Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008320.1 Hibiscus syriacus cultivar Beakdansim tig00111023_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: 269452
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1725 original size:24 final size:24
Alignment explanation
Indices: 1691--1737 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1681 CTGAAACATC
1691 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1715 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1738 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2446 original size:20 final size:20
Alignment explanation
Indices: 2418--2783 Score: 440
Period size: 20 Copynumber: 18.4 Consensus size: 20
2408 AAATTTCAGT
* * * *
2418 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2438 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2458 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2478 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2498 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2518 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2538 GTTGCGATTTACGGATAC-C
1 GTTGCGATTTACGGATACGC
2557 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2577 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2597 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2617 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2637 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2657 GTTGCGATATAC-GATACGC
1 GTTGCGATTTACGGATACGC
* **
2676 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2696 GTTGCGATTTAC-GATACAC
1 GTTGCGATTTACGGATACGC
2715 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2735 GTTGCGATTTACGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2755 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2775 GTTGCGATT
1 GTTGCGATT
2784 ATGGAAAATC
Statistics
Matches: 308, Mismatches: 27, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
19 58 0.19
20 245 0.80
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2582 original size:119 final size:117
Alignment explanation
Indices: 2418--2783 Score: 427
Period size: 119 Copynumber: 3.1 Consensus size: 117
2408 AAATTTCAGT
* * * * *
2418 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATCG-TTGCGATTTACAGATTCTCGTTG
1 GTTGCGATTTAC-GATACGCGTTGCGATTTACGGA-TA-CGCTTGCGATTTAC-GATACACGTTG
* *
2482 CGATTTACGGATTA-TCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATTA-TC
62 CGATTTACGGA-TACACGTTGCGATTTACGGATACGCGTTGCGATTTACGGA-TACGC
*
2538 GTTGCGATTTACGGATAC-CGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGC
1 GTTGCGATTTAC-GATACGCGTTGCGATTTACGGATACGC-TTGCGATTTAC-GATACACGTTGC
*
2602 GATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGCGATTTACGGATACGC
63 GATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
* * **
2657 GTTGCGATATACGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGATACACGTTGCGA
1 GTTGCGATTTACGATACGCGTTGCGATTTACGGATACGC-TTGCGATTTACGATACACGTTGCGA
* * * ** *
2722 TTTACGGATACGCGTTGCGATTTACGTG-TTCGCGTTGCGATTTTCATATTCGC
65 TTTACGGATACACGTTGCGATTTACG-GATACGCGTTGCGATTTACGGATACGC
2775 GTTGCGATT
1 GTTGCGATT
2784 ATGGAAAATC
Statistics
Matches: 217, Mismatches: 23, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
117 2 0.01
118 76 0.35
119 124 0.57
120 15 0.07
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (117 bp):
GTTGCGATTTACGATACGCGTTGCGATTTACGGATACGCTTGCGATTTACGATACACGTTGCGAT
TTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
Found at i:2780 original size:99 final size:100
Alignment explanation
Indices: 2418--2783 Score: 458
Period size: 99 Copynumber: 3.7 Consensus size: 100
2408 AAATTTCAGT
* * * * * * *
2418 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTG
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACAGATTCGCATTG
* *
2482 CGATTTACGGATTA-TCGTTGCGATTTACGGATACGC
65 CGATTTACGGA-TACGCGTTGCGATTTACGGATACAC
* * *
2518 GTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATAC-CGTTGCGATTTACGGATACGCATTG
1 GTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATTCGCATTG
2581 CGATTTACGGATACGCGTTGCGATTTACGGATACAC
65 CGATTTACGGATACGCGTTGCGATTTACGGATACAC
* * *
2617 GTTGCGGTTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATATAC-GATACGCATTGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATTCGCATTGC
**
2681 GATTTACCCATACGCGTTGCGATTTAC-GATACAC
66 GATTTACGGATACGCGTTGCGATTTACGGATACAC
* * * *
2715 GTTGCGATTTACGGATACGCGTTGCGATTTACGTG-TTCGCGTTGCGATTTTCATATTCGCGTTG
1 GTTGCGATTTACGGATACGCGTTGCGATTTACG-GATACGCGTTGCGATTTACAGATTCGCATTG
2779 CGATT
65 CGATT
2784 ATGGAAAATC
Statistics
Matches: 238, Mismatches: 21, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
98 57 0.24
99 138 0.58
100 42 0.18
101 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (100 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATTCGCATTGC
GATTTACGGATACGCGTTGCGATTTACGGATACAC
Found at i:28876 original size:20 final size:20
Alignment explanation
Indices: 28808--28887 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
28798 CAGAACCCCA
* * *
28808 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCTTAT
* * *
28828 GGGGGGATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCCTT--AT
*
28851 GGGGGAATCGGTTCCCTTAT
1 GGGGGAATCGATTCCCTTAT
28871 GGGGGAATCGATTCCCT
1 GGGGGAATCGATTCCCT
28888 CTGTACCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
20 28 0.57
21 4 0.08
22 5 0.10
23 12 0.24
ACGTcount: A:0.15, C:0.24, G:0.35, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAT
Found at i:41346 original size:2 final size:2
Alignment explanation
Indices: 41341--41365 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41331 CACACATGTG
41341 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
41366 CAGATTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42353 original size:43 final size:42
Alignment explanation
Indices: 42300--42650 Score: 396
Period size: 43 Copynumber: 8.1 Consensus size: 42
42290 TGAGAACCAA
*
42300 AAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
*
42343 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTATGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTT-TGGAAC
* * * *
42386 AAACGCTGCAAAAGATCATATATATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* **** * * *
42428 AAACACAATGAAAGGTCAGATCTATAGCGGCATTTTTTTAGAAT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGC--GTTTTTGGAAC
* *
42472 AAACGCCGCAAAAGGTCAGATCTATAGCGGTGTTTTTTGGAAG
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
* *
42515 AAACGCCGCAAAAGGTCAGATATATAGCGACGTTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
* * * ** *
42558 AAACGCCGCAAAAGATCAAATATATAGCATCTTTTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGC--GTTTTTGGAAC
*
42602 AAACGCCGCAAAAGGTCAGATCTATAACGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
42645 AAACGC
1 AAACGC
42651 ATAATTTCCT
Statistics
Matches: 260, Mismatches: 41, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
42 56 0.22
43 136 0.52
44 68 0.26
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:42377 original size:87 final size:83
Alignment explanation
Indices: 42280--42636 Score: 338
Period size: 87 Copynumber: 4.1 Consensus size: 83
42270 CCGCTAAAGG
* * *
42280 TAGCGGCGTTTGAGAACCAAAAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTGGAACAA
1 TAGCGGCGTTTGAGAA-C--AAACGCCGCAAAAGATC-AGATATATAGCGGCGTTTTTGGAACAA
*
42345 ACGCCGCAATAGGTCAGATCTA
62 ACGCCGCAAAAGGTCAGATCTA
* * *
42367 TAGCGGCGTTTTATGGAACAAACGCTGCAAAAGATCATATATATAGCGGCGTTTTTGGAACAAAC
1 TAGCGGCGTTTGA--GAACAAACGCCGCAAAAGATCAGATATATAGCGGCGTTTTTGGAACAAAC
* ****
42432 ACAATGAAAGGTCAGATCTA
64 GCCGCAAAAGGTCAGATCTA
* * * * * * *
42452 TAGCGGCATTTTTTTAGAATAAACGCCGCAAAAGGTCAGATCTATAGCGGTGTTTTTTGGAAGAA
1 TAGCGGC---GTTTGAGAACAAACGCCGCAAAAGATCAGATATATAGCGGCG-TTTTTGGAACAA
*
42517 ACGCCGCAAAAGGTCAGATATA
62 ACGCCGCAAAAGGTCAGATCTA
* * ** *
42539 TAGCGACGTTTTTTG-GAACAAACGCCGCAAAAGATCAAATATATAGCATCTTTTTTTTGGAACA
1 TAGCGGCG---TTTGAGAACAAACGCCGCAAAAGATCAGATATATAGCGGC--GTTTTTGGAACA
42603 AACGCCGCAAAAGGTCAGATCTA
61 AACGCCGCAAAAGGTCAGATCTA
*
42626 TAACGGCGTTT
1 TAGCGGCGTTT
42637 TTGGATACAA
Statistics
Matches: 218, Mismatches: 41, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
84 3 0.01
85 48 0.22
86 72 0.33
87 86 0.39
88 6 0.03
89 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (83 bp):
TAGCGGCGTTTGAGAACAAACGCCGCAAAAGATCAGATATATAGCGGCGTTTTTGGAACAAACGC
CGCAAAAGGTCAGATCTA
Found at i:46189 original size:41 final size:41
Alignment explanation
Indices: 46125--46436 Score: 226
Period size: 41 Copynumber: 7.6 Consensus size: 41
46115 AACTTGCGGT
* * *
46125 GTTTATAAAACAAACGCCACTAAAGCATGAGTCTATAGCGAC
1 GTTTATATAA-AAACGCCACTAAAGTACGAGTCTATAGCGAC
* ** * *
46167 GATTGCATAAAAACGCCACTAAAGTACGAGTCTCTAGCGGC
1 GTTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGAC
* * * ** *
46208 ATTTGA-ATACAAA-TCCACTAAAGTTTGAGT-TTTAGCGAC
1 GTTT-ATATAAAAACGCCACTAAAGTACGAGTCTATAGCGAC
* * * * * *
46247 GTTTGTATAAAAAC-CCACTAAGGTATGAATCTACAGCGGC
1 GTTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGAC
* * *
46287 GTTTATAAACACAAACACCACTAAA-TCACGAGTCTATAGCGGC
1 GTTTATATA-A-AAACGCCACTAAAGT-ACGAGTCTATAGCGAC
* * *
46330 GTTTATATAAAAACGTCACTAAAGTACGATTCTATAGCAAC
1 GTTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGAC
* * *
46371 GTTTATATAAAAATGCCACTAAAGTAC-AATCTTTAGC-AGC
1 GTTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGA-C
* *
46411 GCATT-TATAGAAACGCCACTAAAGTA
1 G-TTTATATAAAAACGCCACTAAAGTA
46437 TAGTATTTAG
Statistics
Matches: 214, Mismatches: 45, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
39 30 0.14
40 56 0.26
41 87 0.41
42 13 0.06
43 28 0.13
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (41 bp):
GTTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGAC
Found at i:46429 original size:40 final size:39
Alignment explanation
Indices: 46323--46464 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 39
46313 CACGAGTCTA
* * * *
46323 TAGCGGCGTTTATATAAAAACGTCACTAAAGTACGATTCTA
1 TAGCAGCGTTT-TATAAAAACGCCACTAAAGTAC-AATCTT
* *
46364 TAGCAACGTTTATATAAAAATGCCACTAAAGTACAATCTT
1 TAGCAGCGTTT-TATAAAAACGCCACTAAAGTACAATCTT
* * * * *
46404 TAGCAGCGCATTTATAGAAACGCCACTAAAGTATAGTATT
1 TAGCAGCG-TTTTATAAAAACGCCACTAAAGTACAATCTT
* *
46444 TAGCGGCGTTTTTATAGAAAC
1 TAGCAGCG-TTTTATAAAAAC
46465 ATCGCTAAAG
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
40 52 0.62
41 32 0.38
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (39 bp):
TAGCAGCGTTTTATAAAAACGCCACTAAAGTACAATCTT
Found at i:46949 original size:25 final size:25
Alignment explanation
Indices: 46921--46973 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
46911 GCATCAACTT
46921 CCAACTGTCACCATCAAGCCTGCTG
1 CCAACTGTCACCATCAAGCCTGCTG
46946 CCAACTGTCACCATCAAGCCTGCTG
1 CCAACTGTCACCATCAAGCCTGCTG
46971 CCA
1 CCA
46974 CGTCCCAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.42, G:0.15, T:0.19
Consensus pattern (25 bp):
CCAACTGTCACCATCAAGCCTGCTG
Found at i:47799 original size:2 final size:2
Alignment explanation
Indices: 47792--47818 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47782 TTGAATACAT
47792 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
47819 TGTAGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48145 original size:2 final size:2
Alignment explanation
Indices: 48131--48176 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
48121 TAAAAAAAAC
48131 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48170 TA T- TA TA
1 TA TA TA TA
48177 AATTTACTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54509 original size:13 final size:13
Alignment explanation
Indices: 54491--54529 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
54481 GTCATAAATC
*
54491 TATGACACGCATT
1 TATGACGCGCATT
*
54504 TATGACGCTCATT
1 TATGACGCGCATT
54517 TATGACGCGCATT
1 TATGACGCGCATT
54530 GAGCGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:57188 original size:43 final size:43
Alignment explanation
Indices: 57133--57313 Score: 229
Period size: 43 Copynumber: 4.2 Consensus size: 43
57123 TGAGAACAAA
* * *
57133 AAACGTCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
* * * *
57176 AAACGCCACAAAAGGTCGAGATCTATAGTGACGTTTTTAGAAT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
* *
57219 AAACGCCGCAAAAGGTCAACATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
* * * *
57262 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTTGATTC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGA-AC
57305 AAACGCCGC
1 AAACGCCGC
57314 TAATTACCTT
Statistics
Matches: 119, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 19 0.16
43 100 0.84
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
Found at i:59717 original size:20 final size:20
Alignment explanation
Indices: 59692--59730 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
59682 GGCAGGTTCT
59692 AATTCCCAGCCTGTAGTGCA
1 AATTCCCAGCCTGTAGTGCA
59712 AATTCCCAGCCTGTAGTGC
1 AATTCCCAGCCTGTAGTGC
59731 CATTTGCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (20 bp):
AATTCCCAGCCTGTAGTGCA
Found at i:61681 original size:41 final size:41
Alignment explanation
Indices: 61510--61733 Score: 209
Period size: 43 Copynumber: 5.3 Consensus size: 41
61500 CTTTAAGCTT
* * * *
61510 TAGCGGCGTTTTTAAACATAAACGCCACTAAAGTACGAGTTTA
1 TAGCGGCGTTTGTATA-A-AAACGCCACTAAAGTATGAGTCTA
* * * * *
61553 TAGCTGCATTTTTAAACACAAACGCCACTAAATTATGAGTCTA
1 TAGCGGCGTTTGTATA-A-AAACGCCACTAAAGTATGAGTCTA
* *
61596 TAGCGGCGTTT-TAAAACATAAACGCCACTAAAGTATGAGCCTA
1 TAGCGGCGTTTGT-ATA-A-AAACGCCACTAAAGTATGAGTCTA
* *
61639 TAGCGGCGTTTGTATAAAAATGCCATTAAAGTATGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTA
* * *
61680 TAGCGGCGTTTGCATATAAACGCCACTAAAGTACT-ACTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTA-TGAGTCTA
*
61721 TTGCGGCGTTTGT
1 TAGCGGCGTTTGT
61734 TGAAAATTCC
Statistics
Matches: 156, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
41 66 0.42
42 3 0.02
43 86 0.55
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTA
Found at i:61727 original size:82 final size:84
Alignment explanation
Indices: 61510--61747 Score: 252
Period size: 86 Copynumber: 2.8 Consensus size: 84
61500 CTTTAAGCTT
* * ** * * * *
61510 TAGCGGCGTTTTTAAACATAAACGCCACTAAAGTACGAGTTTATAGCTGCATTTTTAAACACAAA
1 TAGCGGCGTTTTAAAACATAAACGCCACTAAAGTATGAGCCTATAGCGGCGTTTGTATA-A-AAA
* *
61575 CGCCACTAAATTATGAGTCTA
64 TGCCACTAAAGTATGAGTCTA
61596 TAGCGGCGTTTTAAAACATAAACGCCACTAAAGTATGAGCCTATAGCGGCGTTTGTATAAAAATG
1 TAGCGGCGTTTTAAAACATAAACGCCACTAAAGTATGAGCCTATAGCGGCGTTTGTATAAAAATG
*
61661 CCATTAAAGTATGAGTCTA
66 CCACTAAAGTATGAGTCTA
** * * *
61680 TAGCGGCG-TTT-GCATATAAACGCCACTAAAGTACT-A-CTCTATTGCGGCGTTTGT-TGAAAA
1 TAGCGGCGTTTTAAAACATAAACGCCACTAAAGTA-TGAGC-CTATAGCGGCGTTTGTATAAAAA
*
61740 TTCCACTA
64 TGCCACTA
61748 TAGATGAATC
Statistics
Matches: 132, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
81 12 0.09
82 35 0.27
83 4 0.03
84 29 0.22
85 1 0.01
86 51 0.39
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (84 bp):
TAGCGGCGTTTTAAAACATAAACGCCACTAAAGTATGAGCCTATAGCGGCGTTTGTATAAAAATG
CCACTAAAGTATGAGTCTA
Found at i:61762 original size:40 final size:41
Alignment explanation
Indices: 61718--61821 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 41
61708 AAGTACTACT
* * * * *
61718 CTATTGCGGCGTTTGTT-GAAAATTCCACTATAGATGAATC
1 CTATTACGGCGTTTATTAAAAAATGCCACTATAGATGAACC
* *
61758 CTATTACGACGTTTATTAAAAAATGCCACTATAGATTAACC
1 CTATTACGGCGTTTATTAAAAAATGCCACTATAGATGAACC
*
61799 CTATTACGGCATTTATATAAAAA
1 CTATTACGGCGTTTAT-TAAAAA
61822 CGCCGCTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 14 0.26
41 33 0.62
42 6 0.11
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (41 bp):
CTATTACGGCGTTTATTAAAAAATGCCACTATAGATGAACC
Found at i:61900 original size:82 final size:82
Alignment explanation
Indices: 61758--61915 Score: 210
Period size: 82 Copynumber: 1.9 Consensus size: 82
61748 TAGATGAATC
* * * *
61758 CTATTACGACGTTTATTAAAAAATGCCACTATAGATTAACCCTATTACGGCATTTATATAAAAAC
1 CTATCACGACGTTTATTAAAAAACGCCACTATAGATGAACCCTATCACGGCATTTATATAAAAAC
61823 GCCGCTAAAGTACTACT
66 GCCGCTAAAGTACTACT
* * * ** *
61840 CTATCACGACGTTTGTTGAAAAAACGCCACTATTGATGAA-CCTATCGCGGTGTTTGTATAAAAA
1 CTATCACGACGTTTATT-AAAAAACGCCACTATAGATGAACCCTATCACGGCATTTATATAAAAA
61904 CGCCGCTAAAGT
65 CGCCGCTAAAGT
61916 TACCATTTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
82 46 0.71
83 19 0.29
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (82 bp):
CTATCACGACGTTTATTAAAAAACGCCACTATAGATGAACCCTATCACGGCATTTATATAAAAAC
GCCGCTAAAGTACTACT
Found at i:71065 original size:2 final size:2
Alignment explanation
Indices: 71056--71120 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
71046 TATGTGTATC
71056 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71097 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
71121 AACAGTAACA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:78439 original size:21 final size:20
Alignment explanation
Indices: 78415--78547 Score: 85
Period size: 21 Copynumber: 6.5 Consensus size: 20
78405 GCCGCATAAA
78415 ATGTTCCGAAGGACAACATAT
1 ATGTTCCGAAGGAC-ACATAT
78436 ATG-TCCTGAAGGACCACATA-
1 ATGTTCC-GAAGGA-CACATAT
*
78456 AT-TGTCCTGTAGGACACATAT
1 ATGT-TCC-GAAGGACACATAT
* * *
78477 ATGTTCCAAAGGAC-CAAAC
1 ATGTTCCGAAGGACACATAT
* *
78496 ATATCCCGAAGGATCACATAT
1 ATGTTCCGAAGGA-CACATAT
* * *
78517 ATATTCCCAAGGATTACATAT
1 ATGTTCCGAAGGA-CACATAT
*
78538 ATGTCCCGAA
1 ATGTTCCGAA
78548 TGACCGCATA
Statistics
Matches: 88, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
19 13 0.15
20 17 0.19
21 56 0.64
22 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (20 bp):
ATGTTCCGAAGGACACATAT
Found at i:83285 original size:98 final size:99
Alignment explanation
Indices: 83171--83356 Score: 329
Period size: 98 Copynumber: 1.9 Consensus size: 99
83161 AAAAAATTTA
* *
83171 AAATATTTGGTTTGATTTTATAATTGGTAAAAGTTGAAGAATCATGTTGGGAATAATTATTTATA
1 AAATATTTGGTTTGATTTTATAATTGGTAAAAGTAGAAGAATCATGTTGGGAATAATTATGTATA
83236 GAATTGAATAAGTATTTT-ATAATGAAATTGCAT
66 GAATTGAATAAGTATTTTGATAATGAAATTGCAT
* *
83269 AAATATTTGGTTTGATTTTATAATTGGTAAAAGTAGAAGAATCGTGTTGGGAATAATTATGTATG
1 AAATATTTGGTTTGATTTTATAATTGGTAAAAGTAGAAGAATCATGTTGGGAATAATTATGTATA
83334 GAATTGAATAAGTATTTTGATAA
66 GAATTGAATAAGTATTTTGATAA
83357 GTTTGAAGTT
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 79 0.95
99 4 0.05
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (99 bp):
AAATATTTGGTTTGATTTTATAATTGGTAAAAGTAGAAGAATCATGTTGGGAATAATTATGTATA
GAATTGAATAAGTATTTTGATAATGAAATTGCAT
Found at i:83897 original size:36 final size:36
Alignment explanation
Indices: 83854--83956 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
83844 AGTTGAGTAT
* *
83854 TATCAGCTTTGATACATTTGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
83890 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
83926 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
83957 CCAGCACCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:86113 original size:18 final size:18
Alignment explanation
Indices: 86090--86182 Score: 89
Period size: 18 Copynumber: 4.9 Consensus size: 18
86080 ACTGAATATT
86090 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
86108 TGTCCCGAATGACCACTGA
1 TGTCCCGAATGACCACT-A
*
86127 TTGTTCCGAA-GAACCACTA
1 -TGTCCCGAATG-ACCACTA
* * *
86146 TGTTCCGAAGGACCACTGTT
1 TGTCCCGAATGACCAC--TA
*
86166 TGTCCCGAAAGACCACT
1 TGTCCCGAATGACCACT
86183 GATAATCCCT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
18 32 0.49
19 4 0.06
20 29 0.45
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:86142 original size:20 final size:20
Alignment explanation
Indices: 86119--86185 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
86109 GTCCCGAATG
86119 ACCACTGATTGTTCCGAAGA
1 ACCACTGATTGTTCCGAAGA
*
86139 ACCACT-A-TGTTCCGAAGG
1 ACCACTGATTGTTCCGAAGA
* *
86157 ACCACTGTTTGTCCCGAA-A
1 ACCACTGATTGTTCCGAAGA
86176 GACCACTGAT
1 -ACCACTGAT
86186 AATCCCTCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 16 0.41
19 1 0.03
20 22 0.56
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (20 bp):
ACCACTGATTGTTCCGAAGA
Found at i:86143 original size:38 final size:38
Alignment explanation
Indices: 86089--86182 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
86079 CACTGAATAT
* *
86089 TTGTCCCGAATGACCACTATGTCCCGAATGACCACTGA
1 TTGTCCCGAAAGACCACTATGTCCCGAAGGACCACTGA
* * *
86127 TTGTTCCG-AAGAACCACTATGTTCCGAAGGACCACTGT
1 TTGTCCCGAAAG-ACCACTATGTCCCGAAGGACCACTGA
86165 TTGTCCCGAAAGACCACT
1 TTGTCCCGAAAGACCACT
86183 GATAATCCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.04
38 43 0.90
39 3 0.06
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (38 bp):
TTGTCCCGAAAGACCACTATGTCCCGAAGGACCACTGA
Found at i:91606 original size:18 final size:17
Alignment explanation
Indices: 91577--91645 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 17
91567 AATATTTGTC
*
91577 CCGAATGACCACTATAT
1 CCGAAGGACCACTATAT
91594 CCTGAAGGACCACTGATCATT
1 CC-GAAGGACCACT-AT-A-T
* *
91615 CCGAAGAACCACTATGT
1 CCGAAGGACCACTATAT
*
91632 CCCGAAGGATCACT
1 -CCGAAGGACCACT
91646 GTTTGTCCCG
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.07
18 21 0.50
19 4 0.10
20 11 0.26
21 3 0.07
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.20
Consensus pattern (17 bp):
CCGAAGGACCACTATAT
Found at i:91657 original size:38 final size:38
Alignment explanation
Indices: 91571--91657 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 38
91561 GCACTGAATA
*
91571 TTTGTCCCGAATGACCACTATATCCTGAAGGACCACTG
1 TTTGTCCCGAATGACCACTATATCCCGAAGGACCACTG
* ** * * *
91609 ATCATTCCGAA-GAACCACTATGTCCCGAAGGATCACTG
1 TTTGTCCCGAATG-ACCACTATATCCCGAAGGACCACTG
91647 TTTGTCCCGAA
1 TTTGTCCCGAA
91658 AGACTACTGA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (38 bp):
TTTGTCCCGAATGACCACTATATCCCGAAGGACCACTG
Found at i:92084 original size:21 final size:21
Alignment explanation
Indices: 92060--92099 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
92050 AAACCTAAAT
**
92060 ATCATATATTGTTCATATATA
1 ATCATATATACTTCATATATA
92081 ATCATATATACTTCATATA
1 ATCATATATACTTCATATA
92100 GTACATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (21 bp):
ATCATATATACTTCATATATA
Found at i:93522 original size:12 final size:12
Alignment explanation
Indices: 93507--93566 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
93497 CAGAAATAAA
93507 AACAGAATTCAG
1 AACAGAATTCAG
*
93519 AACAG-ATATCAT
1 AACAGAAT-TCAG
*
93531 AACAGAATCCAG
1 AACAGAATTCAG
* *
93543 ATCAGAAATCAG
1 AACAGAATTCAG
93555 AACAGAATTCAG
1 AACAGAATTCAG
93567 GTCATGTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:93534 original size:24 final size:24
Alignment explanation
Indices: 93497--93566 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
93487 ATGGAGATAT
* *
93497 CAGAAATAAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * *
93521 CAGATATCATAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
93545 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAGAACAGAATTCAG
93567 GTCATGTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.16
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:109153 original size:22 final size:22
Alignment explanation
Indices: 109128--109179 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
109118 CCAAAGTGCC
109128 ACATAGAATGTCCCGAAAGACA
1 ACATAGAATGTCCCGAAAGACA
* * * *
109150 ACATA-TATGTCCTGAAGGACC
1 ACATAGAATGTCCCGAAAGACA
109171 ACATAGAAT
1 ACATAGAAT
109180 TGTCATGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
ACATAGAATGTCCCGAAAGACA
Found at i:109275 original size:21 final size:21
Alignment explanation
Indices: 109229--109271 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
109219 ATATATTTTG
*
109229 AAGGATTACATATATGTTCCC
1 AAGGATCACATATATGTTCCC
109250 AAGGATCACATATATG-TCCC
1 AAGGATCACATATATGTTCCC
109270 AA
1 AA
109272 AGGACCGCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (21 bp):
AAGGATCACATATATGTTCCC
Found at i:123199 original size:4 final size:4
Alignment explanation
Indices: 123190--123318 Score: 215
Period size: 4 Copynumber: 32.2 Consensus size: 4
123180 ATCAACTGTG
123190 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123238 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
123286 CACT- CATA CATA CAAA TATA CGTA CATA CATA C
1 CA-TA CATA CATA CATA CATA CATA CATA CATA C
123319 CTCGATGATG
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
3 1 0.01
4 115 0.98
5 1 0.01
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:126460 original size:189 final size:189
Alignment explanation
Indices: 126131--126884 Score: 1129
Period size: 189 Copynumber: 4.0 Consensus size: 189
126121 AGCAAAATTT
* * **
126131 GGCAAGCAATATAAACTCAGACGATAGCTAATTCAACGAGATATCTTAAACAGAATCATAGCTAT
1 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
* * * ** * *
126196 CACAATGAAACTCAAATTCAAAAATGAAATTCTGGATAACTCGAAAATGTAGTTCATACTCCCTA
66 CACAATGAAACTCATATTCGAAAACGAAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCTA
* * *
126261 GCAATTTAATCTATGATTCATGGTCTAGAATGGTAAAAATATATAACATCAATATGATA
131 GCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
* * *
126320 GGCAAGCAATATAAACTCAGACGATAGCTAATCCAATGAGATATTTTAAACAGAATCATAGCTAT
1 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
*
126385 CACAATGAAACTCATATTCGAAAACGAAATTCCGGAGAACTCGAAAATGTAGTCCATACTCCCTA
66 CACAATGAAACTCATATTCGAAAACGAAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCTA
* * * * * *
126450 GTAGTTTAATCTCTTATTCAAGGTCTATAATGGTACAAGTATATAACATCAATATGATG
131 GCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
* *
126509 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATCTCTTAAACAGAATCATAGCTAC
1 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
* * *
126574 CACATTGGAACTCATATTTGAAAACGAAAATT-CAGAGAACTCGAAAATGTAGTCCATACTCCCT
66 CACAATGAAACTCATATTCGAAAACG-AAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCT
*
126638 AGCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATG
130 AGCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
*
126698 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATCTCTTAAACAGAATCATAGCTAT
1 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
* * * * *
126763 CACAAAGGAAA-TCATATTCTAAAACGAAATTTCAGAGAACTCGAAAATGCAATCCATACTCCCT
66 CAC-AATGAAACTCATATTCGAAAACGAAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCT
*
126827 AGCAGTTTAACCTATGATTCATGGTCTAGAATGGTACAAGTATAT-ACATC-ATATGATA
130 AGCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
126885 TAGGCAACAC
Statistics
Matches: 520, Mismatches: 42, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
187 7 0.01
188 10 0.02
189 494 0.95
190 9 0.02
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (189 bp):
GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
CACAATGAAACTCATATTCGAAAACGAAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCTA
GCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
Found at i:128472 original size:15 final size:15
Alignment explanation
Indices: 128454--128483 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
128444 AAAACCATGT
128454 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
128469 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
128484 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:128490 original size:15 final size:15
Alignment explanation
Indices: 128457--128491 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
128447 ACCATGTTAG
* *
128457 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
128472 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
128487 ATAAA
1 ATAAA
128492 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:128621 original size:9 final size:8
Alignment explanation
Indices: 128596--128671 Score: 62
Period size: 8 Copynumber: 8.5 Consensus size: 8
128586 GATAAAGAAG
128596 AAAAAATA
1 AAAAAATA
* *
128604 TAGAAATA
1 AAAAAATA
128612 AAACAAATA
1 AAA-AAATA
128621 AATAAAATAA
1 AA-AAAAT-A
128631 TAAAAAAGTA
1 -AAAAAA-TA
128641 AAAAAATA
1 AAAAAATA
128649 TATATAAAATA
1 -A-A-AAAATA
128660 AAAAAATA
1 AAAAAATA
128668 AAAA
1 AAAA
128672 GTAATATATA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
8 19 0.34
9 19 0.34
10 9 0.16
11 9 0.16
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (8 bp):
AAAAAATA
Found at i:128644 original size:43 final size:43
Alignment explanation
Indices: 128587--128670 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
128577 AAAAATAAAG
* * *
128587 ATAAAGAAGAAAAAATATAGAAATAAAACAAATAAATAAAATA
1 ATAAAAAAGAAAAAAAATAGAAATAAAACAAAAAAATAAAATA
* * * *
128630 ATAAAAAAGTAAAAAAATATATATAAAATAAAAAAATAAAA
1 ATAAAAAAGAAAAAAAATAGAAATAAAACAAAAAAATAAAA
128671 AGTAATATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (43 bp):
ATAAAAAAGAAAAAAAATAGAAATAAAACAAAAAAATAAAATA
Found at i:128648 original size:19 final size:18
Alignment explanation
Indices: 128574--128668 Score: 84
Period size: 19 Copynumber: 5.1 Consensus size: 18
128564 AGTAAGTAAT
*
128574 ATAAAAAATAAAGATAAAGA
1 ATAAAAAATAAA-A-AAATA
* * *
128594 AGAAAAAATATAGAAATA
1 ATAAAAAATAAAAAAATA
*
128612 A-AACAAATAAATAAAATA
1 ATAAAAAATAAA-AAAATA
128630 ATAAAAAAGTAAAAAAATA
1 ATAAAAAA-TAAAAAAATA
*
128649 TATATAAAATAAAAAAATA
1 -ATAAAAAATAAAAAAATA
128668 A
1 A
128669 AAAGTAATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
17 8 0.13
18 12 0.19
19 21 0.34
20 21 0.34
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (18 bp):
ATAAAAAATAAAAAAATA
Found at i:128659 original size:35 final size:33
Alignment explanation
Indices: 128618--128702 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
128608 AATAAAACAA
128618 ATAAATAAAATAATAAAAAAGTAAAAAAATATAT
1 ATAAATAAAATAATAAAAAAGT-AAAAAATATAT
* * *
128652 ATAAAATAAAAAAAT-AAAAAGTAATATATATAT
1 AT-AAATAAAATAATAAAAAAGTAAAAAATATAT
* *
128685 ATATATAAATTAATAAAA
1 ATAAATAAAATAATAAAA
128703 CTGATAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
32 9 0.21
33 14 0.33
34 9 0.21
35 11 0.26
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (33 bp):
ATAAATAAAATAATAAAAAAGTAAAAAATATAT
Found at i:128664 original size:27 final size:28
Alignment explanation
Indices: 128607--128702 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 28
128597 AAAAATATAG
* *
128607 AAATAAAACAAATAAATAAAATAATAAAA
1 AAATAAAA-AAATATATATAATAATAAAA
*
128636 AAGTAAAAAAATATATATAA-AATAAAA
1 AAATAAAAAAATATATATAATAATAAAA
*
128663 AAATAAAAAGTAATATATATATATATATAAAT
1 AAATAAAAA--AATATATATA-ATA-ATAAAA
*
128695 TAATAAAA
1 AAATAAAA
128703 CTGATAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
27 15 0.27
28 10 0.18
29 17 0.30
30 1 0.02
31 1 0.02
32 12 0.21
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (28 bp):
AAATAAAAAAATATATATAATAATAAAA
Found at i:128664 original size:29 final size:28
Alignment explanation
Indices: 128571--128702 Score: 94
Period size: 28 Copynumber: 4.6 Consensus size: 28
128561 AATAGTAAGT
* * *
128571 AATATAAAAAATAAAGATAAAGA-AGAAAA
1 AATATAAAAAATAAA-A-AAATATATATAA
*
128600 AATAT-AGAAATAAAACAAATA-A-ATAA
1 AATATAAAAAATAAAA-AAATATATATAA
128626 AATAATAAAAAAGTAAAAAAATATATATAA
1 AAT-ATAAAAAA-TAAAAAAATATATATAA
128656 AATA-AAAAAATAAAAAGTAATATATATATA
1 AATATAAAAAATAAAAA--AATATATATA-A
* *
128686 TATATAAATTAATAAAA
1 AATATAAA-AAATAAAA
128703 CTGATAATAA
Statistics
Matches: 86, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
26 6 0.07
27 14 0.16
28 23 0.27
29 22 0.26
30 11 0.13
31 3 0.03
32 7 0.08
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.23
Consensus pattern (28 bp):
AATATAAAAAATAAAAAAATATATATAA
Found at i:128799 original size:21 final size:20
Alignment explanation
Indices: 128747--128800 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
128737 TAAAAAAAAT
128747 AAAAATATATAC-TAAAGTAA
1 AAAAATAT-TACATAAAGTAA
*
128767 AAAGAA-AATACATAAATGTAA
1 AAA-AATATTACATAAA-GTAA
128788 AAAAATATTACAT
1 AAAAATATTACAT
128801 GAAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 3 0.11
20 10 0.36
21 15 0.54
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (20 bp):
AAAAATATTACATAAAGTAA
Found at i:128873 original size:14 final size:15
Alignment explanation
Indices: 128854--128892 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
128844 AAATGTGCTT
*
128854 ATAAATAAAATTA-A
1 ATAAATAAAATAATA
128868 ATAAATAAAATAATA
1 ATAAATAAAATAATA
*
128883 ATAATTAAAA
1 ATAAATAAAA
128893 CGTAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:129144 original size:35 final size:36
Alignment explanation
Indices: 129074--129173 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
129064 GTGCTTGTGG
* * *
129074 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
129111 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
129146 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
129174 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 11 0.20
37 18 0.32
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:130563 original size:105 final size:105
Alignment explanation
Indices: 129634--131027 Score: 1476
Period size: 105 Copynumber: 13.3 Consensus size: 105
129624 AATATTGTTC
* * *
129634 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTGTTGACA
** * * * * * *
129699 GTCAGTCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
129740 CGAGTCTAATATCCTTCGTTGTGAAGATGAAATTGACTCTG-AAC---GAAA-TCTTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTGTTGACAA
*
129800 TCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * * *
129840 CGAGTCCAATATCCTTCGCTACGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTGTTGACA
129905 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * ** *
129946 CGAGTGGCACGATATCCTCCG-TCGTGGAGTTGAAA-TCGCGGATGAAACT-GAAAAGTTGTTCG
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-TCTGAAACTGGGAAA-TTGTT-G
* *
130008 TTGACAACCAACCGTCCCTTCGTTGTGATGTTGAACTTGTGTTGTCT
59 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * *
130055 CGGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTGTT
*
130119 GACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
130164 CGAGTCCAATATCCTTCGCTGTAAAGTTGAGATTGGCT-T----C---GAAATTGCTTGTCGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTGTTGACA
** * * * *
130221 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
130262 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTGTTGACA
130327 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
130368 CGAGTCCAATATCCTTCGCTGTGAACTT-AAGATTGGCT-T----C---GAAATTGCTTGTCGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAA-ATTGGCTCTGAAACTGGGAAATTG-TTGTTGAC
** * * * *
130424 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
130466 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTGTTGACAA
130531 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
130571 CGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTGTTGACAA
* * * **
130636 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
130676 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTGTTGACAA
* * * * *
130741 GCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
130781 -GAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTTGTTGTTGACA
1 CG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTGTTGACA
* * * *
130845 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
130886 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGAAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTGTTGACA
* *
130951 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
130992 CGAGTGCCACAATATCCTCCG-TCGTGGAGTTGAAAT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAAT
131028 CGCGGATGGC
Statistics
Matches: 1117, Mismatches: 129, Indels: 81
0.84 0.10 0.06
Matches are distributed among these distances:
98 166 0.15
99 4 0.00
100 78 0.07
101 4 0.00
102 4 0.00
103 2 0.00
104 4 0.00
105 395 0.35
106 250 0.22
107 2 0.00
108 14 0.01
109 186 0.17
110 8 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:131712 original size:37 final size:37
Alignment explanation
Indices: 131649--131720 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
131639 TGAGAAACGG
*
131649 TCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAATTA
1 TCTCAAGAGAGACAAAATTTTATTTCAAGGGAAATTA
131686 TCTCAAGAGAGACGAAAA-TTTATTTCAAGGGAAAT
1 TCTCAAGAGAGAC-AAAATTTTATTTCAAGGGAAAT
131721 GTTTTCAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (37 bp):
TCTCAAGAGAGACAAAATTTTATTTCAAGGGAAATTA
Found at i:131854 original size:35 final size:35
Alignment explanation
Indices: 131735--131854 Score: 102
Period size: 35 Copynumber: 3.4 Consensus size: 35
131725 TCAATGTTTA
*
131735 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAAT-T
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATCT
* *
131771 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC-
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATCT
* * * *
131806 T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATCT
1 TGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATCT
*
131842 TGTTTTAAGAAAA
1 TGTTTCAAGAAAA
131855 ACAATCATGA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
34 3 0.05
35 32 0.48
36 28 0.42
37 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (35 bp):
TGTTTCAAGAAAACTGTCTCAAGAGAGACAAATCT
Found at i:132312 original size:18 final size:18
Alignment explanation
Indices: 132285--132320 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
132275 TGTTGAATCC
*
132285 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
132303 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
132321 TTGATGTTGA
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:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:132746 original size:22 final size:22
Alignment explanation
Indices: 132721--132771 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
132711 TTGTGTTTGG
132721 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
132743 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
132765 TCAAAGG
1 TCAAAGG
132772 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:133437 original size:8 final size:7
Alignment explanation
Indices: 133425--133496 Score: 54
Period size: 8 Copynumber: 9.1 Consensus size: 7
133415 TGATTTTTGC
133425 TCTTTTT
1 TCTTTTT
133432 TCCTTTTGT
1 T-CTTTT-T
133441 TCTTGTTT
1 TCTT-TTT
*
133449 CTCTTGTT
1 -TCTTTTT
133457 TCTTTGTT
1 TCTTT-TT
*
133465 TTTTTTT
1 TCTTTTT
133472 TGCTTTTT
1 T-CTTTTT
133480 TGCTTCTTT
1 T-CTT-TTT
133489 TCTTTTT
1 TCTTTTT
133496 T
1 T
133497 GTTCTTGATT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
7 12 0.22
8 30 0.56
9 12 0.22
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.76
Consensus pattern (7 bp):
TCTTTTT
Found at i:133493 original size:16 final size:16
Alignment explanation
Indices: 133469--133502 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
133459 TTTGTTTTTT
133469 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
133486 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
133501 TT
1 TT
133503 GATTGGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:137072 original size:15 final size:15
Alignment explanation
Indices: 137054--137083 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
137044 AAAACCATGT
137054 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
*
137069 TAGATAAAAATGTAA
1 TAGATAAAAAGGTAA
137084 GAAATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:137273 original size:41 final size:41
Alignment explanation
Indices: 137228--137309 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
137218 TAAAACAAAT
137228 AAATAAAATAATAA-TAAAAAAGTAAAAATA-ATATATATATA
1 AAATAAAA-AA-AATTAAAAAAGTAAAAATATATATATATATA
*
137269 AAATAAAAAAAATTAAAAAAGTAAATATATATATATATATA
1 AAATAAAAAAAATTAAAAAAGTAAAAATATATATATATATA
137310 TATATATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
39 2 0.05
40 17 0.45
41 19 0.50
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (41 bp):
AAATAAAAAAAATTAAAAAAGTAAAAATATATATATATATA
Found at i:137280 original size:33 final size:35
Alignment explanation
Indices: 137237--137303 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
137227 TAAATAAAAT
137237 AATAATAAAAAAGT-AAAAA-T-AATATATATATAA
1 AATAA-AAAAAAGTAAAAAAGTAAATATATATATAA
*
137270 AATAAAAAAAATTAAAAAAGTAAATATATATATA
1 AATAAAAAAAAGTAAAAAAGTAAATATATATATA
137304 TATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.23
33 10 0.33
34 1 0.03
35 12 0.40
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (35 bp):
AATAAAAAAAAGTAAAAAAGTAAATATATATATAA
Found at i:137298 original size:2 final size:2
Alignment explanation
Indices: 137293--137329 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
137283 AAAAAAGTAA
137293 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
137330 AATTAATAAA
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:137423 original size:23 final size:23
Alignment explanation
Indices: 137374--137441 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
137364 ATATATAATC
* *
137374 TAAAAAAAATAAAATATACTAAA-G
1 TAAAAAAAATAATACATA--AAATG
137398 TAAAAAAGAA-AATACATAAAATG
1 TAAAAAA-AATAATACATAAAATG
*
137421 TAAAAAAAATATTACATAAAA
1 TAAAAAAAATAATACATAAAA
137442 AAAAATAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.13
23 18 0.47
24 13 0.34
25 2 0.05
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (23 bp):
TAAAAAAAATAATACATAAAATG
Found at i:137780 original size:35 final size:36
Alignment explanation
Indices: 137710--137809 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
137700 GTGCTTGTGG
* * *
137710 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
137747 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
137782 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
137810 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 11 0.20
37 18 0.32
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:139100 original size:28 final size:29
Alignment explanation
Indices: 139056--139117 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
139046 AGTCTTTATA
* *
139056 TTTAAAAAATATGATCAAATGAACCCTTG
1 TTTAAAAAATAGGATCAAATCAACCCTTG
139085 TTTAAAAAAT-GGATCAAATCAACCCTTG
1 TTTAAAAAATAGGATCAAATCAACCCTTG
139113 TTTAA
1 TTTAA
139118 TAATTTTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 21 0.68
29 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (29 bp):
TTTAAAAAATAGGATCAAATCAACCCTTG
Found at i:139991 original size:31 final size:29
Alignment explanation
Indices: 139945--140041 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 29
139935 CATTGAAGTT
*
139945 TCAAAAGTTATAAAATAATTATTAAATTTA
1 TCAAAA-TTACAAAATAATTATTAAATTTA
* * *
139975 TCAAACTATTACAAAATGATCATTAATATTTT
1 TCAAA--ATTACAAAATAATTATTAA-ATTTA
*** *
140007 TCCAAAATTTTTAAATAATTATTAAATTCA
1 T-CAAAATTACAAAATAATTATTAAATTTA
140037 TCAAA
1 TCAAA
140042 TTTTATGATA
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
29 4 0.08
30 9 0.17
31 29 0.56
32 6 0.12
33 4 0.08
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.40
Consensus pattern (29 bp):
TCAAAATTACAAAATAATTATTAAATTTA
Found at i:152665 original size:67 final size:67
Alignment explanation
Indices: 152557--152690 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
152547 TGGTCGCGTG
* *
152557 GCCCTAGGGTGATGATACCCTAGGGTTTGTTACTGGGATCATCTGGACCGTTGGATCTAAGTTAG
1 GCCCTAAGGTGATGATACCCTAGGGTTTGTTACTGGGATCATCTAGACCGTTGGATCTAAGTTAG
152622 AT
66 AT
*
152624 GCCCTAAGGTGATGATACCCTAGGGTTTGTTGCTGGGATCATCTAGACCGTTGGATCTAAGTTAG
1 GCCCTAAGGTGATGATACCCTAGGGTTTGTTACTGGGATCATCTAGACCGTTGGATCTAAGTTAG
152689 AT
66 AT
152691 CCAACGGCTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (67 bp):
GCCCTAAGGTGATGATACCCTAGGGTTTGTTACTGGGATCATCTAGACCGTTGGATCTAAGTTAG
AT
Found at i:152838 original size:3 final size:3
Alignment explanation
Indices: 152832--152901 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
152822 AATAATTATT
* *
152832 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
152875 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
152902 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:152877 original size:18 final size:18
Alignment explanation
Indices: 152821--152901 Score: 94
Period size: 18 Copynumber: 4.3 Consensus size: 18
152811 TCTGGGCTTG
152821 TAATAATTATTTAATAATAA
1 TAATAA-TATTT-ATAATAA
*
152841 T-ATAATATATATAATATAA
1 TAATAATATTTAT-A-ATAA
152860 TAATAATATTTATAATAA
1 TAATAATATTTATAATAA
152878 TAATAATAATTT-TAATAA
1 TAATAAT-ATTTATAATAA
152896 TAATAA
1 TAATAA
152902 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.04
18 28 0.51
19 14 0.25
20 11 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATATTTATAATAA
Found at i:153160 original size:76 final size:76
Alignment explanation
Indices: 153058--153770 Score: 1230
Period size: 76 Copynumber: 9.4 Consensus size: 76
153048 GAGGTCTTAA
* * *
153058 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153123 AGGCTTTTTGG
66 AGGCTTTTTGG
153134 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153199 AGGCTTTTTGG
66 AGGCTTTTTGG
*
153210 AAACATCATGCACTGTAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153275 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
153286 AAACATCATGTACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAACCTCCAGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153350 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
153361 AAACATCATGCACTGTAGGACTTACAGATGACCCAAAGGCTTTGGAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153426 AGGCTTTTTGG
66 AGGCTTTTTGG
*
153437 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153502 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
153513 AAACATCATGCACTGAAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153578 AGGCTTTTTGG
66 AGGCTTTTTGG
*
153589 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153654 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * * *
153665 AAACACCATGCACTGCAGAACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153730 AGGCTTTTTGG
66 AGGCTTTTTGG
*
153741 AAACATCATGCACTGTTGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
153771 TGGGAAATAG
Statistics
Matches: 604, Mismatches: 32, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 0.12
76 533 0.88
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:153611 original size:303 final size:304
Alignment explanation
Indices: 153058--153770 Score: 1248
Period size: 303 Copynumber: 2.3 Consensus size: 304
153048 GAGGTCTTAA
* *
153058 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153123 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
*
153188 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAAGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAAGACTTACAGATGACCCTAAGGCTTT
* *
153253 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGTACTGTAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
153318 CCGAAGG-TTTGAAAACATCAAAAACCTCCAGAAGGCTTTTTGG
261 CCGAAGGCTTTGAAAACATCAAAAACCTCCAGAAGGCTTTTTGG
* * *
153361 AAACATCATGCACTGTAGGACTTACAGATGACCCAAAGGCTTTGGAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTCCCGA
153426 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
*
153491 AAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGAAAGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAAGACTTACAGATGACCCTAAGGCTTT
153556 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
* * *
153621 CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
261 CCGAAGGCTTTGAAAACATCAAAAACCTCCAGAAGGCTTTTTGG
* * * ** *
153665 AAACACCATGCACTGCAGAACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
153730 AGGCTTTTTGGAAACATCATGCACTGTTGGACTTACAGATG
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
153771 TGGGAAATAG
Statistics
Matches: 388, Mismatches: 21, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
303 257 0.66
304 131 0.34
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (304 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAAGACTTACAGATGACCCTAAGGCTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
CCGAAGGCTTTGAAAACATCAAAAACCTCCAGAAGGCTTTTTGG
Found at i:154474 original size:22 final size:22
Alignment explanation
Indices: 154446--154544 Score: 164
Period size: 22 Copynumber: 4.5 Consensus size: 22
154436 AATAAAGCTT
154446 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
154468 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
154490 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
154512 TCATCTTT-ATAAAGAGAATCTA
1 TCATCTTTGA-AAAGAGAATCTA
154534 TCATCTTTGAA
1 TCATCTTTGAA
154545 GAATGTAGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.01
22 69 0.97
23 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:154509 original size:44 final size:44
Alignment explanation
Indices: 154446--154546 Score: 184
Period size: 44 Copynumber: 2.3 Consensus size: 44
154436 AATAAAGCTT
*
154446 TCATCTTTGAAAAGAGAATCTATCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATCTA
*
154490 TCATCTTTGAAGAGAGAATCTATCATCTTTATAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATCTA
154534 TCATCTTTGAAGA
1 TCATCTTTGAAGA
154547 ATGTAGATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (44 bp):
TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATCTA
Found at i:159260 original size:17 final size:17
Alignment explanation
Indices: 159240--159329 Score: 67
Period size: 17 Copynumber: 5.9 Consensus size: 17
159230 TTTTTCCCTT
159240 TTTTTCCTTTTTTCTCA
1 TTTTTCCTTTTTTCTCA
159257 TTTTTCC--TTTT-TCA
1 TTTTTCCTTTTTTCTCA
*
159271 ----AC-TTTTTTCT--
1 TTTTTCCTTTTTTCTCA
*
159281 TTTTTTCTTTTTTCTCA
1 TTTTTCCTTTTTTCTCA
159298 TTTTT-CTTTTTTCATCA
1 TTTTTCCTTTTTTC-TCA
*
159315 TTTTTCTTTTTTTCT
1 TTTTTCCTTTTTTCT
159330 TTCTTTGCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 24
0.67 0.05 0.28
Matches are distributed among these distances:
10 1 0.02
11 4 0.07
12 1 0.02
14 3 0.05
15 12 0.21
16 8 0.14
17 21 0.37
18 7 0.12
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCCTTTTTTCTCA
Found at i:159296 original size:41 final size:41
Alignment explanation
Indices: 159237--159331 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
159227 TTCTTTTTCC
*
159237 CTTTTTTTCCTTTTTTCTCATTTTTCCTTTTTCAACTTTTTT
1 CTTTTTTT-CTTTTTTCTCATTTTTCCTTTTTCAACATTTTT
* *
159279 CTTTTTTTCTTTTTTCTCATTTTTCTTTTTTCATCATTTTT
1 CTTTTTTTCTTTTTTCTCATTTTTCCTTTTTCAACATTTTT
159320 CTTTTTTTCTTT
1 CTTTTTTTCTTT
159332 CTTTGCTAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
41 42 0.84
42 8 0.16
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (41 bp):
CTTTTTTTCTTTTTTCTCATTTTTCCTTTTTCAACATTTTT
Found at i:159302 original size:34 final size:32
Alignment explanation
Indices: 159224--159358 Score: 91
Period size: 33 Copynumber: 4.0 Consensus size: 32
159214 ATTTCTCCCA
* *
159224 TTTT-TCTTTTTCCCTTTTTTTCCTTTTTTCTCAT
1 TTTTCTCTTTTTCAC-TTTTTT-CTTTTTT-TCTT
159258 TTTTC-CTTTTTCAACTTTTTTCTTTTTTTCTT
1 TTTTCTCTTTTTC-ACTTTTTTCTTTTTTTCTT
*
159290 TTTTCTCATTTTT--CTTTTTTCATCATTTTTCTT
1 TTTTCTC-TTTTTCACTTTTTTC-T-TTTTTTCTT
**
159323 TTTT-TCTTTCTTTGCTAGATTTTTCTTTTTTTCTT
1 TTTTCTC-TT-TTT-C-ACTTTTTTCTTTTTTTCTT
159358 T
1 T
159359 CTTTGCTGGA
Statistics
Matches: 83, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
31 8 0.10
32 13 0.16
33 23 0.28
34 22 0.27
35 10 0.12
36 1 0.01
37 6 0.07
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (32 bp):
TTTTCTCTTTTTCACTTTTTTCTTTTTTTCTT
Found at i:159344 original size:27 final size:27
Alignment explanation
Indices: 159314--159365 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
159304 TTTTTTCATC
159314 ATTTTTCTTTTTTTCTTTCTTTGCTAG
1 ATTTTTCTTTTTTTCTTTCTTTGCTAG
159341 ATTTTTCTTTTTTTCTTTCTTTGCT
1 ATTTTTCTTTTTTTCTTTCTTTGCT
159366 GGATGAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (27 bp):
ATTTTTCTTTTTTTCTTTCTTTGCTAG
Found at i:162553 original size:20 final size:20
Alignment explanation
Indices: 162530--162568 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
162520 CGAACGTAAA
*
162530 AATGCAAATATAAAAATGTG
1 AATGCAAACATAAAAATGTG
* *
162550 AATGTAACCATAAAAATGT
1 AATGCAAACATAAAAATGT
162569 AAATTATGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGCAAACATAAAAATGTG
Found at i:165900 original size:21 final size:23
Alignment explanation
Indices: 165858--165903 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
165848 TTTCTCTCCT
165858 CTTTTTTCGTGGCTATTCGTCTC
1 CTTTTTTCGTGGCTATTCGTCTC
165881 CTTTTTTC-TGG-T-TTCTGTCTC
1 CTTTTTTCGTGGCTATTC-GTCTC
165902 CT
1 CT
165904 CTCTTCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.14
21 8 0.36
22 3 0.14
23 8 0.36
ACGTcount: A:0.02, C:0.26, G:0.15, T:0.57
Consensus pattern (23 bp):
CTTTTTTCGTGGCTATTCGTCTC
Found at i:166376 original size:3 final size:3
Alignment explanation
Indices: 166370--166439 Score: 67
Period size: 3 Copynumber: 24.0 Consensus size: 3
166360 AATAATTATT
* *
166370 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
166413 TAA TAA TAA TAA -ATT TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA
166440 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
2 7 0.13
3 44 0.80
4 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:166415 original size:18 final size:18
Alignment explanation
Indices: 166359--166439 Score: 85
Period size: 18 Copynumber: 4.3 Consensus size: 18
166349 TCTGGGCTTG
166359 TAATAATTATTTAATAATAA
1 TAATAA-TATTT-ATAATAA
*
166379 T-ATAATATATATAATATAA
1 TAATAATATTTAT-A-ATAA
166398 TAATAATATTTATAATAA
1 TAATAATATTTATAATAA
*
166416 TAATAATAAATT-TAATAA
1 TAATAAT-ATTTATAATAA
166434 TAATAA
1 TAATAA
166440 ATTAAGTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.04
18 28 0.52
19 13 0.24
20 11 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATATTTATAATAA
Found at i:170407 original size:23 final size:22
Alignment explanation
Indices: 170381--170444 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
170371 TAAATGTTAA
*
170381 ATATAATTTAAAAAATAAAATTT
1 ATATAATTTAAAAAATAAAA-AT
**
170404 ATATACCTTAATAAAATAAAAAT
1 ATATAATTTAA-AAAATAAAAAT
*
170427 A-ATAATTTAAATAATAAA
1 ATATAATTTAAAAAATAAA
170445 CGTGTAGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 7 0.21
22 7 0.21
23 11 0.32
24 9 0.26
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (22 bp):
ATATAATTTAAAAAATAAAAAT
Found at i:171056 original size:23 final size:21
Alignment explanation
Indices: 171020--171071 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
171010 CGGTTCAACC
171020 TAAATTTTTT--TATTTTTTAT
1 TAAATTTTTTGGTA-TTTTTAT
171040 TAAATATTTTTGGTATTTTTAT
1 TAAAT-TTTTTGGTATTTTTAT
*
171062 TTAATTTTTT
1 TAAATTTTTT
171072 AAATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 10 0.36
22 11 0.39
23 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TAAATTTTTTGGTATTTTTAT
Found at i:180478 original size:23 final size:23
Alignment explanation
Indices: 180450--180493 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
180440 AACACAAACG
* *
180450 AACGAACATAATAAATGAACATA
1 AACGAACACAATAAACGAACATA
180473 AACGAACACAATAAACGAACA
1 AACGAACACAATAAACGAACA
180494 ACACAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.11
Consensus pattern (23 bp):
AACGAACACAATAAACGAACATA
Found at i:180486 original size:13 final size:13
Alignment explanation
Indices: 180436--180493 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
180426 AACGAATGTG
180436 AACGAACACAA-A
1 AACGAACACAATA
*
180448 CGAACGAACATAATA
1 --AACGAACACAATA
*
180463 AATG-A-AC-ATA
1 AACGAACACAATA
180473 AACGAACACAATA
1 AACGAACACAATA
180486 AACGAACA
1 AACGAACA
180494 ACACAAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 3 0.08
13 14 0.39
14 10 0.28
15 1 0.03
ACGTcount: A:0.60, C:0.21, G:0.10, T:0.09
Consensus pattern (13 bp):
AACGAACACAATA
Found at i:180771 original size:14 final size:14
Alignment explanation
Indices: 180752--180780 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
180742 ACCCTTTGTT
180752 CGAACATAAATGAA
1 CGAACATAAATGAA
180766 CGAACATAAATGAA
1 CGAACATAAATGAA
180780 C
1 C
180781 ATATAATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:195102 original size:27 final size:27
Alignment explanation
Indices: 195072--195144 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
195062 TAAAATTTAG
*
195072 ATTATTTAATAATTTCAT-AAAAATAAT
1 ATTATTTAATAA-TTAATAAAAAATAAT
* * *
195099 ATTATTAAATTATTAATAAAAAATTAT
1 ATTATTTAATAATTAATAAAAAATAAT
*
195126 ATTATTTATATATTTAATA
1 ATTATTTA-ATAATTAATA
195145 TTAATATAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 4 0.11
27 25 0.68
28 8 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTATTTAATAATTAATAAAAAATAAT
Found at i:195815 original size:24 final size:23
Alignment explanation
Indices: 195740--195842 Score: 88
Period size: 23 Copynumber: 4.5 Consensus size: 23
195730 TTTGAGCATA
* * *
195740 TAAACGAACAT-TTCGCGAACGT
1 TAAACAAACATGTTGGCAAACGT
*
195762 TAAACAAACATGTTGGAGAATAC--
1 TAAACAAACATGTTGG-CAA-ACGT
*
195785 TAAACAAATATGTTGGCAAACGT
1 TAAACAAACATGTTGGCAAACGT
* *
195808 ATAAACAAACATGTTGACGAACGT
1 -TAAACAAACATGTTGGCAAACGT
195832 TAAAC-AACATG
1 TAAACAAACATG
195843 GCCGCATACA
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.03
22 18 0.27
23 23 0.35
24 21 0.32
25 2 0.03
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.22
Consensus pattern (23 bp):
TAAACAAACATGTTGGCAAACGT
Found at i:206702 original size:16 final size:17
Alignment explanation
Indices: 206675--206708 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
206665 CTTAGTATTT
206675 ATAATATAATTTCATAA
1 ATAATATAATTTCATAA
206692 ATAAT-TAATTTCATAA
1 ATAATATAATTTCATAA
206708 A
1 A
206709 AGAGACTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATATAATTTCATAA
Found at i:208258 original size:80 final size:80
Alignment explanation
Indices: 208122--208283 Score: 308
Period size: 80 Copynumber: 2.0 Consensus size: 80
208112 GTTAAGGAGG
208122 TTACTCGTGATGAAATTAAAGATGCATTTTTTTCTCAAGGTAACGATAAAGCTCCCGGTCCGGAT
1 TTACTCGTGATGAAATTAAAGATGCATTTTTTTCTCAAGGTAACGATAAAGCTCCCGGTCC-GAT
208187 GGTTACACTCCATATT
65 GGTTACACTCCATATT
208203 TTACTCGTGATGAAATTAAAGATGC-TTTTTTTCTCAAGGTAACGATAAAGCTCCCGGTCCGATG
1 TTACTCGTGATGAAATTAAAGATGCATTTTTTTCTCAAGGTAACGATAAAGCTCCCGGTCCGATG
208267 GTTACACTCCATATT
66 GTTACACTCCATATT
208282 TT
1 TT
208284 TCAAGAAAGC
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
79 21 0.26
80 35 0.43
81 25 0.31
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (80 bp):
TTACTCGTGATGAAATTAAAGATGCATTTTTTTCTCAAGGTAACGATAAAGCTCCCGGTCCGATG
GTTACACTCCATATT
Found at i:211250 original size:31 final size:32
Alignment explanation
Indices: 211212--211279 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 32
211202 ACTGCTACTA
*
211212 CTACACAG-ACTTTTTCAGGAAAAAAATTCTT
1 CTACACAGTACTTTTTCAGAAAAAAAATTCTT
211243 CTACACAGACTTACTTTTTCAGAAAAAAAATTCTT
1 CTACACAG---TACTTTTTCAGAAAAAAAATTCTT
211278 CT
1 CT
211280 TGAAGTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.25
35 24 0.75
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (32 bp):
CTACACAGTACTTTTTCAGAAAAAAAATTCTT
Found at i:216358 original size:20 final size:22
Alignment explanation
Indices: 216313--216370 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
216303 GCATGGGTAG
216313 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
216337 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
216357 TGCATCGATTCACT
1 TGCATCGATGCACT
216371 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:220566 original size:15 final size:15
Alignment explanation
Indices: 220546--220577 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
220536 ATAATATTTC
*
220546 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
220561 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
220576 TT
1 TT
220578 GGATCTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:223214 original size:24 final size:24
Alignment explanation
Indices: 223182--223231 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
223172 TTCTCATAAT
223182 CATCTTTGTTATTTGTTTCGAAAA
1 CATCTTTGTTATTTGTTTCGAAAA
223206 CATCTTTGTTATTTGTTTCGAAAA
1 CATCTTTGTTATTTGTTTCGAAAA
223230 CA
1 CA
223232 CCATGCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (24 bp):
CATCTTTGTTATTTGTTTCGAAAA
Found at i:225074 original size:28 final size:28
Alignment explanation
Indices: 225031--225094 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
225021 TTAGATTGAG
225031 GTTGAACAAAAAGAATGGAGTTATTACT
1 GTTGAACAAAAAGAATGGAGTTATTACT
* *
225059 GTTGAACAAAAGGAATGGAGTTATTATT
1 GTTGAACAAAAAGAATGGAGTTATTACT
225087 GTTGAACA
1 GTTGAACA
225095 TATTAGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.30
Consensus pattern (28 bp):
GTTGAACAAAAAGAATGGAGTTATTACT
Found at i:225584 original size:16 final size:17
Alignment explanation
Indices: 225563--225595 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
225553 TTACTATTCA
225563 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
225579 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
225596 TGTCGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:239343 original size:21 final size:20
Alignment explanation
Indices: 239303--239345 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
239293 AAATTTTATA
*
239303 TTAGAATTTAGAGCTTAGAT
1 TTAGAATTTAAAGCTTAGAT
239323 TTAGAAATTTAAAG-TTCAGAT
1 TTAG-AATTTAAAGCTT-AGAT
239344 TT
1 TT
239346 TAAAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
TTAGAATTTAAAGCTTAGAT
Found at i:244318 original size:19 final size:19
Alignment explanation
Indices: 244296--244332 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
244286 TAGATTTGGT
*
244296 ATACCTTTGGATTCAAATG
1 ATACCTTTGGAGTCAAATG
*
244315 ATACTTTTGGAGTCAAAT
1 ATACCTTTGGAGTCAAAT
244333 ATGTCTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (19 bp):
ATACCTTTGGAGTCAAATG
Found at i:257782 original size:2 final size:2
Alignment explanation
Indices: 257777--257807 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
257767 ATATATATAT
257777 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
257808 TTACATCAAC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:259049 original size:31 final size:30
Alignment explanation
Indices: 259014--259077 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
259004 TATCAAATCT
259014 AAATTAAAATTTTATATAAATAACTAAACTA
1 AAATTAAAATTTTATATAAATAACTAAA-TA
* * * *
259045 AAATTTAAATTTTATGTACATAATTAAATA
1 AAATTAAAATTTTATATAAATAACTAAATA
259075 AAA
1 AAA
259078 CCAAAGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (30 bp):
AAATTAAAATTTTATATAAATAACTAAATA
Found at i:259199 original size:95 final size:95
Alignment explanation
Indices: 259036--259226 Score: 355
Period size: 95 Copynumber: 2.0 Consensus size: 95
259026 TATATAAATA
*
259036 ACTAAACTAAAATTTAAATTTTATGTACATAATTAAATAAAACCAAAGTTCATATATGATATTAT
1 ACTAAACTAAAATTTAAATTTTATGTACATAATTAAATAAAACCAAAGTTCATATATAATATTAT
259101 AGATTTAATGTAATTTTACGTACAATTTTG
66 AGATTTAATGTAATTTTACGTACAATTTTG
* *
259131 ACTAAACTAAAATTTAAATTTTATGTACATAATTAAATAAAACCAAAGTTCTTTTATAATATTAT
1 ACTAAACTAAAATTTAAATTTTATGTACATAATTAAATAAAACCAAAGTTCATATATAATATTAT
259196 AGATTTAATGTAATTTTACGTACAATTTTG
66 AGATTTAATGTAATTTTACGTACAATTTTG
259226 A
1 A
259227 TATTTAATCC
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (95 bp):
ACTAAACTAAAATTTAAATTTTATGTACATAATTAAATAAAACCAAAGTTCATATATAATATTAT
AGATTTAATGTAATTTTACGTACAATTTTG
Found at i:259687 original size:2 final size:2
Alignment explanation
Indices: 259680--259708 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
259670 AACAAACGGG
259680 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 A
259709 GTCACCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:261449 original size:8 final size:8
Alignment explanation
Indices: 261438--262150 Score: 724
Period size: 8 Copynumber: 89.1 Consensus size: 8
261428 TACATAATTT
261438 ATACATAC
1 ATACATAC
261446 ATACATAC
1 ATACATAC
*
261454 ATACATGC
1 ATACATAC
*
261462 ATACATGC
1 ATACATAC
*
261470 ATACATGC
1 ATACATAC
*
261478 ATACATGC
1 ATACATAC
*
261486 ATACATGC
1 ATACATAC
*
261494 ATACATGC
1 ATACATAC
*
261502 ATACATGC
1 ATACATAC
*
261510 ATACATGC
1 ATACATAC
*
261518 ATACATGC
1 ATACATAC
*
261526 ATACATGC
1 ATACATAC
*
261534 ATACATGC
1 ATACATAC
*
261542 ATACATGC
1 ATACATAC
*
261550 ATACATGC
1 ATACATAC
* *
261558 ATGCATGC
1 ATACATAC
*
261566 ATACATGC
1 ATACATAC
* *
261574 ATGCATGC
1 ATACATAC
*
261582 ATACATGC
1 ATACATAC
* *
261590 ATGCATGC
1 ATACATAC
*
261598 ATACATGC
1 ATACATAC
*
261606 ATACATGC
1 ATACATAC
*
261614 ATACATGC
1 ATACATAC
* *
261622 ATGCATGC
1 ATACATAC
*
261630 ATGCATAC
1 ATACATAC
* *
261638 ATGCATGC
1 ATACATAC
*
261646 ATACATGC
1 ATACATAC
* *
261654 ATGCATGC
1 ATACATAC
* *
261662 ATGCATGC
1 ATACATAC
* *
261670 ATGCATTC
1 ATACATAC
**
261678 ATGGATAC
1 ATACATAC
*
261686 ATGCATAC
1 ATACATAC
*
261694 ATACATGC
1 ATACATAC
*
261702 ATGCATAC
1 ATACATAC
* *
261710 ATGCATGC
1 ATACATAC
261718 ATACATAC
1 ATACATAC
*
261726 ATGCATAC
1 ATACATAC
* *
261734 ATGCATGC
1 ATACATAC
*
261742 ATGCATAC
1 ATACATAC
*
261750 ATGCATAC
1 ATACATAC
* *
261758 ATGCATGC
1 ATACATAC
*
261766 ATACATGC
1 ATACATAC
*
261774 ATACATGC
1 ATACATAC
* *
261782 ATGCATGC
1 ATACATAC
* *
261790 ATGCATGC
1 ATACATAC
* *
261798 ATGCATTC
1 ATACATAC
**
261806 ATGGATAC
1 ATACATAC
* *
261814 ATGCATGC
1 ATACATAC
* *
261822 ATGCATGC
1 ATACATAC
* *
261830 ATGCATGC
1 ATACATAC
* **
261838 ATTCATGG
1 ATACATAC
*
261846 ATACATGC
1 ATACATAC
261854 ATACATAC
1 ATACATAC
*
261862 ATGCATAC
1 ATACATAC
*
261870 ATGCATAC
1 ATACATAC
*
261878 ATGCATAC
1 ATACATAC
261886 ATACATAC
1 ATACATAC
261894 ATACATAC
1 ATACATAC
261902 ATACATAC
1 ATACATAC
261910 ATACATAC
1 ATACATAC
261918 ATACATAC
1 ATACATAC
261926 ATACATAC
1 ATACATAC
261934 ATACATAC
1 ATACATAC
261942 ATACATAC
1 ATACATAC
261950 ATACATAC
1 ATACATAC
*
261958 ATACATAT
1 ATACATAC
261966 ATACATAC
1 ATACATAC
261974 ATACATAC
1 ATACATAC
261982 ATACATAC
1 ATACATAC
261990 ATACATAC
1 ATACATAC
261998 ATACATAC
1 ATACATAC
262006 ATACATAC
1 ATACATAC
262014 ATACATAC
1 ATACATAC
262022 ATACATAC
1 ATACATAC
262030 ATACATAC
1 ATACATAC
262038 ATACATAC
1 ATACATAC
262046 ATACATAC
1 ATACATAC
262054 ATACATAC
1 ATACATAC
262062 ATACATAC
1 ATACATAC
262070 ATACATAC
1 ATACATAC
262078 ATACATAC
1 ATACATAC
262086 ATACATAC
1 ATACATAC
262094 ATACATAC
1 ATACATAC
262102 ATACATAC
1 ATACATAC
262110 ATACATAC
1 ATACATAC
262118 ATACATAC
1 ATACATAC
* *
262126 ATGCATGC
1 ATACATAC
*
262134 ATACATGC
1 ATACATAC
*
262142 ATGCATAC
1 ATACATAC
262150 A
1 A
262151 CCATAAAATT
Statistics
Matches: 657, Mismatches: 48, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 657 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (8 bp):
ATACATAC
Found at i:268203 original size:18 final size:18
Alignment explanation
Indices: 268182--268217 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
268172 TTTTAAAACA
268182 ATTTTTAAGAAAAAAATC
1 ATTTTTAAGAAAAAAATC
* *
268200 ATTTTTTAGACAAAAATC
1 ATTTTTAAGAAAAAAATC
268218 GGTATGTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (18 bp):
ATTTTTAAGAAAAAAATC
Found at i:268797 original size:33 final size:33
Alignment explanation
Indices: 268754--268853 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
268744 AGTTTACGAT
* *
268754 AATTAAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
268787 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
* *
268820 AATTCAAATACTTAAAAACTTACAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
268853 A
1 A
268854 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTTGATA
Found at i:268873 original size:21 final size:21
Alignment explanation
Indices: 268848--268889 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
268838 CTTACAAGTT
268848 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
268869 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
268890 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Done.