Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 35
Found at i:3078627 original size:20 final size:20
Alignment explanation
Indices: 3078604--3078770 Score: 189
Period size: 20 Copynumber: 8.3 Consensus size: 20
3078594 AATCTGTAAA
3078604 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
3078624 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
3078644 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
3078664 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
3078684 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
3078704 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
3078724 TC-CAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * * *
3078743 TCGTAACGCGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
3078764 TCGCAAC
1 TCGCAAC
3078771 TGAATTTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
19 20 0.16
20 89 0.72
21 15 0.12
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:3078627 original size:40 final size:40
Alignment explanation
Indices: 3078583--3078770 Score: 267
Period size: 40 Copynumber: 4.7 Consensus size: 40
3078573 AGTTTCCAAT
* *
3078583 TTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-AT-AGTCAAATTCGCAACACAAAAGTCAAA
3078623 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
*
3078663 TTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
3078703 TTCGCAACGCGATAGTCAAATTC-CAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
* *
3078742 TTCGTAACGCGGA-ATTTCAAATTCGCAAC
1 TTCGCAACGC-GATA-GTCAAATTCGCAAC
3078771 TGAATTTCAA
Statistics
Matches: 137, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.22
40 101 0.74
41 4 0.03
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (40 bp):
TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:3078763 original size:21 final size:19
Alignment explanation
Indices: 3078737--3078828 Score: 78
Period size: 19 Copynumber: 4.7 Consensus size: 19
3078727 AACACAAAAG
*
3078737 TCAAATTCGTAACGCGGAATT
1 TCAAATTCGCAA--CGGAATT
*
3078758 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACGGAATT
* *
3078777 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAAC-GGAATT
* *
3078797 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-GGAATT
*
3078817 T-AATTTCGCAAC
1 TCAAATTCGCAAC
3078829 AGGTTTTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 28 0.47
20 21 0.35
21 11 0.18
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACGGAATT
Found at i:3078803 original size:20 final size:19
Alignment explanation
Indices: 3078753--3078828 Score: 91
Period size: 19 Copynumber: 3.9 Consensus size: 19
3078743 TCGTAACGCG
3078753 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
3078772 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
* * *
3078791 AGATTTTCGAATTCGCAACAC
1 -GAATTTCAAATTCGCAAC-T
*
3078812 GAATTT-AATTTCGCAAC
1 GAATTTCAAATTCGCAAC
3078829 AGGTTTTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 28 0.57
20 21 0.43
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:3078816 original size:40 final size:39
Alignment explanation
Indices: 3078583--3078828 Score: 241
Period size: 40 Copynumber: 6.2 Consensus size: 39
3078573 AGTTTCCAAT
*
3078583 TTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-AT-AGTCAAATTCGCAACAC-GAAGTCAAA
*
3078623 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACAC-GAAGTCAAA
3078663 TTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACAC-GAAGTCAAA
*
3078703 TTCGCAACGCGATAGTCAAATTC-CAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACAC-GAAGTCAAA
* * * *
3078742 TTCGTAACGCGGA-ATTTCAAATTCGCAAC-TGAATTTCAAA
1 TTCGCAACGC-GATA-GTCAAATTCGCAACACGAA-GTCAAA
** ** * * * *
3078782 TTCGCAACTAGATTTTCGAATTCGCAACACGAATTTAAT
1 TTCGCAACGCGATAGTCAAATTCGCAACACGAAGTCAAA
3078821 TTCGCAAC
1 TTCGCAAC
3078829 AGGTTTTAAT
Statistics
Matches: 181, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
38 2 0.01
39 59 0.33
40 116 0.64
41 4 0.02
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (39 bp):
TTCGCAACGCGATAGTCAAATTCGCAACACGAAGTCAAA
Found at i:3078829 original size:19 final size:19
Alignment explanation
Indices: 3078802--3078848 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3078792 GATTTTCGAA
3078802 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
**
3078821 TTCGCAACA-GGTTTTAAT
1 TTCGCAACACGAATTTAAT
*
3078839 TTTGCAACAC
1 TTCGCAACAC
3078849 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:3079004 original size:14 final size:16
Alignment explanation
Indices: 3078985--3079021 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3078975 TCCTCATCTC
3078985 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
3078999 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
3079015 TAATTTT
1 TAATTTT
3079022 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:3079635 original size:12 final size:12
Alignment explanation
Indices: 3079614--3079647 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3079604 ACCACATTTT
*
3079614 CAATACCAAACA
1 CAATATCAAACA
3079626 CAATATCAAACA
1 CAATATCAAACA
*
3079638 CAATCTCAAA
1 CAATATCAAA
3079648 ACCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:3079824 original size:24 final size:24
Alignment explanation
Indices: 3079767--3079826 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3079757 TAGTCAGTAT
3079767 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* *
3079791 -CCAGACTTTGATCTTGGTCAATAC
1 TCGA-AATTTGATCTTGGTCAATAC
*
3079815 TCGAATTTTGAT
1 TCGAAATTTGAT
3079827 GATATGATGG
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
Found at i:3080009 original size:3 final size:3
Alignment explanation
Indices: 3080001--3080037 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3079991 ATATAACCCT
*
3080001 GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
3080038 TCCCCGAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3082140 original size:20 final size:21
Alignment explanation
Indices: 3082117--3082159 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3082107 GATCAACGCG
3082117 AAAGTCAAATTCACAACG-AA
1 AAAGTCAAATTCACAACGTAA
*
3082137 AAAGTCAAATTCGCAACGTAA
1 AAAGTCAAATTCACAACGTAA
3082158 AA
1 AA
3082160 TAAGCGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (21 bp):
AAAGTCAAATTCACAACGTAA
Found at i:3082219 original size:14 final size:14
Alignment explanation
Indices: 3082181--3082219 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3082171 ATAGTCAAAT
3082181 TCGCAACGCG-AAA
1 TCGCAACGCGAAAA
3082194 TCGCAAAC-CGAAAA
1 TCGC-AACGCGAAAA
3082208 TCGCAACGCGAA
1 TCGCAACGCGAA
3082220 TTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.41, C:0.31, G:0.21, T:0.08
Consensus pattern (14 bp):
TCGCAACGCGAAAA
Found at i:3082238 original size:20 final size:20
Alignment explanation
Indices: 3082215--3082296 Score: 68
Period size: 20 Copynumber: 4.4 Consensus size: 20
3082205 AAATCGCAAC
3082215 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
* * *
3082235 GCGAATTTGACTATCAC--A
1 GCGAATTTGACTTTCGCGTT
* *
3082253 ACG--CTT-A-TTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
3082269 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
*
3082289 GCAAATTT
1 GCGAATTT
3082297 TACTATTGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
14 4 0.09
15 1 0.02
16 4 0.09
18 4 0.09
19 1 0.02
20 31 0.69
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:3082302 original size:54 final size:54
Alignment explanation
Indices: 3082215--3082350 Score: 200
Period size: 54 Copynumber: 2.5 Consensus size: 54
3082205 AAATCGCAAC
*
3082215 GCGAATTTGACTTTCGCGTTGCGAATTTGACTATCACAACGCTTATTTCGCGTT
1 GCGAATTTGACTTTCGCGTTGCGAATTTGACTATCACAACGCTTATTTCGCATT
* * ** *
3082269 GCGAATTTGACTTTCGCGTTGCAAATTTTACTATTGCAACGCTTCTTTCGCATT
1 GCGAATTTGACTTTCGCGTTGCGAATTTGACTATCACAACGCTTATTTCGCATT
* *
3082323 GCAAATTTTACTTTCGCGTTGCGAATTT
1 GCGAATTTGACTTTCGCGTTGCGAATTT
3082351 ACCTTACCTT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (54 bp):
GCGAATTTGACTTTCGCGTTGCGAATTTGACTATCACAACGCTTATTTCGCATT
Found at i:3082338 original size:20 final size:20
Alignment explanation
Indices: 3082313--3082379 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 20
3082303 TGCAACGCTT
*
3082313 CTTTCGCATTGCAAATTTTA
1 CTTTCGCGTTGCAAATTTTA
*
3082333 CTTTCGCGTTGCGAATTTACCTTA
1 CTTTCGCGTTGC-AAATT---TTA
3082357 CCTTTCGCGTTGCAAATTTTA
1 -CTTTCGCGTTGCAAATTTTA
3082378 CT
1 CT
3082380 ATTGCAACGC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 13 0.33
21 7 0.18
24 7 0.18
25 12 0.31
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.43
Consensus pattern (20 bp):
CTTTCGCGTTGCAAATTTTA
Found at i:3082514 original size:25 final size:25
Alignment explanation
Indices: 3082476--3082525 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3082466 AAATCAATTA
*
3082476 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
3082501 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
3082526 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:3082937 original size:18 final size:18
Alignment explanation
Indices: 3082916--3082952 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3082906 GTAATTGGAG
3082916 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3082934 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3082952 T
1 T
3082953 ATAAATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3082959 original size:24 final size:24
Alignment explanation
Indices: 3082908--3082960 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3082898 TTTCATATGT
* * *
3082908 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
3082932 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
3082956 AATTT
1 AATTT
3082961 CAGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:3084298 original size:20 final size:21
Alignment explanation
Indices: 3084275--3084326 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
3084265 TCGCAACACG
*
3084275 AATTTGA-CTTTCGCGTTGCA
1 AATTTGACCTTTCACGTTGCA
*
3084295 AATTT-ACCTTTCACGTTGCG
1 AATTTGACCTTTCACGTTGCA
3084315 AATTTGTACCTT
1 AATTTG-ACCTT
3084327 CAACAGGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 21 0.78
22 5 0.19
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (21 bp):
AATTTGACCTTTCACGTTGCA
Found at i:3086181 original size:65 final size:65
Alignment explanation
Indices: 3086044--3086203 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
3086034 TGCACTAAGA
* *
3086044 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
3086108 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
3086171 AG
65 -G
* *
3086173 GTGTATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
3086204 CAATTTAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 29 0.34
65 54 0.63
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:3088376 original size:13 final size:13
Alignment explanation
Indices: 3088348--3088386 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3088338 TGGGCAATGT
*
3088348 TTTGAAAA-ACTA
1 TTTGAAAATAATA
3088360 TTTGAAAATAATA
1 TTTGAAAATAATA
*
3088373 TTTGTAAATAATA
1 TTTGAAAATAATA
3088386 T
1 T
3088387 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:3094802 original size:18 final size:17
Alignment explanation
Indices: 3094748--3094796 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3094738 TTGGACCCTT
* *
3094748 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3094766 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3094784 AGTGCATTCGATG
1 AGTGCA-TCGATG
3094797 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3094910 original size:65 final size:65
Alignment explanation
Indices: 3094768--3094927 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
3094758 TGCACTAAGA
* * * *
3094768 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATTGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTACATCGATGCATGGCTG
* * *
3094832 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTACATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTACATCGATGCATGGCT
3094895 AG
65 -G
* *
3094897 GTGTATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
3094928 CAATTTAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 29 0.35
65 52 0.62
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTACATCGATGCATGGCTG
Found at i:3094965 original size:20 final size:20
Alignment explanation
Indices: 3094940--3094995 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
3094930 ATTTAATTAA
3094940 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
3094960 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
3094980 TGGTGCATCGGTGCAT
1 TGGTGCATCGATGCAT
3094996 CACTCTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:3094970 original size:65 final size:63
Alignment explanation
Indices: 3094768--3094976 Score: 199
Period size: 65 Copynumber: 3.2 Consensus size: 63
3094758 TGCACTAAGA
* * * * * *
3094768 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATTGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCATAAA-ATCTA-AGTGCATCGATGCATGGTTG
* * * * *
3094832 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTACATCGGTGCATGGTAG
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCATAAAAT-CTAAGTGCATCGATGCATGGTTG
* **
3094897 GTGTATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TAATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-ATAAAATCTAA--GTGCATCGATGCATGG-T
3094960 TG
62 TG
3094962 GTGCATCGATGCATG
1 GTGCATCGATGCATG
3094977 GATTGGTGCA
Statistics
Matches: 120, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
62 2 0.02
63 3 0.03
64 47 0.39
65 64 0.53
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCATAAAATCTAAGTGCATCGATGCATGGTTG
Found at i:3095838 original size:21 final size:21
Alignment explanation
Indices: 3095777--3095894 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 21
3095767 ATGAATCGGG
* ** *
3095777 CTCTTGAACGGTGGTCGGGAC
1 CTCTTGAACGATGGGAGGGGC
* * *
3095798 CTATTGAATGATGGAAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
3095819 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* * * *
3095840 TTCTTCAATGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
3095861 CTCTTGAACGATAGGAGGCGC
1 CTCTTGAACGATGGGAGGGGC
*
3095882 CTCTTGAATGATG
1 CTCTTGAACGATG
3095895 ATAGGTGCAT
Statistics
Matches: 74, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:3095850 original size:42 final size:43
Alignment explanation
Indices: 3095777--3095894 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 43
3095767 ATGAATCGGG
** * *
3095777 CTCTTGAACGGTGGTCGGGACCTATTGAATGATGGA-AGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGGAGAGGGGC
* *
3095819 CTCTTGAACGGTGGGAGGGGCTTCTTCAATGAT-GAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGGAGAGGGGC
* * *
3095861 CTCTTGAACGATAGGAGGCGCCTCTTGAATGATG
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATG
3095895 ATAGGTGCAT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.03
42 61 0.97
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (43 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGGAGAGGGGC
Found at i:3097253 original size:18 final size:17
Alignment explanation
Indices: 3097219--3097258 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
3097209 CCCCCTAGAA
3097219 ATTTTAAATTCTCTTAT
1 ATTTTAAATTCTCTTAT
* *
3097236 ATTTTATAATTTTTTTAT
1 ATTTTA-AATTCTCTTAT
3097254 ATTTT
1 ATTTT
3097259 TTATTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTAAATTCTCTTAT
Found at i:3100356 original size:20 final size:21
Alignment explanation
Indices: 3100312--3100367 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
3100302 CAGTTTCCAA
* *
3100312 ATTCGCAACGCGAATATCCAG
1 ATTCGCAACGCGATTATCAAG
*
3100333 ATTCGCAACGCGATTGT-AAG
1 ATTCGCAACGCGATTATCAAG
*
3100353 ATTCGCAACGTGATT
1 ATTCGCAACGCGATT
3100368 TTGAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (21 bp):
ATTCGCAACGCGATTATCAAG
Found at i:3100421 original size:22 final size:22
Alignment explanation
Indices: 3100367--3100423 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
3100357 GCAACGTGAT
* *
3100367 TTTGAAAAATATGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAAAG
3100389 -TT--AAAATGTGTTGCGAAAG
1 TTTGAAAAATGTGTTGCGAAAG
*
3100408 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
3100424 TTGCGATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 15 0.52
20 2 0.07
21 2 0.07
22 10 0.34
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAAAG
Found at i:3100490 original size:20 final size:21
Alignment explanation
Indices: 3100436--3100491 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
3100426 GCGATAGTCA
3100436 AAATCGCGTTGCGA-ATCTGG
1 AAATCGCGTTGCGATATCTGG
** *
3100456 AAA-CTGATTTACGATA-CTGG
1 AAATC-GCGTTGCGATATCTGG
3100476 AAATCGCGTTGCGATA
1 AAATCGCGTTGCGATA
3100492 GTCAGAATCG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (21 bp):
AAATCGCGTTGCGATATCTGG
Found at i:3100500 original size:20 final size:20
Alignment explanation
Indices: 3100476--3100542 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
3100466 ACGATACTGG
*
3100476 AAATCGCGTTGCGATAGTCA
1 AAATCGCGATGCGATAGTCA
* * *
3100496 GAATCGCGCTGCGAT-TTACA
1 AAATCGCGATGCGATAGT-CA
* *
3100516 TAATCGCAATGCGATAGTCA
1 AAATCGCGATGCGATAGTCA
3100536 AAATCGC
1 AAATCGC
3100543 AGCGCGAATC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (20 bp):
AAATCGCGATGCGATAGTCA
Found at i:3100549 original size:20 final size:20
Alignment explanation
Indices: 3100486--3100549 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
3100476 AAATCGCGTT
*
3100486 GCGATAGTCAGAATCGC-GC
1 GCGATAGTCAAAATCGCAGC
* * **
3100505 TGCGAT-TTACATAATCGCAAT
1 -GCGATAGT-CAAAATCGCAGC
3100526 GCGATAGTCAAAATCGCAGC
1 GCGATAGTCAAAATCGCAGC
3100546 GCGA
1 GCGA
3100550 ATCTGGAAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (20 bp):
GCGATAGTCAAAATCGCAGC
Found at i:3100587 original size:20 final size:19
Alignment explanation
Indices: 3100564--3100609 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3100554 GGAAACTGAT
* *
3100564 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
3100584 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
3100603 TTGCGAT
1 TTGCGAT
3100610 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:3100599 original size:19 final size:19
Alignment explanation
Indices: 3100575--3100611 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3100565 TGCGATACTG
*
3100575 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
3100594 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
3100612 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:3102499 original size:6 final size:6
Alignment explanation
Indices: 3102488--3102662 Score: 350
Period size: 6 Copynumber: 29.2 Consensus size: 6
3102478 CTGAGCCATC
3102488 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
3102536 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
3102584 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
3102632 TATACA TATACA TATACA TATACA TATACA T
1 TATACA TATACA TATACA TATACA TATACA T
3102663 GTATACAGCT
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 169 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TATACA
Found at i:3104201 original size:12 final size:12
Alignment explanation
Indices: 3104186--3104220 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
3104176 GTTATTTAAA
3104186 CGGGTATTGGGT
1 CGGGTATTGGGT
3104198 CGGGTATTGGGT
1 CGGGTATTGGGT
3104210 CGGGTATTGGG
1 CGGGTATTGGG
3104221 CCGAGAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.51, T:0.31
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:3104237 original size:24 final size:24
Alignment explanation
Indices: 3104186--3104240 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
3104176 GTTATTTAAA
* * * * *
3104186 CGGGTATTGGGTCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGC
3104210 CGGGTATTGGGCCGAGAATCGGGC
1 CGGGTATTGGGCCGAGAATCGGGC
3104234 CGGGTAT
1 CGGGTAT
3104241 ATATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGC
Found at i:3104245 original size:2 final size:2
Alignment explanation
Indices: 3104238--3104329 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
3104228 TCGGGCCGGG
* * * *
3104238 TA TA TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
3104279 TA T- TT TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- 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
3104316 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
3104330 AATAATTATT
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
1 6 0.09
2 61 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3104380 original size:13 final size:13
Alignment explanation
Indices: 3104350--3104398 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
3104340 TTTAATATTT
*
3104350 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
3104362 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
3104375 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
3104388 ATCGGGGCGGG
1 ATCGGGGCGGG
3104399 GATTACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 11 0.31
13 24 0.69
ACGTcount: A:0.12, C:0.16, G:0.55, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:3104398 original size:26 final size:25
Alignment explanation
Indices: 3104350--3104398 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
3104340 TTTAATATTT
*
3104350 ATCGGGTCGGGTATCGGGGCGGGTA
1 ATCGGGGCGGGTATCGGGGCGGGTA
3104375 ATCGGGGCGGGTAATCGGGGCGGG
1 ATCGGGGCGGGT-ATCGGGGCGGG
3104399 GATTACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.12, C:0.16, G:0.55, T:0.16
Consensus pattern (25 bp):
ATCGGGGCGGGTATCGGGGCGGGTA
Found at i:3108551 original size:35 final size:35
Alignment explanation
Indices: 3108505--3108580 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
3108495 AAAACAGACA
* * *
3108505 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
3108540 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
3108575 TCAATT
1 TCAATT
3108581 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:3109130 original size:130 final size:130
Alignment explanation
Indices: 3108977--3109224 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
3108967 TATTTATATA
* **
3108977 ATCAATTTGATCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
3109042 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
* *
3109107 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATTATTTAACCAGGATCTGACATGTG
1 ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
3109172 TTAACGCATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
3109225 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:3109255 original size:130 final size:129
Alignment explanation
Indices: 3108991--3109255 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
3108981 ATTTGATCCT
* ** *
3108991 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
3109056 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
* *
3109121 AAATTAAATAAAATTTAATAAATTAATTATTTAACCAGGATCTGACATGTGTTAACGCATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
3109186 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
3109250 -A
128 CA
3109251 AAATT
1 AAATT
3109256 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:3109586 original size:28 final size:27
Alignment explanation
Indices: 3109555--3109617 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
3109545 AGTTGATACA
*
3109555 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
3109583 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
3109611 ATATTTT
1 ATATTTT
3109618 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:3109710 original size:16 final size:18
Alignment explanation
Indices: 3109689--3109722 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3109679 ATTTCTTATT
3109689 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
3109705 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
3109723 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:3111903 original size:354 final size:355
Alignment explanation
Indices: 3111242--3111948 Score: 1308
Period size: 354 Copynumber: 2.0 Consensus size: 355
3111232 TAGTTCCCCA
*
3111242 GAACTGCATCCATAAGGGCTTACCCTAAGCACACAGCAAAGAGAGTCAACCTAAGGGTATGCCTT
1 GAACTGCATCAATAAGGGCTTACCCTAAGCACACAGCAAAGAGAGTCAACCTAAGGGTATGCCTT
3111307 GGGGCTCATGGGCCTACCCAAGGGTATCATTAATTCCATAAGAATTTACCAGATGGATCAGGCCT
66 GGGGCTCATGGGCCTACCCAAGGGTATCATTAATTCCATAAGAATTTACCAGATGGATCAGGCCT
3111372 CCATACTCCAGAATCCTACTCAAATAAAAATCCAGTAGAAATCAGTTTTAACTGTAAACTGTAAT
131 CCATACTCCAGAATCCTACTCAAATAAAAATCCAGTAGAAATCAGTTTTAACTGTAAACTGTAAT
* *
3111437 ATCTGGATCGTAATCTAGTAATATCTCATAATCGTGATAATGAAATAAATCATATAATTGATCTC
196 ATATGGATCGTAATCTAGTAATATCTCATAATCGTGATAATGAAATAAATCATATAACTGATCTC
*
3111502 TACCTGTGCACCATATATAGTTCCATGATTAACCCAAGTGAGTACCTTGGGGCCTGAGAGCCTAC
261 TACCTGTACACCATATATAGTTCCATGATTAACCCAAGTGAGTACCTTGGGGCCTGAGAGCCTAC
3111567 CCAAGGGTCACCTTAGATCCATAAAGATGG
326 CCAAGGGTCACCTTAGATCCATAAAGATGG
* *
3111597 GAACTGTATCAATAAGGGCTTACCCTAAGCACACAGCAAAGAGAGTCAACCTAAGGG-ATGTCTT
1 GAACTGCATCAATAAGGGCTTACCCTAAGCACACAGCAAAGAGAGTCAACCTAAGGGTATGCCTT
* *
3111661 GGGGCTTATGGGCCTACCCAAGGGTATCATTAATTCCATAAGGATTTACCAGATGGATCAGGCCT
66 GGGGCTCATGGGCCTACCCAAGGGTATCATTAATTCCATAAGAATTTACCAGATGGATCAGGCCT
* *
3111726 CCATACTCCAGAATCCTACTCATATAAAAATCCAGTAGAAATTAGTTTTAACTGTAAACTGTAAT
131 CCATACTCCAGAATCCTACTCAAATAAAAATCCAGTAGAAATCAGTTTTAACTGTAAACTGTAAT
3111791 ATATGGATCGTAATCTAGTAATATCTCATAATCGTGATAATGAAATAAATCATATAACTGATCTC
196 ATATGGATCGTAATCTAGTAATATCTCATAATCGTGATAATGAAATAAATCATATAACTGATCTC
3111856 TACCTGTACACCATATATAGTTCCATGATTAACCCAAGTGAGTACCTTGGGGCCTGAGAGCCTAC
261 TACCTGTACACCATATATAGTTCCATGATTAACCCAAGTGAGTACCTTGGGGCCTGAGAGCCTAC
*
3111921 CCAAGGGTCACCTTAGGTCCATAAAGAT
326 CCAAGGGTCACCTTAGATCCATAAAGAT
3111949 TTACCAGCTT
Statistics
Matches: 341, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
354 286 0.84
355 55 0.16
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (355 bp):
GAACTGCATCAATAAGGGCTTACCCTAAGCACACAGCAAAGAGAGTCAACCTAAGGGTATGCCTT
GGGGCTCATGGGCCTACCCAAGGGTATCATTAATTCCATAAGAATTTACCAGATGGATCAGGCCT
CCATACTCCAGAATCCTACTCAAATAAAAATCCAGTAGAAATCAGTTTTAACTGTAAACTGTAAT
ATATGGATCGTAATCTAGTAATATCTCATAATCGTGATAATGAAATAAATCATATAACTGATCTC
TACCTGTACACCATATATAGTTCCATGATTAACCCAAGTGAGTACCTTGGGGCCTGAGAGCCTAC
CCAAGGGTCACCTTAGATCCATAAAGATGG
Found at i:3113313 original size:9 final size:9
Alignment explanation
Indices: 3113301--3113504 Score: 50
Period size: 9 Copynumber: 21.9 Consensus size: 9
3113291 ATTTTTTATT
3113301 TTTTATTTA
1 TTTTATTTA
3113310 TTTTATATATA
1 TTTTAT-T-TA
*
3113321 TATTATTT-
1 TTTTATTTA
3113329 TTACTT-TTTA
1 TT--TTATTTA
3113339 TTATTATTT-
1 TT-TTATTTA
* *
3113348 TATTTGTTTG
1 T-TTTATTTA
3113358 TTTTATTTA
1 TTTTATTTA
* *
3113367 TATATATTTT
1 T-TTTATTTA
*
3113377 TTCTTCTTT-
1 TT-TTATTTA
3113386 TTCTTAATTT-
1 TT-TT-ATTTA
*
3113396 TTTTATTTT
1 TTTTATTTA
3113405 TTTATATTTA
1 TTT-TATTTA
3113415 TTTTACTTACTA
1 TTTTA-TT--TA
3113427 TTTTATCTTTA
1 TTTTA--TTTA
* *
3113438 CTTTCTTTA
1 TTTTATTTA
* *
3113447 TCTTA--TC
1 TTTTATTTA
3113454 TTTTATTTA
1 TTTTATTTA
*
3113463 ATTTATTT-
1 TTTTATTTA
*
3113471 TTTT-TTCA
1 TTTTATTTA
3113479 TTTTTATTTA
1 -TTTTATTTA
* *
3113489 ATTAATTTA
1 TTTTATTTA
3113498 -TTTATTT
1 TTTTATTT
3113505 CTTACATTTT
Statistics
Matches: 146, Mismatches: 27, Indels: 45
0.67 0.12 0.21
Matches are distributed among these distances:
7 7 0.05
8 14 0.10
9 63 0.43
10 40 0.27
11 12 0.08
12 7 0.05
13 3 0.02
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTTATTTA
Found at i:3113317 original size:36 final size:35
Alignment explanation
Indices: 3113279--3113350 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
3113269 TATATATATA
* *
3113279 TATATATATACTATTTTTTATTTTTTA-T-TTATTT
1 TATATATATATTA-TTTTTACTTTTTATTATTATTT
3113313 TATATATATATTATTTTTACTTTTTATTATTATTT
1 TATATATATATTATTTTTACTTTTTATTATTATTT
3113348 TAT
1 TAT
3113351 TTGTTTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 12 0.35
34 13 0.38
35 9 0.26
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (35 bp):
TATATATATATTATTTTTACTTTTTATTATTATTT
Found at i:3113337 original size:24 final size:22
Alignment explanation
Indices: 3113310--3113378 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 22
3113300 TTTTTATTTA
3113310 TTTTATATATATATTATTTTTACT-
1 TTTTAT-TATATATTATTTTT--TG
*
3113334 TTTTATTATTATTTTATTTGTTTG
1 TTTTATTA-TATATTATTT-TTTG
3113358 TTTTATT-TATATATATTTTTT
1 TTTTATTATATAT-TATTTTTT
3113379 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 7 0.18
23 8 0.21
24 22 0.56
25 2 0.05
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.72
Consensus pattern (22 bp):
TTTTATTATATATTATTTTTTG
Found at i:3113363 original size:48 final size:46
Alignment explanation
Indices: 3113299--3113411 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 46
3113289 CTATTTTTTA
3113299 TTTTTTATTTATTTTATATATATATTATTTTTACTT-TTTATTATT-AT
1 TTTTTTATTT-TTTTATATATATA-TATTTTTACTTCTTT-TTATTAAT
* * * *
3113346 TTTATTTGTTTGTTTTATTTATATATATTTTTTCTTCTTTTTCTTAAT
1 TTT-TTTATTT-TTTTATATATATATATTTTTACTTCTTTTTATTAAT
3113394 TTTTTTATTTTTTTATAT
1 TTTTTTATTTTTTTATAT
3113412 TTATTTTACT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
46 7 0.12
47 23 0.41
48 26 0.46
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (46 bp):
TTTTTTATTTTTTTATATATATATATTTTTACTTCTTTTTATTAAT
Found at i:3113413 original size:48 final size:46
Alignment explanation
Indices: 3113299--3113415 Score: 130
Period size: 47 Copynumber: 2.5 Consensus size: 46
3113289 CTATTTTTTA
*
3113299 TTTTTTATTTATTTTATATATATATTATTTTTACTTTTTATTATTAT
1 TTTTTTATTT-TTTTATATTTATATTATTTTTACTTTTTATTATTAT
* * * *
3113346 TTTATTTGTTTGTTT-TATTTATATATATTTTTTCTTCTTT-TTCTTAAT
1 TTT-TTTATTTTTTTATATTTATAT-TATTTTTACTT-TTTATTATT-AT
3113394 TTTTTTATTTTTTTATATTTAT
1 TTTTTTATTTTTTTATATTTAT
3113416 TTTACTTACT
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
46 8 0.14
47 29 0.50
48 21 0.36
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (46 bp):
TTTTTTATTTTTTTATATTTATATTATTTTTACTTTTTATTATTAT
Found at i:3113415 original size:52 final size:51
Alignment explanation
Indices: 3113292--3113417 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 51
3113282 ATATATACTA
* *
3113292 TTTTTTATTTTTTATTTATTT-TATATATATATTATTTTTACTTTTTATTAT
1 TTTTTTATTTTTT-TATATTTATTTATATATATTATTTTTACTTTTTATTAT
* * * * *
3113343 TATTTTATTTGTTTGT-TTTATTTATATATATT-TTTTCTTCTTTTTCTTAAT
1 TTTTTTATTTTTTTATATTTATTTATATATATTATTTT-TACTTTTTATT-AT
3113394 TTTTTTATTTTTTTATATTTATTT
1 TTTTTTATTTTTTTATATTTATTT
3113418 TACTTACTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
49 7 0.11
50 22 0.35
51 26 0.42
52 7 0.11
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (51 bp):
TTTTTTATTTTTTTATATTTATTTATATATATTATTTTTACTTTTTATTAT
Found at i:3113489 original size:26 final size:28
Alignment explanation
Indices: 3113454--3113505 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
3113444 TTATCTTATC
*
3113454 TTTTATTTAATTTATTT-TTT-TTTCAT
1 TTTTATTTAATTAATTTATTTATTTCAT
3113480 TTTTATTTAATTAATTTATTTATTTC
1 TTTTATTTAATTAATTTATTTATTTC
3113506 TTACATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.70
27 3 0.13
28 4 0.17
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTATTTAATTAATTTATTTATTTCAT
Found at i:3113496 original size:30 final size:32
Alignment explanation
Indices: 3113455--3113517 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
3113445 TATCTTATCT
* *
3113455 TTTATTTAATTTATTT-TTT-TTTCATTTTTA
1 TTTAATTAATTTATTTATTTCTTACATTTTTA
3113485 TTTAATTAATTTATTTATTTCTTACATTTTTA
1 TTTAATTAATTTATTTATTTCTTACATTTTTA
3113517 T
1 T
3113518 CTAACATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 15 0.52
31 3 0.10
32 11 0.38
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (32 bp):
TTTAATTAATTTATTTATTTCTTACATTTTTA
Found at i:3114364 original size:27 final size:26
Alignment explanation
Indices: 3114334--3114385 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
3114324 AAATACTTTA
3114334 GGCCATTTAACACTTTAGGGGCATTTT
1 GGCCATTTAACACTTTA-GGGCATTTT
*
3114361 GGCCATTTTACACTTTAGGGCATTT
1 GGCCATTTAACACTTTAGGGCATTT
3114386 CTATAAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (26 bp):
GGCCATTTAACACTTTAGGGCATTTT
Found at i:3116684 original size:15 final size:15
Alignment explanation
Indices: 3116666--3116698 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3116656 AAATTCTAAA
3116666 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
3116681 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
3116696 TAT
1 TAT
3116699 ATTTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:3118930 original size:35 final size:35
Alignment explanation
Indices: 3118884--3118956 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
3118874 AGAAATCTAA
*
3118884 GAGAAGCTGCTAAATGTGTTAATTGTTATCAATCC
1 GAGAAGCTGCTAAAGGTGTTAATTGTTATCAATCC
*
3118919 GAGAAGCTGCTAAGGGTGTTAATTGTTATCAATCC
1 GAGAAGCTGCTAAAGGTGTTAATTGTTATCAATCC
3118954 GAG
1 GAG
3118957 CTCAAGAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (35 bp):
GAGAAGCTGCTAAAGGTGTTAATTGTTATCAATCC
Found at i:3122366 original size:19 final size:19
Alignment explanation
Indices: 3122342--3122379 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3122332 ATATTTCCTT
3122342 GTACTCCAAGGTAGTAGAA
1 GTACTCCAAGGTAGTAGAA
3122361 GTACTCCAAGGTAGTAGAA
1 GTACTCCAAGGTAGTAGAA
3122380 AGGATCATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (19 bp):
GTACTCCAAGGTAGTAGAA
Found at i:3124565 original size:3 final size:3
Alignment explanation
Indices: 3124557--3124587 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3124547 GATAAAGATG
*
3124557 AGA AGA AGA AGA AGA AGA AGA AGA GGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3124588 AGGGTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3134711 original size:22 final size:23
Alignment explanation
Indices: 3134662--3134710 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3134652 AGAATCGATA
3134662 CCCCC-TTGAAGGGGAACCAATT
1 CCCCCTTTGAAGGGGAACCAATT
* **
3134684 CCCCCTTTGAATGGGAACTGATT
1 CCCCCTTTGAAGGGGAACCAATT
3134707 CCCC
1 CCCC
3134711 TCTGTAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACCAATT
Found at i:3142245 original size:13 final size:14
Alignment explanation
Indices: 3142211--3142247 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3142201 TATTTGATTT
3142211 ATAAATAATATTAA
1 ATAAATAATATTAA
3142225 ATAAATAATA-T-A
1 ATAAATAATATTAA
3142237 ATGAAATAATA
1 AT-AAATAATA
3142248 CTTTATTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 9 0.41
14 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
ATAAATAATATTAA
Found at i:3154082 original size:41 final size:41
Alignment explanation
Indices: 3154037--3154114 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
3154027 TACTAAGAAG
* * *
3154037 TAAGAACTCGATCTGGGTATTTGATTATTTTCCATTTTGAC
1 TAAGAACTCGAACTGGGTATTTGAGTATTTGCCATTTTGAC
* *
3154078 TAAGAACTTGAACTGGGTATTTGGGTATTTGCCATTT
1 TAAGAACTCGAACTGGGTATTTGAGTATTTGCCATTT
3154115 CCTTCATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (41 bp):
TAAGAACTCGAACTGGGTATTTGAGTATTTGCCATTTTGAC
Found at i:3154285 original size:19 final size:19
Alignment explanation
Indices: 3154261--3154297 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3154251 TAAGTAGAGG
3154261 TAAGATAATAGATTGTCTT
1 TAAGATAATAGATTGTCTT
3154280 TAAGATAATAGATTGTCT
1 TAAGATAATAGATTGTCT
3154298 CTAATATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (19 bp):
TAAGATAATAGATTGTCTT
Found at i:3161112 original size:29 final size:29
Alignment explanation
Indices: 3161070--3161154 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
3161060 CTGACGGATC
*
3161070 TACTTTTATTTTAAGGTATTCATCCTAAA
1 TACTTTTATTTTAAGGTATTCGTCCTAAA
3161099 TACTTTTATTTTAAGGTATTCGTCCT-AA
1 TACTTTTATTTTAAGGTATTCGTCCTAAA
*
3161127 -AGTTTTATTTTAAGGTATTCGTCCTAAA
1 TACTTTTATTTTAAGGTATTCGTCCTAAA
3161155 GTTTTATTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
27 24 0.45
28 4 0.08
29 25 0.47
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (29 bp):
TACTTTTATTTTAAGGTATTCGTCCTAAA
Found at i:3161140 original size:27 final size:27
Alignment explanation
Indices: 3161073--3161163 Score: 146
Period size: 27 Copynumber: 3.3 Consensus size: 27
3161063 ACGGATCTAC
* *
3161073 TTTTATTTTAAGGTATTCATCCTAAATAC
1 TTTTATTTTAAGGTATTCGTCCT-AA-AG
3161102 TTTTATTTTAAGGTATTCGTCCTAAAG
1 TTTTATTTTAAGGTATTCGTCCTAAAG
3161129 TTTTATTTTAAGGTATTCGTCCTAAAG
1 TTTTATTTTAAGGTATTCGTCCTAAAG
3161156 TTTTATTT
1 TTTTATTT
3161164 GTGTTTATTG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 36 0.60
28 2 0.03
29 22 0.37
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (27 bp):
TTTTATTTTAAGGTATTCGTCCTAAAG
Found at i:3162412 original size:70 final size:70
Alignment explanation
Indices: 3162299--3162440 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
3162289 CCAGCAGGTT
3162299 TTCAAAACTTTAATATTATACTATATAAGTTATCTATTATTGGTTTTCTTGTTTTGATAACTGGC
1 TTCAAAACTTTAATATTATACTATATAAGTTATCTATTATTGGTTTTCTTGTTTTGATAACTGGC
3162364 TTCTC
66 TTCTC
3162369 TTCAAAACTTTAATATTATACTATATAAGTTATCTATTATTGGTTTTCTTGTTTTGATAACTGGC
1 TTCAAAACTTTAATATTATACTATATAAGTTATCTATTATTGGTTTTCTTGTTTTGATAACTGGC
3162434 TTCTC
66 TTCTC
3162439 TT
1 TT
3162441 TTGCAGGGAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.51
Consensus pattern (70 bp):
TTCAAAACTTTAATATTATACTATATAAGTTATCTATTATTGGTTTTCTTGTTTTGATAACTGGC
TTCTC
Found at i:3163342 original size:22 final size:21
Alignment explanation
Indices: 3163290--3163349 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
3163280 GATTTCTGGG
3163290 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
3163311 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
3163331 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
3163350 CTCAAACGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:3163427 original size:23 final size:22
Alignment explanation
Indices: 3163383--3163427 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3163373 AATCTCATGG
*
3163383 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
3163405 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
3163428 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:3164944 original size:103 final size:103
Alignment explanation
Indices: 3164724--3164936 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
3164714 GGGTCTACGC
3164724 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
3164789 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTATTAAGGAATGATATGT
3164827 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
3164892 CCCTAGTATATGTATATGGTTATTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTATTAAGGAATGATATGT
3164930 GGTCCTT
1 GGTCCTT
3164937 ATGGACATTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTATTAAGGAATGATATGT
Found at i:3166454 original size:17 final size:17
Alignment explanation
Indices: 3166432--3166468 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3166422 AGCAAGAGTG
3166432 TGCCTATAATAAGGGTT
1 TGCCTATAATAAGGGTT
3166449 TGCCTATAATAAGGGTT
1 TGCCTATAATAAGGGTT
3166466 TGC
1 TGC
3166469 ATTCTAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (17 bp):
TGCCTATAATAAGGGTT
Found at i:3166892 original size:177 final size:177
Alignment explanation
Indices: 3166596--3166950 Score: 692
Period size: 177 Copynumber: 2.0 Consensus size: 177
3166586 ATACAGTTGT
3166596 ATATTTGGATCATAATAAATGTGGATTTGATAAGTTAAGTAAACTATTGCTGAGATAATTCCGAC
1 ATATTTGGATCATAATAAATGTGGATTTGATAAGTTAAGTAAACTATTGCTGAGATAATTCCGAC
3166661 TGGAATGAATGTATATGAATGGTTCGATGAAGGTTTATGCTTTAGATTGGAATAATTGGTGGTGA
66 TGGAATGAATGTATATGAATGGTTCGATGAAGGTTTATGCTTTAGATTGGAATAATTGGTGGTGA
3166726 CTAACAGAATTATGTGATGGTAAGTGTATCAAAGGTAAAGGATTAGA
131 CTAACAGAATTATGTGATGGTAAGTGTATCAAAGGTAAAGGATTAGA
3166773 ATATTTGGATCATAATAAATGTGGATTTGATAAGTTAAGTAAACTATTGCTGAGATAATTCCGAC
1 ATATTTGGATCATAATAAATGTGGATTTGATAAGTTAAGTAAACTATTGCTGAGATAATTCCGAC
*
3166838 TGGAATGAATGTATATGAATGGTTCGATGAATGTTTATGCTTTAGATTGGAATAATTGGTGGTGA
66 TGGAATGAATGTATATGAATGGTTCGATGAAGGTTTATGCTTTAGATTGGAATAATTGGTGGTGA
*
3166903 CTAACAGAATTATGTGATGGTAAGTGTATCAAAGGTAAATGATTAGA
131 CTAACAGAATTATGTGATGGTAAGTGTATCAAAGGTAAAGGATTAGA
3166950 A
1 A
3166951 GATGATGTCA
Statistics
Matches: 176, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 176 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (177 bp):
ATATTTGGATCATAATAAATGTGGATTTGATAAGTTAAGTAAACTATTGCTGAGATAATTCCGAC
TGGAATGAATGTATATGAATGGTTCGATGAAGGTTTATGCTTTAGATTGGAATAATTGGTGGTGA
CTAACAGAATTATGTGATGGTAAGTGTATCAAAGGTAAAGGATTAGA
Found at i:3168777 original size:22 final size:21
Alignment explanation
Indices: 3168725--3168784 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
3168715 GATTTCTGGG
3168725 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
3168746 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
3168766 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
3168785 CTCAAACGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:3170216 original size:103 final size:103
Alignment explanation
Indices: 3170037--3170249 Score: 374
Period size: 103 Copynumber: 2.1 Consensus size: 103
3170027 GGGTCTACGC
3170037 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGAT
* *
3170102 CCTTGGCATATGTATATGATTCTTAAGGAATGATATG-
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
3170139 GGTCCTTCGGGACATATATGTATTTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 GGTCCTTCGGGACATATATGTA-TTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGA
*
3170204 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
65 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
3170243 GGTCCTT
1 GGTCCTT
3170250 ATGGACATTA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
102 22 0.21
103 76 0.72
104 7 0.07
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:3170326 original size:23 final size:23
Alignment explanation
Indices: 3170264--3170328 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
3170254 ACATTATTAT
*
3170264 GTGGCACTACGGTGCAATTCTAC
1 GTGGCACTTCGGTGCAATTCTAC
* *
3170287 GCGGCAC-TCTGGCGCAATTCTAC
1 GTGGCACTTC-GGTGCAATTCTAC
3170310 GTGGCACTTCGGTGCAATT
1 GTGGCACTTCGGTGCAATT
3170329 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.91
24 2 0.06
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
GTGGCACTTCGGTGCAATTCTAC
Found at i:3188318 original size:55 final size:55
Alignment explanation
Indices: 3188252--3188362 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
3188242 AAGAACCACC
3188252 GGTTGATTGTTCCTTTTTTCCTCCTGAAAATATGAACTGCATGTTTCCAGTATTG
1 GGTTGATTGTTCCTTTTTTCCTCCTGAAAATATGAACTGCATGTTTCCAGTATTG
3188307 GGTTGATTGTTCCTTTTTTCCTCCTGAAAATATGAACTGCATGTTTCCAGTATTG
1 GGTTGATTGTTCCTTTTTTCCTCCTGAAAATATGAACTGCATGTTTCCAGTATTG
3188362 G
1 G
3188363 CTCCTGTATG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (55 bp):
GGTTGATTGTTCCTTTTTTCCTCCTGAAAATATGAACTGCATGTTTCCAGTATTG
Found at i:3190774 original size:21 final size:20
Alignment explanation
Indices: 3190731--3190771 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 20
3190721 CCGAAAATAT
3190731 TAAAAAAATAATATTTTAAA
1 TAAAAAAATAATATTTTAAA
3190751 TAAAAATAATAATATTATTAA
1 TAAAAA-AATAATATT-TTAA
3190772 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAAAATAATATTTTAAA
Found at i:3196733 original size:60 final size:61
Alignment explanation
Indices: 3196639--3196754 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 61
3196629 TTCCTTCAAT
*
3196639 TATGACTCTCATTCTAAATTGGCCCCTAAAC-TTTTAAACATTTCATTTTCATCCCCAAAC
1 TATGACTCTCATTCTAAATTGGCCCCTAAACTTTTTAAACATTTCAATTTCATCCCCAAAC
* *
3196699 TATGA-TCTTCATTCTAAATTGGTCCCC-AAGCTTTTTTAACATTTCAATTTCATCCC
1 TATGACTC-TCATTCTAAATTGG-CCCCTAAACTTTTTAAACATTTCAATTTCATCCC
3196755 AAATTATATG
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
59 2 0.04
60 22 0.44
61 26 0.52
ACGTcount: A:0.28, C:0.27, G:0.06, T:0.40
Consensus pattern (61 bp):
TATGACTCTCATTCTAAATTGGCCCCTAAACTTTTTAAACATTTCAATTTCATCCCCAAAC
Found at i:3197038 original size:60 final size:60
Alignment explanation
Indices: 3196916--3197065 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
3196906 CAAAAGTCTG
* * * * * * ** *
3196916 AGGACCAATTTAGAATGATACTCATAGTTTAGAGACGAAAATAGAATGTTCAAAGTTTTA
1 AGGATCAATTTAGAATGAGAATCATAGTTTACAGACGAAAATAAAATATTCAAAAATGTA
* * * * *
3196976 AGG-GCTAATTTAGAATGAGAGTCATAGTTTACAGATGAAATTAAAATATTTAAAAATGTA
1 AGGATC-AATTTAGAATGAGAATCATAGTTTACAGACGAAAATAAAATATTCAAAAATGTA
3197036 AGGATCAATTT-GAGATGAGAATCATAGTTT
1 AGGATCAATTTAGA-ATGAGAATCATAGTTT
3197066 GAGGACATGT
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
59 3 0.04
60 69 0.95
61 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.31
Consensus pattern (60 bp):
AGGATCAATTTAGAATGAGAATCATAGTTTACAGACGAAAATAAAATATTCAAAAATGTA
Found at i:3198077 original size:21 final size:20
Alignment explanation
Indices: 3197991--3198148 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
3197981 AAATGACCAA
**
3197991 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3198010 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3198030 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3198050 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3198071 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3198092 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3198112 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
3198133 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3198149 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3198210 original size:20 final size:20
Alignment explanation
Indices: 3198116--3198464 Score: 427
Period size: 20 Copynumber: 17.4 Consensus size: 20
3198106 GATTTTCAAT
* ** *
3198116 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3198136 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3198156 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3198176 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
3198196 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
3198216 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3198236 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3198256 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3198276 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3198296 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3198316 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3198336 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
3198356 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3198376 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3198396 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3198416 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3198436 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3198456 AATCACAAC
1 AATCGCAAC
3198465 ACTGAAATTT
Statistics
Matches: 287, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 281 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3199180 original size:24 final size:24
Alignment explanation
Indices: 3199141--3199187 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3199131 AAATTTGGTC
3199141 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3199165 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3199188 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3199379 original size:12 final size:12
Alignment explanation
Indices: 3199362--3199386 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3199352 ATATAATCCT
3199362 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3199374 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3199386 G
1 G
3199387 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3201692 original size:19 final size:19
Alignment explanation
Indices: 3201670--3201943 Score: 336
Period size: 19 Copynumber: 15.4 Consensus size: 19
3201660 CGGAAAATAC
*
3201670 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3201689 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3201703 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3201723 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3201737 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3201756 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
*
3201775 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3201789 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3201808 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
3201827 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
3201846 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3201865 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3201884 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3201898 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3201917 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3201936 AATCGCAA
1 AATCGCAA
3201944 CGAGATAATC
Statistics
Matches: 222, Mismatches: 12, Indels: 42
0.80 0.04 0.15
Matches are distributed among these distances:
14 39 0.18
15 2 0.01
16 11 0.05
17 10 0.05
18 3 0.01
19 144 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3201757 original size:33 final size:35
Alignment explanation
Indices: 3201670--3201965 Score: 264
Period size: 33 Copynumber: 8.5 Consensus size: 35
3201660 CGGAAAATAC
* *
3201670 AATCGCAACGCGAAATGAAAATCCCAA-C-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCGATGAA
*
3201703 AATCGCAATGCGGAAATGAAAATCGCAA-CGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAAGCGATGAA
*
3201737 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG--ATGAA
*
3201775 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG--ATGAA
* *
3201808 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG--ATGAA
3201846 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG--ATGAA
3201884 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG--ATGAA
*
3201917 AATCGCAATGCGAAATGAAAATCGCAA-CGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAAGCGATGAA
3201950 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
3201966 TATAAACGCA
Statistics
Matches: 233, Mismatches: 13, Indels: 34
0.83 0.05 0.12
Matches are distributed among these distances:
33 99 0.42
34 31 0.13
35 11 0.05
36 10 0.04
37 2 0.01
38 80 0.34
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (35 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGATGAA
Found at i:3201872 original size:109 final size:105
Alignment explanation
Indices: 3201698--3201965 Score: 441
Period size: 109 Copynumber: 2.5 Consensus size: 105
3201688 AAATCCCAAC
3201698 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAAATGAAAATCGC
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGC
*
3201762 AATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAA
65 AATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAA
* *
3201803 ATGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGAT-G-AATCGCAATGCGAAATGAAAAT
*
3201868 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
62 CGCAATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAA
3201912 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAAT
3201966 TATAAACGCA
Statistics
Matches: 152, Mismatches: 6, Indels: 11
0.90 0.04 0.07
Matches are distributed among these distances:
104 31 0.20
105 16 0.11
106 4 0.03
107 5 0.03
108 1 0.01
109 95 0.62
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (105 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:3201981 original size:52 final size:52
Alignment explanation
Indices: 3201698--3201965 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
3201688 AAATCCCAAC
3201698 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3201751 ATGAAAATCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
3201803 ATGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
3201860 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3201912 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3201964 AT
1 AT
3201966 TATAAACGCA
Statistics
Matches: 204, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
52 132 0.65
53 17 0.08
54 4 0.02
55 5 0.02
56 1 0.00
57 45 0.22
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3202062 original size:19 final size:19
Alignment explanation
Indices: 3201972--3202054 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
3201962 AAATTATAAA
3201972 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3201991 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3202011 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3202027 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3202044 CGCATTGCGAT
1 CGCATTGCGAT
3202055 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3202180 original size:14 final size:14
Alignment explanation
Indices: 3202161--3202197 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3202151 CATCAATTAC
3202161 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3202175 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3202189 ACAAATCAA
1 ACAAATCAA
3202198 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3204166 original size:14 final size:14
Alignment explanation
Indices: 3204147--3204203 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3204137 GCGAAATGAA
*
3204147 AATCGCAACGACAG
1 AATCGCAACGAAAG
3204161 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3204178 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3204194 AATCGCAACG
1 AATCGCAACG
3204204 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3204174 original size:33 final size:33
Alignment explanation
Indices: 3204128--3204220 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3204118 GCGAAACCAA
*
3204128 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3204161 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3204194 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3204221 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3204185 original size:19 final size:19
Alignment explanation
Indices: 3204091--3204225 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3204081 TAGTTTACTT
* *
3204091 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3204111 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3204130 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3204149 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3204163 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3204182 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3204196 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3204215 TCGCAATGCGA
1 TCGCAACGCGA
3204226 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3204275 original size:19 final size:19
Alignment explanation
Indices: 3204221--3204349 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
3204211 AAAATCGCAA
3204221 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3204240 TGCAATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3204254 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3204273 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3204287 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3204306 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3204325 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3204345 TGCGA
1 TGCGA
3204350 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3204309 original size:33 final size:34
Alignment explanation
Indices: 3204221--3204312 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 34
3204211 AAAATCGCAA
*
3204221 TGCGATTTTGGTTTCGCGTTGC-AATCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
3204254 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
3204287 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3204313 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 52 0.95
34 3 0.05
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:3204563 original size:92 final size:93
Alignment explanation
Indices: 3204393--3204771 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
3204383 TTGAATGGAT
3204393 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3204458 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3204486 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3204550 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3204578 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3204642 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3204670 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3204735 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3204763 AAATTTACT
1 AAATTTACT
3204772 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3204722 original size:185 final size:185
Alignment explanation
Indices: 3204393--3204771 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
3204383 TTGAATGGAT
3204393 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3204458 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3204523 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
3204578 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3204642 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
3204707 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
3204763 AAATTTACT
1 AAATTTACT
3204772 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 100 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3206497 original size:14 final size:14
Alignment explanation
Indices: 3206478--3206567 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3206468 TTGAAATGAA
3206478 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3206492 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
3206509 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
3206525 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3206544 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3206558 AATCGCAACG
1 AATCGCAACG
3206568 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3206515 original size:33 final size:33
Alignment explanation
Indices: 3206470--3206584 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3206460 TCTTTTGGTT
3206470 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3206503 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3206536 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3206569 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3206585 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3206516 original size:19 final size:18
Alignment explanation
Indices: 3206477--3206589 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
3206467 GTTGAAATGA
3206477 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
3206492 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
3206509 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
3206525 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
3206542 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
3206558 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
3206575 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
3206590 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:3206620 original size:14 final size:14
Alignment explanation
Indices: 3206601--3206655 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3206591 TTTGGTTTCG
3206601 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3206615 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3206634 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3206648 CGTTGCGA
1 CGTTGCGA
3206656 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3206633 original size:33 final size:33
Alignment explanation
Indices: 3206585--3206655 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3206575 AAAATCGCAA
**
3206585 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3206618 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3206651 TGCGA
1 TGCGA
3206656 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3206663 original size:33 final size:33
Alignment explanation
Indices: 3206596--3206677 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
3206586 GCGATTTTGG
***
3206596 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
3206629 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
3206662 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
3206678 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:3206682 original size:20 final size:20
Alignment explanation
Indices: 3206608--3206696 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
3206598 TCGCGTTGCG
3206608 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3206628 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
3206641 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
3206661 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3206681 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
3206697 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3206818 original size:33 final size:33
Alignment explanation
Indices: 3206776--3206846 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3206766 AATACTAACT
*
3206776 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3206809 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3206842 TGAAA
1 TGAAA
3206847 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3207079 original size:22 final size:22
Alignment explanation
Indices: 3207027--3207081 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3207017 TGGTTGTGAG
**
3207027 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3207049 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3207071 GGATTTCTTCG
1 GGATTTCTTCG
3207082 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3207252 original size:20 final size:20
Alignment explanation
Indices: 3207227--3207419 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
3207217 CTTTAAATAT
3207227 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3207247 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3207269 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3207288 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3207308 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3207328 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3207348 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3207368 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3207388 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3207408 CGCGTTGCGATT
1 CGCGTTGCGATT
3207420 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3207414 original size:60 final size:60
Alignment explanation
Indices: 3207227--3207419 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
3207217 CTTTAAATAT
**
3207227 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3207288 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3207348 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3207408 CGCGTTGCGATT
1 CGCGTTGCGATT
3207420 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3208921 original size:334 final size:339
Alignment explanation
Indices: 3208264--3208937 Score: 1022
Period size: 334 Copynumber: 2.0 Consensus size: 339
3208254 ATATTAAATT
* ** *
3208264 ATAATTTTATTAGCAATGAATAAACATTATTAACTGTTGTTAAAAAATAATAATTAATGAATAAT
1 ATAAATTTATTAAAAATGAATAAACATTATTAACTGTTGATAAAAAATAATAATTAATGAATAAT
*
3208329 AATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTATTTTATATTTTTAAACAA
66 AATTCATTTGATCCCTCAATTGTAATTAAAAGATTATTTT-ATATTA-TTTATATTTTTAAACAA
3208394 TTAATTTTAAAAGTCAATAAATTTTTTAAAAAATATATGAAATTTATAATTTTTTAAATTATAAA
129 TTAATTTTAAAAGTCAATAAATTTTTTAAAAAATATATGAAATTTATAATTTTTTAAATTATAAA
* * * **
3208459 ATATTTATCATCATCATCGTCATCATTTTGTAAAAGAAATACTGGTTATAAAACTTTTATAAAAT
194 ATATTTATCATCATCATCATAATCATTTTATAAAAGAAATACTAATTATAAAACTTTTATAAAAT
* * * * *
3208524 TATTTATATTTTAAAATATTTACCCTCAAAGTTTTTCTATACTATATTATACGTATTGTGTAATT
259 TATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAAATTATACATATTGTGTAATT
3208589 TCATGCAAAAATCAAA
324 TCATGCAAAAATCAAA
* *
3208605 ATAAATTTATTAAAAATTAATAAACATTATTAATTGTTGAT-AAAAATAATAATTAATGAATAAT
1 ATAAATTTATTAAAAATGAATAAACATTATTAACTGTTGATAAAAAATAATAATTAATGAATAAT
3208669 AATTCATTTGATCCCTCAATTGTAATTAAAAGATTATTTT-T-TTA-TT-T-TTTTTAAACAATT
66 AATTCATTTGATCCCTCAATTGTAATTAAAAGATTATTTTATATTATTTATATTTTTAAACAATT
* * *
3208729 AA-TTTAAAATTCAATACA-TTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
131 AATTTTAAAAGTCAATAAATTTTTTAAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
* * *
3208792 ATTTATTATTATCATCATTATAATCATTTTATAACAGAAATACTAATTATAAAACTTTTATAAAA
196 A--T-TTATCATCATCATCATAATCATTTTATAAAAGAAATACTAATTATAAAACTTTTATAAAA
* *
3208857 TTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATATTAAATTGTACATATTGTGTAAT
258 TTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAAATTATACATATTGTGTAAT
3208922 TTCATGCAAAAATCAA
323 TTCATGCAAAAATCAA
3208938 TATCTATCGT
Statistics
Matches: 305, Mismatches: 25, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
331 45 0.15
332 14 0.05
333 16 0.05
334 127 0.42
335 2 0.01
337 3 0.01
338 1 0.00
340 62 0.20
341 35 0.11
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (339 bp):
ATAAATTTATTAAAAATGAATAAACATTATTAACTGTTGATAAAAAATAATAATTAATGAATAAT
AATTCATTTGATCCCTCAATTGTAATTAAAAGATTATTTTATATTATTTATATTTTTAAACAATT
AATTTTAAAAGTCAATAAATTTTTTAAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
ATTTATCATCATCATCATAATCATTTTATAAAAGAAATACTAATTATAAAACTTTTATAAAATTA
TTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAAATTATACATATTGTGTAATTTC
ATGCAAAAATCAAA
Found at i:3212290 original size:24 final size:24
Alignment explanation
Indices: 3212263--3212314 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3212253 CGTTCATTTA
*
3212263 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* ***
3212287 CGTTTATGTTTGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
3212311 CGTT
1 CGTT
3212315 TATGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.13, G:0.27, T:0.50
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:3212315 original size:24 final size:24
Alignment explanation
Indices: 3212274--3212320 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
3212264 GTTCGTGAAC
3212274 GTTCGGTTATGTTCGTTTATGTTT
1 GTTCGGTTATGTTCGTTTATGTTT
3212298 GTTCGGTTATGTTCGTTTATGTT
1 GTTCGGTTATGTTCGTTTATGTT
3212321 CATTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.26, T:0.57
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTTATGTTT
Found at i:3212331 original size:24 final size:24
Alignment explanation
Indices: 3212279--3212334 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
3212269 TGAACGTTCG
** *
3212279 GTTATGTTCGTTTATGTTTGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
3212303 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
3212327 TTTATGTT
1 GTTATGTT
3212335 TAACTCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.09, G:0.20, T:0.59
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:3213431 original size:16 final size:16
Alignment explanation
Indices: 3213410--3213476 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
3213400 GTCTCCAACG
3213410 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
**
3213426 TTTATGTTCGTGTTTG
1 TTTATGTTCGTGTTCA
*
3213442 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
3213458 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
3213472 TTTAT
1 TTTAT
3213477 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:3222039 original size:21 final size:21
Alignment explanation
Indices: 3221997--3222039 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3221987 TTTCTGGGCT
* * *
3221997 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
3222018 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
3222039 A
1 A
3222040 ACGAACAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:3222446 original size:19 final size:18
Alignment explanation
Indices: 3222411--3222460 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3222401 GAGTTTGTTA
**
3222411 TGATTATATGTGCTATAT
1 TGATTATATGTATTATAT
3222429 GTGATTATATGTATTATAT
1 -TGATTATATGTATTATAT
* *
3222448 TAATTGTATGTAT
1 TGATTATATGTAT
3222461 GCATGACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (18 bp):
TGATTATATGTATTATAT
Found at i:3223661 original size:23 final size:23
Alignment explanation
Indices: 3223627--3223694 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
3223617 CATCTTATAT
3223627 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
3223650 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
3223673 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
3223695 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3232247 original size:75 final size:74
Alignment explanation
Indices: 3232059--3232247 Score: 211
Period size: 74 Copynumber: 2.5 Consensus size: 74
3232049 TTTAATATTT
* * *
3232059 TTCTACACTTAATATTAT-GATTTCAATCTTAAGATTTGACACTTTAATATTATGGTTTGATTAT
1 TTCTAAACTTAATATTATAG-TTTGAATCTTAAGATTTGACACTTTAATATTATGATTTGATTAT
3232123 GGATTTACTA
65 GGATTTACTA
* * * * *
3232133 TTCTAGAGTTAATATTATGGTTTGAATCTTAAGATTTGACATTTTAATATTGTGATTT-ATTTAT
1 TTCTAAACTTAATATTATAGTTTGAATCTTAAGATTTGACACTTTAATATTATGATTTGA-TTAT
* *
3232197 GGATTTTATTG
65 GGA-TTTACTA
* * * *
3232208 TTCTAAACTTAATATTGTAGTTTGAGTCTTGATATTTGAC
1 TTCTAAACTTAATATTATAGTTTGAATCTTAAGATTTGAC
3232248 TTTATTTATA
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
73 1 0.01
74 57 0.59
75 39 0.40
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (74 bp):
TTCTAAACTTAATATTATAGTTTGAATCTTAAGATTTGACACTTTAATATTATGATTTGATTATG
GATTTACTA
Found at i:3232295 original size:19 final size:19
Alignment explanation
Indices: 3232250--3232291 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
3232240 TATTTGACTT
3232250 TATTTATAATTTTTAAATC
1 TATTTATAATTTTTAAATC
3232269 TATTTATAATTTTTAAAT-
1 TATTTATAATTTTTAAATC
3232287 TATTT
1 TATTT
3232292 TATATGTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATAATTTTTAAATC
Found at i:3232375 original size:12 final size:12
Alignment explanation
Indices: 3232360--3232404 Score: 90
Period size: 12 Copynumber: 3.8 Consensus size: 12
3232350 TCCCCGTCTC
3232360 CGTATCCGTCCT
1 CGTATCCGTCCT
3232372 CGTATCCGTCCT
1 CGTATCCGTCCT
3232384 CGTATCCGTCCT
1 CGTATCCGTCCT
3232396 CGTATCCGT
1 CGTATCCGT
3232405 ATCAGTGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.09, C:0.40, G:0.18, T:0.33
Consensus pattern (12 bp):
CGTATCCGTCCT
Found at i:3232379 original size:18 final size:19
Alignment explanation
Indices: 3232339--3232380 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3232329 TTTAAAAATT
* *
3232339 TCCGTTTCCTGTCCCCGTC
1 TCCGTATCCTGTCCCCGTA
*
3232358 TCCGTATCC-GTCCTCGTA
1 TCCGTATCCTGTCCCCGTA
3232376 TCCGT
1 TCCGT
3232381 CCTCGTATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.05, C:0.43, G:0.17, T:0.36
Consensus pattern (19 bp):
TCCGTATCCTGTCCCCGTA
Found at i:3244371 original size:21 final size:21
Alignment explanation
Indices: 3244347--3244405 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3244337 CGCAGTCGTT
3244347 TCAGATGGCACTGCAGCCATA
1 TCAGATGGCACTGCAGCCATA
* * *
3244368 TCAGATGGCACCGTAGCCATT
1 TCAGATGGCACTGCAGCCATA
* *
3244389 TCATATGCCACTGCAGC
1 TCAGATGGCACTGCAGC
3244406 TAGGTCAGAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (21 bp):
TCAGATGGCACTGCAGCCATA
Done.