Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 7 of 325
Found at i:1561680 original size:71 final size:72
Alignment explanation
Indices: 1561498--1561821 Score: 382
Period size: 74 Copynumber: 4.5 Consensus size: 72
1561488 TTGTTTTTTC
* * * * *
1561498 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
*
1561563 CTGCTTTT
66 ATGC-TTT
* *** * *
1561571 TAGTTCATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATT
1 CA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATT
1561636 TATG-TTT
65 TATGCTTT
* * * *
1561643 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
*
1561708 CTGCTTTT
66 ATGC-TTT
* *** *
1561716 TAGTTCATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATT
1 CA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATT
1561781 TATG-TTT
65 TATGCTTT
* *
1561788 CAAAAATCAACTCATATTACGAGAGGTGGGTTGA
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1561822 ACCTTTTAAT
Statistics
Matches: 208, Mismatches: 39, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
71 83 0.40
72 8 0.04
73 5 0.02
74 112 0.54
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (72 bp):
CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
ATGCTTT
Found at i:1561761 original size:145 final size:145
Alignment explanation
Indices: 1561498--1561821 Score: 603
Period size: 145 Copynumber: 2.2 Consensus size: 145
1561488 TTGTTTTTTC
*
1561498 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
1561563 CTGCTTTTTAGTTCATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAA
66 CTGCTTTTTAGTTCATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAA
1561628 TTTCAATTTATGTTT
131 TTTCAATTTATGTTT
1561643 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1561708 CTGCTTTTTAGTTCATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAA
66 CTGCTTTTTAGTTCATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAA
1561773 TTTCAATTTATGTTT
131 TTTCAATTTATGTTT
* * *
1561788 CAAAAATCAACTCATATTACGAGAGGTGGGTTGA
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
1561822 ACCTTTTAAT
Statistics
Matches: 174, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 174 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (145 bp):
CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
CTGCTTTTTAGTTCATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAA
TTTCAATTTATGTTT
Found at i:1561950 original size:141 final size:140
Alignment explanation
Indices: 1561773--1562047 Score: 437
Period size: 141 Copynumber: 1.9 Consensus size: 140
1561763 GTTGAGGTAA
*
1561773 TTTCAATTTATGTTTCAAAAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTCTAC
1 TTTCAATTTACGTTTCAAAAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTCTAC
* *
1561838 TTTTTCAAAATCAGCTCATATTGCGAAAGGTGAGTTGAGCCTCAGG-TCAC-GTTGAGGTATTTT
66 TTTTTCAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGTTCACAGTCGAGGTATTTT
1561901 CAATTTCTGT
131 CAATTTCTGT
1561911 TTTCAATTTACGTTGTTCAAAGAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTC
1 TTTCAATTTACG-T-TTCAAA-AATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTC
* * **
1561976 TACTTTTTCAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTTGGGTTCACATGTCGAGGTA
63 TACTTTTTCAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGTTCACA-GTCGAGGTA
1562041 TTTTCAA
127 TTTTCAA
1562048 AATCTACTTT
Statistics
Matches: 124, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
138 11 0.09
139 1 0.01
140 6 0.05
141 87 0.70
142 4 0.03
144 15 0.12
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (140 bp):
TTTCAATTTACGTTTCAAAAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTCTAC
TTTTTCAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGTTCACAGTCGAGGTATTTT
CAATTTCTGT
Found at i:1562457 original size:68 final size:67
Alignment explanation
Indices: 1562323--1562499 Score: 223
Period size: 68 Copynumber: 2.6 Consensus size: 67
1562313 TGTTTTTTTT
1562323 TTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTTTCAAAATCT
1 TTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTTTCAAAATCT
1562388 AC
66 AC
* * * **
1562390 TTTTCAAAGTATTAACTCATGTTGCGAGAGGTGAGTTGAGCCTTCTAA-TTTC-TTCTTTTAATT
1 TTTTCAAAG-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-TAATTTTCGTT-TTTCAAAA
1562453 TCTAC
63 TCTAC
* * * **
1562458 GTTTCAAAAATCAACCCATATTGCGAGAAATGAGTTGAGCCT
1 TTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1562500 CAGTTCACTT
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
67 39 0.41
68 53 0.56
69 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (67 bp):
TTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTTTCAAAATCT
AC
Found at i:1563223 original size:22 final size:23
Alignment explanation
Indices: 1563162--1563233 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1563152 TGTGCCGCAA
*
1563162 CCACTACAACCAGCCCCATACCC
1 CCACTACAACAAGCCCCATACCC
1563185 CCACTACAACAAGCCCCATACCC
1 CCACTACAACAAGCCCCATACCC
* *
1563208 CCACTGCAACAA-CCCCATACCG
1 CCACTACAACAAGCCCCATACCC
1563230 CCAC
1 CCAC
1563234 AGTCCTCGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 13 0.28
23 33 0.72
ACGTcount: A:0.32, C:0.54, G:0.06, T:0.08
Consensus pattern (23 bp):
CCACTACAACAAGCCCCATACCC
Found at i:1564341 original size:13 final size:14
Alignment explanation
Indices: 1564317--1564347 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1564307 ATCATTATCA
1564317 ATATTAATATATGT
1 ATATTAATATATGT
1564331 ATATT-ATATATGT
1 ATATTAATATATGT
1564344 ATAT
1 ATAT
1564348 ATTCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
ATATTAATATATGT
Found at i:1564900 original size:15 final size:13
Alignment explanation
Indices: 1564870--1564927 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
1564860 TCATGTATAT
1564870 TATTATATATGTA
1 TATTATATATGTA
*
1564883 TATTGTATATGTTCA
1 TATTATATATG-T-A
* *
1564898 TATTAAATATAT-
1 TATTATATATGTA
1564910 TATGTATATATGTA
1 TAT-TATATATGTA
1564924 TATT
1 TATT
1564928 TCTCACGTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
12 3 0.09
13 18 0.51
14 5 0.14
15 9 0.26
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (13 bp):
TATTATATATGTA
Found at i:1566469 original size:22 final size:22
Alignment explanation
Indices: 1566412--1566470 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
1566402 ACCATATCAC
* *
1566412 TAGGCACCAAAGTGCTGAGCAG
1 TAGGCACCAAAGTGCTGAACAA
* ** *
1566434 TAAGCACCGGAGTGTTGAACAA
1 TAGGCACCAAAGTGCTGAACAA
*
1566456 TAGGCACCATAGTGC
1 TAGGCACCAAAGTGC
1566471 AAATCAGTAG
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.22, G:0.29, T:0.17
Consensus pattern (22 bp):
TAGGCACCAAAGTGCTGAACAA
Found at i:1566507 original size:20 final size:22
Alignment explanation
Indices: 1566466--1566514 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
1566456 TAGGCACCAT
1566466 AGTGCAAATCAGTAGCCACCGA
1 AGTGCAAATCAGTAGCCACCGA
*
1566488 AGTGCAAA-CAGT-GGCACCGA
1 AGTGCAAATCAGTAGCCACCGA
1566508 AGTGCAA
1 AGTGCAA
1566515 TCCTGTACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
22 8 0.31
ACGTcount: A:0.37, C:0.24, G:0.27, T:0.12
Consensus pattern (22 bp):
AGTGCAAATCAGTAGCCACCGA
Found at i:1567059 original size:32 final size:32
Alignment explanation
Indices: 1567022--1567085 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1567012 CACTCTTCTA
1567022 AAGCCCTCTGATTTCAGTAATTACAGAAATTT
1 AAGCCCTCTGATTTCAGTAATTACAGAAATTT
*
1567054 AAGCCCTTTGATTTCAGTAATTACAGAAATTT
1 AAGCCCTCTGATTTCAGTAATTACAGAAATTT
1567086 CATGTCAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
AAGCCCTCTGATTTCAGTAATTACAGAAATTT
Found at i:1567680 original size:3 final size:3
Alignment explanation
Indices: 1567672--1567712 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1567662 AAGTAAAAGA
1567672 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1567713 ATGTTAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1569036 original size:23 final size:23
Alignment explanation
Indices: 1569010--1569100 Score: 57
Period size: 23 Copynumber: 4.0 Consensus size: 23
1569000 AAATAATAAT
1569010 AATAAAACATTTTAAAATAAATA
1 AATAAAACATTTTAAAATAAATA
* * * *
1569033 AAT---AGAGTTCAAAATAAGGTA
1 AATAAAACATTTTAAAATAA-ATA
* * *
1569054 TATAAAACAATTTAAAATAAGT-
1 AATAAAACATTTTAAAATAAATA
1569076 AATCAAAACAATTTT-AAATAAATA
1 AAT-AAAAC-ATTTTAAAATAAATA
1569100 A
1 A
1569101 TATATAATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 13
0.68 0.15 0.18
Matches are distributed among these distances:
20 11 0.22
21 4 0.08
22 2 0.04
23 17 0.34
24 16 0.32
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (23 bp):
AATAAAACATTTTAAAATAAATA
Found at i:1569071 original size:24 final size:23
Alignment explanation
Indices: 1569043--1569101 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
1569033 AATAGAGTTC
1569043 AAAATAAGGTATAT-AAAACAATTT
1 AAAATAA-GTA-ATCAAAACAATTT
1569067 AAAATAAGTAATCAAAACAATTT
1 AAAATAAGTAATCAAAACAATTT
* *
1569090 TAAATAAATAAT
1 AAAATAAGTAAT
1569102 ATATAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 2 0.06
23 23 0.72
24 7 0.22
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (23 bp):
AAAATAAGTAATCAAAACAATTT
Found at i:1569222 original size:5 final size:5
Alignment explanation
Indices: 1569212--1569243 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1569202 TTCATTTAAA
*
1569212 AAAAT AAAAT AAAAT ACAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1569244 TATATAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1571719 original size:40 final size:40
Alignment explanation
Indices: 1571672--1571754 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 40
1571662 TATGGGATAT
** * *
1571672 TGAATATTGTTTTGAATACTGAATTGAACTGTGAAATTCC
1 TGAATATTGTTACGAATACTGAATTAAACTGTAAAATTCC
* * *
1571712 TGAATATTGTTACGTATACTGCATTAAACTGTAAAATTTC
1 TGAATATTGTTACGAATACTGAATTAAACTGTAAAATTCC
1571752 TGA
1 TGA
1571755 TGAAACGAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.40
Consensus pattern (40 bp):
TGAATATTGTTACGAATACTGAATTAAACTGTAAAATTCC
Found at i:1572071 original size:6 final size:6
Alignment explanation
Indices: 1572053--1572096 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
1572043 GTGTGTTGAA
* * *
1572053 TACTGT TATTGT TACTGT TACTGC TATTGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
1572097 TAGCTACTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.18, C:0.14, G:0.16, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:1572080 original size:18 final size:19
Alignment explanation
Indices: 1572053--1572094 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1572043 GTGTGTTGAA
*
1572053 TACTGTTATTGTTACTG-T
1 TACTGCTATTGTTACTGAT
1572071 TACTGCTATTGTTACTGAT
1 TACTGCTATTGTTACTGAT
1572090 TACTG
1 TACTG
1572095 TTTAGCTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (19 bp):
TACTGCTATTGTTACTGAT
Found at i:1574651 original size:26 final size:26
Alignment explanation
Indices: 1574614--1574749 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
1574604 TGATACAAAT
* *
1574614 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
1574640 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
1574666 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
1574692 TGATAATGGGTTAAGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
1574718 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
1574744 TGATAA
1 TGATAA
1574750 GAATATCATG
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:1576786 original size:137 final size:137
Alignment explanation
Indices: 1576540--1576826 Score: 529
Period size: 137 Copynumber: 2.1 Consensus size: 137
1576530 GAGTAGTCTC
1576540 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGACCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGACCTATGGGCCATAC
*
1576605 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTTGCCCAGTACC
66 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
1576670 ACTGTTA
131 ACTGTTA
*
1576677 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGACCTATGGGCCATAC
*
1576742 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
1576807 ACTGTTA
131 ACTGTTA
**
1576814 CCTGAATGGGCTT
1 CCCAAATGGGCTT
1576827 AGGCCCAATA
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 145 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGACCTATGGGCCATAC
TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:1579944 original size:26 final size:26
Alignment explanation
Indices: 1579915--1579972 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
1579905 CATGAAATTC
1579915 TTATCATAAAACATTTACCTAACCCA
1 TTATCATAAAACATTTACCTAACCCA
** *
1579941 TTATCATGGAACATTTACCTAACCTA
1 TTATCATAAAACATTTACCTAACCCA
1579967 TTATCA
1 TTATCA
1579973 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (26 bp):
TTATCATAAAACATTTACCTAACCCA
Found at i:1581686 original size:38 final size:38
Alignment explanation
Indices: 1581598--1581712 Score: 185
Period size: 39 Copynumber: 3.0 Consensus size: 38
1581588 ATTCCACTCC
* * *
1581598 CCCCATGCTACTTTGTTTTATTATTAATTAAAACTACTT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACCA-TT
1581637 CCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
1581675 CCCCATACTATTTTGTTTTTATTATTAATTAAAACCAT
1 CCCCATACTATTTTG-TTTTATTATTAATTAAAACCAT
1581713 ACTTTATTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
38 17 0.24
39 55 0.76
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.47
Consensus pattern (38 bp):
CCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
Found at i:1581904 original size:7 final size:7
Alignment explanation
Indices: 1581892--1581922 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1581882 AACCGTCATG
1581892 CCGGTCA
1 CCGGTCA
1581899 CCGGTCA
1 CCGGTCA
1581906 CCGGTCA
1 CCGGTCA
*
1581913 CCGGCCA
1 CCGGTCA
1581920 CCG
1 CCG
1581923 ACGGCGGCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.48, G:0.29, T:0.10
Consensus pattern (7 bp):
CCGGTCA
Found at i:1582365 original size:22 final size:22
Alignment explanation
Indices: 1582340--1582384 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1582330 ATACAATTTC
1582340 TTCTCTCC-CAAAATACAATCGA
1 TTCT-TCCTCAAAATACAATCGA
*
1582362 TTCTTCCTCAAAATACCATCGA
1 TTCTTCCTCAAAATACAATCGA
1582384 T
1 T
1582385 CCCCCCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (22 bp):
TTCTTCCTCAAAATACAATCGA
Found at i:1605955 original size:36 final size:37
Alignment explanation
Indices: 1605891--1605966 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
1605881 TATAATTTTC
* ** * *
1605891 AAAATAAAAATATGTTAGAATTTTTAAAAAATTGTAA
1 AAAATAAAAATATATTAGAAAATGTAAAAAAGTGTAA
*
1605928 AAAATAAAAAT-TATTAGAAAATGTAAAATAGTGTAA
1 AAAATAAAAATATATTAGAAAATGTAAAAAAGTGTAA
1605964 AAA
1 AAA
1605967 TAATTAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 22 0.67
37 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (37 bp):
AAAATAAAAATATATTAGAAAATGTAAAAAAGTGTAA
Found at i:1605965 original size:29 final size:29
Alignment explanation
Indices: 1605932--1605996 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
1605922 TTGTAAAAAA
*
1605932 TAAAAATTATTAGAAAATGTA-AAATAGTG
1 TAAAAATAATTA-AAAATGTATAAATAGTG
*
1605961 TAAAAATAATTAAAAATTTATAAATAGT-
1 TAAAAATAATTAAAAATGTATAAATAGTG
*
1605989 AAAAAATA
1 TAAAAATA
1605997 TTGTATCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (29 bp):
TAAAAATAATTAAAAATGTATAAATAGTG
Found at i:1607540 original size:14 final size:14
Alignment explanation
Indices: 1607521--1607550 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1607511 CAAATTTGTC
*
1607521 TTTTTTTTAGTTTT
1 TTTTTTTTACTTTT
1607535 TTTTTTTTACTTTT
1 TTTTTTTTACTTTT
1607549 TT
1 TT
1607551 ATAGAACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.03, G:0.03, T:0.87
Consensus pattern (14 bp):
TTTTTTTTACTTTT
Found at i:1607907 original size:25 final size:23
Alignment explanation
Indices: 1607873--1607936 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
1607863 TTTTTATTTG
* *
1607873 TTTTTCATTTGTTTCTTTTTCTGA
1 TTTTT-ATTTGTTTCCTTTTCCGA
1607897 TTCTTTTATTTGTTTGTCCTTTTCCGA
1 -T-TTTTATTTG-TT-TCCTTTTCCGA
1607924 TTTTTATTTGTTT
1 TTTTTATTTGTTT
1607937 TTCTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 1 0.03
24 2 0.06
25 15 0.44
26 7 0.21
27 9 0.26
ACGTcount: A:0.08, C:0.12, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTTTATTTGTTTCCTTTTCCGA
Found at i:1608162 original size:22 final size:22
Alignment explanation
Indices: 1608109--1608185 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
1608099 TTATTATTTG
* *
1608109 TTTTATAATATTTTAAATGTATA
1 TTTT-TAAAATTTTAAATATATA
** *
1608132 TTTCAAAAATTTTAAATATATT
1 TTTTTAAAATTTTAAATATATA
* *
1608154 TTTTTAAAA-TTTAAATTTAAA
1 TTTTTAAAATTTTAAATATATA
1608175 TTTTTAAAATT
1 TTTTTAAAATT
1608186 ATTTTTAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 18 0.42
22 22 0.51
23 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (22 bp):
TTTTTAAAATTTTAAATATATA
Found at i:1608168 original size:21 final size:21
Alignment explanation
Indices: 1608137--1608185 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1608127 GTATATTTCA
**
1608137 AAAATTTTAAATATATTTTTTT
1 AAAA-TTTAAATATAAATTTTT
*
1608159 AAAATTTAAATTTAAATTTTT
1 AAAATTTAAATATAAATTTTT
1608180 AAAATT
1 AAAATT
1608186 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATTTAAATATAAATTTTT
Found at i:1608189 original size:12 final size:12
Alignment explanation
Indices: 1608174--1608230 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
1608164 TTAAATTTAA
1608174 ATTTTTAAAATT
1 ATTTTTAAAATT
1608186 ATTTTT-AAA-T
1 ATTTTTAAAATT
*
1608196 A-TATTAAAACTT
1 ATTTTTAAAA-TT
1608208 -TTTTT-AAATT
1 ATTTTTAAAATT
*
1608218 ATATTTAAAATT
1 ATTTTTAAAATT
1608230 A
1 A
1608231 AAAAATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
9 3 0.08
10 7 0.19
11 10 0.28
12 16 0.44
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTTTAAAATT
Found at i:1608192 original size:20 final size:21
Alignment explanation
Indices: 1608154--1608217 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1608144 TAAATATATT
* **
1608154 TTTTTAAAATTTAAATTTAAA
1 TTTTTAAAACTTATTTTTAAA
1608175 TTTTTAAAA-TTATTTTTAAA
1 TTTTTAAAACTTATTTTTAAA
*
1608195 TATATTAAAACTT-TTTTTAAA
1 T-TTTTAAAACTTATTTTTAAA
1608216 TT
1 TT
1608218 ATATTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 11 0.29
21 25 0.66
22 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTAAAACTTATTTTTAAA
Found at i:1613165 original size:26 final size:26
Alignment explanation
Indices: 1613114--1613172 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1613104 AAAGTAAATG
*
1613114 AGGAAAAACAAATAAAAAAACGAAAA
1 AGGAAAAACAAATAAAAAAACAAAAA
* *
1613140 AGGACAAACAAATAAAAGAATAAAAAAA
1 AGGAAAAACAAATAAAA-AA-ACAAAAA
1613168 AGGAA
1 AGGAA
1613173 GAAATGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 2 0.07
28 9 0.33
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (26 bp):
AGGAAAAACAAATAAAAAAACAAAAA
Found at i:1614351 original size:3 final size:3
Alignment explanation
Indices: 1614343--1614590 Score: 144
Period size: 3 Copynumber: 84.7 Consensus size: 3
1614333 TAGTACCATG
* * * *
1614343 ATA ATA ATA AGA ATA ATA ATA ATA A-A ATA ATA AAA ATA ACA AT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
1614389 TTA CTA ATA ATA ATA ATAA ATA A-A A-A ATG ATA ATA A-A TATA TATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA -ATA -ATA
* * *
1614434 A-A ATA ATA GTA ACA GTA ATA A-A ATA A-A TATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * * * *
1614476 ATA ATCA A-A ATA AAA ATA ATA A-C ATG TTA CTA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
1614520 ATA AGTA ATA ATA TATA ATA ATA ACA GTA ATA A-A ATA ATA ATG GTG
1 ATA A-TA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1614566 ATA ATA TTA A-A ATA ATG ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1614591 GTCAAATTAA
Statistics
Matches: 189, Mismatches: 38, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
2 23 0.12
3 149 0.79
4 17 0.09
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1614380 original size:20 final size:20
Alignment explanation
Indices: 1614343--1614561 Score: 91
Period size: 20 Copynumber: 11.1 Consensus size: 20
1614333 TAGTACCATG
* *
1614343 ATAATAATAAGAATAATAATA
1 ATAA-AATAATAAAAATAATA
*
1614364 ATAAAATAATAAAAATAACA
1 ATAAAATAATAAAAATAATA
*** * *
1614384 ATATGTTACTAATAATAATA
1 ATAAAATAATAAAAATAATA
*
1614404 AT-AAAT-A-AAAAATGATA
1 ATAAAATAATAAAAATAATA
1614421 AT-AAATATATATAAAATAATA
1 ATAAAATA-ATA-AAAATAATA
* *
1614442 GTAACAGTAAT-AAAAT-A-A
1 ATAA-AATAATAAAAATAATA
* *
1614460 ATATAAT-ATAATAATAATA
1 ATAAAATAATAAAAATAATA
*
1614479 AT-CAA-AATAAAAATAATA
1 ATAAAATAATAAAAATAATA
* *** * *
1614497 ACATGTTACTAATAATAATA
1 ATAAAATAATAAAAATAATA
*
1614517 ATAATAAGTAATAATATATAATA
1 ATAA-AA-TAATAA-AAATAATA
*
1614540 ATAACAGTAAT-AAAATAATA
1 ATAA-AATAATAAAAATAATA
1614560 AT
1 AT
1614562 GGTGATAATA
Statistics
Matches: 143, Mismatches: 40, Indels: 31
0.67 0.19 0.14
Matches are distributed among these distances:
16 2 0.01
17 20 0.14
18 18 0.13
19 6 0.04
20 57 0.40
21 14 0.10
22 12 0.08
23 14 0.10
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (20 bp):
ATAAAATAATAAAAATAATA
Found at i:1614380 original size:29 final size:29
Alignment explanation
Indices: 1614343--1614561 Score: 123
Period size: 29 Copynumber: 7.5 Consensus size: 29
1614333 TAGTACCATG
* *
1614343 ATAATAATAAGAATAATAATAATAAAATA
1 ATAAAAATAATAATAATAATAATAAAATA
* ** *
1614372 ATAAAAATAACAAT-ATGTTACTAATAATA
1 ATAAAAATAATAATAATAATAATAA-AATA
*
1614401 ATAATAAATAA-AA-AATGATAAT-AAATA
1 ATAA-AAATAATAATAATAATAATAAAATA
* * *
1614428 TATATAAAATAATAGTAACAGTAATAAAATA
1 -ATA-AAAATAATAATAATAATAATAAAATA
*
1614459 A-ATATAAT-ATAATAATAATAATCAAAATA
1 ATA-AAAATAATAATAATAATAAT-AAAATA
* ** *
1614488 A-AAATAATAA-CATGTTACTAATAATAATA
1 ATAAA-AATAATAATAATAATAATAA-AATA
* *
1614517 ATAATAAGTAATAATATATAATAATAACAGTA
1 ATAA-AAATAATAATA-ATAATAATAA-AATA
1614549 AT-AAAATAATAAT
1 ATAAAAATAATAAT
1614562 GGTGATAATA
Statistics
Matches: 146, Mismatches: 28, Indels: 31
0.71 0.14 0.15
Matches are distributed among these distances:
27 4 0.03
28 31 0.21
29 60 0.41
30 29 0.20
31 9 0.06
32 13 0.09
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (29 bp):
ATAAAAATAATAATAATAATAATAAAATA
Found at i:1616474 original size:8 final size:8
Alignment explanation
Indices: 1616461--1616485 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1616451 ACCTATTAAA
1616461 TTTAAAAT
1 TTTAAAAT
1616469 TTTAAAAT
1 TTTAAAAT
1616477 TTTAAAAT
1 TTTAAAAT
1616485 T
1 T
1616486 AGTTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1616546 original size:19 final size:20
Alignment explanation
Indices: 1616514--1616557 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1616504 TCTACTTGAC
1616514 ATTTTTTAACATA-TTTAAA
1 ATTTTTTAACATATTTTAAA
1616533 ATTTCTTTAA-ATATTTTAAA
1 ATTT-TTTAACATATTTTAAA
1616553 ATTTT
1 ATTTT
1616558 AAATATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTTAACATATTTTAAA
Found at i:1616558 original size:8 final size:9
Alignment explanation
Indices: 1616517--1616563 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 9
1616507 ACTTGACATT
1616517 TTTTAACATA
1 TTTTAA-ATA
* *
1616527 TTTAAAATT
1 TTTTAAATA
1616536 TCTTTAAATA
1 T-TTTAAATA
1616546 TTTTAAA-A
1 TTTTAAATA
1616554 TTTTAAATA
1 TTTTAAATA
1616563 T
1 T
1616564 ATTACAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
8 8 0.26
9 11 0.35
10 12 0.39
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTAAATA
Found at i:1616617 original size:8 final size:8
Alignment explanation
Indices: 1616604--1616705 Score: 78
Period size: 8 Copynumber: 12.0 Consensus size: 8
1616594 AAAAAATATA
1616604 TTAAAATT
1 TTAAAATT
1616612 TTAAAATT
1 TTAAAATT
1616620 TTAAAATAT
1 TTAAAAT-T
*
1616629 TTAAAATA
1 TTAAAATT
1616637 TTAATATATT
1 TTAA-A-ATT
* *
1616647 TAAAAAAAT
1 T-TAAAATT
* *
1616656 TGAATATAT
1 TTAAAAT-T
1616665 TTAAAATTT
1 TTAAAA-TT
* *
1616674 TTAACATA
1 TTAAAATT
*
1616682 TTACAATT
1 TTAAAATT
1616690 TTAAAATT
1 TTAAAATT
1616698 TTAAAATT
1 TTAAAATT
1616706 GGTTATACTT
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
8 43 0.59
9 23 0.32
10 5 0.07
11 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (8 bp):
TTAAAATT
Found at i:1616633 original size:17 final size:17
Alignment explanation
Indices: 1616604--1616705 Score: 93
Period size: 17 Copynumber: 6.0 Consensus size: 17
1616594 AAAAAATATA
1616604 TTAAAAT-TTTAAAATT
1 TTAAAATATTTAAAATT
*
1616620 TTAAAATATTTAAAATA
1 TTAAAATATTTAAAATT
* *
1616637 TTAATATATTTAAAAAAAT
1 TTAAAATATTT--AAAATT
* *
1616656 TGAATATATTTAAAATTT
1 TTAAAATATTTAAAA-TT
* *
1616674 TTAACATA-TTACAATT
1 TTAAAATATTTAAAATT
1616690 TTAAAAT-TTTAAAATT
1 TTAAAATATTTAAAATT
1616706 GGTTATACTT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
16 22 0.31
17 27 0.39
18 7 0.10
19 14 0.20
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (17 bp):
TTAAAATATTTAAAATT
Found at i:1616661 original size:19 final size:18
Alignment explanation
Indices: 1616620--1616670 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
1616610 TTTTAAAATT
* *
1616620 TTAAAATATTT-AAAATA
1 TTAATATATTTAAAAAAA
1616637 TTAATATATTTAAAAAAA
1 TTAATATATTTAAAAAAA
1616655 TTGAATATATTTAAAA
1 TT-AATATATTTAAAA
1616671 TTTTTAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.33
18 7 0.23
19 13 0.43
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAATATATTTAAAAAAA
Found at i:1616731 original size:69 final size:70
Alignment explanation
Indices: 1616658--1616822 Score: 223
Period size: 71 Copynumber: 2.4 Consensus size: 70
1616648 AAAAAAATTG
* *
1616658 AATATATTTAAAATTTTTAACATATTACAAT-T-TTAAAATTTTAAAATTGGTTATACTTAAC-T
1 AATATATTTAAAATTTTTAATATATTA-AATATATTAAAATTTTAAAATTAGTTATACTTAACAT
1616720 TTTTTT
65 TTTTTT
* *
1616726 AAATATATTT-AATTTTTTCAAATATATTAAATATATTAAAATTTTAAAATTAGTTATATTTAAC
1 -AATATATTTAAAATTTTT--AATATATTAAATATATTAAAATTTTAAAATTAGTTATACTTAAC
1616790 ATTTTTTT
63 ATTTTTTT
1616798 AATATATTTAAAA-TTTTAATATATT
1 AATATATTTAAAATTTTTAATATATT
1616823 TAATTTTTTT
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
68 7 0.08
69 20 0.24
70 9 0.11
71 40 0.47
72 9 0.11
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (70 bp):
AATATATTTAAAATTTTTAATATATTAAATATATTAAAATTTTAAAATTAGTTATACTTAACATT
TTTTT
Found at i:1616737 original size:20 final size:19
Alignment explanation
Indices: 1616709--1616753 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1616699 TAAAATTGGT
* *
1616709 TATACTTAACTTTTTTTAAA
1 TATATTTAA-TTTTTTCAAA
1616729 TATATTTAATTTTTTCAAA
1 TATATTTAATTTTTTCAAA
1616748 TATATT
1 TATATT
1616754 AAATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTTAATTTTTTCAAA
Found at i:1616816 original size:17 final size:18
Alignment explanation
Indices: 1616611--1616858 Score: 119
Period size: 18 Copynumber: 14.1 Consensus size: 18
1616601 ATATTAAAAT
1616611 TTTAAAATTTTAAA-ATA
1 TTTAAAATTTTAAATATA
*
1616628 TTTAAAATATT-AATATA
1 TTTAAAATTTTAAATATA
** *
1616645 TTTAAAAAAATTGAATATA
1 TTT-AAAATTTTAAATATA
* *
1616664 TTTAAAATTTTTAACATA
1 TTTAAAATTTTAAATATA
*
1616682 -TTACAATTTTAAA-AT-
1 TTTAAAATTTTAAATATA
*
1616697 TTTAAAATTGGT---TATA
1 TTTAAAATT-TTAAATATA
* **
1616713 CTTAACTTTTTTTAAATATA
1 TTTAA--AATTTTAAATATA
**
1616733 TTTAATTTTTTCAAATATA
1 TTTAAAATTTT-AAATATA
*
1616752 -TTAAATATATTAAA-AT-
1 TTTAAA-ATTTTAAATATA
**
1616768 TTTAAAA--TTAGTTATA
1 TTTAAAATTTTAAATATA
* *
1616784 TTTAACATTTTTTTAATATA
1 TTTAA-A-ATTTTAAATATA
1616804 TTTAAAATTTT-AATATA
1 TTTAAAATTTTAAATATA
** * *
1616821 TTTAATTTTTTTAAATTTT
1 TTTAA-AATTTTAAATATA
1616840 TTTAAAATTTTAAATATA
1 TTTAAAATTTTAAATATA
1616858 T
1 T
1616859 AGATTTTCTT
Statistics
Matches: 175, Mismatches: 33, Indels: 45
0.69 0.13 0.18
Matches are distributed among these distances:
14 3 0.02
15 4 0.02
16 21 0.12
17 48 0.27
18 51 0.29
19 29 0.17
20 19 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTAAAATTTTAAATATA
Found at i:1616827 original size:15 final size:16
Alignment explanation
Indices: 1616794--1616829 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1616784 TTTAACATTT
1616794 TTTTAATATATTTAAAA
1 TTTTAATATATTT-AAA
1616811 TTTTAATATATTT-AA
1 TTTTAATATATTTAAA
1616826 TTTT
1 TTTT
1616830 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
17 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAATATATTTAAA
Found at i:1616901 original size:9 final size:9
Alignment explanation
Indices: 1616887--1616960 Score: 55
Period size: 9 Copynumber: 8.1 Consensus size: 9
1616877 CTATTAAAAT
1616887 ATATATTAA
1 ATATATTAA
1616896 ATATATTAA
1 ATATATTAA
*
1616905 A-ATTTTAA
1 ATATATTAA
*
1616913 ATATACTAAAA
1 ATATA-T-TAA
1616924 TATATATTAA
1 -ATATATTAA
*
1616934 ATATTTTAA
1 ATATATTAA
*
1616943 A-ATTTTAA
1 ATATATTAA
1616951 A-ATACTTAA
1 ATATA-TTAA
1616960 A
1 A
1616961 AAAAATCACA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
8 17 0.31
9 26 0.48
10 3 0.06
11 3 0.06
12 5 0.09
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATATTAA
Found at i:1616904 original size:21 final size:21
Alignment explanation
Indices: 1616878--1616945 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
1616868 TAGTTTTACC
1616878 TATTAAAATATATATTAAATA
1 TATTAAAATATATATTAAATA
1616899 TATT-AAA-AT-T-TTAAATA
1 TATTAAAATATATATTAAATA
*
1616916 TACTAAAATATATATTAAATA
1 TATTAAAATATATATTAAATA
*
1616937 TTTTAAAAT
1 TATTAAAAT
1616946 TTTAAAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 10 0.25
18 4 0.10
19 4 0.10
20 4 0.10
21 18 0.45
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTAAAATATATATTAAATA
Found at i:1616914 original size:17 final size:18
Alignment explanation
Indices: 1616892--1616961 Score: 74
Period size: 17 Copynumber: 3.9 Consensus size: 18
1616882 AAAATATATA
1616892 TTAAATATA-TTAAAATT
1 TTAAATATACTTAAAATT
*
1616909 TTAAATATACTAAAATATAT
1 TTAAATATACTTAAA-AT-T
*
1616929 ATTAAATAT-TTTAAAATT
1 -TTAAATATACTTAAAATT
1616947 TTAAA-ATACTTAAAA
1 TTAAATATACTTAAAA
1616962 AAAATCACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
16 2 0.05
17 20 0.45
18 5 0.11
19 4 0.09
20 5 0.11
21 8 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATATACTTAAAATT
Found at i:1616925 original size:38 final size:38
Alignment explanation
Indices: 1616880--1616961 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
1616870 GTTTTACCTA
1616880 TTAAAATATATATTAAATATATTAAAATTTTAAATATAC
1 TTAAAATATATATTAAATATATTAAAATTTTAAA-ATAC
*
1616919 -TAAAATATATATTAAATATTTTAAAATTTTAAAATAC
1 TTAAAATATATATTAAATATATTAAAATTTTAAAATAC
1616956 TTAAAA
1 TTAAAA
1616962 AAAATCACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 4 0.10
38 37 0.90
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (38 bp):
TTAAAATATATATTAAATATATTAAAATTTTAAAATAC
Found at i:1617127 original size:28 final size:28
Alignment explanation
Indices: 1617096--1617159 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
1617086 ACTTTCAAGA
*
1617096 TAAATTTTAAATCATTTACA-TATTTAAT
1 TAAATTTTAAATCATTTA-ATTAATTAAT
*** *
1617124 TAAAAAATAAGTCATTTAATTAATTAAT
1 TAAATTTTAAATCATTTAATTAATTAAT
1617152 TAAATTTT
1 TAAATTTT
1617160 TTTAGTTAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
TAAATTTTAAATCATTTAATTAATTAAT
Found at i:1626692 original size:2 final size:2
Alignment explanation
Indices: 1626685--1626713 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1626675 AACTCCATAA
1626685 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1626714 TAGATTGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1627440 original size:3 final size:3
Alignment explanation
Indices: 1627432--1627457 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1627422 ACGAACACTG
1627432 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
1627458 GATGGGTGGA
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1638619 original size:8 final size:8
Alignment explanation
Indices: 1638606--1638632 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1638596 TTGGAGTAAA
1638606 AGAAAAAG
1 AGAAAAAG
1638614 AGAAAAAG
1 AGAAAAAG
1638622 AGAAAAAG
1 AGAAAAAG
1638630 AGA
1 AGA
1638633 TGACAGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AGAAAAAG
Found at i:1640267 original size:6 final size:6
Alignment explanation
Indices: 1640232--1640286 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
1640222 ACTTTATAAT
* * * * *
1640232 TATTTA GATTTG TATTTG TAATTA TA-TTA TATTTA TATTTA TATCTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1640279 TATTTA TA
1 TATTTA TA
1640287 ATATTAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
5 5 0.12
6 36 0.88
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (6 bp):
TATTTA
Found at i:1640270 original size:23 final size:22
Alignment explanation
Indices: 1640228--1640271 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1640218 TTTTACTTTA
*
1640228 TAATTATTTAGATTTGTATTTG
1 TAATTATTTAGATTTATATTTG
*
1640250 TAATTATATTATATTTATATTT
1 TAATTAT-TTAGATTTATATTT
1640272 ATATCTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TAATTATTTAGATTTATATTTG
Found at i:1640931 original size:18 final size:20
Alignment explanation
Indices: 1640894--1640940 Score: 71
Period size: 18 Copynumber: 2.4 Consensus size: 20
1640884 ATTTAATTTT
1640894 TTTATATATTTAATAATAATA
1 TTTAT-TATTTAATAATAATA
1640915 TTTATTATTT-A-AATAATA
1 TTTATTATTTAATAATAATA
1640933 TTTATTAT
1 TTTATTAT
1640941 ATTTTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.58
19 1 0.04
20 5 0.19
21 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTATTTAATAATAATA
Found at i:1640940 original size:21 final size:20
Alignment explanation
Indices: 1640895--1640944 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
1640885 TTTAATTTTT
*
1640895 TTATATATTTAATAATA-ATA
1 TTAT-TATTTAATAATATTTA
1640915 TTTATTATTTAAATAATATTTA
1 -TTATTATTT-AATAATATTTA
1640937 TTA-TATTT
1 TTATTATTT
1640945 TTTGTACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 10 0.38
21 14 0.54
22 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTTAATAATATTTA
Found at i:1643816 original size:10 final size:9
Alignment explanation
Indices: 1643793--1643825 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1643783 CGATTCAAGA
1643793 AAAAATAAT
1 AAAAATAAT
1643802 AAAAATAAT
1 AAAAATAAT
1643811 ATAAAATAA-
1 A-AAAATAAT
1643820 AAAAAT
1 AAAAAT
1643826 TTGATCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.22
9 11 0.48
10 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:1648434 original size:2 final size:2
Alignment explanation
Indices: 1648427--1648462 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1648417 AAAACTAATA
*
1648427 AT AT AT AT AT GT 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
1648463 CAATTATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1649495 original size:2 final size:2
Alignment explanation
Indices: 1649478--1649518 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1649468 CAAATTTTTG
*
1649478 TA TA -A TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1649519 AATGCAGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1652259 original size:42 final size:42
Alignment explanation
Indices: 1652176--1652273 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 42
1652166 CATGGTTCAA
* * *
1652176 CTATGGTCTTACACATCTTTACATAATGATGTCATAGCCCAG
1 CTATGGTCTTACACATCATTACATAATGATGCCATAACCCAG
*
1652218 CTATGGTCTTACACAT-ATT-CATATGTCGATGCCATAACCCAG
1 CTATGGTCTTACACATCATTACATA-AT-GATGCCATAACCCAG
1652260 CTATGGTCTTACAC
1 CTATGGTCTTACAC
1652274 GAATCACATA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 4 0.08
41 3 0.06
42 43 0.86
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (42 bp):
CTATGGTCTTACACATCATTACATAATGATGCCATAACCCAG
Found at i:1652347 original size:47 final size:46
Alignment explanation
Indices: 1652244--1652367 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 46
1652234 ATTCATATGT
* * * * *
1652244 CGATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
1652290 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
1652337 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
1652368 GAAATCACTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:1652427 original size:31 final size:31
Alignment explanation
Indices: 1652392--1652602 Score: 325
Period size: 31 Copynumber: 6.8 Consensus size: 31
1652382 CTTGTCACTT
*
1652392 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
1652423 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1652454 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1652485 GTAGTCGGAA-CTACCACTTTTCACTGATCAG
1 GTAG-CCGAAGCTACCACTTTTCACTGATCAG
*
1652516 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1652547 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
1652578 GTAGCTGAAGCTGCCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
1652603 TGTCATTTGT
Statistics
Matches: 169, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
30 4 0.02
31 162 0.96
32 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:1652684 original size:50 final size:51
Alignment explanation
Indices: 1652578--1652706 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
1652568 CACTGATCAG
* ** *
1652578 GTAGCTGAAGCTGCCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
1652629 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
*
1652679 GTAGCCAAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
1652707 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 44 0.63
51 26 0.37
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:1657816 original size:108 final size:108
Alignment explanation
Indices: 1657620--1657962 Score: 605
Period size: 108 Copynumber: 3.2 Consensus size: 108
1657610 GTATAACTAT
* *
1657620 ATAAATCTCAACCTTTTGTTATTAACTATCATAATAAAAATGACGTAAACCCTAAATCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
* *
1657685 ACTCAACACAACCTTATTTCCTACCCCATCCAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTA
*
1657728 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAACTCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
*
1657793 ACTCAACACAACCCTATTCCCTACCCCATCTAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTA
* * *
1657836 ATAAATCTCAACCTTTTGTTATTAGCTAGCATAACAAAAATGACATAAACCCTAAATTGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
1657901 ACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTA
1657944 ATAAATCTCAACCTTTTGT
1 ATAAATCTCAACCTTTTGT
1657963 GACGTAAACC
Statistics
Matches: 224, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 224 1.00
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.30
Consensus pattern (108 bp):
ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
ACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTA
Found at i:1658189 original size:251 final size:252
Alignment explanation
Indices: 1657729--1658211 Score: 806
Period size: 251 Copynumber: 1.9 Consensus size: 252
1657719 CTCTTTGTAA
* *
1657729 TAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAACTCGATCTAAA
1 TAAATCTCAACATTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAAA
* * *
1657794 CTCAACACAACCCTATTCCCTACCCCATCTAACCTCTTTGTAATAAATCTCAACCTTTTGTTATT
66 CTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATT
* *
1657859 AGCTAGCATAACAAAAATGACATAAACCCTAAATTGATCTAAACTCAACACAACCCTATTCCCTA
131 AACTAGCATAACAAAAATGACATAAACCCTAAACTGATCTAAACTCAACACAACCCTATTCCCTA
*
1657924 CCCCATCCAACCTCTTTGTAATAAATCTCAACCTTTTGTGACGTAAACCCTATGAAC
196 CCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTGTGACGTAAACCCTATGAAC
* * *
1657981 TAAA-CTCAACATTTTTTTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAA
1 TAAATCTCAACATTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAAA
*
1658045 CTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATT
66 CTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATT
** * *
1658110 AACTAGCATAACAAAAATGATGTAAACCTTAAACTGATTTAAACTCAACACAACCCTATTCCCTA
131 AACTAGCATAACAAAAATGACATAAACCCTAAACTGATCTAAACTCAACACAACCCTATTCCCTA
*
1658175 TCCCATCCAACCTCTTTGTAATAAATCTCAACATTTT
196 CCCCATCCAACCTCTTTGTAATAAATCTCAACATTTT
1658212 ATTATTAACT
Statistics
Matches: 214, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
251 210 0.98
252 4 0.02
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.30
Consensus pattern (252 bp):
TAAATCTCAACATTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAAA
CTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATT
AACTAGCATAACAAAAATGACATAAACCCTAAACTGATCTAAACTCAACACAACCCTATTCCCTA
CCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTGTGACGTAAACCCTATGAAC
Found at i:1658300 original size:359 final size:366
Alignment explanation
Indices: 1657621--1658583 Score: 1357
Period size: 359 Copynumber: 2.6 Consensus size: 366
1657611 TATAACTATA
* * * * * *
1657621 TAAATCTCAACCTTTTGTTATTAACTATCATAATAAAAATGACGTAAACCCTAAATCGATCTAAA
1 TAAA-CTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAA
* * * * *
1657686 CTCAACACAACCTTATTTCCTACCCCATCCAACCTCTTTGTAATAAATCTCAACCTTTTGTTATT
65 CTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATT
* *
1657751 AACTAGCATAACAAAAATGACGTAAACCCT-AACTCGATCTAAACTCAACACAACCCTATTCCCT
130 AACTAGCATAACAAAAATGACGTAAACCTTAAACT-GATTTAAACTCAACACAACCCTATTCCCT
* * * * *
1657815 ACCCCATCTAACCTCTTTGTAATAAATCTCAACCTTTTGTTATTAGCTAGCATAACAAAAATGAC
194 AACCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGAC
**
1657880 ATAAACCCTAAATTGATCTAAACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTAA
259 ATAAACCCTAAACCGATCTAAACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTAA
1657945 TAAATCTCAACCTTTTG-T-G-AC-G-TAAACCCT-AT-GAAC
324 TAAATCTCAACCTTTTGTTAGAACAGATAAACCCTAATCGAAC
*
1657981 TAAACTCAACATTTTTTTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAAC
1 TAAACTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAAC
1658046 TCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTA
66 TCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTA
* *
1658111 ACTAGCATAACAAAAATGATGTAAACCTTAAACTGATTTAAACTCAACACAACCCTATTCCCTAT
131 ACTAGCATAACAAAAATGACGTAAACCTTAAACTGATTTAAACTCAACACAACCCTATTCCCTAA
**
1658176 CCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGATGT
196 CCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGACAT
* * *
1658241 AAACCTTAAACCGATTTAAACTCAACACAACCCTATTCCCTACCCCATCCAATCTCTTTGTAATA
261 AAACCCTAAACCGATCTAAACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTAATA
1658306 AATCTCAACCTTTTGTTATTAATTAGCATAACAAAAATGACATAAACCCTAAATCGAAC
326 AATCTCAACCTTTTG-------TTAG---AAC----A-G--ATAAACCCT-AATCGAAC
* * *
1658365 TAAACTTAACATTTTATTATTAATTAGCATAACAAAAATGACGTAAACCTTAAATCAATTTAAAC
1 TAAACTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAAC
* *
1658430 TCAACACAACCCTATTCCCTATCCCATCTAACCTTTTTGTAATAAATCTCAACATTTTATTATTA
66 TCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTA
* *
1658495 ACTGGCATAACAAAAATGACGTAAACCTTAAACCGATTTAAACTCAACACAACCCTATTCCCTAA
131 ACTAGCATAACAAAAATGACGTAAACCTTAAACTGATTTAAACTCAACACAACCCTATTCCCTAA
*
1658560 CCCATCCAACCTCTCTGTATATAA
196 CCCATCCAACCTCTTTGTA-ATAA
1658584 CTAAATATTG
Statistics
Matches: 539, Mismatches: 37, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
359 305 0.57
360 8 0.01
367 1 0.00
368 1 0.00
372 2 0.00
378 1 0.00
381 8 0.01
383 2 0.00
384 207 0.38
385 4 0.01
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.30
Consensus pattern (366 bp):
TAAACTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAAC
TCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTA
ACTAGCATAACAAAAATGACGTAAACCTTAAACTGATTTAAACTCAACACAACCCTATTCCCTAA
CCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGACAT
AAACCCTAAACCGATCTAAACTCAACACAACCCTATTCCCTACCCCATCCAACCTCTTTGTAATA
AATCTCAACCTTTTGTTAGAACAGATAAACCCTAATCGAAC
Found at i:1658370 original size:108 final size:108
Alignment explanation
Indices: 1657981--1658362 Score: 642
Period size: 108 Copynumber: 3.5 Consensus size: 108
1657971 CCCTATGAAC
*
1657981 TAAA-CTCAACATTTTTTTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAA
1 TAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAA
1658045 CTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAA
66 CTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAA
*
1658088 TAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGATGTAAACCTTAAA-CTGATTTAA
1 TAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATC-GATTTAA
1658152 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAA
65 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAA
* *
1658196 TAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGATGTAAACCTTAAACCGATTTAAA
1 TAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAA
* *
1658261 CTCAACACAACCCTATTCCCTACCCCATCCAATCTCTTTGTAA
66 CTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAA
* * * * *
1658304 TAAATCTCAACCTTTTGTTATTAATTAGCATAACAAAAATGACATAAACCCTAAATCGA
1 TAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGA
1658363 ACTAAACTTA
Statistics
Matches: 261, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
107 5 0.02
108 255 0.98
109 1 0.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.31
Consensus pattern (108 bp):
TAAATCTCAACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAATCGATTTAAA
CTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTAA
Found at i:1658405 original size:168 final size:168
Alignment explanation
Indices: 1658204--1658526 Score: 520
Period size: 168 Copynumber: 1.9 Consensus size: 168
1658194 AATAAATCTC
* *
1658204 AACATTTTATTATTAACTAGCATAACAAAAATGATGTAAACCTTAAACCGATTTAAACTCAACAC
1 AACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAACCAATTTAAACTCAACAC
* * * *
1658269 AACCCTATTCCCTACCCCATCCAATCTCTTTGTAATAAATCTCAACCTTTTGTTATTAATTAGCA
66 AACCCTATTCCCTACCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTAACTAGCA
1658334 TAACAAAAATGACATAAACCCTAAATCGAACTAAACTT
131 TAACAAAAATGACATAAACCCTAAATCGAACTAAACTT
* *
1658372 AACATTTTATTATTAATTAGCATAACAAAAATGACGTAAACCTTAAATCAATTTAAACTCAACAC
1 AACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAACCAATTTAAACTCAACAC
* * * *
1658437 AACCCTATTCCCTATCCCATCTAACCTTTTTGTAATAAATCTCAACATTTTATTATTAACTGGCA
66 AACCCTATTCCCTACCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTAACTAGCA
* *
1658502 TAACAAAAATGACGTAAACCTTAAA
131 TAACAAAAATGACATAAACCCTAAA
1658527 CCGATTTAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
168 141 1.00
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.31
Consensus pattern (168 bp):
AACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAACCAATTTAAACTCAACAC
AACCCTATTCCCTACCCCATCCAACCTCTTTGTAATAAATCTCAACATTTTATTATTAACTAGCA
TAACAAAAATGACATAAACCCTAAATCGAACTAAACTT
Found at i:1658429 original size:60 final size:60
Alignment explanation
Indices: 1658304--1658435 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 60
1658294 CTCTTTGTAA
* *
1658304 TAAATCTCAACCTTTTGTTATTAATTAGCATAACAAAAATGACATAAACCCTAAATCGAAC
1 TAAA-CTCAACATTTTATTATTAATTAGCATAACAAAAATGACATAAACCCTAAATCGAAC
* * * *
1658365 TAAACTTAACATTTTATTATTAATTAGCATAACAAAAATGACGTAAACCTTAAATC-AATT
1 TAAACTCAACATTTTATTATTAATTAGCATAACAAAAATGACATAAACCCTAAATCGAA-C
1658425 TAAACTCAACA
1 TAAACTCAACA
1658436 CAACCCTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 2 0.03
60 57 0.90
61 4 0.06
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.31
Consensus pattern (60 bp):
TAAACTCAACATTTTATTATTAATTAGCATAACAAAAATGACATAAACCCTAAATCGAAC
Found at i:1658507 original size:108 final size:108
Alignment explanation
Indices: 1658372--1658571 Score: 346
Period size: 108 Copynumber: 1.9 Consensus size: 108
1658362 AACTAAACTT
* *
1658372 AACATTTTATTATTAATTAGCATAACAAAAATGACGTAAACCTTAAATCAATTTAAACTCAACAC
1 AACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAACCAATTTAAACTCAACAC
* *
1658437 AACCCTATTCCCTATCCCATCTAACCTTTTTGTAATAAATCTC
66 AACCCTATTCCCTAACCCATCCAACCTTTTTGTAATAAATCTC
* *
1658480 AACATTTTATTATTAACTGGCATAACAAAAATGACGTAAACCTTAAACCGATTTAAACTCAACAC
1 AACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAACCAATTTAAACTCAACAC
1658545 AACCCTATTCCCTAACCCATCCAACCT
66 AACCCTATTCCCTAACCCATCCAACCT
1658572 CTCTGTATAT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 86 1.00
ACGTcount: A:0.40, C:0.26, G:0.04, T:0.30
Consensus pattern (108 bp):
AACATTTTATTATTAACTAGCATAACAAAAATGACGTAAACCTTAAACCAATTTAAACTCAACAC
AACCCTATTCCCTAACCCATCCAACCTTTTTGTAATAAATCTC
Found at i:1660131 original size:216 final size:221
Alignment explanation
Indices: 1659560--1660139 Score: 579
Period size: 215 Copynumber: 2.7 Consensus size: 221
1659550 ACATATCTAG
** * * **
1659560 TTCAACATAAAAAATTCAGTTTTTTGGACTAAAAATGATAGCTGTCATGGGTCAAAGATCTATGG
1 TTCAACATTGAAAATTCAGTCTTTTGGAC-AAAAATGATAGCTTTCATATGTCAAAGATCTATGG
* * * *
1659625 TGAATTTGAGGTGACTGATGATCTAATTGGATTTATGGAG-TTTCTCTTTCCTTAATTATTAATT
65 TGAATTTGA-G-G--TGATGATCTAATTGGATTGATGGAGTTTTC-CTTCCCTTAATGATTAATA
* * * * *
1659689 TATACAGTTCTTCTCTACTTCAGTGTAAAGGGTGTTTTGCTATCTTTCTAGATTGATTAATTAGT
125 TATACAGTTCTTCTCTACTTAAATGTAAAGGGTGTTTTGCCATCTTTCTACATTGAATAATTAGT
* * *
1659754 TATCATGTTTGGTTTCATCATCTGCTCTATGTAA
190 TATCA-GTTTGATTTCAT-ATCTGATCAATGTAA
* *
1659788 TTCAACATTGAAAATTCACTCTTTTGGACTAAAATGATAGCTTTCATATGTCAAAGATCTAT-G-
1 TTCAACATTGAAAATTCAGTCTTTTGGACAAAAATGATAGCTTTCATATGTCAAAGATCTATGGT
* * * *
1659851 G----T--GGTGATGATCTAATTGGATTGATGGTGTTTTTCTTGCCTGT-ATGATTAATATGTAC
66 GAATTTGAGGTGATGATCTAATTGGATTGATGGAGTTTTCCTTCCCT-TAATGATTAATATATAC
*
1659909 AGTTCTTCTCTACTTAAATGTAGAGGGTGTTTTGCCATCTCTTC-ACATTGAATAATTAGTT-T-
130 AGTTCTTCTCTACTTAAATGTAAAGGGTGTTTTGCCATCT-TTCTACATTGAATAATTAGTTATC
1659971 A-TTT-ATTT-AT-T-T-ATCAAAT-TACA
194 AGTTTGATTTCATATCTGATC-AATGTA-A
* * *** * *
1659994 TTGAATATTAGTTGATTCAGTCTTGTTGGACCAAAATGATAGATTTCATATGTCAAAGATCTATG
1 TTCAACATT-GAAAATTCAGTCTT-TTGGACAAAAATGATAGCTTTCATATGTCAAAGATCTATG
* *
1660059 GTGAATTTGAGGTGATGATCCAATTGGATTGATGGGGTTTTCCTTCCCTTAATGATTAATATATA
64 GTGAATTTGAGGTGATGATCTAATTGGATTGATGGAGTTTTCCTTCCCTTAATGATTAATATATA
*
1660124 TAGTTCTTCTCTACTT
129 CAGTTCTTCTCTACTT
1660140 GAGAGTTACG
Statistics
Matches: 298, Mismatches: 38, Indels: 44
0.78 0.10 0.12
Matches are distributed among these distances:
205 4 0.01
206 11 0.04
207 11 0.04
208 37 0.12
209 3 0.01
210 4 0.01
211 3 0.01
213 1 0.00
214 2 0.01
215 93 0.31
216 70 0.23
217 1 0.00
218 1 0.00
221 1 0.00
225 1 0.00
226 1 0.00
227 29 0.10
228 25 0.08
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (221 bp):
TTCAACATTGAAAATTCAGTCTTTTGGACAAAAATGATAGCTTTCATATGTCAAAGATCTATGGT
GAATTTGAGGTGATGATCTAATTGGATTGATGGAGTTTTCCTTCCCTTAATGATTAATATATACA
GTTCTTCTCTACTTAAATGTAAAGGGTGTTTTGCCATCTTTCTACATTGAATAATTAGTTATCAG
TTTGATTTCATATCTGATCAATGTAA
Found at i:1660155 original size:216 final size:221
Alignment explanation
Indices: 1659560--1660175 Score: 576
Period size: 216 Copynumber: 2.8 Consensus size: 221
1659550 ACATATCTAG
** * * **
1659560 TTCAACATAAAAAATTCAGTTTTTTGGACTAAAAATGATAGCTGTCATGGGTCAAAGATCTATGG
1 TTCAACATTGAAAATTCAGTCTTTTGGAC-AAAAATGATAGCTTTCATATGTCAAAGATCTATGG
* * * *
1659625 TGAATTTGAGGTGACTGATGATCTAATTGGATTTATGGAG-TTTCTCTTTCCTTAATTATTAATT
65 TGAATTTGA-G-G--TGATGATCTAATTGGATTGATGGAGTTTTC-CTTCCCTTAATGATTAATA
* * * * *
1659689 TATACAGTTCTTCTCTACTTCAGTGTAAAGGGTGTTTTGCTATCT-TTCTAGATTGATTAATTAG
125 TATACAGTTCTTCTCTACTT-AGAGTTAAGGGTGTTTTGCCATCTCTTCTACATTGAATAATTAG
* * *
1659753 TTATCATGTTTGGTTTCATCATCTGCTCTATGTAA
189 TTATCA-GTTTGATTTCAT-ATCTGATCAATGTAA
* *
1659788 TTCAACATTGAAAATTCACTCTTTTGGACTAAAATGATAGCTTTCATATGTCAAAGATCTAT-G-
1 TTCAACATTGAAAATTCAGTCTTTTGGACAAAAATGATAGCTTTCATATGTCAAAGATCTATGGT
* * * *
1659851 G----T--GGTGATGATCTAATTGGATTGATGGTGTTTTTCTTGCCTGT-ATGATTAATATGTAC
66 GAATTTGAGGTGATGATCTAATTGGATTGATGGAGTTTTCCTTCCCT-TAATGATTAATATATAC
*
1659909 AGTTCTTCTCTACTTA-AATGTAGAGGGTGTTTTGCCATCTCTTC-ACATTGAATAATTAGTT-T
130 AGTTCTTCTCTACTTAGAGT-TA-AGGGTGTTTTGCCATCTCTTCTACATTGAATAATTAGTTAT
1659971 -A-TTT-ATTT-AT-T-T-ATCAAAT-TACA
193 CAGTTTGATTTCATATCTGATC-AATGTA-A
* * *** * *
1659994 TTGAATATTAGTTGATTCAGTCTTGTTGGACCAAAATGATAGATTTCATATGTCAAAGATCTATG
1 TTCAACATT-GAAAATTCAGTCTT-TTGGACAAAAATGATAGCTTTCATATGTCAAAGATCTATG
* *
1660059 GTGAATTTGAGGTGATGATCCAATTGGATTGATGGGGTTTTCCTTCCCTTAATGATTAATATATA
64 GTGAATTTGAGGTGATGATCTAATTGGATTGATGGAGTTTTCCTTCCCTTAATGATTAATATATA
* * * *
1660124 TAGTTCTTCTCTACTTGAGAGTTACGGGTGTTTTTCCATCTCTT-TAGATTGA
129 CAGTTCTTCTCTACTT-AGAGTTAAGGGTGTTTTGCCATCTCTTCTACATTGA
1660176 TTAAGATATG
Statistics
Matches: 325, Mismatches: 42, Indels: 54
0.77 0.10 0.13
Matches are distributed among these distances:
205 4 0.01
206 11 0.03
207 11 0.03
208 37 0.11
209 3 0.01
210 4 0.01
211 3 0.01
213 2 0.01
214 4 0.01
215 88 0.27
216 94 0.29
217 4 0.01
218 3 0.01
221 1 0.00
225 1 0.00
226 1 0.00
227 29 0.09
228 25 0.08
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (221 bp):
TTCAACATTGAAAATTCAGTCTTTTGGACAAAAATGATAGCTTTCATATGTCAAAGATCTATGGT
GAATTTGAGGTGATGATCTAATTGGATTGATGGAGTTTTCCTTCCCTTAATGATTAATATATACA
GTTCTTCTCTACTTAGAGTTAAGGGTGTTTTGCCATCTCTTCTACATTGAATAATTAGTTATCAG
TTTGATTTCATATCTGATCAATGTAA
Found at i:1667199 original size:6 final size:6
Alignment explanation
Indices: 1667188--1667221 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1667178 TAAGACAGAA
1667188 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG -GAGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGG
1667222 AAGTCAACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:1674903 original size:20 final size:19
Alignment explanation
Indices: 1674867--1674905 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1674857 TGCCGAAATT
*
1674867 TATTTTTTTTTCCTTCTTC
1 TATTTTTTATTCCTTCTTC
1674886 TATTTTTTATT-CTT-TTC
1 TATTTTTTATTCCTTCTTC
1674903 TAT
1 TAT
1674906 CCTTCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTATTCCTTCTTC
Found at i:1675591 original size:8 final size:8
Alignment explanation
Indices: 1675578--1675602 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1675568 CTAGATCGAT
1675578 AAAAGCCG
1 AAAAGCCG
1675586 AAAAGCCG
1 AAAAGCCG
1675594 AAAAGCCG
1 AAAAGCCG
1675602 A
1 A
1675603 CATTTGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.24, T:0.00
Consensus pattern (8 bp):
AAAAGCCG
Found at i:1676254 original size:20 final size:21
Alignment explanation
Indices: 1676211--1676256 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1676201 ACTGTTTTGT
1676211 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
1676231 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
1676250 TATGGGC
1 TATGGGC
1676257 AAGACCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:1680115 original size:19 final size:18
Alignment explanation
Indices: 1680079--1680117 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1680069 GTTTTTCTTA
*
1680079 TAGAATAAGTTATTTTAT
1 TAGAATAAGTTATATTAT
1680097 TAGAATAATGTTATATTAT
1 TAGAATAA-GTTATATTAT
1680116 TA
1 TA
1680118 ATATTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (18 bp):
TAGAATAAGTTATATTAT
Found at i:1681340 original size:21 final size:21
Alignment explanation
Indices: 1681292--1681343 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1681282 GTGGAAAATA
*
1681292 AAAAAAATAATTCATAAATTT
1 AAAAAAATAACTCATAAATTT
* *
1681313 TAAAAAATAACTC-TTAATTT
1 AAAAAAATAACTCATAAATTT
1681333 AAAGAAAATAA
1 AAA-AAAATAA
1681344 ACATAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAAAATAACTCATAAATTT
Found at i:1682229 original size:31 final size:31
Alignment explanation
Indices: 1682194--1682257 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1682184 CTTAATAGCC
**
1682194 CAGTGACTAAAATAAAAGTTTTTGAATAGTT
1 CAGTGACTAAAATAAAAACTTTTGAATAGTT
* *
1682225 CAGTGATTTAAATAAAAACTTTTGAATAGTT
1 CAGTGACTAAAATAAAAACTTTTGAATAGTT
1682256 CA
1 CA
1682258 ATGATCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (31 bp):
CAGTGACTAAAATAAAAACTTTTGAATAGTT
Found at i:1683295 original size:25 final size:25
Alignment explanation
Indices: 1683267--1683314 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1683257 AAGAACATTT
1683267 TAATTAATAATAAAGTTAAATATAA
1 TAATTAATAATAAAGTTAAATATAA
*
1683292 TAATTAATAATAAATTTAAATAT
1 TAATTAATAATAAAGTTAAATAT
1683315 GTTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TAATTAATAATAAAGTTAAATATAA
Found at i:1686135 original size:3 final size:3
Alignment explanation
Indices: 1686127--1686155 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1686117 TTTCCCTATA
1686127 CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
1686156 ACCGCCACCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:1687786 original size:31 final size:31
Alignment explanation
Indices: 1687748--1687818 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1687738 TATAATACTA
*
1687748 TCACTAAATTAATTAAAAATTTTTATTTAAG
1 TCACTAAATTAATTAAAAATTTTTATTCAAG
* * * *
1687779 TCACTAAACTATTTGAAATTTTTTATTCAAG
1 TCACTAAATTAATTAAAAATTTTTATTCAAG
*
1687810 TTACTAAAT
1 TCACTAAAT
1687819 AGTTAAGCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (31 bp):
TCACTAAATTAATTAAAAATTTTTATTCAAG
Found at i:1688960 original size:25 final size:23
Alignment explanation
Indices: 1688931--1688976 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
1688921 TATAAAGACT
1688931 AATTTTTAATAATAAAAATAAATAA
1 AATTTTTAA-AA-AAAAATAAATAA
*
1688956 AATTTTTAACAAAAAATAAAT
1 AATTTTTAAAAAAAAATAAAT
1688977 TTACTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 1 0.05
25 9 0.45
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AATTTTTAAAAAAAAATAAATAA
Found at i:1689367 original size:20 final size:20
Alignment explanation
Indices: 1689345--1689381 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1689335 AAAAGGTTAA
*
1689345 AAAATAT-TTAAAATTTTAG
1 AAAATATCTGAAAATTTTAG
1689364 AAAATATCTGAAAATTTT
1 AAAATATCTGAAAATTTT
1689382 TAAAATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
AAAATATCTGAAAATTTTAG
Found at i:1690055 original size:13 final size:13
Alignment explanation
Indices: 1690019--1690061 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1690009 TTTATTTTTA
*
1690019 TAATATTATTAAT
1 TAATATTAATAAT
*
1690032 TAAT-TTAAATAGT
1 TAATATT-AATAAT
1690045 TAATATTAATAAT
1 TAATATTAATAAT
1690058 TAAT
1 TAAT
1690062 CAAAATTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
TAATATTAATAAT
Found at i:1691608 original size:31 final size:31
Alignment explanation
Indices: 1691573--1691634 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1691563 CTTAATAGCC
*
1691573 CAATGACTAAAAT-AAAAGTTTTTGAATAGTT
1 CAATGACTAAAATGAAAA-CTTTTGAATAGTT
* *
1691604 CAATGATTTAAATGAAAACTTTTGAATAGTT
1 CAATGACTAAAATGAAAACTTTTGAATAGTT
1691635 TAAGGATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (31 bp):
CAATGACTAAAATGAAAACTTTTGAATAGTT
Found at i:1693156 original size:75 final size:75
Alignment explanation
Indices: 1693037--1693208 Score: 205
Period size: 75 Copynumber: 2.4 Consensus size: 75
1693027 CATGGCAAAG
** *
1693037 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
1693096 CCATACTGAGC
65 CCATACCGAGC
1693107 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
1693172 CATACCGAGT
66 CATACCGAGC
***
1693182 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
1693209 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 1 0.01
75 46 0.53
76 18 0.21
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:1693175 original size:35 final size:35
Alignment explanation
Indices: 1693040--1693206 Score: 167
Period size: 35 Copynumber: 4.6 Consensus size: 35
1693030 GGCAAAGTGT
* **
1693040 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
1693075 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
1693110 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
1693150 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
1693186 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
1693207 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
35 64 0.55
36 21 0.18
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:1693198 original size:36 final size:35
Alignment explanation
Indices: 1693136--1693206 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
1693126 ATTATCAAAT
* *
1693136 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
*
1693171 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC
1693207 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (35 bp):
CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
Found at i:1695742 original size:17 final size:19
Alignment explanation
Indices: 1695707--1695748 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
1695697 AAAAAAATTA
1695707 TTTTAACTCTTTATTTAAT
1 TTTTAACTCTTTATTTAAT
1695726 TTTTAA-TCTTT-TTTAAT
1 TTTTAACTCTTTATTTAAT
1695743 TTTTAA
1 TTTTAA
1695749 AGTTACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTAACTCTTTATTTAAT
Found at i:1699032 original size:31 final size:31
Alignment explanation
Indices: 1698951--1699021 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1698941 CCTAAAGCGG
* * **
1698951 GAACAGTTGCCTAATCTAGGTCCCCGTGTAA
1 GAACAATTGCCTAATTTAGGTCCCAATGTAA
*
1698982 GAACAATTGCCTAATTTAGGTCCCAATGTGA
1 GAACAATTGCCTAATTTAGGTCCCAATGTAA
1699013 GAACAATTG
1 GAACAATTG
1699022 TCAAGTTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (31 bp):
GAACAATTGCCTAATTTAGGTCCCAATGTAA
Found at i:1703402 original size:40 final size:40
Alignment explanation
Indices: 1703357--1703434 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1703347 TCACACCATG
* * * *
1703357 TGGGGATAAAATTGACCCATCCATCCCTGCGCACCATATA
1 TGGGGATAAAATCGACCCATCCAACCCTACACACCATATA
*
1703397 TGGGGATATAATCGACCCATCCAACCCTACACACCATA
1 TGGGGATAAAATCGACCCATCCAACCCTACACACCATA
1703435 AGGTACCACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCATCCAACCCTACACACCATATA
Found at i:1705206 original size:18 final size:18
Alignment explanation
Indices: 1705183--1705218 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1705173 GAGCAATAGA
*
1705183 GGAGCCACAAAATTAGTT
1 GGAGCCAAAAAATTAGTT
1705201 GGAGCCAAAAAATTAGTT
1 GGAGCCAAAAAATTAGTT
1705219 ATGTACTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (18 bp):
GGAGCCAAAAAATTAGTT
Found at i:1708962 original size:16 final size:18
Alignment explanation
Indices: 1708941--1708978 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
1708931 TTTTTTTTAG
1708941 ATTTTAAGA-TTA-TTTT
1 ATTTTAAGATTTATTTTT
*
1708957 ATTTTAATATTTATTTTT
1 ATTTTAAGATTTATTTTT
1708975 ATTT
1 ATTT
1708979 GAAAAGACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTAAGATTTATTTTT
Found at i:1710406 original size:2 final size:2
Alignment explanation
Indices: 1710399--1710433 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1710389 TGACCACATA
*
1710399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1710434 AGTTAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1714080 original size:2 final size:2
Alignment explanation
Indices: 1714073--1714103 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1714063 ATTGTGGAAT
1714073 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 T
1714104 GAAATAGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1714434 original size:35 final size:37
Alignment explanation
Indices: 1714395--1714463 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
1714385 ATTTATTTGA
1714395 CTAGTGCAAGGCAC-AA-CTACTATCGATTTATCCAG
1 CTAGTGCAAGGCACAAATCTACTATCGATTTATCCAG
** *
1714430 CTAGTGCTGGGCACAAATCTACTATCGGTTTATC
1 CTAGTGCAAGGCACAAATCTACTATCGATTTATC
1714464 TGTTTAGCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 12 0.41
36 2 0.07
37 15 0.52
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (37 bp):
CTAGTGCAAGGCACAAATCTACTATCGATTTATCCAG
Found at i:1714514 original size:36 final size:35
Alignment explanation
Indices: 1714474--1714589 Score: 88
Period size: 36 Copynumber: 3.1 Consensus size: 35
1714464 TGTTTAGCGC
1714474 TGGGCGCAAATCTTTGTCGGTTAATTTAGCTAGTGT
1 TGGGCGCAAATCTTTGTCGGTTAATTT-GCTAGTGT
* * * * * *
1714510 TGGGCACACATTTAATATCGTCGGTTTATTTGACTAGCGC
1 TGGGCGCAAATCT--T-T-GTCGGTTAATTTG-CTAGTGT
* * *
1714550 TGAGTGTAAATCTTTGTCGGTTAATTTGGCTAGTGT
1 TGGGCGCAAATCTTTGTCGGTTAATTT-GCTAGTGT
1714586 TGGG
1 TGGG
1714590 AACACATTTA
Statistics
Matches: 58, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
36 29 0.50
37 2 0.03
38 2 0.03
39 2 0.03
40 23 0.40
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.39
Consensus pattern (35 bp):
TGGGCGCAAATCTTTGTCGGTTAATTTGCTAGTGT
Found at i:1714514 original size:73 final size:74
Alignment explanation
Indices: 1714428--1714853 Score: 216
Period size: 71 Copynumber: 5.8 Consensus size: 74
1714418 CGATTTATCC
* * ** *
1714428 AGCTAGTGCTGGGCACAAATCTACTA-TCGGTTTATCTGTTTAGCGCTGGGCGCAAATCTTTGTC
1 AGCTAGTGTTGGGCACAAATCTAATACTCGGTTTATCTGACTAGCGCTGAGCGCAAATCTTTGTC
1714492 GGTTAATTT
66 GGTTAATTT
* * * * *
1714501 AGCTAGTGTTGGGCACACATTTAATATCGTCGGTTTATTTGACTAGCGCTGAGTGTAAATCTTTG
1 AGCTAGTGTTGGGCACAAATCTAATA-C-TCGGTTTATCTGACTAGCGCTGAGCGCAAATCTTTG
1714566 TCGGTTAATTT
64 TCGGTTAATTT
* * * * * * * * *
1714577 GGCTAGTGTTGGGAACACATTTAATATTTTCGGTTTAT-TCAACTAGC-TTCAGATGCAAATCTT
1 AGCTAGTGTTGGGCACAAATCTAATA--CTCGGTTTATCT-GACTAGCGCTGAG-CGCAAATCTT
* *
1714640 TGTCGATTTA-TT
62 TGTCGGTTAATTT
* * ** * * *
1714652 CGACTAGTGTAGGGCAC--ATCT-ATTGTCGGTTTACCTGACTAGCGCTGAGCACAAATCTTTAT
1 AG-CTAGTGTTGGGCACAAATCTAATACTCGGTTTATCTGACTAGCGCTGAGCGCAAATCTTTGT
* *
1714714 CGATTTATTT
65 CGGTTAATTT
*** ** * * * * *
1714724 -GACTAGTGCAAGGCAC--ATCT-ATTGTCGGTTTACCCGACTAGCACTGGGCGCAAATCTTTAT
1 AG-CTAGTGTTGGGCACAAATCTAATACTCGGTTTATCTGACTAGCGCTGAGCGCAAATCTTTGT
** *
1714785 CCATTTATTT
65 CGGTTAATTT
* ** * * * *
1714795 -GATTAGTGCAGGGCAC--ATCTACTA-TCGGTTTACCCGACTAGCGCTGGGCGCAAATCTTT
1 AG-CTAGTGTTGGGCACAAATCTAATACTCGGTTTATCTGACTAGCGCTGAGCGCAAATCTTT
1714854 ATCGATTTAT
Statistics
Matches: 298, Mismatches: 44, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
71 147 0.49
72 7 0.02
73 24 0.08
74 3 0.01
75 7 0.02
76 109 0.37
77 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (74 bp):
AGCTAGTGTTGGGCACAAATCTAATACTCGGTTTATCTGACTAGCGCTGAGCGCAAATCTTTGTC
GGTTAATTT
Found at i:1714561 original size:76 final size:76
Alignment explanation
Indices: 1714454--1714711 Score: 242
Period size: 76 Copynumber: 3.5 Consensus size: 76
1714444 AAATCTACTA
* ** * *
1714454 TCGGTTTATCTGTTTAGCGCTGGGCGCAAATCTTTGTCGGTTAATTTAGCTAGTGTTGGGCACAC
1 TCGGTTTATTTGACTAGCGCTGAGCGCAAATCTTTGTCGGTTAATTTAGCTAGTGTTGGGAACAC
1714519 ATTTAATATCG
66 ATTTAATATCG
* * *
1714530 TCGGTTTATTTGACTAGCGCTGAGTGTAAATCTTTGTCGGTTAATTTGGCTAGTGTTGGGAACAC
1 TCGGTTTATTTGACTAGCGCTGAGCGCAAATCTTTGTCGGTTAATTTAGCTAGTGTTGGGAACAC
**
1714595 ATTTAATATTT
66 ATTTAATATCG
** * * * * * * *
1714606 TCGGTTTATTCAACTAGC-TTCAGATGCAAATCTTTGTCGATTTA-TTCGACTAGTGTAGGG--C
1 TCGGTTTATTTGACTAGCGCTGAG-CGCAAATCTTTGTCGGTTAATTTAG-CTAGTGTTGGGAAC
*
1714667 ACATCT-AT-T-G
64 ACATTTAATATCG
** *
1714677 TCGGTTTACCTGACTAGCGCTGAGCACAAATCTTT
1 TCGGTTTATTTGACTAGCGCTGAGCGCAAATCTTT
1714712 ATCGATTTAT
Statistics
Matches: 150, Mismatches: 29, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
71 23 0.15
72 4 0.03
73 2 0.01
74 6 0.04
75 6 0.04
76 109 0.73
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (76 bp):
TCGGTTTATTTGACTAGCGCTGAGCGCAAATCTTTGTCGGTTAATTTAGCTAGTGTTGGGAACAC
ATTTAATATCG
Found at i:1714707 original size:71 final size:71
Alignment explanation
Indices: 1714631--1714918 Score: 443
Period size: 71 Copynumber: 4.1 Consensus size: 71
1714621 AGCTTCAGAT
* * * * *
1714631 GCAAATCTTTGTCGATTTATTCGACTAGTGTAGGGCACATCTATTGTCGGTTTACCTGACTAGCG
1 GCAAATCTTTATCGATTTATTTGACTAGTGCAGGGCACATCTACTGTCGGTTTACCCGACTAGCG
*
1714696 CTGAGC
66 CTGGGC
* * * *
1714702 ACAAATCTTTATCGATTTATTTGACTAGTGCAAGGCACATCTATTGTCGGTTTACCCGACTAGCA
1 GCAAATCTTTATCGATTTATTTGACTAGTGCAGGGCACATCTACTGTCGGTTTACCCGACTAGCG
1714767 CTGGGC
66 CTGGGC
* * *
1714773 GCAAATCTTTATCCATTTATTTGATTAGTGCAGGGCACATCTACTATCGGTTTACCCGACTAGCG
1 GCAAATCTTTATCGATTTATTTGACTAGTGCAGGGCACATCTACTGTCGGTTTACCCGACTAGCG
1714838 CTGGGC
66 CTGGGC
*
1714844 GCAAATCTTTATCGATTTATTTGACTAGTGCAGGGCACATCTACTGTCAGTTTA-CCGACTAGCG
1 GCAAATCTTTATCGATTTATTTGACTAGTGCAGGGCACATCTACTGTCGGTTTACCCGACTAGCG
1714908 CTGGGC
66 CTGGGC
1714914 GCAAA
1 GCAAA
1714919 AATTTGTTAC
Statistics
Matches: 198, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
70 21 0.11
71 177 0.89
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (71 bp):
GCAAATCTTTATCGATTTATTTGACTAGTGCAGGGCACATCTACTGTCGGTTTACCCGACTAGCG
CTGGGC
Found at i:1714728 original size:36 final size:36
Alignment explanation
Indices: 1714632--1714882 Score: 147
Period size: 36 Copynumber: 7.1 Consensus size: 36
1714622 GCTTCAGATG
* * *
1714632 CAAATCTTTGTCGATTTATTCGACTAGTG-TAGGGCA
1 CAAATCTTTATCGATTTATTTGACTAGCGCT-GGGCA
* * ** *
1714668 C--ATCTATTGTCGGTTTACCTGACTAGCGCTGAGCA
1 CAAATCT-TTATCGATTTATTTGACTAGCGCTGGGCA
* **
1714703 CAAATCTTTATCGATTTATTTGACTAGTGCAAGGCA
1 CAAATCTTTATCGATTTATTTGACTAGCGCTGGGCA
* * *** * *
1714739 C--ATCTATTGTCGGTTTACCCGACTAGCACTGGGCG
1 CAAATCT-TTATCGATTTATTTGACTAGCGCTGGGCA
* * * *
1714774 CAAATCTTTATCCATTTATTTGATTAGTGCAGGGCA
1 CAAATCTTTATCGATTTATTTGACTAGCGCTGGGCA
* * *** *
1714810 C--ATCTACTATCGGTTTACCCGACTAGCGCTGGGCG
1 CAAATCT-TTATCGATTTATTTGACTAGCGCTGGGCA
* *
1714845 CAAATCTTTATCGATTTATTTGACTAGTGCAGGGCA
1 CAAATCTTTATCGATTTATTTGACTAGCGCTGGGCA
1714881 CA
1 CA
1714883 TCTACTGTCA
Statistics
Matches: 152, Mismatches: 53, Indels: 20
0.68 0.24 0.09
Matches are distributed among these distances:
34 12 0.08
35 62 0.41
36 66 0.43
37 12 0.08
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (36 bp):
CAAATCTTTATCGATTTATTTGACTAGCGCTGGGCA
Found at i:1719503 original size:25 final size:26
Alignment explanation
Indices: 1719456--1719511 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
1719446 AACCCTACTT
1719456 TTATATTATATATTGAAAAATTATTTTA
1 TTATATTATATATT-AAAAATTA-TTTA
*
1719484 TTATA-TATATATT-AATATTATTTA
1 TTATATTATATATTAAAAATTATTTA
1719508 TTAT
1 TTAT
1719512 CTATTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 8 0.30
25 6 0.22
27 8 0.30
28 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTATATTATATATTAAAAATTATTTA
Found at i:1720243 original size:30 final size:29
Alignment explanation
Indices: 1720207--1720277 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
1720197 TGTATTATTC
*
1720207 TTTTTGTATGTCATGCATTATTTTATTACT
1 TTTTTGTATGTCATGCATTATTTAATTA-T
* *
1720237 TTTTTGTATATCATGTATTATTTAATTAT
1 TTTTTGTATGTCATGCATTATTTAATTAT
*
1720266 TAATTTGTATGT
1 T-TTTTGTATGT
1720278 TTGTACGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.06
30 33 0.94
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.61
Consensus pattern (29 bp):
TTTTTGTATGTCATGCATTATTTAATTAT
Found at i:1722776 original size:27 final size:24
Alignment explanation
Indices: 1722716--1722781 Score: 62
Period size: 28 Copynumber: 2.6 Consensus size: 24
1722706 TAGTATTTAA
1722716 TTAATTTTTTAAATTTAAAAATAT
1 TTAATTTTTTAAATTTAAAAATAT
*
1722740 TTATTCTTTTTATATATTTTAAATAAT-T
1 TTAAT-TTTTTA-A-A-TTTAAA-AATAT
*
1722768 TTAATTTTTAAAAT
1 TTAATTTTTTAAAT
1722782 GTTTTTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
24 5 0.15
25 7 0.21
26 2 0.06
27 6 0.18
28 11 0.32
29 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TTAATTTTTTAAATTTAAAAATAT
Found at i:1725934 original size:26 final size:26
Alignment explanation
Indices: 1725905--1725980 Score: 143
Period size: 26 Copynumber: 2.9 Consensus size: 26
1725895 ATTGATAAAA
*
1725905 GGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATG
1725931 GGTTAGGTAAATGTTTCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATG
1725957 GGTTAGGTAAATGTTTCATGATAA
1 GGTTAGGTAAATGTTTCATGATAA
1725981 GAATTTCATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (26 bp):
GGTTAGGTAAATGTTTCATGATAATG
Found at i:1727507 original size:25 final size:25
Alignment explanation
Indices: 1727459--1727507 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1727449 ACAGTTTTAC
1727459 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
1727484 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
1727508 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:1731712 original size:26 final size:26
Alignment explanation
Indices: 1731651--1731743 Score: 152
Period size: 26 Copynumber: 3.5 Consensus size: 26
1731641 AATTGATAAA
1731651 GGTTAGGTAAATGTTCCATGATAAT-
1 GGTTAGGTAAATGTTCCATGATAATG
1731676 GGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTCCATGATAATG
*
1731702 GGTTAGGTAAATGTTTCATGATAATG
1 GGTTAGGTAAATGTTCCATGATAATG
1731728 GAGTTAGGTAATATGT
1 G-GTTAGGTAA-ATGT
1731744 GATAATGGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
25 25 0.39
26 26 0.41
27 9 0.14
28 4 0.06
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (26 bp):
GGTTAGGTAAATGTTCCATGATAATG
Found at i:1733277 original size:26 final size:26
Alignment explanation
Indices: 1733248--1733300 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1733238 TTTACAGTTT
*
1733248 TACCCCTAGGAGATAAA-TTACCGAAA
1 TACCCATAGG-GATAAATTTACCGAAA
* *
1733274 TACCCATAGGGTTAAATTTACCTAAA
1 TACCCATAGGGATAAATTTACCGAAA
1733300 T
1 T
1733301 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (26 bp):
TACCCATAGGGATAAATTTACCGAAA
Found at i:1735566 original size:27 final size:28
Alignment explanation
Indices: 1735530--1735669 Score: 193
Period size: 27 Copynumber: 5.2 Consensus size: 28
1735520 AGCATGGCTG
*
1735530 CCAGA-ACAGATA-ATGTGGCAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
1735556 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
1735584 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
1735611 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
1735638 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
1735665 CCAGA
1 CCAGA
1735670 ACGCTTCCTC
Statistics
Matches: 107, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
26 5 0.05
27 84 0.79
28 18 0.17
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:1735837 original size:29 final size:26
Alignment explanation
Indices: 1735774--1735848 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 26
1735764 AAATTAACCC
* * *
1735774 TAGGGGTATAACGGTAATTTTGCACC
1 TAGGGGTATAACAGTAATTTTCCACA
1735800 TAGGGGTATAACAGTAAATTTTCCATACA
1 TAGGGGTATAACAGT-AATTTTCC--ACA
* *
1735829 TAGGGGTATTATAGTAATTT
1 TAGGGGTATAACAGTAATTT
1735849 AGCTACTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 14 0.34
27 7 0.17
28 5 0.12
29 15 0.37
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.35
Consensus pattern (26 bp):
TAGGGGTATAACAGTAATTTTCCACA
Found at i:1737329 original size:26 final size:26
Alignment explanation
Indices: 1737293--1737402 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
1737283 CATAAAATTC
1737293 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1737319 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
1737345 TTATCATGGAACATTTGCCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
1737371 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
1737397 TTATCA
1 TTATCA
1737403 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1737943 original size:29 final size:28
Alignment explanation
Indices: 1737897--1737954 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1737887 CCGAACATAT
1737897 TATGTTATAAAAATATTATATTAATTATA
1 TATGTTATAAAAATATTATA-TAATTATA
* *
1737926 TATGTTA-AATAATAATTATATATTTATA
1 TATGTTATAAAAAT-ATTATATAATTATA
1737954 T
1 T
1737955 TTATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
TATGTTATAAAAATATTATATAATTATA
Found at i:1740472 original size:3 final size:3
Alignment explanation
Indices: 1740367--1740453 Score: 158
Period size: 3 Copynumber: 29.0 Consensus size: 3
1740357 AAAATTTAGA
1740367 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1740415 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T AGTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
1740454 TTAAGACCTT
Statistics
Matches: 82, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.02
3 78 0.95
4 2 0.02
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1740545 original size:2 final size:2
Alignment explanation
Indices: 1740538--1740568 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1740528 TAATTAATAC
1740538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1740569 GTTTATATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1740728 original size:2 final size:2
Alignment explanation
Indices: 1740721--1740745 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1740711 TATCAGTATT
1740721 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 T
1740746 TATTTACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1744858 original size:2 final size:2
Alignment explanation
Indices: 1744851--1744880 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1744841 TATTTATAAG
1744851 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1744881 AATAAGAGAC
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):
TA
Found at i:1747858 original size:5 final size:6
Alignment explanation
Indices: 1747844--1747868 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1747834 TGTTTCCCTT
1747844 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
1747869 CAAAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1756707 original size:13 final size:13
Alignment explanation
Indices: 1756689--1756713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1756679 TGTCTCGTAG
1756689 TGATTCCAGGCCA
1 TGATTCCAGGCCA
1756702 TGATTCCAGGCC
1 TGATTCCAGGCC
1756714 TCGAATCTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (13 bp):
TGATTCCAGGCCA
Done.