Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008179.1 Hibiscus syriacus cultivar Beakdansim tig00110776_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: 726026
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 3
Found at i:7371 original size:20 final size:21
Alignment explanation
Indices: 7326--7379 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
7316 ACATTCATGA
7326 GGTATCGATA-CATGAAGAAC
1 GGTATCGATACCATGAAGAAC
** *
7346 AATATCGATACCAT-AAGGAC
1 GGTATCGATACCATGAAGAAC
7366 GGTATCGATACCAT
1 GGTATCGATACCAT
7380 CTTTGAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (21 bp):
GGTATCGATACCATGAAGAAC
Found at i:9456 original size:13 final size:13
Alignment explanation
Indices: 9440--9475 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
9430 GCCCCGATTA
*
9440 CCCGATTATCCGC
1 CCCGATTACCCGC
9453 CCCGATTACCCGC
1 CCCGATTACCCGC
9466 CCCGA-TACCC
1 CCCGATTACCC
9476 AACCCGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.17, C:0.53, G:0.14, T:0.17
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:9543 original size:27 final size:27
Alignment explanation
Indices: 9484--9544 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
9474 CCAACCCGAT
* *
9484 AAATATTAAAAATAATTATTTATATATA
1 AAATATTAAAAAT-ATTATTTAAATAAA
*
9512 TAATATTAAAAAT-TTAATTTAAATAAA
1 AAATATTAAAAATATT-ATTTAAATAAA
9539 AAATAT
1 AAATAT
9545 ATTTAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 14 0.50
28 12 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AAATATTAAAAATATTATTTAAATAAA
Found at i:9548 original size:17 final size:18
Alignment explanation
Indices: 9505--9551 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
9495 ATAATTATTT
* *
9505 ATATATATAATATTAAAA
1 ATATATTTAATATAAAAA
*
9523 ATTTAATTTAA-ATAAAAA
1 ATAT-ATTTAATATAAAAA
9541 ATATATTTAAT
1 ATATATTTAAT
9552 TTAATATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATTTAATATAAAAA
Found at i:9580 original size:12 final size:12
Alignment explanation
Indices: 9563--9591 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
9553 TAATATATAT
9563 ATACCTGGCCCA
1 ATACCTGGCCCA
9575 ATACCTGGCCCA
1 ATACCTGGCCCA
9587 ATACC
1 ATACC
9592 CGTTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.41, G:0.14, T:0.17
Consensus pattern (12 bp):
ATACCTGGCCCA
Found at i:13970 original size:77 final size:77
Alignment explanation
Indices: 13841--13992 Score: 180
Period size: 77 Copynumber: 2.0 Consensus size: 77
13831 GCTATGAAAT
* * * * *
13841 AGTTATCCTGAAGGAGCTTTAAGTTGATATGAAATAATTAATTTAACCATGTATATTTAGTGGAA
1 AGTTAACCCGAAGGAGCTTTAAATCGATATGAAATAATTAATTTAACCATGTATATGTAGTGGAA
13906 AAGTGTTGAAGA
66 AAGTGTTGAAGA
* * * * *
13918 AGTTAACCCGAAGGATCTTTAAATCGATGTGAAAT-ATCTAATTTTACTATGTATGTGTAGTGGA
1 AGTTAACCCGAAGGAGCTTTAAATCGATATGAAATAAT-TAATTTAACCATGTATATGTAGTGGA
**
13982 AACTTGTTGAA
65 AAAGTGTTGAA
13993 ACAGGCAAAC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
76 2 0.03
77 60 0.97
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (77 bp):
AGTTAACCCGAAGGAGCTTTAAATCGATATGAAATAATTAATTTAACCATGTATATGTAGTGGAA
AAGTGTTGAAGA
Found at i:16067 original size:24 final size:24
Alignment explanation
Indices: 16023--16069 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16013 ATAAAGAACC
*
16023 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
16047 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
16070 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:19382 original size:19 final size:20
Alignment explanation
Indices: 19360--19403 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19350 GAGAAAAGGT
19360 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
19379 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
19399 AAAAG
1 AAAAG
19404 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:26297 original size:24 final size:24
Alignment explanation
Indices: 26253--26299 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
26243 ATAAAGAACC
*
26253 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
26277 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
26300 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:32725 original size:38 final size:38
Alignment explanation
Indices: 32674--32749 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
32664 ATGAATGTCA
32674 AATGGTTTGTGAAAAACGAGGGAGTGTACTCAAGAAAG
1 AATGGTTTGTGAAAAACGAGGGAGTGTACTCAAGAAAG
32712 AATGGTTTGTGAAAAACGAGGGAGTGTACTCAAGAAAG
1 AATGGTTTGTGAAAAACGAGGGAGTGTACTCAAGAAAG
32750 TTTAAAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.08, G:0.32, T:0.21
Consensus pattern (38 bp):
AATGGTTTGTGAAAAACGAGGGAGTGTACTCAAGAAAG
Found at i:46405 original size:64 final size:63
Alignment explanation
Indices: 46312--46451 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 63
46302 ATATTGAATG
* *
46312 TGCATCGATGCACTCTTTAAAGAAGAAACACCAAATGCAATTGGTGCATCGATGCATAAGGAA
1 TGCATCGATGCACCCTTTAAAGAAGAAACACCAAAGGCAATTGGTGCATCGATGCATAAGGAA
* * * * * * * * *
46375 TGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGAGTAG
1 TGCATCGATGCA-CCCTTTAAAGAAG-AAACACCAAAGGCAATTGGTGCATCGATGCATAAGGAA
46439 TGCATCGATGCAC
1 TGCATCGATGCAC
46452 ATGTTAAAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 15 0.23
64 49 0.77
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACCCTTTAAAGAAGAAACACCAAAGGCAATTGGTGCATCGATGCATAAGGAA
Found at i:46484 original size:20 final size:22
Alignment explanation
Indices: 46439--46496 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
46429 GCATGAGTAG
46439 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
46463 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
46483 TGCATCGATGCACT
1 TGCATCGATGCACT
46497 TCAAGGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:47416 original size:31 final size:31
Alignment explanation
Indices: 47378--47436 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
47368 GAGTCGAGGG
*
47378 TTTACCTATGTTCTAAGGAACATATGGACAT
1 TTTACCTAGGTTCTAAGGAACATATGGACAT
** *
47409 TTTACCTAGGTTCTTCGGAACCTATGGA
1 TTTACCTAGGTTCTAAGGAACATATGGA
47437 TAGTTACCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (31 bp):
TTTACCTAGGTTCTAAGGAACATATGGACAT
Found at i:47467 original size:30 final size:30
Alignment explanation
Indices: 47428--47589 Score: 306
Period size: 30 Copynumber: 5.4 Consensus size: 30
47418 GTTCTTCGGA
*
47428 ACCTATGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
47458 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
47488 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
47518 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
*
47548 ACCTCTGGATAGTTACCGATGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
47578 ACCTCTGGATAG
1 ACCTCTGGATAG
47590 GTCCTTCGGG
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 130 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:48540 original size:83 final size:83
Alignment explanation
Indices: 48400--48563 Score: 312
Period size: 83 Copynumber: 2.0 Consensus size: 83
48390 GCCGATTCTA
48400 GGCTTAAACCGAAGTCAAATGAGTTTTAAAAATGTGTACATGCCAACATAGAGTGAAAATTTCTG
1 GGCTTAAACCGAAGTCAAATGAGTTTTAAAAATGTGTACATGCCAACATAGAGTGAAAATTTCTG
48465 ATCTGATAGGGTAAGGAGT
66 ATCTGATA-GGTAAGGAGT
48484 GGCTTAAACCG-AGTCAAATGAGTTTTAAAAATGTGTACATGCCAACATAGAGTGAAAATTTCTG
1 GGCTTAAACCGAAGTCAAATGAGTTTTAAAAATGTGTACATGCCAACATAGAGTGAAAATTTCTG
48548 ATCTGATAGGTAAGGA
66 ATCTGATAGGTAAGGA
48564 TGTGATGTCG
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
82 8 0.10
83 61 0.76
84 11 0.14
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.27
Consensus pattern (83 bp):
GGCTTAAACCGAAGTCAAATGAGTTTTAAAAATGTGTACATGCCAACATAGAGTGAAAATTTCTG
ATCTGATAGGTAAGGAGT
Found at i:50832 original size:63 final size:62
Alignment explanation
Indices: 50744--50903 Score: 180
Period size: 63 Copynumber: 2.5 Consensus size: 62
50734 ATTATGGCAA
* * * *
50744 GGTGTATCGATGCATATGATGTGCATCGATGCACTCTTTAAAGAAG-AAACATCGAATGCAATT
1 GGTGCATCGATGCATAAG-TGTGCATCGATGCACCCTTTAAA-AAGAAAACATCGAAGGCAATT
* *
50807 GGTGCATCGATGCATAAG-GAATGCATCGATGCATCCCTTTAAAATGAAAACATCGAAGGTAATT
1 GGTGCATCGATGCATAAGTG--TGCATCGATGCA-CCCTTTAAAAAGAAAACATCGAAGGCAATT
* * *
50871 TGTGTATCGATGCATGAGTGTGCATCGATGCAC
1 GGTGCATCGATGCATAAGTGTGCATCGATGCAC
50904 ATGTTAAAGA
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 42 0.51
64 38 0.46
65 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (62 bp):
GGTGCATCGATGCATAAGTGTGCATCGATGCACCCTTTAAAAAGAAAACATCGAAGGCAATT
Found at i:50936 original size:20 final size:22
Alignment explanation
Indices: 50891--50948 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
50881 TGCATGAGTG
50891 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
50915 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
50935 TGCATCGATGCACT
1 TGCATCGATGCACT
50949 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:51914 original size:29 final size:29
Alignment explanation
Indices: 51846--51995 Score: 185
Period size: 29 Copynumber: 5.4 Consensus size: 29
51836 GGTTCTTCGG
*
51846 GACCTATGGATAGTTACCGA-GATCTTTAT
1 GACCTCTGGATAG-TACCGAGGATCTTTAT
51875 G---TCTGGATAGTACCGAGGATCTTTAT
1 GACCTCTGGATAGTACCGAGGATCTTTAT
51901 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAG-TACCGAGGATCTTTAT
51931 GACC-CTGGATAGT---GAGGATC-TTAT
1 GACCTCTGGATAGTACCGAGGATCTTTAT
* *
51955 GACCTCTGGATAGTTCCGATGATCTTTAT
1 GACCTCTGGATAGTACCGAGGATCTTTAT
51984 GACCTCT-GATAG
1 GACCTCTGGATAG
51996 GTCCTTCGGG
Statistics
Matches: 109, Mismatches: 2, Indels: 21
0.83 0.02 0.16
Matches are distributed among these distances:
24 8 0.07
25 22 0.20
26 18 0.17
28 12 0.11
29 29 0.27
30 20 0.18
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (29 bp):
GACCTCTGGATAGTACCGAGGATCTTTAT
Found at i:51948 original size:55 final size:54
Alignment explanation
Indices: 51846--51995 Score: 193
Period size: 55 Copynumber: 2.8 Consensus size: 54
51836 GGTTCTTCGG
* *
51846 GACCTATGGATAGTTACCGAGATCTTTATG--TCTGGATAGTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGATCTTTATGACCCTGGATAGT--CGAGGATC-TTAT
51901 GACCTCTGGATAGTTACCGAGGATCTTTATGACCCTGGATAGT-GAGGATCTTAT
1 GACCTCTGGATAGTTACCGA-GATCTTTATGACCCTGGATAGTCGAGGATCTTAT
51955 GACCTCTGGATAGTT-CCGATGATCTTTATGACCTCT-GATAG
1 GACCTCTGGATAGTTACCGA-GATCTTTATGACC-CTGGATAG
51996 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
53 22 0.25
54 21 0.24
55 26 0.30
56 10 0.11
58 9 0.10
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (54 bp):
GACCTCTGGATAGTTACCGAGATCTTTATGACCCTGGATAGTCGAGGATCTTAT
Found at i:59874 original size:2 final size:2
Alignment explanation
Indices: 59867--59909 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
59857 GCAAAGGTGA
59867 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
59909 C
1 C
59910 ACACACACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:76050 original size:13 final size:13
Alignment explanation
Indices: 76032--76063 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
76022 TTGCTTTCGT
76032 AGCAACCAAAATC
1 AGCAACCAAAATC
76045 AGCAACCAAAATC
1 AGCAACCAAAATC
*
76058 AACAAC
1 AGCAAC
76064 TTTTCCCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.31, G:0.06, T:0.06
Consensus pattern (13 bp):
AGCAACCAAAATC
Found at i:90206 original size:23 final size:23
Alignment explanation
Indices: 90178--90221 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
90168 TAACGAATAT
90178 TAAAAAT-ATTTTAATTAAAATTA
1 TAAAAATGA-TTTAATTAAAATTA
*
90201 TAAAAATGATTTATTTAAAAT
1 TAAAAATGATTTAATTAAAAT
90222 ATGAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAAAATGATTTAATTAAAATTA
Found at i:91538 original size:40 final size:40
Alignment explanation
Indices: 91483--91605 Score: 237
Period size: 40 Copynumber: 3.1 Consensus size: 40
91473 CTGCATATCG
91483 TAAGGAGCCAAGCCAAAGCTCTAGTTACAAGGAATGCTTC
1 TAAGGAGCCAAGCCAAAGCTCTAGTTACAAGGAATGCTTC
*
91523 TAAGGAGCCCAGCCAAAGCTCTAGTTACAAGGAATGCTTC
1 TAAGGAGCCAAGCCAAAGCTCTAGTTACAAGGAATGCTTC
91563 TAAGGAGCCAAGCCAAAGCTCTAGTTACAAGGAATGCTTC
1 TAAGGAGCCAAGCCAAAGCTCTAGTTACAAGGAATGCTTC
91603 TAA
1 TAA
91606 CATATCTGCA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (40 bp):
TAAGGAGCCAAGCCAAAGCTCTAGTTACAAGGAATGCTTC
Found at i:98734 original size:7 final size:7
Alignment explanation
Indices: 98729--98848 Score: 119
Period size: 7 Copynumber: 18.1 Consensus size: 7
98719 TCATTTTTTC
98729 TTTT-TT
1 TTTTCTT
98735 TTTTCTT
1 TTTTCTT
98742 TTTTCTT
1 TTTTCTT
98749 TTTTC-T
1 TTTTCTT
98755 TTTT-TT
1 TTTTCTT
*
98761 TTTTATT
1 TTTTCTT
*
98768 TTTTATT
1 TTTTCTT
*
98775 TTTTATT
1 TTTTCTT
98782 TTTTCTT
1 TTTTCTT
98789 TTTTCTT
1 TTTTCTT
98796 TTTTCTT
1 TTTTCTT
*
98803 TTTT-TC
1 TTTTCTT
*
98809 CTTT-TT
1 TTTTCTT
*
98815 TTTTCAT
1 TTTTCTT
98822 TTTTC-T
1 TTTTCTT
*
98828 TTTTCAT
1 TTTTCTT
*
98835 TTTTC-A
1 TTTTCTT
98841 TTTTCTT
1 TTTTCTT
98848 T
1 T
98849 CATTTTTCCT
Statistics
Matches: 100, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
6 33 0.33
7 67 0.67
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:98788 original size:40 final size:40
Alignment explanation
Indices: 98722--98855 Score: 159
Period size: 40 Copynumber: 3.3 Consensus size: 40
98712 TTTTCAGTCA
*
98722 TTTTTTCTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTT-T
1 TTTTTTCTTTTTTTTTTATTTTTTCTTTTTTCTTTTTTCT
98761 TTTTATT-TTTTATTTTTTATTTTTTCTTTTTTCTTTTTTCT
1 TTTT-TTCTTTT-TTTTTTATTTTTTCTTTTTTCTTTTTTCT
* *
98802 TTTTTTCCTTTTTTTTTCA-TTTTTC-TTTTTCATTTTTCAT
1 TTTTTT-CTTTTTTTTTTATTTTTTCTTTTTTCTTTTTTC-T
*
98842 TTTCTTTCATTTTT
1 TTT-TTTCTTTTTT
98856 CCTCTTTTTT
Statistics
Matches: 84, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
39 20 0.24
40 46 0.55
41 14 0.17
42 4 0.05
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (40 bp):
TTTTTTCTTTTTTTTTTATTTTTTCTTTTTTCTTTTTTCT
Found at i:98792 original size:47 final size:46
Alignment explanation
Indices: 98729--98872 Score: 166
Period size: 47 Copynumber: 3.0 Consensus size: 46
98719 TCATTTTTTC
*
98729 TTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTT-TTTTATTTTTTATT
1 TTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTTCTTTT-TTTTTCATT
98775 TTTTATTTTTTCTTTTTTCTTTTTTCTTTTTTTCCTTTTTTTTTCA-T
1 TTTT-TTTTTTCTTTTTTCTTTTTTCTTTTTTT-CTTTTTTTTTCATT
* * * *
98822 TTTTCTTTTTCATTTTTCATTTTCTTTCATTTTTCCTCTTTTTTTTCATT
1 TTTTTTTTTTCTTTTTTC--TTT-TTTCTTTTTTTCT-TTTTTTTTCATT
98872 T
1 T
98873 CTTATTCAAG
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
46 16 0.19
47 33 0.39
48 11 0.13
49 23 0.27
50 2 0.02
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (46 bp):
TTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTTCTTTTTTTTTCATT
Found at i:98838 original size:1 final size:1
Alignment explanation
Indices: 98722--98818 Score: 86
Period size: 1 Copynumber: 97.0 Consensus size: 1
98712 TTTTCAGTCA
* * * * * * * *
98722 TTTTTTCTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTTTTTTATTTTTTATTTTTTATTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * **
98787 TTTTTTCTTTTTTCTTTTTTTCCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
98819 CATTTTTCTT
Statistics
Matches: 74, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:98856 original size:7 final size:6
Alignment explanation
Indices: 98723--98848 Score: 91
Period size: 6 Copynumber: 20.5 Consensus size: 6
98713 TTTCAGTCAT
* *
98723 TTTTTC TTTTT- TTTTTC TTTTTTC TTTTTTC TTTTTT TTTTTA TTTTT-
1 TTTTTC TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC
* * *
98771 TATTT- TTTAT- TTTTTC TTTTTTC TTTTTTC TTTTT- TTCCTTTT TTTTTC
1 TTTTTC TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTTC TT--TTTC TTTTTC
*
98820 ATTTTTC TTTTTC ATTTTTC ATTTTC TTT
1 -TTTTTC TTTTTC -TTTTTC TTTTTC TTT
98849 CATTTTTCCT
Statistics
Matches: 102, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
5 18 0.18
6 41 0.40
7 41 0.40
8 2 0.02
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:98865 original size:40 final size:36
Alignment explanation
Indices: 98722--98865 Score: 121
Period size: 33 Copynumber: 4.2 Consensus size: 36
98712 TTTTCAGTCA
98722 TTTTTTCTTTTT-TTTTTC--TTTTTTC-TTTTTTC
1 TTTTTTCTTTTTCTTTTTCATTTTTTTCATTTTTTC
* *
98754 TTTTTT-TTTTTATTTTTTA-TTTTTT-ATTTTTTC
1 TTTTTTCTTTTTCTTTTTCATTTTTTTCATTTTTTC
**
98787 TTTTTTCTTTTTTCTTTTT--TTCCTTT--TTTTTTC
1 TTTTTTC-TTTTTCTTTTTCATTTTTTTCATTTTTTC
*
98820 ATTTTTCTTTTTCATTTTTCATTTTCTTTCATTTTTCCTC
1 TTTTTTCTTTTTC-TTTTTCATTTT-TTTCATTTTT--TC
98860 TTTTTT
1 TTTTTT
98866 TTCATTTCTT
Statistics
Matches: 90, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
31 5 0.06
32 17 0.19
33 37 0.41
34 4 0.04
35 12 0.13
36 3 0.03
38 5 0.06
40 7 0.08
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (36 bp):
TTTTTTCTTTTTCTTTTTCATTTTTTTCATTTTTTC
Found at i:98873 original size:24 final size:22
Alignment explanation
Indices: 98803--98875 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 22
98793 CTTTTTTCTT
98803 TTTTTCCTTTTTTTTTCATTTTTC
1 TTTTTCCTTTTTTTTTCA--TTTC
*
98827 TTTTTCATTTTTCATTTTC-TTTC
1 TTTTTCCTTTTT--TTTTCATTTC
98850 ATTTTTCCTCTTTTTTTTCATTTC
1 -TTTTTCCT-TTTTTTTTCATTTC
98874 TT
1 TT
98876 ATTCAAGCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
23 11 0.26
24 22 0.52
25 4 0.10
26 5 0.12
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTCCTTTTTTTTTCATTTC
Found at i:107899 original size:38 final size:37
Alignment explanation
Indices: 107855--107997 Score: 120
Period size: 34 Copynumber: 3.9 Consensus size: 37
107845 TTAAAAATAA
*
107855 TTTTTGAAAAAATATA-ATATATGATTTTTAGAAAACGG
1 TTTTTGAAAAAATATATATATAT-AGTTTT-GAAAACGG
* *
107893 TTTTTGAATATATATATATATATAGTTTTGAAAAC--
1 TTTTTGAAAAAATATATATATATAGTTTTGAAAACGG
* * * *
107928 ATTTCGAAAATATATATATTATATAG-TTTG-AAA--T
1 TTTTTGAAAAAATATATA-TATATAGTTTTGAAAACGG
*
107962 TTTTTGAAAACATATATAATATATAGTTTTTGAAAA
1 TTTTTGAAAAAATATAT-ATATATAG-TTTTGAAAA
107998 TATATATAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
34 24 0.27
35 20 0.22
36 11 0.12
37 9 0.10
38 19 0.21
39 6 0.07
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAAAATATATATATATAGTTTTGAAAACGG
Found at i:107977 original size:36 final size:35
Alignment explanation
Indices: 107899--108098 Score: 143
Period size: 37 Copynumber: 5.8 Consensus size: 35
107889 ACGGTTTTTG
107899 AATATATATATATATATAGTTTTGAAAACATTTCGAA
1 AATATATATAT-TATATAG-TTTGAAAACATTTCGAA
** *
107936 AATATATATATTATATAGTTTG-AAATTTTTTGAA
1 AATATATATATTATATAGTTTGAAAACATTTCGAA
* *
107970 AACATATATAATATATAG-TT-------TTT-GAA
1 AATATATATATTATATAGTTTGAAAACATTTCGAA
* **
107996 AATATATATAATATATAGTTTTTG-AAACATTTTTAA
1 AATATATATATTATATAG--TTTGAAAACATTTCGAA
* * * *
108032 TATATATATATAATATAGTTTTCAAAACATTTTTGAA
1 AATATATATATTATATAG-TTTGAAAACA-TTTCGAA
*
108069 AACATATATATTATATAGTTTTGAAAACAT
1 AATATATATATTATATAG-TTTGAAAACAT
108099 ATATATAATA
Statistics
Matches: 135, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
26 20 0.15
27 3 0.02
29 2 0.01
33 2 0.01
34 25 0.19
35 11 0.08
36 30 0.22
37 42 0.31
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (35 bp):
AATATATATATTATATAGTTTGAAAACATTTCGAA
Found at i:108009 original size:24 final size:26
Alignment explanation
Indices: 107962--108128 Score: 134
Period size: 26 Copynumber: 6.6 Consensus size: 26
107952 AGTTTGAAAT
107962 TTTTTGAAAACATATATAATATATAG
1 TTTTTGAAAACATATATAATATATAG
*
107988 TTTTTGAAAATATATATAATATATAG
1 TTTTTGAAAACATATATAATATATAG
* *
108014 TTTTTG-AAACATTTTTAATATATA-
1 TTTTTGAAAACATATATAATATATAG
* * * * * *
108038 TATAT-AATATAGT-TTTCAA-A-ACA-
1 TTTTTGAAAACA-TATAT-AATATATAG
*
108061 TTTTTGAAAACATATATATTATATAG
1 TTTTTGAAAACATATATAATATATAG
108087 -TTTTGAAAACATATATATAATATATAG
1 TTTTTGAAAAC--ATATATAATATATAG
* *
108114 TTTTTTAAAAAATAT
1 TTTTTGAAAACATAT
108129 TTTGAAAACA
Statistics
Matches: 111, Mismatches: 19, Indels: 22
0.73 0.12 0.14
Matches are distributed among these distances:
23 7 0.06
24 17 0.15
25 30 0.27
26 35 0.32
27 14 0.13
28 8 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (26 bp):
TTTTTGAAAACATATATAATATATAG
Found at i:108040 original size:62 final size:60
Alignment explanation
Indices: 107933--108053 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 60
107923 AAAACATTTC
* *
107933 GAAAATATATATATTATATAGTTTGAAATTTTTTGAAAACATATATA-ATATATAGTTTTT
1 GAAAATATATATAATATATAGTTTGAAAATTTTTGAAAACATATATATA-ATATAGTTTTT
* *
107993 GAAAATATATATAATATATAGTTTTTGAAACATTTTT-AATATATATATATAATATAGTTTT
1 GAAAATATATATAATATATAG--TTTGAAA-ATTTTTGAAAACATATATATAATATAGTTTT
108054 CAAAACATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
60 20 0.38
62 27 0.51
63 6 0.11
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (60 bp):
GAAAATATATATAATATATAGTTTGAAAATTTTTGAAAACATATATATAATATAGTTTTT
Found at i:108046 original size:64 final size:63
Alignment explanation
Indices: 107933--108209 Score: 179
Period size: 68 Copynumber: 4.1 Consensus size: 63
107923 AAAACATTTC
* * *
107933 GAAAATATATATATTATATAG-TTTGAAA-TTTTTTGAA-A-ACATATATAATATATAGTTTTT
1 GAAAATATATATAATATATAGTTTTGAAACATTTTT-AATATATATATATAATATATAGTTTTT
107993 GAAAATATATATAATATATAGTTTTTGAAACATTTTTAATATATATATATAATATAGTTTTCAAA
1 GAAAATATATATAATATATAG-TTTTGAAACATTTTTAATATATATATATAATATA----T----
*
108058 ACATTTTT
57 A-GTTTTT
* * * * * * *
108066 GAAAACATATATATTATATAGTTTTGAAAACATATATATAATATATAGTTTTTTAAAAAATA--T
1 GAAAATATATATAATATATAGTTTTG-AAACAT-T-TTTAATATATA--TATATAATATATAGTT
108129 TTT
61 TTT
* *
108132 GAAAACATATATATAATATATAGTTTTAAAAAAACATTTTGAATATATATATATATAATATATAG
1 G-AAA-ATATATATAATATATAGTTTT---GAAACATTTT-TA-ATATATATATATAATATATAG
*
108197 TTTTG
59 TTTTT
108202 GAAAATAT
1 GAAAATAT
108210 TTTTGAAAAT
Statistics
Matches: 168, Mismatches: 21, Indels: 48
0.71 0.09 0.20
Matches are distributed among these distances:
60 20 0.12
62 9 0.05
63 6 0.04
64 13 0.08
66 5 0.03
67 3 0.02
68 34 0.20
69 6 0.04
70 17 0.10
72 6 0.04
73 31 0.18
74 1 0.01
75 10 0.06
77 7 0.04
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (63 bp):
GAAAATATATATAATATATAGTTTTGAAACATTTTTAATATATATATATAATATATAGTTTTT
Found at i:108110 original size:133 final size:134
Alignment explanation
Indices: 107848--108239 Score: 347
Period size: 133 Copynumber: 2.8 Consensus size: 134
107838 ATAATTTTTA
*
107848 AAAATAATTTTTGAAAA-A-ATATAATATAT-GATTTTTAGAAAACGGTTTTTGAATATATATAT
1 AAAA-AATTTTTGAAAATATATATAATATATAG-TTTTT-G-AAAC-ATTTTT-AATATATATAT
* *** *
107910 AT-ATATAGTTTTGAAAACA-TTTCGAAAATATATATATTATATAG-TTTGAAATTTTTTGAAAA
60 ATAATATAGTTTTGAAAACATTTTTGAAAA-ATATATATTATATAGTTTTGAAAACATATGAAAA
107972 CATATATA-AT
124 CATATATATAT
* * *
107982 ATATAGTTTTTGAAAATATATATAATATATAGTTTTTGAAACATTTTTAATATATATATATAATA
1 AAAAAATTTTTGAAAATATATATAATATATAGTTTTTGAAACATTTTTAATATATATATATAATA
* *
108047 TAGTTTTCAAAACATTTTTGAAAACATATATATTATATAGTTTTGAAAACATAT-ATATAATATA
66 TAGTTTTGAAAACATTTTTGAAAA-ATATATATTATATAGTTTTGAAAACATATGA-A-AACATA
* *
108111 TAGTTTTTT
128 TA--TATAT
** *
108120 AAAAAATATTTTGAAAACATATATATAATATATAGTTTTAAAAAAACATTTTGAATATATATATA
1 AAAAAAT-TTTTG-AAA-ATATATATAATATATAGTTTT--TGAAACATTTT-TA-ATATATATA
* *
108185 TATAATATATAGTTTTGGAAAATATTTTTG--AAA-ATATATTATATAGTTTTAAAAA
59 TAT-A-ATATAGTTTT-GAAAACATTTTTGAAAAATATATATTATATAGTTTTGAAAA
108240 ACAATTTTTG
Statistics
Matches: 214, Mismatches: 23, Indels: 32
0.80 0.09 0.12
Matches are distributed among these distances:
131 13 0.06
132 21 0.10
133 39 0.18
134 14 0.07
135 23 0.11
136 1 0.00
137 1 0.00
138 5 0.02
139 5 0.02
140 3 0.01
141 21 0.10
143 9 0.04
144 22 0.10
145 13 0.06
146 3 0.01
147 10 0.05
148 11 0.05
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (134 bp):
AAAAAATTTTTGAAAATATATATAATATATAGTTTTTGAAACATTTTTAATATATATATATAATA
TAGTTTTGAAAACATTTTTGAAAAATATATATTATATAGTTTTGAAAACATATGAAAACATATAT
ATAT
Found at i:108133 original size:66 final size:67
Alignment explanation
Indices: 108031--108163 Score: 191
Period size: 66 Copynumber: 2.0 Consensus size: 67
108021 AACATTTTTA
* *
108031 ATATATATATATAATATAGTTTTCAAAACATTTTTGAAAACATATATAT-TATATAGTTTTGAAA
1 ATATATATATATAATATAGTTTTCAAAAAATTTTTGAAAACATATATATATATATAGTTTTAAAA
108095 AC
66 AC
*
108097 ATATATATA-AT-ATATAGTTTTTTAAAAAATATTTTGAAAACATATATATAATATATAGTTTTA
1 ATATATATATATAATATAG-TTTTCAAAAAAT-TTTTGAAAACATATATAT-ATATATAGTTTTA
108160 AAAA
63 AAAA
108164 AACATTTTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
64 6 0.10
65 12 0.20
66 27 0.45
68 15 0.25
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (67 bp):
ATATATATATATAATATAGTTTTCAAAAAATTTTTGAAAACATATATATATATATAGTTTTAAAA
AC
Found at i:108134 original size:41 final size:41
Alignment explanation
Indices: 108087--108260 Score: 186
Period size: 41 Copynumber: 4.4 Consensus size: 41
108077 TATTATATAG
*
108087 TTTTGAAAACATATATATAATATATAGTTTTTTAAAAAATA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAAATA
*
108128 TTTTGAAAACATATATATAATATATAG-TTTTAAAAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAAATA
* ** *
108168 TTTTGAATATATATATATATAATATATAGTTTTGGAAAATAT-
1 TTTTGAA-A-ACATATATATAATATATAGTTTTTAAAAAAATA
*
108210 TTTTG--AA-A-ATATAT--TATATAGTTTTAAAAAACAAT-
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAA-AATA
*
108245 TTTTGAAAATATATAT
1 TTTTGAAAACATATAT
108261 TATAGGGTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
34 15 0.13
35 7 0.06
36 6 0.05
37 3 0.03
38 2 0.02
39 5 0.04
40 18 0.16
41 28 0.24
42 23 0.20
43 8 0.07
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (41 bp):
TTTTGAAAACATATATATAATATATAGTTTTTAAAAAAATA
Found at i:108265 original size:35 final size:35
Alignment explanation
Indices: 108182--108276 Score: 113
Period size: 35 Copynumber: 2.7 Consensus size: 35
108172 GAATATATAT
** *
108182 ATATATAATATATAGTTTTGGAAAATATTTTTGAAA
1 ATATAT-ATATATAGTTTTAAAAAAAATTTTTGAAA
108218 ATATAT-TATATAGTTTTAAAAAACAATTTTTGAAA
1 ATATATATATATAGTTTTAAAAAA-AATTTTTGAAA
108253 ATATATAT-TATAGGGTTTTAAAAA
1 ATATATATATATA--GTTTTAAAAA
108277 CTTATAATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
34 15 0.29
35 20 0.38
36 7 0.13
37 10 0.19
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.43
Consensus pattern (35 bp):
ATATATATATATAGTTTTAAAAAAAATTTTTGAAA
Found at i:108271 original size:37 final size:35
Alignment explanation
Indices: 108184--108276 Score: 109
Period size: 34 Copynumber: 2.6 Consensus size: 35
108174 ATATATATAT
* ** *
108184 ATATAATATATAGTTTTGGAAAA-TATTTTTGAAA
1 ATATATTATATAGTTTTAAAAAACAATTTTTGAAA
108218 ATATATTATATAGTTTTAAAAAACAATTTTTGAAA
1 ATATATTATATAGTTTTAAAAAACAATTTTTGAAA
108253 ATATA-TATTATAGGGTTTTAAAAA
1 ATATATTA-TATA--GTTTTAAAAA
108277 CTTATAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
34 22 0.43
35 19 0.37
37 10 0.20
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.43
Consensus pattern (35 bp):
ATATATTATATAGTTTTAAAAAACAATTTTTGAAA
Found at i:108720 original size:20 final size:21
Alignment explanation
Indices: 108690--108728 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
108680 AACAACACAC
*
108690 AACATCAAACCAAGATCGGGG
1 AACATCAAACCAACATCGGGG
108711 AACA-CAAACCAACATCGG
1 AACATCAAACCAACATCGG
108729 TGGACCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (21 bp):
AACATCAAACCAACATCGGGG
Found at i:108769 original size:22 final size:22
Alignment explanation
Indices: 108744--108793 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
108734 CATGACGAAA
*
108744 AACAAAGAGGCAACCACTACAC
1 AACAAAGAGGCAACCAATACAC
*
108766 AACAAAGGGGCAACCAATACAC
1 AACAAAGAGGCAACCAATACAC
108788 AACAAA
1 AACAAA
108794 TGAGATACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.54, C:0.28, G:0.14, T:0.04
Consensus pattern (22 bp):
AACAAAGAGGCAACCAATACAC
Found at i:109557 original size:7 final size:7
Alignment explanation
Indices: 109547--109606 Score: 68
Period size: 7 Copynumber: 8.1 Consensus size: 7
109537 AATTTTAACA
109547 TTTTTAT
1 TTTTTAT
109554 TTTTTA-
1 TTTTTAT
109560 TTTTTAT
1 TTTTTAT
*
109567 TTTTGAT
1 TTTTTAT
109574 TTATTTAAT
1 TT-TTT-AT
109583 ATTTTTAT
1 -TTTTTAT
109591 TTTTTAT
1 TTTTTAT
109598 TTTCTTAT
1 TTT-TTAT
109606 T
1 T
109607 GTATTTTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
6 6 0.13
7 24 0.52
8 9 0.20
9 5 0.11
10 2 0.04
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTTAT
Found at i:109563 original size:5 final size:6
Alignment explanation
Indices: 109546--109600 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
109536 AAATTTTAAC
*
109546 ATTTTT ATTTTTT ATTTTT ATTTTT GA--TTT ATTTAAT ATTTTT ATTTTTT
1 ATTTTT A-TTTTT ATTTTT ATTTTT -ATTTTT ATTT-TT ATTTTT A-TTTTT
109596 ATTTT
1 ATTTT
109601 CTTATTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 19 0.46
7 18 0.44
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:109564 original size:13 final size:13
Alignment explanation
Indices: 109546--109600 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 13
109536 AAATTTTAAC
109546 ATTTTTATTTTTT
1 ATTTTTATTTTTT
*
109559 ATTTTTATTTTTG
1 ATTTTTATTTTTT
**
109572 A--TTTATTTAAT
1 ATTTTTATTTTTT
109583 ATTTTTATTTTTT
1 ATTTTTATTTTTT
109596 ATTTT
1 ATTTT
109601 CTTATTGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 8 0.24
13 26 0.76
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:109579 original size:24 final size:24
Alignment explanation
Indices: 109549--109599 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
109539 TTTTAACATT
**
109549 TTTATTTTTTATTTTTATTTTTGA
1 TTTATTTAATATTTTTATTTTTGA
*
109573 TTTATTTAATATTTTTATTTTTTA
1 TTTATTTAATATTTTTATTTTTGA
109597 TTT
1 TTT
109600 TCTTATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTATTTAATATTTTTATTTTTGA
Found at i:109585 original size:18 final size:16
Alignment explanation
Indices: 109539--109596 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 16
109529 TACTTTTAAA
*
109539 TTTTAACATTTTTATT
1 TTTTAATATTTTTATT
*
109555 TTTTATTTTTATTTTTGATT
1 TTTTA---ATATTTTT-ATT
109575 TATTTAATATTTTTATT
1 T-TTTAATATTTTTATT
109592 TTTTA
1 TTTTA
109597 TTTTCTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 9 0.26
17 4 0.12
18 7 0.21
19 6 0.18
20 4 0.12
21 4 0.12
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTAATATTTTTATT
Found at i:110549 original size:20 final size:20
Alignment explanation
Indices: 110509--110556 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
110499 AATCATATTG
*
110509 CCCATGGGTACAGATTCCCC
1 CCCAGGGGTACAGATTCCCC
110529 CCCAAGGGGTACAGATT-CCC
1 CCC-AGGGGTACAGATTCCCC
110549 CCCAGGGG
1 CCCAGGGG
110557 GAACATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 9 0.35
21 12 0.46
ACGTcount: A:0.21, C:0.38, G:0.27, T:0.15
Consensus pattern (20 bp):
CCCAGGGGTACAGATTCCCC
Found at i:110566 original size:20 final size:20
Alignment explanation
Indices: 110518--110566 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
110508 GCCCATGGGT
*
110518 ACAGATTCCCCCCCAAGGGGT
1 ACAGATT-CCCCCCAAGGGGA
*
110539 ACAGATTCCCCCCAGGGGGA
1 ACAGATTCCCCCCAAGGGGA
*
110559 ACATATTC
1 ACAGATTC
110567 ATTTTAATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.16
Consensus pattern (20 bp):
ACAGATTCCCCCCAAGGGGA
Found at i:110671 original size:165 final size:165
Alignment explanation
Indices: 110399--110722 Score: 621
Period size: 165 Copynumber: 2.0 Consensus size: 165
110389 TGTTTCAAAG
*
110399 TTCATTTTAATCCTTACTAAAGTGTAAAATTATGTTTTATACTTAAATTATTTTTAAAACAATTT
1 TTCATTTTAATCCTTACTAAAGTGTAAAATTATGTTTTATACTTAAACTATTTTTAAAACAATTT
*
110464 TACAAAGTATTTCGAACCGTTTCAAAGCCAAGAAAAATCATATTGCCCATGGGTACAGATTCCCC
66 TACAAAGTATTTCGAACCGTTTCAAAGCCAAGAAAAATCATATTGCCCAGGGGTACAGATTCCCC
110529 CCCAAGGGGTACAGATTCCCCCCAGGGGGAACATA
131 CCCAAGGGGTACAGATTCCCCCCAGGGGGAACATA
*
110564 TTCATTTTAATCCTTACTAAAGTGTAAAATTGTGTTTTATACTTAAACTATTTTTAAAACAATTT
1 TTCATTTTAATCCTTACTAAAGTGTAAAATTATGTTTTATACTTAAACTATTTTTAAAACAATTT
110629 TACAAAGTATTTCGAACCGTTTCAAAGCCAAGAAAAATCATATTGCCCAGGGGTACAGATTCCCC
66 TACAAAGTATTTCGAACCGTTTCAAAGCCAAGAAAAATCATATTGCCCAGGGGTACAGATTCCCC
110694 CCCAAGGGGTACAGATTCCCCCCAGGGGG
131 CCCAAGGGGTACAGATTCCCCCCAGGGGG
110723 TACCGATTCC
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 156 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (165 bp):
TTCATTTTAATCCTTACTAAAGTGTAAAATTATGTTTTATACTTAAACTATTTTTAAAACAATTT
TACAAAGTATTTCGAACCGTTTCAAAGCCAAGAAAAATCATATTGCCCAGGGGTACAGATTCCCC
CCCAAGGGGTACAGATTCCCCCCAGGGGGAACATA
Found at i:110701 original size:21 final size:21
Alignment explanation
Indices: 110677--110735 Score: 93
Period size: 20 Copynumber: 2.9 Consensus size: 21
110667 CATATTGCCC
110677 AGGGGTACAGATTCCCCCCCA
1 AGGGGTACAGATTCCCCCCCA
110698 AGGGGTACAGATT-CCCCCCA
1 AGGGGTACAGATTCCCCCCCA
* *
110718 GGGGGTACCGATTCCCCC
1 AGGGGTACAGATTCCCCC
110736 TGTCTAACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.15
Consensus pattern (21 bp):
AGGGGTACAGATTCCCCCCCA
Found at i:111121 original size:34 final size:32
Alignment explanation
Indices: 111082--111151 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
111072 TTTTGTAAAG
*
111082 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
111116 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
111148 GGGA
1 GGGA
111152 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:113046 original size:2 final size:2
Alignment explanation
Indices: 113039--113069 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
113029 AGCAATATTA
113039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
113070 ACACTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113883 original size:44 final size:44
Alignment explanation
Indices: 113815--113950 Score: 218
Period size: 44 Copynumber: 3.1 Consensus size: 44
113805 CATTGTCTGA
*
113815 TATCGATACTACTATATATAGAAGTATCGACACTCCTTGGACGG
1 TATCGATACTACTATATATAGAAGTATCGATACTCCTTGGACGG
* * * **
113859 TATCGATACTACTATATATGGAAGTATCGATATTCATTGGATTG
1 TATCGATACTACTATATATAGAAGTATCGATACTCCTTGGACGG
113903 TATCGATACTACTATATATAGAAGTATCGATACTCCTTGGACGG
1 TATCGATACTACTATATATAGAAGTATCGATACTCCTTGGACGG
113947 TATC
1 TATC
113951 TATATTGTTG
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 81 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (44 bp):
TATCGATACTACTATATATAGAAGTATCGATACTCCTTGGACGG
Found at i:113885 original size:24 final size:24
Alignment explanation
Indices: 113815--113936 Score: 93
Period size: 24 Copynumber: 5.4 Consensus size: 24
113805 CATTGTCTGA
*
113815 TATCGATACTACTATATATAGAAG
1 TATCGATACTACTATATATGGAAG
** *
113839 TATCG--AC-ACT-CCT-TGGACGG
1 TATCGATACTACTATATATGGA-AG
113859 TATCGATACTACTATATATGGAAG
1 TATCGATACTACTATATATGGAAG
* *
113883 TATCGATA-T--T-CAT-TGGATTG
1 TATCGATACTACTATATATGGA-AG
*
113903 TATCGATACTACTATATATAGAAG
1 TATCGATACTACTATATATGGAAG
113927 TATCGATACT
1 TATCGATACT
113937 CCTTGGACGG
Statistics
Matches: 74, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
19 7 0.09
20 18 0.24
21 5 0.07
22 4 0.05
23 5 0.07
24 28 0.38
25 7 0.09
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (24 bp):
TATCGATACTACTATATATGGAAG
Found at i:114270 original size:15 final size:15
Alignment explanation
Indices: 114250--114280 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
114240 ATTATCAATG
114250 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
114265 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
114280 A
1 A
114281 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:114970 original size:6 final size:6
Alignment explanation
Indices: 114961--114995 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
114951 AATTAAGATG
114961 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAA
114996 ATCTGTGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (6 bp):
GAAAAT
Found at i:119804 original size:33 final size:33
Alignment explanation
Indices: 119757--119850 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
119747 ACCCGACCTA
* *
119757 ACCCGAAAACTATACATCCTCCACCCAAAGCCT
1 ACCCGAAAAATATACACCCTCCACCCAAAGCCT
* * ** *
119790 ACCCGAAAATTATACACCCTTCACCTGAATCCT
1 ACCCGAAAAATATACACCCTCCACCCAAAGCCT
* * *
119823 ATCTGAAAAATATATACCCTCCACCCAA
1 ACCCGAAAAATATACACCCTCCACCCAA
119851 TTAATTTTTT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.37, C:0.37, G:0.05, T:0.20
Consensus pattern (33 bp):
ACCCGAAAAATATACACCCTCCACCCAAAGCCT
Found at i:122943 original size:15 final size:15
Alignment explanation
Indices: 122925--122953 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
122915 TTTTTATCAC
122925 GATAATCCTTATTAT
1 GATAATCCTTATTAT
122940 GATAATCCTTATTA
1 GATAATCCTTATTA
122954 GATGAAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (15 bp):
GATAATCCTTATTAT
Found at i:126263 original size:41 final size:39
Alignment explanation
Indices: 126218--126391 Score: 190
Period size: 42 Copynumber: 4.3 Consensus size: 39
126208 ACTTCGACTA
*
126218 TCGCATTGCGATTTACATATTCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATTTACAAATT--CGTTGCGATAGTCCAAGT
* **
126259 TCGCATTGCGATTTTCCAAATTTATTGCGATAGTCCAAGT
1 TCGCATTGCGA-TTTACAAATTCGTTGCGATAGTCCAAGT
** *
126299 TCGCGCTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAGT
1 TCGCATTGCGATTTA---CAAATTCGTTGCGATAGTCCAAGT
*
126341 TCGCGTTGCGATTATTACAAATTCGTTGCGATAGTCCAAGT
1 TCGCATTGCGA-T-TTACAAATTCGTTGCGATAGTCCAAGT
126382 TCG--TTGCGAT
1 TCGCATTGCGAT
126392 AGTCGAAGTT
Statistics
Matches: 117, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
38 1 0.01
39 9 0.08
40 25 0.21
41 37 0.32
42 41 0.35
43 1 0.01
44 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (39 bp):
TCGCATTGCGATTTACAAATTCGTTGCGATAGTCCAAGT
Found at i:126267 original size:21 final size:21
Alignment explanation
Indices: 126237--126454 Score: 168
Period size: 21 Copynumber: 10.6 Consensus size: 21
126227 GATTTACATA
126237 TTCGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
126258 TTCGCATTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
**
126279 TT--TATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
126298 TTCGCGCTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
126321 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
126340 TTCGCGTTGCGATTATTACAAA
1 TTCGCGTTGCGA-TAGTCCAAG
126362 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
126381 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
126400 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
126423 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
126442 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
126455 TTATTCTAAA
Statistics
Matches: 153, Mismatches: 31, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
19 58 0.38
20 8 0.05
21 62 0.41
22 8 0.05
23 17 0.11
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:126295 original size:19 final size:20
Alignment explanation
Indices: 126243--126437 Score: 76
Period size: 19 Copynumber: 9.6 Consensus size: 20
126233 CATATTCGCG
*
126243 TTGCGATAGTCCAAGTTCGCA
1 TTGCGATAGTCCAAATTC-CA
** *
126264 TTGCGATTTTCCAAATT-TA
1 TTGCGATAGTCCAAATTCCA
* *
126283 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATTC-CA
* * **
126304 CTGCGATTTATTCCAAATT-TG
1 TTGCGA--TAGTCCAAATTCCA
* *
126325 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATTC-CA
* * *
126346 TTGCGATTATTACAAATT-CG
1 TTGCGA-TAGTCCAAATTCCA
* *
126366 TTGCGATAGTCCAAGTT-CG
1 TTGCGATAGTCCAAATTCCA
* * *
126385 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATTC-CA
* *
126406 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAATTCCA
126427 TTGCGATAGTC
1 TTGCGATAGTC
126438 GAAGTTCGCG
Statistics
Matches: 135, Mismatches: 28, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
19 54 0.40
20 8 0.06
21 48 0.36
22 8 0.06
23 17 0.13
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCCAAATTCCA
Found at i:126331 original size:42 final size:41
Alignment explanation
Indices: 126242--126391 Score: 225
Period size: 42 Copynumber: 3.7 Consensus size: 41
126232 ACATATTCGC
*
126242 GTTGCGATAGTCCAAGTTCGCATTGCGATT-TTCCAAATTT
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAATTT
* *
126282 ATTGCGATAGTCCAAGTTCGCGCTGCGATTTATTCCAAATTT
1 GTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATTT
* *
126324 GTTGCGATAGTCCAAGTTCGCGTTGCGATTATTACAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAATTT
126365 GTTGCGATAGTCCAAGTT--CGTTGCGAT
1 GTTGCGATAGTCCAAGTTCGCGTTGCGAT
126392 AGTCGAAGTT
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
39 9 0.09
40 25 0.25
41 31 0.31
42 36 0.36
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
GTTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAATTT
Found at i:126389 original size:102 final size:103
Alignment explanation
Indices: 126283--126482 Score: 332
Period size: 102 Copynumber: 2.0 Consensus size: 103
126273 TCCAAATTTA
*
126283 TTGCGATAGTCCAAGTTCGCGCTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGCTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTT
126348 GCGA-TTATTAC-AAATTCGTTGCGATAGTCCAAGTTCG
66 GCGATTTATT-CTAAATTCGTTGCGATAGTCCAAGTTCG
* * *
126385 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGCTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTT
*
126450 GCGATTTATTCTAAATTCGTTGTGATAGTCCAA
66 GCGATTTATTCTAAATTCGTTGCGATAGTCCAA
126483 AATCGCAACG
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
102 66 0.73
103 25 0.27
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (103 bp):
TTGCGATAGTCCAAGTTCGCGCTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTT
GCGATTTATTCTAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:126390 original size:60 final size:61
Alignment explanation
Indices: 126315--126454 Score: 210
Period size: 60 Copynumber: 2.3 Consensus size: 61
126305 TGCGATTTAT
* *
126315 TCCAAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTACAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
* *
126375 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
*
126436 TCGAAGTTCGCGTTGCGAT
1 TCCAAGTT--CGTTGCGAT
126455 TTATTCTAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
60 34 0.47
61 29 0.40
63 9 0.12
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
Found at i:126427 original size:42 final size:42
Alignment explanation
Indices: 126375--126479 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
126365 GTTGCGATAG
*
126375 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
126417 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
126459 TCTAAATTCGTTGTGATAGTC
1 TCCAAATTCGTTGCGATAGTC
126480 CAAAATCGCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:126470 original size:21 final size:21
Alignment explanation
Indices: 126305--126471 Score: 100
Period size: 19 Copynumber: 8.1 Consensus size: 21
126295 AAGTTCGCGC
*
126305 TGCGATTTATTCCAAATTTGT
1 TGCGATTTATTCCAAATTCGT
* *
126326 TGCGA--TAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATT--CGT
*
126347 TGCGA-TTATTACAAATTCGT
1 TGCGATTTATTCCAAATTCGT
* *
126367 TGCGA--TAGTCCAAGTTCGT
1 TGCGATTTATTCCAAATTCGT
* * *
126386 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATT--CGT
126407 TGCGATTTATTCCAAATTCGT
1 TGCGATTTATTCCAAATTCGT
* * *
126428 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATT--CGT
*
126449 TGCGATTTATTCTAAATTCGT
1 TGCGATTTATTCCAAATTCGT
126470 TG
1 TG
126472 TGATAGTCCA
Statistics
Matches: 116, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
19 43 0.37
20 8 0.07
21 41 0.35
22 8 0.07
23 16 0.14
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (21 bp):
TGCGATTTATTCCAAATTCGT
Found at i:126483 original size:61 final size:59
Alignment explanation
Indices: 126241--126454 Score: 162
Period size: 61 Copynumber: 3.5 Consensus size: 59
126231 TACATATTCG
** * ** *
126241 CGTTGCGATAGTCCAAGTTCGCATTGCGATTTTCCAAATT-TATTGCGA-TAGTCCAAGTT
1 CGTTGCGATAGTCCAAGTTCG--TTGCGATAGTCGAAATTCCGTTGCGATTAGTCCAAATT
* * * * * * * *
126300 CGCGCTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTATTACAAATT
1 --CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAATTC-CGTTGCGATTAGTCCAAATT
* *
126364 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAATTC-CGTTGCGA-TTAGTCCAAATT
*
126425 CGTTGCGATAGTCGAAGTTCGCGTTGCGAT
1 CGTTGCGATAGTCCAAGTT--CGTTGCGAT
126455 TTATTCTAAA
Statistics
Matches: 126, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
60 36 0.29
61 50 0.40
62 7 0.06
63 25 0.20
64 8 0.06
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (59 bp):
CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAATTCCGTTGCGATTAGTCCAAATT
Found at i:127414 original size:42 final size:42
Alignment explanation
Indices: 127352--127668 Score: 562
Period size: 42 Copynumber: 7.5 Consensus size: 42
127342 TGCGATTTTG
*
127352 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
127394 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
127436 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
127478 GACTATCGCAACGAACTTGGAATAAATCACAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
127520 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
127562 GACTATCGCAACGAACTTGGAATATATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
127604 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
127646 GACTATCGTAACGTGAACTTGGA
1 GACTATCGCAAC--GAACTTGGA
127669 CTATCGCAAC
Statistics
Matches: 263, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
42 254 0.97
44 9 0.03
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:131850 original size:18 final size:18
Alignment explanation
Indices: 131827--131869 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
131817 ATCACTTTAT
*
131827 TACTTGTTCGATTGTGTA
1 TACTTGCTCGATTGTGTA
131845 TACTTGCTCGATTGTGTA
1 TACTTGCTCGATTGTGTA
131863 TACTTGC
1 TACTTGC
131870 ACACATATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (18 bp):
TACTTGCTCGATTGTGTA
Found at i:133101 original size:15 final size:15
Alignment explanation
Indices: 133081--133137 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
133071 CCAGATATTA
133081 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
133096 CGGGTACCCGAATTTT
1 CGGGTACCCG-GTAAT
*
133112 GCGGGTACTCGGTAAT
1 -CGGGTACCCGGTAAT
133128 CGGGTACCCG
1 CGGGTACCCG
133138 ATACCCGGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 19 0.59
16 4 0.12
17 9 0.28
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:142994 original size:41 final size:41
Alignment explanation
Indices: 142917--143029 Score: 156
Period size: 41 Copynumber: 2.7 Consensus size: 41
142907 CGCCGCCGCC
* *
142917 ATCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACT
1 ATCGCAACGAATTTGGAAA--ATCGCAACGACAACTGTAGACT
142960 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
*
143001 ATCGCAACGCGAA-ATGGAAAATCGCAACG
1 ATCGCAA--CGAATTTGGAAAATCGCAACG
143030 CGAAATGGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
41 28 0.43
42 15 0.23
43 22 0.34
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
Found at i:143009 original size:22 final size:21
Alignment explanation
Indices: 142917--143009 Score: 82
Period size: 22 Copynumber: 4.4 Consensus size: 21
142907 CGCCGCCGCC
** *
142917 ATCGCAACGAATTTGTAAACT
1 ATCGCAACGAAACTGTAGACT
*
142938 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
* * **
142960 ATCGCAACG-AA-TTTGGAAA
1 ATCGCAACGAAACTGTAGACT
142979 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
143001 ATCGCAACG
1 ATCGCAACG
143010 CGAAATGGAA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
19 13 0.24
20 2 0.04
21 11 0.20
22 29 0.53
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAAACTGTAGACT
Found at i:143026 original size:20 final size:20
Alignment explanation
Indices: 143001--143096 Score: 183
Period size: 20 Copynumber: 4.8 Consensus size: 20
142991 ACTGTAGACT
143001 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
143021 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
143041 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
143061 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
143081 ATCGCAATGCGAAATG
1 ATCGCAACGCGAAATG
143097 CAACGCGAAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:144295 original size:23 final size:24
Alignment explanation
Indices: 144253--144315 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 24
144243 TTTGAAAGTA
*
144253 TTTGTTTATATTTTCGTGAACATG
1 TTTGTTTATATGTTCGTGAACATG
144277 TTTGTTTA-ATGTTCGTGAACATG
1 TTTGTTTATATGTTCGTGAACATG
* * *
144300 TTCGCTTATATATTCG
1 TTTGTTTATATGTTCG
144316 CGAATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.51
Consensus pattern (24 bp):
TTTGTTTATATGTTCGTGAACATG
Found at i:144510 original size:2 final size:2
Alignment explanation
Indices: 144503--144539 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
144493 CCGATACTTA
144503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
144540 AAGTAATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:155794 original size:19 final size:19
Alignment explanation
Indices: 155765--155801 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
155755 TGACATTGGT
155765 GATTTAATTTTATACTGGA
1 GATTTAATTTTATACTGGA
155784 GATTTAATTTTATACTGG
1 GATTTAATTTTATACTGG
155802 TGAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (19 bp):
GATTTAATTTTATACTGGA
Found at i:155810 original size:19 final size:19
Alignment explanation
Indices: 155769--155810 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
155759 ATTGGTGATT
**
155769 TAATTTTATACTGGAGATT
1 TAATTTTATACTGGAGAAA
*
155788 TAATTTTATACTGGTGAAA
1 TAATTTTATACTGGAGAAA
155807 TAAT
1 TAAT
155811 AAGTTTTGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (19 bp):
TAATTTTATACTGGAGAAA
Found at i:161716 original size:9 final size:9
Alignment explanation
Indices: 161704--161760 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
161694 TTATATTTAG
161704 TAATTTATT
1 TAATTTATT
161713 TAATTTATT
1 TAATTTATT
161722 TAATTTATT
1 TAATTTATT
161731 TAA-TTATT
1 TAATTTATT
161739 TAA--TATT
1 TAATTTATT
* *
161746 TTATTTAAT
1 TAATTTATT
161755 TAATTT
1 TAATTT
161761 TTTTTGCAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
7 6 0.14
8 8 0.19
9 29 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATTTATT
Found at i:161727 original size:26 final size:26
Alignment explanation
Indices: 161690--161742 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
161680 TAAGGTATAT
161690 TTTATTATATTTA-GTAATTTATTTAA
1 TTTATTATATTTATGTAA-TTATTTAA
*
161716 TTTATT-TAATTTATTTAATTATTTAA
1 TTTATTAT-ATTTATGTAATTATTTAA
161742 T
1 T
161743 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.04
26 20 0.83
27 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTATTATATTTATGTAATTATTTAA
Found at i:171796 original size:14 final size:12
Alignment explanation
Indices: 171765--171790 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
171755 AGTGTGATAG
171765 TACCAACACTAA
1 TACCAACACTAA
171777 TACCAACACTAA
1 TACCAACACTAA
171789 TA
1 TA
171791 TACCAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (12 bp):
TACCAACACTAA
Found at i:174705 original size:24 final size:24
Alignment explanation
Indices: 174673--174723 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
174663 TGACAGATGA
174673 TTAAAATAAAACTAAAACTTAACG
1 TTAAAATAAAACTAAAACTTAACG
174697 TTAAAATAAAACTAAAACTTAACG
1 TTAAAATAAAACTAAAACTTAACG
174721 TTA
1 TTA
174724 GATATGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (24 bp):
TTAAAATAAAACTAAAACTTAACG
Found at i:179808 original size:9 final size:9
Alignment explanation
Indices: 179793--179836 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
179783 AAGATATATT
179793 AAAATAAAA
1 AAAATAAAA
*
179802 TAAATAAAA
1 AAAATAAAA
179811 AAAATAAAA
1 AAAATAAAA
*
179820 AAAATAATA
1 AAAATAAAA
*
179829 ATAATAAA
1 AAAATAAA
179837 TAGTAATAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAAAA
Found at i:179849 original size:16 final size:16
Alignment explanation
Indices: 179824--179854 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
179814 ATAAAAAAAA
179824 TAATAATAATAAATAG
1 TAATAATAATAAATAG
*
179840 TAATAGTAATAAATA
1 TAATAATAATAAATA
179855 TAAAATGAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TAATAATAATAAATAG
Found at i:179924 original size:21 final size:22
Alignment explanation
Indices: 179891--179931 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
179881 GGTTAAAATA
179891 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
179913 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
179932 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:183587 original size:16 final size:17
Alignment explanation
Indices: 183562--183602 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
183552 TTAATTAAAA
183562 ACTTAAATTTTT-TCTC
1 ACTTAAATTTTTATCTC
*
183578 ACTTATATTTTTATCT-
1 ACTTAAATTTTTATCTC
183594 -CTTAAATTT
1 ACTTAAATTT
183603 AAAAATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.59
Consensus pattern (17 bp):
ACTTAAATTTTTATCTC
Found at i:186318 original size:27 final size:27
Alignment explanation
Indices: 186288--186339 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
186278 ATTTCTTCAA
*
186288 AGAGCATTTCAGGAAGTGTTTCCTTAT
1 AGAGCATTTCAGGAAGCGTTTCCTTAT
186315 AGAGCATTTCAGGAAGCGTTTCCTT
1 AGAGCATTTCAGGAAGCGTTTCCTT
186340 GGACATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (27 bp):
AGAGCATTTCAGGAAGCGTTTCCTTAT
Found at i:186349 original size:27 final size:27
Alignment explanation
Indices: 186290--186349 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
186280 TTCTTCAAAG
* * *
186290 AGCATTTCAGGAAGTGTTTCCTTATAG
1 AGCATTTCAGGAAGCGTTTCCTTAGAC
*
186317 AGCATTTCAGGAAGCGTTTCCTTGGAC
1 AGCATTTCAGGAAGCGTTTCCTTAGAC
*
186344 ATCATT
1 AGCATT
186350 ATTTGAGTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (27 bp):
AGCATTTCAGGAAGCGTTTCCTTAGAC
Found at i:189429 original size:65 final size:65
Alignment explanation
Indices: 189357--189520 Score: 199
Period size: 65 Copynumber: 2.5 Consensus size: 65
189347 TTGGACTCTC
* * *
189357 AGTGCATCGGTGCACTAAGA-GTGCATCGAATGCATAAAATGCATTCAATGTTTTGA-AAAAGCC
1 AGTGCATCGATGCA-TAAGATGTGCATCG-ATGCATAAAATGCATTCAATGTTTTCATAAAACCC
189420 TG
64 TG
* * * *
189422 AGTGCATCGATGCATGATATGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTG
1 AGTGCATCGATGCATAAGATGTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAACCCTG
* *
189487 AGTGCATCGATACAT-GGTATGTGCATCGATGCAT
1 AGTGCATCGATGCATAAG-ATGTGCATCGATGCAT
189521 GGTATGTGCA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 27 0.31
65 59 0.69
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCATAAGATGTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAACCCTG
Found at i:189512 original size:19 final size:19
Alignment explanation
Indices: 189488--189535 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
189478 AAAACCCTGA
189488 GTGCATCGATACATGGTAT
1 GTGCATCGATACATGGTAT
*
189507 GTGCATCGATGCATGGTAT
1 GTGCATCGATACATGGTAT
189526 GTGCATCGAT
1 GTGCATCGAT
189536 TCATCAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (19 bp):
GTGCATCGATACATGGTAT
Found at i:189596 original size:84 final size:83
Alignment explanation
Indices: 189423--189605 Score: 235
Period size: 84 Copynumber: 2.2 Consensus size: 83
189413 AAAAGCCTGA
*
189423 GTGCATCGATGCATGATATGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGA
1 GTGCATCGATGCATGATATGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAACCATGA
*
189488 GTGCATCGATACATGGTAT
65 GTGCATCGATACATAGTAT
* * * *
189507 GTGCATCGATGCATGGTATGTGCATCGATTCATCAAATGCATTCGATG-TTCAATTAAATCATCG
1 GTGCATCGATGCATGATATGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAACCAT-G
* *
189571 -GTGCATCGATGCATAGTTT
64 AGTGCATCGATACATAGTAT
*
189590 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
189606 CCTTTGAATA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
82 3 0.03
83 24 0.28
84 60 0.69
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (83 bp):
GTGCATCGATGCATGATATGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAACCATGAG
TGCATCGATACATAGTAT
Found at i:203886 original size:13 final size:13
Alignment explanation
Indices: 203865--203902 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
203855 CTAACTCGGT
203865 TGAGTCAACTCAC
1 TGAGTCAACTCAC
*
203878 TGAGCCAACTCAC
1 TGAGTCAACTCAC
*
203891 TAAGTCAACTCA
1 TGAGTCAACTCA
203903 TTGACTCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.21
Consensus pattern (13 bp):
TGAGTCAACTCAC
Found at i:206142 original size:2 final size:2
Alignment explanation
Indices: 206135--206175 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
206125 GGGCAAATAC
206135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
206176 ATTTTGTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:208199 original size:18 final size:18
Alignment explanation
Indices: 208084--208186 Score: 170
Period size: 18 Copynumber: 5.7 Consensus size: 18
208074 TTTGTCCCAT
208084 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
208102 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
*
208120 AGGACCATTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
208138 AGGACCATTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
208156 AGGACCATTATGTCCCGA
1 AGGACCACTATGTCCCGA
208174 AGGACCACTATGT
1 AGGACCACTATGT
208187 GTCGAATGAC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 81 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.20
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:209079 original size:24 final size:20
Alignment explanation
Indices: 209006--209083 Score: 111
Period size: 20 Copynumber: 3.7 Consensus size: 20
208996 TTCCCTTTGA
209006 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
209026 AATGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
209046 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
209069 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
209084 CTAGCCATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
20 35 0.67
22 1 0.02
23 3 0.06
24 13 0.25
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:212540 original size:18 final size:18
Alignment explanation
Indices: 212519--212596 Score: 104
Period size: 18 Copynumber: 4.3 Consensus size: 18
212509 TATCTCGTAG
212519 GACCACTATATCCCGAAT
1 GACCACTATATCCCGAAT
*
212537 GACCACTATGTCCCGAA-
1 GACCACTATATCCCGAAT
* *
212554 GAACCATTATGTCCCGAAT
1 G-ACCACTATATCCCGAAT
*
212573 GACCACTATATCCCGAAG
1 GACCACTATATCCCGAAT
212591 GACCAC
1 GACCAC
212597 GTAGACCCTC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
17 1 0.02
18 51 0.96
19 1 0.02
ACGTcount: A:0.32, C:0.33, G:0.15, T:0.19
Consensus pattern (18 bp):
GACCACTATATCCCGAAT
Found at i:212576 original size:36 final size:36
Alignment explanation
Indices: 212520--212596 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
212510 ATCTCGTAGG
*
212520 ACCACTATATCCCGAATGACCACTATGTCCCGAAGA
1 ACCACTATATCCCGAATGACCACTATATCCCGAAGA
* * *
212556 ACCATTATGTCCCGAATGACCACTATATCCCGAAGG
1 ACCACTATATCCCGAATGACCACTATATCCCGAAGA
212592 ACCAC
1 ACCAC
212597 GTAGACCCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.19
Consensus pattern (36 bp):
ACCACTATATCCCGAATGACCACTATATCCCGAAGA
Found at i:213556 original size:64 final size:63
Alignment explanation
Indices: 213469--213609 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
213459 TATTTAACAT
* * *
213469 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCAATATTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCAAT-GTTTCATCTTTAAAGA
* * * * * *
213532 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCAATGTTTCATCTTTAAAGA
213596 GTGCATCGATGCAC
1 GTGCATCGATGCAC
213610 ATTGAATGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 21 0.32
64 45 0.68
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCAATGTTTCATCTTTAAAGA
Found at i:215840 original size:19 final size:19
Alignment explanation
Indices: 215816--215854 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
215806 ATCTACCACA
215816 CATACTTATTAATCCTACC
1 CATACTTATTAATCCTACC
215835 CATACTTATTAATCCTACC
1 CATACTTATTAATCCTACC
215854 C
1 C
215855 TGACATGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (19 bp):
CATACTTATTAATCCTACC
Found at i:217357 original size:63 final size:64
Alignment explanation
Indices: 217238--217378 Score: 153
Period size: 63 Copynumber: 2.2 Consensus size: 64
217228 ATGCACATGA
* ** * *
217238 AGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATCAGTGTATCGATGCAAAAG-T
1 AGTGCATCGATGCACTCCCCTAAAATAAAAACATCGAATGGCATCAGTGTACCGATGC-AAAGTT
* * * * *
217302 GGTGCATCGATGCAC-CCCCTAAAATACAAACATCGAATGGGATTTA-TGTACCGATGCATAGTT
1 AGTGCATCGATGCACTCCCCTAAAATAAAAACATCGAATGGCA-TCAGTGTACCGATGCAAAGTT
217365 AGTGCATCGATGCA
1 AGTGCATCGATGCA
217379 TAGTTAGTGC
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
62 3 0.05
63 46 0.72
64 15 0.23
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (64 bp):
AGTGCATCGATGCACTCCCCTAAAATAAAAACATCGAATGGCATCAGTGTACCGATGCAAAGTT
Found at i:217377 original size:19 final size:19
Alignment explanation
Indices: 217353--217397 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
217343 ATTTATGTAC
217353 CGATGCATAGTTAGTGCAT
1 CGATGCATAGTTAGTGCAT
217372 CGATGCATAGTTAGTGCAT
1 CGATGCATAGTTAGTGCAT
217391 CGATGCA
1 CGATGCA
217398 CCCGTTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (19 bp):
CGATGCATAGTTAGTGCAT
Found at i:217993 original size:18 final size:18
Alignment explanation
Indices: 217970--218004 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
217960 AGGGATTATC
217970 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
217988 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
218005 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:224523 original size:18 final size:18
Alignment explanation
Indices: 224497--224531 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
224487 CGGAATAATC
224497 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
224515 AGTGTTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
224532 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:225665 original size:46 final size:46
Alignment explanation
Indices: 225570--225667 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 46
225560 ATGAAAATAA
*
225570 AAATAATAATAATAAATCAAAAGATGAAGAAAAAAAAACAATAAAT
1 AAATAATAATAATAAATCAAAAGAGGAAGAAAAAAAAACAATAAAT
* *
225616 AAATAATAATAATAAATCGAAAG-GGAA-AATAAAATAAA-AATATATT
1 AAATAATAATAATAAATCAAAAGAGGAAGAA-AAAA-AAACAATA-AAT
225662 AAATAA
1 AAATAA
225668 ATCAAAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 2 0.04
45 11 0.24
46 33 0.72
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.20
Consensus pattern (46 bp):
AAATAATAATAATAAATCAAAAGAGGAAGAAAAAAAAACAATAAAT
Found at i:225723 original size:24 final size:27
Alignment explanation
Indices: 225663--225724 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 27
225653 AAATATATTA
225663 AATAAATCAAAAGAAAGAAAGAAATGT
1 AATAAATCAAAAGAAAGAAAGAAATGT
225690 AA-AAAT-AAAA-AAAGAATA-AAA-G-
1 AATAAATCAAAAGAAAGAA-AGAAATGT
225712 AATAAATCAAAAG
1 AATAAATCAAAAG
225725 GAGAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
22 2 0.06
23 5 0.16
24 13 0.42
25 5 0.16
26 4 0.13
27 2 0.06
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.13
Consensus pattern (27 bp):
AATAAATCAAAAGAAAGAAAGAAATGT
Found at i:225748 original size:32 final size:30
Alignment explanation
Indices: 225707--225766 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
225697 AAAAAAGAAT
*
225707 AAAAGAATAA-ATCAAAAGGAGAAAAAAATTA
1 AAAAGAATAATA-AAAAAGGA-AAAAAAATTA
225738 AAAAGAAATAATAAAAAAGGAAAAAAAAT
1 AAAAG-AATAATAAAAAAGGAAAAAAAAT
225767 CAAAGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 13 0.50
32 12 0.46
33 1 0.04
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12
Consensus pattern (30 bp):
AAAAGAATAATAAAAAAGGAAAAAAAATTA
Found at i:225789 original size:28 final size:25
Alignment explanation
Indices: 225758--225828 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
225748 ATAAAAAAGG
*
225758 AAAAAAAATCAAAGAAAAAAAAT-G
1 AAAAAAAATCAAAGAAAAAAAATAT
* *
225782 AAATAAAA-CAAAACACAAAAAAATAT
1 AAAAAAAATC-AAAGA-AAAAAAATAT
225808 AAAAATAAATCAAAGAAAAAA
1 AAAAA-AAATCAAAGAAAAAA
225829 TGAATAGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
23 1 0.03
24 11 0.30
25 8 0.22
26 9 0.24
27 7 0.19
28 1 0.03
ACGTcount: A:0.79, C:0.07, G:0.04, T:0.10
Consensus pattern (25 bp):
AAAAAAAATCAAAGAAAAAAAATAT
Found at i:226002 original size:28 final size:29
Alignment explanation
Indices: 225959--226031 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
225949 ATAAGGTAGG
**
225959 GACTAAAATGCAAAAATAA-TAAATTCAG-
1 GACTAAAATATAAAAA-AATTAAATTCAGT
* *
225987 GATTAAAATATTAAAAAATTAAATTCAGT
1 GACTAAAATATAAAAAAATTAAATTCAGT
226016 GACTAAAATATAAAAA
1 GACTAAAATATAAAAA
226032 GTATAACTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 2 0.05
28 21 0.57
29 14 0.38
ACGTcount: A:0.59, C:0.07, G:0.08, T:0.26
Consensus pattern (29 bp):
GACTAAAATATAAAAAAATTAAATTCAGT
Found at i:227410 original size:10 final size:10
Alignment explanation
Indices: 227391--227468 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 10
227381 CATTTAAATG
227391 ATAAACGAAC
1 ATAAACGAAC
*
227401 ATAAAAGAAC
1 ATAAACGAAC
*
227411 GTAAACGAAC
1 ATAAACGAAC
*
227421 ACAAACGAAC
1 ATAAACGAAC
227431 GAATATAAACGAAC
1 ----ATAAACGAAC
*
227445 ATAATAAAGGAAC
1 ---ATAAACGAAC
227458 ATAAACGAAC
1 ATAAACGAAC
227468 A
1 A
227469 ACACAAACAC
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
10 35 0.65
13 10 0.19
14 9 0.17
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:227968 original size:7 final size:7
Alignment explanation
Indices: 227958--227997 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
227948 AAATTAAATT
227958 AAATATA
1 AAATATA
227965 AAATATA
1 AAATATA
227972 AAATATA
1 AAATATA
*
227979 AAA-ATG
1 AAATATA
227985 AAATA-A
1 AAATATA
227991 AAATATA
1 AAATATA
227998 TTGTTATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (7 bp):
AAATATA
Found at i:228951 original size:21 final size:22
Alignment explanation
Indices: 228911--228953 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
228901 CATTTTTTAA
228911 TATTAATCATTGATATTTGATT
1 TATTAATCATTGATATTTGATT
228933 TATTAATCAATT-A-ATTTGATT
1 TATTAATC-ATTGATATTTGATT
228954 CAAGTACCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 9 0.45
23 3 0.15
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (22 bp):
TATTAATCATTGATATTTGATT
Found at i:229272 original size:19 final size:19
Alignment explanation
Indices: 229240--229276 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
229230 ATGACCAACA
*
229240 AAATCACAATGCGATCTCT
1 AAATCACAACGCGATCTCT
*
229259 AAATCGCAACGCGATCTC
1 AAATCACAACGCGATCTC
229277 CATTATCGCA
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:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCACAACGCGATCTCT
Found at i:229387 original size:20 final size:20
Alignment explanation
Indices: 229362--229414 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
229352 GATTTTAGAT
229362 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
229382 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
*
229402 AATCGCAACGCGA
1 AATCGCAATGCGA
229415 TTCTGACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:229451 original size:22 final size:20
Alignment explanation
Indices: 229403--229490 Score: 140
Period size: 20 Copynumber: 4.3 Consensus size: 20
229393 GAATATGTAA
229403 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
229423 ATCGCAACGCGATTCTGACAT
1 ATCGCAACGCGATTCTGAC-T
229444 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
229465 ATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
229485 AACGCA
1 ATCGCA
229491 TCACTGAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
20 43 0.67
21 2 0.03
22 19 0.30
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:229451 original size:42 final size:42
Alignment explanation
Indices: 229403--229483 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
229393 GAATATGTAA
229403 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACATG
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACATG
*
229445 ATCGCAACGCGATTCTGACTATCGCAACGTGATTCTGAC
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGAC
229484 TAACGCATCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (42 bp):
ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACATG
Found at i:240792 original size:20 final size:20
Alignment explanation
Indices: 240731--240792 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
240721 CAAATAACTG
*
240731 AAAACATGTCA-AAAATAGAA
1 AAAATATGTCATAAAATA-AA
* **
240751 GAAATAAATCATAAATATAAA
1 AAAATATGTCATAAA-ATAAA
240772 AAAATATGTCATAAAATAAA
1 AAAATATGTCATAAAATAAA
240792 A
1 A
240793 TTATTAAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 13 0.39
21 17 0.52
22 3 0.09
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.21
Consensus pattern (20 bp):
AAAATATGTCATAAAATAAA
Found at i:246450 original size:32 final size:34
Alignment explanation
Indices: 246409--246486 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
246399 TTTAAATAGT
*
246409 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
*
246441 TATTATTTTTT-TATTAAATAATATTTATATAAT
1 TATTATTTTTTATATTAAATAATATTTATATAAA
246474 TATTATTTATTTA
1 TATTATTT-TTTA
246487 GAATTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 4 0.10
32 14 0.35
33 19 0.47
34 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:246460 original size:18 final size:19
Alignment explanation
Indices: 246431--246466 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
246421 TATTAATATA
*
246431 TTTATGTAAATATTATTTT
1 TTTATGTAAATAATATTTT
246450 TTTAT-TAAATAATATTT
1 TTTATGTAAATAATATTT
246467 ATATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTATGTAAATAATATTTT
Found at i:248280 original size:21 final size:21
Alignment explanation
Indices: 248254--248347 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
248244 TATGCCATCT
* *
248254 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
248275 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
248296 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
248317 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
248338 CCGCAGGGTT
1 CCGCAGGGTT
248348 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:248929 original size:33 final size:34
Alignment explanation
Indices: 248870--248966 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
248860 AAATGTTTTT
*
248870 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
248904 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
248937 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
248967 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Done.