGGTTCAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTC
402473 TTATTACGAACTCCTTCTAGAAACATTGATGCTGCTC
451 TTATTACGAACTCCTTCTAGAAACATTGATGCTGCTC
*
402510 TATCTCCTTCT-CTGATAGAATCGAGCAAAAAATTGAATAAGTTCTTCAGATTATGAACTTTTTC
1 TATCTCCTTCTGC-GATAGAATCGAGCAAAAAATTGAATAAGTTCTTCAGATTATGAACTTCTTC
* * * *
402574 TTCCTCTTCAGATTAGTTCTTCTTATCACGAACTCTTTCTGGAAATGTAGATGTTGCTCTATCTC
65 TTCCTCTTCAGATGAGTTCTTCTTATCACGAACTCTTTCTGGAAACGTAGATGCTGCTCTATCGC
* * *
402639 CTTTTGCGATAGAATCAAGCAAAAAGTT-TAA-TTCAGATTATGAACTTCTTCTTCCTCTTCAGA
130 CTTCTGCGATAGAATCAAGAAAAAAGTTATAATTTCAGATTATGAACTTCTTCTTCATCTTCAGA
* * ** *
402702 TTAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATG-TTGCTTTATCTCCTTCTGCGATA
195 TTAGTTATTCTTATTAAGAACTCCTTCCAGAAATATTGATGCTT-CTTTATCTCCTTCTGCGATA
* *
402766 GAATCGAGTAAAAGATTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTT
259 GAATCGAGCAAAAGATTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATAAGTT
* * * * *
402831 CTTCTTATTACGAACTCCTTTTGGAAATGTTGATGTTTCTCTATCTCCTTCTGCGATAGAATCGA
324 CTTCTTATCACAAACTCCTTCTGGAAATGTTGATGTTGCTATATCTCCTTCTGCGATAGAATCGA
402896 GCAAAAGGTTCAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTA
389 GCAAAAGGTTCAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTA
402961 TTACGAACTCCTTCT
454 TTACGAACTCCTTCT
402976 TTCCTGAAAT
Statistics
Matches: 433, Mismatches: 31, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
484 2 0.00
485 285 0.66
489 3 0.01
491 1 0.00
492 142 0.33
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (487 bp):
TATCTCCTTCTGCGATAGAATCGAGCAAAAAATTGAATAAGTTCTTCAGATTATGAACTTCTTCT
TCCTCTTCAGATGAGTTCTTCTTATCACGAACTCTTTCTGGAAACGTAGATGCTGCTCTATCGCC
TTCTGCGATAGAATCAAGAAAAAAGTTATAATTTCAGATTATGAACTTCTTCTTCATCTTCAGAT
TAGTTATTCTTATTAAGAACTCCTTCCAGAAATATTGATGCTTCTTTATCTCCTTCTGCGATAGA
ATCGAGCAAAAGATTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCT
TCTTATCACAAACTCCTTCTGGAAATGTTGATGTTGCTATATCTCCTTCTGCGATAGAATCGAGC
AAAAGGTTCAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
ACGAACTCCTTCTAGAAACATTGATGCTGCTC
Found at i:403868 original size:54 final size:53
Alignment explanation
Indices: 403786--403947 Score: 207
Period size: 54 Copynumber: 3.0 Consensus size: 53
403776 ATAACAACTG
* * * *
403786 GTTCGTAAAACTTTTGACCACACATTCATCATTTCCTGTGGTTTCTGCCCAGAT
1 GTTCGTAAAA-TTTTGACAACAAATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
* * * *
403840 GTTCGTAAAATGTTTGACAACATATTCATCCTTTCCTATGGCTTCTACCTAGAT
1 GTTCGTAAAAT-TTTGACAACAAATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
* *
403894 GTTCGTAAAACATTTGACAAAAAATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAA-TTTTGACAACAAATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
403948 TTCTTATCAG
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 92 0.99
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (53 bp):
GTTCGTAAAATTTTGACAACAAATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
Found at i:404487 original size:1 final size:1
Alignment explanation
Indices: 404481--404528 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
404471 ATAACCTCTC
* * * * *
404481 TTTTTTTTTCTTTTTTTTCTTTTTTTCTTTTTTTTCTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
404529 GCTATTTGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:404496 original size:8 final size:8
Alignment explanation
Indices: 404483--404528 Score: 67
Period size: 8 Copynumber: 5.8 Consensus size: 8
404473 AACCTCTCTT
404483 TTTTTTTC
1 TTTTTTTC
404491 TTTTTTTTC
1 -TTTTTTTC
404500 TTTTTTTC
1 TTTTTTTC
404508 TTTTTTT-
1 TTTTTTTC
*
404515 TCTTTTTC
1 TTTTTTTC
404523 TTTTTT
1 TTTTTT
404529 GCTATTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 6 0.18
8 20 0.59
9 8 0.24
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTC
Found at i:404496 original size:9 final size:9
Alignment explanation
Indices: 404482--404521 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
404472 TAACCTCTCT
404482 TTTTTTTTC
1 TTTTTTTTC
404491 TTTTTTTTC
1 TTTTTTTTC
404500 -TTTTTTTC
1 TTTTTTTTC
404508 TTTTTTTTC
1 TTTTTTTTC
404517 TTTTT
1 TTTTT
404522 CTTTTTTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:404528 original size:17 final size:17
Alignment explanation
Indices: 404483--404521 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
404473 AACCTCTCTT
404483 TTTTTTTCTTTTTTTTC
1 TTTTTTTCTTTTTTTTC
404500 TTTTTTTCTTTTTTTTC
1 TTTTTTTCTTTTTTTTC
404517 TTTTT
1 TTTTT
404522 CTTTTTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTTC
Found at i:408057 original size:2 final size:2
Alignment explanation
Indices: 408050--408079 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
408040 ATAATTAAAG
408050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408080 AGTAGGGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:409481 original size:3 final size:3
Alignment explanation
Indices: 409473--409558 Score: 120
Period size: 3 Copynumber: 28.3 Consensus size: 3
409463 ATTCGGGCCT
* *
409473 ATA ATA ATA AT- ATCA TTA ATA ATA ATA ATA TTAA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
*
409519 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
409559 AATGGAGAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:416560 original size:2 final size:2
Alignment explanation
Indices: 416553--416587 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
416543 ACATAGTCAT
416553 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
416588 TAAAGAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:419683 original size:23 final size:23
Alignment explanation
Indices: 419650--419713 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
419640 AGGCGATGAC
* *
419650 ATCAGCACCTTGTAGAAGGTCCA
1 ATCAGCGCCTTGTAGAAGATCCA
*
419673 GTCAGCGCCTTGTAGAAGATCCA
1 ATCAGCGCCTTGTAGAAGATCCA
*
419696 ATCAGCG-CTTCTAGAAGA
1 ATCAGCGCCTTGTAGAAGA
419714 ACGAATGGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 10 0.28
23 26 0.72
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (23 bp):
ATCAGCGCCTTGTAGAAGATCCA
Found at i:420799 original size:12 final size:13
Alignment explanation
Indices: 420777--420820 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
420767 ATTTAAAACG
420777 ATTTATATTTTATT
1 ATTT-TATTTTATT
420791 A-TTTATTTTATT
1 ATTTTATTTTATT
420803 ATTTTATTCTTATT
1 ATTTTATT-TTATT
420817 -TTTT
1 ATTTT
420821 TTATCTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.36
13 12 0.43
14 6 0.21
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTTATTTTATT
Found at i:422025 original size:21 final size:22
Alignment explanation
Indices: 421988--422032 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
421978 TTTTTTTAAA
*
421988 TTTGATGATTGAAAATAATCTT
1 TTTGAAGATTGAAAATAATCTT
*
422010 TTTGAAGATT-AAAATATTCTT
1 TTTGAAGATTGAAAATAATCTT
422031 TT
1 TT
422033 AAATCGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (22 bp):
TTTGAAGATTGAAAATAATCTT
Found at i:423588 original size:51 final size:51
Alignment explanation
Indices: 423528--423629 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
423518 GGATAGAGAC
* *
423528 TCTCGAGGTTTGTGGAGACCTTCATCCTCTCAGTCTCAGAGGACGAGAAAG
1 TCTCGAGGTTCGCGGAGACCTTCATCCTCTCAGTCTCAGAGGACGAGAAAG
*
423579 TCTCTAGGTTCGCGGAGACCTTCATCCTCTCAGTCTCAGAGGACGAGAAAG
1 TCTCGAGGTTCGCGGAGACCTTCATCCTCTCAGTCTCAGAGGACGAGAAAG
423630 GGCTTAACTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (51 bp):
TCTCGAGGTTCGCGGAGACCTTCATCCTCTCAGTCTCAGAGGACGAGAAAG
Found at i:427429 original size:19 final size:20
Alignment explanation
Indices: 427401--427449 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
427391 TCCAAGAGCG
*
427401 TGTATCTTCATT-AAAATCA
1 TGTATTTTCATTAAAAATCA
427420 TGTATTTTCATTAAAAATCA
1 TGTATTTTCATTAAAAATCA
427440 TGTATTTTCA
1 TGTATTTTCA
427450 AAGGGCTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (20 bp):
TGTATTTTCATTAAAAATCA
Found at i:428266 original size:303 final size:303
Alignment explanation
Indices: 427719--428318 Score: 1146
Period size: 303 Copynumber: 2.0 Consensus size: 303
427709 CTTACTTAAG
427719 TTTATAGAGAACGAGGATAAGCTTTCTATAGCTTTTCTTCTTCTTTGGCTTATTTAAGATACTAC
1 TTTATAGAGAACGAGGATAAGCTTTCTATAGCTTTTCTTCTTCTTTGGCTTATTTAAGATACTAC
*
427784 TTAAACCATCACTGTCATCATCTTCTTCACGCCATCACCTTCACCATTCCATTATCATTTCATCA
66 TTAAACCATCACCGTCATCATCTTCTTCACGCCATCACCTTCACCATTCCATTATCATTTCATCA
* *
427849 CCATTAAAGCCATCCTTCACTCATCATTGAAGTAACATCCAACAACATCATTGGAGGCCAATTCT
131 CCATTAAAGCCATCATTCACTCATCATTGAAGTAACATCCAACAACATCATTGGAGGCCAATTCG
427914 TGATCTATTGAAGGATAATTATTCATCATTTTCACAGCCCAGTTTGATAACCATTCTAATCCTTT
196 TGATCTATTGAAGGATAATTATTCATCATTTTCACAGCCCAGTTTGATAACCATTCTAATCCTTT
427979 ATTTCTTATTAAATTCTTTTCAATCTTTCATTTCTTTTTATCA
261 ATTTCTTATTAAATTCTTTTCAATCTTTCATTTCTTTTTATCA
*
428022 TTTATAGAGAACGGGGATAAGCTTTCTATAGCTTTTCTTCTTCTTTGGCTTATTTAAGATACTAC
1 TTTATAGAGAACGAGGATAAGCTTTCTATAGCTTTTCTTCTTCTTTGGCTTATTTAAGATACTAC
428087 TTAAACCATCACCGTCATCATCTTCTTCACGCCATCACCTTCACCATTCCATTATCATTTCATCA
66 TTAAACCATCACCGTCATCATCTTCTTCACGCCATCACCTTCACCATTCCATTATCATTTCATCA
428152 CCATTAAAGCCATCATTCACTCATCATTGAAGTAACATCCAACAACATCATTGGAGGCCAATTCG
131 CCATTAAAGCCATCATTCACTCATCATTGAAGTAACATCCAACAACATCATTGGAGGCCAATTCG
**
428217 TGATCTATTGAAGGATAATTATTCATCATTTTCGTAGCCCAGTTTGATAACCATTCTAATCCTTT
196 TGATCTATTGAAGGATAATTATTCATCATTTTCACAGCCCAGTTTGATAACCATTCTAATCCTTT
428282 ATTTCTTATTAAATTCTTTTCAATCTTTCATTTCTTT
261 ATTTCTTATTAAATTCTTTTCAATCTTTCATTTCTTT
428319 CATTCATTTT
Statistics
Matches: 291, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
303 291 1.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (303 bp):
TTTATAGAGAACGAGGATAAGCTTTCTATAGCTTTTCTTCTTCTTTGGCTTATTTAAGATACTAC
TTAAACCATCACCGTCATCATCTTCTTCACGCCATCACCTTCACCATTCCATTATCATTTCATCA
CCATTAAAGCCATCATTCACTCATCATTGAAGTAACATCCAACAACATCATTGGAGGCCAATTCG
TGATCTATTGAAGGATAATTATTCATCATTTTCACAGCCCAGTTTGATAACCATTCTAATCCTTT
ATTTCTTATTAAATTCTTTTCAATCTTTCATTTCTTTTTATCA
Found at i:428505 original size:13 final size:13
Alignment explanation
Indices: 428489--428513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
428479 CTGCAACAAA
428489 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
428502 AAGAAAAAGAAA
1 AAGAAAAAGAAA
428514 AAAAGAAAAG
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAG
Found at i:428522 original size:6 final size:6
Alignment explanation
Indices: 428486--428515 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
428476 GTGCTGCAAC
428486 AAAAAG AAAAAG AAAGAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAA
428516 AAGAAAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:428524 original size:19 final size:19
Alignment explanation
Indices: 428486--428524 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
428476 GTGCTGCAAC
*
428486 AAAAAGAAAAAGAAAGAAG
1 AAAAAGAAAAAGAAAAAAG
428505 AAAAAGAAAAA-AAGAAAAG
1 AAAAAGAAAAAGAA-AAAAG
428524 A
1 A
428525 CTCATACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAAAG
Found at i:429636 original size:21 final size:20
Alignment explanation
Indices: 429612--429651 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
429602 AAGAAGATGT
*
429612 TGGAGTTGAAAAGGATGAATA
1 TGGAGATGAAAAGGA-GAATA
*
429633 TGGAGATGAAGAGGAGAAT
1 TGGAGATGAAAAGGAGAAT
429652 GAAGAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (20 bp):
TGGAGATGAAAAGGAGAATA
Found at i:436328 original size:90 final size:90
Alignment explanation
Indices: 436175--436352 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
436165 CCTAACACAC
* * *
436175 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
436240 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
436265 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
436330 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
436353 TTCAGGATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:441615 original size:13 final size:13
Alignment explanation
Indices: 441596--441633 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
441586 AAAAGAATAC
441596 AAAAAGAAAAA-G
1 AAAAAGAAAAATG
441608 ATAAAAGAAAAATG
1 A-AAAAGAAAAATG
441622 AAAGAAGAAAAA
1 AAA-AAGAAAAA
441634 AAAGGCGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 12 0.52
14 10 0.43
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAAAGAAAAATG
Found at i:443110 original size:80 final size:79
Alignment explanation
Indices: 442898--443181 Score: 327
Period size: 80 Copynumber: 3.5 Consensus size: 79
442888 CATCACCATT
** * * * *
442898 TTGTTCAACATTTGCTTGATTTCATCACAGAAGGAGGTGGATCAACATTTTCGATAAAAGAAGTT
1 TTGTTCAACCCTTGCTCGATTTCATCACAGAAGGAGGTGGATCAGCATTTCCGATAAACG-AGTT
*
442963 CATAATGAGAAGAAC
65 CATAATGAGAAAAAC
* * * * * *
442978 TTGTTC-ACCATTTTGCTCGAATCCATCACATAATGAGTTGGATCAGCATTTCCGATGAAACGAG
1 TTGTTCAACC--CTTGCTCGATTTCATCACAGAAGGAGGTGGATCAGCATTTCCGAT-AAACGAG
443042 TTCATAATGAGAAAAAC
63 TTCATAATGAGAAAAAC
* * * * * *
443059 TTGTTCAACCCTTGCTCGATTTCATTATAGAATGAGGTGGATCAGCGTTTCCGATAAAACAAGTC
1 TTGTTCAACCCTTGCTCGATTTCATCACAGAAGGAGGTGGATCAGCATTTCCGAT-AAACGAGTT
* *
443124 CATAATGAGAATAAT
65 CATAATGAGAAAAAC
443139 TTGTTCAACCCTTGCTCGATTTCATCACAGAAGGAGGTGGATC
1 TTGTTCAACCCTTGCTCGATTTCATCACAGAAGGAGGTGGATC
443182 GACATTTTTA
Statistics
Matches: 173, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
79 2 0.01
80 103 0.60
81 61 0.35
82 7 0.04
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (79 bp):
TTGTTCAACCCTTGCTCGATTTCATCACAGAAGGAGGTGGATCAGCATTTCCGATAAACGAGTTC
ATAATGAGAAAAAC
Found at i:446984 original size:21 final size:21
Alignment explanation
Indices: 446960--447001 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
446950 TGCAAGATGA
446960 TTAAATAGTGGATGGAAGAGT
1 TTAAATAGTGGATGGAAGAGT
446981 TTAAATAGTGGATGGAAGAGT
1 TTAAATAGTGGATGGAAGAGT
447002 CTAAGTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (21 bp):
TTAAATAGTGGATGGAAGAGT
Found at i:459248 original size:52 final size:52
Alignment explanation
Indices: 459166--459271 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
459156 GTTACAACCA
* *
459166 ATAAAAGACCCTTTGATTTATGCATCTTGTTCTTATGAGTAGTGGAGATTTG
1 ATAAAAGACCCTTTGATTTATGCATCTTGTTCATATGAGTAGTAGAGATTTG
*
459218 ATAAAAGACCCTTTGATTTATGCATTTTGTTCATATGAGTAGTAGAGATTTG
1 ATAAAAGACCCTTTGATTTATGCATCTTGTTCATATGAGTAGTAGAGATTTG
459270 AT
1 AT
459272 TTACTTGCAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (52 bp):
ATAAAAGACCCTTTGATTTATGCATCTTGTTCATATGAGTAGTAGAGATTTG
Found at i:459754 original size:18 final size:18
Alignment explanation
Indices: 459742--459785 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
459732 CTCTTTTTAC
459742 TTTTCAAGTTCTTTTCAT
1 TTTTCAAGTTCTTTTCAT
459760 TTTTCAAGTTCTTTTCAT
1 TTTTCAAGTTCTTTTCAT
459778 TTTTCAAG
1 TTTTCAAG
459786 CATTGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.59
Consensus pattern (18 bp):
TTTTCAAGTTCTTTTCAT
Found at i:460406 original size:18 final size:19
Alignment explanation
Indices: 460378--460416 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
460368 TTCTCTTATT
*
460378 TTTACTTTAATTGCTTTTA
1 TTTACTTTAATCGCTTTTA
*
460397 TTTA-TTTAATCGTTTTTA
1 TTTACTTTAATCGCTTTTA
460415 TT
1 TT
460417 ACTATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTACTTTAATCGCTTTTA
Found at i:461249 original size:26 final size:26
Alignment explanation
Indices: 461198--461250 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
461188 ATAAAAAAAT
* *
461198 AAAAGTTAATAAAAATATTTTTTTAC
1 AAAAGTTAATAAAAATATTCTGTTAC
*
461224 AAAAGTTAATAAAGATATTCTGTTAC
1 AAAAGTTAATAAAAATATTCTGTTAC
461250 A
1 A
461251 CATATAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.38
Consensus pattern (26 bp):
AAAAGTTAATAAAAATATTCTGTTAC
Found at i:462210 original size:34 final size:35
Alignment explanation
Indices: 462172--462238 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
462162 TAAATTGATA
*
462172 ATTTAT-TCTTAAATTATTTTGAGTTCATAAAAAG
1 ATTTATATCATAAATTATTTTGAGTTCATAAAAAG
* **
462206 ATTTATAATGATATTTTATTTTGAGTTCATAAA
1 ATTTAT-ATCATAAATTATTTTGAGTTCATAAA
462239 TTGGGTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 6 0.22
36 21 0.78
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.49
Consensus pattern (35 bp):
ATTTATATCATAAATTATTTTGAGTTCATAAAAAG
Found at i:462446 original size:16 final size:16
Alignment explanation
Indices: 462427--462460 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
462417 ATTTGGGGAG
462427 TTAATAATTTTTTATT
1 TTAATAATTTTTTATT
**
462443 TTAATTTTTTTTTATT
1 TTAATAATTTTTTATT
462459 TT
1 TT
462461 TAATGTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTAATAATTTTTTATT
Found at i:462461 original size:17 final size:17
Alignment explanation
Indices: 462434--462469 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
462424 GAGTTAATAA
462434 TTTTTTATTTTAAT-TT
1 TTTTTTATTTTAATGTT
462450 TTTTTTATTTTTAATGTT
1 TTTTTTA-TTTTAATGTT
462468 TT
1 TT
462470 GGGTTTCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTTTATTTTAATGTT
Found at i:463073 original size:6 final size:6
Alignment explanation
Indices: 463062--463107 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
463052 AGGTTCTTTT
463062 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
463108 TATATTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:463999 original size:14 final size:15
Alignment explanation
Indices: 463980--464008 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
463970 ATGACTTGTT
463980 ATGAAATAA-AAAGA
1 ATGAAATAATAAAGA
463994 ATGAAATAATAAAGA
1 ATGAAATAATAAAGA
464009 GAATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (15 bp):
ATGAAATAATAAAGA
Found at i:466584 original size:6 final size:6
Alignment explanation
Indices: 466531--466583 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
466521 CACCTCACTT
* *
466531 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCT CTCTCT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
466579 CTCTC
1 CTCTC
466584 TGGTTTCTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CTCTCC
Found at i:466881 original size:22 final size:21
Alignment explanation
Indices: 466847--466887 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
466837 ATAATTATTT
466847 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
466868 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
466888 ATTTTGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:469285 original size:161 final size:161
Alignment explanation
Indices: 469039--469341 Score: 525
Period size: 161 Copynumber: 1.9 Consensus size: 161
469029 TTGTTTCGAT
* *
469039 ACTCTCCATTCACAATAGAAGGGATTAATCATCAAATCATCGACTAACTTCATTGTTTTCTACCT
1 ACTCTCCATTCACAATAGAAGAGATGAATCATCAAATCATCGACTAACTTCATTGTTTTCTACCT
* *
469104 TCTAAACCATCATGAGCTATCACTTAACATGTTGTTCATCAATATTTGGTGCAGTGAGTAAGAAC
66 TCTAAACCATCATGAGCTATCACTTAACATGTTGTTCATCAATATTTGGTGCAGTGAATAAGAAA
469169 AAACTTATAATCGAACTTTGATCGATTCACG
131 AAACTTATAATCGAACTTTGATCGATTCACG
* * *
469200 ACTCTCCATTCACAATAGAAGAGATGAATCATCAAATCATTGACTAACTTCTTTGTTTTTTACCT
1 ACTCTCCATTCACAATAGAAGAGATGAATCATCAAATCATCGACTAACTTCATTGTTTTCTACCT
**
469265 TCTAAACCATCATGAGCTATCGGTTAACATGTTGTTCATCAATATTTGGTGCAGTGAATAAGAAA
66 TCTAAACCATCATGAGCTATCACTTAACATGTTGTTCATCAATATTTGGTGCAGTGAATAAGAAA
469330 AAACTTATAATC
131 AAACTTATAATC
469342 CAAGGAATTA
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
161 133 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (161 bp):
ACTCTCCATTCACAATAGAAGAGATGAATCATCAAATCATCGACTAACTTCATTGTTTTCTACCT
TCTAAACCATCATGAGCTATCACTTAACATGTTGTTCATCAATATTTGGTGCAGTGAATAAGAAA
AAACTTATAATCGAACTTTGATCGATTCACG
Found at i:469397 original size:23 final size:23
Alignment explanation
Indices: 469369--469424 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
469359 TACAAAATCT
469369 AGAAATTAAATTAGGGTCAGTTA
1 AGAAATTAAATTAGGGTCAGTTA
469392 AGAAATTAAATTAGGGTCAGTTA
1 AGAAATTAAATTAGGGTCAGTTA
*
469415 GGAAATTAAA
1 AGAAATTAAA
469425 AGTAATATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (23 bp):
AGAAATTAAATTAGGGTCAGTTA
Found at i:476377 original size:15 final size:16
Alignment explanation
Indices: 476352--476399 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
476342 TAACATGTTT
*
476352 AAAAATAAAAACTTAA
1 AAAAATAAAAACTGAA
476368 AAAAAT-AAAACTGAA
1 AAAAATAAAAACTGAA
* *
476383 AAAGAAAAAAAAATGAA
1 AAA-AATAAAAACTGAA
476400 GAACTTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 8 0.30
17 8 0.30
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAATAAAAACTGAA
Found at i:476672 original size:16 final size:16
Alignment explanation
Indices: 476653--476685 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
476643 CTAACTGGAC
476653 CTTCTAGAAACTGCCA
1 CTTCTAGAAACTGCCA
476669 CTTCTAGAAACTGCCA
1 CTTCTAGAAACTGCCA
476685 C
1 C
476686 GTCAGATCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.24
Consensus pattern (16 bp):
CTTCTAGAAACTGCCA
Found at i:484274 original size:34 final size:34
Alignment explanation
Indices: 484229--484295 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
484219 AATAGGAATT
*
484229 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATG
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATG
484264 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
484296 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATG
Found at i:486852 original size:5 final size:5
Alignment explanation
Indices: 486842--486871 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
486832 GTATTATTTA
*
486842 TTATT TTATT TTATT CTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
486872 ACTTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:486861 original size:15 final size:15
Alignment explanation
Indices: 486843--486871 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
486833 TATTATTTAT
486843 TATTTTATTTTATTC
1 TATTTTATTTTATTC
486858 TATTTTATTTTATT
1 TATTTTATTTTATT
486872 ACTTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTATTTTATTC
Found at i:486957 original size:3 final size:3
Alignment explanation
Indices: 486949--486979 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
486939 TCATTATGAC
486949 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
486980 ACGTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:486971 original size:14 final size:14
Alignment explanation
Indices: 486952--486979 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
486942 TTATGACTAT
486952 TATTATTATTATTA
1 TATTATTATTATTA
486966 TATTATTATTATTA
1 TATTATTATTATTA
486980 ACGTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:487038 original size:20 final size:19
Alignment explanation
Indices: 487013--487060 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
487003 TTTTATTCTT
*
487013 TTTTTATTGTTGTTTTTTCC
1 TTTTTATT-TTATTTTTTCC
487033 TTTTTA-TTTATTTTTTCC
1 TTTTTATTTTATTTTTTCC
*
487051 TCTTTATTTT
1 TTTTTATTTT
487061 CTGTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.60
19 4 0.16
20 6 0.24
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTATTTTTTCC
Found at i:487079 original size:86 final size:86
Alignment explanation
Indices: 486983--487144 Score: 199
Period size: 86 Copynumber: 1.9 Consensus size: 86
486973 ATTATTAACG
* * * *
486983 TATATATTTTACT-TTTTTATTTT-TAT-TCTTTTTTTATTGTTGTTTTTTCCTTTTTATTTATT
1 TATATATTTTA-TATTTTTATTTTCTATATCTTTATTTATT-TT-CTATTTCCTTTATATTTATT
487045 TT-TTCCTCTTTATTTTCTGTAATTT
63 TTGTT--TCTTTATTTTCTGTAATTT
*
487070 TATAT-TTTTATATTTTTATTTTCTTTATCTTTATTTATTTTCTATTTCCTTTATATTTATTTTG
1 TATATATTTTATATTTTTATTTTCTATATCTTTATTTATTTTCTATTTCCTTTATATTTATTTTG
487134 TTTCTTTATTT
66 TTTCTTTATTT
487145 ATTTCTATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
85 10 0.15
86 34 0.52
87 11 0.17
88 11 0.17
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.73
Consensus pattern (86 bp):
TATATATTTTATATTTTTATTTTCTATATCTTTATTTATTTTCTATTTCCTTTATATTTATTTTG
TTTCTTTATTTTCTGTAATTT
Found at i:487102 original size:15 final size:15
Alignment explanation
Indices: 487051--487105 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
487041 TATTTTTTCC
*
487051 TCTTTATTTTCTGTAA
1 TCTTTATTTTCT-TTA
487067 T-TTTATATTT-TTATA
1 TCTTTAT-TTTCTT-TA
*
487082 TTTTTATTTTCTTTA
1 TCTTTATTTTCTTTA
487097 TCTTTATTT
1 TCTTTATTT
487106 ATTTTCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 1 0.03
15 21 0.64
16 11 0.33
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (15 bp):
TCTTTATTTTCTTTA
Found at i:487108 original size:19 final size:18
Alignment explanation
Indices: 487084--487148 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
487074 TTTTTATATT
487084 TTTATTTTCTTTATCTTTA
1 TTTATTTTCTTT-TCTTTA
487103 TTTATTTTCTATTTCCTTTATA
1 TTTATTTTCT-TTT-C-TT-TA
*
487125 TTTATTTT-GTTTCTTTA
1 TTTATTTTCTTTTCTTTA
487142 TTTATTT
1 TTTATTT
487149 CTATTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
17 9 0.22
18 2 0.05
19 12 0.29
20 6 0.15
21 2 0.05
22 10 0.24
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTTTCTTTTCTTTA
Found at i:487122 original size:26 final size:25
Alignment explanation
Indices: 487068--487131 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
487058 TTTCTGTAAT
*
487068 TTTATATTT-TTATATTTTTATTTTC
1 TTTATATTTATT-TATTTTTATTTCC
*
487093 TTTATCTTTATTTATTTTCTATTTCC
1 TTTATATTTATTTATTTT-TATTTCC
487119 TTTATATTTATTT
1 TTTATATTTATTT
487132 TGTTTCTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTATATTTATTTATTTTTATTTCC
Found at i:487153 original size:23 final size:23
Alignment explanation
Indices: 487119--487178 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 23
487109 TTCTATTTCC
487119 TTTATATTTATTTTGTTT-CTTTA
1 TTTATATTTATTTT-TTTGCTTTA
*
487142 TTTAT-TTCTATTTTTTTGTTTTA
1 TTTATATT-TATTTTTTTGCTTTA
487165 TTTAATTATTTATT
1 TTT-A-TATTTATT
487179 ATATTATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
22 5 0.16
23 18 0.58
24 1 0.03
25 5 0.16
26 2 0.06
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (23 bp):
TTTATATTTATTTTTTTGCTTTA
Found at i:487307 original size:19 final size:17
Alignment explanation
Indices: 487252--487308 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
487242 TTTATCTCAT
*
487252 TTTATTTA-TTTATTTA
1 TTTATTTACTTTATTTC
*
487268 TTTATTTCCTCTTATTTTC
1 TTTATTTACT-TTA-TTTC
487287 TTTATTTACTTTCATTATC
1 TTTATTTACTTT-ATT-TC
487306 TTT
1 TTT
487309 TCCTCTAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 7 0.21
17 1 0.03
18 7 0.21
19 18 0.55
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTACTTTATTTC
Found at i:498018 original size:21 final size:20
Alignment explanation
Indices: 497967--498018 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
497957 AAAACCTTCG
*
497967 AAGAGTTCAAGATCGAGAATC
1 AAGAG-TCAAGATCCAGAATC
* *
497988 AAAACTTCAAGATTCCAGAATC
1 AAGA-GTCAAGA-TCCAGAATC
498010 AAGAGTCAA
1 AAGAGTCAA
498019 CAAGACAGGC
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.19
Consensus pattern (20 bp):
AAGAGTCAAGATCCAGAATC
Found at i:498360 original size:124 final size:124
Alignment explanation
Indices: 498211--498576 Score: 574
Period size: 124 Copynumber: 2.9 Consensus size: 124
498201 CATTTACTCG
*
498211 AGATTGGATTTCAACTTCAT-GACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGAGG
1 AGATTGGATTTCAACTTC-TCGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGG
* *
498275 CCATCCACGATTTTAACTTCACGACGAAGGATATTGTGCCCACCAGCAACATTCATCTTT
65 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTT
* * * *
498335 AGATTGGATTTCAACTTCTCAACGAATGATATCCAATTCAAGGCTCAACTTCATAACGAAGGGGC
1 AGATTGGATTTCAACTTCTCGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGC
*
498400 CATCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCACCAG-AAGCATTCATCTTT
66 CATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAA-CATTCATCTTT
* *
498459 AGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGG
1 AGATTGGATTTCAACTTCTCGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAA-GGGG
* * *
498524 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCATT
65 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATT
498577 GGATTTCAAC
Statistics
Matches: 220, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
123 3 0.01
124 165 0.75
125 51 0.23
126 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (124 bp):
AGATTGGATTTCAACTTCTCGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGC
CATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTT
Found at i:498857 original size:251 final size:250
Alignment explanation
Indices: 498459--499062 Score: 913
Period size: 251 Copynumber: 2.4 Consensus size: 250
498449 ATTCATCTTT
*
498459 AGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGG
1 AGATTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAGGCTCAACTTCACAA-GAA-GGGG
498524 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCATTGGATTTCAACTT
64 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCATTGGATTTCAACTT
* * *
498589 CACAACGAAGAATATCCAATTCAAAGCTCTACTTCATAGC-AAAGGGACTTCCCAGTTTCATTCA
129 CACAACAAAGAATATCCAATTCAAAGCTCAACTTCACAGCGAAAGGGA-TTCCCAGTTTCATTCA
* * *
498653 AAGCCAATTTTAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAACTTACATA
193 AAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAACTTACACA
* * *
498711 AGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGC
1 AGATTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAGGCTCAACTTCACAA-GAAGGGGC
* *
498776 CATCCACGATTTCAACTTCACGACGAATGATATCGTGCTCACAAGTAGCATTGGATTTCAACTTC
65 CATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCATTGGATTTCAACTTC
* * * * *
498841 ACAACAAAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGATTCCCTGTTTCATTTAGA
130 ACAACAAAGAATATCCAATTCAAAGCTCAACTTCACAGCGAAAGGGATTCCCAGTTTCATTCAAA
* *
498906 GCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACGCAACTTGCACA
195 GCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAACTTACACA
* * * * *
498962 AGATTGGATTTTAACTTCATGAAGAAGGATATCTAATTTAAGGCTTAACTTCACGAAGAAGGGGC
1 AGATTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAGGCTCAACTTCAC-AAGAAGGGGC
** *
499027 CATCCATAATTTCAACTTCACAACGAAGGATATCGT
65 CATCCACGATTTCAACTTCACGACGAAGGATATCGT
499063 ACCCTAAAGA
Statistics
Matches: 319, Mismatches: 31, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
251 254 0.80
252 65 0.20
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (250 bp):
AGATTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAGGCTCAACTTCACAAGAAGGGGCC
ATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTCACAAGCAGCATTGGATTTCAACTTCA
CAACAAAGAATATCCAATTCAAAGCTCAACTTCACAGCGAAAGGGATTCCCAGTTTCATTCAAAG
CCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAACTTACACA
Found at i:500626 original size:12 final size:13
Alignment explanation
Indices: 500604--500645 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
500594 ATTTAATCCT
500604 TTTTA-TTATTTA
1 TTTTATTTATTTA
500616 -TTTATTTATTTA
1 TTTTATTTATTTA
500628 TTTTA-TT-TTTA
1 TTTTATTTATTTA
500639 TTTTATT
1 TTTTATT
500646 ACTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 13 0.48
12 10 0.37
13 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:500651 original size:27 final size:30
Alignment explanation
Indices: 500603--500660 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 30
500593 AATTTAATCC
*
500603 TTTTTATTATTTATTTATTTAT-TTATTTTA
1 TTTTTATTATTTATTTACTTATATT-TTTTA
500633 TTTTTA-T-TTTA-TTACTTATATTTTTTA
1 TTTTTATTATTTATTTACTTATATTTTTTA
500660 T
1 T
500661 ATACTTCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 13 0.50
28 6 0.23
29 1 0.04
30 6 0.23
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTTATTATTTATTTACTTATATTTTTTA
Found at i:502320 original size:84 final size:84
Alignment explanation
Indices: 502179--502430 Score: 477
Period size: 84 Copynumber: 3.0 Consensus size: 84
502169 CAATCTATCT
*
502179 CATCGTGTTCGTTCATACTAAAATCGATCACCATTTATAGTATGTTAACACCTTCAATGCTTCGT
1 CATCGTGTTCGTTCATACTGAAATCGATCACCATTTATAGTATGTTAACACCTTCAATGCTTCGT
502244 AATCTTGGGGGAGCTCTCC
66 AATCTTGGGGGAGCTCTCC
502263 CATCGTGTTCGTTCATACTGAAATCGATCACCATTTATAGTATGTTAACACCTTCAATGCTTCGT
1 CATCGTGTTCGTTCATACTGAAATCGATCACCATTTATAGTATGTTAACACCTTCAATGCTTCGT
502328 AATCTTGGGGGAGCTCTCC
66 AATCTTGGGGGAGCTCTCC
*
502347 CATCGTGTTCGTTCATACTGAAATCGATCACCATTTATAGTTTGTTAACACCTTCAATGCTTCGT
1 CATCGTGTTCGTTCATACTGAAATCGATCACCATTTATAGTATGTTAACACCTTCAATGCTTCGT
*
502412 AATCTTGGGGGAACTCTCC
66 AATCTTGGGGGAGCTCTCC
502431 TAAGAAAATA
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 165 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (84 bp):
CATCGTGTTCGTTCATACTGAAATCGATCACCATTTATAGTATGTTAACACCTTCAATGCTTCGT
AATCTTGGGGGAGCTCTCC
Found at i:506803 original size:31 final size:31
Alignment explanation
Indices: 506760--506828 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
506750 ATACATATAC
* * *
506760 AAACATTCAAGTATAAATAATTCAAATATTA
1 AAACATTAAAGTACAAATAATTCAAATATGA
*
506791 AAACATTAAAGTACAAATAGTTCAAATATGA
1 AAACATTAAAGTACAAATAATTCAAATATGA
*
506822 AATCATT
1 AAACATT
506829 GAGGCATGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (31 bp):
AAACATTAAAGTACAAATAATTCAAATATGA
Found at i:509737 original size:51 final size:53
Alignment explanation
Indices: 509682--509783 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 53
509672 GTGTTATTGT
* * *
509682 TTTTCCTTCTCTCATTCTTCTTCACAATA-TTTTTT-CTCACACTTTATCTGC
1 TTTTCCTCCCCTCATTCTTCTACACAATATTTTTTTCCTCACACTTTATCTGC
* **
509733 TTTTCCTCCCCTCTTTCTTCTACACTCTATTTTTTTCCTCACACTTTATCT
1 TTTTCCTCCCCTCATTCTTCTACACAATATTTTTTTCCTCACACTTTATCT
509784 TCAACTTCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 23 0.53
52 6 0.14
53 14 0.33
ACGTcount: A:0.14, C:0.32, G:0.01, T:0.53
Consensus pattern (53 bp):
TTTTCCTCCCCTCATTCTTCTACACAATATTTTTTTCCTCACACTTTATCTGC
Found at i:511059 original size:51 final size:53
Alignment explanation
Indices: 511004--511106 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 53
510994 GTGTTCTTGT
* * *
511004 TTTTCCTTCTCTCATTCTTCTTCA-CAATATTTTTT-CTCACACTTTATCTGC
1 TTTTCCTCCCCTCATTCTTCTCCACCAATATTTTTTCCTCACACTTTATCTGC
* * *
511055 TTTTCCTCCCCTCTTTCTTCTCCACTCTATTTTTTTTCCTCACACTTTATCT
1 TTTTCCTCCCCTCATTCTTCTCCAC-CAATATTTTTTCCTCACACTTTATCT
511107 TCAACTTCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
51 20 0.47
53 9 0.21
54 14 0.33
ACGTcount: A:0.13, C:0.33, G:0.01, T:0.53
Consensus pattern (53 bp):
TTTTCCTCCCCTCATTCTTCTCCACCAATATTTTTTCCTCACACTTTATCTGC
Found at i:511961 original size:2 final size:2
Alignment explanation
Indices: 511954--511979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
511944 TATCTACATA
511954 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
511980 TCATTTGTCA
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:513116 original size:21 final size:21
Alignment explanation
Indices: 513087--513146 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
513077 TTCCCTAAAA
*
513087 TTTTTATGAAG-GCTGATTTAG
1 TTTTAATGAAGAG-TGATTTAG
513108 TTTTAATG-AGAGTGATTTAG
1 TTTTAATGAAGAGTGATTTAG
513128 TTTTAATG-AGAGTGATTTA
1 TTTTAATGAAGAGTGATTTA
513147 ATTTGCTTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 29 0.78
21 8 0.22
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (21 bp):
TTTTAATGAAGAGTGATTTAG
Found at i:513123 original size:20 final size:20
Alignment explanation
Indices: 513100--513146 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
513090 TTATGAAGGC
513100 TGATTTAGTTTTAATGAGAG
1 TGATTTAGTTTTAATGAGAG
513120 TGATTTAGTTTTAATGAGAG
1 TGATTTAGTTTTAATGAGAG
513140 TGATTTA
1 TGATTTA
513147 ATTTGCTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (20 bp):
TGATTTAGTTTTAATGAGAG
Found at i:522597 original size:17 final size:18
Alignment explanation
Indices: 522572--522616 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
522562 TTGTTAAAGT
*
522572 ATAACTTAAA-TAAATTA
1 ATAATTTAAACTAAATTA
*
522589 ATAATTTAAACTTAATTA
1 ATAATTTAAACTAAATTA
*
522607 ATATTTTAAA
1 ATAATTTAAA
522617 AATTCTAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTTAAACTAAATTA
Found at i:547996 original size:13 final size:13
Alignment explanation
Indices: 547967--548001 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
547957 GGGGAGTAAT
547967 TTTTCAAAAATGA
1 TTTTCAAAAATGA
547980 -TTTCAAAAATGA
1 TTTTCAAAAATGA
547992 TTTTCAAAAA
1 TTTTCAAAAA
548002 AAATCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:548588 original size:166 final size:168
Alignment explanation
Indices: 548305--548639 Score: 656
Period size: 166 Copynumber: 2.0 Consensus size: 168
548295 ATCGAGCCAA
548305 AAATGAGTTTTAAGTAGGGGTGTACCGATACACTCTTTGAATGTACTGATACCCCTGAATTTCGA
1 AAATGAGTTTTAAGTAGGGGTGTACCGATACACTCTTTGAATGTACTGATACCCCTGAATTTCGA
548370 ATGTAATAAGGGTACCGATACATAGCCAAATGTACCGATACCCCTTATGTTAAATTTGGCTTCGA
66 ATGTAATAAGGGTACCGATACATAGCCAAATGTACCGATACCCCTTATGTTAAATTTGGCTTCGA
548435 GAAACATCGAATTCCATAGGTGTACCGATACCCCTGGG
131 GAAACATCGAATTCCATAGGTGTACCGATACCCCTGGG
548473 AAATGAG-TTTAAGTAGGGGTGTACCGATACACTCTTTGAA-GTACTGATACCCCTGAATTTCGA
1 AAATGAGTTTTAAGTAGGGGTGTACCGATACACTCTTTGAATGTACTGATACCCCTGAATTTCGA
548536 ATGTAATAAGGGTACCGATACATAGCCAAATGTACCGATACCCCTTATGTTAAATTTGGCTTCGA
66 ATGTAATAAGGGTACCGATACATAGCCAAATGTACCGATACCCCTTATGTTAAATTTGGCTTCGA
548601 GAAACATCGAATTCCATAGGTGTACCGATACCCCTGGG
131 GAAACATCGAATTCCATAGGTGTACCGATACCCCTGGG
548639 A
1 A
548640 GGTACCGATA
Statistics
Matches: 167, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
166 127 0.76
167 33 0.20
168 7 0.04
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (168 bp):
AAATGAGTTTTAAGTAGGGGTGTACCGATACACTCTTTGAATGTACTGATACCCCTGAATTTCGA
ATGTAATAAGGGTACCGATACATAGCCAAATGTACCGATACCCCTTATGTTAAATTTGGCTTCGA
GAAACATCGAATTCCATAGGTGTACCGATACCCCTGGG
Found at i:549726 original size:21 final size:19
Alignment explanation
Indices: 549682--549754 Score: 78
Period size: 18 Copynumber: 3.8 Consensus size: 19
549672 ATATACAACA
549682 AAATATATAACTATAATAT
1 AAATATATAACTATAATAT
* *
549701 AAATATATACACTTTATTAT
1 AAATATATA-ACTATAATAT
549721 ATAATATATAAC-AT-ATAT
1 A-AATATATAACTATAATAT
*
549739 AATATATATAAATATA
1 AA-ATATATAACTATA
549755 TATTGTAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
17 1 0.02
18 12 0.27
19 12 0.27
20 11 0.25
21 8 0.18
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATATAACTATAATAT
Found at i:549736 original size:9 final size:8
Alignment explanation
Indices: 549718--549756 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 8
549708 TACACTTTAT
549718 TATAT-AA
1 TATATAAA
549725 TATATAACA
1 TATATAA-A
549734 TATATAATA
1 TATATAA-A
549743 TATATAAA
1 TATATAAA
549751 TATATA
1 TATATA
549757 TTGTAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 5 0.17
8 8 0.28
9 16 0.55
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (8 bp):
TATATAAA
Found at i:549822 original size:44 final size:45
Alignment explanation
Indices: 549772--549865 Score: 108
Period size: 44 Copynumber: 2.1 Consensus size: 45
549762 ATTATAATGG
549772 TAATATT-TAATATATAA-AAAT-CTAATATAAACTA-TATACTATATA
1 TAATATTGT-ATA-ATAATAAATACT-ATATAAA-TATTATACTATATA
*
549817 -AATATTGTATAATAATACATACTATATAAATATTATACTATATA
1 TAATATTGTATAATAATAAATACTATATAAATATTATACTATATA
549861 TAATA
1 TAATA
549866 CCATATCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
43 6 0.14
44 30 0.70
45 7 0.16
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (45 bp):
TAATATTGTATAATAATAAATACTATATAAATATTATACTATATA
Found at i:549866 original size:28 final size:30
Alignment explanation
Indices: 549807--549889 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 30
549797 TATAAACTAT
*
549807 ATACTATATAAATATTGTA-TA-ATAATAC
1 ATACTATATAAATATTATACTATATAATAC
549835 ATACTATATAAATATTATACTATAT-ATA-
1 ATACTATATAAATATTATACTATATAATAC
549863 ATACCATATCATATAATA-TATACTATA
1 ATA-C-TAT-ATA-AATATTATACTATA
549890 GAAAATAATG
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
28 21 0.44
29 6 0.12
30 5 0.10
31 12 0.25
32 4 0.08
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (30 bp):
ATACTATATAAATATTATACTATATAATAC
Found at i:552122 original size:72 final size:71
Alignment explanation
Indices: 552028--552324 Score: 348
Period size: 72 Copynumber: 4.2 Consensus size: 71
552018 ATTTTTTTTT
* * * * * *
552028 AGTGAGAC-ACAAATTTTTAAGGGAAATATCTCAAGTGAAATGAAAATTTGTTTTGAGAGAAACT
1 AGTGAGACAAAAAAATTTCAAGGGAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAACT
552092 GTCTCG
66 GTCTCG
* ** *
552098 AGTGAGACGAAAAAAATTTCAAGGGAAAATATCTCAAGTGAGATGTAATTTTAATTCGAGTGAAA
1 AGTGAGAC-AAAAAAATTTCAAGGG-AAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAA
* *
552163 TTGTCTCA
64 CTGTCTCG
* * *
552171 AGTGAGACAGAAAAATTTCAAAGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGTGAAAC
1 AGTGAGACAAAAAAATTTC-AAGGGAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAAC
*
552236 TTTCTCG
65 TGTCTCG
** * *
552243 AGTGAGAC-AAAATTTTTCAAGGGAATTATCTCAA-TAGAGATGAAATTTTGTTTCAAGAGAAAC
1 AGTGAGACAAAAAAATTTCAAGGGAAATATCTCAAGT-GAGATGAAATTTTGTTTCGAGAGAAAC
*
552306 TGTATCG
65 TGTCTCG
552313 AGTGAGACAAAA
1 AGTGAGACAAAA
552325 TTTTTCAAAG
Statistics
Matches: 192, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
69 1 0.01
70 60 0.31
71 10 0.05
72 71 0.37
73 50 0.26
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (71 bp):
AGTGAGACAAAAAAATTTCAAGGGAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAACT
GTCTCG
Found at i:552293 original size:70 final size:70
Alignment explanation
Indices: 552028--552338 Score: 365
Period size: 70 Copynumber: 4.4 Consensus size: 70
552018 ATTTTTTTTT
* * *
552028 AGTGAGACACAAATTTTT-AAGGGAAATATCTCAAGTGAAATGAAAATTTGTTTTGAGAGAAACT
1 AGTGAGACA-AAATTTTTCAAGGGAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAACT
552092 GTCTCG
65 GTCTCG
** * ** *
552098 AGTGAGACGAAAAAAATTTCAAGGGAAAATATCTCAAGTGAGATGTAATTTTAATTCGAGTGAAA
1 AGTGAGAC--AAAATTTTTCAAGGG-AAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAA
* *
552163 TTGTCTCA
63 CTGTCTCG
** * *
552171 AGTGAGACAGAAAAATTTCAAAGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGTGAAAC
1 AGTGAGACA-AAATTTTTC-AAGGGAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAAC
*
552236 TTTCTCG
64 TGTCTCG
* *
552243 AGTGAGACAAAATTTTTCAAGGGAATTATCTCAA-TAGAGATGAAATTTTGTTTCAAGAGAAACT
1 AGTGAGACAAAATTTTTCAAGGGAAATATCTCAAGT-GAGATGAAATTTTGTTTCGAGAGAAACT
*
552307 GTATCG
65 GTCTCG
*
552313 AGTGAGACAAAATTTTTCAAAGGAAA
1 AGTGAGACAAAATTTTTCAAGGGAAA
552339 ACCGTCTTGA
Statistics
Matches: 206, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
69 1 0.00
70 76 0.37
71 14 0.07
72 65 0.32
73 50 0.24
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (70 bp):
AGTGAGACAAAATTTTTCAAGGGAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAACTG
TCTCG
Found at i:552355 original size:142 final size:144
Alignment explanation
Indices: 552046--552369 Score: 359
Period size: 142 Copynumber: 2.2 Consensus size: 144
552036 ACAAATTTTT
* * * * *
552046 AAGGGAAATATCTCAAGTGAAATGAAAATTTGTTTTGAGAGAAACTGTCTCGAGTGAGACGAAAA
1 AAGGAAAACATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGAC-AAAA
* * * * *
552111 AAATTTCAAGGGAAAATATCTCAAGTGAGATGTAATTTTAATTCGAGTGAAATTGTCTCAAGTGA
65 AAATTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTAATTCAAGAGAAACTGTATCAAGTGA
552176 GACAGAAAAATTTCA
130 GACAGAAAAATTTCA
* * *
552191 AAGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGTGAAACTTTCTCGAGTGAGAC-AAAA
1 AAGGAAAACATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACAAAAA
** * ** *
552255 TTTTTCAAGGG-AATTATCTCAA-TAGAGATGAAATTTTGTTTCAAGAGAAACTGTATCGAGTGA
66 AATTTCAAGGGAAAATATCTCAAGT-GAGATGAAATTTTAATTCAAGAGAAACTGTATCAAGTGA
**
552318 GACA-AAATTTTTCA
130 GACAGAAAAATTTCA
* ** *
552332 AAGGAAAACCGTCTTGAGTGAGATAAAATTTTTGTTTC
1 AAGGAAAA-CATCTCAAGTGAGATGAAA-TTTTGTTTC
552370 AAGGAGATTG
Statistics
Matches: 152, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
141 17 0.11
142 59 0.39
143 22 0.14
145 54 0.36
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (144 bp):
AAGGAAAACATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACAAAAA
AATTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTAATTCAAGAGAAACTGTATCAAGTGAG
ACAGAAAAATTTCA
Found at i:557796 original size:114 final size:114
Alignment explanation
Indices: 557596--557823 Score: 456
Period size: 114 Copynumber: 2.0 Consensus size: 114
557586 GGTATAGAGC
557596 TTAAGATGTGTGCCTTTTCAAAAGCTGAAATTAATAGAAAATAATTAGTCCAGCTATTTATTTGA
1 TTAAGATGTGTGCCTTTTCAAAAGCTGAAATTAATAGAAAATAATTAGTCCAGCTATTTATTTGA
557661 GAAAAAAATATAATGAAAGGTAAATAAATGGATCAAACATAAATTAAAA
66 GAAAAAAATATAATGAAAGGTAAATAAATGGATCAAACATAAATTAAAA
557710 TTAAGATGTGTGCCTTTTCAAAAGCTGAAATTAATAGAAAATAATTAGTCCAGCTATTTATTTGA
1 TTAAGATGTGTGCCTTTTCAAAAGCTGAAATTAATAGAAAATAATTAGTCCAGCTATTTATTTGA
557775 GAAAAAAATATAATGAAAGGTAAATAAATGGATCAAACATAAATTAAAA
66 GAAAAAAATATAATGAAAGGTAAATAAATGGATCAAACATAAATTAAAA
557824 CATAAACTTA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (114 bp):
TTAAGATGTGTGCCTTTTCAAAAGCTGAAATTAATAGAAAATAATTAGTCCAGCTATTTATTTGA
GAAAAAAATATAATGAAAGGTAAATAAATGGATCAAACATAAATTAAAA
Found at i:560044 original size:30 final size:30
Alignment explanation
Indices: 560009--560072 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
559999 AGAAAAGTCT
* *
560009 AAAATACAAATAGTAAAACTTAATTAAGGA
1 AAAATACAAAGAATAAAACTTAATTAAGGA
**
560039 AAAATATGAAGAATAAAACTTAATTAAGGA
1 AAAATACAAAGAATAAAACTTAATTAAGGA
560069 AAAA
1 AAAA
560073 AAAGATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (30 bp):
AAAATACAAAGAATAAAACTTAATTAAGGA
Found at i:560530 original size:13 final size:13
Alignment explanation
Indices: 560512--560542 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
560502 AATTTCTCGC
*
560512 CCTTTTTTTCTCT
1 CCTTTTTTTCTAT
560525 CCTTTTTTTCTAT
1 CCTTTTTTTCTAT
560538 CCTTT
1 CCTTT
560543 CTGTGTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (13 bp):
CCTTTTTTTCTAT
Found at i:562983 original size:19 final size:20
Alignment explanation
Indices: 562959--563037 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
562949 ATTAAGCACT
* *
562959 TATGAATAGTTCTG-TACTA
1 TATGAATAGTACCGATACTA
* *
562978 TATGAACAGTACCGATACTG
1 TATGAATAGTACCGATACTA
* *
562998 TATGAATAGTATCGATACTG
1 TATGAATAGTACCGATACTA
* *
563018 TGTGAACAGTACCGATACTA
1 TATGAATAGTACCGATACTA
563038 AAAAACATCG
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
19 11 0.22
20 38 0.78
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (20 bp):
TATGAATAGTACCGATACTA
Found at i:563001 original size:20 final size:20
Alignment explanation
Indices: 562973--563036 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
562963 AATAGTTCTG
*
562973 TACTATATGAACAGTACCGA
1 TACTGTATGAACAGTACCGA
* *
562993 TACTGTATGAATAGTATCGA
1 TACTGTATGAACAGTACCGA
*
563013 TACTGTGTGAACAGTACCGA
1 TACTGTATGAACAGTACCGA
563033 TACT
1 TACT
563037 AAAAAACATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
TACTGTATGAACAGTACCGA
Found at i:563029 original size:40 final size:39
Alignment explanation
Indices: 562959--563036 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
562949 ATTAAGCACT
562959 TATGAATAGTTCTGTACTATATGAACAGTACCGATACTG
1 TATGAATAGTTCTGTACTATATGAACAGTACCGATACTG
* *
562998 TATGAATAGTATC-GATACTGTGTGAACAGTACCGATACT
1 TATGAATAGT-TCTG-TACTATATGAACAGTACCGATACT
563037 AAAAAACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 11 0.31
40 24 0.69
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (39 bp):
TATGAATAGTTCTGTACTATATGAACAGTACCGATACTG
Found at i:565048 original size:20 final size:19
Alignment explanation
Indices: 565007--565049 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
564997 AATAATTTGG
*
565007 TTTTGAAAACAAAAGTAGA
1 TTTTGAAAACAAAAGTAAA
565026 TTTTGAAAATCAAAA-TGAAA
1 TTTTGAAAA-CAAAAGT-AAA
565046 TTTT
1 TTTT
565050 ACAAAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (19 bp):
TTTTGAAAACAAAAGTAAA
Found at i:566198 original size:90 final size:91
Alignment explanation
Indices: 566091--566277 Score: 313
Period size: 91 Copynumber: 2.1 Consensus size: 91
566081 AAAGGGGGAG
* * *
566091 AAATATGAGTTTGAAAAATTCAATTTTATTAATGAAAAA-GGGGAGCTGAACATTTTTACATATT
1 AAATATGAGTTTAAAAAATTCAATTGTATTAATGAAAAAGGGGGAGCTGAACATTTTCACATATT
*
566155 TTCCAAAAATTGGTATCTTTTTCATT
66 TTCCAAAAATTAGTATCTTTTTCATT
*
566181 AAATATGAGTTTAAAAAATTCAATTGTATTAATGAAAAAGGGGGAGTTGAACATTTTCACATATT
1 AAATATGAGTTTAAAAAATTCAATTGTATTAATGAAAAAGGGGGAGCTGAACATTTTCACATATT
*
566246 TTCCAACAATTAGTATCTTTTTCATT
66 TTCCAAAAATTAGTATCTTTTTCATT
566272 AAATAT
1 AAATAT
566278 TTTATTAAGG
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 37 0.41
91 53 0.59
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (91 bp):
AAATATGAGTTTAAAAAATTCAATTGTATTAATGAAAAAGGGGGAGCTGAACATTTTCACATATT
TTCCAAAAATTAGTATCTTTTTCATT
Found at i:566506 original size:20 final size:20
Alignment explanation
Indices: 566467--566545 Score: 97
Period size: 20 Copynumber: 4.0 Consensus size: 20
566457 CAATATTTTT
* *
566467 TATGAATAGTACTG-TACTG
1 TATGAACAGTACCGATACTG
* *
566486 TATGAACAATATCGATACTG
1 TATGAACAGTACCGATACTG
* *
566506 TATGAATAGTACCGGTACTG
1 TATGAACAGTACCGATACTG
566526 TATGAACAGTACCGATACTG
1 TATGAACAGTACCGATACTG
566546 CTACAATTGT
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
19 10 0.20
20 39 0.80
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
TATGAACAGTACCGATACTG
Found at i:566512 original size:39 final size:40
Alignment explanation
Indices: 566467--566545 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
566457 CAATATTTTT
* *
566467 TATGAATAGTA-CTGTACTGTATGAACAATATCGATACTG
1 TATGAATAGTACCGGTACTGTATGAACAATACCGATACTG
*
566506 TATGAATAGTACCGGTACTGTATGAACAGTACCGATACTG
1 TATGAATAGTACCGGTACTGTATGAACAATACCGATACTG
566546 CTACAATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 11 0.31
40 25 0.69
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (40 bp):
TATGAATAGTACCGGTACTGTATGAACAATACCGATACTG
Found at i:566565 original size:40 final size:40
Alignment explanation
Indices: 566471--566565 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
566461 ATTTTTTATG
* * *
566471 AATAGTACTG-TACTGTATGAACAATATCGATACTGTATG
1 AATAGTACCGATACTGTATGAACAATACCGATACTGTATC
* *
566510 AATAGTACCGGTACTGTATGAACAGTACCGATACTGCTA-C
1 AATAGTACCGATACTGTATGAACAATACCGATACTG-TATC
* *
566550 AATTGTATCGATACTG
1 AATAGTACCGATACTG
566566 CTACAGTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 9 0.19
40 36 0.77
41 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (40 bp):
AATAGTACCGATACTGTATGAACAATACCGATACTGTATC
Found at i:566578 original size:20 final size:20
Alignment explanation
Indices: 566538--566578 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
566528 TGAACAGTAC
**
566538 CGATACTGCTACAATTGTAT
1 CGATACTGCTACAATAATAT
*
566558 CGATACTGCTACAGTAATAT
1 CGATACTGCTACAATAATAT
566578 C
1 C
566579 AAGCCCAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (20 bp):
CGATACTGCTACAATAATAT
Found at i:569496 original size:33 final size:33
Alignment explanation
Indices: 569435--569498 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
569425 AAGGGGTTTT
* * *
569435 GGTTCTAGCTGAGCATGTGAAAAGCTAGGGAAA
1 GGTTCTAGCTGAGCACGTAAAAAACTAGGGAAA
* *
569468 GGTTCTAGTTTAGCACGTAAAAAACTAGGGA
1 GGTTCTAGCTGAGCACGTAAAAAACTAGGGA
569499 GTTTGTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.23
Consensus pattern (33 bp):
GGTTCTAGCTGAGCACGTAAAAAACTAGGGAAA
Found at i:569778 original size:27 final size:27
Alignment explanation
Indices: 569732--569783 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
569722 TCTGCAAATC
* *
569732 CCAACAATTTTATATTTAATTATTTGA
1 CCAACAATTTTATATCTAATGATTTGA
569759 CCAA-AATTTTATATACTAATGATTT
1 CCAACAATTTTATAT-CTAATGATTT
569784 TGTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (27 bp):
CCAACAATTTTATATCTAATGATTTGA
Found at i:575151 original size:21 final size:21
Alignment explanation
Indices: 575105--575175 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
575095 AATTGTAACA
* **
575105 AAGGGATCGATCATTTTTATTG
1 AAGGGATCGATC-CTTTTGGTG
575127 -AGGGATCGATCCTTTTGGTG
1 AAGGGATCGATCCTTTTGGTG
575147 AAGGGATCGATCCTTTTGGTG
1 AAGGGATCGATCCTTTTGGTG
575168 AAGGGATC
1 AAGGGATC
575176 AATACCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 6 0.13
21 39 0.87
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.34
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTGGTG
Found at i:579344 original size:11 final size:11
Alignment explanation
Indices: 579302--579376 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
579292 TCGAAACTCG
579302 AGCTCGATTCA
1 AGCTCGATTCA
* **
579313 AGCTCAATTGTG
1 AGCTCGATT-CA
*
579325 AGCTTGATTCA
1 AGCTCGATTCA
**
579336 AGCTCGATTGTG
1 AGCTCGATT-CA
579348 AGCTCGATTCA
1 AGCTCGATTCA
579359 AGCTCGACTT-A
1 AGCTCGA-TTCA
579370 AGCTCGA
1 AGCTCGA
579377 GGATGGGTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
11 31 0.63
12 18 0.37
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:579364 original size:23 final size:23
Alignment explanation
Indices: 579301--579365 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
579291 CTCGAAACTC
*
579301 GAGCTCGATTCAAGCTCAATTGT
1 GAGCTCGATTCAAGCTCGATTGT
*
579324 GAGCTTGATTCAAGCTCGATTGT
1 GAGCTCGATTCAAGCTCGATTGT
579347 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTCAAGCTCGA
579366 CTTAAGCTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTGT
Found at i:579632 original size:18 final size:18
Alignment explanation
Indices: 579609--579648 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
579599 ATCTTGCTAA
579609 TCTTTTCTCGTTTCATAT
1 TCTTTTCTCGTTTCATAT
579627 TCTTTTCTCGTTTCATAT
1 TCTTTTCTCGTTTCATAT
579645 TCTT
1 TCTT
579649 CTATCGTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.23, G:0.05, T:0.62
Consensus pattern (18 bp):
TCTTTTCTCGTTTCATAT
Found at i:579655 original size:18 final size:18
Alignment explanation
Indices: 579616--579655 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
579606 TAATCTTTTC
* *
579616 TCGTTTCATATTCTTTTC
1 TCGTTTCATATTCTTCTA
579634 TCGTTTCATATTCTTCTA
1 TCGTTTCATATTCTTCTA
579652 TCGT
1 TCGT
579656 CTCCATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.07, T:0.57
Consensus pattern (18 bp):
TCGTTTCATATTCTTCTA
Found at i:581494 original size:7 final size:7
Alignment explanation
Indices: 581450--581657 Score: 113
Period size: 7 Copynumber: 29.9 Consensus size: 7
581440 GTGCATAACT
581450 TAAACCC
1 TAAACCC
*
581457 TAAACTC
1 TAAACCC
581464 T-AACCC
1 TAAACCC
581470 T-AACTCC
1 TAAAC-CC
*
581477 T-AACACA
1 TAAAC-CC
581484 TAAACCC
1 TAAACCC
581491 TAAACCC
1 TAAACCC
581498 TAAACCC
1 TAAACCC
* *
581505 T-ATCACA
1 TAAAC-CC
581512 TAAACCC
1 TAAACCC
*
581519 TAAGCCC
1 TAAACCC
*
581526 TAAACAC
1 TAAACCC
*
581533 TGAACCC
1 TAAACCC
581540 TAAACCC
1 TAAACCC
581547 TAAACCC
1 TAAACCC
*
581554 TAAATCC
1 TAAACCC
* *
581561 T-ATCACA
1 TAAAC-CC
*
581568 TAAACTC
1 TAAACCC
581575 TAAACCC
1 TAAACCC
* *
581582 TAAATCT
1 TAAACCC
581589 TAAACCC
1 TAAACCC
* *
581596 TAAATCT
1 TAAACCC
* *
581603 TAAATCA
1 TAAACCC
* *
581610 T-ATCACA
1 TAAAC-CC
**
581617 TAAACTA
1 TAAACCC
**
581624 TAAACTA
1 TAAACCC
581631 TAAACCC
1 TAAACCC
*
581638 TAAACTC
1 TAAACCC
581645 TAAACCC
1 TAAACCC
581652 TAAACC
1 TAAACC
581658 TGATCACATA
Statistics
Matches: 155, Mismatches: 38, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
6 12 0.08
7 134 0.86
8 9 0.06
ACGTcount: A:0.44, C:0.34, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:581586 original size:28 final size:28
Alignment explanation
Indices: 581457--581587 Score: 151
Period size: 28 Copynumber: 4.7 Consensus size: 28
581447 ACTTAAACCC
* *
581457 TAAACTCT-AACCCTAACTCCTAACACA
1 TAAACCCTAAACCCTAAATCCTAACACA
* *
581484 TAAACCCTAAACCCTAAACCCTATCACA
1 TAAACCCTAAACCCTAAATCCTAACACA
* *
581512 TAAACCCTAAGCCCTAAA-CACTGAAC-CC
1 TAAACCCTAAACCCTAAATC-CT-AACACA
*
581540 TAAACCCTAAACCCTAAATCCTATCACA
1 TAAACCCTAAACCCTAAATCCTAACACA
*
581568 TAAACTCTAAACCCTAAATC
1 TAAACCCTAAACCCTAAATC
581588 TTAAACCCTA
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
27 10 0.11
28 75 0.85
29 3 0.03
ACGTcount: A:0.42, C:0.37, G:0.02, T:0.20
Consensus pattern (28 bp):
TAAACCCTAAACCCTAAATCCTAACACA
Found at i:581664 original size:49 final size:49
Alignment explanation
Indices: 581535--581668 Score: 171
Period size: 49 Copynumber: 2.7 Consensus size: 49
581525 CTAAACACTG
* *
581535 AACCCTAAACCCTAAACCCTAAATCCTATCACATAAACTCTAAACCCTA
1 AACCCTAAACCCTAAACCCTAAATCCTATCACATAAACTATAAACCATA
* * * * * *
581584 AATCTTAAACCCTAAATCTTAAATCATATCACATAAACTATAAACTATA
1 AACCCTAAACCCTAAACCCTAAATCCTATCACATAAACTATAAACCATA
*
581633 AACCCTAAACTCTAAACCCTAAA-CCTGATCACATAA
1 AACCCTAAACCCTAAACCCTAAATCCT-ATCACATAA
581669 TTAGAAGGAA
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
48 2 0.03
49 68 0.97
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.24
Consensus pattern (49 bp):
AACCCTAAACCCTAAACCCTAAATCCTATCACATAAACTATAAACCATA
Found at i:582066 original size:14 final size:14
Alignment explanation
Indices: 582049--582089 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
582039 TTTATTCATC
582049 AATAATGTATTTTT
1 AATAATGTATTTTT
582063 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
582074 AATAATGTAATTTT
1 AATAATGTATTTTT
582088 AA
1 AA
582090 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:585250 original size:54 final size:54
Alignment explanation
Indices: 585175--585352 Score: 230
Period size: 54 Copynumber: 3.3 Consensus size: 54
585165 GTACACCCCT
* * *
585175 TGCCAATACCGAAATTCATAAACTTATTATAAATTTCTTAGTTTGCACACATAG
1 TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
* * *
585229 TGCCAATAAGGAAATTTATAAACTTATTATGAATTTCTTAGGTTGCATACATAG
1 TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
* ** * * *
585283 AGAAAATACGAAAATTCATAAACTTATTATGCATTTCTTAGGTTGAACACATAG
1 TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
* *
585337 TGTCAATATGGAAATT
1 TGCCAATACGGAAATT
585353 ACAATATATA
Statistics
Matches: 104, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (54 bp):
TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
Found at i:585839 original size:20 final size:22
Alignment explanation
Indices: 585793--585839 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
585783 TCGATACCCA
585793 CATC-AGTATCGATACTGATTG
1 CATCTAGTATCGATACTGATTG
585814 CA--TAGTATCGATACTG-TT-
1 CATCTAGTATCGATACTGATTG
585832 CATCTAGT
1 CATCTAGT
585840 TTCTTCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 2 0.09
19 2 0.09
20 17 0.74
21 2 0.09
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (22 bp):
CATCTAGTATCGATACTGATTG
Found at i:589439 original size:23 final size:21
Alignment explanation
Indices: 589383--589478 Score: 84
Period size: 23 Copynumber: 4.3 Consensus size: 21
589373 TCGAGGGTTC
* *
589383 TATGCGGTCCTTCGGGATAATT
1 TATGTGGTCCTTCGGGA-CATT
*
589405 CTACGTGGTCCTTCGGGACATT
1 -TATGTGGTCCTTCGGGACATT
* * *
589427 TATGTGCGATCCTTTGAGACATA
1 TATGTG-G-TCCTTCGGGACATT
*
589450 TATGTGGTTCTTCGGGACATT
1 TATGTGGTCCTTCGGGACATT
589471 CTATGTGG
1 -TATGTGG
589479 CACTTCGATG
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
21 15 0.25
22 12 0.20
23 32 0.54
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATT
Found at i:589911 original size:14 final size:15
Alignment explanation
Indices: 589892--589921 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
589882 TGATTTATGC
589892 TATATG-TATTTTGT
1 TATATGTTATTTTGT
589906 TATATGTTATTTTGT
1 TATATGTTATTTTGT
589921 T
1 T
589922 GGCATGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (15 bp):
TATATGTTATTTTGT
Found at i:591219 original size:15 final size:15
Alignment explanation
Indices: 591199--591230 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
591189 TATAATCAAG
591199 GTTAAGCTAAACAGT
1 GTTAAGCTAAACAGT
591214 GTTAAGCTAAACAGT
1 GTTAAGCTAAACAGT
591229 GT
1 GT
591231 CAGCATTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (15 bp):
GTTAAGCTAAACAGT
Found at i:597176 original size:15 final size:16
Alignment explanation
Indices: 597156--597190 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
597146 AATTTCCACT
597156 ATGTTTT-AAAAGTTA
1 ATGTTTTGAAAAGTTA
597171 ATGTTTTGAAAAGTTA
1 ATGTTTTGAAAAGTTA
597187 ATGT
1 ATGT
597191 GACACCTCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (16 bp):
ATGTTTTGAAAAGTTA
Found at i:601428 original size:54 final size:54
Alignment explanation
Indices: 601305--601428 Score: 203
Period size: 54 Copynumber: 2.3 Consensus size: 54
601295 GCACACTCAT
* *
601305 TGCCAATATGGAAATTCATAAACTTATTATGGATTTCTTAGGTTGCACACATAG
1 TGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAGATTGCACACATAG
* * *
601359 TGCTAATACGAAAATTCATAAACTTATTATGAATTTCTTAGATTGCACACATAG
1 TGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAGATTGCACACATAG
601413 TGCCAATATGGAAATT
1 TGCCAATATGGAAATT
601429 ACAATATATA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (54 bp):
TGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAGATTGCACACATAG
Found at i:604758 original size:25 final size:25
Alignment explanation
Indices: 604730--604779 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
604720 ATAAAAACCC
*
604730 TAAATAAA-AACTAAATAATAATAAA
1 TAAATAAATAAAT-AATAATAATAAA
*
604755 TAAATAAATAAATTATAATAATAAA
1 TAAATAAATAAATAATAATAATAAA
604780 GGAATAATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (25 bp):
TAAATAAATAAATAATAATAATAAA
Found at i:604772 original size:22 final size:21
Alignment explanation
Indices: 604730--604779 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
604720 ATAAAAACCC
*
604730 TAAATAAAAACTAAATAATAA
1 TAAATAAAAAATAAATAATAA
*
604751 TAAATAAATAAATAAATTATAA
1 TAAATAAA-AAATAAATAATAA
604773 T-AATAAA
1 TAAATAAA
604780 GGAATAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAATAAAAAATAAATAATAA
Done.