Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007113.1 Hibiscus syriacus cultivar Beakdansim tig00018586_pilon, whole genome shotgun sequence
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: 836039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:1502 original size:21 final size:20
Alignment explanation
Indices: 1483--1601 Score: 121
Period size: 21 Copynumber: 5.7 Consensus size: 20
1473 GATGCACCTG
* *
1483 TCATCGTTCAAAAGGCACCT
1 TCATCGTTCAAGAGGCCCCT
*
1503 CCTATCGTTCAAGAGGCCCCT
1 TC-ATCGTTCAAGAGGCCCCT
1524 ATCATCGTTCAAGAGGCCCCT
1 -TCATCGTTCAAGAGGCCCCT
* *
1545 TCCACCGTTCAATAGGCCCCT
1 T-CATCGTTCAAGAGGCCCCT
*
1566 GTCATCGTTCAAGAGGTCCCT
1 -TCATCGTTCAAGAGGCCCCT
* *
1587 CCCACCGTTCAAGAG
1 -TCATCGTTCAAGAG
1602 CCCGATTCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.02
21 79 0.95
22 2 0.02
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCCT
Found at i:1554 original size:42 final size:42
Alignment explanation
Indices: 1483--1601 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 42
1473 GATGCACCTG
* * *
1483 TCATCGTTCAAAAGGCACC-TCCTATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTTCC-ACCGTTCAAGAGGCCCCTA
* *
1525 TCATCGTTCAAGAGGCCCCTTCCACCGTTCAATAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTTCCACCGTTCAAGAGGCCCCTA
* *
1567 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTTCCACCGTTCAAGAG
1602 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 65 0.96
43 3 0.04
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTTCCACCGTTCAAGAGGCCCCTA
Found at i:6628 original size:15 final size:16
Alignment explanation
Indices: 6592--6629 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6582 AAATCATTAA
*
6592 AAAATTATATAGAAAT
1 AAAATTATATAGAAAC
*
6608 AAAATTATGTA-AAAC
1 AAAATTATATAGAAAC
6623 AAAATTA
1 AAAATTA
6630 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATTATATAGAAAC
Found at i:6852 original size:19 final size:19
Alignment explanation
Indices: 6824--6876 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
6814 TCGAAAACCG
6824 AGTTGCGAATTTGAAATTC
1 AGTTGCGAATTTGAAATTC
*
6843 AGTTGTGAATTTGAAATTC
1 AGTTGCGAATTTGAAATTC
6862 AGTGTTGCGAATTTG
1 A--GTTGCGAATTTG
6877 GCAAACGCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 19 0.63
21 11 0.37
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.40
Consensus pattern (19 bp):
AGTTGCGAATTTGAAATTC
Found at i:6943 original size:20 final size:21
Alignment explanation
Indices: 6905--6949 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
6895 TGGCTTTTTT
*
6905 GTTGCGATTTTCTAAATTCGC
1 GTTGCGATTTACTAAATTCGC
6926 GTTGCGATTTAC-AAATTCGC
1 GTTGCGATTTACTAAATTCGC
6946 GTTG
1 GTTG
6950 TGAATTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (21 bp):
GTTGCGATTTACTAAATTCGC
Found at i:8943 original size:85 final size:85
Alignment explanation
Indices: 8776--9357 Score: 671
Period size: 85 Copynumber: 6.8 Consensus size: 85
8766 TACCATACGG
* * * * * * *** *
8776 TTGATATGTCATTGAGCTGAATGGAATCGAACTCGACA-ATTTTTGTTGACAGATAAATTTTCTT
1 TTGATATGCCCTTGAGCTGAATGTAATTGAACTCGA-AGGTATTTGTTGACAGATAACCCTTCTC
* * *
8840 GACTTAAGCTATGCTGTAAAT
65 GCCTTGAGTTATGCTGTAAAT
* * * *
8861 TTGACATGCCCTTGAGCTGAATGAAATTGAACTCGAAGGTATTTATTGACAGTTAACCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCG
*
8926 CCTTGAGTTATGATGTAAAT
66 CCTTGAGTTATGCTGTAAAT
* * * * * * * * *
8946 TTGATATGTCCTTGAGTTGAGTGTAATCGAACTCGAAGGTTTTTGTTGACATATAGCCCTTTTCT
1 TTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCG
9011 CCTTGAGTTATGCTGTAAAT
66 CCTTGAGTTATGCTGTAAAT
* * * * * *
9031 TTGATATGCCCTTCAGCTGAATATAATTGAACTTGAAGGTCTTTGCTGACAGATAACCCTTATCG
1 TTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCG
9096 CCTTGAGTTATGCTGTAAAT
66 CCTTGAGTTATGCTGTAAAT
** * * *
9116 TTGATATGCCCTTGAGCTGAATGTAATCAAATTCAAAGGTATTTGCTGACAGATAACCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCG
9181 CCTTGAGTTATGCTGTAAAT
66 CCTTGAGTTATGCTGTAAAT
* * * * *
9201 TTGATATGCCTTTGAGCTGAATGTAATTGAACTAGAAGGTCTTGGTTAACAGATAACCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCG
9266 CCTTGAGTTATGCTGTAAAT
66 CCTTGAGTTATGCTGTAAAT
* * * * * * * **
9286 TTGATATGTCATTGAGCTGAGTGTAATTGAACTCGATGGTCTTTTGCTGGCAGATAGTCCTTCTC
1 TTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTCTC
9351 GCCTTGA
65 GCCTTGA
9358 ACTATACAAC
Statistics
Matches: 420, Mismatches: 75, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
84 1 0.00
85 395 0.94
86 24 0.06
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (85 bp):
TTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCG
CCTTGAGTTATGCTGTAAAT
Found at i:9539 original size:86 final size:86
Alignment explanation
Indices: 9433--9735 Score: 408
Period size: 86 Copynumber: 3.5 Consensus size: 86
9423 TTTCTTTACT
* * * **
9433 TGACTCCCCTTCACAGGAAAGCCAAGTGGTATATTCTTCAAGTGGTTCCCCTTCACGGGTCTGAA
1 TGACTCCCCTTCACAGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGTGGGTCTGAA
* *
9498 CCAAGTGAGATGATATTTGGA
66 CCAGGTGAGATGATCTTTGGA
* * * *
9519 TGACTCCCCTTCACATGAAAGTCGTGTGGTATATTCTTTAGGTGGTTCCACTTCGTGGGTCTGAA
1 TGACTCCCCTTCACAGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGTGGGTCTGAA
9584 CCAGGTGAGATGATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
* * * * *
9605 TGACTCGCCTTCACGGGAAAGTCATGTGGTATATTCTTCTGGTGGTTCCCTTTTGTGGGTCTGAA
1 TGACTCCCCTTCACAGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGTGGGTCTGAA
9670 CCAGGTGAGATGATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
* * ** * *
9691 CGACTCCCATTCATGGGAAAGTCATATGGTCTATTCTTCAGGTGG
1 TGACTCCCCTTCACAGGAAAGTCATGTGGTATATTCTTCAGGTGG
9736 CTCCTCTTTA
Statistics
Matches: 190, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 190 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (86 bp):
TGACTCCCCTTCACAGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGTGGGTCTGAA
CCAGGTGAGATGATCTTTGGA
Found at i:10717 original size:22 final size:22
Alignment explanation
Indices: 10689--10732 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
10679 ACTATAACAG
10689 GTGTTCCTTAACACCCTTAGTC
1 GTGTTCCTTAACACCCTTAGTC
*
10711 GTGTTCCTTAACTCCCTTAGTC
1 GTGTTCCTTAACACCCTTAGTC
10733 TATCTTTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.14, T:0.39
Consensus pattern (22 bp):
GTGTTCCTTAACACCCTTAGTC
Found at i:11016 original size:99 final size:99
Alignment explanation
Indices: 10845--11041 Score: 331
Period size: 99 Copynumber: 2.0 Consensus size: 99
10835 GGACAACTCA
* * * *
10845 ATATTATAATCACCTTTATTAGGCTAGCAGAATCTTATCTATAAAGCCGCGTCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCAGAATCTTATCCATAAAGCCGCGGCCTTTAACCAATT
10910 GCTTTAGAGGGACAACTCAAGCTTTATTGTATAG
66 GCTTTAGAGGGACAACTCAAGCTTTATTGTATAG
* *
10944 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCCTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCAGAATCTTATCCATAAAGCCGCGGCCTTTAACCAATT
*
11009 GCTTTAGAGGGATAACTCAAGCTTTATTGTATA
66 GCTTTAGAGGGACAACTCAAGCTTTATTGTATA
11042 TATAATATTA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGCTAGCAGAATCTTATCCATAAAGCCGCGGCCTTTAACCAATT
GCTTTAGAGGGACAACTCAAGCTTTATTGTATAG
Found at i:15281 original size:31 final size:30
Alignment explanation
Indices: 15205--15283 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 30
15195 ACCTATAAAC
15205 AAAAAAATAAAAAAAAAGGATATAAATAATA
1 AAAAAAAT-AAAAAAAAGGATATAAATAATA
**
15236 AAACAAAACCAAAAAAAGGA-A-AAATAAAATA
1 AAA-AAAATAAAAAAAAGGATATAAAT--AATA
15267 TAAAAAAATAAAAAAAA
1 -AAAAAAATAAAAAAAA
15284 TAAAACAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
29 4 0.10
30 1 0.03
31 28 0.70
32 7 0.17
ACGTcount: A:0.80, C:0.04, G:0.05, T:0.11
Consensus pattern (30 bp):
AAAAAAATAAAAAAAAGGATATAAATAATA
Found at i:15545 original size:2 final size:2
Alignment explanation
Indices: 15538--15570 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
15528 AAAGAAAAAC
*
15538 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15571 ATAAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:15577 original size:10 final size:11
Alignment explanation
Indices: 15538--15584 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
15528 AAAGAAAAAC
*
15538 ATATATATAT-
1 ATATAAATATA
*
15548 ATATATATATA
1 ATATAAATATA
15559 TATATAAATATA
1 -ATATAAATATA
15571 ATA-AAATATA
1 ATATAAATATA
15581 ATAT
1 ATAT
15585 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 20 0.61
11 3 0.09
12 10 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATAAATATA
Found at i:15610 original size:21 final size:23
Alignment explanation
Indices: 15562--15610 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
15552 ATATATATAT
* *
15562 ATAAATATAATAAAATATAATAT
1 ATAAATATAATAAAATATAAGAA
*
15585 TTAAATA-AATAAAA-ATAAGAA
1 ATAAATATAATAAAATATAAGAA
15606 ATAAA
1 ATAAA
15611 AAAGAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 9 0.41
22 7 0.32
23 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
ATAAATATAATAAAATATAAGAA
Found at i:24286 original size:22 final size:21
Alignment explanation
Indices: 24248--24298 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
24238 TTTTAAAATT
*
24248 AATAAATAAATTTTTATAATA
1 AATAAATAAATTATTATAATA
* *
24269 AATAATATTAATTATTATATTA
1 AATAA-ATAAATTATTATAATA
24291 AATAAATA
1 AATAAATA
24299 TCATAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAAATAAATTATTATAATA
Found at i:24876 original size:30 final size:28
Alignment explanation
Indices: 24811--24877 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
24801 TAATTAGCAT
*
24811 AAAAATAATTAATTAATAAATTTAAATA
1 AAAAATAATTAATAAATAAATTTAAATA
* * *
24839 AATAATAATTATATAAATATTATTTTAATA
1 AAAAATAATTA-ATAAATA-AATTTAAATA
24869 AAAAATAAT
1 AAAAATAAT
24878 ATTTATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 10 0.31
29 6 0.19
30 16 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAAATAATTAATAAATAAATTTAAATA
Found at i:24936 original size:33 final size:35
Alignment explanation
Indices: 24834--24942 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 35
24824 TAATAAATTT
* * *
24834 AAATAAATAATAATTATATAA--ATATTATTTTAA
1 AAATAAATAATATTTATATAATTATATTACTATAA
24867 TAAA-AAATAATATTTATATAATTATATTACTATAA
1 -AAATAAATAATATTTATATAATTATATTACTATAA
*
24902 AATATAAATACTATTTA-A-AA-TATATTAACT-TAA
1 AA-ATAAATAATATTTATATAATTATATT-ACTATAA
24935 AAATAAAT
1 AAATAAAT
24943 TTATTACTAC
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
32 6 0.09
33 27 0.41
34 10 0.15
35 12 0.18
36 11 0.17
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (35 bp):
AAATAAATAATATTTATATAATTATATTACTATAA
Found at i:26638 original size:31 final size:31
Alignment explanation
Indices: 26603--26673 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
26593 AAAACATAAT
26603 ATTTGATCACTTTCATTTTTATTTAATTAAG
1 ATTTGATCACTTTCATTTTTATTTAATTAAG
*
26634 ATTTGATCACTTTTATTTTTATTTAATTAAG
1 ATTTGATCACTTTCATTTTTATTTAATTAAG
*
26665 ATGTGATCA
1 ATTTGATCA
26674 TTGAGGGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (31 bp):
ATTTGATCACTTTCATTTTTATTTAATTAAG
Found at i:26805 original size:124 final size:123
Alignment explanation
Indices: 26640--26891 Score: 396
Period size: 124 Copynumber: 2.0 Consensus size: 123
26630 TAAGATTTGA
* * * * *
26640 TCACTTTTATTTTTATTTAATTAAGATGTGATCATTGAGGGTTAATTGTCGTTAGACCTTTAACG
1 TCACTTTTATTTTTATTTAATTAAGATGTGACCACTGAGGGTTAATTATCGTTAAACCTTTAACA
* * *
26705 GATTGCTAATGCAACACAGTGAATTTATAAAATTAAAAAGGATAAACTACATAAATAG
66 GACTGCTAACGCAACACAGTGAATTTATAAAATTAAAAAGCATAAACTACATAAATAG
26763 TCACTTTTAGTTTTTATTTAATTAAGATGTGACCACTGAGGGTTAATTATCGTTAAACCTTTAAC
1 TCACTTTTA-TTTTTATTTAATTAAGATGTGACCACTGAGGGTTAATTATCGTTAAACCTTTAAC
***
26828 AGACTGCTAACGTTGCACAGTGAATTTATAAAATTAAAAAGCATAAACTACATAAATAG
65 AGACTGCTAACGCAACACAGTGAATTTATAAAATTAAAAAGCATAAACTACATAAATAG
26887 TCACT
1 TCACT
26892 AATGTTTGAG
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
123 9 0.08
124 108 0.92
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (123 bp):
TCACTTTTATTTTTATTTAATTAAGATGTGACCACTGAGGGTTAATTATCGTTAAACCTTTAACA
GACTGCTAACGCAACACAGTGAATTTATAAAATTAAAAAGCATAAACTACATAAATAG
Found at i:31991 original size:3 final size:3
Alignment explanation
Indices: 31983--32017 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
31973 TCAACCAATA
31983 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
32018 ATCAAATAAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:32098 original size:18 final size:18
Alignment explanation
Indices: 32075--32111 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
32065 TACCCAATAT
*
32075 CCAAACCCAAACCCTAGC
1 CCAAACCAAAACCCTAGC
32093 CCAAACCAAAACCCTAGC
1 CCAAACCAAAACCCTAGC
32111 C
1 C
32112 GTAGCCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.49, G:0.05, T:0.05
Consensus pattern (18 bp):
CCAAACCAAAACCCTAGC
Found at i:33099 original size:24 final size:23
Alignment explanation
Indices: 33045--33124 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
33035 GAATGTAAAT
* * * **
33045 GAACATAAACGAACACAATAATT
1 GAACGTAAACGAACAAAACAAAC
* *
33068 GAACGTAAATGAACATAAACGAAC
1 GAACGTAAACGAACA-AAACAAAC
33092 GAACGTAAACGAACAAAACAAAC
1 GAACGTAAACGAACAAAACAAAC
*
33115 GAACATAAAC
1 GAACGTAAAC
33125 TACCACAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
23 29 0.63
24 17 0.37
ACGTcount: A:0.57, C:0.19, G:0.12, T:0.11
Consensus pattern (23 bp):
GAACGTAAACGAACAAAACAAAC
Found at i:33135 original size:23 final size:23
Alignment explanation
Indices: 33001--33124 Score: 86
Period size: 24 Copynumber: 5.3 Consensus size: 23
32991 CATTTAAATG
* * *
33001 ATAAACGAAAATAAATAAACGACC
1 ATAAACGAACA-AAACAAACGAAC
*** *
33025 ATAAACGAACGAATGTAAATGAAC
1 ATAAACGAAC-AAAACAAACGAAC
* * **
33049 ATAAACGAACACAATAATTGAAC
1 ATAAACGAACAAAACAAACGAAC
* * *
33072 GTAAATGAACATAAACGAACGAAC
1 ATAAACGAACA-AAACAAACGAAC
*
33096 GTAAACGAACAAAACAAACGAAC
1 ATAAACGAACAAAACAAACGAAC
33119 ATAAAC
1 ATAAAC
33125 TACCACAACA
Statistics
Matches: 79, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
23 34 0.43
24 44 0.56
25 1 0.01
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.13
Consensus pattern (23 bp):
ATAAACGAACAAAACAAACGAAC
Found at i:33647 original size:24 final size:23
Alignment explanation
Indices: 33563--33661 Score: 112
Period size: 24 Copynumber: 4.3 Consensus size: 23
33553 GATTGATCTA
* *
33563 AACATAAACGAATGAAAGTAAACG
1 AACATAAACGAA-CAAAGTAAATG
*
33587 AACATAAACGACCGAAAGTAAATG
1 AACATAAACGAAC-AAAGTAAATG
*
33611 AACATAAACGAACAAACATAAATG
1 AACATAAACGAACAAA-GTAAATG
*
33635 AACATAAACGAACATA--AAATG
1 AACATAAACGAACAAAGTAAATG
33656 AACATA
1 AACATA
33662 TTACTGAATG
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
21 11 0.16
23 3 0.04
24 53 0.79
ACGTcount: A:0.60, C:0.15, G:0.12, T:0.13
Consensus pattern (23 bp):
AACATAAACGAACAAAGTAAATG
Found at i:33660 original size:11 final size:10
Alignment explanation
Indices: 33625--33661 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
33615 TAAACGAACA
33625 AACATAAATG
1 AACATAAATG
*
33635 AACATAAACG
1 AACATAAATG
33645 AACATAAAATG
1 AACAT-AAATG
33656 AACATA
1 AACATA
33662 TTACTGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.62, C:0.14, G:0.08, T:0.16
Consensus pattern (10 bp):
AACATAAATG
Found at i:35954 original size:35 final size:36
Alignment explanation
Indices: 35882--35956 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
35872 TGAATATTTA
*
35882 ATTTCTTAGATTTTAATTTAAATATTTCTTTTGTTT
1 ATTTCTTAGATTTTAATTTAAATATTTATTTTGTTT
**
35918 ATTTCTTA-ATTTTAATTTATTTAATTTATTTT-TTT
1 ATTTCTTAGATTTTAATTTAAAT-ATTTATTTTGTTT
35953 ATTT
1 ATTT
35957 TGAATTTGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (36 bp):
ATTTCTTAGATTTTAATTTAAATATTTATTTTGTTT
Found at i:43738 original size:19 final size:19
Alignment explanation
Indices: 43714--43762 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
43704 CGGGAAAATA
43714 TTCTTTTTACTTTA-TTCC
1 TTCTTTTTACTTTATTTCC
*
43732 TT-TCTTTTATTTTATTTCC
1 TTCT-TTTTACTTTATTTCC
*
43751 TTATTTTTACTT
1 TTCTTTTTACTT
43763 ATCTCTCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 11 0.42
19 13 0.50
20 1 0.04
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCTTTTTACTTTATTTCC
Found at i:46029 original size:3 final size:3
Alignment explanation
Indices: 46021--46114 Score: 188
Period size: 3 Copynumber: 31.3 Consensus size: 3
46011 ACGTAGAAAC
46021 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46069 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
46115 ATTTATCAAG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:49335 original size:20 final size:20
Alignment explanation
Indices: 49310--49353 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
49300 AGACCCAAAG
49310 GAAGTAAGCGCAAGATCCCA
1 GAAGTAAGCGCAAGATCCCA
49330 GAAGTAAGCGCAAGATCCCA
1 GAAGTAAGCGCAAGATCCCA
49350 GAAG
1 GAAG
49354 AAAGAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (20 bp):
GAAGTAAGCGCAAGATCCCA
Found at i:53428 original size:32 final size:32
Alignment explanation
Indices: 53326--53462 Score: 131
Period size: 32 Copynumber: 4.3 Consensus size: 32
53316 CCTCAAAAAT
* * *
53326 TGTCCATAGGTCCCGAAAA-ACCTAGGTAA-AC
1 TGTCCATATGTCCC-AAAAGACATAGGTAATTC
** *
53357 TGTCCATATGCTCCTTAGA-ACATAGGT-ATAT-
1 TGTCCATATG-TCCCAAAAGACATAGGTAAT-TC
* *
53388 TGTCCATATGTCTCAAAAGATATAGGTAATTC
1 TGTCCATATGTCCCAAAAGACATAGGTAATTC
*
53420 TGTCCATATGTCCCGAAAGACATAGGTAATTC
1 TGTCCATATGTCCCAAAAGACATAGGTAATTC
53452 TGTCCATATGT
1 TGTCCATATGT
53463 TCCGTAGAAC
Statistics
Matches: 86, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
30 5 0.06
31 36 0.42
32 45 0.52
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTCCATATGTCCCAAAAGACATAGGTAATTC
Found at i:53475 original size:32 final size:32
Alignment explanation
Indices: 53348--53480 Score: 123
Period size: 32 Copynumber: 4.2 Consensus size: 32
53338 CCGAAAAACC
* * *
53348 TAGGTAA-ACTGTCCATATGCTCCTTAGAACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACA
*** *
53379 TAGGT-ATAT-TGTCCATATGTCTCAAAAG-ATA
1 TAGGTAAT-TCTGTCCATATGT-TCCGTAGAACA
* *
53410 TAGGTAATTCTGTCCATATGTCCCG-AAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGA-ACA
53442 TAGGTAATTCTGTCCATATGTTCCGTAGAACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACA
53474 TAGGTAA
1 TAGGTAA
53481 ACCCTAGACT
Statistics
Matches: 81, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
30 2 0.02
31 24 0.30
32 53 0.65
33 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (32 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACA
Found at i:56593 original size:23 final size:24
Alignment explanation
Indices: 56567--56616 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
56557 CCAAATTTTT
* *
56567 TTTTGATTTCTAATC-TTTTATTA
1 TTTTGACTTCAAATCATTTTATTA
* *
56590 TTTTTACTTCAAATCATTTTTTTA
1 TTTTGACTTCAAATCATTTTATTA
56614 TTT
1 TTT
56617 AAAAATCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTGACTTCAAATCATTTTATTA
Found at i:58054 original size:20 final size:20
Alignment explanation
Indices: 58007--58054 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
57997 ATTATCAAAC
58007 TATCATTTATTTATTATTCT
1 TATCATTTATTTATTATTCT
*
58027 TA-CTATTT-TTTATATATTTT
1 TATC-ATTTATTTAT-TATTCT
58047 TATCATTT
1 TATCATTT
58055 CCAACATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 6 0.25
20 17 0.71
21 1 0.04
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TATCATTTATTTATTATTCT
Found at i:67616 original size:17 final size:17
Alignment explanation
Indices: 67594--67661 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
67584 ATATTATGCT
67594 TAAAAAATGAAAATGAA
1 TAAAAAATGAAAATGAA
*
67611 TAAAAAA-GAAAAAAGAA
1 TAAAAAATG-AAAATGAA
*
67628 -AAAAAATGAAAA-AAA
1 TAAAAAATGAAAATGAA
*
67643 TGAAAAAGGTGAAAATGAA
1 T-AAAAA-ATGAAAATGAA
67662 AATGAGGGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 2 0.05
16 11 0.27
17 20 0.49
18 6 0.15
19 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
TAAAAAATGAAAATGAA
Found at i:67649 original size:10 final size:10
Alignment explanation
Indices: 67603--67649 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
67593 TTAAAAAATG
67603 AAAATGAATAA
1 AAAATGAA-AA
67614 AAAA-G--AA
1 AAAATGAAAA
67621 AAAA-GAAAA
1 AAAATGAAAA
67630 AAAATG-AAA
1 AAAATGAAAA
67639 AAAATGAAAA
1 AAAATGAAAA
67649 A
1 A
67650 GGTGAAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.22
9 15 0.47
10 6 0.19
11 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.09
Consensus pattern (10 bp):
AAAATGAAAA
Found at i:68891 original size:118 final size:118
Alignment explanation
Indices: 68683--68905 Score: 367
Period size: 118 Copynumber: 1.9 Consensus size: 118
68673 AACATTTCTG
*
68683 TGGAAGGGTTCGTAATGAGAAAAACTCATTCGATGAGCAAGAAGAAGTTCATAATGAGAAGAACT
1 TGGAAGAGTTCGTAATGAGAAAAACTCATTCGATGAGCAAGAAGAAGTTCATAATGAGAAGAACT
68748 TATTCAACCTTAGCTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCAA
66 TATTCAACCTTAGCTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCAA
* * **
68801 TGGAAGAGTTTGTAATGAGAAGAACTCA-TCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAAC
1 TGGAAGAGTTCGTAATGAGAAAAACTCATTC-GATGAGCAAGAAGAAGTTCATAATGAGAAGAAC
* *
68865 TTATTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGA
65 TTATTCAACCTTAGCTCGATTCCATCACAGAAGGAGATGGA
68906 ATAGCACCGA
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
117 2 0.02
118 95 0.98
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (118 bp):
TGGAAGAGTTCGTAATGAGAAAAACTCATTCGATGAGCAAGAAGAAGTTCATAATGAGAAGAACT
TATTCAACCTTAGCTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCAA
Found at i:71690 original size:20 final size:21
Alignment explanation
Indices: 71667--71744 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 21
71657 TTGGTGCAGA
*
71667 GGGAATCGATCCCCCCATGA-
1 GGGAACCGATCCCCCCATGAG
**
71687 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGA-TCCCCCCATG-AG
*
71710 GGGAACCGATCCCCCCA-CAG
1 GGGAACCGATCCCCCCATGAG
* *
71730 GGGAATCGATACCCC
1 GGGAACCGATCCCCC
71745 TGGGGTTCTG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 23 0.49
21 8 0.17
22 7 0.15
23 9 0.19
ACGTcount: A:0.24, C:0.36, G:0.26, T:0.14
Consensus pattern (21 bp):
GGGAACCGATCCCCCCATGAG
Found at i:73705 original size:17 final size:18
Alignment explanation
Indices: 73667--73705 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
73657 TTTTAACATT
*
73667 TTGAATATTTTGGAATGT
1 TTGAATATTTTGGAATGA
*
73685 TTGAAT-TTTTGGATTGA
1 TTGAATATTTTGGAATGA
73702 TTGA
1 TTGA
73706 CTTTGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (18 bp):
TTGAATATTTTGGAATGA
Found at i:78255 original size:36 final size:37
Alignment explanation
Indices: 78188--78264 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
78178 TTTTTATATT
78188 TTTAATTTTGTAAAAAAATTTATATAAATATTATA-AA
1 TTTAATTTTGTAAAAAAA-TTATATAAATATTATACAA
* *
78225 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTATACAA
78262 TTT
1 TTT
78265 GTATATTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 14 0.39
37 18 0.50
38 4 0.11
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATACAA
Found at i:81993 original size:18 final size:18
Alignment explanation
Indices: 81972--82009 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
81962 AAAATAATCT
81972 GTAATGACCAAAATA-TGA
1 GTAAT-ACCAAAATAGTGA
*
81990 GTAATACGAAAATAGTGA
1 GTAATACCAAAATAGTGA
82008 GT
1 GT
82010 GAACTAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (18 bp):
GTAATACCAAAATAGTGA
Found at i:85808 original size:29 final size:29
Alignment explanation
Indices: 85762--85818 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
85752 TGCTGCAATA
*
85762 CAATAGCTTTTAATTACAAACCATATAAG
1 CAATAGCTTTTAACTACAAACCATATAAG
*
85791 CAATAGCTTTTCACTACAAACCATATAA
1 CAATAGCTTTTAACTACAAACCATATAA
85819 ACATACCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (29 bp):
CAATAGCTTTTAACTACAAACCATATAAG
Found at i:88273 original size:2 final size:2
Alignment explanation
Indices: 88266--88349 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
88256 GCTACAAACA
88266 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
88308 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
88350 TGCAGAGATA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96952 original size:55 final size:55
Alignment explanation
Indices: 96885--96994 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
96875 TAGAATTGAG
*
96885 CCTCTGACTGAATTTTTCATGTCCATGTATTCAGCCAAATGTG-TTCTAGTATGTA
1 CCTCTAACTGAATTTTTCATGTCCATGTATTCAGCCAAATG-GATTCTAGTATGTA
* *
96940 CCTCTAACTGAATTTTTCATTTCCATGTATTGAGCCAAATGGATTCTAGTATGTA
1 CCTCTAACTGAATTTTTCATGTCCATGTATTCAGCCAAATGGATTCTAGTATGTA
96995 GAAATATTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 1 0.02
55 50 0.98
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (55 bp):
CCTCTAACTGAATTTTTCATGTCCATGTATTCAGCCAAATGGATTCTAGTATGTA
Found at i:97961 original size:32 final size:32
Alignment explanation
Indices: 97920--97984 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
97910 TGGGAGACTG
97920 TTGTTCCCTTAACAAATCACTCAATGCACTTA
1 TTGTTCCCTTAACAAATCACTCAATGCACTTA
97952 TTGTTCCCTTAACAAATCACTCAATGCACTTA
1 TTGTTCCCTTAACAAATCACTCAATGCACTTA
97984 T
1 T
97985 AAAGCAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (32 bp):
TTGTTCCCTTAACAAATCACTCAATGCACTTA
Found at i:100535 original size:94 final size:95
Alignment explanation
Indices: 100416--100603 Score: 279
Period size: 96 Copynumber: 2.0 Consensus size: 95
100406 CCAATTATAC
* * *
100416 TATTTAAATCTTAAAGAATTAA-TTTTTTCAAAGAAATTTCTTTGGTTGATCGACTAACGATCTA
1 TATTTAAATCTTAAAGAATTAATTTTTTTCAAAGAAATTTCTTTAGATGATCAACTAACGATCTA
100480 TATTCTTACTAACATGATGTGATAACATAA
66 TATTCTTACTAACATGATGTGATAACATAA
* * * *
100510 TATTTAAATCTTAAAAATATTATTTTTTTTCAAAGAAGTTTCTTTAGATGATCAACTAGCGATCT
1 TATTTAAATCTTAAAGA-ATTAATTTTTTTCAAAGAAATTTCTTTAGATGATCAACTAACGATCT
* *
100575 ATATTCTTATTAACGTGATGTGATAACAT
65 ATATTCTTACTAACATGATGTGATAACAT
100604 GATCTGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 16 0.19
95 4 0.05
96 63 0.76
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (95 bp):
TATTTAAATCTTAAAGAATTAATTTTTTTCAAAGAAATTTCTTTAGATGATCAACTAACGATCTA
TATTCTTACTAACATGATGTGATAACATAA
Found at i:101504 original size:24 final size:24
Alignment explanation
Indices: 101477--101530 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
101467 GTATTCGAAA
101477 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
101501 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
101525 TTTGAT
1 TTTGAT
101531 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:103988 original size:20 final size:20
Alignment explanation
Indices: 103963--104051 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
103953 CAACGCGGAA
103963 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
103983 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
104003 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
104023 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
104043 ATCACAACG
1 ATCGCAACG
104052 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 58 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:104111 original size:34 final size:33
Alignment explanation
Indices: 104023--104118 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
104013 GGAATTGACT
* ** *
104023 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
104057 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
104090 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
104119 CAAAATTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:104190 original size:33 final size:33
Alignment explanation
Indices: 104133--104217 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
104123 ATTAGTTTCG
104133 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
104167 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
104200 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
104218 CGCGTTGCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:104349 original size:14 final size:14
Alignment explanation
Indices: 104330--104366 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
104320 CATCAATTAA
104330 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
104344 ACAAATCATCTTTT
1 ACAAATCAACATTT
104358 ACAAATCAA
1 ACAAATCAA
104367 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:106313 original size:20 final size:20
Alignment explanation
Indices: 106290--106463 Score: 142
Period size: 20 Copynumber: 9.3 Consensus size: 20
106280 GAAACTTAAA
*
106290 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
106310 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
106330 ATCGCAATGCAAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
106350 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
*
106370 ATCGCAA--CG-AGA-GA--
1 ATCGCAATGCGAAAATGACT
**
106384 ATCGCAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGACT
106403 ATCGCAA--C-AACAA--A--
1 ATCGCAATGCGAA-AATGACT
* *
106417 ATTGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
106437 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
106457 ATCGCAA
1 ATCGCAA
106464 CGAGAGAATC
Statistics
Matches: 127, Mismatches: 13, Indels: 28
0.76 0.08 0.17
Matches are distributed among these distances:
14 13 0.10
16 10 0.08
17 7 0.06
18 5 0.04
19 7 0.06
20 85 0.67
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:106535 original size:20 final size:20
Alignment explanation
Indices: 106472--106633 Score: 154
Period size: 20 Copynumber: 8.8 Consensus size: 20
106462 AACGAGAGAA
*
106472 TCGCAATGCGATTA-TCA-TT
1 TCGCATTGCGA-TAGTCATTT
106491 TCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTT
**
106507 TCG--TTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTT
106525 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
106545 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
106565 TCGCATTGCGAT--TC--TC
1 TCGCATTGCGATAGTCATTT
106581 TCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
** *
106599 TCGTGTTGTGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
106619 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
106634 AAACTATTCT
Statistics
Matches: 121, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
14 14 0.12
16 13 0.11
17 2 0.02
18 11 0.09
19 10 0.08
20 71 0.59
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:106592 original size:74 final size:73
Alignment explanation
Indices: 106472--106633 Score: 236
Period size: 74 Copynumber: 2.2 Consensus size: 73
106462 AACGAGAGAA
* *
106472 TCGCAATGCGATTA-TCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGA
1 TCGCATTGCGA-TAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGA
106536 TAGTCATTT
65 TAGTCATTT
** ** *
106545 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGTGTTGTGA
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGA
106610 TAGTCATTT
65 TAGTCATTT
106619 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
106634 AAACTATTCT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 2 0.03
73 13 0.16
74 65 0.81
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (73 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGAT
AGTCATTT
Found at i:106596 original size:34 final size:34
Alignment explanation
Indices: 106489--106601 Score: 145
Period size: 34 Copynumber: 3.1 Consensus size: 34
106479 GCGATTATCA
*
106489 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAA
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
*
106523 ATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCAT
*
106563 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
106597 TTTCG
1 TTTCG
106602 TGTTGTGATA
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
34 31 0.45
36 6 0.09
38 7 0.10
40 25 0.36
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
Found at i:108548 original size:19 final size:20
Alignment explanation
Indices: 108504--108550 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
108494 CTGAAACTTT
108504 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
108524 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
108543 AAATCGCA
1 AAATCGCA
108551 TTGCGATTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:108590 original size:20 final size:20
Alignment explanation
Indices: 108565--108611 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
108555 GATTCTCTCG
108565 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
108585 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
108605 TTGCGAT
1 TTGCGAT
108612 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:109222 original size:20 final size:20
Alignment explanation
Indices: 109199--109350 Score: 234
Period size: 20 Copynumber: 7.7 Consensus size: 20
109189 CGATAGTCAG
*
109199 ATTCGCATTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
109219 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
109239 A-ACGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
109258 ATTCGCGTTTCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
109278 AATCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
109298 ATTCGCGTTTCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
109318 AATCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
109338 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
109351 ATTAGGAAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 18 0.15
20 101 0.85
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACGT
Found at i:109296 original size:40 final size:40
Alignment explanation
Indices: 109201--109343 Score: 261
Period size: 40 Copynumber: 3.6 Consensus size: 40
109191 ATAGTCAGAT
* *
109201 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTAA
1 TCGCGTTGCGATTTACGTATTCGCGTTTCGATTTACGTAA
109241 -CGCGTTGCGATTTACGTATTCGCGTTTCGATTTACGTAA
1 TCGCGTTGCGATTTACGTATTCGCGTTTCGATTTACGTAA
109280 TCGCGTTGCGATTTACGTATTCGCGTTTCGATTTACGTAA
1 TCGCGTTGCGATTTACGTATTCGCGTTTCGATTTACGTAA
109320 TCGCGTTGCGATTTACGTATTCGC
1 TCGCGTTGCGATTTACGTATTCGC
109344 ATTGCGAATT
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
39 37 0.37
40 63 0.63
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGTATTCGCGTTTCGATTTACGTAA
Found at i:109371 original size:21 final size:21
Alignment explanation
Indices: 109347--109392 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
109337 TATTCGCATT
109347 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
109368 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
109389 GCGA
1 GCGA
109393 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:114573 original size:18 final size:19
Alignment explanation
Indices: 114552--114597 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
114542 AACGATGGCA
114552 ATGTGGTAGC-AAATGGAT
1 ATGTGGTAGCAAAATGGAT
* *
114570 ATGTTGTGGCAAAATGGAT
1 ATGTGGTAGCAAAATGGAT
114589 -TGTGAGTAG
1 ATGTG-GTAG
114598 TGCGATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.30
Consensus pattern (19 bp):
ATGTGGTAGCAAAATGGAT
Found at i:115958 original size:20 final size:20
Alignment explanation
Indices: 115929--115967 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
115919 ATTTCACCAC
*
115929 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
115949 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
115968 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:124440 original size:20 final size:20
Alignment explanation
Indices: 124411--124449 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
124401 ATTTCACCAC
*
124411 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
124431 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
124450 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:125261 original size:100 final size:98
Alignment explanation
Indices: 125117--125401 Score: 287
Period size: 100 Copynumber: 2.9 Consensus size: 98
125107 AAACCCCTAG
** * *
125117 AAATTAGGCTTAATTTCTTTCAAAATTCATTTGAAATCATCAAGAAACCCTTGAAAATCAAACTT
1 AAATTAGGCTTAGCTT-TTTCAAAATTCATTTGAAAACATCAAGAAACCCTTGAAAATCAAGCTT
125182 AGCTTCTTTAAAAAAATCATTTGAAGGCA-TCAAGA
65 AGCTTCTTTAAAAAAATCATTTGAA-G-ATTCAAGA
* * *
125217 AAATTAGGCTTAGCTTATTTCAAAATTCATTTGAAAACATCAAGAAACCCATGAAAAT-TAGGTT
1 AAATTAGGCTTAGCTT-TTTCAAAATTCATTTGAAAACATCAAGAAACCCTTGAAAATCAAGCTT
* * * * **
125281 AGATTCTTT-CAGAAATCA--TCAAGATTCTCGA
65 AGCTTCTTTAAAAAAATCATTTGAAGATTCAAGA
* * * *
125312 AAATT-GAACTTAGCTCTTTTAAAAATT-ATTTGAAAACATCAAGAAATCCTTGAAAATCAGGCT
1 AAATTAG-GCTTAGCT-TTTTCAAAATTCATTTGAAAACATCAAGAAACCCTTGAAAATCAAGCT
* *
125375 TAGCTTCTTTAAGAATATTCATTTGAA
64 TAGCTTCTTTAA-AAAAATCATTTGAA
125402 AATATCATAT
Statistics
Matches: 150, Mismatches: 27, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
94 30 0.20
95 37 0.25
96 4 0.03
97 5 0.03
98 7 0.05
99 14 0.09
100 53 0.35
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (98 bp):
AAATTAGGCTTAGCTTTTTCAAAATTCATTTGAAAACATCAAGAAACCCTTGAAAATCAAGCTTA
GCTTCTTTAAAAAAATCATTTGAAGATTCAAGA
Found at i:130306 original size:22 final size:21
Alignment explanation
Indices: 130281--130323 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
130271 GAGAAAAAGT
130281 AAAAGTTAAAAAATGAAAGAGA
1 AAAAGTT-AAAAATGAAAGAGA
*
130303 AAAAGTTAATAATGAAAGAGA
1 AAAAGTTAAAAATGAAAGAGA
130324 GAAGAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (21 bp):
AAAAGTTAAAAATGAAAGAGA
Found at i:130349 original size:26 final size:24
Alignment explanation
Indices: 130263--130355 Score: 71
Period size: 26 Copynumber: 3.6 Consensus size: 24
130253 GATGATGAAT
*
130263 AAATGAGAGAGAAAAAGTAAAAGTTAAA
1 AAATGAGAGAGAAAAAGT-TAA---AAA
* *
130291 AAATGAAAGAGAAAAAGTTAATAATG
1 AAATGAGAGAGAAAAAGTTAA-AA-A
130317 AAA-GAGAGAAGAAAAAGTTAAAAA
1 AAATGAGAG-AGAAAAAGTTAAAAA
*
130341 AAATTGAGAGGGAAA
1 AAA-TGAGAGAGAAA
130356 TGGGTGATAG
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
24 3 0.05
25 13 0.24
26 20 0.36
27 2 0.04
28 17 0.31
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (24 bp):
AAATGAGAGAGAAAAAGTTAAAAA
Found at i:134514 original size:21 final size:21
Alignment explanation
Indices: 134490--134535 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
134480 AATTGTTTTT
134490 CCTTGGCATCAAATTCTGGTG
1 CCTTGGCATCAAATTCTGGTG
134511 CCTTGGCATCAAATTCTGGTG
1 CCTTGGCATCAAATTCTGGTG
134532 CCTT
1 CCTT
134536 AGTAGAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (21 bp):
CCTTGGCATCAAATTCTGGTG
Found at i:137172 original size:23 final size:23
Alignment explanation
Indices: 137146--137191 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
137136 AATAACCAAG
*
137146 ATAAA-TATAAACCTACCATTAAA
1 ATAAAGTATAAA-CAACCATTAAA
*
137169 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGTATAAACAACCATTAAA
137192 CCAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (23 bp):
ATAAAGTATAAACAACCATTAAA
Found at i:141116 original size:16 final size:17
Alignment explanation
Indices: 141095--141126 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
141085 TACTATTCAT
141095 GTGAATAGT-AAATTTC
1 GTGAATAGTGAAATTTC
141111 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
141127 TGTCGGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (17 bp):
GTGAATAGTGAAATTTC
Found at i:153807 original size:2 final size:2
Alignment explanation
Indices: 153800--153831 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
153790 CTTGCTTCAA
153800 AT AT AT AT AT AT AT -T A- 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
153832 GTTTTGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153820 original size:16 final size:16
Alignment explanation
Indices: 153799--153829 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
153789 CCTTGCTTCA
153799 AATATATATATATATT
1 AATATATATATATATT
153815 AATATATATATATAT
1 AATATATATATATAT
153830 ATGTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATATATATATATT
Found at i:157427 original size:14 final size:14
Alignment explanation
Indices: 157408--157437 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
157398 TCCTTCCAAC
157408 TTATTTATTTATTT
1 TTATTTATTTATTT
157422 TTATTTATTTATTT
1 TTATTTATTTATTT
157436 TT
1 TT
157438 TTGCTTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:162552 original size:180 final size:179
Alignment explanation
Indices: 162197--162732 Score: 722
Period size: 180 Copynumber: 3.0 Consensus size: 179
162187 CCAACCAAAT
** * *
162197 TTTCTGCATAACATAGTTAATAACCATTGCCT-TCTCCAAGTTCATTATCATCTTCTGCATAACC
1 TTTCTGCATAACATAGTTAATAACCATT-ATTATTTCTAAGTTCATTATCATCTTCTGCATAACC
*
162261 AAGAACTTATCAGAAGAAAAAAAAAACATACTTTGAACAGTAGAAGCATGCTTTGATGTTTTCTG
65 AAGAACTTATCAGAAGAAAAAAAAAACATACTTTGAACAGTAGAAGCATCCTTTGATGTTTTCTG
* *
162326 ATAAATTGCACTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
130 ACAACTTGCACTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
* *
162376 TTTCTGCATAACATAGGTAATAACCATTATTATTTCTAAATTCATTATCATCTTCTGCATAACCA
1 TTTCTGCATAACATAGTTAATAACCATTATTATTTCTAAGTTCATTATCATCTTCTGCATAACCA
* *
162441 ATAACTTATCAGAAGAAAAAAAACAACATACTTTGAACAGTAGAAACATCCTTTGATGTTTTCTG
66 AGAACTTATCAGAAGAAAAAAAA-AACATACTTTGAACAGTAGAAGCATCCTTTGATGTTTTCTG
* *
162506 ACAACTTGCATTCTTGGGTAATGAGTGGTCATTGAGCAAGCTCTTCTTAG
130 ACAACTTGCACTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
* * ** **
162556 TTTCTGGACAACATAGTTAAGGACCATTATTATTTCTAAGTTCATTATCATCTTCTGCA-ATATT
1 TTTCTGCATAACATAGTTAATAACCATTATTATTTCTAAGTTCATTATCATCTTCTGCATA-ACC
* * * * *** * *
162620 AAGAAATAACCGGAAG--AAAAATGGCATACTTCGAACAGCAGAAGCATCCTTTGATGTTTTCTG
65 AAGAACTTATCAGAAGAAAAAAAAAACATACTTTGAACAGTAGAAGCATCCTTTGATGTTTTCTG
* * *
162683 ATC-ACTTGCACTCTTGGGTGATGAGTGATCATTGTGCAAACTCTTCTTAG
130 A-CAACTTGCACTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
162733 CTATGATTTT
Statistics
Matches: 316, Mismatches: 37, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
177 79 0.25
178 7 0.02
179 80 0.25
180 150 0.47
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (179 bp):
TTTCTGCATAACATAGTTAATAACCATTATTATTTCTAAGTTCATTATCATCTTCTGCATAACCA
AGAACTTATCAGAAGAAAAAAAAAACATACTTTGAACAGTAGAAGCATCCTTTGATGTTTTCTGA
CAACTTGCACTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
Found at i:167068 original size:19 final size:20
Alignment explanation
Indices: 167046--167093 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
167036 ATCGTCATAC
*
167046 TTCTTATTTTTTAT-TTATT
1 TTCTTATTTTATATCTTATT
**
167065 TTCTTAAATTATATCTTATT
1 TTCTTATTTTATATCTTATT
167085 TT-TTATTTT
1 TTCTTATTTT
167094 CAATAATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (20 bp):
TTCTTATTTTATATCTTATT
Found at i:186616 original size:64 final size:63
Alignment explanation
Indices: 186531--186691 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
186521 TTGTTTAAGG
* * * *
186531 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
186595 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
186659 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
186692 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:187704 original size:31 final size:30
Alignment explanation
Indices: 187666--187761 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
187656 GTCAAAGAAC
187666 TACCTATG-TCTTTCGAGACATATGGACAGT
1 TACCTATGTTCTTT-GAGACATATGGACAGT
** *
187696 ATACCTATGTTCTAAG-GAACATATGGATAGTT
1 -TACCTATGTTCTTTGAG-ACATATGGACAG-T
* * *
187728 TACCTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATGTTCTTTGAGACATATGGACAGT
187758 TACC
1 TACC
187762 GAGGATCTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
30 6 0.11
31 42 0.79
32 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (30 bp):
TACCTATGTTCTTTGAGACATATGGACAGT
Found at i:187771 original size:30 final size:30
Alignment explanation
Indices: 187717--187816 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
187707 CTAAGGAACA
* * *
187717 TATGGATAGTTTACCTAGGTTCTTTGGGACC
1 TATGGATAG-TTACCGAGGATCTTTAGGACC
* **
187748 TATGGACAGTTACCGAGGATCTTTATTACC
1 TATGGATAGTTACCGAGGATCTTTAGGACC
* *
187778 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTAGGACC
*
187808 TCTGGATAG
1 TATGGATAG
187817 GTCTTACGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
30 52 0.87
31 8 0.13
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTAGGACC
Found at i:188744 original size:41 final size:41
Alignment explanation
Indices: 188698--188798 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 41
188688 TTTATGGATT
* * *
188698 GCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA-TAGAT-
1 GCCCGAAGGACTTATCATCATGCTCGAAAGACTTACT-GATA
* *
188738 GACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATA
1 G-CCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACTGATA
188781 GCCCGAAGGACTTATCAT
1 GCCCGAAGGACTTATCAT
188799 ATGTGAGATT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
40 1 0.02
41 15 0.30
42 32 0.64
43 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (41 bp):
GCCCGAAGGACTTATCATCATGCTCGAAAGACTTACTGATA
Found at i:188975 original size:215 final size:215
Alignment explanation
Indices: 188572--189360 Score: 1201
Period size: 215 Copynumber: 3.7 Consensus size: 215
188562 GTGTTACACA
* * *
188572 AAGGACTTAT-AAATTGCGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTTTT
1 AAGGACTTATCAAA-TGTGAAATTCTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTT
* ** * * * * *
188636 AAAACATCATTTTCTCATTTTC-CTTTCATGTGAAAACATCATACCCGAAAGTTTTATGGATTGC
65 AAAACATCACTTTCTCATTTTCAAATTCTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGC
188700 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
130 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
*
188765 GAAAGACTTACTGATAGCCCG
195 GAAAGACTTACTGATGGCCCG
* *
188786 AAGGACTTATCATATGTGAGATTCTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTA
1 AAGGACTTATCAAATGTGAAATTCTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTA
*
188851 AAACATCACTTTCTCATTTTCAAATTCTTGTGAAAACATCCTACCAGAAGGTCTTATGGATGGCC
66 AAACATCACTTTCTCATTTTCAAATTCTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCC
* * * *
188916 CGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGATCCGAAGGATTTACGCATCATTCTCG
131 CGAAGGACTTATCATCTTGCTCTAAAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCG
*
188981 AAAGACTTACTGATGGCCTG
196 AAAGACTTACTGATGGCCCG
* *
189001 AAGGACTTAT-AAATTGTGAAATTCTAAAAATCGCATTCTTCATTTTCAAAAATTTCATCTTCTT
1 AAGGACTTATCAAA-TGTGAAATTCTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTT
189065 AAAACATCACTTTCTCATTTTCAAATTCTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGC
65 AAAACATCACTTTCTCATTTTCAAATTCTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGC
* *
189130 CCGAAGGACTTATCATCTTACTCTAAAGGCTTATAGATGACCCGAAGAATTTAAAGCATCATGCT
130 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTATAGATGACCCGAAGGATTT-AAGCATCATGCT
189195 CGAAAGACTTACTGATGGCCCG
194 CGAAAGACTTACTGATGGCCCG
* * *
189217 AAGGACTTA-CAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAATTTTCATCTTCTT
1 AAGGACTTATCAAAT-GTGAAATTCTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTT
* * *
189281 CAAAACATTATTTTTTCTCATTCTCAAATTCATT-TGAAAACATCCTACCCGAAGGTCTTATGGA
65 -AAAACATCA--CTTTCTCATTTTCAAATTC-TTGTGAAAACATCCTACCCGAAGGTCTTATGGA
189345 TGGCCCGAAGGACTTA
126 TGGCCCGAAGGACTTA
189361 ACTTGATGGC
Statistics
Matches: 525, Mismatches: 40, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
214 79 0.15
215 286 0.54
216 87 0.17
217 8 0.02
219 63 0.12
220 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (215 bp):
AAGGACTTATCAAATGTGAAATTCTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTA
AAACATCACTTTCTCATTTTCAAATTCTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCC
CGAAGGACTTATCATCTTGCTCTAAAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCG
AAAGACTTACTGATGGCCCG
Found at i:192989 original size:11 final size:11
Alignment explanation
Indices: 192964--193000 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
192954 TTCCTTATTA
192964 TTTTTATTTTC
1 TTTTTATTTTC
192975 -TTTTATTTTC
1 TTTTTATTTTC
192985 TTTTT-TTTCTC
1 TTTTTATTT-TC
192996 TTTTT
1 TTTTT
193001 CTTCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 13 0.54
11 11 0.46
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTTC
Found at i:192994 original size:9 final size:9
Alignment explanation
Indices: 192965--193045 Score: 83
Period size: 9 Copynumber: 8.7 Consensus size: 9
192955 TCCTTATTAT
192965 TTTTATTTTC
1 TTTT-TTTTC
192975 TTTTATTTTC
1 TTTT-TTTTC
192985 TTTTTTTTC
1 TTTTTTTTC
192994 TCTTTTTCTTC
1 T-TTTTT-TTC
*
193005 TTTTTCTTC
1 TTTTTTTTC
193014 -TTTTTTTC
1 TTTTTTTTC
*
193022 TTCTTTTTC
1 TTTTTTTTC
* *
193031 TTCTTCTTC
1 TTTTTTTTC
193040 TTTTTT
1 TTTTTT
193046 CCTTTTTTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
8 7 0.11
9 28 0.45
10 23 0.37
11 4 0.06
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:193005 original size:3 final size:3
Alignment explanation
Indices: 192994--193041 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
192984 CTTTTTTTTC
* * * *
192994 TCT TTT TCT TCT TTT TCT TCT T-T TTT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
193041 T
1 T
193042 TTTTCCTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (3 bp):
TCT
Found at i:193005 original size:20 final size:20
Alignment explanation
Indices: 192964--193053 Score: 83
Period size: 20 Copynumber: 4.3 Consensus size: 20
192954 TTCCTTATTA
*
192964 TTTTTATTT-TCTTTTATTTTC
1 TTTTT-TTTCTCTTTT-TCTTC
192985 TTTTTTTTCTCTTTTTCTTC
1 TTTTTTTTCTCTTTTTCTTC
* *
193005 TTTTTCTTCTTTTTTTCTTC
1 TTTTTTTTCTCTTTTTCTTC
* *
193025 TTTTTCTTCTTCTTCTTTTTTCC
1 TTTTTTTTC-TCTT-TTTCTT-C
193048 TTTTTT
1 TTTTTT
193054 CTTTCATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
20 34 0.58
21 14 0.24
22 5 0.08
23 6 0.10
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTTCTCTTTTTCTTC
Found at i:193009 original size:26 final size:27
Alignment explanation
Indices: 192970--193045 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 27
192960 ATTATTTTTA
*
192970 TTTTCTTTTATTTTCTTTTTTTTC-TCT
1 TTTTCTTCT-TTTTCTTTTTTTTCTTCT
192997 TTTTCTTCTTTTTCTTCTTTTTTTCTTCT
1 TTTTCTTCTTTTTC-T-TTTTTTTCTTCT
*
193026 TTTTCTTCTTCTTCTTTTTT
1 TTTTCTTCTTTTTCTTTTTT
193046 CCTTTTTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.11
27 14 0.32
28 9 0.20
29 16 0.36
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTCTTCTTTTTCTTTTTTTTCTTCT
Found at i:193052 original size:9 final size:8
Alignment explanation
Indices: 192987--193057 Score: 72
Period size: 9 Copynumber: 8.4 Consensus size: 8
192977 TTATTTTCTT
192987 TTTTTTCTC
1 TTTTTT-TC
192996 TTTTTCTTC
1 TTTTT-TTC
193005 TTTTTCTTC
1 TTTTT-TTC
193014 TTTTTTTC
1 TTTTTTTC
193022 TTCTTTTTC
1 TT-TTTTTC
*
193031 TTCTTCTTC
1 TT-TTTTTC
193040 -TTTTTTC
1 TTTTTTTC
*
193047 CTTTTTTC
1 TTTTTTTC
193055 TTT
1 TTT
193058 CATTTTTCGA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
7 5 0.09
8 15 0.27
9 35 0.62
10 1 0.02
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:193064 original size:12 final size:11
Alignment explanation
Indices: 192972--193056 Score: 83
Period size: 11 Copynumber: 8.2 Consensus size: 11
192962 TATTTTTATT
*
192972 TTCTTTTATT-
1 TTCTTTTTTTC
192982 TTC-TTTTTT-
1 TTCTTTTTTTC
*
192991 TTCTCTTTTTC
1 TTCTTTTTTTC
193002 TTC--TTTTTC
1 TTCTTTTTTTC
193011 TTCTTTTTTTC
1 TTCTTTTTTTC
193022 TTCTTTTTCTTC
1 TTCTTTTT-TTC
*
193034 TTCTTCTTTT-
1 TTCTTTTTTTC
*
193044 TTCCTTTTTTC
1 TTCTTTTTTTC
193055 TT
1 TT
193057 TCATTTTTCG
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
9 17 0.27
10 16 0.25
11 21 0.33
12 10 0.16
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:196165 original size:2 final size:2
Alignment explanation
Indices: 196158--196244 Score: 58
Period size: 2 Copynumber: 46.0 Consensus size: 2
196148 AATGATTATT
* *
196158 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
196197 TA -A TT TA AA TA AA AA TA TA TA TA TT TA -A TT TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
196237 TA TA TA TA
1 TA TA TA TA
196245 CCCGGCCCGA
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
1 5 0.08
2 59 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:196290 original size:12 final size:12
Alignment explanation
Indices: 196242--196295 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
196232 ATATATATAT
*
196242 ATACCCGGCCCG
1 ATACCCGGCCCA
* *
196254 ATTCCTGGCCCA
1 ATACCCGGCCCA
*
196266 ATA-CCGACCCA
1 ATACCCGGCCCA
196277 ATACCCGGCCCA
1 ATACCCGGCCCA
196289 ATACCCG
1 ATACCCG
196296 TTTAAATAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 9 0.26
12 25 0.74
ACGTcount: A:0.24, C:0.46, G:0.17, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:199838 original size:2 final size:2
Alignment explanation
Indices: 199831--199868 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
199821 GGGTATTACA
199831 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
199869 TAACAACTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:200165 original size:21 final size:21
Alignment explanation
Indices: 200136--200188 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
200126 ATTCTGACTA
200136 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
200157 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTCCCAAAT
*
200178 TCGCAATGCGA
1 TCGCATTGCGA
200189 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:200203 original size:20 final size:20
Alignment explanation
Indices: 200178--200264 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
200168 TTTTCCGAAT
200178 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
200198 TCGCAACGCGAATTTA-GAAAA
1 TCGCAATGCGAA--TACGTAAA
* *
200219 TCGCAATGTGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
200239 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
200259 TCGCAA
1 TCGCAA
200265 CGAGATTCTG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
19 3 0.05
20 37 0.67
21 13 0.24
22 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:200224 original size:41 final size:40
Alignment explanation
Indices: 200178--200264 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 40
200168 TTTTCCGAAT
*
200178 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTAGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCT-GAAAA
* * * *
200219 TCGCAATGTGATTACGTAAATCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
200259 TCGCAA
1 TCGCAA
200265 CGAGATTCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 10 0.24
41 31 0.76
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
Found at i:200274 original size:20 final size:20
Alignment explanation
Indices: 200193--200274 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
200183 ATGCGAATAC
200193 GTAAATCGCAACGCGAATT-T
1 GTAAATCGCAACGCG-ATTCT
* * *
200213 AGAAAATCGCAATGTGATTAC-
1 -GTAAATCGCAACGCGATT-CT
* *
200234 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGCGATTCT
*
200254 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGCGATTCT
200274 G
1 G
200275 ACTATCGCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 36 0.73
21 12 0.24
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (20 bp):
GTAAATCGCAACGCGATTCT
Found at i:201153 original size:24 final size:24
Alignment explanation
Indices: 201126--201179 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
201116 ATATTCAAAA
* *
201126 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
201150 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
201174 TTTGAT
1 TTTGAT
201180 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:203646 original size:20 final size:20
Alignment explanation
Indices: 203623--203696 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
203613 CAACGCGAAT
203623 ATGACTATCGCAACACGGAA
1 ATGACTATCGCAACACGGAA
*
203643 ATGACTATCGCAACGCGGAA
1 ATGACTATCGCAACACGGAA
* *
203663 TTGACTATCACAACACGGAA
1 ATGACTATCGCAACACGGAA
203683 ATGACTATCGCAAC
1 ATGACTATCGCAAC
203697 GAGAGAATCG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
ATGACTATCGCAACACGGAA
Found at i:203668 original size:40 final size:40
Alignment explanation
Indices: 203612--203697 Score: 147
Period size: 40 Copynumber: 2.1 Consensus size: 40
203602 CGCGGAAATT
*
203612 GCAACGCGAATATGACTATCGCAACACGGAAATGACTATC
1 GCAACGCGAATATGACTATCACAACACGGAAATGACTATC
203652 GCAACGCGGAAT-TGACTATCACAACACGGAAATGACTATC
1 GCAACGC-GAATATGACTATCACAACACGGAAATGACTATC
203692 GCAACG
1 GCAACG
203698 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (40 bp):
GCAACGCGAATATGACTATCACAACACGGAAATGACTATC
Found at i:203726 original size:33 final size:34
Alignment explanation
Indices: 203689--203764 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
203679 GGAAATGACT
203689 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
*
203722 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
203756 ATCGCAACG
1 ATCGCAACG
203765 CGAAATTAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 23 0.56
34 18 0.44
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:203760 original size:20 final size:20
Alignment explanation
Indices: 203702--203769 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
203692 GCAACGAGAG
203702 AATCGCAATGC-AAAATGAA
1 AATCGCAATGCGAAAATGAA
*
203721 AATCGCAA--CG--AGTG--
1 AATCGCAATGCGAAAATGAA
203735 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
203755 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
203770 TTAGTTTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
14 8 0.21
16 5 0.13
17 1 0.03
18 3 0.08
19 8 0.21
20 14 0.36
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:203842 original size:33 final size:33
Alignment explanation
Indices: 203779--203874 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
203769 ATTAGTTTCG
**
203779 CGTTGCGATTTTCATTTTCGCATTATGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
203813 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* ** *
203846 CGTTGTGATAGTCATTTCCGTATTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
203875 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:205468 original size:42 final size:42
Alignment explanation
Indices: 205389--205470 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
205379 CCTCTTCAAC
* *
205389 GATGACAGCGGCCTCTTGAACGGTATGAGGGGACTCTTGAGG
1 GATGACAGCGGCCTCTTGAACGATAAGAGGGGACTCTTGAGG
* * *
205431 GATGATAGGGGCCTCTTGAACGATAAG-GGAGGCCTCTTGA
1 GATGACAGCGGCCTCTTGAACGATAAGAGG-GGACTCTTGA
205471 ACAATGACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (42 bp):
GATGACAGCGGCCTCTTGAACGATAAGAGGGGACTCTTGAGG
Found at i:205983 original size:20 final size:20
Alignment explanation
Indices: 205960--206066 Score: 169
Period size: 20 Copynumber: 5.3 Consensus size: 20
205950 GAAACTTAAA
*
205960 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
205980 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
206000 ATCGCAATACGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
206020 ATCGCAATACGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
206040 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
206060 ATCGCAA
1 ATCGCAA
206067 CGAGAGAATC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:206138 original size:20 final size:20
Alignment explanation
Indices: 206113--206217 Score: 123
Period size: 20 Copynumber: 5.5 Consensus size: 20
206103 GATTCTTTTG
206113 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
206133 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
* *
206153 TTTTCGAT--TC--TCTCG--
1 -TTGCGATAGTCATTTTCGCA
*
206168 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
206188 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
206208 TTGCGATAGT
1 TTGCGATAGT
206218 AAACTATTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.08
16 2 0.03
17 3 0.04
18 4 0.06
19 2 0.03
20 48 0.68
21 6 0.08
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:206177 original size:55 final size:55
Alignment explanation
Indices: 206102--206209 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
206092 TTTTGCATTG
* *
206102 CGATTCTTTTGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCACATTTT
1 CGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCACATTTT
* *
206157 CGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATT
1 CGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCACATT
206210 GCGATAGTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (55 bp):
CGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCACATTTT
Found at i:208142 original size:20 final size:20
Alignment explanation
Indices: 208094--208143 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
208084 GAAACTTTAA
*
208094 ATCGCAACACGAAAATGAAT
1 ATCGCAACGCGAAAATGAAT
** *
208114 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGAAT
208134 ATCGCAACGC
1 ATCGCAACGC
208144 AAGAATCGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGAAT
Found at i:208626 original size:22 final size:22
Alignment explanation
Indices: 208565--208626 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
208555 TGACCGTGAA
* *
208565 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
208587 TG-TTATCGTC---G-TGGGGAC
1 TGATT-TCGTCGGAGATGGGGAC
208605 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
208627 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 13 0.41
19 3 0.09
21 3 0.09
22 13 0.41
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:208849 original size:20 final size:20
Alignment explanation
Indices: 208821--208995 Score: 224
Period size: 20 Copynumber: 8.7 Consensus size: 20
208811 CGATAGTCAG
208821 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
**
208841 ATTTACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
208861 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
208881 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
208902 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
208922 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
208942 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
208963 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
208983 ATTCGCATTGCGA
1 ATTCGCATTGCGA
208996 ATTAGGAAAA
Statistics
Matches: 129, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
20 98 0.76
21 31 0.24
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:208923 original size:41 final size:41
Alignment explanation
Indices: 208803--208957 Score: 181
Period size: 40 Copynumber: 3.9 Consensus size: 41
208793 GCTATGTAAA
** *
208803 TCGCATTGCGATAGT-CAGATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTAT
** * **
208843 TTACATTGCGATTTACGTAA-TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTAT
*
208883 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTAT
* **
208924 TCGCATTGCGATTTACGTAA-TCGCATTGCGATTT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTT
208958 TCCAAATTCG
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 58 0.61
41 37 0.39
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTAT
Found at i:208934 original size:61 final size:61
Alignment explanation
Indices: 208848--208995 Score: 278
Period size: 61 Copynumber: 2.4 Consensus size: 61
208838 CGTATTTACA
* *
208848 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCG
208909 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCG
208970 TTGCGATTTACGTATTCGCATTGCGA
1 TTGCGATTTACGTATTCGCATTGCGA
208996 ATTAGGAAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 85 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (61 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCG
Found at i:208937 original size:81 final size:80
Alignment explanation
Indices: 208803--208957 Score: 247
Period size: 81 Copynumber: 1.9 Consensus size: 80
208793 GCTATGTAAA
* *
208803 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTTACATTGCGATTTACGTAATCGCA
1 TCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGTAATCGCA
208868 TTGCGATTTACGTAT
66 TTGCGATTTACGTAT
** * *
208883 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGC
1 TCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGTAATCGC
208948 ATTGCGATTT
65 ATTGCGATTT
208958 TCCAAATTCG
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 13 0.19
81 55 0.81
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (80 bp):
TCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGTAATCGCA
TTGCGATTTACGTAT
Found at i:208967 original size:41 final size:40
Alignment explanation
Indices: 208823--208995 Score: 229
Period size: 41 Copynumber: 4.3 Consensus size: 40
208813 ATAGTCAGAT
**
208823 TCGCATTGCGATTTACGTATTTACATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
* **
208863 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
*
208903 TTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAA
1 -TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
* ** * *
208944 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGA-TTTACGTATTCGCATTGCGATTTACGTAA
208985 TCGCATTGCGA
1 TCGCATTGCGA
208996 ATTAGGAAAA
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
40 45 0.39
41 71 0.61
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
Found at i:209037 original size:21 final size:21
Alignment explanation
Indices: 208985--209037 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
208975 ATTTACGTAT
*
208985 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
209006 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
*
209027 TCGTAATGCGA
1 TCGCAATGCGA
209038 TAGTCAGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:215952 original size:106 final size:110
Alignment explanation
Indices: 215736--216063 Score: 549
Period size: 111 Copynumber: 3.0 Consensus size: 110
215726 ATTACAAAAA
* *
215736 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATAATTA-TAATAATTTAAATTA
*
215801 AATTAAAACGTTAAAATGTTACCGTATCAGCAGAGTGTCGAGATAT
65 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
215847 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATAATT-T-A-AA-TTAAATTAA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATAATTATAATAATTTAAATTAA
215908 ATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 ATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
215953 TTAATTATTAATCTAATAATCATGCATTAAATAAATCAACTAA-ATATTACTAATAATTTAAATT
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATA-ATTA-TAATAATTTAAATT
*
216017 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
64 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
216064 ATGATTTCTA
Statistics
Matches: 206, Mismatches: 5, Indels: 12
0.92 0.02 0.05
Matches are distributed among these distances:
105 1 0.00
106 98 0.48
107 2 0.01
108 2 0.01
109 2 0.01
110 2 0.01
111 99 0.48
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (110 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATAATTATAATAATTTAAATTAA
ATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:216738 original size:2 final size:2
Alignment explanation
Indices: 216731--216776 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
216721 CCATTAGATA
216731 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
216773 AT AT
1 AT AT
216777 GCCATTCTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234024 original size:19 final size:19
Alignment explanation
Indices: 234000--234041 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
233990 GACATGTCAT
*
234000 TTCTATTATATTTGGTTTG
1 TTCTATTACATTTGGTTTG
*
234019 TTCTATTACATTTTGTTTG
1 TTCTATTACATTTGGTTTG
234038 TTCT
1 TTCT
234042 CTCATTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.64
Consensus pattern (19 bp):
TTCTATTACATTTGGTTTG
Found at i:244259 original size:17 final size:18
Alignment explanation
Indices: 244227--244260 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
244217 CATCTTTAAA
*
244227 TAAAAAATTATTAAAATT
1 TAAAAAATTATAAAAATT
244245 TAAAAAA-TATAAAAAT
1 TAAAAAATTATAAAAAT
244261 AGTAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAATTATAAAAATT
Found at i:244519 original size:23 final size:22
Alignment explanation
Indices: 244478--244529 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
244468 ATTTAAAATA
244478 AAAAATATTAATTAAAATTATT
1 AAAAATATTAATTAAAATTATT
*
244500 TAAAAT-TTAATTATATAATTATT
1 AAAAATATTAATTA-A-AATTATT
244523 AAAAATA
1 AAAAATA
244530 AAAATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 6 0.24
23 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATATTAATTAAAATTATT
Found at i:246422 original size:6 final size:6
Alignment explanation
Indices: 246406--246448 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
246396 ACCCAACTTA
246406 ACCCA- ACCCAT ACCCAT ACCCAT ACCCAT ACCCAT ACCCAT AC
1 ACCCAT ACCCAT ACCCAT ACCCAT ACCCAT ACCCAT ACCCAT AC
246449 TTGTGTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.35, C:0.51, G:0.00, T:0.14
Consensus pattern (6 bp):
ACCCAT
Found at i:249835 original size:29 final size:29
Alignment explanation
Indices: 249802--249869 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
249792 AAACAAACTT
249802 GGTTCAGACCAAATTGGTTGATTCGGGGC
1 GGTTCAGACCAAATTGGTTGATTCGGGGC
249831 GGTTCAGACCAAATTGGTTGATTCGGGGC
1 GGTTCAGACCAAATTGGTTGATTCGGGGC
*
249860 GGTCCAGACC
1 GGTTCAGACC
249870 GACTGGGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (29 bp):
GGTTCAGACCAAATTGGTTGATTCGGGGC
Found at i:249878 original size:29 final size:29
Alignment explanation
Indices: 249806--249878 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
249796 AAACTTGGTT
* *
249806 CAGACCAAATTGGTTGATTCGGGGCGGTT
1 CAGACCAAATGGGTTGATTCGGGGCGGTC
*
249835 CAGACCAAATTGGTTGATTCGGGGCGGTC
1 CAGACCAAATGGGTTGATTCGGGGCGGTC
* *
249864 CAGACCGACTGGGTT
1 CAGACCAAATGGGTT
249879 TTGGTCGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (29 bp):
CAGACCAAATGGGTTGATTCGGGGCGGTC
Found at i:256175 original size:2 final size:2
Alignment explanation
Indices: 256168--256205 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
256158 TGTGCATGAT
256168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
256206 GATGGATAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:260760 original size:20 final size:20
Alignment explanation
Indices: 260704--260774 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
260694 GCGATTTTTC
*
260704 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
260724 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
260744 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
*
260764 GACTGTCGCAA
1 GACTATCGCAA
260775 CACTGCATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:261647 original size:24 final size:24
Alignment explanation
Indices: 261590--261649 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
261580 TAGTCGGTAT
261590 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* *
261614 -CCAGACTTTGATCTTGGTCAATAC
1 TCGA-AATTTGATCTTGGTCAATAC
*
261638 TCGAATTTTGAT
1 TCGAAATTTGAT
261650 GATTTTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 26 0.87
25 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Done.