Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008574.1 Hibiscus syriacus cultivar Beakdansim tig00111503_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: 414859
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:281869 original size:18 final size:18
Alignment explanation
Indices: 281846--281886 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
281836 ATTGTATATA
281846 ATTACTTTTTATAAATAG
1 ATTACTTTTTATAAATAG
281864 ATTACTTTTTATAAATAG
1 ATTACTTTTTATAAATAG
281882 ATTAC
1 ATTAC
281887 GCGGTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTACTTTTTATAAATAG
Found at i:285755 original size:2 final size:2
Alignment explanation
Indices: 285748--285863 Score: 120
Period size: 2 Copynumber: 59.0 Consensus size: 2
285738 ATATAAAATG
285748 AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT GAT AT GAT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT -AT
* *
285789 AT GAT AT A- AT -T AT -T AA AT AT AT A- AT AT AT TT AGT -T AT AT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
285828 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
285864 TAAATATAAA
Statistics
Matches: 98, Mismatches: 4, Indels: 24
0.78 0.03 0.19
Matches are distributed among these distances:
1 7 0.07
2 82 0.84
3 9 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:285934 original size:2 final size:2
Alignment explanation
Indices: 285927--285972 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
285917 AAATCTAAAT
285927 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
285968 TA TA T
1 TA TA T
285973 GAAATCAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:287020 original size:16 final size:16
Alignment explanation
Indices: 287001--287033 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
286991 TAAAAACTAT
287001 AAATAAAAAGAAAATA
1 AAATAAAAAGAAAATA
*
287017 AAATAAAAAGAAGATA
1 AAATAAAAAGAAAATA
287033 A
1 A
287034 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:287556 original size:23 final size:23
Alignment explanation
Indices: 287510--287558 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
287500 ATAAAGAACC
*
287510 AAAATAAACTTAAATATATCATT
1 AAAATAAACTTAAACATATCATT
*
287533 AAAATAAAGTTAAAACATAT-ATT
1 AAAATAAACTT-AAACATATCATT
287556 AAA
1 AAA
287559 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATAAACTTAAACATATCATT
Found at i:292655 original size:16 final size:16
Alignment explanation
Indices: 292636--292668 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
292626 TAAAAACTGT
292636 AAATAAAAAGAAAATA
1 AAATAAAAAGAAAATA
*
292652 AAATAAAAAGAAGATA
1 AAATAAAAAGAAAATA
292668 A
1 A
292669 TCCTCACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:293190 original size:23 final size:23
Alignment explanation
Indices: 293145--293193 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
293135 ATTAAGAACC
*
293145 AAAATAAACTTAAATATATCATT
1 AAAATAAACTTAAATACATCATT
*
293168 AAAATAAAGTTAAA-ACATCCATT
1 AAAATAAACTTAAATACAT-CATT
293191 AAA
1 AAA
293194 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTTAAATACATCATT
Found at i:298387 original size:62 final size:61
Alignment explanation
Indices: 298286--298406 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 61
298276 CCGGCTCTGA
* *
298286 GTATTTTTTAGCTCGGGGAGAAATAAAAGAAATAGACCCCTATTTATGTTTTTTATTTTTTG
1 GTATTTTTTAGCTCGGAGAGAAATAAAAGAAATAGACCCCTATTTATGTTCTTT-TTTTTTG
*
298348 GTATTTTTTGGCTC-GAGACGAAATAAAAGAAAT-GAACCCCTATTTATGTTCTTTTTTTT
1 GTATTTTTTAGCTCGGAGA-GAAATAAAAGAAATAG-ACCCCTATTTATGTTCTTTTTTTT
298407 GGCCCGGGAC
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
61 9 0.17
62 45 0.83
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (61 bp):
GTATTTTTTAGCTCGGAGAGAAATAAAAGAAATAGACCCCTATTTATGTTCTTTTTTTTTG
Found at i:298611 original size:13 final size:13
Alignment explanation
Indices: 298564--298616 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
298554 ATCTTAATTC
298564 AAATTTTAAAAAT
1 AAATTTTAAAAAT
298577 AATATTATTAATAAAT
1 AA-ATT-TTAA-AAAT
*
298593 ATAATTTTAAATAT
1 A-AATTTTAAAAAT
*
298607 AAATTATAAA
1 AAATTTTAAA
298617 GTAAACGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 10 0.29
14 7 0.21
15 8 0.24
16 8 0.24
17 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:304526 original size:21 final size:21
Alignment explanation
Indices: 304482--304526 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
304472 AAACTATACA
*
304482 TTTAGTACCTAAATTATCAGT
1 TTTAGTACCTAAATTATCAAT
304503 TTTAGTACCTAAACTT-TCAAT
1 TTTAGTACCTAAA-TTATCAAT
304524 TTT
1 TTT
304527 TTCAAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTAGTACCTAAATTATCAAT
Found at i:312842 original size:18 final size:18
Alignment explanation
Indices: 312780--312843 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
312770 TTTATTGAAA
*
312780 AACCGATAAACCGAACCG
1 AACCGAAAAACCGAACCG
312798 AACCGAAAAACCCGAACCG
1 AACCGAAAAA-CCGAACCG
*
312817 TTAA---AAAAACCAAACCG
1 --AACCGAAAAACCGAACCG
312834 AACCGAAAAA
1 AACCGAAAAA
312844 ACCGGTTTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 7 0.18
18 19 0.50
19 8 0.21
21 2 0.05
ACGTcount: A:0.53, C:0.30, G:0.12, T:0.05
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:329344 original size:18 final size:18
Alignment explanation
Indices: 329302--329347 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
329292 CCTTGATTTT
329302 ATTAA-AATAATATCTAAA
1 ATTAATAAT-ATATCTAAA
* *
329320 ACT-ATAATATATCTATA
1 ATTAATAATATATCTAAA
329337 ATTAATAATAT
1 ATTAATAATAT
329348 TTTATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTAATAATATATCTAAA
Found at i:332587 original size:81 final size:81
Alignment explanation
Indices: 332447--332688 Score: 340
Period size: 81 Copynumber: 3.0 Consensus size: 81
332437 CTAGGATTGA
** * * *
332447 TACTGATTTATCTCCTCTGCGAAAACGGAGGGTTCGGAATGAAACACCATCACCTGAACCTTTAG
1 TACTGATTTATCTCCTCCACGAAAACGGAGGGTTCGGAATGATACACAATCACCAGAACCTTTAG
*
332512 TAAACAGTGCAGATGG
66 TAAACAGAGCAGATGG
* * *
332528 TACTGATTTATCTCCTCCACGGAAACAGAGGGTTCGGAATGATACACAATCATCAGAACCTTTAG
1 TACTGATTTATCTCCTCCACGAAAACGGAGGGTTCGGAATGATACACAATCACCAGAACCTTTAG
*
332593 TGAACAGAGCAGATGG
66 TAAACAGAGCAGATGG
* * * * * *
332609 TACTGATTTATCTCCTCCACGTAAATGGAGGGCTCGGAATGATACACATTCACCAAAACCTTTAA
1 TACTGATTTATCTCCTCCACGAAAACGGAGGGTTCGGAATGATACACAATCACCAGAACCTTTAG
332674 TAAACAGAGCAGATG
66 TAAACAGAGCAGATG
332689 CTGATTTATC
Statistics
Matches: 142, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 142 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (81 bp):
TACTGATTTATCTCCTCCACGAAAACGGAGGGTTCGGAATGATACACAATCACCAGAACCTTTAG
TAAACAGAGCAGATGG
Found at i:332740 original size:78 final size:78
Alignment explanation
Indices: 332448--332733 Score: 288
Period size: 81 Copynumber: 3.6 Consensus size: 78
332438 TAGGATTGAT
** * * * * **
332448 ACTGATTTATCTCCTCTGCGAAAACGGAGGGTTCGGAATGAAACACCATCACCTGAACCTTTAGT
1 ACTGATTTATCTCCTCCACGGAAATGGAGGG-T-GGAATGATACACAATCACCAAAACCTTTAGT
*
332513 AAACAGTGCAGATGG
64 AAACAGAGCAGATGG
** * *
332528 TACTGATTTATCTCCTCCACGGAAACAGAGGGTTCGGAATGATACACAATCATCAGAACCTTTAG
1 -ACTGATTTATCTCCTCCACGGAAATGGAGGG-T-GGAATGATACACAATCACCAAAACCTTTAG
*
332593 TGAACAGAGCAGATGG
63 TAAACAGAGCAGATGG
* * *
332609 TACTGATTTATCTCCTCCACGTAAATGGAGGGCTCGGAATGATACACATTCACCAAAACCTTTAA
1 -ACTGATTTATCTCCTCCACGGAAATGGAGGG-T-GGAATGATACACAATCACCAAAACCTTTAG
332674 TAAACAGAGCAGAT-G
63 TAAACAGAGCAGATGG
* * *
332689 -CTGATTTATCACCACCTCGGAAATGGAGGGTGAGAAATGATACAC
1 ACTGATTTATCTCCTCCACGGAAATGGAGGGTG-G-AATGATACAC
332734 CTTCACCGAA
Statistics
Matches: 180, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
76 1 0.01
77 2 0.01
78 36 0.20
80 1 0.01
81 140 0.78
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (78 bp):
ACTGATTTATCTCCTCCACGGAAATGGAGGGTGGAATGATACACAATCACCAAAACCTTTAGTAA
ACAGAGCAGATGG
Found at i:336361 original size:2 final size:2
Alignment explanation
Indices: 336350--336439 Score: 76
Period size: 2 Copynumber: 50.5 Consensus size: 2
336340 GAACCCAAAA
* *
336350 AT AT -T AT AT AT A- AT A- AT AT A- AA AT AT AT A- AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
336387 A- AT A- AT -T AT AT -T A- AA AT AT AT AT AT AT AT -T 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
336423 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
336440 ATCGAGGCGG
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
1 11 0.15
2 62 0.85
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:336391 original size:29 final size:29
Alignment explanation
Indices: 336349--336441 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 29
336339 CGAACCCAAA
336349 AATA-TTATATATAATAATATAAAATATAT
1 AATATTTATA-ATAATAATATAAAATATAT
*
336378 AATATTTATAATAATTATATTAAAATATAT
1 AATATTTATAATAATAATA-TAAAATATAT
*
336408 ATATATATTAT-AT-ATATATATATATATATAT
1 A-ATAT-TTATAATAATA-ATATA-AAATATAT
336439 AAT
1 AAT
336442 CGAGGCGGGT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
29 12 0.22
30 22 0.40
31 17 0.31
32 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AATATTTATAATAATAATATAAAATATAT
Found at i:336428 original size:23 final size:23
Alignment explanation
Indices: 336350--336439 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 23
336340 GAACCCAAAA
*
336350 ATATTATATATA-ATAATATAAAAT
1 ATATTATATATATAT-ATAT-ATAT
* *
336374 ATATAATATTTATA-ATA-AT-T
1 ATATTATATATATATATATATAT
*
336394 ATATTA-AAATATATATATATAT
1 ATATTATATATATATATATATAT
336416 -TA-TATATATATATATATATAT
1 ATATTATATATATATATATATAT
336437 ATA
1 ATA
336440 ATCGAGGCGG
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
19 5 0.09
20 11 0.21
21 20 0.38
22 3 0.06
23 3 0.06
24 10 0.19
25 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTATATATATATATATATAT
Found at i:338729 original size:81 final size:81
Alignment explanation
Indices: 338575--338733 Score: 180
Period size: 81 Copynumber: 2.0 Consensus size: 81
338565 AGAGGTTATT
*** * * *
338575 GATACTGTAAGGCCAGTATCGATACCAAGGGTATGGTTTGAGCTTTAAAGCAAGAGTAAGTGTAG
1 GATACTGTAAGGCCAGTATCGATACCAAGGGTATGAAATGAGCTTTAAAGCAAGAGAAAATATAG
338640 AGGCAAGTGAGGTGTC
66 AGGCAAGTGAGGTGTC
* *
338656 GATATTGTAAGGCCAGTATCGATACCAA-GGTCGA-GAAATGGGCTTT-AAGTCAAGAGAAAATA
1 GATACTGTAAGGCCAGTATCGATACCAAGGGT--ATGAAATGAGCTTTAAAG-CAAGAGAAAATA
* *
338718 TATAGGTAAGTGAGGT
63 TAGAGGCAAGTGAGGT
338734 TTTGCACAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
80 6 0.09
81 58 0.89
82 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (81 bp):
GATACTGTAAGGCCAGTATCGATACCAAGGGTATGAAATGAGCTTTAAAGCAAGAGAAAATATAG
AGGCAAGTGAGGTGTC
Found at i:342052 original size:81 final size:81
Alignment explanation
Indices: 341854--342077 Score: 319
Period size: 79 Copynumber: 2.8 Consensus size: 81
341844 GCTTGCCCTC
* * *
341854 AGCACACAGCAAAAAGGGAAGCCAACCTAAGGATATACCTT-AGATCTACCCAAGGACATCCTTA
1 AGCACACAGC-AAAAGGGAA-CCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTA
*
341918 GATCCGTAGGGTTACCTTA
63 GATCCATAGGGTTACCTTA
* *
341937 AGCAC-CAGC-TAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGT
1 AGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGAT
342000 CCATAGGGTTACCTTA
66 CCATAGGGTTACCTTA
* *
342016 TGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATACCTT
1 AGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATAT-CCTT
342078 GGGACCTACC
Statistics
Matches: 128, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
79 50 0.39
80 20 0.16
81 45 0.35
82 8 0.06
83 5 0.04
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (81 bp):
AGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGAT
CCATAGGGTTACCTTA
Found at i:342072 original size:23 final size:23
Alignment explanation
Indices: 342045--342099 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
342035 CCAACCTAAG
342045 GATATACCTTGGGACCTACCCAA
1 GATATACCTTGGGACCTACCCAA
342068 GATATACCTTGGGACCTACCCAA
1 GATATACCTTGGGACCTACCCAA
342091 GATAT-CCTT
1 GATATACCTT
342100 AGGTCCGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (23 bp):
GATATACCTTGGGACCTACCCAA
Found at i:342087 original size:104 final size:103
Alignment explanation
Indices: 341964--342179 Score: 389
Period size: 104 Copynumber: 2.1 Consensus size: 103
341954 CCAACCTAAG
*
341964 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCTTATGCACACAACAAA
1 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTAACTTATGCACACAAC-AA
342029 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
65 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
* *
342068 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
1 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTAACTTATGCACACAACAAA
342133 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
66 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
342171 GATAT-CCTT
1 GATATACCTT
342180 AGGTCCGTAG
Statistics
Matches: 109, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
102 4 0.04
103 46 0.42
104 59 0.54
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (103 bp):
GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTAACTTATGCACACAACAAA
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
Found at i:342201 original size:80 final size:80
Alignment explanation
Indices: 342068--342268 Score: 366
Period size: 80 Copynumber: 2.5 Consensus size: 80
342058 ACCTACCCAA
342068 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
1 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
342133 GGGAACCAACCTAAG
66 GGGAACCAACCTAAG
*
342148 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAA
1 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
342213 GGGAACCAACCTAAG
66 GGGAACCAACCTAAG
* * *
342228 GATATGCCTTGGGGCCTACCTAAGATATCCTTAGGTCCGTA
1 GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTA
342269 AGGACTTACA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 117 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (80 bp):
GATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAAA
GGGAACCAACCTAAG
Found at i:342230 original size:183 final size:183
Alignment explanation
Indices: 341885--342261 Score: 607
Period size: 184 Copynumber: 2.1 Consensus size: 183
341875 CCAACCTAAG
* * *
341885 GATATACCTTAGATCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACCAGCTAAG
1 GATATACCTTAGACCTACCCAAGGACATCCTTAGATCCGTAGGGTTAACTTAAGCACCAGCAAAG
341950 GGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCTT
66 GGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCTT
342015 ATGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
131 ATGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
* * * *
342068 GATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTAACTTATGCACACAGCAA
1 GATATACCTT-AGACCTACCCAAGGACATCCTTAGATCCGTAGGGTTAACTTAAGCAC-CAGCAA
*
342132 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACC
64 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACC
* * * *
342197 TTATGCACACAGC-AAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCTAA
129 TTATGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
342251 GATAT-CCTTAG
1 GATATACCTTAG
342262 GTCCGTAAGG
Statistics
Matches: 179, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
181 1 0.01
182 4 0.02
183 83 0.46
184 91 0.51
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (183 bp):
GATATACCTTAGACCTACCCAAGGACATCCTTAGATCCGTAGGGTTAACTTAAGCACCAGCAAAG
GGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCTT
ATGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
Found at i:344131 original size:17 final size:18
Alignment explanation
Indices: 344098--344131 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
344088 TCCATTCTGT
344098 CTTATTATTTAATTCCAA
1 CTTATTATTTAATTCCAA
344116 CTTATTATTT-ATTCCA
1 CTTATTATTTAATTCCA
344132 GACCTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
CTTATTATTTAATTCCAA
Found at i:351157 original size:76 final size:76
Alignment explanation
Indices: 351031--351182 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
351021 GACATGGTTT
351031 GCAAACAATTTGAGATAAGAAAACTTACACTCTATTTAGTTGATGTTTTTGCTAGTTTCCCTTCA
1 GCAAACAATTTGAGATAAGAAAACTTACACTCTATTTAGTTGATGTTTTTGCTAGTTTCCCTTCA
351096 CTATCTATTAA
66 CTATCTATTAA
351107 GCAAACAATTTGAGATAAGAAAACTTACACTCTATTTAGTTGATGTTTTTGCTAGTTTCCCTTCA
1 GCAAACAATTTGAGATAAGAAAACTTACACTCTATTTAGTTGATGTTTTTGCTAGTTTCCCTTCA
351172 CTATCTATTAA
66 CTATCTATTAA
351183 TTTTTAGTTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (76 bp):
GCAAACAATTTGAGATAAGAAAACTTACACTCTATTTAGTTGATGTTTTTGCTAGTTTCCCTTCA
CTATCTATTAA
Found at i:351388 original size:25 final size:24
Alignment explanation
Indices: 351351--351404 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
351341 TTTGTTTTCG
*
351351 CCCTCCTAAAATTTTATAAGTTCA
1 CCCTCCTAAAATTTTAAAAGTTCA
*
351375 TCCCTCCTACAATTTTAAAAGTTCA
1 -CCCTCCTAAAATTTTAAAAGTTCA
351400 CCCTC
1 CCCTC
351405 TAACATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.30, C:0.31, G:0.04, T:0.35
Consensus pattern (24 bp):
CCCTCCTAAAATTTTAAAAGTTCA
Found at i:358586 original size:24 final size:24
Alignment explanation
Indices: 358540--358591 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
358530 CATACTTATT
*
358540 TATTGACTCGTTTATAAGTTCATA
1 TATTGACTCGTTTATAAGCTCATA
* *
358564 TATTGACTCGTTTATTAGCTCATT
1 TATTGACTCGTTTATAAGCTCATA
358588 TATT
1 TATT
358592 CGGTTCTCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (24 bp):
TATTGACTCGTTTATAAGCTCATA
Found at i:369257 original size:15 final size:15
Alignment explanation
Indices: 369239--369268 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
369229 ACCACGGTGC
369239 TCCCGGAATCCTGCG
1 TCCCGGAATCCTGCG
369254 TCCCGGAATCCTGCG
1 TCCCGGAATCCTGCG
369269 CGATTGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.27, T:0.20
Consensus pattern (15 bp):
TCCCGGAATCCTGCG
Found at i:370854 original size:21 final size:21
Alignment explanation
Indices: 370825--370877 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
370815 TGAACTCGGC
* *
370825 ATACGGATTGCTATCCTGTAG
1 ATACAGATTACTATCCTGTAG
370846 ATACAGATTACTATCCTGTAG
1 ATACAGATTACTATCCTGTAG
370867 ATACAGATTAC
1 ATACAGATTAC
370878 CAATATCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (21 bp):
ATACAGATTACTATCCTGTAG
Found at i:384477 original size:35 final size:35
Alignment explanation
Indices: 384437--384506 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
384427 TGGTTTTGAA
384437 AAATATTTAACGTTCATTCTTACATTCTTATTTTT
1 AAATATTTAACGTTCATTCTTACATTCTTATTTTT
384472 AAATATTTAACGTTCATTCTTACATTCTTATTTTT
1 AAATATTTAACGTTCATTCTTACATTCTTATTTTT
384507 TTTCAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (35 bp):
AAATATTTAACGTTCATTCTTACATTCTTATTTTT
Found at i:386237 original size:14 final size:14
Alignment explanation
Indices: 386218--386252 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
386208 TAAATTAAGA
386218 TTTATGATTTAGAG
1 TTTATGATTTAGAG
*
386232 TTTATGTTTTAGAG
1 TTTATGATTTAGAG
*
386246 GTTATGA
1 TTTATGA
386253 GGTTAGGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (14 bp):
TTTATGATTTAGAG
Found at i:392880 original size:22 final size:22
Alignment explanation
Indices: 392823--392880 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
392813 AATTTTAACA
* *
392823 TTCAGTATTGTTCACGGTACTG
1 TTCATTATTATTCACGGTACTG
* * *
392845 TTTATTACTATTCACGGTATTG
1 TTCATTATTATTCACGGTACTG
*
392867 TTCATTATTTTTCA
1 TTCATTATTATTCA
392881 TACCGTATAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.50
Consensus pattern (22 bp):
TTCATTATTATTCACGGTACTG
Found at i:393176 original size:2 final size:2
Alignment explanation
Indices: 393171--393200 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
393161 TGTTTTTTAA
393171 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
393201 GTTTTTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:393219 original size:12 final size:12
Alignment explanation
Indices: 393202--393400 Score: 69
Period size: 12 Copynumber: 16.1 Consensus size: 12
393192 TATAATATAG
*
393202 TTTTTAAGAATA
1 TTTTTAAAAATA
393214 TTTTTAAAAATA
1 TTTTTAAAAATA
* * *
393226 TATATAATATATGA
1 TTTTTAA-AAAT-A
*
393240 TTTTTGAAAATA
1 TTTTTAAAAATA
*
393252 TTTTTGAAAATA
1 TTTTTAAAAATA
* * *
393264 TATATAATATATA
1 TTTTTAA-AAATA
* * *
393277 GTTTAAAAAACA
1 TTTTTAAAAATA
*
393289 TTTTGAAAACATA
1 TTTTTAAAA-ATA
* * *
393302 TATATTATATATA
1 T-TTTTAAAAATA
**
393315 TTTTTGGAAATA
1 TTTTTAAAAATA
* * *
393327 TATAT-AATATA
1 TTTTTAAAAATA
*
393338 GTTTTTGAAAATA
1 -TTTTTAAAAATA
393351 TTTTT-AAAATA
1 TTTTTAAAAATA
* * * *
393362 TATATAATATATGG
1 TTTTTAA-AAAT-A
393376 TTTTTAAAAATA
1 TTTTTAAAAATA
*
393388 TTTTGAAAAATA
1 TTTTTAAAAATA
393400 T
1 T
393401 ATATAATATA
Statistics
Matches: 132, Mismatches: 45, Indels: 20
0.67 0.23 0.10
Matches are distributed among these distances:
11 13 0.10
12 74 0.56
13 31 0.23
14 14 0.11
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (12 bp):
TTTTTAAAAATA
Found at i:393227 original size:38 final size:37
Alignment explanation
Indices: 393183--393573 Score: 195
Period size: 35 Copynumber: 10.7 Consensus size: 37
393173 ATATATATAT
393183 ATATATATATATAATATAGTTTTTAAGAATATTTTTAAA
1 ATATATATATAT-ATATAGTTTTTAA-AATATTTTTAAA
393222 A-ATATATATA-ATATATGATTTTTGAAAATATTTTTGAAA
1 ATATATATATATATATA-G-TTTTT-AAAATATTTTT-AAA
** * *
393261 ATATATATA-ATATATAGTTTAAAAAACATTTTGAAA
1 ATATATATATATATATAGTTTTTAAAATATTTTTAAA
* **
393297 ACATATATAT-TATATA-----T---AT-TTTTGGAA
1 ATATATATATATATATAGTTTTTAAAATATTTTTAAA
* **
393324 ATATATATA-ATATAGT--TTTTGAAAATATTTTTAAA--
1 ATATATATATATATA-TAGTTTTTAAAATA--TTTTTAAA
* *
393359 ATATATATA-ATATATGGTTTTTAAAAATATTTTGAAA
1 ATATATATATATATATAGTTTTT-AAAATATTTTTAAA
* *
393396 A-ATATATATAATATATAGTTTTTAAAACATTTTGAAA
1 ATATATATAT-ATATATAGTTTTTAAAATATTTTTAAA
* * *
393433 A-CTATATA-ATATAT-GATTTTGAAAACATTTTTAGAA
1 ATATATATATATATATAG-TTTTTAAAATATTTTTA-AA
* *
393469 TATATATATATATATATATATAATTTTAAAATATTATTTGAA
1 -ATATATATATATATATA-GT--TTTTAAAATATT-TTTAAA
* * *
393511 A-ACATATAT-TATAT-GATTTTAAAATATTTTTTTAA
1 ATATATATATATATATAGTTTTTAAAATA-TTTTTAAA
* * *
393546 ACATATATATAGTATATAATATTTAAAA
1 ATATATATATA-TATATAGTTTTTAAAA
393574 ATGTTCTTTT
Statistics
Matches: 277, Mismatches: 34, Indels: 82
0.70 0.09 0.21
Matches are distributed among these distances:
27 19 0.07
28 2 0.01
34 4 0.01
35 55 0.20
36 44 0.16
37 41 0.15
38 49 0.18
39 27 0.10
40 20 0.07
41 1 0.00
42 12 0.04
43 3 0.01
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (37 bp):
ATATATATATATATATAGTTTTTAAAATATTTTTAAA
Found at i:393234 original size:36 final size:35
Alignment explanation
Indices: 393187--393561 Score: 247
Period size: 38 Copynumber: 10.4 Consensus size: 35
393177 ATATATATAT
393187 ATATATATAATATAGTTTTTAAGAATATTTTTAAAA
1 ATATATATAATATAGTTTTTAA-AATATTTTTAAAA
*
393223 ATATATATAATATATGATTTTTGAAAATATTTTTGAAA
1 ATATATATAATATA-G-TTTTT-AAAATATTTTTAAAA
** * *
393261 ATATATATAATATATAGTTTAAAAAACATTTTGAAAA
1 ATATATAT-A-ATATAGTTTTTAAAATATTTTTAAAA
**
393298 CATATATAT--TATA-----T---ATATTTTTGGAA
1 -ATATATATAATATAGTTTTTAAAATATTTTTAAAA
393324 ATATATATAATATAGTTTTTGAAAATATTTTT-AAA
1 ATATATATAATATAGTTTTT-AAAATATTTTTAAAA
*
393359 ATATATATAATATATGGTTTTTAAAAATATTTTGAAAA
1 ATATATATAATATA--GTTTTT-AAAATATTTTTAAAA
* *
393397 ATATATATAATATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATAT-A-ATATAGTTTTTAAAATATTTTTAAAA
* * *
393433 A-CTATATAATATATGATTTTGAAAACATTTTTAGAATA
1 ATATATATAATATA-G-TTTTTAAAATATTTTTA-AA-A
* *
393471 TATATATATATATATATATAATTTTAAAATATTATTTGAAA
1 -ATATATATA-ATATA-GT--TTTTAAAATATT-TTTAAAA
* * * *
393512 ACATATATTATAT-GATTTTAAAATATTTTTTTAAAC
1 ATATATATAATATAGTTTTTAAAATA--TTTTTAAAA
*
393548 ATATATATAGTATA
1 ATATATATAATATA
393562 TAATATTTAA
Statistics
Matches: 269, Mismatches: 34, Indels: 71
0.72 0.09 0.19
Matches are distributed among these distances:
25 8 0.03
26 8 0.03
27 4 0.01
32 1 0.00
33 5 0.02
34 6 0.02
35 41 0.15
36 48 0.18
37 38 0.14
38 54 0.20
39 10 0.04
40 24 0.09
41 7 0.03
42 12 0.04
43 3 0.01
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (35 bp):
ATATATATAATATAGTTTTTAAAATATTTTTAAAA
Found at i:393336 original size:25 final size:24
Alignment explanation
Indices: 393289--393351 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
393279 TTAAAAAACA
*
393289 TTTTGAAAACATATATATTATATATAT
1 TTTTG-AAA-ATATATATAATATA-AT
* *
393316 TTTTGGAAATATATATAATATAGT
1 TTTTGAAAATATATATAATATAAT
393340 TTTTGAAAATAT
1 TTTTGAAAATAT
393352 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 12 0.38
25 13 0.41
26 2 0.06
27 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTTGAAAATATATATAATATAAT
Found at i:393379 original size:37 final size:36
Alignment explanation
Indices: 393312--393562 Score: 208
Period size: 35 Copynumber: 6.7 Consensus size: 36
393302 TATATTATAT
*
393312 ATATTTTTGGAAATATATATAATATA-GTTTTTGAAA
1 ATATTTTT-AAAATATATATAATATATGTTTTTGAAA
*
393348 ATATTTTTAAAATATATATAATATATGGTTTTTAAAA
1 ATATTTTTAAAATATATATAATATAT-GTTTTTGAAA
*
393385 ATATTTTGAAAAATATATATAATATATAGTTTTT-AAA
1 ATATTTT-TAAAATATATATAATATAT-GTTTTTGAAA
* * * *
393422 ACATTTTGAAAA-CTATATAATATATGATTTTGAAA
1 ATATTTTTAAAATATATATAATATATGTTTTTGAAA
* * *
393457 ACATTTTTAGAATATATATATATATATATATATAATTTTAAA
1 ATATTTTTA-AA-ATATATATA-ATATATGT-T--TTTGAAA
* *
393499 ATATTATTTGAAAACATATAT--TATATGATTTT-AAA
1 ATATT-TTT-AAAATATATATAATATATGTTTTTGAAA
*
393534 ATATTTTTTTAAACATATATATAGTATAT
1 ATA--TTTTTAAA-ATATATATAATATAT
393563 AATATTTAAA
Statistics
Matches: 179, Mismatches: 18, Indels: 34
0.77 0.08 0.15
Matches are distributed among these distances:
34 5 0.03
35 48 0.27
36 27 0.15
37 28 0.16
38 36 0.20
39 11 0.06
40 1 0.01
42 17 0.09
43 5 0.03
44 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (36 bp):
ATATTTTTAAAATATATATAATATATGTTTTTGAAA
Found at i:393400 original size:73 final size:72
Alignment explanation
Indices: 393314--393573 Score: 233
Period size: 73 Copynumber: 3.5 Consensus size: 72
393304 TATTATATAT
*
393314 ATTTTTG-GAAATATATATA-ATATAGTTTTTGAAAATATTTTTAAAATATATATAATATATGGT
1 ATTTTTGAAAAATATATATATATATAGTTTTT-AAAATATTTTTAAAA-ATATATAATATATGGT
393377 TTTTAAAA-
64 TTTTAAAAC
* * * *
393385 ATATTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACTATATAATATATGAT
1 AT-TTTTGAAAAATATATAT-ATATATAGTTTTTAAAATATTTTTAAAAATATATAATATATGGT
*
393450 TTTGAAAAC
64 TTTTAAAAC
* * *
393459 ATTTTTAGAATATATATATATATATATATA-TAATTTTAAAATATTATTTGAAAACATATATTAT
1 ATTTTT-GAA-A-A-ATATATATATATATAGT--TTTTAAAATATT-TTTAAAAATATATAATAT
* *
393523 AT-GATTTTAAAAT
59 ATGGTTTTTAAAAC
* * * *
393536 ATTTTTTTAAACATATATATAGTATATAATATTTAAAA
1 A-TTTTTGAAAAATATATATA-TATATAGTTTTTAAAA
393574 ATGTTCTTTT
Statistics
Matches: 155, Mismatches: 19, Indels: 27
0.77 0.09 0.13
Matches are distributed among these distances:
71 2 0.01
72 5 0.03
73 35 0.23
74 35 0.23
75 19 0.12
76 10 0.06
77 29 0.19
78 20 0.13
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (72 bp):
ATTTTTGAAAAATATATATATATATAGTTTTTAAAATATTTTTAAAAATATATAATATATGGTTT
TTAAAAC
Found at i:393452 original size:98 final size:98
Alignment explanation
Indices: 393211--393425 Score: 247
Period size: 98 Copynumber: 2.2 Consensus size: 98
393201 GTTTTTAAGA
* * *
393211 ATATTTTTAAAAATATATATAATATA-TGATTTTTGAAAATATTTTTGAAAATATATATAATATA
1 ATATTTTTGAAAACATATATAATATACT-A--TATGAAAATATTTTT-AAAATATATATAATATA
*
393275 TAGTTTAAAAAACATTTTGAAAACATATATATTATAT
62 TAGTTTAAAAAACATTTTGAAAACATATATATAATAT
* * * * * *
393312 ATATTTTTGGAAATATATATAATATAGTTTTTGAAAATATTTTTAAAATATATATAATATATGGT
1 ATATTTTTGAAAACATATATAATATACTATATGAAAATATTTTTAAAATATATATAATATATAG-
* *
393377 TTTTAAAAATATTTTGAAAA-ATATATATAATAT
65 TTTAAAAAACATTTTGAAAACATATATATAATAT
393410 ATAGTTTTT-AAAACAT
1 ATA-TTTTTGAAAACAT
393426 TTTGAAAACT
Statistics
Matches: 102, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
98 39 0.38
99 38 0.37
101 24 0.24
102 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (98 bp):
ATATTTTTGAAAACATATATAATATACTATATGAAAATATTTTTAAAATATATATAATATATAGT
TTAAAAAACATTTTGAAAACATATATATAATAT
Found at i:393524 original size:43 final size:42
Alignment explanation
Indices: 393435--393524 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
393425 TTTTGAAAAC
* * *
393435 TATATAATATATGATTTTGAAAACATTTTTAGAATATATATA
1 TATATAATATATAATTTTGAAAACATTTTTAAAACATATATA
*
393477 TATATATATATATAATTTT-AAAATATTATTTGAAAACATATAT-
1 TATATA-ATATATAATTTTGAAAACATT-TTT-AAAACATATATA
393520 TATAT
1 TATAT
393525 GATTTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 13 0.32
43 19 0.46
44 9 0.22
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (42 bp):
TATATAATATATAATTTTGAAAACATTTTTAAAACATATATA
Found at i:393594 original size:6 final size:6
Alignment explanation
Indices: 393583--393642 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
393573 AATGTTCTTT
* *
393583 TTTTTA TTTTTA TTTTTA TTTTTA TTATTCA --TTTA TTGTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA
*
393630 TTTAT- TTTTTA TT
1 TTTTTA TTTTTA TT
393643 CATTTCTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 3 0.07
5 4 0.09
6 34 0.77
7 3 0.07
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:393617 original size:17 final size:17
Alignment explanation
Indices: 393597--393653 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 17
393587 TATTTTTATT
393597 TTTATTTTTATTATTCA
1 TTTATTTTTATTATTCA
* *
393614 TTTATTGTTATT-TTTA
1 TTTATTTTTATTATTCA
393630 TTTA-TTTT-TTATTCA
1 TTTATTTTTATTATTCA
*
393645 TTTCTTTTT
1 TTTATTTTT
393654 CTTTTTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 2 0.06
15 9 0.27
16 11 0.33
17 11 0.33
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTATTTTTATTATTCA
Found at i:393640 original size:23 final size:23
Alignment explanation
Indices: 393575--393642 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
393565 TATTTAAAAA
*
393575 TGTTCTTTTT-TTTA-TTTTTAT
1 TGTTATTTTTATTTATTTTTTAT
* *
393596 TTTTATTTTTA-TTATTCATTTAT
1 TGTTATTTTTATTTATT-TTTTAT
393619 TGTTATTTTTATTTATTTTTTAT
1 TGTTATTTTTATTTATTTTTTAT
393642 T
1 T
393643 CATTTCTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 11 0.29
22 1 0.03
23 21 0.55
24 5 0.13
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (23 bp):
TGTTATTTTTATTTATTTTTTAT
Found at i:394915 original size:17 final size:17
Alignment explanation
Indices: 394883--394924 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
394873 CCCATTTATT
394883 TTATTTTTTTGTTTTTA
1 TTATTTTTTTGTTTTTA
394900 TTATTATTTTT-TTTTT-
1 TTATT-TTTTTGTTTTTA
*
394916 TTGTTTTTT
1 TTATTTTTT
394925 ACTAACCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
17 10 0.43
18 5 0.22
ACGTcount: A:0.10, C:0.00, G:0.05, T:0.86
Consensus pattern (17 bp):
TTATTTTTTTGTTTTTA
Found at i:394973 original size:13 final size:14
Alignment explanation
Indices: 394940--394977 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
394930 CCTTTTTATT
*
394940 ATTATTCTTATTCTT
1 ATTATT-TTATTCTA
394955 ATTATTTTATT-TA
1 ATTATTTTATTCTA
394968 ATTATTTTAT
1 ATTATTTTAT
394978 ATTTCCTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 5 0.23
15 6 0.27
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTATTTTATTCTA
Found at i:395052 original size:136 final size:141
Alignment explanation
Indices: 394757--395052 Score: 358
Period size: 136 Copynumber: 2.1 Consensus size: 141
394747 TTTAATTTTT
*
394757 TTATTAT-T-TATTTATTTGTTTTTTACTAACCTTTTTATTATTCTTATTCTTATTATTTTATTT
1 TTATTATATATATTT-TTTGTTTTTTACTAACCTTTTTATTA-T-TTATTCTTATTATCTTATTT
*
394820 AATTATTATTTAATTATTTTCTATTTCCTTTGTTTTAACTTTTGTTTATATTTCCCATTTATTTT
63 AATTATTATTTAATTATTTTATATTTCCTTTGTTTTAACTTTTGTTTATATTTCCCATTTATTTT
* * * **
394885 ATTTTTTTGTTTTTA
128 A-TTTATTATATCAA
* * *
394900 TTATTATTTTTTTTTTTTGTTTTTTACTAACCTTTTTATTA-TTATTCTTA-T-TCTTA-TT-AT
1 TTATTATATATATTTTTTGTTTTTTACTAACCTTTTTATTATTTATTCTTATTATCTTATTTAAT
* *
394960 T-TTATTTAATTATTTTATATTTCCTTTGTTTTAACTTTTGTTTATATTTTCCATTTCTTTTA-T
66 TATTATTTAATTATTTTATATTTCCTTTGTTTTAACTTTTGTTTATATTTCCCATTTATTTTATT
395023 TATTATATCAA
131 TATTATATCAA
*
395034 TGTGTGTATATATATTTTT
1 T-TAT-TATATATATTTTT
395053 CCTTTTCTTC
Statistics
Matches: 135, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
134 8 0.06
135 2 0.01
136 68 0.50
137 3 0.02
138 2 0.01
139 4 0.03
140 1 0.01
141 9 0.07
143 7 0.05
144 27 0.20
145 4 0.03
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (141 bp):
TTATTATATATATTTTTTGTTTTTTACTAACCTTTTTATTATTTATTCTTATTATCTTATTTAAT
TATTATTTAATTATTTTATATTTCCTTTGTTTTAACTTTTGTTTATATTTCCCATTTATTTTATT
TATTATATCAA
Found at i:398513 original size:69 final size:69
Alignment explanation
Indices: 398424--398552 Score: 213
Period size: 69 Copynumber: 1.9 Consensus size: 69
398414 AGAAGCAATC
* *
398424 ATAATATGATAAATATTGATATTTTACAAATTTATTTTATTATAAAATATTTTAAGAATACCTTT
1 ATAATATGATAAATATTGATATTTTACAAATTTATTTAATTATAAAATATTTTAAAAATACCTTT
398489 TTAA
66 TTAA
* * *
398493 ATAATATGATAAGTTTTGATATTTTATAAATTTATTTAATTATAAAATATTTTAAAAATA
1 ATAATATGATAAATATTGATATTTTACAAATTTATTTAATTATAAAATATTTTAAAAATA
398553 TCATTTAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (69 bp):
ATAATATGATAAATATTGATATTTTACAAATTTATTTAATTATAAAATATTTTAAAAATACCTTT
TTAA
Found at i:399069 original size:18 final size:19
Alignment explanation
Indices: 399032--399070 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
399022 ACCGAGTAAA
399032 TTATGTATTAGTTATTTAT
1 TTATGTATTAGTTATTTAT
399051 TTAT-TATTA-TTATTATAT
1 TTATGTATTAGTTATT-TAT
399069 TT
1 TT
399071 TAATTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TTATGTATTAGTTATTTAT
Found at i:400300 original size:35 final size:35
Alignment explanation
Indices: 400252--400363 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
400242 TCTAAACCTT
* * *
400252 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * * *
400287 TAATTGAATTATTTTGGAATTTAGAGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * *
400322 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
400357 AAATTGA
1 AAATTGA
400364 TGGTTGTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
Found at i:401635 original size:24 final size:22
Alignment explanation
Indices: 401604--401647 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
401594 GAATTTCATG
401604 ATTAATATTTATATTTCATATAA
1 ATTAATATTTAT-TTTCATATAA
*
401627 ATTATATATTTATTTTTATAT
1 ATTA-ATATTTATTTTCATAT
401648 TTTATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTAATATTTATTTTCATATAA
Found at i:411516 original size:35 final size:35
Alignment explanation
Indices: 411470--411541 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
411460 ATTTATATTC
411470 TGTAGATAGAAACTGAGGAATGAAGGTCGCAAACT
1 TGTAGATAGAAACTGAGGAATGAAGGTCGCAAACT
411505 TGTAGATAGAAACTGAGGAATGAAGGTCGCAAACT
1 TGTAGATAGAAACTGAGGAATGAAGGTCGCAAACT
411540 TG
1 TG
411542 ACGCTCTGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (35 bp):
TGTAGATAGAAACTGAGGAATGAAGGTCGCAAACT
Done.