Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 30
Found at i:2035203 original size:21 final size:20
Alignment explanation
Indices: 2035151--2035211 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
2035141 GATTACATAT
*
2035151 GTCCTTCGGGACATATAGATAG
1 GTCCTTCGGGAC--ATAGATAC
*
2035173 GTCATTCGGGACATAGATGAC
1 GTCCTTCGGGACATAGAT-AC
2035194 GTCCTTCGGGACATAGAT
1 GTCCTTCGGGACATAGAT
2035212 TTCATATGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.17
21 18 0.51
22 11 0.31
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (20 bp):
GTCCTTCGGGACATAGATAC
Found at i:2044632 original size:12 final size:12
Alignment explanation
Indices: 2044617--2044671 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
2044607 ATTATTTAAA
2044617 CGGGTATTGGGC
1 CGGGTATTGGGC
*
2044629 CGGGTATTGGGT
1 CGGGTATTGGGC
2044641 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
2044653 CGAGAATCGGGC
1 CGGGTATTGGGC
2044665 CGGGTAT
1 CGGGTAT
2044672 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:2044870 original size:6 final size:6
Alignment explanation
Indices: 2044859--2044883 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2044849 AAATGGGTTT
2044859 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
2044884 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:2045088 original size:4 final size:4
Alignment explanation
Indices: 2045079--2045194 Score: 56
Period size: 4 Copynumber: 28.0 Consensus size: 4
2045069 ATATCTCTTC
* * * * **
2045079 AAAT AAAT AAAT AAAT ATATTT GAAAC AAAC AAAC AAAT AAAT AAAT TCA-
1 AAAT AAAT AAAT AAAT A-A-AT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* ** * *
2045129 AAAT AACT AAAT AAAT TCA- AAAT AAAC ACAT AAAT AAAT AAAT CCAACAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AA-AT
*
2045179 AATT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT
2045195 TTGGAATAAA
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
3 2 0.02
4 72 0.86
5 3 0.04
6 4 0.05
7 3 0.04
ACGTcount: A:0.66, C:0.09, G:0.01, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2045134 original size:46 final size:45
Alignment explanation
Indices: 2045083--2045260 Score: 144
Period size: 46 Copynumber: 3.8 Consensus size: 45
2045073 CTCTTCAAAT
* *
2045083 AAATAAATAAATATATTTGAAACAAACAAACAAATAAATAAATTCA
1 AAATAAATAAATAAATTTAAAACAAACAAA-AAATAAATAAATTCA
* * * * *
2045129 AAATAACTAAATAAATTCAAAATAAACACATAAATAAATAAATCCAA
1 AAATAAATAAATAAATTTAAAACAAACA-AAAAATAAATAAATTC-A
** * *
2045176 CATAATTAAATAAATAAATTTGGAATAAACGAAAAAATAAAT-TATTCA
1 -A-AA-TAAATAAATAAATTTAAAACAAAC-AAAAAATAAATAAATTCA
* * *
2045224 AAATAATTAAA-AATTTTAAAACAAATCAATAAATAAA
1 AAATAAATAAATAAATTTAAAACAAA-CAAAAAATAAA
2045261 AATTACCTCA
Statistics
Matches: 105, Mismatches: 20, Indels: 16
0.74 0.14 0.11
Matches are distributed among these distances:
44 19 0.18
45 8 0.08
46 38 0.36
47 3 0.03
48 2 0.02
49 5 0.05
50 29 0.28
51 1 0.01
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.25
Consensus pattern (45 bp):
AAATAAATAAATAAATTTAAAACAAACAAAAAATAAATAAATTCA
Found at i:2045144 original size:27 final size:28
Alignment explanation
Indices: 2045078--2045144 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
2045068 CATATCTCTT
* *
2045078 CAAA-TAAATAAATAAATATATTTGAAA
1 CAAACTAAATAAATAAATATAATTCAAA
*
2045105 CAAAC-AAACAAATAAATA-AATTCAAA
1 CAAACTAAATAAATAAATATAATTCAAA
2045131 -ATAACTAAATAAAT
1 CA-AACTAAATAAAT
2045145 TCAAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 1 0.03
26 9 0.27
27 23 0.70
ACGTcount: A:0.66, C:0.09, G:0.01, T:0.24
Consensus pattern (28 bp):
CAAACTAAATAAATAAATATAATTCAAA
Found at i:2045163 original size:19 final size:19
Alignment explanation
Indices: 2045117--2045153 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2045107 AACAAACAAA
2045117 TAAATAAATTCAAAATAAC
1 TAAATAAATTCAAAATAAC
2045136 TAAATAAATTCAAAATAA
1 TAAATAAATTCAAAATAA
2045154 ACACATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAATAAATTCAAAATAAC
Found at i:2045188 original size:27 final size:27
Alignment explanation
Indices: 2045129--2045194 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
2045119 AATAAATTCA
* *
2045129 AAATAACTAAATAAATTCAAAATAAAC
1 AAATAAATAAATAAATCCAAAATAAAC
* * **
2045156 ACATAAATAAATAAATCCAACATAATT
1 AAATAAATAAATAAATCCAAAATAAAC
2045183 AAATAAATAAAT
1 AAATAAATAAAT
2045195 TTGGAATAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (27 bp):
AAATAAATAAATAAATCCAAAATAAAC
Found at i:2045214 original size:50 final size:48
Alignment explanation
Indices: 2045076--2045234 Score: 155
Period size: 46 Copynumber: 3.3 Consensus size: 48
2045066 TTCATATCTC
* * *
2045076 TTCAAATAAATAAATAAATATATTTGAAACAAACAAACAAATAAATAAA
1 TTCAAATAATTAAATAAATAAATTTGAAATAAACAAA-AAATAAATAAA
* ** *
2045125 TTC-AA-AA-TAACTAAATAAATTCAAAATAAACACATAAATAAATAAA
1 TTCAAATAATTAAATAAATAAATTTGAAATAAACA-AAAAATAAATAAA
* * *
2045171 TCCAACATAATTAAATAAATAAATTTGGAATAAACGAAAAAATAAAT-TA
1 TTCAA-ATAATTAAATAAATAAATTTGAAATAAAC-AAAAAATAAATAAA
2045220 TTCAAAATAATTAAA
1 TTC-AAATAATTAAA
2045235 AATTTTAAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
46 33 0.37
47 4 0.04
48 3 0.03
49 17 0.19
50 31 0.35
51 1 0.01
ACGTcount: A:0.63, C:0.09, G:0.03, T:0.26
Consensus pattern (48 bp):
TTCAAATAATTAAATAAATAAATTTGAAATAAACAAAAAATAAATAAA
Found at i:2046375 original size:51 final size:50
Alignment explanation
Indices: 2046320--2046446 Score: 121
Period size: 51 Copynumber: 2.5 Consensus size: 50
2046310 GCAGTAAAGT
* ** *
2046320 GCGCCCCCTGAACCACGCTATATGCTGATTTGGCG-CCACGTGGGGTATAGC
1 GCGCCCCCTGAACCACGCTATACGCTGACATGG-GTACACGT-GGGTATAGC
** * *
2046371 GCGCCCTATGTACCACGCTATACGCTGACATGGGTTACACGTGTGTATAGC
1 GCGCCCCCTGAACCACGCTATACGCTGACATGGG-TACACGTGGGTATAGC
* **
2046422 GCGCCCCCTGATCCGTGCTATACGC
1 GCGCCCCCTGAACCACGCTATACGC
2046447 CACGTAGGGG
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
50 1 0.02
51 54 0.90
52 5 0.08
ACGTcount: A:0.18, C:0.32, G:0.27, T:0.23
Consensus pattern (50 bp):
GCGCCCCCTGAACCACGCTATACGCTGACATGGGTACACGTGGGTATAGC
Found at i:2046463 original size:41 final size:41
Alignment explanation
Indices: 2046415--2046498 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
2046405 TTACACGTGT
* ** *
2046415 GTATAGCGCGCCCCCTGATCCGTGCTATACGCCACGTAGGG
1 GTATAGCGCGCACCAGGAGCCGTGCTATACGCCACGTAGGG
* * *
2046456 GTATAGCGCGGATCAGGGGCCGTGCTATACGCCACGTAGGG
1 GTATAGCGCGCACCAGGAGCCGTGCTATACGCCACGTAGGG
2046497 GT
1 GT
2046499 TAATTATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.18, C:0.29, G:0.35, T:0.19
Consensus pattern (41 bp):
GTATAGCGCGCACCAGGAGCCGTGCTATACGCCACGTAGGG
Found at i:2049482 original size:21 final size:21
Alignment explanation
Indices: 2049439--2049531 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
2049429 TTTTCCCAAT
** *
2049439 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
*
2049459 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
** *
2049480 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
2049500 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
2049521 TCGCAATGCGA
1 TCGCAATGCGA
2049532 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:2049545 original size:20 final size:20
Alignment explanation
Indices: 2049520--2049614 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
2049510 AATTGGGAAA
*
2049520 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2049540 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2049561 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2049581 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2049601 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2049615 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2049551 original size:41 final size:41
Alignment explanation
Indices: 2049439--2049531 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
2049429 TTTTCCCAAT
*
2049439 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
2049480 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
2049521 TCGCAATGCGA
1 TCGCAATGCGA
2049532 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
Found at i:2049562 original size:41 final size:41
Alignment explanation
Indices: 2049517--2049594 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
2049507 GCGAATTGGG
* * *
2049517 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
2049558 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
2049595 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:2049566 original size:21 final size:20
Alignment explanation
Indices: 2049439--2049567 Score: 66
Period size: 20 Copynumber: 6.3 Consensus size: 20
2049429 TTTTCCCAAT
*
2049439 TCGCAATGCG-AATAAGTAAA
1 TCGCAATGCGAAATAA-AAAA
* * **
2049459 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAAAT-AAAAAA
*
2049480 TCGCAATGCG-AATAAGTAAA
1 TCGCAATGCGAAATAA-AAAA
* **
2049500 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAAAT-AAAAAA
* * **
2049521 TCGCAATGCGATACT-GACTA
1 TCGCAATGCGA-AATAAAAAA
2049541 TCGCAATGCGATAATAAAAAA
1 TCGCAATGCGA-AATAAAAAA
2049562 TCGCAA
1 TCGCAA
2049568 CGAGATACTT
Statistics
Matches: 81, Mismatches: 21, Indels: 13
0.70 0.18 0.11
Matches are distributed among these distances:
20 41 0.51
21 38 0.47
22 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAAATAAAAAA
Found at i:2049830 original size:22 final size:22
Alignment explanation
Indices: 2049802--2049845 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2049792 CACTCTCTCA
2049802 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2049824 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2049846 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2050134 original size:20 final size:20
Alignment explanation
Indices: 2050109--2050146 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2050099 CGATTCTCTC
2050109 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
2050129 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
2050147 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:2051487 original size:18 final size:18
Alignment explanation
Indices: 2051466--2051510 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2051456 TCCACTTCGG
*
2051466 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2051484 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2051502 GAGCCATCA
1 GAGCCATCA
2051511 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2051916 original size:6 final size:6
Alignment explanation
Indices: 2051907--2051947 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
2051897 TTTGTTAGTA
* *
2051907 TTTGTT TTTGGT TTTGTT TTTGGT TTTGTT TTTGTCT TTTG
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGT-T TTTG
2051948 GTTGAAGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.02, G:0.22, T:0.76
Consensus pattern (6 bp):
TTTGTT
Found at i:2051924 original size:12 final size:12
Alignment explanation
Indices: 2051907--2051940 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
2051897 TTTGTTAGTA
2051907 TTTGTTTTTGGT
1 TTTGTTTTTGGT
2051919 TTTGTTTTTGGT
1 TTTGTTTTTGGT
2051931 TTTGTTTTTG
1 TTTGTTTTTG
2051941 TCTTTTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (12 bp):
TTTGTTTTTGGT
Found at i:2051933 original size:18 final size:19
Alignment explanation
Indices: 2051907--2051950 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
2051897 TTTGTTAGTA
*
2051907 TTTGTTTTTGGTTTTGT-T
1 TTTGGTTTTGGTTTTGTCT
*
2051925 TTTGGTTTTGTTTTTGTCT
1 TTTGGTTTTGGTTTTGTCT
2051944 TTTGGTT
1 TTTGGTT
2051951 GAAGTAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.00, C:0.02, G:0.23, T:0.75
Consensus pattern (19 bp):
TTTGGTTTTGGTTTTGTCT
Found at i:2052058 original size:19 final size:20
Alignment explanation
Indices: 2052004--2052049 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2051994 TAGTTTACTT
* *
2052004 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2052024 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
2052044 TCGCAA
1 TCGCAA
2052050 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2052078 original size:14 final size:14
Alignment explanation
Indices: 2052059--2052116 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2052049 ATGTGAAATG
2052059 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2052073 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
2052089 ATGAAATAGCAACGAC
1 A--AAATCGCAACGAC
2052105 AAAATCGCAACG
1 AAAATCGCAACG
2052117 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2052100 original size:18 final size:18
Alignment explanation
Indices: 2052004--2052133 Score: 69
Period size: 19 Copynumber: 7.3 Consensus size: 18
2051994 TAGTTTACTT
* *
2052004 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGA-AA
**
2052024 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAAT-GAAA
* *
2052044 TCGCAATGTGAAATGAAAA
1 TCGCAACGCGAAATG-AAA
*
2052063 TCGCAA--CGACA--AAA
1 TCGCAACGCGAAATGAAA
2052077 TCGCAACGCGAAATGAAA
1 TCGCAACGCGAAATGAAA
* *
2052095 TAGCAA--CGACA--AAA
1 TCGCAACGCGAAATGAAA
2052109 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATG-AAA
2052128 TCGCAA
1 TCGCAA
2052134 TGCAATTTGT
Statistics
Matches: 85, Mismatches: 13, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
14 17 0.20
16 12 0.14
17 3 0.04
18 9 0.11
19 21 0.25
20 21 0.25
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (18 bp):
TCGCAACGCGAAATGAAA
Found at i:2052106 original size:32 final size:32
Alignment explanation
Indices: 2052043--2052126 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 32
2052033 GGAAATGGCT
* * *
2052043 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATAGCAACGACAAA
2052076 ATCGCAACGCGAAATGAAATAGCAACGACAAA
1 ATCGCAACGCGAAATGAAATAGCAACGACAAA
2052108 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2052127 ATCGCAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 34 0.71
33 14 0.29
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.12
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATAGCAACGACAAA
Found at i:2052169 original size:14 final size:14
Alignment explanation
Indices: 2052150--2052207 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2052140 TTGTGTTTCG
2052150 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2052164 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2052180 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2052196 CGTTGCGATTTT
1 CGTTGCGATTTT
2052208 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2052186 original size:32 final size:33
Alignment explanation
Indices: 2052145--2052223 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2052135 GCAATTTGTG
2052145 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
2052177 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2052210 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2052224 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2052222 original size:19 final size:19
Alignment explanation
Indices: 2052164--2052281 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
2052154 GCGATTTTGT
2052164 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2052182 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
2052196 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
2052215 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
2052235 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2052254 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
2052274 TGTTGCGA
1 CGTTGCGA
2052282 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2054152 original size:14 final size:14
Alignment explanation
Indices: 2054133--2054168 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2054123 ATTGTTTAAT
2054133 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2054147 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2054161 TGATTTGT
1 TGATTTGT
2054169 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2054307 original size:19 final size:19
Alignment explanation
Indices: 2054285--2054352 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
2054275 ATCGCAACGA
2054285 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2054304 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2054323 GAAAATCGCAA-G-G--A-
1 GAAAATCGCAATGCGAAAT
2054337 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2054353 TTTTTATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 2 0.04
16 1 0.02
17 1 0.02
18 1 0.02
19 30 0.65
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2054428 original size:20 final size:20
Alignment explanation
Indices: 2054371--2054428 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2054361 TCGCATTGCG
* * *
2054371 ATTTTCTCGTTGTGATAACC
1 ATTTTCGCGTTGCGATAGCC
2054391 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2054411 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2054429 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2055580 original size:24 final size:24
Alignment explanation
Indices: 2055524--2055582 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
2055514 AGTCAGTATT
* *
2055524 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
2055548 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
2055572 CGAATTTTGAT
1 CGAAATTTGAT
2055583 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:2055773 original size:12 final size:12
Alignment explanation
Indices: 2055756--2055780 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2055746 ATATAATCCT
2055756 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2055768 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2055780 G
1 G
2055781 TCCCTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2058096 original size:19 final size:19
Alignment explanation
Indices: 2058074--2058204 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
2058064 AGAAATTACT
2058074 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2058093 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2058107 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2058126 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
2058140 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2058159 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2058173 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2058192 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2058205 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2058116 original size:33 final size:33
Alignment explanation
Indices: 2058074--2058200 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
2058064 AGAAATTACT
2058074 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
2058107 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2058139 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2058173 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2058201 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2058181 original size:66 final size:66
Alignment explanation
Indices: 2058075--2058207 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2058065 GAAATTACTA
*
2058075 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2058140 T
66 T
*
2058141 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2058206 T
66 T
2058207 T
1 T
2058208 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:2058222 original size:19 final size:20
Alignment explanation
Indices: 2058200--2058239 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2058190 AAATCGCAAC
2058200 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
2058219 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
2058239 G
1 G
2058240 TGATTCTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:2058402 original size:14 final size:14
Alignment explanation
Indices: 2058383--2058419 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2058373 CATCAATTAA
2058383 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2058397 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2058411 ACAAATCAA
1 ACAAATCAA
2058420 TTAAACAAAC
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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2059825 original size:21 final size:21
Alignment explanation
Indices: 2059796--2059876 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
2059786 GAATTGTGGG
*
2059796 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
2059817 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
2059838 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
2059859 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
2059877 AGGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:2059858 original size:42 final size:42
Alignment explanation
Indices: 2059812--2059903 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
2059802 CTCTTCAACG
* * * *
2059812 ATGATAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
1 ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
* * *
2059854 ATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGGG
1 ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
2059896 ATGATAGG
1 ATGATAGG
2059904 CGAGTCGGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.23
Consensus pattern (42 bp):
ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
Found at i:2061936 original size:20 final size:19
Alignment explanation
Indices: 2061905--2062098 Score: 94
Period size: 20 Copynumber: 10.8 Consensus size: 19
2061895 TCTTTTGGTT
2061905 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
2061924 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
2061945 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2061964 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
2061978 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
* *
2061994 -ACA-GAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
2062011 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
2062027 -CCA-GACAATCGCAACGT
1 GAAATGAAAATCGCAACGA
*
2062044 GAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAAC-GA
* *
2062064 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
2062083 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2062099 TGTGATTTTG
Statistics
Matches: 130, Mismatches: 27, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
14 23 0.18
15 3 0.02
16 6 0.05
17 6 0.05
18 3 0.02
19 41 0.32
20 46 0.35
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2061987 original size:33 final size:32
Alignment explanation
Indices: 2061930--2062060 Score: 172
Period size: 33 Copynumber: 4.0 Consensus size: 32
2061920 ACGAGATAAT
2061930 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAAC-A
2061964 GAGAATCGCAACGCGAAATGACTATCGCGAACA
1 GAGAATCGCAACGCGAAATGACTATCGC-AACA
* *
2061997 GAAAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGC-AACA
* * **
2062030 GACAATCGCAACGTGAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
2062061 TGCGAAATAA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.02
33 70 0.79
34 17 0.19
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.12
Consensus pattern (32 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACA
Found at i:2062011 original size:19 final size:19
Alignment explanation
Indices: 2061997--2062098 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
2061987 ATCGCGAACA
2061997 GAAAATCGCAACGCGAAAT
1 GAAAATCGCAACGCGAAAT
** *
2062016 GACTATCGCGAC-C---A-
1 GAAAATCGCAACGCGAAAT
* *
2062030 GACAATCGCAACGTGAAAT
1 GAAAATCGCAACGCGAAAT
2062049 GAAAATCGCAACTGCGAAAT
1 GAAAATCGCAAC-GCGAAAT
*
2062069 AAAAATCGCAACGCGAAAT
1 GAAAATCGCAACGCGAAAT
2062088 GAAAATCGCAA
1 GAAAATCGCAA
2062099 TGTGATTTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
18 2 0.03
19 37 0.55
20 17 0.25
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAACGCGAAAT
Found at i:2062721 original size:20 final size:20
Alignment explanation
Indices: 2062696--2062768 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
2062686 GCGCTATGTA
2062696 AATCGCGTTGCGAAAGTCAT
1 AATCGCGTTGCGAAAGTCAT
*
2062716 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAT
2062736 AATCGCGTTGCGAAAGTCAGT
1 AATCGCGTTGCGAAAGTCA-T
*
2062757 -ATCTCGTTGCGA
1 AATCGCGTTGCGA
2062769 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAT
Found at i:2062802 original size:20 final size:20
Alignment explanation
Indices: 2062777--2062830 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2062767 GATTTTGTAT
2062777 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2062797 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2062817 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2062831 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2062802 original size:61 final size:61
Alignment explanation
Indices: 2062717--2062833 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
2062707 GAAAGTCATA
* * * * *
2062717 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
2062778 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
2062834 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:2062849 original size:61 final size:61
Alignment explanation
Indices: 2062717--2062851 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
2062707 GAAAGTCATA
* * * * * ** *
2062717 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
2062778 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
2062840 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2062852 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:2063661 original size:25 final size:24
Alignment explanation
Indices: 2063633--2063681 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2063623 AATTATAAAT
*
2063633 TAAGTTATTAGTAA-AATATATTTAA
1 TAAGTTAATA-TAATAATAT-TTTAA
2063658 TAAGTTAATATAATAATATTTTAA
1 TAAGTTAATATAATAATATTTTAA
2063682 GTGAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAAGTTAATATAATAATATTTTAA
Found at i:2063994 original size:39 final size:39
Alignment explanation
Indices: 2063947--2064052 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 39
2063937 ATTAAAAAAT
2063947 AATTTAGAACGTTAATGTGAAATAATTTAAAAAATTAAG
1 AATTTAGAACGTTAATGTGAAATAATTTAAAAAATTAAG
* * *
2063986 AATTTAGAACGTT-ATGGTGTCAA-AATTTAAGAAATTAGG
1 AATTTAGAACGTTAAT-GTG-AAATAATTTAAAAAATTAAG
** *
2064025 TTTTTAGAATGTTAGA-GTGAAATAATTT
1 AATTTAGAACGTTA-ATGTGAAATAATTT
2064053 GAGAATTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 4 0.07
39 48 0.87
40 2 0.04
41 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (39 bp):
AATTTAGAACGTTAATGTGAAATAATTTAAAAAATTAAG
Found at i:2064507 original size:31 final size:31
Alignment explanation
Indices: 2064440--2064515 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
2064430 TTAACTTGGG
* *
2064440 GTGACCACATCTTAATTAAATAAAAATGAAA
1 GTGACCAAATCTTAATTAAATAAAAATCAAA
* **
2064471 ATGACCAAATCTTGTTTAAATAAAAA-CATAA
1 GTGACCAAATCTTAATTAAATAAAAATCA-AA
*
2064502 GTGACCATATCTTA
1 GTGACCAAATCTTA
2064516 TGTATTTTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (31 bp):
GTGACCAAATCTTAATTAAATAAAAATCAAA
Found at i:2064819 original size:21 final size:21
Alignment explanation
Indices: 2064790--2064838 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2064780 TATTTTAATA
2064790 AAAAT-AAAAATAAAAGTAT-T
1 AAAATAAAAAATAAAA-TATGT
* *
2064810 AAATTAAAAAATTAAATATGT
1 AAAATAAAAAATAAAATATGT
2064831 AAAATAAA
1 AAAATAAA
2064839 TTTTAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAATAAAAAATAAAATATGT
Found at i:2066290 original size:19 final size:19
Alignment explanation
Indices: 2066266--2066303 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2066256 AAATTATATT
2066266 AAATATATATTAAAATAAA
1 AAATATATATTAAAATAAA
*
2066285 AAATATATATTAAATTAAA
1 AAATATATATTAAAATAAA
2066304 TTAAAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATATATATTAAAATAAA
Found at i:2066776 original size:60 final size:60
Alignment explanation
Indices: 2066682--2066876 Score: 221
Period size: 60 Copynumber: 3.2 Consensus size: 60
2066672 CTTCCTTATA
* *
2066682 TCCATTATGAAAGATACAAACGTCCACAAGGACTTACCCTAGACCACTAAGATCTTGA-AG
1 TCCATTATGAAAGATACAAACATCCACAAGGACTTACCCTAGACCACTAAGAT-TTAAGAG
* * * *
2066742 TCCATTATAAAAGATACAAACATCCACAATGACTTACCCTAGATCATTAAGATTTAAGAG
1 TCCATTATGAAAGATACAAACATCCACAAGGACTTACCCTAGACCACTAAGATTTAAGAG
* * * * ** * *
2066802 TCCAATATGGAAGATACAAATATCCATAAGGACTTACAGTAGACCACTAAAATGTAAGAG
1 TCCATTATGAAAGATACAAACATCCACAAGGACTTACCCTAGACCACTAAGATTTAAGAG
* * *
2066862 TTCAATATAAAAGAT
1 TCCATTATGAAAGAT
2066877 CAGAACAGAC
Statistics
Matches: 113, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
59 3 0.03
60 110 0.97
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (60 bp):
TCCATTATGAAAGATACAAACATCCACAAGGACTTACCCTAGACCACTAAGATTTAAGAG
Found at i:2068577 original size:18 final size:18
Alignment explanation
Indices: 2068517--2068564 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
2068507 TTTTATTATT
*
2068517 ATTATATTAATAAATATAG
1 ATTAAATTAA-AAATATAG
* *
2068536 ATTAAAATAAAAATATAT
1 ATTAAATTAAAAATATAG
2068554 ATTAAATTAAA
1 ATTAAATTAAA
2068565 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTAAATTAAAAATATAG
Found at i:2072180 original size:77 final size:77
Alignment explanation
Indices: 2072053--2072214 Score: 252
Period size: 77 Copynumber: 2.1 Consensus size: 77
2072043 GAGAATGAGA
* * *
2072053 TGAAGATGTCATTGATAGCCTTTATCAAAGGCTTCAATCGACCCTCCAAGACGAGATTATCTTAG
1 TGAAGATGTCATTGATAACCTTTATCAAAGGCTCCAATCAACCCTCCAAGACGAGATTATCTTAG
**
2072118 TAATTCGAAGTG
66 TAACCCGAAGTG
* * *
2072130 TGAAGATGTTATTGATAACCTTTATTAAAGGCTCCAATCAACCCTCCAAGACGTGATTATCTTAG
1 TGAAGATGTCATTGATAACCTTTATCAAAGGCTCCAATCAACCCTCCAAGACGAGATTATCTTAG
2072195 TAACCCGAAGTG
66 TAACCCGAAGTG
2072207 TGAAGATG
1 TGAAGATG
2072215 ACTTCACCAC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (77 bp):
TGAAGATGTCATTGATAACCTTTATCAAAGGCTCCAATCAACCCTCCAAGACGAGATTATCTTAG
TAACCCGAAGTG
Found at i:2074426 original size:60 final size:60
Alignment explanation
Indices: 2074258--2074436 Score: 225
Period size: 60 Copynumber: 3.0 Consensus size: 60
2074248 CCAAAACAAG
* * * **
2074258 CATCCATAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCTATTATAAAAGATACAGA
1 CATCCAGAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACAGA
* * * * * * *
2074318 CGTCCATAAGGACTTACCCTAGATCACTAAGATTTAAGAGTCCAATATGGAAGATATAGA
1 CATCCAGAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACAGA
* *
2074378 CATTCAGAAGGACTTACCATAAACCACTAAGATCTAGGAGTCCAATATGGAAGAT-CAGA
1 CATCCAGAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACAGA
2074437 ACAGATAAGA
Statistics
Matches: 100, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 3 0.03
60 97 0.97
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (60 bp):
CATCCAGAAGGACTTACCCTAAACCACTAAGATCTAGGAGTCCAATATGGAAGATACAGA
Found at i:2075509 original size:21 final size:21
Alignment explanation
Indices: 2075462--2075509 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
2075452 TCGAACTAAT
* * * *
2075462 AAAAAATAATATTTTTATTTA
1 AAAAAACAATACTTTAATTGA
2075483 ATAAAAACAATACTTTAATTGA
1 A-AAAAACAATACTTTAATTGA
2075505 AAAAA
1 AAAAA
2075510 TTATATATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAAACAATACTTTAATTGA
Found at i:2081476 original size:15 final size:17
Alignment explanation
Indices: 2081456--2081488 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2081446 ATGGATTTCC
2081456 TTAA-TTTGTAT-ATCA
1 TTAATTTTGTATCATCA
2081471 TTAATTTTGTATCATCA
1 TTAATTTTGTATCATCA
2081488 T
1 T
2081489 ACACAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (17 bp):
TTAATTTTGTATCATCA
Found at i:2083782 original size:20 final size:20
Alignment explanation
Indices: 2083757--2083798 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2083747 TGTGTAGATA
2083757 TCATATCATTGTCGATAGGT
1 TCATATCATTGTCGATAGGT
2083777 TCATATCATTGTCGATAGGT
1 TCATATCATTGTCGATAGGT
2083797 TC
1 TC
2083799 TAACGAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (20 bp):
TCATATCATTGTCGATAGGT
Found at i:2084968 original size:15 final size:15
Alignment explanation
Indices: 2084950--2084982 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2084940 GGAGGAGAAT
2084950 GAGGAGGTGGAGGTA
1 GAGGAGGTGGAGGTA
2084965 GAGGAGGTGGAGGTA
1 GAGGAGGTGGAGGTA
2084980 GAG
1 GAG
2084983 AAGGAAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.61, T:0.12
Consensus pattern (15 bp):
GAGGAGGTGGAGGTA
Found at i:2090914 original size:14 final size:14
Alignment explanation
Indices: 2090895--2090928 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2090885 TATCTATTGA
2090895 TACATTATACGAGG
1 TACATTATACGAGG
*
2090909 TACATTATATGAGG
1 TACATTATACGAGG
2090923 TACATT
1 TACATT
2090929 CGTGTACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (14 bp):
TACATTATACGAGG
Found at i:2091025 original size:28 final size:29
Alignment explanation
Indices: 2090963--2091032 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
2090953 TGGTGCAATT
* *
2090963 TATATGAGGCACTTTCGAGTGCAGATTAC
1 TATATGAGGCACTTTCAAGTACAGATTAC
*
2090992 T-GATGAGGCACTTTCAAGTACA-ATTGA-
1 TATATGAGGCACTTTCAAGTACAGATT-AC
2091019 TATATGAGGCACTT
1 TATATGAGGCACTT
2091033 GCCAGTGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 4 0.11
28 30 0.86
29 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (29 bp):
TATATGAGGCACTTTCAAGTACAGATTAC
Found at i:2092999 original size:30 final size:30
Alignment explanation
Indices: 2092963--2093029 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
2092953 AATGAACCGG
* *
2092963 CGGTTCAAACCGGTTTTGCCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTACAGGTTTTCAGC
**
2092993 CGGTTCACCCCGGTTTTACAGGTTTTCAGC
1 CGGTTCAAACCGGTTTTACAGGTTTTCAGC
2093023 CGGTTCA
1 CGGTTCA
2093030 TTGCCAGACC
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:0.13, C:0.28, G:0.25, T:0.33
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTACAGGTTTTCAGC
Found at i:2093653 original size:17 final size:17
Alignment explanation
Indices: 2093633--2093671 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2093623 AACATACTTT
2093633 TAAT-TTATAATAATAAA
1 TAATATTAT-ATAATAAA
*
2093650 TAATATTATATTATAAA
1 TAATATTATATAATAAA
2093667 TAATA
1 TAATA
2093672 AAATAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATATTATATAATAAA
Found at i:2093681 original size:17 final size:17
Alignment explanation
Indices: 2093639--2093681 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2093629 CTTTTAATTT
**
2093639 ATAATAATAAATAATATT
1 ATAAT-ATAAATAATAAA
*
2093657 ATATTATAAATAATAAA
1 ATAATATAAATAATAAA
2093674 ATAATATA
1 ATAATATA
2093682 TTAAATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATATAAATAATAAA
Found at i:2093682 original size:27 final size:23
Alignment explanation
Indices: 2093632--2093690 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 23
2093622 AAACATACTT
*
2093632 TTAATTTATAATAATAAATAATA
1 TTAAATTATAATAATAAATAATA
*
2093655 TTATATTATAAATAATAAAATAATATA
1 TTAAATTAT-AATAAT-AAAT-A-ATA
2093682 TTAAATTAT
1 TTAAATTAT
2093691 TCAAACTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 7 0.24
24 6 0.21
25 4 0.14
26 1 0.03
27 11 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAAATTATAATAATAAATAATA
Found at i:2094670 original size:17 final size:16
Alignment explanation
Indices: 2094639--2094674 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2094629 AACAATTTAA
*
2094639 TATGTTATTTATTATT
1 TATGTTATATATTATT
2094655 TATGTTATAATATTATT
1 TATGTTAT-ATATTATT
2094672 TAT
1 TAT
2094675 TACTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATGTTATATATTATT
Found at i:2099512 original size:2 final size:2
Alignment explanation
Indices: 2099505--2099534 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2099495 CCTTGGAATG
2099505 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
2099535 TGTTGAGAAA
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:2101874 original size:3 final size:3
Alignment explanation
Indices: 2101866--2101912 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
2101856 AAACTTTAGT
*
2101866 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2101913 TTTGTGTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2103859 original size:73 final size:71
Alignment explanation
Indices: 2103740--2103885 Score: 238
Period size: 73 Copynumber: 2.0 Consensus size: 71
2103730 TTGCCTTGAT
*
2103740 TATTACAATCCGGCAATCGGAAAATAATACTAAGAAGTAAGAAATTCCCTTATCGTTATATTTAT
1 TATTACAATCCGGCAATCGAAAAATAATACTAAGAAGTAAGAAATTCCCTTATCGTTATA--TAT
2103805 ATAGAAAA
64 ATAGAAAA
* * *
2103813 TATTATAATCCGGCAATCGAAAAATAATACTAAGAAGTGAGAAATTCCCTTATCGTTGTATATAT
1 TATTACAATCCGGCAATCGAAAAATAATACTAAGAAGTAAGAAATTCCCTTATCGTTATATATAT
2103878 AGAAAA
66 AGAAAA
2103884 TA
1 TA
2103886 GAAAGCCAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 13 0.19
73 56 0.81
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (71 bp):
TATTACAATCCGGCAATCGAAAAATAATACTAAGAAGTAAGAAATTCCCTTATCGTTATATATAT
AGAAAA
Found at i:2107183 original size:16 final size:16
Alignment explanation
Indices: 2107162--2107195 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2107152 GAAAAATACT
2107162 ACTCCCCCTTACTTTA
1 ACTCCCCCTTACTTTA
2107178 ACTCCCCCTTACTTTA
1 ACTCCCCCTTACTTTA
2107194 AC
1 AC
2107196 ACTTTCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (16 bp):
ACTCCCCCTTACTTTA
Found at i:2129054 original size:75 final size:75
Alignment explanation
Indices: 2128931--2129078 Score: 260
Period size: 75 Copynumber: 2.0 Consensus size: 75
2128921 GCTAGTTTCC
* * *
2128931 CACAGTATGGGTTAACTGAGCAAACACTCCTTCAATACTTTTACGAAGGATTAACTCCTCTGGAA
1 CACAGCATGAGTTAACTGAGCAAACACTCCTTCAATACTTTTACGAAGGATTAACTCCCCTGGAA
2128996 ATGAAGATCT
66 ATGAAGATCT
*
2129006 CACAGCATGAGTTAATTGAGCAAACACTCCTTCAATACTTTTACGAAGGATTAACTCCCCTGGAA
1 CACAGCATGAGTTAACTGAGCAAACACTCCTTCAATACTTTTACGAAGGATTAACTCCCCTGGAA
2129071 ATGAAGAT
66 ATGAAGAT
2129079 GATCGATGCT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (75 bp):
CACAGCATGAGTTAACTGAGCAAACACTCCTTCAATACTTTTACGAAGGATTAACTCCCCTGGAA
ATGAAGATCT
Found at i:2142215 original size:14 final size:15
Alignment explanation
Indices: 2142196--2142224 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2142186 AAAATAATAT
2142196 AAAAAAT-TAAATTA
1 AAAAAATATAAATTA
2142210 AAAAAATATAAATTA
1 AAAAAATATAAATTA
2142225 TTTAGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAAATATAAATTA
Found at i:2151050 original size:20 final size:20
Alignment explanation
Indices: 2151027--2151104 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
2151017 AGCTTTAAGA
*
2151027 ATCGATACCCCATAAACATC
1 ATCGATACCCAATAAACATC
**
2151047 ATCGATACCACAATAAGAGGT-
1 ATCGATACC-CAATAA-ACATC
*
2151068 ATCGATACCCTATAAACATC
1 ATCGATACCCAATAAACATC
*
2151088 ATTGATACCACAATAAA
1 ATCGATACC-CAATAAA
2151105 AAGTATCAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
19 2 0.04
20 22 0.48
21 20 0.43
22 2 0.04
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.22
Consensus pattern (20 bp):
ATCGATACCCAATAAACATC
Found at i:2151076 original size:41 final size:41
Alignment explanation
Indices: 2151027--2151118 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
2151017 AGCTTTAAGA
* *
2151027 ATCGATACCCCATAAACATCATCGATACCACAATAAGAGGT
1 ATCGATACCCCATAAACATCATCGATACCACAATAAAAAGT
* *
2151068 ATCGATACCCTATAAACATCATTGATACCACAATAAAAAGT
1 ATCGATACCCCATAAACATCATCGATACCACAATAAAAAGT
*
2151109 ATCAATACCC
1 ATCGATACCC
2151119 TCTTACCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (41 bp):
ATCGATACCCCATAAACATCATCGATACCACAATAAAAAGT
Found at i:2161375 original size:18 final size:20
Alignment explanation
Indices: 2161342--2161424 Score: 82
Period size: 20 Copynumber: 4.1 Consensus size: 20
2161332 ATAACCAGAA
2161342 CCCTCAGGGGGTATCGATTC
1 CCCTCAGGGGGTATCGATTC
2161362 CCCT-AGGGGG-ATCGATTC
1 CCCTCAGGGGGTATCGATTC
* *
2161380 CCCTTCAAAGGGGGAATCGGTT-
1 CCC-TC--AGGGGGTATCGATTC
*
2161402 CCCTCATGGGGGTATGGATTC
1 CCCTCA-GGGGGTATCGATTC
2161423 CC
1 CC
2161425 TCTGCACCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
18 11 0.21
19 8 0.15
20 14 0.27
21 4 0.08
22 9 0.17
23 6 0.12
ACGTcount: A:0.17, C:0.28, G:0.31, T:0.24
Consensus pattern (20 bp):
CCCTCAGGGGGTATCGATTC
Found at i:2165291 original size:785 final size:785
Alignment explanation
Indices: 2163781--2165310 Score: 2684
Period size: 785 Copynumber: 1.9 Consensus size: 785
2163771 CCGAAAATAA
* *
2163781 CCCAAAAATATTTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTATTCTAAATTTCGA
1 CCCAAAAATATTTTGGCAAATTATTTTCACAAAGCATAGTTCTAGCCATTTATTCTAAATTTCGA
* *
2163846 TTTTTCTTCTCAACAACTCCATTTTGTTAAGGGGTTCTAGGTGCTAAAAAATTATGGCTAATACC
66 TTTTTCCTCTCAACAACTCCATTTTGTTAAGGGGTTCTAGGTGCTAAAAAATTATGACTAATACC
*
2163911 ATTAGAATTACAAAACTCAATAAATTCAAGATTTTCAAATTCAGTGCCATGATCACTCCTAACAC
131 ATTAGAATTACAAAACTCAATAAATCCAAGATTTTCAAATTCAGTGCCATGATCACTCCTAACAC
* *
2163976 TAGTTATAGAGTAACCTTTTTCATTTTGGATTATTTTTGAAAATGTGATGAAACGTTCTAATGCT
196 TAGTTATAGAGTAACCTTTATCATTTTGGATTACTTTTGAAAATGTGATGAAACGTTCTAATGCT
*
2164041 TCATCTTTAGTTCTTAAAAATAGAACCCAAGTATATCTAGAATAGTCATCTACCAAGACAAATGA
261 TCATCTTTAGTACTTAAAAATAGAACCCAAGTATATCTAGAATAGTCATCTACCAAGACAAATGA
*
2164106 ATATTGTTTTCCACCCAAGCTAGTAGTCCTATTTGGCCCAAAAAGATCTATATGGATCAATTGTA
326 ATATTGTTTTCCACCCAAGCTAGTAGTCCTAGTTGGCCCAAAAAGATCTATATGGATCAATTGTA
2164171 ATACTCTACTAGTTGATACATCATTAATGGATTTAAAAGAAACTCGCTTTTGTTTTCCTTTAGCA
391 ATACTCTACTAGTTGATACATCATTAATGGATTTAAAAGAAACTCGCTTTTGTTTTCCTTTAGCA
* * * * *
2164236 CAAGCATCACAGATTTTATCATTATCAAATTTTAGTTTAGGCAGCCCTCAAACTAATTCTCCTTG
456 CAAGCATCACAGATTTTATCATTATCAAATTTAAGCTTAGGCAACCCTCAAACTAAATCACCTTG
* *
2164301 AACTAACCATTGCAAAACACTCATGCTAGCATGTCTTAGTCTCCTATGCCATAACCAACTATCAT
521 AACTAACCATTGCAAAACACTCATACTAGCATGTCCTAGTCTCCTATGCCATAACCAACTATCAT
2164366 GCTCATCCTTAGCAACTAGGCACAAATTAGTCATATCAATAGAATCTAAATGCACCATGTATATG
586 GCTCATCCTTAGCAACTAGGCACAAATTAGTCATATCAATAGAATCTAAATGCACCATGTATATG
*
2164431 ATTCCTATTCTATGACCAATAAGCATAACCCGATTAGATGCAATGTCAATGACTTTACAACCATT
651 ATTCCTATTCTATGACCAACAAGCATAACCCGATTAGATGCAATGTCAATGACTTTACAACCATT
* *
2164496 AATTTCAAACATGACATTGAATCCCTTATCGCATAATTTCAAACATAACAAGCGGTATTTGTGGC
716 AATATCAAACATGACATTAAATCCCTTATCGCATAATTTCAAACATAACAAGCGGTATTTGTGGC
2164561 TTCCG
781 TTCCG
*
2164566 CCCAAAAATATTTTGGCAAATTATTTTCACAAAGCATAGTTCTAGCCATTTCTTCTAAAGTTT-G
1 CCCAAAAATATTTTGGCAAATTATTTTCACAAAGCATAGTTCTAGCCATTTATTCTAAA-TTTCG
* *
2164630 ATTTTTCCTCTCAACAACTCCATTTTGTTGAGGGGTTCTAGGTGCTGAAAAATTATGACTAATAC
65 ATTTTTCCTCTCAACAACTCCATTTTGTTAAGGGGTTCTAGGTGCTAAAAAATTATGACTAATAC
*
2164695 CATTAGAATTACAAAACTCAGTAAATCCAAGATTTTCAAATTCAGTGCCATGATCACTCCTAACA
130 CATTAGAATTACAAAACTCAATAAATCCAAGATTTTCAAATTCAGTGCCATGATCACTCCTAACA
* ***
2164760 CTAGTTATAGAGTAACCTTTATCGTTTTGGATTACTTTTGAAAATGTGATGAATTTTTCTAATGC
195 CTAGTTATAGAGTAACCTTTATCATTTTGGATTACTTTTGAAAATGTGATGAAACGTTCTAATGC
* *
2164825 TTCATCTTTAGTACTTAAGAATAGAACCCAAGTATATCTAGAATAGTCATCTACCAAGACATATG
260 TTCATCTTTAGTACTTAAAAATAGAACCCAAGTATATCTAGAATAGTCATCTACCAAGACAAATG
*
2164890 CATATTGTTTTCCACCCAAGCTAGTAGTCCTAGTTGGCCCAAAAAGATCTATATGGATCAATTGT
325 AATATTGTTTTCCACCCAAGCTAGTAGTCCTAGTTGGCCCAAAAAGATCTATATGGATCAATTGT
**
2164955 AATACTCTACTAGTTGATATGTCATTAATGGATTTAAAAGAAACTCGCTTTTGTTTTCCTTTAGC
390 AATACTCTACTAGTTGATACATCATTAATGGATTTAAAAGAAACTCGCTTTTGTTTTCCTTTAGC
**
2165020 ACAAGCATCACAGATTTTATCATTATCAAATTTAAGCTTAGGCAACCCTTGAACTAAATCACCTT
455 ACAAGCATCACAGATTTTATCATTATCAAATTTAAGCTTAGGCAACCCTCAAACTAAATCACCTT
* *
2165085 GAATTAACCGTTGCAAAACACTCATACTAGCATGTCCTAGTCTCCTATGCCATAACCAACTATCA
520 GAACTAACCATTGCAAAACACTCATACTAGCATGTCCTAGTCTCCTATGCCATAACCAACTATCA
* *
2165150 TGTTCATCCTTAGCAACTAGGCACAAATTAGTCATATCAATAGAATCTAAGTGCACCATGTATAT
585 TGCTCATCCTTAGCAACTAGGCACAAATTAGTCATATCAATAGAATCTAAATGCACCATGTATAT
* *
2165215 GTTTCCTATTCTATGACCAACAAGCATAATCCGATTAGATGCAATGTCAATGACTTTACAACCAT
650 GATTCCTATTCTATGACCAACAAGCATAACCCGATTAGATGCAATGTCAATGACTTTACAACCAT
2165280 TAATATCAAACATGACATTAAATCCCTTATC
715 TAATATCAAACATGACATTAAATCCCTTATC
2165311 ACAAAATTGA
Statistics
Matches: 704, Mismatches: 40, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
785 701 1.00
786 3 0.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (785 bp):
CCCAAAAATATTTTGGCAAATTATTTTCACAAAGCATAGTTCTAGCCATTTATTCTAAATTTCGA
TTTTTCCTCTCAACAACTCCATTTTGTTAAGGGGTTCTAGGTGCTAAAAAATTATGACTAATACC
ATTAGAATTACAAAACTCAATAAATCCAAGATTTTCAAATTCAGTGCCATGATCACTCCTAACAC
TAGTTATAGAGTAACCTTTATCATTTTGGATTACTTTTGAAAATGTGATGAAACGTTCTAATGCT
TCATCTTTAGTACTTAAAAATAGAACCCAAGTATATCTAGAATAGTCATCTACCAAGACAAATGA
ATATTGTTTTCCACCCAAGCTAGTAGTCCTAGTTGGCCCAAAAAGATCTATATGGATCAATTGTA
ATACTCTACTAGTTGATACATCATTAATGGATTTAAAAGAAACTCGCTTTTGTTTTCCTTTAGCA
CAAGCATCACAGATTTTATCATTATCAAATTTAAGCTTAGGCAACCCTCAAACTAAATCACCTTG
AACTAACCATTGCAAAACACTCATACTAGCATGTCCTAGTCTCCTATGCCATAACCAACTATCAT
GCTCATCCTTAGCAACTAGGCACAAATTAGTCATATCAATAGAATCTAAATGCACCATGTATATG
ATTCCTATTCTATGACCAACAAGCATAACCCGATTAGATGCAATGTCAATGACTTTACAACCATT
AATATCAAACATGACATTAAATCCCTTATCGCATAATTTCAAACATAACAAGCGGTATTTGTGGC
TTCCG
Found at i:2174470 original size:23 final size:23
Alignment explanation
Indices: 2174407--2174457 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
2174397 GGGTGATACG
2174407 CCATAGCAATCCTATGTCGTACT
1 CCATAGCAATCCTATGTCGTACT
2174430 CCATAGCAATCCTATGTCGTACT
1 CCATAGCAATCCTATGTCGTACT
2174453 CCATA
1 CCATA
2174458 TCACTTCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.29
Consensus pattern (23 bp):
CCATAGCAATCCTATGTCGTACT
Found at i:2176361 original size:22 final size:22
Alignment explanation
Indices: 2176333--2176385 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
2176323 TTCATGACTA
*
2176333 CCTTCTTTGTAATTGGATTGAG
1 CCTTCTTTGTAATTAGATTGAG
2176355 CCTTCTTTGTAATTAGATTGAG
1 CCTTCTTTGTAATTAGATTGAG
2176377 CCTTCTTTG
1 CCTTCTTTG
2176386 AGGTTCCACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (22 bp):
CCTTCTTTGTAATTAGATTGAG
Found at i:2182153 original size:18 final size:18
Alignment explanation
Indices: 2182130--2182165 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2182120 TTTATTAAAT
2182130 AGAGAAAAAAAATAAAAA
1 AGAGAAAAAAAATAAAAA
**
2182148 AGAGAACTAAAATAAAAA
1 AGAGAAAAAAAATAAAAA
2182166 TAAAAATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (18 bp):
AGAGAAAAAAAATAAAAA
Found at i:2182522 original size:22 final size:22
Alignment explanation
Indices: 2182494--2182563 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
2182484 TAAATCATGC
* *
2182494 AAGTGCCTTAGCACTTATA-ATA
1 AAGTGCCTCAACACTTATACA-A
2182516 AAGTGCCTCAACACTTATACAA
1 AAGTGCCTCAACACTTATACAA
* *
2182538 AAGTGCATTC-ACACTAATACAA
1 AAGTGC-CTCAACACTTATACAA
2182560 AAGT
1 AAGT
2182564 TCCATAGCAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 39 0.93
23 3 0.07
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (22 bp):
AAGTGCCTCAACACTTATACAA
Found at i:2182860 original size:20 final size:20
Alignment explanation
Indices: 2182837--2182876 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2182827 TACCGATTTG
2182837 GGCTTATCAATATCGATACT
1 GGCTTATCAATATCGATACT
* * *
2182857 GGCTTTTGAGTATCGATACT
1 GGCTTATCAATATCGATACT
2182877 AGCCCGAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (20 bp):
GGCTTATCAATATCGATACT
Found at i:2187101 original size:15 final size:17
Alignment explanation
Indices: 2187081--2187129 Score: 77
Period size: 16 Copynumber: 3.1 Consensus size: 17
2187071 TTCACTTTCC
2187081 CCTTTTCC-TTTT-TTT
1 CCTTTTCCATTTTCTTT
2187096 CCTTTTCCATTTTCTTT
1 CCTTTTCCATTTTCTTT
2187113 -CTTTTCCATTTTCTTT
1 CCTTTTCCATTTTCTTT
2187129 C
1 C
2187130 ATCCTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.26
16 20 0.65
17 3 0.10
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (17 bp):
CCTTTTCCATTTTCTTT
Found at i:2187108 original size:22 final size:23
Alignment explanation
Indices: 2187083--2187125 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2187073 CACTTTCCCC
2187083 TTTTCCTTT-TTTTCC-TTTTCCA
1 TTTT-CTTTCTTTTCCATTTTCCA
2187105 TTTTCTTTCTTTTCCATTTTC
1 TTTTCTTTCTTTTCCATTTTC
2187126 TTTCATCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTCTTTCTTTTCCATTTTCCA
Found at i:2189055 original size:2 final size:2
Alignment explanation
Indices: 2189043--2189132 Score: 171
Period size: 2 Copynumber: 45.0 Consensus size: 2
2189033 TAACGTATGG
*
2189043 AT AT TT 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
2189085 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
2189127 AT AT AT
1 AT AT AT
2189133 TTCTTTTTCT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2189202 original size:5 final size:5
Alignment explanation
Indices: 2189184--2189250 Score: 66
Period size: 5 Copynumber: 13.2 Consensus size: 5
2189174 TGTATATATA
* *
2189184 TATTT TA-TT CATTT TATTT TATTT TATTT TATTTT TATTTT TATTT TATGT
1 TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TA-TTT TATTT TATTT
*
2189235 T-TTT TGTCTT TATTT T
1 TATTT TAT-TT TATTT T
2189251 TATTACTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
4 6 0.11
5 32 0.60
6 15 0.28
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:2189232 original size:32 final size:32
Alignment explanation
Indices: 2189194--2189254 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2189184 TATTTTATTC
*
2189194 ATTTTATTTTATTTTAT-TTTATTTTTATTTTT
1 ATTTTATGTT-TTTTATCTTTATTTTTATTTTT
*
2189226 ATTTTATGTTTTTTGTCTTTATTTTTATT
1 ATTTTATGTTTTTTATCTTTATTTTTATT
2189255 ACTTTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (32 bp):
ATTTTATGTTTTTTATCTTTATTTTTATTTTT
Found at i:2193652 original size:14 final size:14
Alignment explanation
Indices: 2193630--2193662 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2193620 AGGGAGGGGA
*
2193630 CTCCAGTAAGAAGC
1 CTCCCGTAAGAAGC
2193644 CTCCCGTAAGAAGC
1 CTCCCGTAAGAAGC
2193658 CTCCC
1 CTCCC
2193663 ATGAAGAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (14 bp):
CTCCCGTAAGAAGC
Found at i:2196995 original size:17 final size:17
Alignment explanation
Indices: 2196957--2196997 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2196947 TAAGTCGAAG
2196957 AAGA-AAAATAAAAAGA
1 AAGATAAAATAAAAAGA
2196973 AA-ATAAAATAACAAA-A
1 AAGATAAAATAA-AAAGA
2196989 AAGATAAAA
1 AAGATAAAA
2196998 ACGTTTAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 12 0.55
17 9 0.41
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.10
Consensus pattern (17 bp):
AAGATAAAATAAAAAGA
Found at i:2198050 original size:42 final size:43
Alignment explanation
Indices: 2197999--2198096 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 43
2197989 AATGGGTCAT
*
2197999 CACGATTTCAACTCCACGATGGAGGATATCATACCCA-A-AATC
1 CACGATTTCAACTCCACGATAGAGGATATCATACCCACACAA-C
* * *
2198041 CACTATTTCAACTCCACGATAGAGGATATCGTGCCCACACAAC
1 CACGATTTCAACTCCACGATAGAGGATATCATACCCACACAAC
2198084 CACGATTTCAACT
1 CACGATTTCAACT
2198097 TCATGACGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 33 0.67
43 14 0.29
44 2 0.04
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.22
Consensus pattern (43 bp):
CACGATTTCAACTCCACGATAGAGGATATCATACCCACACAAC
Found at i:2200139 original size:8 final size:8
Alignment explanation
Indices: 2200110--2200162 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
2200100 TATTTAATCC
2200110 TTTTTATTA
1 TTTTT-TTA
2200119 TTATTTATTA
1 TT-TTT-TTA
2200129 TTTTTTTA
1 TTTTTTTA
2200137 TTTTTTTA
1 TTTTTTTA
**
2200145 TTTAGTTA
1 TTTTTTTA
2200153 TCTTTTTTA
1 T-TTTTTTA
2200162 T
1 T
2200163 ACTTTGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 18 0.47
9 11 0.29
10 9 0.24
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2200147 original size:16 final size:16
Alignment explanation
Indices: 2200110--2200162 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
2200100 TATTTAATCC
2200110 TTTTTATTATTATTTATTA
1 TTTTT-TTATT-TTT-TTA
2200129 TTTTTTTATTTTTTTA
1 TTTTTTTATTTTTTTA
**
2200145 TTTAGTTATCTTTTTTA
1 TTTTTTTAT-TTTTTTA
2200162 T
1 T
2200163 ACTTTGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 10 0.32
17 11 0.35
18 5 0.16
19 5 0.16
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTTTTATTTTTTTA
Found at i:2200188 original size:2 final size:2
Alignment explanation
Indices: 2200181--2200216 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2200171 TATACGGTAT
2200181 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
2200217 ACTATTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2200306 original size:8 final size:9
Alignment explanation
Indices: 2200291--2200315 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2200281 ATATTAATAT
2200291 TTCTTTTTC
1 TTCTTTTTC
2200300 TTCTTTTTC
1 TTCTTTTTC
2200309 TTCTTTT
1 TTCTTTT
2200316 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:2200340 original size:2 final size:2
Alignment explanation
Indices: 2200333--2200363 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2200323 TTATTATCAT
2200333 TA 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 TA T
2200364 TATTCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2200398 original size:25 final size:25
Alignment explanation
Indices: 2200369--2200421 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2200359 TATATTATTC
2200369 ATTTTAT-TTATTTTTATTTATTTTT
1 ATTTTATGTT-TTTTTATTTATTTTT
* *
2200394 ATTTTATGTTTTTTTCTTTGTTTTT
1 ATTTTATGTTTTTTTATTTATTTTT
2200419 ATT
1 ATT
2200422 ACTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (25 bp):
ATTTTATGTTTTTTTATTTATTTTT
Found at i:2200407 original size:15 final size:15
Alignment explanation
Indices: 2200369--2200432 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
2200359 TATATTATTC
*
2200369 ATTTTATTTATTTTT
1 ATTTTTTTTATTTTT
2200384 ATTTATTTTTA-TTTT
1 ATTT-TTTTTATTTTT
* *
2200399 ATGTTTTTT-TCTTT
1 ATTTTTTTTATTTTT
* * *
2200413 GTTTTTATTACTTTT
1 ATTTTTTTTATTTTT
2200428 ATTTT
1 ATTTT
2200433 CACTATCTCC
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
14 14 0.38
15 18 0.49
16 5 0.14
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (15 bp):
ATTTTTTTTATTTTT
Found at i:2200408 original size:10 final size:10
Alignment explanation
Indices: 2200370--2200397 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2200360 ATATTATTCA
2200370 TTTTATTTAT
1 TTTTATTTAT
2200380 TTTTATTTAT
1 TTTTATTTAT
2200390 TTTTATTT
1 TTTTATTT
2200398 TATGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:2202597 original size:12 final size:12
Alignment explanation
Indices: 2202580--2202606 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2202570 TGACGATGAT
2202580 TGATGATGGTGA
1 TGATGATGGTGA
2202592 TGATGATGGTGA
1 TGATGATGGTGA
2202604 TGA
1 TGA
2202607 AAAGACCATT
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:0.26, C:0.00, G:0.41, T:0.33
Consensus pattern (12 bp):
TGATGATGGTGA
Found at i:2203665 original size:28 final size:28
Alignment explanation
Indices: 2203633--2203688 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
2203623 ATGACTAATA
*
2203633 TAACCATTTTATTATCATTAATAAAAAT
1 TAACCATTTTATTACCATTAATAAAAAT
2203661 TAACCATTTTATTACCATTAATAAAAAT
1 TAACCATTTTATTACCATTAATAAAAAT
2203689 AAACTCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (28 bp):
TAACCATTTTATTACCATTAATAAAAAT
Found at i:2203706 original size:27 final size:28
Alignment explanation
Indices: 2203642--2203707 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
2203632 ATAACCATTT
* * **
2203642 TATTATCATTAATAAAAATTAACCATTT
1 TATTACCATTAATAAAAATAAACCATGC
2203670 TATTACCATTAATAAAAATAAACTCATGC
1 TATTACCATTAATAAAAATAAAC-CATGC
2203699 T-TTA-CATTA
1 TATTACCATTA
2203708 CATCCGACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 5 0.15
28 24 0.73
29 4 0.12
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (28 bp):
TATTACCATTAATAAAAATAAACCATGC
Found at i:2204068 original size:30 final size:30
Alignment explanation
Indices: 2204032--2204098 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
2204022 TAAAGTTTGT
* *
2204032 AAAAGTTTAGGG-ACAAAAAATGTACTTTTC
1 AAAAGTTTAGGGAAC-AAAAATGTAATTTCC
*
2204062 AAAAGTTTAGGGAACAAAAGTGTAATTTCC
1 AAAAGTTTAGGGAACAAAAATGTAATTTCC
2204092 AAAAGTT
1 AAAAGTT
2204099 ATGTATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (30 bp):
AAAAGTTTAGGGAACAAAAATGTAATTTCC
Found at i:2208202 original size:59 final size:59
Alignment explanation
Indices: 2208130--2208264 Score: 191
Period size: 59 Copynumber: 2.3 Consensus size: 59
2208120 TATGCACCGC
* * *
2208130 AGTGCTAACCCAAATATGAAACATGAGGTCGTGCCCACCATTAGCACTAGTTATACTTT
1 AGTGCTAACCCAAATATGAAACATAAAGTCGTGCCCACCATTAGCACTAGTTATACTTA
* * **
2208189 AGTGCTAGCCCAAATATGACACATAAAGTCGTGCCCACCATTTTCACTAGTTATACTTA
1 AGTGCTAACCCAAATATGAAACATAAAGTCGTGCCCACCATTAGCACTAGTTATACTTA
2208248 AGTGC-AACCCCAAATAT
1 AGTGCTAA-CCCAAATAT
2208265 ATAGCATATT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 1 0.01
59 66 0.99
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (59 bp):
AGTGCTAACCCAAATATGAAACATAAAGTCGTGCCCACCATTAGCACTAGTTATACTTA
Found at i:2214806 original size:108 final size:108
Alignment explanation
Indices: 2214685--2215726 Score: 1330
Period size: 108 Copynumber: 9.6 Consensus size: 108
2214675 GGAGTATGGA
* * *
2214685 ACTCGAATAATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
*
2214750 TTCATCAATCGCGTCTGCCCTCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
2214793 ACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATATT-TTCAGAGAGTATAAGACTCGAACA
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTAT-TTCTTCAGAGAGTATAAGAC-C-CACA
* * * * * * *
2214857 ATCTTTAAT-GATCGTGTCTGCCCCCTATATATTTAGGGAGTATAAG
63 ATC-TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
2214903 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATC
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
* * *
2214966 TTCATCAATCGTGTTTGCCCCCTATTTTTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** * * * *
2215009 ACTCGAACAATCTTCAATGATCGTGTTTGCCCCCTATATCTTTAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
*
2215074 TTCATCAATCGCGTCTGCCTCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2215117 ACTCGAACGATCTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
2215182 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
2215225 ACTCGAACAATCTTCAACGATCGTGTATGCCCCCTATATCTTCAGAGAGTATAATACCCACAATC
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
* * **
2215290 TTCAACGATTACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2215333 ACCCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAATATAAGACCCGAACAA
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCC--ACAA
* * *
2215398 TCTTCAACTATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2215443 AC-C-CACAATCTTCATCAATCGCGTCTGCCGCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
* * * *
2215506 TCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAAAGAGTATAAG
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
2215551 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAA
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCC--ACAA
* * *
2215614 TCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2215659 AC-C-CACAATCTTCATCAATCGCGTTTGCTCCCTATTTCTTCAGAGAGTATAAGACCCGAACAA
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCC--ACAA
2215722 TCTTC
64 TCTTC
2215727 TTTTACTTCA
Statistics
Matches: 847, Mismatches: 73, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
105 4 0.00
106 39 0.05
107 4 0.00
108 703 0.83
109 6 0.01
110 87 0.10
111 4 0.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (108 bp):
ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:2214955 original size:163 final size:162
Alignment explanation
Indices: 2214685--2215726 Score: 1407
Period size: 163 Copynumber: 6.4 Consensus size: 162
2214675 GGAGTATGGA
* * * *
2214685 ACTCGAATAATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
*
2214750 TTCATCAATCGCGTCTGCCCTCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATC
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACGATC
*
2214815 GTGTCTGCCCCCTATATT-TTCAGAGAGTATAAG
130 GCGTCTGCCCCCTAT-TTCTTCAGAGAGTATAAG
* * * * * * *
2214848 ACTCGAACAATCTTTAATGATCGTGTCTGCCCCCTATATATTTAGGGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
* *
2214913 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-ACAATCTTCATCAATCG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACGATCG
* * *
2214977 TGTTTGCCCCCTATTTTTTCAGAGAGTATAAG
131 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
2215009 ACTCGAACAATCTTCAATGATCGTGTTTGCCCCCTATATCTTTAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
* *
2215074 TTCATCAATCGCGTCTGCCTCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATC
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACGATC
* *
2215139 GTGTCTGCCCCCTATATCTTCAGAGAGTATAAG
130 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2215172 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
* * * * * * *
2215235 TCTTCAACGATCGTGTATGCCCCCTATATCTTCAGAGAGTATAATAC-CCACAATCTTCAACGAT
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACGAT
**
2215299 TACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
129 CGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
2215333 ACCCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAATATAAGACCCGAACAA
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCC--ACAA
* * * * * *
2215398 TCTTCAACTATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-CCACAATCTTCATCAAT
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACGAT
*
2215462 CGCGTCTGCCGCCTATTTCTTCAGAGAGTATAAG
129 CGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
2215496 ACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAAAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
* *
2215561 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACGATT
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACGATC
2215626 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
130 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
2215659 AC-C-CACAATCTTCATCAATCGCGTTTGCTCCCTATTTCTTCAGAGAGTATAAGACCCGAACAA
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCC--ACAA
2215722 TCTTC
64 TCTTC
2215727 TTTTACTTCA
Statistics
Matches: 787, Mismatches: 79, Indels: 26
0.88 0.09 0.03
Matches are distributed among these distances:
160 2 0.00
161 335 0.43
162 7 0.01
163 443 0.56
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (162 bp):
ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACGATCG
CGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:2216792 original size:128 final size:127
Alignment explanation
Indices: 2216500--2216908 Score: 599
Period size: 128 Copynumber: 3.2 Consensus size: 127
2216490 TCTCATCATG
* *
2216500 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACAGGCCTTTCAAAATGCCCCTATT
1 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCC-TTCAAAATGCCCC-ATC
* ** * *
2216565 ACCTCAAATTGTAAGGCTCATTCTTCATGCC-TC--CTTGGTCTGAATCTTTTCATCTCAACATG
64 ACCTCAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAAT-TTTTCATCTCAACCTA
2216627 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCAC
1 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCAC
* *
2216692 CTTAGTTTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTTATCATCTCAACCTA
66 CTCAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTT-TCATCTCAACCTA
* * * *
2216755 ATGTGGGTTCAGTCATGCCCCAACATTATCTTGTACTGGTACGAGCCTTCAAAATGTCCCATCAC
1 ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCAC
* *
2216820 CTCAGATTGTAAGGCTTATTCTTCATGCCTTCTTCTTCTTCTGAATCTTGTCATCTCAACCTA
66 CTCAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAAT-TTTTCATCTCAACCTA
* *
2216883 ATGTGGGTTCAGCCGTGCCACAACAT
1 ATGTGGGTTCAGTCGTGCCCCAACAT
2216909 ATCGCAACTT
Statistics
Matches: 257, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
125 30 0.12
126 15 0.06
127 49 0.19
128 161 0.63
129 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (127 bp):
ATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCAC
CTCAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTTTCATCTCAACCTA
Found at i:2218170 original size:16 final size:16
Alignment explanation
Indices: 2218152--2218181 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2218142 TTCATTCTTT
2218152 TTTTC-ATTTTTCTCA
1 TTTTCAATTTTTCTCA
2218167 TTTTCAATTTTTCTC
1 TTTTCAATTTTTCTC
2218182 TTTCTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCAATTTTTCTCA
Found at i:2218208 original size:6 final size:6
Alignment explanation
Indices: 2218151--2218243 Score: 59
Period size: 6 Copynumber: 15.2 Consensus size: 6
2218141 TTTCATTCTT
* *
2218151 TTTTTC ATTTTTC TCATTTTC AATTTTTC TCTTTC TTTTCC TTTTT- TATTTTC
1 TTTTTC -TTTTTC T--TTTTC --TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC
* * *
2218204 TTTTTC -ATTTC ATTTT- TTTTTC -TTTTC TTTTTC TCTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
2218244 ATATTTCTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
5 14 0.20
6 37 0.54
7 7 0.10
8 10 0.14
10 1 0.01
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:2218225 original size:16 final size:16
Alignment explanation
Indices: 2218198--2218235 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2218188 TTCCTTTTTT
2218198 ATTTTCTTTTTCATTTC
1 ATTTT-TTTTTCATTTC
*
2218215 ATTTTTTTTTCTTTTC
1 ATTTTTTTTTCATTTC
2218231 -TTTTT
1 ATTTTT
2218236 CTCTTTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 10 0.50
17 5 0.25
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTTTTTTCATTTC
Found at i:2218250 original size:14 final size:12
Alignment explanation
Indices: 2218174--2218258 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 12
2218164 TCATTTTCAA
2218174 TTTTTCTCTTTC
1 TTTTTCTCTTTC
* *
2218186 TTTTCCT-TTTT
1 TTTTTCTCTTTC
*
2218197 TATTTTCTTTTTC
1 T-TTTTCTCTTTC
*
2218210 -ATTTCAT-TTT-
1 TTTTTC-TCTTTC
2218220 TTTTTCT-TTTC
1 TTTTTCTCTTTC
2218231 TTTTTCTCTTTC
1 TTTTTCTCTTTC
2218243 TATATTTCTC-TTC
1 T-T-TTTCTCTTTC
2218256 TTT
1 TTT
2218259 CTCTTTATGA
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
10 4 0.07
11 23 0.39
12 18 0.31
13 8 0.14
14 6 0.10
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTCTCTTTC
Found at i:2220572 original size:6 final size:6
Alignment explanation
Indices: 2220551--2220585 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
2220541 AAACAAATAC
2220551 ATGC-A ATGCAAA ATGCAA ATGCAA ATGCAA ATGCA
1 ATGCAA ATGC-AA ATGCAA ATGCAA ATGCAA ATGCA
2220586 CGAGGTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.14
6 19 0.68
7 5 0.18
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGCAA
Found at i:2228312 original size:42 final size:42
Alignment explanation
Indices: 2228224--2228505 Score: 321
Period size: 43 Copynumber: 6.6 Consensus size: 42
2228214 TATGAAGTGG
2228224 TATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * **
2228267 TATAGGTCTGATCTTTTGCGGCGTTTGTTCCAAAAACGATGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * **
2228309 TATAGGTCTGACATTTTGCGGCGTTTGTTCCAAAAACGGTGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * * *
2228351 TATAGGTATGACCTTTTGCGGCGTTTGTTTCATAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * *
2228393 TATATATCATGACTTTTTGCGGCGTTTGTTCCAGAAACGCCGC
1 TATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * * *
2228436 TATAGATATTGACCTTTTGCGGCGTTTATTCTAAAAACGTCGC
1 TATAGAT-CTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * * *
2228479 GATAGATCTTGGCCTATTGCTGCGTTT
1 TATAGATC-TGACCTTTTGCGGCGTTT
2228506 TTTGTTCTCA
Statistics
Matches: 205, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
42 92 0.45
43 113 0.55
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (42 bp):
TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
Found at i:2230387 original size:13 final size:15
Alignment explanation
Indices: 2230357--2230388 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2230347 CGTTTAGATT
2230357 TTTTTAAATTATATA
1 TTTTTAAATTATATA
2230372 TTTTTAAA-TA-ATA
1 TTTTTAAATTATATA
2230385 TTTT
1 TTTT
2230389 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAAATTATATA
Found at i:2231959 original size:68 final size:67
Alignment explanation
Indices: 2231818--2231965 Score: 172
Period size: 68 Copynumber: 2.2 Consensus size: 67
2231808 TTATTTAATG
* * * * * *
2231818 ACCTAATTATGTTATTTCAGGTACTTGCACGGGAGTCTCAAAGAATTAGAGTGACTCGCGCGGGA
1 ACCTAATCATGTTATTTCAGGTACTCGCACGAGAGTCTCAAAGAATTAGAGTAACTCGCACGAGA
**
2231883 GT
66 AC
* * *
2231885 AACTAATCATGTTATTTCAGGTGACTCGTATGAGAGTCTCAAA-AGATTAGAGTAACTCGCACGA
1 ACCTAATCATGTTATTTCAGGT-ACTCGCACGAGAGTCTCAAAGA-ATTAGAGTAACTCGCACGA
2231949 GAAC
64 GAAC
2231953 ACCTAATCATGTT
1 ACCTAATCATGTT
2231966 TTTTGGGTGG
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
67 21 0.31
68 46 0.69
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (67 bp):
ACCTAATCATGTTATTTCAGGTACTCGCACGAGAGTCTCAAAGAATTAGAGTAACTCGCACGAGA
AC
Found at i:2248344 original size:15 final size:14
Alignment explanation
Indices: 2248324--2248362 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2248314 CATTTAGATC
2248324 TTTTAAAAAAATATT
1 TTTTAAAAAAA-ATT
2248339 TTTTAAAAAAAATT
1 TTTTAAAAAAAATT
* *
2248353 ATTCAAAAAA
1 TTTTAAAAAA
2248363 TATAAACGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTTAAAAAAAATT
Found at i:2248346 original size:14 final size:14
Alignment explanation
Indices: 2248324--2248365 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2248314 CATTTAGATC
2248324 TTTTAAAAAAATATT
1 TTTTAAAAAAATA-T
2248339 TTTTAAAAAAA-AT
1 TTTTAAAAAAATAT
* *
2248352 TATTCAAAAAATAT
1 TTTTAAAAAAATAT
2248366 AAACGTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.42
14 3 0.12
15 11 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TTTTAAAAAAATAT
Found at i:2250796 original size:304 final size:305
Alignment explanation
Indices: 2250233--2250842 Score: 1053
Period size: 304 Copynumber: 2.0 Consensus size: 305
2250223 ATAAATCGAC
* * *
2250233 ATGATTAATTGGTTTTTTCTTGAAAATTTTGACGTTCCATGCATTTTTTTGGTTGAATTGATAGC
1 ATGATTAATTGGTGTTTTCTTGAAAATTTTGACATTCCATGCATTTTTTTGGTTGAATTGATAAC
*
2250298 ATGACTTAGTGCAATTAAACCTTTAATGTAAGTTTTGAGCCTAATGAGCATACATTTTCTTTCTT
66 ATGACTTAGTGCAATTAAACCTTTAATGTAAGTTTTGAGCCTAATGAGCATACATTTACTTTCTT
*
2250363 TCTTTTTATTTGATTTGAGTGTGCCGACTAATTATTTGCATTCTAGAACTTCTAGCATAATGCTT
131 TCTATTTATTTGATTTGAGTGTGCCGACTAATTATTTGCATTCTAGAACTTCTAGCATAATGCTT
* *
2250428 GTCGGGACTATACGATTGAATGTGATGGATTAGCATGATAGAGGCATTAGGATTCAACCCTTTTG
196 GTCGGGACTACACGATTGAATGTGATGCATTAGCATGATAGAGGCATTAGGATTCAACCCTTTTG
2250493 ACTTCCCAAAAAATAGCCTACCCTTTGTTTAATTACCCATTAGAT
261 ACTTCCCAAAAAATAGCCTACCCTTTGTTTAATTACCCATTAGAT
2250538 ATGATTAATTGG-GTTTTCTTGAAAATTTTGACATTCCATGCATTTTTTTGGTTGAATTGATAAC
1 ATGATTAATTGGTGTTTTCTTGAAAATTTTGACATTCCATGCATTTTTTTGGTTGAATTGATAAC
* * *
2250602 ATGACTTAGTGCAATTAAACTTTTAATGTGAGTTTT-AGGCCTAATGAGCATATATTTACTTTCT
66 ATGACTTAGTGCAATTAAACCTTTAATGTAAGTTTTGA-GCCTAATGAGCATACATTTACTTTCT
* *
2250666 TTCTATTTGTTTGATTTGAGTGTGCCGACTAATTATTTGCATTCTAGAACTTGTAGCATAATGCT
130 TTCTATTTATTTGATTTGAGTGTGCCGACTAATTATTTGCATTCTAGAACTTCTAGCATAATGCT
* *
2250731 TGTCGGGGCTACACGATTGAATGTGATGCATTAGCATGATAGAGGCATTAGGATTTAACCCTTTT
195 TGTCGGGACTACACGATTGAATGTGATGCATTAGCATGATAGAGGCATTAGGATTCAACCCTTTT
* *
2250796 GACTTCCCAAAAAATAGCCTACCCTTTGTTTAGTTACCCCTTAGAT
260 GACTTCCCAAAAAATAGCCTACCCTTTGTTTAATTACCCATTAGAT
2250842 A
1 A
2250843 GCCAATTTTG
Statistics
Matches: 288, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
303 1 0.00
304 275 0.95
305 12 0.04
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (305 bp):
ATGATTAATTGGTGTTTTCTTGAAAATTTTGACATTCCATGCATTTTTTTGGTTGAATTGATAAC
ATGACTTAGTGCAATTAAACCTTTAATGTAAGTTTTGAGCCTAATGAGCATACATTTACTTTCTT
TCTATTTATTTGATTTGAGTGTGCCGACTAATTATTTGCATTCTAGAACTTCTAGCATAATGCTT
GTCGGGACTACACGATTGAATGTGATGCATTAGCATGATAGAGGCATTAGGATTCAACCCTTTTG
ACTTCCCAAAAAATAGCCTACCCTTTGTTTAATTACCCATTAGAT
Found at i:2252101 original size:23 final size:24
Alignment explanation
Indices: 2252054--2252112 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2252044 AGCAATTAGG
*
2252054 GGAATTGTCTTTTTCAATTTATTA
1 GGAATTATCTTTTTCAATTTATTA
*
2252078 GGGATTATCTTTTGT-AATTT-TTA
1 GGAATTATCTTTT-TCAATTTATTA
2252101 GGAATTATCTTT
1 GGAATTATCTTT
2252113 GCATTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.45
24 16 0.52
25 1 0.03
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (24 bp):
GGAATTATCTTTTTCAATTTATTA
Found at i:2252265 original size:20 final size:20
Alignment explanation
Indices: 2252240--2252279 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2252230 TTGTTTTATA
2252240 AAGTTTTTACTTTT-CTTTTC
1 AAGTTTTTA-TTTTACTTTTC
2252260 AAGTTTTTATTTTACTTTTC
1 AAGTTTTTATTTTACTTTTC
2252280 TTTTAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.65
Consensus pattern (20 bp):
AAGTTTTTATTTTACTTTTC
Done.