Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007838.1 Hibiscus syriacus cultivar Beakdansim tig00110187_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: 3429202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:2025703 original size:36 final size:36
Alignment explanation
Indices: 2025663--2025746 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 36
2025653 TTGACAACAG
* *
2025663 AGGATCATTGATGAAAGAATTGAACATCGATAATAT
1 AGGATCATCGATGAAAGAATTAAACATCGATAATAT
* *
2025699 AGGATTATCGATGAAAGAATTAAACATTGATAATAT
1 AGGATCATCGATGAAAGAATTAAACATCGATAATAT
*
2025735 AAGATCATCGAT
1 AGGATCATCGAT
2025747 TTTTACATCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (36 bp):
AGGATCATCGATGAAAGAATTAAACATCGATAATAT
Found at i:2034035 original size:33 final size:33
Alignment explanation
Indices: 2033993--2034100 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
2033983 TTTTCTTCTT
2033993 TCTTCTTCCCGCTGCTTCTCGCGCTGCAATCTC
1 TCTTCTTCCCGCTGCTTCTCGCGCTGCAATCTC
*
2034026 TCTTCTTCCCACTGCTTCTCGCGCTGCAATCTC
1 TCTTCTTCCCGCTGCTTCTCGCGCTGCAATCTC
* ** *
2034059 TCTTCTTCACGCTGCTTCTTACGCAT-CAACCTC
1 TCTTCTTCCCGCTGCTTCTCGCGC-TGCAATCTC
2034092 TCTTCTTCC
1 TCTTCTTCC
2034101 TTCCTTCTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 66 0.99
34 1 0.01
ACGTcount: A:0.09, C:0.42, G:0.11, T:0.38
Consensus pattern (33 bp):
TCTTCTTCCCGCTGCTTCTCGCGCTGCAATCTC
Found at i:2035336 original size:3 final size:3
Alignment explanation
Indices: 2035328--2035353 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2035318 TTTTGCAACA
2035328 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
2035354 ATATGAATTC
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:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2037313 original size:20 final size:19
Alignment explanation
Indices: 2037278--2037336 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
2037268 ATCGATCAAC
*
2037278 AATGATATAACAGGTAAAA
1 AATGATAAAACAGGTAAAA
* *
2037297 ATATGATAAAACTGGTATCAA
1 A-ATGATAAAACAGGTA-AAA
* *
2037318 AATGATGAAACCGGTAAAA
1 AATGATAAAACAGGTAAAA
2037337 CGCTACCGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (19 bp):
AATGATAAAACAGGTAAAA
Found at i:2037414 original size:181 final size:180
Alignment explanation
Indices: 2037079--2037550 Score: 649
Period size: 181 Copynumber: 2.6 Consensus size: 180
2037069 GATCCAAATT
* * * * * ** *
2037079 AAAAATTATAGATCCACAATGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGGTAA
1 AAAAATTATCGATCAACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAA
* * * * * *
2037144 AACCGGTAAAGCGGTACCGAATATATTTAAAGTGTCGGTATTTTAATATAAGGATCGACACTTCG
66 AACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
* *
2037209 TTAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAGTGTCGATACTTTCA
131 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT-A
* *
2037260 AAAAATATATCGATCAACAATGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAAT-TATCGATCAACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
2037325 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
65 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
2037389 GTGAATTTAAATGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
130 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
* * *
2037440 AAAAATGTATCGATCAAACAACGATTTAACAGGTAAAAATATGATAAAACCGATATCAAAATGAT
1 AAAAAT-TATCGATC-AACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
* *
2037505 AAAACCGGTAAAATGATACCAGATATATTAAAAGTGTCGATACTTT
64 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
2037551 CGTAAGTACG
Statistics
Matches: 257, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
180 15 0.06
181 156 0.61
182 86 0.33
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (180 bp):
AAAAATTATCGATCAACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAA
AACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
Found at i:2038004 original size:18 final size:19
Alignment explanation
Indices: 2037981--2038018 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2037971 CTTTTATTAA
*
2037981 ATATTATAG-GTATAAATG
1 ATATTACAGTGTATAAATG
2037999 ATATTACAGTTGTATAAATG
1 ATATTACAG-TGTATAAATG
2038019 TGCCGACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (19 bp):
ATATTACAGTGTATAAATG
Found at i:2038357 original size:182 final size:184
Alignment explanation
Indices: 2038139--2038485 Score: 610
Period size: 183 Copynumber: 1.9 Consensus size: 184
2038129 ATATCAGCAT
*
2038139 AAAGTGTCGATACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACC-ATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACCAACAATTATAATGTA
* *
2038203 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGA-AATATGTATACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTATACAACC
2038267 TATATCGACACTTTTTAATATTGTGTCGC-TACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTC-CATACTTTATGTCCAGAATGGATGAAA
*
2038321 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCAACAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACCAACAATTATAATGTA
* *
2038386 ATAGGTAATTTTTTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTATACAACC
2038451 TATATCGACACTTTTTAATATTGTGTCCATACTTT
131 TATATCGACACTTTTTAATATTGTGTCCATACTTT
2038486 TAAGTAACGC
Statistics
Matches: 156, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
182 49 0.31
183 61 0.39
184 46 0.29
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACCAACAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTATACAACC
TATATCGACACTTTTTAATATTGTGTCCATACTTTATGTCCAGAATGGATGAAA
Found at i:2041803 original size:182 final size:182
Alignment explanation
Indices: 2041182--2042015 Score: 1373
Period size: 182 Copynumber: 4.6 Consensus size: 182
2041172 TTTTACCTTT
** *
2041182 TTTAAAAGAGAAGAAGTTATATTGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
2041247 AACAATATAACAGGTAAAAATATGACAAAACCGG--TCGAAATGAAAAAACAGGCAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
2041310 CGATTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
2041362 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTAT-AAAATGTATCGAT-CAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
2041424 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAA-CGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
2041488 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTT-GAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
2041537 -TTAATAAGAGAAGAAGTTATAGCGCCAATAATGTGTCGATATTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * *
2041601 TAACAATATAACATGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAATAGGTAAAGTGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
2041666 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* * * *
2041719 TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATATTTTATAAAATTGTATCAATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
2041784 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
2041849 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTAGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
2041901 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * **
2041966 AATAATATAACATGTAAAAATATGATAAAACCGGTCTATAAATGACAAAA
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
2042016 TGTGAACGCA
Statistics
Matches: 611, Mismatches: 32, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
174 4 0.01
175 11 0.02
176 37 0.06
177 49 0.08
178 116 0.19
179 95 0.16
180 13 0.02
181 6 0.01
182 276 0.45
183 4 0.01
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:2042255 original size:87 final size:87
Alignment explanation
Indices: 2042151--2042313 Score: 283
Period size: 87 Copynumber: 1.9 Consensus size: 87
2042141 AAATAGGTCA
*
2042151 ATATAAGCGCTACCTATTACATTATATAAG-TTCTACCTAATATGTTATTGTACTTGATAATATT
1 ATATAAGCGCTACCTATTACATTATATAAGCGT-TACCTAATATGTTATTGTACTTGATAATATT
2042215 TCCGGTTAAATACCTATTTTATT
65 TCCGGTTAAATACCTATTTTATT
* *
2042238 ATATAAGCGCTATCTATTATATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
2042303 CCGGTTAAATA
66 CCGGTTAAATA
2042314 ATATAATATA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
87 71 0.99
88 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:2042285 original size:23 final size:23
Alignment explanation
Indices: 2042225--2042285 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2042215 TCCGGTTAAA
* *
2042225 TACCTATTTTATTATATAAGCGC
1 TACCTAATATATTATATAAGCGC
* * *
2042248 TATCTATTATATTATATAAGCGT
1 TACCTAATATATTATATAAGCGC
*
2042271 TACCTAATATGTTAT
1 TACCTAATATATTAT
2042286 TGTACTTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (23 bp):
TACCTAATATATTATATAAGCGC
Found at i:2046008 original size:60 final size:58
Alignment explanation
Indices: 2045893--2046012 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 58
2045883 TTCAATGCAT
* * * * *
2045893 ATCCATAATCACAATACAACATCAAGGATAAGGCTCAGTTCACGAAGCTCAAACACTC
1 ATCCATAAACACAATACAACATCAAGGATAAGACTCAGGTCACAAAACTCAAACACTC
* * * *
2045951 ATCCATAACACACAATACCACAATCAAGGATGAGACTCGGGTCACAAAACTCGAACACTC
1 ATCCATAA-ACACAATACAAC-ATCAAGGATAAGACTCAGGTCACAAAACTCAAACACTC
2046011 AT
1 AT
2046013 TTACAACATA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 8 0.16
59 10 0.20
60 33 0.65
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.17
Consensus pattern (58 bp):
ATCCATAAACACAATACAACATCAAGGATAAGACTCAGGTCACAAAACTCAAACACTC
Found at i:2051576 original size:22 final size:21
Alignment explanation
Indices: 2051549--2051601 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2051539 GTATGAACAA
2051549 TATCGATACCATATGAA-AGGGG
1 TATCGATACC-TATGAAGA-GGG
**
2051571 TATCGATACCTATGTGGAGGG
1 TATCGATACCTATGAAGAGGG
2051592 TATCGATACC
1 TATCGATACC
2051602 CAGGGAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (21 bp):
TATCGATACCTATGAAGAGGG
Found at i:2065189 original size:17 final size:17
Alignment explanation
Indices: 2065169--2065202 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2065159 AATTTAATAA
*
2065169 AAATTATTTTATGTATT
1 AAATTATTTTATATATT
2065186 AAATTATTTTATATATT
1 AAATTATTTTATATATT
2065203 GCAAAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
AAATTATTTTATATATT
Found at i:2069803 original size:29 final size:29
Alignment explanation
Indices: 2069768--2069849 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2069758 AAACTAAATT
* *
2069768 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
2069797 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
2069826 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2069850 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:2074506 original size:29 final size:29
Alignment explanation
Indices: 2074471--2074552 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2074461 AAACTAAATT
* *
2074471 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
2074500 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
2074529 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2074553 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:2080586 original size:18 final size:18
Alignment explanation
Indices: 2080563--2080614 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
2080553 ACTTAGAATT
*
2080563 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
2080581 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
2080599 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
2080615 ATATCACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2081575 original size:21 final size:22
Alignment explanation
Indices: 2081550--2081602 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2081540 AAGTTCCACG
2081550 GGTATCGATAC-CCTCCACATA-
1 GGTATCGATACACCTCC-CATAT
*
2081571 GGTATCGATACACCTTCCATAT
1 GGTATCGATACACCTCCCATAT
2081593 GGTATCGATA
1 GGTATCGATA
2081603 TTGTTCATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (22 bp):
GGTATCGATACACCTCCCATAT
Found at i:2082918 original size:19 final size:19
Alignment explanation
Indices: 2082896--2082951 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
2082886 CTTATAGTTC
2082896 ACTTTCAATGTTAACTTTG
1 ACTTTCAATGTTAACTTTG
*
2082915 ACTTTCAAT-TTGACTTTG
1 ACTTTCAATGTTAACTTTG
* **
2082933 ATTTTTTATGTTAACTTTG
1 ACTTTCAATGTTAACTTTG
2082952 CTCTTACCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (19 bp):
ACTTTCAATGTTAACTTTG
Found at i:2083879 original size:20 final size:20
Alignment explanation
Indices: 2083828--2083866 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2083818 GTTCTTACAG
2083828 TATCAATACTGCATGAACAA
1 TATCAATACTGCATGAACAA
2083848 TATCAATACTGCATGAACA
1 TATCAATACTGCATGAACA
2083867 GTACTGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (20 bp):
TATCAATACTGCATGAACAA
Found at i:2087334 original size:25 final size:26
Alignment explanation
Indices: 2087299--2087351 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
2087289 AATTGACTTT
* *
2087299 TACTTTTATTATTA-TTAATATTTGA
1 TACTTTCATTATTATTTAAAATTTGA
2087324 TACTTTCATTATTATTTAAAATTTGA
1 TACTTTCATTATTATTTAAAATTTGA
2087350 TA
1 TA
2087352 ATATTTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (26 bp):
TACTTTCATTATTATTTAAAATTTGA
Found at i:2088460 original size:32 final size:35
Alignment explanation
Indices: 2088387--2088473 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 35
2088377 TATCGTTAAG
2088387 TTTTATTAAAATTTAAATTAATTATATACCGATAAATA
1 TTTTATTAAAATTTAAATTAATTATATACC---AAATA
*
2088425 TTTTATTAAAATTTTAATTAATTATATA-C-AA-A
1 TTTTATTAAAATTTAAATTAATTATATACCAAATA
*
2088457 TTTTAGT-AAATTTAAAT
1 TTTTATTAAAATTTAAAT
2088474 AAAAATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 9 0.20
32 7 0.15
33 2 0.04
37 1 0.02
38 27 0.59
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (35 bp):
TTTTATTAAAATTTAAATTAATTATATACCAAATA
Found at i:2094032 original size:38 final size:38
Alignment explanation
Indices: 2093979--2094054 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
2093969 CGTTAAATTA
*
2093979 TTATTTTCGTTAAATGTTAACAACAGATGATTTGATTG
1 TTATTTTCGTCAAATGTTAACAACAGATGATTTGATTG
2094017 TTATTTTCGTCAAATGTTAACAACAGATGATTTGATTG
1 TTATTTTCGTCAAATGTTAACAACAGATGATTTGATTG
2094055 GTAATACATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (38 bp):
TTATTTTCGTCAAATGTTAACAACAGATGATTTGATTG
Found at i:2094907 original size:20 final size:20
Alignment explanation
Indices: 2094864--2094912 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
2094854 GAACTCTAAT
2094864 TTCGCAACACAGTTTTTCAAA
1 TTCGCAACACAG-TTTTCAAA
*
2094885 TTCGCAACTCAG-TTTCGAAA
1 TTCGCAACACAGTTTTC-AAA
2094905 TTCGCAAC
1 TTCGCAAC
2094913 GCTAATTACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 11 0.42
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (20 bp):
TTCGCAACACAGTTTTCAAA
Found at i:2094998 original size:74 final size:75
Alignment explanation
Indices: 2094877--2095043 Score: 230
Period size: 74 Copynumber: 2.2 Consensus size: 75
2094867 GCAACACAGT
* *
2094877 TTTTCAAATTCGCAACTCAGTTTCGAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
1 TTTTCAAATTCGCAACACAGTTTCGAAATCCGCAACGCTAATTACCGACATAGGTAAACAGTACT
*
2094942 ATCGTAA-GA
66 ATCGCAACGA
* * * *
2094951 TTTTCAAATCCGCAACACGATTTTC-AAATCCGCAATGCTAATTACCGATATAGGTAAACAGTAC
1 TTTTCAAATTCGCAACAC-AGTTTCGAAATCCGCAACGCTAATTACCGACATAGGTAAACAGTAC
2095015 TATCGCAACGCGA
65 TATCGCAA--CGA
2095028 TTTTCAAATTCGCAAC
1 TTTTCAAATTCGCAAC
2095044 GCTAATTACC
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
74 59 0.73
75 5 0.06
77 17 0.21
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (75 bp):
TTTTCAAATTCGCAACACAGTTTCGAAATCCGCAACGCTAATTACCGACATAGGTAAACAGTACT
ATCGCAACGA
Found at i:2095074 original size:57 final size:57
Alignment explanation
Indices: 2094961--2095082 Score: 190
Period size: 57 Copynumber: 2.1 Consensus size: 57
2094951 TTTTCAAATC
* **
2094961 CGCAACACGATTTTCAAATCCGCAATGCTAATTACCGATATAGGTAAACAGTACTAT
1 CGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACACAACTAT
* *
2095018 CGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTAT
1 CGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACACAACTAT
*
2095075 CACAACAC
1 CGCAACAC
2095083 AAATTTCGCA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (57 bp):
CGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACACAACTAT
Found at i:2095583 original size:20 final size:20
Alignment explanation
Indices: 2095560--2095607 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2095550 AGAAATTCGC
*
2095560 GTTGCGATTTTCGAAACTGA
1 GTTGCGAATTTCGAAACTGA
* *
2095580 GTTGCGAATTTGGAAACTGT
1 GTTGCGAATTTCGAAACTGA
2095600 GTTGCGAA
1 GTTGCGAA
2095608 ATTGGAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTCGAAACTGA
Found at i:2095612 original size:20 final size:20
Alignment explanation
Indices: 2095572--2095613 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2095562 TGCGATTTTC
*
2095572 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
2095592 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
2095612 GA
1 GA
2095614 GTTCGCGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:2097962 original size:18 final size:18
Alignment explanation
Indices: 2097939--2097977 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2097929 CAAAATATAC
2097939 TACTCTCAATTATCGACA
1 TACTCTCAATTATCGACA
2097957 TACTCTCAATTATCGACA
1 TACTCTCAATTATCGACA
2097975 TAC
1 TAC
2097978 ATGCATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (18 bp):
TACTCTCAATTATCGACA
Found at i:2110150 original size:107 final size:105
Alignment explanation
Indices: 2110017--2110272 Score: 263
Period size: 107 Copynumber: 2.4 Consensus size: 105
2110007 AAAATATATT
* * * *
2110017 TTTTGAAATATATATTATATAGTTTTTTAAAACGTTTTT-GAAAACTTATGTACAATATATAAGT
1 TTTTGAAATATATAATATATAATTTTTAAAAACGTTTTTGGAAAA-TT-TATACAATATAT-AGT
*
2110081 TTT-AAAACATTTT-GAAAA-TTATATAGTGTATAGTTTTGAAATCA
63 TTTAAAAACATTTTGGAAAACTTATATA----ATAGTTTTAAAATCA
* *
2110125 TTTTGAAA-ATATAATATATAATTTTTAAAAACATTTTTTGGAAAATTTATATAATATATAGTTT
1 TTTTGAAATATATAATATATAATTTTTAAAAAC-GTTTTTGGAAAATTTATACAATATATAGTTT
* *
2110189 TAACAAAACATTTTGGAAAACTTATATAATATTTTTAAAATTA
65 T-A-AAAACATTTTGGAAAACTTATATAATAGTTTTAAAATCA
*
2110232 TCTTTGAAAATTATATAATATATAA-TTTTGAAAACGTTTTT
1 T-TTTG-AAA-TATATAATATATAATTTTTAAAAACGTTTTT
2110273 AAATATAATA
Statistics
Matches: 126, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
106 6 0.05
107 44 0.35
108 19 0.15
109 23 0.18
110 14 0.11
111 20 0.16
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (105 bp):
TTTTGAAATATATAATATATAATTTTTAAAAACGTTTTTGGAAAATTTATACAATATATAGTTTT
AAAAACATTTTGGAAAACTTATATAATAGTTTTAAAATCA
Found at i:2110178 original size:40 final size:39
Alignment explanation
Indices: 2110133--2110220 Score: 124
Period size: 39 Copynumber: 2.2 Consensus size: 39
2110123 CATTTTGAAA
* *
2110133 ATATAATATATAATTTTTA-AAAACATTTTTTGGAAAATTT
1 ATATAATATATAATTTTAACAAAACA--TTTTGGAAAACTT
*
2110173 ATATAATATATAGTTTTAACAAAACATTTTGGAAAACTT
1 ATATAATATATAATTTTAACAAAACATTTTGGAAAACTT
2110212 ATATAATAT
1 ATATAATAT
2110221 TTTTAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 21 0.48
40 17 0.39
41 6 0.14
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (39 bp):
ATATAATATATAATTTTAACAAAACATTTTGGAAAACTT
Found at i:2110203 original size:39 final size:39
Alignment explanation
Indices: 2110133--2110265 Score: 129
Period size: 40 Copynumber: 3.6 Consensus size: 39
2110123 CATTTTGAAA
* *
2110133 ATATAATATATAATTTTTAAAAACATTTTTTGGAAAATTT
1 ATATAATATATAATTTTAAAAAACA-TTTTTGGAAAACTT
*
2110173 ATATAATATATAGTTTTAACAAAACA-TTTTGGAAAACTT
1 ATATAATATATAATTTTAA-AAAACATTTTTGGAAAACTT
** *
2110212 ATAT-A-ATAT--TTTT-AAAATTATCTTT-GAAAA-TT
1 ATATAATATATAATTTTAAAAAACATTTTTGGAAAACTT
*
2110244 ATATAATATATAATTTTGAAAA
1 ATATAATATATAATTTTAAAAA
2110266 CGTTTTTAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 17
0.78 0.06 0.17
Matches are distributed among these distances:
32 6 0.08
33 10 0.12
34 8 0.10
35 4 0.05
36 4 0.05
37 8 0.10
38 1 0.01
39 16 0.20
40 17 0.21
41 6 0.08
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (39 bp):
ATATAATATATAATTTTAAAAAACATTTTTGGAAAACTT
Found at i:2110331 original size:16 final size:16
Alignment explanation
Indices: 2110310--2110348 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
2110300 TTTTTGAAAC
2110310 ATATATATTA-TA-TA
1 ATATATATTATTATTA
2110324 ATATATATTATTATTA
1 ATATATATTATTATTA
*
2110340 ATATTTATT
1 ATATATATT
2110349 TCATTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 2 0.09
16 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATATATTATTATTA
Found at i:2111539 original size:2 final size:2
Alignment explanation
Indices: 2111532--2111574 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2111522 TTTCCATTAT
2111532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2111574 T
1 T
2111575 TTATGGTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2115093 original size:75 final size:75
Alignment explanation
Indices: 2115000--2115146 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
2114990 CATGGCAAAG
* *
2115000 CAATTCATATCAATACAAGTATGCAATATTCATAATACTATTAAAGCATTTAAAGATATTTTATC
1 CAATACATATCAATACAAGTATGCAATATTCATAATACTATCAAAGCATTTAAAGATATTTTATC
2115065 GAATTTATAT
66 GAATTTATAT
* * *
2115075 CAATACATATCGATACAAGTATGCAATATTCGTAATATTATCAAAGCATTTAAAGATATTTTATC
1 CAATACATATCAATACAAGTATGCAATATTCATAATACTATCAAAGCATTTAAAGATATTTTATC
2115140 GAATTTA
66 GAATTTA
2115147 GTTTAATGGT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (75 bp):
CAATACATATCAATACAAGTATGCAATATTCATAATACTATCAAAGCATTTAAAGATATTTTATC
GAATTTATAT
Found at i:2120222 original size:59 final size:60
Alignment explanation
Indices: 2120106--2120223 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
2120096 CTCCACGATG
* * * * * *
2120106 TCGACATTTAGGTCGAACAAGCTGGTAGTTGAATGTCTTCCCCTTGAACTTGAAGGCATT
1 TCGACATTGAGGTCGAACAAGCTCGCAATTGAATATCTTCCCCTGGAACTTGAAGGCATT
* *
2120166 TCGATATTGAGGTCGAAGAAGCTCGCAATTGAATATC-TCCCCTGGAACTTGAAGGCAT
1 TCGACATTGAGGTCGAACAAGCTCGCAATTGAATATCTTCCCCTGGAACTTGAAGGCAT
2120224 CGTATTAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
59 20 0.40
60 30 0.60
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (60 bp):
TCGACATTGAGGTCGAACAAGCTCGCAATTGAATATCTTCCCCTGGAACTTGAAGGCATT
Found at i:2123140 original size:24 final size:25
Alignment explanation
Indices: 2123112--2123165 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
2123102 TAAAAAAAGG
2123112 GTAAACAG-ACTTATAAACAT-GTCA
1 GTAAACAGAACTTATAAA-ATAGTCA
*
2123136 GTAAA-TGAACTTATAAAATAGTCA
1 GTAAACAGAACTTATAAAATAGTCA
*
2123160 ATAAAC
1 GTAAAC
2123166 GTGTTTGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (25 bp):
GTAAACAGAACTTATAAAATAGTCA
Found at i:2125126 original size:18 final size:19
Alignment explanation
Indices: 2125091--2125127 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2125081 CACGGAATGT
2125091 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2125111 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2125128 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2128487 original size:43 final size:43
Alignment explanation
Indices: 2128425--2128553 Score: 240
Period size: 43 Copynumber: 3.0 Consensus size: 43
2128415 CGTTTTATTA
* *
2128425 ACTCAAATGATATTGCAGAGTAGAGTAGATTACTACAATATGC
1 ACTCAAATGATGTTTCAGAGTAGAGTAGATTACTACAATATGC
2128468 ACTCAAATGATGTTTCAGAGTAGAGTAGATTACTACAATATGC
1 ACTCAAATGATGTTTCAGAGTAGAGTAGATTACTACAATATGC
2128511 ACTCAAATGATGTTTCAGAGTAGAGTAGATTACTACAATATGC
1 ACTCAAATGATGTTTCAGAGTAGAGTAGATTACTACAATATGC
2128554 TTGCTACTCT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (43 bp):
ACTCAAATGATGTTTCAGAGTAGAGTAGATTACTACAATATGC
Found at i:2136032 original size:43 final size:45
Alignment explanation
Indices: 2135968--2136058 Score: 141
Period size: 43 Copynumber: 2.1 Consensus size: 45
2135958 GCTTTCTGTC
* *
2135968 GGTGTCTATTTAAATCGCCTTTGCTGGCAACTATAACTG-AAAAT
1 GGTGTCTATTTAAATCACCTTTGCTGGCAACTAAAACTGAAAAAT
*
2136012 GGTGTCTA-TTAAATCACCTTTGCTGGCTACTAAAACTGAAAAAT
1 GGTGTCTATTTAAATCACCTTTGCTGGCAACTAAAACTGAAAAAT
2136056 GGT
1 GGT
2136059 TGCAATCCAG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 27 0.63
44 16 0.37
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (45 bp):
GGTGTCTATTTAAATCACCTTTGCTGGCAACTAAAACTGAAAAAT
Found at i:2157335 original size:12 final size:12
Alignment explanation
Indices: 2157318--2157347 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2157308 GGCAAGGACT
2157318 TAATTATTAGTA
1 TAATTATTAGTA
*
2157330 TAATTATTAGTT
1 TAATTATTAGTA
2157342 TAATTA
1 TAATTA
2157348 AACTAGTTAA
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:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
TAATTATTAGTA
Found at i:2159241 original size:2 final size:2
Alignment explanation
Indices: 2159234--2159272 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
2159224 GTGTTCGTTC
*
2159234 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
2159273 CAAGTGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2159431 original size:22 final size:20
Alignment explanation
Indices: 2159383--2159431 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 20
2159373 CACTAGCACA
*
2159383 TAATATTTGTTCATTTTTATT
1 TAAT-TTTGTGCATTTTTATT
2159404 TAAATTTTGTGCATTTTTTCATT
1 T-AATTTTGTGCA-TTTTT-ATT
2159427 TAATT
1 TAATT
2159432 CAAAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.33
22 12 0.50
23 4 0.17
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (20 bp):
TAATTTTGTGCATTTTTATT
Found at i:2164543 original size:18 final size:20
Alignment explanation
Indices: 2164506--2164546 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2164496 GATATAAGAA
2164506 GATGAAAAAAAAAGAGAAAT
1 GATGAAAAAAAAAGAGAAAT
*
2164526 GATG-AAAATAAAGA-AAAT
1 GATGAAAAAAAAAGAGAAAT
2164544 GAT
1 GAT
2164547 ATTTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.15
Consensus pattern (20 bp):
GATGAAAAAAAAAGAGAAAT
Found at i:2175904 original size:33 final size:35
Alignment explanation
Indices: 2175844--2175912 Score: 124
Period size: 33 Copynumber: 2.0 Consensus size: 35
2175834 AGGTGAAACA
2175844 CGAGTACCTTCATAAAATATCTTGTTAAATCAATT
1 CGAGTACCTTCATAAAATATCTTGTTAAATCAATT
2175879 CGAGTACCTTCAT-AAA-ATCTTGTTAAATCAATT
1 CGAGTACCTTCATAAAATATCTTGTTAAATCAATT
2175912 C
1 C
2175913 CATAACCACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 18 0.53
34 3 0.09
35 13 0.38
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (35 bp):
CGAGTACCTTCATAAAATATCTTGTTAAATCAATT
Found at i:2176342 original size:29 final size:29
Alignment explanation
Indices: 2176299--2176472 Score: 258
Period size: 29 Copynumber: 6.0 Consensus size: 29
2176289 TTATCACCTT
* *
2176299 TTTTAAGAAATATTTACGAAAATAACACCC
1 TTTTAA-AAATATTTACAAAAATAACACCA
* * *
2176329 TTTTAAAAATATTTACAAAAACAACATCT
1 TTTTAAAAATATTTACAAAAATAACACCA
2176358 TTTTAAAAATATTTACAAAAATAACACCA
1 TTTTAAAAATATTTACAAAAATAACACCA
*
2176387 TTTTAAAAATATTTACGAAAATAACACCA
1 TTTTAAAAATATTTACAAAAATAACACCA
* * *
2176416 TTTTAAAAATATTTACGAAAATAAAACCT
1 TTTTAAAAATATTTACAAAAATAACACCA
2176445 TTTTAAAAATATTTACAAAAATAACACC
1 TTTTAAAAATATTTACAAAAATAACACC
2176473 CGGTAAATGT
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
29 126 0.95
30 6 0.05
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (29 bp):
TTTTAAAAATATTTACAAAAATAACACCA
Found at i:2176409 original size:87 final size:88
Alignment explanation
Indices: 2176299--2176472 Score: 296
Period size: 87 Copynumber: 2.0 Consensus size: 88
2176289 TTATCACCTT
* * *
2176299 TTTTAAGAAATATTTACGAAAATAACACCCTTTTAAAAATATTTACAAAAACAACATCTTTTTAA
1 TTTTAAGAAATATTTACGAAAATAACACCATTTTAAAAATATTTACAAAAACAAAACCTTTTTAA
2176364 AAATATTTACAAAAATAACACCA
66 AAATATTTACAAAAATAACACCA
* *
2176387 TTTTAA-AAATATTTACGAAAATAACACCATTTTAAAAATATTTACGAAAATAAAACCTTTTTAA
1 TTTTAAGAAATATTTACGAAAATAACACCATTTTAAAAATATTTACAAAAACAAAACCTTTTTAA
2176451 AAATATTTACAAAAATAACACC
66 AAATATTTACAAAAATAACACC
2176473 CGGTAAATGT
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 75 0.93
88 6 0.07
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (88 bp):
TTTTAAGAAATATTTACGAAAATAACACCATTTTAAAAATATTTACAAAAACAAAACCTTTTTAA
AAATATTTACAAAAATAACACCA
Found at i:2183702 original size:21 final size:20
Alignment explanation
Indices: 2183660--2183702 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2183650 GAAAGGTTGA
* *
2183660 AGAAGAAAGGGGGGAGAGGG
1 AGAAGAAAGGAGGGAAAGGG
*
2183680 AGAAGAAAGTGAGGGAAATGG
1 AGAAGAAAG-GAGGGAAAGGG
2183701 AG
1 AG
2183703 GAACAGATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.51, T:0.05
Consensus pattern (20 bp):
AGAAGAAAGGAGGGAAAGGG
Found at i:2186531 original size:114 final size:117
Alignment explanation
Indices: 2186302--2186533 Score: 416
Period size: 114 Copynumber: 2.0 Consensus size: 117
2186292 TTTAAAACCT
*
2186302 TCGAAGTTTTATGTCTTTCGTCGTACTATAGTCTCTCGACATGATCGCTGTCAATCCCATTATTA
1 TCGAAGTTTTATGTCCTTCGTCGTACTATAG-CTCTCGACATGATCGCTGTCAATCCCATTATTA
2186367 GTTTGACTATCTAATAGTTGGATCTATCTTTGTCAACTCATCAACAACAATCA
65 GTTTGACTATCTAATAGTTGGATCTATCTTTGTCAACTCATCAACAACAATCA
2186420 TCGAAGTTTTATGTCCTTCGTCGTACTATAG-TCTCGACATGATCGCTGTCAATCCCATTATTAG
1 TCGAAGTTTTATGTCCTTCGTCGTACTATAGCTCTCGACATGATCGCTGTCAATCCCATTATTAG
*
2186484 TTT-CCTATCTAA-AGTTGGATCTATCTTTGTCAACTCATCAACAACAATCA
66 TTTGACTATCTAATAGTTGGATCTATCTTTGTCAACTCATCAACAACAATCA
2186534 ATTCTAGGAC
Statistics
Matches: 112, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
114 38 0.34
115 8 0.07
116 36 0.32
118 30 0.27
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (117 bp):
TCGAAGTTTTATGTCCTTCGTCGTACTATAGCTCTCGACATGATCGCTGTCAATCCCATTATTAG
TTTGACTATCTAATAGTTGGATCTATCTTTGTCAACTCATCAACAACAATCA
Found at i:2189915 original size:6 final size:6
Alignment explanation
Indices: 2189901--2189977 Score: 127
Period size: 6 Copynumber: 12.8 Consensus size: 6
2189891 ATTCGAGCCG
* * *
2189901 TTGCTT TTGCAT TTGCAT TTGCTT TTGCAT TTGCTT TTGCAT TTGCAT
1 TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT
2189949 TTGCAT TTGCAT TTGCAT TTGCAT TTGCA
1 TTGCAT TTGCAT TTGCAT TTGCAT TTGCA
2189978 GGGTGTGTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (6 bp):
TTGCAT
Found at i:2199226 original size:147 final size:148
Alignment explanation
Indices: 2198959--2199256 Score: 589
Period size: 147 Copynumber: 2.0 Consensus size: 148
2198949 GACAAATAGT
2198959 GTTAACAGTTAAGTATTATTTGATACGGATGATGTCCTTTAGATGTGTCAAAGACAGCAAAATAA
1 GTTAACAGTTAAGTATTATTTGATACGGATGATGTCCTTTAGATGTGTCAAAGACAGCAAAATAA
2199024 AGCATGTATGTTTGATAAAAAAGAATAATAGATAAAATGCTATGAAATCTGGTATAGAAAATGAT
66 AGCATGTATGTTTGATAAAAAAGAATAATAGATAAAATGCTATGAAATCTGGTATAGAAAATGAT
2199089 -ATATAAGACTTAACCTC
131 AATATAAGACTTAACCTC
2199106 GTTAACAGTTAAGTATTATTTGATACGGATGATGTCCTTTAGATGTGTCAAAGACAGCAAAATAA
1 GTTAACAGTTAAGTATTATTTGATACGGATGATGTCCTTTAGATGTGTCAAAGACAGCAAAATAA
2199171 AGCATGTATGTTTGATAAAAAAGAATAATAGATAAAATGCTATGAAATCTGGTATAGAAAATGAT
66 AGCATGTATGTTTGATAAAAAAGAATAATAGATAAAATGCTATGAAATCTGGTATAGAAAATGAT
2199236 AATATAAGACTTAACCTC
131 AATATAAGACTTAACCTC
2199254 GTT
1 GTT
2199257 CTGAAAGTAA
Statistics
Matches: 150, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 130 0.87
148 20 0.13
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (148 bp):
GTTAACAGTTAAGTATTATTTGATACGGATGATGTCCTTTAGATGTGTCAAAGACAGCAAAATAA
AGCATGTATGTTTGATAAAAAAGAATAATAGATAAAATGCTATGAAATCTGGTATAGAAAATGAT
AATATAAGACTTAACCTC
Found at i:2200789 original size:39 final size:39
Alignment explanation
Indices: 2200740--2200818 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
2200730 ATTTTTTGTG
2200740 AACAAAAAAGGGTGTATAAAATAAAAATGTTTTCTTTTT
1 AACAAAAAAGGGTGTATAAAATAAAAATGTTTTCTTTTT
*
2200779 AACAAAAAAGGGTGTGTAAAATAAAAATGTTTTCTTTTT
1 AACAAAAAAGGGTGTATAAAATAAAAATGTTTTCTTTTT
2200818 A
1 A
2200819 TAATCTTCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (39 bp):
AACAAAAAAGGGTGTATAAAATAAAAATGTTTTCTTTTT
Found at i:2205533 original size:30 final size:31
Alignment explanation
Indices: 2205487--2205548 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
2205477 TTTAATCTTT
*
2205487 AGTTTAGTGGTCAAAAT-GATATTACATCTAA
1 AGTTTAGTGATCAAAATAG-TATTACATCTAA
*
2205518 AGTTTA-TGATCAAAATAGTATTATATCTAA
1 AGTTTAGTGATCAAAATAGTATTACATCTAA
2205548 A
1 A
2205549 TATCAAGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (31 bp):
AGTTTAGTGATCAAAATAGTATTACATCTAA
Found at i:2206663 original size:21 final size:21
Alignment explanation
Indices: 2206633--2206698 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
2206623 TGTCCTTGCA
2206633 ATAAACCCTAAACCCTAAACT
1 ATAAACCCTAAACCCTAAACT
* *
2206654 ATAAATCCTAAACCTTAAACT
1 ATAAACCCTAAACCCTAAACT
* * *
2206675 ATAAGCCATAAACCCTAAATT
1 ATAAACCCTAAACCCTAAACT
2206696 ATA
1 ATA
2206699 CTTACCTCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (21 bp):
ATAAACCCTAAACCCTAAACT
Found at i:2206805 original size:21 final size:21
Alignment explanation
Indices: 2206753--2206805 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2206743 CAATAAATCT
2206753 TAAACTCTAAACCATAAACCA
1 TAAACTCTAAACCATAAACCA
* *
2206774 TAAACTATAAA-CATTAAACCC
1 TAAACTCTAAACCA-TAAACCA
*
2206795 TAAAATCTAAA
1 TAAACTCTAAA
2206806 TCTGATTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACTCTAAACCATAAACCA
Found at i:2207218 original size:18 final size:18
Alignment explanation
Indices: 2207195--2207231 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2207185 TTTTGGTTAT
2207195 GGAGTACCTTAGTCATTA
1 GGAGTACCTTAGTCATTA
2207213 GGAGTACCTTAGTCATTA
1 GGAGTACCTTAGTCATTA
2207231 G
1 G
2207232 TACTAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (18 bp):
GGAGTACCTTAGTCATTA
Found at i:2208501 original size:22 final size:22
Alignment explanation
Indices: 2208473--2208530 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
2208463 TGGTGAGCAC
*
2208473 TTGAGTTTGTATCAAGCTTAAA
1 TTGAGTTTGAATCAAGCTTAAA
** *
2208495 TTGAGTTTGAATTGAGCTTGAA
1 TTGAGTTTGAATCAAGCTTAAA
2208517 TTGAGCTCTTGAAT
1 TTGAG-T-TTGAAT
2208531 TTTTTTTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 23 0.77
23 1 0.03
24 6 0.20
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (22 bp):
TTGAGTTTGAATCAAGCTTAAA
Found at i:2208529 original size:13 final size:12
Alignment explanation
Indices: 2208493--2208531 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
2208483 ATCAAGCTTA
2208493 AATTGAGT-TTG
1 AATTGAGTCTTG
2208504 AATTGAG-CTTG
1 AATTGAGTCTTG
2208515 AATTGAGCTCTTG
1 AATTGAG-TCTTG
2208528 AATT
1 AATT
2208532 TTTTTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 17 0.68
13 8 0.32
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (12 bp):
AATTGAGTCTTG
Found at i:2216663 original size:22 final size:23
Alignment explanation
Indices: 2216613--2216674 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
2216603 TATATTAATA
*
2216613 TTAAATATATTAAGTAATATTGTT
1 TTAAACATATTAA-TAATATTGTT
2216637 TTAAA-ATATTAATATATATT-TT
1 TTAAACATATTAATA-ATATTGTT
2216659 TTAAACAT-TTAATAAT
1 TTAAACATATTAATAAT
2216675 TAATATATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.06
22 15 0.42
23 14 0.39
24 5 0.14
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (23 bp):
TTAAACATATTAATAATATTGTT
Found at i:2217257 original size:19 final size:19
Alignment explanation
Indices: 2217233--2217288 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
2217223 TGCCTTTTGC
2217233 ATTTGATGATTGATAAT-T
1 ATTTGATGATTGATAATGT
*
2217251 GATTTGACTGAATG-TAATGT
1 -ATTTGA-TGATTGATAATGT
2217271 ACTTTGATGATTTGATAA
1 A-TTTGATGA-TTGATAA
2217289 CAGATTGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 14 0.47
20 13 0.43
21 3 0.10
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (19 bp):
ATTTGATGATTGATAATGT
Found at i:2229764 original size:227 final size:230
Alignment explanation
Indices: 2229367--2229824 Score: 895
Period size: 227 Copynumber: 2.0 Consensus size: 230
2229357 TTTTCTTGCG
2229367 TGAAGTGAAGGAGTGTCAAGCTAAGGCCAGAGGGATTCCATATAAGAAGAAGAAGAAGAAGAAGA
1 TGAAGTGAAGGAGTGTCAAGCTAAGGCCAGAGGGATTCCATATAAGAAGAAGAAGAAGAAGAAGA
2229432 TTCAAATTAAACCCAACGTGAAGGACGAGGCTAATTCATCGTCAAAGCAGCACCCAGCCCTTCTT
66 TTCAAATTAAACCCAACGTGAAGGACGAGGCTAATTCATCGTCAAAGCAGCACCCAGCCCTTCTT
2229497 AGCTCTAACTAAGAGCTTTTTACGGTAATTCCTTTTACTTTGATATGCACGCTCCTCCATTGCCA
131 AGCTCTAACTAAGAGCTTTTTACGGTAATTCCTTTTACTTTGATATGCACGCTCCTCCATTGCCA
2229562 TGATGATGATGGTGATGA-TTAAGAATAAAACTCT
196 TGATGATGATGGTGATGATTTAAGAATAAAACTCT
2229596 TGAAGTGAAGGAGTGTCAAGCTAAGGCCAGAGGGATTCCATATAAGAAGAAGAAGAAG-A-AAGA
1 TGAAGTGAAGGAGTGTCAAGCTAAGGCCAGAGGGATTCCATATAAGAAGAAGAAGAAGAAGAAGA
2229659 TTCAAATTAAACCCAACGTGAAGGACGAGGCTAATTCATCGTCAAAGCAGCACCCAGCCCTTCTT
66 TTCAAATTAAACCCAACGTGAAGGACGAGGCTAATTCATCGTCAAAGCAGCACCCAGCCCTTCTT
2229724 AGCTCTAACTAAGAGCTTTTTACGGTAATTCCTTTTACTTTGATATGCACGCTCCTCCATTGCCA
131 AGCTCTAACTAAGAGCTTTTTACGGTAATTCCTTTTACTTTGATATGCACGCTCCTCCATTGCCA
2229789 TGATGATGATGGTGATGATTTAAGAATAAAACTCT
196 TGATGATGATGGTGATGATTTAAGAATAAAACTCT
2229824 T
1 T
2229825 AGATTTCTTG
Statistics
Matches: 228, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
227 152 0.67
228 18 0.08
229 58 0.25
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (230 bp):
TGAAGTGAAGGAGTGTCAAGCTAAGGCCAGAGGGATTCCATATAAGAAGAAGAAGAAGAAGAAGA
TTCAAATTAAACCCAACGTGAAGGACGAGGCTAATTCATCGTCAAAGCAGCACCCAGCCCTTCTT
AGCTCTAACTAAGAGCTTTTTACGGTAATTCCTTTTACTTTGATATGCACGCTCCTCCATTGCCA
TGATGATGATGGTGATGATTTAAGAATAAAACTCT
Found at i:2231381 original size:15 final size:16
Alignment explanation
Indices: 2231361--2231390 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2231351 ATTTAATCAA
2231361 AATTAAAAC-ATTAAG
1 AATTAAAACAATTAAG
2231376 AATTAAAACAATTAA
1 AATTAAAACAATTAA
2231391 AAAATAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (16 bp):
AATTAAAACAATTAAG
Found at i:2237162 original size:2 final size:2
Alignment explanation
Indices: 2237155--2237185 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2237145 TCATGGGTAC
2237155 AT AT AT AT AT AT A- 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
2237186 TGGAACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2237473 original size:31 final size:31
Alignment explanation
Indices: 2237433--2237495 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2237423 ATTTTTTTTC
* *
2237433 TATTCGTATACACTTTCAAATTTTCTCACTT
1 TATTCGTATAAACTTGCAAATTTTCTCACTT
* *
2237464 TATTTGTATAAACTTGCAATTTTTCTCACTT
1 TATTCGTATAAACTTGCAAATTTTCTCACTT
2237495 T
1 T
2237496 TTAATTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.51
Consensus pattern (31 bp):
TATTCGTATAAACTTGCAAATTTTCTCACTT
Found at i:2238449 original size:24 final size:24
Alignment explanation
Indices: 2238405--2238467 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
2238395 CATAAAGAAT
* * *
2238405 GTGTCACAAGAGCAGACAAAAAGA
1 GTGTCACAAGAACATACAAAAACA
*
2238429 GTGTCACAAGAACATAGAAAAACA
1 GTGTCACAAGAACATACAAAAACA
* *
2238453 -AGTCACAAGGACATA
1 GTGTCACAAGAACATA
2238468 TATTCTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.51, C:0.17, G:0.21, T:0.11
Consensus pattern (24 bp):
GTGTCACAAGAACATACAAAAACA
Found at i:2239430 original size:60 final size:60
Alignment explanation
Indices: 2239298--2239437 Score: 194
Period size: 60 Copynumber: 2.3 Consensus size: 60
2239288 AGTATATACG
* * *
2239298 TATAGTTTGGGATGAAATTGGAATGTTCAAAAACTTTGAGGACCAATTTAGAATGAAGGT
1 TATAGTTTGGGATGAAATTGAAATGTTCAAAAACGTTGAGGACCAATTTAAAATGAAGGT
* * *
2239358 CATAGTTTGGGATGAAATTGAAATGTTC-AAAAGGTTGAGGACTAATTTAAAATGATA-GT
1 TATAGTTTGGGATGAAATTGAAATGTTCAAAAACGTTGAGGACCAATTTAAAATGA-AGGT
2239417 TATAGTTTAGGGATGAAATTG
1 TATAGTTT-GGGATGAAATTG
2239438 GAACATTTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
59 32 0.45
60 39 0.55
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (60 bp):
TATAGTTTGGGATGAAATTGAAATGTTCAAAAACGTTGAGGACCAATTTAAAATGAAGGT
Found at i:2239464 original size:59 final size:57
Alignment explanation
Indices: 2239298--2239484 Score: 184
Period size: 59 Copynumber: 3.2 Consensus size: 57
2239288 AGTATATACG
*
2239298 TATAGTTTGGGATGAAATTGG-AATGTTCAAAAACTTTGAGGACCAATTTAGAATGAAGGT
1 TATAGTTTGGGATGAAATTGGAAAT-TT--AAAACTTTGAGGACCAATTTAAAATGAA-GT
* ** *
2239358 CATAGTTTGGGATGAAATT-GAAATGTTCAAAAGGTTGAGGACTAATTTAAAATGATAGT
1 TATAGTTTGGGATGAAATTGGAAAT-TT-AAAACTTTGAGGACCAATTTAAAATGA-AGT
*
2239417 TATAGTTTAGGGATGAAATTGGAACATTTAAAA-TTT-AGGGACCAATTTAAAATAAGAGT
1 TATAGTTT-GGGATGAAATTGGAA-ATTTAAAACTTTGA-GGACCAATTTAAAATGA-AGT
*
2239476 TATAATTTG
1 TATAGTTTG
2239485 AGGACATGTG
Statistics
Matches: 109, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
58 2 0.02
59 60 0.55
60 40 0.37
61 5 0.05
62 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.33
Consensus pattern (57 bp):
TATAGTTTGGGATGAAATTGGAAATTTAAAACTTTGAGGACCAATTTAAAATGAAGT
Found at i:2239716 original size:59 final size:60
Alignment explanation
Indices: 2239603--2239716 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 60
2239593 ATAGTTTGAT
** * * *
2239603 GATGAAATTAAAATATTCAAAAGTTACAAGATTAATTTAAAATAAAAATCATAATGTAAA
1 GATGAAATTAAAATATTCAAAAAATACAAAAATAATTTAAAATAAAAACCATAATGTAAA
2239663 GATGAAATTAAAATATTCAAAAAATA-AAAAATAATTTAAAATAAAAACCATAAT
1 GATGAAATTAAAATATTCAAAAAATACAAAAATAATTTAAAATAAAAACCATAAT
2239717 TTGATGACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 25 0.51
60 24 0.49
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (60 bp):
GATGAAATTAAAATATTCAAAAAATACAAAAATAATTTAAAATAAAAACCATAATGTAAA
Found at i:2247368 original size:60 final size:60
Alignment explanation
Indices: 2247292--2247424 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
2247282 ACTTGTATTG
* * * *
2247292 AAATTTTATCTCTATTTCGTAATAAGATAATGATAAGCTAAAAG-ATGTAATTTATAATTT
1 AAATTCTATCTCTATTTCGTAATAAGATAAGGATAAG-TAAAAGAATGTAATCTACAATTT
* * * *
2247352 AAATTCTATCTTTATTTCGTAATAGGATTAGGATAAGTCAAAGAATGTAATCTACAATTT
1 AAATTCTATCTCTATTTCGTAATAAGATAAGGATAAGTAAAAGAATGTAATCTACAATTT
* *
2247412 AAACTCTTTCTCT
1 AAATTCTATCTCT
2247425 TCTCCTATTT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 5 0.08
60 56 0.92
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (60 bp):
AAATTCTATCTCTATTTCGTAATAAGATAAGGATAAGTAAAAGAATGTAATCTACAATTT
Found at i:2248458 original size:3 final size:3
Alignment explanation
Indices: 2248450--2248478 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2248440 GTTCAGTTAA
2248450 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2248479 ATGAAGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2248890 original size:31 final size:30
Alignment explanation
Indices: 2248855--2248913 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2248845 AAACTACAAG
*
2248855 TTTAGTACTTAAACTATCACTTTTGTTTCGT
1 TTTAGTACCTAAACTATCA-TTTTGTTTCGT
* *
2248886 TTTAGTACCTAAACTTTCATTTTTTTTC
1 TTTAGTACCTAAACTATCATTTTGTTTC
2248914 AAAATCATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (30 bp):
TTTAGTACCTAAACTATCATTTTGTTTCGT
Found at i:2248955 original size:31 final size:32
Alignment explanation
Indices: 2248920--2248988 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
2248910 TTTCAAAATC
*
2248920 ATACCTAAC-GTTTACTTTTTGTTTCATTTTA
1 ATACCTAACTGTTAACTTTTTGTTTCATTTTA
**
2248951 ATACCCCACTGTTAACTTTTTGTTTCATTTTA
1 ATACCTAACTGTTAACTTTTTGTTTCATTTTA
*
2248983 GTACCT
1 ATACCT
2248989 TAATTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (32 bp):
ATACCTAACTGTTAACTTTTTGTTTCATTTTA
Found at i:2249834 original size:201 final size:202
Alignment explanation
Indices: 2249489--2249891 Score: 790
Period size: 201 Copynumber: 2.0 Consensus size: 202
2249479 CATTGACAAA
2249489 ATTGAATTTAAAGATCGGCGAGCTAGAGCATGGGCTGCATTGTTTGCTTCTTACTGTAATGTTTA
1 ATTGAATTTAAAGATCGGCGAGCTAGAGCATGGGCTGCATTGTTTGCTTCTTACTGTAATGTTTA
2249554 CGATTATTTAGAGTTGAATTTGATATGCTGAGAATGAAAAACACAAAAAAATCGATGATTACGTT
66 CGATTATTTAGAGTTGAATTTGATATGCTGAGAATGAAAAACACAAAAAAATCGATGATTACGTT
2249619 AATCGAATGAAAACCATCGTGAATGAAACAATTGACAATGTTAGAGTGG-TGAAAAGATTTGGAT
131 AATCGAATGAAAACCATCGTGAATGAAACAATTGACAATGTTAGAGTGGTTGAAAAGATTTGGAT
2249683 GAGACTT
196 GAGACTT
*
2249690 ATTGAATTTAAAGATCGGCGAGCTAGAGCATGGGCTGCATTGTTTGCTTCTTATTGTAATGTTTA
1 ATTGAATTTAAAGATCGGCGAGCTAGAGCATGGGCTGCATTGTTTGCTTCTTACTGTAATGTTTA
2249755 CGATTATTTAGAGTTGAATTTGATATGCTGAGAATGAAAAACACAAAAAAATCGATGATTACGTT
66 CGATTATTTAGAGTTGAATTTGATATGCTGAGAATGAAAAACACAAAAAAATCGATGATTACGTT
2249820 AATCGAATGAAAACCATCGTGAATGAAACAATTGACAATGTTAGAGTGGTTGAAAAGATTTGGAT
131 AATCGAATGAAAACCATCGTGAATGAAACAATTGACAATGTTAGAGTGGTTGAAAAGATTTGGAT
2249885 GAGACTT
196 GAGACTT
2249892 GAGTCACATA
Statistics
Matches: 200, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
201 178 0.89
202 22 0.11
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (202 bp):
ATTGAATTTAAAGATCGGCGAGCTAGAGCATGGGCTGCATTGTTTGCTTCTTACTGTAATGTTTA
CGATTATTTAGAGTTGAATTTGATATGCTGAGAATGAAAAACACAAAAAAATCGATGATTACGTT
AATCGAATGAAAACCATCGTGAATGAAACAATTGACAATGTTAGAGTGGTTGAAAAGATTTGGAT
GAGACTT
Found at i:2251680 original size:18 final size:18
Alignment explanation
Indices: 2251654--2251690 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2251644 GTATATTACA
* *
2251654 TAGTTTATATTATATAGT
1 TAGTATATACTATATAGT
2251672 TAGTATATACTATATAGT
1 TAGTATATACTATATAGT
2251690 T
1 T
2251691 TGCATGTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TAGTATATACTATATAGT
Found at i:2251845 original size:11 final size:12
Alignment explanation
Indices: 2251820--2251850 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2251810 AATATATACA
2251820 TAAAAAATATAT
1 TAAAAAATATAT
2251832 TAAAAAATAT-T
1 TAAAAAATATAT
2251843 TAAAAAAT
1 TAAAAAAT
2251851 CCTAAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAAAATATAT
Found at i:2252359 original size:2 final size:2
Alignment explanation
Indices: 2252352--2252482 Score: 52
Period size: 2 Copynumber: 61.0 Consensus size: 2
2252342 ATACGTAAAC
*
2252352 TA TA TA TA TA T- TA TA TA GTA TA TA AA TA TCA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA TA TA -TA TA
* * * * *
2252394 TA GTT TA TA TA TA AA CTA TA GTT TT TA TA TA TA GT- TCA TA TG TA
1 TA -TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA -TA T-A TA TA TA
* * *
2252438 AA CTA TA TA -A TA TA TA TA GTT TA TA TA TT TA GTA TA TA CTA TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA
2252481 TA
1 TA
2252483 AATAGTTTAT
Statistics
Matches: 98, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
1 3 0.03
2 78 0.80
3 17 0.17
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2252368 original size:7 final size:6
Alignment explanation
Indices: 2252352--2252482 Score: 52
Period size: 7 Copynumber: 20.3 Consensus size: 6
2252342 ATACGTAAAC
* *
2252352 TATATA TATAT- TATATA GTATATA AATATCA TATATA GTATATA GTTTATA
1 TATATA TATATA TATATA -TATATA TATAT-A TATATA -TATATA -TATATA
* * * * *
2252403 TATAAA CTATAGTT TTTATA TATAGT- TCATATG TAAACTA TATA-A TATATA
1 TATATA -TATA-TA TATATA TATA-TA T-ATATA TATA-TA TATATA TATATA
* *
2252454 TAGTTTA TATATT TAGTATA TACTATA TA
1 TA-TATA TATATA TA-TATA TA-TATA TA
2252483 AATAGTTTAT
Statistics
Matches: 94, Mismatches: 18, Indels: 25
0.69 0.13 0.18
Matches are distributed among these distances:
5 10 0.11
6 29 0.31
7 55 0.59
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:2252370 original size:31 final size:30
Alignment explanation
Indices: 2252328--2252463 Score: 140
Period size: 31 Copynumber: 4.6 Consensus size: 30
2252318 CTATATAGTT
*
2252328 TATATATATAGTTCATACGTAAACTATATA
1 TATATATATAGTTCATATGTAAACTATATA
2252358 TATATTATATAG-T-ATA--TAAA-TATCATA
1 TATA-TATATAGTTCATATGTAAACTAT-ATA
* * *
2252385 TATAGTATATAGTTTATATATAAACTATAGTT
1 TATA-TATATAGTTCATATGTAAACTATA-TA
*
2252417 TTTATATATAGTTCATATGTAAACTATATA
1 TATATATATAGTTCATATGTAAACTATATA
*
2252447 -ATATATATAGTTTATAT
1 TATATATATAGTTCATAT
2252464 ATTTAGTATA
Statistics
Matches: 90, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
26 3 0.03
27 18 0.20
28 1 0.01
29 21 0.23
30 6 0.07
31 34 0.38
32 7 0.08
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (30 bp):
TATATATATAGTTCATATGTAAACTATATA
Found at i:2252375 original size:20 final size:20
Alignment explanation
Indices: 2252352--2252482 Score: 70
Period size: 20 Copynumber: 6.2 Consensus size: 20
2252342 ATACGTAAAC
2252352 TATATATATATTATATAGTA
1 TATATATATATTATATAGTA
*
2252372 TATAAATATCA-TATATAGTA
1 TATATATAT-ATTATATAGTA
* *
2252392 TATAGTTTATATATAAACTATAGTT
1 TATA---TATATAT-TA-TATAGTA
*
2252417 TTTATATATAGTTCATAT-GTA
1 TATATATATA-TT-ATATAGTA
* *
2252438 AACTATATA-ATATATATAGTT
1 TA-TATATATAT-TATATAGTA
* * *
2252459 TATATATTTAGTATATACTA
1 TATATATATATTATATAGTA
2252479 TATA
1 TATA
2252483 AATAGTTTAT
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
20 42 0.51
21 9 0.11
22 16 0.19
23 6 0.07
24 1 0.01
25 9 0.11
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (20 bp):
TATATATATATTATATAGTA
Found at i:2252475 original size:89 final size:90
Alignment explanation
Indices: 2252321--2252492 Score: 228
Period size: 89 Copynumber: 1.9 Consensus size: 90
2252311 AGCTCAACTA
2252321 TATAGTTTATATATATAGTTCATACGTAAACTATATATATATTATATAGTATATAAATATCATAT
1 TATAGTTTATATATATAGTTCATACGTAAACTATATATATATTATATAGTATATAAATATCATAT
2252386 A-TAGTAT-ATAGTTTATATATAAAC
66 ACTA-TATAATAGTTTATATATAAAC
* * **
2252410 TATAGTTTTTATATATAGTTCATATGTAAACTATATA-ATA-TATATAGTTTATATATTTAGT-A
1 TATAGTTTATATATATAGTTCATACGTAAACTATATATATATTATATAG--TATATAAATA-TCA
2252472 TATACTATATAAATAGTTTAT
63 TATACTATAT-AATAGTTTAT
2252493 TAATTAATGT
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
87 7 0.10
88 3 0.04
89 51 0.70
90 3 0.04
91 9 0.12
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (90 bp):
TATAGTTTATATATATAGTTCATACGTAAACTATATATATATTATATAGTATATAAATATCATAT
ACTATATAATAGTTTATATATAAAC
Found at i:2252949 original size:2 final size:2
Alignment explanation
Indices: 2252942--2252990 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2252932 TAATATAAAC
2252942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2252984 TA T- TA TA
1 TA TA TA TA
2252991 AACCATATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2258518 original size:15 final size:15
Alignment explanation
Indices: 2258495--2258525 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2258485 GATCAGGATG
*
2258495 TATTTTACTTTTTTA
1 TATTCTACTTTTTTA
2258510 TATTCTACTTTTTTA
1 TATTCTACTTTTTTA
2258525 T
1 T
2258526 TTGATTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTCTACTTTTTTA
Found at i:2273098 original size:20 final size:21
Alignment explanation
Indices: 2273065--2273112 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
2273055 AAAATATTAA
*
2273065 AATATTTGTGTA-TTAAATTT
1 AATATTTGTATATTTAAATTT
* *
2273085 AATATTTTTATATTTAAATAT
1 AATATTTGTATATTTAAATTT
2273106 -ATATTTG
1 AATATTTG
2273113 GTACATGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
AATATTTGTATATTTAAATTT
Found at i:2275234 original size:15 final size:15
Alignment explanation
Indices: 2275210--2275243 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2275200 TTTCATGGAT
2275210 ATAA-GTTGGTTTAA
1 ATAATGTTGGTTTAA
*
2275224 GTAATGTTGGTTTAA
1 ATAATGTTGGTTTAA
2275239 ATAAT
1 ATAAT
2275244 TGTAGTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (15 bp):
ATAATGTTGGTTTAA
Found at i:2275846 original size:16 final size:17
Alignment explanation
Indices: 2275815--2275852 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2275805 ATGATATACA
2275815 TGAT-TATATGCATATG
1 TGATATATATGCATATG
2275831 TGATATATATGC-TATG
1 TGATATATATGCATATG
*
2275847 AGATAT
1 TGATAT
2275853 GACCAATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (17 bp):
TGATATATATGCATATG
Found at i:2275890 original size:22 final size:20
Alignment explanation
Indices: 2275865--2275906 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2275855 CCAATGTGAA
2275865 ATGAAATAAGCTATATGAATAT
1 ATGAAATAA-C-ATATGAATAT
*
2275887 ATGAAATGACATATGAATAT
1 ATGAAATAACATATGAATAT
2275907 GCAATATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGAAATAACATATGAATAT
Found at i:2280679 original size:60 final size:61
Alignment explanation
Indices: 2280586--2280725 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 61
2280576 TAGCATATCG
*
2280586 ATAGTTTAGAGATGAAATTAGAATGTATAAAAGTTT-GGGGA-CTAATTTAGAATGAAGGTT
1 ATAGTTTAGAGATGAAATTAGAATATATAAAAGTTTAGGGGATC-AATTTAGAATGAAGGTT
* * * * * * *
2280646 ATAGTTT-GAGGATGGAATTGGAATATTTAAAAGTTTAGTGGATCAATTTAGAATAAAAGTC
1 ATAGTTTAGA-GATGAAATTAGAATATATAAAAGTTTAGGGGATCAATTTAGAATGAAGGTT
*
2280707 ATAATTTTA-AGATGAAATT
1 AT-AGTTTAGAGATGAAATT
2280726 GGAACGTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
59 2 0.03
60 29 0.45
61 28 0.43
62 6 0.09
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (61 bp):
ATAGTTTAGAGATGAAATTAGAATATATAAAAGTTTAGGGGATCAATTTAGAATGAAGGTT
Found at i:2280726 original size:61 final size:60
Alignment explanation
Indices: 2280590--2280729 Score: 147
Period size: 61 Copynumber: 2.3 Consensus size: 60
2280580 ATATCGATAG
* * * * * *
2280590 TTTAGAGATGAAATTAGAATGTATAAAAGTTTGGGGACTAATTTAGAATGAAGGTTATAGT
1 TTTA-AGATGAAATTGGAATATATAAAAGTTTGGGGACTAATTTAGAATAAAAGTCATAAT
* * * * *
2280651 TTGAGGATGGAATTGGAATATTTAAAAGTTTAGTGGA-TCAATTTAGAATAAAAGTCATAAT
1 TTTAAGATGAAATTGGAATATATAAAAGTTT-GGGGACT-AATTTAGAATAAAAGTCATAAT
2280712 TTTAAGATGAAATTGGAA
1 TTTAAGATGAAATTGGAA
2280730 CGTTAAAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
60 23 0.37
61 40 0.63
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (60 bp):
TTTAAGATGAAATTGGAATATATAAAAGTTTGGGGACTAATTTAGAATAAAAGTCATAAT
Found at i:2281825 original size:2 final size:2
Alignment explanation
Indices: 2281820--2281851 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2281810 TGAAAGATGC
*
2281820 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2281852 GGGTAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2283524 original size:91 final size:90
Alignment explanation
Indices: 2283362--2283599 Score: 244
Period size: 91 Copynumber: 2.6 Consensus size: 90
2283352 GTTGAGAGTG
* * * * * ** *
2283362 TTAACCTAAAATATGATCATATTTATTCTAAAATATTACACAATTTG-TAGTAATTTCGATTACA
1 TTAACTTAAAATGTGACCATATCTACTCTAAAA-GCTACACAA-TTGATAATAATTTCGATTACA
** * * *
2283426 ATTAAGAATGTTATATTAAAACGTGTT
64 ACCAAGAATGTTACATTAAAACATATT
* * * * *
2283453 TTAACTTAAAATGTGACCTTATCTACTCTAAAAAGCTACACGATTGGTAATATTTTCGATTAGAA
1 TTAACTTAAAATGTGACCATATCTACTCT-AAAAGCTACACAATTGATAATAATTTCGATTACAA
**
2283518 CCAAGAATGTTACATTGCAACATATT
65 CCAAGAATGTTACATTAAAACATATT
* *
2283544 TTAACTTAAAATGTGACCATATGTACTCTAAAAGTTACACAATTGATAATAATTTC
1 TTAACTTAAAATGTGACCATATCTACTCTAAAAGCTACACAATTGATAATAATTTC
2283600 AGTTATAACA
Statistics
Matches: 120, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
90 26 0.22
91 90 0.75
92 4 0.03
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (90 bp):
TTAACTTAAAATGTGACCATATCTACTCTAAAAGCTACACAATTGATAATAATTTCGATTACAAC
CAAGAATGTTACATTAAAACATATT
Found at i:2285763 original size:18 final size:18
Alignment explanation
Indices: 2285737--2285771 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2285727 ATTTATTTAA
* *
2285737 TATTTAAATGTTTAAAAG
1 TATTAAAATATTTAAAAG
2285755 TATTAAAATATTTAAAA
1 TATTAAAATATTTAAAA
2285772 ATAAAATACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
TATTAAAATATTTAAAAG
Found at i:2288077 original size:13 final size:13
Alignment explanation
Indices: 2288059--2288083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2288049 GGTTTGGTAT
2288059 TTTTATTTATTTA
1 TTTTATTTATTTA
2288072 TTTTATTTATTT
1 TTTTATTTATTT
2288084 TTGGTTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:2290752 original size:22 final size:22
Alignment explanation
Indices: 2290711--2290756 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2290701 ATCTTGACTA
2290711 CTAAAAAATATTAAATAATTATG
1 CTAAAAAATATTAAATAATT-TG
2290734 CTAAAAAA-ATTAGAA-AATTTG
1 CTAAAAAATATTA-AATAATTTG
2290755 CT
1 CT
2290757 GAGATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.33
Consensus pattern (22 bp):
CTAAAAAATATTAAATAATTTG
Found at i:2291134 original size:14 final size:15
Alignment explanation
Indices: 2291094--2291136 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
2291084 GATAAATATT
2291094 TAAATATAATA-AAA
1 TAAATATAATATAAA
* *
2291108 TAACTATAGTATAAA
1 TAAATATAATATAAA
2291123 TAAATA-AATATAAA
1 TAAATATAATATAAA
2291137 AATATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
TAAATATAATATAAA
Found at i:2297582 original size:14 final size:14
Alignment explanation
Indices: 2297565--2297604 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2297555 TCCTCCTTTT
2297565 TTATTTATATTATA
1 TTATTTATATTATA
*
2297579 TTATTTTTATTATA
1 TTATTTATATTATA
2297593 TATATCTTATAT
1 T-TAT-TTATAT
2297605 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:2297772 original size:16 final size:17
Alignment explanation
Indices: 2297736--2297786 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
2297726 TTTGTTTTTA
*
2297736 TTTATTTATA-TA-TAT
1 TTTATTTTTACTATTAT
*
2297751 TATATTTTTACT-TTAT
1 TTTATTTTTACTATTAT
*
2297767 TTTATTTTTTCTATTAT
1 TTTATTTTTACTATTAT
2297784 TTT
1 TTT
2297787 TTCCTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.28
16 14 0.48
17 7 0.24
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTTACTATTAT
Found at i:2297775 original size:17 final size:17
Alignment explanation
Indices: 2297731--2297786 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2297721 CTATTTTTGT
*
2297731 TTTTATTTATTTA-TATA
1 TTTTATTT-TTTACTTTA
*
2297748 TATTATATTTTTACTTTA
1 TTTTAT-TTTTTACTTTA
2297766 TTTTATTTTTT-CTATTA
1 TTTTATTTTTTACT-TTA
2297783 TTTT
1 TTTT
2297787 TTCCTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 21 0.64
18 10 0.30
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTACTTTA
Found at i:2298056 original size:26 final size:27
Alignment explanation
Indices: 2298009--2298062 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
2297999 TTATTTTTAT
2298009 TATTTTTTACGTGTTTTGTTATT-TTC
1 TATTTTTTACGTGTTTTGTTATTATTC
* *
2298035 TATTTTTT-CTTGTTTTATTTATTATTC
1 TATTTTTTACGTGTTTT-GTTATTATTC
2298062 T
1 T
2298063 CACGTTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 13 0.54
27 4 0.17
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.72
Consensus pattern (27 bp):
TATTTTTTACGTGTTTTGTTATTATTC
Found at i:2300928 original size:563 final size:563
Alignment explanation
Indices: 2299862--2300981 Score: 2116
Period size: 563 Copynumber: 2.0 Consensus size: 563
2299852 CAATCATTGC
* *
2299862 AGAAGAACTGGCATAGGAAGGTTCGTTGGGTGTATTTAGCTCATTCAAATCTGGATTCACATCCA
1 AGAAGAACTGGCAGAGGAAGGTTCGTTGGGTGTATTTAGCTCATTCAAATCTGGATTCACAGCCA
*
2299927 CTTTTGGAAGACTAATGGGGTATCCTATCGCCGATTCAGCACTACCTATTCACTTTTGGGAGAAT
66 CTTTTGGAAGACTAATGGGGTAGCCTATCGCCGATTCAGCACTACCTATTCACTTTTGGGAGAAT
* *
2299992 TCATCACTAGGAAATGGCATGAAGGTGCTTCAAAGGAAAAGTGGATGAAAGTTTTTACACTTCTT
131 TCATCACTAGGAAATGGCATGAAGGTGCTTCAAAGGAAAAGTAGATGAAAGTTTTTACACATCTT
2300057 CAGGATCGGGATATTACCTGGAGAGCCCCCTGGTTGTTCCTCAGTGATGTTCTTTTCCGGTGTGG
196 CAGGATCGGGATATTACCTGGAGAGCCCCCTGGTTGTTCCTCAGTGATGTTCTTTTCCGGTGTGG
2300122 GGATTCTGATACTATGACCTTACTTGGACTTTGGGATGCAGTTGGGTATGCCCCGTTGTTAGCAC
261 GGATTCTGATACTATGACCTTACTTGGACTTTGGGATGCAGTTGGGTATGCCCCGTTGTTAGCAC
2300187 TTAGACAGTATGGGGCACGTCAGTTTATCCCGGTAACATGCAGGCTAGCTAGATCAGAGTTTGTG
326 TTAGACAGTATGGGGCACGTCAGTTTATCCCGGTAACATGCAGGCTAGCTAGATCAGAGTTTGTG
*
2300252 TATAATGGTGACAGTTATAAGAAGAGGATCAAGGAAACAGATGATTCATGGAAGAAAGTATGTCA
391 TATAAAGGTGACAGTTATAAGAAGAGGATCAAGGAAACAGATGATTCATGGAAGAAAGTATGTCA
2300317 GATGGATGTTGTGGCTGTCAGAGAAATGCTTACTCTGGATTATGTGGAGTGGCGAAGACTGAGAA
456 GATGGATGTTGTGGCTGTCAGAGAAATGCTTACTCTGGATTATGTGGAGTGGCGAAGACTGAGAA
2300382 AGAATGATAACATCCCGGTGCCAGAATGTGAAGACACTTTTGG
521 AGAATGATAACATCCCGGTGCCAGAATGTGAAGACACTTTTGG
2300425 AGAAGAACTGGCAGAGGAAGGTTCGTTGGGTGTATTTAGCTCATTCAAATCTGGATTCACAGCCA
1 AGAAGAACTGGCAGAGGAAGGTTCGTTGGGTGTATTTAGCTCATTCAAATCTGGATTCACAGCCA
*
2300490 CTTTTGGAAGACTAATGGGGTAGCCTATCGTCGATTCAGCACTACCTATTCACTTTTGGGAGAAT
66 CTTTTGGAAGACTAATGGGGTAGCCTATCGCCGATTCAGCACTACCTATTCACTTTTGGGAGAAT
2300555 TCATCACTAGGAAATGGCATGAAGGTGCTTCAAAGGAAAAGTAGATGAAAGTTTTTACACATCTT
131 TCATCACTAGGAAATGGCATGAAGGTGCTTCAAAGGAAAAGTAGATGAAAGTTTTTACACATCTT
2300620 CAGGATCGGGATATTACCTGGAGAGCCCCCTGGTTGTTCCTCAGTGATGTTCTTTTCCGGTGTGG
196 CAGGATCGGGATATTACCTGGAGAGCCCCCTGGTTGTTCCTCAGTGATGTTCTTTTCCGGTGTGG
2300685 GGATTCTGATACTATGACCTTACTTGGACTTTGGGATGCAGTTGGGTATGCCCCGTTGTTAGCAC
261 GGATTCTGATACTATGACCTTACTTGGACTTTGGGATGCAGTTGGGTATGCCCCGTTGTTAGCAC
*
2300750 TTAGACAGTATGGGGCACGTCAGTTTGTCCCGGTAACATG-AGGGCTAGCTAGATCAGAGTTTGT
326 TTAGACAGTATGGGGCACGTCAGTTTATCCCGGTAACATGCA-GGCTAGCTAGATCAGAGTTTGT
* * * *
2300814 GTATAAAGGTTACAGTTATAAGAAGAGGATCAAGGAAGCAGCTGATTCGTGGAAGAAAGTATGTC
390 GTATAAAGGTGACAGTTATAAGAAGAGGATCAAGGAAACAGATGATTCATGGAAGAAAGTATGTC
2300879 AGATGGATGTTGTGGCTGTCAGAGAAATGCTTACTCTGGATTATGTGGAGTGGCGAAGACTGAGA
455 AGATGGATGTTGTGGCTGTCAGAGAAATGCTTACTCTGGATTATGTGGAGTGGCGAAGACTGAGA
2300944 AAGAATGATAACATCCCGGTGCCAGAATGTGAAGACAC
520 AAGAATGATAACATCCCGGTGCCAGAATGTGAAGACAC
2300982 CCGGACCATG
Statistics
Matches: 544, Mismatches: 12, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
562 1 0.00
563 543 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (563 bp):
AGAAGAACTGGCAGAGGAAGGTTCGTTGGGTGTATTTAGCTCATTCAAATCTGGATTCACAGCCA
CTTTTGGAAGACTAATGGGGTAGCCTATCGCCGATTCAGCACTACCTATTCACTTTTGGGAGAAT
TCATCACTAGGAAATGGCATGAAGGTGCTTCAAAGGAAAAGTAGATGAAAGTTTTTACACATCTT
CAGGATCGGGATATTACCTGGAGAGCCCCCTGGTTGTTCCTCAGTGATGTTCTTTTCCGGTGTGG
GGATTCTGATACTATGACCTTACTTGGACTTTGGGATGCAGTTGGGTATGCCCCGTTGTTAGCAC
TTAGACAGTATGGGGCACGTCAGTTTATCCCGGTAACATGCAGGCTAGCTAGATCAGAGTTTGTG
TATAAAGGTGACAGTTATAAGAAGAGGATCAAGGAAACAGATGATTCATGGAAGAAAGTATGTCA
GATGGATGTTGTGGCTGTCAGAGAAATGCTTACTCTGGATTATGTGGAGTGGCGAAGACTGAGAA
AGAATGATAACATCCCGGTGCCAGAATGTGAAGACACTTTTGG
Found at i:2303115 original size:23 final size:25
Alignment explanation
Indices: 2303089--2303134 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
2303079 ATCAGAACAA
2303089 AAAGAGAAAA-AAAAAGA-AAAAGC
1 AAAGAGAAAATAAAAAGAGAAAAGC
2303112 AAAGAGAAAATAAAAAGAGAAAA
1 AAAGAGAAAATAAAAAGAGAAAA
2303135 AAAAACAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.48
24 7 0.33
25 4 0.19
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (25 bp):
AAAGAGAAAATAAAAAGAGAAAAGC
Found at i:2303119 original size:13 final size:11
Alignment explanation
Indices: 2303082--2303138 Score: 62
Period size: 11 Copynumber: 4.9 Consensus size: 11
2303072 AGATTCAATC
*
2303082 AGAACAAAAAG
1 AGAAAAAAAAG
2303093 AGAAAAAAAA-
1 AGAAAAAAAAG
2303103 AGAAAAAGCAAAG
1 AGAAAAA--AAAG
2303116 AGAAAATAAAAAG
1 AG-AAA-AAAAAG
2303129 AGAAAAAAAA
1 AGAAAAAAAA
2303139 ACAAAGGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 7 0.17
11 14 0.35
12 6 0.15
13 8 0.20
14 3 0.08
15 2 0.05
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:2303139 original size:13 final size:13
Alignment explanation
Indices: 2303087--2303139 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
2303077 CAATCAGAAC
2303087 AAAAAGAG--AAA
1 AAAAAGAGAAAAA
2303098 AAAAA-AGAAAAA
1 AAAAAGAGAAAAA
** *
2303110 GCAAAGAGAAAAT
1 AAAAAGAGAAAAA
2303123 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
2303136 AAAA
1 AAAA
2303140 CAAAGGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 2 0.06
11 5 0.15
12 6 0.18
13 20 0.61
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:2304258 original size:32 final size:31
Alignment explanation
Indices: 2304222--2304339 Score: 139
Period size: 31 Copynumber: 3.7 Consensus size: 31
2304212 GGAACAATGA
2304222 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATGTTG
* * *
2304254 GGGCATTTTTTAGATTTAACATCAAATGTT-
1 GGGCATCTTTGAGATTCAACATCAAATGTTG
* * *
2304284 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
*
2304316 GGGCATCTTTGGGAATTCAACATC
1 GGGCATCTTTGAG-ATTCAACATC
2304340 CTGATGCAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.07
31 45 0.61
32 24 0.32
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATGTTG
Found at i:2305310 original size:36 final size:36
Alignment explanation
Indices: 2305212--2305330 Score: 166
Period size: 36 Copynumber: 3.3 Consensus size: 36
2305202 TATGTTTTAT
* *
2305212 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTC
* * *
2305248 TTGGAACTAAGTTTTGTCTCCCTTGAGACAGTTTCTC
1 TTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTCTC
* *
2305285 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCC
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTC
2305321 TTGAAACAAA
1 TTGAAACAAA
2305331 ATCTTTGAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
36 41 0.57
37 31 0.43
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (36 bp):
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTC
Found at i:2305392 original size:65 final size:65
Alignment explanation
Indices: 2305288--2305461 Score: 226
Period size: 65 Copynumber: 2.6 Consensus size: 65
2305278 GTTTCTCTTG
* * * **
2305288 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
*
2305353 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
2305418 TA
64 TA
* *
2305420 AAACAAAATTTTGTTTCCCTTGAGATC-GTTT-TCATGAAACAA
1 AAAC-AAATTTTGTCTCCCTTGAGA-CAGTTTCTCTTGAAACAA
2305462 CAGATATCTT
Statistics
Matches: 97, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
65 37 0.38
66 4 0.04
67 32 0.33
68 23 0.24
69 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:2305458 original size:67 final size:67
Alignment explanation
Indices: 2305288--2305460 Score: 219
Period size: 67 Copynumber: 2.6 Consensus size: 67
2305278 GTTTCTCTTG
* * * * **
2305288 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
2305351 TA
66 TA
* *
2305353 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
2305418 TA
66 TA
*
2305420 AAACAAAATTTTGTTTCCCTTGAGATC-GTTT-TCATGAAACA
1 AAAC-AAATTTTGTCTCCCTTGAGA-CAGTTTCTCATGAAACA
2305461 ACAGATATCT
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
65 33 0.34
66 2 0.02
67 37 0.39
68 23 0.24
69 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:2306360 original size:106 final size:106
Alignment explanation
Indices: 2306170--2306522 Score: 496
Period size: 106 Copynumber: 3.3 Consensus size: 106
2306160 ACGAAGGGGC
* * *
2306170 TTCCTAGTTTCAGAGCCAATTTTAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAACACAAGCT
* *
2306235 CAACTTCACAACGAAGGGGCGGCTGGCTGTCAATAAACATT
66 CAACTTCACAACGAAGGGGCGACTGGCTGTCAACAAACATT
*
2306276 TTCCCAGTTTCAGAGCCAATTTTAACTTCACAACGAGGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAACACAAGCT
**
2306341 CAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAACTT
66 CAACTTCACAACGAAGGGGCGACTGGCTGTCAACAAAC-A-TT
* * *
2306384 TT--CAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATT-GAGCTCGAGACAACAC
1 TTCCCAG--T--TTCAGAGCCAATTTCAACTTCACAACGAGGGATATTGGA-CTCAAGACAACAC
* *
2306446 AAGCTCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAAT
61 AAGCTCAACTTCACAACGAAGGGGCGACTGGCTGTCAACAAACATT
*
2306492 TTCCCAGTTCCAGAGCCAATTTCAACTTCAC
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCAC
2306523 GACGGATATC
Statistics
Matches: 222, Mismatches: 16, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
106 121 0.55
107 1 0.00
108 9 0.04
109 3 0.01
110 88 0.40
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAACACAAGCT
CAACTTCACAACGAAGGGGCGACTGGCTGTCAACAAACATT
Found at i:2307848 original size:14 final size:15
Alignment explanation
Indices: 2307832--2307908 Score: 79
Period size: 14 Copynumber: 5.2 Consensus size: 15
2307822 CCTCCTTTTT
2307832 TATTTATATTATAT-
1 TATTTATATTATATA
*
2307846 TATTTGTATTATATA
1 TATTTATATTATATA
*
2307861 TATCTTATATCAT-TA
1 TAT-TTATATTATATA
*
2307876 TATATATA-TATATA
1 TATTTATATTATATA
*
2307890 TATATATATATATATA
1 TATTTATAT-TATATA
2307906 TAT
1 TAT
2307909 GTATTAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
13 2 0.04
14 27 0.51
15 8 0.15
16 16 0.30
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (15 bp):
TATTTATATTATATA
Found at i:2307862 original size:2 final size:2
Alignment explanation
Indices: 2307855--2307908 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
2307845 TTATTTGTAT
*
2307855 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
2307896 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
2307909 GTATTAATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2307955 original size:24 final size:25
Alignment explanation
Indices: 2307898--2307957 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
2307888 TATATATATA
2307898 TATATATATATGTATTAATTTTTCTC
1 TATATAT-TATGTATTAATTTTTCTC
* *
2307924 TATTTATTATGTATATATTTTTTCT-
1 TATATATTATGTAT-TAATTTTTCTC
2307949 TA-ATATTAT
1 TATATATTAT
2307958 ATTTTATACG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.20
25 9 0.30
26 15 0.50
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (25 bp):
TATATATTATGTATTAATTTTTCTC
Found at i:2307978 original size:39 final size:36
Alignment explanation
Indices: 2307935--2308018 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 36
2307925 ATTTATTATG
*
2307935 TATATATTTTTTCTTAATATTATATTTTATACGTTTTTA
1 TATATATATTTTCTTAATATTATATTTT-T--GTTTTTA
*
2307974 TATATATATTTTCTTAATATTCTATTTTTGTTTTTA
1 TATATATATTTTCTTAATATTATATTTTTGTTTTTA
*
2308010 TTTATATAT
1 TATATATAT
2308019 ATATTATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 15 0.36
38 1 0.02
39 26 0.62
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (36 bp):
TATATATATTTTCTTAATATTATATTTTTGTTTTTA
Found at i:2308047 original size:17 final size:18
Alignment explanation
Indices: 2308010--2308058 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
2308000 TTTGTTTTTA
*
2308010 TTTATATATATATTATATT
1 TTTATAT-TATTTTATATT
*
2308029 TTTATTTTATTTTAT-TT
1 TTTATATTATTTTATATT
*
2308046 TTTCTATTATTTT
1 TTTATATTATTTT
2308059 TTTCCTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 13 0.50
18 7 0.27
19 6 0.23
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATATTATTTTATATT
Found at i:2308286 original size:19 final size:19
Alignment explanation
Indices: 2308264--2308325 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
2308254 ATTTTATTCA
2308264 TTTTGTTTATTTTTTTATT
1 TTTTGTTTATTTTTTTATT
* *
2308283 TTTTTTTTATTTTTTTACGTG
1 TTTTGTTTATTTTTTTA--TT
*
2308304 TTTTG-TTATTTTTTCATT
1 TTTTGTTTATTTTTTTATT
2308322 TTTT
1 TTTT
2308326 CTTGTTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.14
19 16 0.44
20 10 0.28
21 5 0.14
ACGTcount: A:0.10, C:0.03, G:0.06, T:0.81
Consensus pattern (19 bp):
TTTTGTTTATTTTTTTATT
Found at i:2308287 original size:11 final size:11
Alignment explanation
Indices: 2308273--2308298 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2308263 ATTTTGTTTA
2308273 TTTTTTTATTT
1 TTTTTTTATTT
2308284 TTTTTTTATTT
1 TTTTTTTATTT
2308295 TTTT
1 TTTT
2308299 ACGTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:2308307 original size:20 final size:19
Alignment explanation
Indices: 2308264--2308317 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2308254 ATTTTATTCA
* *
2308264 TTTTGTTTATTTTTTTATTT
1 TTTT-TTTATTTTTTTAGTG
2308284 TTTTTTTATTTTTTTACGTG
1 TTTTTTTATTTTTTTA-GTG
*
2308304 TTTTGTTATTTTTT
1 TTTTTTTATTTTTT
2308318 CATTTTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.81
Consensus pattern (19 bp):
TTTTTTTATTTTTTTAGTG
Found at i:2308339 original size:27 final size:29
Alignment explanation
Indices: 2308254--2308340 Score: 58
Period size: 27 Copynumber: 3.1 Consensus size: 29
2308244 TTTTTTTAAC
* *
2308254 ATTTTATTCATTTTGTTTA-TTTTTTTATTT
1 ATTTT-TTCATTTT-TTTACGTGTTTTATTT
* ** *
2308284 TTTTTTTATTTT-TTTACGTGTTTT-GTT
1 ATTTTTTCATTTTTTTACGTGTTTTATTT
*
2308311 ATTTTTTCA-TTTTTT-CTTGTTTTATTT
1 ATTTTTTCATTTTTTTACGTGTTTTATTT
2308338 ATT
1 ATT
2308341 ATTCTCACAT
Statistics
Matches: 43, Mismatches: 11, Indels: 9
0.68 0.17 0.14
Matches are distributed among these distances:
26 9 0.21
27 20 0.47
28 5 0.12
29 5 0.12
30 4 0.09
ACGTcount: A:0.13, C:0.05, G:0.06, T:0.77
Consensus pattern (29 bp):
ATTTTTTCATTTTTTTACGTGTTTTATTT
Found at i:2311336 original size:20 final size:20
Alignment explanation
Indices: 2311313--2311387 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
2311303 CAACGCGAAC
*
2311313 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACACAGTT
*
2311333 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCGCAACACAGTT
* * *
2311353 TCGGAAA-TCGCAACGCGATTT
1 TC-CAAATTCGCAACAC-AGTT
2311374 TCCAAATTCGCAAC
1 TCCAAATTCGCAAC
2311388 GGTAATTACC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (20 bp):
TCCAAATTCGCAACACAGTT
Found at i:2311451 original size:57 final size:57
Alignment explanation
Indices: 2311359--2311503 Score: 245
Period size: 57 Copynumber: 2.5 Consensus size: 57
2311349 AGTTTCGGAA
* *
2311359 ATCGCAACGCGATTTTCCAAATTCGCAACGGTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAATGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
2311417 ATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
* *
2311474 ATCGCAATGAGGTTTTCAAATTCGCAACGC
1 ATCGCAATGCGATTTTCAAATTCGCAACGC
2311504 GATTTTCAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
57 68 0.82
58 15 0.18
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (57 bp):
ATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
Found at i:2311500 original size:20 final size:20
Alignment explanation
Indices: 2311475--2311522 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2311465 AACAGTACTA
*
2311475 TCGCAATGAGGTTTTCAAAT
1 TCGCAATGAGATTTTCAAAT
* *
2311495 TCGCAACGCGATTTTCAAAT
1 TCGCAATGAGATTTTCAAAT
2311515 TCGCAATG
1 TCGCAATG
2311523 CTAATTACCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (20 bp):
TCGCAATGAGATTTTCAAAT
Found at i:2311508 original size:77 final size:76
Alignment explanation
Indices: 2311418--2311650 Score: 290
Period size: 77 Copynumber: 3.0 Consensus size: 76
2311408 AACAGTACTA
2311418 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATG
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATG
2311483 AGGTTTTCAAAT
66 -GGTTTTCAAAT
* * *
2311495 TCGCAACGCGATTTTCAAATTCGCAATGCTAATTACCGATATAGGTAAACGGTACTATCGCAAT-
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATG
***
2311559 -GTAAACAATACT
66 GGTTTTCAA-A-T
** * * *
2311571 ATTTCATTGCGATTTTCAAATTCGCAACGCTAATTCCCGATATAGGTAAACAGTACTATCGTAAT
1 -TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
* *
2311636 GCGATTTTCATAT
65 G-GGTTTTCAAAT
2311649 TC
1 TC
2311651 ACGTTGCGAT
Statistics
Matches: 130, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
74 5 0.04
75 1 0.01
76 1 0.01
77 118 0.91
78 1 0.01
79 1 0.01
80 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (76 bp):
TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATG
GGTTTTCAAAT
Found at i:2311660 original size:20 final size:20
Alignment explanation
Indices: 2311635--2311702 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
2311625 ACTATCGTAA
*
2311635 TGCGATTTTCATATTCACGT
1 TGCGATTTACATATTCACGT
2311655 TGCGATTTACATATT-ATCGT
1 TGCGATTTACATATTCA-CGT
* *
2311675 TGCGATTTACCTATTCGCGT
1 TGCGATTTACATATTCACGT
*
2311695 TGCAATTT
1 TGCGATTT
2311703 TGGAACCTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.98
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (20 bp):
TGCGATTTACATATTCACGT
Done.