Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 26
Found at i:3351806 original size:25 final size:27
Alignment explanation
Indices: 3351773--3351825 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
3351763 AACAAACAAT
*
3351773 TTTTCAAAAAAAT-TTA-ATTTCGAAA
1 TTTTAAAAAAAATATTAGATTTCGAAA
3351798 TTTTAAAAAAAATATTATGATTTCGAAA
1 TTTTAAAAAAAATATTA-GATTTCGAAA
3351826 ATTAGTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
28 9 0.38
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (27 bp):
TTTTAAAAAAAATATTAGATTTCGAAA
Found at i:3352966 original size:21 final size:21
Alignment explanation
Indices: 3352924--3352967 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3352914 ACTCCGGGAG
* *
3352924 CTAGTTCCTCACGAGTTGCTC
1 CTAGTTCCTCACGAGCTCCTC
* *
3352945 CTAGTTCCTCTCGTGCTCCTC
1 CTAGTTCCTCACGAGCTCCTC
3352966 CT
1 CT
3352968 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGTTCCTCACGAGCTCCTC
Found at i:3353531 original size:2 final size:2
Alignment explanation
Indices: 3353524--3353548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3353514 CAGCTTAAGC
3353524 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3353549 TTAATCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3357463 original size:15 final size:15
Alignment explanation
Indices: 3357440--3357478 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3357430 AATGAAATGC
*
3357440 AGATGCAAAATGTAA
1 AGATGCAAAATGCAA
*
3357455 AGATACAAAATGCAA
1 AGATGCAAAATGCAA
3357470 AGATGCAAA
1 AGATGCAAA
3357479 TGCTGATCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.15
Consensus pattern (15 bp):
AGATGCAAAATGCAA
Found at i:3359770 original size:32 final size:31
Alignment explanation
Indices: 3359716--3359805 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 31
3359706 AATGATGAAA
* *
3359716 AATG-ACACAATCAAAAGAAAATAAATAGGTT
1 AATGTACACAAACAAAAGGAAATAAATA-GTT
* * *
3359747 AGTGTACATAAACAAAAGGAAATAAATTATTT
1 AATGTACACAAACAAAAGGAAATAAA-TAGTT
*
3359779 AATGTACACAAACAAAAGGAAAGAAAT
1 AATGTACACAAACAAAAGGAAATAAAT
3359806 CATTTAATAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 4 0.08
32 43 0.88
33 2 0.04
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.20
Consensus pattern (31 bp):
AATGTACACAAACAAAAGGAAATAAATAGTT
Found at i:3359811 original size:32 final size:32
Alignment explanation
Indices: 3359749--3359813 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3359739 AATAGGTTAG
* * *
3359749 TGTACATAAACAAAAGGAAATAAATTATTTAA
1 TGTACACAAACAAAAGGAAAGAAATCATTTAA
3359781 TGTACACAAACAAAAGGAAAGAAATCATTTAA
1 TGTACACAAACAAAAGGAAAGAAATCATTTAA
3359813 T
1 T
3359814 ACAGGTGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (32 bp):
TGTACACAAACAAAAGGAAAGAAATCATTTAA
Found at i:3363414 original size:45 final size:44
Alignment explanation
Indices: 3363306--3363429 Score: 133
Period size: 45 Copynumber: 2.7 Consensus size: 44
3363296 GATGAACCAT
3363306 TATGCATTTTCATTTATGGCATTCTTTCATTGCCAATAATGCACTCA
1 TATGCATTTT-ATTTATGGCA-TCTTTCA-TGCCAATAATGCACTCA
* * * ** *
3363353 TATGTATTTCAATTATGGCATCATTTCATGCTGATAATGTA-TCTA
1 TATGCATTTTATTTATGGCATC-TTTCATGCCAATAATGCACTC-A
3363398 TATGCATTTTATTTATGGCATCCTTTCATGCC
1 TATGCATTTTATTTATGGCAT-CTTTCATGCC
3363430 CTTTTATACG
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
44 2 0.03
45 39 0.61
46 15 0.23
47 8 0.12
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (44 bp):
TATGCATTTTATTTATGGCATCTTTCATGCCAATAATGCACTCA
Found at i:3363493 original size:45 final size:46
Alignment explanation
Indices: 3363402--3363496 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 46
3363392 TATCTATATG
* *
3363402 CATTTTATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATA
1 CATTTCATTTATGGCATCCTTTCATGCCCTTTTATACACTATTATA
3363448 CATTTCATTTATGGCATCCTTTCATG-CCTTTTATACAAC-ATTATA
1 CATTTCATTTATGGCATCCTTTCATGCCCTTTTATAC-ACTATTATA
3363493 CATT
1 CATT
3363497 GTCACACATC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 20 0.43
46 26 0.57
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (46 bp):
CATTTCATTTATGGCATCCTTTCATGCCCTTTTATACACTATTATA
Found at i:3363910 original size:31 final size:30
Alignment explanation
Indices: 3363864--3363943 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
3363854 TTCAATAATA
*
3363864 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
3363895 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
3363926 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
3363944 TTTTTTAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.86
32 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:3363921 original size:19 final size:20
Alignment explanation
Indices: 3363897--3363946 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3363887 GATAAATTTA
*
3363897 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
3363916 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
3363937 TT-ATAATTTT
1 TTAATAATTTT
3363947 TTTAAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:3365282 original size:55 final size:55
Alignment explanation
Indices: 3365169--3365742 Score: 691
Period size: 55 Copynumber: 10.5 Consensus size: 55
3365159 TATATGGTAG
* ** *
3365169 TTCATCAACTCAGGATGAATTATGTGG-GTTGCACACATC-GTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACA-CAGTGCATGTACGGTTA
* * *
3365223 TTCATCAACTCATGATGAATTCCGTGGATTTGCATACACAATGCATGTACGGTTT
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACACAGTGCATGTACGGTTA
* * *
3365278 TTCATCAAATCATGATGAATTCCATGGATTTGCACACATAGTGTC-TGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACACAGTG-CATGTACGGTTA
* * *
3365333 TTCATCAACTCATGATGAATTTCGTGGATTTGCACAC-CTAGTGCCTGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACAC-AGTGCATGTACGGTTA
* * *
3365388 TTCATCAACTCATGATGAATTCTGTGGATTTGCACAC-CTAGTGTC-TATACGGATA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACAC-AGTG-CATGTACGGTTA
* *
3365443 TTCATCAACTCATGATGAATTCTGTGGATTTGCACACATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACACAGTGCATGTACGGTTA
* *
3365498 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACACAGTGCATGTACGGTTA
* * *
3365553 TTCATCAACTCATGATGAATTCCATGGATTTACACACATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACACAGTGCATGTACGGTTA
* * * * * *
3365608 TTAATCAACTCATGATGAATTTCGT-GAATTACACACATC-GTACCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACA-CAGTGCATGTACGGTTA
* * * * *
3365662 TTCATCAACTCATGATGAATTCTGTGGATTTGCACACATAGTTCCTGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACACAGTGCATGTACGGTTA
*
3365717 TTCATTC-ACAT-AGGATGAATTCCGTG
1 TTCA-TCAAC-TCATGATGAATTCCGTG
3365743 AAATGCACAC
Statistics
Matches: 459, Mismatches: 48, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
54 73 0.16
55 381 0.83
56 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCCGTGGATTTGCACACACAGTGCATGTACGGTTA
Found at i:3366255 original size:20 final size:21
Alignment explanation
Indices: 3366230--3366282 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
3366220 TATGTGATCA
3366230 ATGGTATCGATACCAT-CC-TC
1 ATGGTATCGATA-CATCCCTTC
3366250 ATGGTATCGATA-ATCCCTTC
1 ATGGTATCGATACATCCCTTC
*
3366270 TTGGTATCGATAC
1 ATGGTATCGATAC
3366283 TACTCAACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 25 0.86
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (21 bp):
ATGGTATCGATACATCCCTTC
Found at i:3368681 original size:2 final size:2
Alignment explanation
Indices: 3368674--3368712 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3368664 ATCATCAAGC
3368674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3368713 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3368961 original size:20 final size:20
Alignment explanation
Indices: 3368932--3369090 Score: 101
Period size: 20 Copynumber: 7.8 Consensus size: 20
3368922 ATTCGCACTG
*
3368932 CATTTAGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
3368952 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
3368973 AAAATCGCGTTGCGGTTTTC
1 CATTTCGCGTTGCGATTTTC
* *
3368993 CATTTCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGAT--TTTC
*
3369015 CA-GT-GTCGTTGCGATTTTC
1 CATTTCG-CGTTGCGATTTTC
* *
3369034 CATTTCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGAT--TTTC
* *
3369056 CA-GT-GTCGTTGTGATTTTC
1 CATTTCG-CGTTGCGATTTTC
3369075 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
3369091 AGTTTTAAAA
Statistics
Matches: 101, Mismatches: 27, Indels: 22
0.67 0.18 0.15
Matches are distributed among these distances:
19 8 0.08
20 50 0.50
21 35 0.35
22 8 0.08
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:3368995 original size:41 final size:41
Alignment explanation
Indices: 3368939--3369093 Score: 242
Period size: 41 Copynumber: 3.8 Consensus size: 41
3368929 CTGCATTTAG
* *
3368939 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGT-GT
*
3368980 CGTTGCGGTTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
3369021 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
*
3369062 CGTTGTGATTTTCCATTTCGCGTTGCGATAGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT
3369094 TTTAAAAAAA
Statistics
Matches: 107, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
40 1 0.01
41 105 0.98
42 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
Found at i:3369026 original size:21 final size:21
Alignment explanation
Indices: 3369000--3369066 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
3368990 TTCCATTTCG
3369000 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
3369021 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
3369039 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
3369062 CGTTG
1 CGTTG
3369067 TGATTTTCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 9 0.26
21 14 0.40
22 4 0.11
23 2 0.06
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:3369190 original size:6 final size:6
Alignment explanation
Indices: 3369179--3369240 Score: 82
Period size: 6 Copynumber: 11.3 Consensus size: 6
3369169 GACACGTATT
3369179 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-C-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3369224 ACC-CG ACC-CG ACC-CG AC
1 ACCACG ACCACG ACCACG AC
3369241 GGCGGCGCGC
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
4 3 0.05
5 21 0.38
6 31 0.56
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3369234 original size:15 final size:17
Alignment explanation
Indices: 3369183--3369240 Score: 79
Period size: 15 Copynumber: 3.6 Consensus size: 17
3369173 CGTATTACCA
3369183 CGACCACGACCACGACC
1 CGACCACGACCACGACC
3369200 ACGACCACGACCACGA-C
1 -CGACCACGACCACGACC
3369217 CGACC-CGACC-CGACC
1 CGACCACGACCACGACC
3369232 CGACC-CGAC
1 CGACCACGAC
3369241 GGCGGCGCGC
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.08
15 15 0.38
16 5 0.13
17 1 0.03
18 15 0.38
ACGTcount: A:0.28, C:0.53, G:0.19, T:0.00
Consensus pattern (17 bp):
CGACCACGACCACGACC
Found at i:3370092 original size:21 final size:21
Alignment explanation
Indices: 3370063--3370174 Score: 65
Period size: 21 Copynumber: 5.4 Consensus size: 21
3370053 CAAATGGAAA
*
3370063 ATCGTAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
3370084 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
* *
3370104 ACCGCAACGATACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
3370125 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
3370145 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
3370166 ATCGCAACG
1 ATCGCAACG
3370175 CGAAATGGAA
Statistics
Matches: 64, Mismatches: 17, Indels: 20
0.63 0.17 0.20
Matches are distributed among these distances:
19 6 0.09
20 22 0.34
21 30 0.47
22 6 0.09
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:3370113 original size:41 final size:41
Alignment explanation
Indices: 3370054--3370263 Score: 266
Period size: 41 Copynumber: 5.1 Consensus size: 41
3370044 AAATTATCGC
*
3370054 AAATGGAAAATCGTAACGACACTGTAGACTATCGCAACGCG
1 AAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCG
* *
3370095 AAATGGAAAACCGCAACGATACTGTAGACTATCGCAACGCG
1 AAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCG
3370136 AAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCG
1 AAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCG
* * * *
3370177 AAATGGAAAACCGCAAC-ACGATTTTCA-ACTATCACAACGCG
1 AAATGGAAAATCGCAACGAC-ACTGT-AGACTATCGCAACGCG
* * *
3370218 AAATGAAAAATCGCAACG-CGATTTTTA-ACTATCGCAACGCG
1 AAATGGAAAATCGCAACGAC-A-CTGTAGACTATCGCAACGCG
3370259 AAATG
1 AAATG
3370264 CAGCGCGAAT
Statistics
Matches: 153, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.01
41 146 0.95
42 5 0.03
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (41 bp):
AAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCG
Found at i:3370150 original size:20 final size:20
Alignment explanation
Indices: 3370084--3370238 Score: 75
Period size: 20 Copynumber: 7.6 Consensus size: 20
3370074 ACTGTAGACT
3370084 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
3370104 ACCGCAA--CGATACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
3370125 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
3370145 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
3370166 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * ** ** *
3370186 ACCGCAACACGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
* *
3370207 ATCACAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
3370227 ATCGCAACGCGA
1 ATCGCAACGCGA
3370239 TTTTTAACTA
Statistics
Matches: 94, Mismatches: 30, Indels: 22
0.64 0.21 0.15
Matches are distributed among these distances:
18 6 0.06
19 6 0.06
20 41 0.44
21 29 0.31
22 6 0.06
23 6 0.06
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:3371203 original size:60 final size:60
Alignment explanation
Indices: 3371079--3371203 Score: 133
Period size: 60 Copynumber: 2.1 Consensus size: 60
3371069 AGGGAGGAGC
* * * ** *
3371079 AAAGGAGGGCAAACAAGGAGGGAGCAGCTAGGGAGAGAAGGGCACCAGGAGCTGGGAAGC
1 AAAGGAGGGCAAACAAGGAAGGAGCAGATAGGGAGAGAAGGGCACCAAGAAATGGGAAGA
* * * * * **
3371139 AAAGGTGGTCAAACAAGGAAGGATCAGATAGGGAGTGAAGGGTACCAAGAAATGGGCCGA
1 AAAGGAGGGCAAACAAGGAAGGAGCAGATAGGGAGAGAAGGGCACCAAGAAATGGGAAGA
3371199 AAAGG
1 AAAGG
3371204 CGGAAGGAAT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.41, T:0.07
Consensus pattern (60 bp):
AAAGGAGGGCAAACAAGGAAGGAGCAGATAGGGAGAGAAGGGCACCAAGAAATGGGAAGA
Found at i:3371857 original size:2 final size:2
Alignment explanation
Indices: 3371850--3371877 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3371840 TATTAATAAT
3371850 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
3371878 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3373223 original size:57 final size:57
Alignment explanation
Indices: 3373160--3373274 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
3373150 TTCTGGGTGC
3373160 ACACTTTAAAGTCATTGATTAGTAACCCTTTTATATAATTTCGATAATGACCCAAAT
1 ACACTTTAAAGTCATTGATTAGTAACCCTTTTATATAATTTCGATAATGACCCAAAT
3373217 ACACTTTAAAGTCATTGATTAGTAACCCTTTTATATAATTTCGATAATGACCCAAAT
1 ACACTTTAAAGTCATTGATTAGTAACCCTTTTATATAATTTCGATAATGACCCAAAT
3373274 A
1 A
3373275 TTATTTTAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (57 bp):
ACACTTTAAAGTCATTGATTAGTAACCCTTTTATATAATTTCGATAATGACCCAAAT
Found at i:3382189 original size:113 final size:113
Alignment explanation
Indices: 3381991--3382217 Score: 454
Period size: 113 Copynumber: 2.0 Consensus size: 113
3381981 TTTGATTAAA
3381991 CATGTATTTTAAATCTCACATGTGTAGGGCCCGAATTTGTCTGACCATATTAATGGTAATGGAGA
1 CATGTATTTTAAATCTCACATGTGTAGGGCCCGAATTTGTCTGACCATATTAATGGTAATGGAGA
3382056 GGCAATCAAGAGAGCTGCTTCAAGTATGATTCGGACCCATAGTATATC
66 GGCAATCAAGAGAGCTGCTTCAAGTATGATTCGGACCCATAGTATATC
3382104 CATGTATTTTAAATCTCACATGTGTAGGGCCCGAATTTGTCTGACCATATTAATGGTAATGGAGA
1 CATGTATTTTAAATCTCACATGTGTAGGGCCCGAATTTGTCTGACCATATTAATGGTAATGGAGA
3382169 GGCAATCAAGAGAGCTGCTTCAAGTATGATTCGGACCCATAGTATATC
66 GGCAATCAAGAGAGCTGCTTCAAGTATGATTCGGACCCATAGTATATC
3382217 C
1 C
3382218 GGTGACCTAC
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (113 bp):
CATGTATTTTAAATCTCACATGTGTAGGGCCCGAATTTGTCTGACCATATTAATGGTAATGGAGA
GGCAATCAAGAGAGCTGCTTCAAGTATGATTCGGACCCATAGTATATC
Found at i:3387277 original size:29 final size:28
Alignment explanation
Indices: 3387238--3387307 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
3387228 TAAGTTTCGG
* * *
3387238 GGGTTTGTGATTGAGGGTTATGAGTTTTA
1 GGGTTTATGATTAAGGG-TATGAATTTTA
* *
3387267 GTGTTTATGATTTAAGGGTGTGAATTTTA
1 GGGTTTATGA-TTAAGGGTATGAATTTTA
3387296 GGGTTTATGATT
1 GGGTTTATGATT
3387308 TAAGAACATC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 2 0.06
29 26 0.76
30 6 0.18
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (28 bp):
GGGTTTATGATTAAGGGTATGAATTTTA
Found at i:3387308 original size:15 final size:15
Alignment explanation
Indices: 3387238--3387308 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
3387228 TAAGTTTCGG
* *
3387238 GGGTTTGTGA-TTGA
1 GGGTTTATGATTTTA
3387252 GGG-TTATGAGTTTTA
1 GGGTTTATGA-TTTTA
* *
3387267 GTGTTTATGATTTAA
1 GGGTTTATGATTTTA
*
3387282 GGG--TGTGAATTTTA
1 GGGTTTATG-ATTTTA
3387296 GGGTTTATGATTT
1 GGGTTTATGATTT
3387309 AAGAACATCT
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
13 8 0.19
14 11 0.26
15 15 0.35
16 9 0.21
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (15 bp):
GGGTTTATGATTTTA
Found at i:3387497 original size:45 final size:45
Alignment explanation
Indices: 3387433--3387521 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
3387423 GACTATCACT
3387433 TGTCAATCACCTACTACCCAATGAGCATTTCCCGATACGATCTCG
1 TGTCAATCACCTACTACCCAATGAGCATTTCCCGATACGATCTCG
*
3387478 TGTCAATCACCTACTACCCAATGAGCATTTCCTGATACGATCTC
1 TGTCAATCACCTACTACCCAATGAGCATTTCCCGATACGATCTC
3387522 TGACGATCAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.28
Consensus pattern (45 bp):
TGTCAATCACCTACTACCCAATGAGCATTTCCCGATACGATCTCG
Found at i:3391468 original size:58 final size:59
Alignment explanation
Indices: 3391335--3391473 Score: 149
Period size: 59 Copynumber: 2.4 Consensus size: 59
3391325 AACATAATGA
* *
3391335 ATAGTCGGTGATCATTTTGTAACTTTTAATAGTCGAGGGACTCAATAAAACAACTCCTT
1 ATAGTCGGGGATCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACTCCTT
* * * * * *
3391394 ATAGTTGAGAATCATTTTGTAACTTTTAATAGTC-AGGGATTTAACAAAGCAGTA-T-CTT
1 ATAGTCGGGGATCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACA--ACTCCTT
*
3391452 ATAGTCGGGGACCATTTGTGTA
1 ATAGTCGGGGATCATTT-TGTA
3391474 TTTTACCCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
58 29 0.45
59 35 0.54
60 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (59 bp):
ATAGTCGGGGATCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACTCCTT
Found at i:3391627 original size:44 final size:46
Alignment explanation
Indices: 3391545--3391631 Score: 115
Period size: 44 Copynumber: 1.9 Consensus size: 46
3391535 ATAATCACGC
* * *
3391545 TTTATATAAATATAATTTTTTAAATAGTCTATGGTGATTATAATGT
1 TTTATATAAATATAATTTTTTAAATAATATAAGGTGATTATAATGT
* *
3391591 TTTATAT-AA-ATAGTTTTTTAAATAATATAAGTTGATTATAA
1 TTTATATAAATATAATTTTTTAAATAATATAAGGTGATTATAA
3391632 GATAGTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 27 0.75
45 2 0.06
46 7 0.19
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.49
Consensus pattern (46 bp):
TTTATATAAATATAATTTTTTAAATAATATAAGGTGATTATAATGT
Found at i:3391978 original size:22 final size:23
Alignment explanation
Indices: 3391930--3391983 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
3391920 AAATTTAGTG
* *
3391930 TTAATTATTATTATTTATATCATA
1 TTAA-TATTATTATTAATATCACA
3391954 TT-ATATTATTATATAATAT-ACA
1 TTAATATTATTAT-TAATATCACA
3391976 TTAATATT
1 TTAATATT
3391984 TACGTAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 13 0.50
23 11 0.42
24 2 0.08
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATATTATTATTAATATCACA
Found at i:3395595 original size:24 final size:25
Alignment explanation
Indices: 3395568--3395621 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
3395558 TAGTAATAAT
*
3395568 TAAAAAATAAT-AAACATCTTTTTA
1 TAAAAAATAATAAAACAACTTTTTA
*
3395592 T-AAATATAATAAAACAACTTTTTA
1 TAAAAAATAATAAAACAACTTTTTA
3395616 -AAAAAA
1 TAAAAAA
3395622 CATATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAAAAATAATAAAACAACTTTTTA
Found at i:3395918 original size:21 final size:21
Alignment explanation
Indices: 3395867--3395919 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3395857 ATTATGACTA
3395867 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
3395888 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
3395909 TCGCAATGCGA
1 TCGCAATGCGA
3395920 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:3395934 original size:20 final size:21
Alignment explanation
Indices: 3395909--3395960 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3395899 TTTTCCCAAT
*
3395909 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3395929 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3395950 TCGCAATGCGA
1 TCGCAATGCGA
3395961 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3395973 original size:41 final size:41
Alignment explanation
Indices: 3395946--3396023 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
3395936 GCGAATTGGG
*
3395946 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
3395987 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
3396024 CTGACTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3395974 original size:20 final size:20
Alignment explanation
Indices: 3395949--3396036 Score: 106
Period size: 20 Copynumber: 4.3 Consensus size: 20
3395939 AATTGGGAAA
*
3395949 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
3395969 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
3395990 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3396010 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3396030 TTCGCAA
1 ATCGCAA
3396037 TGAGATAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.03
20 40 0.68
21 15 0.25
22 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3396043 original size:20 final size:20
Alignment explanation
Indices: 3395991--3396043 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3395981 TAATACAAAA
*
3395991 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
*
3396011 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
*
3396031 TCGCAATGAGATA
1 TCGCAACGAGATA
3396044 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:3396568 original size:20 final size:20
Alignment explanation
Indices: 3396514--3396572 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3396504 TTTATTCTCT
**
3396514 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
3396534 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
3396554 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
3396573 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:3397906 original size:18 final size:18
Alignment explanation
Indices: 3397885--3397932 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3397875 TCCACTTCGG
3397885 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
3397903 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3397921 GAGCCATCACCT
1 GAGCCATCACCT
3397933 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3398532 original size:19 final size:19
Alignment explanation
Indices: 3398510--3398592 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
3398500 TCAAATGGCT
*
3398510 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3398529 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3398543 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3398562 ATCACAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3398581 ATCGCAATGCGA
1 ATCGCAATGCGA
3398593 TTTGTGTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 37 0.71
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3398623 original size:14 final size:14
Alignment explanation
Indices: 3398604--3398662 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3398594 TTGTGTTTCG
3398604 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3398618 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
3398635 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3398651 CGTTGCGATTTT
1 CGTTGCGATTTT
3398663 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3398636 original size:33 final size:33
Alignment explanation
Indices: 3398599--3398681 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
3398589 GCGATTTGTG
*
3398599 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
3398632 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
3398665 TTTCGCATTGCAATTTT
1 TTTCGCATTGCGATTTT
3398682 CATTTCGCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:3398644 original size:19 final size:19
Alignment explanation
Indices: 3398620--3398697 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
3398610 GATTTTGTCG
3398620 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3398639 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
3398653 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
3398672 TTGCAATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3398691 TTGCGAT
1 TTGCGAT
3398698 AGCCATTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 29 0.59
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3398734 original size:21 final size:21
Alignment explanation
Indices: 3398704--3398744 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3398694 CGATAGCCAT
3398704 TTTCGCGTTGCGAAAGTAAAG
1 TTTCGCGTTGCGAAAGTAAAG
*
3398725 TTTCGTGTTGCGAAAGTAAA
1 TTTCGCGTTGCGAAAGTAAA
3398745 CTATTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (21 bp):
TTTCGCGTTGCGAAAGTAAAG
Found at i:3399102 original size:21 final size:20
Alignment explanation
Indices: 3399076--3399144 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
3399066 CTGTCATCCC
3399076 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
3399097 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
3399118 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
3399138 TCAAGAG
1 TCAAGAG
3399145 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:3399156 original size:41 final size:42
Alignment explanation
Indices: 3399066--3399156 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
3399056 CCCGACTCAC
* *
3399066 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
3399108 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
3399149 CTGTCATC
1 CTGTCATC
3399157 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:3400602 original size:14 final size:14
Alignment explanation
Indices: 3400568--3400606 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3400558 TTGATTGTTT
3400568 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3400582 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
3400596 TGTTGATTTGT
1 AATTGATTTGT
3400607 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3400752 original size:14 final size:14
Alignment explanation
Indices: 3400733--3400786 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
3400723 GAAACTGACT
*
3400733 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
3400747 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
3400766 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3400780 ATCGCAA
1 ATCGCAA
3400787 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:3400770 original size:19 final size:17
Alignment explanation
Indices: 3400746--3400791 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
3400736 GCAACGAGAG
3400746 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
3400765 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
3400779 AATCGCAATGCGA
1 AATCGCAATGCGA
3400792 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:3403030 original size:12 final size:12
Alignment explanation
Indices: 3403013--3403037 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3403003 TCTTCGGGGA
3403013 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3403025 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3403037 C
1 C
3403038 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3403246 original size:24 final size:24
Alignment explanation
Indices: 3403212--3403265 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3403202 CTGAAACATC
*
3403212 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
3403236 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3403260 ATCAAA
1 ATCAAA
3403266 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3404039 original size:20 final size:20
Alignment explanation
Indices: 3404016--3404162 Score: 172
Period size: 20 Copynumber: 7.3 Consensus size: 20
3404006 TATTATCTCA
* *
3404016 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGTATCGCG
* *
3404036 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCAGTATCGCG
*
3404056 TTGCGAAAGTCAGTATCGCG
1 TTGCGATAGTCAGTATCGCG
*
3404076 TTGCGAAAGTCAGTATCGCG
1 TTGCGATAGTCAGTATCGCG
* *
3404096 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--TAGTCAGTATCGCG
*
3404117 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCG
3404137 TTGCGATAGTCA-TAATCGCG
1 TTGCGATAGTCAGT-ATCGCG
3404157 TTGCGA
1 TTGCGA
3404163 ATCTGGAAAC
Statistics
Matches: 113, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
19 4 0.04
20 93 0.82
21 14 0.12
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCG
Found at i:3405388 original size:29 final size:29
Alignment explanation
Indices: 3405355--3405437 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
3405345 CTGAAAATGG
* *
3405355 AGGTCGCCATGTATGTCGGGCGGCCTTAT
1 AGGTCGCCATGTATGCCGGGCGACCTTAT
*
3405384 AGGTCACCATGTATGCCGGGCGACCTTAT
1 AGGTCGCCATGTATGCCGGGCGACCTTAT
*
3405413 AGGTCGCCATGTGAT-CCCGGCGACC
1 AGGTCGCCATGT-ATGCCGGGCGACC
3405438 AAACCTGCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTATGCCGGGCGACCTTAT
Found at i:3411688 original size:20 final size:20
Alignment explanation
Indices: 3411642--3411688 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3411632 GATACCTTTA
*
3411642 GAAAATAGAAGGCCATAATG
1 GAAAATGGAAGGCCATAATG
* *
3411662 GAAAATGGAATGCCATAGTG
1 GAAAATGGAAGGCCATAATG
3411682 GAAAATG
1 GAAAATG
3411689 AGACTGATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.17
Consensus pattern (20 bp):
GAAAATGGAAGGCCATAATG
Found at i:3414233 original size:18 final size:18
Alignment explanation
Indices: 3414207--3414295 Score: 160
Period size: 18 Copynumber: 4.9 Consensus size: 18
3414197 GTTCAGTATT
3414207 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3414225 TGCCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3414243 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3414261 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3414279 CGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3414296 GGATACGTCC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.27, C:0.36, G:0.22, T:0.15
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3418437 original size:18 final size:18
Alignment explanation
Indices: 3418414--3418511 Score: 153
Period size: 18 Copynumber: 5.3 Consensus size: 18
3418404 CCAGTAATTC
3418414 TATTCCCTGGTAATCTTT
1 TATTCCCTGGTAATCTTT
3418432 TATTCCCTGGTAATCTTT
1 TATTCCCTGGTAATCTTT
3418450 TATTCCCTGGTAATCTTT
1 TATTCCCTGGTAATCTTT
*
3418468 TATTCCCTAGTAATCTTT
1 TATTCCCTGGTAATCTTT
3418486 TATTCCCACTGGTAAT-TTT
1 TATT-CC-CTGGTAATCTTT
3418505 ATATTCC
1 -TATTCC
3418512 GTGAACCAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
18 57 0.76
19 7 0.09
20 11 0.15
ACGTcount: A:0.19, C:0.22, G:0.09, T:0.49
Consensus pattern (18 bp):
TATTCCCTGGTAATCTTT
Found at i:3425879 original size:35 final size:35
Alignment explanation
Indices: 3425803--3425880 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
3425793 TTAAATACAG
*
3425803 CAAACTTACAATAAGAATTAAATGGTAAATGATAA
1 CAAAATTACAATAAGAATTAAATGGTAAATGATAA
*
3425838 CCAAATTACAATAACTGATATTAAATGGT-AAT-A-AA
1 CAAAATTACAATAA--GA-ATTAAATGGTAAATGATAA
3425873 CAAAATTA
1 CAAAATTA
3425881 ACTGAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 21 0.57
36 1 0.03
37 5 0.14
38 10 0.27
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (35 bp):
CAAAATTACAATAAGAATTAAATGGTAAATGATAA
Found at i:3426105 original size:3 final size:3
Alignment explanation
Indices: 3426099--3426157 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
3426089 GCTGTCATCA
* * * * * *
3426099 TCG TCG TCG TCG TCG TCG TCG TCA CCG TCA TCA TCG TCA TCG TCA TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
3426147 TCG TCG TCG TC
1 TCG TCG TCG TC
3426158 CTGAGCATGT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.08, C:0.36, G:0.24, T:0.32
Consensus pattern (3 bp):
TCG
Found at i:3428044 original size:111 final size:111
Alignment explanation
Indices: 3427907--3428128 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
3427897 ATTACAAAAA
*
3427907 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAATTATCACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATCACTAATAATTTAAATTA
* *
3427972 AATTAAAACGTTAAAATATTACCTTATCAGCAAAGTATCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTATAGAGATAT
* *
3428018 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATCACTAATAATTTAAATTA
* *
3428083 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTATAGAGATAT
3428129 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATCACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTATAGAGATAT
Found at i:3428800 original size:20 final size:20
Alignment explanation
Indices: 3428777--3428828 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3428767 AACGCGATCC
3428777 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
3428797 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
3428817 CCAAAATCGCAA
1 CCAGAATCGCAA
3428829 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:3428845 original size:21 final size:20
Alignment explanation
Indices: 3428818--3428916 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
3428808 AATCAGTTTC
3428818 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3428839 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3428860 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3428880 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3428901 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3428917 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3428945 original size:20 final size:20
Alignment explanation
Indices: 3428883--3429076 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3428873 CGATTTTCCA
* ** *
3428883 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3428903 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3428923 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3428943 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3428963 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3428983 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3429003 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
3429023 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
3429043 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
3429064 AAATCGCAACGCG
1 AAATCGCAACGCG
3429077 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3428967 original size:60 final size:60
Alignment explanation
Indices: 3428883--3429076 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3428873 CGATTTTCCA
* ** * *
3428883 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
3428943 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
3429003 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
3429064 AAATCGCAACGCG
1 AAATCGCAACGCG
3429077 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:3429498 original size:33 final size:33
Alignment explanation
Indices: 3429459--3429529 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3429449 TTCACTTAGA
*
3429459 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3429492 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3429525 TTTCA
1 TTTCA
3429530 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3429669 original size:14 final size:14
Alignment explanation
Indices: 3429650--3429704 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3429640 AGAATGACTG
3429650 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
3429664 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
3429683 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3429697 TCGCAACG
1 TCGCAACG
3429705 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:3429717 original size:33 final size:33
Alignment explanation
Indices: 3429650--3429720 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3429640 AGAATGACTG
***
3429650 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3429683 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3429716 TCGCA
1 TCGCA
3429721 TTGCGATTTT
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:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:3429738 original size:19 final size:19
Alignment explanation
Indices: 3429716--3429813 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3429706 GAAACCAAAA
*
3429716 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3429735 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3429749 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3429768 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3429782 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
3429801 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3429814 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3429757 original size:14 final size:14
Alignment explanation
Indices: 3429738--3429827 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3429728 TTTCATTTCG
3429738 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3429752 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3429771 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3429785 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
3429802 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
3429818 CGTTGCGATT
1 CGTTGCGATT
3429828 TTCATTTCAA
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:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3429763 original size:33 final size:33
Alignment explanation
Indices: 3429721--3429835 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3429711 CAAAATCGCA
3429721 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3429754 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3429787 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3429820 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3429836 AACCAAAAGA
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:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3431263 original size:18 final size:18
Alignment explanation
Indices: 3431240--3431285 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
3431230 GATGCTTTAA
3431240 CACTTAGATTAGCCATTT
1 CACTTAGATTAGCCATTT
3431258 CACTTAGATTAGCCATTT
1 CACTTAGATTAGCCATTT
3431276 CACTTAGATT
1 CACTTAGATT
3431286 GCTTAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
CACTTAGATTAGCCATTT
Found at i:3431408 original size:93 final size:93
Alignment explanation
Indices: 3431290--3431669 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
3431280 TAGATTGCTT
*
3431290 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3431355 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3431383 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3431447 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3431475 AGTAAATTTGTTCGGTTGCTGCCAATCCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3431540 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3431568 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3431633 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3431661 AGTAAATTT
1 AGTAAATTT
3431670 ATCCATTCAA
Statistics
Matches: 283, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.32
93 192 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3431602 original size:185 final size:186
Alignment explanation
Indices: 3431290--3431671 Score: 739
Period size: 185 Copynumber: 2.1 Consensus size: 186
3431280 TAGATTGCTT
*
3431290 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATCCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3431355 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3431420 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3431475 AGTAAATTTGTTCGGTTGCTGCCAATCCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATCCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3431540 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3431605 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3431661 AGTAAATTTAT
1 AGTAAATTTAT
3431672 CCATTCAAGT
Statistics
Matches: 193, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
185 153 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATCCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3431753 original size:19 final size:19
Alignment explanation
Indices: 3431713--3431841 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3431703 TAGTTTACTT
* *
3431713 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3431733 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3431752 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3431771 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3431785 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3431804 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3431818 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3431837 TCGCA
1 TCGCA
3431842 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3431792 original size:33 final size:32
Alignment explanation
Indices: 3431749--3431841 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
3431739 CGCGAAACCA
**
3431749 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3431781 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3431814 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3431842 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3431839 original size:52 final size:52
Alignment explanation
Indices: 3431713--3431841 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
3431703 TAGTTTACTT
**
3431713 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
3431765 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
3431818 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
3431842 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:3431859 original size:19 final size:19
Alignment explanation
Indices: 3431837--3431971 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
3431827 GAAACCAAAA
*
3431837 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3431856 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3431872 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3431889 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3431905 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3431922 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3431941 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3431961 TCGTGTTGCGA
1 TCGCGTTGCGA
3431972 AAGTAAACTA
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:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3431878 original size:14 final size:14
Alignment explanation
Indices: 3431859--3431915 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3431849 TTTCATTTCG
3431859 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3431873 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3431890 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
3431906 CGTTGCGATT
1 CGTTGCGATT
3431916 TTCATTTCGC
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:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3431884 original size:33 final size:33
Alignment explanation
Indices: 3431842--3431934 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
3431832 CAAAATCGCA
*
3431842 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3431875 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3431908 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3431935 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3433832 original size:38 final size:38
Alignment explanation
Indices: 3433789--3433861 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
3433779 AATTGATTGT
*
3433789 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
3433827 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
3433862 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:3433848 original size:19 final size:19
Alignment explanation
Indices: 3433784--3433848 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
3433774 AGTTTAATTG
*
3433784 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
3433803 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
3433821 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
3433841 ATTGATTT
1 ATTGATTT
3433849 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:3433862 original size:14 final size:14
Alignment explanation
Indices: 3433843--3433878 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3433833 ATTGTTTAAT
3433843 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3433857 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3433871 TGATTTGT
1 TGATTTGT
3433879 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3434001 original size:19 final size:19
Alignment explanation
Indices: 3433985--3434086 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3433975 AAAAATGACT
3433985 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3434004 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3434023 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3434037 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3434056 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3434076 ATCGCAATGCG
1 ATCGCAATGCG
3434087 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3434143 original size:19 final size:19
Alignment explanation
Indices: 3434115--3434440 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
3434105 GATTATCTCG
3434115 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3434134 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3434153 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3434167 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3434186 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3434205 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
3434224 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
3434243 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3434262 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3434276 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3434295 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3434314 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3434328 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3434347 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3434366 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3434380 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3434400 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3434414 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3434433 TTGCGATT
1 TTGCGATT
3434441 GTATTTTCCG
Statistics
Matches: 267, Mismatches: 14, Indels: 52
0.80 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 158 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3434155 original size:52 final size:52
Alignment explanation
Indices: 3434093--3434412 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
3434083 TGCGTTTATA
* *
3434093 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGTGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3434145 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
3434197 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
3434254 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
3434306 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
3434358 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
3434411 AT
1 AT
3434413 GTTGGGATTT
Statistics
Matches: 256, Mismatches: 6, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 181 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3434190 original size:71 final size:72
Alignment explanation
Indices: 3434115--3434440 Score: 380
Period size: 71 Copynumber: 4.6 Consensus size: 72
3434105 GATTATCTCG
*
3434115 TTGCGATTTTCATTTCGCATTGTGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
3434179 TTTCGCA
66 TTTCGCA
* *
3434186 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
3434251 TTCATTTCGCA
62 TTCATTTCGCA
*
3434262 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
3434320 TTC-TCTCG--
62 TTCATTTCGCA
*
3434328 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
3434392 TTTCCGCA
66 TTT-CGCA
* *
3434400 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
3434441 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 12, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 108 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.48
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:3434358 original size:161 final size:157
Alignment explanation
Indices: 3434093--3434412 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 157
3434083 TGCGTTTATA
*
3434093 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGTGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
3434158 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
3434223 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
3434254 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
3434319 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
3434384 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
3434411 AT
1 AT
3434413 GTTGGGATTT
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 115 0.75
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:3434384 original size:33 final size:33
Alignment explanation
Indices: 3434138--3434440 Score: 272
Period size: 33 Copynumber: 8.7 Consensus size: 33
3434128 TTCGCATTGT
*
3434138 GATTTTCATTTCGCATTGCGATTCTTTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
3434171 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGC
* * *
3434209 GATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGA--TT-CTCTCG--TTGC
3434247 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
3434280 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGC
* * * * *
3434318 GATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGC
1 GATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGC
3434351 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
* *
3434384 GATTTTCATTTCCGCATTGCGATTTTCAT-GTTGG
1 GATTTTCATTT-CGCATTGCGATTCTC-TCGTTGC
*
3434418 GATTTTCATTTCGCGTTGCGATT
1 GATTTTCATTTCGCATTGCGATT
3434441 GTATTTTCCG
Statistics
Matches: 231, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 83 0.36
34 29 0.13
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
Found at i:3436763 original size:12 final size:12
Alignment explanation
Indices: 3436746--3436770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3436736 TCTTCGGGGA
3436746 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3436758 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3436770 C
1 C
3436771 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3436979 original size:24 final size:24
Alignment explanation
Indices: 3436945--3436991 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3436935 CTGAAACATC
3436945 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3436969 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3436992 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3437693 original size:20 final size:20
Alignment explanation
Indices: 3437665--3438033 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
3437655 AAATTTCAGT
* * * *
3437665 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3437685 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3437705 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3437725 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3437745 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3437765 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3437785 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3437805 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3437825 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3437845 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
3437865 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3437885 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3437905 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
3437925 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
3437945 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3437965 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3437985 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
3438005 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
3438025 GTTGCGATT
1 GTTGCGATT
3438034 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3450989 original size:42 final size:43
Alignment explanation
Indices: 3450879--3450998 Score: 161
Period size: 44 Copynumber: 2.8 Consensus size: 43
3450869 GACATTCTAT
*
3450879 ACACTGATCGCATATACAGATTACTTGTGAAACATTCTATACGC
1 ACACTGATCGCATATACAGATTACTTGTGAAACATTCCATAC-C
* *
3450923 ACACTGATCGCATATGCAAATTACTTGTGAAACATTCCATA-C
1 ACACTGATCGCATATACAGATTACTTGTGAAACATTCCATACC
* * * *
3450965 ACACTGATCCCGTATACAGGTTACTTGTAAAACA
1 ACACTGATCGCATATACAGATTACTTGTGAAACA
3450999 GCCGGTGCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 29 0.43
44 38 0.57
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (43 bp):
ACACTGATCGCATATACAGATTACTTGTGAAACATTCCATACC
Found at i:3481254 original size:9 final size:9
Alignment explanation
Indices: 3481240--3481275 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3481230 TTTAATATTT
3481240 TGTATTTAA
1 TGTATTTAA
*
3481249 TTTATTTAA
1 TGTATTTAA
3481258 -GTATTTAA
1 TGTATTTAA
3481266 TGTATTTAA
1 TGTATTTAA
3481275 T
1 T
3481276 ATTTTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
TGTATTTAA
Found at i:3481281 original size:17 final size:17
Alignment explanation
Indices: 3481241--3481279 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3481231 TTAATATTTT
*
3481241 GTATTTAATTTATTTAA
1 GTATTTAATGTATTTAA
3481258 GTATTTAATGTATTTAA
1 GTATTTAATGTATTTAA
3481275 -TATTT
1 GTATTT
3481280 TACTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (17 bp):
GTATTTAATGTATTTAA
Found at i:3483634 original size:33 final size:33
Alignment explanation
Indices: 3483593--3483662 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
3483583 ACTTACTTTA
3483593 ATTTGTT-AATATGGTTGGATTTATT-TTAATTT
1 ATTTGTTAAAT-TGGTTGGATTTATTGTTAATTT
* *
3483625 ATTTCGTTAAATTTGTTGGATTTTTTGTTAATTT
1 ATTT-GTTAAATTGGTTGGATTTATTGTTAATTT
3483659 ATTT
1 ATTT
3483663 TGCTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 4 0.12
33 15 0.45
34 14 0.42
ACGTcount: A:0.23, C:0.01, G:0.14, T:0.61
Consensus pattern (33 bp):
ATTTGTTAAATTGGTTGGATTTATTGTTAATTT
Found at i:3483661 original size:34 final size:34
Alignment explanation
Indices: 3483606--3483676 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
3483596 TGTTAATATG
3483606 GTTGGATTTATTTTAATTTATTTCG-TTAAATTT
1 GTTGGATTTATTTTAATTTATTTCGCTTAAATTT
* * *
3483639 GTTGGATTTTTTGTTAATTTATTTTGCTTAATTTT
1 GTTGGATTTATT-TTAATTTATTTCGCTTAAATTT
3483674 GTT
1 GTT
3483677 TATTACCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 11 0.33
34 12 0.36
35 10 0.30
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (34 bp):
GTTGGATTTATTTTAATTTATTTCGCTTAAATTT
Found at i:3484753 original size:17 final size:17
Alignment explanation
Indices: 3484731--3484767 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3484721 AGTTTAAAAG
3484731 TGCGACAATATTATATC
1 TGCGACAATATTATATC
3484748 TGCGACAATATTATATC
1 TGCGACAATATTATATC
3484765 TGC
1 TGC
3484768 AAAAAAAACA
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:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (17 bp):
TGCGACAATATTATATC
Found at i:3488614 original size:138 final size:137
Alignment explanation
Indices: 3488353--3488695 Score: 345
Period size: 138 Copynumber: 2.5 Consensus size: 137
3488343 GTTGCCATTT
* * * *
3488353 CAAGT-CTTTGTCCTCTTGATGAATCAGGTTTGGCATCTTTCGTTTTGAAGTCACTGATCGTCTT
1 CAAGTCCTTT-TCCTCTTGATGAATCAGGTTTGACATCCTTCATTTTGAAGTCACTGATTGTCTT
* * * * *
3488417 TCCCTTAGCATCTTCATACATAGGAACCGGAGGACTTTTCACATATCACTTTCCGAAGTTCCTAA
65 TCCCTCAACATCTTCACACATAGGAACCGGAGGACTTTTCACATATCAC-TTCCAAAGTTCCCAA
3488482 TTCCAAATC
129 TTCCAAATC
* * * *
3488491 GAATTCCTTTTCCTCTTGATGAATCAGATTTGACATCCTTCATTTTAAAGTCACTGATTGTCTTT
1 CAAGTCCTTTTCCTCTTGATGAATCAGGTTTGACATCCTTCATTTTGAAGTCACTGATTGTCTTT
* * * ** * * *
3488556 TCCTCAACATGTTCACACGTAGGAATTGGAGGATTTTTCACATTTTCCAAC-T-CAAAGTTCCCG
66 CCCTCAACATCTTCACACATAGGAACCGGAGGACTTTTCACA-TAT-C-ACTTCCAAAGTTCCCA
* *
3488619 GTTCCAAGTC
128 ATTCCAAATC
* * * *
3488629 CAAGTCCTTGTT--TGTTACATGAATCAGGTCTGACATCCTTCATTTTGAAGTCAGTGATTGTCT
1 CAAGTCCTT-TTCCTCTT-GATGAATCAGGTTTGACATCCTTCATTTTGAAGTCACTGATTGTCT
3488692 TTCC
64 TTCC
3488696 ATCAGCCTGA
Statistics
Matches: 167, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
137 3 0.02
138 152 0.91
139 9 0.05
140 1 0.01
141 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (137 bp):
CAAGTCCTTTTCCTCTTGATGAATCAGGTTTGACATCCTTCATTTTGAAGTCACTGATTGTCTTT
CCCTCAACATCTTCACACATAGGAACCGGAGGACTTTTCACATATCACTTCCAAAGTTCCCAATT
CCAAATC
Found at i:3490603 original size:23 final size:22
Alignment explanation
Indices: 3490556--3490604 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3490546 AACATCTCTA
*
3490556 TTCATGAAAATAGTTAAGTTTT
1 TTCATGAAAATAGTTAAGTTAT
3490578 TTCATGAAAATTAGTTAA-TTCAT
1 TTCATGAAAA-TAGTTAAGTT-AT
3490601 TTCA
1 TTCA
3490605 CCCAAAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (22 bp):
TTCATGAAAATAGTTAAGTTAT
Found at i:3493468 original size:25 final size:25
Alignment explanation
Indices: 3493431--3493481 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
3493421 TCGAGAGTGA
3493431 AATTGATTACATCATGCAAAATCAT
1 AATTGATTACATCATGCAAAATCAT
* *
3493456 AATTGATTCCATCATGTAAAATCAT
1 AATTGATTACATCATGCAAAATCAT
3493481 A
1 A
3493482 TGTGGGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (25 bp):
AATTGATTACATCATGCAAAATCAT
Found at i:3497215 original size:8 final size:7
Alignment explanation
Indices: 3497153--3497213 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
3497143 TATTTTAAAA
*
3497153 TTTAAAT
1 TTTAATT
*
3497160 TTAAATT
1 TTTAATT
3497167 TTTATATT
1 TTTA-ATT
*
3497175 TATAATT
1 TTTAATT
3497182 TATT-ATT
1 T-TTAATT
*
3497189 TTATAACT
1 TT-TAATT
3497197 TTTAATT
1 TTTAATT
3497204 TTTAATT
1 TTTAATT
3497211 TTT
1 TTT
3497214 TACTTAAAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
6 1 0.02
7 31 0.72
8 11 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTAATT
Found at i:3501820 original size:21 final size:21
Alignment explanation
Indices: 3501791--3501832 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3501781 CATCGTCTGT
*
3501791 CGCCACTCGATCTCCTTCGAC
1 CGCCACTCGATCTCCCTCGAC
* *
3501812 CGCCGCTCGTTCTCCCTCGAC
1 CGCCACTCGATCTCCCTCGAC
3501833 TCGAACGCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.50, G:0.17, T:0.24
Consensus pattern (21 bp):
CGCCACTCGATCTCCCTCGAC
Found at i:3502262 original size:56 final size:56
Alignment explanation
Indices: 3502176--3502294 Score: 229
Period size: 56 Copynumber: 2.1 Consensus size: 56
3502166 CCCTGTGAGT
3502176 AATATTAGATCATCAAAGGGTTAAAAGTTACTCCAAAACTTAAAAACATAAGATCG
1 AATATTAGATCATCAAAGGGTTAAAAGTTACTCCAAAACTTAAAAACATAAGATCG
*
3502232 AATATTAGATCATCAAAGGGTTAAAAGTTACTCCAAAACTTAAAAACATAAGATTG
1 AATATTAGATCATCAAAGGGTTAAAAGTTACTCCAAAACTTAAAAACATAAGATCG
3502288 AATATTA
1 AATATTA
3502295 AAGATTATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.27
Consensus pattern (56 bp):
AATATTAGATCATCAAAGGGTTAAAAGTTACTCCAAAACTTAAAAACATAAGATCG
Found at i:3503350 original size:2 final size:2
Alignment explanation
Indices: 3503343--3503379 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3503333 TTTTCTCTTC
3503343 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3503380 TTAATGTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3503366 original size:17 final size:17
Alignment explanation
Indices: 3503344--3503377 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3503334 TTTCTCTTCA
3503344 TATATATATATATATAT
1 TATATATATATATATAT
3503361 TATATATATATATATAT
1 TATATATATATATATAT
3503378 ATTTAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:3503367 original size:19 final size:19
Alignment explanation
Indices: 3503343--3503380 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3503333 TTTTCTCTTC
3503343 ATATATATATATATATATT
1 ATATATATATATATATATT
3503362 ATATATATATATATATATT
1 ATATATATATATATATATT
3503381 TAATGTAGAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATATATATATATATT
Found at i:3504219 original size:4 final size:4
Alignment explanation
Indices: 3504175--3504203 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3504165 ACATGTGTTA
3504175 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
3504204 TTGAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:3504267 original size:19 final size:21
Alignment explanation
Indices: 3504228--3504268 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
3504218 TAAAAAACTT
3504228 AAAATTACTATTGTTTATTAA
1 AAAATTACTATTGTTTATTAA
*
3504249 AAAATT-CTATT-TTTTTTAA
1 AAAATTACTATTGTTTATTAA
3504268 A
1 A
3504269 TATTAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
AAAATTACTATTGTTTATTAA
Found at i:3505118 original size:229 final size:228
Alignment explanation
Indices: 3504707--3505156 Score: 785
Period size: 229 Copynumber: 2.0 Consensus size: 228
3504697 GTAAATTATC
* * *
3504707 TATCCTTTTTATAAAAGTGTCCAATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAG
1 TATCATTTTTATAAAAGTGTCCAATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAG
**
3504772 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
66 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
*
3504837 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
131 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
3504902 GAAACATAAATTACATAACTTTCAAAAAAGTATA
196 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
3504936 TATCATTTTTATAAAAGTGTCC-ATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTG
1 TATCATTTTTATAAAAGTGTCCAATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTA
*
3505000 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
65 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
* *
3505065 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAAT
130 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAAT
3505130 TGAAACATAAATTACATAACTTTAAAA
195 TGAAACATAAATTACATAACTTTAAAA
3505157 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 19 0.09
229 191 0.91
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCAATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAG
TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:3505245 original size:20 final size:19
Alignment explanation
Indices: 3505222--3505268 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
3505212 CGATATACCA
3505222 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
3505242 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
3505262 GGTAAAA
1 GGTAAAA
3505269 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:3505412 original size:20 final size:19
Alignment explanation
Indices: 3505389--3505435 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3505379 CGATATAACA
*
3505389 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
3505409 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
3505429 GGTAAAA
1 GGTAAAA
3505436 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:3507776 original size:33 final size:33
Alignment explanation
Indices: 3507734--3507799 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3507724 AAATAGATGG
*
3507734 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
3507767 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
3507800 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:3509639 original size:19 final size:19
Alignment explanation
Indices: 3509595--3509638 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3509585 AATGTCGAGT
3509595 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3509614 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
3509633 T-ATTTT
1 TAATTTT
3509639 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3510261 original size:199 final size:199
Alignment explanation
Indices: 3509721--3511137 Score: 2610
Period size: 199 Copynumber: 7.1 Consensus size: 199
3509711 TTAAGGGTCA
* *
3509721 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
3509786 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
3509851 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3509916 AATG
196 AATG
3509920 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
*
3509984 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCCAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
3510049 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3510114 AATG
196 AATG
*
3510118 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
*
3510183 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
3510248 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3510313 AATG
196 AATG
*
3510317 TGTCGACACTAATATTGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
3510381 AATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
3510445 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3510510 AATG
196 AATG
* *
3510514 TGTCGACACTAATATTGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
3510579 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
3510644 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3510709 AATG
196 AATG
* *
3510713 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
*
3510778 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
3510843 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3510908 AATG
196 AATG
*
3510912 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
* *
3510977 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
3511042 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3511107 AATG
196 AATG
3511111 TGTCGACACTAATAT--TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
3511138 CTAATTTAAA
Statistics
Matches: 1193, Mismatches: 22, Indels: 8
0.98 0.02 0.01
Matches are distributed among these distances:
197 160 0.13
198 292 0.24
199 741 0.62
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:3510536 original size:396 final size:397
Alignment explanation
Indices: 3509721--3511137 Score: 2624
Period size: 396 Copynumber: 3.6 Consensus size: 397
3509711 TTAAGGGTCA
* * *
3509721 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
3509786 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
3509851 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3509916 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
*
3509981 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCCAAATCATCGAACCCAAAAGTATA
261 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
3510046 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
3510111 AATAATG
391 AATAATG
3510118 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
3510183 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
3510248 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
3510313 AATGTGTCGACACTAATATTGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
3510378 ATCAATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
261 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
3510442 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
3510507 AATAATG
391 AATAATG
* * *
3510514 TGTCGACACTAATATTGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
3510579 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
3510644 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
3510709 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTG
* *
3510774 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
260 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
*
3510839 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCT
325 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
3510904 AAATAATG
390 AAATAATG
3510912 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
3510977 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
3511042 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3511107 AATGTGTCGACACTAATAT--TTTGTGTCGATA
196 AATGTGTCGACACTAATATAGTTTGTGTCGATA
3511138 CTAATTTAAA
Statistics
Matches: 991, Mismatches: 27, Indels: 5
0.97 0.03 0.00
Matches are distributed among these distances:
396 351 0.35
397 325 0.33
398 315 0.32
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (397 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
AATAATG
Found at i:3510882 original size:595 final size:595
Alignment explanation
Indices: 3509721--3511137 Score: 2651
Period size: 595 Copynumber: 2.4 Consensus size: 595
3509711 TTAAGGGTCA
*
3509721 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
3509786 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
3509851 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
3509916 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
195 AATGTGTCGACACTAATATTGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
*
3509981 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCCAAATCATCGAACCCAAAAGTATA
260 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
3510046 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
325 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTA
*
3510111 AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAG
390 AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAG
3510176 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
455 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
*
3510241 TATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
520 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
3510306 TCTAAATAATG
585 TCTAAATAATG
*
3510317 TGTCGACACTAATATTGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
3510382 ATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
3510446 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
3510511 ATGTGTCGACACTAATATTGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGC
196 ATGTGTCGACACTAATATTGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGC
3510576 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
260 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
3510641 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTA
325 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTA
3510706 AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAG
390 AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAG
3510771 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
455 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
*
3510836 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
520 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
3510901 TCTAAATAATG
585 TCTAAATAATG
*
3510912 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
* *
3510977 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
3511042 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3511107 AATGTGTCGACACTAATA-T-TTTGTGTCGATA
195 AATGTGTCGACACTAATATTGTTTGTGTCGATA
3511138 CTAATTTAAA
Statistics
Matches: 802, Mismatches: 16, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
594 140 0.17
595 465 0.58
596 75 0.09
597 122 0.15
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (595 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATGTGTCGACACTAATATTGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
TCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAA
ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGG
TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
CTAAATAATG
Found at i:3512619 original size:12 final size:12
Alignment explanation
Indices: 3512602--3512693 Score: 69
Period size: 12 Copynumber: 7.4 Consensus size: 12
3512592 GGTCGCAGAA
*
3512602 GATGAAGCTGAC
1 GATGAAGATGAC
3512614 GATGAAGATGAC
1 GATGAAGATGAC
3512626 GATGATGATGATGAC
1 GATGA--A-GATGAC
*
3512641 GATGAA-ACTGGC
1 GATGAAGA-TGAC
*
3512653 GATGAAGATGAT
1 GATGAAGATGAC
* * *
3512665 GACGATGATGAT
1 GATGAAGATGAC
* *
3512677 GATGATGATGAA
1 GATGAAGATGAC
3512689 GATGA
1 GATGA
3512694 TGATCCAAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
11 1 0.01
12 52 0.78
13 2 0.03
14 1 0.01
15 11 0.16
ACGTcount: A:0.37, C:0.08, G:0.34, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:3512638 original size:15 final size:15
Alignment explanation
Indices: 3512614--3512696 Score: 84
Period size: 15 Copynumber: 5.7 Consensus size: 15
3512604 TGAAGCTGAC
*
3512614 GATGAAGATGACGAT
1 GATGATGATGACGAT
3512629 GATGATGATGACGAT
1 GATGATGATGACGAT
*
3512644 GA--A--ACTGGCGAT
1 GATGATGA-TGACGAT
*
3512656 GAAGATGATGACGAT
1 GATGATGATGACGAT
*
3512671 GATGATGATGATGAT
1 GATGATGATGACGAT
*
3512686 GAAGATGATGA
1 GATGATGATGA
3512697 TCCAAACAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
11 1 0.02
12 8 0.14
13 1 0.02
14 1 0.02
15 45 0.79
16 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.34, T:0.23
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:3512640 original size:27 final size:27
Alignment explanation
Indices: 3512610--3512693 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
3512600 AAGATGAAGC
3512610 TGACGATGAAGATGACGATGATGATGA
1 TGACGATGAAGATGACGATGATGATGA
* *
3512637 TGACGATGAA-ACTGGCGATGAAGATGA
1 TGACGATGAAGA-TGACGATGATGATGA
* * *
3512664 TGACGATGATGATGATGATGATGAAGA
1 TGACGATGAAGATGACGATGATGATGA
3512691 TGA
1 TGA
3512694 TGATCCAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
26 1 0.02
27 46 0.96
28 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (27 bp):
TGACGATGAAGATGACGATGATGATGA
Found at i:3514372 original size:184 final size:184
Alignment explanation
Indices: 3514063--3514918 Score: 1622
Period size: 184 Copynumber: 4.7 Consensus size: 184
3514053 CTTTCAACAT
**
3514063 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
3514128 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
3514193 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
3514247 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
3514312 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
3514377 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
3514431 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTATTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
3514496 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTAGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
3514561 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
3514615 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
3514680 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
3514745 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* * *
3514799 ATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
3514864 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
3514919 CCATTTAAAA
Statistics
Matches: 660, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 660 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:3517508 original size:23 final size:23
Alignment explanation
Indices: 3517477--3517539 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
3517467 ATAGGTAAAC
*
3517477 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
3517500 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
3517523 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
3517540 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Done.