Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014046.1 Kokia drynarioides strain JFW-HI SEQ_129077, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 246777
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:963 original size:16 final size:17
Alignment explanation
Indices: 942--973 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
932 TCTTACCTCA
942 TAATATAA-TATATTTT
1 TAATATAATTATATTTT
958 TAATATAATTATATTT
1 TAATATAATTATATTT
974 ATACAGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATATAATTATATTTT
Found at i:4771 original size:21 final size:20
Alignment explanation
Indices: 4706--4779 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
4696 AAAAATATCC
*
4706 TTAAAATCTTAAAAA--AAA
1 TTAAAATTTTAAAAATTAAA
*
4724 TTAATATTTTTAAAAATTAACA
1 TTAA-AATTTTAAAAATTAA-A
*
4746 -GAAAATTTTAAAAATTAAA
1 TTAAAATTTTAAAAATTAAA
*
4765 TTTAAAAATTTAAAA
1 -TTAAAATTTTAAAA
4780 GCTTAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 4 0.09
19 10 0.23
20 14 0.32
21 15 0.34
22 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (20 bp):
TTAAAATTTTAAAAATTAAA
Found at i:7361 original size:22 final size:22
Alignment explanation
Indices: 7333--7376 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
7323 ATTATATATA
7333 CTTTTTCGGTGATAATAATCGG
1 CTTTTTCGGTGATAATAATCGG
7355 CTTTTTCGGTGATAATAATCGG
1 CTTTTTCGGTGATAATAATCGG
7377 TACATACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.41
Consensus pattern (22 bp):
CTTTTTCGGTGATAATAATCGG
Found at i:18652 original size:79 final size:79
Alignment explanation
Indices: 18550--18852 Score: 412
Period size: 79 Copynumber: 3.9 Consensus size: 79
18540 GCTCGTAAAC
* * *
18550 ATAAATT-GAATAATTCTGTTTCAAGATTTATTCCTGCCGTTCAACAGAATTAATTCGAGTTTCT
1 ATAAATTAAAATAATTCTGTTTCAAGATTTATTCCTACCGTTCAATAGAATTAATTCGAGTTTCT
*
18614 GTTTCAAAACAAGA
66 GTTTCAAAACAAAA
* * *
18628 ATAAATTAAAATAATTCTGTTTCAAGATTTATTTCTACCGTTCAATAGAATTAATTTGAGTTTTT
1 ATAAATTAAAATAATTCTGTTTCAAGATTTATTCCTACCGTTCAATAGAATTAATTCGAGTTTCT
18693 GTTTCAAAACAAAA
66 GTTTCAAAACAAAA
* * * *** * * *
18707 AAAAATTAAAATAATTATGTTTCAGGATTTATTCCCGTCGTTCAATAGAATTCATTCAAGTTTTT
1 ATAAATTAAAATAATTCTGTTTCAAGATTTATTCCTACCGTTCAATAGAATTAATTCGAGTTTCT
*
18772 GTTTCCAAACAAAA
66 GTTTCAAAACAAAA
* * *
18786 ATAAATTAAAATAATTCTGTTTCAGGATTTATTTCTACCGTTCAATAGAATTTATTCGA-TTTCT
1 ATAAATTAAAATAATTCTGTTTCAAGATTTATTCCTACCGTTCAATAGAATTAATTCGAGTTTCT
18850 GTT
66 GTT
18853 GTTAACAGTA
Statistics
Matches: 197, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
78 14 0.07
79 183 0.93
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (79 bp):
ATAAATTAAAATAATTCTGTTTCAAGATTTATTCCTACCGTTCAATAGAATTAATTCGAGTTTCT
GTTTCAAAACAAAA
Found at i:19114 original size:31 final size:31
Alignment explanation
Indices: 19076--19160 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
19066 GACTTTATTA
*
19076 TTAAATTGTGGCCTTAAATTGTGACAAAACC
1 TTAAATTGTGGCATTAAATTGTGACAAAACC
* ** *
19107 TTAAATTGTGGTATTAAATTAAGACAAAAGC
1 TTAAATTGTGGCATTAAATTGTGACAAAACC
* *
19138 TTAAATTGTAGCTTTAAATTGTG
1 TTAAATTGTGGCATTAAATTGTG
19161 GCATCAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (31 bp):
TTAAATTGTGGCATTAAATTGTGACAAAACC
Found at i:22902 original size:15 final size:15
Alignment explanation
Indices: 22884--22929 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
22874 ATGACAAATA
*
22884 TTAAAATAATTTAAT
1 TTAAAATGATTTAAT
*
22899 TTAAACTGATTTAAT
1 TTAAAATGATTTAAT
*
22914 TTAAATTGATTTAAT
1 TTAAAATGATTTAAT
22929 T
1 T
22930 GATTTAATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (15 bp):
TTAAAATGATTTAAT
Found at i:29519 original size:33 final size:33
Alignment explanation
Indices: 29477--29544 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
29467 TTAAATTATA
29477 AAGTGTTAGGTTATAATTCCAAAAAGCACAAAT
1 AAGTGTTAGGTTATAATTCCAAAAAGCACAAAT
29510 AAGTGTTAGGTTATAATTCCAAAAAGCACAAAT
1 AAGTGTTAGGTTATAATTCCAAAAAGCACAAAT
29543 AA
1 AA
29545 TTTGACCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (33 bp):
AAGTGTTAGGTTATAATTCCAAAAAGCACAAAT
Found at i:32395 original size:26 final size:26
Alignment explanation
Indices: 32366--32447 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
32356 GTCATCGAAC
32366 CTCATAATTCGTAAAGGATTCATATA
1 CTCATAATTCGTAAAGGATTCATATA
* * * * **
32392 CTCATGA-T-G-ACACGTAGTCATCGGA
1 CTCATAATTCGTA-AAGGATTCAT-ATA
32417 CCTCATAATTCGTAAAGGATTCATATA
1 -CTCATAATTCGTAAAGGATTCATATA
32444 CTCA
1 CTCA
32448 CGATGACACA
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
23 1 0.03
24 8 0.21
25 2 0.05
26 16 0.42
27 2 0.05
28 8 0.21
29 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (26 bp):
CTCATAATTCGTAAAGGATTCATATA
Found at i:32397 original size:52 final size:52
Alignment explanation
Indices: 32337--32499 Score: 281
Period size: 52 Copynumber: 3.1 Consensus size: 52
32327 GTTTCATTTA
*
32337 ATACTCATGATGACACATAGTCATCGAACCTCATAATTCGTAAAGGATTCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
*
32389 ATACTCATGATGACACGTAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
* * *
32441 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
32493 ATACTCA
1 ATACTCA
32500 CGATTTTTGC
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 105 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (52 bp):
ATACTCATGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
Found at i:43734 original size:17 final size:17
Alignment explanation
Indices: 43712--43746 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
43702 CTTTATAAGC
43712 TTTTTGAAGTAGATTTT
1 TTTTTGAAGTAGATTTT
43729 TTTTTGAAGTAGATTTT
1 TTTTTGAAGTAGATTTT
43746 T
1 T
43747 AGTGGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (17 bp):
TTTTTGAAGTAGATTTT
Found at i:47291 original size:30 final size:28
Alignment explanation
Indices: 47239--47627 Score: 210
Period size: 30 Copynumber: 13.2 Consensus size: 28
47229 ATTCGGGATA
* *
47239 AAAATGTAATTTTCGAGGAATTTAGGGGTC
1 AAAATGTAATTTTGGA-AAATTT-GGGGTC
* * *
47269 AAAATTGAAATTTTGGAAAATTTGGGATT
1 AAAA-TGTAATTTTGGAAAATTTGGGGTC
* * *
47298 AAAATTGCACTTTTGGAAAATTTGAGGTC
1 AAAA-TGTAATTTTGGAAAATTTGGGGTC
*
47327 GAAAATGTGACTTTTGG-AAATTTGGGGGT-
1 -AAAATGT-AATTTTGGAAAATTT-GGGGTC
* ** *
47356 AAAATGGTAATTTTTGAATGTTTGGGGGC
1 AAAAT-GTAATTTTGGAAAATTTGGGGTC
* * * *
47385 -AAATGGTAATTTTTGGATGAGTTT-GGTTG
1 AAAAT-GTAA-TTTTGGA-AAATTTGGGGTC
* * *
47414 AAAATGTAATTTTGAGAAAGTTTAGGGTTA
1 AAAATGTAATTTTG-GAAAATTT-GGGGTC
** *
47444 AAAATACAATTTTGGAAAAGTTTGGGGTT
1 AAAATGTAATTTTGGAAAA-TTTGGGGTC
* * * *
47473 AAAATGTAATTTTAGAGAAGTTTGAGAGTT
1 AAAATGTAATTTTGGA-AAATTTG-GGGTC
**
47503 AAAATGGGATTTTGGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGAAAA-TTT-GGGGTC
* *
47533 AAAATGTAATTTTAGAGAAGTTTGGTGGTC
1 AAAATGTAATTTTGGA-AAATTTGG-GGTC
* * *
47563 AAAATGTAATTTTAGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAA-TTT-GGGGTC
* *
47593 AAAATGTAATTTTAGAAAAGTTTAGGGTTC
1 AAAATGTAATTTTGGAAAA-TTT-GGGGTC
47623 AAAAT
1 AAAAT
47628 ATGATTTTTG
Statistics
Matches: 286, Mismatches: 51, Indels: 44
0.75 0.13 0.12
Matches are distributed among these distances:
28 34 0.12
29 87 0.30
30 151 0.53
31 14 0.05
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAATTTGGGGTC
Found at i:47370 original size:29 final size:29
Alignment explanation
Indices: 47338--47426 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
47328 AAAATGTGAC
47338 TTTTGGAA-ATTTGGGGGTAAAATGGTAAT
1 TTTTGGAATATTTGGGGG-AAAATGGTAAT
* *
47367 TTTT-GAATGTTTGGGGGCAAATGGTAAT
1 TTTTGGAATATTTGGGGGAAAATGGTAAT
**
47395 TTTTGG-ATGAGTTTGGTTGAAAAT-GTAAT
1 TTTTGGAAT-A-TTTGGGGGAAAATGGTAAT
47424 TTT
1 TTT
47427 GAGAAAGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 19 0.38
29 21 0.42
30 10 0.20
ACGTcount: A:0.27, C:0.01, G:0.29, T:0.43
Consensus pattern (29 bp):
TTTTGGAATATTTGGGGGAAAATGGTAAT
Found at i:47537 original size:60 final size:60
Alignment explanation
Indices: 47409--47627 Score: 268
Period size: 60 Copynumber: 3.6 Consensus size: 60
47399 GGATGAGTTT
*
47409 GGTTGAAAATGTAATTTT-GAGAAAGTTT-AGGGTTAAAAATACAATTTTGGAAAAGTTT-GG
1 GGTT-AAAATGTAATTTTAGAG-AAGTTTGAGGGTT-AAAATGCAATTTTGGAAAAGTTTAGG
* **
47469 GGTTAAAATGTAATTTTAGAGAAGTTTGAGAGTTAAAATGGGATTTTGGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTAGAGAAGTTTGAGGGTTAAAATGCAATTTTGGAAAAGTTTAGG
* * * * *
47529 GGTCAAAATGTAATTTTAGAGAAGTTTG-GTGGTCAAAATGTAATTTTAGAAAAGTTTAAG
1 GGTTAAAATGTAATTTTAGAGAAGTTTGAG-GGTTAAAATGCAATTTTGGAAAAGTTTAGG
*
47589 GGTTAAAATGTAATTTTAGAAAAGTTT-AGGGTTCAAAAT
1 GGTTAAAATGTAATTTTAGAGAAGTTTGAGGGTT-AAAAT
47628 ATGATTTTTG
Statistics
Matches: 139, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
59 43 0.31
60 96 0.69
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (60 bp):
GGTTAAAATGTAATTTTAGAGAAGTTTGAGGGTTAAAATGCAATTTTGGAAAAGTTTAGG
Found at i:47635 original size:30 final size:29
Alignment explanation
Indices: 47409--47627 Score: 242
Period size: 30 Copynumber: 7.3 Consensus size: 29
47399 GGATGAGTTT
47409 GGTTGAAAATGTAATTTT-GAGAAAGTTTAG
1 GGTT-AAAATGTAATTTTAGA-AAAGTTTAG
** * *
47439 GGTTAAAAATACAATTTTGGAAAAGTTTGG
1 GGTT-AAAATGTAATTTTAGAAAAGTTTAG
*
47469 GGTTAAAATGTAATTTTAGAGAAGTTTGAG
1 GGTTAAAATGTAATTTTAGAAAAGTTT-AG
* ** *
47499 AGTTAAAATGGGATTTTGGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTAGAAAAGTTTA-G
* * *
47529 GGTCAAAATGTAATTTTAGAGAAGTTTGG
1 GGTTAAAATGTAATTTTAGAAAAGTTTAG
*
47558 TGGTCAAAATGTAATTTTAGAAAAGTTTAAG
1 -GGTTAAAATGTAATTTTAGAAAAGTTT-AG
47589 GGTTAAAATGTAATTTTAGAAAAGTTTAG
1 GGTTAAAATGTAATTTTAGAAAAGTTTAG
47618 GGTTCAAAAT
1 GGTT-AAAAT
47628 ATGATTTTTG
Statistics
Matches: 159, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
29 27 0.17
30 129 0.81
31 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
GGTTAAAATGTAATTTTAGAAAAGTTTAG
Found at i:47635 original size:90 final size:88
Alignment explanation
Indices: 47409--47640 Score: 293
Period size: 90 Copynumber: 2.6 Consensus size: 88
47399 GGATGAGTTT
* * * *
47409 GGTTGAAAATGTAATTTTGAGAAAGTTTAGGGTTAAAAATACAATTTTGGAAAAGTTTGGGGTTA
1 GGTT-AAAATGTAATTTTGA-AAAGTTTAGGGTTCAAAATATAATTTTAGAAAAGTTTGGGGTCA
* *
47474 AAATGTAATTTTAGAGAAGTTTGAG
64 AAATGTAATTTTAGAAAAGTTTAAG
* ** * * *
47499 AGTTAAAATGGGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAAGTTTGGTGGTCA
1 GGTTAAAATGTAATTTT-GAAAAGTTTAGGGTTCAAAATATAATTTTAGAAAAGTTTGG-GGTCA
47564 AAATGTAATTTTAGAAAAGTTTAAG
64 AAATGTAATTTTAGAAAAGTTTAAG
* *
47589 GGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTCAAAATATGATTTTTGAAA
1 GGTTAAAATGTAATTTT-GAAAAGTTTAGGGTTCAAAATATAATTTTAGAAA
47641 GAAAATAGGG
Statistics
Matches: 119, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
89 44 0.37
90 75 0.63
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (88 bp):
GGTTAAAATGTAATTTTGAAAAGTTTAGGGTTCAAAATATAATTTTAGAAAAGTTTGGGGTCAAA
ATGTAATTTTAGAAAAGTTTAAG
Found at i:48575 original size:20 final size:20
Alignment explanation
Indices: 48550--48588 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48540 TTTAAACTTC
* *
48550 TTATTTATTATTATTATTAT
1 TTATTTAATATTATAATTAT
48570 TTATTTAATATTATAATTA
1 TTATTTAATATTATAATTA
48589 ATATGCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTAATATTATAATTAT
Found at i:49945 original size:39 final size:39
Alignment explanation
Indices: 49902--50353 Score: 302
Period size: 39 Copynumber: 11.6 Consensus size: 39
49892 GATGGCTACA
*
49902 ATCTGCCCCAGGCTCGGGGTGAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** * * *
49941 ATCTGTCATAGGCTTGGGATAAAAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
*
49980 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * ** *** **
50019 ATCTGTCCCAAGCTCGGGATAAAAGATCGAATGGCAGCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * *
50058 ATTTGCCCTAAGCTCGGGGTAAGAGATTTGTTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* *
50097 ATTTGCCCCAGGCTCGGGGTAAAAGATT-G--GATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGG-TG
* ** * *
50134 CAATCTACCTAAGGCTCGGGGTAAGAGATTGGATGATAGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * * * *
50175 ATCTACCCTAGGCTCGGGGTAAAAGATCGGATGGTTGTA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
** * *
50214 ATCTGCCTTAGGCTCGGGGTAAGAGATTGGCTTATTGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * ** * **
50253 ATTTGCCCCAAGG-TTGGGGTAAAAGATAAGATGACT-GCA
1 ATCTGCCCC-AGGCTCGGGGTAAGAGATTGGCTGA-TGGTG
* * * *
50292 ATCTGCCTCAAGCTCGGGGTAAGAGATTAGCTGATGGTA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* *
50331 ATCTACCCTAGGCTCGGGGTAAG
1 ATCTGCCCCAGGCTCGGGGTAAG
50354 TGATCAGAAT
Statistics
Matches: 317, Mismatches: 86, Indels: 20
0.75 0.20 0.05
Matches are distributed among these distances:
36 5 0.02
37 2 0.01
38 4 0.01
39 295 0.93
40 5 0.02
41 2 0.01
42 4 0.01
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:50349 original size:156 final size:157
Alignment explanation
Indices: 49795--50352 Score: 565
Period size: 156 Copynumber: 3.6 Consensus size: 157
49785 TACCCCATGA
* * * * * * * ** *
49795 TTGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGATAAGAGATCGAATGATT
1 TTGGGGTAAAAGATTGGATGA---CTGCAATCTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATG
* * * * * * *
49860 GCAATCTGCCCTAGGCTCGAGGTAAAAGTTCGGATGGCTACAATCTGCCCCAGGCTCGGGGTGAG
63 GTAATCTACCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAG
* * *
49925 AGATTGGCTGATGGTGATCTG--TCATAGGC
128 AGATTGGCTTATGGTGATTTGCCCCA-AGGC
* * ** *
49954 TTGGGATAAAAGATTGGCTGA-TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGT
1 TTGGGGTAAAAGATTGGATGACT-GCAATCTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGT
* * * * * * * *
50018 GATCTGTCCC-AAGCTCGGGATAAAAGATCGAATGGCAGCAATTTGCCCTAAGCTCGGGGTAAGA
65 AATCT-ACCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGA
*
50082 GATTTG-TTGATGGTGATTTGCCCC-AGGC
129 GATTGGCTT-ATGGTGATTTGCCCCAAGGC
* * * * *
50110 TCGGGGTAAAAGATTGGATGGCTGCAATCTACCT-AAGGCTCGGGGTAAGAGATTGGATGATAGT
1 TTGGGGTAAAAGATTGGATGACTGCAATCTGCCTCAA-GCTCGGGGTAAGAGATTGGCTGATGGT
* * * *
50174 GATCTACCCTAGGCTCGGGGTAAAAGATCGGATGGTTGTAATCTGCCTTAGGCTCGGGGTAAGAG
65 AATCTACCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAG
*
50239 ATTGGCTTATTGTGATTTGCCCCAAGG-
130 ATTGGCTTATGGTGATTTGCCCCAAGGC
** *
50266 TTGGGGTAAAAGATAAGATGACTGCAATCTGCCTCAAGCTCGGGGTAAGAGATTAGCTGATGGTA
1 TTGGGGTAAAAGATTGGATGACTGCAATCTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGTA
50331 ATCTACCCTAGGCTCGGGGTAA
66 ATCTACCCTAGGCTCGGGGTAA
50353 GTGATCAGAA
Statistics
Matches: 326, Mismatches: 62, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
155 7 0.02
156 289 0.89
157 11 0.03
158 1 0.00
159 18 0.06
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (157 bp):
TTGGGGTAAAAGATTGGATGACTGCAATCTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGTA
ATCTACCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGA
TTGGCTTATGGTGATTTGCCCCAAGGC
Found at i:50350 original size:78 final size:78
Alignment explanation
Indices: 49863--50352 Score: 499
Period size: 78 Copynumber: 6.3 Consensus size: 78
49853 AATGATTGCA
* * * * * *
49863 ATCTGCCCTAGGCTCGAGGTAAAAGTTCGGATGGCTACAATCTGCCCCAGGCTCGGGGTGAGAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCTCAAGCTCGGGGTAAGAGA
49928 TTGGCTGATGGTG
66 TTGGCTGATGGTG
* * * * * *
49941 ATCTGTCATAGGCTTGGGATAAAAGATTGGCTGATGG-TG--ATCTGCCCCAAGCTCGGGGTAAG
1 ATCTGCCCTAGGCTCGGGGTAAAAGA-T--CGGATGGCTGCAATCTGCCTCAAGCTCGGGGTAAG
50003 AGATTGGCTGATGGTG
63 AGATTGGCTGATGGTG
* * * * *
50019 ATCTGTCCC-AAGCTCGGGATAAAAGATCGAATGGCAGCAATTTGCC-CTAAGCTCGGGGTAAGA
1 ATCTG-CCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCTC-AAGCTCGGGGTAAGA
* *
50082 GATTTGTTGATGGTG
64 GATTGGCTGATGGTG
* * * *
50097 ATTTGCCCCAGGCTCGGGGTAAAAGATTGGATGGCTGCAATCTACCT-AAGGCTCGGGGTAAGAG
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCTCAA-GCTCGGGGTAAGAG
* *
50161 ATTGGATGATAGTG
65 ATTGGCTGATGGTG
* * * * *
50175 ATCTACCCTAGGCTCGGGGTAAAAGATCGGATGGTTGTAATCTGCCTTAGGCTCGGGGTAAGAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCTCAAGCTCGGGGTAAGAGA
* *
50240 TTGGCTTATTGTG
66 TTGGCTGATGGTG
* * * ** *
50253 ATTTGCCCCAAGG-TTGGGGTAAAAGATAAGATGACTGCAATCTGCCTCAAGCTCGGGGTAAGAG
1 ATCTG-CCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCTCAAGCTCGGGGTAAGAG
* *
50317 ATTAGCTGATGGTA
65 ATTGGCTGATGGTG
*
50331 ATCTACCCTAGGCTCGGGGTAA
1 ATCTGCCCTAGGCTCGGGGTAA
50353 GTGATCAGAA
Statistics
Matches: 337, Mismatches: 61, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
75 5 0.01
76 1 0.00
77 13 0.04
78 302 0.90
79 9 0.03
80 1 0.00
81 6 0.02
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (78 bp):
ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCTCAAGCTCGGGGTAAGAGA
TTGGCTGATGGTG
Found at i:55623 original size:6 final size:6
Alignment explanation
Indices: 55598--55636 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
55588 ACAACTAATA
* * *
55598 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
55637 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:60317 original size:32 final size:33
Alignment explanation
Indices: 60274--60348 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 33
60264 TCCAGTATAA
*
60274 GAGTATTACATACAATGTCCGA-AATTAAAAAC
1 GAGTATAACATACAATGTCCGAGAATTAAAAAC
60306 GAGTATAACATACAATGTCCGAGAATTAAAAAC
1 GAGTATAACATACAATGTCCGAGAATTAAAAAC
60339 GAGTATAACA
1 GAGTATAACA
60349 AAATTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 21 0.51
33 20 0.49
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.23
Consensus pattern (33 bp):
GAGTATAACATACAATGTCCGAGAATTAAAAAC
Found at i:69211 original size:279 final size:284
Alignment explanation
Indices: 68699--69274 Score: 790
Period size: 279 Copynumber: 2.0 Consensus size: 284
68689 TGACTTATGC
* * *
68699 TAAAAACGATTGATTCAATATGCCACATGTTGTGCAAATTTAATAGCTCAATTACGCTTATGCCT
1 TAAAAACGATTGATCCAATATGCCACATGTTGTACAAATTTAATAGCCCAATTACGCTTATGCCT
*
68764 CAAATGCAAATTTATGGATGATAGTCATCCATGTTCTCTAGATCTATTAGAATTCCTTGGAACAT
66 CAAACGCAAATTTATGGATGATAG--ATCCATG-----T-GATCTATTAGAATTCCTTGGAACAT
* *
68829 CCCAAACTATCATAATACCTCACTCGGTTGATGCCACTCAATGTAGGAAAACCATATAAGGGAAA
123 CCCAAACTATCATAATACCTCACTCAGTTGATGCCACTCAATATAGGAAAACCATATAAGGGAAA
* *
68894 TGTGGATAGTAAAAACATGGTTGTGCACACATGCCCCTAGTGGTAGTATGGTTACAATATA-TTC
188 TGTGGATAGTAAAAACATGGTTGTACACACATGCCCCTAGTCGTAGTATGGTTACAATATATTTC
* * *
68958 TGCTTGGTACGACATCCACAAAAATTGC-AAAA
253 -GCTTGGTACGACATCCAAAAAAACTACAAAAA
68990 TAAAAACGATTGATCCAATATGCCACATGTTGTACAAATTTAATAGCCCAATTACGCTTATGCCT
1 TAAAAACGATTGATCCAATATGCCACATGTTGTACAAATTTAATAGCCCAATTACGCTTATGCCT
* * * * *
69055 CGACCG-AAATTTTTGGATGATAG-T-CATG-GATTTGTTAGAA-TCACTTGGAACATCCCAAAC
66 CAAACGCAAATTTATGGATGATAGATCCATGTGATCTATTAGAATTC-CTTGGAACATCCCAAAC
* * * *
69115 TATTATAATACCTCACTCAGTTGATGCCACTCGATATAGGAAAAGCATATAAGAGG-CATGTGGA
130 TATCATAATACCTCACTCAGTTGATGCCACTCAATATAGGAAAACCATATAAG-GGAAATGTGGA
* *
69179 TGGTAAAAACATGGTTGTACACACATGCCCCTAGTCGTAGTATGGTTACAATATCTTTCGCTTGG
194 TAGTAAAAACATGGTTGTACACACATGCCCCTAGTCGTAGTATGGTTACAATATATTTCGCTTGG
*
69244 TACGATATCCAAAAAAACTACAAAAA
259 TACGACATCCAAAAAAACTACAAAAA
69270 TAAAA
1 TAAAA
69275 TTATTGAATT
Statistics
Matches: 258, Mismatches: 23, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
278 2 0.01
279 156 0.60
280 14 0.05
286 4 0.02
287 1 0.00
290 16 0.06
291 65 0.25
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (284 bp):
TAAAAACGATTGATCCAATATGCCACATGTTGTACAAATTTAATAGCCCAATTACGCTTATGCCT
CAAACGCAAATTTATGGATGATAGATCCATGTGATCTATTAGAATTCCTTGGAACATCCCAAACT
ATCATAATACCTCACTCAGTTGATGCCACTCAATATAGGAAAACCATATAAGGGAAATGTGGATA
GTAAAAACATGGTTGTACACACATGCCCCTAGTCGTAGTATGGTTACAATATATTTCGCTTGGTA
CGACATCCAAAAAAACTACAAAAA
Found at i:73259 original size:15 final size:17
Alignment explanation
Indices: 73226--73262 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
73216 TAGGTTCATA
*
73226 ATATATTATATTATGTT
1 ATATATTATATTATATT
73243 ATATA-TATA-TATATT
1 ATATATTATATTATATT
73258 ATATA
1 ATATA
73263 ATTTATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 4 0.21
17 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATTATATTATATT
Found at i:76417 original size:25 final size:25
Alignment explanation
Indices: 76389--76457 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
76379 TCAATCAAAT
76389 TTATCAATTAAAATCA-TATTAAAAA
1 TTATCAATTAAAAT-ATTATTAAAAA
*
76414 TTATCAATTAAAATATTATTAAATA
1 TTATCAATTAAAATATTATTAAAAA
76439 TT-T-AATTAAAA-ATTCATTA
1 TTATCAATTAAAATATT-ATTA
76458 CTAATAAAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
22 3 0.07
23 12 0.29
24 2 0.05
25 24 0.59
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (25 bp):
TTATCAATTAAAATATTATTAAAAA
Found at i:76570 original size:34 final size:34
Alignment explanation
Indices: 76525--76593 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
76515 TCAACCTTTC
* * * *
76525 ATCTCCTTTGACTTTTAACTTTTCATCTTCCTTA
1 ATCTCCCTTGACCTTTAACCTTCCATCTTCCTTA
* *
76559 ATCTCCCTTGACCTTTAGCCTTCCATCTTTCTTA
1 ATCTCCCTTGACCTTTAACCTTCCATCTTCCTTA
76593 A
1 A
76594 CCTTTTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.17, C:0.30, G:0.04, T:0.48
Consensus pattern (34 bp):
ATCTCCCTTGACCTTTAACCTTCCATCTTCCTTA
Found at i:77096 original size:35 final size:33
Alignment explanation
Indices: 77057--77133 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
77047 GTATTTTTCT
* * *
77057 CTTATATTATGCTTGAAAGTTTTGTTAAGGGATTA
1 CTTATATT-TGCTTGAAA-ATTTGTTAAAGGACTA
*
77092 CTTATGTTTGCTTGAAAATTTGTTAAAGGACTA
1 CTTATATTTGCTTGAAAATTTGTTAAAGGACTA
*
77125 CTGATATTT
1 CTTATATTT
77134 ACATTAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 20 0.56
34 9 0.25
35 7 0.19
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (33 bp):
CTTATATTTGCTTGAAAATTTGTTAAAGGACTA
Found at i:82011 original size:17 final size:17
Alignment explanation
Indices: 81989--82047 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
81979 CCCTTGACTT
81989 TTAACCTTCCATTTTCC
1 TTAACCTTCCATTTTCC
* **
82006 TTAACC-TCCCTTGACC
1 TTAACCTTCCATTTTCC
*
82022 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATTTTCC
82040 TTAACCTT
1 TTAACCTT
82048 TCATATTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 7 0.21
17 20 0.61
18 6 0.18
ACGTcount: A:0.19, C:0.37, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAACCTTCCATTTTCC
Found at i:82020 original size:34 final size:34
Alignment explanation
Indices: 81977--82046 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
81967 AACCTTTCAT
* *
81977 CTCCCTTGACTTTTAACCTTCCATTTTCCTTAAC
1 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
82011 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
1 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
82045 CT
1 CT
82047 TTCATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.17, C:0.39, G:0.03, T:0.41
Consensus pattern (34 bp):
CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
Found at i:82904 original size:15 final size:16
Alignment explanation
Indices: 82883--82920 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
82873 AAATAAAAAC
82883 ATAAAAATAT-AATTT
1 ATAAAAATATAAATTT
* *
82898 TTAAAAATCTAAATTT
1 ATAAAAATATAAATTT
82914 ATAAAAA
1 ATAAAAA
82921 AAACTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAAAATATAAATTT
Found at i:82949 original size:21 final size:21
Alignment explanation
Indices: 82907--82963 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
82897 TTTAAAAATC
* *
82907 TAAATTTATAAAAAA-AACTT
1 TAAATATAAAAAAAATAACTT
*
82927 TATAAT-TAAAAAAAATAATTT
1 TA-AATATAAAAAAAATAACTT
*
82948 TAAATATATAAAAAAT
1 TAAATATAAAAAAAAT
82964 TTCCAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATAAAAAAAATAACTT
Found at i:87895 original size:59 final size:61
Alignment explanation
Indices: 87824--87939 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 61
87814 ATCACTTTAA
* * * *
87824 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
87883 TATTAAAATAATAAAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTA
1 TATTAAAATAATAAAATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTA
87940 TGATAACATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (61 bp):
TATTAAAATAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:90398 original size:39 final size:39
Alignment explanation
Indices: 90324--90459 Score: 101
Period size: 39 Copynumber: 3.5 Consensus size: 39
90314 ATGAAATTAG
* **
90324 TAGTGACACTGTAAACACTACAATATTATGTTGAACCGA
1 TAGTGACACTGTAAACACTACAATACTATACTGAACCGA
* * * * *
90363 TAGTGACACTGTAAACACTGCATTGCTATACTGAACTGG
1 TAGTGACACTGTAAACACTACAATACTATACTGAACCGA
** * ** * * ** *
90402 CGGTGATACTGTAAACACCGCAATACTGTACTAAAGTGG
1 TAGTGACACTGTAAACACTACAATACTATACTGAACCGA
*
90441 TAGTGACACTATAAACACT
1 TAGTGACACTGTAAACACT
90460 CTCAGACTGT
Statistics
Matches: 75, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (39 bp):
TAGTGACACTGTAAACACTACAATACTATACTGAACCGA
Found at i:91032 original size:26 final size:26
Alignment explanation
Indices: 91002--91072 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
90992 AATGTGTTAA
*
91002 CTGATTTGTGATTGAACTGTTACCAG
1 CTGATTTGTGATTGAACTGATACCAG
* * * *
91028 CTGATCTCTGACTGAACTGATATCAG
1 CTGATTTGTGATTGAACTGATACCAG
*
91054 TTG-TTATGTGATTGAACTG
1 CTGATT-TGTGATTGAACTG
91073 CTAACTGACG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGATTTGTGATTGAACTGATACCAG
Found at i:98832 original size:18 final size:18
Alignment explanation
Indices: 98809--98848 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
98799 TTTGTTCGTC
*
98809 TATTTATAATGTCCAAAA
1 TATTTATAATATCCAAAA
98827 TATTTATAATATCCAAAA
1 TATTTATAATATCCAAAA
98845 TATT
1 TATT
98849 ACAAGTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (18 bp):
TATTTATAATATCCAAAA
Found at i:99467 original size:38 final size:38
Alignment explanation
Indices: 99416--99492 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
99406 TGTCCTCAAG
99416 TAAACAAAAATAAACAAAGTCCCAATTAGAAATGTCAC
1 TAAACAAAAATAAACAAAGTCCCAATTAGAAATGTCAC
99454 TAAACAAAAATAAACAAAGTCCCAATTAGAAATGTCAC
1 TAAACAAAAATAAACAAAGTCCCAATTAGAAATGTCAC
99492 T
1 T
99493 GCAATCATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.55, C:0.18, G:0.08, T:0.19
Consensus pattern (38 bp):
TAAACAAAAATAAACAAAGTCCCAATTAGAAATGTCAC
Found at i:110928 original size:53 final size:53
Alignment explanation
Indices: 110847--111201 Score: 424
Period size: 53 Copynumber: 6.7 Consensus size: 53
110837 TTGTGCAAAA
* * *
110847 GATTAAAGGTCCGATGACTCTATTTCATCGTGAGTTATATGAATCCTATCACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
* * *
110900 GATTAAAGGTCTGATGACCCTGTGTCATCGTTAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
** * * * * **
110953 GATTAAAGGTCAAATGACTCTGTGTTATCATGAGTTATATGAACCCTATGACA
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
* * * *
111006 GATTAAAGGTCTGATAACTCTGTGTCCTCGTGAGTTATATAAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
* * * * * *
111059 AATTTAAGGTCCGATGACTATTTGTCATCGTGAGTTATATGAATCTTATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
* * * *
111112 GATTAAGGGTCCAATGACTTTGTGTCATCGTGAGTTACATGAATCC-ATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
* * *
111164 GATTAAAGGTCCGATGACTCTGTATCATCTTTAGTTAT
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
111202 CAAATGCGAA
Statistics
Matches: 249, Mismatches: 53, Indels: 1
0.82 0.17 0.00
Matches are distributed among these distances:
52 36 0.14
53 213 0.86
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
Found at i:111925 original size:20 final size:21
Alignment explanation
Indices: 111881--111936 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
111871 TAGAAGTAAG
*
111881 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAAGAGTC
111902 ACTTGTATCGGTA-AA-AGTTC
1 ACTTGTATCGGTAGAAGAG-TC
*
111922 ACTTATATCGGTAGA
1 ACTTGTATCGGTAGA
111937 GGTTTGCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.52
21 13 0.42
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGAGTC
Found at i:118195 original size:53 final size:53
Alignment explanation
Indices: 118115--118416 Score: 419
Period size: 53 Copynumber: 5.7 Consensus size: 53
118105 TTATGCCAAA
* * *
118115 GATTAAAGGTCCGATGACTTTGTGTCATCGTGTGTTATATGAATCCTATCACG
1 GATTAAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* *
118168 GATTAAAGGTTCGATGACTCTGTGTCATCGTAAGTTATATGAATCTTATCACG
1 GATTAAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * *
118221 GATTAAAGGTTTGATGACTCTGTGTCATTGTGAGTTATATGAATCCTATCATG
1 GATTAAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* *
118274 GATTAAAGG-TCTGATGACTATGTGTCATCGTGAGTTATATGAATCCTATTACG
1 GATTAAAGGTTC-GATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * * * * * *
118327 GATTAAGGGTCCGATGACTTTGTGTCATCATGAGTTACACGAATCC-ATCAAG
1 GATTAAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
*
118379 GATAAAAGGTTCGATGACTCTGTGTCATCGTGAGTTAT
1 GATTAAAGGTTCGATGACTCTGTGTCATCGTGAGTTAT
118417 CAAATGTGAA
Statistics
Matches: 218, Mismatches: 29, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
52 37 0.17
53 180 0.83
54 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (53 bp):
GATTAAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
Found at i:124318 original size:77 final size:77
Alignment explanation
Indices: 124191--124345 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 77
124181 AAAGAGAAAG
* *
124191 TAACGGAATAGTCCCTGTACCTTGACGAATACTGCAACTTAGTCTGGTAAGTTCGTACTATTTAT
1 TAACGGAATAGTCCCTATACCTTGACGAATACTGCAACTTAGTCTAGTAAGTTCGTACTATTTAT
124256 TTCTCCATTTAA
66 TTCTCCATTTAA
*
124268 TAACGGAATAGTCCCTATACCTTGACGAATACTGTAACTTAGTCTAGTAAGTTCGTACTATTTAT
1 TAACGGAATAGTCCCTATACCTTGACGAATACTGCAACTTAGTCTAGTAAGTTCGTACTATTTAT
124333 TTCTCCATTTAA
66 TTCTCCATTTAA
124345 T
1 T
124346 GCTTGCAAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (77 bp):
TAACGGAATAGTCCCTATACCTTGACGAATACTGCAACTTAGTCTAGTAAGTTCGTACTATTTAT
TTCTCCATTTAA
Found at i:124483 original size:28 final size:28
Alignment explanation
Indices: 124409--124485 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
124399 GCTTGAGAAA
* * *
124409 TATTCTGTATTCTGGCTCAAAAGAACGT
1 TATTCTGTATTTTGGCTCGAAAGAACAT
*
124437 TATTCTGTATTTTGGCTCGAAAGAGCAT
1 TATTCTGTATTTTGGCTCGAAAGAACAT
*
124465 TATTTTGTATTTTGGCTCGAA
1 TATTCTGTATTTTGGCTCGAA
124486 GCATTTTTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (28 bp):
TATTCTGTATTTTGGCTCGAAAGAACAT
Found at i:143842 original size:23 final size:23
Alignment explanation
Indices: 143816--143859 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
143806 TTCATTTAAC
*
143816 TTAATCGAACATGTTCACGAATA
1 TTAAACGAACATGTTCACGAATA
*
143839 TTAAACGAATATGTTCACGAA
1 TTAAACGAACATGTTCACGAA
143860 CATATTCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (23 bp):
TTAAACGAACATGTTCACGAATA
Found at i:144371 original size:40 final size:39
Alignment explanation
Indices: 144310--144386 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 39
144300 AATGAGTTTC
144310 TAGAAAAAGGAATATAAGTGATAATGGTAATGAATATTG
1 TAGAAAAAGGAATATAAGTGATAATGGTAATGAATATTG
144349 TAGAAAAAGGAAATATAAGTGATAATGGTAATGAATAT
1 TAGAAAAAGG-AATATAAGTGATAATGGTAATGAATAT
144387 GGTACGTAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 10 0.27
40 27 0.73
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (39 bp):
TAGAAAAAGGAATATAAGTGATAATGGTAATGAATATTG
Found at i:148484 original size:16 final size:17
Alignment explanation
Indices: 148454--148486 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
148444 ATCAAACATT
*
148454 TACTTTTTAGATGTGAA
1 TACTTTTGAGATGTGAA
148471 TACTTTTGAG-TGTGAA
1 TACTTTTGAGATGTGAA
148487 CACGCATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.45
Consensus pattern (17 bp):
TACTTTTGAGATGTGAA
Found at i:150681 original size:16 final size:17
Alignment explanation
Indices: 150660--150692 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
150650 TAAATTAAGA
150660 GGTTTAA-ATTTTTTAT
1 GGTTTAACATTTTTTAT
150676 GGTTTAACTATTTTTTA
1 GGTTTAAC-ATTTTTTA
150693 ATAATTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.61
Consensus pattern (17 bp):
GGTTTAACATTTTTTAT
Found at i:151858 original size:72 final size:73
Alignment explanation
Indices: 151721--151861 Score: 221
Period size: 75 Copynumber: 1.9 Consensus size: 73
151711 ACCCTAACTC
* * *
151721 CATCTTCTTCTATTTTTTCATTTTGTTTTCACCATTTTTTCCCTCCCTCACCTCACCATCATTTT
1 CATCTTCTTCTATTTTTTCATTTCGATTTCACCATTGTTT--CTCCCTCACCTCACCATCATTTT
151786 CCCTCATCCT
64 CCCTCATCCT
*
151796 CATCTTCTTCTATTTTTTCATTTCGATTTCACCATTGTTT-TCCCTCACCTCACCATCGTTTTCC
1 CATCTTCTTCTATTTTTTCATTTCGATTTCACCATTGTTTCTCCCTCACCTCACCATCATTTTCC
151860 CT
66 CT
151862 TTTCTCTTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 25 0.40
75 37 0.60
ACGTcount: A:0.13, C:0.35, G:0.03, T:0.49
Consensus pattern (73 bp):
CATCTTCTTCTATTTTTTCATTTCGATTTCACCATTGTTTCTCCCTCACCTCACCATCATTTTCC
CTCATCCT
Found at i:152806 original size:23 final size:23
Alignment explanation
Indices: 152776--152845 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
152766 TCAAATTAAA
152776 CATTGTATCTAAAAAAAACCATC
1 CATTGTATCTAAAAAAAACCATC
* * *
152799 CATTGTATATAATAAGAACCATC
1 CATTGTATCTAAAAAAAACCATC
*
152822 CATTGTATC--AATAAAACCATC
1 CATTGTATCTAAAAAAAACCATC
152843 CAT
1 CAT
152846 CTATCTCCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 12 0.30
23 28 0.70
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (23 bp):
CATTGTATCTAAAAAAAACCATC
Found at i:156143 original size:21 final size:21
Alignment explanation
Indices: 156119--156191 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 21
156109 AATTATACAT
156119 ACATAATACATATAACAGTAA
1 ACATAATACATATAACAGTAA
156140 ACATAACATACATGATATACA-TAA
1 ACAT-A-ATACAT-ATA-ACAGTAA
*
156164 AAAT-ATACAAATATAACAGTAA
1 ACATAATAC--ATATAACAGTAA
156186 ACATAA
1 ACATAA
156192 CATACATAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
21 11 0.26
22 10 0.24
23 9 0.21
24 9 0.21
25 3 0.07
ACGTcount: A:0.59, C:0.14, G:0.04, T:0.23
Consensus pattern (21 bp):
ACATAATACATATAACAGTAA
Found at i:156152 original size:9 final size:9
Alignment explanation
Indices: 156140--156263 Score: 53
Period size: 9 Copynumber: 13.6 Consensus size: 9
156130 ATAACAGTAA
156140 ACATAACAT
1 ACATAACAT
* *
156149 ACATGATAT
1 ACATAACAT
156158 ACATAA-A-
1 ACATAACAT
*
156165 A-ATATACAA
1 ACATA-ACAT
*
156174 ATATAACAGT
1 ACATAACA-T
156184 AAACATAACAT
1 -A-CATAACAT
156195 ACATAACAT
1 ACATAACAT
156204 ACAT-ACA-
1 ACATAACAT
*
156211 A-ATAGACAA
1 ACATA-ACAT
*
156220 ACAAAACACT
1 ACATAACA-T
*
156230 AAATATAACAT
1 --ACATAACAT
*
156241 ACATAATAT
1 ACATAACAT
*
156250 ACATATCAT
1 ACATAACAT
156259 ACATA
1 ACATA
156264 CAAATATTCT
Statistics
Matches: 88, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.06
7 3 0.03
8 8 0.09
9 51 0.58
10 6 0.07
11 3 0.03
12 12 0.14
ACGTcount: A:0.58, C:0.17, G:0.02, T:0.23
Consensus pattern (9 bp):
ACATAACAT
Found at i:156193 original size:46 final size:46
Alignment explanation
Indices: 156078--156300 Score: 218
Period size: 46 Copynumber: 4.7 Consensus size: 46
156068 ATAAACAGCC
* * *
156078 ATACAAACATAACAATAAACATAACATACAGAATTATACATACATA-
1 ATACAAACATAACAGTAAACATAACATACATAA-TATACATACAAAT
* * *
156124 ATAC--ATATAACAGTAAACATAACATACATGATATACATAAAAAT
1 ATACAAACATAACAGTAAACATAACATACATAATATACATACAAAT
* *
156168 ATACAAATATAACAGTAAACATAACATACATAACATACATACAAAT
1 ATACAAACATAACAGTAAACATAACATACATAATATACATACAAAT
* * * *
156214 AGACAAACAAAACACTAAATATAACATACATAATATACATATCATACAT
1 ATACAAACATAACAGTAAACATAACATACATAATATACATA-CA-A-AT
*
156263 ACAAATATTCTAACATAACAGTAAACATAACATACATA
1 ----ATA--CAAACATAACAGTAAACATAACATACATA
156301 GCAGTATGGA
Statistics
Matches: 145, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
43 10 0.07
44 27 0.19
46 76 0.52
47 2 0.01
48 1 0.01
49 2 0.01
53 2 0.01
55 25 0.17
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (46 bp):
ATACAAACATAACAGTAAACATAACATACATAATATACATACAAAT
Found at i:156199 original size:55 final size:53
Alignment explanation
Indices: 156140--156300 Score: 165
Period size: 55 Copynumber: 3.1 Consensus size: 53
156130 ATAACAGTAA
*
156140 ACATAACATACATGATATACATAAAAATATACAAATATAACAGTAAACATAACAT
1 ACATAACATACAT-ATATACAT-AAAATATACAAACATAACAGTAAACATAACAT
* * * *
156195 ACATAACATAC----ATAC---AAATAGACAAACAAAACACTAAATATAACAT
1 ACATAACATACATATATACATAAAATATACAAACATAACAGTAAACATAACAT
* * *
156241 ACATAATATACATATCATACATACAAATATTCTAACATAACAGTAAACATAACAT
1 ACATAACATACATAT-ATACATA-AAATATACAAACATAACAGTAAACATAACAT
156296 ACATA
1 ACATA
156301 GCAGTATGGA
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
46 36 0.42
50 4 0.05
51 4 0.05
55 41 0.48
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.23
Consensus pattern (53 bp):
ACATAACATACATATATACATAAAATATACAAACATAACAGTAAACATAACAT
Found at i:156533 original size:30 final size:30
Alignment explanation
Indices: 156470--156533 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
156460 CAACAAAAAC
* *
156470 AAAAAATAAAAGCTAGATATGATACCAATT
1 AAAAAATAAAAGCTAGATATAATACCAAAT
* * *
156500 AAAAAATAAAAGTTATATATAATACGAAAT
1 AAAAAATAAAAGCTAGATATAATACCAAAT
156530 AAAA
1 AAAA
156534 TAGAGTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.23
Consensus pattern (30 bp):
AAAAAATAAAAGCTAGATATAATACCAAAT
Found at i:157125 original size:28 final size:28
Alignment explanation
Indices: 157085--157139 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
157075 CAATGGATGG
*
157085 AAAAAAAGTTTAGGTACCAATCTGGGAC
1 AAAAAAACTTTAGGTACCAATCTGGGAC
157113 AAAAAAACTTTAGGTACCAATCTGGGA
1 AAAAAAACTTTAGGTACCAATCTGGGA
157140 GAAGTGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.22
Consensus pattern (28 bp):
AAAAAAACTTTAGGTACCAATCTGGGAC
Found at i:160838 original size:6 final size:6
Alignment explanation
Indices: 160827--160873 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
160817 TATAACAATA
160827 TTTCTT TTTCTT TTCTCTT TTTCTCT TTT-TCT TTTCTT TTT-TT TTTC
1 TTTCTT TTTCTT TT-TCTT TTTCT-T TTTCT-T TTTCTT TTTCTT TTTC
160874 ATTCACAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.14
6 21 0.57
7 11 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:160854 original size:21 final size:21
Alignment explanation
Indices: 160829--160869 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
160819 TAACAATATT
160829 TCTTTTTCTTTTCTCTTTTTC
1 TCTTTTTCTTTTCTCTTTTTC
*
160850 TCTTTTTCTTTTCTTTTTTT
1 TCTTTTTCTTTTCTCTTTTT
160870 TTTCATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TCTTTTTCTTTTCTCTTTTTC
Found at i:180111 original size:16 final size:15
Alignment explanation
Indices: 180087--180133 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
180077 AACATTTAAA
180087 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
180102 TTTTTCTTTCTTTTTC
1 TTTTT-TTTCTTTTTC
*
180118 TCATTTTTTCTTTTTC
1 T-TTTTTTTCTTTTTC
180134 AAGTGACTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 5 0.17
16 21 0.72
17 3 0.10
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:193634 original size:23 final size:22
Alignment explanation
Indices: 193602--193703 Score: 105
Period size: 23 Copynumber: 4.5 Consensus size: 22
193592 GCTGGGGAAA
*
193602 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
193624 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
193647 CAGTAGGCACATATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
* * *
193670 TAGTAGGCACACAAAGTGCGAAA
1 CAGTAGGCACACACAGTGC-AAT
*
193693 CAGTAAGCACA
1 CAGTAGGCACA
193704 TGAAGTGCGA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.24
23 50 0.76
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:193657 original size:45 final size:46
Alignment explanation
Indices: 193598--193703 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 46
193588 AAGTGCTGGG
* *
193598 GAAACAGTAAGCACACACAGTGC-AATCCAGTAGGCACACACAGTGC
1 GAAACAGTAAGCACACACAGCGCAAAT-CAGTAGGCACACAAAGTGC
* * * * *
193644 -AATCAGTAGGCACATATAGCGCAAATTAGTAGGCACACAAAGTGC
1 GAAACAGTAAGCACACACAGCGCAAATCAGTAGGCACACAAAGTGC
193689 GAAACAGTAAGCACA
1 GAAACAGTAAGCACA
193704 TGAAGTGCGA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
45 34 0.69
46 15 0.31
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.13
Consensus pattern (46 bp):
GAAACAGTAAGCACACACAGCGCAAATCAGTAGGCACACAAAGTGC
Found at i:204120 original size:16 final size:15
Alignment explanation
Indices: 204099--204142 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
204089 AATTTAAAAT
204099 AAATTAAAAAGTTAA
1 AAATTAAAAAGTTAA
*
204114 CAAATTAAATAAATTAA
1 -AAATTAAA-AAGTTAA
204131 AAATTAGAAAAG
1 AAATTA-AAAAG
204143 AATTTTCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (15 bp):
AAATTAAAAAGTTAA
Found at i:204129 original size:25 final size:26
Alignment explanation
Indices: 204084--204133 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
204074 GTCTAAACTA
*
204084 TTAACAATTTAAAATAAATTAAAAAG
1 TTAACAAATTAAAATAAATTAAAAAG
204110 TTAACAAATT-AAATAAATTAAAAA
1 TTAACAAATTAAAATAAATTAAAAA
204134 TTAGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (26 bp):
TTAACAAATTAAAATAAATTAAAAAG
Found at i:204914 original size:14 final size:13
Alignment explanation
Indices: 204891--204920 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
204881 TCAATTTATT
204891 AAAAATAAAATAA
1 AAAAATAAAATAA
204904 AAAACATAAAATAA
1 AAAA-ATAAAATAA
204918 AAA
1 AAA
204921 CTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:212993 original size:33 final size:28
Alignment explanation
Indices: 212925--212980 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
212915 AAGTACACAT
212925 GAATTCTAGGTTAAATGTTATTTTATTC
1 GAATTCTAGGTTAAATGTTATTTTATTC
212953 GAATTCTAGGTTAAATGTTATTTTATTC
1 GAATTCTAGGTTAAATGTTATTTTATTC
212981 AACCTTGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (28 bp):
GAATTCTAGGTTAAATGTTATTTTATTC
Found at i:231142 original size:41 final size:43
Alignment explanation
Indices: 231046--231149 Score: 149
Period size: 43 Copynumber: 2.4 Consensus size: 43
231036 AACTCGATAT
* * *
231046 TTAAATGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
1 TTAAA-GGAAGACTCATGTCTCGAGATGAGAATGAGAATTTATA
*
231090 TTAAGGGAAGACTCATGTCTCGAGATGAGAATGAG-A-TTATA
1 TTAAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATTTATA
231131 TTAAAGGAAGACTCATGTC
1 TTAAAGGAAGACTCATGTC
231150 GTAAAATGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
41 23 0.42
42 1 0.02
43 27 0.49
44 4 0.07
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.29
Consensus pattern (43 bp):
TTAAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATTTATA
Found at i:231159 original size:41 final size:41
Alignment explanation
Indices: 231046--231165 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 41
231036 AACTCGATAT
**** *
231046 TTAAATGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
1 TTAAA-GGAAGACTCATGTCTCAAAATGAGAATGAG-A-TTATA
* * *
231090 TTAAGGGAAGACTCATGTCTCGAGATGAGAATGAGATTATA
1 TTAAAGGAAGACTCATGTCTCAAAATGAGAATGAGATTATA
*
231131 TTAAAGGAAGACTCATGTCGT-AAAATGAGCATGAG
1 TTAAAGGAAGACTCATGTC-TCAAAATGAGAATGAG
231166 GTTTGTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 34 0.51
42 2 0.03
43 27 0.40
44 4 0.06
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (41 bp):
TTAAAGGAAGACTCATGTCTCAAAATGAGAATGAGATTATA
Found at i:234552 original size:14 final size:12
Alignment explanation
Indices: 234522--234553 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
234512 ACTGTTTGAA
234522 GACACACGGGCT
1 GACACACGGGCT
234534 GACACACGGGCT
1 GACACACGGGCT
234546 GACACACG
1 GACACACG
234554 AGTGTTTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.34, G:0.31, T:0.06
Consensus pattern (12 bp):
GACACACGGGCT
Found at i:237843 original size:24 final size:24
Alignment explanation
Indices: 237816--237862 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
237806 ACAAAATTAA
* *
237816 CTCTCGCGAGCCTAGAAAGGTTAG
1 CTCTCACGAGCCCAGAAAGGTTAG
* *
237840 CTCTTACGAGCCCAGAATGGTTA
1 CTCTCACGAGCCCAGAAAGGTTA
237863 ACCAATAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (24 bp):
CTCTCACGAGCCCAGAAAGGTTAG
Found at i:240711 original size:172 final size:173
Alignment explanation
Indices: 240424--240774 Score: 661
Period size: 172 Copynumber: 2.0 Consensus size: 173
240414 CGCCGTAATA
240424 TTGCACAATGAAAATCTTATGAAACTTAACTTTCCTGTTATATCTAAGACTCAAATATTCACACT
1 TTGCACAATGAAAATCTTATGAAACTTAACTTTCCTGTTATATCTAAGACTCAAATATTCACACT
240489 AACCACACCATCCAGTGCTCGCAATGCAACATATTCAAGAACAAGTGGATTAAATTCCTTCAATC
66 AACCACACCATCCAGTGCTCGCAATGCAACATATTCAAGAACAAGTGGATTAAATTCCTTCAATC
240554 CCCAAGCAACTTCCATTGT-TATGCTTGTTTACTTAATTTGTCG
131 CCCAAGCAACTTCCATTGTCT-TGCTTGTTTACTTAATTTGTCG
240597 -TGCACAATGAAAATCTTATGAAACTTAACTTTCCTGTTATATCTAAGACTCAAATATTCACACT
1 TTGCACAATGAAAATCTTATGAAACTTAACTTTCCTGTTATATCTAAGACTCAAATATTCACACT
* *
240661 AACCACACCATCCAGTGTTCGCAATGCAACATATTCAAGAACAAGTGGATTAAATTCCTTCAATT
66 AACCACACCATCCAGTGCTCGCAATGCAACATATTCAAGAACAAGTGGATTAAATTCCTTCAATC
240726 CCCAAGCAACTTCCATTGTCTTGCTTGTTTACTTAATTTGTCG
131 CCCAAGCAACTTCCATTGTCTTGCTTGTTTACTTAATTTGTCG
240769 TTGCAC
1 TTGCAC
240775 CTTCCAGTGC
Statistics
Matches: 174, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
172 168 0.97
173 6 0.03
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (173 bp):
TTGCACAATGAAAATCTTATGAAACTTAACTTTCCTGTTATATCTAAGACTCAAATATTCACACT
AACCACACCATCCAGTGCTCGCAATGCAACATATTCAAGAACAAGTGGATTAAATTCCTTCAATC
CCCAAGCAACTTCCATTGTCTTGCTTGTTTACTTAATTTGTCG
Done.