Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013620.1 Kokia drynarioides strain JFW-HI SEQ_128648, 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: 249751
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:246 original size:13 final size:13
Alignment explanation
Indices: 228--252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
218 CAATCTCATG
228 ACCATCTTCAACC
1 ACCATCTTCAACC
241 ACCATCTTCAAC
1 ACCATCTTCAAC
253 ATCCACTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (13 bp):
ACCATCTTCAACC
Found at i:1864 original size:29 final size:29
Alignment explanation
Indices: 1813--2259 Score: 374
Period size: 29 Copynumber: 15.8 Consensus size: 29
1803 GAAGGTCCCT
*
1813 AAACTATCCAAAAATTTCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* * * * * *
1843 GAACTTCTAAAAATCCCATTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
1872 AAACTTCTAAAAATTTCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * *
1901 AAACTTCTAAAAATCCCATTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCCC
1930 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
1959 GAACTTCCAAAAATTCCATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCCC
*
1989 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
2018 AAACTTCCAAAAATCCCATTTTT------
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
2041 -AAC-CCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
2068 AAACTTCCAAAAA-TCTCATTTTT------
1 AAACTTCCAAAAATTC-CATTTTTACCCCC
* *
2091 -AAC-CCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
2118 AAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* * *
2148 AAAATTCCAAAAATTCCATTTTTACCTCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
2177 AAACTTTCAAAAA-TCTCATTTTCAACCCCA
1 AAACTTCCAAAAATTC-CATTTT-TACCCCC
2207 AAACTTCCAAAAATTCCATTTTTACCCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCC-C
* *
2237 GAA-TGTCTAAAAATTCCATTTTT
1 AAACT-TCCAAAAATTCCATTTTT
2260 TAAACCACAA
Statistics
Matches: 335, Mismatches: 57, Indels: 50
0.76 0.13 0.11
Matches are distributed among these distances:
21 30 0.09
22 8 0.02
28 10 0.03
29 190 0.57
30 95 0.28
31 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:2013 original size:59 final size:58
Alignment explanation
Indices: 1813--2234 Score: 471
Period size: 59 Copynumber: 7.5 Consensus size: 58
1803 GAAGGTCCCT
* * * *
1813 AAACTATCCAAAAATTTCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTAACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCTCA
* * * *
1872 AAACTTCTAAAAATTTCATTTTTACCCTCAAACTTCTAAAAATCCCATTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCTCA
* * * *
1930 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTT-AACCTCA
*
1989 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTT----T--
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCTCA
* * *
2041 -AAC-CCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTT----T--
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCTCA
* * *
2091 -AAC-CCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTTAACCTCA
* * * * * *
2148 AAAATTCCAAAAATTCCATTTTTACCTCTAAACTTTCAAAAATCTCATTTTCAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTT-AACCTCA
2207 AAACTTCCAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
2235 TCGAATGTCT
Statistics
Matches: 324, Mismatches: 28, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
50 89 0.27
51 7 0.02
54 1 0.00
58 100 0.31
59 127 0.39
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCTCA
Found at i:2054 original size:50 final size:50
Alignment explanation
Indices: 1995--2156 Score: 315
Period size: 50 Copynumber: 3.2 Consensus size: 50
1985 CTCGAAACTT
1995 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACC
1 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACC
*
2045 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTAACC
1 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACC
2095 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACC
1 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACC
2145 CCAAAAATTCCA
1 CCAAAAATTCCA
2157 AAAATTCCAT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 110 1.00
ACGTcount: A:0.37, C:0.31, G:0.00, T:0.31
Consensus pattern (50 bp):
CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACC
Found at i:2076 original size:20 final size:21
Alignment explanation
Indices: 2024--2070 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
2014 CCTCAAACTT
*
2024 CCAAAAATCCCATTTTTAACC
1 CCAAAAATTCCATTTTTAACC
2045 CCAAAAATTCCATTTTT-ACC
1 CCAAAAATTCCATTTTTAACC
2065 CTCAAA
1 C-CAAA
2071 CTTCCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.30
Consensus pattern (21 bp):
CCAAAAATTCCATTTTTAACC
Found at i:2126 original size:20 final size:21
Alignment explanation
Indices: 2074--2120 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
2064 CCTCAAACTT
2074 CCAAAAA-TCTCATTTTTAACC
1 CCAAAAATTC-CATTTTTAACC
2095 CCAAAAATTCCATTTTT-ACC
1 CCAAAAATTCCATTTTTAACC
2115 CTCAAA
1 C-CAAA
2121 CTTCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.17
21 18 0.75
22 2 0.08
ACGTcount: A:0.38, C:0.30, G:0.00, T:0.32
Consensus pattern (21 bp):
CCAAAAATTCCATTTTTAACC
Found at i:7168 original size:12 final size:12
Alignment explanation
Indices: 7146--7188 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
7136 TATGTGGAAT
*
7146 AAATTATATTAA
1 AAATTAAATTAA
*
7158 GAATTAAATTATA
1 AAATTAAATTA-A
7171 TAAATTAAATTAA
1 -AAATTAAATTAA
7184 AAATT
1 AAATT
7189 TAAACGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 14 0.54
13 2 0.08
14 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
AAATTAAATTAA
Found at i:7178 original size:14 final size:17
Alignment explanation
Indices: 7145--7182 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
7135 ATATGTGGAA
7145 TAAATTATATTAAGAAT
1 TAAATTATATTAAGAAT
7162 TAAATTATA-T-A-AAT
1 TAAATTATATTAAGAAT
7176 TAAATTA
1 TAAATTA
7183 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 1 0.05
17 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATTATATTAAGAAT
Found at i:9583 original size:30 final size:29
Alignment explanation
Indices: 9405--9841 Score: 350
Period size: 30 Copynumber: 14.8 Consensus size: 29
9395 TTCTCAAGGA
* *
9405 AAAAATGGTAATTTTGGGAAAGTTCGGGGGTT
1 AAAAATGG-AATTTTTGG-AAGTTTGGGGG-T
*
9437 AAAAATGGAATTTTTAGACA-TTTGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTGGGGGT
* ***
9466 -AAAAGGGTAA-TTTT-GAGAGTTTTAAGGT
1 AAAAATGG-AATTTTTGGA-AGTTTGGGGGT
* * *
9494 CGAAAATGGAGTTTTTGGACA--TTCGGGG-
1 -AAAAATGGAATTTTTGGA-AGTTTGGGGGT
* * * *
9522 CAAAATGGTAATTTTTGAAAGTTTCGAGGT
1 AAAAATGG-AATTTTTGGAAGTTTGGGGGT
* * *
9552 AAAAAATGGAAATTTTGGAGGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
9582 AAAAATGTAATTTTT-GAGAGTTTTGAGGGT
1 AAAAATGGAATTTTTGGA-AG-TTTGGGGGT
* * *
9612 AAAAATAGAATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* **
9641 AAAAATGGAATTTTTAGAAGTTTTAAGGGT
1 AAAAATGGAATTTTTGGAAG-TTTGGGGGT
* * *
9671 AAAAATGGAATTTTTAGAAATTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
*
9700 AAAAATGGAATTTTTGGAAGTTTTTGGGGT
1 AAAAATGGAATTTTTGGAAG-TTTGGGGGT
*
9730 CAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * *
9760 AAAAATTGAATTTTTGGAAGTTTTGAGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
9789 AAAAAATGTAATTTTTGGAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
9819 AAAAATGGAATTTTTGGACAGTT
1 AAAAATGGAATTTTTGGA-AGTT
9842 CCTTTGATTT
Statistics
Matches: 333, Mismatches: 52, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
27 11 0.03
28 26 0.08
29 123 0.37
30 125 0.38
31 40 0.12
32 8 0.02
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGGT
Found at i:9617 original size:59 final size:61
Alignment explanation
Indices: 9432--9834 Score: 383
Period size: 59 Copynumber: 6.8 Consensus size: 61
9422 GAAAGTTCGG
* * **
9432 GGGTTAAAAATGGAATTTTTAGACA-TTTGGGGGTAAAAGGGTAA-TTTTGAG-AGTTTT-A
1 GGGTAAAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTTGA
* ** * * * *
9490 AGGTCGAAAATGGAGTTTTTGGACA--TTCGGGG-CAAAATGGTAATTTTTGA-AAGTTTCGA
1 GGGTAAAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAAT-GTAATTTTTGAGAAGTTTTGA
* * *
9549 -GGTAAAAAATGGAAATTTTGGAGGTTCGGGGGTAAAAATGTAATTTTTGAG-AGTTTTGA
1 GGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTTGA
* * * * *
9608 GGGT-AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTT-AGAAGTTTTAA
1 GGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTTGA
* * * *
9667 GGGT-AAAAATGGAATTTTTAGAAATTTAGGGGTAAAAATGGAATTTTTG-GAAGTTTTTG-
1 GGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAG-TTTTGA
* *
9726 GGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAAT-TGAATTTTTG-GAAGTTTTGA
1 GGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGT-AATTTTTGAGAAGTTTTGA
* * *
9786 -GGTAAAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTG
1 GGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTG
9835 GACAGTTCCT
Statistics
Matches: 289, Mismatches: 40, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
56 3 0.01
57 10 0.03
58 51 0.18
59 168 0.58
60 57 0.20
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.35
Consensus pattern (61 bp):
GGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTTGA
Found at i:9976 original size:10 final size:10
Alignment explanation
Indices: 9961--10006 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
9951 TTTCAATTTT
9961 TTATTAATAA
1 TTATTAATAA
9971 TTATTAATAA
1 TTATTAATAA
*
9981 -TATTATTAA
1 TTATTAATAA
9990 TTATTTAATAA
1 TTA-TTAATAA
*
10001 ATATTA
1 TTATTA
10007 TCTTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 8 0.26
10 15 0.48
11 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTATTAATAA
Found at i:9987 original size:12 final size:12
Alignment explanation
Indices: 9961--10052 Score: 50
Period size: 12 Copynumber: 7.8 Consensus size: 12
9951 TTTCAATTTT
9961 TTATTAAT-A-A
1 TTATTAATAATA
9971 TTATTAATAATA
1 TTATTAATAATA
*
9983 TTATTAATTAT-
1 TTATTAATAATA
* *
9994 TTAATAAATATTA
1 TT-ATTAATAATA
*
10007 TCT-TTAATAAAA
1 T-TATTAATAATA
* *
10019 TTATTATTATTA
1 TTATTAATAATA
*
10031 TCATTAATGAA-A
1 TTATTAAT-AATA
10043 TTATTTAATA
1 TTA-TTAATA
10053 TATAATATAT
Statistics
Matches: 60, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
10 8 0.13
11 4 0.07
12 40 0.67
13 7 0.12
14 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (12 bp):
TTATTAATAATA
Found at i:10013 original size:24 final size:19
Alignment explanation
Indices: 9962--10030 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 19
9952 TTCAATTTTT
*
9962 TATTAATAATTATTAATAA
1 TATTATTAATTATTAATAA
9981 TATTATTAATTATTTAATAA
1 TATTATTAATTA-TTAATAA
10001 -A-TATT-ATCT-TTAATAA
1 TATTATTAAT-TATTAATAA
*
10017 AATTATT-ATTATTA
1 TATTATTAATTATTA
10031 TCATTAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
16 7 0.16
17 4 0.09
18 14 0.32
19 12 0.27
20 7 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTATTAATTATTAATAA
Found at i:10014 original size:16 final size:15
Alignment explanation
Indices: 9993--10022 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9983 TTATTAATTA
9993 TTTAATAAATATTATC
1 TTTAATAAA-ATTATC
10009 TTTAATAAAATTAT
1 TTTAATAAAATTAT
10023 TATTATTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATAAAATTATC
Found at i:10031 original size:24 final size:24
Alignment explanation
Indices: 10002--10047 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
9992 ATTTAATAAA
*
10002 TATTATCTTTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
*
10026 TATTATCATTAATGAAATTATT
1 TATTATCATTAATAAAATTATT
10048 TAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:10121 original size:17 final size:17
Alignment explanation
Indices: 10099--10133 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
10089 TGGCCAAAAT
10099 TAATAGCAAATAATAAC
1 TAATAGCAAATAATAAC
10116 TAATAGCAAATAATAAC
1 TAATAGCAAATAATAAC
10133 T
1 T
10134 TAGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (17 bp):
TAATAGCAAATAATAAC
Found at i:10845 original size:6 final size:6
Alignment explanation
Indices: 10822--10899 Score: 56
Period size: 6 Copynumber: 13.3 Consensus size: 6
10812 GTTCTAAATC
* * **
10822 AATTTG AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
**
10869 AAGATA AATTTA AATTTA AGA--TA AATTTA AA
1 AATTTA AATTTA AATTTA A-ATTTA AATTTA AA
10900 ACCAATCTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
4 1 0.02
5 10 0.18
6 40 0.71
7 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:10848 original size:17 final size:18
Alignment explanation
Indices: 10837--10899 Score: 94
Period size: 17 Copynumber: 3.6 Consensus size: 18
10827 GAATTTTAAT
10837 TAAATTTAAATTTAAAG-
1 TAAATTTAAATTTAAAGA
*
10854 CAAATTTAAATTTAAAAGA
1 TAAATTTAAATTT-AAAGA
10873 TAAATTTAAATTT-AAGA
1 TAAATTTAAATTTAAAGA
10890 TAAATTTAAA
1 TAAATTTAAA
10900 ACCAATCTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 26 0.62
18 4 0.10
19 12 0.29
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTTAAAGA
Found at i:11561 original size:193 final size:195
Alignment explanation
Indices: 11230--11854 Score: 679
Period size: 206 Copynumber: 3.1 Consensus size: 195
11220 TGACTTGGCC
* * * ** * * *
11230 TTCTTCTCAGTATCTTATCAGGAAGACGACCGCATCACTTGTTTTGATCCATTTCTCTGTGTTTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTATCTC
* * * * * *
11295 ATCAGGAAAACGGATTTGGTTCACTTCTCCGTATTTCATCAGGAAGCTAACCTCTTTATTGCTTC
66 ATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTTATTGCTTC
*
11360 -ATCCTGCTTCTCAATATCTTATCAAGAAGCTGGGG-TCGAAGATTTGTTCGCATT-GAGTTGGT
131 GA-CCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCGAAGATTTGTTCGCATTAGAGTTGGT
11422 A
195 A
* *
11423 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTATCTC
* * *
11488 ATAAAGAAGACGAATTTGG-TCAACTTCTCAGTATCTCATCAGGAAGCTAACATTTTTATTGTTT
66 ATCAGGAAGACGAATTTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTAACATTTTTATTGCTT
* * * * *
11552 CGCCCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTTGCATTAAGCGTGGG
130 CGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCGAAGATTTGTTCGCATT-AGAGTTGG
11617 TTTGA
194 --T-A
* * *
11622 TTTGGTCTTCTTCTCAGTATCTCATTAGGAATG-TGATCGCATCGCTTGTTTCAATCCACTTCTC
1 --T--TCTTC-TCT--GTATCTCATCAGGAA-GATGACCGCATCACTTGTTTCAATCCACTTCTC
* ** *
11686 TGTATCTTATCAGGAAGATAAATTTGGTTCACTTCTCAGCATCTCATCAGGAAGCTAACCA-TTT
58 TGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAA-CATTTT
* * * *
11750 TATTGCTACGACCTGCTTCTCAGTATCTCAT-AAGGTAGCTGGGGTTCGAAGATTTGCTCGCATT
122 TATTGCTTCGACCTGCTTCTCAATATCTCATCAA-GAAGCTGGGGTTCGAAGATTTGTTCGCATT
11814 GAGCCTCAAGTTGGTA
186 -AG-----AGTTGGTA
11830 TTCTTCTCTGTATCTCATCAGGAAG
1 TTCTTCTCTGTATCTCATCAGGAAG
11855 CTAACCATTT
Statistics
Matches: 360, Mismatches: 48, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
192 2 0.01
193 139 0.39
194 18 0.05
196 5 0.01
198 1 0.00
199 1 0.00
200 1 0.00
201 15 0.04
203 8 0.02
204 8 0.02
205 1 0.00
206 150 0.42
207 5 0.01
208 1 0.00
209 1 0.00
211 4 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (195 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTATCTC
ATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTTATTGCTTC
GACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCGAAGATTTGTTCGCATTAGAGTTGGTA
Found at i:11914 original size:115 final size:115
Alignment explanation
Indices: 11717--11931 Score: 351
Period size: 115 Copynumber: 1.9 Consensus size: 115
11707 ATTTGGTTCA
11717 CTTCTCAGCATCTCATCAGGAAGCTAACCATTTTATTGCTACGACCTGCTTCTCAGTATCTCATA
1 CTTCTCAGCATCTCATCAGGAAGCTAACCATTTTATTGCTACGACCTGCTTCTCAGTATCTCATA
*
11782 AGGTAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCAAGTTGGTATT
66 AGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCAAGTTGGTATT
* * ** *
11832 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGCATCTCATCAGGAAGCTAACCATTTTATTGCTACGACCTGCTTCTCAGTATCTCATA
*
11897 AGGAAGCTGTGGG-TCGAAGATTTGTTCGCATTGAG
66 AGGAAGCTG-GGGTTCGAAGATTTGCTCGCATTGAG
11932 TTGGTATACT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
115 89 0.97
116 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (115 bp):
CTTCTCAGCATCTCATCAGGAAGCTAACCATTTTATTGCTACGACCTGCTTCTCAGTATCTCATA
AGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCAAGTTGGTATT
Found at i:23740 original size:59 final size:59
Alignment explanation
Indices: 23669--23909 Score: 190
Period size: 59 Copynumber: 4.1 Consensus size: 59
23659 CCTGAGGGGC
* * * **
23669 AAAATGGTAATTTTGGA-TTCTCGGGGGT-AAAATGATAA-TTTTTGAAAGTTTTGGGGTCA
1 AAAATGGAAATTTTGGAGGT-TCGAGGGTAAAAAT-ATAATTTTTTG-AAGTTTCAGGGTCA
* *
23728 AAAATGGAAATTTTAGAGGTTCGAGGGTAAAAATATAATTTTTTGAAGTTTCAGGGTTA
1 AAAATGGAAATTTTGGAGGTTCGAGGGTAAAAATATAATTTTTTGAAGTTTCAGGGTCA
* * * ** * * *
23787 AAAATGGAATTTTTGGAAGTTAGAGGGTAAAAATGGAATTTTTGGAAGTCTC-GAGGTAA
1 AAAATGGAAATTTTGGAGGTTCGAGGGTAAAAATATAATTTTTTGAAGTTTCAG-GGTCA
* * * *
23846 AAAATGGAATTTTTGGAAGTTTCGA-GGTAAAAA-ATGGAATTTTTGGAAG-TTCGAGGGTAA
1 AAAATGGAAATTTTGG-AGGTTCGAGGGTAAAAATAT--AATTTTTTGAAGTTTC-AGGGTCA
23906 AAAA
1 AAAA
23910 GTACTTTTCA
Statistics
Matches: 151, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
58 1 0.01
59 111 0.74
60 38 0.25
61 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (59 bp):
AAAATGGAAATTTTGGAGGTTCGAGGGTAAAAATATAATTTTTTGAAGTTTCAGGGTCA
Found at i:23791 original size:30 final size:30
Alignment explanation
Indices: 23705--23909 Score: 208
Period size: 30 Copynumber: 6.9 Consensus size: 30
23695 GTAAAATGAT
* ** *
23705 AATTTTTGAAAGTTTTGGGGTCAAAAATGG
1 AATTTTTGGAAGTTTCAGGGTAAAAAATGG
* * *
23735 AAATTTTAG-AGGTTCGAGGGTAAAAATAT--
1 AATTTTTGGAAGTTTC-AGGGTAAAAA-ATGG
* *
23764 AATTTTTTGAAGTTTCAGGGTTAAAAATGG
1 AATTTTTGGAAGTTTCAGGGTAAAAAATGG
**
23794 AATTTTTGGAAGTTAGAGGGT-AAAAATGG
1 AATTTTTGGAAGTTTCAGGGTAAAAAATGG
*
23823 AATTTTTGGAAGTCTC-GAGGTAAAAAATGG
1 AATTTTTGGAAGTTTCAG-GGTAAAAAATGG
23853 AATTTTTGGAAGTTTC-GAGGTAAAAAATGG
1 AATTTTTGGAAGTTTCAG-GGTAAAAAATGG
23883 AATTTTTGGAAG-TTCGAGGGTAAAAAA
1 AATTTTTGGAAGTTTC-AGGGTAAAAAA
23910 GTACTTTTCA
Statistics
Matches: 148, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.02
29 47 0.32
30 95 0.64
31 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (30 bp):
AATTTTTGGAAGTTTCAGGGTAAAAAATGG
Found at i:23849 original size:89 final size:88
Alignment explanation
Indices: 23705--23908 Score: 252
Period size: 89 Copynumber: 2.3 Consensus size: 88
23695 GTAAAATGAT
* * * *
23705 AATTTTTGAAAGTTTTG-GGGTCAAAAATGGAAATTTTAGAGGTTCGAGGGTAAAAATATAATTT
1 AATTTTTGGAAG-TTAGAGGGT-AAAAATGGAAATTTTAGAAGTTCGAGGGTAAAAATAGAATTT
* *
23769 TTTGAAGTTTC-AGGGTTAAAAATGG
64 TTGGAAGTTTCGA-GGTAAAAAATGG
* * *
23794 AATTTTTGGAAGTTAGAGGGTAAAAATGGAATTTTTGGAAGTCTCGA-GGTAAAAAATGGAATTT
1 AATTTTTGGAAGTTAGAGGGTAAAAATGGAAATTTTAGAAGT-TCGAGGGT-AAAAATAGAATTT
23858 TTGGAAGTTTCGAGGTAAAAAATGG
64 TTGGAAGTTTCGAGGTAAAAAATGG
*
23883 AATTTTTGGAAGTTCGAGGGTAAAAA
1 AATTTTTGGAAGTTAGAGGGTAAAAA
23909 AGTACTTTTC
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
88 24 0.24
89 76 0.75
90 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (88 bp):
AATTTTTGGAAGTTAGAGGGTAAAAATGGAAATTTTAGAAGTTCGAGGGTAAAAATAGAATTTTT
GGAAGTTTCGAGGTAAAAAATGG
Found at i:24964 original size:32 final size:29
Alignment explanation
Indices: 24898--24965 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
24888 CAATTTCTTT
* *
24898 TTTATTATTAATGTTTTTATTAAAAAATA
1 TTTATTATTAATATTATTATTAAAAAATA
* *
24927 CTTATTATTATTATTATTATTAATTAATAATA
1 TTTATTATTAATATTATTATTAA--AA-AATA
24959 TTTATTA
1 TTTATTA
24966 ATGTCATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 19 0.61
31 2 0.06
32 10 0.32
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TTTATTATTAATATTATTATTAAAAAATA
Found at i:25705 original size:24 final size:24
Alignment explanation
Indices: 25678--25725 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
25668 CTTGTTTGTA
*
25678 ATGGGTTAGGGATATAGGTCTGTT
1 ATGGGTTAAGGATATAGGTCTGTT
*
25702 ATGGGTTAAGGATATGGGTCTGTT
1 ATGGGTTAAGGATATAGGTCTGTT
25726 TGGTATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.04, G:0.38, T:0.38
Consensus pattern (24 bp):
ATGGGTTAAGGATATAGGTCTGTT
Found at i:28122 original size:30 final size:30
Alignment explanation
Indices: 28088--28293 Score: 222
Period size: 30 Copynumber: 6.9 Consensus size: 30
28078 TAAAATCGGA
** * *
28088 TCAAATTTGAATTTTTGGAAACTTCAGGTG
1 TCAAATTCAAATTTTTGGAAAATTTAGGTG
**
28118 TCAAA-TCAAAAATTTGGAAAATTTAGG-G
1 TCAAATTCAAATTTTTGGAAAATTTAGGTG
** *
28146 TCAAATTGGAATTTTTGGAAAATTTAGATG
1 TCAAATTCAAATTTTTGGAAAATTTAGGTG
*
28176 TCAAATTCAAATTTTTGGAAAATTTAGGGG
1 TCAAATTCAAATTTTTGGAAAATTTAGGTG
* *
28206 TCAAATTTCAAATTTTTGGAAAGTTTAGGGG
1 TCAAA-TTCAAATTTTTGGAAAATTTAGGTG
*
28237 TCAAATT-AGAATTTTTGGAAAGTTT-GGTGG
1 TCAAATTCA-AATTTTTGGAAAATTTAGGT-G
* *
28267 TCAAATTCAAATTTTTGAAAAAATTAG
1 TCAAATTCAAATTTTTGGAAAATTTAG
28294 AGGTCGAAAA
Statistics
Matches: 149, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.04
29 36 0.24
30 76 0.51
31 31 0.21
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37
Consensus pattern (30 bp):
TCAAATTCAAATTTTTGGAAAATTTAGGTG
Found at i:28240 original size:61 final size:60
Alignment explanation
Indices: 28088--28293 Score: 231
Period size: 61 Copynumber: 3.5 Consensus size: 60
28078 TAAAATCGGA
** * * **
28088 TCAAATTTGAATTTTTGGAAACTTCAGGTGTCAAA-TCAAAAATTTGGAAAATTTA-GGG
1 TCAAATTCAAATTTTTGGAAAATTTAGGTGTCAAATTCAAATTTTTGGAAAATTTAGGGG
** *
28146 TCAAATTGGAATTTTTGGAAAATTTAGATGTCAAATTCAAATTTTTGGAAAATTTAGGGG
1 TCAAATTCAAATTTTTGGAAAATTTAGGTGTCAAATTCAAATTTTTGGAAAATTTAGGGG
* * *
28206 TCAAATTTCAAATTTTTGGAAAGTTTAGGGGTCAAATT-AGAATTTTTGGAAAGTTT-GGTGG
1 TCAAA-TTCAAATTTTTGGAAAATTTAGGTGTCAAATTCA-AATTTTTGGAAAATTTAGG-GG
* *
28267 TCAAATTCAAATTTTTGAAAAAATTAG
1 TCAAATTCAAATTTTTGGAAAATTTAG
28294 AGGTCGAAAA
Statistics
Matches: 128, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
58 31 0.24
59 18 0.14
60 30 0.23
61 49 0.38
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37
Consensus pattern (60 bp):
TCAAATTCAAATTTTTGGAAAATTTAGGTGTCAAATTCAAATTTTTGGAAAATTTAGGGG
Found at i:28270 original size:91 final size:88
Alignment explanation
Indices: 28088--28298 Score: 253
Period size: 91 Copynumber: 2.4 Consensus size: 88
28078 TAAAATCGGA
** * * *
28088 TCAAATTTGAATTTTTGGAAACTTCAGGTGTCAAATCAAAAATTTGGAAAATTTAGGGTCAAATT
1 TCAAATTCAAATTTTTGGAAAATTTAGGGGTCAAATCAAAAATTTGGAAAATTTAGGGTCAAATT
*
28153 GGAATTTTTGGAAAATTTAGATG
66 AGAATTTTTGGAAAATTTAGATG
** *
28176 TCAAATTCAAATTTTTGGAAAATTTAGGGGTCAAATTTCAAATTTTTGGAAAGTTTAGGGGTCAA
1 TCAAATTCAAATTTTTGGAAAATTTAGGGGTCAAA--TCAAAAATTTGGAAAATTTA-GGGTCAA
* *
28241 ATTAGAATTTTTGGAAAGTTT-GGTGG
63 ATTAGAATTTTTGGAAAATTTAGAT-G
* * *
28267 TCAAATTCAAATTTTTGAAAAAATTAGAGGTC
1 TCAAATTCAAATTTTTGGAAAATTTAGGGGTC
28299 GAAAAATAAT
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
88 30 0.29
90 19 0.18
91 56 0.53
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (88 bp):
TCAAATTCAAATTTTTGGAAAATTTAGGGGTCAAATCAAAAATTTGGAAAATTTAGGGTCAAATT
AGAATTTTTGGAAAATTTAGATG
Found at i:28312 original size:60 final size:60
Alignment explanation
Indices: 28130--28331 Score: 180
Period size: 60 Copynumber: 3.4 Consensus size: 60
28120 AAATCAAAAA
* * ** * * * *
28130 TTTGGAAAATTTAGGGTCAAA-TTGGAATTTTTGGAAAATTTAGATGTCAAATTCA-AATT
1 TTTGGAAAGTTTGGGGTCAAATTTCAAATTTTTGAAAAAATTAGAGGTCAAA-TAAGAATT
* * ** * *
28189 TTTGGAAAATTTAGGGGTCAAATTTCAAATTTTTGGAAAGTTTAGGGGTCAAATTAGAATT
1 TTTGGAAAGTTT-GGGGTCAAATTTCAAATTTTTGAAAAAATTAGAGGTCAAATAAGAATT
*
28250 TTTGGAAAGTTTGGTGGTCAAA-TTCAAATTTTTGAAAAAATTAGAGGTCGAAA-AATAATT
1 TTTGGAAAGTTTGG-GGTCAAATTTCAAATTTTTGAAAAAATTAGAGGTC-AAATAAGAATT
28310 TTT-GAATAGTTTGAGGGTCAAA
1 TTTGGAA-AGTTTG-GGGTCAAA
28332 GAATAATTTT
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
59 15 0.12
60 56 0.46
61 51 0.42
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (60 bp):
TTTGGAAAGTTTGGGGTCAAATTTCAAATTTTTGAAAAAATTAGAGGTCAAATAAGAATT
Found at i:29604 original size:4 final size:4
Alignment explanation
Indices: 29597--29638 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
29587 TTATTTATTT
* *
29597 ATAA AT-A ATAA ATAA ATAA AAAA ATTAA ATGA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA A-TAA ATAA ATAA ATAA AT
29639 TTTGGCCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 26 0.81
5 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:29631 original size:17 final size:17
Alignment explanation
Indices: 29605--29639 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29595 TTATAAATAA
29605 TAAATAAATAAAAAAAT
1 TAAATAAATAAAAAAAT
* *
29622 TAAATGAATAAATAAAT
1 TAAATAAATAAAAAAAT
29639 T
1 T
29640 TTGGCCTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAATAAATAAAAAAAT
Found at i:30476 original size:39 final size:39
Alignment explanation
Indices: 30346--30478 Score: 119
Period size: 39 Copynumber: 3.4 Consensus size: 39
30336 ATAGCTTTAA
* * *
30346 GGGTAA-ATGATTGAATTGCTTCAATTTGTCTCATGGTCG
1 GGGTAAGA-GATTGGATTGCTTCAATTTGCCCCATGGTCG
* * * * **
30385 AGGTAAGAGATCGGATGGTCTTCAATTTACCCTC-TGGTTA
1 GGGTAAGAGATTGGATTG-CTTCAATTTGCCC-CATGGTCG
* *
30425 GGG-AAAAGATTGGATTGCTTCAATCTGCCCCATGGTCG
1 GGGTAAGAGATTGGATTGCTTCAATTTGCCCCATGGTCG
30463 GGGTAAGAGATTGGAT
1 GGGTAAGAGATTGGAT
30479 GGTATTCACT
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
37 1 0.01
38 18 0.25
39 34 0.48
40 17 0.24
41 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.32
Consensus pattern (39 bp):
GGGTAAGAGATTGGATTGCTTCAATTTGCCCCATGGTCG
Found at i:30642 original size:50 final size:50
Alignment explanation
Indices: 30495--30659 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 50
30485 CACTCCATTT
* * * * * *
30495 TAGCTTCAGGAGTATAAGATTCGTCCTTG-AGACTTCAAT-CAGCCCCTCTA
1 TAGCTTTAGGTGTATGAGATTTGTCATTGCAG-CTTCAATCCA-CTCCTCTA
* ** **
30545 CAGCTTTAGGTCAATGAGATTTGTCATTGCAGCTTCAATCTGCTCCTCTA
1 TAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCCACTCCTCTA
* *
30595 TAGCTTTAGGTGTATGAGATTTGTCATTGCGGCTTCAATCCATTCCTCTA
1 TAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCCACTCCTCTA
*
30645 TAGCTTTAGGGGTAT
1 TAGCTTTAGGTGTAT
30660 AGGACTCGTC
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
50 92 0.98
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (50 bp):
TAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCCACTCCTCTA
Found at i:42183 original size:22 final size:21
Alignment explanation
Indices: 42153--42209 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
42143 CACATAATTT
42153 ACAAATATAAATAATAATA-AA
1 ACAAATATAAATAATAA-ACAA
*
42174 ACAAAATATACATAA-AAACAA
1 AC-AAATATAAATAATAAACAA
42195 ACAAATA-AAATAATA
1 ACAAATATAAATAATA
42210 TACATATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 5 0.16
20 7 0.23
21 8 0.26
22 11 0.35
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (21 bp):
ACAAATATAAATAATAAACAA
Found at i:42385 original size:60 final size:61
Alignment explanation
Indices: 42321--42456 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 61
42311 AAAACCAAGA
* * *
42321 CAAATTTTAATTTTTAG-AAACTTC-AGGGATCAAA-TCAAAAATTTTGGAAAATTTTAGGGT
1 CAAATTATAATTTTTAGAAAACTTCGAGGG-TCAAATTC-AAAATTTTAGAAAATTTAAGGGT
* * * *
42381 CAAATTCA-AATTTTT-GAAAAGTTCGATGGTTAAATTCAAATTTTTAGAAAATTTAAGGGT
1 CAAATT-ATAATTTTTAGAAAACTTCGAGGGTCAAATTCAAAATTTTAGAAAATTTAAGGGT
*
42441 CAAAATATAATTTTTA
1 CAAATTATAATTTTTA
42457 AATAGTTTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
59 2 0.03
60 55 0.89
61 5 0.08
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.38
Consensus pattern (61 bp):
CAAATTATAATTTTTAGAAAACTTCGAGGGTCAAATTCAAAATTTTAGAAAATTTAAGGGT
Found at i:42396 original size:30 final size:29
Alignment explanation
Indices: 42359--42444 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
42349 ATCAAATCAA
* *
42359 AAATTTTGGAAAATTTTAGGGTCAAATTC
1 AAATTTTTGAAAATTTAAGGGTCAAATTC
** * *
42388 AAATTTTTGAAAAGTTCGATGGTTAAATTC
1 AAATTTTTGAAAA-TTTAAGGGTCAAATTC
42418 AAATTTTTAGAAAATTTAAGGGTCAAA
1 AAATTTTT-GAAAATTTAAGGGTCAAA
42445 ATATAATTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 12 0.26
30 29 0.63
31 5 0.11
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (29 bp):
AAATTTTTGAAAATTTAAGGGTCAAATTC
Found at i:42472 original size:60 final size:60
Alignment explanation
Indices: 42362--42474 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
42352 AAATCAAAAA
* * * *
42362 TTTTGGAAAATTTTAGGGTCAAATTCAAATTTTTGAAAAGTTCGATGGTTAAATTCAAAT
1 TTTTAGAAAATTTAAGGGTCAAAATCAAATTTTTGAAAAGTTCGAGGGTTAAATTCAAAT
*
42422 TTTTAGAAAATTTAAGGGTCAAAAT-ATAATTTTT-AAATAGTTTGAGGGTTAAA
1 TTTTAGAAAATTTAAGGGTCAAAATCA-AATTTTTGAAA-AGTTCGAGGGTTAAA
42475 GAATAACTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (60 bp):
TTTTAGAAAATTTAAGGGTCAAAATCAAATTTTTGAAAAGTTCGAGGGTTAAATTCAAAT
Found at i:46492 original size:17 final size:18
Alignment explanation
Indices: 46467--46503 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
46457 TCTTTTAAAA
46467 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
46485 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
46502 AT
1 AT
46504 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:47866 original size:61 final size:61
Alignment explanation
Indices: 47696--47885 Score: 193
Period size: 61 Copynumber: 3.1 Consensus size: 61
47686 ATCTTAAATA
* * ** ** * *
47696 TAAAAAAATTCAATAAGTTT-ACCCTTAATGTTTACAAAAAAATTTCATTTTAGTTTTAATTC
1 TAAAAAAATT-AATAAATTTGACCCTCAACATTTAC-AAACTATTTCAATTTAGTTCTAATTC
* * *
47758 TAAAACAATTAATAAATTTGTCCCTCAACATTTACAAACTATGTCAATTTAGTTCTAATTC
1 TAAAAAAATTAATAAATTTGACCCTCAACATTTACAAACTATTTCAATTTAGTTCTAATTC
* * ** * * *
47819 TAAAAAAATTAATAAATTTGACCCTCAATATTTATAATTTTTTTCAATTTAGTACTAACTC
1 TAAAAAAATTAATAAATTTGACCCTCAACATTTACAAACTATTTCAATTTAGTTCTAATTC
47880 TAAAAA
1 TAAAAA
47886 TTAAAAAGTA
Statistics
Matches: 106, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
61 86 0.81
62 20 0.19
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (61 bp):
TAAAAAAATTAATAAATTTGACCCTCAACATTTACAAACTATTTCAATTTAGTTCTAATTC
Found at i:50058 original size:17 final size:18
Alignment explanation
Indices: 50026--50068 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
50016 AAAAAAATAT
* *
50026 TATTTTCAAGTCTTTTTA
1 TATTTTCAAATCTTTTAA
*
50044 T-TTTTCAAATTTTTTAA
1 TATTTTCAAATCTTTTAA
50061 TATTTTCA
1 TATTTTCA
50069 TGGTATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (18 bp):
TATTTTCAAATCTTTTAA
Found at i:53361 original size:4 final size:4
Alignment explanation
Indices: 53350--53379 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
53340 TAAATATTCA
53350 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
53380 AGAAGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:63609 original size:34 final size:34
Alignment explanation
Indices: 63570--63635 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
63560 CAAAATATTG
* *
63570 TTTTTTAATTTTTAAGGGCCTCAATTTTTTTTTT
1 TTTTTTAACTTTTAAGGGCCTAAATTTTTTTTTT
**
63604 TTTTTTTGCTTTTAAGGGCCTAAATTTTTTTT
1 TTTTTTAACTTTTAAGGGCCTAAATTTTTTTT
63636 ACCAACTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.64
Consensus pattern (34 bp):
TTTTTTAACTTTTAAGGGCCTAAATTTTTTTTTT
Found at i:65110 original size:13 final size:13
Alignment explanation
Indices: 65092--65116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65082 CTAAGTCAAC
65092 TTGTTTATATTGA
1 TTGTTTATATTGA
65105 TTGTTTATATTG
1 TTGTTTATATTG
65117 CAAGCTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGTTTATATTGA
Found at i:70959 original size:46 final size:46
Alignment explanation
Indices: 70904--70996 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
70894 TTGTAATCCA
*
70904 TTAAGTAAATATCTTATCTGCTTGAAAACCTTTTTAATTTAGTGAT
1 TTAAGTAAATATCTAATCTGCTTGAAAACCTTTTTAATTTAGTGAT
70950 TTAAGTAAATATCTAATCTGCTTGAAAACCTTTTTAATTTAGTGAT
1 TTAAGTAAATATCTAATCTGCTTGAAAACCTTTTTAATTTAGTGAT
70996 T
1 T
70997 AATATATGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (46 bp):
TTAAGTAAATATCTAATCTGCTTGAAAACCTTTTTAATTTAGTGAT
Found at i:71728 original size:18 final size:18
Alignment explanation
Indices: 71705--71739 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
71695 TGCTTTTAAT
*
71705 AAATATTTTTGGGATAAA
1 AAATATTTTTGAGATAAA
71723 AAATATTTTTGAGATAA
1 AAATATTTTTGAGATAA
71740 CAACATTGTT
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:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (18 bp):
AAATATTTTTGAGATAAA
Found at i:74701 original size:19 final size:19
Alignment explanation
Indices: 74677--74714 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
74667 AAAGTTAATA
*
74677 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTAAGGTGG
74696 ACAAATTTGATTAAGGTGG
1 ACAAATTTGATTAAGGTGG
74715 GTGACAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (19 bp):
ACAAATTTGATTAAGGTGG
Found at i:82837 original size:34 final size:35
Alignment explanation
Indices: 82799--82869 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
82789 CTAAGCCTCG
*
82799 AACTTTA-A-CTCACAAACCCAAATCTTGAACCTTA
1 AACTTTATATCTCA-AAACCCAAATCTTAAACCTTA
* *
82833 AACTTTATATCTCAAACCCCAAATTTTAAACCTTA
1 AACTTTATATCTCAAAACCCAAATCTTAAACCTTA
82868 AA
1 AA
82870 TTTCAAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 7 0.22
35 21 0.66
36 4 0.12
ACGTcount: A:0.42, C:0.27, G:0.01, T:0.30
Consensus pattern (35 bp):
AACTTTATATCTCAAAACCCAAATCTTAAACCTTA
Found at i:86400 original size:23 final size:23
Alignment explanation
Indices: 86351--86415 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
86341 GCAGAATATG
*
86351 AAATAATTTATTCAA-TCAATCA
1 AAATAATTTATTCAATTTAATCA
*
86373 AAATAATTTGTTCAATTTAATCA
1 AAATAATTTATTCAATTTAATCA
* *
86396 GAATAATTTATTTAATTTAA
1 AAATAATTTATTCAATTTAA
86416 AATCAATCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (23 bp):
AAATAATTTATTCAATTTAATCA
Found at i:90580 original size:23 final size:22
Alignment explanation
Indices: 90523--90580 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
90513 ATTAACGAAT
90523 TGATCC-CACAAAAAATTTGAAA
1 TGATCCAC-CAAAAAATTTGAAA
* *
90545 TG-CCCTACAAAAAAATTTGAAAA
1 TGATCC-ACCAAAAAATTTG-AAA
90568 TGATCCACCAAAA
1 TGATCCACCAAAA
90581 TTATACATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
21 2 0.07
22 12 0.43
23 12 0.43
24 2 0.07
ACGTcount: A:0.50, C:0.21, G:0.09, T:0.21
Consensus pattern (22 bp):
TGATCCACCAAAAAATTTGAAA
Found at i:98094 original size:18 final size:18
Alignment explanation
Indices: 98054--98103 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
98044 GCAGCCTGAC
*
98054 CAGATGCGATCACAAAACT
1 CAGATGCAATCAC-AAACT
*
98073 -AGATGCAATCACATACT
1 CAGATGCAATCACAAACT
*
98090 CAGATGCAACCACA
1 CAGATGCAATCACA
98104 GGTTCAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16
Consensus pattern (18 bp):
CAGATGCAATCACAAACT
Found at i:102422 original size:24 final size:24
Alignment explanation
Indices: 102395--102440 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
102385 AATTTTTCTG
*
102395 TTAATTT-TTGTCTTTTAGTTTACT
1 TTAATTTGTT-TCTTTAAGTTTACT
102419 TTAATTTGTTTCTTTAAGTTTA
1 TTAATTTGTTTCTTTAAGTTTA
102441 TAAAAGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.65
Consensus pattern (24 bp):
TTAATTTGTTTCTTTAAGTTTACT
Found at i:104064 original size:21 final size:22
Alignment explanation
Indices: 104040--104090 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
104030 GTATTACTGC
104040 AGAAAAAGAAAGA-AAAGAAGA
1 AGAAAAAGAAAGAGAAAGAAGA
104061 AGAAAAAG-AAGAGAAAGAAGA
1 AGAAAAAGAAAGAGAAAGAAGA
*
104082 AAAAAAAGA
1 AGAAAAAGA
104091 TGTTGCCTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
AGAAAAAGAAAGAGAAAGAAGA
Found at i:104067 original size:12 final size:12
Alignment explanation
Indices: 104040--104090 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
104030 GTATTACTGC
104040 AGAAAAAG-A-A
1 AGAAAAAGAAGA
104050 AG-AAAAGAAGA
1 AGAAAAAGAAGA
104061 AGAAAAAGAAG-
1 AGAAAAAGAAGA
104072 AG--AAAGAAGA
1 AGAAAAAGAAGA
*
104082 AAAAAAAGA
1 AGAAAAAGA
104091 TGTTGCCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
9 12 0.35
10 4 0.12
11 5 0.15
12 13 0.38
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAGA
Found at i:104508 original size:17 final size:17
Alignment explanation
Indices: 104483--104526 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
104473 CATGCATTTC
104483 TTTTAATTGTCAT-TGCA
1 TTTTAATTGTC-TCTGCA
*
104500 TTTTTATTGTCTCTGCA
1 TTTTAATTGTCTCTGCA
*
104517 TTTTATTTGT
1 TTTTAATTGT
104527 TCTATCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.61
Consensus pattern (17 bp):
TTTTAATTGTCTCTGCA
Found at i:110364 original size:21 final size:21
Alignment explanation
Indices: 110332--110393 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
110322 TTGGTTTGAC
110332 TCAAAA-GGTTTGGGTTTGGT
1 TCAAAAGGGTTTGGGTTTGGT
*
110352 TCAAAAGGGTTTGGTTTTGGT
1 TCAAAAGGGTTTGGGTTTGGT
*
110373 TCATAAGGGTTTGGGTTTGGT
1 TCAAAAGGGTTTGGGTTTGGT
110394 GTTGATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.18, C:0.05, G:0.35, T:0.42
Consensus pattern (21 bp):
TCAAAAGGGTTTGGGTTTGGT
Found at i:112725 original size:28 final size:28
Alignment explanation
Indices: 112667--112777 Score: 114
Period size: 28 Copynumber: 4.0 Consensus size: 28
112657 CACGAGACTG
* * * * **
112667 ATTTGCTCACATAAGTTATAAAATTCAA
1 ATTTGCTCACACAAGCTATGATATTTGA
* ** *
112695 ATTTGCTCACCCGTGCTATGGTATTTGA
1 ATTTGCTCACACAAGCTATGATATTTGA
*
112723 ATTTGCTCACACAAGCTGTGATATTTGA
1 ATTTGCTCACACAAGCTATGATATTTGA
*
112751 ATTTTCTCACACAAGCTATGATATTTG
1 ATTTGCTCACACAAGCTATGATATTTG
112778 GGATACTCAT
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (28 bp):
ATTTGCTCACACAAGCTATGATATTTGA
Found at i:127201 original size:2 final size:2
Alignment explanation
Indices: 127196--127239 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
127186 ACAAACAAAC
127196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127238 AT
1 AT
127240 TGTAATTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127305 original size:42 final size:46
Alignment explanation
Indices: 127259--127347 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
127249 AAACTGTATT
127259 GTTTTTCTATCT-A-ATATATATATA-A-AAAAGTATAAGTTTAGA
1 GTTTTTCTATCTAATATATATATATATATAAAAGTATAAGTTTAGA
127301 GTTTTTCTATCTAATATATATATATATATAAAAGTATAAGTTTAGA
1 GTTTTTCTATCTAATATATATATATATATAAAAGTATAAGTTTAGA
127347 G
1 G
127348 AAACTTTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
42 12 0.28
43 1 0.02
44 11 0.26
45 1 0.02
46 18 0.42
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (46 bp):
GTTTTTCTATCTAATATATATATATATATAAAAGTATAAGTTTAGA
Found at i:130365 original size:3 final size:3
Alignment explanation
Indices: 130357--130387 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
130347 TATTTGATCC
130357 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
130388 AAGAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:131484 original size:34 final size:34
Alignment explanation
Indices: 131439--131528 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 34
131429 AGAATATGAA
*
131439 AAGTTAAGGAAGATGAAAGGTTAAAGATCAAGGG
1 AAGTTAAGGAAGATGAAAGGTTAAAGATCAAAGG
* * * *
131473 AGGTTAAGGAAGATGGAAGGCTAAAGGTCAAAGG
1 AAGTTAAGGAAGATGAAAGGTTAAAGATCAAAGG
131507 AAGTTAAGGAAGATGAAAGGTT
1 AAGTTAAGGAAGATGAAAGGTT
131529 GAACATCCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.44, C:0.03, G:0.34, T:0.18
Consensus pattern (34 bp):
AAGTTAAGGAAGATGAAAGGTTAAAGATCAAAGG
Found at i:136933 original size:34 final size:34
Alignment explanation
Indices: 136888--136980 Score: 145
Period size: 34 Copynumber: 2.7 Consensus size: 34
136878 AGAATATGAA
*
136888 AAGTTAAGGAAGATGGAAGGTTAAAGAG-C-AAGG
1 AAGTTAAGGAAGATGGAAGGTTAAAG-GTCAAAAG
136921 AAGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAAG
1 AA-GTTAAGGAAGATGGAAGGTTAAAGGTCAAAAG
136956 AAGTTAAGGAAGATGGAAGGTTAAA
1 AAGTTAAGGAAGATGGAAGGTTAAA
136981 AGATGAAAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
33 3 0.05
34 48 0.86
35 5 0.09
ACGTcount: A:0.46, C:0.02, G:0.34, T:0.17
Consensus pattern (34 bp):
AAGTTAAGGAAGATGGAAGGTTAAAGGTCAAAAG
Found at i:136978 original size:17 final size:17
Alignment explanation
Indices: 136890--136992 Score: 92
Period size: 17 Copynumber: 6.2 Consensus size: 17
136880 AATATGAAAA
136890 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
* *
136907 GTTAAAG-AGCAAGGAAG
1 GTTAAGGAAG-ATGGAAG
136924 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
*
136941 GTTAAAGGTCAA-A-AGAA-
1 GTT-AAGG--AAGATGGAAG
136958 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
*
136975 GTTAA--AAGATGAAAG
1 GTTAAGGAAGATGGAAG
136990 GTT
1 GTT
136993 GAACATCCAT
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.03
15 13 0.18
16 9 0.13
17 35 0.49
18 9 0.13
19 1 0.01
20 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.35, T:0.18
Consensus pattern (17 bp):
GTTAAGGAAGATGGAAG
Found at i:144435 original size:14 final size:14
Alignment explanation
Indices: 144416--144445 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
144406 ATTTCTTTAG
*
144416 TTGAGATAGTAAAA
1 TTGAGAGAGTAAAA
144430 TTGAGAGAGTAAAA
1 TTGAGAGAGTAAAA
144444 TT
1 TT
144446 TATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (14 bp):
TTGAGAGAGTAAAA
Found at i:146080 original size:105 final size:103
Alignment explanation
Indices: 145818--146318 Score: 755
Period size: 103 Copynumber: 4.9 Consensus size: 103
145808 AAATGATAAA
*
145818 ATGGTAGAAATTTTTTAGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTTT
1 ATGGTAGAAATTTTTTGGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTTT
145883 GATGGGAAGAAAATATAAGAAAATGGGTTCTCATCTTC
66 GATGGGAAGAAAATATAAGAAAATGGGTTCTCATCTTC
* *
145921 ATGGTAGAAATTTTTTGAGTGTTTGATTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTTT
1 ATGGTAGAAATTTTTTGGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTTT
* *
145986 TATGGGAAAAAAAATATAAGAAAATGGGTTCTCATCTTC
66 GATGGG-AAGAAAATATAAGAAAATGGGTTCTCATCTTC
* *
146025 ATGGTAGAAAATTTTTTGGGTGTTTGATTGATGAGAAAATGGAAGAAAATATAGTAAAAATTGTT
1 ATGGTAG-AAATTTTTTGGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTT
* *
146090 TTATGGGAAGAAAATATAAG-AAA----CTCTCATCTTC
65 TGATGGGAAGAAAATATAAGAAAATGGGTTCTCATCTTC
* *
146124 ATGGT-GAAATTTTTTGGGTGTTTGGTTGATGAGAAAATGTAAAAAAATATAGTAAAATTTGTTT
1 ATGGTAGAAATTTTTTGGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTTT
* * *
146188 AATGAGAAGAAAATATAAGAAAATGGATTCTCATCTTC
66 GATGGGAAGAAAATATAAGAAAATGGGTTCTCATCTTC
* * * * *
146226 ATGGTAGAAATTTTTTGAGTGTTTGGTTGATAAAAAAATATAAAAAAATATAGTAAAAATTGTTT
1 ATGGTAGAAATTTTTTGGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTTT
146291 GATGGGAAGAAAATATATA-AAAATGGGT
66 GATGGGAAGAAAATATA-AGAAAATGGGT
146319 AAAATAAATA
Statistics
Matches: 365, Mismatches: 24, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
97 71 0.19
98 4 0.01
99 15 0.04
102 15 0.04
103 147 0.40
104 51 0.14
105 62 0.17
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (103 bp):
ATGGTAGAAATTTTTTGGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTTT
GATGGGAAGAAAATATAAGAAAATGGGTTCTCATCTTC
Found at i:148259 original size:40 final size:39
Alignment explanation
Indices: 148199--148276 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 39
148189 CAACTCTCTT
148199 AAAACGGAATCTACTTCAAACAAATATGCCATGGTTCCTC
1 AAAACGGAATCTACTTCAAACAAA-ATGCCATGGTTCCTC
*
148239 AAAACGGAATCTA-TTCCAAACATAATGCCATGGTTCCT
1 AAAACGGAATCTACTT-CAAACAAAATGCCATGGTTCCT
148277 TACTTCGACA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 16 0.44
40 20 0.56
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (39 bp):
AAAACGGAATCTACTTCAAACAAAATGCCATGGTTCCTC
Found at i:158406 original size:17 final size:18
Alignment explanation
Indices: 158384--158419 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
158374 TAAATGAGTT
158384 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
158401 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
158419 A
1 A
158420 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:160029 original size:21 final size:21
Alignment explanation
Indices: 159992--160045 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
159982 AACCAAAGTG
*
159992 AACCAAATCC-ATGTGAACCAA
1 AACCAAACCCAAT-TGAACCAA
**
160013 GTCCAAACCCAATTGAACCAA
1 AACCAAACCCAATTGAACCAA
160034 AACCAAACCCAA
1 AACCAAACCCAA
160046 ACCAAGTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.48, C:0.33, G:0.07, T:0.11
Consensus pattern (21 bp):
AACCAAACCCAATTGAACCAA
Found at i:161189 original size:14 final size:14
Alignment explanation
Indices: 161166--161199 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
161156 AATTTACATC
* *
161166 ATTTTATTATTATT
1 ATTTTGTTATTAAT
161180 ATTTTGTTATTAAT
1 ATTTTGTTATTAAT
161194 ATTTTG
1 ATTTTG
161200 GTTTTGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
ATTTTGTTATTAAT
Found at i:165826 original size:126 final size:126
Alignment explanation
Indices: 165601--165856 Score: 503
Period size: 126 Copynumber: 2.0 Consensus size: 126
165591 AATGGTATAC
*
165601 TTATGTGTCTCTAATGAATGGGTTATCAATGTTGCTTTGAAAATTTACATTAATTGAATGAAATG
1 TTATGTGTCTCTAATGAATGGGTTATCAATGCTGCTTTGAAAATTTACATTAATTGAATGAAATG
165666 GTTAAAATTGTGTTTTGGACTATTTGAAATATTGGGGAAGTTTTTAAGTTGTTTCAGGGGG
66 GTTAAAATTGTGTTTTGGACTATTTGAAATATTGGGGAAGTTTTTAAGTTGTTTCAGGGGG
165727 TTATGTGTCTCTAATGAATGGGTTATCAATGCTGCTTTGAAAATTTACATTAATTGAATGAAATG
1 TTATGTGTCTCTAATGAATGGGTTATCAATGCTGCTTTGAAAATTTACATTAATTGAATGAAATG
165792 GTTAAAATTGTGTTTTGGACTATTTGAAATATTGGGGAAGTTTTTAAGTTGTTTCAGGGGG
66 GTTAAAATTGTGTTTTGGACTATTTGAAATATTGGGGAAGTTTTTAAGTTGTTTCAGGGGG
165853 TTAT
1 TTAT
165857 TACTAAGTTT
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 129 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (126 bp):
TTATGTGTCTCTAATGAATGGGTTATCAATGCTGCTTTGAAAATTTACATTAATTGAATGAAATG
GTTAAAATTGTGTTTTGGACTATTTGAAATATTGGGGAAGTTTTTAAGTTGTTTCAGGGGG
Found at i:170838 original size:6 final size:6
Alignment explanation
Indices: 170827--170865 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
170817 TGATCAAAAA
* * *
170827 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
170866 TACTGGGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:178320 original size:25 final size:25
Alignment explanation
Indices: 178278--178332 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
178268 CTGAAAATTG
178278 AAAAAAGGGAAAAGAAAACAAAGG-C
1 AAAAAAGGGAAAAGAAAA-AAAGGCC
*
178303 AAAAAGGGGTAAAA-AAAAAAAGGCC
1 AAAAAAGGG-AAAAGAAAAAAAGGCC
178328 AAAAA
1 AAAAA
178333 TTCAAATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 18 0.67
26 4 0.15
ACGTcount: A:0.69, C:0.07, G:0.22, T:0.02
Consensus pattern (25 bp):
AAAAAAGGGAAAAGAAAAAAAGGCC
Found at i:179318 original size:6 final size:6
Alignment explanation
Indices: 179307--179333 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
179297 GACACTTTTT
179307 CTCTGA CTCTGA CTCTGA CTCTGA CTC
1 CTCTGA CTCTGA CTCTGA CTCTGA CTC
179334 ACTGGGTTTC
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:0.37, G:0.15, T:0.33
Consensus pattern (6 bp):
CTCTGA
Found at i:179885 original size:24 final size:26
Alignment explanation
Indices: 179846--179900 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
179836 TTCAATCCCA
*
179846 AATTTAAATTAAATTA-AATAAT-TT
1 AATTTAAATTAAATTATAAAAATATT
**
179870 AATTTAAATTTGATTATAAAAATATT
1 AATTTAAATTAAATTATAAAAATATT
179896 AATTT
1 AATTT
179901 TACTGTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 14 0.54
25 5 0.19
26 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
AATTTAAATTAAATTATAAAAATATT
Found at i:181433 original size:12 final size:12
Alignment explanation
Indices: 181418--181555 Score: 92
Period size: 12 Copynumber: 11.9 Consensus size: 12
181408 TTTGGTACTG
181418 TTTTTGTTGTTA
1 TTTTTGTTGTTA
*
181430 TTTTTATTGTT-
1 TTTTTGTTGTTA
* *
181441 GTTTTGTCT-ATA
1 TTTTTGT-TGTTA
*
181453 TTTTTGCTGTTA
1 TTTTTGTTGTTA
* *
181465 TTTTTGTTGCTG
1 TTTTTGTTGTTA
*
181477 TTTTTGTTATTA
1 TTTTTGTTGTTA
181489 TTTTTGTTG---
1 TTTTTGTTGTTA
*
181498 TTTTTGTTATT-
1 TTTTTGTTGTTA
* *
181509 GTTTTATTGTTA
1 TTTTTGTTGTTA
*
181521 TTTTTGTT-TCTG
1 TTTTTGTTGT-TA
*
181533 TTTTGGTTGTTA
1 TTTTTGTTGTTA
*
181545 TTTTAGTTGTT
1 TTTTTGTTGTT
181556 TTGATGTTAT
Statistics
Matches: 94, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
9 8 0.09
11 16 0.17
12 69 0.73
13 1 0.01
ACGTcount: A:0.09, C:0.03, G:0.17, T:0.72
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:181443 original size:35 final size:34
Alignment explanation
Indices: 181395--181528 Score: 114
Period size: 35 Copynumber: 3.9 Consensus size: 34
181385 ATTTTTGTGC
* * * *
181395 TTTTTGTTATTGTTTTGGTACTGTTTTTGTTGTTA
1 TTTTTATTGTTGTTTTGCTA-TATTTTTGTTGTTA
*
181430 TTTTTATTGTTGTTTTGTCTATATTTTTGCTGTTA
1 TTTTTATTGTTGTTTTG-CTATATTTTTGTTGTTA
* * *
181465 TTTTTGTTGCTGTTTTTGTTATTATTTTTGTTGTT-
1 TTTTTATTGTTG-TTTTGCTA-TATTTTTGTTGTTA
181500 TTTGTTATTGTT-TTATTG-T-TATTTTTGTT
1 TTT-TTATTGTTGTT-TTGCTATATTTTTGTT
181529 TCTGTTTTGG
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
32 10 0.12
34 3 0.04
35 45 0.54
36 25 0.30
ACGTcount: A:0.09, C:0.03, G:0.16, T:0.72
Consensus pattern (34 bp):
TTTTTATTGTTGTTTTGCTATATTTTTGTTGTTA
Found at i:181486 original size:21 final size:21
Alignment explanation
Indices: 181460--181513 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
181450 ATATTTTTGC
181460 TGTTATT-TTTGTTGCTGTTTT
1 TGTTATTATTT-TTGCTGTTTT
*
181481 TGTTATTATTTTTGTTGTTTT
1 TGTTATTATTTTTGCTGTTTT
*
181502 TGTTATTGTTTT
1 TGTTATTATTTT
181514 ATTGTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.07, C:0.02, G:0.17, T:0.74
Consensus pattern (21 bp):
TGTTATTATTTTTGCTGTTTT
Found at i:181525 original size:44 final size:44
Alignment explanation
Indices: 181477--181569 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
181467 TTTGTTGCTG
* *
181477 TTTTTGTTAT-TATTTTTGTTGTTTTTGTTA-TTGTTTT-ATTGTTA
1 TTTTTGTT-TCTATTTTGGTTGTTATT-TTAGTTGTTTTGA-TGTTA
*
181521 TTTTTGTTTCTGTTTTGGTTGTTATTTTAGTTGTTTTGATGTTA
1 TTTTTGTTTCTATTTTGGTTGTTATTTTAGTTGTTTTGATGTTA
181565 TTTTT
1 TTTTT
181570 ATACGTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
43 4 0.09
44 38 0.88
45 1 0.02
ACGTcount: A:0.10, C:0.01, G:0.16, T:0.73
Consensus pattern (44 bp):
TTTTTGTTTCTATTTTGGTTGTTATTTTAGTTGTTTTGATGTTA
Found at i:181535 original size:35 final size:36
Alignment explanation
Indices: 181480--181555 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 36
181470 GTTGCTGTTT
* *
181480 TTGTTATTATTTTTGTTGTTTTTGTTATTGTTTTA-
1 TTGTTATTATTTTTGTTGTTTTGGTTATTATTTTAG
*
181515 TTGTTATT-TTTGTT-TCTGTTTTGGTTGTTATTTTAG
1 TTGTTATTATTT-TTGT-TGTTTTGGTTATTATTTTAG
181551 TTGTT
1 TTGTT
181556 TTGATGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.11
35 26 0.74
36 5 0.14
ACGTcount: A:0.09, C:0.01, G:0.17, T:0.72
Consensus pattern (36 bp):
TTGTTATTATTTTTGTTGTTTTGGTTATTATTTTAG
Found at i:181546 original size:56 final size:55
Alignment explanation
Indices: 181415--181569 Score: 184
Period size: 56 Copynumber: 2.7 Consensus size: 55
181405 TGTTTTGGTA
* *
181415 CTGTTTTTGTTGTTATTTTTATTGTTGTTTTGTCTATATTTTTGCTGTTATTTTTGTTG
1 CTGTTTTTGTTGTTATTTTTGTTG-T-TTTTGT-TAT-TTTTTACTGTTATTTTTGTTG
* * *
181474 CTGTTTTTGTTATTATTTTTGTTGTTTTTGTTATTGTTTTATTGTTATTTTTGTTT
1 CTGTTTTTGTTGTTATTTTTGTTGTTTTTGTTATT-TTTTACTGTTATTTTTGTTG
* *
181530 CTGTTTTGGTTGTTATTTTAGTTGTTTTGATGTTATTTTT
1 CTGTTTTTGTTGTTATTTTTGTTGTTTT--TGTTATTTTT
181570 ATACGTTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
55 1 0.01
56 45 0.53
57 9 0.11
58 8 0.09
59 22 0.26
ACGTcount: A:0.09, C:0.03, G:0.17, T:0.71
Consensus pattern (55 bp):
CTGTTTTTGTTGTTATTTTTGTTGTTTTTGTTATTTTTTACTGTTATTTTTGTTG
Found at i:182600 original size:17 final size:17
Alignment explanation
Indices: 182555--182603 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
182545 AAATTAAAAA
*
182555 TAATAAAATAAAATATTT
1 TAATTAAAT-AAATATTT
* *
182573 TTA-TAATTAAATATTT
1 TAATTAAATAAATATTT
182589 TAATTAAATAAATAT
1 TAATTAAATAAATAT
182604 AATTTTTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 10 0.40
17 13 0.52
18 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTAAATAAATATTT
Found at i:182609 original size:36 final size:34
Alignment explanation
Indices: 182555--182622 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 34
182545 AAATTAAAAA
182555 TAATAAAATAAAATATTTTTATA-ATTAAATATTT
1 TAATAAAATAAAATATTTTTATATA-TAAATATTT
*
182589 TAATTAAATAAATATAATTTTTATATATAAATAT
1 TAATAAAATAAA-AT-ATTTTTATATATAAATAT
182623 GATAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 11 0.37
35 2 0.07
36 16 0.53
37 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (34 bp):
TAATAAAATAAAATATTTTTATATATAAATATTT
Found at i:183475 original size:26 final size:26
Alignment explanation
Indices: 183427--183483 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
183417 AAAAAGCCAC
*
183427 TCATTTTATAAAAAAAATCATT-ATT
1 TCATTATATAAAAAAAATCATTAATT
*
183452 TCATTATATAAAAACAAATTATTAATT
1 TCATTATATAAAAA-AAATCATTAATT
183479 T-ATTA
1 TCATTA
183484 AGAAAACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 13 0.46
26 11 0.39
27 4 0.14
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (26 bp):
TCATTATATAAAAAAAATCATTAATT
Found at i:187755 original size:29 final size:29
Alignment explanation
Indices: 187722--187791 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
187712 AGTTTGGGTT
*
187722 ATTTACACTTTTAGTCCT-TCAACTTTTGA
1 ATTTACACTTTTA-ACCTCTCAACTTTTGA
**
187751 ATTTATGC-TTTAACCTCTCAACTTTTGA
1 ATTTACACTTTTAACCTCTCAACTTTTGA
187779 ATATTCACACTTT
1 AT-TT-ACACTTT
187792 GACCTATCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 3 0.09
28 17 0.53
29 8 0.25
30 2 0.06
31 2 0.06
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (29 bp):
ATTTACACTTTTAACCTCTCAACTTTTGA
Found at i:192843 original size:13 final size:13
Alignment explanation
Indices: 192825--192861 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
192815 TTCTTGTTAA
*
192825 AATAAAATACAAT
1 AATAAAATAAAAT
192838 AATAAAATAAAAT
1 AATAAAATAAAAT
192851 -A-AAAATAAAAT
1 AATAAAATAAAAT
192862 CCAAATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 12 0.52
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:192845 original size:18 final size:16
Alignment explanation
Indices: 192822--192861 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
192812 GAATTCTTGT
192822 TAAAATAAAATACAATAA
1 TAAAATAAAATA-AA-AA
192840 TAAAATAAAATAAAAA
1 TAAAATAAAATAAAAA
192856 TAAAAT
1 TAAAAT
192862 CCAAATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:194992 original size:22 final size:21
Alignment explanation
Indices: 194958--194998 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
194948 TTTAAAACGC
194958 TTAAAAATATTTTAAATTATA
1 TTAAAAATATTTTAAATTATA
*
194979 TTAAAAAGTGTTTTAAATTA
1 TTAAAAA-TATTTTAAATTA
194999 AAGTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TTAAAAATATTTTAAATTATA
Found at i:195005 original size:22 final size:21
Alignment explanation
Indices: 194959--195005 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
194949 TTAAAACGCT
* *
194959 TAAAAATATTTTAAATTATAT
1 TAAAAATATTTTAAATTAAAG
*
194980 TAAAAAGTGTTTTAAATTAAAG
1 TAAAAA-TATTTTAAATTAAAG
195002 TAAA
1 TAAA
195006 TTTGCTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
TAAAAATATTTTAAATTAAAG
Found at i:195278 original size:20 final size:19
Alignment explanation
Indices: 195253--195290 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
195243 TACTTCCCTC
*
195253 TCTCTCTTTGTTTTCTTTCT
1 TCTCTCTTT-TTTCCTTTCT
195273 TCTCTCTTTTTTCCTTTC
1 TCTCTCTTTTTTCCTTTC
195291 ATAACAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (19 bp):
TCTCTCTTTTTTCCTTTCT
Found at i:195284 original size:18 final size:21
Alignment explanation
Indices: 195253--195290 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
195243 TACTTCCCTC
195253 TCTCTCTTTGTTTT-CTTTCT
1 TCTCTCTTTGTTTTCCTTTCT
195273 TCTCTC-TT-TTTTCCTTTC
1 TCTCTCTTTGTTTTCCTTTC
195291 ATAACAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (21 bp):
TCTCTCTTTGTTTTCCTTTCT
Found at i:200214 original size:17 final size:17
Alignment explanation
Indices: 200194--200228 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
200184 CACAAGACTT
200194 TATTTAAATTTAAATTA
1 TATTTAAATTTAAATTA
*
200211 TATTTAATTTTAAATTA
1 TATTTAAATTTAAATTA
200228 T
1 T
200229 CTTTTAAGCA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTTAAATTTAAATTA
Found at i:203194 original size:3 final size:3
Alignment explanation
Indices: 203186--203216 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
203176 ACACACATAT
203186 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
203217 ATATCATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:205601 original size:64 final size:64
Alignment explanation
Indices: 205533--205733 Score: 169
Period size: 64 Copynumber: 3.1 Consensus size: 64
205523 AATATCATCT
*
205533 TTAATTTAATACACATATAAACCAATTTGTTATTTAAATATATCTAAATCATTAATTTTAATAC
1 TTAATTTAATACACATATAAACCAATTTATTATTTAAATATATCTAAATCATTAATTTTAATAC
* * * * * * * * ** *
205597 TTAA-TTATTTAAATATGTCCAAAACAATATTATT-TTCAAAGTTTGAACTCGTATCA-TAA-TA
1 TTAATTTA-ATACACATAT--AAACCAAT-TTATTATTTAAA-TAT-ATCT-AAATCATTAATTT
*
205658 TCAT-C
59 TAATAC
*
205663 TTTAATTTAATACACATATAAACCAATTTATTATTTAAATATATCCAAATCATTAATTTTAATAC
1 -TTAATTTAATACACATATAAACCAATTTATTATTTAAATATATCTAAATCATTAATTTTAATAC
205728 TTAATT
1 TTAATT
205734 AATTAATTTC
Statistics
Matches: 98, Mismatches: 26, Indels: 26
0.65 0.17 0.17
Matches are distributed among these distances:
62 4 0.04
63 8 0.08
64 27 0.28
65 13 0.13
66 13 0.13
67 20 0.20
68 9 0.09
69 4 0.04
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.43
Consensus pattern (64 bp):
TTAATTTAATACACATATAAACCAATTTATTATTTAAATATATCTAAATCATTAATTTTAATAC
Found at i:205607 original size:67 final size:67
Alignment explanation
Indices: 205536--205740 Score: 172
Period size: 67 Copynumber: 3.1 Consensus size: 67
205526 ATCATCTTTA
*
205536 ATTTAATACACATATAAACCAATTTGTTATTTAAATATATCTAAATCATTAATTTTAATACTTAA
1 ATTTAATACACATATAAACCAATTTATTATTTAAATATATCTAAATCATTAATTTTAATACTTAA
205601 TT
66 TT
* ** ** * * * * ** * *
205603 ATTTAA-ATATGTCCAAAACAATATTATT-TTCAAAGTTTGAACTCGTATCA-TAA-TATCAT-C
1 ATTTAATACACATATAAACCAAT-TTATTATTTAAA-TAT-ATCT-AAATCATTAATTTTAATAC
*
205663 TT--TA
62 TTAATT
*
205667 ATTTAATACACATATAAACCAATTTATTATTTAAATATATCCAAATCATTAATTTTAATACTTAA
1 ATTTAATACACATATAAACCAATTTATTATTTAAATATATCTAAATCATTAATTTTAATACTTAA
205732 TT
66 TT
*
205734 AATTAAT
1 ATTTAAT
205741 TTCACAATCA
Statistics
Matches: 96, Mismatches: 31, Indels: 22
0.64 0.21 0.15
Matches are distributed among these distances:
62 4 0.04
63 5 0.05
64 18 0.19
65 18 0.19
66 18 0.19
67 23 0.24
68 6 0.06
69 4 0.04
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (67 bp):
ATTTAATACACATATAAACCAATTTATTATTTAAATATATCTAAATCATTAATTTTAATACTTAA
TT
Found at i:205686 original size:131 final size:131
Alignment explanation
Indices: 205488--205739 Score: 459
Period size: 131 Copynumber: 1.9 Consensus size: 131
205478 TACTTTTCTC
*
205488 AACAATATTATTTTCAAAGTTTGAACGCGTGTCATAATATCATCTTTAATTTAATACACATATAA
1 AACAATATTATTTTCAAAGTTTGAACGCGTATCATAATATCATCTTTAATTTAATACACATATAA
* * *
205553 ACCAATTTGTTATTTAAATATATCTAAATCATTAATTTTAATACTTAATTATTTAAATATGTCCA
66 ACCAATTTATTATTTAAATATATCCAAATCATTAATTTTAATACTTAATTAATTAAATATGTCCA
205618 A
131 A
*
205619 AACAATATTATTTTCAAAGTTTGAACTCGTATCATAATATCATCTTTAATTTAATACACATATAA
1 AACAATATTATTTTCAAAGTTTGAACGCGTATCATAATATCATCTTTAATTTAATACACATATAA
205684 ACCAATTTATTATTTAAATATATCCAAATCATTAATTTTAATACTTAATTAATTAA
66 ACCAATTTATTATTTAAATATATCCAAATCATTAATTTTAATACTTAATTAATTAA
205740 TTTCACAATC
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
131 116 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (131 bp):
AACAATATTATTTTCAAAGTTTGAACGCGTATCATAATATCATCTTTAATTTAATACACATATAA
ACCAATTTATTATTTAAATATATCCAAATCATTAATTTTAATACTTAATTAATTAAATATGTCCA
A
Found at i:206897 original size:13 final size:13
Alignment explanation
Indices: 206879--206904 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
206869 CCCGGATAAT
206879 TGAATTATTGAAG
1 TGAATTATTGAAG
206892 TGAATTATTGAAG
1 TGAATTATTGAAG
206905 ATGTGAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
TGAATTATTGAAG
Found at i:214551 original size:6 final size:6
Alignment explanation
Indices: 214540--214594 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
214530 GCAGATATTT
* * *
214540 CCTTCC CCTTCC CCTTCC CCTTTC CCTGCC CC-TCC CC-TCC CCTCCC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC
*
214586 CCTCCC CCT
1 CCTTCC CCT
214595 CATCACTCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
5 9 0.21
6 34 0.79
ACGTcount: A:0.00, C:0.71, G:0.02, T:0.27
Consensus pattern (6 bp):
CCTTCC
Found at i:214566 original size:18 final size:17
Alignment explanation
Indices: 214540--214592 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
214530 GCAGATATTT
*
214540 CCTTCCCCTTCCCCTTCC
1 CCTTCCCCTGCCCC-TCC
*
214558 CCTTTCCCTGCCCCTCC
1 CCTTCCCCTGCCCCTCC
*
214575 CC-TCCCCTCCCCCTCC
1 CCTTCCCCTGCCCCTCC
214591 CC
1 CC
214593 CTCATCACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 14 0.45
17 5 0.16
18 12 0.39
ACGTcount: A:0.00, C:0.72, G:0.02, T:0.26
Consensus pattern (17 bp):
CCTTCCCCTGCCCCTCC
Found at i:216496 original size:25 final size:25
Alignment explanation
Indices: 216456--216505 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
216446 TCTTTTCCAA
216456 TCATTTACGATAATTACTATTTGTT
1 TCATTTACGATAATTACTATTTGTT
* *
216481 TCATTTACTATTATTACTATTTGTT
1 TCATTTACGATAATTACTATTTGTT
216506 ATTTTCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (25 bp):
TCATTTACGATAATTACTATTTGTT
Found at i:222966 original size:29 final size:30
Alignment explanation
Indices: 222934--222991 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
222924 ATGATTTAAT
222934 GTGCAATTGTACACAT-AAATTTTGATTTC
1 GTGCAATTGTACACATGAAATTTTGATTTC
* * *
222963 GTGCAATTTTATACATGAAATTTTTATTT
1 GTGCAATTGTACACATGAAATTTTGATTT
222992 GATACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (30 bp):
GTGCAATTGTACACATGAAATTTTGATTTC
Found at i:225165 original size:23 final size:23
Alignment explanation
Indices: 225139--225186 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
225129 TTTTATTTTT
*
225139 TAACA-AAAAATATTTTTATATAA
1 TAACATAAAAAGATTTTTATA-AA
*
225162 TAACATAATAAGATTTTTATAAA
1 TAACATAAAAAGATTTTTATAAA
225185 TA
1 TA
225187 TATAACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
TAACATAAAAAGATTTTTATAAA
Found at i:225611 original size:19 final size:20
Alignment explanation
Indices: 225572--225620 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
225562 ATTACAAAAT
225572 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTCAAA
225592 AATTCAAAAT-ATTTAT-AAA
1 AATTCAAAATAATTT-TCAAA
225611 AATTCTAAAA
1 AATTC-AAAA
225621 CTTATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTCAAAATAATTTTCAAA
Found at i:225625 original size:18 final size:19
Alignment explanation
Indices: 225572--225626 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
225562 ATTACAAAAT
* *
225572 AATTCAAAATAATTTTCAAA
1 AATTCAAAATACTTAT-AAA
*
225592 AATTCAAAATATTTATAAA
1 AATTCAAAATACTTATAAA
*
225611 AATTCTAAA-ACTTATA
1 AATTCAAAATACTTATA
225627 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 6 0.19
19 11 0.35
20 14 0.45
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCAAAATACTTATAAA
Found at i:226104 original size:2 final size:2
Alignment explanation
Indices: 226097--226121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
226087 ATTAAACATA
226097 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
226122 AGAAACTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:226474 original size:23 final size:23
Alignment explanation
Indices: 226448--226491 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
226438 AACTCGAAGT
*
226448 ACTT-ATTAGAGTTGACTCAAATA
1 ACTTGATTAGA-TTAACTCAAATA
*
226471 ACTTGATTCGATTAACTCAAA
1 ACTTGATTAGATTAACTCAAA
226492 ATTAGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (23 bp):
ACTTGATTAGATTAACTCAAATA
Found at i:238038 original size:17 final size:17
Alignment explanation
Indices: 238003--238034 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
237993 AATATTAATT
238003 AATTAAATTAATTTTTC
1 AATTAAATTAATTTTTC
238020 AATTAAA-TAATTTTT
1 AATTAAATTAATTTTT
238035 TCAACTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTAAATTAATTTTTC
Found at i:240991 original size:14 final size:14
Alignment explanation
Indices: 240972--241003 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
240962 GCTATTTCAC
240972 TATTATATTGCTAT
1 TATTATATTGCTAT
*
240986 TATTATATTGTTAT
1 TATTATATTGCTAT
241000 TATT
1 TATT
241004 TGGATATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (14 bp):
TATTATATTGCTAT
Found at i:248211 original size:16 final size:17
Alignment explanation
Indices: 248177--248211 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
248167 ATTCAAGAAA
*
248177 TGGGTTTAAGGAAATAT
1 TGGGTTTAAGGAAAAAT
248194 TGGGTTTAA-GAAAAAT
1 TGGGTTTAAGGAAAAAT
248210 TG
1 TG
248212 AGAATACGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (17 bp):
TGGGTTTAAGGAAAAAT
Found at i:249420 original size:11 final size:10
Alignment explanation
Indices: 249407--249442 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
249397 AAATTGAAGG
249407 AAAAAAGAAA
1 AAAAAAGAAA
249417 GAAAAAAGAGAA
1 -AAAAAAGA-AA
249429 AAAAAAGAAA
1 AAAAAAGAAA
249439 AAAA
1 AAAA
249443 GAAAAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.25
11 16 0.67
12 2 0.08
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:249428 original size:9 final size:9
Alignment explanation
Indices: 249406--249448 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
249396 AAAATTGAAG
249406 GAAAAAAGAAA
1 GAAAAAAG--A
249417 GAAAAAAGA
1 GAAAAAAGA
*
249426 GAAAAAAAA
1 GAAAAAAGA
249435 GAAAAAA-A
1 GAAAAAAGA
249443 GAAAAA
1 GAAAAA
249449 GGAAGAAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
8 7 0.23
9 16 0.52
11 8 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
GAAAAAAGA
Found at i:249454 original size:18 final size:19
Alignment explanation
Indices: 249408--249455 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
249398 AATTGAAGGA
249408 AAAAAGAAAGAAAAAAGAG
1 AAAAAGAAAGAAAAAAGAG
249427 AAAAA-AAAGAAAAAA-AG
1 AAAAAGAAAGAAAAAAGAG
*
249444 AAAAAGGAAGAA
1 AAAAAGAAAGAA
249456 GGAGAAGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.26
18 15 0.56
19 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAAGAG
Done.