Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002126.1 Hibiscus syriacus cultivar Beakdansim tig00004355_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: 1482737
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1355851 original size:20 final size:20
Alignment explanation
Indices: 1355826--1355875 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1355816 GATGCAATCA
1355826 GTATCGATA-T-TGAGAGAAAG
1 GTATCGATACTATGAG-G-AAG
1355846 GTATCGATACTATGAGGAAG
1 GTATCGATACTATGAGGAAG
1355866 GTATCGATAC
1 GTATCGATAC
1355876 CATTGATCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 22 0.79
21 2 0.07
22 4 0.14
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGATACTATGAGGAAG
Found at i:1355951 original size:22 final size:21
Alignment explanation
Indices: 1355914--1355970 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
1355904 CGGTACCGTA
1355914 ATAGAGTATC-AGTACCATAGT
1 ATAGAGTATCGA-TACCATAGT
*
1355935 ATAGTAGTATCGATACCATGGT
1 ATAG-AGTATCGATACCATAGT
*
1355957 AT-GGGTATCGATAC
1 ATAGAGTATCGATAC
1355971 TAATGAGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.31
21 5 0.16
22 16 0.50
23 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (21 bp):
ATAGAGTATCGATACCATAGT
Found at i:1356549 original size:108 final size:107
Alignment explanation
Indices: 1356342--1356668 Score: 404
Period size: 108 Copynumber: 3.0 Consensus size: 107
1356332 TTCCGTACAG
* * * *
1356342 GCACTAAGTGTGCAACCCACTGAATTCATCATATGTTGATAACATATGAACAATCATTTCACCAC
1 GCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGAT--GA-AT-AAC---CGTTTCAACAC
*
1356407 CAAGTGTGCAACCCATGAAATTCATCATATGTTGATGAACAACCGTTTC
59 TAAGTGTGCAACCCATGAAATTCATCATATGTTGATGAACAACCGTTTC
*
1356456 AGCACTAAGTGTGCAACCCACGGAATTAATCATATGTTGATGAATAACCGTTTCAACACTAAGTG
1 -GCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAATAACCGTTTCAACACTAAGTG
*
1356521 TGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTTC
65 TGCAACCCATGAAATTCATCATATGTTGATGAACAACCGTTTC
* * * * *
1356564 GACACTAAGTGTGCAACCCACGAAATTCATCATATGTTAATGAACAACCG-TACAAGCACTATGT
1 G-CACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAATAACCGTTTCAA-CACTAAGT
* * * * *
1356628 GTGCAACTCATGGAATTCATTATAGGTTGATGAACTACCGT
64 GTGCAACCCATGAAATTCATCATATGTTGATGAACAACCGT
1356669 ATAGGAACTA
Statistics
Matches: 191, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
107 5 0.03
108 142 0.74
111 3 0.02
112 2 0.01
113 1 0.01
115 38 0.20
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (107 bp):
GCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAATAACCGTTTCAACACTAAGTGT
GCAACCCATGAAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:1356599 original size:162 final size:163
Alignment explanation
Indices: 1356343--1356661 Score: 421
Period size: 162 Copynumber: 1.9 Consensus size: 163
1356333 TCCGTACAGG
*
1356343 CACTAAGTGTGCAACCCACTGAATTCATCATATGTTGATAACATATGAACAATCATTTCACCACC
1 CACTAAGTGTGCAACCCACTGAATTCATCATATGTTG-----A-ATGAACAACCATTTCACCACC
* * *
1356408 AAGTGTGCAACCCATGAAATTCATCATATGTTGATGAACAACCGTTTC-AGCACTAAGTGTGCAA
60 AAGTGTGCAACCCACGAAATTCATCATATGTTAATGAACAACCG-TACAAGCACTAAGTGTGCAA
*
1356472 CCCACGGAATTAATCATATGTTGATGAATAACCGTTTCAA
124 CCCACGGAATTAATCATAGGTTGATGAATAACCGTTTCAA
* *
1356512 CACTAAGTGTGCAACCCAC-GAAATTCATCATATGTTG-ATGAACAACCGTTTCGA-CACTAAGT
1 CACTAAGTGTGCAACCCACTG-AATTCATCATATGTTGAATGAACAACCATTTC-ACCACCAAGT
* * *
1356574 GTGCAACCCACGAAATTCATCATATGTTAATGAACAACCGTACAAGCACTATGTGTGCAACTCAT
64 GTGCAACCCACGAAATTCATCATATGTTAATGAACAACCGTACAAGCACTAAGTGTGCAACCCAC
* *
1356639 GGAATTCATTATAGGTTGATGAA
129 GGAATTAATCATAGGTTGATGAA
1356662 CTACCGTATA
Statistics
Matches: 135, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
161 2 0.01
162 96 0.71
163 1 0.01
168 1 0.01
169 35 0.26
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (163 bp):
CACTAAGTGTGCAACCCACTGAATTCATCATATGTTGAATGAACAACCATTTCACCACCAAGTGT
GCAACCCACGAAATTCATCATATGTTAATGAACAACCGTACAAGCACTAAGTGTGCAACCCACGG
AATTAATCATAGGTTGATGAATAACCGTTTCAA
Found at i:1356669 original size:54 final size:54
Alignment explanation
Indices: 1356387--1356668 Score: 377
Period size: 54 Copynumber: 5.2 Consensus size: 54
1356377 TTGATAACAT
* * * * *
1356387 ATGAACAATCATTTCACCACCAAGTGTGCAACCCATGAAATTCATCATATGTTG
1 ATGAACAACCGTTTCAACACTAAGTGTGCAACCCACGAAATTCATCATATGTTG
* * *
1356441 ATGAACAACCGTTTCAGCACTAAGTGTGCAACCCACGGAATTAATCATATGTTG
1 ATGAACAACCGTTTCAACACTAAGTGTGCAACCCACGAAATTCATCATATGTTG
*
1356495 ATGAATAACCGTTTCAACACTAAGTGTGCAACCCACGAAATTCATCATATGTTG
1 ATGAACAACCGTTTCAACACTAAGTGTGCAACCCACGAAATTCATCATATGTTG
* *
1356549 ATGAACAACCGTTTCGACACTAAGTGTGCAACCCACGAAATTCATCATATGTTA
1 ATGAACAACCGTTTCAACACTAAGTGTGCAACCCACGAAATTCATCATATGTTG
* * * * * * *
1356603 ATGAACAACCG-TACAAGCACTATGTGTGCAACTCATGGAATTCATTATAGGTTG
1 ATGAACAACCGTTTCAA-CACTAAGTGTGCAACCCACGAAATTCATCATATGTTG
*
1356657 ATGAACTACCGT
1 ATGAACAACCGT
1356669 ATAGGAACTA
Statistics
Matches: 202, Mismatches: 24, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
53 3 0.01
54 199 0.99
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (54 bp):
ATGAACAACCGTTTCAACACTAAGTGTGCAACCCACGAAATTCATCATATGTTG
Found at i:1356686 original size:162 final size:162
Alignment explanation
Indices: 1356310--1356686 Score: 406
Period size: 162 Copynumber: 2.3 Consensus size: 162
1356300 AAAACTAAGA
* * * *
1356310 AATTCATAATAAGTTTATGAATTTCCGTACAGGCACTAAGTGTGCAACCCACTGAATTCATCATA
1 AATTCATAATAAGTTGATGAA-TACCGTATAGGAACTAAGTGTGCAACCCACTGAATTCATCATA
* *
1356375 TGTTGATAACATATGAACAATCATTTCACCACCAAGTGTGCAACCCATGAAATTCATCATATGTT
65 TGTTG-----A-ATGAACAACCATTTCACCACCAAGTGTGCAACCCACGAAATTCATCATATGTT
* *
1356440 GATGAACAACCGTTTCAGCACTAAGTGTGCAACCCACGG
124 AATGAACAACCGTTACAGCACTAAGTGTGCAACCCACGG
* * * *
1356479 AATTAATCATATGTTGATGAATAACCGTTTCA--ACACTAAGTGTGCAACCCAC-GAAATTCATC
1 AATTCATAATAAGTTGATGAAT-ACCGTAT-AGGA-ACTAAGTGTGCAACCCACTG-AATTCATC
* *
1356541 ATATGTTG-ATGAACAACCGTTTCGA-CACTAAGTGTGCAACCCACGAAATTCATCATATGTTAA
62 ATATGTTGAATGAACAACCATTTC-ACCACCAAGTGTGCAACCCACGAAATTCATCATATGTTAA
* * *
1356604 TGAACAACCG-TACAAGCACTATGTGTGCAACTCATGG
126 TGAACAACCGTTAC-AGCACTAAGTGTGCAACCCACGG
* * *
1356641 AATTCATTATAGGTTGATGAACTACCGTATAGGAACTACGTGTGCA
1 AATTCATAATAAGTTGATGAA-TACCGTATAGGAACTAAGTGTGCA
1356687 TCTTAATAAA
Statistics
Matches: 177, Mismatches: 22, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
161 3 0.02
162 113 0.64
163 3 0.02
168 2 0.01
169 55 0.31
170 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (162 bp):
AATTCATAATAAGTTGATGAATACCGTATAGGAACTAAGTGTGCAACCCACTGAATTCATCATAT
GTTGAATGAACAACCATTTCACCACCAAGTGTGCAACCCACGAAATTCATCATATGTTAATGAAC
AACCGTTACAGCACTAAGTGTGCAACCCACGG
Found at i:1357036 original size:21 final size:21
Alignment explanation
Indices: 1356967--1357036 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
1356957 ATTTGACATA
* *
1356967 AAAGGCATGAAAAGATGCCAT
1 AAAGACATGAAATGATGCCAT
* *
1356988 AAATGAAAATGCATAATGGTG-CATT
1 AAA-G-ACATG-A-AATGATGCCA-T
1357013 AAAGACATGAAATGATGCCAT
1 AAAGACATGAAATGATGCCAT
1357034 AAA
1 AAA
1357037 TGAAATGCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
21 13 0.35
22 4 0.11
23 7 0.19
24 4 0.11
25 9 0.24
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (21 bp):
AAAGACATGAAATGATGCCAT
Found at i:1357068 original size:45 final size:46
Alignment explanation
Indices: 1356967--1357056 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
1356957 ATTTGACATA
*
1356967 AAAGGCATGAAAAGATGCCATAAATGAAAATGCATAATGGTGCATT
1 AAAGACATGAAAAGATGCCATAAATGAAAATGCATAATGGTGCATT
*
1357013 AAAGACATGAAATGATGCCATAAATG-AAATGCATAATGGTGCAT
1 AAAGACATGAAAAGATGCCATAAATGAAAATGCATAATGGTGCAT
1357057 AACAGAGATG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 18 0.43
46 24 0.57
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (46 bp):
AAAGACATGAAAAGATGCCATAAATGAAAATGCATAATGGTGCATT
Found at i:1357079 original size:45 final size:46
Alignment explanation
Indices: 1356967--1357083 Score: 132
Period size: 45 Copynumber: 2.6 Consensus size: 46
1356957 ATTTGACATA
* * *
1356967 AAAGGCATGAAAAGATGCCATAAATGAAAATGCATAATGGTGCATT
1 AAAGACATGAAAGGATACCATAAATGAAAATGCATAATGGTGCATT
* *
1357013 AAAGACATGAAATGATGCCATAAATG-AAATGCATAATGGTGCA-T
1 AAAGACATGAAAGGATACCATAAATGAAAATGCATAATGGTGCATT
* *
1357057 AACAGAGATGAAGGGCA-ACCATAAATG
1 AA-AGACATGAAAGG-ATACCATAAATG
1357084 TGAAATTGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 3 0.05
45 35 0.56
46 25 0.40
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (46 bp):
AAAGACATGAAAGGATACCATAAATGAAAATGCATAATGGTGCATT
Found at i:1358911 original size:43 final size:46
Alignment explanation
Indices: 1358807--1358915 Score: 161
Period size: 47 Copynumber: 2.4 Consensus size: 46
1358797 ATTTATCCCG
1358807 TAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTTCA
1 TAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTT-AATTTCA
* * *
1358854 TAAGCTCGTAAGCTTATTTTATCAATATACTTGCCA-TT-A-TTCA
1 TAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAATTTCA
1358897 TAAGCTCGTAAGCTTATTT
1 TAAGCTCGTAAGCTTATTT
1358916 GCATACTTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
43 23 0.39
44 1 0.02
46 2 0.03
47 33 0.56
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.40
Consensus pattern (46 bp):
TAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAATTTCA
Found at i:1358923 original size:38 final size:41
Alignment explanation
Indices: 1358807--1358929 Score: 126
Period size: 47 Copynumber: 2.9 Consensus size: 41
1358797 ATTTATCCCG
*
1358807 TAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTTCA
1 TAAGCTCGTAAGCTTATTTTAGC--AATACTTACCA-TT--A-TTCA
* *
1358854 TAAGCTCGTAAGCTTATTTTATCAATATACTTGCCATTATTCA
1 TAAGCTCGTAAGCTTATTTTAGC-A-ATACTTACCATTATTCA
1358897 TAAGCTCGTAAGCTTA-TTT-GC-ATACTTACCATT
1 TAAGCTCGTAAGCTTATTTTAGCAATACTTACCATT
1358930 TATTAACCAT
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
38 11 0.15
41 1 0.01
42 3 0.04
43 20 0.28
44 1 0.01
46 4 0.06
47 31 0.44
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.40
Consensus pattern (41 bp):
TAAGCTCGTAAGCTTATTTTAGCAATACTTACCATTATTCA
Found at i:1360299 original size:13 final size:13
Alignment explanation
Indices: 1360281--1360316 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1360271 TAGGTTCTTC
1360281 ATCAATTCTTACA
1 ATCAATTCTTACA
1360294 ATCAATTCTTACA
1 ATCAATTCTTACA
*
1360307 ATTAATTCTT
1 ATCAATTCTT
1360317 TAAAATCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.44
Consensus pattern (13 bp):
ATCAATTCTTACA
Found at i:1365827 original size:12 final size:12
Alignment explanation
Indices: 1365810--1365845 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1365800 TTATTGTTCA
1365810 TGCTACAGTAAC
1 TGCTACAGTAAC
1365822 TGCTACAGT-AC
1 TGCTACAGTAAC
*
1365833 TGTTACAGTAAC
1 TGCTACAGTAAC
1365845 T
1 T
1365846 TCCAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (12 bp):
TGCTACAGTAAC
Found at i:1367329 original size:23 final size:23
Alignment explanation
Indices: 1367293--1367356 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1367283 CAGCTCATAT
*
1367293 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCTAAGTGCCACGTAG
* * *
1367316 AATTGCACCTAAGTACCGCGTAG
1 AAATGCACCTAAGTGCCACGTAG
1367339 AAATGCA-CTGAAGTGCCA
1 AAATGCACCT-AAGTGCCA
1367357 TATAAGATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
AAATGCACCTAAGTGCCACGTAG
Found at i:1367619 original size:21 final size:21
Alignment explanation
Indices: 1367594--1367648 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1367584 TATTACCTAG
1367594 GCACGTAGTCTCATAGTTTTT
1 GCACGTAGTCTCATAGTTTTT
1367615 GCACGTAGTCTCATAGTTTTT
1 GCACGTAGTCTCATAGTTTTT
*
1367636 GCACATAG-CTCAT
1 GCACGTAGTCTCAT
1367649 TATCACATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
GCACGTAGTCTCATAGTTTTT
Found at i:1367863 original size:41 final size:41
Alignment explanation
Indices: 1367790--1367872 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 41
1367780 AATTTATCAT
1367790 TTATTCACATAAATCAATTACTCATAGCATTTC-CTATAGAA
1 TTATTCACATAAATCAATTACTCATAGCATTTCAC-ATAGAA
* *
1367831 TTATTCACATAGAA-C-ATATACTTATAGTATTTCACATAGAA
1 TTATTCACATA-AATCAAT-TACTCATAGCATTTCACATAGAA
1367872 T
1 T
1367873 ATACATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
40 2 0.05
41 32 0.86
42 3 0.08
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (41 bp):
TTATTCACATAAATCAATTACTCATAGCATTTCACATAGAA
Found at i:1372386 original size:2 final size:2
Alignment explanation
Indices: 1372379--1372434 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1372369 GATGTCAGAA
1372379 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
1372421 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1372435 CTTTTATGGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1375706 original size:54 final size:53
Alignment explanation
Indices: 1375646--1376091 Score: 518
Period size: 54 Copynumber: 8.3 Consensus size: 53
1375636 TTTTTGTACA
* *
1375646 GACACTAAGGGTGCAACCCACAGAATTCATCATATGTTAATGAACAACCGTTTC
1 GACACTAAGTGTGCAACCCAC-GAATTCATCATATGTTGATGAACAACCGTTTC
* * * *
1375700 GGCACTAAGTATTCAACCCACAGAATTCATCATATGTTGATGAACAACCGTTTT
1 GACACTAAGTGTGCAACCCAC-GAATTCATCATATGTTGATGAACAACCGTTTC
* * * * *
1375754 GGCACTAAGTTTGCAACCCACGAAATTCATCATATGTTGATGAATAGCAGTTTC
1 GACACTAAGTGTGCAACCCACG-AATTCATCATATGTTGATGAACAACCGTTTC
*
1375808 GACACTAAGTGCGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTTTC
1 GACACTAAGTGTGCAACCCAC-GAATTCATCATATGTTGATGAACAACCGTTTC
* * *
1375862 GGCACTAAGTGTGCAACCCACGCAATTCATTATATGTTGATGAACAA-CATTTC
1 GACACTAAGTGTGCAACCCACG-AATTCATCATATGTTGATGAACAACCGTTTC
* * *
1375915 GACATTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAATCGTTTC
1 GACACTAAGTGTGCAACCCACG-AATTCATCATATGTTGATGAACAACCGTTTC
* * *
1375969 GACATTAAGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCG-TAC
1 GACACTAAGTGTGCAACCCAC-GAATTCATCATATGTTGATGAACAACCGTTTC
* * * * * * * *
1376022 AAGCACTATGTGTGCAACTCATGAAATTCATCATAGGTTGATGAACGACCGTATA
1 GA-CACTAAGTGTGCAACCCACG-AATTCATCATATGTTGATGAACAACCGTTTC
* *
1376077 GGCACTACGTGTGCA
1 GACACTAAGTGTGCA
1376092 TCTTAATAAA
Statistics
Matches: 340, Mismatches: 44, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
53 53 0.16
54 285 0.84
55 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (53 bp):
GACACTAAGTGTGCAACCCACGAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:1376514 original size:45 final size:46
Alignment explanation
Indices: 1376371--1376533 Score: 233
Period size: 46 Copynumber: 3.6 Consensus size: 46
1376361 ATTTGACATA
1376371 AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATT
1 AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATT
* * * *
1376417 AAAGACATGAACA-AATGTCATAAATGAAAATACATAACGGTGCATT
1 AAAGGCATGAA-AGGATGCCATAAATGAAAATGCATAACGGTGCATT
*
1376463 AAAGGCATGAAAGGATGCCATAAATG-AAATGCATAATGGTGCA-T
1 AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATT
*
1376507 AACAGGCATGAAGGGATGCCATAAATG
1 AA-AGGCATGAAAGGATGCCATAAATG
1376534 TGAAATTGAT
Statistics
Matches: 104, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
44 3 0.03
45 39 0.38
46 61 0.59
47 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.20
Consensus pattern (46 bp):
AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATT
Found at i:1377931 original size:3 final size:3
Alignment explanation
Indices: 1377923--1377979 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
1377913 CCCTCAACAC
1377923 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
1377969 AAT AAT AAT AA
1 AAT AAT AAT AA
1377980 ATTATGTGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1389239 original size:17 final size:18
Alignment explanation
Indices: 1389214--1389259 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1389204 AAAAAAAATT
1389214 ATAATAGTAAAAT-ATTAA
1 ATAA-AGTAAAATGATTAA
*
1389232 ATAAAGTAAAATGCTTAA
1 ATAAAGTAAAATGATTAA
*
1389250 ATAAATTAAA
1 ATAAAGTAAA
1389260 TACATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (18 bp):
ATAAAGTAAAATGATTAA
Found at i:1389833 original size:15 final size:15
Alignment explanation
Indices: 1389809--1389881 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
1389799 TTGGTTTTTC
1389809 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
1389824 GGAATTTGAATTACT
1 GGAAAATGAATTACT
*
1389839 GGAAAATAAATTACT
1 GGAAAATGAATTACT
***
1389854 GGAGTTTGAATT-CT
1 GGAAAATGAATTACT
1389868 GGAAAATGAATTAC
1 GGAAAATGAATTAC
1389882 ATTTCTGGAA
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
14 11 0.24
15 34 0.76
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:1389879 original size:29 final size:30
Alignment explanation
Indices: 1389809--1389881 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
1389799 TTGGTTTTTC
1389809 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATTACT
* *
1389839 GGAAAATAAATTACTGGAGTTTGAATT-CT
1 GGAAAATGAATTACTGGAATTTGAATTACT
1389868 GGAAAATGAATTAC
1 GGAAAATGAATTAC
1389882 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTGGAATTTGAATTACT
Found at i:1389922 original size:14 final size:14
Alignment explanation
Indices: 1389883--1389923 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1389873 ATGAATTACA
* *
1389883 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
1389897 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
1389911 TTTCCGTAAAATG
1 TTTCCGGAAAATG
1389924 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:1390202 original size:11 final size:11
Alignment explanation
Indices: 1390186--1390223 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1390176 TTAAATATCT
1390186 TTATTAAAATA
1 TTATTAAAATA
1390197 TTATTAAAATA
1 TTATTAAAATA
*
1390208 -TATAAATAATA
1 TTATTAA-AATA
1390219 TTATT
1 TTATT
1390224 CATTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 5 0.22
11 15 0.65
12 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:1390238 original size:19 final size:20
Alignment explanation
Indices: 1390186--1390238 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1390176 TTAAATATCT
1390186 TTATTAAA-ATATTATTAAA
1 TTATTAAATATATTATTAAA
* *
1390205 ATATATAAATAATATTATT-CA
1 TTAT-TAAAT-ATATTATTAAA
1390226 TTATTAAATATAT
1 TTATTAAATATAT
1390239 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 4 0.14
22 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTAAATATATTATTAAA
Found at i:1390252 original size:24 final size:28
Alignment explanation
Indices: 1390195--1390253 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1390185 TTTATTAAAA
1390195 TATTATTAAAATATATAAATAATATTATT
1 TATTATTAAAATATATAAAT-ATATTATT
*
1390224 CATTATT-AAATATATAAAT-T-TT-TT
1 TATTATTAAAATATATAAATATATTATT
1390248 TATTAT
1 TATTAT
1390254 ATATTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 7 0.25
25 2 0.07
26 1 0.04
28 12 0.43
29 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TATTATTAAAATATATAAATATATTATT
Found at i:1390321 original size:15 final size:16
Alignment explanation
Indices: 1390283--1390359 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 16
1390273 ATAATATCTT
1390283 ATATTATTATAATATA
1 ATATTATTATAATATA
*
1390299 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
1390316 ATATTA--AAAATATA
1 ATATTATTATAATATA
1390330 ATATTA-TATTAATA-A
1 ATATTATTA-TAATATA
*
1390345 ATATTAATA-AATATA
1 ATATTATTATAATATA
1390360 TTTTAAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.30
15 13 0.26
16 8 0.16
17 8 0.16
18 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:1390330 original size:14 final size:15
Alignment explanation
Indices: 1390311--1390359 Score: 66
Period size: 14 Copynumber: 3.3 Consensus size: 15
1390301 TGATTATTTT
1390311 ATATAATATTAA-AA
1 ATATAATATTAATAA
*
1390325 ATATAATATTATATTA
1 ATATAATATTA-ATAA
1390341 ATA-AATATTAATAA
1 ATATAATATTAATAA
1390355 ATATA
1 ATATA
1390360 TTTTAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 17 0.57
15 9 0.30
16 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATAATATTAATAA
Found at i:1390347 original size:29 final size:32
Alignment explanation
Indices: 1390283--1390359 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 32
1390273 ATAATATCTT
* *
1390283 ATATTATTATAATATAATTGATTATTTTATATA
1 ATATTAATA-AATATAATTGATTATTTAATATA
1390316 ATATTAA-AAATATAA-T-ATTATATTAATA-A
1 ATATTAATAAATATAATTGATTAT-TTAATATA
1390345 ATATTAATAAATATA
1 ATATTAATAAATATA
1390360 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 13 0.32
30 13 0.32
31 7 0.17
32 1 0.03
33 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
ATATTAATAAATATAATTGATTATTTAATATA
Found at i:1390348 original size:10 final size:10
Alignment explanation
Indices: 1390315--1390358 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
1390305 TATTTTATAT
1390315 AATATTAA-A
1 AATATTAATA
1390324 AATA-TAATA
1 AATATTAATA
*
1390333 TTATATTAATA
1 -AATATTAATA
1390344 AATATTAATA
1 AATATTAATA
1390354 AATAT
1 AATAT
1390359 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 3 0.10
9 5 0.17
10 17 0.57
11 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:1390617 original size:42 final size:42
Alignment explanation
Indices: 1390558--1390718 Score: 277
Period size: 42 Copynumber: 3.8 Consensus size: 42
1390548 ATGAATTACG
1390558 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
**
1390600 TTCCGGAAAACGAATTACGTGAAACAAACACCAGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
1390642 TTCCGGAAAACGAATTACGTGAAACAAACAGGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
1390684 TTCCGGAAAACGAATTACATGAAAGAAACACGGGA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGA
1390719 TTTTTGGGAA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 111 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1400687 original size:22 final size:22
Alignment explanation
Indices: 1400656--1400714 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1400646 TTGGTGCAGA
*
1400656 GGGAATCGATATCCCCTTGAAG
1 GGGAACCGATATCCCCTTGAAG
* *
1400678 TGGAACCGAT-TCCCCTTGTAG
1 GGGAACCGATATCCCCTTGAAG
*
1400699 GGGAACCGATACCCCC
1 GGGAACCGATATCCCC
1400715 ATGGGGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATATCCCCTTGAAG
Found at i:1402631 original size:17 final size:16
Alignment explanation
Indices: 1402602--1402667 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
1402592 CATTTTGGAT
*
1402602 ATTTTGGAATGTTTGA
1 ATTTTGGATTGTTTGA
1402618 ATTTGTGGATTGTTTG-
1 ATTT-TGGATTGTTTGA
* *
1402634 ACTTTGAATTTGTTTGA
1 ATTTTGGA-TTGTTTGA
1402651 ATTTATGGA-TGTTTGA
1 ATTT-TGGATTGTTTGA
1402667 A
1 A
1402668 CTTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.07
16 22 0.54
17 13 0.32
18 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (16 bp):
ATTTTGGATTGTTTGA
Found at i:1402942 original size:25 final size:25
Alignment explanation
Indices: 1402911--1402991 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 25
1402901 TAACAAAAAG
1402911 GGGGAGAAATGTTAAAGTGTTTAAA
1 GGGGAGAAATGTTAAAGTGTTTAAA
** *
1402936 GGGGAGATGTGTT--AGAG--TAAA
1 GGGGAGAAATGTTAAAGTGTTTAAA
1402957 -GGG-G--ATGTTAAAGTGTTTAAA
1 GGGGAGAAATGTTAAAGTGTTTAAA
*
1402978 GGGGAGAAGTGTTA
1 GGGGAGAAATGTTA
1402992 GAGTAAAGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
17 4 0.10
19 4 0.10
20 3 0.07
21 8 0.19
22 3 0.07
23 4 0.10
25 16 0.38
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (25 bp):
GGGGAGAAATGTTAAAGTGTTTAAA
Found at i:1402956 original size:21 final size:21
Alignment explanation
Indices: 1402932--1403000 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1402922 TTAAAGTGTT
1402932 TAAAGGGGAGATGTGTTAGAG
1 TAAAGGGGAGATGTGTTAGAG
* *
1402953 TAAA-GGG-GATGT-TAAAGTG
1 TAAAGGGGAGATGTGT-TAGAG
*
1402972 TTTAAAGGGGAGAAGTGTTAGAG
1 --TAAAGGGGAGATGTGTTAGAG
1402995 TAAAGG
1 TAAAGG
1403001 AGAGTAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
18 1 0.03
19 8 0.22
20 3 0.08
21 14 0.38
22 3 0.08
23 7 0.19
24 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.25
Consensus pattern (21 bp):
TAAAGGGGAGATGTGTTAGAG
Found at i:1402974 original size:42 final size:42
Alignment explanation
Indices: 1402919--1403000 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
1402909 AGGGGGAGAA
*
1402919 ATGTTAAAGTGTTTAAAGGGGAGATGTGTTAGAGTAAAGGGG
1 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAAGGGG
1402961 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAAGG
1 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAAGG
1403001 AGAGTAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (42 bp):
ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAAGGGG
Found at i:1402989 original size:17 final size:17
Alignment explanation
Indices: 1402925--1402990 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 17
1402915 AGAAATGTTA
1402925 AAGTGTTTAAAGGGGAG
1 AAGTGTTTAAAGGGGAG
*
1402942 ATGTGTTAGAGTAAAGGGGATG
1 AAGTGTT----TAAAGGGGA-G
1402964 TTAAAGTGTTTAAAGGGGAG
1 ---AAGTGTTTAAAGGGGAG
1402984 AAGTGTT
1 AAGTGTT
1402991 AGAGTAAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
17 13 0.33
20 1 0.03
21 18 0.46
22 1 0.03
25 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (17 bp):
AAGTGTTTAAAGGGGAG
Found at i:1407887 original size:20 final size:20
Alignment explanation
Indices: 1407844--1407892 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1407834 CTGTACTACC
* *
1407844 TGAATAGTACTGATACTGTA
1 TGAATAGTACCGATACTATA
*
1407864 TGAATAGTACCGATACTATG
1 TGAATAGTACCGATACTATA
*
1407884 TGAACAGTA
1 TGAATAGTA
1407893 ATGAACAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
TGAATAGTACCGATACTATA
Found at i:1412655 original size:20 final size:20
Alignment explanation
Indices: 1412630--1412667 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1412620 AAATCTTACT
*
1412630 GGAAAAGAATCTAACGCAGG
1 GGAAAAGAATCAAACGCAGG
*
1412650 GGAAAATAATCAAACGCA
1 GGAAAAGAATCAAACGCA
1412668 AAATAAGACG
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:0.50, C:0.16, G:0.24, T:0.11
Consensus pattern (20 bp):
GGAAAAGAATCAAACGCAGG
Found at i:1414073 original size:34 final size:34
Alignment explanation
Indices: 1414011--1414075 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
1414001 AATGGGTTTT
* *
1414011 GGTTCTAGTTAAGCTCGCTAAAAGCTAGGGATAA
1 GGTTCTAGTTAAGCCCGCTAAAAACTAGGGATAA
*
1414045 GGTTCTAGTTTAGCCCG-TGAAAAACTAGGGA
1 GGTTCTAGTTAAGCCCGCT-AAAAACTAGGGA
1414076 GTTGTAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 1 0.04
34 26 0.96
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (34 bp):
GGTTCTAGTTAAGCCCGCTAAAAACTAGGGATAA
Found at i:1421731 original size:12 final size:12
Alignment explanation
Indices: 1421698--1421731 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1421688 CGATTATTAT
1421698 CGGCCTGATACC
1 CGGCCTGATACC
*
1421710 CGTCCTGATACC
1 CGGCCTGATACC
*
1421722 CGGCCCGATA
1 CGGCCTGATA
1421732 AATATTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.41, G:0.24, T:0.18
Consensus pattern (12 bp):
CGGCCTGATACC
Found at i:1425289 original size:16 final size:15
Alignment explanation
Indices: 1425264--1425294 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1425254 ATTTTTATAA
1425264 TTATATTTAATTTAT
1 TTATATTTAATTTAT
1425279 TTATCATTTAATTTAT
1 TTAT-ATTTAATTTAT
1425295 ATAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTAATTTAT
Found at i:1425316 original size:17 final size:16
Alignment explanation
Indices: 1425294--1425359 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 16
1425284 ATTTAATTTA
1425294 TATAATATATTGAGTAC
1 TATAATAT-TTGAGTAC
* * *
1425311 TATAATATCTAATTA-
1 TATAATATTTGAGTAC
*
1425326 TATAATATGTTGAGTAA
1 TATAATAT-TTGAGTAC
1425343 TATAATAGTTTGAGTAC
1 TATAATA-TTTGAGTAC
1425360 ACAATCTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
15 8 0.21
16 8 0.21
17 22 0.56
18 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (16 bp):
TATAATATTTGAGTAC
Found at i:1436757 original size:21 final size:21
Alignment explanation
Indices: 1436731--1436776 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1436721 TACAATCTCA
* *
1436731 TCTTCTTTTTCCATTTCTTCT
1 TCTTCTTCTTCCATTTCTTCC
* *
1436752 TCTTCTTCTTCTATTTTTTCC
1 TCTTCTTCTTCCATTTCTTCC
1436773 TCTT
1 TCTT
1436777 TGAAGCTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.67
Consensus pattern (21 bp):
TCTTCTTCTTCCATTTCTTCC
Found at i:1439477 original size:13 final size:14
Alignment explanation
Indices: 1439445--1439492 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
1439435 GATCATATAA
*
1439445 TATGTGATAGAGAGC
1 TATGTGATA-AGAAC
1439460 TATGTGA-AAGAAC
1 TATGTGATAAGAAC
*
1439473 TATGTGATATGAA-
1 TATGTGATAAGAAC
1439486 TATGTGA
1 TATGTGA
1439493 ATGTGTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 18 0.60
14 5 0.17
15 7 0.23
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (14 bp):
TATGTGATAAGAAC
Found at i:1439604 original size:18 final size:18
Alignment explanation
Indices: 1439581--1439632 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
1439571 GGGTCTACGC
*
1439581 GGTCCTTTGAGACATAGT
1 GGTCCTTCGAGACATAGT
*
1439599 GGTCCTTCGGGACATAGT
1 GGTCCTTCGAGACATAGT
*
1439617 GGTCCTTCGGGACATA
1 GGTCCTTCGAGACATA
1439633 TGTGTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGAGACATAGT
Found at i:1441759 original size:2 final size:2
Alignment explanation
Indices: 1441752--1441788 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1441742 GCCAATTGAT
1441752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1441789 CTTAAGCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1442373 original size:18 final size:18
Alignment explanation
Indices: 1442327--1442378 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1442317 ATCCTCTGGT
1442327 TGTTCTTGTTCCTC-TGC
1 TGTTCTTGTTCCTCGTGC
*
1442344 TCGTGCTTGTTCCTCGTGC
1 T-GTTCTTGTTCCTCGTGC
* *
1442363 TGTTCTGGTTCATCGT
1 TGTTCTTGTTCCTCGT
1442379 CGGAGTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 1 0.03
18 24 0.83
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.23, T:0.48
Consensus pattern (18 bp):
TGTTCTTGTTCCTCGTGC
Found at i:1455028 original size:20 final size:20
Alignment explanation
Indices: 1455003--1455055 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1454993 AATGTACTTA
1455003 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
*
1455023 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGAT
* *
1455043 ATGCATCCATGCA
1 GTGCATCGATGCA
1455056 CGAAGGCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:1456245 original size:19 final size:20
Alignment explanation
Indices: 1456221--1456268 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
1456211 AATGATTTTC
1456221 TTTTGAAAACAAAAAT-AAA
1 TTTTGAAAACAAAAATGAAA
* *
1456240 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1456260 TTTTGAAAA
1 TTTTGAAAA
1456269 AAATTTAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1459018 original size:19 final size:20
Alignment explanation
Indices: 1458994--1459041 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1458984 AATGATTTTC
*
1458994 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1459013 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1459033 TTTTGAAAA
1 TTTTGAAAA
1459042 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1460469 original size:20 final size:20
Alignment explanation
Indices: 1460444--1460517 Score: 114
Period size: 20 Copynumber: 3.7 Consensus size: 20
1460434 AATACACTTA
1460444 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
1460464 GTGCATCGATGCATCCT-ACT
1 GTGCATCGATGCATCCTGA-T
*
1460484 GTGCATCGATGCATCTTGAT
1 GTGCATCGATGCATCCTGAT
*
1460504 GTGCATCCATGCAT
1 GTGCATCGATGCAT
1460518 GAAGGCTGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:1465812 original size:19 final size:19
Alignment explanation
Indices: 1465788--1465827 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1465778 ATATATTTTC
* *
1465788 TTTCATACTCCCTTACCCT
1 TTTCATACTACCTTACACT
*
1465807 TTTCATATTACCTTACACT
1 TTTCATACTACCTTACACT
1465826 TT
1 TT
1465828 CCTATCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTCATACTACCTTACACT
Found at i:1467781 original size:28 final size:28
Alignment explanation
Indices: 1467745--1467825 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
1467735 AAATGACCAC
* *
1467745 TATGTCCCGAATGACCACATAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
* * *
1467773 TATGGCCCGAAGGACCATGTAGAACATA
1 TATGTCCCGAAGGACCACGTAGAACACA
*
1467801 TATGTCTCGAAGGACCACGTAGAAC
1 TATGTCCCGAAGGACCACGTAGAAC
1467826 CCTCGACTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACGTAGAACACA
Found at i:1470187 original size:23 final size:23
Alignment explanation
Indices: 1470161--1470221 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1470151 CACCACAGCT
*
1470161 CATATAATTGCATCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
1470184 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
1470207 CGTAGAATTGCACCG
1 CATATAATTGCACCG
1470222 TAGCCATATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1470376 original size:103 final size:103
Alignment explanation
Indices: 1470261--1470682 Score: 785
Period size: 103 Copynumber: 4.1 Consensus size: 103
1470251 TAATGTCCAT
* * *
1470261 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1470326 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1470364 AAAGACCACATATCATTCTTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1470429 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1470467 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1470532 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1470570 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1470635 GACTTCACACATGTTCCAAAGAAT--ATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1470671 AAGGACCACATA
1 AAGGACCACATA
1470683 GACCCTCGAC
Statistics
Matches: 312, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
101 24 0.08
103 288 0.92
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1476207 original size:23 final size:23
Alignment explanation
Indices: 1476181--1476264 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
1476171 CACATATAAA
1476181 TGCACCGGAGTGCCGCGTAGAAT
1 TGCACCGGAGTGCCGCGTAGAAT
* * *** *
1476204 TGCACCGTATTGCCATATAATAAT
1 TGCACCGGAGTGCCGCGT-AGAAT
**
1476228 TGCACTAGAGTGCCGCGTAGAAT
1 TGCACCGGAGTGCCGCGTAGAAT
*
1476251 TGCACCGTAGTGCC
1 TGCACCGGAGTGCC
1476265 ATATAATAAT
Statistics
Matches: 43, Mismatches: 17, Indels: 2
0.69 0.27 0.03
Matches are distributed among these distances:
23 28 0.65
24 15 0.35
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (23 bp):
TGCACCGGAGTGCCGCGTAGAAT
Found at i:1476415 original size:103 final size:103
Alignment explanation
Indices: 1476284--1476704 Score: 754
Period size: 103 Copynumber: 4.1 Consensus size: 103
1476274 TGTCCATAAG
*** *
1476284 GACCACATATCATTCCTTAAGAATCATATACATATATTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
1476349 TTCACACATGTTCCAAAGAATACATATATATCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
1476387 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
1476452 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
1476490 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
1476555 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
1476593 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAAAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1476658 TTCACACATGTTCCAAAGAATACATATATGTCCC-AAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
1476695 GGACCACATA
1 -GACCACATA
1476705 CCCCTCGACT
Statistics
Matches: 309, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
102 2 0.01
103 307 0.99
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:1482116 original size:23 final size:23
Alignment explanation
Indices: 1482088--1482209 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
1482078 GTCACCACAT
* *
1482088 CATATAATTACACCGAAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
* *
1482111 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGTAGTGCCA
*
1482134 C--GTAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
* *
1482155 TATAATAATTGCACCG-AGTGCCG
1 CAT-ATAATTGCACCGTAGTGCCA
*
1482178 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
*
1482201 TATAATAAT
1 CAT-ATAAT
1482210 GTCCATAAGG
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
21 17 0.21
22 11 0.14
23 37 0.46
24 15 0.19
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGTAGTGCCA
Found at i:1482174 original size:44 final size:45
Alignment explanation
Indices: 1482091--1482209 Score: 170
Period size: 44 Copynumber: 2.6 Consensus size: 45
1482081 ACCACATCAT
* * *
1482091 ATAATTACACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCGC
1 ATAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGC
*
1482135 GTAATTGCACCGTAGTGCCATATAATAATTGCACC-GAGTGCCGC
1 ATAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGC
1482179 ATAGAATTGCACCGTAGTGCCATATAATAAT
1 AT--AATTGCACCGTAGTGCCATATAATAAT
1482210 GTCCATAAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
44 29 0.43
45 11 0.16
46 27 0.40
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (45 bp):
ATAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGC
Found at i:1482198 original size:46 final size:46
Alignment explanation
Indices: 1482088--1482209 Score: 169
Period size: 46 Copynumber: 2.7 Consensus size: 46
1482078 GTCACCACAT
* * *
1482088 CATATAATTACACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCG
1 CATA-AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCG
*
1482134 CGT-AATTGCACCGTAGTGCCATATAATAATTGCACC-GAGTGCCG
1 CATAAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCG
1482178 CATAGAATTGCACCGTAGTGCCATATAATAAT
1 CATA-AATTGCACCGTAGTGCCATATAATAAT
1482210 GTCCATAAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
44 28 0.41
45 11 0.16
46 29 0.43
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (46 bp):
CATAAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCG
Found at i:1482411 original size:99 final size:100
Alignment explanation
Indices: 1482216--1482525 Score: 445
Period size: 96 Copynumber: 3.1 Consensus size: 100
1482206 TAATGTCCAT
*** * *
1482216 AAGGACCACATATCATTCCTTAAGAATCATATACATATATTAGGGATCAAGTATTTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATC--ATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1482281 GACTTCACACATGTTCCAAAGAATACATATATGTCCG
64 GACTTCACACATGTTCCAAAGAATACATATATGTCCG
*
1482318 AAGGACCACATATCATTCCTTAAGAATCATACATATGCCAAGGATCAAGTATGTGTCTCA-CATA
1 AAGGACCACATATCATTCCTTAAGAATCATACATATGCCAAGGATCAAGTATGTGTCTCACCAGA
1482382 CTTCACACATGTTCCAAAGAATACATATAT-TCCG
66 CTTCACACATGTTCCAAAGAATACATATATGTCCG
* * *
1482416 AA--ACAATCAT-TCGATCCCTTAAG-AT-ATACATATGCCAAGGATCCAGTATGTGTCTCACCA
1 AAGGACCA-CATATC-ATTCCTTAAGAATCATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1482476 GACTTCACACATGTTCCAAAGAATACATATATGTCCG
64 GACTTCACACATGTTCCAAAGAATACATATATGTCCG
1482513 AATGGACCACATA
1 AA-GGACCACATA
1482526 GACCCTCGAC
Statistics
Matches: 189, Mismatches: 11, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
95 31 0.16
96 40 0.21
97 18 0.10
98 6 0.03
99 36 0.19
100 30 0.16
102 28 0.15
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (100 bp):
AAGGACCACATATCATTCCTTAAGAATCATACATATGCCAAGGATCAAGTATGTGTCTCACCAGA
CTTCACACATGTTCCAAAGAATACATATATGTCCG
Done.