Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 7 of 333
Found at i:1711542 original size:23 final size:25
Alignment explanation
Indices: 1711499--1711544 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1711489 TGTACCTAAT
1711499 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
1711524 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
1711545 ACAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:1712068 original size:30 final size:30
Alignment explanation
Indices: 1712032--1712146 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
1712022 TAGGTACAAG
* *
1712032 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
1712062 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
1712092 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1712122 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
1712147 TAAGAAAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:1713953 original size:21 final size:21
Alignment explanation
Indices: 1713929--1713968 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1713919 TTTTAATTTA
**
1713929 AAAATCATTTAAATAATAAAT
1 AAAATCATGGAAATAATAAAT
*
1713950 AAAATGATGGAAATAATAA
1 AAAATCATGGAAATAATAA
1713969 TAATAAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (21 bp):
AAAATCATGGAAATAATAAAT
Found at i:1719812 original size:21 final size:21
Alignment explanation
Indices: 1719783--1719824 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1719773 CAAACTCATC
1719783 AAGCACATCATTG-GCCTCGT
1 AAGCACATCATTGAGCCTCGT
*
1719803 AAGCAACATCTTTGAGCCTCGT
1 AAGC-ACATCATTGAGCCTCGT
1719825 CAACCAACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (21 bp):
AAGCACATCATTGAGCCTCGT
Found at i:1720846 original size:20 final size:21
Alignment explanation
Indices: 1720816--1720870 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1720806 TTTTAATTTT
1720816 TTAATTTTTTTAAAAT-TTAAA
1 TTAA-TTTTTTAAAATGTTAAA
* *
1720837 TTAATTTTTTACAATGTTATA
1 TTAATTTTTTAAAATGTTAAA
1720858 -TATATTTTTTAAA
1 TTA-ATTTTTTAAA
1720871 TTTGTTTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTAATTTTTTAAAATGTTAAA
Found at i:1726075 original size:210 final size:209
Alignment explanation
Indices: 1725711--1726522 Score: 1139
Period size: 210 Copynumber: 3.9 Consensus size: 209
1725701 TGGAAAGCTC
* * * * * * * *
1725711 TCCAATTTGTTGCACCAGTT-AATTGACAGGTTTTGAAGGGAGGAAAATCCTTCCAAATCTGGAA
1 TCCAATTTGTCGCAACA-TTGAACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGA
* * * * * *
1725775 TTGAACTTAAATTAGAGCAAAACTC-TAGATCTAATTTTTTGAGACAACTGGAGGTAGATAATCC
65 TCGAACTTAAATTAG-G-ACAACCCATAAATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCC
*
1725839 ATCTCCAATCTTGCTTAATTTTTCACAACTGAAAATGTGAAGCTTTTCAAGAGATGAACATCCTC
128 ATCTCCAATCTTGCTTAATTTTTCACAACTGAAAATGCGAAGCTTTTCAAGAGATGAACATCCTC
1725904 CAGTTATTGGAAGAACT
193 CAGTTATTGGAAGAACT
* *
1725921 TCCAATTTGTCGCAACATTGAACTGACAGATATTGAAGAGAGAAAAATCCTTCCAAATTTGAGAT
1 TCCAATTTGTCGCAACATTGAACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGAT
* *
1725986 CGAACTTAAATTAGGACAACCCAATAAATCTAATTTTTTGAGACAAGTGGAAGTAGATAATCCAT
66 CGAACTTAAATTAGGACAACCC-ATAAATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCAT
* * * *
1726051 CTCCAATCTTGCTTAATGTTTCACAACTGGAAATGCTAAGCTTTTCAAGAGATGAACATCCTCCG
130 CTCCAATCTTGCTTAATTTTTCACAACTGAAAATGCGAAGCTTTTCAAGAGATGAACATCCTCCA
*
1726116 GTTATAGGAAGAACT
195 GTTATTGGAAGAACT
* * *
1726131 TCCAATTTGTCACAGCCA-TCAACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGA
1 TCCAATTTGTCGCA-ACATTGAACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGA
*
1726195 TCGAACTTAAATTAGGACATCCCCATAAATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCA
65 TCGAACTTAAATTAGGACA-ACCCATAAATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCA
*
1726260 TCTCCAATCTTGTTTAATTTTTCACAACT-AGAAATGCGAAGCTTTTCAAGAGATGAACATCCTC
129 TCTCCAATCTTGCTTAATTTTTCACAACTGA-AAATGCGAAGCTTTTCAAGAGATGAACATCCTC
1726324 CAGTTATTGGAAGAACT
193 CAGTTATTGGAAGAACT
* * *
1726341 TCCAATTTGTTGCAACTTTGAACTGACAGATATTGAAGAGAGGAAATTCCTTCCAAATTTGGGAT
1 TCCAATTTGTCGCAACATTGAACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGAT
**** * * *
1726406 CGAACTTAAATTAGGACAATAGTTTAAATGTAATTCTTTGAGACAAGTGGAGGTTGATAATCCGT
66 CGAACTTAAATTAGGACAA-CCCATAAATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCAT
* *
1726471 CTCCAATCTTGCTTAATTTGTCACATAATG-AAATGCGAAGCTTTTCAAGAGA
130 CTCCAATCTTGCTTAATTTTTCACA-ACTGAAAATGCGAAGCTTTTCAAGAGA
1726523 ATAACATTGT
Statistics
Matches: 539, Mismatches: 53, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
208 5 0.01
209 4 0.01
210 523 0.97
211 7 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (209 bp):
TCCAATTTGTCGCAACATTGAACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGAT
CGAACTTAAATTAGGACAACCCATAAATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATC
TCCAATCTTGCTTAATTTTTCACAACTGAAAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAG
TTATTGGAAGAACT
Found at i:1729691 original size:6 final size:6
Alignment explanation
Indices: 1729672--1729709 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1729662 TCTAGAACAG
*
1729672 TCTTATT TCCTTT TCTTTT TCTTTT TCTTTT T-TTTT TC
1 TCTT-TT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC
1729710 AAAACAGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 5 0.18
6 20 0.71
7 3 0.11
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:1733759 original size:16 final size:16
Alignment explanation
Indices: 1733693--1733759 Score: 89
Period size: 16 Copynumber: 4.2 Consensus size: 16
1733683 TGAATTATTT
* *
1733693 ATTACAGGTCTATTCT
1 ATTACAGCTCTATTCC
*
1733709 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
* *
1733725 ATTACAACTCTATTAC
1 ATTACAGCTCTATTCC
1733741 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
1733757 ATT
1 ATT
1733760 CCTTCCAACC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.28, C:0.24, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:1737013 original size:14 final size:15
Alignment explanation
Indices: 1736994--1737023 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1736984 TTAAATTAGG
1736994 ACAATTCTTT-AGAC
1 ACAATTCTTTGAGAC
1737008 ACAATTCTTTGAGAC
1 ACAATTCTTTGAGAC
1737023 A
1 A
1737024 AGTGGAGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (15 bp):
ACAATTCTTTGAGAC
Found at i:1737289 original size:210 final size:209
Alignment explanation
Indices: 1736941--1737522 Score: 767
Period size: 210 Copynumber: 2.8 Consensus size: 209
1736931 ATCAACTGAT
* * *
1736941 AGATTTTGAAGAGATGAAAATCCTTCCAAATTTGGGATCGAACTTAAATTAGGACAATTCTTTAG
1 AGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATAAGGACAA-TCTTAAG
* *
1737006 A-CACAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCGATCTTGCTTAACTTTTCACAT
65 ATC-TAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCGATCTTGCTTAACTTTTCACAA
* * *
1737070 GATGAAATGCTAAGATTTTCAAGAAAAGAACATCCTCCGGTTATTGGAAGTACTTCCAATTCGTT
129 CAGGAAATGCTAAGATTTTCAAGAAAAGAACATCCTCCGGTTATTGGAAGTACTTCCAATTCGTA
* *
1737135 GCACCATT-TAATTGAC
194 GCAAC-TTAGAATTGAC
* *
1737151 AGATTTTGAAGAGAGGAAAATCCTTCCAAATTAGGAATCGAACTTAAATAAGGACAATCTTCAAG
1 AGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATAAGGACAATCTT-AAG
* * * * *
1737216 ATCTAATTCTTTGAGACAAGTGGAGGTTGATAATCCATCTCCAATCTTGCTTAATTTTTCGCAAC
65 ATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCGATCTTGCTTAACTTTTCACAAC
* * * * *
1737281 CGGAAATGCTAAGCTTTTCAAGAGATGAACATCGTCCGGTTATTGGAAGTACTTCCAATTCGTAG
130 AGGAAATGCTAAGATTTTCAAGAAAAGAACATCCTCCGGTTATTGGAAGTACTTCCAATTCGTAG
1737346 CAACTTAGAATTGAC
195 CAACTTAGAATTGAC
* * * *
1737361 AGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATTAA-AACACTCATATA
1 AGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAA-TAAGGACAATCTTA-A
*
1737425 GATATAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCGATCTTGCTTAAAC-TTTCACA
64 GATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCGATCTTGCTT-AACTTTTCACA
** * * * * *
1737489 TGATGAAATGCGAAGCTTTTCAAGAGAATAACAT
128 ACAGGAAATGCTAAGATTTTCAAGAAAAGAACAT
1737523 TGTCCCGTTA
Statistics
Matches: 325, Mismatches: 41, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
209 7 0.02
210 312 0.96
211 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (209 bp):
AGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATAAGGACAATCTTAAGA
TCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCGATCTTGCTTAACTTTTCACAACA
GGAAATGCTAAGATTTTCAAGAAAAGAACATCCTCCGGTTATTGGAAGTACTTCCAATTCGTAGC
AACTTAGAATTGAC
Found at i:1743307 original size:17 final size:17
Alignment explanation
Indices: 1743287--1743320 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1743277 AAATAGATTT
1743287 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
1743304 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
1743321 ACTTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:1744003 original size:17 final size:17
Alignment explanation
Indices: 1743983--1744016 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1743973 ATGTTTAGGT
1743983 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
1744000 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
1744017 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:1744371 original size:16 final size:15
Alignment explanation
Indices: 1744352--1744405 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 15
1744342 ATATGTAATT
1744352 ATTAATTAATTTAAAA
1 ATTAATTAATTT-AAA
1744368 ATTAATTAAAGATTTAAA
1 ATTAATT--A-ATTTAAA
*
1744386 ATAAATTAATTTAAA
1 ATTAATTAATTTAAA
1744401 ATTAA
1 ATTAA
1744406 AAAGCTTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 11 0.33
16 8 0.24
18 10 0.30
19 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTAATTAATTTAAA
Found at i:1744408 original size:22 final size:22
Alignment explanation
Indices: 1744366--1744408 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1744356 ATTAATTTAA
*
1744366 AAATTAATTAAAGATTTAAAAT
1 AAATTAATTAAAGATTAAAAAT
1744388 AAATTAATTTAAA-ATTAAAAA
1 AAATTAA-TTAAAGATTAAAAA
1744409 GCTTCACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATTAATTAAAGATTAAAAAT
Found at i:1746399 original size:47 final size:47
Alignment explanation
Indices: 1746290--1746400 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
1746280 CCGGAATAAG
* * *
1746290 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * * *
1746337 CACAAAGTACTTCATCGGAACAAATCTGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
1746384 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
1746401 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 1 0.02
47 50 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:1747172 original size:4 final size:4
Alignment explanation
Indices: 1747163--1747197 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1747153 CCCTTTTCTA
*
1747163 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TCTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1747198 TTTTTTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:1749703 original size:24 final size:24
Alignment explanation
Indices: 1749658--1749710 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1749648 TTGTCTTTTT
1749658 CTTTTATTCTTTTTCTTATTTTAA
1 CTTTTATTCTTTTTCTTATTTTAA
*
1749682 GTTTTATT-TTTTT-TTAACTTTTAA
1 CTTTTATTCTTTTTCTT-A-TTTTAA
1749706 CTTTT
1 CTTTT
1749711 TCTCAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 2 0.08
23 6 0.24
24 17 0.68
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (24 bp):
CTTTTATTCTTTTTCTTATTTTAA
Found at i:1749790 original size:50 final size:54
Alignment explanation
Indices: 1749728--1749909 Score: 153
Period size: 57 Copynumber: 3.3 Consensus size: 54
1749718 TTTAAAAAAC
*
1749728 TTTAAATGTATA-TTTTA-AAT-TT-GTTTATTTATTTATTATTAATTTTAAAT
1 TTTAAATATATATTTTTATAATCTTAGTTTATTTATTTATTATTAATTTTAAAT
* *
1749778 TTTAAATATATATTTTTTATTTATCCTTATTTTATTTATTTATTATTAATTTTAAAT
1 TTTAAATATATA-TTTTTA-TAAT-CTTAGTTTATTTATTTATTATTAATTTTAAAT
* * * * *
1749835 TTTAAAATTTAAATGTTGTCT-TTATCCTTA-TTTATTTTATTTATTTTTTATTCTT-AAT
1 TTT-AAATATATAT-TT-T-TATAAT-CTTAGTTTA-TTTATTTATTATTAATT-TTAAAT
1749893 TTTAAATATATATTTTT
1 TTTAAATATATATTTTT
1749910 GAAATTATTT
Statistics
Matches: 110, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
50 11 0.10
52 5 0.05
54 3 0.03
55 1 0.01
56 4 0.04
57 43 0.39
58 39 0.35
59 3 0.03
60 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (54 bp):
TTTAAATATATATTTTTATAATCTTAGTTTATTTATTTATTATTAATTTTAAAT
Found at i:1749869 original size:57 final size:58
Alignment explanation
Indices: 1749751--1749904 Score: 197
Period size: 58 Copynumber: 2.7 Consensus size: 58
1749741 TTTAAATTTG
* * *
1749751 TTTATTTATTTATTATTAATTTTAAATTTT-AAATATATATTTTTTATTTATCCTTAT
1 TTTATTTATTTATTATTAATTTTAAATTTTAAAATATAAATGTTGTATTTATCCTTAT
* *
1749808 TTTATTTATTTATTATTAATTTTAAATTTTAAAATTTAAATGTTGTCTTTATCCTTA-
1 TTTATTTATTTATTATTAATTTTAAATTTTAAAATATAAATGTTGTATTTATCCTTAT
* *
1749865 TTTATTTTATTTATTTTTTATTCTT-AATTTTAAATATATA
1 TTTA-TTTATTTATTATTAATT-TTAAATTTTAAA-ATATA
1749905 TTTTTGAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
57 34 0.40
58 45 0.53
59 6 0.07
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (58 bp):
TTTATTTATTTATTATTAATTTTAAATTTTAAAATATAAATGTTGTATTTATCCTTAT
Found at i:1750059 original size:20 final size:19
Alignment explanation
Indices: 1750034--1750089 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
1750024 TTTATAATAT
1750034 TTTAAATGTATATTTTAAAA
1 TTTAAAT-TATATTTTAAAA
*
1750054 TTTAAAATT-TATTTTTTAAA
1 TTT-AAATTATA-TTTTAAAA
1750074 TATTAAA-TATATTTTA
1 T-TTAAATTATATTTTA
1750090 TTTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 7 0.23
20 17 0.57
21 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTAAATTATATTTTAAAA
Found at i:1750061 original size:21 final size:22
Alignment explanation
Indices: 1750023--1750077 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1750013 TTATTATTAG
*
1750023 TTTTATAATATTTTAAATGTATA
1 TTTTA-AATATTTAAAATGTATA
* *
1750046 TTTTAAA-ATTTAAAATTTATT
1 TTTTAAATATTTAAAATGTATA
1750067 TTTTAAATATT
1 TTTTAAATATT
1750078 AAATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 18 0.64
22 5 0.18
23 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAAATATTTAAAATGTATA
Found at i:1750079 original size:21 final size:21
Alignment explanation
Indices: 1750023--1750088 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
1750013 TTATTATTAG
* *
1750023 TTTTATAATATTTTAAATGTATA
1 TTTTA-AATA-TTTAAATATATT
*
1750046 TTTTAAA-ATTTAAAATTTATT
1 TTTTAAATATTT-AAATATATT
1750067 TTTTAAATA-TTAAATATATT
1 TTTTAAATATTTAAATATATT
1750087 TT
1 TT
1750089 ATTTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 13 0.34
21 17 0.45
22 3 0.08
23 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTAAATATTTAAATATATT
Found at i:1750427 original size:17 final size:18
Alignment explanation
Indices: 1750407--1750441 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1750397 TAAAGTTTTT
*
1750407 TTAAAA-TTAAGAAAAAG
1 TTAAAAGTTAAAAAAAAG
1750424 TTAAAAGTTAAAAAAAAG
1 TTAAAAGTTAAAAAAAAG
1750442 AAAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (18 bp):
TTAAAAGTTAAAAAAAAG
Found at i:1750459 original size:24 final size:25
Alignment explanation
Indices: 1750415--1750465 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
1750405 TTTTAAAATT
* *
1750415 AAGAAAAAGTTAAAAGTTAAAA-AA
1 AAGAAAAAGTAAAAAGATAAAAGAA
1750439 AAGAAAAAG-AAAAAGAATAAAAGAA
1 AAGAAAAAGTAAAAAG-ATAAAAGAA
1750464 AA
1 AA
1750466 AGACAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 14 0.61
25 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (25 bp):
AAGAAAAAGTAAAAAGATAAAAGAA
Found at i:1751794 original size:144 final size:144
Alignment explanation
Indices: 1751561--1751972 Score: 513
Period size: 144 Copynumber: 2.9 Consensus size: 144
1751551 TACACAGCCT
** ** * * *
1751561 CCTTAGAGAAGAGAGATTTCTGAATGACTGTGGCAAGGCTTCTATTCCTTGAAACTCTTCTATCG
1 CCTTAGAGAAGAGAGATTTCCCAACCACTCTGGCAAGGCTTCTATTCCATGAAACCCTTCTATCG
* * * * *
1751626 TTAAATATTCAAGGGTAGAAAGGAGTTGAAGTTGGTGAGTAAAACTCTTTAGC-TTCCGAAAACC
66 TCAAATCTTCAAGGGTAGTAAGGAGTTGAAGTTGGTGAGGAAGACTCTTTAGCTTTCC-AAAACC
*
1751690 ACTCAAATATAGATG
130 ACTCAAATATAGACG
* * ** *
1751705 CCTTAGAGAAGAGAGATTTCCCAACCATTCTGGCAAGGCTTCTATTTCATGAAACCCCAGC-ATA
1 CCTTAGAGAAGAGAGATTTCCCAACCACTCTGGCAAGGCTTCTATTCCATGAAA-CCCTTCTATC
* * * *
1751769 GTCAAATCTTCAAGGGCAGTGAGGAGTTGCAGCTGGTGAGGAAGACTCTTTAGCTTTCCAAAACC
65 GTCAAATCTTCAAGGGTAGTAAGGAGTTGAAGTTGGTGAGGAAGACTCTTTAGCTTTCCAAAACC
1751834 ACTCAAATATAGACG
130 ACTCAAATATAGACG
* ** *
1751849 CCTTAGAGAAGAGAGATTTCCCAACCAGTCTGGCAAGGCTTCTATTCCACCAAACCTTTCTATCG
1 CCTTAGAGAAGAGAGATTTCCCAACCACTCTGGCAAGGCTTCTATTCCATGAAACCCTTCTATCG
* * * *
1751914 TCAAATCTTCAAGGGTGGTTAGGAGTTGAAATTGGTGAGGGAGACTCTTTAGCGTTTCC
66 TCAAATCTTCAAGGGTAGTAAGGAGTTGAAGTTGGTGAGGAAGACTCTTTAGC-TTTCC
1751973 CAACCAATCA
Statistics
Matches: 227, Mismatches: 37, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
143 3 0.01
144 212 0.93
145 12 0.05
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (144 bp):
CCTTAGAGAAGAGAGATTTCCCAACCACTCTGGCAAGGCTTCTATTCCATGAAACCCTTCTATCG
TCAAATCTTCAAGGGTAGTAAGGAGTTGAAGTTGGTGAGGAAGACTCTTTAGCTTTCCAAAACCA
CTCAAATATAGACG
Found at i:1752728 original size:210 final size:207
Alignment explanation
Indices: 1752365--1753567 Score: 1276
Period size: 210 Copynumber: 5.7 Consensus size: 207
1752355 CAACGGATAC
* * * * **
1752365 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATCGAACTTAAATTAGGACAACATTTTAGAT
1 ATTTTGAAGAGAGGAAAATCCTTTC-AATTTGGAATGGAACTTAAATTAGGACAATA-CATAG-T
* * * * ** * *
1752430 C-TAATTCTTTAAGAAAAGTGGAGGTAGATAATCCGTCTCCAATCTTACTTAACTTTTT-GCAAT
63 CGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCAATCTTGCTTAA-TTTTTCGCAAC
* * * * *
1752493 CGAAAATGCTAAG-TTTTATAAGAGATGAACATCCTCCGGTAATCGGAAGAACTTCCAATTCGCT
127 CGGAAATGCTAAGCTTTT-CAAGAGATGAACATCCTCCGGTTATCGGAAGAACTCCCAATTC-TT
1752557 GCACCATCT-AATTGACAG
190 GCACC-TCTCAATTGACAG
* * ** * * *
1752575 ATTTTGAAGAGACGAAAATCCTTTCAATTCCGGAATTAAAATCAAGTTAGGACAATTACATAGTC
1 ATTTTGAAGAGAGGAAAATCCTTTCAATT-TGGAATGGAACTTAAATTAGGACAA-TACATAGTC
* * *
1752640 GTAATTTTTTGAGACAAGTAGAGGTTGACAGCCCGTCTCCAATCTTGCTTAATTTTTCGCAAAC-
64 GTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCAATCTTGCTTAATTTTTCGCAACCG
* * * * *
1752704 GATAATGCTAAGCTCTTCAAGAGATGAACATTCTCCCGTTATCGGAAGAACTTCCAATTTTTTGC
129 GA-AATGCTAAGCTTTTCAAGAGATGAACATCCTCCGGTTATCGGAAGAACTCCCAA-TTCTTGC
1752769 ACCTCTCAATTGACAG
192 ACCTCTCAATTGACAG
* * * **
1752785 ATTTTGAAGAGAGGAAAATCTTTTCAAGTTAGGAATAGAACTTAAATTAGGACAATATTTTAGAT
1 ATTTTGAAGAGAGGAAAATCCTTTCAA-TTTGGAATGGAACTTAAATTAGGACAATA-CATAG-T
* * ** *
1752850 C-TAATT-TTCTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTTTTCGCAAC
63 CGTAATTCTT-TGAGACAAGTGGAGGTTGACAGCCCGTCTCCAATCTTGCTTAATTTTTCGCAAC
* * * *
1752913 CAGAAAT-CTTAAGCTTTTGAAGAGATGAACATCCTCCGGTTATTGGAAGAACTCCCAATTTTTT
127 CGGAAATGC-TAAGCTTTTCAAGAGATGAACATCCTCCGGTTATCGGAAGAACTCCCAA-TTCTT
*
1752977 GCAGCTCTCAATTGACAG
190 GCACCTCTCAATTGACAG
* * * * * *
1752995 ATATTGAAGAGAGGAAAAGCCTTCCAAATTTGGAATGGAACTTACATTAGGACAATCCGATAGAC
1 ATTTTGAAGAGAGGAAAATCCTTTC-AATTTGGAATGGAACTTAAATTAGGACAATAC-ATAG-T
*
1753060 CG-AATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTGCTTAATTTTTCGCAACC
63 CGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCAATCTTGCTTAATTTTTCGCAACC
* * * *
1753124 GGAAATCCTAAGCTTTTCAAGGGATGAACATCCTCCGATTATCGGAAGAACTCCCAAATCCTTGC
128 GGAAATGCTAAGCTTTTCAAGAGATGAACATCCTCCGGTTATCGGAAGAACTCCC-AATTCTTGC
* *
1753189 ACCTGTAAATTGACAG
192 ACCTCTCAATTGACAG
* * * * *
1753205 ATTTTGAAGAGACGATAATCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATCAAATAGAC
1 ATTTTGAAGAGAGGAAAATCCTTTC-AATTTGGAATGGAACTTAAATTAGGACAAT-ACATAGTC
* *
1753270 CTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCGATCTTGCTTAATTTTTCGCAACCG
64 GTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCAATCTTGCTTAATTTTTCGCAACCG
* * * *
1753335 GATATTCTAAGCTTTTCAAGAGATGAACATCCTCCGATAATCGGAAGAACTCCCAATTTCTTGCA
129 GAAATGCTAAGCTTTTCAAGAGATGAACATCCTCCGGTTATCGGAAGAACTCCCAA-TTCTTGCA
** *
1753400 GTTCTCAATTGACAA
193 CCTCTCAATTGACAG
* * *
1753415 ATTTTGAAGAGAGGAAAATCCTTCTAAATTTGGAATCGAACTTAAATTAGGACAA-GCATGTAGG
1 ATTTTGAAGAGAGGAAAATCCTT-TCAATTTGGAATGGAACTTAAATTAGGACAATACA--TA-G
* * ** * * * *
1753479 T-GTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTTTCCAATCTTACTTAATTTTTCACAAA
62 TCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCAATCTTGCTTAATTTTTCGCAAC
**
1753543 ATGAAATGCTAAGCTTTTCAAGAGA
127 CGGAAATGCTAAGCTTTTCAAGAGA
1753568 AGAGCATTGT
Statistics
Matches: 844, Mismatches: 122, Indels: 54
0.83 0.12 0.05
Matches are distributed among these distances:
208 1 0.00
209 23 0.03
210 800 0.95
211 20 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (207 bp):
ATTTTGAAGAGAGGAAAATCCTTTCAATTTGGAATGGAACTTAAATTAGGACAATACATAGTCGT
AATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCAATCTTGCTTAATTTTTCGCAACCGGA
AATGCTAAGCTTTTCAAGAGATGAACATCCTCCGGTTATCGGAAGAACTCCCAATTCTTGCACCT
CTCAATTGACAG
Found at i:1753152 original size:420 final size:417
Alignment explanation
Indices: 1752365--1753584 Score: 1467
Period size: 420 Copynumber: 2.9 Consensus size: 417
1752355 CAACGGATAC
* *
1752365 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATCGAACTTAAATTAGGACAACATTTTAGAT
1 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATAGAACTTAAATTAGGACAATATTTTAGAT
* * * *
1752430 CTAATTCTTTAAGAAAAGTGGAGGTAGATAATCCGTCTCCAATCTTACTTAACTTTTT-GCAATC
66 CTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAA-TTTTTCGCAACC
* * *
1752494 GAAAATGC-TAAG-TTTTATAAGAGATGAACATCCTCCGGTAATCGGAAGAACTTCCAA-TTCGC
130 G-AAAT-CTTAAGCTTTT-CAAGAGATGAACATCCTCCGGTAATCGGAAGAACTCCCAATTTC-T
* * * * ** * *
1752556 TGCACCATCT-AATTGACAGATTTTGAAGAGACGAAAATCCTTTC-AATTCCGGAATTAAAATCA
191 TGCAGC-TCTCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATT-TGGAATCGAACTTA
* * * * *
1752619 AGTTAGGACAATTAC-ATAGTCGTAATTTTTTGAGACAAGTAGAGGTTGACAGCCCGTCTCCAAT
254 A-TTAGGACAA-TCCGATAGCCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAAT
*
1752683 CTTGCTTAATTTTTCGCAAACGATAATGCTAAGCTCTTCAAGAGATGAACATTCTCCCGTTATCG
317 CTTGCTTAATTTTTCGCAAACGA-AATGCTAAGCTTTTCAAGAGATGAACATTCTCCCGTTATCG
* * ** *
1752748 GAAGAACTTCCAATTTTTTGCACCTCTCAATTGACAG
381 GAAGAACTCCCAAATCCTTGCACCTCTAAATTGACAG
* * * * *
1752785 ATTTTGAAGAGAGGAAAATCTTTTCAAGTTAGGAATAGAACTTAAATTAGGACAATATTTTAGAT
1 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATAGAACTTAAATTAGGACAATATTTTAGAT
*
1752850 CTAATT-TTCTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTTTTCGCAACC
66 CTAATTCTT-TGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACC
* * * *
1752914 AGAAATCTTAAGCTTTTGAAGAGATGAACATCCTCCGGTTATTGGAAGAACTCCCAATTTTTTGC
130 -GAAATCTTAAGCTTTTCAAGAGATGAACATCCTCCGGTAATCGGAAGAACTCCCAATTTCTTGC
* * *
1752979 AGCTCTCAATTGACAGATATTGAAGAGAGGAAAAGCCTTCCAAATTTGGAATGGAACTTACATTA
194 AGCTCTCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGAATCGAACTTA-ATTA
1753044 GGACAATCCGATAGACCG-AATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTGC
258 GGACAATCCGATAG-CCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTGC
* * * *
1753108 TTAATTTTTCGCAACCGGAAATCCTAAGCTTTTCAAGGGATGAACATCCT-CCGATTATCGGAAG
322 TTAATTTTTCGCAAAC-GAAATGCTAAGCTTTTCAAGAGATGAACATTCTCCCG-TTATCGGAAG
*
1753172 AACTCCCAAATCCTTGCACCTGTAAATTGACAG
385 AACTCCCAAATCCTTGCACCTCTAAATTGACAG
* * **
1753205 ATTTTGAAGAGACGATAATCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATCA-AATAGA
1 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATAGAACTTAAATTAGGACAAT-ATTTTAGA
* * * ** *
1753269 CCTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCGATCTTGCTTAATTTTTCGCAACC
65 TCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACC
* *
1753334 GGATAT-TCTAAGCTTTTCAAGAGATGAACATCCTCCGATAATCGGAAGAACTCCCAATTTCTTG
130 -GAAATCT-TAAGCTTTTCAAGAGATGAACATCCTCCGGTAATCGGAAGAACTCCCAATTTCTTG
* * *
1753398 CAGTTCTCAATTGACAAATTTTGAAGAGAGGAAAATCCTTCTAAATTTGGAATCGAACTTAAATT
193 CAGCTCTCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGAATCGAACTT-AATT
* * ** * * ** * *
1753463 AGGACAAGCATG-TAGGTGTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTTTCCAATCTTA
257 AGGACAATC-CGATAGCCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTG
* * * * *
1753527 CTTAATTTTTCACAAAATGAAATGCTAAGCTTTTCAAGAGAAGAGCATTGTCCCGTTA
321 CTTAATTTTTCGC-AAACGAAATGCTAAGCTTTTCAAGAGATGAACATTCTCCCGTTA
1753585 GTGGAACACT
Statistics
Matches: 687, Mismatches: 92, Indels: 42
0.84 0.11 0.05
Matches are distributed among these distances:
419 18 0.03
420 643 0.94
421 26 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (417 bp):
ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATAGAACTTAAATTAGGACAATATTTTAGAT
CTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACCG
AAATCTTAAGCTTTTCAAGAGATGAACATCCTCCGGTAATCGGAAGAACTCCCAATTTCTTGCAG
CTCTCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGAATCGAACTTAATTAGGA
CAATCCGATAGCCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTGCTTAA
TTTTTCGCAAACGAAATGCTAAGCTTTTCAAGAGATGAACATTCTCCCGTTATCGGAAGAACTCC
CAAATCCTTGCACCTCTAAATTGACAG
Found at i:1754386 original size:15 final size:15
Alignment explanation
Indices: 1754366--1754396 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1754356 AAAACAATAT
1754366 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
1754381 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
1754396 A
1 A
1754397 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:1757766 original size:15 final size:15
Alignment explanation
Indices: 1757756--1757785 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1757746 TCCCTTCTTG
1757756 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
1757771 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
1757786 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:1758553 original size:17 final size:18
Alignment explanation
Indices: 1758527--1758565 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1758517 CAAATTGTGG
1758527 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
1758543 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
1758561 AAAAT
1 AAAAT
1758566 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:1758742 original size:15 final size:15
Alignment explanation
Indices: 1758722--1758752 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1758712 AAAACAATAT
1758722 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
1758737 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
1758752 A
1 A
1758753 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:1761238 original size:20 final size:20
Alignment explanation
Indices: 1761215--1761252 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1761205 TTATTTTTAC
1761215 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
1761235 ATATATTAATAAATTTAT
1 ATATATTAATAAATTTAT
1761253 TGCAATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:1763728 original size:6 final size:6
Alignment explanation
Indices: 1763714--1763768 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
1763704 GATGGGTGAG
* *
1763714 GGGGAA GGAGAA GGAGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
1763762 GGGGAA G
1 GGGGAA G
1763769 AAGCTTCAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:1764212 original size:17 final size:17
Alignment explanation
Indices: 1764192--1764247 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
1764182 TTTATAATTA
1764192 TAAAAAATTTTAAAAAT
1 TAAAAAATTTTAAAAAT
1764209 TAAAAAGATTTT-AAAAT
1 TAAAAA-ATTTTAAAAAT
*
1764226 TCAAAAAGAATTATAAAAAT
1 T--AAAA-AATTTTAAAAAT
1764246 TA
1 TA
1764248 TATAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 12 0.36
18 6 0.18
19 8 0.24
20 7 0.21
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
TAAAAAATTTTAAAAAT
Found at i:1764214 original size:18 final size:18
Alignment explanation
Indices: 1764187--1764247 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
1764177 AATAATTTAT
1764187 AATTATAAAAAATTTTAAA
1 AATTA-AAAAAATTTTAAA
*
1764206 AATTAAAAAGATTTT-AA
1 AATTAAAAAAATTTTAAA
*
1764223 AATTCAAAAAGAATTATAAA
1 AATT-AAAAA-AATTTTAAA
1764243 AATTA
1 AATTA
1764248 TATAAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 6 0.17
18 14 0.39
19 10 0.28
20 6 0.17
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (18 bp):
AATTAAAAAAATTTTAAA
Found at i:1764584 original size:24 final size:23
Alignment explanation
Indices: 1764531--1764586 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
1764521 GTAAGCGAAT
1764531 AAAGGAATAAGAAAGACAAATAG
1 AAAGGAATAAGAAAGACAAATAG
1764554 AAA-GAATAATGTAAAAGA-AAATA-
1 AAAGGAATAA-G--AAAGACAAATAG
1764577 AAAGGAATAA
1 AAAGGAATAA
1764587 AAAATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 6 0.21
23 7 0.24
24 11 0.38
25 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.12
Consensus pattern (23 bp):
AAAGGAATAAGAAAGACAAATAG
Found at i:1765114 original size:29 final size:29
Alignment explanation
Indices: 1765082--1765140 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1765072 CGATTTTGGG
1765082 TGATCATTTGATTTTAATAGTGAATTTTA
1 TGATCATTTGATTTTAATAGTGAATTTTA
1765111 TGATCATTTGATTTTAATAGTGAATTTTA
1 TGATCATTTGATTTTAATAGTGAATTTTA
1765140 T
1 T
1765141 ACTCTTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (29 bp):
TGATCATTTGATTTTAATAGTGAATTTTA
Found at i:1769131 original size:38 final size:38
Alignment explanation
Indices: 1769072--1769177 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
1769062 CATTTTTAAG
*
1769072 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
1769109 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
1769147 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
1769178 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:1769570 original size:19 final size:17
Alignment explanation
Indices: 1769546--1769662 Score: 59
Period size: 16 Copynumber: 6.9 Consensus size: 17
1769536 TAATACTAGA
1769546 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
1769565 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
*
1769585 AAAATATATACAATGA-T
1 AAAATATATATAAT-ATT
* * *
1769602 AATATATATAAAAGA-T
1 AAAATATATATAATATT
* *
1769618 -ATATGTATAT-ATAATT
1 AAAATATATATAAT-ATT
*
1769634 -ATATA-ATATAATATT
1 AAAATATATATAATATT
1769649 AAAATATA-ATAATA
1 AAAATATATATAATA
1769663 CGACATAAGA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
14 1 0.01
15 16 0.20
16 19 0.24
17 17 0.21
18 2 0.03
19 8 0.10
20 9 0.11
21 2 0.03
22 6 0.08
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:1769875 original size:3 final size:3
Alignment explanation
Indices: 1769860--1769895 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1769850 AAGCATAAAC
* *
1769860 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1769896 CATTGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1770051 original size:6 final size:6
Alignment explanation
Indices: 1770009--1770042 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1769999 ATAAAAATAT
*
1770009 ATACTA ATACATA ATAGTA ATACTA ATACTA ATA
1 ATACTA ATAC-TA ATACTA ATACTA ATACTA ATA
1770043 ATACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (6 bp):
ATACTA
Found at i:1770542 original size:11 final size:11
Alignment explanation
Indices: 1770526--1770561 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1770516 AGAAAAAAAA
1770526 GAAGAGAGAGG
1 GAAGAGAGAGG
*
1770537 GAAGAGAGAAG
1 GAAGAGAGAGG
1770548 GAAGAGAGAAGG
1 GAAGAGAG-AGG
1770560 GA
1 GA
1770562 GGGGGGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAGG
Found at i:1770690 original size:17 final size:17
Alignment explanation
Indices: 1770668--1770706 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1770658 AGGTAAAAAA
* * *
1770668 TTTATTTTTTGTTTTTT
1 TTTATTTGTTGTATATT
1770685 TTTATTTGTTGTATATT
1 TTTATTTGTTGTATATT
1770702 TTTAT
1 TTTAT
1770707 GTTAAATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (17 bp):
TTTATTTGTTGTATATT
Found at i:1771277 original size:21 final size:21
Alignment explanation
Indices: 1771252--1771307 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
1771242 TTGAAAGTTT
1771252 ATAATATTT-AAATATTAAAAA
1 ATAATATTTAAAAT-TTAAAAA
1771273 ATAATATTTAAAATTTAAAAA
1 ATAATATTTAAAATTTAAAAA
1771294 AGTAAT-TTTAAAAT
1 A-TAATATTTAAAAT
1771308 ATATATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 25 0.76
22 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATATTTAAAATTTAAAAA
Found at i:1771373 original size:21 final size:22
Alignment explanation
Indices: 1771349--1771390 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1771339 TTAAAATTTT
*
1771349 TAAAATTAATA-ATAAATAAAA
1 TAAAATAAATAGATAAATAAAA
1771370 TAAAATAAATAGATAAATAAA
1 TAAAATAAATAGATAAATAAA
1771391 GAGAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
TAAAATAAATAGATAAATAAAA
Found at i:1771385 original size:18 final size:18
Alignment explanation
Indices: 1771359--1771415 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1771349 TAAAATTAAT
*
1771359 AATAAATAAAATAAAATA
1 AATAGATAAAATAAAATA
*
1771377 AATAGAT-AAATAAAGAGA
1 AATAGATAAAATAAA-ATA
* *
1771395 AAAAGATAAAAGAAAAGTA
1 AATAGATAAAATAAAA-TA
1771414 AA
1 AA
1771416 AAAAAGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.23
18 15 0.48
19 9 0.29
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AATAGATAAAATAAAATA
Found at i:1771422 original size:10 final size:10
Alignment explanation
Indices: 1771394--1771438 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
1771384 AAATAAAGAG
1771394 AAAAAGATAAA
1 AAAAAG-TAAA
1771405 AGAAAAGTAAA
1 A-AAAAGTAAA
1771416 AAAAAGT--A
1 AAAAAGTAAA
1771424 AAAAAGTAAA
1 AAAAAGTAAA
1771434 AAAAA
1 AAAAA
1771439 AAGTACTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.26
10 12 0.39
11 6 0.19
12 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (10 bp):
AAAAAGTAAA
Found at i:1777170 original size:51 final size:51
Alignment explanation
Indices: 1777099--1777218 Score: 213
Period size: 51 Copynumber: 2.4 Consensus size: 51
1777089 CTGATCACAT
1777099 TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
1777150 TTATCACTTATTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
* *
1777201 TTGTCACTTGTCACTGAT
1 TTATCACTTGTTACTGAT
1777219 AAACATGTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (51 bp):
TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:1777248 original size:24 final size:24
Alignment explanation
Indices: 1777220--1777267 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1777210 GTCACTGATA
1777220 AACATGTCAAATTGCATATTTTTT
1 AACATGTCAAATTGCATATTTTTT
*
1777244 AACATGTCAACTTGCATATTTTTT
1 AACATGTCAAATTGCATATTTTTT
1777268 GTGCTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (24 bp):
AACATGTCAAATTGCATATTTTTT
Found at i:1782764 original size:50 final size:50
Alignment explanation
Indices: 1782640--1782938 Score: 393
Period size: 50 Copynumber: 5.8 Consensus size: 50
1782630 GATAATAACA
* ** *
1782640 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGG
* * * *
1782691 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
*
1782741 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1782791 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
* * * *
1782841 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TC-T-CGG
*
1782896 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1782939 TTACCCAAAT
Statistics
Matches: 219, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
49 1 0.00
50 141 0.64
51 33 0.15
52 1 0.00
53 2 0.01
54 1 0.00
55 2 0.01
56 38 0.17
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
Found at i:1783054 original size:13 final size:13
Alignment explanation
Indices: 1783033--1783064 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1783023 GCTTGGATCA
*
1783033 TCATCAAATAAAT
1 TCATAAAATAAAT
1783046 TCATAAAATAAAT
1 TCATAAAATAAAT
1783059 TCATAA
1 TCATAA
1783065 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1783310 original size:30 final size:30
Alignment explanation
Indices: 1783276--1783333 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1783266 CCTTGACTCT
*
1783276 AACTTTTTCAAAATTACAATTTTACCCCTA
1 AACTTTTACAAAATTACAATTTTACCCCTA
* * *
1783306 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTACCCC
1783334 AAGGCTTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTACCCCTA
Found at i:1786668 original size:17 final size:17
Alignment explanation
Indices: 1786638--1786678 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1786628 TTAGGTTGAT
* *
1786638 TAATTGAAATTTCTTTC
1 TAATTAAAACTTCTTTC
1786655 TAATTAAAACTTCTTTC
1 TAATTAAAACTTCTTTC
1786672 TAATTAA
1 TAATTAA
1786679 CTCAATCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (17 bp):
TAATTAAAACTTCTTTC
Found at i:1787468 original size:28 final size:28
Alignment explanation
Indices: 1787436--1787490 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1787426 AGAAATCAGT
1787436 CAGATACAGTCTGGGCCTGAGCCCATTA
1 CAGATACAGTCTGGGCCTGAGCCCATTA
* * *
1787464 CAGATTCAGTTTGGGCCTTAGCCCATT
1 CAGATACAGTCTGGGCCTGAGCCCATT
1787491 TGGATACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (28 bp):
CAGATACAGTCTGGGCCTGAGCCCATTA
Found at i:1789858 original size:19 final size:20
Alignment explanation
Indices: 1789806--1789865 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
1789796 AAAAAAAACC
*
1789806 TTAAAAATTGTAAAAAAGAATAT
1 TTAAAAATT-TACAAAA-AA-AT
1789829 TTAAAAA-TTACAAAAAAA-
1 TTAAAAATTTACAAAAAAAT
1789847 TTAAAAATTTACAAAAAAA
1 TTAAAAATTTACAAAAAAA
1789866 ATATAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 7 0.20
19 12 0.34
20 2 0.06
21 6 0.17
22 1 0.03
23 7 0.20
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (20 bp):
TTAAAAATTTACAAAAAAAT
Found at i:1789949 original size:9 final size:8
Alignment explanation
Indices: 1789903--1789949 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
1789893 AATATTTAAA
*
1789903 AAAATATT
1 AAAATTTT
1789911 AGAAATTTT
1 A-AAATTTT
*
1789920 AAATTTTT
1 AAAATTTT
1789928 AAAATTTT
1 AAAATTTT
1789936 AAAATTTT
1 AAAATTTT
1789944 ATAAAT
1 A-AAAT
1789950 CACATCTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 23 0.68
9 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
AAAATTTT
Found at i:1797246 original size:19 final size:20
Alignment explanation
Indices: 1797217--1797260 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
1797207 ATAGATTGAA
1797217 ATTCTCCAAAAATAAAATTT
1 ATTCTCCAAAAATAAAATTT
1797237 ATTC-CCAAAAATAAAATTT
1 ATTCTCCAAAAATAAAATTT
1797256 ATTCT
1 ATTCT
1797261 ATGTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTCTCCAAAAATAAAATTT
Found at i:1802500 original size:49 final size:49
Alignment explanation
Indices: 1802428--1802521 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
1802418 TGCTATGCAA
* *
1802428 TGCTAAACTTGGTCTTTCACTGTCTACACTCTTATCACTGTTTATACAT
1 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTATACAT
1802477 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTAT
1 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTAT
1802522 CCCTTCTAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.43
Consensus pattern (49 bp):
TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTATACAT
Found at i:1808606 original size:5 final size:6
Alignment explanation
Indices: 1808589--1808614 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1808579 TTAATCATTA
1808589 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
1808615 GAAATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:1809905 original size:23 final size:23
Alignment explanation
Indices: 1809879--1809924 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1809869 TACAGGTGAG
1809879 GAAGTTAGTGCCAAAGACTATAA
1 GAAGTTAGTGCCAAAGACTATAA
1809902 GAAGTTAGTGCCAAAGACTATAA
1 GAAGTTAGTGCCAAAGACTATAA
1809925 AGTCTACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (23 bp):
GAAGTTAGTGCCAAAGACTATAA
Found at i:1810229 original size:192 final size:192
Alignment explanation
Indices: 1809902--1810336 Score: 735
Period size: 192 Copynumber: 2.3 Consensus size: 192
1809892 AAGACTATAA
*
1809902 GAAGTTAGTGCCAAAGACTATAAAGTCTACTCAATTTGGGGCCACTAGTGCTATCTTAAATAAAG
1 GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGCTATCTTAAATAAAG
* * * *
1809967 CATGGTCAACAATGGCGGGTTTTACGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
66 AATGGTCAACAATGGCAGGTTTCAAGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
* * *
1810032 TCACACTTTCATTTGTAGGTTACGGTGATGGACTTATATTTTTTGAGCAAAATACAGATGAG
131 TCACACTTTCATTTGTAGGTGACGGTGATGGACTTACAGTTTTTGAGCAAAATACAGATGAG
* *
1810094 GAAGTTAGTGCCAAAGACTACAAAGTCCACTCAATTTGGGGCAACTAGTGCTATCTTAAATAAAG
1 GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGCTATCTTAAATAAAG
*
1810159 AATGGTCAACAATGGTAGGTTTCAAGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
66 AATGGTCAACAATGGCAGGTTTCAAGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
* * * *
1810224 TCACACTTTCATTTGTAGGTGATGGTGATGGACTTACGGTTTTTGAGCAAGATATAGATGAG
131 TCACACTTTCATTTGTAGGTGACGGTGATGGACTTACAGTTTTTGAGCAAAATACAGATGAG
1810286 GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGC
1 GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGC
1810337 ATTTCACATT
Statistics
Matches: 226, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
192 226 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (192 bp):
GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGCTATCTTAAATAAAG
AATGGTCAACAATGGCAGGTTTCAAGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
TCACACTTTCATTTGTAGGTGACGGTGATGGACTTACAGTTTTTGAGCAAAATACAGATGAG
Found at i:1841839 original size:15 final size:15
Alignment explanation
Indices: 1841821--1841850 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1841811 TAAATTTCAG
1841821 TTAATTCAATTAATC
1 TTAATTCAATTAATC
*
1841836 TTAATTGAATTAATC
1 TTAATTCAATTAATC
1841851 GAAATATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAATTCAATTAATC
Found at i:1846174 original size:39 final size:39
Alignment explanation
Indices: 1846115--1846215 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
1846105 ATCGTGATTT
** * *
1846115 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
*
1846154 GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
*
1846193 GAAGCCCGAAGGCTAATTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
1846216 TCACCAGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.15
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
Found at i:1846197 original size:21 final size:21
Alignment explanation
Indices: 1846133--1846197 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1846123 AAATCTAGCT
* *
1846133 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAATGCTAAATG
** * *
1846154 GAAGC-C-CGAAGGCTAACT-
1 GAAGCACATAAATGCTAAATG
1846172 GAAGCACATAAATGCTAAATG
1 GAAGCACATAAATGCTAAATG
1846193 GAAGC
1 GAAGC
1846198 CCGAAGGCTA
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 5 0.16
19 7 0.23
20 9 0.29
21 10 0.32
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.14
Consensus pattern (21 bp):
GAAGCACATAAATGCTAAATG
Found at i:1849434 original size:30 final size:30
Alignment explanation
Indices: 1849387--1849443 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1849377 CATCAAATTA
1849387 AAACTTATATATCAAATTACATATTTAACT
1 AAACTTATATATCAAATTACATATTTAACT
*
1849417 AAACTTCATATAT-AAATTTCATATTTA
1 AAACTT-ATATATCAAATTACATATTTA
1849444 TCCCTAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (30 bp):
AAACTTATATATCAAATTACATATTTAACT
Found at i:1849512 original size:12 final size:12
Alignment explanation
Indices: 1849495--1849519 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1849485 GAAATCACCC
1849495 ATCATTTAATTA
1 ATCATTTAATTA
1849507 ATCATTTAATTA
1 ATCATTTAATTA
1849519 A
1 A
1849520 AGCTTCTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
ATCATTTAATTA
Found at i:1850643 original size:23 final size:24
Alignment explanation
Indices: 1850617--1850667 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
1850607 ATGATTTAGG
1850617 AAATTATAATTTTATTTC-ATCAA
1 AAATTATAATTTTATTTCAATCAA
1850640 AAA-TATAATTTTATTTCAATCAA
1 AAATTATAATTTTATTTCAATCAA
*
1850663 TAATT
1 AAATT
1850668 TTAAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 14 0.56
23 10 0.40
24 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTATAATTTTATTTCAATCAA
Found at i:1851857 original size:17 final size:16
Alignment explanation
Indices: 1851831--1851861 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1851821 CAATTAATTT
1851831 ATTTTTAAAAATTAAG
1 ATTTTTAAAAATTAAG
1851847 ATTTTTAAAAATTAA
1 ATTTTTAAAAATTAA
1851862 AAAAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTTTTAAAAATTAAG
Found at i:1853293 original size:17 final size:17
Alignment explanation
Indices: 1853266--1853306 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1853256 ACTTTTTTAA
1853266 TAAAAAT-AATA-AATAT
1 TAAAAATAAATATAA-AT
1853282 TAAAAATAAATATAAAT
1 TAAAAATAAATATAAAT
*
1853299 TACAAATA
1 TAAAAATA
1853307 TACATATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 13 0.59
18 2 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAATAAATATAAAT
Found at i:1863339 original size:23 final size:23
Alignment explanation
Indices: 1863310--1863356 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1863300 ACAAGCTTGA
1863310 TGAGAGATTATTTCCCATACATT
1 TGAGAGATTATTTCCCATACATT
*
1863333 TGAGAGATTATTTCCCATATATT
1 TGAGAGATTATTTCCCATACATT
1863356 T
1 T
1863357 TTACCTACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (23 bp):
TGAGAGATTATTTCCCATACATT
Found at i:1865327 original size:50 final size:50
Alignment explanation
Indices: 1865252--1865351 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
1865242 AAGCTTGCAA
*
1865252 CACCATTGATAGATAAGTCACTTTTGTTTAAAATTAATGATATTTGTCTT
1 CACCATTGATAGATAAGTCACTTTTGTTTAAAATTAACGATATTTGTCTT
1865302 CACCATTGATAGATTAA-TCACTTTTGTTTAAAATTAACGATATTTGTCTT
1 CACCATTGATAGA-TAAGTCACTTTTGTTTAAAATTAACGATATTTGTCTT
1865352 ACATTCATAC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 45 0.94
51 3 0.06
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (50 bp):
CACCATTGATAGATAAGTCACTTTTGTTTAAAATTAACGATATTTGTCTT
Found at i:1870626 original size:23 final size:24
Alignment explanation
Indices: 1870572--1870620 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1870562 GTAAGAAAAA
1870572 AACACTTTAGCCATTTTTATAGAT
1 AACACTTTAGCCATTTTTATAGAT
1870596 AACACTTTAGCCATTTTTATAGAT
1 AACACTTTAGCCATTTTTATAGAT
1870620 A
1 A
1870621 CCCTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (24 bp):
AACACTTTAGCCATTTTTATAGAT
Found at i:1881233 original size:132 final size:132
Alignment explanation
Indices: 1881097--1881348 Score: 294
Period size: 131 Copynumber: 1.9 Consensus size: 132
1881087 TTGAACATCA
* * *
1881097 CCTTCGTTTTAAAGTGTTTTCTTA-AAAACATGAGTAAAAACCTAAAGGAATATTCGAATGTTTT
1 CCTTCGTTTTAAAG-GATTT-TTAGAAAACACGAGTAAAAACCTAAAGGAATATTCGAATATTTT
* * *
1881161 GACCAAACGAGAAGTCACAACCCAACACGA-TAGGGCATGATTCC-CGAATTGTCAAACACAAAG
64 GACCAAACGAGAAATCACAACCCAACAC-ATTAGGGCACGATTCCGCGAATTGCCAAACACAAAG
1881224 TATTG
128 TATTG
* * *** * * *
1881229 CCTTCGTTTTAAAGGATTTTTAGAAGACACGAGTGAAATTTTGAAGGGATATTCGATTATTTTGA
1 CCTTCGTTTTAAAGGATTTTTAGAAAACACGAGTAAAAACCTAAAGGAATATTCGAATATTTTGA
* * **
1881294 GCAAACGCGAAATTGCAACCCAACACATTAGGGCACGATTCCGCGAATTGCCAAA
66 CCAAACGAGAAATCACAACCCAACACATTAGGGCACGATTCCGCGAATTGCCAAA
1881349 TATCGAATCT
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
130 4 0.04
131 70 0.71
132 25 0.25
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (132 bp):
CCTTCGTTTTAAAGGATTTTTAGAAAACACGAGTAAAAACCTAAAGGAATATTCGAATATTTTGA
CCAAACGAGAAATCACAACCCAACACATTAGGGCACGATTCCGCGAATTGCCAAACACAAAGTAT
TG
Found at i:1881381 original size:131 final size:131
Alignment explanation
Indices: 1881141--1881381 Score: 290
Period size: 131 Copynumber: 1.8 Consensus size: 131
1881131 TAAAAACCTA
* * *
1881141 AAGGAATATTCGAATGTTTTGACCAAACGAGAAGTCACAACCCAACACGATAGGGCATGATTCCC
1 AAGGAATATTCGAATATTTTGACCAAACGAGAAATCACAACCCAACACGATAGGGCACGATTCCC
* * *
1881206 GAATTGTCAAACACAAAGTATTGCCTTCGTTTTAAAGGATTTTTAGAAGACACGAGTGAAATTTT
66 GAATTGCCAAACACAAAGTATCGCCTTCGTTTTAAAGGAATTTTAGAAGACACGAGTGAAATTTT
1881271 G
131 G
* * * * **
1881272 AAGGGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACAC-ATTAGGGCACGATTCC
1 AAGGAATATTCGAATATTTTGACCAAACGAGAAATCACAACCCAACACGA-TAGGGCACGATTCC
* * * *
1881336 GCGAATTGCCAAATATCGAA-TCTCGTCTTCGTTTTAAA-GAATTTTA
65 -CGAATTGCCAAACA-CAAAGTATCGCCTTCGTTTTAAAGGAATTTTA
1881382 AAAAATTGTG
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
130 1 0.01
131 60 0.66
132 27 0.30
133 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (131 bp):
AAGGAATATTCGAATATTTTGACCAAACGAGAAATCACAACCCAACACGATAGGGCACGATTCCC
GAATTGCCAAACACAAAGTATCGCCTTCGTTTTAAAGGAATTTTAGAAGACACGAGTGAAATTTT
G
Found at i:1882413 original size:28 final size:28
Alignment explanation
Indices: 1882373--1882428 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1882363 AGAGTACATA
1882373 TATACACATATAGAAGAGCACTTTAAAC
1 TATACACATATAGAAGAGCACTTTAAAC
1882401 TATACACATATAGAAGAGCACTTTAAAC
1 TATACACATATAGAAGAGCACTTTAAAC
1882429 AGACAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (28 bp):
TATACACATATAGAAGAGCACTTTAAAC
Found at i:1882445 original size:28 final size:28
Alignment explanation
Indices: 1882380--1882442 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
1882370 ATATATACAC
* * *
1882380 ATATAGAAGAGCACTTTAAACTATACAC
1 ATATAAAAGAGCACTTTAAACTAGACAA
*
1882408 ATATAGAAGAGCACTTTAAAC-AGACAA
1 ATATAAAAGAGCACTTTAAACTAGACAA
*
1882435 ATTTAAAA
1 ATATAAAA
1882443 AGAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 10 0.32
28 21 0.68
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (28 bp):
ATATAAAAGAGCACTTTAAACTAGACAA
Found at i:1884758 original size:13 final size:14
Alignment explanation
Indices: 1884737--1884768 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1884727 ATAAAAACTA
1884737 TAAACAAAAGTTAT
1 TAAACAAAAGTTAT
1884751 TAAA-AAAAGTTA-
1 TAAACAAAAGTTAT
1884763 TAAACA
1 TAAACA
1884769 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 9 0.53
14 4 0.24
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (14 bp):
TAAACAAAAGTTAT
Found at i:1884782 original size:17 final size:18
Alignment explanation
Indices: 1884755--1884790 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1884745 AGTTATTAAA
1884755 AAAAGTTATAAACATTTT
1 AAAAGTTATAAACATTTT
*
1884773 AAAA-TTATAAATATTTT
1 AAAAGTTATAAACATTTT
1884790 A
1 A
1884791 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAAGTTATAAACATTTT
Found at i:1885768 original size:107 final size:107
Alignment explanation
Indices: 1885581--1885801 Score: 293
Period size: 107 Copynumber: 2.1 Consensus size: 107
1885571 ATCCCTACAA
** *
1885581 TGCAAAATTTGGAGGGGGTGAAACATAAAACTTTGGACTTATTTGAATCCGACCAAATTATACTA
1 TGCAAAATTTGGAGGGGGAAAAACATAAAACTTTGGACTTATTTGAATCCGACCAAATTACACTA
* * *
1885646 AAACCCATTTGAAAGCAATTGATGAGGAAAGCTTTGACATTT
66 AAACACATTTAAAAGCAATTGACGAGGAAAGCTTTGACATTT
** * **
1885688 TGCAAAATTTGGAGGGGGAAAAACATAAAACTTTGGACTTATTTGAATTTTG-CTATTTTACACT
1 TGCAAAATTTGGAGGGGGAAAAACATAAAACTTTGGACTTATTTGAA-TCCGACCAAATTACACT
* * *
1885752 AAAACACATTTAAAAGCATTTGGCGAGGAAAGTTTTGACATTT
65 AAAACACATTTAAAAGCAATTGACGAGGAAAGCTTTGACATTT
1885795 T-CAAAAT
1 TGCAAAAT
1885802 AAGATAGCAA
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
106 6 0.06
107 91 0.92
108 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (107 bp):
TGCAAAATTTGGAGGGGGAAAAACATAAAACTTTGGACTTATTTGAATCCGACCAAATTACACTA
AAACACATTTAAAAGCAATTGACGAGGAAAGCTTTGACATTT
Found at i:1907994 original size:12 final size:13
Alignment explanation
Indices: 1907979--1908012 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1907969 AATTAACATC
1907979 CCACTAAACCA-A
1 CCACTAAACCACA
*
1907991 CCACTAAACCACC
1 CCACTAAACCACA
1908004 CCACTAAAC
1 CCACTAAAC
1908013 TATCCCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.44, C:0.47, G:0.00, T:0.09
Consensus pattern (13 bp):
CCACTAAACCACA
Found at i:1908019 original size:13 final size:13
Alignment explanation
Indices: 1907975--1908019 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1907965 AACTAATTAA
1907975 CATCCCACTAAAC
1 CATCCCACTAAAC
*
1907988 CA-ACCACTAAAC
1 CATCCCACTAAAC
*
1908000 CACCCCACTAAAC
1 CATCCCACTAAAC
*
1908013 TATCCCA
1 CATCCCA
1908020 TTAACTCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.13
Consensus pattern (13 bp):
CATCCCACTAAAC
Found at i:1908547 original size:15 final size:14
Alignment explanation
Indices: 1908491--1908604 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 14
1908481 TTATTATGTT
*
1908491 TCTATTTATATTTA
1 TCTATTTTTATTTA
*
1908505 T-T-TTGTTATTCTAA
1 TCTATTTTTATT-T-A
*
1908519 TACTATTATTATTTA
1 T-CTATTTTTATTTA
1908534 TCTAATTTTTATTTA
1 TCT-ATTTTTATTTA
*
1908549 TCTATTTATATTTCA
1 TCTATTTTTATTT-A
* *
1908564 ACTATTATTATATT-
1 TCTATTTTTAT-TTA
1908578 TCTATTTATTATATT-
1 TCTATTT-TTAT-TTA
*
1908593 TCTATTTCTATT
1 TCTATTTTTATT
1908605 AATATACTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.08
13 3 0.04
14 22 0.28
15 38 0.47
16 4 0.05
17 7 0.09
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.63
Consensus pattern (14 bp):
TCTATTTTTATTTA
Found at i:1908568 original size:44 final size:44
Alignment explanation
Indices: 1908520--1908604 Score: 113
Period size: 44 Copynumber: 1.9 Consensus size: 44
1908510 TTATTCTAAT
1908520 ACTATTATTAT-TTATCTAATTT-TTAT-TTATCTATTTATATTTCA
1 ACTATTATTATATT-TCT-ATTTATTATATT-TCTATTTATATTTCA
*
1908564 ACTATTATTATATTTCTATTTATTATATTTCTATTTCTATT
1 ACTATTATTATATTTCTATTTATTATATTTCTATTTATATT
1908605 AATATACTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
43 4 0.11
44 29 0.78
45 4 0.11
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (44 bp):
ACTATTATTATATTTCTATTTATTATATTTCTATTTATATTTCA
Found at i:1908597 original size:29 final size:29
Alignment explanation
Indices: 1908479--1908598 Score: 88
Period size: 29 Copynumber: 4.1 Consensus size: 29
1908469 TTATTGCTAT
* *
1908479 TATTATTATGTTTCTATTTA-TATTTATTT
1 TATTATTATATTTCTATTTATTATTTA-TC
* * * *
1908508 TGTTATTCTAATACTA-TTATTATTTATC
1 TATTATTATATTTCTATTTATTATTTATC
* *
1908536 TAATTTTTAT-TTATCTATTTA-TATTTCAAC
1 T-ATTATTATATT-TCTATTTATTATTT-ATC
1908566 TATTATTATATTTCTATTTATTATATT-TC
1 TATTATTATATTTCTATTTATTAT-TTATC
1908595 TATT
1 TATT
1908599 TCTATTAATA
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
28 6 0.09
29 50 0.72
30 11 0.16
31 2 0.03
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (29 bp):
TATTATTATATTTCTATTTATTATTTATC
Found at i:1908686 original size:6 final size:6
Alignment explanation
Indices: 1908675--1908702 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1908665 TAACATTCTA
1908675 TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTA
1908703 CGTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:1908804 original size:24 final size:23
Alignment explanation
Indices: 1908713--1908805 Score: 62
Period size: 24 Copynumber: 3.9 Consensus size: 23
1908703 CGTTTTTTGT
* *
1908713 TATTATCTATTTTAACTTTT-TA
1 TATTATGTATTTTAAATTTTATA
* *
1908735 TATAATGTTCATTTCAAATTTTTATA
1 TATTATG-T-ATTTTAAA-TTTTATA
* * * *
1908761 CATTGTTTACTTTAATATTTTCATA
1 TATTATGTATTTTAA-ATTTT-ATA
1908786 TATTATGTATTTTAAATTTT
1 TATTATGTATTTTAAATTTT
1908806 TTTACACATT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
22 5 0.10
23 1 0.02
24 20 0.39
25 20 0.39
26 5 0.10
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (23 bp):
TATTATGTATTTTAAATTTTATA
Found at i:1908806 original size:25 final size:24
Alignment explanation
Indices: 1908713--1908840 Score: 80
Period size: 25 Copynumber: 5.2 Consensus size: 24
1908703 CGTTTTTTGT
* *
1908713 TATTATCTATTTTAACTTTTTATA
1 TATTATGTATTTTAAATTTTTATA
*
1908737 TA--ATGTTCATTTCAAATTTTTATA
1 TATTATG-T-ATTTTAAATTTTTATA
* * * * *
1908761 CATTGTTTACTTTAATATTTTCATA
1 TATTATGTATTTTAA-ATTTTTATA
*
1908786 TATTATGTATTTTAAATTTTTTTACA
1 TATTATGTATTTTAAA--TTTTTATA
* * *
1908812 CATTATATATTTTGAATTGTTTATA
1 TATTATGTATTTTAAATT-TTTATA
1908837 TATT
1 TATT
1908841 TGAAGAGTTT
Statistics
Matches: 76, Mismatches: 20, Indels: 15
0.68 0.18 0.14
Matches are distributed among these distances:
22 2 0.03
23 1 0.01
24 25 0.33
25 28 0.37
26 20 0.26
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (24 bp):
TATTATGTATTTTAAATTTTTATA
Found at i:1910717 original size:15 final size:15
Alignment explanation
Indices: 1910697--1910748 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1910687 ACTACAAAAC
1910697 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
1910712 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
1910731 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
1910746 ATT
1 ATT
1910749 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:1910851 original size:22 final size:22
Alignment explanation
Indices: 1910811--1910866 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1910801 AATAAAATTG
*
1910811 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
1910831 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
1910853 TATTAATAATTTAT
1 AAATAATAAATTAT
1910867 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:1914477 original size:31 final size:32
Alignment explanation
Indices: 1914442--1914502 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
1914432 AAAAAGGCTT
1914442 AATAGTCTAATAACTTAAAT-AATTTTTTTTG
1 AATAGTCTAATAACTTAAATGAATTTTTTTTG
* *
1914473 AATAGTTTAGTAACTTAAATGAATTTTTTT
1 AATAGTCTAATAACTTAAATGAATTTTTTT
1914503 ATGTAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (32 bp):
AATAGTCTAATAACTTAAATGAATTTTTTTTG
Found at i:1920757 original size:15 final size:15
Alignment explanation
Indices: 1920737--1920768 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1920727 CTCTGCTAAC
*
1920737 TTAAGTTATTGTATA
1 TTAAGTTATCGTATA
1920752 TTAAGTTATCGTATA
1 TTAAGTTATCGTATA
1920767 TT
1 TT
1920769 CTATAGGTTA
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:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (15 bp):
TTAAGTTATCGTATA
Found at i:1922039 original size:17 final size:17
Alignment explanation
Indices: 1922017--1922067 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
1922007 ATTGCAAAAT
1922017 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
1922034 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
*
1922053 CATATCTTCGAAGAT
1 CATATCTTCTAAGAT
1922068 CATGTTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:1923773 original size:22 final size:22
Alignment explanation
Indices: 1923745--1923791 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1923735 AAATGCGTCA
1923745 GCTACAATGTTGGCACTCCCCG
1 GCTACAATGTTGGCACTCCCCG
1923767 GCTACAATGTTGGCACTCCCCG
1 GCTACAATGTTGGCACTCCCCG
1923789 GCT
1 GCT
1923792 TGTATTCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.23
Consensus pattern (22 bp):
GCTACAATGTTGGCACTCCCCG
Found at i:1929679 original size:19 final size:20
Alignment explanation
Indices: 1929639--1929682 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1929629 GTCTCTTTAG
* *
1929639 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
1929658 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
1929677 GCATTA
1 GCATTA
1929683 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:1932213 original size:20 final size:19
Alignment explanation
Indices: 1932188--1932251 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 19
1932178 AAAATCAAAG
1932188 TCAAAATGAAAATGAAAAAA
1 TCAAAAT-AAAATGAAAAAA
1932208 TCAAAAATAAAAAT-AAAAAA
1 TC-AAAAT-AAAATGAAAAAA
* *
1932228 ACAAAA-AGAA-GAAAAAA
1 TCAAAATAAAATGAAAAAA
1932245 TCAAAAT
1 TCAAAAT
1932252 CAAGATCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 14 0.38
19 4 0.11
20 9 0.24
21 10 0.27
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (19 bp):
TCAAAATAAAATGAAAAAA
Found at i:1932220 original size:21 final size:20
Alignment explanation
Indices: 1932190--1932234 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1932180 AATCAAAGTC
* *
1932190 AAAATGAAAATGAAAAAATCA
1 AAAATAAAAAT-AAAAAAACA
1932211 AAAATAAAAATAAAAAAACA
1 AAAATAAAAATAAAAAAACA
1932231 AAAA
1 AAAA
1932235 GAAGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.11
Consensus pattern (20 bp):
AAAATAAAAATAAAAAAACA
Found at i:1933203 original size:15 final size:16
Alignment explanation
Indices: 1933183--1933212 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1933173 GAAGAAGAAG
1933183 ATGAAAAA-TAAAAAA
1 ATGAAAAAGTAAAAAA
1933198 ATGAAAAAGTAAAAA
1 ATGAAAAAGTAAAAA
1933213 TGGAGAGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (16 bp):
ATGAAAAAGTAAAAAA
Found at i:1934602 original size:88 final size:88
Alignment explanation
Indices: 1934445--1935005 Score: 735
Period size: 88 Copynumber: 6.4 Consensus size: 88
1934435 ATGAAGTTGC
* * *
1934445 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTTGGTTG
1934510 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
1934533 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTTCCTCTCTTGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTTGGTTG
1934598 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * * *
1934621 GGATCTTGCATTTCTGCATTGATAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT-TTCGGTT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTT-GGTT
*
1934685 GTGATAGAGCTGGTTGAAGACAAA
65 GTGATGGAGCTGGTTGAAGACAAA
*
1934709 AGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT-TTCGGTT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTT-GGTT
*
1934773 GTGATAGAGCTGGTTGAAGACAAA
65 GTGATGGAGCTGGTTGAAGACAAA
* * *
1934797 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTTGGTTG
* **
1934862 T-AGTGGAGCTGGTTAAAGA-AGC
66 TGA-TGGAGCTGGTTGAAGACAAA
* * * * *
1934884 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCATC-CATCGAT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTC-TTGGT
* * * **
1934946 TG-CAGTGGAGCTAGTTAAAGA-AGC
64 TGTGA-TGGAGCTGGTTGAAGACAAA
* *
1934970 AGATCTTGCCTTCCTGCATTAACAGCAAAGCAGATC
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATC
1935006 AAAAAAAAAA
Statistics
Matches: 437, Mismatches: 30, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
85 6 0.01
86 69 0.16
87 39 0.09
88 322 0.74
89 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTTGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:1935288 original size:44 final size:45
Alignment explanation
Indices: 1935240--1935389 Score: 121
Period size: 44 Copynumber: 3.4 Consensus size: 45
1935230 CCAGAAATCC
* *
1935240 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGAGA-GATCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATGAAACGATCT
* * * * ** * * *
1935284 TATCTTCC-GGAGATTACAGCGGAGTAGA-TCGAA-GACACTATCC
1 TATCTCCCTGAAG-TTACAGTGGAGTGGATTAAAATGAAACGATCT
* *
1935327 TATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAAT-AAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATGAAACGATCT
* *
1935371 TATCTCTCTGAGGTTACAG
1 TATCTCCCTGAAGTTACAG
1935390 CAGAGTAGGT
Statistics
Matches: 78, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
42 3 0.04
43 28 0.36
44 47 0.60
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (45 bp):
TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATGAAACGATCT
Found at i:1935331 original size:87 final size:87
Alignment explanation
Indices: 1935236--1935397 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 87
1935226 AAAGCCAGAA
*
1935236 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAT-GAGAGATCTTATCT-TCCGGAGATT
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG-GATCTTATCTCT-CGGAGATT
*
1935299 ACAGCGGAGTAGATCGAAGACACT
64 ACAGCAGAGTAGATCGAAGACACT
* * * *
1935323 ATCCTATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCTTATCTCTCTGAGGTTAC
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCGGAGATTAC
1935388 AGCAGAGTAG
66 AGCAGAGTAG
1935398 GTCGCATCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 64 0.96
88 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (87 bp):
ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCGGAGATTAC
AGCAGAGTAGATCGAAGACACT
Found at i:1936949 original size:3 final size:3
Alignment explanation
Indices: 1936943--1936992 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
1936933 TTTAGCCACT
*
1936943 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1936987 CTTA TT
1 -TTA TT
1936993 TGTTTATGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
2 4 0.10
3 33 0.79
4 5 0.12
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1939374 original size:17 final size:17
Alignment explanation
Indices: 1939352--1939402 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
1939342 ATTGCAAAAT
1939352 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
1939369 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
*
1939388 CATATCTTCAAAGAT
1 CATATCTTCTAAGAT
1939403 CATGTTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:1941156 original size:43 final size:43
Alignment explanation
Indices: 1941100--1941186 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
1941090 TCATATTTCA
* *
1941100 TTTCTCATTTCATAATAATTTCTCATATTTTCCATTTCAATAT
1 TTTCTCATCTCATAATAATTTCTCATATTTCCCATTTCAATAT
* * * *
1941143 TTTCTCATCTCATATTCATTTCTCATCTTTCCCATTTCATTAT
1 TTTCTCATCTCATAATAATTTCTCATATTTCCCATTTCAATAT
1941186 T
1 T
1941187 AATCACATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (43 bp):
TTTCTCATCTCATAATAATTTCTCATATTTCCCATTTCAATAT
Found at i:1941157 original size:15 final size:14
Alignment explanation
Indices: 1941120--1941158 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1941110 CATAATAATT
1941120 TCTCATATTTTCCA
1 TCTCATATTTTCCA
*
1941134 TTTCAATATTTTCTCA
1 TCTC-ATATTTTC-CA
1941150 TCTCATATT
1 TCTCATATT
1941159 CATTTCTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 13 0.62
16 5 0.24
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (14 bp):
TCTCATATTTTCCA
Found at i:1969132 original size:22 final size:24
Alignment explanation
Indices: 1969101--1969151 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
1969091 TGAGTTTCAC
*
1969101 ATGATTTATAAAATGTG-AAATAT
1 ATGATATATAAAATGTGTAAATAT
* *
1969124 -TGATATATATATTGTGTAAATAT
1 ATGATATATAAAATGTGTAAATAT
1969147 ATGAT
1 ATGAT
1969152 CAGCATGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.57
23 6 0.26
24 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (24 bp):
ATGATATATAAAATGTGTAAATAT
Found at i:1969389 original size:47 final size:47
Alignment explanation
Indices: 1969283--1969395 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
1969273 AAGAATGAAG
* * *
1969283 AAGTGATAGTTTATCTACAAAAGTGGTGGCTTGTCCATAATATTATA
1 AAGTGATAGTTTATCTGCAAAAGTGGTGGCTTATCCACAATATTATA
* * * *
1969330 AAGTGGTGGTTTATTTGCAAAAGTGGTGGCTTATCCACAATATTATT
1 AAGTGATAGTTTATCTGCAAAAGTGGTGGCTTATCCACAATATTATA
*
1969377 AAGTGACAGTTTATCTGCA
1 AAGTGATAGTTTATCTGCA
1969396 TTACTGTGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (47 bp):
AAGTGATAGTTTATCTGCAAAAGTGGTGGCTTATCCACAATATTATA
Found at i:1987014 original size:5 final size:5
Alignment explanation
Indices: 1987004--1987057 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
1986994 ATCCTAAATT
*
1987004 AATAA AATAA AA-ATA AATAA AA-AT AATAA AACT-A AATAA AATAA AATAA
1 AATAA AATAA AATA-A AATAA AATAA AATAA AA-TAA AATAA AATAA AATAA
1987053 AATAA
1 AATAA
1987058 TATCTTCTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 5 0.12
5 35 0.83
6 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:1987020 original size:19 final size:19
Alignment explanation
Indices: 1986998--1987054 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1986988 AGCCTAATCC
1986998 TAAATTAATAAAATAAAAA
1 TAAATTAATAAAATAAAAA
* *
1987017 TAAA-TAAAAATAATAAAAC
1 TAAATTAATAA-AATAAAAA
*
1987036 TAAATAAAATAAAATAAAA
1 TAAAT-TAATAAAATAAAA
1987055 TAATATCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 5 0.16
19 15 0.48
20 7 0.23
21 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAATTAATAAAATAAAAA
Found at i:1987030 original size:24 final size:24
Alignment explanation
Indices: 1987003--1987049 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1986993 AATCCTAAAT
1987003 TAATAAAA-TAAAAATAAATAAAAA
1 TAATAAAACTAAAAA-AAATAAAAA
*
1987027 TAATAAAACTAAATAAAATAAAA
1 TAATAAAACTAAAAAAAATAAAA
1987050 TAAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (24 bp):
TAATAAAACTAAAAAAAATAAAAA
Found at i:1992279 original size:3 final size:3
Alignment explanation
Indices: 1992253--1992324 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
1992243 TTCTCATTGC
* * * *
1992253 TAT TTT TAT T-T TATT TAC TAT TAT TAT TAT TAT T-T TAC TAG TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1992297 TATT TAT TATT TAT TAT TAT TAC TAT TA
1 TA-T TAT TA-T TAT TAT TAT TAT TAT TA
1992325 CTGTCATTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 4 0.07
3 42 0.76
4 9 0.16
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1992484 original size:3 final size:3
Alignment explanation
Indices: 1992476--1992517 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1992466 TCCCTTTTAT
1992476 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1992518 CACTCATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1992724 original size:3 final size:3
Alignment explanation
Indices: 1992718--1992754 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1992708 ACTTAACTAC
1992718 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1992755 TATTCATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1992913 original size:9 final size:9
Alignment explanation
Indices: 1992899--1992943 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
1992889 TTCTATTATC
1992899 TATTTATTT
1 TATTTATTT
1992908 TATTTA-TT
1 TATTTATTT
1992916 TATTTATTAT
1 TATTTATT-T
1992926 TA-TTATTAT
1 TATTTATT-T
1992935 TA-TTATTT
1 TATTTATTT
1992943 T
1 T
1992944 TACATATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
8 10 0.29
9 21 0.62
10 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTATTT
Found at i:1992919 original size:17 final size:18
Alignment explanation
Indices: 1992894--1992945 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 18
1992884 TGCCCTTCTA
1992894 TTATCTATTTATT-TTAT
1 TTATCTATTTATTATTAT
*
1992911 TTATTTATTTATTATTA-
1 TTATCTATTTATTATTAT
1992928 TTAT-TA-TTATTATT-T
1 TTATCTATTTATTATTAT
1992943 TTA
1 TTA
1992946 CATATTACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 11 0.34
16 2 0.06
17 16 0.50
18 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATCTATTTATTATTAT
Found at i:1992934 original size:12 final size:13
Alignment explanation
Indices: 1992892--1992942 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
1992882 TGTGCCCTTC
1992892 TATTATCTATTTAT
1 TATTAT-TATTTAT
1992906 T-TTATTTATTTATT
1 TATTA-TTATTTA-T
1992920 TATTATTA-TTAT
1 TATTATTATTTAT
1992932 TATTATTATTT
1 TATTATTATTT
1992943 TTACATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 9 0.27
13 14 0.42
14 7 0.21
15 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:1996766 original size:37 final size:37
Alignment explanation
Indices: 1996711--1996785 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1996701 TACTACGTAC
*
1996711 GTAGTACAGAGCCGATGGTCTACTTATCTAAAATAAT
1 GTAGTACAGAGCCAATGGTCTACTTATCTAAAATAAT
*
1996748 GTAGTACAGAGCCAATGGTCTACTTTTCTAAAATAAT
1 GTAGTACAGAGCCAATGGTCTACTTATCTAAAATAAT
1996785 G
1 G
1996786 AAGTTCAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (37 bp):
GTAGTACAGAGCCAATGGTCTACTTATCTAAAATAAT
Found at i:2006641 original size:18 final size:18
Alignment explanation
Indices: 2006618--2006707 Score: 126
Period size: 18 Copynumber: 5.0 Consensus size: 18
2006608 CCCAACTACT
*
2006618 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
2006636 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
2006654 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
**
2006672 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
*
2006690 GTATACGTGGATAGTACC
1 GTATACGTGAATAGTACC
2006708 ATAAACGGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:2006670 original size:36 final size:36
Alignment explanation
Indices: 2006619--2006707 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
2006609 CCAACTACTG
*
2006619 TATACGTGAACAGTACCGTATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
* *
2006655 TATACGTGAATAGTACCGTATACGTGAATAGTGTCG
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
*
2006691 TATACGTGGATAGTACC
1 TATACGTGAATAGTACC
2006708 ATAAACGGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
Found at i:2011746 original size:54 final size:54
Alignment explanation
Indices: 2011687--2011824 Score: 170
Period size: 54 Copynumber: 2.6 Consensus size: 54
2011677 CATGGCTGTT
*
2011687 AGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAACCACC
1 AGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAACCACC
* * * *
2011741 AGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCAGAGCCACC
1 AGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCACC
* * * * *
2011795 AGATCAGATATTTGTGGCATAACCACCAGA
1 AGAACAGATATATGTGACAGAGCCACCAGA
2011825 ACGCTTCCTC
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 56 0.76
55 18 0.24
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
AGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCACC
Found at i:2011747 original size:27 final size:26
Alignment explanation
Indices: 2011687--2011826 Score: 154
Period size: 27 Copynumber: 5.2 Consensus size: 26
2011677 CATGGCTGTT
* *
2011687 AGAACAGATAATGTGACAGAGTCACC
1 AGAACAGATAATGTGGCAGAGCCACC
*
2011713 AGATACAGATAATCGTGGCAGAACCACC
1 AGA-ACAGATAAT-GTGGCAGAGCCACC
2011741 AGAACAGATATATGTGGCAGAGCCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
* *
2011768 AGATCAGATATTTGTGGCAGAGCCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
* * * *
2011795 AGATCAGATATTTGTGGCATAACCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
2011822 AGAAC
1 AGAAC
2011827 GCTTCCTCCA
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.03
27 83 0.81
28 16 0.16
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
AGAACAGATAATGTGGCAGAGCCACC
Done.