Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008010.1 Hibiscus syriacus cultivar Beakdansim tig00110472_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: 3152856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2898108 original size:26 final size:26
Alignment explanation
Indices: 2898048--2898102 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
2898038 TTTTTAAATT
2898048 TGTCCTTTTATCTAACATTTATTCGG
1 TGTCCTTTTATCTAACATTTATTCGG
2898074 TGTCCTTTTATCTAACATTTATTCGG
1 TGTCCTTTTATCTAACATTTATTCGG
2898100 TGT
1 TGT
2898103 TTTTTTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (26 bp):
TGTCCTTTTATCTAACATTTATTCGG
Found at i:2898544 original size:17 final size:18
Alignment explanation
Indices: 2898507--2898547 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2898497 ATATTATGTA
*
2898507 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2898525 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2898542 TTTACT
1 TTTACT
2898548 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2900739 original size:25 final size:26
Alignment explanation
Indices: 2900706--2900754 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2900696 ATGTTTCGGG
*
2900706 TATATTTG-TTTG-GTTTGGAGAATAA
1 TATAATTGTTTTGAGTTT-GAGAATAA
2900731 TATAATTGTTTTGAGTTTGAGAAT
1 TATAATTGTTTTGAGTTTGAGAAT
2900755 TTATTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 10 0.48
27 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (26 bp):
TATAATTGTTTTGAGTTTGAGAATAA
Found at i:2921549 original size:28 final size:28
Alignment explanation
Indices: 2921514--2921578 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
2921504 TATGTAATTT
2921514 ATATATTTCT-TTATAATTTTTACTAATA
1 ATATATTT-TATTATAATTTTTACTAATA
* *
2921542 ATATATTTTATTATATTTTTTACTTATA
1 ATATATTTTATTATAATTTTTACTAATA
2921570 ATATATTTT
1 ATATATTTT
2921579 CGTTTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATATTTTATTATAATTTTTACTAATA
Found at i:2923870 original size:2 final size:2
Alignment explanation
Indices: 2923863--2923894 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2923853 AATTTATAAG
2923863 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
2923895 ACTTATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2928919 original size:20 final size:20
Alignment explanation
Indices: 2928894--2928950 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
2928884 TCTTATTCCT
2928894 TGGTAATCTTACATTCCCAC
1 TGGTAATCTTACATTCCCAC
* *
2928914 TGGTAATCTTGCATACCCAC
1 TGGTAATCTTACATTCCCAC
2928934 TGGTAATCTTACATTCC
1 TGGTAATCTTACATTCC
2928951 GTGAACCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (20 bp):
TGGTAATCTTACATTCCCAC
Found at i:2930304 original size:54 final size:54
Alignment explanation
Indices: 2930245--2930352 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
2930235 TAATAAAACT
* *** *
2930245 GTAACATATGACATGTTTTTATTGATTGTTGTTTATATTTTGAGGAAAAAAAAA
1 GTAACATACGACATGTTTTTATTGATTACCGTTAATATTTTGAGGAAAAAAAAA
** * *
2930299 GTAACATACGGTATGTTTTTATTGATTACCGTTAATATTTTGAGGTAAATAAAA
1 GTAACATACGACATGTTTTTATTGATTACCGTTAATATTTTGAGGAAAAAAAAA
2930353 TAAAATGATC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (54 bp):
GTAACATACGACATGTTTTTATTGATTACCGTTAATATTTTGAGGAAAAAAAAA
Found at i:2934151 original size:2 final size:2
Alignment explanation
Indices: 2934144--2934180 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2934134 GTCAAGAAGA
2934144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2934181 ATTAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2949875 original size:21 final size:21
Alignment explanation
Indices: 2949849--2949888 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2949839 CCCCCTTTGA
*
2949849 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2949870 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2949889 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2951865 original size:17 final size:17
Alignment explanation
Indices: 2951843--2951876 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2951833 TTCAATATTT
*
2951843 TGGATTGTTTGATTTTA
1 TGGATTGTTGGATTTTA
2951860 TGGATTGTTGGATTTTA
1 TGGATTGTTGGATTTTA
2951877 GATTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTA
Found at i:2955949 original size:29 final size:29
Alignment explanation
Indices: 2955909--2956049 Score: 230
Period size: 29 Copynumber: 4.9 Consensus size: 29
2955899 GTGACAGCAT
*
2955909 AGGTCGCCATGCACGCCCGGTGTCCT-TA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
*
2955937 TAGGTCACCATGCACGCCCGGCGTCCTATA
1 -AGGTCGCCATGCACGCCCGGCGTCCTATA
2955967 AGGTCGCCATGCACGCCCGGCGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
*
2955996 AGGTCGCCATGCACGCCCGACGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
*
2956025 AGGTCGCCATGCACGCCCGACGTCC
1 AGGTCGCCATGCACGCCCGGCGTCC
2956050 ATCATTCTTT
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
29 105 0.98
30 2 0.02
ACGTcount: A:0.18, C:0.38, G:0.26, T:0.18
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGTCCTATA
Found at i:2956322 original size:26 final size:27
Alignment explanation
Indices: 2956286--2956354 Score: 104
Period size: 26 Copynumber: 2.5 Consensus size: 27
2956276 CCATGGCCGG
2956286 CGACATGGTAGGTCGCCATGGAGT-GC
1 CGACATGGTAGGTCGCCATGGAGTCGC
*
2956312 CGACATGGTAGGTCGCCATGGAGTCCCGG
1 CGACATGGTAGGTCGCCATGGAGT--CGC
2956341 CGACATGGTAGGTC
1 CGACATGGTAGGTC
2956355 ATGAGTCCGG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 24 0.62
29 15 0.38
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (27 bp):
CGACATGGTAGGTCGCCATGGAGTCGC
Found at i:2956331 original size:13 final size:13
Alignment explanation
Indices: 2956289--2956332 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2956279 TGGCCGGCGA
2956289 CATGGTAGGTCGC
1 CATGGTAGGTCGC
* *
2956302 CATGG-AGTGCCGA
1 CATGGTAG-GTCGC
2956315 CATGGTAGGTCGC
1 CATGGTAGGTCGC
2956328 CATGG
1 CATGG
2956333 AGTCCCGGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.18, C:0.23, G:0.39, T:0.20
Consensus pattern (13 bp):
CATGGTAGGTCGC
Found at i:2956354 original size:29 final size:29
Alignment explanation
Indices: 2956282--2956416 Score: 150
Period size: 29 Copynumber: 4.6 Consensus size: 29
2956272 GTTGCCATGG
2956282 CCGGCGACATGGTAGGTCGCCATGGAGT-
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
*
2956310 --GCCGACATGGTAGGTCGCCATGGAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
*** * *
2956337 CCGGCGACATGGTAGGTCATGAGTCCGGCGAC
1 CCGGCGACATGGTAGGTCGCCA-T--GGAGTC
*
2956369 ACCGACGACATGGTAGGTCGCCATGGAGTC
1 -CCGGCGACATGGTAGGTCGCCATGGAGTC
2956399 CCGGCGACATGGTAGGTC
1 CCGGCGACATGGTAGGTC
2956417 TGCATCATCA
Statistics
Matches: 86, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
26 25 0.29
29 33 0.38
30 5 0.06
32 5 0.06
33 18 0.21
ACGTcount: A:0.19, C:0.27, G:0.37, T:0.17
Consensus pattern (29 bp):
CCGGCGACATGGTAGGTCGCCATGGAGTC
Found at i:2956357 original size:26 final size:26
Alignment explanation
Indices: 2956282--2956369 Score: 94
Period size: 26 Copynumber: 3.3 Consensus size: 26
2956272 GTTGCCATGG
2956282 CCGGCGACATGGTAGGTCGCCATGGAGT
1 CCGGCGACATGGTAGGT--CCATGGAGT
*
2956310 --GCCGACATGGTAGGTCGCCATGGAGT
1 CCGGCGACATGGTAGGT--CCATGGAGT
2956336 CCCGGCGACATGGTAGGT-CAT-GAGT
1 -CCGGCGACATGGTAGGTCCATGGAGT
2956361 CCGGCGACA
1 CCGGCGACA
2956370 CCGACGACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
24 9 0.16
25 4 0.07
26 28 0.51
29 14 0.25
ACGTcount: A:0.19, C:0.26, G:0.38, T:0.17
Consensus pattern (26 bp):
CCGGCGACATGGTAGGTCCATGGAGT
Found at i:2956951 original size:21 final size:21
Alignment explanation
Indices: 2956926--2956969 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2956916 AATCTAGTTA
2956926 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
2956947 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
2956968 AT
1 AT
2956970 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:2957491 original size:17 final size:17
Alignment explanation
Indices: 2957469--2957528 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
2957459 AGATAATTTT
2957469 TGTTTAAAAAAATATTG
1 TGTTTAAAAAAATATTG
* *
2957486 TGTTTAAAAATATTTAGTG
1 TGTTTAAAAA-A-ATATTG
*
2957505 TTGTTTTAAAAAAATATTT
1 -TG-TTTAAAAAAATATTG
2957524 TGTTT
1 TGTTT
2957529 TATTTATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 13 0.38
18 3 0.09
19 7 0.21
20 3 0.09
21 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (17 bp):
TGTTTAAAAAAATATTG
Found at i:2960546 original size:13 final size:13
Alignment explanation
Indices: 2960528--2960569 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
2960518 AACGGTCAAC
2960528 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2960541 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
* *
2960553 GGTAAACGGTTCG
1 GGTCAACGGGTCG
2960566 GGTC
1 GGTC
2960570 GGGTAAACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2960551 original size:7 final size:7
Alignment explanation
Indices: 2960506--2960536 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2960496 AGAATAGCAC
2960506 CGGTCAA
1 CGGTCAA
*
2960513 CGATCAA
1 CGGTCAA
2960520 CGGTCAA
1 CGGTCAA
2960527 CGGTCAA
1 CGGTCAA
2960534 CGG
1 CGG
2960537 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:2960553 original size:12 final size:12
Alignment explanation
Indices: 2960528--2960569 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
2960518 AACGGTCAAC
2960528 GGTCAACGGGTCG
1 GGTCAAC-GGTCG
2960541 GGTCAACGGTCG
1 GGTCAACGGTCG
*
2960553 GGTAAACGGTTCG
1 GGTCAACGG-TCG
2960566 GGTC
1 GGTC
2960570 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 13 0.50
13 13 0.50
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.19
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:2960600 original size:18 final size:18
Alignment explanation
Indices: 2960548--2960601 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
2960538 TCGGGTCAAC
*
2960548 GGTCGGGTAAACGGTTCG
1 GGTCGGGTAAACGGGTCG
*
2960566 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
2960584 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
2960602 TGACCGGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.46, T:0.20
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:2967730 original size:29 final size:28
Alignment explanation
Indices: 2967690--2967744 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
2967680 TATCATTTTG
* *
2967690 TTTCGAAAAATTACTATAATAGCACCCA
1 TTTCGAAAAATTACCAGAATAGCACCCA
* *
2967718 TTTCGAATTAATTCCCAGAATAGCACC
1 TTTCGAA-AAATTACCAGAATAGCACC
2967745 AAAACCGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 7 0.32
29 15 0.68
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (28 bp):
TTTCGAAAAATTACCAGAATAGCACCCA
Found at i:2967806 original size:12 final size:13
Alignment explanation
Indices: 2967781--2967822 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2967771 ACCGATTAAC
2967781 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2967794 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
2967806 GGTAAACGGGTCG
1 GGTCAACGGGTCG
2967819 GGTC
1 GGTC
2967823 GGGTAAACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2967824 original size:18 final size:18
Alignment explanation
Indices: 2967801--2967836 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2967791 TCGGGTCAAC
2967801 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
2967819 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
2967837 TGACCGGTCA
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:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:2967836 original size:13 final size:13
Alignment explanation
Indices: 2967785--2967821 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
2967775 ATTAACGGTC
*
2967785 AACGGGTCGGGTC
1 AACGGGTCGGGTA
2967798 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
2967810 AACGGGTCGGGT
1 AACGGGTCGGGT
2967822 CGGGTAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:2967852 original size:10 final size:10
Alignment explanation
Indices: 2967839--2967884 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
2967829 ACGGGTCGTG
2967839 ACCGGTCAAA
1 ACCGGTCAAA
2967849 ACCGGTTCAAA
1 ACCGG-TCAAA
*
2967860 ACCGGT-TAA
1 ACCGGTCAAA
2967869 ACCGGTCAAA
1 ACCGGTCAAA
2967879 ACCGGT
1 ACCGGT
2967885 TTCCAGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 8 0.25
10 14 0.44
11 10 0.31
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:2967860 original size:11 final size:11
Alignment explanation
Indices: 2967839--2967885 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
2967829 ACGGGTCGTG
2967839 ACCGG-TCAAA
1 ACCGGTTCAAA
2967849 ACCGGTTCAAA
1 ACCGGTTCAAA
2967860 ACCGGTT--AA
1 ACCGGTTCAAA
2967869 ACCGG-TCAAA
1 ACCGGTTCAAA
2967879 ACCGGTT
1 ACCGGTT
2967886 TCCAGCGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 7 0.21
10 12 0.36
11 13 0.39
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (11 bp):
ACCGGTTCAAA
Found at i:2967879 original size:19 final size:20
Alignment explanation
Indices: 2967847--2967885 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
2967837 TGACCGGTCA
2967847 AAACCGGTTCAAAACCGGTT
1 AAACCGGTTCAAAACCGGTT
2967867 AAACCGG-TCAAAACCGGTT
1 AAACCGGTTCAAAACCGGTT
2967886 TCCAGCGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AAACCGGTTCAAAACCGGTT
Found at i:2969334 original size:49 final size:49
Alignment explanation
Indices: 2969277--2969999 Score: 647
Period size: 60 Copynumber: 13.3 Consensus size: 49
2969267 TTATAAGATT
* *
2969277 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
2969335 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2969386 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2969435 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG--A
2969486 GTAATGATTTAGCAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 -T-A-G---T---AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* * * * *
2969544 TAGTAATGATTTAATAATGATTAGTAATAATGAAATTGTT-ATTAATATTTAATGATTTGA
1 TAGTAATGA-TTAGTAAT-A--A-TGA-AAT--TATTATTAATT--T-TTA-ATGATTTGA
* *
2969604 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATGAT--T--TGA
*
2969662 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
2969713 TAGTAATGATTTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGA
1 TAGTAATGA-TTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
2969772 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* * *
2969823 TAGTAATGATTTAATAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
1 TAGTAATGA-TTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATGAT--T--TGA
* *
2969882 TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
2969933 TAGTAATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
2969982 TAGTAATAATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
2970000 GATTTGATAG
Statistics
Matches: 573, Mismatches: 31, Indels: 128
0.78 0.04 0.17
Matches are distributed among these distances:
49 174 0.30
50 67 0.12
51 19 0.03
52 7 0.01
53 13 0.02
54 12 0.02
55 28 0.05
56 9 0.02
57 13 0.02
58 6 0.01
59 23 0.04
60 184 0.32
61 18 0.03
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:2969390 original size:39 final size:45
Alignment explanation
Indices: 2969368--2969494 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 45
2969358 AAATTATTAT
2969368 TAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTAT
1 TAATTTTTAA-GA-TTGATA-T-ATGATTAGTAATAATGAAATTATTAT
2969417 TAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTAT
1 TAATTTTTAA-GA-TTGATA-T-ATGATTAGTAATAATGAAATTATTAT
2969466 TAATTTTTAATGATTTGATAGTAATGATT
1 TAATTTTTAA-GA-TTGATA-T-ATGATT
2969495 TAGCAATGAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 78 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (45 bp):
TAATTTTTAAGATTGATATATGATTAGTAATAATGAAATTATTAT
Found at i:2969418 original size:109 final size:109
Alignment explanation
Indices: 2969277--2970029 Score: 1124
Period size: 109 Copynumber: 6.9 Consensus size: 109
2969267 TTATAAGATT
* * *
2969277 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
*
2969342 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
2969386 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
* * * * * * *
2969450 AT-AAT-GAAATTAT--TATTAATTTTTAATGATTTGAT-AGTAATGA
66 ATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGA-T-TTGA
* *
2969493 TTTAGCAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAG
*
2969558 TAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGA
64 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* *
2969604 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
2969669 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
2969713 TAGTAATGATTTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATTTAGT
1 TAGTAATGA-TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGT
*
2969778 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
65 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * *
2969823 TAGTAATGATTTAATAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGT
1 TAGTAATGA-TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGT
*
2969888 AATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGA
65 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* *
2969933 TAGTAATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATAATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
* * * *
2969998 ATGATTTGATAGTAATG-ATTTATTATAAATAT
66 ATGATTAG-TAATAATGAAATTATTATTAATAT
2970030 GTCGAATTTG
Statistics
Matches: 584, Mismatches: 46, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
104 3 0.01
105 9 0.02
106 12 0.02
107 5 0.01
108 8 0.01
109 295 0.51
110 223 0.38
111 5 0.01
112 13 0.02
113 8 0.01
114 3 0.01
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (109 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:2969479 original size:35 final size:34
Alignment explanation
Indices: 2969438--2969600 Score: 92
Period size: 35 Copynumber: 5.2 Consensus size: 34
2969428 GATTTGATAG
2969438 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * * *
2969473 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
2969498 CAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * *
2969533 TAATGATT--TGAT-A-GTAATGA-T-TTAA---
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
2969558 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
2969593 TAATGATT
1 TAATGATT
2969601 TGATAGTAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 40
0.61 0.11 0.27
Matches are distributed among these distances:
25 15 0.16
27 6 0.07
28 3 0.03
29 15 0.16
30 4 0.04
31 16 0.18
32 3 0.03
33 6 0.07
35 23 0.25
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (34 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTT
Found at i:2969508 original size:60 final size:60
Alignment explanation
Indices: 2969435--2970003 Score: 682
Period size: 60 Copynumber: 10.2 Consensus size: 60
2969425 AATGATTTGA
2969435 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
*
2969495 TAGCAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* * *
2969555 TAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA-T
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* * * * ** *
2969614 TAGTAAT-AAT-G-AA-ATTG---TTATTAATATTTAATG---ATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
*
2969664 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT-A--A--
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
*
2969719 T-G--AT--TTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
2969774 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA--
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* *
2969832 T--T--T-A--A-TAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* *
2969884 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA-T
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
*
2969943 TAG---T-A--A-TAAT--T-AAATTATTATTAATTTTTAATGATTTGATAGTAATAATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
2969993 TAGTAATGATT
1 TAGTAATGATT
2970004 TGATAGTAAT
Statistics
Matches: 440, Mismatches: 31, Indels: 80
0.80 0.06 0.15
Matches are distributed among these distances:
49 49 0.11
50 98 0.22
51 4 0.01
52 17 0.04
53 6 0.01
54 7 0.02
55 6 0.01
56 6 0.01
57 13 0.03
58 5 0.01
59 13 0.03
60 216 0.49
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (60 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
Found at i:2969648 original size:35 final size:35
Alignment explanation
Indices: 2969607--2969709 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
2969597 GATTTGATAG
2969607 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
* * *
2969642 TAATGATT--TGAT-A-GTAA-TG--ATT--TA-G
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
*
2969667 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
2969702 TAATGATT
1 TAATGATT
2969710 TGATAGTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 20
0.65 0.09 0.26
Matches are distributed among these distances:
25 8 0.16
26 2 0.04
27 3 0.06
28 4 0.08
29 3 0.06
30 3 0.06
31 3 0.06
32 4 0.08
33 3 0.06
34 2 0.04
35 16 0.31
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.46
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTGTTATTAATATT
Found at i:2969782 original size:110 final size:109
Alignment explanation
Indices: 2969499--2970029 Score: 884
Period size: 110 Copynumber: 4.9 Consensus size: 109
2969489 ATGATTTAGC
*
2969499 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATAATGA
1 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGA
*
2969564 TTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGT
66 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
* *
2969608 AATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
1 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGA
2969673 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
66 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
*
2969717 AATGATTTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATTTAGTAATG
1 AATGA-TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATG
*
2969782 ATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGT
65 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
* * *
2969827 AATGATTTAATAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATG
1 AATGA-TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATG
*
2969892 ATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGT
65 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
* *
2969937 AATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATAATTTAGTAATGA
1 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGA
* * * *
2970002 TTTGATAGTAATG-ATTTATTATAAATAT
66 TTAG-TAATAATGAAATTATTATTAATAT
2970030 GTCGAATTTG
Statistics
Matches: 396, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
109 180 0.45
110 216 0.55
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (109 bp):
AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGA
TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
Found at i:2969831 original size:14 final size:14
Alignment explanation
Indices: 2969812--2969845 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2969802 TATTAATTTT
* *
2969812 TAATGATTTGATAG
1 TAATGATTTAATAA
2969826 TAATGATTTAATAA
1 TAATGATTTAATAA
2969840 TAATGA
1 TAATGA
2969846 AATTGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:2969866 original size:36 final size:35
Alignment explanation
Indices: 2969826--2969929 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 35
2969816 GATTTGATAG
2969826 TAATGATTTAATAATAATGAAATTGTTATTAATATT
1 TAATGA-TTAATAATAATGAAATTGTTATTAATATT
* * *
2969862 TAATGATT--TGAT-A-GTAA-TG--ATT--TA-G
1 TAATGATTAATAATAATGAAATTGTTATTAATATT
*
2969887 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAATAATAATGAAATTGTTATTAATATT
2969922 TAATGATT
1 TAATGATT
2969930 TGATAGTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 21
0.66 0.08 0.27
Matches are distributed among these distances:
25 8 0.15
26 2 0.04
27 3 0.06
28 4 0.08
29 3 0.06
30 4 0.08
31 3 0.06
32 4 0.08
33 3 0.06
34 2 0.04
35 10 0.19
36 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (35 bp):
TAATGATTAATAATAATGAAATTGTTATTAATATT
Found at i:2969993 original size:14 final size:14
Alignment explanation
Indices: 2969971--2970018 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
2969961 TATTAATTTT
2969971 TAATGATTTGATAG
1 TAATGATTTGATAG
*
2969985 TAAT-AATT--TAG
1 TAATGATTTGATAG
2969996 TAATGATTTGATAG
1 TAATGATTTGATAG
2970010 TAATGATTT
1 TAATGATTT
2970019 ATTATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 7 0.24
12 3 0.10
13 3 0.10
14 16 0.55
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:2970000 original size:25 final size:25
Alignment explanation
Indices: 2969922--2970019 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 25
2969912 TATTAATATT
*
2969922 TAATGATTTGATAGTAATGA-TTAG
1 TAATGATTTGATAGTAATAATTTAG
* ** * * *
2969946 TAATAATTAAATTATTATTAATTT-T
1 TAATGATTTGA-TAGTAATAATTTAG
2969971 TAATGATTTGATAGTAATAATTTAG
1 TAATGATTTGATAGTAATAATTTAG
*
2969996 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATAATTTA
2970020 TTATAAATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
24 18 0.32
25 37 0.65
26 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATAATTTAG
Found at i:2972166 original size:15 final size:16
Alignment explanation
Indices: 2972146--2972179 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2972136 CAAAAAAATT
2972146 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
2972161 TAATATAATAAACTTA
1 TAATATAATAAACTTA
2972177 TAA
1 TAA
2972180 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:2972266 original size:30 final size:30
Alignment explanation
Indices: 2972232--2972331 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 30
2972222 TTTCTTTAAA
2972232 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
2972262 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
2972292 AAACTAATAAAATATTTTTTAATTATAA-TT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
*
2972322 C-ACTACTAAA
1 CAACTAATAAA
2972332 AAACCTAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.12
30 51 0.80
31 5 0.08
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:2972284 original size:15 final size:16
Alignment explanation
Indices: 2972236--2972290 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
2972226 TTTAAACAAC
2972236 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
2972251 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
2972266 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
2972281 TAATATAACT
1 TAATATAACT
2972291 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:2972490 original size:17 final size:17
Alignment explanation
Indices: 2972468--2972503 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2972458 TAAATGTTTT
2972468 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
2972485 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
2972502 AC
1 AC
2972504 AAACTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (17 bp):
ACCCTAACCCTAAACTA
Found at i:2972733 original size:27 final size:27
Alignment explanation
Indices: 2972695--2972747 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2972685 GGTCGGCTGC
2972695 CATGCACCAATAATTGAAGAATCACGT
1 CATGCACCAATAATTGAAGAATCACGT
2972722 CATGCACCAATAATTGAAGAATCACG
1 CATGCACCAATAATTGAAGAATCACG
2972748 AGCCGTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.21
Consensus pattern (27 bp):
CATGCACCAATAATTGAAGAATCACGT
Found at i:2973037 original size:12 final size:12
Alignment explanation
Indices: 2973020--2973048 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2973010 ACACGACCCT
2973020 CGTCGGAAGCCA
1 CGTCGGAAGCCA
2973032 CGTCGGAAGCCA
1 CGTCGGAAGCCA
2973044 CGTCG
1 CGTCG
2973049 TAGGTCGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.34, G:0.34, T:0.10
Consensus pattern (12 bp):
CGTCGGAAGCCA
Found at i:2975332 original size:24 final size:24
Alignment explanation
Indices: 2975304--2975349 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2975294 ACGTCAACGA
*
2975304 CGACT-TGTCACCGAAGAAAACAAC
1 CGACTCTGTCACC-AAAAAAACAAC
*
2975328 CGACTCTTTCACCAAAAAAACA
1 CGACTCTGTCACCAAAAAAACA
2975350 TTTCTAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.43, C:0.30, G:0.11, T:0.15
Consensus pattern (24 bp):
CGACTCTGTCACCAAAAAAACAAC
Found at i:2978110 original size:35 final size:35
Alignment explanation
Indices: 2978024--2978215 Score: 178
Period size: 35 Copynumber: 5.5 Consensus size: 35
2978014 AAAGTTTGCA
* ** *
2978024 TCGATTCAAGTCGAACTGAAGGAAACATCA-AATT
1 TCGATTCAAGTCGAACGGAAGGAGGCATCACATTT
* *
2978058 TCAATTCAAGTCGAACGGAAGGAGTCATCACATTT
1 TCGATTCAAGTCGAACGGAAGGAGGCATCACATTT
** * *
2978093 TCGATTCAAGTTTAACGGAATGAGGCATCACACTT
1 TCGATTCAAGTCGAACGGAAGGAGGCATCACATTT
* * *
2978128 TCGATTCAAGTAGAACAGG-AGGAAGCAT-ACA-CT
1 TCGATTCAAGTCGAAC-GGAAGGAGGCATCACATTT
*
2978161 TCTGATTCAAGTCGAACGGAAGGAGGCATCGCACTTT
1 TC-GATTCAAGTCGAACGGAAGGAGGCATCACA-TTT
* *
2978198 T-GATTCAACTAGAACGGA
1 TCGATTCAAGTCGAACGGA
2978216 TGGTTTACTA
Statistics
Matches: 129, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
33 5 0.04
34 50 0.39
35 70 0.54
36 2 0.02
37 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (35 bp):
TCGATTCAAGTCGAACGGAAGGAGGCATCACATTT
Found at i:2979484 original size:31 final size:33
Alignment explanation
Indices: 2979428--2979514 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 33
2979418 AGTATTTTTT
* *
2979428 TAAATAGTTATTATACTTTATATTAAT-ATATTTATG
1 TAAATA-TTATT-TA-TTTAT-TAAATAATATTTATA
*
2979464 TAAATATTATTTTTTTATTAAAATAATATTTATA
1 TAAATATTATTTATTTATT-AAATAATATTTATA
*
2979498 TAATTATTATTTATTTA
1 TAAATATTATTTATTTA
2979515 GAATTAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
32 1 0.02
33 8 0.18
34 24 0.55
35 5 0.11
36 6 0.14
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (33 bp):
TAAATATTATTTATTTATTAAATAATATTTATA
Found at i:2979677 original size:17 final size:17
Alignment explanation
Indices: 2979655--2979708 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2979645 AATGTTAATA
2979655 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
2979672 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
2979689 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
2979706 TTT
1 TTT
2979709 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:2981266 original size:21 final size:21
Alignment explanation
Indices: 2981223--2981267 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2981213 GCAGGGGTAC
* *
2981223 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
2981244 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
2981265 ATG
1 ATG
2981268 TCATCTCTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.13, T:0.24
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:2981300 original size:21 final size:21
Alignment explanation
Indices: 2981276--2981367 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
2981266 TGTCATCTCT
*
2981276 GCAGGGTTACATTCCGAGCCT
1 GCAGGGTTACATTCCGAGCCC
2981297 GCAGGGTTACATTCCGAGCCC
1 GCAGGGTTACATTCCGAGCCC
* *
2981318 GTAGGGTTACATTCCTAGCCC
1 GCAGGGTTACATTCCGAGCCC
* * *
2981339 GCCA-GGTTACATGCCTAACCC
1 G-CAGGGTTACATTCCGAGCCC
2981360 GCAGGGTT
1 GCAGGGTT
2981368 TTATACCATA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
20 2 0.03
21 60 0.95
22 1 0.02
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (21 bp):
GCAGGGTTACATTCCGAGCCC
Found at i:2981907 original size:34 final size:34
Alignment explanation
Indices: 2981869--2981966 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
2981859 AAATGTTTTT
*
2981869 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
2981903 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
2981937 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
2981967 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:2982606 original size:127 final size:127
Alignment explanation
Indices: 2982367--2982609 Score: 398
Period size: 127 Copynumber: 1.9 Consensus size: 127
2982357 TTACCTGATT
*
2982367 TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTC
1 TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2982432 TGACAAAATAATGGAAGGCGCCACCCGGGAACACGCCTTAATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCCACCCGGGAACACGCCTTAATATGAATAGTGAAATAATAGG
* * *
2982494 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGTAATTATAACATATTCT-
1 TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
2982558 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGT
66 TGACAAAATAATGGAAGGCGC-CACCCGGGAACACGCCTTAATATGAATAGT
2982610 ACTCCGATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
126 21 0.20
127 86 0.80
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (127 bp):
TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCCACCCGGGAACACGCCTTAATATGAATAGTGAAATAATAGG
Found at i:2982693 original size:8 final size:8
Alignment explanation
Indices: 2982680--2982717 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2982670 TCACAAGCTT
2982680 TCAAATTC
1 TCAAATTC
2982688 TCAAATTC
1 TCAAATTC
* *
2982696 CCAAACTC
1 TCAAATTC
2982704 T-AAATTC
1 TCAAATTC
2982711 TCAAATT
1 TCAAATT
2982718 ATCTGAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:2994716 original size:32 final size:31
Alignment explanation
Indices: 2994679--2994755 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 31
2994669 TATCAGATCA
**
2994679 TTATAAAATAATATTATTTTTTAATATAATTT
1 TTATAAAATAATATTAACTTTTAATA-AATTT
*
2994711 TTATAAAATAATTATTAACTTTTATTAAATTT
1 TTATAAAATAA-TATTAACTTTTAATAAATTT
*
2994743 ATATAAAATAATA
1 TTATAAAATAATA
2994756 AATTTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 2 0.05
32 26 0.65
33 12 0.30
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TTATAAAATAATATTAACTTTTAATAAATTT
Found at i:2994777 original size:19 final size:18
Alignment explanation
Indices: 2994736--2994769 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2994726 TAACTTTTAT
2994736 TAAATTTATATAAAATAA
1 TAAATTTATATAAAATAA
2994754 TAAATTTAT-TAAAATA
1 TAAATTTATATAAAATA
2994770 TTATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATTTATATAAAATAA
Found at i:2994788 original size:29 final size:28
Alignment explanation
Indices: 2994710--2994795 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
2994700 TAATATAATT
*
2994710 TTTATAAAATAATTATTAACTTTTATT-AAA
1 TTTAT-AAATAATAATTAA--TTTATTAAAA
*
2994740 TTTATATAA-AATAATAAATTTATTAAAA
1 TTTATA-AATAATAATTAATTTATTAAAA
*
2994768 TATTATAAATAATCATTAATTTATTAAA
1 T-TTATAAATAATAATTAATTTATTAAA
2994796 GGTCATAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
27 6 0.12
28 6 0.12
29 29 0.60
30 7 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTATAAATAATAATTAATTTATTAAAA
Found at i:3009562 original size:17 final size:19
Alignment explanation
Indices: 3009523--3009564 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
3009513 CATTAAACCT
3009523 TTTTATATTAAATATATAA
1 TTTTATATTAAATATATAA
*
3009542 TTTTATA-TATATATA-AA
1 TTTTATATTAAATATATAA
3009559 TTTTAT
1 TTTTAT
3009565 GAATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 7 0.32
19 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTATATTAAATATATAA
Found at i:3012979 original size:16 final size:16
Alignment explanation
Indices: 3012953--3012986 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3012943 TCCATTTCCA
3012953 TTTCAATTCTAA-AAT
1 TTTCAATTCTAACAAT
3012968 TTTCATATTCTAACAAT
1 TTTCA-ATTCTAACAAT
3012985 TT
1 TT
3012987 GCATTAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTCAATTCTAACAAT
Found at i:3016365 original size:21 final size:21
Alignment explanation
Indices: 3016339--3016379 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3016329 TAAATAAAGC
3016339 AATTTCGGACAACAAAAAATT
1 AATTTCGGACAACAAAAAATT
3016360 AATTTCGGACAACAAAAAAT
1 AATTTCGGACAACAAAAAAT
3016380 CCACACTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.22
Consensus pattern (21 bp):
AATTTCGGACAACAAAAAATT
Found at i:3022641 original size:16 final size:16
Alignment explanation
Indices: 3022604--3022660 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
3022594 GTTTACTTCA
*
3022604 GAATGATT-AAACGCT
1 GAATGATTCAAATGCT
*
3022619 AAATGATTCAAATGCT
1 GAATGATTCAAATGCT
*
3022635 GAATGATTCAAATACT
1 GAATGATTCAAATGCT
3022651 GAATGATTCA
1 GAATGATTCA
3022661 GAGGTTCTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 7 0.19
16 30 0.81
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:3023199 original size:6 final size:6
Alignment explanation
Indices: 3023188--3023213 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3023178 AACAGAAAAA
3023188 ACTATC ACTATC ACTATC ACTATC AC
1 ACTATC ACTATC ACTATC ACTATC AC
3023214 ATACAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (6 bp):
ACTATC
Found at i:3027779 original size:74 final size:76
Alignment explanation
Indices: 3027691--3027871 Score: 231
Period size: 77 Copynumber: 2.4 Consensus size: 76
3027681 ATTCGGGTTT
* *
3027691 GAGTATGAGGGTTGGATACATGTATATGT-TGACATAGGTTGCAAGTGCTAT-ATTTAAACTATT
1 GAGTATGAGTGTTGGATACAAGTATATGTCTGACATAGGTTGCAAGTGCTATAATTTAAACTATT
*
3027754 TACTTGGAATC
66 TACTAGGAATC
** * *
3027765 GAGTATGAGTGTTGGATACAAGTATATGTCTGGTATAGGTTGCAAGTGCTATAAATTTACACTCT
1 GAGTATGAGTGTTGGATACAAGTATATGTCTGACATAGGTTGCAAGTGCTAT-AATTTAAACTAT
*
3027830 TTACTAGGACTC
65 TTACTAGGAATC
* * * *
3027842 AAGTAGGACTGTTGGATACAGGTATATGTC
1 GAGTATGAGTGTTGGATACAAGTATATGTC
3027872 CGGCACGTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 27 0.29
75 20 0.22
77 45 0.49
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (76 bp):
GAGTATGAGTGTTGGATACAAGTATATGTCTGACATAGGTTGCAAGTGCTATAATTTAAACTATT
TACTAGGAATC
Found at i:3029834 original size:247 final size:245
Alignment explanation
Indices: 3029391--3029885 Score: 915
Period size: 247 Copynumber: 2.0 Consensus size: 245
3029381 CTCTCTCAAA
3029391 GGAAATAGCATTTGCAGGACAAACATTTTCACAAGGCCTAGGGCAGTCAGAAGGACAATTCTCTG
1 GGAAATAGCATTTGCAGGACAAACATTTTCACAAGGCCTAGGGCAGTCAGAAGGACAATTCTCTG
3029456 GATCAAATTCTAAGATAAAGAGTACTAAGATCAGGACCAATGAAAGCACTAAGAAATCTACGCAC
66 GATCAAATTCTAAGATAAAGAGTACTAAGATCAGGACCAATGAAAGCACTAAGAAATCTACGCAC
3029521 TCAACAAGTGCTTAAAGTCGGTTGATCCAGAAGTAACTTCTTCATTCAAGGACTCAAATCTTAAA
131 TCAACAAGTGCTTAAAGTCGGTTGATCCAGAAGTAACTTCTTCATTCAAGGACTCAAATCTTAAA
3029586 GTTTTATGTCTTTAAGGGTTCAAATCATGCAGGGTCTTGGCTATTTTTGGTTG
196 G-TTTATGTC-TTAAGGGTTCAAATCATGCAGGGTC-TGGCTATTTTTGGTTG
3029639 GGAAAT-GCATTTGCAGGACAAACATTTTTCACAAGGCCTAGGGCAGTCAGAAGGACAATTCTCT
1 GGAAATAGCATTTGCAGGACAAACA-TTTTCACAAGGCCTAGGGCAGTCAGAAGGACAATTCTCT
3029703 GGATC-AATTCTAAGATAAAGAGTACTAAGATCAGGACCAATGAAAGCACTAAGAAATCATACGC
65 GGATCAAATTCTAAGATAAAGAGTACTAAGATCAGGACCAATGAAAGCACTAAGAAATC-TACGC
3029767 A-TCAACAAGTGCTTAAAGTCGGTTGATCCAGAAGTAACTTCTTCATTCAAGGACTCAAATCTTA
129 ACTCAACAAGTGCTTAAAGTCGGTTGATCCAGAAGTAACTTCTTCATTCAAGGACTCAAATCTTA
*
3029831 AAGTTTATGTCTTACGGGTTCAAATCATGCAGGGTCTGGCTATTTTTGGTTG
194 AAGTTTATGTCTTAAGGGTTCAAATCATGCAGGGTCTGGCTATTTTTGGTTG
3029883 GGA
1 GGA
3029886 TCATTCAAGT
Statistics
Matches: 244, Mismatches: 1, Indels: 8
0.96 0.00 0.03
Matches are distributed among these distances:
244 19 0.08
245 24 0.10
246 8 0.03
247 137 0.56
248 56 0.23
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (245 bp):
GGAAATAGCATTTGCAGGACAAACATTTTCACAAGGCCTAGGGCAGTCAGAAGGACAATTCTCTG
GATCAAATTCTAAGATAAAGAGTACTAAGATCAGGACCAATGAAAGCACTAAGAAATCTACGCAC
TCAACAAGTGCTTAAAGTCGGTTGATCCAGAAGTAACTTCTTCATTCAAGGACTCAAATCTTAAA
GTTTATGTCTTAAGGGTTCAAATCATGCAGGGTCTGGCTATTTTTGGTTG
Found at i:3036454 original size:37 final size:38
Alignment explanation
Indices: 3036369--3036458 Score: 157
Period size: 38 Copynumber: 2.4 Consensus size: 38
3036359 TTTTCACCCT
3036369 AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
3036407 AAACCCGACCCGA-CTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACCT-GACCCGAATATCACACTTAAAA
3036444 AAACCCGACCCGACC
1 AAACCCGACCCGACC
3036459 CGAACAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
37 18 0.36
38 32 0.64
ACGTcount: A:0.38, C:0.40, G:0.11, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
Found at i:3041191 original size:57 final size:57
Alignment explanation
Indices: 3041103--3041215 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
3041093 ACCCATCTGC
* *
3041103 ATCAATGCCGAGTTATTTTGGTTACTTTGCACGCCATGAGAAGCAACTTGCATATTG
1 ATCAATGCCGAGTTATTTTGGCTACTTTGCACACCATGAGAAGCAACTTGCATATTG
* *
3041160 ATCAATGCCGAGTTATTTTGGCTACTTTGCACACCATGTGAAGCGACTTGCATATT
1 ATCAATGCCGAGTTATTTTGGCTACTTTGCACACCATGAGAAGCAACTTGCATATT
3041216 TATGTTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (57 bp):
ATCAATGCCGAGTTATTTTGGCTACTTTGCACACCATGAGAAGCAACTTGCATATTG
Found at i:3045652 original size:54 final size:54
Alignment explanation
Indices: 3045572--3045994 Score: 605
Period size: 54 Copynumber: 7.8 Consensus size: 54
3045562 ATATATCAGT
* * *
3045572 ACTATGTGTGCAACCCACGGGATTCATCATGAGTTGATGAATAACCGTACAGGT
1 ACTATGTGTGCAACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATGC
* *
3045626 ACTATGTGTGCAACCCACGGGATTCATCATGAGTTGATGAATAACAGTACATGC
1 ACTATGTGTGCAACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATGC
*
3045680 ACTATGTGTGTAACCCAC-GAGATTCATCATGAGTTGATGAATAACCGTACATGC
1 ACTATGTGTGCAACCCACAG-GATTCATCATGAGTTGATGAATAACCGTACATGC
* * ** *
3045734 ATTATGTGTGCAAATCCATGGGATTCATCATGAGTTGATGAATAACCGTACATGT
1 ACTATGTGTGC-AACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATGC
* * * * *
3045789 ACTATGCGTGCAAATCCACATGATTCATCATTAGTTGATGAATAACTGTACATGC
1 ACTATGTGTGC-AACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATGC
*
3045844 ACTATGTGTGCAAACCCACATGATTCATCATGAGTTGATGAATAACCGTACATGC
1 ACTATGTGTGC-AACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATGC
* *
3045899 ACTATGTGTGCAACCCACAAGATTCATCATGAGTTGATGAATAACCGTACAGGC
1 ACTATGTGTGCAACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATGC
* * *
3045953 ACTATGTGTGCAACCCACAGAATTTATCATGAGATGATGAAT
1 ACTATGTGTGCAACCCACAGGATTCATCATGAGTTGATGAAT
3045995 TACCATATAG
Statistics
Matches: 338, Mismatches: 28, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
53 1 0.00
54 189 0.56
55 147 0.43
56 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (54 bp):
ACTATGTGTGCAACCCACAGGATTCATCATGAGTTGATGAATAACCGTACATGC
Found at i:3049000 original size:59 final size:59
Alignment explanation
Indices: 3048908--3049027 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 59
3048898 ATGAATCGAC
* *
3048908 GAACACTCATATTAACCGTAGAATTTTATTAATTTTTGTTATTTAAAGGTTTTGTTTGA
1 GAACACTCATATTAACCGTAGAATTTTATTAATTTTTGTTATTCAAAGGTATTGTTTGA
* ** * * *
3048967 GAACACTCTTATTAATTGTGGAGTTTTTTTAATTTTTGTTATTCAAAGGTATTGTTTGA
1 GAACACTCATATTAACCGTAGAATTTTATTAATTTTTGTTATTCAAAGGTATTGTTTGA
3049026 GA
1 GA
3049028 TTTAGTTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.48
Consensus pattern (59 bp):
GAACACTCATATTAACCGTAGAATTTTATTAATTTTTGTTATTCAAAGGTATTGTTTGA
Found at i:3050510 original size:43 final size:42
Alignment explanation
Indices: 3050453--3050564 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 42
3050443 CGCGGCGTTT
*
3050453 GTTAA-CAAAAAACGCCGCAATAGGTGACGATATATAGCGGC
1 GTTAATCAACAAACGCCGCAATAGGTGACGATATATAGCGGC
** *
3050494 GCTTAATCAACAAACGCCGCAATAGGTGTTGATATTTAGCGGC
1 G-TTAATCAACAAACGCCGCAATAGGTGACGATATATAGCGGC
** * *
3050537 GTTTGTTAGACAAACGCCGCAGTAGGTG
1 GTTAATCA-ACAAACGCCGCAATAGGTG
3050565 TTGATGTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 1 0.02
42 8 0.13
43 51 0.85
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (42 bp):
GTTAATCAACAAACGCCGCAATAGGTGACGATATATAGCGGC
Found at i:3050618 original size:85 final size:85
Alignment explanation
Indices: 3050503--3050755 Score: 350
Period size: 85 Copynumber: 3.0 Consensus size: 85
3050493 CGCTTAATCA
* * * * *
3050503 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTAGACAAACGCCGCAGTAGGTGTTG
1 ACAAACGACGCAGTAGGTGTTGATGTTTAGCGACGTTT-TTACACAAACGCCGCAGTAGGTGTTG
*
3050568 ATGTTTAGCGGCATTTTT-CC
65 ATGTTTAGCGGCGTTTTTCCC
* * *
3050588 ACAAACGACGCAGTAGGTGTTGACGTTTAGCGTCGTTTTTCCCACAAACGCCGCAGTAGGTGTTG
1 ACAAACGACGCAGTAGGTGTTGATGTTTAGCGACGTTTTT-ACACAAACGCCGCAGTAGGTGTTG
3050653 ATGTTTAGCGGCGTTTTTCCC
65 ATGTTTAGCGGCGTTTTTCCC
* *
3050674 ACAAACGTCGCAGTAGGTGTTAATGTTTAGCGACG-TTTTACCACAAACGCCGCAGTAGGTGTTG
1 ACAAACGACGCAGTAGGTGTTGATGTTTAGCGACGTTTTTA-CACAAACGCCGCAGTAGGTGTTG
3050738 A-GATTTAGCGGCGTTTTT
65 ATG-TTTAGCGGCGTTTTT
3050756 ATCAAAAATG
Statistics
Matches: 151, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
84 3 0.02
85 115 0.76
86 33 0.22
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (85 bp):
ACAAACGACGCAGTAGGTGTTGATGTTTAGCGACGTTTTTACACAAACGCCGCAGTAGGTGTTGA
TGTTTAGCGGCGTTTTTCCC
Found at i:3050690 original size:128 final size:128
Alignment explanation
Indices: 3050503--3050786 Score: 383
Period size: 128 Copynumber: 2.2 Consensus size: 128
3050493 CGCTTAATCA
* *
3050503 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTAGACAAACGCCGCAGTAGGTGTTG
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTACACAAACGCCGCAGTAGGTGTTA
* * *
3050568 ATGTTTAGCGGCATTTTTCCACAAACGACGCAGTAGGTGTTGACG-TTTAGCGTCGTTTTTCCC
66 ATGTTTAGCGACATTTTACCACAAACGACGCAGTAGGTGTTGA-GATTTAGCGGCGTTTTTCCC
* * * *
3050631 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTT-TTCCCACAAACGTCGCAGTAGGTGTT
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTT-ACACAAACGCCGCAGTAGGTGTT
* * **
3050695 AATGTTTAGCGACGTTTTACCACAAACGCCGCAGTAGGTGTTGAGATTTAGCGGCGTTTTTATC
65 AATGTTTAGCGACATTTTACCACAAACGACGCAGTAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* * * *
3050759 AAAAATGCCGCAATAGATGTTGAGATTT
1 ACAAACGCCGCAATAGGTGTTGATATTT
3050787 CTTGGTGCTT
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
127 3 0.02
128 132 0.98
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (128 bp):
ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTACACAAACGCCGCAGTAGGTGTTA
ATGTTTAGCGACATTTTACCACAAACGACGCAGTAGGTGTTGAGATTTAGCGGCGTTTTTCCC
Found at i:3050786 original size:43 final size:43
Alignment explanation
Indices: 3050503--3050781 Score: 359
Period size: 43 Copynumber: 6.5 Consensus size: 43
3050493 CGCTTAATCA
* * *
3050503 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTA-G
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTT-TTACC
*
3050546 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCATTTTT-CC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTACC
* * * *
3050588 ACAAACGACGCAGTAGGTGTTGACGTTTAGCGTCGTTTTTCCC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTACC
*
3050631 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTACC
* * *
3050674 ACAAACGTCGCAGTAGGTGTTAATGTTTAGCGACG-TTTTACC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTACC
*
3050716 ACAAACGCCGCAGTAGGTGTTGA-GATTTAGCGGCGTTTTTATC
1 ACAAACGCCGCAGTAGGTGTTGATG-TTTAGCGGCGTTTTTACC
* * * *
3050759 AAAAATGCCGCAATAGATGTTGA
1 ACAAACGCCGCAGTAGGTGTTGA
3050782 GATTTCTTGG
Statistics
Matches: 209, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.00
42 74 0.35
43 134 0.64
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (43 bp):
ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTACC
Found at i:3060172 original size:12 final size:12
Alignment explanation
Indices: 3060155--3060179 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3060145 GGAAACTTTG
3060155 CGTCATGCATGT
1 CGTCATGCATGT
3060167 CGTCATGCATGT
1 CGTCATGCATGT
3060179 C
1 C
3060180 TTACAATGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (12 bp):
CGTCATGCATGT
Found at i:3061954 original size:23 final size:23
Alignment explanation
Indices: 3061898--3061954 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
3061888 AGTAATAGTG
3061898 TTATATTATTTTTAAAAATATTAA
1 TTATATTA-TTTTAAAAATATTAA
* *
3061922 TTAGTA-TATTTTAAATATATTTA
1 TTA-TATTATTTTAAAAATATTAA
3061945 TTATATTATT
1 TTATATTATT
3061955 ATATTAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 20 0.69
24 5 0.17
25 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATATTATTTTAAAAATATTAA
Found at i:3061983 original size:32 final size:34
Alignment explanation
Indices: 3061932--3061996 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
3061922 TTAGTATATT
** *
3061932 TTAAATATATTTATTATATTATT-A-TATTAATG
1 TTAAATATATAAATAATATTATTCATTATTAATG
3061964 TTAAATATATAAATAATATTATTCATTATTAAT
1 TTAAATATATAAATAATATTATTCATTATTAAT
3061997 AATTTAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 20 0.71
33 1 0.04
34 7 0.25
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (34 bp):
TTAAATATATAAATAATATTATTCATTATTAATG
Found at i:3062144 original size:22 final size:23
Alignment explanation
Indices: 3062116--3062162 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3062106 TTGATTATTT
*
3062116 TATTATAATCTTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
3062138 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
3062161 TA
1 TA
3062163 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:3062149 original size:30 final size:34
Alignment explanation
Indices: 3062089--3062168 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
3062079 ATAACATCTT
* *
3062089 ATATTATTATAATATAATTGATTATTTTATTAT-A
1 ATATTAATA-AATATAATTGATTATATTATTATAA
*
3062123 ATCTTAA-AAATATAA-T-ATTATATTATTATAA
1 ATATTAATAAATATAATTGATTATATTATTATAA
3062154 ATATTAATAAATATA
1 ATATTAATAAATATA
3062169 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 12 0.30
31 8 0.20
32 14 0.35
33 1 0.03
34 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
ATATTAATAAATATAATTGATTATATTATTATAA
Found at i:3062449 original size:42 final size:42
Alignment explanation
Indices: 3062401--3062481 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
3062391 ACCAAACACT
*
3062401 GGAAAATATTTTCCGAAAAATGAATTATGTGAAACAAACGCA
1 GGAAAATATTTTCCGAAAAATGAATTACGTGAAACAAACGCA
*
3062443 GGAAAATATTTTTCGAAAAATGAATTACGTGAAACAAAC
1 GGAAAATATTTTCCGAAAAATGAATTACGTGAAACAAAC
3062482 ACATGATTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (42 bp):
GGAAAATATTTTCCGAAAAATGAATTACGTGAAACAAACGCA
Found at i:3064936 original size:108 final size:108
Alignment explanation
Indices: 3064745--3064955 Score: 368
Period size: 108 Copynumber: 2.0 Consensus size: 108
3064735 GTGAGTAATT
*
3064745 AAATAATTAAATTAGACATTCATTGATTTCAAATTATCATATTCTTTATTAATATTCACTTTCTA
1 AAATAATTAAATCAGACATTCATTGATTTCAAATTATCATATTCTTTATTAATATTCACTTTCTA
*
3064810 AAGTCCTTATTACTATTTCATTATTTAATTTATCATTATCTAA
66 AAGTCCTTATTACAATTTCATTATTTAATTTATCATTATCTAA
* * * *
3064853 AAATAATTCAATCAGACATTCATTGATTTCAAATTATCATATTCTTTATTGATATTTACTTTTTA
1 AAATAATTAAATCAGACATTCATTGATTTCAAATTATCATATTCTTTATTAATATTCACTTTCTA
3064918 AAGTCCTTATTACAATTTCATTATTTAATTTATCATTA
66 AAGTCCTTATTACAATTTCATTATTTAATTTATCATTA
3064956 ACTTAAATCA
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.48
Consensus pattern (108 bp):
AAATAATTAAATCAGACATTCATTGATTTCAAATTATCATATTCTTTATTAATATTCACTTTCTA
AAGTCCTTATTACAATTTCATTATTTAATTTATCATTATCTAA
Found at i:3067426 original size:29 final size:29
Alignment explanation
Indices: 3067391--3067472 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3067381 AAACTAAATT
*
3067391 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3067420 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3067449 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3067473 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3072196 original size:29 final size:29
Alignment explanation
Indices: 3072161--3072242 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3072151 AAACTAAATT
*
3072161 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3072190 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3072219 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3072243 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3073591 original size:19 final size:19
Alignment explanation
Indices: 3073557--3073593 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3073547 ATGACCAACA
*
3073557 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
3073576 AAATCGCAACGTGATCTC
1 AAATCGCAACGCGATCTC
3073594 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:3073671 original size:20 final size:20
Alignment explanation
Indices: 3073640--3073711 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
3073630 TAATACATAA
* *
3073640 TCGCAACACGATTCTAACTA
1 TCGCAACGCGATTCTAACTG
* *
3073660 TCGTAACGCGATTCTGACTG
1 TCGCAACGCGATTCTAACTG
*
3073680 TCGCAACGCGATTCTTACTG
1 TCGCAACGCGATTCTAACTG
3073700 TCGCAACGCGAT
1 TCGCAACGCGAT
3073712 AATACAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTAACTG
Found at i:3073905 original size:22 final size:22
Alignment explanation
Indices: 3073877--3073927 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3073867 CATCGGCGAC
3073877 ATCCGTCCACATCTCCGACGAA
1 ATCCGTCCACATCTCCGACGAA
*
3073899 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCACATCTCCGACGAA
3073921 ATCCGTC
1 ATCCGTC
3073928 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.43, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCACATCTCCGACGAA
Found at i:3074337 original size:19 final size:20
Alignment explanation
Indices: 3074313--3074367 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3074303 GATAGTCAAA
3074313 TTCGCGTTGCGATTTTCA-T
1 TTCGCGTTGCGATTTTCATT
**
3074332 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCATT
* *
3074352 TTTGTGTTGCGATTTT
1 TTCGCGTTGCGATTTT
3074368 AAGTTTCAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:3075636 original size:19 final size:21
Alignment explanation
Indices: 3075612--3075654 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3075602 ATATGTTGTG
3075612 ATGAT-ATAAACCATATG-AT
1 ATGATAATAAACCATATGAAT
*
3075631 ATGATAATAAACTATATGAAT
1 ATGATAATAAACCATATGAAT
3075652 ATG
1 ATG
3075655 TGATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGATAATAAACCATATGAAT
Found at i:3076225 original size:31 final size:31
Alignment explanation
Indices: 3076187--3076342 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
3076177 AGGGTCGAGG
3076187 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3076218 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3076249 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3076280 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3076311 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
3076342 G
1 G
3076343 GTCCTTCGGG
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 120 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3079695 original size:21 final size:21
Alignment explanation
Indices: 3079669--3079713 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3079659 GATTTCTGGG
* *
3079669 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3079690 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3079711 CAA
1 CAA
3079714 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3080175 original size:19 final size:21
Alignment explanation
Indices: 3080151--3080193 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3080141 ATATGTTGTG
3080151 ATGAT-ATAAACCATATG-AT
1 ATGATAATAAACCATATGAAT
*
3080170 ATGATAATAAACTATATGAAT
1 ATGATAATAAACCATATGAAT
3080191 ATG
1 ATG
3080194 TGATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGATAATAAACCATATGAAT
Found at i:3080764 original size:31 final size:31
Alignment explanation
Indices: 3080726--3080868 Score: 234
Period size: 31 Copynumber: 4.6 Consensus size: 31
3080716 AGGGTCGAGG
3080726 GTTTACCTATGTTCTTCGGGACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
3080757 GTTTACCTATGTTCTTCGGGACATATGGACTA
1 GTTTACCTATGTTCTTCGGGACATATGGAC-A
*
3080789 -TTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACA
*
3080819 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* *
3080850 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
3080869 AATCTATGGA
Statistics
Matches: 107, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
31 106 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACA
Found at i:3083336 original size:20 final size:20
Alignment explanation
Indices: 3083311--3083379 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
3083301 CGAAACTTAA
3083311 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
3083331 ATCGCAAAGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
3083351 ATCGCAACGCGAAGTTGACT
1 ATCGCAACGCGAAAATGACT
3083371 ATCGCAACG
1 ATCGCAACG
3083380 GGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3083493 original size:33 final size:33
Alignment explanation
Indices: 3083445--3083525 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
3083435 ACTATCGCAA
* * *
3083445 TGCGA-ATTTAGTTTCGTGTTGCGATTTTCTCGT
1 TGCGATATTTA-TTTCGTATTGCGATTATCCCGT
*
3083478 TGCGATTTTTATTTCGTATTGCGATTATCCCGT
1 TGCGATATTTATTTCGTATTGCGATTATCCCGT
*
3083511 TGCGATATTCATTTC
1 TGCGATATTTATTTC
3083526 CGCGTTGCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 37 0.90
34 4 0.10
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (33 bp):
TGCGATATTTATTTCGTATTGCGATTATCCCGT
Found at i:3083533 original size:20 final size:20
Alignment explanation
Indices: 3083508--3083556 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3083498 GCGATTATCC
* *
3083508 CGTTGCGATATTCATTTCCG
1 CGTTGCAATAGTCATTTCCG
*
3083528 CGTTGCAATAGTCATTTTCG
1 CGTTGCAATAGTCATTTCCG
3083548 CGTTGCAAT
1 CGTTGCAAT
3083557 TTAAGTTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.39
Consensus pattern (20 bp):
CGTTGCAATAGTCATTTCCG
Found at i:3084157 original size:21 final size:21
Alignment explanation
Indices: 3084062--3084169 Score: 83
Period size: 21 Copynumber: 5.1 Consensus size: 21
3084052 GCCCGACTCA
*
3084062 CCTGTCATCGTTCAAGAGGCT
1 CCTGTCATCGTTCAAGAGGCC
* *
3084083 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* * ** *
3084104 CCTATCTTCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
3084125 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
3084146 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
3084167 CCT
1 CCT
3084170 CCTACCATTT
Statistics
Matches: 64, Mismatches: 21, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 1 0.02
21 62 0.97
22 1 0.02
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:3084170 original size:42 final size:42
Alignment explanation
Indices: 3084062--3084171 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
3084052 GCCCGACTCA
* * *
3084062 CCTGTCATCGTTCAAGAGG-CTTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTC-CCTCCCACCGTTCAAGAGGCC
* * **
3084104 CCTATCTTCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCC
*
3084146 CCTGTCATCGTTGAAGAGGTCCCTCC
1 CCTGTCATCGTTCAAGAGGTCCCTCC
3084172 TACCATTTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.02
42 49 0.92
43 3 0.06
ACGTcount: A:0.18, C:0.37, G:0.19, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCC
Found at i:3085469 original size:42 final size:42
Alignment explanation
Indices: 3085404--3085711 Score: 535
Period size: 42 Copynumber: 7.3 Consensus size: 42
3085394 CGTTGCGATT
3085404 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
** *
3085446 TTCAACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
3085488 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACTCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
3085530 TTCGACTATCGCAATGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
3085572 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
3085614 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
3085656 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
3085698 TTGGACTATCGCAA
1 TTGGACTATCGCAA
3085712 TGCGAATATG
Statistics
Matches: 248, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 248 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:3092726 original size:24 final size:20
Alignment explanation
Indices: 3092674--3092731 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
3092664 TTTCCCTTGA
3092674 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
* *
3092694 AGTGTATCGATGCATCCCTTTAC
1 AGTGCATCGATGCAT---TCTAC
3092717 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3092732 CTAATTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
23 5 0.16
24 12 0.39
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:3103604 original size:2 final size:2
Alignment explanation
Indices: 3103597--3103623 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3103587 ACAAATTTTA
3103597 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3103624 GTAAAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3104550 original size:16 final size:16
Alignment explanation
Indices: 3104529--3104562 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3104519 ATGAATTATT
3104529 ATTTATTGAAAATTAA
1 ATTTATTGAAAATTAA
* *
3104545 ATTTATTTAAATTTAA
1 ATTTATTGAAAATTAA
3104561 AT
1 AT
3104563 ATAAAGTATT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTATTGAAAATTAA
Found at i:3117909 original size:25 final size:25
Alignment explanation
Indices: 3117881--3117943 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
3117871 CAAAATTTGA
3117881 TTTCAATTTGATTAGGTTACTAGAC
1 TTTCAATTTGATTAGGTTACTAGAC
3117906 TTTCAATTTGATTAGGTTACTAGAC
1 TTTCAATTTGATTAGGTTACTAGAC
3117931 TTTCAATTTGATT
1 TTTCAATTTGATT
3117944 TCAATCAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (25 bp):
TTTCAATTTGATTAGGTTACTAGAC
Found at i:3118654 original size:20 final size:20
Alignment explanation
Indices: 3118629--3118666 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3118619 AATCTTTATA
* *
3118629 TTAACTTTTTCAATTAAATT
1 TTAACTTTATCAAATAAATT
3118649 TTAACTTTATCAAATAAA
1 TTAACTTTATCAAATAAA
3118667 ATTAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAACTTTATCAAATAAATT
Found at i:3122203 original size:15 final size:15
Alignment explanation
Indices: 3122183--3122228 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
3122173 AAAACATCGG
*
3122183 TTTAATTTTTAACTT
1 TTTAATTTTTAAATT
3122198 TTTAATTTTTCAAATT
1 TTTAATTTTT-AAATT
*
3122214 TTATAAATTTTAAAT
1 TT-TAATTTTTAAAT
3122229 CCAATTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 10 0.37
16 10 0.37
17 7 0.26
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATTTTTAAATT
Found at i:3125837 original size:18 final size:20
Alignment explanation
Indices: 3125814--3125853 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3125804 AAATATAATT
*
3125814 TTTAAATA-AT-TATGTATA
1 TTTAAATATATATATATATA
3125832 TTTAAATATATATATATATA
1 TTTAAATATATATATATATA
3125852 TT
1 TT
3125854 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTAAATATATATATATATA
Found at i:3125885 original size:17 final size:17
Alignment explanation
Indices: 3125850--3125885 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3125840 TATATATATA
*
3125850 TATTATTTTTTATTAAT
1 TATTATTTTTAATTAAT
*
3125867 TATTATTTTTAATTTAT
1 TATTATTTTTAATTAAT
3125884 TA
1 TA
3125886 ATCACTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTTTTAATTAAT
Found at i:3126452 original size:21 final size:21
Alignment explanation
Indices: 3126406--3126461 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3126396 GATTCTGACT
3126406 ATCGCATTGCGA-TTTCCCAA
1 ATCGCATTGCGATTTTCCCAA
* *
3126426 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTTCCCAA
*
3126448 ATCGCAATGCGATT
1 ATCGCATTGCGATT
3126462 ACGTAAATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 21 0.70
22 8 0.27
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCCAA
Found at i:3126716 original size:20 final size:20
Alignment explanation
Indices: 3126691--3126779 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
3126681 CAACGCGGAA
*
3126691 ATCGCAACGC-AAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
3126711 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
3126731 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
3126751 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
3126771 ATCGCAACG
1 ATCGCAACG
3126780 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:3126839 original size:34 final size:33
Alignment explanation
Indices: 3126751--3126844 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
3126741 GGAATTGACT
* **
3126751 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
3126785 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3126818 ATCGCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
3126845 ACCGAAATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3126898 original size:33 final size:33
Alignment explanation
Indices: 3126856--3126936 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 33
3126846 CCGAAATTAG
**
3126856 TTTCGCATTGCGATTCACTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
*
3126889 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
*
3126922 TTTCCGCGTTGCGAT
1 TTT-CGCATTGCGAT
3126937 AGTCTGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.77
34 10 0.23
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.41
Consensus pattern (33 bp):
TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
Found at i:3127115 original size:33 final size:33
Alignment explanation
Indices: 3127073--3127153 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 33
3127063 GCGAAATTAG
**
3127073 TTTCGCATTGCGATTCACTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
*
3127106 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
*
3127139 TTTCCGCGTTGCGAT
1 TTT-CGCATTGCGAT
3127154 AGTCTGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.77
34 10 0.23
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.41
Consensus pattern (33 bp):
TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
Found at i:3127205 original size:217 final size:217
Alignment explanation
Indices: 3126827--3127261 Score: 827
Period size: 217 Copynumber: 2.0 Consensus size: 217
3126817 AATCGCAATG
3126827 CGAAAATGAAAATCGCAAACCGAAATTAGTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTT
1 CGAAAATGAAAATCGCAAACCGAAATTAGTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTT
3126892 CGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAACA
66 CGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAACA
* *
3126957 TAATGCAAATTGAAATCAACAAATTAACTATTACATTTCAATCAATTAAACAAGCACAAATATTA
131 TAATGCAAATTAAAATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATTA
3127022 TGTACACATCAATTAAACAAAT
196 TGTACACATCAATTAAACAAAT
3127044 CGAAAATGAAAATCGC-AACGCGAAATTAGTTTCGCATTGCGATTCACTCGTTGCGATTTTCATT
1 CGAAAATGAAAATCGCAAAC-CGAAATTAGTTTCGCATTGCGATTCACTCGTTGCGATTTTCATT
3127108 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAAC
65 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAAC
*
3127173 ATAATGCAGATTAAAATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATT
130 ATAATGCAAATTAAAATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATT
3127238 ATGTACACATCAATTAAACAAAT
195 ATGTACACATCAATTAAACAAAT
3127261 C
1 C
3127262 AACATTTACA
Statistics
Matches: 214, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
216 3 0.01
217 211 0.99
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (217 bp):
CGAAAATGAAAATCGCAAACCGAAATTAGTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCATTCAACA
TAATGCAAATTAAAATCAACAAATCAACTATTACATTTCAATCAATTAAACAAGCACAAATATTA
TGTACACATCAATTAAACAAAT
Found at i:3127274 original size:14 final size:14
Alignment explanation
Indices: 3127255--3127291 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3127245 CATCAATTAA
3127255 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3127269 ACAAATCATCTTTT
1 ACAAATCAACATTT
3127283 ACAAATCAA
1 ACAAATCAA
3127292 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:3128742 original size:42 final size:42
Alignment explanation
Indices: 3128663--3128755 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
3128653 CCTCTTCAAC
* * *
3128663 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
3128705 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
3128747 GATGACAGG
1 GATGACAGG
3128756 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:3129258 original size:20 final size:20
Alignment explanation
Indices: 3129235--3129303 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
3129225 GAAACTTAAA
3129235 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
3129255 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
3129275 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3129295 ATCGCAACG
1 ATCGCAACG
3129304 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3129377 original size:20 final size:20
Alignment explanation
Indices: 3129348--3129551 Score: 285
Period size: 20 Copynumber: 10.5 Consensus size: 20
3129338 GATTCTTTCG
**
3129348 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
3129368 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
3129388 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
3129408 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
3129428 TTGCGATTGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
3129448 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* * *
3129468 TT--G-TA---ATTCTCTCG
1 TTGCGATAGTCATTTTCGCA
*
3129482 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
3129502 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
3129522 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
3129542 TTGCGATAGT
1 TTGCGATAGT
3129552 AAACCATTAT
Statistics
Matches: 164, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
14 8 0.05
16 1 0.01
17 4 0.02
18 1 0.01
20 150 0.91
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:3129435 original size:94 final size:91
Alignment explanation
Indices: 3129327--3129551 Score: 258
Period size: 94 Copynumber: 2.4 Consensus size: 91
3129317 GCGATTTTCG
* *
3129327 TTTCGCATTGCGAT-TC-TTT-CGTTGCGATAGTCAAATTCGCATTGTGATAGTCATTTTCGCAT
1 TTTCGCATTGCGATGTCATTTACATTGCGATAGTCAAATTCGCATTGT-A-AGTC--TCTCG--T
3129389 TGCGATAGTCATTTTCGCATTGCGATAGTCAT
60 TGCGATAGTCATTTTCGCATTGCGATAGTCAT
** *
3129421 TTTCGCATTGCGATTGTCATTTTCACATTGCGATAGTCATTTTCGCATTGTAATTCTCTCGTTGC
1 TTTCGCATTGCGA-TGTCA-TTT-ACATTGCGATAGTCAAATTCGCATTGTAAGTCTCTCGTTGC
*
3129486 GATAGTCATTTTCGCGTTGCGATAGTCAT
63 GATAGTCATTTTCGCATTGCGATAGTCAT
*
3129515 TTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1 TTTCGCATTGCGAT-GTCA-TTT-ACATTGCGATAGT
3129552 AAACCATTAT
Statistics
Matches: 117, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
93 1 0.01
94 79 0.68
95 1 0.01
96 6 0.05
98 6 0.05
99 1 0.01
100 23 0.20
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (91 bp):
TTTCGCATTGCGATGTCATTTACATTGCGATAGTCAAATTCGCATTGTAAGTCTCTCGTTGCGAT
AGTCATTTTCGCATTGCGATAGTCAT
Found at i:3131461 original size:20 final size:20
Alignment explanation
Indices: 3131426--3131485 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
3131416 TCGTAACACG
**
3131426 ACGAAAATGAAAATCGCAAC
1 ACGAAAATGACTATCGCAAC
*
3131446 ACGAAAATGACTATCGCAAT
1 ACGAAAATGACTATCGCAAC
* **
3131466 GCGAATTTGACTATCGCAAC
1 ACGAAAATGACTATCGCAAC
3131486 GCAAGAATCG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (20 bp):
ACGAAAATGACTATCGCAAC
Found at i:3131963 original size:22 final size:22
Alignment explanation
Indices: 3131902--3131963 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
3131892 TGACCGTGAA
*
3131902 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
3131924 TG-TTATCGTC---G-TGGGGAC
1 TGATT-TCGTCGGAGATGGGGAC
3131942 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
3131964 GGATGTCGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 13 0.39
19 3 0.09
21 3 0.09
22 14 0.42
ACGTcount: A:0.18, C:0.15, G:0.39, T:0.29
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:3139250 original size:122 final size:123
Alignment explanation
Indices: 3139032--3139273 Score: 459
Period size: 122 Copynumber: 2.0 Consensus size: 123
3139022 AACTTCTGAT
3139032 TTTATCACTCAACTTCTGATTTCATCTTTTTTGGTCACCCAATAAATTTTTTTTAAAGTAGAATT
1 TTTATCACTCAACTTCTGATTTCATCTTTTTTGGTCACCCAATAAATTTTTTTTAAAGTAGAATT
3139097 ATCATATATTCATTGACCGAATAAAACATAAACAACAATCATACATGAAAAACACGAA
66 ATCATATATTCATTGACCGAATAAAACATAAACAACAATCATACATGAAAAACACGAA
*
3139155 TTTATCACTCAACTTCTGATTTCATCTTTTTTGGTCACCCAATCAA-TTTTTTTAAAGTAGAATT
1 TTTATCACTCAACTTCTGATTTCATCTTTTTTGGTCACCCAATAAATTTTTTTTAAAGTAGAATT
*
3139219 ATCATATATTCATTGACCGAATAAAACATAAACAACAATCATACATGACAAACAC
66 ATCATATATTCATTGACCGAATAAAACATAAACAACAATCATACATGAAAAACAC
3139274 ATTCGTGTCT
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
122 72 0.62
123 45 0.38
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (123 bp):
TTTATCACTCAACTTCTGATTTCATCTTTTTTGGTCACCCAATAAATTTTTTTTAAAGTAGAATT
ATCATATATTCATTGACCGAATAAAACATAAACAACAATCATACATGAAAAACACGAA
Found at i:3149102 original size:33 final size:33
Alignment explanation
Indices: 3149060--3149124 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
3149050 AAGTAGTATT
3149060 CAGGAGGATGAGTCCTTTCCAGAGAGACCTGGG
1 CAGGAGGATGAGTCCTTTCCAGAGAGACCTGGG
3149093 CAGGAGGATGAGTCCTTTCCAGAGAGACCTGG
1 CAGGAGGATGAGTCCTTTCCAGAGAGACCTGG
3149125 ACAACCAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.35, T:0.18
Consensus pattern (33 bp):
CAGGAGGATGAGTCCTTTCCAGAGAGACCTGGG
Found at i:3151471 original size:29 final size:30
Alignment explanation
Indices: 3151438--3151503 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
3151428 ATGATTGTTT
*
3151438 TAATTATT-AATTT-TTAAAAAATTGTAAAA
1 TAATTATTAAATTTATT-AAAAATTATAAAA
**
3151467 TAATTATTAAATTTATTAAATGTTATAAAA
1 TAATTATTAAATTTATTAAAAATTATAAAA
3151497 TAATTAT
1 TAATTAT
3151504 ATATAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 8 0.25
30 22 0.69
31 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (30 bp):
TAATTATTAAATTTATTAAAAATTATAAAA
Done.