Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008606.1 Hibiscus syriacus cultivar Beakdansim tig00111562_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: 365242
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 1 of 2
Found at i:2829 original size:3 final size:3
Alignment explanation
Indices: 2821--2848 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2811 CAGAAAACAA
2821 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
2849 CTCAAGGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:20473 original size:472 final size:471
Alignment explanation
Indices: 19394--20775 Score: 2054
Period size: 472 Copynumber: 2.9 Consensus size: 471
19384 TGGTAGAACT
* * * * * * *
19394 TATACGGTGGGAGACGCCAGCGGTTGGCGTGTCCCGACAGGAAATGATGATTTGTATGATGATTG
1 TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAATAATGATTTTTATGATGATTG
* **
19459 GAACGACAACAAGGATTTCTTTGTTGGGGATGTTCTATGTGAGTCGCTTAGCTCAAAATCTAA-C
66 GAACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTAGCTCAAAATCTAACC
* * * * * * * ** **
19523 -A---TGAATTTGATCATTAG-AGTACGCATGTATTTACTATTTATTGTCTACTGGTGCGTGTTT
131 TATTCTTAATTGGATCATTGGTAGTA--CATATA-TGA--ATGT-TGGT-T--T--TGTATGTGA
19583 TTTGCAGTGTTCAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGA
185 TTT-CAGTGTTCAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGA
* * *
19648 CAACTGCAACGCTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGGATTACCCTCGACA
249 CAACTGCAACGCTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACA
* * * * *
19713 GGACTGGTGATCACTACTTCATTTGCGGTTTCCCCGGTCATTGTGCCGCCGGCCAAAAGCTCAAT
314 GGACCGGTGACCACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCCGGCCAAAAGCTGAGT
* * * * * * ** * * * *
19778 GTTGAAG-TCAGAAATGGCAACCGCAAC-GGCACTGCT--C-CTACT-CC--TAGACCAAGTCCC
379 ATCGATGTTGA-AAACGGCAACCGC-CCTGGCACCACTCCCACAACTCCCGGAACACCAAGCCCC
*
19835 ACCACGCCTGCAACCCCAAGCGGTATGACC
442 ACCACGCCAGCAACCCCAAGCGGTATGACC
19865 TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAATAATGATTTTTATGATGATTG
1 TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAATAATGATTTTTATGATGATTG
*
19930 GAACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTGGCTCAAAATCTAACC
66 GAACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTAGCTCAAAATCTAACC
19995 TATTCTTAATTGGATCATTGGGTAGTACATATATGAATGTTGGTTTTGTATGTGATTTCAGTGTT
131 TATTCTTAATTGGATCATT-GGTAGTACATATATGAATGTTGGTTTTGTATGTGATTTCAGTGTT
20060 CAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACG
195 CAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACG
20125 CTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGAC
260 CTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGAC
*
20190 CACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCAGGCCAAAAGCTGAGTATCGATGTTGA
325 CACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCCGGCCAAAAGCTGAGTATCGATGTTGA
20255 AAACGGCAACCGCCCTGGCACCACTCCCACAACTCCCGGAACACCAAGCCCCACCACGCCAGCAA
390 AAACGGCAACCGCCCTGGCACCACTCCCACAACTCCCGGAACACCAAGCCCCACCACGCCAGCAA
20320 CCCCAAGCGGTATGACC
455 CCCCAAGCGGTATGACC
* *
20337 TATACGGTGGGAGACTCCACCGGTTGGCGAGTACCTACCGGAAATAATGATTTTTACGATGATTG
1 TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAATAATGATTTTTATGATGATTG
* *
20402 GAACGACAACAAGGATTTCTATGTTGGCGATGTTCTCTGTGAGTATCTTAGCTCAAAATCTAACC
66 GAACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTAGCTCAAAATCTAACC
*
20467 TATTCTTAATTGGATCATTAGGTAGTACATATATGAATGTTGGTTTTGTATATGATTTCAGTGTT
131 TATTCTTAATTGGATCATT-GGTAGTACATATATGAATGTTGGTTTTGTATGTGATTTCAGTGTT
20532 CAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACG
195 CAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACG
*
20597 TTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGAC
260 CTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGAC
*
20662 CACTACTTCATTTGCGGTTTCCCGGGTCATTGTACCGCCGGCCAAAAGCTGAGTATCGATGTTGA
325 CACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCCGGCCAAAAGCTGAGTATCGATGTTGA
*
20727 AAACGGCAACCGCCCTGGCACCACTCCCACAACACCCGGAACACCAAGC
390 AAACGGCAACCGCCCTGGCACCACTCCCACAACTCCCGGAACACCAAGC
20776 GCCTCCGCAC
Statistics
Matches: 841, Mismatches: 55, Indels: 29
0.91 0.06 0.03
Matches are distributed among these distances:
465 1 0.00
466 205 0.24
467 10 0.01
468 1 0.00
469 5 0.01
470 2 0.00
471 118 0.14
472 471 0.56
473 4 0.00
475 2 0.00
476 17 0.02
477 1 0.00
478 4 0.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (471 bp):
TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAATAATGATTTTTATGATGATTG
GAACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTAGCTCAAAATCTAACC
TATTCTTAATTGGATCATTGGTAGTACATATATGAATGTTGGTTTTGTATGTGATTTCAGTGTTC
AACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACGC
TGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGACC
ACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCCGGCCAAAAGCTGAGTATCGATGTTGAA
AACGGCAACCGCCCTGGCACCACTCCCACAACTCCCGGAACACCAAGCCCCACCACGCCAGCAAC
CCCAAGCGGTATGACC
Found at i:22063 original size:42 final size:42
Alignment explanation
Indices: 22016--22095 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
22006 GATGAATTGT
22016 CACGTTAATACTATGGATAACCATATCAATATCGTGAACTGA
1 CACGTTAATACTATGGATAACCATATCAATATCGTGAACTGA
22058 CACGTTAATACTATGGATAACCATATCAATATCGTGAA
1 CACGTTAATACTATGGATAACCATATCAATATCGTGAA
22096 TTGATACATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (42 bp):
CACGTTAATACTATGGATAACCATATCAATATCGTGAACTGA
Found at i:27011 original size:21 final size:20
Alignment explanation
Indices: 26960--27013 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
26950 TCATCGTTTG
*
26960 CTATTACAGTGCTGAAGTGA
1 CTATTACGGTGCTGAAGTGA
26980 CTATTACGGTGCTGAAGTGA
1 CTATTACGGTGCTGAAGTGA
27000 -TAATTCACGGTGCT
1 CT-ATT-ACGGTGCT
27014 AACGTGGTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 22 0.71
21 8 0.26
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (20 bp):
CTATTACGGTGCTGAAGTGA
Found at i:27939 original size:18 final size:17
Alignment explanation
Indices: 27914--27950 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
27904 ATAACAACTT
27914 TTTATATAATAATTAAA
1 TTTATATAATAATTAAA
*
27931 TTTATTATAATACTTAAA
1 TTTA-TATAATAATTAAA
27949 TT
1 TT
27951 GTTGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTATATAATAATTAAA
Found at i:31122 original size:7 final size:7
Alignment explanation
Indices: 31110--31140 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
31100 CCACTGTCTG
31110 TCACTGT
1 TCACTGT
31117 TCACTGT
1 TCACTGT
31124 TCACTGT
1 TCACTGT
*
31131 TCACTAT
1 TCACTGT
31138 TCA
1 TCA
31141 TATCATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (7 bp):
TCACTGT
Found at i:38668 original size:25 final size:25
Alignment explanation
Indices: 38634--38685 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
38624 AAGTCCCTAT
38634 TATCATTAACGGGGACGGAGCTGTA
1 TATCATTAACGGGGACGGAGCTGTA
* *
38659 TATCGTTAACGGGGACGGATCTGTA
1 TATCATTAACGGGGACGGAGCTGTA
38684 TA
1 TA
38686 GGGGTGCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (25 bp):
TATCATTAACGGGGACGGAGCTGTA
Found at i:50241 original size:6 final size:6
Alignment explanation
Indices: 50230--50259 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
50220 CTGGGTTTTC
50230 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
50260 GTGTTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTCAT
Found at i:51583 original size:32 final size:31
Alignment explanation
Indices: 51547--51623 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
51537 CGGGGCCGTG
*
51547 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
51579 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
51610 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
51624 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:51606 original size:63 final size:63
Alignment explanation
Indices: 51500--51623 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
51490 CCCTAAGGGA
* * ** *
51500 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
51563 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
51624 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:52503 original size:7 final size:7
Alignment explanation
Indices: 52491--52521 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
52481 GTCAAAGAAA
52491 GTCAACG
1 GTCAACG
52498 GTCAACG
1 GTCAACG
52505 GTCAACG
1 GTCAACG
52512 GTCAACG
1 GTCAACG
52519 GTC
1 GTC
52522 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:52528 original size:5 final size:5
Alignment explanation
Indices: 52518--52558 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
52508 AACGGTCAAC
*
52518 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
52559 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:52539 original size:22 final size:22
Alignment explanation
Indices: 52511--52559 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
52501 AACGGTCAAC
52511 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
52533 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
52555 GGTCA
1 GGTCA
52560 GACCGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:52573 original size:9 final size:9
Alignment explanation
Indices: 52555--52653 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
52545 GGTCGGGTCG
*
52555 GGTCAGACC
1 GGTCAAACC
52564 GGTCAAACC
1 GGTCAAACC
* *
52573 GATTCAGACC
1 G-GTCAAACC
52583 GGTCAAACC
1 GGTCAAACC
*
52592 GGTTCGAACC
1 GG-TCAAACC
*
52602 GGTTGAAACC
1 GG-TCAAACC
52612 GGTCAAACC
1 GGTCAAACC
52621 GGTCAGAACC
1 GGTCA-AACC
*
52631 GGTTGAAAACC
1 GG-T-CAAACC
52642 GGTCAAACC
1 GGTCAAACC
52651 GGT
1 GGT
52654 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:52579 original size:19 final size:19
Alignment explanation
Indices: 52557--52654 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
52547 TCGGGTCGGG
*
52557 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
52576 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
52595 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
52614 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
52634 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
52654 T
1 T
52655 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:52612 original size:29 final size:31
Alignment explanation
Indices: 52580--52654 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
52570 ACCGATTCAG
52580 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
52609 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
52639 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
52655 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:58910 original size:32 final size:31
Alignment explanation
Indices: 58874--58950 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
58864 CGGGGCCGTG
*
58874 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
58906 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
58937 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
58951 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:58933 original size:63 final size:63
Alignment explanation
Indices: 58827--58950 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
58817 CCCTAAGGGA
* * ** *
58827 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
58890 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
58951 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:59861 original size:17 final size:17
Alignment explanation
Indices: 59839--59878 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
59829 AACGGTCAAC
59839 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
59856 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
59873 GGTCAA
1 GGTCAA
59879 ACCGATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:59866 original size:7 final size:7
Alignment explanation
Indices: 59819--59849 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
59809 GTCAAAGAAA
59819 GTCAACG
1 GTCAACG
59826 GTCAACG
1 GTCAACG
59833 GTCAACG
1 GTCAACG
59840 GTCAACG
1 GTCAACG
59847 GTC
1 GTC
59850 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:59911 original size:9 final size:9
Alignment explanation
Indices: 59873--59962 Score: 72
Period size: 10 Copynumber: 9.3 Consensus size: 9
59863 GGTCGGGTCG
59873 GGTCAAACC
1 GGTCAAACC
*
59882 GATCAAACC
1 GGTCAAACC
* *
59891 GATTCAGACC
1 G-GTCAAACC
59901 GGTCAAACC
1 GGTCAAACC
*
59910 GGTTCGAACC
1 GG-TCAAACC
*
59920 GGTTGAAACC
1 GG-TCAAACC
59930 GGTCAGAACC
1 GGTCA-AACC
*
59940 GGTTGAAAACC
1 GG-T-CAAACC
59951 GGTCAAACC
1 GGTCAAACC
59960 GGT
1 GGT
59963 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
9 27 0.42
10 30 0.46
11 7 0.11
12 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:59920 original size:19 final size:19
Alignment explanation
Indices: 59878--59942 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
59868 GGTCGGGTCA
* *
59878 AACCGATCAAACCGATTC-
1 AACCGGTCAAACCGGTTCG
59896 AGACCGGTCAAACCGGTTCG
1 A-ACCGGTCAAACCGGTTCG
*
59916 AACCGGTTGAAACCGG-TCAG
1 AACCGG-TCAAACCGGTTC-G
59936 AACCGGT
1 AACCGGT
59943 TGAAAACCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 23 0.57
20 16 0.40
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (19 bp):
AACCGGTCAAACCGGTTCG
Found at i:59930 original size:20 final size:20
Alignment explanation
Indices: 59905--59963 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
59895 CAGACCGGTC
59905 AAACCGGTTCGAACCGGTTG-
1 AAACCGG-TCGAACCGGTTGA
59925 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTC-GAACCGGTTGA
*
59946 AAACCGGTCAAACCGGTT
1 AAACCGGTCGAACCGGTT
59964 TCCAGCAGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 2 0.06
20 25 0.69
21 9 0.25
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (20 bp):
AAACCGGTCGAACCGGTTGA
Found at i:68493 original size:12 final size:12
Alignment explanation
Indices: 68478--68509 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
68468 GATTTTGTCC
68478 TTTCATCATTAA
1 TTTCATCATTAA
68490 TTTCATCATTAA
1 TTTCATCATTAA
68502 TTTCATCA
1 TTTCATCA
68510 GATCTGCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTCATCATTAA
Found at i:80807 original size:21 final size:21
Alignment explanation
Indices: 80783--80828 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
80773 TAATCACATG
80783 TTAAGATTTTACTTAATTCCT
1 TTAAGATTTTACTTAATTCCT
*
80804 TTAAGATTTTACTTAATTTCT
1 TTAAGATTTTACTTAATTCCT
80825 TTAA
1 TTAA
80829 TAGATCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.54
Consensus pattern (21 bp):
TTAAGATTTTACTTAATTCCT
Found at i:86938 original size:7 final size:7
Alignment explanation
Indices: 86928--86953 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
86918 ATTTAAAATT
86928 ATTTTAG
1 ATTTTAG
86935 ATTTTAG
1 ATTTTAG
86942 ATTTTAG
1 ATTTTAG
86949 ATTTT
1 ATTTT
86954 TTAATGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
ATTTTAG
Found at i:87868 original size:23 final size:23
Alignment explanation
Indices: 87841--87895 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
87831 TGAATAATTA
* **
87841 TGTTTTTGTGACATGTTTATCTC
1 TGTTTTTGTGAAACATTTATCTC
87864 TGTTTTTGTGAAACATTTATCTC
1 TGTTTTTGTGAAACATTTATCTC
87887 TGTCTTTTG
1 TGT-TTTTG
87896 GCACTTTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.15, C:0.13, G:0.16, T:0.56
Consensus pattern (23 bp):
TGTTTTTGTGAAACATTTATCTC
Found at i:93667 original size:2 final size:2
Alignment explanation
Indices: 93660--93688 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
93650 ATAACGACTT
93660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93689 TATTAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94524 original size:31 final size:34
Alignment explanation
Indices: 94478--94542 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 34
94468 TAAATTTTAA
94478 AAAAGTTAAGAGTTTAAATACTAAA-ATA-GATT
1 AAAAGTTAAGAGTTTAAATACTAAATATATGATT
* **
94510 AAAAG-TAATAGTTTAGGTACTAAATATATGATT
1 AAAAGTTAAGAGTTTAAATACTAAATATATGATT
94543 TATTCGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 16 0.57
32 8 0.29
33 4 0.14
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (34 bp):
AAAAGTTAAGAGTTTAAATACTAAATATATGATT
Found at i:102445 original size:19 final size:19
Alignment explanation
Indices: 102421--102461 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
102411 CACAACCACT
102421 GCATCAAATCAATCACCCA
1 GCATCAAATCAATCACCCA
102440 GCATCAAATCAATCACCCA
1 GCATCAAATCAATCACCCA
102459 GCA
1 GCA
102462 AGAATAAACT
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:0.41, C:0.37, G:0.07, T:0.15
Consensus pattern (19 bp):
GCATCAAATCAATCACCCA
Found at i:109841 original size:30 final size:31
Alignment explanation
Indices: 109783--109842 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
109773 TGATCTTAAA
*
109783 AAAATTAAAAGTTCAGATACTAAAACATATC
1 AAAATTAAAAGTTAAGATACTAAAACATATC
*
109814 AAAATTAATAGTTTAAG-TACT-AAACATAT
1 AAAATTAAAAG-TTAAGATACTAAAACATAT
109843 AAATTACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 14 0.54
32 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (31 bp):
AAAATTAAAAGTTAAGATACTAAAACATATC
Found at i:115082 original size:13 final size:13
Alignment explanation
Indices: 115064--115092 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
115054 AATCCATATT
115064 GTTTCTTCTACAG
1 GTTTCTTCTACAG
115077 GTTTCTTCTACAG
1 GTTTCTTCTACAG
115090 GTT
1 GTT
115093 CAGACTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (13 bp):
GTTTCTTCTACAG
Found at i:125607 original size:121 final size:121
Alignment explanation
Indices: 125393--125629 Score: 438
Period size: 121 Copynumber: 2.0 Consensus size: 121
125383 TGCAAAAGGT
* *
125393 AAGAAGCCAATGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTCACAACTTTATTTA
1 AAGAAGCCAAAGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTAACAACTTTATTTA
*
125458 TTCTTGTTTCCTTAGTTAATGAACAAGATGGACTGTAGAGGCTAGTTAGCTAATGG
66 TGCTTGTTTCCTTAGTTAATGAACAAGATGGACTGTAGAGGCTAGTTAGCTAATGG
125514 AAGAAGCCAAAGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTAACAACTTTATTTA
1 AAGAAGCCAAAGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTAACAACTTTATTTA
*
125579 TGCTTGTTTCCTTAGTTAATGAACAAGATGGATTGTAGAGGCTAGTTAGCT
66 TGCTTGTTTCCTTAGTTAATGAACAAGATGGACTGTAGAGGCTAGTTAGCT
125630 GGTGCAGCAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 112 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (121 bp):
AAGAAGCCAAAGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTAACAACTTTATTTA
TGCTTGTTTCCTTAGTTAATGAACAAGATGGACTGTAGAGGCTAGTTAGCTAATGG
Found at i:129607 original size:3 final size:3
Alignment explanation
Indices: 129599--129642 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
129589 TTTTTATCTT
129599 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
129643 TTCATCTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:131367 original size:682 final size:682
Alignment explanation
Indices: 130023--131371 Score: 2405
Period size: 682 Copynumber: 2.0 Consensus size: 682
130013 TATCATTTTG
* * * **
130023 AGACGAGTTTAAATAAAAGTATATTATTTAAACGAATTCGTCACATTAAAGTGATGAGTTTATTA
1 AGACGAGTTTAAATAAAAATATATTATTTAAAC-AATTCATCACATTAAAGTAACAAGTTTATTA
* *
130088 AATACTGTAGTAAATTCCATAGATCTCAAATTAAAAGTAATCCTAATTTTTTTTTCTAAGTGCGG
65 AATACTATAGCAAATTCCATAGATCTCAAATTAAAAGTAATCCTAATTTTTTTTTCTAAGTGCGG
130153 TATTGGGCAATTTCGCCCAGAGCCAAAGCATTATTGAAGCATGGTTTTCCTAATTGTTGTACTCA
130 TATTGGGCAATTTCGCCCAGAGCCAAAGCATTATTGAAGCATGGTTTTCCTAATTGTTGTACTCA
*
130218 GAACAGGGATGACAAAGAAATATTTATCTAATGGGATTTTTATCAATTTGGTACGTATCTAAATA
195 GAACAGGGATGACAAAGAAATATTTATCTAATGGGATCTTTATCAATTTGGTACGTATCTAAATA
*
130283 TTCAGTTTTAGTCTGTTTTAGTGTCTAAACTTTCTATTTATTAAATTTGACGTTAAATTTTGAAC
260 TTCAGTTTTAGTCTGTTTTAGTGTCTAAACTTTCTATTTATTAAATTTGACATTAAATTTTGAAC
130348 ATGAATACTAAAATGAAACAAAAATTAAACTTTAGGTATGATTTAAAAATATTGCAAGTTTAGAT
325 ATGAATACTAAAATGAAACAAAAATTAAACTTTAGGTATGATTTAAAAATATTGCAAGTTTAGAT
130413 ATTAAAATGAATCAAAACTAATAATTTAAGTACTAAACATGTAATTTACTCTAAAATTTAAATTT
390 ATTAAAATGAATCAAAACTAATAATTTAAGTACTAAACATGTAATTTACTCTAAAATTTAAATTT
130478 TAAACCGATTTTAGGGAGAATTTGCTTTGTCTTATTTTAAGATAATTACAAAAATATCTTTCAAG
455 TAAACCGATTTTAGGGAGAATTTGCTTTGTCTTATTTTAAGATAATTACAAAAATATCTTTCAAG
* *
130543 TATTTGTGTATTATTATTTGGTTTTGACAAAGTATATAAAAAATAGTATTTTTCAAATTTAATAT
520 TATTTGTATATTATTATTTGGTTTTGACAAAGTATATAAAAAATAGTATATTTCAAATTTAATAT
* * * *
130608 TGGAATAAAAATGGATTTGACATCGCCACGCCTAATCAATATTACGCTTATTTGTTATCATGTTG
585 TGGAATAAAAATGGATTTGACATCGCCACGCCTAATCAAGATGACACTTATTTGTTATCATATTG
130673 ATATTCTTTGTTTTGGGTTCTCGGATTAATTTC
650 ATATTCTTTGTTTTGGGTTCTCGGATTAATTTC
* *
130706 AGACGAGTTTAAATAAAAATATATTATTTGAA-AATTCATCACATTGAAGTAACAAGTTTATTAA
1 AGACGAGTTTAAATAAAAATATATTATTTAAACAATTCATCACATTAAAGTAACAAGTTTATTAA
* *
130770 ATACTATAGCAAATTCCGTAGATCTTAAATTAAAAGTAATCCTAATTTTTTTTTTCTAAGTGCGG
66 ATACTATAGCAAATTCCATAGATCTCAAATTAAAAGTAATCCTAA-TTTTTTTTTCTAAGTGCGG
130835 TATTGGGCAATTTCGCCCAGAGCCAAAGCATTATTGAAGCATGGTTTTCCTAATTGTTGTACTCA
130 TATTGGGCAATTTCGCCCAGAGCCAAAGCATTATTGAAGCATGGTTTTCCTAATTGTTGTACTCA
*
130900 GAACAGGGATGGCAAAGAAATATTTATCTAATGGGATCTTTATCAATTTGGTACGTATCTAAATA
195 GAACAGGGATGACAAAGAAATATTTATCTAATGGGATCTTTATCAATTTGGTACGTATCTAAATA
*
130965 TTCAGTTTTAGTCTGTTTTAGTGTCTAATCTTTCTATTTATTAAATTTGACATTAAATTTTGAAC
260 TTCAGTTTTAGTCTGTTTTAGTGTCTAAACTTTCTATTTATTAAATTTGACATTAAATTTTGAAC
*
131030 ATGAATACTAAAATGAAATAAAAATTAAACTTTAGGTATGATTTAAAAATATTGCAAGTTTAGAT
325 ATGAATACTAAAATGAAACAAAAATTAAACTTTAGGTATGATTTAAAAATATTGCAAGTTTAGAT
* *
131095 ATTAAAATGGATTAAAACTAA-AATTTAAGTACTAAACATGTAATTTACTCTAAAATTTAAATTT
390 ATTAAAATGAATCAAAACTAATAATTTAAGTACTAAACATGTAATTTACTCTAAAATTTAAATTT
131159 TAAACCGATTTTAGGGAGAATTTGCTTTGTCTTATTTTAAGATAATTACAAAAATATCTTTCAAA
455 TAAACCGATTTTAGGGAGAATTTGCTTTGTCTTATTTTAAGATAATTACAAAAATATCTTTC-AA
131224 GTATTTGTATATTATTATTTGGTTTTGACAAAGTATATAAAAAATAGTATATTTCAAATTTAATA
519 GTATTTGTATATTATTATTTGGTTTTGACAAAGTATATAAAAAATAGTATATTTCAAATTTAATA
* * *
131289 TTGGAATAAAAATGGATTTGATATCGTCACGCCTGATCAAGATGACACTTATTTGTTATCATATT
584 TTGGAATAAAAATGGATTTGACATCGCCACGCCTAATCAAGATGACACTTATTTGTTATCATATT
*
131354 GATTTTCTTTGTTTTGGG
649 GATATTCTTTGTTTTGGG
131372 CCCTCAGATC
Statistics
Matches: 636, Mismatches: 28, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
681 173 0.27
682 433 0.68
683 30 0.05
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (682 bp):
AGACGAGTTTAAATAAAAATATATTATTTAAACAATTCATCACATTAAAGTAACAAGTTTATTAA
ATACTATAGCAAATTCCATAGATCTCAAATTAAAAGTAATCCTAATTTTTTTTTCTAAGTGCGGT
ATTGGGCAATTTCGCCCAGAGCCAAAGCATTATTGAAGCATGGTTTTCCTAATTGTTGTACTCAG
AACAGGGATGACAAAGAAATATTTATCTAATGGGATCTTTATCAATTTGGTACGTATCTAAATAT
TCAGTTTTAGTCTGTTTTAGTGTCTAAACTTTCTATTTATTAAATTTGACATTAAATTTTGAACA
TGAATACTAAAATGAAACAAAAATTAAACTTTAGGTATGATTTAAAAATATTGCAAGTTTAGATA
TTAAAATGAATCAAAACTAATAATTTAAGTACTAAACATGTAATTTACTCTAAAATTTAAATTTT
AAACCGATTTTAGGGAGAATTTGCTTTGTCTTATTTTAAGATAATTACAAAAATATCTTTCAAGT
ATTTGTATATTATTATTTGGTTTTGACAAAGTATATAAAAAATAGTATATTTCAAATTTAATATT
GGAATAAAAATGGATTTGACATCGCCACGCCTAATCAAGATGACACTTATTTGTTATCATATTGA
TATTCTTTGTTTTGGGTTCTCGGATTAATTTC
Found at i:132114 original size:27 final size:28
Alignment explanation
Indices: 132080--132144 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 28
132070 AATTATTATA
132080 TATTTTATATATTTTTTATT-AAAATTT
1 TATTTTATATATTTTTTATTAAAAATTT
132107 TATTTTATTTATATATTTTTTATTAAAAATTT
1 TA---T-TTTATATATTTTTTATTAAAAATTT
132139 TATTTT
1 TATTTT
132145 CATCTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
27 2 0.06
28 3 0.09
29 1 0.03
30 1 0.03
31 17 0.52
32 9 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
TATTTTATATATTTTTTATTAAAAATTT
Found at i:132118 original size:31 final size:32
Alignment explanation
Indices: 132066--132144 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
132056 TATTGAAAAT
*
132066 TTAAAATTATTA-TATATTTTATATATTTTTTA
1 TTAAAATT-TTATTTTATTTTATATATTTTTTA
132098 TTAAAATTTTATTTTA-TTTATATATTTTTTA
1 TTAAAATTTTATTTTATTTTATATATTTTTTA
132129 TTAAAAATTTTATTTT
1 TT-AAAATTTTATTTT
132145 CATCTTTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 20 0.45
32 24 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
TTAAAATTTTATTTTATTTTATATATTTTTTA
Found at i:141834 original size:74 final size:75
Alignment explanation
Indices: 141749--141897 Score: 196
Period size: 75 Copynumber: 2.0 Consensus size: 75
141739 GGCAAGCATA
* * * *
141749 AATAAAATTTTAGGTTGAAAC-T-ATCAATAAAATGAGTCATTAATCGAAGAAAATT-GAGATTT
1 AATAAAATTTTAGGAT-AAACATCATCAATAAAATAAATCATTAATCAAAGAAAATTCGA-ATTT
*
141811 CAGGGTGGACAC
64 CAGGATGGACAC
* *
141823 AATAAAATTTTAGGATATACATCATCAATAAAATAAATGATTAATCAAAGAAAATTCGAATTTCA
1 AATAAAATTTTAGGATAAACATCATCAATAAAATAAATCATTAATCAAAGAAAATTCGAATTTCA
141888 GGATGGACAC
66 GGATGGACAC
141898 GTGTTTACGC
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
73 3 0.05
74 16 0.25
75 44 0.68
76 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (75 bp):
AATAAAATTTTAGGATAAACATCATCAATAAAATAAATCATTAATCAAAGAAAATTCGAATTTCA
GGATGGACAC
Found at i:143638 original size:20 final size:20
Alignment explanation
Indices: 143544--143932 Score: 498
Period size: 20 Copynumber: 19.4 Consensus size: 20
143534 GATTTTCCAT
* ** *
143544 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
143564 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
143584 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
143604 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
143624 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
143644 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
143664 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
143684 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
143704 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
143724 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
143744 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
143764 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
143784 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
143804 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
143824 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
143844 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
143864 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
143884 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
143904 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
143924 AATCACAAC
1 AATCGCAAC
143933 ACTGAAATTT
Statistics
Matches: 325, Mismatches: 36, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 319 0.98
21 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:144651 original size:24 final size:23
Alignment explanation
Indices: 144612--144657 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
144602 AAATTTGGTC
144612 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
144636 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
144658 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:147159 original size:19 final size:19
Alignment explanation
Indices: 147137--147442 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
147127 CGGAAAATAC
*
147137 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
147156 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
147170 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
147190 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
147204 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
147223 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
147242 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
147256 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
147275 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
147294 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
147308 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
147327 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
147346 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
147365 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
147384 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
147398 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
147417 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
147435 AATCGCAA
1 AATCGCAA
147443 CGAGATAATC
Statistics
Matches: 251, Mismatches: 10, Indels: 53
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 15 0.06
17 15 0.06
18 12 0.05
19 146 0.58
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:147252 original size:52 final size:52
Alignment explanation
Indices: 147165--147442 Score: 379
Period size: 52 Copynumber: 5.2 Consensus size: 52
147155 AAATCCCAAC
147165 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
147218 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
147270 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
147322 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
147379 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
147431 ATG-AAATCGCAA
1 ATGAAAATCGCAA
147443 CGAGATAATC
Statistics
Matches: 215, Mismatches: 5, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
51 9 0.04
52 153 0.71
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 28 0.13
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:147288 original size:71 final size:71
Alignment explanation
Indices: 147204--147442 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
147194 GCAACGAGAG
*
147204 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
147269 AATGAA
66 AATGAA
* *
147275 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAA
147335 TGCGAAATGAA
61 TGCGAAATGAA
*
147346 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
147411 AATGAA
66 AATGAA
147417 AATCGCAATGCGAAATG-AAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
147443 CGAGATAATC
Statistics
Matches: 152, Mismatches: 6, Indels: 21
0.85 0.03 0.12
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 4 0.03
70 10 0.07
71 111 0.73
72 1 0.01
73 4 0.03
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:147580 original size:19 final size:19
Alignment explanation
Indices: 147471--147572 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
147461 AAATTATAAA
147471 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
147490 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
147510 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
147526 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
147543 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
147562 CGCATTGCGAT
1 CGCATTGCGAT
147573 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:147698 original size:14 final size:14
Alignment explanation
Indices: 147679--147715 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
147669 CATCAATTAC
147679 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
147693 ACAAATCATCTTTT
1 ACAAATCAACTTTT
147707 ACAAATCAA
1 ACAAATCAA
147716 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:149696 original size:19 final size:19
Alignment explanation
Indices: 149637--149770 Score: 92
Period size: 19 Copynumber: 7.6 Consensus size: 19
149627 TAGTTTACTT
* *
149637 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
*
149657 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATCAAAA
*
149675 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAATCAAAA
*
149694 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
* *
149708 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
149727 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAATCAAAA
*
149741 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
149760 TCGCAATGCGA
1 TCGCAACGCGA
149771 TTTTGGTTTC
Statistics
Matches: 91, Mismatches: 12, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
14 18 0.20
15 1 0.01
16 6 0.07
17 6 0.07
18 17 0.19
19 31 0.34
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:149711 original size:14 final size:14
Alignment explanation
Indices: 149692--149748 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
149682 GCGAAATTAA
*
149692 AATCGCAACGACAG
1 AATCGCAACGAAAG
149706 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
149723 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
149739 AATCGCAACG
1 AATCGCAACG
149749 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:149719 original size:33 final size:33
Alignment explanation
Indices: 149637--149765 Score: 159
Period size: 33 Copynumber: 3.8 Consensus size: 33
149627 TAGTTTACTT
* * *
149637 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAA
1 TCGCAACGCGAAA-TGAAAATCGCAA--CGAAA--GAA
* *
149675 TCGCAACGCGAAATTAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
*
149708 TCGCAATGCGAAATGAAAATCGCAACGAAAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
149741 TCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAATGAAAATCGCAA
149766 TGCGATTTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 56 0.67
35 4 0.05
37 12 0.14
38 12 0.14
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.12
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
Found at i:149788 original size:19 final size:19
Alignment explanation
Indices: 149766--149894 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
149756 AAAATCGCAA
149766 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
149785 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
149799 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
149818 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
149832 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
149851 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
149870 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
149890 TGCGA
1 TGCGA
149895 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:149808 original size:33 final size:33
Alignment explanation
Indices: 149766--149857 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
149756 AAAATCGCAA
149766 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
149799 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
149832 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
149858 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:150410 original size:92 final size:93
Alignment explanation
Indices: 149938--151055 Score: 2178
Period size: 93 Copynumber: 12.1 Consensus size: 93
149928 TTGAATGGAT
149938 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150003 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150031 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150096 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150124 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150189 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150217 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150279 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150307 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150371 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150399 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150464 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150492 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150557 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150585 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150650 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150678 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150743 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150771 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150835 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150863 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
150927 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
150955 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
151019 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
151047 AAATTTACT
1 AAATTTACT
151056 AAGCAATCTA
Statistics
Matches: 1020, Mismatches: 1, Indels: 9
0.99 0.00 0.01
Matches are distributed among these distances:
90 87 0.09
91 25 0.02
92 317 0.31
93 591 0.58
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:152778 original size:14 final size:14
Alignment explanation
Indices: 152759--152848 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
152749 TTGAAATGAA
152759 AATCGCAACGAGAG
1 AATCGCAACGAGAG
152773 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
152790 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
152806 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
152825 AATCGCAACGAGAG
1 AATCGCAACGAGAG
152839 AATCGCAACG
1 AATCGCAACG
152849 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:152796 original size:33 final size:33
Alignment explanation
Indices: 152751--152865 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
152741 TCTTTTGGTT
152751 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
152784 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
152817 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
152850 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
152866 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:152797 original size:19 final size:18
Alignment explanation
Indices: 152758--152870 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
152748 GTTGAAATGA
152758 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
152773 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
152790 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
152806 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
152823 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
152839 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
152856 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
152871 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:152901 original size:14 final size:14
Alignment explanation
Indices: 152882--152936 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
152872 TTTGGTTTCG
152882 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
152896 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
152915 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
152929 CGTTGCGA
1 CGTTGCGA
152937 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:152914 original size:33 final size:33
Alignment explanation
Indices: 152866--152936 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
152856 AAAATCGCAA
**
152866 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
152899 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
152932 TGCGA
1 TGCGA
152937 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:152944 original size:33 final size:33
Alignment explanation
Indices: 152877--152958 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
152867 GCGATTTTGG
***
152877 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
152910 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
152943 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
152959 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:152963 original size:20 final size:20
Alignment explanation
Indices: 152889--152977 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
152879 TCGCGTTGCG
152889 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
152909 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
152922 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
152942 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
152962 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
152978 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:153099 original size:33 final size:33
Alignment explanation
Indices: 153057--153126 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
153047 AATACTAACT
*
153057 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
153090 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
153123 TGAA
1 TGAA
153127 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:153360 original size:22 final size:22
Alignment explanation
Indices: 153308--153362 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
153298 TGGTTGTGAG
**
153308 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
153330 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
153352 GGATTTCTTCG
1 GGATTTCTTCG
153363 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:153533 original size:20 final size:20
Alignment explanation
Indices: 153508--153700 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
153498 CTTTAAATAT
153508 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
153528 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
153550 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
153569 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
153589 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
153609 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
153629 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
153649 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
153669 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
153689 CGCGTTGCGATT
1 CGCGTTGCGATT
153701 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:153695 original size:60 final size:60
Alignment explanation
Indices: 153508--153700 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
153498 CTTTAAATAT
**
153508 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
153569 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
153629 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
153689 CGCGTTGCGATT
1 CGCGTTGCGATT
153701 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:153781 original size:20 final size:20
Alignment explanation
Indices: 153756--153807 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
153746 AAGAATCGCG
*
153756 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
153776 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
153796 TTGCGATTCTGG
1 TTGCGATTCTGG
153808 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:154464 original size:18 final size:17
Alignment explanation
Indices: 154431--154464 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
154421 TTAATTAATA
*
154431 ATTTTTATTAAAAAAAT
1 ATTTTTATAAAAAAAAT
154448 ATTTTTGATAAAAAAAA
1 ATTTTT-ATAAAAAAAA
154465 ATAACGGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTTTTATAAAAAAAAT
Found at i:157607 original size:160 final size:160
Alignment explanation
Indices: 157326--157638 Score: 402
Period size: 160 Copynumber: 2.0 Consensus size: 160
157316 CCCGACAAAG
* * * * * *
157326 CATGGTAAATAATAGGGTATTAAATTAGACTAAAATTGATAGTTTTAGTAATTATATTTTTAATT
1 CATGGTAAATAATAGGGTACTAAATTAGACCAAAATCGATAATTTTAATAATTACATTTTTAATT
* * * * *
157391 TTAGTTCATTTTAATACTTAAATTTTTATTTTTAAAAATTATATTTACAATTTAATTTTTATTTT
66 TTAATCCATTTTAATACCTAAATTTTTATTTTTAAAAATTATACTTACAATTTAATTTTTATTTC
*
157456 ATTTTAGTGT-TTCTGTTCAAAATGTAACAT
131 ATTTTAGT-TCTTCTATTCAAAATGTAACAT
*
157486 CATGGTAAATAATA-GGTACTAAATT-GAACCAAAATCGATAATTTTAATATTTACATTTTTTAA
1 CATGGTAAATAATAGGGTACTAAATTAG-ACCAAAATCGATAATTTTAATAATTACA-TTTTTAA
* * *
157549 TTTTAATCCGTTTTAATACCT-AATTTTTTTATTTTAAAAGTTATACTTA-AATTTTAATTTTTA
64 TTTTAATCCATTTTAATACCTAAATTTTTAT-TTTTAAAAATTATACTTACAA-TTTAATTTTTA
157612 TTTCATTTTAGTTCTTCTATTCAAAAT
127 TTTCATTTTAGTTCTTCTATTCAAAAT
157639 AGACCCAAAT
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
158 1 0.01
159 43 0.33
160 88 0.67
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (160 bp):
CATGGTAAATAATAGGGTACTAAATTAGACCAAAATCGATAATTTTAATAATTACATTTTTAATT
TTAATCCATTTTAATACCTAAATTTTTATTTTTAAAAATTATACTTACAATTTAATTTTTATTTC
ATTTTAGTTCTTCTATTCAAAATGTAACAT
Found at i:166578 original size:60 final size:60
Alignment explanation
Indices: 166486--166642 Score: 171
Period size: 60 Copynumber: 2.6 Consensus size: 60
166476 GTATATGAGT
* * * * * *
166486 ATAGTTT-GGGATAAAATTGGAACGTTCAAAAAGTTTAGGGACCAATTTAGAATGA-AGGTC
1 ATAGTTTAGGGATGAAATTGAAACATT-TAAAAGTTTAAGGACCAATGTAGAATGATA-GTC
*
166546 ATAGTTT-GGGAATGAAATT-AAA-ATGATTAAAAGTTTAAGGACTAATGTAGAATGATAGTC
1 ATAGTTTAGGG-ATGAAATTGAAACAT--TTAAAAGTTTAAGGACCAATGTAGAATGATAGTC
166606 ATAGTTTAGGGATGAAATTGAAACATTTAAAAGTTTA
1 ATAGTTTAGGGATGAAATTGAAACATTTAAAAGTTTA
166643 TATACCAGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
59 1 0.01
60 65 0.78
61 15 0.18
62 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.31
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAATTGAAACATTTAAAAGTTTAAGGACCAATGTAGAATGATAGTC
Found at i:170939 original size:11 final size:11
Alignment explanation
Indices: 170923--170988 Score: 87
Period size: 11 Copynumber: 5.9 Consensus size: 11
170913 AGCTCAAGAC
170923 TCAAGCTCGAT
1 TCAAGCTCGAT
*
170934 TCAAGCTTGAT
1 TCAAGCTCGAT
**
170945 TGTGAGCTCGAT
1 T-CAAGCTCGAT
170957 TCAAGCTCGAT
1 TCAAGCTCGAT
170968 TCAAGCTCGAT
1 TCAAGCTCGAT
*
170979 TTAAGCTCGA
1 TCAAGCTCGA
170989 GGATGGGTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 39 0.83
12 8 0.17
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (11 bp):
TCAAGCTCGAT
Found at i:170956 original size:23 final size:22
Alignment explanation
Indices: 170923--170988 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 22
170913 AGCTCAAGAC
*
170923 TCAAGCTCGATTCAAGCTTGAT
1 TCAAGCTCGATTCAAGCTCGAT
**
170945 TGTGAGCTCGATTCAAGCTCGAT
1 T-CAAGCTCGATTCAAGCTCGAT
*
170968 TCAAGCTCGATTTAAGCTCGA
1 TCAAGCTCGATTCAAGCTCGA
170989 GGATGGGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 18 0.49
23 19 0.51
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (22 bp):
TCAAGCTCGATTCAAGCTCGAT
Found at i:170963 original size:34 final size:33
Alignment explanation
Indices: 170923--170988 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
170913 AGCTCAAGAC
* *
170923 TCAAGCTCGATTCAAGCTTGATTGTGAGCTCGAT
1 TCAAGCTCGATTCAAGCTCGATT-TAAGCTCGAT
170957 TCAAGCTCGATTCAAGCTCGATTTAAGCTCGA
1 TCAAGCTCGATTCAAGCTCGATTTAAGCTCGA
170989 GGATGGGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (33 bp):
TCAAGCTCGATTCAAGCTCGATTTAAGCTCGAT
Found at i:172919 original size:15 final size:15
Alignment explanation
Indices: 172899--172942 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
172889 CCTAACCCCT
172899 AACCCTTAACATATA
1 AACCCTTAACATATA
*
172914 AACCCTAAACATATA
1 AACCCTTAACATATA
172929 AA-CCTTAATCATAT
1 AACCCTTAA-CATAT
172943 CACATAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (15 bp):
AACCCTTAACATATA
Found at i:172957 original size:7 final size:7
Alignment explanation
Indices: 172947--173184 Score: 67
Period size: 7 Copynumber: 33.7 Consensus size: 7
172937 TCATATCACA
172947 TAAACTC
1 TAAACTC
172954 TAAAACTC
1 T-AAACTC
*
172962 TGAACTC
1 TAAACTC
*
172969 TAAACCC
1 TAAACTC
*
172976 TAAACCC
1 TAAACTC
172983 TAAAC-C
1 TAAACTC
172989 TTAAA-TC
1 -TAAACTC
* *
172996 ATATCAC-A
1 -TA-AACTC
173004 TAAACTC
1 TAAACTC
*
173011 TAAAACTT
1 T-AAACTC
* *
173019 TGAATTC
1 TAAACTC
173026 TAAACTC
1 TAAACTC
*
173033 TAAACCC
1 TAAACTC
173040 TAAAC-C
1 TAAACTC
173046 TTAACAC-C
1 -TAA-ACTC
173054 TAAAC-C
1 TAAACTC
173060 TTAAAC-C
1 -TAAACTC
173067 ATAAA-TAC
1 -TAAACT-C
*
173075 TAAACCC
1 TAAACTC
173082 TAAAC-C
1 TAAACTC
173088 TTAAA-TCC
1 -TAAACT-C
* *
173096 TATTAC-A
1 TA-AACTC
173103 TAAACTC
1 TAAACTC
173110 TAAACTC
1 TAAACTC
173117 TAAAC-C
1 TAAACTC
*
173123 ATAAACCC
1 -TAAACTC
173131 TAAAC-C
1 TAAACTC
173137 TTAAA-TC
1 -TAAACTC
* *
173144 -ATATCATA
1 TA-AAC-TC
173152 TAAACTC
1 TAAACTC
173159 TAAACTC
1 TAAACTC
173166 TAAAC-C
1 TAAACTC
173172 TTAAACTC
1 -TAAACTC
173180 TAAAC
1 TAAAC
173185 CTTAAACCTT
Statistics
Matches: 177, Mismatches: 25, Indels: 58
0.68 0.10 0.22
Matches are distributed among these distances:
5 1 0.01
6 14 0.08
7 136 0.77
8 25 0.14
9 1 0.01
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACTC
Found at i:172996 original size:57 final size:57
Alignment explanation
Indices: 172912--173049 Score: 215
Period size: 57 Copynumber: 2.4 Consensus size: 57
172902 CCTTAACATA
**
172912 TAAACCCTAAACATATAAACCTT-AATCATATCACATAAACTCTAAAACTCTGAACTC
1 TAAACCCTAAAC-CCTAAACCTTAAATCATATCACATAAACTCTAAAACTCTGAACTC
* *
172969 TAAACCCTAAACCCTAAACCTTAAATCATATCACATAAACTCTAAAACTTTGAATTC
1 TAAACCCTAAACCCTAAACCTTAAATCATATCACATAAACTCTAAAACTCTGAACTC
*
173026 TAAACTCTAAACCCTAAACCTTAA
1 TAAACCCTAAACCCTAAACCTTAA
173050 CACCTAAACC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
56 8 0.11
57 67 0.89
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (57 bp):
TAAACCCTAAACCCTAAACCTTAAATCATATCACATAAACTCTAAAACTCTGAACTC
Found at i:173009 original size:49 final size:49
Alignment explanation
Indices: 172956--173203 Score: 266
Period size: 49 Copynumber: 5.0 Consensus size: 49
172946 ATAAACTCTA
*
172956 AAACTCTGAACTCTAAACCCTAAACCCTAAACCTTAAATCATATCACAT
1 AAACTCTAAACTCTAAACCCTAAACCCTAAACCTTAAATCATATCACAT
* * ** * * * * * *
173005 AAACTCTAAAACTTTGAATTCTAAACTCTAAACCCTAAACCTTAACACCT
1 AAACTCT-AAACTCTAAACCCTAAACCCTAAACCTTAAATCATATCACAT
** * *
173055 AAAC-CTTAAAC-CATAAATACTAAACCCTAAACCTTAAATCCTATTACAT
1 AAACTC-TAAACTC-TAAACCCTAAACCCTAAACCTTAAATCATATCACAT
* *
173104 AAACTCTAAACTCTAAACCATAAACCCTAAACCTTAAATCATATCATAT
1 AAACTCTAAACTCTAAACCCTAAACCCTAAACCTTAAATCATATCACAT
* * * *
173153 AAACTCTAAACTCTAAACCTTAAACTCTAAACCTTAAACCTTATCACAT
1 AAACTCTAAACTCTAAACCCTAAACCCTAAACCTTAAATCATATCACAT
173202 AA
1 AA
173204 TTTGAAGGAA
Statistics
Matches: 162, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
49 124 0.77
50 38 0.23
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (49 bp):
AAACTCTAAACTCTAAACCCTAAACCCTAAACCTTAAATCATATCACAT
Found at i:173042 original size:14 final size:14
Alignment explanation
Indices: 173025--173191 Score: 83
Period size: 14 Copynumber: 11.4 Consensus size: 14
173015 ACTTTGAATT
173025 CTAAACTCTAAACC
1 CTAAACTCTAAACC
*
173039 CTAAAC-CTTAACAC
1 CTAAACTCTAAAC-C
173053 CTAAAC-CTTAAACC
1 CTAAACTC-TAAACC
*
173067 ATAAA-TACTAAACC
1 CTAAACT-CTAAACC
*
173081 CTAAAC-CTTAAATC
1 CTAAACTC-TAAACC
* * *
173095 CTATTAC-ATAAACT
1 CTA-AACTCTAAACC
173109 CTAAACTCTAAACC
1 CTAAACTCTAAACC
* *
173123 ATAAACCCTAAACC
1 CTAAACTCTAAACC
* *
173137 TTAAATCATATCATATAAACT
1 CTAAA-C---TC---TAAACC
173158 CTAAACTCTAAACC
1 CTAAACTCTAAACC
*
173172 TTAAACTCTAAACC
1 CTAAACTCTAAACC
*
173186 TTAAAC
1 CTAAAC
173192 CTTATCACAT
Statistics
Matches: 118, Mismatches: 20, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
13 8 0.07
14 89 0.75
15 8 0.07
17 2 0.02
18 1 0.01
20 1 0.01
21 9 0.08
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
CTAAACTCTAAACC
Found at i:173192 original size:21 final size:21
Alignment explanation
Indices: 173026--173195 Score: 122
Period size: 21 Copynumber: 8.1 Consensus size: 21
173016 CTTTGAATTC
*
173026 TAAACTCTAAACCCTAAACCT
1 TAAACTCTAAACCATAAACCT
* *
173047 TAACAC-CTAAACCTTAAACCA
1 TAA-ACTCTAAACCATAAACCT
*
173068 TAAA-TACTAAACCCTAAACCT
1 TAAACT-CTAAACCATAAACCT
*
173089 TAAA-TCCTATTA-CATAAA-CT
1 TAAACT-CTA-AACCATAAACCT
*
173109 CTAAACTCTAAACCATAAACCC
1 -TAAACTCTAAACCATAAACCT
* * *
173131 TAAAC-CTTAAATCAT-ATCAT
1 TAAACTC-TAAACCATAAACCT
173151 ATAAACTCTAAACTC-TAAACCT
1 -TAAACTCTAAAC-CATAAACCT
*
173173 TAAACTCTAAACCTTAAACCT
1 TAAACTCTAAACCATAAACCT
173194 TA
1 TA
173196 TCACATAATT
Statistics
Matches: 119, Mismatches: 16, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
20 8 0.07
21 101 0.85
22 10 0.08
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACTCTAAACCATAAACCT
Found at i:182767 original size:22 final size:24
Alignment explanation
Indices: 182724--182770 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
182714 CTGTGATTAA
182724 TAATAATATAATATATAAATATAAC
1 TAATAATATAATATAT-AATATAAC
*
182749 TAATAAT-TAATCTATATATATA
1 TAATAATATAATATATA-ATATA
182771 TTCCTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 12 0.60
25 7 0.35
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
TAATAATATAATATATAATATAAC
Found at i:189279 original size:2 final size:2
Alignment explanation
Indices: 189272--189311 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
189262 GTGAATAATT
189272 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
189312 ATTTTAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:189332 original size:10 final size:10
Alignment explanation
Indices: 189273--189332 Score: 57
Period size: 10 Copynumber: 6.0 Consensus size: 10
189263 TGAATAATTT
*
189273 ATATATATAT
1 ATATATATAA
*
189283 ATATATATAT
1 ATATATATAA
*
189293 ATATATATAT
1 ATATATATAA
189303 ATATATATAA
1 ATATATATAA
* * *
189313 TTTTAAATAA
1 ATATATATAA
*
189323 ATATACATAA
1 ATATATATAA
189333 TAAAATTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 43 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
ATATATATAA
Found at i:190129 original size:4 final size:4
Alignment explanation
Indices: 190120--190148 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
190110 TTTAACTTTG
190120 AAGA AAGA AAGA AAGA AAGA AAG- AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
190149 AACATGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:192851 original size:38 final size:36
Alignment explanation
Indices: 192794--192871 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 36
192784 AATTTAACGT
192794 TAAATTTTGAATGGGGTACTAAAAT-AAA-ATAAAAC
1 TAAATTTTGAATGGGGTACTAAAATGAAACA-AAAAC
*
192829 TAAAGTTTTTAATGGTGAGTACTAAAATGAAACAAAAAC
1 TAAA-TTTTGAATGG-G-GTACTAAAATGAAACAAAAAC
192868 TAAA
1 TAAA
192872 ATTTAGATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 4 0.11
36 9 0.24
37 1 0.03
38 10 0.27
39 12 0.32
40 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.28
Consensus pattern (36 bp):
TAAATTTTGAATGGGGTACTAAAATGAAACAAAAAC
Found at i:197693 original size:22 final size:21
Alignment explanation
Indices: 197655--197696 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
197645 TGAAAAGTAT
197655 TAATATTATATCAATAAATTA
1 TAATATTATATCAATAAATTA
* *
197676 TAATATTTTTATCCATAAATT
1 TAATA-TTATATCAATAAATT
197697 TATCAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATTATATCAATAAATTA
Found at i:199305 original size:16 final size:17
Alignment explanation
Indices: 199286--199321 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
199276 GTTGATTTAA
*
199286 TTTTGT-AAATATATAT
1 TTTTGTAAAACATATAT
199302 TTTTGTAAAACATATAT
1 TTTTGTAAAACATATAT
199319 TTT
1 TTT
199322 AGAAGAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTGTAAAACATATAT
Found at i:204066 original size:57 final size:58
Alignment explanation
Indices: 203990--204143 Score: 204
Period size: 57 Copynumber: 2.7 Consensus size: 58
203980 GCTTGGCGGT
* * * *
203990 TTCAATTACTTCCTAAGTCCCTACTAGTTTT-AAATTATGCACCCCAAATTTGGTGGG
1 TTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACTATGCACCCCAAATTTAGTGGC
*
204047 TTCAATTACTTCCCGAGTCCCTACTAGTTTTGAAACTATGCACCCCAAATTTAGTGGC
1 TTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACTATGCACCCCAAATTTAGTGGC
* *** *
204105 TTCAATGACTTTTGAAGT-CCTAGTAGTTTTGAAACTATG
1 TTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACTATG
204144 AAAAATAAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
57 49 0.58
58 36 0.42
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (58 bp):
TTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACTATGCACCCCAAATTTAGTGGC
Found at i:207416 original size:22 final size:23
Alignment explanation
Indices: 207372--207417 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
207362 GTTAATTCGG
*
207372 TTCAAAATCATTTAATTAATTAA
1 TTCAAAATCATTTAAATAATTAA
* *
207395 TTCAAAATTA-TTAAATATTTAA
1 TTCAAAATCATTTAAATAATTAA
207417 T
1 T
207418 ATATTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (23 bp):
TTCAAAATCATTTAAATAATTAA
Found at i:210882 original size:60 final size:60
Alignment explanation
Indices: 210772--210886 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
210762 GTTTGGGGAT
*
210772 TAATTTAGAATGAAGATCACAATTTGAGGATGAATATGAAACATTAAAAAGTTTAAAGAC
1 TAATTTAGAATGAAGATCACAATTTGAGGATGAATATAAAACATTAAAAAGTTTAAAGAC
* * * * *
210832 TAATTTAGAATGATAG-TTATAGTTTGAGGATGAA-ATTAAAATATTTAAAAGTTTA
1 TAATTTAGAATGA-AGATCACAATTTGAGGATGAATA-TAAAACATTAAAAAGTTTA
210887 GGGATCACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 44 0.94
61 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (60 bp):
TAATTTAGAATGAAGATCACAATTTGAGGATGAATATAAAACATTAAAAAGTTTAAAGAC
Found at i:214316 original size:33 final size:33
Alignment explanation
Indices: 214274--214353 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
214264 TAACCACGTT
*
214274 AAGTCTCGTCTCTTCGAGGAATACTTTCGGATG
1 AAGTCTCGTCTCTTCGAGGAACACTTTCGGATG
* * * **
214307 AAGTCTCGTCTATTTGAGGAGCGTTTTCGGATG
1 AAGTCTCGTCTCTTCGAGGAACACTTTCGGATG
* *
214340 AATTATCGTCTCTT
1 AAGTCTCGTCTCTT
214354 TGGGGAGAGC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (33 bp):
AAGTCTCGTCTCTTCGAGGAACACTTTCGGATG
Found at i:216415 original size:74 final size:74
Alignment explanation
Indices: 216286--216427 Score: 257
Period size: 74 Copynumber: 1.9 Consensus size: 74
216276 AGTGATCAAT
* *
216286 TTGTAACAAACGATAACGTTAGCTTTCTCAATTTGTGACTTTTCAAATATTAATAGTGAAAACGA
1 TTGTAACAAACGATAACGTTAGCTTTCTCAATTTGTGACTTTTCAAACATCAATAGTGAAAACGA
216351 ACACTCATA
66 ACACTCATA
*
216360 TTGTAACAAACGATAACGTTAGTTTTCTCAATTTGTGACTTTTCAAACATCAATAGTGAAAACGA
1 TTGTAACAAACGATAACGTTAGCTTTCTCAATTTGTGACTTTTCAAACATCAATAGTGAAAACGA
216425 ACA
66 ACA
216428 TTTATCTAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (74 bp):
TTGTAACAAACGATAACGTTAGCTTTCTCAATTTGTGACTTTTCAAACATCAATAGTGAAAACGA
ACACTCATA
Found at i:221315 original size:20 final size:20
Alignment explanation
Indices: 221277--221315 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
221267 GTGCTCCCAC
*
221277 TAAGAAGCACCCCATAAGCT
1 TAAGAAGCACCCCAGAAGCT
* *
221297 TAAGAATCACCCCGGAAGC
1 TAAGAAGCACCCCAGAAGC
221316 CATCTCTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
TAAGAAGCACCCCAGAAGCT
Found at i:235862 original size:21 final size:21
Alignment explanation
Indices: 235836--235898 Score: 126
Period size: 21 Copynumber: 3.0 Consensus size: 21
235826 TCCCTGTATT
235836 TTAGAAACAGTGAGAGATGAG
1 TTAGAAACAGTGAGAGATGAG
235857 TTAGAAACAGTGAGAGATGAG
1 TTAGAAACAGTGAGAGATGAG
235878 TTAGAAACAGTGAGAGATGAG
1 TTAGAAACAGTGAGAGATGAG
235899 CATACTTCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.43, C:0.05, G:0.33, T:0.19
Consensus pattern (21 bp):
TTAGAAACAGTGAGAGATGAG
Found at i:241171 original size:2 final size:2
Alignment explanation
Indices: 241164--241197 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
241154 CTCAGGTCTA
*
241164 TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
241198 ACGCATACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:241892 original size:17 final size:17
Alignment explanation
Indices: 241870--241903 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
241860 CACACCAAAG
241870 AATGAACTAACCAAGAA
1 AATGAACTAACCAAGAA
241887 AATGAACTAACCAAGAA
1 AATGAACTAACCAAGAA
241904 TGTACTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.12
Consensus pattern (17 bp):
AATGAACTAACCAAGAA
Found at i:246592 original size:31 final size:30
Alignment explanation
Indices: 246495--246596 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
246485 TGTGTCATAT
* *
246495 GTCCTCAAACTATGAATCTCATTTTAAATTG
1 GTCCTTAAACTATGAATCT-ATTTTAAATTA
* * *
246526 GTCCCTAAACTTTTGAA--TATTTTAATTTCA
1 GTCCTTAAAC-TATGAATCTATTTTAAATT-A
*
246556 -TCCTTAAACTATGAATCTAATTCTAAATTA
1 GTCCTTAAACTATGAATCT-ATTTTAAATTA
246586 GTCCTTAAACT
1 GTCCTTAAACT
246597 CTTAAACATT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
28 5 0.09
29 17 0.30
30 3 0.05
31 26 0.46
32 5 0.09
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (30 bp):
GTCCTTAAACTATGAATCTATTTTAAATTA
Found at i:246595 original size:60 final size:60
Alignment explanation
Indices: 246496--246678 Score: 217
Period size: 60 Copynumber: 3.0 Consensus size: 60
246486 GTGTCATATG
* * * * *
246496 TCCTCAAACTATGAATCTCATTTTAAATTGGTCCCTAAACTTTTGAATATTTTAATTTCA
1 TCCTTAAACTATGAATCTAATTCTAAATTGGTCCATAAACTTTTGAATATTCTAATTTCA
* * * * *
246556 TCCTTAAACTATGAATCTAATTCTAAATTAGTCCTTAAACTCTTAAACATTCTAATTTCA
1 TCCTTAAACTATGAATCTAATTCTAAATTGGTCCATAAACTTTTGAATATTCTAATTTCA
* * *
246616 TCAC-TAAACTATG-ATCTTATTTCTAAATTGGTCCATAAACTTTTGAATATTCAAAATTCA
1 TC-CTTAAACTATGAATC-TAATTCTAAATTGGTCCATAAACTTTTGAATATTCTAATTTCA
246676 TCC
1 TCC
246679 CCAAATCTAT
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
59 4 0.04
60 99 0.95
61 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.41
Consensus pattern (60 bp):
TCCTTAAACTATGAATCTAATTCTAAATTGGTCCATAAACTTTTGAATATTCTAATTTCA
Found at i:247240 original size:14 final size:14
Alignment explanation
Indices: 247221--247253 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
247211 ACTTATCAAA
247221 TTCACATTCA-TAAG
1 TTCACATT-ATTAAG
247235 TTCACATTATTAAG
1 TTCACATTATTAAG
247249 TTCAC
1 TTCAC
247254 TAGCCCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (14 bp):
TTCACATTATTAAG
Found at i:247355 original size:23 final size:22
Alignment explanation
Indices: 247329--247395 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
247319 CACCACAACT
*
247329 CGTATAATTGCACCGAAGTGCAA
1 CGTAGAATTGCACCGAAGTGC-A
* * *
247352 CGTAGAATTGCATCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTG-CA
*
247375 CGTAGAATTGCACCGTAGTGC
1 CGTAGAATTGCACCGAAGTGC
247396 CATATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (22 bp):
CGTAGAATTGCACCGAAGTGCA
Found at i:247651 original size:30 final size:30
Alignment explanation
Indices: 247610--247678 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
247600 ACATAGTTTG
* *
247610 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATCATTTTCATACCTT
247640 TATCACATAGACATATCATTTTCATACCTT
1 TATCACATAGACATATCATTTTCATACCTT
247670 TATCACATA
1 TATCACATA
247679 ACTCATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (30 bp):
TATCACATAGACATATCATTTTCATACCTT
Found at i:249640 original size:174 final size:174
Alignment explanation
Indices: 249350--249699 Score: 664
Period size: 174 Copynumber: 2.0 Consensus size: 174
249340 TGATTAGTTG
249350 TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
1 TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
*
249415 AGTGATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
66 AGTAATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
**
249480 TGAGCATTCAATGTCGAACTGTTGAGAGATAATATCAACTATCA
131 TGAGCATTCAATGTCGAAAGGTTGAGAGATAATATCAACTATCA
249524 TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
1 TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
*
249589 CGTAATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
66 AGTAATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
249654 TGAGCATTCAATGTCGAAAGGTTGAGAGATAATATCAACTATCA
131 TGAGCATTCAATGTCGAAAGGTTGAGAGATAATATCAACTATCA
249698 TT
1 TT
249700 ATTATCTCAA
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 172 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (174 bp):
TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
AGTAATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
TGAGCATTCAATGTCGAAAGGTTGAGAGATAATATCAACTATCA
Found at i:253610 original size:19 final size:20
Alignment explanation
Indices: 253582--253619 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
253572 TATTTAAATT
*
253582 AATTATAAACT-TTTTTTTG
1 AATTAAAAACTATTTTTTTG
253601 AATTAAAAACTATTTTTTT
1 AATTAAAAACTATTTTTTT
253620 TATATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
AATTAAAAACTATTTTTTTG
Found at i:253626 original size:180 final size:180
Alignment explanation
Indices: 253243--253614 Score: 573
Period size: 180 Copynumber: 2.0 Consensus size: 180
253233 ATTAAATTTT
* * *
253243 AAATTTTAAATATATTATATATAACATATGGGGTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTATATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
* ** *
253308 TTTAAGATCCAATAATTTTTAAACCTAAATCAATATTAATTAATTAAAATTTTATATAAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTA
*
253373 TATTTTATAATTATATTATTTAAATTAATTGTAAACTTTTTTTAATTAAA
131 TATTTTATAATTATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
* * * *
253423 AAATATTATATATATTATATATAACATATGGGCTCTGCCTAAATCATTTAAAATTCAATTAATAA
1 AAATATTATATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
*
253488 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAAATTATATAAAATTT
253553 ATATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
130 ATATTTTATAA-T-TATATTATTTAAATTAATTATAAAC-TTTTTTT-AATTAAA
*
253608 AACTATT
1 AAATATT
253615 TTTTTTATAT
Statistics
Matches: 173, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
180 102 0.59
181 26 0.15
182 1 0.01
183 24 0.14
184 7 0.04
185 13 0.08
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (180 bp):
AAATATTATATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTA
TATTTTATAATTATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
Found at i:254053 original size:60 final size:60
Alignment explanation
Indices: 253985--254136 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
253975 TTGATGAATT
* * * * * *
253985 GGGATGAAATTGGAA-GATCTAAATATTTTGA-GACAAATTTAGAATGAGATTCATAGTTTG
1 GGGATGAAATTGGAATG-T-TAAAAAGTTTAAGGACAAATTTAAAATGAGAGTCATACTTTG
*
254045 GGGATGAAATTGGAATGTTAAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATACTTTG
1 GGGATGAAATTGGAATGTTAAAAAGTTTAAGGACAAATTTAAAATGAGAGTCATACTTTG
* * *
254105 AGGATGAAATAT-GAATGTTTAAAATTTTAAGG
1 GGGATGAAAT-TGGAATGTTAAAAAGTTTAAGG
254137 GTCATAGTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
59 9 0.11
60 68 0.86
61 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (60 bp):
GGGATGAAATTGGAATGTTAAAAAGTTTAAGGACAAATTTAAAATGAGAGTCATACTTTG
Found at i:254465 original size:20 final size:18
Alignment explanation
Indices: 254423--254465 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
254413 AATAATTATT
* *
254423 TAATTTAAACATGTGTCA
1 TAATTTAAACATGTATAA
254441 TAATTTAGAACATGGTATAA
1 TAATTTA-AACAT-GTATAA
254461 TAATT
1 TAATT
254466 GAATTGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 5 0.24
20 9 0.43
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (18 bp):
TAATTTAAACATGTATAA
Found at i:270669 original size:43 final size:43
Alignment explanation
Indices: 270621--270734 Score: 180
Period size: 41 Copynumber: 2.7 Consensus size: 43
270611 CACAAATTCG
270621 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTGT
* *
270664 CGTTGCGAT-TTTCG-AAAT-TCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTT-GAAAATCGCGTTGCGATAGTCTACAGTTGT
270705 CGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CGTTGCGATAGTTGAAAATCGCGTTGCGAT
270735 TTTCCATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
41 32 0.51
42 12 0.19
43 19 0.30
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (43 bp):
CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTGT
Found at i:271399 original size:6 final size:6
Alignment explanation
Indices: 271378--271450 Score: 132
Period size: 6 Copynumber: 12.5 Consensus size: 6
271368 TCCCGTCTCG
271378 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
271424 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
271451 AATACGTGTC
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.15
6 57 0.85
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:271633 original size:20 final size:20
Alignment explanation
Indices: 271610--271670 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
271600 AGATCGCGTT
271610 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
* ** *
271630 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTTCAACTATCGCAAC
271650 GCGATTTTCAACTATCGCAAC
1 GCGA-TTTCAACTATCGCAAC
271671 ACGAATTTGC
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
19 1 0.03
20 17 0.57
21 12 0.40
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Found at i:278375 original size:44 final size:44
Alignment explanation
Indices: 278312--278401 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
278302 GATAAATTAT
*
278312 ACCGTTCCTAACTAAACTTTACTCTCTCCTATTTTACTCACTAA
1 ACCGTTCCTAACTAAACTTTACTCTCTCCTATTTTACTAACTAA
*
278356 ACCGTTCTTAACTAAACTTTACTCTCTCCTATTTTACTAACTAA
1 ACCGTTCCTAACTAAACTTTACTCTCTCCTATTTTACTAACTAA
278400 AC
1 AC
278402 TTTTTAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.29, C:0.30, G:0.02, T:0.39
Consensus pattern (44 bp):
ACCGTTCCTAACTAAACTTTACTCTCTCCTATTTTACTAACTAA
Found at i:279612 original size:3 final size:3
Alignment explanation
Indices: 279600--279629 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
279590 TTACCCTATT
279600 ATA ATAA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT
279630 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:279901 original size:2 final size:2
Alignment explanation
Indices: 279894--279919 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
279884 GCACCTAGGT
279894 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
279920 AAGGCTGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:283364 original size:4 final size:4
Alignment explanation
Indices: 283355--283379 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
283345 TGATTCATTG
283355 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
283380 TGTATAGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:286248 original size:6 final size:6
Alignment explanation
Indices: 286237--286273 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
286227 ATGTATTTTA
286237 TTATAT TTATAT TTATAT TTATAT TTATATT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATA-T TTATAT
286274 GCAAGTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:286708 original size:12 final size:11
Alignment explanation
Indices: 286685--286718 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
286675 ACAATCGAAA
286685 ATAATATTTTT
1 ATAATATTTTT
286696 ATAATACTTTTT
1 ATAATA-TTTTT
*
286708 ATTATATTTTT
1 ATAATATTTTT
286719 TCTATTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
ATAATATTTTT
Found at i:287887 original size:23 final size:23
Alignment explanation
Indices: 287861--287907 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
287851 AAAATATTCT
287861 TCTTTTGTCATTGAATAAAAAAA
1 TCTTTTGTCATTGAATAAAAAAA
287884 TCTTTTGTCATTGAATAAAAAAA
1 TCTTTTGTCATTGAATAAAAAAA
287907 T
1 T
287908 TCTACGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (23 bp):
TCTTTTGTCATTGAATAAAAAAA
Found at i:288056 original size:2 final size:2
Alignment explanation
Indices: 288049--288073 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
288039 CAATTTTGTA
288049 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
288074 AATTTTATGA
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:288264 original size:35 final size:35
Alignment explanation
Indices: 288218--288297 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
288208 TTATTCCTTT
*
288218 AACCAAACACTGTAATCTTACATTCCTGCTAAACG
1 AACCAAACACTGTAATCTTACATTACTGCTAAACG
*
288253 AACCAAACACTGTAATCTTACATTACTGTTAAACG
1 AACCAAACACTGTAATCTTACATTACTGCTAAACG
288288 AACCAAACAC
1 AACCAAACAC
288298 AACAATGCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (35 bp):
AACCAAACACTGTAATCTTACATTACTGCTAAACG
Found at i:288356 original size:18 final size:18
Alignment explanation
Indices: 288313--288357 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
288303 TGCAATATTC
* * *
288313 CCGGTAATCTTATTTCCG
1 CCGGTAATCCTATTCCCA
*
288331 CCGATAATCCTATTCCCA
1 CCGGTAATCCTATTCCCA
288349 CCGGTAATC
1 CCGGTAATC
288358 TTACATTCCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.31
Consensus pattern (18 bp):
CCGGTAATCCTATTCCCA
Found at i:296373 original size:23 final size:23
Alignment explanation
Indices: 296346--296428 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
296336 CGAACGAGAA
296346 ATGAACATTAAATGAACATGTTC
1 ATGAACATTAAATGAACATGTTC
* * **
296369 GTGAACATATAAACGAACACATTC
1 ATGAACAT-TAAATGAACATGTTC
*
296393 ATGAACATTAAGTGAACATGTTC
1 ATGAACATTAAATGAACATGTTC
*
296416 ATGAACAATAAAT
1 ATGAACATTAAAT
296429 AAACGAACAC
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 29 0.60
24 19 0.40
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (23 bp):
ATGAACATTAAATGAACATGTTC
Found at i:296409 original size:47 final size:49
Alignment explanation
Indices: 296346--296438 Score: 145
Period size: 47 Copynumber: 1.9 Consensus size: 49
296336 CGAACGAGAA
*
296346 ATGAACATTAAATGAACATGTTCGTGAAC-AT-ATAAACGAACACATTC
1 ATGAACATTAAATGAACATGTTCATGAACAATAATAAACGAACACATTC
*
296393 ATGAACATTAAGTGAACATGTTCATGAACAATAAATAAACGAACAC
1 ATGAACATTAAATGAACATGTTCATGAACAAT-AATAAACGAACAC
296439 GAACATAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 27 0.66
48 2 0.05
50 12 0.29
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (49 bp):
ATGAACATTAAATGAACATGTTCATGAACAATAATAAACGAACACATTC
Found at i:300444 original size:3 final size:3
Alignment explanation
Indices: 300430--300523 Score: 170
Period size: 3 Copynumber: 31.3 Consensus size: 3
300420 AGAGAGAGAG
*
300430 AGA AGA ATA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
300478 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
300524 AATGAGAGAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:307257 original size:15 final size:15
Alignment explanation
Indices: 307237--307266 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
307227 CTTTCTCATA
307237 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
307252 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
307267 TCAGCCTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:309474 original size:103 final size:103
Alignment explanation
Indices: 309367--309572 Score: 385
Period size: 103 Copynumber: 2.0 Consensus size: 103
309357 TTTAGTACTT
*
309367 AAATTATTAGTTTTGGTCTGTTTTAGTACTTAAATTTTCATTTTTTCCGAAACTTAATGTTAATT
1 AAATTATTAGTTTTGGTCTGTTTTAGTACCTAAATTTTCATTTTTTCCGAAACTTAATGTTAATT
*
309432 TTTAGCTGGATATTTTTTTTGAATTAATCACTGGTATC
66 TTTAGCCGGATATTTTTTTTGAATTAATCACTGGTATC
*
309470 AAATTATTAGTTTTGGTTTGTTTTAGTACCTAAATTTTCATTTTTTCCGAAACTTAATGTTAATT
1 AAATTATTAGTTTTGGTCTGTTTTAGTACCTAAATTTTCATTTTTTCCGAAACTTAATGTTAATT
309535 TTTAGCCGGATATTTTTTTTGAATTAATCACTGGTATC
66 TTTAGCCGGATATTTTTTTTGAATTAATCACTGGTATC
309573 CGATCTATTA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (103 bp):
AAATTATTAGTTTTGGTCTGTTTTAGTACCTAAATTTTCATTTTTTCCGAAACTTAATGTTAATT
TTTAGCCGGATATTTTTTTTGAATTAATCACTGGTATC
Found at i:310429 original size:15 final size:15
Alignment explanation
Indices: 310409--310445 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
310399 TGCCCGGTTT
310409 AAGAACGAATCGCTA
1 AAGAACGAATCGCTA
310424 AAGAACGAATCGCTA
1 AAGAACGAATCGCTA
310439 AAGAACG
1 AAGAACG
310446 CTCCGATCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.11
Consensus pattern (15 bp):
AAGAACGAATCGCTA
Done.