Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold290.1
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: 1360782
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 12027 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:2651 original size:28 final size:27
Alignment explanation
Indices: 2588--2739 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
2578 ATATTAAGTC
* * *
2588 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
2615 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
2643 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
2670 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
2698 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
2725 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2740 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:2672 original size:55 final size:55
Alignment explanation
Indices: 2588--2739 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
2578 ATATTAAGTC
* * *
2588 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
2643 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
2698 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
2740 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:10843 original size:28 final size:27
Alignment explanation
Indices: 10780--10931 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
10770 ATATTAAGTC
* *
10780 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
10807 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
10835 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
10862 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
10890 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
10917 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10932 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:10864 original size:55 final size:55
Alignment explanation
Indices: 10780--10959 Score: 261
Period size: 55 Copynumber: 3.3 Consensus size: 55
10770 ATATTAAGTC
* * *
10780 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
10835 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
10890 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAACT
*
10946 CGCACACGTAGTGC
1 CGCACACTTAGTGC
10960 CAATCTCGTG
Statistics
Matches: 113, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
55 95 0.84
56 18 0.16
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:18893 original size:28 final size:28
Alignment explanation
Indices: 18832--19738 Score: 1723
Period size: 28 Copynumber: 32.5 Consensus size: 28
18822 ATATTAAGTC
* * *
18832 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAGTCAAACT
18859 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
18887 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
18914 CGCACACTTAGGGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
18942 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
18970 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
18998 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19026 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19054 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19082 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19110 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19138 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19166 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19194 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19222 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19250 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19278 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19306 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19334 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19362 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19390 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19418 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19446 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19474 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19502 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19530 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19558 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19586 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
19614 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
19642 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTCAAACT
19669 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
19697 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTCAAACT
19724 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19739 GCACAATTTA
Statistics
Matches: 867, Mismatches: 10, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
27 89 0.10
28 778 0.90
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAGTCAAACT
Found at i:22142 original size:29 final size:29
Alignment explanation
Indices: 22100--22166 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
22090 ACATGGCTTG
22100 GAAT-TGATTCGGGCCAAATGGACCATAT
1 GAATGTGATTCGGGCCAAATGGACCATAT
* * *
22128 GAATGTGATTTGGGCCTAATGGGCCATAT
1 GAATGTGATTCGGGCCAAATGGACCATAT
*
22157 GAATGAGATT
1 GAATGTGATT
22167 AGGCCTAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (29 bp):
GAATGTGATTCGGGCCAAATGGACCATAT
Found at i:22180 original size:28 final size:29
Alignment explanation
Indices: 22111--22185 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
22101 AATTGATTCG
* * * *
22111 GGCCAAATGGACCATATGAATGTGATTTG
1 GGCCTAATGGGCCATATGAATGAGATTTA
22140 GGCCTAATGGGCCATATGAATGAGA-TTA
1 GGCCTAATGGGCCATATGAATGAGATTTA
*
22168 GGCCTAGTGGGCCATATG
1 GGCCTAATGGGCCATATG
22186 CATGTATGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (29 bp):
GGCCTAATGGGCCATATGAATGAGATTTA
Found at i:37334 original size:30 final size:32
Alignment explanation
Indices: 37278--37340 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
37268 CACCTGTCTA
37278 AAACCTTATTTTGATGAGAATGATAGCAGGAAT
1 AAACCTTATTTTGA-GAGAATGATAGCAGGAAT
*
37311 AAACCTTATTTT-A-AGATTGATAGCAGGAAT
1 AAACCTTATTTTGAGAGAATGATAGCAGGAAT
37341 GAGGAGTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 16 0.55
32 1 0.03
33 12 0.41
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (32 bp):
AAACCTTATTTTGAGAGAATGATAGCAGGAAT
Found at i:38197 original size:18 final size:19
Alignment explanation
Indices: 38155--38199 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
38145 CAAAATAATC
*
38155 ATCATTTTTCTCATACTATT
1 ATCATTTTGCTCATA-TATT
*
38175 TTCATTTTGCTCAT-TATT
1 ATCATTTTGCTCATATATT
38193 ATCATTT
1 ATCATTT
38200 ACTTTGCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.22, C:0.18, G:0.02, T:0.58
Consensus pattern (19 bp):
ATCATTTTGCTCATATATT
Found at i:39747 original size:39 final size:40
Alignment explanation
Indices: 39668--39745 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
39658 ATGAAAATGT
**
39668 TTAAAAATATTTATTTATTATTTTATGTTTTTAATTTTTA
1 TTAAAAATATTTATTTATTATTTTATAATTTTAATTTTTA
*
39708 TTAAAACTATTT-TTTATTAGATTTTATAATTTT-ATTTT
1 TTAAAAATATTTATTTATT--ATTTTATAATTTTAATTTT
39746 ATAATTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 6 0.18
40 16 0.48
41 11 0.33
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (40 bp):
TTAAAAATATTTATTTATTATTTTATAATTTTAATTTTTA
Found at i:45733 original size:7 final size:6
Alignment explanation
Indices: 45686--45732 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
45676 ATAATTTAAT
* *
45686 AAATAA AAATAA AAATCTAA AACTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAA
45733 ACATATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 32 0.86
8 5 0.14
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:45766 original size:9 final size:9
Alignment explanation
Indices: 45752--45846 Score: 127
Period size: 9 Copynumber: 10.6 Consensus size: 9
45742 TTTATACAAA
45752 TAATTCGGT
1 TAATTCGGT
45761 TAATTCGGT
1 TAATTCGGT
*
45770 TAATTTGGT
1 TAATTCGGT
*
45779 TAATTTGGT
1 TAATTCGGT
* *
45788 TAATTTGGG
1 TAATTCGGT
*
45797 TAATTCGGG
1 TAATTCGGT
*
45806 TAATTCGGG
1 TAATTCGGT
*
45815 TAATTCGAT
1 TAATTCGGT
45824 TAATTCGGT
1 TAATTCGGT
45833 TAATTCGGT
1 TAATTCGGT
45842 TAATT
1 TAATT
45847 TTATACTTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 80 1.00
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.45
Consensus pattern (9 bp):
TAATTCGGT
Found at i:51921 original size:18 final size:18
Alignment explanation
Indices: 51898--51934 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
51888 AAATTAAGTT
51898 TTTTAGCTCTTGAATAAA
1 TTTTAGCTCTTGAATAAA
51916 TTTTAGCTCTTGAATAAA
1 TTTTAGCTCTTGAATAAA
51934 T
1 T
51935 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
TTTTAGCTCTTGAATAAA
Found at i:55550 original size:21 final size:21
Alignment explanation
Indices: 55524--55567 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
55514 AATAAATAGA
55524 CTACCTTTGTTTTTGAAACTT
1 CTACCTTTGTTTTTGAAACTT
*
55545 CTACCTTTGTTTTTGAAATTT
1 CTACCTTTGTTTTTGAAACTT
55566 CT
1 CT
55568 CTTTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (21 bp):
CTACCTTTGTTTTTGAAACTT
Found at i:56345 original size:94 final size:94
Alignment explanation
Indices: 56225--56715 Score: 479
Period size: 94 Copynumber: 5.2 Consensus size: 94
56215 TCGTTACAAA
* ** * ** * * * *
56225 TTCAAGGAGATAAGATTTGTTGTTGTAGTTTTATTCTAACCCACTGTAACTTTAGAAGCATAAGA
1 TTCAGGGAGATAAGATTTGTCATTGTAGTTTTAATCCGACCCACTGCAACTTCAGAAGTATAGGA
* *
56290 TTTATAGCTTCATCTTACTCCATTGCAAT
66 TTTATAGCTTCATCTTACTCCACTGCAAC
* * **
56319 TTCAGGGAGATAAGATTTTTTATTGTAGTTTTAA-CCTGACCCACTGCAACTTCAGGGGTATAGG
1 TTCAGGGAGATAAGATTTGTCATTGTAGTTTTAATCC-GACCCACTGCAACTTCAGAAGTATAGG
* * *
56383 ATTTATAGTTTTATCTT-GTCCCACTGCAAC
65 ATTTATAGCTTCATCTTACT-CCACTGCAAC
* * * **
56413 TTCAGAGAGATAAGATTCGTCATTGTAGTTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGA
1 TTCAGGGAGATAAGATTTGTCATTGTAGTTTTAATCCGACCCACTGCAACTTCAGAAGTATAGGA
* ** *
56478 TTTGTAGCTTCATCTTGTTCCACTGCAAT
66 TTTATAGCTTCATCTTACTCCACTGCAAC
* * *
56507 TTTAGGGAGATAAGATTTGTCATTTGTAGTTTTAATCCGACCCACTGCAACTTTA-AAGGTTTAG
1 TTCAGGGAGATAAGATTTGTCA-TTGTAGTTTTAATCCGACCCACTGCAACTTCAGAA-GTATAG
* *
56571 GATTTGTAGCTTCATCTTACTCCACTGTAAC
64 GATTTATAGCTTCATCTTACTCCACTGCAAC
* * * * * * **
56602 TTCAGGGAGATAAGATTCGTCATTATAGTTTCATTCCGACCTACTGCAACTTTAGGGGTATAGGA
1 TTCAGGGAGATAAGATTTGTCATTGTAGTTTTAATCCGACCCACTGCAACTTCAGAAGTATAGGA
* * **
56667 ATTGTAGCTTCAATCCGAC-CCACTGCAAC
66 TTTATAGCTTC-ATCTTACTCCACTGCAAC
*
56696 TTCAGGG-GTATAGGATTTGT
1 TTCAGGGAG-ATAAGATTTGT
56716 AGCTTCATCT
Statistics
Matches: 334, Mismatches: 54, Indels: 18
0.82 0.13 0.04
Matches are distributed among these distances:
93 3 0.01
94 241 0.72
95 90 0.27
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (94 bp):
TTCAGGGAGATAAGATTTGTCATTGTAGTTTTAATCCGACCCACTGCAACTTCAGAAGTATAGGA
TTTATAGCTTCATCTTACTCCACTGCAAC
Found at i:56373 original size:50 final size:49
Alignment explanation
Indices: 56313--56559 Score: 153
Period size: 44 Copynumber: 5.2 Consensus size: 49
56303 CTTACTCCAT
*
56313 TGCAATTTCAGGGAGATAAGATTTTTTATTGTAGTTTTAACCTGACCCAC
1 TGCAACTTCAGGGAGATAAGA-TTTTTATTGTAGTTTTAACCTGACCCAC
* * * *
56363 TGCAACTTCAGGG-GTATAGGA--TTTA---TAGTTTTATCTTGTCCCAC
1 TGCAACTTCAGGGAG-ATAAGATTTTTATTGTAGTTTTAACCTGACCCAC
* * * *
56407 TGCAACTTCAGAGAGATAAGATTCGTCATTGTAGTTTCAATCC-GACCCAC
1 TGCAACTTCAGGGAGATAAGATT-TTTATTGTAGTTTTAA-CCTGACCCAC
* * * * * **
56457 TGCAACTTCAGGG-GTATAGGA----T-TTGTAGCTTCATCTTGTTCCAC
1 TGCAACTTCAGGGAG-ATAAGATTTTTATTGTAGTTTTAACCTGACCCAC
* * *
56501 TGCAATTTTAGGGAGATAAGATTTGTCATTTGTAGTTTTAATCC-GACCCAC
1 TGCAACTTCAGGGAGATAAGATTT-TTA-TTGTAGTTTTAA-CCTGACCCAC
56552 TGCAACTT
1 TGCAACTT
56560 TAAAGGTTTA
Statistics
Matches: 145, Mismatches: 32, Indels: 39
0.67 0.15 0.18
Matches are distributed among these distances:
43 1 0.01
44 64 0.44
45 2 0.01
47 6 0.04
49 2 0.01
50 47 0.32
51 22 0.15
52 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (49 bp):
TGCAACTTCAGGGAGATAAGATTTTTATTGTAGTTTTAACCTGACCCAC
Found at i:56406 original size:44 final size:44
Alignment explanation
Indices: 56344--56741 Score: 148
Period size: 44 Copynumber: 8.6 Consensus size: 44
56334 TTTTTTATTG
* *
56344 TAGTTTTAACCTGACCCACTGCAACTTCAGGGGTATAGGATTTA
1 TAGTTTTATCTTGACCCACTGCAACTTCAGGGGTATAGGATTTA
* * *
56388 TAGTTTTATCTTGTCCCACTGCAACTTCAGAGAG-ATAAGATTCGTCA
1 TAGTTTTATCTTGACCCACTGCAACTTCAG-GGGTATAGGATT--T-A
* * *
56435 TTGTAGTTTCAATC-CGACCCACTGCAACTTCAGGGGTATAGGATTTG
1 ---TAGTTT-TATCTTGACCCACTGCAACTTCAGGGGTATAGGATTTA
* * ** * * *
56482 TAGCTTCATCTTGTTCCACTGCAATTTTAGGGAG-ATAAGATTTGTCATTTG
1 TAGTTTTATCTTGACCCACTGCAACTTCAGGG-GTAT-AG----G--ATTTA
* * ** * *
56533 TAGTTTTAATC-CGACCCACTGCAACTTTAAAGGTTTAGGATTTG
1 TAGTTTT-ATCTTGACCCACTGCAACTTCAGGGGTATAGGATTTA
* * * *
56577 TAGCTTCATCTT-ACTCCACTGTAACTTCAGGGAG-ATAAGATTCGTCATTA
1 TAGTTTTATCTTGAC-CCACTGCAACTTCAGGG-GTATAGGA----T--TTA
* * * * * *
56627 TAGTTTCAT-TCCGACCTACTGCAACTTTAGGGGTATAGGAATTG
1 TAGTTTTATCT-TGACCCACTGCAACTTCAGGGGTATAGGATTTA
** * *
56671 TAGCTTCAATC-CGACCCACTGCAACTTCAGGGGTATAGGATTTG
1 TAG-TTTTATCTTGACCCACTGCAACTTCAGGGGTATAGGATTTA
* *
56715 TAGCTTCATCTTG-CTCCACTGCAACTT
1 TAGTTTTATCTTGAC-CCACTGCAACTT
56742 TAAGGAGATA
Statistics
Matches: 264, Mismatches: 54, Indels: 72
0.68 0.14 0.18
Matches are distributed among these distances:
43 13 0.05
44 135 0.51
45 10 0.04
46 2 0.01
47 1 0.00
48 2 0.01
49 5 0.02
50 62 0.23
51 31 0.12
52 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (44 bp):
TAGTTTTATCTTGACCCACTGCAACTTCAGGGGTATAGGATTTA
Found at i:56617 original size:189 final size:188
Alignment explanation
Indices: 56225--56715 Score: 567
Period size: 189 Copynumber: 2.6 Consensus size: 188
56215 TCGTTACAAA
* * ** * ** * ** * *
56225 TTCAAGGAGATAAGATTTGTTGTTGTAGTTTTATTCTAACCCACTGTAACTTTAGAAGCATAAGA
1 TTCAGGGAGATAAGATTCGTCATTGTAGTTTCATTCCGACCCACTGCAACTTTAGGGGTATAGGA
* * * *
56290 TTTATAGCTTCATCTTACTCCATTGCAATTTCAGGGAGATAAGATTTTTTATTGTAGTTTTAACC
66 TTTGTAGCTTCATCTTACTCCACTGCAATTTCAGGGAGATAAGATTTGTCATTGTAGTTTTAACC
** * * *
56355 TGACCCACTGCAACTTCAGGGGTATAGGATTTATAGTTTTATCTTGTCCCACTGCAAC
131 TGACCCACTGCAACTTCAAAGGTATAGGATTTATAGCTTCATCTTCTCCCACTGCAAC
* * *
56413 TTCAGAGAGATAAGATTCGTCATTGTAGTTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGA
1 TTCAGGGAGATAAGATTCGTCATTGTAGTTTCATTCCGACCCACTGCAACTTTAGGGGTATAGGA
** *
56478 TTTGTAGCTTCATCTTGTTCCACTGCAATTTTAGGGAGATAAGATTTGTCATTTGTAGTTTTAAT
66 TTTGTAGCTTCATCTTACTCCACTGCAATTTCAGGGAGATAAGATTTGTCA-TTGTAGTTTTAA-
* * * *
56543 CC-GACCCACTGCAACTTTAAAGGTTTAGGATTTGTAGCTTCATCTTACT-CCACTGTAAC
129 CCTGACCCACTGCAACTTCAAAGGTATAGGATTTATAGCTTCATCTT-CTCCCACTGCAAC
* *
56602 TTCAGGGAGATAAGATTCGTCATTATAGTTTCATTCCGACCTACTGCAACTTTAGGGGTATAGGA
1 TTCAGGGAGATAAGATTCGTCATTGTAGTTTCATTCCGACCCACTGCAACTTTAGGGGTATAGGA
* ** * *
56667 ATTGTAGCTTCAATCCGAC-CCACTGCAACTTCAGGG-GTATAGGATTTGT
66 TTTGTAGCTTC-ATCTTACTCCACTGCAATTTCAGGGAG-ATAAGATTTGT
56716 AGCTTCATCT
Statistics
Matches: 254, Mismatches: 44, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
188 95 0.37
189 153 0.60
190 6 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (188 bp):
TTCAGGGAGATAAGATTCGTCATTGTAGTTTCATTCCGACCCACTGCAACTTTAGGGGTATAGGA
TTTGTAGCTTCATCTTACTCCACTGCAATTTCAGGGAGATAAGATTTGTCATTGTAGTTTTAACC
TGACCCACTGCAACTTCAAAGGTATAGGATTTATAGCTTCATCTTCTCCCACTGCAAC
Found at i:56710 original size:138 final size:138
Alignment explanation
Indices: 56530--56816 Score: 412
Period size: 138 Copynumber: 2.1 Consensus size: 138
56520 GATTTGTCAT
* * * *
56530 TTGTAGTTTTAATCCGACCCACTGCAACTTTAAAGGTTTAGGATTTGTAGCTTCATCTTACTCCA
1 TTGTAGCTTCAATCCGACCCACTGCAACTTCAAAGGTATAGGATTTGTAGCTTCATCTTACTCCA
* * * * * *
56595 CTGTAACTTCAGGGAGATAAGATTCGTCATTATAGTTTCATTCCGACCTACTGCAACTTTAGGGG
66 CTGCAACTTCAAGGAGATAAGATTCGCCATTATAATTTCATTCCGACCTACTGCAACTTCAAGGG
56660 TATAGGAA
131 TATAGGAA
** *
56668 TTGTAGCTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCA
1 TTGTAGCTTCAATCCGACCCACTGCAACTTCAAAGGTATAGGATTTGTAGCTTCATCTTACTCCA
* * * * *
56733 CTGCAACTTTAAGGAGATAAGATTCGCCATTGTAATTTTATTCTGACCTACTGCAAGTTCAAGGG
66 CTGCAACTTCAAGGAGATAAGATTCGCCATTATAATTTCATTCCGACCTACTGCAACTTCAAGGG
56798 TATAGGAA
131 TATAGGAA
56806 TTGTAGCTTCA
1 TTGTAGCTTCA
56817 TCTGTTTCCC
Statistics
Matches: 131, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 131 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (138 bp):
TTGTAGCTTCAATCCGACCCACTGCAACTTCAAAGGTATAGGATTTGTAGCTTCATCTTACTCCA
CTGCAACTTCAAGGAGATAAGATTCGCCATTATAATTTCATTCCGACCTACTGCAACTTCAAGGG
TATAGGAA
Found at i:68901 original size:56 final size:54
Alignment explanation
Indices: 68786--68948 Score: 265
Period size: 56 Copynumber: 3.0 Consensus size: 54
68776 GTGACCCGAA
* *
68786 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAACATAAATTAAAAG
1 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAG
*
68839 GCTCAACTCATCTCTCGTAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAG
1 GCTCAACTCACCTCTCGTAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAG
68895 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAA
1 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAA
68949 TACCTCAGCG
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
53 28 0.27
54 19 0.19
55 9 0.09
56 46 0.45
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (54 bp):
GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAG
Found at i:69029 original size:54 final size:55
Alignment explanation
Indices: 68966--69075 Score: 213
Period size: 54 Copynumber: 2.0 Consensus size: 55
68956 GCGTGTATTG
68966 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATT-AAA
1 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA
69020 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA
1 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA
69075 A
1 A
69076 TGCCTCAGCG
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 51 0.93
55 4 0.07
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (55 bp):
AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA
Found at i:69065 original size:127 final size:127
Alignment explanation
Indices: 68837--69187 Score: 648
Period size: 127 Copynumber: 2.7 Consensus size: 127
68827 ATAAATTAAA
*
68837 AGGCTCAACTCATCTCTCGTAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAGGCTCAAC
1 AGGCTCAACTCACCTCTCGTAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAGGCTCAAC
68902 TCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTATTG
64 TCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTATTG
68966 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
1 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
*
69031 ACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATGCCTCAGCGTGTATTG
66 ACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTATTG
* *
69093 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTA
1 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
69158 ACCTCTCGTAATATGAGTTGATTTTTGAAA
66 ACCTCTCGTAATATGAGTTGATTTTTGAAA
69188 CTTAACTTGA
Statistics
Matches: 218, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
127 187 0.86
129 31 0.14
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (127 bp):
AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
ACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTATTG
Found at i:69341 original size:90 final size:88
Alignment explanation
Indices: 69149--69379 Score: 268
Period size: 90 Copynumber: 2.6 Consensus size: 88
69139 AAATTAAAAG
* * * * * **
69149 GCTCAACTAACCTCTCGTAATATGAGTTGA-TTTTTGAAACTTAACTTGAAAAGCAGATTTTGAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAACATAAATTGAAAAACAGAAATTGAA
*
69213 AATACCTCGACATGTGACCCGAA
66 AATACCTCGACATGTGAACCGAA
69236 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTGAAAGAACAGAAATTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAACATAAATTGAAA-AACAGAAATTG
* * * *
69301 GAAATGCCTC-AGTATGTGAACCGAG
64 AAAATACCTCGA-CATGTGAACCGAA
* * *
69326 GTTCAACTCATCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG--AAACATAAATTGAAA
69380 TTACCTCAGC
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
87 28 0.23
89 27 0.22
90 54 0.44
91 14 0.11
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (88 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAACATAAATTGAAAAACAGAAATTGAA
AATACCTCGACATGTGAACCGAA
Found at i:77848 original size:4 final size:4
Alignment explanation
Indices: 77839--77878 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
77829 TGGGATATGC
* * *
77839 AATG AATG AATG AATA AATG AATG AATG CATA AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
77879 CCAATCACGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:77860 original size:16 final size:16
Alignment explanation
Indices: 77839--77878 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
77829 TGGGATATGC
77839 AATGAATGAATGAATA
1 AATGAATGAATGAATA
*
77855 AATGAATGAATGCATA
1 AATGAATGAATGAATA
77871 AATGAATG
1 AATGAATG
77879 CCAATCACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.25
Consensus pattern (16 bp):
AATGAATGAATGAATA
Found at i:82354 original size:21 final size:19
Alignment explanation
Indices: 82323--82371 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
82313 CTATTTTTTA
82323 ATATAT-ATATTAGAAATAT
1 ATATATAATATTAGAAA-AT
82342 ATATAGTAATATTAGAAAAT
1 ATATA-TAATATTAGAAAAT
82362 ATATATAATA
1 ATATATAATA
82372 GTACAGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.36
20 8 0.29
21 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
ATATATAATATTAGAAAAT
Found at i:82431 original size:36 final size:38
Alignment explanation
Indices: 82391--82462 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
82381 ATATATGACT
82391 AATAATATTA-AAA-CACA-TACATAATAATACATAAAA
1 AATAATATTAGAAAGCACAGTACATAAT-ATACATAAAA
*
82427 AATAATATTAGAAAGCATATGTACATAATATACATA
1 AATAATATTAGAAAGCACA-GTACATAATATACATA
82463 TGGAAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 10 0.32
37 3 0.10
38 3 0.10
39 7 0.23
40 8 0.26
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.28
Consensus pattern (38 bp):
AATAATATTAGAAAGCACAGTACATAATATACATAAAA
Found at i:84984 original size:15 final size:16
Alignment explanation
Indices: 84960--84996 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
84950 TAATCATACA
84960 TAAT-AATAATC-ATT
1 TAATAAATAATCAATT
84974 TAATAAATAATCAATT
1 TAATAAATAATCAATT
*
84990 TCATAAA
1 TAATAAA
84997 CTCATCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 9 0.45
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAAATAATCAATT
Found at i:86212 original size:25 final size:24
Alignment explanation
Indices: 86178--86231 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
86168 CTTTGTTTTA
* *
86178 TTTTATTTCTTTTATTTTATGTTATG
1 TTTTATTTCTATTA--TTATATTATG
86204 TTTTA-TTCTATTATTATATTATG
1 TTTTATTTCTATTATTATATTATG
86227 TTTTA
1 TTTTA
86232 GTAATAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 14 0.54
25 7 0.27
26 5 0.19
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (24 bp):
TTTTATTTCTATTATTATATTATG
Found at i:87208 original size:3 final size:3
Alignment explanation
Indices: 87131--87197 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
87121 ATTAATAAGA
* * * *
87131 AAT AAT AAT AAC AAT AAT AAT AAT ATT CAATT AAT AAT ACT ATAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AA-T AAT AAT AAT A-AT AAT
87179 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
87198 GTGAAATAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
3 48 0.91
4 4 0.08
5 1 0.02
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:88387 original size:1 final size:1
Alignment explanation
Indices: 88377--88418 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
88367 ATGATATTAG
* *
88377 TTTTTGTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
88419 CTATTCCTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.02, G:0.02, T:0.95
Consensus pattern (1 bp):
T
Found at i:88408 original size:20 final size:20
Alignment explanation
Indices: 88383--88420 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
88373 TTAGTTTTTG
88383 TTTTTTTTTTTTTTTTCTTT
1 TTTTTTTTTTTTTTTTCTTT
88403 TTTTTTTTTTTTTTTTCT
1 TTTTTTTTTTTTTTTTCT
88421 ATTCCTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTCTTT
Found at i:88479 original size:14 final size:16
Alignment explanation
Indices: 88455--88487 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
88445 CTCTCTACTC
88455 TTTGTTCTTTTT-TTT
1 TTTGTTCTTTTTCTTT
88470 TTTG-TCTTTTTCTTT
1 TTTGTTCTTTTTCTTT
88485 TTT
1 TTT
88488 TTGCAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (16 bp):
TTTGTTCTTTTTCTTT
Found at i:89212 original size:31 final size:31
Alignment explanation
Indices: 89174--89257 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 31
89164 TTTATTTTTA
*
89174 AAAATATTTAAATTATTTAA-ATTATTAATAT
1 AAAATATTTAAATTATTTAATATTATTAA-AC
*
89205 AAAATA-TTATAGTT-TTTAATATTATTAAAC
1 AAAATATTTA-AATTATTTAATATTATTAAAC
*
89235 AAACATATTT-TATTATTT-ATATT
1 AAA-ATATTTAAATTATTTAATATT
89258 TAGCCATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
30 19 0.43
31 23 0.52
32 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (31 bp):
AAAATATTTAAATTATTTAATATTATTAAAC
Found at i:89302 original size:16 final size:15
Alignment explanation
Indices: 89265--89310 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
89255 ATTTAGCCAT
*
89265 ATAATAAATTACT-A
1 ATAATAAATTATTAA
*
89279 AT-ATAATTTATTAA
1 ATAATAAATTATTAA
*
89293 ATAATAAATTATTTA
1 ATAATAAATTATTAA
89308 ATA
1 ATA
89311 TTTTAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 13 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAAATTATTAA
Found at i:89337 original size:13 final size:14
Alignment explanation
Indices: 89321--89362 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
89311 TTTTAATTTT
89321 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
89334 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
89349 ATTTTAAATAATAT
1 ATTTT-AATAATAT
89363 TCTTCACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:89347 original size:16 final size:16
Alignment explanation
Indices: 89325--89361 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
89315 AATTTTATTT
89325 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
89342 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
89357 TAATA
1 TAATA
89362 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:89951 original size:14 final size:14
Alignment explanation
Indices: 89915--89953 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
89905 CCAAGAAATT
89915 AAGTCATTTTCCAG
1 AAGTCATTTTCCAG
*
89929 AAATCATTTTCCAG
1 AAGTCATTTTCCAG
*
89943 AAGTTATTTTC
1 AAGTCATTTTC
89954 AATGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (14 bp):
AAGTCATTTTCCAG
Found at i:95920 original size:29 final size:29
Alignment explanation
Indices: 95862--95921 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
95852 TGATTTTCAC
* *
95862 ATTTATACACATGTAATAGGATTTTTAAT
1 ATTTATACACATGTAATAGCATTTTAAAT
95891 ATTTATA-ACATGTAA-AGCAGTTTGTAAAT
1 ATTTATACACATGTAATAGCA-TTT-TAAAT
95920 AT
1 AT
95922 GAGTGTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 11 0.41
29 13 0.48
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (29 bp):
ATTTATACACATGTAATAGCATTTTAAAT
Found at i:96670 original size:20 final size:21
Alignment explanation
Indices: 96642--96684 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
96632 CACGAATTTA
*
96642 TTAGTTTTTTTAT-ATTAATT
1 TTAGATTTTTTATGATTAATT
*
96662 TTAGATTTTTTATGGTTAATT
1 TTAGATTTTTTATGATTAATT
96683 TT
1 TT
96685 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (21 bp):
TTAGATTTTTTATGATTAATT
Found at i:96685 original size:22 final size:21
Alignment explanation
Indices: 96636--96686 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
96626 AACCATCACG
*
96636 AATTTATTAGTTTTTTTATATT
1 AATTT-TTAGATTTTTTATATT
*
96658 AA-TTTTAGATTTTTTATGGTT
1 AATTTTTAGATTTTTTAT-ATT
96679 AATTTTTA
1 AATTTTTA
96687 AATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.48
21 6 0.24
22 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (21 bp):
AATTTTTAGATTTTTTATATT
Found at i:97964 original size:12 final size:12
Alignment explanation
Indices: 97925--97964 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
97915 TTTAATAATA
97925 TAAAA-ATAT-T
1 TAAAATATATAT
*
97935 TAAAACATATAT
1 TAAAATATATAT
97947 TAAAATATATAT
1 TAAAATATATAT
97959 TAAAAT
1 TAAAAT
97965 GAAAAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 5 0.19
11 4 0.15
12 18 0.67
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAATATATAT
Found at i:107218 original size:15 final size:15
Alignment explanation
Indices: 107198--107236 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
107188 TCCTCAGAAG
107198 AAGTTATCGACGAGA
1 AAGTTATCGACGAGA
*
107213 AAGTTATCGACGATA
1 AAGTTATCGACGAGA
107228 AAGTTATCG
1 AAGTTATCG
107237 CTGAAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (15 bp):
AAGTTATCGACGAGA
Found at i:107414 original size:25 final size:26
Alignment explanation
Indices: 107371--107420 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
107361 GCATATGGTA
107371 TTGTCTTATTTTTTTGTTTTTATTTG
1 TTGTCTTATTTTTTTGTTTTTATTTG
107397 TTGTCTTA-TTTTTTGTTTTTATTT
1 TTGTCTTATTTTTTTGTTTTTATTT
107421 TATGTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.08, C:0.04, G:0.10, T:0.78
Consensus pattern (26 bp):
TTGTCTTATTTTTTTGTTTTTATTTG
Found at i:107421 original size:13 final size:13
Alignment explanation
Indices: 107380--107426 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
107370 ATTGTCTTAT
107380 TTTTTTGTTTTTA
1 TTTTTTGTTTTTA
* *
107393 TTTGTTG-TCTTA
1 TTTTTTGTTTTTA
107405 TTTTTTGTTTTTA
1 TTTTTTGTTTTTA
*
107418 TTTTATGTT
1 TTTTTTGTT
107427 AATTGAATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.09, C:0.02, G:0.11, T:0.79
Consensus pattern (13 bp):
TTTTTTGTTTTTA
Found at i:110609 original size:3 final size:3
Alignment explanation
Indices: 110601--110656 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
110591 CCATCCAAAC
110601 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
110649 AAT AAT AA
1 AAT AAT AA
110657 GGGATAAAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:113528 original size:26 final size:26
Alignment explanation
Indices: 113499--113556 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
113489 CCCGATATAT
*
113499 GGCTGTTCATGAGCTTCCAGATTAAA
1 GGCTCTTCATGAGCTTCCAGATTAAA
** * *
113525 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTCATGAGCTTCCAGATTAAA
113551 GGCTCT
1 GGCTCT
113557 CCGGAGCTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCAGATTAAA
Found at i:113673 original size:24 final size:23
Alignment explanation
Indices: 113646--113693 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
113636 TACCCGTTAT
*
113646 TGGCTCGTATGAGCTTCCTAATTA
1 TGGCTCGTATGAACTTCCT-ATTA
*
113670 TGGCTCTTATGAACTTCCTATTA
1 TGGCTCGTATGAACTTCCTATTA
113693 T
1 T
113694 ACAGCCCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (23 bp):
TGGCTCGTATGAACTTCCTATTA
Found at i:123332 original size:14 final size:14
Alignment explanation
Indices: 123313--123342 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
123303 TATCTTATAA
123313 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
123327 ATATGCGTTAATCT
1 ATATGCGTGAATCT
123341 AT
1 AT
123343 GTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:124855 original size:11 final size:10
Alignment explanation
Indices: 124817--124868 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
124807 ATAAAAAGGG
124817 TAATAAATAAA
1 TAAT-AATAAA
*
124828 TAGATGAATAGA
1 TA-AT-AATAAA
124840 TAATAATGAAA
1 TAATAAT-AAA
*
124851 TAATAATAGA
1 TAATAATAAA
124861 TAATAATA
1 TAATAATA
124869 TACCAATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 13 0.37
11 13 0.37
12 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (10 bp):
TAATAATAAA
Found at i:124865 original size:10 final size:10
Alignment explanation
Indices: 124834--124868 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
124824 TAAATAGATG
124834 AATAGATAAT
1 AATAGATAAT
*
124844 AATGAAATAAT
1 AAT-AGATAAT
124855 AATAGATAAT
1 AATAGATAAT
124865 AATA
1 AATA
124869 TACCAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (10 bp):
AATAGATAAT
Found at i:125741 original size:10 final size:11
Alignment explanation
Indices: 125725--125754 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
125715 GGATAGATTT
125725 AAAAAAAAAAC
1 AAAAAAAAAAC
125736 AAAAAAAAAAC
1 AAAAAAAAAAC
*
125747 AACAAAAA
1 AAAAAAAA
125755 CGAAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:125744 original size:14 final size:14
Alignment explanation
Indices: 125725--125754 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
125715 GGATAGATTT
125725 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
*
125739 AAAAAAACAACAAA
1 AAAAAAAAAACAAA
125753 AA
1 AA
125755 CGAAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:126894 original size:31 final size:31
Alignment explanation
Indices: 126856--126919 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
126846 ATTTATTTAA
* *
126856 ATATATACAATTGAATCAAAATCAAAATTTT
1 ATATATACAATTAAATCAAAATCAAAAATTT
* * *
126887 ATATATACATTTAAATCACAATTAAAAATTT
1 ATATATACAATTAAATCAAAATCAAAAATTT
126918 AT
1 AT
126920 GTGTATAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (31 bp):
ATATATACAATTAAATCAAAATCAAAAATTT
Found at i:127609 original size:14 final size:13
Alignment explanation
Indices: 127589--127620 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
127579 TATATATATA
127589 AATTAACACTAAT
1 AATTAACACTAAT
127602 AGATTAACACTAAT
1 A-ATTAACACTAAT
127616 AATTA
1 AATTA
127621 TTATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (13 bp):
AATTAACACTAAT
Found at i:135416 original size:14 final size:16
Alignment explanation
Indices: 135378--135414 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
135368 ATCTTTTTTA
135378 TTAT-TATTATAAAGT
1 TTATATATTATAAAGT
*
135393 TTATATATTATAAATT
1 TTATATATTATAAAGT
135409 TTATAT
1 TTATAT
135415 TACTTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTATATATTATAAAGT
Found at i:143355 original size:22 final size:22
Alignment explanation
Indices: 143313--143355 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
143303 AATTGGTCTT
**
143313 AAATTTCAAAATATTCTTATCG
1 AAATTTCAAAATATTAGTATCG
*
143335 AAATTTTAAAATATTAGTATC
1 AAATTTCAAAATATTAGTATC
143356 TTATTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATTTCAAAATATTAGTATCG
Found at i:145111 original size:14 final size:14
Alignment explanation
Indices: 145071--145122 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
145061 AAACACCATT
145071 AAAA-ATAAT-TAA
1 AAAATATAATATAA
* *
145083 AAAATAAAATTTAA
1 AAAATATAATATAA
145097 AAAATATAATATAA
1 AAAATATAATATAA
* *
145111 ATAATTTAATAT
1 AAAATATAATAT
145123 TCGTAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 4 0.12
13 4 0.12
14 25 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATATAATATAA
Found at i:165233 original size:13 final size:14
Alignment explanation
Indices: 165217--165252 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
165207 CAATCTCATA
165217 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
165230 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
165243 TCTC-ATTTCA
1 TCTCAATTTCA
165253 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:165235 original size:26 final size:25
Alignment explanation
Indices: 165197--165259 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
165187 AACCTTTTGG
*
165197 TTCATATTTTCAATCTC-ATATCTCAAT
1 TTCA-ATTCTCAAT-TCAATATCTC-AT
*
165224 TTCAATTCTCAATTCAATTTCTCAT
1 TTCAATTCTCAATTCAATATCTCAT
165249 TTC-ATTC-CAAT
1 TTCAATTCTCAAT
165260 AGTTCAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 4 0.12
24 4 0.12
25 7 0.21
26 14 0.42
27 4 0.12
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.48
Consensus pattern (25 bp):
TTCAATTCTCAATTCAATATCTCAT
Found at i:165242 original size:18 final size:19
Alignment explanation
Indices: 165204--165244 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
165194 TGGTTCATAT
165204 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
165223 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
165241 TTTC
1 TTTC
165245 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:165458 original size:23 final size:21
Alignment explanation
Indices: 165406--165480 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
165396 CCTGATCAGT
** *
165406 ATACGACACATAAAGTGCCTG
1 ATACGACACACGAGGTGCCTG
165427 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
*
165448 ATACGACACACGAGGCGCCTG
1 ATACGACACACGAGGTGCCTG
165469 AAATACGACACA
1 --ATACGACACA
165481 TAAAGTGCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 38 0.79
23 10 0.21
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.13
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:165490 original size:23 final size:21
Alignment explanation
Indices: 165406--165490 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
165396 CCTGATCAGT
*
165406 ATACGACACATAAAGTGCCTG
1 ATACGACACACAAAGTGCCTG
* *
165427 ATACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
* * *
165448 ATACGACACACGAGGCGCCTG
1 ATACGACACACAAAGTGCCTG
*
165469 AAATACGACACATAAAGTGCCT
1 --ATACGACACACAAAGTGCCT
165491 AAATGGTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
21 38 0.70
23 16 0.30
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.15
Consensus pattern (21 bp):
ATACGACACACAAAGTGCCTG
Found at i:165888 original size:15 final size:15
Alignment explanation
Indices: 165863--165920 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
165853 TCATATATAT
165863 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
165879 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
165894 AATAATTTCAATCAA
1 TATAAATTCAATCAA
165909 TATAAATTCAAT
1 TATAAATTCAAT
165921 AAAACAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:165905 original size:30 final size:28
Alignment explanation
Indices: 165866--165924 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
165856 TATATATTAT
165866 ATAATTCAATCAATATAAATTCAATCAAA
1 ATAATTCAATCAATATAAATTCAAT-AAA
165895 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
165924 A
1 A
165925 CAGATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:167646 original size:24 final size:25
Alignment explanation
Indices: 167619--167665 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
167609 ATCATATTAG
167619 TTTAACAT-TTTGTATA-ATATTTCA
1 TTTAA-ATGTTTGTATATATATTTCA
*
167643 TTTAAATGTTTTTATATATATTT
1 TTTAAATGTTTGTATATATATTT
167666 ATACATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 12 0.60
25 6 0.30
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTAAATGTTTGTATATATATTTCA
Found at i:169291 original size:53 final size:51
Alignment explanation
Indices: 169221--169319 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 51
169211 TACTTGGGTA
169221 TTATATTATATATATTTTTATATGTTATA-TA-TATACTTTTAATATTGTATT
1 TTATATTATATATATTTTTA-ATGTTATATTATTATA-TTTTAATATTGTATT
*
169272 TTATATATATCATATATTTTTAATGTTGTATTATTATATTTTAATATT
1 TTATAT-TAT-ATATATTTTTAATGTTATATTATTATATTTTAATATT
169320 ATACTACATA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
51 6 0.14
52 10 0.23
53 23 0.53
54 4 0.09
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (51 bp):
TTATATTATATATATTTTTAATGTTATATTATTATATTTTAATATTGTATT
Found at i:169293 original size:32 final size:32
Alignment explanation
Indices: 169246--169310 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
169236 TTTTATATGT
169246 TATATATATACTTTTAATATTGTATT-TTATA
1 TATATATATACTTTTAATATTGTATTATTATA
* *
169277 TATATCATATATTTTTAATGTTGTATTATTATA
1 TATAT-ATATACTTTTAATATTGTATTATTATA
169310 T
1 T
169311 TTTAATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.17
32 19 0.63
33 6 0.20
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (32 bp):
TATATATATACTTTTAATATTGTATTATTATA
Found at i:169331 original size:53 final size:52
Alignment explanation
Indices: 169222--169332 Score: 127
Period size: 53 Copynumber: 2.1 Consensus size: 52
169212 ACTTGGGTAT
* * **
169222 TATATTATATATATTTTTATATGTTATATATATACTTTTAATATTGTATTTTA
1 TATA-TATATATATTTTTATATGTTATATATATACTTTTAATATTATACTACA
*
169275 TATATATCATATATTTTTA-ATGTTGTATTATTATA-TTTTAATATTATACTACA
1 TATATAT-ATATATTTTTATATGTTATA-TA-TATACTTTTAATATTATACTACA
169328 TATAT
1 TATAT
169333 TTTCATATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
52 10 0.20
53 36 0.72
54 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (52 bp):
TATATATATATATTTTTATATGTTATATATATACTTTTAATATTATACTACA
Found at i:169359 original size:26 final size:26
Alignment explanation
Indices: 169317--169405 Score: 90
Period size: 26 Copynumber: 3.3 Consensus size: 26
169307 ATATTTTAAT
169317 ATTATACTACATATATTTTCATATTAC
1 ATTATA-TACATATATTTTCATATTAC
* *
169344 ATTATATACATATATTTTTATA-TAT
1 ATTATATACATATATTTTCATATTAC
** *
169369 ATTATCATGTATATATTTTGATATTAC
1 ATTAT-ATACATATATTTTCATATTAC
169396 TAGTTATATA
1 -A-TTATATA
169406 TTACTTATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
25 7 0.14
26 29 0.57
27 8 0.16
28 3 0.06
29 4 0.08
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTATATACATATATTTTCATATTAC
Found at i:180166 original size:12 final size:12
Alignment explanation
Indices: 180149--180173 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
180139 TCTCTGCACA
180149 TTGTTTCAGCAT
1 TTGTTTCAGCAT
180161 TTGTTTCAGCAT
1 TTGTTTCAGCAT
180173 T
1 T
180174 GAAAAAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (12 bp):
TTGTTTCAGCAT
Found at i:182420 original size:74 final size:74
Alignment explanation
Indices: 182325--182928 Score: 606
Period size: 75 Copynumber: 8.1 Consensus size: 74
182315 TATGTGGATG
* *
182325 TTTC-ATTTCTGTTTTCAAAAAAATCAACTCATAATTGCGAAAGGTGAGTTGAGCCTCGGGGCAC
1 TTTCAATTTCTGCTTTCAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
*
182389 GCCGAGGTAT
65 GCTGAGGTAT
* * * * ***
182399 TTTCAAATTCTACTTTCAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTTACG
1 TTTCAATTTCTGCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
* *
182464 -TGTTGAGTCAC
66 CTG-AG-GT-AT
** * *
182475 TTTCAATTTCTG-TTT-----TTATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCGGGGCATG
1 TTTCAATTTCTGCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
*
182534 CTGAGGCAT
66 CTGAGGTAT
* * * *
182543 TTTCAATTTATGTTTTTC--AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TTTCAATTTCTG-CTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
182606 GCTGAGGTAT
65 GCTGAGGTAT
* * * * *
182616 TTTCAATTTCTACTTTCCAAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTCAGGAG-AC
1 TTTCAATTTCTGCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGGCAC
182680 GCTGAGGTGA-
65 GCTGAGGT-AT
* * * *
182690 TTTCAATTTATGTTTGTCAAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGG
1 TTTCAATTTCTGCTT-TC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGG
182755 CACGCTGAGGTAT
62 CACGCTGAGGTAT
* * *
182768 TTTCGATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTCAATTTCTGCT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
*
182833 GCTGAGGTAA
65 GCTGAGGTAT
* * * * **
182843 TTTCAATTTATGTTTGTC--AAAAATCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCAC
1 TTTCAATTTCTGCTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
*
182906 ATGCTGAGGTCT
65 --GCTGAGGTAT
182918 TTTCAATTTCT
1 TTTCAATTTCT
182929 ATTTTTAATT
Statistics
Matches: 438, Mismatches: 68, Indels: 47
0.79 0.12 0.08
Matches are distributed among these distances:
68 12 0.03
69 1 0.00
70 39 0.09
71 2 0.00
72 4 0.01
73 97 0.22
74 90 0.21
75 119 0.27
76 11 0.03
77 3 0.01
78 59 0.13
79 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (74 bp):
TTTCAATTTCTGCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
CTGAGGTAT
Found at i:182512 original size:70 final size:69
Alignment explanation
Indices: 182425--182937 Score: 280
Period size: 73 Copynumber: 7.0 Consensus size: 69
182415 CAAAAAAATT
* * * * * *
182425 AACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTTACGTGTTGAGTCACTTTCAATTTCTGTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACATGCTGAGGCACTTTCAATTTATGTTT
182490 TT-ATC
64 TTAATC
* * *
182495 AACTCATATTGCGAGAGGTGAGTGGAGCCTCGGGGCATGCTGAGGCATTTTCAATTTATGTTTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGCACTTTCAATTTATGTTTTT
182560 CAAAAATC
66 ----AATC
* * * * * *
182568 AGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG-CACGCTGAGGTATTTTCAATTTCTACTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACATGCTGAGGCACTTTCAATTTAT-GTTT
**
182632 CCAAAAAATC
64 ----TTAATC
* * * * * *
182642 AACTCATATTGTGAGAAGTGAGTTGAGCCTCAGGAGACGCTGAGGTGA-TTTCAATTTATGTTTG
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGG-CACTTTCAATTTATGTTT-
*
182706 TCAAAAAAAAAATC
64 T--------TAATC
* * * * * *
182720 AACTCATATTGCGAGAGATGAGTTGAGCCTCAGGG-CACGCTGAGGTATTTTCGATTTCTGCTCT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACATGCTGAGGCACTTTCAATTTATG-T-T
**
182784 TCAAAAAAATC
63 T----TTAATC
* * * *
182795 AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTTGT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGCACTTTCAATTTATGTTT-T
*
182860 CAAAAATC
65 ---TAATC
* * * * * *
182868 AACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACATGCTGAGGTC-TTTTCAATTTCTATT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACATGCTGAGG-CACTTTCAATTTATGTT
182932 TTTAAT
63 TTTAAT
182938 TTCTGTTTTT
Statistics
Matches: 354, Mismatches: 54, Indels: 69
0.74 0.11 0.14
Matches are distributed among these distances:
68 25 0.07
70 31 0.09
71 3 0.01
73 95 0.27
74 61 0.17
75 81 0.23
77 1 0.00
78 52 0.15
79 3 0.01
80 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (69 bp):
AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGCACTTTCAATTTATGTTTTT
AATC
Found at i:183051 original size:89 final size:87
Alignment explanation
Indices: 182843--183255 Score: 508
Period size: 89 Copynumber: 4.6 Consensus size: 87
182833 GCTGAGGTAA
* * *
182843 TTTCAATTTATGTTTGTCAAAAATCAACTCATATCGCGAGAGGTGAGTTAAGCCTC-GGCTCACA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
* *
182907 TGCTGAGGTCTTTTCAATTTCTATT
63 TGCTGAGGTATTTTCAATTTCTGTT
* * *
182932 TTT-AATTTCTGTTTTTCAAAAATCAACTCATACTACGAGAGGTGAGTTGAGCCTCAGGACATGC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGC
*
182996 TGAGGTAATTTCAATTTCTGTT
66 TGAGGTATTTTCAATTTCTGTT
* * *
183018 TTCTCCAATTTATGTTTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TT-T-CAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAT
183083 GCTGAGGTATTTTCAATTTCTGTT
64 GCTGAGGTATTTTCAATTTCTGTT
** *
183107 TTTCAATTT-TCACTTTTCAAAAAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGC
1 TTTCAATTTAT-GTTTTTC-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-
* *
183171 TCACATGCTGAGGTATTTTCAATTTATGTTT
59 -GACATGCTGAGGTATTTTCAATTTCTG-TT
* *
183202 TTTCAATTTATATTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
183256 GTGGGTTCAC
Statistics
Matches: 283, Mismatches: 27, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
86 28 0.10
87 12 0.04
88 47 0.17
89 83 0.29
90 34 0.12
92 38 0.13
94 23 0.08
95 17 0.06
96 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (87 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGC
TGAGGTATTTTCAATTTCTGTT
Found at i:183206 original size:15 final size:15
Alignment explanation
Indices: 183186--183218 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
183176 TGCTGAGGTA
*
183186 TTTTCAATTTATGTT
1 TTTTCAATTTATATT
183201 TTTTCAATTTATATT
1 TTTTCAATTTATATT
183216 TTT
1 TTT
183219 CAAAGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTCAATTTATATT
Found at i:184608 original size:26 final size:26
Alignment explanation
Indices: 184569--184647 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
184559 NNNNNNNNNN
184569 ATATATTTTCATATTACATTATATAC
1 ATATATTTTCATATTACATTATATAC
* * **
184595 ATATATTTTTATA-TATATTATCATGT
1 ATATATTTTCATATTACATTAT-ATAC
*
184621 ATATATTTTGATATTACTAGTTATATA
1 ATATATTTTCATATTAC-A-TTATATA
184648 TTACTTATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
25 7 0.17
26 26 0.62
27 2 0.05
28 3 0.07
29 4 0.10
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (26 bp):
ATATATTTTCATATTACATTATATAC
Found at i:185012 original size:22 final size:24
Alignment explanation
Indices: 184986--185044 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
184976 TCCGTATATC
*
184986 ATATTATTCATTTTTAT-ACTTAT
1 ATATTATTCATTATTATCACTTAT
*
185009 -TATT-TTCATTATTGTCACTTAT
1 ATATTATTCATTATTATCACTTAT
185031 ATATTATT-ATTATT
1 ATATTATTCATTATT
185045 TGGTGTACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 9 0.29
22 10 0.32
23 10 0.32
24 2 0.06
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATTATTCATTATTATCACTTAT
Found at i:187490 original size:26 final size:26
Alignment explanation
Indices: 187461--187535 Score: 150
Period size: 26 Copynumber: 2.9 Consensus size: 26
187451 TTAAATGAAA
187461 ATATATATAACAAAAAACTAAAAAAT
1 ATATATATAACAAAAAACTAAAAAAT
187487 ATATATATAACAAAAAACTAAAAAAT
1 ATATATATAACAAAAAACTAAAAAAT
187513 ATATATATAACAAAAAACTAAAA
1 ATATATATAACAAAAAACTAAAA
187536 CAAATTTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (26 bp):
ATATATATAACAAAAAACTAAAAAAT
Found at i:194051 original size:26 final size:26
Alignment explanation
Indices: 194014--194071 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
194004 TGATACAAAT
194014 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
194040 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
194066 TGATAA
1 TGATAA
194072 GAATTTCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:196749 original size:7 final size:7
Alignment explanation
Indices: 196737--196769 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
196727 GTTTAGAAAA
196737 TAAATTT
1 TAAATTT
196744 TAAATTT
1 TAAATTT
196751 TAAATTT
1 TAAATTT
196758 TAAATTT
1 TAAATTT
196765 TAAAT
1 TAAAT
196770 CAATCCAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TAAATTT
Found at i:199318 original size:37 final size:37
Alignment explanation
Indices: 199277--199353 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
199267 GAGAATTAAA
* *
199277 GTCGGTCTGGATTTAATGTAAAGTATATTTAAATTAT
1 GTCGGTCTGGATTTAACGTAAAGCATATTTAAATTAT
*
199314 GTCGGTGTGGATTTAACGTAAAGCATATTTAAATTAT
1 GTCGGTCTGGATTTAACGTAAAGCATATTTAAATTAT
199351 GTC
1 GTC
199354 AATAAGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (37 bp):
GTCGGTCTGGATTTAACGTAAAGCATATTTAAATTAT
Found at i:199366 original size:37 final size:37
Alignment explanation
Indices: 199286--199363 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
199276 AGTCGGTCTG
* * ** **
199286 GATTTAATGTAAAGTATATTTAAATTATGTCGGTGTG
1 GATTTAACGTAAAGCATATTTAAATTATGTCAATGAA
199323 GATTTAACGTAAAGCATATTTAAATTATGTCAAT-AA
1 GATTTAACGTAAAGCATATTTAAATTATGTCAATGAA
199359 GATTT
1 GATTT
199364 TAAATGTGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
36 5 0.14
37 30 0.86
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (37 bp):
GATTTAACGTAAAGCATATTTAAATTATGTCAATGAA
Found at i:201198 original size:41 final size:41
Alignment explanation
Indices: 201152--201329 Score: 250
Period size: 41 Copynumber: 4.3 Consensus size: 41
201142 ATAGAGCAAT
*
201152 AAACGCCGCTAAAAACCAGAGCAATAGCGGCGCTTTTGGTA
1 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTA
* *
201193 AAACGCCACTAAAAACTAGAGCATTAGCGGCGCTTTTGGTA
1 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTA
*
201234 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGTTTTTGGTA
1 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTA
* * * * *
201275 AAATGCCGCTAAAAATC-GAAGTATTAGCGACGCTTTCGGTA
1 AAACGCCGCTAAAAACCAG-AGCATTAGCGGCGCTTTTGGTA
*
201316 AAACGCTGCTAAAA
1 AAACGCCGCTAAAA
201330 GTCATATAAC
Statistics
Matches: 122, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 1 0.01
41 121 0.99
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (41 bp):
AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTA
Found at i:201396 original size:22 final size:23
Alignment explanation
Indices: 201371--201418 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
201361 AAAAAATCAT
*
201371 AAACACT-AA-TCTATAATCCTTA
1 AAACACTAAACTCT-TAAACCTTA
201393 AAACACTAAACTCTTAAACCTTA
1 AAACACTAAACTCTTAAACCTTA
201416 AAA
1 AAA
201419 AATTTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 13 0.57
24 3 0.13
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (23 bp):
AAACACTAAACTCTTAAACCTTA
Found at i:201669 original size:15 final size:15
Alignment explanation
Indices: 201633--201665 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
201623 TATTTTAAGT
*
201633 TTTATGGATTATGAG
1 TTTAGGGATTATGAG
201648 TTTAGGGATTATG-G
1 TTTAGGGATTATGAG
201662 TTTA
1 TTTA
201666 AGGGTTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
TTTAGGGATTATGAG
Found at i:201966 original size:14 final size:15
Alignment explanation
Indices: 201932--201968 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
201922 ACTATTTTAA
201932 GGTTTATGAATTATG
1 GGTTTATGAATTATG
201947 GGTTTAGTG-ATTAT-
1 GGTTTA-TGAATTATG
201961 GGTTTATG
1 GGTTTATG
201969 GTTTAAGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 6 0.29
15 11 0.52
16 2 0.10
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (15 bp):
GGTTTATGAATTATG
Found at i:205414 original size:26 final size:26
Alignment explanation
Indices: 205363--205415 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
205353 TCAAACATGC
*
205363 ATTTAGGTCAATTTAACTCTAGGGGT
1 ATTTAGGTCAATTTAACTCTAAGGGT
* *
205389 ATTTCGGT-AATTTATCTACTAAGGGT
1 ATTTAGGTCAATTTAACT-CTAAGGGT
205415 A
1 A
205416 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACTCTAAGGGT
Found at i:206941 original size:26 final size:26
Alignment explanation
Indices: 206903--206960 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
206893 CATGAAATTC
206903 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
206929 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
206955 TTATCA
1 TTATCA
206961 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:209756 original size:20 final size:20
Alignment explanation
Indices: 209694--209757 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 20
209684 AAATTTCAAA
*
209694 AATTAAACATAATATAATATTT
1 AATTAAA-ATAAAAT-ATATTT
*
209716 AACATAGAAAT-AAATATTATTT
1 AA-TTA-AAATAAAATA-TATTT
209738 AATTAAAATAAAATATATTT
1 AATTAAAATAAAATATATTT
209758 TTTAAAGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
20 9 0.26
21 8 0.23
22 12 0.34
23 4 0.11
24 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (20 bp):
AATTAAAATAAAATATATTT
Found at i:209861 original size:42 final size:42
Alignment explanation
Indices: 209774--209956 Score: 204
Period size: 42 Copynumber: 4.3 Consensus size: 42
209764 GTTCATGATT
* * * *
209774 TTTAGCGGCGTTTGTGAGAAAAGCGCTGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGT-AAAAAAGCGCCGCTAAAGGTCCTGGTC
* * * *
209817 TTTAGTGGCGTTTGTAAAAAAACACTGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGTCCTGGTC
* * * *
209859 TTTAGCGGCGTTTCTTAAAAGAGCTCCGCTAAAGGTCCAGGTC
1 TTTAGCGGCGTTT-GTAAAAAAGCGCCGCTAAAGGTCCTGGTC
* * * *
209902 TTTAGCGGCGTTTTTATAAAAGCGCCGCGAAAGATCCTGGTC
1 TTTAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGTCCTGGTC
209944 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
209957 TTTAGATTTG
Statistics
Matches: 120, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
42 70 0.58
43 50 0.42
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGTCCTGGTC
Found at i:209890 original size:85 final size:85
Alignment explanation
Indices: 209774--209956 Score: 217
Period size: 85 Copynumber: 2.2 Consensus size: 85
209764 GTTCATGATT
* * *
209774 TTTAGCGGCGTTTGTGAGAAAAGCGCTGCTAAAGGT-CATGATCTTTAGTGGCGTTTGTAAAAAA
1 TTTAGCGGCGTTTCTGAGAAAAGCGCCGCTAAAGGTCCA-GATCTTTAGCGGCGTTTGTAAAAAA
* * *
209838 ACACTGCTAAAGGTCCTGGTC
65 ACACCGCGAAAGATCCTGGTC
* * * * *
209859 TTTAGCGGCGTTTCTTA-AAAGAGCTCCGCTAAAGGTCCAGGTCTTTAGCGGCGTTTTTATAAAA
1 TTTAGCGGCGTTTCTGAGAAA-AGCGCCGCTAAAGGTCCAGATCTTTAGCGGCGTTTGTAAAAAA
* *
209923 GCGCCGCGAAAGATCCTGGTC
65 ACACCGCGAAAGATCCTGGTC
209944 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
209957 TTTAGATTTG
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
84 3 0.04
85 78 0.94
86 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (85 bp):
TTTAGCGGCGTTTCTGAGAAAAGCGCCGCTAAAGGTCCAGATCTTTAGCGGCGTTTGTAAAAAAA
CACCGCGAAAGATCCTGGTC
Found at i:212984 original size:82 final size:82
Alignment explanation
Indices: 212842--213004 Score: 308
Period size: 82 Copynumber: 2.0 Consensus size: 82
212832 GGCACACATG
*
212842 CGGCACTCATGGGCAGTTGGGGCTAGGGTTTGCTGTTGCTGAAAGTTTGTTATGGGCTATTAGGT
1 CGGCACTCATGGGCAGTTGGGGCTACGGTTTGCTGTTGCTGAAAGTTTGTTATGGGCTATTAGGT
212907 TTGGGCTTGAATTTGGA
66 TTGGGCTTGAATTTGGA
*
212924 CGGCGCTCATGGGCAGTTGGGGCTACGGTTTGCTGTTGCTGAAAGTTTGTTATGGGCTATTAGGT
1 CGGCACTCATGGGCAGTTGGGGCTACGGTTTGCTGTTGCTGAAAGTTTGTTATGGGCTATTAGGT
212989 TTGGGCTTGAATTTGG
66 TTGGGCTTGAATTTGG
213005 GTTTGGGCAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.15, C:0.13, G:0.37, T:0.36
Consensus pattern (82 bp):
CGGCACTCATGGGCAGTTGGGGCTACGGTTTGCTGTTGCTGAAAGTTTGTTATGGGCTATTAGGT
TTGGGCTTGAATTTGGA
Found at i:213521 original size:44 final size:44
Alignment explanation
Indices: 213407--213828 Score: 354
Period size: 44 Copynumber: 9.6 Consensus size: 44
213397 TTCTCTGCCA
* * *
213407 AATACAGGAAGGCAAGATCTGCAATCTTCGATCTACTTCAACACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACC
* * * * *
213452 AGTATGGGAAGACAAGATCTG-TATCTTGGATCCACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACC
* * * *
213495 AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
* * * * *
213539 AATAAATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACC
* * * *
213584 AATATGGGAAGACAAGATCTGC-ATCTTGGATCCACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACC
* * * *
213627 AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
* * * * *
213671 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACC
* * * * *
213716 AATATGGGAAGACAAGATCTGC-GTCGTCGATCCACTTC-CAATC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACC
* * * * * *
213759 ATTATAGGAAGATAGGACCTGCTAGCTTCGATCTACTTCACGCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
* *
213803 AATACATGAAGACAAGATCTGC-ATCT
1 AATATAGGAAGACAAGATCTGCTATCT
213829 GACTTTAATC
Statistics
Matches: 289, Mismatches: 77, Indels: 24
0.74 0.20 0.06
Matches are distributed among these distances:
42 3 0.01
43 60 0.21
44 162 0.56
45 64 0.22
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (44 bp):
AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
Found at i:213574 original size:132 final size:132
Alignment explanation
Indices: 213384--213824 Score: 693
Period size: 132 Copynumber: 3.3 Consensus size: 132
213374 TAAGACTGTA
* * * * * ** * **
213384 ATCTTCGATTTGCTTCTCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCGATCTACTTCAAC
1 ATCTTCGATCTACTTCAC-GCC-AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCC
* *
213449 ACCAGTATGGGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACC
64 ACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACC
213514 TGCT
129 TGCT
*
213518 ATCTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
213583 CAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTG
66 CAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTG
213648 CT
131 CT
213650 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
* * * * *
213715 CAATATGGGAAGACAAGATCTGCGTCGTCGATCCACTTCCAATCATTATAGGAAGATAGGACCTG
66 CAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTG
213780 CT
131 CT
*
213782 AGCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
213825 ATCTGACTTT
Statistics
Matches: 287, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
132 269 0.94
133 3 0.01
134 15 0.05
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (132 bp):
ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
CAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTG
CT
Found at i:227066 original size:42 final size:43
Alignment explanation
Indices: 226999--227081 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 43
226989 TGAGATTGAT
226999 TCTTAAGAAATAAAAAAAACATGAATAAGTAAATAAATGGAGA
1 TCTTAAGAAATAAAAAAAACATGAATAAGTAAATAAATGGAGA
* *
227042 TCTTGAGAAATAAAAAAGA-ATGAATAAGTAAATAAATGGA
1 TCTTAAGAAATAAAAAAAACATGAATAAGTAAATAAATGGA
227082 TAGCAAGCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 21 0.55
43 17 0.45
ACGTcount: A:0.59, C:0.04, G:0.16, T:0.22
Consensus pattern (43 bp):
TCTTAAGAAATAAAAAAAACATGAATAAGTAAATAAATGGAGA
Found at i:232039 original size:29 final size:29
Alignment explanation
Indices: 231997--232052 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
231987 AAGTAAATAG
*
231997 CTAACTAAGCTAACAGAAAATTACAGCAA
1 CTAACTAAGCTAACAAAAAATTACAGCAA
232026 CTAACTAAGCTAACAAAAAATTACAGC
1 CTAACTAAGCTAACAAAAAATTACAGC
232053 TAGATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.52, C:0.21, G:0.09, T:0.18
Consensus pattern (29 bp):
CTAACTAAGCTAACAAAAAATTACAGCAA
Found at i:232186 original size:24 final size:24
Alignment explanation
Indices: 232144--232195 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
232134 AATCAAAGTC
** *
232144 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
232168 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
232192 AAAT
1 AAAT
232196 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:232501 original size:31 final size:31
Alignment explanation
Indices: 232466--232533 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
232456 CTACAAAATG
*
232466 GTCACTAAATTAT-TCAAAAATTTTCATTTAA
1 GTCACTAAATTATAT-AAAAATTGTCATTTAA
* *
232497 GTCACTAAATTATATGAAAGTTGTCATTTAA
1 GTCACTAAATTATATAAAAATTGTCATTTAA
232528 GTCACT
1 GTCACT
232534 GAGCTATTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (31 bp):
GTCACTAAATTATATAAAAATTGTCATTTAA
Found at i:234626 original size:20 final size:20
Alignment explanation
Indices: 234601--234645 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
234591 CTCAACTATG
* *
234601 ATATGAAGTACATT-TAAAA
1 ATATGAACTAAATTGTAAAA
234620 CATATGAACTAAATTGTAAAA
1 -ATATGAACTAAATTGTAAAA
234641 ATATG
1 ATATG
234646 TGTACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (20 bp):
ATATGAACTAAATTGTAAAA
Found at i:235062 original size:32 final size:32
Alignment explanation
Indices: 235017--235084 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
235007 CCCTGCTTAT
235017 TGTT-TGATTCACATGTTTTAAATATGTTTCG
1 TGTTATGATTCACATGTTTTAAATATGTTTCG
235048 TGTTATGATTCACATGTTTTAAATATGTTTCG
1 TGTTATGATTCACATGTTTTAAATATGTTTCG
235080 TGTTA
1 TGTTA
235085 GGTCCAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (32 bp):
TGTTATGATTCACATGTTTTAAATATGTTTCG
Found at i:239646 original size:45 final size:45
Alignment explanation
Indices: 239582--239667 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
239572 TAAAAATGTT
*
239582 AAAACTCGAGCCTGACCCAACCTGTTCGTATTAATTTTTTTATGA
1 AAAACTCGAACCTGACCCAACCTGTTCGTATTAATTTTTTTATGA
239627 AAAACTCGAACCTGACCCAACCTGTTCGTATTAATTTTTTT
1 AAAACTCGAACCTGACCCAACCTGTTCGTATTAATTTTTTT
239668 TATATAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (45 bp):
AAAACTCGAACCTGACCCAACCTGTTCGTATTAATTTTTTTATGA
Found at i:245023 original size:22 final size:20
Alignment explanation
Indices: 244973--245023 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 20
244963 TTAATCAAGT
*
244973 TAAAAAAATAACTTTTAATT
1 TAAAAAAATAACTTTTAATC
244993 TAAAGAAAATAAACTTAATT-ATC
1 TAAA-AAAAT-AACTT--TTAATC
245016 TAAAAAAA
1 TAAAAAAA
245024 AGTTTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 9 0.35
23 6 0.23
24 2 0.08
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAAAAATAACTTTTAATC
Found at i:247538 original size:30 final size:30
Alignment explanation
Indices: 247502--247561 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
247492 ATTTTTAGAC
* *
247502 TAAAGTTTATACCAGACAATAATATACAAA
1 TAAAGTTCATACCAAACAATAATATACAAA
247532 TAAAGTTCATACCAAACAATAATATACAAA
1 TAAAGTTCATACCAAACAATAATATACAAA
247562 GAATGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (30 bp):
TAAAGTTCATACCAAACAATAATATACAAA
Found at i:248658 original size:25 final size:27
Alignment explanation
Indices: 248612--248666 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
248602 ATTTTTTATT
248612 TTAATTTTTTTTGGTTTAATT-AAAATA
1 TTAATTTTTTTT-GTTTAATTAAAAATA
248639 TTAATTTTTTATT-TTT-ATTAAAAATA
1 TTAATTTTTT-TTGTTTAATTAAAAATA
248665 TT
1 TT
248667 TAAATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 3 0.12
26 11 0.42
27 10 0.38
28 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TTAATTTTTTTTGTTTAATTAAAAATA
Found at i:248669 original size:27 final size:27
Alignment explanation
Indices: 248611--248669 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
248601 AATTTTTTAT
248611 TTTAATTTTTTTTGGTTTAATTAAAATA
1 TTTAATTTTTTTT-GTTTAATTAAAATA
248639 -TTAATTTTTTATT-TTT-ATTAAAAATA
1 TTTAATTTTTT-TTGTTTAATT-AAAATA
248665 TTTAA
1 TTTAA
248670 ATATAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
25 3 0.11
26 9 0.32
27 14 0.50
28 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (27 bp):
TTTAATTTTTTTTGTTTAATTAAAATA
Found at i:248835 original size:20 final size:20
Alignment explanation
Indices: 248810--248850 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
248800 TGTTGCTACA
248810 CCACCATGCTGCTGTCCCTT
1 CCACCATGCTGCTGTCCCTT
*
248830 CCACCATGCTGTTGTCCCTT
1 CCACCATGCTGCTGTCCCTT
248850 C
1 C
248851 AATGGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.44, G:0.15, T:0.32
Consensus pattern (20 bp):
CCACCATGCTGCTGTCCCTT
Found at i:250325 original size:50 final size:49
Alignment explanation
Indices: 250208--250455 Score: 196
Period size: 50 Copynumber: 4.9 Consensus size: 49
250198 GAATATAACA
* * * * * * *
250208 TGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT-TCTCATAT-CGG
* *
250257 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TTCTCATATCGG
* * ** * *
250307 TGCCCATGCCATGTCCCAGACATGGTCTGACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TTCTCATATCGG
* * * *
250357 TGCCAACGCTATGTCCCAAACATGGTCTTACATGGGATCTCTCATAGTCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT-TCTCATA---TC---GG
*
250413 TGCCAATGCCATGTCCCAGACATGATCTTACATGGGA-TCTCAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATTCTCAT
250456 CACCCAAATG
Statistics
Matches: 157, Mismatches: 32, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
48 1 0.01
49 36 0.23
50 78 0.50
53 2 0.01
54 6 0.04
56 34 0.22
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATTCTCATATCGG
Found at i:251757 original size:14 final size:13
Alignment explanation
Indices: 251703--251765 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
251693 GTATCCACTG
251703 GAAGAGAGAAAGAA
1 GAAGA-AGAAAGAA
*
251717 -AAGAGAGAAAAAA
1 GAAGA-AGAAAGAA
* *
251730 GAATAA-AAAAAA
1 GAAGAAGAAAGAA
251742 GAAG-AG-AAGAA
1 GAAGAAGAAAGAA
251753 GAAGAAGAAAGAA
1 GAAGAAGAAAGAA
251766 AGAAAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.22
12 11 0.27
13 18 0.44
14 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (13 bp):
GAAGAAGAAAGAA
Found at i:252000 original size:60 final size:60
Alignment explanation
Indices: 251934--252052 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
251924 TTGCTTTTTA
* ** * *
251934 TAATTATTTTAAAATTAATTTGTTAGTAATTTGGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGTTATAAATTGTTGTGTTTG
251994 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGTTATAAATTGTTGTGTTT
252053 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTAAGTTATAAATTGTTGTGTTTG
Found at i:257880 original size:13 final size:14
Alignment explanation
Indices: 257852--257885 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
257842 AAATACCTTA
257852 TTCTTCTTCTTGTT
1 TTCTTCTTCTTGTT
*
257866 TTCTT-TTCTTTTT
1 TTCTTCTTCTTGTT
257879 TTCTTCT
1 TTCTTCT
257886 CCCTATCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
TTCTTCTTCTTGTT
Found at i:258045 original size:27 final size:27
Alignment explanation
Indices: 258015--258101 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
258005 CCACTATTCA
* *
258015 CGCCTCTGAGTTAGGCACAACTAGTCG
1 CGCCTCTGAGATAGGCTCAACTAGTCG
* * *
258042 CGCCTGTCAGATAGGCTTAACTAGTCG
1 CGCCTCTGAGATAGGCTCAACTAGTCG
*
258069 CGCCTTTGAGATAGGCTCAACTAGTCG
1 CGCCTCTGAGATAGGCTCAACTAGTCG
*
258096 TGCCTC
1 CGCCTC
258102 GTATCTATAC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (27 bp):
CGCCTCTGAGATAGGCTCAACTAGTCG
Found at i:258564 original size:21 final size:21
Alignment explanation
Indices: 258538--258593 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
258528 AATAGCGGTG
*
258538 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
258559 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
258580 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
258594 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:258799 original size:30 final size:29
Alignment explanation
Indices: 258762--258887 Score: 180
Period size: 30 Copynumber: 4.2 Consensus size: 29
258752 ATTCATTTAA
258762 TAAAATACACTACATATATTTTTTTATTT
1 TAAAATACACTACATATATTTTTTTATTT
*
258791 CTAGAATACACTACATATATTTTTTTATTT
1 -TAAAATACACTACATATATTTTTTTATTT
*
258821 TGAAAATACACTACATGTATTTTTTTATTTT
1 T-AAAATACACTACATATATTTTTTTA-TTT
* *
258852 TAAAATCCATTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTA-TTT
258882 TAAAAT
1 TAAAAT
258888 TTTAAATACA
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
29 1 0.01
30 83 0.94
31 4 0.05
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (29 bp):
TAAAATACACTACATATATTTTTTTATTT
Found at i:258995 original size:58 final size:59
Alignment explanation
Indices: 258911--259069 Score: 166
Period size: 58 Copynumber: 2.7 Consensus size: 59
258901 AAATCCCATC
* * *
258911 TCCCCTCTTCCACCGTATCCTTCTCCCATTTCCCATTCCCATGCAATACCC-ATTCC-C-AT
1 TCCCCTATTCCACCGTACCCTCCTCCCATTTCCCATTCCCAT-C--TACCCTATTCCACGAT
* * * *
258970 TTCCC-ATTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATCTCCCCTCTTCCATCGAT
1 TCCCCTATTCCACCGTACCCTCCTCCCATTTCCCATTCCCATCTACCCTATTCCA-CGAT
* *
259029 TCCCCTCTTCCACCGTTCCCTCCTCCCA-TTCCCATTCCCAT
1 TCCCCTATTCCACCGTACCCTCCTCCCATTTCCCATTCCCAT
259070 TCCCATTATC
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
55 4 0.05
56 4 0.05
57 1 0.01
58 33 0.39
59 23 0.27
60 20 0.24
ACGTcount: A:0.13, C:0.51, G:0.04, T:0.32
Consensus pattern (59 bp):
TCCCCTATTCCACCGTACCCTCCTCCCATTTCCCATTCCCATCTACCCTATTCCACGAT
Found at i:259004 original size:28 final size:28
Alignment explanation
Indices: 258964--259066 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 28
258954 CAATACCCAT
*
258964 TCCCATTTCCCATTCCACCGTGCCCTCC
1 TCCCATTTCCCATTCCACCGTCCCCTCC
* *
258992 TCCCATTTCCCATTCCCATC-TCCCCTCT
1 TCCCATTTCCCATT-CCACCGTCCCCTCC
* * *
259020 TCCATCGATTCCCCTCTTCCACCGTTCCCTCC
1 TCC--C-ATTTCCC-ATTCCACCGTCCCCTCC
259052 TCCCA-TTCCCATTCC
1 TCCCATTTCCCATTCC
259067 CATTCCCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.07
28 27 0.46
29 5 0.08
30 2 0.03
31 10 0.17
32 11 0.19
ACGTcount: A:0.11, C:0.53, G:0.04, T:0.32
Consensus pattern (28 bp):
TCCCATTTCCCATTCCACCGTCCCCTCC
Found at i:259060 original size:21 final size:21
Alignment explanation
Indices: 258971--259060 Score: 50
Period size: 21 Copynumber: 4.4 Consensus size: 21
258961 CATTCCCATT
*
258971 TCCCATTCCACCGTGCCCTCC
1 TCCCATTCCACCGTTCCCTCC
* *
258992 TCCCATTTC-CCATTCCCAT-C
1 TCCCATTCCACCGTTCCC-TCC
* *
259012 TCCCCTCTTCCATCGATT-CC-CC
1 T-CCC-ATTCCACCG-TTCCCTCC
259034 T--C-TTCCACCGTTCCCTCC
1 TCCCATTCCACCGTTCCCTCC
259052 TCCCATTCC
1 TCCCATTCC
259061 CATTCCCATT
Statistics
Matches: 50, Mismatches: 8, Indels: 22
0.62 0.10 0.28
Matches are distributed among these distances:
16 2 0.04
17 9 0.18
18 3 0.06
19 1 0.02
20 9 0.18
21 16 0.32
22 5 0.10
23 3 0.06
24 2 0.04
ACGTcount: A:0.10, C:0.54, G:0.04, T:0.31
Consensus pattern (21 bp):
TCCCATTCCACCGTTCCCTCC
Found at i:259063 original size:6 final size:6
Alignment explanation
Indices: 259052--259076 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
259042 CGTTCCCTCC
259052 TCCCAT TCCCAT TCCCAT TCCCAT T
1 TCCCAT TCCCAT TCCCAT TCCCAT T
259077 ATCAACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.48, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCCAT
Found at i:268155 original size:17 final size:17
Alignment explanation
Indices: 268130--268172 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
268120 GTCAAGCATT
*
268130 AGCGGCGCATTCTGTTA
1 AGCGACGCATTCTGTTA
268147 AGCGACGCATTCTGTTA
1 AGCGACGCATTCTGTTA
*
268164 AGCGCCGCA
1 AGCGACGCA
268173 AAAAGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (17 bp):
AGCGACGCATTCTGTTA
Found at i:268410 original size:25 final size:25
Alignment explanation
Indices: 268382--268442 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
268372 CGGTTTAAGG
* *
268382 TTTATAGTTTATATATGTTTTATGA
1 TTTAGAGTTTATATATGTTCTATGA
*
268407 TTTAGGGTTTATATATGTTCTATGA
1 TTTAGAGTTTATATATGTTCTATGA
* *
268432 TTCAGGGTTTA
1 TTTAGAGTTTA
268443 AGGAATATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (25 bp):
TTTAGAGTTTATATATGTTCTATGA
Found at i:268538 original size:21 final size:21
Alignment explanation
Indices: 268494--268539 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
268484 TAGTTGGGGT
* * *
268494 TTAAGGTTTAAGTGTTTAGGG
1 TTAAGGGTTAAGGGTTTAGAG
*
268515 TTAAGGGTTAAGGGTTTATAG
1 TTAAGGGTTAAGGGTTTAGAG
268536 TTAA
1 TTAA
268540 TGTTTTATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.41
Consensus pattern (21 bp):
TTAAGGGTTAAGGGTTTAGAG
Done.