Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 37
Found at i:6527792 original size:18 final size:18
Alignment explanation
Indices: 6527769--6527803 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6527759 CCACTATGAA
6527769 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
6527787 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
6527804 GTAGAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:6530744 original size:55 final size:54
Alignment explanation
Indices: 6530671--6531108 Score: 437
Period size: 55 Copynumber: 8.1 Consensus size: 54
6530661 TCTTCAAATG
* *
6530671 ACGGGTCCGCTCCTTATTCATTCA-AGGAGTATA-AGACTCGAACAATCTTCAGCAA
1 ACGGGTCCGCTCCCTATTC-TTCAGA-GAGTATAGA-ACTCGAACAATCTTCAACAA
* * * * * *
6530726 ACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCAAACAATTTTCAATAA
1 ACGGGTCCGCTCCCTATTC-TTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
6530781 ACGGGTCCGCTCCCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
1 ACGGGTCCGCTCCCTATTC-TTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
*
6530836 ACGGGTCCGCTCTCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AA
1 ACGGGTCCGCTCCCTA-TTCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAA
* * *
6530891 ATGGGTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AA
1 ACGGGTCCGCTCCCTATT-CTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAA
* * * **
6530946 ACGGGTCCGCTCTCTATTCATTCAGAGAGTATAGAACTTGATCAATCTGAAACAA
1 ACGGGTCCGCTCCCTATTC-TTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
*** * * *
6531001 ATATGTCCGCTCCCTATTTCTTCAGAGAGTAT-GGACTTGAACAATCTTCAACGA
1 ACGGGTCCGCTCCCTA-TTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
*** * *
6531055 ATTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAA
1 ACGGGTCCGCTCCCTATT-CTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
6531106 ACG
1 ACG
6531109 ACTTTGCTTC
Statistics
Matches: 334, Mismatches: 39, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
51 13 0.04
53 2 0.01
54 48 0.14
55 263 0.79
56 8 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (54 bp):
ACGGGTCCGCTCCCTATTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
Found at i:6530950 original size:165 final size:163
Alignment explanation
Indices: 6530671--6531095 Score: 495
Period size: 165 Copynumber: 2.6 Consensus size: 163
6530661 TCTTCAAATG
* *
6530671 ACGGGTCCGCTCCT-TATTCATTCA-AGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTC
1 ACGGGTCCGCTCCTAT-TTC-TTCAGA-GAGTATAGA-ACTCGAACAATCTTCA-AAAATGTGTC
* * *
6530733 TGCTCCCTATTCGTTCAGGGAGTATA-AGACTCAAACAATTTTCAATAAACGGGTCCGCTCCCTA
61 TGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCAAACAATCTTCAATAAACGGGTCCGCTCCCTA
* **
6530797 TTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
125 TTCATTCAGAGAGTATAGAACTCGAACAATCTGAAACAA
*
6530836 ACGGGTCCGCTCTCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGGGT-TCG
1 ACGGGTCCGCTC-CTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAATGTGTCT-G
* * *
6530900 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTC-ATAAAACGGGTCCGCTCTCTATT
63 CTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAAT-AAACGGGTCCGCTCCCTATT
* *
6530964 CATTCAGAGAGTATAGAACTTGATCAATCTGAAACAA
127 CATTCAGAGAGTATAGAACTCGAACAATCTGAAACAA
*** * * * *
6531001 ATATGTCCGCTCCCTATTTCTTCAGAGAGTAT-GGACTTGAACAATCTTCAACGAATTTGTCTGC
1 ACGGGTCCGCT-CCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAATGTGTCTGC
*
6531065 TCCCTATTCCTTCAGAGAGTATAGGACTCAA
64 TCCCTATTCCTTCAGAGAGTATAGAACTCAA
6531096 TCTTCAACAA
Statistics
Matches: 224, Mismatches: 26, Indels: 21
0.83 0.10 0.08
Matches are distributed among these distances:
163 1 0.00
164 54 0.24
165 159 0.71
166 9 0.04
167 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (163 bp):
ACGGGTCCGCTCCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAATGTGTCTGCTC
CCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAATAAACGGGTCCGCTCCCTATTCATT
CAGAGAGTATAGAACTCGAACAATCTGAAACAA
Found at i:6531434 original size:17 final size:17
Alignment explanation
Indices: 6531402--6531436 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6531392 TATCTTCATC
6531402 TCAATGCTTCAATATCT
1 TCAATGCTTCAATATCT
6531419 TCAAT-CTTCAACTATCT
1 TCAATGCTTCAA-TATCT
6531436 T
1 T
6531437 TGGAAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.43
Consensus pattern (17 bp):
TCAATGCTTCAATATCT
Found at i:6532514 original size:57 final size:61
Alignment explanation
Indices: 6532447--6532591 Score: 142
Period size: 58 Copynumber: 2.4 Consensus size: 61
6532437 TTGAACCCCC
6532447 CTTTTATTTCTTTTTCTTTTTTCATCATTTTT-TC-TTTCTCA-TTTTTCC-TT-CCA-TTTT
1 CTTTT-TTTCTTTTTCTTTTTTCATC-TTTTTATCATTTCTCATTTTTTCCTTTCCCATTTTT
* *
6532504 CTATTTTTTCTGTTTCCTTTTTT-TTCTTTTTCATCATTTCTCATTTTTTCCATTTTCCCATTTT
1 CT-TTTTTTCT-TTTTCTTTTTTCATCTTTTT-ATCATTTCTCATTTTTTCC--TTTCCCATTTT
6532568 T
61 T
*
6532569 CTTTTCTTCTTTTTCTTCTTTTC
1 CTTTTTTTCTTTTTCTT-TTTTC
6532592 GTTTTTCATT
Statistics
Matches: 71, Mismatches: 4, Indels: 18
0.76 0.04 0.19
Matches are distributed among these distances:
56 5 0.07
57 9 0.13
58 15 0.21
59 7 0.10
60 7 0.10
63 8 0.11
64 14 0.20
65 6 0.08
ACGTcount: A:0.08, C:0.22, G:0.01, T:0.70
Consensus pattern (61 bp):
CTTTTTTTCTTTTTCTTTTTTCATCTTTTTATCATTTCTCATTTTTTCCTTTCCCATTTTT
Found at i:6532553 original size:24 final size:22
Alignment explanation
Indices: 6532523--6532583 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
6532513 CTGTTTCCTT
*
6532523 TTTTTTCTTTTTCATCATTTCTC
1 TTTTTTCTTTTTC-CCATTTCTC
* *
6532546 ATTTTTTCCATTTTCCCATTTTTC
1 -TTTTTT-CTTTTTCCCATTTCTC
6532570 TTTTCTTCTTTTTC
1 TTTT-TTCTTTTTC
6532584 TTCTTTTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 10 0.32
24 15 0.48
25 6 0.19
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTTCTTTTTCCCATTTCTC
Found at i:6541308 original size:45 final size:45
Alignment explanation
Indices: 6541251--6541369 Score: 220
Period size: 45 Copynumber: 2.6 Consensus size: 45
6541241 AAAAGGAAAT
6541251 CCTAACCGCATGATATCTAATTCGCATGCTTGTTCAAAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATGCTTGTTCAAAAAATAAA
*
6541296 CCTAACCTCATGATATCTAATTCGCATGCTTGTTCAAAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATGCTTGTTCAAAAAATAAA
*
6541341 CCTAACCGCATGATATCTAGTTCGCATGC
1 CCTAACCGCATGATATCTAATTCGCATGC
6541370 ATTTATTCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (45 bp):
CCTAACCGCATGATATCTAATTCGCATGCTTGTTCAAAAAATAAA
Found at i:6545665 original size:7 final size:7
Alignment explanation
Indices: 6545653--6545695 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
6545643 CTAAAGCAAC
6545653 AGGAGGA
1 AGGAGGA
6545660 AGGAGGA
1 AGGAGGA
6545667 AGGAGGA
1 AGGAGGA
6545674 AGGAGGA
1 AGGAGGA
6545681 AGGAGGA
1 AGGAGGA
*
6545688 AGAAGGA
1 AGGAGGA
6545695 A
1 A
6545696 AAAGGAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (7 bp):
AGGAGGA
Found at i:6545701 original size:14 final size:14
Alignment explanation
Indices: 6545653--6545705 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
6545643 CTAAAGCAAC
*
6545653 AGGAGGAAGGAGGA
1 AGGAGGAAGAAGGA
*
6545667 AGGAGGAAGGAGGA
1 AGGAGGAAGAAGGA
6545681 AGGAGGAAGAAGGA
1 AGGAGGAAGAAGGA
**
6545695 AAAAGGAAGAA
1 AGGAGGAAGAA
6545706 AATGTTCTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (14 bp):
AGGAGGAAGAAGGA
Found at i:6545701 original size:21 final size:21
Alignment explanation
Indices: 6545656--6545703 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
6545646 AAGCAACAGG
* **
6545656 AGGAAGGAGGAAGGAGGAAGG
1 AGGAAGGAGGAAGAAGGAAAA
6545677 AGGAAGGAGGAAGAAGGAAAA
1 AGGAAGGAGGAAGAAGGAAAA
6545698 AGGAAG
1 AGGAAG
6545704 AAAATGTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (21 bp):
AGGAAGGAGGAAGAAGGAAAA
Found at i:6546989 original size:33 final size:33
Alignment explanation
Indices: 6546951--6547065 Score: 230
Period size: 33 Copynumber: 3.5 Consensus size: 33
6546941 TACAAATCCA
6546951 AATAATAAACAATAAATTTATGTATAGTTATTT
1 AATAATAAACAATAAATTTATGTATAGTTATTT
6546984 AATAATAAACAATAAATTTATGTATAGTTATTT
1 AATAATAAACAATAAATTTATGTATAGTTATTT
6547017 AATAATAAACAATAAATTTATGTATAGTTATTT
1 AATAATAAACAATAAATTTATGTATAGTTATTT
6547050 AATAATAAACAATAAA
1 AATAATAAACAATAAA
6547066 AAATATTTAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.39
Consensus pattern (33 bp):
AATAATAAACAATAAATTTATGTATAGTTATTT
Found at i:6548168 original size:42 final size:42
Alignment explanation
Indices: 6548109--6548190 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
6548099 CTAGCCGAGC
* *
6548109 TCGAGTCGATTCCATTCGATTCGAGTATTTATCGAGCCTTGA
1 TCGAGTCAATTCCATTCGATCCGAGTATTTATCGAGCCTTGA
*
6548151 TCGAGTCAATTTCATTCGATCCGAGTATTTATCGAGCCTT
1 TCGAGTCAATTCCATTCGATCCGAGTATTTATCGAGCCTT
6548191 TATCAAATCG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (42 bp):
TCGAGTCAATTCCATTCGATCCGAGTATTTATCGAGCCTTGA
Found at i:6551392 original size:43 final size:43
Alignment explanation
Indices: 6551345--6551631 Score: 147
Period size: 43 Copynumber: 6.7 Consensus size: 43
6551335 TGTATTGGTG
* *
6551345 TTTAGCGGCGTTTTCCCTACAAACGCCGTAGTAGGTGTTGAGA
1 TTTAGCGGCGTTTTACCTACAAACGCCGCAGTAGGTGTTGAGA
* * *
6551388 TTTAGCTGCGTTTTACTTACAAACGCCGCAGTAGGTGTTGATA
1 TTTAGCGGCGTTTTACCTACAAACGCCGCAGTAGGTGTTGAGA
* ** * ** * *
6551431 TTTTA-CGGCTTTTTTTC-ACAAATGCCGCAAAAGATGATGATG-
1 -TTTAGCGGCGTTTTACCTACAAACGCCGCAGTAGGTGTTGA-GA
* * * * * *
6551473 TTTAGCGGCATTTTTCCCACAAACGTCGCAGTAGGTTTTTCAGA
1 TTTAGCGGCGTTTTACCTACAAACGCCGCAGTAGG-TGTTGAGA
* * * * * * * *
6551517 TTTAACCGTGTTTGTATCGA-AAATGACGCAATAAGG-GTTGAGA
1 TTTAGCGGCGTTT-TACCTACAAACGCCGCAGT-AGGTGTTGAGA
* * ** * *
6551560 ATTAGCGGCGTTTTTA-TTGA-AAACGTTGTAATAGGTGTTGAGA
1 TTTAGCGGCG-TTTTACCT-ACAAACGCCGCAGTAGGTGTTGAGA
* *
6551603 TTTAGCGGCGTTTTTCATACAAACGCCGC
1 TTTAGCGGCGTTTTACCTACAAACGCCGC
6551632 TAAAGTTGGG
Statistics
Matches: 177, Mismatches: 54, Indels: 26
0.69 0.21 0.10
Matches are distributed among these distances:
41 4 0.02
42 36 0.20
43 103 0.58
44 28 0.16
45 6 0.03
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTTACCTACAAACGCCGCAGTAGGTGTTGAGA
Found at i:6551666 original size:43 final size:43
Alignment explanation
Indices: 6551619--6551763 Score: 197
Period size: 43 Copynumber: 3.4 Consensus size: 43
6551609 GGCGTTTTTC
*
6551619 ATACAAACGCCGCTAAAGTTGGGTATCTCGCGGCGTTTCTAGT
1 ATACAAACGCCGCTAAAGTTGGGTATATCGCGGCGTTTCTAGT
6551662 ATACAAACGCCGCTAAAGTTGGGTATATCGCGGCGTTTCTAGT
1 ATACAAACGCCGCTAAAGTTGGGTATATCGCGGCGTTTCTAGT
* * * *
6551705 ATACAAACGCCGCTAAATGTAT-GGTATATTGCGACATTT-T-TT
1 ATACAAACGCCGCTAAA-GT-TGGGTATATCGCGGCGTTTCTAGT
*
6551747 TTACAAACGCCGCTAAA
1 ATACAAACGCCGCTAAA
6551764 TAACACAAAA
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
42 17 0.18
43 60 0.64
44 16 0.17
45 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
ATACAAACGCCGCTAAAGTTGGGTATATCGCGGCGTTTCTAGT
Found at i:6554965 original size:22 final size:22
Alignment explanation
Indices: 6554935--6555016 Score: 146
Period size: 22 Copynumber: 3.7 Consensus size: 22
6554925 TTCAGTATTT
6554935 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
6554957 GTCCTGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
6554979 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
6555001 GTCCCAAAGGACCACT
1 GTCCCGAAGGACCACT
6555017 ATGTCCCGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.15
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:6555044 original size:18 final size:18
Alignment explanation
Indices: 6555010--6555044 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6555000 CGTCCCAAAG
*
6555010 GACCACTATGTCCCGAAT
1 GACCACTATATCCCGAAT
*
6555028 GACCACTATATCTCGAA
1 GACCACTATATCCCGAA
6555045 GGACTAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.23
Consensus pattern (18 bp):
GACCACTATATCCCGAAT
Found at i:6555709 original size:64 final size:63
Alignment explanation
Indices: 6555596--6555757 Score: 172
Period size: 65 Copynumber: 2.5 Consensus size: 63
6555586 TCCCTTGACG
* * * *
6555596 GGTGCATCGATGCACTACC-CATGAATCGGTGCATAAATCATATTCGATGTT-TGTATTTTAAGC
1 GGTGCATCGATGCACT-CCTTATGCATCGATGCATAAATCATATTCGATGTTAT-TAATTTAA--
6555659 A-
62 AT
*
6555660 GGTGCATCGATGCACTCCTTATGCATCGATGCATTAATGGCAT-TT-GATGTTCATTAATTTAAA
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAAT--CATATTCGATGTT-ATTAATTTAAA
6555723 T
63 T
6555724 GAGTGCATCGATGCACTCCTTATGCATCGATGCA
1 G-GTGCATCGATGCACTCCTTATGCATCGATGCA
6555758 CCTTCAACAA
Statistics
Matches: 86, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
63 3 0.03
64 38 0.44
65 41 0.48
66 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (63 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTATTAATTTAAAT
Found at i:6556445 original size:2 final size:2
Alignment explanation
Indices: 6556438--6556479 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6556428 CTAAATAATC
6556438 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
6556480 CTTTATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6561866 original size:18 final size:18
Alignment explanation
Indices: 6561820--6561890 Score: 106
Period size: 18 Copynumber: 3.7 Consensus size: 18
6561810 GTTCAGTATT
6561820 TGTCCCGAAGGACCACTGGA
1 TGTCCCGAAGGACCACT--A
6561840 TACGTCCCGAAGGACCACTA
1 T--GTCCCGAAGGACCACTA
6561860 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
6561878 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
6561891 TAATATACCC
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
18 30 0.61
20 3 0.06
22 16 0.33
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.15
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:6569969 original size:21 final size:21
Alignment explanation
Indices: 6569943--6570045 Score: 179
Period size: 21 Copynumber: 4.9 Consensus size: 21
6569933 GCGTAGAATT
*
6569943 TGTCCCGAAGGACCACGTAGA
1 TGTCCCGAAGGACCACATAGA
*
6569964 TGTCCCGAAGGACGACATAGA
1 TGTCCCGAAGGACCACATAGA
*
6569985 TGTCCCGAAGGACGACATAGA
1 TGTCCCGAAGGACCACATAGA
6570006 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
6570027 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
6570046 TAACACATAT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.32, C:0.27, G:0.26, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:6570874 original size:20 final size:20
Alignment explanation
Indices: 6570849--6570906 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
6570839 TTCCCATTGA
*
6570849 AGTGCATCAGTGTATTCTAC
1 AGTGCATCAGTGCATTCTAC
6570869 AGTGCATCAGTGCATTCTAC
1 AGTGCATCAGTGCATTCTAC
6570889 AGTGCATC-GATGCATTCT
1 AGTGCATCAG-TGCATTCT
6570907 TTAATAGGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 1 0.03
20 35 0.97
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCAGTGCATTCTAC
Found at i:6572358 original size:41 final size:41
Alignment explanation
Indices: 6572313--6572459 Score: 120
Period size: 41 Copynumber: 3.6 Consensus size: 41
6572303 TCTATTATAT
* *
6572313 TGCGGCATTTGTATAAAAACGCCGCTATAGATTATATCTAC
1 TGCGGCGTTTGTACAAAAACGCCGCTATAGATTATATCTAC
** * * * *
6572354 TGCGGCGTTTGTACAAAAATACCGCTAAAG-TTCTATTATAT
1 TGCGGCGTTTGTACAAAAACGCCGCTATAGATTATA-TCTAC
* * * * *
6572395 TGTGGTGTTTGTATAAAAACGCTGCAATAGA-TATAATCTAC
1 TGCGGCGTTTGTACAAAAACGCCGCTATAGATTAT-ATCTAC
*
6572436 TAG-GGTGTTTGTACAAAAACGCCG
1 T-GCGGCGTTTGTACAAAAACGCCG
6572460 TTAAAGTGCT
Statistics
Matches: 81, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (41 bp):
TGCGGCGTTTGTACAAAAACGCCGCTATAGATTATATCTAC
Found at i:6572384 original size:82 final size:82
Alignment explanation
Indices: 6572295--6572454 Score: 234
Period size: 82 Copynumber: 2.0 Consensus size: 82
6572285 TAAAATCGTT
*
6572295 GCTAAAGTTCTATTATATTGCGGCATTTGTATAAAAACGCCGCTATAGAT-TATATCTACT-GCG
1 GCTAAAGTTCTATTATATTGCGGCATTTGTATAAAAACGCCGCAATAGATATA-ATCTACTAG-G
6572358 GCGTTTGTACAAAAATACC
64 GCGTTTGTACAAAAATACC
* ** * *
6572377 GCTAAAGTTCTATTATATTGTGGTGTTTGTATAAAAACGCTGCAATAGATATAATCTACTAGGGT
1 GCTAAAGTTCTATTATATTGCGGCATTTGTATAAAAACGCCGCAATAGATATAATCTACTAGGGC
6572442 GTTTGTACAAAAA
66 GTTTGTACAAAAA
6572455 CGCCGTTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
82 67 0.96
83 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (82 bp):
GCTAAAGTTCTATTATATTGCGGCATTTGTATAAAAACGCCGCAATAGATATAATCTACTAGGGC
GTTTGTACAAAAATACC
Found at i:6574016 original size:42 final size:42
Alignment explanation
Indices: 6573962--6574098 Score: 165
Period size: 42 Copynumber: 3.3 Consensus size: 42
6573952 TAAACAAACA
*
6573962 TATTGCGACGTTTTTACTATAAACGCCGCTAAATTATTACTC
1 TATTGCGGCGTTTTTACTATAAACGCCGCTAAATTATTACTC
*
6574004 TATTGCGGCGTTTTTAC-ACAAACGCCGCTAAATTATTACTC
1 TATTGCGGCGTTTTTACTATAAACGCCGCTAAATTATTACTC
** **
6574045 TACAGCGGCGTTTGTT--TGATAAACGCCGCTAAATTACCACTC
1 TATTGCGGCGTTT-TTACT-ATAAACGCCGCTAAATTATTACTC
*
6574087 TGTTGC-GCGTTT
1 TATTGCGGCGTTT
6574099 GTTAGAAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
41 40 0.49
42 42 0.51
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (42 bp):
TATTGCGGCGTTTTTACTATAAACGCCGCTAAATTATTACTC
Found at i:6574038 original size:41 final size:42
Alignment explanation
Indices: 6573962--6574112 Score: 173
Period size: 41 Copynumber: 3.6 Consensus size: 42
6573952 TAAACAAACA
*
6573962 TATTGCGACGTTT-TTACTATAAACGCCGCTAAATTATTACTC
1 TATTGCGGCGTTTGTTAC-ATAAACGCCGCTAAATTATTACTC
*
6574004 TATTGCGGCGTTT-TTACACAAACGCCGCTAAATTATTACTC
1 TATTGCGGCGTTTGTTACATAAACGCCGCTAAATTATTACTC
** ** **
6574045 TACAGCGGCGTTTGTTTGATAAACGCCGCTAAATTACCACTC
1 TATTGCGGCGTTTGTTACATAAACGCCGCTAAATTATTACTC
* * *
6574087 TGTTGC-GCGTTTGTTAGAAAAACGCC
1 TATTGCGGCGTTTGTTACATAAACGCC
6574113 ACTATAAACG
Statistics
Matches: 94, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
41 52 0.55
42 42 0.45
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (42 bp):
TATTGCGGCGTTTGTTACATAAACGCCGCTAAATTATTACTC
Found at i:6574138 original size:41 final size:41
Alignment explanation
Indices: 6574050--6574140 Score: 96
Period size: 41 Copynumber: 2.2 Consensus size: 41
6574040 TACTCTACAG
* * * * *
6574050 CGGCGTTTGTTTGATAAACGCCGCTAAATTACCACTCTGTTG
1 CGGCGTTTGTTAGAAAAACGCCACTAAA-TACCACCCTGTTC
*
6574092 C-GCGTTTGTTAGAAAAACGCCACTATAA-ACGACCCTGTTC
1 CGGCGTTTGTTAGAAAAACGCCACTA-AATACCACCCTGTTC
6574132 CGGCGTTTG
1 CGGCGTTTG
6574141 ATCTACAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
40 10 0.24
41 28 0.68
42 3 0.07
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (41 bp):
CGGCGTTTGTTAGAAAAACGCCACTAAATACCACCCTGTTC
Found at i:6582131 original size:99 final size:99
Alignment explanation
Indices: 6581960--6582159 Score: 391
Period size: 99 Copynumber: 2.0 Consensus size: 99
6581950 GGAGTGACTA
*
6581960 ACTGTTCTTCTTCATCACAAGGATCTTTACTCTGAATCAAGTTGCGATATGGGGAACAATCAATG
1 ACTGTTCTTCTTCATCACAAGGATCTTTACTCTGAATCAAGTTGCGATATGGGGAACAATCAAAG
6582025 GAATCTGGTGAACCACATGGAATGATCGACGATG
66 GAATCTGGTGAACCACATGGAATGATCGACGATG
6582059 ACTGTTCTTCTTCATCACAAGGATCTTTACTCTGAATCAAGTTGCGATATGGGGAACAATCAAAG
1 ACTGTTCTTCTTCATCACAAGGATCTTTACTCTGAATCAAGTTGCGATATGGGGAACAATCAAAG
6582124 GAATCTGGTGAACCACATGGAATGATCGACGATG
66 GAATCTGGTGAACCACATGGAATGATCGACGATG
6582158 AC
1 AC
6582160 GATGGAGATG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (99 bp):
ACTGTTCTTCTTCATCACAAGGATCTTTACTCTGAATCAAGTTGCGATATGGGGAACAATCAAAG
GAATCTGGTGAACCACATGGAATGATCGACGATG
Found at i:6584511 original size:31 final size:31
Alignment explanation
Indices: 6584476--6584565 Score: 73
Period size: 31 Copynumber: 3.0 Consensus size: 31
6584466 TATTTTCTCA
6584476 AATATCATTTTAAATTATCCCTAAACTTTTC
1 AATATCATTTTAAATTATCCCTAAACTTTTC
* * * *
6584507 -A-AT-ATTTTAATTTCATCCCTGAAC-TATG
1 AATATCATTTTAAATT-ATCCCTAAACTTTTC
*
6584535 ACTATCATTTTAAATTAGT-CCTCAAACTTTT
1 AATATCATTTTAAATTA-TCCCT-AAACTTTT
6584566 GAACATTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
28 11 0.25
29 11 0.25
30 7 0.16
31 13 0.30
32 2 0.05
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (31 bp):
AATATCATTTTAAATTATCCCTAAACTTTTC
Found at i:6584585 original size:29 final size:30
Alignment explanation
Indices: 6584553--6584618 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
6584543 TTTAAATTAG
*
6584553 TCCTCAAAC-TTTTGAACATTTCAATTTCA
1 TCCTCAAACTTTTTGAACATTCCAATTTCA
* *
6584582 TCCTCAAACTTTTTGAGCATTCCAATTTTA
1 TCCTCAAACTTTTTGAACATTCCAATTTCA
6584612 TCC-CAAA
1 TCCTCAAA
6584619 TTATATGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (30 bp):
TCCTCAAACTTTTTGAACATTCCAATTTCA
Found at i:6589489 original size:22 final size:21
Alignment explanation
Indices: 6589447--6589486 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6589437 GAGTTTATTT
*
6589447 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
6589468 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
6589487 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:6592434 original size:12 final size:12
Alignment explanation
Indices: 6592417--6592442 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6592407 TTGTTATGCT
6592417 TGCTCCTCGGGC
1 TGCTCCTCGGGC
6592429 TGCTCCTCGGGC
1 TGCTCCTCGGGC
6592441 TG
1 TG
6592443 TTCAGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.35, T:0.27
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:6594138 original size:20 final size:21
Alignment explanation
Indices: 6594090--6594150 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
6594080 TTCCCCTGTG
6594090 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGGTTCCC--TCAAA
*
6594113 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
6594133 GGGGGAATCGGTTCCCTC
1 GGGGGAATCGGTTCCCTC
6594151 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 19 0.51
21 2 0.05
23 16 0.43
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:6599776 original size:23 final size:23
Alignment explanation
Indices: 6599750--6599813 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
6599740 CAGCTCGTAT
6599750 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
6599773 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
* *
6599796 AATTACACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
6599814 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:6600000 original size:103 final size:103
Alignment explanation
Indices: 6599829--6600144 Score: 560
Period size: 103 Copynumber: 3.1 Consensus size: 103
6599819 TAATGTCCAT
* * * *
6599829 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
6599894 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
6599932 AAGTACCATATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
6599997 GACTTTACACATGTTCCAAAGAATACATATATGCCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
6600035 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
6600100 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
6600138 AAGGACC
1 AAGGACC
6600145 GCGTAGACCC
Statistics
Matches: 201, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 201 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:6604478 original size:20 final size:20
Alignment explanation
Indices: 6604453--6604490 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6604443 CACATGTTAA
6604453 AGAATGCATCAATGCACTGT
1 AGAATGCATCAATGCACTGT
*
6604473 AGAATGCATCGATGCACT
1 AGAATGCATCAATGCACT
6604491 TCAAGGGGAA
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:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATGCATCAATGCACTGT
Found at i:6604966 original size:20 final size:19
Alignment explanation
Indices: 6604918--6604968 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
6604908 AAATGACCAA
*
6604918 CAAATTCGCAATGTGATCT
1 CAAATTCGCAACGTGATCT
6604937 CAAATTCGCAACGTGAAT-T
1 CAAATTCGCAACGTG-ATCT
6604956 CAAATTTCGCAAC
1 CAAA-TTCGCAAC
6604969 CCAGGTTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (19 bp):
CAAATTCGCAACGTGATCT
Found at i:6605000 original size:20 final size:20
Alignment explanation
Indices: 6604977--6605060 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
6604967 ACCCAGGTTC
*
6604977 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAAAAGT
* *
6604997 CAAATTCGAAACACATAAGT
1 CAAATTCGCAACACAAAAGT
*
6605017 CAAATTCGCAACGCAAAAGT
1 CAAATTCGCAACACAAAAGT
* *
6605037 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACACAAAAGT
6605057 CAAA
1 CAAA
6605061 ATTTGCAACG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.15
Consensus pattern (20 bp):
CAAATTCGCAACACAAAAGT
Found at i:6605057 original size:40 final size:40
Alignment explanation
Indices: 6604977--6605071 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
6604967 ACCCAGGTTC
* *
6604977 CAAATTCGCAACACAGAAGTCAAATTCGAAACACATAAGT
1 CAAATTCGCAACGCAAAAGTCAAATTCGAAACACATAAGT
* *
6605017 CAAATTCGCAACGCAAAAGTCAAATTCGCAACGCGA-AAGT
1 CAAATTCGCAACGCAAAAGTCAAATTCGAAACAC-ATAAGT
*
6605057 CAAAATTTGCAACGC
1 C-AAATTCGCAACGC
6605072 GATACTCCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 35 0.73
41 13 0.27
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (40 bp):
CAAATTCGCAACGCAAAAGTCAAATTCGAAACACATAAGT
Found at i:6605068 original size:21 final size:20
Alignment explanation
Indices: 6604977--6605073 Score: 108
Period size: 20 Copynumber: 4.8 Consensus size: 20
6604967 ACCCAGGTTC
*
6604977 CAAATTCGCAACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
* *
6604997 CAAATTCGAAACAC-ATAAGT
1 CAAATTCGCAACGCGA-AAGT
*
6605017 CAAATTCGCAACGCAAAAGT
1 CAAATTCGCAACGCGAAAGT
6605037 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
6605057 CAAAATTTGCAACGCGA
1 C-AAATTCGCAACGCGA
6605074 TACTCCAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
20 54 0.78
21 15 0.22
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:6606080 original size:40 final size:41
Alignment explanation
Indices: 6606022--6606127 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 41
6606012 AACAAATGCA
* * *
6606022 TTGCGATTTTGGAGTATCGTGTTGCAAATCTT-AAATCGCG
1 TTGCGAATTTCGATTATCGTGTTGCAAATCTTAAAATCGCG
*
6606062 TTGCGAATTTCGATTATCGCGTTGCAAATCTTAAAATCGCG
1 TTGCGAATTTCGATTATCGTGTTGCAAATCTTAAAATCGCG
6606103 TTGCGAATTTCGACTT-TCGTGTTGC
1 TTGCGAATTTCGA-TTATCGTGTTGC
6606128 GAATTTGGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
40 28 0.47
41 29 0.49
42 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
TTGCGAATTTCGATTATCGTGTTGCAAATCTTAAAATCGCG
Found at i:6606111 original size:41 final size:40
Alignment explanation
Indices: 6606022--6606115 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 40
6606012 AACAAATGCA
* * *
6606022 TTGCGATTTTGGAGTATCGTGTTGCAAATCTTAAATCGCG
1 TTGCGAATTTCGAGTATCGCGTTGCAAATCTTAAATCGCG
*
6606062 TTGCGAATTTCGATTATCGCGTTGCAAATCTTAAAATCGCG
1 TTGCGAATTTCGAGTATCGCGTTGCAAATCTT-AAATCGCG
6606103 TTGCGAATTTCGA
1 TTGCGAATTTCGA
6606116 CTTTCGTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 28 0.57
41 21 0.43
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (40 bp):
TTGCGAATTTCGAGTATCGCGTTGCAAATCTTAAATCGCG
Found at i:6606166 original size:20 final size:20
Alignment explanation
Indices: 6606057--6606173 Score: 87
Period size: 21 Copynumber: 5.8 Consensus size: 20
6606047 AAATCTTAAA
*
6606057 TCGCGTTGCGAATTTCGATT
1 TCGCGTTGCGAATTTCGAAT
* * *
6606077 ATCGCGTTGCAAATCTT-AAAA
1 -TCGCGTTGCGAAT-TTCGAAT
*
6606098 TCGCGTTGCGAATTTCGACTT
1 TCGCGTTGCGAATTTCGA-AT
* *
6606119 TCGTGTTGCGAATTTGGAA-
1 TCGCGTTGCGAATTTCGAAT
* *
6606138 CCTGGGTTGCGAAATTT-GAAT
1 TC-GCGTTGCG-AATTTCGAAT
6606159 TCGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
6606174 GTTGGTCATT
Statistics
Matches: 75, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
19 8 0.11
20 30 0.40
21 35 0.47
22 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGAATTTCGAAT
Found at i:6606675 original size:30 final size:30
Alignment explanation
Indices: 6606630--6606696 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
6606620 AAGGAACATA
* * * *
6606630 TGGACAGTTATCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTCTATAACCTC
6606660 TGGATAGTTACCGAGGATCTCTATAACCTC
1 TGGATAGTTACCGAGGATCTCTATAACCTC
6606690 TGGATAG
1 TGGATAG
6606697 GTCCTTCGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTCTATAACCTC
Found at i:6610820 original size:42 final size:40
Alignment explanation
Indices: 6610741--6610834 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 40
6610731 AAATAACCAA
6610741 CAAATTCGCAACGCAAACTCCAATTTCGCAACACAGTTTC
1 CAAATTCGCAACGCAAACTCCAATTTCGCAACACAGTTTC
* * * *
6610781 CAAATTCGCAACGTGAAATTCCCAGA-TTCGCAACTCAGTTTT
1 CAAATTCGCAACG-CAAACT-CCA-ATTTCGCAACACAGTTTC
*
6610823 GAAATTCGCAAC
1 CAAATTCGCAAC
6610835 TCGAATTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 13 0.28
41 4 0.09
42 28 0.61
43 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (40 bp):
CAAATTCGCAACGCAAACTCCAATTTCGCAACACAGTTTC
Found at i:6610895 original size:20 final size:20
Alignment explanation
Indices: 6610870--6610977 Score: 207
Period size: 20 Copynumber: 5.4 Consensus size: 20
6610860 TTTCCAAATT
6610870 CGCGACGCGAATCTGTAATC
1 CGCGACGCGAATCTGTAATC
6610890 CGCGACGCGAATCTGTAATC
1 CGCGACGCGAATCTGTAATC
6610910 CGCGACGCGAATCTGTAATC
1 CGCGACGCGAATCTGTAATC
6610930 CGCGACGCGAATCTGTAATC
1 CGCGACGCGAATCTGTAATC
6610950 CGCGACGCGAATCTGTAATC
1 CGCGACGCGAATCTGTAATC
*
6610970 TGCGACGC
1 CGCGACGC
6610978 TAATTTCGAA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (20 bp):
CGCGACGCGAATCTGTAATC
Found at i:6611016 original size:20 final size:20
Alignment explanation
Indices: 6610993--6611042 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
6610983 TCGAATTCAC
*
6610993 AATTCACGACCCTAATTTCG
1 AATTCACAACCCTAATTTCG
*
6611013 AATTCACAACGCTAATTTCG
1 AATTCACAACCCTAATTTCG
*
6611033 AATTCGCAAC
1 AATTCACAAC
6611043 ACAAATCCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (20 bp):
AATTCACAACCCTAATTTCG
Found at i:6611305 original size:20 final size:20
Alignment explanation
Indices: 6611233--6611306 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
6611223 TCGTGAATTT
6611233 CGAA-TTCACAATTCGCGACG
1 CGAATTTCA-AATTCGCGACG
* * * *
6611253 CTAATATCGAATTTGCGACG
1 CGAATTTCAAATTCGCGACG
* * * *
6611273 CTAATTCCTAATTGGCGACG
1 CGAATTTCAAATTCGCGACG
6611293 CGAATTTCAAATTC
1 CGAATTTCAAATTC
6611307 ACAATTCGCG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (20 bp):
CGAATTTCAAATTCGCGACG
Found at i:6611321 original size:47 final size:47
Alignment explanation
Indices: 6611262--6611372 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 47
6611252 GCTAATATCG
* * * * *
6611262 AATTTGCGACGCTAATTCCTAATTGGCGACGCGAATTTCAAATTCAC
1 AATTCGCGACGCTAATTCCGAATTCGCAACACGAATTTCAAATTCAC
* * *
6611309 AATTCGCGACGCTAATTCCGAATTCGCAATACTAATTTCGAATTCAC
1 AATTCGCGACGCTAATTCCGAATTCGCAACACGAATTTCAAATTCAC
*
6611356 AATTCGCGATGCTAATT
1 AATTCGCGACGCTAATT
6611373 TTACATGGTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (47 bp):
AATTCGCGACGCTAATTCCGAATTCGCAACACGAATTTCAAATTCAC
Found at i:6611332 original size:27 final size:27
Alignment explanation
Indices: 6611282--6611373 Score: 81
Period size: 27 Copynumber: 3.7 Consensus size: 27
6611272 GCTAATTCCT
* * *
6611282 AATTGGCGACGCGAATTTCAAATTCAC
1 AATTCGCGACGCTAATTTCGAATTCAC
* *
6611309 AATTCGCGACGCTAATTCCGAATTCGC
1 AATTCGCGACGCTAATTTCGAATTCAC
6611336 AA-T----A--CTAATTTCGAATTCAC
1 AATTCGCGACGCTAATTTCGAATTCAC
*
6611356 AATTCGCGATGCTAATTT
1 AATTCGCGACGCTAATTT
6611374 TACATGGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
20 16 0.31
21 1 0.02
22 1 0.02
25 1 0.02
26 1 0.02
27 31 0.61
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (27 bp):
AATTCGCGACGCTAATTTCGAATTCAC
Found at i:6611343 original size:20 final size:20
Alignment explanation
Indices: 6611320--6611358 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6611310 ATTCGCGACG
*
6611320 CTAATTCCGAATTCGCAATA
1 CTAATTCCGAATTCACAATA
*
6611340 CTAATTTCGAATTCACAAT
1 CTAATTCCGAATTCACAAT
6611359 TCGCGATGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (20 bp):
CTAATTCCGAATTCACAATA
Found at i:6611601 original size:20 final size:20
Alignment explanation
Indices: 6611550--6611594 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6611540 TTCGCGTCAA
* *
6611550 GAATTCGGAATTAGCGTTGC
1 GAATTAGGAATTAGCGTCGC
*
6611570 GAATTAGGAATTAGTGTCGC
1 GAATTAGGAATTAGCGTCGC
6611590 GAATT
1 GAATT
6611595 GTGAATTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (20 bp):
GAATTAGGAATTAGCGTCGC
Found at i:6611620 original size:20 final size:20
Alignment explanation
Indices: 6611597--6611641 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
6611587 CGCGAATTGT
6611597 GAATTCAAAATTAGCGTCGC
1 GAATTCAAAATTAGCGTCGC
* *
6611617 GAATTCGAAATTAGCGTCGT
1 GAATTCAAAATTAGCGTCGC
6611637 GAATT
1 GAATT
6611642 TGGAAAATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (20 bp):
GAATTCAAAATTAGCGTCGC
Found at i:6611694 original size:20 final size:21
Alignment explanation
Indices: 6611665--6611703 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
6611655 TGCGGAAAAG
6611665 AAATTCGAGTTGCGAATTTCA
1 AAATTCGAGTTGCGAATTTCA
6611686 AAATT-GAGTTGCGAATTT
1 AAATTCGAGTTGCGAATTT
6611704 GGAAACTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (21 bp):
AAATTCGAGTTGCGAATTTCA
Found at i:6611716 original size:20 final size:20
Alignment explanation
Indices: 6611671--6611726 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
6611661 AAAGAAATTC
** *
6611671 GAGTTGCGAATTTCAAAATT
1 GAGTTGCGAATTTGGAAACT
6611691 GAGTTGCGAATTTGGAAACT
1 GAGTTGCGAATTTGGAAACT
* *
6611711 GTGTTGCGAAATTGGA
1 GAGTTGCGAATTTGGA
6611727 GTTCGCGTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.32
Consensus pattern (20 bp):
GAGTTGCGAATTTGGAAACT
Found at i:6611958 original size:20 final size:20
Alignment explanation
Indices: 6611935--6611980 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6611925 AATTTCTTTC
*
6611935 TCGCAACATAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
6611955 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
6611975 TCGCAA
1 TCGCAA
6611981 AGCGCGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:6612557 original size:20 final size:20
Alignment explanation
Indices: 6612519--6612581 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
6612509 AAATCGCAAC
* *
6612519 GCGATTTT-AGTTTCACGTT
1 GCGATTTTCATTTTCGCGTT
6612538 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
* * *
6612558 ACGAATTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
6612578 GCGA
1 GCGA
6612582 ATTTAAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.16, C:0.17, G:0.21, T:0.46
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:6612593 original size:20 final size:20
Alignment explanation
Indices: 6612529--6612585 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
6612519 GCGATTTTAG
* *
6612529 TTTCACGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTCAT
*
6612549 TTTCGCGTTACGAATTTCAT
1 TTTCGCGTTGCGAATTTCAT
*
6612569 TTTCGTGTTGCGAATTT
1 TTTCGCGTTGCGAATTT
6612586 AAGTTTCGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTCAT
Found at i:6614536 original size:4 final size:4
Alignment explanation
Indices: 6614527--6614564 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
6614517 TTTTTCGGCA
* *
6614527 TTAT TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
6614565 TTAGCGGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:6614791 original size:23 final size:22
Alignment explanation
Indices: 6614708--6614805 Score: 100
Period size: 21 Copynumber: 4.6 Consensus size: 22
6614698 AATTCACCTG
6614708 TCATCGTTCAAGAGGCTCCTC-C
1 TCATCGTTCAAGAGG-TCCTCTC
*
6614730 -CA-CTATTCAAGAGGT-CTCTC
1 TCATC-GTTCAAGAGGTCCTCTC
* *
6614750 CCATAGTTCAAGAGG-CCTCTC
1 TCATCGTTCAAGAGGTCCTCTC
6614771 TCATCGTTCAAGAGGTCC-CTC
1 TCATCGTTCAAGAGGTCCTCTC
*
6614792 TCACCGTTCAAGAG
1 TCATCGTTCAAGAG
6614806 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.05
20 3 0.05
21 56 0.88
22 2 0.03
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (22 bp):
TCATCGTTCAAGAGGTCCTCTC
Found at i:6616446 original size:20 final size:20
Alignment explanation
Indices: 6616423--6616477 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
6616413 GTGTTGCGAA
6616423 TTTGATTTTCGCGTTACGAT
1 TTTGATTTTCGCGTTACGAT
6616443 TTTGACTTTT-GCGTTACGAT
1 TTTGA-TTTTCGCGTTACGAT
**
6616463 TTTGGCTTTCGCGTT
1 TTTGATTTTCGCGTT
6616478 GCGAATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.77
21 4 0.13
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (20 bp):
TTTGATTTTCGCGTTACGAT
Found at i:6616709 original size:18 final size:18
Alignment explanation
Indices: 6616686--6616721 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6616676 AAGCCGGTTG
*
6616686 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
6616704 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
6616722 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:6619435 original size:16 final size:16
Alignment explanation
Indices: 6619396--6619438 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
6619386 ACCCGGAAGT
*
6619396 TCCGAGTACCCGAAAA
1 TCCGGGTACCCGAAAA
*
6619412 T-TGGGTACCCGAAAA
1 TCCGGGTACCCGAAAA
6619427 TCCGGGTACCCG
1 TCCGGGTACCCG
6619439 GATTTGCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (16 bp):
TCCGGGTACCCGAAAA
Found at i:6619700 original size:12 final size:12
Alignment explanation
Indices: 6619667--6619700 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6619657 GGTTGTGGGT
*
6619667 TTTGATATTCTG
1 TTTGATATTGTG
6619679 TTTGATATTGTG
1 TTTGATATTGTG
*
6619691 TTTGGTATTG
1 TTTGATATTG
6619701 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.03, G:0.24, T:0.59
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:6620331 original size:14 final size:15
Alignment explanation
Indices: 6620295--6620332 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6620285 GAAATCATAG
6620295 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
6620310 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
6620325 AAAAATTA
1 AAAAATTA
6620333 GAGATAGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:6620606 original size:40 final size:41
Alignment explanation
Indices: 6620493--6620609 Score: 143
Period size: 40 Copynumber: 2.9 Consensus size: 41
6620483 TTGTGAAATT
*
6620493 AAAATTCGTGTTGCGAATTC-GAAAATCGAGTTGTGAAAAC
1 AAAATTCGTGTTGCGAATTCAGAAAATCGAGTTGCGAAAAC
* **
6620533 AAAATTCGTGTTGCG-ATTTAGAAAATCTTGTTGCGAAAA-
1 AAAATTCGTGTTGCGAATTCAGAAAATCGAGTTGCGAAAAC
* *
6620572 AGAAATTCGCGTTGCGAATTCAG-AAATAGAGTTGCGAA
1 A-AAATTCGTGTTGCGAATTCAGAAAATCGAGTTGCGAA
6620610 TTTGAAAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
39 4 0.06
40 56 0.86
41 5 0.08
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (41 bp):
AAAATTCGTGTTGCGAATTCAGAAAATCGAGTTGCGAAAAC
Found at i:6620639 original size:21 final size:20
Alignment explanation
Indices: 6620580--6620649 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
6620570 AAAGAAATTC
*
6620580 GCGTTGCGAA-TTCAGAAATA
1 GCGTTGCGAATTTGA-AAATA
*
6620600 GAGTTGCGAATTTGAAAATA
1 GCGTTGCGAATTTGAAAATA
* *
6620620 GCGTTGTGAATTTGGAAAATC
1 GCGTTGCGAATTT-GAAAATA
6620641 GCGTTGCGA
1 GCGTTGCGA
6620650 TTGCAGAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.60
21 17 0.40
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATA
Found at i:6620696 original size:61 final size:61
Alignment explanation
Indices: 6620573--6620696 Score: 137
Period size: 61 Copynumber: 2.0 Consensus size: 61
6620563 TTGCGAAAAA
* ** *
6620573 GAAATTCGCGTTGCGAATTCAGAAATAGAGTTGCGAATTTGAAAATAGCGTTGTGAATTTG
1 GAAAATCGCGTTGCGAATTCAGAAATAGAGTTGCGAATTTGAAAATAGCGTTGCAAAATTG
* * *
6620634 GAAAATCGCGTTGCG-ATTGCAGAAACT-GAGTTGTGAATTTGGAAACT-GTGTTGCAAAATTG
1 GAAAATCGCGTTGCGAATT-CAGAAA-TAGAGTTGCGAATTT-GAAAATAGCGTTGCAAAATTG
6620695 GA
1 GA
6620697 GTTCGCGTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
60 3 0.06
61 44 0.83
62 6 0.11
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.30
Consensus pattern (61 bp):
GAAAATCGCGTTGCGAATTCAGAAATAGAGTTGCGAATTTGAAAATAGCGTTGCAAAATTG
Found at i:6620801 original size:40 final size:40
Alignment explanation
Indices: 6620757--6620838 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 40
6620747 GTTAAAATCG
*
6620757 TATATTATAAGGCATTATT-GGTCACTGAAGTTATTTTCTC
1 TATATTATAAGGCATT-TTCGGCCACTGAAGTTATTTTCTC
6620797 TATATTATAAGGCATTTTCGGCCACTGAAGTTATTTTCTC
1 TATATTATAAGGCATTTTCGGCCACTGAAGTTATTTTCTC
6620837 TA
1 TA
6620839 ATATCAATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 2 0.05
40 38 0.95
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (40 bp):
TATATTATAAGGCATTTTCGGCCACTGAAGTTATTTTCTC
Found at i:6623101 original size:34 final size:33
Alignment explanation
Indices: 6623076--6623153 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 33
6623066 TCGATCTACC
6623076 AAGGAGAAAACAATGATAATTCTCTCTTGATAAA
1 AAGGAGAAAACAATGATAATTCTCTC-TGATAAA
6623110 AAGGAGAAAACAATGATAATTCTCTCTTGATAAA
1 AAGGAGAAAACAATGATAATTCTCTC-TGATAAA
6623144 AAGGAGAAAA
1 AAGGAGAAAA
6623154 TAACTCTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (33 bp):
AAGGAGAAAACAATGATAATTCTCTCTGATAAA
Found at i:6630484 original size:2 final size:2
Alignment explanation
Indices: 6630477--6630506 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6630467 GTGCAACCAA
6630477 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
6630507 CATCTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6631541 original size:2 final size:2
Alignment explanation
Indices: 6631534--6631571 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6631524 TCATATTCAC
*
6631534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6631572 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6631681 original size:25 final size:28
Alignment explanation
Indices: 6631653--6631704 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
6631643 GTGTAACAAT
6631653 TTTATTAAA-AAT-ATT-AATATCTAAA
1 TTTATTAAACAATGATTGAATATCTAAA
*
6631678 TTTATTAAACAATGATTGTATATCTAA
1 TTTATTAAACAATGATTGAATATCTAA
6631705 TTTGCTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 9 0.39
26 3 0.13
27 3 0.13
28 8 0.35
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (28 bp):
TTTATTAAACAATGATTGAATATCTAAA
Found at i:6632147 original size:2 final size:2
Alignment explanation
Indices: 6632140--6632169 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6632130 CTACTTAAGG
6632140 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6632170 CTGTGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6638746 original size:19 final size:15
Alignment explanation
Indices: 6638702--6638744 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
6638692 TTCGGTTGTA
6638702 AGAAGAAAGAAAGGG
1 AGAAGAAAGAAAGGG
6638717 AGAAGAAAGAAAGGG
1 AGAAGAAAGAAAGGG
6638732 AGAAGAAAGAAAG
1 AGAAGAAAGAAAG
6638745 AAGAAGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
AGAAGAAAGAAAGGG
Found at i:6638909 original size:10 final size:10
Alignment explanation
Indices: 6638894--6638922 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6638884 TTGTTTGTTG
6638894 AATTATATTA
1 AATTATATTA
6638904 AATTATATTA
1 AATTATATTA
6638914 AATT-TATTA
1 AATTATATTA
6638923 TATGTCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTATATTA
Found at i:6639063 original size:33 final size:33
Alignment explanation
Indices: 6639024--6639101 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
6639014 GAAGTTATAA
* * *
6639024 TATATATTAAAATTAGTTAATTAGTTTTTTATT
1 TATATATTAAAAATAGTTAATTAGTTTGTTAGT
* *
6639057 TATATATAAAAAATATTTAATTAGTTTGTTAGT
1 TATATATTAAAAATAGTTAATTAGTTTGTTAGT
*
6639090 TAAATAGTTAAA
1 TATATA-TTAAA
6639102 GTTATATTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 33 0.89
34 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (33 bp):
TATATATTAAAAATAGTTAATTAGTTTGTTAGT
Found at i:6641630 original size:18 final size:17
Alignment explanation
Indices: 6641573--6641640 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 17
6641563 TTCGAAATGG
6641573 AGTGCATGGATGCACTC
1 AGTGCATGGATGCACTC
* *
6641590 AGGGTGCATCGATG-AAT-
1 A--GTGCATGGATGCACTC
6641607 AGTGCATGGATGCACTGC
1 AGTGCATGGATGCACT-C
6641625 AGTGCATGGATGCACT
1 AGTGCATGGATGCACT
6641641 TTGACACCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
15 10 0.24
16 2 0.05
17 2 0.05
18 18 0.43
19 10 0.24
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (17 bp):
AGTGCATGGATGCACTC
Found at i:6641891 original size:21 final size:21
Alignment explanation
Indices: 6641862--6641901 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6641852 ATGTTTAATG
6641862 AAAAAGATA-CAAATTGTTAAC
1 AAAAAGATATC-AATTGTTAAC
*
6641883 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
6641902 CCAATTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:6644917 original size:20 final size:20
Alignment explanation
Indices: 6644892--6644929 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6644882 CCGTTGCAGC
*
6644892 CAGGGTACATGGATGCACAA
1 CAGGGTACATCGATGCACAA
*
6644912 CAGGGTGCATCGATGCAC
1 CAGGGTACATCGATGCAC
6644930 TAATTGCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.24, G:0.32, T:0.16
Consensus pattern (20 bp):
CAGGGTACATCGATGCACAA
Found at i:6645026 original size:20 final size:19
Alignment explanation
Indices: 6644953--6645036 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
6644943 AATGGAGTGT
6644953 ATGGATGCACT-CAGGGTGC
1 ATGGATGCACTACA-GGTGC
*
6644972 ATCGATG--C-ACA-GTGC
1 ATGGATGCACTACAGGTGC
*
6644987 ATGGATGCACTGCAGGTGC
1 ATGGATGCACTACAGGTGC
*
6645006 ATGGATGCACTATAGGGTGC
1 ATGGATGCACTACA-GGTGC
6645026 ATGGATGCACT
1 ATGGATGCACT
6645037 TTGACACCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
15 10 0.19
17 4 0.07
18 2 0.04
19 22 0.41
20 16 0.30
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (19 bp):
ATGGATGCACTACAGGTGC
Found at i:6645033 original size:39 final size:34
Alignment explanation
Indices: 6644948--6645015 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
6644938 TTCGAAATGG
*
6644948 AGTGTATGGATGCACTCAGGGTGCATCGATGCAC
1 AGTGCATGGATGCACTCAGGGTGCATCGATGCAC
*
6644982 AGTGCATGGATGCACTGCA-GGTGCATGGATGCAC
1 AGTGCATGGATGCACT-CAGGGTGCATCGATGCAC
6645016 TATAGGGTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.22
Consensus pattern (34 bp):
AGTGCATGGATGCACTCAGGGTGCATCGATGCAC
Found at i:6646378 original size:17 final size:17
Alignment explanation
Indices: 6646356--6646414 Score: 73
Period size: 17 Copynumber: 3.3 Consensus size: 17
6646346 CTAATATAAA
6646356 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
*
6646373 TTAAACAACAATAAATATTT
1 TTAAACAA-AAT--ATTTTT
*
6646393 TTAAACAAAATATTATT
1 TTAAACAAAATATTTTT
6646410 TTAAA
1 TTAAA
6646415 TGTGAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 17 0.47
18 3 0.08
19 3 0.08
20 13 0.36
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:6647412 original size:28 final size:28
Alignment explanation
Indices: 6647349--6647453 Score: 167
Period size: 28 Copynumber: 3.7 Consensus size: 28
6647339 CTTGGTCACC
* *
6647349 GGGCGTACATGGCGACCTAGCATGTCG-T
1 GGGCGTGCATGGCGACCTA-CAGGTCGCT
6647377 GGGGCGTGCATGGCGACCTACAGGTCGCT
1 -GGGCGTGCATGGCGACCTACAGGTCGCT
6647406 GGGCGTGCATGGCGACCTACAGGTCGCT
1 GGGCGTGCATGGCGACCTACAGGTCGCT
6647434 GGGCGTGCATGGCGACCTAC
1 GGGCGTGCATGGCGACCTAC
6647454 CCCTTCGTGC
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
28 54 0.74
29 19 0.26
ACGTcount: A:0.15, C:0.28, G:0.39, T:0.18
Consensus pattern (28 bp):
GGGCGTGCATGGCGACCTACAGGTCGCT
Found at i:6647725 original size:19 final size:19
Alignment explanation
Indices: 6647701--6647741 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
6647691 CATTTTAAAC
6647701 TTTTATAGAATTTAAATAT
1 TTTTATAGAATTTAAATAT
6647720 TTTTATAGAATTTAAATAT
1 TTTTATAGAATTTAAATAT
6647739 TTT
1 TTT
6647742 AAATTTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTATAGAATTTAAATAT
Found at i:6655532 original size:60 final size:60
Alignment explanation
Indices: 6655462--6655615 Score: 215
Period size: 60 Copynumber: 2.5 Consensus size: 60
6655452 TTTTGGATTG
6655462 GTCCCTAAACTTTTAAATATTTCAATTTCAT-CTCTAAACTATGA-TTATCATTCTAAATTA
1 GTCCCTAAACTTTTAAATATTTCAATTTCATCCT-TAAACTATGACTT-TCATTCTAAATTA
* *
6655522 GT-CCTCAAACTTTTAAACATTTCAATTTCATCCTTAAACTATGACTTTCATTCTAAATTG
1 GTCCCT-AAACTTTTAAATATTTCAATTTCATCCTTAAACTATGACTTTCATTCTAAATTA
* *
6655582 GTCCCTAAACTCTTTGAATATTCCAATTTCATCC
1 GTCCCTAAACT-TTTAAATATTTCAATTTCATCC
6655616 CAAATTATAC
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
59 3 0.04
60 55 0.65
61 26 0.31
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (60 bp):
GTCCCTAAACTTTTAAATATTTCAATTTCATCCTTAAACTATGACTTTCATTCTAAATTA
Found at i:6655555 original size:29 final size:29
Alignment explanation
Indices: 6655468--6655561 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
6655458 ATTGGTCCCT
*
6655468 AAACTTTTAAATATTTCAATTTCAT-CTC
1 AAACTTTTAAACATTTCAATTTCATCCTC
* *
6655496 TAAACTATGATT-ATCA-TTCTAAATT-AGTCCTC
1 -AAACT-T--TTAAACATTTC-AATTTCA-TCCTC
*
6655528 AAACTTTTAAACATTTCAATTTCATCCTT
1 AAACTTTTAAACATTTCAATTTCATCCTC
6655557 AAACT
1 AAACT
6655562 ATGACTTTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
28 2 0.04
29 21 0.42
30 10 0.20
31 12 0.24
32 5 0.10
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (29 bp):
AAACTTTTAAACATTTCAATTTCATCCTC
Found at i:6655829 original size:60 final size:60
Alignment explanation
Indices: 6655736--6655853 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
6655726 CATATTTGGT
* **
6655736 GGATGAAATTGGAATATTCAAAAGTTTGGGGACTAATATAGAAA-GAGGGTGATAGTTTAG
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATATA-AAATGAGGGTGATAGTTTAG
* * * *
6655796 GGATGAAATTAGAATGTTCAAAAGTTTAAGGACTGATTTAAAATGAGGGTTATAGTTT
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATATAAAATGAGGGTGATAGTTT
6655854 GAGAATATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 3 0.06
60 47 0.94
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.31
Consensus pattern (60 bp):
GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATATAAAATGAGGGTGATAGTTTAG
Found at i:6656524 original size:19 final size:19
Alignment explanation
Indices: 6656493--6656529 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6656483 AATTTTGTCA
6656493 AAAATATATTTTATAACAAT
1 AAAATATATTTTA-AACAAT
6656513 AAAATA-ATTTTAAACAA
1 AAAATATATTTTAAACAA
6656530 AATGATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATATATTTTAAACAAT
Found at i:6664403 original size:29 final size:29
Alignment explanation
Indices: 6664339--6664432 Score: 111
Period size: 29 Copynumber: 3.2 Consensus size: 29
6664329 TAGTTAATTT
* *
6664339 TTAAGTTGATCCTTAAACTTTAGTCTAAATA
1 TTAATTTGAT-CTTAAACTTTAGAC-AAATA
6664370 TTAATTTGATCTTAAACTTTTA-ACAAATA
1 TTAATTTGATCTTAAAC-TTTAGACAAATA
*
6664399 TTAATTTGA-CTTCTAACTTTAGACAAATA
1 TTAATTTGATCTT-AAACTTTAGACAAATA
6664428 TTAAT
1 TTAAT
6664433 ATAACCTCTA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
28 7 0.12
29 29 0.51
30 8 0.14
31 13 0.23
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (29 bp):
TTAATTTGATCTTAAACTTTAGACAAATA
Found at i:6664442 original size:29 final size:28
Alignment explanation
Indices: 6664388--6664443 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
6664378 ATCTTAAACT
* * *
6664388 TTTAACAAATATTAATTTGACTTCTAAC
1 TTTAACAAATATTAATATAACCTCTAAC
6664416 TTTAGACAAATATTAATATAACCTCTAA
1 TTTA-ACAAATATTAATATAACCTCTAA
6664444 ATATGATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (28 bp):
TTTAACAAATATTAATATAACCTCTAAC
Found at i:6666511 original size:19 final size:19
Alignment explanation
Indices: 6666473--6666542 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
6666463 ACACAAAGTC
*
6666473 AAATTCGCAATGCGGAATTTG
1 AAATTCGCAA--CCGAATTTG
*
6666494 AAATTCGCAACTGAATTTG
1 AAATTCGCAACCGAATTTG
6666513 AAATTCGCAACGCGAATTT-
1 AAATTCGCAAC-CGAATTTG
*
6666532 AATTTCGCAAC
1 AAATTCGCAAC
6666543 AGGTTTTAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 29 0.64
20 6 0.13
21 10 0.22
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AAATTCGCAACCGAATTTG
Found at i:6667316 original size:12 final size:12
Alignment explanation
Indices: 6667295--6667328 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6667285 ACCACATTTC
*
6667295 CAATACCAAACA
1 CAATATCAAACA
6667307 CAATATCAAACA
1 CAATATCAAACA
*
6667319 CAATCTCAAA
1 CAATATCAAA
6667329 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:6667481 original size:24 final size:24
Alignment explanation
Indices: 6667454--6667507 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6667444 GTATTCGAAA
6667454 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
6667478 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
6667502 TTTGAT
1 TTTGAT
6667508 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:6669786 original size:18 final size:18
Alignment explanation
Indices: 6669763--6669798 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6669753 AAGCAAAAGG
*
6669763 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
6669781 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
6669799 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:6670109 original size:20 final size:20
Alignment explanation
Indices: 6670084--6670122 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6670074 ATGTTGCAAT
*
6670084 CAACGCGAACGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
6670104 CAACGCGAAAGTCAAATTC
1 CAACGCGAAAGTCAAATTC
6670123 ACAAACCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:6670619 original size:18 final size:18
Alignment explanation
Indices: 6670598--6670634 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6670588 GTAATTGGAG
6670598 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
6670616 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
6670634 T
1 T
6670635 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:6670641 original size:24 final size:24
Alignment explanation
Indices: 6670590--6670642 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
6670580 TTTCATATGT
* * *
6670590 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
6670614 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
6670638 AATTT
1 AATTT
6670643 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:6670989 original size:39 final size:39
Alignment explanation
Indices: 6670946--6671032 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
6670936 TCCGATGCTC
6670946 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
6670985 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
6671024 ATCAAAATC
1 ATCAAAATC
6671033 TACACCTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:6671826 original size:21 final size:21
Alignment explanation
Indices: 6671802--6671904 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 21
6671792 GCGGGCGGGA
6671802 CCTCTTGAACGATGATAGGGG
1 CCTCTTGAACGATGATAGGGG
* **
6671823 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGATAGGGG
* * *
6671844 CTTCTTCG-ATGATGATAGGGC
1 CCTCTT-GAACGATGATAGGGG
* * *
6671865 CCTCTTGAACTAT-AGGAGGCG
1 CCTCTTGAACGATGA-TAGGGG
*
6671886 CCTCTTGAATGATGATAGG
1 CCTCTTGAACGATGATAGG
6671905 CGCATCGGGC
Statistics
Matches: 60, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.26
Consensus pattern (21 bp):
CCTCTTGAACGATGATAGGGG
Found at i:6671883 original size:42 final size:42
Alignment explanation
Indices: 6671802--6671904 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
6671792 GCGGGCGGGA
* * * * *
6671802 CCTCTTGAACGATGATAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGATAGGGCCCTCTTGAACGATAGGAGGCG
* *
6671844 CTTCTTCG-ATGATGATAGGGCCCTCTTGAACTATAGGAGGCG
1 CCTCTT-GAATGATGATAGGGCCCTCTTGAACGATAGGAGGCG
6671886 CCTCTTGAATGATGATAGG
1 CCTCTTGAATGATGATAGG
6671905 CGCATCGGGC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 49 0.96
43 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.26
Consensus pattern (42 bp):
CCTCTTGAATGATGATAGGGCCCTCTTGAACGATAGGAGGCG
Found at i:6672336 original size:21 final size:21
Alignment explanation
Indices: 6672308--6672357 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
6672298 ACCATTATCT
**
6672308 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAACACCGACCTCA
*
6672329 TGACGTAAAACACCGACCTCA
1 TCACGTAAAACACCGACCTCA
6672350 TCACGTAA
1 TCACGTAA
6672358 TTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.18
Consensus pattern (21 bp):
TCACGTAAAACACCGACCTCA
Found at i:6674352 original size:20 final size:21
Alignment explanation
Indices: 6674327--6674370 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
6674317 ATGAGAGATG
6674327 GAGATA-GACGGATTTCGTCA
1 GAGATAGGACGGATTTCGTCA
6674347 GAGATAGGGACGGATTTCGTCA
1 GAGATA-GGACGGATTTCGTCA
6674369 GA
1 GA
6674371 TATGGGGACG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.27
22 16 0.73
ACGTcount: A:0.30, C:0.14, G:0.34, T:0.23
Consensus pattern (21 bp):
GAGATAGGACGGATTTCGTCA
Found at i:6674361 original size:22 final size:22
Alignment explanation
Indices: 6674333--6674383 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
6674323 GATGGAGATA
6674333 GACGGATTTCGTCAGAGATAGG
1 GACGGATTTCGTCAGAGATAGG
* *
6674355 GACGGATTTCGTCAGATATGGG
1 GACGGATTTCGTCAGAGATAGG
6674377 GACGGAT
1 GACGGAT
6674384 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCAGAGATAGG
Found at i:6674536 original size:20 final size:20
Alignment explanation
Indices: 6674511--6674639 Score: 141
Period size: 20 Copynumber: 6.5 Consensus size: 20
6674501 GCGTAAAAAC
* *
6674511 ATTTGACTTTCGTGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
6674531 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
***
6674551 ATTTGACTTTTTTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
***
6674571 ATTTGACTTTTTTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
**
6674591 ATTTGACTACCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
**
6674611 ATTTGACTACCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
6674631 ATTTGACTT
1 ATTTGACTT
6674640 CTGTGTTGCG
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 96 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:6674556 original size:40 final size:40
Alignment explanation
Indices: 6674511--6674650 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
6674501 GCGTAAAAAC
*
6674511 ATTTGACTTTCGTGTTACGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTGCGA
** * ***
6674551 ATTTGACTTTTTTGTTGCGAATTTGACTTTTTTGTTGCGA
1 ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTGCGA
** * *
6674591 ATTTGACTACCGCGTTGCGAATTTGACTACCGCGTTGCGA
1 ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTGCGA
6674631 ATTTGAC-TTCTGTGTTGCGA
1 ATTTGACTTTC-GTGTTGCGA
6674651 TTTACAGATT
Statistics
Matches: 79, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 1 0.01
40 78 0.99
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (40 bp):
ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:6674592 original size:60 final size:60
Alignment explanation
Indices: 6674511--6674650 Score: 190
Period size: 60 Copynumber: 2.3 Consensus size: 60
6674501 GCGTAAAAAC
* * * *****
6674511 ATTTGACTTTCGTGTTACGAATTTGACTATCGCGTTGCGAATTTGACTTTTTTGTTGCGA
1 ATTTGACTTTTGTGTTGCGAATTTGACTACCGCGTTGCGAATTTGACTACCGCGTTGCGA
*
6674571 ATTTGACTTTTTTGTTGCGAATTTGACTACCGCGTTGCGAATTTGACTACCGCGTTGCGA
1 ATTTGACTTTTGTGTTGCGAATTTGACTACCGCGTTGCGAATTTGACTACCGCGTTGCGA
*
6674631 ATTTGACTTCTGTGTTGCGA
1 ATTTGACTTTTGTGTTGCGA
6674651 TTTACAGATT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (60 bp):
ATTTGACTTTTGTGTTGCGAATTTGACTACCGCGTTGCGAATTTGACTACCGCGTTGCGA
Found at i:6687892 original size:42 final size:42
Alignment explanation
Indices: 6687845--6687945 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
6687835 CAAACATAAT
* * *
6687845 TCTTTATTCATATTTGAGTAGCTTAATTTGAAAATGTAGGTA
1 TCTTTATTCATATTTGAGTAGCTTAATCTGAAAAGGTAAGTA
* * *
6687887 TCTTTATTCATATTTGAGTAGTTTTATCTGTAAAGGTAAGTA
1 TCTTTATTCATATTTGAGTAGCTTAATCTGAAAAGGTAAGTA
6687929 TCTTTATTCATATTTGA
1 TCTTTATTCATATTTGA
6687946 AAATATATCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.49
Consensus pattern (42 bp):
TCTTTATTCATATTTGAGTAGCTTAATCTGAAAAGGTAAGTA
Found at i:6690472 original size:29 final size:29
Alignment explanation
Indices: 6690430--6690493 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
6690420 TCAATTGAAC
* *
6690430 CATTCAGTGCTGAACACTAAATCGTTCAA
1 CATTCAGCGCTGAACACTAAACCGTTCAA
* * *
6690459 CATTCAGCGCTGAACGCTGAACCGTTCAG
1 CATTCAGCGCTGAACACTAAACCGTTCAA
6690488 CATTCA
1 CATTCA
6690494 ACGCGTTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (29 bp):
CATTCAGCGCTGAACACTAAACCGTTCAA
Found at i:6690533 original size:15 final size:15
Alignment explanation
Indices: 6690513--6690555 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
6690503 TTTCGTACCT
6690513 CTGACTGATTCAGTG
1 CTGACTGATTCAGTG
6690528 CTGACTGATTCAGTG
1 CTGACTGATTCAGTG
*
6690543 CTGATTGATTCAG
1 CTGACTGATTCAG
6690556 CAAAACAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (15 bp):
CTGACTGATTCAGTG
Found at i:6702532 original size:15 final size:16
Alignment explanation
Indices: 6702512--6702551 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
6702502 AGTAATTTTT
6702512 AAATATTTATTA-TAA
1 AAATATTTATTATTAA
* *
6702527 AAATATTAATTATTTA
1 AAATATTTATTATTAA
6702543 AAATATTTA
1 AAATATTTA
6702552 AAACAATCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTTATTATTAA
Found at i:6704163 original size:20 final size:20
Alignment explanation
Indices: 6704138--6704176 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6704128 TATTTATTAT
6704138 TTAATTTTATATATCTAAAA
1 TTAATTTTATATATCTAAAA
*
6704158 TTAATTTTATATTTCTAAA
1 TTAATTTTATATATCTAAA
6704177 TTTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTTTATATATCTAAAA
Found at i:6709181 original size:20 final size:20
Alignment explanation
Indices: 6709156--6709220 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
6709146 AAATCTGAAA
* *
6709156 AAAAATTTGGTTTGAGGTTT
1 AAAAATTCGGTTTGGGGTTT
* *
6709176 AAAAATCCGGTCTGGGGTTT
1 AAAAATTCGGTTTGGGGTTT
6709196 AAAAATTCGGTTTGGGGTTT
1 AAAAATTCGGTTTGGGGTTT
6709216 AAAAA
1 AAAAA
6709221 ATTGGATGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (20 bp):
AAAAATTCGGTTTGGGGTTT
Found at i:6709563 original size:43 final size:43
Alignment explanation
Indices: 6709502--6709589 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
6709492 TCGTAAACTT
6709502 TTTAGCTTCCATCACATTGGATCTGTTAATATTTCATTACTGA
1 TTTAGCTTCCATCACATTGGATCTGTTAATATTTCATTACTGA
*
6709545 TTTAGCTTCCATCACATTGGATCTGTTAATATTTCATTAGTGA
1 TTTAGCTTCCATCACATTGGATCTGTTAATATTTCATTACTGA
6709588 TT
1 TT
6709590 GATCTCTACG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (43 bp):
TTTAGCTTCCATCACATTGGATCTGTTAATATTTCATTACTGA
Found at i:6715949 original size:17 final size:17
Alignment explanation
Indices: 6715927--6715960 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6715917 TTTTCTTTTA
*
6715927 ATTTAATTAATTAAATT
1 ATTTAACTAATTAAATT
*
6715944 ATTTAACTATTTAAATT
1 ATTTAACTAATTAAATT
6715961 GTGTCAATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAACTAATTAAATT
Found at i:6718330 original size:12 final size:12
Alignment explanation
Indices: 6718313--6718339 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6718303 AGATTATTTT
6718313 TTTAAAATGTAA
1 TTTAAAATGTAA
6718325 TTTAAAATGTAA
1 TTTAAAATGTAA
6718337 TTT
1 TTT
6718340 CTAGTATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTAAAATGTAA
Found at i:6731925 original size:2 final size:2
Alignment explanation
Indices: 6731913--6731955 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
6731903 TGCAGCCTGT
6731913 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6731953 TA T
1 TA T
6731956 GGCCGGCAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6734788 original size:5 final size:5
Alignment explanation
Indices: 6734778--6734823 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
6734768 AAAACCGATA
* *
6734778 AACCG AACCG AACCG AATCG AA--A AACCCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA-CCG AACCG AACCG AACCG AA
6734824 TACACCCCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
3 2 0.06
5 31 0.89
6 2 0.06
ACGTcount: A:0.46, C:0.35, G:0.17, T:0.02
Consensus pattern (5 bp):
AACCG
Found at i:6738706 original size:7 final size:7
Alignment explanation
Indices: 6738694--6738743 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
6738684 CAGCAATAGA
6738694 CAACAGG
1 CAACAGG
6738701 CAACAGG
1 CAACAGG
6738708 CAACAGG
1 CAACAGG
6738715 CAACAGG
1 CAACAGG
6738722 CAACAGG
1 CAACAGG
6738729 CAACAGG
1 CAACAGG
6738736 CAACAGG
1 CAACAGG
6738743 C
1 C
6738744 CAAAGTTTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.42, C:0.30, G:0.28, T:0.00
Consensus pattern (7 bp):
CAACAGG
Found at i:6742619 original size:18 final size:18
Alignment explanation
Indices: 6742587--6742621 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6742577 ACTGAATATT
* *
6742587 TGTCCCGATGGACCACTA
1 TGTCCCGAAGAACCACTA
6742605 TGTCCCGAAGAACCACT
1 TGTCCCGAAGAACCACT
6742622 GATAATCCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:6744534 original size:22 final size:21
Alignment explanation
Indices: 6744490--6744530 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6744480 TTTACCTCGA
6744490 TTATTCCCTAAATTTTAGGGT
1 TTATTCCCTAAATTTTAGGGT
6744511 TTATATCCCT-AATTTTAGGG
1 TTAT-TCCCTAAATTTTAGGG
6744531 GTTTTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (21 bp):
TTATTCCCTAAATTTTAGGGT
Done.