Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 6 of 15
Found at i:627019 original size:57 final size:57
Alignment explanation
Indices: 626957--627066 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
626947 CATTTGATTG
* *
626957 TCAATTGA-GAGATAATTTAGTGAATAAAAGGAAATGGAAGGATAAACATTTAAAGGA
1 TCAATTGATAAGA-AATTTAGTGAATAAAAGCAAATGGAAGGATAAACATTTAAAGGA
* * * *
627014 TCAATTGATAAGAAATTTAGTTAATAAATGCAAGTTGAAGGATAAACATTTAA
1 TCAATTGATAAGAAATTTAGTGAATAAAAGCAAATGGAAGGATAAACATTTAA
627067 GGGGTAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 43 0.93
58 3 0.07
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (57 bp):
TCAATTGATAAGAAATTTAGTGAATAAAAGCAAATGGAAGGATAAACATTTAAAGGA
Found at i:630486 original size:18 final size:18
Alignment explanation
Indices: 630463--630498 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
630453 AGCAAAAAGC
630463 AAAGAATCAATCATGGAG
1 AAAGAATCAATCATGGAG
630481 AAAGAATCAATCATGGAG
1 AAAGAATCAATCATGGAG
630499 GGTCACTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.22, T:0.17
Consensus pattern (18 bp):
AAAGAATCAATCATGGAG
Found at i:632075 original size:50 final size:50
Alignment explanation
Indices: 632021--632194 Score: 210
Period size: 50 Copynumber: 3.4 Consensus size: 50
632011 TTAAAATATT
632021 AAAATATTATTTTTATATTATTAGTATATATTTATAATTAAAATTAAATA
1 AAAATATTATTTTTATATTATTAGTATATATTTATAATTAAAATTAAATA
* * ** *
632071 AAAATATTA-TTTT-TATTATTA-AATAATAATTTATTATTATTTATTATATCATT
1 AAAATATTATTTTTATATTATTAGTAT-AT-ATTTATAATTA-AAATTA-A--ATA
*
632124 AAAATATTATTTTTATATTATTAGTATATGTTTATAATTAAAATTAAATA
1 AAAATATTATTTTTATATTATTAGTATATATTTATAATTAAAATTAAATA
632174 AAAATATTATTTTTATTATTA
1 AAAATATTATTTTTA-TATTA
632195 AATAATAATT
Statistics
Matches: 103, Mismatches: 11, Indels: 19
0.77 0.08 0.14
Matches are distributed among these distances:
47 2 0.02
48 10 0.10
49 14 0.14
50 30 0.29
51 6 0.06
52 1 0.01
53 15 0.15
54 13 0.13
55 10 0.10
56 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (50 bp):
AAAATATTATTTTTATATTATTAGTATATATTTATAATTAAAATTAAATA
Found at i:632091 original size:25 final size:25
Alignment explanation
Indices: 632063--632199 Score: 100
Period size: 25 Copynumber: 5.4 Consensus size: 25
632053 TATAATTAAA
632063 ATTAAATAAAAATATTATTTTTATT
1 ATTAAATAAAAATATTATTTTTATT
*
632088 ATTAAATAATAATTTATTATTATTTATT
1 ATTAAATAA-AA-ATATTATT-TTTATT
* *
632116 A-TATCATTAAAATATTATTTTTA-T
1 ATTA-AATAAAAATATTATTTTTATT
* * * * ** **
632140 ATT-ATTAGTATATGTTTATAATTAAA
1 ATTAAATA-AAAAT-ATTATTTTTATT
632166 ATTAAATAAAAATATTATTTTTATT
1 ATTAAATAAAAATATTATTTTTATT
632191 ATTAAATAA
1 ATTAAATAA
632200 TAATTTAAGT
Statistics
Matches: 82, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
23 1 0.01
24 5 0.06
25 37 0.45
26 15 0.18
27 14 0.17
28 10 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (25 bp):
ATTAAATAAAAATATTATTTTTATT
Found at i:632134 original size:103 final size:103
Alignment explanation
Indices: 632018--632206 Score: 369
Period size: 103 Copynumber: 1.8 Consensus size: 103
632008 TCATTAAAAT
632018 ATTAAAATATTATTTTTATATTATTAGTATATATTTATAATTAAAATTAAATAAAAATATTATTT
1 ATTAAAATATTATTTTTATATTATTAGTATATATTTATAATTAAAATTAAATAAAAATATTATTT
632083 TTATTATTAAATAATAATTTATTATTATTTATTATATC
66 TTATTATTAAATAATAATTTATTATTATTTATTATATC
*
632121 ATTAAAATATTATTTTTATATTATTAGTATATGTTTATAATTAAAATTAAATAAAAATATTATTT
1 ATTAAAATATTATTTTTATATTATTAGTATATATTTATAATTAAAATTAAATAAAAATATTATTT
632186 TTATTATTAAATAATAATTTA
66 TTATTATTAAATAATAATTTA
632207 AGTCAAGTTG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 85 1.00
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (103 bp):
ATTAAAATATTATTTTTATATTATTAGTATATATTTATAATTAAAATTAAATAAAAATATTATTT
TTATTATTAAATAATAATTTATTATTATTTATTATATC
Found at i:634120 original size:16 final size:16
Alignment explanation
Indices: 634099--634136 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
634089 ATTTTTATTA
*
634099 TAAATTTAAGTAATA-T
1 TAAATTTAA-AAATACT
634115 TAAATTTAAAAATACT
1 TAAATTTAAAAATACT
634131 TAAATT
1 TAAATT
634137 AATTATTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTAAAAATACT
Found at i:635330 original size:17 final size:18
Alignment explanation
Indices: 635308--635365 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
635298 AAGTTAGGTA
635308 AAAAAGAAAGAAAG-AAG
1 AAAAAGAAAGAAAGAAAG
*
635325 ATAAAG-AAGAAAGAAAG
1 AAAAAGAAAGAAAGAAAG
* *
635342 AAAAAGAAAAAAAAAAAGG
1 AAAAAGAAAGAAAGAAA-G
635361 AAAAA
1 AAAAA
635366 ATATGAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 7 0.21
17 13 0.38
18 8 0.24
19 6 0.18
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAGAAAGAAAG
Found at i:635334 original size:20 final size:20
Alignment explanation
Indices: 635306--635343 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
635296 AAAAGTTAGG
635306 TAAAAAAGAAAGAAAGAAGA
1 TAAAAAAGAAAGAAAGAAGA
*
635326 TAAAGAAGAAAGAAAGAA
1 TAAAAAAGAAAGAAAGAA
635344 AAAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (20 bp):
TAAAAAAGAAAGAAAGAAGA
Found at i:643217 original size:27 final size:27
Alignment explanation
Indices: 643180--644001 Score: 1266
Period size: 27 Copynumber: 30.0 Consensus size: 27
643170 GTGGCATTTT
* *
643180 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
643208 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
643235 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
643263 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
643290 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
643317 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
643344 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
643371 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
643399 CTTTTAAGTCTACAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
643427 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
643454 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
643481 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
643509 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
643536 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
643564 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
643592 CTTTTAAGACCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
643619 CTTTTAAGTCCACAATTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
643646 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
643673 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
643701 CTTTTAAGTTCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
643728 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
643756 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
643783 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
643810 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
643838 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
643865 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
643893 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
643920 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
643947 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
643974 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
644001 C
1 C
644002 ATTCCAATGC
Statistics
Matches: 734, Mismatches: 52, Indels: 17
0.91 0.06 0.02
Matches are distributed among these distances:
27 478 0.65
28 256 0.35
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:643477 original size:137 final size:137
Alignment explanation
Indices: 643180--644001 Score: 1321
Period size: 137 Copynumber: 6.0 Consensus size: 137
643170 GTGGCATTTT
* * * *
643180 CTTTTAAAGTCCACAACTCTGTGGCATCTTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
643245 CCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCCGTGGCACCT-TTTTAAGTCCACAACTCC
65 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCC
643309 GTGGCACC
130 GTGGCACC
643317 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
643381 CACAACTCCGTGGCATCCCTTTTAAGTCTACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCC
66 CACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCC
*
643446 ATGGCACC
130 GTGGCACC
* *
643454 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGA
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
* *
643518 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCCACAACTCC
65 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCC
643583 GTGGCATCC
130 GTGGCA-CC
* * *
643592 CTTTT-AAGACCACAACTCTGTGGCACCCTTTTAAGTCCACAATTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * * * *
643656 CACAACTCTGTGGCACCCTTTTAAGTCCATAACTCTGTGGCATCTCTTTTAAGTTCACAACTCTG
66 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCCG
643721 TGGCACC
131 TGGCACC
* *
643728 CTTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * *
643793 CACAACTCTGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTG
66 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCCG
643858 TGGCACC
131 TGGCACC
*
643865 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
643930 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATC-CTTTTAAATCCACAACTCTG
66 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCCG
643994 TGGCACC
131 TGGCACC
644001 C
1 C
644002 ATTCCAATGC
Statistics
Matches: 643, Mismatches: 37, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
135 20 0.03
136 111 0.17
137 436 0.68
138 76 0.12
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (137 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCCG
TGGCACC
Found at i:644016 original size:110 final size:108
Alignment explanation
Indices: 643180--644001 Score: 1266
Period size: 110 Copynumber: 7.5 Consensus size: 108
643170 GTGGCATTTT
* * * *
643180 CTTTTAAAGTCCACAACTCTGTGGCATCTTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
*
643245 CCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
643290 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
643355 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
643399 CTTTTAAGTCTACAACTCCGTGGCATCTCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
643464 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* *
643509 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
* *
643574 CACAACTCCGTGGCATCCCTTTTAAGACCACAACTCTGTGGCACC
65 CACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* *
643619 CTTTTAAGTCCACAATTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * * * *
643684 ATAACTCTGTGGCATCTCTTTTAAGTTCACAACTCTGTGGCACC
66 ACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* *
643728 CTTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * *
643793 CACAACTCTGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCT
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* *
643838 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
643903 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
643947 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAATCCACAACTCTGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC
644002 ATTCCAATGC
Statistics
Matches: 660, Mismatches: 45, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
108 67 0.10
109 235 0.36
110 332 0.50
111 26 0.04
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (108 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:644039 original size:32 final size:32
Alignment explanation
Indices: 643984--644430 Score: 734
Period size: 32 Copynumber: 14.0 Consensus size: 32
643974 CTTTTAAATC
* * *
643984 CACAACTCTGTGGC-ACCCATTCCAATGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
644015 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* *
644047 CACAAGTCGGTAGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
644079 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
644111 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
644143 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
644175 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
644207 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
644239 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
644271 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
644303 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* * *
644335 CATAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* * * *
644367 CACAAGTCGGGGGCGACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
**
644399 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
644431 TGCAAATCAA
Statistics
Matches: 396, Mismatches: 19, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
31 12 0.03
32 384 0.97
ACGTcount: A:0.31, C:0.36, G:0.19, T:0.15
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
Found at i:645719 original size:17 final size:18
Alignment explanation
Indices: 645697--645753 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
645687 AAGTTAGGTA
645697 AAAAAGAAAGAAAG-AAG
1 AAAAAGAAAGAAAGAAAG
*
645714 ATAAAG-AAGAAAGAAAG
1 AAAAAGAAAGAAAGAAAG
*
645731 AAAAAGAAA-AAAAAAAGG
1 AAAAAGAAAGAAAGAAA-G
645749 AAAAA
1 AAAAA
645754 ATATGAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 7 0.21
17 19 0.56
18 8 0.24
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAGAAAGAAAG
Found at i:645723 original size:20 final size:20
Alignment explanation
Indices: 645695--645732 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
645685 AAAAGTTAGG
645695 TAAAAAAGAAAGAAAGAAGA
1 TAAAAAAGAAAGAAAGAAGA
*
645715 TAAAGAAGAAAGAAAGAA
1 TAAAAAAGAAAGAAAGAA
645733 AAAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (20 bp):
TAAAAAAGAAAGAAAGAAGA
Found at i:649157 original size:29 final size:29
Alignment explanation
Indices: 649119--649181 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
649109 ATTTTCTTTA
* *
649119 TATTTCATCGTTTAATATCTAATTAATAT
1 TATTACATCGTTTAATAGCTAATTAATAT
649148 TATTACATCGTTTAATAGCTAATTAATAT
1 TATTACATCGTTTAATAGCTAATTAATAT
649177 TATTA
1 TATTA
649182 TGTGTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (29 bp):
TATTACATCGTTTAATAGCTAATTAATAT
Found at i:649901 original size:2 final size:2
Alignment explanation
Indices: 649888--649917 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
649878 AGTTTATTAC
*
649888 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
649918 TAATTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:650242 original size:32 final size:32
Alignment explanation
Indices: 650206--650270 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
650196 TGATTTACTT
650206 CTTTTTGGATATTGAATTTTCATTTACACATC
1 CTTTTTGGATATTGAATTTTCATTTACACATC
650238 CTTTTTGGATATTGAATTTTCATTTACACATC
1 CTTTTTGGATATTGAATTTTCATTTACACATC
650270 C
1 C
650271 ATTCATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.49
Consensus pattern (32 bp):
CTTTTTGGATATTGAATTTTCATTTACACATC
Found at i:650820 original size:17 final size:17
Alignment explanation
Indices: 650798--650830 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
650788 ACTTAAAAAT
650798 ATAAATTAAAATATATA
1 ATAAATTAAAATATATA
650815 ATAAATTAAAATATAT
1 ATAAATTAAAATATAT
650831 TTATAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAATTAAAATATATA
Found at i:651303 original size:20 final size:19
Alignment explanation
Indices: 651259--651308 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
651249 AAAAAATTAG
651259 ATAA-TATTTTAAATTTTT
1 ATAATTATTTTAAATTTTT
*
651277 ATTATTATTTTAAAATATTTT
1 ATAATTATTTT-AAAT-TTTT
651298 A-AATTAATTTT
1 ATAATT-ATTTT
651309 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.12
19 6 0.23
20 7 0.27
21 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATAATTATTTTAAATTTTT
Found at i:651326 original size:18 final size:18
Alignment explanation
Indices: 651301--651337 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
651291 ATATTTTAAA
*
651301 TTAATTTTTTTA-TTTTT
1 TTAAATTTTTTAGTTTTT
651318 TTAAATTTTTTAGTTTTT
1 TTAAATTTTTTAGTTTTT
651336 TT
1 TT
651338 TATTATGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (18 bp):
TTAAATTTTTTAGTTTTT
Found at i:651711 original size:2 final size:2
Alignment explanation
Indices: 651706--651748 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
651696 TATAGTTATT
* *
651706 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
651748 T
1 T
651749 CCTTTTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:657243 original size:17 final size:17
Alignment explanation
Indices: 657220--657260 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
657210 CGTTTAAGTC
657220 ATAAATTTTTAATT-TTA
1 ATAAATTTTT-ATTATTA
*
657237 TTAAATTTTTATTATTA
1 ATAAATTTTTATTATTA
657254 ATAAATT
1 ATAAATT
657261 AAATTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAAATTTTTATTATTA
Found at i:657262 original size:22 final size:22
Alignment explanation
Indices: 657236--657277 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
657226 TTTTAATTTT
657236 ATTAAATT-TTTATTATTAATAA
1 ATTAAATTATTTA-TATTAATAA
657258 ATTAAATTATTTATATTAAT
1 ATTAAATTATTTATATTAAT
657278 TTTATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAAATTATTTATATTAATAA
Found at i:657780 original size:12 final size:12
Alignment explanation
Indices: 657765--657830 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
657755 TTTATTTTAT
657765 TATTTAAAATAA
1 TATTTAAAATAA
*
657777 TATTAAAAATAA
1 TATTTAAAATAA
*
657789 TATTTATAATTAA
1 TATTTA-AAATAA
657802 -ATTT-AAATAA
1 TATTTAAAATAA
* * *
657812 AAATAAAAATAA
1 TATTTAAAATAA
*
657824 TTTTTAA
1 TATTTAA
657831 TTATTTAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
10 5 0.12
11 2 0.05
12 29 0.71
13 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:660723 original size:53 final size:51
Alignment explanation
Indices: 660657--660760 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 51
660647 AAACCTTTAT
** *
660657 ATTTTTATTATATTTAAATAAATTTTTAATATTTAATTTTTATCTAAATAA
1 ATTTTTATTATATTTAAATAAATCGTTAATATTTAATTTATATCTAAATAA
*
660708 ATTTTTAATTTATATTTAAATAACTCGTTAATATTTAATTTATATCTAAATAA
1 ATTTTT-A-TTATATTTAAATAAATCGTTAATATTTAATTTATATCTAAATAA
660761 TATCTTAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
51 6 0.13
52 1 0.02
53 40 0.85
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (51 bp):
ATTTTTATTATATTTAAATAAATCGTTAATATTTAATTTATATCTAAATAA
Found at i:660738 original size:23 final size:23
Alignment explanation
Indices: 660689--660739 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
660679 TTTTTAATAT
* **
660689 TTAATTTTTATCTAAATAAATTT
1 TTAATTTATATCTAAATAAATCG
* *
660712 TTAATTTATATTTAAATAACTCG
1 TTAATTTATATCTAAATAAATCG
660735 TTAAT
1 TTAAT
660740 ATTTAATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATTTATATCTAAATAAATCG
Found at i:660769 original size:30 final size:30
Alignment explanation
Indices: 660711--660771 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
660701 TAAATAAATT
* *
660711 TTTAATTTATATTTAAATAACTCGTTAATA
1 TTTAATTTATATCTAAATAAATCGTTAATA
660741 TTTAATTTATATCTAAATAATATC-TTAATA
1 TTTAATTTATATCTAAATAA-ATCGTTAATA
660771 T
1 T
660772 AATCATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTAATTTATATCTAAATAAATCGTTAATA
Found at i:660861 original size:21 final size:21
Alignment explanation
Indices: 660818--660877 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
660808 TAAAAAACAA
* *
660818 ATAATAAAAATTTATATAA-TT
1 ATAATAAAAATATA-AAAATTT
660839 ATAATAAAAATATAAAAATTT
1 ATAATAAAAATATAAAAATTT
* *
660860 AT--TTAAAATAAAAAAATT
1 ATAATAAAAATATAAAAATT
660878 CAAGAGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 14 0.41
20 3 0.09
21 17 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATAAAAATATAAAAATTT
Found at i:661486 original size:16 final size:16
Alignment explanation
Indices: 661446--661498 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
661436 TAGTAAAAAA
661446 TATTAT-AAATAATTT
1 TATTATAAAATAATTT
*
661461 AAATTA-AAAATTAATTT
1 -TATTATAAAA-TAATTT
661478 T-TTATAAAATAATTT
1 TATTATAAAATAATTT
661493 TATTAT
1 TATTAT
661499 TTTTATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 10 0.32
16 15 0.48
17 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTATAAAATAATTT
Found at i:661640 original size:16 final size:17
Alignment explanation
Indices: 661619--661687 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 17
661609 AATCTTATCA
661619 TTATTATATTTAA-ATT
1 TTATTATATTTAATATT
*
661635 TTATTATTTTTAATATT
1 TTATTATATTTAATATT
661652 TTAATT-T-TTCATAATATT
1 TT-ATTATATT--TAATATT
661670 TT-TTA-ATTTAAATATT
1 TTATTATATTT-AATATT
661686 TT
1 TT
661688 TCAATTATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
15 1 0.02
16 24 0.53
17 8 0.18
18 12 0.27
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATATTTAATATT
Found at i:661654 original size:103 final size:103
Alignment explanation
Indices: 661546--661745 Score: 230
Period size: 103 Copynumber: 1.9 Consensus size: 103
661536 TTTTTTTGGC
* * * * * *
661546 ATTTTAATTTTTTATTAT-TTTATTTAA-TTCAATTTTTTTAAAAAATAATAT-TAATTAATTTT
1 ATTTTAATTTTTCATAATATTT-TTTAATTTAAATATTTTTAAAAAATAATATCAAATTAATCTT
661608 TAATCTTATCATTATTAT-AT-TTAAATTTTATTATTTTTAAT
65 TAA--TT-TCATTATTATGATATTAAA-TTTATTATTTTTAAT
* ** *
661649 ATTTTAATTTTTCATAATATTTTTTAATTTAAATATTTTTCAATTATAATATCAAATTCATCTTT
1 ATTTTAATTTTTCATAATATTTTTTAATTTAAATATTTTTAAAAAATAATATCAAATTAATCTTT
661714 AATTTCATTATTATGATATTAAATTTATTATT
66 AATTTCATTATTATGATATTAAATTTATTATT
661746 ATAATAATTG
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
102 10 0.12
103 34 0.41
104 27 0.33
105 11 0.13
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (103 bp):
ATTTTAATTTTTCATAATATTTTTTAATTTAAATATTTTTAAAAAATAATATCAAATTAATCTTT
AATTTCATTATTATGATATTAAATTTATTATTTTTAAT
Found at i:661699 original size:16 final size:16
Alignment explanation
Indices: 661662--661700 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
661652 TTAATTTTTC
*
661662 ATAATATTTTTTAATT
1 ATAATATTTTTCAATT
661678 -TAAATATTTTTCAATT
1 AT-AATATTTTTCAATT
661694 ATAATAT
1 ATAATAT
661701 CAAATTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATAATATTTTTCAATT
Found at i:663093 original size:36 final size:36
Alignment explanation
Indices: 663046--663118 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
663036 ACTTTGCTGA
663046 ATATATGAGAACCAGATACCAGGTAAAACTTGTTGC
1 ATATATGAGAACCAGATACCAGGTAAAACTTGTTGC
**
663082 ATATATGAGAACCAGATATTAGGTAAAACTTGTTGC
1 ATATATGAGAACCAGATACCAGGTAAAACTTGTTGC
663118 A
1 A
663119 ATCTGTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
ATATATGAGAACCAGATACCAGGTAAAACTTGTTGC
Found at i:664784 original size:24 final size:22
Alignment explanation
Indices: 664760--664801 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
664750 GGATATGAAT
664760 ATAT-AAATAAAAAAGTTAAAAA
1 ATATCAAAT-AAAAAGTTAAAAA
*
664782 ATATCAAATCAAAAGTTAAA
1 ATATCAAATAAAAAGTTAAA
664802 TTGATATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (22 bp):
ATATCAAATAAAAAGTTAAAAA
Found at i:664850 original size:19 final size:21
Alignment explanation
Indices: 664819--664861 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
664809 GATTTTCGAT
*
664819 TTTTAACTTA-TTTAAAAGGA
1 TTTTAACTTATTTTAAAAGAA
664839 TTTTAA-TTATTTTAAAAGAA
1 TTTTAACTTATTTTAAAAGAA
664859 TTT
1 TTT
664862 AATGTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTTAACTTATTTTAAAAGAA
Found at i:665197 original size:16 final size:17
Alignment explanation
Indices: 665164--665219 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
665154 ACATATTAAA
665164 ATTAATA-ATATAAATT
1 ATTAATATATATAAATT
*
665180 ATTAATATAT-TAATTT
1 ATTAATATATATAAATT
665196 ATATAA-ATATATAATATT
1 AT-TAATATATATAA-ATT
*
665214 TTTAAT
1 ATTAAT
665220 TTGACATCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 18 0.56
17 11 0.34
18 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAATATATATAAATT
Found at i:665203 original size:25 final size:26
Alignment explanation
Indices: 665171--665221 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
665161 AAAATTAATA
665171 ATATAAAT-TATTAATA-TATTAATTT
1 ATATAAATATA-TAATATTATTAATTT
*
665196 ATATAAATATATAATATTTTTAATTT
1 ATATAAATATATAATATTATTAATTT
665222 GACATCACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATATAAATATATAATATTATTAATTT
Found at i:669456 original size:27 final size:25
Alignment explanation
Indices: 669396--669461 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
669386 ACATAATGAG
*
669396 TGAAAAA-TATATTTTGAAAAATAAA
1 TGAAAAATTATA-TTTAAAAAATAAA
*
669421 TAAATAAATTATATTTAAAAAATTAAA
1 TGAA-AAATTATATTTAAAAAA-TAAA
*
669448 TTGAAAAATAATAT
1 -TGAAAAATTATAT
669462 GTAATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 3 0.09
26 11 0.33
27 16 0.48
28 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.35
Consensus pattern (25 bp):
TGAAAAATTATATTTAAAAAATAAA
Found at i:676201 original size:2 final size:2
Alignment explanation
Indices: 676190--676236 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
676180 TTAATGAACT
676190 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
676231 TA TA TA
1 TA TA TA
676237 AATTTTCATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:676365 original size:4 final size:4
Alignment explanation
Indices: 676356--676383 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
676346 ACGAAGCTTC
676356 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
676384 TGGGTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:676544 original size:27 final size:28
Alignment explanation
Indices: 676512--676581 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
676502 TAAAATTATA
676512 ATTTATTTTAAAATAAAAATA-AAAAAT
1 ATTTATTTTAAAATAAAAATACAAAAAT
* *
676539 ATTTATATTATAAA-AAAAGTACAAAAAT
1 ATTTATTTTA-AAATAAAAATACAAAAAT
* *
676567 GTTTAATTCTAAAAT
1 ATTT-ATTTTAAAAT
676582 TTAAAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 15 0.44
28 15 0.44
29 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (28 bp):
ATTTATTTTAAAATAAAAATACAAAAAT
Found at i:677005 original size:17 final size:16
Alignment explanation
Indices: 676975--677016 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
676965 ATATTAAATA
*
676975 AATA-TTAAATATAATT
1 AATATTTAAAAATAA-T
676991 AATATTTAAAAATAAT
1 AATATTTAAAAATAAT
677007 ATATATTTAA
1 A-ATATTTAA
677017 CTAAATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATTTAAAAATAAT
Found at i:677112 original size:14 final size:14
Alignment explanation
Indices: 677076--677114 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
677066 CTTATTAATT
677076 AAAATAAAATT-TTA
1 AAAAT-AAATTATTA
677090 AAAATAAATTATTA
1 AAAATAAATTATTA
677104 AAAATAAATTA
1 AAAATAAATTA
677115 AAATCTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAAATTATTA
Found at i:680263 original size:20 final size:21
Alignment explanation
Indices: 680228--680267 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
680218 TTATAATTAA
680228 ATTTAAATAAAATAATTTTATT
1 ATTTAAAT-AAATAATTTTATT
680250 ATTTAAAT-AATAATTTTA
1 ATTTAAATAAATAATTTTA
680268 ATTAAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAAATAAATAATTTTATT
Found at i:680617 original size:12 final size:13
Alignment explanation
Indices: 680600--680660 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 13
680590 TTAAGCATTA
680600 AAAATATTAAT-T
1 AAAATATTAATAT
680612 AAAATA-TAATAT
1 AAAATATTAATAT
680624 AAAATA-TAATATTT
1 AAAATATTAATA--T
*
680638 AAAA-AATAATAT
1 AAAATATTAATAT
680650 AAATATATTAA
1 AAA-ATATTAA
680661 AAAATATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
11 4 0.10
12 22 0.52
13 2 0.05
14 14 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATATTAATAT
Found at i:680646 original size:14 final size:14
Alignment explanation
Indices: 680599--680649 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
680589 ATTAAGCATT
* *
680599 AAAAATATTAATTA
1 AAAAATAATATTTA
*
680613 AAATATAATA--TA
1 AAAAATAATATTTA
*
680625 AAATATAATATTTA
1 AAAAATAATATTTA
680639 AAAAATAATAT
1 AAAAATAATAT
680650 AAATATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 12 0.38
14 20 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAATAATATTTA
Found at i:680675 original size:21 final size:21
Alignment explanation
Indices: 680626--680672 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
680616 TATAATATAA
680626 AATAT-AATAT-TTAAAAAAT
1 AATATAAATATATTAAAAAAT
680645 AATATAAATATATTAAAAAAT
1 AATATAAATATATTAAAAAAT
680666 -ATATAAA
1 AATATAAA
680673 ATAAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.19
20 12 0.46
21 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATATAAATATATTAAAAAAT
Found at i:680677 original size:51 final size:52
Alignment explanation
Indices: 680598--680745 Score: 122
Period size: 51 Copynumber: 2.8 Consensus size: 52
680588 TATTAAGCAT
* * *
680598 TAAAAATATTAATTAAAATATAATATAAAATATAATATT-TAAAAAATAATA
1 TAAATATATTAATAAAAATATAAAATAAAATATAATATTGTAAAAAATAATA
* * *
680649 TAAATATATTAA-AAAATATATAAAATAAATTATTATTTTGTTAAAAATTATAAAATA
1 TAAATATATTAATAAAA-ATATAAAATAAAATATAATATTG-TAAAAA--AT--AATA
* * *
680706 TATAATATTTTTAATAAAATTATAATA-AAAATATAATATT
1 TA-AATA-TATTAATAAAAATATAAAATAAAATATAATATT
680746 AATACATAAC
Statistics
Matches: 75, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
50 3 0.04
51 29 0.39
53 6 0.08
55 2 0.03
57 6 0.08
58 14 0.19
59 11 0.15
60 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (52 bp):
TAAATATATTAATAAAAATATAAAATAAAATATAATATTGTAAAAAATAATA
Found at i:680680 original size:21 final size:21
Alignment explanation
Indices: 680608--680680 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 21
680598 TAAAAATATT
*
680608 AATTAAAATATAATATAAAATATA
1 AATTAAAAAAT-ATAT-AAA-ATA
680632 ATATTTAAAAAATA-ATATAAATA
1 A-A-TTAAAAAATATATA-AAATA
*
680655 TATTAAAAAATATATAAAATA
1 AATTAAAAAATATATAAAATA
680676 AATTA
1 AATTA
680681 TTATTTTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
21 19 0.45
22 4 0.10
23 4 0.10
24 5 0.12
25 2 0.05
26 8 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTAAAAAATATATAAAATA
Found at i:680701 original size:30 final size:28
Alignment explanation
Indices: 680640--680745 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 28
680630 TAATATTTAA
*
680640 AAAATAATATAA-ATATATTAAAAAATATAT
1 AAAATAA-ATAATAT-TTTTAAAAAAT-TAT
* *
680670 AAAATAAATTATTATTTTGTTAAAAATTAT
1 AAAATAAA-TAATATTTT-TAAAAAATTAT
*
680700 AAAATATATAATATTTTTAATAAAATTAT
1 AAAATAAATAATATTTTTAA-AAAATTAT
*
680729 AATAAAAATATAATATT
1 AA-AATAA-ATAATATT
680746 AATACATAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
28 2 0.03
29 19 0.31
30 24 0.39
31 17 0.27
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
AAAATAAATAATATTTTTAAAAAATTAT
Found at i:682236 original size:42 final size:40
Alignment explanation
Indices: 682190--682267 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
682180 TTGATAAATT
682190 ATTATTTAAATTTAAT-TATTAAATATATAAATATTAATAAAA
1 ATTATTT-AATTTAATATATTAAATA-ATAAAT-TTAATAAAA
** *
682232 ATTATTTTTTTTAATATTTTAAATAATAAATTTAAT
1 ATTATTTAATTTAATATATTAAATAATAAATTTAAT
682268 TTATAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 5 0.16
41 12 0.38
42 15 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
ATTATTTAATTTAATATATTAAATAATAAATTTAATAAAA
Found at i:682273 original size:13 final size:13
Alignment explanation
Indices: 682257--682283 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
682247 ATTTTAAATA
682257 ATAAATTTAATTT
1 ATAAATTTAATTT
682270 ATAAATTTAATTT
1 ATAAATTTAATTT
682283 A
1 A
682284 ATTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAATTTAATTT
Found at i:683461 original size:17 final size:18
Alignment explanation
Indices: 683421--683463 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
683411 TATATAAAAT
**
683421 ATATAATATTTAAATATA
1 ATATAATATAAAAATATA
683439 ATTATAATATAAAAAT-TA
1 A-TATAATATAAAAATATA
683457 ATATAAT
1 ATATAAT
683464 TATGATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 4 0.18
19 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAATATAAAAATATA
Found at i:683609 original size:2 final size:2
Alignment explanation
Indices: 683602--683632 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
683592 AACATATTCC
683602 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
683633 ATGTAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:685043 original size:14 final size:14
Alignment explanation
Indices: 685024--685053 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
685014 GAATTCAAGG
685024 TTTAATTTAATTTA
1 TTTAATTTAATTTA
*
685038 TTTAATTTATTTTA
1 TTTAATTTAATTTA
685052 TT
1 TT
685054 ATTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAATTTAATTTA
Found at i:686483 original size:23 final size:24
Alignment explanation
Indices: 686457--686537 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 24
686447 TATTTATTAA
686457 TAATAAAAATAATATTTTAAAT-T
1 TAATAAAAATAATATTTTAAATAT
* *
686480 TAATTATAAA-AATA-TATAAATAT
1 TAA-TAAAAATAATATTTTAAATAT
*
686503 TAATATAAAAAATAATATTTTAATTAT
1 T-A-AT-AAAAATAATATTTTAAATAT
686530 ATAATAAA
1 -TAATAAA
686538 TATGTCTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
22 6 0.13
23 9 0.20
24 7 0.16
25 8 0.18
26 6 0.13
27 8 0.18
28 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAATAAAAATAATATTTTAAATAT
Found at i:686488 original size:26 final size:27
Alignment explanation
Indices: 686451--686534 Score: 90
Period size: 26 Copynumber: 3.3 Consensus size: 27
686441 TCAAATTATT
*
686451 TATTAATAATAAAAATAATATTTTAAA
1 TATTAATTATAAAAATAATATTTTAAA
686478 T-TTAATTATAAAAAT-ATA---TAAA
1 TATTAATTATAAAAATAATATTTTAAA
*
686500 TATTAA-TATAAAAAATAATATTTTAAT
1 TATTAATTAT-AAAAATAATATTTTAAA
686527 TATATAAT
1 TAT-TAAT
686535 AAATATGTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
22 8 0.17
23 10 0.21
24 3 0.06
25 3 0.06
26 13 0.28
27 7 0.15
28 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TATTAATTATAAAAATAATATTTTAAA
Found at i:686802 original size:3 final size:3
Alignment explanation
Indices: 686794--686840 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
686784 TAGAAAAATA
* *
686794 AAT AAT AAT AAT AAT AAT AAT GAC AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
686841 GGTCCATGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:687508 original size:19 final size:19
Alignment explanation
Indices: 687484--687527 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
687474 GGTGAATATA
*
687484 TTTTTAGAACAAATTTTAT
1 TTTTTAGAACAAATTTAAT
**
687503 TTTTTA-TTCAAATTTAAT
1 TTTTTAGAACAAATTTAAT
687521 TTTTTAG
1 TTTTTAG
687528 TTTAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTAGAACAAATTTAAT
Found at i:687574 original size:19 final size:18
Alignment explanation
Indices: 687550--687585 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
687540 ATTTAAATTT
*
687550 TTTTAAATATTATATAAAG
1 TTTTAAAT-TTAAATAAAG
687569 TTTTAAATTTAAATAAA
1 TTTTAAATTTAAATAAA
687586 TAATTTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTAAATTTAAATAAAG
Found at i:689757 original size:82 final size:81
Alignment explanation
Indices: 689610--690067 Score: 441
Period size: 82 Copynumber: 5.6 Consensus size: 81
689600 CTTTGGGAAG
* ** *
689610 TGCATTGAAACGAACATTCGTTTAATAGGCATTACATAT--GAAATAGTGCATTTGATCACATGT
1 TGCA-TGAAACGAACATTCCTGCAATAGGCATTACAT-TCCG-AATAGTGCATTTGATCACACGT
*
689673 TACTTATTTCATTATGACC
63 TACTTATTTCATTACGACC
* ** * * * *
689692 TGCACTGAAACGAACCTTCCTTTAACAGGCATAACATTCCGAATAGTGCATGTGATTACACGTTA
1 TGCA-TGAAACGAACATTCCTGCAATAGGCATTACATTCCGAATAGTGCATTTGATCACACGTTA
*
689757 CTTATTTCATCACGACC
65 CTTATTTCATTACGACC
* * * *
689774 TGTATCGAAACGAACATTCCTGCAATAGGCATTACATACC-AAGTAGTGCATTTGCTCACACGCT
1 TGCAT-GAAACGAACATTCCTGCAATAGGCATTACATTCCGAA-TAGTGCATTTGATCACACGTT
* *
689838 ACTTATTTCATCACAACC
64 ACTTATTTCATTACGACC
* * * *
689856 TGCATCGGAACGAACATTCCTGCAATAGGCATTACATACCAAAT-GTTGCATTTGATCACATGCT
1 TGCAT-GAAACGAACATTCCTGCAATAGGCATTACATTCCGAATAG-TGCATTTGATCACACG-T
*
689920 T-CTTATTTCATTATGACC
63 TACTTATTTCATTACGACC
* * * *
689938 AGCATTGAGACGAACATTCCTGCAAAAGGCATTAC-TTACCGAATGGTGCATTTGATCACAC-TC
1 TGCA-TGAAACGAACATTCCTGCAATAGGCATTACATT-CCGAATAGTGCATTTGATCACACGT-
* *
690001 TGCTTATTTTATTACGACC
63 TACTTATTTCATTACGACC
* *
690020 TGCATCG--A-GAACATTCCTGCAATAGGCATTACATACCAAATAGTGCAT
1 TGCAT-GAAACGAACATTCCTGCAATAGGCATTACATTCCGAATAGTGCAT
690068 GACGATTACA
Statistics
Matches: 318, Mismatches: 44, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
79 34 0.11
80 3 0.01
81 8 0.03
82 267 0.84
83 6 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (81 bp):
TGCATGAAACGAACATTCCTGCAATAGGCATTACATTCCGAATAGTGCATTTGATCACACGTTAC
TTATTTCATTACGACC
Found at i:689927 original size:164 final size:163
Alignment explanation
Indices: 689611--690068 Score: 505
Period size: 164 Copynumber: 2.8 Consensus size: 163
689601 TTTGGGAAGT
* * ** ** * *
689611 GCATTGAAACGAACATTCGTTTAATAGGCATTACATATGAAATAGTGCATTTGATCACATGTTAC
1 GCATCGAAACGAACATTCCTGCAATAGGCATTACATA-CCAATAGTGCATTTGATCACACGCTAC
* * * ** * * * *
689676 TTATTTCATTATGACCTGCA-CTGAAACGAACCTTCCTTTAACAGGCATAACATTCCGAATAGTG
65 TTATTTCATTACGACCTGCATC-GGAACGAACATTCCTGCAATAGGCATTACATACCAAATAGTG
* *
689740 CATGTGATTACACGTTACTTATTTCATCACGACCT
129 CATGTGATCACACGTTACTTATTTCATCACGACCA
* *
689775 GTATCGAAACGAACATTCCTGCAATAGGCATTACATACCAAGTAGTGCATTTGCTCACACGCTAC
1 GCATCGAAACGAACATTCCTGCAATAGGCATTACATACCAA-TAGTGCATTTGATCACACGCTAC
* *
689840 TTATTTCATCACAACCTGCATCGGAACGAACATTCCTGCAATAGGCATTACATACCAAAT-GTTG
65 TTATTTCATTACGACCTGCATCGGAACGAACATTCCTGCAATAGGCATTACATACCAAATAG-TG
* * * *
689904 CATTTGATCACATGCTT-CTTATTTCATTATGACCA
129 CATGTGATCACACG-TTACTTATTTCATCACGACCA
* * * * * * *
689939 GCATTGAGACGAACATTCCTGCAAAAGGCATTACTTACCGAATGGTGCATTTGATCACACTCTGC
1 GCATCGAAACGAACATTCCTGCAATAGGCATTACATACC-AATAGTGCATTTGATCACACGCTAC
*
690004 TTATTTTATTACGACCTGCATC-G-A-GAACATTCCTGCAATAGGCATTACATACCAAATAGTGC
65 TTATTTCATTACGACCTGCATCGGAACGAACATTCCTGCAATAGGCATTACATACCAAATAGTGC
690066 ATG
130 ATG
690069 ACGATTACAG
Statistics
Matches: 248, Mismatches: 40, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
161 38 0.15
162 2 0.01
163 4 0.02
164 199 0.80
165 5 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (163 bp):
GCATCGAAACGAACATTCCTGCAATAGGCATTACATACCAATAGTGCATTTGATCACACGCTACT
TATTTCATTACGACCTGCATCGGAACGAACATTCCTGCAATAGGCATTACATACCAAATAGTGCA
TGTGATCACACGTTACTTATTTCATCACGACCA
Found at i:696198 original size:397 final size:389
Alignment explanation
Indices: 695577--696311 Score: 1319
Period size: 397 Copynumber: 1.9 Consensus size: 389
695567 GGGGGGGGGG
* *
695577 AATCAGGTGTTTGGGGTTGAGAATAGATTTGCTTTATGGTGCTGTTTAGTTGTAGATTGCTGAAT
1 AATCAGGTGTTTGGGGTTGAGAATAGATTTGCTTTATGGTGCTGCTTAGTTGTAGATTGCCGAAT
*
695642 GCACTTAATATATGTGCTAACATTTTTATTTTTTTTTGCTGTCAGCTTTACAAAACTCGCGAGGA
66 GCACTTAATATATGTGCTAACATTTTTATTTTTTTTTGCTGGCAGCTTTACAAAACTCGCGAGGA
695707 GAAGTATCTGCTGGATCTTCAGAGGGTTCAGGGGCCACAGTTTCTCTTCTTGGATCTTTGTGCTG
131 GAAGTATCTGCTGGATCTTCAGAGGGTTCAGGGGCCACAGTTTCTCTTCTTGGATCTTTGTGCTG
*
695772 CATTCCTTGCACAGCTCCGGGTCCTCTAAATGAGAAGGTTATATTTCAGCGACCTTTGTCCATGA
196 CATTCCTTGCACAGCTCCGGGTCCTCTAAATGAGAAGGTTATATTTCAACGACCTTTGTCCATGA
* *
695837 CCATGAATCTTCTACGATGGATGTGAATAAGAACATTCGATGTATATAATTTTCTTTTTCCTTTT
261 CCATGAATCTTCTACGATGCATGTGAATAAGAACATTCGATGTATATAATTTCCTTTTTCCTTTT
695902 TCATTTTTTAGTCTAACTGATTATCCTCCGAGCAAAGGGTTTTTTTTTTTTTTTTTCCTGAGGA
326 TCATTTTTTAGTCTAACTGATTATCCTCCGAGCAAAGGGTTTTTTTTTTTTTTTTTCCTGAGGA
695966 AATCAGGTGTTTGGGGTTGAGAATAGATTTGCTTTATGGTGCTGCTTAGTTGTAGATTGCCGAAT
1 AATCAGGTGTTTGGGGTTGAGAATAGATTTGCTTTATGGTGCTGCTTAGTTGTAGATTGCCGAAT
*
696031 GCACTTAATATATGTGCTAACATTTTT-TTTTTTGCTGTCGTGGGTGCCAGCAGCTTTACAAAAC
66 GCACTTAATATATGTGCTAACATTTTTATTTTTT--T-T--T-GCTG---GCAGCTTTACAAAAC
696095 TCGCGAGGAGAAGTATCTGCTGGATCTTCAGAGGGTTCAGGGGCCACAGTTTCTCTTCTTGGATC
122 TCGCGAGGAGAAGTATCTGCTGGATCTTCAGAGGGTTCAGGGGCCACAGTTTCTCTTCTTGGATC
696160 TTTGTGCTGCATTCCTTGCACAGCTCCGGGTCCTCTAAATGAGAAGGTTATATTTCAACGACCTT
187 TTTGTGCTGCATTCCTTGCACAGCTCCGGGTCCTCTAAATGAGAAGGTTATATTTCAACGACCTT
696225 TGTCCATGACCATGAATCTTCTACGATGCATGTGAATAAGAACATTCGATGTATATAATTTCCTT
252 TGTCCATGACCATGAATCTTCTACGATGCATGTGAATAAGAACATTCGATGTATATAATTTCCTT
696290 TTTCCTTTTTCATTTTTTAGTC
317 TTTCCTTTTTCATTTTTTAGTC
696312 CGACTAAACC
Statistics
Matches: 330, Mismatches: 7, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
388 6 0.02
389 90 0.27
390 1 0.00
391 1 0.00
393 1 0.00
394 3 0.01
397 228 0.69
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (389 bp):
AATCAGGTGTTTGGGGTTGAGAATAGATTTGCTTTATGGTGCTGCTTAGTTGTAGATTGCCGAAT
GCACTTAATATATGTGCTAACATTTTTATTTTTTTTTGCTGGCAGCTTTACAAAACTCGCGAGGA
GAAGTATCTGCTGGATCTTCAGAGGGTTCAGGGGCCACAGTTTCTCTTCTTGGATCTTTGTGCTG
CATTCCTTGCACAGCTCCGGGTCCTCTAAATGAGAAGGTTATATTTCAACGACCTTTGTCCATGA
CCATGAATCTTCTACGATGCATGTGAATAAGAACATTCGATGTATATAATTTCCTTTTTCCTTTT
TCATTTTTTAGTCTAACTGATTATCCTCCGAGCAAAGGGTTTTTTTTTTTTTTTTTCCTGAGGA
Found at i:697368 original size:24 final size:25
Alignment explanation
Indices: 697323--697377 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
697313 TTTATAATTA
697323 TTTTATAATTTAGAAAATTTTATTT
1 TTTTATAATTTAGAAAATTTTATTT
*
697348 TTTTATAAGTTTA-ATAA-TTTATTT
1 TTTTATAA-TTTAGAAAATTTTATTT
*
697372 TATTAT
1 TTTTAT
697378 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 11 0.41
26 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTTATAATTTAGAAAATTTTATTT
Found at i:700890 original size:2 final size:2
Alignment explanation
Indices: 700883--700911 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
700873 TTGCTCTTGT
700883 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
700912 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:701703 original size:22 final size:22
Alignment explanation
Indices: 701668--701709 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
701658 ATTTTTTATT
701668 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
701690 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
701710 ATTTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:705202 original size:17 final size:17
Alignment explanation
Indices: 705180--705219 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
705170 TAAAATTTTT
705180 TCATGACGTAACTCGAC
1 TCATGACGTAACTCGAC
705197 TCATGACGTAACTCGAC
1 TCATGACGTAACTCGAC
705214 TCATGA
1 TCATGA
705220 ATATCCCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (17 bp):
TCATGACGTAACTCGAC
Found at i:709813 original size:162 final size:160
Alignment explanation
Indices: 709256--709818 Score: 720
Period size: 160 Copynumber: 3.5 Consensus size: 160
709246 TTTTCCCAAC
* * * * *
709256 ACCCACATATCTAAAACACAAATATATTGAGAAAACAAATAAAAAAAGTGAACTTCTTGTTGATG
1 ACCCAAATATCTAAAACCCAAATATATTGAGAAAACAAGTAAAAAAAATGAACTTCTTGATGATG
* *
709321 ATACTCAAAATAATAAAAACACCCCAAGACTAAAAATCATAACTTTGAGTTAATCAAAGGTACAT
66 ATACTCAAAATAATAAAAACACCCCAAGACTAAGAATCATAACTTTGAGTTAATCAAAGGTAAAT
* * *
709386 TTCCAATAAATTAAGCTCTACTTCTTTTATT
131 TTCCAAT-CATTAAGCTCTACTTTTTTTAAT
* * *
709417 ACCCAAATCTCTAAAACCCAAATATATTGAGAAAACAA-TTAAAAAAGTGAACTTCTTGATGATG
1 ACCCAAATATCTAAAACCCAAATATATTGAGAAAACAAGTAAAAAAAATGAACTTCTTGATGATG
* * *
709481 ATATTCAAAATAATAAAACCACCCCAAGACTAAGAATCATCATATCTTTTAGTTAATCAAAGGTA
66 ATACTCAAAATAATAAAAACACCCCAAGACTAAGAATCAT-A-A-CTTTGAGTTAATCAAAGGTA
709546 AATTTCCAATCATTAAAGCTCTACATTTTTTTCTAAT
128 AATTTCCAATCATT-AAGCTCTAC--TTTTTT-TAAT
* * * * * *
709583 -CCAAAATATCTGAAACCCATATAGACTGAGAAAACAAGTAAAAAAGAT-AACTTCTTGATGATG
1 ACCCAAATATCTAAAACCCAAATATATTGAGAAAACAAGTAAAAAAAATGAACTTCTTGATGATG
* * * *
709646 ATACTCAAAATAATAAAAGCATCCCAAAACTAAGAATCATAACTTTGAGTTAATCAAAGGTAAAC
66 ATACTCAAAATAATAAAAACACCCCAAGACTAAGAATCATAACTTTGAGTTAATCAAAGGTAAAT
709711 TTCCAATCATTGAA-CTCTACTTTTTTTAAAT
131 TTCCAATCATT-AAGCTCTACTTTTTTT-AAT
* * * * *
709742 ACCCACATATCCAAAATCCATATATATTGAGAAAACAAGTAACAAAAAATGAACTTCATGATGAT
1 ACCCAAATATCTAAAACCCAAATATATTGAGAAAACAAGTAA-AAAAAATGAACTTCTTGATGAT
709807 GATACTCAAAAT
65 GATACTCAAAAT
709819 GATAGAACAA
Statistics
Matches: 352, Mismatches: 38, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
158 1 0.00
159 9 0.03
160 95 0.27
161 48 0.14
162 63 0.18
163 38 0.11
164 1 0.00
165 87 0.25
166 10 0.03
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (160 bp):
ACCCAAATATCTAAAACCCAAATATATTGAGAAAACAAGTAAAAAAAATGAACTTCTTGATGATG
ATACTCAAAATAATAAAAACACCCCAAGACTAAGAATCATAACTTTGAGTTAATCAAAGGTAAAT
TTCCAATCATTAAGCTCTACTTTTTTTAAT
Found at i:711162 original size:17 final size:18
Alignment explanation
Indices: 711142--711175 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
711132 TTTTTTAATA
*
711142 ATTTTACTAATA-AAAAG
1 ATTTAACTAATATAAAAG
711159 ATTTAACTAATATAAAA
1 ATTTAACTAATATAAAA
711176 CGTTAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATTTAACTAATATAAAAG
Found at i:714126 original size:18 final size:19
Alignment explanation
Indices: 714099--714143 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
714089 TTAGAATTTT
714099 TTTATAAAT-ATAATAAA-A
1 TTTATAAATAATAA-AAATA
*
714117 TTTATTAATAATAAAAATA
1 TTTATAAATAATAAAAATA
714136 TTTA-AAAT
1 TTTATAAAT
714144 GACAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTATAAATAATAAAAATA
Found at i:714720 original size:16 final size:18
Alignment explanation
Indices: 714689--714721 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
714679 TCTGATTAAA
714689 TTAAATCTATTAAATAAT
1 TTAAATCTATTAAATAAT
714707 TTAAAT-TA-TAAATAA
1 TTAAATCTATTAAATAA
714722 ATTTGTGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATCTATTAAATAAT
Found at i:714724 original size:17 final size:19
Alignment explanation
Indices: 714685--714725 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
714675 TTAATCTGAT
714685 TAAA-TTAAATCTATTAAA
1 TAAATTTAAATCTATTAAA
714703 T-AATTTAAAT-TA-TAAA
1 TAAATTTAAATCTATTAAA
714719 TAAATTT
1 TAAATTT
714726 GTGTGCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATTTAAATCTATTAAA
Found at i:714997 original size:21 final size:21
Alignment explanation
Indices: 714958--714997 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
714948 AATTATTTTA
*
714958 TTTAAATTTAATATTAATTAT
1 TTTAAATTTAATATAAATTAT
714979 TTTAAATATTAA-ATAAATT
1 TTTAAAT-TTAATATAAATT
714998 TATGAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAAATTTAATATAAATTAT
Found at i:715887 original size:10 final size:10
Alignment explanation
Indices: 715805--715887 Score: 51
Period size: 10 Copynumber: 8.0 Consensus size: 10
715795 ATTTTTAATA
*
715805 TATAAAATAT
1 TATAAATTAT
*
715815 TATAAAGTAT
1 TATAAATTAT
715825 TATAAATTATTT
1 TATAAATTA--T
*
715837 TAAAAATTAT
1 TATAAATTAT
** *
715847 TATATTTTTT
1 TATAAATTAT
* *
715857 TATGATTATAGT
1 TATAAAT-TA-T
715869 TAT-AATTAT
1 TATAAATTAT
715878 TATAAATTAT
1 TATAAATTAT
715888 GCAAAATAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
9 4 0.07
10 37 0.65
11 3 0.05
12 13 0.23
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (10 bp):
TATAAATTAT
Found at i:716235 original size:20 final size:19
Alignment explanation
Indices: 716180--716243 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
716170 TTAATAATTT
* *
716180 ATATTATATAAATTT-TAAA
1 ATATT-TATATATTTATATA
*
716199 ATATTTATATATTTATATC
1 ATATTTATATATTTATATA
*
716218 ATATTTATATTTTTTATATA
1 ATATTTATA-TATTTATATA
716238 ATATTT
1 ATATTT
716244 TAATTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
18 8 0.21
19 16 0.42
20 14 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTTATATATTTATATA
Found at i:717575 original size:22 final size:23
Alignment explanation
Indices: 717550--717598 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
717540 TTAAGACGAA
717550 TTAATTAAGTTAGA-AATTAAAT
1 TTAATTAAGTTAGATAATTAAAT
* * *
717572 TTAATTAATTTATATAATTATAT
1 TTAATTAAGTTAGATAATTAAAT
717595 TTAA
1 TTAA
717599 AAAATAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TTAATTAAGTTAGATAATTAAAT
Found at i:720697 original size:20 final size:21
Alignment explanation
Indices: 720672--720729 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
720662 TTAATTAATT
720672 ATATTTAAATATATTA-TATC
1 ATATTTAAATATATTATTATC
* *
720692 ATATTT-ATTATATTATTTTC
1 ATATTTAAATATATTATTATC
720712 ATATTTATAAATATATTA
1 ATA-TT-TAAATATATTA
720730 AGTTGGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 8 0.26
20 12 0.39
21 2 0.06
22 1 0.03
23 8 0.26
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTTAAATATATTATTATC
Found at i:722006 original size:22 final size:22
Alignment explanation
Indices: 721981--722022 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
721971 AATTATTAAA
*
721981 ATATTTTTAT-ATTAATATTTTT
1 ATATTTTAATAATTAA-ATTTTT
722003 ATATTTTAATAATTAAATTT
1 ATATTTTAATAATTAAATTT
722023 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTTTAATAATTAAATTTTT
Found at i:722013 original size:16 final size:14
Alignment explanation
Indices: 721980--722007 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
721970 CAATTATTAA
721980 AATATTTTTATATT
1 AATATTTTTATATT
721994 AATATTTTTATATT
1 AATATTTTTATATT
722008 TTAATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:725060 original size:3 final size:3
Alignment explanation
Indices: 725052--725077 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
725042 GACTCAAGGT
725052 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
725078 CCACCACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:725594 original size:20 final size:19
Alignment explanation
Indices: 725566--725651 Score: 73
Period size: 19 Copynumber: 4.9 Consensus size: 19
725556 ATATTTAAAG
725566 AATTTT-ATAT-TTATATA
1 AATTTTAATATATTATATA
725583 AATTTTAATATATTA-AT-
1 AATTTTAATATATTATATA
725600 AA--TT--TATATTATATA
1 AATTTTAATATATTATATA
*
725615 AATTTTAAAATATT-TATA
1 AATTTTAATATATTATATA
* *
725633 TATTTATATTATATTATAT
1 AATTT-TAATATATTATAT
725652 TATAATTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
13 7 0.13
14 2 0.04
15 4 0.07
17 10 0.18
18 14 0.25
19 15 0.27
20 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTAATATATTATATA
Found at i:725615 original size:32 final size:33
Alignment explanation
Indices: 725569--725646 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 33
725559 TTTAAAGAAT
*
725569 TTTATATTTATATAAATTTTAATATATTAATA-A
1 TTTATA-TTATATAAATTTTAAAATATTAATATA
*
725602 TTTATATTATATAAATTTTAAAATATTTATATA
1 TTTATATTATATAAATTTTAAAATATTAATATA
725635 TTTATATTATAT
1 TTTATATTATAT
725647 TATATTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 23 0.55
33 19 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTATATTATATAAATTTTAAAATATTAATATA
Found at i:725641 original size:14 final size:14
Alignment explanation
Indices: 725628--725674 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
725618 TTTAAAATAT
725628 TTATATATTTAT-A
1 TTATATATTTATAA
725641 TTATATTATATTATAA
1 TTATA-TAT-TTATAA
* *
725657 TTATTTTTTTATAA
1 TTATATATTTATAA
725671 TTAT
1 TTAT
725675 GTATGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 5 0.17
14 13 0.45
15 6 0.21
16 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATATATTTATAA
Found at i:725662 original size:33 final size:32
Alignment explanation
Indices: 725569--725662 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 32
725559 TTTAAAGAAT
*
725569 TTTATATT-TATATAAATTTTAATATATTAATAA
1 TTTATATTATAT-TAAATTTTAAT-TATTTATAA
*
725602 TTTATATTATA-TAAATTTTAAAATATTTATATA
1 TTTATATTATATTAAATTTT-AATTATTTATA-A
* *
725635 TTTATATTATATTATATTATAATTATTT
1 TTTATATTATATTAAATTTTAATTATTT
725663 TTTTATAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
32 15 0.29
33 29 0.56
34 8 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTATATTATATTAAATTTTAATTATTTATAA
Found at i:728303 original size:17 final size:19
Alignment explanation
Indices: 728281--728326 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
728271 GCCCTTTTTA
728281 TTATAAAATT-TATATATT
1 TTATAAAATTATATATATT
*
728299 TATAATATAATTATATATATT
1 T-T-ATAAAATTATATATATT
728320 TTATAAA
1 TTATAAA
728327 TATAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 1 0.04
19 5 0.22
20 8 0.35
21 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATAAAATTATATATATT
Found at i:728306 original size:11 final size:11
Alignment explanation
Indices: 728292--728338 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
728282 TATAAAATTT
*
728292 ATATATTTATA
1 ATATAATTATA
728303 ATATAATTAT-
1 ATATAATTATA
*
728313 ATATATTTTATAA
1 ATATA-ATTAT-A
728326 ATATAATTATA
1 ATATAATTATA
728337 AT
1 AT
728339 TTTATTTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 5 0.17
11 16 0.53
12 4 0.13
13 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATAATTATA
Found at i:728314 original size:19 final size:21
Alignment explanation
Indices: 728287--728340 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
728277 TTTATTATAA
728287 AATTTATATATTTAT-AATAT
1 AATTTATATATTTATAAATAT
728307 AATTATATATATTTTATAAATAT
1 AATT-TATATA-TTTATAAATAT
728330 AA-TTATA-ATTT
1 AATTTATATATTT
728341 TATTTTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.10
20 5 0.16
21 10 0.32
22 6 0.19
23 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTATATATTTATAAATAT
Found at i:728328 original size:23 final size:21
Alignment explanation
Indices: 728277--728343 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 21
728267 ATAAGCCCTT
* *
728277 TTTATTATAAAATT-TATATA
1 TTTATAATATAATTATATATA
728297 TTTATAATATAATTATATATA
1 TTTATAATATAATTATATATA
728318 TTTTATAAATATAATTATA-AT-
1 -TTTAT-AATATAATTATATATA
728339 TTTAT
1 TTTAT
728344 TTTACTAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 17 0.40
21 6 0.14
22 7 0.17
23 12 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATAATATAATTATATATA
Found at i:729376 original size:12 final size:11
Alignment explanation
Indices: 729345--729381 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
729335 GTTAATATAA
729345 AAATA-TTTTT
1 AAATATTTTTT
729355 AAA-ATTTTTT
1 AAATATTTTTT
729365 AAATATTATTTT
1 AAATATT-TTTT
729377 AAATA
1 AAATA
729382 ATAAAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 11 0.46
11 3 0.12
12 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:730238 original size:20 final size:19
Alignment explanation
Indices: 730205--730279 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 19
730195 AAATTAAGTA
730205 ATTTG-TTTAATTTAATTG
1 ATTTGATTTAATTTAATTG
730223 ATTTGATTTAAATTTAAATATG
1 ATTTGATTT-AATTT-AAT-TG
730245 ATTTTTGGTGATTTAATTTAATTTG
1 A---TT--TGATTTAATTTAA-TTG
730270 ATTTGATTTA
1 ATTTGATTTA
730280 GATTATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
18 5 0.11
19 3 0.06
20 12 0.26
21 3 0.06
22 5 0.11
25 7 0.15
26 6 0.13
27 6 0.13
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (19 bp):
ATTTGATTTAATTTAATTG
Found at i:730519 original size:5 final size:5
Alignment explanation
Indices: 730472--730535 Score: 62
Period size: 5 Copynumber: 13.2 Consensus size: 5
730462 GATAATTTTA
* * * *
730472 AATAT AATAA AAAAT AATAT -ATTT AATA- AATAT AAAAAT AATAT AATA-
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
730520 AATAT AATAT AATAT A
1 AATAT AATAT AATAT A
730536 TTTAAATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
4 11 0.23
5 32 0.68
6 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:730533 original size:34 final size:34
Alignment explanation
Indices: 730470--730552 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 34
730460 TTGATAATTT
*
730470 TAAATATAATAAAAAATAATATATTTAATAAATA
1 TAAATATAATAAAAAATAATATATATAATAAATA
* * *
730504 TAAAAATAATATAATAAAT-ATA-ATATAATATATT
1 TAAATATAATA-AA-AAATAATATATATAATAAATA
*
730538 TAAATATAATTAAAA
1 TAAATATAATAAAAA
730553 TAACCTGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
32 2 0.05
33 2 0.05
34 28 0.68
35 5 0.12
36 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (34 bp):
TAAATATAATAAAAAATAATATATATAATAAATA
Found at i:730543 original size:10 final size:10
Alignment explanation
Indices: 730469--730555 Score: 58
Period size: 10 Copynumber: 9.0 Consensus size: 10
730459 TTTGATAATT
730469 TTAAATATAA
1 TTAAATATAA
* *
730479 TAAAAAATAA
1 TTAAATATAA
* *
730489 -TATATTTAA
1 TTAAATATAA
730498 -TAAATATAA
1 TTAAATATAA
**
730507 AAATAATATAA
1 TTA-AATATAA
730518 -TAAATATAA
1 TTAAATATAA
*
730527 -TATAATATAT
1 TTA-AATATAA
730537 TTAAATATAA
1 TTAAATATAA
730547 TTAAA-ATAA
1 TTAAATATAA
730556 CCTGTTTAAC
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
9 25 0.41
10 27 0.44
11 9 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAATATAA
Found at i:730543 original size:24 final size:22
Alignment explanation
Indices: 730483--730540 Score: 84
Period size: 20 Copynumber: 2.7 Consensus size: 22
730473 ATATAATAAA
730483 AAATAATATATTTAATAAATAT
1 AAATAATATATTTAATAAATAT
*
730505 AAA-AATA-ATATAATAAATAT
1 AAATAATATATTTAATAAATAT
730525 AATATAATATATTTAA
1 AA-ATAATATATTTAA
730541 ATATAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 14 0.45
21 5 0.16
22 7 0.23
23 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATAATATATTTAATAAATAT
Found at i:730547 original size:20 final size:19
Alignment explanation
Indices: 730472--730547 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
730462 GATAATTTTA
*
730472 AATATAATAAAAAATAATAT
1 AATATAAT-AAATATAATAT
* *
730492 -ATTTAATAAATATAAAAAT
1 AATATAATAAATAT-AATAT
730511 AATATAATAAATATAATAT
1 AATATAATAAATATAATAT
*
730530 AATATATTTAAATATAAT
1 AATATA-ATAAATATAAT
730548 TAAAATAACC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.11
19 20 0.43
20 22 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATAATAAATATAATAT
Found at i:730555 original size:24 final size:25
Alignment explanation
Indices: 730468--730555 Score: 93
Period size: 24 Copynumber: 3.8 Consensus size: 25
730458 TTTTGATAAT
*
730468 TTTAAATATAATAAAAAATAATATA
1 TTTAAATATAATATAAAATAATATA
730493 TTT-AATA-AATAT-AAA-AATA-A
1 TTTAAATATAATATAAAATAATATA
* *
730513 TAT-AATA-AATATAATATAATATA
1 TTTAAATATAATATAAAATAATATA
730536 TTTAAATATAAT-TAAAATAA
1 TTTAAATATAATATAAAATAA
730556 CCTGTTTAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
20 12 0.23
21 6 0.11
22 7 0.13
23 7 0.13
24 15 0.28
25 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TTTAAATATAATATAAAATAATATA
Found at i:730594 original size:19 final size:18
Alignment explanation
Indices: 730571--730618 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
730561 TTAACCTATA
730571 TATATTTATTTAA-AATT
1 TATATTTATTTAATAATT
*
730588 T-TAATATATTTAATAATT
1 TAT-ATTTATTTAATAATT
730606 TATATTATATTTA
1 TATATT-TATTTA
730619 CATTTACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.04
17 10 0.40
18 7 0.28
19 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTTATTTAATAATT
Found at i:730599 original size:17 final size:19
Alignment explanation
Indices: 730577--730618 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
730567 TATATATATT
730577 TATTTAA-AATTT-TAATA
1 TATTTAATAATTTATAATA
*
730594 TATTTAATAATTTATATTA
1 TATTTAATAATTTATAATA
730613 TATTTA
1 TATTTA
730619 CATTTACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 5 0.23
19 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTAATAATTTATAATA
Found at i:730765 original size:58 final size:58
Alignment explanation
Indices: 730698--730813 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
730688 AATGAGAAAG
** * *
730698 CTAAAATGGAAGACTTAAATGCAATGGTTTGTGCCGACGGGTGATCAGAGGCAAAGTT
1 CTAAAATGGAAGACTTAAATGCAATGGCGTGAGCCGACGGCTGATCAGAGGCAAAGTT
730756 CTAAAATGGAAGACTTAAATGCAATGGCGTGAGCCGACGGCTGATCAGAGGCAAAGTT
1 CTAAAATGGAAGACTTAAATGCAATGGCGTGAGCCGACGGCTGATCAGAGGCAAAGTT
730814 GTGATGGGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (58 bp):
CTAAAATGGAAGACTTAAATGCAATGGCGTGAGCCGACGGCTGATCAGAGGCAAAGTT
Found at i:738133 original size:24 final size:24
Alignment explanation
Indices: 738106--738180 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
738096 TCAAATTAAT
738106 TTTTTATATGAATAAAATTATAAA
1 TTTTTATATGAATAAAATTATAAA
* * *
738130 TTTTTTTATAAAT-AATTTAT-AA
1 TTTTTATATGAATAAAATTATAAA
* *
738152 TTTTTATACGGATAAAATTATAAA
1 TTTTTATATGAATAAAATTATAAA
738176 TTTTT
1 TTTTT
738181 TTTACAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 11 0.27
23 12 0.29
24 18 0.44
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTTTATATGAATAAAATTATAAA
Found at i:738149 original size:23 final size:24
Alignment explanation
Indices: 738116--738191 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 24
738106 TTTTTATATG
*
738116 AATAAAATTATAAATTTTTTTATA
1 AATAAAATTATAAATTTTTTTACA
* * *
738140 AAT-AATTTAT-AATTTTTATACG
1 AATAAAATTATAAATTTTTTTACA
*
738162 GATAAAATTATAAATTTTTTTTACA
1 AATAAAATTATAAA-TTTTTTTACA
738187 AATAA
1 AATAA
738192 TTAATAACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
22 11 0.28
23 12 0.30
24 5 0.12
25 12 0.30
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
AATAAAATTATAAATTTTTTTACA
Found at i:738159 original size:46 final size:47
Alignment explanation
Indices: 738099--738222 Score: 164
Period size: 47 Copynumber: 2.7 Consensus size: 47
738089 TAAAATATCA
* * *
738099 AATTAAT--TTTTTATATGAATAAAATTATAAA-TTTTTTTATAAAT
1 AATTAATAATTTTTATACGGATAAAATTATAAATTTTTTTTACAAAT
*
738143 AATTTATAATTTTTATACGGATAAAATTATAAATTTTTTTTACAAAT
1 AATTAATAATTTTTATACGGATAAAATTATAAATTTTTTTTACAAAT
* * *
738190 AATTAATAACTTTTGTACGGATAAAATCATAAA
1 AATTAATAATTTTTATACGGATAAAATTATAAA
738223 CCTTTAAACC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
44 6 0.09
46 22 0.32
47 41 0.59
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (47 bp):
AATTAATAATTTTTATACGGATAAAATTATAAATTTTTTTTACAAAT
Found at i:738193 original size:23 final size:22
Alignment explanation
Indices: 738121--738203 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 22
738111 ATATGAATAA
*
738121 AATTATAAATTTTTTTATAAAT
1 AATTATAAATTTTTTTACAAAT
*
738143 AATT-TATAATTTTTATACGGATAA-
1 AATTATA-AATTTTTTTAC--A-AAT
738167 AATTATAAATTTTTTTTACAAAT
1 AATTATAAA-TTTTTTTACAAAT
*
738190 AATTAATAACTTTT
1 AATT-ATAAATTTT
738204 GTACGGATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
21 2 0.04
22 15 0.31
23 9 0.18
24 11 0.22
25 12 0.24
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTATAAATTTTTTTACAAAT
Found at i:738573 original size:16 final size:15
Alignment explanation
Indices: 738537--738567 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
738527 TTTAACTATC
738537 TAAAATTTTTCTTTA
1 TAAAATTTTTCTTTA
738552 TAAAATTTTT-TTTA
1 TAAAATTTTTCTTTA
738566 TA
1 TA
738568 CCAAATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TAAAATTTTTCTTTA
Found at i:738762 original size:15 final size:15
Alignment explanation
Indices: 738742--738820 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
738732 AATTAAGAAA
738742 AAAATTTAAAATATT
1 AAAATTTAAAATATT
*
738757 AAAATTTAAATTA-T
1 AAAATTTAAAATATT
738771 -AAATTTATTAAATATT
1 AAAATTTA--AAATATT
*** *
738787 ATTTTTTAAATTATT
1 AAAATTTAAAATATT
*
738802 AAATTTTAAAATTATT
1 AAAATTTAAAA-TATT
738818 AAA
1 AAA
738821 TAATATATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
13 7 0.14
14 1 0.02
15 30 0.60
16 8 0.16
17 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTTAAAATATT
Found at i:738783 original size:16 final size:16
Alignment explanation
Indices: 738746--738821 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
738736 AAGAAAAAAA
* *
738746 TTTAAAATATTAAA-A
1 TTTAAATTATTAAATT
738761 TTTAAATTA-TAAATT
1 TTTAAATTATTAAATT
*
738776 TATTAAA-TATT-ATTT
1 T-TTAAATTATTAAATT
738791 TTTAAATTATTAAATT
1 TTTAAATTATTAAATT
*
738807 TTAAAATTATTAAAT
1 TTTAAATTATTAAAT
738822 AATATATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.18
15 19 0.37
16 23 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATTATTAAATT
Found at i:738804 original size:38 final size:38
Alignment explanation
Indices: 738762--738834 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
738752 ATATTAAAAT
* * *
738762 TTAAATTATAAATTTATTAAATATTATTTTTTAAATTA
1 TTAAATTATAAAATTATTAAATAATATATTTTAAATTA
*
738800 TTAAATTTTAAAATTATTAAATAATATATTTTAAA
1 TTAAATTATAAAATTATTAAATAATATATTTTAAA
738835 AATAATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TTAAATTATAAAATTATTAAATAATATATTTTAAATTA
Found at i:738805 original size:8 final size:8
Alignment explanation
Indices: 738747--738821 Score: 61
Period size: 8 Copynumber: 9.8 Consensus size: 8
738737 AGAAAAAAAT
*
738747 TTAAAATA
1 TTAAATTA
*
738755 TTAAAAT-
1 TTAAATTA
738762 TTAAATTA
1 TTAAATTA
738770 -TAAATTTA
1 TTAAA-TTA
738778 TTAAA-TA
1 TTAAATTA
* *
738785 TT-ATTTT
1 TTAAATTA
738792 TTAAATTA
1 TTAAATTA
738800 TTAAATT-
1 TTAAATTA
738807 TTAAAATTA
1 TT-AAATTA
738816 TTAAAT
1 TTAAAT
738822 AATATATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
6 1 0.02
7 19 0.35
8 29 0.53
9 6 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TTAAATTA
Found at i:740095 original size:15 final size:14
Alignment explanation
Indices: 740070--740099 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
740060 CCAAAGTTTC
740070 ATTAATTTTTATAT
1 ATTAATTTTTATAT
740084 ATTAATTTTT-TAT
1 ATTAATTTTTATAT
740097 ATT
1 ATT
740100 TTTAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTAATTTTTATAT
Found at i:741276 original size:2 final size:2
Alignment explanation
Indices: 741269--741303 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
741259 GCTTGATACA
741269 AT AT AT AT 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 AT AT AT AT A
741304 AACCATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:743298 original size:17 final size:16
Alignment explanation
Indices: 743272--743314 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
743262 TTTTTAATTC
*
743272 ATTATATTTTAAAGAAA
1 ATTATTTTTTAAA-AAA
*
743289 ATTATTTTTTTTAAAAA
1 ATTA-TTTTTTAAAAAA
743306 ATTATTTTT
1 ATTATTTTT
743315 CACCCACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 11 0.48
18 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTATTTTTTAAAAAA
Found at i:743744 original size:26 final size:23
Alignment explanation
Indices: 743714--743772 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 23
743704 GCCTGATTGA
*
743714 ATTATATAAATTATATTAATTTTAT
1 ATTATATAAATTAT-GTAATTTT-T
**
743739 ATTTATATATCTTATGTAATTTTT
1 A-TTATATAAATTATGTAATTTTT
743763 ATTATATAAA
1 ATTATATAAA
743773 GAATAAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 7 0.25
24 2 0.07
25 8 0.29
26 11 0.39
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTATATAAATTATGTAATTTTT
Found at i:743875 original size:18 final size:19
Alignment explanation
Indices: 743836--743875 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
743826 TTATATTTTA
* *
743836 AAATTTAATAAAAAATATT
1 AAATTTAATAAAAAAAACT
743855 AAATTTAA-AAAAAAAACT
1 AAATTTAATAAAAAAAACT
743873 AAA
1 AAA
743876 AATAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATTTAATAAAAAAAACT
Found at i:744500 original size:23 final size:22
Alignment explanation
Indices: 744400--744505 Score: 70
Period size: 23 Copynumber: 4.6 Consensus size: 22
744390 TTACATAAAT
* *
744400 AAAAATTATAAATTTTCATCACA
1 AAAAATTATAAATTTT-ATAATA
* * *
744423 AACAACTAATAACTTTTA-AATA
1 AA-AAATTATAAATTTTATAATA
* * *
744445 AATGAACTATAAATTTTTTAATA
1 AA-AAATTATAAATTTTATAATA
**
744468 AATATTTTATAAATTTTATACATA
1 AA-AAATTATAAATTTTATA-ATA
744492 AAAAATTATAAATT
1 AAAAATTATAAATT
744506 ATTACCTTAC
Statistics
Matches: 61, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
22 13 0.21
23 32 0.52
24 16 0.26
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.40
Consensus pattern (22 bp):
AAAAATTATAAATTTTATAATA
Found at i:744902 original size:18 final size:17
Alignment explanation
Indices: 744881--744922 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
744871 TTATGAATTT
744881 TAAAAA-AAAAATGATAAA
1 TAAAAATAAAAAT-A-AAA
744899 TAAAAATTAAAAATAAAA
1 TAAAAA-TAAAAATAAAA
744917 TAAAAA
1 TAAAAA
744923 GTTATTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.68
19 1 0.05
20 6 0.27
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (17 bp):
TAAAAATAAAAATAAAA
Found at i:745412 original size:20 final size:20
Alignment explanation
Indices: 745371--745414 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
745361 ATTATTAAAC
*
745371 ATAAATATATTTATATATTA
1 ATAAATATATTTATATAATA
*
745391 ATAAATTTATTTA-ATTAATA
1 ATAAATATATTTATA-TAATA
745411 ATAA
1 ATAA
745415 TACAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAATATATTTATATAATA
Found at i:745611 original size:15 final size:14
Alignment explanation
Indices: 745586--745615 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
745576 CCAAAGTTTC
745586 ATTAATTTTTATAT
1 ATTAATTTTTATAT
745600 ATTAATTTTT-TAT
1 ATTAATTTTTATAT
745613 ATT
1 ATT
745616 TTTAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTAATTTTTATAT
Found at i:745888 original size:26 final size:25
Alignment explanation
Indices: 745833--745894 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
745823 TTTTTTAAAA
745833 AAATTT-ATTTGATAAAATATAATTT
1 AAATTTAATTTGATAAAATATAA-TT
*
745858 TAATTTAATTTGATAAAAATATTAA-T
1 AAATTTAATTTGAT-AAAATA-TAATT
*
745884 AAATTAAATTT
1 AAATTTAATTT
745895 AAATTTGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 5 0.16
26 17 0.55
27 6 0.19
28 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (25 bp):
AAATTTAATTTGATAAAATATAATT
Found at i:745950 original size:15 final size:15
Alignment explanation
Indices: 745911--745952 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
745901 GATTTTAATC
*
745911 AAATAATT-AAATTC
1 AAATAATTAAAATTA
*
745925 GAATAATTTAAAATTA
1 AAATAA-TTAAAATTA
745941 AAATAATTAAAA
1 AAATAATTAAAA
745953 ATCAAATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AAATAATTAAAATTA
Found at i:745959 original size:15 final size:15
Alignment explanation
Indices: 745907--745959 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
745897 ATTTGATTTT
745907 AATCAAATAATT-AA
1 AATCAAATAATTAAA
* *
745921 ATTCGAATAATTTAAA
1 AATCAAATAA-TTAAA
* *
745937 ATTAAAATAATTAAA
1 AATCAAATAATTAAA
745952 AATCAAAT
1 AATCAAAT
745960 GACTAAACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 8 0.26
15 13 0.42
16 10 0.32
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (15 bp):
AATCAAATAATTAAA
Done.