Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold982
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: 106087
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:2301 original size:26 final size:25
Alignment explanation
Indices: 2247--2326 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
2237 TTGAATTAAA
* *
2247 TAAATTTTATTAATTATTAATATAT
1 TAAATTTTATTAAATATAAATATAT
*
2272 TAAATTTTATATAAATATAAATATTT
1 TAAATTTTAT-TAAATATAAATATAT
*
2298 TAAA-TATATTATAATATAAA-ATAT
1 TAAATTTTATTA-AATATAAATATAT
*
2322 AAAAT
1 TAAAT
2327 AAGATAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
24 8 0.17
25 22 0.48
26 16 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAATTTTATTAAATATAAATATAT
Found at i:3419 original size:14 final size:14
Alignment explanation
Indices: 3400--3426 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3390 ATGGTTGATA
3400 TTTAAAGTTTAGGG
1 TTTAAAGTTTAGGG
3414 TTTAAAGTTTAGG
1 TTTAAAGTTTAGG
3427 AATCTTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
TTTAAAGTTTAGGG
Found at i:3751 original size:17 final size:17
Alignment explanation
Indices: 3738--3780 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3728 GATTTGACCT
*
3738 TTGACTTTGGTTGATAG
1 TTGACTTTGGTTGACAG
*
3755 TTGACTTTGGTTGATAG
1 TTGACTTTGGTTGACAG
*
3772 TTGATTTTG
1 TTGACTTTG
3781 ATTGTTGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.16, C:0.05, G:0.28, T:0.51
Consensus pattern (17 bp):
TTGACTTTGGTTGACAG
Found at i:8828 original size:24 final size:25
Alignment explanation
Indices: 8795--8858 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
8785 CTAATTCTCC
*
8795 TTATATATATTTTTTTATTTTTT-A
1 TTATAGATATTTTTTTATTTTTTGA
8819 TTATAGATATAATTTTTTATTTTTTGA
1 TTATAGATAT--TTTTTTATTTTTTGA
8846 TTAT-G-TATTTTTT
1 TTATAGATATTTTTT
8859 GGATTTTCAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 5 0.14
24 9 0.25
25 3 0.08
26 14 0.39
27 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (25 bp):
TTATAGATATTTTTTTATTTTTTGA
Found at i:8835 original size:26 final size:27
Alignment explanation
Indices: 8799--8849 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
8789 TTCTCCTTAT
*
8799 ATATATTTTTTTATTTTTT-ATTATAG
1 ATATAATTTTTTATTTTTTGATTATAG
8825 ATATAATTTTTTATTTTTTGATTAT
1 ATATAATTTTTTATTTTTTGATTAT
8850 GTATTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (27 bp):
ATATAATTTTTTATTTTTTGATTATAG
Found at i:9581 original size:15 final size:15
Alignment explanation
Indices: 9558--9603 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9548 TCTCTTTTTT
*
9558 ATTTATTATTATTTA
1 ATTTTTTATTATTTA
9573 ATTTTTTATT-TTTAA
1 ATTTTTTATTATTT-A
*
9588 AATTTTTA-TATTTA
1 ATTTTTTATTATTTA
9602 AT
1 AT
9604 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTTATTATTTA
Found at i:12994 original size:21 final size:19
Alignment explanation
Indices: 12970--13021 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
12960 TAATTGTGTT
12970 TTAAATTTTAAATTTTTATGA
1 TTAAATTTTAAATTTTTA--A
*
12991 TTAAAATTT-AATTTTTAA
1 TTAAATTTTAAATTTTTAA
13009 -T-AATTTTAAATTT
1 TTAAATTTTAAATTT
13022 AAAAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 5 0.18
17 6 0.21
18 1 0.04
20 8 0.29
21 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTAAATTTTAAATTTTTAA
Found at i:13019 original size:22 final size:21
Alignment explanation
Indices: 12968--13023 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
12958 ATTAATTGTG
*
12968 TTTTAAATTTTAAATTTTTATGA
1 TTTTAAA-TTT-AATTTTTATAA
*
12991 -TTAAAATTTAATTTTTAATAA
1 TTTTAAATTTAATTTTT-ATAA
13012 TTTTAAATTTAA
1 TTTTAAATTTAA
13024 AAAAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.25
21 6 0.21
22 15 0.54
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTAAATTTAATTTTTATAA
Found at i:18990 original size:16 final size:16
Alignment explanation
Indices: 18969--19014 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
18959 GTTTTTCTAA
18969 AAAATATATTATTTTT
1 AAAATATATTATTTTT
* *
18985 AAAATATAATTACTTAT
1 AAAATAT-ATTATTTTT
19002 -AAATAT-TTATTTT
1 AAAATATATTATTTT
19015 CATTAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 5 0.20
16 13 0.52
17 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAATATATTATTTTT
Found at i:20463 original size:18 final size:19
Alignment explanation
Indices: 20440--20486 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
20430 TTAAAAAAAG
20440 AATAAAAATAAATA-ATAA
1 AATAAAAATAAATACATAA
*
20458 AATAAAAA-ATATACATAA
1 AATAAAAATAAATACATAA
*
20476 AATAATAATAA
1 AATAAAAATAA
20487 TAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 19 0.79
19 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAAAAATAAATACATAA
Found at i:20489 original size:14 final size:14
Alignment explanation
Indices: 20435--20495 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 14
20425 TTTTTTTAAA
* *
20435 AAAAGAATAAAAAT
1 AAAATAATAATAAT
20449 -AAATAATAA-AAT
1 AAAATAATAATAAT
20461 AAAA-AAT-ATACAT
1 AAAATAATAATA-AT
20474 AAAATAATAATAAT
1 AAAATAATAATAAT
*
20488 AAATTAAT
1 AAAATAAT
20496 TAAAAGGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 1 0.03
12 7 0.17
13 17 0.43
14 12 0.30
15 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:20718 original size:19 final size:20
Alignment explanation
Indices: 20681--20722 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
20671 AAGAAGAGAG
20681 GAATCGAAACAAGAAAAAAA
1 GAATCGAAACAAGAAAAAAA
*
20701 GAATTGAAACAA-AAAAAAA
1 GAATCGAAACAAGAAAAAAA
20720 GAA
1 GAA
20723 AACAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.71, C:0.07, G:0.14, T:0.07
Consensus pattern (20 bp):
GAATCGAAACAAGAAAAAAA
Found at i:22000 original size:22 final size:21
Alignment explanation
Indices: 21970--22016 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
21960 CATCGGGTAC
*
21970 AAAATGAAATTTTCAAAATTTA-
1 AAAACGAAA-TTT-AAAATTTAG
21992 AAAACGAAATTTAAAATTTAG
1 AAAACGAAATTTAAAATTTAG
22013 AAAA
1 AAAA
22017 GTTTAGTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 7 0.30
22 8 0.35
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (21 bp):
AAAACGAAATTTAAAATTTAG
Found at i:26223 original size:15 final size:16
Alignment explanation
Indices: 26203--26232 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26193 AGCATGATAA
26203 AAAAAG-AAAAAAAAG
1 AAAAAGCAAAAAAAAG
26218 AAAAAGCAAAAAAAA
1 AAAAAGCAAAAAAAA
26233 ATAGAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAGCAAAAAAAAG
Found at i:27633 original size:89 final size:87
Alignment explanation
Indices: 27462--27770 Score: 323
Period size: 89 Copynumber: 3.5 Consensus size: 87
27452 TTCAAGGAAA
* ** * *
27462 ACACAGTTCTTAATCATATCCCCTTCAATCAGCC-CTTAGATGGTATTGATGCATCATAAAGCTT
1 ACACA-TTCTTAATCATATCCCCTTTACCCAACCAC-TAGATGGTATTGATGCATCACAAAGCTT
*
27526 GGTTTCTTGGGGGTAAGGTGCAACCC
64 GATTTCTT--GGGTAAGGTGCAACCC
** ** * *
27552 ACGTATTCCCAATCATATTCCCTTCACCCAACCACTAGATGGTATTGATGCATCACAAAGCTTGA
1 ACACATTCTTAATCATATCCCCTTTACCCAACCACTAGATGGTATTGATGCATCACAAAGCTTGA
* ** *
27617 TCTCATTGAATAAAGGTGCAGCCC
66 TTTC-TTGGGT-AAGGTGCAACCC
* * * *
27641 ATACATTCTTAATCATATCCCCTTTTACCCGACCACTAGATGGTATTGGTGCATCACAAAGTTTG
1 ACACATTCTTAATCATATCCCC-TTTACCCAACCACTAGATGGTATTGATGCATCACAAAGCTTG
* *
27706 TTTTCCTTGGGGCAAGGTGCAACCC
65 ATTT-CTT-GGGTAAGGTGCAACCC
*
27731 ACACATTCTTAATCATATCCCCTTTATCCAACCACTAGAT
1 ACACATTCTTAATCATATCCCCTTTACCCAACCACTAGAT
27771 AATACTAATG
Statistics
Matches: 180, Mismatches: 33, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
88 2 0.01
89 96 0.53
90 80 0.44
91 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (87 bp):
ACACATTCTTAATCATATCCCCTTTACCCAACCACTAGATGGTATTGATGCATCACAAAGCTTGA
TTTCTTGGGTAAGGTGCAACCC
Found at i:28000 original size:47 final size:47
Alignment explanation
Indices: 27930--28478 Score: 513
Period size: 47 Copynumber: 11.8 Consensus size: 47
27920 AATTCCACCT
* * * * *
27930 TCGTTGGACTATATTGGCATTAGGACCTAGCCAAACTCTTCTTATGC
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCC
* * * * * *
27977 TCGTTTGATTGTATTGGTGTTAGGAGCTGGTTAAA-TACTTCTCA-CC
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACT-CTTCTTATCC
* * * * *
28023 TCATTTGACTCTTTTAGCATTAGGACCTGGTCAAACTCTT-TTCA-CC
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTT-ATCC
* * * * **
28069 TTCGTTTGACTGTATTAGCATTAGGACCTGGTCAAACTCTTCTCATAA
1 -TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCC
* * ** * *
28117 TCGTTCGACTGTATTGGCG-TAAAACCTGGTCAAACTCTTCTCA-CAT
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATC-C
** *
28163 TCGTTTGAC-ATATTGATGTTAGGGCCTGGTCAAACTCTTCTTATCC
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCC
* * * * * *
28209 TTGTTTGACTGTATTGGCATTAAGACTTGGTCAAACTCTTCTTATTC
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCC
* * *
28256 TCGTTTGACTATATTGGCGTTAGGACCTAGTCAAACTCTTCTCA-CAT
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATC-C
* * * *
28303 TCGTTTGACTATATTGGCATTAAGACCTGATCAAATTCTTCTTATCC
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCC
* *
28350 TCGTTTGACTATATTAGCGTTAGGACATGGTCAAACTCTTCTTATCC
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCC
** * *
28397 TCGTTTGACTATATTGGTATTAGGACCTGGTCAAACTCTTCTCA-CT
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCC
* * *
28443 TCATTTGACTGTATTGGCGTTAGGACCTAGTCAAAC
1 TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAAC
28479 ATTACTCATT
Statistics
Matches: 405, Mismatches: 85, Indels: 25
0.79 0.17 0.05
Matches are distributed among these distances:
45 7 0.02
46 124 0.31
47 272 0.67
48 2 0.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (47 bp):
TCGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCC
Found at i:28552 original size:42 final size:42
Alignment explanation
Indices: 28506--30159 Score: 643
Period size: 42 Copynumber: 39.4 Consensus size: 42
28496 GTCTGTCGGT
** **
28506 TTTGACCCTAAAGACTTTCTTACCCTCAGTCTGTTTGTCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
** * * *
28548 TTTGA-CCTCGGAGACTACCTCA-TCTCAAGTCTACCTGTCGAC
1 TTTGACCCT-GGAGACTTTCTTACCCTC-AGTCTGCCTGTCGAC
* * * *
28590 TTTGACCTTGGAGACATTCTTACCTTCAGTCTGCCTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * ** * * * * *
28632 TTTGACTCTAGAGACTGCCTCA-TCTCAAGTTTACTTGTCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGAC
* * * * *
28674 TTTGACCCTAGAGACTTTATTACCTTCAGTCTGTCTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* ** * * * * * *
28716 TTTGACCTTGGAGACTACCTCA-TCTCAAGTCTGTCTATTGGC
1 TTTGACCCTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGAC
* * * *
28758 TTTGACCTTGGAGACTTTCTTACCCTTAAGTTTGCCTATCGAC
1 TTTGACCCTGGAGACTTTCTTACCC-TCAGTCTGCCTGTCGAC
* * * * *
28801 TTTGACCCTTGAGACTTTCTTACCTTTAATCTGCCTATCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
28843 TTTGACCCTGGAGAC-TTCTTTACCCTCAAGTCTGCCTGTCGAC
1 TTTGACCCTGGAGACTTTC-TTACCCTC-AGTCTGCCTGTCGAC
* ** * * * *
28886 TTTGACCTTACAGACTTTCTTACCTTCAATCTGCCTGTTGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* ** * * * * * * *
28928 TTTAACTTTGGAGA-TTGCCT-CATCTCAAGTGTGTCTATCGGC
1 TTTGACCCTGGAGACTTTCTTAC-CCTC-AGTCTGCCTGTCGAC
* * * * * *
28970 TTTGACCTTGGAGACTTTCTTACCTTCTGTATGCCTATCAAC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * *
29012 TTTGATCTTGGAGACTTTCTTACCCTCAACTTTGCCTGTCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGAC
* * * * *
29055 TTTGA-CCTAGAGACTTTTTTAACTTCAATCTGCCTGTC-AGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGA-C
* ** * * * * *
29096 TTTGACCTTAAAGAC-TGCTT-CATCTCAGGTCTGCATGTTGGC
1 TTTGACCCTGGAGACTTTCTTAC-CCTCA-GTCTGCCTGTCGAC
* * * * * *
29138 TTTAACCCTCGAGACTTTTTTACCTTTAGTTTGCCTGTCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * * * *
29180 TTTGATCCTAGAGA-TTGCCT-CATCTCAAGTCTGCCTGTCGGC
1 TTTGACCCTGGAGACTTTCTTAC-CCTC-AGTCTGCCTGTCGAC
* * * * **
29222 TTTGAACCTGGAGACTTTCTTACCTTTAATCTGCCTGTCGGT
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * ** * * * *
29264 TTTAACCCTAGAGACTGCCTCA-TCTCAAGTCTGCCTATCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGAC
* * * * *
29306 TTTGACCTTAGAGACTTCCTTACCCTCAAGTCTGTCTGTTGAC
1 TTTGACCCTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGAC
* * * * * *
29349 TTTGATCTTGGAAACTTTCTTAACTTCAGTCTGCCTATCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * * *
29391 TTTGACCTTGGAG-C---CTCA-TCTCAAGTCTGCTTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGAC
* * * * * *
29429 TTTGACCTTAGAGA-TTTTTCTACCTTTAGTCTACCTGTC-AGC
1 TTTGACCCTGGAGACTTTCT-TACCCTCAGTCTGCCTGTCGA-C
* * * * * * * *
29471 TTTGACCTTAGAGA-TTGCCT-CATCTCAAGTATGCTTGTCGGC
1 TTTGACCCTGGAGACTTTCTTAC-CCTC-AGTCTGCCTGTCGAC
* * * *** * * *
29513 TTTAACCCTAGAGACTTTTTTATTTTAAGTTTGCCTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * ** *
29555 TTTGACTCTGGGGACTTTCCTA-CCTCAAGTCTGTTTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGAC
* * * * * * *
29597 TTTGACCTTGAAGACTTTTTTACCTTAAGTCTGCTTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * *
29639 TTTGACCTTGGAGA-TTGCCT-CATCTCAAGTCTGCCTGTCGAC
1 TTTGACCCTGGAGACTTTCTTAC-CCTC-AGTCTGCCTGTCGAC
* * * * * * *
29681 TTTGACCTTGAAAATTTTCTTACCTTCAATCTACCTGTCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * * * * *
29723 TTTGACCTTGGAGACTGTCTTATCTTAAGTCTGTCTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * ** *
29765 TATGACCTTGGAGACTTTCTTGCTTTCAGTCTGCCTATCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * * *
29807 TTTGACCTTGGAGATTTTCTTACCTTTAGTCTGCCTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * * * *
29849 TTTGACCTTGGAGACTGTC-T-CGTCTCAAGTCTGCTTATCGGC
1 TTTGACCCTGGAGACTTTCTTAC-CCTC-AGTCTGCCTGTCGAC
* * * * *
29891 TTTGACCTTCGAGACTTTCTTACCTTCAGTCTGTCTGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * * *
29933 TTTGACCCTAGAGACTGTCTTATCAC-AAGTCTGCCTATC-AGC
1 TTTGACCCTGGAGACTTTCTTA-CCCTCAGTCTGCCTGTCGA-C
* * * * * *
29975 TTTAACCTTGGAGAC-TTCTTTACCCTTAAATCTGTCTGTCGGC
1 TTTGACCCTGGAGACTTTC-TTACCC-TCAGTCTGCCTGTCGAC
* * * * * * * * *
30018 TTTGACCTTAGAAACTTTCTTACCTTTAGTTTGCTTGTTGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * * * * * * *
30060 TTTTACCTTGGAGACTTCCTCATCTTAAGTTTGTCTGTCGAC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* * * * * * *
30102 TTTGACCTTGAAGACATTCTTATCTTCAGTCTGCCAGTCGGC
1 TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
* *
30144 TTTGTCCCTAGAGACT
1 TTTGACCCTGGAGACT
30160 GCCTTATCTC
Statistics
Matches: 1191, Mismatches: 361, Indels: 120
0.71 0.22 0.07
Matches are distributed among these distances:
37 2 0.00
38 27 0.02
40 6 0.01
41 61 0.05
42 898 0.75
43 185 0.16
44 12 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (42 bp):
TTTGACCCTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGAC
Found at i:28646 original size:84 final size:84
Alignment explanation
Indices: 28498--30252 Score: 1067
Period size: 84 Copynumber: 20.9 Consensus size: 84
28488 TTTAGTTTGT
* * ** * ** * *
28498 CTGTCGGTTTTGACCCTAAAGACTTTCTTACCCTCAGTCTGTTTGTCGACTTTGACCTCGGAGAC
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * * *
28563 TACCTCATCTCAAGTCTAC
66 TTCCTTACCTCAAGTCTGC
* * *
28582 CTGTCGACTTTGACCTTGGAGACATTCTTACCTTCAGTCTGCCTGTCGGCTTTGA-CTCTAGAGA
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCT-TGGAGA
* * * * *
28646 CTGCCTCATCTCAAGTTTAC
65 CTTCCTTACCTCAAGTCTGC
* * * * * *
28666 TTGTCGACTTTGACCCTAGAGACTTTATTACCTTCAGTCTGTCTGTCGGCTTTGACCTTGGAGAC
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * * *
28731 TACCTCATCTCAAGTCTGT
66 TTCCTTACCTCAAGTCTGC
* * * * * *
28750 CTATTGGCTTTGACCTTGGAGACTTTCTTACCCTTAAGTTTGCCTATCGACTTTGACCCTT-GAG
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTA-CCTTCAGTCTGCCTGTCGGCTTTGA-CCTTGGAG
* *
28814 ACTTTCTTACCTTTAA-TCTGC
64 ACTTCCTTACC-TCAAGTCTGC
* * * * * **
28835 CTATCGACTTTGACCCTGGAGAC-TTCTTTACCCTCAAGTCTGCCTGTCGACTTTGACCTTACAG
1 CTGTCGGCTTTGACCTTGGAGACTTTC-TTACCTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAG
*
28899 ACTTTCTTACCTTCAA-TCTGC
64 ACTTCCTTACC-TCAAGTCTGC
* * * * * * * * *
28920 CTGTTGGCTTTAACTTTGGAGA-TTGCCT-CATCTCAAGTGTGTCTATCGGCTTTGACCTTGGAG
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCT-TC-AGTCTGCCTGTCGGCTTTGACCTTGGAG
* * *
28983 ACTTTCTTACCTTC-TGTATGC
64 ACTTCCTTACC-TCAAGTCTGC
* ** * * * * * *
29004 CTATCAACTTTGATCTTGGAGACTTTCTTACCCTCAACTTTGCCTGTCGACTTTGACC-TAGAGA
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGA
** *
29068 CTTTTTTAACTTCAA-TCTGC
65 CTTCCTT-ACCTCAAGTCTGC
* ** * * * * * * *
29088 CTGTCAGCTTTGACCTTAAAGAC-TGCTT-CATCTCAGGTCTGCATGTTGGCTTTAACCCTCGAG
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCT-TCA-GTCTGCCTGTCGGCTTTGACCTTGGAG
** ** *
29151 ACTTTTTTACCTTTAGTTTGC
64 ACTTCCTTACCTCAAGTCTGC
* * * * *
29172 CTGTCGACTTTGATCC-TAGAGA-TTGCCT-CATCTCAAGTCTGCCTGTCGGCTTTGAACC-TGG
1 CTGTCGGCTTTGA-CCTTGGAGACTTTCTTACCT-TC-AGTCTGCCTGTCGGCTTTG-ACCTTGG
* *
29233 AGACTTTCTTACCTTTAA-TCTGC
62 AGACTTCCTTACC-TCAAGTCTGC
* * * * ** * * * *
29256 CTGTCGGTTTTAACCCTAGAGACTGCCTCATC-TCAAGTCTGCCTATCGGCTTTGACCTTAGAGA
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGA
*
29320 CTTCCTTACCCTCAAGTCTGT
65 CTTCCTTA-CCTCAAGTCTGC
* * * * * * *
29341 CTGTTGACTTTGATCTTGGAAACTTTCTTAACTTCAGTCTGCCTATCGACTTTGACCTTGGAG--
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* *
29404 --CCTCATCTCAAGTCTGC
66 TTCCTTACCTCAAGTCTGC
* * * * * * *
29421 TTGTCGGCTTTGACCTTAGAGA-TTTTTCTACCTTTAGTCTACCTGTCAGCTTTGACCTTAGAGA
1 CTGTCGGCTTTGACCTTGGAGACTTTCT-TACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * *
29485 -TTGCCTCATCTCAAGTATGC
65 CTT-CCTTACCTCAAGTCTGC
* * * * * ** * * *
29505 TTGTCGGCTTTAACCCTAGAGACTTTTTTATTTTAAGTTTGCCTGTCGGCTTTGA-CTCTGGGGA
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCT-TGGAGA
*
29569 CTTTCC-TACCTCAAGTCTGT
65 C-TTCCTTACCTCAAGTCTGC
* * * * *
29589 TTGTCGGCTTTGACCTTGAAGACTTTTTTACCTTAAGTCTGCTTGTCGGCTTTGACCTTGGAGA-
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* *
29653 TTGCCTCATCTCAAGTCTGC
66 TT-CCTTACCTCAAGTCTGC
* * * * * * *
29673 CTGTCGACTTTGACCTTGAAAATTTTCTTACCTTCAATCTACCTGTCGACTTTGACCTTGGAGAC
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * *
29738 TGT-CTTATCTTAAGTCTGT
66 T-TCCTTACCTCAAGTCTGC
* * * * * *
29757 CTGTCGGCTATGACCTTGGAGACTTTCTTGCTTTCAGTCTGCCTATCGACTTTGACCTTGGAGAT
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* **
29822 TTTCTTACCTTTAGTCTGC
66 TTCCTTACCTCAAGTCTGC
* * * * *
29841 CTGTCGGCTTTGACCTTGGAGACTGTC-T-CGTCTCAAGTCTGCTTATCGGCTTTGACCTTCGAG
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCT-TC-AGTCTGCCTGTCGGCTTTGACCTTGGAG
* *
29904 ACTTTCTTACCTTC-AGTCTGT
64 ACTTCCTTACC-TCAAGTCTGC
* * * * * * * *
29925 CTGTCGGCTTTGACCCTAGAGACTGTCTTATC-ACAAGTCTGCCTATCAGCTTTAACCTTGGAGA
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * * *
29989 CTTCTTTACCCTTAAATCTGT
65 CTTCCTTA-CCTCAAGTCTGC
* * * * * * *
30010 CTGTCGGCTTTGACCTTAGAAACTTTCTTACCTTTAGTTTGCTTGTTGGCTTTTACCTTGGAGAC
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * * * *
30075 TTCCTCATCTTAAGTTTGT
66 TTCCTTACCTCAAGTCTGC
* * * * * * * *
30094 CTGTCGACTTTGACCTTGAAGACATTCTTATCTTCAGTCTGCCAGTCGGCTTTGTCCCTAGAGAC
1 CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * *
30159 TGCCTTATCTCAATTCTGC
66 TTCCTTACCTCAAGTCTGC
* * * * * * * * *
30178 TTGTCGGTTTTGACCCTAGAGAC-TTCATTACCTTTAAGTCTGCTTATTGGCTTT-AACTTGGAG
1 CTGTCGGCTTTGACCTTGGAGACTTTC-TTACC-TTCAGTCTGCCTGTCGGCTTTGACCTTGGAG
30241 ACTTCCTTACCT
64 ACTTCCTTACCT
30253 TTAGTTTTCC
Statistics
Matches: 1317, Mismatches: 298, Indels: 112
0.76 0.17 0.06
Matches are distributed among these distances:
79 4 0.00
80 54 0.04
81 4 0.00
82 6 0.00
83 44 0.03
84 893 0.68
85 299 0.23
86 13 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (84 bp):
CTGTCGGCTTTGACCTTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
TTCCTTACCTCAAGTCTGC
Found at i:28705 original size:126 final size:125
Alignment explanation
Indices: 28575--30253 Score: 990
Period size: 126 Copynumber: 13.3 Consensus size: 125
28565 CCTCATCTCA
*
28575 AGTCTACCTGTCGACTTTGACCTTGGAGACATTCTTACCTTCAGTCTGCCTGTCGGCTTTGA-CT
1 AGTCTGCCTGTCGACTTTGACCTTGGAGAC-TTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCT
** * * * * *
28639 CTAGAGACTGCCTCATCTCAAGTTTACTTGTCGACTTTGACCCTAGAGACTTTATTACCTTC
65 -TAGAGACTTTCTTATCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
* * * * * * * *
28701 AGTCTGTCTGTCGGCTTTGACCTTGGAGACTACCT-CATCTCAAGTCTGTCTATTGGCTTTGACC
1 AGTCTGCCTGTCGACTTTGACCTTGGAGACTTCTTACCT-TC-AGTCTGCCTGTCGGCTTTGACC
* * * * * * *
28765 TTGGAGACTTTCTTACCCTTAAGTTTGCCTATCGACTTTGACCCTTGAGACTTTCTTACCTTT
64 TTAGAGACTTTCTTA-TCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
* * * * *
28828 AATCTGCCTATCGACTTTGACCCTGGAGACTTCTTTACCCTCAAGTCTGCCTGTCGACTTTGACC
1 AGTCTGCCTGTCGACTTTGACCTTGGAGACTTC-TTACCTTC-AGTCTGCCTGTCGGCTTTGACC
* * * * * ** * * * *
28893 TTACAGACTTTCTTACCTTCAA-TCTGCCTGTTGGCTTTAACTTTGGAGA-TTGCCT-CATCTC
64 TTAGAGACTTTCTTATC-TCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCT-TC
* * * * * * * ** *
28954 AAGTGTGTCTATCGGCTTTGACCTTGGAGACTTTCTTACCTTCTGTATGCCTATCAACTTTGATC
1 -AGTCTGCCTGTCGACTTTGACCTTGGAGAC-TTCTTACCTTCAGTCTGCCTGTCGGCTTTGACC
* * * * * *
29019 TTGGAGACTTTCTTACCCTCAACTTTGCCTGTCGACTTTGA-CCTAGAGACTTTTTTAACTTC
64 TTAGAGACTTTCTTA-TCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
* ** * * * * *
29081 AATCTGCCTGTC-AGCTTTGACCTTAAAGACTGCTT-CATCTCAGGTCTGCATGTTGGCTTTAAC
1 AGTCTGCCTGTCGA-CTTTGACCTTGGAGACTTCTTACCT-TCA-GTCTGCCTGTCGGCTTTGAC
* * * * ** * * * * *
29144 CCTCGAGACTTTTTTACCTTTAGTTTGCCTGTCGACTTTGATCCTAGAGA-TTGCCT-CATCTC
63 CTTAGAGACTTTCTTATCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCT-TC
* * * * *
29206 AAGTCTGCCTGTCGGCTTTGAACC-TGGAGACTTTCTTACCTTTAATCTGCCTGTCGGTTTTAAC
1 -AGTCTGCCTGTCGACTTTG-ACCTTGGAGAC-TTCTTACCTTCAGTCTGCCTGTCGGCTTTGAC
* ** * * * * * *
29270 CCTAGAGACTGCCTCATCTCAAGTCTGCCTATCGGCTTTGACCTTAGAGACTTCCTTACCCTC
63 CTTAGAGACTTTCTTATCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
* * * * * * *
29333 AAGTCTGTCTGTTGACTTTGATCTTGGAAACTTTCTTAACTTCAGTCTGCCTATCGACTTTGACC
1 -AGTCTGCCTGTCGACTTTGACCTTGGAGAC-TTCTTACCTTCAGTCTGCCTGTCGGCTTTGACC
* * * * * * *
29398 TTGGAG-C---CTCATCTCAAGTCTGCTTGTCGGCTTTGACCTTAGAGA-TTTTTCTACCTTT
64 TTAGAGACTTTCTTATCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCT-TACCTTC
* * * * * * *
29456 AGTCTACCTGTC-AGCTTTGACCTTAGAGA-TTGCCT-CATCTCAAGTATGCTTGTCGGCTTTAA
1 AGTCTGCCTGTCGA-CTTTGACCTTGGAGACTT-CTTACCT-TC-AGTCTGCCTGTCGGCTTTGA
* * * * * * * *
29518 CCCTAGAGACTTTTTTATTTTAAGTTTGCCTGTCGGCTTTGACTCTGGGGACTTTCCTACC-TC
62 CCTTAGAGACTTTCTTATCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
** * * * * *
29581 AAGTCTGTTTGTCGGCTTTGACCTTGAAGACTTTTTTACCTTAAGTCTGCTTGTCGGCTTTGACC
1 -AGTCTGCCTGTCGACTTTGACCTTGGAGAC-TTCTTACCTTCAGTCTGCCTGTCGGCTTTGACC
* * * * * * * *
29646 TTGGAGA-TTGCCTCATCTCAAGTCTGCCTGTCGACTTTGA-CCTTGAAAATTTTCTTACCTTC
64 TTAGAGACTT-TCTTATCTCAAGTTTGCCTGTCGGCTTTGACCCTAG-AGACTTTCTTACCTTC
* * * * * *
29708 AATCTACCTGTCGACTTTGACCTTGGAGACTGTCTTATCTTAAGTCTGTCTGTCGGCTATGACCT
1 AGTCTGCCTGTCGACTTTGACCTTGGAGACT-TCTTACCTTCAGTCTGCCTGTCGGCTTTGACCT
* * * * * * * * * *
29773 TGGAGACTTTCTTGCTTTC-AGTCTGCCTATCGACTTTGACCTTGGAGATTTTCTTACCTTT
65 TAGAGACTTTCTT-ATCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
* * * *
29834 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGTC-T-CGTCTCAAGTCTGCTTATCGGCTTTGAC
1 AGTCTGCCTGTCGACTTTGACCTTGGAGACT-TCTTACCT-TC-AGTCTGCCTGTCGGCTTTGAC
* * * * * * *
29897 CTTCGAGACTTTCTTACCTTC-AGTCTGTCTGTCGGCTTTGACCCTAGAGACTGTCTTATC-AC
63 CTTAGAGACTTTCTTATC-TCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
* * * * *
29959 AAGTCTGCCTATC-AGCTTTAACCTTGGAGACTTCTTTACCCTTAAATCTGTCTGTCGGCTTTGA
1 -AGTCTGCCTGTCGA-CTTTGACCTTGGAGACTTC-TTA-CCTTCAGTCTGCCTGTCGGCTTTGA
* * ** * * * * * * * * *
30023 CCTTAGAAACTTTCTTACCTTTAGTTTGCTTGTTGGCTTTTACCTTGGAGACTTCCTCATCTTA
62 CCTTAGAGACTTTCTTATCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
* * * * * * *
30087 AGTTTGTCTGTCGACTTTGACCTTGAAGACATTCTTATCTTCAGTCTGCCAGTCGGCTTTGTCCC
1 AGTCTGCCTGTCGACTTTGACCTTGGAGAC-TTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCT
** * * *
30152 TAGAGACTGCCTTATCTCAA-TTCTGCTTGTCGGTTTTGACCCTAGAGAC-TTCATTACCTTTA
65 TAGAGACTTTCTTATCTCAAGTT-TGCCTGTCGGCTTTGACCCTAGAGACTTTC-TTACC-TTC
* * * * *
30214 AGTCTGCTTATTGGCTTT-AACTTGGAGACTTCCTTACCTT
1 AGTCTGCCTGTCGACTTTGACCTTGGAGACTT-CTTACCTT
30254 TAGTTTTCCC
Statistics
Matches: 1177, Mismatches: 310, Indels: 132
0.73 0.19 0.08
Matches are distributed among these distances:
120 3 0.00
121 5 0.00
122 45 0.04
123 42 0.04
124 6 0.01
125 57 0.05
126 632 0.54
127 330 0.28
128 54 0.05
129 3 0.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (125 bp):
AGTCTGCCTGTCGACTTTGACCTTGGAGACTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTT
AGAGACTTTCTTATCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTC
Found at i:29455 original size:207 final size:210
Alignment explanation
Indices: 29151--29529 Score: 507
Period size: 207 Copynumber: 1.8 Consensus size: 210
29141 AACCCTCGAG
* * * * *
29151 ACTTTTTTACCTTTAGTTTGCCTGTCGACTTTGATCCTAGAGATTGCCTCATCTCAAGTCTGCCT
1 ACTTTCTTAACTTCAGTCTGCCTATCGACTTTGATCCTAGAGA-TGCCTCATCTCAAGTCTGCCT
* * * *
29216 GTCGGCTTTGAACCTGGAGACTTTCTTACCTTTAATCTGCCTGTCGGTTTTAACCCTAGAGACTG
65 GTCGGCTTTGAACCTAGAGACTTTCTTACCTTTAATCTACCTGTCAGCTTTAACCCTAGAGACTG
* * *
29281 CCTCATCTCAAGTCTGCCTATCGGCTTTGACCTTAGAGACTTCCTTACCCTCAAGTCTGTCTGTT
130 CCTCATCTCAAGTATGCCTATCGGCTTTAACCCTAGAGACTTCCTTACCCTCAAGTCTGTCTGTT
29346 GACTTTGATCTTGGAA
195 GACTTTGATCTTGGAA
* *
29362 ACTTTCTTAACTTCAGTCTGCCTATCGACTTTGA-CCTTG-GA-GCCTCATCTCAAGTCTGCTTG
1 ACTTTCTTAACTTCAGTCTGCCTATCGACTTTGATCCTAGAGATGCCTCATCTCAAGTCTGCCTG
* * * * *
29424 TCGGCTTTG-ACCTTAGAGA-TTTTTCTACCTTTAGTCTACCTGTCAGCTTTGACCTTAGAGATT
66 TCGGCTTTGAACC-TAGAGACTTTCT-TACCTTTAATCTACCTGTCAGCTTTAACCCTAGAGACT
* *
29487 GCCTCATCTCAAGTATGCTTGTCGGCTTTAACCCTAGAGACTT
129 GCCTCATCTCAAGTATGCCTATCGGCTTTAACCCTAGAGACTT
29530 TTTTATTTTA
Statistics
Matches: 145, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
206 7 0.05
207 103 0.71
209 2 0.01
210 4 0.03
211 29 0.20
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.37
Consensus pattern (210 bp):
ACTTTCTTAACTTCAGTCTGCCTATCGACTTTGATCCTAGAGATGCCTCATCTCAAGTCTGCCTG
TCGGCTTTGAACCTAGAGACTTTCTTACCTTTAATCTACCTGTCAGCTTTAACCCTAGAGACTGC
CTCATCTCAAGTATGCCTATCGGCTTTAACCCTAGAGACTTCCTTACCCTCAAGTCTGTCTGTTG
ACTTTGATCTTGGAA
Found at i:30869 original size:14 final size:13
Alignment explanation
Indices: 30845--30895 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
30835 GTTAATTTTA
30845 AAAAAATAATAAT
1 AAAAAATAATAAT
30858 AAAAAAT-A-AAT
1 AAAAAATAATAAT
* * *
30869 AAATAATATTCAT
1 AAAAAATAATAAT
30882 AAAATAATAATAAT
1 AAAA-AATAATAAT
30896 TAATTAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 12 0.41
14 7 0.24
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:31098 original size:23 final size:21
Alignment explanation
Indices: 31071--31128 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
31061 ACAAAAACAG
*
31071 AACAAAAAGAAGAGAGAAATCGA
1 AACAAAAA-AAGAAAG-AATCGA
31094 AACAAAAAAA-AAAGAATCGA
1 AACAAAAAAAGAAAGAATCGA
31114 AACAAAAAAAAGAAA
1 AAC-AAAAAAAGAAA
31129 ACAAAAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 9 0.28
21 10 0.31
22 5 0.16
23 8 0.25
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (21 bp):
AACAAAAAAAGAAAGAATCGA
Found at i:31129 original size:23 final size:24
Alignment explanation
Indices: 31065--31129 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 24
31055 AAGAAAACAA
31065 AAACAGAACAAAAAGAAGAGAGAAATCG
1 AAACA-AA-AAAAAGAA-A-AGAAATCG
31093 AAAC--AAAAAA-AAAAG-AATCG
1 AAACAAAAAAAAGAAAAGAAATCG
31113 AAACAAAAAAAAGAAAA
1 AAACAAAAAAAAGAAAA
31130 CAAAAAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
20 9 0.26
21 2 0.06
22 7 0.21
23 6 0.18
24 5 0.15
25 1 0.03
28 4 0.12
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (24 bp):
AAACAAAAAAAAGAAAAGAAATCG
Found at i:31325 original size:28 final size:28
Alignment explanation
Indices: 31259--31327 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
31249 AAACAGCACA
31259 CAAGCAACAGCAAGCAACTCTAGCAATC
1 CAAGCAACAGCAAGCAACTCTAGCAATC
*
31287 CAA-AAATCAGCAAGCAACTCTAGCAATC
1 CAAGCAA-CAGCAAGCAACTCTAGCAATC
*
31315 TAAGCAACAGCAA
1 CAAGCAACAGCAA
31328 TCGAAACACA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.06
28 32 0.89
29 2 0.06
ACGTcount: A:0.46, C:0.29, G:0.13, T:0.12
Consensus pattern (28 bp):
CAAGCAACAGCAAGCAACTCTAGCAATC
Found at i:31381 original size:9 final size:9
Alignment explanation
Indices: 31367--31398 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
31357 CTGAAGACAC
*
31367 AGCAAAGTA
1 AGCAAAGAA
31376 AGCAAAGAA
1 AGCAAAGAA
31385 AGCAAAGAA
1 AGCAAAGAA
31394 AGCAA
1 AGCAA
31399 CGCAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.62, C:0.12, G:0.22, T:0.03
Consensus pattern (9 bp):
AGCAAAGAA
Found at i:37176 original size:16 final size:16
Alignment explanation
Indices: 37155--37212 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
37145 TAATTGTTCG
*
37155 GGTCATTTCGAGTTTC
1 GGTCATTTCGAGTTTA
*
37171 GGTCATTTCGAATTTA
1 GGTCATTTCGAGTTTA
* * *
37187 GGTTATTATAG-GTTTG
1 GGTCATT-TCGAGTTTA
37203 GGTCATTTCG
1 GGTCATTTCG
37213 GATTCGTGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
15 2 0.06
16 29 0.88
17 2 0.06
ACGTcount: A:0.17, C:0.12, G:0.26, T:0.45
Consensus pattern (16 bp):
GGTCATTTCGAGTTTA
Found at i:37859 original size:24 final size:25
Alignment explanation
Indices: 37832--37885 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
37822 AAATATGTTA
* *
37832 TATTTATTATATTATTTTTATA-TT
1 TATTTAATATATTATGTTTATATTT
*
37856 TATTAAATATATTATGTTTATATTT
1 TATTTAATATATTATGTTTATATTT
37881 TATTT
1 TATTT
37886 TCATGTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TATTTAATATATTATGTTTATATTT
Found at i:37861 original size:38 final size:37
Alignment explanation
Indices: 37803--37886 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 37
37793 CTACATTAAA
*
37803 ATATT-TTTTTAATATAATTAAATATGTTATATTTATT
1 ATATTATTTTTAATATAATTAAATATATTATATTTA-T
* *
37840 ATATTATTTTT-ATATTTATTAAATATATTATGTTTAT
1 ATATTATTTTTAATA-TAATTAAATATATTATATTTAT
*
37877 ATTTTATTTT
1 ATATTATTTT
37887 CATGTCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 18 0.44
38 23 0.56
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (37 bp):
ATATTATTTTTAATATAATTAAATATATTATATTTAT
Found at i:39190 original size:3 final size:3
Alignment explanation
Indices: 39127--39174 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
39117 AAATAGTTAC
39127 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39175 CAGCTTTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42925 original size:22 final size:22
Alignment explanation
Indices: 42876--42971 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 22
42866 AGGGATTGAT
* *
42876 ATTTTCTTAAGAAAGATCAATG
1 ATTTTTTTAAGAAAGATCAATA
** *
42898 CCTTTTTTAAGAAGGATCAATA
1 ATTTTTTTAAGAAAGATCAATA
*
42920 ATTTTTTTAA-AATAAAT-AATCA
1 ATTTTTTTAAGAA-AGATCAAT-A
42942 A-TTTTTTAAGAGAA-ATCAAT-
1 ATTTTTTTAAGA-AAGATCAATA
*
42962 ATCTTTTTAA
1 ATTTTTTTAA
42972 AAATGATAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.02
21 22 0.38
22 34 0.59
23 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (22 bp):
ATTTTTTTAAGAAAGATCAATA
Found at i:44948 original size:11 final size:12
Alignment explanation
Indices: 44928--44958 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
44918 AGATTGCACA
44928 TTTATTTTATTT
1 TTTATTTTATTT
44940 TTT-TTTTATTT
1 TTTATTTTATTT
44951 TTTATTTT
1 TTTATTTT
44959 TGCTTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:47814 original size:5 final size:5
Alignment explanation
Indices: 47800--47832 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
47790 ATTCTCTGGG
*
47800 CATCT TATCT CATCT CATCT CATCT CATCT CAT
1 CATCT CATCT CATCT CATCT CATCT CATCT CAT
47833 AATGTCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.42
Consensus pattern (5 bp):
CATCT
Found at i:48293 original size:2 final size:2
Alignment explanation
Indices: 48286--48320 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48276 GTGACTCAGC
48286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48321 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49181 original size:21 final size:21
Alignment explanation
Indices: 49149--49198 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
49139 TCATTATTAC
49149 TATTATTTATTAGTTGCGTTA-T
1 TATTA-TTATTAGTTGC-TTATT
*
49171 TATTATTATTATTTGCTTATT
1 TATTATTATTAGTTGCTTATT
49192 TATTATT
1 TATTATT
49199 TATAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.69
22 5 0.19
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (21 bp):
TATTATTATTAGTTGCTTATT
Found at i:49369 original size:7 final size:7
Alignment explanation
Indices: 49357--49389 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
49347 GTGAATGGGA
49357 TTGAATT
1 TTGAATT
49364 TTGAATT
1 TTGAATT
49371 TTGAATT
1 TTGAATT
49378 TTGAATT
1 TTGAATT
49385 TTGAA
1 TTGAA
49390 ACGATTGAAT
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:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (7 bp):
TTGAATT
Found at i:49504 original size:12 final size:12
Alignment explanation
Indices: 49489--49523 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
49479 TATATAGATT
49489 TTTATATATTTA
1 TTTATATATTTA
*
49501 TTTATTTATTTA
1 TTTATATATTTA
49513 TTT-TATATTTA
1 TTTATATATTTA
49524 GATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATATATTTA
Found at i:49533 original size:17 final size:17
Alignment explanation
Indices: 49511--49551 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
49501 TTTATTTATT
49511 TATTTTATATTTAGATTA
1 TATTTTATA-TTAGATTA
*
49529 T-TTTTATATTATATTA
1 TATTTTATATTAGATTA
49545 TATTTTA
1 TATTTTA
49552 GTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 8 0.38
17 12 0.57
18 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TATTTTATATTAGATTA
Found at i:49544 original size:16 final size:15
Alignment explanation
Indices: 49486--49551 Score: 52
Period size: 17 Copynumber: 4.5 Consensus size: 15
49476 TTGTATATAG
49486 ATTTTTATA-TATTT
1 ATTTTTATATTATTT
49500 A--TTTAT-TTATTT
1 ATTTTTATATTATTT
*
49512 A-TTTTATATTTAGATT
1 ATTTTTATA-TTA-TTT
49528 ATTTTTATATTATATT
1 ATTTTTATATTAT-TT
49544 ATATTTTA
1 AT-TTTTA
49552 GTTTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
12 11 0.26
13 5 0.12
14 1 0.02
15 3 0.07
16 10 0.24
17 12 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
ATTTTTATATTATTT
Found at i:49749 original size:22 final size:22
Alignment explanation
Indices: 49723--49771 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
49713 ATTTTATATA
49723 AATTTTGATACGTTTATCTATT
1 AATTTTGATACGTTTATCTATT
49745 AATTTTGATACGTTTATCTATT
1 AATTTTGATACGTTTATCTATT
49767 AATTT
1 AATTT
49772 ATGTTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (22 bp):
AATTTTGATACGTTTATCTATT
Found at i:53309 original size:3 final size:3
Alignment explanation
Indices: 53301--53327 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53291 TTGATAAAAA
53301 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
53328 ATAATTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54067 original size:29 final size:32
Alignment explanation
Indices: 54035--54110 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 32
54025 CATTATTTTT
54035 ATTTAAATTTAAAA-ATTT-AA-TTAATTTAA
1 ATTTAAATTTAAAAGATTTAAACTTAATTTAA
*
54064 ATTTAAATTTAAAATGATTTAAACTTTAATTTGA
1 ATTTAAATTTAAAA-GATTTAAAC-TTAATTTAA
54098 ATGTTAAATTTAA
1 AT-TTAAATTTAA
54111 TTGAATCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 14 0.35
31 4 0.10
32 2 0.05
34 10 0.25
35 10 0.25
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (32 bp):
ATTTAAATTTAAAAGATTTAAACTTAATTTAA
Found at i:54144 original size:21 final size:21
Alignment explanation
Indices: 54120--54160 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54110 ATTGAATCAA
*
54120 ATTTAAA-TAATTAATTTAAAT
1 ATTTAAACTAA-TAATATAAAT
54141 ATTTAAACTAATAATATAAA
1 ATTTAAACTAATAATATAAA
54161 CTCTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAAACTAATAATATAAAT
Found at i:54449 original size:4 final size:4
Alignment explanation
Indices: 54440--54465 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
54430 ATTATGTCAC
54440 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
54466 ACCTCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:54728 original size:6 final size:6
Alignment explanation
Indices: 54717--54751 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
54707 AGCAAGCACG
* *
54717 CACATA CACATA CACAAA CACAAA CACAAA CACAA
1 CACAAA CACAAA CACAAA CACAAA CACAAA CACAA
54752 TGGTAAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.60, C:0.34, G:0.00, T:0.06
Consensus pattern (6 bp):
CACAAA
Found at i:59571 original size:16 final size:17
Alignment explanation
Indices: 59550--59593 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
59540 TATAAATGTT
59550 AATTAATTATTAAAA-A
1 AATTAATTATTAAAATA
59566 AATTAATTA-TAAAATA
1 AATTAATTATTAAAATA
59582 AATT--TTATTAAA
1 AATTAATTATTAAA
59594 TAATAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 14 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTAATTATTAAAATA
Found at i:59592 original size:30 final size:29
Alignment explanation
Indices: 59556--59618 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
59546 TGTTAATTAA
59556 TTATTAAAAAAATTAATTATA-AAATAAATT
1 TTATT-AAAAAA-TAATTATATAAATAAATT
* **
59586 TTATTAAATAATAATTATATATTTAAATT
1 TTATTAAAAAATAATTATATAAATAAATT
59615 TTAT
1 TTAT
59619 ATTAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 8 0.28
29 16 0.55
30 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATTAAAAAATAATTATATAAATAAATT
Found at i:59712 original size:21 final size:22
Alignment explanation
Indices: 59678--59721 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
59668 TCAATTATTT
59678 TAAATATATCA-TTTAAAAAAA
1 TAAATATATCATTTTAAAAAAA
* * *
59699 TAAATATTTTATTTTAAATAAA
1 TAAATATATCATTTTAAAAAAA
59721 T
1 T
59722 TATTTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATATCATTTTAAAAAAA
Found at i:59778 original size:14 final size:14
Alignment explanation
Indices: 59759--59797 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
59749 TTATAGACCT
*
59759 ATTATTTTAAATAA
1 ATTATTTAAAATAA
59773 ATTATTTAAAATAA
1 ATTATTTAAAATAA
**
59787 AAAATTTAAAA
1 ATTATTTAAAA
59798 AATAAATATT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATTTAAAATAA
Found at i:59808 original size:15 final size:15
Alignment explanation
Indices: 59767--59808 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
59757 CTATTATTTT
59767 AAATAAATTATTTAAA
1 AAATAAA-TATTTAAA
59783 ATAA-AAA-ATTTAAA
1 A-AATAAATATTTAAA
59797 AAATAAATATTT
1 AAATAAATATTT
59809 TATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.09
14 11 0.48
15 4 0.17
16 4 0.17
17 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATAAATATTTAAA
Found at i:60724 original size:13 final size:13
Alignment explanation
Indices: 60693--60724 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
60683 TATATTACAA
*
60693 ATTTAATATCTAT
1 ATTTATTATCTAT
60706 ATTTATTATCTAT
1 ATTTATTATCTAT
60719 ATTTAT
1 ATTTAT
60725 GTCTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTATTATCTAT
Found at i:60771 original size:14 final size:13
Alignment explanation
Indices: 60732--60773 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
60722 TATGTCTTTT
60732 AATTCTATTTAATA
1 AATTCTATTTAA-A
*
60746 AATT-TTTTTAAA
1 AATTCTATTTAAA
60758 AATTCGTATTTAAA
1 AATTC-TATTTAAA
60772 AA
1 AA
60774 GAAAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 5 0.21
13 6 0.25
14 13 0.54
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (13 bp):
AATTCTATTTAAA
Found at i:61418 original size:21 final size:22
Alignment explanation
Indices: 61370--61411 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
61360 GCATAAGTTT
* *
61370 AGATCTATTTATAAATTAGATG
1 AGATTTATTTATAAATTAAATG
61392 AGATTTATTT-TAAATTAAAT
1 AGATTTATTTATAAATTAAAT
61412 TGAATTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (22 bp):
AGATTTATTTATAAATTAAATG
Found at i:64213 original size:11 final size:13
Alignment explanation
Indices: 64195--64226 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
64185 TAATTAAATT
64195 AATATTTA-TTTA
1 AATATTTATTTTA
64207 AAT-TTTATTTTA
1 AATATTTATTTTA
64219 AATATTTA
1 AATATTTA
64227 AGAATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 10 0.56
13 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTTATTTTA
Found at i:64247 original size:23 final size:20
Alignment explanation
Indices: 64197--64247 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
64187 ATTAAATTAA
64197 TATTTATTTAAATTTTATTT
1 TATTTATTTAAATTTTATTT
**
64217 TAAATATTTAAGAATCTTTATTT
1 TATTTATTT-A-AAT-TTTATTT
64240 TATTTATT
1 TATTTATT
64248 CTTCTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 3 0.12
23 13 0.54
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTTATTTAAATTTTATTT
Found at i:64615 original size:19 final size:19
Alignment explanation
Indices: 64587--64628 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
64577 AATATTAAAA
* *
64587 TTTTTCATTTTATTTTATT
1 TTTTTCATTTTAATTAATT
*
64606 TTTTTTATTTTAATTAATT
1 TTTTTCATTTTAATTAATT
64625 TTTT
1 TTTT
64629 ATCACTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCATTTTAATTAATT
Found at i:64853 original size:17 final size:18
Alignment explanation
Indices: 64831--64864 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
64821 TAATTTATTT
*
64831 TTTAAATTATGA-ATAAA
1 TTTAAAATATGATATAAA
64848 TTTAAAATATGATATAA
1 TTTAAAATATGATATAA
64865 TTAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
TTTAAAATATGATATAAA
Found at i:65633 original size:14 final size:14
Alignment explanation
Indices: 65611--65681 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 14
65601 TTATATAAAT
65611 TTTTATATATTTTTA
1 TTTT-TATATTTTTA
65626 TTTTTATA-TTTTA
1 TTTTTATATTTTTA
65639 --TTTATATTATATTA
1 TTTTTATATT-T-TTA
65653 TTTATTAT-TTTTTA
1 TTT-TTATATTTTTA
* *
65667 -TATTATATTTATA
1 TTTTTATATTTTTA
65680 TT
1 TT
65682 ATATTTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
11 6 0.13
12 5 0.11
13 12 0.26
14 11 0.24
15 5 0.11
16 3 0.07
17 4 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTATATTTTTA
Found at i:65642 original size:11 final size:11
Alignment explanation
Indices: 65623--65687 Score: 76
Period size: 11 Copynumber: 5.7 Consensus size: 11
65613 TTATATATTT
*
65623 TTATTTTTATA
1 TTATATTTATA
*
65634 TTTTATTTATA
1 TTATATTTATA
*
65645 TTATATTATTTA
1 TTATATT-TATA
*
65657 TTATTTTTTATA
1 TTA-TATTTATA
65669 TTATATTTATA
1 TTATATTTATA
65680 TTATATTT
1 TTATATTT
65688 TAAATCATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
11 30 0.67
12 12 0.27
13 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATATTTATA
Found at i:65651 original size:24 final size:23
Alignment explanation
Indices: 65609--65681 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
65599 ATTTATATAA
* *
65609 ATTTTTATATAT-TTTTATTTTT
1 ATTTTTATTTATATTATATTTTT
65631 ATATTTTATTTATATTATATTATTT
1 AT-TTTTATTTATATTATATT-TTT
*
65656 ATTATTT-TTTATATTATATTTAT
1 ATT-TTTATTTATATTATATTTTT
65679 ATT
1 ATT
65682 ATATTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 2 0.05
23 14 0.32
24 20 0.45
25 8 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTTTTATTTATATTATATTTTT
Found at i:65665 original size:35 final size:33
Alignment explanation
Indices: 65613--65686 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 33
65603 ATATAAATTT
*
65613 TTATA-TATTTTTATTTTTATATTTTATTTATA
1 TTATATTATTTTTATTTTTATATTATATTTATA
65645 TTATATTATTTATTATTTTTTATATTATATTTATA
1 TTATATTATTT-TTA-TTTTTATATTATATTTATA
65680 TTATATT
1 TTATATT
65687 TTAAATCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
32 5 0.13
33 5 0.13
34 3 0.08
35 25 0.66
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (33 bp):
TTATATTATTTTTATTTTTATATTATATTTATA
Found at i:65673 original size:40 final size:39
Alignment explanation
Indices: 65599--65686 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 39
65589 TCAACAATTA
*
65599 ATTTATA-TAAATTTTTATATATTTTTATTTTTATATTTT
1 ATTTATATTAAATTTTTATATATTTTTATTATTATA-TTT
*
65638 ATTTATATTATATTATTTAT-TATTTTT-TATATTATATTT
1 ATTTATATTAAATT-TTTATATATTTTTAT-TATTATATTT
65677 ATATTATATT
1 AT-TTATATT
65687 TTAAATCATT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
39 13 0.30
40 25 0.58
41 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (39 bp):
ATTTATATTAAATTTTTATATATTTTTATTATTATATTT
Found at i:66774 original size:26 final size:26
Alignment explanation
Indices: 66743--66814 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 26
66733 TGTAAATGAT
66743 TAAAAATTAATTAATAAAATAGAAACA
1 TAAAAATTAATTAATAAAATAGAAA-A
* *
66770 T-AAAA-TACATTATTAAAA-ATAAAA
1 TAAAAATTA-ATTAATAAAATAGAAAA
66794 TAAAAATTAATTAATAAAATA
1 TAAAAATTAATTAATAAAATA
66815 ATTTTCTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 2 0.05
25 19 0.50
26 16 0.42
27 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (26 bp):
TAAAAATTAATTAATAAAATAGAAAA
Found at i:67754 original size:29 final size:27
Alignment explanation
Indices: 67720--67781 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
67710 ATCAAAATAT
*
67720 TAATATTTTAAATAGTAATATTATTATAA
1 TAATATTTT-AATAGTAA-AATATTATAA
* *
67749 TAATA-TTTAATATTAAAATATTATAT
1 TAATATTTTAATAGTAAAATATTATAA
67775 TAATATT
1 TAATATT
67782 AAATACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 13 0.45
27 8 0.28
28 3 0.10
29 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TAATATTTTAATAGTAAAATATTATAA
Found at i:67762 original size:18 final size:18
Alignment explanation
Indices: 67741--67786 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
67731 ATAGTAATAT
67741 TATTATAATAATAT-TTAA
1 TATTA-AATAATATATTAA
*
67759 TATTAAAATATTATATTAA
1 TATT-AAATAATATATTAA
67778 TATTAAATA
1 TATTAAATA
67787 CTTAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAAATAATATATTAA
Found at i:67797 original size:19 final size:19
Alignment explanation
Indices: 67756--67799 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
67746 TAATAATATT
* *
67756 TAATATTAAAATATTATAT
1 TAATATTAAAATATTAAAA
67775 TAATATT-AAATACTTAAAA
1 TAATATTAAAATA-TTAAAA
67794 TAATAT
1 TAATAT
67800 ATTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATATTAAAATATTAAAA
Found at i:67806 original size:25 final size:25
Alignment explanation
Indices: 67751--67807 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
67741 TATTATAATA
* *
67751 ATATTTAATATTAAAATATTATATT
1 ATATTAAATATTAAAATAATATATT
67776 AATATTAAATACTTAAAATAATATATT
1 -ATATTAAATA-TTAAAATAATATATT
67803 -TATTA
1 ATATTA
67808 TTAAAACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.18
26 9 0.32
27 14 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATTAAATATTAAAATAATATATT
Found at i:67813 original size:20 final size:20
Alignment explanation
Indices: 67738--67869 Score: 81
Period size: 20 Copynumber: 6.2 Consensus size: 20
67728 TAAATAGTAA
*
67738 TATTATTATAATA--ATATT
1 TATTATTAAAATATTATATT
*
67756 TAATATTAAAATATTATATT
1 TATTATTAAAATATTATATT
*
67776 AATATTAAATACTTAAAATAATATATT
1 --TA-T---TA-TTAAAATATTATATT
*
67803 TATTATTAAAACATTA-ATT
1 TATTATTAAAATATTATATT
*
67822 ATATTAATATATAAATATTATAGT
1 -TATT-AT-TA-AAATATTATATT
* *
67846 TATTTTTAAAATATTATTTT
1 TATTATTAAAATATTATATT
67866 TATT
1 TATT
67870 TTTTTTAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 26
0.71 0.09 0.21
Matches are distributed among these distances:
18 11 0.12
19 3 0.03
20 32 0.36
21 6 0.07
22 5 0.06
23 11 0.12
24 3 0.03
25 2 0.02
26 2 0.02
27 14 0.16
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (20 bp):
TATTATTAAAATATTATATT
Found at i:67819 original size:28 final size:28
Alignment explanation
Indices: 67744--67838 Score: 80
Period size: 26 Copynumber: 3.6 Consensus size: 28
67734 GTAATATTAT
* * *
67744 TATAATAATATTTAATA--TTAAAATAT
1 TATATTAATATTAAATACATTAAAATAA
67770 TATATTAATATTAAATAC-TTAAAATAA
1 TATATTAATATTAAATACATTAAAATAA
*
67797 TATATTTATTATTAAA-ACATT--AAT--
1 TATA-TTAATATTAAATACATTAAAATAA
67821 TATATTAATATATAAATA
1 TATATTAATAT-TAAATA
67839 TTATAGTTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
23 6 0.10
24 8 0.14
25 1 0.02
26 18 0.31
27 14 0.24
28 12 0.20
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
TATATTAATATTAAATACATTAAAATAA
Found at i:67863 original size:23 final size:22
Alignment explanation
Indices: 67788--67888 Score: 68
Period size: 23 Copynumber: 4.7 Consensus size: 22
67778 TATTAAATAC
* *
67788 TTAAAATAATA-TAT-TTATTA
1 TTAAAATATTATTATATTATTT
* *
67808 TTAAAACATTAATTATATTA-AT
1 TTAAAATATT-ATTATATTATTT
* *
67830 ATATAAATATTA-TA-GTTATTT
1 TTA-AAATATTATTATATTATTT
* *
67851 TTAAAATATTATTTTTATTTTTT
1 TTAAAATATTA-TTATATTATTT
67874 TTAAAATATTATTAT
1 TTAAAATATTATTAT
67889 TGACATAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
20 19 0.32
21 6 0.10
22 10 0.17
23 25 0.42
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (22 bp):
TTAAAATATTATTATATTATTT
Found at i:68426 original size:41 final size:41
Alignment explanation
Indices: 68368--68462 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
68358 TGGTTTTTTT
* *
68368 TATTTTAATCATATAAATATGAGCATAATAAAATTATT-ATA
1 TATTTTAATAATATAAATATGAACATAATAAAA-TATTAATA
*
68409 TATTTTAA-AATATTAAATATGAATATAATAAAATATTAAATA
1 TATTTTAATAATA-TAAATATGAACATAATAAAATATT-AATA
*
68451 TATTTTATTAAT
1 TATTTTAATAAT
68463 TATATTAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
40 7 0.15
41 26 0.57
42 10 0.22
43 3 0.07
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (41 bp):
TATTTTAATAATATAAATATGAACATAATAAAATATTAATA
Found at i:68521 original size:24 final size:25
Alignment explanation
Indices: 68501--68555 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
68491 TAATATTTGT
*
68501 TATTATATTTTTATATT-TATTAAA
1 TATTATATTTTTATATTATATTTAA
*
68525 TATTTTATTTTTATATTATATTTAA
1 TATTATATTTTTATATTATATTTAA
*
68550 AATTAT
1 TATTAT
68556 TAATTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTATATTTTTATATTATATTTAA
Found at i:68522 original size:17 final size:16
Alignment explanation
Indices: 68500--68541 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
68490 GTAATATTTG
68500 TTATTATATTTTTATAT
1 TTATTATATTTTT-TAT
* *
68517 TTATTAAATATTTTAT
1 TTATTATATTTTTTAT
68533 TT-TTATATT
1 TTATTATATT
68542 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATATTTTTTAT
Found at i:68545 original size:18 final size:18
Alignment explanation
Indices: 68501--68547 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
68491 TAATATTTGT
68501 TATTATATTTTTATATTTA
1 TATTATA-TTTTATATTTA
* *
68520 T-TAAATATTTTATTTTTA
1 TAT-TATATTTTATATTTA
68538 TATTATATTT
1 TATTATATTT
68548 AAAATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTATATTTTATATTTA
Found at i:69168 original size:29 final size:31
Alignment explanation
Indices: 69124--69187 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
69114 TTATTTTTTA
* * *
69124 TTTATTATAATTTAAAAA-TA-TAATAATTT
1 TTTATTAAAATATAAAAATTATTAATAAATT
69153 TTTATTAAAATATAAAAATTATTAATAAATT
1 TTTATTAAAATATAAAAATTATTAATAAATT
69184 TTTA
1 TTTA
69188 CCGAAGTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 16 0.53
30 2 0.07
31 12 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TTTATTAAAATATAAAAATTATTAATAAATT
Found at i:69882 original size:23 final size:23
Alignment explanation
Indices: 69846--69889 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
69836 TAACACAATT
69846 AAATATTATAAATATAATATAAA
1 AAATATTATAAATATAATATAAA
*
69869 AAATAATTAT-AATATGATATA
1 AAAT-ATTATAAATATAATATA
69890 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATATTATAAATATAATATAAA
Found at i:69891 original size:39 final size:37
Alignment explanation
Indices: 69848--69926 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 37
69838 ACACAATTAA
* *
69848 ATATTATAAATATAAT-ATAAAAAATAATTATAATATGAT
1 ATATTATAAAAAAAATAATAAAAAATAA-TATAA-AT-AT
*
69887 ATATTTTAAAAAAAATAATAAAAAATAATATAAATAT
1 ATATTATAAAAAAAATAATAAAAAATAATATAAATAT
69924 ATA
1 ATA
69927 AACATATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 5 0.14
38 2 0.06
39 18 0.50
40 11 0.31
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (37 bp):
ATATTATAAAAAAAATAATAAAAAATAATATAAATAT
Found at i:69959 original size:10 final size:10
Alignment explanation
Indices: 69897--69960 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
69887 ATATTTTAAA
69897 AAAAATA-AT
1 AAAAATATAT
69906 AAAAA-ATAAT
1 AAAAATAT-AT
*
69916 ATAAATATAT
1 AAAAATATAT
*
69926 AAACATAT-T
1 AAAAATATAT
*
69935 -AAAATTTAT
1 AAAAATATAT
*
69944 ATAAATATAT
1 AAAAATATAT
69954 AAAAATA
1 AAAAATA
69961 ATATTATACA
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
8 6 0.14
9 7 0.17
10 27 0.64
11 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAATATAT
Found at i:69968 original size:14 final size:14
Alignment explanation
Indices: 69947--69980 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
69937 AATTTATATA
69947 AATA-TATAAAAAT
1 AATATTATAAAAAT
*
69960 AATATTATACAAAT
1 AATATTATAAAAAT
69974 AATATTA
1 AATATTA
69981 ATAGAACGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATTATAAAAAT
Found at i:70637 original size:21 final size:22
Alignment explanation
Indices: 70586--70642 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
70576 AAAATATATT
* * *
70586 TTAAATTTAAATATTATTTTTA
1 TTAAATTTATATATTATTATAA
70608 TTAATATTTATATATT-TTATAA
1 TTAA-ATTTATATATTATTATAA
70630 TTAAATTTATATA
1 TTAAATTTATATA
70643 AATTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.29
22 12 0.39
23 10 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAAATTTATATATTATTATAA
Found at i:70640 original size:19 final size:19
Alignment explanation
Indices: 70580--70641 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
70570 AATATAAAAA
70580 TATATTTTA-AATTTAAATAT
1 TATATTTTATAA-TTAAAT-T
*
70600 TAT-TTTTATTAA-T-ATTT
1 TATATTTTA-TAATTAAATT
70617 ATATATTTTATAATTAAATT
1 -TATATTTTATAATTAAATT
70637 TATAT
1 TATAT
70642 AAATTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
17 1 0.03
18 8 0.24
19 17 0.50
20 6 0.18
21 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTTTATAATTAAATT
Found at i:73959 original size:17 final size:17
Alignment explanation
Indices: 73924--73959 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
73914 AAAAAATTAA
*
73924 ATATATTTATGTTAGAT
1 ATATATTTATATTAGAT
*
73941 ATATATTTATATTATAT
1 ATATATTTATATTAGAT
73958 AT
1 AT
73960 TTACACTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
ATATATTTATATTAGAT
Found at i:74982 original size:15 final size:15
Alignment explanation
Indices: 74937--74979 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 15
74927 TGATCATAAC
74937 TTTG-CTTTTTG-A-
1 TTTGTCTTTTTGTAT
74949 TTT-TCTTTTTGTAT
1 TTTGTCTTTTTGTAT
74963 TTTGTCTTTTT-TAT
1 TTTGTCTTTTTGTAT
74977 TTT
1 TTT
74980 TGTAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.37
13 1 0.04
14 9 0.33
15 7 0.26
ACGTcount: A:0.07, C:0.07, G:0.09, T:0.77
Consensus pattern (15 bp):
TTTGTCTTTTTGTAT
Found at i:75512 original size:2 final size:2
Alignment explanation
Indices: 75505--75532 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75495 CAACAGTGCA
75505 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75533 TTGTGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76877 original size:22 final size:22
Alignment explanation
Indices: 76849--76893 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
76839 GAAAGAAAAC
*
76849 TCAACCATTAATCACTCTCTGA
1 TCAACCATTAATCACGCTCTGA
*
76871 TCAACCATTAGTCACGCTCTGA
1 TCAACCATTAATCACGCTCTGA
76893 T
1 T
76894 TACATAGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (22 bp):
TCAACCATTAATCACGCTCTGA
Found at i:77529 original size:2 final size:2
Alignment explanation
Indices: 77522--77552 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
77512 AATTTATTTC
77522 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77553 GAAAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:79083 original size:1 final size:1
Alignment explanation
Indices: 79077--79101 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
79067 ATGTAAATGA
79077 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
79102 TTTAATTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:81708 original size:19 final size:18
Alignment explanation
Indices: 81666--81712 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
81656 GAAAATTTGC
*
81666 TAATTTTTTTATATATAA
1 TAATATTTTTATATATAA
*
81684 -AA-ATTTTTATAATGTAA
1 TAATATTTTTAT-ATATAA
81701 TAATATTTTTAT
1 TAATATTTTTAT
81713 CAAATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 2 0.08
19 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TAATATTTTTATATATAA
Found at i:83406 original size:2 final size:2
Alignment explanation
Indices: 83399--83430 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
83389 AGCATCGCAA
83399 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
83431 GGGGTAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:88325 original size:1 final size:1
Alignment explanation
Indices: 88319--88387 Score: 138
Period size: 1 Copynumber: 69.0 Consensus size: 1
88309 TTGAACATCA
88319 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
88384 CCCC
1 CCCC
88388 AACAAAACAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:90322 original size:24 final size:24
Alignment explanation
Indices: 90255--90327 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
90245 AGATTAAAAA
* * *
90255 TAATAATAATAGTA-AAATTAATTA
1 TAATAATAAGAGTATAAAAT-ATTG
* *
90279 TTATAATAATGAG-ATTAAATATTG
1 TAATAATAA-GAGTATAAAATATTG
90303 TAATAATAAGAGTATAAAATTATTG
1 TAATAATAAGAGTATAAAA-TATTG
90328 ATGAGATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
23 3 0.08
24 25 0.66
25 10 0.26
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (24 bp):
TAATAATAAGAGTATAAAATATTG
Found at i:91046 original size:2 final size:2
Alignment explanation
Indices: 91039--91088 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
91029 ATTTACAACC
91039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
91081 AT AT AT AT
1 AT AT AT AT
91089 CACAAATCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98434 original size:28 final size:28
Alignment explanation
Indices: 98394--98451 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
98384 AGCATAGAGT
98394 TATGATTTATTATTCTTTTTTGTAAATA
1 TATGATTTATTATTCTTTTTTGTAAATA
*
98422 TATGATTTATTATTCTTTTTTGTACATA
1 TATGATTTATTATTCTTTTTTGTAAATA
98450 TA
1 TA
98452 AACCATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (28 bp):
TATGATTTATTATTCTTTTTTGTAAATA
Found at i:101068 original size:19 final size:19
Alignment explanation
Indices: 101041--101083 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
101031 TTATAAATAA
* *
101041 ATTTAAATA-AAAATATATT
1 ATTTTAATAGAAAA-ATACT
101060 ATTTTAATAGAAAAATACT
1 ATTTTAATAGAAAAATACT
101079 ATTTT
1 ATTTT
101084 GACTTGATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTTTAATAGAAAAATACT
Found at i:103137 original size:51 final size:51
Alignment explanation
Indices: 103050--103166 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 51
103040 AGAAATTGTA
* ** *
103050 GGGTTGGAGTATTCTCAAAGATGAAAAATTTGACATTTTGGAAGTAAAAATG
1 GGGTTAGAGTA-TCTCAAAGATGAAAAATTCAACATTTTGAAAGTAAAAATG
* * *
103102 GGGTTAGAGTATCTTAGAGATTAAAAATTCAACATTTTGAAAGTAAAAATG
1 GGGTTAGAGTATCTCAAAGATGAAAAATTCAACATTTTGAAAGTAAAAATG
** *
103153 AAGTTAAAGTATCT
1 GGGTTAGAGTATCT
103167 ATTCGGAGAT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 45 0.82
52 10 0.18
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (51 bp):
GGGTTAGAGTATCTCAAAGATGAAAAATTCAACATTTTGAAAGTAAAAATG
Found at i:103226 original size:80 final size:79
Alignment explanation
Indices: 103142--103363 Score: 213
Period size: 78 Copynumber: 2.8 Consensus size: 79
103132 AACATTTTGA
* * *
103142 AAGTAAAAATGAAGTTAAAGTATCTATTCGGAGATAGTGGGGTTGAAGTATCCCTAGAGATGAAA
1 AAGTAAAAATGAGGTTAGAGTATCT-TTCGGAGATGGTGGGGTTGAAGTATCCC-AGAGATGAAA
*
103207 AA-TTTGGCATTCTAG
64 AACTTTGGCATTATAG
* * * *
103222 AAGTAGAAAT-AGGGTTGGAGTATCCCCTT-GGATATGGTGGGGTT-AGAGTAT-CCAGAGAT-A
1 AAGTAAAAATGA-GGTTAGAGTAT--CTTTCGGAGATGGTGGGGTTGA-AGTATCCCAGAGATGA
*
103282 AAAACTTTGGCATTATGG
62 AAAACTTTGGCATTATAG
* * * * *
103300 AAATAAAAATGGGGTTAGAGTATCTCTCGAAGATGGTGGGGGTTGGAGTATCCCAGAGATGAAA
1 AAGTAAAAATGAGGTTAGAGTATCTTTCGGAGATGGT-GGGGTTGAAGTATCCCAGAGATGAAA
103364 TTTGATGTTT
Statistics
Matches: 113, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
76 2 0.02
77 12 0.11
78 46 0.41
79 12 0.11
80 38 0.34
81 2 0.02
82 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.27
Consensus pattern (79 bp):
AAGTAAAAATGAGGTTAGAGTATCTTTCGGAGATGGTGGGGTTGAAGTATCCCAGAGATGAAAAA
CTTTGGCATTATAG
Found at i:105862 original size:4 final size:4
Alignment explanation
Indices: 105847--105886 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
105837 TTTCATATTC
*
105847 TCTT TTTT TCTT TCTT TC-T TC-T TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC
105887 GTTTGATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 6 0.18
4 27 0.82
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:105871 original size:14 final size:14
Alignment explanation
Indices: 105854--105880 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
105844 TTCTCTTTTT
105854 TTCTTTCTTTCTTC
1 TTCTTTCTTTCTTC
105868 TTCTTTCTTTCTT
1 TTCTTTCTTTCTT
105881 TCTTTCGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTTCTTTCTTC
Done.