Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 99 of 120
Found at i:28495599 original size:85 final size:85
Alignment explanation
Indices: 28495450--28495684 Score: 303
Period size: 85 Copynumber: 2.8 Consensus size: 85
28495440 AAACGTCGCT
* * * * *
28495450 CTTTCCTCACAAACGCAACTAAAGAACATGGTCTTTAGTGGCGTTTTTCTCACAAACGCCGCTAA
1 CTTTTCTCACAAATGCAACTAAAG-ACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAA
*
28495515 AGAACATGGTCTTTAGC-AGCG
65 AGAACATGATCTTTAGCGA-CG
* * * *
28495536 CTTTTCTCACAAATGTC-ACTAAAGACATGGTCTTTAACGGTGCTTTTCCCACAAATGTCGCTAA
1 CTTTTCTCACAAATG-CAACTAAAGACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAA
28495600 AGAACATGATCTTTAGCGACG
65 AGAACATGATCTTTAGCGACG
* ** *
28495621 CTTTTCGCACAAATGCTGCTAAAGACATGGTCTTTAGCGACGCTTTTCCCACAAACGCCGCTAA
1 CTTTTCTCACAAATGCAACTAAAGACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAA
28495685 TATTAACAGA
Statistics
Matches: 129, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 106 0.82
86 21 0.16
87 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (85 bp):
CTTTTCTCACAAATGCAACTAAAGACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
GAACATGATCTTTAGCGACG
Found at i:28497537 original size:41 final size:41
Alignment explanation
Indices: 28497450--28497653 Score: 179
Period size: 41 Copynumber: 5.0 Consensus size: 41
28497440 TTTAATAAAC
* * * *
28497450 TAGCGACGCTTATGGGAAACGCT-GCTATTGCT-TAACCTT
1 TAGCGGCGCTTATCGGAAACGCTCGCTAATGCTCTGACCTT
*
28497489 TAGCGGCGCTTATGGGAAA-GCATCGCTAATGCTCTGACCTT
1 TAGCGGCGCTTATCGGAAACGC-TCGCTAATGCTCTGACCTT
**
28497530 TAGCGGCGCTT-TCCCATAAACG-TCGCTAATGCTCTGACCTT
1 TAGCGGCGCTTAT--CGGAAACGCTCGCTAATGCTCTGACCTT
** **
28497571 TAGCGGCGCTTCCCATAAACGC-CGCTAATGCTCTGACCTT
1 TAGCGGCGCTTATCGGAAACGCTCGCTAATGCTCTGACCTT
* * ** *
28497611 TAGCGACGCTTTCTCATAAACGC-CGCTAATGTTCTGACCTT
1 TAGCGGCGC-TTATCGGAAACGCTCGCTAATGCTCTGACCTT
28497652 TA
1 TA
28497654 ATGACGTTTT
Statistics
Matches: 146, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 19 0.13
40 43 0.29
41 78 0.53
42 3 0.02
43 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
TAGCGGCGCTTATCGGAAACGCTCGCTAATGCTCTGACCTT
Found at i:28497597 original size:40 final size:41
Alignment explanation
Indices: 28497512--28497699 Score: 245
Period size: 41 Copynumber: 4.6 Consensus size: 41
28497502 GGGAAAGCAT
*
28497512 CGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCATAAACGT
1 CGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCATAAACGC
28497553 CGCTAATGCTCTGACCTTTAGCGGCGC-TTCCCATAAACGC
1 CGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCATAAACGC
* *
28497593 CGCTAATGCTCTGACCTTTAGCGACGCTTTCTCATAAACGC
1 CGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCATAAACGC
* ** * * *
28497634 CGCTAATGTTCTGACCTTTAATGACGTTTTTCCTATAAACGC
1 CGCTAATGCTCTGACCTTTAGCGGCG-CTTTCCCATAAACGC
* * *
28497676 CGCTATTGCT-TTACCTTTTGCGGC
1 CGCTAATGCTCTGACCTTTAGCGGC
28497700 ATTTATGCAA
Statistics
Matches: 129, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
40 38 0.29
41 71 0.55
42 20 0.16
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (41 bp):
CGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCATAAACGC
Found at i:28497858 original size:21 final size:23
Alignment explanation
Indices: 28497812--28497862 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
28497802 ATAAATATTT
*
28497812 AATATAAATGTTTTATAGTATAA
1 AATATGAATGTTTTATAGTATAA
28497835 AATATGAAT-TTTTACTA-TAT-A
1 AATATGAATGTTTTA-TAGTATAA
28497856 AATATGA
1 AATATGA
28497863 TTATTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 8 0.31
23 10 0.38
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (23 bp):
AATATGAATGTTTTATAGTATAA
Found at i:28502335 original size:10 final size:10
Alignment explanation
Indices: 28502322--28502352 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
28502312 TTAAATTTTT
28502322 TTAAAAATAA
1 TTAAAAATAA
28502332 TTAAAAATAA
1 TTAAAAATAA
28502342 TTAAAAATAA
1 TTAAAAATAA
28502352 T
1 T
28502353 GTAGTGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:28506654 original size:74 final size:74
Alignment explanation
Indices: 28506562--28506713 Score: 286
Period size: 74 Copynumber: 2.1 Consensus size: 74
28506552 GATACCTAAG
* *
28506562 TGAAGTATACAAGCATCATCGTGTATTTTATATTAAACTCATATTTTATTAATTTTCAATAACAA
1 TGAAGTATACAAGCATCATAGTGTATTTTATATTAAACTCATATTTTATCAATTTTCAATAACAA
28506627 TATTTAATA
66 TATTTAATA
28506636 TGAAGTATACAAGCATCATAGTGTATTTTATATTAAACTCATATTTTATCAATTTTCAATAACAA
1 TGAAGTATACAAGCATCATAGTGTATTTTATATTAAACTCATATTTTATCAATTTTCAATAACAA
28506701 TATTTAATA
66 TATTTAATA
28506710 TGAA
1 TGAA
28506714 TTAAGTTTTA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (74 bp):
TGAAGTATACAAGCATCATAGTGTATTTTATATTAAACTCATATTTTATCAATTTTCAATAACAA
TATTTAATA
Found at i:28506782 original size:25 final size:27
Alignment explanation
Indices: 28506739--28506794 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 27
28506729 TTTTATTTTT
28506739 TATATATAATACTAGATATATG-AACAA
1 TATATATAATACTAGATATATGCAA-AA
*
28506766 TATATAT-ATA-TATATATATGCAAAA
1 TATATATAATACTAGATATATGCAAAA
28506791 TATA
1 TATA
28506795 AAAATCATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 15 0.56
26 5 0.19
27 7 0.26
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (27 bp):
TATATATAATACTAGATATATGCAAAA
Found at i:28521673 original size:22 final size:23
Alignment explanation
Indices: 28521633--28521685 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
28521623 CGCCATTATT
* *
28521633 ATTTTTAAAATATTTTATAATTA
1 ATTTTTAAAATAGTATATAATTA
*
28521656 ATTTTTAAAA-AGTATATAATTT
1 ATTTTTAAAATAGTATATAATTA
*
28521678 ATTATTAA
1 ATTTTTAA
28521686 TAGTAATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTTAAAATAGTATATAATTA
Found at i:28524035 original size:24 final size:25
Alignment explanation
Indices: 28523981--28524037 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
28523971 TATTTTTATA
* **
28523981 GAATAATATTTGATGTATTTTCGGT
1 GAATAATATTTGATGTATTATCAAT
* *
28524006 GTATAA-ATTTTATGTATTATCAAT
1 GAATAATATTTGATGTATTATCAAT
28524030 GAATAATA
1 GAATAATA
28524038 ACATAACACA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.46
Consensus pattern (25 bp):
GAATAATATTTGATGTATTATCAAT
Found at i:28525458 original size:81 final size:81
Alignment explanation
Indices: 28525318--28526910 Score: 2528
Period size: 81 Copynumber: 19.7 Consensus size: 81
28525308 TTTGTTCCGA
* *
28525318 AATCA-AATGTTTTGTGAAAGTAAGCTGTCGAATATTTGTCTTCCAAACCCTTCATTTCTTTCCC
1 AATCAGAA-GTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCC
28525382 TTCGCCATGGCTTTCAG
65 TTCGCCATGGCTTTCAG
* * * * * * *
28525399 AATCAGAAGTTTTGTGCAAGTAAAGAT-TTGCATATTTATCTTCCAAATCCTTCACTTCTTTCTC
1 AATCAGAAGTTTTGTGAAAGT-AAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCC
*
28525463 TTCGCCATGGCATTCAG
65 TTCGCCATGGCTTTCAG
* * **** * * * *
28525480 AATCAGAAGTTTTATGGAAGTAAAAACTAGCATATTTATCTTCCAAACCCTTCACTTTTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28525545 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
28525561 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28525626 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
*
28525642 AATCAGAAGTTTTGTGAAAGTAAGCTGCGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28525707 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
*
28525723 AATCAGAAGTTTTGTGAAAGTAAGCTGCGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28525788 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
* * * *
28525804 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATCTGTCTTCCAAACCCTTCATTTCCTTCCGT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28525869 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
*
28525885 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTACCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28525950 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
28525966 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
*
28526031 TCGCCATGGATTTCAG
66 TCGCCATGGCTTTCAG
* * *
28526047 AATCAGAAGTTTTGTGAAAGTAAGCTATGGAATATCTGTCTTCCAAACCCTTCATTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28526112 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
* * * * * * *
28526128 AATCAGAAGTTTTGTGCAAGTAAAGAT-TTGCATATTTATCTTCCAAATCCTTCACTTCTTTCTC
1 AATCAGAAGTTTTGTGAAAGT-AAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCC
*
28526192 TTCGCCATGGCATTCAG
65 TTCGCCATGGCTTTCAG
* * **** * * * *
28526209 AATCAGAAGTTTTATGGAAGTAAAAACTAGCATATTTATCTTCCAAACCCTTCACTTTTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28526274 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
28526290 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28526355 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
*
28526371 AATCAGAAGTTTTGTGAAAGTAAGCTGCGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28526436 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
28526452 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28526517 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
* * * *
28526533 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATCTGTCTTCCAAACCCTTCATTTCCTTCCGT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28526598 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
*
28526614 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTACCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28526679 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
28526695 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
*
28526760 TCGCCATGGATTTCAG
66 TCGCCATGGCTTTCAG
* * * *
28526776 AATCAGAAGTTTTGTGAAAGTAAGCTATGGAATATCTGTCTTCCAAACCCTTCATTTCCTTCCCT
1 AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
28526841 TCGCCATGGCTTTCAG
66 TCGCCATGGCTTTCAG
* * * * *
28526857 AATCAGAAGTTTTGTGGAAGTAAAGAT-TAGCATATTTTTCTTCCAAATCCCTTC
1 AATCAGAAGTTTTGTGAAAGT-AAGCTGTGGAATATTTGTCTTCCAAA-CCCTTC
28526911 CTGCATTGCC
Statistics
Matches: 1407, Mismatches: 98, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
80 6 0.00
81 1381 0.98
82 20 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (81 bp):
AATCAGAAGTTTTGTGAAAGTAAGCTGTGGAATATTTGTCTTCCAAACCCTTCACTTCTTTCCCT
TCGCCATGGCTTTCAG
Found at i:28531608 original size:3 final size:3
Alignment explanation
Indices: 28531600--28531633 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28531590 CTTTCTGTAT
28531600 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28531634 CTTTTATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28533837 original size:14 final size:14
Alignment explanation
Indices: 28533820--28533850 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28533810 TAAGTGTTGG
28533820 AAAAATAAATATTA
1 AAAAATAAATATTA
*
28533834 AAAAATAAGTATTA
1 AAAAATAAATATTA
28533848 AAA
1 AAA
28533851 TTAAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAATAAATATTA
Found at i:28541929 original size:77 final size:77
Alignment explanation
Indices: 28541802--28541955 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
28541792 AAGGCACGTC
28541802 AAAATGCCATTGATAGTTTTTGCAATGGTCGAGATGCACAAATTTGATTGTGAGTGATGTAACGA
1 AAAATGCCATTGATAGTTTTTGCAATGGTCGAGATGCACAAATTTGATTGTGAGTGATGTAACGA
28541867 TCCTACAAAGCA
66 TCCTACAAAGCA
28541879 AAAATGCCATTGATAGTTTTTGCAATGGTCGAGATGCACAAATTTGATTGTGAGTGATGTAACGA
1 AAAATGCCATTGATAGTTTTTGCAATGGTCGAGATGCACAAATTTGATTGTGAGTGATGTAACGA
28541944 TCCTACAAAGCA
66 TCCTACAAAGCA
28541956 CGCTTTGTGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (77 bp):
AAAATGCCATTGATAGTTTTTGCAATGGTCGAGATGCACAAATTTGATTGTGAGTGATGTAACGA
TCCTACAAAGCA
Found at i:28543761 original size:3 final size:3
Alignment explanation
Indices: 28543755--28543784 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28543745 TTTATTATTA
*
28543755 TTG TTG TTG TTG ATG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
28543785 ATATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.63
Consensus pattern (3 bp):
TTG
Found at i:28547633 original size:6 final size:6
Alignment explanation
Indices: 28547622--28547647 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28547612 AGTTGTCGAT
28547622 GAAGAG GAAGAG GAAGAG GAAGAG GA
1 GAAGAG GAAGAG GAAGAG GAAGAG GA
28547648 TGATGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:28555623 original size:6 final size:6
Alignment explanation
Indices: 28555602--28555635 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
28555592 GTCGATGAAA
28555602 AGGAAG ACGG-AG AGGAAG AGGAAG AGGAAG AGGA
1 AGGAAG A-GGAAG AGGAAG AGGAAG AGGAAG AGGA
28555636 TGATGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.08
6 22 0.85
7 2 0.08
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGAAG
Found at i:28557177 original size:180 final size:179
Alignment explanation
Indices: 28556875--28557220 Score: 484
Period size: 180 Copynumber: 1.9 Consensus size: 179
28556865 ATTGGGACCT
** * * * *
28556875 TCTTTTGACTGGTGGCATTTTCATCATGAAGCTTTCTTTTATATTTTAGAAAATGATTAAATTTT
1 TCTTTTGACACGTGACACTTTCATCATGAAGCTTTCCTTTACATTTTAGAAAATGATTAAATTTT
* * * * *
28556940 AGTTTTAGTCTTTATATGTTTAAATTTAGTTTTTACTTTATACTTTAATTTCTAATATAATTTGG
66 AGTTTTAGTCTTTATATGTTTAAATTGAGTATTTACTCTATACTTCAATTTCTAATATAATATGG
* *
28557005 TTTTTATATTTTATAATGTT-AATAGTTAATATCGTTAATTTTTATTTC
131 TCTCTATATTTTATAATGTTCAATAGTTAATATCGTTAATTTTTATTTC
*
28557053 TCTTTTGACACGTGACACTTTCATCAT-AAGCTTTCCTTTACATTTTAGAAAAT-AGTTAAGTTT
1 TCTTTTGACACGTGACACTTTCATCATGAAGCTTTCCTTTACATTTTAGAAAATGA-TTAAATTT
*
28557116 TAGTTTTGGTCCTTCTATTATGTTTAAATATGA-TATTTACTCTATACTTCAATTTCTAATATAA
65 TAGTTTTAGT-CTT-TA-TATGTTTAAAT-TGAGTATTTACTCTATACTTCAATTTCTAATATAA
28557180 TATGGTCTCTATATTTTATAATGTTCAATAGTTAATATCGT
126 TATGGTCTCTATATTTTATAATGTTCAATAGTTAATATCGT
28557221 GAAATATAAT
Statistics
Matches: 147, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
176 1 0.01
177 40 0.27
178 26 0.18
179 2 0.01
180 61 0.41
181 17 0.12
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (179 bp):
TCTTTTGACACGTGACACTTTCATCATGAAGCTTTCCTTTACATTTTAGAAAATGATTAAATTTT
AGTTTTAGTCTTTATATGTTTAAATTGAGTATTTACTCTATACTTCAATTTCTAATATAATATGG
TCTCTATATTTTATAATGTTCAATAGTTAATATCGTTAATTTTTATTTC
Found at i:28557688 original size:19 final size:18
Alignment explanation
Indices: 28557665--28557703 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
28557655 AAAATTACCA
28557665 AAAAATTTCAAAATATTTAT
1 AAAAA-TTCAAAAT-TTTAT
*
28557685 AAAAATTCCAAATTTTAT
1 AAAAATTCAAAATTTTAT
28557703 A
1 A
28557704 TTATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTCAAAATTTTAT
Found at i:28561582 original size:19 final size:19
Alignment explanation
Indices: 28561558--28561595 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
28561548 TTGAAAAGAA
28561558 AAAAGCCACA-AATAAATAG
1 AAAAGCCACAGAA-AAATAG
28561577 AAAAGCCACAGAAAAATAG
1 AAAAGCCACAGAAAAATAG
28561596 TACATACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.63, C:0.16, G:0.13, T:0.08
Consensus pattern (19 bp):
AAAAGCCACAGAAAAATAG
Found at i:28562837 original size:45 final size:44
Alignment explanation
Indices: 28562786--28562871 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
28562776 AATATAGATA
* *
28562786 AGAAAAAAAAAGCTATGTGGAAGCAATCACAACCAAAGAAAAATT
1 AGAAAAAAAAAGCAATGTGGAAGCAACCACAACC-AAGAAAAATT
** *
28562831 AGAAAAAGGAAGCAATGTGGAAGTAACCACAACCAAGAAAA
1 AGAAAAAAAAAGCAATGTGGAAGCAACCACAACCAAGAAAA
28562872 GAAGCCATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 7 0.19
45 29 0.81
ACGTcount: A:0.57, C:0.14, G:0.19, T:0.10
Consensus pattern (44 bp):
AGAAAAAAAAAGCAATGTGGAAGCAACCACAACCAAGAAAAATT
Found at i:28563790 original size:15 final size:15
Alignment explanation
Indices: 28563770--28563799 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28563760 GTTGCTTTCC
28563770 TTTCTTTCTTTCTTT
1 TTTCTTTCTTTCTTT
*
28563785 TTTCTTTTTTTCTTT
1 TTTCTTTCTTTCTTT
28563800 AGTAAGACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTCTTTCTTT
Found at i:28571686 original size:16 final size:17
Alignment explanation
Indices: 28571655--28571696 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
28571645 AATTATAAAA
*
28571655 AAAATAAAAGATTTTCC
1 AAAATAATAGATTTTCC
*
28571672 AAAATAATA-ATTTTCG
1 AAAATAATAGATTTTCC
28571688 AAAACTAAT
1 AAAA-TAAT
28571697 TAATGATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (17 bp):
AAAATAATAGATTTTCC
Found at i:28571774 original size:15 final size:16
Alignment explanation
Indices: 28571739--28571775 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28571729 CTTTAAACTT
28571739 TTTTAAATATATATGG
1 TTTTAAATATATATGG
28571755 TTTTAAAT-T-TATGTG
1 TTTTAAATATATATG-G
28571770 TTTTAA
1 TTTTAA
28571776 CATGAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 8 0.40
16 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTTAAATATATATGG
Found at i:28573052 original size:7 final size:7
Alignment explanation
Indices: 28573040--28573064 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28573030 TGGCAACACC
28573040 AACCCTA
1 AACCCTA
28573047 AACCCTA
1 AACCCTA
28573054 AACCCTA
1 AACCCTA
28573061 AACC
1 AACC
28573065 TCCATACCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:28576977 original size:18 final size:18
Alignment explanation
Indices: 28576954--28576996 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28576944 GTTCAAGGTA
28576954 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
28576972 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
28576990 TAATTAA
1 TAATTAA
28576997 AAACCTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:28587620 original size:33 final size:33
Alignment explanation
Indices: 28587578--28587642 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
28587568 TCATCATTAC
*
28587578 CGTTGTTTTTACATTAATTACAAATAAACGCAT
1 CGTTATTTTTACATTAATTACAAATAAACGCAT
28587611 CGTTATTTTTACATTAATTACAAATAAACGCA
1 CGTTATTTTTACATTAATTACAAATAAACGCA
28587643 CTGTTCATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (33 bp):
CGTTATTTTTACATTAATTACAAATAAACGCAT
Found at i:28589554 original size:19 final size:17
Alignment explanation
Indices: 28589529--28589576 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 17
28589519 GAAAGGTTAT
28589529 AAAGGAGAAAAGCAAAAA
1 AAAGGAGAAAAG-AAAAA
28589547 AGAAGGAGAGAAAAGAAAAA
1 A-AA-G-GAGAAAAGAAAAA
28589567 AAAGGA-AAAA
1 AAAGGAGAAAA
28589577 TTACAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 4 0.15
17 2 0.07
18 2 0.07
19 4 0.15
20 7 0.26
21 8 0.30
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (17 bp):
AAAGGAGAAAAGAAAAA
Found at i:28589559 original size:21 final size:19
Alignment explanation
Indices: 28589533--28589572 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
28589523 GGTTATAAAG
28589533 GAGAAAAGCAAAAAAGAAGGA
1 GAGAAAAG-AAAAAA-AAGGA
28589554 GAGAAAAGAAAAAAAAGGA
1 GAGAAAAGAAAAAAAAGGA
28589573 AAAATTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 8 0.42
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (19 bp):
GAGAAAAGAAAAAAAAGGA
Found at i:28592719 original size:30 final size:29
Alignment explanation
Indices: 28592678--28593000 Score: 277
Period size: 30 Copynumber: 10.8 Consensus size: 29
28592668 ACCGAGGTCA
* * *
28592678 AAAATGAAATTTTGGAAGGTTTGGGGGTTT
1 AAAATGTAATTTTGGAAAGTTTTGGGG-TT
* *
28592708 AAAATGTAATTTTGTAAAAGTTTTGGGGTC
1 AAAATGTAATTTTG-GAAAGTTTTGGGGTT
** *
28592738 AAAATGTAACATTGGAAAAGTTTTTAGGGTT
1 AAAATGTAATTTTGG-AAAG-TTTTGGGGTT
*
28592769 AAAATGTAATATTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGG-AAAGTTTTGGGGTT
* *
28592799 AAAATGTAATTTTGGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGG-AAAGTTTTGGGGTT
* * * *
28592829 AAATTATAATTTTGGAAAAGTTTTGAGGCT
1 AAAATGTAATTTTGG-AAAGTTTTGGGGTT
** *
28592859 AAAATGTAATTTTGGAAAAATTTAGGGTT
1 AAAATGTAATTTTGGAAAGTTTTGGGGTT
* * * *
28592888 AAAATGTAATTTTAGAAAAGTTTTAGTGTC
1 AAAATGTAATTTT-GGAAAGTTTTGGGGTT
* *
28592918 AAAATGTAATTTTAGAAAAGTTTTAGGGTT
1 AAAATGTAATTTT-GGAAAGTTTTGGGGTT
* ** *
28592948 AAAATATAATTTTCAAAAAGTTTTGGGATT
1 AAAATGTAATTTT-GGAAAGTTTTGGGGTT
* *
28592978 AAAATATAATTTTTGGATAGTTT
1 AAAATGTAA-TTTTGGAAAGTTT
28593001 AGGGACCTAC
Statistics
Matches: 245, Mismatches: 43, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
29 22 0.09
30 182 0.74
31 41 0.17
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGTTTTGGGGTT
Found at i:28592742 original size:60 final size:60
Alignment explanation
Indices: 28592673--28592990 Score: 363
Period size: 60 Copynumber: 5.3 Consensus size: 60
28592663 GTAAAACCGA
* * ** *
28592673 GGTCAAAAATGAAATTTTGG-AAGGTTTGGGGGTTTAAAATGTAATTTTGTAAAAGTTTTGG
1 GGTC-AAAATGTAATTTTGGAAAAGTTTTAGGG-TTAAAATGTAATTTTGGAAAAGTTTTGG
** *
28592734 GGTCAAAATGTAACATTGGAAAAGTTTTTAGGGTTAAAATGTAATATTGGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAG-TTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGG
* * * * *
28592795 GGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAATTATAATTTTGGAAAAGTTTTGA
1 GGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGG
* * *
28592855 GG-CTAAAATGTAATTTTGGAAAA-ATTTAGGGTTAAAATGTAATTTTAGAAAAGTTTTAG
1 GGTC-AAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGG
* * * **
28592914 TGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTTAAAATATAATTTTCAAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGG
* * *
28592974 GATTAAAATATAATTTT
1 GGTCAAAATGTAATTTT
28592991 TGGATAGTTT
Statistics
Matches: 217, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
59 48 0.22
60 109 0.50
61 54 0.25
62 6 0.03
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (60 bp):
GGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGG
Found at i:28592936 original size:119 final size:119
Alignment explanation
Indices: 28592708--28592990 Score: 361
Period size: 119 Copynumber: 2.4 Consensus size: 119
28592698 TTGGGGGTTT
* * * ** *
28592708 AAAATGTAATTTTGTAAAAGTTTTGGGGTCAAAATGTAACATTGGAAAAGTTTTTAGGGTTAAAA
1 AAAATATAATTTTGAAAAAGTTTTGGGCT-AAAATGTAATTTTGGAAAAG-ATTTAGGGTTAAAA
* * * *
28592773 TGTAATATTGGAAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTC
64 TGTAATATTAGAAAAGTTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTC
* *
28592829 AAATTATAATTTTGGAAAAGTTTTGAGGCTAAAATGTAATTTTGGAAAA-ATTTAGGGTTAAAAT
1 AAAATATAATTTTGAAAAAGTTTTG-GGCTAAAATGTAATTTTGGAAAAGATTTAGGGTTAAAAT
* * *
28592893 GTAATTTTAGAAAAGTTTTAGTGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTT
65 GTAATATTAGAAAAGTTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTC
* * *
28592948 AAAATATAATTTTCAAAAAGTTTTGGGATTAAAATATAATTTT
1 AAAATATAATTTTGAAAAAGTTTTGGG-CTAAAATGTAATTTT
28592991 TGGATAGTTT
Statistics
Matches: 141, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
118 2 0.01
119 97 0.69
121 39 0.28
122 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (119 bp):
AAAATATAATTTTGAAAAAGTTTTGGGCTAAAATGTAATTTTGGAAAAGATTTAGGGTTAAAATG
TAATATTAGAAAAGTTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTC
Found at i:28593713 original size:21 final size:22
Alignment explanation
Indices: 28593673--28593713 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28593663 CCTTTCGTTT
*
28593673 TTTATTTTATTATTACTAAATA
1 TTTATTTTATTATCACTAAATA
*
28593695 TTTA-TTTATTATCATTAAA
1 TTTATTTTATTATCACTAAA
28593714 CAACATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTTTATTATCACTAAATA
Found at i:28594317 original size:18 final size:18
Alignment explanation
Indices: 28594294--28594328 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28594284 CTGGTTTTGG
*
28594294 TTATGGGTTGAAAATGGT
1 TTATGGGATGAAAATGGT
*
28594312 TTATGGGATGTAAATGG
1 TTATGGGATGAAAATGG
28594329 GTTGGGTTTA
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:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (18 bp):
TTATGGGATGAAAATGGT
Found at i:28594486 original size:17 final size:16
Alignment explanation
Indices: 28594464--28594542 Score: 86
Period size: 17 Copynumber: 4.7 Consensus size: 16
28594454 TTTTAAAAAA
*
28594464 AAATTTATAATAATATT
1 AAATTTAAAATAA-ATT
*
28594481 AAATTTAAATTTAAATT
1 AAATTTAAA-ATAAATT
28594498 AAATTTAAAATAAATTT
1 AAATTTAAAATAAA-TT
*
28594515 AAAATTAAAATAAATT
1 AAATTTAAAATAAATT
*
28594531 TAATTTCAAAAT
1 AAATTT-AAAAT
28594543 GGTTTGGGCC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
16 10 0.19
17 40 0.75
18 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTTAAAATAAATT
Found at i:28594490 original size:6 final size:6
Alignment explanation
Indices: 28594479--28594533 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
28594469 TATAATAATA
* *
28594479 TTAAAT TTAAAT TTAAA- TTAAAT TTAAA- ATAAAT TTAAAA TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
28594524 ATAAAT TTAA
1 TTAAAT TTAA
28594534 TTTCAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 13 0.32
6 28 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:28594501 original size:11 final size:11
Alignment explanation
Indices: 28594479--28594536 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
28594469 TATAATAATA
28594479 TTAAATTTAAAT
1 TTAAA-TTAAAT
28594491 TTAAATTAAAT
1 TTAAATTAAAT
*
28594502 TTAAAATAAAT
1 TTAAATTAAAT
28594513 TTAAAATTAAA-
1 TT-AAATTAAAT
* *
28594524 ATAAATTTAAT
1 TTAAATTAAAT
28594535 TT
1 TT
28594537 CAAAATGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 7 0.18
11 20 0.51
12 12 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:28605017 original size:18 final size:18
Alignment explanation
Indices: 28604994--28605036 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28604984 ATTCAATGTG
28604994 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
28605012 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
28605030 TAATTAA
1 TAATTAA
28605037 AAACTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:28611184 original size:24 final size:24
Alignment explanation
Indices: 28611131--28611187 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
28611121 ATAAGATTAT
28611131 TATTAA-ATATAATTTAATAAAAA
1 TATTAATATATAATTTAATAAAAA
* *
28611154 TAATAATATATAATTTAATAAAAT
1 TATTAATATATAATTTAATAAAAA
*
28611178 TCTTAATATA
1 TATTAATATA
28611188 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TATTAATATATAATTTAATAAAAA
Found at i:28611230 original size:33 final size:33
Alignment explanation
Indices: 28611193--28611256 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
28611183 ATATAATTAT
28611193 TTTTATATTAAACTATATTAAAATATTTTTTAG
1 TTTTATATTAAACTATATTAAAATATTTTTTAG
* * *
28611226 TTTTATATTAAATTATATTCAAATCTTTTTT
1 TTTTATATTAAACTATATTAAAATATTTTTT
28611257 TATATTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (33 bp):
TTTTATATTAAACTATATTAAAATATTTTTTAG
Found at i:28613624 original size:54 final size:54
Alignment explanation
Indices: 28613566--28613676 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
28613556 ATTTTATAAT
28613566 AAAACATAATTAAATTAATTAAATTTGATTAATAAAATGATATATAATAAAATG
1 AAAACATAATTAAATTAATTAAATTTGATTAATAAAATGATATATAATAAAATG
28613620 AAAACATAATTAAATTAATTAAATTTGATTAATAAAATGATATATAATAAAATG
1 AAAACATAATTAAATTAATTAAATTTGATTAATAAAATGATATATAATAAAATG
28613674 AAA
1 AAA
28613677 TTTTATAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (54 bp):
AAAACATAATTAAATTAATTAAATTTGATTAATAAAATGATATATAATAAAATG
Found at i:28613684 original size:15 final size:15
Alignment explanation
Indices: 28613595--28613677 Score: 52
Period size: 15 Copynumber: 5.9 Consensus size: 15
28613585 TAAATTTGAT
*
28613595 TAATAAAATGATATA
1 TAATAAAATGAAATA
28613610 TAATAAAATGAAA-A
1 TAATAAAATGAAATA
* *
28613624 -CAT--AATTAAAT-
1 TAATAAAATGAAATA
* ***
28613635 TAATTAAATTTGAT-
1 TAATAAAATGAAATA
*
28613649 TAATAAAATGATATA
1 TAATAAAATGAAATA
28613664 TAATAAAATGAAAT
1 TAATAAAATGAAAT
28613678 TTTATAATAA
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
11 6 0.12
12 2 0.04
13 2 0.04
14 17 0.33
15 25 0.48
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (15 bp):
TAATAAAATGAAATA
Found at i:28615408 original size:2 final size:2
Alignment explanation
Indices: 28615401--28615425 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28615391 CCTCAATTAT
28615401 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28615426 GACTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28616848 original size:58 final size:57
Alignment explanation
Indices: 28616774--28617078 Score: 314
Period size: 58 Copynumber: 5.3 Consensus size: 57
28616764 ACCCGGAGGC
* **
28616774 AAAATTGTAATTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGGGACT
1 AAAATGGTAATTTTGG-TGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGGGGGT
* * ** * *
28616832 GAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTTGGGGGT
1 AAAATGGTAATTTTGGTGAAAT-TGGGTCAAAACGAGAATTTTGGAAAGTTCGGGGGT
*
28616890 AAAATGGTAATTTTTGGTTGAAATTGGGTCATAACGAGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAA-TTTTGG-TGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGGGGGT
** * *
28616949 GGAATGGTAATTTTGGTGAAATTGGGGTCAAAAATG-GAATTTTGGAAGGTTCGGGGGT
1 AAAATGGTAATTTTGGTGAAATT-GGGTC-AAAACGAGAATTTTGGAAAGTTCGGGGGT
* * * * * *
28617007 AAAATGGTAATTTTTGGT-AAATCGAGTAAAAATG-GAATTTTGGAAAACTT-GGGGAT
1 AAAATGGTAA-TTTTGGTGAAATTGGGTCAAAACGAGAATTTTGG-AAAGTTCGGGGGT
28617063 AAAAAT-GTAATTTTGG
1 -AAAATGGTAATTTTGG
28617079 AAAGTTTTAG
Statistics
Matches: 210, Mismatches: 29, Indels: 19
0.81 0.11 0.07
Matches are distributed among these distances:
55 6 0.03
56 24 0.11
57 25 0.12
58 95 0.45
59 54 0.26
60 6 0.03
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.32
Consensus pattern (57 bp):
AAAATGGTAATTTTGGTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGGGGGT
Found at i:28616901 original size:29 final size:29
Alignment explanation
Indices: 28616869--28617020 Score: 75
Period size: 29 Copynumber: 5.2 Consensus size: 29
28616859 TCAAAAATAG
28616869 AATTTTGGAAGGTTTGGGGGTAAAATGGT
1 AATTTTGGAAGGTTTGGGGGTAAAATGGT
** ** * *
28616898 AATTTTTGGTTGAAATT--GGGTCATAACGAG-
1 AA-TTTTGGAAG-GTTTGGGGGT-AAAATG-GT
* * **
28616928 AATTTTGGAAAGTTCGGGGGTGGAATGGT
1 AATTTTGGAAGGTTTGGGGGTAAAATGGT
*
28616957 AATTTTGGTGAA--ATT-GGGGTCAAAAATGG-
1 AATTTT-G-GAAGGTTTGGGGGT--AAAATGGT
*
28616986 AATTTTGGAAGGTTCGGGGGTAAAATGGT
1 AATTTTGGAAGGTTTGGGGGTAAAATGGT
28617015 AATTTT
1 AATTTT
28617021 TGGTAAATCG
Statistics
Matches: 87, Mismatches: 21, Indels: 30
0.63 0.15 0.22
Matches are distributed among these distances:
27 3 0.03
28 15 0.17
29 35 0.40
30 28 0.32
31 6 0.07
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (29 bp):
AATTTTGGAAGGTTTGGGGGTAAAATGGT
Found at i:28616941 original size:117 final size:117
Alignment explanation
Indices: 28616774--28617024 Score: 423
Period size: 117 Copynumber: 2.2 Consensus size: 117
28616764 ACCCGGAGGC
*
28616774 AAAATTGTAA-TTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGGGACTGAAATG
1 AAAATGGTAATTTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGGGACTGAAATG
*
28616838 GTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTTGGGGGT
66 GTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTCGGGGGT
* ** *
28616890 AAAATGGTAATTTTTGGTTGAAATTGGGTCATAACGAGAATTTTGGAAAGTTCGGGGGTGGAATG
1 AAAATGGTAATTTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGGGACTGAAATG
* *
28616955 GTAATTTTGGTGAAATTGGGGTCAAAAATGGAATTTTGGAAGGTTCGGGGGT
66 GTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTCGGGGGT
28617007 AAAATGGTAATTTTTGGT
1 AAAATGGTAATTTTTGGT
28617025 AAATCGAGTA
Statistics
Matches: 126, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
116 9 0.07
117 117 0.93
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGGGACTGAAATG
GTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTCGGGGGT
Found at i:28617161 original size:60 final size:59
Alignment explanation
Indices: 28617064--28617247 Score: 226
Period size: 60 Copynumber: 3.1 Consensus size: 59
28617054 CTTGGGGATA
* * *
28617064 AAAATGTAATTTTGGAAAGTTTTAGGGTCAAAATGTAATTTACAAAAATTTTTAGGGTT
1 AAAATGTAATTTTGGAAAATTTTAGGGTCAAAATGTAATTTACAAAAAGTTTTAGGGTC
* * *
28617123 AAAATATAATTTTGGAAAAATTTAGGGGTCAAAATGTAATTTATAAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAATTTTA-GGGTCAAAATGTAATTTACAAAAAGTTTTAGGGTC
* * * ***
28617183 AAAATGTGATTTTGGAAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAG-TTTAGGGGTC
1 AAAATGTAATTTTGGAAAA-TTTTAGGGTCAAAATGTAATTTACAAAAAGTTTTA-GGGTC
28617243 AAAAT
1 AAAAT
28617248 ATAGTTTTTA
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
59 25 0.23
60 79 0.73
61 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (59 bp):
AAAATGTAATTTTGGAAAATTTTAGGGTCAAAATGTAATTTACAAAAAGTTTTAGGGTC
Found at i:28617185 original size:90 final size:89
Alignment explanation
Indices: 28617042--28617247 Score: 290
Period size: 90 Copynumber: 2.3 Consensus size: 89
28617032 GTAAAAATGG
* * **
28617042 AATTTTGG-AAAACTT-GGGGATAAAAATGTAATTTTGGAAAGTTTTAGGGTCAAAATGTAATTT
1 AATTTTGGAAAAATTTAGGGG-TCAAAATGTAATTTTAAAAAGTTTTAGGGTCAAAATGTAATTT
*
28617105 ACAAAAATTTTTAGGGTTAAAATAT
65 ACAAAAAGTTTTAGGGTTAAAATAT
*
28617130 AATTTTGGAAAAATTTAGGGGTCAAAATGTAATTTATAAAAAGTTTTAGGGTCAAAATGTGATTT
1 AATTTTGGAAAAATTTAGGGGTCAAAATGTAATTT-TAAAAAGTTTTAGGGTCAAAATGTAATTT
***
28617195 TGGAAAAGTTTTAGGGTTAAAATAT
65 ACAAAAAGTTTTAGGGTTAAAATAT
*
28617220 AATTTTGGAAAAGTTTAGGGGTCAAAAT
1 AATTTTGGAAAAATTTAGGGGTCAAAAT
28617248 ATAGTTTTTA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
88 8 0.08
89 19 0.18
90 78 0.74
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (89 bp):
AATTTTGGAAAAATTTAGGGGTCAAAATGTAATTTTAAAAAGTTTTAGGGTCAAAATGTAATTTA
CAAAAAGTTTTAGGGTTAAAATAT
Found at i:28617250 original size:30 final size:29
Alignment explanation
Indices: 28617035--28617247 Score: 198
Period size: 30 Copynumber: 7.2 Consensus size: 29
28617025 AAATCGAGTA
* * * *
28617035 AAAATGGAATTTTGGAAAA-CTTGGGGATA
1 AAAATGTAATTTTGGAAAAGTTTAGGG-TC
28617064 AAAATGTAATTTTGG-AAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAG-TTTAGGGTC
*** * *
28617093 AAAATGTAATTTACAAAAATTTTTAGGGTT
1 AAAATGTAATTTTGGAAAA-GTTTAGGGTC
* *
28617123 AAAATATAATTTTGGAAAAATTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTC
*
28617153 AAAATGTAATTTAT-AAAAAGTTTTAGGGTC
1 AAAATGTAATTT-TGGAAAAG-TTTAGGGTC
* *
28617183 AAAATGTGATTTTGGAAAAGTTTTAGGGTT
1 AAAATGTAATTTTGGAAAAG-TTTAGGGTC
*
28617213 AAAATATAATTTTGGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTC
28617243 AAAAT
1 AAAAT
28617248 ATAGTTTTTA
Statistics
Matches: 151, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.02
29 36 0.24
30 107 0.71
31 5 0.03
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTC
Found at i:28618820 original size:17 final size:16
Alignment explanation
Indices: 28618781--28618856 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 16
28618771 TGGACACTAT
* *
28618781 TAAATTTATAATAATTT
1 TAAATTTA-ATTAATTC
28618798 TAAAATTTACATTAATTC
1 T-AAATTTA-ATTAATTC
28618816 TAAATTTAAATTAAATT-
1 TAAATTT-AATT-AATTC
*
28618833 TAAATTTAA-TAAATC
1 TAAATTTAATTAATTC
28618848 TAAATTTAA
1 TAAATTTAA
28618857 AATAAATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
14 3 0.06
15 10 0.20
16 2 0.04
17 17 0.33
18 19 0.37
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTAATTAATTC
Found at i:28618827 original size:6 final size:6
Alignment explanation
Indices: 28618811--28618909 Score: 77
Period size: 6 Copynumber: 17.3 Consensus size: 6
28618801 AATTTACATT
*
28618811 AATTCTA AATTTA AA-TTA AATTTA AATTT- AA--TA AATCTA AATTTA
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * * *
28618856 AA-ATA AATTTA ACTTTA ACA--TA AATTTA ATTTTA AAATTA AATTTA
1 AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA AATTTA AATTTA
*
28618902 ATTTTA AA
1 AATTTA AA
28618910 ATGATATGGC
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
3 1 0.01
4 3 0.04
5 14 0.19
6 51 0.70
7 4 0.05
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:28618832 original size:11 final size:11
Alignment explanation
Indices: 28618816--28618902 Score: 70
Period size: 11 Copynumber: 7.8 Consensus size: 11
28618806 ACATTAATTC
28618816 TAAATTTAAAT
1 TAAATTTAAAT
28618827 TAAATTTAAAT
1 TAAATTTAAAT
*
28618838 TTAA--TAAAT
1 TAAATTTAAAT
*
28618847 CTAAATTTAAAA
1 -TAAATTTAAAT
*
28618859 TAAATTTAACT
1 TAAATTTAAAT
* **
28618870 TTAACATAAATT
1 TAAATTTAAA-T
*
28618882 TAATTTTAAAAT
1 TAAATTT-AAAT
28618894 TAAATTTAA
1 TAAATTTAA
28618903 TTTTAAAATG
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
9 5 0.09
10 3 0.05
11 31 0.54
12 15 0.26
13 3 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:28618860 original size:17 final size:17
Alignment explanation
Indices: 28618780--28618911 Score: 126
Period size: 17 Copynumber: 7.8 Consensus size: 17
28618770 TTGGACACTA
* *
28618780 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
* *
28618797 TTAAAATTT-ACATTAAT
1 TT-AAATTTAAAATAAAT
*
28618814 TCTAAATTTAAATTAAAT
1 T-TAAATTTAAAATAAAT
28618832 TTAAATTT--AATAAAT
1 TTAAATTTAAAATAAAT
*
28618847 CTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
28618864 TTAACTTTAACATAAAT
1 TTAAATTTAAAATAAAT
*
28618881 TTAATTTTAAAATTAAAT
1 TTAAATTTAAAA-TAAAT
*
28618899 TTAATTTTAAAAT
1 TTAAATTTAAAAT
28618912 GATATGGCTG
Statistics
Matches: 95, Mismatches: 14, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
15 13 0.14
17 52 0.55
18 30 0.32
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:28618894 original size:67 final size:67
Alignment explanation
Indices: 28618781--28618908 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 67
28618771 TGGACACTAT
* * *
28618781 TAAATTTATAATAATTTTAAAATTTACATTAATTCTAAATTTAAATTAAATTTAAATTTAATAAA
1 TAAATTTAAAATAAATTTAAAATTTACATAAATTCTAAATTTAAATTAAATTTAAATTTAATAAA
28618846 TC
66 TC
* * *
28618848 TAAATTTAAAATAAATTT-AACTTTAACATAAATT-TAATTTTAAAATTAAATTTAATTTTAA
1 TAAATTTAAAATAAATTTAAAATTT-ACATAAATTCTAAATTT-AAATTAAATTTAAATTTAA
28618909 AATGATATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 11 0.21
67 42 0.79
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (67 bp):
TAAATTTAAAATAAATTTAAAATTTACATAAATTCTAAATTTAAATTAAATTTAAATTTAATAAA
TC
Found at i:28619332 original size:92 final size:92
Alignment explanation
Indices: 28619172--28619929 Score: 1372
Period size: 92 Copynumber: 8.2 Consensus size: 92
28619162 GAGGTTTTAT
* * *
28619172 CTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTTACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
*
28619237 TGAAAATTCATCTTGTTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
* * *
28619264 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAATTTCAAGAGGATAAGAATTGGCACT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
28619329 TGAAAATTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
*
28619356 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTTCTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
*
28619421 TGAAAATTCATATTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
*
28619448 CTTCAGAGAGATAAAGATCCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
*
28619513 TGAAAATTCACCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
* *
28619540 CTTTAGAGAGATAAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
*
28619605 TGAAATTTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
28619632 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
*
28619697 TGAAATTTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
28619724 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
28619789 TGAAAATTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
28619816 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
28619881 TGAAAATTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
*
28619908 CTTCAGAAAGATAAAGATTCGT
1 CTTCAGAGAGATAAAGATTCGT
28619930 CGTCGTGGAT
Statistics
Matches: 641, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 641 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (92 bp):
CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
TGAAAATTCATCTTGCTCTTACTATAA
Found at i:28619645 original size:52 final size:51
Alignment explanation
Indices: 28619571--28619921 Score: 254
Period size: 52 Copynumber: 7.5 Consensus size: 51
28619561 TTATCCAACT
28619571 TTACTATAACTTCA-AGAGGATAAGAATTGACATTTGAAATTTCATCTTGCTC
1 TTACTATAACTTCAGAGA-GATAAGAATTGACATTTGAAA-TTCATCTTGCTC
* ***
28619623 TTACTATAACTTCAGAGAGAT-A-AA--G--ATTCG---TT-ATCCAACT-
1 TTACTATAACTTCAGAGAGATAAGAATTGACATTTGAAATTCATCTTGCTC
28619663 TTACTATAACTTCA-AGAGGATAAGAATTGACATTTGAAATTTCATCTTGCTC
1 TTACTATAACTTCAGAGA-GATAAGAATTGACATTTGAAA-TTCATCTTGCTC
* ***
28619715 TTACTATAACTTCAGAGAGAT-A-AA--G--ATTCG---TT-ATCCAACT-
1 TTACTATAACTTCAGAGAGATAAGAATTGACATTTGAAATTCATCTTGCTC
28619755 TTACTATAACTTCA-AGAGGATAAGAATTGACATTTGAAAATTCATCTTGCTC
1 TTACTATAACTTCAGAGA-GATAAGAATTGACATTTG-AAATTCATCTTGCTC
* ***
28619807 TTACTATAACTTCAGAGAGAT-A-AA--G--ATTCG---TT-ATCCAACT-
1 TTACTATAACTTCAGAGAGATAAGAATTGACATTTGAAATTCATCTTGCTC
28619847 TTACTATAACTTCA-AGAGGATAAGAATTGACATTTGAAAATTCATCTTGCTC
1 TTACTATAACTTCAGAGA-GATAAGAATTGACATTTG-AAATTCATCTTGCTC
*
28619899 TTACTATAACTTCAGAAAGATAA
1 TTACTATAACTTCAGAGAGATAA
28619922 AGATTCGTCG
Statistics
Matches: 231, Mismatches: 25, Indels: 86
0.68 0.07 0.25
Matches are distributed among these distances:
39 9 0.04
40 51 0.22
41 18 0.08
42 12 0.05
44 3 0.01
46 24 0.10
48 3 0.01
50 12 0.05
51 18 0.08
52 70 0.30
53 11 0.05
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (51 bp):
TTACTATAACTTCAGAGAGATAAGAATTGACATTTGAAATTCATCTTGCTC
Found at i:28627963 original size:58 final size:58
Alignment explanation
Indices: 28627901--28628185 Score: 325
Period size: 58 Copynumber: 4.9 Consensus size: 58
28627891 TTTGGATACC
* * * * *
28627901 CGGGGGCAAAATGATAATTTTGATTGAAAT-TGGCTC-AAAATGAGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTG-GTGAAATCGGGGTCAAAAATG-GAATTTTGGAAAGTT
* *
28627959 CGGGGGTGAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGGTT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT
* * ** *
28628017 CGCGGGTAATATGGTAATTTTGGTTGAAAT-TAGGTC-AAAACGAGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTGG-TGAAATCGGGGTCAAAAATG-GAATTTTGGAAAGTT
* *
28628075 CAGGGGTGAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTT-GAAAGGTT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAA-GTT
*
28628133 CGGAGGTAAAATGGTAATTTTTGGT-AAATC-GGG-CAAAAATGGAATTTTGGAAA
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAA
28628186 ACTTGGGGAT
Statistics
Matches: 194, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
56 15 0.08
57 28 0.14
58 127 0.65
59 24 0.12
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT
Found at i:28627990 original size:29 final size:29
Alignment explanation
Indices: 28627958--28628182 Score: 88
Period size: 29 Copynumber: 7.8 Consensus size: 29
28627948 TTTGGAAAGT
*
28627958 TCGGGGGTGAAATGGTAATTTTGGTGAAA
1 TCGGGGGTAAAATGGTAATTTTGGTGAAA
*
28627987 TC-GGGGTCAAAAATGG-AATTTT-G-GAAGGT
1 TCGGGGGT--AAAATGGTAATTTTGGTGAA--A
* *
28628016 TCGCGGGTAATATGGTAATTTTGGTTGAAA
1 TCGGGGGTAAAATGGTAATTTTGG-TGAAA
** *
28628046 T--TAGGTCAAAACGAG-AATTTT-G-GAAA
1 TCGGGGGT-AAAATG-GTAATTTTGGTGAAA
* *
28628072 GTTCAGGGGTGAAATGGTAATTTTGGTGAAA
1 --TCGGGGGTAAAATGGTAATTTTGGTGAAA
28628103 TC-GGGGTCAAAAATGG-AA-TTT--TGAAA
1 TCGGGGGT--AAAATGGTAATTTTGGTGAAA
*
28628129 GGTTCGGAGGTAAAATGGTAATTTTTGGT-AAA
1 ---TCGGGGGTAAAATGGTAA-TTTTGGTGAAA
**
28628161 TC-GGGCAAAAATGG-AATTTTGG
1 TCGGGGGTAAAATGGTAATTTTGG
28628183 AAAACTTGGG
Statistics
Matches: 149, Mismatches: 18, Indels: 61
0.65 0.08 0.27
Matches are distributed among these distances:
26 15 0.10
27 5 0.03
28 42 0.28
29 46 0.31
30 27 0.18
31 7 0.05
32 6 0.04
33 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.31
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTGGTGAAA
Found at i:28628119 original size:116 final size:116
Alignment explanation
Indices: 28627908--28628153 Score: 406
Period size: 116 Copynumber: 2.1 Consensus size: 116
28627898 ACCCGGGGGC
* * *
28627908 AAAATGATAATTTTGATTGAAATTGGCTCAAAATGAGAATTTTGGAAAGTTCGGGGGTGAAATGG
1 AAAATGGTAATTTTGATTGAAATTGGCTCAAAACGAGAATTTTGGAAAGTTCAGGGGTGAAATGG
*
28627973 TAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGGTTCGCG-GGT
66 TAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGAAAGGTTCG-GAGGT
* *
28628024 AATATGGTAATTTTGGTTGAAATTAGG-TCAAAACGAGAATTTTGGAAAGTTCAGGGGTGAAATG
1 AAAATGGTAATTTTGATTGAAATT-GGCTCAAAACGAGAATTTTGGAAAGTTCAGGGGTGAAATG
28628088 GTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGAAAGGTTCGGAGGT
65 GTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGAAAGGTTCGGAGGT
28628140 AAAATGGTAATTTT
1 AAAATGGTAATTTT
28628154 TGGTAAATCG
Statistics
Matches: 121, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
115 1 0.01
116 118 0.98
117 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (116 bp):
AAAATGGTAATTTTGATTGAAATTGGCTCAAAACGAGAATTTTGGAAAGTTCAGGGGTGAAATGG
TAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGAAAGGTTCGGAGGT
Found at i:28628199 original size:28 final size:27
Alignment explanation
Indices: 28627937--28628214 Score: 70
Period size: 29 Copynumber: 9.7 Consensus size: 27
28627927 AAATTGGCTC
* *
28627937 AAAATGAGAATTTTGGAAAGTTCGGGGGT
1 AAAATG-GAATTTTGGAAAATT-GGGGAT
* * *
28627966 GAAATGGTAATTTTGGTGAAATCGGGG-T
1 AAAATGG-AATTTTGG-AAAATTGGGGAT
**
28627994 CAAAAATGGAATTTTGGAAGGTTCGCGGG-T
1 --AAAATGGAATTTTGGAAAATT-G-GGGAT
* * *
28628024 AATATGGTAATTTTGGTTGAAATT-AGG-T
1 AAAATGG-AATTTTGG--AAAATTGGGGAT
* *
28628052 CAAAACGAGAATTTTGGAAAGTTCAGGGG-T
1 -AAAATG-GAATTTTGGAAAATT--GGGGAT
* * *
28628082 GAAATGGTAATTTTGGTGAAATCGGGG-T
1 AAAATGG-AATTTTGG-AAAATTGGGGAT
*
28628110 CAAAAATGGAATTTT-GAAAGGTTCGGAGG-T
1 --AAAATGGAATTTTGGAAA-ATT-GG-GGAT
* * *
28628140 AAAATGGTAATTTTTGGTAAATCGGGCA-
1 AAAATGG-AA-TTTTGGAAAATTGGGGAT
28628168 AAAATGGAATTTTGGAAAACTTGGGGAT
1 AAAATGGAATTTTGGAAAA-TTGGGGAT
* *
28628196 AAAAATGTAATTTTAGAAA
1 -AAAATGGAATTTTGGAAA
28628215 GTTTTAGGGT
Statistics
Matches: 184, Mismatches: 37, Indels: 56
0.66 0.13 0.20
Matches are distributed among these distances:
26 9 0.05
27 13 0.07
28 36 0.20
29 86 0.47
30 34 0.18
31 6 0.03
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.30
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAAATTGGGGAT
Found at i:28628246 original size:30 final size:30
Alignment explanation
Indices: 28628197--28628355 Score: 177
Period size: 29 Copynumber: 5.4 Consensus size: 30
28628187 CTTGGGGATA
*
28628197 AAAATGTAATTT-TAGAAAGTTTTAGGGTT
1 AAAATGTAATTTATAAAAAGTTTTAGGGTT
*
28628226 AAAATGTAATTTACAAAAAGTTTTA-GGTT
1 AAAATGTAATTTATAAAAAGTTTTAGGGTT
* *
28628255 AAAATATAATTT-TGGAAAAG-TTTAGGGGTT
1 AAAATGTAATTTAT-AAAAAGTTTTA-GGGTT
* *
28628285 AAAATGTAATTTATAGAAAGTTTTAGGGTC
1 AAAATGTAATTTATAAAAAGTTTTAGGGTT
*
28628315 AAAATGTGATTT-TAAAAATGTTTT-GGGTT
1 AAAATGTAATTTATAAAAA-GTTTTAGGGTT
*
28628344 AAAATATAATTT
1 AAAATGTAATTT
28628356 TGGAAAAGTT
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.04
29 51 0.47
30 49 0.45
31 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.40
Consensus pattern (30 bp):
AAAATGTAATTTATAAAAAGTTTTAGGGTT
Found at i:28628287 original size:59 final size:58
Alignment explanation
Indices: 28628197--28628415 Score: 208
Period size: 59 Copynumber: 3.7 Consensus size: 58
28628187 CTTGGGGATA
* * * *
28628197 AAAATGTAATTTTAG-AAAGTTTTAGGGTTAAAATGTAATTTACAAAAAGTTTTAGGTT
1 AAAATATAATTTTGGAAAAG-TTTAGGGTTAAAATATAATTTACAAAAAGTTTTAGGTC
* * *
28628255 AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTC
1 AAAATATAATTTTGGAAAAGTTTA-GGGTTAAAATATAATTTACAAAAAGTTTTA-GGTC
* * * * *** ** *
28628315 AAAATGTGATTTT-AAAAATGTTTTGGGTTAAAATATAATTTTGGAAAAGTTTGGGGGAC
1 AAAATATAATTTTGGAAAA-GTTTAGGGTTAAAATATAATTTACAAAAAGTTT-TAGGTC
*
28628374 AAAATATAATTTTGGAAAAGTTTAAGGGTCAAAATATAATTT
1 AAAATATAATTTTGGAAAAGTTT-AGGGTTAAAATATAATTT
28628416 TTGGATTGTT
Statistics
Matches: 132, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
58 17 0.13
59 77 0.58
60 38 0.29
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (58 bp):
AAAATATAATTTTGGAAAAGTTTAGGGTTAAAATATAATTTACAAAAAGTTTTAGGTC
Found at i:28628309 original size:89 final size:86
Alignment explanation
Indices: 28628175--28628415 Score: 313
Period size: 89 Copynumber: 2.7 Consensus size: 86
28628165 GCAAAAATGG
* *
28628175 AATTTTGGAAAA-CTTGGGGATAAAAATGTAATTTTAGAAAGTTTTAGGGTTAAAATGTAATTTA
1 AATTTTGGAAAAGTTTGGGG-TAAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATGTAATTTA
28628239 CAAAAAGTTTTAGGTTAAAATAT
65 -AAAAAGTTTTAGGTTAAAATAT
* *
28628262 AATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATGTGATTT
1 AATTTTGGAAAAGTTT-GGGGTAAAAATGTAATTT-TAGAAAGTTTTAGGGTCAAAATGT-AATT
* *
28628327 TAAAAATGTTTTGGGTTAAAATAT
63 TAAAAAAGTTTTAGGTTAAAATAT
* * * * *
28628351 AATTTTGGAAAAGTTTGGGGGACAAAATATAATTTTGGAAAAGTTTAAGGGTCAAAATATAATTT
1 AATTTTGGAAAAGTTTGGGGTA-AAAATGTAATTTTAG-AAAGTTTTAGGGTCAAAATGTAATTT
28628416 TTGGATTGTT
Statistics
Matches: 135, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
87 12 0.09
88 25 0.19
89 93 0.69
90 5 0.04
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (86 bp):
AATTTTGGAAAAGTTTGGGGTAAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATGTAATTTAA
AAAAGTTTTAGGTTAAAATAT
Found at i:28628380 original size:30 final size:30
Alignment explanation
Indices: 28628197--28628416 Score: 180
Period size: 30 Copynumber: 7.4 Consensus size: 30
28628187 CTTGGGGATA
* * * *
28628197 AAAATGTAATTTTAG-AAAGTTTTAGGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTC
* *** * *
28628226 AAAATGTAATTTACAAAAAGTTTTA-GGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTC
* *
28628255 AAAATATAATTTTGGAAAAGTTTAGGGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTC
* * *
28628285 AAAATGTAATTTATAG-AAAGTTTTAGGGTC
1 AAAATATAATTT-TGGAAAAGTTTAAGGGTC
* * * * *
28628315 AAAATGTGATTTT-AAAAATGTTT-TGGGTT
1 AAAATATAATTTTGGAAAA-GTTTAAGGGTC
** *
28628344 AAAATATAATTTTGGAAAAGTTTGGGGGAC
1 AAAATATAATTTTGGAAAAGTTTAAGGGTC
28628374 AAAATATAATTTTGGAAAAGTTTAAGGGTC
1 AAAATATAATTTTGGAAAAGTTTAAGGGTC
28628404 AAAATATAATTTT
1 AAAATATAATTTT
28628417 TGGATTGTTT
Statistics
Matches: 157, Mismatches: 27, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
29 58 0.37
30 97 0.62
31 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (30 bp):
AAAATATAATTTTGGAAAAGTTTAAGGGTC
Found at i:28629990 original size:17 final size:16
Alignment explanation
Indices: 28629951--28630026 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 16
28629941 GACACTCTAT
* *
28629951 TAAATTTATAATAATTT
1 TAAATTTA-ATTAATTC
28629968 TAAAATTTACATTAATTC
1 T-AAATTTA-ATTAATTC
28629986 TAAATTTAAATTAAATT-
1 TAAATTT-AATT-AATTC
*
28630003 TAAATTTAA-TAAATC
1 TAAATTTAATTAATTC
28630018 TAAATTTAA
1 TAAATTTAA
28630027 AATAAATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
14 3 0.06
15 10 0.20
16 2 0.04
17 17 0.33
18 19 0.37
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTAATTAATTC
Found at i:28629997 original size:6 final size:6
Alignment explanation
Indices: 28629981--28630061 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
28629971 AATTTACATT
*
28629981 AATTCTA AATTTA AA-TTA AATTTA AATTT- AA--TA AATCTA AATTTA
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
28630026 AA-ATA AATTTA ACTTTA ACA--TA AATTTA ATTTTA AA
1 AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA AA
28630062 ATGAATTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
3 1 0.02
4 3 0.05
5 14 0.24
6 37 0.63
7 4 0.07
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:28630002 original size:11 final size:11
Alignment explanation
Indices: 28629986--28630037 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
28629976 ACATTAATTC
28629986 TAAATTTAAAT
1 TAAATTTAAAT
28629997 TAAATTTAAAT
1 TAAATTTAAAT
*
28630008 TTAA--TAAAT
1 TAAATTTAAAT
*
28630017 CTAAATTTAAAA
1 -TAAATTTAAAT
28630029 TAAATTTAA
1 TAAATTTAA
28630038 CTTTAACATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 5 0.14
10 3 0.09
11 23 0.66
12 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:28630030 original size:17 final size:17
Alignment explanation
Indices: 28629950--28630069 Score: 111
Period size: 17 Copynumber: 7.1 Consensus size: 17
28629940 GGACACTCTA
* *
28629950 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
* *
28629967 TTAAAATTT-ACATTAAT
1 TT-AAATTTAAAATAAAT
*
28629984 TCTAAATTTAAATTAAAT
1 T-TAAATTTAAAATAAAT
28630002 TTAAATTT--AATAAAT
1 TTAAATTTAAAATAAAT
*
28630017 CTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
28630034 TTAACTTTAACATAAAT
1 TTAAATTTAAAATAAAT
* *
28630051 TTAATTTTAAAATGAAT
1 TTAAATTTAAAATAAAT
28630068 TT
1 TT
28630070 TAAAATGATT
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
15 13 0.16
17 57 0.69
18 13 0.16
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:28630068 original size:12 final size:12
Alignment explanation
Indices: 28630053--28630077 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28630043 ACATAAATTT
28630053 AATTTTAAAATG
1 AATTTTAAAATG
28630065 AATTTTAAAATG
1 AATTTTAAAATG
28630077 A
1 A
28630078 TTTGGCTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:28631957 original size:23 final size:23
Alignment explanation
Indices: 28631878--28632090 Score: 133
Period size: 23 Copynumber: 9.5 Consensus size: 23
28631868 TAAACGGAAC
* * *
28631878 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
28631900 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
28631922 GGGCAACAAAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
28631948 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
28631968 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
28631987 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
28632010 AATCGGAGAGCACACATAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
28632033 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
28632058 -AACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
28632080 AATCAGAGAGC
1 AAACAGAGAGC
28632091 GCGCTAGTGT
Statistics
Matches: 147, Mismatches: 27, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 3 0.02
22 34 0.23
23 59 0.40
24 1 0.01
25 27 0.18
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:28631986 original size:39 final size:39
Alignment explanation
Indices: 28631932--28632006 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
28631922 GGGCAACAAA
*
28631932 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
28631971 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
28632007 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:28634675 original size:22 final size:22
Alignment explanation
Indices: 28634650--28634695 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
28634640 TCAATGACTA
28634650 AAATGTTACAACACGATAACGC
1 AAATGTTACAACACGATAACGC
28634672 AAATGTTACAACACGATAACGC
1 AAATGTTACAACACGATAACGC
28634694 AA
1 AA
28634696 GTGACTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (22 bp):
AAATGTTACAACACGATAACGC
Found at i:28634894 original size:17 final size:17
Alignment explanation
Indices: 28634872--28634915 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
28634862 ACCAAACCAT
28634872 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
28634889 TTTAAATCTATTTTAAA
1 TTTAAATTTATTTTAAA
28634906 TTTAAATTTA
1 TTTAAATTTA
28634916 ATCAATGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:28636614 original size:30 final size:30
Alignment explanation
Indices: 28636590--28636801 Score: 162
Period size: 30 Copynumber: 7.1 Consensus size: 30
28636580 AAACTTCTCC
*
28636590 AAAATTTTATTTTGACCCCTAAACTTTCTA
1 AAAATTATATTTTGACCCCTAAACTTTCTA
* *
28636620 AAAATTATATTTTGACCCCTAAACTTTTTT
1 AAAATTATATTTTGACCCCTAAACTTTCTA
* * * *
28636650 AAAATTACATTTT-AACCTTAAAACTTT-TCC
1 AAAATTATATTTTGACCCCT-AAACTTTCT-A
* * * * * *
28636680 AAATTTATATTTTGACCACAAAAATTTTTG
1 AAAATTATATTTTGACCCCTAAACTTTCTA
* * * *
28636710 AAAATTACATTTTAACCCATAAACTTT-TC
1 AAAATTATATTTTGACCCCTAAACTTTCTA
* * *
28636739 AAAATTATATTTTAACCTCAAAACTTTCTA
1 AAAATTATATTTTGACCCCTAAACTTTCTA
* * *
28636769 AAAATTACCA-TTTCACCCCTAAACTTTCCA
1 AAAATTA-TATTTTGACCCCTAAACTTTCTA
28636799 AAA
1 AAA
28636802 TTCCATTTTT
Statistics
Matches: 143, Mismatches: 33, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
29 29 0.20
30 110 0.77
31 4 0.03
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAACTTTCTA
Found at i:28636761 original size:59 final size:59
Alignment explanation
Indices: 28636598--28636803 Score: 227
Period size: 60 Copynumber: 3.5 Consensus size: 59
28636588 CCAAAATTTT
* * * * *
28636598 ATTTTGACCCCTAAACTTTCTAAAAATTATATTTTGACCCCTAAACTTTTTTAAAATTAC
1 ATTTTAACCCCTAAACTTT-TCAAAATTATATTTTGACCACAAAACTTTTTAAAAATTAC
* * * *
28636658 ATTTTAA-CCTTAAAACTTTTCCAAATTTATATTTTGACCACAAAAATTTTTGAAAATTAC
1 ATTTTAACCCCT-AAACTTTT-CAAAATTATATTTTGACCACAAAACTTTTTAAAAATTAC
* * * *
28636718 ATTTTAACCCATAAACTTTTCAAAATTATATTTTAACCTCAAAACTTTCTAAAAATTACC
1 ATTTTAACCCCTAAACTTTTCAAAATTATATTTTGACCACAAAACTTTTTAAAAATTA-C
* *
28636778 A-TTTCACCCCTAAACTTTCCAAAATT
1 ATTTTAACCCCTAAACTTTTCAAAATT
28636804 CCATTTTTAA
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
59 58 0.47
60 63 0.51
61 3 0.02
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (59 bp):
ATTTTAACCCCTAAACTTTTCAAAATTATATTTTGACCACAAAACTTTTTAAAAATTAC
Found at i:28636810 original size:59 final size:58
Alignment explanation
Indices: 28636604--28636803 Score: 204
Period size: 59 Copynumber: 3.4 Consensus size: 58
28636594 TTTTATTTTG
* * * * *
28636604 ACCCCTAAACTTTCTAAAAATTATATTTTGACCCCTAAACTTTTTTAAAATTACATTTTA
1 ACCCCTAAACTTTC-CAAAATTATATTTTAACCACAAAACTTTTTAAAAATTACA-TTTA
* * * * *
28636664 A-CCTTAAAACTTTTCCAAATTTATATTTTGACCACAAAAATTTTTGAAAATTACATTTTA
1 ACCCCT-AAAC-TTTCCAAAATTATATTTTAACCACAAAACTTTTTAAAAATTACA-TTTA
* * * * *
28636724 ACCCATAAACTTTTCAAAATTATATTTTAACCTCAAAACTTTCTAAAAATTACCATTTC
1 ACCCCTAAACTTTCCAAAATTATATTTTAACCACAAAACTTTTTAAAAATTA-CATTTA
28636783 ACCCCTAAACTTTCCAAAATT
1 ACCCCTAAACTTTCCAAAATT
28636804 CCATTTTTAA
Statistics
Matches: 118, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
59 60 0.51
60 51 0.43
61 7 0.06
ACGTcount: A:0.39, C:0.20, G:0.01, T:0.39
Consensus pattern (58 bp):
ACCCCTAAACTTTCCAAAATTATATTTTAACCACAAAACTTTTTAAAAATTACATTTA
Found at i:28636817 original size:29 final size:29
Alignment explanation
Indices: 28636710--28636929 Score: 125
Period size: 29 Copynumber: 7.5 Consensus size: 29
28636700 AAAATTTTTG
* *
28636710 AAAATTACA-TTTTAACCCATAAACTTTTC
1 AAAATTCCATTTTTAACCC-TAAACTTTCC
* *
28636739 AAAATT--ATATTTTAACCTCAAAACTTTCTA
1 AAAATTCCAT-TTTTAACC-CTAAACTTTC-C
* *
28636769 AAAATTACCA-TTTCACCCCTAAACTTTCC
1 AAAATT-CCATTTTTAACCCTAAACTTTCC
*
28636798 AAAATTCCATTTTTAACCCT-GA-TTTCACC
1 AAAATTCCATTTTTAACCCTAAACTTT--CC
** **
28636827 AAAAATAACATTTTT-ACCCTCAAGTTTTCC
1 -AAAATTCCATTTTTAACCCT-AAACTTTCC
* *
28636857 ATAATTCCATTTTTAACCCT-AATTTTACC
1 AAAATTCCATTTTTAACCCTAAACTTT-CC
* *
28636886 AAAAATTACCA-TTTTACCCCCAAACTTTCC
1 -AAAATT-CCATTTTTAACCCTAAACTTTCC
*
28636916 AAAATCCCATTTTT
1 AAAATTCCATTTTT
28636930 GGCCCAATTT
Statistics
Matches: 148, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
27 4 0.03
28 12 0.08
29 64 0.43
30 50 0.34
31 14 0.09
32 3 0.02
33 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAATTCCATTTTTAACCCTAAACTTTCC
Found at i:28636831 original size:59 final size:59
Alignment explanation
Indices: 28636710--28636963 Score: 220
Period size: 59 Copynumber: 4.3 Consensus size: 59
28636700 AAAATTTTTG
* * * *
28636710 AAAATTA-CATTTTAACCCATAAACTTTTCAAAATT--ATATTTTAACCTCAAAACTTT--CTA
1 AAAATTACCATTTT-ACCCCTAAACTTTCCAAAATTCCAT-TTTTAACC-C-TAA-TTTCACCA
* *
28636769 AAAATTACCATTTCACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCA
* ** * *
28636828 AAAA-TAACATTTTTA-CCCTCAAGTTTTCCATAATTCCATTTTTAACCCTAATTTTACCA
1 AAAATTACCA-TTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCA
* * ** *
28636887 AAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTGGCCC-AATTTTAACC-
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAA-TTTCACCA
*
28636945 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
28636964 CCGGGTATCC
Statistics
Matches: 162, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
57 3 0.02
58 29 0.18
59 108 0.67
60 20 0.12
61 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCA
Found at i:28636901 original size:30 final size:30
Alignment explanation
Indices: 28636710--28636919 Score: 127
Period size: 30 Copynumber: 7.1 Consensus size: 30
28636700 AAAATTTTTG
28636710 AAAATTA-CATTTTAACCCATAAACTTTT-C-
1 AAAATTACCATTTTAACCC-TAAA-TTTTCCA
* * * *
28636739 AAAATTA-TATTTTAACCTCAAAACTTTCTA
1 AAAATTACCATTTTAACC-CTAAATTTTCCA
* * *
28636769 AAAATTACCATTTCACCCCTAAACTTTCC-
1 AAAATTACCATTTTAACCCTAAATTTTCCA
* *
28636798 AAAATT-CCATTTTTAACCCT-GATTTCACCA
1 AAAATTACCA-TTTTAACCCTAAATTT-TCCA
* * *
28636828 AAAA-TAACATTTTTACCCTCAAGTTTTCC-
1 AAAATTACCATTTTAACCCT-AAATTTTCCA
*
28636857 ATAATT-CCATTTTTAACCCT-AATTTTACCA
1 AAAATTACCA-TTTTAACCCTAAATTTT-CCA
* * *
28636887 AAAATTACCATTTTACCCCCAAACTTTCCA
1 AAAATTACCATTTTAACCCTAAATTTTCCA
28636917 AAA
1 AAA
28636920 TCCCATTTTT
Statistics
Matches: 138, Mismatches: 27, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
28 14 0.10
29 52 0.38
30 54 0.39
31 18 0.13
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCTAAATTTTCCA
Found at i:28636958 original size:30 final size:30
Alignment explanation
Indices: 28636769--28636958 Score: 119
Period size: 29 Copynumber: 6.5 Consensus size: 30
28636759 AAACTTTCTA
* * *
28636769 AAAATTACCA-TTTCACCCCTAAACTTT-CC
1 AAAATTACCATTTTTAACCC-AAATTTTACC
** *
28636798 AAAATT-CCATTTTTAACCCTGATTTCACC
1 AAAATTACCATTTTTAACCCAAATTTTACC
* * * *
28636827 AAAAATAACATTTTTACCCTCAAGTTTT-CC
1 AAAATTACCATTTTTAACC-CAAATTTTACC
* *
28636857 ATAATT-CCATTTTTAACCCTAATTTTACC
1 AAAATTACCATTTTTAACCCAAATTTTACC
* *
28636886 AAAAATTACCA-TTTTACCCCCAAACTTT-CC
1 -AAAATTACCATTTTTA-ACCCAAATTTTACC
* **
28636916 AAAA-TCCCATTTTTGGCCC-AATTTTAACC
1 AAAATTACCATTTTTAACCCAAATTTT-ACC
28636945 AAAATTACCATTTT
1 AAAATTACCATTTT
28636959 GCCCCCCGGG
Statistics
Matches: 121, Mismatches: 28, Indels: 23
0.70 0.16 0.13
Matches are distributed among these distances:
27 5 0.04
28 19 0.16
29 46 0.38
30 36 0.30
31 15 0.12
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTTAACCCAAATTTTACC
Found at i:28636965 original size:59 final size:58
Alignment explanation
Indices: 28636769--28636964 Score: 232
Period size: 59 Copynumber: 3.3 Consensus size: 58
28636759 AAACTTTCTA
* * * *
28636769 AAAATTACCATTTCACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACC
* * * ** *
28636827 AAAAATAACATTTTTACCCTCAAGTTTTCCATAATTCCATTTTTAACCCTAATTTTACC
1 AAAATTACCA-TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACC
* **
28636886 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTGGCCC-AATTTTAACC
1 -AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTT-ACC
*
28636945 AAAATTACCATTTTGCCCCC
1 AAAATTACCATTTTACCCCC
28636965 CGGGTATCCA
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
58 33 0.29
59 74 0.64
60 8 0.07
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACC
Found at i:28639004 original size:17 final size:17
Alignment explanation
Indices: 28638980--28639025 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
28638970 TATTGTATTT
28638980 TAATTTTTTTAATAATA
1 TAATTTTTTTAATAATA
* * **
28638997 TTATTTTTTAAATGCTA
1 TAATTTTTTTAATAATA
28639014 TAATTTTTTTAA
1 TAATTTTTTTAA
28639026 AAAAAATGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TAATTTTTTTAATAATA
Found at i:28644333 original size:24 final size:24
Alignment explanation
Indices: 28644306--28644376 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
28644296 TGACTCAAAC
* *
28644306 AAATAAATATACTTTAATTGAAAT
1 AAATAAACAGACTTTAATTGAAAT
* *
28644330 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAGACTTTAATTGAAAT
* * *
28644354 AATTAAACAGAGTTTAACTGAAA
1 AAATAAACAGACTTTAATTGAAA
28644377 GATTATTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.30
Consensus pattern (24 bp):
AAATAAACAGACTTTAATTGAAAT
Found at i:28646333 original size:24 final size:24
Alignment explanation
Indices: 28646305--28646361 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
28646295 TAGACTAATA
*
28646305 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTCAAACAAATAAAC
* *
28646329 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAATTCAAACAAATAAAC
28646353 AGAGTTTAA
1 AGAGTTTAA
28646362 CTGAAAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (24 bp):
AGAGTTTAATTCAAACAAATAAAC
Found at i:28646366 original size:24 final size:24
Alignment explanation
Indices: 28646317--28646367 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
28646307 AGTTTGATTC
*
28646317 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
*
28646341 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
28646365 AAA
1 AAA
28646368 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:28647940 original size:4 final size:4
Alignment explanation
Indices: 28647931--28647963 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
28647921 CCAAAGGGTA
*
28647931 AGTG AGTG AGTG AGTG AATG AGTG AGTG AGTG A
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
28647964 AGATCTTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.24
Consensus pattern (4 bp):
AGTG
Found at i:28647954 original size:16 final size:16
Alignment explanation
Indices: 28647933--28647964 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28647923 AAAGGGTAAG
28647933 TGAGTGAGTGAGTGAA
1 TGAGTGAGTGAGTGAA
28647949 TGAGTGAGTGAGTGAA
1 TGAGTGAGTGAGTGAA
28647965 GATCTTGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (16 bp):
TGAGTGAGTGAGTGAA
Found at i:28657654 original size:29 final size:30
Alignment explanation
Indices: 28657620--28657681 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
28657610 ATCTTACGTG
* *
28657620 TATAATT-ACATTAAATTAAAATTTATGTA
1 TATAATTAACATTAAATCAAAATTAATGTA
28657649 TATAATTACACATTAAATCAAAATTAATGTA
1 TATAATTA-ACATTAAATCAAAATTAATGTA
28657680 TA
1 TA
28657682 ATTAAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
31 22 0.76
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (30 bp):
TATAATTAACATTAAATCAAAATTAATGTA
Found at i:28657682 original size:29 final size:28
Alignment explanation
Indices: 28657618--28657686 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 28
28657608 GAATCTTACG
* *
28657618 TGTATAATT-ACATTAAATTAAAATTTA
1 TGTATAATTAACATTAAATCAAAATTAA
28657645 TGTATATAATTACACATTAAATCAAAATTAA
1 TG--TATAATTA-ACATTAAATCAAAATTAA
28657676 TGTATAATTAA
1 TGTATAATTAA
28657687 AGTTTAGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 15 0.42
31 18 0.50
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (28 bp):
TGTATAATTAACATTAAATCAAAATTAA
Found at i:28662593 original size:19 final size:20
Alignment explanation
Indices: 28662556--28662594 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28662546 AAAATTTATA
*
28662556 TTTAAAAAAAATTTGAAAAT
1 TTTAAAAAAAATCTGAAAAT
28662576 TTTAAAAAAAATCT-AAAAT
1 TTTAAAAAAAATCTGAAAAT
28662595 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
TTTAAAAAAAATCTGAAAAT
Found at i:28665460 original size:18 final size:18
Alignment explanation
Indices: 28665437--28665473 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28665427 AAATCAAATT
* *
28665437 AATTCGGTTAATTGATCG
1 AATTCGGTGAATCGATCG
28665455 AATTCGGTGAATCGATCG
1 AATTCGGTGAATCGATCG
28665473 A
1 A
28665474 TTAATAATTT
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:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (18 bp):
AATTCGGTGAATCGATCG
Found at i:28666592 original size:2 final size:2
Alignment explanation
Indices: 28666585--28666620 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
28666575 ATGGCTGCCT
28666585 TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28666621 GTTTGTTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:28670993 original size:23 final size:24
Alignment explanation
Indices: 28670944--28670993 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
28670934 CTAGTATTTT
* *
28670944 TTTTATTTTCAAGCAATTGAGTTG
1 TTTTATTTTCAAGAAATTGAGTCG
28670968 TTTTATTTTCAA-AAATTTG-GTCG
1 TTTTATTTTCAAGAAA-TTGAGTCG
28670991 TTT
1 TTT
28670994 GTTTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.54
Consensus pattern (24 bp):
TTTTATTTTCAAGAAATTGAGTCG
Found at i:28679916 original size:5 final size:5
Alignment explanation
Indices: 28679886--28679915 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
28679876 ACCAAAACCA
*
28679886 AAATC AAATC AAATC AAATC AAATC TAATC
1 AAATC AAATC AAATC AAATC AAATC AAATC
28679916 TTACTCGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATC
Found at i:28696350 original size:2 final size:2
Alignment explanation
Indices: 28696309--28696334 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28696299 AAAAAAAAAA
28696309 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
28696335 TCTTTTTATG
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:28699304 original size:16 final size:16
Alignment explanation
Indices: 28699283--28699317 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28699273 TTGCTTTTAA
28699283 AAAGCACTTTTGG-GAC
1 AAAGCAC-TTTGGAGAC
28699299 AAAGCACTTTGGAGAC
1 AAAGCACTTTGGAGAC
28699315 AAA
1 AAA
28699318 AGTATTCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (16 bp):
AAAGCACTTTGGAGAC
Found at i:28704846 original size:59 final size:57
Alignment explanation
Indices: 28704754--28704895 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 57
28704744 GAAATATCAT
* *
28704754 GGACTAACTTGGACCCAAAAACAGTTCAGCCCCAATAT-AGGAACAATTACAAAGTTC-AG
1 GGACTAACTTGGA--CAAAAAAAGTTAAGCCCCAATATGA-GAACAATTACAAAG-TCAAG
* * *
28704813 GGACTAACTTGGACAAAAAAATGTTTAAGCCCCAATGTGAGAGCAATTACCAAGTCAAG
1 GGACTAACTTGGACAAAAAAA-G-TTAAGCCCCAATATGAGAACAATTACAAAGTCAAG
* *
28704872 GCACTAACTTGGAAAAAAAAAGTT
1 GGACTAACTTGGACAAAAAAAGTT
28704896 CAAGTCCGAA
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
57 9 0.12
58 4 0.06
59 58 0.81
60 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (57 bp):
GGACTAACTTGGACAAAAAAAGTTAAGCCCCAATATGAGAACAATTACAAAGTCAAG
Found at i:28706441 original size:30 final size:28
Alignment explanation
Indices: 28706405--28706567 Score: 102
Period size: 30 Copynumber: 5.5 Consensus size: 28
28706395 AAAATTCAGA
28706405 GTAAAATGGTAATTTTTGGTAAAATCGGG
1 GTAAAATGG-AATTTTTGGTAAAATCGGG
* *
28706434 GTCAAAATGGGA-TTTT-G-AAAAGTTTGGGGG
1 GT-AAAATGGAATTTTTGGTAAAA---T-CGGG
*
28706464 GTAAAATGGTAATTTTTGGTAAAATTGGG
1 GTAAAATGG-AATTTTTGGTAAAATCGGG
*
28706493 GTTAAAATGGAA-TTTTGG-AAAGTTCGAGG
1 G-TAAAATGGAATTTTTGGTAAA-ATCG-GG
* * **
28706522 GTAAAATAGTAACTTTTGGTAAAATCAAG
1 GTAAAAT-GGAATTTTTGGTAAAATCGGG
28706551 GTCAAAAATGGAATTTT
1 GT--AAAATGGAATTTT
28706568 GGAAAGTTGA
Statistics
Matches: 105, Mismatches: 12, Indels: 33
0.70 0.08 0.22
Matches are distributed among these distances:
26 4 0.04
27 4 0.04
28 18 0.17
29 26 0.25
30 36 0.34
31 12 0.11
32 1 0.01
33 4 0.04
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (28 bp):
GTAAAATGGAATTTTTGGTAAAATCGGG
Found at i:28706477 original size:59 final size:58
Alignment explanation
Indices: 28706405--28706596 Score: 251
Period size: 59 Copynumber: 3.3 Consensus size: 58
28706395 AAAATTCAGA
* *
28706405 GTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAATGGGATTTTGAAAAGTTTGGGGG
1 GTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAATGGAATTTTGGAAAG-TTGGGGG
* * * *
28706464 GTAAAATGGTAATTTTTGGTAAAATTGGGGTTAAAATGGAATTTTGGAAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAATGGAATTTTGGAAAGTTGGGGG
* * ** *
28706522 GTAAAATAGTAACTTTTGGTAAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTGAGGG
1 GTAAAATGGTAATTTTTGGTAAAATCGGGGTC-AAAATGGAATTTTGGAAAGTTGGGGG
28706581 GTAAAAAT-GTAATTTT
1 GT-AAAATGGTAATTTT
28706597 AGAAAGTTTT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
58 31 0.27
59 79 0.69
60 5 0.04
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
GTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAATGGAATTTTGGAAAGTTGGGGG
Found at i:28706617 original size:117 final size:117
Alignment explanation
Indices: 28706352--28706641 Score: 286
Period size: 117 Copynumber: 2.5 Consensus size: 117
28706342 TCGGGGGCAG
* * * * * * * *
28706352 AATGGTAATTTTGATTGAAATT-AGGTCAAAACGGGGATTTTGGAAAATTC-AGAGTAAAATGGT
1 AATGGTAATTTTTAGTAAAATTGAGGTCAAAA-TGGAATTTTGGAAAGTTCGAGGGTAAAATAGT
* ** * *
28706415 AATTTTTGGTAAAATCGGGGTCAAAATGGGATTTTGAAAAGTTTGGGGGGTAA
65 AACTTTTGGTAAAATCAAGGTCAAAATGGAATTTTGAAAAGTTTGAGGGGTAA
* * *
28706468 AATGGTAATTTTTGGTAAAATTGGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATAGTA
1 AATGGTAATTTTTAGTAAAATTGAGGTCAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATAGTA
*
28706533 ACTTTTGGTAAAATCAAGGTCAAAAATGGAATTTTGGAAAG-TTGAGGGGTAAA
66 ACTTTTGGTAAAATCAAGGTC-AAAATGGAATTTTGAAAAGTTTGAGGGGT-AA
* ** * *
28706586 AAT-GTAA-TTTTAG-AAAGTTTTGAGGTCAAAATATAATTTTGAAATAGTTTGAGGGT
1 AATGGTAATTTTTAGTAAA--ATTGAGGTCAAAATGGAATTTTGGAA-AGTTCGAGGGT
28706642 CCAAATGTAA
Statistics
Matches: 142, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
115 3 0.02
116 38 0.27
117 69 0.49
118 32 0.23
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (117 bp):
AATGGTAATTTTTAGTAAAATTGAGGTCAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATAGTA
ACTTTTGGTAAAATCAAGGTCAAAATGGAATTTTGAAAAGTTTGAGGGGTAA
Found at i:28706653 original size:30 final size:29
Alignment explanation
Indices: 28706432--28706835 Score: 230
Period size: 30 Copynumber: 13.6 Consensus size: 29
28706422 GGTAAAATCG
** *
28706432 GGGTCAAAATGGGATTTTGAAAAGTTTGGG
1 GGGTCAAAATGTAATTTTGAAAAGTTT-GA
28706462 GGGT-AAAATGGTAATTTTTGGTAAAA--TTG-
1 GGGTCAAAAT-GTAA-TTTT-G-AAAAGTTTGA
* * * *
28706491 GGGTTAAAATGGAATTTTGGAAAGTTCGA
1 GGGTCAAAATGTAATTTTGAAAAGTTTGA
*
28706520 GGGT-AAAATAGTAACTTTTGGTAAAA---TCA
1 GGGTCAAAAT-GTAA-TTTT-G-AAAAGTTTGA
* * *
28706549 AGGTCAAAAATGGAATTTTGGAAAG-TTGA
1 GGGTC-AAAATGTAATTTTGAAAAGTTTGA
*
28706578 GGGGTAAAAATGTAATTTT-AGAAAGTTTTGA
1 -GGGTCAAAATGTAATTTTGA-AAAG-TTTGA
*
28706609 -GGTCAAAATATAATTTTGAAATAGTTTGA
1 GGGTCAAAATGTAATTTTGAAA-AGTTTGA
* *
28706638 GGGTCCAAATGTAATTTTTAGAAAGTTTTG-
1 GGGTCAAAATGTAATTTTGA-AAAG-TTTGA
*
28706668 GGGTCAAAATGTAATTTTTAGAAAA-TTTTA
1 GGGTCAAAATGTAA-TTTT-GAAAAGTTTGA
*
28706698 GGGTCAAAATATAATTTTAGAAAAGTTT-A
1 GGGTCAAAATGTAATTTT-GAAAAGTTTGA
* * *
28706727 GGGGTAAAAATGCAATTTTTAGAAAGTTTTG-
1 -GGGTCAAAATGTAATTTTGA-AAAG-TTTGA
* *
28706758 GGGTTAAAATATAATTTTAGAAAAGTTT-A
1 GGGTCAAAATGTAATTTT-GAAAAGTTTGA
*
28706787 GGGGTCAAAATGTAATTATTAGAAAGGTTTGA
1 -GGGTCAAAATGTAATT-TT-GAAAAGTTTGA
* *
28706819 -TGTTAAAATGTAATTTT
1 GGGTCAAAATGTAATTTT
28706836 TGGACAGTCT
Statistics
Matches: 297, Mismatches: 39, Indels: 77
0.72 0.09 0.19
Matches are distributed among these distances:
26 3 0.01
27 4 0.01
28 12 0.04
29 87 0.29
30 137 0.46
31 44 0.15
32 6 0.02
33 4 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGAAAAGTTTGA
Found at i:28706666 original size:60 final size:59
Alignment explanation
Indices: 28706431--28706835 Score: 280
Period size: 60 Copynumber: 6.8 Consensus size: 59
28706421 TGGTAAAATC
** * * *
28706431 GGGGTCAAAATGGGATTTTGAAAAGTTTGGGGGGT-AAAATGGTAATTTTTGGTAAAA--TT-
1 GGGGTCAAAATGTAATTTTGAAAAGTTT-GAGGGTCAAAAT-ATAA-TTTTAG-AAAAGTTTA
* * * * * *
28706490 GGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATAGTAACTTTTGGTAAAA--TCA
1 GGGGTCAAAATGTAATTTTGAAAAGTTTGAGGGTCAAAATA-TAA-TTTTAG-AAAAGTTTA
* * * * * *
28706549 -AGGTCAAAAATGGAATTTTGGAAAG-TTGAGGGGTAAAAATGTAATTTTAG-AAAGTTTT
1 GGGGTC-AAAATGTAATTTTGAAAAGTTTGA-GGGTCAAAATATAATTTTAGAAAAGTTTA
* * * * *
28706607 GAGGTCAAAATATAATTTTGAAATAGTTTGAGGGTCCAAATGTAATTTTTAG-AAAGTTTT
1 GGGGTCAAAATGTAATTTTGAAA-AGTTTGAGGGTCAAAATATAA-TTTTAGAAAAGTTTA
*
28706667 GGGGTCAAAATGTAATTTTTAGAAAA-TTTTAGGGTCAAAATATAATTTTAGAAAAGTTTA
1 GGGGTCAAAATGTAA-TTTT-GAAAAGTTTGAGGGTCAAAATATAATTTTAGAAAAGTTTA
* * * *
28706727 GGGGTAAAAATGCAATTTTTAGAAAGTTTTG-GGGTTAAAATATAATTTTAGAAAAGTTTA
1 GGGGTCAAAATGTAATTTTGA-AAAG-TTTGAGGGTCAAAATATAATTTTAGAAAAGTTTA
* * * *
28706787 GGGGTCAAAATGTAATTATTAGAAAGGTTTGA-TGTTAAAATGTAATTTT
1 GGGGTCAAAATGTAATT-TT-GAAAAGTTTGAGGGTCAAAATATAATTTT
28706836 TGGACAGTCT
Statistics
Matches: 289, Mismatches: 37, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
56 3 0.01
58 52 0.18
59 82 0.28
60 134 0.46
61 13 0.04
62 5 0.02
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (59 bp):
GGGGTCAAAATGTAATTTTGAAAAGTTTGAGGGTCAAAATATAATTTTAGAAAAGTTTA
Found at i:28706827 original size:90 final size:89
Alignment explanation
Indices: 28706549--28706836 Score: 332
Period size: 90 Copynumber: 3.2 Consensus size: 89
28706539 GGTAAAATCA
* * ** * *
28706549 AGGTCAAAAATGGAA-TTTTGGAAAGTTGAGGGGTAAAAATGTAATTTTAG-AAAGTTTTGAGGT
1 AGGT-AAAAATGTAATTTTTAGAAAGTTTTGGGGTAAAAATGTAATTTTAGAAAAGTTTAGGGGT
28706612 CAAAATATAATTTT-GAAATAGTTTG
65 CAAAATATAATTTTAGAAA-AGTTTG
** * *
28706637 AGGGTCCAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAATTTTA-GGG
1 A-GGTAAAAATGTAATTTTTAGAAAGTTTTGGGGTAAAAATGTAA-TTTTAGAAAAGTTTAGGGG
28706701 TCAAAATATAATTTTAGAAAAGTTTAG
64 TCAAAATATAATTTTAGAAAAGTTT-G
* * * *
28706728 GGGTAAAAATGCAATTTTTAGAAAGTTTTGGGGTTAAAATATAATTTTAGAAAAGTTTAGGGGTC
1 AGGTAAAAATGTAATTTTTAGAAAGTTTTGGGGTAAAAATGTAATTTTAGAAAAGTTTAGGGGTC
* *
28706793 AAAATGTAATTATTAGAAAGGTTTG
66 AAAATATAATT-TTAGAAAAGTTTG
* *
28706818 ATGTTAAAATGTAATTTTT
1 AGGTAAAAATGTAATTTTT
28706837 GGACAGTCTA
Statistics
Matches: 169, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
88 8 0.05
89 42 0.25
90 97 0.57
91 22 0.13
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.37
Consensus pattern (89 bp):
AGGTAAAAATGTAATTTTTAGAAAGTTTTGGGGTAAAAATGTAATTTTAGAAAAGTTTAGGGGTC
AAAATATAATTTTAGAAAAGTTTG
Found at i:28708228 original size:26 final size:26
Alignment explanation
Indices: 28708166--28708228 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
28708156 TTGTAATTGA
* *
28708166 ATTGATTTCTCAGAAAGGGTTCATGT
1 ATTGATTTCTCACAAAGGGTTCATAT
*
28708192 ATTGATTTTTCTTC-CAAAGGGTTCGTAT
1 ATTGA--TTTC-TCACAAAGGGTTCATAT
28708220 ATTGATTTC
1 ATTGATTTC
28708229 AAGAACAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 9 0.29
28 20 0.65
29 2 0.06
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (26 bp):
ATTGATTTCTCACAAAGGGTTCATAT
Found at i:28708743 original size:20 final size:20
Alignment explanation
Indices: 28708685--28708737 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
28708675 AATTTGATTG
*
28708685 AATTTAAATTT--AAAG-CA
1 AATTTAAATTTAAAAAGATA
28708702 AATTTAAATTTAAAAAGATA
1 AATTTAAATTTAAAAAGATA
28708722 AATTTAAATTTAAAAA
1 AATTTAAATTTAAAAA
28708738 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 11 0.34
19 4 0.12
20 17 0.53
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (20 bp):
AATTTAAATTTAAAAAGATA
Found at i:28708749 original size:14 final size:14
Alignment explanation
Indices: 28708707--28708749 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
28708697 AAGCAAATTT
* *
28708707 AAATTTAAAAAGAT
1 AAATTTAAAAATAA
**
28708721 AAATTTAAATTTAA
1 AAATTTAAAAATAA
28708735 AAATTTAAAAATAA
1 AAATTTAAAAATAA
28708749 A
1 A
28708750 TTTGAATCAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAATTTAAAAATAA
Found at i:28708749 original size:20 final size:20
Alignment explanation
Indices: 28708706--28708752 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28708696 AAAGCAAATT
**
28708706 TAAATTTAAAAAGATAAATT
1 TAAATTTAAAAAGATAAAAA
**
28708726 TAAATTTAAAAATTTAAAAA
1 TAAATTTAAAAAGATAAAAA
28708746 TAAATTT
1 TAAATTT
28708753 GAATCAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAATTTAAAAAGATAAAAA
Found at i:28709055 original size:17 final size:17
Alignment explanation
Indices: 28709025--28709058 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28709015 TTTTTGACCA
**
28709025 TTTAAATTTTTAAAAAT
1 TTTAAATTAATAAAAAT
28709042 TTTAAATTAATAAAAAT
1 TTTAAATTAATAAAAAT
28709059 AAAATTACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAATAAAAAT
Found at i:28709504 original size:17 final size:18
Alignment explanation
Indices: 28709482--28709515 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28709472 TTTATAAGTT
28709482 TTTTTATAAAA-ATTATA
1 TTTTTATAAAACATTATA
28709499 TTTTTATAAAACATTAT
1 TTTTTATAAAACATTAT
28709516 GAAAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTATAAAACATTATA
Found at i:28711453 original size:14 final size:14
Alignment explanation
Indices: 28711436--28711462 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28711426 AACATAAAAA
28711436 TTAAAAATATATAT
1 TTAAAAATATATAT
28711450 TTAAAAATATATA
1 TTAAAAATATATA
28711463 AATTTATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:28720933 original size:26 final size:26
Alignment explanation
Indices: 28720900--28720960 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
28720890 GGTCCAAAAT
*
28720900 ATTTTTTTTATCTTTTAA-ACACCAAC
1 ATTTTTTTTAACTTTTAAGACACC-AC
* *
28720926 ATTTTTTTTAACTTTTAAGAGACCCC
1 ATTTTTTTTAACTTTTAAGACACCAC
28720952 ATTTTTTTT
1 ATTTTTTTT
28720961 TTTAGTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.26, C:0.16, G:0.03, T:0.54
Consensus pattern (26 bp):
ATTTTTTTTAACTTTTAAGACACCAC
Found at i:28722821 original size:30 final size:29
Alignment explanation
Indices: 28722776--28723031 Score: 168
Period size: 30 Copynumber: 8.7 Consensus size: 29
28722766 TGGACTTTCA
28722776 GGGGT-AAAATGGTAATTTTGAGAAAATTTT
1 GGGGTAAAAAT-GTAATTTTG-GAAAATTTT
* *
28722806 GGGTTAAAAATGTAATTTTTGG--AATTTGA
1 GGGGTAAAAATGTAA-TTTTGGAAAATTT-T
*
28722835 GGGGTAAAAATGTAATTTTAGG-AAGTTTT
1 GGGGTAAAAATGTAATTTT-GGAAAATTTT
* *
28722864 GGGGTTAAAAATGGAATTTTTTG--AATTTT
1 GGGG-TAAAAATGTAA-TTTTGGAAAATTTT
* * * *
28722893 AGGGTTAAAAATGTAATTTTTGAAAAGTTC
1 -GGGGTAAAAATGTAATTTTGGAAAATTTT
* * * *
28722923 GAGGGCAAAAATATAATTTTTGAAAAGTTTG
1 G-GGGTAAAAATGTAATTTTGGAAAA-TTTT
* *
28722954 GGGGTAAAAATATAATTTTTGG-AAGTTTT
1 GGGGTAAAAATGTAA-TTTTGGAAAATTTT
* *
28722983 GGGATTAAAAA-GTAATTTTGGAGAAGTTTT
1 GGG-GTAAAAATGTAATTTTGGA-AAATTTT
* *
28723013 GGGGTCAAAATATAATTTT
1 GGGGTAAAAATGTAATTTT
28723032 TGGATAGTTT
Statistics
Matches: 183, Mismatches: 26, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
28 21 0.11
29 50 0.27
30 90 0.49
31 22 0.12
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.38
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTGGAAAATTTT
Found at i:28722826 original size:59 final size:59
Alignment explanation
Indices: 28722753--28723001 Score: 222
Period size: 59 Copynumber: 4.2 Consensus size: 59
28722743 TACCCGGGGG
*
28722753 AAAATGCTAA-TTTTGGACTTTCAGGGGT-AAAATGGTAATTTTGAGAAAATTTT-GGGTTA
1 AAAATG-TAATTTTTGGAATTTCAGGGGTAAAAAT-GTAATTTT-AGAAAATTTTGGGGTTA
* * *
28722812 AAAATGTAATTTTTGGAATTTGAGGGGTAAAAATGTAATTTTAGGAAGTTTTGGGGTTA
1 AAAATGTAATTTTTGGAATTTCAGGGGTAAAAATGTAATTTTAGAAAATTTTGGGGTTA
* * * * * * * *
28722871 AAAATGGAATTTTTTGAATTTTAGGGTTAAAAATGTAATTTTTGAAAAGTTCGAGGG-CA
1 AAAATGTAATTTTTGGAATTTCAGGGGTAAAAATGTAATTTTAGAAAATTTTG-GGGTTA
* * * * * * * *
28722930 AAAATATAATTTTTGAAAAGTTT-GGGGGTAAAAATATAATTTTTGGAAGTTTTGGGATTA
1 AAAATGTAATTTTTG-GAA-TTTCAGGGGTAAAAATGTAATTTTAGAAAATTTTGGGGTTA
28722990 AAAA-GTAATTTT
1 AAAATGTAATTTT
28723002 GGAGAAGTTT
Statistics
Matches: 155, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
58 11 0.07
59 102 0.66
60 39 0.25
61 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAATTTCAGGGGTAAAAATGTAATTTTAGAAAATTTTGGGGTTA
Found at i:28723017 original size:59 final size:59
Alignment explanation
Indices: 28722802--28723046 Score: 223
Period size: 59 Copynumber: 4.1 Consensus size: 59
28722792 TTTGAGAAAA
* * *
28722802 TTTTGGG-TTAAAAATGTAATTTTTG-GAATTTGAGGGGTAAAAATGTAATTTTAGGAAG
1 TTTTGGGATTAAAAATGTAATTTTTGAGAATTT-TGGGGTAAAAATATAATTTTTGGAAG
* * * * * *
28722860 TTTTGGGGTTAAAAATGGAATTTTT-TGAATTTTAGGGTTAAAAATGTAATTTTTGAAAAG
1 TTTTGGGATTAAAAATGTAATTTTTGAGAATTTT-GGGGTAAAAATATAATTTTTG-GAAG
* ** * * *
28722920 -TTCGAGG-GCAAAAATATAATTTTTGAAAAGTTTGGGGGTAAAAATATAATTTTTGGAAG
1 TTTTG-GGATTAAAAATGTAATTTTTGAGAA-TTTTGGGGTAAAAATATAATTTTTGGAAG
* *
28722979 TTTTGGGATTAAAAA-GTAATTTTGGAGAAGTTTTGGGGTCAAAATATAATTTTTGGATAG
1 TTTTGGGATTAAAAATGTAATTTTTGAGAA-TTTTGGGGTAAAAATATAATTTTTGGA-AG
*
28723039 TTTAGGGA
1 TTTTGGGA
28723047 CCTCCAAAGC
Statistics
Matches: 152, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
58 7 0.05
59 99 0.65
60 43 0.28
61 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.39
Consensus pattern (59 bp):
TTTTGGGATTAAAAATGTAATTTTTGAGAATTTTGGGGTAAAAATATAATTTTTGGAAG
Found at i:28723041 original size:30 final size:29
Alignment explanation
Indices: 28722802--28723041 Score: 200
Period size: 30 Copynumber: 8.1 Consensus size: 29
28722792 TTTGAGAAAA
* *
28722802 TTTTGGGTTAAAAATGTAATTTTTGGAA-
1 TTTTGGGGTAAAAATATAATTTTTGGAAG
* * *
28722830 TTTGAGGGGTAAAAATGTAATTTTAGGAAG
1 TTT-TGGGGTAAAAATATAATTTTTGGAAG
** *
28722860 TTTTGGGGTTAAAAATGGAATTTTTTGAA-
1 TTTTGGGG-TAAAAATATAATTTTTGGAAG
* * *
28722889 TTTTAGGGTTAAAAATGTAATTTTTGAAAAG
1 TTTT-GGGGTAAAAATATAATTTTTG-GAAG
* * *
28722920 -TTCGAGGGCAAAAATATAATTTTTGAAAAG
1 TTTTG-GGGTAAAAATATAATTTTTG-GAAG
*
28722950 TTTGGGGGTAAAAATATAATTTTTGGAAG
1 TTTTGGGGTAAAAATATAATTTTTGGAAG
* * *
28722979 TTTTGGGATTAAAAA-GTAATTTTGGAGAAG
1 TTTTGGG-GTAAAAATATAATTTTTG-GAAG
*
28723009 TTTTGGGGTCAAAATATAATTTTTGGATAG
1 TTTTGGGGTAAAAATATAATTTTTGGA-AG
28723039 TTT
1 TTT
28723042 AGGGACCTCC
Statistics
Matches: 174, Mismatches: 26, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.02
29 70 0.40
30 98 0.56
31 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.40
Consensus pattern (29 bp):
TTTTGGGGTAAAAATATAATTTTTGGAAG
Found at i:28725040 original size:58 final size:58
Alignment explanation
Indices: 28724961--28725098 Score: 154
Period size: 59 Copynumber: 2.4 Consensus size: 58
28724951 TTTTGGATAC
* * ** * *
28724961 TCGGGGGCAAAATGGTAATTTTGGTTGAAA-TTGGGTCAAAAATGGGATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTGG-TAAAACCGGGGTCAAAAATGGAATTTTAGAAAGT
* * *
28725019 TCGGGGGTAATATGGTAATTTTTGGTAAAACCGGGGTTAAAAATGGAATTTTAGAAGGT
1 TCGGGGGTAAAATGGTAA-TTTTGGTAAAACCGGGGTCAAAAATGGAATTTTAGAAAGT
*
28725078 TCGAGGGTAAAAT-GTAATTTT
1 TCGGGGGTAAAATGGTAATTTT
28725099 TAGAAAGTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
57 4 0.06
58 24 0.36
59 39 0.58
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (58 bp):
TCGGGGGTAAAATGGTAATTTTGGTAAAACCGGGGTCAAAAATGGAATTTTAGAAAGT
Found at i:28725042 original size:30 final size:30
Alignment explanation
Indices: 28725008--28725253 Score: 84
Period size: 30 Copynumber: 8.3 Consensus size: 30
28724998 AAAAATGGGA
* *
28725008 TTTTGGAAAGTTCGGGGGTAATATGGTAAT
1 TTTTAGAAAGTTCGGGGGTAAAATGGTAAT
* ** *
28725038 TTTTGGTAAA-ACCGGGGTTAAAAATGG-AA-
1 TTTTAG-AAAGTTCGGGGGT-AAAATGGTAAT
* *
28725067 TTTTAGAAGGTTCGAGGGTAAAAT-GTAAT
1 TTTTAGAAAGTTCGGGGGTAAAATGGTAAT
*** *
28725096 TTTTAGAAAGTTTTAGGGTCAAAAT-ATAAT
1 TTTTAGAAAGTTCGGGGGT-AAAATGGTAAT
* ***
28725126 TTTGGAGAAA-TTTAAGGGTCAAAAT-GTAAT
1 TTT-TAGAAAGTTCGGGGGT-AAAATGGTAAT
* *
28725156 TTTTAGAAAGTTTAGGGGTTAAAAT-GTAAT
1 TTTTAGAAAG-TTCGGGGGTAAAATGGTAAT
* * ** * * *
28725186 ATTCA-AAAGGTTTTGAGGTTAAAT-ATAA-
1 TTTTAGAAA-GTTCGGGGGTAAAATGGTAAT
* * *
28725214 TTTTGGAGAAGTTTGGGGTTAAAAT-GTAAT
1 TTTTAGA-AAGTTCGGGGGTAAAATGGTAAT
28725244 TTTTAGAAAG
1 TTTTAGAAAG
28725254 CTTTAGGGTT
Statistics
Matches: 164, Mismatches: 39, Indels: 27
0.71 0.17 0.12
Matches are distributed among these distances:
27 1 0.01
28 11 0.07
29 64 0.39
30 69 0.42
31 19 0.12
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
TTTTAGAAAGTTCGGGGGTAAAATGGTAAT
Found at i:28725265 original size:30 final size:29
Alignment explanation
Indices: 28725052--28725268 Score: 185
Period size: 30 Copynumber: 7.3 Consensus size: 29
28725042 GGTAAAACCG
* * *
28725052 GGGTTAAAAATGGAA-TTTTAGAAGGTTCGA
1 GGGTT-AAAATGTAATTTTTAGAAAGTT-TA
28725082 GGG-TAAAATGTAATTTTTAGAAAGTTTTA
1 GGGTTAAAATGTAATTTTTAGAAAG-TTTA
* * *
28725111 GGGTCAAAATATAATTTTGGAGAAA-TTTAA
1 GGGTTAAAATGTAATTTT-TAGAAAGTTT-A
*
28725141 GGGTCAAAATGTAATTTTTAGAAAGTTTA
1 GGGTTAAAATGTAATTTTTAGAAAGTTTA
* * *
28725170 GGGGTTAAAATGTAATATTCA-AAAGGTTTT
1 -GGGTTAAAATGTAATTTTTAGAAA-GTTTA
* * *
28725200 GAGGTT-AAATATAA-TTTTGGAGAAGTTTG
1 G-GGTTAAAATGTAATTTTTAGA-AAGTTTA
28725229 GGGTTAAAATGTAATTTTTAGAAAGCTTTA
1 GGGTTAAAATGTAATTTTTAGAAAG-TTTA
28725259 GGGTTAAAAT
1 GGGTTAAAAT
28725269 ACCATTTTTG
Statistics
Matches: 153, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
28 14 0.09
29 50 0.33
30 84 0.55
31 5 0.03
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTTAGAAAGTTTA
Found at i:28725987 original size:14 final size:14
Alignment explanation
Indices: 28725970--28726000 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28725960 TTCTCTTTTC
28725970 CTTTTTCTTTTGTT
1 CTTTTTCTTTTGTT
*
28725984 CTTTTTGTTTTGTT
1 CTTTTTCTTTTGTT
28725998 CTT
1 CTT
28726001 AAACTTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (14 bp):
CTTTTTCTTTTGTT
Found at i:28727032 original size:6 final size:6
Alignment explanation
Indices: 28727018--28727074 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
28727008 GATTTTTTAA
* * * *
28727018 TTAATT TTAAAT TTAAAT TCAAA- TTAAAT TTAAAC TT-AAT TAAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
28727064 TTAAAC TTAAA
1 TTAAAT TTAAA
28727075 AGAAAAGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 7 0.17
6 34 0.83
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:28727036 original size:17 final size:17
Alignment explanation
Indices: 28727018--28727073 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
28727008 GATTTTTTAA
28727018 TTAATTTTAAATTTAAA-
1 TTAA-TTTAAATTTAAAC
*
28727035 TTCAAATTAAATTTAAAC
1 TT-AATTTAAATTTAAAC
*
28727053 TTAATTAAAATTTAAAC
1 TTAATTTAAATTTAAAC
28727070 TTAA
1 TTAA
28727074 AAGAAAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATTTAAATTTAAAC
Done.