Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold109
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: 1855911
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.34
Warning! 69956 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:1761031 original size:51 final size:51
Alignment explanation
Indices: 1760955--1761059 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
1760945 AGCCCTTGTG
*
1760955 TTAAATGAACTCTATCCCAGCTTAGTCATTGATTAGGATTTAAACATGCTT
1 TTAAATGAACTCCATCCCAGCTTAGTCATTGATTAGGATTTAAACATGCTT
*
1761006 TTAAATGAACTCCATCCCAGTTTAGTCATTGATTAGGATTTAAACATGCTT
1 TTAAATGAACTCCATCCCAGCTTAGTCATTGATTAGGATTTAAACATGCTT
1761057 TTA
1 TTA
1761060 CTTTTGGATC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (51 bp):
TTAAATGAACTCCATCCCAGCTTAGTCATTGATTAGGATTTAAACATGCTT
Found at i:1772612 original size:20 final size:21
Alignment explanation
Indices: 1772587--1772638 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
1772577 TTTTAAACAC
1772587 GTATCGATACATTCAA-TTA-T
1 GTATCGATACATT-AACTTATT
1772607 GTATCGATACATTAACTTATT
1 GTATCGATACATTAACTTATT
*
1772628 GTATTGATACA
1 GTATCGATACA
1772639 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 11 0.38
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (21 bp):
GTATCGATACATTAACTTATT
Found at i:1773458 original size:2 final size:2
Alignment explanation
Indices: 1773451--1773484 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1773441 TTACAGCCGC
1773451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1773485 ATAATTAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1775389 original size:21 final size:22
Alignment explanation
Indices: 1775365--1775427 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
1775355 TATATTTTAA
1775365 AATTTAAATTTTAAATTTAT-G
1 AATTTAAATTTTAAATTTATAG
** *
1775386 AATTTATTTTTTAAAATAATTATAT
1 AATTTAAATTTT-AAAT--TTATAG
*
1775411 AAATTAAATTTTAAATT
1 AATTTAAATTTTAAATT
1775428 CATTAATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
21 10 0.31
22 5 0.16
24 8 0.25
25 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTTAAATTTTAAATTTATAG
Found at i:1777253 original size:2 final size:2
Alignment explanation
Indices: 1777246--1777286 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1777236 ATTTAGTGTT
1777246 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1777287 TACAAATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1777701 original size:16 final size:18
Alignment explanation
Indices: 1777665--1777706 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
1777655 AATAATATGC
*
1777665 ATTTATAAAAAAATTATA
1 ATTTATAAAAAAATTAAA
1777683 ATTTA-AAAAAAA-TAAA
1 ATTTATAAAAAAATTAAA
1777699 ATTT-TAAA
1 ATTTATAAA
1777707 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.45
17 7 0.32
18 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTTATAAAAAAATTAAA
Found at i:1778291 original size:19 final size:20
Alignment explanation
Indices: 1778254--1778291 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1778244 ATATAAAATT
* *
1778254 TTAAAAAATTATTTTTAAAA
1 TTAAAAAATTATATCTAAAA
1778274 TTAAAAAA-TATATCTAAA
1 TTAAAAAATTATATCTAAA
1778292 CATAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAAAAATTATATCTAAAA
Found at i:1778637 original size:2 final size:2
Alignment explanation
Indices: 1778620--1778656 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1778610 TTCCACGTAT
* *
1778620 TA TA CA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1778657 TTGTTTATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1778866 original size:24 final size:25
Alignment explanation
Indices: 1778809--1778868 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
1778799 AATTTTTATA
* *
1778809 TTAATATAT-AATTAATATAATAAT
1 TTAATATTTAAATAAATATAATAAT
*
1778833 TTAATCTTTAAATAAATA-AATAAAT
1 TTAATATTTAAATAAATATAAT-AAT
1778858 TTAA-ATTTAAA
1 TTAATATTTAAA
1778869 ATTAAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAATATTTAAATAAATATAATAAT
Found at i:1778958 original size:22 final size:23
Alignment explanation
Indices: 1778920--1778971 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1778910 AGATATCATA
*
1778920 TAAAA-ATGATATGAAAAATAAT
1 TAAAATATAATATGAAAAATAAT
*
1778942 TAAAATATAATAT-AAAAATAGT
1 TAAAATATAATATGAAAAATAAT
*
1778964 AAAAATAT
1 TAAAATAT
1778972 GATTTTGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (23 bp):
TAAAATATAATATGAAAAATAAT
Found at i:1779040 original size:10 final size:10
Alignment explanation
Indices: 1779022--1779055 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1779012 ATTATTAATA
*
1779022 TATAAAAATT
1 TATATAAATT
1779032 TATATAAATT
1 TATATAAATT
*
1779042 TACATAAATT
1 TATATAAATT
1779052 TATA
1 TATA
1779056 ATAATTTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATAAATT
Found at i:1779411 original size:18 final size:18
Alignment explanation
Indices: 1779371--1779412 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1779361 TATTTAACAT
1779371 AAAAA-ATAACATAAATA
1 AAAAATATAACATAAATA
**
1779388 CGAAATATAACATAAATA
1 AAAAATATAACATAAATA
1779406 AAAAATA
1 AAAAATA
1779413 AATATATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAATATAACATAAATA
Found at i:1779747 original size:2 final size:2
Alignment explanation
Indices: 1779740--1779783 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1779730 TTCCTGGTTC
1779740 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
1779782 AT
1 AT
1779784 CCTCCTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1781843 original size:24 final size:25
Alignment explanation
Indices: 1781811--1781864 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1781801 AATTGTTAAA
* * * *
1781811 TTTAAAAATAT-TTTATATTAATAT
1 TTTATAAATATATTTAAATAAAAAT
1781835 TTTATAAATATATTTAAATAAAAAT
1 TTTATAAATATATTTAAATAAAAAT
1781860 TTTAT
1 TTTAT
1781865 TATTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTATAAATATATTTAAATAAAAAT
Found at i:1783719 original size:18 final size:16
Alignment explanation
Indices: 1783663--1783720 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 16
1783653 ACATTAAAAT
1783663 TTAAATTTA-AAATTA
1 TTAAATTTATAAATTA
*
1783678 TTAAATATTATATATTTA
1 TTAAAT-TTATA-AATTA
*
1783696 TAAAATTTAATAAATTAA
1 TTAAATTT-ATAAATT-A
1783714 TTAAATT
1 TTAAATT
1783721 AAACTTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 6 0.18
16 3 0.09
17 6 0.18
18 19 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATTTATAAATTA
Found at i:1787170 original size:16 final size:16
Alignment explanation
Indices: 1787151--1787181 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1787141 CTTATTTCTA
*
1787151 TTTATTTTTATTCATT
1 TTTATTTTAATTCATT
1787167 TTTATTTTAATTCAT
1 TTTATTTTAATTCAT
1787182 ACATGAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTTTAATTCATT
Found at i:1789072 original size:14 final size:14
Alignment explanation
Indices: 1789053--1789079 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1789043 AAAGCATATG
1789053 AAAAAGAAAAAAAC
1 AAAAAGAAAAAAAC
1789067 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
1789080 TACTAAATAA
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:0.89, C:0.04, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAC
Found at i:1790624 original size:20 final size:18
Alignment explanation
Indices: 1790578--1790627 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1790568 GAAAAATATA
*
1790578 TAAAAAATCAGAAAAATG
1 TAAAAAATCAAAAAAATG
* *
1790596 TAGAAAATCAAAAAAGATTT
1 TAAAAAATCAAAAAA-A-TG
1790616 TAAAAAATCAAA
1 TAAAAAATCAAA
1790628 TAGCATACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
19 1 0.04
20 12 0.46
ACGTcount: A:0.66, C:0.06, G:0.08, T:0.20
Consensus pattern (18 bp):
TAAAAAATCAAAAAAATG
Found at i:1793324 original size:33 final size:33
Alignment explanation
Indices: 1793248--1793324 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
1793238 AAATTACATA
* *
1793248 AATATAATATAAATATACGAATATATCAAAATT
1 AATATAATATAAATATACGAACATAACAAAATT
* * **
1793281 TATATGATATAAATAT-TTAACATAACAAAATT
1 AATATAATATAAATATACGAACATAACAAAATT
1793313 AATATAAATATA
1 AATAT-AATATA
1793325 TGAAAATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 16 0.46
33 19 0.54
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (33 bp):
AATATAATATAAATATACGAACATAACAAAATT
Found at i:1793350 original size:26 final size:27
Alignment explanation
Indices: 1793311--1793362 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
1793301 CATAACAAAA
1793311 TTAATATAAATATATGAAAATAATATT
1 TTAATATAAATATATGAAAATAATATT
*
1793338 TTAA-ATAAATATATGAATATAATAT
1 TTAATATAAATATATGAAAATAATAT
1793363 AAATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
TTAATATAAATATATGAAAATAATATT
Found at i:1793361 original size:13 final size:14
Alignment explanation
Indices: 1793313--1793363 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
1793303 TAACAAAATT
1793313 AATATAAATATATG
1 AATATAAATATATG
* * *
1793327 AAAAT-AATATTTT
1 AATATAAATATATG
1793340 AA-ATAAATATATG
1 AATATAAATATATG
1793353 AATAT-AATATA
1 AATATAAATATA
1793364 AATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 2 0.07
13 22 0.73
14 6 0.20
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AATATAAATATATG
Found at i:1794413 original size:16 final size:16
Alignment explanation
Indices: 1794390--1794431 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
1794380 ATGTAGGTGT
1794390 AAATTTTAAAA-TTAA
1 AAATTTTAAAATTTAA
1794405 AAATATTTAAAATTTAA
1 AAAT-TTTAAAATTTAA
1794422 AAATTTTAAA
1 AAATTTTAAA
1794432 TATCAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTTAAAATTTAA
Found at i:1794540 original size:16 final size:16
Alignment explanation
Indices: 1794519--1794552 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1794509 ATTTTATTTT
*
1794519 AAATATAATTATAAAA
1 AAATATAATAATAAAA
*
1794535 AAATATCATAATAAAA
1 AAATATAATAATAAAA
1794551 AA
1 AA
1794553 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATATAATAATAAAA
Found at i:1794989 original size:21 final size:22
Alignment explanation
Indices: 1794965--1795006 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1794955 AAATGAATTA
1794965 TTTTATTATGAT-ATTTTTCTT
1 TTTTATTATGATAATTTTTCTT
* *
1794986 TTTTTTTATTATAATTTTTCT
1 TTTTATTATGATAATTTTTCT
1795007 CCCTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTATGATAATTTTTCTT
Found at i:1795281 original size:15 final size:15
Alignment explanation
Indices: 1795227--1795288 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
1795217 TTGAATTGAG
*
1795227 TTATTTTAAATTTAGA
1 TTATTTTTAATTTA-A
*
1795243 TTTATTTTAAATTTAA
1 -TTATTTTTAATTTAA
*
1795259 TTACTTTTAATTTGAA
1 TTATTTTTAATTT-AA
1795275 -TATTTTTGAATTTA
1 TTATTTTT-AATTTA
1795289 GTTTTTTCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 18 0.45
16 8 0.20
17 14 0.35
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (15 bp):
TTATTTTTAATTTAA
Found at i:1796502 original size:32 final size:30
Alignment explanation
Indices: 1796461--1796519 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1796451 TGCAAAAATA
*
1796461 TTTAAGAATTAAAAAAATTTTATTTTATTGAT
1 TTTAAGAATT--AAAAATTATATTTTATTGAT
* *
1796493 TTTAGGAATTGAAAATTATATTTTATT
1 TTTAAGAATTAAAAATTATATTTTATT
1796520 TAAATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.62
32 9 0.38
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTAAGAATTAAAAATTATATTTTATTGAT
Found at i:1796992 original size:23 final size:25
Alignment explanation
Indices: 1796924--1796993 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 25
1796914 AAAAATTCAC
1796924 TATT-AATCATTTTTATTGATAATAAAT
1 TATTAAAT-ATTTTT-TT-ATAATAAAT
** *
1796951 TATTAAATATAATTATATAAT-AAT
1 TATTAAATATTTTTTTATAATAAAT
1796975 TA-TAAATATTTTTTTATAA
1 TATTAAATATTTTTTTATAA
1796994 ATTAAATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
23 14 0.39
24 5 0.14
25 5 0.14
26 1 0.03
27 8 0.22
28 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
TATTAAATATTTTTTTATAATAAAT
Found at i:1796996 original size:21 final size:21
Alignment explanation
Indices: 1796945--1797008 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
1796935 TTTATTGATA
**
1796945 ATAAATTATTAAATATAATTAT
1 ATAAATTA-TAAATATTTTTAT
*
1796967 ATAATAATTATAAATATTTTTTT
1 AT-A-AATTATAAATATTTTTAT
1796990 ATAAA-T-TAAATATTTTTAT
1 ATAAATTATAAATATTTTTAT
1797009 TTAAGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 12 0.33
20 1 0.03
21 2 0.06
22 3 0.08
23 13 0.36
24 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAAATTATAAATATTTTTAT
Found at i:1797050 original size:34 final size:34
Alignment explanation
Indices: 1797012--1797081 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
1797002 TTTTTATTTA
*
1797012 AGAAAATTTTAATCATTTATTTATTTATACTTTT
1 AGAAAAATTTAATCATTTATTTATTTATACTTTT
1797046 AGAAAAATTTAATCATTTATTTATTTATACTTTT
1 AGAAAAATTTAATCATTTATTTATTTATACTTTT
1797080 AG
1 AG
1797082 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (34 bp):
AGAAAAATTTAATCATTTATTTATTTATACTTTT
Found at i:1797252 original size:15 final size:15
Alignment explanation
Indices: 1797231--1797296 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
1797221 TTTCGGATTG
1797231 AATTTTTGTAAATATA
1 AATTTTTGTAAAT-TA
*
1797247 AATTTTTTTAAATTA
1 AATTTTTGTAAATTA
*
1797262 AATTTTTTTAAAATTTA
1 AATTTTTGT-AAA-TTA
* *
1797279 AAATTTT-TAATTTA
1 AATTTTTGTAAATTA
1797293 AATT
1 AATT
1797297 GTAAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
14 6 0.14
15 13 0.30
16 16 0.36
17 9 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
AATTTTTGTAAATTA
Found at i:1797266 original size:31 final size:31
Alignment explanation
Indices: 1797231--1797296 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1797221 TTTCGGATTG
*
1797231 AATTTTTGT-AAATATAAATTTTTTTAAATTA
1 AATTTTTGTAAAATATAAA-ATTTTTAAATTA
* * *
1797262 AATTTTTTTAAAATTTAAAATTTTTAATTTA
1 AATTTTTGTAAAATATAAAATTTTTAAATTA
1797293 AATT
1 AATT
1797297 GTAAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
AATTTTTGTAAAATATAAAATTTTTAAATTA
Found at i:1797315 original size:22 final size:22
Alignment explanation
Indices: 1797269--1797348 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
1797259 TTAAATTTTT
* * *
1797269 TTAAAATTTAAAATTTTT-AAT
1 TTAAATTTTAAATTTTTTCAAA
*
1797290 TTAAATTGTAAATTTTTTCAAA
1 TTAAATTTTAAATTTTTTCAAA
**
1797312 TTAAATTTTAAATTAATTCAAA
1 TTAAATTTTAAATTTTTTCAAA
1797334 -TAAATTTTTAAATTT
1 TTAAA-TTTTAAATTT
1797349 AAACTTGGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 19 0.39
22 30 0.61
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (22 bp):
TTAAATTTTAAATTTTTTCAAA
Found at i:1797318 original size:15 final size:15
Alignment explanation
Indices: 1797231--1797320 Score: 81
Period size: 15 Copynumber: 5.4 Consensus size: 15
1797221 TTTCGGATTG
*
1797231 AATTTTTGTAAATATA
1 AATTTTTTTAAAT-TA
1797247 AATTTTTTTAAATTA
1 AATTTTTTTAAATTA
1797262 AATTTTTTTAAAATTTAA
1 AATTTTTTT-AAA-TT-A
1797280 AATTTTTAATTTAAATTGTA
1 AA-TTTT--TTTAAA-T-TA
*
1797300 AATTTTTTCAAATTA
1 AATTTTTTTAAATTA
1797315 AATTTT
1 AATTTT
1797321 AAATTAATTC
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
15 19 0.29
16 16 0.25
17 7 0.11
18 3 0.05
19 8 0.12
20 8 0.12
21 4 0.06
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (15 bp):
AATTTTTTTAAATTA
Found at i:1797788 original size:28 final size:28
Alignment explanation
Indices: 1797748--1797804 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1797738 AATTTGAGGG
1797748 ATCGTTTTTTTTGTTCTCAGACAAAGTT
1 ATCGTTTTTTTTGTTCTCAGACAAAGTT
1797776 ATCGTTTTTTTTGTTCTCAGACAAAGTT
1 ATCGTTTTTTTTGTTCTCAGACAAAGTT
1797804 A
1 A
1797805 AGTTTTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (28 bp):
ATCGTTTTTTTTGTTCTCAGACAAAGTT
Found at i:1797811 original size:28 final size:28
Alignment explanation
Indices: 1797751--1797811 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
1797741 TTGAGGGATC
*
1797751 GTTTTTTTTGTTCTCAGACAAAGTTATC
1 GTTTTTTTTGTTCTCAGACAAAGTTATA
1797779 GTTTTTTTTGTTCTCAGACAAAGTTA-A
1 GTTTTTTTTGTTCTCAGACAAAGTTATA
1797806 GTTTTT
1 GTTTTT
1797812 GCAGAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.52
Consensus pattern (28 bp):
GTTTTTTTTGTTCTCAGACAAAGTTATA
Found at i:1799060 original size:2 final size:2
Alignment explanation
Indices: 1799053--1799090 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1799043 GTTGAGCGAC
1799053 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
1799091 GTTGGTTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1800008 original size:2 final size:2
Alignment explanation
Indices: 1800001--1800047 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1799991 AATTCCTCAT
1800001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1800043 TA TA T
1 TA TA T
1800048 TACTGTTCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1800780 original size:30 final size:30
Alignment explanation
Indices: 1800744--1800832 Score: 151
Period size: 30 Copynumber: 3.0 Consensus size: 30
1800734 AACTTTCTAG
*
1800744 CTGGGACATGCTTTGTATCTCCATGCGTTT
1 CTGGGACATGCTCTGTATCTCCATGCGTTT
*
1800774 CTGGGACATGCTCTGTATCTCCATACGTTT
1 CTGGGACATGCTCTGTATCTCCATGCGTTT
*
1800804 CTGGGACATGCTCTGTATCTCTATGCGTT
1 CTGGGACATGCTCTGTATCTCCATGCGTT
1800833 GGGTCTAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (30 bp):
CTGGGACATGCTCTGTATCTCCATGCGTTT
Found at i:1800879 original size:3 final size:3
Alignment explanation
Indices: 1800873--1800899 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1800863 AACAATAATA
1800873 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1800900 TTTCTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1806267 original size:2 final size:2
Alignment explanation
Indices: 1806260--1806298 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1806250 TGAACTGTTC
1806260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1806299 TTGAAGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1809155 original size:15 final size:15
Alignment explanation
Indices: 1809132--1809161 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1809122 AAAAAAAAAA
*
1809132 TAAATATATTTTTAT
1 TAAAAATATTTTTAT
1809147 TAAAAATATTTTTAT
1 TAAAAATATTTTTAT
1809162 ATTTGATATT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAAAATATTTTTAT
Found at i:1809645 original size:16 final size:16
Alignment explanation
Indices: 1809624--1809655 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1809614 TAATAATATG
1809624 TGTCACATTATTATTA
1 TGTCACATTATTATTA
1809640 TGTCACATTATTATTA
1 TGTCACATTATTATTA
1809656 ATTAAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTCACATTATTATTA
Found at i:1814424 original size:13 final size:13
Alignment explanation
Indices: 1814406--1814430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1814396 AACTCACTCA
1814406 GTATCGATACATT
1 GTATCGATACATT
1814419 GTATCGATACAT
1 GTATCGATACAT
1814431 GGTCAAATGA
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:1814872 original size:23 final size:23
Alignment explanation
Indices: 1814846--1814889 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1814836 GTATTCAACC
*
1814846 TTGGTGTACAATCTTTT-AAGAAT
1 TTGGGGTACAAT-TTTTGAAGAAT
*
1814869 TTGGGGTATAATTTTTGAAGA
1 TTGGGGTACAATTTTTGAAGA
1814890 GATTGAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (23 bp):
TTGGGGTACAATTTTTGAAGAAT
Found at i:1815970 original size:3 final size:3
Alignment explanation
Indices: 1815964--1815988 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1815954 ATCAATAATA
1815964 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
1815989 AGTTGACTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1823166 original size:52 final size:52
Alignment explanation
Indices: 1823088--1823216 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1823078 CGAAATATGA
1823088 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * **
1823140 AAATTTGACTGCATGTATCAATACATTTTTTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1823192 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1823217 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1823227 original size:52 final size:51
Alignment explanation
Indices: 1823088--1823236 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 51
1823078 CGAAATATGA
1823088 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTCATAGTGTATCGATACATCTGGGC
* * **
1823140 AAATTTGACTGCATGTATCAATACATTTTTTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTCATAGTGTATCGATACATCTGGGC
* ***
1823192 AAATTTGCCTACATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTCAT-AGTGTATCGATACA
1823237 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 1 0.01
52 84 0.99
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTCATAGTGTATCGATACATCTGGGC
Found at i:1823243 original size:13 final size:13
Alignment explanation
Indices: 1823225--1823249 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1823215 CAAAGATCAG
1823225 TGTATCGATACAA
1 TGTATCGATACAA
1823238 TGTATCGATACA
1 TGTATCGATACA
1823250 TTTGAGTAAT
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:1823316 original size:19 final size:18
Alignment explanation
Indices: 1823292--1823352 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
1823282 TAGCTTACAT
1823292 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1823311 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1823324 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1823343 TGTATCGATA
1 TGTATCGATA
1823353 TATTGCATCG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1823328 original size:32 final size:32
Alignment explanation
Indices: 1823287--1823387 Score: 157
Period size: 32 Copynumber: 3.1 Consensus size: 32
1823277 GGCAGTAGCT
*
1823287 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1823319 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
* * *
1823351 TATATTGCATCGATACAACACTTTATGTGTCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1823384 TACA
1 TACA
1823388 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1823329 original size:13 final size:13
Alignment explanation
Indices: 1823311--1823335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1823301 ACAAAACTTA
1823311 TGTATCGATACAT
1 TGTATCGATACAT
1823324 TGTATCGATACA
1 TGTATCGATACA
1823336 ACACTTATGT
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:1824406 original size:43 final size:43
Alignment explanation
Indices: 1824345--1824671 Score: 375
Period size: 43 Copynumber: 7.2 Consensus size: 43
1824335 TAAAGATGAC
1824345 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1824388 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1824431 AAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ---A-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
** * * * *
1824481 GGAGTTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1824524 AAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 --A-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1824573 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1824616 AAAGATGAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -AA-A-G---GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1824665 AAAGGTG
1 AAAGGTG
1824672 AAAAAAAAAA
Statistics
Matches: 241, Mismatches: 24, Indels: 38
0.80 0.08 0.13
Matches are distributed among these distances:
43 116 0.48
44 4 0.02
45 1 0.00
46 4 0.02
47 3 0.01
48 3 0.01
49 73 0.30
50 37 0.15
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:1824558 original size:49 final size:49
Alignment explanation
Indices: 1824233--1824964 Score: 755
Period size: 49 Copynumber: 15.1 Consensus size: 49
1824223 CTTAGGAATG
* * *
1824233 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
** * *
1824282 TTAAAGATGACAAAGACGCCAATACGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
1824334 TTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * *
1824386 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
1824429 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
1824479 TT---G--G-AGTTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
1824522 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
1824571 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
1824614 TTAAAGATGAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * * *
1824663 TTAAAGGTGAAAAAAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAAC
1 TTAAAGATG--------AAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
1824721 TTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
1824773 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
1824816 TTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
1824865 TTAAA-ACG-A--TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
**
1824910 TTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1824959 TTAAAG
1 TTAAAG
1824965 GAAGATGCCA
Statistics
Matches: 582, Mismatches: 59, Indels: 84
0.80 0.08 0.12
Matches are distributed among these distances:
43 152 0.26
44 1 0.00
45 39 0.07
46 4 0.01
47 4 0.01
48 6 0.01
49 171 0.29
50 38 0.07
52 120 0.21
53 5 0.01
57 3 0.01
58 38 0.07
59 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
Found at i:1824582 original size:92 final size:92
Alignment explanation
Indices: 1824307--1824671 Score: 604
Period size: 92 Copynumber: 3.9 Consensus size: 92
1824297 ACGCCAATAC
* *
1824307 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGC
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGC
1824372 CAGCGATATTGGACTTAAAGGTGCCAATGT
63 CAGCGATATTGGACTTAAAGGTGCCAATGT
* * *
1824402 GCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCA
1 GCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCA
** *
1824467 GCGATATTGGACTTGGAGTTGCCAATGT
65 GCGATATTGGACTTAAAGGTGCCAATGT
*
1824495 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAG
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAG
1824560 CGATATTGGACTTAAAGGTGCCAATGT
66 CGATATTGGACTTAAAGGTGCCAATGT
*
1824587 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGTGCCAATATGCTGATTCAAGGCCAG
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAG
1824652 CGATATTGGACTTAAAGGTG
66 CGATATTGGACTTAAAGGTG
1824672 AAAAAAAAAA
Statistics
Matches: 255, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
92 142 0.56
93 79 0.31
95 27 0.11
96 7 0.03
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (92 bp):
GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAG
CGATATTGGACTTAAAGGTGCCAATGT
Found at i:1824777 original size:110 final size:106
Alignment explanation
Indices: 1824573--1824965 Score: 435
Period size: 94 Copynumber: 3.9 Consensus size: 106
1824563 TATTGGACTT
*
1824573 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAAGTGCCAATATGC
1824638 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAAAAAA
66 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAAAAAA
*
1824679 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT-G-AAA-GTGCCAAT
*
1824744 ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T--------
62 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAAAAAA
* * *
1824775 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAAGTGCCAATATGC
* *
1824840 TGATTCAAGGCCAACTATATTGGAC-T-----T------AA
66 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAAAAAA
* * * *
1824869 AACGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-CAAAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAA-GTGCCAATATG
*
1824933 CTGATTCAAGGCCAGCTATATTGGACTTAAAGG
65 CTGATTCAAGGCCAGCGATATTGGACTTAAAGG
1824966 AAGATGCCAC
Statistics
Matches: 261, Mismatches: 13, Indels: 32
0.85 0.04 0.10
Matches are distributed among these distances:
92 38 0.15
93 4 0.02
94 83 0.32
95 42 0.16
96 5 0.02
104 1 0.00
106 5 0.02
107 42 0.16
108 1 0.00
109 4 0.02
110 36 0.14
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (106 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAAGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAAAAAA
Found at i:1825047 original size:32 final size:31
Alignment explanation
Indices: 1824970--1825158 Score: 227
Period size: 32 Copynumber: 5.9 Consensus size: 31
1824960 TAAAGGAAGA
*
1824970 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAG--GGT
*
1825003 TGCCACCGACTTGTGTGGGCTTTAGAAGGGAT
1 TGCCACCAACTTGTGTGGGCTTTAGAAGGG-T
*
1825035 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAG--AAGGGT
*
1825068 TGCCACCAACTTGCGTGGGCTTTGAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-AGAAGGGT
** *
1825100 TGCCACTGACTTGTGTGGGCTTTGGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAG-AAGGGT
* *
1825132 TGCCATCGACTTGTGTGGGCTTT-GAAG
1 TGCCACCAACTTGTGTGGGCTTTAGAAG
1825159 AATGGTGAAA
Statistics
Matches: 139, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
30 3 0.02
31 4 0.03
32 77 0.55
33 49 0.35
34 6 0.04
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.29
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAGGGT
Found at i:1825074 original size:65 final size:63
Alignment explanation
Indices: 1824970--1825158 Score: 263
Period size: 65 Copynumber: 3.0 Consensus size: 63
1824960 TAAAGGAAGA
*
1824970 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGAT
1 TGCCACCAACTTGTGTGGGC-TTTGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGG-T
* *
1825035 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCAACTTGCGTGGGCTTTGAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAAAAAGGTTGCCACCGACTTGTGTGGGCTTT-AGAAGGGT
** * * *
1825100 TGCCACTGACTTGTGTGGGCTTTGGAAAGGGTTGCCATCGACTTGTGTGGGCTTT-GAAG
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAG
1825159 AATGGTGAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
62 4 0.04
64 30 0.27
65 71 0.63
66 7 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.29
Consensus pattern (63 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGT
Found at i:1825144 original size:97 final size:98
Alignment explanation
Indices: 1824970--1825154 Score: 286
Period size: 97 Copynumber: 1.9 Consensus size: 98
1824960 TAAAGGAAGA
*
1824970 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGAT
1 TGCCACCAACTTGCGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGAT
1825035 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGT
66 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGT
* *
1825068 TGCCACCAACTTGCGTGGGC-TTTG-AGAAGGGTTGCCACTGACTTGTGTGGGCTTTGGAAAGGG
1 TGCCACCAACTTGCGTGGGCTTTTGAAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG-AAGGG
* *
1825131 -TTGCCATCGACTTGTGTGGGCTTT
64 ATTGCCACCAACTTGTGTGGGCTTT
1825155 GAAGAATGGT
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
96 4 0.05
97 52 0.65
98 24 0.30
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (98 bp):
TGCCACCAACTTGCGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGAT
TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGT
Found at i:1825213 original size:33 final size:33
Alignment explanation
Indices: 1825166--1825808 Score: 600
Period size: 34 Copynumber: 19.8 Consensus size: 33
1825156 AAGAATGGTG
* * *
1825166 AAAGATGCCACGAAGTTGTAGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1825199 CAAGGTGCCACGAAGTTGTGGACTTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAA-GGAA
* **
1825234 AAAGAGTGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1825266 GAAGGTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1825299 CAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAA-GGAA
*
1825334 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-G--
1 AAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
1825366 ---GGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1825396 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
1825431 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1825464 AAAGAGTGCCACGGAATTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
1825499 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1825532 AAAGAGTGCCACGGAGTTGTGGGCTTAAAA-G--
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1825563 ---GGTGCCACGAAGTTATGGACTTAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1825592 AAAAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
* *
1825626 AAAGATGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1825659 CAAGGTGCCACGGAGTTGTGGACTTTAAAGGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGG-AA
*
1825693 AAAGGGTGCCACGGAGTCGTGGACTTAAAA-G--
1 AAA-GGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * **
1825724 ---GGTGCCACGAAGTTGTGG-GTTTTAA--AA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1825751 AGA-GTGCCACAGAGTTGTGGACTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* *
1825784 AAAGGTGCCACGAAGTCGTGGACTT
1 AAAGGTGCCACGGAGTTGTGGACTT
1825809 TGAGAAAGGA
Statistics
Matches: 504, Mismatches: 68, Indels: 76
0.78 0.10 0.12
Matches are distributed among these distances:
26 4 0.01
27 44 0.09
28 20 0.04
29 16 0.03
31 23 0.05
32 24 0.05
33 117 0.23
34 150 0.30
35 65 0.13
36 41 0.08
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:1825561 original size:27 final size:27
Alignment explanation
Indices: 1825531--1825774 Score: 128
Period size: 27 Copynumber: 8.0 Consensus size: 27
1825521 CTTAGAAGGA
*
1825531 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
* * *
1825558 AAAAGGGTGCCACGAAGTTATGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
1825585 AAAAGAAAAAAGTGCCACGGAGTTGTGGACTTT
1 AAAAG-----AGTGCCACGGAGTTGTGGAC-TT
*
1825618 AAAAGGAAAAAGATGCCACAGAGTTGTGGACTT
1 AAAA-G----AG-TGCCACGGAGTTGTGGACTT
1825651 AAAAGGAACAAGGTGCCACGGAGTTGTGGACTTT
1 AAAA-G----A-GTGCCACGGAGTTGTGGAC-TT
* *
1825685 AAAGGAAAAAAGGGTGCCACGGAGTCGTGGACTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
* * **
1825719 AAAAGGGTGCCACGAAGTTGTGGGTTTT
1 AAAAGAGTGCCACGGAGTTGT-GGACTT
*
1825747 AAAAAGAGTGCCACAGAGTTGTGGACTT
1 -AAAAGAGTGCCACGGAGTTGTGGACTT
1825775 TGAAAAGAAA
Statistics
Matches: 177, Mismatches: 21, Indels: 37
0.75 0.09 0.16
Matches are distributed among these distances:
27 47 0.27
28 8 0.05
29 18 0.10
32 17 0.10
33 41 0.23
34 23 0.13
35 18 0.10
40 1 0.01
41 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.21
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTTGTGGACTT
Found at i:1825609 original size:161 final size:158
Alignment explanation
Indices: 1825166--1825818 Score: 599
Period size: 161 Copynumber: 4.0 Consensus size: 158
1825156 AAGAATGGTG
* * * * *
1825166 AAAGATGCCACGAAGTTGTAGACTTAAAAGGAACAA-GGTGCCACGAAGTTGTGGACTTTAAAAG
1 AAAGGTGCCACGGAGTTGTGGACTT-AAAGGAAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA-
* ** * * *
1825230 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA-AAGAAGGTGCCACGGAGTCGTGGACTTAAA
63 -G-----G-GTGCCACGAAGTTGT-GGCTTAAAAGAAAAAAGTGCCACGGAGTTGTGGACTTAAA
* * *
1825294 AGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGA
120 AGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA-GGAA
* *
1825334 AAAGAGTGCCACGGAGTTGTGGGCTT-----TAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGG
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAGGAAAAAGGGTGCCACGGAGTTGTGGACTT------
* * * *
1825394 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGA
59 -AAAAGGGTGCCACGAAGTTGT-GGC-TT-AAAAGAAAAAAGTGCCACGGAGTTGTGGACTTAAA
* * *
1825459 AGGAAAAAGAGTGCCACGGAATTGTGGGCTTTAAAAAGAA
120 AGGAAAAAG-GTGCCACGGAGTTGTGGACTTTAAAAGGAA
* *
1825499 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG
1 AAAGGTGCCACGGAGTTGTGGACTTA-AAGGAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
*
1825564 GTGCCACGAAGTTATGGACTTAAAAGAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAA
65 GTGCCACGAAGTTGTGG-CTTAAAAGAAAAAAGTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAA
* *
1825629 GATGCCACAGAGTTGTGGAC-TTAAAAGGAA
128 GGTGCCACGGAGTTGTGGACTTTAAAAGGAA
* *
1825659 CAAGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAAGGGTGCCACGGAGTCGTGGACTTAAAAG
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAGG-AAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* ** * *
1825724 GGTGCCACGAAGTTGTGGGTT-TTA-AAAAGAGTGCCACAGAGTTGTGGACTTTGAAAA-GAAAA
64 GGTGCCACGAAGTTGTGGCTTAAAAGAAAAAAGTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAA
* *
1825786 AGGTGCCACGAAGTCGTGGACTTTGAGAAAGGA
127 AGGTGCCACGGAGTTGTGGACTTT-A-AAAGGA
1825819 TTTGAAGAAT
Statistics
Matches: 411, Mismatches: 47, Indels: 61
0.79 0.09 0.12
Matches are distributed among these distances:
158 48 0.12
159 7 0.02
160 38 0.09
161 100 0.24
162 36 0.09
163 26 0.06
164 41 0.10
165 41 0.10
166 23 0.06
168 5 0.01
169 17 0.04
170 29 0.07
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (158 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAGGAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
TGCCACGAAGTTGTGGCTTAAAAGAAAAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGT
GCCACGGAGTTGTGGACTTTAAAAGGAA
Found at i:1825793 original size:34 final size:36
Alignment explanation
Indices: 1825747--1825816 Score: 101
Period size: 34 Copynumber: 2.0 Consensus size: 36
1825737 TGTGGGTTTT
*
1825747 AAAAAGAGTGCCAC-AGAGTTGTGGACTTTGA-AAAG
1 AAAAAGAGTGCCACGA-AGTCGTGGACTTTGAGAAAG
1825782 AAAAAG-GTGCCACGAAGTCGTGGACTTTGAGAAAG
1 AAAAAGAGTGCCACGAAGTCGTGGACTTTGAGAAAG
1825817 GATTTGAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 21 0.66
35 11 0.34
ACGTcount: A:0.39, C:0.13, G:0.30, T:0.19
Consensus pattern (36 bp):
AAAAAGAGTGCCACGAAGTCGTGGACTTTGAGAAAG
Found at i:1825945 original size:16 final size:17
Alignment explanation
Indices: 1825914--1825951 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1825904 GATGCAAATA
* *
1825914 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
1825931 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
1825947 ATGAT
1 ATGAT
1825952 TACAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:1826795 original size:16 final size:16
Alignment explanation
Indices: 1826766--1826807 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1826756 GGGTTTTTCC
1826766 TTTCTTCTTTT-TTTT-
1 TTTCTT-TTTTGTTTTG
*
1826781 TTCCTTTTTTGTTTTG
1 TTTCTTTTTTGTTTTG
1826797 TTTCTTTTTTG
1 TTTCTTTTTTG
1826808 GAAAAGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 10 0.43
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (16 bp):
TTTCTTTTTTGTTTTG
Found at i:1834014 original size:13 final size:13
Alignment explanation
Indices: 1833996--1834020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1833986 CAAAGATCAG
1833996 TGTATCGATACAA
1 TGTATCGATACAA
1834009 TGTATCGATACA
1 TGTATCGATACA
1834021 TTTTTTGGCA
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:1837497 original size:19 final size:20
Alignment explanation
Indices: 1837454--1837502 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1837444 TACCCAGATA
1837454 TATCGATACATATTGCTTAG
1 TATCGATACATATTGCTTAG
*
1837474 TATCGATACA-AGTT-CTTGG
1 TATCGATACATA-TTGCTTAG
1837493 TATCGATACA
1 TATCGATACA
1837503 CAGTAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
TATCGATACATATTGCTTAG
Found at i:1837588 original size:13 final size:13
Alignment explanation
Indices: 1837551--1837588 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1837541 AACTCACTCC
*
1837551 GTATCGATACAGT
1 GTATCGATACATT
*
1837564 GTATCAATACATT
1 GTATCGATACATT
1837577 GTATCGATACAT
1 GTATCGATACAT
1837589 GGTCAAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1839611 original size:97 final size:97
Alignment explanation
Indices: 1839386--1839632 Score: 325
Period size: 97 Copynumber: 2.5 Consensus size: 97
1839376 TTTTTGATTG
** * * * *
1839386 AAAAACGAAGTTGGAGTATCCCCTCGGAGGAATGAGGTTGGAGTGTCCCTGATGATGACAATTTA
1 AAAAACGGGGTTGGAGTATCCCCTCAGAGGAAGGGGGTTGGAGTGTCCCCGATGATGACAATTTA
1839451 AATGAGAATAAAATTTAAACTTTGATGCGTTT
66 AATGAGAATAAAATTTAAACTTTGATGCGTTT
* *
1839483 AAAAACGGGGTTGGAGTATCCCCTCAGAGGAAGGGGGTTGAAGTGTCCCCGATGGTGACAATTTA
1 AAAAACGGGGTTGGAGTATCCCCTCAGAGGAAGGGGGTTGGAGTGTCCCCGATGATGACAATTTA
* * *
1839548 AGTGAGAATAAGATTTAAACTTTGATGTGTTT
66 AATGAGAATAAAATTTAAACTTTGATGCGTTT
* * * * * *
1839580 AAAAGCGGGGTTGTAGTATCCTCT-TGAAGGAATGGGGTTGGAGTATCCCCGAT
1 AAAAACGGGGTTGGAGTATCCCCTCAG-AGGAAGGGGGTTGGAGTGTCCCCGAT
1839633 AAATAAAATT
Statistics
Matches: 131, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
96 1 0.01
97 130 0.99
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28
Consensus pattern (97 bp):
AAAAACGGGGTTGGAGTATCCCCTCAGAGGAAGGGGGTTGGAGTGTCCCCGATGATGACAATTTA
AATGAGAATAAAATTTAAACTTTGATGCGTTT
Found at i:1841354 original size:11 final size:11
Alignment explanation
Indices: 1841338--1841369 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1841328 CTATTTCTCC
1841338 TCTCTTTTCTT
1 TCTCTTTTCTT
1841349 TCTCTTTT-TT
1 TCTCTTTTCTT
1841359 T-TCTTTTCTT
1 TCTCTTTTCTT
1841369 T
1 T
1841370 TTAGTTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.30
10 6 0.30
11 8 0.40
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TCTCTTTTCTT
Found at i:1841368 original size:14 final size:15
Alignment explanation
Indices: 1841342--1841371 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1841332 TTCTCCTCTC
1841342 TTTTCTTTCTCTTTT
1 TTTTCTTTCTCTTTT
1841357 TTTTCTTT-TCTTTT
1 TTTTCTTTCTCTTTT
1841371 T
1 T
1841372 AGTTGAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTCTCTTTT
Found at i:1845863 original size:142 final size:137
Alignment explanation
Indices: 1845602--1845869 Score: 313
Period size: 142 Copynumber: 1.9 Consensus size: 137
1845592 AATAAACTTG
* * *
1845602 AGCTTTCAAATTGTTTTATGAGATTATAATTACGTGTTTAAATTACAATAGAAATCAATAAATTA
1 AGCTTTCAAATTGTTTTATGAAATTATAATTACGTGTTCAAATTACAATAGAAATAAATAAATTA
* * *** ** * * *
1845667 TATATAACTAGATAAATTTAATGTGAAATTATGGGCAATTGATACATGATTAAATTTGAACGCGA
66 CATAGAACTAGATAAATTTAATACAAAATTATGACCAATTGATACAGGAATAAATCTGAACGCGA
1845732 CAGCAAA
131 CAGCAAA
* **
1845739 AGCTTTCACATTGTTTTCATGAAATTATAATTGTGTGTTCAAATTACAATAGGAACCATTAAATA
1 AGCTTTCAAATTGTTTT-ATGAAATTATAATTACGTGTTCAAATTACAATA-GAA--A-TAAATA
* *
1845804 AATTACATAGAACTAGATAAATTTAATACAAAATTA-GACCAAATTTATATAGGAATAAATCTGA
61 AATTACATAGAACTAGATAAATTTAATACAAAATTATGACC-AATTGATACAGGAATAAATCTGA
1845868 AC
125 AC
1845870 ATAAGAATTT
Statistics
Matches: 107, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
137 16 0.15
138 29 0.27
139 3 0.03
141 3 0.03
142 56 0.52
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (137 bp):
AGCTTTCAAATTGTTTTATGAAATTATAATTACGTGTTCAAATTACAATAGAAATAAATAAATTA
CATAGAACTAGATAAATTTAATACAAAATTATGACCAATTGATACAGGAATAAATCTGAACGCGA
CAGCAAA
Found at i:1847202 original size:5 final size:6
Alignment explanation
Indices: 1847154--1847199 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
1847144 AATTAATAAT
* **
1847154 TTTTAA TTTTTA GATTAA TTTTAA TTTTAA TTTTAA TTTT-A TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
1847200 TTTCTTAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:1847316 original size:26 final size:26
Alignment explanation
Indices: 1847287--1847336 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1847277 AATTAAAATA
*
1847287 ATTTAATTTATTAATTAAT-TATTTTT
1 ATTTAATTT-TTAAATAATATATTTTT
*
1847313 ATTTGATTTTTAAATAATATATTT
1 ATTTAATTTTTAAATAATATATTT
1847337 AAAGTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTAATTTTTAAATAATATATTTTT
Found at i:1851451 original size:2 final size:2
Alignment explanation
Indices: 1851444--1851538 Score: 131
Period size: 2 Copynumber: 47.0 Consensus size: 2
1851434 TTTTAACCTT
1851444 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1851486 TA TA TA TA TA TGA TA CA CTGA -A TG TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA
1851527 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1851539 ATAATAAGCT
Statistics
Matches: 84, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
1 2 0.02
2 79 0.94
3 2 0.02
4 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1851702 original size:14 final size:16
Alignment explanation
Indices: 1851657--1851703 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
1851647 TTTGATACCA
*
1851657 ATATATAAATACAAAAT
1 ATATATAAAT-TAAAAT
1851674 ATATATAAATT-AAAT
1 ATATATAAATTAAAAT
1851689 -TATA-AAATTAAAAT
1 ATATATAAATTAAAAT
1851703 A
1 A
1851704 ATCGAACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.19
14 8 0.30
15 4 0.15
17 10 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATATAAATTAAAAT
Found at i:1852838 original size:26 final size:26
Alignment explanation
Indices: 1852802--1852855 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1852792 GGTGCCCTAC
*
1852802 TTTCTGTTACATGGGCTAGGGGTTCA
1 TTTCTGTTACATAGGCTAGGGGTTCA
1852828 TTTCTGTTACATAGGCTAGGGGTTCA
1 TTTCTGTTACATAGGCTAGGGGTTCA
1852854 TT
1 TT
1852856 AGCTTACGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.41
Consensus pattern (26 bp):
TTTCTGTTACATAGGCTAGGGGTTCA
Done.