Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 83 of 135
Found at i:27930162 original size:27 final size:26
Alignment explanation
Indices: 27930131--27930182 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
27930121 AAATTTTGTT
*
27930131 CAGTTTTTATTTAAACATTTTTAAATA
1 CAGTTTTTATATAAA-ATTTTTAAATA
*
27930158 CAGTTTTTATATCAAATTTTTAAAT
1 CAGTTTTTATATAAAATTTTTAAAT
27930183 GTATACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.52
Consensus pattern (26 bp):
CAGTTTTTATATAAAATTTTTAAATA
Found at i:27931587 original size:94 final size:94
Alignment explanation
Indices: 27931479--27931667 Score: 342
Period size: 94 Copynumber: 2.0 Consensus size: 94
27931469 TATGTCTAAA
* * *
27931479 TTTTCAAAACATACGTACGTTTTTTAATTGTTTTATTTACATTTTATTTGTATTTGTTTATAATT
1 TTTTCAAAAAATACGTACGTTTTTTAATTGTTTTATTTACATTTTATTTGTATTTGGTTATAACT
27931544 ATTTACAACTTTTTATATTTTTAGGTTTT
66 ATTTACAACTTTTTATATTTTTAGGTTTT
*
27931573 TTTTCAAAAAATACGTACGTTTTTTGATTGTTTTATTTACATTTTATTTGTATTTGGTTATAACT
1 TTTTCAAAAAATACGTACGTTTTTTAATTGTTTTATTTACATTTTATTTGTATTTGGTTATAACT
27931638 ATTTACAACTTTTTATATTTTTAGGTTTT
66 ATTTACAACTTTTTATATTTTTAGGTTTT
27931667 T
1 T
27931668 AGTTGTGATT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.25, C:0.07, G:0.08, T:0.59
Consensus pattern (94 bp):
TTTTCAAAAAATACGTACGTTTTTTAATTGTTTTATTTACATTTTATTTGTATTTGGTTATAACT
ATTTACAACTTTTTATATTTTTAGGTTTT
Found at i:27931819 original size:17 final size:18
Alignment explanation
Indices: 27931783--27931821 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
27931773 AAATCAAATT
*
27931783 AATTTGATTAATCGATTA
1 AATTTAATTAATCGATTA
27931801 AATTTAATTAATCGA-TA
1 AATTTAATTAATCGATTA
27931818 AATT
1 AATT
27931822 AATCGAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (18 bp):
AATTTAATTAATCGATTA
Found at i:27935124 original size:96 final size:96
Alignment explanation
Indices: 27934960--27935154 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 96
27934950 ATTTTTATTA
*
27934960 TCAAACTAGACAATTGTAACTTAACACTGTCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
1 TCAAACTAGACAATTGTAACTTAACACTGCCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
27935025 AGTACCATAATCAGGTGGAGGTTCAATCAAG
66 AGTACCATAATCAGGTGGAGGTTCAATCAAG
27935056 TCAAACTAGACAATTGTAACTTAACACTGCCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
1 TCAAACTAGACAATTGTAACTTAACACTGCCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
27935121 AGTACCATAATCAGGTGGAGGTTCAATCAAG
66 AGTACCATAATCAGGTGGAGGTTCAATCAAG
27935152 TCA
1 TCA
27935155 TTGTCAGGGT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (96 bp):
TCAAACTAGACAATTGTAACTTAACACTGCCAAAGCTTGAAATTAGGAAGAAATAGGGGAATCTT
AGTACCATAATCAGGTGGAGGTTCAATCAAG
Found at i:27940167 original size:27 final size:27
Alignment explanation
Indices: 27940122--27940184 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
27940112 GGTACAAGGG
* *
27940122 GTGGTGCCTATCTGACAGGCGACACTA
1 GTGGTGCCTACCTGACAGGCGACACCA
* *
27940149 GTGGTGCCTACCTGCCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGACACCA
*
27940176 ATGGTGCCT
1 GTGGTGCCT
27940185 TTCTGTCAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.21
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGACACCA
Found at i:27941375 original size:5 final size:5
Alignment explanation
Indices: 27941367--27941394 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27941357 TTAAAAAAGA
27941367 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
27941395 ATTTGACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:27941465 original size:27 final size:27
Alignment explanation
Indices: 27941403--27941466 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
27941393 AAATTTGACA
*
27941403 AGTGGTGCCTTTAGGGTAGGCGGCACC
1 AGTGGTGCCTCTAGGGTAGGCGGCACC
* * *
27941430 AATGTTGCCTACT-GGGTAGGCGGCACT
1 AGTGGTGCCT-CTAGGGTAGGCGGCACC
27941457 AGTGGTGCCT
1 AGTGGTGCCT
27941467 TTGTCAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.38, T:0.25
Consensus pattern (27 bp):
AGTGGTGCCTCTAGGGTAGGCGGCACC
Found at i:27941583 original size:25 final size:25
Alignment explanation
Indices: 27941553--27941609 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
27941543 AAATTTTAAC
* *
27941553 AACAAATTTTTGAAGAAGGAAAGGA
1 AACAAAGTTTTGAAGAAGAAAAGGA
*
27941578 AGCAAAAGTTTTGAAGAAGAAAAGGA
1 AAC-AAAGTTTTGAAGAAGAAAAGGA
27941604 AACAAA
1 AACAAA
27941610 AGGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.16
Consensus pattern (25 bp):
AACAAAGTTTTGAAGAAGAAAAGGA
Found at i:27941589 original size:26 final size:26
Alignment explanation
Indices: 27941560--27941611 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
27941550 AACAACAAAT
* *
27941560 TTTTGAAGAAGGAAAGGAAGCAAAAG
1 TTTTGAAGAAGAAAAGGAAACAAAAG
27941586 TTTTGAAGAAGAAAAGGAAACAAAAG
1 TTTTGAAGAAGAAAAGGAAACAAAAG
27941612 GTTAGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.27, T:0.15
Consensus pattern (26 bp):
TTTTGAAGAAGAAAAGGAAACAAAAG
Found at i:27944799 original size:33 final size:33
Alignment explanation
Indices: 27944757--27944829 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
27944747 TACTGTAACG
* *
27944757 GGCTGAAAGGATTAGAGAACTGTGATGGTATCA
1 GGCTGAAAGGAATAGAGAACTGTGATAGTATCA
* *
27944790 GGCTGAAAGGAATAGAGAACTGTGGTAGTATCG
1 GGCTGAAAGGAATAGAGAACTGTGATAGTATCA
27944823 GGCTGAA
1 GGCTGAA
27944830 GATATCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.33, C:0.10, G:0.36, T:0.22
Consensus pattern (33 bp):
GGCTGAAAGGAATAGAGAACTGTGATAGTATCA
Found at i:27945025 original size:6 final size:6
Alignment explanation
Indices: 27945014--27945040 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27945004 ATAGTGCTGC
27945014 GGCTCA GGCTCA GGCTCA GGCTCA GGC
1 GGCTCA GGCTCA GGCTCA GGCTCA GGC
27945041 AACTGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (6 bp):
GGCTCA
Found at i:27947789 original size:17 final size:17
Alignment explanation
Indices: 27947767--27947800 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27947757 CTTACAATAA
*
27947767 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
27947784 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
27947801 AAATTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:27950605 original size:27 final size:26
Alignment explanation
Indices: 27950557--27950607 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
27950547 AGGTATTGTC
*
27950557 CGAAAAAAATATTAAATCAGTTAATT
1 CGAAAAAAATATTAAATAAGTTAATT
* *
27950583 CGAAAAATATATTGAATGAAGTTAA
1 CGAAAAAAATATTAAAT-AAGTTAA
27950608 AAATCAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (26 bp):
CGAAAAAAATATTAAATAAGTTAATT
Found at i:27950978 original size:18 final size:18
Alignment explanation
Indices: 27950955--27950997 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27950945 GAATAGTTTT
27950955 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
27950973 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
27950991 TTAATTA
1 TTAATTA
27950998 TACCGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:27962063 original size:28 final size:28
Alignment explanation
Indices: 27962032--27962126 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 28
27962022 TTTATGCTGA
*
27962032 TCAGCTTATATATATGCGTTTACGTTCG
1 TCAGCTTATATATATGCGTTTACGCTCG
** * * *
27962060 TCAGC-T-TGCACA--CGCTTATGCTCG
1 TCAGCTTATATATATGCGTTTACGCTCG
* * *
27962084 TCAGCTTATATATATGTGTTTACACTCA
1 TCAGCTTATATATATGCGTTTACGCTCG
27962112 TCAGCTTATATATAT
1 TCAGCTTATATATAT
27962127 ATATATATAT
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
24 14 0.29
25 1 0.02
26 6 0.12
27 1 0.02
28 27 0.55
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (28 bp):
TCAGCTTATATATATGCGTTTACGCTCG
Found at i:27962064 original size:52 final size:52
Alignment explanation
Indices: 27962007--27962106 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
27961997 ATTTATGCTT
* *
27962007 GTCAGCTTGTACACGTTTATGCT-GATCAGCTTATATATATGCGTTTACGTTC
1 GTCAGCTTGCACACGCTTATGCTCG-TCAGCTTATATATATGCGTTTACGTTC
*
27962059 GTCAGCTTGCACACGCTTATGCTCGTCAGCTTATATATATGTGTTTAC
1 GTCAGCTTGCACACGCTTATGCTCGTCAGCTTATATATATGCGTTTAC
27962107 ACTCATCAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 43 0.98
53 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (52 bp):
GTCAGCTTGCACACGCTTATGCTCGTCAGCTTATATATATGCGTTTACGTTC
Found at i:27962116 original size:52 final size:52
Alignment explanation
Indices: 27962008--27962118 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 52
27961998 TTTATGCTTG
* * ** *
27962008 TCAGCTTGTACACGTTTATGCTGATCAGCTTATATATATGCGTTTACGTTCG
1 TCAGCTTGCACACGCTTATGCTGATCAGCTTATATATATGCGTTTACACTCA
*
27962060 TCAGCTTGCACACGCTTATGCTCG-TCAGCTTATATATATGTGTTTACACTCA
1 TCAGCTTGCACACGCTTATGCT-GATCAGCTTATATATATGCGTTTACACTCA
27962112 TCAGCTT
1 TCAGCTT
27962119 ATATATATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 51 0.98
53 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.39
Consensus pattern (52 bp):
TCAGCTTGCACACGCTTATGCTGATCAGCTTATATATATGCGTTTACACTCA
Found at i:27962125 original size:2 final size:2
Alignment explanation
Indices: 27962118--27962142 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27962108 CTCATCAGCT
27962118 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
27962143 GCGTTTGCGC
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:27963520 original size:24 final size:24
Alignment explanation
Indices: 27963493--27963547 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
27963483 ACAATCAATT
27963493 CATTTTATATTACATTTGCACTGA
1 CATTTTATATTACATTTGCACTGA
*
27963517 CATTTTATATTACTTTTGCACTGA
1 CATTTTATATTACATTTGCACTGA
27963541 CAATTTT
1 C-ATTTT
27963548 TACTCTTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.49
Consensus pattern (24 bp):
CATTTTATATTACATTTGCACTGA
Found at i:27968037 original size:29 final size:29
Alignment explanation
Indices: 27967995--27968053 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
27967985 ATAGGATGAA
27967995 AGGTTCCTTAGGAGAAAAGGGACGGTGGT
1 AGGTTCCTTAGGAGAAAAGGGACGGTGGT
*
27968024 AGGTTCCTTAGGAGAAAAGGGATGGTGGT
1 AGGTTCCTTAGGAGAAAAGGGACGGTGGT
27968053 A
1 A
27968054 ATAGGCAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.41, T:0.22
Consensus pattern (29 bp):
AGGTTCCTTAGGAGAAAAGGGACGGTGGT
Found at i:27980710 original size:16 final size:16
Alignment explanation
Indices: 27980689--27980721 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
27980679 TCTTTCATTT
27980689 TCACCATTGTTTTCCC
1 TCACCATTGTTTTCCC
27980705 TCACCATTGTTTTCCC
1 TCACCATTGTTTTCCC
27980721 T
1 T
27980722 TTTTTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.36, G:0.06, T:0.45
Consensus pattern (16 bp):
TCACCATTGTTTTCCC
Found at i:27980731 original size:74 final size:74
Alignment explanation
Indices: 27980648--27980785 Score: 226
Period size: 74 Copynumber: 1.9 Consensus size: 74
27980638 CATGTTCCGA
*
27980648 TTTTTCTTCAAAGAAA-ATTTAACCCATTTTTTCTTTC-ATTTTCACCATTGTTTTCCCTCACCA
1 TTTTTCTTCAAAGAAATA-TTAACCCATTTTTTCTTTCGA-TTTCACCATCGTTTTCCCTCACCA
27980711 TTGTTTTCCCT
64 TTGTTTTCCCT
*
27980722 TTTTTCTTCAAAGAAATATTAACCCTTTTTTTCTTTCGATTTCACCATCGTTTTCCCTCACCAT
1 TTTTTCTTCAAAGAAATATTAACCCATTTTTTCTTTCGATTTCACCATCGTTTTCCCTCACCAT
27980786 CATTTATCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
74 58 0.97
75 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.04, T:0.49
Consensus pattern (74 bp):
TTTTTCTTCAAAGAAATATTAACCCATTTTTTCTTTCGATTTCACCATCGTTTTCCCTCACCATT
GTTTTCCCT
Found at i:27980847 original size:22 final size:22
Alignment explanation
Indices: 27980799--27980852 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
27980789 TTATCATTTC
* * *
27980799 CTTTCGTTTTGCCTCTGCATCT
1 CTTTCGTTTTCCCTCAGCAACT
* *
27980821 ATTTCGTTTTCCCTCAGTAACT
1 CTTTCGTTTTCCCTCAGCAACT
*
27980843 CTTTCATTTT
1 CTTTCGTTTT
27980853 TTGTTTCATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.11, C:0.28, G:0.09, T:0.52
Consensus pattern (22 bp):
CTTTCGTTTTCCCTCAGCAACT
Found at i:27986239 original size:20 final size:20
Alignment explanation
Indices: 27986052--27986230 Score: 200
Period size: 20 Copynumber: 9.0 Consensus size: 20
27986042 AAATGAAGAA
27986052 GTGCCCCTGTATGCACTTCG
1 GTGCCCCTGTATGCACTTCG
* *
27986072 GTGCCCCTATTTGCACTTCG
1 GTGCCCCTGTATGCACTTCG
* * **
27986092 ATGCCCCTGTTTGCACTTTT
1 GTGCCCCTGTATGCACTTCG
*
27986112 GTGCTCCTGTATGCACTTCG
1 GTGCCCCTGTATGCACTTCG
* *
27986132 ATGCCCTTGTATGCACTTCG
1 GTGCCCCTGTATGCACTTCG
* *
27986152 GTGCCCCTGTTTGCACTTTG
1 GTGCCCCTGTATGCACTTCG
* * *
27986172 GTGCCTCTATTTGCACTTCG
1 GTGCCCCTGTATGCACTTCG
*
27986192 GTGCCCCTG-ATGCACACTC-
1 GTGCCCCTGTATGCAC-TTCG
27986211 GTGCCCCTGTATGCACTTCG
1 GTGCCCCTGTATGCACTTCG
27986231 ATGTCCCTGA
Statistics
Matches: 130, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
19 16 0.12
20 114 0.88
ACGTcount: A:0.11, C:0.33, G:0.22, T:0.35
Consensus pattern (20 bp):
GTGCCCCTGTATGCACTTCG
Found at i:27988209 original size:4 final size:4
Alignment explanation
Indices: 27988195--27988254 Score: 57
Period size: 4 Copynumber: 13.8 Consensus size: 4
27988185 ATAACAGTAA
* *
27988195 ACAT AACAT ACAT ACAA ATAT ACAT AACAT ACAT AACAT ACAT AACAAT
1 ACAT -ACAT ACAT ACAT ACAT ACAT -ACAT ACAT -ACAT ACAT -AC-AT
27988244 ACAT ACAT ACA
1 ACAT ACAT ACA
27988255 AAAATAGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
4 29 0.62
5 16 0.34
6 2 0.04
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:27988226 original size:9 final size:9
Alignment explanation
Indices: 27988194--27988254 Score: 74
Period size: 9 Copynumber: 6.9 Consensus size: 9
27988184 TATAACAGTA
27988194 AACATAACAT
1 AACAT-ACAT
27988204 -ACATACA-
1 AACATACAT
*
27988211 AATATACAT
1 AACATACAT
27988220 AACATACAT
1 AACATACAT
27988229 AACATACAT
1 AACATACAT
27988238 AACAATACAT
1 AAC-ATACAT
27988248 -ACATACA
1 AACATACA
27988255 AAAATAGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
8 14 0.30
9 26 0.57
10 6 0.13
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (9 bp):
AACATACAT
Found at i:27988231 original size:30 final size:27
Alignment explanation
Indices: 27988195--27988254 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 27
27988185 ATAACAGTAA
27988195 ACATAACATACATACAAATATACATAACAT
1 ACATAACATACATA-AAA-ATACAT-ACAT
*
27988225 ACATAACATACATAACAATACATACAT
1 ACATAACATACATAAAAATACATACAT
27988252 ACA
1 ACA
27988255 AAAATAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 7 0.24
28 6 0.21
29 2 0.07
30 14 0.48
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (27 bp):
ACATAACATACATAAAAATACATACAT
Found at i:27988426 original size:30 final size:30
Alignment explanation
Indices: 27988363--27988426 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
27988353 CAATAAAAAC
**
27988363 AAAAAATAAAAGTTAGATATAATACGACTT
1 AAAAAATAAAAGTTAGATATAATACGAAAT
* *
27988393 AAAAAATAAAAGTTATATATAATACTAAAT
1 AAAAAATAAAAGTTAGATATAATACGAAAT
27988423 AAAA
1 AAAA
27988427 CAATCAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (30 bp):
AAAAAATAAAAGTTAGATATAATACGAAAT
Found at i:27989176 original size:29 final size:29
Alignment explanation
Indices: 27989131--27989187 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
27989121 CAGTGGACGA
* *
27989131 AAAAAAAAGTTTGGGTACCAATCTGGGAC
1 AAAAAAAACTTTAGGTACCAATCTGGGAC
27989160 AAAAAAAACTTTAGGTACCAATCTGGGA
1 AAAAAAAACTTTAGGTACCAATCTGGGA
27989188 GAAGTGGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (29 bp):
AAAAAAAACTTTAGGTACCAATCTGGGAC
Found at i:27989305 original size:21 final size:22
Alignment explanation
Indices: 27989281--27989330 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
27989271 ACTTCTACTG
*
27989281 ATACAAGTGACAGTTTTATC-A
1 ATACAAGTGACACTTTTATCGA
* *
27989302 ATACAAGAGACTCTTTTATCGA
1 ATACAAGTGACACTTTTATCGA
27989324 A-ACAAGT
1 ATACAAGT
27989331 CATACATCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (22 bp):
ATACAAGTGACACTTTTATCGA
Found at i:28009720 original size:15 final size:15
Alignment explanation
Indices: 28009702--28009757 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
28009692 CTGAGATTGT
*
28009702 TGCTGTTGTTGTTGA
1 TGCTGTTGCTGTTGA
*
28009717 TGCTGTTGCTGTTGC
1 TGCTGTTGCTGTTGA
* *
28009732 TGCTGTTGCTGCTGC
1 TGCTGTTGCTGTTGA
*
28009747 TGCTGCTGCTG
1 TGCTGTTGCTG
28009758 CTGCTGCTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.02, C:0.20, G:0.34, T:0.45
Consensus pattern (15 bp):
TGCTGTTGCTGTTGA
Found at i:28009723 original size:9 final size:9
Alignment explanation
Indices: 28009699--28009781 Score: 82
Period size: 9 Copynumber: 9.6 Consensus size: 9
28009689 TTGCTGAGAT
*
28009699 TGTTGCTGT
1 TGTTGCTGC
* *
28009708 TGTTGTTGA
1 TGTTGCTGC
* *
28009717 TGCTGTTGC
1 TGTTGCTGC
28009726 TGTTGCTGC
1 TGTTGCTGC
28009735 TGTTGCTGC
1 TGTTGCTGC
28009744 ---TGCTGC
1 TGTTGCTGC
*
28009750 TGCTGCTGC
1 TGTTGCTGC
*
28009759 TGCTGCTGC
1 TGTTGCTGC
28009768 TGTTGCTGC
1 TGTTGCTGC
28009777 TGTTG
1 TGTTG
28009782 TCGGTGATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
6 6 0.09
9 58 0.91
ACGTcount: A:0.01, C:0.20, G:0.34, T:0.45
Consensus pattern (9 bp):
TGTTGCTGC
Found at i:28009731 original size:6 final size:6
Alignment explanation
Indices: 28009717--28009778 Score: 88
Period size: 6 Copynumber: 10.3 Consensus size: 6
28009707 TTGTTGTTGA
* * *
28009717 TGCTGT TGCTGT TGCTGC TGTTGC TGCTGC TGCTGC TGCTGC TGCTGC
1 TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC
*
28009765 TGCTGT TGCTGC TG
1 TGCTGC TGCTGC TG
28009779 TTGTCGGTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.00, C:0.26, G:0.34, T:0.40
Consensus pattern (6 bp):
TGCTGC
Found at i:28009758 original size:15 final size:15
Alignment explanation
Indices: 28009717--28009778 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
28009707 TTGTTGTTGA
* *
28009717 TGCTGTTGCTGTTGC
1 TGCTGCTGCTGCTGC
*
28009732 TGCTGTTGCTGCTGC
1 TGCTGCTGCTGCTGC
28009747 TGCTGCTGCTGCTGC
1 TGCTGCTGCTGCTGC
*
28009762 TGCTGCTGTTGCTGC
1 TGCTGCTGCTGCTGC
28009777 TG
1 TG
28009779 TTGTCGGTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.00, C:0.26, G:0.34, T:0.40
Consensus pattern (15 bp):
TGCTGCTGCTGCTGC
Found at i:28021847 original size:70 final size:67
Alignment explanation
Indices: 28021716--28021848 Score: 169
Period size: 70 Copynumber: 1.9 Consensus size: 67
28021706 ATAAACAATA
* * * *
28021716 TAATGGTTTTACCTTTTAACTTAATAAGTATACATTTATTAAAACGACGTAATTTTACCTTTTAA
1 TAATGGTTTTACCTTTTAACTTAAAAAGTAAACATTTATCAAAACAACGTAATTTTACCTTTTAA
28021781 CT
66 CT
* *
28021783 TAATGGTTTTGA-CTTTTAACTTTAGAAAAGATAAACATTTATCAAAACAACGTAGTTTTCCCTT
1 TAATGGTTTT-ACCTTTTAAC-TTA-AAAAG-TAAACATTTATCAAAACAACGTAATTTTACCTT
28021847 TT
62 TT
28021849 CTTATTCAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
67 18 0.32
68 4 0.07
69 4 0.07
70 30 0.54
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTACCTTTTAACTTAAAAAGTAAACATTTATCAAAACAACGTAATTTTACCTTTTAA
CT
Found at i:28022729 original size:28 final size:28
Alignment explanation
Indices: 28022682--28022837 Score: 147
Period size: 28 Copynumber: 5.6 Consensus size: 28
28022672 TAGTAAATGT
*
28022682 TCTGTATTCTGGGCTAGTAAGAGCGTAAC
1 TCTGTATTCT-GGCTCGTAAGAGCGTAAC
* * *
28022711 TTTGTATTTTGGCTCGTAAGAGCGTATC
1 TCTGTATTCTGGCTCGTAAGAGCGTAAC
*
28022739 TCTGCATTCTGGCTCGTAAGAGCGTAAC
1 TCTGTATTCTGGCTCGTAAGAGCGTAAC
* * * *
28022767 TCTGTACTCTGGCTCGCAAGAGC-AATAT
1 TCTGTATTCTGGCTCGTAAGAGCGTA-AC
* * * *
28022795 TCTAG-ATTTTGGCTCGAAAGAGCGTTAT
1 TCT-GTATTCTGGCTCGTAAGAGCGTAAC
28022823 TCTGT-TTCTGGCTCG
1 TCTGTATTCTGGCTCG
28022838 AAAGGAGCAT
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
27 11 0.11
28 84 0.81
29 9 0.09
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (28 bp):
TCTGTATTCTGGCTCGTAAGAGCGTAAC
Found at i:28022780 original size:56 final size:55
Alignment explanation
Indices: 28022681--28022864 Score: 169
Period size: 56 Copynumber: 3.3 Consensus size: 55
28022671 TTAGTAAATG
* * * * *
28022681 TTCTGTATTCTGGGCTAGTAAGAGCGTAACTTTGTATTTTGGCTCGTAAGAGC-GTA
1 TTCTG-ATTCT-GGCTCGTAAGAGCGTAACTCTGTATTCTGGCTCGCAAGAGCAATA
*
28022737 TCTCTGCATTCTGGCTCGTAAGAGCGTAACTCTGTACTCTGGCTCGCAAGAGCAATA
1 T-TCTG-ATTCTGGCTCGTAAGAGCGTAACTCTGTATTCTGGCTCGCAAGAGCAATA
* * * * * *
28022794 TTCTAGATTTTGGCTCGAAAGAGCGTTATTCTGT-TTCTGGCTCGAAAGGAGCATTA
1 TTCT-GATTCTGGCTCGTAAGAGCGTAACTCTGTATTCTGGCTCGCAA-GAGCAATA
28022850 CTT-TG-TTCTGGCTCG
1 -TTCTGATTCTGGCTCG
28022865 AATGAGCTAT
Statistics
Matches: 108, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
54 9 0.08
55 12 0.11
56 72 0.67
57 15 0.14
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (55 bp):
TTCTGATTCTGGCTCGTAAGAGCGTAACTCTGTATTCTGGCTCGCAAGAGCAATA
Found at i:28022805 original size:84 final size:82
Alignment explanation
Indices: 28022716--28022880 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 82
28022706 GTAACTTTGT
* * *
28022716 ATTTTGGCTCGTAAGAGCG-TATCTCTGCATTCTGGCTCGTAA-GAGCGTAACTCTGTACTCTGG
1 ATTTTGGCTCGAAAGAGCGTTAT-TCTG-ATTCTGGCTCGAAAGGAGCATAACTCTGT--TCTGG
28022779 CTCGCAA-GAGCAATATTCTAG
62 CTCG-AATGAGCAATATTCTAG
* * *
28022800 ATTTTGGCTCGAAAGAGCGTTATTCTGTTTCTGGCTCGAAAGGAGCATTACTTTGTTCTGGCTCG
1 ATTTTGGCTCGAAAGAGCGTTATTCTGATTCTGGCTCGAAAGGAGCATAACTCTGTTCTGGCTCG
*
28022865 AATGAGCTATATTCTA
66 AATGAGCAATATTCTA
28022881 TTCTAGGCTC
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
81 2 0.03
82 21 0.30
83 12 0.17
84 33 0.46
85 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (82 bp):
ATTTTGGCTCGAAAGAGCGTTATTCTGATTCTGGCTCGAAAGGAGCATAACTCTGTTCTGGCTCG
AATGAGCAATATTCTAG
Found at i:28022845 original size:28 final size:27
Alignment explanation
Indices: 28022720--28022898 Score: 118
Period size: 28 Copynumber: 6.5 Consensus size: 27
28022710 CTTTGTATTT
* *
28022720 TGGCTCGTAAGAGCG-TATCTCTGCATTC
1 TGGCTCGAAAGAGCGTTAT-TCTG-TTTC
* * * *
28022748 TGGCTCGTAAGAGCGTAACTCTGTACTC
1 TGGCTCGAAAGAGCGTTATTCTGT-TTC
* **
28022776 TGGCTCGCAAGAGCAATATTCTAGATTT-
1 TGGCTCGAAAGAGCGTTATTCT-G-TTTC
28022804 TGGCTCGAAAGAGCGTTATTCTGTTTC
1 TGGCTCGAAAGAGCGTTATTCTGTTTC
*
28022831 TGGCTCGAAAGGAGCATTACTT-TG-TTC
1 TGGCTCGAAA-GAGCGTTA-TTCTGTTTC
* *
28022858 TGGCTCGAATGAGC-TATATTCT-ATTC
1 TGGCTCGAAAGAGCGT-TATTCTGTTTC
*
28022884 TAGGCTCGAATGAGC
1 T-GGCTCGAAAGAGC
28022899 AATAATTTTC
Statistics
Matches: 125, Mismatches: 15, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
25 3 0.02
26 14 0.11
27 36 0.29
28 66 0.53
29 5 0.04
30 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (27 bp):
TGGCTCGAAAGAGCGTTATTCTGTTTC
Found at i:28022878 original size:54 final size:52
Alignment explanation
Indices: 28022804--28022934 Score: 133
Period size: 54 Copynumber: 2.5 Consensus size: 52
28022794 TTCTAGATTT
* * *
28022804 TGGCTCGAAAGAGCGT-TATTCTGTTTCT-GGCTCGAAAGGAGCATTACTTTGTTC
1 TGGCTCGAATGAGC-TATATTCTGTTTCTAGGCTCG-AAGGAGCAATA-ATT-TTC
* *
28022858 TGGCTCGAATGAGCTATATTCT-ATTCTAGGCTCGAATGAGCAATAATTTTC
1 TGGCTCGAATGAGCTATATTCTGTTTCTAGGCTCGAAGGAGCAATAATTTTC
*
28022909 TAGGCTCGAATAAGCTATACTTCTGT
1 T-GGCTCGAATGAGCTATA-TTCTGT
28022935 AACGGCTCGA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
51 4 0.06
52 18 0.28
53 18 0.28
54 25 0.38
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (52 bp):
TGGCTCGAATGAGCTATATTCTGTTTCTAGGCTCGAAGGAGCAATAATTTTC
Found at i:28022915 original size:25 final size:27
Alignment explanation
Indices: 28022855--28022919 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
28022845 CATTACTTTG
* *
28022855 TTCT-GGCTCGAATGAGCTATATTCTA
1 TTCTAGGCTCGAATGAGCAATAATCTA
28022881 TTCTAGGCTCGAATGAGCAATAAT-T-
1 TTCTAGGCTCGAATGAGCAATAATCTA
28022906 TTCTAGGCTCGAAT
1 TTCTAGGCTCGAAT
28022920 AAGCTATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 14 0.39
26 5 0.14
27 17 0.47
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (27 bp):
TTCTAGGCTCGAATGAGCAATAATCTA
Found at i:28035260 original size:21 final size:21
Alignment explanation
Indices: 28035214--28035262 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
28035204 AATAGTGCAG
*
28035214 ACTTCTACCGATACAAGTGACT
1 ACTTCTACCGACACAAGT-ACT
28035236 -CTTCTACCGACACAAGT-CTT
1 ACTTCTACCGACACAAGTAC-T
28035256 ACTTCTA
1 ACTTCTA
28035263 TCGGTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 22 0.92
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (21 bp):
ACTTCTACCGACACAAGTACT
Found at i:28041673 original size:28 final size:28
Alignment explanation
Indices: 28041614--28041683 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
28041604 CTCTGTATTC
* * *
28041614 TGGCTCGTAAGAGCGTATCTATGCATTC
1 TGGCTCGTAAGAGCGTAACTATGCACTA
* *
28041642 TGGCTCGTAAGAGCGTAACTTTGTACTA
1 TGGCTCGTAAGAGCGTAACTATGCACTA
*
28041670 TGGCTCGCAAGAGC
1 TGGCTCGTAAGAGC
28041684 AATATTCTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (28 bp):
TGGCTCGTAAGAGCGTAACTATGCACTA
Found at i:28041788 original size:27 final size:26
Alignment explanation
Indices: 28041698--28041793 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 26
28041688 TTCTGGATTC
* * *
28041698 TGGCTTGAAAGAGTGTTATTCTGTTTT
1 TGGCTCGAATGAGTATTATTCTG-TTT
* *
28041725 TGGCTCGAAAGGAGTATTACTCTGTTT
1 TGGCTCG-AATGAGTATTATTCTGTTT
28041752 TGGCTCGAATGAGCTA-TATTCTGTTCT
1 TGGCTCGAATGAG-TATTATTCTGTT-T
* *
28041779 GGGCTCGAATAAGTA
1 TGGCTCGAATGAGTA
28041794 ATAATTTTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
26 15 0.26
27 30 0.52
28 13 0.22
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.39
Consensus pattern (26 bp):
TGGCTCGAATGAGTATTATTCTGTTT
Found at i:28043820 original size:25 final size:26
Alignment explanation
Indices: 28043748--28043820 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
28043738 CTATTTTCTT
* *
28043748 AAAATTTTACCAGGGGCAAAATCATC
1 AAAATTTTACTAGGGGTAAAATCATC
*
28043774 AAAATTTTACTAGGGGTAAAATCGTC
1 AAAATTTTACTAGGGGTAAAATCATC
* *
28043800 AAAATTTT-GTTGGGGTAAAAT
1 AAAATTTTACTAGGGGTAAAAT
28043821 AGGATGAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 11 0.26
26 31 0.74
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (26 bp):
AAAATTTTACTAGGGGTAAAATCATC
Found at i:28049214 original size:24 final size:24
Alignment explanation
Indices: 28049178--28049242 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
28049168 TATATATACA
* *
28049178 TTTACACTTGCCAGCTTGCACATG
1 TTTACGCTCGCCAGCTTGCACATG
28049202 TTTACGCTCGCCAGCTTGCACATG
1 TTTACGCTCGCCAGCTTGCACATG
* *
28049226 TTTATGCTCGTCAGCTT
1 TTTACGCTCGCCAGCTT
28049243 ATATATGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.35
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTTGCACATG
Found at i:28049229 original size:75 final size:74
Alignment explanation
Indices: 28049103--28049248 Score: 213
Period size: 75 Copynumber: 2.0 Consensus size: 74
28049093 TTCATTGCGT
* * *
28049103 TTTACACTCACCAGCTTTCATATGTTTACGCTCCTCAGCTTGCACACGTTTATGCTCGTTAGCTA
1 TTTACACTCACCAGCTTGCACATGTTTACGCTCCTCAGCTTGCACACGTTTATGCTCGTCAGCT-
28049168 TATATATACA
65 TATATATACA
** *
28049178 TTTACACTTGCCAGCTTGCACATGTTTACGCTCGC-CAGCTTGCACATGTTTATGCTCGTCAGCT
1 TTTACACTCACCAGCTTGCACATGTTTACGCTC-CTCAGCTTGCACACGTTTATGCTCGTCAGCT
28049242 TATATAT
65 TATATAT
28049249 GTATATATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
74 7 0.11
75 56 0.88
76 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (74 bp):
TTTACACTCACCAGCTTGCACATGTTTACGCTCCTCAGCTTGCACACGTTTATGCTCGTCAGCTT
ATATATACA
Found at i:28049384 original size:50 final size:50
Alignment explanation
Indices: 28049256--28049837 Score: 522
Period size: 50 Copynumber: 11.3 Consensus size: 50
28049246 TATGTATATA
* * * * * *
28049256 TATACATGCGTTTACGCTCGCTAGCTTGCACACATTTACGCTCATTAGCTT
1 TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGC-T
** * * *
28049307 ATATATATATGTTTACGCTCGCTAGCTTGCACACGTTTACACTCGTCAGCT
1 -TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * *
28049358 TATATATGTGTTTATGCTTGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATAT
1 TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGC-----T
* * * *
28049413 ATATATATGCGTTTACGCTCGCCAGCTTGCACACGTTTACACTCATCAACT
1 -TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* *
28049464 TATATATGCGTTT-TGGCTCGCCAACTTGCACACGTTTACGCTCGTTAGCT
1 TATATATGCGTTTAT-GCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * * * * *
28049514 TATATATGCGGTTATGCTTGCTAGCTTGCACATGTTTATGCTCGTCTGCTTATAT
1 TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGC-----T
** **
28049569 ATATATATGCGTTTACACTCGGTAGCTTGCACACGTTTACGCTCGTCAGCT
1 -TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
*
28049620 TATATATGTGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCCTAT
1 TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAG-C--T
* * * * * *
28049673 ATATATATGCATTTACGCTTGCCAGCTTGCACACGTTTATGCTCGTTAGCC
1 -TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * * * *
28049724 TATATATGCATTT-TCGCTTGCCAGCTTGCACACGTTTATGCTCGTTAGCC
1 TATATATGCGTTTAT-GCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * * * *
28049774 TATATATGCATTT-TCGCTTGCCAGCTTGAACACGTTTACACTCGTCATCT
1 TATATATGCGTTTAT-GCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
*
28049824 TATATATGCATTTA
1 TATATATGCGTTTA
28049838 ATTTCTTTAA
Statistics
Matches: 449, Mismatches: 61, Indels: 41
0.81 0.11 0.07
Matches are distributed among these distances:
50 273 0.61
51 5 0.01
52 42 0.09
53 2 0.00
54 42 0.09
55 2 0.00
56 83 0.18
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (50 bp):
TATATATGCGTTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
Found at i:28049406 original size:24 final size:24
Alignment explanation
Indices: 28049315--28049408 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
28049305 TTATATATAT
28049315 ATGTTTACGCTCG-CTAGCTTGCAC
1 ATGTTTACGCTCGTC-AGCTTGCAC
* * ** *
28049339 ACGTTTACACTCGTCAGCTTATAT
1 ATGTTTACGCTCGTCAGCTTGCAC
* * *
28049363 ATGTGTTTATGCTTGCCAGCTTGCAC
1 A--TGTTTACGCTCGTCAGCTTGCAC
28049389 ATGTTTACGCTCGTCAGCTT
1 ATGTTTACGCTCGTCAGCTT
28049409 ATATATATAT
Statistics
Matches: 51, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
24 34 0.67
25 1 0.02
26 16 0.31
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (24 bp):
ATGTTTACGCTCGTCAGCTTGCAC
Found at i:28049446 original size:106 final size:101
Alignment explanation
Indices: 28049256--28049837 Score: 519
Period size: 106 Copynumber: 5.6 Consensus size: 101
28049246 TATGTATATA
* * * * * * * **
28049256 TATACATGCGTTTACGCTCGCTAGCTTGCACACATTTACGCTCATTAGCTTATATATATATGTTT
1 TATATATGCGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGC-TATATATATGCGTTT
* *
28049321 ACGCTCGCTAGCTTGCACACGTTTACACTCGTCAGCT
65 ACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* *
28049358 TATATATGTGTTTATGCTTGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATATATATATATGC
1 TATATATGCGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGC-----TATATATATGC
* * *
28049423 GTTTACGCTCGCCAGCTTGCACACGTTTACACTCATCAACT
61 GTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * * *
28049464 TATATATGCGTTT-TGGCTCGCCAACTTGCACACGTTTACGCTCGTTAGCT-TATATATGCGGTT
1 TATATATGCGTTTAT-GCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTATATATATGCGTTT
* * * * * *
28049527 ATGCTTGCTAGCTTGCACATGTTTATGCTCGTCTGCTTATAT
65 ACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGC-----T
** * ** *
28049569 ATATATATGCGTTTACACTCGGTAGCTTGCACACGTTTACGCTCGTCAGCT-TATATATGTGTTT
1 -TATATATGCGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTATATATATGCGTTT
*
28049633 ATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCCTAT
65 ACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAG-C--T
* * * * * *
28049673 ATATATATGCATTTACGCTTGCCAGCTTGCACACGTTTATGCTCGTTAGC-CTATATATGCATTT
1 -TATATATGCGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTATATATATGCGTTT
* * * * *
28049737 TCGCTTGCCAGCTTGCACACGTTTATGCTCGTTAGCC
65 ACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * * * *
28049774 TATATATGCATTT-TCGCTTGCCAGCTTGAACACGTTTACACTCGTCATCT-TATATATGCATTT
1 TATATATGCGTTTAT-GCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTATATATATGCGTTT
28049837 A
65 A
28049838 ATTTCTTTAA
Statistics
Matches: 399, Mismatches: 65, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
100 94 0.24
101 1 0.00
102 40 0.10
103 1 0.00
104 87 0.22
105 2 0.01
106 173 0.43
107 1 0.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (101 bp):
TATATATGCGTTTATGCTTGCCAGCTTGCACACGTTTACGCTCGTCAGCTATATATATGCGTTTA
CGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
Found at i:28049506 original size:24 final size:24
Alignment explanation
Indices: 28049422--28049507 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
28049412 TATATATATG
*
28049422 CGTTTACGCTCGCCAGCTTGCACA
1 CGTTTACGCTCGCCAACTTGCACA
* ** ** *
28049446 CGTTTACACTCATCAACTTATATA
1 CGTTTACGCTCGCCAACTTGCACA
**
28049470 TGCGTTTTGGCTCGCCAACTTGCACA
1 --CGTTTACGCTCGCCAACTTGCACA
28049496 CGTTTACGCTCG
1 CGTTTACGCTCG
28049508 TTAGCTTATA
Statistics
Matches: 43, Mismatches: 17, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
24 27 0.63
26 16 0.37
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.31
Consensus pattern (24 bp):
CGTTTACGCTCGCCAACTTGCACA
Found at i:28049540 original size:156 final size:156
Alignment explanation
Indices: 28049201--28049837 Score: 703
Period size: 156 Copynumber: 4.0 Consensus size: 156
28049191 GCTTGCACAT
* *
28049201 GTTTACGCTCGCCAGCTTGCACATGTTTATGCTCGTCAGCTTATATATGTATATATATACATGCG
1 GTTTATGCTTGCCAGCTTGCACATGTTTATGCTCGTCAGC---T-TA--TATATATAT--ATGCG
* * * ** * *
28049266 TTTACGCTCGCTAGCTTGCACACATTTACGCTCATTAGCTTATATATATATGTTTACGCTCGCTA
58 TTTACGCTCGCCAGCTTGCACACGTTTACGCTCATCAGC-T-TATATATGCGTTTTCGCTCGCCA
*
28049331 GCTTGCACACGTTTACACTCGTCAGCTTATATATGT
121 GCTTGCACACGTTTACACTCGTCAGCTTATATATGC
*
28049367 GTTTATGCTTGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATATATATATATGCGTTTACGCT
1 GTTTATGCTTGCCAGCTTGCACATGTTTATGCTCGTCAGCTTATATATATATATGCGTTTACGCT
* * * *
28049432 CGCCAGCTTGCACACGTTTACACTCATCAACTTATATATGCGTTTTGGCTCGCCAACTTGCACAC
66 CGCCAGCTTGCACACGTTTACGCTCATCAGCTTATATATGCGTTTTCGCTCGCCAGCTTGCACAC
* *
28049497 GTTTACGCTCGTTAGCTTATATATGC
131 GTTTACACTCGTCAGCTTATATATGC
* * * *
28049523 GGTTATGCTTGCTAGCTTGCACATGTTTATGCTCGTCTGCTTATATATATATATGCGTTTACACT
1 GTTTATGCTTGCCAGCTTGCACATGTTTATGCTCGTCAGCTTATATATATATATGCGTTTACGCT
** * *
28049588 CGGTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGTGTTTAT-GCTCGCCAGCTTGCACA
66 CGCCAGCTTGCACACGTTTACGCTCATCAGCTTATATATGCGTTT-TCGCTCGCCAGCTTGCACA
*
28049652 CGTTTACGCTCGTCAGCCTATATATATATGC
130 CGTTTACACTCGTCAG-C--T-TATATATGC
* * * * * * *
28049683 ATTTACGCTTGCCAGCTTGCACACGTTTATGCTCGTTAGC------CTATATATGCATTTTCGCT
1 GTTTATGCTTGCCAGCTTGCACATGTTTATGCTCGTCAGCTTATATATATATATGCGTTTACGCT
* * * * * * * *
28049742 TGCCAGCTTGCACACGTTTATGCTCGTTAGCCTATATATGCATTTTCGCTTGCCAGCTTGAACAC
66 CGCCAGCTTGCACACGTTTACGCTCATCAGCTTATATATGCGTTTTCGCTCGCCAGCTTGCACAC
*
28049807 GTTTACACTCGTCATCTTATATATGC
131 GTTTACACTCGTCAGCTTATATATGC
*
28049833 ATTTA
1 GTTTA
28049838 ATTTCTTTAA
Statistics
Matches: 412, Mismatches: 53, Indels: 28
0.84 0.11 0.06
Matches are distributed among these distances:
150 14 0.03
151 1 0.00
153 2 0.00
154 81 0.20
156 180 0.44
157 3 0.01
158 39 0.09
159 1 0.00
160 51 0.12
162 2 0.00
163 1 0.00
166 37 0.09
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (156 bp):
GTTTATGCTTGCCAGCTTGCACATGTTTATGCTCGTCAGCTTATATATATATATGCGTTTACGCT
CGCCAGCTTGCACACGTTTACGCTCATCAGCTTATATATGCGTTTTCGCTCGCCAGCTTGCACAC
GTTTACACTCGTCAGCTTATATATGC
Found at i:28049668 original size:24 final size:24
Alignment explanation
Indices: 28049578--28049668 Score: 85
Period size: 24 Copynumber: 3.7 Consensus size: 24
28049568 TATATATATG
*
28049578 CGTTTACACTCGGT-AGCTTGCACA
1 CGTTTACGCTC-GTCAGCTTGCACA
** *
28049602 CGTTTACGCTCGTCAGCTTATATA
1 CGTTTACGCTCGTCAGCTTGCACA
* * *
28049626 TGTGTTTATGCTCGCCAGCTTGCACA
1 --CGTTTACGCTCGTCAGCTTGCACA
28049652 CGTTTACGCTCGTCAGC
1 CGTTTACGCTCGTCAGC
28049669 CTATATATAT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
23 2 0.04
24 31 0.61
26 18 0.35
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.33
Consensus pattern (24 bp):
CGTTTACGCTCGTCAGCTTGCACA
Found at i:28055556 original size:20 final size:20
Alignment explanation
Indices: 28055519--28055559 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28055509 TAAAAATACA
* *
28055519 TATAATTATTCATCTAATAT
1 TATAACTATTCAACTAATAT
*
28055539 TATAACTATTCAAGTAATAT
1 TATAACTATTCAACTAATAT
28055559 T
1 T
28055560 GTTTGAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.46
Consensus pattern (20 bp):
TATAACTATTCAACTAATAT
Found at i:28059634 original size:26 final size:26
Alignment explanation
Indices: 28059604--28059655 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
28059594 AAATCTCTCT
* *
28059604 ATTACAGTCTCGTAAATATCCTAGCA
1 ATTACAGTCTAGCAAATATCCTAGCA
*
28059630 ATTACAGTCTAGCAAATATTCTAGCA
1 ATTACAGTCTAGCAAATATCCTAGCA
28059656 TGAGCATTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.31
Consensus pattern (26 bp):
ATTACAGTCTAGCAAATATCCTAGCA
Found at i:28064960 original size:17 final size:17
Alignment explanation
Indices: 28064938--28064977 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28064928 AACTAAAATG
28064938 AATGCAA-CGACAATAAA
1 AATGCAAGC-ACAATAAA
*
28064955 AATGCAAGCACAATAAG
1 AATGCAAGCACAATAAA
28064972 AATGCA
1 AATGCA
28064978 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.55, C:0.17, G:0.15, T:0.12
Consensus pattern (17 bp):
AATGCAAGCACAATAAA
Found at i:28083819 original size:2 final size:2
Alignment explanation
Indices: 28083812--28083839 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28083802 TGACATATGA
28083812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28083840 GTATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28084321 original size:19 final size:20
Alignment explanation
Indices: 28084278--28084321 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28084268 TCATCCGGCC
*
28084278 CAAAAAAACCCAAAAATAAA
1 CAAAAAAACCCAAAAACAAA
*
28084298 CAAAAAAA-CCAAAACCAAA
1 CAAAAAAACCCAAAAACAAA
*
28084317 TAAAA
1 CAAAA
28084322 CATAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.75, C:0.20, G:0.00, T:0.05
Consensus pattern (20 bp):
CAAAAAAACCCAAAAACAAA
Found at i:28100078 original size:21 final size:21
Alignment explanation
Indices: 28100052--28100091 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28100042 ATAGGGTATA
28100052 TAATGTCCGCATCTAACCATT
1 TAATGTCCGCATCTAACCATT
28100073 TAATGTCCGCATCTAACCA
1 TAATGTCCGCATCTAACCA
28100092 GTTGCGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (21 bp):
TAATGTCCGCATCTAACCATT
Found at i:28117358 original size:26 final size:26
Alignment explanation
Indices: 28117314--28117371 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
28117304 AAAAGGCAGT
* *
28117314 TTTCT-TCTTTTCTTGACTTAAAATC
1 TTTCTCTCTTCTCTTAACTTAAAATC
28117339 TTTCTCTCTTCTCTTAACTTAAAATC
1 TTTCTCTCTTCTCTTAACTTAAAATC
28117365 TTTCTCT
1 TTTCTCT
28117372 AAGTATGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.19, C:0.24, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTCTCTCTTCTCTTAACTTAAAATC
Found at i:28148401 original size:43 final size:43
Alignment explanation
Indices: 28148352--28148440 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
28148342 TAGTATTAAG
* *
28148352 ATTACTTGTTTAAAATTTAATTTACTCTTTAAATGCAACCCAA
1 ATTACTTGTTTAAAATTTAAATTACTCTTTAAATACAACCCAA
*
28148395 ATTACTTGTTTAAAATTTAAATTACTCTTTAAATACAATCCAA
1 ATTACTTGTTTAAAATTTAAATTACTCTTTAAATACAACCCAA
28148438 ATT
1 ATT
28148441 TCATCGAGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.43
Consensus pattern (43 bp):
ATTACTTGTTTAAAATTTAAATTACTCTTTAAATACAACCCAA
Found at i:28148455 original size:23 final size:23
Alignment explanation
Indices: 28148429--28148486 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
28148419 CTCTTTAAAT
28148429 ACAATCCAAATTTCATCGAGATG
1 ACAATCCAAATTTCATCGAGATG
28148452 ACAATCCAAATTTCATCGAGATG
1 ACAATCCAAATTTCATCGAGATG
28148475 ACAATCCAAATT
1 ACAATCCAAATT
28148487 ATGCAATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.26
Consensus pattern (23 bp):
ACAATCCAAATTTCATCGAGATG
Found at i:28150228 original size:19 final size:19
Alignment explanation
Indices: 28150201--28150257 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
28150191 ATGCACACAT
* *
28150201 GATTTCACTAATCATACAC
1 GATTCCACTAATCAAACAC
* *
28150220 GATTCCACTAATCAGACAT
1 GATTCCACTAATCAAACAC
* *
28150239 AATTCAACTAATCAAACAC
1 GATTCCACTAATCAAACAC
28150258 CATTAACGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (19 bp):
GATTCCACTAATCAAACAC
Found at i:28158339 original size:15 final size:16
Alignment explanation
Indices: 28158319--28158356 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28158309 AAATTCCACT
28158319 AGAAAATAAGCAA-AA
1 AGAAAATAAGCAATAA
*
28158334 AGAAAA-CAGCAATAA
1 AGAAAATAAGCAATAA
28158349 AGAAAATA
1 AGAAAATA
28158357 TTAACTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.71, C:0.08, G:0.13, T:0.08
Consensus pattern (16 bp):
AGAAAATAAGCAATAA
Found at i:28160625 original size:216 final size:216
Alignment explanation
Indices: 28160336--28164831 Score: 5073
Period size: 216 Copynumber: 20.9 Consensus size: 216
28160326 TAAAACACTT
* * * * *
28160336 CATGCTCGAGAAATCGCATCATTTAGCCCAAATAGTTTTTCATTTTGTAAACAACTTTTAGT-TT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
28160400 CTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACT
66 -TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACT
** * * * * *
28160465 TACCAATCTTTTACGAGTTCTTTTATAACATCGGTTTCTTAAAGTATTAAAGACGATCAATTCCT
130 TTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCT
*
28160530 TCGAGCAATTTTCCAAACATTC
195 TCGAGCAATTTTCCGAACATTC
* * * *
28160552 CATGCTCGAGAAATCGCATC-TTCTAGTCCAAATAGTTTGCCATTTTGTAAAAAACTTTTGGTCT
1 CATGCTCGGGAAATCGCATCATT-TGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * * *
28160616 TTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGATTCTTGGCCGAACTTTCGTAC-
65 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACT
* * * *
28160680 TTGCTAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTAAAGATGATTCATTCC
130 TTTC-AAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCC
* *
28160745 TTCGAGCAATTTTCTGAACATTT
194 TTCGAGCAATTTTCCGAACATTC
** * * * * **
28160768 CATGCTTAGGAAATTGCATCATTTGATCCAAATAGTTTGACATTTTGTACACAACTTTCAGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * *
28160833 TAAATTAAAAATTTATTTACGTGACAATTGTTTCTCTCTTGGTTCATGGTCGAACTTCCAAACTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* ** * **
28160898 GTCAATGTTTTACGAGTTCTTTTACAACTTCAATTCCTTAAAGTATTCAAGACGATCCATTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
* *
28160963 CGAGCAAATTTCTGAACATTC
196 CGAGCAATTTTCCGAACATTC
** * * *
28160984 CATGCTTAGGAAATCTCATCATCTGGTCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
28161049 TAAATTAAAAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTTTTGGCCGAACTTCCGAACTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * * * * *
28161114 TTTAAACTTTTACGAGTTATTTTATAACTTCAGTTCTTTAAAGTATTCAAAATGATCCATTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
* **
28161179 CGAGTAATTTTTTGAACATTC
196 CGAGCAATTTTCCGAACATTC
* * *
28161200 TATGCTCGGGAAATCGTATCATTTGGTCCAAATAGATTGTCATTTTGTAAA-AACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * *
28161264 TGAATTAAAAACTTATTTACATGAAAATTGTTTCTCT-TTAGGTTCTAGGTCGAACTTCCAAACG
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT-GGTTCTTGGCCGAACTTCCGAACT
* **
28161328 TTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACAATCCATTTTT
130 TTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCT
* *
28161393 TCGAGAAATTTTCCGAAGATTC
195 TCGAGCAATTTTCCGAACATTC
** *
28161415 CATGCTCAAGAAATCACATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * *
28161480 TCAATTAAAAACTTATTTACGTGCA-AATTGTTTCTCTGTTGGTTCTTGGTCAAACTTCCGAACT
66 TGAATTAAAAACTTATTTACGTG-AGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACT
* * * *
28161544 TGT-AAAATTTTACGAGTTTTTTTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCT
130 TTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCT
*
28161608 TC--G---TATT-CGAGACGA-TC
195 TCGAGCAATTTTCCGA-AC-ATTC
* * * * * ** *
28161625 CATTCCTTCGAGCAATTTTTCGAACATTCCATGCTTGG--GAAATCG--CATCATTTGGTCCAAA
1 CA-TGC-TCG-GGAA---ATCG--CA-T-CAT--TTGGTCCAAATAGTTTGTCATTTTGT--AAA
* * * * * * * *
28161686 -TA-GTTT-GTCAATTTG---TAAACAACTT-TTGTTCTTTGGATTAAAAACTTATTTATATGAG
52 CAACTTTTGGTC--TTTGAATTAAA-AACTTATT-TAC----G--TGAGAA-TTGTTTCTCT---
* * **** * * * *
28161744 AATTGTTTCTCTATTTGTTA-TTGGCCAAACTTCCGAACTTTTAAAACTTTTTCGAGTTCTTTTA
103 -CTTGGTTCT-TGGCCG-AACTT--CC-GA-------ACTTTTCAAACTTTTACGAGTTCTTTTA
* * *
28161808 TAAATTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCTAACATTC
155 TAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * *
28161870 CATGCTCGCGAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* *
28161935 TAAATTAAAAACGTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTT--G-----
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * * ** *
28161993 -TCAAACTTTTACAAGTTATTTTATAACTTCAGTTCCTTAAAGTATTCAAGATAATCCGTTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
* ** *
28162057 CGAGAAATTTTTTGAACACTC
196 CGAGCAATTTTCCGAACATTC
* *
28162078 CATGCTCGGGAAATCGCGTCATTTGGTCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *** * * * *
28162143 TGAATTAAAACCTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGATAAACATCTGACCTA
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * * * * *
28162208 GTCAAACTTTTGCGAGTTCTTTTATAACTTCAGTTCCTTATAGTATTCTAGACGATTCATTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
** *
28162273 CGAGCAATTTTTTGAATATTC
196 CGAGCAATTTTCCGAACATTC
* * * *
28162294 CATGCTCGGGAAATCACATCATTTAGTCCAAAAAGTTTGTCATTTTGTAAACAAATTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * * *
28162359 TGGATTAAAAACTTATTTCCATGAGAAATGTTTCTCTTTTGGTTCTTAGCCGAACTTCCAAACTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* ** *
28162424 TTTAAA-TTTTTTGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTA
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
* *
28162488 CGAGAAATTTTTCG------C
196 CGAGCAATTTTCCGAACATTC
*
28162503 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
28162568 TGAATTAAAAACTTATTTACGTGAGAATTATTTTTCTCCTT-GTTCTTGGCCGAACTTTCGAACT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT-CTTGGTTCTTGGCCGAACTTCCGAACT
* * * * *
28162632 TGTAAAAATTTTATGAGTTCTTTTATAACTTCGGTTCTTTAAAGTATTCAAGACGATCCATTCCT
130 TTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCT
* * *
28162697 TTGACCAATTTTTCGAACATTC
195 TCGAGCAATTTTCCGAACATTC
* * *
28162719 CATGCTCGGGAAATCGGATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGTTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* ** * * * *
28162784 TGGATTAAAAACTTATTTATATGAGAATTGTTTCTCTATTTGTTATTGGCCAAACTT-CGAACTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * *
28162848 TTAAAACTTTTTCGAGTTCTTTTATAAATTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
* *
28162913 CGAGCAATTTTTCTAACATTC
196 CGAGCAATTTTCCGAACATTC
* * *
28162934 CATGCTCGCGAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* *
28162999 TAAATTAAAAACGTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTT--G-----
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * * **
28163057 -TCAAACTTTTACAAGTTATTTTATAACTTCAGTTCCTTAAAGTATTCAAGATAATCCATTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
* ** *
28163121 CGAGAAATTTTTTGAACACTC
196 CGAGCAATTTTCCGAACATTC
* *
28163142 CATGCTCGGGAAATCGCGTCATTTGGTCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *** * * * *
28163207 TGAATTAAAACCTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGATAAACATCTGACCTA
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * * * * *
28163272 GTCAAACTTTTGCGAGTTCTTTTATAACTTCAGTTCCTTATAGTATTCTAGACGATTCATTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
** *
28163337 CGAGCAATTTTTTGAATATTC
196 CGAGCAATTTTCCGAACATTC
* * * *
28163358 CATGCTCGGGAAATCACATCATTTAGTCCAAAAAGTTTGTCATTTTGTAAACAAATTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * * *
28163423 TGGATTAAAAACTTATTTCCATGAGAAATGTTTCTCTTTTGGTTCTTAGCCGAACTTCCAAACTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * *
28163488 TTTAAA-TTTT-TGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTA
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
* *
28163551 CGAGAAATTTTTCG------C
196 CGAGCAATTTTCCGAACATTC
*
28163566 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
28163631 TGAATTAAAAACTTATTTACGTGAGAATTATTTTTCTCCTT-GTTCTTGGCCGAACTTTCGAACT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT-CTTGGTTCTTGGCCGAACTTCCGAACT
* * * * *
28163695 TGTAAAACTTTTATGAGTTCTTTTATAACTTTGGTTCTTTAAAGTATTCAAGACGATCCATTCCT
130 TTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCT
* * *
28163760 TTGACCAATTTTTCGAACATTC
195 TCGAGCAATTTTCCGAACATTC
* *
28163782 CATGCTCGGGAAATCGGATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTGTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * *
28163847 TGGATTAAAAACTTATTTACATGAGAATTGTTTCTTTCTTGGTTCTTGGTCGAACATCCGAGCTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * * * * * **
28163912 TTAAAACTTTTTCGAGTTCTTTTATAACTTTGTTTCCTTACAGTATTCAAGATGATTGATTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
*
28163977 CGAGCAATTTTCCAAACATTC
196 CGAGCAATTTTCCGAACATTC
* * * * *
28163998 CATGCTCGAGAAATCGCATCATTTAGCCCAAATAGTTTTTCATTTTGTAAACAACTTTTAGT-TT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
28164062 CTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACT
66 -TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACT
** * * * * *
28164127 TACCAATCTTTTACGAGTTCTTTTATAACATCGGTTTCTTAAAGTATTAAAGACGATCAATTCCT
130 TTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCT
*
28164192 TCGAGCAATTTTCCAAACATTC
195 TCGAGCAATTTTCCGAACATTC
* * * * *
28164214 CATGCTCGAGAAATCGCATCATTTGGTCAAAATAGTTTGTCATTTTCTAAAAAACTTTTGGTATT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
28164279 TGAATTAAAAACTTATTTACGTGAGACTTGTTTCTCTCTTAGTTCTTGGCCAAACTTCCGAACTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
** * * * ** * *
28164344 ACCAAACTGTTATGAGTTATTTTATAACTTCTTTTCCTTAAAGTATTCAAGACAATCCATTCCAT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
28164409 CGAGCAATTTTCCGAACATTC
196 CGAGCAATTTTCCGAACATTC
** * * *
28164430 CATGCTCAAGAAATCACATAATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * * *
28164495 TGAATTAAAAACTTTTTTACGTAAGAATTATTTCTCTCTTGGTTCTTAGCCAAACTTTCGAAGTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * *
28164560 GTAAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
* * * *
28164625 CAAGTATTTTTCCGAACACTC
196 CGAGCAATTTTCCGAACATTC
*
28164646 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
1 CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * *
28164711 TGGATTAAAAACTTATTTACATGAGAATTGTCTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTT
66 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
* * * *
28164776 TTCAAACTTTTCCAAGTTATTTTATAACTTCGGTTCTTTAAAGTATTCAAGACGAT
131 TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
28164832 TGTAACGCGT
Statistics
Matches: 3634, Mismatches: 536, Indels: 220
0.83 0.12 0.05
Matches are distributed among these distances:
208 480 0.13
209 126 0.03
210 139 0.04
211 3 0.00
212 2 0.00
213 3 0.00
214 62 0.02
215 512 0.14
216 2069 0.57
217 21 0.01
218 13 0.00
219 5 0.00
220 11 0.00
221 1 0.00
222 5 0.00
223 3 0.00
224 7 0.00
225 1 0.00
226 4 0.00
227 7 0.00
228 7 0.00
229 4 0.00
230 1 0.00
231 9 0.00
232 5 0.00
233 3 0.00
234 1 0.00
235 11 0.00
236 5 0.00
237 13 0.00
238 9 0.00
239 14 0.00
240 58 0.02
242 3 0.00
243 3 0.00
244 3 0.00
245 9 0.00
246 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (216 bp):
CATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT
TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT
CGAGCAATTTTCCGAACATTC
Found at i:28161620 original size:24 final size:24
Alignment explanation
Indices: 28161586--28161634 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
28161576 ATTCCTTAAA
28161586 GTATTCAAGACGATCCATTCCTTC
1 GTATTCAAGACGATCCATTCCTTC
*
28161610 GTATTCGAGACGATCCATTCCTTC
1 GTATTCAAGACGATCCATTCCTTC
28161634 G
1 G
28161635 AGCAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (24 bp):
GTATTCAAGACGATCCATTCCTTC
Found at i:28162415 original size:424 final size:425
Alignment explanation
Indices: 28161610--28164831 Score: 3912
Period size: 424 Copynumber: 7.5 Consensus size: 425
28161600 CCATTCCTTC
* *
28161610 GTATTCGAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTTGGGAAATCGCATCA
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
* * * *
28161675 TTTGGTCCAAATAGTTTGTCAATTTGTAAACAACTTTTGTTCTTTGGATTAAAAACTTATTTATA
66 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACA
* * * * * *
28161740 TGAGAATTGTTTCTCTATTTGTTATTGGCCAAACTTCCGAACTTTTAAAACTTTTTCGAGTTCTT
131 TGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCTT
* *
28161805 TTATAAATTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCTAACATTC
196 TTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTC
* *
28161870 CATGCTCGCGAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
261 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
28161935 TAAATTAAAAACGTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGC-CGAACTTGTCAAAC
326 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCTCGAACTTGTCAAAC
* * *
28161999 TTTTACAAGTTATTTTATAACTTCAGTTCCTTAAA
391 TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
** * * * * *
28162034 GTATTCAAGATAATCCGTTCCTTCGAGAAATTTTTTGAACACTCCATGCTCGGGAAATCGCGTCA
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
* * *
28162099 TTTGGTCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAACCTTATTTACG
66 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACA
* *** * * * ** *
28162164 TGAGAATTATTTCTCTCTTGGTTCTTGGATAAACATCTGACCTAGTCAAACTTTTGCGAGTTCTT
131 TGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCTT
* * * * * *
28162229 TTATAACTTCAGTTCCTTATAGTATTCTAGACGATTCATTCCTTCGAGCAATTTTTTGAATATTC
196 TTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTC
* * * * *
28162294 CATGCTCGGGAAATCACATCATTTAGTCCAAAAAGTTTGTCATTTTGTAAACAAATTTTGGTCTT
261 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * *
28162359 TGGATTAAAAACTTATTTCCATGAGAAATGTTTCTCTTTTGGTTCTTAGC-CGAACTT-CCAAAC
326 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCTCGAACTTGTCAAAC
*
28162422 TTTTTAAATTTTTTGAGTTCTTTTATAACTTCGGTTCCTTAAA
391 -TTTT--A-----CGAGTTCTTTTATAACTTCGGTTCCTTAAA
* *
28162465 GTATTCAAGACGATCCATTCCTACGAGAAATTTTTCG------CCATGCTCGGGAAATCGCATCA
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
* *
28162524 TTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACG
66 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACA
* * * * * * *
28162589 TGAGAATTATTTTTCTCCTT-GTTCTTGGCCGAACTTTCGAACTTGTAAAAATTTTATGAGTTCT
131 TGAGAATTGTTTCTCT-CTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCT
* * *
28162653 TTTATAACTTCGGTTCTTTAAAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATT
195 TTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATT
* *
28162718 CCATGCTCGGGAAATCGGATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGTTCT
260 CCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* ** * * * *
28162783 TTGGATTAAAAACTTATTTATATGAGAATTGTTTCTCTATTTGTTATTGGCCAAACTTCGAACTT
325 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTT-----AGC-TCGAACTT
* * * *
28162848 TTAAAACTTTTTCGAGTTCTTTTATAAATTCGGTTCCTTAAA
384 GTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
* *
28162890 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGCGAAATCGCATCA
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
* * * * *
28162955 TTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACGTATTTACG
66 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACA
* *
28163020 TGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTT--G------TCAAACTTTTACAAGTTATT
131 TGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCTT
* ** * * *
28163077 TTATAACTTCAGTTCCTTAAAGTATTCAAGATAATCCATTCCTTCGAGAAATTTTTTGAACACTC
196 TTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTC
* * *
28163142 CATGCTCGGGAAATCGCGTCATTTGGTCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTT
261 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * *
28163207 TGAATTAAAACCTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGATAAACATCTGACCTA
326 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTC-T---T-AGC-TC-GAACTT
* * *
28163272 GTCAAACTTTTGCGAGTTCTTTTATAACTTCAGTTCCTTATA
384 GTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
* * * * *
28163314 GTATTCTAGACGATTCATTCCTTCGAGCAATTTTTTGAATATTCCATGCTCGGGAAATCACATCA
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
* * * * *
28163379 TTTAGTCCAAAAAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGGATTAAAAACTTATTTCCA
66 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACA
* * * * * *
28163444 TGAGAAATGTTTCTCTTTTGGTTCTTAGCCGAACTTCCAAACTTTTTAAA-TTTT-TGAGTTCTT
131 TGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCTT
* *
28163507 TTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTACGAGAAATTTTTCG------C
196 TTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTC
28163566 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
261 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
28163631 TGAATTAAAAACTTATTTACGTGAGAATTATTTTTCTCCTT-GTTCTTGGCCGAACTTTCGAACT
326 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT-CTTGGTTCTT-----AGC--TCGAACT
* * * *
28163695 TGTAAAACTTTTATGAGTTCTTTTATAACTTTGGTTCTTTAAA
383 TGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
* * *
28163738 GTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGCTCGGGAAATCGGATCA
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
* *
28163803 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTGTTTGGATTAAAAACTTATTTACA
66 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACA
* * * * * *
28163868 TGAGAATTGTTTCTTTCTTGGTTCTTGGTCGAACATCCGAGCTTTTAAAACTTTTTCGAGTTCTT
131 TGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCTT
* * * * ** * *
28163933 TTATAACTTTGTTTCCTTACAGTATTCAAGATGATTGATTCCTTCGAGCAATTTTCCAAACATTC
196 TTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTC
* * * * * *
28163998 CATGCTCGAGAAATCGCATCATTTAGCCCAAATAGTTTTTCATTTTGTAAACAACTTTTAGT-TT
261 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
*
28164062 CTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGC-CGAACTTCCGAAC
326 -TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCTCGAACTT--G---
* * *
28164126 TTACCAATCTTTTACGAGTTCTTTTATAACATCGGTTTCTTAAA
385 -T--CAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
* * * * *
28164170 GTATTAAAGACGATCAATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATCA
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
* * * * *
28164235 TTTGGTCAAAATAGTTTGTCATTTTCTAAAAAACTTTTGGTATTTGAATTAAAAACTTATTTACG
66 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACA
* * * ** * * *
28164300 TGAGACTTGTTTCTCTCTTAGTTCTTGGCCAAACTTCCGAACTTACCAAACTGTTATGAGTTATT
131 TGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCTT
** * * *
28164365 TTATAACTTCTTTTCCTTAAAGTATTCAAGACAATCCATTCCATCGAGCAATTTTCCGAACATTC
196 TTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTC
** * *
28164430 CATGCTCAAGAAATCACATAATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
261 CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * *
28164495 TGAATTAAAAACTTTTTTACGTAAGAATTATTTCTCTCTTGGTTCTTAGCCAAACTTTCGAAGTT
326 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAG-----C--TCGAACTT
* *
28164560 GTAAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAA
384 GTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
* * *
28164602 GTATTCAAGACGATCCATTCCTTCAAG-TATTTTTCCGAACACTCCATGCTCGGGAAATCGCATC
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTT-CGAACATTCCATGCTCGGGAAATCGCATC
* *
28164666 ATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGGATTAAAAACTTATTTAC
65 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAC
* * * * *
28164731 ATGAGAATTGTCTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTTTCAAACTTTTCCAAGTTAT
130 ATGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCT
*
28164796 TTTATAACTTCGGTTCTTTAAAGTATTCAAGACGAT
195 TTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
28164832 TGTAACGCGT
Statistics
Matches: 2399, Mismatches: 328, Indels: 134
0.84 0.11 0.05
Matches are distributed among these distances:
420 1 0.00
423 180 0.08
424 834 0.35
425 357 0.15
426 61 0.03
427 2 0.00
429 1 0.00
430 65 0.03
431 185 0.08
432 698 0.29
433 6 0.00
434 1 0.00
437 1 0.00
438 1 0.00
440 6 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (425 bp):
GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACA
TGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTACGAGTTCTT
TTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTC
CATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCTCGAACTTGTCAAAC
TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
Found at i:28187076 original size:19 final size:19
Alignment explanation
Indices: 28187049--28187090 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
28187039 TAGCAGCACC
28187049 AAAAGAAAAGTAAAA-AAAT
1 AAAAGAAAA-TAAAAGAAAT
*
28187068 AAAATAAAATAAAAGAAAT
1 AAAAGAAAATAAAAGAAAT
28187087 AAAA
1 AAAA
28187091 ATATCTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAGAAAATAAAAGAAAT
Found at i:28196795 original size:37 final size:37
Alignment explanation
Indices: 28196762--28196905 Score: 140
Period size: 37 Copynumber: 4.1 Consensus size: 37
28196752 TCAGGCTATG
**
28196762 TGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTGG
1 TGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTCA
*
28196799 TGCCGATG---T-A---TATGTGCCTAGTAGGCTTCA
1 TGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTCA
* * * *
28196829 TGCTGTTGTTTTCAGGCTATGTGTCTAGTAGGCTTCA
1 TGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTCA
* * * *
28196866 TGCTGGTGTATTCGGGCTATGTGCCTAGCAGGCTTTA
1 TGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTCA
28196903 TGC
1 TGC
28196906 TGGTAATCCA
Statistics
Matches: 88, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
30 24 0.27
33 2 0.02
34 2 0.02
37 60 0.68
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.36
Consensus pattern (37 bp):
TGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTCA
Found at i:28196906 original size:37 final size:37
Alignment explanation
Indices: 28196809--28196909 Score: 148
Period size: 37 Copynumber: 2.7 Consensus size: 37
28196799 TGCCGATGTA
* *
28196809 TATGTGCCTAGTAGGCTTCATGCTGTTGTTTTCAGGC
1 TATGTGCCTAGTAGGCTTCATGCTGGTGTATTCAGGC
* *
28196846 TATGTGTCTAGTAGGCTTCATGCTGGTGTATTCGGGC
1 TATGTGCCTAGTAGGCTTCATGCTGGTGTATTCAGGC
* *
28196883 TATGTGCCTAGCAGGCTTTATGCTGGT
1 TATGTGCCTAGTAGGCTTCATGCTGGT
28196910 AATCCAAGAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.14, C:0.18, G:0.30, T:0.39
Consensus pattern (37 bp):
TATGTGCCTAGTAGGCTTCATGCTGGTGTATTCAGGC
Found at i:28197274 original size:75 final size:75
Alignment explanation
Indices: 28197146--28197292 Score: 276
Period size: 75 Copynumber: 2.0 Consensus size: 75
28197136 CATGTATGTA
*
28197146 GGATGTTTTGGTAGTTACCTTGTTGGGGAATAGTTCTTGTTAAAACTTCAGCCTAAGCATCTTTT
1 GGATGTTTTGGTAGCTACCTTGTTGGGGAATAGTTCTTGTTAAAACTTCAGCCTAAGCATCTTTT
28197211 GAAGTATATG
66 GAAGTATATG
*
28197221 GGATGTTTTGGTAGCTACCTTGTTGGGGAATAGTTCTTGTTAAAACTTTAGCCTAAGCATCTTTT
1 GGATGTTTTGGTAGCTACCTTGTTGGGGAATAGTTCTTGTTAAAACTTCAGCCTAAGCATCTTTT
28197286 GAAGTAT
66 GAAGTAT
28197293 TTACATGTAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (75 bp):
GGATGTTTTGGTAGCTACCTTGTTGGGGAATAGTTCTTGTTAAAACTTCAGCCTAAGCATCTTTT
GAAGTATATG
Found at i:28198372 original size:24 final size:24
Alignment explanation
Indices: 28198340--28198387 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28198330 ACAAAATGAA
28198340 AGGGAAACTCAAAGGCCCGAAAAT
1 AGGGAAACTCAAAGGCCCGAAAAT
28198364 AGGGAAACTCAAAGGCCCGAAAAT
1 AGGGAAACTCAAAGGCCCGAAAAT
28198388 GTTACACCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.08
Consensus pattern (24 bp):
AGGGAAACTCAAAGGCCCGAAAAT
Found at i:28203901 original size:37 final size:37
Alignment explanation
Indices: 28203853--28203990 Score: 152
Period size: 37 Copynumber: 3.7 Consensus size: 37
28203843 TGCATCTAAT
* *
28203853 TATTTAGGCTATGTGCCTCGTAGGCTAT-GTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCT-TCGTGCCGGTG
* * *
28203890 TATTCAAGCTATGTGTCTAGTAGGCTTCGTGCCAGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTG
* * * * *
28203927 TTTTCAGGTTATGTGTCTAGTAGGCTTCATGCGGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTG
* *
28203964 TATTCGGGCTATGTGCCTAGCAGGCTT
1 TATTCAGGCTATGTGCCTAGTAGGCTT
28203991 TGTGTATGTA
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
36 1 0.01
37 83 0.99
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.36
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTG
Found at i:28211178 original size:15 final size:15
Alignment explanation
Indices: 28211158--28211213 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
28211148 CATAAAAAAA
28211158 TAAATATAAAATTAT
1 TAAATATAAAATTAT
*
28211173 TAAATATTAAAA-TAA
1 TAAATA-TAAAATTAT
*
28211188 TATAATATAAATATTTT
1 TA-AATATAAA-ATTAT
*
28211205 TAAAAATAA
1 TAAATATAA
28211214 TACGAACGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 14 0.42
16 16 0.48
17 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATATAAAATTAT
Found at i:28211198 original size:31 final size:31
Alignment explanation
Indices: 28211150--28211208 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
28211140 GGTATTTTCA
28211150 TAAAAAAATAAATATAAA-ATTATTAAATAT
1 TAAAAAAATAAATATAAATATTATTAAATAT
* *
28211180 TAAAATAATATAATATAAATATTTTTAAA
1 TAAAAAAATA-AATATAAATATTATTAAA
28211209 AATAATACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 8 0.32
32 8 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
TAAAAAAATAAATATAAATATTATTAAATAT
Found at i:28213012 original size:6 final size:7
Alignment explanation
Indices: 28212995--28213020 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28212985 CCAAAGATAA
28212995 AAAAAAT
1 AAAAAAT
28213002 AAAAAAT
1 AAAAAAT
28213009 AAAAAAT
1 AAAAAAT
28213016 AAAAA
1 AAAAA
28213021 CCTTGAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:28214456 original size:15 final size:15
Alignment explanation
Indices: 28214436--28214486 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
28214426 TTATCTCATA
28214436 TTATATTTTAATCAC
1 TTATATTTTAATCAC
*
28214451 TTATATTTAAAAT-A-
1 TTATATTT-TAATCAC
*
28214465 TTACATTTTAATCAC
1 TTATATTTTAATCAC
28214480 TTATATT
1 TTATATT
28214487 ATCGTTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 3 0.10
14 8 0.28
15 15 0.52
16 3 0.10
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATATTTTAATCAC
Found at i:28218327 original size:6 final size:6
Alignment explanation
Indices: 28218316--28218355 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
28218306 GGCAATCCAA
* * *
28218316 TTTTAT TTTTAT TTTTAG TTTTAG TTTTAG TTTCAG TTTT
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTT
28218356 TTTCTTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (6 bp):
TTTTAG
Found at i:28219302 original size:106 final size:106
Alignment explanation
Indices: 28219125--28219319 Score: 263
Period size: 106 Copynumber: 1.8 Consensus size: 106
28219115 ATAAAAAAAA
*
28219125 TAAATTAGGAGTGTGTTGGACTAAGTAATCGGGATGGAGTGCTTGAGTTGTCATTCCATTTCGCA
1 TAAATTAGGAGTGTGTTGGACTAAGTAACCGGGATGGAGTGCTTGAGTTGTCATTCCATTTCGCA
* *
28219190 TTAAAAGGGCCAATACA-TCTTAAGTAAAAAAATGATGATAT
66 -TAAAAAGACCAATACATTCTTAAGTAAAAAAATGATGATAT
* *
28219231 TAAATT-GAGAGTGTGTTGGGCTAAGTAACCGGGATGGGGTGCTTCG-GTTGT-ATTCCATTTCG
1 TAAATTAG-GAGTGTGTTGGACTAAGTAACCGGGATGGAGTGCTT-GAGTTGTCATTCCATTTCG
* *
28219293 CGTCAAAAAGACCAATATATTCTTAAG
64 CAT-AAAAAGACCAATACATTCTTAAG
28219320 CAAGAGGAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
104 1 0.01
105 25 0.32
106 51 0.65
107 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (106 bp):
TAAATTAGGAGTGTGTTGGACTAAGTAACCGGGATGGAGTGCTTGAGTTGTCATTCCATTTCGCA
TAAAAAGACCAATACATTCTTAAGTAAAAAAATGATGATAT
Found at i:28225328 original size:21 final size:21
Alignment explanation
Indices: 28225304--28225348 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28225294 AAATGCCTTG
** *
28225304 CGTGGCATGACACACGATGTC
1 CGTGGCACAACACACAATGTC
*
28225325 CGTGGCGCAACACACAATGTC
1 CGTGGCACAACACACAATGTC
28225346 CGT
1 CGT
28225349 ATTGCAACAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (21 bp):
CGTGGCACAACACACAATGTC
Found at i:28225355 original size:21 final size:21
Alignment explanation
Indices: 28225313--28225362 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
28225303 GCGTGGCATG
* *
28225313 ACACACGATGTCCGTGGCGCA
1 ACACACAATGTCCGTAGCGCA
**
28225334 ACACACAATGTCCGTATTGCA
1 ACACACAATGTCCGTAGCGCA
28225355 ACACACAA
1 ACACACAA
28225363 CCTTGTGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (21 bp):
ACACACAATGTCCGTAGCGCA
Found at i:28225411 original size:21 final size:21
Alignment explanation
Indices: 28225359--28225411 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
28225349 ATTGCAACAC
28225359 ACAACCTTGTGTTAAGCCACA
1 ACAACCTTGTGTTAAGCCACA
* * *
28225380 ACAGCCCTGTGTTGAGCCACA
1 ACAACCTTGTGTTAAGCCACA
28225401 ACAACCTTGTG
1 ACAACCTTGTG
28225412 GTGCACTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (21 bp):
ACAACCTTGTGTTAAGCCACA
Found at i:28229398 original size:17 final size:17
Alignment explanation
Indices: 28229373--28229407 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28229363 TACTATAACA
*
28229373 AATGGAAATGCAATGAC
1 AATGCAAATGCAATGAC
28229390 AATGCAAATGCAATGAC
1 AATGCAAATGCAATGAC
28229407 A
1 A
28229408 GTTAAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.17
Consensus pattern (17 bp):
AATGCAAATGCAATGAC
Found at i:28229415 original size:17 final size:17
Alignment explanation
Indices: 28229373--28229427 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
28229363 TACTATAACA
*
28229373 AATGGAAATGCAATGAC
1 AATGAAAATGCAATGAC
*
28229390 AATGCAAATGCAATGAC
1 AATGAAAATGCAATGAC
* * * *
28229407 AGTTAAAATGTAATGAT
1 AATGAAAATGCAATGAC
28229424 AATG
1 AATG
28229428 GGAATGTGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (17 bp):
AATGAAAATGCAATGAC
Found at i:28238494 original size:26 final size:26
Alignment explanation
Indices: 28238441--28238495 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
28238431 TTTTGGACGT
** **
28238441 AATTCTGGATGTGCTCATGCAGTGAC
1 AATTCTGGACATGCTCATGCAGCAAC
*
28238467 AATTCTGGACATGTTCATGCAGCAAC
1 AATTCTGGACATGCTCATGCAGCAAC
28238493 AAT
1 AAT
28238496 AGTAGTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (26 bp):
AATTCTGGACATGCTCATGCAGCAAC
Found at i:28240685 original size:17 final size:19
Alignment explanation
Indices: 28240646--28240687 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
28240636 ATAATTCTAG
28240646 TAAAA-TAACTTCAATTCT
1 TAAAATTAACTTCAATTCT
28240664 TAAAATTAAC-TCAATT-T
1 TAAAATTAACTTCAATTCT
28240681 TAAAATT
1 TAAAATT
28240688 CTAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 11 0.48
19 4 0.17
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATTAACTTCAATTCT
Found at i:28241517 original size:16 final size:16
Alignment explanation
Indices: 28241492--28241537 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
28241482 GGGGAATGTG
28241492 TAAA-AAACAT-AAATA
1 TAAATAAACATGAAA-A
28241507 TAAATAAACATGAAAA
1 TAAATAAACATGAAAA
*
28241523 TAAATAAAGATGAAA
1 TAAATAAACATGAAA
28241538 TAAGCATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 4 0.14
16 21 0.75
17 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:28245593 original size:48 final size:48
Alignment explanation
Indices: 28245541--28245666 Score: 216
Period size: 48 Copynumber: 2.6 Consensus size: 48
28245531 TAATTATGCT
28245541 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTCGTTTAATAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTCGTTTAATAATCTGCA
* *
28245589 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTCGTTTAATAATCTGCA
* *
28245637 TTATTAAATGTTTTGTTTGTTAAATGCATC
1 TCATTAAGTGTTTTGTTTGTTAAATGCATC
28245667 CTAGTTAAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTCGTTTAATAATCTGCA
Found at i:28247816 original size:21 final size:21
Alignment explanation
Indices: 28247747--28247817 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 21
28247737 TTTTTTTATG
* * *
28247747 AAAGAAAATGAAACAAAAAG-
1 AAAGGAAATGAGAGAAAAAGA
*
28247767 AAAGGAGATTGAGAGAAGAAA-A
1 AAAGGA-AATGAGAGAA-AAAGA
*
28247789 AAA-GAAATGAGGGAAAAAGA
1 AAAGGAAATGAGAGAAAAAGA
28247809 AAAGGAAAT
1 AAAGGAAAT
28247818 AAAAAGAGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.08
20 17 0.43
21 14 0.35
22 6 0.15
ACGTcount: A:0.66, C:0.01, G:0.25, T:0.07
Consensus pattern (21 bp):
AAAGGAAATGAGAGAAAAAGA
Found at i:28249335 original size:31 final size:31
Alignment explanation
Indices: 28249283--28249345 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
28249273 TTTAGTTGAA
* *
28249283 TAAGTGTTTGCATCTTTAATTATGTCTTGCAT
1 TAAGTGTTTGCA-CTTTAATTAAGTCATGCAT
28249315 TAAGTGTTTTGCA-TTTAATTAAGTCATGCAT
1 TAAGTG-TTTGCACTTTAATTAAGTCATGCAT
28249346 AAAATTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 6 0.21
33 6 0.21
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (31 bp):
TAAGTGTTTGCACTTTAATTAAGTCATGCAT
Found at i:28249473 original size:48 final size:48
Alignment explanation
Indices: 28249411--28249552 Score: 203
Period size: 48 Copynumber: 2.9 Consensus size: 48
28249401 GAAAGTTGTT
*
28249411 TAATTATGCTTCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAA
1 TAATT-TGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAA
*
28249460 TAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAG
1 TAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAA
* * * * * *
28249508 TAATCTGTATTATTAAATGTTTTATTTGTTAAATGCATCTCTGTT
1 TAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
28249553 AAATGCCTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
48 80 0.94
49 5 0.06
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (48 bp):
TAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAA
Found at i:28253755 original size:147 final size:149
Alignment explanation
Indices: 28253572--28253866 Score: 452
Period size: 147 Copynumber: 2.0 Consensus size: 149
28253562 TTTTAAATGA
** * *
28253572 AATCACTACTTTTCTTAATGATCAAAAGTTTTATTTCAAAAT-AGTTAAAAATATCAAAACTTTT
1 AATCACTACTTTTCTTAAAAATCAAAAGTTTTATTTC-AAATCAGTTAAAAAAATCAAAACTTTG
*
28253636 TTTAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTATATTTTTAAAAATATAA
65 CTTAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTATATTTTTAAAAATATAA
28253701 ACATTCT-TTTTCTAAAAAG
130 ACATTCTCTTTTCTAAAAAG
* *
28253720 AATCAC-ACTTTTCTTAAAAATCAAAGGTTTTATTTCGAATCAGTTAAAAAAATCAAAACTTTGC
1 AATCACTACTTTTCTTAAAAATCAAAAGTTTTATTTCAAATCAGTTAAAAAAATCAAAACTTTGC
* * * *
28253784 TTAGAAATTTAAATTTTTTCCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAAA
66 TTAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTATATTTTTAAAAATATAAA
*
28253849 CTTTCTCTTTTCTAAAAA
131 CATTCTCTTTTCTAAAAA
28253867 AATATCAAAA
Statistics
Matches: 133, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
146 3 0.02
147 113 0.85
148 17 0.13
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (149 bp):
AATCACTACTTTTCTTAAAAATCAAAAGTTTTATTTCAAATCAGTTAAAAAAATCAAAACTTTGC
TTAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTATATTTTTAAAAATATAAA
CATTCTCTTTTCTAAAAAG
Found at i:28254405 original size:15 final size:15
Alignment explanation
Indices: 28254385--28254419 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
28254375 TGCTTCTACA
28254385 AATCCGAAGGTGTCT
1 AATCCGAAGGTGTCT
28254400 AATCCGAAGGTGTCT
1 AATCCGAAGGTGTCT
28254415 AATCC
1 AATCC
28254420 TTCGATGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (15 bp):
AATCCGAAGGTGTCT
Found at i:28255136 original size:21 final size:20
Alignment explanation
Indices: 28255110--28255150 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28255100 TTCAAAATAG
28255110 TTAAAAATATCAAAACTTTTT
1 TTAAAAA-ATCAAAACTTTTT
**
28255131 TTAAAAAATTTAAACTTTTT
1 TTAAAAAATCAAAACTTTTT
28255151 CCTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAAAATCAAAACTTTTT
Found at i:28255316 original size:146 final size:150
Alignment explanation
Indices: 28255066--28255360 Score: 447
Period size: 146 Copynumber: 2.0 Consensus size: 150
28255056 TTTTAAATGA
** *
28255066 AATCACTACTTTTCTTAAGGATCAAAACTTTTATTTCAAAATAGTTAAAAATATCAAAACTTTTT
1 AATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCAAAATAGTTAAAAATATCAAAACTTTGT
*
28255131 TTAAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTATATTTTTAAAAATTTAA
66 TTAAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTATATTTTTAAAAATCTAA
28255196 ACATTCT-TTTTCTAAAAAG
131 ACATTCTCTTTTCTAAAAAG
** *
28255215 AATCAC-ACTTTTCTTAAAAATCAAAGGTTTTATTTC-GAATCAGTTAAAAA-ATCAAAACTTTG
1 AATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCAAAAT-AGTTAAAAATATCAAAACTTTG
* * *
28255277 TTT-AGAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAATATATTTTTATTTTTAAAAATCTA
65 TTTAAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTATATTTTTAAAAATCTA
*
28255341 AACTTTCTCTTTTCTAAAAA
130 AACATTCTCTTTTCTAAAAA
28255361 AATATCAAAA
Statistics
Matches: 133, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
146 64 0.48
147 28 0.21
148 35 0.26
149 6 0.05
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (150 bp):
AATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCAAAATAGTTAAAAATATCAAAACTTTGT
TTAAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTATATTTTTAAAAATCTAA
ACATTCTCTTTTCTAAAAAG
Found at i:28255811 original size:3 final size:3
Alignment explanation
Indices: 28255763--28255794 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28255753 CCTTGTGCCC
28255763 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28255795 GTTATGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28256391 original size:4 final size:4
Alignment explanation
Indices: 28256375--28256409 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
28256365 ACAAATGAGC
* *
28256375 GAAT GAGT GAAT GAAT GGAT GAAT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
28256410 ATTGGGGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:28257863 original size:37 final size:37
Alignment explanation
Indices: 28257813--28257887 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
28257803 AGAACGATGA
28257813 AGAACGCGACAACAGTTCTTGAGAAATTACCGGATTT
1 AGAACGCGACAACAGTTCTTGAGAAATTACCGGATTT
*
28257850 AGAACGCGACAACAGTTCTTGAGAAATTACTGGATTT
1 AGAACGCGACAACAGTTCTTGAGAAATTACCGGATTT
28257887 A
1 A
28257888 ATCTTATTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (37 bp):
AGAACGCGACAACAGTTCTTGAGAAATTACCGGATTT
Found at i:28263221 original size:18 final size:18
Alignment explanation
Indices: 28263198--28263243 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
28263188 AAGAAATGGT
28263198 ATTGATATCGCTTAGAAA
1 ATTGATATCGCTTAGAAA
28263216 ATTGATATCGCTTAGAAA
1 ATTGATATCGCTTAGAAA
28263234 ATTGATATCG
1 ATTGATATCG
28263244 AATTAGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (18 bp):
ATTGATATCGCTTAGAAA
Found at i:28265848 original size:58 final size:58
Alignment explanation
Indices: 28265758--28265878 Score: 233
Period size: 58 Copynumber: 2.1 Consensus size: 58
28265748 GCCAACCATC
28265758 ATTTTGTTGGAAGCTTATAAATTGGCAGATTAACCACCTAAGTGTGCCAATCTAGATA
1 ATTTTGTTGGAAGCTTATAAATTGGCAGATTAACCACCTAAGTGTGCCAATCTAGATA
*
28265816 ATTTTGTTGGAAGCTTATAAATTGGCGGATTAACCACCTAAGTGTGCCAATCTAGATA
1 ATTTTGTTGGAAGCTTATAAATTGGCAGATTAACCACCTAAGTGTGCCAATCTAGATA
28265874 ATTTT
1 ATTTT
28265879 CACAACTATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (58 bp):
ATTTTGTTGGAAGCTTATAAATTGGCAGATTAACCACCTAAGTGTGCCAATCTAGATA
Found at i:28269742 original size:3 final size:3
Alignment explanation
Indices: 28269734--28269760 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28269724 TTCACCGATT
28269734 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
28269761 GATAAGGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28282268 original size:37 final size:37
Alignment explanation
Indices: 28282193--28282277 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
28282183 TGCCGATGTA
* *
28282193 TATGTGCCTAGTAGGCTTCATGCTATTGTTTTCAGGC
1 TATGTGCCTAGTAAGCTTCATGCTAGTGTTTTCAGGC
* * *
28282230 TATGTGTCTAGTAAGCTTCATGCTGGTGTATTT-GGGC
1 TATGTGCCTAGTAAGCTTCATGCTAGTGT-TTTCAGGC
28282267 TATGTGCCTAG
1 TATGTGCCTAG
28282278 CAGGCTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 38 0.93
38 3 0.07
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.40
Consensus pattern (37 bp):
TATGTGCCTAGTAAGCTTCATGCTAGTGTTTTCAGGC
Found at i:28297198 original size:13 final size:13
Alignment explanation
Indices: 28297176--28297223 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
28297166 GTAGAGAATC
*
28297176 TCATGCCTTATTT
1 TCATACCTTATTT
*
28297189 TCATATCTTATTT
1 TCATACCTTATTT
*
28297202 TCATACCTTAATT
1 TCATACCTTATTT
*
28297215 TCTTACCTT
1 TCATACCTT
28297224 GAGCAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.54
Consensus pattern (13 bp):
TCATACCTTATTT
Found at i:28314580 original size:10 final size:10
Alignment explanation
Indices: 28314543--28314571 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
28314533 CATTTCATCA
28314543 ATACATATAC
1 ATACATATAC
28314553 ATACATATAC
1 ATACATATAC
28314563 ATACATATA
1 ATACATATA
28314572 TATATATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (10 bp):
ATACATATAC
Found at i:28335799 original size:12 final size:12
Alignment explanation
Indices: 28335778--28335812 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
28335768 ATTTCTTCTC
*
28335778 TTCTTCTTCTTT
1 TTCTTTTTCTTT
28335790 TTCTTTTTCTTT
1 TTCTTTTTCTTT
28335802 TTCTTTTTCTT
1 TTCTTTTTCTT
28335813 CCTTTTTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTCTTTTTCTTT
Found at i:28335805 original size:18 final size:18
Alignment explanation
Indices: 28335778--28335812 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28335768 ATTTCTTCTC
28335778 TTCTTCTTCTTTTTCTTT
1 TTCTTCTTCTTTTTCTTT
*
28335796 TTCTTTTTCTTTTTCTT
1 TTCTTCTTCTTTTTCTT
28335813 CCTTTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCTTCTTCTTTTTCTTT
Found at i:28336432 original size:19 final size:19
Alignment explanation
Indices: 28336408--28336460 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
28336398 CTAACTTAAC
28336408 AAAAATGCAATGAAAAAAT
1 AAAAATGCAATGAAAAAAT
*
28336427 AAAAATGCAATGACAAAAT
1 AAAAATGCAATGAAAAAAT
28336446 AAAAATGC-ATGAAAA
1 AAAAATGCAATGAAAA
28336461 CTATCTACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 6 0.19
19 26 0.81
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.15
Consensus pattern (19 bp):
AAAAATGCAATGAAAAAAT
Found at i:28349288 original size:23 final size:20
Alignment explanation
Indices: 28349239--28349288 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
28349229 ACGATATTAG
28349239 ACAAATAAATAAATTTATGC
1 ACAAATAAATAAATTTATGC
*
28349259 ACGAATAAATAAATCTAATATGC
1 ACAAATAAATAAAT-T--TATGC
28349282 ACAAATA
1 ACAAATA
28349289 CTAAAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.52
21 1 0.04
23 11 0.44
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (20 bp):
ACAAATAAATAAATTTATGC
Found at i:28350188 original size:16 final size:16
Alignment explanation
Indices: 28350167--28350208 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
28350157 ATGTGTGAAA
28350167 AAACAT-AAATATAAAT
1 AAACATGAAA-ATAAAT
28350183 AAACATGAAAATAAAT
1 AAACATGAAAATAAAT
*
28350199 AAAGATGAAA
1 AAACATGAAA
28350209 TAAGCATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (16 bp):
AAACATGAAAATAAAT
Found at i:28353784 original size:21 final size:22
Alignment explanation
Indices: 28353743--28353784 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28353733 TTCTGGTCTT
* *
28353743 TTTAAATTAGAACTCTAGTCCG
1 TTTAAATTACAAATCTAGTCCG
28353765 TTTAAATTACAAAT-TAGTCC
1 TTTAAATTACAAATCTAGTCC
28353785 TATAACTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTAAATTACAAATCTAGTCCG
Found at i:28355580 original size:69 final size:69
Alignment explanation
Indices: 28355464--28355602 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
28355454 ATTGTCTTTC
* * * *
28355464 ATCGGGCTATGTTTTATTGATCTCCGATTGTTATTGAAGTATGGAAACTGATTTGTTTTTATTGT
1 ATCGAGCTATGTTTTATTGATCTCCGATTGTTATTGAAATATGGAAACTAATTTGGTTTTATTGT
28355529 ATTA
66 ATTA
**
28355533 ATCGAGCTATGTTTTATTGATCTTTGATTGTTATTGAAATATGGAAACTAATTTGGTTTTATTGT
1 ATCGAGCTATGTTTTATTGATCTCCGATTGTTATTGAAATATGGAAACTAATTTGGTTTTATTGT
28355598 ATTA
66 ATTA
28355602 A
1 A
28355603 GCATTACTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (69 bp):
ATCGAGCTATGTTTTATTGATCTCCGATTGTTATTGAAATATGGAAACTAATTTGGTTTTATTGT
ATTA
Found at i:28356666 original size:21 final size:21
Alignment explanation
Indices: 28356591--28356701 Score: 123
Period size: 21 Copynumber: 5.3 Consensus size: 21
28356581 TTACTGAGTT
* * *
28356591 ACACGGGCGAGTAGAATAGCC
1 ACACGGGCGTGTGGGATAGCC
* * * *
28356612 ACACAGGCATGTAGAATAGCC
1 ACACGGGCGTGTGGGATAGCC
* *
28356633 ACAAGGGCATGTGGGATAGCC
1 ACACGGGCGTGTGGGATAGCC
* *
28356654 ACACGGGTGTGTGGGATGGCC
1 ACACGGGCGTGTGGGATAGCC
28356675 ACACGGGCGTGTGGGATAGCC
1 ACACGGGCGTGTGGGATAGCC
28356696 ACACGG
1 ACACGG
28356702 CCATGGTTGG
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.27, C:0.23, G:0.37, T:0.14
Consensus pattern (21 bp):
ACACGGGCGTGTGGGATAGCC
Found at i:28359538 original size:52 final size:52
Alignment explanation
Indices: 28359450--28359644 Score: 309
Period size: 52 Copynumber: 3.8 Consensus size: 52
28359440 AAATGTAAAA
* *
28359450 AGGTCCGATGACTATGTGTCATCTTGAGTATATGAATCCTTTAAGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
28359502 AGGTTCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
28359554 AGGTCCAATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
28359606 AGGTCCGATGACTATGTGTCATTGTGAGCATATGGATCC
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC
28359645 AGGTCTGATG
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 130 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:28360575 original size:21 final size:21
Alignment explanation
Indices: 28360546--28360596 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
28360536 GGAGTTTTTA
*
28360546 GTATCGGTAGAAG-CATGACAT
1 GTATCGGTAGAAGTCA-CACAT
*
28360567 GTTTCGGTAGAAGTCACACAT
1 GTATCGGTAGAAGTCACACAT
28360588 GTATCGGTA
1 GTATCGGTA
28360597 ATATTATCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (21 bp):
GTATCGGTAGAAGTCACACAT
Found at i:28365892 original size:13 final size:14
Alignment explanation
Indices: 28365874--28365903 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
28365864 AACAACAACG
28365874 AAAGAAAT-AAAAT
1 AAAGAAATCAAAAT
28365887 AAAGAAATCAAAAT
1 AAAGAAATCAAAAT
28365901 AAA
1 AAA
28365904 AGATACTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAGAAATCAAAAT
Found at i:28386762 original size:26 final size:26
Alignment explanation
Indices: 28386706--28386763 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
28386696 TATATGGATG
*
28386706 CAATTTTGGACATCCTCATGCAGCGA
1 CAATTATGGACATCCTCATGCAGCGA
* ** * *
28386732 TAATTATGGACATGTTCATGTAGTGA
1 CAATTATGGACATCCTCATGCAGCGA
28386758 CAATTA
1 CAATTA
28386764 GTAGTAAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (26 bp):
CAATTATGGACATCCTCATGCAGCGA
Found at i:28388382 original size:17 final size:18
Alignment explanation
Indices: 28388337--28388383 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
28388327 TTGGGTTTCC
* *
28388337 TCCCCTTCACCAGGGATT
1 TCCCATTCAGCAGGGATT
*
28388355 TCCCTTTCAGCAGGGATT
1 TCCCATTCAGCAGGGATT
28388373 T-CCATTCAGCA
1 TCCCATTCAGCA
28388384 ACATTTGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.19, C:0.34, G:0.17, T:0.30
Consensus pattern (18 bp):
TCCCATTCAGCAGGGATT
Found at i:28394304 original size:20 final size:20
Alignment explanation
Indices: 28394279--28394321 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28394269 CATATGCTCC
28394279 TGCATTAAAGCTTCAAGTGA
1 TGCATTAAAGCTTCAAGTGA
28394299 TGCATTAAAGCTTCAAGTGA
1 TGCATTAAAGCTTCAAGTGA
28394319 TGC
1 TGC
28394322 TAATGAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (20 bp):
TGCATTAAAGCTTCAAGTGA
Found at i:28396808 original size:26 final size:26
Alignment explanation
Indices: 28396770--28396826 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
28396760 TATCTGGGTG
* *
28396770 CAATTTTGGACATGCTCATGCAGCGA
1 CAATTCTGGACATGCTAATGCAGCGA
* * *
28396796 CAATTCTGTACATGTTAATGCAGTGA
1 CAATTCTGGACATGCTAATGCAGCGA
28396822 CAATT
1 CAATT
28396827 AGTAGTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (26 bp):
CAATTCTGGACATGCTAATGCAGCGA
Found at i:28434230 original size:22 final size:22
Alignment explanation
Indices: 28434205--28434247 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28434195 AAAATATTTC
28434205 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAATTTGGG-TTAATTA
*
28434227 ATTATTTAATTTGGGTTAATT
1 ATTATATAATTTGGGTTAATT
28434248 TTATTCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (22 bp):
ATTATATAATTTGGGTTAATTA
Done.