Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 71 of 290
Found at i:23482405 original size:36 final size:36
Alignment explanation
Indices: 23482358--23482429 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
23482348 CTTTGGATAC
23482358 ATTTCTCGGTAGTTTCCAATCAACAACTATCGAAAT
1 ATTTCTCGGTAGTTTCCAATCAACAACTATCGAAAT
23482394 ATTTCTCGGTAGTTTCCAATCAACAACTATCGAAAT
1 ATTTCTCGGTAGTTTCCAATCAACAACTATCGAAAT
23482430 CTTACTCAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (36 bp):
ATTTCTCGGTAGTTTCCAATCAACAACTATCGAAAT
Found at i:23484776 original size:46 final size:45
Alignment explanation
Indices: 23484709--23484883 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 45
23484699 CGTAACCCGC
*
23484709 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCAT
* *
23484755 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGCAT
* * * * * *
23484801 ACATTTCA-CGAACTCAGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCAT
*
23484848 CCATAAGTAAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
23484884 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
45 3 0.03
46 66 0.63
47 32 0.30
48 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGCAT
Found at i:23484828 original size:93 final size:93
Alignment explanation
Indices: 23484717--23484888 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
23484707 GCCCATAAGT
* * * *
23484717 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
23484782 CGAGTTCGGATGCTTAGTTACATTTCAC
66 CGAGTTCGGATGCTTAGTTACATTTCAC
* *
23484810 GAACTCAGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
23484875 CGAGTTCGGATGCT
66 CGAGTTCGGATGCT
23484889 CAACCATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
CGAGTTCGGATGCTTAGTTACATTTCAC
Found at i:23487186 original size:25 final size:27
Alignment explanation
Indices: 23487149--23487207 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
23487139 CCTGAACCCT
*
23487149 TATGAGATGAAA-TGACTATTTTTCCC
1 TATGAGATGAAATTGACAATTTTTCCC
*
23487175 TATGTGAT-AAATTGACAATTTTTCCC
1 TATGAGATGAAATTGACAATTTTTCCC
23487201 TTATGAG
1 -TATGAG
23487208 GTAAAATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 3 0.11
26 20 0.71
27 5 0.18
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (27 bp):
TATGAGATGAAATTGACAATTTTTCCC
Found at i:23487205 original size:27 final size:27
Alignment explanation
Indices: 23487145--23487344 Score: 145
Period size: 27 Copynumber: 7.4 Consensus size: 27
23487135 CGTACCTGAA
* * *
23487145 CCCTTATGAGATGAAATGACTATTTTT
1 CCCTTATGTGATAAAATGACTATTTTG
* * *
23487172 CCC-TATGTGATAAATTGACAATTTTT
1 CCCTTATGTGATAAAATGACTATTTTG
* * *
23487198 CCCTTATGAGGTAAAATGACGT-GTTTG
1 CCCTTATGTGATAAAATGAC-TATTTTG
* **
23487225 CGCTTATGTGGCAAAATGACTATTTTG
1 CCCTTATGTGATAAAATGACTATTTTG
* *
23487252 CCCTTATGTGATAAAATAACGATTTTG
1 CCCTTATGTGATAAAATGACTATTTTG
* * **
23487279 CCCTTATGAGGTAAAATGACGGTCTTT-
1 CCCTTATGTGATAAAATGACTAT-TTTG
* * * * *
23487306 CCTTTATGAGGTAAAATGAATGTTTTG
1 CCCTTATGTGATAAAATGACTATTTTG
*
23487333 CCCCTATGTGAT
1 CCCTTATGTGAT
23487345 GTATATGTAT
Statistics
Matches: 138, Mismatches: 30, Indels: 10
0.78 0.17 0.06
Matches are distributed among these distances:
26 26 0.19
27 109 0.79
28 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (27 bp):
CCCTTATGTGATAAAATGACTATTTTG
Found at i:23487283 original size:81 final size:80
Alignment explanation
Indices: 23487158--23487344 Score: 234
Period size: 81 Copynumber: 2.3 Consensus size: 80
23487148 TTATGAGATG
* * * *
23487158 AAATGACTATTTTTCCCTATGTGATAAATTGACAATTTTTCCCTTATGAGGTAAAATGACGTGT-
1 AAATGACTATTTTGCCCTATGTGATAAAATAACAATTTTGCCCTTATGAGGTAAAATGACG-GTC
*
23487222 TTGCGC-TTATGTGGCA
65 TTGC-CTTTATGAGGCA
*
23487238 AAATGACTATTTTGCCCTTATGTGATAAAATAACGATTTTGCCCTTATGAGGTAAAATGACGGTC
1 AAATGACTATTTTGCCC-TATGTGATAAAATAACAATTTTGCCCTTATGAGGTAAAATGACGGTC
* *
23487303 TTTCCTTTATGAGGTA
65 TTGCCTTTATGAGGCA
* *
23487319 AAATGAATGTTTTGCCCCTATGTGAT
1 AAATGACTATTTTG-CCCTATGTGAT
23487345 GTATATGTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
80 19 0.20
81 71 0.76
82 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (80 bp):
AAATGACTATTTTGCCCTATGTGATAAAATAACAATTTTGCCCTTATGAGGTAAAATGACGGTCT
TGCCTTTATGAGGCA
Found at i:23492251 original size:14 final size:13
Alignment explanation
Indices: 23492232--23492264 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
23492222 ATAACGTGAT
23492232 TTACCATAATCTCA
1 TTACCATAAT-TCA
23492246 TTACCATAATTCA
1 TTACCATAATTCA
23492259 TT-CCAT
1 TTACCAT
23492265 CACAAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 5 0.26
14 10 0.53
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (13 bp):
TTACCATAATTCA
Found at i:23498563 original size:33 final size:33
Alignment explanation
Indices: 23498526--23498598 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
23498516 ATTCGATCTC
23498526 ATCTATAGTAACAATATATAACGGATCCGACCG
1 ATCTATAGTAACAATATATAACGGATCCGACCG
23498559 ATCTATAGTAACAATATATAACGGATCCGACCG
1 ATCTATAGTAACAATATATAACGGATCCGACCG
23498592 ATACTAT
1 AT-CTAT
23498599 CTTAGTATCG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 35 0.90
34 4 0.10
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (33 bp):
ATCTATAGTAACAATATATAACGGATCCGACCG
Found at i:23508253 original size:20 final size:20
Alignment explanation
Indices: 23508230--23508267 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23508220 GTTTGAATTG
*
23508230 TGTATTTTATAATGTTTGAA
1 TGTATTTTAAAATGTTTGAA
23508250 TGTATTTTAAAATGTTTG
1 TGTATTTTAAAATGTTTG
23508268 CAAATTGGTA
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:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (20 bp):
TGTATTTTAAAATGTTTGAA
Found at i:23510868 original size:14 final size:14
Alignment explanation
Indices: 23510846--23510877 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
23510836 TGTTATTTTT
*
23510846 TTTTTAAAAATTAA
1 TTTTAAAAAATTAA
23510860 TTTTAAAAAATTAA
1 TTTTAAAAAATTAA
23510874 TTTT
1 TTTT
23510878 TTATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAAAAAATTAA
Found at i:23510888 original size:11 final size:11
Alignment explanation
Indices: 23510872--23510915 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
23510862 TTAAAAAATT
23510872 AATTTTTTATA
1 AATTTTTTATA
23510883 AATTTTTCTTATA
1 AA-TTTT-TTATA
*
23510896 ATTTTTTTATA
1 AATTTTTTATA
23510907 AATTTTTTA
1 AATTTTTTA
23510916 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 15 0.52
12 8 0.28
13 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
AATTTTTTATA
Found at i:23510896 original size:13 final size:12
Alignment explanation
Indices: 23510874--23510914 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
23510864 AAAAAATTAA
23510874 TTTTTTATAAAT
1 TTTTTTATAAAT
23510886 TTTTCTTAT-AAT
1 TTTT-TTATAAAT
23510898 TTTTTTATAAAT
1 TTTTTTATAAAT
23510910 TTTTT
1 TTTTT
23510915 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.15
12 19 0.70
13 4 0.15
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTATAAAT
Found at i:23510942 original size:10 final size:10
Alignment explanation
Indices: 23510929--23510955 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
23510919 TTTAAAAGAG
23510929 TTTAATTGAT
1 TTTAATTGAT
23510939 TTTAATTGAT
1 TTTAATTGAT
23510949 TTTAATT
1 TTTAATT
23510956 TGTTACTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (10 bp):
TTTAATTGAT
Found at i:23514388 original size:6 final size:6
Alignment explanation
Indices: 23514377--23514411 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
23514367 TTATAGTGTA
23514377 TTATTC TTATTC TTATTC TTATTC TTATTC TTATT
1 TTATTC TTATTC TTATTC TTATTC TTATTC TTATT
23514412 ATTAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATTC
Found at i:23515829 original size:21 final size:22
Alignment explanation
Indices: 23515790--23515838 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
23515780 AGGCACTTTA
*
23515790 TGTGTCGTATTTCAAGCACGTCG
1 TGTGTCGTA-TTCAAGCACCTCG
*
23515813 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAAGCACCTCG
23515834 TGTGT
1 TGTGT
23515839 TATTTCAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.62
23 9 0.38
ACGTcount: A:0.14, C:0.22, G:0.29, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAAGCACCTCG
Found at i:23515846 original size:21 final size:21
Alignment explanation
Indices: 23515797--23515850 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
23515787 TTATGTGTCG
* *
23515797 TATTTCAAGCACGTCGTGTGT
1 TATTTCAGGCACCTCGTGTGT
** *
23515818 CGTATCAGGCACCTCGTGTGT
1 TATTTCAGGCACCTCGTGTGT
23515839 TATTTCAGGCAC
1 TATTTCAGGCAC
23515851 TTATGTGTCG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (21 bp):
TATTTCAGGCACCTCGTGTGT
Found at i:23517142 original size:63 final size:63
Alignment explanation
Indices: 23517043--23517168 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
23517033 ATAAGCTTAA
*
23517043 TTACATTATCAATTCACGAATTAGAGTGATTATTCATGACATAGGTAAATTCACCTTTAGAAT
1 TTACATTATCAATTCACGAATTAGAGTGATTATTCATGACATAGGTAAATCCACCTTTAGAAT
23517106 TTACATTATCAATTCACGAATTAGAGTGATTATTCATGACATAGGTAAATCCACCTTTAGAAT
1 TTACATTATCAATTCACGAATTAGAGTGATTATTCATGACATAGGTAAATCCACCTTTAGAAT
23517169 AAGTAAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (63 bp):
TTACATTATCAATTCACGAATTAGAGTGATTATTCATGACATAGGTAAATCCACCTTTAGAAT
Found at i:23518003 original size:34 final size:35
Alignment explanation
Indices: 23517884--23518010 Score: 141
Period size: 35 Copynumber: 3.6 Consensus size: 35
23517874 AGTACATCAA
* * * * *
23517884 TAATCCAACCAAAACACAGCAAATTCTCATAAAAGC
1 TAATCCATCCGAAACACA-CCAATGCTCATAAGAGC
*
23517920 TAATCCATCC-AGAGCACACCAATGCTCATAAGAGC
1 TAATCCATCCGA-AACACACCAATGCTCATAAGAGC
* *
23517955 TAATCCATCTGAAACACACTAATGCTCATAAGAG-
1 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
*
23517989 TTATCCATCCGAAACACACCAA
1 TAATCCATCCGAAACACACCAA
23518011 AACAGAGAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
34 19 0.24
35 44 0.56
36 15 0.19
ACGTcount: A:0.43, C:0.29, G:0.09, T:0.19
Consensus pattern (35 bp):
TAATCCATCCGAAACACACCAATGCTCATAAGAGC
Found at i:23519449 original size:30 final size:29
Alignment explanation
Indices: 23519415--23519503 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 29
23519405 TTTTTAAAGT
*
23519415 CACCCATATCCCTACTAACTCCCATTAAAC
1 CACCCATATCCC-ACTAACTCCCACTAAAC
23519445 CACCCATATCCCCACTAACTCCCACTAAAC
1 CACCCATAT-CCCACTAACTCCCACTAAAC
* *
23519475 CACTCATATTCCCGCTAACTCCCACTAAA
1 CACCCATA-TCCCACTAACTCCCACTAAA
23519504 TCTGATAGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
30 50 0.93
31 4 0.07
ACGTcount: A:0.33, C:0.45, G:0.01, T:0.21
Consensus pattern (29 bp):
CACCCATATCCCACTAACTCCCACTAAAC
Found at i:23521723 original size:11 final size:11
Alignment explanation
Indices: 23521707--23521731 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23521697 CTAGCTATAC
23521707 ATGCCATATTT
1 ATGCCATATTT
23521718 ATGCCATATTT
1 ATGCCATATTT
23521729 ATG
1 ATG
23521732 AATTGCGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (11 bp):
ATGCCATATTT
Found at i:23529321 original size:30 final size:28
Alignment explanation
Indices: 23529268--23529326 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
23529258 AAGTTGAGAG
23529268 AAAAAAAAAAGAAGAAGGTTTTTTTTTA
1 AAAAAAAAAAGAAGAAGGTTTTTTTTTA
* *
23529296 AAAAACAAAGAAGAGGAATGTTTTTTTTTA
1 AAAAA-AAA-AAGAAGAAGGTTTTTTTTTA
23529326 A
1 A
23529327 TTTTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.19
29 3 0.11
30 19 0.70
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (28 bp):
AAAAAAAAAAGAAGAAGGTTTTTTTTTA
Found at i:23533051 original size:8 final size:8
Alignment explanation
Indices: 23533034--23533068 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
23533024 TTTTGGTTCA
*
23533034 TTTTAGTT
1 TTTTATTT
23533042 TTTTATTT
1 TTTTATTT
23533050 TTTTATTT
1 TTTTATTT
*
23533058 CTTTATTT
1 TTTTATTT
23533066 TTT
1 TTT
23533069 AATGTTGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:23534631 original size:57 final size:57
Alignment explanation
Indices: 23534519--23534629 Score: 179
Period size: 57 Copynumber: 2.0 Consensus size: 57
23534509 GATTATCCAA
* * * *
23534519 AGGCAAAGTTGAGCAATTAATCCACCGACGTATTGATTTTCGGAGGACCAATTTTAG
1 AGGCAAAATTCAGCAATTAATCCACCGACATATAGATTTTCGGAGGACCAATTTTAG
23534576 AGGCAAAATTCAGCAATTAATCCACCGACATATAGATTTT-GGAGGACCAATTTT
1 AGGCAAAATTCAGCAATTAATCCACCGACATATAGATTTTCGGAGGACCAATTTT
23534630 TAATTTATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 14 0.28
57 36 0.72
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (57 bp):
AGGCAAAATTCAGCAATTAATCCACCGACATATAGATTTTCGGAGGACCAATTTTAG
Found at i:23536471 original size:25 final size:25
Alignment explanation
Indices: 23536443--23536498 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
23536433 GGAAGAAGAA
23536443 AATTATGATTTCTGCTTCAAGGTTC
1 AATTATGATTTCTGCTTCAAGGTTC
23536468 AATTATGATTTCTGCTTCAAGGTTC
1 AATTATGATTTCTGCTTCAAGGTTC
*
23536493 ACTTAT
1 AATTAT
23536499 ACAAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (25 bp):
AATTATGATTTCTGCTTCAAGGTTC
Found at i:23541384 original size:43 final size:43
Alignment explanation
Indices: 23541333--23541565 Score: 189
Period size: 43 Copynumber: 5.5 Consensus size: 43
23541323 CCTAATTTCA
* *
23541333 TCACCGGCAAT-CAGCCTGCTAGACCTTTAAGTCCGATATCATT
1 TCACCGGCATTAC-GCCTGCTAGACCTTTAAGCCCGATATCATT
* **
23541376 TCACCGGCATTACGCCTGCTAG--GTTCGGAGCCCGATA--ATAT
1 TCACCGGCATTACGCCTGCTAGACCTT-TAAGCCCGATATCAT-T
* * *
23541417 TCACCAGC-TTAAAGCTTGCTAGACCTTTAAGCCCGATATCATT
1 TCACCGGCATT-ACGCCTGCTAGACCTTTAAGCCCGATATCATT
* * **
23541460 TCATCGGCATTACGCCTGCTAG-GCTCGAAGCCCGATA--ATAT
1 TCACCGGCATTACGCCTGCTAGACCTTTAAGCCCGATATCAT-T
* * * * *
23541501 TCACCAGC-TTAAAGCTTGCTAGACCTTTAAGTCTGATATCATT
1 TCACCGGCATT-ACGCCTGCTAGACCTTTAAGCCCGATATCATT
23541544 TCACCGGCATTACGCCTGCTAG
1 TCACCGGCATTACGCCTGCTAG
23541566 GCTCAAAGCC
Statistics
Matches: 145, Mismatches: 30, Indels: 30
0.71 0.15 0.15
Matches are distributed among these distances:
40 8 0.06
41 35 0.24
42 39 0.27
43 54 0.37
44 9 0.06
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (43 bp):
TCACCGGCATTACGCCTGCTAGACCTTTAAGCCCGATATCATT
Found at i:23541437 original size:41 final size:41
Alignment explanation
Indices: 23541392--23541522 Score: 124
Period size: 41 Copynumber: 3.1 Consensus size: 41
23541382 GCATTACGCC
*
23541392 TGCTAGGTTCGGAGCCCGATAATATTCACCAGCTTAAAGCT
1 TGCTAGGTTCGAAGCCCGATAATATTCACCAGCTTAAAGCT
* * * * * *
23541433 TGCTAGACCTT-TAAGCCCGAT-ATCATTTCATCGGCATT-ACGCC
1 TGCTAG--GTTCGAAGCCCGATAAT-A-TTCACCAGC-TTAAAGCT
*
23541476 TGCTAGGCTCGAAGCCCGATAATATTCACCAGCTTAAAGCT
1 TGCTAGGTTCGAAGCCCGATAATATTCACCAGCTTAAAGCT
23541517 TGCTAG
1 TGCTAG
23541523 ACCTTTAAGT
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
40 2 0.03
41 25 0.37
42 19 0.28
43 20 0.29
44 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (41 bp):
TGCTAGGTTCGAAGCCCGATAATATTCACCAGCTTAAAGCT
Found at i:23541450 original size:42 final size:42
Alignment explanation
Indices: 23541404--23541531 Score: 145
Period size: 42 Copynumber: 3.0 Consensus size: 42
23541394 CTAGGTTCGG
23541404 AGCCCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTA
1 AGCCCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTA
* * * * * **
23541446 AGCCCGAT-ATCATTTCATCGGCATT-ACGCCTGCTAG-GCTCGA
1 AGCCCGATAAT-A-TTCACCAGC-TTAAAGCTTGCTAGACCTTTA
23541488 AGCCCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTA
1 AGCCCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTA
23541530 AG
1 AG
23541532 TCTGATATCA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
40 2 0.03
41 18 0.27
42 26 0.39
43 18 0.27
44 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (42 bp):
AGCCCGATAATATTCACCAGCTTAAAGCTTGCTAGACCTTTA
Found at i:23541589 original size:84 final size:84
Alignment explanation
Indices: 23541349--23541576 Score: 402
Period size: 84 Copynumber: 2.7 Consensus size: 84
23541339 GCAATCAGCC
* *
23541349 TGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTGCTAGGTTCGGAGCCCGATAA
1 TGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTGCTAGGCTCGAAGCCCGATAA
23541414 TATTCACCAGCTTAAAGCT
66 TATTCACCAGCTTAAAGCT
* *
23541433 TGCTAGACCTTTAAGCCCGATATCATTTCATCGGCATTACGCCTGCTAGGCTCGAAGCCCGATAA
1 TGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTGCTAGGCTCGAAGCCCGATAA
23541498 TATTCACCAGCTTAAAGCT
66 TATTCACCAGCTTAAAGCT
* *
23541517 TGCTAGACCTTTAAGTCTGATATCATTTCACCGGCATTACGCCTGCTAGGCTCAAAGCCC
1 TGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTGCTAGGCTCGAAGCCC
23541577 AAAATTTATC
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 136 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (84 bp):
TGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTGCTAGGCTCGAAGCCCGATAA
TATTCACCAGCTTAAAGCT
Found at i:23545945 original size:8 final size:8
Alignment explanation
Indices: 23545932--23545963 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
23545922 ATCCCACGAG
23545932 CGCTCGCA
1 CGCTCGCA
23545940 CGCTCGCA
1 CGCTCGCA
23545948 CGCTCGCA
1 CGCTCGCA
23545956 CGCTCGCA
1 CGCTCGCA
23545964 AGTTCTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.50, G:0.25, T:0.12
Consensus pattern (8 bp):
CGCTCGCA
Found at i:23549893 original size:60 final size:59
Alignment explanation
Indices: 23549780--23549909 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 59
23549770 AACTGGCCCT
* * *
23549780 TAGCCCATATCACTATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATATTGGGCC
1 TAGCCCATATAACTATTAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATATTGGGCA
* * *
23549840 TAGCCCATATAAGTATTAATCTGGGTCGTAGCCCTATTACA-AGTC-GAGATATATTGGGCA
1 TAGCCCATATAACTATTAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TATATTGGGCA
*
23549900 TTGCCCATAT
1 TAGCCCATAT
23549910 TAACACAGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 4 0.07
60 51 0.85
61 5 0.08
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (59 bp):
TAGCCCATATAACTATTAATCTGGGCCATAGCCCATTACAGATCAGAGTATATTGGGCA
Found at i:23553983 original size:26 final size:28
Alignment explanation
Indices: 23553939--23553996 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
23553929 GCGCGACTCT
* *
23553939 TTTTTTTATATTAAAATATT-TTTTTTG
1 TTTTTTTATAATAAAATATTATTTTTTA
*
23553966 TTTTTTTA-AATAAGATATTATTTTTTA
1 TTTTTTTATAATAAAATATTATTTTTTA
23553993 TTTT
1 TTTT
23553997 CGGATCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTTTATAATAAAATATTATTTTTTA
Found at i:23554078 original size:27 final size:27
Alignment explanation
Indices: 23554038--23554110 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
23554028 TACAGATTGC
* * *
23554038 GCCTATCTCTGAGGCGCAACTAGTTGA-
1 GCCTATCTCAGAGGCGCAACTA-ATCAT
* *
23554065 GCCTTTCTCAGAGGCGCGACTAATCAT
1 GCCTATCTCAGAGGCGCAACTAATCAT
23554092 GCCTATCTCAGAGGCGCAA
1 GCCTATCTCAGAGGCGCAA
23554111 ATGGTGGAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCAACTAATCAT
Found at i:23554473 original size:60 final size:62
Alignment explanation
Indices: 23554389--23554521 Score: 200
Period size: 60 Copynumber: 2.2 Consensus size: 62
23554379 ATACTAAACT
* * * *
23554389 AAACAC-AACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA-C
1 AAACACAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTATA
23554449 AAACACAAAAAATTT-TAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTATA
1 AAACACAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTATA
*
23554510 AAAAACAAAAAA
1 AAACACAAAAAA
23554522 ATTACATTCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 48 0.73
61 18 0.27
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (62 bp):
AAACACAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTATA
Found at i:23558395 original size:22 final size:22
Alignment explanation
Indices: 23558370--23558454 Score: 57
Period size: 22 Copynumber: 3.7 Consensus size: 22
23558360 AAACCCTAAT
23558370 TTCTCTTTTTTATTTTCTTTTA
1 TTCTCTTTTTTATTTTCTTTTA
* * *
23558392 TTCTTTCTTTCTTTCTATTTCGTTTC
1 TTC--TCTTT-TTTAT-TTTCTTTTA
* *
23558418 TTCTCTATTTT-TTTTCTTGTTT
1 TTCTCTTTTTTATTTTCTT-TTA
23558440 TTCT-TTATTTTATTT
1 TTCTCTT-TTTTATTT
23558455 ATTCTCTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
21 6 0.12
22 14 0.29
23 6 0.12
24 9 0.18
25 4 0.08
26 10 0.20
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.75
Consensus pattern (22 bp):
TTCTCTTTTTTATTTTCTTTTA
Found at i:23558404 original size:16 final size:16
Alignment explanation
Indices: 23558383--23558480 Score: 53
Period size: 16 Copynumber: 6.0 Consensus size: 16
23558373 TCTTTTTTAT
23558383 TTTCTTTTATTCTTTC
1 TTTCTTTTATTCTTTC
23558399 TTTCTTTCTATTTCGTTTC
1 TTTCTTT-TA-TTC-TTTC
*
23558418 -TTC-TCTATT-TTT-
1 TTTCTTTTATTCTTTC
* *
23558430 TTTCTTGTTTTTCTTTA
1 TTTCTT-TTATTCTTTC
* *
23558447 TTT-TATTTATTCTCTA
1 TTTCT-TTTATTCTTTC
23558463 TTTCATTTTATTTCTTTC
1 TTTC-TTTTA-TTCTTTC
23558481 ATTTACTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
13 6 0.10
14 1 0.02
15 5 0.08
16 24 0.38
17 11 0.17
18 12 0.19
19 4 0.06
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTCTTTTATTCTTTC
Found at i:23558619 original size:3 final size:3
Alignment explanation
Indices: 23558611--23558641 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
23558601 CAATTAATTG
23558611 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
23558642 GTAAATATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:23558667 original size:26 final size:26
Alignment explanation
Indices: 23558638--23558699 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
23558628 AATAATAATA
23558638 ATAAGTAAATATCTTTTACTTAATTT
1 ATAAGTAAATATCTTTTACTTAATTT
*
23558664 ATAAGTAAGTATCTTTTACTTAATTT
1 ATAAGTAAATATCTTTTACTTAATTT
23558690 ATAAGTAAAT
1 ATAAGTAAAT
23558700 TTATATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (26 bp):
ATAAGTAAATATCTTTTACTTAATTT
Found at i:23559284 original size:26 final size:26
Alignment explanation
Indices: 23559255--23559305 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
23559245 AAATTACAAG
*
23559255 TTATTAGCAATTAATATTAATTAATA
1 TTATTAGCAATTAATATTAAGTAATA
* **
23559281 TTATTTGTTATTAATATTAAGTAAT
1 TTATTAGCAATTAATATTAAGTAAT
23559306 TAATAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (26 bp):
TTATTAGCAATTAATATTAAGTAATA
Found at i:23559519 original size:41 final size:41
Alignment explanation
Indices: 23559474--23559556 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
23559464 TCAAAAAAAG
*
23559474 AAAAGAGAGAAAAGAATGATAGGTGAACTAAGCGGGTTCAC
1 AAAAGAGAGAAAAGAATGATAGGTGAACTAAGCAGGTTCAC
23559515 AAAAGAGAGAAAAGAATGATAGGTGAACTAAGCAGGTTCAC
1 AAAAGAGAGAAAAGAATGATAGGTGAACTAAGCAGGTTCAC
23559556 A
1 A
23559557 CTTAGGTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.48, C:0.10, G:0.28, T:0.14
Consensus pattern (41 bp):
AAAAGAGAGAAAAGAATGATAGGTGAACTAAGCAGGTTCAC
Found at i:23560356 original size:21 final size:20
Alignment explanation
Indices: 23560332--23560371 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
23560322 ATAATTATTT
*
23560332 TAATTTTTATGTAAAAATAAG
1 TAATTTATAT-TAAAAATAAG
*
23560353 TAATTTATATTCAAAATAA
1 TAATTTATATTAAAAATAA
23560372 TGAAGATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
TAATTTATATTAAAAATAAG
Found at i:23567859 original size:16 final size:16
Alignment explanation
Indices: 23567840--23567872 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
23567830 TTATAGAACC
*
23567840 ATTTTTTTAAATAATA
1 ATTTTATTAAATAATA
23567856 ATTTTATTAAATAATA
1 ATTTTATTAAATAATA
23567872 A
1 A
23567873 ATAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTATTAAATAATA
Found at i:23567877 original size:23 final size:21
Alignment explanation
Indices: 23567847--23567893 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
23567837 ACCATTTTTT
*
23567847 TAAATAATAATTTTATTAAATAA
1 TAAATAAT-ATTTT-TTAAACAA
23567870 TAAATAATATTTTTTAAACAA
1 TAAATAATATTTTTTAAACAA
23567891 TAA
1 TAA
23567894 CTGTTAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.43
22 5 0.22
23 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATAATATTTTTTAAACAA
Found at i:23568315 original size:22 final size:22
Alignment explanation
Indices: 23568268--23568310 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
23568258 ATTACAATTT
* *
23568268 ATTTTTAATTAAATTTTTTAAA
1 ATTTTTAATCAAATTATTTAAA
23568290 ATTTTTAATCAAATCTATTTA
1 ATTTTTAATCAAAT-TATTTA
23568311 GATTTAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTAATCAAATTATTTAAA
Found at i:23570399 original size:28 final size:28
Alignment explanation
Indices: 23570342--23570407 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
23570332 TTTTACCTCA
**
23570342 TATTTATATTTTAAGTTAATTTAATTAT
1 TATTTATATTTTAAGTTAATTTAACCAT
* *
23570370 TATTTATTTTTTAA-TTAAATTTGACCAT
1 TATTTATATTTTAAGTT-AATTTAACCAT
23570398 TAATTT-TATT
1 T-ATTTATATT
23570408 ATATATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 2 0.06
28 25 0.81
29 4 0.13
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
TATTTATATTTTAAGTTAATTTAACCAT
Found at i:23576511 original size:22 final size:21
Alignment explanation
Indices: 23576486--23576535 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
23576476 TGATTAATTA
23576486 ATTTTTTAAAAATTTAAAAAAT
1 ATTTTTTAAAAATTT-AAAAAT
* * *
23576508 ATTTTCTTGATAATTTTAAAAT
1 ATTTT-TTAAAAATTTAAAAAT
23576530 ATTTTT
1 ATTTTT
23576536 ACTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTTTTAAAAATTTAAAAAT
Found at i:23583926 original size:10 final size:10
Alignment explanation
Indices: 23583911--23583936 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23583901 TCAATGTTAG
23583911 ATTTTTTATA
1 ATTTTTTATA
23583921 ATTTTTTATA
1 ATTTTTTATA
23583931 ATTTTT
1 ATTTTT
23583937 AAAAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:23583935 original size:9 final size:9
Alignment explanation
Indices: 23583913--23583979 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
23583903 AATGTTAGAT
23583913 TTTTTATAA
1 TTTTTATAA
23583922 TTTTTTATAA
1 -TTTTTATAA
23583932 TTTTTA-AA
1 TTTTTATAA
**
23583940 -AATTATAA
1 TTTTTATAA
* **
23583948 ATTTTGGAA
1 TTTTTATAA
23583957 TTTTTATAA
1 TTTTTATAA
23583966 TTTTT-TAAA
1 TTTTTAT-AA
23583975 TTTTT
1 TTTTT
23583980 GTTGAGAGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
7 3 0.07
8 5 0.11
9 28 0.62
10 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:23584302 original size:55 final size:55
Alignment explanation
Indices: 23584218--23584329 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
23584208 AATCTAATTA
23584218 TGCTTATTAATACGATGTGTGTTGTATAGAGAGATGTTGATTTGCCTAAGTGTGT
1 TGCTTATTAATACGATGTGTGTTGTATAGAGAGATGTTGATTTGCCTAAGTGTGT
*
23584273 TGCTTCTTAATACGATGTGTGTTGTATAGAGAGATGTTGATTTGCCTAAGTGTGT
1 TGCTTATTAATACGATGTGTGTTGTATAGAGAGATGTTGATTTGCCTAAGTGTGT
23584328 TG
1 TG
23584330 TATAGAGAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.22, C:0.08, G:0.28, T:0.42
Consensus pattern (55 bp):
TGCTTATTAATACGATGTGTGTTGTATAGAGAGATGTTGATTTGCCTAAGTGTGT
Found at i:23584326 original size:33 final size:33
Alignment explanation
Indices: 23584289--23584357 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
23584279 TTAATACGAT
23584289 GTGTGTTGTATAGAGAGATGTTGATTTGCCTAA
1 GTGTGTTGTATAGAGAGATGTTGATTTGCCTAA
23584322 GTGTGTTGTATAGAGAGATGTTGATTTGCCTAA
1 GTGTGTTGTATAGAGAGATGTTGATTTGCCTAA
23584355 GTG
1 GTG
23584358 GTCCACTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.23, C:0.06, G:0.32, T:0.39
Consensus pattern (33 bp):
GTGTGTTGTATAGAGAGATGTTGATTTGCCTAA
Found at i:23589226 original size:3 final size:3
Alignment explanation
Indices: 23589220--23589245 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23589210 CTACTACTAC
23589220 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
23589246 TCAACATCCA
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:23593493 original size:23 final size:22
Alignment explanation
Indices: 23593381--23593494 Score: 65
Period size: 23 Copynumber: 5.0 Consensus size: 22
23593371 ATATATATGT
*
23593381 ATATATA-ATAATAT-TTAAGA
1 ATATATACATAATATATTAAAA
*
23593401 ATATATACATAAGATGA-TATAAA
1 ATATATACATAATAT-ATTA-AAA
* * *
23593424 ATACATACATGGAATAGTATGAGAA
1 ATATATACAT--AATA-TATTAAAA
**
23593449 ATATATA-ACTAATGGCATTAAAA
1 ATATATACA-TAAT-ATATTAAAA
23593472 ATATATACATAATATATATAAAA
1 ATATATACATAATATAT-TAAAA
23593495 TGCATATAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 21
0.67 0.13 0.20
Matches are distributed among these distances:
20 7 0.10
21 6 0.09
22 4 0.06
23 35 0.51
24 2 0.03
25 13 0.19
26 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (22 bp):
ATATATACATAATATATTAAAA
Found at i:23595560 original size:24 final size:24
Alignment explanation
Indices: 23595533--23595584 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
23595523 GTGGAATATC
* *
23595533 ATTAAGCTCCAATCTATCAAGTCA
1 ATTAAGCTCCAATCCATCAAGCCA
23595557 ATTAAGCTCCAATCCATCAAGCCA
1 ATTAAGCTCCAATCCATCAAGCCA
23595581 ATTA
1 ATTA
23595585 TAATATATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (24 bp):
ATTAAGCTCCAATCCATCAAGCCA
Found at i:23596883 original size:42 final size:42
Alignment explanation
Indices: 23596837--23596916 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
23596827 GAACTATGGA
**
23596837 CACACGGTCGTGTCCTCACTTGTGTAACTCTCTAAGTATGAT
1 CACACGGTCGTGTCCTCACCCGTGTAACTCTCTAAGTATGAT
23596879 CACACGGTCGTGTCCTCACCCGTGTAACTCTCTAAGTA
1 CACACGGTCGTGTCCTCACCCGTGTAACTCTCTAAGTA
23596917 CAATCACATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (42 bp):
CACACGGTCGTGTCCTCACCCGTGTAACTCTCTAAGTATGAT
Found at i:23597931 original size:35 final size:36
Alignment explanation
Indices: 23597798--23597948 Score: 173
Period size: 36 Copynumber: 4.2 Consensus size: 36
23597788 CAATCCTATC
* *
23597798 AAACACACAAGATGCTCATAAGAGCTAGTCCA-TCTG
1 AAACACACTAGATGCTCATAAGAGCTAATCCATTC-G
* * *
23597834 AAACACACTAGATGCTTATAAGAGCTAATTCATCCG
1 AAACACACTAGATGCTCATAAGAGCTAATCCATTCG
* *
23597870 AAAATACACCA-ATGCTCATAAGAGCTAATCCATTCG
1 -AAACACACTAGATGCTCATAAGAGCTAATCCATTCG
* * *
23597906 AAACACACTA-ATGTTCATAAGAGCTAGTCCAATCG
1 AAACACACTAGATGCTCATAAGAGCTAATCCATTCG
23597941 AAACACAC
1 AAACACAC
23597949 CAAAACAGAG
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
35 38 0.39
36 51 0.52
37 9 0.09
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.21
Consensus pattern (36 bp):
AAACACACTAGATGCTCATAAGAGCTAATCCATTCG
Found at i:23618282 original size:19 final size:19
Alignment explanation
Indices: 23618244--23618282 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
23618234 TTTATTTGTC
*
23618244 ATAATTATTTTAAAATATT
1 ATAATTATTTTAAAAGATT
* *
23618263 ATAATTCTTTTGAAAGATT
1 ATAATTATTTTAAAAGATT
23618282 A
1 A
23618283 AATATTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (19 bp):
ATAATTATTTTAAAAGATT
Found at i:23618703 original size:30 final size:30
Alignment explanation
Indices: 23618669--23618730 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
23618659 CTTAACAAGT
*
23618669 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAAAAACAAAATTAAC
*
23618699 AAATGCCTTTAAAATAAAAACAAAATTAAC
1 AAATGCCTCTAAAATAAAAACAAAATTAAC
23618729 AA
1 AA
23618731 TAAAGTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.15, G:0.03, T:0.23
Consensus pattern (30 bp):
AAATGCCTCTAAAATAAAAACAAAATTAAC
Found at i:23619703 original size:12 final size:11
Alignment explanation
Indices: 23619686--23619732 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
23619676 TGAATGTTTT
23619686 AACAAAAACAAA
1 AACAAAAA-AAA
23619698 AACAAAAAAAA
1 AACAAAAAAAA
23619709 AGA-AAAAGAAAA
1 A-ACAAAA-AAAA
*
23619721 AAGAAAAAAAA
1 AACAAAAAAAA
23619732 A
1 A
23619733 GAGACCATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 14 0.44
12 18 0.56
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAAAAA
Found at i:23619715 original size:17 final size:17
Alignment explanation
Indices: 23619689--23619734 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
23619679 ATGTTTTAAC
*
23619689 AAAAACAAAA-ACAAAA
1 AAAAAAAAAAGACAAAA
23619705 AAAAAGAAAAAGA-AAAA
1 AAAAA-AAAAAGACAAAA
23619722 AGAAAAAAAAAGA
1 A-AAAAAAAAAGA
23619735 GACCATGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.19
17 16 0.62
18 5 0.19
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGACAAAA
Found at i:23619720 original size:13 final size:12
Alignment explanation
Indices: 23619701--23619732 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
23619691 AAACAAAAAC
23619701 AAAAAAAAAGAA
1 AAAAAAAAAGAA
23619713 AAAGAAAAAAGAA
1 AAA-AAAAAAGAA
23619726 AAAAAAA
1 AAAAAAA
23619733 GAGACCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:23620263 original size:5 final size:5
Alignment explanation
Indices: 23620253--23620284 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
23620243 CCTACTGTGA
23620253 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
23620285 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:23620278 original size:9 final size:9
Alignment explanation
Indices: 23620254--23620284 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
23620244 CTACTGTGAA
23620254 AAATAAAAT
1 AAATAAAAT
23620263 AAAATAAAAT
1 -AAATAAAAT
23620273 AAATAAAAT
1 AAATAAAAT
23620282 AAA
1 AAA
23620285 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:23621150 original size:22 final size:24
Alignment explanation
Indices: 23621118--23621162 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
23621108 AAAAAAAACA
23621118 TAAAAATTAAAATTAAC-CAAATT
1 TAAAAATTAAAATTAACTCAAATT
*
23621141 TAAAAA-TAAAATTGACTCAAAT
1 TAAAAATTAAAATTAACTCAAAT
23621163 ATATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (24 bp):
TAAAAATTAAAATTAACTCAAATT
Found at i:23626668 original size:25 final size:25
Alignment explanation
Indices: 23626631--23626678 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
23626621 TCTCTTAAAT
* *
23626631 TTTATTTACAAATAAAAATTATATA
1 TTTATATAAAAATAAAAATTATATA
* *
23626656 TTTATATAAAAATATATATTATA
1 TTTATATAAAAATAAAAATTATA
23626679 AATACCCGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTATATAAAAATAAAAATTATATA
Found at i:23646183 original size:18 final size:18
Alignment explanation
Indices: 23646157--23646207 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
23646147 TCTTCTTTAA
*
23646157 CCTTTAACCTTTCATCTT
1 CCTTAAACCTTTCATCTT
*
23646175 CCTTAAACCGTTCATCTT
1 CCTTAAACCTTTCATCTT
*
23646193 CTTGTAAACCCTTTC
1 CCT-TAAA-CCTTTC
23646208 CTATTTATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 18 0.67
19 4 0.15
20 5 0.19
ACGTcount: A:0.20, C:0.33, G:0.04, T:0.43
Consensus pattern (18 bp):
CCTTAAACCTTTCATCTT
Found at i:23648142 original size:43 final size:43
Alignment explanation
Indices: 23648090--23648177 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
23648080 GAACCTTAAG
23648090 ACCGAGTCACTTTGGGTGTCCGTGATTAACCTACTGAACACGT
1 ACCGAGTCACTTTGGGTGTCCGTGATTAACCTACTGAACACGT
*
23648133 ACCGAGTCACTTTGGGTGTCCGTGATTAACCTCCTGAACACGT
1 ACCGAGTCACTTTGGGTGTCCGTGATTAACCTACTGAACACGT
23648176 AC
1 AC
23648178 TTGTCTGGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (43 bp):
ACCGAGTCACTTTGGGTGTCCGTGATTAACCTACTGAACACGT
Found at i:23649080 original size:17 final size:17
Alignment explanation
Indices: 23649036--23649084 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
23649026 TCGTTTAAAT
*
23649036 ATTAATTTTTTTTATTA
1 ATTAATTTTTTTAATTA
*
23649053 A-TAATAGTTTTTAATTA
1 ATTAAT-TTTTTTAATTA
23649070 ATTAATTTTTTTAAT
1 ATTAATTTTTTTAAT
23649085 AAAGATGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTAATTTTTTTAATTA
Found at i:23651184 original size:7 final size:7
Alignment explanation
Indices: 23651170--23651198 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
23651160 TTTTTATTTT
23651170 AATA-AA
1 AATATAA
23651176 AATATAA
1 AATATAA
23651183 AATATAA
1 AATATAA
23651190 AATATAA
1 AATATAA
23651197 AA
1 AA
23651199 ATTGTAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AATATAA
Found at i:23654130 original size:4 final size:4
Alignment explanation
Indices: 23654121--23654232 Score: 84
Period size: 4 Copynumber: 28.0 Consensus size: 4
23654111 TTTAATTCTG
* * * * **
23654121 TTAT TTAT TTAT TCAT CTAC TTGT TTAT TTA- TTCC TTAT TTCAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TTAT
* * * * * *
23654169 TTCAT TCAT TTAT TTGT TTAT TTAC TCAT TTAT TTAT ATA- TTAT TCAT
1 TT-AT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
23654217 TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT
23654233 GTTTCAATCC
Statistics
Matches: 81, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
3 4 0.05
4 70 0.86
5 7 0.09
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (4 bp):
TTAT
Found at i:23654149 original size:20 final size:20
Alignment explanation
Indices: 23654121--23654232 Score: 129
Period size: 20 Copynumber: 5.6 Consensus size: 20
23654111 TTTAATTCTG
* *
23654121 TTATTTATTTATTCATCTAC
1 TTATTTATTTATTCATTTAT
* *
23654141 TTGTTTATTTATTC-CTTAT
1 TTATTTATTTATTCATTTAT
23654160 TTCATTTATTTCATTCATTTAT
1 TT-ATTTATTT-ATTCATTTAT
* *
23654182 TTGTTTATTTACTCATTTAT
1 TTATTTATTTATTCATTTAT
*
23654202 TTATATA-TTATTCATTTAT
1 TTATTTATTTATTCATTTAT
23654221 TTATTTATTTAT
1 TTATTTATTTAT
23654233 GTTTCAATCC
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
19 21 0.28
20 38 0.50
21 11 0.14
22 6 0.08
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATTTATTTATTCATTTAT
Found at i:23654454 original size:12 final size:12
Alignment explanation
Indices: 23654437--23654462 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23654427 TTTTATTCAT
23654437 TTATTATCATTA
1 TTATTATCATTA
23654449 TTATTATCATTA
1 TTATTATCATTA
23654461 TT
1 TT
23654463 TTTTTATCTT
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:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTATCATTA
Found at i:23654564 original size:13 final size:13
Alignment explanation
Indices: 23654546--23654570 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23654536 GGCATCTAGC
23654546 ATTTTTATTTTTT
1 ATTTTTATTTTTT
23654559 ATTTTTATTTTT
1 ATTTTTATTTTT
23654571 ATCACTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:23664138 original size:22 final size:22
Alignment explanation
Indices: 23664110--23664153 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
23664100 AGCAAGAGAA
23664110 TGTAAAACCTATCTAGATGAGT
1 TGTAAAACCTATCTAGATGAGT
*
23664132 TGTAAAACCTATTTAGATGAGT
1 TGTAAAACCTATCTAGATGAGT
23664154 ATTTTTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (22 bp):
TGTAAAACCTATCTAGATGAGT
Found at i:23666679 original size:46 final size:46
Alignment explanation
Indices: 23666620--23666968 Score: 432
Period size: 46 Copynumber: 7.6 Consensus size: 46
23666610 GCCATAGTGC
* * ** *
23666620 CTTTCAACTATGGTCTTACTCATTTTTTGTCATGTTGCCATGGTAT
1 CTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTAT
*
23666666 CTTTCAACCATGGTCTTGTTCATTTCATGTCACGTTGCCATGGTAT
1 CTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTAT
*
23666712 CTTTCAACCATGGTCCTATTCATTTCATGTCA-GCTT-CCATGGTAT
1 CTTTCAACCATGGTCTTATTCATTTCATGTCACG-TTGCCATGGTAT
* *** * *
23666757 CTTTCAACTATGGTCTTATTCATTTCCCATCATGTTGCTATGGTAT
1 CTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTAT
* *
23666803 CTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTTCCATGGTAT
1 CTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTAT
* * * *
23666849 CTTTCAACCATTGTCTTATCCTTTTCATGTCACGTTTCCATGGTAT
1 CTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTAT
* ** * * *
23666895 TTTTCAACCATGGTCTTACACATTTCATATCATGTTACCATGGTAT
1 CTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTAT
**
23666941 CTTTCAACCATGGTCTTACACATTTCAT
1 CTTTCAACCATGGTCTTATTCATTTCAT
23666969 TTCAGAAAGT
Statistics
Matches: 267, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
45 39 0.15
46 228 0.85
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (46 bp):
CTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTAT
Found at i:23666875 original size:137 final size:138
Alignment explanation
Indices: 23666620--23666968 Score: 502
Period size: 137 Copynumber: 2.5 Consensus size: 138
23666610 GCCATAGTGC
** * *
23666620 CTTTCAACTATGGTCTTACTCATTTTTTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTGT
1 CTTTCAACTATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTAT
*
23666685 TCATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCCTATTCATTTCATGTCA-GCTTC
66 TCATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCCTATCCATTTCATGTCACGCTTC
23666749 CATGGTAT
131 CATGGTAT
* ** *
23666757 CTTTCAACTATGGTCTTATTCATTTCCCATCATGTTGCTATGGTATCTTTCAACCATGGTCTTAT
1 CTTTCAACTATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTAT
* * * * * *
23666822 TCTTTTCATGTCACGTTTCCATGGTATCTTTCAACCATTGTCTTATCCTTTTCATGTCACGTTTC
66 TCATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCCTATCCATTTCATGTCACGCTTC
23666887 CATGGTAT
131 CATGGTAT
* * * * *
23666895 TTTTCAACCATGGTCTTACACATTTCATATCATGTTACCATGGTATCTTTCAACCATGGTCTTAC
1 CTTTCAACTATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTAT
*
23666960 ACATTTCAT
66 TCATTTCAT
23666969 TTCAGAAAGT
Statistics
Matches: 186, Mismatches: 25, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
137 111 0.60
138 75 0.40
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (138 bp):
CTTTCAACTATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTAT
TCATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCCTATCCATTTCATGTCACGCTTC
CATGGTAT
Found at i:23668862 original size:31 final size:30
Alignment explanation
Indices: 23668827--23668902 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
23668817 CTAATGAAAT
*
23668827 AATAAAAAATATCTTATTAAA-ATATTAATAA
1 AATAAAAAATATCTAATTAAATA-ATT-ATAA
* **
23668858 AATAATATTTATCTAATTAAATAATTATAA
1 AATAAAAAATATCTAATTAAATAATTATAA
*
23668888 AATATCAAAATATCT
1 AATA-AAAAATATCT
23668903 CTAGCATCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
30 8 0.23
31 26 0.74
32 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (30 bp):
AATAAAAAATATCTAATTAAATAATTATAA
Found at i:23670479 original size:25 final size:25
Alignment explanation
Indices: 23670447--23670494 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
23670437 GAATATGCTA
23670447 AATGTGCTAATAATCAGAGAGCACT
1 AATGTGCTAATAATCAGAGAGCACT
*
23670472 AATGTGCTAGTAATCAGAGAGCA
1 AATGTGCTAATAATCAGAGAGCA
23670495 TGCTGAGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (25 bp):
AATGTGCTAATAATCAGAGAGCACT
Found at i:23671816 original size:46 final size:46
Alignment explanation
Indices: 23671775--23672079 Score: 430
Period size: 46 Copynumber: 6.6 Consensus size: 46
23671765 TGCCATAATG
* *
23671775 TCTTTCAACCATGGTCTTGTTCATTTCATGTCACATTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* *
23671821 TCTTTCAACCATGGTCTTGTTCATTTCATGTCACATTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* *
23671867 TCTTTGAACCATGGTCTTATTCATTTCATGTCACGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
** *
23671913 TCTTTCAATAATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* * * *
23671959 TCTTTCAACCATTGTCTTATCCTTTTCATGTCACGTTTCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* ** * *
23672005 TTTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
**
23672051 TCTTTCAACCATGGTCTTACACATTTCAT
1 TCTTTCAACCATGGTCTTATTCATTTCAT
23672080 TTCAGAAAAC
Statistics
Matches: 236, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 236 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
Found at i:23673370 original size:15 final size:15
Alignment explanation
Indices: 23673352--23673381 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23673342 GATTTAATTT
23673352 AATATTTTATTCATC
1 AATATTTTATTCATC
23673367 AATATTTTATTCATC
1 AATATTTTATTCATC
23673382 CTATAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTTTATTCATC
Found at i:23673943 original size:11 final size:11
Alignment explanation
Indices: 23673927--23673974 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
23673917 CTTTATATAC
23673927 TAATAAAATAA
1 TAATAAAATAA
*
23673938 TAATAAAATATCT
1 TAATAAAATA--A
* *
23673951 TATTAAAATAT
1 TAATAAAATAA
23673962 TAATAAAATAA
1 TAATAAAATAA
23673973 TA
1 TA
23673975 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:23674954 original size:44 final size:44
Alignment explanation
Indices: 23674886--23675516 Score: 406
Period size: 44 Copynumber: 14.1 Consensus size: 44
23674876 ATCATTATGG
* *
23674886 CAAATCTTATCTCCCTGAATTTGCAGTGGAGCAGATTGAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * *
23674930 CAAATCTGATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
23674974 CTAATCTTATTTCCCTAAAGTTGCAGTGGAGCAAATTGGAA-ATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-GAAGCTA
* * ** * * *
23675018 GTAAATCTTGTCTCTTTGAAGTTGCAGTAGAGCAGGTTAAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
23675063 TAAACCTTATCTCCATGGAGTTGCAGTGGAGCAGGTTGAAG-TCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT-A
* * * * * * *
23675107 CTAATCTTATCTTCCTGAAGTTACAGTGAAGCAGATTAAAACCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * * *
23675151 CAAGTCTCATATCTCTGAAGTTGCAGTGGAGCAAATTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * *
23675195 GCAAGTCTCATTTCCCTGAAGTTGCAGTGG-GACAGGTTGAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCTA
* * * *
23675240 TCATAGTGAATCTGATCTCCCTGAAGTAGCAGTGGAGCAGATTAAAGATA
1 -C--A---AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
23675290 GCAAATCTCATCTCTCTGAAATTGCAGTAGAGCAGATTAAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * ** * *
23675335 TAAA-CTTTATCTCCCTAAAGCTATAATGGAGCAGATTGAAGTTA
1 CAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * * *
23675379 CAAGTCTTATTTCCCTAAATTTGCAGTGGAGCAGATTAAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
** * * ** *
23675423 GTGAATCTTATCTCCCCGAAGTTGTAGTGGAATAGATTGACGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* ** * * * * * *
23675468 CTAATCTTATCTCATTGAGGATGTAGTAGAGTAGATTGAAGCGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
23675512 CAAAT
1 CAAAT
23675517 TCTACACCTC
Statistics
Matches: 449, Mismatches: 122, Indels: 32
0.74 0.20 0.05
Matches are distributed among these distances:
43 2 0.00
44 273 0.61
45 137 0.31
47 1 0.00
48 1 0.00
50 34 0.08
51 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
Found at i:23675128 original size:133 final size:133
Alignment explanation
Indices: 23674887--23675139 Score: 310
Period size: 133 Copynumber: 1.9 Consensus size: 133
23674877 TCATTATGGC
* * * * *
23674887 AAATCTTATCTCCCTGAATTTGCAGTGGAGCAGATTGAAGCCACAAATCTGATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTGATCTCCATGAAGTT
* *
23674952 GCAGTGGAGCAAATTAAAGCCACTAATCTTATTTCCCTAAAGTTGCAGTGGAGCAAATTGGAAAT
66 GCAGTGGAGCAAATTAAAGCCACTAATCTTATTTCCCTAAAGTTACAGTGAAGCAAATTGGAAAT
23675017 AGT
131 AGT
* ** * * * * *
23675020 AAATCTTGTCTCTTTGAAGTTGCAGTAGAGCAGGTTAAAGCTATAAACCTTATCTCCATGGAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTGATCTCCATGAAGTT
** * * *
23675085 GCAGTGGAGCAGGTTGAAGTCACTAATCTTATCTT-CCTGAAGTTACAGTGAAGCA
66 GCAGTGGAGCAAATTAAAGCCACTAATCTTAT-TTCCCTAAAGTTACAGTGAAGCA
23675140 GATTAAAACC
Statistics
Matches: 99, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
133 97 0.98
134 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (133 bp):
AAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTGATCTCCATGAAGTT
GCAGTGGAGCAAATTAAAGCCACTAATCTTATTTCCCTAAAGTTACAGTGAAGCAAATTGGAAAT
AGT
Found at i:23675217 original size:177 final size:177
Alignment explanation
Indices: 23674891--23675240 Score: 427
Period size: 177 Copynumber: 2.0 Consensus size: 177
23674881 TATGGCAAAT
* * *
23674891 CTTATCTCCCTGAATTTGCAGTGGAGCAGATTGAAGCCACAAATCTGATCTCCCTGAAGTTGCAG
1 CTTATCTCCATGAAGTTGCAGTGGAGCAGATTGAAGCCACAAATCTGATCTCCCTGAAGTTACAG
* * * * *
23674956 TGGAGCAAATTAAAGCCACTAATCTTATTTCCCTAAAGTTGCAGTGGAGCAAATTGGAAATAGTA
66 TGAAGCAAATTAAAACCACTAATCTCATATCCCTAAAGTTGCAGTGGAGCAAATTGGAAATAGCA
** **
23675021 AATCTTGTCTCTTTGAAGTTGCAGT-AGAGCAGGTTAAAGCTATAAAC
131 AATCTCATCTCCCTGAAGTTGCAGTGAGA-CAGGTTAAAGCTATAAAC
* * * * * *
23675068 CTTATCTCCATGGAGTTGCAGTGGAGCAGGTTGAAGTCACTAATCTTATCTTCCTGAAGTTACAG
1 CTTATCTCCATGAAGTTGCAGTGGAGCAGATTGAAGCCACAAATCTGATCTCCCTGAAGTTACAG
* * *
23675133 TGAAGCAGATTAAAACCAC-AAGTCTCATATCTCTGAAGTTGCAGTGGAGCAAATT-GAAGATAG
66 TGAAGCAAATTAAAACCACTAA-TCTCATATCCCTAAAGTTGCAGTGGAGCAAATTGGAA-ATAG
* * * *
23675196 CAAGTCTCATTTCCCTGAAGTTGCAGTGGGACAGGTTGAAGCTAT
129 CAAATCTCATCTCCCTGAAGTTGCAGTGAGACAGGTTAAAGCTAT
23675241 CATAGTGAAT
Statistics
Matches: 145, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
176 5 0.03
177 138 0.95
178 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (177 bp):
CTTATCTCCATGAAGTTGCAGTGGAGCAGATTGAAGCCACAAATCTGATCTCCCTGAAGTTACAG
TGAAGCAAATTAAAACCACTAATCTCATATCCCTAAAGTTGCAGTGGAGCAAATTGGAAATAGCA
AATCTCATCTCCCTGAAGTTGCAGTGAGACAGGTTAAAGCTATAAAC
Found at i:23677315 original size:19 final size:19
Alignment explanation
Indices: 23677253--23677305 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
23677243 CACTTATTTC
*
23677253 ATTCATTTATTTGT-TCATTT
1 ATTCATTTATTTATAT-A-TT
*
23677273 ACTCATTTATTTATATATT
1 ATTCATTTATTTATATATT
23677292 ATTCATTTATTTAT
1 ATTCATTTATTTAT
23677306 TTTTGTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 15 0.52
20 13 0.45
21 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTCATTTATTTATATATT
Found at i:23677630 original size:24 final size:23
Alignment explanation
Indices: 23677593--23677638 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
23677583 GGCATCTAGA
*
23677593 ATTTTTATTATTTATTTATTTTT
1 ATTTTTATCATTTATTTATTTTT
23677616 ATTTTTATCACTTTATTTATTTT
1 ATTTTTATCA-TTTATTTATTTT
23677639 ATACCATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (23 bp):
ATTTTTATCATTTATTTATTTTT
Found at i:23683825 original size:7 final size:7
Alignment explanation
Indices: 23683811--23683847 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
23683801 ATCATTTCAA
23683811 TCGAATC
1 TCGAATC
*
23683818 TTGAATC
1 TCGAATC
23683825 TCGAATC
1 TCGAATC
23683832 TCGAATC
1 TCGAATC
23683839 TCGAATC
1 TCGAATC
23683846 TC
1 TC
23683848 TAACCTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (7 bp):
TCGAATC
Found at i:23683913 original size:6 final size:6
Alignment explanation
Indices: 23683905--23683951 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
23683895 TTTAGAATTT
* *
23683905 GAGTTT GAGTTT GAGTTC GAGTTC GAGTTC GAGTTC GAGTTC GAGTT
1 GAGTTC GAGTTC GAGTTC GAGTTC GAGTTC GAGTTC GAGTTC GAGTT
23683952 TAAGGTTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.11, G:0.34, T:0.38
Consensus pattern (6 bp):
GAGTTC
Found at i:23684774 original size:17 final size:16
Alignment explanation
Indices: 23684719--23684781 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 16
23684709 ATTTTAATAT
23684719 AATTTCTATGAAGTTCTAA
1 AATTTCTAT-AA-TT-TAA
* *
23684738 AATTTATATCTATTTAA
1 AATTTCTAT-AATTTAA
23684755 AATTTCTATAATTTATA
1 AATTTCTATAATTTA-A
*
23684772 AATTTTTATA
1 AATTTCTATA
23684782 GTATTCATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
16 5 0.14
17 21 0.57
18 2 0.05
19 9 0.24
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (16 bp):
AATTTCTATAATTTAA
Found at i:23684779 original size:26 final size:27
Alignment explanation
Indices: 23684732--23684807 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 27
23684722 TTCTATGAAG
* ** *
23684732 TTCTAAAATTTATATCTATTTAAAAT-
1 TTCTATAATTTATAAATTTTTAAAATA
* *
23684758 TTCTATAATTTATAAATTTTTATAGTA
1 TTCTATAATTTATAAATTTTTAAAATA
23684785 TTCATATAATATTATATAATTTT
1 TTC-TATAAT-TTATA-AATTTT
23684808 CATATATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 20 0.50
27 3 0.08
28 6 0.15
29 5 0.12
30 6 0.15
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (27 bp):
TTCTATAATTTATAAATTTTTAAAATA
Found at i:23684802 original size:21 final size:20
Alignment explanation
Indices: 23684778--23684818 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
23684768 TATAAATTTT
*
23684778 TATAGTATTCATATAATATTA
1 TATAATATTCATAT-ATATTA
*
23684799 TATAATTTTCATATATATTA
1 TATAATATTCATATATATTA
23684819 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (20 bp):
TATAATATTCATATATATTA
Found at i:23684828 original size:21 final size:21
Alignment explanation
Indices: 23684785--23684826 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
23684775 TTTTATAGTA
23684785 TTCATATAATATTATATAATT
1 TTCATATAATATTATATAATT
*
23684806 TTCATAT-ATATTA-ATATTT
1 TTCATATAATATTATATAATT
23684825 TT
1 TT
23684827 TTAACATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 6 0.30
21 7 0.35
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTCATATAATATTATATAATT
Found at i:23687331 original size:39 final size:39
Alignment explanation
Indices: 23687270--23687408 Score: 233
Period size: 39 Copynumber: 3.6 Consensus size: 39
23687260 TCGTGATTTA
* * *
23687270 AAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACGG
1 AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
* *
23687309 AAGCCCGAAGGCTAACTAAAGCACACAAGTGTTAAACGG
1 AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
23687348 AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
1 AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
23687387 AAGCCCGAAGGCTAACTGAAGC
1 AAGCCCGAAGGCTAACTGAAGC
23687409 TTATCAGAGC
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.38, C:0.24, G:0.25, T:0.12
Consensus pattern (39 bp):
AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
Found at i:23689362 original size:46 final size:46
Alignment explanation
Indices: 23689310--23689583 Score: 406
Period size: 46 Copynumber: 6.0 Consensus size: 46
23689300 AGTGTGCTCT
*
23689310 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
23689356 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
23689402 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
23689448 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
23689494 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
23689540 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
23689584 TCATGTCAAA
Statistics
Matches: 216, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 1 0.00
46 215 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:23689825 original size:16 final size:17
Alignment explanation
Indices: 23689804--23689836 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23689794 ATGATGGAGC
23689804 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
23689820 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
23689837 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:23694233 original size:46 final size:46
Alignment explanation
Indices: 23694181--23694316 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
23694171 AGTGTGCTTT
*
23694181 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAAC
*
23694227 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAAC
* * * * * *
23694273 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACAATGGCA
23694317 TCATGTCAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 80 0.99
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAAC
Found at i:23695509 original size:229 final size:229
Alignment explanation
Indices: 23695108--23695561 Score: 872
Period size: 229 Copynumber: 2.0 Consensus size: 229
23695098 TGAAACTCAT
*
23695108 ATGAGTTAACGGAAGCTCGTAAGAGCTAAACGAAAAGCAAACACGAGAATTCACAACAAATGCTG
1 ATGAGTTAACGGAAGCTCGTAAGAGCTAAACGAAAAGAAAACACGAGAATTCACAACAAATGCTG
23695173 AATCTCGATTTACTTGGGTAATTTACCGTCAATTCATCTTTTTCACTGAACAATTGTACTCATTT
66 AATCTCGATTTACTTGGGTAATTTACCGTCAATTCATCTTTTTCACTGAACAATTGTACTCATTT
*
23695238 CCTGCGTTCCGTTCCTCCGAAATACTCAGTTCGATTTCATAACTTTTGTACATAATTTACTTATT
131 CCTGCATTCCGTTCCTCCGAAATACTCAGTTCGATTTCATAACTTTTGTACATAATTTACTTATT
23695303 TTCAACAATTAACATACATAAATATTAATCCCTG
196 TTCAACAATTAACATACATAAATATTAATCCCTG
23695337 ATGAGTTAACGGAAGCTCGTAAGAGCTAAACGAAAAGAAAACACGAGAATTCACAACAAATGCTG
1 ATGAGTTAACGGAAGCTCGTAAGAGCTAAACGAAAAGAAAACACGAGAATTCACAACAAATGCTG
*
23695402 AATCTCGATTTACTTGGGTAATTTACCGTCAATTCATCTTTTTCACTGAACGATTGTACTCATTT
66 AATCTCGATTTACTTGGGTAATTTACCGTCAATTCATCTTTTTCACTGAACAATTGTACTCATTT
*
23695467 CCTGCATTCCGTTCCTCTGAAATACTCAGTTCGATTTCATAACTTTTGTACATAATTTACTTATT
131 CCTGCATTCCGTTCCTCCGAAATACTCAGTTCGATTTCATAACTTTTGTACATAATTTACTTATT
23695532 TTCAACAATTAACATACATAAATATTAATC
196 TTCAACAATTAACATACATAAATATTAATC
23695562 ACCATTCATA
Statistics
Matches: 221, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
229 221 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (229 bp):
ATGAGTTAACGGAAGCTCGTAAGAGCTAAACGAAAAGAAAACACGAGAATTCACAACAAATGCTG
AATCTCGATTTACTTGGGTAATTTACCGTCAATTCATCTTTTTCACTGAACAATTGTACTCATTT
CCTGCATTCCGTTCCTCCGAAATACTCAGTTCGATTTCATAACTTTTGTACATAATTTACTTATT
TTCAACAATTAACATACATAAATATTAATCCCTG
Found at i:23699899 original size:15 final size:14
Alignment explanation
Indices: 23699882--23699919 Score: 53
Period size: 12 Copynumber: 2.8 Consensus size: 14
23699872 TATACATTTA
23699882 AAAAAATTATAATT
1 AAAAAATTATAATT
23699896 --AAAATTATTAATT
1 AAAAAATTA-TAATT
23699909 AAAAAATTATA
1 AAAAAATTATA
23699920 CTAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
12 7 0.33
13 5 0.24
14 2 0.10
15 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAAATTATAATT
Found at i:23699901 original size:12 final size:13
Alignment explanation
Indices: 23699884--23699912 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23699874 TACATTTAAA
23699884 AAAATTA-TAATT
1 AAAATTATTAATT
23699896 AAAATTATTAATT
1 AAAATTATTAATT
23699909 AAAA
1 AAAA
23699913 AATTATACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTATTAATT
Found at i:23701752 original size:29 final size:30
Alignment explanation
Indices: 23701702--23701761 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
23701692 TGGACTTGAA
*
23701702 TTTTTAAATAAAAAAGTTGAAGGAA-TAAAT
1 TTTTTAAATAAAAAAGTAGAA-GAATTAAAT
23701732 TTTTTAAA-ATAAAAA-TAGAAGAATTAAAT
1 TTTTTAAATA-AAAAAGTAGAAGAATTAAAT
23701761 T
1 T
23701762 CTAAATGCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.11
29 11 0.41
30 13 0.48
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (30 bp):
TTTTTAAATAAAAAAGTAGAAGAATTAAAT
Found at i:23705939 original size:60 final size:59
Alignment explanation
Indices: 23705818--23705956 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 59
23705808 ATCAGAGTTA
* *
23705818 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAATAT
1 ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAATAT
* * * *
23705879 ACTGGGCCTAGCCCATGTTAGTATCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATAT
1 ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGA-ATAT
* *
23705939 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTAGCCCATAT
23705957 TAACACAGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 3 0.05
60 50 0.76
61 13 0.20
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (59 bp):
ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAATAT
Found at i:23705974 original size:20 final size:20
Alignment explanation
Indices: 23705949--23705994 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
23705939 ATTGGGCCTT
23705949 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
23705969 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
23705988 GCCCATA
1 GCCCATA
23705995 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:23706003 original size:19 final size:20
Alignment explanation
Indices: 23705961--23706004 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
23705951 CCATATTAAC
** *
23705961 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
23705981 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
23706000 ACAGT
1 ACAGT
23706005 CTTATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:23707630 original size:32 final size:32
Alignment explanation
Indices: 23707591--23707655 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
23707581 TAAATCCCAT
* *
23707591 CCAAATTCCTTGCACCATCAGTAGCAGTCCAC
1 CCAAATTCCTTGCACCATCAGCAACAGTCCAC
23707623 CCAAATTCCTTGCACCATCAGCAACAGTCCAC
1 CCAAATTCCTTGCACCATCAGCAACAGTCCAC
23707655 C
1 C
23707656 GCTTGACCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.40, G:0.11, T:0.20
Consensus pattern (32 bp):
CCAAATTCCTTGCACCATCAGCAACAGTCCAC
Found at i:23708707 original size:72 final size:71
Alignment explanation
Indices: 23708590--23708893 Score: 305
Period size: 72 Copynumber: 4.3 Consensus size: 71
23708580 TATTGGGTGT
* * * *
23708590 TGCTCGCACAAGCTTCAGAGATTC-CATAACATGTGTTGGATCTCAAGCCACCGATAAAGAATGA
1 TGCTCACACAAGCTTCAGAGAATCGC--AACATATGTCGGATCTCAAGCCACCGATAAAGAATGA
23708654 TTCGATAC
64 TTCGATAC
*
23708662 TGCTCACACAAACTTCAGAGAATCCGCAACATATGTCGGATCTCAAGCCACCGATAAAGAATGAT
1 TGCTCACACAAGCTTCAGAGAAT-CGCAACATATGTCGGATCTCAAGCCACCGATAAAGAATGAT
*
23708727 TCCATGA-
65 TCGAT-AC
* * * * * * *
23708734 TGCTCACACAAACCTCAGAGAAT-GCATCATATGTCAGATCTCAAACCATCGATAAAGAATGGTT
1 TGCTCACACAAGCTTCAGAGAATCGCAACATATGTCGGATCTCAAGCCACCGATAAAGAATGATT
*
23708798 CGATGC
66 CGATAC
* * * * * * *
23708804 TCCTCACACAAGCTTTAAAGAATC-C-ACA-ATGCCTGATCTCAAGCCATCAATAAAGAATGATT
1 TGCTCACACAAGCTTCAGAGAATCGCAACATATGTCGGATCTCAAGCCACCGATAAAGAATGATT
* *
23708866 CAATTC
66 CGATAC
* *
23708872 TGTTCACACAAGCTTGAGAGAA
1 TGCTCACACAAGCTTCAGAGAA
23708894 GGATCTCATG
Statistics
Matches: 196, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
68 51 0.26
69 2 0.01
70 58 0.30
72 82 0.42
73 2 0.01
74 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (71 bp):
TGCTCACACAAGCTTCAGAGAATCGCAACATATGTCGGATCTCAAGCCACCGATAAAGAATGATT
CGATAC
Found at i:23708810 original size:70 final size:69
Alignment explanation
Indices: 23708628--23708893 Score: 291
Period size: 70 Copynumber: 3.8 Consensus size: 69
23708618 ACATGTGTTG
*
23708628 GATCTCAAGCCACCGATAAAGAATGATTCGATACTGCTCACACAAACTTCAGAGAATCCGCAACA
1 GATCTCAAGCCACCGATAAAGAATGATTCGATGCTGCTCACACAAACTTCAGAGAAT--GC-ACA
*
23708693 TATGTCG
63 TATGTCA
* * *
23708700 GATCTCAAGCCACCGATAAAGAATGATTCCATGATGCTCACACAAACCTCAGAGAATGCATCATA
1 GATCTCAAGCCACCGATAAAGAATGATTCGATGCTGCTCACACAAACTTCAGAGAATGCA-CATA
23708765 TGTCA
65 TGTCA
* * * * * * * *
23708770 GATCTCAAACCATCGATAAAGAATGGTTCGATGCTCCTCACACAAGCTTTAAAGAATCCACA-AT
1 GATCTCAAGCCACCGATAAAGAATGATTCGATGCTGCTCACACAAACTTCAGAGAATGCACATAT
* *
23708834 GCCT
66 GTCA
* * * * * * *
23708838 GATCTCAAGCCATCAATAAAGAATGATTCAATTCTGTTCACACAAGCTTGAGAGAA
1 GATCTCAAGCCACCGATAAAGAATGATTCGATGCTGCTCACACAAACTTCAGAGAA
23708894 GGATCTCATG
Statistics
Matches: 166, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
68 51 0.31
69 3 0.02
70 59 0.36
72 53 0.32
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23
Consensus pattern (69 bp):
GATCTCAAGCCACCGATAAAGAATGATTCGATGCTGCTCACACAAACTTCAGAGAATGCACATAT
GTCA
Found at i:23711861 original size:13 final size:13
Alignment explanation
Indices: 23711843--23711873 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
23711833 CGCTTCTCTA
23711843 TATTCAACATAAT
1 TATTCAACATAAT
23711856 TATTCAACATAAT
1 TATTCAACATAAT
23711869 TATTC
1 TATTC
23711874 TTATCACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (13 bp):
TATTCAACATAAT
Found at i:23713715 original size:53 final size:53
Alignment explanation
Indices: 23713653--23713760 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 53
23713643 AATGTGAACT
*
23713653 ATGGATTAAATTGAATATTAAGAT-TACTTAATTGATTGAAATTATCTTTTTAA
1 ATGGATTAAATTGAATATTAA-ATATACTTAATTGATTGAAATTATCTATTTAA
* *
23713706 ATGGATTAAATTGAATATTAACTATGCTTAATTGATTGAAATTATCTATTTAA
1 ATGGATTAAATTGAATATTAAATATACTTAATTGATTGAAATTATCTATTTAA
23713759 AT
1 AT
23713761 CAAGATAAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 1 0.02
53 50 0.98
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (53 bp):
ATGGATTAAATTGAATATTAAATATACTTAATTGATTGAAATTATCTATTTAA
Found at i:23714803 original size:52 final size:52
Alignment explanation
Indices: 23714725--23714832 Score: 207
Period size: 52 Copynumber: 2.1 Consensus size: 52
23714715 TTAAAAATTA
23714725 TGTTTGGTTGGTGCACTTTAATGTTTACCAAATGTTGTCATTTTAGGTCACT
1 TGTTTGGTTGGTGCACTTTAATGTTTACCAAATGTTGTCATTTTAGGTCACT
*
23714777 TGTTTGGTTGGTGCACTTTAATGTTTACCAAATGTTGTCATTTTTGGTCACT
1 TGTTTGGTTGGTGCACTTTAATGTTTACCAAATGTTGTCATTTTAGGTCACT
23714829 TGTT
1 TGTT
23714833 AAGGATTGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.48
Consensus pattern (52 bp):
TGTTTGGTTGGTGCACTTTAATGTTTACCAAATGTTGTCATTTTAGGTCACT
Found at i:23715947 original size:25 final size:27
Alignment explanation
Indices: 23715916--23715974 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
23715906 TTTATTACTT
23715916 ATATTAATAGT-ATT-TTATT-AATTTA
1 ATATTAATAGTGATTATT-TTAAATTTA
23715941 ATATTAA-AGTGATTATTTTAAATTTA
1 ATATTAATAGTGATTATTTTAAATTTA
23715967 AT-TTAATA
1 ATATTAATA
23715975 TTATCTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 3 0.10
25 16 0.53
26 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (27 bp):
ATATTAATAGTGATTATTTTAAATTTA
Found at i:23716691 original size:12 final size:12
Alignment explanation
Indices: 23716668--23716702 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
23716658 GATATACTTT
23716668 CATAATCAGATG
1 CATAATCAGATG
23716680 CA-AATGCAGATG
1 CATAAT-CAGATG
23716692 CATAATCAGAT
1 CATAATCAGAT
23716703 ACATTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (12 bp):
CATAATCAGATG
Found at i:23719102 original size:72 final size:72
Alignment explanation
Indices: 23718913--23719112 Score: 238
Period size: 72 Copynumber: 2.8 Consensus size: 72
23718903 CATATTTGGG
* * * *
23718913 CTGCTCACACAAGCTTCAGAGAATTCGCAACATGTTTCGAATCTCAAGCCACCGATAAAAAATGA
1 CTGCTCACACAAGCTTCAGAGAATCCGCAACATATATCGAATCTCAAGCCATCGATAAAAAATGA
** * *
23718978 TTTGGTG
66 TCCGATA
* * * * *
23718985 CTGCTCACACAAGCTTCAAAGAATCCACAACATATGTCGAATCTCAAGTCATCGATAAAGAATGA
1 CTGCTCACACAAGCTTCAGAGAATCCGCAACATATATCGAATCTCAAGCCATCGATAAAAAATGA
23719050 TCCGATA
66 TCCGATA
* * * **
23719057 CTGCTCACACAAGCTTTAGAGAATCCGCGATATATATCGGGTCTCAAGCCATCGAT
1 CTGCTCACACAAGCTTCAGAGAATCCGCAACATATATCGAATCTCAAGCCATCGAT
23719113 CATTAAATCC
Statistics
Matches: 107, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 107 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (72 bp):
CTGCTCACACAAGCTTCAGAGAATCCGCAACATATATCGAATCTCAAGCCATCGATAAAAAATGA
TCCGATA
Found at i:23720808 original size:23 final size:23
Alignment explanation
Indices: 23720779--23720834 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
23720769 TTTCATGTAT
23720779 TTTTTATTTTACTATTAT-TTAC
1 TTTTTATTTTACTATTATCTTAC
* *
23720801 TTATTTA-TTTATTATTGTCTTAC
1 TT-TTTATTTTACTATTATCTTAC
23720824 TTTTTATTTTA
1 TTTTTATTTTA
23720835 AAATTTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTTATTTTACTATTATCTTAC
Found at i:23720919 original size:17 final size:17
Alignment explanation
Indices: 23720874--23720925 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
23720864 TTTTCGCTTG
* *
23720874 TTATTTATTTATATATA
1 TTATTTATATATACATA
*
23720891 TTTTTTACATATATACATA
1 TTATTT--ATATATACATA
*
23720910 TTATTTATATTTACAT
1 TTATTTATATATACAT
23720926 TCGTTATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 14 0.50
19 14 0.50
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTTATATATACATA
Found at i:23722394 original size:18 final size:19
Alignment explanation
Indices: 23722373--23722422 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
23722363 ATGTATTAGA
23722373 TATTAAATAA-ATATTTAT
1 TATTAAATAAGATATTTAT
23722391 TATTTTATAA-AAGATATTTAT
1 TA--TTA-AATAAGATATTTAT
23722412 TAATTAAATAA
1 T-ATTAAATAA
23722423 TTATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 10 0.38
21 11 0.42
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTAAATAAGATATTTAT
Found at i:23724657 original size:46 final size:46
Alignment explanation
Indices: 23724599--23724864 Score: 280
Period size: 46 Copynumber: 6.0 Consensus size: 46
23724589 CGTGTGCTCT
*
23724599 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
23724645 CTGATATGAAA----T--G--CATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
23724683 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAAG
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
23724729 GTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** ** * *
23724775 ATGACGGGAAATGAATAAGACTATGGTTGAAAGATACCATGACAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
23724821 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATACTATGGCA
1 CTGACATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
23724865 TCATGTCGAA
Statistics
Matches: 189, Mismatches: 22, Indels: 18
0.83 0.10 0.08
Matches are distributed among these distances:
38 36 0.19
40 1 0.01
42 2 0.01
44 1 0.01
45 1 0.01
46 148 0.78
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:23724671 original size:38 final size:38
Alignment explanation
Indices: 23724620--23724695 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
23724610 TGTGTAAGAC
23724620 CATGGTTGAAAGATACCATGGCAACCTGATATGAAATG
1 CATGGTTGAAAGATACCATGGCAACCTGATATGAAATG
23724658 CATGGTTGAAAGATACCATGGCAACCTGATATGAAATG
1 CATGGTTGAAAGATACCATGGCAACCTGATATGAAATG
23724696 TGTAAGACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (38 bp):
CATGGTTGAAAGATACCATGGCAACCTGATATGAAATG
Found at i:23724863 original size:138 final size:130
Alignment explanation
Indices: 23724604--23724864 Score: 335
Period size: 138 Copynumber: 1.9 Consensus size: 130
23724594 GCTCTCTGAA
* * * *
23724604 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGCATGGTTGAAA
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACCGGAAATGAAAAGCATGGTTGAAA
* * * * * *
23724669 GATACCATGGCAACCTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAAGGTGAC
66 GATACCATGACAACATGACATGAAACGAGTAAAACCATAGTTGAAAGATACCATGGCAAGGTGAC
23724734 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGACGGGAAATGAATAAGACTAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC----C-GGAAATGAA-AAG-C-AT
*
23724799 GGTTGAAAGATACCATGACAACATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATACTATGG
58 GGTTGAAAGATACCATGACAACATGACATG-AAACGAGTAAAACCATAGTTGAAAGATACCATGG
23724863 CA
122 CA
23724865 TCATGTCGAA
Statistics
Matches: 111, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
130 40 0.36
134 1 0.01
135 7 0.06
136 2 0.02
137 2 0.02
138 59 0.53
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (130 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACCGGAAATGAAAAGCATGGTTGAAA
GATACCATGACAACATGACATGAAACGAGTAAAACCATAGTTGAAAGATACCATGGCAAGGTGAC
Found at i:23729674 original size:46 final size:45
Alignment explanation
Indices: 23729624--23729797 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
23729614 TGTTTGGGCA
23729624 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
23729670 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * *
23729717 TCCGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
23729763 CCCGAGCTCGTTGAGTTGAATCCGAGTTCACTTAT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT
23729798 CGGCGGGTTA
Statistics
Matches: 105, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 65 0.62
47 31 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:23729779 original size:93 final size:93
Alignment explanation
Indices: 23729620--23729791 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
23729610 AGGATGTTTG
* * * *
23729620 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
*
23729685 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAATCCGAGTTCGAGAGATGTAACTA
* *
23729713 GGCATCCGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
23729778 TTGAATCCGAGTTC
66 TTGAATCCGAGTTC
23729792 ACTTATCGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
TTGAATCCGAGTTCGAGAGATGTAACTA
Found at i:23732290 original size:20 final size:20
Alignment explanation
Indices: 23732265--23732305 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
23732255 ATTCACATAT
23732265 ACATATAATAACTCATTCTC
1 ACATATAATAACTCATTCTC
23732285 ACATATAATAACTCATTCTC
1 ACATATAATAACTCATTCTC
23732305 A
1 A
23732306 TACTTATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (20 bp):
ACATATAATAACTCATTCTC
Found at i:23732590 original size:42 final size:42
Alignment explanation
Indices: 23732477--23732594 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 42
23732467 TGGAAAGTTC
* * *
23732477 ATACAATGCCAACGTCCTAGACATGGTCTTACATGTAATCAA
1 ATACGATGCCAACGTCCCAGACATGGTCTTACATGAAATCAA
* * *
23732519 ATACCGATGCC-TCTGTCCCAGGCAAGGTCTTACATGAAATCAA
1 ATA-CGATGCCAAC-GTCCCAGACATGGTCTTACATGAAATCAA
*
23732562 ATACGATGCCAACGTCCCAGACGTGGTCTTACA
1 ATACGATGCCAACGTCCCAGACATGGTCTTACA
23732595 CGATAACACA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
42 28 0.44
43 35 0.56
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (42 bp):
ATACGATGCCAACGTCCCAGACATGGTCTTACATGAAATCAA
Done.