Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 43
Found at i:1567218 original size:12 final size:12
Alignment explanation
Indices: 1567203--1567269 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 12
1567193 AACAAAAAAG
1567203 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
1567215 AAAAACAAAGAA
1 AAAAAAAAAGAA
*
1567227 AATAAAAAGAGAA
1 AA-AAAAAAAGAA
*
1567240 ACAAAAACAAAGGA
1 A-AAAAA-AAAGAA
**
1567254 AAAAATGAAGAA
1 AAAAAAAAAGAA
1567266 AAAA
1 AAAA
1567270 GAAGAGACGC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
12 21 0.48
13 17 0.39
14 6 0.14
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:1567257 original size:39 final size:38
Alignment explanation
Indices: 1567203--1567276 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 38
1567193 AACAAAAAAG
1567203 AAAAAAAAAGAAAAAAACAAAGAAAATAAAAAGAGAAAC
1 AAAAAAAAAGAAAAAAACAAAGAAAA-AAAAAGAGAAAC
* * ** *
1567242 AAAAACAAAGGAAAAAATGAAGAAAAAAGAAGAGA
1 AAAAAAAAAGAAAAAAACAAAGAAAAAAAAAGAGA
1567277 CGCATATGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 8 0.27
39 22 0.73
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.03
Consensus pattern (38 bp):
AAAAAAAAAGAAAAAAACAAAGAAAAAAAAAGAGAAAC
Found at i:1568373 original size:32 final size:32
Alignment explanation
Indices: 1568320--1568407 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
1568310 GGAACAATGT
* * *
1568320 GGGCATCTTCGAAGATTCAACATCAAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATAGTG
* * *
1568352 GGGTATTTTTGGAGATTCAACAAT-GAATAGTG
1 GGGCATCTTTGGAGATTCAAC-ATCAAATAGTG
*
1568384 GGGCATCTTTGGGGATTCAACATC
1 GGGCATCTTTGGAGATTCAACATC
1568408 CTGATGCGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
31 2 0.04
32 41 0.91
33 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATAGTG
Found at i:1570089 original size:7 final size:7
Alignment explanation
Indices: 1570070--1570107 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
1570060 CGAAATATAC
1570070 ATATATAT
1 ATATAT-T
1570078 ATATATT
1 ATATATT
1570085 ATATATT
1 ATATATT
1570092 ATATATGT
1 ATATAT-T
1570100 AT-TATT
1 ATATATT
1570106 AT
1 AT
1570108 TTGTTAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 3 0.10
7 17 0.59
8 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (7 bp):
ATATATT
Found at i:1570096 original size:18 final size:17
Alignment explanation
Indices: 1570073--1570108 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1570063 AATATACATA
1570073 TATATATATATTATATAT
1 TATATATATATTAT-TAT
*
1570091 TATATATGTATTATTAT
1 TATATATATATTATTAT
1570108 T
1 T
1570109 TGTTAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TATATATATATTATTAT
Found at i:1571415 original size:34 final size:29
Alignment explanation
Indices: 1571354--1571416 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
1571344 TATACATATG
1571354 TTATTTTTTTTTTTTTTTTTTTCTTTATA
1 TTATTTTTTTTTTTTTTTTTTTCTTTATA
1571383 TTATTTTATTTTTATTTTTATTGTTTCTTT-TA
1 TTATTTT-TTTTT-TTTTT-TT-TTTCTTTATA
1571415 TT
1 TT
1571417 TTAATCAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 7 0.23
30 5 0.17
31 5 0.17
32 6 0.20
33 7 0.23
ACGTcount: A:0.13, C:0.03, G:0.02, T:0.83
Consensus pattern (29 bp):
TTATTTTTTTTTTTTTTTTTTTCTTTATA
Found at i:1575171 original size:2 final size:2
Alignment explanation
Indices: 1575160--1575190 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1575150 TTCAAAGTTA
1575160 AT AT -T 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
1575191 TAAAATTTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1583813 original size:19 final size:20
Alignment explanation
Indices: 1583789--1583897 Score: 102
Period size: 20 Copynumber: 5.5 Consensus size: 20
1583779 AATGACCAAC
1583789 AAAATCGCAATG-CGAAACA-
1 AAAATCGCAATGTCGAAA-AG
* *
1583808 AAAATCGCAACG-CGATTTAA-
1 AAAATCGCAATGTCGA--AAAG
*
1583828 AAAATCGCAATGTTGAAAAG
1 AAAATCGCAATGTCGAAAAG
*
1583848 AAAATCGCAATGTTGAAAAG
1 AAAATCGCAATGTCGAAAAG
*
1583868 AAAATCGCAACGGTC-AAAAG
1 AAAATCGCAA-TGTCGAAAAG
1583888 AAAATCGCAA
1 AAAATCGCAA
1583898 CGCGATCTTC
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.21
20 57 0.73
21 5 0.06
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATCGCAATGTCGAAAAG
Found at i:1583832 original size:20 final size:20
Alignment explanation
Indices: 1583789--1583966 Score: 84
Period size: 20 Copynumber: 8.8 Consensus size: 20
1583779 AATGACCAAC
*
1583789 AAAATCGCAATGCGA--AACA
1 AAAATCGCAACGCGATTAA-A
*
1583808 AAAATCGCAACGCGATTTAA
1 AAAATCGCAACGCGATTAAA
* *
1583828 AAAATCGCAATGTTGA--AAA
1 AAAATCGCAACG-CGATTAAA
* *
1583847 GAAAATCGCAATGTTGA--AAA
1 -AAAATCGCAACG-CGATTAAA
*
1583867 GAAAATCGCAACG-G-TCAAAA
1 -AAAATCGCAACGCGAT-TAAA
**
1583887 GAAAATCGCAACGCGATCTTCCA
1 -AAAATCGCAACGCGA--TTAAA
* * * *
1583910 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTAAA
* *
1583930 AAAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAA
1583950 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
1583967 CCAAGAATCG
Statistics
Matches: 132, Mismatches: 16, Indels: 21
0.78 0.09 0.12
Matches are distributed among these distances:
18 1 0.01
19 16 0.12
20 96 0.73
21 4 0.03
22 13 0.10
23 1 0.01
24 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAA
Found at i:1583979 original size:20 final size:20
Alignment explanation
Indices: 1583886--1583967 Score: 94
Period size: 20 Copynumber: 4.0 Consensus size: 20
1583876 AACGGTCAAA
1583886 AGAAAATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGA--TT-C
* * *
1583909 A-AGAATCGCAATGCGATTG
1 AGAAAATCGCAACGCGATTC
*
1583928 AGAAAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATTC
1583948 AGAAAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTC
1583968 CAAGAATCGC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 37 0.71
22 13 0.25
23 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
AGAAAATCGCAACGCGATTC
Found at i:1584096 original size:6 final size:6
Alignment explanation
Indices: 1584085--1584116 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1584075 AGACACGTAT
1584085 GACCAC GACCAC GACCAC GACCAC GACC-C GAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GAC
1584117 GAGACGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1584856 original size:6 final size:6
Alignment explanation
Indices: 1584845--1584889 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1584835 TCTCGTCTCG
1584845 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1584890 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1585036 original size:20 final size:20
Alignment explanation
Indices: 1585020--1585107 Score: 133
Period size: 20 Copynumber: 4.4 Consensus size: 20
1585010 TGGAATCACA
1585020 TTGCGATTTTCTCAATCGCG
1 TTGCGATTTTCTCAATCGCG
**
1585040 TTGCGATTCTT-GGAATCGCG
1 TTGCGATT-TTCTCAATCGCG
1585060 TTGCGATTTTCTCAATCGCG
1 TTGCGATTTTCTCAATCGCG
*
1585080 TTGCGATTTTCTCGATCGCG
1 TTGCGATTTTCTCAATCGCG
1585100 TTGCGATT
1 TTGCGATT
1585108 CTTCGAAGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 2 0.03
20 57 0.93
21 2 0.03
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCTCAATCGCG
Found at i:1585098 original size:40 final size:40
Alignment explanation
Indices: 1585003--1585131 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
1584993 TGCCGTTTTA
* * *
1585003 CGATTCTTGGAATCACATTGCGATTTTCTCAATCGCGTTG
1 CGATTCTTCGAATCGCGTTGCGATTTTCTCAATCGCGTTG
*
1585043 CGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCGTTG
1 CGATTCTTCGAATCGCGTTGCGATTTTCTCAATCGCGTTG
* ** *
1585083 CGATTTTCTCG-ATCGCGTTGCGATTCTTCGAAGATCGCATTG
1 CGATTCT-TCGAATCGCGTTGCGATT-TTCTCA-ATCGCGTTG
1585125 CGATTCT
1 CGATTCT
1585132 GCGATTCTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
40 58 0.74
41 6 0.08
42 14 0.18
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.37
Consensus pattern (40 bp):
CGATTCTTCGAATCGCGTTGCGATTTTCTCAATCGCGTTG
Found at i:1585195 original size:20 final size:20
Alignment explanation
Indices: 1585170--1585219 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1585160 TGGAAGAATG
* *
1585170 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
1585190 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
1585210 CGTTGCGATT
1 CGTTGCGATT
1585220 CTCTAAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:1585233 original size:20 final size:19
Alignment explanation
Indices: 1585210--1585261 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1585200 TTCTTTTCAA
1585210 CGTTGCGATTCTCT-AAATCG
1 CGTTGCGATT-T-TGAAATCG
*
1585230 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
1585249 CGTTGCGATTTTG
1 CGTTGCGATTTTG
1585262 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 19 0.63
20 10 0.33
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:1588333 original size:82 final size:81
Alignment explanation
Indices: 1588190--1588393 Score: 268
Period size: 82 Copynumber: 2.5 Consensus size: 81
1588180 CTTGAGTGAA
* * *
1588190 ATAATTTAAACAACTTTT-AAAAAATGGGTGAAATAGTAGTGCATTATCATCTTCTGTAACTTTT
1 ATAATTTAAACAACTTTTCAGAAAA-GGGTGAAATAGTGGTGCATTATCATATTCTGTAACTTTT
*
1588254 CAGAGGTCATTCAATGC
65 CAGAGGCCATTCAATGC
* *
1588271 ATAATTTAAATAACTTTTCAGAAAACGGGTGAAATAGTGGTGCATTATCATATT-TTTCAACTTT
1 ATAATTTAAACAACTTTTCAGAAAA-GGGTGAAATAGTGGTGCATTATCATATTCTGT-AACTTT
* *
1588335 TTAGAGGCCATTTAATGC
64 TCAGAGGCCATTCAATGC
* *
1588353 ATAATTTAAACAACATTTCAGACAAAGGATGAAATAGTGGT
1 ATAATTTAAACAACTTTTCAGA-AAAGGGTGAAATAGTGGT
1588394 ATCTCATCAC
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
81 19 0.18
82 86 0.80
83 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (81 bp):
ATAATTTAAACAACTTTTCAGAAAAGGGTGAAATAGTGGTGCATTATCATATTCTGTAACTTTTC
AGAGGCCATTCAATGC
Found at i:1588414 original size:82 final size:81
Alignment explanation
Indices: 1588190--1588420 Score: 209
Period size: 82 Copynumber: 2.8 Consensus size: 81
1588180 CTTGAGTGAA
* * * * * ***
1588190 ATAATTTAAACAAC-TTTTAAAAAATGGGTGAAATAGTAGTGCATTATCATC-TTCTGTAACTTT
1 ATAATTTAAACAACATTTCAGAAAACGGATGAAATAGTGGT-CATTATCA-CATTCAACAACTTT
* *
1588253 TCAGAGGTCATTCAATGC
64 TTAGAGGCCATTCAATGC
* * * * ***
1588271 ATAATTTAAATAACTTTTCAGAAAACGGGTGAAATAGTGGTGCATTATCATATTTTTCAACTTTT
1 ATAATTTAAACAACATTTCAGAAAACGGATGAAATAGTGGT-CATTATCACATTCAACAACTTTT
*
1588336 TAGAGGCCATTTAATGC
65 TAGAGGCCATTCAATGC
*
1588353 ATAATTTAAACAACATTTCAGACAAA-GGATGAAATAGTGGT-ATCTCATCACCTTCAACAACTT
1 ATAATTTAAACAACATTTCAGA-AAACGGATGAAATAGTGGTCAT-T-ATCACATTCAACAACTT
1588416 TTTAG
63 TTTAG
1588421 TGATGTATCA
Statistics
Matches: 125, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
80 2 0.02
81 14 0.11
82 106 0.85
83 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (81 bp):
ATAATTTAAACAACATTTCAGAAAACGGATGAAATAGTGGTCATTATCACATTCAACAACTTTTT
AGAGGCCATTCAATGC
Found at i:1591132 original size:13 final size:13
Alignment explanation
Indices: 1591114--1591139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1591104 TCAGTATAGT
1591114 CTATAATATAGAA
1 CTATAATATAGAA
1591127 CTATAATATAGAA
1 CTATAATATAGAA
1591140 ACCCCCCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
CTATAATATAGAA
Found at i:1592816 original size:15 final size:15
Alignment explanation
Indices: 1592798--1592836 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1592788 TAACCGGTTT
1592798 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
1592813 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
1592828 CGATTTTAA
1 CGGTTTTAA
1592837 TATTCCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:1593054 original size:21 final size:21
Alignment explanation
Indices: 1593005--1593055 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1592995 ACACTTAGAG
1593005 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
* *
1593026 AACTGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
1593047 TACCGATTC
1 AACCGATTC
1593056 TCCCATGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:1593277 original size:13 final size:13
Alignment explanation
Indices: 1593256--1593310 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1593246 AAGTTCGATA
*
1593256 AATTCAAATACTT
1 AATTGAAATACTT
1593269 AATTGAAATACTT
1 AATTGAAATACTT
* *
1593282 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1593296 AATTGAAATACTT
1 AATTGAAATACTT
1593309 AA
1 AA
1593311 ATACTTCAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1593361 original size:33 final size:32
Alignment explanation
Indices: 1593296--1593392 Score: 151
Period size: 32 Copynumber: 3.0 Consensus size: 32
1593286 AACTCAACAT
* * *
1593296 AATTGAAATACTTAAATACTTCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCAAGTTCGATA
1593328 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1593361 AATTCAAATAC-TAAAAACTTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCAAGTTCGATA
1593392 A
1 A
1593393 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
31 12 0.20
32 28 0.46
33 21 0.34
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (32 bp):
AATTCAAATACTTAAAAACTTCAAGTTCGATA
Found at i:1593411 original size:21 final size:21
Alignment explanation
Indices: 1593387--1593426 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1593377 ACTTCAAGTT
1593387 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1593408 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
1593427 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1595725 original size:15 final size:13
Alignment explanation
Indices: 1595694--1595746 Score: 72
Period size: 15 Copynumber: 3.9 Consensus size: 13
1595684 TTCGGATAAA
1595694 AACCGG-TTTTTT
1 AACCGGTTTTTTT
1595706 AACCGGTTTTTTT
1 AACCGGTTTTTTT
1595719 CAGACCGGTTTTTTT
1 -A-ACCGGTTTTTTT
1595734 AAACCGGTTTTTT
1 -AACCGGTTTTTT
1595747 ATCCGGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 6 0.16
13 6 0.16
14 12 0.32
15 13 0.35
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (13 bp):
AACCGGTTTTTTT
Found at i:1595730 original size:14 final size:12
Alignment explanation
Indices: 1595694--1595753 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 12
1595684 TTCGGATAAA
1595694 AACCGGTTTTTT
1 AACCGGTTTTTT
1595706 AACCGGTTTTTTT
1 AACCGG-TTTTTT
1595719 CAGACCGGTTTTTTT
1 -A-ACCGG-TTTTTT
1595734 AAACCGGTTTTTT
1 -AACCGGTTTTTT
*
1595747 ATCCGGT
1 AACCGGT
1595754 AAAAAAACCG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
12 12 0.28
13 12 0.28
14 6 0.14
15 13 0.30
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:1595753 original size:12 final size:13
Alignment explanation
Indices: 1595693--1595747 Score: 67
Period size: 13 Copynumber: 4.1 Consensus size: 13
1595683 TTTCGGATAA
1595693 AAACCGGTTTTTT
1 AAACCGGTTTTTT
1595706 -AACCGGTTTTTTT
1 AAACCGG-TTTTTT
*
1595719 CAGACCGGTTTTTTT
1 -AAACCGG-TTTTTT
1595734 AAACCGGTTTTTT
1 AAACCGGTTTTTT
1595747 A
1 A
1595748 TCCGGTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 6 0.16
13 13 0.35
14 6 0.16
15 12 0.32
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (13 bp):
AAACCGGTTTTTT
Found at i:1596555 original size:3 final size:3
Alignment explanation
Indices: 1596547--1596606 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1596537 TTGCTATTGT
1596547 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1596595 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1596607 GGCTTAATAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1597439 original size:3 final size:3
Alignment explanation
Indices: 1597431--1597474 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1597421 TATTCAAGTC
*
1597431 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1597475 ACAAATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1600745 original size:8 final size:8
Alignment explanation
Indices: 1600729--1600769 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1600719 AATTTGACCC
*
1600729 TTATGTTA
1 TTATTTTA
1600737 TTATTTTA
1 TTATTTTA
1600745 TTATTTTA
1 TTATTTTA
*
1600753 -TATTAT-
1 TTATTTTA
1600759 TTATTTTA
1 TTATTTTA
1600767 TTA
1 TTA
1600770 CATATACGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
7 10 0.36
8 18 0.64
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
TTATTTTA
Found at i:1600870 original size:2 final size:2
Alignment explanation
Indices: 1600863--1600899 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1600853 TTAAAGTTAT
1600863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1600900 TTTATAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1601090 original size:2 final size:2
Alignment explanation
Indices: 1601083--1601109 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1601073 TTTTATTTAG
1601083 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1601110 TTTGTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1601210 original size:14 final size:13
Alignment explanation
Indices: 1601139--1601212 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 13
1601129 TATATTCATC
1601139 TTATTTTT-TTAT
1 TTATTTTTCTTAT
* *
1601151 TGACTTTATCTTAT
1 TTA-TTTTTCTTAT
* *
1601165 CTTGTTCTTCTTAT
1 -TTATTTTTCTTAT
* *
1601179 TTGTTTTT-TTAA
1 TTATTTTTCTTAT
1601191 TTATTTTATCTTAT
1 TTATTTT-TCTTAT
1601205 TTATTTTT
1 TTATTTTT
1601213 GTCACACTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
12 11 0.23
13 13 0.28
14 22 0.47
15 1 0.02
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTTTTCTTAT
Found at i:1602133 original size:4 final size:4
Alignment explanation
Indices: 1602126--1602150 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1602116 TTTCGTCATA
1602126 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1602151 TACTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1611414 original size:23 final size:23
Alignment explanation
Indices: 1611384--1611431 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1611374 CTTTTCCGGA
1611384 GGGGCCCTTGTCCTGGCCGAAAT
1 GGGGCCCTTGTCCTGGCCGAAAT
1611407 GGGGCCCTTGTCCTGGCCGAAAT
1 GGGGCCCTTGTCCTGGCCGAAAT
1611430 GG
1 GG
1611432 ACGGACCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.21
Consensus pattern (23 bp):
GGGGCCCTTGTCCTGGCCGAAAT
Found at i:1612809 original size:106 final size:106
Alignment explanation
Indices: 1612382--1613332 Score: 1477
Period size: 106 Copynumber: 9.0 Consensus size: 106
1612372 GGAGGATATC
* * *
1612382 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGT---C-AACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
1612442 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1612484 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGTTAGTTGTTAAC-AACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1612548 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1612589 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1612653 AATTTCAGAGCCAATTTCAACTTCATAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1612694 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1612759 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1612800 ATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAATTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1612865 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1612906 ACTCCAGACGACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1612971 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1613012 ACTCCAGACGACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1613077 AATTCCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1613118 ACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1613183 AATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * **
1613224 ACTCCATACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1613289 AGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1613330 ACT
1 ACT
1613333 TGGAAGGGGC
Statistics
Matches: 792, Mismatches: 51, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
102 40 0.05
103 2 0.00
105 202 0.26
106 548 0.69
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1615465 original size:9 final size:9
Alignment explanation
Indices: 1615437--1615497 Score: 68
Period size: 9 Copynumber: 6.6 Consensus size: 9
1615427 TATATATATA
*
1615437 TATTTTTTT
1 TATTTATTT
1615446 TATATTCATTT
1 TAT-TT-ATTT
1615457 TATTTATTT
1 TATTTATTT
1615466 TATTTATTT
1 TATTTATTT
* *
1615475 TGTTTGTTT
1 TATTTATTT
*
1615484 CATTTATTT
1 TATTTATTT
1615493 TATTT
1 TATTT
1615498 TTACCTTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
9 33 0.77
10 4 0.09
11 6 0.14
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (9 bp):
TATTTATTT
Found at i:1615553 original size:2 final size:2
Alignment explanation
Indices: 1615546--1615572 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1615536 TTTTATTTAG
1615546 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1615573 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1618815 original size:27 final size:27
Alignment explanation
Indices: 1618777--1618832 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1618767 ATAAACTCAT
1618777 AACTCGCTTACTAAAGAACTGTCACCC
1 AACTCGCTTACTAAAGAACTGTCACCC
1618804 AACTCGCTTACTAAAGAACTGTCACCC
1 AACTCGCTTACTAAAGAACTGTCACCC
1618831 AA
1 AA
1618833 GGTCTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.21
Consensus pattern (27 bp):
AACTCGCTTACTAAAGAACTGTCACCC
Found at i:1621223 original size:60 final size:59
Alignment explanation
Indices: 1621146--1621332 Score: 211
Period size: 60 Copynumber: 3.1 Consensus size: 59
1621136 TTATATGTCT
* * *
1621146 TCAAATTATGATCCTCATTTCAAATTAGTCCATAAATTTTTAAACATTCCAATTTCATCC
1 TCAAACTATGAT-CTCATTTCAAATTTGTCCATAAACTTTTAAACATTCCAATTTCATCC
* * *
1621206 TCAAACTATGACTCTCA-TTCTAAATTTGTCCTTAAACTTTTGAACATTCCAATTTTATCC
1 TCAAACTATGA-TCTCATTTC-AAATTTGTCCATAAACTTTTAAACATTCCAATTTCATCC
*
1621266 TCAAACTATGAATCTCATTGT-AAATTTGTCCATAAACTTTTATATC-TTCTC-ATTTCATCC
1 TCAAACTATG-ATCTCATT-TCAAATTTGTCCATAAACTTTTA-AACATTC-CAATTTCATCC
*
1621326 CCAAACT
1 TCAAACT
1621333 CATCCAAATA
Statistics
Matches: 109, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
59 3 0.03
60 99 0.91
61 6 0.06
62 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (59 bp):
TCAAACTATGATCTCATTTCAAATTTGTCCATAAACTTTTAAACATTCCAATTTCATCC
Found at i:1621243 original size:31 final size:30
Alignment explanation
Indices: 1621203--1621296 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
1621193 TCCAATTTCA
1621203 TCCTCAAACTATGACTCTCATTCTAAATTTG
1 TCCTCAAACTATGA-TCTCATTCTAAATTTG
* * * * * *
1621234 TCCTTAAACTTTTGA--ACATTCCAATTTTA
1 TCCTCAAAC-TATGATCTCATTCTAAATTTG
*
1621263 TCCTCAAACTATGAATCTCATTGTAAATTTG
1 TCCTCAAACTATG-ATCTCATTCTAAATTTG
1621294 TCC
1 TCC
1621297 ATAAACTTTT
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
28 3 0.07
29 19 0.41
31 20 0.43
32 4 0.09
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (30 bp):
TCCTCAAACTATGATCTCATTCTAAATTTG
Found at i:1621601 original size:27 final size:28
Alignment explanation
Indices: 1621529--1621608 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
1621519 GATGAAAACG
* **
1621529 AAATGTTCAAAAGTTTAAGGACTAATTTA
1 AAATGTTTAAAAGTTTAAGGA-TAATAAA
* *
1621558 GAATGATTGTAATAGTTTAAGGATAA-AAA
1 AAATG-TT-TAAAAGTTTAAGGATAATAAA
*
1621587 AAATGTTTAAAAGTTTAGGGAT
1 AAATGTTTAAAAGTTTAAGGAT
1621609 CAATTTGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
27 13 0.32
28 2 0.05
29 9 0.22
30 5 0.12
31 12 0.29
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.34
Consensus pattern (28 bp):
AAATGTTTAAAAGTTTAAGGATAATAAA
Found at i:1623918 original size:19 final size:19
Alignment explanation
Indices: 1623894--1623931 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1623884 AAGGTTGGTA
1623894 CCTTCTTTAAGCTGTAGGG
1 CCTTCTTTAAGCTGTAGGG
1623913 CCTTCTTTAAGCTGTAGGG
1 CCTTCTTTAAGCTGTAGGG
1623932 GTAATCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (19 bp):
CCTTCTTTAAGCTGTAGGG
Found at i:1632684 original size:2 final size:2
Alignment explanation
Indices: 1632677--1632729 Score: 79
Period size: 2 Copynumber: 25.5 Consensus size: 2
1632667 CTCTTGAATC
*
1632677 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TGA GTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA
1632721 TA TA TA TA T
1 TA TA TA TA T
1632730 TTGAGTTGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 45 0.96
3 1 0.02
4 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1632714 original size:24 final size:24
Alignment explanation
Indices: 1632687--1632735 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1632677 TATATATATA
1632687 TATATATATATATATATATTTGAG
1 TATATATATATATATATATTTGAG
1632711 TATATATATATATATATATTTGAG
1 TATATATATATATATATATTTGAG
1632735 T
1 T
1632736 TGTGGTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (24 bp):
TATATATATATATATATATTTGAG
Found at i:1633677 original size:13 final size:13
Alignment explanation
Indices: 1633659--1633686 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1633649 AGCAGCAAGA
1633659 TAGAATGGATCCT
1 TAGAATGGATCCT
1633672 TAGAATGGATCCT
1 TAGAATGGATCCT
1633685 TA
1 TA
1633687 CCTCTCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (13 bp):
TAGAATGGATCCT
Found at i:1634334 original size:27 final size:27
Alignment explanation
Indices: 1634292--1634359 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1634282 GTGTAGGAAT
1634292 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1634317 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1634344 TATAGATATATGATTT
1 TATAGAGATATGATTT
1634360 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1637984 original size:27 final size:27
Alignment explanation
Indices: 1637942--1638009 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1637932 GTGTAGGAAT
1637942 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1637967 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1637994 TATAGATATATGATTT
1 TATAGAGATATGATTT
1638010 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1641933 original size:21 final size:21
Alignment explanation
Indices: 1641907--1641953 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1641897 TTTACTGCAA
1641907 AAAATTCCTAAAAATATCAAC
1 AAAATTCCTAAAAATATCAAC
1641928 AAAATTCCTAAAAATATCAAC
1 AAAATTCCTAAAAATATCAAC
1641949 AAAAT
1 AAAAT
1641954 ACCAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATTCCTAAAAATATCAAC
Found at i:1648403 original size:18 final size:18
Alignment explanation
Indices: 1648380--1648435 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
1648370 AAAAAGAAGG
1648380 TAATTTTTTTGTTTAAAT
1 TAATTTTTTTGTTTAAAT
1648398 TAA----TTTGTATT-AAT
1 TAATTTTTTTGT-TTAAAT
*
1648412 TTATTTTTTTGTTTAAAT
1 TAATTTTTTTGTTTAAAT
1648430 TAATTT
1 TAATTT
1648436 AGATTACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 10 0.33
15 2 0.07
17 2 0.07
18 16 0.53
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TAATTTTTTTGTTTAAAT
Found at i:1650849 original size:31 final size:31
Alignment explanation
Indices: 1650813--1650879 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1650803 ACAAATGGGG
*
1650813 TCATTTAAATAGAAATAAAGCTTACAAACAT
1 TCATTTAAATACAAATAAAGCTTACAAACAT
** * *
1650844 TCATTTAAATACAAATAGGGTTTACAAATAT
1 TCATTTAAATACAAATAAAGCTTACAAACAT
1650875 TCATT
1 TCATT
1650880 CAATTATGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (31 bp):
TCATTTAAATACAAATAAAGCTTACAAACAT
Found at i:1652018 original size:24 final size:24
Alignment explanation
Indices: 1651967--1652018 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1651957 ATCTGCCGTG
* * * **
1651967 TAGAATTTGCACTGAAGTTCCATG
1 TAGAATATGCACCGAAGTACCACA
1651991 TAGAATATGCACCGAAGTACCACA
1 TAGAATATGCACCGAAGTACCACA
1652015 TAGA
1 TAGA
1652019 TTTTTCCCGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TAGAATATGCACCGAAGTACCACA
Found at i:1652035 original size:23 final size:23
Alignment explanation
Indices: 1652002--1652086 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 23
1651992 AGAATATGCA
* * *
1652002 CCGAAGTACCACATAGATTTTTC
1 CCGAAGGACCACATAGAATTGTC
*
1652025 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACATAGAATTGTC
**
1652048 CCGAATAACCACA-A-AATTGTC
1 CCGAAGGACCACATAGAATTGTC
*
1652069 CCGAATGACCACATAGAA
1 CCGAAGGACCACATAGAA
1652087 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
21 19 0.37
22 2 0.04
23 31 0.60
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (23 bp):
CCGAAGGACCACATAGAATTGTC
Found at i:1652067 original size:21 final size:21
Alignment explanation
Indices: 1652041--1652081 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1652031 GACCACGTAG
1652041 AATTGTCCCGAATAACCACAA
1 AATTGTCCCGAATAACCACAA
*
1652062 AATTGTCCCGAATGACCACA
1 AATTGTCCCGAATAACCACA
1652082 TAGAACCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (21 bp):
AATTGTCCCGAATAACCACAA
Found at i:1653851 original size:20 final size:20
Alignment explanation
Indices: 1653826--1653863 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1653816 TTCAATATTG
*
1653826 ACCTCTAGGTATCGATACTA
1 ACCTCTAGGCATCGATACTA
1653846 ACCTCTAGGCATCGATAC
1 ACCTCTAGGCATCGATAC
1653864 AACTGACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (20 bp):
ACCTCTAGGCATCGATACTA
Found at i:1653963 original size:18 final size:19
Alignment explanation
Indices: 1653899--1653967 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 19
1653889 AAATGGTTGC
*
1653899 TATCGATACTTTTTCTTGAG
1 TATCGATAC-TTTTCCTGAG
1653919 TATCGATACTTCTGGTCCGTG-G
1 TATCGATACTT-T--TCC-TGAG
1653941 TATCGATAC-TTTCCTGAG
1 TATCGATACTTTTCCTGAG
1653959 TATCGATAC
1 TATCGATAC
1653968 CAAATTTGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
17 2 0.05
18 13 0.30
19 2 0.05
20 11 0.26
21 1 0.02
22 12 0.28
23 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (19 bp):
TATCGATACTTTTCCTGAG
Found at i:1657618 original size:22 final size:22
Alignment explanation
Indices: 1657577--1657644 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
1657567 CTCGTATAAA
1657577 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1657600 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1657622 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1657644 T
1 T
1657645 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1657905 original size:30 final size:31
Alignment explanation
Indices: 1657864--1657923 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1657854 TAGACATAGT
*
1657864 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
1657894 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
1657924 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:1657980 original size:29 final size:29
Alignment explanation
Indices: 1657938--1658009 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
1657928 TTTTCTGCAT
*
1657938 ATTCATGTCATGTAATACATATAAT-CTGA
1 ATTCATGTCATGTAATACATATAATAC-AA
*
1657967 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
1657996 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1658010 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:1658461 original size:66 final size:67
Alignment explanation
Indices: 1658312--1658485 Score: 201
Period size: 67 Copynumber: 2.6 Consensus size: 67
1658302 TTTTTCTCAT
* * *
1658312 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTTAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATTCATATACG
1658377 AGGA
64 AGGA
* * *
1658381 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCT-TAAGCAATCTGGAAATTCATATACGA
*
1658444 TGA
65 GGA
* *
1658447 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
1658486 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
65 6 0.06
66 18 0.19
67 56 0.60
68 1 0.01
69 12 0.13
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATTCATATACGAG
GA
Found at i:1663772 original size:20 final size:19
Alignment explanation
Indices: 1663747--1663806 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
1663737 TTTTGGTGCA
*
1663747 GAGGGAATCGATATCCCCAT
1 GAGGGAACCGAT-TCCCCAT
*
1663767 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATT-CCCC-AT
1663788 GAAGGGGAACCGATTCCCC
1 G-A-GGGAACCGATTCCCC
1663807 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 2 0.06
22 5 0.15
23 11 0.32
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCAT
Found at i:1663829 original size:21 final size:21
Alignment explanation
Indices: 1663790--1663849 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
1663780 CCCCCTTTGA
* *
1663790 AGGGGAACCGAT-TCCCCCAC
1 AGGGGAATCGATACCCCCCAC
1663810 AGGGGAATCGATACCCCCCAC
1 AGGGGAATCGATACCCCCCAC
1663831 AGGGGAATCGATACCCCCC
1 AGGGGAATCGATACCCCCC
1663850 TGGGGTTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
20 11 0.30
21 26 0.70
ACGTcount: A:0.27, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAATCGATACCCCCCAC
Found at i:1664251 original size:4 final size:4
Alignment explanation
Indices: 1664238--1664271 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1664228 GAAATTTTCG
*
1664238 AAAT -AAT AAAT AAAT AAAT ATAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1664272 AATTTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1664262 original size:16 final size:15
Alignment explanation
Indices: 1664238--1664271 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
1664228 GAAATTTTCG
1664238 AAATAATAAATAAAT
1 AAATAATAAATAAAT
1664253 AAATATATAAATAAAT
1 AAATA-ATAAATAAAT
1664269 AAA
1 AAA
1664272 AATTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:1668757 original size:65 final size:64
Alignment explanation
Indices: 1668688--1668877 Score: 254
Period size: 65 Copynumber: 2.9 Consensus size: 64
1668678 TACACCTGGG
* * * *
1668688 ATGCATTGGTACACTAATTACATTCGATGTTTCAAAAGAGCCAGGAGTGTATCGATGCATTATCT
1 ATGCATTGGTACACAAAATACATTCGATGTTTCAAAA-AACCAAGAGTGTATCGATGCATTATCT
* *
1668753 ATGCATTGGCACACAAAATACATTCGATGTTTCAATAAAACCAAGAGTGTATCGATGCATTGTCT
1 ATGCATTGGTACACAAAATACATTCGATGTTTCAA-AAAACCAAGAGTGTATCGATGCATTATCT
* * * * *
1668818 GTGCATTGCTACACAAAATGCATTCGATGTTTAAATAAAACAAAGAGTGTATCGATGCAT
1 ATGCATTGGTACACAAAATACATTCGATGTTTCAA-AAAACCAAGAGTGTATCGATGCAT
1668878 CAAAGTTTGT
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
65 110 0.98
66 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (64 bp):
ATGCATTGGTACACAAAATACATTCGATGTTTCAAAAAACCAAGAGTGTATCGATGCATTATCT
Found at i:1670879 original size:13 final size:12
Alignment explanation
Indices: 1670846--1670881 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1670836 TAATGGGCAA
1670846 AATTTTGAAAAC
1 AATTTTGAAAAC
*
1670858 TATTTTGAAAAC
1 AATTTTGAAAAC
1670870 AATATTTGAAAA
1 AAT-TTTGAAAA
1670882 ATCATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (12 bp):
AATTTTGAAAAC
Found at i:1671410 original size:23 final size:23
Alignment explanation
Indices: 1671380--1671454 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
1671370 TGTATCGATG
1671380 CACATTCAAGGAATGCATCGGTA
1 CACATTCAAGGAATGCATCGGTA
* * * *
1671403 CACCTTCATA-G--TGTATCGATG
1 CACATTCA-AGGAATGCATCGGTA
*
1671424 CATATTCAAGGAATGCATCGGTA
1 CACATTCAAGGAATGCATCGGTA
*
1671447 CACTTTCA
1 CACATTCA
1671455 TAGTGTATCA
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
20 1 0.03
21 14 0.38
23 21 0.57
24 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (23 bp):
CACATTCAAGGAATGCATCGGTA
Found at i:1671420 original size:44 final size:44
Alignment explanation
Indices: 1671368--1671470 Score: 179
Period size: 44 Copynumber: 2.3 Consensus size: 44
1671358 TACACTGCAG
1671368 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCAT
* *
1671412 AGTGTATCGATGCATATTCAAGGAATGCATCGGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCAT
*
1671456 AGTGTATCAATGCAC
1 AGTGTATCGATGCAC
1671471 TTAGCACAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCAT
Found at i:1677336 original size:65 final size:64
Alignment explanation
Indices: 1677250--1677438 Score: 236
Period size: 65 Copynumber: 2.9 Consensus size: 64
1677240 ACACCTGGGG
* * *
1677250 TGCATCAGTACACTAATTACATTTGATGTTTCAAAAGAGCCAAGAGTGTATCGATGCATTGTCTA
1 TGCATCAGTACACAAAATACATTCGATGTTTCAAAAGA-CCAAGAGTGTATCGATGCATTGTCTA
* * * * *
1677315 TGCATCGGTACACAAAATACATTCGATGTTTCAATAAAACCAAGAGTATATCGATGTATTGTCTG
1 TGCATCAGTACACAAAATACATTCGATGTTTCAA-AAGACCAAGAGTGTATCGATGCATTGTCTA
* * *
1677380 TGCATCAGTACACAAAATGCATTCGATGTTT-AAATAGAACAAGAAATGTATCGATGCAT
1 TGCATCAGTACACAAAATACATTCGATGTTTCAAA-AGACCAAG-AGTGTATCGATGCAT
1677439 CAAAGTGTGT
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 8 0.08
65 94 0.89
66 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (64 bp):
TGCATCAGTACACAAAATACATTCGATGTTTCAAAAGACCAAGAGTGTATCGATGCATTGTCTA
Found at i:1678810 original size:11 final size:11
Alignment explanation
Indices: 1678794--1678831 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1678784 TTATTAGATG
1678794 AATAATATATA
1 AATAATATATA
1678805 AATAATATAT-
1 AATAATATATA
1678815 -ATAATATATTA
1 AATAATATA-TA
1678826 AATAAT
1 AATAAT
1678832 TAATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.33
10 1 0.04
11 10 0.42
12 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATAATATATA
Found at i:1685080 original size:24 final size:21
Alignment explanation
Indices: 1685051--1685104 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1685041 TATTGAATTT
*
1685051 TTTTAAAAATATAAAATTTAATA
1 TTTTAAAAAT-T-AAATTTAAAA
* *
1685074 TTATTAATAATTGAATTTAAAA
1 TT-TTAAAAATTAAATTTAAAA
1685096 TTTTAAAAA
1 TTTTAAAAA
1685105 CTAATGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 6 0.23
22 10 0.38
23 3 0.12
24 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTTAAAAATTAAATTTAAAA
Found at i:1686401 original size:19 final size:19
Alignment explanation
Indices: 1686377--1686417 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1686367 TCGATAAAAA
1686377 TATCACTATTGATATTTTC
1 TATCACTATTGATATTTTC
1686396 TATCACTATTGATATTTTC
1 TATCACTATTGATATTTTC
1686415 TAT
1 TAT
1686418 AAAAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.54
Consensus pattern (19 bp):
TATCACTATTGATATTTTC
Found at i:1707694 original size:13 final size:13
Alignment explanation
Indices: 1707673--1707702 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1707663 TAATTTTTAA
1707673 TTAAATTGATTCT
1 TTAAATTGATTCT
*
1707686 TTAACTTGATTCT
1 TTAAATTGATTCT
1707699 TTAA
1 TTAA
1707703 TTTTGTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (13 bp):
TTAAATTGATTCT
Found at i:1713214 original size:55 final size:55
Alignment explanation
Indices: 1713146--1713345 Score: 346
Period size: 55 Copynumber: 3.6 Consensus size: 55
1713136 ATTGTTTGAG
*
1713146 TGTGTATCGGTACACTGAGGAGTGTATCGATATCCTCAAAACATCGAATTCCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATTCCATT
1713201 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATTCCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATTCCATT
* * *
1713256 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAGTGCTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATTCCATT
* *
1713311 TGTATATTGGTACACTGAGGAGTGTATCGATACCC
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCC
1713346 CCCAAGCATG
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 139 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATTCCATT
Found at i:1714842 original size:64 final size:64
Alignment explanation
Indices: 1714706--1714866 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
1714696 ATTGTTCAGT
* *
1714706 GTGTATCGATGCACAGGAAGTGCATCGATGCACCCATTAGAAATGGAAACATCGAATGCAGGTA
1 GTGTATCGATGCATAGGAAGTGCATCGATGCACCCATTAGAAATGAAAACATCGAATGCAGGTA
* *
1714770 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTA-AAATGAAAACATCGAAT--ATGA
1 GTGTATCGATGCAT-AGGAAGTGCATCGATGCA-CCCATTAGAAATGAAAACATCGAATGCA-G-
* *
1714831 TTG
62 GTA
* *
1714834 GTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 GTGTATCGATGCATAGGAAGTGCATCGATGCAC
1714867 ATGTTAAAGA
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.05
64 70 0.83
65 9 0.11
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (64 bp):
GTGTATCGATGCATAGGAAGTGCATCGATGCACCCATTAGAAATGAAAACATCGAATGCAGGTA
Found at i:1714899 original size:20 final size:22
Alignment explanation
Indices: 1714854--1714911 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1714844 GCATGGGTAG
1714854 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1714878 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
1714898 TGTATCGATGCACT
1 TGCATCGATGCACT
1714912 TCAAGAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1715393 original size:2 final size:2
Alignment explanation
Indices: 1715386--1715415 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1715376 GTGTTTGCGG
1715386 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
1715416 GAATAAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1715689 original size:18 final size:18
Alignment explanation
Indices: 1715666--1715734 Score: 129
Period size: 18 Copynumber: 3.8 Consensus size: 18
1715656 GGGTCTACAC
1715666 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
1715684 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
*
1715702 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACACAGT
1715720 GGTCCTTCGGGACAC
1 GGTCCTTCGGGACAC
1715735 TTCATAGTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (18 bp):
GGTCCTTCGGGACACAGT
Found at i:1716744 original size:19 final size:20
Alignment explanation
Indices: 1716720--1716761 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1716710 TCTAAGAGCT
1716720 CATTTAGG-CCATATAGATG
1 CATTTAGGACCATATAGATG
* *
1716739 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1716759 CAT
1 CAT
1716762 GTGGTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1718278 original size:23 final size:23
Alignment explanation
Indices: 1718251--1718294 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1718241 AATACAATTT
*
1718251 AATTTGCCAAGACATTTCCATCC
1 AATTTGCCAAGACATATCCATCC
*
1718274 AATTTGCCACGACATATCCAT
1 AATTTGCCAAGACATATCCAT
1718295 TTGCTACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.30
Consensus pattern (23 bp):
AATTTGCCAAGACATATCCATCC
Found at i:1723775 original size:96 final size:96
Alignment explanation
Indices: 1723611--1723785 Score: 271
Period size: 96 Copynumber: 1.8 Consensus size: 96
1723601 AATCTACATG
* *
1723611 AGTGAGAAGGATTAGTCATCTTCTATGAAAAATAATGGACCATTTTTGTAGTACACTTACTAGAA
1 AGTGAGAAGGATTAGCCATCTTCTATGAAAAATAATGGACCATTTTTCTAGTACACTTACTAGAA
*
1723676 TCATGAGGAAAAAATGATATGTATATATATA
66 TCATAAGGAAAAAATGATATGTATATATATA
** **
1723707 AGTGAGAAGGATTAGCCA-CATTCTATGAAAAATGTTGGGTCATTTTTCTAGTACACTTACTAGA
1 AGTGAGAAGGATTAGCCATC-TTCTATGAAAAATAATGGACCATTTTTCTAGTACACTTACTAGA
1723771 ATCATAAGGAAAAAA
65 ATCATAAGGAAAAAA
1723786 GGCTATATGT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
95 1 0.01
96 70 0.99
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (96 bp):
AGTGAGAAGGATTAGCCATCTTCTATGAAAAATAATGGACCATTTTTCTAGTACACTTACTAGAA
TCATAAGGAAAAAATGATATGTATATATATA
Found at i:1724537 original size:18 final size:18
Alignment explanation
Indices: 1724497--1724537 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1724487 TTGTCTCAAA
1724497 TAATTCTAACATAAACCC
1 TAATTCTAACATAAACCC
*
1724515 CAATT-TAACATAAATCCC
1 TAATTCTAACATAAA-CCC
1724533 TAATT
1 TAATT
1724538 GGGATTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATTCTAACATAAACCC
Found at i:1728050 original size:21 final size:22
Alignment explanation
Indices: 1728002--1728050 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1727992 ATTCCCCTGT
1728002 GGGGGGAATCGATTCCCTTTCAA
1 GGGGGGAATCGATTCCC-TTCAA
* *
1728025 AGGGGGAATCGGTTCCC-TCAA
1 GGGGGGAATCGATTCCCTTCAA
1728046 GGGGG
1 GGGGG
1728051 ATAGATTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.35
23 15 0.65
ACGTcount: A:0.20, C:0.20, G:0.39, T:0.20
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCTTCAA
Found at i:1738074 original size:53 final size:53
Alignment explanation
Indices: 1738008--1738115 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
1737998 TACTAAACGT
*
1738008 ATTAAGTTTTTAATGGAAGGGTACTAAAATGAAATAAAAACTAAATGTCAGGC
1 ATTAAGTTTTTAATGGAAAGGTACTAAAATGAAATAAAAACTAAATGTCAGGC
* *
1738061 ATTAAGTTTTTAATGGAAATGTACTAAAATGAAATAAAAACTAAATGTTAGGC
1 ATTAAGTTTTTAATGGAAAGGTACTAAAATGAAATAAAAACTAAATGTCAGGC
1738114 AT
1 AT
1738116 AGTTTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (53 bp):
ATTAAGTTTTTAATGGAAAGGTACTAAAATGAAATAAAAACTAAATGTCAGGC
Found at i:1738553 original size:22 final size:21
Alignment explanation
Indices: 1738491--1738565 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
1738481 TAATTTTAAA
*
1738491 AAAATAAAAATAAAATAATATGT
1 AAAATAAATATAAAA-AATAT-T
**
1738514 AAATATAAATAT-TTAAATATT
1 AAA-ATAAATATAAAAAATATT
*
1738535 CAAAATAAATATAAAAAATACTA
1 -AAAATAAATATAAAAAATA-TT
1738558 AAAATAAA
1 AAAATAAA
1738566 AATTAAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
21 9 0.21
22 21 0.50
23 5 0.12
24 7 0.17
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (21 bp):
AAAATAAATATAAAAAATATT
Found at i:1738602 original size:36 final size:38
Alignment explanation
Indices: 1738562--1738636 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 38
1738552 ATACTAAAAA
1738562 TAAAAAT-TA-AA-TTACTAAAAAATTAAATATATATTT
1 TAAAAATATATAATTTACTAAAAAA-TAAATATATATTT
*
1738598 TAAAAATACTATTAATTTTCTAAAAAATAAATATATATT
1 TAAAAATA-TA-TAATTTACTAAAAAATAAATATATATT
1738637 ATAAGCTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 7 0.21
38 2 0.06
40 14 0.42
41 10 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (38 bp):
TAAAAATATATAATTTACTAAAAAATAAATATATATTT
Found at i:1740274 original size:20 final size:19
Alignment explanation
Indices: 1740235--1740286 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
1740225 TTTCCCAAAA
* *
1740235 AGTTTCGATACTTTTCAAG
1 AGTTTCGAAACTTCTCAAG
1740254 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACT-TCTCAAG
*
1740274 AGTTTCAAAACTT
1 AGTTTCGAAACTT
1740287 TACCTAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (19 bp):
AGTTTCGAAACTTCTCAAG
Found at i:1741652 original size:15 final size:16
Alignment explanation
Indices: 1741615--1741657 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
1741605 TATGGAAAAT
1741615 AAGAAAG-AACAAGAA
1 AAGAAAGAAACAAGAA
1741630 GAAGAGAAGAAACAAGAA
1 -AAGA-AAGAAACAAGAA
1741648 AAGAAAGAAA
1 AAGAAAGAAA
1741658 AATGTGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.40
17 7 0.28
18 8 0.32
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAACAAGAA
Found at i:1751951 original size:100 final size:100
Alignment explanation
Indices: 1751655--1752082 Score: 332
Period size: 102 Copynumber: 4.2 Consensus size: 100
1751645 AAACATTTTA
* * * * * *
1751655 ATAAGTATAACATTACAGGTAGTGCA-TTTTTTTATACTTATCAATAGTTTACATTATATATTTG
1 ATAAGTATAACATTATAGGTA--GCACCTTTTTTA-A-TTGTCAA-CGTTTACATTATATGTTTC
* * *
1751719 AAACCTTTTATATTATGAAAAAGTGAGACAAAACATGTTT
61 AAACCTTTTATATTATGAGAAAGTTAGACAAAACAAGTTT
* * * * * **
1751759 ATAAGTATAACATTGTAGGTTGCACCTTATTTTAATTAG-CAACCGTTAAGATTATTTCATTCAA
1 ATAAGTATAACATTATAGGTAGCACCTT-TTTTAATT-GTCAA-CGTTTACATTATATGTTTCAA
* * *
1751823 CCCGTTTT-TATTATGCA-ATAG-TATGACAAAACAAGTTG
63 ACC-TTTTATATTATG-AGAAAGTTA-GACAAAACAAGTTT
** * *
1751861 ATAAGTCCAACATTATATGTAGCGCCTTTTTTAATTGTCAACGTTTACATTATATGTTTCAAACC
1 ATAAGTATAACATTATAGGTAGCACCTTTTTTAATTGTCAACGTTTACATTATATGTTTCAAACC
1751926 TTTTATATTATGAGAAAGTTAGACAAAACAAGTTT
66 TTTTATATTATGAGAAAGTTAGACAAAACAAGTTT
* * * ** ***
1751961 ACAAGTATAACATTATAGGATA-CACATTTTTTTAATTATCAGTTGTTGGGATTATATGTTTCAA
1 ATAAGTATAACATTATAGG-TAGCAC-CTTTTTTAATTGTCA-ACGTTTACATTATATGTTTCAA
* * * *
1752025 A-TTATTTTTACTAT-AGAATAGTTAGACAAAACGAGTTT
63 ACCT-TTTATATTATGAGAA-AGTTAGACAAAACAAGTTT
*
1752063 ATAAGTCTAACATTATAGGT
1 ATAAGTATAACATTATAGGT
1752083 TACGTCTTCT
Statistics
Matches: 259, Mismatches: 50, Indels: 33
0.76 0.15 0.10
Matches are distributed among these distances:
99 5 0.02
100 59 0.23
101 35 0.14
102 129 0.50
103 8 0.03
104 23 0.09
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (100 bp):
ATAAGTATAACATTATAGGTAGCACCTTTTTTAATTGTCAACGTTTACATTATATGTTTCAAACC
TTTTATATTATGAGAAAGTTAGACAAAACAAGTTT
Found at i:1752055 original size:202 final size:202
Alignment explanation
Indices: 1751701--1752079 Score: 474
Period size: 202 Copynumber: 1.9 Consensus size: 202
1751691 CTTATCAATA
* * *
1751701 GTTTACATTATATATTTGAAACCTTTTATATTATGAAAAAGTGAGACAAAACATGTTTATAAGTA
1 GTTTACATTATATATTTCAAACCTTTTATATTATGAAAAAGTGAGACAAAACAAGTTTACAAGTA
* * * * * * *
1751766 TAACATTGTAGGTTGCACCTTATTTTAATTAGCAACCGTTAAGATTATTTCATTCAACCCGTTTT
66 TAACATTATAGGATACACATTATTTTAATTAGCAACCGTTAAGATTATATCATTCAAACCATTTT
*
1751831 TATTATGCAATAGTATGACAAAACAAGTTGATAAGTCCAACATTATATGTAGCGCCTTTTTTAAT
131 TACTATGCAATAGTATGACAAAACAAGTTGATAAGTCCAACATTATATGTAGCGCCTTTTTTAAT
1751896 TGTCAAC
196 TGTCAAC
* * *
1751903 GTTTACATTATATGTTTCAAACCTTTTATATTATGAGAAAGTTAGACAAAACAAGTTTACAAGTA
1 GTTTACATTATATATTTCAAACCTTTTATATTATGAAAAAGTGAGACAAAACAAGTTTACAAGTA
* * *** ** ** **
1751968 TAACATTATAGGATACACATTTTTTTAATTATCAGTTGTTGGGATTATATGTTTCAAATTATTTT
66 TAACATTATAGGATACACATTATTTTAATTAGCAACCGTTAAGATTATATCATTCAAACCATTTT
* * *
1752033 TACTATAG-AATAGT-TAGACAAAACGAGTTTATAAGTCTAACATTATA
131 TACTAT-GCAATAGTAT-GACAAAACAAGTTGATAAGTCCAACATTATA
1752080 GGTTACGTCT
Statistics
Matches: 147, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
201 1 0.01
202 145 0.99
203 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (202 bp):
GTTTACATTATATATTTCAAACCTTTTATATTATGAAAAAGTGAGACAAAACAAGTTTACAAGTA
TAACATTATAGGATACACATTATTTTAATTAGCAACCGTTAAGATTATATCATTCAAACCATTTT
TACTATGCAATAGTATGACAAAACAAGTTGATAAGTCCAACATTATATGTAGCGCCTTTTTTAAT
TGTCAAC
Found at i:1752773 original size:3 final size:3
Alignment explanation
Indices: 1752765--1752849 Score: 98
Period size: 3 Copynumber: 27.0 Consensus size: 3
1752755 CTAAAACTCT
* * *
1752765 TTC TTC TTC TTC TTC TTC TCC TCCC TTC TTC TTC TTC TCCC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC T-TC TTC TTC
*
1752812 TTC TTC TCCC TTC TTC TTC TTC TCTC TTC TTC TTC TTC
1 TTC TTC T-TC TTC TTC TTC TTC T-TC TTC TTC TTC TTC
1752850 CTCCTCCTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
3 62 0.86
4 10 0.14
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (3 bp):
TTC
Found at i:1752792 original size:16 final size:16
Alignment explanation
Indices: 1752773--1752849 Score: 136
Period size: 16 Copynumber: 4.8 Consensus size: 16
1752763 CTTTCTTCTT
*
1752773 CTTCTTCTTCTCCTCC
1 CTTCTTCTTCTTCTCC
1752789 CTTCTTCTTCTTCTCC
1 CTTCTTCTTCTTCTCC
1752805 CTTCTTCTTCTTCTCC
1 CTTCTTCTTCTTCTCC
*
1752821 CTTCTTCTTCTTCTCT
1 CTTCTTCTTCTTCTCC
1752837 CTTCTTCTTCTTC
1 CTTCTTCTTCTTC
1752850 CTCCTCCTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (16 bp):
CTTCTTCTTCTTCTCC
Found at i:1753927 original size:2 final size:2
Alignment explanation
Indices: 1753920--1753953 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1753910 GAGCTATGTG
1753920 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
1753954 GAACATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1754253 original size:22 final size:22
Alignment explanation
Indices: 1754223--1754283 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
1754213 GGGTCTATGT
*
1754223 GGTCATTCGGGACATATACATA
1 GGTCATTCGGGACAAATACATA
*
1754245 GGTCCTTCGGGACAAATACATA
1 GGTCATTCGGGACAAATACATA
1754267 GGTCATTCGGGACAAAT
1 GGTCATTCGGGACAAAT
1754284 TTCATATGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCATTCGGGACAAATACATA
Found at i:1754995 original size:20 final size:21
Alignment explanation
Indices: 1754970--1755010 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1754960 GTAGCAGTAT
*
1754970 TATAGCA-AGGTATCGGTACC
1 TATAGCAGAGGTATCGATACC
*
1754990 TATAGCAGGGGTATCGATACC
1 TATAGCAGAGGTATCGATACC
1755011 CCTGAAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (21 bp):
TATAGCAGAGGTATCGATACC
Found at i:1755611 original size:102 final size:98
Alignment explanation
Indices: 1755294--1755628 Score: 277
Period size: 102 Copynumber: 3.3 Consensus size: 98
1755284 TGAAAAAGTG
* * * * * *
1755294 AGACAAAACATGTTTATAAGTATAACATTGTAGGTTGCACCTTCTTTTAATTAGCAACCGTTAAG
1 AGACAAAACAAGTTTATAAGTATAACATTATAGG-TACA-CTTTTTTTAATTATCAATCGTTAAG
* * *
1755359 ATTATTTCA-TTCAAACCGTTTTTATTATGCAATAG-T
64 ATTATAT-ATTTCAAA-C-TTTTTACTATGGAATAGTT
* * * * * * *
1755395 ATGACAAAACAAGTTGATAAGTCTAACATTATAGGTAGCGC-CTTTTTAATTGTTAAT-GTTTAC
1 A-GACAAAACAAGTTTATAAGTATAACATTATAGGTA-CACTTTTTTTAATTATCAATCG-TTAA
* * * *
1755458 G-TTATATGTTTCAAACCTTTTACATTATACGAA-AGTA
63 GATTATATATTTCAAACTTTTTAC--TAT-GGAATAGTT
**
1755495 AGACAAAACAAGTTTATAAGTATAACATTATAGGATACACATTTTTTTAATTATCAATCGTTGGG
1 AGACAAAACAAGTTTATAAGTATAACATTATAGG-TACAC-TTTTTTTAATTATCAATCGTTAAG
1755560 ATTATATATTTCAAACTATTTTTACTATGGAATAGTT
64 ATTATATATTTCAAAC--TTTTTACTATGGAATAGTT
* *
1755597 AGACAAAACGAGTTTATAAGTCTAACATTATA
1 AGACAAAACAAGTTTATAAGTATAACATTATA
1755629 AGTTACGTCT
Statistics
Matches: 184, Mismatches: 34, Indels: 31
0.74 0.14 0.12
Matches are distributed among these distances:
97 5 0.03
98 1 0.01
99 50 0.27
100 19 0.10
101 22 0.12
102 81 0.44
104 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (98 bp):
AGACAAAACAAGTTTATAAGTATAACATTATAGGTACACTTTTTTTAATTATCAATCGTTAAGAT
TATATATTTCAAACTTTTTACTATGGAATAGTT
Found at i:1757283 original size:75 final size:76
Alignment explanation
Indices: 1757190--1757369 Score: 222
Period size: 77 Copynumber: 2.4 Consensus size: 76
1757180 CAAAACCTCG
* * *
1757190 ACATTCTTGGGCGCAACCTATTTTA-TAA-AAAATATTAATATTACAGATCACAACATACTTTCA
1 ACATTCTTGGGAGCAACCTATTTTATTAATAAAATATTAACATTACAGATCACAAC-TAATTTCA
*
1757253 TAGTGAATCATA
65 TAGTGAACCATA
* * *
1757265 ACATTCTTGGGAGTAACCTATTTTATTAATTAAAATATTAACATTACATATCACAACTAATTTCT
1 ACATTCTTGGGAGCAACCTATTTTATTAA-TAAAATATTAACATTACAGATCACAACTAATTTCA
*
1757330 TAGTGAACCATG
65 TAGTGAACCATA
* *
1757342 ACATTATTGGGTGCAACC-ATATTTATTA
1 ACATTCTTGGGAGCAACCTAT-TTTATTA
1757370 TATATTTTCA
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
75 23 0.26
76 5 0.06
77 38 0.42
78 24 0.27
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (76 bp):
ACATTCTTGGGAGCAACCTATTTTATTAATAAAATATTAACATTACAGATCACAACTAATTTCAT
AGTGAACCATA
Found at i:1757743 original size:265 final size:264
Alignment explanation
Indices: 1757240--1758036 Score: 1120
Period size: 263 Copynumber: 3.0 Consensus size: 264
1757230 TTACAGATCA
* * * * * *
1757240 CAACATACTTTCATAGTGAATCATAACATTCTTGGGAGTAACCTATTTTATTAATTAAAATATTA
1 CAACATACTTTCTTAGTGAACCATGACATTCTTGGGTGCAACCTATTTTATTAATAAAAATATTA
* * * **
1757305 ACATTACATATCACAAC-TAATTTCTTAGTGAACCATGACATTATTGGGTGCAACCATATTTATT
66 ACATTAAAGATCACAACATAATTTCTTATTGAACCATGACATTATT-GG-GCAACTGTATTTATT
* * * * *
1757369 ATATATTTTCATAACTTTTTTCAGCTTTTAACTTATTTTCTTATCGTGGGAAACTCTAAAGCTCC
129 ATACATATTCATAAC-ATTTTCAGGTTTTAACTTATTTTCTTATCGTGGGAAACTCCAAAGCTCC
1757434 ATCAACTTAAACTTTGATAATATTTTAGGCGCAACCCATTTTATTATTAAAAATAGTAAGATTCC
193 ATCAACTTAAACTTTGATAATATTTTAGGCGCAACCCATTTTATTATTAAAAATAGTAAGATTCC
1757499 AAAATTG
258 AAAATTG
* *
1757506 CAACATACTTTCTTAGTGAACCATGACATTCTTGGGTGCAATCTATTTTATTAATAAAAATACTA
1 CAACATACTTTCTTAGTGAACCATGACATTCTTGGGTGCAACCTATTTTATTAATAAAAATATTA
* *
1757571 ACATTAAAGATCACAACATAATTT-TTATTCAACCATGAAATTATTGGGCACAACTGTATTTATT
66 ACATTAAAGATCACAACATAATTTCTTATTGAACCATGACATTATTGGG--CAACTGTATTTATT
* ** *
1757635 ATACATATTCATAACATTTTCAGGTTTTAACTTATTTTCTTATCATGAAAAACTCCAATGCTCCA
129 ATACATATTCATAACATTTTCAGGTTTTAACTTATTTTCTTATCGTGGGAAACTCCAAAGCTCCA
* *
1757700 TCAGCTTAAACTTTGATAATATTTTAGGCGCAACCCATTTTATTAATAAAAATAGTAAGATTCC-
194 TCAACTTAAACTTTGATAATATTTTAGGCGCAACCCATTTTATTATTAAAAATAGTAAGATTCCA
*
1757764 ATATTG
259 AAATTG
* * *
1757770 CAACATGCTTTCTTAGTGAACCAAGAAATTCTTGGGTGCAACCTA-TTTATTAATAAAAATATTA
1 CAACATACTTTCTTAGTGAACCATGACATTCTTGGGTGCAACCTATTTTATTAATAAAAATATTA
* **
1757834 ACATTAAAGATCACAACAT-ATTTCTTATTGAACCATTACATTATTAGAGGTTACTGTATTTATT
66 ACATTAAAGATCACAACATAATTTCTTATTGAACCATGACATTATT-G-GGCAACTGTATTTATT
* ** *
1757898 ATACATATTCATAACATTTTCATGTTTTAACTTATTTTCTTATCGTGGGAAACAGCAAGGCTCCA
129 ATACATATTCATAACATTTTCAGGTTTTAACTTATTTTCTTATCGTGGGAAACTCCAAAGCTCCA
** *
1757963 TCAACTTAAACTTTGATAATATTTTAGGCGCAACTTATTTTATTATTAAAAATAGTAAG-TTTCA
194 TCAACTTAAACTTTGATAATATTTTAGGCGCAACCCATTTTATTATTAAAAATAGTAAGATTCCA
*
1758027 AGATTG
259 AAATTG
1758033 CAAC
1 CAAC
1758037 CTCATTCTTT
Statistics
Matches: 474, Mismatches: 50, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
262 7 0.01
263 189 0.40
264 48 0.10
265 109 0.23
266 115 0.24
267 6 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (264 bp):
CAACATACTTTCTTAGTGAACCATGACATTCTTGGGTGCAACCTATTTTATTAATAAAAATATTA
ACATTAAAGATCACAACATAATTTCTTATTGAACCATGACATTATTGGGCAACTGTATTTATTAT
ACATATTCATAACATTTTCAGGTTTTAACTTATTTTCTTATCGTGGGAAACTCCAAAGCTCCATC
AACTTAAACTTTGATAATATTTTAGGCGCAACCCATTTTATTATTAAAAATAGTAAGATTCCAAA
ATTG
Found at i:1758291 original size:158 final size:158
Alignment explanation
Indices: 1757993--1758310 Score: 433
Period size: 158 Copynumber: 2.0 Consensus size: 158
1757983 ATTTTAGGCG
* * * * *
1757993 CAACTTATTTTATTATTAAAAATAGTAAGTTTCAAGATTGCAACCTCATTCTTTACTGAAAGAAG
1 CAACCTATTTTATTATTAAAAATAGTAAGATTCAAGATTACAACCTCATTCCTTACTGAAACAAG
*
1758058 ACATTATTGGGCGCAACTGTATTTACTATATATGTTCATAACATTTTCAGTATTTAGCTTATTTA
66 ACATTATTGGGCGCAACCGTATTTACTATATATGTTCATAACATTTTCAGTATTTAGCTTATTTA
*
1758123 CATATTGTAGGAAATTAAAAGGCTCCAT
131 CATATCGTAGGAAATTAAAAGGCTCCAT
* * * * *
1758151 CAACCTATTTTATTGTTAAAAATATTAAGATTCCATATTACAACTTTC-TTCCTTACTGAAACAA
1 CAACCTATTTTATTATTAAAAATAGTAAGATTCAAGATTACAAC-CTCATTCCTTACTGAAACAA
* * * *
1758215 GACATTATTGGGCGCAACCGTATTTATTATATGTGTTCATAACATTTTTAGTCTTATA-CTTATT
65 GACATTATTGGGCGCAACCGTATTTACTATATATGTTCATAACATTTTCAGTATT-TAGCTTATT
***
1758279 TTGTTATCGTAGGAAATTAAAAGGCTCCAT
129 TACATATCGTAGGAAATTAAAAGGCTCCAT
1758309 CA
1 CA
1758311 GCTTTAACTC
Statistics
Matches: 139, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
158 135 0.97
159 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (158 bp):
CAACCTATTTTATTATTAAAAATAGTAAGATTCAAGATTACAACCTCATTCCTTACTGAAACAAG
ACATTATTGGGCGCAACCGTATTTACTATATATGTTCATAACATTTTCAGTATTTAGCTTATTTA
CATATCGTAGGAAATTAAAAGGCTCCAT
Found at i:1758766 original size:24 final size:21
Alignment explanation
Indices: 1758739--1758873 Score: 56
Period size: 22 Copynumber: 6.1 Consensus size: 21
1758729 ATAACTTATG
1758739 ATATATATTTAATTTTAAAAAAT
1 ATATATATTTAATTTT--AAAAT
* * *
1758762 AATATAATTTTTAGTATTTGAAAT
1 -ATAT-ATATTTAAT-TTTAAAAT
** *
1758786 ATATATATTTAATTTTTTAGT
1 ATATATATTTAATTTTAAAAT
* **
1758807 A-ATTTAATTTAATTTTTAGTAT
1 ATATAT-ATTTAA-TTTTAAAAT
* * *
1758829 TTTTATATTTATTTTTTAAAAT
1 ATATATATTTA-ATTTTAAAAT
* * *
1758851 ATTTATATTTAAATTTAAGAT
1 ATATATATTTAATTTTAAAAT
1758872 AT
1 AT
1758874 TTTTATTTTT
Statistics
Matches: 82, Mismatches: 23, Indels: 15
0.68 0.19 0.12
Matches are distributed among these distances:
20 3 0.04
21 21 0.26
22 34 0.41
23 6 0.07
24 8 0.10
25 7 0.09
26 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
ATATATATTTAATTTTAAAAT
Found at i:1758838 original size:22 final size:22
Alignment explanation
Indices: 1758784--1758881 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
1758774 AGTATTTGAA
*
1758784 ATATATATATTTAATTTTTTAGT
1 ATATTTATATTTAA-TTTTTAGT
1758807 A-ATTTA-ATTTAATTTTTAGT
1 ATATTTATATTTAATTTTTAGT
* * **
1758827 ATTTTTATATTTATTTTTTAAA
1 ATATTTATATTTAATTTTTAGT
* *
1758849 ATATTTATATTTAAATTTAAG-
1 ATATTTATATTTAATTTTTAGT
*
1758870 ATATTTTTATTT
1 ATATTTATATTT
1758882 TTTAAAAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.15
21 21 0.34
22 31 0.50
23 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (22 bp):
ATATTTATATTTAATTTTTAGT
Found at i:1758855 original size:43 final size:45
Alignment explanation
Indices: 1758789--1758879 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 45
1758779 TTGAAATATA
** * *
1758789 TATATTTAATTTTTTAGTAATTTA-ATTTAATTTTTAG-TATTTT
1 TATATTTAATTTTTTAAAAATTTATATTTAAATTTAAGATATTTT
1758832 TATATTT-ATTTTTTAAAATATTTATATTTAAATTTAAGATATTTT
1 TATATTTAATTTTTTAAAA-ATTTATATTTAAATTTAAGATATTTT
1758877 TAT
1 TAT
1758880 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 9 0.22
43 12 0.29
44 11 0.27
45 9 0.22
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (45 bp):
TATATTTAATTTTTTAAAAATTTATATTTAAATTTAAGATATTTT
Found at i:1758873 original size:21 final size:21
Alignment explanation
Indices: 1758784--1758881 Score: 74
Period size: 21 Copynumber: 4.6 Consensus size: 21
1758774 AGTATTTGAA
* *
1758784 ATATATATATTTAATTTTTTAG
1 ATATTTATATTTAA-TTTTAAG
*
1758806 -TAATTTA-ATTTAATTTTTAG
1 AT-ATTTATATTTAATTTTAAG
* * *
1758826 TATTTTTATATTTATTTTTTAAA
1 -ATATTTATATTTA-ATTTTAAG
*
1758849 ATATTTATATTTAAATTTAAG
1 ATATTTATATTTAATTTTAAG
*
1758870 ATATTTTTATTT
1 ATATTTATATTT
1758882 TTTAAAAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
20 7 0.11
21 27 0.44
22 22 0.36
23 5 0.08
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATATTTATATTTAATTTTAAG
Found at i:1763220 original size:58 final size:58
Alignment explanation
Indices: 1763139--1763288 Score: 291
Period size: 58 Copynumber: 2.6 Consensus size: 58
1763129 ATTTTTTTGT
1763139 TTGTCAATGAGCCTCTTAACATAGATGTTATATACTTATATAGGTTTACTTGTTTGAA
1 TTGTCAATGAGCCTCTTAACATAGATGTTATATACTTATATAGGTTTACTTGTTTGAA
1763197 TTGTCAATGAGCCTCTTAACATAGATGTTATATACTTATATAGGTTTACTTGTTTGAA
1 TTGTCAATGAGCCTCTTAACATAGATGTTATATACTTATATAGGTTTACTTGTTTGAA
*
1763255 TTGTCAATGAGCCTCTTAACATATATGTTATATA
1 TTGTCAATGAGCCTCTTAACATAGATGTTATATA
1763289 GGTTTACTTG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 91 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (58 bp):
TTGTCAATGAGCCTCTTAACATAGATGTTATATACTTATATAGGTTTACTTGTTTGAA
Found at i:1768867 original size:93 final size:93
Alignment explanation
Indices: 1768704--1768895 Score: 339
Period size: 93 Copynumber: 2.1 Consensus size: 93
1768694 GAAGCCTTCC
* *
1768704 AAACAACCTTCACAGTGTGCATCTTAGGGTACTTCTACTACGGTCAATGCTGCCAGCAGTTGGTC
1 AAACAACCTTCACAGTGTGCACCTTAGGGTAATTCTACTACGGTCAATGCTGCCAGCAGTTGGTC
*
1768769 TTTTAGTCAACAACAAATGGAGGAGCGA
66 CTTTAGTCAACAACAAATGGAGGAGCGA
*
1768797 AAACAACCTTCACAGTGTGTACCTTAGGGTAATTCTACTACGGTCAATGCTGCCAGCAGTTGGTC
1 AAACAACCTTCACAGTGTGCACCTTAGGGTAATTCTACTACGGTCAATGCTGCCAGCAGTTGGTC
*
1768862 CTTTAGTCAACAACTAATGGAGGAGCGA
66 CTTTAGTCAACAACAAATGGAGGAGCGA
1768890 AAACAA
1 AAACAA
1768896 ATTTTTGTTC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (93 bp):
AAACAACCTTCACAGTGTGCACCTTAGGGTAATTCTACTACGGTCAATGCTGCCAGCAGTTGGTC
CTTTAGTCAACAACAAATGGAGGAGCGA
Found at i:1775516 original size:2 final size:2
Alignment explanation
Indices: 1775509--1775560 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1775499 TGTCAATTTA
1775509 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
1775551 AT AT AT AT AT
1 AT AT AT AT AT
1775561 GAAATTGACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1776213 original size:23 final size:23
Alignment explanation
Indices: 1776177--1776221 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1776167 ATAACAATAT
*
1776177 TAATTATTAAAATATATTATTAA
1 TAATTATTAAAATATAATATTAA
1776200 TAATT-TTAATAATATAATATTA
1 TAATTATTAA-AATATAATATTA
1776222 TATGTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTATTAAAATATAATATTAA
Found at i:1776245 original size:54 final size:54
Alignment explanation
Indices: 1776179--1776306 Score: 131
Period size: 54 Copynumber: 2.4 Consensus size: 54
1776169 AACAATATTA
* *
1776179 ATTATTAAAATATATTATTAA-TA-ATTTTAATAATATA-ATATTATATGTTTTACT
1 ATTA-TAAAATATATTATTAATTATATTATAATAATATAGATATTATATATTTT--T
1776233 ATTATAACAATATATTA--AATTATATTATAATAATATATGATATTATATATTTTT
1 ATTATAA-AATATATTATTAATTATATTATAATAATATA-GATATTATATATTTTT
* *
1776287 ATTTTAATAATATATAATTA
1 ATTATAA-AATATATTATTA
1776307 GTCATTAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
52 2 0.03
53 5 0.08
54 41 0.66
56 14 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (54 bp):
ATTATAAAATATATTATTAATTATATTATAATAATATAGATATTATATATTTTT
Found at i:1776258 original size:23 final size:23
Alignment explanation
Indices: 1776232--1776280 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1776222 TATGTTTTAC
*
1776232 TATTATAACAATATATTAAATTA
1 TATTATAACAATATATGAAATTA
* *
1776255 TATTATAATAATATATGATATTA
1 TATTATAACAATATATGAAATTA
1776278 TAT
1 TAT
1776281 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTATAACAATATATGAAATTA
Found at i:1776275 original size:28 final size:31
Alignment explanation
Indices: 1776206--1776301 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 31
1776196 TTAATAATTT
* *
1776206 TAATAATATA--ATATTATATGTTT-TACTA
1 TAATAATATATGATATTATATATTTATATTA
* *
1776234 TTATAACA-AT-ATATTA-A-A-TTATATTA
1 TAATAATATATGATATTATATATTTATATTA
* *
1776260 TAATAATATATGATATTATATATTTTTATTT
1 TAATAATATATGATATTATATATTTATATTA
1776291 TAATAATATAT
1 TAATAATATAT
1776302 AATTAGTCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
25 2 0.04
26 10 0.19
27 4 0.08
28 18 0.34
29 1 0.02
30 1 0.02
31 17 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (31 bp):
TAATAATATATGATATTATATATTTATATTA
Found at i:1780273 original size:24 final size:23
Alignment explanation
Indices: 1780213--1780274 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
1780203 GAATAATAAT
* *
1780213 AAAATAAATAAAATAGATGAATA
1 AAAATAAATAAAATTGATAAATA
* *
1780236 AAGATAAATGAAATTGAGTAAATA
1 AAAATAAATAAAATTGA-TAAATA
*
1780260 AAAATAAAAAAAATT
1 AAAATAAATAAAATT
1780275 AAAAAGGGGT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (23 bp):
AAAATAAATAAAATTGATAAATA
Found at i:1782445 original size:85 final size:85
Alignment explanation
Indices: 1782327--1782952 Score: 824
Period size: 85 Copynumber: 7.4 Consensus size: 85
1782317 TCAACATTTT
* ** * * * * * *
1782327 TTTGTTGACAGATAGCTTTTCTTGACTTAAGTTATGCTGTAAATTTTACATGCCCTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
* * *
1782392 TAG-AATCAAACTC-ACAGATA
66 T-GTAATCGAACTCGA-AGGTC
* * * * *
1782412 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATACTATAAATTTGATATGTCATTGAGTTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
1782477 TGTAATCGAACTCGAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * * * * *
1782497 TTTTTTGACAGATATCCCTTCTCGTCTGGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
1782562 TGTAATCGAACTCGAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * * * *
1782582 TTTGCTGATAGATAACCCTTCTCACCTTGAATTATGCTATAAATTTGATATGCCTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
1782647 TGTAATCGAACTCGAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * * *
1782667 TTTGCTGACAGATAACCCTTATCGCCTTGAGTTATGATGTAAATTTGATATGCATTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
*
1782732 TGTAATCGAACTAGAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * * *
1782752 TTGGTTGACAGATATCCATTCTTGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
1782817 TGTAATCGAACTCGAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * *
1782837 TTTGCTGATAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTCGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
*
1782902 TGTAATCGAACTCAAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * *
1782922 TTGGTTGATAGATAGCCCTTCTCGCCTTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAG
1782953 CTAAGCTGCA
Statistics
Matches: 477, Mismatches: 62, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
84 1 0.00
85 475 1.00
86 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA
TGTAATCGAACTCGAAGGTC
Found at i:1783230 original size:42 final size:42
Alignment explanation
Indices: 1783182--1783333 Score: 105
Period size: 42 Copynumber: 3.6 Consensus size: 42
1783172 TCTGAACAAA
1783182 GTGAGATGATCTTTGGATGACTCCCCTTCACGGTAAAGTCAT
1 GTGAGATGATCTTTGGATGACTCCCCTTCACGGTAAAGTCAT
* ** ** * * *
1783224 GTGAGATGTTCCTCAGG-TGGTTCCCCTT-AGCGGGTCTGAA-CCAA
1 GTGAGATGAT-CTTTGGATGACTCCCCTTCA-C-GG--TAAAGTCAT
* * * *
1783268 GTAAGATGATCTTTGAATGACTCCCATTCACGGGAAAGTCAT
1 GTGAGATGATCTTTGGATGACTCCCCTTCACGGTAAAGTCAT
*
1783310 GTGAGATGTTCTTT-GAGTGACTCC
1 GTGAGATGATCTTTGGA-TGACTCC
1783334 TCTTTGTGAG
Statistics
Matches: 78, Mismatches: 23, Indels: 18
0.66 0.19 0.15
Matches are distributed among these distances:
41 4 0.05
42 40 0.51
43 11 0.14
44 19 0.24
45 4 0.05
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (42 bp):
GTGAGATGATCTTTGGATGACTCCCCTTCACGGTAAAGTCAT
Found at i:1783320 original size:86 final size:86
Alignment explanation
Indices: 1783019--1783312 Score: 401
Period size: 86 Copynumber: 3.4 Consensus size: 86
1783009 CGATCATAAT
* * * * *
1783019 TCTTTAGATGACTCCCCTTCACGGGAAAGCCAAGTGGCATATTCTTCATGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGCATATTCCTCAGGTGGTTCCCCTTAGCG
*
1783084 GGTCTGAACCAGGTGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* * * *
1783105 TATTTGGATGACTCCCTTTCATGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTAGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGCATATTCCTCAGGTGGTTCCCCTTAGCG
* *
1783170 GATCTGAACAAAGTGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* * *
1783191 TCTTTGGATGACTCCCCTTCACGGTAAAGTCATGTGAG-ATGTTCCTCAGGTGGTTCCCCTTAGC
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTG-GCATATTCCTCAGGTGGTTCCCCTTAGC
*
1783255 GGGTCTGAACCAAGTAAGATGA
65 GGGTCTGAACCAAGTGAGATGA
* * *
1783277 TCTTTGAATGACTCCCATTCACGGGAAAGTCATGTG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTG
1783313 AGATGTTCTT
Statistics
Matches: 183, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 182 0.99
87 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (86 bp):
TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGCATATTCCTCAGGTGGTTCCCCTTAGCG
GGTCTGAACCAAGTGAGATGA
Found at i:1784660 original size:99 final size:99
Alignment explanation
Indices: 1784488--1784689 Score: 302
Period size: 99 Copynumber: 2.0 Consensus size: 99
1784478 GGCCAGTTCA
* *
1784488 ATATTATAATCACGTTTACCAGACTAGCTGAATCTTATCCACAAAGCCAGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTACCAGACTAGCTGAATCTTATCCACAAAGCCAGGGCGTTTAACCAAAT
* *
1784553 GCCTTAGAGGGACAGCTCAAGCTTTATTGTATAT
66 GCCTTAGAGGGACAACTCAAGCTTTATTGTATAC
* *
1784587 ATATTATAATCACCTTTATCA-ATCTAGCTGAATCTTATCCATAAAGCC-GGAGCGTTTAACCAA
1 ATATTATAATCACCTTTACCAGA-CTAGCTGAATCTTATCCACAAAGCCAGG-GCGTTTAACCAA
1784650 ATG-CTCTAGAGGGACAACTCAAGCTTTATTGTATAC
64 ATGCCT-TAGAGGGACAACTCAAGCTTTATTGTATAC
1784686 ATAT
1 ATAT
1784690 AATATTATAA
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
98 5 0.05
99 89 0.95
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (99 bp):
ATATTATAATCACCTTTACCAGACTAGCTGAATCTTATCCACAAAGCCAGGGCGTTTAACCAAAT
GCCTTAGAGGGACAACTCAAGCTTTATTGTATAC
Found at i:1788584 original size:13 final size:13
Alignment explanation
Indices: 1788568--1788592 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1788558 TTAATCGTGA
1788568 AAATTAAAATTTT
1 AAATTAAAATTTT
1788581 AAATTAAAATTT
1 AAATTAAAATTT
1788593 AAAAACCCGA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTAAAATTTT
Found at i:1790037 original size:2 final size:2
Alignment explanation
Indices: 1790030--1790102 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
1790020 CATTGTAATA
1790030 AT AT AT AT -T 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
1790071 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
1790103 GTCCAGACGA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1790997 original size:2 final size:2
Alignment explanation
Indices: 1790990--1791027 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1790980 TTAAAACAAC
*
1790990 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1791028 AATAAGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1791046 original size:23 final size:23
Alignment explanation
Indices: 1791011--1791054 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1791001 ATATATATAT
*
1791011 ATATATATATATTTATAAATAAG
1 ATATATATATATTTAAAAATAAG
* *
1791034 ATATTTATTTATTTAAAAATA
1 ATATATATATATTTAAAAATA
1791055 TCTGAATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATATATATATTTAAAAATAAG
Found at i:1791371 original size:11 final size:11
Alignment explanation
Indices: 1791357--1791382 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1791347 GACTAAAATA
1791357 AAATAATAATT
1 AAATAATAATT
1791368 AAATAATAATT
1 AAATAATAATT
1791379 AAAT
1 AAAT
1791383 TACTAATTTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAATAATT
Done.