Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003795.1 Hibiscus syriacus cultivar Beakdansim tig00008118_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: 171163
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:609 original size:45 final size:45
Alignment explanation
Indices: 465--668 Score: 335
Period size: 45 Copynumber: 4.6 Consensus size: 45
455 ATGAAATGGT
465 TAATGAA-TTATTAAAATGTTATATATTTTGTTAATAGAA-AGTC
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
508 TAATGAAGTTATTAAAAT-TTATATATTTTGTTAATA-AATAGTC
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
551 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
* *
596 TAATGAAGGTATTAAAATGTTATATATTTTGTTAATATAATAGTC
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
* *
641 TAATGAAGCTATTAAAAATGTGATATAT
1 TAATGAAGTTATT-AAAATGTTATATAT
669 AAATATTTTG
Statistics
Matches: 152, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
42 2 0.01
43 47 0.31
44 28 0.18
45 62 0.41
46 13 0.09
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (45 bp):
TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
Found at i:620 original size:87 final size:89
Alignment explanation
Indices: 465--668 Score: 342
Period size: 87 Copynumber: 2.3 Consensus size: 89
455 ATGAAATGGT
*
465 TAATGAA-TTATTAAAATGTTATATATTTTGTTAATAGAAAGTCTAATGAAGTTATTAAAAT-TT
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAAAGTCTAATGAAGGTATTAAAATGTT
528 ATATATTTTGTTAATA-AATAGTC
66 ATATATTTTGTTAATATAATAGTC
551 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTCTAATGAAGGTATTAAAATGT
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAA-AGTCTAATGAAGGTATTAAAATGT
616 TATATATTTTGTTAATATAATAGTC
65 TATATATTTTGTTAATATAATAGTC
* *
641 TAATGAAGCTATTAAAAATGTGATATAT
1 TAATGAAGTTATT-AAAATGTTATATAT
669 AAATATTTTG
Statistics
Matches: 110, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
86 7 0.06
87 32 0.29
88 21 0.19
89 18 0.16
90 19 0.17
91 13 0.12
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (89 bp):
TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAAAGTCTAATGAAGGTATTAAAATGTT
ATATATTTTGTTAATATAATAGTC
Found at i:6612 original size:25 final size:25
Alignment explanation
Indices: 6584--6632 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
6574 TGAAATAATT
*
6584 TGAAATTAAATAAAAA-ATAATAAAA
1 TGAAAATAAA-AAAAATATAATAAAA
6609 TGAAAATAAAAAAAATATAATAAA
1 TGAAAATAAAAAAAATATAATAAA
6633 CCGGGTACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (25 bp):
TGAAAATAAAAAAAATATAATAAAA
Found at i:8464 original size:17 final size:17
Alignment explanation
Indices: 8442--8483 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
8432 GATTGGACAG
8442 AAAAAAATAA-GAATAAT
1 AAAAAAA-AATGAATAAT
*
8459 AAAAAAAAATTAATAAT
1 AAAAAAAAATGAATAAT
8476 AAAAAAAA
1 AAAAAAAA
8484 TAAACAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAAAAAATGAATAAT
Found at i:8467 original size:20 final size:19
Alignment explanation
Indices: 8442--8483 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
8432 GATTGGACAG
8442 AAAAAAATAAGAATAATAAA
1 AAAAAAATAAGAATAA-AAA
* *
8462 AAAAAATTAATAATAAAAA
1 AAAAAAATAAGAATAAAAA
8481 AAA
1 AAA
8484 TAAACAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAAAATAAGAATAAAAA
Found at i:8472 original size:14 final size:14
Alignment explanation
Indices: 8455--8496 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
8445 AAAATAAGAA
8455 TAATAAAAAAAAAT
1 TAATAAAAAAAAAT
*
8469 TAATAATAAAAAAAA
1 TAATAA-AAAAAAAT
*
8484 TAA-ACAAAAAAAT
1 TAATAAAAAAAAAT
8497 AAAATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 7 0.29
14 7 0.29
15 10 0.42
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
TAATAAAAAAAAAT
Found at i:8485 original size:26 final size:26
Alignment explanation
Indices: 8445--8502 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
8435 TGGACAGAAA
* * *
8445 AAAATAAGAATAATAAA-AAAAAATT
1 AAAATAAAAAAAATAAACAAAAAAAT
8470 AATAATAAAAAAAATAAACAAAAAAAT
1 AA-AATAAAAAAAATAAACAAAAAAAT
8497 AAAATA
1 AAAATA
8503 TTAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 17 0.61
27 9 0.32
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (26 bp):
AAAATAAAAAAAATAAACAAAAAAAT
Found at i:8495 original size:16 final size:16
Alignment explanation
Indices: 8459--8502 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
8449 TAAGAATAAT
* *
8459 AAAAAAAAATTAATAA
1 AAAAAAAAATAAACAA
*
8475 TAAAAAAAATAAACAA
1 AAAAAAAAATAAACAA
8491 AAAAATAAAATA
1 AAAAA-AAAATA
8503 TTAAATATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAAAAATAAACAA
Found at i:8589 original size:35 final size:36
Alignment explanation
Indices: 8535--8769 Score: 201
Period size: 35 Copynumber: 6.8 Consensus size: 36
8525 TCAAAAAATT
* * *
8535 TGTTTTCAAAAAACCATTTTTAAAATTATATA-TACA
1 TGTTTTC-AAAAACCATTTTAAAAACTATATACTATA
8571 TGTTTTCAAAAACCATTTTAAAAACTATATACTATA
1 TGTTTTCAAAAACCATTTTAAAAACTATATACTATA
* *
8607 TGTTTTCAAAAA-TATTTTAAAAACTATATATTATA
1 TGTTTTCAAAAACCATTTTAAAAACTATATACTATA
*
8642 TGTTTTCAAAAA-C----T--ATACTATATA-TATA
1 TGTTTTCAAAAACCATTTTAAAAACTATATACTATA
* * *
8670 --TATTCAAAAA-TATTTTAAAAACTATATATTATA
1 TGTTTTCAAAAACCATTTTAAAAACTATATACTATA
* * *
8703 TGTTTTCAAAAA-TATGTTTTCAAAACTATATATTATA
1 TGTTTTCAAAAACCA--TTTTAAAAACTATATACTATA
* *
8740 TGTTTTCCAAAACCGATTTAAAAAAACTAT
1 TGTTTTCAAAAACC-ATTT-TAAAAACTAT
8770 GTTGAACTAT
Statistics
Matches: 168, Mismatches: 16, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
26 9 0.05
28 4 0.02
29 9 0.05
30 1 0.01
31 1 0.01
32 9 0.05
33 4 0.02
35 66 0.39
36 22 0.13
37 34 0.20
38 8 0.05
39 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (36 bp):
TGTTTTCAAAAACCATTTTAAAAACTATATACTATA
Found at i:8656 original size:24 final size:26
Alignment explanation
Indices: 8618--8679 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
8608 GTTTTCAAAA
8618 ATATTTT-AAAAACTATA-TAT-TAT
1 ATATTTTCAAAAACTATACTATATAT
*
8641 ATGTTTTCAAAAACTATACTATATAT
1 ATATTTTCAAAAACTATACTATATAT
*
8667 ATATATTCAAAAA
1 ATATTTTCAAAAA
8680 TATTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.18
24 10 0.30
25 3 0.09
26 14 0.42
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (26 bp):
ATATTTTCAAAAACTATACTATATAT
Found at i:8683 original size:61 final size:59
Alignment explanation
Indices: 8586--8714 Score: 208
Period size: 61 Copynumber: 2.2 Consensus size: 59
8576 TCAAAAACCA
*
8586 TTTT-AAAAACTATATACTATATGTTTTCAAAAATATTTTAAAAACTATATATTATATG
1 TTTTCAAAAACTATATACTATATATTTTCAAAAATATTTTAAAAACTATATATTATATG
8644 TTTTCAAAAACTATACTA-TATATATATATTCAAAAATATTTTAAAAACTATATATTATATG
1 TTTTCAAAAACTATA-TACTATATAT-T-TTCAAAAATATTTTAAAAACTATATATTATATG
8705 TTTTCAAAAA
1 TTTTCAAAAA
8715 TATGTTTTCA
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
58 4 0.06
59 16 0.24
60 3 0.05
61 43 0.65
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (59 bp):
TTTTCAAAAACTATATACTATATATTTTCAAAAATATTTTAAAAACTATATATTATATG
Found at i:8719 original size:14 final size:14
Alignment explanation
Indices: 8700--8727 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8690 ACTATATATT
8700 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
8714 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
8728 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:8741 original size:37 final size:37
Alignment explanation
Indices: 8639--8751 Score: 149
Period size: 37 Copynumber: 3.0 Consensus size: 37
8629 ACTATATATT
* *
8639 ATATGTTTTCAAAAACTATACTATATATATATATTCAAAA
1 ATATGTTTTC-AAAACTATA-TAT-TATATGTTTTCAAAA
*
8679 ATA--TTTTAAAAACTATATATTATATGTTTTCAAAA
1 ATATGTTTTCAAAACTATATATTATATGTTTTCAAAA
*
8714 ATATGTTTTCAAAACTATATATTATATGTTTTCCAAA
1 ATATGTTTTCAAAACTATATATTATATGTTTTCAAAA
8751 A
1 A
8752 CCGATTTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
35 16 0.24
36 3 0.05
37 40 0.61
38 4 0.06
40 3 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (37 bp):
ATATGTTTTCAAAACTATATATTATATGTTTTCAAAA
Found at i:8831 original size:34 final size:30
Alignment explanation
Indices: 8793--8861 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
8783 TTGATATAAC
8793 AATTTAAGGCAAAACGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAA-GGTTTTTGGACTT-AATTG
*
8827 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAAGGTTTTTGGACTTAATTG
8856 AATTTA
1 AATTTA
8862 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 12 0.36
31 5 0.15
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAAGGTTTTTGGACTTAATTG
Found at i:8966 original size:21 final size:21
Alignment explanation
Indices: 8940--9059 Score: 147
Period size: 21 Copynumber: 5.7 Consensus size: 21
8930 AAGGTGTCAA
8940 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
8961 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGC
8982 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
9003 AGTGCATCCATGCA--CTTGCAC
1 AGTGCATCCATGCACCCCTG--C
** *
9024 TAGTGCATAGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
9045 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
9060 TCAAACACTG
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
19 3 0.03
20 12 0.14
21 56 0.65
22 12 0.14
23 3 0.03
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:8999 original size:42 final size:43
Alignment explanation
Indices: 8940--9061 Score: 167
Period size: 42 Copynumber: 2.9 Consensus size: 43
8930 AAGGTGTCAA
**
8940 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCAC-CCCTGT
1 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTCCCACT
**
8982 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTTGCACT
1 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTCCCACT
** *
9025 AGTGCATAGATGCA-CCATGCAGTGCATCCATGCACTC
1 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTC
9062 AAACACTGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 57 0.80
43 14 0.20
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (43 bp):
AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTCCCACT
Found at i:9125 original size:21 final size:21
Alignment explanation
Indices: 9080--9224 Score: 163
Period size: 21 Copynumber: 7.0 Consensus size: 21
9070 AATGCAATTA
***
9080 GTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCAAGGCT
*
9100 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATCAAGGCT
*
9121 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATCAAGGCT
9142 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
**
9163 GTGCATCGATGCATC-CTGCT
1 GTGCATCGATGCATCAAGGCT
**
9183 GTGCATCGATGCATC-CTGCT
1 GTGCATCGATGCATCAAGGCT
*
9203 GTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATC-AAGGCT
9224 G
1 G
9225 CAACGTCTAT
Statistics
Matches: 112, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 50 0.45
21 61 0.54
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.28
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:9347 original size:21 final size:21
Alignment explanation
Indices: 9318--9357 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
9308 TTTGAGTAGA
9318 AAAATCATCCCTAAACGGCTCC
1 AAAATCATCCC-AAACGGCTCC
*
9340 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
9358 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:9933 original size:37 final size:38
Alignment explanation
Indices: 9873--9964 Score: 114
Period size: 37 Copynumber: 2.4 Consensus size: 38
9863 AAATCCCAAC
* * *
9873 AAACTATATATTATATACGTTTTCAAAAATATGTTTTCA
1 AAACTATATA-TATATACATTTTCAAAAACATGCTTTCA
* *
9912 AAACTATATAT-TATACATTTTCAAAAGCGTGCTTTCA
1 AAACTATATATATATACATTTTCAAAAACATGCTTTCA
*
9949 AAACCATATATATATA
1 AAACTATATATATATA
9965 TATATATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 31 0.67
38 5 0.11
39 10 0.22
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (38 bp):
AAACTATATATATATACATTTTCAAAAACATGCTTTCA
Found at i:9961 original size:2 final size:2
Alignment explanation
Indices: 9954--9987 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9944 TTTCAAAACC
9954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9988 TCAAAAACCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10052 original size:40 final size:37
Alignment explanation
Indices: 10008--10095 Score: 122
Period size: 40 Copynumber: 2.3 Consensus size: 37
9998 TTTTTTTAAA
10008 AAAAACTATATATTATATGCTTTCAAAAAAACTATTTTC
1 AAAAACTATATATTATATGCTTTC-AAAAAA-TATTTTC
* **
10047 TAAAAATTATATATTATATTTTTTCAAAAAATATTTTC
1 -AAAAACTATATATTATATGCTTTCAAAAAATATTTTC
10085 AAAAACTATAT
1 AAAAACTATAT
10096 TATATTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 10 0.23
38 7 0.16
39 6 0.14
40 21 0.48
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (37 bp):
AAAAACTATATATTATATGCTTTCAAAAAATATTTTC
Found at i:11390 original size:20 final size:20
Alignment explanation
Indices: 11335--11401 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
11325 GCGATCGATA
* *
11335 ATTCGCAACGTGATCTCC-G
1 ATTCGCAACGCGATTTCCAG
** *
11354 ATATCGCAAATCAATTTCCAG
1 AT-TCGCAACGCGATTTCCAG
*
11375 ATTCGCAACGCGATTTTCCAA
1 ATTCGCAACGCGA-TTTCCAG
11396 ATTCGC
1 ATTCGC
11402 GTTGCGATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 2 0.06
20 19 0.53
21 15 0.42
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTCGCAACGCGATTTCCAG
Found at i:11408 original size:21 final size:22
Alignment explanation
Indices: 11384--11529 Score: 128
Period size: 21 Copynumber: 6.9 Consensus size: 22
11374 GATTCGCAAC
11384 GCGATT-TTCCAAATTCGCGTT
1 GCGATTATTCCAAATTCGCGTT
*
11405 GCGATTTATTCCAAGTT--CGTT
1 GCGA-TTATTCCAAATTCGCGTT
* * *
11426 GCGA-TAGTCGAAGTTCGCGTT
1 GCGATTATTCCAAATTCGCGTT
11447 GCGATTTATTCCAAATT--CGTT
1 GCGA-TTATTCCAAATTCGCGTT
11468 GCGATTTATTCCAAATTCGCGTT
1 GCGA-TTATTCCAAATTCGCGTT
* * *
11491 GCGA-TAGTCGAAGTTCGCGTT
1 GCGATTATTCCAAATTCGCGTT
* *
11512 GCGA-TAGTCCAAAATCGC
1 GCGATTATTCCAAATTCGC
11530 AACGACTGGT
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.09
21 70 0.67
22 2 0.02
23 24 0.23
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (22 bp):
GCGATTATTCCAAATTCGCGTT
Found at i:11443 original size:42 final size:42
Alignment explanation
Indices: 11391--11529 Score: 165
Period size: 42 Copynumber: 3.3 Consensus size: 42
11381 AACGCGATTT
11391 TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
* * * *
11433 TCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
1 TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAG
* *
11477 TCCAAATTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATAG
*
11519 TCCAAAATCGC
1 TCCAAATTCGC
11530 AACGACTGGT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
42 56 0.68
44 26 0.32
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
Found at i:11497 original size:65 final size:64
Alignment explanation
Indices: 11390--11516 Score: 211
Period size: 65 Copynumber: 2.0 Consensus size: 64
11380 CAACGCGATT
*
11390 TTCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAAATTC-CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
11455 TTCCAAATT-CGTTGCGATTTATTCCAAATTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGAT
1 TTCCAAATTCCGTTGCGATTTATTCCAAATT--CGTTGCGATAGTCGAAGTTCGCGTTGCGAT
11517 AGTCCAAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
63 20 0.34
65 39 0.66
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (64 bp):
TTCCAAATTCCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
Found at i:12285 original size:6 final size:6
Alignment explanation
Indices: 12264--12300 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
12254 GTCCGTCTCG
12264 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
12301 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:12413 original size:21 final size:21
Alignment explanation
Indices: 12384--12473 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
12374 ACCAGTCGTT
* *
12384 GCGATTTTGGACTATCGCAAC
1 GCGAATTTCGACTATCGCAAC
* **
12405 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTCGACTATCGCAAC
*
12426 GCGAACTTCGACTATCGCAAC
1 GCGAATTTCGACTATCGCAAC
* * *
12447 GCGAACTTCGATTATCGCAAT
1 GCGAATTTCGACTATCGCAAC
12468 GCGAAT
1 GCGAAT
12474 ATGTAAATCG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.23
Consensus pattern (21 bp):
GCGAATTTCGACTATCGCAAC
Found at i:12464 original size:42 final size:42
Alignment explanation
Indices: 12393--12472 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
12383 TGCGATTTTG
* *
12393 GACTATCGCAACGCGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTCGAAAATCGCAACGCGAACTTC
** *
12435 GACTATCGCAACGCGAACTTCGATTATCGCAATGCGAA
1 GACTATCGCAACGCGAACTTCGAAAATCGCAACGCGAA
12473 TATGTAAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGCGAACTTCGAAAATCGCAACGCGAACTTC
Found at i:13548 original size:34 final size:34
Alignment explanation
Indices: 13508--13576 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
13498 CACATTTTCA
* *
13508 ACTTTTAATCTCAACTATCACTTAACACTGATTC
1 ACTTTTAATCTCAACTATCACTCAACACTAATTC
13542 ACTTTTAATCTCAACTATCACTCAACACTAATTC
1 ACTTTTAATCTCAACTATCACTCAACACTAATTC
13576 A
1 A
13577 ATGGTCCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (34 bp):
ACTTTTAATCTCAACTATCACTCAACACTAATTC
Found at i:13720 original size:21 final size:21
Alignment explanation
Indices: 13687--13741 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
13677 GAATGGTTTC
*
13687 CAAAGTTGACATCTTTATAAA
1 CAAAGCTGACATCTTTATAAA
*
13708 CAAAGCTGGCATCTTTATAAA
1 CAAAGCTGACATCTTTATAAA
13729 CAAAGCTTGACAT
1 CAAAGC-TGACAT
13742 AAGCCAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (21 bp):
CAAAGCTGACATCTTTATAAA
Found at i:26689 original size:38 final size:38
Alignment explanation
Indices: 26621--26694 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
26611 GGTCGGATCG
* * *
26621 AGTGAAAAATATATATTTTTGTATTCGAGTCAAATTCA
1 AGTGAAAAATATATATTTTTGAAGTAGAGTCAAATTCA
*
26659 AGTGAATAATATATATATTTT-AAGTAGAGTCAAATT
1 AGTGAAAAATATATAT-TTTTGAAGTAGAGTCAAATT
26695 GACCAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 27 0.87
39 4 0.13
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (38 bp):
AGTGAAAAATATATATTTTTGAAGTAGAGTCAAATTCA
Found at i:27104 original size:22 final size:22
Alignment explanation
Indices: 27079--27126 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
27069 CTACGGTGAC
27079 ATCCTTCCCCATCTCCAACGAA
1 ATCCTTCCCCATCTCCAACGAA
*
27101 ATCCTTCCCCATCTCCGACGAA
1 ATCCTTCCCCATCTCCAACGAA
27123 ATCC
1 ATCC
27127 GTCTATCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.46, G:0.06, T:0.23
Consensus pattern (22 bp):
ATCCTTCCCCATCTCCAACGAA
Found at i:27235 original size:17 final size:16
Alignment explanation
Indices: 27205--27249 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
27195 GGGTTAGTTT
*
27205 TTTTTAATTATTTTTA
1 TTTTTAATTTTTTTTA
27221 TTTTTAATTTTTTTTA
1 TTTTTAATTTTTTTTA
*
27237 TTATTAGATTTTT
1 TTTTTA-ATTTTT
27250 CATATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTTAATTTTTTTTA
Found at i:27508 original size:19 final size:19
Alignment explanation
Indices: 27484--27617 Score: 117
Period size: 19 Copynumber: 7.4 Consensus size: 19
27474 AAAACACAAC
27484 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
* *
27503 GCGATTTTTATTTCGTGTT
1 GCGATTTTCATTTCGCGTT
27522 GCGA---T--TTTCGCGTT
1 GCGATTTTCATTTCGCGTT
27536 GCGA--TT--TTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
27551 GCGATTTTCATTTCGTGTT
1 GCGATTTTCATTTCGCGTT
**
27570 ATGATTTTCATTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
27590 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
*
27610 ACGATTTT
1 GCGATTTT
27618 AAGTTTTAGA
Statistics
Matches: 99, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.12
15 14 0.14
16 1 0.01
17 2 0.02
19 36 0.36
20 34 0.34
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:27536 original size:14 final size:14
Alignment explanation
Indices: 27513--27559 Score: 76
Period size: 14 Copynumber: 3.3 Consensus size: 14
27503 GCGATTTTTA
*
27513 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
27527 TTTCGCGTTGCGATT
1 TTTCGCGTTGCGA-T
27542 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
27556 TTTC
1 TTTC
27560 ATTTCGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.06, C:0.19, G:0.26, T:0.49
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:27546 original size:15 final size:15
Alignment explanation
Indices: 27494--27558 Score: 78
Period size: 15 Copynumber: 4.1 Consensus size: 15
27484 GCGATTTTAG
27494 TTTCGCGTTGCGATTTTT
1 TTTCGCGTTGCGA---TT
*
27512 ATTTCGTGTTGCGA-T
1 -TTTCGCGTTGCGATT
27527 TTTCGCGTTGCGATT
1 TTTCGCGTTGCGATT
27542 TTTCGCGTTGCGATT
1 TTTCGCGTTGCGATT
27557 TT
1 TT
27559 CATTTCGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
14 12 0.28
15 19 0.44
19 12 0.28
ACGTcount: A:0.08, C:0.17, G:0.25, T:0.51
Consensus pattern (15 bp):
TTTCGCGTTGCGATT
Found at i:27594 original size:39 final size:40
Alignment explanation
Indices: 27541--27617 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
27531 GCGTTGCGAT
* *
27541 TTTTCGCGTTGCGATTTTCA-TTTCGTGTTATGATTTTCA
1 TTTTCGCGTTGCGATTTTCATTTTCGCGTTACGATTTTCA
27580 TTTTCGCGTTGCGATTTTCATTTTCGCGTTACGATTTT
1 TTTTCGCGTTGCGATTTTCATTTTCGCGTTACGATTTT
27618 AAGTTTTAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 20 0.57
40 15 0.43
ACGTcount: A:0.12, C:0.17, G:0.18, T:0.53
Consensus pattern (40 bp):
TTTTCGCGTTGCGATTTTCATTTTCGCGTTACGATTTTCA
Found at i:27595 original size:20 final size:20
Alignment explanation
Indices: 27541--27617 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
27531 GCGTTGCGAT
*
27541 TTTTCGCGTTGCGATTTTCA
1 TTTTCGCGTTACGATTTTCA
* *
27561 -TTTCGTGTTATGATTTTCA
1 TTTTCGCGTTACGATTTTCA
*
27580 TTTTCGCGTTGCGATTTTCA
1 TTTTCGCGTTACGATTTTCA
27600 TTTTCGCGTTACGATTTT
1 TTTTCGCGTTACGATTTT
27618 AAGTTTTAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.33
20 33 0.67
ACGTcount: A:0.12, C:0.17, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTTCGCGTTACGATTTTCA
Found at i:29384 original size:21 final size:23
Alignment explanation
Indices: 29360--29457 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 23
29350 TGGTGCATGG
29360 CGTGATGAGGTA-CGGT-CTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
29381 CGTGGTGAGGTAGAGGT--TTTA
1 CGTGATGAGGTAGCGGTACTTTA
* * ** *
29402 CGCGATGA--CAATGGTGCTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
29423 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTAGCGGTACTTTA
29444 CGTGATGAGGTAGC
1 CGTGATGAGGTAGC
29458 CGCTCTACGT
Statistics
Matches: 57, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
19 4 0.07
21 49 0.86
22 3 0.05
23 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.35, T:0.32
Consensus pattern (23 bp):
CGTGATGAGGTAGCGGTACTTTA
Found at i:29432 original size:63 final size:63
Alignment explanation
Indices: 29335--29456 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
29325 AGGTCGACAC
* * *
29335 TTTACGTGAAGACAATGGTGCATGGCGTGATGAGGTA-CGGT-CTTTACGTGGTGAGGTAGAGGT
1 TTTACGCGAAGACAATGGTGCATGACGTGATGAGGTATC--TACTTTACGTGATGAGGTAGAGGT
* * * *
29398 TTTACGCGATGACAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTAG
1 TTTACGCGAAGACAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAG
29457 CCGCTCTACG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 48 0.96
64 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.34, T:0.31
Consensus pattern (63 bp):
TTTACGCGAAGACAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAGAGGT
Found at i:29784 original size:21 final size:21
Alignment explanation
Indices: 29755--29934 Score: 168
Period size: 21 Copynumber: 8.6 Consensus size: 21
29745 AGCACCTGTC
*
29755 ATCGTTCAAGAGGCCACTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* *
29776 ATTGTTCAAGAGGCCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
* *
29796 CATCCTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
29818 ACCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* *
29839 ATCGTTCAAGAGGCCCAT-AT
1 ATCGTTCAAGAGGCCCCTCCT
* *
29859 CATCCTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
29881 ACCGTTCAAGAGGCCCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
* *
29901 CATCGTTCAAGAGGTCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
29923 ACCGTTCAAGAG
1 ATCGTTCAAGAG
29935 CTCGATTCAC
Statistics
Matches: 125, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.02
21 123 0.98
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:29829 original size:63 final size:63
Alignment explanation
Indices: 29757--29914 Score: 255
Period size: 63 Copynumber: 2.5 Consensus size: 63
29747 CACCTGTCAT
* *
29757 CGTTCAAGAGGCCACTCCTATTGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCACTCCTATCGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
*
29820 CGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCACTCCTATCGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
* *
29883 CGTTCAAGAGGCCCCT-GTCATCGTTCAAGAGG
1 CGTTCAAGAGGCCACTCCT-ATCGTTCAAGAGG
29915 TCCCTCCCAC
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 1 0.01
63 88 0.99
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (63 bp):
CGTTCAAGAGGCCACTCCTATCGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
Found at i:29920 original size:42 final size:41
Alignment explanation
Indices: 29757--29934 Score: 187
Period size: 42 Copynumber: 4.2 Consensus size: 41
29747 CACCTGTCAT
* * **
29757 CGTTCAAGAGGCCACTCCTATTGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGCCCCTCC-ATCGTTCAAGAGGCCCCTCCCA-C
* * * *
29800 C-TTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCCCT-CCATCGTTCAAGAGGCCCCTCCCAC
* * *
29841 CGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCT-CCATCGTTCAAGAGGCCCCTCCCAC
* *
29883 CGTTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCT-CCATCGTTCAAGAGGCCCCTCCCAC
29925 CGTTCAAGAG
1 CGTTCAAGAG
29935 CTCGATTCAC
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 109 0.96
43 3 0.03
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (41 bp):
CGTTCAAGAGGCCCCTCCATCGTTCAAGAGGCCCCTCCCAC
Found at i:31773 original size:18 final size:18
Alignment explanation
Indices: 31752--31787 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31742 AAGCCGGTTA
*
31752 TGATTGTGATTTTGATTT
1 TGATTGCGATTTTGATTT
31770 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
31788 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.22, T:0.58
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:32708 original size:18 final size:18
Alignment explanation
Indices: 32661--32708 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
32651 TAGTGGAGCC
32661 GAAATT-TATATTGAAATT
1 GAAATTCTA-ATTGAAATT
* * *
32679 CAAACTCAAATTGAAATT
1 GAAATTCTAATTGAAATT
32697 GAAATTCTAATT
1 GAAATTCTAATT
32709 ACATATGAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (18 bp):
GAAATTCTAATTGAAATT
Found at i:33121 original size:25 final size:25
Alignment explanation
Indices: 33087--33136 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
33077 TATTATTTTC
*
33087 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
33112 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
33137 TAATTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:33181 original size:20 final size:20
Alignment explanation
Indices: 33156--33206 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
33146 ATCTGCATTA
*
33156 TGTTGAAGGTAAAAGAGACC
1 TGTTGAAGGTAAAAAAGACC
33176 TGTTGAAGGTAAAAAAGACC
1 TGTTGAAGGTAAAAAAGACC
33196 TGTTGAAGGTA
1 TGTTGAAGGTA
33207 CACTTTCGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.29, T:0.24
Consensus pattern (20 bp):
TGTTGAAGGTAAAAAAGACC
Found at i:35899 original size:12 final size:12
Alignment explanation
Indices: 35878--35911 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35868 GGTTGTGGGT
*
35878 TTTGAGATTGTG
1 TTTGATATTGTG
35890 TTTGATATTGTG
1 TTTGATATTGTG
*
35902 TTTGGTATTG
1 TTTGATATTG
35912 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:36728 original size:20 final size:19
Alignment explanation
Indices: 36684--36792 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 19
36674 CAAAACATTT
*
36684 GTGTTGCGAAAATAAAA-C
1 GTGTTGCGAAATTAAAATC
*
36702 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
36722 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
*
36742 GAGTTGCG-AATTCAGAAATC
1 GTGTTGCGAAATT-A-AAATC
* * *
36762 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
36782 AGTGTTGCGAA
1 -GTGTTGCGAA
36793 TTTGTAAATC
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
18 15 0.20
19 5 0.07
20 38 0.51
21 17 0.23
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:36813 original size:20 final size:20
Alignment explanation
Indices: 36724--36876 Score: 159
Period size: 20 Copynumber: 7.6 Consensus size: 20
36714 TAAAATTCGT
* *
36724 GTTGCGAATTCGAAAATCGA-
1 GTTGCGAATTTGGAAATC-AC
**
36744 GTTGCGAATTCAGAAATCGA-
1 GTTGCGAATTTGGAAATC-AC
*
36764 GTTGCGAATTT-GAAATTCAGT
1 GTTGCGAATTTGGAAA-TCA-C
*
36785 GTTGCGAATTTGTAAATCAC
1 GTTGCGAATTTGGAAATCAC
*
36805 GTTGGGAATTTGGAAATCAC
1 GTTGCGAATTTGGAAATCAC
36825 GTTGCGAATTTGGAAATCAC
1 GTTGCGAATTTGGAAATCAC
* * *
36845 ATTTCGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCAC
36865 GTTGCGAATTTG
1 GTTGCGAATTTG
36877 ACTTCTGTGT
Statistics
Matches: 116, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
19 5 0.04
20 94 0.81
21 14 0.12
22 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCAC
Found at i:52329 original size:22 final size:22
Alignment explanation
Indices: 52290--52341 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
52280 GGACTTGAAC
*
52290 ATGCATGGCCGTAGGTTACAAA
1 ATGCATGGCCGAAGGTTACAAA
* * *
52312 ATGCATGGCTGAATGTTACAAT
1 ATGCATGGCCGAAGGTTACAAA
*
52334 TTGCATGG
1 ATGCATGG
52342 TCTCAGGGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (22 bp):
ATGCATGGCCGAAGGTTACAAA
Found at i:52486 original size:16 final size:16
Alignment explanation
Indices: 52461--52502 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
52451 GTGATGGCTG
* **
52461 GTGGAAACAAAGTTAA
1 GTGGAGACAAAGCCAA
52477 GTGGAGACAAAGCCAA
1 GTGGAGACAAAGCCAA
52493 GTGGAGACAA
1 GTGGAGACAA
52503 GCAATCTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.31, T:0.12
Consensus pattern (16 bp):
GTGGAGACAAAGCCAA
Found at i:56489 original size:34 final size:35
Alignment explanation
Indices: 56433--56498 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
56423 AGACAAGTAA
56433 TCTTCCAAGCACATGGGCTGTTT-ATAGTGCATTG
1 TCTTCCAAGCACATGGGCTGTTTCATAGTGCATTG
* *
56467 TCTTCTAATGCACAT-GGTTGTTTCATAGTGCA
1 TCTTCCAA-GCACATGGGCTGTTTCATAGTGCA
56499 ATGGTATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (35 bp):
TCTTCCAAGCACATGGGCTGTTTCATAGTGCATTG
Found at i:64185 original size:15 final size:15
Alignment explanation
Indices: 64160--64195 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
64150 AAGGAAATGC
64160 AAATGGAAATGGAAAG
1 AAAT-GAAATGGAAAG
*
64176 AAATGAAATGGATAG
1 AAATGAAATGGAAAG
64191 AAATG
1 AAATG
64196 TTATCAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.17
Consensus pattern (15 bp):
AAATGAAATGGAAAG
Found at i:65749 original size:6 final size:6
Alignment explanation
Indices: 65738--65781 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
65728 GTTATATGAG
* *
65738 TCTTTT TCTTTT TCTTTT TCTTTT TGTTCTT TCATTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
65782 GTTGCTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:65770 original size:19 final size:19
Alignment explanation
Indices: 65738--65789 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
65728 GTTATATGAG
* *
65738 TCTTTTTCTT-TTTCTTTT
1 TCTTTTTGTTCTTTCATTT
65756 TCTTTTTGTTCTTTCATTT
1 TCTTTTTGTTCTTTCATTT
65775 TCTTTTTGTTGCTTT
1 TCTTTTTGTT-CTTT
65790 TGTTGCAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 9 0.30
19 17 0.57
20 4 0.13
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (19 bp):
TCTTTTTGTTCTTTCATTT
Found at i:69795 original size:6 final size:6
Alignment explanation
Indices: 69780--69824 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
69770 GTTGTAGGAG
*
69780 TCTTTT TCTTTC TCTTTT TCTTTT TCTTCTT TCTTCTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTT-TT TCTTTT T
69825 GTTGCTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 23 0.64
7 13 0.36
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:69812 original size:7 final size:7
Alignment explanation
Indices: 69780--69821 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
69770 GTTGTAGGAG
69780 TCTTT-T
1 TCTTTCT
69786 TCTTTCT
1 TCTTTCT
*
69793 CTTTTTCT
1 -TCTTTCT
69801 T-TTTCT
1 TCTTTCT
69807 TCTTTCT
1 TCTTTCT
69814 TCTTTCT
1 TCTTTCT
69821 T
1 T
69822 TTTGTTGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
6 11 0.34
7 15 0.47
8 6 0.19
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TCTTTCT
Found at i:75692 original size:11 final size:11
Alignment explanation
Indices: 75676--75720 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
75666 GGATCATTAA
75676 GAAAGGAAATG
1 GAAAGGAAATG
75687 GAAAGGAAATG
1 GAAAGGAAATG
* *
75698 GAAATGAAA-A
1 GAAAGGAAATG
*
75708 GAAATGAAATG
1 GAAAGGAAATG
75719 GA
1 GA
75721 TAGAAATGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.11
Consensus pattern (11 bp):
GAAAGGAAATG
Found at i:78683 original size:22 final size:22
Alignment explanation
Indices: 78652--78693 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
78642 GGAATTAAGT
78652 GGATGATGATGGTCTTGATGGA
1 GGATGATGATGGTCTTGATGGA
* *
78674 GGATGTTGATGGTGTTGATG
1 GGATGATGATGGTCTTGATG
78694 TTGAAATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.02, G:0.43, T:0.36
Consensus pattern (22 bp):
GGATGATGATGGTCTTGATGGA
Found at i:78940 original size:19 final size:20
Alignment explanation
Indices: 78890--78932 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
78880 GAAACCCCTT
78890 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
78910 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
78929 TGAA
1 TGAA
78933 GATTCATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:89262 original size:23 final size:21
Alignment explanation
Indices: 89236--89277 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
89226 AATGCGAAAT
*
89236 TGATGGTTTTTGATGGATGAAGA
1 TGATGG-TGTTGAT-GATGAAGA
89259 TGATGGTGTTGATGATGAA
1 TGATGGTGTTGATGATGAA
89278 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (21 bp):
TGATGGTGTTGATGATGAAGA
Found at i:93467 original size:13 final size:12
Alignment explanation
Indices: 93449--93490 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
93439 GCTTGCTTTC
93449 TCTTTTTGAATTT
1 TCTTTTT-AATTT
*
93462 TCTTTTT-CTTT
1 TCTTTTTAATTT
93473 TCTTTTCTAATTT
1 TCTTTT-TAATTT
93486 TCTTT
1 TCTTT
93491 CTTTTTGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (12 bp):
TCTTTTTAATTT
Found at i:93486 original size:18 final size:18
Alignment explanation
Indices: 93465--93515 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
93455 TGAATTTTCT
93465 TTTTCTTTTCTTTTCT-AA
1 TTTTCTTTTCTTTT-TGAA
**
93483 TTTTC-TTTCTTTTTGTC
1 TTTTCTTTTCTTTTTGAA
93500 TTTTCTTTTCTTTTTG
1 TTTTCTTTTCTTTTTG
93516 CACTCTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 13 0.45
18 15 0.52
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGAA
Found at i:98695 original size:19 final size:19
Alignment explanation
Indices: 98671--98707 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
98661 TAGGAGTCTT
*
98671 TTCTTTTTTTTTCTTTTTC
1 TTCTTTCTTTTTCTTTTTC
*
98690 TTCTTTCTTTTTGTTTTT
1 TTCTTTCTTTTTCTTTTT
98708 GTTGCAGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (19 bp):
TTCTTTCTTTTTCTTTTTC
Found at i:98901 original size:5 final size:5
Alignment explanation
Indices: 98891--98932 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
98881 GGATCATTAA
* *
98891 GAAAT GAAAT GGAAAT GAAAA GAAAA GAAAT GAAAT GAAAT G
1 GAAAT GAAAT -GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT G
98933 GATATAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (5 bp):
GAAAT
Found at i:98942 original size:15 final size:16
Alignment explanation
Indices: 98891--98934 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
98881 GGATCATTAA
98891 GAAATGAAATGGAAAT
1 GAAATGAAATGGAAAT
* *
98907 GAAAAGAAA-AGAAAT
1 GAAATGAAATGGAAAT
98922 GAAATGAAATGGA
1 GAAATGAAATGGA
98935 TATAAATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (16 bp):
GAAATGAAATGGAAAT
Found at i:99108 original size:32 final size:30
Alignment explanation
Indices: 99060--99118 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
99050 ATTCAATGAT
99060 GGAGGAATGGTAATGGAAGGATGATGATATA
1 GGAGGAATGGTAATGGAA-GATGATGATATA
* *
99091 GGAGTGAATGGTGATGGAAGATGGTGAT
1 GGAG-GAATGGTAATGGAAGATGATGAT
99119 GGTTAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.34, C:0.00, G:0.42, T:0.24
Consensus pattern (30 bp):
GGAGGAATGGTAATGGAAGATGATGATATA
Found at i:100785 original size:30 final size:30
Alignment explanation
Indices: 100751--100820 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
100741 AGAATATAAA
*
100751 ATAAGTTAAGAAATTAAATGGGTATAAATG
1 ATAAGTTAAGAAATTAAATGGGTATAAAGG
100781 ATAAGTTAAGAAATTAAATGGGTATAAAGG
1 ATAAGTTAAGAAATTAAATGGGTATAAAGG
100811 ATAAGTTAAG
1 ATAAGTTAAG
100821 TGATAAGATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (30 bp):
ATAAGTTAAGAAATTAAATGGGTATAAAGG
Found at i:104612 original size:19 final size:19
Alignment explanation
Indices: 104557--104604 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
104547 GAAACCCCTT
104557 TGAAAATTCATGATTTTTAA
1 TGAAAATTCATGA-TTTTAA
*
104577 TGAAAATACATGATTTTAA
1 TGAAAATTCATGATTTTAA
104596 TGAAAATTC
1 TGAAAATTC
104605 TTGCTTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (19 bp):
TGAAAATTCATGATTTTAA
Found at i:106624 original size:104 final size:104
Alignment explanation
Indices: 106444--106661 Score: 427
Period size: 104 Copynumber: 2.1 Consensus size: 104
106434 TTGTTTATTG
*
106444 AAACATGCTTGAATGCATAACATGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
1 AAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
106509 AGATATTAATATGCATGACATGAATTTGAGAATGAATGA
66 AGATATTAATATGCATGACATGAATTTGAGAATGAATGA
106548 AAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
1 AAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
106613 AGATATTAATATGCATGACATGAATTTGAGAATGAATGA
66 AGATATTAATATGCATGACATGAATTTGAGAATGAATGA
106652 AAACATGCTT
1 AAACATGCTT
106662 AATATGTATG
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 113 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (104 bp):
AAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
AGATATTAATATGCATGACATGAATTTGAGAATGAATGA
Found at i:106650 original size:51 final size:50
Alignment explanation
Indices: 106489--106655 Score: 153
Period size: 51 Copynumber: 3.2 Consensus size: 50
106479 AAATGCTAAG
106489 ATGAATGCAAAACTACTATGAGATATTAATATGCATGACATGAATTTGAGA
1 ATGAATG-AAAACTACTATGAGATATTAATATGCATGACATGAATTTGAGA
* * * * * * * *
106540 ATGAATGAAAACATGCT-TGA-ATGCA-TAACACGTGAATCATCTTAAATGCTAAG-
1 ATGAATGAAAAC-TACTATGAGAT--ATTAATA--TGCATGA-CATGAAT-TTGAGA
106593 ATGAATGCAAAACTACTATGAGATATTAATATGCATGACATGAATTTGAGA
1 ATGAATG-AAAACTACTATGAGATATTAATATGCATGACATGAATTTGAGA
106644 ATGAATGAAAAC
1 ATGAATGAAAAC
106656 ATGCTTAATA
Statistics
Matches: 88, Mismatches: 16, Indels: 25
0.68 0.12 0.19
Matches are distributed among these distances:
49 2 0.02
50 20 0.23
51 23 0.26
52 10 0.11
53 16 0.18
54 15 0.17
55 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (50 bp):
ATGAATGAAAACTACTATGAGATATTAATATGCATGACATGAATTTGAGA
Found at i:109236 original size:29 final size:29
Alignment explanation
Indices: 109203--109301 Score: 83
Period size: 29 Copynumber: 3.2 Consensus size: 29
109193 GAGATAGGAA
*
109203 CCACAAGTATCAAGGTGAAAGGAATGATG
1 CCACAAGTATCAAGGTGAAAGGAATGACG
* * **
109232 CCACAAGCAT-AAGCTTGATAAGTCGGGTTTGACG
1 CCACAAGTATCAAG-GTGA-AA----GGAATGACG
*
109266 CCACAAGTACCAAGGTGAAAGGAATGACG
1 CCACAAGTATCAAGGTGAAAGGAATGACG
109295 CCACAAG
1 CCACAAG
109302 CATAAGCTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
28 3 0.06
29 26 0.49
30 2 0.04
33 2 0.04
34 17 0.32
35 3 0.06
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.16
Consensus pattern (29 bp):
CCACAAGTATCAAGGTGAAAGGAATGACG
Found at i:109302 original size:63 final size:63
Alignment explanation
Indices: 109203--109342 Score: 253
Period size: 63 Copynumber: 2.2 Consensus size: 63
109193 GAGATAGGAA
* *
109203 CCACAAGTATCAAGGTGAAAGGAATGATGCCACAAGCATAAGCTTGATAAGTCGGGTTTGACG
1 CCACAAGTAACAAGGTGAAAGGAATGACGCCACAAGCATAAGCTTGATAAGTCGGGTTTGACG
*
109266 CCACAAGTACCAAGGTGAAAGGAATGACGCCACAAGCATAAGCTTGATAAGTCGGGTTTGACG
1 CCACAAGTAACAAGGTGAAAGGAATGACGCCACAAGCATAAGCTTGATAAGTCGGGTTTGACG
109329 CCACAAGTAACAAG
1 CCACAAGTAACAAG
109343 TTACTTGATA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 74 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (63 bp):
CCACAAGTAACAAGGTGAAAGGAATGACGCCACAAGCATAAGCTTGATAAGTCGGGTTTGACG
Found at i:109333 original size:34 final size:34
Alignment explanation
Indices: 109231--109335 Score: 114
Period size: 34 Copynumber: 3.2 Consensus size: 34
109221 AAGGAATGAT
109231 GCCACAAGCATAAGCTTGATAAGTCGGGTTTGAC
1 GCCACAAGCATAAGCTTGATAAGTCGGGTTTGAC
* * * **
109265 GCCACAAGTACCAAG-GTGA-AA----GGAATGAC
1 GCCACAAGCA-TAAGCTTGATAAGTCGGGTTTGAC
109294 GCCACAAGCATAAGCTTGATAAGTCGGGTTTGAC
1 GCCACAAGCATAAGCTTGATAAGTCGGGTTTGAC
109328 GCCACAAG
1 GCCACAAG
109336 TAACAAGTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
28 3 0.06
29 18 0.33
30 2 0.04
33 2 0.04
34 26 0.48
35 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (34 bp):
GCCACAAGCATAAGCTTGATAAGTCGGGTTTGAC
Found at i:110552 original size:117 final size:117
Alignment explanation
Indices: 110420--110654 Score: 407
Period size: 117 Copynumber: 2.0 Consensus size: 117
110410 ATGTTGTTTA
* * * *
110420 TTGAAACATGTTTGAATACATAACACGTGAATCATGTTAAATGCTAAGATGCATGCAAAACTACT
1 TTGAAACATGCTTGAATACATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAAATACT
*
110485 ATGAGATATTAATATGCATGACATGAATTTAAGAATGAATGAAAATATGCTT
66 ATGAGATATTAATATGCATGACATGAATTTAAGAATGAATGAAAACATGCTT
*
110537 TTGAAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAAATACT
1 TTGAAACATGCTTGAATACATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAAATACT
*
110602 ATGAGATATTAATATGCATGACATGAATTTGAGAATGAATGAAAACATGCTT
66 ATGAGATATTAATATGCATGACATGAATTTAAGAATGAATGAAAACATGCTT
110654 T
1 T
110655 GATACAGTTC
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 111 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (117 bp):
TTGAAACATGCTTGAATACATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAAATACT
ATGAGATATTAATATGCATGACATGAATTTAAGAATGAATGAAAACATGCTT
Found at i:111464 original size:10 final size:10
Alignment explanation
Indices: 111449--111477 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
111439 TTTGGCTTCT
111449 TGCATGAATA
1 TGCATGAATA
111459 TGCATGAATA
1 TGCATGAATA
111469 TGCATGAAT
1 TGCATGAAT
111478 GGATGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (10 bp):
TGCATGAATA
Found at i:115427 original size:23 final size:23
Alignment explanation
Indices: 115401--115449 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
115391 ATAAAGAACC
*
115401 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAAGAT-CCATT
*
115424 AAAATAAAGTTTAAAGATCCATT
1 AAAATAAAGCTTAAAGATCCATT
115447 AAA
1 AAA
115450 CTAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAAGATCCATT
Found at i:118752 original size:20 final size:19
Alignment explanation
Indices: 118705--118753 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
118695 ATAAGAGAAA
118705 AAAG-TAAAAGTTAAAATG
1 AAAGATAAAAGTTAAAATG
* * *
118723 AAATAGAAAAGTTAAGGATG
1 AAAGATAAAAGTTAA-AATG
118743 AAAGATAAAAG
1 AAAGATAAAAG
118754 AAAAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.18
Consensus pattern (19 bp):
AAAGATAAAAGTTAAAATG
Found at i:125646 original size:23 final size:23
Alignment explanation
Indices: 125620--125668 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
125610 ATAAAGAACC
*
125620 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
125643 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
125666 AAA
1 AAA
125669 CAAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:127463 original size:18 final size:18
Alignment explanation
Indices: 127440--127510 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
127430 GTTCTTAAGG
*
127440 AGTGGTCCTTCGGGATAT
1 AGTGGTCATTCGGGATAT
* *
127458 AGTGGTCATTCGAGACAT
1 AGTGGTCATTCGGGATAT
*
127476 AGTGGTCCTTCGGGATAT
1 AGTGGTCATTCGGGATAT
*
127494 AATGGTCATTCGGGATA
1 AGTGGTCATTCGGGATA
127511 ATTTCTACGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (18 bp):
AGTGGTCATTCGGGATAT
Found at i:129845 original size:20 final size:20
Alignment explanation
Indices: 129820--129857 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
129810 TTTATGGTGG
*
129820 GTAGTATCGGTACTCTAGCT
1 GTAGTATCGATACTCTAGCT
129840 GTAGTATCGATACTCTAG
1 GTAGTATCGATACTCTAG
129858 GGTCAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
GTAGTATCGATACTCTAGCT
Found at i:141039 original size:42 final size:42
Alignment explanation
Indices: 140972--141063 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
140962 GTGGATTGGA
*
140972 TTAAGGATCCAGGCGGTTGTCTGGCTTTTGTTTCTTTCCTAG
1 TTAAGGATCCAGGCGATTGTCTGGCTTTTGTTTCTTTCCTAG
*
141014 TTAAGGATCCAGGCGATTGTTTGGCTTTTGTTTCTTTCCTAG
1 TTAAGGATCCAGGCGATTGTCTGGCTTTTGTTTCTTTCCTAG
141056 TTAAGGAT
1 TTAAGGAT
141064 ATTGCTAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.43
Consensus pattern (42 bp):
TTAAGGATCCAGGCGATTGTCTGGCTTTTGTTTCTTTCCTAG
Found at i:147054 original size:8 final size:8
Alignment explanation
Indices: 147041--147067 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
147031 GTGTGTCCTT
147041 TTTCTTCC
1 TTTCTTCC
147049 TTTCTTCC
1 TTTCTTCC
147057 TTTCTTCC
1 TTTCTTCC
147065 TTT
1 TTT
147068 TCATAGAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTCTTCC
Found at i:159659 original size:8 final size:8
Alignment explanation
Indices: 159647--159677 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
159637 AGAATATCTG
*
159647 CTCTCTCG
1 CTCTCTCA
159655 CTCTCTCA
1 CTCTCTCA
159663 CTCTCTCA
1 CTCTCTCA
159671 CTCTCTC
1 CTCTCTC
159678 CATTTCTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.06, C:0.52, G:0.03, T:0.39
Consensus pattern (8 bp):
CTCTCTCA
Found at i:165176 original size:23 final size:23
Alignment explanation
Indices: 165150--165193 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
165140 CCATACCAGA
165150 TTTTTT-TCCAGATAAAAAATCAG
1 TTTTTTATCC-GATAAAAAATCAG
*
165173 TTTTTTATCCGGTAAAAAATC
1 TTTTTTATCCGATAAAAAATC
165194 CGGTCGTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (23 bp):
TTTTTTATCCGATAAAAAATCAG
Found at i:167666 original size:21 final size:21
Alignment explanation
Indices: 167640--167685 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
167630 TGATTTATTA
167640 TTATGGAGTTCAAGTTGGTTG
1 TTATGGAGTTCAAGTTGGTTG
* *
167661 TTATGGATTTCAAGTTTGTTG
1 TTATGGAGTTCAAGTTGGTTG
167682 TTAT
1 TTAT
167686 AGATGTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.04, G:0.26, T:0.50
Consensus pattern (21 bp):
TTATGGAGTTCAAGTTGGTTG
Found at i:167694 original size:21 final size:21
Alignment explanation
Indices: 167649--167698 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
167639 ATTATGGAGT
* * *
167649 TCAAGTTGGTTGTTATGGATT
1 TCAAGTTTGTTGTTATAGATG
167670 TCAAGTTTGTTGTTATAGATG
1 TCAAGTTTGTTGTTATAGATG
167691 TCAAGTTT
1 TCAAGTTT
167699 ATTGAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.06, G:0.24, T:0.48
Consensus pattern (21 bp):
TCAAGTTTGTTGTTATAGATG
Done.