Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 14 of 39
Found at i:1785084 original size:13 final size:13
Alignment explanation
Indices: 1785066--1785090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1785056 ACATTTGGTC
1785066 ATGTATCGATACA
1 ATGTATCGATACA
1785079 ATGTATCGATAC
1 ATGTATCGATAC
1785091 TGTGCAACAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1787569 original size:13 final size:13
Alignment explanation
Indices: 1787547--1787582 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1787537 ATAATCCCCT
*
1787547 TGTATCGATACAG
1 TGTATCGATACAA
*
1787560 TGTATAGATACAA
1 TGTATCGATACAA
1787573 TGTATCGATA
1 TGTATCGATA
1787583 TAGAGAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1792148 original size:9 final size:9
Alignment explanation
Indices: 1792134--1792164 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1792124 TCTGAGTCAC
*
1792134 CATCATCAT
1 CATCATCTT
1792143 CATCATCTT
1 CATCATCTT
1792152 CATCATCTT
1 CATCATCTT
1792161 CATC
1 CATC
1792165 GTCCTTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (9 bp):
CATCATCTT
Found at i:1793792 original size:13 final size:13
Alignment explanation
Indices: 1793774--1793798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1793764 CATTTTATGG
1793774 TGTATCGATACAA
1 TGTATCGATACAA
1793787 TGTATCGATACA
1 TGTATCGATACA
1793799 TACTGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1793814 original size:32 final size:33
Alignment explanation
Indices: 1793751--1793818 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1793741 CGTTACAAGC
**
1793751 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
1793784 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1793816 CAA
1 CAA
1793819 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1793897 original size:20 final size:21
Alignment explanation
Indices: 1793850--1793902 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1793840 GCCAATGACC
**
1793850 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
1793871 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
1793891 TGTATCGATACA
1 TGTATCGATACA
1793903 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:1793908 original size:13 final size:13
Alignment explanation
Indices: 1793890--1793914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1793880 ACATTTGGTC
1793890 ATGTATCGATACA
1 ATGTATCGATACA
1793903 ATGTATCGATAC
1 ATGTATCGATAC
1793915 TGTGCAACAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1795490 original size:26 final size:26
Alignment explanation
Indices: 1795436--1795495 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
1795426 ATACTTAAGA
*
1795436 TGCCATTTCCAACTTTTGGTTAGTAT
1 TGCCATTTCCAACTTTTGGTTACTAT
*
1795462 TGCCATTTCCAACTTTTGGTTACTTT
1 TGCCATTTCCAACTTTTGGTTACTAT
*
1795488 TGCAATTT
1 TGCCATTT
1795496 AATTCCTAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.48
Consensus pattern (26 bp):
TGCCATTTCCAACTTTTGGTTACTAT
Found at i:1796772 original size:13 final size:13
Alignment explanation
Indices: 1796754--1796778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1796744 TATTTTACTA
1796754 TGTATCGATACAT
1 TGTATCGATACAT
1796767 TGTATCGATACA
1 TGTATCGATACA
1796779 AATAGCGATA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1796863 original size:19 final size:19
Alignment explanation
Indices: 1796809--1796863 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1796799 TGTCAGTTTT
**
1796809 ATATATCGATACAATTGTTC
1 ATATATCGATACAA-TGAGC
* * *
1796829 ATGTATTGATATAATGAGC
1 ATATATCGATACAATGAGC
1796848 ATATATCGATACAATG
1 ATATATCGATACAATG
1796864 TATCAATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATATATCGATACAATGAGC
Found at i:1803187 original size:3 final size:3
Alignment explanation
Indices: 1803179--1803213 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1803169 CGAGTCAACT
*
1803179 TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1803214 CTTGATAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:1804835 original size:13 final size:13
Alignment explanation
Indices: 1804817--1804841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1804807 TATTTTACTA
1804817 TGTATCGATACAT
1 TGTATCGATACAT
1804830 TGTATCGATACA
1 TGTATCGATACA
1804842 ATGTCCCATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1806168 original size:26 final size:25
Alignment explanation
Indices: 1806131--1806179 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1806121 ACAAGTAATC
1806131 AAAATAAAATAAAA-AATTATAACA
1 AAAATAAAATAAAATAATTATAACA
*
1806155 AAAACTAAGAATAAAATATTTATAA
1 AAAA-TAA-AATAAAATAATTATAA
1806180 AATGTGTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 3 0.14
26 7 0.33
27 7 0.33
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAATAAAATAAAATAATTATAACA
Found at i:1808004 original size:24 final size:23
Alignment explanation
Indices: 1807975--1808020 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1807965 TCCTCAAAAT
1807975 AAATAATAA-CATTTCATATAATAA
1 AAATAA-AATCATTTCAT-TAATAA
*
1807999 AAATAAAATCATTTTATTAATA
1 AAATAAAATCATTTCATTAATA
1808021 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATAAAATCATTTCATTAATAA
Found at i:1808106 original size:26 final size:26
Alignment explanation
Indices: 1808052--1808115 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
1808042 GTTAAAATAC
*
1808052 AAATTATAATATTAAAATATTTAATAAT
1 AAATTA-AA-ATTAAAATATATAATAAT
1808080 AAATTAAAATTAAAATTATATAA-AAT
1 AAATTAAAATTAAAA-TATATAATAAT
**
1808106 ATGTTAAAAT
1 AAATTAAAAT
1808116 ACAAAGATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 18 0.56
27 8 0.25
28 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AAATTAAAATTAAAATATATAATAAT
Found at i:1815258 original size:19 final size:21
Alignment explanation
Indices: 1815228--1815267 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1815218 TGTGGAGATC
1815228 TTATACTTTATATAT-TTATT
1 TTATACTTTATATATATTATT
1815248 TTATA-TTTATATATATTATT
1 TTATACTTTATATATATTATT
1815268 ATATTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATACTTTATATATATTATT
Found at i:1815260 original size:8 final size:8
Alignment explanation
Indices: 1815229--1815378 Score: 56
Period size: 9 Copynumber: 17.1 Consensus size: 8
1815219 GTGGAGATCT
1815229 TATACTTTA
1 TATA-TTTA
1815238 TATATTTA
1 TATATTTA
1815246 TTTTATATTTA
1 ---TATATTTA
1815257 TATATATTA
1 TATAT-TTA
1815266 TTATATTATAA
1 -TATATT-T-A
*
1815277 TTATATTAAA
1 -TATATT-TA
*
1815287 AATATTTA
1 TATATTTA
1815295 -ATATTTA
1 TATATTTA
*
1815302 TATATATTT
1 TATAT-TTA
1815311 TAATATTT-
1 T-ATATTTA
1815319 TAATAATTT-
1 T-AT-ATTTA
1815328 T-TATTATA
1 TATATT-TA
*
1815336 TAAATTTA
1 TATATTTA
* *
1815344 AAAATTATA
1 TATATT-TA
*
1815353 TATATTCA
1 TATATTTA
1815361 TATATTTA
1 TATATTTA
1815369 TATTATTTA
1 TA-TATTTA
1815378 T
1 T
1815379 TTTTGTCACA
Statistics
Matches: 115, Mismatches: 10, Indels: 32
0.73 0.06 0.20
Matches are distributed among these distances:
6 3 0.03
7 9 0.08
8 36 0.31
9 39 0.34
10 11 0.10
11 17 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATTTA
Found at i:1815366 original size:49 final size:46
Alignment explanation
Indices: 1815254--1815374 Score: 115
Period size: 49 Copynumber: 2.6 Consensus size: 46
1815244 TATTTTATAT
* * *
1815254 TTATATATATTAT-TATATTATAATTATATTAAAAATATTTAATAT
1 TTATATATATTATATATTTTATAATTATATTAAAAATATTTAAAAA
* * *
1815299 TTATATATATTTTAATATTTTAATAATTTTTATTATATAA-ATTTAAAAA
1 TTATATATATTAT-ATATTTT-ATAA-TTATATTA-AAAATATTTAAAAA
1815348 TTATATATATTCATATA-TTTAT-ATTAT
1 TTATATATATT-ATATATTTTATAATTAT
1815375 TTATTTTTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
45 15 0.24
46 1 0.02
47 7 0.11
48 7 0.11
49 28 0.45
50 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (46 bp):
TTATATATATTATATATTTTATAATTATATTAAAAATATTTAAAAA
Found at i:1818425 original size:31 final size:31
Alignment explanation
Indices: 1818387--1818456 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
1818377 TGTTTTTCTC
1818387 TATAATGGAACAATAATGTGAATCCATTGTT
1 TATAATGGAACAATAATGTGAATCCATTGTT
1818418 TATAATGGAACAATAATGTGAATCCATTGTT
1 TATAATGGAACAATAATGTGAATCCATTGTT
1818449 TATAATGG
1 TATAATGG
1818457 TTATAATCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (31 bp):
TATAATGGAACAATAATGTGAATCCATTGTT
Found at i:1818520 original size:38 final size:38
Alignment explanation
Indices: 1818437--1818511 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
1818427 ACAATAATGT
1818437 GAATCCATTGTTTATAATGGTTATAATCTAGCCTATGC
1 GAATCCATTGTTTATAATGGTTATAATCTAGCCTATGC
1818475 GAATCCATTGTTTATAATGGTTATAATCTAGCCTATG
1 GAATCCATTGTTTATAATGGTTATAATCTAGCCTATG
1818512 ATGGTCCATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (38 bp):
GAATCCATTGTTTATAATGGTTATAATCTAGCCTATGC
Found at i:1820293 original size:18 final size:18
Alignment explanation
Indices: 1820272--1820310 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1820262 AATTATAAAT
*
1820272 ATTAAAATTTAAATATAA
1 ATTAAAAATTAAATATAA
*
1820290 ATTAAAAATTAAATTTAA
1 ATTAAAAATTAAATATAA
1820308 ATT
1 ATT
1820311 GATATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAAAAATTAAATATAA
Found at i:1820318 original size:24 final size:25
Alignment explanation
Indices: 1820261--1820309 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
1820251 GTTATAAAAA
1820261 AAATTATAAATATTAAAATTTAAATAT
1 AAATTA-AAA-ATTAAAATTTAAATAT
1820288 AAATTAAAAATT-AAATTTAAAT
1 AAATTAAAAATTAAAATTTAAAT
1820310 TGATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
25 3 0.14
26 3 0.14
27 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATTAAAAATTAAAATTTAAATAT
Found at i:1821425 original size:16 final size:17
Alignment explanation
Indices: 1821406--1821438 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1821396 TATTTGAAAT
1821406 AAAT-TTTTAAATATTA
1 AAATATTTTAAATATTA
*
1821422 AAATATTTTAATTATTA
1 AAATATTTTAAATATTA
1821439 GTAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATATTTTAAATATTA
Found at i:1821548 original size:24 final size:24
Alignment explanation
Indices: 1821505--1821617 Score: 76
Period size: 24 Copynumber: 4.7 Consensus size: 24
1821495 AGTAGTTATA
**
1821505 TTTTTAA-AT-TTAATTTTAATAT
1 TTTTTAATATATTAATAATAATAT
1821527 TTTTTAATATATTAATAATAAT-T
1 TTTTTAATATATTAATAATAATAT
* *
1821550 TTTTTAAATATATTATATTAGAATATT
1 TTTTT-AATATATTA-ATAATAATA-T
*
1821577 TATTATTAATATA-TATTAA-AATAT
1 T-TT-TTAATATATTAATAATAATAT
*
1821601 TTTTCTAA-ATAATAATA
1 TTTT-TAATATATTAATA
1821618 TCATTTTAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
22 11 0.15
23 17 0.23
24 20 0.27
25 10 0.14
26 2 0.03
27 4 0.05
28 8 0.11
29 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (24 bp):
TTTTTAATATATTAATAATAATAT
Found at i:1821560 original size:22 final size:23
Alignment explanation
Indices: 1821505--1821560 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1821495 AGTAGTTATA
**
1821505 TTTTTAAAT-TTAATTTTAATAT
1 TTTTTAAATATTAATAATAATAT
1821527 TTTTTAATATATTAATAATAAT-T
1 TTTTTAA-ATATTAATAATAATAT
1821550 TTTTTAAATAT
1 TTTTTAAATAT
1821561 ATTATATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 11 0.37
23 10 0.33
24 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTTAAATATTAATAATAATAT
Found at i:1821574 original size:15 final size:15
Alignment explanation
Indices: 1821553--1821594 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1821543 AATAATTTTT
1821553 TTAAATATATTA-TA
1 TTAAATATATTATTA
1821567 TTAGAATAT-TTATTA
1 TTA-AATATATTATTA
1821582 TTAATATATATTA
1 TTAA-ATATATTA
1821595 AAATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 7 0.29
15 14 0.58
16 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
TTAAATATATTATTA
Found at i:1821575 original size:13 final size:13
Alignment explanation
Indices: 1821534--1821601 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
1821524 TATTTTTTAA
1821534 TATATTAATAATAAT
1 TATATTAA-AAT-AT
* *
1821549 TTTTTTAAATATAT
1 TATATTAAA-ATAT
*
1821563 TATATTAGAATAT
1 TATATTAAAATAT
*
1821576 T-TATTATTAATA-
1 TATATTA-AAATAT
1821588 TATATTAAAATAT
1 TATATTAAAATAT
1821601 T
1 T
1821602 TTTCTAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 10 0.24
13 15 0.36
14 9 0.21
15 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (13 bp):
TATATTAAAATAT
Found at i:1823208 original size:2 final size:2
Alignment explanation
Indices: 1823201--1823252 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1823191 TTACAGAGCA
1823201 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
1823243 AT AT AT -T AT A
1 AT AT AT AT AT A
1823253 CACACACACA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1824402 original size:34 final size:34
Alignment explanation
Indices: 1824364--1824446 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
1824354 GAGGAATCAA
* *
1824364 ATAATTTTTATTTGTTT-ATTTATAAAATTATAAT
1 ATAATTTATATTTATTTAATTTA-AAAATTATAAT
*
1824398 ATAATTTATATTTATTTAATTTAAAAATTATATT
1 ATAATTTATATTTATTTAATTTAAAAATTATAAT
*
1824432 TTATATTT-TATTTAT
1 ATA-ATTTATATTTAT
1824447 ATAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 34 0.79
35 9 0.21
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (34 bp):
ATAATTTATATTTATTTAATTTAAAAATTATAAT
Found at i:1824458 original size:29 final size:29
Alignment explanation
Indices: 1824369--1824470 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 29
1824359 ATCAAATAAT
*
1824369 TTTTATTTGTTTATTTATA-AAATTATAATA
1 TTTTATAT-TTTATTTATATAAATTAT-ATA
* *
1824399 TAATTTATA-TTTATTTAATTTAAA-AATTATA
1 T--TTTATATTTTATTT-ATATAAATTA-TATA
1824430 TTTTATATTTTATTTATATAAATTATATA
1 TTTTATATTTTATTTATATAAATTATATA
* *
1824459 TATTAAATTTTA
1 TTTTATATTTTA
1824471 AATAAAATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
29 26 0.45
30 16 0.28
31 7 0.12
32 9 0.16
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (29 bp):
TTTTATATTTTATTTATATAAATTATATA
Found at i:1827774 original size:350 final size:351
Alignment explanation
Indices: 1827133--1827839 Score: 1382
Period size: 350 Copynumber: 2.0 Consensus size: 351
1827123 AGAGGATTTC
1827133 ATATTTTTTTTTCAATATAATCAGTCATACATTAATGGCTCTGCATGCACGTGATAAAAAAATCT
1 ATATTTTTTTTTCAATATAATCAGTCATACATTAATGGCTCTGCATGCACGTGATAAAAAAATCT
1827198 ATATTCTCATATGAAAATGATGAATCTATAAAGAAAAAATTTTGTTTTTAAATAATTCCTTTACA
66 ATATTCTCATATGAAAATGATGAATCTATAAAGAAAAAATTTTGTTTTTAAATAATTCCTTTACA
1827263 AATTTTGAAGATTACTTTTGCGGATTATATCATAATCAAATTTCCTATTTTCATGAATTTTTTGA
131 AATTTTGAAGATTACTTTTGCGGATTATATCATAATCAAATTTCCTATTTTCATGAATTTTTTGA
1827328 TAATTTTCTATAATATTTGAAAAATTAATTGTCGTATATTTTTACCAATACTAGTGAGATTTTTA
196 TAATTTTCTATAATATTTGAAAAATTAATTGTCGTATATTTTTACCAATACTAGTGAGATTTTTA
1827393 TGCCGATATTTGCCCAAAAAATCATAAATATTC-AAAAAAATATGTATTATCATTTTTACCACGC
261 TGCCGATATTTGCCCAAAAAATCATAAATATTCAAAAAAAATATGTATTATCATTTTTACCACGC
*
1827457 AGTTCAAATTGTGAATTTTGTAAATT
326 AGTTCAAATTGTGAATTTTATAAATT
1827483 ATATTTTTTTTTCAATATAATCAGTCATACATTAATGGCTCTGCATGCACGTGATAAAAAAATCT
1 ATATTTTTTTTTCAATATAATCAGTCATACATTAATGGCTCTGCATGCACGTGATAAAAAAATCT
*
1827548 ATATTCTCATATGAAAATGATGAATCTATAAAGAAAATATTTTGTTTTTAAATAATTCCTTTACA
66 ATATTCTCATATGAAAATGATGAATCTATAAAGAAAAAATTTTGTTTTTAAATAATTCCTTTACA
1827613 AATTTTGAAGATTACTTTTGCGGATTATATCATAATCAAATTTCCTATTTTCATGAATTTTTTGA
131 AATTTTGAAGATTACTTTTGCGGATTATATCATAATCAAATTTCCTATTTTCATGAATTTTTTGA
1827678 TAATTTTCTATAATATTTGAAAAATTAATTGTCGTATATTTTTACCAATACTAGTGAGATTTTTA
196 TAATTTTCTATAATATTTGAAAAATTAATTGTCGTATATTTTTACCAATACTAGTGAGATTTTTA
1827743 TGCCGATATTTGCCCAAAAAATCATAAATATTCAAAAAAAATATGTATTATCATTTTTACCACGC
261 TGCCGATATTTGCCCAAAAAATCATAAATATTCAAAAAAAATATGTATTATCATTTTTACCACGC
1827808 AGTTCAAATTGTGAATTTTATAAATT
326 AGTTCAAATTGTGAATTTTATAAATT
1827834 A-ATTTT
1 ATATTTT
1827840 GAATTTTCAT
Statistics
Matches: 354, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
350 297 0.84
351 57 0.16
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (351 bp):
ATATTTTTTTTTCAATATAATCAGTCATACATTAATGGCTCTGCATGCACGTGATAAAAAAATCT
ATATTCTCATATGAAAATGATGAATCTATAAAGAAAAAATTTTGTTTTTAAATAATTCCTTTACA
AATTTTGAAGATTACTTTTGCGGATTATATCATAATCAAATTTCCTATTTTCATGAATTTTTTGA
TAATTTTCTATAATATTTGAAAAATTAATTGTCGTATATTTTTACCAATACTAGTGAGATTTTTA
TGCCGATATTTGCCCAAAAAATCATAAATATTCAAAAAAAATATGTATTATCATTTTTACCACGC
AGTTCAAATTGTGAATTTTATAAATT
Found at i:1828403 original size:154 final size:154
Alignment explanation
Indices: 1828107--1828772 Score: 713
Period size: 153 Copynumber: 4.3 Consensus size: 154
1828097 ATTACGAGAG
* * * * * * **
1828107 AATCAGTTTTAAAAAATTAAATTTATTTTATAAGTTATAAAATTTTTCCTATTATCAAAATACAA
1 AATCAATTTTAAAAAATTCAATTTATTTTATAAGTTTTAGAATTTTTTCTATTATCGAAATACGG
* * *
1828172 AGTTTTTTTCTCCGTAAATTTTTGTCAATAAGATTTTTCTAAGTTTATAATTTTTAAAATTCTTC
66 AGTTTTCTTCTCCGTAAATTTTT-TCAGTAAGATTTTTCTAAGTTTATAATTTTCAAAATTCTTC
1828237 AAATATTATTTTTTAATTGATATTA
130 AAATATTATTTTTTAATTGATATTA
* * * *
1828262 AATCTATTTTGAAAAATTCAATTTA-TTTATAAGTTTTAGAATTTTTTCTGTCATCGAAATACGG
1 AATCAATTTTAAAAAATTCAATTTATTTTATAAGTTTTAGAATTTTTTCTATTATCGAAATACGG
* * *
1828326 AGTTTTCTTCTCCTTAAATTTTTTCGGTAAGATTTTTCTAAGTTTATAATTTTCAAAATTTTTCA
66 AGTTTTCTTCTCCGTAAATTTTTTCAGTAAGATTTTTCTAAGTTTATAATTTTCAAAATTCTTCA
*
1828391 AATATTATTTTTTAATTAATATTA
131 AATATTATTTTTTAATTGATATTA
* * **
1828415 AATCAATTTTAAAAAATTCAATTTATTTTATGAGTTTTAGAA-TTTTTCAATTATCGGCATACGG
1 AATCAATTTTAAAAAATTCAATTTATTTTATAAGTTTTAGAATTTTTTCTATTATCGAAATACGG
* *
1828479 AGTTTTCTTCTTCGTAAA-TTTTTCAGTAAGATTTTTCTAAGTCTATAATTTTCAAAATTCTTCA
66 AGTTTTCTTCTCCGTAAATTTTTTCAGTAAGATTTTTCTAAGTTTATAATTTTCAAAATTCTTCA
* **
1828543 AATATTATTATTTAATTGATGCTA
131 AATATTATTTTTTAATTGATATTA
* * * * * *
1828567 AATCAATTTTGAAAATTTTAATTTATTTTATAAGTTTTATAATATTTTT-TGTT-TCCAAA-ACA
1 AATCAATTTTAAAAAATTCAATTTATTTTATAAGTTTTAGAAT-TTTTTCTATTATCGAAATAC-
* * * * * ** ** * * *
1828629 TAGAATTTTCTACTCCATAAATTTTTT-TGTTGGATTTTT-TGCGATTCAAAATTTTTAAAATTC
64 -GGAGTTTTCTTCTCCGTAAATTTTTTCAGTAAGATTTTTCTAAG-TTTATAATTTTCAAAATTC
** * *
1828692 AACAAATATT-TTTATTAAATTCATATTA
127 TTCAAATATTATTT-TTTAATTGATATTA
* * * *
1828720 AATCAATTTTAGAAAATTCAATTTATTTTTTTAGTTTT-GATTTTTTTCATATT
1 AATCAATTTTAAAAAATTCAATTTATTTTATAAGTTTTAGAATTTTTTC-TATT
1828773 CTTTAATTTT
Statistics
Matches: 425, Mismatches: 76, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
151 7 0.02
152 109 0.26
153 211 0.50
154 77 0.18
155 21 0.05
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (154 bp):
AATCAATTTTAAAAAATTCAATTTATTTTATAAGTTTTAGAATTTTTTCTATTATCGAAATACGG
AGTTTTCTTCTCCGTAAATTTTTTCAGTAAGATTTTTCTAAGTTTATAATTTTCAAAATTCTTCA
AATATTATTTTTTAATTGATATTA
Found at i:1828768 original size:305 final size:307
Alignment explanation
Indices: 1828107--1828765 Score: 778
Period size: 305 Copynumber: 2.2 Consensus size: 307
1828097 ATTACGAGAG
* * * * * * *** **
1828107 AATCAGTTTTAAAAAATTAAATTTATTTTATAAGTTATAAAATTTTTCCTATTATCAAAATACAA
1 AATCAATTTTAAAAAATTCAATTTATTTTATGAGTTTTAGAATTTTT-CAATTATCGGCATACGG
* * *
1828172 AGTTTTTTTCTCCGTAAATTTTTGTCAATAAGATTTTTCTAAGTTTATAATTTTTAAAATTCTTC
65 AGTTTTCTTCTCCGTAAATTTTTGTCAATAAGATTTTTCTAAGTCTATAATTTTCAAAATTCTTC
* * *
1828237 AAATATTATTTTTTAATTGATATTAAATCTATTTTGAAAAATTCAATTTATTTATAAGTTTTAGA
130 AAATATTATTATTTAATTGATACTAAATCAATTTTGAAAAATTCAATTTATTTATAAGTTTTAGA
* * * * *
1828302 ATTTTTTCTGTCATCGAAATACGGAGTTTTCTTCTCCTTAAATTTTTTCGGTAAGATTTTTCTAA
195 ATTTTTTCTGTCATCCAAATACAGAATTTTCTACTCCATAAATTTTTTCGGTAAGATTTTTCTAA
* * *** *
1828367 GTTTATAATTTTCAAAATTTTTCAAATATTATTTTTTAATTAATATTA
260 GTTCAAAATTTTCAAAATTCAACAAATATTATTTTTAAATTAATATTA
1828415 AATCAATTTTAAAAAATTCAATTTATTTTATGAGTTTTAGAATTTTTCAATTATCGGCATACGGA
1 AATCAATTTTAAAAAATTCAATTTATTTTATGAGTTTTAGAATTTTTCAATTATCGGCATACGGA
* *
1828480 GTTTTCTTCTTCGTAAA-TTTT-TCAGTAAGATTTTTCTAAGTCTATAATTTTCAAAATTCTTCA
66 GTTTTCTTCTCCGTAAATTTTTGTCAATAAGATTTTTCTAAGTCTATAATTTTCAAAATTCTTCA
* * * *
1828543 AATATTATTATTTAATTGATGCTAAATCAATTTTGAAAATTTTAATTTATTTTATAAGTTTTATA
131 AATATTATTATTTAATTGATACTAAATCAATTTTGAAAAATTCAATTTA-TTTATAAGTTTTAGA
* * **
1828608 ATATTTTT-TGT-TTCCAAA-ACATAGAATTTTCTACTCCATAAATTTTTT-TGTTGGATTTTT-
195 AT-TTTTTCTGTCATCCAAATAC--AGAATTTTCTACTCCATAAATTTTTTCGGTAAGATTTTTC
** * *
1828668 TGCGATTCAAAATTTTTAAAATTCAACAAATATT-TTTATTAAATTCATATTA
257 TAAG-TTCAAAATTTTCAAAATTCAACAAATATTATTT-TTAAATTAATATTA
* * * *
1828720 AATCAATTTTAGAAAATTCAATTTATTTTTTTAGTTTT-GATTTTTT
1 AATCAATTTTAAAAAATTCAATTTATTTTATGAGTTTTAGAATTTTT
1828766 TCATATTCTT
Statistics
Matches: 299, Mismatches: 46, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
304 14 0.05
305 166 0.56
306 45 0.15
307 32 0.11
308 42 0.14
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (307 bp):
AATCAATTTTAAAAAATTCAATTTATTTTATGAGTTTTAGAATTTTTCAATTATCGGCATACGGA
GTTTTCTTCTCCGTAAATTTTTGTCAATAAGATTTTTCTAAGTCTATAATTTTCAAAATTCTTCA
AATATTATTATTTAATTGATACTAAATCAATTTTGAAAAATTCAATTTATTTATAAGTTTTAGAA
TTTTTTCTGTCATCCAAATACAGAATTTTCTACTCCATAAATTTTTTCGGTAAGATTTTTCTAAG
TTCAAAATTTTCAAAATTCAACAAATATTATTTTTAAATTAATATTA
Found at i:1829631 original size:201 final size:201
Alignment explanation
Indices: 1829286--1829663 Score: 747
Period size: 201 Copynumber: 1.9 Consensus size: 201
1829276 TAATCTTTGG
*
1829286 ATATTTTCTTTATCTTTCTTTCTTTTAGTGAGCCTAAATCTTGTTCTAGTTCACAGAATTTCATC
1 ATATTTTCTTTATCTTTCTTTCTTTTAGTGAGCCTAAATCTTGTTCTAGCTCACAGAATTTCATC
1829351 CATGCTGAAAGGCATAACAAGTTGGCAATGATAAATATTTTTGATTTAGTTGTTATGTTTAGATT
66 CATGCTGAAAGGCATAACAAGTTGGCAATGATAAATATTTTTGATTTAGTTGTTATGTTTAGATT
1829416 TCTTGATGATAGCTTGGTTTTTCTTATGAAATAGGTTGATTATTGGTTTTTCTTATAAATATTTT
131 TCTTGATGATAGCTTGGTTTTTCTTATGAAATAGGTTGATTATTGGTTTTTCTTATAAATATTTT
1829481 TGATAA
196 TGATAA
1829487 ATATTTTCTTTATCTTTCTTTCTTTTAGTGAGCCTAAATCTTGTTCTAGCTCACAGAATTTCATC
1 ATATTTTCTTTATCTTTCTTTCTTTTAGTGAGCCTAAATCTTGTTCTAGCTCACAGAATTTCATC
1829552 CATGCTGAAAGGCATAACAAGTTGGCAATGATAAATATTTTTGATTTAGTTGTTATGTTTAGATT
66 CATGCTGAAAGGCATAACAAGTTGGCAATGATAAATATTTTTGATTTAGTTGTTATGTTTAGATT
1829617 TCTTGATGATAGCTTGGTTTTTCTTATGAAATAGGTTGATTATTGGT
131 TCTTGATGATAGCTTGGTTTTTCTTATGAAATAGGTTGATTATTGGT
1829664 GTAATCTTTA
Statistics
Matches: 176, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
201 176 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (201 bp):
ATATTTTCTTTATCTTTCTTTCTTTTAGTGAGCCTAAATCTTGTTCTAGCTCACAGAATTTCATC
CATGCTGAAAGGCATAACAAGTTGGCAATGATAAATATTTTTGATTTAGTTGTTATGTTTAGATT
TCTTGATGATAGCTTGGTTTTTCTTATGAAATAGGTTGATTATTGGTTTTTCTTATAAATATTTT
TGATAA
Found at i:1830744 original size:331 final size:331
Alignment explanation
Indices: 1830137--1830802 Score: 1260
Period size: 331 Copynumber: 2.0 Consensus size: 331
1830127 GGAATACAAA
*
1830137 TGAGCTTTGAAAAAATAACAATAAAGAATACAAAAGCTCTTTGAAGTGTAGAAATTGATAAAACT
1 TGAGATTTGAAAAAATAACAATAAAGAATACAAAAGCTCTTTGAAGTGTAGAAATTGATAAAACT
1830202 TGAATGTTTTGATTTCTTAATGTTTCTTGTAAGTTCTTATTTTTCTTCAGCTGTTAAAAACTTAT
66 TGAATGTTTTGATTTCTTAATGTTTCTTGTAAGTTCTTATTTTTCTTCAGCTGTTAAAAACTTAT
1830267 ATTTATAGGCTAGAATGTTGATATACTCGTTGGAGGTTGAATGATTGTGTTTGTAGCCTTTGTTG
131 ATTTATAGGCTAGAATGTTGATATACTCGTTGGAGGTTGAATGATTGTGTTTGTAGCCTTTGTTG
1830332 ACTTGTTTGGAGCTTGTTTCCGCGCATTCACGCTCTTATATAGCAATACAATTCATAATGTATCG
196 ACTTGTTTGGAGCTTGTTTCCGCGCATTCACGCTCTTATATAGCAATACAATTCATAATGTATCG
* *
1830397 ATACATACATTTGAAATTTATAGCCGTTGGCCTCAATGTATTGATATATTTCACCATGTATCGAT
261 ATACATACATTTGAAATTTATAGCCATTGGCCTCAATGTATTGATACATTTCACCATGTATCGAT
1830462 ACAATG
326 ACAATG
*
1830468 TGAGATTTGAAAGAATAACAATAAAGAATACAAAAGCTCTTTGAAGTGTAGAAATTGATAAAACT
1 TGAGATTTGAAAAAATAACAATAAAGAATACAAAAGCTCTTTGAAGTGTAGAAATTGATAAAACT
1830533 TGAATGTTTTGATTTCTTAATGTTTCTTGTAAGTTCTTATTTTTCTTCAGCTGTTAAAAACTTAT
66 TGAATGTTTTGATTTCTTAATGTTTCTTGTAAGTTCTTATTTTTCTTCAGCTGTTAAAAACTTAT
1830598 ATTTATAGGCTAGAATGTTGATATACTCGTTGGAGGTTGAATGATTGTGTTTGTAGCCTTTGTTG
131 ATTTATAGGCTAGAATGTTGATATACTCGTTGGAGGTTGAATGATTGTGTTTGTAGCCTTTGTTG
* * *
1830663 ACTTGTTTGGAGTTTGTTTTCGCGCATTCACGCTCTTATATATCAATACAATTCATAATGTATCG
196 ACTTGTTTGGAGCTTGTTTCCGCGCATTCACGCTCTTATATAGCAATACAATTCATAATGTATCG
*
1830728 ATACATACATTTGAAATTTATAGCTATTGGCCTCAATGTATTGATACATTTCACCATGTATCGAT
261 ATACATACATTTGAAATTTATAGCCATTGGCCTCAATGTATTGATACATTTCACCATGTATCGAT
1830793 ACAATG
326 ACAATG
1830799 TGAG
1 TGAG
1830803 TTTTAGCTAC
Statistics
Matches: 327, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
331 327 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (331 bp):
TGAGATTTGAAAAAATAACAATAAAGAATACAAAAGCTCTTTGAAGTGTAGAAATTGATAAAACT
TGAATGTTTTGATTTCTTAATGTTTCTTGTAAGTTCTTATTTTTCTTCAGCTGTTAAAAACTTAT
ATTTATAGGCTAGAATGTTGATATACTCGTTGGAGGTTGAATGATTGTGTTTGTAGCCTTTGTTG
ACTTGTTTGGAGCTTGTTTCCGCGCATTCACGCTCTTATATAGCAATACAATTCATAATGTATCG
ATACATACATTTGAAATTTATAGCCATTGGCCTCAATGTATTGATACATTTCACCATGTATCGAT
ACAATG
Found at i:1831593 original size:23 final size:21
Alignment explanation
Indices: 1831550--1831596 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1831540 AAAACTCCCC
**
1831550 CTTAATAAAATTTTTCTCTCT
1 CTTAATAAAATTTTAATCTCT
1831571 CTTAATAAAATATTTAATACTCT
1 CTTAATAAAAT-TTTAAT-CTCT
1831594 CTT
1 CTT
1831597 TGTTAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 4 0.18
23 7 0.32
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (21 bp):
CTTAATAAAATTTTAATCTCT
Found at i:1833829 original size:9 final size:9
Alignment explanation
Indices: 1833815--1833851 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
1833805 GATCAATCAA
1833815 ATATGGCAT
1 ATATGGCAT
1833824 ATATGGCAT
1 ATATGGCAT
1833833 ATAT-GCAT
1 ATATGGCAT
1833841 ATATGGCAT
1 ATATGGCAT
1833850 AT
1 AT
1833852 CATGTGACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (9 bp):
ATATGGCAT
Found at i:1833842 original size:17 final size:18
Alignment explanation
Indices: 1833815--1833851 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
1833805 GATCAATCAA
1833815 ATATGGCATATATGGCAT
1 ATATGGCATATATGGCAT
1833833 ATAT-GCATATATGGCAT
1 ATATGGCATATATGGCAT
1833850 AT
1 AT
1833852 CATGTGACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (18 bp):
ATATGGCATATATGGCAT
Found at i:1833870 original size:18 final size:18
Alignment explanation
Indices: 1833847--1833885 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1833837 GCATATATGG
1833847 CATATCATGTGACCAAAA
1 CATATCATGTGACCAAAA
1833865 CATATCATGTGACCAAAA
1 CATATCATGTGACCAAAA
1833883 CAT
1 CAT
1833886 GCATATATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (18 bp):
CATATCATGTGACCAAAA
Found at i:1835499 original size:13 final size:13
Alignment explanation
Indices: 1835481--1835505 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1835471 ATAATGCACA
1835481 GTATCGATACATT
1 GTATCGATACATT
1835494 GTATCGATACAT
1 GTATCGATACAT
1835506 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1835623 original size:13 final size:13
Alignment explanation
Indices: 1835605--1835630 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1835595 TACACACAAG
1835605 ATGTATCGATACA
1 ATGTATCGATACA
1835618 ATGTATCGATACA
1 ATGTATCGATACA
1835631 TCCCAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1835648 original size:33 final size:32
Alignment explanation
Indices: 1835587--1835650 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1835577 CTTAACTGTT
1835587 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAGATGTATCGATACAA
*
1835619 TGTATCGATACATCCCAA-ATTGTATCGATACA
1 TGTATCGATACA-CACAAGA-TGTATCGATACA
1835651 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAGATGTATCGATACAA
Found at i:1839421 original size:13 final size:13
Alignment explanation
Indices: 1839403--1839427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1839393 CAAAGATCAG
1839403 TGTATCGATACAA
1 TGTATCGATACAA
1839416 TGTATCGATACA
1 TGTATCGATACA
1839428 GTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1839509 original size:32 final size:33
Alignment explanation
Indices: 1839468--1839601 Score: 182
Period size: 32 Copynumber: 4.0 Consensus size: 33
1839458 AGTAGCTTAA
*
1839468 ATTGTATCGATACAAAAC-TTATGTATCGATAT
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
* *
1839500 ATTGTATCGATACAACAC-TTGTGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
1839532 AATGTATCGATACAACAACACTTTATGTATCGATAC
1 ATTGTATCGATAC-A-AA-ACTTTATGTATCGATAC
*
1839568 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
1839601 A
1 A
1839602 AAAAAAATTT
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
32 41 0.46
33 19 0.21
34 2 0.02
35 3 0.03
36 25 0.28
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:1839539 original size:13 final size:13
Alignment explanation
Indices: 1839521--1839546 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1839511 ACAACACTTG
1839521 TGTATCGATACAA
1 TGTATCGATACAA
1839534 TGTATCGATACAA
1 TGTATCGATACAA
1839547 CAACACTTTA
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1839566 original size:68 final size:65
Alignment explanation
Indices: 1839470--1839602 Score: 205
Period size: 68 Copynumber: 2.0 Consensus size: 65
1839460 TAGCTTAAAT
* *
1839470 TGTATCGATACAAAACTTATGTATCGATATATTGTATCGATACAACAC-TTGTGTATCGATACAA
1 TGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCGATACAA
1839534 TGTATCGATACAACAACACTTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCGAT
1 TGTATCGATAC-A-AA-AC-TTATGTATCGATACATTGTATCGATACAACACTTTATGTATCGAT
1839599 ACAA
62 ACAA
1839603 AAAAAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
64 11 0.18
65 1 0.02
66 2 0.03
67 2 0.03
68 31 0.50
69 15 0.24
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (65 bp):
TGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCGATACAA
Found at i:1839575 original size:13 final size:13
Alignment explanation
Indices: 1839557--1839581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1839547 CAACACTTTA
1839557 TGTATCGATACAT
1 TGTATCGATACAT
1839570 TGTATCGATACA
1 TGTATCGATACA
1839582 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1840434 original size:49 final size:48
Alignment explanation
Indices: 1840312--1840445 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 48
1840302 CAGTTAGACT
* * * *
1840312 TGAAGGTGACAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAG
** * * *
1840360 ACAAGGTGCCAATATGTTGATTCAAGGCTAGCTATATTGGGCTTAAAGG
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA-G
*
1840409 TGAAGGTGCCAATATGCTAATTCAAGGCCAGCGATAT
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
1840446 CAGACTTAGA
Statistics
Matches: 70, Mismatches: 15, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
48 38 0.54
49 32 0.46
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (48 bp):
TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAG
Found at i:1840532 original size:28 final size:28
Alignment explanation
Indices: 1840475--1840632 Score: 187
Period size: 28 Copynumber: 5.6 Consensus size: 28
1840465 CACCAACTTG
1840475 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-AACT
* * *
1840504 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTAACT
*
1840532 TGTGGGCTTTTAAAGATTGCCACTAACT
1 TGTGGGCTTTTAAAGGTTGCCACTAACT
*
1840560 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTAACT
*
1840588 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTAACT
*
1840618 TGTGGG-TTTAAAAGG
1 TGTGGGCTTTTAAAGG
1840633 AAAAAGAGTG
Statistics
Matches: 113, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
27 8 0.07
28 70 0.62
29 14 0.12
30 21 0.19
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTAACT
Found at i:1840569 original size:56 final size:57
Alignment explanation
Indices: 1840475--1840632 Score: 207
Period size: 56 Copynumber: 2.8 Consensus size: 57
1840465 CACCAACTTG
* * *
1840475 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACTTGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAA-GATTGCCACT-AACTTGTGGGCTTTTAAAGGTTGCCACTGACT
1840532 TGTGGGCTTTT-AAAGATTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGATTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACT
** *
1840588 TGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGG-TTTAAAAGG
1 TGTGGGCTTTTG-AAAGATTGCCACTAACTTGTGGGCTTTTAAAGG
1840633 AAAAAGAGTG
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
55 4 0.04
56 46 0.51
57 20 0.22
58 21 0.23
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (57 bp):
TGTGGGCTTTTGAAAGATTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:1840655 original size:34 final size:35
Alignment explanation
Indices: 1840617--1840691 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1840607 TGCCACTAAC
* * *
1840617 TTGTGGGTTTA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
*
1840651 TTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
1840686 TTGTGG
1 TTGTGG
1840692 ACTTTGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 9 0.26
35 26 0.74
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.23
Consensus pattern (35 bp):
TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
Found at i:1840710 original size:29 final size:29
Alignment explanation
Indices: 1840667--1840748 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
1840657 GCTTACAAAA
* *
1840667 GAAAAAGAGTGCCACGGAGTTGTGGACTTT
1 GAAAAAGA-TGCCACCGACTTGTGGACTTT
*
1840697 GAAAAAGATGCCACCGACTTGTGGGCTTT
1 GAAAAAGATGCCACCGACTTGTGGACTTT
*
1840726 GAAAAAGATGCCACTGACTTGTG
1 GAAAAAGATGCCACCGACTTGTG
1840749 CGCTTTTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 40 0.83
30 8 0.17
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (29 bp):
GAAAAAGATGCCACCGACTTGTGGACTTT
Found at i:1856091 original size:13 final size:13
Alignment explanation
Indices: 1856073--1856097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1856063 CAAAGATCAG
1856073 TGTATCGATACAA
1 TGTATCGATACAA
1856086 TGTATCGATACA
1 TGTATCGATACA
1856098 GTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1856183 original size:32 final size:33
Alignment explanation
Indices: 1856142--1856203 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1856132 GCTTAAATTG
1856142 TATCGATACAAAAC-TTATGTATCGATACATTA
1 TATCGATACAAAACTTTATGTATCGATACATTA
*
1856174 TATCGATACAACACTTTATGTATCGATACA
1 TATCGATACAAAACTTTATGTATCGATACA
1856204 AAAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (33 bp):
TATCGATACAAAACTTTATGTATCGATACATTA
Found at i:1856291 original size:21 final size:21
Alignment explanation
Indices: 1856229--1856284 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1856219 GTTGGGACCT
1856229 TGTATCGATACATTCTAACAA
1 TGTATCGATACATTCTAACAA
1856250 TGTATCGATACATTCTAACAA
1 TGTATCGATACATTCTAACAA
1856271 TGTATCGATACATT
1 TGTATCGATACATT
1856285 TGGACAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAACAA
Found at i:1862038 original size:13 final size:13
Alignment explanation
Indices: 1862020--1862057 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1862010 CAGCATTCTC
*
1862020 TGTATCGATACAT
1 TGTATCGATACAG
1862033 TGTATCGATACAG
1 TGTATCGATACAG
1862046 TGTATCGATACA
1 TGTATCGATACA
1862058 AAGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1863961 original size:54 final size:55
Alignment explanation
Indices: 1863873--1864001 Score: 206
Period size: 54 Copynumber: 2.3 Consensus size: 55
1863863 TTCTGTAAAT
*
1863873 AAATTTATGATTAAGGGGGAGTAAGAAACATGTGATTATTTTATTAAGGGGGAG-
1 AAATTTATGATTAAGGGGGAGTAAAAAACATGTGATTATTTTATTAAGGGGGAGA
*
1863927 AAATTTATGATTAAGGGGGAGTAAAAAACTTGTGATTATTTTATTAAGGGGGAGA
1 AAATTTATGATTAAGGGGGAGTAAAAAACATGTGATTATTTTATTAAGGGGGAGA
*
1863982 AAATTTTTTTGATTAAGGGG
1 AAA--TTTATGATTAAGGGG
1864002 AAGAGAAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
54 52 0.75
55 3 0.04
57 14 0.20
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (55 bp):
AAATTTATGATTAAGGGGGAGTAAAAAACATGTGATTATTTTATTAAGGGGGAGA
Found at i:1864600 original size:20 final size:21
Alignment explanation
Indices: 1864575--1864625 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1864565 CGATACATTA
*
1864575 TATCGATACATG-ACCA-AATG
1 TATCGATACATGCA-AAGAATG
*
1864595 TATCGATACTTGCAAAGAATG
1 TATCGATACATGCAAAGAATG
1864616 TATCGATACA
1 TATCGATACA
1864626 AGTGATTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (21 bp):
TATCGATACATGCAAAGAATG
Found at i:1864703 original size:13 final size:13
Alignment explanation
Indices: 1864685--1864743 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
1864675 TACACACAAG
1864685 ATGTATCGATACA
1 ATGTATCGATACA
1864698 ATGTATCGATACATCCCAA
1 ATGTATCGAT--A---C-A
1864717 ATTGTATCGATACA
1 A-TGTATCGATACA
1864731 ATGTATCGATACA
1 ATGTATCGATACA
1864744 TCCCAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.56
14 2 0.05
15 2 0.05
18 2 0.05
19 2 0.05
20 9 0.23
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1864724 original size:20 final size:20
Alignment explanation
Indices: 1864699--1864764 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1864689 ATCGATACAA
1864699 TGTATCGATACATCCCAAAT
1 TGTATCGATACATCCCAAAT
1864719 TGTATCGAT--A---C-AA-
1 TGTATCGATACATCCCAAAT
1864732 TGTATCGATACATCCCAAAT
1 TGTATCGATACATCCCAAAT
*
1864752 TGCATCGATACAT
1 TGTATCGATACAT
1864765 TGGCTTGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 2 0.05
18 2 0.05
19 2 0.05
20 21 0.55
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATCCCAAAT
Found at i:1864724 original size:33 final size:33
Alignment explanation
Indices: 1864686--1864763 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
1864676 ACACACAAGA
1864686 TGTATCGATACAATGTATCGATACATCCCAAAT
1 TGTATCGATACAATGTATCGATACATCCCAAAT
1864719 TGTATCGATACAATGTATCGATACATCCCAAAT
1 TGTATCGATACAATGTATCGATACATCCCAAAT
*
1864752 TGCATCGATACA
1 TGTATCGATACA
1864764 TTGGCTTGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACATCCCAAAT
Found at i:1868658 original size:267 final size:267
Alignment explanation
Indices: 1868183--1868722 Score: 1044
Period size: 267 Copynumber: 2.0 Consensus size: 267
1868173 GCTCTTCCTG
* * **
1868183 AGCCATAATATATAGATTTGTGACTTCTTCATCGTCATCGGATGAGTTGCTATCACTCCATGTGG
1 AGCCATAAGATATAGATTTATGACTTCTTCATCGTCATCGGATGAGTCACTATCACTCCATGTGG
1868248 CCACCATAGCCTTCTTCTTTGGCTTATTTAAATTCTTCTTCTTCAATGTCAAACAATCAAACTTT
66 CCACCATAGCCTTCTTCTTTGGCTTATTTAAATTCTTCTTCTTCAATGTCAAACAATCAAACTTT
1868313 ATATGCCCTGGTTTCTTGCACTCATAGCATATAATTTGATCTTTGTCCTTCTTGCTCGATTCTCC
131 ATATGCCCTGGTTTCTTGCACTCATAGCATATAATTTGATCTTTGTCCTTCTTGCTCGATTCTCC
1868378 TTTTACCATGGCTTTTCTTTGAGGTTTTCTTGATTTCATCTTCAAGAATTTGTTGAACTTTCTAG
196 TTTTACCATGGCTTTTCTTTGAGGTTTTCTTGATTTCATCTTCAAGAATTTGTTGAACTTTCTAG
1868443 GCATCAT
261 GCATCAT
1868450 AGCCATAAGATATAGATTTATGACTTCTTCATCGTCATCGGATGAGTCACTATCACTCCATGTGG
1 AGCCATAAGATATAGATTTATGACTTCTTCATCGTCATCGGATGAGTCACTATCACTCCATGTGG
1868515 CCACCATAGCCTTCTTCTTTGGCTTATTTAAATTCTTCTTCTTCAATGTCAAACAATCAAACTTT
66 CCACCATAGCCTTCTTCTTTGGCTTATTTAAATTCTTCTTCTTCAATGTCAAACAATCAAACTTT
1868580 ATATGCCCTGGTTTCTTGCACTCATAGCATATAATTTGATCTTTGTCCTTCTTGCTCGATTCTCC
131 ATATGCCCTGGTTTCTTGCACTCATAGCATATAATTTGATCTTTGTCCTTCTTGCTCGATTCTCC
1868645 TTTTACCATGGCTTTTCTTTGAGGTTTTCTTGATTTCATCTTCAAGAATTTGTTGAACTTTCTAG
196 TTTTACCATGGCTTTTCTTTGAGGTTTTCTTGATTTCATCTTCAAGAATTTGTTGAACTTTCTAG
1868710 GCATCAT
261 GCATCAT
1868717 AGCCAT
1 AGCCAT
1868723 TTCTTCATCC
Statistics
Matches: 269, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
267 269 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (267 bp):
AGCCATAAGATATAGATTTATGACTTCTTCATCGTCATCGGATGAGTCACTATCACTCCATGTGG
CCACCATAGCCTTCTTCTTTGGCTTATTTAAATTCTTCTTCTTCAATGTCAAACAATCAAACTTT
ATATGCCCTGGTTTCTTGCACTCATAGCATATAATTTGATCTTTGTCCTTCTTGCTCGATTCTCC
TTTTACCATGGCTTTTCTTTGAGGTTTTCTTGATTTCATCTTCAAGAATTTGTTGAACTTTCTAG
GCATCAT
Found at i:1870409 original size:13 final size:13
Alignment explanation
Indices: 1870391--1870420 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1870381 ACAATCCTTC
1870391 ATGTATCGATACA
1 ATGTATCGATACA
*
1870404 ATGTATTGATACA
1 ATGTATCGATACA
1870417 ATGT
1 ATGT
1870421 GAGTTTTAGC
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:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1870489 original size:19 final size:20
Alignment explanation
Indices: 1870465--1870515 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1870455 TATTTTAGTG
*
1870465 TGTATCGATACAATG-AATA
1 TGTATCGATACAAAGCAATA
1870484 TGTATCGATACAAAGCAATA
1 TGTATCGATACAAAGCAATA
1870504 TGTATCGATACA
1 TGTATCGATACA
1870516 TCTGGGCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAGCAATA
Found at i:1875563 original size:19 final size:18
Alignment explanation
Indices: 1875541--1875596 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1875531 CATTGTATAT
1875541 ATACAACACTTATGTATCG
1 ATACAACA-TTATGTATCG
1875560 AT---ACA-T-TGTATCG
1 ATACAACATTATGTATCG
1875573 ATACAACATTTATGTATCG
1 ATACAACA-TTATGTATCG
1875592 ATACA
1 ATACA
1875597 TTTACTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 9 0.29
14 1 0.03
16 6 0.19
18 1 0.03
19 14 0.45
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (18 bp):
ATACAACATTATGTATCG
Found at i:1875567 original size:32 final size:32
Alignment explanation
Indices: 1875521--1875598 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
1875511 GTAGTAGCTT
* *
1875521 TGTAGCGATACATTGTATATATACAACACTTA
1 TGTATCGATACATTGTATAGATACAACACTTA
* *
1875553 TGTATCGATACATTGTATCGATACAACATTTA
1 TGTATCGATACATTGTATAGATACAACACTTA
1875585 TGTATCGATACATT
1 TGTATCGATACATT
1875599 TACTGTTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATTGTATAGATACAACACTTA
Found at i:1875571 original size:13 final size:13
Alignment explanation
Indices: 1875553--1875577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1875543 ACAACACTTA
1875553 TGTATCGATACAT
1 TGTATCGATACAT
1875566 TGTATCGATACA
1 TGTATCGATACA
1875578 ACATTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1879279 original size:155 final size:154
Alignment explanation
Indices: 1878951--1879320 Score: 426
Period size: 155 Copynumber: 2.4 Consensus size: 154
1878941 TAGTGTCCAC
* * *
1878951 TAGGGATATCGAGATACTTTCACGTCGAAGGTATCCCTTAGGGTCATTTTTGTAATTTTTTAGAA
1 TAGGGATATCG-GGTACTTTCATGTCGAAGGTATCCC-TAGGGTCATTTTCGTAATTTTTTAGAA
* * * * *
1879016 CTAAGTCCTAGGTTATCACTAGGTCCGCTTTTATGCCACAGGTAGGTATTTAGGATAGGTTCACT
64 CCAACTCCTAGGTCATCACTAGGTCCGCTTTTATACCACAGGTAGATATTTAGGATAGGTTCACT
**
1879081 CTTTTTCTATCCTTTTTAAGTCCTTG
129 CTTTTTAAATCCTTTTTAAGTCCTTG
* * *
1879107 AAAGG-TACCGGGATACTTTCATGTCGAAGGTATCCGCTAGGGTCATTTTCGTAATTTTTTAGAA
1 TAGGGATATCGGG-TACTTTCATGTCGAAGGTATCC-CTAGGGTCATTTTCGTAATTTTTTAGAA
* * *
1879171 CCAACTCCTAGGTCGTCACTGGGTCTGCTTTTATACCGA-AGGTAGATATTTAGGATAGGTTCA-
64 CCAACTCCTAGGTCATCACTAGGTCCGCTTTTATACC-ACAGGTAGATATTTAGGATAGGTTCAC
*
1879234 TCCTTTTTAAAATCCTATTTT-GGTCCTT-
128 T-CTTTTT-AAATCCT-TTTTAAGTCCTTG
* * * * *
1879262 TAGGGATATTGGGTACTTTTATGTCAAAGGTATCTCTTAGGGACATTTTCGTAATTTTT
1 TAGGGATATCGGGTACTTTCATGTCGAAGGTATC-CCTAGGGTCATTTTCGTAATTTTT
1879321 CTTGAACTTA
Statistics
Matches: 181, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
154 2 0.01
155 153 0.85
156 22 0.12
157 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (154 bp):
TAGGGATATCGGGTACTTTCATGTCGAAGGTATCCCTAGGGTCATTTTCGTAATTTTTTAGAACC
AACTCCTAGGTCATCACTAGGTCCGCTTTTATACCACAGGTAGATATTTAGGATAGGTTCACTCT
TTTTAAATCCTTTTTAAGTCCTTG
Found at i:1883111 original size:17 final size:17
Alignment explanation
Indices: 1883073--1883105 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1883063 GGAAAGATTG
*
1883073 TGAAAGAGAAGAAAAAA
1 TGAAAAAGAAGAAAAAA
1883090 TGAAAAAGAAGAAAAA
1 TGAAAAAGAAGAAAAA
1883106 GAGAAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (17 bp):
TGAAAAAGAAGAAAAAA
Found at i:1883620 original size:112 final size:110
Alignment explanation
Indices: 1883421--1883677 Score: 263
Period size: 112 Copynumber: 2.3 Consensus size: 110
1883411 AAATTCATGT
* * * * ** *
1883421 TTTATACATTTTGATCCATTTGTGCCTAGGAAACTGGGCATGTATCTTGTCAGTTTCGATCTTTT
1 TTTATACA-TTTGATCCATTTGTGCCTAGGAAACTGAGCACGTATCTTATCAGTTTCAAAATCTT
*
1883486 TAAGCCCCGTAACATTCGATTTGCTT-GATTTTCG-AATAAA-TTCACA
65 TAAGCCCCGTAACATTCAATTTG-TTGGATTTT-GAAATAAACTT-ACA
* * *
1883532 CTTTATTCATTTCGATCCATTCGTGCCTAGGAAA-TAGAGCACGTATCTTATCAGTTTTAAAATC
1 -TTTATACATTT-GATCCATTTGTGCCTAGGAAACT-GAGCACGTATCTTATCAGTTTCAAAATC
* * *
1883596 TTTGAGCCCTGTAACA-TCAAATTTGTTGGATTTTGAAATAAACTTATA
63 TTTAAGCCCCGTAACATTC-AATTTGTTGGATTTTGAAATAAACTTACA
1883644 TTTCATACGATTTGATCCATTTGTGCCTAGGAAA
1 TTT-ATAC-ATTTGATCCATTTGTGCCTAGGAAA
1883678 ATGGGGCATA
Statistics
Matches: 121, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
111 12 0.10
112 103 0.85
113 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (110 bp):
TTTATACATTTGATCCATTTGTGCCTAGGAAACTGAGCACGTATCTTATCAGTTTCAAAATCTTT
AAGCCCCGTAACATTCAATTTGTTGGATTTTGAAATAAACTTACA
Found at i:1884224 original size:89 final size:86
Alignment explanation
Indices: 1884014--1884228 Score: 200
Period size: 89 Copynumber: 2.4 Consensus size: 86
1884004 GCCTTCCAAT
* *
1884014 TGATGCTTGCATTTGCATCATTTCACTTGCATCTACATTTTACATAACATTGATATCTGCATTAT
1 TGATGCTTGCATTTGCATCATTTCA-TTGCATCTACACTTTACATAACATTGATATCTGCATCAT
*
1884079 TCCATATGCATTTGCTCTTTTA
65 TCCATATGCATTTACTCTTTTA
* * * * * * * * * * *
1884101 TAAATGTTTGCATTTGCATTATTTCACATACATCTGCACTTTAGATGACGTTTGGTATTTGCATC
1 T-GATGCTTGCATTTGCATCATTTCA-TTGCATCTACACTTTACATAAC-ATTGATATCTGCATC
*
1884166 A-TCTTATATGCATTTAC-CATTTTA
63 ATTC-CATATGCATTTACTC-TTTTA
*
1884190 CTGATGCTTGCATTTACATCATTTCATGTGCATCTACAC
1 -TGATGCTTGCATTTGCATCATTTCAT-TGCATCTACAC
1884229 CATTAGATGT
Statistics
Matches: 100, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
87 1 0.01
88 41 0.41
89 57 0.57
90 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.44
Consensus pattern (86 bp):
TGATGCTTGCATTTGCATCATTTCATTGCATCTACACTTTACATAACATTGATATCTGCATCATT
CCATATGCATTTACTCTTTTA
Found at i:1885186 original size:44 final size:44
Alignment explanation
Indices: 1885105--1885438 Score: 206
Period size: 44 Copynumber: 7.7 Consensus size: 44
1885095 TTCATTTTGA
* * *
1885105 TTTGACGTA-GGTTACCACCCCGGTC-AAGTCCTCCTCATTCACG
1 TTTGACGTATGGTTACCACCCTGGTCAAACT-CTTCTCATTCACG
* *
1885148 TTTGATGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTC-GG
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCA-TTCACG
* * * * *
1885192 TCTGACGTATGGTTACTATCCTGGTCAAATTCTTTTCATCTCAC-
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCAT-TCACG
* * * * * * * *
1885236 -TTAACCTATGGTTACCACCTTGGTTAGATTCTTTTCA-TCTCG
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTCACG
* * * ** * *
1885278 CTTGACATATGGTTACCACCCTTGTCAATTTTTTCTTTCATTCATG
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTC--TCATTCACG
* * * * *
1885324 TTTGACGTATGGTTACCACCCAGGTCGAACTCTTTTTATTTCA-A
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCA-TTCACG
* * *
1885368 TTTGACGTATGG----CACCCAGGTCAAA-TCTTCCTTATTCATG
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTT-CTCATTCACG
* *
1885408 TTTGATGTATGGTTACCACCCTGGACAAACT
1 TTTGACGTATGGTTACCACCCTGGTCAAACT
1885439 TATGGTTACC
Statistics
Matches: 224, Mismatches: 49, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
39 8 0.04
40 26 0.12
41 3 0.01
43 63 0.28
44 81 0.36
45 14 0.06
46 29 0.13
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (44 bp):
TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTCACG
Found at i:1885412 original size:40 final size:41
Alignment explanation
Indices: 1885317--1885420 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 41
1885307 TTTTTCTTTC
* *
1885317 ATTCATGTTTGACGTATGGTTACCACCCAGGTCGAACTCTTTTT
1 ATTCATGTTTGACGTATGG-T--CACCCAGGTCGAAATCTTCTT
*
1885361 ATTTCA-ATTTGACGTATGG-CACCCAGGTC-AAATCTTCCTT
1 A-TTCATGTTTGACGTATGGTCACCCAGGTCGAAATCTT-CTT
*
1885401 ATTCATGTTTGATGTATGGT
1 ATTCATGTTTGACGTATGGT
1885421 TACCACCCTG
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
39 10 0.20
40 24 0.47
44 13 0.25
45 4 0.08
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (41 bp):
ATTCATGTTTGACGTATGGTCACCCAGGTCGAAATCTTCTT
Found at i:1894174 original size:69 final size:69
Alignment explanation
Indices: 1894095--1894288 Score: 257
Period size: 69 Copynumber: 2.8 Consensus size: 69
1894085 ATTTCGTCCC
* * *
1894095 TATTTATTCTACTAAGGAGTTGAAAATATATAGTAACATAGATAAATAATTATATTTAATATTAA
1 TATTTATTCTAATAAGGAGTTGAAAATATATAGTAACATAGATAAATAACTATATTTAATACTAA
1894160 ATAT
66 ATAT
* *
1894164 TATTTATTCTAGT-AGAGAGTTGAAAATATATTA-TAACATAGATAAATAACTATTTTTAATACT
1 TATTTATTCTAATAAG-GAGTTGAAAATATA-TAGTAACATAGATAAATAACTATATTTAATACT
1894227 AAATAT
64 AAATAT
* * * * *
1894233 CATATTATTCCAATAGGGAGTTAAAAACATATAGTAACATAGATAAATAACTATAT
1 TAT-TTATTCTAATAAGGAGTTGAAAATATATAGTAACATAGATAAATAACTATAT
1894289 CCATTGTTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
68 2 0.02
69 63 0.58
70 43 0.39
71 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (69 bp):
TATTTATTCTAATAAGGAGTTGAAAATATATAGTAACATAGATAAATAACTATATTTAATACTAA
ATAT
Found at i:1898397 original size:121 final size:121
Alignment explanation
Indices: 1898231--1898480 Score: 383
Period size: 121 Copynumber: 2.1 Consensus size: 121
1898221 TCAAATATAT
* * *
1898231 GAATATATCAAAATCCATATAAACAGTAATATCATTATGTCAAAATTTATATAAATATATAATAT
1 GAATATATCAAAATCCATATAAAAAGTAATATCACTATATCAAAATTTATATAAATATATAATAT
* *
1898296 ATTAAATACAATTTAACTGAAGAAGATAACATAAATACATATACAAACACAAACAC
66 ATTAAATACAATATAACTGAAGAAAATAACATAAATACATATACAAACACAAACAC
* * * * * *
1898352 GAATATATCAAAATCTATGTAAAAATTATTATTACTATATTAAAATTTATATAAATATATAATAT
1 GAATATATCAAAATCCATATAAAAAGTAATATCACTATATCAAAATTTATATAAATATATAATAT
*
1898417 ATTCAATACAATATAACTGAAGAAAATAACATAAATACATATACAAACACAAACAC
66 ATTAAATACAATATAACTGAAGAAAATAACATAAATACATATACAAACACAAACAC
*
1898473 GAACATAT
1 GAATATAT
1898481 AAATTTTTTT
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 116 1.00
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (121 bp):
GAATATATCAAAATCCATATAAAAAGTAATATCACTATATCAAAATTTATATAAATATATAATAT
ATTAAATACAATATAACTGAAGAAAATAACATAAATACATATACAAACACAAACAC
Found at i:1906062 original size:16 final size:16
Alignment explanation
Indices: 1906041--1906073 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1906031 AAGCCTCCCC
1906041 TGTTTGGATAATATTT
1 TGTTTGGATAATATTT
1906057 TGTTTGGATAATATTT
1 TGTTTGGATAATATTT
1906073 T
1 T
1906074 AATTAAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TGTTTGGATAATATTT
Found at i:1906568 original size:15 final size:15
Alignment explanation
Indices: 1906550--1906581 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1906540 TTTAAAACCC
*
1906550 TTACTTTTCTTTCTT
1 TTACTTTACTTTCTT
1906565 TTACTTTACTTTCTT
1 TTACTTTACTTTCTT
1906580 TT
1 TT
1906582 TTTAACATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (15 bp):
TTACTTTACTTTCTT
Found at i:1907674 original size:14 final size:14
Alignment explanation
Indices: 1907657--1907683 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1907647 TTTATTTTTT
1907657 AAATATATTTTATG
1 AAATATATTTTATG
1907671 AAATATATTTTAT
1 AAATATATTTTAT
1907684 ATCATTAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
AAATATATTTTATG
Found at i:1908900 original size:21 final size:22
Alignment explanation
Indices: 1908863--1908909 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1908853 AGACTTAACG
* *
1908863 AAAAAAATAATGCAAAA-CTAA
1 AAAAAAATAAAGCAAAATCGAA
*
1908884 AAAAAAATAAAGTAAAATCGAA
1 AAAAAAATAAAGCAAAATCGAA
1908906 AAAA
1 AAAA
1908910 TATTACAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (22 bp):
AAAAAAATAAAGCAAAATCGAA
Found at i:1909350 original size:26 final size:26
Alignment explanation
Indices: 1909325--1909375 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1909315 ATGATAAAAT
1909325 TTAAAAA-AATTAAATAAATTATAAA
1 TTAAAAAGAATTAAATAAATTATAAA
** *
1909350 TTAAAAAGTTTTATATAAATTATAAA
1 TTAAAAAGAATTAAATAAATTATAAA
1909376 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
TTAAAAAGAATTAAATAAATTATAAA
Found at i:1909737 original size:10 final size:12
Alignment explanation
Indices: 1909722--1909781 Score: 62
Period size: 10 Copynumber: 5.5 Consensus size: 12
1909712 GCTTCATAAA
1909722 CTCTTA-TCTC-
1 CTCTTACTCTCT
1909732 CTCTTACTCTCT
1 CTCTTACTCTCT
1909744 CTC-T-CTCTCT
1 CTCTTACTCTCT
1909754 CTC-T-CTCTCT
1 CTCTTACTCTCT
1909764 CTCTCT-CTCTCT
1 CTCT-TACTCTCT
1909776 CTCTTA
1 CTCTTA
1909782 TAGACTCTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
10 25 0.56
11 6 0.13
12 14 0.31
ACGTcount: A:0.05, C:0.45, G:0.00, T:0.50
Consensus pattern (12 bp):
CTCTTACTCTCT
Found at i:1909745 original size:2 final size:2
Alignment explanation
Indices: 1909738--1909779 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1909728 TCTCCTCTTA
1909738 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1909780 TATAGACTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1912116 original size:41 final size:41
Alignment explanation
Indices: 1912031--1912137 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
1912021 AGTTCTATTT
**
1912031 CTTTTAAGATATGTAATTATCAC--T--GGTAAGTTTTATG
1 CTTTTAAGATATGTAATTATCACTTTAGGGTAAGACTTATG
* *
1912068 CTGTTAAGATATGTAACTATCACTTTAGGGTAAGACTTATG
1 CTTTTAAGATATGTAATTATCACTTTAGGGTAAGACTTATG
* *
1912109 CTTTTAAGACAAGTAATTATCACTTTAGG
1 CTTTTAAGATATGTAATTATCACTTTAGG
1912138 ATAAATATGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 21 0.36
39 1 0.02
41 36 0.62
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (41 bp):
CTTTTAAGATATGTAATTATCACTTTAGGGTAAGACTTATG
Found at i:1914152 original size:2 final size:2
Alignment explanation
Indices: 1914141--1914174 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1914131 CGAAATCAGC
1914141 AT AT -T 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 AT AT A
1914175 CAAGTTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1914785 original size:20 final size:20
Alignment explanation
Indices: 1914762--1914819 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 20
1914752 TTATGCATGC
1914762 TATATATTT-TTTAATAAATT
1 TATATATTTATTT-ATAAATT
*
1914782 TATATATTTATTTTTAAATT
1 TATATATTTATTTATAAATT
1914802 TATATTATTTATGTTATA
1 TATA-TATTTAT-TTATA
1914820 TTATATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 19 0.58
21 10 0.30
22 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATATATTTATTTATAAATT
Found at i:1914827 original size:25 final size:25
Alignment explanation
Indices: 1914799--1914856 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
1914789 TTATTTTTAA
1914799 ATTTATATTATTTATGT-TAT-ATTAT
1 ATTTATATTATTT-T-TATATAATTAT
1914824 ATTT-TAATTATTTTTATATAATTAT
1 ATTTAT-ATTATTTTTATATAATTAT
1914849 A-TTATATT
1 ATTTATATT
1914857 TAAAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
23 1 0.03
24 10 0.34
25 18 0.62
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTTATATTATTTTTATATAATTAT
Found at i:1915368 original size:25 final size:27
Alignment explanation
Indices: 1915315--1915389 Score: 91
Period size: 25 Copynumber: 2.8 Consensus size: 27
1915305 TTATTATGTT
*
1915315 ATATTTTTATAATTATAAATATAATAA
1 ATATTGTTATAATTATAAATATAATAA
*
1915342 ATATTGTTATAA-T-TAATTATAATAA
1 ATATTGTTATAATTATAAATATAATAA
* *
1915367 ATATTAATTATAAATATAAATAT
1 ATATT-GTTATAATTATAAATAT
1915390 TAAAAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 16 0.39
26 7 0.17
27 12 0.29
28 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATTGTTATAATTATAAATATAATAA
Found at i:1916017 original size:7 final size:7
Alignment explanation
Indices: 1915992--1916032 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
1915982 TAAATTTAAC
1915992 TATAAAA
1 TATAAAA
1915999 TTATATAAA
1 -TATA-AAA
1916008 TATAAAA
1 TATAAAA
1916015 TATAAAA
1 TATAAAA
1916022 TATAAAA
1 TATAAAA
1916029 -ATAA
1 TATAA
1916033 TTTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.12
7 17 0.53
8 8 0.25
9 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TATAAAA
Found at i:1919093 original size:73 final size:72
Alignment explanation
Indices: 1919016--1919277 Score: 268
Period size: 72 Copynumber: 3.6 Consensus size: 72
1919006 GATTATAAGG
*
1919016 GTTTAAA-TTTTTAAAATATTATTTATTTTTATTTGTATAAATTTAAATTTAATTTTTAGGTATG
1 GTTTAAATTTTTTAAAATATAATTTATTTTTATTTGTA-AAATTTAAATTTAATTTTTAGGT-TG
1919080 ATTATATAA
64 ATTATATAA
* * *
1919089 GTTTAAATTTTTTTAAAATATGATTTATTTTTATTTATAAAAATTT-AATTTAATTTTTTAGTTT
1 GTTTAAA-TTTTTTAAAATATAATTTATTTTTATTTGT-AAAATTTAAATTTAA-TTTTTAGGTT
*
1919153 TATTATATGAA
63 GATTATAT-AA
* * * * **
1919164 -TTTAAA-ATTTTAATATATAATTTATTTTTCTTTGTACAAGTTTAAATTTGTTTTTTAAGG-TG
1 GTTTAAATTTTTTAAAATATAATTTATTTTTATTTGTA-AAATTTAAATTTAATTTTT-AGGTTG
1919226 ATTATA-AGA
64 ATTATATA-A
* *
1919235 G-TTAAATTTTTTTGAAGTATAATTTATTTTTATTTGTAAAATT
1 GTTTAAA-TTTTTTAAAATATAATTTATTTTTATTTGTAAAATT
1919278 AGTTTAATTT
Statistics
Matches: 157, Mismatches: 20, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
70 1 0.01
71 7 0.04
72 45 0.29
73 39 0.25
74 21 0.13
75 43 0.27
76 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (72 bp):
GTTTAAATTTTTTAAAATATAATTTATTTTTATTTGTAAAATTTAAATTTAATTTTTAGGTTGAT
TATATAA
Found at i:1919247 original size:147 final size:144
Alignment explanation
Indices: 1919017--1919288 Score: 361
Period size: 147 Copynumber: 1.9 Consensus size: 144
1919007 ATTATAAGGG
* * *
1919017 TTTAAATTTTTAAAATATTATTTATTTTTATTTGTATAAATTTAAATTTAATTTTTAGGTATGAT
1 TTTAAAATTTTAAAATATAATTTATTTTTATTTGTACAAATTTAAATTTAATTTTTAGG-ATGAT
*
1919082 TATATAAGTTTAAATTTTTTTAAAATATGATTTATTTTTATTTATAAAAATTTAATTTAATTTTT
65 TATATAAGTTTAAATTTTTTTAAAATATAATTTATTTTTATTTAT-AAAA-TTAATTTAATTTTT
1919147 TAGTTTTATTATATGAA
128 TAGTTTTATTATATGAA
* * * **
1919164 TTTAAAATTTTAATATATAATTTATTTTTCTTTGTACAAGTTTAAATTTGTTTTTTAAGG-TGAT
1 TTTAAAATTTTAAAATATAATTTATTTTTATTTGTACAAATTTAAATTTAATTTTT-AGGATGAT
* * * *
1919228 TATA-AGAG-TTAAATTTTTTTGAAGTATAATTTATTTTTATTTGTAAAATTAGTTTAATTTT
65 TATATA-AGTTTAAATTTTTTTAAAATATAATTTATTTTTATTTATAAAATTAATTTAATTTT
1919289 ATTTTGATTA
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
143 12 0.11
144 4 0.04
145 33 0.30
146 10 0.09
147 48 0.44
148 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (144 bp):
TTTAAAATTTTAAAATATAATTTATTTTTATTTGTACAAATTTAAATTTAATTTTTAGGATGATT
ATATAAGTTTAAATTTTTTTAAAATATAATTTATTTTTATTTATAAAATTAATTTAATTTTTTAG
TTTTATTATATGAA
Found at i:1919313 original size:25 final size:24
Alignment explanation
Indices: 1919259--1919316 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
1919249 AAGTATAATT
*
1919259 TATTTTTA-TTTGTAAAATTAGTT
1 TATTTTTATTTTGTAAAATTAGTG
* * *
1919282 TAATTTTATTTTGATTACATTAGTG
1 TATTTTTATTTTG-TAAAATTAGTG
1919307 TATTTTTATT
1 TATTTTTATT
1919317 GAAATATTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 7 0.25
24 4 0.14
25 17 0.61
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (24 bp):
TATTTTTATTTTGTAAAATTAGTG
Found at i:1919383 original size:39 final size:39
Alignment explanation
Indices: 1919340--1919418 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
1919330 ATTGGTATTT
1919340 TAAATAAAAATATAAATTATTTGGTAATAATTAAAATTA
1 TAAATAAAAATATAAATTATTTGGTAATAATTAAAATTA
*
1919379 TAAATGAAAATATAAATTATTTGGTAATAATTAAAATTA
1 TAAATAAAAATATAAATTATTTGGTAATAATTAAAATTA
1919418 T
1 T
1919419 TTTTGTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.39
Consensus pattern (39 bp):
TAAATAAAAATATAAATTATTTGGTAATAATTAAAATTA
Found at i:1919413 original size:19 final size:20
Alignment explanation
Indices: 1919353--1919420 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1919343 ATAAAAATAT
1919353 AAATTATTTGGTAATAATTA
1 AAATTATTTGGTAATAATTA
*
1919373 AAATTATAAAT-G-AA-AA-TA
1 AAATTAT--TTGGTAATAATTA
1919391 TAAATTATTTGGTAATAATTA
1 -AAATTATTTGGTAATAATTA
1919412 AAATTATTT
1 AAATTATTT
1919421 TTGTTATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
17 1 0.03
18 3 0.08
19 11 0.28
20 20 0.51
21 3 0.08
22 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (20 bp):
AAATTATTTGGTAATAATTA
Found at i:1919431 original size:21 final size:21
Alignment explanation
Indices: 1919353--1919443 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 21
1919343 ATAAAAATAT
*
1919353 AAATTA-TTTGGTAATAATTA
1 AAATTATTTTTGTAATAATTA
***
1919373 AAATTATAAATG-AA-AA-TA
1 AAATTATTTTTGTAATAATTA
*
1919391 TAAATTA-TTTGGTAATAATTA
1 -AAATTATTTTTGTAATAATTA
*
1919412 AAATTATTTTTGTTATAATTA
1 AAATTATTTTTGTAATAATTA
* *
1919433 CATTTATTTTT
1 AAATTATTTTT
1919444 TTAGTTGTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
18 3 0.06
19 10 0.19
20 16 0.30
21 24 0.45
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (21 bp):
AAATTATTTTTGTAATAATTA
Found at i:1920778 original size:26 final size:25
Alignment explanation
Indices: 1920732--1920780 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1920722 TCTAATAAAA
*
1920732 TTATGACATGCCTCATACTAGAGGT
1 TTATGACATGCCACATACTAGAGGT
1920757 TTATGAACATAGCCACAT-CTAGAG
1 TTATG-ACAT-GCCACATACTAGAG
1920781 TGCAAATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 10 0.48
27 6 0.29
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (25 bp):
TTATGACATGCCACATACTAGAGGT
Found at i:1930189 original size:36 final size:36
Alignment explanation
Indices: 1930148--1930219 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1930138 CTTATGTTAG
*
1930148 GTTTATACAAAACTTGACATATAGTCTATAGTAGAA
1 GTTTATACAAAACTTGACATACAGTCTATAGTAGAA
1930184 GTTTATACAAAACTTGACATACAGTCTATAGTAGAA
1 GTTTATACAAAACTTGACATACAGTCTATAGTAGAA
1930220 AATGCTTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (36 bp):
GTTTATACAAAACTTGACATACAGTCTATAGTAGAA
Found at i:2147953 original size:79 final size:79
Alignment explanation
Indices: 2147846--2148048 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
2147836 TAATAACAGG
* * * * * * *
2147846 GTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGAGGA-TTA
1 GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATC-AAGATTTA
**
2147910 GAAAAAAAAATCGG-
65 GAAAAAAAAGCCGGA
* * *
2147924 GATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTT
1 G-TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAGATTTA
** *
2147989 GGGAATAAAGCCGGA
65 GAAAAAAAAGCCGGA
* *
2148004 GTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
2148049 GAAATAACGA
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
78 3 0.03
79 100 0.96
80 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAGATTTAG
AAAAAAAAGCCGGA
Found at i:2148044 original size:28 final size:28
Alignment explanation
Indices: 2148004--2148071 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
2147994 TAAAGCCGGA
** * *
2148004 GTTGGAGTATCCCCTCGGAAGTAACGGG
1 GTTGGAGTATCCCCGAGGAAATAACGAG
*
2148032 GTTGGAGTATCCCCGATGAAATAACGAG
1 GTTGGAGTATCCCCGAGGAAATAACGAG
2148060 GTTGGAGTATCC
1 GTTGGAGTATCC
2148072 TCGATTATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (28 bp):
GTTGGAGTATCCCCGAGGAAATAACGAG
Found at i:2148123 original size:52 final size:52
Alignment explanation
Indices: 2148060--2148393 Score: 179
Period size: 52 Copynumber: 6.3 Consensus size: 52
2148050 AAATAACGAG
*
2148060 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * * ** * *
2148112 GTTGGAGTATCCTCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * * *
2148165 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
2148216 GTTGGAGTATCCCC--TCA-GAAAAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTATGAAAAA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
* *
2148270 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGA
* * * *
2148325 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
2148376 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
2148394 GTGGAGAATT
Statistics
Matches: 213, Mismatches: 43, Indels: 53
0.69 0.14 0.17
Matches are distributed among these distances:
48 6 0.03
50 1 0.00
51 36 0.17
52 79 0.37
53 26 0.12
54 30 0.14
55 26 0.12
56 3 0.01
57 3 0.01
58 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:2148246 original size:27 final size:27
Alignment explanation
Indices: 2148207--2148283 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
2148197 TTTTAGCGAT
* *
2148207 AAAACCGGAGTTGGAGTATCCCCTCA-G
1 AAAAACGGGGTTGGAGTATCCCC-CATG
*
2148234 AAAAACGGGGTTGGAGTATCCCCGATG
1 AAAAACGGGGTTGGAGTATCCCCCATG
**
2148261 ATTAACGGGGTTGGAGTATCCCC
1 AAAAACGGGGTTGGAGTATCCCC
2148284 GATTGTGAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.02
27 43 0.98
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (27 bp):
AAAAACGGGGTTGGAGTATCCCCCATG
Found at i:2148340 original size:55 final size:51
Alignment explanation
Indices: 2148274--2148401 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 51
2148264 AACGGGGTTG
* *
2148274 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTG-AGAAATTAGTG---TTTTGAAAATAAAATCGGAGTTA
* *
2148329 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGAGTTA
* *
2148380 GAATATCCTCGATTGTGGAGAA
1 GAGTATCCCCGATTGT-GAGAA
2148402 TTGATAAACT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
51 34 0.54
52 2 0.03
53 4 0.06
54 8 0.13
55 15 0.24
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
Found at i:2148380 original size:106 final size:102
Alignment explanation
Indices: 2148060--2148396 Score: 251
Period size: 106 Copynumber: 3.2 Consensus size: 102
2148050 AAATAACGAG
* *
2148060 GTTGGAGTATCCTCGATTATGAAAAATTG-GTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTGTGT-TTTTTGGAAATAAAATCGGAGTTGGAGTATCC
* * *
2148124 TCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
65 CCGATTAAA-GAAAATTAGTGTTTTGAAAATAAAA-C-GGA
* *
2148165 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTG-TTTTAGCG--ATAAAACCGGAGTTGGAGTAT
1 GTTGGAGTATCCCCGATTGT-GAAAAATT-GTGTTTTTTG-GAAATAAAATCGGAGTTGGAGTAT
* * * *** ** * *
2148226 CCCC--TCAGAA-AAACGGGGTTGGAGTATCCCCGATGAT-TAACGGG
63 CCCCGATTA-AAGAAA----ATT--AGTGT-TTTGAAAATAAAACGGA
*
2148270 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTAGAGTAT
1 GTTGGAGTATCCCCGATTGTGAA-AAATT-GTG-TTTTTTGGAAATAAAATCGGAGTTGGAGTAT
*
2148335 CCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
63 CCCCGATTAAAGAAAATTAGTGTTTTGAAAATAAAA-CGGA
* *
2148376 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
2148397 GAGAATTGAT
Statistics
Matches: 175, Mismatches: 34, Indels: 45
0.69 0.13 0.18
Matches are distributed among these distances:
101 3 0.02
102 2 0.01
103 2 0.01
104 44 0.25
105 26 0.15
106 52 0.30
107 8 0.05
108 9 0.05
109 23 0.13
110 1 0.01
111 5 0.03
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (102 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
CGATTAAAGAAAATTAGTGTTTTGAAAATAAAACGGA
Found at i:2148395 original size:212 final size:212
Alignment explanation
Indices: 2147993--2148398 Score: 604
Period size: 212 Copynumber: 1.9 Consensus size: 212
2147983 TATTTTGGGA
* * *
2147993 ATAAAGCCGGAGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAGAAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
2148058 AGGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * *
2148123 CTCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCAGGATTGGAATATCCCCGATTGTGGAA
2148188 AAATTAGTGTTTTAGCG
196 AAATTAGTGTTTTAGCG
*
2148205 ATAAAACCGGAGTTGGAGTATCCCCTCAGAA-AAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAGAAACGGGGTTGGAGTATCCCCGATGAAATAACG
* * *
2148268 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTAGAGT
66 AGGTTGGAGTATCCCCGATTATGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGAGTTAGAGT
* * * *
2148333 ATCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATC-GGAGTTGGAATATCCTCGATTGT
128 ATCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCAGGA-TTGGAATATCCCCGATTGT
2148396 GGA
192 GGA
2148399 GAATTGATAA
Statistics
Matches: 174, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
210 28 0.16
211 32 0.18
212 74 0.43
213 40 0.23
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCAGAAGAAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCAGGATTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:2150769 original size:13 final size:13
Alignment explanation
Indices: 2150751--2150776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2150741 ACAAAGATCC
2150751 ATGTATCGATACA
1 ATGTATCGATACA
2150764 ATGTATCGATACA
1 ATGTATCGATACA
2150777 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2150772 original size:33 final size:33
Alignment explanation
Indices: 2150730--2150796 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2150720 AAAATTTCCA
***
2150730 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2150763 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2150796 A
1 A
2150797 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2150840 original size:19 final size:18
Alignment explanation
Indices: 2150816--2150883 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2150806 CAGTAGCTAA
2150816 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2150835 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2150850 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2150867 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2150884 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2150856 original size:13 final size:13
Alignment explanation
Indices: 2150838--2150862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2150828 ACAATACTTA
2150838 TGTATCGATACAT
1 TGTATCGATACAT
2150851 TGTATCGATACA
1 TGTATCGATACA
2150863 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2150860 original size:32 final size:32
Alignment explanation
Indices: 2150819--2150881 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2150809 TAGCTAATTA
*
2150819 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2150851 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2150882 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2150963 original size:21 final size:21
Alignment explanation
Indices: 2150939--2150995 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2150929 CATTTGTAGG
2150939 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2150960 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
2150981 ATGTATCGATACATT
1 ATGTATCGATACATT
2150996 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2151026 original size:17 final size:17
Alignment explanation
Indices: 2151004--2151037 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2150994 TTTAATTTTT
2151004 TTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTCAA
2151021 TTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTCAA
2151038 ACACTTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTTTTCAA
Found at i:2154884 original size:10 final size:10
Alignment explanation
Indices: 2154869--2154922 Score: 71
Period size: 10 Copynumber: 5.8 Consensus size: 10
2154859 CCTTCGTACC
2154869 AAAAAAAACT
1 AAAAAAAACT
2154879 AAAAAAAACT
1 AAAAAAAACT
2154889 AAAAAAAA-T
1 AAAAAAAACT
2154898 AAAAAAAAC-
1 AAAAAAAACT
*
2154907 -AAACAAAC-
1 AAAAAAAACT
2154915 AAAAAAAA
1 AAAAAAAA
2154923 AGAAGGGTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
8 7 0.17
9 15 0.38
10 18 0.45
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAAAAAACT
Found at i:2154894 original size:19 final size:18
Alignment explanation
Indices: 2154870--2154922 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
2154860 CTTCGTACCA
2154870 AAAAAAACTAAAAAAAAC
1 AAAAAAACTAAAAAAAAC
*
2154888 TAAAAAAAATAAAAAAAAC
1 -AAAAAAACTAAAAAAAAC
*
2154907 AAACAAAC-AAAAAAAA
1 AAAAAAACTAAAAAAAA
2154923 AGAAGGGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 8 0.26
18 6 0.19
19 17 0.55
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAACTAAAAAAAAC
Found at i:2156155 original size:13 final size:12
Alignment explanation
Indices: 2156110--2156182 Score: 58
Period size: 13 Copynumber: 5.6 Consensus size: 12
2156100 TAATTCACCA
2156110 TTTGTCAAGAAAT
1 TTTGTC-AGAAAT
* *
2156123 TATCGTCAAAAACT
1 T-TTGTCAGAAA-T
2156137 TTTGTC-GACAAT
1 TTTGTCAGA-AAT
2156149 GTTTGTCAGAAAT
1 -TTTGTCAGAAAT
2156162 TTTGTCAAGAAAT
1 TTTGTC-AGAAAT
2156175 TTTCGTCA
1 TTT-GTCA
2156183 ATACGACCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
12 8 0.16
13 30 0.61
14 11 0.22
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (12 bp):
TTTGTCAGAAAT
Found at i:2156569 original size:202 final size:205
Alignment explanation
Indices: 2156279--2156683 Score: 498
Period size: 202 Copynumber: 2.0 Consensus size: 205
2156269 TGGCATCCTT
* * * * * * * *
2156279 TCAAAGCCCACATGTAAGTGGCATCTTTTCAAATCCCATAGGTTAGTGGCATCCTCTCAAAGCCC
1 TCAAAGCCCACAAGTAAGTAGCACCCTTTCAAAACCCACAAGTTAGTGGCACCCTCTCAAAGCCC
* * * *
2156344 ACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTT-AAGCCTACACAAGTT
66 ACAAGTCAGTAGCAACCTTTCAAAGCCCACAAATCAGTGGCA-CCCTTTAAAGCCCACACAAGTT
* *
2156408 AGTGGCAACCTT-TCTCGAAGCC-CACAAGTCAGTGGC-ACC-CCTTCAAGCCCACACAAGTTGG
130 AGTGGCAACCTTCTCT-AAAGCCACACAAGTCAGTGGCAACCTCCTTAAAGCCCACACAAGTTGG
2156469 TGGCAACCTCTC
194 TGGCAACCTCTC
* * *
2156481 TCAAAGCCCACAAGTCAGTAGCACCCTTTCAAAACCCACAAGTTAGTGGCACCCTTTCTAAGCCC
1 TCAAAGCCCACAAGTAAGTAGCACCCTTTCAAAACCCACAAGTTAGTGGCACCCTCTCAAAGCCC
* * *
2156546 ACAAGTTAGTAG-AACCTTTTCAAAGCCCACAAATTAGTGGCACCTTTTCAAAGCCCACACAAGT
66 ACAAGTCAGTAGCAACC-TTTCAAAGCCCACAAATCAGTGGCACCCTTT-AAAGCCCACACAAGT
* * * **
2156610 TGGTGGCAACCTTCTCTAAAGCCTATACAAGTCGGTGGCAACCTTTTTAAAGCCCACACAAGTTG
129 TAGTGGCAACCTTCTCTAAAGCC-ACACAAGTCAGTGGCAACCTCCTTAAAGCCCACACAAGTTG
2156675 GTGGCAACC
193 GTGGCAACC
2156684 CTTCTAAACC
Statistics
Matches: 170, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
201 8 0.05
202 87 0.51
203 30 0.18
204 3 0.02
205 12 0.07
206 3 0.02
207 27 0.16
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (205 bp):
TCAAAGCCCACAAGTAAGTAGCACCCTTTCAAAACCCACAAGTTAGTGGCACCCTCTCAAAGCCC
ACAAGTCAGTAGCAACCTTTCAAAGCCCACAAATCAGTGGCACCCTTTAAAGCCCACACAAGTTA
GTGGCAACCTTCTCTAAAGCCACACAAGTCAGTGGCAACCTCCTTAAAGCCCACACAAGTTGGTG
GCAACCTCTC
Found at i:2156595 original size:84 final size:84
Alignment explanation
Indices: 2156188--2156667 Score: 378
Period size: 84 Copynumber: 5.6 Consensus size: 84
2156178 CGTCAATACG
** * * * ** *
2156188 ACCCTTCTCAAAGCCCGTAAGTCAATGGC-ACCCTTTCAAAGCCCATGAGTCAGTGGCATCCTTT
1 ACCCTT-TCAAAGCCCACAAGTTAGTGGCAACCTTTTCAAAGCCCACAAGTTAGTGGCA-CCTTT
* * *
2156252 CAAAGCCCATAAATAAGTGGC
64 CAAAGCCCACAAGTCAGTGGC
* * * * * * * *
2156273 ATCCTTTCAAAGCCCACATGTAAGTGGC-ATCTTTTCAAATCCCATAGGTTAGTGGCATCCTCTC
1 ACCCTTTCAAAGCCCACAAGTTAGTGGCAACCTTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTC
2156337 AAAGCCCACAAGTCAGTGGC
65 AAAGCCCACAAGTCAGTGGC
* * * *
2156357 ATCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTT--AAGCCTACACAAGTTAGTGGCAACCTT
1 ACCCTTTCAAAGCCCACAAGTTAGTGGCAACCTTTTCAAAGCC--CACAAGTTAGTGGC-ACC-T
*
2156420 TCTCGAAGCCCACAAGTCAGTGGC
62 T-TCAAAGCCCACAAGTCAGTGGC
* * * * *
2156444 ACCCCTTC-AAGCCCACACAAGTTGGTGGCAACCTCTCTCAAAGCCCACAAGTCAGTAGCACCCT
1 ACCCTTTCAAAG-CC-CACAAGTTAGTGGCAACCT-TTTCAAAGCCCACAAGTTAGTGGCA-CCT
* *
2156508 TTCAAAACCCACAAGTTAGTGGC
62 TTCAAAGCCCACAAGTCAGTGGC
* * *
2156531 ACCCTTTCTAAGCCCACAAGTTAGTAG-AACCTTTTCAAAGCCCACAAATTAGTGGCACCTTTTC
1 ACCCTTTCAAAGCCCACAAGTTAGTGGCAACCTTTTCAAAGCCCACAAGTTAGTGGCACC-TTTC
**
2156595 AAAGCCCACACAAGTTGGTGGC
65 AAAG-CC-CACAAGTCAGTGGC
* * ** *
2156617 AACCTTCTCTAAAGCCTATACAAGTCGGTGGCAACCTTTTTAAAGCCCACA
1 ACCCTT-TC-AAAGCC--CACAAGTTAGTGGCAACCTTTTCAAAGCCCACA
2156668 CAAGTTGGTG
Statistics
Matches: 320, Mismatches: 54, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
83 6 0.02
84 117 0.37
85 30 0.09
86 34 0.11
87 59 0.18
88 26 0.08
89 16 0.05
90 9 0.03
91 23 0.07
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (84 bp):
ACCCTTTCAAAGCCCACAAGTTAGTGGCAACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTTCA
AAGCCCACAAGTCAGTGGC
Found at i:2156603 original size:28 final size:28
Alignment explanation
Indices: 2156190--2156667 Score: 340
Period size: 28 Copynumber: 16.6 Consensus size: 28
2156180 TCAATACGAC
* ** * *
2156190 CCTTCTCAAAGCCCGTAAGTCAATGGCA
1 CCTTTTCAAAGCCCACAAGTTAGTGGCA
* ** *
2156218 CCCTTTCAAAGCCCATGAGTCAGTGGCA
1 CCTTTTCAAAGCCCACAAGTTAGTGGCA
* * *
2156246 TCC-TTTCAAAGCCCATAAATAAGTGGCA
1 -CCTTTTCAAAGCCCACAAGTTAGTGGCA
* *
2156274 TCC-TTTCAAAGCCCACATGTAAGTGGCA
1 -CCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * *
2156302 TCTTTTCAAATCCCATAGGTTAGTGGCA
1 CCTTTTCAAAGCCCACAAGTTAGTGGCA
* *
2156330 TCC-TCTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTTCAAAGCCCACAAGTTAGTGGCA
*
2156358 TCC-TTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTTCAAAGCCCACAAGTTAGTGGCA
*
2156386 CCCCTTT--AAGCCTACACAAGTTAGTGGCAA
1 -CCTTTTCAAAGCC--CACAAGTTAGTGGC-A
* *
2156416 CCTTTCTCGAAGCCCACAAGTCAGTGGCA
1 CCTTT-TCAAAGCCCACAAGTTAGTGGCA
** *
2156445 CCCCTTC-AAGCCCACACAAGTTGGTGGCAA
1 CCTTTTCAAAG-CC-CACAAGTTAGTGGC-A
* * *
2156475 CCTCTCTCAAAGCCCACAAGTCAGTAGCA
1 CCT-TTTCAAAGCCCACAAGTTAGTGGCA
* *
2156504 CCCTTTCAAAACCCACAAGTTAGTGGCA
1 CCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * *
2156532 CCCTTTCTAAGCCCACAAGTTAGTAGAA
1 CCTTTTCAAAGCCCACAAGTTAGTGGCA
*
2156560 CCTTTTCAAAGCCCACAAATTAGTGGCA
1 CCTTTTCAAAGCCCACAAGTTAGTGGCA
*
2156588 CCTTTTCAAAGCCCACACAAGTTGGTGGCAA
1 CCTTTTCAAAG-CC-CACAAGTTAGTGGC-A
* * **
2156619 CCTTCTCTAAAGCCTATACAAGTCGGTGGCAA
1 CCTTTTC-AAAGCC--CACAAGTTAGTGGC-A
*
2156651 CCTTTTTAAAGCCCACA
1 CCTTTTCAAAGCCCACA
2156668 CAAGTTGGTG
Statistics
Matches: 371, Mismatches: 59, Indels: 39
0.79 0.13 0.08
Matches are distributed among these distances:
27 9 0.02
28 223 0.60
29 47 0.13
30 41 0.11
31 19 0.05
32 32 0.09
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (28 bp):
CCTTTTCAAAGCCCACAAGTTAGTGGCA
Found at i:2162995 original size:97 final size:97
Alignment explanation
Indices: 2162879--2163066 Score: 295
Period size: 97 Copynumber: 1.9 Consensus size: 97
2162869 TGTTTTCGAC
* * *
2162879 GATGATAATTTAGGCAAAAATAGGATTTAAATCATGACAAGTTTAAAAACGGGGTTAGAGTATCC
1 GATGATAATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAACGAGGTTAGAGTATCC
* * *
2162944 CCTCGAAAGAATGGGGTCAGAGTATCTCTGAT
66 CCTCGAAAAAATAGAGTCAGAGTATCTCTGAT
* *
2162976 GATGATAATTTAAGTAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACGAGGTTAGAGTATCC
1 GATGATAATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAACGAGGTTAGAGTATCC
*
2163041 CCTCGAAAAAATAGAGTTAGAGTATC
66 CCTCGAAAAAATAGAGTCAGAGTATC
2163067 CCGATGAATA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 82 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (97 bp):
GATGATAATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAACGAGGTTAGAGTATCC
CCTCGAAAAAATAGAGTCAGAGTATCTCTGAT
Found at i:2165497 original size:51 final size:52
Alignment explanation
Indices: 2165383--2165505 Score: 124
Period size: 51 Copynumber: 2.4 Consensus size: 52
2165373 TGATACATTG
* * * **
2165383 AAGAACGTATCGATACATTTTGGTCAAAAACTCAAAATGTATTGATAAAATA
1 AAGAATGTATCGATACATTTAGGTCAAAAACCCAAAATGTATCAATAAAATA
* * ** *
2165435 AAGAATATATCGATACATTTAGGT-TAAAACCCGTAATGTATCAATATAATGA
1 AAGAATGTATCGATACATTTAGGTCAAAAACCCAAAATGTATCAATAAAAT-A
*
2165487 AA-AATGTATCGAAACATTT
1 AAGAATGTATCGATACATTT
2165506 TCATTCTAGA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
51 34 0.59
52 24 0.41
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (52 bp):
AAGAATGTATCGATACATTTAGGTCAAAAACCCAAAATGTATCAATAAAATA
Found at i:2169060 original size:13 final size:13
Alignment explanation
Indices: 2169042--2169067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2169032 TACACAAAGT
2169042 ATGTATCGATACA
1 ATGTATCGATACA
2169055 ATGTATCGATACA
1 ATGTATCGATACA
2169068 CCAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2169065 original size:32 final size:33
Alignment explanation
Indices: 2169024--2169087 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2169014 TAGCCAAACT
*
2169024 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAT-TGTATCGATACAA
2169056 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
2169088 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Done.