Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 341 of 356
Found at i:109128823 original size:2 final size:2
Alignment explanation
Indices: 109128816--109128858 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
109128806 AGAATAGACT
109128816 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
109128858 A
1 A
109128859 AAAAAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:109128875 original size:22 final size:22
Alignment explanation
Indices: 109128850--109128894 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
109128840 ACACACACAC
109128850 ACACACACAAA-AAAAAAAAACA
1 ACACA-ACAAACAAAAAAAAACA
*
109128872 ACACAACAAACAAACAAAAACA
1 ACACAACAAACAAAAAAAAACA
109128894 A
1 A
109128895 AAACTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (22 bp):
ACACAACAAACAAAAAAAAACA
Found at i:109131684 original size:22 final size:21
Alignment explanation
Indices: 109131642--109131693 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
109131632 ATAAGATTTT
*
109131642 AATATATTATTTAAAATTTAAA
1 AATATTTTATTTAAAATTT-AA
*
109131664 AATATTTTATATTAATA-TTAA
1 AATATTTTAT-TTAAAATTTAA
*
109131685 TATATTTTA
1 AATATTTTA
109131694 ATTCAAGCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.38
22 11 0.42
23 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATTTTATTTAAAATTTAA
Found at i:109131893 original size:15 final size:15
Alignment explanation
Indices: 109131873--109131903 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109131863 AGTCTTCTAG
109131873 ACGAATCAAAATTTT
1 ACGAATCAAAATTTT
109131888 ACGAATCAAAATTTT
1 ACGAATCAAAATTTT
109131903 A
1 A
109131904 TTTCTTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (15 bp):
ACGAATCAAAATTTT
Found at i:109134407 original size:16 final size:14
Alignment explanation
Indices: 109134379--109134410 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
109134369 TCAGTTTGAT
109134379 TAAAAAATTATAAA
1 TAAAAAATTATAAA
109134393 TAAAAAA-T-TAAA
1 TAAAAAATTATAAA
109134405 TAAAAA
1 TAAAAA
109134411 TTACTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAAAATTATAAA
Found at i:109139981 original size:46 final size:44
Alignment explanation
Indices: 109139873--109139991 Score: 139
Period size: 46 Copynumber: 2.6 Consensus size: 44
109139863 GTGTGCTCTC
* *
109139873 TGAAATGAAATGACCATGGTTGAAAGATACCATGGCAACATGATA
1 TGAAATGAAAT-ACCATGGTTGAAAGATACCATAGCAACATGACA
* * *
109139918 TGAAATGTGTAAGACCATGGTTGAAAGATACCATAGCAACGTGACA
1 TGAAA--TGAAATACCATGGTTGAAAGATACCATAGCAACATGACA
*
109139964 TGAAATGAACGATACCATAGTTGAAAGA
1 TGAAATGAA--ATACCATGGTTGAAAGA
109139992 CACTATGGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
44 3 0.05
45 5 0.08
46 50 0.81
47 4 0.06
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (44 bp):
TGAAATGAAATACCATGGTTGAAAGATACCATAGCAACATGACA
Found at i:109141710 original size:15 final size:16
Alignment explanation
Indices: 109141692--109141721 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
109141682 AGGTGTGCAT
109141692 GGGCCAGG-TCGGGCC
1 GGGCCAGGTTCGGGCC
109141707 GGGCCAGGTTCGGGC
1 GGGCCAGGTTCGGGC
109141722 TTAAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.30, G:0.53, T:0.10
Consensus pattern (16 bp):
GGGCCAGGTTCGGGCC
Found at i:109141866 original size:15 final size:17
Alignment explanation
Indices: 109141830--109141866 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
109141820 AAAGATTTTA
*
109141830 AAATATATTAAATAATC
1 AAATACATTAAATAATC
109141847 AAATACATTAAA-AA-C
1 AAATACATTAAATAATC
109141862 AAATA
1 AAATA
109141867 TTAAAACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 2 0.11
17 11 0.58
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATACATTAAATAATC
Found at i:109141991 original size:23 final size:23
Alignment explanation
Indices: 109141956--109142001 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
109141946 ATTATATTAA
*
109141956 AATTAAAATTAAAATATAAATAT
1 AATTAAAATTAAAAAATAAATAT
*
109141979 AATTAAAGA-TAAAAAATATATAT
1 AATTAAA-ATTAAAAAATAAATAT
109142002 TTTTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAAATTAAAAAATAAATAT
Found at i:109151859 original size:9 final size:10
Alignment explanation
Indices: 109151836--109151861 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
109151826 TATGCTCAAT
109151836 TTTTTCTACA
1 TTTTTCTACA
109151846 TTTTTCTACA
1 TTTTTCTACA
109151856 TTTTTC
1 TTTTTC
109151862 GTACGTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTCTACA
Found at i:109158331 original size:37 final size:37
Alignment explanation
Indices: 109158281--109158354 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
109158271 CGAATTGTGC
109158281 CTATGATATTTTGGTTGACCTAATGAAAGGTTTTCCT
1 CTATGATATTTTGGTTGACCTAATGAAAGGTTTTCCT
109158318 CTATGATATTTTGGTTGACCTAATGAAAGGTTTTCCT
1 CTATGATATTTTGGTTGACCTAATGAAAGGTTTTCCT
109158355 ATTGGTGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (37 bp):
CTATGATATTTTGGTTGACCTAATGAAAGGTTTTCCT
Found at i:109160279 original size:21 final size:21
Alignment explanation
Indices: 109160255--109160302 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
109160245 GTATAATTAT
*
109160255 TTTAATAAATA-CATATTAAAA
1 TTTAATAAACATC-TATTAAAA
109160276 TTTAATAAACATCTATTAAAA
1 TTTAATAAACATCTATTAAAA
*
109160297 TATAAT
1 TTTAAT
109160303 TAAAACCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAATAAACATCTATTAAAA
Found at i:109164607 original size:10 final size:10
Alignment explanation
Indices: 109164592--109164616 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
109164582 AGAAATTGGC
109164592 GAGAGAGAGG
1 GAGAGAGAGG
109164602 GAGAGAGAGG
1 GAGAGAGAGG
109164612 GAGAG
1 GAGAG
109164617 CTAAACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGG
Found at i:109165824 original size:16 final size:17
Alignment explanation
Indices: 109165792--109165824 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
109165782 AAATAATTGT
*
109165792 AATAATTATACATTTAA
1 AATAATTATAAATTTAA
109165809 AATAATT-TAAATTTAA
1 AATAATTATAAATTTAA
109165825 TTTACAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAATTATAAATTTAA
Found at i:109167049 original size:15 final size:16
Alignment explanation
Indices: 109167029--109167059 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
109167019 ACCTTGTTTG
109167029 ATAAATC-ATTAAAAA
1 ATAAATCAATTAAAAA
109167044 ATAAATCAATTAAAAA
1 ATAAATCAATTAAAAA
109167060 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAATCAATTAAAAA
Found at i:109167082 original size:17 final size:18
Alignment explanation
Indices: 109167060--109167100 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
109167050 CAATTAAAAA
* *
109167060 TTAATATTTTTAGTA-AT
1 TTAATATTTTAAGCACAT
109167077 TTAATATTTTAAGCACAT
1 TTAATATTTTAAGCACAT
109167095 TTAATA
1 TTAATA
109167101 ATCTATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (18 bp):
TTAATATTTTAAGCACAT
Found at i:109177582 original size:100 final size:100
Alignment explanation
Indices: 109177409--109177609 Score: 296
Period size: 100 Copynumber: 2.0 Consensus size: 100
109177399 AAATAACGTG
* * * *
109177409 TAAGACAAATATTGTAATGTCAACATAAATTATAAGTGGATTGTCATGCGAGTTGCAACATCAAC
1 TAAGACAAATAATGTAATGTCAACATAAATTATAAGTGAATTATCATGCAAGTTGCAACATCAAC
*
109177474 ATCGTTAAAAATAATATTATTATTAATATTTTTGT
66 ATCGTTAAAAATAATAATATTATTAATATTTTTGT
* * * *
109177509 TAAGACAAATAATGTAACT-TCAACGTGAATTATACGTGAATTATTATGCAAGTTGCAACATCAA
1 TAAGACAAATAATGTAA-TGTCAACATAAATTATAAGTGAATTATCATGCAAGTTGCAACATCAA
*
109177573 TATCGTTAAAAATAATAATATTATTAATATTTTTGT
65 CATCGTTAAAAATAATAATATTATTAATATTTTTGT
109177609 T
1 T
109177610 TAAAAACAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 89 0.99
101 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (100 bp):
TAAGACAAATAATGTAATGTCAACATAAATTATAAGTGAATTATCATGCAAGTTGCAACATCAAC
ATCGTTAAAAATAATAATATTATTAATATTTTTGT
Found at i:109180611 original size:21 final size:20
Alignment explanation
Indices: 109180587--109180628 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
109180577 TAATGTCACA
*
109180587 TCAGTAATTTTATTCTGAATT
1 TCAGGAATTTTATT-TGAATT
*
109180608 TCAGGATTTTTATTTGAATT
1 TCAGGAATTTTATTTGAATT
109180628 T
1 T
109180629 AATTCTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (20 bp):
TCAGGAATTTTATTTGAATT
Found at i:109183995 original size:3 final size:3
Alignment explanation
Indices: 109183987--109184108 Score: 63
Period size: 3 Copynumber: 40.3 Consensus size: 3
109183977 TAATTTAATC
* * * *
109183987 TAT TAT TAT TATT TAT TA- TAG TAC TAT TAT TAT CT-T CTGT TAT CAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT
* * ** **
109184033 TAC TAT TAT TAT TCT TGC TAT TATT TAT TAT CGT TAT TAT TAT TCA-
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT
* *
109184079 TAT TAT TAT TAT TAT TAC CAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
109184109 TGTTTTATTT
Statistics
Matches: 91, Mismatches: 20, Indels: 16
0.72 0.16 0.13
Matches are distributed among these distances:
2 5 0.05
3 77 0.85
4 9 0.10
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:109184292 original size:3 final size:3
Alignment explanation
Indices: 109184268--109184376 Score: 62
Period size: 3 Copynumber: 36.7 Consensus size: 3
109184258 TCAAATTTTA
* * *
109184268 TAT TAT GAT TAT T-T TAAT TAT TAT TAT TAT TAT TAT TAG TAC TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
109184313 CT-T TAT TAC TAT TAT TTT TAT TAC TAT CAC TAT TAC TAC TAC TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
109184358 TAC TA- TAT TGT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
109184377 CTATCATATT
Statistics
Matches: 81, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
2 5 0.06
3 73 0.90
4 3 0.04
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:109184346 original size:27 final size:27
Alignment explanation
Indices: 109184289--109184359 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
109184279 TTTTAATTAT
* **
109184289 TATTATTATTATTATTAGTACTATCTT
1 TATTACTATTATTATTAGTACTATCAC
* *
109184316 TATTACTATTATTTTTATTACTATCAC
1 TATTACTATTATTATTAGTACTATCAC
* *
109184343 TATTACTACTACTATTA
1 TATTACTATTATTATTA
109184360 CTATATTGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.01, T:0.55
Consensus pattern (27 bp):
TATTACTATTATTATTAGTACTATCAC
Found at i:109184377 original size:17 final size:16
Alignment explanation
Indices: 109184355--109184408 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
109184345 TTACTACTAC
*
109184355 TATTACTATATTGTTAT
1 TATTACTATA-TATTAT
109184372 TATTACTATCATATTAT
1 TATTACTAT-ATATTAT
* *
109184389 CATTACTATACTATTTT
1 TATTACTATA-TATTAT
109184406 TAT
1 TAT
109184409 CTATTACTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 29 0.94
18 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (16 bp):
TATTACTATATATTAT
Found at i:109194043 original size:28 final size:29
Alignment explanation
Indices: 109194003--109194059 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
109193993 GTTTTAATAT
109194003 TCTATAGGATTTTCTACCAAAAAA-AAAA
1 TCTATAGGATTTTCTACCAAAAAAGAAAA
*
109194031 TCTATAGGATTTTTTACCAAAAAAGAAAA
1 TCTATAGGATTTTCTACCAAAAAAGAAAA
109194060 GTATTCTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (29 bp):
TCTATAGGATTTTCTACCAAAAAAGAAAA
Found at i:109195153 original size:21 final size:22
Alignment explanation
Indices: 109195129--109195179 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
109195119 TTAAAAACGT
109195129 TTTAATTATTATTATTTTT-TA
1 TTTAATTATTATTATTTTTATA
**
109195150 TTTAAAAATTATTATTTTTATA
1 TTTAATTATTATTATTTTTATA
109195172 TTTAATTA
1 TTTAATTA
109195180 ATAAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTAATTATTATTATTTTTATA
Found at i:109195170 original size:27 final size:27
Alignment explanation
Indices: 109195132--109195187 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 27
109195122 AAAACGTTTT
*
109195132 AATTATTATTATT-T-TTTATTTAA-A
1 AATTATTATTATTATATTTAATTAATA
*
109195156 AATTATTATTTTTATATTTAATTAATA
1 AATTATTATTATTATATTTAATTAATA
109195183 AATTA
1 AATTA
109195188 AAAAAATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 1 0.04
26 8 0.30
27 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
AATTATTATTATTATATTTAATTAATA
Found at i:109195964 original size:19 final size:18
Alignment explanation
Indices: 109195909--109195964 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
109195899 TTTAATAATT
109195909 TTTAAATATTTTATAAAA
1 TTTAAATATTTTATAAAA
109195927 TTTAAATATTTTATAAAA
1 TTTAAATATTTTATAAAA
*
109195945 TTTAAACATTTTATTAAAA
1 TTTAAATATTTTA-TAAAA
109195964 T
1 T
109195965 AACATCTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 30 0.83
19 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATATTTTATAAAA
Found at i:109196621 original size:29 final size:27
Alignment explanation
Indices: 109196589--109196647 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
109196579 TAAATACAAA
*
109196589 AATTAAATCAAAATTAAAATTATATATAT
1 AATTAAACCAAAA-TAAAATTA-ATATAT
* *
109196618 AATTACACCAAAATAAAATTAATATCT
1 AATTAAACCAAAATAAAATTAATATAT
109196645 AAT
1 AAT
109196648 ATTACGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 8 0.30
28 8 0.30
29 11 0.41
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (27 bp):
AATTAAACCAAAATAAAATTAATATAT
Found at i:109200792 original size:18 final size:18
Alignment explanation
Indices: 109200757--109200792 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
109200747 CATTTTCCTT
* *
109200757 CATTTGTTTAATGGAAAA
1 CATTTGATTAATGAAAAA
109200775 CATTTGATTAATGAAAAA
1 CATTTGATTAATGAAAAA
109200793 TGGTTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (18 bp):
CATTTGATTAATGAAAAA
Found at i:109201126 original size:14 final size:14
Alignment explanation
Indices: 109201109--109201138 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
109201099 TATACATTAC
*
109201109 TAATTATAAATATT
1 TAATAATAAATATT
109201123 TAATAATAAATATT
1 TAATAATAAATATT
109201137 TA
1 TA
109201139 TACTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATAATAAATATT
Found at i:109211000 original size:41 final size:41
Alignment explanation
Indices: 109210955--109211036 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
109210945 ACTTTAGTCC
*
109210955 TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
1 TAATTTTAAGTAAATCAATAAACATATAAAATTGTTCAATT
109210996 TAATTTTAAGTAAATCAATAAACATATAAAATTGTTCAATT
1 TAATTTTAAGTAAATCAATAAACATATAAAATTGTTCAATT
109211037 GGATAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (41 bp):
TAATTTTAAGTAAATCAATAAACATATAAAATTGTTCAATT
Found at i:109211230 original size:31 final size:32
Alignment explanation
Indices: 109211185--109211247 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
109211175 TTGTTAATTT
109211185 GAGATTAAAAAGTTAATAATTAAGCCATTTTC
1 GAGATTAAAAAGTTAATAATTAAGCCATTTTC
109211217 GAGATT-AAAAGTTAATAATTAAGCCATTTTC
1 GAGATTAAAAAGTTAATAATTAAGCCATTTTC
109211248 TTCTATACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (32 bp):
GAGATTAAAAAGTTAATAATTAAGCCATTTTC
Found at i:109217601 original size:17 final size:17
Alignment explanation
Indices: 109217579--109217612 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
109217569 CTTTTAAGTG
109217579 TTTATAACTGTTATTGA
1 TTTATAACTGTTATTGA
109217596 TTTATAACTGTTATTGA
1 TTTATAACTGTTATTGA
109217613 AGTGCATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (17 bp):
TTTATAACTGTTATTGA
Found at i:109222050 original size:14 final size:14
Alignment explanation
Indices: 109222013--109222069 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
109222003 GAATTTTTTG
* *
109222013 TTAAATTTATTTCA
1 TTAAATTTTTTTAA
109222027 TTACAATTTTTTTAA
1 TTA-AATTTTTTTAA
109222042 TTAAATTTTTTATAA
1 TTAAATTTTTT-TAA
*
109222057 GTAAATTTTTTTA
1 TTAAATTTTTTTA
109222070 TTTCAAAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 13 0.34
15 25 0.66
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (14 bp):
TTAAATTTTTTTAA
Found at i:109228093 original size:15 final size:16
Alignment explanation
Indices: 109228073--109228109 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
109228063 CCGTGTAAAC
*
109228073 ACAAAACAAACAAAA-
1 ACAAAACAAAAAAAAT
109228088 ACAAAACAAAAAAAAT
1 ACAAAACAAAAAAAAT
109228104 ACAAAA
1 ACAAAA
109228110 AATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.03
Consensus pattern (16 bp):
ACAAAACAAAAAAAAT
Found at i:109228094 original size:11 final size:11
Alignment explanation
Indices: 109228069--109228110 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
109228059 GGGCCCGTGT
109228069 AAACACAAAAC-
1 AAACA-AAAACA
109228080 AAACAAAAACA
1 AAACAAAAACA
109228091 AAACAAAAA-A
1 AAACAAAAACA
109228101 AATACAAAAA
1 AA-ACAAAAA
109228111 ATATATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (11 bp):
AAACAAAAACA
Found at i:109230902 original size:130 final size:130
Alignment explanation
Indices: 109230722--109231094 Score: 406
Period size: 130 Copynumber: 2.9 Consensus size: 130
109230712 AAAATTATTC
* * ** *
109230722 AAAACAAAGACGAAATTTGATGTTCAGCGATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * *
109230787 TTTCGCGTTCGCTCAAAATAATCGAATTTCCCTTTGAAATTTCATTCATATCTTTTAAAATCCCT
66 TTTCGCATTCGCTCAAAATAATCGAATATCACTTTAAAATTTCACTCATATCTTTTAAAATCCCT
* * * *
109230852 TAAATGAAGATGAGATTTGATGTTTGGCAATTCGCGGAATTGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * ** * * *
109230917 TTTCGCATTTGTTCAAAATAATCGAATATCATTTTAAAATTTTGCTCGTGTCTTTTAAAATCTCT
66 TTTCGCATTCGCTCAAAATAATCGAATATCACTTTAAAATTTCACTCATATCTTTTAAAATCCCT
* * * * * * *
109230982 AAAACGAAGGCGATATGTGATATTTGGCAATTCACGGGATCGTGCCCTAACGTGTTGGGTAGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * *
109231047 TTCCCCGATT-GTTTAAAATAATCAAATATCCCTTCAAAATTTCACTCA
66 TTTCGC-ATTCGCTCAAAATAATCGAATATCACTTTAAAATTTCACTCA
109231095 GCCCCTCTAA
Statistics
Matches: 199, Mismatches: 43, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
130 196 0.98
131 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (130 bp):
AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTCGCTCAAAATAATCGAATATCACTTTAAAATTTCACTCATATCTTTTAAAATCCCT
Found at i:109233674 original size:162 final size:161
Alignment explanation
Indices: 109233190--109233675 Score: 618
Period size: 163 Copynumber: 3.0 Consensus size: 161
109233180 ATTGAGTCGA
* * *
109233190 GGCAAGGTGGATTTTATCTAAAACCG-CCCCAA-TATGCCCTGAAAATTTCAGCCAAGCAACTAA
1 GGCAAGGTGGATTTTATCTAAAACCGCCCCCAACT-TGCCCTGAAAATTTCAGCTAAGAAACCAA
* * * **
109233253 CATGCCTAGCCTCTGAACTTGATTGTCAGATAAAAGAAAGACCCATAAGGTGAGGTTGAAACCTG
65 CATGCCTAGCCTCCGAACTTGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCA
* * *
109233318 AAAAGTTGGGTTATTTTTCCTCATATATGTTCGG
130 AAAAGTT-CGTT-TTTTTCCCCATATAAGTTCGG
* * * * *
109233352 GGCAATGTGGATTTTATCTACAACCACTCCCAACCTGCCCTGAAAATTTCAGCTAAGAAACCAAC
1 GGCAAGGTGGATTTTATCTAAAACCGCCCCCAACTTGCCCTGAAAATTTCAGCTAAGAAACCAAC
* *
109233417 ATGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGCCCTATAGGGTGAGGTTGAAACCCAA
66 ATGCCTAGCCTCCGAACTTGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCAA
* * *
109233482 AAAGTTCGCTTGTTTCTCCCATATAAGTTCGT
131 AAAGTTCGTTTTTTTC-CCCATATAAGTTCGG
* * * *
109233514 GGCAAGGTGGATTTTATCTAGAACTGCCCCACAACTTGCCCCGAAAATTTCAGATAAGAAACCAA
1 GGCAAGGTGGATTTTATCTAAAACCGCCCC-CAACTTGCCCTGAAAATTTCAGCTAAGAAACCAA
* * *
109233579 CATGCCTAGCCTCCGAACTTGATTGTGAGATAAAA-AAAGACATATAGGGGGAGGTTGAAACCCA
65 CATGCCTAGCCTCCGAACTTGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCA
* **
109233643 AAAATTTCAGTTTTTTTCCCCATGCAAGTTCGG
130 AAAAGTTC-GTTTTTTTCCCCATATAAGTTCGG
109233676 TTGAAACTCG
Statistics
Matches: 279, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
161 5 0.02
162 107 0.38
163 167 0.60
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (161 bp):
GGCAAGGTGGATTTTATCTAAAACCGCCCCCAACTTGCCCTGAAAATTTCAGCTAAGAAACCAAC
ATGCCTAGCCTCCGAACTTGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCAA
AAAGTTCGTTTTTTTCCCCATATAAGTTCGG
Found at i:109234224 original size:29 final size:29
Alignment explanation
Indices: 109234182--109234239 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
109234172 AAACAAAAGA
109234182 AAGTCAAATTATTGCCCAGATTGTTCGTT
1 AAGTCAAATTATTGCCCAGATTGTTCGTT
109234211 AAGTCAAATTATTGCCCAGATTGTTCGTT
1 AAGTCAAATTATTGCCCAGATTGTTCGTT
109234240 GTTGTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (29 bp):
AAGTCAAATTATTGCCCAGATTGTTCGTT
Found at i:109235263 original size:14 final size:15
Alignment explanation
Indices: 109235211--109235261 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
109235201 ATAAAACGTT
109235211 AATATAAATAATTAA
1 AATATAAATAATTAA
* *
109235226 AATAT-AATACTTTA
1 AATATAAATAATTAA
109235240 AATATAAATAATTAA
1 AATATAAATAATTAA
109235255 AATATAA
1 AATATAA
109235262 TATGAGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:109236627 original size:17 final size:17
Alignment explanation
Indices: 109236599--109236632 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
109236589 TTCATTTTTC
109236599 TTAAAAAAAA-TTAGTA
1 TTAAAAAAAATTTAGTA
109236615 TTAAAACAAAATTTAGTA
1 TTAAAA-AAAATTTAGTA
109236633 CAAATGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAAAAAAAATTTAGTA
Found at i:109237397 original size:21 final size:21
Alignment explanation
Indices: 109237373--109237412 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
109237363 TGAATTAACT
109237373 CAACTTTATCCAAAATTTATA
1 CAACTTTATCCAAAATTTATA
* *
109237394 CAACTTTTTCCGAAATTTA
1 CAACTTTATCCAAAATTTA
109237413 CACACCCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (21 bp):
CAACTTTATCCAAAATTTATA
Found at i:109244758 original size:28 final size:28
Alignment explanation
Indices: 109244700--109244769 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
109244690 TATTTAAATG
** *
109244700 TTTAATTTTTATTTTTCTCATAATTTAA
1 TTTAATTTTTATTTTAATCATAATATAA
*
109244728 TTTAATTTTTATTTTAAT-ATAGTATATA
1 TTTAATTTTTATTTTAATCATAATATA-A
*
109244756 TTTTATTTATTATT
1 TTTAATTT-TTATT
109244770 AATTAATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 6 0.17
28 24 0.69
29 5 0.14
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTAATTTTTATTTTAATCATAATATAA
Found at i:109254119 original size:17 final size:18
Alignment explanation
Indices: 109254092--109254127 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
109254082 CTCCCTAAAA
*
109254092 TTTACATTTTTAAACTTT
1 TTTACATTTTTAAAATTT
109254110 TTTA-ATTTTTAAAATTT
1 TTTACATTTTTAAAATTT
109254127 T
1 T
109254128 AAATTTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTACATTTTTAAAATTT
Found at i:109254127 original size:16 final size:17
Alignment explanation
Indices: 109254092--109254138 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
109254082 CTCCCTAAAA
*
109254092 TTTACATTTTTAAACTTT
1 TTTA-ATTTTTAAACATT
109254110 TTTAATTTTTAAA-ATT
1 TTTAATTTTTAAACATT
* *
109254126 TTAAATTTGTAAA
1 TTTAATTTTTAAA
109254139 TGTAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 13 0.50
17 9 0.35
18 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAATTTTTAAACATT
Found at i:109260575 original size:14 final size:15
Alignment explanation
Indices: 109260549--109260579 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
109260539 TCCTGGCTCA
109260549 TCAACACATTTTTCT
1 TCAACACATTTTTCT
109260564 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
109260578 TC
1 TC
109260580 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:109263176 original size:17 final size:18
Alignment explanation
Indices: 109263154--109263187 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
109263144 ATGACTTCTA
109263154 TTAAAT-TATAATTATTT
1 TTAAATGTATAATTATTT
*
109263171 TTAAATGTATATTTATT
1 TTAAATGTATAATTATT
109263188 ACGACTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTAAATGTATAATTATTT
Found at i:109264553 original size:26 final size:25
Alignment explanation
Indices: 109264495--109264560 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
109264485 AACATACTTC
*
109264495 TAATTATTTTTATTTCATTAATTATA
1 TAATTATTTTTA-TTAATTAATTATA
* * *
109264521 TATTTATTTTTATTAATTAGTGTATT
1 TAATTATTTTTATTAATTAAT-TATA
*
109264547 TAATTATTATTATT
1 TAATTATTTTTATT
109264561 TAAAGATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 7 0.21
26 26 0.79
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (25 bp):
TAATTATTTTTATTAATTAATTATA
Found at i:109264576 original size:24 final size:22
Alignment explanation
Indices: 109264543--109264586 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
109264533 TTAATTAGTG
109264543 TATTTAATTATTATTATTTAAAGA
1 TATTTAATTA-T-TTATTTAAAGA
*
109264567 TATTTGATTATTTATTTAAA
1 TATTTAATTATTTATTTAAA
109264587 AATGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 1 0.05
24 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTTAATTATTTATTTAAAGA
Found at i:109264602 original size:22 final size:23
Alignment explanation
Indices: 109264549--109264603 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
109264539 AGTGTATTTA
* *
109264549 ATTATTATTATTTAAAGATATTTG
1 ATTATT-TTATTTAAAAATATATG
*
109264573 ATTA-TTTATTTAAAAATGTAT-
1 ATTATTTTATTTAAAAATATATG
109264594 ATTATTTTAT
1 ATTATTTTAT
109264604 GTAATGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 1 0.04
24 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (23 bp):
ATTATTTTATTTAAAAATATATG
Found at i:109267386 original size:20 final size:20
Alignment explanation
Indices: 109267367--109267404 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
109267357 TAAATTATTA
*
109267367 ATAATTTTTTTTAA-ACATT
1 ATAATTATTTTTAATACATT
*
109267386 ATTATTATTTTTAATACAT
1 ATAATTATTTTTAATACAT
109267405 GCATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
ATAATTATTTTTAATACATT
Found at i:109267627 original size:29 final size:29
Alignment explanation
Indices: 109267591--109267651 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
109267581 TTATTTATCG
109267591 TTATT-ATA-AATA-TATTGTTTT-CATTC
1 TTATTAATATAATATTATTGTTTTCCA-TC
*
109267617 TTATTAATATATTATTATTGTTTTCCATC
1 TTATTAATATAATATTATTGTTTTCCATC
109267646 TTATTA
1 TTATTA
109267652 TTATTAGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 3 0.10
28 3 0.10
29 17 0.57
30 2 0.07
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (29 bp):
TTATTAATATAATATTATTGTTTTCCATC
Found at i:109267655 original size:3 final size:3
Alignment explanation
Indices: 109267533--109267585 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
109267523 ACTATTATGC
* *
109267533 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT CAT TCAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
109267579 TAT TAT T
1 TAT TAT T
109267586 TATCGTTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:109280582 original size:87 final size:85
Alignment explanation
Indices: 109280483--109280683 Score: 212
Period size: 87 Copynumber: 2.3 Consensus size: 85
109280473 TTCATAAGAT
* **
109280483 CTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGT-AGATCTTATTTCCCTAAGCC-G-TAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATT-TAAGATC-TAAATCCCTAA-CCGGTTAG
* *
109280545 TGGAGCAGATCGAA-GATTGACAAGC
63 -GAAACAGATC-AATGA-TGACAAGC
* * ****
109280570 CTTAACCCCCTAAACAGTAGGGTAACTGGTTGAATTTACAGATCTAAATCCCTAACCGGTTAGGA
1 CTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATTTA-AGATCTAAATCCCTAACCGGTTAGGA
109280635 AACAGATCAATGATGACAAGC
65 AACAGATCAATGATGACAAGC
109280656 CTTAACCCCCTAAGCAGTAGGGTAACAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAG
109280684 GCTGAAAATC
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
86 39 0.41
87 49 0.51
88 8 0.08
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (85 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATTTAAGATCTAAATCCCTAACCGGTTAGGAA
ACAGATCAATGATGACAAGC
Found at i:109282284 original size:3 final size:3
Alignment explanation
Indices: 109282278--109282346 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
109282268 TTATTAATCG
* *
109282278 TAT TAT TAC TAT TAT T-T CT-T TAT TTT TAT T-T TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
109282319 TCAT TAT TAGT TAT TAT TAT TAT TAT TA
1 T-AT TAT TA-T TAT TAT TAT TAT TAT TA
109282347 GTTTTAGCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
2 8 0.15
3 41 0.75
4 6 0.11
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:109282333 original size:19 final size:19
Alignment explanation
Indices: 109282311--109282349 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
109282301 TTTTATTTTA
109282311 TATTA-TATTCATTATTAGT
1 TATTATTATT-ATTATTAGT
109282330 TATTATTATTATTATTAGT
1 TATTATTATTATTATTAGT
109282349 T
1 T
109282350 TTAGCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TATTATTATTATTATTAGT
Found at i:109282425 original size:18 final size:20
Alignment explanation
Indices: 109282402--109282438 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
109282392 ATTATTAATA
109282402 ATTATT-TTTTTAA-ACATT
1 ATTATTATTTTTAATACATT
109282420 ATTATTATTTTTAATACAT
1 ATTATTATTTTTAATACAT
109282439 GCATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTATTTTTAATACATT
Found at i:109282652 original size:29 final size:29
Alignment explanation
Indices: 109282616--109282676 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
109282606 TTATTTATCG
109282616 TTATT-ATA-AATA-TATTGTTTT-CATTC
1 TTATTAATATAATATTATTGTTTTCCA-TC
*
109282642 TTATTAATATATTATTATTGTTTTCCATC
1 TTATTAATATAATATTATTGTTTTCCATC
109282671 TTATTA
1 TTATTA
109282677 TTATTACTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 3 0.10
28 3 0.10
29 17 0.57
30 2 0.07
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (29 bp):
TTATTAATATAATATTATTGTTTTCCATC
Found at i:109282680 original size:3 final size:3
Alignment explanation
Indices: 109282567--109282610 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
109282557 ACTATTATGC
* *
109282567 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT CAT TCAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T
109282611 TATCGTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:109284081 original size:32 final size:32
Alignment explanation
Indices: 109284045--109284110 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
109284035 TTACGACAGT
*
109284045 GAACATTTCATAATTTCATTCTAATCAAGTCA
1 GAACATTTCATAATATCATTCTAATCAAGTCA
*
109284077 GAACATTTGATAATATCATTCTAATCAAGTCA
1 GAACATTTCATAATATCATTCTAATCAAGTCA
109284109 GA
1 GA
109284111 GGAAAATTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (32 bp):
GAACATTTCATAATATCATTCTAATCAAGTCA
Found at i:109292627 original size:26 final size:25
Alignment explanation
Indices: 109292569--109292634 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
109292559 AACATACTTC
*
109292569 TAATTATTTTTATTTCATTAATTAAT
1 TAATTATTTTTA-TTAATTAATTAAT
* * *
109292595 TATTTATTTTTATTAATTAGTTTATT
1 TAATTATTTTTATTAATTA-ATTAAT
*
109292621 TAATTATTATTATT
1 TAATTATTTTTATT
109292635 TAAAGATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 6 0.18
26 27 0.82
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TAATTATTTTTATTAATTAATTAAT
Found at i:109292671 original size:21 final size:22
Alignment explanation
Indices: 109292625--109292674 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
109292615 TTTATTTAAT
*
109292625 TATTA-TTATTTAAAGATATAA
1 TATTATTTATTTAAAAATATAA
* *
109292646 GATTATTTATTTAAAAATGT-A
1 TATTATTTATTTAAAAATATAA
109292667 TATTATTT
1 TATTATTT
109292675 TATGTAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (22 bp):
TATTATTTATTTAAAAATATAA
Found at i:109292676 original size:22 final size:23
Alignment explanation
Indices: 109292623--109292677 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
109292613 AGTTTATTTA
*
109292623 ATTATTATTATTTAAAGATATAAG
1 ATTATT-TTATTTAAAAATATAAG
* *
109292647 ATTA-TTTATTTAAAAATGT-AT
1 ATTATTTTATTTAAAAATATAAG
109292668 ATTATTTTAT
1 ATTATTTTAT
109292678 GTAATGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 1 0.04
24 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
ATTATTTTATTTAAAAATATAAG
Found at i:109293700 original size:18 final size:17
Alignment explanation
Indices: 109293667--109293700 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
109293657 AAAAGAAAGT
*
109293667 AAAAGAAAGAAGAACAG
1 AAAAGAAACAAGAACAG
109293684 AAAAGAAACAGAGAACA
1 AAAAGAAACA-AGAACA
109293701 AAACGAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.09, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAAACAAGAACAG
Found at i:109294151 original size:17 final size:17
Alignment explanation
Indices: 109294115--109294148 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
109294105 TAAAAGAGTT
*
109294115 AATTAGGATTAAATTGG
1 AATTAGGAATAAATTGG
109294132 AATTAAGGAATAAATTG
1 AATT-AGGAATAAATTG
109294149 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (17 bp):
AATTAGGAATAAATTGG
Found at i:109294687 original size:27 final size:27
Alignment explanation
Indices: 109294647--109294726 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
109294637 ATGCCTTATT
* *
109294647 GGTGTATTTGGGAGGATATGA-TATACC
1 GGTGTGTTTAGGAGGATAT-ATTATACC
* *
109294674 GGTGTGTTTAGGAGGCTATATTATACT
1 GGTGTGTTTAGGAGGATATATTATACC
109294701 GGTGTG-TTATGGAGGATTTATATTAT
1 GGTGTGTTTA-GGAGGA--TATATTAT
109294727 TCTGGGTGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 32 0.73
29 8 0.18
ACGTcount: A:0.24, C:0.05, G:0.31, T:0.40
Consensus pattern (27 bp):
GGTGTGTTTAGGAGGATATATTATACC
Found at i:109295687 original size:20 final size:19
Alignment explanation
Indices: 109295650--109295688 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
109295640 TATATAGCTG
*
109295650 ATTAACTACTTTAACAACT
1 ATTAACTACTTGAACAACT
*
109295669 ATTAACTGACTTGACCAACT
1 ATTAACT-ACTTGAACAACT
109295689 TACTAACCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (19 bp):
ATTAACTACTTGAACAACT
Found at i:109300240 original size:20 final size:19
Alignment explanation
Indices: 109300203--109300241 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
109300193 TATATAGCTA
* *
109300203 ATTAACTACTTTAGCAACT
1 ATTAACTACTTGACCAACT
109300222 ATTAACTGACTTGACCAACT
1 ATTAACT-ACTTGACCAACT
109300242 TACTAACCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (19 bp):
ATTAACTACTTGACCAACT
Found at i:109302156 original size:25 final size:26
Alignment explanation
Indices: 109302098--109302171 Score: 116
Period size: 25 Copynumber: 2.9 Consensus size: 26
109302088 TGAGCTTTCC
*
109302098 AATGTGCAAGCTGCAAG-TTCAGCAAA
1 AATGTGTAAGCTGCAAGCTT-AGCAAA
109302124 AATGTGTAAGCTGCAAGCTTAGC-AA
1 AATGTGTAAGCTGCAAGCTTAGCAAA
109302149 AATGTGTAAGCTGCAAGCTTAGC
1 AATGTGTAAGCTGCAAGCTTAGC
109302172 GAGAAGTGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 25 0.54
26 19 0.41
27 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (26 bp):
AATGTGTAAGCTGCAAGCTTAGCAAA
Found at i:109304508 original size:51 final size:51
Alignment explanation
Indices: 109304409--109304509 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
109304399 GGTATGTATA
* * * *
109304409 TAAAGGGATTACATCATTTTCGGTCAAATAAGGTGGTTTGAACCGACTTTG
1 TAAAGGGATTACACCAGTTTCGGTCAAATAAGGTGATTTGAACAGACTTTG
* * * * *
109304460 TAAAGGGATTACACCAGTTTCGGTGAGATAAGTTGATTTTAATAGACTTT
1 TAAAGGGATTACACCAGTTTCGGTCAAATAAGGTGATTTGAACAGACTTT
109304510 TATGCATTCC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (51 bp):
TAAAGGGATTACACCAGTTTCGGTCAAATAAGGTGATTTGAACAGACTTTG
Found at i:109305454 original size:21 final size:21
Alignment explanation
Indices: 109305425--109305464 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
109305415 TTTGATTTTT
109305425 TTCAAGATGAAAATACTGAAA
1 TTCAAGATGAAAATACTGAAA
* * *
109305446 TTCAGGATGAGAATGCTGA
1 TTCAAGATGAAAATACTGA
109305465 TATGGCATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (21 bp):
TTCAAGATGAAAATACTGAAA
Found at i:109312051 original size:15 final size:16
Alignment explanation
Indices: 109312031--109312060 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
109312021 TAACTAATGT
109312031 AAAATAAT-GTTATTC
1 AAAATAATAGTTATTC
109312046 AAAATAATAGTTATT
1 AAAATAATAGTTATT
109312061 TAACATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
AAAATAATAGTTATTC
Found at i:109313086 original size:31 final size:31
Alignment explanation
Indices: 109313051--109313117 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
109313041 CTTCCTGCAT
* *
109313051 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * * *
109313082 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
109313113 TAAAA
1 TAAAA
109313118 AATACAAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.60, C:0.18, G:0.04, T:0.18
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:109313389 original size:21 final size:20
Alignment explanation
Indices: 109313365--109313422 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
109313355 TCTGCTACCA
*
109313365 TCGCTCGTGCCTCTGCCTCTC
1 TCGCT-GTGCCTCTGCCTCCC
*
109313386 TCGCTGTAGCCGCTGCCTCCC
1 TCGCTGT-GCCTCTGCCTCCC
*
109313407 TCTCTGCTGCCTCTGC
1 TCGCTG-TGCCTCTGC
109313423 TCTAAGTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.02, C:0.47, G:0.21, T:0.31
Consensus pattern (20 bp):
TCGCTGTGCCTCTGCCTCCC
Found at i:109318984 original size:9 final size:9
Alignment explanation
Indices: 109318970--109319189 Score: 131
Period size: 9 Copynumber: 23.9 Consensus size: 9
109318960 TATTTAAGTA
109318970 TTATGTAAG
1 TTATGTAAG
*
109318979 TTATGTAAT
1 TTATGTAAG
*
109318988 TTATGATATG
1 TTATG-TAAG
* * *
109318998 ATATAT-AT
1 TTATGTAAG
*
109319006 TTATGTAAA
1 TTATGTAAG
* *
109319015 TTATAT-AT
1 TTATGTAAG
*
109319023 TTATCTAAG
1 TTATGTAAG
*
109319032 TTATATAAG
1 TTATGTAAG
109319041 TTATGTAAG
1 TTATGTAAG
*
109319050 TTATGTAAA
1 TTATGTAAG
*
109319059 TTATGATATAAAA
1 TTATG---T-AAG
*
109319072 TATATTTAAG
1 T-TATGTAAG
*
109319082 TATTTTGTAAG
1 --TTATGTAAG
109319093 TTATGTAAG
1 TTATGTAAG
* *
109319102 TTATAT-AT
1 TTATGTAAG
*
109319110 TTATCTAAG
1 TTATGTAAG
*
109319119 TTATATAAG
1 TTATGTAAG
*
109319128 TTATATAAG
1 TTATGTAAG
*
109319137 TTATGTATG
1 TTATGTAAG
*
109319146 TTATATAAG
1 TTATGTAAG
109319155 TTATGTAAG
1 TTATGTAAG
* *
109319164 TTATATATG
1 TTATGTAAG
*
109319173 TTATATAAG
1 TTATGTAAG
109319182 TTATGTAA
1 TTATGTAA
109319190 ATTAAGATAT
Statistics
Matches: 164, Mismatches: 36, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
8 16 0.10
9 125 0.76
10 7 0.04
11 7 0.04
12 2 0.01
13 4 0.02
14 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:109319049 original size:18 final size:18
Alignment explanation
Indices: 109318970--109319185 Score: 150
Period size: 18 Copynumber: 11.7 Consensus size: 18
109318960 TATTTAAGTA
* *
109318970 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
109318988 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
* *
109319006 TTATGTAAATTATAT-AT
1 TTATGTAAGTTATATAAG
*
109319023 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
109319041 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
* *
109319059 TTATGATATAAAATATATTTAAG
1 TTATG---T-AAGT-TATATAAG
* *
109319082 TATTTTGTAAGTTATGTAAG
1 --TTATGTAAGTTATATAAG
* * *
109319102 TTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
*
109319119 TTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAG
*
109319137 TTATGTATGTTATATAAG
1 TTATGTAAGTTATATAAG
*
109319155 TTATGTAAGTTATATATG
1 TTATGTAAGTTATATAAG
*
109319173 TTATATAAGTTAT
1 TTATGTAAGTTAT
109319186 GTAAATTAAG
Statistics
Matches: 159, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
17 37 0.23
18 90 0.57
19 7 0.04
20 7 0.04
21 4 0.03
22 4 0.03
23 6 0.04
25 4 0.03
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.49
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:109319062 original size:27 final size:27
Alignment explanation
Indices: 109319023--109319189 Score: 147
Period size: 27 Copynumber: 6.0 Consensus size: 27
109319013 AATTATATAT
*
109319023 TTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* * *
109319050 TTATGTAAATTATGATATAAAATATATTTAAG
1 TTATGT-AAGT-T-ATAT-AAGT-TATGTAAG
* * * *
109319082 TATTTTGTAAGTTATGTAAGTTATAT-AT
1 --TTATGTAAGTTATATAAGTTATGTAAG
* *
109319110 TTATCTAAGTTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
*
109319137 TTATGTATGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* *
109319164 TTATATATGTTATATAAGTTATGTAA
1 TTATGTAAGTTATATAAGTTATGTAA
109319190 ATTAAGATAT
Statistics
Matches: 114, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
26 21 0.18
27 55 0.48
28 4 0.04
29 5 0.04
30 7 0.06
31 6 0.05
32 8 0.07
33 3 0.03
34 5 0.04
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATATAAGTTATGTAAG
Found at i:109319080 original size:114 final size:114
Alignment explanation
Indices: 109318946--109319167 Score: 304
Period size: 114 Copynumber: 1.9 Consensus size: 114
109318936 ACTAGTTATG
* * * *
109318946 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAATTTATGATATGATATAT-ATTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-ATATATAAGTTAT
* *
109319010 GTAAATTATAT-ATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
64 ATAAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
* * *
109319060 TATGATATAAAATATATTTAAGTATTTTGTAAGTTATGTAAGTTATATATTTATCTAAGTTATAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
* * *
109319125 AAGTTATATAAGTTATGTATGTTATATAAGTTATGTAAGTTAT
66 AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTAT
109319168 ATATGTTATA
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
112 4 0.04
113 18 0.19
114 72 0.77
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
Found at i:109319320 original size:15 final size:15
Alignment explanation
Indices: 109319300--109319355 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
109319290 AAGTAGCGGG
109319300 ATTAAATAATATTTA
1 ATTAAATAATATTTA
109319315 ATTAAATAATATTT-
1 ATTAAATAATATTTA
109319329 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
109319344 ATTAAATAATAT
1 ATTAAATAATAT
109319356 ACATGTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:109319560 original size:24 final size:24
Alignment explanation
Indices: 109319532--109319599 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
109319522 ACTTAAATGG
109319532 TAAAACGGACGATAATATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
* *
109319556 TAAAACGGA-GAATAGTATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
*
109319580 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
109319600 CAATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:109320312 original size:371 final size:372
Alignment explanation
Indices: 109319680--109320591 Score: 1754
Period size: 372 Copynumber: 2.5 Consensus size: 372
109319670 AATTGAAACA
*
109319680 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATGATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
109319745 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
*
109319810 AATAAGGTTGGAGAGAATGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
131 AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
109319875 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAATAGTAATTTGAATAT
196 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAATAGTAATTTGAATAT
*
109319940 AATAATATC-AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATA
261 AATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTAGAAATAAATTAAGGTTATA
109320004 TAAATATTCAATAGTAAATGAGCTCGATAAAACTGTTTTCAAGTCTT
326 TAAATATTCAATAGTAAATGAGCTCGATAAAACTGTTTTCAAGTCTT
*
109320051 TTTGAATTTTTTAAGATTCATGATACGTGGCGTTGTTACACCTAAGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATGATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
109320116 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
*
109320181 AATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
131 AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
*
109320246 GAAATTTAAAAATGTTAAATATTAAAATAAAACATTATTAATATAAAAAATAGTAATTTGAATAT
196 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAATAGTAATTTGAATAT
109320311 AATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTAGAAATAAATTAAGGTTATA
261 AATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTAGAAATAAATTAAGGTTATA
*
109320376 TAAATATTCAATAGTAAATGAGCTCGATAGAACTGTTTTCAAGTCTT
326 TAAATATTCAATAGTAAATGAGCTCGATAAAACTGTTTTCAAGTCTT
109320423 TTTGAATTTTTTAAGATTCATGATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATGATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
109320488 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
109320553 AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTT
131 AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTT
109320592 AATGGACAAG
Statistics
Matches: 532, Mismatches: 8, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
371 265 0.50
372 267 0.50
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (372 bp):
TTTGAATTTTTTAAGATTCATGATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAATAGTAATTTGAATAT
AATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTAGAAATAAATTAAGGTTATA
TAAATATTCAATAGTAAATGAGCTCGATAAAACTGTTTTCAAGTCTT
Found at i:109324034 original size:14 final size:15
Alignment explanation
Indices: 109324010--109324039 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
109324000 CACAAACTTC
109324010 AGAATTTATGTATTT
1 AGAATTTATGTATTT
109324025 AGAA-TTATGTATTT
1 AGAATTTATGTATTT
109324039 A
1 A
109324040 TATAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
AGAATTTATGTATTT
Found at i:109326019 original size:28 final size:28
Alignment explanation
Indices: 109325949--109326041 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
109325939 TTTTTGTGGG
109325949 GGGTTTAGGGTTT-TGGAGTTTATAGA-TTA
1 GGGTTTAGGGTTTAT-GA-TTTA-AGATTTA
* * * *
109325978 GTGTTTATGTTTTATGATTTAAAATTTA
1 GGGTTTAGGGTTTATGATTTAAGATTTA
109326006 GGGTTTAGGGTTTAATG-TTTAAGATTTAA
1 GGGTTTAGGGTTT-ATGATTTAAGATTT-A
109326035 GGGTTTA
1 GGGTTTA
109326042 CAGAAAGCCA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.04
28 26 0.50
29 23 0.44
30 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (28 bp):
GGGTTTAGGGTTTATGATTTAAGATTTA
Found at i:109326376 original size:41 final size:40
Alignment explanation
Indices: 109326331--109326588 Score: 193
Period size: 41 Copynumber: 6.6 Consensus size: 40
109326321 AACTTTTTGC
*
109326331 GGCGTTTGGACCAAAAACGCCGCTATTAATCAGTTTTTAGT
1 GGCGTTTGGA-CAAAAACGCCGCTATTGATCAGTTTTTAGT
* * *
109326372 GGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTT-GT
1 GGCG-TTTGGACAAAAACGCCGCTATTGATCAG-TTTTTAGT
109326413 GGCGTTTGGGACAAAAACGCCGC-----A--A---TTTAGT
1 GGCGTTT-GGACAAAAACGCCGCTATTGATCAGTTTTTAGT
** * *
109326444 GGCGTTTGAGATTAAAACGCCACTATTGATCAGCTTTTAGT
1 GGCGTTTG-GACAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * *
109326485 GGCGTTTTGATAAAAACGCCGCTATTGACCAATTTTTAGT
1 GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * * *
109326525 GGCGTTTTTGG-CAAAAATGCCGCTATAGTTTAGCTTTTAGT
1 GGCG--TTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
109326566 GGCGTTTCGGAC--AAACGCCGCTA
1 GGCGTTT-GGACAAAAACGCCGCTA
109326589 ATGTATATTA
Statistics
Matches: 173, Mismatches: 25, Indels: 40
0.73 0.11 0.17
Matches are distributed among these distances:
30 4 0.02
31 20 0.12
34 1 0.01
36 2 0.01
38 1 0.01
39 13 0.08
40 36 0.21
41 81 0.47
42 15 0.09
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (40 bp):
GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
Found at i:109326461 original size:72 final size:71
Alignment explanation
Indices: 109326366--109326506 Score: 212
Period size: 72 Copynumber: 2.0 Consensus size: 71
109326356 TTAATCAGTT
*
109326366 TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTTGTGGCGTTTGGGACAAAAAC
1 TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTT-GGACAAAAAC
109326431 GCCGCAA
65 GCCGCAA
* * * *
109326438 TTTAGTGGCG-TTTGAGATTAAAACGCCACTATTGATCAGCTTTTAGTGGCGTTTTGATAAAAAC
1 TTTAGTGGCGTTTTG-GATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTTGGACAAAAAC
109326502 GCCGC
65 GCCGC
109326507 TATTGACCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 17 0.27
72 46 0.73
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (71 bp):
TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTTGGACAAAAACG
CCGCAA
Found at i:109331915 original size:21 final size:22
Alignment explanation
Indices: 109331886--109331932 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
109331876 CAGAAGGAGT
*
109331886 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
109331908 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
109331929 GAGT
1 GAGT
109331933 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:109340078 original size:13 final size:13
Alignment explanation
Indices: 109340058--109340091 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
109340048 GGTAGTGGGT
109340058 TTAA-TGGGTAGG
1 TTAATTGGGTAGG
109340070 TTAATTGGGTAGG
1 TTAATTGGGTAGG
109340083 TTAATTGGG
1 TTAATTGGG
109340092 CTGAAGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
TTAATTGGGTAGG
Found at i:109344066 original size:25 final size:23
Alignment explanation
Indices: 109344037--109344101 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
109344027 AATAAAAAAC
*
109344037 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAAT-AAATACA
109344062 TTTAAAACATAAAAATAAAT--A
1 TTTAAAACATAAAAATAAATACA
*
109344083 -TTAAAACA-AAAAACAAATA
1 TTTAAAACATAAAAATAAATA
109344102 AAAAATGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 4 0.11
24 4 0.11
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAATAAATACA
Found at i:109344094 original size:19 final size:20
Alignment explanation
Indices: 109344063--109344101 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
109344053 TCAAATACAT
*
109344063 TTAAAACATAAAAATAAATA
1 TTAAAACATAAAAACAAATA
109344083 TTAAAACA-AAAAACAAATA
1 TTAAAACATAAAAACAAATA
109344102 AAAAATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:109344982 original size:17 final size:17
Alignment explanation
Indices: 109344949--109344982 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
109344939 TTTAATTAAG
109344949 TAAATTATTAAAAATTA
1 TAAATTATTAAAAATTA
109344966 TAAA-TATTAAAATATTA
1 TAAATTATTAAAA-ATTA
109344983 GATAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTATTAAAAATTA
Found at i:109346057 original size:40 final size:40
Alignment explanation
Indices: 109346013--109346088 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
109346003 TTTATTCTAT
109346013 TTTTTAATTTGTGTATTGTTTTAAAAATTGTTTTAATATA
1 TTTTTAATTTGTGTATTGTTTTAAAAATTGTTTTAATATA
* * * * *
109346053 TTTTTTATTTGTTTCTTGTTTTAATATTTGTTTTAA
1 TTTTTAATTTGTGTATTGTTTTAAAAATTGTTTTAA
109346089 ATGTATTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.66
Consensus pattern (40 bp):
TTTTTAATTTGTGTATTGTTTTAAAAATTGTTTTAATATA
Found at i:109348073 original size:24 final size:24
Alignment explanation
Indices: 109348046--109348093 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
109348036 CATAAACTTA
*
109348046 TATATATTATAAATACAAAAAAAT
1 TATATATTAAAAATACAAAAAAAT
109348070 TATATATTAAAAATACAAAAAAAT
1 TATATATTAAAAATACAAAAAAAT
109348094 AATAAATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
TATATATTAAAAATACAAAAAAAT
Found at i:109348696 original size:22 final size:22
Alignment explanation
Indices: 109348671--109348725 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
109348661 TTAATTTTAA
*
109348671 TATTATGTA-TACTATTATATTT
1 TATTATCTATTACTATTATA-TT
*
109348693 TATTA-CTATTATTATTATATT
1 TATTATCTATTACTATTATATT
*
109348714 TATTATTTATTA
1 TATTATCTATTA
109348726 GCATTAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTATCTATTACTATTATATT
Found at i:109348716 original size:28 final size:30
Alignment explanation
Indices: 109348671--109348738 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 30
109348661 TTAATTTTAA
109348671 TATTATGTATACTATTA-TATTTTATTA-CTAT
1 TATTAT-TATACTATTATTA-TTTATTAGC-AT
109348702 TATTATTATA-T-TTATTATTTATTAGCAT
1 TATTATTATACTATTATTATTTATTAGCAT
*
109348730 TAGTATTAT
1 TATTATTAT
109348739 TTTCACTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 20 0.59
29 4 0.12
30 4 0.12
31 6 0.18
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (30 bp):
TATTATTATACTATTATTATTTATTAGCAT
Found at i:109348731 original size:22 final size:21
Alignment explanation
Indices: 109348684--109348736 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
109348674 TATGTATACT
**
109348684 ATTATATTTTATTACTATTATT
1 ATTATA-TTTATTACTATTAGC
*
109348706 ATTATATTTATTATTTATTAGC
1 ATTATATTTATTA-CTATTAGC
109348728 ATTAGTATT
1 ATTA-TATT
109348737 ATTTTCACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 7 0.27
22 15 0.58
23 4 0.15
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (21 bp):
ATTATATTTATTACTATTAGC
Found at i:109349220 original size:23 final size:22
Alignment explanation
Indices: 109349183--109349234 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
109349173 TTTTAACACT
*
109349183 ATATTATGTATATATATATTTTA
1 ATATTATGTACATAT-TATTTTA
* *
109349206 ATGTTATGTACATATTTTTTTA
1 ATATTATGTACATATTATTTTA
109349228 ATATTAT
1 ATATTAT
109349235 ATTTTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (22 bp):
ATATTATGTACATATTATTTTA
Found at i:109349238 original size:16 final size:16
Alignment explanation
Indices: 109349221--109349250 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
109349211 ATGTACATAT
109349221 TTTTTTA-ATATTATA
1 TTTTTTATATATTATA
109349236 TTTTTTATATATTAT
1 TTTTTTATATATTAT
109349251 TATGTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTATATATTATA
Found at i:109349729 original size:19 final size:19
Alignment explanation
Indices: 109349680--109349733 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
109349670 CGTTTTCAAT
*
109349680 ATATTGTATATAT-TTTTA
1 ATATAGTATATATGTTTTA
*
109349698 ATCTAGTATTATATGTTTTA
1 ATATAGTA-TATATGTTTTA
109349718 TATATA-TATATATGTT
1 -ATATAGTATATATGTT
109349734 CCCCACTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.20
19 13 0.43
20 7 0.23
21 4 0.13
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (19 bp):
ATATAGTATATATGTTTTA
Found at i:109364693 original size:18 final size:18
Alignment explanation
Indices: 109364670--109364705 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
109364660 GATGCTGGTG
109364670 TTGCCTTGTTGTAAGGGT
1 TTGCCTTGTTGTAAGGGT
109364688 TTGCCTTGTTGTAAGGGT
1 TTGCCTTGTTGTAAGGGT
109364706 GAGGGACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (18 bp):
TTGCCTTGTTGTAAGGGT
Found at i:109366149 original size:30 final size:30
Alignment explanation
Indices: 109366113--109366173 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
109366103 TGCTTTTCAT
109366113 TGCAGCAATGCATGAATCTTGAAAGCAAAC
1 TGCAGCAATGCATGAATCTTGAAAGCAAAC
109366143 TGCAGCAATGCATGAATCTTGAAAGCAAAC
1 TGCAGCAATGCATGAATCTTGAAAGCAAAC
109366173 T
1 T
109366174 TATAGCAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (30 bp):
TGCAGCAATGCATGAATCTTGAAAGCAAAC
Found at i:109372738 original size:68 final size:69
Alignment explanation
Indices: 109372610--109372747 Score: 217
Period size: 68 Copynumber: 2.0 Consensus size: 69
109372600 ATAATTCACC
* *
109372610 CTCCAATAATTGCCTGCTATATATACCATATAACCATTGCCAAATATATACACCCCTGTAAACAT
1 CTCCAATAATTGCCTGCTATATATACCA-ATAACCATCGCCAAATAAATACACCCCTGTAAACAT
109372675 GGAGT
65 GGAGT
*
109372680 CTCCAATAATTGCTTGCTATATATACC-ATAACCATCGCCAAATAAATAC-CCCACTGTAAACAT
1 CTCCAATAATTGCCTGCTATATATACCAATAACCATCGCCAAATAAATACACCC-CTGTAAACAT
109372743 GGAGT
65 GGAGT
109372748 GGACCTCTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
67 3 0.05
68 35 0.55
70 26 0.41
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (69 bp):
CTCCAATAATTGCCTGCTATATATACCAATAACCATCGCCAAATAAATACACCCCTGTAAACATG
GAGT
Found at i:109373747 original size:22 final size:23
Alignment explanation
Indices: 109373720--109373765 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
109373710 CGTTTAGCCC
*
109373720 AACAAATCAAAGCCCCAA-CCCA
1 AACAAATCAAAGCCCAAATCCCA
*
109373742 AACAAATCAAGGCCCAAATCCCA
1 AACAAATCAAAGCCCAAATCCCA
109373765 A
1 A
109373766 GTTAAGCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.50, C:0.37, G:0.07, T:0.07
Consensus pattern (23 bp):
AACAAATCAAAGCCCAAATCCCA
Found at i:109375572 original size:24 final size:24
Alignment explanation
Indices: 109375545--109375590 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
109375535 ATTATTTAAA
109375545 TTATCATTATAATTATTATTTTCG
1 TTATCATTATAATTATTATTTTCG
* * *
109375569 TTATCATTGTCATTTTTATTTT
1 TTATCATTATAATTATTATTTT
109375591 GCCATGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (24 bp):
TTATCATTATAATTATTATTTTCG
Found at i:109385742 original size:17 final size:17
Alignment explanation
Indices: 109385709--109385742 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
109385699 TTTAATTAAG
109385709 TAAATTATTAAAAATTA
1 TAAATTATTAAAAATTA
109385726 TAAA-TATTAAAATATTA
1 TAAATTATTAAAA-ATTA
109385743 GATAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTATTAAAAATTA
Found at i:109395922 original size:14 final size:15
Alignment explanation
Indices: 109395896--109395926 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
109395886 TCCAGGTTCA
109395896 TCAACACATTTTTCT
1 TCAACACATTTTTCT
109395911 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
109395925 TC
1 TC
109395927 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:109397540 original size:11 final size:11
Alignment explanation
Indices: 109397524--109397554 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
109397514 AAGTATGGGT
109397524 AGGTATGGGAA
1 AGGTATGGGAA
*
109397535 AGGTATGGGCA
1 AGGTATGGGAA
109397546 AGGTATGGG
1 AGGTATGGG
109397555 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:109401631 original size:18 final size:18
Alignment explanation
Indices: 109401608--109401664 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
109401598 CCTAACTACT
*
109401608 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
109401626 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
109401644 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
109401662 GTA
1 GTA
109401665 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:109402224 original size:11 final size:11
Alignment explanation
Indices: 109402208--109402238 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
109402198 AAGTATGGGT
109402208 AGGTATGGGAA
1 AGGTATGGGAA
*
109402219 AGGTATGGGCA
1 AGGTATGGGAA
109402230 AGGTATGGG
1 AGGTATGGG
109402239 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:109407795 original size:26 final size:27
Alignment explanation
Indices: 109407764--109407834 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 27
109407754 TGATTATATA
*
109407764 TAAAAATTCAAAAAAAATTAAAAT-AG
1 TAAAAATTCAAAAAAAATAAAAATAAG
109407790 TAAAAAATTC-AAAAAAATAAAAATAAG
1 T-AAAAATTCAAAAAAAATAAAAATAAG
*
109407817 TAAGAATTCAAAATAAAA
1 TAAAAATTCAAAA-AAAA
109407835 ATTATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 21 0.54
27 14 0.36
28 4 0.10
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (27 bp):
TAAAAATTCAAAAAAAATAAAAATAAG
Found at i:109407797 original size:27 final size:27
Alignment explanation
Indices: 109407765--109407851 Score: 90
Period size: 26 Copynumber: 3.2 Consensus size: 27
109407755 GATTATATAT
109407765 AAAAATTCAAAAAAAATTAAAATAGTA
1 AAAAATTCAAAAAAAATTAAAATAGTA
*
109407792 AAAAATTC-AAAAAAATAAAAATAAGT-
1 AAAAATTCAAAAAAAATTAAAAT-AGTA
* *
109407818 AAGAATTCAAAATAAAAATTATAAA-AATA
1 AAAAATTC-AAA-AAAAATTA-AAATAGTA
109407847 AAAAA
1 AAAAA
109407852 ATGATGAGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
26 20 0.41
27 11 0.22
28 4 0.08
29 11 0.22
30 3 0.06
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.21
Consensus pattern (27 bp):
AAAAATTCAAAAAAAATTAAAATAGTA
Found at i:109415842 original size:27 final size:27
Alignment explanation
Indices: 109415754--109415825 Score: 144
Period size: 27 Copynumber: 2.7 Consensus size: 27
109415744 TTGGGTGTAT
109415754 CGCCTATCAGATAGGCACAACCAGTGC
1 CGCCTATCAGATAGGCACAACCAGTGC
109415781 CGCCTATCAGATAGGCACAACCAGTGC
1 CGCCTATCAGATAGGCACAACCAGTGC
109415808 CGCCTATCAGATAGGCAC
1 CGCCTATCAGATAGGCAC
109415826 GATTAGTACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.29, C:0.33, G:0.22, T:0.15
Consensus pattern (27 bp):
CGCCTATCAGATAGGCACAACCAGTGC
Found at i:109417086 original size:21 final size:18
Alignment explanation
Indices: 109417019--109417080 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
109417009 TGTGAAAATG
109417019 ATATAAACATATTAATAT-
1 ATATAAA-ATATTAATATA
*
109417037 AT-CAAAAT-TT-ATATA
1 ATATAAAATATTAATATA
*
109417052 ATATAAATTATTAATATA
1 ATATAAAATATTAATATA
109417070 ATAATAAAATA
1 AT-ATAAAATA
109417081 GTTTAAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
14 4 0.11
15 4 0.11
16 6 0.17
17 5 0.14
18 9 0.26
19 7 0.20
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAAATATTAATATA
Found at i:109422382 original size:16 final size:16
Alignment explanation
Indices: 109422363--109422396 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
109422353 TACATGCAAT
*
109422363 ACATGTCACATTAGAC
1 ACATGTCACATTAAAC
*
109422379 ACATGTGACATTAAAC
1 ACATGTCACATTAAAC
109422395 AC
1 AC
109422397 CAGTAATAAT
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:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (16 bp):
ACATGTCACATTAAAC
Found at i:109427966 original size:16 final size:16
Alignment explanation
Indices: 109427931--109427984 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
109427921 AAAAAATATG
* * *
109427931 TTTTCTATCATTTTAG
1 TTTTCTATCCTTCTAA
109427947 TTTTCTATCCCTTC-AA
1 TTTTCTAT-CCTTCTAA
*
109427963 TTTTTTATCCTTCTAA
1 TTTTCTATCCTTCTAA
109427979 TTTTCT
1 TTTTCT
109427985 TTTCACTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 5 0.16
16 23 0.74
17 3 0.10
ACGTcount: A:0.17, C:0.20, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTCTATCCTTCTAA
Found at i:109433434 original size:87 final size:87
Alignment explanation
Indices: 109433287--109433455 Score: 297
Period size: 87 Copynumber: 1.9 Consensus size: 87
109433277 TTTTCAGCAG
*
109433287 TGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAATGCGCCCGAA-CCT
1 TGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCGCCCGAATCC-
109433351 ACTAAATTGCATACTTCACGTAT
65 ACTAAATTGCATACTTCACGTAT
109433374 TGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCAG-CCGAATCC
1 TGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGC-GCCCGAATCC
109433438 ACTAAATTGCATACTTCA
65 ACTAAATTGCATACTTCA
109433456 AGTGAAGAAC
Statistics
Matches: 79, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
87 76 0.96
88 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (87 bp):
TGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCGCCCGAATCCA
CTAAATTGCATACTTCACGTAT
Found at i:109433770 original size:15 final size:15
Alignment explanation
Indices: 109433750--109433780 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109433740 GTCATGTAAG
109433750 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
109433765 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
109433780 T
1 T
109433781 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:109433972 original size:17 final size:17
Alignment explanation
Indices: 109433939--109433977 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
109433929 TAAGCTTTTG
109433939 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
109433956 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
109433973 ATTTT
1 ATTTT
109433978 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:109438111 original size:15 final size:15
Alignment explanation
Indices: 109438091--109438121 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109438081 GTCATGTAAA
109438091 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
109438106 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
109438121 T
1 T
109438122 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:109438312 original size:17 final size:17
Alignment explanation
Indices: 109438279--109438317 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
109438269 TAAGCTTTTG
109438279 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
109438296 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
109438313 ATTTT
1 ATTTT
109438318 CCACACCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:109440173 original size:14 final size:15
Alignment explanation
Indices: 109440148--109440177 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
109440138 CCAGGTTCAC
109440148 CAACACATTTTTCTT
1 CAACACATTTTTCTT
109440163 CAACA-ATTTTTCTT
1 CAACACATTTTTCTT
109440177 C
1 C
109440178 CCATTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
CAACACATTTTTCTT
Found at i:109450161 original size:16 final size:16
Alignment explanation
Indices: 109450136--109450187 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
109450126 AAAAGTTATG
109450136 TTTTTCATCCTTCTAA
1 TTTTTCATCCTTCTAA
* * *
109450152 TTTTTTATCCCTCCAA
1 TTTTTCATCCTTCTAA
* *
109450168 TTTTTCATGCTTTTAA
1 TTTTTCATCCTTCTAA
109450184 TTTT
1 TTTT
109450188 CTTTTCACTC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTCATCCTTCTAA
Done.