Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008075.1 Hibiscus syriacus cultivar Beakdansim tig00110577_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: 1947163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1338682 original size:15 final size:15
Alignment explanation
Indices: 1338652--1338707 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
1338642 ATCTGGAATA
* *
1338652 TTAAAATCGATTTTT
1 TTAAAACCGGTTTTT
*
1338667 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1338682 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1338699 TTAAAACCG
1 TTAAAACCG
1338708 AAACCGGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.61
17 13 0.39
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1338716 original size:21 final size:18
Alignment explanation
Indices: 1338671--1338704 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1338661 ATTTTTTTAT
1338671 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1338688 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1338705 CCGAAACCGG
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:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1338824 original size:15 final size:17
Alignment explanation
Indices: 1338798--1338829 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1338788 TTCTATGGAA
1338798 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1338814 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1338830 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1344663 original size:3 final size:3
Alignment explanation
Indices: 1344641--1344732 Score: 98
Period size: 3 Copynumber: 31.0 Consensus size: 3
1344631 ATTTGGTTTT
* * *
1344641 TTA TTA -TA TTTA TTA CTA TTA TTA TTA TTT TTA TTA TTA ATA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
1344686 TTT TTA TTA TTA ATA TTA TTT TTA TTA TTA ATA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1344733 CAGATACAAC
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
2 4 0.06
3 66 0.92
4 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1346247 original size:23 final size:22
Alignment explanation
Indices: 1346212--1346255 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1346202 ATATAGTCAT
*
1346212 ATAAATATAAATAATATATATA
1 ATAAATAAAAATAATATATATA
*
1346234 ATAAATAAATAATAATTTATAT
1 ATAAATAAA-AATAATATATAT
1346256 TAAATCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAATAAAAATAATATATATA
Found at i:1357685 original size:11 final size:11
Alignment explanation
Indices: 1357660--1357717 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
1357650 ATTATGCTTG
1357660 AAGAAAAAATGAA
1 AAGAAAAAA--AA
1357673 AAGAAAAAAAA
1 AAGAAAAAAAA
* * *
1357684 AAGAGAAGAAG
1 AAGAAAAAAAA
*
1357695 AAGGAAAAAAA
1 AAGAAAAAAAA
1357706 AAGAAAAAAAA
1 AAGAAAAAAAA
1357717 A
1 A
1357718 GGTCAAGATA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 28 0.76
13 9 0.24
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1358109 original size:19 final size:17
Alignment explanation
Indices: 1358067--1358115 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
1358057 TATTTTCTCT
1358067 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
1358083 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
1358101 AAAATTCAACTTATT
1 -AAATTCAATTTATT
1358116 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:1358614 original size:114 final size:114
Alignment explanation
Indices: 1358409--1358745 Score: 548
Period size: 114 Copynumber: 3.0 Consensus size: 114
1358399 TGCCACGTTA
* * *
1358409 TCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1358474 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
*
1358523 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
1358588 TTTGGTATAAACCCCAAAACTAATTATTAGATTTAAAAGATGAATTTGC
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
1358637 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* ** * * * * *
1358702 TTCGGTAGGAACCACAGAACCAATCACTAGAATTGAAAGATGAA
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAA
1358746 CTGTATGATT
Statistics
Matches: 206, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 206 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
Found at i:1359654 original size:112 final size:112
Alignment explanation
Indices: 1359457--1360115 Score: 880
Period size: 112 Copynumber: 6.0 Consensus size: 112
1359447 GCAAAGATTT
* *
1359457 AAATCCATCA-TTCAATGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTT-GATGGATCAACTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
1359521 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTTAACCTTTTGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* *
1359569 AAATCCATCACTTGATGGATCATCTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATATGAAGA
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
1359634 ATGAAGAATAAGTTCATAATGAGAAGAGCTTGTTTAACCTTTTGCTC
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
*
1359681 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
1359746 AGGAAGAAGAAGTTCATAATGAAAAGAGCTTATTTAACCTTTTGCTC
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
** ***
1359793 AAATCCATCACTTGATGGAAGAA----GGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGAAG
*
1359854 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * *
1359902 AAATCCATTACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
1359967 AAAGAAAAAGAAGTTCATAATGAGAAGAACCTGTTCAA-CTTTT-CGC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * *
1360013 ---T---T-ACTGGATGGATCAACTTTTCCAGAGAAAGTTCATAATAAAAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAG
1360071 -AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1360116 ATGACTCTAT
Statistics
Matches: 498, Mismatches: 40, Indels: 25
0.88 0.07 0.04
Matches are distributed among these distances:
103 34 0.07
104 58 0.12
105 2 0.00
108 6 0.01
109 94 0.19
111 2 0.00
112 234 0.47
113 67 0.13
114 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (112 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:1360023 original size:104 final size:104
Alignment explanation
Indices: 1359909--1360113 Score: 340
Period size: 104 Copynumber: 2.0 Consensus size: 104
1359899 CTCAAATCCA
* *
1359909 TTACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAA
1 TTACTGGATGGATCAACATTTCCAGAGAAAGTTCATAATAAAAAGAACTCATCTGAAG-AAGAAA
1359974 AAGAAGTTCATAATGAGAAGAACCTGTTCAA-CTTTTCGC
65 AAGAAGTTCATAATGAGAAGAACCTGTTCAACCTTTTCGC
* * *
1360013 TTACTGGATGGATCAACTTTTCCAGAGAAAGTTCATAATAAAAAGAACTCATCTGAAGAGGAAGA
1 TTACTGGATGGATCAACATTTCCAGAGAAAGTTCATAATAAAAAGAACTCATCTGAAGAAGAAAA
*
1360078 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
66 AGAAGTTCATAATGAGAAGAACCTGTTCAACCTTTT
1360114 GCATGACTCT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 34 0.36
104 60 0.64
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (104 bp):
TTACTGGATGGATCAACATTTCCAGAGAAAGTTCATAATAAAAAGAACTCATCTGAAGAAGAAAA
AGAAGTTCATAATGAGAAGAACCTGTTCAACCTTTTCGC
Found at i:1360232 original size:84 final size:84
Alignment explanation
Indices: 1360083--1360245 Score: 247
Period size: 84 Copynumber: 1.9 Consensus size: 84
1360073 GAAGAAGAAG
* * * **
1360083 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATTAGCA
1 TTCATAATAAGAAGAACTTGTTCAACCTTTTGCAAGACTCTATCACAGAAGAAGATAGACCAGCA
*
1360148 T-ACACTTTTCCAGAGAAAA
66 TCA-ACATTTCCAGAGAAAA
*
1360167 TTCATAATAAGAAGAACTTGTTCAACCTTTTGCAAGATTCTATCACAGAAGAAGATAGACCAGCA
1 TTCATAATAAGAAGAACTTGTTCAACCTTTTGCAAGACTCTATCACAGAAGAAGATAGACCAGCA
1360232 TCAACATTTCCAGA
66 TCAACATTTCCAGA
1360246 AGTGTTCATA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
84 70 0.99
85 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (84 bp):
TTCATAATAAGAAGAACTTGTTCAACCTTTTGCAAGACTCTATCACAGAAGAAGATAGACCAGCA
TCAACATTTCCAGAGAAAA
Found at i:1360549 original size:18 final size:18
Alignment explanation
Indices: 1360528--1360589 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
1360518 ATTTGGTTTT
1360528 TTATTA-TATTTATTACTA
1 TTATTATTATTT-TTACTA
*
1360546 TTATTATTATTTTTATTA
1 TTATTATTATTTTTACTA
* *
1360564 TTAATATTATTTTTAATA
1 TTATTATTATTTTTACTA
1360582 TTATTATT
1 TTATTATT
1360590 TTATTACAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 34 0.87
19 5 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTATTATTTTTACTA
Found at i:1360550 original size:3 final size:3
Alignment explanation
Indices: 1360528--1360595 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
1360518 ATTTGGTTTT
* * *
1360528 TTA TTA -TA TTTA TTA CTA TTA TTA TTA TTT TTA TTA TTA ATA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1360573 TTT TTA ATA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1360596 CAGATACAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
4 2 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1363608 original size:27 final size:28
Alignment explanation
Indices: 1363560--1363620 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
1363550 TATACAACAT
* *
1363560 AAATTCATGTTTTTAATCAAATTTTGAA
1 AAATTAATATTTTTAATCAAATTTTGAA
*
1363588 AAATTAATATTTTTTAT-AAATTTTGAA
1 AAATTAATATTTTTAATCAAATTTTGAA
1363615 AAATTA
1 AAATTA
1363621 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (28 bp):
AAATTAATATTTTTAATCAAATTTTGAA
Found at i:1363627 original size:28 final size:28
Alignment explanation
Indices: 1363569--1363627 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
1363559 TAAATTCATG
*
1363569 TTTTTAATCAAATTTTGAAAAATTAATA
1 TTTTTAATCAAATTTTGAAAAATTAAAA
*
1363597 TTTTTTAT-AAATTTTGAAAAATTATAAA
1 TTTTTAATCAAATTTTGAAAAATTA-AAA
1363625 TTT
1 TTT
1363628 AAAATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (28 bp):
TTTTTAATCAAATTTTGAAAAATTAAAA
Found at i:1364154 original size:21 final size:21
Alignment explanation
Indices: 1364103--1364155 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1364093 ATTATGACTA
1364103 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1364124 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1364145 TCGCAATGCGA
1 TCGCAATGCGA
1364156 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1364175 original size:41 final size:41
Alignment explanation
Indices: 1364130--1364361 Score: 132
Period size: 41 Copynumber: 5.7 Consensus size: 41
1364120 AATTTCGCGT
*
1364130 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * * *
1364171 TGCGAATTTGGAAAATCGCAATACG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
1364212 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
1364253 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
1364294 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * *
1364335 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAATTCGCAATGCGAAT
1364362 CTTACTATCG
Statistics
Matches: 144, Mismatches: 40, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
39 2 0.01
40 26 0.18
41 114 0.79
43 1 0.01
44 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:1364188 original size:21 final size:20
Alignment explanation
Indices: 1364145--1364192 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1364135 TTTTCCCAAT
*
1364145 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
1364165 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1364186 TCGCAAT
1 TCGCAAT
1364193 ACGATACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1364240 original size:21 final size:21
Alignment explanation
Indices: 1364206--1364278 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
1364196 ATACTGACTA
* *
1364206 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
1364227 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
1364247 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
1364268 TCGCAATGCGA
1 TCGCAATGCGA
1364279 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:1364293 original size:20 final size:20
Alignment explanation
Indices: 1364268--1364379 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
1364258 TTTTCATAAT
1364268 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1364288 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1364308 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1364329 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1364349 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
1364369 TCGCAATGCGA
1 TCGCAATGCGA
1364380 TTTATATAGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1364962 original size:19 final size:19
Alignment explanation
Indices: 1364938--1364982 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1364928 GCAACGAGAG
**
1364938 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
1364957 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1364976 AATCGCA
1 AATCGCA
1364983 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1365036 original size:24 final size:19
Alignment explanation
Indices: 1364978--1365123 Score: 112
Period size: 19 Copynumber: 7.1 Consensus size: 19
1364968 GAAACCAAAA
*
1364978 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1364997 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1365016 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1365035 TCGCGTTACGATTCTCTCATTGCGATT
1 TCGCGTTGCGA---T-T--TT-C-ATT
* **
1365062 CTCTCGTTGCGATAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1365082 TCCGTGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
1365102 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1365122 TC
1 TC
1365124 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
19 48 0.48
20 33 0.33
21 2 0.02
22 2 0.02
25 2 0.02
26 1 0.01
27 3 0.03
28 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1365062 original size:14 final size:14
Alignment explanation
Indices: 1365043--1365074 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1365033 TTTCGCGTTA
1365043 CGATTCTCTCATTG
1 CGATTCTCTCATTG
*
1365057 CGATTCTCTCGTTG
1 CGATTCTCTCATTG
1365071 CGAT
1 CGAT
1365075 AGTCATTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.41
Consensus pattern (14 bp):
CGATTCTCTCATTG
Found at i:1365100 original size:20 final size:20
Alignment explanation
Indices: 1365064--1365123 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1365054 TTGCGATTCT
**
1365064 CTCGTTGCGATAGTCATTTC
1 CTCGTTGCGATTTTCATTTC
1365084 CGT-GTTGCGATTTTCATTAT-
1 C-TCGTTGCGATTTTCATT-TC
1365104 CTCGTTGCGATTTTCATTTC
1 CTCGTTGCGATTTTCATTTC
1365124 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (20 bp):
CTCGTTGCGATTTTCATTTC
Found at i:1367270 original size:21 final size:21
Alignment explanation
Indices: 1367246--1367312 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1367236 TCATTCCTCG
1367246 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1367267 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1367288 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1367309 AGAG
1 AGAG
1367313 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1367270 original size:42 final size:42
Alignment explanation
Indices: 1367194--1367312 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1367184 GACTCGCCTG
* * * * * * *
1367194 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1367236 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1367278 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1367313 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1368681 original size:14 final size:14
Alignment explanation
Indices: 1368661--1368711 Score: 86
Period size: 14 Copynumber: 3.6 Consensus size: 14
1368651 GATTGTTTAA
1368661 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
1368674 TGTGATTTGTAAAAG
1 T-TGATTTGTAAAAG
1368689 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1368703 TTGATTTGT
1 TTGATTTGT
1368712 TTAATTGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 1 0.03
14 34 0.94
15 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1368840 original size:19 final size:19
Alignment explanation
Indices: 1368818--1368876 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1368808 AAAAATTACT
1368818 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1368837 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
1368851 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1368870 ATCGCAA
1 ATCGCAA
1368877 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1368860 original size:33 final size:33
Alignment explanation
Indices: 1368818--1368911 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
1368808 AAAAATTACT
* *
1368818 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1368851 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1368884 ATCGCAACGTGAAACT-AAAATCGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
1368912 CGAAACTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1368905 original size:19 final size:19
Alignment explanation
Indices: 1368850--1368926 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
1368840 GCAACGAGAT
*
1368850 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
1368869 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
1368883 AATCGCAACGTGAAACTAA
1 AATCGCAACGCGAAACTAA
1368902 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
1368921 ATTCGC
1 AATCGC
1368927 GTTACGATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 1 0.02
17 2 0.04
18 2 0.04
19 33 0.67
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:1368953 original size:19 final size:18
Alignment explanation
Indices: 1368931--1369052 Score: 88
Period size: 19 Copynumber: 7.2 Consensus size: 18
1368921 ATTCGCGTTA
1368931 CGATTTTCATTTCGCTTTG
1 CGATTTTCATTTCGC-TTG
**
1368950 CGA--TTC-CCTCG-TTG
1 CGATTTTCATTTCGCTTG
1368964 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGC-TTG
*
1368983 CGA--TTC-TCTCG-TTG
1 CGATTTTCATTTCGCTTG
1368997 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGC-TTG
*
1369016 CGA--TT-ATCTCG-TTG
1 CGATTTTCATTTCGCTTG
1369030 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGC-TTG
1369049 CGAT
1 CGAT
1369053 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 8, Indels: 30
0.68 0.07 0.25
Matches are distributed among these distances:
14 18 0.22
16 20 0.25
17 20 0.25
19 22 0.28
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (18 bp):
CGATTTTCATTTCGCTTG
Found at i:1368973 original size:33 final size:33
Alignment explanation
Indices: 1368926--1369052 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
1368916 ACTAAATTCG
* * *
1368926 CGTTACGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1368959 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1368992 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1369025 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1369053 AGTAATTTCC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1368999 original size:14 final size:14
Alignment explanation
Indices: 1368947--1369034 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1368937 TCATTTCGCT
*
1368947 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
1368961 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1368978 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1368994 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
1369011 CATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
1369027 TTGCGATT
1 TTGCGATT
1369035 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1369118 original size:20 final size:20
Alignment explanation
Indices: 1369046--1369118 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1369036 TCATTTCGCA
* *
1369046 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
1369066 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
1369086 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
1369107 TTGCGATAGTCA
1 TTGCGATAGTCA
1369119 AATGATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:1371611 original size:24 final size:24
Alignment explanation
Indices: 1371577--1371630 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1371567 CTGAAACATC
* *
1371577 ATCAAAATCCGATTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1371601 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1371625 ATCAAA
1 ATCAAA
1371631 TTTTGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1372499 original size:20 final size:20
Alignment explanation
Indices: 1372474--1372530 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1372464 TAATACAAAA
*
1372474 TCGCAACGTGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
1372494 TCGCAACGAGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
1372514 TCGCAAAGAGATTCTGA
1 TCGCAACGAGATTCTGA
1372531 AAATCGCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:1372537 original size:20 final size:20
Alignment explanation
Indices: 1372470--1372539 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1372460 GAGATAATAC
*
1372470 AAAATCGCAACGTGATTCTG
1 AAAATCGCAACGAGATTCTG
***
1372490 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
*** *
1372510 ACTTTCGCAAAGAGATTCTG
1 AAAATCGCAACGAGATTCTG
1372530 AAAATCGCAA
1 AAAATCGCAA
1372540 TCATCTTCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:1372842 original size:21 final size:20
Alignment explanation
Indices: 1372818--1372862 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1372808 TGCATTGCGA
1372818 TTTTCTCGTTGCGATAGTCAG
1 TTTTCT-GTTGCGATAGTCAG
* *
1372839 TTTTGTGTTGCGATAGTCTG
1 TTTTCTGTTGCGATAGTCAG
1372859 TTTT
1 TTTT
1372863 GCCTTCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.11, C:0.13, G:0.24, T:0.51
Consensus pattern (20 bp):
TTTTCTGTTGCGATAGTCAG
Found at i:1372850 original size:20 final size:20
Alignment explanation
Indices: 1372825--1372863 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1372815 CGATTTTCTC
1372825 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
1372845 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
1372864 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:1374461 original size:41 final size:42
Alignment explanation
Indices: 1374407--1374498 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
1374397 CCTCTTCAAC
* *
1374407 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* * *
1374448 GATGATAGGGGCCTCTTGAATGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
1374490 GATGACAGG
1 GATGACAGG
1374499 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 19 0.43
42 25 0.57
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:1374463 original size:21 final size:21
Alignment explanation
Indices: 1374434--1374494 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1374424 GAACGGTGGG
*
1374434 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
1374455 GGGGCCTCTTGAATGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
1374476 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1374495 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.11, G:0.43, T:0.25
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1374861 original size:20 final size:20
Alignment explanation
Indices: 1374836--1374874 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1374826 GAAGAATAGT
1374836 TTACTTTCACAACACGAAAC
1 TTACTTTCACAACACGAAAC
* *
1374856 TTACTTTCGCAACGCGAAA
1 TTACTTTCACAACACGAAA
1374875 ATGACTATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (20 bp):
TTACTTTCACAACACGAAAC
Found at i:1374885 original size:20 final size:20
Alignment explanation
Indices: 1374862--1374948 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
1374852 AAACTTACTT
*
1374862 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
1374882 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1374902 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1374922 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1374941 TCGCAACG
1 TCGCAACG
1374949 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 14 0.23
20 46 0.77
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1374917 original size:40 final size:39
Alignment explanation
Indices: 1374862--1374981 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 39
1374852 AAACTTACTT
**
1374862 TCGCAACGCGAAAATGACTATCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTATCGCAACGC-GAAATGAAAA
* * *
1374902 TCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAACGCGAAATGAAAA
* *
1374941 TCGCAA--CGACAA--A--ATCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAACGCGAAATGAAAA
1374974 TCGCAACG
1 TCGCAACG
1374982 ACAAAATCGC
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
33 26 0.37
37 4 0.06
39 14 0.20
40 26 0.37
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (39 bp):
TCGCAACGCGAAAATGACTATCGCAACGCGAAATGAAAA
Found at i:1374956 original size:14 final size:14
Alignment explanation
Indices: 1374937--1374995 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1374927 ATGCGAAATG
1374937 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1374951 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1374970 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1374984 AAAATCGCAACG
1 AAAATCGCAACG
1374996 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1375011 original size:33 final size:33
Alignment explanation
Indices: 1374921--1375000 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
1374911 GGAAATGGCT
1374921 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1374954 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1374987 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1375001 CACAAATCGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1375029 original size:19 final size:19
Alignment explanation
Indices: 1375007--1375103 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
1374997 GAAACACAAA
1375007 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1375026 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1375042 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1375059 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1375075 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1375092 TTGCATTGCGAT
1 TCGCATTGCGAT
1375104 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 7 0.11
18 6 0.10
19 24 0.38
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1375050 original size:14 final size:14
Alignment explanation
Indices: 1375031--1375087 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1375021 TCATTTCGCA
1375031 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
1375045 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
1375062 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
1375078 TTGCGATTTT
1 TTGCGATTTT
1375088 CATTTTGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:1375054 original size:33 final size:33
Alignment explanation
Indices: 1375012--1375103 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
1375002 ACAAATCGCA
1375012 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1375045 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1375078 TTGCGATTTTCATTTTGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1375104 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1375122 original size:20 final size:20
Alignment explanation
Indices: 1375097--1375142 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1375087 TCATTTTGCA
1375097 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
1375117 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
1375137 TTGCGA
1 TTGCGA
1375143 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1375706 original size:18 final size:18
Alignment explanation
Indices: 1375683--1375730 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1375673 CGGGTCGATC
1375683 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1375701 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1375719 AGGTGATGGCTC
1 AGGTGATGGCTC
1375731 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1377090 original size:20 final size:20
Alignment explanation
Indices: 1377042--1377100 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1377032 AATAGTTTCT
* *
1377042 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
1377062 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
1377082 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
1377101 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:1377388 original size:22 final size:22
Alignment explanation
Indices: 1377361--1377404 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1377351 GATGGAGATA
1377361 GACGGATTTCGCCGGAGATGGT
1 GACGGATTTCGCCGGAGATGGT
*
1377383 GACGGATTTCGTCGGAGATGGT
1 GACGGATTTCGCCGGAGATGGT
1377405 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.41, T:0.25
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGT
Found at i:1377604 original size:21 final size:22
Alignment explanation
Indices: 1377572--1377667 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 22
1377562 CGCTTTGAAA
* *
1377572 ATCGCATTGCGATTATGT-ATT
1 ATCGCGTTGCGATTATGTCAGT
* *
1377593 ATCTCGTTGCGA--AAGTCAGT
1 ATCGCGTTGCGATTATGTCAGT
* * *
1377613 ATTGCGTTGCGATTCTGT-ATT
1 ATCGCGTTGCGATTATGTCAGT
1377634 ATCGCGTTGCGA-TA-GTCAGT
1 ATCGCGTTGCGATTATGTCAGT
1377654 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
1377668 TTCCAAATTC
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.09
20 27 0.47
21 24 0.41
22 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (22 bp):
ATCGCGTTGCGATTATGTCAGT
Found at i:1377635 original size:41 final size:41
Alignment explanation
Indices: 1377572--1377667 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
1377562 CGCTTTGAAA
* *
1377572 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
1377613 ATTGCGTTGCGATTCTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1377654 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
1377668 TTCCAAATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1377684 original size:21 final size:21
Alignment explanation
Indices: 1377655--1377727 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
1377645 ATAGTCAGTA
*
1377655 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
1377676 TCGCATTGCGATTTTCAAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
1377697 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
1377717 TCGCATTGCGA
1 TCGCATTGCGA
1377728 ATTGGGAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1377685 original size:41 final size:41
Alignment explanation
Indices: 1377599--1377687 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
1377589 TATTATCTCG
* * ** * *
1377599 TTGCGAAAGTCAGTATTGCGTTGCGATTCTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTCTCAAATATCGCA
*
1377640 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTCT-CAAATATCGCA
1377681 TTGCGAT
1 TTGCGAT
1377688 TTTCAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 38 0.95
42 2 0.05
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTCTCAAATATCGCA
Found at i:1377769 original size:21 final size:22
Alignment explanation
Indices: 1377717--1377769 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1377707 ATTTACTTAT
1377717 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1377738 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1377759 TCGCATTGCGA
1 TCGCATTGCGA
1377770 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1385896 original size:29 final size:29
Alignment explanation
Indices: 1385864--1385922 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1385854 TAATTTATAG
* *
1385864 TAATTAAATTTTGATATAAT-GATTTTAAA
1 TAATTAAACTTT-ATAAAATAGATTTTAAA
*
1385893 TAATTAAACTTTATAAAATATATTTTAAA
1 TAATTAAACTTTATAAAATAGATTTTAAA
1385922 T
1 T
1385923 GGTATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (29 bp):
TAATTAAACTTTATAAAATAGATTTTAAA
Found at i:1386822 original size:36 final size:36
Alignment explanation
Indices: 1386775--1386848 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
1386765 AGCTGTCACA
*
1386775 GAGTGAATGGACATGGTAAGAACCGCACTAATCAAG
1 GAGTGAATGGACATGGTAAGAACCACACTAATCAAG
*
1386811 GAGTGAATGGACATGGTAAGAACCACACTAATCGAG
1 GAGTGAATGGACATGGTAAGAACCACACTAATCAAG
1386847 GA
1 GA
1386849 ACGATTTGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.16
Consensus pattern (36 bp):
GAGTGAATGGACATGGTAAGAACCACACTAATCAAG
Found at i:1389548 original size:26 final size:25
Alignment explanation
Indices: 1389500--1389549 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1389490 TATATTACAG
*
1389500 AAAAAATAAGAGAAACTTGTAAAAT
1 AAAAAATAAGAGAAAATTGTAAAAT
1389525 AAAAAATAAGA-AAATATTGATAAAA
1 AAAAAATAAGAGAAA-ATTG-TAAAA
1389550 AATATTTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.64
26 5 0.23
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (25 bp):
AAAAAATAAGAGAAAATTGTAAAAT
Found at i:1391260 original size:67 final size:66
Alignment explanation
Indices: 1391162--1391298 Score: 265
Period size: 67 Copynumber: 2.1 Consensus size: 66
1391152 CATGCATGAT
1391162 CTTAAGCAAGTGTTACATACTTTGGGTTTAACTGATCTATCACTGAAGTAGGAGTTTCATGCTTT
1 CTTAAGCAAGTGTTACATACTTTGGGTTTAACTGATCTATCACTGAAGTAGGAGTTTCATGCTTT
1391227 C
66 C
1391228 CTTATAGCAAGTGTTACATACTTTGGGTTTAACTGATCTATCACTGAAGTAGGAGTTTCATGCTT
1 CTTA-AGCAAGTGTTACATACTTTGGGTTTAACTGATCTATCACTGAAGTAGGAGTTTCATGCTT
1391293 TC
65 TC
1391295 CTTA
1 CTTA
1391299 CTCCTCTATT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 4 0.06
67 66 0.94
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (66 bp):
CTTAAGCAAGTGTTACATACTTTGGGTTTAACTGATCTATCACTGAAGTAGGAGTTTCATGCTTT
C
Found at i:1397032 original size:33 final size:33
Alignment explanation
Indices: 1396990--1397056 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1396980 CCTAGTACAG
1396990 ATGGTGGACACGACCTTATGTGTCATACGAATT
1 ATGGTGGACACGACCTTATGTGTCATACGAATT
* *
1397023 ATGGTGGACACGACCTTATGTGTTATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGAATT
1397056 A
1 A
1397057 GCACTACGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGAATT
Found at i:1397184 original size:44 final size:44
Alignment explanation
Indices: 1397135--1397326 Score: 296
Period size: 44 Copynumber: 4.3 Consensus size: 44
1397125 TGGTATATGG
*
1397135 TTATGGA-ATAATGGAAAGTGTATTGGTAAAATAAGCTTACAAGC
1 TTATGGATA-AATGGTAAGTGTATTGGTAAAATAAGCTTACAAGC
1397179 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACAAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACAAGC
*
1397223 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACAAGC
* * * *
1397267 TTATGGATAAATGGTAAGTATATTGGTAAAATAATCTTACGAGT
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACAAGC
1397311 TTATGGTATTAAATGG
1 TTATGG-A-TAAATGG
1397327 AAAAATATTG
Statistics
Matches: 140, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
44 131 0.94
45 2 0.01
46 7 0.05
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACAAGC
Found at i:1397233 original size:25 final size:25
Alignment explanation
Indices: 1397161--1397233 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
1397151 AGTGTATTGG
1397161 TAAAATAAGCTTACAAGCTTATGGA
1 TAAAATAAGCTTACAAGCTTATGGA
* **
1397186 T-AAAT--G-GT--AAGTGTATTGG-
1 TAAAATAAGCTTACAAGCTTA-TGGA
1397205 TAAAATAAGCTTACAAGCTTATGGA
1 TAAAATAAGCTTACAAGCTTATGGA
1397230 TAAA
1 TAAA
1397234 TGGTAAGTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 16
0.61 0.11 0.29
Matches are distributed among these distances:
19 6 0.18
20 7 0.21
21 1 0.03
22 2 0.06
23 1 0.03
24 7 0.21
25 10 0.29
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.30
Consensus pattern (25 bp):
TAAAATAAGCTTACAAGCTTATGGA
Found at i:1397234 original size:24 final size:24
Alignment explanation
Indices: 1397163--1397234 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
1397153 TGTATTGGTA
1397163 AAATAAGCTTACAAGCTTATGGAT
1 AAATAAGCTTACAAGCTTATGGAT
*
1397187 AAAT--G-GT--AAG-TGTATTGG-T
1 AAATAAGCTTACAAGCT-TA-TGGAT
1397206 AAAATAAGCTTACAAGCTTATGGAT
1 -AAATAAGCTTACAAGCTTATGGAT
1397231 AAAT
1 AAAT
1397235 GGTAAGTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 6 0.17
20 7 0.19
21 1 0.03
22 2 0.06
23 1 0.03
24 11 0.31
25 6 0.17
26 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (24 bp):
AAATAAGCTTACAAGCTTATGGAT
Found at i:1398960 original size:18 final size:19
Alignment explanation
Indices: 1398937--1398973 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1398927 CTCATAATCC
1398937 TATTCT-CTGATAATCTTT
1 TATTCTACTGATAATCTTT
1398955 TATTCTCACTGATAATCTT
1 TATTCT-ACTGATAATCTT
1398974 ACATTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTCTACTGATAATCTTT
Found at i:1398979 original size:20 final size:20
Alignment explanation
Indices: 1398943--1398981 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1398933 ATCCTATTCT
**
1398943 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTACATTCTCA
1398963 CTGATAATCTTACATTCTC
1 CTGATAATCTTACATTCTC
1398982 TTAACCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (20 bp):
CTGATAATCTTACATTCTCA
Found at i:1400061 original size:3 final size:3
Alignment explanation
Indices: 1400053--1400078 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1400043 TCACAACCCG
1400053 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
1400079 AACCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1400918 original size:157 final size:157
Alignment explanation
Indices: 1400632--1400947 Score: 623
Period size: 157 Copynumber: 2.0 Consensus size: 157
1400622 GTCAAGTTCA
1400632 ATTAGAAATAAGAAGTTCAGGAACTAGCCTCGTAATTTGTCCAAAACCAAAGGAGAATGCCCAAG
1 ATTAGAAATAAGAAGTTCAGGAACTAGCCTCGTAATTTGTCCAAAACCAAAGGAGAATGCCCAAG
1400697 AATTCTAGAGATTTCTTTTCCCCATTTAAAATCAAGCAAACCCGGAAAAAAAAACATTTTATCTT
66 AATTCTAGAGATTTCTTTTCCCCATTTAAAATCAAGCAAACCCGGAAAAAAAAACATTTTATCTT
*
1400762 CACCAGTCGCCCGCACCGTACTTCTCC
131 CACCAGTCGCCCCCACCGTACTTCTCC
1400789 ATTAGAAATAAGAAGTTCAGGAACTAGCCTCGTAATTTGTCCAAAACCAAAGGAGAATGCCCAAG
1 ATTAGAAATAAGAAGTTCAGGAACTAGCCTCGTAATTTGTCCAAAACCAAAGGAGAATGCCCAAG
1400854 AATTCTAGAGATTTCTTTTCCCCATTTAAAATCAAGCAAACCCGGAAAAAAAAACATTTTATCTT
66 AATTCTAGAGATTTCTTTTCCCCATTTAAAATCAAGCAAACCCGGAAAAAAAAACATTTTATCTT
1400919 CACCAGTCGCCCCCACCGTACTTCTCC
131 CACCAGTCGCCCCCACCGTACTTCTCC
1400946 AT
1 AT
1400948 CATTCACATG
Statistics
Matches: 158, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (157 bp):
ATTAGAAATAAGAAGTTCAGGAACTAGCCTCGTAATTTGTCCAAAACCAAAGGAGAATGCCCAAG
AATTCTAGAGATTTCTTTTCCCCATTTAAAATCAAGCAAACCCGGAAAAAAAAACATTTTATCTT
CACCAGTCGCCCCCACCGTACTTCTCC
Found at i:1402901 original size:2 final size:2
Alignment explanation
Indices: 1402894--1402924 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1402884 GATTGTTGAA
1402894 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
1402925 GAAAATACCA
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:1406949 original size:17 final size:18
Alignment explanation
Indices: 1406918--1406952 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1406908 AAAGCTTTTA
1406918 TCTCTTTCATCTCCTTCT
1 TCTCTTTCATCTCCTTCT
*
1406936 TCTC-TTCATTTCCTTCT
1 TCTCTTTCATCTCCTTCT
1406953 CGTTTCCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.06, C:0.37, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTCTTTCATCTCCTTCT
Found at i:1407588 original size:17 final size:17
Alignment explanation
Indices: 1407566--1407598 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1407556 TTTTTTACCG
1407566 ATTTTATTATTTAAAAA
1 ATTTTATTATTTAAAAA
1407583 ATTTTATTATTTAAAA
1 ATTTTATTATTTAAAA
1407599 TAATAATAAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATTATTTAAAAA
Found at i:1410818 original size:14 final size:15
Alignment explanation
Indices: 1410781--1410818 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1410771 CTGTCTATAT
*
1410781 GCAGAGATTTTTTAC
1 GCAGAGATTTATTAC
*
1410796 GCAGGGATTTATTA-
1 GCAGAGATTTATTAC
1410810 GCAGAGATT
1 GCAGAGATT
1410819 ACTTTCCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (15 bp):
GCAGAGATTTATTAC
Found at i:1412474 original size:2 final size:2
Alignment explanation
Indices: 1412467--1412502 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1412457 TTGGATTGTC
1412467 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
1412503 TGCTTTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1413631 original size:16 final size:16
Alignment explanation
Indices: 1413597--1413636 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1413587 TTTACTTCAT
* *
1413597 AATGATT-AAGTGTTG
1 AATGATTCAAATGCTG
1413612 AATGATTCAAATGCTG
1 AATGATTCAAATGCTG
1413628 AATGATTCA
1 AATGATTCA
1413637 GAGATTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (16 bp):
AATGATTCAAATGCTG
Found at i:1418453 original size:4 final size:4
Alignment explanation
Indices: 1418446--1418516 Score: 142
Period size: 4 Copynumber: 17.8 Consensus size: 4
1418436 ATACATATAT
1418446 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1418494 ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATA
1418517 AAGTGTTACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:1419985 original size:11 final size:11
Alignment explanation
Indices: 1419969--1419993 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1419959 GTTTAAAGGT
1419969 AATTATTTTTA
1 AATTATTTTTA
1419980 AATTATTTTTA
1 AATTATTTTTA
1419991 AAT
1 AAT
1419994 GATAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTATTTTTA
Found at i:1420031 original size:87 final size:85
Alignment explanation
Indices: 1419935--1420225 Score: 357
Period size: 87 Copynumber: 3.4 Consensus size: 85
1419925 ATTTATCATT
*
1419935 AAAAATAATATATAATTTAAATTTGTTTAAAGGTAATTATTTTTAAATTATTTTTAAATGATAAA
1 AAAAATAATATATAATTTAAATTTGTTTAAA-ATAATTATTTTTAAATTATTTTTAAATGATAAA
*
1420000 TGAATAATAAACATCGTAAGAA
65 TGAATAA-AAACATTGTAAGAA
*
1420022 AAAAATAATATATAATTTTAATTTGTTTTAAAATAATTA-TTTTATAATTATTTTTAAATG---A
1 AAAAATAATATATAATTTAAATTTG-TTTAAAATAATTATTTTTA-AATTATTTTTAAATGATAA
1420083 ATGAATAACAAACATTGTAAGAAAGA
64 ATGAATAA-AAACATTGTAAG--A-A
*
1420109 AAAAATAATATATAATTTAAAATTT-TTTAAAAATAATTATTTTAAAATTATTTTTAAATGATAA
1 AAAAATAATATATAATTT-AAATTTGTTT-AAAATAATTATTTTTAAATTATTTTTAAATGATAA
* *
1420173 ATGAATAAAAACGTTGTAA-TA
64 ATGAATAAAAACATTGTAAGAA
*
1420194 AATAATATATATATAATTT-AA-TT-TTTAAAATA
1 AAAAATA-ATATATAATTTAAATTTGTTTAAAATA
1420226 TAAAAAATTT
Statistics
Matches: 183, Mismatches: 9, Indels: 29
0.83 0.04 0.13
Matches are distributed among these distances:
82 6 0.03
83 5 0.03
84 22 0.12
85 7 0.04
86 20 0.11
87 89 0.49
88 15 0.08
89 10 0.05
90 9 0.05
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (85 bp):
AAAAATAATATATAATTTAAATTTGTTTAAAATAATTATTTTTAAATTATTTTTAAATGATAAAT
GAATAAAAACATTGTAAGAA
Found at i:1420152 original size:25 final size:28
Alignment explanation
Indices: 1420109--1420162 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 28
1420099 GTAAGAAAGA
1420109 AAAAATAATATATAATTTAAAATT-TTTT
1 AAAAATAATATAT-ATTTAAAATTATTTT
1420137 AAAAATAAT-TAT-TTTAAAATTATTTT
1 AAAAATAATATATATTTAAAATTATTTT
1420163 TAAATGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 9 0.36
26 4 0.16
27 3 0.12
28 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AAAAATAATATATATTTAAAATTATTTT
Found at i:1420226 original size:23 final size:22
Alignment explanation
Indices: 1420208--1420265 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 22
1420198 ATATATATAT
1420208 AATTTAATTTTTAAAATATAAAA
1 AATTTAATTTTTAAAATAT-AAA
1420231 AATTTAATTTTTAAAATATAAA
1 AATTTAATTTTTAAAATATAAA
1420253 AATTTTAATTTTT
1 AA-TTTAATTTTT
1420266 TTAACCTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTAATTTTTAAAATATAAA
Found at i:1420646 original size:17 final size:18
Alignment explanation
Indices: 1420614--1420653 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1420604 CCTGATTAGA
*
1420614 AAATTAATATTTAGAATT
1 AAATTAATAATTAGAATT
1420632 AAATTAA-AATTAGAATT
1 AAATTAATAATTAGAATT
1420649 AAATT
1 AAATT
1420654 GATAGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
AAATTAATAATTAGAATT
Found at i:1421523 original size:13 final size:13
Alignment explanation
Indices: 1421507--1421544 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1421497 TTAAAATTGA
1421507 ATTTTTTATTTTT
1 ATTTTTTATTTTT
1421520 ATTTTATTA-TTTT
1 ATTTT-TTATTTTT
*
1421533 ATTTGTTATTTT
1 ATTTTTTATTTT
1421545 ATATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 3 0.14
13 16 0.73
14 3 0.14
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:1421532 original size:20 final size:20
Alignment explanation
Indices: 1421510--1421546 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1421500 AAATTGAATT
1421510 TTTTATTT-TTATTTTATTA
1 TTTTATTTGTTATTTTATTA
1421529 TTTTATTTGTTATTTTAT
1 TTTTATTTGTTATTTTAT
1421547 ATAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTATTTGTTATTTTATTA
Found at i:1428994 original size:29 final size:29
Alignment explanation
Indices: 1428962--1429080 Score: 96
Period size: 29 Copynumber: 4.1 Consensus size: 29
1428952 ATAAGATTTG
* *
1428962 ATCCTTGTCCTCATTCTGCAAGAAATTAT
1 ATCCATGTCCTCATTCTGCAAGAGATTAT
* ** *
1428991 ATCCATATATTGATTCTGCATAG-GATTAT
1 ATCCATGTCCTCATTCTGCA-AGAGATTAT
** * * *
1429020 ATCCCCGTCCTAATTCTGTATGAGATTAT
1 ATCCATGTCCTCATTCTGCAAGAGATTAT
* * *
1429049 ATCCATGTCATCATTATGCATGAGATTAT
1 ATCCATGTCCTCATTCTGCAAGAGATTAT
1429078 ATC
1 ATC
1429081 TTCGTCTTGA
Statistics
Matches: 68, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
28 1 0.01
29 65 0.96
30 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (29 bp):
ATCCATGTCCTCATTCTGCAAGAGATTAT
Found at i:1429117 original size:29 final size:29
Alignment explanation
Indices: 1428974--1429124 Score: 115
Period size: 29 Copynumber: 5.2 Consensus size: 29
1428964 CCTTGTCCTC
* * ** *
1428974 ATTCTGCAAGAAATTATATCCATATATTG
1 ATTCTGCATGAGATTATATCCACGTCTTG
* * *
1429003 ATTCTGCAT-AGGATTATATCCCCGTCCTA
1 ATTCTGCATGA-GATTATATCCACGTCTTG
* * * *
1429032 ATTCTGTATGAGATTATATCCATGTCATC
1 ATTCTGCATGAGATTATATCCACGTCTTG
* **
1429061 ATTATGCATGAGATTATATCTTCGTCTTG
1 ATTCTGCATGAGATTATATCCACGTCTTG
* * *
1429090 ATTCTGCATGGGATTATATCCCCATCTTG
1 ATTCTGCATGAGATTATATCCACGTCTTG
*
1429119 TTTCTG
1 ATTCTG
1429125 TTTGAGATCT
Statistics
Matches: 94, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
28 1 0.01
29 92 0.98
30 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (29 bp):
ATTCTGCATGAGATTATATCCACGTCTTG
Found at i:1430002 original size:20 final size:20
Alignment explanation
Indices: 1429977--1430032 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1429967 TTCTGCACAC
1429977 AAAGTTTTGAAACTCTAGGG
1 AAAGTTTTGAAACTCTAGGG
*
1429997 AAAGTTTTGAAACTCTGGGG
1 AAAGTTTTGAAACTCTAGGG
*
1430017 AAAGTTTCGAAACTCT
1 AAAGTTTTGAAACTCT
1430033 TCGAAAGAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (20 bp):
AAAGTTTTGAAACTCTAGGG
Found at i:1430142 original size:19 final size:20
Alignment explanation
Indices: 1430099--1430142 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1430089 TAAAGTTTTG
*
1430099 AAACTCTTGAGATAGTTTCA
1 AAACTCTTGAGAAAGTTTCA
1430119 AAACTCTTGA-AAAGTATT-A
1 AAACTCTTGAGAAAGT-TTCA
1430138 AAACT
1 AAACT
1430143 TTTTGGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (20 bp):
AAACTCTTGAGAAAGTTTCA
Found at i:1432382 original size:15 final size:15
Alignment explanation
Indices: 1432358--1432391 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1432348 CCATAGGACC
1432358 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
1432373 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
1432388 ACTA
1 ACTA
1432392 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1432518 original size:29 final size:29
Alignment explanation
Indices: 1432476--1432556 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
1432466 TTCCATATGT
1432476 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1432504 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1432533 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1432557 ATATCACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1438953 original size:21 final size:21
Alignment explanation
Indices: 1438927--1438971 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1438917 GATTTCTGGG
* *
1438927 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1438948 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1438969 CAA
1 CAA
1438972 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1439894 original size:62 final size:62
Alignment explanation
Indices: 1439774--1439898 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 62
1439764 AGGGTCGAGG
* * * * *
1439774 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
**
1439836 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATTTATGGACT
1 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
1439898 G
1 G
1439899 GTCCTTCGGG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
Found at i:1439898 original size:31 final size:31
Alignment explanation
Indices: 1439774--1439883 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
1439764 AGGGTCGAGG
1439774 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1439805 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1439836 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1439867 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
1439884 AGAATTTATG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1441249 original size:15 final size:15
Alignment explanation
Indices: 1441225--1441258 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1441215 CCGTAGGACC
1441225 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
1441240 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
1441255 ACTA
1 ACTA
1441259 TTATACCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1441386 original size:29 final size:29
Alignment explanation
Indices: 1441343--1441452 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
1441333 TTTCATATGT
1441343 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
1441371 TCATGTACCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
1441400 TCATGCAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1441429 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1441453 ATATCACATA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.09
29 65 0.84
30 5 0.06
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1446333 original size:2 final size:2
Alignment explanation
Indices: 1446326--1446376 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1446316 ACTAAAACAA
*
1446326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1446368 AT AT AT AT A
1 AT AT AT AT A
1446377 ATTCTTATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1457756 original size:103 final size:100
Alignment explanation
Indices: 1457329--1457833 Score: 780
Period size: 103 Copynumber: 5.0 Consensus size: 100
1457319 GCGCGGCACT
* * * * *
1457329 TTTTAATGGAACCCAGTTCTGATAATTAAGTTGTATGTGCGTTCCCGATGATCTCCAATCTCTAG
1 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
*
1457394 TTTTTCCAATTTCCCTTTCTTTCCCGTCAACCCACGTA
66 TTTTTCCAATTTCCCTTTCTTCCCCGTCAA--C-CGTA
* * *
1457432 TTTTAATGAAACCCTGTCCTGATAATTAAGTTGTATGTACATTCCCAACGATCTCCAA-CCACTA
1 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCC-CTA
* *
1457496 CTTTTTCCAA-TTCCCTTTCTTTCCCGTCAACCGTA
65 GTTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTA
*
1457531 TTTTAATGGAACCCTATCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
1 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
1457596 TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTA
66 TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTA
*
1457631 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAATGATCTCCAATCCCTAT
1 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTA-
*
1457696 TTTTTTTCCCAATTTCCCTTTCTTCCCCGTCAACCGTA
65 -GTTTTT-CCAATTTCCCTTTCTTCCCCGTCAACCGTA
* * *
1457734 TTTTAATGGAACCTTGTCCTGATAATTAAGTTGTATGTGCGCTCCCAACGATCTCCAATCCCTAT
1 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
1457799 TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTA
66 TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTA
1457834 ATTTCGCTTC
Statistics
Matches: 375, Mismatches: 21, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
99 70 0.19
100 119 0.32
101 6 0.02
102 26 0.07
103 154 0.41
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (100 bp):
TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTA
Found at i:1457782 original size:203 final size:199
Alignment explanation
Indices: 1457329--1457833 Score: 787
Period size: 203 Copynumber: 2.5 Consensus size: 199
1457319 GCGCGGCACT
* * * * *
1457329 TTTTAATGGAACCCAGTTCTGATAATTAAGTTGTATGTGCGTTCCCGATGATCTCCAATCTCTAG
1 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
*
1457394 TTTTTCCAATTTCCCTTTCTTTCCCGTCAACCCACGTATTTTAATGAAACCCTGTCCTGATAATT
66 TTTTTCCAATTTCCCTTTCTTCCCCGTCAA--C-CGTATTTTAATGAAACCCTGTCCTGATAATT
*
1457459 AAGTTGTATGTACATTCCCAACGATCTCCAACCACTACTTTTTCCAATTCCCTTTCTTTCCCGTC
128 AAGTTGTATGTACATTCCCAACGATCTCCAACCACTACTTTTTCCAATTCCCTTTCTTCCCCGTC
1457524 AACCGTA
193 AACCGTA
*
1457531 TTTTAATGGAACCCTATCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
1 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
*
1457596 TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTATTTTAATGGAACCCTGTCCTGATAATTAAG
66 TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTATTTTAATGAAACCCTGTCCTGATAATTAAG
* * * *
1457661 TTGTATGTGCGTTCCCAATGATCTCCAATCC-CTATTTTTTTTCCCAATTTCCCTTTCTTCCCCG
131 TTGTATGTACATTCCCAACGATCTCCAA-CCACTA--CTTTTT-CCAA-TTCCCTTTCTTCCCCG
1457725 TCAACCGTA
191 TCAACCGTA
* * *
1457734 TTTTAATGGAACCTTGTCCTGATAATTAAGTTGTATGTGCGCTCCCAACGATCTCCAATCCCTAT
1 TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
1457799 TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTA
66 TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTA
1457834 ATTTCGCTTC
Statistics
Matches: 281, Mismatches: 17, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
199 61 0.22
200 3 0.01
201 5 0.02
202 92 0.33
203 120 0.43
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (199 bp):
TTTTAATGGAACCCTGTCCTGATAATTAAGTTGTATGTGCGTTCCCAACGATCTCCAATCCCTAG
TTTTTCCAATTTCCCTTTCTTCCCCGTCAACCGTATTTTAATGAAACCCTGTCCTGATAATTAAG
TTGTATGTACATTCCCAACGATCTCCAACCACTACTTTTTCCAATTCCCTTTCTTCCCCGTCAAC
CGTA
Found at i:1460765 original size:46 final size:44
Alignment explanation
Indices: 1460697--1460800 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 44
1460687 TCATTCAATA
* *
1460697 GGTACCGATACCCTCTCAAACGAGAAAAATTTCAGAATGTCAT-AGG
1 GGTACCGATACCCCCTCAAAC--GAAAAATTACAGAATGTCATGA-G
* **
1460743 GGTACCGATGCCCCCTTGAACGAAAAATTACAGAATGTCATGAG
1 GGTACCGATACCCCCTCAAACGAAAAATTACAGAATGTCATGAG
1460787 GGTACCGATACCCC
1 GGTACCGATACCCC
1460801 TAATAGGGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 33 0.65
45 1 0.02
46 17 0.33
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (44 bp):
GGTACCGATACCCCCTCAAACGAAAAATTACAGAATGTCATGAG
Found at i:1462665 original size:23 final size:23
Alignment explanation
Indices: 1462597--1462665 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1462587 CAATATTATA
* * *
1462597 TGGCACTTCGGTGCTTTTTTACA
1 TGGCACTTCGGTGCATTTATACG
* * * *
1462620 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTATACG
1462643 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTATACG
1462666 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTATACG
Found at i:1467889 original size:23 final size:23
Alignment explanation
Indices: 1467856--1467923 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1467846 AATATTATAT
1467856 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
1467879 GGCACTACGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
1467902 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1467924 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1469190 original size:15 final size:16
Alignment explanation
Indices: 1469170--1469224 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 16
1469160 TTTAATCAAG
1469170 TTGTTGAATATT-TAT
1 TTGTTGAATATTATAT
1469185 TTGTTGAATATTGA-AT
1 TTGTTGAATATT-ATAT
1469201 TT-TT--AT-TTATAT
1 TTGTTGAATATTATAT
1469213 TTGTTGAATATT
1 TTGTTGAATATT
1469225 GGGCTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
11 1 0.03
12 6 0.18
13 4 0.12
15 16 0.48
16 6 0.18
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (16 bp):
TTGTTGAATATTATAT
Found at i:1469310 original size:15 final size:15
Alignment explanation
Indices: 1469292--1469323 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1469282 ATTATTTATA
1469292 TTGTTTTTATTAAAT
1 TTGTTTTTATTAAAT
1469307 TTGTTTTTATTAAAT
1 TTGTTTTTATTAAAT
1469322 TT
1 TT
1469324 AAAAAATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
TTGTTTTTATTAAAT
Found at i:1474048 original size:7 final size:7
Alignment explanation
Indices: 1474036--1474073 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1474026 CCGCGCTCCT
1474036 TTTTTCC
1 TTTTTCC
1474043 TTTTTCC
1 TTTTTCC
1474050 TTTTTCC
1 TTTTTCC
1474057 TTTTTCC
1 TTTTTCC
1474064 TTTTTCC
1 TTTTTCC
1474071 TTT
1 TTT
1474074 CTTCTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCC
Found at i:1479516 original size:58 final size:58
Alignment explanation
Indices: 1479443--1479560 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
1479433 ATCCATAATC
1479443 GTATCAACTTCTCTCAAGTGTAAATCAATGTTGCATGAAAGCTCATGATCGATCACCA
1 GTATCAACTTCTCTCAAGTGTAAATCAATGTTGCATGAAAGCTCATGATCGATCACCA
* *
1479501 GTATCGACTTCTCTCAAGTGTCAATCAATGTTGCATGAAAGCTCATGATCGATCACCA
1 GTATCAACTTCTCTCAAGTGTAAATCAATGTTGCATGAAAGCTCATGATCGATCACCA
1479559 GT
1 GT
1479561 TCCAGCTTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (58 bp):
GTATCAACTTCTCTCAAGTGTAAATCAATGTTGCATGAAAGCTCATGATCGATCACCA
Found at i:1480742 original size:14 final size:15
Alignment explanation
Indices: 1480718--1480746 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1480708 TTTATTTTTC
1480718 AAATGTTTAAATATA
1 AAATGTTTAAATATA
1480733 AAAT-TTTAAATATA
1 AAATGTTTAAATATA
1480747 CAATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAATGTTTAAATATA
Found at i:1483267 original size:37 final size:36
Alignment explanation
Indices: 1483208--1483327 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
1483198 ATCCCATTAT
* *
1483208 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
1483244 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1483280 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1483315 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
1483328 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:1483283 original size:21 final size:21
Alignment explanation
Indices: 1483259--1483319 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1483249 TTCAAAGAAA
1483259 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1483280 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1483294 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1483315 CATTT
1 CATTT
1483320 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1483336 original size:35 final size:36
Alignment explanation
Indices: 1483210--1483354 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
1483200 CCCATTATCA
*
1483210 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
1483245 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
1483282 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
1483318 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
1483352 TTT
1 TTT
1483355 AATAATTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:1487404 original size:12 final size:12
Alignment explanation
Indices: 1487384--1487413 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1487374 AATTTTCTAT
*
1487384 TAACATGAATAG
1 TAACCTGAATAG
1487396 TAACCTGAATAG
1 TAACCTGAATAG
1487408 TAACCT
1 TAACCT
1487414 CGCAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (12 bp):
TAACCTGAATAG
Found at i:1487871 original size:21 final size:21
Alignment explanation
Indices: 1487847--1487907 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1487837 TTCAAAGAAA
1487847 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1487868 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1487882 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1487903 CATTT
1 CATTT
1487908 TTTTCAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1487881 original size:35 final size:35
Alignment explanation
Indices: 1487799--1487908 Score: 168
Period size: 35 Copynumber: 3.1 Consensus size: 35
1487789 CCCATTTCAT
* * *
1487799 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
1487834 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1487870 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1487905 TTTT
1 TTTT
1487909 TTTCAAAGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 39 0.56
36 11 0.16
37 20 0.29
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:1493630 original size:43 final size:42
Alignment explanation
Indices: 1493542--1493637 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 42
1493532 GTTACAATGG
* *
1493542 AAAATATTATGAAAAATATAATATTTTAAGTTGCATCCAATT
1 AAAATATTATGAAAAATACAATATTTTAAGTTGCATCCAACT
* * * *
1493584 AAAATATTTATGAATAATGCAATATTTTAAGTTGCGTCTAACT
1 AAAATA-TTATGAAAAATACAATATTTTAAGTTGCATCCAACT
*
1493627 AAAATGTTATG
1 AAAATATTATG
1493638 TTTTTGATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 11 0.24
43 35 0.76
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (42 bp):
AAAATATTATGAAAAATACAATATTTTAAGTTGCATCCAACT
Found at i:1494685 original size:47 final size:47
Alignment explanation
Indices: 1494634--1494771 Score: 249
Period size: 47 Copynumber: 2.9 Consensus size: 47
1494624 AACTCTCTCT
*
1494634 AAAAGAGGGATTACAAATTTAGCAAATAAAAGAAAACTTCACAATCC
1 AAAAGAGGGATTACAAATCTAGCAAATAAAAGAAAACTTCACAATCC
1494681 AAAAGAGGGATTACAAATCTAGCAAATAAAAGAAAACTTCACAATCC
1 AAAAGAGGGATTACAAATCTAGCAAATAAAAGAAAACTTCACAATCC
* *
1494728 AAAAGAGGGATTATAAATCTAGAAAATAAAAGAAAACTTCACAA
1 AAAAGAGGGATTACAAATCTAGCAAATAAAAGAAAACTTCACAA
1494772 AGGCAAATGT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 88 1.00
ACGTcount: A:0.55, C:0.14, G:0.13, T:0.18
Consensus pattern (47 bp):
AAAAGAGGGATTACAAATCTAGCAAATAAAAGAAAACTTCACAATCC
Found at i:1498196 original size:22 final size:22
Alignment explanation
Indices: 1498168--1498210 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1498158 ACTATATTGT
* *
1498168 ATGAACATTACCGTGAACAGTA
1 ATGAACAATACCATGAACAGTA
*
1498190 ATGAACAATACTATGAACAGT
1 ATGAACAATACCATGAACAGT
1498211 GCTACAGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (22 bp):
ATGAACAATACCATGAACAGTA
Found at i:1498240 original size:21 final size:21
Alignment explanation
Indices: 1498210--1498250 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1498200 CTATGAACAG
* *
1498210 TGCTACAGTGTACCGATGCAT
1 TGCTACAGTGCACCAATGCAT
*
1498231 TGCTATAGTGCACCAATGCA
1 TGCTACAGTGCACCAATGCA
1498251 CAAAATTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGCACCAATGCAT
Found at i:1498928 original size:48 final size:49
Alignment explanation
Indices: 1498829--1498930 Score: 118
Period size: 49 Copynumber: 2.1 Consensus size: 49
1498819 CAACTCGTAT
* * * *
1498829 AAATTTTCACCGAAGTGCCACGTAGAATTTGTCATAAAGGACCGCGTAG
1 AAATTTGCACCGAAGTGCCACATAGAATTTGTCATAAAGGACCACATAG
* * *
1498878 AAATTTGCACCGTAGTGCCATATAGGA-TTGTCCAT-AAGGACCACATAG
1 AAATTTGCACCGAAGTGCCACATAGAATTTGT-CATAAAGGACCACATAG
1498926 AAATT
1 AAATT
1498931 CCTTAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
48 20 0.44
49 25 0.56
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (49 bp):
AAATTTGCACCGAAGTGCCACATAGAATTTGTCATAAAGGACCACATAG
Found at i:1499174 original size:30 final size:31
Alignment explanation
Indices: 1499140--1499203 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1499130 TTATATCGCG
1499140 TAGACATATCA-TTTACATACCTTTATCACA
1 TAGACATATCATTTTACATACCTTTATCACA
*
1499170 TAGACATATCATTTTCCATACCTTTATCACA
1 TAGACATATCATTTTACATACCTTTATCACA
1499201 TAG
1 TAG
1499204 CTCATATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (31 bp):
TAGACATATCATTTTACATACCTTTATCACA
Found at i:1505328 original size:21 final size:21
Alignment explanation
Indices: 1505302--1505341 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1505292 TAATGAACAG
*
1505302 TGCTACAGTGTACCGATGCAT
1 TGCTACAGTGCACCGATGCAT
*
1505323 TGCTACAGTGCATCGATGC
1 TGCTACAGTGCACCGATGC
1505342 TCAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (21 bp):
TGCTACAGTGCACCGATGCAT
Found at i:1505944 original size:25 final size:25
Alignment explanation
Indices: 1505916--1505989 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
1505906 CACCACAACT
1505916 CGTATAAATTTGCACCGAAGTGCCA
1 CGTATAAATTTGCACCGAAGTGCCA
* *
1505941 CGTA-GAATTTGTC-CCGAA-TGAC-
1 CGTATAAATTTG-CACCGAAGTGCCA
*
1505963 CGTATAGAAATTTGCACCGTAGTGCCA
1 CGTAT--AAATTTGCACCGAAGTGCCA
1505990 TATAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
22 4 0.11
23 3 0.08
24 12 0.32
25 15 0.41
26 3 0.08
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (25 bp):
CGTATAAATTTGCACCGAAGTGCCA
Done.