Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015376.1 Kokia drynarioides strain JFW-HI SEQ_130423, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 193640
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:202 original size:110 final size:111
Alignment explanation
Indices: 1--209 Score: 287
Period size: 110 Copynumber: 1.9 Consensus size: 111
* ** * *
1 ATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCA
1 ATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGA-CGT--GCCTGAGTTGGTATTCTTCTCA
* *
66 GTATCTTATCAGGAAGATGACTGCATCGCTTGTTTCAATCTGCTTCTCTC
63 GTATCTCATCAGGAAGATGACCGCATCGC-TGTTTCAATCTGCTTCTCTC
* *
116 ATCAGGAAGCTGGGGTTCAAAGATTTGCTCGCATCGA-GT-CCTGAGTTGGTATTCTTCTCGGTA
1 ATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGACGTGCCTGAGTTGGTATTCTTCTCAGTA
179 TCTCATCAGGAAGATGACCGCATCGCTGTTT
66 TCTCATCAGGAAGATGACCGCATCGCTGTTT
210 GTGGATGGTC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
109 5 0.06
110 43 0.51
113 2 0.02
115 35 0.41
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.33
Consensus pattern (111 bp):
ATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGACGTGCCTGAGTTGGTATTCTTCTCAGTA
TCTCATCAGGAAGATGACCGCATCGCTGTTTCAATCTGCTTCTCTC
Found at i:7641 original size:22 final size:21
Alignment explanation
Indices: 7616--7658 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
7606 AATTCCTTGT
7616 ATCGCGTCG-ATTTTCTCCTCTA
1 ATCGC-TCGTATTTT-TCCTCTA
*
7638 ATCGCTTGTATTTTTCCTCTA
1 ATCGCTCGTATTTTTCCTCTA
7659 TTTGTCTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.14, C:0.28, G:0.12, T:0.47
Consensus pattern (21 bp):
ATCGCTCGTATTTTTCCTCTA
Found at i:11654 original size:96 final size:96
Alignment explanation
Indices: 11480--11661 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 96
11470 AAGGATGTTC
* ** * * * *
11480 GATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGTAACTTTTCAGAATTGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTCAGAATCGAAGA
*
11545 TAAGGAAACATTGCCTCGATTAAGGGTATTT
66 TAAAGAAACATTGCCTCGATTAAGGGTATTT
*
11576 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTC-GAAACTCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTCAG-AA-TCGAA
*
11640 -ATAAA-AGAATATTGCCTCGATT
64 GATAAAGA-AACATTGCCTCGATT
11662 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 2 0.03
96 67 0.92
97 4 0.05
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTCAGAATCGAAGA
TAAAGAAACATTGCCTCGATTAAGGGTATTT
Found at i:12044 original size:30 final size:30
Alignment explanation
Indices: 11999--12292 Score: 356
Period size: 29 Copynumber: 10.0 Consensus size: 30
11989 TTTTTGGACA
*
11999 TTCGAGGGT-AAAATGGTAATTTTTGAAAGT
1 TTCGAGGGTCAAAATGG-AATTTTTGGAAGT
* *
12029 TTCG-GGGTCAAAATGGAAATTTTGG-AGG
1 TTCGAGGGTCAAAATGGAATTTTTGGAAGT
*
12057 TTCGAGGGTAAAAATGGAA-TTTTGGAAGT
1 TTCGAGGGTCAAAATGGAATTTTTGGAAGT
* * *
12086 TTCGAGGTTGAAAATGGAGTTTTTGGAAG-
1 TTCGAGGGTCAAAATGGAATTTTTGGAAGT
* * *
12115 TTCGAGGGTAAAAATGTAATTTTT-GAAGG
1 TTCGAGGGTCAAAATGGAATTTTTGGAAGT
* *
12144 TTCGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGAGGGTCAAAATGGAATTTTTGGAAGT
*
12174 TTC-AAGGTCGAAAATGGAATTTTTGGAAGT
1 TTCGAGGGTC-AAAATGGAATTTTTGGAAGT
12204 TTCG-GGGTCAAAAATGGAATTTTTGGAAG-
1 TTCGAGGGTC-AAAATGGAATTTTTGGAAGT
*
12233 TTCGAGGGTGAAAATGGAATTTTTGGAAGT
1 TTCGAGGGTCAAAATGGAATTTTTGGAAGT
12263 TTCG-GGGTCGAAAATGGAATTTTTGGAAGT
1 TTCGAGGGTC-AAAATGGAATTTTTGGAAGT
12293 ACAAAAAGGA
Statistics
Matches: 231, Mismatches: 22, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
28 16 0.07
29 114 0.49
30 101 0.44
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (30 bp):
TTCGAGGGTCAAAATGGAATTTTTGGAAGT
Found at i:12290 original size:59 final size:59
Alignment explanation
Indices: 11975--12292 Score: 407
Period size: 59 Copynumber: 5.4 Consensus size: 59
11965 AGAGTTTTGA
* * *
11975 GGTCAAAAATAGAGTTTTTGGACA-TTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTCGG
1 GGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTTGGAAGTTTCGG
* * *
12034 GGTC-AAAATGGAAATTTTGGAGGTTCGAGGGTAAAAATGGAA-TTTTGGAAGTTTCGA
1 GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGG
** * * *
12091 GGTTGAAAATGGAGTTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTT-GAAGGTTCGGG
1 GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTC-GG
* *
12150 GGT-AAAAATGGAATTTTTGGAAGTTTC-AAGGTCGAAAATGGAATTTTTGGAAGTTTCGG
1 GGTCAAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTCGG
*
12209 GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTGAAAATGGAATTTTTGGAAGTTTCGG
1 GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGG
*
12268 GGTCGAAAATGGAATTTTTGGAAGT
1 GGTCAAAAATGGAATTTTTGGAAGT
12293 ACAAAAAGGA
Statistics
Matches: 228, Mismatches: 21, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
57 16 0.07
58 88 0.39
59 93 0.41
60 31 0.14
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (59 bp):
GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGG
Found at i:13866 original size:6 final size:6
Alignment explanation
Indices: 13855--13941 Score: 69
Period size: 6 Copynumber: 15.2 Consensus size: 6
13845 ATTATTTAAA
13855 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* * * * *
13901 TAATTT TAAA-A TAAACT TAATTT TAAA-A TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T
13942 TGTTAGGCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
4 5 0.08
5 11 0.17
6 43 0.67
7 5 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:13880 original size:23 final size:23
Alignment explanation
Indices: 13848--13895 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
13838 ATGAGACATT
13848 ATTTAAATAAATTTAAATTT-AA
1 ATTTAAATAAATTTAAATTTCAA
13870 ATTTATAATAAATTTAAATTTCAA
1 ATTTA-AATAAATTTAAATTTCAA
13894 AT
1 AT
13896 AAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTCAA
Found at i:13883 original size:17 final size:17
Alignment explanation
Indices: 13861--13941 Score: 117
Period size: 17 Copynumber: 4.8 Consensus size: 17
13851 TAAATAAATT
*
13861 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
13878 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
13895 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
* *
13912 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
13929 TAAATTTAAATTT
1 TAAATTTAAATTT
13942 TGTTAGGCCT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:17857 original size:27 final size:26
Alignment explanation
Indices: 17813--17863 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
17803 ATAGATGAGT
**
17813 ATATAATAATATTTTATTATCTTTAAA
1 ATATAATAATATGATATTAT-TTTAAA
*
17840 ATATAATAATGTGATATTATTTTA
1 ATATAATAATATGATATTATTTTA
17864 TTGATATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (26 bp):
ATATAATAATATGATATTATTTTAAA
Found at i:20846 original size:51 final size:51
Alignment explanation
Indices: 20735--20846 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
20725 AAATGTTATA
* * * *
20735 GGTTAAATTTGTTAAATCATGATCAAATTGATAAAATGTGTAAATGTTGCC
1 GGTTAAATTTGTTAAACCAAGATCAAATTGACAAAATGTGTAAATGTTGAC
* *
20786 GGCTAAATTTGTTAAACCAAGA-CAAAATTGACAGAATGTGTAAACT-TTGAC
1 GGTTAAATTTGTTAAACCAAGATC-AAATTGACAAAATGTGTAAA-TGTTGAC
*
20837 GGTTGAATTT
1 GGTTAAATTT
20847 ATTATTATAC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.02
51 49 0.96
52 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.34
Consensus pattern (51 bp):
GGTTAAATTTGTTAAACCAAGATCAAATTGACAAAATGTGTAAATGTTGAC
Found at i:27287 original size:26 final size:26
Alignment explanation
Indices: 27245--27502 Score: 111
Period size: 26 Copynumber: 10.2 Consensus size: 26
27235 ATCTTATACA
* *
27245 CGTTTACACTAGTCAGCTTAGTTATG
1 CGTTTACGCTCGTCAGCTTAGTTATG
* * **
27271 CGTTTACGCTCGCCAGCTT-G-CACA
1 CGTTTACGCTCGTCAGCTTAGTTATG
* * * **
27295 CGTTTATGCTCGCCAGCTT-G-CACA
1 CGTTTACGCTCGTCAGCTTAGTTATG
* * *
27319 CGTTTATGCTCGTCAACTTATTTATG
1 CGTTTACGCTCGTCAGCTTAGTTATG
* * * * **
27345 TGTTTACACTCGCCAACTT-G-TACA
1 CGTTTACGCTCGTCAGCTTAGTTATG
* ** *
27369 CGTTTATGCTTATCAGCTTATTTATG
1 CGTTTACGCTCGTCAGCTTAGTTATG
* * * **
27395 CGTTTACACTCAAT-AGCTT-G-CACA
1 CGTTTACGCTC-GTCAGCTTAGTTATG
*
27419 CGTTTACGCTCGTCAGCTTATTTATG
1 CGTTTACGCTCGTCAGCTTAGTTATG
* * * *
27445 TGTTTACGCTTGTCAACTTATTTATG
1 CGTTTACGCTCGTCAGCTTAGTTATG
* *
27471 CGTTTACGCTCGTCAGGTTATTTATG
1 CGTTTACGCTCGTCAGCTTAGTTATG
*
27497 TGTTTA
1 CGTTTA
27503 TTACAATTCG
Statistics
Matches: 173, Mismatches: 51, Indels: 16
0.72 0.21 0.07
Matches are distributed among these distances:
23 1 0.01
24 71 0.41
25 1 0.01
26 98 0.57
27 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (26 bp):
CGTTTACGCTCGTCAGCTTAGTTATG
Found at i:27305 original size:24 final size:24
Alignment explanation
Indices: 27271--27330 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
27261 CTTAGTTATG
*
27271 CGTTTACGCTCGCCAGCTTGCACA
1 CGTTTATGCTCGCCAGCTTGCACA
27295 CGTTTATGCTCGCCAGCTTGCACA
1 CGTTTATGCTCGCCAGCTTGCACA
27319 CGTTTATGCTCG
1 CGTTTATGCTCG
27331 TCAACTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.15, C:0.33, G:0.22, T:0.30
Consensus pattern (24 bp):
CGTTTATGCTCGCCAGCTTGCACA
Found at i:27350 original size:50 final size:50
Alignment explanation
Indices: 27303--27451 Score: 208
Period size: 50 Copynumber: 3.0 Consensus size: 50
27293 CACGTTTATG
*
27303 CTCGCCAGCTTGCACACGTTTATGCTCGTCAACTTATTTATGTGTTTACA
1 CTCGCCAGCTTGCACACGTTTATGCTCGTCAGCTTATTTATGTGTTTACA
* * ** *
27353 CTCGCCAACTTGTACACGTTTATGCTTATCAGCTTATTTATGCGTTTACA
1 CTCGCCAGCTTGCACACGTTTATGCTCGTCAGCTTATTTATGTGTTTACA
*** *
27403 CTCAATAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATGTGTTTAC
1 CTCGCCAGCTTGCACACGTTTATGCTCGTCAGCTTATTTATGTGTTTAC
27452 GCTTGTCAAC
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (50 bp):
CTCGCCAGCTTGCACACGTTTATGCTCGTCAGCTTATTTATGTGTTTACA
Found at i:27386 original size:74 final size:74
Alignment explanation
Indices: 27242--27387 Score: 184
Period size: 74 Copynumber: 2.0 Consensus size: 74
27232 GCCATCTTAT
* * * *
27242 ACACGTTTACACTAGTCAGCTTAGTTATGCGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCG
1 ACACGTTTACACTAGTCAACTTAGTTATGCGTTTACACTCGCCAACTTGCACACGTTTATGCTCA
27307 CCAGCTTGC
66 CCAGCTTGC
** * * * * *
27316 ACACGTTTATGCTCGTCAACTTATTTATGTGTTTACACTCGCCAACTTGTACACGTTTATGCTTA
1 ACACGTTTACACTAGTCAACTTAGTTATGCGTTTACACTCGCCAACTTGCACACGTTTATGCTCA
*
27381 TCAGCTT
66 CCAGCTT
27388 ATTTATGCGT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.36
Consensus pattern (74 bp):
ACACGTTTACACTAGTCAACTTAGTTATGCGTTTACACTCGCCAACTTGCACACGTTTATGCTCA
CCAGCTTGC
Found at i:31887 original size:29 final size:30
Alignment explanation
Indices: 31855--32102 Score: 203
Period size: 29 Copynumber: 8.4 Consensus size: 30
31845 TAAATTTTCC
*
31855 AAAATTACATTTTTGCCCCT-AAACTTCTA
1 AAAATCACATTTTTGCCCCTCAAACTTCTA
*
31884 AAAATCACATTTTT-ACCCTCAAACTTCTCA
1 AAAATCACATTTTTGCCCCTCAAACTTCT-A
* *
31914 AAATTTACATTTTTGCCCC-CAAACTT-TCA
1 AAAATCACATTTTTGCCCCTCAAACTTCT-A
* * *
31943 AAAATCACATTTTT-ACCCTCGAACTTTTCA
1 AAAATCACATTTTTGCCCCTCAAACTTCT-A
* * * *
31973 AAAATTACA-TTTTACCACT-AAACTTCCA
1 AAAATCACATTTTTGCCCCTCAAACTTCTA
32001 AAAATCACATTTTTG-CCCTCAAACTTTTCTA
1 AAAATCACATTTTTGCCCCTCAAAC--TTCTA
* * *
32032 AAAA-AACAATTTTGCCCC-CGAACTTCTA
1 AAAATCACATTTTTGCCCCTCAAACTTCTA
* * *
32060 AACATCACATTTTTG-CCCTCGAACATCTA
1 AAAATCACATTTTTGCCCCTCAAACTTCTA
*
32089 AAAATTACCATTTT
1 AAAATCA-CATTTT
32103 ACCCCCTAGC
Statistics
Matches: 177, Mismatches: 28, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
28 30 0.17
29 81 0.46
30 52 0.29
31 14 0.08
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATCACATTTTTGCCCCTCAAACTTCTA
Found at i:31946 original size:59 final size:58
Alignment explanation
Indices: 31854--32102 Score: 277
Period size: 59 Copynumber: 4.2 Consensus size: 58
31844 CTAAATTTTC
*
31854 CAAAATTACATTTTTGCCCCTAAACTTCTAAAAATCACATTTTTACCCTCAAACTTCT
1 CAAAATTACATTTTTGCCCCCAAACTTCTAAAAATCACATTTTTACCCTCAAACTTCT
* *
31912 CAAAATTTACATTTTTGCCCCCAAACTT-TCAAAAATCACATTTTTACCCTCGAACTTTT
1 CAAAA-TTACATTTTTGCCCCCAAACTTCT-AAAAATCACATTTTTACCCTCAAACTTCT
* * * * * *
31971 CAAAAATTACA-TTTTACCACTAAACTTCCAAAAATCACATTTTTGCCCTCAAACTTTT
1 C-AAAATTACATTTTTGCCCCCAAACTTCTAAAAATCACATTTTTACCCTCAAACTTCT
** * * * * * *
32029 CTAAAAAAACAATTTTGCCCCCGAACTTCTAAACATCACATTTTTGCCCTCGAACATCT
1 C-AAAATTACATTTTTGCCCCCAAACTTCTAAAAATCACATTTTTACCCTCAAACTTCT
*
32088 AAAAATTACCATTTT
1 CAAAATTA-CATTTT
32103 ACCCCCTAGC
Statistics
Matches: 160, Mismatches: 25, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
58 59 0.37
59 97 0.61
60 4 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (58 bp):
CAAAATTACATTTTTGCCCCCAAACTTCTAAAAATCACATTTTTACCCTCAAACTTCT
Found at i:32056 original size:117 final size:117
Alignment explanation
Indices: 31849--32105 Score: 331
Period size: 117 Copynumber: 2.2 Consensus size: 117
31839 GGTCCCTAAA
* * * *
31849 TTTTCCAAAATTACATTTTTGCCCCTAAACTTCTAAAAATCACATTTTTACCCTCAAACTTCTCA
1 TTTTCAAAAATTACA-TTTTACCACTAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCTCA
** *
31914 AAATTTACATTTTTGCCCCCAAACTT-TCAAAAATCACATTTTTACCCTCGAAC
65 AAATAAACAATTTTGCCCCCAAACTTCT-AAAAATCACATTTTTACCCTCGAAC
* *
31967 TTTTCAAAAATTACATTTTACCACTAAACTTCCAAAAATCACATTTTTGCCCTCAAACTTTTCTA
1 TTTTCAAAAATTACATTTTACCACTAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCTC-A
* * *
32032 AAA-AAACAATTTTGCCCCCGAACTTCTAAACATCACATTTTTGCCCTCGAAC
65 AAATAAACAATTTTGCCCCCAAACTTCTAAAAATCACATTTTTACCCTCGAAC
* *
32084 ATCT-AAAAATTACCATTTTACC
1 TTTTCAAAAATTA-CATTTTACC
32106 CCCTAGCATT
Statistics
Matches: 122, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
116 8 0.07
117 95 0.78
118 19 0.16
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (117 bp):
TTTTCAAAAATTACATTTTACCACTAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCTCAA
AATAAACAATTTTGCCCCCAAACTTCTAAAAATCACATTTTTACCCTCGAAC
Found at i:32130 original size:59 final size:57
Alignment explanation
Indices: 31855--32131 Score: 197
Period size: 59 Copynumber: 4.7 Consensus size: 57
31845 TAAATTTTCC
** * * *
31855 AAAATTA-CATTTTTGCCCCTAAACTTCTAAAAATCACATTTTTACCCTCAAACTTCTCA
1 AAAATTACCATTTTACCCCCTACA-TTC-AAAAATCACATTTTTGCCCTCGAACTTCT-A
* * * * * *
31914 AAATTTA-CATTTTTGCCCCCAAACTTTCAAAAATCACATTTTTACCCTCGAACTTTTCA
1 AAAATTACCA-TTTTACCCCC-TACATTCAAAAATCACATTTTTGCCCTCGAACTTCT-A
* * *
31973 AAAATTA-CATTTTA-CCACTAAACTTCCAAAAATCACATTTTTGCCCTCAAACTTTTCTA
1 AAAATTACCATTTTACCCCCTACA-TT-CAAAAATCACATTTTTGCCCTCGAAC--TTCTA
* * * * * *
32032 AAAA-AACAATTTTGCCCCCGA-ACTTCTAAACATCACATTTTTGCCCTCGAACATCTA
1 AAAATTACCATTTTACCCCCTACA-TTC-AAAAATCACATTTTTGCCCTCGAACTTCTA
*
32089 AAAATTACCATTTTACCCCCTAGCATTCAAAAATTACCATTTT
1 AAAATTACCATTTTACCCCCTA-CATTCAAAAATCA-CATTTT
32132 GCACTCAAGT
Statistics
Matches: 174, Mismatches: 31, Indels: 26
0.75 0.13 0.11
Matches are distributed among these distances:
56 1 0.01
57 13 0.07
58 49 0.28
59 91 0.52
60 19 0.11
61 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCTACATTCAAAAATCACATTTTTGCCCTCGAACTTCTA
Found at i:32158 original size:28 final size:30
Alignment explanation
Indices: 32135--32208 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
32125 CCATTTTGCA
*
32135 CTCAAGTTTT-CAAAATTCACATTTTCAAC
1 CTCAAATTTTCCAAAATTCACATTTTCAAC
32164 CTCAAATTTTCCAAAAGTTCA-ATTTT-AATC
1 CTCAAATTTTCCAAAA-TTCACATTTTCAA-C
32194 CT-AAATTTTCCAAAA
1 CTCAAATTTTCCAAAA
32209 ATTTCAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
29 24 0.59
30 13 0.32
31 4 0.10
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
CTCAAATTTTCCAAAATTCACATTTTCAAC
Found at i:32199 original size:29 final size:29
Alignment explanation
Indices: 32135--32231 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 29
32125 CCATTTTGCA
*
32135 CTCAAGTTTT-CAAAATTCACATTTTCAA-C
1 CTCAAATTTTCCAAAATTCA-ATTTT-AATC
32164 CTCAAATTTTCCAAAAGTTCAATTTTAATC
1 CTCAAATTTTCCAAAA-TTCAATTTTAATC
*
32194 CT-AAATTTTCCAAAAATTTCAATTTTGATC
1 CTCAAATTTTCC-AAAA-TTCAATTTTAATC
*
32224 CCCAAATT
1 CTCAAATT
32232 CCTTAAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
29 20 0.34
30 30 0.51
31 9 0.15
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (29 bp):
CTCAAATTTTCCAAAATTCAATTTTAATC
Found at i:42846 original size:57 final size:58
Alignment explanation
Indices: 42777--42896 Score: 156
Period size: 57 Copynumber: 2.1 Consensus size: 58
42767 CCTTTGTGAC
* *
42777 AAACTCTGGAAAGATAAG-CCTCTGTGGCAAACCTCTTAAAGGAATA-ACCTTCATGGAA
1 AAACTCTGGAAAGATAAGCCCT-TATGGCAAACCTCTAAAAGGAA-ACACCTTCATGGAA
* * *
42835 AAACTCT-GAAAGGTGAGCCCTTATGGCAAACCTCTAAAAGGAAACACCTTCTTGGAA
1 AAACTCTGGAAAGATAAGCCCTTATGGCAAACCTCTAAAAGGAAACACCTTCATGGAA
42892 AAACT
1 AAACT
42897 TTAGAAGGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
56 1 0.02
57 44 0.80
58 10 0.18
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (58 bp):
AAACTCTGGAAAGATAAGCCCTTATGGCAAACCTCTAAAAGGAAACACCTTCATGGAA
Found at i:42884 original size:28 final size:29
Alignment explanation
Indices: 42801--42885 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 29
42791 TAAGCCTCTG
*
42801 TGGCAAACCTCTTAAAGGAATA-ACCTTCA
1 TGGCAAACCTCTAAAAGGAA-ACACCTTCA
* * * * *
42830 TGGAAAAACTCTGAAAGGTGAGC-CCTT-A
1 TGGCAAACCTCTAAAAGG-AAACACCTTCA
42858 TGGCAAACCTCTAAAAGGAAACACCTTC
1 TGGCAAACCTCTAAAAGGAAACACCTTC
42886 TTGGAAAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
27 2 0.05
28 20 0.48
29 19 0.45
30 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (29 bp):
TGGCAAACCTCTAAAAGGAAACACCTTCA
Found at i:42992 original size:28 final size:28
Alignment explanation
Indices: 42940--43122 Score: 160
Period size: 28 Copynumber: 6.6 Consensus size: 28
42930 AAGGAAATGT
* * * *
42940 CTTTGTGGCAATATTTG-TAAAGGAAAC
1 CTTTGTGGCGATCTCTGTTAAAGGAAGC
*
42967 ATTTGTGGCGATCTCTGTTAAAGGAAGC
1 CTTTGTGGCGATCTCTGTTAAAGGAAGC
*
42995 CTTTAG-GGTGATCTCTGTTAAA-GACAGC
1 CTTT-GTGGCGATCTCTGTTAAAGGA-AGC
* * *
43023 CTTTGTGGCAATTTTTGTTAAAGGAAGC
1 CTTTGTGGCGATCTCTGTTAAAGGAAGC
** * *
43051 CTTTGTGGTAATCT-TTTCTAAAGGAAGT
1 CTTTGTGGCGATCTCTGT-TAAAGGAAGC
*
43079 CTTTGTGGCGATCTCTATTAAAGGAAGTC
1 CTTTGTGGCGATCTCTGTTAAAGGAAG-C
*
43108 C-TTGTGGCAATCTCT
1 CTTTGTGGCGATCTCT
43123 ATTGAAGAAA
Statistics
Matches: 128, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
27 18 0.14
28 104 0.81
29 6 0.05
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (28 bp):
CTTTGTGGCGATCTCTGTTAAAGGAAGC
Found at i:43056 original size:84 final size:84
Alignment explanation
Indices: 42940--43118 Score: 206
Period size: 84 Copynumber: 2.1 Consensus size: 84
42930 AAGGAAATGT
*
42940 CTTTGTGGCAATATTTGTAAAGGAAACATTTGTGGCGATCTCTGT-TAAAGGAAGCCTTTAG-GG
1 CTTTGTGGCAATATTTGTAAAGGAAACATTTGTGGCAATCT-TGTCTAAAGGAAGCCTTT-GTGG
* *
43003 TGATCTCTGTTAAA-GACAG-C
64 CGATCTCTATTAAAGGA-AGTC
* * * * * *
43023 CTTTGTGGCAATTTTTGTTAAAGGAAGCCTTTGTGGTAATCTTTTCTAAAGGAAGTCTTTGTGGC
1 CTTTGTGGCAATATTTG-TAAAGGAAACATTTGTGGCAATCTTGTCTAAAGGAAGCCTTTGTGGC
43088 GATCTCTATTAAAGGAAGTC
65 GATCTCTATTAAAGGAAGTC
43108 C-TTGTGGCAAT
1 CTTTGTGGCAAT
43119 CTCTATTGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
83 19 0.23
84 59 0.72
85 4 0.05
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (84 bp):
CTTTGTGGCAATATTTGTAAAGGAAACATTTGTGGCAATCTTGTCTAAAGGAAGCCTTTGTGGCG
ATCTCTATTAAAGGAAGTC
Found at i:43123 original size:28 final size:27
Alignment explanation
Indices: 42969--43190 Score: 114
Period size: 28 Copynumber: 8.0 Consensus size: 27
42959 AAGGAAACAT
* *
42969 TTGTGGCGATCTCTGTTAAAGGAAGCC
1 TTGTGGCAATCTCTATTAAAGGAAGCC
** *
42996 TT-TAGGGTGATCTCTGTTAAA-GACAGCC
1 TTGT--GGCAATCTCTATTAAAGGA-AGCC
* * *
43024 TTTGTGGCAATTTTTGTTAAAGGAAGCC
1 -TTGTGGCAATCTCTATTAAAGGAAGCC
* * *
43052 TTTGTGGTAATCT-TTTCTAAAGGAAGTCT
1 -TTGTGGCAATCTCTAT-TAAAGGAAG-CC
*
43081 TTGTGGCGATCTCTATTAAAGGAAGTCC
1 TTGTGGCAATCTCTATTAAAGGAAG-CC
* * *
43109 TTGTGGCAATCTCTATTGAAGAAAGTCG
1 TTGTGGCAATCTCTATTAAAGGAAG-CC
* ** * *
43137 TTGTAGTGATCTTTA-TAAAGGAAACCC
1 TTGTGGCAATCTCTATTAAAGG-AAGCC
*
43164 TTGTGGCTAAT-TAT-TTAAAGGAAGCC
1 TTGTGGC-AATCTCTATTAAAGGAAGCC
43190 T
1 T
43191 CTATGGCTAA
Statistics
Matches: 153, Mismatches: 30, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
26 6 0.04
27 24 0.16
28 115 0.75
29 7 0.05
30 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (27 bp):
TTGTGGCAATCTCTATTAAAGGAAGCC
Found at i:43135 original size:56 final size:55
Alignment explanation
Indices: 42968--43170 Score: 160
Period size: 56 Copynumber: 3.6 Consensus size: 55
42958 AAAGGAAACA
* ** * * *
42968 TTTGTGGCGATCTCTGTTAAAGGAAGCCTT-TAGGGTGATCTCTGTTAAAGACAGCC
1 TTTGTGGCGATCTCTATTAAAGGAAGCCTTGT--GGCAATCTCTATTAAAGAAAGTC
* * * * * * *
43024 TTTGTGGCAATTTTTGTTAAAGGAAGCCTTTGTGGTAATCT-TTTCTAAAGGAAGTC
1 TTTGTGGCGATCTCTATTAAAGGAAGCC-TTGTGGCAATCTCTAT-TAAAGAAAGTC
*
43080 TTTGTGGCGATCTCTATTAAAGGAAGTCCTTGTGGCAATCTCTATTGAAGAAAGTC
1 TTTGTGGCGATCTCTATTAAAGGAAG-CCTTGTGGCAATCTCTATTAAAGAAAGTC
* * * * *
43136 GTTGTAGTGATCTTTA-TAAAGGAAACCCTTGTGGC
1 TTTGTGGCGATCTCTATTAAAGG-AAGCCTTGTGGC
43171 TAATTATTTA
Statistics
Matches: 120, Mismatches: 21, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
55 17 0.14
56 96 0.80
57 6 0.05
58 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (55 bp):
TTTGTGGCGATCTCTATTAAAGGAAGCCTTGTGGCAATCTCTATTAAAGAAAGTC
Found at i:43182 original size:27 final size:27
Alignment explanation
Indices: 43151--43223 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
43141 AGTGATCTTT
*
43151 ATAAAGGAAACCCTTGTGGCTAATTAT
1 ATAAAGGAAACCCTTGTGGCTAATTAA
* * *
43178 TTAAAGG-AAGCCTCTATGGCTAATTAA
1 ATAAAGGAAACCCT-TGTGGCTAATTAA
* *
43205 ATAAAGGAAGCCCATGTGG
1 ATAAAGGAAACCCTTGTGG
43224 TTATCTAAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
26 5 0.14
27 27 0.77
28 3 0.09
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (27 bp):
ATAAAGGAAACCCTTGTGGCTAATTAA
Found at i:45827 original size:27 final size:26
Alignment explanation
Indices: 45797--45946 Score: 113
Period size: 27 Copynumber: 5.6 Consensus size: 26
45787 CCCATATCCA
*
45797 CCACAAAGGCTTCCTTTACTCAGACAG
1 CCACAAAGGCTTCCTTTACT-AGATAG
* *
45824 CCACAAAGGCTTCCATTATA-AAGATTG
1 CCACAAAGGCTTCC-TT-TACTAGATAG
* * * *
45851 CCACGAAGGATTCTTTTACTTAGATAA
1 CCACAAAGGCTTCCTTTAC-TAGATAG
* * *
45878 CCATAAAGGCTTCCTTTACGGAGATTG
1 CCACAAAGGCTTCCTTTAC-TAGATAG
* * *
45905 CCACAATGACTTCCTTTACATAGTTAG
1 CCACAAAGGCTTCCTTTAC-TAGATAG
*
45932 CCACAAAGGGTTCCT
1 CCACAAAGGCTTCCT
45947 GTATAGAGAT
Statistics
Matches: 92, Mismatches: 27, Indels: 8
0.72 0.21 0.06
Matches are distributed among these distances:
25 2 0.02
26 2 0.02
27 84 0.91
28 2 0.02
29 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (26 bp):
CCACAAAGGCTTCCTTTACTAGATAG
Found at i:45923 original size:54 final size:54
Alignment explanation
Indices: 45797--45966 Score: 171
Period size: 54 Copynumber: 3.1 Consensus size: 54
45787 CCCATATCCA
* * * * *
45797 CCACAAAGGCTTCCTTTACTCAGACAGCCACAAAGGCTTCCATTATAAAGATTG
1 CCACAAAGACTTCCTTTACTTAGATAGCCACAAAGGCTTCCTTTATAGAGATTG
* * * * **
45851 CCACGAAGGA-TTCTTTTACTTAGATAACCATAAAGGCTTCCTTTACGGAGATTG
1 CCAC-AAAGACTTCCTTTACTTAGATAGCCACAAAGGCTTCCTTTATAGAGATTG
* * * * * *
45905 CCACAATGACTTCCTTTACATAGTTAGCCACAAAGGGTTCCTGTATAGAGATTA
1 CCACAAAGACTTCCTTTACTTAGATAGCCACAAAGGCTTCCTTTATAGAGATTG
45959 CCACAAAG
1 CCACAAAG
45967 GCTTTCATGT
Statistics
Matches: 91, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
53 4 0.04
54 84 0.92
55 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (54 bp):
CCACAAAGACTTCCTTTACTTAGATAGCCACAAAGGCTTCCTTTATAGAGATTG
Found at i:46800 original size:23 final size:25
Alignment explanation
Indices: 46774--46819 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
46764 CCAATTAGGG
46774 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
46797 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
46820 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:49815 original size:27 final size:27
Alignment explanation
Indices: 49785--49923 Score: 116
Period size: 27 Copynumber: 5.0 Consensus size: 27
49775 ATTTGTGTTA
* * *
49785 ATCTTTGTAAATGAAGTCTTTGTGGCG
1 ATCTTTGTAAAGGAAGCCTTTATGGCG
* * *
49812 ATCTCTATAAAGGAAGCCTTTATGGTG
1 ATCTTTGTAAAGGAAGCCTTTATGGCG
* * * *
49839 ATCTTTGTAAAGGAATCCCTTGTGGTG
1 ATCTTTGTAAAGGAAGCCTTTATGGCG
* * **
49866 ATCTCTGTTAAAGGAATCCTTTATGGTA
1 ATCTTTG-TAAAGGAAGCCTTTATGGCG
*
49894 ATCTCTTTTAAAGGAATGCCTTTATGGCG
1 ATCT-TTGTAAAGGAA-GCCTTTATGGCG
49923 A
1 A
49924 ACCTTGAAAG
Statistics
Matches: 89, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
27 49 0.55
28 29 0.33
29 11 0.12
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (27 bp):
ATCTTTGTAAAGGAAGCCTTTATGGCG
Found at i:49849 original size:54 final size:55
Alignment explanation
Indices: 49783--49915 Score: 162
Period size: 54 Copynumber: 2.4 Consensus size: 55
49773 CAATTTGTGT
* *
49783 TAATCTTTGTAAATGAAGT-CTTTGTGGCGATCTCT-ATAAAGGAAGCCTTTATGG
1 TAATCTTTGTAAAGGAA-TCCCTTGTGGCGATCTCTGATAAAGGAAGCCTTTATGG
* * * *
49837 TGATCTTTGTAAAGGAATCCCTTGTGGTGATCTCTGTTAAAGGAATCCTTTATGG
1 TAATCTTTGTAAAGGAATCCCTTGTGGCGATCTCTGATAAAGGAAGCCTTTATGG
* *
49892 TAATCTCTTTTAAAGGAATGCCTT
1 TAATCT-TTGTAAAGGAATCCCTT
49916 TATGGCGAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 29 0.43
55 22 0.33
56 15 0.22
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (55 bp):
TAATCTTTGTAAAGGAATCCCTTGTGGCGATCTCTGATAAAGGAAGCCTTTATGG
Found at i:49878 original size:28 final size:28
Alignment explanation
Indices: 49811--49920 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 28
49801 TCTTTGTGGC
* * *
49811 GATCTCT-ATAAAGGAAGCCTTTATGGT
1 GATCTCTGTTAAAGGAATCCCTTATGGT
* *
49838 GATCTTTG-TAAAGGAATCCCTTGTGGT
1 GATCTCTGTTAAAGGAATCCCTTATGGT
*
49865 GATCTCTGTTAAAGGAATCCTTTATGGT
1 GATCTCTGTTAAAGGAATCCCTTATGGT
* * *
49893 AATCTCTTTTAAAGGAATGCCTTTATGG
1 GATCTCTGTTAAAGGAAT-CCCTTATGG
49921 CGAACCTTGA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
27 29 0.41
28 33 0.46
29 9 0.13
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (28 bp):
GATCTCTGTTAAAGGAATCCCTTATGGT
Found at i:61149 original size:21 final size:21
Alignment explanation
Indices: 61123--61178 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
61113 GGTTGGTTCA
*
61123 AAGGACAAGAAGAAGAAGCGC
1 AAGGACAAAAAGAAGAAGCGC
*
61144 AAGGACAAAAAGAAGAAGCAC
1 AAGGACAAAAAGAAGAAGCGC
*
61165 AATGAGCAAAAAGA
1 AAGGA-CAAAAAGA
61179 GCGCCTAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.59, C:0.12, G:0.27, T:0.02
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAGCGC
Found at i:65778 original size:87 final size:87
Alignment explanation
Indices: 65675--65854 Score: 299
Period size: 87 Copynumber: 2.1 Consensus size: 87
65665 ATGATTATGA
*
65675 TTGACATTATGTTTTTGTTTTTGTTTGCACCACATTGGTTGACAATATAGTTTATGGTATAGGAA
1 TTGACATTATGTTTTTGTTTTTGTTTGCACCACATTGGTTGACAATATAGTTTATGATATA-GAA
* *
65740 -CTTGTGGCTATTGTGACAATGG
65 GCTTCTGGCTATTATGACAATGG
*
65762 TTGACATTATGTTTTTGTTTTTGTTTGCACCACATTGGTTGACAATATGGTTTATGATATAGAAG
1 TTGACATTATGTTTTTGTTTTTGTTTGCACCACATTGGTTGACAATATAGTTTATGATATAGAAG
*
65827 CTTCTTGCTATTATGACAATGG
66 CTTCTGGCTATTATGACAATGG
65849 TTGACA
1 TTGACA
65855 ATAAGATACA
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 3 0.03
87 84 0.97
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (87 bp):
TTGACATTATGTTTTTGTTTTTGTTTGCACCACATTGGTTGACAATATAGTTTATGATATAGAAG
CTTCTGGCTATTATGACAATGG
Found at i:68581 original size:28 final size:28
Alignment explanation
Indices: 68535--68612 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
68525 AGATAGCTTA
*
68535 GCTCTTACGAGCCCA-AAATCAGAATAAT
1 GCTCTTTCGAG-CCAGAAATCAGAATAAT
* *
68563 GCTCTTTCGAGCTAGAAATCAAAATAAT
1 GCTCTTTCGAGCCAGAAATCAGAATAAT
68591 GCTCTTTCGAGCCAG-AATCAGA
1 GCTCTTTCGAGCCAGAAATCAGA
68613 TTACTCCTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
27 8 0.18
28 36 0.82
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (28 bp):
GCTCTTTCGAGCCAGAAATCAGAATAAT
Found at i:76229 original size:103 final size:103
Alignment explanation
Indices: 76094--76286 Score: 341
Period size: 103 Copynumber: 1.9 Consensus size: 103
76084 ATCTATAATT
76094 AGTCTTTTAAATTTAGTTTAGTTTTCTTTCTTTCATAGGTTTTTAGAATTTATTTTCAGTTGTTT
1 AGTCTTTTAAATTTAGTTTAGTTTTCTTTCTTTCATAGGTTTTTAGAATTTATTTTCAGTTGTTT
* *
76159 TCTTTTTTCAAGAGATTTGATTTGTGGAGCCTAGAATG
66 TATGTTTTCAAGAGATTTGATTTGTGGAGCCTAGAATG
**
76197 AGTCTTTTAAATTTAGTTTAGTTTTCTTTCTTTTGTAGGTTTTTAGAATTTATTTTCAGTTGTTT
1 AGTCTTTTAAATTTAGTTTAGTTTTCTTTCTTTCATAGGTTTTTAGAATTTATTTTCAGTTGTTT
*
76262 TATGTTTTCAAGAGATTTTATTTGT
66 TATGTTTTCAAGAGATTTGATTTGT
76287 AGAGATCATC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 85 1.00
ACGTcount: A:0.21, C:0.07, G:0.16, T:0.56
Consensus pattern (103 bp):
AGTCTTTTAAATTTAGTTTAGTTTTCTTTCTTTCATAGGTTTTTAGAATTTATTTTCAGTTGTTT
TATGTTTTCAAGAGATTTGATTTGTGGAGCCTAGAATG
Found at i:78767 original size:29 final size:31
Alignment explanation
Indices: 78706--78777 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 31
78696 TAATATTTTT
* * *
78706 TTTATTATGATATTTATATTTTTATAAAATG
1 TTTAATATGGTATGTATATTTTTATAAAATG
*
78737 TTTAATGTGGTATGTATA-TTTTA-AAAATG
1 TTTAATATGGTATGTATATTTTTATAAAATG
78766 TTTAATATGGTA
1 TTTAATATGGTA
78778 CTTAAACTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 17 0.47
30 5 0.14
31 14 0.39
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (31 bp):
TTTAATATGGTATGTATATTTTTATAAAATG
Found at i:91552 original size:42 final size:41
Alignment explanation
Indices: 91505--91723 Score: 224
Period size: 42 Copynumber: 5.2 Consensus size: 41
91495 AGTCATAAGC
91505 CTTCCTTTAATCATATTCTCATTCTCATCCAGAGACATGAGT
1 CTTCCTTTAATCATATTCTCATTCTCATCC-GAGACATGAGT
* * * *
91547 CTTCCTTTAATCATAATCTCATTTTAATCTCGAGACATCAGT
1 CTTCCTTTAATCATATTCTCATTCTCATC-CGAGACATGAGT
*
91589 CTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATGAGT
1 CTTCCTTTAATCATATTCTCATTCTCATC-CGAGACATGAGT
* * * * * * *
91631 CTTCCTTTAATCATATTTTCGTGCTTATTTCGAGTCAAGAGT
1 CTTCCTTTAATCATATTCTCATTCTCA-TCCGAGACATGAGT
* * * *
91673 CTTCCATTT-ATACAAATTCTCATGCTCAACCTGAGACATGAGG
1 CTTCC-TTTAAT-CATATTCTCATTCTCATCC-GAGACATGAGT
91716 CTTCCTTT
1 CTTCCTTT
91724 TTATACATCA
Statistics
Matches: 148, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
42 118 0.80
43 30 0.20
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.39
Consensus pattern (41 bp):
CTTCCTTTAATCATATTCTCATTCTCATCCGAGACATGAGT
Found at i:91664 original size:84 final size:84
Alignment explanation
Indices: 91505--91723 Score: 248
Period size: 84 Copynumber: 2.6 Consensus size: 84
91495 AGTCATAAGC
* *
91505 CTTCCTTTAATCATATTCTCATTCTCATCCAGAGACATGAGTCTTCCTTTAATCATAATCTCATT
1 CTTCCTTTAATCATAATCTCATTCTCATCCAGAGACATGAGTCTTCCTTTAATCATAATCTCATC
*
91570 TTAATCTCGAGACATCAGT
66 TTAATCTCGAGACAACAGT
* * *
91589 CTTCCTTTAATCATAATCTCATTCTCATCTC-GAGACATGAGTCTTCCTTTAATCATATTTTCGT
1 CTTCCTTTAATCATAATCTCATTCTCATC-CAGAGACATGAGTCTTCCTTTAATCATAATCTCAT
* * *
91653 GCTT-ATTTCGAGTCAAGAGT
65 -CTTAATCTCGAGACAACAGT
* * * *
91673 CTTCCATTT-ATACA-AATTCTCATGCTCAACCTGAGACATGAGGCTTCCTTT
1 CTTCC-TTTAAT-CATAA-TCTCATTCTCATCCAGAGACATGAGTCTTCCTTT
91724 TTATACATCA
Statistics
Matches: 117, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
84 80 0.68
85 37 0.32
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.39
Consensus pattern (84 bp):
CTTCCTTTAATCATAATCTCATTCTCATCCAGAGACATGAGTCTTCCTTTAATCATAATCTCATC
TTAATCTCGAGACAACAGT
Found at i:92985 original size:27 final size:28
Alignment explanation
Indices: 92928--92988 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
92918 AAACACCAGT
* * *
92928 AAAGAATGCTTTTGTGGAAAATCTTTAA
1 AAAGAACGCCTTTGTGGAAAATCTCTAA
*
92956 AAAGAACGCCTTTGTGG-CAATCTCTAA
1 AAAGAACGCCTTTGTGGAAAATCTCTAA
92983 AAAGAA
1 AAAGAA
92989 TCTCTATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (28 bp):
AAAGAACGCCTTTGTGGAAAATCTCTAA
Found at i:93111 original size:142 final size:142
Alignment explanation
Indices: 92855--93130 Score: 455
Period size: 142 Copynumber: 1.9 Consensus size: 142
92845 GTTCTCAATG
*
92855 TGTTTCGGGACGATAAGGGGAAAACCTCACGAAATGTGAGTCTAGACAAATCCTTATCACCTAAA
1 TGTTTCGGGACGATAAGGGGAAAACCTCACGAAATGTGAGTCTAGACAAATCCTTATCACATAAA
* **
92920 ACACCAGTAAAGAATGCTTTTGTGGAAAATCTTTAAAAAGAACGCCTTTGTGGCAATCTCTAAAA
66 ACACCAGTAAAGAACGCTTTTGTGGAAAATCTCCAAAAAGAACGCCTTTGTGGCAATCTCTAAAA
92985 AGAATCTCTATA
131 AGAATCTCTATA
*
92997 TGTTTCGGGACGATGAGGGGAAAACCTCACGAAATGTGAGTCTA-AGCAAATCCTTATCACATAA
1 TGTTTCGGGACGATAAGGGGAAAACCTCACGAAATGTGAGTCTAGA-CAAATCCTTATCACATAA
* ** *
93061 AACACCAGTAAAGAACGCTTTTGTGGAAAATCTCCAGAAAGAATTCCTTTGTGGCAATCTCTAGA
65 AACACCAGTAAAGAACGCTTTTGTGGAAAATCTCCAAAAAGAACGCCTTTGTGGCAATCTCTAAA
93126 AAGAA
130 AAGAA
93131 CGCCTTTGTA
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 1 0.01
142 123 0.99
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (142 bp):
TGTTTCGGGACGATAAGGGGAAAACCTCACGAAATGTGAGTCTAGACAAATCCTTATCACATAAA
ACACCAGTAAAGAACGCTTTTGTGGAAAATCTCCAAAAAGAACGCCTTTGTGGCAATCTCTAAAA
AGAATCTCTATA
Found at i:93127 original size:27 final size:28
Alignment explanation
Indices: 93065--93139 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
93055 ACATAAAACA
*
93065 CCAGTAAAGAACGCTTTTGTGGAAAATCT
1 CCAG-AAAGAACGCCTTTGTGGAAAATCT
** *
93094 CCAGAAAGAATTCCTTTGTGG-CAATCT
1 CCAGAAAGAACGCCTTTGTGGAAAATCT
*
93121 CTAGAAAGAACGCCTTTGT
1 CCAGAAAGAACGCCTTTGT
93140 AACAAAACTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 21 0.54
28 14 0.36
29 4 0.10
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (28 bp):
CCAGAAAGAACGCCTTTGTGGAAAATCT
Found at i:93173 original size:28 final size:28
Alignment explanation
Indices: 93070--93520 Score: 135
Period size: 28 Copynumber: 15.9 Consensus size: 28
93060 AAACACCAGT
* * *
93070 AAAGAACGCTTTTGTGG-AAAATCTCCAG
1 AAAGAACACCTTTGTGGCAAAA-CTCTAG
** *
93098 AAAGAATTCCTTTGTGGC-AATCTCTAG
1 AAAGAACACCTTTGTGGCAAAACTCTAG
* **
93125 AAAGAACGCCTTTGTAACAAAACTCTA-
1 AAAGAACACCTTTGTGGCAAAACTCTAG
* * *
93152 AAAGGAACACCTTTGTGGCAAAGCTTTGG
1 AAA-GAACACCTTTGTGGCAAAACTCTAG
** * * *
93181 AAAGAATGCCTTTGTCGCAAAACTTTGGG
1 AAAGAACACCTTTGTGGCAAAACTCT-AG
* * * * *
93210 AAAGAATACCTTTGTGGCGGAACCTCGAA
1 AAAGAACACCTTTGTGGC-AAAACTCTAG
* * **
93239 AAAGAGCGCCTTTGTGGTGAAACTCT-G
1 AAAGAACACCTTTGTGGCAAAACTCTAG
* * * * *
93266 AAAAAAAGTACCTTTATGGCAAAACTTTGG
1 -AAAGAA-CACCTTTGTGGCAAAACTCTAG
* * ** * *
93296 AAAAGAA-AGCCTCTGTGGCGATGCTTTGG
1 -AAAGAACA-CCTTTGTGGCAAAACTCTAG
* * * *
93325 AAAGAACGCCTTTGTGGTAAAGCTCTGGG
1 AAAGAACACCTTTGTGGCAAAACTCT-AG
* * *
93354 AAAGAA-AGCCTTTGTGGTAAAGCTCTGGG
1 AAAGAACA-CCTTTGTGGCAAAACTCT-AG
* ** ** * * *
93383 ATAGAATGCCTTTGTGGTGAAATTATGG
1 AAAGAACACCTTTGTGGCAAAACTCTAG
* * * * *
93411 AAAGAACGCTTTTGTGACGAAACTCTGG
1 AAAGAACACCTTTGTGGCAAAACTCTAG
* * * * *
93439 AAAGGAACAACTCTATGACAAAGCTCTAG
1 AAA-GAACACCTTTGTGGCAAAACTCTAG
* * *
93468 AAAGAACGCCTTTGTGGCGAACCTCT-G
1 AAAGAACACCTTTGTGGCAAAACTCTAG
*
93495 AAAGGAAAACCTTTGTGGC-AAACTCT
1 AAA-GAACACCTTTGTGGCAAAACTCT
93521 GGAATGGTAA
Statistics
Matches: 320, Mismatches: 87, Indels: 33
0.73 0.20 0.08
Matches are distributed among these distances:
27 32 0.10
28 145 0.45
29 132 0.41
30 11 0.03
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (28 bp):
AAAGAACACCTTTGTGGCAAAACTCTAG
Found at i:93314 original size:29 final size:29
Alignment explanation
Indices: 93161--93399 Score: 146
Period size: 29 Copynumber: 8.3 Consensus size: 29
93151 AAAAGGAACA
* *
93161 CCTTTGTGGCAAAGCTTTGG-AAAGAATG
1 CCTTTGTGGCAAAACTTTGGAAAAGAAAG
* *
93189 CCTTTGTCGCAAAACTTTGGGAAAGAATA-
1 CCTTTGTGGCAAAACTTTGGAAAAGAA-AG
** * * * **
93218 CCTTTGTGGCGGAACCTCGAAAAAGAGCG
1 CCTTTGTGGCAAAACTTTGGAAAAGAAAG
** *
93247 CCTTTGTGGTGAAACTCT-GAAAA-AAAG
1 CCTTTGTGGCAAAACTTTGGAAAAGAAAG
*
93274 TACCTTTATGGCAAAACTTTGGAAAAGAAAG
1 --CCTTTGTGGCAAAACTTTGGAAAAGAAAG
* * ** *
93305 CCTCTGTGGCGATGCTTTGG-AAAGAACG
1 CCTTTGTGGCAAAACTTTGGAAAAGAAAG
* * * *
93333 CCTTTGTGGTAAAGCTCTGGGAAAGAAAG
1 CCTTTGTGGCAAAACTTTGGAAAAGAAAG
* * * * * *
93362 CCTTTGTGGTAAAGCTCTGGGATAGAATG
1 CCTTTGTGGCAAAACTTTGGAAAAGAAAG
93391 CCTTTGTGG
1 CCTTTGTGG
93400 TGAAATTATG
Statistics
Matches: 165, Mismatches: 38, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
27 2 0.01
28 44 0.27
29 110 0.67
30 5 0.03
31 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (29 bp):
CCTTTGTGGCAAAACTTTGGAAAAGAAAG
Found at i:93399 original size:86 final size:84
Alignment explanation
Indices: 93156--93442 Score: 249
Period size: 86 Copynumber: 3.3 Consensus size: 84
93146 ACTCTAAAAG
* * * * * *
93156 GAACACCTTTGTGGCAAAGCTTTGGAAAGAATGCCTTTGTCGCAAAACTTTGGGAAAGAATACCT
1 GAACGCCTTTGTGGTAAAGCTCTGGAAAGAAAGCCTTTGTGGCAAAACTTTGGGAAAGAATGCCT
* * *
93221 TTGTGGCGGAACCTCGAAAAA
66 TTGTGGC-GAACTTTG-GAAA
* * * * *
93242 GAGCGCCTTTGTGGTGAAA-CTCT-GAAAAAAAGTACCTTTATGGCAAAACTTTGGAAAAGAAAG
1 GAACGCCTTTGTGGT-AAAGCTCTGGAAAGAAAG--CCTTTGTGGCAAAACTTTGGGAAAGAATG
* *
93305 CCTCTGTGGCGATGCTTTGGAAA
63 CCTTTGTGGCGA-ACTTTGGAAA
* * * *
93328 GAACGCCTTTGTGGTAAAGCTCTGGGAAAGAAAGCCTTTGTGGTAAAGCTCTGGGATAGAATGCC
1 GAACGCCTTTGTGGTAAAGCTCT-GGAAAGAAAGCCTTTGTGGCAAAACTTTGGGAAAGAATGCC
* *
93393 TTTGTGGTGAAATTATGGAAA
65 TTTGTGGCGAACTT-TGGAAA
*
93414 GAACGCTTTTGTGACG-AAA-CTCTGGAAAG
1 GAACGCCTTTGTG--GTAAAGCTCTGGAAAG
93443 GAACAACTCT
Statistics
Matches: 161, Mismatches: 30, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
85 18 0.11
86 92 0.57
87 42 0.26
88 9 0.06
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (84 bp):
GAACGCCTTTGTGGTAAAGCTCTGGAAAGAAAGCCTTTGTGGCAAAACTTTGGGAAAGAATGCCT
TTGTGGCGAACTTTGGAAA
Found at i:93588 original size:21 final size:22
Alignment explanation
Indices: 93549--93591 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
93539 GGCAATCTTT
93549 GTAAAGGAAACCTTTGTGACTA
1 GTAAAGGAAACCTTTGTGACTA
*
93571 GTAAAGGAAGCC-TTGTGACTA
1 GTAAAGGAAACCTTTGTGACTA
93592 ATGATGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.26
Consensus pattern (22 bp):
GTAAAGGAAACCTTTGTGACTA
Found at i:95983 original size:21 final size:20
Alignment explanation
Indices: 95915--95985 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 20
95905 TTGGCCTTAT
*
95915 TTTTTTTTGGAAATATGTATGTTA
1 TTTTTTTT-GAAATAT-T-TG-AA
*
95939 TTTTTTTTGAAA-ATTTCAACA
1 TTTTTTTTGAAATATTT-GA-A
95960 TTTTTTTTGTAAATATTTGAA
1 TTTTTTTTG-AAATATTTGAA
95981 TTTTT
1 TTTTT
95986 AATTTTAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
20 1 0.03
21 17 0.43
22 6 0.15
23 8 0.20
24 8 0.20
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTTTTTTGAAATATTTGAA
Found at i:99080 original size:18 final size:18
Alignment explanation
Indices: 99041--99083 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
99031 AAAAGGTTTG
* *
99041 AAAAAATATATTAGATTC
1 AAAAAATAGATTAGAGTC
99059 AAAAAATAGATTTAGAGT-
1 AAAAAATAGA-TTAGAGTC
99077 AAAAAAT
1 AAAAAAT
99084 TAAGATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.28
Consensus pattern (18 bp):
AAAAAATAGATTAGAGTC
Found at i:99147 original size:16 final size:17
Alignment explanation
Indices: 99126--99159 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
99116 GAGTCCGACT
99126 TATTTTAAATT-TATAA
1 TATTTTAAATTATATAA
*
99142 TATTTTATATTATATAA
1 TATTTTAAATTATATAA
99159 T
1 T
99160 TTAGAACACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTAAATTATATAA
Found at i:105167 original size:12 final size:12
Alignment explanation
Indices: 105150--105189 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
105140 TTCACCTGTC
105150 TTACCTACTGAA
1 TTACCTACTGAA
* *
105162 TTACCTTCTGTA
1 TTACCTACTGAA
*
105174 TTACCTACTGAG
1 TTACCTACTGAA
105186 TTAC
1 TTAC
105190 ATTCTGTGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (12 bp):
TTACCTACTGAA
Found at i:105172 original size:24 final size:24
Alignment explanation
Indices: 105145--105196 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
105135 TCTTCTTCAC
* *
105145 CTGTCTTACCTACTGAATTACCTT
1 CTGTATTACCTACTGAATTACATT
*
105169 CTGTATTACCTACTGAGTTACATT
1 CTGTATTACCTACTGAATTACATT
105193 CTGT
1 CTGT
105197 GTCTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (24 bp):
CTGTATTACCTACTGAATTACATT
Found at i:116779 original size:30 final size:30
Alignment explanation
Indices: 116745--116808 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
116735 AATTAAATAG
*
116745 AATAAAAGGA-TTAAA-AAATTTTAAAAGAAA
1 AATAAAAGGATTTAAATAAA-TATAAAA-AAA
116775 AATAAAAGGATTTAAATAAATATAAAAAAA
1 AATAAAAGGATTTAAATAAATATAAAAAAA
116805 AATA
1 AATA
116809 GAATAAAGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 17 0.55
31 11 0.35
32 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (30 bp):
AATAAAAGGATTTAAATAAATATAAAAAAA
Found at i:118326 original size:46 final size:46
Alignment explanation
Indices: 118270--118630 Score: 423
Period size: 46 Copynumber: 8.0 Consensus size: 46
118260 ATTTGCTTCT
*
118270 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGCAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
* * * *
118316 GTAGCTTCAATTTGCCCCTCTTGACTTAAGGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
* * * * *
118362 TTGGCTTCAATCTGCCCTTCTTGATTTACGGGTAAAAGATTGGATA
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
* **
118408 GTGGCTTCAATCT-ACCCTC-T-GGTT-AGGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
* * *
118450 GTGGCTTCAATCTGCCCCTCTTGATTTAAGGGTAAAAGATTTGATA
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
*
118496 GTGGCTTCAATTTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
* * *
118542 GTGGCTTCAATCCGCCCCTC-TAGACTTAGGGGTAAAAGATT--A-G
1 GTGGCTTCAATCTGCCCCTCTTA-ATTTAAGGGTAAAAGATTGGATG
* * * * * *
118585 ATGACTTCAATCTACCCTTCTTAATTTAGGGGTAAAAGAATGGATG
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
118631 TGGTGATGTA
Statistics
Matches: 267, Mismatches: 39, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
42 29 0.11
43 39 0.15
44 5 0.02
45 9 0.03
46 185 0.69
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (46 bp):
GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGATTGGATG
Found at i:118546 original size:134 final size:137
Alignment explanation
Indices: 118270--118631 Score: 425
Period size: 134 Copynumber: 2.7 Consensus size: 137
118260 ATTTGCTTCT
* * * * * *
118270 GTGGCTTCAATCTGCCCCTCTTA-ATTTAAGGGCAAAAGATTGGATGGTAGCTTCAATTTGCCCC
1 GTGGCTTCAATCCGACCCTC-TAGACTT-AGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCC
* * * *
118334 TCTTGACTTAAGGGTAAAAGATTGGATGTTGGCTTCAATCTGCCCTTCTTGATTTACGGGTAAAA
64 TCTTGATTTAAGGGTAAAAGATTGGATGTTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAA
118399 GATTGGATA
129 GATTGGATA
* *
118408 GTGGCTTCAAT-CTACCCTCT-G-GTTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTC
1 GTGGCTTCAATCCGACCCTCTAGACTTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTC
* *
118470 TTGATTTAAGGGTAAAAGATTTGATAG-TGGCTTCAATTTGCCCCTCTTAATTTAAGGGTAAAAG
66 TTGATTTAAGGGTAAAAGATTGGAT-GTTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAG
*
118534 ATTGGATG
130 ATTGGATA
* * * * *
118542 GTGGCTTCAATCCGCCCCTCTAGACTTAGGGGTAAAAGATT--A-GATGACTTCAATCTACCCTT
1 GTGGCTTCAATCCGACCCTCTAGACTTA-GGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCT
* * *
118604 CTTAATTTAGGGGTAAAAGAATGGATGT
65 CTTGATTTAAGGGTAAAAGATTGGATGT
118632 GGTGATGTAG
Statistics
Matches: 192, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
134 110 0.57
135 48 0.25
136 3 0.02
137 8 0.04
138 23 0.12
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (137 bp):
GTGGCTTCAATCCGACCCTCTAGACTTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTC
TTGATTTAAGGGTAAAAGATTGGATGTTGGCTTCAATCTGCCCCTCTTAATTTAAGGGTAAAAGA
TTGGATA
Found at i:118577 original size:180 final size:177
Alignment explanation
Indices: 118270--118602 Score: 504
Period size: 180 Copynumber: 1.9 Consensus size: 177
118260 ATTTGCTTCT
*
118270 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGCAAAAGATTGGATGGTAGCTTCAATTTGCCCCT
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGCAAAAGATTGGATAGTAGCTTCAATTTGCCCCT
* * * * * *
118335 CTTGACTTAAGGGTAAAAGATTGGATGTTGGCTTCAATCTGCCCTTCTTGATTTACGGGTAAAAG
66 CTTAACTTAAGGGTAAAAGATTGGATGGTGGCTTCAATCCGCCCCTCTAGACTTACGGGTAAAAG
* *
118400 ATTGGATAGTGGCTTCAATCTACCCTCTGGTTAGGGTAAAAGATTGGATG
131 ATT--AGA-TGACTTCAATCTACCCTCTGGTTAGGGTAAAAGATTGGATG
* * * *
118450 GTGGCTTCAATCTGCCCCTCTTGATTTAAGGGTAAAAGATTTGATAGTGGCTTCAATTTGCCCCT
1 GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGCAAAAGATTGGATAGTAGCTTCAATTTGCCCCT
* *
118515 CTTAATTTAAGGGTAAAAGATTGGATGGTGGCTTCAATCCGCCCCTCTAGACTTAGGGGTAAAAG
66 CTTAACTTAAGGGTAAAAGATTGGATGGTGGCTTCAATCCGCCCCTCTAGACTTACGGGTAAAAG
118580 ATTAGATGACTTCAATCTACCCT
131 ATTAGATGACTTCAATCTACCCT
118603 TCTTAATTTA
Statistics
Matches: 138, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
177 16 0.12
178 2 0.01
180 120 0.87
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (177 bp):
GTGGCTTCAATCTGCCCCTCTTAATTTAAGGGCAAAAGATTGGATAGTAGCTTCAATTTGCCCCT
CTTAACTTAAGGGTAAAAGATTGGATGGTGGCTTCAATCCGCCCCTCTAGACTTACGGGTAAAAG
ATTAGATGACTTCAATCTACCCTCTGGTTAGGGTAAAAGATTGGATG
Found at i:124950 original size:109 final size:110
Alignment explanation
Indices: 124745--124955 Score: 282
Period size: 109 Copynumber: 1.9 Consensus size: 110
124735 AGGACATTCG
* * * * *
124745 TTGATTTTAAATAGGATGTTCGATTACTTTGGTTCAAGGAAAAAGTCATACCTAGCACATTAGGG
1 TTGATTTTAAATAGGATATTCGATTACTTAGATTCAAGGAAAAACTCATACCCAGCACATTAGGG
* *
124810 CACAATTTTTCAAGTCCCCTAAAGTAAAAGAACATTGAACATTTA
66 CACAATTTCTCAAGTCCCCTAAAATAAAAGAACATTGAACATTTA
* * *
124855 TTGATTTTAAATAGGATATTCGATTACTTAGATTCGAA-GAATAACT-ATACCCAGCACGTTTGG
1 TTGATTTTAAATAGGATATTCGATTACTTAGATTC-AAGGAAAAACTCATACCCAGCACATTAGG
* * *
124918 GCACAATTTCTCGAGTTCCCTAAAATACAAGAACATTG
65 GCACAATTTCTCAAGTCCCCTAAAATAAAAGAACATTG
124956 CCTTGATTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
109 47 0.54
110 38 0.44
111 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (110 bp):
TTGATTTTAAATAGGATATTCGATTACTTAGATTCAAGGAAAAACTCATACCCAGCACATTAGGG
CACAATTTCTCAAGTCCCCTAAAATAAAAGAACATTGAACATTTA
Found at i:128176 original size:6 final size:6
Alignment explanation
Indices: 128165--128245 Score: 80
Period size: 6 Copynumber: 14.0 Consensus size: 6
128155 TTTAATTTAT
* *
128165 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* * *
128211 -TTAAA TTTAAA TTTAAA TTTGAT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
128246 AAGTCCATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
4 2 0.03
5 11 0.18
6 47 0.76
7 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:128180 original size:17 final size:17
Alignment explanation
Indices: 128158--128245 Score: 113
Period size: 17 Copynumber: 5.1 Consensus size: 17
128148 GCCCCTTTTT
128158 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
128175 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* * *
128192 AATTAATCTTAAAATTA
1 AATTTATTTTAAATTTA
* *
128209 AATTAAATTTAAATTTA
1 AATTTATTTTAAATTTA
*
128226 AATTTGATTTTAAAATTA
1 AATTT-ATTTTAAATTTA
128244 AA
1 AA
128246 AAGTCCATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
17 49 0.80
18 12 0.20
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:128197 original size:11 final size:11
Alignment explanation
Indices: 128165--128229 Score: 62
Period size: 11 Copynumber: 5.7 Consensus size: 11
128155 TTTAATTTAT
128165 TTTAAATTTAAA
1 TTTAAA-TTAAA
**
128177 TTTATTTTAAA
1 TTTAAATTAAA
128188 TTTAAATT-AA
1 TTTAAATTAAA
128198 TCTTAAAATTAAA
1 T-TT-AAATTAAA
128211 -TTAAATTTAAA
1 TTTAAA-TTAAA
128222 TTTAAATT
1 TTTAAATT
128230 TGATTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 6 0.14
11 22 0.50
12 14 0.32
13 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:129006 original size:20 final size:20
Alignment explanation
Indices: 128981--129018 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
128971 CTTTAATGCT
128981 ATTAATAAATAATAATAATA
1 ATTAATAAATAATAATAATA
*
129001 ATTAATAATTAATAATAA
1 ATTAATAAATAATAATAA
129019 CGTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTAATAAATAATAATAATA
Found at i:129016 original size:7 final size:7
Alignment explanation
Indices: 128981--129016 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
128971 CTTTAATGCT
128981 ATTAATA
1 ATTAATA
*
128988 AATAATA
1 ATTAATA
128995 A-TAATA
1 ATTAATA
129001 ATTAATA
1 ATTAATA
129008 ATTAATA
1 ATTAATA
129015 AT
1 AT
129017 AACGTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
ATTAATA
Found at i:134018 original size:22 final size:21
Alignment explanation
Indices: 133977--134019 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
133967 CCCAGACAAA
*
133977 TAGAAGAAAAATACAGGCGAT
1 TAGAAGAAAAATACACGCGAT
133998 TAGAAGAGAAAAT-CGACGCGAT
1 TAGAAGA-AAAATAC-ACGCGAT
134020 GCAGGGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.14
Consensus pattern (21 bp):
TAGAAGAAAAATACACGCGAT
Found at i:141815 original size:206 final size:206
Alignment explanation
Indices: 141532--142118 Score: 827
Period size: 206 Copynumber: 2.8 Consensus size: 206
141522 AAGCGAGCAG
* * * *
141532 ATCTTCAAACCCTAGCTTCGTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCT
1 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
*
141597 TCCTGATGAGATACTGAGAAGTGAACCAAATTCTTCTTCCTGATTAGATACAGAGAAGCAGATTG
66 TCCTGATGAGATACTGAGAAGTGAACCAAATTCTTCTTCCTGATAAGATACAGAGAAGCAGATTG
*
141662 AAACAAGCGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGTTC
131 AAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTC
141727 GATGTAAATAA
196 GATGTAAATAA
*
141738 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAATGGTTAGCT
1 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
* * * *
141803 TCCTGATGAGATACTGAGAAGTGAATCAAATT-TGCCTTCCTGATGAGATACAGAGAAGCGGATT
66 TCCTGATGAGATACTGAGAAGTGAACCAAATTCT-TCTTCCTGATAAGATACAGAGAAGCAGATT
*
141867 GAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGTT
130 GAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTT
* *
141932 CGATGTGAGTAA
195 CGATGTAAATAA
** * * *
141944 ATCTTCGAACTTCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAACGGTTAGCT
1 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
* * * ** * * * * * *
142009 TCCCGATGAAATA-TGGGGAAGTGAACCAAAACCATCTTCCTGATAAAACACGGAGAAGTAGATC
66 TCCTGATGAGATACT-GAGAAGTGAACCAAATTCTTCTTCCTGATAAGATACAGAGAAGCAGATT
* * ** *
142073 AAAACAAGTGATATGGTCATCTTCCTGATAAGATACTGAGAAGAAG
130 GAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAG
142119 GTCAAGTCAA
Statistics
Matches: 338, Mismatches: 40, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
205 2 0.01
206 336 0.99
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (206 bp):
ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
TCCTGATGAGATACTGAGAAGTGAACCAAATTCTTCTTCCTGATAAGATACAGAGAAGCAGATTG
AAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTC
GATGTAAATAA
Found at i:142456 original size:17 final size:17
Alignment explanation
Indices: 142433--142503 Score: 97
Period size: 17 Copynumber: 4.1 Consensus size: 17
142423 GCCCCTTTTT
142433 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
142450 TATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
142467 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
*
142484 AATTTGATTTTAAAATTA
1 AATTT-ATTTTAAATTTA
142502 AA
1 AA
142504 AAGTCCATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 34 0.74
18 12 0.26
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:142467 original size:6 final size:6
Alignment explanation
Indices: 142440--142503 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
142430 TTTAATTTAT
* *
142440 TTTAAA TTTATA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* * *
142486 TTTGAT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA
142504 AAGTCCATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
4 2 0.04
5 5 0.11
6 35 0.78
7 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:142470 original size:23 final size:23
Alignment explanation
Indices: 142440--142488 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
142430 TTTAATTTAT
* * *
142440 TTTAAATTTATATTTATTTTAAA
1 TTTAAATTAATATTAAATTTAAA
*
142463 TTTAAATTAATCTTAAATTTAAA
1 TTTAAATTAATATTAAATTTAAA
142486 TTT
1 TTT
142489 GATTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAAATTAATATTAAATTTAAA
Found at i:143195 original size:7 final size:7
Alignment explanation
Indices: 143172--143207 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
143162 CTTTAATGCT
143172 ATTAATA
1 ATTAATA
*
143179 AATAAT-
1 ATTAATA
143185 ATTAATA
1 ATTAATA
143192 ATTAATA
1 ATTAATA
143199 ATTAATA
1 ATTAATA
143206 AT
1 AT
143208 AACGCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTAATA
Found at i:144446 original size:29 final size:29
Alignment explanation
Indices: 144299--144607 Score: 255
Period size: 29 Copynumber: 10.8 Consensus size: 29
144289 GGAGGTCCCT
** * *
144299 AAACTATCCAAAAATTATATTTTTACCCCCA
1 AAACT-TCCAAAAATTCCATTTTTA-CCTCG
**
144330 AAACTT-CAAAAACCCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
144359 AAACTTCCAAAAATTCCATTTTTACC-C-
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* * *
144386 AAACTTTCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
144416 AAACTTCCAAAAATTCTATTTTTACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* **
144445 AAACTTCCAAAAATTCCATTTTAACCTTA
1 AAACTTCCAAAAATTCCATTTTTACCTCG
*
144474 AAACCTCCAAAAATTCCATTTTTA-C-C-
1 AAACTTCCAAAAATTCCATTTTTACCTCG
** *
144500 ---CTTGAAAAAATTCTATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* *
144527 AAACTCCCATAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* *
144556 AAACTTCCAAAAAATCCTTTTTTTACCCTCG
1 AAACTTCCAAAAATTCC-ATTTTTA-CCTCG
* *
144587 -AACCT-CTAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
144608 GCCCCAGGAT
Statistics
Matches: 225, Mismatches: 38, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
23 16 0.07
24 1 0.00
25 1 0.00
26 1 0.00
27 21 0.09
28 10 0.04
29 100 0.44
30 70 0.31
31 5 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:144529 original size:23 final size:23
Alignment explanation
Indices: 144482--144529 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
144472 TAAAACCTCC
*
144482 AAAAATTCCATTTTTACCCTTGA
1 AAAAATTCCATTTTTACCCTCGA
*
144505 AAAAATTCTATTTTTGA-CCTCGA
1 AAAAATTCCATTTTT-ACCCTCGA
144528 AA
1 AA
144530 CTCCCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
AAAAATTCCATTTTTACCCTCGA
Found at i:144598 original size:111 final size:111
Alignment explanation
Indices: 144306--144607 Score: 279
Period size: 111 Copynumber: 2.7 Consensus size: 111
144296 CCTAAACTAT
** * * ** * *
144306 CCAAAAATTATATTTTTACCCCCAAAACTT-CAAAAACCCCATTTTTAA-CCTCGAAACTTCCAA
1 CCAAAAATTCCATTTTTA-CCTCGAAACTTCCAAAAAATCCA-TTTTAACCCT-AAAACCTCCAA
** *
144369 AAATTCCATTTTTACCCAAACTTTCAAAAATCCCATTTTTAACCCCGAAACTT
63 AAATTCCATTTTTA-CC---CTTGAAAAAATCCCATTTTTAACCCCGAAACTC
* * *
144422 CCAAAAATTCTATTTTTACCTCGAAACTTCCAAAAATTCCATTTTAACCTTAAAACCTCCAAAAA
1 CCAAAAATTCCATTTTTACCTCGAAACTTCCAAAAAATCCATTTTAACCCTAAAACCTCCAAAAA
* * * *
144487 TTCCATTTTTACCCTTGAAAAAATTCTATTTTTGACCTCGAAACTC
66 TTCCATTTTTACCCTTGAAAAAATCCCATTTTTAACCCCGAAACTC
* * * ** *
144533 CCATAAATTCCATTTTTACCCTC-AAACTTCCAAAAAATCCTTTTTTTACCCTCGAACCT-CTAA
1 CCAAAAATTCCATTTTTA-CCTCGAAACTTCCAAAAAATCC-ATTTTAACCCTAAAACCTCCAAA
144596 AATTCCATTTTT
64 AATTCCATTTTT
144608 GCCCCAGGAT
Statistics
Matches: 158, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
111 73 0.46
112 17 0.11
114 2 0.01
115 38 0.24
116 28 0.18
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (111 bp):
CCAAAAATTCCATTTTTACCTCGAAACTTCCAAAAAATCCATTTTAACCCTAAAACCTCCAAAAA
TTCCATTTTTACCCTTGAAAAAATCCCATTTTTAACCCCGAAACTC
Found at i:147587 original size:27 final size:26
Alignment explanation
Indices: 147555--147639 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
147545 AAAAGAATTT
**
147555 AATTGAAATTAATAATATTATTGTAAA
1 AATTGAAAAAAATAATATTATT-TAAA
*
147582 AATTGAAAAAAATAATTTTATTTAAA
1 AATTGAAAAAAATAATATTATTTAAA
* * *
147608 TATTATT-AAAAATATAAAATTATTTAAT
1 -A--ATTGAAAAAAATAATATTATTTAAA
147636 AATT
1 AATT
147640 TGTAAAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 21 0.44
28 17 0.35
29 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AATTGAAAAAAATAATATTATTTAAA
Found at i:147898 original size:15 final size:16
Alignment explanation
Indices: 147868--147902 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
147858 TTTTCAATTA
*
147868 TTTTATTTTTTGTAAT
1 TTTTATTTTTTATAAT
147884 TTTTA-TTTTTATAAT
1 TTTTATTTTTTATAAT
147899 TTTT
1 TTTT
147903 TATAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATTTTTTATAAT
Found at i:147903 original size:16 final size:16
Alignment explanation
Indices: 147863--147905 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
147853 AATTTTTTTC
*
147863 AATTATTTTATTTTTTGT
1 AATT-TTTTA-TTTTTAT
147881 AA-TTTTTATTTTTAT
1 AATTTTTTATTTTTAT
147896 AATTTTTTAT
1 AATTTTTTAT
147906 AATTTATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 12 0.52
17 1 0.04
18 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
AATTTTTTATTTTTAT
Found at i:147919 original size:17 final size:16
Alignment explanation
Indices: 147899--147959 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
147889 TTTTTATAAT
147899 TTTTTATAATTTATATG
1 TTTTTA-AATTTATATG
* *
147916 TTTTTAGATTATATATA
1 TTTTTAAATT-TATATG
* *
147933 TTTCTAAATTTTTATG
1 TTTTTAAATTTATATG
*
147949 TATTTATAATT
1 TTTTTA-AATT
147960 ATTTTATATA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 11 0.32
17 23 0.68
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTAAATTTATATG
Found at i:147978 original size:20 final size:19
Alignment explanation
Indices: 147890--147978 Score: 56
Period size: 19 Copynumber: 4.5 Consensus size: 19
147880 TAATTTTTAT
147890 TTTTATAATTTTTTATA-A
1 TTTTATAATTTTTTATATA
**
147908 TTTATATGTTTTTAGATTATATA
1 TTT-TATAATTTT---TTATATA
* * *
147931 TATTTCTAAATTTTTATGTA
1 T-TTTATAATTTTTTATATA
147951 -TTTATAATTATTTTATATA
1 TTTTATAATT-TTTTATATA
*
147970 TTTTTTAAT
1 TTTTATAAT
147979 GTGTATATAC
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
18 10 0.19
19 15 0.29
20 13 0.25
22 5 0.10
23 7 0.13
24 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTATATA
Found at i:149171 original size:17 final size:17
Alignment explanation
Indices: 149149--149185 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
149139 AACAAATACT
* *
149149 AATGCTAGCATTTTGAA
1 AATGCTAACATTTTAAA
149166 AATGCTAACATTTTAAA
1 AATGCTAACATTTTAAA
149183 AAT
1 AAT
149186 CTTAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (17 bp):
AATGCTAACATTTTAAA
Found at i:157712 original size:41 final size:41
Alignment explanation
Indices: 157655--157736 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
157645 TATGTAATTA
157655 AGTTTGAAATTACATTCTAGTATGTAAAATCGGAGATAAAT
1 AGTTTGAAATTACATTCTAGTATGTAAAATCGGAGATAAAT
157696 AGTTTGAAATTACATTCTAGTATGTAAAATCGGAGATAAAT
1 AGTTTGAAATTACATTCTAGTATGTAAAATCGGAGATAAAT
157737 TGAAATATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (41 bp):
AGTTTGAAATTACATTCTAGTATGTAAAATCGGAGATAAAT
Found at i:161163 original size:112 final size:111
Alignment explanation
Indices: 160964--161183 Score: 334
Period size: 112 Copynumber: 2.0 Consensus size: 111
160954 TTCAAGTAAC
* * * *
160964 TTATCACAAACCTCAATTCGAATGTTCTTAAACATCTTGAGTTGTGATCTTAAATCAACAAACTC
1 TTATCACAAACCTCAATTCAAATGTTCTTAAACATCCTGAGTTATAATCTTAAATCAACAAACTC
* *
161029 AAAGAAAATTAGGTTACGATCTTAAATCAACTAATCTTAAGCATTAA
66 AAAGAAAATTAGGTTACAATCTT-AATCAACTAACCTTAAGCATTAA
* *
161076 TTATCACCAATCTCAATTCAAATGTTCTTAAACATCCTGAGTTATAATCTTAAATCAGA-AAACT
1 TTATCACAAACCTCAATTCAAATGTTCTTAAACATCCTGAGTTATAATCTTAAATCA-ACAAACT
*
161140 CAAAGAAAATTAGGTTACAATCTTAATCAACTAACCTTGAGCAT
65 CAAAGAAAATTAGGTTACAATCTTAATCAACTAACCTTAAGCAT
161184 CAGTTGGGAA
Statistics
Matches: 98, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
111 18 0.18
112 79 0.81
113 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (111 bp):
TTATCACAAACCTCAATTCAAATGTTCTTAAACATCCTGAGTTATAATCTTAAATCAACAAACTC
AAAGAAAATTAGGTTACAATCTTAATCAACTAACCTTAAGCATTAA
Found at i:161324 original size:20 final size:20
Alignment explanation
Indices: 161299--161341 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
161289 CAATAATAAA
161299 TAGGCGAGCCTTTATAATGT
1 TAGGCGAGCCTTTATAATGT
*
161319 TAGGCGAGCTTTTATAATGT
1 TAGGCGAGCCTTTATAATGT
161339 TAG
1 TAG
161342 TTGGGAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.37
Consensus pattern (20 bp):
TAGGCGAGCCTTTATAATGT
Found at i:161452 original size:69 final size:69
Alignment explanation
Indices: 161329--161461 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 69
161319 TAGGCGAGCT
* * * * *
161329 TTTATAATGTTAGTTGGGAACATAGGTTCACTAGCTATTTTGGAAATTATGATCATAAATCGACA
1 TTTATAATGTTAGCTGGGAACATAGGTCCACCAGCTATTTTGGAAACTACGATCATAAATCGACA
161394 AGCA
66 AGCA
* * ** *
161398 TTTATAATTTTAGCTGGGAACATAGGTCCACCATCTATTTTGGAGGCTGCGATCATAAATCGAC
1 TTTATAATGTTAGCTGGGAACATAGGTCCACCAGCTATTTTGGAAACTACGATCATAAATCGAC
161462 GAGCCTTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (69 bp):
TTTATAATGTTAGCTGGGAACATAGGTCCACCAGCTATTTTGGAAACTACGATCATAAATCGACA
AGCA
Found at i:161485 original size:69 final size:69
Alignment explanation
Indices: 161329--161487 Score: 174
Period size: 69 Copynumber: 2.3 Consensus size: 69
161319 TAGGCGAGCT
* * * * * *
161329 TTTATAATGTTAGTTGGGAACATAGGTTCACTAGCTATTTTGGAAATTATGATCATAAATCGACA
1 TTTATAATATCAGTTGGGAACATAGGTCCACCAGCTATTTTGGAAACTACGATCATAAATCGACA
161394 AGCA
66 AGCA
* * * * ** * *
161398 TTTATAATTTTAGCTGGGAACATAGGTCCACCATCTATTTTGGAGGCTGCGATCATAAATCGACG
1 TTTATAATATCAGTTGGGAACATAGGTCCACCAGCTATTTTGGAAACTACGATCATAAATCGACA
*
161463 AGCC
66 AGCA
*
161467 TTTGTAATATCAGTTGGGAAC
1 TTTATAATATCAGTTGGGAAC
161488 GTATGTCTAC
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (69 bp):
TTTATAATATCAGTTGGGAACATAGGTCCACCAGCTATTTTGGAAACTACGATCATAAATCGACA
AGCA
Found at i:163699 original size:24 final size:24
Alignment explanation
Indices: 163667--163714 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
163657 AGTCTTTCTT
163667 GTCCAAATGATCATCTGTTCCTTA
1 GTCCAAATGATCATCTGTTCCTTA
163691 GTCCAAATGATCATCTGTTCCTTA
1 GTCCAAATGATCATCTGTTCCTTA
163715 CAATGTGCGA
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:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (24 bp):
GTCCAAATGATCATCTGTTCCTTA
Found at i:180548 original size:20 final size:20
Alignment explanation
Indices: 180525--180565 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
180515 TTCAAATAAC
180525 TTAAAAATAGTTAATCCAAG
1 TTAAAAATAGTTAATCCAAG
180545 TTAAAAATAGTTAATCCAAG
1 TTAAAAATAGTTAATCCAAG
180565 T
1 T
180566 CTATGACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (20 bp):
TTAAAAATAGTTAATCCAAG
Found at i:191356 original size:3 final size:3
Alignment explanation
Indices: 191348--191372 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
191338 GATCTTTTAT
191348 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
191373 AAAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:192133 original size:21 final size:21
Alignment explanation
Indices: 192085--192140 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
192075 ATGCGTAAAA
*
192085 AAAATAAATATAAATAGAAATG
1 AAAATAAATA-AAATAGAAATC
192107 AAAATAAATAAAGAT-GAAATC
1 AAAATAAATAAA-ATAGAAATC
*
192128 AGAATAAATAAAA
1 AAAATAAATAAAA
192141 ATTATACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 18 0.58
22 12 0.39
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (21 bp):
AAAATAAATAAAATAGAAATC
Found at i:192925 original size:19 final size:19
Alignment explanation
Indices: 192897--192940 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
192887 GAAATAGTTA
*
192897 AAAAAATTAAACTTTATTT
1 AAAAATTTAAACTTTATTT
*
192916 AAAAATTTAAACTTTTTTT
1 AAAAATTTAAACTTTATTT
*
192935 TAAAAT
1 AAAAAT
192941 GCTTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATTTAAACTTTATTT
Done.