Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 93 of 120
Found at i:27626306 original size:51 final size:52
Alignment explanation
Indices: 27626237--27626380 Score: 144
Period size: 51 Copynumber: 2.9 Consensus size: 52
27626227 TTAAGATTTT
*
27626237 AAGGTTTTATGGTTTAGGGTTATTA-A-TTTA-AGGATTT-AGGGTTTTAAGTTA
1 AAGG-TTTAGGGTTTAGGGTTATTAGAGTTTAGA-G-TTTAAGGGTTTTAAGTTA
* *
27626288 ATGGTTTAGGGTTTTAGGG-T-TTAGAGTTTAGAGTTTAAGGTTTTTAAGTTA
1 AAGGTTTAGGG-TTTAGGGTTATTAGAGTTTAGAGTTTAAGGGTTTTAAGTTA
* *
27626339 AAGGTTTAGGGTTTAGGGTTA--AG-GTTTATAGGTTAAGGGTTT
1 AAGGTTTAGGGTTTAGGGTTATTAGAGTTTAGAGTTTAAGGGTTT
27626381 ATGTGTTTAG
Statistics
Matches: 79, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
49 19 0.24
50 20 0.25
51 39 0.49
52 1 0.01
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (52 bp):
AAGGTTTAGGGTTTAGGGTTATTAGAGTTTAGAGTTTAAGGGTTTTAAGTTA
Found at i:27626315 original size:29 final size:29
Alignment explanation
Indices: 27626234--27626331 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
27626224 AGTTTAAGAT
* * *
27626234 TTTAAGGTTTTATGGTTTAGGGTTATTAA
1 TTTAAGGTTTTAGGGTTTAGAGTTAATAA
* **
27626263 TTTAAGGATTTAGGGTTTTA-AGTTAATGG
1 TTTAAGGTTTTAGGG-TTTAGAGTTAATAA
* * * *
27626292 TTTAGGGTTTTAGGGTTTAGAGTTTAGAG
1 TTTAAGGTTTTAGGGTTTAGAGTTAATAA
27626321 TTTAAGGTTTT
1 TTTAAGGTTTT
27626332 TAAGTTAAAG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
28 4 0.07
29 47 0.85
30 4 0.07
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (29 bp):
TTTAAGGTTTTAGGGTTTAGAGTTAATAA
Found at i:27626323 original size:22 final size:22
Alignment explanation
Indices: 27626291--27626354 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
27626281 TAAGTTAATG
*
27626291 GTTTAGGGTTTTAGGGTTTAGA
1 GTTTAGAGTTTTAGGGTTTAGA
* *
27626313 GTTTAGAGTTTAAGGTTTTTA-A
1 GTTTAGAGTTTTAGG-GTTTAGA
* *
27626335 G-TTAAAGGTTTAGGGTTTAG
1 GTTTAGAGTTTTAGGGTTTAG
27626355 GGTTAAGGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
20 4 0.12
21 10 0.30
22 15 0.45
23 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.45
Consensus pattern (22 bp):
GTTTAGAGTTTTAGGGTTTAGA
Found at i:27626330 original size:14 final size:14
Alignment explanation
Indices: 27626263--27626477 Score: 91
Period size: 15 Copynumber: 14.8 Consensus size: 14
27626253 GGGTTATTAA
27626263 TTTAAGGATTTAGGG
1 TTTAAGG-TTTAGGG
* *
27626278 TTTTAA-GTTAATGG
1 -TTTAAGGTTTAGGG
*
27626292 TTTAGGGTTTTAGGG
1 TTTAAGG-TTTAGGG
*
27626307 TTT-AGAGTTTAGAG
1 TTTAAG-GTTTAGGG
*
27626321 TTTAAGGTTTTTA-AG
1 TTTAAGG--TTTAGGG
*
27626336 TTAAAGGTTTAGGG
1 TTTAAGGTTTAGGG
* *
27626350 TTT-AGGGTTAAGG
1 TTTAAGGTTTAGGG
*
27626363 TTTATAGGTTAAGGG
1 TTTA-AGGTTTAGGG
*
27626378 TTTATGTGTTTAGGG
1 TTTAAG-GTTTAGGG
*
27626393 TTTTAAAGTTTTAGGG
1 -TTT-AAGGTTTAGGG
* *
27626409 TTTAAGATTTTTA-AG
1 TTTAAG--GTTTAGGG
*
27626424 TTAAAGG-TTAGGG
1 TTTAAGGTTTAGGG
* * *
27626437 TTTTAGGTTAAGTG
1 TTTAAGGTTTAGGG
*
27626451 TTTATGGTTTTTAGGG
1 TTTAAGG--TTTAGGG
*
27626467 TTTAGGGTTTA
1 TTTAAGGTTTA
27626478 AAGTTTTTAA
Statistics
Matches: 149, Mismatches: 32, Indels: 38
0.68 0.15 0.17
Matches are distributed among these distances:
12 3 0.02
13 25 0.17
14 37 0.25
15 47 0.32
16 35 0.23
17 2 0.01
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:27626452 original size:65 final size:63
Alignment explanation
Indices: 27626383--27626737 Score: 285
Period size: 65 Copynumber: 5.4 Consensus size: 63
27626373 AAGGGTTTAT
* *
27626383 GTGTTTAGGGTTTTAAAGTTTTAGGGTTTAAGATTTTTAAGTTAAAGGTTAGGGTTTTAGGTTAA
1 GTGTTTAGGGTTTT-AAG-TTAAGGGTTTAAGATTTTTAAGTTAAAGGTTAGGGTTTTAAGTTAA
* * * *
27626448 GTGTTTATGGTTTTTAGGGTTTAGGGTTTAA-AGTTTTTAAG-TAAAGAATTTAGGG-TTTATAG
1 GTGTTTA-GGGTTTTA-AGTTAAGGGTTTAAGA-TTTTTAAGTTAAAG--GTTAGGGTTTTA-AG
*
27626510 TTTTA
60 -TTAA
* ** *
27626515 -TGATTTAGGAATTTTAAGTTAAGGGTTT-AGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTA
1 GTG-TTTAGG-GTTTTAAGTTAAGGGTTTAAGATTTTTAAGTTAAAGGTTAGGG-TTTTAAGTTA
27626578 A
63 A
* * * * *
27626579 GGGTTTATGGATTTTAAAGTTTAGGGTTTAA-AGTTTTTAGGTTAAGGGTTGAGGGTTTTAAGTT
1 GTGTTTA-GGGTTTT-AAGTTAAGGGTTTAAGA-TTTTTAAGTTAAAGGTT-AGGGTTTTAAGTT
27626643 AA
62 AA
* * * *
27626645 G-GGTTAGGGTTTGTAAGTTAAGGGTTTATGGTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTTA
1 GTGTTTAGGGTTT-TAAGTTAAGGGTTTAAGATTTTTAAGTTAAAGG-TTAGGG-TTTTAAGTTA
27626709 A
63 A
*
27626710 GAG-TTAGGGTTTTTAAGTTAAGGGTTTA
1 GTGTTTAGGG-TTTTAAGTTAAGGGTTTA
27626738 GGGTTAGGGT
Statistics
Matches: 239, Mismatches: 26, Indels: 50
0.76 0.08 0.16
Matches are distributed among these distances:
64 59 0.25
65 96 0.40
66 68 0.28
67 16 0.07
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (63 bp):
GTGTTTAGGGTTTTAAGTTAAGGGTTTAAGATTTTTAAGTTAAAGGTTAGGGTTTTAAGTTAA
Found at i:27626464 original size:22 final size:22
Alignment explanation
Indices: 27626023--27626742 Score: 459
Period size: 21 Copynumber: 33.0 Consensus size: 22
27626013 TCAAATTATA
27626023 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
27626044 TTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * **
27626065 TTTTATTTAATGG-TTACAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
27626086 TTAAAG-TAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
27626107 TTTAATTTAAGGG-TTAGGG--
1 TTTAAGTTAAGGGTTTAGGGTT
*
27626126 TTT---TTAAGGTTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
27626145 TTTAATTTAAG-GATTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
27626166 TTTAAGGTTTTAGAGTTTAAGGTT
1 TTTAA-G-TTAAGGGTTTAGGGTT
* *
27626190 TTTAATTTAAGGGTTTATGGGGT
1 TTTAAGTTAAGGGTTTA-GGGTT
* * *
27626213 TTTAAGTTAAGAGTTTA-AGAT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
27626234 TTTAAGGTTTTATGGTTTAGGGTT
1 TTTAA-G-TTAAGGGTTTAGGGTT
* * *
27626258 ATTAATTTAAGGATTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
*
27626279 TTTAAGTTAATGGTTTAGGGTTTT
1 TTTAAGTTAAGGGTTTAGGG--TT
* * *
27626303 AGGGTTTAGAGTTTAGAGTTTAAGGTT
1 ----TTTA-AGTTAAGGGTTTAGGGTT
*
27626330 TTTAAGTTAAAGGTTTAGGG--
1 TTTAAGTTAAGGGTTTAGGGTT
* *
27626350 TTTAGGGTTAA-GGTTTATAGG--
1 TTTA-AGTTAAGGGTTTA-GGGTT
* *
27626371 -TTAAGGGTTTATGTGTTTAGGGTT
1 TTTAA--G-TTAAGGGTTTAGGGTT
* * * *
27626395 TTAAAGTTTTAGGGTTTAAGATT
1 TTTAAG-TTAAGGGTTTAGGGTT
*
27626418 TTTAAGTTAAAGG-TTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
27626438 TTTAGGTTAAGTGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * **
27626460 TTTAGGGTTTAGGGTTTAAAGTT
1 TTTA-AGTTAAGGGTTTAGGGTT
* **
27626483 TTTAAGTAAAGAATTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * * **
27626505 TAT-AGTTTTATGATTTAGGAAT
1 TTTAAG-TTAAGGGTTTAGGGTT
27626527 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
27626548 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
27626569 TTTAAGTTAAGGGTTTATGGATT
1 TTTAAGTTAAGGGTTTA-GGGTT
* * **
27626592 TTAAAGTTTAGGGTTTAAAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
27626614 TTTAGGTTAAGGGTTGAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
27626635 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
27626656 TGTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
27626678 TTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
27626700 TTTAATTTAAGAG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
27626721 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
27626743 AGGGTTTTTA
Statistics
Matches: 535, Mismatches: 121, Indels: 85
0.72 0.16 0.11
Matches are distributed among these distances:
16 6 0.01
17 6 0.01
19 6 0.01
20 40 0.07
21 182 0.34
22 157 0.29
23 96 0.18
24 21 0.04
25 3 0.01
27 2 0.00
28 4 0.01
29 12 0.02
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:27626624 original size:87 final size:86
Alignment explanation
Indices: 27626526--27626742 Score: 310
Period size: 87 Copynumber: 2.5 Consensus size: 86
27626516 GATTTAGGAA
*
27626526 TTTTAAGTTAAGGGTTTAGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTATGGAT
1 TTTTAAGTTAAGGGTTTAGGGTTTTAAGTTAAGGGTTAGGGTTTGTAAGTTAAGGGTTTATGG-T
* *
27626591 TTTAAAGTTTAGGGTTTAAAGT
65 TTTAAAGTTAAAGGTTTAAAGT
* *
27626613 TTTTAGGTTAAGGGTTGAGGGTTTTAAGTTAAGGGTTAGGGTTTGTAAGTTAAGGGTTTATGGTT
1 TTTTAAGTTAAGGGTTTAGGGTTTTAAGTTAAGGGTTAGGGTTTGTAAGTTAAGGGTTTATGGTT
* **
27626678 TTTAAGTTAAAGGTTTAGGGT
66 TTAAAGTTAAAGGTTTAAAGT
* *
27626699 TTTTAATTTAAGAG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGG-TTAGGGTT
27626743 AGGGTTTTTA
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
85 5 0.04
86 43 0.37
87 68 0.59
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (86 bp):
TTTTAAGTTAAGGGTTTAGGGTTTTAAGTTAAGGGTTAGGGTTTGTAAGTTAAGGGTTTATGGTT
TTAAAGTTAAAGGTTTAAAGT
Found at i:27626743 original size:28 final size:28
Alignment explanation
Indices: 27626705--27626770 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
27626695 GGGTTTTTAA
27626705 TTTAAGAGTTAGGGTTTTTAAGTTAAGGG
1 TTTAAG-GTTAGGGTTTTTAAGTTAAGGG
* *
27626734 TTTAGGGTTAGGGTTTTTAGGTTAAGGG
1 TTTAAGGTTAGGGTTTTTAAGTTAAGGG
27626762 TTTAAGGTT
1 TTTAAGGTT
27626771 TGTCAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (28 bp):
TTTAAGGTTAGGGTTTTTAAGTTAAGGG
Found at i:27626764 original size:43 final size:43
Alignment explanation
Indices: 27626620--27626745 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 43
27626610 AGTTTTTAGG
* * * * *
27626620 TTAAGGGTTGAGGG-TTTTAAGTT-AAGGGTTAGGGTTTGTAAG
1 TTAAGAGTT-AGGGTTTTTAAGTTAAAGGTTTAGGGTTAGGAAT
* * ***
27626662 TTAAGGGTTTATGGTTTTTAAGTTAAAGGTTTAGGGTTTTTAAT
1 TTAAGAG-TTAGGGTTTTTAAGTTAAAGGTTTAGGGTTAGGAAT
*
27626706 TTAAGAGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTAGG
1 TTAAGAGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTTAGG
27626746 GTTTTTAGGT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
42 10 0.14
43 39 0.55
44 22 0.31
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.43
Consensus pattern (43 bp):
TTAAGAGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTTAGGAAT
Found at i:27627354 original size:18 final size:18
Alignment explanation
Indices: 27627314--27627357 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
27627304 GGACTCGAAA
* *
27627314 AAGGAAACATATAAGGGT
1 AAGGAAACATAAAAGGGC
* *
27627332 TAGGATACATAAAAGGGC
1 AAGGAAACATAAAAGGGC
27627350 AAGGAAAC
1 AAGGAAAC
27627358 GCACTTGGCA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.27, T:0.14
Consensus pattern (18 bp):
AAGGAAACATAAAAGGGC
Found at i:27628139 original size:20 final size:21
Alignment explanation
Indices: 27628097--27628140 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
27628087 TAATTTTGTT
*
27628097 TTTTAAAAATCTACATAATAA
1 TTTTAAAAATCTACATAAAAA
27628118 TTTT-AAAATCTA-ATATAAAA
1 TTTTAAAAATCTACATA-AAAA
27628138 TTT
1 TTT
27628141 ACCTCGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTAAAAATCTACATAAAAA
Found at i:27628692 original size:27 final size:27
Alignment explanation
Indices: 27628662--27628714 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
27628652 GTCTAAAGTG
27628662 ATAGTGCACTCTCCACATGAAAGATGA
1 ATAGTGCACTCTCCACATGAAAGATGA
27628689 ATAGTGCACTCTCCACATGAAAGATG
1 ATAGTGCACTCTCCACATGAAAGATG
27628715 GAATGTGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (27 bp):
ATAGTGCACTCTCCACATGAAAGATGA
Found at i:27629105 original size:16 final size:16
Alignment explanation
Indices: 27629084--27629115 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27629074 GTTTAAAAAA
27629084 TTTTTAAAAATAATTT
1 TTTTTAAAAATAATTT
*
27629100 TTTTTAAAAATTATTT
1 TTTTTAAAAATAATTT
27629116 AAAAAGAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAAAAATAATTT
Found at i:27629213 original size:12 final size:11
Alignment explanation
Indices: 27629177--27629231 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
27629167 TTAAATATGG
27629177 ATTTGAGAGAA
1 ATTTGAGAGAA
*
27629188 ATTTG-GAAAGA
1 ATTTGAGAGA-A
27629199 ATTTGAGAGTAA
1 ATTTGAGAG-AA
27629211 A-TTGAGAGGAA
1 ATTTGAGA-GAA
27629222 ATTTGAGAGA
1 ATTTGAGAGA
27629232 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.08
11 22 0.59
12 11 0.30
13 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:27639040 original size:11 final size:12
Alignment explanation
Indices: 27639019--27639044 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27639009 TTCTTGGGGG
27639019 AAAAGGAAAAAA
1 AAAAGGAAAAAA
27639031 AAAAGGAAAAAA
1 AAAAGGAAAAAA
27639043 AA
1 AA
27639045 TATTTTCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAAAA
Found at i:27640779 original size:16 final size:16
Alignment explanation
Indices: 27640731--27640772 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
27640721 TTCATTGTAT
27640731 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
**
27640747 TATAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
27640763 TGGAATAGAG
1 TGGAATAGAG
27640773 ATGTAATAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:27640854 original size:44 final size:45
Alignment explanation
Indices: 27640761--27640855 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 45
27640751 ATAGAGGCGT
* * *
27640761 AATGGAATAGAGATGTAATAGCAATTCAATTGTTTGGTTGAATGT
1 AATGGAATAGAGACGTAATAGCAATTCAATTGTTTAGTTGAATGG
* *
27640806 AATGGAATAGAGACGTAATAG-TATTC-TTGTGTTTAGTTGAATGG
1 AATGGAATAGAGACGTAATAGCAATTCAAT-TGTTTAGTTGAATGG
27640850 AATGGA
1 AATGGA
27640856 GGTGTAATAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (45 bp):
AATGGAATAGAGACGTAATAGCAATTCAATTGTTTAGTTGAATGG
Found at i:27641047 original size:17 final size:18
Alignment explanation
Indices: 27641014--27641047 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27641004 TATTATTAAC
*
27641014 TATATTTTAATTAAAATA
1 TATAATTTAATTAAAATA
27641032 TATAATTTAA-TAAAAT
1 TATAATTTAATTAAAAT
27641048 TCTTAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAATTTAATTAAAATA
Found at i:27641206 original size:120 final size:120
Alignment explanation
Indices: 27640993--27641454 Score: 843
Period size: 120 Copynumber: 3.9 Consensus size: 120
27640983 TTAATCATAT
* * * *
27640993 TTTAACATAATTATTATTAACTATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
**
27641058 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATGCTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
*
27641113 TTTAAAATTATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
27641178 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
27641233 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
27641298 AAATATTCTTATATGAATTTACTAAAATTATAATATATAATAATATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
*
27641353 TTTAAAATAATTATAATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
27641418 AAATATTCTTATATGAATTTACTAAAATCATAATATA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATA
27641455 NNNNNNNNNN
Statistics
Matches: 331, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 331 1.00
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
Found at i:27641255 original size:26 final size:26
Alignment explanation
Indices: 27641225--27641383 Score: 78
Period size: 26 Copynumber: 6.5 Consensus size: 26
27641215 TAATAATATA
27641225 AAATATAATTTAAAATAATTATTATT
1 AAATATAATTTAAAATAATTATTATT
*
27641251 AAATATAATTTAATAA-AAATA-TA-T
1 AAATATAATTTAA-AATAATTATTATT
* ** *
27641275 -AATTTAA--TAAAATTCTTAATATT
1 AAATATAATTTAAAATAATTATTATT
* *
27641298 AAATAT--TCTT-ATATGAA-T-TTACTA
1 AAATATAAT-TTAAAAT-AATTATTA-TT
* *
27641322 AAATTATAATATATAATAA-TA-TA--
1 AAA-TATAATTTAAAATAATTATTATT
*
27641345 AAATATAATTTAAAATAATTATAATT
1 AAATATAATTTAAAATAATTATTATT
27641371 AAATATAATTTAA
1 AAATATAATTTAA
27641384 TAAAAATATA
Statistics
Matches: 97, Mismatches: 17, Indels: 38
0.64 0.11 0.25
Matches are distributed among these distances:
20 2 0.02
21 5 0.05
22 15 0.15
23 14 0.14
24 14 0.14
25 6 0.06
26 36 0.37
27 5 0.05
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (26 bp):
AAATATAATTTAAAATAATTATTATT
Found at i:27641408 original size:28 final size:28
Alignment explanation
Indices: 27641307--27641408 Score: 88
Period size: 28 Copynumber: 3.7 Consensus size: 28
27641297 TAAATATTCT
*
27641307 TATATGAATTTACTAAAATTATAATATATAA
1 TATAT-AATTTAATAAAATT-TAATA-ATAA
*
27641338 TAATATAA---AATATAATTTAA-AATAA
1 T-ATATAATTTAATAAAATTTAATAATAA
* * *
27641363 T-TATAATTAAATATAATTTAATAAAAA
1 TATATAATTTAATAAAATTTAATAATAA
27641390 TATATAATTTAATAAAATT
1 TATATAATTTAATAAAATT
27641409 CTTAATATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
23 5 0.08
25 5 0.08
26 13 0.22
27 8 0.13
28 22 0.37
31 3 0.05
32 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
TATATAATTTAATAAAATTTAATAATAA
Found at i:27641419 original size:18 final size:18
Alignment explanation
Indices: 27641253--27641406 Score: 80
Period size: 18 Copynumber: 7.9 Consensus size: 18
27641243 TTATTATTAA
27641253 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
27641271 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
* ****
27641289 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAAAT
*
27641308 ATATGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
*
27641326 -TATAATATATAATAATATAAA
1 ATATAAT-T-TAATAA-A-AAT
27641347 ATATAATTTAAAATAATTATAATT
1 ATATAATTT--AATAA--A-AA-T
27641371 AAATATAATTTAATAAAAAT
1 --ATATAATTTAATAAAAAT
27641391 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
27641407 TTCTTAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
16 3 0.03
17 8 0.08
18 40 0.38
19 10 0.09
20 6 0.06
21 8 0.08
22 12 0.11
23 5 0.05
24 5 0.05
26 9 0.08
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.42
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:27642179 original size:7 final size:7
Alignment explanation
Indices: 27642167--27642192 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27642157 AAGGAAATAT
27642167 ATATCCA
1 ATATCCA
27642174 ATATCCA
1 ATATCCA
27642181 ATATCCA
1 ATATCCA
27642188 ATATC
1 ATATC
27642193 ACTAGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (7 bp):
ATATCCA
Found at i:27646279 original size:19 final size:19
Alignment explanation
Indices: 27646255--27646308 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
27646245 AATCATATCT
27646255 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
27646274 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
27646293 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
27646309 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:27646304 original size:38 final size:40
Alignment explanation
Indices: 27646232--27646308 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
27646222 AAATTAAATC
27646232 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
27646274 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
27646309 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:27646639 original size:43 final size:42
Alignment explanation
Indices: 27646592--27646696 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 42
27646582 TAAAAAATAT
*
27646592 ATATATGTATGTGTATATA-CATAAAATTATAAAAATATGAAAA
1 ATATATGTATGTATATATATCATAAAATTAT-AAAATAT-AAAA
**
27646635 ATATATGTATGTATATATATTTTAAAATTATAAAATATAAAA
1 ATATATGTATGTATATATATCATAAAATTATAAAATATAAAA
* * *
27646677 ATATATCTAAGTATGTATAT
1 ATATATGTATGTATATATAT
27646697 ATACATATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 21 0.38
43 25 0.45
44 9 0.16
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (42 bp):
ATATATGTATGTATATATATCATAAAATTATAAAATATAAAA
Found at i:27646696 original size:42 final size:44
Alignment explanation
Indices: 27646613--27646696 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 44
27646603 TGTATATACA
* *
27646613 TAAAATTATAAAAATATGAAAAATATATGTATGTATATATATTT
1 TAAAATTATAAAAATATGAAAAATATATCTAAGTATATATATTT
*
27646657 TAAAATTAT-AAAATAT-AAAAATATATCTAAGTATGTATAT
1 TAAAATTATAAAAATATGAAAAATATATCTAAGTATATATAT
27646697 ATACATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 21 0.57
43 7 0.19
44 9 0.24
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (44 bp):
TAAAATTATAAAAATATGAAAAATATATCTAAGTATATATATTT
Found at i:27646697 original size:2 final size:2
Alignment explanation
Indices: 27646692--27646755 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
27646682 TCTAAGTATG
* * * * *
27646692 TA TA TA TA CA TA TA TA TG TA TA TA AA T- TA -A AA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
27646732 TA TA TA TG TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
27646756 AAAATTATGA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:27646714 original size:10 final size:10
Alignment explanation
Indices: 27646688--27646755 Score: 63
Period size: 10 Copynumber: 7.0 Consensus size: 10
27646678 TATATCTAAG
27646688 TATGTATATA
1 TATGTATATA
*
27646698 TA--CATATA
1 TATGTATATA
27646706 TATGTATATA
1 TATGTATATA
* *
27646716 AAT-TA-AAA
1 TATGTATATA
27646724 TATGTATATATA
1 TATG--TATATA
27646736 TATGTATATA
1 TATGTATATA
27646746 TATGTATATA
1 TATGTATATA
27646756 AAAATTATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
8 11 0.24
9 2 0.04
10 25 0.54
11 2 0.04
12 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (10 bp):
TATGTATATA
Found at i:27646726 original size:18 final size:20
Alignment explanation
Indices: 27646705--27646757 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
27646695 ATATACATAT
27646705 ATATGTATATAAAT-TA-AA
1 ATATGTATATAAATGTATAA
*
27646723 ATATGTATATATATATGTATAT
1 ATATGTATATA-A-ATGTATAA
27646745 ATATGTATATAAA
1 ATATGTATATAAA
27646758 AATTATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
20 3 0.10
21 3 0.10
22 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATGTATATAAATGTATAA
Found at i:27648793 original size:60 final size:60
Alignment explanation
Indices: 27648691--27648822 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 60
27648681 TACACTAGTA
* ** *
27648691 GTCAGCCAACTATTAATAAATTTATCTTTTGGTCATTTAACTATGAAAAGTTATAAAATG
1 GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
* * * * *
27648751 GTTATCCAACTATTAGTAAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
1 GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
27648811 GTCACCCAACTA
1 GTCACCCAACTA
27648823 CTCAATTTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (60 bp):
GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
Found at i:27648843 original size:60 final size:59
Alignment explanation
Indices: 27648719--27648845 Score: 139
Period size: 60 Copynumber: 2.1 Consensus size: 59
27648709 AATTTATCTT
** * * * * *
27648719 TTGGTCATTTAACTATGAAAAGTTATAAAATGGTTATCCAACTATTAGTAAATTTCTTTT
1 TTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTATCAG-AAATTTCTTTC
**
27648779 TTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTACTCA-ATTTTGTCTTTC
1 TTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTA-TCAGAAATT-TCTTTC
27648839 TTGGTCA
1 TTGGTCA
27648846 CTAACTGGCT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 3 0.05
60 51 0.91
61 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (59 bp):
TTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTATCAGAAATTTCTTTC
Found at i:27652114 original size:31 final size:31
Alignment explanation
Indices: 27652077--27652141 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
27652067 AGCCAGCTGG
*
27652077 TGACCAAAAAAGATAA-A-ATTGAATAGTTGGA
1 TGACCAAAAAAGA-AATATACT-AATAGTTGGA
27652108 TGACCAAAAAAGAAATATACTAATAGTTGGA
1 TGACCAAAAAAGAAATATACTAATAGTTGGA
27652139 TGA
1 TGA
27652142 TAACTAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 2 0.06
31 27 0.87
32 2 0.06
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.23
Consensus pattern (31 bp):
TGACCAAAAAAGAAATATACTAATAGTTGGA
Found at i:27655138 original size:39 final size:39
Alignment explanation
Indices: 27655093--27655210 Score: 148
Period size: 39 Copynumber: 3.3 Consensus size: 39
27655083 TAAAATTTAA
27655093 TATTAAGATAATCACTTTATTATTAATTTAATAAAATAC
1 TATTAAGATAATCACTTTATTATTAATTTAATAAAATAC
* *
27655132 TATTAAGATAA--A---TATTA--AATTTAAT---TTAA
1 TATTAAGATAATCACTTTATTATTAATTTAATAAAATAC
27655161 TATTAAGATAATCACTTTATTATTAATTTAATAAAATAC
1 TATTAAGATAATCACTTTATTATTAATTTAATAAAATAC
27655200 TATTAAGATAA
1 TATTAAGATAA
27655211 ATATTAAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
29 13 0.20
31 1 0.02
32 8 0.12
34 10 0.15
36 8 0.12
37 1 0.02
39 24 0.37
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (39 bp):
TATTAAGATAATCACTTTATTATTAATTTAATAAAATAC
Found at i:27655148 original size:31 final size:32
Alignment explanation
Indices: 27655113--27655224 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 32
27655103 ATCACTTTAT
27655113 TATT-AATTTAATAAAATACTATTAAGATAAA
1 TATTAAATTTAATAAAATACTATTAAGATAAA
* *
27655144 TATTAAATTTAAT---TTAATATTAAGATAATCA
1 TATTAAATTTAATAAAATACTATTAAGATAA--A
27655175 CTTTATTATTAATTTAATAAAATACTATTAAGATAAA
1 ---TATTA--AATTTAATAAAATACTATTAAGATAAA
27655212 TATTAAATTTAAT
1 TATTAAATTTAAT
27655225 TTAATATTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
29 13 0.20
31 5 0.08
32 16 0.24
34 10 0.15
36 8 0.12
37 1 0.02
39 13 0.20
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (32 bp):
TATTAAATTTAATAAAATACTATTAAGATAAA
Found at i:27655160 original size:68 final size:68
Alignment explanation
Indices: 27655086--27655234 Score: 298
Period size: 68 Copynumber: 2.2 Consensus size: 68
27655076 TTATCTATAA
27655086 AATTTAATATTAAGATAATCACTTTATTATTAATTTAATAAAATACTATTAAGATAAATATTAAA
1 AATTTAATATTAAGATAATCACTTTATTATTAATTTAATAAAATACTATTAAGATAAATATTAAA
27655151 TTT
66 TTT
27655154 AATTTAATATTAAGATAATCACTTTATTATTAATTTAATAAAATACTATTAAGATAAATATTAAA
1 AATTTAATATTAAGATAATCACTTTATTATTAATTTAATAAAATACTATTAAGATAAATATTAAA
27655219 TTT
66 TTT
27655222 AATTTAATATTAA
1 AATTTAATATTAA
27655235 ATGTATTAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 81 1.00
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (68 bp):
AATTTAATATTAAGATAATCACTTTATTATTAATTTAATAAAATACTATTAAGATAAATATTAAA
TTT
Found at i:27655162 original size:37 final size:37
Alignment explanation
Indices: 27655115--27655230 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 37
27655105 CACTTTATTA
27655115 TTAATTTAATAAAATACTATTAAGATAAATATTAAAT
1 TTAATTTAATAAAATACTATTAAGATAAATATTAAAT
* *
27655152 TTAA-TT--T---A-A-TATTAAGAT-AATCACTTTATT
1 TTAATTTAATAAAATACTATTAAGATAAAT-A-TTAAAT
27655182 ATTAATTTAATAAAATACTATTAAGATAAATATTAAAT
1 -TTAATTTAATAAAATACTATTAAGATAAATATTAAAT
27655220 TTAATTTAATA
1 TTAATTTAATA
27655231 TTAAATGTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 24
0.69 0.04 0.26
Matches are distributed among these distances:
28 3 0.05
29 10 0.16
30 5 0.08
31 5 0.08
32 2 0.03
34 2 0.03
36 2 0.03
37 16 0.25
38 5 0.08
39 10 0.16
40 3 0.05
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (37 bp):
TTAATTTAATAAAATACTATTAAGATAAATATTAAAT
Found at i:27655251 original size:37 final size:37
Alignment explanation
Indices: 27655183--27655253 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
27655173 CACTTTATTA
*
27655183 TTAATTTAATAAAATACTATTAAGATAAATATTAAAT
1 TTAATTTAATAAAATACTATTAAAATAAATATTAAAT
*
27655220 TTAATTTAATATTAAAT-GTATTAAAAT-AATATTA
1 TTAATTTAATA--AAATACTATTAAAATAAATATTA
27655254 TTTCCAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
37 18 0.60
38 8 0.27
39 4 0.13
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (37 bp):
TTAATTTAATAAAATACTATTAAAATAAATATTAAAT
Found at i:27655253 original size:68 final size:68
Alignment explanation
Indices: 27655086--27655253 Score: 230
Period size: 68 Copynumber: 2.5 Consensus size: 68
27655076 TTATCTATAA
*** *
27655086 AATTTAATATTAAGATAATCACTTTATTATTAATTTAATAAAATACTATTAAGATAAATATTAAA
1 AATTTAATATTAAGATAATCAAAATAATATTAATTTAATAAAATACTATTAAGATAAATATTAAA
27655151 TTT
66 TTT
*** *
27655154 AATTTAATATTAAGATAATCACTTTATTATTAATTTAATAAAATACTATTAAGATAAATATTAAA
1 AATTTAATATTAAGATAATCAAAATAATATTAATTTAATAAAATACTATTAAGATAAATATTAAA
27655219 TTT
66 TTT
* *
27655222 AATTTAATATTAA-ATGTATTAAAATAATATTA
1 AATTTAATATTAAGAT-AATCAAAATAATATTA
27655254 TTTCCAGAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
67 2 0.02
68 91 0.98
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (68 bp):
AATTTAATATTAAGATAATCAAAATAATATTAATTTAATAAAATACTATTAAGATAAATATTAAA
TTT
Found at i:27655505 original size:19 final size:19
Alignment explanation
Indices: 27655481--27655517 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27655471 GACCATTGGC
27655481 CCGATTTCACATAACAAGT
1 CCGATTTCACATAACAAGT
*
27655500 CCGATTTCACATAGCAAG
1 CCGATTTCACATAACAAG
27655518 CCTGGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (19 bp):
CCGATTTCACATAACAAGT
Found at i:27660533 original size:42 final size:42
Alignment explanation
Indices: 27660470--27660553 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
27660460 GGATGGTTTC
* * *
27660470 GTTTCCCATTTGGGATTTTTTGGGTATCTCAGGATTGCCTTT
1 GTTTCCCATTTGGGATATTTTGAGTATCCCAGGATTGCCTTT
*
27660512 GTTTCCCGTTTGGGATATTTTGAGTATCCCAGGATTGCCTTT
1 GTTTCCCATTTGGGATATTTTGAGTATCCCAGGATTGCCTTT
27660554 CTTGCCTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (42 bp):
GTTTCCCATTTGGGATATTTTGAGTATCCCAGGATTGCCTTT
Found at i:27662497 original size:41 final size:39
Alignment explanation
Indices: 27662382--27662517 Score: 132
Period size: 41 Copynumber: 3.5 Consensus size: 39
27662372 ACCAGTTTGG
* * * *
27662382 CACCCAGTGCCTCATCGGATAATTCTAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGAATAA-TCCAAGTAGTAAATTGA
* * * * * *
27662422 CACCTAGTGTCTCATCGACTAAACC--GAAGTAAATTGG
1 CACCCAGTGCCTCATCGAATAATCCAAGTAGTAAATTGA
27662459 CACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCC-AAGTAGTAAATTGA
*
27662500 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
27662518 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 24 0.32
38 5 0.07
39 1 0.01
40 18 0.24
41 27 0.36
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAATCCAAGTAGTAAATTGA
Found at i:27664325 original size:20 final size:21
Alignment explanation
Indices: 27664302--27664358 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
27664292 AATAAATACC
27664302 AAAAATTTATTTTAAAAATTA
1 AAAAATTTATTTTAAAAATTA
**
27664323 AAAAAAGTATTTT-AAAATT-
1 AAAAATTTATTTTAAAAATTA
*
27664342 -AAAATTTTTTTTAAAAA
1 AAAAATTTATTTTAAAAA
27664359 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.30
19 4 0.13
20 6 0.20
21 11 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAAATTTATTTTAAAAATTA
Found at i:27664374 original size:11 final size:11
Alignment explanation
Indices: 27664350--27664420 Score: 71
Period size: 11 Copynumber: 6.7 Consensus size: 11
27664340 TTAAAATTTT
27664350 TTTTAAAAAGTA
1 TTTTAAAAA-TA
27664362 TTTTAAAAATA
1 TTTTAAAAATA
27664373 TTTT--AAA-A
1 TTTTAAAAATA
27664381 -TTTAAAAATA
1 TTTTAAAAATA
* *
27664391 -ATAAAAAAGTA
1 TTTTAAAAA-TA
27664402 TTTTAAAAATA
1 TTTTAAAAATA
27664413 TTTTAAAA
1 TTTTAAAA
27664421 TTAAAAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
7 3 0.06
8 1 0.02
9 6 0.12
10 7 0.14
11 18 0.36
12 15 0.30
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:27664426 original size:17 final size:17
Alignment explanation
Indices: 27664404--27664450 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
27664394 AAAAAGTATT
*
27664404 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
27664421 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
27664438 ATAAATATATTTA
1 TTAAAAATATTTA
27664451 TTACCCGGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:27664436 original size:40 final size:40
Alignment explanation
Indices: 27664324--27664438 Score: 144
Period size: 40 Copynumber: 2.8 Consensus size: 40
27664314 TAAAAATTAA
*** *
27664324 AAAAAGTATTTTAAAATTAAAATTTTTTTTAAAAAGTATTTT
1 AAAAA-TATTTTAAAATTAAAA-AAATTTAAAAAAGTATTTT
27664366 AAAAATATTTTAAAATTTAAAAATAA--TAAAAAAGTATTTT
1 AAAAATATTTTAAAA-TTAAAAA-AATTTAAAAAAGTATTTT
27664406 AAAAATATTTTAAAATTAAAAAAATTTAAAAAA
1 AAAAATATTTTAAAATTAAAAAAATTTAAAAAA
27664439 TAAATATATT
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
38 2 0.03
39 7 0.11
40 35 0.54
41 10 0.15
42 11 0.17
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (40 bp):
AAAAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTT
Found at i:27669379 original size:35 final size:35
Alignment explanation
Indices: 27669340--27669427 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
27669330 CTCTTTACGA
* *
27669340 GGTGTCTCATTAAAGGGCCTATAAACCGTTTACAT
1 GGTGTCTCATTGAAGGACCTATAAACCGTTTACAT
* * *
27669375 GGTGTTGTC-TCGAAGGACCTATAAATCGTTTACAT
1 GGTG-TCTCATTGAAGGACCTATAAACCGTTTACAT
*
27669410 GGTGTCGCATTGAAGGAC
1 GGTGTCTCATTGAAGGAC
27669428 AAGTCGATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
34 2 0.05
35 38 0.88
36 3 0.07
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (35 bp):
GGTGTCTCATTGAAGGACCTATAAACCGTTTACAT
Found at i:27674650 original size:29 final size:31
Alignment explanation
Indices: 27674603--27674668 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 31
27674593 AAAAAATGAC
*
27674603 TATATAAAATATTTCAATA-AA-TAAAATAA
1 TATATAAAATATATCAATATAATTAAAATAA
27674632 TATATAAAAT-TATCAAATATTCAATTAAAATAA
1 TATATAAAATATATC-AATA-T-AATTAAAATAA
27674665 TATA
1 TATA
27674669 AATATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 3 0.10
29 14 0.45
32 2 0.06
33 12 0.39
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (31 bp):
TATATAAAATATATCAATATAATTAAAATAA
Found at i:27675248 original size:49 final size:50
Alignment explanation
Indices: 27675124--27675254 Score: 151
Period size: 49 Copynumber: 2.7 Consensus size: 50
27675114 ATATTGTATC
*
27675124 ATAATTATTTT-TCTCTAATTACTTTAAATTAATTAAGAGATAAAAATAA
1 ATAATTATTTTATCTCTAATTACATTAAATTAATTAAGAGATAAAAATAA
* * * * * * * * *
27675173 A-AAATAATTTATCACTACTTAGATTAAAATAATTAAGTGATAATATTAA
1 ATAATTATTTTATCTCTAATTACATTAAATTAATTAAGAGATAAAAATAA
27675222 ATAATTATTTTATCTCTAATTA-ATTAAATTAAT
1 ATAATTATTTTATCTCTAATTACATTAAATTAAT
27675255 AGAAGATAAA
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
48 7 0.11
49 42 0.65
50 16 0.25
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (50 bp):
ATAATTATTTTATCTCTAATTACATTAAATTAATTAAGAGATAAAAATAA
Found at i:27675285 original size:126 final size:126
Alignment explanation
Indices: 27675139--27675394 Score: 512
Period size: 126 Copynumber: 2.0 Consensus size: 126
27675129 TATTTTTCTC
27675139 TAATTACTTTAAATTAATTAAGAGATAAAAATAAAAAATAATTTATCACTACTTAGATTAAAATA
1 TAATTACTTTAAATTAATTAAGAGATAAAAATAAAAAATAATTTATCACTACTTAGATTAAAATA
27675204 ATTAAGTGATAATATTAAATAATTATTTTATCTCTAATTAATTAAATTAATAGAAGATAAA
66 ATTAAGTGATAATATTAAATAATTATTTTATCTCTAATTAATTAAATTAATAGAAGATAAA
27675265 TAATTACTTTAAATTAATTAAGAGATAAAAATAAAAAATAATTTATCACTACTTAGATTAAAATA
1 TAATTACTTTAAATTAATTAAGAGATAAAAATAAAAAATAATTTATCACTACTTAGATTAAAATA
27675330 ATTAAGTGATAATATTAAATAATTATTTTATCTCTAATTAATTAAATTAATAGAAGATAAA
66 ATTAAGTGATAATATTAAATAATTATTTTATCTCTAATTAATTAAATTAATAGAAGATAAA
27675391 TAAT
1 TAAT
27675395 ACATAAAAGA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 130 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (126 bp):
TAATTACTTTAAATTAATTAAGAGATAAAAATAAAAAATAATTTATCACTACTTAGATTAAAATA
ATTAAGTGATAATATTAAATAATTATTTTATCTCTAATTAATTAAATTAATAGAAGATAAA
Found at i:27675374 original size:49 final size:49
Alignment explanation
Indices: 27675273--27675380 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
27675263 AATAATTACT
*
27675273 TTAAATTAATTAAGAGATAAAAATAAAAAATAATTTATCACTACTTAGA
1 TTAAATTAATTAAGAGATAAAAATAAAAAATAATTTATCACTAATTAGA
* * * * * * *
27675322 TTAAAATAATTAAGTGATAATATTAAATAATTATTTTATCTCTAATTA-A
1 TTAAATTAATTAAGAGATAAAAATAAA-AAATAATTTATCACTAATTAGA
27675371 TTAAATTAAT
1 TTAAATTAAT
27675381 AGAAGATAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 33 0.67
50 16 0.33
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (49 bp):
TTAAATTAATTAAGAGATAAAAATAAAAAATAATTTATCACTAATTAGA
Found at i:27685663 original size:33 final size:33
Alignment explanation
Indices: 27685602--27685704 Score: 118
Period size: 33 Copynumber: 3.1 Consensus size: 33
27685592 CAATGAACTT
* * * *
27685602 GAGCCGGAAGGAGTGGAGTACAGCGGTGGATAC
1 GAGCCGGAAGGAGCGGAATACTGAGGTGGATAC
*
27685635 -AGGCTGGAAGGAGCGGAATACTGAGGTGGATAC
1 GA-GCCGGAAGGAGCGGAATACTGAGGTGGATAC
* * *
27685668 GAGCCGGAAGGTGCGGACTACTAAGGTGGATAC
1 GAGCCGGAAGGAGCGGAATACTGAGGTGGATAC
27685701 GAGC
1 GAGC
27685705 TATGATGACT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.02
33 57 0.97
34 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.43, T:0.14
Consensus pattern (33 bp):
GAGCCGGAAGGAGCGGAATACTGAGGTGGATAC
Found at i:27687885 original size:46 final size:46
Alignment explanation
Indices: 27687821--27687917 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
27687811 AAGAATCTTA
*
27687821 ATTATGAGTTTTGAGAAACGCTTTTAATTGATACTATTAATGTATT
1 ATTATGAGTTTTGAGAAACGCTTTTAATCGATACTATTAATGTATT
27687867 ATTATGAGTTTTGAGAAACGCTTTTAATCGATACTATTAATGTATT
1 ATTATGAGTTTTGAGAAACGCTTTTAATCGATACTATTAATGTATT
27687913 ATTAT
1 ATTAT
27687918 CGACTTTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (46 bp):
ATTATGAGTTTTGAGAAACGCTTTTAATCGATACTATTAATGTATT
Found at i:27688341 original size:60 final size:60
Alignment explanation
Indices: 27688257--27688371 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
27688247 ATACTAAACT
** * *
27688257 AAACACACCAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATATTTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATATTTAC
*
27688317 AAACACAAAAATTTGTAACATAATCCTAAATTACTAACAAATTAATTTTAAAATA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATA
27688372 ATTATAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATATTTAC
Found at i:27688557 original size:8 final size:8
Alignment explanation
Indices: 27688544--27688632 Score: 59
Period size: 8 Copynumber: 11.5 Consensus size: 8
27688534 TACCTTTTTT
27688544 TTTCTTTC
1 TTTCTTTC
27688552 TTTCTTTC
1 TTTCTTTC
27688560 TTTCTTTC
1 TTTCTTTC
27688568 -TTC-TTC
1 TTTCTTTC
27688574 -TTC-TTC
1 TTTCTTTC
27688580 -TTCTCTTC
1 TTTCT-TTC
27688588 -TTC-TTC
1 TTTCTTTC
27688594 -TTCTTTTC
1 TTTC-TTTC
27688602 TTCTCCTTTC
1 TT-T-CTTTC
*
27688612 TCTCTTTTC
1 TTTC-TTTC
*
27688621 TTTCTCTC
1 TTTCTTTC
27688629 TTTC
1 TTTC
27688633 GGTGGATGGG
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
6 18 0.26
7 3 0.04
8 33 0.47
9 9 0.13
10 6 0.09
11 1 0.01
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTCTTTC
Found at i:27688569 original size:20 final size:18
Alignment explanation
Indices: 27688544--27688632 Score: 73
Period size: 17 Copynumber: 5.0 Consensus size: 18
27688534 TACCTTTTTT
27688544 TTTCTTTC-T-TTCTTTC
1 TTTCTTTCTTCTTCTTTC
27688560 TTTCTTTCTTCTTC-TTC
1 TTTCTTTCTTCTTCTTTC
27688577 -TTCTTCTCTTCTTC-TTC
1 TTTCTT-TCTTCTTCTTTC
*
27688594 -TTCTTTTCTTCTCCTTTC
1 TTTC-TTTCTTCTTCTTTC
*
27688612 TCTCTTTTCTTTCTCTCTTTC
1 TTTC-TTTC-TTCT-TCTTTC
27688633 GGTGGATGGG
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
16 13 0.21
17 25 0.40
18 8 0.13
19 7 0.11
20 4 0.06
21 5 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTCTTTCTTCTTCTTTC
Found at i:27688573 original size:3 final size:3
Alignment explanation
Indices: 27688565--27688605 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
27688555 CTTTCTTTCT
27688565 TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TT- TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
27688606 CCTTTCTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:27688586 original size:17 final size:16
Alignment explanation
Indices: 27688561--27688630 Score: 73
Period size: 14 Copynumber: 4.8 Consensus size: 16
27688551 CTTTCTTTCT
27688561 TTCTTTCTTCTTCTTC
1 TTCTTTCTTCTTCTTC
27688577 TTC-TTC-TCTTCTTC
1 TTCTTTCTTCTTCTTC
27688591 TTC-TTCTT-TTCTTC
1 TTCTTTCTTCTTCTTC
*
27688605 TCCTTTC-TC-TCTT-
1 TTCTTTCTTCTTCTTC
27688618 TTCTTTCTCTCTT
1 TTCTTTCT-TCTT
27688631 TCGGTGGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
13 6 0.13
14 27 0.59
15 9 0.20
16 4 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTTTCTTCTTCTTC
Found at i:27703081 original size:33 final size:33
Alignment explanation
Indices: 27703030--27703098 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
27703020 TATCGAATCT
* *
27703030 ACTTCCCCTAAAGCATACCTGTTAGTTTACTTC
1 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
27703063 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
1 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
27703096 ACT
1 ACT
27703099 ATTTGCTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (33 bp):
ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
Found at i:27713707 original size:20 final size:20
Alignment explanation
Indices: 27713682--27713721 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27713672 CGTAAAATGA
*
27713682 TTTCTGGAAAATATTTTACT
1 TTTCTGGAAAATAATTTACT
*
27713702 TTTCTGTAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
27713722 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:27713711 original size:34 final size:35
Alignment explanation
Indices: 27713667--27713733 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
27713657 CAGTAAAATA
*
27713667 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
*
27713701 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
27713734 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:27714897 original size:30 final size:30
Alignment explanation
Indices: 27714861--27714918 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
27714851 GACCATGCCA
*
27714861 GTCATAGCAAATTGGTACTTATGGTCTTAT
1 GTCATAGCAAATTGGTACTTATGATCTTAT
*
27714891 GTCATAGCAAATTGGTAGTTATGATCTT
1 GTCATAGCAAATTGGTACTTATGATCTT
27714919 GTACAAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (30 bp):
GTCATAGCAAATTGGTACTTATGATCTTAT
Found at i:27716360 original size:18 final size:18
Alignment explanation
Indices: 27716337--27716381 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
27716327 GCTTCGAAAC
* *
27716337 GGGAAAGGGAAGGGGTAG
1 GGGAAAGGGAAGGAGAAG
27716355 GGGAAAGGGAAGGAGAAG
1 GGGAAAGGGAAGGAGAAG
27716373 GGGAAAGGG
1 GGGAAAGGG
27716382 GAGAAGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (18 bp):
GGGAAAGGGAAGGAGAAG
Found at i:27716389 original size:18 final size:18
Alignment explanation
Indices: 27716337--27716389 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
27716327 GCTTCGAAAC
** *
27716337 GGGAAAGGGAAGGGGTAG
1 GGGAAAGGGAAGAAGAAG
*
27716355 GGGAAAGGGAAGGAGAAG
1 GGGAAAGGGAAGAAGAAG
*
27716373 GGGAAAGGGGAGAAGAA
1 GGGAAAGGGAAGAAGAA
27716390 TGGGTCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.57, T:0.02
Consensus pattern (18 bp):
GGGAAAGGGAAGAAGAAG
Found at i:27716986 original size:15 final size:15
Alignment explanation
Indices: 27716966--27716997 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
27716956 TCAAATCAAG
27716966 ATGTGAGAGCCTGAT
1 ATGTGAGAGCCTGAT
27716981 ATGTGAGAGCCTGAT
1 ATGTGAGAGCCTGAT
27716996 AT
1 AT
27716998 TCTCAAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.28
Consensus pattern (15 bp):
ATGTGAGAGCCTGAT
Found at i:27723958 original size:2 final size:2
Alignment explanation
Indices: 27723951--27723975 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27723941 ATCGCCTCTA
27723951 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27723976 ATTTATTGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27727799 original size:22 final size:21
Alignment explanation
Indices: 27727774--27727822 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
27727764 AAGAATGCCC
27727774 AACAACTAATCCTTACCAAAGG
1 AACAAC-AATCCTTACCAAAGG
* * *
27727796 AACAACCATGCTTACCTAAGG
1 AACAACAATCCTTACCAAAGG
27727817 AACAAC
1 AACAAC
27727823 CACGAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.45, C:0.29, G:0.10, T:0.16
Consensus pattern (21 bp):
AACAACAATCCTTACCAAAGG
Found at i:27727811 original size:21 final size:21
Alignment explanation
Indices: 27727785--27727824 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27727775 ACAACTAATC
27727785 CTTACCAAAGGAACAACCATG
1 CTTACCAAAGGAACAACCATG
*
27727806 CTTACCTAAGGAACAACCA
1 CTTACCAAAGGAACAACCA
27727825 CGAAACATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.15
Consensus pattern (21 bp):
CTTACCAAAGGAACAACCATG
Found at i:27728276 original size:20 final size:22
Alignment explanation
Indices: 27728242--27728281 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
27728232 AAAATTTAAA
*
27728242 AAAAAAATATTAATT-AAAACT
1 AAAAAAATATAAATTGAAAACT
27728263 AAAAAAATA-AAATTGAAAA
1 AAAAAAATATAAATTGAAAA
27728282 GAAAATGCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (22 bp):
AAAAAAATATAAATTGAAAACT
Found at i:27728761 original size:25 final size:27
Alignment explanation
Indices: 27728705--27728762 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
27728695 ACTTATTTTA
*
27728705 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTA--TT-AAGACAT
27728735 TTGTTAATTTTGTTATTA-T-AGACAT
1 TTGTTAATTTTGTTATTATTAAGACAT
27728760 TTG
1 TTG
27728763 CTTATTAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.30
27 1 0.04
30 18 0.67
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (27 bp):
TTGTTAATTTTGTTATTATTAAGACAT
Found at i:27731514 original size:30 final size:30
Alignment explanation
Indices: 27731479--27731625 Score: 156
Period size: 30 Copynumber: 4.9 Consensus size: 30
27731469 CAAAAAATAA
*
27731479 AAAATTGCATTTTGACCCCTAAAATTTTTT
1 AAAATTACATTTTGACCCCTAAAATTTTTT
* * * *
27731509 AAAATTATATTTTAACCCCTAAACTTGTTT
1 AAAATTACATTTTGACCCCTAAAATTTTTT
* * *
27731539 GAAATTACATTTTAACCCATAAAATTTTTT
1 AAAATTACATTTTGACCCCTAAAATTTTTT
*
27731569 -AAATTACGTTTTGACCCC-AAAATTTTCTT
1 AAAATTACATTTTGACCCCTAAAATTTT-TT
* *
27731598 AAAATTACGTTTAGACCCC-AGAAATTTT
1 AAAATTACATTTTGACCCCTA-AAATTTT
27731626 ACTACAATTG
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
28 8 0.08
29 17 0.17
30 68 0.68
31 7 0.07
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAAATTTTTT
Found at i:27731840 original size:12 final size:12
Alignment explanation
Indices: 27731823--27731853 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
27731813 ACTTGCGAAA
27731823 AAGAGAAAAAAG
1 AAGAGAAAAAAG
27731835 AAGAGAAAAAAG
1 AAGAGAAAAAAG
27731847 -AGAGAAA
1 AAGAGAAA
27731854 GAGAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAGAAAAAAG
Found at i:27732269 original size:16 final size:14
Alignment explanation
Indices: 27732246--27732283 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
27732236 GGCCCAGTGG
27732246 AGAAAAAAAAAGAGA
1 AGAAAAAAAAA-AGA
27732261 AGAAAAAAAAAAGA
1 AGAAAAAAAAAAGA
27732275 AGAAAAAAA
1 AGAAAAAAA
27732284 GGGAGTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAAGA
Found at i:27732405 original size:5 final size:5
Alignment explanation
Indices: 27732395--27732422 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27732385 TATTTATATT
27732395 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
27732423 TAAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:27732827 original size:17 final size:17
Alignment explanation
Indices: 27732785--27733054 Score: 201
Period size: 17 Copynumber: 15.4 Consensus size: 17
27732775 TTCCATTTTC
* *
27732785 CAAAATTTTTCGTGTCTT
1 CAAAAATTTCCGTGT-TT
27732803 CTAAAAATTTCCGTGTTT
1 C-AAAAATTTCCGTGTTT
* *
27732821 CAAAAATTTTCTTGTTTT
1 CAAAAATTTCCGTG-TTT
*
27732839 CAAAAATTTCTGTGTTT
1 CAAAAATTTCCGTGTTT
*
27732856 CAAAAATTTTCGTGTTTT
1 CAAAAATTTCCGTG-TTT
*
27732874 C-AAAATATTGCGTGTTT
1 CAAAAAT-TTCCGTGTTT
27732891 CAAAAATATT--GATGTTTT
1 CAAAAAT-TTCCG-TG-TTT
27732909 CAAAAA-TTCCGGTGTTT
1 CAAAAATTTCC-GTGTTT
*
27732926 CAAAAAATTCCCGTGTTT
1 C-AAAAATTTCCGTGTTT
* *
27732944 TAAAAAATTCCGTGTTTT
1 CAAAAATTTCCGTG-TTT
*
27732962 C-AAAATTTTCGTGTTTT
1 CAAAAATTTCCGTG-TTT
* * *
27732979 CAAAATTTTTCGTATTT
1 CAAAAATTTCCGTGTTT
*
27732996 CAAAAA-TCCTCGTGTTTT
1 CAAAAATTTC-CGTG-TTT
*
27733014 CAAAAATTTCGGTGTTT
1 CAAAAATTTCCGTGTTT
* *
27733031 TAAAAATTTTCGTGTTTT
1 CAAAAATTTCCGTG-TTT
27733049 CAAAAA
1 CAAAAA
27733055 AAAAATCTCG
Statistics
Matches: 205, Mismatches: 29, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
16 4 0.02
17 92 0.45
18 91 0.44
19 18 0.09
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (17 bp):
CAAAAATTTCCGTGTTT
Found at i:27732844 original size:35 final size:35
Alignment explanation
Indices: 27732785--27733054 Score: 307
Period size: 35 Copynumber: 7.7 Consensus size: 35
27732775 TTCCATTTTC
* *
27732785 CAAAATTTTTCGTGTCTTCTAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAATTTCCGTGTTT
* *
27732821 CAAAAATTTTCTTGTTTTCAAAAATTTCTGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
*
27732856 CAAAAATTTTCGTGTTTTC-AAAATATTGCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAAT-TTCCGTGTTT
*
27732891 CAAAAATATT-GATGTTTTCAAAAA-TTCCGGTGTTT
1 CAAAAATTTTCG-TGTTTTCAAAAATTTCC-GTGTTT
** *
27732926 CAAAAAATTCCCGTGTTTT-AAAAAATTCCGTGTTTT
1 C-AAAAATTTTCGTGTTTTCAAAAATTTCCGTG-TTT
* * *
27732962 C-AAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
** *
27732996 CAAAAATCCTCGTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
*
27733031 TAAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
27733055 AAAAATCTCG
Statistics
Matches: 197, Mismatches: 27, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
34 27 0.14
35 129 0.65
36 40 0.20
37 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (35 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
Found at i:27734001 original size:17 final size:17
Alignment explanation
Indices: 27733962--27734005 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
27733952 TTTATTGCTC
*
27733962 TATTAACTAT-TAAAAT
1 TATTAAATATATAAAAT
27733978 T-TTAAATATATAAAAT
1 TATTAAATATATAAAAT
27733994 TATTAAATATAT
1 TATTAAATATAT
27734006 TTAAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 8 0.32
17 10 0.40
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAAATATATAAAAT
Found at i:27734010 original size:19 final size:17
Alignment explanation
Indices: 27733969--27734012 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
27733959 CTCTATTAAC
27733969 TATTAAAATTTTAAATA
1 TATTAAAATTTTAAATA
27733986 TA-TAAAATTATTAAATA
1 TATTAAAATT-TTAAATA
27734003 TATTTAAAAT
1 TA-TTAAAAT
27734013 GAAAGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 11 0.46
19 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAAAATTTTAAATA
Found at i:27747521 original size:25 final size:25
Alignment explanation
Indices: 27747493--27747545 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
27747483 CAAGTGAAAA
*
27747493 GTCTGTTCTGACTAGGATAAAATGT
1 GTCTGTTCTGACTAAGATAAAATGT
27747518 GTCTGTTCTGACTAAGATAAAATGT
1 GTCTGTTCTGACTAAGATAAAATGT
27747543 GTC
1 GTC
27747546 GACTTAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (25 bp):
GTCTGTTCTGACTAAGATAAAATGT
Found at i:27759111 original size:15 final size:15
Alignment explanation
Indices: 27759073--27759112 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
27759063 AGAGGGGGGC
27759073 GTTTGTTTTTTTTAT
1 GTTTGTTTTTTTTAT
*
27759088 GTTTATTTTTTTTAT
1 GTTTGTTTTTTTTAT
27759103 -TTTCGTTTTT
1 GTTT-GTTTTT
27759113 GAAAAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.07, C:0.03, G:0.10, T:0.80
Consensus pattern (15 bp):
GTTTGTTTTTTTTAT
Found at i:27770327 original size:9 final size:9
Alignment explanation
Indices: 27770313--27770448 Score: 62
Period size: 10 Copynumber: 14.2 Consensus size: 9
27770303 CACGTGGCGA
27770313 AAAAATTAT
1 AAAAATTAT
27770322 AAAAATTAT
1 AAAAATTAT
* *
27770331 TAAAATCAAT
1 AAAAAT-TAT
27770341 AAAAA-TATT
1 AAAAATTA-T
27770350 AAAAATTAT
1 AAAAATTAT
*
27770359 AGAATTATATAT
1 A-AA-AAT-TAT
*
27770371 AGAAATATAT
1 AAAAAT-TAT
*
27770381 AGAAATATAT
1 AAAAAT-TAT
** *
27770391 TCAATTTAT
1 AAAAATTAT
27770400 GAAAAATTAT
1 -AAAAATTAT
*
27770410 TAAAA-TAT
1 AAAAATTAT
*
27770418 GAAAATTACT
1 AAAAATTA-T
27770428 -AAAATATAT
1 AAAAAT-TAT
27770437 AAAAATATAT
1 AAAAAT-TAT
27770447 AA
1 AA
27770449 TTTTTTAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
8 8 0.08
9 37 0.37
10 49 0.49
11 3 0.03
12 4 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:27770424 original size:17 final size:18
Alignment explanation
Indices: 27770397--27770434 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
27770387 ATATTCAATT
*
27770397 TATGAAAAATTATTAAAA
1 TATGAAAAATTACTAAAA
27770415 TATG-AAAATTACTAAAA
1 TATGAAAAATTACTAAAA
27770432 TAT
1 TAT
27770435 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
TATGAAAAATTACTAAAA
Found at i:27770450 original size:26 final size:26
Alignment explanation
Indices: 27770402--27770475 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
27770392 CAATTTATGA
* *
27770402 AAAAT-TATTAAAATATGAAAATTACT
1 AAAATATATAAAAATAT-ATAATTACT
**
27770428 AAAATATATAAAAATATATAATTTTT
1 AAAATATATAAAAATATATAATTACT
* *
27770454 TAAATATATATAAAATTTATAA
1 AAAATATATA-AAAATATATAA
27770476 GATTTAACCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 20 0.50
27 20 0.50
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (26 bp):
AAAATATATAAAAATATATAATTACT
Found at i:27770481 original size:26 final size:26
Alignment explanation
Indices: 27770429--27770482 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
27770419 AAAATTACTA
**
27770429 AAATATATAAAAATATATAATTTTTT
1 AAATATATAAAAATATATAATGATTT
*
27770455 AAATATATATAAAATTTATAA-GATTT
1 AAATATATA-AAAATATATAATGATTT
27770481 AA
1 AA
27770483 CCTCTGCCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AAATATATAAAAATATATAATGATTT
Found at i:27771164 original size:20 final size:20
Alignment explanation
Indices: 27771139--27771176 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
27771129 CATGATCCGA
27771139 TTAAAACACGAGAATTTTTT
1 TTAAAACACGAGAATTTTTT
27771159 TTAAAACACGAGAATTTT
1 TTAAAACACGAGAATTTT
27771177 GAAGCACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAAAACACGAGAATTTTTT
Found at i:27771246 original size:19 final size:19
Alignment explanation
Indices: 27771206--27771263 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
27771196 TTTAAAAGTT
*
27771206 TTTTTTA-AATCACGAAAA
1 TTTTTTAGAAACACGAAAA
*
27771224 -TTTTT-GCAAACACGAGAA
1 TTTTTTAG-AAACACGAAAA
27771242 TTTTTTAGAAACACGAAAA
1 TTTTTTAGAAACACGAAAA
27771261 TTT
1 TTT
27771264 CTGAAAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 5 0.15
18 9 0.27
19 18 0.55
20 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (19 bp):
TTTTTTAGAAACACGAAAA
Found at i:27771307 original size:17 final size:17
Alignment explanation
Indices: 27771287--27771379 Score: 62
Period size: 17 Copynumber: 5.4 Consensus size: 17
27771277 AAAATTTTAC
*
27771287 AACACGAAAATTTGCGA
1 AACACGAAAATTTTCGA
* * *
27771304 AACATGACAATTTTTGA
1 AACACGAAAATTTTCGA
* **
27771321 AAAACGAGAAATTTTTAA
1 AACACGA-AAATTTTCGA
*
27771339 GAACGCGAAAA-TTTCGA
1 -AACACGAAAATTTTCGA
* **
27771356 AACACGGAAATTTTTAA
1 AACACGAAAATTTTCGA
27771373 AACACGA
1 AACACGA
27771380 GGATTTTTTT
Statistics
Matches: 56, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
16 8 0.14
17 32 0.57
18 11 0.20
19 5 0.09
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (17 bp):
AACACGAAAATTTTCGA
Found at i:27771322 original size:53 final size:52
Alignment explanation
Indices: 27771249--27771368 Score: 134
Period size: 53 Copynumber: 2.3 Consensus size: 52
27771239 GAATTTTTTA
27771249 GAAACACGAAAATTTCTGAAAAATCAAAAAAATTTT-ACAACACGAAAATTTGC
1 GAAACACGAAAATTTCTGAAAAA-CAAAAAAATTTTAACAACACGAAAATTT-C
* * * * * * * *
27771302 GAAACATGACAATTTTTGAAAAACGAGAAATTTTTAAGAACGCGAAAATTTC
1 GAAACACGAAAATTTCTGAAAAACAAAAAAATTTTAACAACACGAAAATTTC
*
27771354 GAAACACGGAAATTT
1 GAAACACGAAAATTT
27771369 TTAAAACACG
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
52 22 0.40
53 33 0.60
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.24
Consensus pattern (52 bp):
GAAACACGAAAATTTCTGAAAAACAAAAAAATTTTAACAACACGAAAATTTC
Found at i:27771417 original size:19 final size:19
Alignment explanation
Indices: 27771392--27771433 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
27771382 ATTTTTTTTT
27771392 ATTTTTTT--AATACACAGA
1 ATTTTTTTGAAATACA-AGA
27771410 ATTTTTTTGAAATACAAGA
1 ATTTTTTTGAAATACAAGA
27771429 ATTTT
1 ATTTT
27771434 AAAGACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 8 0.36
20 6 0.27
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (19 bp):
ATTTTTTTGAAATACAAGA
Found at i:27771550 original size:19 final size:18
Alignment explanation
Indices: 27771528--27771587 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
27771518 AATTTTTATT
*
27771528 TTTTTTTGAAACGTGAGAA
1 TTTTTTTGAAACATGA-AA
*
27771547 --TTTTTGAAACACGAAA
1 TTTTTTTGAAACATGAAA
27771563 TTTTCTTTGAAACATGAAA
1 TTTT-TTTGAAACATGAAA
27771582 TTTTTT
1 TTTTTT
27771588 ATATCACCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 2 0.06
17 12 0.34
18 4 0.11
19 17 0.49
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (18 bp):
TTTTTTTGAAACATGAAA
Found at i:27771617 original size:18 final size:17
Alignment explanation
Indices: 27771594--27771645 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
27771584 TTTTATATCA
*
27771594 CCAGAAGTTTTGAAAAC
1 CCAGAATTTTTGAAAAC
27771611 CCGAGAATTTTTGAAATA-
1 CC-AGAATTTTTGAAA-AC
27771629 CCAGAATTTTTGAAAAC
1 CCAGAATTTTTGAAAAC
27771646 ATGAGAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 1 0.03
17 15 0.48
18 14 0.45
19 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (17 bp):
CCAGAATTTTTGAAAAC
Found at i:27771652 original size:18 final size:18
Alignment explanation
Indices: 27771542--27771786 Score: 127
Period size: 18 Copynumber: 13.8 Consensus size: 18
27771532 TTTGAAACGT
27771542 GAGAATTTTTG-AAACAC
1 GAGAATTTTTGAAAACAC
*
27771559 GA-AATTTTCTTTG-AAACAT
1 GAGAA--TT-TTTGAAAACAC
* * *
27771578 GA-AATTTTTTATATCAC
1 GAGAATTTTTGAAAACAC
* * *
27771595 CAGAAGTTTTGAAAACCC
1 GAGAATTTTTGAAAACAC
27771613 GAGAATTTTTGAAATAC-C
1 GAGAATTTTTGAAA-ACAC
*
27771631 -AGAATTTTTGAAAACAT
1 GAGAATTTTTGAAAACAC
*
27771648 GAGAATTTAT-AAAACA-
1 GAGAATTTTTGAAAACAC
* * *
27771664 GGGAAATTTTTCTAAAAAAC
1 GAG-AATTTTT-GAAAACAC
* * *
27771684 AAGAAAGTTTTTG-AAATAT
1 GAG-AA-TTTTTGAAAACAC
*
27771703 GGGAATTTTTGAAAACAC
1 GAGAATTTTTGAAAACAC
* *
27771721 G-GAAATTATTGAAAACGC
1 GAG-AATTTTTGAAAACAC
27771739 GAGAATTTTT-AAAACAC
1 GAGAATTTTTGAAAACAC
* * *
27771756 GACAA-TTTTGAAGACAT
1 GAGAATTTTTGAAAACAC
*
27771773 GAAAATTTTTGAAA
1 GAGAATTTTTGAAA
27771787 TACGAATTTT
Statistics
Matches: 174, Mismatches: 36, Indels: 35
0.71 0.15 0.14
Matches are distributed among these distances:
16 13 0.07
17 59 0.34
18 67 0.39
19 26 0.15
20 4 0.02
21 5 0.03
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (18 bp):
GAGAATTTTTGAAAACAC
Found at i:27771733 original size:35 final size:33
Alignment explanation
Indices: 27771692--27771786 Score: 86
Period size: 35 Copynumber: 2.7 Consensus size: 33
27771682 ACAAGAAAGT
27771692 TTTTGAAATATGGGAATTTTTGAAAACACGGA-AA
1 TTTTGAAA-ATGGGAATTTTTGAAAACAC-GACAA
*
27771726 TTATTGAAAACGCGAGAATTTTT-AAAACACGACAA
1 TT-TTGAAAATG-G-GAATTTTTGAAAACACGACAA
**
27771761 TTTTGAAGACATGAAAATTTTTGAAA
1 TTTTGAA-A-ATGGGAATTTTTGAAA
27771787 TACGAATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
34 18 0.36
35 22 0.44
36 10 0.20
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (33 bp):
TTTTGAAAATGGGAATTTTTGAAAACACGACAA
Found at i:27771762 original size:17 final size:16
Alignment explanation
Indices: 27771706--27771797 Score: 60
Period size: 17 Copynumber: 5.4 Consensus size: 16
27771696 GAAATATGGG
27771706 AATTTTTGAAAACACGGA
1 AATTTTT-AAAACAC-GA
* *
27771724 AATTATTGAAAACGCGA
1 AATT-TTTAAAACACGA
27771741 GAATTTTTAAAACACGA
1 -AATTTTTAAAACACGA
* * *
27771758 CAATTTTGAAGACATGAA
1 -AATTTTTAAAACACG-A
* *
27771776 AATTTTTGAAATACG-
1 AATTTTTAAAACACGA
27771791 AATTTTT
1 AATTTTT
27771798 TCTTTTAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
15 7 0.12
17 34 0.59
18 15 0.26
19 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (16 bp):
AATTTTTAAAACACGA
Found at i:27771780 original size:34 final size:34
Alignment explanation
Indices: 27771706--27771792 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
27771696 GAAATATGGG
* *
27771706 AATTTTTGAAAACACGGAAATTATTGAAAACGCGAG
1 AATTTTT-AAAACAC-GAAATTATTGAAAACACGAA
* *
27771742 AATTTTTAAAACACGACAATT-TTGAAGACATGAA
1 AATTTTTAAAACACGA-AATTATTGAAAACACGAA
* *
27771776 AATTTTTGAAATACGAA
1 AATTTTTAAAACACGAA
27771793 TTTTTTCTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
33 1 0.02
34 25 0.57
35 11 0.25
36 7 0.16
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (34 bp):
AATTTTTAAAACACGAAATTATTGAAAACACGAA
Found at i:27772221 original size:3 final size:3
Alignment explanation
Indices: 27772213--27772277 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
27772203 TGCATTAAAA
27772213 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27772261 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
27772278 ATAAATATGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:27772390 original size:19 final size:19
Alignment explanation
Indices: 27772362--27772398 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27772352 AACACCATTT
*
27772362 AAATACATTAAATAAAATA
1 AAATACATTAAAGAAAATA
*
27772381 AAATAGATTAAAGAAAAT
1 AAATACATTAAAGAAAAT
27772399 TACCAAAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (19 bp):
AAATACATTAAAGAAAATA
Found at i:27772669 original size:12 final size:11
Alignment explanation
Indices: 27772661--27772732 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 11
27772651 ACTTTTTTAT
27772661 TTTCTTTTTTC
1 TTTCTTTTTTC
27772672 TTTC-TTTTTC
1 TTTCTTTTTTC
*
27772682 TATC-TTTTTC
1 TTTCTTTTTTC
***
27772692 TTTCTCCCTTC
1 TTTCTTTTTTC
**
27772703 -TTCTTCTTCCC
1 TTTCTT-TTTTC
27772714 TTTTCTTTTTTC
1 -TTTCTTTTTTC
27772726 TTTCTTT
1 TTTCTTT
27772733 CAAACCCAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
10 22 0.49
11 15 0.33
12 3 0.07
13 5 0.11
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:27772679 original size:10 final size:10
Alignment explanation
Indices: 27772661--27772696 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
27772651 ACTTTTTTAT
27772661 TTTCTTTTTTC
1 TTTC-TTTTTC
27772672 TTTCTTTTTC
1 TTTCTTTTTC
*
27772682 TATCTTTTTC
1 TTTCTTTTTC
27772692 TTTCT
1 TTTCT
27772697 CCCTTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:27772690 original size:27 final size:27
Alignment explanation
Indices: 27772660--27772732 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
27772650 TACTTTTTTA
*
27772660 TTTTCTTTTTTCTTTCTTTTTCTAT-CT
1 TTTTCTTTTTTCTTTCTTTTTCT-TCCC
* * * *
27772687 TTTTCTTTCTCCCTTCTTCTTCTTCCC
1 TTTTCTTTTTTCTTTCTTTTTCTTCCC
27772714 TTTTCTTTTTTCTTTCTTT
1 TTTTCTTTTTTCTTTCTTT
27772733 CAAACCCAAG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTCTTTTTTCTTTCTTTTTCTTCCC
Found at i:27772695 original size:24 final size:23
Alignment explanation
Indices: 27772652--27772696 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
27772642 TATCGGGCTA
*
27772652 CTTTTTTATTTTCTTTTTTCTTT
1 CTTTTTTATTTTCTTCTTTCTTT
27772675 CTTTTTCTATCTTT-TTCTTTCT
1 CTTTTT-TAT-TTTCTTCTTTCT
27772697 CCCTTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 10 0.53
25 3 0.16
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
CTTTTTTATTTTCTTCTTTCTTT
Found at i:27772867 original size:18 final size:17
Alignment explanation
Indices: 27772834--27772871 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
27772824 TTCCTCCTTT
27772834 TCTTCTTTTCCTTTTTC
1 TCTTCTTTTCCTTTTTC
27772851 TCTTCTCTTTCAC-TTTTC
1 TCTTCT-TTTC-CTTTTTC
27772869 TCT
1 TCT
27772872 CCTTCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 12 0.63
19 1 0.05
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (17 bp):
TCTTCTTTTCCTTTTTC
Found at i:27773459 original size:29 final size:28
Alignment explanation
Indices: 27773426--27773578 Score: 85
Period size: 30 Copynumber: 5.2 Consensus size: 28
27773416 GCAAAAATGC
27773426 AATTTTAGGAAAATATAGGGCTAAAGTGT
1 AATTTTA-GAAAATATAGGGCTAAAGTGT
* *
27773455 AATTTTTAGAAAGTTTAGGGGGCT-AAGTGT
1 AA-TTTTAGAAAATATA--GGGCTAAAGTGT
* * * *
27773485 AA-TTTACAAAGTATTAGGGGTCAAGATGT
1 AATTTTAGAAAATA-TAGGGCTAAAG-TGT
* * *
27773514 AATTTTTGAAAAATTTAAGGGCTAAAATGT
1 AATTTTAG-AAAATAT-AGGGCTAAAGTGT
* * * *
27773544 AATTTTTGAAAAGTTTTGGGGCTAAAATGT
1 AATTTTAGAAAA--TATAGGGCTAAAGTGT
27773574 AATTT
1 AATTT
27773579 ATTTTTTTGT
Statistics
Matches: 100, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
27 4 0.04
28 12 0.12
29 20 0.20
30 45 0.45
31 19 0.19
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (28 bp):
AATTTTAGAAAATATAGGGCTAAAGTGT
Found at i:27773483 original size:30 final size:31
Alignment explanation
Indices: 27773443--27773578 Score: 119
Period size: 30 Copynumber: 4.5 Consensus size: 31
27773433 GGAAAATATA
27773443 GGGCTAAAGTGTAATTTTT-AGAAAGTTTAGG
1 GGGCTAAAGTGTAATTTTTGA-AAAGTTTAGG
27773474 GGGCT-AAGTGTAA--TTT-ACAAAGTATTA-G
1 GGGCTAAAGTGTAATTTTTGA-AAAGT-TTAGG
* * *
27773502 GGG-TCAAGATGTAATTTTTGAAAAATTTA-A
1 GGGCTAAAG-TGTAATTTTTGAAAAGTTTAGG
* *
27773532 GGGCTAAAATGTAATTTTTGAAAAGTTT-TG
1 GGGCTAAAGTGTAATTTTTGAAAAGTTTAGG
*
27773562 GGGCTAAAATGTAATTT
1 GGGCTAAAGTGTAATTT
27773579 ATTTTTTTGT
Statistics
Matches: 90, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.01
28 16 0.18
29 8 0.09
30 49 0.54
31 15 0.17
32 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.36
Consensus pattern (31 bp):
GGGCTAAAGTGTAATTTTTGAAAAGTTTAGG
Found at i:27773504 original size:28 final size:29
Alignment explanation
Indices: 27773443--27773504 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
27773433 GGAAAATATA
*
27773443 GGGCTAAAGTGTAATTTTTAGAAAGTTTAGG
1 GGGCTAAAGTGTAA--TTTACAAAGTTTAGG
27773474 GGGCT-AAGTGTAATTTACAAAGTATTAGG
1 GGGCTAAAGTGTAATTTACAAAGT-TTAGG
27773503 GG
1 GG
27773505 TCAAGATGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.31
29 7 0.24
30 8 0.28
31 5 0.17
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (29 bp):
GGGCTAAAGTGTAATTTACAAAGTTTAGG
Found at i:27776439 original size:18 final size:19
Alignment explanation
Indices: 27776411--27776447 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
27776401 GAAAATAAAA
27776411 GTAATAAATATATATATAT
1 GTAATAAATATATATATAT
*
27776430 GTAA-AAATATGTATATAT
1 GTAATAAATATATATATAT
27776448 ATTTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
GTAATAAATATATATATAT
Found at i:27776624 original size:3 final size:3
Alignment explanation
Indices: 27776616--27776657 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
27776606 ATAAGCAATT
* *
27776616 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27776658 TGAAATTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:27783022 original size:29 final size:28
Alignment explanation
Indices: 27782964--27783024 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
27782954 AAAATATTTA
* **
27782964 AAAAATATAAAAAATTGTAAAATTTTAT
1 AAAAATATAAAAAATTATAAAATTGCAT
27782992 AAAAATCATAAAAAAATTATAAAA-TGCAT
1 AAAAAT-AT-AAAAAATTATAAAATTGCAT
27783021 AAAA
1 AAAA
27783025 GACCCTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 9 0.32
30 13 0.46
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (28 bp):
AAAAATATAAAAAATTATAAAATTGCAT
Found at i:27783222 original size:20 final size:21
Alignment explanation
Indices: 27783197--27783252 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
27783187 TTTGGTACAA
27783197 TAATTTTTATAATTTTTTA-C
1 TAATTTTTATAATTTTTTACC
27783217 TAA-TTTTAT-ATTTCTTTACC
1 TAATTTTTATAATTT-TTTACC
*
27783237 T-TTTTTTATAATTTTT
1 TAATTTTTATAATTTTT
27783253 ATGACTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.13
19 10 0.32
20 13 0.42
21 4 0.13
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (21 bp):
TAATTTTTATAATTTTTTACC
Found at i:27783317 original size:23 final size:22
Alignment explanation
Indices: 27783266--27783315 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
27783256 ACTTTATAAA
27783266 ATTTTATAA--TTTTTTTCTAT
1 ATTTTATAATTTTTTTTTCTAT
27783286 ATTTTATAATTTTTTTTTCTA-
1 ATTTTATAATTTTTTTTTCTAT
27783307 ATTTT-TAAT
1 ATTTTATAAT
27783316 AAATATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.46
21 5 0.18
22 10 0.36
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTATAATTTTTTTTTCTAT
Found at i:27783371 original size:29 final size:29
Alignment explanation
Indices: 27783299--27783372 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
27783289 TTATAATTTT
* *
27783299 TTTTTCTAATTTTTAATAAATATTAAGTA
1 TTTTTATAATTTTTATTAAATATTAAGTA
27783328 TTTTTAT-ATTTTTATTAAA-ATTTAA-TAA
1 TTTTTATAATTTTTATTAAATA-TTAAGT-A
27783356 TTTTTATAATTTTTATT
1 TTTTTATAATTTTTATT
27783373 GGTTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 2 0.05
28 23 0.57
29 15 0.38
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTTTATAATTTTTATTAAATATTAAGTA
Found at i:27791521 original size:43 final size:44
Alignment explanation
Indices: 27791473--27791655 Score: 157
Period size: 43 Copynumber: 4.2 Consensus size: 44
27791463 TTTTGGAAAT
* *
27791473 AAACGCCACTATAGACCATGACCTTTAGCGGCGCTTTCCT-C-AC
1 AAACGCCACTATAGATCAAGACCTTTAGCGGCGCTTT-CTACAAC
* *
27791516 AAACGCCACTATAGATCAGGATCTTTAGCGGCGC-TTCTACAAC
1 AAACGCCACTATAGATCAAGACCTTTAGCGGCGCTTTCTACAAC
* * *
27791559 AAACACCGCTATAGATCAAGACCTTTTAGCGGCGCTTATATA-AA-
1 AAACGCCACTATAGATCAAGACC-TTTAGCGGCGCTT-TCTACAAC
* * * * * *
27791603 AAACGCCGCTATAGAACAA-ACTTTTAGTGACGC-TTCTTGCAA-
1 AAACGCCACTATAGATCAAGACCTTTAGCGGCGCTTTC-TACAAC
27791645 AAACGCCACTA
1 AAACGCCACTA
27791656 AAAACATAAC
Statistics
Matches: 117, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.01
41 4 0.03
42 24 0.21
43 54 0.46
44 28 0.24
45 3 0.03
46 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.23
Consensus pattern (44 bp):
AAACGCCACTATAGATCAAGACCTTTAGCGGCGCTTTCTACAAC
Found at i:27791702 original size:20 final size:19
Alignment explanation
Indices: 27791672--27791724 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
27791662 TAACATTTAA
27791672 AAATA-TTATTTTAATCAA-
1 AAATATTTATTTTAAT-AAT
*
27791690 ATAATATTTATTTTTATAAT
1 A-AATATTTATTTTAATAAT
27791710 AAATATTTTATTTTA
1 AAATA-TTTATTTTA
27791725 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 10 0.34
20 18 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATATTTATTTTAATAAT
Found at i:27792526 original size:45 final size:45
Alignment explanation
Indices: 27792472--27792573 Score: 204
Period size: 45 Copynumber: 2.3 Consensus size: 45
27792462 CCCACTATCA
27792472 CCACATAAAGGTAATTAACTCAATAAGGCATACTCAAACAATTAG
1 CCACATAAAGGTAATTAACTCAATAAGGCATACTCAAACAATTAG
27792517 CCACATAAAGGTAATTAACTCAATAAGGCATACTCAAACAATTAG
1 CCACATAAAGGTAATTAACTCAATAAGGCATACTCAAACAATTAG
27792562 CCACATAAAGGT
1 CCACATAAAGGT
27792574 TTAACATTCC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.22
Consensus pattern (45 bp):
CCACATAAAGGTAATTAACTCAATAAGGCATACTCAAACAATTAG
Found at i:27801076 original size:45 final size:45
Alignment explanation
Indices: 27801011--27801646 Score: 884
Period size: 45 Copynumber: 14.2 Consensus size: 45
27801001 CTCAGAGAAC
*
27801011 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
27801056 AGATCGAAGATAGCATATCTTGTCTTCCAGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * *
27801101 AGATCGAAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCAAAAT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* **
27801146 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTAGCAGTAAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
27801191 AGATCGAGGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * * *
27801236 AGATCGAGGATAACAAATCTTGTCTTTCTATATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
27801281 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAACGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
27801326 AGATCGAAGATAGCAGATCTTGTC-TCCTATATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
27801370 AGATCGAGGATAGCAGATCTTGTCTTCCAGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
27801415 AGATCGAAGATAGCAGATATTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
27801460 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* ** *
27801505 AGATCGAAGATAGCAGATCTTATCTTCCTGTATTGGCAGTAAAGC
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * * ** * * *
27801550 AGATCGAAGACACCAG-CCTTGCCTTCCTGTGCTGACAACGAAGC
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
27801594 AGA-CTGAAGATAGCAGATCATG-CATTCCTGTACTGGCAGCAAAGC
1 AGATC-GAAGATAGCAGATCTTGTC-TTCCTGTATTGGCAGCGAAGT
27801639 AGATCGAA
1 AGATCGAA
27801647 AAACAACGAA
Statistics
Matches: 530, Mismatches: 56, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
43 1 0.00
44 74 0.14
45 454 0.86
46 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (45 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
Found at i:27803148 original size:3 final size:3
Alignment explanation
Indices: 27803140--27803192 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
27803130 TATTTTAATG
* * *
27803140 TTA TTA TTA TTG TTA TCA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27803188 -TA TTA
1 TTA TTA
27803193 ATATAATTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:27806030 original size:2 final size:2
Alignment explanation
Indices: 27806023--27806049 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27806013 GAAATTTGAA
27806023 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
27806050 CCATTAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27807755 original size:3 final size:3
Alignment explanation
Indices: 27807747--27807783 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
27807737 TAAAAACCTT
27807747 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 A
27807784 CAGGTTGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:27811732 original size:24 final size:24
Alignment explanation
Indices: 27811705--27811757 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
27811695 TGGCTCTTCA
*
27811705 GAGCTGTCC-GTTACTGGCTCGCAT
1 GAGCTGTCCAATTA-TGGCTCGCAT
*
27811729 GAGCTTTCCAATTATGGCTCGCAT
1 GAGCTGTCCAATTATGGCTCGCAT
27811753 GAGCT
1 GAGCT
27811758 TTCTGTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (24 bp):
GAGCTGTCCAATTATGGCTCGCAT
Found at i:27819665 original size:23 final size:25
Alignment explanation
Indices: 27819625--27819677 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
27819615 TCTGATTAAT
*
27819625 TGGCTCGCATAAGCTTCCC-A-ATA
1 TGGCTCGCATAAACTTCCCGATATA
* *
27819648 TGGCTCGCTTAAATTTCCCGATATA
1 TGGCTCGCATAAACTTCCCGATATA
27819673 TGGCT
1 TGGCT
27819678 ATCCGAAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.64
24 1 0.04
25 8 0.32
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (25 bp):
TGGCTCGCATAAACTTCCCGATATA
Done.