Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 14 of 15
Found at i:1964442 original size:44 final size:44
Alignment explanation
Indices: 1964379--1964470 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
1964369 TTTTGTGTTG
*
1964379 TAATCGTGTCATGTCGTATCATATTAATATAAACAGATCAAGTT
1 TAATCGTGTCATATCGTATCATATTAATATAAACAGATCAAGTT
1964423 TAATCGTGTCATATCGTATCATATTAATATAAACAGATCAAGTT
1 TAATCGTGTCATATCGTATCATATTAATATAAACAGATCAAGTT
1964467 TAAT
1 TAAT
1964471 TATGTCATGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (44 bp):
TAATCGTGTCATATCGTATCATATTAATATAAACAGATCAAGTT
Found at i:1966153 original size:13 final size:13
Alignment explanation
Indices: 1966135--1966160 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1966125 CAATTTTTTG
1966135 TGTATCGATACAT
1 TGTATCGATACAT
1966148 TGTATCGATACAT
1 TGTATCGATACAT
1966161 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1968720 original size:13 final size:13
Alignment explanation
Indices: 1968702--1968740 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1968692 ATAAACACCC
*
1968702 TGTATCGATACAG
1 TGTATCGATACAA
1968715 TGTATCGATACAA
1 TGTATCGATACAA
1968728 TGTATCGATACAA
1 TGTATCGATACAA
1968741 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1968751 original size:20 final size:20
Alignment explanation
Indices: 1968726--1968804 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1968716 GTATCGATAC
1968726 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1968746 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1968771 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1968791 CATGTATCGATACA
1 AATGTATCGATACA
1968805 TTTTAGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1970839 original size:15 final size:15
Alignment explanation
Indices: 1970819--1970849 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1970809 ATTTCGTTTG
*
1970819 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1970834 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1970849 G
1 G
1970850 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1972677 original size:21 final size:23
Alignment explanation
Indices: 1972652--1972699 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
1972642 GCAAGTTTTC
*
1972652 ATTTTTC-TTAGCTAAC-TCATT
1 ATTTTTCATTAGCCAACTTCATT
*
1972673 A-TTTTCATTAGCCAACTTCTTT
1 ATTTTTCATTAGCCAACTTCATT
1972695 ATTTT
1 ATTTT
1972700 AACTTGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 5 0.23
23 3 0.14
ACGTcount: A:0.23, C:0.19, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTTTTCATTAGCCAACTTCATT
Found at i:1972699 original size:22 final size:20
Alignment explanation
Indices: 1972654--1972699 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1972644 AAGTTTTCAT
*
1972654 TTTTCTTAGCTAACTCATTA
1 TTTTCTTAGCCAACTCATTA
*
1972674 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAAC-TCATTA
1972696 TTTT
1 TTTT
1972700 AACTTGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 8 0.36
22 9 0.41
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTCTTAGCCAACTCATTA
Found at i:1974933 original size:13 final size:13
Alignment explanation
Indices: 1974915--1974940 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1974905 CAATTTTTTG
1974915 TGTATCGATACAT
1 TGTATCGATACAT
1974928 TGTATCGATACAT
1 TGTATCGATACAT
1974941 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1975458 original size:25 final size:25
Alignment explanation
Indices: 1975424--1975482 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
1975414 GCTAATTCTT
1975424 TCTTTTAATTGTTGACCTTTGTAGC
1 TCTTTTAATTGTTGACCTTTGTAGC
1975449 TCTTTTAATTGTTGACCTTTGTAGC
1 TCTTTTAATTGTTGACCTTTGTAGC
1975474 TCTTTTAAT
1 TCTTTTAAT
1975483 AGTCTTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.17, C:0.15, G:0.14, T:0.54
Consensus pattern (25 bp):
TCTTTTAATTGTTGACCTTTGTAGC
Found at i:1976508 original size:7 final size:7
Alignment explanation
Indices: 1976496--1976525 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1976486 AGGACTTAAA
1976496 AAAATAG
1 AAAATAG
1976503 AAAATA-
1 AAAATAG
1976509 AAAATAG
1 AAAATAG
1976516 AAAATAG
1 AAAATAG
1976523 AAA
1 AAA
1976526 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (7 bp):
AAAATAG
Found at i:1976513 original size:13 final size:13
Alignment explanation
Indices: 1976495--1976526 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1976485 TAGGACTTAA
1976495 AAAAATAGAAAAT
1 AAAAATAGAAAAT
1976508 AAAAATAGAAAAT
1 AAAAATAGAAAAT
*
1976521 AGAAAT
1 AAAAAT
1976527 TAATAAAAAT
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:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (13 bp):
AAAAATAGAAAAT
Found at i:1978425 original size:70 final size:70
Alignment explanation
Indices: 1978297--1978431 Score: 182
Period size: 70 Copynumber: 1.9 Consensus size: 70
1978287 TATATTTTTT
* *
1978297 AATGTATCGATATATTCTGTCTTTTACCCAGATGCATCGATACATGTATGAATGTATCGATACAT
1 AATGTATCGATATATTCTGTCTTTTAACCAGATGCATCGATACATGTATGAATATATCGATACAT
1978362 TCTTC
66 TCTTC
* * * * * *
1978367 AATGTATCGATATATTTTGTCTTTTTAACCAGATGTATCGATA-TTTTTTTAATATATCGATACA
1 AATGTATCGATATATTCTGTC-TTTTAACCAGATGCATCGATACATGTATGAATATATCGATACA
1978431 T
65 T
1978432 CTAGTTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 37 0.66
71 19 0.34
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (70 bp):
AATGTATCGATATATTCTGTCTTTTAACCAGATGCATCGATACATGTATGAATATATCGATACAT
TCTTC
Found at i:1981842 original size:18 final size:18
Alignment explanation
Indices: 1981821--1981874 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
1981811 AGCCAAATAT
1981821 AAGTTTTATAAAAGTGTA
1 AAGTTTTATAAAAGTGTA
* *
1981839 AAG--TT-TCAAA-TAT-
1 AAGTTTTATAAAAGTGTA
1981852 AAGTTTTATAAAAGTGTA
1 AAGTTTTATAAAAGTGTA
1981870 AAGTT
1 AAGTT
1981875 GTCTTTCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
13 3 0.11
14 2 0.07
15 6 0.22
16 6 0.22
17 2 0.07
18 8 0.30
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.39
Consensus pattern (18 bp):
AAGTTTTATAAAAGTGTA
Found at i:1981851 original size:31 final size:31
Alignment explanation
Indices: 1981814--1981874 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
1981804 AGTTATAAGC
1981814 CAAATATAAGTTTTATAAAAGTGTAAAGTTT
1 CAAATATAAGTTTTATAAAAGTGTAAAGTTT
1981845 CAAATATAAGTTTTATAAAAGTGTAAAGTT
1 CAAATATAAGTTTTATAAAAGTGTAAAGTT
1981875 GTCTTTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (31 bp):
CAAATATAAGTTTTATAAAAGTGTAAAGTTT
Found at i:1982136 original size:19 final size:19
Alignment explanation
Indices: 1982112--1982151 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1982102 AAACCTTAGA
1982112 ATAATTTATTTCTCAACCC
1 ATAATTTATTTCTCAACCC
1982131 ATAATTTATTTCTCAACCC
1 ATAATTTATTTCTCAACCC
1982150 AT
1 AT
1982152 TAAAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATTTATTTCTCAACCC
Found at i:1985949 original size:3 final size:3
Alignment explanation
Indices: 1985941--1985978 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1985931 TCTCCACCGC
1985941 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1985979 AATTAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1986644 original size:21 final size:19
Alignment explanation
Indices: 1986620--1986669 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
1986610 GAATTGATTT
*
1986620 AAAATATTATTTATTTTATA
1 AAAATATTATTT-TTTAATA
1986640 AAAA-ATTATTTTTTAATCA
1 AAAATATTATTTTTTAAT-A
1986659 AAAATAATTAT
1 AAAAT-ATTAT
1986670 AAAATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 12 0.46
20 4 0.15
21 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATATTATTTTTTAATA
Found at i:1986908 original size:2 final size:2
Alignment explanation
Indices: 1986903--1986937 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1986893 ATATATATAT
1986903 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1986938 TTGGCTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1987390 original size:6 final size:6
Alignment explanation
Indices: 1987379--1987473 Score: 58
Period size: 6 Copynumber: 15.8 Consensus size: 6
1987369 AAATTACATT
*
1987379 ATATAA ATATAA AT-TAA TTA-AA ATAATAA ATATATA ATAT-- ATATAA
1 ATATAA ATATAA ATATAA ATATAA AT-ATAA ATATA-A ATATAA ATATAA
* * *
1987425 ATATAA ATAATAA TTAATTAA A-AT-A ATAAAA ATATAA TATATTA ATATA
1 ATATAA AT-ATAA AT-A-TAA ATATAA ATATAA ATATAA -ATATAA ATATA
1987474 TTAATTTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
4 6 0.09
5 9 0.13
6 31 0.44
7 21 0.30
8 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAA
Found at i:1987392 original size:25 final size:24
Alignment explanation
Indices: 1987364--1987463 Score: 59
Period size: 23 Copynumber: 4.2 Consensus size: 24
1987354 ATTTTAGATA
* *
1987364 AAATAAAATTACATTATATAAATAT
1 AAATAAAATTAAAATA-ATAAATAT
*
1987389 AAAT-TAATTAAAATAATAAATAT
1 AAATAAAATTAAAATAATAAATAT
*
1987412 --ATAATATATATAAAT-ATAAATA-
1 AAATAAAAT-TA-AAATAATAAATAT
* *
1987434 ATAAT-TAATTAAAATAATAAAAAT
1 A-AATAAAATTAAAATAATAAATAT
1987458 ATAATA
1 A-AATA
1987464 TATTAATATA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
21 2 0.03
22 6 0.10
23 25 0.43
24 19 0.33
25 6 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAAATTAAAATAATAAATAT
Found at i:1987411 original size:23 final size:24
Alignment explanation
Indices: 1987381--1987462 Score: 102
Period size: 23 Copynumber: 3.5 Consensus size: 24
1987371 ATTACATTAT
1987381 ATAAATATA-AATTAATTAAAATA
1 ATAAATATATAATTAATTAAAATA
1987404 ATAAATATATAA-T-ATATATAAAT-
1 ATAAATATATAATTAAT-TA-AAATA
1987427 ATAAATA-ATAATTAATTAAAATA
1 ATAAATATATAATTAATTAAAATA
*
1987450 ATAAAAATATAAT
1 ATAAATATATAAT
1987463 ATATTAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
22 10 0.20
23 28 0.55
24 13 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAATATATAATTAATTAAAATA
Found at i:1987440 original size:46 final size:46
Alignment explanation
Indices: 1987378--1987474 Score: 153
Period size: 46 Copynumber: 2.1 Consensus size: 46
1987368 AAAATTACAT
*
1987378 TATATAAATATAAATTAATTAAAATAATAAATATATAATATATATAA
1 TATATAAATATAAATTAATTAAAATAATAAAAATATAATATAT-TAA
1987425 -ATATAAATA-ATAATTAATTAAAATAATAAAAATATAATATATTAA
1 TATATAAATATA-AATTAATTAAAATAATAAAAATATAATATATTAA
1987470 TATAT
1 TATAT
1987475 TAATTTATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
45 4 0.09
46 43 0.91
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (46 bp):
TATATAAATATAAATTAATTAAAATAATAAAAATATAATATATTAA
Found at i:1987448 original size:16 final size:16
Alignment explanation
Indices: 1987390--1987453 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
1987380 TATAAATATA
1987390 AATTAATTAAAATAAT
1 AATTAATTAAAATAAT
* *
1987406 AAAT-A-TATAAT-AT
1 AATTAATTAAAATAAT
*
1987419 -ATATAAATATAAATAAT
1 AAT-TAATTA-AAATAAT
1987436 AATTAATTAAAATAAT
1 AATTAATTAAAATAAT
1987452 AA
1 AA
1987454 AAATATAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
12 1 0.03
13 3 0.08
14 6 0.16
15 3 0.08
16 15 0.41
17 7 0.19
18 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTAATTAAAATAAT
Found at i:1987534 original size:15 final size:15
Alignment explanation
Indices: 1987456--1987536 Score: 51
Period size: 15 Copynumber: 5.2 Consensus size: 15
1987446 AATAATAAAA
*
1987456 ATATAATATATTAAT
1 ATATAATATTTTAAT
1987471 ATATTAAT-TTATATAAT
1 ATA-TAATATT-T-TAAT
1987488 ATA-AAT-TTTTGATAT
1 ATATAATATTTT-A-AT
* * *
1987503 AAAAAATTATGTTAAT
1 ATATAA-TATTTTAAT
1987519 ATATAATATTTTAAT
1 ATATAATATTTTAAT
1987534 ATA
1 ATA
1987537 ACTATAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
13 1 0.02
14 2 0.04
15 24 0.46
16 13 0.25
17 9 0.17
18 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATAATATTTTAAT
Found at i:1989600 original size:21 final size:20
Alignment explanation
Indices: 1989552--1989603 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1989542 ATTATTTAAA
* *
1989552 AAATAAAAAATATTTAAATT
1 AAATATAAAATATATAAATT
1989572 AAATTATAAAATATATAAATAT
1 AAA-TATAAAATATATAAAT-T
*
1989594 TAATATAAAA
1 AAATATAAAA
1989604 ATAATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATAAAATATATAAATT
Found at i:1990060 original size:3 final size:3
Alignment explanation
Indices: 1990052--1990086 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1990042 TTATCTTCAA
1990052 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1990087 GAAAATTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1992342 original size:19 final size:20
Alignment explanation
Indices: 1992320--1992362 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1992310 TTGGATTTTA
*
1992320 CTTTAAACTTT-TTCTCTTT
1 CTTTAAACTTTATTCCCTTT
*
1992339 CTTTAATCTTTATTCCCTTT
1 CTTTAAACTTTATTCCCTTT
1992359 -TTTA
1 CTTTA
1992363 TAATCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (20 bp):
CTTTAAACTTTATTCCCTTT
Found at i:1994054 original size:23 final size:23
Alignment explanation
Indices: 1994007--1994050 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1993997 TTGTTTCATT
*
1994007 TTATGATTTATTCTTTTCTTTTC
1 TTATCATTTATTCTTTTCTTTTC
*
1994030 TTATCATTT-TTCTTTTTTTTT
1 TTATCATTTATTCTTTTCTTTT
1994051 TCTTTAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75
Consensus pattern (23 bp):
TTATCATTTATTCTTTTCTTTTC
Found at i:1996192 original size:2 final size:2
Alignment explanation
Indices: 1996185--1996225 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1996175 GTTTACCTTT
1996185 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
1996226 TATCTTTATT
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:2002622 original size:15 final size:15
Alignment explanation
Indices: 2002575--2002623 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2002565 CCGAATGTTG
* *
2002575 AATCCGATTAACCCG
1 AATCAGATTAACCCA
* *
2002590 AATCTAGAATAACACA
1 AATC-AGATTAACCCA
2002606 AATCAGATTAACCCA
1 AATCAGATTAACCCA
2002621 AAT
1 AAT
2002624 GTTATAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.20
Consensus pattern (15 bp):
AATCAGATTAACCCA
Found at i:2003382 original size:11 final size:11
Alignment explanation
Indices: 2003362--2003392 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2003352 CTAAATACAT
2003362 AAAA-ATTTTA
1 AAAATATTTTA
2003372 AAAATATTTTA
1 AAAATATTTTA
2003383 AAAATATTTT
1 AAAATATTTT
2003393 TATAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:2003393 original size:12 final size:12
Alignment explanation
Indices: 2003367--2003401 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
2003357 TACATAAAAA
2003367 TTTTAAAAATA-
1 TTTTAAAAATAT
2003378 TTTTAAAAATAT
1 TTTTAAAAATAT
*
2003390 TTTTATAAATAT
1 TTTTAAAAATAT
2003402 ATATTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTTAAAAATAT
Found at i:2004706 original size:2 final size:2
Alignment explanation
Indices: 2004699--2004725 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2004689 ATTTGAAGGT
2004699 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2004726 TACGTCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2005335 original size:59 final size:59
Alignment explanation
Indices: 2005270--2005391 Score: 226
Period size: 59 Copynumber: 2.1 Consensus size: 59
2005260 GTATTTGACA
*
2005270 CTCTCTTCCAATAACAAAATTCAAAATGTTACAGAGGAGCAACTCAAGTTGTTTTTACT
1 CTCTCTTCCAATAACAAAATTCAAAATGTTACAGAGGACCAACTCAAGTTGTTTTTACT
*
2005329 CTCTCTTCCAATAACAAAATTCAAAATGTTACAGGGGACCAACTCAAGTTGTTTTTACT
1 CTCTCTTCCAATAACAAAATTCAAAATGTTACAGAGGACCAACTCAAGTTGTTTTTACT
2005388 CTCT
1 CTCT
2005392 TATAAAGGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (59 bp):
CTCTCTTCCAATAACAAAATTCAAAATGTTACAGAGGACCAACTCAAGTTGTTTTTACT
Found at i:2006367 original size:32 final size:32
Alignment explanation
Indices: 2006329--2006397 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
2006319 ATACGAGACT
* *
2006329 TTATATTGGTATTATATTT-ATATATTTTATTA
1 TTATATTAGTATTATATTTAAAATATTTT-TTA
*
2006361 TTATATTATTATTATATTTAAAATATTTTTTA
1 TTATATTAGTATTATATTTAAAATATTTTTTA
*
2006393 ATATA
1 TTATA
2006398 AAAGATATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 24 0.75
33 8 0.25
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (32 bp):
TTATATTAGTATTATATTTAAAATATTTTTTA
Found at i:2006371 original size:11 final size:11
Alignment explanation
Indices: 2006338--2006378 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2006328 TTTATATTGG
2006338 TATTATA-T-T
1 TATTATATTAT
*
2006347 TATATATTTTAT
1 TAT-TATATTAT
2006359 TATTATATTAT
1 TATTATATTAT
2006370 TATTATATT
1 TATTATATT
2006379 TAAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 3 0.11
10 3 0.11
11 17 0.63
12 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTATATTAT
Found at i:2011964 original size:21 final size:23
Alignment explanation
Indices: 2011925--2011969 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
2011915 GAAAATAAGT
* *
2011925 AATAATTATTAAATGATTATATA
1 AATAATTATAAAATGATTAAATA
2011948 AATAATT-TAAAAT-ATTAAATA
1 AATAATTATAAAATGATTAAATA
2011969 A
1 A
2011970 TTATAAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AATAATTATAAAATGATTAAATA
Found at i:2011968 original size:17 final size:17
Alignment explanation
Indices: 2011946--2012004 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
2011936 AATGATTATA
2011946 TAAATAATTTAAAATAT
1 TAAATAATTTAAAATAT
*
2011963 TAAATAATTATAAAGTTATT
1 TAAATAATT-TAAA-ATA-T
* *
2011983 TAAATGATTTTAAATAT
1 TAAATAATTTAAAATAT
*
2012000 AAAAT
1 TAAAT
2012005 GAAGTATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 14 0.41
18 6 0.18
19 5 0.15
20 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATAATTTAAAATAT
Found at i:2011998 original size:37 final size:39
Alignment explanation
Indices: 2011925--2012015 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 39
2011915 GAAAATAAGT
*
2011925 AATAATTATTAAATGATTATATAAATAATTTAAAATATTA
1 AATAATTA-TAAATGATTATATAAATAATTTAAAATATAA
* * *
2011965 AATAATTATAAA-G-TTATTTAAATGATTTTAAATATAA
1 AATAATTATAAATGATTATATAAATAATTTAAAATATAA
*
2012002 AATGAAGTATAAAT
1 AAT-AATTATAAAT
2012016 AATATTAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
37 23 0.52
38 9 0.20
39 4 0.09
40 8 0.18
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (39 bp):
AATAATTATAAATGATTATATAAATAATTTAAAATATAA
Found at i:2014001 original size:3 final size:3
Alignment explanation
Indices: 2013993--2014024 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2013983 GATGCAATTA
2013993 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2014025 ACAACTGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2018659 original size:22 final size:21
Alignment explanation
Indices: 2018612--2018660 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2018602 ATTAAAATAT
**
2018612 TATTTTATATTAATTTTTATA
1 TATTTTATATTAATTTAGATA
2018633 TATTTTATAATTAAATTTAGATA
1 TATTTTAT-ATT-AATTTAGATA
2018656 -ATTTT
1 TATTTT
2018661 TTTTTACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 8 0.33
23 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TATTTTATATTAATTTAGATA
Found at i:2018821 original size:14 final size:15
Alignment explanation
Indices: 2018802--2018836 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2018792 ATTCAATCAT
2018802 ATTTAATAT-ATAAA
1 ATTTAATATGATAAA
*
2018816 ATTTAATATGTTAAA
1 ATTTAATATGATAAA
2018831 ATTTAA
1 ATTTAA
2018837 ATTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
ATTTAATATGATAAA
Found at i:2018829 original size:22 final size:21
Alignment explanation
Indices: 2018800--2018849 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
2018790 TCATTCAATC
*
2018800 ATATTTAATATATAAAATTTA
1 ATATTTAAAATATAAAATTTA
* *
2018821 ATATGTTAAAATTTAAATTTTA
1 ATAT-TTAAAATATAAAATTTA
2018843 ATATTTA
1 ATATTTA
2018850 TAATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTTAAAATATAAAATTTA
Found at i:2020434 original size:2 final size:2
Alignment explanation
Indices: 2020418--2020460 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2020408 TTTATACCAA
*
2020418 AT AT A- AT AC 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
2020459 AT
1 AT
2020461 CAAAGCTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2023211 original size:133 final size:133
Alignment explanation
Indices: 2022973--2023236 Score: 456
Period size: 133 Copynumber: 2.0 Consensus size: 133
2022963 AAACACAAGC
*
2022973 ATTCACCACAGAAAATCTGGACTAGTATAACTAAATTTATATGGACAATTGGATTTATCCCCCAA
1 ATTCACCACAGAAAATCTGGACTAGTATAACTAAATTTATATGGACAATTGGATTTATCCCCAAA
* ** *
2023038 AATCTCAGCCCATTCACAAAAATAAATGAAACAAGCTCACTGATGTTTTAGTTCAGCTTGTTTAT
66 AATCTCAGCCCATTCACAAAAATAAACGAAACAAGCTCACTGATGTTACAATTCAGCTTGTTTAT
2023103 TCA
131 TCA
* *
2023106 ATTCACCACAGAAAATCTGGACTAGTATAACTAAATTTATATGGATAATTGGATTTATTCCCAAA
1 ATTCACCACAGAAAATCTGGACTAGTATAACTAAATTTATATGGACAATTGGATTTATCCCCAAA
*
2023171 AATCTCAGCCCATTCACAAACATAAACGAAACAAGCTCACTGATGTTACAATTCAGCTTGTTTAT
66 AATCTCAGCCCATTCACAAAAATAAACGAAACAAGCTCACTGATGTTACAATTCAGCTTGTTTAT
2023236 T
131 T
2023237 AAATGAGTTT
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 123 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.31
Consensus pattern (133 bp):
ATTCACCACAGAAAATCTGGACTAGTATAACTAAATTTATATGGACAATTGGATTTATCCCCAAA
AATCTCAGCCCATTCACAAAAATAAACGAAACAAGCTCACTGATGTTACAATTCAGCTTGTTTAT
TCA
Found at i:2024365 original size:2 final size:2
Alignment explanation
Indices: 2024360--2024390 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2024350 AAACAAATGC
2024360 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2024391 ACAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2030345 original size:15 final size:16
Alignment explanation
Indices: 2030321--2030362 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2030311 ATAAACTTTG
*
2030321 ATTTTGTTTTGAT-TT
1 ATTTTATTTTGATATT
2030336 ATTTTATTTT-ATATT
1 ATTTTATTTTGATATT
2030351 ATTTTATATTTG
1 ATTTTAT-TTTG
2030363 TTGGTTAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 18 0.78
16 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (16 bp):
ATTTTATTTTGATATT
Found at i:2030649 original size:19 final size:20
Alignment explanation
Indices: 2030625--2030670 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
2030615 TAGCTTGCAA
*
2030625 TTTTAATCAATTTTT-TTAT
1 TTTTAATAAATTTTTATTAT
2030644 TTTTAATAAATTTTTATTAT
1 TTTTAATAAATTTTTATTAT
2030664 TTTTAAT
1 TTTTAAT
2030671 TAGTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATAAATTTTTATTAT
Found at i:2032184 original size:16 final size:17
Alignment explanation
Indices: 2032154--2032185 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2032144 TATCCATTTT
2032154 ACATAATATATTGTAAA
1 ACATAATATATTGTAAA
2032171 ACATAATA-ATTGTAA
1 ACATAATATATTGTAA
2032186 TTAAGCATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
ACATAATATATTGTAAA
Found at i:2037250 original size:5 final size:5
Alignment explanation
Indices: 2037232--2037381 Score: 72
Period size: 5 Copynumber: 28.6 Consensus size: 5
2037222 AGTAAATTTA
* * *
2037232 ATAAT ATTATAT ATAAT ATAAAT ATATT ATAAA ATAAT -TAAA ATTAAT
1 ATAAT A-TA-AT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT A-TAAT
* * * * * *
2037280 ATATT ATAAA ATAATT AAAAT ATAAT ATAAAAT TTAAT ATATT ATAAAA
1 ATAAT ATAAT ATAA-T ATAAT ATAAT AT--AAT ATAAT ATAAT AT-AAT
* * * *
2037329 ATAAT ATAAT ATATAA ATAAT TTAAT ATTAAT ATTAT ATAA- ATTAT -TAAT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT
2037379 ATA
1 ATA
2037382 TAAAAATTTA
Statistics
Matches: 106, Mismatches: 26, Indels: 26
0.67 0.16 0.16
Matches are distributed among these distances:
4 9 0.08
5 62 0.58
6 28 0.26
7 7 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:2037280 original size:25 final size:25
Alignment explanation
Indices: 2037252--2037370 Score: 107
Period size: 25 Copynumber: 4.5 Consensus size: 25
2037242 ATATAATATA
2037252 AATATATTATAAAATAATTAAAATT
1 AATATATTATAAAATAATTAAAATT
2037277 AATATATTATAAAATAATTAAAATAT
1 AATATATTATAAAATAATTAAAAT-T
* * *
2037303 AATATAAAATT-TAATATATTATAAAAAT
1 AATAT---ATTATAAAATAAT-TAAAATT
* *
2037331 AATATAATATATAAATAATTTAATATT
1 AATATATTATA-AAATAA-TTAAAATT
2037358 AATAT-TATATAAA
1 AATATAT-TATAAA
2037371 TTATTAATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
25 26 0.34
26 10 0.13
27 18 0.24
28 14 0.18
29 8 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AATATATTATAAAATAATTAAAATT
Found at i:2037291 original size:16 final size:16
Alignment explanation
Indices: 2037232--2037446 Score: 85
Period size: 16 Copynumber: 13.2 Consensus size: 16
2037222 AGTAAATTTA
*
2037232 ATAATATTATATATAAT
1 ATAAAATTA-ATATAAT
* *
2037249 ATAAATATATTATAAAAT
1 ATAAA-AT-TAATATAAT
2037267 AATTAAAATTAATATATTAT
1 -A-TAAAATTAATATA--AT
*
2037287 AAAATAATTAAAATATAAT
1 ATAA-AATT--AATATAAT
*
2037306 ATAAAATTTAATATATT
1 ATAAAA-TTAATATAAT
*
2037323 ATAAAAATAATATAAT
1 ATAAAATTAATATAAT
*
2037339 ATATAAA-TAATTTAAT
1 ATA-AAATTAATATAAT
*
2037355 ATTAATATT-ATATAA-
1 A-TAAAATTAATATAAT
*
2037370 AT--TATTAATAT-AT
1 ATAAAATTAATATAAT
*
2037383 A-AAAATTTATATAAAT
1 ATAAAATTAATAT-AAT
*
2037399 ATAAAA-TAATTTAA-
1 ATAAAATTAATATAAT
* * *
2037413 ATATAATT-ATAAAAA
1 ATAAAATTAATATAAT
2037428 ATAAAA-TACATA-AAT
1 ATAAAATTA-ATATAAT
2037443 ATAA
1 ATAA
2037447 CGTATAAATA
Statistics
Matches: 152, Mismatches: 22, Indels: 50
0.68 0.10 0.22
Matches are distributed among these distances:
12 5 0.03
13 5 0.03
14 18 0.12
15 15 0.10
16 37 0.24
17 27 0.18
18 17 0.11
19 16 0.11
20 6 0.04
21 6 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAAATTAATATAAT
Found at i:2037317 original size:38 final size:38
Alignment explanation
Indices: 2037240--2037426 Score: 149
Period size: 38 Copynumber: 4.9 Consensus size: 38
2037230 TAATAATATT
*
2037240 ATATATAATATAAATATATTATAAA-ATAAT-TAAAA-TTA
1 ATATATTATA-AAATA-ATTA-AAATATAATATAAAATTTA
2037278 ATATATTATAAAATAATTAAAATATAATATAAAATTTA
1 ATATATTATAAAATAATTAAAATATAATATAAAATTTA
*
2037316 ATATATTATAAAAATAA-TATAATAT-ATA-AATAATTTA
1 ATATATTAT-AAAATAATTAAAATATAATATAA-AATTTA
* * * *
2037353 ATATTAATATTATATAAATTATTAATAT-ATA-AAAATTT-
1 ATA-TATTATAAAAT-AATTA-AAATATAATATAAAATTTA
* *
2037391 ATATAAATATAAAATAATTTAAATATAATTATAAAA
1 ATAT-ATTATAAAATAATTAAAATATAA-TATAAAA
2037427 AATAAAATAC
Statistics
Matches: 127, Mismatches: 9, Indels: 25
0.79 0.06 0.16
Matches are distributed among these distances:
35 3 0.02
36 16 0.13
37 31 0.24
38 48 0.38
39 18 0.14
40 11 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (38 bp):
ATATATTATAAAATAATTAAAATATAATATAAAATTTA
Found at i:2037369 original size:81 final size:76
Alignment explanation
Indices: 2037225--2037418 Score: 202
Period size: 81 Copynumber: 2.5 Consensus size: 76
2037215 CGCGTTAAGT
*
2037225 AAATTTAATAATATTATATATAATATAAATATATTATA-AAATAATTAAAATTAATATATTATAA
1 AAATTTAAT-ATATTATATA-AA-AT-AATATAATATATAAATAATTAAAATTAATATATTAT-A
2037289 AATAATTAAAATATAATATA
61 AATAATT--AATAT-ATA-A
*
2037309 AAATTTAATATATTATA-AAAATAATATAATATATAAATAATTTAATATTAATAT-TATATAAAT
1 AAATTTAATATATTATATAAAATAATATAATATATAAATAA-TTAAAATTAATATAT-TATAAAT
*
2037372 TATTAATATATAA
64 AATTAATATATAA
* *
2037385 AAATTT-ATATA-AATATAAAATAATTTAA-ATATAA
1 AAATTTAATATATTATATAAAATAATATAATATATAA
2037419 TTATAAAAAA
Statistics
Matches: 101, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
74 9 0.09
75 16 0.16
76 7 0.07
77 3 0.03
78 5 0.05
79 10 0.10
80 16 0.16
81 17 0.17
82 1 0.01
83 8 0.08
84 9 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (76 bp):
AAATTTAATATATTATATAAAATAATATAATATATAAATAATTAAAATTAATATATTATAAATAA
TTAATATATAA
Found at i:2037393 original size:25 final size:25
Alignment explanation
Indices: 2037338--2037399 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
2037328 AATAATATAA
*
2037338 TATATAAATAATTTAATATTAATAT
1 TATATAAATAATTTAATATTAAAAT
*
2037363 TATATAAATTA-TTAATATATAAAAATT
1 TATATAAATAATTTAATAT-T-AAAA-T
2037390 TATATAAATA
1 TATATAAATA
2037400 TAAAATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 7 0.23
25 11 0.35
26 3 0.10
27 10 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TATATAAATAATTTAATATTAAAAT
Found at i:2041309 original size:21 final size:20
Alignment explanation
Indices: 2041276--2041323 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
2041266 ATGGAAATGT
2041276 TGGACAT-G-TTAAAATGCA
1 TGGACATGGTTTAAAATGCA
2041294 TGGAACATGGTTTAAAATGCA
1 TGG-ACATGGTTTAAAATGCA
2041315 TGGACATGG
1 TGGACATGG
2041324 ACTGTTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.11
19 4 0.15
20 7 0.26
21 13 0.48
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.27
Consensus pattern (20 bp):
TGGACATGGTTTAAAATGCA
Found at i:2042316 original size:51 final size:52
Alignment explanation
Indices: 2042219--2042319 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 52
2042209 ACATTCTTCA
*
2042219 ATGTATTGATACATATAGGTCAAAAACCCAGAATATATCGATACAATGAAGC
1 ATGTATCGATACATATAGGTCAAAAACCCAGAATATATCGATACAATGAAGC
* * *
2042271 ATGTATCGATACATTTAGGTC-AAAACTCAGAATGTATCGATACAATGAA
1 ATGTATCGATACATATAGGTCAAAAACCCAGAATATATCGATACAATGAA
2042320 AAATGTATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 26 0.58
52 19 0.42
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.27
Consensus pattern (52 bp):
ATGTATCGATACATATAGGTCAAAAACCCAGAATATATCGATACAATGAAGC
Found at i:2045735 original size:19 final size:19
Alignment explanation
Indices: 2045695--2045736 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2045685 TTAAAGTATT
* *
2045695 AAAATATATATTATAATTA
1 AAAATATATACTATAATCA
2045714 AAAATATTATACTATAA-CA
1 AAAATA-TATACTATAATCA
2045733 AAAA
1 AAAA
2045737 CTTACTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATATACTATAATCA
Found at i:2045761 original size:11 final size:12
Alignment explanation
Indices: 2045745--2045774 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2045735 AACTTACTTG
2045745 AAAAATAA-TAA
1 AAAAATAATTAA
2045756 AAAAATAATTAA
1 AAAAATAATTAA
2045768 AAAAATA
1 AAAAATA
2045775 TAAGATTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAATAATTAA
Found at i:2046707 original size:33 final size:33
Alignment explanation
Indices: 2046670--2046752 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
2046660 ACTCAAATTC
2046670 AAAAAATTTCAAACTTAAAAAAATTAAAATTTA
1 AAAAAATTTCAAACTTAAAAAAATTAAAATTTA
* * *
2046703 AAAAAATTTTAAA-TCTAAATAAATTCAAATTTA
1 AAAAAATTTCAAACT-TAAAAAAATTAAAATTTA
2046736 AAAAAA-TTCAAACTTAA
1 AAAAAATTTCAAACTTAA
2046753 TTATCGACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
32 9 0.20
33 35 0.80
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (33 bp):
AAAAAATTTCAAACTTAAAAAAATTAAAATTTA
Found at i:2046752 original size:16 final size:16
Alignment explanation
Indices: 2046626--2046752 Score: 98
Period size: 16 Copynumber: 7.8 Consensus size: 16
2046616 AATATGAAAT
*
2046626 AATTCGAACTTAAAAA
1 AATTCAAACTTAAAAA
* *
2046642 GAA-TCAAAATAAAAAA
1 -AATTCAAACTTAAAAA
*
2046658 TAACTCAAA-TTCAAAAA
1 -AATTCAAACTT-AAAAA
*
2046675 ATTTCAAACTTAAAAA
1 AATTCAAACTTAAAAA
* *
2046691 AATTAAAATTTAAAAA
1 AATTCAAACTTAAAAA
* *
2046707 AATTTTAAA-TCTAAATA
1 AA-TTCAAACT-TAAAAA
*
2046724 AATTCAAATTTAAAAA
1 AATTCAAACTTAAAAA
2046740 AATTCAAACTTAA
1 AATTCAAACTTAA
2046753 TTATCGACTA
Statistics
Matches: 89, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
16 62 0.70
17 27 0.30
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (16 bp):
AATTCAAACTTAAAAA
Found at i:2047663 original size:20 final size:21
Alignment explanation
Indices: 2047638--2047679 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2047628 GACATTATAT
*
2047638 TTTTA-TTGTTTTTTATTTCG
1 TTTTATTTATTTTTTATTTCG
2047658 TTTTATTTATTTTTTATTTCG
1 TTTTATTTATTTTTTATTTCG
2047679 T
1 T
2047680 AATAATCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTATTTATTTTTTATTTCG
Found at i:2047690 original size:22 final size:21
Alignment explanation
Indices: 2047646--2047690 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2047636 ATTTTTATTG
* * *
2047646 TTTTTTATTTCGTTTTATTTA
1 TTTTTTATTTCGTATAATCTA
2047667 TTTTTTATTTCGTAATAATCTA
1 TTTTTTATTTCGT-ATAATCTA
2047689 TT
1 TT
2047691 GGTCGAGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTTTATTTCGTATAATCTA
Found at i:2048340 original size:17 final size:19
Alignment explanation
Indices: 2048302--2048342 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
2048292 ATATTCTTTT
*
2048302 AATTTTAAATTGATATCAA
1 AATTTCAAATTGATATCAA
2048321 AATTTCAAA-TGATA-CAA
1 AATTTCAAATTGATATCAA
2048338 AATTT
1 AATTT
2048343 TAAGAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 5 0.24
19 8 0.38
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (19 bp):
AATTTCAAATTGATATCAA
Found at i:2049539 original size:2 final size:2
Alignment explanation
Indices: 2049532--2049562 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2049522 ATGCTTTTTG
*
2049532 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2049563 ATCATACAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2051308 original size:2 final size:2
Alignment explanation
Indices: 2051301--2051326 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2051291 AAATAATTGA
2051301 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
2051327 CTAGTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2055430 original size:15 final size:15
Alignment explanation
Indices: 2055410--2055536 Score: 83
Period size: 15 Copynumber: 8.5 Consensus size: 15
2055400 GATGCATTGA
2055410 TTATTATCATCTACT
1 TTATTATCATCTACT
2055425 TTATTATCATGC-ACT
1 TTATTATCAT-CTACT
2055440 TTATTATCATCTAC-
1 TTATTATCATCTACT
*
2055454 --ATTGTCATCTACT
1 TTATTATCATCTACT
2055467 TTATTTGATGCAT-TGA--
1 TTA-TT-AT-CATCT-ACT
2055483 TTATTATCAATCTACT
1 TTATTATC-ATCTACT
*
2055499 TTATTTGATGCAT-T-GT
1 TTA-TT-AT-CATCTACT
*
2055515 TTATTGTCATCTACT
1 TTATTATCATCTACT
2055530 TTATTAT
1 TTATTAT
2055537 AGTTTTAGTC
Statistics
Matches: 88, Mismatches: 6, Indels: 36
0.68 0.05 0.28
Matches are distributed among these distances:
12 11 0.12
13 4 0.05
14 8 0.09
15 38 0.43
16 13 0.15
17 5 0.06
18 8 0.09
19 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (15 bp):
TTATTATCATCTACT
Found at i:2055530 original size:31 final size:31
Alignment explanation
Indices: 2055454--2055534 Score: 135
Period size: 32 Copynumber: 2.6 Consensus size: 31
2055444 TATCATCTAC
2055454 ATTGTCATCTACTTTATTTGATGCATTGATT
1 ATTGTCATCTACTTTATTTGATGCATTGATT
* *
2055485 ATTATCAATCTACTTTATTTGATGCATTGTTT
1 ATTGTC-ATCTACTTTATTTGATGCATTGATT
2055517 ATTGTCATCTACTTTATT
1 ATTGTCATCTACTTTATT
2055535 ATAGTTTTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 17 0.37
32 29 0.63
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.53
Consensus pattern (31 bp):
ATTGTCATCTACTTTATTTGATGCATTGATT
Found at i:2055972 original size:19 final size:19
Alignment explanation
Indices: 2055948--2055987 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2055938 TAAAATTGTA
* *
2055948 AAAATAATTTATACATTAT
1 AAAATAAATAATACATTAT
*
2055967 AAAATAAATAATACTTTAT
1 AAAATAAATAATACATTAT
2055986 AA
1 AA
2055988 TAAATGGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATAAATAATACATTAT
Found at i:2057298 original size:26 final size:26
Alignment explanation
Indices: 2057242--2057299 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2057232 AAATAAAGTT
*
2057242 TATATTATATTTATTGGAACTTTTAA
1 TATATTATATTGATTGGAACTTTTAA
* *
2057268 GATATTATATTGATT-GAATTTTTTAA
1 TATATTATATTGATTGGAA-CTTTTAA
2057294 TATATT
1 TATATT
2057300 TTTAAGCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (26 bp):
TATATTATATTGATTGGAACTTTTAA
Found at i:2057611 original size:22 final size:21
Alignment explanation
Indices: 2057586--2057628 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
2057576 GTTATTTTAA
2057586 ATTAGGTTAAATTTAATATTAT
1 ATTAGGTTAAATTTAA-ATTAT
** *
2057608 ATTATTTTGAATTTAAATTAT
1 ATTAGGTTAAATTTAAATTAT
2057629 TTTTTATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTAGGTTAAATTTAAATTAT
Found at i:2057920 original size:22 final size:22
Alignment explanation
Indices: 2057894--2057955 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
2057884 TAATATAATT
2057894 ATTAAATAATTAAAAAAAATAA
1 ATTAAATAATTAAAAAAAATAA
***
2057916 ATTAATATAA-TAATTTAAATAA
1 ATTAA-ATAATTAAAAAAAATAA
2057938 ATTAAAATATATTAAAAA
1 ATT-AAATA-ATTAAAAA
2057956 TATAATTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
22 20 0.67
23 7 0.23
24 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATTAAATAATTAAAAAAAATAA
Found at i:2057927 original size:26 final size:26
Alignment explanation
Indices: 2057885--2057939 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2057875 ATTGAATATT
*
2057885 AATATAATTATTAAATAATTAAAAAA
1 AATATAATTAATAAATAATTAAAAAA
* *
2057911 AATA-AATTAATATAATAATTTAAATA
1 AATATAATTAATA-AATAATTAAAAAA
2057937 AAT
1 AAT
2057940 TAAAATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AATATAATTAATAAATAATTAAAAAA
Found at i:2059157 original size:2 final size:2
Alignment explanation
Indices: 2059150--2059199 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2059140 TTCGTGAGGC
2059150 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
2059192 AT AT AT AT
1 AT AT AT AT
2059200 TTCAATTATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2065327 original size:16 final size:17
Alignment explanation
Indices: 2065296--2065331 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2065286 TTTTAAAATT
2065296 TTCGAGTTATTTTCGGG
1 TTCGAGTTATTTTCGGG
2065313 TTCGAGTTA-TTTCGGG
1 TTCGAGTTATTTTCGGG
2065329 TTC
1 TTC
2065332 AGATCATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.11, C:0.14, G:0.28, T:0.47
Consensus pattern (17 bp):
TTCGAGTTATTTTCGGG
Found at i:2066599 original size:30 final size:32
Alignment explanation
Indices: 2066563--2066645 Score: 136
Period size: 30 Copynumber: 2.7 Consensus size: 32
2066553 AAAAGTCACA
*
2066563 TTTTTACACAGATGTATCGATACATTCT-T-T
1 TTTTTACCCAGATGTATCGATACATTCTGTCT
2066593 TTTTTACCCAGATGTATCGATACATTCTGTCT
1 TTTTTACCCAGATGTATCGATACATTCTGTCT
2066625 TTTTT-CCCAGATGTATCGATA
1 TTTTTACCCAGATGTATCGATA
2066646 TATTTTTCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
30 27 0.54
31 17 0.34
32 6 0.12
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (32 bp):
TTTTTACCCAGATGTATCGATACATTCTGTCT
Found at i:2070004 original size:16 final size:16
Alignment explanation
Indices: 2069971--2070028 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
2069961 TATCCGATTC
* *
2069971 ATTTCGGGTTCAAATT
1 ATTTCGGGTTCGAGTT
* * *
2069987 ATTTTGGGTTTGGGTT
1 ATTTCGGGTTCGAGTT
2070003 ATTTCGGGTTCGAGTT
1 ATTTCGGGTTCGAGTT
*
2070019 ATTTCAGGTT
1 ATTTCGGGTT
2070029 TTGGGTTGGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.16, C:0.09, G:0.28, T:0.48
Consensus pattern (16 bp):
ATTTCGGGTTCGAGTT
Found at i:2070029 original size:32 final size:33
Alignment explanation
Indices: 2069971--2070035 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
2069961 TATCCGATTC
* *
2069971 ATTTCGGGTTCAAATTATTT-TGGGTTTGGGTT
1 ATTTCGGGTTCAAATTATTTCAGGTTTTGGGTT
* *
2070003 ATTTCGGGTTCGAGTTATTTCAGGTTTTGGGTT
1 ATTTCGGGTTCAAATTATTTCAGGTTTTGGGTT
2070036 GGTCGGTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.14, C:0.08, G:0.29, T:0.49
Consensus pattern (33 bp):
ATTTCGGGTTCAAATTATTTCAGGTTTTGGGTT
Found at i:2074614 original size:93 final size:91
Alignment explanation
Indices: 2074498--2074674 Score: 275
Period size: 93 Copynumber: 1.9 Consensus size: 91
2074488 GGAGTTTGGG
* * *
2074498 ATTGTTTAATCTGCTCAAGTAGAGTTTGTAATGATCCTTTGGGCTGAGTTGGAGTTTGTTTAATC
1 ATTGTTTAACCTGCTCAAGTAGAGTTTGTAATGATCCCTTGGGCTGAGGTGGAGTTTGTTTAATC
2074563 TGCATC-AAGTAGAGCTTTGCAATTGTA
66 TGC-TCAAAGTAGAG-TTTGCAATTGTA
*
2074590 ATTGTTTAACCCTGCTCCAGTAGAGTTTGTAATGATCCCTTGGGCTGAGGTGGAGTTTGTTTAAT
1 ATTGTTTAA-CCTGCTCAAGTAGAGTTTGTAATGATCCCTTGGGCTGAGGTGGAGTTTGTTTAAT
2074655 CTGCTCGAAAGTAGAGTTTG
65 CTGCTC-AAAGTAGAGTTTG
2074675 TGATGATCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
92 11 0.14
93 59 0.76
94 8 0.10
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (91 bp):
ATTGTTTAACCTGCTCAAGTAGAGTTTGTAATGATCCCTTGGGCTGAGGTGGAGTTTGTTTAATC
TGCTCAAAGTAGAGTTTGCAATTGTA
Found at i:2081954 original size:33 final size:35
Alignment explanation
Indices: 2081912--2081994 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 35
2081902 GTTTTGCCTA
*
2081912 CCCAACCTAC-C-CAAACTCAAACACAGCATCAGT
1 CCCAACCTACACTCAAACTCAAACACAACATCAGT
2081945 CCCAACCTACACAATCTCAAACTCAAACACAACATCAGT
1 CCCAACCT--AC-A-CTCAAACTCAAACACAACATCAGT
*
2081984 CCCAATCTACA
1 CCCAACCTACA
2081995 AAGTCACAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
33 8 0.19
35 2 0.05
36 1 0.02
37 2 0.05
38 1 0.02
39 28 0.67
ACGTcount: A:0.41, C:0.41, G:0.04, T:0.14
Consensus pattern (35 bp):
CCCAACCTACACTCAAACTCAAACACAACATCAGT
Found at i:2085319 original size:105 final size:105
Alignment explanation
Indices: 2085132--2085345 Score: 410
Period size: 105 Copynumber: 2.0 Consensus size: 105
2085122 TTTTCAAATC
*
2085132 TTAAACTATCATAAGGAATCCAAATGTTCACAAGTGTCCTCCATGCCACACGGAAATTCAGTATA
1 TTAAACTATCATAAGGAATCCAAATGTTCACAAGTGTCCTCCACGCCACACGGAAATTCAGTATA
2085197 CATTTGATTGAACGGATAACTTTCATCAGATAACATCATA
66 CATTTGATTGAACGGATAACTTTCATCAGATAACATCATA
2085237 TTAAACTATCATAAGGAATCCAAATGTTCACAAGTGTCCTCCACGCCACACGGAAATTCAGTATA
1 TTAAACTATCATAAGGAATCCAAATGTTCACAAGTGTCCTCCACGCCACACGGAAATTCAGTATA
*
2085302 CATTTGATTGAATGGATAACTTTCATCAGATAACATCATA
66 CATTTGATTGAACGGATAACTTTCATCAGATAACATCATA
2085342 TTAA
1 TTAA
2085346 TTAAAGTATA
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 107 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (105 bp):
TTAAACTATCATAAGGAATCCAAATGTTCACAAGTGTCCTCCACGCCACACGGAAATTCAGTATA
CATTTGATTGAACGGATAACTTTCATCAGATAACATCATA
Found at i:2093394 original size:2 final size:2
Alignment explanation
Indices: 2093389--2093420 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2093379 AAAAAAAATC
2093389 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
2093421 AAATAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2096945 original size:14 final size:15
Alignment explanation
Indices: 2096926--2096962 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2096916 ATTTGGTAAA
2096926 AAAATTAA-TAATTT
1 AAAATTAATTAATTT
2096940 AAAATTAATTAATTT
1 AAAATTAATTAATTT
*
2096955 AAATTTAA
1 AAAATTAA
2096963 AAATAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTAATTAATTT
Found at i:2096961 original size:21 final size:23
Alignment explanation
Indices: 2096935--2096980 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
2096925 AAAAATTAAT
*
2096935 AATTTAAAATTAA-TT-AATTTA
1 AATTTAAAAATAATTTGAATTTA
2096956 AATTTAAAAATAATTTGAATTTA
1 AATTTAAAAATAATTTGAATTTA
2096979 AA
1 AA
2096981 ATTACTCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 2 0.09
23 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTTAAAAATAATTTGAATTTA
Found at i:2096971 original size:17 final size:17
Alignment explanation
Indices: 2096932--2096981 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
2096922 TAAAAAAATT
*
2096932 AATAATTTAAAATT--A
1 AATAATTTAAATTTAAA
*
2096947 ATTAATTTAAATTTAAA
1 AATAATTTAAATTTAAA
*
2096964 AATAATTTGAATTTAAA
1 AATAATTTAAATTTAAA
2096981 A
1 A
2096982 TTACTCGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 12 0.41
17 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AATAATTTAAATTTAAA
Found at i:2097031 original size:16 final size:16
Alignment explanation
Indices: 2097010--2097056 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
2097000 ATCTGAATCC
2097010 GAAATGCTTCGAACTT
1 GAAATGCTTCGAACTT
*
2097026 GAAATGAC-TCGAACCT
1 GAAATG-CTTCGAACTT
*
2097042 GAAATGATTCGAACT
1 GAAATGCTTCGAACT
2097057 CAAAATAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (16 bp):
GAAATGCTTCGAACTT
Found at i:2097062 original size:16 final size:16
Alignment explanation
Indices: 2097009--2097103 Score: 57
Period size: 16 Copynumber: 6.5 Consensus size: 16
2096999 AATCTGAATC
*
2097009 CGAAATGCTTCGAACT
1 CGAAATGATTCGAACT
* *
2097025 TGAAATGACTCGAAC-
1 CGAAATGATTCGAACT
2097040 CTGAAATGATTCGAACT
1 C-GAAATGATTCGAACT
2097057 C-AAA--A-T--AACT
1 CGAAATGATTCGAACT
* *
2097067 TG-AATAATT--AACT
1 CGAAATGATTCGAACT
*
2097080 TGAAATGATTCGAACT
1 CGAAATGATTCGAACT
2097096 CGAAATGA
1 CGAAATGA
2097104 CCTGAATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
10 6 0.10
12 2 0.03
13 8 0.13
14 6 0.10
15 3 0.05
16 36 0.58
17 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (16 bp):
CGAAATGATTCGAACT
Found at i:2097087 original size:39 final size:39
Alignment explanation
Indices: 2097041--2097134 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
2097031 GACTCGAACC
*
2097041 TGAAATGATTCGAACTCAAAATAACTTGAATAATTAACT
1 TGAAATGATTCGAACTCAAAATAACCTGAATAATTAACT
* *
2097080 TGAAATGATTCGAACTCGAAATGACCTGAATAATTAACT
1 TGAAATGATTCGAACTCAAAATAACCTGAATAATTAACT
* *
2097119 CGAAATGATCCGAACT
1 TGAAATGATTCGAACT
2097135 TAAATTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (39 bp):
TGAAATGATTCGAACTCAAAATAACCTGAATAATTAACT
Found at i:2102850 original size:16 final size:16
Alignment explanation
Indices: 2102831--2102909 Score: 65
Period size: 16 Copynumber: 4.9 Consensus size: 16
2102821 CGAATTAATC
2102831 CGAACCCGAAATGACT
1 CGAACCCGAAATGACT
* *
2102847 CGAATCTGAAATGAAC-
1 CGAACCCGAAATG-ACT
* *
2102863 CGAACCCAAAATGACC
1 CGAACCCGAAATGACT
*
2102879 CGAATCC-AAAGTGA-T
1 CGAACCCGAAA-TGACT
2102894 CCGAACCCGAAATGAC
1 -CGAACCCGAAATGAC
2102910 CAAAACCCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 5 0.10
16 39 0.80
17 5 0.10
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.13
Consensus pattern (16 bp):
CGAACCCGAAATGACT
Found at i:2102920 original size:32 final size:31
Alignment explanation
Indices: 2102798--2102920 Score: 102
Period size: 32 Copynumber: 3.9 Consensus size: 31
2102788 TCCGATTGAC
* * * *
2102798 CCGAACCTGAAATGACCTAAACCCGAATTAAT
1 CCGAACCCGAAATGACCAAAACCC-AAATGAT
* * ** *
2102830 CCGAACCCGAAATGACTCGAATCTGAAATGAA
1 CCGAACCCGAAATGAC-CAAAACCCAAATGAT
* ** *
2102862 CCGAACCCAAAATGACCCGAATCCAAAGTGAT
1 CCGAACCCGAAATGACCAAAACCCAAA-TGAT
2102894 CCGAACCCGAAATGACCAAAACCCAAA
1 CCGAACCCGAAATGACCAAAACCCAAA
2102921 AATAACTCGA
Statistics
Matches: 69, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
31 5 0.07
32 60 0.87
33 4 0.06
ACGTcount: A:0.42, C:0.30, G:0.15, T:0.13
Consensus pattern (31 bp):
CCGAACCCGAAATGACCAAAACCCAAATGAT
Found at i:2102960 original size:15 final size:15
Alignment explanation
Indices: 2102942--2102972 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2102932 AATTTTATAG
2102942 CCGAAATAACCCAAC
1 CCGAAATAACCCAAC
*
2102957 CCGAAATAAGCCAAC
1 CCGAAATAACCCAAC
2102972 C
1 C
2102973 TAAAACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.39, G:0.10, T:0.06
Consensus pattern (15 bp):
CCGAAATAACCCAAC
Found at i:2103118 original size:2 final size:2
Alignment explanation
Indices: 2103113--2103140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2103103 AAAAGAAAAG
2103113 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2103141 AAACTCTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2107587 original size:12 final size:12
Alignment explanation
Indices: 2107569--2107607 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2107559 TGTTTGGCTG
2107569 AAATGTGGTTGA
1 AAATGTGGTTGA
*
2107581 TAATGTGGTTGA
1 AAATGTGGTTGA
*
2107593 AAATGTGATTGA
1 AAATGTGGTTGA
2107605 AAA
1 AAA
2107608 GATGATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.33
Consensus pattern (12 bp):
AAATGTGGTTGA
Found at i:2109782 original size:20 final size:20
Alignment explanation
Indices: 2109757--2109796 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2109747 TTTTTAAGGG
2109757 CGAGAAAAATTACCTTAATA
1 CGAGAAAAATTACCTTAATA
2109777 CGAGAAAAATTACCTTAATA
1 CGAGAAAAATTACCTTAATA
2109797 ATGGCAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
CGAGAAAAATTACCTTAATA
Found at i:2111575 original size:18 final size:18
Alignment explanation
Indices: 2111552--2111586 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2111542 AGAAATAACC
2111552 AAATTTACAATCTTGAGT
1 AAATTTACAATCTTGAGT
* *
2111570 AAATTTATAATTTTGAG
1 AAATTTACAATCTTGAG
2111587 ATGTATTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (18 bp):
AAATTTACAATCTTGAGT
Found at i:2115472 original size:295 final size:295
Alignment explanation
Indices: 2114938--2115517 Score: 844
Period size: 295 Copynumber: 2.0 Consensus size: 295
2114928 AATGCAAACG
* * *
2114938 TTAGTTATGCATATTAGTGTTAATTTTGTTAAAAACCCAGATTTAGCTTATGCGGGAAGGGATGT
1 TTAGTTATGCATATTAGTGGTAATTTTCTTAAAAACCCAGATTTAGCTTATGCGGGAAAGGATGT
* *
2115003 GCAAGAATGGTCTATAAATCTTGATTTTTTATCTTAGATGTATTAGATAATATGGTAAAGAAATT
66 ACAAGAATGGTCTATAAATCTTGATTTTTTATCTTAGATGTATTAGATAATATGGTAAAGAAACT
* * *
2115068 GGTTATGCCATAATAAATTATTTTTCTCTCCTAAAACTAAGAGATGATATAAATAATGGACTTAA
131 AGTTATGCCATAATAAATTAGTCTTCTCTCCTAAAACTAAGAGATGATATAAATAATGGACTTAA
* * * *
2115133 GGTATGCTATGATAATGCGTCTTTGGTGTCAATGATAAATCATATAGAAAACATGGGGGTCGTGC
196 GGTATGCTATGATAATGCATCTTCGGTGTCAATGATAAATCATATAGAAAACATAGGGGTCATGC
2115198 ATGTTTATCCAT-G-GCATGAAATTAAGTGGTGAGTA
261 ATGTTTAT--ATAGAGCATGAAATTAAGTGGTGAGTA
** *
2115233 TTAGTTATGCATATTAGTGGTAATTTTCTTAAAAACCTTGATTTAGCTTATGTGGGAAAGGA-GT
1 TTAGTTATGCATATTAGTGGTAATTTTCTTAAAAACCCAGATTTAGCTTATGCGGGAAAGGATGT
* * * * *
2115297 ACAAGAATGGTTTATAAATCTTGATTTTTTATCTTATGGTGTCTTATATAATATGGTAAAGAAGC
66 ACAAGAATGGTCTATAAATCTTGATTTTTTATCTTA-GATGTATTAGATAATATGGTAAAGAAAC
* * *
2115362 TAGTTATGCCTTATTAAATTAGTCTTCT-TACCTGAAACTAAGAGATGATATAAATAATGGACTT
130 TAGTTATGCCATAATAAATTAGTCTTCTCT-CCTAAAACTAAGAGATGATATAAATAATGGACTT
* * * * *
2115426 AGGGTTTGCTATGATAATGCATCTTCGGTGTCAATGGTAGATCATATAGAGAACATAGGGGTCAT
194 AAGGTATGCTATGATAATGCATCTTCGGTGTCAATGATAAATCATATAGAAAACATAGGGGTCAT
2115491 GCATGTTTATATAGAGCATGAAATTAA
259 GCATGTTTATATAGAGCATGAAATTAA
2115518 CATAGTAAAA
Statistics
Matches: 253, Mismatches: 28, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
293 2 0.01
294 38 0.15
295 213 0.84
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (295 bp):
TTAGTTATGCATATTAGTGGTAATTTTCTTAAAAACCCAGATTTAGCTTATGCGGGAAAGGATGT
ACAAGAATGGTCTATAAATCTTGATTTTTTATCTTAGATGTATTAGATAATATGGTAAAGAAACT
AGTTATGCCATAATAAATTAGTCTTCTCTCCTAAAACTAAGAGATGATATAAATAATGGACTTAA
GGTATGCTATGATAATGCATCTTCGGTGTCAATGATAAATCATATAGAAAACATAGGGGTCATGC
ATGTTTATATAGAGCATGAAATTAAGTGGTGAGTA
Found at i:2116042 original size:24 final size:24
Alignment explanation
Indices: 2116010--2116089 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
2116000 ACAGCTAAGG
*
2116010 ATGAGGGTGAGAGCAATGACTCTA
1 ATGACGGTGAGAGCAATGACTCTA
* * *
2116034 ATGACGGTGAAAAC-A-G-CT-AA
1 ATGACGGTGAGAGCAATGACTCTA
*
2116054 GGATGAGGGTGAGAGCAATGACTCTA
1 --ATGACGGTGAGAGCAATGACTCTA
2116080 ATGACGGTGA
1 ATGACGGTGA
2116090 AGGGGACCAT
Statistics
Matches: 41, Mismatches: 9, Indels: 12
0.66 0.15 0.19
Matches are distributed among these distances:
20 1 0.02
21 2 0.05
22 12 0.29
23 2 0.05
24 21 0.51
25 2 0.05
26 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.34, T:0.19
Consensus pattern (24 bp):
ATGACGGTGAGAGCAATGACTCTA
Found at i:2116063 original size:46 final size:46
Alignment explanation
Indices: 2115996--2116090 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
2115986 AGAAAAAAAA
2115996 GAAAACAGCTAAGGATGAGGGTGAGAGCAATGACTCTAATGACGGT
1 GAAAACAGCTAAGGATGAGGGTGAGAGCAATGACTCTAATGACGGT
2116042 GAAAACAGCTAAGGATGAGGGTGAGAGCAATGACTCTAATGACGGT
1 GAAAACAGCTAAGGATGAGGGTGAGAGCAATGACTCTAATGACGGT
2116088 GAA
1 GAA
2116091 GGGGACCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.38, C:0.13, G:0.33, T:0.17
Consensus pattern (46 bp):
GAAAACAGCTAAGGATGAGGGTGAGAGCAATGACTCTAATGACGGT
Found at i:2117200 original size:24 final size:24
Alignment explanation
Indices: 2117173--2117220 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2117163 AGAGAAAGAG
*
2117173 AATTATAAATAAAT-AATAACCAAA
1 AATTATAAA-AAATCAAGAACCAAA
*
2117197 AATTTTAAAAAATCAAGAACCAAA
1 AATTATAAAAAATCAAGAACCAAA
2117221 TGAAACATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (24 bp):
AATTATAAAAAATCAAGAACCAAA
Found at i:2121735 original size:22 final size:22
Alignment explanation
Indices: 2121701--2121742 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2121691 TTAAAGGGAG
** *
2121701 AAAAAAATTTATCTTTTAATTA
1 AAAAAAAACTATCTCTTAATTA
2121723 AAAAAAAACTATCTCTTAAT
1 AAAAAAAACTATCTCTTAAT
2121743 AACATCCAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAAAAACTATCTCTTAATTA
Found at i:2129392 original size:2 final size:2
Alignment explanation
Indices: 2129385--2129418 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2129375 GTAAAAAGAC
2129385 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2129419 AGAAACATAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2130035 original size:25 final size:27
Alignment explanation
Indices: 2130000--2130054 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2129990 TATTACGTAT
*
2130000 TAATATATTAAA-A-ATTTATAATATA
1 TAATATATTAAATATAATTATAATATA
*
2130025 TAATATCTTAAATATAATTATAATATA
1 TAATATATTAAATATAATTATAATATA
2130052 TAA
1 TAA
2130055 AAATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 11 0.42
26 1 0.04
27 14 0.54
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TAATATATTAAATATAATTATAATATA
Found at i:2131364 original size:21 final size:23
Alignment explanation
Indices: 2131338--2131380 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
2131328 ATTTGCTGTA
2131338 ATTTTTTATT-ATTT-AATTTTG
1 ATTTTTTATTAATTTAAATTTTG
2131359 ATTTTTTATTAATTTAAATTTT
1 ATTTTTTATTAATTTAAATTTT
2131381 AATGAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
22 4 0.20
23 6 0.30
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTTTTTATTAATTTAAATTTTG
Found at i:2133588 original size:36 final size:36
Alignment explanation
Indices: 2133542--2133619 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
2133532 TATTACATTG
2133542 GAGATTTTTTATTGCACATAAATTATGTAAATGGTC
1 GAGATTTTTTATTGCACATAAATTATGTAAATGGTC
* * *
2133578 GAGATTTTTTATTGCACATGATTTATTTAAATGGTC
1 GAGATTTTTTATTGCACATAAATTATGTAAATGGTC
2133614 GA-ATTT
1 GAGATTT
2133620 GTTTGAGTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 4 0.10
36 35 0.90
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.45
Consensus pattern (36 bp):
GAGATTTTTTATTGCACATAAATTATGTAAATGGTC
Found at i:2133877 original size:14 final size:15
Alignment explanation
Indices: 2133858--2133893 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2133848 GACATGAGTA
2133858 TAAATATAATTTTTT
1 TAAATATAATTTTTT
*
2133873 AAATATATAATTTTTT
1 TAA-ATATAATTTTTT
2133889 TAAAT
1 TAAAT
2133894 TAAGTATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAATATAATTTTTT
Found at i:2133882 original size:16 final size:17
Alignment explanation
Indices: 2133861--2133893 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2133851 ATGAGTATAA
2133861 ATATAA-TTTTTTAAAT
1 ATATAATTTTTTTAAAT
2133877 ATATAATTTTTTTAAAT
1 ATATAATTTTTTTAAAT
2133894 TAAGTATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATAATTTTTTTAAAT
Found at i:2134181 original size:2 final size:2
Alignment explanation
Indices: 2134174--2134200 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2134164 TGAACAAATT
2134174 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2134201 GAAAACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2138870 original size:20 final size:19
Alignment explanation
Indices: 2138842--2138888 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2138832 AATTATTATT
2138842 TATTTTATTAAAATATATA
1 TATTTTATTAAAATATATA
* *
2138861 TATTTATATTAAATTTTATA
1 TATTT-TATTAAAATATATA
2138881 TATTTTAT
1 TATTTTAT
2138889 AAATAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTATTAAAATATATA
Found at i:2139123 original size:25 final size:25
Alignment explanation
Indices: 2139065--2139143 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 25
2139055 TAAATTTTAA
* *
2139065 TATATTAAAATTTATATATTTTATA
1 TATATTAAATTTTATATATTTTATT
* *
2139090 TGTA-T-AATTTTTTATATTTTATT
1 TATATTAAATTTTATATATTTTATT
* *
2139113 TATATTAAATTTTAAATAATTATATT
1 TATATTAAATTTTATAT-ATTTTATT
2139139 TATAT
1 TATAT
2139144 GGTATAATGA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
23 18 0.42
24 2 0.05
25 11 0.26
26 12 0.28
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
TATATTAAATTTTATATATTTTATT
Found at i:2139125 original size:23 final size:23
Alignment explanation
Indices: 2139058--2139126 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
2139048 TATCATATAA
2139058 ATTTTA-ATATATTAAAATTTATAT
1 ATTTTATATATATT-AAATTT-TAT
* *
2139082 ATTTTATATGTA-TAATTTTTTAT
1 ATTTTATATATATTAA-ATTTTAT
*
2139105 ATTTTATTTATATTAAATTTTA
1 ATTTTATATATATTAAATTTTA
2139127 AATAATTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 20 0.54
24 13 0.35
25 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (23 bp):
ATTTTATATATATTAAATTTTAT
Found at i:2139823 original size:27 final size:29
Alignment explanation
Indices: 2139787--2139868 Score: 116
Period size: 30 Copynumber: 2.9 Consensus size: 29
2139777 TTAAACTTCA
2139787 TAATTT-TATTTAAATAAATTTTTATTTT
1 TAATTTATATTTAAATAAATTTTTATTTT
*
2139815 T-A-TTATATTAAAATAAATTTTTATTTTT
1 TAATTTATATTTAAATAAATTTTTA-TTTT
*
2139843 TAATTTATATATAAATAAATTTTTAT
1 TAATTTATATTTAAATAAATTTTTAT
2139869 ATCAAATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 2 0.04
27 18 0.38
28 6 0.13
29 2 0.04
30 19 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TAATTTATATTTAAATAAATTTTTATTTT
Found at i:2139869 original size:16 final size:17
Alignment explanation
Indices: 2139844--2139878 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2139834 TTTATTTTTT
2139844 AATTTATATAT-AAATA
1 AATTTATATATCAAATA
*
2139860 AATTTTTATATCAAATA
1 AATTTATATATCAAATA
2139877 AA
1 AA
2139879 ATAATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTATATATCAAATA
Found at i:2140008 original size:29 final size:30
Alignment explanation
Indices: 2139962--2140028 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
2139952 TTTAAAGTTG
2139962 TTTAAATATAAAATAAAAAATAAAAAATAA
1 TTTAAATATAAAATAAAAAATAAAAAATAA
*
2139992 TTTAAATAT--AATAAAAACATAAAAAATTA
1 TTTAAATATAAAATAAAAA-ATAAAAAATAA
2140021 TTTAAATA
1 TTTAAATA
2140029 AAATTACAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 8 0.23
29 18 0.51
30 9 0.26
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (30 bp):
TTTAAATATAAAATAAAAAATAAAAAATAA
Found at i:2140673 original size:12 final size:12
Alignment explanation
Indices: 2140656--2140684 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2140646 TCAAGTTAGA
2140656 TTATTTAAAATT
1 TTATTTAAAATT
2140668 TTATTTAAAATT
1 TTATTTAAAATT
2140680 TTATT
1 TTATT
2140685 GAAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTAAAATT
Found at i:2145968 original size:5 final size:5
Alignment explanation
Indices: 2145951--2145985 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
2145941 ATAAGCTGTA
* *
2145951 TATTT TATGT TATTT TATTT TATTT TATTT CATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT
2145986 ATTCTCTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:2146630 original size:2 final size:2
Alignment explanation
Indices: 2146623--2146661 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2146613 CCTCAACTAC
* * *
2146623 AT AT AT AT AT AT AT AT AT AT AC AT TT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2146662 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2146653 original size:18 final size:18
Alignment explanation
Indices: 2146630--2146666 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2146620 TACATATATA
* *
2146630 TATATATATATATACATT
1 TATATATAAATATAAATT
2146648 TATATATAAATATAAATT
1 TATATATAAATATAAATT
2146666 T
1 T
2146667 TAAAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATATAAATATAAATT
Found at i:2146704 original size:16 final size:16
Alignment explanation
Indices: 2146661--2146704 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2146651 ATATAAATAT
* *
2146661 AAATTTTAAAATTATA
1 AAATTTTAAAACTACA
*
2146677 AAAATTTAAAACTACA
1 AAATTTTAAAACTACA
*
2146693 AAATTTTTAAAC
1 AAATTTTAAAAC
2146705 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTTTAAAACTACA
Found at i:2148480 original size:28 final size:30
Alignment explanation
Indices: 2148431--2148486 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
2148421 CTCATCCATA
*
2148431 AAAAATAAAAGATTACCTACAAAAAAAGAT
1 AAAAATAAAAGATTACCAACAAAAAAAGAT
* *
2148461 AAAAA-AAAA-ATTAGCAACAATAAAAG
1 AAAAATAAAAGATTACCAACAAAAAAAG
2148487 TTATTTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 4 0.17
30 5 0.22
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (30 bp):
AAAAATAAAAGATTACCAACAAAAAAAGAT
Found at i:2154389 original size:2 final size:2
Alignment explanation
Indices: 2154384--2154417 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2154374 CGAGAGAAGA
2154384 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
2154418 GGAGATACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.