Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011719.1 Kokia drynarioides strain JFW-HI SEQ_126713, 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: 137763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:2403 original size:23 final size:24
Alignment explanation
Indices: 2373--2417 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
2363 GTCATAAAGT
2373 AAAAGCGTGCCAC-AAGGCAGAGG
1 AAAAGCGTGCCACAAAGGCAGAGG
2396 AAAAGCGTGCCACAAAGGCAGA
1 AAAAGCGTGCCACAAAGGCAGA
2418 TAAAAACTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.42, C:0.22, G:0.31, T:0.04
Consensus pattern (24 bp):
AAAAGCGTGCCACAAAGGCAGAGG
Found at i:2422 original size:23 final size:23
Alignment explanation
Indices: 2370--2422 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2360 CATGTCATAA
2370 AGTAAAAGCGTGCCACAAGGCAG
1 AGTAAAAGCGTGCCACAAGGCAG
*
2393 AGGAAAAGCGTGCCACAAAGGCAG
1 AGTAAAAGCGTGCCAC-AAGGCAG
2417 A-TAAAA
1 AGTAAAA
2423 ACTAGAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.45, C:0.19, G:0.28, T:0.08
Consensus pattern (23 bp):
AGTAAAAGCGTGCCACAAGGCAG
Found at i:4008 original size:27 final size:26
Alignment explanation
Indices: 3977--4040 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 26
3967 TTCATTGAGG
*
3977 TTATTAGTTTATCGATAAATAAATATT
1 TTATTAATTTATCGATAAATAAATA-T
*
4004 TTATTAATTTATCGATAAATTAATAT
1 TTATTAATTTATCGATAAATAAATAT
4030 TTATTAATTTA
1 TTATTAATTTA
4041 GAAAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATAAATAT
Found at i:6527 original size:12 final size:11
Alignment explanation
Indices: 6504--6593 Score: 54
Period size: 11 Copynumber: 7.6 Consensus size: 11
6494 CAAATATCTC
6504 TAAAATAATAA
1 TAAAATAATAA
6515 TAAAATAAATAA
1 TAAAAT-AATAA
* *
6527 TAAAACACAATATT
1 T-AAA-ATAATA-A
*
6541 TAAACAATAACAA
1 T-AA-AATAATAA
*
6554 CAAAATAATAA
1 TAAAATAATAA
* *
6565 TAATATAATAG
1 TAAAATAATAA
*
6576 TAAAATGATAA
1 TAAAATAATAA
*
6587 CAAAATA
1 TAAAATA
6594 TTGTTTTTTT
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
11 34 0.58
12 8 0.14
13 7 0.12
14 9 0.15
15 1 0.02
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:6549 original size:21 final size:22
Alignment explanation
Indices: 6520--6560 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6510 AATAATAAAA
* *
6520 TAAATAATAA-AACACAATATT
1 TAAACAATAACAACAAAATATT
6541 TAAACAATAACAACAAAATA
1 TAAACAATAACAACAAAATA
6561 ATAATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACAATAACAACAAAATATT
Found at i:15040 original size:29 final size:29
Alignment explanation
Indices: 14988--15072 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
14978 ATTTGAGGTC
* *
14988 AAAATTGAAATTTTTTAAAAATTTGGGATT-
1 AAAATT-AAACTTTTGAAAAATTTGGG-TTA
15018 AAAATTAAACTTTTGAAAAATTTGAGGTTA
1 AAAATTAAACTTTTGAAAAATTTG-GGTTA
*
15048 AAAATGT-GACTTTTG-AAAATTTGGG
1 AAAAT-TAAACTTTTGAAAAATTTGGG
15073 GGCAAAATGA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
28 2 0.04
29 26 0.53
30 20 0.41
31 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.39
Consensus pattern (29 bp):
AAAATTAAACTTTTGAAAAATTTGGGTTA
Found at i:15052 original size:30 final size:29
Alignment explanation
Indices: 14977--15050 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
14967 ATTTTCGAGG
* * *
14977 AATTTGAGGTCAAAATTGAAATTTTTTAAA
1 AATTTGAGGTTAAAATT-AAACTTTTGAAA
15007 AATTTG-GGATTAAAATTAAACTTTTGAAA
1 AATTTGAGG-TTAAAATTAAACTTTTGAAA
15036 AATTTGAGGTTAAAA
1 AATTTGAGGTTAAAA
15051 ATGTGACTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (29 bp):
AATTTGAGGTTAAAATTAAACTTTTGAAA
Found at i:15138 original size:30 final size:29
Alignment explanation
Indices: 15048--15323 Score: 211
Period size: 29 Copynumber: 9.5 Consensus size: 29
15038 TTTGAGGTTA
* * *
15048 AAAATGTGACTTTTGAAAATTT-GGGGGC
1 AAAATGTAATTTTTGAAAATTTAGGGGTC
* * * *
15076 AAAATGATGATTTTT--AGATGTTTGTGGT-
1 AAAATG-TAATTTTTGAAAAT-TTAGGGGTC
*
15104 AAAATGTAATTTTAGAGAAATTTAGGGGTC
1 AAAATGTAATTTTTGA-AAATTTAGGGGTC
* * * *
15134 AAAATGCAATTTTGGAAATTTTTGGGGTC
1 AAAATGTAATTTTTGAAAATTTAGGGGTC
* *
15163 AAAATGTAATTTTGGAAAAGTTTAGGGCT-
1 AAAATGTAATTTTTGAAAA-TTTAGGGGTC
* * * *
15192 AAAATGTAATTTTTGAGAAGTTAAGGCTC
1 AAAATGTAATTTTTGAAAATTTAGGGGTC
* * ***
15221 AAAATGTAATTTTGGAAAATTTTGGAAACC
1 AAAATGTAATTTTTGAAAATTTAGG-GGTC
* * *
15251 AATATGTAATTTTTGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTTGAAAA-TTTAGGGGTC
* *
15281 AAAATGTAATTTTTGATAATTTAAGGGTC
1 AAAATGTAATTTTTGAAAATTTAGGGGTC
15310 AAAATGTAATTTTT
1 AAAATGTAATTTTT
15324 ACGAAGTTAG
Statistics
Matches: 197, Mismatches: 40, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
27 9 0.05
28 21 0.11
29 104 0.53
30 59 0.30
31 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAATTTAGGGGTC
Found at i:15166 original size:87 final size:87
Alignment explanation
Indices: 15058--15322 Score: 252
Period size: 87 Copynumber: 3.0 Consensus size: 87
15048 AAAATGTGAC
* * * *
15058 TTTT-GAAAA-TTTGGGGGCAAAATGATGATTTT-TAGATGTTT-GTGG-TAAAATGTAATTTTA
1 TTTTGGAAAATTTTGGGGGCAAAATG-TAATTTTGGAAAAGTTTAG-GGCTAAAATGTAATTTTA
* * *
15118 GAGAAATTTAGGGGTCAAAATGCAA
64 GAG-AAGTTAAGGCTCAAAATGCAA
* * *
15143 TTTTGGAAATTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGCTAAAATGTAATTTTTGA
1 TTTTGGAAAATTTTGGGGGCAAAATGTAATTTTGGAAAAGTTTAGGGCTAAAATGTAATTTTAGA
*
15208 GAAGTTAAGGCTCAAAATGTAA
66 GAAGTTAAGGCTCAAAATGCAA
*** * * * *
15230 TTTTGGAAAATTTTGGAAACCAATATGTAATTTTTGAAAAGTTTAAGGGTTAAAATGTAATTTTT
1 TTTTGGAAAATTTTGG-GGGCAAAATGTAATTTTGGAAAAGTTT-AGGGCTAAAATGTAATTTTA
* * * *
15295 GATAATTTAAGGGTCAAAATGTAA
64 GAGAAGTTAAGGCTCAAAATGCAA
15319 TTTT
1 TTTT
15323 TACGAAGTTA
Statistics
Matches: 152, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
85 4 0.03
86 10 0.07
87 54 0.36
88 40 0.26
89 44 0.29
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (87 bp):
TTTTGGAAAATTTTGGGGGCAAAATGTAATTTTGGAAAAGTTTAGGGCTAAAATGTAATTTTAGA
GAAGTTAAGGCTCAAAATGCAA
Found at i:15206 original size:59 final size:58
Alignment explanation
Indices: 15104--15323 Score: 207
Period size: 59 Copynumber: 3.7 Consensus size: 58
15094 TGTTTGTGGT
* * * **
15104 AAAATGTAATTTTAGAGAAATTTAGGGGTCAAAATGCAA-TTTTGGAAATTTTTGGGGTC
1 AAAATGTAATTTTGGA-AAATTTAGGGCTCAAAATGTAATTTTTGGAAA-TTTAAGGGTC
* *
15163 AAAATGTAATTTTGGAAAAGTTTAGGGCT-AAAATGTAATTTTT-GAGAAGTTAAGGCTC
1 AAAATGTAATTTTGGAAAA-TTTAGGGCTCAAAATGTAATTTTTGGA-AATTTAAGGGTC
* * * * *
15221 AAAATGTAATTTTGGAAAATTTTGGAAAC-CAATATGTAATTTTTGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAATTTAGG--GCTCAAAATGTAATTTTTGGAAA-TTTAAGGGTC
* *
15281 AAAATGTAATTTTTGATAATTTAAGGG-TCAAAATGTAATTTTT
1 AAAATGTAATTTTGGAAAATTT-AGGGCTCAAAATGTAATTTTT
15324 ACGAAGTTAG
Statistics
Matches: 132, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
57 5 0.04
58 38 0.29
59 59 0.45
60 28 0.21
61 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAATTTAGGGCTCAAAATGTAATTTTTGGAAATTTAAGGGTC
Found at i:15340 original size:30 final size:29
Alignment explanation
Indices: 15104--15361 Score: 182
Period size: 29 Copynumber: 8.8 Consensus size: 29
15094 TGTTTGTGGT
* * *
15104 AAAATGTAATTTTAGAGAAATTTAGGGGTC
1 AAAATGTAATTTTTGAG-AAGTTAAGGGTC
* * * **
15134 AAAATGCAATTTTGGA-AATTTTTGGGGTC
1 AAAATGTAATTTTTGAGAA-GTTAAGGGTC
* * *
15163 AAAATGTAATTTTGGAAAAGTTTAGGG-C
1 AAAATGTAATTTTTGAGAAGTTAAGGGTC
*
15191 TAAAATGTAATTTTTGAGAAGTTAAGGCTC
1 -AAAATGTAATTTTTGAGAAGTTAAGGGTC
* * ** **
15221 AAAATGTAATTTTGGA-AAATTTTGGAAACC
1 AAAATGTAATTTTTGAGAAGTTAAGG--GTC
* * *
15251 AATATGTAATTTTTGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTTGAGAAG-TTAAGGGTC
* *
15281 AAAATGTAATTTTTGATAATTTAAGGGTC
1 AAAATGTAATTTTTGAGAAGTTAAGGGTC
15310 AAAATGTAATTTTT-ACGAAGTTAGAGGGTC
1 AAAATGTAATTTTTGA-GAAGTTA-AGGGTC
* * *
15340 ATAATATGATTTTTGAGAAGTT
1 AAAATGTAATTTTTGAGAAGTT
15362 TGAGGACCTC
Statistics
Matches: 184, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
28 10 0.05
29 95 0.52
30 72 0.39
31 3 0.02
32 4 0.02
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTTAAGGGTC
Found at i:15355 original size:89 final size:87
Alignment explanation
Indices: 15103--15322 Score: 226
Period size: 89 Copynumber: 2.5 Consensus size: 87
15093 ATGTTTGTGG
* * * * * ** * *** *
15103 TAAAATGTAATTTTAGAGAAATTTAGGGGTCAAAATGCAATTTTGGAAATTTTTGG-GGTCAAAA
1 TAAAATGTAATTTTTGAG-AAGTTAAGGCTCAAAATGTAATTTTGGAAAAGTTAGGAAACCAATA
*
15167 TGTAATTTTGGAAAAGTTTAGGGC
65 TG-AATTTTTGAAAAGTTTAGGGC
* *
15191 TAAAATGTAATTTTTGAGAAGTTAAGGCTCAAAATGTAATTTTGGAAAATTTTGGAAACCAATAT
1 TAAAATGTAATTTTTGAGAAGTTAAGGCTCAAAATGTAATTTTGGAAAAGTTAGGAAACCAATAT
*
15256 GTAATTTTTGAAAAGTTTAAGGGT
66 G-AATTTTTGAAAAGTTT-AGGGC
* * *
15280 TAAAATGTAATTTTTGATAATTTAAGGGTCAAAATGTAATTTT
1 TAAAATGTAATTTTTGAGAAGTTAAGGCTCAAAATGTAATTTT
15323 TACGAAGTTA
Statistics
Matches: 115, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
87 32 0.28
88 39 0.34
89 44 0.38
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (87 bp):
TAAAATGTAATTTTTGAGAAGTTAAGGCTCAAAATGTAATTTTGGAAAAGTTAGGAAACCAATAT
GAATTTTTGAAAAGTTTAGGGC
Found at i:16227 original size:11 final size:11
Alignment explanation
Indices: 16191--16238 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
16181 ACTTCTCTTT
16191 TTTATTA-TTA
1 TTTATTATTTA
* *
16201 TTTAATATAATA
1 TTTATTAT-TTA
16213 TTTATTATTTA
1 TTTATTATTTA
*
16224 TTTATTAATTA
1 TTTATTATTTA
16235 TTTA
1 TTTA
16239 ATAGACATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 6 0.19
11 16 0.52
12 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:19658 original size:7 final size:7
Alignment explanation
Indices: 19646--19674 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
19636 AGTAAACCCC
19646 TCAATTA
1 TCAATTA
19653 TCAATTA
1 TCAATTA
19660 TCAATTA
1 TCAATTA
19667 TCAATTA
1 TCAATTA
19674 T
1 T
19675 TTGAATTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (7 bp):
TCAATTA
Found at i:23684 original size:16 final size:15
Alignment explanation
Indices: 23645--23688 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
23635 AAAATAAATA
23645 AAAATTTTAAAATTT
1 AAAATTTTAAAATTT
**
23660 ATATTTTTTAAAATTAT
1 A-AAATTTTAAAATT-T
23677 AAAATTTTAAAA
1 AAAATTTTAAAA
23689 AATATTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.04
16 20 0.87
17 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTTTAAAATTT
Found at i:24865 original size:2 final size:2
Alignment explanation
Indices: 24860--24884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24850 TTCATATATA
24860 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
24885 CTTCTTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:29403 original size:9 final size:8
Alignment explanation
Indices: 29393--29433 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
29383 AACATGATTA
29393 AAAAATAT
1 AAAAATAT
*
29401 AAACATCAT
1 AAAAAT-AT
29410 AAAAATAT
1 AAAAATAT
29418 -AAAATAT
1 AAAAATAT
29425 AAAAA-AT
1 AAAAATAT
29432 AA
1 AA
29434 TTAATTGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 11 0.38
8 11 0.38
9 7 0.24
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:29413 original size:17 final size:15
Alignment explanation
Indices: 29393--29433 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
29383 AACATGATTA
29393 AAAAATATAAACATCAT
1 AAAAATATAAA-AT-AT
29410 AAAAATATAAAATAT
1 AAAAATATAAAATAT
29425 AAAAA-ATAA
1 AAAAATATAA
29434 TTAATTGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 2 0.08
17 11 0.46
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAAATATAAAATAT
Found at i:29414 original size:19 final size:17
Alignment explanation
Indices: 29352--29430 Score: 54
Period size: 17 Copynumber: 4.4 Consensus size: 17
29342 TTAAAATTTA
29352 AAAAAAATATAAAATTAAT
1 AAAAAAATATAAAA-T-AT
* *
29371 AAATAAATTATTAACATGAT
1 AAA-AAAATA-TAAAAT-AT
*
29391 TAAAAAATATAAACATCAT
1 AAAAAAATATAAA-AT-AT
29410 --AAAAATATAAAATAT
1 AAAAAAATATAAAATAT
29425 AAAAAA
1 AAAAAA
29431 TAATTAATTG
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
15 2 0.04
16 2 0.04
17 15 0.31
18 3 0.06
19 12 0.25
20 10 0.21
21 4 0.08
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (17 bp):
AAAAAAATATAAAATAT
Found at i:36748 original size:42 final size:42
Alignment explanation
Indices: 36689--36778 Score: 180
Period size: 42 Copynumber: 2.1 Consensus size: 42
36679 ACAGCAACAA
36689 GAAGAAGATATAGTTGAAAGAAGTCAAGCAGAAATCAATGCT
1 GAAGAAGATATAGTTGAAAGAAGTCAAGCAGAAATCAATGCT
36731 GAAGAAGATATAGTTGAAAGAAGTCAAGCAGAAATCAATGCT
1 GAAGAAGATATAGTTGAAAGAAGTCAAGCAGAAATCAATGCT
36773 GAAGAA
1 GAAGAA
36779 CTAACTGTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.49, C:0.09, G:0.24, T:0.18
Consensus pattern (42 bp):
GAAGAAGATATAGTTGAAAGAAGTCAAGCAGAAATCAATGCT
Found at i:42424 original size:9 final size:9
Alignment explanation
Indices: 42410--42452 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
42400 AGAGAATGAT
42410 GAAGAAAAA
1 GAAGAAAAA
*
42419 GAAGAAGAA
1 GAAGAAAAA
* *
42428 GGAGAGAAA
1 GAAGAAAAA
*
42437 GAAGAGAAA
1 GAAGAAAAA
42446 GAAGAAA
1 GAAGAAA
42453 CTGAACCTGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:49076 original size:27 final size:27
Alignment explanation
Indices: 49045--49100 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
49035 TACTGACTTG
49045 ACTTCTATCGATACTTGTCCAATAGGT
1 ACTTCTATCGATACTTGTCCAATAGGT
*
49072 ACTTCTATCGATACTTGTCCTATAGGT
1 ACTTCTATCGATACTTGTCCAATAGGT
49099 AC
1 AC
49101 CAGTAGAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (27 bp):
ACTTCTATCGATACTTGTCCAATAGGT
Found at i:60936 original size:24 final size:24
Alignment explanation
Indices: 60909--61035 Score: 175
Period size: 24 Copynumber: 5.3 Consensus size: 24
60899 TTTAGCCCAC
60909 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
* *
60933 ACGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
* **
60957 ACGAGCCCAAAATGGCTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
*
60981 ATGAAG-CCAGAATGATTAGCTCTT
1 ACG-AGCCCAGAATGATTAGCTCTT
*
61005 ACAAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
61029 ACGAGCC
1 ACGAGCC
61036 TAGATAGAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 2 0.02
24 87 0.96
25 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:70301 original size:23 final size:23
Alignment explanation
Indices: 70275--70319 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
70265 AGCGTACAAA
70275 AACTAAGACTAATCAAAACATAG
1 AACTAAGACTAATCAAAACATAG
70298 AACTAAGACTAATCAAAACATA
1 AACTAAGACTAATCAAAACATA
70320 ACAAACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.18, G:0.07, T:0.18
Consensus pattern (23 bp):
AACTAAGACTAATCAAAACATAG
Found at i:70843 original size:34 final size:34
Alignment explanation
Indices: 70770--70845 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 34
70760 AAACTAAACT
*
70770 CAAATATTTTTAATTTTTTACCTTTTATCTTATC
1 CAAATATTTTTAATTTTTTACCTTTTATCTTACC
*
70804 TAAATATTTTTAATTTTTTACCTTTTA-CTTTACC
1 CAAATATTTTTAATTTTTTACCTTTTATC-TTACC
70838 CAAATATT
1 CAAATATT
70846 GTATAATCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 1 0.03
34 37 0.97
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (34 bp):
CAAATATTTTTAATTTTTTACCTTTTATCTTACC
Found at i:78255 original size:3 final size:3
Alignment explanation
Indices: 78249--78346 Score: 61
Period size: 3 Copynumber: 32.7 Consensus size: 3
78239 AATTGTTGTT
* * * * * * * * *
78249 GTG GTG GTG GTG GTA GTA GTA GTG GTA GTG GTA GTA GTA ATG GTA GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
* * * * * *
78297 GTG GTG GTG GTG GTG ATG GTA GTA GTA ATG GTA GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
78345 GT
1 GT
78347 TGTAACACCC
Statistics
Matches: 77, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.15, C:0.00, G:0.51, T:0.34
Consensus pattern (3 bp):
GTG
Found at i:78258 original size:6 final size:6
Alignment explanation
Indices: 78252--78346 Score: 84
Period size: 6 Copynumber: 15.8 Consensus size: 6
78242 TGTTGTTGTG
* * * * *
78252 GTGGTG GTGGTA GTAGTA GTGGTA GTGGTA GTAGTA ATGGTA GTGGTG
1 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA
* * * * *
78300 GTGGTG GTGGT- GATGGTA GTAGTA ATGGTA GTGGTG GTGGTG GTGGT
1 GTGGTA GTGGTA G-TGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGT
78347 TGTAACACCC
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
5 1 0.01
6 72 0.97
7 1 0.01
ACGTcount: A:0.16, C:0.00, G:0.51, T:0.34
Consensus pattern (6 bp):
GTGGTA
Found at i:78310 original size:36 final size:36
Alignment explanation
Indices: 78277--78346 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
78267 GTAGTGGTAG
78277 TGGTAGTAGTAATGGTAGTGGTGGTGGTGGTGGTGA
1 TGGTAGTAGTAATGGTAGTGGTGGTGGTGGTGGTGA
78313 TGGTAGTAGTAATGGTAGTGGTGGTGGTGGTGGT
1 TGGTAGTAGTAATGGTAGTGGTGGTGGTGGTGGT
78347 TGTAACACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (36 bp):
TGGTAGTAGTAATGGTAGTGGTGGTGGTGGTGGTGA
Found at i:83321 original size:3 final size:3
Alignment explanation
Indices: 83313--83352 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
83303 ATATTATGTT
83313 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
83353 AATTATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:88635 original size:12 final size:12
Alignment explanation
Indices: 88618--88642 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88608 GACAGGTTCT
88618 TCTTCTTCTTTC
1 TCTTCTTCTTTC
88630 TCTTCTTCTTTC
1 TCTTCTTCTTTC
88642 T
1 T
88643 TTTCCTCGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTTCTTCTTTC
Found at i:88635 original size:15 final size:16
Alignment explanation
Indices: 88615--88644 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88605 CTTGACAGGT
88615 TCTTCTTC-TTCTTTC
1 TCTTCTTCTTTCTTTC
88630 TCTTCTTCTTTCTTT
1 TCTTCTTCTTTCTTT
88645 TCCTCGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TCTTCTTCTTTCTTTC
Found at i:110790 original size:17 final size:18
Alignment explanation
Indices: 110768--110808 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
110758 TTAGTTTTCA
110768 TGCATTCTT-ATTGTGC-T
1 TGCATTCTTAATTGT-CAT
110785 TGCATT-TTAATTGTCAT
1 TGCATTCTTAATTGTCAT
110802 TGCATTC
1 TGCATTC
110809 ATTTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (18 bp):
TGCATTCTTAATTGTCAT
Found at i:116430 original size:18 final size:18
Alignment explanation
Indices: 116381--116423 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
116371 GATGCTAATG
116381 CTGCTGAGGAAGAGACTC
1 CTGCTGAGGAAGAGACTC
116399 CTGCTGAGGAAGAGACTC
1 CTGCTGAGGAAGAGACTC
116417 CTGCTGA
1 CTGCTGA
116424 TGGAGAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.33, T:0.19
Consensus pattern (18 bp):
CTGCTGAGGAAGAGACTC
Found at i:116924 original size:17 final size:17
Alignment explanation
Indices: 116892--116954 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 17
116882 TTGTTAGTAA
**
116892 TCATTGTCATCACATTC
1 TCATTGTCATTGCATTC
*
116909 TCATTGTCATTGCATTT
1 TCATTGTCATTGCATTC
* *
116926 TAATTGTCACTGCATTC
1 TCATTGTCATTGCATTC
*
116943 GCATTGTCATTG
1 TCATTGTCATTG
116955 TAATTCCATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (17 bp):
TCATTGTCATTGCATTC
Found at i:119205 original size:33 final size:33
Alignment explanation
Indices: 119154--119409 Score: 144
Period size: 33 Copynumber: 7.6 Consensus size: 33
119144 TGATCCAACC
* *
119154 ATGGTCTT-ACGTTAGAATGTCATAGCCCAGCT
1 ATGGTCTTAACATCAGAATGTCATAGCCCAGCT
* * ** *
119186 ATAGTCTTAACATCAGAATGCCATAGCATATCT
1 ATGGTCTTAACATCAGAATGTCATAGCCCAGCT
* * * * * *
119219 ATGGTCTT-ACATCTATATACACTGCCATGGTCCAACC
1 ATGGTCTTAACATC---AGA-A-TGTCATAGCCCAGCT
* ** *
119256 ATGATCTT-ATGTCAGAATGTCATAGCGCAGCT
1 ATGGTCTTAACATCAGAATGTCATAGCCCAGCT
*
119288 ATGGTCTTAACATCTGAATGTCATAGCCCAGCT
1 ATGGTCTTAACATCAGAATGTCATAGCCCAGCT
* * * * * * *
119321 ATGGTCTTGCATCTATATACAATGTCATGGTCCAACC
1 ATGGTCTT--AAC-AT-CAGAATGTCATAGCCCAGCT
* *
119358 ATGGTCTT-ACATTAGAATGTCATAGCTCAGCT
1 ATGGTCTTAACATCAGAATGTCATAGCCCAGCT
119390 ATGGTCTTATA-ATCAGAATG
1 ATGGTCTTA-ACATCAGAATG
119410 CAGCCTATCT
Statistics
Matches: 165, Mismatches: 46, Indels: 25
0.70 0.19 0.11
Matches are distributed among these distances:
32 50 0.30
33 64 0.39
34 4 0.02
35 4 0.02
36 3 0.02
37 40 0.24
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (33 bp):
ATGGTCTTAACATCAGAATGTCATAGCCCAGCT
Found at i:119295 original size:102 final size:102
Alignment explanation
Indices: 119119--119410 Score: 415
Period size: 102 Copynumber: 2.9 Consensus size: 102
119109 TAACGCGATC
* *
119119 GGTCTTACATATATATACACTGCCATGATCCAACCATGGTCTTACGTTAGAATGTCATAGCCCAG
1 GGTCTTACATCTATATACACTGCCATGGTCCAACCATGGTCTTACGTTAGAATGTCATAGCCCAG
* * *
119184 CTATAGTCTTAACATCAGAATGCCATAGCATATCTAT
66 CTATGGTCTTAACATCAGAATGCCATAGCACAGCTAT
* * * *
119221 GGTCTTACATCTATATACACTGCCATGGTCCAACCATGATCTTATGTCAGAATGTCATAGCGCAG
1 GGTCTTACATCTATATACACTGCCATGGTCCAACCATGGTCTTACGTTAGAATGTCATAGCCCAG
* * *
119286 CTATGGTCTTAACATCTGAATGTCATAGCCCAGCTAT
66 CTATGGTCTTAACATCAGAATGCCATAGCACAGCTAT
* * * * *
119323 GGTCTTGCATCTATATACAATGTCATGGTCCAACCATGGTCTTACATTAGAATGTCATAGCTCAG
1 GGTCTTACATCTATATACACTGCCATGGTCCAACCATGGTCTTACGTTAGAATGTCATAGCCCAG
119388 CTATGGTCTTATA-ATCAGAATGC
66 CTATGGTCTTA-ACATCAGAATGC
119411 AGCCTATCTC
Statistics
Matches: 167, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
102 166 0.99
103 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (102 bp):
GGTCTTACATCTATATACACTGCCATGGTCCAACCATGGTCTTACGTTAGAATGTCATAGCCCAG
CTATGGTCTTAACATCAGAATGCCATAGCACAGCTAT
Found at i:125823 original size:39 final size:39
Alignment explanation
Indices: 125769--126057 Score: 159
Period size: 39 Copynumber: 7.5 Consensus size: 39
125759 TAGTCATCTG
*
125769 ATCT-TTACTCCGAGCCTGGGGCAAATCACCATTAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAAATCACCATTAACCA
* * * *
125807 ATCTCTTACCCCGAGCCTGGGGTAGATCATCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAAATCACCATTAACCA
* * * * ** * *
125846 ATCTTTTACCCCGAGCTTGGGGCAGATTA-CAGCAATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAAATCACCATTAA-CCA
* * * *
125885 ATCTTTTACCCCAAGCCTGAGGCAGATTGCAACCA-T--CCA
1 ATCTCTTACCCCGAGCCTGGGGCA-AAT-C-ACCATTAACCA
* * * * *
125924 ATTTCTTA-CCCGAGCTTAGGG-AAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAA-ATCACCATTAACCA
* **
125962 ATCTCTTACCCCGAGCCT-GGGCAGATTGCAGCCA-T--CTG
1 ATCTCTTACCCCGAGCCTGGGGCA-AAT-CA-CCATTAACCA
* * * *
126000 ATCTCATACCCCGAGCTTGGGGCAGATCACTATTAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAAATCACCATTAACCA
*
126039 ATCTCTTACCCTGAGCCTG
1 ATCTCTTACCCCGAGCCTG
126058 AGGTAGATTG
Statistics
Matches: 187, Mismatches: 45, Indels: 37
0.70 0.17 0.14
Matches are distributed among these distances:
35 4 0.02
36 4 0.02
37 5 0.03
38 49 0.26
39 115 0.61
40 4 0.02
41 3 0.02
42 1 0.01
43 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAAATCACCATTAACCA
Found at i:125925 original size:78 final size:78
Alignment explanation
Indices: 125763--126185 Score: 383
Period size: 78 Copynumber: 5.5 Consensus size: 78
125753 AGATCATAGT
* * * * * * *
125763 CATCTGATC-TTTACTCCGAGCCTGGGGCAAATCACCATTAACCAATCTCTTACCCCGAGCCTGG
1 CATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTGA
* *
125827 GGTAGA-T-CATCAT
66 GGCAGATTGCA--AC
* * * * * * * * *
125840 CAACCAATCTTTTACCCCGAGCTTGGGGCAGATTA-CAGCAATTCGATCTTTTACCCCAAGCCTG
1 CATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAA-CCAATCTCTTACCCCGAGCCTG
125904 AGGCAGATTGCAAC
65 AGGCAGATTGCAAC
* * *
125918 CATCCAAT-TTCTTA-CCCGAGCTTAGGGAAGATCACCATCAGCCAATCTCTTACCCCGAGCCTG
1 CATCCGATCTT-TTACCCCGAGCTTAGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTG
*
125981 -GGCAGATTGCAGC
65 AGGCAGATTGCAAC
* ** * * * *
125994 CATCTGATCTCATACCCCGAGCTTGGGGCAGATCACTATTAACCAATCTCTTACCCTGAGCCTGA
1 CATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTGA
*
126059 GGTAGATTGCAAC
66 GGCAGATTGCAAC
* * * * *
126072 CATCCGATCTTTTACCTCGAGCTTAAGGTAGATCATCATCAACCAATCTCTTACCCTGAGCCTGA
1 CATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTGA
* *
126137 GGCAAATTACAAC
66 GGCAGATTGCAAC
* * * * *
126150 CGTCCGATCTTTTACCCCAAGTTTACGGCAAATCAC
1 CATCCGATCTTTTACCCCGAGCTTAGGGCAGATCAC
126186 TGTCAGCTAA
Statistics
Matches: 277, Mismatches: 60, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
76 20 0.07
77 91 0.33
78 163 0.59
79 1 0.00
80 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (78 bp):
CATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTGA
GGCAGATTGCAAC
Found at i:126087 original size:39 final size:38
Alignment explanation
Indices: 125807--126166 Score: 110
Period size: 39 Copynumber: 9.3 Consensus size: 38
125797 CCATTAACCA
* * * * *
125807 ATCTCTTACCCCGAGCCTGGGGTAGA-TCATCATCAACCA
1 ATCTCTTACCCTGAGCCTGAGGTAGATTCA--ACCATCCG
* * * * * * * *
125846 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCAATTCG
1 ATCTCTTACCCTGAGCCTGAGGTAGATT-CAACCATCCG
* ** * *
125885 ATCTTTTACCCCAAGCCTGAGGCAGATTGCAACCATCCA
1 ATCTCTTACCCTGAGCCTGAGGTAGATT-CAACCATCCG
* * * *
125924 ATTTCTTACCC-GAG-CTTAGGGAAGA-TC-ACCATCAGCCA
1 ATCTCTTACCCTGAGCCTGA-GGTAGATTCAACCAT---CCG
* * * *
125962 ATCTCTTACCCCGAGCCTG-GGCAGATTGCAGCCATCTG
1 ATCTCTTACCCTGAGCCTGAGGTAGATT-CAACCATCCG
* * * * * * *
126000 ATCTCATACCCCGAGCTTGGGGCAGA-TC-ACTATTAACCA
1 ATCTCTTACCCTGAGCCTGAGGTAGATTCAACCA-T--CCG
126039 ATCTCTTACCCTGAGCCTGAGGTAGATTGCAACCATCCG
1 ATCTCTTACCCTGAGCCTGAGGTAGATT-CAACCATCCG
* * * * * *
126078 ATCTTTTA-CCTCGAGCTTAAGGTAGA-TCATCATCAACCA
1 ATCTCTTACCCT-GAGCCTGAGGTAGATTCA--ACCATCCG
* * *
126117 ATCTCTTACCCTGAGCCTGAGGCAAATTACAACCGTCCG
1 ATCTCTTACCCTGAGCCTGAGGTAGATT-CAACCATCCG
*
126156 ATCTTTTACCC
1 ATCTCTTACCC
126167 CAAGTTTACG
Statistics
Matches: 240, Mismatches: 57, Indels: 48
0.70 0.17 0.14
Matches are distributed among these distances:
35 5 0.02
36 3 0.01
37 8 0.03
38 48 0.20
39 154 0.64
40 9 0.04
41 10 0.04
42 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (38 bp):
ATCTCTTACCCTGAGCCTGAGGTAGATTCAACCATCCG
Found at i:126296 original size:39 final size:39
Alignment explanation
Indices: 126216--126904 Score: 315
Period size: 39 Copynumber: 17.7 Consensus size: 39
126206 CCATCAGCCA
* * * *
126216 ATCTTTTACCCCGAGCTTGGGGCAGGTTACAATCGTTCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * *
126255 ATCTTTTACCTCGAGCTTGGGGTAGATTGCAACCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * * * * * * * * * *
126294 ATCTATTATCCCAAGCATGGAGAAGATCACCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * * ** * *
126333 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* ** *
126372 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGTCATTCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
** * * *** * *
126411 ATCTCATACCCAGAGCTTGGGGCAGATCACTGTCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* ** * * * * * *
126450 ATCTCTTACCCTAAGCCTGAGGTAGATTGCAGCCATCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * * * *
126489 ATCTCTTACCCCGAGCTTGGGGCAGATCATC-ATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTA-CAACCATCCG
* ** * * * * * *
126528 ATCTCTTACCCTAAGCCTAGGGCAAATTATAGCCGTCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * * * *** * *
126567 ATCTTTTACCTCAAGCTTGAGGCAGATCACTGTCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* ** * * * *
126606 ATCTCTTATTCCAAGCCTGGGGCAAATTGCAACCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * * * * *
126645 ATCTCTTACCTCAAGCCTGGGGCAGATTACAGCCATCTG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * * * * *
126684 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * *
126723 ATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * * * * *
126762 ATCTTTTACCCCGAGCCTGGAGCAGATCATCATCC-GCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTA-CAACCATCCG
* * * * * * *
126801 ATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
* * * * * *
126840 ATCTCTTACTCCGAGCATAGGGCATATTGCAGA-CATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACA-ACCATCCG
*
126879 ATCTCTTA-CCCGAGCTTGGGGCAGAT
1 ATCTTTTACCCCGAGCTTGGGGCAGAT
126905 CACCATCAGT
Statistics
Matches: 488, Mismatches: 157, Indels: 11
0.74 0.24 0.02
Matches are distributed among these distances:
38 16 0.03
39 466 0.95
40 6 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATTACAACCATCCG
Found at i:126413 original size:117 final size:116
Alignment explanation
Indices: 126199--126926 Score: 621
Period size: 117 Copynumber: 6.2 Consensus size: 116
126189 CAGCTAATGA
* * * * *** * *
126199 CAGATCACCATCAGCCAATCTTTTACCCCGAGCTTGGGGCAGGTTACAATCGTTCGATCTTTTAC
1 CAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATCTCTTAC
* * * * *
126264 CTCGAGCTTGGGGTAGATTGCAACCATCCGATCTATTATCCCAAGCATGGAG
66 CCCGAGCTTGGGGCAGATTGCAACCATCCGATCTCTTA-CCCAAGCCTGGGG
* * *
126316 AAGATCACCATCAACCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAACCAATCTCTTAC
1 CAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATCTCTTAC
* ** * * *
126381 CCCGAGCTTGGGGCAGATTACAGTCATTCGATCTCATACCCAGAGCTTGGGG
66 CCCGAGCTTGGGGCAGATTGCAACCATCCGATCTCTTACCCA-AGCCTGGGG
** * ** * * *
126433 CAGATCACTGTCAACCAATCTCTTACCCTAAGCCTGAGGTAGATTGCAGCCAT---CCAATCTCT
1 CAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAACCAATCTCT
* * * *
126495 TACCCCGAGCTTGGGGCAGA-T-CATCATCAGCCAATCTCTTACCCTAAGCCTAGGG
63 TACCCCGAGCTTGGGGCAGATTGCA--ACCATCCGATCTCTTACCC-AAGCCTGGGG
* * * * * * * * * * ** *
126550 CAAATTA-TAGCCGTCCGATCTTTTACCTCAAGCTTGAGGCAGATCACTGTCAGCCAATCTCTTA
1 CAGATCACCATCAG-CCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATCTCTTA
** * * *
126614 TTCCAAGCCTGGGGCAAATTGCAACCATCCGATCTCTTACCTCAAGCCTGGGG
65 CCCCGAGCTTGGGGCAGATTGCAACCATCCGATCTCTTACC-CAAGCCTGGGG
* *
126667 CAGATTACAGCCATCTG---ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCT
1 CAGA-T-CA-CCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATCTCT
* * * *
126729 TACCCCGAGCTTGGGGTAGATTGCAACCATCCGATCTTTTACCCCGAGCCTGGAG
63 TACCCCGAGCTTGGGGCAGATTGCAACCATCCGATCTCTTA-CCCAAGCCTGGGG
* * *
126784 CAGATCATCATCCGCCAATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAACCAATCTCTTAC
1 CAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATCTCTTAC
* * * * * *
126849 TCCGAGCATAGGGCATATTGCAGA-CATCCGATCTCTTACCCGAGCTTGGGG
66 CCCGAGCTTGGGGCAGATTGCA-ACCATCCGATCTCTTACCCAAGCCTGGGG
* *
126900 CAGATCACCATCAGTCAGTCTCTTACC
1 CAGATCACCATCAGCCAATCTCTTACC
126927 TCGCGATAAG
Statistics
Matches: 492, Mismatches: 96, Indels: 47
0.77 0.15 0.07
Matches are distributed among these distances:
114 7 0.01
115 6 0.01
116 43 0.09
117 416 0.85
118 8 0.02
119 5 0.01
120 4 0.01
121 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (116 bp):
CAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATCTCTTAC
CCCGAGCTTGGGGCAGATTGCAACCATCCGATCTCTTACCCAAGCCTGGGG
Found at i:126427 original size:78 final size:77
Alignment explanation
Indices: 126199--126926 Score: 499
Period size: 78 Copynumber: 9.3 Consensus size: 77
126189 CAGCTAATGA
* * * * * * *
126199 CAGATCACCATCAGCCAATCTTTTACCCCGAGCTTGGGGCAGGTTACAATCGTTCGATCTTTTAC
1 CAGATCACCATCA-CCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGTCATCCGATCTCTTAC
*
126264 CTCGAGCTTGGGG
65 CCCGAGCTTGGGG
* * * * * * * * * * *
126277 TAGATTGCAACCAT--CCGATCTATTATCCCAAGCATGGAGAAGATCACCA-TCAACCAATCTCT
1 CAGA-T-C-ACCATCACCAATCTCTTACCCCGAGCCTGGGGCAGATTA-CAGTCATCCGATCTCT
126339 TACCCCGAGCTTGGGG
62 TACCCCGAGCTTGGGG
* * * *
126355 CAGATCACCATTAACCAATCTCTTACCCCGAGCTTGGGGCAGATTACAGTCATTCGATCTCATAC
1 CAGATCACCA-TCACCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGTCATCCGATCTCTTAC
*
126420 CCAGAGCTTGGGG
65 CCCGAGCTTGGGG
** ** * * * * *
126433 CAGATCACTGTCAACCAATCTCTTACCCTAAGCCTGAGGTAGATTGCAGCCATCCAATCTCTTAC
1 CAGATCACCATC-ACCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGTCATCCGATCTCTTAC
126498 CCCGAGCTTGGGG
65 CCCGAGCTTGGGG
* ** * * * * * *
126511 CAGATCATCATCAGCCAATCTCTTACCCTAAGCCTAGGGCAAATTATAGCCGTCCGATCTTTTAC
1 CAGATCACCATCA-CCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGTCATCCGATCTCTTAC
* * *
126576 CTCAAGCTTGAGG
65 CCCGAGCTTGGGG
** ** * * * **
126589 CAGATCACTGTCAGCCAATCTCTTATTCCAAGCCTGGGGCAAATTGCAACCATCCGATCTCTTAC
1 CAGATCACCATCA-CCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGTCATCCGATCTCTTAC
* * *
126654 CTCAAGCCTGGGG
65 CCCGAGCTTGGGG
** * * * *
126667 CAGATTACAGCCAT--CTGATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCAATCTCT
1 CAGA-T-CA-CCATCACCAATCTCTTACCCCGAGCCTGGGGCAGATTA-CAGTCATCCGATCTCT
126729 TACCCCGAGCTTGGGG
62 TACCCCGAGCTTGGGG
* * * *
126745 TAGATTGCAACCAT--CCGATCTTTTACCCCGAGCCTGGAGCAGA-T-CA-TCATCCGCCAATCT
1 CAGA-T-C-ACCATCACCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGTCATCCG---ATCT
126805 CTTACCCCGAGCTTGGGG
60 CTTACCCCGAGCTTGGGG
* * * * * * *
126823 TAGATCACCATCAACCAATCTCTTACTCCGAGCATAGGGCATATTGCAGACATCCGATCTCTTA-
1 CAGATCACCATC-ACCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGTCATCCGATCTCTTAC
126887 CCCGAGCTTGGGG
65 CCCGAGCTTGGGG
* *
126900 CAGATCACCATCAGTCAGTCTCTTACC
1 CAGATCACCATCA-CCAATCTCTTACC
126927 TCGCGATAAG
Statistics
Matches: 514, Mismatches: 111, Indels: 51
0.76 0.16 0.08
Matches are distributed among these distances:
75 16 0.03
76 4 0.01
77 40 0.08
78 428 0.83
79 8 0.02
80 5 0.01
81 13 0.03
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (77 bp):
CAGATCACCATCACCAATCTCTTACCCCGAGCCTGGGGCAGATTACAGTCATCCGATCTCTTACC
CCGAGCTTGGGG
Found at i:127992 original size:11 final size:11
Alignment explanation
Indices: 127978--128024 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
127968 AAATGTCTAT
127978 TAAATAATTAA
1 TAAATAATTAA
*
127989 TAAATAAATAA
1 TAAATAATTAA
128000 TAAAT-ATTATA
1 TAAATAATTA-A
128011 TTAAATAA-TAA
1 -TAAATAATTAA
128022 TAA
1 TAA
128025 TAAAAGAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
10 6 0.19
11 17 0.55
12 7 0.23
13 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAATAATTAA
Found at i:129014 original size:30 final size:30
Alignment explanation
Indices: 128848--129081 Score: 228
Period size: 30 Copynumber: 7.8 Consensus size: 30
128838 AGGAGGTCTC
* * *
128848 CAAACTTCTCAAAAATAATATTTTGACCC-
1 CAAACTTCTCTAAAATTACATTTTGACCCT
* *
128877 CTTAACTTCAT-AAAAATTACATTTTGACCCT
1 C-AAACTTC-TCTAAAATTACATTTTGACCCT
* *
128908 CAAACTT-TTTAAAAATTACATTTTAACCCT
1 CAAACTTCTCT-AAAATTACATTTTGACCCT
128938 CAAACTTCT-TAAAAATTACATTTT-AGCCCT
1 CAAACTTCTCT-AAAATTACATTTTGA-CCCT
* *
128968 CAAACTTTTCCAAAATTACATTTTGACCCT
1 CAAACTTCTCTAAAATTACATTTTGACCCT
* *
128998 CAAACTTCTCTAAAATTAGATTTT-AACCT
1 CAAACTTCTCTAAAATTACATTTTGACCCT
* * *
129027 CGAACTTTTCTAAAATTACATTTTAACCCT
1 CAAACTTCTCTAAAATTACATTTTGACCCT
* *
129057 CAAACTTATCCAAAATTACCATTTT
1 CAAACTTCTCTAAAATTA-CATTTT
129082 CCCCCAAATT
Statistics
Matches: 175, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.01
29 27 0.15
30 137 0.78
31 10 0.06
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
CAAACTTCTCTAAAATTACATTTTGACCCT
Found at i:129057 original size:59 final size:59
Alignment explanation
Indices: 128889--129089 Score: 264
Period size: 60 Copynumber: 3.4 Consensus size: 59
128879 TAACTTCATA
128889 AAAATTACATTTTGACCCTCAAACTTTT-TAAAAATTACATTTTAACCCTCAAACTTCT-T
1 AAAATTACATTTT-ACCCTCAAACTTTTCT-AAAATTACATTTTAACCCTCAAACTTCTCT
* *
128948 AAAAATTACATTTTAGCCCTCAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTCTCT
1 -AAAATTACATTTTA-CCCTCAAACTTTTCTAAAATTACATTTTAACCCTCAAACTTCTCT
* * * * *
129009 AAAATTAGATTTTAACCTCGAACTTTTCTAAAATTACATTTTAACCCTCAAACTTATCC
1 AAAATTACATTTTACCCTCAAACTTTTCTAAAATTACATTTTAACCCTCAAACTTCTCT
*
129068 AAAATTACCATTTT-CCCCCAAA
1 AAAATTA-CATTTTACCCTCAAA
129090 TTTCCAAAAG
Statistics
Matches: 124, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
59 52 0.42
60 71 0.57
61 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAATTACATTTTACCCTCAAACTTTTCTAAAATTACATTTTAACCCTCAAACTTCTCT
Found at i:129178 original size:30 final size:30
Alignment explanation
Indices: 128887--129179 Score: 218
Period size: 30 Copynumber: 9.9 Consensus size: 30
128877 CTTAACTTCA
*
128887 TAAAAATTACATTTTGACCCTCAAACTTTT-
1 TAAAAATTACATTTTAACCCTCAAA-TTTTC
*
128917 TAAAAATTACATTTTAACCCTCAAA-CTTC
1 TAAAAATTACATTTTAACCCTCAAATTTTC
*
128946 TTAAAAATTACATTTTAGCCCTCAAACTTTTC
1 -TAAAAATTACATTTTAACCCTCAAA-TTTTC
* * *
128978 -CAAAATTACATTTTGACCCTCAAACTTCTC
1 TAAAAATTACATTTTAACCCTCAAA-TTTTC
* *
129008 T-AAAATTAGATTTTAA-CCTCGAACTTTTC
1 TAAAAATTACATTTTAACCCTC-AAATTTTC
*
129037 T-AAAATTACATTTTAACCCTCAAACTTATC
1 TAAAAATTACATTTTAACCCTCAAA-TTTTC
* *
129067 -CAAAATTACCATTTT--CCCCCAAA-TTTC
1 TAAAAATTA-CATTTTAACCCTCAAATTTTC
* * * *
129094 CAAAAGTCACATTTTCGA-CCTCAAATTTTC
1 TAAAAATTACATTTT-AACCCTCAAATTTTC
* * *
129124 TAAAAGTT-CGATTTAAATCC-CAAATTTTC
1 TAAAAATTAC-ATTTTAACCCTCAAATTTTC
* *
129153 TAAAAATTTCAATTTTGACCC-CAAATT
1 TAAAAATTAC-ATTTTAACCCTCAAATT
129180 CCTCAAAAAT
Statistics
Matches: 215, Mismatches: 30, Indels: 36
0.77 0.11 0.13
Matches are distributed among these distances:
27 9 0.04
28 7 0.03
29 56 0.26
30 134 0.62
31 6 0.03
32 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
TAAAAATTACATTTTAACCCTCAAATTTTC
Found at i:133443 original size:28 final size:26
Alignment explanation
Indices: 133387--133446 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
133377 TAAGATAACT
* *
133387 ATATAAAAAATTTCAATTATTGAAAA
1 ATATAAAAAATTTCAAATATTAAAAA
* *
133413 ATATATAAAATTATTAAATATTAAAATA
1 ATATAAAAAATT-TCAAATATTAAAA-A
133441 ATATAA
1 ATATAA
133447 TATAAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 11 0.41
27 10 0.37
28 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
ATATAAAAAATTTCAAATATTAAAAA
Found at i:133984 original size:4 final size:4
Alignment explanation
Indices: 133975--134000 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
133965 TAAAAATAAT
133975 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
134001 AAATTAAGGC
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:134356 original size:18 final size:19
Alignment explanation
Indices: 134321--134363 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
134311 AAAATTCAAA
*
134321 AAAAAATAAAAAATATTTT
1 AAAAAATAAAAAATATTTC
* *
134340 AAAAAATCAACAA-ATTTC
1 AAAAAATAAAAAATATTTC
134358 AAAAAA
1 AAAAAA
134364 GTTATAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAAATAAAAAATATTTC
Found at i:135825 original size:29 final size:29
Alignment explanation
Indices: 135768--135825 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
135758 GACGAAATTA
* *
135768 AAAGTTCAAGTACCACATTGTACATTTTG
1 AAAGTACAAGTACCACATTGTAAATTTTG
*
135797 AAAGTACATGTACCACATTG-AAATATTTG
1 AAAGTACAAGTACCACATTGTAAAT-TTTG
135826 TTAAAGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (29 bp):
AAAGTACAAGTACCACATTGTAAATTTTG
Found at i:136346 original size:7 final size:7
Alignment explanation
Indices: 136311--136360 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
136301 AATATTTAAA
136311 ATATTTGT
1 ATATTT-T
136319 ATA-TTT
1 ATATTTT
136325 ACTATTTT
1 A-TATTTT
*
136333 CAAATTTT
1 -ATATTTT
136341 ATATTTT
1 ATATTTT
136348 ATA-TTT
1 ATATTTT
136354 ATATTTT
1 ATATTTT
136361 CTCATCAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
6 8 0.22
7 16 0.44
8 11 0.31
9 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (7 bp):
ATATTTT
Found at i:137736 original size:17 final size:17
Alignment explanation
Indices: 137709--137748 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
137699 ATAAATTCTA
*
137709 AATAGACTAAATATAAAT
1 AATA-ACTAAATAGAAAT
137727 AATAACTAAATAGAAAT
1 AATAACTAAATAGAAAT
137744 AATAA
1 AATAA
137749 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (17 bp):
AATAACTAAATAGAAAT
Done.