Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 20
Found at i:2179793 original size:64 final size:65
Alignment explanation
Indices: 2179640--2179800 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
2179630 GAATTAATTG
* * *** *
2179640 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
2179705 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
2179768 A
65 A
2179769 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
2179801 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:2179815 original size:64 final size:64
Alignment explanation
Indices: 2179640--2179820 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
2179630 GAATTAATTG
* * * *
2179640 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
2179705 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
2179769 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
2179821 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:2181533 original size:34 final size:34
Alignment explanation
Indices: 2181482--2181581 Score: 150
Period size: 34 Copynumber: 2.9 Consensus size: 34
2181472 CAAATGAACG
*
2181482 AACGTAAACAGAA-ACAAACAGG-TGAATATAAACA
1 AACGTAAAC-GAACACAAA-TGGATGAATATAAACA
2181516 AACGTAAACGAACACAAATGGATGAATATAAACA
1 AACGTAAACGAACACAAATGGATGAATATAAACA
*
2181550 AATGTAAACGAACACAAATGGATGAATATAAA
1 AACGTAAACGAACACAAATGGATGAATATAAA
2181582 TGAACAAACA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.08
34 57 0.92
ACGTcount: A:0.57, C:0.13, G:0.15, T:0.15
Consensus pattern (34 bp):
AACGTAAACGAACACAAATGGATGAATATAAACA
Found at i:2181790 original size:14 final size:14
Alignment explanation
Indices: 2181771--2181812 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
2181761 CAGGTCTGGA
2181771 GAACATAAACGAAT
1 GAACATAAACGAAT
* *
2181785 GAACATAAATGAAC
1 GAACATAAACGAAT
2181799 GAACATAAACGAAT
1 GAACATAAACGAAT
2181813 AGATTATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACATAAACGAAT
Found at i:2181913 original size:40 final size:40
Alignment explanation
Indices: 2181868--2181959 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
2181858 TCGTGTTCGC
*
2181868 TCATTTAATTAAACGAATATAAAATCTTTTTCATGTCCGT
1 TCATTTAATAAAACGAATATAAAATCTTTTTCATGTCCGT
2181908 TCATTTAATAAAACGAATATAAAATCTTTTTCATGTCCGT
1 TCATTTAATAAAACGAATATAAAATCTTTTTCATGTCCGT
2181948 TCATTTAATAAA
1 TCATTTAATAAA
2181960 TAAACGAACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (40 bp):
TCATTTAATAAAACGAATATAAAATCTTTTTCATGTCCGT
Found at i:2194566 original size:20 final size:20
Alignment explanation
Indices: 2194529--2194590 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 20
2194519 GTTCGTTCAT
** *
2194529 TTATGTTCGTGAACGTTCGG
1 TTATGTTCGTTTATGTTCGG
2194549 TTATGTTCGTTTATGTTCGTTCGG
1 TTATGTTCGTTTA---T-GTTCGG
2194573 TTATGTTCGTTTATGTTC
1 TTATGTTCGTTTATGTTC
2194591 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 15 0.43
21 1 0.03
24 19 0.54
ACGTcount: A:0.11, C:0.13, G:0.24, T:0.52
Consensus pattern (20 bp):
TTATGTTCGTTTATGTTCGG
Found at i:2194569 original size:24 final size:24
Alignment explanation
Indices: 2194542--2194590 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2194532 TGTTCGTGAA
2194542 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
2194566 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
2194590 C
1 C
2194591 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:2194570 original size:14 final size:14
Alignment explanation
Indices: 2194542--2194583 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
2194532 TGTTCGTGAA
2194542 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2194556 CG-T---TTATGTT
1 CGTTCGGTTATGTT
2194566 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2194580 CGTT
1 CGTT
2194584 TATGTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2194600 original size:24 final size:24
Alignment explanation
Indices: 2194548--2194603 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2194538 TGAACGTTCG
* *
2194548 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
2194572 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
2194596 TTTATGTT
1 GTTATGTT
2194604 TAACCCAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:2195119 original size:11 final size:11
Alignment explanation
Indices: 2195103--2195142 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
2195093 TGGGGCAATG
*
2195103 TCGAGCTTGAA
1 TCGAGCTTCAA
2195114 TCGAGCTTCAA
1 TCGAGCTTCAA
*
2195125 TCGAGCATCAA
1 TCGAGCTTCAA
2195136 TCGAGCT
1 TCGAGCT
2195143 CGAGACTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:2195489 original size:16 final size:16
Alignment explanation
Indices: 2195464--2195504 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2195454 AAAAAAATTT
*
2195464 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
2195480 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
2195496 T-TT-ATTTAT
1 TGTTCATTTAT
2195505 TAAATGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 2 0.08
16 16 0.67
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:2199522 original size:39 final size:39
Alignment explanation
Indices: 2199462--2199537 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
2199452 CCTGGCAGTG
*
2199462 CTGGAAGCTGCTGCAACTGATGCGTGGAGGGGCTGCTTA
1 CTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTTA
* * *
2199501 CTGGAAGCTGCTGGAAATGATGTGTGGAGGGGTTGCT
1 CTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
2199538 GGATGGAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.18, C:0.16, G:0.41, T:0.25
Consensus pattern (39 bp):
CTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTTA
Found at i:2200259 original size:73 final size:73
Alignment explanation
Indices: 2200135--2200660 Score: 845
Period size: 73 Copynumber: 7.2 Consensus size: 73
2200125 GAGGTCTTAT
* * *
2200135 CATCTTGCACTGTAGGGCTTACAGATGACCTTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
2200200 TTTGAAAA
66 TTTGAAAA
* * * *
2200208 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTATAAGATCAAAAAGCTTCTGAAGGATT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
*
2200273 TTTGATAA
66 TTTGAAAA
*
2200281 CATCATGCACTGTAGGTCTTACAGATGGCCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
2200346 TTTGAAAA
66 TTTGAAAA
* * *
2200354 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAGATCAAAAAGCTTCTGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
*
2200419 TTTGATAA
66 TTTGAAAA
* * *
2200427 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAGATCAAAAAGCTTCTGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
*
2200492 TTTGATAA
66 TTTGAAAA
*
2200500 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCTCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
2200565 TTTGAAAA
66 TTTGAAAA
*
2200573 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT---AAGATCAAAAAGCTCCCGAAGG
2200638 CTTTTTGAAAA
63 CTTTTTGAAAA
*
2200649 CATCCTGCACTG
1 CATCATGCACTG
2200661 CAAGGCTTAC
Statistics
Matches: 423, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
73 381 0.90
76 42 0.10
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (73 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
TTTGAAAA
Found at i:2200841 original size:11 final size:11
Alignment explanation
Indices: 2200825--2200849 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2200815 AACCTGCATT
2200825 TGCGTGATTCC
1 TGCGTGATTCC
2200836 TGCGTGATTCC
1 TGCGTGATTCC
2200847 TGC
1 TGC
2200850 ATTTGCGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.28, T:0.36
Consensus pattern (11 bp):
TGCGTGATTCC
Found at i:2201359 original size:22 final size:22
Alignment explanation
Indices: 2201308--2201365 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
2201298 GATAAAGCTT
* *
2201308 TCATCTTCGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2201330 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2201352 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
2201366 TGTAGATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:2201816 original size:54 final size:54
Alignment explanation
Indices: 2201734--2201888 Score: 157
Period size: 55 Copynumber: 2.9 Consensus size: 54
2201724 AATTACTGGT
* ** ** *
2201734 TCGTAAAACACTTGACAATGCATTCATCATTTCCTGTGGCTTATGCTTAGAGGC
1 TCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTATGCCCAGAGAC
* * * * * *
2201788 TCGTAAAACATTTGACAACACATTCATCATTCTCATGCGGTTTCTGCCCAGATAT
1 TCGTAAAACATTTGACAACACATTCATCATT-TCCTGTGGCTTATGCCCAGAGAC
* * * *
2201843 TCATAAAACATTTAATAACACATTCATCTTTTCCTGTGGCTTATGC
1 TCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTATGC
2201889 ACAAATTTAT
Statistics
Matches: 80, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
54 39 0.49
55 41 0.51
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (54 bp):
TCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTATGCCCAGAGAC
Found at i:2210360 original size:30 final size:27
Alignment explanation
Indices: 2210320--2210377 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
2210310 AAACATTAAT
* *
2210320 AAAATAAT-ATACATATAAATATTATG
1 AAAATAATAATATATATAAAAATTATG
*
2210346 AAAATAATAGATATATATAAAAATTTTG
1 AAAATAATA-ATATATATAAAAATTATG
2210374 AAAA
1 AAAA
2210378 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
28 19 0.70
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (27 bp):
AAAATAATAATATATATAAAAATTATG
Found at i:2210422 original size:6 final size:7
Alignment explanation
Indices: 2210403--2210427 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2210393 TAAATATATG
2210403 AATTTTT
1 AATTTTT
2210410 AATTTTT
1 AATTTTT
2210417 AATTTTT
1 AATTTTT
2210424 AATT
1 AATT
2210428 AATAGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:2211078 original size:11 final size:11
Alignment explanation
Indices: 2211062--2211095 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
2211052 ATTTTTATTT
2211062 AATAAAAAATA
1 AATAAAAAATA
2211073 AATAAAAAATA
1 AATAAAAAATA
2211084 AATAAACAAATA
1 AATAAA-AAATA
2211096 TTATTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (11 bp):
AATAAAAAATA
Found at i:2212319 original size:39 final size:39
Alignment explanation
Indices: 2212260--2212343 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
2212250 CCGGCAGTGT
* *
2212260 TGGAAGCTGCTGCAACTGATGCGTGGAGGGGCTGCTCGC
1 TGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTCGA
* * * *
2212299 TGGAAGCTGTTGGAAATGATGTGTGGAGGGGCTGCTGGA
1 TGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTCGA
2212338 TGGAAG
1 TGGAAG
2212344 GGGCTGCTCG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.19, C:0.14, G:0.44, T:0.23
Consensus pattern (39 bp):
TGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTCGA
Found at i:2230236 original size:29 final size:30
Alignment explanation
Indices: 2230166--2230241 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
2230156 TGGTTTACAC
*
2230166 AATTCATTTTACGTAAAACAATTTTCATGT
1 AATTCATTTTACGTAAAACAATTTTCAAGT
*
2230196 AATTCATTTTACGTAAAATAATTTT-AAGT
1 AATTCATTTTACGTAAAACAATTTTCAAGT
2230225 AATTCATTTTACGTAAA
1 AATTCATTTTACGTAAA
2230242 TTATTTTCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 20 0.45
30 24 0.55
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (30 bp):
AATTCATTTTACGTAAAACAATTTTCAAGT
Found at i:2230247 original size:14 final size:15
Alignment explanation
Indices: 2230166--2230248 Score: 75
Period size: 15 Copynumber: 5.7 Consensus size: 15
2230156 TGGTTTACAC
2230166 AATTCATTTTACGTA
1 AATTCATTTTACGTA
* *
2230181 AA-ACAATTTTCATGT-
1 AATTC-ATTTT-ACGTA
2230196 AATTCATTTTACGTA
1 AATTCATTTTACGTA
* * *
2230211 AAATAATTTTAAGT-
1 AATTCATTTTACGTA
2230225 AATTCATTTTACGTA
1 AATTCATTTTACGTA
2230240 AATT-ATTTT
1 AATTCATTTT
2230249 CTAGAAAACC
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
14 20 0.38
15 29 0.55
16 4 0.08
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (15 bp):
AATTCATTTTACGTA
Found at i:2231624 original size:143 final size:143
Alignment explanation
Indices: 2231364--2231918 Score: 684
Period size: 143 Copynumber: 3.9 Consensus size: 143
2231354 AATTCGGTGA
* * * * * * *
2231364 CAGAAACTTTTCAATGATATATCAACTCATTTCAGAAAACTTTTTAATAGTGGTATATCAGTTTA
1 CAGAAACTTTTCAGTGATATATCAACTCATTTTAGAAAACTTTTCAGTAGTGATATATCACTTCA
* ** * *
2231429 TATCATAAAAACGTCCATTTCTCATAGGCCATTTAATTTACAATGACCAAAACTTTTCAATGCCC
66 TATCAAAAAAACGTCCATTTCTCATAGGCCATTTAATGCACAATGGCAAAAACTTTTCAATGCCC
*
2231494 AGTAAGTTCTCTT
131 AGTAACTTCTCTT
* * * * *
2231507 CAGAAACTTATCAGTGATATATCAGCTTATTTTAGAAAACTTTTCAGTAGTGATATCTCACTTTA
1 CAGAAACTTTTCAGTGATATATCAACTCATTTTAGAAAACTTTTCAGTAGTGATATATCACTTCA
* * * * *
2231572 TATCATAAAAACGTCCATTTCTTATAGGCCATTTAATGTACAATTGCAAAAACTTTTTAAGTGCC
66 TATCAAAAAAACGTCCATTTCTCATAGGCCATTTAATGCACAATGGCAAAAACTTTTCAA-TGCC
2231637 CAAG-AACTTCTCTT
130 C-AGTAACTTCTCTT
* * *
2231651 TAGAAACTTTTTAGTGATATATCAACTCATTTTAGAAAACTTTTAAGTAGTGATATATCACTTCA
1 CAGAAACTTTTCAGTGATATATCAACTCATTTTAGAAAACTTTTCAGTAGTGATATATCACTTCA
* * * *
2231716 TATTAAAAAAAGCGTCCATTTCTCATAGGCCATTTAATGCACAATGGCATAAACTTTT-AGTTCC
66 TATCAAAAAAA-CGTCCATTTCTCATAGGCCATTTAATGCACAATGGCAAAAACTTTTCAATGCC
* *
2231780 CAATAACTTATCTT
130 CAGTAACTTCTCTT
* * *
2231794 CAGAAACTTTTCAGTGATATATCAACTCATTTAAAAAAACTTTTCAGTTA-TTATATATCACTTC
1 CAGAAACTTTTCAGTGATATATCAACTCATTTTAGAAAACTTTTCAG-TAGTGATATATCACTTC
* * ** *
2231858 ATTTTAGAAAAAAAATCCATTTCTCATAGGCCATTTAATGCACAATGGCAGAAACTTTTCA
65 ATATCA-AAAAAACGTCCATTTCTCATAGGCCATTTAATGCACAATGGCAAAAACTTTTCA
2231919 GTAATATATC
Statistics
Matches: 360, Mismatches: 45, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
142 1 0.00
143 225 0.62
144 90 0.25
145 44 0.12
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (143 bp):
CAGAAACTTTTCAGTGATATATCAACTCATTTTAGAAAACTTTTCAGTAGTGATATATCACTTCA
TATCAAAAAAACGTCCATTTCTCATAGGCCATTTAATGCACAATGGCAAAAACTTTTCAATGCCC
AGTAACTTCTCTT
Found at i:2231948 original size:287 final size:287
Alignment explanation
Indices: 2231365--2231916 Score: 716
Period size: 287 Copynumber: 1.9 Consensus size: 287
2231355 ATTCGGTGAC
* * *
2231365 AGAAACTTTTCAATGATATATCAACTCATTTCAGAAAACTTTTTAATAGTGGTATATCAGTTTAT
1 AGAAACTTTTCAATGATATATCAACTCATTTCAGAAAACTTTTTAATAGTGATATATCACTTCAT
* **
2231430 ATCATAAAAACGTCCATTTCTCATAGGCCATTTAATTTACAATGACCAAAACTTTTCAATGCCCA
66 ATCAAAAAAACGTCCATTTCTCATAGGCCATTTAATGCACAATGACCAAAACTTTTCAATGCCCA
* * * * * * *
2231495 GTAAGTTCTCTTCAGAAACTTATCAGTGATATATCAGCTTATTTTAGAAAACTTTTCAGTAGTGA
131 ATAACTTATCTTCAGAAACTTATCAGTGATATATCAACTCATTTAAAAAAACTTTTCAGTAGTGA
* * * ** * * *
2231560 TATCTCACTTTATATCATAAAAACGTCCATTTCTTATAGGCCATTTAATGTACAATTGCAAAAAC
196 TATATCACTTCATATCAAAAAAAAATCCATTTCTCATAGGCCATTTAATGCACAATGGCAAAAAC
**
2231625 TTTTTAAGTGCCCAAGAACTTCTCTTT
261 TTTTTAAGTGAACAAGAACTTCTCTTT
* * *
2231652 AGAAACTTTTTAGTGATATATCAACTCATTTTAGAAAAC-TTTTAAGTAGTGATATATCACTTCA
1 AGAAACTTTTCAATGATATATCAACTCATTTCAGAAAACTTTTTAA-TAGTGATATATCACTTCA
* * * *
2231716 TATTAAAAAAAGCGTCCATTTCTCATAGGCCATTTAATGCACAATG-GCATAAACTTTT-AGTTC
65 TATCAAAAAAA-CGTCCATTTCTCATAGGCCATTTAATGCACAATGACCA-AAACTTTTCAATGC
*
2231779 CCAATAACTTATCTTCAGAAACTTTTCAGTGATATATCAACTCATTTAAAAAAACTTTTCAGTTA
128 CCAATAACTTATCTTCAGAAACTTATCAGTGATATATCAACTCATTTAAAAAAACTTTTCAG-TA
* * *
2231844 -TTATATATCACTTCATTTTAGAAAAAAAATCCATTTCTCATAGGCCATTTAATGCACAATGGCA
192 GTGATATATCACTTCATATCA-AAAAAAAATCCATTTCTCATAGGCCATTTAATGCACAATGGCA
*
2231908 GAAACTTTT
256 AAAACTTTT
2231917 CAGTAATATA
Statistics
Matches: 227, Mismatches: 33, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
286 6 0.03
287 134 0.59
288 87 0.38
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (287 bp):
AGAAACTTTTCAATGATATATCAACTCATTTCAGAAAACTTTTTAATAGTGATATATCACTTCAT
ATCAAAAAAACGTCCATTTCTCATAGGCCATTTAATGCACAATGACCAAAACTTTTCAATGCCCA
ATAACTTATCTTCAGAAACTTATCAGTGATATATCAACTCATTTAAAAAAACTTTTCAGTAGTGA
TATATCACTTCATATCAAAAAAAAATCCATTTCTCATAGGCCATTTAATGCACAATGGCAAAAAC
TTTTTAAGTGAACAAGAACTTCTCTTT
Found at i:2242915 original size:17 final size:19
Alignment explanation
Indices: 2242893--2242929 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
2242883 GTCCAAACCC
2242893 AAAATA-TTAAAA-CTAAA
1 AAAATATTTAAAATCTAAA
2242910 AAAATATTTAAAATCTAAA
1 AAAATATTTAAAATCTAAA
2242929 A
1 A
2242930 CATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 6 0.33
19 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATATTTAAAATCTAAA
Found at i:2255645 original size:18 final size:17
Alignment explanation
Indices: 2255618--2255666 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2255608 TTGTCTGTGT
*
2255618 AGAAATCAGACTATAGAA
1 AGAAAACAGACTATAG-A
*
2255636 AGAAAACAGACTGTATAGT
1 AGAAAACAGAC--TATAGA
2255655 AGAAAACAGACT
1 AGAAAACAGACT
2255667 GTAGGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 10 0.37
19 11 0.41
20 5 0.19
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.16
Consensus pattern (17 bp):
AGAAAACAGACTATAGA
Found at i:2257643 original size:36 final size:36
Alignment explanation
Indices: 2257595--2257666 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2257585 TTACCTTCTG
*
2257595 TTTCAGATGCAACAGGATCCGAATCTAGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTAGTTCTTGGC
*
2257631 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTAGTTCTTGGC
2257667 GAATGCTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (36 bp):
TTTCAGAGGCAACAGGATCCGAATCTAGTTCTTGGC
Found at i:2259763 original size:18 final size:17
Alignment explanation
Indices: 2259736--2259784 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2259726 GATACCATGT
*
2259736 AGAAATCAGACTATAGAA
1 AGAAAACAGACTATAG-A
*
2259754 AGAAAACAGACTGTATAGT
1 AGAAAACAGAC--TATAGA
2259773 AGAAAACAGACT
1 AGAAAACAGACT
2259785 GTAGGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 10 0.37
19 11 0.41
20 5 0.19
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.16
Consensus pattern (17 bp):
AGAAAACAGACTATAGA
Found at i:2290375 original size:23 final size:23
Alignment explanation
Indices: 2290349--2290448 Score: 182
Period size: 23 Copynumber: 4.3 Consensus size: 23
2290339 AGGAAAACCT
2290349 AATTTTTTAAGAAATTCAAAATC
1 AATTTTTTAAGAAATTCAAAATC
2290372 AATTTTTTAAGAAATTCAAAATC
1 AATTTTTTAAGAAATTCAAAATC
2290395 AATTTTTTAAGAAATTCAAAATC
1 AATTTTTTAAGAAATTCAAAATC
*
2290418 AATTTTTTAAGAAATTCAAAATT
1 AATTTTTTAAGAAATTCAAAATC
*
2290441 GATTTTTT
1 AATTTTTT
2290449 GGGTTTCCTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (23 bp):
AATTTTTTAAGAAATTCAAAATC
Found at i:2291992 original size:129 final size:129
Alignment explanation
Indices: 2291772--2292012 Score: 482
Period size: 129 Copynumber: 1.9 Consensus size: 129
2291762 CATATACTCT
2291772 TATACCTAACATTCGTAATCATCATATAACTCATTTAACCAAGCAATATGCACACAACATCACAT
1 TATACCTAACATTCGTAATCATCATATAACTCATTTAACCAAGCAATATGCACACAACATCACAT
2291837 AAATCATGTAATACATTTCACATAACAAAGCATATATATATATATATCACAAAGCATATATATA
66 AAATCATGTAATACATTTCACATAACAAAGCATATATATATATATATCACAAAGCATATATATA
2291901 TATACCTAACATTCGTAATCATCATATAACTCATTTAACCAAGCAATATGCACACAACATCACAT
1 TATACCTAACATTCGTAATCATCATATAACTCATTTAACCAAGCAATATGCACACAACATCACAT
2291966 AAATCATGTAATACATTTCACATAACAAAGCATATATATATATATAT
66 AAATCATGTAATACATTTCACATAACAAAGCATATATATATATATAT
2292013 ATATATATCA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 112 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (129 bp):
TATACCTAACATTCGTAATCATCATATAACTCATTTAACCAAGCAATATGCACACAACATCACAT
AAATCATGTAATACATTTCACATAACAAAGCATATATATATATATATCACAAAGCATATATATA
Found at i:2292176 original size:25 final size:25
Alignment explanation
Indices: 2292148--2292224 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
2292138 CACTGAGTGC
* *
2292148 CATATAAAATTGTCCTGAAGGACCT
1 CATATAAAATTGTCCCGAAGGACCA
*
2292173 C--ATAGAATTGTCCCGAAGGACCA
1 CATATAAAATTGTCCCGAAGGACCA
* * * *
2292196 C--ATAGAATTGTCTCTAAGAACCA
1 CATATAAAATTGTCCCGAAGGACCA
2292219 CATATA
1 CATATA
2292225 TGTTTCAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
23 40 0.91
25 4 0.09
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (25 bp):
CATATAAAATTGTCCCGAAGGACCA
Found at i:2292181 original size:23 final size:23
Alignment explanation
Indices: 2292155--2292222 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2292145 TGCCATATAA
* *
2292155 AATTGTCCTGAAGGACCTCATAG
1 AATTGTCCCGAAGGACCACATAG
2292178 AATTGTCCCGAAGGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
* * *
2292201 AATTGTCTCTAAGAACCACATA
1 AATTGTCCCGAAGGACCACATA
2292223 TATGTTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:2292265 original size:21 final size:21
Alignment explanation
Indices: 2292241--2292302 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
2292231 AAATGATCAA
2292241 ATATATGTCCCAAAGGACCGC
1 ATATATGTCCCAAAGGACCGC
* * * *
2292262 ATATATATTCCAAAGGATCAC
1 ATATATGTCCCAAAGGACCGC
2292283 ATATATG-CCCGAAA-GACCGC
1 ATATATGTCCC-AAAGGACCGC
2292303 GTAGAACCCT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (21 bp):
ATATATGTCCCAAAGGACCGC
Found at i:2292281 original size:42 final size:41
Alignment explanation
Indices: 2292219--2292302 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 41
2292209 CTAAGAACCA
* * *
2292219 CATATATGTTTCAAATGATCAAATATATGTCCC-AAAGGACCG
1 CATATATATTCCAAAGGATCAAATATATG-CCCGAAA-GACCG
*
2292261 CATATATATTCCAAAGGATCACATATATGCCCGAAAGACCG
1 CATATATATTCCAAAGGATCAAATATATGCCCGAAAGACCG
2292302 C
1 C
2292303 GTAGAACCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 9 0.24
42 28 0.76
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (41 bp):
CATATATATTCCAAAGGATCAAATATATGCCCGAAAGACCG
Found at i:2293041 original size:35 final size:35
Alignment explanation
Indices: 2292979--2293046 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2292969 CATTGTAAAT
* * *
2292979 ATGGTACCGATACTTCCACATTGGTATCGATACTC
1 ATGGCACCGATACTACCACATTAGTATCGATACTC
2293014 ATGGCACCGATACTACCAC-TTCAGTATCGATAC
1 ATGGCACCGATACTACCACATT-AGTATCGATAC
2293047 CCCATGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 2 0.07
35 27 0.93
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (35 bp):
ATGGCACCGATACTACCACATTAGTATCGATACTC
Found at i:2296206 original size:21 final size:21
Alignment explanation
Indices: 2296180--2296319 Score: 136
Period size: 21 Copynumber: 6.6 Consensus size: 21
2296170 TATAAAATTA
*
2296180 TCCCGAATGACCACATATATG
1 TCCCGAAGGACCACATATATG
*
2296201 TCCCGAAGGACCACATAGAATTG
1 TCCCGAAGGACCACATA-TA-TG
* * *
2296224 TCCCTAAAGACCACATATATA
1 TCCCGAAGGACCACATATATG
* * * *
2296245 TTCCAAATGACCAAATATATG
1 TCCCGAAGGACCACATATATG
*
2296266 TCCCGAAGGACCGCATATATG
1 TCCCGAAGGACCACATATATG
* * **
2296287 TTCCAAAGGATAACATATATG
1 TCCCGAAGGACCACATATATG
2296308 TCCCGAAGGACC
1 TCCCGAAGGACC
2296320 GCGTAGAACC
Statistics
Matches: 92, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
21 73 0.79
22 2 0.02
23 17 0.18
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATG
Found at i:2300968 original size:21 final size:21
Alignment explanation
Indices: 2300934--2300990 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
2300924 GTTGGAACAA
*
2300934 AAGGATCAATCCTTTAA-GGG
1 AAGGATCGATCCTTTAAGGGG
2300954 AAGTGAGT-GATCCTTTAAGGGG
1 AAG-GA-TCGATCCTTTAAGGGG
2300976 AAGGATCGATCCTTT
1 AAGGATCGATCCTTT
2300991 TCATCGAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.12
21 21 0.66
22 7 0.22
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (21 bp):
AAGGATCGATCCTTTAAGGGG
Found at i:2301002 original size:21 final size:21
Alignment explanation
Indices: 2300978--2301052 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
2300968 TTAAGGGGAA
2300978 GGATCGATCCTTTTCATCGAG
1 GGATCGATCCTTTTCATCGAG
**
2300999 GGATCGATCCTTTTGGT-GAAG
1 GGATCGATCCTTTTCATCG-AG
* *
2301020 GGATTGATCCTTTTCCTCGAG
1 GGATCGATCCTTTTCATCGAG
2301041 GGATCGATCCTT
1 GGATCGATCCTT
2301053 ATTGTAAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.96
22 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (21 bp):
GGATCGATCCTTTTCATCGAG
Found at i:2301008 original size:42 final size:42
Alignment explanation
Indices: 2300962--2301052 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
2300952 GGAAGTGAGT
2300962 GATCCTTTAAGGGGAA-GGATCGATCCTTTTCATCGAGGGATC
1 GATCCTTT-AGGGGAAGGGATCGATCCTTTTCATCGAGGGATC
* * * *
2301004 GATCCTTTTGGTGAAGGGATTGATCCTTTTCCTCGAGGGATC
1 GATCCTTTAGGGGAAGGGATCGATCCTTTTCATCGAGGGATC
2301046 GATCCTT
1 GATCCTT
2301053 ATTGTAAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 5 0.11
42 39 0.89
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (42 bp):
GATCCTTTAGGGGAAGGGATCGATCCTTTTCATCGAGGGATC
Found at i:2301071 original size:42 final size:42
Alignment explanation
Indices: 2300978--2301071 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
2300968 TTAAGGGGAA
*
2300978 GGATCGATCCTTTTCATCGAGGGATCGATCCTTTTGGTGAAG
1 GGATCGATCCTTTTCATCGAGGGATCGATCCTTTTGGTAAAG
* * *
2301020 GGATTGATCCTTTTCCTCGAGGGATCGATCCTTATT-GTAAAT
1 GGATCGATCCTTTTCATCGAGGGATCGATCCTT-TTGGTAAAG
2301062 GGATCGATCC
1 GGATCGATCC
2301072 CAAACTCACT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (42 bp):
GGATCGATCCTTTTCATCGAGGGATCGATCCTTTTGGTAAAG
Found at i:2306966 original size:17 final size:18
Alignment explanation
Indices: 2306937--2306984 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
2306927 CAAAAAAAAA
*
2306937 TTAATTAAA-TAAAATA-
1 TTAAATAAATTAAAATAT
*
2306953 TTAAA-AAATTTAAATAT
1 TTAAATAAATTAAAATAT
2306970 TTAAATAAATTAAAA
1 TTAAATAAATTAAAA
2306985 ACAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 5 0.19
18 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATAAATTAAAATAT
Found at i:2308236 original size:2 final size:2
Alignment explanation
Indices: 2308229--2308261 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2308219 TTGATAAAAT
2308229 TA 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 TA T
2308262 TTGTTTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2308839 original size:27 final size:27
Alignment explanation
Indices: 2308808--2308863 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2308798 CCTGATGTCG
*
2308808 CCGCCACTATCACATG-GTTTTATGACC
1 CCGCCACCATCACA-GAGTTTTATGACC
*
2308835 CCGCCACCGTCACAGAGTTTTATGACC
1 CCGCCACCATCACAGAGTTTTATGACC
2308862 CC
1 CC
2308864 TCCTGGAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (27 bp):
CCGCCACCATCACAGAGTTTTATGACC
Found at i:2309457 original size:35 final size:32
Alignment explanation
Indices: 2309422--2309502 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
2309412 TTTGGTTAAT
2309422 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAATA-C--TTATTGTAA
2309456 TTTGTTTATCATTTACCATTTAATACTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATACTTATTGTAA
*
2309491 GTTTGTTGTATT
1 -TTTGTTATATT
2309503 TAAAATTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 2 0.05
38 13 0.32
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATACTTATTGTAA
Found at i:2314720 original size:14 final size:14
Alignment explanation
Indices: 2314698--2314730 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2314688 CGTTCGTGAA
*
2314698 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
2314712 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
2314726 CGTTT
1 CGTTT
2314731 ATGTTCATTC
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:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:2315490 original size:10 final size:10
Alignment explanation
Indices: 2315475--2315549 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
2315465 GGGCCTCCAA
2315475 CGTTTATGTT
1 CGTTTATGTT
2315485 CGTTTATGTT
1 CGTTTATGTT
2315495 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
2315506 ATGTTCGTGTT
1 -CGTTTATGTT
2315517 CGTTTATGTT
1 CGTTTATGTT
2315527 CG----TGTT
1 CGTTTATGTT
2315533 CGTTTATGTT
1 CGTTTATGTT
*
2315543 CATTTAT
1 CGTTTAT
2315550 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.66
11 7 0.14
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2315506 original size:16 final size:16
Alignment explanation
Indices: 2315481--2315543 Score: 117
Period size: 16 Copynumber: 3.9 Consensus size: 16
2315471 CCAACGTTTA
2315481 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
2315497 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
2315513 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2315529 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
2315544 ATTTATTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.13, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2327350 original size:44 final size:44
Alignment explanation
Indices: 2327270--2327354 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
2327260 TTGAAATTAT
*
2327270 AAAATTATAACTCAAAACTAATTCGAATTTAATTTTTACGAATC
1 AAAATTATAACTCAAAACTAATTCGAATTGAATTTTTACGAATC
* * * *
2327314 AAAATTATAACTCGAAATTAATT-GGATTCGAGTTTTTACGA
1 AAAATTATAACTCAAAACTAATTCGAATT-GAATTTTTACGA
2327355 GCCAAAATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 4 0.11
44 31 0.89
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (44 bp):
AAAATTATAACTCAAAACTAATTCGAATTGAATTTTTACGAATC
Found at i:2327505 original size:89 final size:89
Alignment explanation
Indices: 2327387--2327564 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
2327377 GCTATACAGA
2327387 GCCAAACAAAAAACGTGGCTTTAATTAATAGGAACTCAACGTCGTGGGATTTCAATATAACATTT
1 GCCAAACAAAAAACGTGGCTTTAATTAATAGGAACTCAACGTCGTGGGATTTCAATATAACATTT
2327452 TTTTAGCTGACTTGTTCTTCATTT
66 TTTTAGCTGACTTGTTCTTCATTT
2327476 GCCAAACAAAAAACGTGGCTTTAATTAATAGGAACTCAACGTCGTGGGATTTCAATATAACATTT
1 GCCAAACAAAAAACGTGGCTTTAATTAATAGGAACTCAACGTCGTGGGATTTCAATATAACATTT
2327541 TTTTAGCTGACTTGTTCTTCATTT
66 TTTTAGCTGACTTGTTCTTCATTT
2327565 ACCTTTCCTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (89 bp):
GCCAAACAAAAAACGTGGCTTTAATTAATAGGAACTCAACGTCGTGGGATTTCAATATAACATTT
TTTTAGCTGACTTGTTCTTCATTT
Found at i:2328619 original size:12 final size:12
Alignment explanation
Indices: 2328596--2328642 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
2328586 GTTTTTTATA
2328596 TAATATATTTTTT
1 TAATA-ATTTTTT
2328609 TAATAATTTTTT
1 TAATAATTTTTT
2328621 TAAT--TTTTTT
1 TAATAATTTTTT
* *
2328631 AAATAAATTTTT
1 TAATAATTTTTT
2328643 AAAATTATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.30
12 16 0.53
13 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TAATAATTTTTT
Found at i:2328635 original size:22 final size:21
Alignment explanation
Indices: 2328602--2328642 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2328592 TATATAATAT
*
2328602 ATTTTTTTAATAATTTTTTTA
1 ATTTTTTTAATAAATTTTTTA
2328623 ATTTTTTTAAATAAATTTTT
1 ATTTTTTT-AATAAATTTTT
2328643 AAAATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTTTTAATAAATTTTTTA
Found at i:2328643 original size:21 final size:21
Alignment explanation
Indices: 2328602--2328644 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2328592 TATATAATAT
*
2328602 ATTTTTTTAATAATTTTTTTA
1 ATTTTTTTAATAATATTTTTA
2328623 ATTTTTTTAAATAA-ATTTTTA
1 ATTTTTTT-AATAATATTTTTA
2328644 A
1 A
2328645 AATTATGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTTTTAATAATATTTTTA
Found at i:2329139 original size:3 final size:3
Alignment explanation
Indices: 2329133--2329179 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2329123 AATAATAATA
2329133 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2329180 CAAATAATAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2336056 original size:62 final size:63
Alignment explanation
Indices: 2335917--2336071 Score: 195
Period size: 62 Copynumber: 2.5 Consensus size: 63
2335907 TTTCCTTGAA
* *
2335917 TCAATCTTTGACTTCCTCGTGAAGAGAAGTAAACTTTTATTATACCCTGACTCCTCAGTAGAG
1 TCAATCTTTGACTTCCTCGTGAAGAGAAGTAAACTTTTATTATACCCTGACTCCCCAATAGAG
* * * * * ** * *
2335980 TCAATTTTTAACTTCCTCTTAAAGAGAAGTTAGTTTTTGTTAT-TCCTGACTCCCCAATAGAG
1 TCAATCTTTGACTTCCTCGTGAAGAGAAGTAAACTTTTATTATACCCTGACTCCCCAATAGAG
*
2336042 TCAATCATTGACTTCCTCGTGAAGAGAAGT
1 TCAATCTTTGACTTCCTCGTGAAGAGAAGT
2336072 CAACCTGTAG
Statistics
Matches: 76, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
62 41 0.54
63 35 0.46
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35
Consensus pattern (63 bp):
TCAATCTTTGACTTCCTCGTGAAGAGAAGTAAACTTTTATTATACCCTGACTCCCCAATAGAG
Found at i:2336096 original size:42 final size:42
Alignment explanation
Indices: 2336037--2336117 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
2336027 GACTCCCCAA
*
2336037 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACCTG
1 TAGAGTCAATCATTGACTTCCTCATGAAGAGAAGTCAACCTG
* *
2336079 TAGAGTCAATCCTTGACTTCCTCATGAATAGAAGTCAAC
1 TAGAGTCAATCATTGACTTCCTCATGAAGAGAAGTCAAC
2336118 ATTTTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (42 bp):
TAGAGTCAATCATTGACTTCCTCATGAAGAGAAGTCAACCTG
Found at i:2336301 original size:62 final size:61
Alignment explanation
Indices: 2336078--2336304 Score: 199
Period size: 62 Copynumber: 3.7 Consensus size: 61
2336068 AAGTCAACCT
* ** *
2336078 GTAGAGTCAATCCTTGACTTCCTCATGAATAGAAGTCAACATTT-TTTATTCCTGGCTCCTCA
1 GTAGAGTCAATCCTTGACTTCCTCATGAAGAGAAGTC-A-ATTTGTTTATTCCTTACTCCCCA
** * * *
2336140 GTAGAGTCAATTTTTAACTTCCTCGTGAAGAGAATTCAACCTTTG-TTATTCCTTAACTCCCCA
1 GTAGAGTCAATCCTTGACTTCCTCATGAAGAGAAGTCAA--TTTGTTTATTCCTT-ACTCCCCA
* * ** * * * *
2336203 G-AGTAGCCAATCCTTGATTTCCTTGTAAATAAAAGTCAATTTGTATTATTTCTTACTCCCCA
1 GTAG-AGTCAATCCTTGACTTCCTCATGAAGAGAAGTCAATTTGT-TTATTCCTTACTCCCCA
* *
2336265 GTAGAGTCAATTCTTGACTTCCTCATTAAGAGAAGTCAAT
1 GTAGAGTCAATCCTTGACTTCCTCATGAAGAGAAGTCAAT
2336305 ATTATAAATT
Statistics
Matches: 129, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
60 1 0.01
61 5 0.04
62 81 0.63
63 42 0.33
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (61 bp):
GTAGAGTCAATCCTTGACTTCCTCATGAAGAGAAGTCAATTTGTTTATTCCTTACTCCCCA
Found at i:2336766 original size:152 final size:150
Alignment explanation
Indices: 2336500--2336944 Score: 370
Period size: 163 Copynumber: 2.9 Consensus size: 150
2336490 TTTATTTGAA
* * * * * * *
2336500 TACCCGAAAAATGGCACAAATCCAGTTTGATCTCCTCTGAATGAATAATAGAGTAGACACATCTT
1 TACCCGAAAAAAGGCACAAATCCAGTCTAATATCCCCTGAATGAATAATAGAGCAGAAACATCTT
* *
2336565 CAAAATTGATTTGAATACCCAAAAAAGTGGCACAGATCCAATCTAATCTCCCCTGAATAAATAGT
66 CAAAATTGATCTGAATACCCAAAAAAGAGGCACAGATCCAATCTAATCTCCCCTGAATAAATAGT
2336630 GGAGCAAAAATTAATCTCAC
131 GGAGCAAAAATTAATCTCAC
* * *
2336650 TACCCGAAAAAGAGGCA-AAGATCCAGTCTAATATCCCCTGAATGAATAGTGGAGCATAAACATC
1 TACCCGAAAAA-AGGCACAA-ATCCAGTCTAATATCCCCTGAATGAATAATAGAGCAGAAACATC
* * * * * *
2336714 TTCAAAAATTGATCTGAATACCCGAAAAAGAGGCACATATCCAGTCTGATCTCCCTTGAATGAAT
64 TTC-AAAATTGATCTGAATACCCAAAAAAGAGGCACAGATCCAATCTAATCTCCCCTGAATAAAT
* * *
2336779 AGTAGAGTAGAAACATCTTCAAAAATTGATCTGAA
128 AGT-G-G-AG---------CAAAAATTAATCTCAC
* * * * * * * * * * * * * *
2336814 TACCCGAAAAAAAGTCACAAATCTATTCTGATCTCCTCTAAATGAATAGTGGGGTAGATACGTTT
1 TACCCG-AAAAAAGGCACAAATCCAGTCTAATATCCCCTGAATGAATAATAGAGCAGAAACATCT
* * * * * *
2336879 TCAAAATTGATCTGAATACCCGAAAGAGAGGCACAGATCCAATCTGATATTCCCTGAATGAATAG
65 TCAAAATTGATCTGAATACCCAAAAAAGAGGCACAGATCCAATCTAATCTCCCCTGAATAAATAG
2336944 T
130 T
2336945 AAAGTAGACC
Statistics
Matches: 238, Mismatches: 40, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
150 13 0.05
151 42 0.18
152 56 0.24
153 1 0.00
154 1 0.00
155 2 0.01
163 58 0.24
164 58 0.24
165 7 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (150 bp):
TACCCGAAAAAAGGCACAAATCCAGTCTAATATCCCCTGAATGAATAATAGAGCAGAAACATCTT
CAAAATTGATCTGAATACCCAAAAAAGAGGCACAGATCCAATCTAATCTCCCCTGAATAAATAGT
GGAGCAAAAATTAATCTCAC
Found at i:2336939 original size:81 final size:81
Alignment explanation
Indices: 2336634--2336944 Score: 372
Period size: 82 Copynumber: 3.8 Consensus size: 81
2336624 AATAGTGGAG
* * * * * *
2336634 CAAAAATTAATCTCACTACCCGAAAAAGAGGCAAAGATCCAGTCTAATATCCCCTGAATGAATAG
1 CAAAAATTGATCTGAATACCCGAAAAAGAGGCACAGATCCAGTCTGATCT-CCCTGAATGAATAG
* *
2336699 TGGAGCATAAACATCTT
65 TGGAGTAGAAACATCTT
*
2336716 CAAAAATTGATCTGAATACCCGAAAAAGAGGCACATATCCAGTCTGATCTCCCTTGAATGAATAG
1 CAAAAATTGATCTGAATACCCGAAAAAGAGGCACAGATCCAGTCTGATCTCCC-TGAATGAATAG
*
2336781 TAGAGTAGAAACATCTT
65 TGGAGTAGAAACATCTT
* * * * * *
2336798 CAAAAATTGATCTGAATACCCGAAAAAAAGTCACAAATCTATTCTGATCTCCTCTAAATGAATAG
1 CAAAAATTGATCTGAATACCCGAAAAAGAGGCACAGATCCAGTCTGATCTCC-CTGAATGAATAG
* * * *
2336863 TGGGGTAGATACGTTTT
65 TGGAGTAGAAACATCTT
* * *
2336880 C-AAAATTGATCTGAATACCCGAAAGAGAGGCACAGATCCAATCTGATATTCCCTGAATGAATAG
1 CAAAAATTGATCTGAATACCCGAAAAAGAGGCACAGATCCAGTCTGAT-CTCCCTGAATGAATAG
2336944 T
65 T
2336945 AAAGTAGACC
Statistics
Matches: 197, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
81 55 0.28
82 141 0.72
83 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (81 bp):
CAAAAATTGATCTGAATACCCGAAAAAGAGGCACAGATCCAGTCTGATCTCCCTGAATGAATAGT
GGAGTAGAAACATCTT
Found at i:2341179 original size:2 final size:2
Alignment explanation
Indices: 2341166--2341200 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
2341156 ATATTATTTG
2341166 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2341201 AGTTTTGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2342865 original size:6 final size:6
Alignment explanation
Indices: 2342854--2342881 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2342844 AATGACTCTC
2342854 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
2342882 TAAAAAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:2343155 original size:21 final size:21
Alignment explanation
Indices: 2343130--2343180 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2343120 TTGTTTGTAT
2343130 TAAAATAATATTATTAATTAA
1 TAAAATAATATTATTAATTAA
** *
2343151 TAAAATTTTATTATTTATTAA
1 TAAAATAATATTATTAATTAA
2343172 -AAAATAATA
1 TAAAATAATA
2343181 AATTAGTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATAATATTATTAATTAA
Found at i:2344050 original size:14 final size:14
Alignment explanation
Indices: 2344018--2344052 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2344008 TTGTTTCACT
*
2344018 GAAAATGTTTTCTG
1 GAAAATGTTTTCCG
2344032 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
*
2344046 TAAAATG
1 GAAAATG
2344053 AATTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (14 bp):
GAAAATGTTTTCCG
Found at i:2344200 original size:14 final size:16
Alignment explanation
Indices: 2344169--2344206 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
2344159 TAAAATAAAT
2344169 AATATTATTTATCATAA
1 AATATTATTTAT-ATAA
2344186 AATATTATTT-T-TAA
1 AATATTATTTATATAA
2344200 AATATTA
1 AATATTA
2344207 AAATAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
16 1 0.05
17 10 0.48
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATTATTTATATAA
Found at i:2344301 original size:24 final size:24
Alignment explanation
Indices: 2344256--2344301 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2344246 TTATTAATAA
* *
2344256 AAATATAAATATTGATATTTATTG
1 AAATAAAAATATTGATAATTATTG
2344280 AAATAAAAATATT-ATAAATTAT
1 AAATAAAAATATTGAT-AATTAT
2344302 ATTAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATAAAAATATTGATAATTATTG
Found at i:2344604 original size:21 final size:24
Alignment explanation
Indices: 2344562--2344633 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 24
2344552 TAATATTAAA
2344562 AATAATATATATTATTAGAAATATT
1 AATAATATATATTATTA-AAATATT
*
2344587 AATAA-ATATATT-TTAAATATTTT
1 AATAATATATATTATTAAA-ATATT
*
2344610 AATAATTAATATTTTGATTAAAAT
1 AATAA-T-ATATATT-ATTAAAAT
2344634 GATATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 2 0.05
23 12 0.31
24 7 0.18
25 5 0.13
26 6 0.15
27 2 0.05
28 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
AATAATATATATTATTAAAATATT
Found at i:2345110 original size:93 final size:93
Alignment explanation
Indices: 2344951--2345136 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
2344941 TTAACTGAAT
* *
2344951 TAATCGATCGGATCGATTAATTCGGTTAAAACCAAAAATAAAAACCCTTGGCGTCAAAAGAGAGC
1 TAATCAATCAGATCGATTAATTCGGTTAAAACCAAAAATAAAAACCCTTGGCGTCAAAAGAGAGC
2345016 CTTATAGAAGGTGTTGTCACCCGGAACC
66 CTTATAGAAGGTGTTGTCACCCGGAACC
2345044 TAATCAATCAGATCGATTAATTCGGTTAAAACCAAAAATAAAAACCCTTGGCGTCAAAAGAGAGC
1 TAATCAATCAGATCGATTAATTCGGTTAAAACCAAAAATAAAAACCCTTGGCGTCAAAAGAGAGC
2345109 CTTATAGAAGGTGTTGTCACCCGGAACC
66 CTTATAGAAGGTGTTGTCACCCGGAACC
2345137 GTCTTTATTT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (93 bp):
TAATCAATCAGATCGATTAATTCGGTTAAAACCAAAAATAAAAACCCTTGGCGTCAAAAGAGAGC
CTTATAGAAGGTGTTGTCACCCGGAACC
Found at i:2347410 original size:2 final size:2
Alignment explanation
Indices: 2347403--2347441 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2347393 TTTCTATAAT
2347403 TA TA TA TA 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 TA TA TA TA T
2347442 TCCGAGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2357324 original size:31 final size:30
Alignment explanation
Indices: 2357259--2357354 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
2357249 ATTAACTTTT
*
2357259 AATTTGACCTTAAACTTTAAATGAAATAC-T-
1 AATTTGACCTTAAATTTTAAAT-AAA-ACATC
2357289 AATTTGACCCTTAAATTTTAAATAAAACATC
1 AATTTGA-CCTTAAATTTTAAATAAAACATC
* * * *
2357320 AATTTGATTCTTGAGTTTTAGAT-AAACATC
1 AATTTGA-CCTTAAATTTTAAATAAAACATC
2357350 AATTT
1 AATTT
2357355 AACTTCTGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
29 2 0.04
30 23 0.40
31 32 0.56
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (30 bp):
AATTTGACCTTAAATTTTAAATAAAACATC
Found at i:2358518 original size:3 final size:3
Alignment explanation
Indices: 2358505--2358562 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
2358495 ACCAAAAATG
* *
2358505 TTA TT- TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2358552 ATA TTA TTA TT
1 TTA TTA TTA TT
2358563 TTTACAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2359930 original size:18 final size:18
Alignment explanation
Indices: 2359907--2359945 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2359897 GCCTAAGCGT
2359907 GCATCTTTCCTATGCGAG
1 GCATCTTTCCTATGCGAG
2359925 GCATCTTTCCTATGCGAG
1 GCATCTTTCCTATGCGAG
2359943 GCA
1 GCA
2359946 CACCGTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (18 bp):
GCATCTTTCCTATGCGAG
Found at i:2360454 original size:60 final size:58
Alignment explanation
Indices: 2360371--2360533 Score: 161
Period size: 59 Copynumber: 2.7 Consensus size: 58
2360361 ACACTTATTT
*
2360371 TAAATTGGTCCCTAAACTTTTAAACAATTCAATTTCATCCTTAAACTATGAC-CATCATTC
1 TAAATTGGTCCC-AAACATTT-AACAATTCAATTTCATCCTTAAACTATG-CTCATCATTC
* * ** *
2360431 TAAATTAGTCCTCAAACATTTAA-AATTCCACTTTCATCCCCAAACTATGCTCTTCATTC
1 TAAATTGGTCC-CAAACATTTAACAATT-CAATTTCATCCTTAAACTATGCTCATCATTC
* *
2360490 TAAATTGGTCCCCAAACTATTTTAACATTTCAATTTAAT-CTTAA
1 TAAATTGGT-CCCAAAC-A-TTTAACAATTCAATTTCATCCTTAA
2360534 TTTATAAGTA
Statistics
Matches: 84, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
58 5 0.06
59 40 0.48
60 23 0.27
61 13 0.15
62 3 0.04
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.37
Consensus pattern (58 bp):
TAAATTGGTCCCAAACATTTAACAATTCAATTTCATCCTTAAACTATGCTCATCATTC
Found at i:2360730 original size:60 final size:60
Alignment explanation
Indices: 2360660--2360790 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
2360650 GATGAATTTG
* *
2360660 GGGATAAAATTGGAA-GATGC-AAACTTTTAGTGACCAATTTAAAATGATATTCATAG-TTT
1 GGGATGAAATTGGAATG-TGCAAAACTTTAAGT-ACCAATTTAAAATGATATTCATAGTTTT
* * * *
2360719 GGGAATGAAATTGGAATGTTCAAAAGTTTAAGTACTAATTTAGAATGATATTCATAGTTTT
1 GGG-ATGAAATTGGAATGTGCAAAACTTTAAGTACCAATTTAAAATGATATTCATAGTTTT
2360780 GGGATGAAATT
1 GGGATGAAATT
2360791 AAAATGTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 3 0.05
60 43 0.69
61 16 0.26
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (60 bp):
GGGATGAAATTGGAATGTGCAAAACTTTAAGTACCAATTTAAAATGATATTCATAGTTTT
Found at i:2360797 original size:60 final size:60
Alignment explanation
Indices: 2360695--2360824 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 60
2360685 TTTAGTGACC
** *
2360695 AATTTAAAATGATATTCATAGTTTGGGAATGAAATTGGAATGTTCAAAAGTTTAAGTACT
1 AATTTAAAATGATATTCATAGTTTGGGAATGAAATTAAAATGTTCAAAAGTTTAAGGACT
* * *
2360755 AATTTAGAATGATATTCATAGTTTTGGG-ATGAAATTAAAATGTTTAAAAGTTTAAGGATT
1 AATTTAAAATGATATTCATAG-TTTGGGAATGAAATTAAAATGTTCAAAAGTTTAAGGACT
*
2360815 AATTTGAAAT
1 AATTTAAAAT
2360825 TAGGGTCATA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 55 0.90
61 6 0.10
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (60 bp):
AATTTAAAATGATATTCATAGTTTGGGAATGAAATTAAAATGTTCAAAAGTTTAAGGACT
Found at i:2363761 original size:3 final size:3
Alignment explanation
Indices: 2363753--2363832 Score: 52
Period size: 3 Copynumber: 26.3 Consensus size: 3
2363743 ATGTTATTTA
* * * * * *
2363753 TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT AAT TAT AAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
2363801 AAT AAT AAT AAT TAT TAT TAA TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
2363833 TAATATTACA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (3 bp):
TAT
Found at i:2363778 original size:21 final size:21
Alignment explanation
Indices: 2363754--2363831 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
2363744 TGTTATTTAT
*
2363754 ATTATTATTATTATTATAATA
1 ATTATTATTATAATTATAATA
2363775 ATTATTATTATAATTATAATA
1 ATTATTATTATAATTATAATA
* * *
2363796 A-TA--ATAATAATAATAATT
1 ATTATTATTATAATTATAATA
*
2363814 ATTATTAATATATATTAT
1 ATTATTATTATA-ATTAT
2363832 TTAATATTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
18 13 0.28
19 2 0.04
20 2 0.04
21 25 0.54
22 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATTATTATAATTATAATA
Found at i:2364354 original size:15 final size:15
Alignment explanation
Indices: 2364334--2364375 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
2364324 ACAACACAGC
2364334 AAAGAAACAGAA-AAG
1 AAAGAAA-AGAAGAAG
2364349 AAAGAAAAGAAGAAG
1 AAAGAAAAGAAGAAG
*
2364364 AAAGAAGAGAAG
1 AAAGAAAAGAAG
2364376 CTTACCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAGAAG
Found at i:2365214 original size:20 final size:20
Alignment explanation
Indices: 2365176--2365214 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2365166 AAATATATCA
*
2365176 TTTTAATTGTATTTTTATTG
1 TTTTAATTGTATTTATATTG
2365196 TTTTAATTGT-TTATATATT
1 TTTTAATTGTATT-TATATT
2365215 TAAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTTAATTGTATTTATATTG
Found at i:2376637 original size:11 final size:11
Alignment explanation
Indices: 2376621--2376678 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
2376611 ATGCTTGAAG
2376621 AAAAAAAAAGA
1 AAAAAAAAAGA
2376632 AAAAAAGAAAGA
1 AAAAAA-AAAGA
*
2376644 AAAGAAAAAGA
1 AAAAAAAAAGA
*
2376655 AATTAAAAAA-A
1 AA-AAAAAAAGA
*
2376666 AAGAAAAAAGA
1 AAAAAAAAAGA
2376677 AA
1 AA
2376679 GAAAGAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 6 0.15
11 19 0.47
12 15 0.38
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:2376653 original size:15 final size:15
Alignment explanation
Indices: 2376631--2376671 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2376621 AAAAAAAAAG
2376631 AAAAAAAGAAA-GAA
1 AAAAAAAGAAATGAA
*
2376645 AAGAAAAAGAAATTAA
1 AA-AAAAAGAAATGAA
2376661 AAAAAAAGAAA
1 AAAAAAAGAAA
2376672 AAAGAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 2 0.08
15 18 0.75
16 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (15 bp):
AAAAAAAGAAATGAA
Found at i:2376662 original size:26 final size:23
Alignment explanation
Indices: 2376618--2376682 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 23
2376608 ATTATGCTTG
*
2376618 AAGAAAAAAAAAG-AAAAAAAGA
1 AAGAAAAAAAAAGAAAAAAAAAA
2376640 AAGAAAAGAAAAAGAAATTAAAAAAA
1 AAGAAAA-AAAAAGAAA--AAAAAAA
2376666 AAGAAAAAAGAAAGAAA
1 AAGAAAAAA-AAAGAAA
2376683 GAGGGGTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 7 0.19
23 6 0.16
24 2 0.05
25 2 0.05
26 20 0.54
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (23 bp):
AAGAAAAAAAAAGAAAAAAAAAA
Found at i:2376679 original size:11 final size:10
Alignment explanation
Indices: 2376618--2376682 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
2376608 ATTATGCTTG
2376618 AAGAAAAAAA
1 AAGAAAAAAA
2376628 AAG--AAAAA
1 AAGAAAAAAA
*
2376636 AAG-AAAGAA
1 AAGAAAAAAA
2376645 AAGAAAAAGAA
1 AAGAAAAA-AA
**
2376656 ATTAAAAAAA
1 AAGAAAAAAA
2376666 AAGAAAAAAGA
1 AAGAAAAAA-A
2376677 AAGAAA
1 AAGAAA
2376683 GAGGGGTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 8 0.18
9 7 0.16
10 15 0.33
11 15 0.33
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:2377967 original size:83 final size:83
Alignment explanation
Indices: 2377828--2378619 Score: 1450
Period size: 83 Copynumber: 9.6 Consensus size: 83
2377818 AAATGCAATG
2377828 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
2377893 GAAATTGGAAGATGAATA
66 GAAATTGGAAGATGAATA
2377911 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
*
2377976 GAAATTGGAAGATAAATA
66 GAAATTGGAAGATGAATA
*
2377994 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA---GATCTAG-TTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
2378055 GAAATTGGAAGATGAATA
66 GAAATTGGAAGATGAATA
*
2378073 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACTAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
2378138 GAAATTGGAAGATGAATA
66 GAAATTGGAAGATGAATA
2378156 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
2378221 GAAATTGGAAGATGAATA
66 GAAATTGGAAGATGAATA
2378239 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
2378304 GAAATTGGAAGATGAATA
66 GAAATTGGAAGATGAATA
*
2378322 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
*
2378387 GAAATTGGAAGATAAATA
66 GAAATTGGAAGATGAATA
2378405 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
2378470 GAAATTGGAAGATGAATA
66 GAAATTGGAAGATGAATA
*
2378488 TGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
* * *
2378553 GAATTTAGAAG-GGTAATA
66 GAAATTGGAAGATG-AATA
*
2378571 TGCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
2378620 AGTAGGAACC
Statistics
Matches: 688, Mismatches: 16, Indels: 10
0.96 0.02 0.01
Matches are distributed among these distances:
79 71 0.10
80 6 0.01
82 7 0.01
83 604 0.88
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
GAAATTGGAAGATGAATA
Found at i:2379540 original size:113 final size:113
Alignment explanation
Indices: 2379342--2379864 Score: 724
Period size: 113 Copynumber: 4.6 Consensus size: 113
2379332 GCAAAGATTT
* *
2379342 AAATCCATCA-TTCAATGGATCAACTTTTCTAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTT-GATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
*
2379406 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
2379455 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
2379520 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
2379568 AAATCCATCACTTGATGAATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
2379633 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * ****
2379681 AAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
2379746 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTACTTGTTTAACCCTTTGCTT
66 AAGGAAGAAGAAATTCATAATGAGAAGAA--T--TTGTTCAACCTTTTGCTC
* * * * **** **** *
2379798 GAATTCATCATTTGATGGATCAGCAGCGCCAAAGAGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
2379863 AA
66 AA
2379865 AAGAAAGTTC
Statistics
Matches: 376, Mismatches: 29, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
113 301 0.80
114 2 0.01
115 1 0.00
117 72 0.19
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:2380143 original size:3 final size:3
Alignment explanation
Indices: 2380135--2380249 Score: 97
Period size: 3 Copynumber: 38.3 Consensus size: 3
2380125 ATGTTATTTA
* * * * *
2380135 TAT TAT TAT TAT TAT TAT AAT TAT TA- TAT TAT AAT TAT AAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
2380182 AAT AAT TAT TAT TAT TAT TAT AAT TAT AAT AAT AAT AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2380230 TAT TAT TAA TAT ATAT TAT T
1 TAT TAT TAT TAT -TAT TAT T
2380250 TAATATTACA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.02
3 93 0.95
4 3 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:2380767 original size:15 final size:15
Alignment explanation
Indices: 2380747--2380782 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2380737 ACAACACAGC
2380747 AAAGAAACAGAA-AAG
1 AAAGAAA-AGAAGAAG
2380762 AAAGAAAAGAAGAAG
1 AAAGAAAAGAAGAAG
2380777 AAAGAA
1 AAAGAA
2380783 GAGGCTTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAGAAG
Found at i:2380996 original size:21 final size:21
Alignment explanation
Indices: 2380971--2381016 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
2380961 CGGTGGCCGG
2380971 CGGCGGAAGAACTCCGACTGA
1 CGGCGGAAGAACTCCGACTGA
2380992 CGGCGGAAGAACTCCGACTGA
1 CGGCGGAAGAACTCCGACTGA
2381013 CGGC
1 CGGC
2381017 TGCCGGCCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.30, G:0.35, T:0.09
Consensus pattern (21 bp):
CGGCGGAAGAACTCCGACTGA
Found at i:2386333 original size:22 final size:22
Alignment explanation
Indices: 2386308--2386352 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2386298 TGAAACCAAA
2386308 ATAGCATAACCAAAGATTAGAC
1 ATAGCATAACCAAAGATTAGAC
2386330 ATAGCATAACCAAAGATTAGAC
1 ATAGCATAACCAAAGATTAGAC
2386352 A
1 A
2386353 AGGGCACCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (22 bp):
ATAGCATAACCAAAGATTAGAC
Found at i:2391037 original size:35 final size:34
Alignment explanation
Indices: 2390952--2391038 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
2390942 ATTTGATATT
*
2390952 TAAATACAACAAACTTACAATAAGAATAAAATGG
1 TAAATACAACAAAATTACAATAAGAATAAAATGG
* * *
2390986 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATAAAATGG
2391024 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2391039 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.25
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATAAAATGG
Found at i:2391243 original size:12 final size:12
Alignment explanation
Indices: 2391226--2391258 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2391216 ACTCCTCGTT
2391226 GTCATCATCATC
1 GTCATCATCATC
2391238 GTCATCATCATC
1 GTCATCATCATC
*
2391250 GTCACCATC
1 GTCATCATC
2391259 GTCATCGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.09, T:0.30
Consensus pattern (12 bp):
GTCATCATCATC
Found at i:2391244 original size:9 final size:9
Alignment explanation
Indices: 2391227--2391279 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
2391217 CTCCTCGTTG
*
2391227 TCATCATCA
1 TCATCGTCA
* *
2391236 TCGTCATCA
1 TCATCGTCA
2391245 TCATCGTCA
1 TCATCGTCA
*
2391254 CCATCGTCA
1 TCATCGTCA
*
2391263 TCGTCGTCA
1 TCATCGTCA
*
2391272 TCGTCGTC
1 TCATCGTC
2391280 GTCCTGAGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.19, C:0.36, G:0.13, T:0.32
Consensus pattern (9 bp):
TCATCGTCA
Found at i:2393277 original size:111 final size:111
Alignment explanation
Indices: 2393139--2393360 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
2393129 ATTACAAAAA
* * *
2393139 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCGTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
2393204 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2393250 TTAATTCGTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCGTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
2393315 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2393361 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCGTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2393498 original size:12 final size:10
Alignment explanation
Indices: 2393484--2393524 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
2393474 ACCTTAAAAA
*
2393484 GAGAGTATTT
1 GAGAGAATTT
2393494 GAGAGAAATTT
1 GAGAG-AATTT
2393505 -AGAGAATTT
1 GAGAGAATTT
2393514 GAGAGAATTT
1 GAGAGAATTT
2393524 G
1 G
2393525 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:2393673 original size:50 final size:49
Alignment explanation
Indices: 2393646--2393743 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 49
2393636 AGATATCCAG
2393646 GTATA-GCGTGGATCAGGGGGCGCGCTATACCCACGTGGCACCAGATCATC
1 GTATACGCG-GGA-CAGGGGGCGCGCTATACCCACGTGGCACCAGATCATC
* *
2393696 GTATATCGCGGGACAGGGGGCGCGCTATACCCACGTGGCGCCAAATCA
1 GTATA-CGCGGGACAGGGGGCGCGCTATACCCACGTGGCACCAGATCA
2393744 GCATATAGCG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 38 0.86
51 3 0.07
52 3 0.07
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (49 bp):
GTATACGCGGGACAGGGGGCGCGCTATACCCACGTGGCACCAGATCATC
Found at i:2393763 original size:50 final size:50
Alignment explanation
Indices: 2393658--2393771 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 50
2393648 ATAGCGTGGA
* * * * *
2393658 TCAGGGGGCGCGCTATACCCACGTGGCACCAGATCATCGTATATCGCGGG
1 TCAGGGGGCGCGCTATACCCACGTGGCACCAAATCAGCATATAGCGCAGG
* * *
2393708 ACAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGCATATAGCGCAGT
1 TCAGGGGGCGCGCTATACCCACGTGGCACCAAATCAGCATATAGCGCAGG
*
2393758 TCAGGGGGAGCGCT
1 TCAGGGGGCGCGCT
2393772 TTCCTGCTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (50 bp):
TCAGGGGGCGCGCTATACCCACGTGGCACCAAATCAGCATATAGCGCAGG
Found at i:2394060 original size:2 final size:2
Alignment explanation
Indices: 2394055--2394092 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2394045 TAACGATAGA
2394055 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
2394093 GGACGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2394219 original size:22 final size:22
Alignment explanation
Indices: 2394193--2394238 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2394183 ATGTGTGTCA
2394193 AATATACATAATTGTAAGAGTC
1 AATATACATAATTGTAAGAGTC
2394215 AATATACATAATTGTAAGAGTC
1 AATATACATAATTGTAAGAGTC
2394237 AA
1 AA
2394239 GCCGCAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (22 bp):
AATATACATAATTGTAAGAGTC
Found at i:2394303 original size:14 final size:15
Alignment explanation
Indices: 2394284--2394312 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2394274 TCTATAGATA
2394284 TATATTTAAA-ATTT
1 TATATTTAAATATTT
2394298 TATATTTAAATATTT
1 TATATTTAAATATTT
2394313 GAAAAGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTTAAATATTT
Found at i:2397008 original size:101 final size:100
Alignment explanation
Indices: 2396815--2397013 Score: 228
Period size: 101 Copynumber: 2.0 Consensus size: 100
2396805 TTTTATTAAT
*
2396815 ATTAACTGACCTTATTCCCATATAAGTAATAGGGTGAGAGAGAGGTAAGATAGTAGGCTGCCTCC
1 ATTAACTGACCTTATTCCCATAT-AGTAATAGGGTGAAAGAGAGGTAAGATAGTAGGCTGCCTCC
* * *
2396880 AACGGGTTGAGAACATATTCTGTGGAAGACCTCCAA
65 AACGGGCTGAGAACATATTCCGAGGAAGACCTCCAA
* * *
2396916 ATTAACTGACCTTATTCCCATAT-GTAAT-GGGAT-AAAGAGATGTATGGTAGTAGGCTGCC-CT
1 ATTAACTGACCTTATTCCCATATAGTAATAGGG-TGAAAGAGAGGTAAGATAGTAGGCTGCCTC-
*
2396977 CAACGTTAGGCTGAGAGCA-ATTTCCGAGGAAGACCTC
64 CAACG---GGCTGAGAACATA-TTCCGAGGAAGACCTC
2397014 TGACAATTAT
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
97 1 0.01
98 30 0.36
99 6 0.07
100 1 0.01
101 46 0.55
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (100 bp):
ATTAACTGACCTTATTCCCATATAGTAATAGGGTGAAAGAGAGGTAAGATAGTAGGCTGCCTCCA
ACGGGCTGAGAACATATTCCGAGGAAGACCTCCAA
Found at i:2398429 original size:27 final size:26
Alignment explanation
Indices: 2398375--2398454 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 26
2398365 TAATATTTTA
* * *
2398375 AAAATAAACAAATATTAT-TAATTTAT
1 AAAATAATCAAATAATATAT-ATTAAT
2398401 AAAATTAATCAAATAATATATATTAAT
1 AAAA-TAATCAAATAATATATATTAAT
* *
2398428 -AAA-AATAAAATAATA-ATACTAAT
1 AAAATAATCAAATAATATATATTAAT
2398451 AAAA
1 AAAA
2398455 ATATTAAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
23 7 0.15
24 14 0.30
26 7 0.15
27 17 0.37
28 1 0.02
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAATAATCAAATAATATATATTAAT
Found at i:2398454 original size:23 final size:24
Alignment explanation
Indices: 2398411--2398457 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2398401 AAAATTAATC
*
2398411 AAATAATATATATTAATAAAAATA
1 AAATAATATATACTAATAAAAATA
2398435 AAATAATA-ATACTAATAAAAATA
1 AAATAATATATACTAATAAAAATA
2398458 TTAAACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAATATATACTAATAAAAATA
Found at i:2399863 original size:3 final size:3
Alignment explanation
Indices: 2399851--2399957 Score: 110
Period size: 3 Copynumber: 35.3 Consensus size: 3
2399841 GATTTGTATT
* * *
2399851 TAA T-A TAA TAA TAA TAA TAA TAA TGTA TAT TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * *
2399896 TAA TAA TGTA TAT TAA TAA TAA -AA TTAA TAA TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
*
2399942 TAA TAA TAA TAG TAA T
1 TAA TAA TAA TAA TAA T
2399958 TTAAGTAAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.05
3 75 0.88
4 6 0.07
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2400274 original size:74 final size:73
Alignment explanation
Indices: 2400138--2400612 Score: 689
Period size: 74 Copynumber: 6.4 Consensus size: 73
2400128 GAGGTATTAT
* * * **
2400138 CATCTTGCACTATAGGTCTTACAGATAACCCTGAGGCTTTAAATATCAAAAATATCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCAAAAAGCTCCCGAAGGCT
*
2400203 TTCTGAAAA
65 TTTTGAAAA
* * *
2400212 CATCATACACTGTATGTCTTACAGATGACTCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCAAAAAGCTCCCGAAGGCT
2400277 TTTTGAAAA
65 TTTTGAAAA
* *
2400286 CATCATGCACTGTAAGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCTGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-T
2400351 TTTTGAAAA
65 TTTTGAAAA
2400360 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-T
2400425 TTTTGAAAA
65 TTTTGAAAA
* * * *
2400434 CATCATCCACTGTAGGTCTTATAGATGACCCTGAGGCTTTAAAATAAAAAAGCTCCCGAAGGTTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGG--C
2400499 TTTTTGAAAA
64 TTTTTGAAAA
* *
2400509 CATCATGCATTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAAAACATCAAAAAGCTCTCGAAG
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT---AAA-ATCAAAAAGCTCCCGAAG
*
2400574 GATTTTTGAAAA
62 GCTTTTTGAAAA
*
2400586 CATCATGCACTGTAGGGCTTACAGATG
1 CATCATGCACTGTAGGTCTTACAGATG
2400613 TGGGAAATAA
Statistics
Matches: 367, Mismatches: 27, Indels: 11
0.91 0.07 0.03
Matches are distributed among these distances:
73 19 0.05
74 246 0.67
75 47 0.13
77 35 0.10
78 3 0.01
79 17 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (73 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
TTTGAAAA
Found at i:2401304 original size:22 final size:22
Alignment explanation
Indices: 2401279--2401332 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
2401269 ATAAAGCGTC
2401279 CATCTTTGAAAAGAGAATCTAT
1 CATCTTTGAAAAGAGAATCTAT
2401301 CATCTTTGAAAAGAGAATCTAT
1 CATCTTTGAAAAGAGAATCTAT
2401323 CATCTTTGAA
1 CATCTTTGAA
2401333 GAGTGTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (22 bp):
CATCTTTGAAAAGAGAATCTAT
Found at i:2402745 original size:75 final size:75
Alignment explanation
Indices: 2402654--2402823 Score: 189
Period size: 75 Copynumber: 2.3 Consensus size: 75
2402644 ACATGATGAT
* * * * ** *
2402654 ATGGGCCTTCAGCATGCCCCTATATTTGTTGATATGATCATTCAAAATACATCAACATTCCTGAT
1 ATGGGCTTTCAGCATGCCCCCACATTTGATGATAAAAACATTCAAAATACATCAACATT-CTGAT
2402719 TT-TAATTGAA
65 TTCTAATTGAA
* *** * **
2402729 ATGGGCTTTCAGCATGCCCCCACATTTGATGATAAAAACGTTCAAAATGTGTCAATATTCTTCTT
1 ATGGGCTTTCAGCATGCCCCCACATTTGATGATAAAAACATTCAAAATACATCAACATTCTGATT
*
2402794 TCTGATTGAA
66 TCTAATTGAA
2402804 ATGGGCTTTCAGCATGCCCC
1 ATGGGCTTTCAGCATGCCCC
2402824 AAAATTTTCT
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
74 5 0.06
75 74 0.94
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (75 bp):
ATGGGCTTTCAGCATGCCCCCACATTTGATGATAAAAACATTCAAAATACATCAACATTCTGATT
TCTAATTGAA
Found at i:2405294 original size:32 final size:32
Alignment explanation
Indices: 2405253--2405347 Score: 156
Period size: 32 Copynumber: 3.0 Consensus size: 32
2405243 TGAAGAAATG
*
2405253 GTTGTTATGCTTAT-TTGATAGAGATACTTCTC
1 GTTGTTATGCTCATATTG-TAGAGATACTTCTC
2405285 GTTGTTATGCTCATATTGTAGAGATACTTCTC
1 GTTGTTATGCTCATATTGTAGAGATACTTCTC
*
2405317 GTTGTTATGCTCATCTTGTAGAGATACTTCT
1 GTTGTTATGCTCATATTGTAGAGATACTTCT
2405348 TGTTTCCAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 57 0.95
33 3 0.05
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (32 bp):
GTTGTTATGCTCATATTGTAGAGATACTTCTC
Found at i:2408702 original size:14 final size:15
Alignment explanation
Indices: 2408683--2408713 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2408673 GTATGAATAC
2408683 AAGATG-AAAATGCA
1 AAGATGTAAAATGCA
2408697 AAGATGTAAAATGCA
1 AAGATGTAAAATGCA
2408712 AA
1 AA
2408714 TGTATGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.58, C:0.06, G:0.19, T:0.16
Consensus pattern (15 bp):
AAGATGTAAAATGCA
Found at i:2411054 original size:17 final size:17
Alignment explanation
Indices: 2411015--2411047 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2411005 AATAGTTGAA
2411015 AATAAAATAAAAATATT
1 AATAAAATAAAAATATT
2411032 AATAAAA-AAATAATAT
1 AATAAAATAAA-AATAT
2411048 ATATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAAATAAAAATATT
Found at i:2412045 original size:27 final size:29
Alignment explanation
Indices: 2411999--2412094 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 29
2411989 CATTTTCTTA
*
2411999 ATATTT-TAAAAATAAACAAATATTAT-T
1 ATATTTATAAAAATAAACAAATAATATAT
* *
2412026 A-ATTTATAAAATTAATCAAATAATATAT
1 ATATTTATAAAAATAAACAAATAATATAT
*
2412054 ATATTAATAAAAATAAA-ATAATAATA-AT
1 ATATTTATAAAAATAAACA-AATAATATAT
*
2412082 A-A-TAATAAAAATA
1 ATATTTATAAAAATA
2412095 TTAAACATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
26 15 0.25
27 19 0.32
28 6 0.10
29 19 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
ATATTTATAAAAATAAACAAATAATATAT
Found at i:2412076 original size:26 final size:26
Alignment explanation
Indices: 2412043--2412094 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2412033 AAAATTAATC
*
2412043 AAATAAT-ATATATATTAATAAAAATA
1 AAATAATAATA-ATAATAATAAAAATA
2412069 AAATAATAATAATAATAATAAAAATA
1 AAATAATAATAATAATAATAAAAATA
2412095 TTAAACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAATAATAATAATAATAAAAATA
Found at i:2412078 original size:3 final size:3
Alignment explanation
Indices: 2412044--2412094 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
2412034 AAATTAATCA
* *
2412044 AAT AAT -AT ATAT ATT AAT AAA AAT AA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2412088 AAA AAT A
1 AAT AAT A
2412095 TTAAACATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2413091 original size:20 final size:22
Alignment explanation
Indices: 2413046--2413091 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
2413036 GTTTTGTGGT
*
2413046 TTGCTTCATGGTTGTTGGCATT
1 TTGCTTCATGGTTGTTGGCATC
2413068 TTGCTTC-TGGTT-TTGGTC-TC
1 TTGCTTCATGGTTGTTGG-CATC
2413088 TTGC
1 TTGC
2413092 CCTCTGTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 9 0.41
21 6 0.27
22 7 0.32
ACGTcount: A:0.04, C:0.17, G:0.26, T:0.52
Consensus pattern (22 bp):
TTGCTTCATGGTTGTTGGCATC
Found at i:2413615 original size:3 final size:3
Alignment explanation
Indices: 2413523--2413599 Score: 100
Period size: 3 Copynumber: 25.3 Consensus size: 3
2413513 GTATTTAATT
* * *
2413523 TAA TAA TAA TAA TAA TAA TGTA TAT TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2413569 TAA TAA TAA TAA TGA TAA TAA TAA TAG TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2413600 TTTAAAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 61 0.97
4 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2414552 original size:23 final size:25
Alignment explanation
Indices: 2414511--2414557 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2414501 GGTATTTTTT
*
2414511 TCCTTCAAGTCTATTTAAC-AATTA
1 TCCTTCAAGTCTATATAACTAATTA
2414535 TCCTTCAA-TCTATATAACTAATT
1 TCCTTCAAGTCTATATAACTAATT
2414558 TCCATTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (25 bp):
TCCTTCAAGTCTATATAACTAATTA
Found at i:2417376 original size:31 final size:30
Alignment explanation
Indices: 2417341--2417401 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
2417331 CAACCATTCA
* *
2417341 CAACTTTTCCAAAATTGCCA-AATTGGTCCCC
1 CAACTATTCAAAAATT-CCATAA-TGGTCCCC
2417372 CAACTATTCAAAAATTCCATAATGGTCCCC
1 CAACTATTCAAAAATTCCATAATGGTCCCC
2417402 AATTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (30 bp):
CAACTATTCAAAAATTCCATAATGGTCCCC
Found at i:2429020 original size:21 final size:21
Alignment explanation
Indices: 2428994--2429033 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2428984 CAGAACCCCA
*
2428994 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2429015 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2429034 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2442069 original size:60 final size:59
Alignment explanation
Indices: 2441975--2442138 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 59
2441965 ACTAAGACCC
* * * * *
2441975 AAACTATAACTCTCATCTTAAATTGATCCTTAAACTTTTGAATAATCGAATTTCATCTCT
1 AAACTATGA-TCTCATTTTAAATTAATCCATAAACTTTTGAATAATCGAATTTCATCCCT
* * * * *
2442035 AAACTATGATTCTCATTTTAAATTAATACATAAACTTTTCAACATTCTAATTTCATCCCT
1 AAACTATGA-TCTCATTTTAAATTAATCCATAAACTTTTGAATAATCGAATTTCATCCCT
* * * * *
2442095 ACACTATGATCTTCTTTTTAAAATAGTCCCTAAACTTTTGAATA
1 AAACTATGATC-TCATTTTAAATTAATCCATAAACTTTTGAATA
2442139 TTTTAAATTC
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 2 0.02
60 82 0.98
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (59 bp):
AAACTATGATCTCATTTTAAATTAATCCATAAACTTTTGAATAATCGAATTTCATCCCT
Found at i:2447496 original size:15 final size:16
Alignment explanation
Indices: 2447485--2447515 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2447475 CTCAAAATAT
2447485 ATTTATTAAAAAAATC
1 ATTTATTAAAAAAATC
*
2447501 TTTTATTAAAAAAAT
1 ATTTATTAAAAAAAT
2447516 GAGTTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTATTAAAAAAATC
Found at i:2452722 original size:29 final size:29
Alignment explanation
Indices: 2452689--2452752 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
2452679 TGATCTAAAG
2452689 GACTCCAACTCCTTAGACCATTTACAAGA
1 GACTCCAACTCCTTAGACCATTTACAAGA
2452718 GACTCCAACTCCTTAGACCATTTACAAGA
1 GACTCCAACTCCTTAGACCATTTACAAGA
2452747 GACTCC
1 GACTCC
2452753 TTATATACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.23
Consensus pattern (29 bp):
GACTCCAACTCCTTAGACCATTTACAAGA
Found at i:2454509 original size:14 final size:14
Alignment explanation
Indices: 2454490--2454526 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2454480 GCCTAAGACC
*
2454490 CTCTCTCTCTCCCA
1 CTCTCTCTCTCACA
*
2454504 CTCTCTCTCTGACA
1 CTCTCTCTCTCACA
2454518 CTCTCTCTC
1 CTCTCTCTC
2454527 ATGATTTCAC
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:0.08, C:0.51, G:0.03, T:0.38
Consensus pattern (14 bp):
CTCTCTCTCTCACA
Found at i:2466497 original size:22 final size:22
Alignment explanation
Indices: 2466472--2466529 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
2466462 GTCTCAGTAC
2466472 TGATACAAAAGTGCATTTGCAA
1 TGATACAAAAGTGCATTTGCAA
* * *
2466494 TGATTCAAAAGTACATTTGCAC
1 TGATACAAAAGTGCATTTGCAA
*
2466516 TGATACTAAAGTGC
1 TGATACAAAAGTGC
2466530 CTTAGTACTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (22 bp):
TGATACAAAAGTGCATTTGCAA
Done.