Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 9 of 14
Found at i:1588779 original size:24 final size:24
Alignment explanation
Indices: 1588708--1588788 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 24
1588698 TATGGTACTA
1588708 CGGTGC-AATTCTACGTGGCACTT
1 CGGTGCAAATTCTACGTGGCACTT
* *
1588731 CGGTGC--ATCTCTATGCGGTCA-TT
1 CGGTGCAAAT-TCTACGTGG-CACTT
1588754 CGG-GACAAATTCTACGTGGCACTT
1 CGGTG-CAAATTCTACGTGGCACTT
1588778 CGGTGCAAATT
1 CGGTGCAAATT
1588789 TATATGAGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
22 3 0.06
23 21 0.45
24 20 0.43
25 3 0.06
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (24 bp):
CGGTGCAAATTCTACGTGGCACTT
Found at i:1589376 original size:21 final size:22
Alignment explanation
Indices: 1589335--1589379 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1589325 TATAGCAGTA
*
1589335 CTGTAGCAGGGGAATCGATTCC
1 CTGTAGCAGGGGAACCGATTCC
*
1589357 CTGTAGCA-GGGTACCGATTCC
1 CTGTAGCAGGGGAACCGATTCC
1589378 CT
1 CT
1589380 ATTTGCATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (22 bp):
CTGTAGCAGGGGAACCGATTCC
Found at i:1590784 original size:29 final size:29
Alignment explanation
Indices: 1590752--1590837 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 29
1590742 TAATCTTTTT
1590752 AAATTTTAAGTTGATCCTCCTAAACTCTA
1 AAATTTTAAGTTGATCCTCCTAAACTCTA
* * ** * * *
1590781 AAATTTTGA-TTTAT-CTTGTAATCTTTTT
1 AAATTTTAAGTTGATCCTCCTAAAC-TCTA
1590809 AAATTTTAAGTTGATCCTCCTAAACTCTA
1 AAATTTTAAGTTGATCCTCCTAAACTCTA
1590838 CCACCAAGTT
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
27 6 0.15
28 14 0.35
29 14 0.35
30 6 0.15
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.45
Consensus pattern (29 bp):
AAATTTTAAGTTGATCCTCCTAAACTCTA
Found at i:1590808 original size:57 final size:58
Alignment explanation
Indices: 1590722--1590837 Score: 216
Period size: 57 Copynumber: 2.0 Consensus size: 58
1590712 AAAATTTTTG
1590722 AAAATTTTGATTTAAACTTGTAATCTTTTTAAATTTTAAGTTGATCCTCCTAAACTCT
1 AAAATTTTGATTTAAACTTGTAATCTTTTTAAATTTTAAGTTGATCCTCCTAAACTCT
*
1590780 AAAATTTTGATTT-ATCTTGTAATCTTTTTAAATTTTAAGTTGATCCTCCTAAACTCT
1 AAAATTTTGATTTAAACTTGTAATCTTTTTAAATTTTAAGTTGATCCTCCTAAACTCT
1590837 A
1 A
1590838 CCACCAAGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
57 44 0.77
58 13 0.23
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (58 bp):
AAAATTTTGATTTAAACTTGTAATCTTTTTAAATTTTAAGTTGATCCTCCTAAACTCT
Found at i:1596802 original size:24 final size:24
Alignment explanation
Indices: 1596775--1596835 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1596765 CAAATGAACA
* **
1596775 AACATAAACAAACGGATGTAAACG
1 AACATAAACAAACGAACCTAAACG
** *
1596799 AACATAAATGAACGAACCTAAATG
1 AACATAAACAAACGAACCTAAACG
1596823 AACATAAACAAAC
1 AACATAAACAAAC
1596836 ACAATAAATG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.57, C:0.18, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAAACAAACGAACCTAAACG
Found at i:1596812 original size:14 final size:14
Alignment explanation
Indices: 1596795--1596825 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1596785 AACGGATGTA
1596795 AACGAACATAAATG
1 AACGAACATAAATG
*
1596809 AACGAACCTAAATG
1 AACGAACATAAATG
1596823 AAC
1 AAC
1596826 ATAAACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:1596892 original size:23 final size:23
Alignment explanation
Indices: 1596866--1596914 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1596856 AACTTGCACA
* *
1596866 AACATAACAAATGAACATAATCG
1 AACACAACAAATGAACATAAACG
* *
1596889 AACACAATAAATGAGCATAAACG
1 AACACAACAAATGAACATAAACG
1596912 AAC
1 AAC
1596915 GTAAACAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (23 bp):
AACACAACAAATGAACATAAACG
Found at i:1597113 original size:24 final size:24
Alignment explanation
Indices: 1597086--1597143 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
1597076 ACTGAATATA
1597086 AACGAACATACACATAAATAAATG
1 AACGAACATACACATAAATAAATG
1597110 AACGAACATACACATAAATAAATG
1 AACGAACATACACATAAATAAATG
1597134 AACGAACATA
1 AACGAACATA
1597144 AACGAACGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.59, C:0.17, G:0.09, T:0.16
Consensus pattern (24 bp):
AACGAACATACACATAAATAAATG
Found at i:1597853 original size:44 final size:44
Alignment explanation
Indices: 1597790--1597881 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
1597780 AATAAGGGGG
1597790 ATGAAGAGAATAGTAGGTATGATGATGATGTATGTATATAATAT
1 ATGAAGAGAATAGTAGGTATGATGATGATGTATGTATATAATAT
*
1597834 ATGAAGAGAATAGTAGGTATGATGCTGATGTATGTATATAATAT
1 ATGAAGAGAATAGTAGGTATGATGATGATGTATGTATATAATAT
1597878 ATGA
1 ATGA
1597882 TAGAAGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.40, C:0.01, G:0.25, T:0.34
Consensus pattern (44 bp):
ATGAAGAGAATAGTAGGTATGATGATGATGTATGTATATAATAT
Found at i:1599401 original size:21 final size:21
Alignment explanation
Indices: 1599345--1599469 Score: 116
Period size: 21 Copynumber: 6.1 Consensus size: 21
1599335 AAATAAATGC
*
1599345 AACTTCGACTATCGCAATGCG
1 AACTTCGACTATCGCAACGCG
*
1599366 AA-TAT-GTA-AATCGCAACGCG
1 AACT-TCG-ACTATCGCAACGCG
1599386 AACTTCGACTATCGCAA--CG
1 AACTTCGACTATCGCAACGCG
* * **
1599405 AATTTGGAAAATCGCAACGCG
1 AACTTCGACTATCGCAACGCG
*
1599426 AACTCCGACTATCGCAACGCG
1 AACTTCGACTATCGCAACGCG
* *
1599447 AACTTAGACTATCGCAATGCG
1 AACTTCGACTATCGCAACGCG
1599468 AA
1 AA
1599470 TATGTAAATC
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
19 15 0.18
20 16 0.20
21 51 0.62
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
AACTTCGACTATCGCAACGCG
Found at i:1599428 original size:40 final size:39
Alignment explanation
Indices: 1599345--1599444 Score: 146
Period size: 40 Copynumber: 2.5 Consensus size: 39
1599335 AAATAAATGC
*
1599345 AACTTCGACTATCGCAATGCGAATATGTAAATCGCAACGCG
1 AACTTCGACTATCGCAA--CGAATATGAAAATCGCAACGCG
*
1599386 AACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCG
1 AACTTCGACTATCGCAACGAATAT-GAAAATCGCAACGCG
*
1599426 AACTCCGACTATCGCAACG
1 AACTTCGACTATCGCAACG
1599445 CGAACTTAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 6 0.11
40 32 0.58
41 17 0.31
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (39 bp):
AACTTCGACTATCGCAACGAATATGAAAATCGCAACGCG
Found at i:1599482 original size:20 final size:21
Alignment explanation
Indices: 1599457--1599509 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1599447 AACTTAGACT
*
1599457 ATCGCAATGCGAATAT-GTAA
1 ATCGCAATGCGAATATGGAAA
* *
1599477 ATCGCAACGCGAATTTGGAAA
1 ATCGCAATGCGAATATGGAAA
1599498 ATCGCAATGCGA
1 ATCGCAATGCGA
1599510 TAGTCGAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (21 bp):
ATCGCAATGCGAATATGGAAA
Found at i:1599501 original size:21 final size:20
Alignment explanation
Indices: 1599355--1599509 Score: 98
Period size: 21 Copynumber: 7.6 Consensus size: 20
1599345 AACTTCGACT
* * *
1599355 ATCGCAATGCGAATATGTAA
1 ATCGCAACGCGAATTTGAAA
* **
1599375 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAA-TTTGAAA
1599396 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAATTT-GAAA
** **
1599415 ATCGCAACGCGAACTCCGACT
1 ATCGCAACGCGAA-TTTGAAA
* **
1599436 ATCGCAACGCGAACTTAGACT
1 ATCGCAACGCGAA-TTTGAAA
* * *
1599457 ATCGCAATGCGAATATGTAA
1 ATCGCAACGCGAATTTGAAA
1599477 ATCGCAACGCGAATTTGGAAA
1 ATCGCAACGCGAATTT-GAAA
*
1599498 ATCGCAATGCGA
1 ATCGCAACGCGA
1599510 TAGTCGAAGT
Statistics
Matches: 104, Mismatches: 25, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
18 2 0.02
19 13 0.12
20 28 0.27
21 60 0.58
22 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGAAA
Found at i:1599568 original size:20 final size:19
Alignment explanation
Indices: 1599545--1599590 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1599535 GGAAACTGAT
* *
1599545 TTGCGATACTGGAGATCGCG
1 TTGCGA-ACTAGAGATCGCA
*
1599565 TTGCGAATTAGAGATCGCA
1 TTGCGAACTAGAGATCGCA
1599584 TTGCGAA
1 TTGCGAA
1599591 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
TTGCGAACTAGAGATCGCA
Found at i:1599580 original size:19 final size:19
Alignment explanation
Indices: 1599556--1599592 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1599546 TGCGATACTG
*
1599556 GAGATCGCGTTGCGAATTA
1 GAGATCGCATTGCGAATTA
1599575 GAGATCGCATTGCGAATT
1 GAGATCGCATTGCGAATT
1599593 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (19 bp):
GAGATCGCATTGCGAATTA
Found at i:1601811 original size:19 final size:18
Alignment explanation
Indices: 1601784--1601822 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1601774 TATCTAATCT
*
1601784 TAATTAATATAAACCTTAA
1 TAATAAATATAAACC-TAA
*
1601803 TAATAAATATTAACCTAA
1 TAATAAATATAAACCTAA
1601821 TA
1 TA
1601823 TAATTTAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAAATATAAACCTAA
Found at i:1609377 original size:17 final size:18
Alignment explanation
Indices: 1609357--1609394 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1609347 ACATTGATAA
*
1609357 TTTATTAACTAAT-AATT
1 TTTATTAACAAATGAATT
*
1609374 TTTATTCACAAATGAATT
1 TTTATTAACAAATGAATT
1609392 TTT
1 TTT
1609395 TATCTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTATTAACAAATGAATT
Found at i:1609490 original size:12 final size:11
Alignment explanation
Indices: 1609466--1609496 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
1609456 TATATTTTCG
1609466 TAAAATAAATT
1 TAAAATAAATT
1609477 TAAAATAGAATT
1 TAAAATA-AATT
1609489 TAAAATAA
1 TAAAATAA
1609497 CTTTTTACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:1609964 original size:22 final size:22
Alignment explanation
Indices: 1609936--1609978 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1609926 CCTTGTCCTG
*
1609936 CGCCTGCTCCCCGCTGCATGCT
1 CGCCTGCTCCCCACTGCATGCT
1609958 CGCCTGCTCCCCACTGCATGC
1 CGCCTGCTCCCCACTGCATGC
1609979 AGGCGACCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.51, G:0.21, T:0.21
Consensus pattern (22 bp):
CGCCTGCTCCCCACTGCATGCT
Found at i:1610044 original size:31 final size:31
Alignment explanation
Indices: 1610009--1610070 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1609999 CATGGCGCAT
*
1610009 GCAAAGCTTCATCCTCTCGCCATAGCTCGTA
1 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
1610040 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
1610071 TAGAACACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
Found at i:1627328 original size:22 final size:24
Alignment explanation
Indices: 1627281--1627339 Score: 86
Period size: 22 Copynumber: 2.5 Consensus size: 24
1627271 AAGGCATAAG
1627281 AAACGTGCAACAAGAGTAGAGAAA
1 AAACGTGCAACAAGAGTAGAGAAA
*
1627305 AAGCGTGCAACAAGAG-A-AGAAA
1 AAACGTGCAACAAGAGTAGAGAAA
*
1627327 AAACGTGTAACAA
1 AAACGTGCAACAA
1627340 TGATAGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 16 0.50
23 1 0.03
24 15 0.47
ACGTcount: A:0.54, C:0.14, G:0.24, T:0.08
Consensus pattern (24 bp):
AAACGTGCAACAAGAGTAGAGAAA
Found at i:1628188 original size:7 final size:7
Alignment explanation
Indices: 1628178--1628225 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
1628168 TCATATCTTT
*
1628178 TAAATCC
1 TAAACCC
*
1628185 TAAATCC
1 TAAACCC
1628192 TAAACCC
1 TAAACCC
1628199 TAAACCC
1 TAAACCC
1628206 TAAACCC
1 TAAACCC
*
1628213 TAAACCT
1 TAAACCC
1628220 TAAACC
1 TAAACC
1628226 AAACTTAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:1632898 original size:15 final size:15
Alignment explanation
Indices: 1632879--1632934 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
1632869 TTCATGGGGT
* *
1632879 AAGAAGACAACGTCT
1 AAGAAGAAAACGTCA
1632894 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
1632909 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
1632924 AAGAAGGAAAA
1 AAGAA-GAAAA
1632935 AGAAAGCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 33 0.87
16 5 0.13
ACGTcount: A:0.59, C:0.12, G:0.21, T:0.07
Consensus pattern (15 bp):
AAGAAGAAAACGTCA
Found at i:1638520 original size:26 final size:27
Alignment explanation
Indices: 1638485--1638535 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1638475 TTTTAGTACT
*
1638485 CTTTAATAGT-T-CATTATATACTTCA
1 CTTTAATAGTATAAATTATATACTTCA
1638510 CTTTAAATAGTATAAATTATATACTT
1 CTTT-AATAGTATAAATTATATACTT
1638536 ATTTCATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 6 0.27
27 1 0.05
28 11 0.50
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (27 bp):
CTTTAATAGTATAAATTATATACTTCA
Found at i:1638806 original size:2 final size:2
Alignment explanation
Indices: 1638794--1638857 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
1638784 TCAATCTACA
1638794 AT AT A- AT AT AT AT AT AT A- 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
1638834 -T AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1638858 AAAATTTCCG
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 56 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1638829 original size:23 final size:23
Alignment explanation
Indices: 1638794--1638858 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
1638784 TCAATCTACA
1638794 ATATA-ATATATATATATAATAT
1 ATATATATATATATATATAATAT
*
1638816 ATATATATATATATATATTATAT
1 ATATATATATATATATATAATAT
1638839 ATATATATATATATATATAA
1 ATATATATATATATATATAA
1638859 AAATTTCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 5 0.12
23 35 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATATATATATATATAATAT
Found at i:1639140 original size:87 final size:86
Alignment explanation
Indices: 1638920--1639128 Score: 289
Period size: 85 Copynumber: 2.4 Consensus size: 86
1638910 GACGTGTGCA
** * * *
1638920 TCAATGACATGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACGCATATATGTATGTC
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATATG-ATGTC
1638985 AAGCAGATTTATGACGGGGGCT
65 AAGCAGATTTATGACGGGGGCT
* * *
1639007 TTAATGACGCGCAATGTAAGTCATACATACGTGTCATAAATTTATGACGCACAAATATG-TGTC-
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATATGATGTCA
*
1639070 ATCTTA-ATTTATGACGGGGGCT
66 AGC--AGATTTATGACGGGGGCT
1639092 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCAT
1639129 CTTAATTTAT
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
84 2 0.02
85 55 0.50
86 1 0.01
87 51 0.47
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (86 bp):
TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATATGATGTCA
AGCAGATTTATGACGGGGGCT
Found at i:1639172 original size:57 final size:57
Alignment explanation
Indices: 1639065--1639185 Score: 165
Period size: 57 Copynumber: 2.1 Consensus size: 57
1639055 GCACAAATAT
* *
1639065 GTGTCATCTTAATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCA-TACATGC
1 GTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAAAGTAAGTCATTA-ATGC
* *
1639122 GTGTCATCTTAATTTATGATGGGGGCTTCAATGACACTCAAAG-AACGTCATTAATGC
1 GTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAAAGTAA-GTCATTAATGC
*
1639179 GCGTCAT
1 GTGTCAT
1639186 AAATTTATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
56 2 0.04
57 53 0.93
58 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (57 bp):
GTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAAAGTAAGTCATTAATGC
Found at i:1639640 original size:4 final size:4
Alignment explanation
Indices: 1639631--1639679 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
1639621 AGATATTTTG
* * * *
1639631 ATAC ATAC ATAC ATGC ATAC ATAC ATGC ATGC ATAC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1639679 A
1 A
1639680 CACGCGCACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:1639673 original size:16 final size:16
Alignment explanation
Indices: 1639631--1639676 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
1639621 AGATATTTTG
*
1639631 ATACATACATACATGC
1 ATACATACATGCATGC
1639647 ATACATACATGCATGC
1 ATACATACATGCATGC
1639663 ATACATACATGCAT
1 ATACATACATGCAT
1639677 ACACACGCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (16 bp):
ATACATACATGCATGC
Found at i:1639692 original size:12 final size:12
Alignment explanation
Indices: 1639677--1639742 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 12
1639667 ATACATGCAT
1639677 ACACACGCGCAC
1 ACACACGCGCAC
* *
1639689 ACACACACGTAC
1 ACACACGCGCAC
* *
1639701 ACGCACGCGTAC
1 ACACACGCGCAC
* * * * *
1639713 GCGCACACACGC
1 ACACACGCGCAC
1639725 ACACACGCGCAC
1 ACACACGCGCAC
1639737 ACACAC
1 ACACAC
1639743 ACATACAACT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.33, C:0.47, G:0.17, T:0.03
Consensus pattern (12 bp):
ACACACGCGCAC
Found at i:1639732 original size:18 final size:18
Alignment explanation
Indices: 1639711--1639745 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1639701 ACGCACGCGT
*
1639711 ACGCGCACACACGCACAC
1 ACGCGCACACACACACAC
1639729 ACGCGCACACACACACA
1 ACGCGCACACACACACA
1639746 TACAACTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.49, G:0.14, T:0.00
Consensus pattern (18 bp):
ACGCGCACACACACACAC
Found at i:1640311 original size:2 final size:2
Alignment explanation
Indices: 1640295--1640341 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1640285 TTTACACATA
1640295 AT AT A- AT AT -T 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
1640335 AT AT AT A
1 AT AT AT A
1640342 ATTTTACGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1655758 original size:64 final size:65
Alignment explanation
Indices: 1655650--1655784 Score: 184
Period size: 64 Copynumber: 2.1 Consensus size: 65
1655640 GTGCACTAAT
* *
1655650 TACATTCAATGTTTCAAACAAGCCTGGAGTGCATCGATGTATGGTCTGTGCGTCGGTACACAAAA
1 TACATTCAATGTTTCAAACAACCCTGGAGTGCATCGATGCATGGTCTGTGCGTCGGTACACAAAA
* * * *
1655715 TACATTCGATGTTTCAATA-AACCCT-GAGTGTATCGATGCATGGTGTGTGCGTCGGTACACTAA
1 TACATTCAATGTTTCAA-ACAACCCTGGAGTGCATCGATGCATGGTCTGTGCGTCGGTACACAAA
1655778 A
65 A
*
1655779 TGCATT
1 TACATT
1655785 AGAAATGGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 40 0.65
65 21 0.34
66 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (65 bp):
TACATTCAATGTTTCAAACAACCCTGGAGTGCATCGATGCATGGTCTGTGCGTCGGTACACAAAA
Found at i:1657736 original size:6 final size:6
Alignment explanation
Indices: 1657725--1657751 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1657715 TATTTGGGTC
1657725 ATTTGG ATTTGG ATTTGG ATTTGG ATT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATT
1657752 AGGTGGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.52
Consensus pattern (6 bp):
ATTTGG
Found at i:1658551 original size:23 final size:23
Alignment explanation
Indices: 1658472--1658551 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
1658462 ACCCGATGGG
*
1658472 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGGGA
* * *
1658495 TGTATC-AGTGCACCTTC-ATGG-
1 TGCATCGA-TGCACATTCAAGGGA
* *
1658516 TGTATCGAAGCACATTCAAGGGA
1 TGCATCGATGCACATTCAAGGGA
1658539 TGCATCGATGCAC
1 TGCATCGATGCAC
1658552 TATCTAGTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
21 13 0.30
22 7 0.16
23 24 0.55
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:1661367 original size:21 final size:21
Alignment explanation
Indices: 1661325--1661367 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1661315 TTTCTGGGCT
* *
1661325 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1661346 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1661367 A
1 A
1661368 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1661925 original size:2 final size:2
Alignment explanation
Indices: 1661918--1661948 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1661908 CATGTTACAG
*
1661918 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1661949 GAGTTGTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1662557 original size:30 final size:30
Alignment explanation
Indices: 1662523--1662775 Score: 479
Period size: 30 Copynumber: 8.4 Consensus size: 30
1662513 GGTTCTTCGG
*
1662523 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1662553 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1662583 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1662613 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1662643 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1662673 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1662703 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1662733 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1662763 GACCTTTGGATAG
1 GACCTCTGGATAG
1662776 GTCTTTCGGA
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 220 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1666150 original size:21 final size:21
Alignment explanation
Indices: 1666108--1666150 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1666098 TTTCTGGGCT
* *
1666108 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1666129 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1666150 A
1 A
1666151 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1666201 original size:20 final size:20
Alignment explanation
Indices: 1666173--1666213 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1666163 TTCCAGAATG
*
1666173 CTAGAGGGGAATCGATACCC
1 CTAGAGGGGAACCGATACCC
* *
1666193 CTAGGGGGGAACCGATTCCC
1 CTAGAGGGGAACCGATACCC
1666213 C
1 C
1666214 CATAATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.15
Consensus pattern (20 bp):
CTAGAGGGGAACCGATACCC
Found at i:1667338 original size:30 final size:30
Alignment explanation
Indices: 1667304--1667556 Score: 470
Period size: 30 Copynumber: 8.4 Consensus size: 30
1667294 GGTTCTTCGG
*
1667304 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1667334 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1667364 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1667394 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1667424 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1667454 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1667484 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1667514 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1667544 GACCTTTGGATAG
1 GACCTCTGGATAG
1667557 GTCTTTCAGA
Statistics
Matches: 218, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 218 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1668710 original size:63 final size:61
Alignment explanation
Indices: 1668590--1668718 Score: 170
Period size: 63 Copynumber: 2.1 Consensus size: 61
1668580 AATGATCCTC
* * *
1668590 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTATCCATATGTTCCGTAGAACATA
* * *
1668651 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAATTATCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTATCCATATGTTCCGTAGAACATA
1668714 GGTAA
1 GGTAA
1668719 ACCCTCGACT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.42
63 29 0.49
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTATCCATATGTTCCGTAGAACATA
Found at i:1668713 original size:32 final size:31
Alignment explanation
Indices: 1668593--1668720 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
1668583 GATCCTCGGT
* * * *
1668593 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
1668624 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
1668655 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
* *
1668687 AATTATCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
1668718 AAC
1 AAC
1668721 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
30 4 0.05
31 50 0.63
32 21 0.27
33 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:1670105 original size:21 final size:21
Alignment explanation
Indices: 1670079--1670124 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1670069 ATTTTATTCG
*
1670079 CTTGAAGGGGTA-TCGGTTCCC
1 CTTGAAGGGGTACT-GATTCCC
*
1670100 CTTGAATGGGTACTGATTCCC
1 CTTGAAGGGGTACTGATTCCC
1670121 CTTG
1 CTTG
1670125 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.15, C:0.24, G:0.28, T:0.33
Consensus pattern (21 bp):
CTTGAAGGGGTACTGATTCCC
Found at i:1671502 original size:41 final size:41
Alignment explanation
Indices: 1671456--1671537 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1671446 TAAATGTGAT
1671456 AAATGGGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAA
1 AAATGGGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAA
1671497 AAATGGGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAA
1 AAATGGGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAA
1671538 CTTGATTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.02, G:0.32, T:0.22
Consensus pattern (41 bp):
AAATGGGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAA
Found at i:1673855 original size:4 final size:4
Alignment explanation
Indices: 1673848--1674507 Score: 1153
Period size: 4 Copynumber: 166.8 Consensus size: 4
1673838 TATATATAAA
*
1673848 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAGG TATG TATTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-TG
*
1673897 TATG TATG TATGG TATG TATG TAGG TATG TATG TATG TATG TATG TATG
1 TATG TATG TAT-G TATG TATG TATG TATG TATG TATG TATG TATG TATG
1673946 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1673992 TATG TATG TATG TATG TATG TATG TATG TTATG TATG TA-- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG -TATG TATG TATG TATG TATG
1674039 TATG TATG -ATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1674086 TATG --TG TATG TATG TATG TAATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG T-ATG TATG TATG TATG TATG TATG TATG
1674133 TATG TATG TA-G TATG TATG TATG TA-G TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1674179 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1674227 TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1674274 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1674322 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1674370 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1674418 TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
1674465 TATG TATG TATG TACG TATG TATA TAAG TATA TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1674508 ATACTTATGT
Statistics
Matches: 629, Mismatches: 12, Indels: 30
0.94 0.02 0.04
Matches are distributed among these distances:
2 6 0.01
3 15 0.02
4 592 0.94
5 16 0.03
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1675941 original size:18 final size:19
Alignment explanation
Indices: 1675908--1675943 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1675898 CTAAATTCCC
1675908 AAAAAAATCAAAATTTCTA
1 AAAAAAATCAAAATTTCTA
*
1675927 AAAAAAAT-AATATTTCT
1 AAAAAAATCAAAATTTCT
1675944 TTTAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAAAATCAAAATTTCTA
Found at i:1675984 original size:2 final size:2
Alignment explanation
Indices: 1675977--1676002 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1675967 TCATTTTTGA
1675977 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
1676003 TAAAATTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1676058 original size:42 final size:43
Alignment explanation
Indices: 1675990--1676095 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
1675980 TATATATATA
* * *
1675990 TATATATATATATTAAAATTTCCAATCTCAAGTAAA-TCATCT
1 TATATGTATATTTTAAATTTTCCAATCTCAAGTAAATTCATCT
* * *
1676032 TATATGTATATTTTAAATTTTTCAATCTCAAGTAAATTCTTTT
1 TATATGTATATTTTAAATTTTCCAATCTCAAGTAAATTCATCT
*
1676075 TATGTGTATATTTTAAATTTT
1 TATATGTATATTTTAAATTTT
1676096 AATAATTATA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 32 0.57
43 24 0.43
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (43 bp):
TATATGTATATTTTAAATTTTCCAATCTCAAGTAAATTCATCT
Found at i:1679619 original size:23 final size:21
Alignment explanation
Indices: 1679593--1679644 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 21
1679583 TTTTATGTAA
*
1679593 AAAAAATACTAATTAAACAATAT
1 AAAAAATAATAATT-AA-AATAT
1679616 AAAATAA-AATAATTAAAATAT
1 AAAA-AATAATAATTAAAATAT
1679637 AATAAAAT
1 AA-AAAAT
1679645 TTAGGGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 9 0.36
22 4 0.16
23 10 0.40
24 2 0.08
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAATAATAATTAAAATAT
Found at i:1679905 original size:35 final size:35
Alignment explanation
Indices: 1679859--1679970 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
1679849 AAAACATTCC
* *
1679859 TCAATTTCATTCTAAACCCCAAATTCCAAAGCAAT
1 TCAATTTCATTCTAAACACCAAATTCCAAAACAAT
* *
1679894 TCAATTTCATTCTAAACACTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACACCAAATTCCAAAACAAT
* * * *
1679929 TCAATTACATTCTAAA-ATCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACA-CCAAATTCCAAAACAAT
1679964 TCAATTT
1 TCAATTT
1679971 AAGGAGGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
34 1 0.01
35 66 0.99
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACACCAAATTCCAAAACAAT
Found at i:1681069 original size:35 final size:33
Alignment explanation
Indices: 1681020--1681132 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 33
1681010 AAAAAAGACA
*
1681020 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTT-GAATTTGGG-TTTAGAAT
*
1681055 GTAATTGAATTATTTTGAAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTG-AATTT-GGGTTTAGAAT
*
1681090 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTA-TTTTGAATTTG-GGTTTAGAAT
*
1681125 AAAATTGA
1 GAAATTGA
1681133 GGATTGTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
34 2 0.03
35 60 0.87
36 7 0.10
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.42
Consensus pattern (33 bp):
GAAATTGAATTATTTTGAATTTGGGTTTAGAAT
Found at i:1684650 original size:83 final size:81
Alignment explanation
Indices: 1684489--1684891 Score: 471
Period size: 83 Copynumber: 5.0 Consensus size: 81
1684479 AGAGAATTTT
* * * * *
1684489 AGAGTTTT-TCTCCAACTAAAACTCTTTTAATATCTAAA---AATATATAATAATATTTTTTAAA
1 AGAGTTTTATCT--AACCAAAACTCTTTTAATATCTAAATTTAAAAAATTATAATATCTTTTAAA
1684550 TTTAAAATATTAAATCTG
64 TTTAAAATATTAAATCTG
* * *
1684568 AGAGTTTTAATTTAACCAAAACTCTTTTGATATCTAAATTTAAACAAATTATAATATCTTTCAAA
1 AGAGTTTT-ATCTAACCAAAACTCTTTTAATATCTAAATTTAAA-AAATTATAATATCTTTTAAA
1684633 TTTAAAATATTAAATCTG
64 TTTAAAATATTAAATCTG
* * *
1684651 CGAGTTTTACTCTAAACAAAACTCTTTTAATATCTAAATTTAAAGAGATTATAATATCTTTTAAA
1 AGAGTTTTA-TCTAACCAAAACTCTTTTAATATCTAAATTTAAA-AAATTATAATATCTTTTAAA
* * *
1684716 TTTATAATATTAAACCTT
64 TTTAAAATATTAAATCTG
* * *
1684734 AAAGTTTTATTCCAACCAAAACTCTTTTAATATCTAAGTTTAAAAAGATTATAATATCTTTTAAA
1 AGAGTTTTA-TCTAACCAAAACTCTTTTAATATCTAAATTTAAAAA-ATTATAATATCTTTTAAA
*
1684799 TTTATAATATTAAATCTG
64 TTTAAAATATTAAATCTG
* * *
1684817 AGAGTTTTA-CT-ACCAAAACTCTTTTAATATCTAAACTTAAATAGATAATAATAT-TGTTTAAA
1 AGAGTTTTATCTAACCAAAACTCTTTTAATATCTAAATTTAAA-AAATTATAATATCT-TTTAAA
1684879 TTT-AAATATTAAA
64 TTTAAAATATTAAA
1684892 CTTTTATTTC
Statistics
Matches: 280, Mismatches: 34, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
79 41 0.15
80 46 0.16
81 4 0.01
82 4 0.01
83 185 0.66
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.42
Consensus pattern (81 bp):
AGAGTTTTATCTAACCAAAACTCTTTTAATATCTAAATTTAAAAAATTATAATATCTTTTAAATT
TAAAATATTAAATCTG
Found at i:1684725 original size:42 final size:41
Alignment explanation
Indices: 1684678--1684813 Score: 98
Period size: 42 Copynumber: 3.3 Consensus size: 41
1684668 AAAACTCTTT
1684678 TAATATCTAAATTTAAAGAGATTATAATATCTTTTAAATTTA
1 TAATAT-TAAATTTAAAGAGATTATAATATCTTTTAAATTTA
* ** *** * ** *
1684720 TAATATTAAACCTTAAAG-TTTTATTCCAAC--CAAAACTCTTT
1 TAATATTAAA-TTTAAAGAGATTATAATATCTTTTAAA-T-TTA
* *
1684761 TAATATCTAAGTTTAAAAAGATTATAATATCTTTTAAATTTA
1 TAATAT-TAAATTTAAAGAGATTATAATATCTTTTAAATTTA
1684803 TAATATTAAAT
1 TAATATTAAAT
1684814 CTGAGAGTTT
Statistics
Matches: 64, Mismatches: 23, Indels: 15
0.63 0.23 0.15
Matches are distributed among these distances:
39 3 0.05
40 1 0.02
41 27 0.42
42 29 0.45
43 1 0.02
44 3 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (41 bp):
TAATATTAAATTTAAAGAGATTATAATATCTTTTAAATTTA
Found at i:1688204 original size:66 final size:64
Alignment explanation
Indices: 1688062--1688219 Score: 221
Period size: 66 Copynumber: 2.4 Consensus size: 64
1688052 TACACTAGGG
*
1688062 TGTGCATCGGTGCAC-AAATCTGC-TTCGATGTTTCAAAATAGCCAGGGTGCATCGATGCATGTC
1 TGTGCATCGGTGCACTAAA--TGCATTCGATGTTTCAAAATAGCCAGGGTGCATCGATGCATGGC
1688125 T
64 T
* ***
1688126 TGTGCATCGGTGCACTTAATGCATTCGATGTTTCAAAATTTTCAGGGGGTGCATCGATGCATGGC
1 TGTGCATCGGTGCACTAAATGCATTCGATGTTTCAAAATAGCCA--GGGTGCATCGATGCATGGC
1688191 T
64 T
1688192 TGTGCATCGGTGCACTAAATGCATTCGA
1 TGTGCATCGGTGCACTAAATGCATTCGA
1688220 AATTCAATTT
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 3 0.04
64 33 0.39
65 2 0.02
66 46 0.55
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (64 bp):
TGTGCATCGGTGCACTAAATGCATTCGATGTTTCAAAATAGCCAGGGTGCATCGATGCATGGCT
Found at i:1690879 original size:23 final size:23
Alignment explanation
Indices: 1690847--1690995 Score: 139
Period size: 23 Copynumber: 6.7 Consensus size: 23
1690837 AAAACCCGAT
*
1690847 GAGTGTATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
1690870 GAGTGCATCGATACACA-AC-A-
1 GAGTGCATCGATGCACATTCAAG
* *
1690890 GAGTGTATCGATGTACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
*
1690913 GAGTTCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
1690936 GAGTGCATCGGTGCACCTTCAA-
1 GAGTGCATCGATGCACATTCAAG
* *
1690958 G-GTGTATCGATGCATATTCAAAG
1 GAGTGCATCGATGCACATTC-AAG
**
1690981 GA-TAAATCGATGCAC
1 GAGTGCATCGATGCAC
1690996 TGTTTAGTGA
Statistics
Matches: 100, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
20 14 0.14
21 16 0.16
22 5 0.05
23 65 0.65
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:1690908 original size:43 final size:43
Alignment explanation
Indices: 1690847--1690929 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
1690837 AAAACCCGAT
1690847 GAGTGTATCGATGCACATTCAAGGAGTGCATCGATACACAACA
1 GAGTGTATCGATGCACATTCAAGGAGTGCATCGATACACAACA
* * *
1690890 GAGTGTATCGATGTACATTCAAGGAGTTCATCGATGCACA
1 GAGTGTATCGATGCACATTCAAGGAGTGCATCGATACACA
1690930 TTCAAGGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (43 bp):
GAGTGTATCGATGCACATTCAAGGAGTGCATCGATACACAACA
Found at i:1690995 original size:44 final size:46
Alignment explanation
Indices: 1690853--1690995 Score: 127
Period size: 43 Copynumber: 3.2 Consensus size: 46
1690843 CGATGAGTGT
* * * **
1690853 ATCGATGCACATTCAAGGAGTGCATCGATACACA-AC-A-GAGTGT
1 ATCGATGCACATTCAAGGAGTTCATCGATGCACATTCAAGGAGTAA
* **
1690896 ATCGATGTACATTCAAGGAGTTCATCGATGCACATTCAAGGAGTGC
1 ATCGATGCACATTCAAGGAGTTCATCGATGCACATTCAAGGAGTAA
* * * *
1690942 ATCGGTGCACCTTCAAGGTG-T-ATCGATGCATATTCAAAGGA-TAA
1 ATCGATGCACATTCAAGGAGTTCATCGATGCACATTC-AAGGAGTAA
1690986 ATCGATGCAC
1 ATCGATGCAC
1690996 TGTTTAGTGA
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
43 31 0.37
44 24 0.29
45 7 0.08
46 21 0.25
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (46 bp):
ATCGATGCACATTCAAGGAGTTCATCGATGCACATTCAAGGAGTAA
Found at i:1694579 original size:330 final size:330
Alignment explanation
Indices: 1693958--1694615 Score: 1203
Period size: 330 Copynumber: 2.0 Consensus size: 330
1693948 CAACTATCAT
*
1693958 GCTCATCCTTAGCAACTAGACATAAATTAGTCATATCTATAGAATCTAAATGCACCATGTATATG
1 GCTCATCCTTAGCAACTAGACATAAATTAGTCATATCTATAGAATCTAAATGCACCATGCATATG
*
1694023 TTTCCTATTCTATGACCAACAAGTATAATCCGATTAGATGCAATGTCAATGACTTTACAACCATT
66 TTTCCTATTCTATGACCAACAAGCATAATCCGATTAGATGCAATGTCAATGACTTTACAACCATT
1694088 AGTTTCAAACATGACATTGAATCCCTTATCACAAATTGACTAATACTTAATAGATTATGCTTTAA
131 AGTTTCAAACATGACATTGAATCCCTTATCACAAATTGACTAATACTTAATAGATTATGCTTTAA
* *
1694153 CCCATTCACATATAAAACATTTTGAATTTGTATGGAAGAGGTATTACTTATAGTGCCTATTCCTT
196 CCCATTCACATATAAAACATTTTGAATTTGTATGGAAGAGGTATTACCTATAGTACCTATTCCTT
* *
1694218 CAATGTGACCTTTTGAATTATCACCAAAGTCACTTCTCCTCTATTTTTTGCATTAAGCTCTATGA
261 CAATGTGACCTTTTGAATTATCACCAAAGTCACTTCTCCTCCATTTTTGGCATTAAGCTCTATGA
1694283 ACCAG
326 ACCAG
1694288 GCTCATCCTTAGCAACTAGACATAAATTAGTCATATCTATAGAATCTAAATGCACCATGCATAT-
1 GCTCATCCTTAGCAACTAGACATAAATTAGTCATATCTATAGAATCTAAATGCACCATGCATATG
1694352 TTTCCTATTCTATGACCAACAAGCATAATCCGATTAGATGCAATGTCAATGACTTTACAACCATT
66 TTTCCTATTCTATGACCAACAAGCATAATCCGATTAGATGCAATGTCAATGACTTTACAACCATT
*
1694417 AGTTTCAAACGTGACATTGAATCCCTTATCACAAAATTGACTAATACTTAATAGATTATGCTTTA
131 AGTTTCAAACATGACATTGAATCCCTTATCAC-AAATTGACTAATACTTAATAGATTATGCTTTA
*
1694482 ACCCATTCACATATAAAACATTTTGAATTTTTATGGAAGAGGTATTACCT-TAGTACCTATTCCT
195 ACCCATTCACATATAAAACATTTTGAATTTGTATGGAAGAGGTATTACCTATAGTACCTATTCCT
*
1694546 TCAATGTGACCTTTTGAATTATCACCAAAAGTCACTTCTCCTCCATTTTTGGCGTTAAGCTCTAT
260 TCAATGTGACCTTTTGAATTATCACC-AAAGTCACTTCTCCTCCATTTTTGGCATTAAGCTCTAT
1694611 GAACC
324 GAACC
1694616 GGTTCTTGTC
Statistics
Matches: 317, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
329 134 0.42
330 183 0.58
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (330 bp):
GCTCATCCTTAGCAACTAGACATAAATTAGTCATATCTATAGAATCTAAATGCACCATGCATATG
TTTCCTATTCTATGACCAACAAGCATAATCCGATTAGATGCAATGTCAATGACTTTACAACCATT
AGTTTCAAACATGACATTGAATCCCTTATCACAAATTGACTAATACTTAATAGATTATGCTTTAA
CCCATTCACATATAAAACATTTTGAATTTGTATGGAAGAGGTATTACCTATAGTACCTATTCCTT
CAATGTGACCTTTTGAATTATCACCAAAGTCACTTCTCCTCCATTTTTGGCATTAAGCTCTATGA
ACCAG
Found at i:1697157 original size:28 final size:28
Alignment explanation
Indices: 1697117--1697184 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
1697107 GTGGGACCAT
1697117 CATCTATGCAGTTGATTATTTTTCAACA
1 CATCTATGCAGTTGATTATTTTTCAACA
1697145 CATCTATGCAGTTGATTATTTTTCAACA
1 CATCTATGCAGTTGATTATTTTTCAACA
1697173 CATCTATGCAGT
1 CATCTATGCAGT
1697185 AGCCATTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (28 bp):
CATCTATGCAGTTGATTATTTTTCAACA
Found at i:1703845 original size:2 final size:2
Alignment explanation
Indices: 1703840--1703870 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1703830 GCTCTTTTTT
1703840 TA TA TA GTA 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
1703871 ATTTCAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1704022 original size:23 final size:24
Alignment explanation
Indices: 1703995--1704054 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
1703985 AAAAAAAATA
1703995 TTTTTAAAAACGTATAATATATAG
1 TTTTTAAAAACGTATAATATATAG
* * *
1704019 TTTTTTGAAAATGTATATTATATAG
1 -TTTTTAAAAACGTATAATATATAG
*
1704044 TTTTGAAAAAC
1 TTTTTAAAAAC
1704055 AATTTTTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (24 bp):
TTTTTAAAAACGTATAATATATAG
Found at i:1704029 original size:25 final size:25
Alignment explanation
Indices: 1703995--1704047 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1703985 AAAAAAAATA
1703995 TTTTTAAAAACGTATAATATATAGT
1 TTTTTAAAAACGTATAATATATAGT
* * *
1704020 TTTTTGAAAATGTATATTATATAGT
1 TTTTTAAAAACGTATAATATATAGT
1704045 TTT
1 TTT
1704048 GAAAAACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (25 bp):
TTTTTAAAAACGTATAATATATAGT
Found at i:1704030 original size:37 final size:36
Alignment explanation
Indices: 1703896--1704030 Score: 121
Period size: 39 Copynumber: 3.6 Consensus size: 36
1703886 TTTGAAAGTA
* * *
1703896 TATAGTATATGTTTTTT-AAAATACTTTTAAAAATG
1 TATAATATATGTTTTTTGAAAATATTTTTAAAAACG
* * *
1703931 TATAATATATG-ATTTTGAAAACATTTCTAAGAAAACG
1 TATAATATATGTTTTTTGAAAATATTT-TTA-AAAACG
* **
1703968 TATAATATATATATTTTAAAAAAAATATTTTTAAAAACG
1 TATAATATATGT-TTTT--TGAAAATATTTTTAAAAACG
1704007 TATAATATATAGTTTTTTGAAAAT
1 TATAATATAT-GTTTTTTGAAAAT
1704031 GTATATTATA
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
34 4 0.05
35 17 0.22
36 2 0.03
37 20 0.26
39 23 0.30
40 3 0.04
41 8 0.10
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (36 bp):
TATAATATATGTTTTTTGAAAATATTTTTAAAAACG
Found at i:1704135 original size:38 final size:36
Alignment explanation
Indices: 1704020--1704197 Score: 112
Period size: 38 Copynumber: 4.8 Consensus size: 36
1704010 AATATATAGT
* *
1704020 TTTTTGAAA-ATGTATATTATATAGTTTTGAAAAACAA
1 TTTTTGAAATATATATA-TATATAGTTTTG-AAAATAA
* * ** **
1704057 TTTTTGAAA-ACATATATATTATGGTTTTGAATTTTT
1 TTTTTGAAATATATATATA-TATAGTTTTGAAAATAA
1704093 TTTTTGAATATATATATATATAATAGTTTTGAAAATAA
1 TTTTTGAA-ATATATATATAT-ATAGTTTTGAAAATAA
* * * * *
1704131 TTTTTGAAATCATATGTAATATTTAGTATTAAAAAT-G
1 TTTTTGAAAT-ATATAT-ATATATAGTTTTGAAAATAA
*
1704168 TTTTTGGAAACCTATATA-ATATATAATTTT
1 TTTTT-GAAA--TATATATATATATAGTTTT
1704198 TTGAAGACAT
Statistics
Matches: 109, Mismatches: 23, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
36 12 0.11
37 41 0.38
38 47 0.43
39 8 0.07
40 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (36 bp):
TTTTTGAAATATATATATATATAGTTTTGAAAATAA
Found at i:1705447 original size:15 final size:15
Alignment explanation
Indices: 1705423--1705465 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1705413 ATTTTATATT
1705423 TTTTAA-ATTATTTA
1 TTTTAATATTATTTA
*
1705437 TTTTATTATTA-TTA
1 TTTTAATATTATTTA
*
1705451 TTTTAATATTTTTTA
1 TTTTAATATTATTTA
1705466 GGACTTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATATTATTTA
Found at i:1706670 original size:25 final size:25
Alignment explanation
Indices: 1706620--1706670 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1706610 TTTAAATACA
* * *
1706620 TATTTAATAGAATATAATTTTGTTT
1 TATTTAATAAAATATAATGTTATTT
1706645 TATTTAATATAAATA-AATGTTATTT
1 TATTTAATA-AAATATAATGTTATTT
1706670 T
1 T
1706671 TATAAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (25 bp):
TATTTAATAAAATATAATGTTATTT
Found at i:1715464 original size:21 final size:20
Alignment explanation
Indices: 1715423--1715466 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1715413 AACCTTTAAA
* *
1715423 TTTAATCAAATTAAATGATT
1 TTTAATAAAAATAAATGATT
* *
1715443 TTTAATAAAAATACATGAAT
1 TTTAATAAAAATAAATGATT
1715463 TTTA
1 TTTA
1715467 TGAACAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
TTTAATAAAAATAAATGATT
Found at i:1718900 original size:6 final size:6
Alignment explanation
Indices: 1718889--1719001 Score: 190
Period size: 6 Copynumber: 18.8 Consensus size: 6
1718879 GACACGTATT
* * * *
1718889 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1718937 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1718985 ACCACG ACCACG ACCAC
1 ACCACG ACCACG ACCAC
1719002 AAGCCGAGCC
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 105 1.00
ACGTcount: A:0.30, C:0.50, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:1719022 original size:10 final size:10
Alignment explanation
Indices: 1719003--1719037 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1718993 CACGACCACA
*
1719003 AGCCGAGCCG
1 AGCCGTGCCG
1719013 AGCCGTGCCG
1 AGCCGTGCCG
*
1719023 TGCCGTGCCG
1 AGCCGTGCCG
1719033 AGCCG
1 AGCCG
1719038 AGACGAGACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.11, C:0.40, G:0.40, T:0.09
Consensus pattern (10 bp):
AGCCGTGCCG
Found at i:1720487 original size:26 final size:24
Alignment explanation
Indices: 1720457--1720504 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1720447 CGACTATCAA
1720457 TATTTTTTATATTATATAAATTTATT
1 TATTTTTT-TATTAT-TAAATTTATT
*
1720483 TATTTTTTTATTATTATATTTA
1 TATTTTTTTATTATTAAATTTA
1720505 AATATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 6 0.29
26 8 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTTTTTATTATTAAATTTATT
Found at i:1721790 original size:7 final size:7
Alignment explanation
Indices: 1721780--1721831 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
1721770 TAAACCTAAA
*
1721780 TTAGAGT
1 TTAGGGT
*
1721787 TTAGGAT
1 TTAGGGT
1721794 TTAGGGT
1 TTAGGGT
1721801 TTAGGGT
1 TTAGGGT
1721808 TTAGGGT
1 TTAGGGT
1721815 TTAGGGT
1 TTAGGGT
1721822 TTAGGGT
1 TTAGGGT
1721829 TTA
1 TTA
1721832 AGTTAGGGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:1722446 original size:12 final size:12
Alignment explanation
Indices: 1722429--1722468 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1722419 GATTCAATCA
1722429 TGCATACACACT
1 TGCATACACACT
*
1722441 TGCATACA-ATCA
1 TGCATACACA-CT
1722453 TGCATACACACT
1 TGCATACACACT
1722465 TGCA
1 TGCA
1722469 AAAGATCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (12 bp):
TGCATACACACT
Found at i:1722455 original size:24 final size:24
Alignment explanation
Indices: 1722423--1722468 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1722413 AGACTAGATT
1722423 CAATCATGCATACACACTTGCATA
1 CAATCATGCATACACACTTGCATA
1722447 CAATCATGCATACACACTTGCA
1 CAATCATGCATACACACTTGCA
1722469 AAAGATCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.24
Consensus pattern (24 bp):
CAATCATGCATACACACTTGCATA
Found at i:1722750 original size:20 final size:20
Alignment explanation
Indices: 1722709--1722750 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1722699 ATTGGTTGTC
* *
1722709 TTAGGATCATATAGATGCAT
1 TTAGGAGCATATAAATGCAT
*
1722729 TTAGGAGCATATAAATGTAT
1 TTAGGAGCATATAAATGCAT
1722749 TT
1 TT
1722751 GGTGGATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (20 bp):
TTAGGAGCATATAAATGCAT
Found at i:1726517 original size:21 final size:21
Alignment explanation
Indices: 1726491--1726530 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1726481 CAGAACCCCA
*
1726491 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1726512 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1726531 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1726559 original size:20 final size:21
Alignment explanation
Indices: 1726513--1726573 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1726503 TTCCCCTGTG
1726513 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1726536 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1726556 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1726574 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1732370 original size:14 final size:14
Alignment explanation
Indices: 1732351--1732380 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1732341 ACTCACTCAC
1732351 TCTATATTACTTAT
1 TCTATATTACTTAT
1732365 TCTATATTACTTAT
1 TCTATATTACTTAT
1732379 TC
1 TC
1732381 GATTGTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (14 bp):
TCTATATTACTTAT
Found at i:1749602 original size:19 final size:19
Alignment explanation
Indices: 1749565--1749631 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
1749555 AAGCTTATTT
* **
1749565 AATTTTTTTAAAAAATAAA
1 AATTATTTTAAAATTTAAA
1749584 AATTATTTTAAAATTTAAATATAA
1 AATTATTTTAAAA-TT---TA-AA
*
1749608 AATTATTTAAAAATTTAAA
1 AATTATTTTAAAATTTAAA
1749627 AATTA
1 AATTA
1749632 AATATAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 19 0.49
20 2 0.05
23 4 0.10
24 14 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTATTTTAAAATTTAAA
Found at i:1749634 original size:24 final size:24
Alignment explanation
Indices: 1749575--1749634 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1749565 AATTTTTTTA
*
1749575 AAAAATAAAAATTATTTTAAAATTT
1 AAAAAT-AAAATTATTTAAAAATTT
*
1749600 AAATATAAAATTATTTAAAAATTT
1 AAAAATAAAATTATTTAAAAATTT
*
1749624 AAAAATTAAAT
1 AAAAATAAAAT
1749635 ATAAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAAATAAAATTATTTAAAAATTT
Found at i:1749650 original size:31 final size:31
Alignment explanation
Indices: 1749590--1749651 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1749580 TAAAAATTAT
* * *
1749590 TTTAAAATTTAAATATAAAATTATTTAAAAA
1 TTTAAAAATTAAATATAAAAATATCTAAAAA
1749621 TTTAAAAATTAAATATAAAAA-ATACTAAAAA
1 TTTAAAAATTAAATATAAAAATAT-CTAAAAA
1749652 AATTAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (31 bp):
TTTAAAAATTAAATATAAAAATATCTAAAAA
Found at i:1749652 original size:32 final size:31
Alignment explanation
Indices: 1749590--1749657 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 31
1749580 TAAAAATTAT
* * * *
1749590 TTTAAAATTTAAATATAAAATTATTTAAAAA
1 TTTAAAAATTAAATATAAAAATACTAAAAAA
1749621 TTTAAAAATTAAATATAAAAAATACTAAAAAA
1 TTTAAAAATTAAATAT-AAAAATACTAAAAAA
*
1749653 ATTAA
1 TTTAA
1749658 TTACTAAGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (31 bp):
TTTAAAAATTAAATATAAAAATACTAAAAAA
Found at i:1752675 original size:24 final size:24
Alignment explanation
Indices: 1752647--1752723 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
1752637 AACTCGTATA
*
1752647 AATTTTCACCGAAGTGCCACGTAG
1 AATTTTCACCGAAGTGCCGCGTAG
*
1752671 AATTTGTC-CCGAAAG-ACCGCGTAG
1 AATTT-TCACCG-AAGTGCCGCGTAG
*
1752695 AAATTTGCACCGAAGTGCCGCGTAG
1 -AATTTTCACCGAAGTGCCGCGTAG
1752720 AATT
1 AATT
1752724 GCACCATAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
24 23 0.52
25 21 0.48
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
AATTTTCACCGAAGTGCCGCGTAG
Found at i:1752734 original size:23 final size:25
Alignment explanation
Indices: 1752641--1752736 Score: 87
Period size: 25 Copynumber: 4.0 Consensus size: 25
1752631 CACCACAACT
* * *
1752641 CGTATAAATTTTCACCGAAGTGCCA
1 CGTAGAAATTTGCACCGAAGTGCCG
*
1752666 CGTAG-AATTTGTC-CCGAAAG-ACCG
1 CGTAGAAATTTG-CACCG-AAGTGCCG
1752690 CGTAGAAATTTGCACCGAAGTGCCG
1 CGTAGAAATTTGCACCGAAGTGCCG
1752715 CGTAG-AA-TTGCACC-ATAGTGCC
1 CGTAGAAATTTGCACCGA-AGTGCC
1752737 ATATAAGATT
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.02
23 13 0.22
24 21 0.35
25 25 0.42
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (25 bp):
CGTAGAAATTTGCACCGAAGTGCCG
Found at i:1752867 original size:21 final size:22
Alignment explanation
Indices: 1752843--1752887 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1752833 CCCAAAGAAT
1752843 ACAT-ATATATCCCGAAGGACC
1 ACATAATATATCCCGAAGGACC
*
1752864 ACATAGAATTTATCCCGAAGGACC
1 ACAT--AATATATCCCGAAGGACC
1752888 GCGTAGACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
24 16 0.80
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.20
Consensus pattern (22 bp):
ACATAATATATCCCGAAGGACC
Found at i:1753081 original size:25 final size:24
Alignment explanation
Indices: 1753053--1753114 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
1753043 CATAATGCAT
* *
1753053 ATAATATGAATTTATGTCATGTATC
1 ATAATATGAATGTA-ATCATGTATC
1753078 ATAATATGGAATGTAATCATGTATC
1 ATAATAT-GAATGTAATCATGTATC
*
1753103 AAAATATTGAAT
1 ATAATA-TGAAT
1753115 CTAGACTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (24 bp):
ATAATATGAATGTAATCATGTATC
Found at i:1754610 original size:20 final size:20
Alignment explanation
Indices: 1754580--1754627 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1754570 AATGATTTTC
*
1754580 TTTTG-AAAGCAAAATTG-GA
1 TTTTGAAAAGCAAAA-TGAAA
1754599 TTTTGAAAAGCAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
1754619 TTTTGAAAA
1 TTTTGAAAA
1754628 ACGATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:1756468 original size:21 final size:21
Alignment explanation
Indices: 1756442--1756491 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1756432 GCTTGATTTT
1756442 GAAACCCCCTTAGGTGGTTTC
1 GAAACCCCCTTAGGTGGTTTC
1756463 GAAACCCCCTTAGGTGGTTTC
1 GAAACCCCCTTAGGTGGTTTC
1756484 GAAACCCC
1 GAAACCCC
1756492 TAGGGAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (21 bp):
GAAACCCCCTTAGGTGGTTTC
Found at i:1759845 original size:14 final size:15
Alignment explanation
Indices: 1759821--1759849 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1759811 TATTATACAT
1759821 AATACTAATTTTTAA
1 AATACTAATTTTTAA
1759836 AATA-TAATTTTTAA
1 AATACTAATTTTTAA
1759850 TTTTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATACTAATTTTTAA
Found at i:1759871 original size:22 final size:22
Alignment explanation
Indices: 1759846--1759887 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1759836 AATATAATTT
*
1759846 TTAATT-TTTTAATAATTTATAA
1 TTAATTATTTT-ATAACTTATAA
1759868 TTAATTATTTTATAACTTAT
1 TTAATTATTTTATAACTTAT
1759888 TATATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAATTATTTTATAACTTATAA
Found at i:1761203 original size:20 final size:21
Alignment explanation
Indices: 1761167--1761205 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1761157 TGGGTTTGAG
*
1761167 TATCGATATTGGGATGAACAA
1 TATCGATACTGGGATGAACAA
1761188 TATCGATACT-GGATGAAC
1 TATCGATACTGGGATGAAC
1761206 TAGGGCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (21 bp):
TATCGATACTGGGATGAACAA
Found at i:1773717 original size:40 final size:40
Alignment explanation
Indices: 1773663--1773750 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
1773653 TAAATTATCC
*
1773663 AGAAAATTTATTTTAAGAAATATTATTAAAAGTACCTTATT
1 AGAAAA-TTATTTTAAGAAATACTATTAAAAGTACCTTATT
*
1773704 AGAAAATTATTTTAAGAAATACTATTAAAATTACCTTATT
1 AGAAAATTATTTTAAGAAATACTATTAAAAGTACCTTATT
1773744 AGAAAAT
1 AGAAAAT
1773751 AAAAAAAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 39 0.87
41 6 0.13
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.39
Consensus pattern (40 bp):
AGAAAATTATTTTAAGAAATACTATTAAAAGTACCTTATT
Found at i:1777107 original size:119 final size:121
Alignment explanation
Indices: 1776875--1777163 Score: 483
Period size: 119 Copynumber: 2.4 Consensus size: 121
1776865 ATGCCGTATG
* * *
1776875 TTAGGATGTAAACATGTCAAGGTTTTAAGAAAAAGTTGTTTGAGCTTTAGAATATTCTCTCTGTT
1 TTAGAATGT-AACATGTCAAGGTTTTAAGTAAAAGTTGTTTGAGCTTTAAAATATTCTCTCTGTT
*
1776940 ACATAATTTTAGGTCTTTGTGATGTATGCCATATAATGTTAGGCTATAGACATCTAC
65 ACATAATTTTAGGTCTTTATGATGTATGCCATATAATGTTAGGCTATAGACATCTAC
*
1776997 TTAGAATGTAACATGTCAAGGTTTTAAGTAAAAGTTGTTTGAGCTTTAAAATA-T-TCTGTGTTA
1 TTAGAATGTAACATGTCAAGGTTTTAAGTAAAAGTTGTTTGAGCTTTAAAATATTCTCTCTGTTA
* * *
1777060 CATAATTTTAGGTCTTTATGATGTATGCCATATATTGTTAGGTTATAGACATGTAC
66 CATAATTTTAGGTCTTTATGATGTATGCCATATAATGTTAGGCTATAGACATCTAC
1777116 TTAGAATGTAACATGTCAAGGTTTTAAGTAAAAGTTGTTTGAGCTTTA
1 TTAGAATGTAACATGTCAAGGTTTTAAGTAAAAGTTGTTTGAGCTTTA
1777164 GCATCATATT
Statistics
Matches: 159, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
119 108 0.68
120 1 0.01
121 42 0.26
122 8 0.05
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (121 bp):
TTAGAATGTAACATGTCAAGGTTTTAAGTAAAAGTTGTTTGAGCTTTAAAATATTCTCTCTGTTA
CATAATTTTAGGTCTTTATGATGTATGCCATATAATGTTAGGCTATAGACATCTAC
Found at i:1780188 original size:21 final size:21
Alignment explanation
Indices: 1780164--1780216 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1780154 TCGGATTTCA
1780164 ATCCGATCCGGATCGGTTTTT
1 ATCCGATCCGGATCGGTTTTT
1780185 ATCCGATCCGGATCGGTTTTT
1 ATCCGATCCGGATCGGTTTTT
1780206 ATCCGATCCGG
1 ATCCGATCCGG
1780217 TTTTTTCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.34
Consensus pattern (21 bp):
ATCCGATCCGGATCGGTTTTT
Found at i:1780340 original size:17 final size:17
Alignment explanation
Indices: 1780315--1780348 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1780305 CCGGTTTCGG
1780315 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
1780332 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
1780349 ATAAAAAACC
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:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:1780763 original size:21 final size:21
Alignment explanation
Indices: 1780737--1780776 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1780727 AATGCTCGGA
1780737 GGGAACCGATTCCCCCATTGG
1 GGGAACCGATTCCCCCATTGG
1780758 GGGAACCGATTCCCCCATT
1 GGGAACCGATTCCCCCATT
1780777 CAACGGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (21 bp):
GGGAACCGATTCCCCCATTGG
Found at i:1781563 original size:32 final size:32
Alignment explanation
Indices: 1781469--1781567 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
1781459 AACTCAACAT
* * *
1781469 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1781502 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
1 AATTCAAATACTTAAAAAC-TTCAAGTTCGATA
1781535 AATTCAAATACTTAAAAACTTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCAAGTTCGATA
1781567 A
1 A
1781568 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 14 0.23
33 46 0.74
34 2 0.03
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTCAAATACTTAAAAACTTCAAGTTCGATA
Found at i:1781586 original size:21 final size:21
Alignment explanation
Indices: 1781562--1781603 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1781552 ACTTCAAGTT
1781562 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1781583 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1781604 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1788992 original size:24 final size:24
Alignment explanation
Indices: 1788940--1789027 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 24
1788930 TTCGATAATC
* *
1788940 CGTTCGTTTATGTTCAT-TCATTT
1 CGTTCGTTTATGTTCATATAAGTT
* * *
1788963 ATGTTCGTATATGTTCATTTAAGTT
1 -CGTTCGTTTATGTTCATATAAGTT
* * *
1788988 CGTTCGTTTATGTCCGTATATGTT
1 CGTTCGTTTATGTTCATATAAGTT
*
1789012 CGTTCGTTTATATTCA
1 CGTTCGTTTATGTTCA
1789028 GCCCAATCTC
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
24 46 0.92
25 4 0.08
ACGTcount: A:0.17, C:0.15, G:0.16, T:0.52
Consensus pattern (24 bp):
CGTTCGTTTATGTTCATATAAGTT
Found at i:1788998 original size:34 final size:34
Alignment explanation
Indices: 1788941--1789012 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1788931 TCGATAATCC
* * *
1788941 GTTCGTTTATGTTCATTCATTTATGTTCGTATAT
1 GTTCATTTAAGTTCATTCATTTATGTCCGTATAT
* *
1788975 GTTCATTTAAGTTCGTTCGTTTATGTCCGTATAT
1 GTTCATTTAAGTTCATTCATTTATGTCCGTATAT
1789009 GTTC
1 GTTC
1789013 GTTCGTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.53
Consensus pattern (34 bp):
GTTCATTTAAGTTCATTCATTTATGTCCGTATAT
Found at i:1789228 original size:23 final size:23
Alignment explanation
Indices: 1789202--1789249 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1789192 TTTTATGTGG
*
1789202 TTATTGTTGTT-GTTTACGTTCAT
1 TTATTG-TGTTCGATTACGTTCAT
*
1789225 TTATTGTGTTCGATTATGTTCAT
1 TTATTGTGTTCGATTACGTTCAT
1789248 TT
1 TT
1789250 GTTATGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.15, C:0.08, G:0.17, T:0.60
Consensus pattern (23 bp):
TTATTGTGTTCGATTACGTTCAT
Found at i:1789920 original size:3 final size:3
Alignment explanation
Indices: 1789912--1789937 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1789902 TTTCATTTAT
1789912 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1789938 TTAATTTATA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1792972 original size:24 final size:24
Alignment explanation
Indices: 1792940--1792996 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1792930 GCCAACCAAA
*
1792940 CATGGGAATGTGGGATTCTCATCC
1 CATGGGAATGTGGGATTCCCATCC
*
1792964 CATGGGAATGTGGGATTCCCATCT
1 CATGGGAATGTGGGATTCCCATCC
1792988 CATGGGAAT
1 CATGGGAAT
1792997 CCCACATTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (24 bp):
CATGGGAATGTGGGATTCCCATCC
Found at i:1793351 original size:2 final size:2
Alignment explanation
Indices: 1793346--1793373 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1793336 AAAATATAAG
1793346 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
1793374 GGTCGGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1802048 original size:23 final size:22
Alignment explanation
Indices: 1802013--1802087 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 22
1802003 TAATACGTTT
*
1802013 GTTTATGTCCATTTATTGTGTTC
1 GTTTAGGT-CATTTATTGTGTTC
*
1802036 GTTTACGGTCATTTGTTTGTGTTC
1 GTTTA-GGTCATTT-ATTGTGTTC
* *
1802060 GTTTATGTTAGTTTATTGTGTTC
1 GTTTAGGTCA-TTTATTGTGTTC
1802083 GTTTA
1 GTTTA
1802088 TGTTCGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 26 0.59
24 18 0.41
ACGTcount: A:0.12, C:0.09, G:0.21, T:0.57
Consensus pattern (22 bp):
GTTTAGGTCATTTATTGTGTTC
Found at i:1802068 original size:10 final size:10
Alignment explanation
Indices: 1802050--1802132 Score: 76
Period size: 10 Copynumber: 7.6 Consensus size: 10
1802040 ACGGTCATTT
*
1802050 GTTTGTGTTC
1 GTTTATGTTC
*
1802060 GTTTATGTTA
1 GTTTATGTTC
1802070 GTTTATTGTGTTC
1 GTTTA---TGTTC
1802083 GTTTATGTTC
1 GTTTATGTTC
1802093 GTTTACATCCGTTC
1 GTTT--AT--GTTC
1802107 GTTTATGTTC
1 GTTTATGTTC
*
1802117 ATTTATGTTC
1 GTTTATGTTC
1802127 GTTTAT
1 GTTTAT
1802133 CATTTAAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
10 40 0.66
12 4 0.07
13 9 0.15
14 8 0.13
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.58
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:1802111 original size:24 final size:23
Alignment explanation
Indices: 1802056--1802132 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
1802046 ATTTGTTTGT
* * **
1802056 GTTCGTTTATGTTAGTTTATTGT
1 GTTCGTTTATGTTCGTTTAATCC
1802079 GTTCGTTTATGTTCGTTTACATCC
1 GTTCGTTTATGTTCGTTTA-ATCC
*
1802103 GTTCGTTTATGTTCATTT-AT--
1 GTTCGTTTATGTTCGTTTAATCC
1802123 GTTCGTTTAT
1 GTTCGTTTAT
1802133 CATTTAAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.21
22 2 0.04
23 18 0.38
24 18 0.38
ACGTcount: A:0.13, C:0.12, G:0.18, T:0.57
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTTAATCC
Found at i:1802122 original size:47 final size:47
Alignment explanation
Indices: 1802008--1802122 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
1801998 TCCTCTAATA
* * *** *
1802008 CGTTTGTTTATGTCCATTTATTGTGTTCGTTTACGGTCATTTGTTTG
1 CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACGGTCATTTACATC
* * * *
1802055 TGTTCGTTTATGTT-AGTTTATTGTGTTCGTTTATGTTCGTTTACATC
1 CGTTCGTTTATGTTCA-TTTATTGTGTTCGTTTACGGTCATTTACATC
1802102 CGTTCGTTTATGTTCATTTAT
1 CGTTCGTTTATGTTCATTTAT
1802123 GTTCGTTTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.96
48 1 0.02
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.57
Consensus pattern (47 bp):
CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACGGTCATTTACATC
Found at i:1802722 original size:3 final size:3
Alignment explanation
Indices: 1802716--1802774 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1802706 ATTTCTTAAT
1802716 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1802764 TTC TTC TTC TT
1 TTC TTC TTC TT
1802775 GTTTCACTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1803770 original size:20 final size:20
Alignment explanation
Indices: 1803754--1803825 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
1803744 GAGAGTATCG
* *
1803754 ATACTTTCCCAAGAGTATCC
1 ATACTTTCCCAAGAGCATCT
* *
1803774 ATGCTTTCCAAAGAGCATCT
1 ATACTTTCCCAAGAGCATCT
*
1803794 ATGCTTTCCCAAGAGCATCT
1 ATACTTTCCCAAGAGCATCT
*
1803814 ATACTTTTCCAA
1 ATACTTTCCCAA
1803826 AGAGGATCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACTTTCCCAAGAGCATCT
Found at i:1820488 original size:6 final size:6
Alignment explanation
Indices: 1820475--1820529 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
1820465 TGAGGTTTTG
* * *
1820475 TTTC-T TTTCTT TTT-GT -TTCTT TTTCTT TTTCCT TTTCCT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
1820520 TTTCTT TTTC
1 TTTCTT TTTC
1820530 GGATTCTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 35 0.81
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:1820490 original size:15 final size:16
Alignment explanation
Indices: 1820470--1820504 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1820460 GAGGTTGAGG
1820470 TTTTGTTTC-TTTTCT
1 TTTTGTTTCTTTTTCT
1820485 TTTTGTTTCTTTTTCT
1 TTTTGTTTCTTTTTCT
1820501 TTTT
1 TTTT
1820505 CCTTTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTGTTTCTTTTTCT
Found at i:1820983 original size:60 final size:60
Alignment explanation
Indices: 1820870--1821004 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
1820860 TGCATCATAG
* * * *
1820870 ATCCCTAAACAATAACCTTCATTTTGAATTAGTCCTTAAACTTTATAATATTCTAATTAC
1 ATCCCTAAACTATGACCTTCATTTTCAATTAGTCCTTAAACTTTATAACATTCTAATTAC
* ** **
1820930 ATCCCTAAACTATGA-CTCTCATTTTCAATTAGTTCTTAAACTTT-TGGGCATTCTAATTTT
1 ATCCCTAAACTATGACCT-TCATTTTCAATTAGTCCTTAAACTTTAT-AACATTCTAATTAC
*
1820990 ATCTCTAAACTATGA
1 ATCCCTAAACTATGA
1821005 TCATCTTTCT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 3 0.05
60 60 0.95
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (60 bp):
ATCCCTAAACTATGACCTTCATTTTCAATTAGTCCTTAAACTTTATAACATTCTAATTAC
Found at i:1821020 original size:18 final size:18
Alignment explanation
Indices: 1820997--1821034 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1820987 TTTATCTCTA
*
1820997 AACTATGATCATCTTTCT
1 AACTATGACCATCTTTCT
1821015 AACTATGACCATCTTTCT
1 AACTATGACCATCTTTCT
1821033 AA
1 AA
1821035 ATTAGTCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (18 bp):
AACTATGACCATCTTTCT
Found at i:1825367 original size:2 final size:2
Alignment explanation
Indices: 1825360--1825401 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1825350 TGTAACATAA
1825360 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
1825402 GGTTTGCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1826217 original size:106 final size:104
Alignment explanation
Indices: 1825908--1826314 Score: 465
Period size: 106 Copynumber: 3.9 Consensus size: 104
1825898 TATTGTTCCC
* * * * * *
1825908 AGTCCAATATCCTCCGCCGTGAAGTTAAAATTGACTC-TGGAACTGGGAAA-TTGTTTGTTG--A
1 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCATGAAACT-GAAAAGTTGTTTGTTGACA
*
1825969 --CAGCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCG
65 GCCAGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
* *
1826007 AGTCTAATATCTTTCACTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGA
1 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTC---ATGAAACTGAAAAGTTGTTTGTTGA
*
1826072 CAGTCAATCA-CCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTG
63 CAG-C---CAGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
* ** * *
1826117 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAACTAGGAAA-TTGTTTGTTGACA
1 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCATGAAACT-GAAAAGTTGTTTGTTGACA
1826180 GCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
65 GCCA---GCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
1826223 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
1 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTC---ATGAAACTGAAAAGTTGTTTGTTGA
*
1826288 CAGCCA-CCCCTTCGCTATGAAGTTGAG
63 CAGCCAGCCCCTTCGCTGTGAAGTTGAG
1826315 TAACCACCAT
Statistics
Matches: 261, Mismatches: 24, Indels: 39
0.81 0.07 0.12
Matches are distributed among these distances:
99 31 0.12
102 6 0.02
103 16 0.06
105 2 0.01
106 108 0.41
107 4 0.02
109 4 0.02
110 88 0.34
111 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (104 bp):
AGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCATGAAACTGAAAAGTTGTTTGTTGACAG
CCAGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
Found at i:1826275 original size:216 final size:205
Alignment explanation
Indices: 1825908--1826314 Score: 598
Period size: 216 Copynumber: 1.9 Consensus size: 205
1825898 TATTGTTCCC
* *
1825908 AGTCCAATATCCTCCGCCGTGAAGTTAAAATTGACTCTGGAACTGGGAAATTGTTTGTTGACAGC
1 AGTCCAATATCCTCCGCCGTGAAGTTAAAATTGACTCTGAAACTAGGAAATTGTTTGTTGACAGC
* *
1825973 CCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCTTTCACTGTGAAGTTGAAAT
66 CCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAAT
*
1826038 TGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTCAATCACCCCTTCGCTGTGAAGTTGAG
131 TGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAG-C---CACCCCTTCGCTATGAAGTTGAG
1826103 CTTGTGTTGTCTTG
192 CTTGTGTTGTCTTG
* * ** * *
1826117 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGACAGC
1 AGTCCAATATCCTCCGCCGTGAAGTTAAAATTGACTCTGAAACTAGGAAATTGTTTGTTG--A--
*
1826182 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAG
62 CA---GCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAG
*
1826247 TTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGCCACCCCTTCGCTATGAAGTT
124 TTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGCCACCCCTTCGCTATGAAGTT
1826312 GAG
189 GAG
1826315 TAACCACCAT
Statistics
Matches: 178, Mismatches: 13, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
209 52 0.29
211 1 0.01
212 22 0.12
213 2 0.01
215 1 0.01
216 100 0.56
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (205 bp):
AGTCCAATATCCTCCGCCGTGAAGTTAAAATTGACTCTGAAACTAGGAAATTGTTTGTTGACAGC
CCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAAT
TGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGCCACCCCTTCGCTATGAAGTTGAGCTTG
TGTTGTCTTG
Found at i:1830395 original size:34 final size:33
Alignment explanation
Indices: 1830357--1830439 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
1830347 AGTCTTACTT
1830357 GGACTCAAA-ATGATTCGGTTTTAGTGTTTCAATA
1 GGACTCAAATATG-TT-GGTTTTAGTGTTTCAATA
*
1830391 GGACTTAAATATGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATATGTTGGTTTTAGTGTTTCAATA
*
1830424 GAACTCAAATATGTTG
1 GGACTCAAATATGTTG
1830440 ATTTATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 32 0.71
34 10 0.22
35 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (33 bp):
GGACTCAAATATGTTGGTTTTAGTGTTTCAATA
Found at i:1830506 original size:5 final size:5
Alignment explanation
Indices: 1830496--1830566 Score: 56
Period size: 5 Copynumber: 13.8 Consensus size: 5
1830486 CTACAAAAGT
*
1830496 AATAA AATAA AAGTAA TAATAA TAATAA TAAT-A AAT-A AATAA AATAT
1 AATAA AATAA AA-TAA -AATAA -AATAA -AATAA AATAA AATAA AATAA
* * *
1830543 AATAT AATAT AATAT AATAA AATA
1 AATAA AATAA AATAA AATAA AATA
1830567 TTTTTGTAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
4 7 0.11
5 36 0.59
6 16 0.26
7 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (5 bp):
AATAA
Done.