Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001277.1 Hibiscus syriacus cultivar Beakdansim tig00002507_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: 391084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:14912 original size:15 final size:15
Alignment explanation
Indices: 14892--14934 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
14882 AACAAGAATT
14892 GAGAAAGAATCAAGA
1 GAGAAAGAATCAAGA
14907 GAGAAAGAATCAAGA
1 GAGAAAGAATCAAGA
*
14922 GAGAAAGCATCAA
1 GAGAAAGAATCAA
14935 ACCTCAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.58, C:0.09, G:0.26, T:0.07
Consensus pattern (15 bp):
GAGAAAGAATCAAGA
Found at i:22657 original size:52 final size:52
Alignment explanation
Indices: 22574--22681 Score: 207
Period size: 52 Copynumber: 2.1 Consensus size: 52
22564 GGAAAAACAA
*
22574 TATCGATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
1 TATCAATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
22626 TATCAATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
1 TATCAATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
22678 TATC
1 TATC
22682 GATACTCATT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.37
Consensus pattern (52 bp):
TATCAATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
Found at i:22669 original size:26 final size:26
Alignment explanation
Indices: 22588--22670 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 26
22578 GATATTGTTC
22588 TTCAATTAGTGTATAATGAAAGAGTT
1 TTCAATTAGTGTATAATGAAAGAGTT
** * **
22614 TTCAAAGGAGAGTATCAAT---ATTGTT
1 TTC-AATTAGTGTAT-AATGAAAGAGTT
22639 CTTCAATTAGTGTATAATGAAAGAGTT
1 -TTCAATTAGTGTATAATGAAAGAGTT
22666 TTCAA
1 TTCAA
22671 AGGAGAGTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
24 3 0.07
25 12 0.29
26 11 0.27
27 12 0.29
28 3 0.07
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.37
Consensus pattern (26 bp):
TTCAATTAGTGTATAATGAAAGAGTT
Found at i:22709 original size:52 final size:52
Alignment explanation
Indices: 22589--22694 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
22579 ATATTGTTCT
* ** *
22589 TCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCAATATTGTTCT
1 TCAAGTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCAATATCATTCA
* *
22641 TCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCGATACTCATTCA
1 TCAAGTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCAATA-TCATTCA
22694 T
1 T
22695 GGAGTATCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 44 0.90
53 5 0.10
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (52 bp):
TCAAGTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCAATATCATTCA
Found at i:28054 original size:3 final size:3
Alignment explanation
Indices: 28046--28157 Score: 152
Period size: 3 Copynumber: 36.7 Consensus size: 3
28036 TTTAAATTTT
** *
28046 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
28094 TTA TTA TAA TTA TTA TTA TCA TTA TTTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
28140 TTA TATA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TT
28158 TAATAAATAA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
3 89 0.94
4 6 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28343 original size:30 final size:27
Alignment explanation
Indices: 28275--28338 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
28265 CCTAGCCACC
*
28275 CCCAGCCGCCTCTGATGCTTCCAGAAT
1 CCCAGCCGCCTCTGATGCTTCAAGAAT
28302 CCCAGCCGCCTCTGATGCTTCAAGAAT
1 CCCAGCCGCCTCTGATGCTTCAAGAAT
28329 CCCAGCCGCC
1 CCCAGCCGCC
28339 GCCTCACTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.19
Consensus pattern (27 bp):
CCCAGCCGCCTCTGATGCTTCAAGAAT
Found at i:28601 original size:15 final size:16
Alignment explanation
Indices: 28581--28612 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
28571 ACGACAAGAA
28581 AAAAAAACAGA-AAAG
1 AAAAAAACAGAGAAAG
28596 AAAAAAACAGAGAAAG
1 AAAAAAACAGAGAAAG
28612 A
1 A
28613 GAACACAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAACAGAGAAAG
Found at i:30481 original size:13 final size:15
Alignment explanation
Indices: 30450--30486 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
30440 ATATATATTT
30450 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
30465 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
30478 TA-TTTATTT
1 TATTTTATTT
30487 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:31946 original size:14 final size:14
Alignment explanation
Indices: 31907--31946 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
31897 TTTACGTTTG
*
31907 TATTTACATTTACA
1 TATTTACATTTGCA
*
31921 TTTTTACATTTGCA
1 TATTTACATTTGCA
31935 TATTTACATTTG
1 TATTTACATTTG
31947 GCATCTTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (14 bp):
TATTTACATTTGCA
Found at i:34525 original size:23 final size:23
Alignment explanation
Indices: 34491--34535 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34481 CTCATACAGC
* *
34491 AAAGAAAGAAGAAGAAGAAAAAG
1 AAAGAAAAAAGAAAAAGAAAAAG
*
34514 AAAGAAAAAAGAAAAAGGAAAA
1 AAAGAAAAAAGAAAAAGAAAAA
34536 TCGAATAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAAGAAAAAGAAAAAG
Found at i:37048 original size:114 final size:114
Alignment explanation
Indices: 36783--37123 Score: 515
Period size: 114 Copynumber: 3.0 Consensus size: 114
36773 AAGTTCCATG
* * *
36783 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATC
* *
36848 TGGTTTGGTATGAACCCCAAAAATCAATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGATTTAAAAGATGAATT
*
36898 TGCTCATAGTAGAAAT-AGGAAGACTCAATAGTATCTTCTGGAAATGTTCTTTGAGTTATCTGAT
1 TGCTCATAGTAGAAATAAGG-AGACTCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGAT
36962 CTGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
65 CTGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
*
37012 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCT-GAAAGTGTTCTTTGAGTTATCTGAT
1 TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAA-TGTTCTTTGAGTTATCTGAT
* * * * * * *
37076 CTGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
65 CTGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
37124 CTGCATGATC
Statistics
Matches: 208, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
113 4 0.02
114 125 0.60
115 79 0.38
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
Found at i:39329 original size:54 final size:53
Alignment explanation
Indices: 39210--39360 Score: 198
Period size: 54 Copynumber: 2.8 Consensus size: 53
39200 AAAGAGATTC
* *
39210 AATG-TTTACGAACATCTGAGCAGAAGCCACA-AAAAAATGAATATGTTGTCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACAGAAAAGATGAATGTGTTGTCA
* * * * * *
39261 AATGTTTTATGAACATCTAAACAGAAACCACATGAAAGGATAAATGTGTTGTCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACA-GAAAAGATGAATGTGTTGTCA
39315 AATGTTTTACGAACATCTGAGCAGAAGCCACAGGAAAAGATGAATG
1 AATGTTTTACGAACATCTGAGCAGAAGCCACA-GAAAAGATGAATG
39361 CACTTATTAA
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
51 4 0.05
52 23 0.28
54 55 0.67
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (53 bp):
AATGTTTTACGAACATCTGAGCAGAAGCCACAGAAAAGATGAATGTGTTGTCA
Found at i:39373 original size:54 final size:53
Alignment explanation
Indices: 39210--39382 Score: 183
Period size: 54 Copynumber: 3.3 Consensus size: 53
39200 AAAGAGATTC
*
39210 AATG-TTTACGAACATCTGAGCAGAAGCCACA-AAAAAATGAAT-ATGTTGTCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACAGAAAAGATGAATGA-GTTGTCA
* * * * * * *
39261 AATGTTTTATGAACATCTAAACAGAAACCACATGAAAGGATAAATGTGTTGTCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACA-GAAAAGATGAATGAGTTGTCA
* * *
39315 AATGTTTTACGAACATCTGAGCAGAAGCCACAGGAAAAGATGAATGCACTTAT-T
1 AATGTTTTACGAACATCTGAGCAGAAGCCACA-GAAAAGATGAATG-AGTTGTCA
39369 AATGTTTTACGAAC
1 AATGTTTTACGAAC
39383 CTGTTATTCT
Statistics
Matches: 98, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
51 4 0.04
52 23 0.23
54 68 0.69
55 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (53 bp):
AATGTTTTACGAACATCTGAGCAGAAGCCACAGAAAAGATGAATGAGTTGTCA
Found at i:39779 original size:22 final size:22
Alignment explanation
Indices: 39751--39805 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
39741 ATCTACACTC
* *
39751 TTCAAAGATGATAGATTATCTT
1 TTCAAAGATGACAAATTATCTT
* *
39773 TTTAAAGATGACAAATTCTCTT
1 TTCAAAGATGACAAATTATCTT
39795 TTCAAAGATGA
1 TTCAAAGATGA
39806 AAACTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAAATTATCTT
Found at i:40602 original size:76 final size:76
Alignment explanation
Indices: 40476--42031 Score: 2981
Period size: 76 Copynumber: 20.5 Consensus size: 76
40466 CTATTTCTCA
40476 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40541 AGCCTTCGGGT
66 AGCCTTCGGGT
*
40552 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40617 AGCCTTCGGGT
66 AGCCTTCGGGT
40628 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40693 AGCCTTCGGGT
66 AGCCTTCGGGT
40704 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40769 AGCCTTCGGGT
66 AGCCTTCGGGT
40780 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
40845 AAGCCTTCGGGT
65 AAGCCTTCGGGT
40857 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
40922 AGTCTTCGGGT
66 AGCCTTCGGGT
40933 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
40998 AAGCCTTCGGGT
65 AAGCCTTCGGGT
41010 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41075 AGCCTTCGGGT
66 AGCCTTCGGGT
41086 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41151 AGCCTTCGGGT
66 AGCCTTCGGGT
41162 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41227 AGCCTTCGGGT
66 AGCCTTCGGGT
41238 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41303 AGCCTTCGGGT
66 AGCCTTCGGGT
*
41314 CATCTATAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41379 AGCCTTCGGGT
66 AGCCTTCGGGT
*
41390 CATCTATAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATG-TTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41453 AGCCTTCGGGT
66 AGCCTTCGGGT
41464 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41529 AGCCTTCGGGT
66 AGCCTTCGGGT
41540 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41605 AGCCTTCGGGT
66 AGCCTTCGGGT
41616 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
41681 AAGCCTTCGGGT
65 AAGCCTTCGGGT
41693 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41758 AGCCTTCGGGT
66 AGCCTTCGGGT
41769 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41834 AGCCTTCGGGT
66 AGCCTTCGGGT
*
41845 CATCTATAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41910 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
41921 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTAATGTTTTCAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
41986 AACCTTCGGGT
66 AGCCTTCGGGT
* *
41997 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAA
42032 CATTTCCATT
Statistics
Matches: 1462, Mismatches: 13, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
74 65 0.04
75 16 0.01
76 1154 0.79
77 227 0.16
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:42165 original size:3 final size:3
Alignment explanation
Indices: 42157--42259 Score: 143
Period size: 3 Copynumber: 33.7 Consensus size: 3
42147 TCATTTAAAT
**
42157 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
42205 TTA TAA TTA TTA TTA TCA TTA TTTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
42251 TATA TTA TT
1 T-TA TTA TT
42260 TAATAAATAA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
3 82 0.93
4 6 0.07
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:42445 original size:30 final size:27
Alignment explanation
Indices: 42377--42440 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
42367 CCTAGCCACC
*
42377 CCCAGCCGCCTCTGATGCTTCCAGAAT
1 CCCAGCCGCCTCTGATGCTTCAAGAAT
42404 CCCAGCCGCCTCTGATGCTTCAAGAAT
1 CCCAGCCGCCTCTGATGCTTCAAGAAT
42431 CCCAGCCGCC
1 CCCAGCCGCC
42441 GCCTCACTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.19
Consensus pattern (27 bp):
CCCAGCCGCCTCTGATGCTTCAAGAAT
Found at i:42699 original size:16 final size:17
Alignment explanation
Indices: 42678--42713 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
42668 AGAGAACGAC
42678 AAGAAAAAAAACAGA-A
1 AAGAAAAAAAACAGAGA
42694 AAG-AAAAAAACAGAGA
1 AAGAAAAAAAACAGAGA
42710 AAGA
1 AAGA
42714 GAACACAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.78, C:0.06, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAACAGAGA
Found at i:54002 original size:23 final size:23
Alignment explanation
Indices: 53976--54028 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
53966 AAAAAAACCA
*
53976 TGTTTATAAGAACCGAAAAACTT
1 TGTTTACAAGAACCGAAAAACTT
* * * *
53999 TGTTTACCATAATCGAAAAATTT
1 TGTTTACAAGAACCGAAAAACTT
54022 TGTTTAC
1 TGTTTAC
54029 CAGAGCTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (23 bp):
TGTTTACAAGAACCGAAAAACTT
Found at i:54041 original size:24 final size:23
Alignment explanation
Indices: 53984--54032 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
53974 CATGTTTATA
*
53984 AGAACCGAAAAACTTTGTTTACC
1 AGAATCGAAAAACTTTGTTTACC
* *
54007 ATAATCGAAAAATTTTGTTTACC
1 AGAATCGAAAAACTTTGTTTACC
54030 AGA
1 AGA
54033 GCTGGAAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (23 bp):
AGAATCGAAAAACTTTGTTTACC
Found at i:57789 original size:42 final size:42
Alignment explanation
Indices: 57725--57844 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
57715 TTTCCCCGAA
*
57725 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
57767 TTCCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
57809 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
57845 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:58090 original size:20 final size:18
Alignment explanation
Indices: 58055--58091 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
58045 ATATTTATTA
58055 ATATTTATAATAATATAT
1 ATATTTATAATAATATAT
* *
58073 ATATTTTTAATATTATAT
1 ATATTTATAATAATATAT
58091 A
1 A
58092 AAATAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTATAATAATATAT
Found at i:58143 original size:22 final size:22
Alignment explanation
Indices: 58118--58198 Score: 54
Period size: 26 Copynumber: 3.2 Consensus size: 22
58108 TATAATAAAG
58118 ATATTATATTTTTATTTTAATA
1 ATATTATATTTTTATTTTAATA
58140 ATATATAATAATTTTTTATATATTAATA
1 ATAT-T-AT-A-TTTTTAT-T-TTAATA
* *
58168 ATGAATATTATTTATATATTTCAATA
1 AT-ATTA-TATTT-T-TATTTTAATA
58194 ATATT
1 ATATT
58199 TTAGTAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
22 4 0.09
23 1 0.02
24 2 0.04
25 3 0.07
26 17 0.37
27 5 0.11
28 13 0.28
29 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (22 bp):
ATATTATATTTTTATTTTAATA
Found at i:58159 original size:48 final size:48
Alignment explanation
Indices: 58058--58159 Score: 113
Period size: 48 Copynumber: 2.1 Consensus size: 48
58048 TTTATTAATA
*
58058 TTTATAATAATATATATATTTTTAATATTATATAAAATAATCAATTAT
1 TTTATAATAAGATATATATTTTTAATATTATATAAAATAATCAATTAT
* *
58106 ATTATAATAAAGATATTATATTTTT-ATTTTA-ATAATATATAAT-AATT-T
1 TTTATAAT-AAGATA-TATATTTTTAATATTATATAA-A-ATAATCAATTAT
58154 TTTATA
1 TTTATA
58160 TATTAATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
48 17 0.37
49 15 0.33
50 14 0.30
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (48 bp):
TTTATAATAAGATATATATTTTTAATATTATATAAAATAATCAATTAT
Found at i:58388 original size:20 final size:20
Alignment explanation
Indices: 58363--58432 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
58353 TTTCCAGATG
*
58363 TTTTCCAGAAATATAATTCA
1 TTTTCCAGAAATGTAATTCA
58383 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
58403 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
58423 TTTTCCAGAA
1 TTTTCCAGAA
58433 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:58441 original size:40 final size:40
Alignment explanation
Indices: 58363--58441 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
58353 TTTCCAGATG
* **
58363 TTTTCCAGAAATATAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATATAATTCATTTTCCAGAAATCAAATTCA
* *
58403 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATATAATTCATTTTCCAGAAATCAAATTC
58442 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATATAATTCATTTTCCAGAAATCAAATTCA
Found at i:58451 original size:15 final size:15
Alignment explanation
Indices: 58415--58496 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
58405 TTACAGAAAT
**
58415 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
58430 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
58444 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
58459 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
58474 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
58489 GTAATTCA
1 GTAATTCA
58497 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:58467 original size:30 final size:30
Alignment explanation
Indices: 58415--58496 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
58405 TTACAGAAAT
58415 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
58444 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
58474 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
58497 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:58489 original size:45 final size:44
Alignment explanation
Indices: 58415--58501 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
58405 TTACAGAAAT
**
58415 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
58459 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
58502 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:59479 original size:188 final size:188
Alignment explanation
Indices: 59150--59504 Score: 525
Period size: 188 Copynumber: 1.9 Consensus size: 188
59140 AAATAAAAAT
* * * *
59150 TTATGTCAAATTTATTTTGTCATAATATTTTTTCAAAATAAAAAATTTTGACAAAGTTATTTAAT
1 TTATGTCAAATATATTTCGTCACAATATTTTTTCAAAATAAAAAATTGTGACAAAGTTATTTAAT
* * * *
59215 CAAAATAATAATGTATAACAAATATTAATTTCTCATCATAAAAAATTGTGACAATTAATATTCTT
66 CAAAATAATAATGTATAACAAATATTAATTTCTCATCATAAAAAATTATGAAAAATAATATTATT
*
59280 TCACGATAACAAATTGCAACAAAATGATTTAGTCACAATAACACGTTAAATTAAACAA
131 TCACAATAACAAATTGCAACAAAATGATTTAGTCACAATAACACGTTAAATTAAACAA
* * * *
59338 TTATGTCAAATATATTTCGTCGCAATATTTTGTT-GAAATAAAAAATTGTGATAAATTTATTTAA
1 TTATGTCAAATATATTTCGTCACAATATTTT-TTCAAAATAAAAAATTGTGACAAAGTTATTTAA
* *
59402 TCAAAATAACT-ATTTATAACAAATATTAATTTCTCATTATAAAAAATTATGAAAAATAATATTA
65 TCAAAATAA-TAATGTATAACAAATATTAATTTCTCATCATAAAAAATTATGAAAAATAATATTA
* *
59466 TTTCACAATAACAAATTGTAACAAAATTATTTAGTCACA
129 TTTCACAATAACAAATTGCAACAAAATGATTTAGTCACA
59505 GTAAAAAAGT
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
188 145 0.98
189 3 0.02
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (188 bp):
TTATGTCAAATATATTTCGTCACAATATTTTTTCAAAATAAAAAATTGTGACAAAGTTATTTAAT
CAAAATAATAATGTATAACAAATATTAATTTCTCATCATAAAAAATTATGAAAAATAATATTATT
TCACAATAACAAATTGCAACAAAATGATTTAGTCACAATAACACGTTAAATTAAACAA
Found at i:70344 original size:26 final size:26
Alignment explanation
Indices: 70308--70372 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
70298 TGACGGCCTC
70308 TTCTTCTTCTTCAGCGCAACCCTTTT
1 TTCTTCTTCTTCAGCGCAACCCTTTT
70334 TTCTTCTTCTTCAGCGCAACCCTTTT
1 TTCTTCTTCTTCAGCGCAACCCTTTT
70360 TTCTTCTTCTTCA
1 TTCTTCTTCTTCA
70373 ACCCAGCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.11, C:0.34, G:0.06, T:0.49
Consensus pattern (26 bp):
TTCTTCTTCTTCAGCGCAACCCTTTT
Found at i:75052 original size:19 final size:18
Alignment explanation
Indices: 75023--75077 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
75013 TTTTAATAAA
75023 TTTTAACATAAAATATATAT
1 TTTTAA-ATAAAATA-ATAT
*
75043 TTTTAAATAAAA-ACTAT
1 TTTTAAATAAAATAATAT
*
75060 TTTTAAATTAAATTAATA
1 TTTTAAA-TAAAATAATA
75078 ATAAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 10 0.33
18 5 0.17
19 9 0.30
20 6 0.20
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAATAAAATAATAT
Found at i:75092 original size:22 final size:22
Alignment explanation
Indices: 75067--75144 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 22
75057 TATTTTTAAA
75067 TTAAATTAATAATAAAATATAT
1 TTAAATTAATAATAAAATATAT
*
75089 TTAATAAGTTAAT-ATAAAAATATTT
1 TT-A-AA-TTAATAAT-AAAATATAT
*
75114 TTAAGTTAATATATATAAA-ATAT
1 TTAAATTAATA-ATA-AAATATAT
75137 TATAAATT
1 T-TAAATT
75145 TAAGTATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
22 7 0.16
23 7 0.16
24 15 0.34
25 15 0.34
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
TTAAATTAATAATAAAATATAT
Found at i:75133 original size:25 final size:24
Alignment explanation
Indices: 75045--75137 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 24
75035 ATATATATTT
* *
75045 TTAAATA-A-AAACTATTTTTAAA
1 TTAAATATATAAAATATTTTTAAG
75067 TTAAATTAATAATAAAATATATTTAATAAG
1 TTAAA-T-AT-ATAAAATAT-TTT--TAAG
75097 TT-AATATA-AAAATATTTTTAAG
1 TTAAATATATAAAATATTTTTAAG
75119 TTAATATATATAAAATATT
1 TTAA-ATATATAAAATATT
75138 ATAAATTTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
22 11 0.19
23 2 0.03
24 9 0.16
25 15 0.26
26 2 0.03
27 8 0.14
28 4 0.07
29 2 0.03
30 5 0.09
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAAATATATAAAATATTTTTAAG
Found at i:76672 original size:11 final size:11
Alignment explanation
Indices: 76656--76686 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
76646 TTGGTTAAAG
76656 AGAGAGAGACA
1 AGAGAGAGACA
76667 AGAGAGAGACA
1 AGAGAGAGACA
76678 AGAGAGAGA
1 AGAGAGAGA
76687 AGGATTGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.55, C:0.06, G:0.39, T:0.00
Consensus pattern (11 bp):
AGAGAGAGACA
Found at i:88905 original size:2 final size:2
Alignment explanation
Indices: 88894--88945 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
88884 AAATTTATTA
88894 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88935 AT AT AT AT AT A
1 AT AT AT AT AT A
88946 ATTATTTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89421 original size:71 final size:72
Alignment explanation
Indices: 89332--89476 Score: 265
Period size: 72 Copynumber: 2.0 Consensus size: 72
89322 GAGATTAATC
*
89332 ATCGGTAACTAGGTATCTAATTC-TTTGTATTCATATGAAGGTAGGGAATGATTGGATGGTGAAG
1 ATCGGTAACTAGGAATCTAATTCTTTTGTATTCATATGAAGGTAGGGAATGATTGGATGGTGAAG
89396 GAGAATA
66 GAGAATA
*
89403 ATCGGTAACTAGGAATCTAATTCTTTTGTATTCTTATGAAGGTAGGGAATGATTGGATGGTGAAG
1 ATCGGTAACTAGGAATCTAATTCTTTTGTATTCATATGAAGGTAGGGAATGATTGGATGGTGAAG
89468 GAGAATA
66 GAGAATA
89475 AT
1 AT
89477 GAATTTCATA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 22 0.31
72 49 0.69
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33
Consensus pattern (72 bp):
ATCGGTAACTAGGAATCTAATTCTTTTGTATTCATATGAAGGTAGGGAATGATTGGATGGTGAAG
GAGAATA
Found at i:90879 original size:188 final size:188
Alignment explanation
Indices: 90546--90892 Score: 525
Period size: 188 Copynumber: 1.8 Consensus size: 188
90536 TCAAAAGATA
* *
90546 AAACTCCTTTTACCATTCAAACTTAAATAGATATTATTTTAATTTGAAATATACAAAAGTATATA
1 AAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTTAATTTCAAATATACAAAAGTATATA
* * * *
90611 ATTATCTTTAATATTCAAAGTTAAAAATATAACAAATATATTTTTAAATTGACATATTCAAAGAG
66 ATTATCTTTAATATTCAAAATTAAAAAGATAACAAATATATTTTTAAATTGACATATTAAAAGAC
* * *
90676 TAATTATCCTACTAATATTTAAATTAAAAAATATATTTAATTTGCAATGGTAAATGGT
131 TAAGTATCATACTAATATTCAAATTAAAAAATATATTTAATTTGCAATGGTAAATGGT
* * * *
90734 AAACTCTTTTTACTATTCAAAGTTAAACATATATTATTTTAATTTCAAATATACAAAAGTATATA
1 AAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTTAATTTCAAATATACAAAAGTATATA
* * *
90799 ATTATCTTTTAATATTCAAAATTATAAAGATAA-AAATATTTTTTTAAATTGACTTATTAAAAGA
66 ATTATC-TTTAATATTCAAAATTAAAAAGATAACAAATATATTTTTAAATTGACATATTAAAAGA
*
90863 CTAGGTATCATACTAATATTCAAATTAAAA
130 CTAAGTATCATACTAATATTCAAATTAAAA
90893 GTTATCTTTT
Statistics
Matches: 141, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
188 118 0.84
189 23 0.16
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (188 bp):
AAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTTAATTTCAAATATACAAAAGTATATA
ATTATCTTTAATATTCAAAATTAAAAAGATAACAAATATATTTTTAAATTGACATATTAAAAGAC
TAAGTATCATACTAATATTCAAATTAAAAAATATATTTAATTTGCAATGGTAAATGGT
Found at i:92077 original size:21 final size:21
Alignment explanation
Indices: 92035--92077 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
92025 TTTCTGGGCT
*
92035 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
92056 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
92077 A
1 A
92078 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:92130 original size:20 final size:20
Alignment explanation
Indices: 92105--92142 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
92095 GAACGCTAGA
*
92105 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
92125 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
92143 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:92944 original size:31 final size:31
Alignment explanation
Indices: 92906--93061 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
92896 AGGGTCGAGG
92906 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
92937 GTTTACCTATGTTCTTCAGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
92968 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
92999 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
93030 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
93061 G
1 G
93062 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:96895 original size:29 final size:29
Alignment explanation
Indices: 96860--96924 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
96850 AGCAAAGTAT
*
96860 GTCGCCATGGAGTCAGGGTGACCTTGTAG
1 GTCGCCATGCAGTCAGGGTGACCTTGTAG
* * *
96889 GTCGCCATGCAGTCGGGGTGTCGTTGTAG
1 GTCGCCATGCAGTCAGGGTGACCTTGTAG
96918 GTCGCCA
1 GTCGCCA
96925 GGTGAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.14, C:0.23, G:0.38, T:0.25
Consensus pattern (29 bp):
GTCGCCATGCAGTCAGGGTGACCTTGTAG
Found at i:101029 original size:15 final size:15
Alignment explanation
Indices: 100975--101033 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
100965 TTATAAAAAA
*
100975 ACTAAATTAAACAAC
1 ACTAACTTAAACAAC
100990 ACTAACTT-AACAA-
1 ACTAACTTAAACAAC
* **
101003 AATATTTTTTAAACAAC
1 ACTA--ACTTAAACAAC
101020 ACTAACTTAAACAA
1 ACTAACTTAAACAA
101034 ATTAATTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
13 3 0.09
14 5 0.15
15 17 0.52
16 5 0.15
17 3 0.09
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (15 bp):
ACTAACTTAAACAAC
Found at i:101043 original size:30 final size:30
Alignment explanation
Indices: 100981--101053 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
100971 AAAAACTAAA
*
100981 TTAAACAACACTAACTTAACAAAATATTTT
1 TTAAACAACACTAACTTAACAAAATATATT
*
101011 TTAAACAACACTAACTTAAACAAATTA-ATT
1 TTAAACAACACTAACTT-AACAAAATATATT
*
101041 TTATACAA-ACTAA
1 TTAAACAACACTAA
101054 ATGAACTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.13
30 26 0.67
31 8 0.21
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (30 bp):
TTAAACAACACTAACTTAACAAAATATATT
Found at i:101576 original size:21 final size:21
Alignment explanation
Indices: 101547--101587 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
101537 CTAATATAAT
*
101547 ATAACTTAAACTAAGAAACTA
1 ATAACTTAAACTAACAAACTA
*
101568 ATAATTTAAACTAACAAACT
1 ATAACTTAAACTAACAAACT
101588 TTTACCCGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:101630 original size:15 final size:15
Alignment explanation
Indices: 101601--101647 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
101591 ACCCGGTTCT
101601 TTCTTCTCCCTTT-C
1 TTCTTCTCCCTTTCC
101615 TTC-T-T-CCTTTCC
1 TTCTTCTCCCTTTCC
*
101627 TTCTTCTCCCTTTCT
1 TTCTTCTCCCTTTCC
101642 TTCTTC
1 TTCTTC
101648 ATAACCGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 5 0.18
12 5 0.18
13 2 0.07
14 4 0.14
15 12 0.43
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
TTCTTCTCCCTTTCC
Found at i:101631 original size:12 final size:11
Alignment explanation
Indices: 101599--101632 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
101589 TTACCCGGTT
*
101599 CTTTCTTCTCC
1 CTTTCTTCTTC
101610 CTTTCTTCTTC
1 CTTTCTTCTTC
101621 CTTTCCTTCTTC
1 CTTT-CTTCTTC
101633 TCCCTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (11 bp):
CTTTCTTCTTC
Found at i:108990 original size:34 final size:33
Alignment explanation
Indices: 108946--109015 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
108936 TTTGTAAAGA
108946 GGAAAAGTTCTAGCTAAGCCCGTGTAAAAGCTAG
1 GGAAAAGTTCTAGCTAAGCCCGTG-AAAAGCTAG
* * * * *
108980 GGAAAGGTTCTAGTTTATCCCGTGAAAATCTAG
1 GGAAAAGTTCTAGCTAAGCCCGTGAAAAGCTAG
109013 GGA
1 GGA
109016 GTTATAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (33 bp):
GGAAAAGTTCTAGCTAAGCCCGTGAAAAGCTAG
Found at i:111739 original size:21 final size:18
Alignment explanation
Indices: 111681--111753 Score: 89
Period size: 15 Copynumber: 4.0 Consensus size: 18
111671 TAACAATTGG
111681 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
111699 TAACAA--G-TATCTTTT
1 TAACAATTGATATCTTTT
111714 TAACAATTGATATTCTTTTGT
1 TAACAATTGATA-TC-TTT-T
111735 TAACAATTGATATCCTTTT
1 TAACAATTGATAT-CTTTT
111754 CATTAAACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
15 14 0.29
16 1 0.02
17 1 0.02
18 8 0.17
19 3 0.06
20 7 0.15
21 14 0.29
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:112112 original size:20 final size:21
Alignment explanation
Indices: 112067--112114 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
112057 AAATTCCAGA
* *
112067 ATGCTACAAGGGTATCGATAC
1 ATGCTACAAGGGTACCAATAC
*
112088 ATGCTACAGGGGTACCAATAC
1 ATGCTACAAGGGTACCAATAC
112109 -TGCTAC
1 ATGCTAC
112115 TGTTCATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
ATGCTACAAGGGTACCAATAC
Found at i:112404 original size:16 final size:16
Alignment explanation
Indices: 112383--112424 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
112373 TTTTCCTTTC
**
112383 TCTTGTAAATATTTGT
1 TCTTGTAAATATTAAT
*
112399 TCTTGT-AAGATTAAT
1 TCTTGTAAATATTAAT
112414 TCTTGTAAATA
1 TCTTGTAAATA
112425 CCTACCTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (16 bp):
TCTTGTAAATATTAAT
Found at i:112531 original size:34 final size:33
Alignment explanation
Indices: 112475--112544 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
112465 TTTGTAAAGA
* *
112475 GGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTAG
1 GGAAAGGTTCTAGCTAAGCCCGT-AAAAAACTAG
* * *
112509 GGAAAGGTTCTAGTTTATCCCGTAAAAAACTAG
1 GGAAAGGTTCTAGCTAAGCCCGTAAAAAACTAG
112542 GGA
1 GGA
112545 GTTGTAAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (33 bp):
GGAAAGGTTCTAGCTAAGCCCGTAAAAAACTAG
Found at i:112892 original size:23 final size:23
Alignment explanation
Indices: 112866--112918 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
112856 TCTCGAAGGA
* *
112866 CCACATAGGTTTGCACCGAAGTG
1 CCACATAGATTTGCAACGAAGTG
112889 CCACATAGATTTGCAACGAAGTG
1 CCACATAGATTTGCAACGAAGTG
112912 CCACATA
1 CCACATA
112919 TTTGTCCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CCACATAGATTTGCAACGAAGTG
Found at i:117457 original size:28 final size:28
Alignment explanation
Indices: 117428--117516 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 28
117418 CAAATTTTAG
*
117428 TTAGTGACAAAAATATAAATTTTAAAAGT
1 TTAGTGAC-AAAGTATAAATTTTAAAAGT
* *
117457 TTAGTGGCAAAGTATAAAGTTTGGAAAAGT
1 TTAGTGACAAAGTATAAA-TTT-TAAAAGT
*
117487 TTAGGGACCAAAGTAT-AATTTTCAAAAGT
1 TTAGTGA-CAAAGTATAAATTTT-AAAAGT
117516 T
1 T
117517 AGGTATTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 9 0.18
29 20 0.40
30 13 0.26
31 8 0.16
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.33
Consensus pattern (28 bp):
TTAGTGACAAAGTATAAATTTTAAAAGT
Found at i:117816 original size:16 final size:16
Alignment explanation
Indices: 117795--117834 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
117785 TTTAGTAACT
117795 AAATTGTAGCTTTCGA
1 AAATTGTAGCTTTCGA
117811 AAATTGTAGCTTTCGA
1 AAATTGTAGCTTTCGA
117827 AAATTGTA
1 AAATTGTA
117835 AGGGCAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (16 bp):
AAATTGTAGCTTTCGA
Found at i:133199 original size:19 final size:18
Alignment explanation
Indices: 133167--133233 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
133157 TGTGTACATA
*
133167 TTTTATTTTTTTTTATTT
1 TTTTATTATTTTTTATTT
* *
133185 TTTTGGTTATTTTTTAATAT
1 TTTT-ATTATTTTTT-ATTT
*
133205 TTTTATTATTTGTTA-TT
1 TTTTATTATTTTTTATTT
*
133222 TTTAATTATTTT
1 TTTTATTATTTT
133234 AATTTAGTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
17 11 0.28
18 5 0.13
19 16 0.41
20 7 0.18
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTATTATTTTTTATTT
Found at i:139564 original size:3 final size:3
Alignment explanation
Indices: 139556--139586 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
139546 GGTGGCAAAT
139556 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
139587 ATAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:140004 original size:13 final size:13
Alignment explanation
Indices: 139997--140050 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
139987 GAAAAAATAT
139997 AGAAAAAAAAGAA
1 AGAAAAAAAAGAA
*
140010 AG-AAAAAATG--
1 AGAAAAAAAAGAA
140020 AGAAAAAAGAA-AA
1 AGAAAAAA-AAGAA
140033 AGAGAAAAAAAGAA
1 AGA-AAAAAAAGAA
140047 AGAA
1 AGAA
140051 TAAAGAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
10 2 0.06
11 5 0.15
12 8 0.24
13 8 0.24
14 10 0.30
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:140015 original size:23 final size:22
Alignment explanation
Indices: 139983--140058 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 22
139973 AAAAAAAGGG
139983 GAAAGAAAAAATATAGAAAAAAAA
1 GAAAG-AAAAA-ATAGAAAAAAAA
140007 GAAAGAAAAAATGAGAAAAAAGAA
1 GAAAGAAAAAAT-AGAAAAAA-AA
*
140031 -AAAGAGAAAAAAAGAAAGAATAAA
1 GAAAGA-AAAAATAGAAA-AA-AAA
140055 GAAA
1 GAAA
140059 ATCGATCAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.04
23 23 0.51
24 16 0.36
25 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (22 bp):
GAAAGAAAAAATAGAAAAAAAA
Found at i:140027 original size:21 final size:24
Alignment explanation
Indices: 139954--140058 Score: 85
Period size: 24 Copynumber: 4.3 Consensus size: 24
139944 ACACAGAGAG
*
139954 AAAG-AAGAAAAGATATAGCAAAAA
1 AAAGAAAGAAAAAATATAG-AAAAA
*
139978 AAGGGGAAAGAAAAAATATAGAAAAA
1 AA--AGAAAGAAAAAATATAGAAAAA
*
140004 AAAGAAAGAAAAAAT-GAGAAAAA
1 AAAGAAAGAAAAAATATAGAAAAA
140027 AGAA-AAAGAGAAAAA-A-AGAAAGAA
1 A-AAGAAAGA-AAAAATATAGAAA-AA
140051 TAAAGAAA
1 -AAAGAAA
140059 ATCGATCAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 17
0.76 0.04 0.19
Matches are distributed among these distances:
23 18 0.26
24 25 0.37
25 4 0.06
26 8 0.12
27 13 0.19
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (24 bp):
AAAGAAAGAAAAAATATAGAAAAA
Found at i:140041 original size:16 final size:16
Alignment explanation
Indices: 140003--140047 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
139993 ATATAGAAAA
140003 AAAAGAAAGAAAAAATG
1 AAAA-AAAGAAAAAATG
140020 AGAAAAAAGAAAAAGA-G
1 A-AAAAAAGAAAAA-ATG
140037 AAAAAAAGAAA
1 AAAAAAAGAAA
140048 GAATAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 10 0.38
17 12 0.46
18 4 0.15
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAAAATG
Found at i:142104 original size:33 final size:33
Alignment explanation
Indices: 142021--142923 Score: 1180
Period size: 33 Copynumber: 27.2 Consensus size: 33
142011 GTAGATCATA
* *
142021 ATCGACATTTAAATCCATCACAGAATGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
142054 ATCGATATTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
142088 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * *
142121 ATCAACGTTCAAATCCATCATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
** *
142154 ATCGATGTTTAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
142187 ATCGACATTCAAATCTATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
142220 ATCGACATTTAAATCCATCACAGAAAGAGGTAG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
142253 ATCGACGTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
142286 ATCGACATTTCAAATCCATCACAGAATGAGGTGA
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * *
142320 ATCGACATTTCAAATCCATTATAGAAGGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
*
142354 ATCGACATTCAAATCCATCACAAAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
142387 AACGATATTTAAAATCCATCACAGAAAGAGATGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
*
142421 ATCGACATTGAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
** *
142454 ATCGATGTTGAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
142487 ATCGACATTCAAATCCATCACAGAAAGAGCTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * *
142520 ATCGATATTCAAATCCATCATAGAAATAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
142553 ATCGACGTTCAAATCCATCATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
142586 ATCGACGTTCAAATCCATCACAGAAGGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
142619 ATCGACATTCAAATCCATCACAGAAAGA-GTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
142651 ATCGACAATCAAATCCATCATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * *
142684 ATCCACGTTCAAATCCATCACAGAAAGATGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
142717 ATCGACATTCAAATCCATCACAGAAATAAGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *** * *
142750 ATCGATATTTTGATCGATCACAGAAAGAGGTGA
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
142783 ATCAACATTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * *
142816 ATCGACATTTCAAATCCATCACAGAAATAGGCGA
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * * * *
142850 ATTGGCATTCAAATTCATCAAAGAAAGAGATGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
142883 ATCGACA-TCTTAATCTATCACAGAAGGAGCTGG
1 ATCGACATTC-AAATCCATCACAGAAAGAGGTGG
*
142916 ATCAACAT
1 ATCGACAT
142924 CAACTTTTTG
Statistics
Matches: 758, Mismatches: 105, Indels: 13
0.87 0.12 0.01
Matches are distributed among these distances:
32 32 0.04
33 579 0.76
34 147 0.19
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (33 bp):
ATCGACATTCAAATCCATCACAGAAAGAGGTGG
Found at i:144335 original size:26 final size:26
Alignment explanation
Indices: 144297--144361 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
144287 TGTGTACATA
* *
144297 TTTT-ATTTTTTTTATTTTTTGGTTATT
1 TTTTAATTATTTTTATTATTT-GTTA-T
144324 TTTTAA-TATTTTTATTATTTGTTAT
1 TTTTAATTATTTTTATTATTTGTTAT
144349 TTTTAATTATTTT
1 TTTTAATTATTTT
144362 AATTTAGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 7 0.21
26 10 0.29
27 16 0.47
28 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTAATTATTTTTATTATTTGTTAT
Found at i:144359 original size:36 final size:36
Alignment explanation
Indices: 144279--144361 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
144269 TCGGTTAAAA
* *
144279 TTAATTATTGTGTACATATTTTATTTTTTTTATTTT
1 TTAATTATTTTGTACATATTTTATTTTTGTTATTTT
** *
144315 TTGGTTATTTTTTA-ATATTTTTATTATTTGTTA-TTT
1 TTAATTATTTTGTACATA-TTTTATT-TTTGTTATTTT
144351 TTAATTATTTT
1 TTAATTATTTT
144362 AATTTAGTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
35 3 0.08
36 29 0.76
37 6 0.16
ACGTcount: A:0.22, C:0.01, G:0.06, T:0.71
Consensus pattern (36 bp):
TTAATTATTTTGTACATATTTTATTTTTGTTATTTT
Found at i:150069 original size:20 final size:20
Alignment explanation
Indices: 150046--150089 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
150036 CAGAGGGAAT
150046 CGATACCCTCATGAGGGGAC
1 CGATACCCTCATGAGGGGAC
150066 CGATACCCTCATGAGGGGAC
1 CGATACCCTCATGAGGGGAC
150086 CGAT
1 CGAT
150090 TCCCCCTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (20 bp):
CGATACCCTCATGAGGGGAC
Found at i:152406 original size:30 final size:30
Alignment explanation
Indices: 152370--152431 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
152360 TAAATGGGAG
152370 AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
1 AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
152400 AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
1 AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
152430 AA
1 AA
152432 CTTGATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (30 bp):
AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
Found at i:152456 original size:32 final size:32
Alignment explanation
Indices: 152415--152478 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
152405 TTAAAGTAAG
152415 GGGGAGTAATTTCAAAACTTGATTTCAAAATC
1 GGGGAGTAATTTCAAAACTTGATTTCAAAATC
152447 GGGGAGTAATTTCAAAACTTGATTTCAAAATC
1 GGGGAGTAATTTCAAAACTTGATTTCAAAATC
152479 TTAAATTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (32 bp):
GGGGAGTAATTTCAAAACTTGATTTCAAAATC
Found at i:154856 original size:42 final size:42
Alignment explanation
Indices: 154755--154859 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 42
154745 ACAAATACCG
* * * * * *
154755 CAAAAGGTCTAGATCTGTAGCGGCGTTTTCCCCACAAATGTCG
1 CAAAAGAT-TAGATCTATAGCAGCGTTTTCCCCACAAACGCCA
* **
154798 CAAAAGATGATG-TCTATAGCAGCGTTTTTTCCACAAACGCCA
1 CAAAAGATTA-GATCTATAGCAGCGTTTTCCCCACAAACGCCA
154840 CAAAAGATTAGATCTATAGC
1 CAAAAGATTAGATCTATAGC
154860 GGAACTTTTC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.02
42 41 0.82
43 8 0.16
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
CAAAAGATTAGATCTATAGCAGCGTTTTCCCCACAAACGCCA
Found at i:156594 original size:29 final size:29
Alignment explanation
Indices: 156559--156640 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
156549 AAACTAAATT
*
156559 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
156588 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
156617 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
156641 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:161361 original size:29 final size:29
Alignment explanation
Indices: 161326--161407 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
161316 AAACTAAATT
*
161326 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
161355 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
161384 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
161408 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:165528 original size:83 final size:83
Alignment explanation
Indices: 165441--165611 Score: 184
Period size: 83 Copynumber: 2.1 Consensus size: 83
165431 GGTGTTTATA
* * *
165441 AAAAAACACCACTAAAGTAGAACTTTGT-AGCGGCATTTGTTAAAAAAAGCCACTATGAA-TGAA
1 AAAAAACACCACTAAAGTACAACTCTATCA-CGGCATTTGTTAAAAAAAGCCACTATGAACT-AA
165504 TCTTATAGCGGCGTTTGTAT
64 TCTTATAGCGGCGTTTGTAT
** ** * * * * * *
165524 AAAAAACGTCGTTAAAGTACTACTCTATCATGGCGTTTTTTGAAAAATGCCACTATGAACTAATC
1 AAAAAACACCACTAAAGTACAACTCTATCACGGCATTTGTTAAAAAAAGCCACTATGAACTAATC
*
165589 TTATTGCGGCGTTTGTAT
66 TTATAGCGGCGTTTGTAT
165607 AAAAA
1 AAAAA
165612 TGCTGCTAGA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
83 70 0.97
84 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (83 bp):
AAAAAACACCACTAAAGTACAACTCTATCACGGCATTTGTTAAAAAAAGCCACTATGAACTAATC
TTATAGCGGCGTTTGTAT
Found at i:177364 original size:52 final size:52
Alignment explanation
Indices: 177286--177392 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
177276 AGCATTGCAC
177286 ATAGTATCGCAGATCTCCCATTTGAAAATCTCTAATATATATATATATATAT
1 ATAGTATCGCAGATCTCCCATTTGAAAATCTCTAATATATATATATATATAT
177338 ATAGTATCGCAGATCTCCCATTTGAAAATCTCTAATATATATATATATATAT
1 ATAGTATCGCAGATCTCCCATTTGAAAATCTCTAATATATATATATATATAT
177390 ATA
1 ATA
177393 TATATATATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (52 bp):
ATAGTATCGCAGATCTCCCATTTGAAAATCTCTAATATATATATATATATAT
Found at i:177379 original size:2 final size:2
Alignment explanation
Indices: 177372--177402 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
177362 AAAATCTCTA
177372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
177403 GTTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:178150 original size:26 final size:26
Alignment explanation
Indices: 178099--178153 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
178089 GTCATAAATC
*
178099 TATGACGCGCATTTATAATACACATT
1 TATGACGCGCATTTATAACACACATT
* * *
178125 TATGACGCTCATTTATAACGCGCATT
1 TATGACGCGCATTTATAACACACATT
178151 TAT
1 TAT
178154 CGTCATTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (26 bp):
TATGACGCGCATTTATAACACACATT
Found at i:185097 original size:30 final size:30
Alignment explanation
Indices: 185031--185105 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
185021 TAAAAAAAAA
* * * *
185031 ATTAAATATTTTAAAAAATTACACTTTTTT
1 ATTAAATATTTCAAAAAATAACAATATTTT
185061 AATTAAATATTTCAAAAAATAACAGATATTTT
1 -ATTAAATATTTCAAAAAATAACA-ATATTTT
*
185093 -TTAAAAATTTCAA
1 ATTAAATATTTCAA
185106 CTTTTATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 12 0.32
31 21 0.55
32 5 0.13
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (30 bp):
ATTAAATATTTCAAAAAATAACAATATTTT
Found at i:185163 original size:16 final size:17
Alignment explanation
Indices: 185137--185185 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
185127 ATGAATGATA
185137 ATTTGTTAATTAAATCTT
1 ATTT-TTAATTAAATCTT
**
185155 A-TTTTAATTAAAAGTT
1 ATTTTTAATTAAATCTT
185171 ATTTTTTAATTAAAT
1 A-TTTTTAATTAAAT
185186 ATTTTTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 2 0.08
18 12 0.46
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTTTAATTAAATCTT
Found at i:185218 original size:17 final size:17
Alignment explanation
Indices: 185196--185228 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
185186 ATTTTTCATT
185196 TTTGTTTACATATTTTA
1 TTTGTTTACATATTTTA
185213 TTTGTTTACATATTTT
1 TTTGTTTACATATTTT
185229 CAAAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTGTTTACATATTTTA
Found at i:197426 original size:9 final size:9
Alignment explanation
Indices: 197412--197445 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
197402 AACATTTAAG
197412 GGTTAATTC
1 GGTTAATTC
*
197421 GTTTAATTC
1 GGTTAATTC
197430 GGTTAATTC
1 GGTTAATTC
*
197439 CGTTAAT
1 GGTTAAT
197446 CGAATTCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (9 bp):
GGTTAATTC
Found at i:201871 original size:29 final size:29
Alignment explanation
Indices: 201805--201873 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
201795 ACGTTTGGTA
201805 ACTGAACTTTAGTTTTTCTTATTTCACTC
1 ACTGAACTTTAGTTTTTCTTATTTCACTC
* * * *
201834 AGTGTACTTTCA-TTTTTTTTAATTT-ACTT
1 ACTGAACTTT-AGTTTTTCTT-ATTTCACTC
201863 ACTGAACTTTA
1 ACTGAACTTTA
201874 TAGATTGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.03
29 26 0.81
30 5 0.16
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (29 bp):
ACTGAACTTTAGTTTTTCTTATTTCACTC
Found at i:207614 original size:27 final size:27
Alignment explanation
Indices: 207583--207650 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
207573 TCTATTTACA
207583 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
207610 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
207637 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
207651 ATTCCTACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:211220 original size:27 final size:27
Alignment explanation
Indices: 211189--211256 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
211179 TCTATTTACA
211189 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
211216 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
211243 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
211257 ATTCCTACAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:214066 original size:13 final size:13
Alignment explanation
Indices: 214042--214071 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
214032 GACAAAGAGA
214042 AATTTCAAAGATT
1 AATTTCAAAGATT
214055 AATTTCAAAGATT
1 AATTTCAAAGATT
214068 AATT
1 AATT
214072 GGGAAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (13 bp):
AATTTCAAAGATT
Found at i:221272 original size:28 final size:29
Alignment explanation
Indices: 221240--221304 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
221230 GCATTTATAT
***
221240 TTTGCATTATGCATTCCCAT-TTTGCATC
1 TTTGCATTATGCATGAACATCTTTGCATC
221268 TTTGCATT-TGCATGAACATCTTTGCATC
1 TTTGCATTATGCATGAACATCTTTGCATC
221296 TTTGCATTA
1 TTTGCATTA
221305 GAACCTATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (29 bp):
TTTGCATTATGCATGAACATCTTTGCATC
Found at i:222684 original size:21 final size:20
Alignment explanation
Indices: 222656--222719 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 20
222646 AAACACACAC
222656 AAAAATAAAGAAAAAAAGAGA
1 AAAAATAAAGAAAAAAAGA-A
*
222677 AAACATAAAGAAAAAAAGAA
1 AAAAATAAAGAAAAAAAGAA
* * *
222697 AAAAAGAAA-AAATAGAGAA
1 AAAAATAAAGAAAAAAAGAA
222716 AAAA
1 AAAA
222720 GAAGAAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 12 0.32
20 8 0.21
21 18 0.47
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (20 bp):
AAAAATAAAGAAAAAAAGAA
Found at i:222706 original size:27 final size:27
Alignment explanation
Indices: 222657--222734 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 27
222647 AACACACACA
222657 AAAATAAAGAAAAAAAGAGAAAACATAAAG
1 AAAA-AAAGAAAAAAAGA-AAAA-ATAAAG
*
222687 AAAAAAAGAAAAAAAGAAAAAATAGAG
1 AAAAAAAGAAAAAAAGAAAAAATAAAG
222714 -AAAAAAGAAGAAAGAAGAAAA
1 AAAAAAAGAA-AAA-AAGAAAA
222735 TAGACAGATC
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
26 9 0.20
27 8 0.18
28 11 0.24
29 13 0.29
30 4 0.09
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (27 bp):
AAAAAAAGAAAAAAAGAAAAAATAAAG
Found at i:222724 original size:21 final size:19
Alignment explanation
Indices: 222656--222726 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 19
222646 AAACACACAC
222656 AAAAATAAAGAAAAAAAGAG
1 AAAAA-AAAGAAAAAAAGAG
222676 AAAACATAAAG-AAAAAA-AG
1 AAAA-A-AAAGAAAAAAAGAG
222695 -AAAAAAAGAAAAAATAGAG
1 AAAAAAAAGAAAAAA-AGAG
222714 AAAAAAGAAGAAA
1 AAAAAA-AAGAAA
222727 GAAGAAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
16 4 0.09
17 6 0.13
18 4 0.09
19 4 0.09
20 15 0.33
21 12 0.27
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.04
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAGAG
Found at i:222732 original size:17 final size:15
Alignment explanation
Indices: 222662--222734 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
222652 ACACAAAAAT
*
222662 AAAGAAAAAAAGAGA
1 AAAGAAAAAAAGAAA
* * *
222677 AAACATAAAGA-AAA
1 AAAGAAAAAAAGAAA
222691 AAAGAAAAAAAGAAAA
1 AAAGAAAAAAAG-AAA
*
222707 AATAGAGAAAAAAGAAG
1 AA-AGA-AAAAAAGAAA
222724 AAAGAAGAAAA
1 AAAGAA-AAAA
222735 TAGACAGATC
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
14 10 0.22
15 9 0.20
16 12 0.27
17 7 0.16
18 7 0.16
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (15 bp):
AAAGAAAAAAAGAAA
Found at i:224499 original size:4 final size:4
Alignment explanation
Indices: 224490--224524 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
224480 AAGTGCATTT
*
224490 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
224525 TATAATTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:224769 original size:55 final size:53
Alignment explanation
Indices: 224703--225007 Score: 308
Period size: 55 Copynumber: 5.6 Consensus size: 53
224693 TGTTTTTTTG
* * * * *
224703 GAAATTAAGTCTGATTTTCAGAAGTTTCTTAACAATTTTCAAATGAGCTTTTAAA
1 GAAACTAAGTCTGATTTTCAGGAGTTTCTTGA-TATTTTCAAATGA-ATTTTAAA
* * * *
224758 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGACCTTTCAAA
1 GAAACTAAGTCTGATTTTCAGGAGTTTCTTGAT-ATTTTCAAATGA-ATTTTAAA
* *
224813 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAAA
1 GAAACTAAGTCTGATTTTCAGGAGTTTCTTGATATTTTCAAATGAATTTTAAA
* * * * *
224866 GAAGCTAAGCCTAATTTTTAGG-GATTTCTTGATGTTTTCAAATGAATTTTCAAA
1 GAAACTAAGTCTGATTTTCAGGAG-TTTCTTGATATTTTCAAATGAATTTT-AAA
* * * *
224920 TAAATTAAG-CTTGATTTTTAGGGGTTTTCTTGATATTTTCAAATGAATTTTTAAA
1 GAAACTAAGTC-TGATTTTCAGGAG-TTTCTTGATATTTTCAAATGAA-TTTTAAA
* * *
224975 GAAACTAAGCCTAATTTTTAGGAGTTTCTTGAT
1 GAAACTAAGTCTGATTTTCAGGAGTTTCTTGAT
225008 GATAACTGAA
Statistics
Matches: 217, Mismatches: 26, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
52 1 0.00
53 51 0.24
54 38 0.18
55 122 0.56
56 5 0.02
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (53 bp):
GAAACTAAGTCTGATTTTCAGGAGTTTCTTGATATTTTCAAATGAATTTTAAA
Found at i:225137 original size:42 final size:41
Alignment explanation
Indices: 225075--225170 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
225065 ATGAATAAGT
* *
225075 CTTTCGGGCCAT-TAGTAAGTCTTTCGAGCATGATGCTTAAATC
1 CTTT-GGGCCATCTA-TAAGTCTTTCGAGCAAGATG-ATAAATC
* *
225118 CTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTC
1 CTTTGGGCCATCTATAAGTCTTTCGAGCAAGATGATAAATC
225159 CTTTGGGCCATC
1 CTTTGGGCCATC
225171 CATATGACCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 16 0.34
42 25 0.53
43 6 0.13
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (41 bp):
CTTTGGGCCATCTATAAGTCTTTCGAGCAAGATGATAAATC
Found at i:225525 original size:275 final size:274
Alignment explanation
Indices: 225031--225573 Score: 813
Period size: 275 Copynumber: 2.0 Consensus size: 274
225021 TGAAAGATTT
* *
225031 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTTCGGGCCATTAGTAAGTC
1 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTTCGGGACATCAGTAAGTC
225096 TTTCGAGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCT
66 TTTCGAGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCT
* * ** * *
225161 TTGGGCCATCCATATGACCTTTGGGCAGAATGTTTTCAAATGAGTTTTTAGAAATTAAGCATGAT
131 TTGGACCATCCATAAGACCTACGAGCAGAATGTTTTCAAATGAGTTTTTAGAAACTAAGCATGAT
* * * * * *
225226 TTTCAGGGGTTTCTTGATGATTATCTCTAAAGAGTTTTTAAAAGGAAGTTAAGTCTATTTTTTAA
196 TTTCAGGGGTTTCTTGAAGATTATCTCCAAAGAATTTTT-AAAGGAAGCTAAGCCTAATTTTTAA
225291 GGGTTCCTTAACAGC
260 GGGTTCCTTAACAGC
* *
225306 TAAGAAACTAATCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTTCTTT-GGGACATCAGTAAGT
1 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAG-TCTTTCGGGACATCAGTAAGT
* ** *
225370 CTTTTGAGTGTGATGCTTAAAT-CTTTCGGGTCATCTATAAGTCTTTCGAGCAAGATTATAAGT-
65 CTTTCGAGCATGATGCTTAAATCCTTT-GGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTC
* *
225433 CTTTCGGACCATCCATAAGACCTACGAGCAGGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCT
129 CTTT-GGACCATCCATAAGACCTACGAGCAGAATGTTTTCAAATGAGTTTTTAGAAACTAAGCAT
*
225498 GATTTTCAGGTGTTTCTTGAAGATTATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTT
193 GATTTTCAGGGGTTTCTTGAAGATTATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTT
*
225563 AGGGGTTCCTT
258 AAGGGTTCCTT
225574 GATGACAACT
Statistics
Matches: 241, Mismatches: 24, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
274 38 0.16
275 198 0.82
276 5 0.02
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (274 bp):
TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTTCGGGACATCAGTAAGTC
TTTCGAGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCT
TTGGACCATCCATAAGACCTACGAGCAGAATGTTTTCAAATGAGTTTTTAGAAACTAAGCATGAT
TTTCAGGGGTTTCTTGAAGATTATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTTAAG
GGTTCCTTAACAGC
Found at i:226145 original size:17 final size:17
Alignment explanation
Indices: 226123--226156 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
226113 TCAAATGGAG
226123 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
226140 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
226157 GCTTGTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
AGTTCATAATGAGAAGA
Found at i:226383 original size:139 final size:139
Alignment explanation
Indices: 226133--226622 Score: 766
Period size: 139 Copynumber: 3.5 Consensus size: 139
226123 AGTTCATAAT
* **
226133 GAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAAATTTAGCTCGATTCATCGCATATGGAGTTGA
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
*
226198 ATCAGCAACACCTCACTCAAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCAT
66 ATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCAT
226263 CCGATGAAG
131 CCGATGAAG
* * * *
226272 GAGAAGAAGTTCATAATGAGAAGAGCTTATTCGACCTTAGCTCGATTCATTGCATATGGAGTTGA
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
* * *
226337 ATCAGCAACGCCTCACTCGAGGGATCAACATTTCTAATGGAGAGTTCATAATGAGAATAACTCAT
66 ATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCAT
226402 CCGATGAAG
131 CCGATGAAG
* *
226411 GAGAAGACGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGA
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
*
226476 ATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCAT
66 ATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCAT
**
226541 TTGAT-AAGG
131 CCGATGAA-G
* * * *
226550 GAGACGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCGCATAAGGAGTTG
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCGCATATGGAGTTG
*
226615 GATCAGCA
65 AATCAGCA
226623 TCATCGTTTC
Statistics
Matches: 321, Mismatches: 28, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
138 2 0.01
139 297 0.93
140 22 0.07
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (139 bp):
GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
ATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCAT
CCGATGAAG
Found at i:232559 original size:289 final size:289
Alignment explanation
Indices: 232040--232618 Score: 1061
Period size: 289 Copynumber: 2.0 Consensus size: 289
232030 AGACCTCTAC
*
232040 GGTTAGGTTCGTTAAAGCAAGAGTTTAGAATGGTCATCTCTGGTTCATTAGGGATATGAATTTAT
1 GGTTAGGTTCGTTAAAGCAAGAGTTTAGAATGGTCATCTCAGGTTCATTAGGGATATGAATTTAT
232105 GGTAGAATAAGAGGTGGATTTTATGGTTTCAAGGAACGACTAGAAGATGACCTAGCTCGTTTAGA
66 GGTAGAATAAGAGGTGGATTTTATGGTTTCAAGGAACGACTAGAAGATGACCTAGCTCGTTTAGA
*
232170 CATGGTTTAAAGAAATCGTAATGGTAAACCTGCAATTAAACAACATATGTATACAACACAATTAA
131 CATGGTTTAAAGAAATCGGAATGGTAAACCTGCAATTAAACAACATATGTATACAACACAATTAA
232235 TCCCAAAACTCAATATAAGTCCTCAATATTCAAGCTTCTCTAACTTAGTGTCTAATGGGAAATAT
196 TCCCAAAACTCAATATAAGTCCTCAATATTCAAGCTTCTCTAACTTAGTGTCTAATGGGAAATAT
*
232300 TGAAAACCAAGTTTGAAAAATCATAATAT
261 TGAAAAACAAGTTTGAAAAATCATAATAT
* * *
232329 GGTTAGGTTCGTTAAAGTAAGAGTTTAGAATGGTCATCTCAGGTTTATTAGGGATATGATTTTAT
1 GGTTAGGTTCGTTAAAGCAAGAGTTTAGAATGGTCATCTCAGGTTCATTAGGGATATGAATTTAT
*
232394 GGTGGAATAAGAGGTGGATTTTATGGTTT-AGAGGAACGACTAGAAGATGACCTAGCTCGTTTAG
66 GGTAGAATAAGAGGTGGATTTTATGGTTTCA-AGGAACGACTAGAAGATGACCTAGCTCGTTTAG
*
232458 ACATGGTTTAAAGAAATTGGAATGGTAAACCTGCAATTAAACAACATATGTATACAACACAATTA
130 ACATGGTTTAAAGAAATCGGAATGGTAAACCTGCAATTAAACAACATATGTATACAACACAATTA
232523 ATCCCAAAACTCAATATAAGTCCTCAATATTCAAGCTTCTCTAACTTAGTGTCTAATGGGAAATA
195 ATCCCAAAACTCAATATAAGTCCTCAATATTCAAGCTTCTCTAACTTAGTGTCTAATGGGAAATA
*
232588 TTGAAAAAGAAGTTTGAAAAATCATAATAT
260 TTGAAAAACAAGTTTGAAAAATCATAATAT
232618 G
1 G
232619 TATAGTTTTC
Statistics
Matches: 280, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
288 1 0.00
289 279 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (289 bp):
GGTTAGGTTCGTTAAAGCAAGAGTTTAGAATGGTCATCTCAGGTTCATTAGGGATATGAATTTAT
GGTAGAATAAGAGGTGGATTTTATGGTTTCAAGGAACGACTAGAAGATGACCTAGCTCGTTTAGA
CATGGTTTAAAGAAATCGGAATGGTAAACCTGCAATTAAACAACATATGTATACAACACAATTAA
TCCCAAAACTCAATATAAGTCCTCAATATTCAAGCTTCTCTAACTTAGTGTCTAATGGGAAATAT
TGAAAAACAAGTTTGAAAAATCATAATAT
Found at i:233254 original size:17 final size:17
Alignment explanation
Indices: 233232--233264 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
233222 TACTGGGTGG
*
233232 CCAGTATCGATACCTAC
1 CCAGTACCGATACCTAC
233249 CCAGTACCGATACCTA
1 CCAGTACCGATACCTA
233265 GTGCACAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.21
Consensus pattern (17 bp):
CCAGTACCGATACCTAC
Found at i:237101 original size:24 final size:24
Alignment explanation
Indices: 237060--237114 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
237050 GTCGGGCAGA
** *
237060 GCTGGCTATGATTTAGCCTGTGTT
1 GCTGGCTATGATCCAGCCTGGGTT
*
237084 GCTGGTTATGATCCAGCCTGGGTT
1 GCTGGCTATGATCCAGCCTGGGTT
*
237108 GTTGGCT
1 GCTGGCT
237115 GAGTACCAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.11, C:0.18, G:0.33, T:0.38
Consensus pattern (24 bp):
GCTGGCTATGATCCAGCCTGGGTT
Found at i:250630 original size:2 final size:2
Alignment explanation
Indices: 250623--250680 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
250613 TTCCTTTATG
250623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250665 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
250681 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252442 original size:12 final size:12
Alignment explanation
Indices: 252425--252458 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
252415 CTAACATTCG
252425 CAATTCTTCCCC
1 CAATTCTTCCCC
252437 CAATTCTTCCCC
1 CAATTCTTCCCC
252449 CAATTCTTCC
1 CAATTCTTCC
252459 TCGCGTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.35
Consensus pattern (12 bp):
CAATTCTTCCCC
Found at i:257570 original size:12 final size:12
Alignment explanation
Indices: 257553--257586 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
257543 CTAACATTCG
257553 CAATTCTTCCCC
1 CAATTCTTCCCC
257565 CAATTCTTCCCC
1 CAATTCTTCCCC
257577 CAATTCTTCC
1 CAATTCTTCC
257587 TCGCGTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.35
Consensus pattern (12 bp):
CAATTCTTCCCC
Found at i:258244 original size:34 final size:34
Alignment explanation
Indices: 258204--258274 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
258194 TCCATATCCA
*
258204 TTTTTGTTAGTTCCTATGTTCATTTGAACATCAT
1 TTTTTGTTAGTTCCTACGTTCATTTGAACATCAT
258238 TTTTTGTTAGTTCCTACGTTCATTTGAACATCAT
1 TTTTTGTTAGTTCCTACGTTCATTTGAACATCAT
258272 TTT
1 TTT
258275 AAGTTGCCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (34 bp):
TTTTTGTTAGTTCCTACGTTCATTTGAACATCAT
Found at i:262078 original size:26 final size:26
Alignment explanation
Indices: 262048--262104 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
262038 CTGGAACATG
262048 TCTCACATTACCAAGTGTTCGAACAA
1 TCTCACATTACCAAGTGTTCGAACAA
262074 TCTCACATTACCAAGTGTTCGAACAA
1 TCTCACATTACCAAGTGTTCGAACAA
262100 TCTCA
1 TCTCA
262105 TCGAACATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (26 bp):
TCTCACATTACCAAGTGTTCGAACAA
Found at i:263338 original size:17 final size:17
Alignment explanation
Indices: 263316--263350 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
263306 ATTTATAGGG
263316 ATAGATACTTGATTACA
1 ATAGATACTTGATTACA
263333 ATAGATACTTGATTACA
1 ATAGATACTTGATTACA
263350 A
1 A
263351 AGGAAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (17 bp):
ATAGATACTTGATTACA
Found at i:266286 original size:19 final size:19
Alignment explanation
Indices: 266258--266298 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
266248 TATATTACCA
*
266258 TTAATGAAATTATAAGATT
1 TTAATAAAATTATAAGATT
*
266277 TTAATAAAATTATGAGATT
1 TTAATAAAATTATAAGATT
266296 TTA
1 TTA
266299 GAGTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (19 bp):
TTAATAAAATTATAAGATT
Found at i:266415 original size:18 final size:18
Alignment explanation
Indices: 266355--266417 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
266345 TTATAATAAA
*
266355 ATATTAATTATGATAATT
1 ATATTAATTATGATTATT
* *
266373 AAATTAATAAATTGACTTATT
1 ATATTAAT-TA-TGA-TTATT
*
266394 ATATTAATTATGATTCTT
1 ATATTAATTATGATTATT
266412 ATATTA
1 ATATTA
266418 TGATTCTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 17 0.47
19 4 0.11
20 4 0.11
21 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATTAATTATGATTATT
Found at i:266439 original size:14 final size:14
Alignment explanation
Indices: 266400--266432 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
266390 TATTATATTA
266400 ATTATGATTCTTAT
1 ATTATGATTCTTAT
266414 ATTATGATTCTTAT
1 ATTATGATTCTTAT
*
266428 GTTAT
1 ATTAT
266433 ATATCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:267236 original size:16 final size:18
Alignment explanation
Indices: 267192--267238 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
267182 ATTGTTTAAA
*
267192 TTATATTATTT-ATTAATT
1 TTATA-TATTTAAATAATT
267210 TTATATATTTAAATAATT
1 TTATATATTTAAATAATT
267228 TT-T-TATTTAAA
1 TTATATATTTAAA
267239 GTATGTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATATTTAAATAATT
Found at i:267362 original size:19 final size:20
Alignment explanation
Indices: 267320--267367 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
267310 TGACACGTGT
*
267320 ATAATGTAT-GTATAACTTA
1 ATAATGTATAGCATAACTTA
*
267339 TTAATGTATAGCATAA-TTA
1 ATAATGTATAGCATAACTTA
*
267358 ATAATATATA
1 ATAATGTATA
267368 ATGTATATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (20 bp):
ATAATGTATAGCATAACTTA
Found at i:267450 original size:4 final size:4
Alignment explanation
Indices: 267441--267466 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
267431 TTAATGTATA
267441 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
267467 ATATAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:267582 original size:18 final size:18
Alignment explanation
Indices: 267559--267703 Score: 105
Period size: 18 Copynumber: 8.6 Consensus size: 18
267549 ATTTTTAGTG
*
267559 TATACTAGATAGTTTATA
1 TATACTATATAGTTTATA
*
267577 TATAC--TA-A-TTAACTA
1 TATACTATATAGTTTA-TA
267592 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
*** *
267610 TATACTA-ATAAACTATG
1 TATACTATATAGTTTATA
267627 TA-A-TATATAGTTTATA
1 TATACTATATAGTTTATA
*
267643 TATACCATATAGTTTATA
1 TATACTATATAGTTTATA
*
267661 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
*
267676 TATAATATATAGTTTATA
1 TATACTATATAGTTTATA
*
267694 TATACCATAT
1 TATACTATAT
267704 TCGGAGGTCT
Statistics
Matches: 96, Mismatches: 18, Indels: 26
0.69 0.13 0.19
Matches are distributed among these distances:
14 4 0.04
15 18 0.19
16 13 0.14
17 14 0.15
18 43 0.45
19 4 0.04
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (18 bp):
TATACTATATAGTTTATA
Found at i:267604 original size:33 final size:33
Alignment explanation
Indices: 267559--267647 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
267549 ATTTTTAGTG
* *
267559 TATACTAGATAGTTTATATATACTAATTAACTA
1 TATACTATATAGTTTATATATACTAATAAACTA
267592 TATACTATATAGTTTATATATACTAATAAACTA
1 TATACTATATAGTTTATATATACTAATAAACTA
* *
267625 TGTAATATATAGTTTATATATAC
1 TATACTATATAGTTTATATATAC
267648 CATATAGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (33 bp):
TATACTATATAGTTTATATATACTAATAAACTA
Found at i:267645 original size:51 final size:51
Alignment explanation
Indices: 267590--267703 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
267580 ACTAATTAAC
* *
267590 TATATACTATATAGTTTATATATACTAATAAACTATGTAATATATAGTTTA
1 TATATACCATATAGTTTATATATACTAATAAACTATATAATATATAGTTTA
*
267641 TATATACCATATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
1 TATATACCATATAGTTTATATATACTAATAAACTATATAATATATAGTTTA
267692 TATATACCATAT
1 TATATACCATAT
267704 TCGGAGGTCT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (51 bp):
TATATACCATATAGTTTATATATACTAATAAACTATATAATATATAGTTTA
Found at i:267930 original size:10 final size:12
Alignment explanation
Indices: 267883--267924 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
267873 CATAGTTTAT
267883 ATATATTATATTA
1 ATATA-TATATTA
267896 ATATATACT-TT-
1 ATATATA-TATTA
267907 ATATATATATTA
1 ATATATATATTA
267919 ATATAT
1 ATATAT
267925 TATAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.04
11 9 0.35
12 10 0.38
13 6 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATATATATTA
Found at i:268839 original size:11 final size:12
Alignment explanation
Indices: 268799--268842 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
268789 TATTTAAACG
*
268799 GGTATTGGGCCA
1 GGTATTGGGTCA
*
268811 GGTATTGGGTCG
1 GGTATTGGGTCA
268823 GGTATTGGGTC-
1 GGTATTGGGTCA
268834 GGTATTGGG
1 GGTATTGGG
268843 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:268841 original size:23 final size:24
Alignment explanation
Indices: 268797--268842 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
268787 ATTATTTAAA
268797 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
268821 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
268843 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:268920 original size:24 final size:25
Alignment explanation
Indices: 268860--268920 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
268850 TCGGGCCGGG
268860 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
268883 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
268907 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
268921 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:269008 original size:13 final size:13
Alignment explanation
Indices: 268952--268995 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
268942 TTTAATATTT
*
268952 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
268964 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
268977 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
268990 ATCGGG
1 ATCGGG
268996 TAATCGGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:273851 original size:36 final size:37
Alignment explanation
Indices: 273780--273864 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
273770 ATCCCATTAT
*
273780 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
273816 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
273852 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
273865 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:278444 original size:21 final size:20
Alignment explanation
Indices: 278417--278480 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
278407 TTTTTCAAAG
278417 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
278437 AAATCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
278452 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
278472 AAACCATTT
1 AAA-CATTT
278481 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:278454 original size:35 final size:36
Alignment explanation
Indices: 278367--278488 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
278357 TTATCCCATT
* *
278367 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
278402 AACTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATC-ATTTTTCAAAGAAACATTTACCAAACTTTGAAA
278439 ATCA-TTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
278474 ACCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
278489 TTGGTTACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 8 0.10
37 34 0.44
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:279726 original size:20 final size:21
Alignment explanation
Indices: 279701--279752 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
279691 TTTTCCCAAT
279701 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* **
279721 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATAAGTAAAA
279742 TCGCAATGCGA
1 TCGCAATGCGA
279753 TACTTACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Done.