Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 128 of 186
Found at i:42390883 original size:5 final size:5
Alignment explanation
Indices: 42390797--42390863 Score: 63
Period size: 5 Copynumber: 14.0 Consensus size: 5
42390787 ATCACCCTAT
* *
42390797 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTA TTATT- TATTA TATT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA
42390845 TTTT- TTATT- TTTTA TTTTA
1 TTTTA TT-TTA TTTTA TTTTA
42390864 CTAACTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
4 13 0.24
5 39 0.72
6 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:42390918 original size:6 final size:6
Alignment explanation
Indices: 42390909--42390940 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
42390899 ATATTTCAAA
42390909 TTAATT TTAATT TTAATT TTAATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TT
42390941 TTTTGCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTAATT
Found at i:42393731 original size:24 final size:24
Alignment explanation
Indices: 42393699--42393747 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42393689 TGTCTCTCTC
42393699 ATTGGTTTATTCGATTATTTTCTT
1 ATTGGTTTATTCGATTATTTTCTT
42393723 ATTGGTTTATTCGATTATTTTCTT
1 ATTGGTTTATTCGATTATTTTCTT
42393747 A
1 A
42393748 CTTTATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.08, G:0.12, T:0.61
Consensus pattern (24 bp):
ATTGGTTTATTCGATTATTTTCTT
Found at i:42398425 original size:24 final size:23
Alignment explanation
Indices: 42398371--42398426 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
42398361 ATTTTCAATT
*
42398371 TTTTAA-ATTATAATTATTTTAA
1 TTTTAATATAATAATTATTTTAA
*
42398393 TTTTAAATATAATAATTTATTTTAC
1 TTTT-AATATAATAA-TTATTTTAA
42398418 TTTTAATAT
1 TTTTAATAT
42398427 TTGATAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.14
23 2 0.07
24 11 0.38
25 12 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTAATATAATAATTATTTTAA
Found at i:42403046 original size:19 final size:19
Alignment explanation
Indices: 42403022--42403062 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
42403012 TATTTTAAAG
*
42403022 TTATTTAAGTAGATATATC
1 TTATTTAAGTAGATAAATC
*
42403041 TTATTTAGGTAGATAAATC
1 TTATTTAAGTAGATAAATC
42403060 TTA
1 TTA
42403063 GAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (19 bp):
TTATTTAAGTAGATAAATC
Found at i:42403146 original size:41 final size:41
Alignment explanation
Indices: 42403099--42403180 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
42403089 ATATTTTATT
*
42403099 TTATCTTTTAGTAGTTGATTAGAATAAGTGAATTATTTTCC
1 TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
*
42403140 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
1 TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
42403181 AAATTAGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
Found at i:42411985 original size:11 final size:11
Alignment explanation
Indices: 42411969--42411999 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42411959 GAAAATTTAA
42411969 TTAATTAATAT
1 TTAATTAATAT
*
42411980 TTAATTAAAAT
1 TTAATTAATAT
42411991 TTAATTAAT
1 TTAATTAAT
42412000 TTACTTGGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTAATTAATAT
Found at i:42422830 original size:5 final size:5
Alignment explanation
Indices: 42422822--42422849 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
42422812 TTTAAATGGT
42422822 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
42422850 TTATAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:42423929 original size:4 final size:4
Alignment explanation
Indices: 42423920--42423949 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
42423910 TACTTTAATC
42423920 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
42423950 ATTTTAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:42427623 original size:40 final size:40
Alignment explanation
Indices: 42427568--42427685 Score: 191
Period size: 40 Copynumber: 3.0 Consensus size: 40
42427558 GAAAAAAAAA
42427568 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
*
42427608 TATAACCGGTTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* * * *
42427648 TTTAACCGGGTTAAGTCCCAAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
42427686 GTTACATCCG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:42431651 original size:42 final size:42
Alignment explanation
Indices: 42431592--42431673 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
42431582 TTGGGCTCAC
42431592 TAATGCCCCTGCGGTATTTATGGATTTGATGAATCGAATCAG
1 TAATGCCCCTGCGGTATTTATGGATTTGATGAATCGAATCAG
42431634 TAATGCCCCTGCGGTATTTATGGATTTGATGAATCGAATC
1 TAATGCCCCTGCGGTATTTATGGATTTGATGAATCGAATC
42431674 TTCATACCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (42 bp):
TAATGCCCCTGCGGTATTTATGGATTTGATGAATCGAATCAG
Found at i:42435964 original size:40 final size:40
Alignment explanation
Indices: 42435909--42436016 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
42435899 AAAAAAAAAA
42435909 TATAACCGGGTTAAGTCCCGAAGGCATTCGTACGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTACGGGTTAT
* *
42435949 TATAATCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTACGGGTTAT
*
42435989 TTTAACCGGGTTAAGTCCCGAAGGCATT
1 TATAACCGGGTTAAGTCCCGAAGGCATT
42436017 TGTGCTGGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTACGGGTTAT
Found at i:42436716 original size:22 final size:21
Alignment explanation
Indices: 42436689--42436731 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42436679 TCTTTTATGT
42436689 TTTTGGGCTAGGGTTTGTTTTG
1 TTTTGGGCTA-GGTTTGTTTTG
* *
42436711 TTTTGGGTTAGTTTTGTTTTG
1 TTTTGGGCTAGGTTTGTTTTG
42436732 GCCATATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.05, C:0.02, G:0.33, T:0.60
Consensus pattern (21 bp):
TTTTGGGCTAGGTTTGTTTTG
Found at i:42436724 original size:16 final size:16
Alignment explanation
Indices: 42436699--42436732 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42436689 TTTTGGGCTA
*
42436699 GGGTTTGTTTTGTTTT
1 GGGTTAGTTTTGTTTT
42436715 GGGTTAGTTTTGTTTT
1 GGGTTAGTTTTGTTTT
42436731 GG
1 GG
42436733 CCATATTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.00, G:0.35, T:0.62
Consensus pattern (16 bp):
GGGTTAGTTTTGTTTT
Found at i:42439197 original size:17 final size:17
Alignment explanation
Indices: 42439175--42439231 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
42439165 TTATTAGACA
*
42439175 ATTTATAATTTTTATTT
1 ATTTATAAATTTTATTT
** *
42439192 ATTTATAAAAGTTATAT
1 ATTTATAAATTTTATTT
42439209 ATATTATAAATTTTATATT
1 AT-TTATAAATTTTAT-TT
42439228 ATTT
1 ATTT
42439232 TTACTTATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 15 0.48
18 13 0.42
19 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTATAAATTTTATTT
Found at i:42442288 original size:17 final size:17
Alignment explanation
Indices: 42442266--42442298 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42442256 CCAATAATGG
42442266 TACCTAACCATAAAAGT
1 TACCTAACCATAAAAGT
42442283 TACCTAACCATAAAAG
1 TACCTAACCATAAAAG
42442299 ACACTAATTT
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:0.48, C:0.24, G:0.06, T:0.21
Consensus pattern (17 bp):
TACCTAACCATAAAAGT
Found at i:42442944 original size:36 final size:38
Alignment explanation
Indices: 42442881--42442955 Score: 136
Period size: 36 Copynumber: 2.0 Consensus size: 38
42442871 TAACCACAAC
42442881 AATTGCATAACATTTATATATATATAAAATATTATAAT
1 AATTGCATAACATTTATATATATATAAAATATTATAAT
42442919 AATTGCATAACA-TT-TATATATATAAAATATTATAAT
1 AATTGCATAACATTTATATATATATAAAATATTATAAT
42442955 A
1 A
42442956 TTTTACTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 23 0.62
37 2 0.05
38 12 0.32
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (38 bp):
AATTGCATAACATTTATATATATATAAAATATTATAAT
Found at i:42444549 original size:56 final size:56
Alignment explanation
Indices: 42444419--42444551 Score: 212
Period size: 56 Copynumber: 2.4 Consensus size: 56
42444409 CCTAGATAGG
* **
42444419 GTCTTACTCGTACACATAAATCAGAATCACATATCGATGCCAACGTATTAAACGTG
1 GTCTTACTCGTACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGCA
* *
42444475 GTCTTACTCGTACTCATATATCAGAATCACATATCGATGTCAACGTATTAAACGCA
1 GTCTTACTCGTACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGCA
*
42444531 GTCTTACTCGCACACATATAT
1 GTCTTACTCGTACACATATAT
42444552 TGATGCCATG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 70 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (56 bp):
GTCTTACTCGTACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGCA
Found at i:42447415 original size:40 final size:40
Alignment explanation
Indices: 42447360--42447584 Score: 317
Period size: 40 Copynumber: 5.6 Consensus size: 40
42447350 TATTCGGATG
*
42447360 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
42447400 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
42447440 ACATCCGGGCGAAGTCCCGAAGGCATTTGTGCAAGTAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTACT
* *
42447483 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
42447523 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
42447563 ATATCC-GGCTAAATCCCTAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
42447585 TACTTGGGTT
Statistics
Matches: 164, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
39 13 0.08
40 115 0.70
43 36 0.22
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:42447503 original size:83 final size:80
Alignment explanation
Indices: 42447362--42447584 Score: 349
Period size: 83 Copynumber: 2.8 Consensus size: 80
42447352 TTCGGATGAT
*
42447362 ATCCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATT
42447427 TGTGCTAGTGACTAC
66 TGTGCTAGTGACTAC
*
42447442 ATCCGGGCGAAGTCCCGAAGGCATTTGTGCAAGTAGTTACTATATCCGGGCTAAGTCCCGAAGGC
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTACTATATCCGGGCTAAGTCCCGAAGGC
*
42447507 ATTTGTGCTAGTGACTAT
63 ATTTGTGCTAGTGACTAC
* * * *
42447525 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCTAAGG
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGG
42447585 TACTTGGGTT
Statistics
Matches: 132, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
79 14 0.11
80 40 0.30
81 1 0.01
82 1 0.01
83 76 0.58
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATT
TGTGCTAGTGACTAC
Found at i:42450320 original size:20 final size:20
Alignment explanation
Indices: 42450294--42450341 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
42450284 AACAAGGGTC
42450294 ACACGCCCGTGTGGTTTGGG
1 ACACGCCCGTGTGGTTTGGG
*
42450314 TCACGCCCGTGTGGTTTGGG
1 ACACGCCCGTGTGGTTTGGG
42450334 ACACGCCC
1 ACACGCCC
42450342 TTGTCCCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.10, C:0.31, G:0.35, T:0.23
Consensus pattern (20 bp):
ACACGCCCGTGTGGTTTGGG
Found at i:42456874 original size:48 final size:48
Alignment explanation
Indices: 42456803--42457134 Score: 396
Period size: 48 Copynumber: 6.9 Consensus size: 48
42456793 GACATTTAGG
* * * *
42456803 TGATATGTGTGCCAGTGTAAGACCATGTCTGAGACATGGCATTGGCAT
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* * *
42456851 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATTGTCAT
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* * * * *
42456899 TGATATGTGCGCTAGTGTAAGACCATGTCTTGGAAATTGCGTCGGCCA-
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CAT
* * * * *
42456947 CGATATGAGAGCCAGTGTAAGACCATTTCTGGGACATGGCATCGACAT
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
**
42456995 TGATATGTGTCCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
** * * *
42457043 TGAGCTGAGAGCTAGTGTAAGAGCATGTCTGGGACATGGCATCGGCCT
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* * * *
42457091 CGACATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCG
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
42457135 ACAATTCACC
Statistics
Matches: 241, Mismatches: 41, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
47 2 0.01
48 237 0.98
49 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (48 bp):
TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
Found at i:42457064 original size:144 final size:144
Alignment explanation
Indices: 42456804--42457137 Score: 479
Period size: 144 Copynumber: 2.3 Consensus size: 144
42456794 ACATTTAGGT
* * * * *
42456804 GATATGTGTGCCAGTGTAAGACCATGTCTGAGACATGGCATTGGCATTGATATGTGTGCTAGTGT
1 GATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGTGTCCTAGTGT
* * * * * *
42456869 AAGACCATGTCTGGGACATGGCATTGTCATTGATATGTGCGCTAGTGTAAGACCATGTCTTGGAA
66 AAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACCATGTCTGGGAA
* *
42456934 ATTGCGTCGGCCAC
131 ATGGCATCGGCCAC
* *
42456948 GATATGAGAGCCAGTGTAAGACCATTTCTGGGACATGGCATCGACATTGATATGTGTCCTAGTGT
1 GATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGTGTCCTAGTGT
* * *
42457013 AAGACCATGTCTGGGACATGGCATCGGCATTGAGCTGAGAGCTAGTGTAAGAGCATGTCTGGGAC
66 AAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACCATGTCTGGGAA
*
42457078 ATGGCATCGGCCTC
131 ATGGCATCGGCCAC
* *
42457092 GACATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGACA
1 GATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACA
42457138 ATTCACCCTC
Statistics
Matches: 167, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
144 167 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (144 bp):
GATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGTGTCCTAGTGT
AAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACCATGTCTGGGAA
ATGGCATCGGCCAC
Found at i:42457804 original size:21 final size:21
Alignment explanation
Indices: 42457778--42457829 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
42457768 CCAATCTCAT
42457778 ACAAAATTTTTCGAAACTTAA
1 ACAAAATTTTTCGAAACTTAA
42457799 ACAAAATTTTTCGAAACTTAA
1 ACAAAATTTTTCGAAACTTAA
42457820 ACAAAATTTT
1 ACAAAATTTT
42457830 CAAAGTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (21 bp):
ACAAAATTTTTCGAAACTTAA
Found at i:42459098 original size:42 final size:42
Alignment explanation
Indices: 42459021--42459151 Score: 167
Period size: 44 Copynumber: 3.0 Consensus size: 42
42459011 TCTTACATGT
* *
42459021 AATCAAATATCGATG-CCACTGTCCCAAACAGGGTCTTAAACGA
1 AATCAAATAT-GATGCCCAC-GTCCCAGACATGGTCTTAAACGA
42459064 AATCAAATATGATGCCCACGTCCCAGACATGGTCTTAAACGTA
1 AATCAAATATGATGCCCACGTCCCAGACATGGTCTTAAACG-A
* *
42459107 AATCATAAGT-TGATGCCAACGTCCCAGACATGGTCTTACACGA
1 AATCA-AA-TATGATGCCCACGTCCCAGACATGGTCTTAAACGA
42459150 AA
1 AA
42459152 ACACATATCG
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
42 24 0.30
43 23 0.29
44 32 0.40
45 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (42 bp):
AATCAAATATGATGCCCACGTCCCAGACATGGTCTTAAACGA
Found at i:42459130 original size:44 final size:43
Alignment explanation
Indices: 42458990--42459144 Score: 174
Period size: 43 Copynumber: 3.6 Consensus size: 43
42458980 AGCTTGTACA
* ** * *
42458990 ATGCCAACGTCCAAGATGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTAAACGTAAATCAAATAT-G
* *
42459033 ATGCC-ACTGTCCCAAACAGGGTCTTAAACG-AAATCAAATATG
1 ATGCCAAC-GTCCCAGACATGGTCTTAAACGTAAATCAAATATG
*
42459075 ATGCCCACGTCCCAGACATGGTCTTAAACGTAAATCATAAGT-TG
1 ATGCCAACGTCCCAGACATGGTCTTAAACGTAAATCA-AA-TATG
42459119 ATGCCAACGTCCCAGACATGGTCTTA
1 ATGCCAACGTCCCAGACATGGTCTTA
42459145 CACGAAAACA
Statistics
Matches: 96, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
42 28 0.29
43 38 0.40
44 29 0.30
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTAAACGTAAATCAAATATG
Found at i:42462194 original size:68 final size:67
Alignment explanation
Indices: 42461987--42462198 Score: 186
Period size: 68 Copynumber: 3.1 Consensus size: 67
42461977 ATATAATTCG
* * * *
42461987 GCTCTCTTGTCTACATGGTGA-ACA-CTTAGTACCACCCATGTGACCTAGC--CAATTTATCTCA
1 GCTCTCTTGTCTACATGGTGATACATCTTAGTATCACACATGTGACCTAGCTACAATATATCTCG
42462048 TA
66 TA
* * * * * * *
42462050 GCTCTCTTGTCTACATGGTG-TCCTTCACTTGGAATCACACATGCGACCTAGCTACATTTATCTC
1 GCTCTCTTGTCTACATGGTGATACAT--CTTAGTATCACACATGTGACCTAGCTACA-ATATATC
42462114 TCCCGTA
63 T--CGTA
* *
42462121 TCTCTCTTGTCTACATGG-GATACATC-TCGTATCACACATGTGACCTAGCTACTACATAGTATC
1 GCTCTCTTGTCTACATGGTGATACATCTTAGTATCACACATGTGACCTAGCTAC-A-ATA-TATC
42462184 TCGTA
63 TCGTA
42462189 GCTCTCTTGT
1 GCTCTCTTGT
42462199 ACACATGATG
Statistics
Matches: 116, Mismatches: 21, Indels: 19
0.74 0.13 0.12
Matches are distributed among these distances:
63 21 0.18
66 20 0.17
68 38 0.33
69 9 0.08
70 5 0.04
71 23 0.20
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (67 bp):
GCTCTCTTGTCTACATGGTGATACATCTTAGTATCACACATGTGACCTAGCTACAATATATCTCG
TA
Found at i:42470795 original size:94 final size:94
Alignment explanation
Indices: 42470633--42471102 Score: 841
Period size: 94 Copynumber: 5.0 Consensus size: 94
42470623 AATGTGACCG
* *
42470633 TATATGCTATTTGAATTAAGTAAGTTGCCATATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
42470698 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
* * *
42470727 GATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAATTAACATTCGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
42470792 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
42470821 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
42470886 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
* *
42470915 TATATGCTATTTGAATTAAGTCAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGTG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
42470980 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
*
42471009 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGGGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
* **
42471074 GAATTAAATGGCACGATGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
42471103 GAATGTCGAT
Statistics
Matches: 360, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 360 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (94 bp):
TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
GAATTAAATGTCACTTTGTGTGCAGATTT
Found at i:42473082 original size:27 final size:27
Alignment explanation
Indices: 42473052--42473146 Score: 95
Period size: 27 Copynumber: 3.5 Consensus size: 27
42473042 ATATTGAGCC
*
42473052 CGCACACTCAGTGCTAT-ATAATCAACT
1 CGCACACTTAGTGC-ATCATAATCAACT
* **
42473079 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCATCATAATCAACT
* **
42473106 CGCACACTTAGTGCAACATAGCCGAA-T
1 CGCACACTTAGTGCATCATAATC-AACT
42473133 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42473147 TGTACAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.03
27 55 0.95
28 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCATCATAATCAACT
Found at i:42477711 original size:51 final size:51
Alignment explanation
Indices: 42477651--42477752 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
42477641 CAATAGTAGG
*
42477651 CTGAGTCTCGCAACAAAGATACAGCACATTTTAGACATTCGTCGGGTGTGC
1 CTGAGTCTCGCAACAAAGATACAGCACATTTTAGACATTCATCGGGTGTGC
42477702 CTGAGTCTCGCAACAAAGATACAGCACATTTTAGACATTCATCGGGTGTGC
1 CTGAGTCTCGCAACAAAGATACAGCACATTTTAGACATTCATCGGGTGTGC
42477753 ATGACAATTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (51 bp):
CTGAGTCTCGCAACAAAGATACAGCACATTTTAGACATTCATCGGGTGTGC
Found at i:42478133 original size:34 final size:34
Alignment explanation
Indices: 42478090--42478158 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
42478080 GAGCAGCCGC
42478090 TACGCTCTCAACGTCATCCGCTAGGGTTCTCTCT
1 TACGCTCTCAACGTCATCCGCTAGGGTTCTCTCT
*
42478124 TACGCTCTCAACGTCATCCGCTAGGGTTCTTTCT
1 TACGCTCTCAACGTCATCCGCTAGGGTTCTCTCT
42478158 T
1 T
42478159 CACCGGGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.14, C:0.33, G:0.17, T:0.35
Consensus pattern (34 bp):
TACGCTCTCAACGTCATCCGCTAGGGTTCTCTCT
Found at i:42479692 original size:27 final size:27
Alignment explanation
Indices: 42479662--42479756 Score: 95
Period size: 27 Copynumber: 3.5 Consensus size: 27
42479652 ATATCGAGTC
*
42479662 CGCACACTCAGTGCTAT-ATAATCAACT
1 CGCACACTTAGTGC-ATCATAATCAACT
* **
42479689 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCATCATAATCAACT
* **
42479716 CGCACACTTAGTGCAACATAGCCGAA-T
1 CGCACACTTAGTGCATCATAATC-AACT
42479743 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42479757 TGTACAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.03
27 55 0.95
28 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCATCATAATCAACT
Found at i:42490209 original size:46 final size:46
Alignment explanation
Indices: 42490063--42490212 Score: 169
Period size: 46 Copynumber: 3.2 Consensus size: 46
42490053 TCACTTATGT
* *
42490063 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGA
* * * * *
42490109 GAGCCAGTGTAAGATCATGTATGGGACATGGCATCGGCATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGA
* *
42490157 GTGCTAGTGTAAGACACGTCTGGGACATGCATCGGCCTCGAGATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-A
42490204 -AGCTAGTGT
1 GAGCTAGTGT
42490213 CCCTATTAGA
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
46 35 0.41
47 26 0.31
48 23 0.27
49 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
Found at i:42491219 original size:46 final size:47
Alignment explanation
Indices: 42491158--42491385 Score: 191
Period size: 46 Copynumber: 4.9 Consensus size: 47
42491148 TTTGGGTCAC
*
42491158 TTATGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A
1 TTATGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGA
* * *
42491204 TTATGAGAGCCAGTGTAAGATCATGTATGGGACATGGCATCGG-CATTGA
1 TTATGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CGA
* * * * *
42491253 -GACGAGTGCTAGTGTAAGACACGTCTGGGACATGCATCGGCCTCGA
1 TTATGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGA
* * * * *
42491299 -GATGTA-AGCTAGTGTAAGAAAGGTCTGGGACATGCATCAGCTACGA
1 TTATG-AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGA
* **
42491345 -GATGATTG-TCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 TTATGAGAGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCG
42491386 ACTTGAGATG
Statistics
Matches: 149, Mismatches: 23, Indels: 18
0.78 0.12 0.09
Matches are distributed among these distances:
45 2 0.01
46 78 0.52
47 41 0.28
48 27 0.18
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (47 bp):
TTATGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGA
Found at i:42491384 original size:94 final size:94
Alignment explanation
Indices: 42491166--42491385 Score: 245
Period size: 94 Copynumber: 2.3 Consensus size: 94
42491156 ACTTATGTGA
* * *
42491166 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGATCATGTA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGATAAGGTA
* *
42491231 TGGGACATGGCATCGGCATTGAGACGAGT
66 TGGGACATGGCATCAGCATCGAGACGAGT
* * *
42491260 GCTAGTGTAAGACACGTCTGGGACATGCATCGGCCTCGA-GATGTA-AGCTAGTGTAAGA-AAGG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATG-AGAGCCAGTGTAAGATAAGG
* * *
42491322 TCTGGGACAT-GCATCAGC-TACGAGATGATT
64 TATGGGACATGGCATCAGCAT-CGAGACGAGT
42491352 G-TCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCG
42491386 ACTTGAGATG
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
91 2 0.02
92 24 0.22
93 24 0.22
94 56 0.52
95 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGATAAGGTA
TGGGACATGGCATCAGCATCGAGACGAGT
Found at i:42491419 original size:140 final size:141
Alignment explanation
Indices: 42491160--42491434 Score: 331
Period size: 140 Copynumber: 2.0 Consensus size: 141
42491150 TGGGTCACTT
* * * * * *
42491160 ATGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAT
1 ATGTAAGCTAGTGTAAGAAAGGTCTGGGACATGCATCAGCCACATGATGAGAGCCAGTGTAAGAC
* * * *
42491225 CATGTATGGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACACGTCTGGGACAT-GCA
66 CATGTATGGGACATGGCATCGACATTGAGACGAGAGCCAATGTAAGACACGTCTGGGACATGGCA
42491289 TCGGCCTCGAG
131 TCGGCCTCGAG
* ** *
42491300 ATGTAAGCTAGTGTAAGAAAGGTCTGGGACATGCATCAGCTACGA-GATGATTGTCAGTGTAAGA
1 ATGTAAGCTAGTGTAAGAAAGGTCTGGGACATGCATCAGCCAC-ATGATGAGAGCCAGTGTAAGA
* * * * **
42491364 CCATGTCTGGGACATGGCATCGAC-TTGAGATGTGAGCCAATGTAGGACTGTGTCTGGGACATGG
65 CCATGTATGGGACATGGCATCGACATTGAGACGAGAGCCAATGTAAGAC-ACGTCTGGGACATGG
42491428 CATCGGC
129 CATCGGC
42491435 ACCTTACCCA
Statistics
Matches: 112, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
139 18 0.16
140 85 0.76
141 9 0.08
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (141 bp):
ATGTAAGCTAGTGTAAGAAAGGTCTGGGACATGCATCAGCCACATGATGAGAGCCAGTGTAAGAC
CATGTATGGGACATGGCATCGACATTGAGACGAGAGCCAATGTAAGACACGTCTGGGACATGGCA
TCGGCCTCGAG
Found at i:42494707 original size:46 final size:46
Alignment explanation
Indices: 42494627--42494794 Score: 137
Period size: 47 Copynumber: 3.6 Consensus size: 46
42494617 AAGTTGGTGC
*
42494627 CATGTCCCAAACATGGTCTTACACT-G-ACTATCGTCTCGTAGCCGATA
1 CATGTCCCAGACAT-GTCTTACACTAGCAC--TCGTCTCGTAGCCGATA
* * *
42494674 CATGTCCCAGACGTGTCTTACACTAGCACTCGTCTCAATA-CCGATGC
1 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTC-GTAGCCGAT-A
* * * * * * * *
42494721 CATGTCCCATACATGATATTACACTGGCTCTCATAAT-GTGGCCGATG
1 CATGTCCCAGACATG-TCTTACACTAGCACTCGT-CTCGTAGCCGATA
42494768 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
42494795 TCACATAAGT
Statistics
Matches: 97, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
46 32 0.33
47 43 0.44
48 21 0.22
49 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGTAGCCGATA
Found at i:42494735 original size:94 final size:94
Alignment explanation
Indices: 42494624--42494794 Score: 236
Period size: 94 Copynumber: 1.8 Consensus size: 94
42494614 CTCAAGTTGG
* * * * *
42494624 TGCCATGTCCCAAACATGGTCTTACACTGACTATCGT-CTCGTAGCCGATACATGTCCCAGACGT
1 TGCCATGTCCCAAACATGATATTACACTGACTATCATAAT-GTAGCCGATACATGTCCCAGACAT
42494688 GTCTTACACTAGCACTCGTCTCAATACCGA
65 GTCTTACACTAGCACTCGTCTCAATACCGA
* * * * *
42494718 TGCCATGTCCCATACATGATATTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATG
1 TGCCATGTCCCAAACATGATATTACACTGACTATCATAATGTAGCCGATACATGTCCCAGACATG
42494783 TCTTACACTAGC
66 TCTTACACTAGC
42494795 TCACATAAGT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
94 65 0.98
95 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (94 bp):
TGCCATGTCCCAAACATGATATTACACTGACTATCATAATGTAGCCGATACATGTCCCAGACATG
TCTTACACTAGCACTCGTCTCAATACCGA
Found at i:42498097 original size:18 final size:18
Alignment explanation
Indices: 42498074--42498109 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42498064 CATATTGACT
42498074 TACTAAGCGTAAAGCTTA
1 TACTAAGCGTAAAGCTTA
42498092 TACTAAGCGTAAAGCTTA
1 TACTAAGCGTAAAGCTTA
42498110 CTCCCCCTTC
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:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (18 bp):
TACTAAGCGTAAAGCTTA
Found at i:42501476 original size:14 final size:15
Alignment explanation
Indices: 42501457--42501485 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42501447 AAAGTTCATA
42501457 TGGATT-TTCTTGTC
1 TGGATTATTCTTGTC
42501471 TGGATTATTCTTGTC
1 TGGATTATTCTTGTC
42501486 CTTGAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.10, C:0.14, G:0.21, T:0.55
Consensus pattern (15 bp):
TGGATTATTCTTGTC
Found at i:42503614 original size:210 final size:210
Alignment explanation
Indices: 42503252--42503671 Score: 840
Period size: 210 Copynumber: 2.0 Consensus size: 210
42503242 ATTTCATGGA
42503252 CTAATGTCTAAATAAACATGGAAATGTGTTGAATTGGATGTACATTGCATTATCAGCTATGCATA
1 CTAATGTCTAAATAAACATGGAAATGTGTTGAATTGGATGTACATTGCATTATCAGCTATGCATA
42503317 ATGAGATACTTGATGAAAAGAGAAAAATTCCGGTTGAATAAAATGGGAAATTCGATGGATAAACC
66 ATGAGATACTTGATGAAAAGAGAAAAATTCCGGTTGAATAAAATGGGAAATTCGATGGATAAACC
42503382 ATGGCTTACATGACTTGAGATCCTGCATGTGCTGCAGCTGCAGAAAAGGATTTCGCCCCGATGGG
131 ATGGCTTACATGACTTGAGATCCTGCATGTGCTGCAGCTGCAGAAAAGGATTTCGCCCCGATGGG
42503447 TAATCTGTTGATCAC
196 TAATCTGTTGATCAC
42503462 CTAATGTCTAAATAAACATGGAAATGTGTTGAATTGGATGTACATTGCATTATCAGCTATGCATA
1 CTAATGTCTAAATAAACATGGAAATGTGTTGAATTGGATGTACATTGCATTATCAGCTATGCATA
42503527 ATGAGATACTTGATGAAAAGAGAAAAATTCCGGTTGAATAAAATGGGAAATTCGATGGATAAACC
66 ATGAGATACTTGATGAAAAGAGAAAAATTCCGGTTGAATAAAATGGGAAATTCGATGGATAAACC
42503592 ATGGCTTACATGACTTGAGATCCTGCATGTGCTGCAGCTGCAGAAAAGGATTTCGCCCCGATGGG
131 ATGGCTTACATGACTTGAGATCCTGCATGTGCTGCAGCTGCAGAAAAGGATTTCGCCCCGATGGG
42503657 TAATCTGTTGATCAC
196 TAATCTGTTGATCAC
42503672 AAATGTAGAA
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 210 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (210 bp):
CTAATGTCTAAATAAACATGGAAATGTGTTGAATTGGATGTACATTGCATTATCAGCTATGCATA
ATGAGATACTTGATGAAAAGAGAAAAATTCCGGTTGAATAAAATGGGAAATTCGATGGATAAACC
ATGGCTTACATGACTTGAGATCCTGCATGTGCTGCAGCTGCAGAAAAGGATTTCGCCCCGATGGG
TAATCTGTTGATCAC
Found at i:42508632 original size:32 final size:32
Alignment explanation
Indices: 42508591--42508657 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
42508581 GCGCGCGAGC
42508591 GCCCGTGTGGGAGCTTTGAGGTGATGGTTGAG
1 GCCCGTGTGGGAGCTTTGAGGTGATGGTTGAG
42508623 GCCCGTGTGGGAGCTTTGAGGTGATGGTTGAG
1 GCCCGTGTGGGAGCTTTGAGGTGATGGTTGAG
42508655 GCC
1 GCC
42508658 ATCATGAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.12, C:0.15, G:0.46, T:0.27
Consensus pattern (32 bp):
GCCCGTGTGGGAGCTTTGAGGTGATGGTTGAG
Found at i:42508876 original size:27 final size:27
Alignment explanation
Indices: 42508795--42509223 Score: 296
Period size: 27 Copynumber: 15.9 Consensus size: 27
42508785 GTAGGCTAGT
* * *
42508795 ATTACTGAAATACCCCTTTA-TGGTAAA
1 ATTACCGAAATA-CCCTTGATTTGTAAA
* * **
42508822 ATTACTGAAATGCCCTTG-TAGGGTAAA
1 ATTACCGAAATACCCTTGAT-TTGTAAA
* * * *
42508849 ACTACTGAAATACCCTTGGTTTGCAAA
1 ATTACCGAAATACCCTTGATTTGTAAA
* * **
42508876 ATTACTG-AATACCCTTGGTTTACAAA
1 ATTACCGAAATACCCTTGATTTGTAAA
* * * *
42508902 ATTACCAAAATACCCTCGATTAGAAAA
1 ATTACCGAAATACCCTTGATTTGTAAA
* *
42508929 ATTACCAAAATACCCCT-AGTTTGTAAA
1 ATTACCGAAATACCCTTGA-TTTGTAAA
* * *
42508956 ATTACCAAAATACCCCTGATTTGTGAA
1 ATTACCGAAATACCCTTGATTTGTAAA
* * * ** *
42508983 ATTACTGAAATACTCTCGACCTATAAA
1 ATTACCGAAATACCCTTGATTTGTAAA
* *
42509010 ATTACCGAAATACCCTCGACTTGTAAA
1 ATTACCGAAATACCCTTGATTTGTAAA
* * *
42509037 ATTAACAAAATACCCTCGATTTGTAAA
1 ATTACCGAAATACCCTTGATTTGTAAA
*
42509064 ATTACCAAAATACCC-TGATTTG-AAA
1 ATTACCGAAATACCCTTGATTTGTAAA
*
42509089 AGTTACCGAAATACCCTTGATTTGGAAA
1 A-TTACCGAAATACCCTTGATTTGTAAA
* * * **
42509117 ATTACAGAAATACCCCTAATTTACAAA
1 ATTACCGAAATACCCTTGATTTGTAAA
*
42509144 ATTACAGAAATACCCTTGACTTT-TAAAA
1 ATTACCGAAATACCCTTGA-TTTGT-AAA
** * * *
42509172 ATTATAGAAATACCATTGGTTTGCAAA
1 ATTACCGAAATACCCTTGATTTGTAAA
* * *
42509199 ACTACCGAAATACCATTGGTTTGTA
1 ATTACCGAAATACCCTTGATTTGTA
42509224 GATTTGCCAA
Statistics
Matches: 333, Mismatches: 57, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
25 4 0.01
26 48 0.14
27 253 0.76
28 28 0.08
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (27 bp):
ATTACCGAAATACCCTTGATTTGTAAA
Found at i:42509513 original size:41 final size:41
Alignment explanation
Indices: 42509468--42509630 Score: 263
Period size: 41 Copynumber: 4.0 Consensus size: 41
42509458 GGAGGAAGAA
* * *
42509468 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACTG
1 ATTGAGGATAGAATGGTTGCTTGACGACCGTGGATCCACCG
42509509 ATTGAGGATAGAATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATAGAATGGTTGCTTGACGACCGTGGATCCACCG
42509550 ATTGAGGATAGAATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATAGAATGGTTGCTTGACGACCGTGGATCCACCG
* * * *
42509591 ATTAAGGATTGCATGGTTGCTTGACGAACGTGGATCCACC
1 ATTGAGGATAGAATGGTTGCTTGACGACCGTGGATCCACC
42509631 AGTGGCTTTT
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 115 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (41 bp):
ATTGAGGATAGAATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:42509814 original size:22 final size:22
Alignment explanation
Indices: 42509789--42509837 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
42509779 ATGGTTTTAC
*
42509789 GCCAACCT-ACATATGGCTCTGT
1 GCCAACCTGA-ATATGGCTATGT
*
42509811 GCCAACCTGATTATGGCTATGT
1 GCCAACCTGAATATGGCTATGT
42509833 GCCAA
1 GCCAA
42509838 ACGTATTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (22 bp):
GCCAACCTGAATATGGCTATGT
Found at i:42511519 original size:46 final size:46
Alignment explanation
Indices: 42511452--42511713 Score: 339
Period size: 46 Copynumber: 5.7 Consensus size: 46
42511442 AACGCCTGAG
42511452 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
*
42511498 CTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCGAATGTCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
*
42511544 CTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCGAATGTCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
*** * * * * *
42511590 CTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-AC-TAGGCCTCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAATG--TCCGAA
* * * *
42511637 CTCGTTGAGTTGAGTCCGTGTTCACTTATGGATGCGAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
* *
42511683 CTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42511714 GCGGGTTACA
Statistics
Matches: 189, Mismatches: 22, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
45 2 0.01
46 152 0.80
47 33 0.17
48 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
Found at i:42514657 original size:15 final size:15
Alignment explanation
Indices: 42514637--42514692 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
42514627 GTATCTTGGG
42514637 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
42514652 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
42514667 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
42514682 TTTCTTTATTC
1 TTTCTTTATTC
42514693 GGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:42518704 original size:45 final size:45
Alignment explanation
Indices: 42518604--42518730 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
42518594 TTTTCTCAAA
* *
42518604 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
42518646 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
42518690 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
42518731 ATCAAGTCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
42 11 0.15
43 14 0.19
44 8 0.11
45 40 0.54
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:42519113 original size:43 final size:43
Alignment explanation
Indices: 42519060--42519192 Score: 148
Period size: 43 Copynumber: 3.1 Consensus size: 43
42519050 CTGGCATTAC
*
42519060 GCCTACTAGGCACGAAGGCCCGAATACACATCACCGGCA-TGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACT-AA
* * * *
42519103 GCTTGCTAGGCAC-AAAGCGTCGAATACACATCACTGGCACTAA
1 GCCTGCTAGGCACGAAGGC-CCGAATACACATCACCGGCACTAA
* * *
42519146 GCCTGCTAGGCACGAAGGCCCGAATATA-AT-ACCAGCACTAG
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
42519187 GCCTGC
1 GCCTGC
42519193 GGGATTTATC
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 14 0.19
42 6 0.08
43 50 0.67
44 5 0.07
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
Found at i:42519218 original size:38 final size:38
Alignment explanation
Indices: 42519164--42519247 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
42519154 GGCACGAAGG
* * *
42519164 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
42519202 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
42519240 CCCGAATA
1 CCCGAATA
42519248 CACATCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:42531278 original size:54 final size:55
Alignment explanation
Indices: 42531173--42531306 Score: 180
Period size: 54 Copynumber: 2.5 Consensus size: 55
42531163 TGTGCCCTTA
* * * *
42531173 GCCCATGTGCAACACTGACTTTAAAACATGGCCATGACACACGCCCATGTGGCCT
1 GCCCGTGTACAACACTGACTTTAAAACATCGACATGACACACGCCCATGTGGCCT
* * *
42531228 GCCTGTGTACAACATTGACTTTAAAACA-CGACATGACACACGCCCGTGTGGCCT
1 GCCCGTGTACAACACTGACTTTAAAACATCGACATGACACACGCCCATGTGGCCT
* *
42531282 GCCCGTGTTCAGCACTGACTTTAAA
1 GCCCGTGTACAACACTGACTTTAAA
42531307 TTTTAAGTGC
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 44 0.65
55 24 0.35
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (55 bp):
GCCCGTGTACAACACTGACTTTAAAACATCGACATGACACACGCCCATGTGGCCT
Found at i:42532251 original size:47 final size:46
Alignment explanation
Indices: 42532045--42532363 Score: 221
Period size: 47 Copynumber: 6.7 Consensus size: 46
42532035 GGGATATGTT
** *
42532045 GCCGATGCCATGTCCTGGACATGGTCTTACACTGGCTCTCATCATCGAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCATC-TCGAG
* * * * * * * **
42532094 GCTGATCCCATGTCCCAGACATGGTTTTATACTAGCTCTCGTCTATACG
1 GCCGAT-GCATGTCCCAGACAT-GTCTTACACTGGCTATCATCTCGA-G
* * *** * * *
42532143 TGCTGATGCCTGTAAAAGACATGTCTTACACTAGC-A-CAACTCTTA-
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCATCTC-GAG
* * *
42532188 GCTGATGCGTGTCCCAGACACGTCTTACACTGGCTATCATCGTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCATC-TCGAG
* ** * *
42532235 GCCGATGCATGTCCCAGACATGTCTTAGACTGGCGCTCATTCTCTAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCA-TCTCGAG
* * * *
42532282 GCCGATGCCATGTCCCAGGCATGGTCTTACACTGGCTATCATATTGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCATCTCGAG
42532330 GCCGATGCATGTCCCAGACATGTCTTACACTGGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC
42532364 ATACAAGTAA
Statistics
Matches: 212, Mismatches: 47, Indels: 25
0.75 0.17 0.09
Matches are distributed among these distances:
44 28 0.13
45 1 0.00
46 20 0.09
47 60 0.28
48 37 0.17
49 60 0.28
50 6 0.03
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCATCTCGAG
Found at i:42534392 original size:23 final size:23
Alignment explanation
Indices: 42534366--42534409 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42534356 AGGTTCATGA
* *
42534366 GGCTTACTATACAAGGTATAAGT
1 GGCTCACTACACAAGGTATAAGT
*
42534389 GGCTCGCTACACAAGGTATAA
1 GGCTCACTACACAAGGTATAA
42534410 CAATTGCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (23 bp):
GGCTCACTACACAAGGTATAAGT
Found at i:42544887 original size:42 final size:42
Alignment explanation
Indices: 42544828--42544930 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
42544818 AGGGTTACTA
* * * *
42544828 AGACTATGTGCAAGACCATATATGGGATAAGGAATCTATATG
1 AGACTTTGTGTAAGACCATATATGAGATAAGGAATCGATATG
* * *
42544870 AGACTTTGTGTAAGACCATATCTGAGATATGGCATCGATATG
1 AGACTTTGTGTAAGACCATATATGAGATAAGGAATCGATATG
*
42544912 AGA-TTTCATGTAAGACCAT
1 AGACTTT-GTGTAAGACCAT
42544931 TCCTGGGCTA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 3 0.06
42 49 0.94
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (42 bp):
AGACTTTGTGTAAGACCATATATGAGATAAGGAATCGATATG
Found at i:42544958 original size:43 final size:42
Alignment explanation
Indices: 42544878--42544991 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 42
42544868 TGAGACTTTG
* * * **
42544878 TGTAAGACCATATCTGAGATATGGCATCGATATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATTGATACGAGATCCCA
*
42544920 TGTAAGACCAT-TCCTGGGCTATTGGCATTGATACGAGATCCCA
1 TGTAAGACCATAT-CTGGGATA-TGGCATTGATACGAGATCCCA
42544963 TGTAAGACCATATCTGGGATATGGCATTG
1 TGTAAGACCATATCTGGGATATGGCATTG
42544992 GTATGGTACC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.02
42 25 0.40
43 35 0.56
44 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATTGATACGAGATCCCA
Found at i:42554758 original size:37 final size:37
Alignment explanation
Indices: 42554708--42554786 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42554698 TTATTACGAA
* * *
42554708 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
42554745 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
42554782 GTCTT
1 GTCTT
42554787 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:42554974 original size:47 final size:47
Alignment explanation
Indices: 42554905--42555331 Score: 836
Period size: 47 Copynumber: 9.1 Consensus size: 47
42554895 CCCTTCGGGA
* *
42554905 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42554952 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42554999 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42555046 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42555093 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42555140 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42555187 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42555234 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42555281 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42555328 CTTA
1 CTTA
42555332 CTATCATTTC
Statistics
Matches: 378, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 378 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42566687 original size:39 final size:41
Alignment explanation
Indices: 42566636--42566722 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 41
42566626 AATTATATTA
* * * *
42566636 AATAT-AGTAAAATGTTTATTATATTTAT-TAGTGTTTTTT
1 AATATAAGTAAAATATCTATTATATTTATGTAGTATTTGTT
42566675 AATATAAG-AAAATATCTATTATATTTATGGTAGTATTTGTT
1 AATATAAGTAAAATATCTATTATATTTAT-GTAGTATTTGTT
42566716 AATATAA
1 AATATAA
42566723 ATACTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 23 0.56
40 2 0.05
41 16 0.39
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.49
Consensus pattern (41 bp):
AATATAAGTAAAATATCTATTATATTTATGTAGTATTTGTT
Found at i:42566891 original size:29 final size:29
Alignment explanation
Indices: 42566849--42566904 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
42566839 AATATAGGCA
42566849 AGTTGAGTCGGGCCCGTGTTTACCTTTAG
1 AGTTGAGTCGGGCCCGTGTTTACCTTTAG
*
42566878 AGTTGGGTCGGGCCCGTGTTTACCTTT
1 AGTTGAGTCGGGCCCGTGTTTACCTTT
42566905 CTTAAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.36
Consensus pattern (29 bp):
AGTTGAGTCGGGCCCGTGTTTACCTTTAG
Found at i:42566918 original size:31 final size:29
Alignment explanation
Indices: 42566855--42566921 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 29
42566845 GGCAAGTTGA
*
42566855 GTCGGGCCCGTGTTTACCTTTAGAGTTGG
1 GTCGGGCCCGTGTTTACCTTTAGAATTGG
42566884 GTCGGGCCCGTGTTTACCTTTCTTA-AATTGG
1 GTCGGGCCCGTGTTTACC--T-TTAGAATTGG
42566915 GTCGGGC
1 GTCGGGC
42566922 TTGGGCAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 18 0.53
31 13 0.38
32 3 0.09
ACGTcount: A:0.10, C:0.22, G:0.33, T:0.34
Consensus pattern (29 bp):
GTCGGGCCCGTGTTTACCTTTAGAATTGG
Found at i:42570827 original size:29 final size:31
Alignment explanation
Indices: 42570761--42570840 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 31
42570751 ATTTATAAAA
42570761 TTTTAAATTAATAATAGTAAAATTGTAATTT-ACC
1 TTTTAAA--AATAATA--AAAATTGTAATTTAACC
* *
42570795 CTTTAAAAATAATAAAAATT-TAATTTAATC
1 TTTTAAAAATAATAAAAATTGTAATTTAACC
*
42570825 TTTTAAAAATTATAAA
1 TTTTAAAAATAATAAA
42570841 CATGTAAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.15
30 22 0.54
32 7 0.17
34 6 0.15
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
TTTTAAAAATAATAAAAATTGTAATTTAACC
Found at i:42571271 original size:44 final size:44
Alignment explanation
Indices: 42571197--42571281 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
42571187 TGAGTTAAAA
* ** *
42571197 ATTTAAAATTAAATAAATAGGACTTATGATAAAATCTCAATTTG
1 ATTTAAAAATAAATAAATAGGACACATGATAAAATCACAATTTG
* *
42571241 ATTTAAAAATAAATAAATATGACACGTGATAAAATCACAAT
1 ATTTAAAAATAAATAAATAGGACACATGATAAAATCACAAT
42571282 CTCATATTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (44 bp):
ATTTAAAAATAAATAAATAGGACACATGATAAAATCACAATTTG
Found at i:42572969 original size:24 final size:24
Alignment explanation
Indices: 42572899--42572972 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
42572889 ACATGTTCCC
* *
42572899 GTTGCTGTTGCTGTTGCTGTTGCT
1 GTTGCTGTTGCTGTTGTTGTTGTT
42572923 GTTGCTGTTGCTGTTGTTGTTGTT
1 GTTGCTGTTGCTGTTGTTGTTGTT
*
42572947 GTTGCTGATGCTGTTGTTGTTGTT
1 GTTGCTGTTGCTGTTGTTGTTGTT
42572971 GT
1 GT
42572973 GGTTTGCCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.01, C:0.11, G:0.34, T:0.54
Consensus pattern (24 bp):
GTTGCTGTTGCTGTTGTTGTTGTT
Found at i:42572972 original size:6 final size:6
Alignment explanation
Indices: 42572899--42572968 Score: 104
Period size: 6 Copynumber: 11.7 Consensus size: 6
42572889 ACATGTTCCC
* *
42572899 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGTT GTTGTT
1 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT
* *
42572947 GTTGCT GATGCT GTTGTT GTTG
1 GTTGCT GTTGCT GTTGCT GTTG
42572969 TTGTGGTTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.01, C:0.11, G:0.34, T:0.53
Consensus pattern (6 bp):
GTTGCT
Found at i:42574764 original size:26 final size:27
Alignment explanation
Indices: 42574726--42574777 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
42574716 TTTTATAAAA
*
42574726 TTTTATAATTTAATTTTTATATATTTTG
1 TTTTATAATTTAATTTCTA-ATATTTTG
42574754 TTTTA-AA-TTAATTTCTAATATTTT
1 TTTTATAATTTAATTTCTAATATTTT
42574778 TATAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 9 0.39
27 2 0.09
28 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTATAATTTAATTTCTAATATTTTG
Found at i:42574826 original size:47 final size:48
Alignment explanation
Indices: 42574708--42574835 Score: 118
Period size: 47 Copynumber: 2.6 Consensus size: 48
42574698 CAAAACGAGG
* * **
42574708 AAATTATTTTTTATAAAATTTTAT-AATTTAATTTTTATATATTTTGTTTT
1 AAATTATTTTTTAT-AAATTTTATAAATTT--TTCTAATATATTTTGTAAT
* * * *
42574758 AAATTAATTTCTA-ATATTTTTATAAATTTTTCTAAT-TTTTTTGTAAT
1 AAATTATTTTTTATA-AATTTTATAAATTTTTCTAATATATTTTGTAAT
*
42574805 AAATTATTTTTTATAAATTTTATAAAATTTT
1 AAATTATTTTTTATAAATTTTATAAATTTTT
42574836 ATGGTTTTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
47 33 0.52
48 7 0.11
49 7 0.11
50 16 0.25
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (48 bp):
AAATTATTTTTTATAAATTTTATAAATTTTTCTAATATATTTTGTAAT
Found at i:42574896 original size:38 final size:37
Alignment explanation
Indices: 42574804--42574901 Score: 92
Period size: 38 Copynumber: 2.6 Consensus size: 37
42574794 TTTTTTGTAA
*
42574804 TAAATTATTTTTTATAAATTTTATAAAATTTTATGGTTT
1 TAAATAATTTTTTAT-AATTTTATAAAATTTTAT-GTTT
* * *
42574843 TAATTAATGTCTTATAATCTTTAT-AAATTTTAAT-TTAT
1 TAAATAATTTTTTATAAT-TTTATAAAATTTT-ATGTT-T
*
42574881 TAAATAATTTTTTATATTTTT
1 TAAATAATTTTTTATAATTTT
42574902 TTATAATTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
37 5 0.10
38 25 0.52
39 18 0.38
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (37 bp):
TAAATAATTTTTTATAATTTTATAAAATTTTATGTTT
Found at i:42581411 original size:11 final size:11
Alignment explanation
Indices: 42581395--42581426 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
42581385 GTCATTCTGC
42581395 TATTATATTGT
1 TATTATATTGT
42581406 TATTATATTGT
1 TATTATATTGT
42581417 TATTACTATT
1 TATTA-TATT
42581427 TGGATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (11 bp):
TATTATATTGT
Found at i:42588784 original size:45 final size:44
Alignment explanation
Indices: 42588718--42588812 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
42588708 GGATTAGAGG
* * *
42588718 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
42588763 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
42588807 TGTAAT
1 TGTAAT
42588813 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:42588995 original size:18 final size:17
Alignment explanation
Indices: 42588974--42589008 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42588964 TTATTATTTA
*
42588974 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42588992 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42589009 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42589002 original size:28 final size:27
Alignment explanation
Indices: 42588932--42589004 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
42588922 TTTATTATCA
*
42588932 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
42588960 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
42588987 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
42589005 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:42589142 original size:18 final size:17
Alignment explanation
Indices: 42589121--42589155 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42589111 TTATTATTAA
*
42589121 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42589139 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42589156 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42589167 original size:147 final size:149
Alignment explanation
Indices: 42588893--42589167 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
42588883 ATGATTATTG
*
42588893 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
42588958 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
42589023 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
* *
42589042 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTACTCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
42589105 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
42589168 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 94 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:42597899 original size:16 final size:17
Alignment explanation
Indices: 42597880--42597911 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42597870 CCAAAAAATA
42597880 TATATTTAA-TAAAAAG
1 TATATTTAATTAAAAAG
42597896 TATATTTAATTAAAAA
1 TATATTTAATTAAAAA
42597912 TAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATATTTAATTAAAAAG
Found at i:42598349 original size:23 final size:23
Alignment explanation
Indices: 42598319--42598365 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
42598309 ATGAATATTG
*
42598319 ACGTGACTAGCGAAAGTAATCAA
1 ACGTGACTAACGAAAGTAATCAA
*
42598342 ACGTGACTAATGAAAGTAATCAA
1 ACGTGACTAACGAAAGTAATCAA
42598365 A
1 A
42598366 AACTAACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (23 bp):
ACGTGACTAACGAAAGTAATCAA
Found at i:42603540 original size:29 final size:29
Alignment explanation
Indices: 42603508--42603565 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
42603498 ATTTAACAAG
42603508 CAAATGCCTATAAAATAATAACAAAATTA
1 CAAATGCCTATAAAATAATAACAAAATTA
*
42603537 CAAATGCCTTTAAAATAATAACAAAATTA
1 CAAATGCCTATAAAATAATAACAAAATTA
42603566 ACAATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.26
Consensus pattern (29 bp):
CAAATGCCTATAAAATAATAACAAAATTA
Found at i:42611152 original size:20 final size:19
Alignment explanation
Indices: 42611108--42611161 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
42611098 AAAAAGACTA
42611108 TTTATTTTATAAAATGAGT
1 TTTATTTTATAAAATGAGT
* *
42611127 TATATTATTAT-AAATGTGTT
1 TTTATT-TTATAAAATGAG-T
*
42611147 TTTATTTTTTAAAAT
1 TTTATTTTATAAAAT
42611162 TATTTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTATTTTATAAAATGAGT
Found at i:42613299 original size:7 final size:7
Alignment explanation
Indices: 42613289--42613315 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
42613279 TATTTTTATT
42613289 TTTAATA
1 TTTAATA
42613296 TTTAATA
1 TTTAATA
42613303 TTTAATA
1 TTTAATA
42613310 TTTAAT
1 TTTAAT
42613316 TATATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAATA
Found at i:42616867 original size:27 final size:26
Alignment explanation
Indices: 42616756--42616907 Score: 115
Period size: 27 Copynumber: 5.7 Consensus size: 26
42616746 ATTCTGTCAA
* * * **
42616756 CCTTTGTAGTGTACTCTGAATGAATCA
1 CCTTTGTGGCGTACTCTGTATG-ATTG
* * * *
42616783 CCTTTGGGGCATACTTTGTATAGATAG
1 CCTTTGTGGCGTACTCTGTAT-GATTG
* **
42616810 CCTTTGTGGCGTACTCTGAATGAATCA
1 CCTTTGTGGCGTACTCTGTATG-ATTG
*
42616837 CCTTTGTGGCGTACTCTGTATAGGTTG
1 CCTTTGTGGCGTACTCTGTAT-GATTG
**
42616864 CCTTTGTGGTATACTCTGTATGGATTG
1 CCTTTGTGGCGTACTCTGTAT-GATTG
*
42616891 CCTTTGTGGGGTACTCT
1 CCTTTGTGGCGTACTCT
42616908 AATTAGATTA
Statistics
Matches: 98, Mismatches: 24, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
26 1 0.01
27 95 0.97
28 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (26 bp):
CCTTTGTGGCGTACTCTGTATGATTG
Found at i:42616895 original size:54 final size:54
Alignment explanation
Indices: 42616756--42616907 Score: 187
Period size: 54 Copynumber: 2.8 Consensus size: 54
42616746 ATTCTGTCAA
* * * *
42616756 CCTTTGTAGTGTACTCTGAATGAATCACCTTTGGGGCATACTTTGTATAGATAG
1 CCTTTGTGGTGTACTCTGAATGAATCACCTTTGTGGCGTACTCTGTATAGATAG
* * *
42616810 CCTTTGTGGCGTACTCTGAATGAATCACCTTTGTGGCGTACTCTGTATAGGTTG
1 CCTTTGTGGTGTACTCTGAATGAATCACCTTTGTGGCGTACTCTGTATAGATAG
* * * ** *
42616864 CCTTTGTGGTATACTCTGTATGGATTGCCTTTGTGGGGTACTCT
1 CCTTTGTGGTGTACTCTGAATGAATCACCTTTGTGGCGTACTCT
42616908 AATTAGATTA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (54 bp):
CCTTTGTGGTGTACTCTGAATGAATCACCTTTGTGGCGTACTCTGTATAGATAG
Found at i:42620659 original size:3 final size:3
Alignment explanation
Indices: 42620651--42620682 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42620641 AATACAATGC
42620651 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
42620683 AACTGTGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:42620774 original size:21 final size:21
Alignment explanation
Indices: 42620749--42620791 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
42620739 GGTTCGCTGT
*
42620749 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
42620770 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
42620791 A
1 A
42620792 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:42620791 original size:16 final size:16
Alignment explanation
Indices: 42620772--42620804 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42620762 TGTATTGGAT
*
42620772 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
42620788 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
42620804 T
1 T
42620805 AGCAAATCAA
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:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:42620849 original size:45 final size:44
Alignment explanation
Indices: 42620783--42620877 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
42620773 GGATTAGAGG
* *
42620783 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
42620828 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
42620872 TGTAAT
1 TGTAAT
42620878 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:42621060 original size:18 final size:17
Alignment explanation
Indices: 42621039--42621073 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42621029 TTATTATTTA
*
42621039 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42621057 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42621074 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42621067 original size:28 final size:27
Alignment explanation
Indices: 42620997--42621069 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
42620987 TTTATTATCA
*
42620997 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
42621025 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
42621052 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
42621070 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:42621204 original size:18 final size:17
Alignment explanation
Indices: 42621183--42621217 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42621173 TTATTATTAA
*
42621183 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42621201 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42621218 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42621228 original size:144 final size:147
Alignment explanation
Indices: 42620958--42621229 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
42620948 ATGATTATTG
42620958 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
42621023 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
42621088 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
42621107 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
42621169 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
42621230 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:42625756 original size:23 final size:24
Alignment explanation
Indices: 42625703--42625756 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
42625693 TCTTTCCCCA
42625703 CCTCTCCTTTCTCTCCACGTGTTT
1 CCTCTCCTTTCTCTCCACGTGTTT
* *
42625727 CAATCTCC-TT-TCTCCACTTGTCTT
1 C-CTCTCCTTTCTCTCCACGTGT-TT
42625751 CCTCTC
1 CCTCTC
42625757 ACCAGCCGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 14 0.56
24 6 0.24
25 5 0.20
ACGTcount: A:0.07, C:0.43, G:0.06, T:0.44
Consensus pattern (24 bp):
CCTCTCCTTTCTCTCCACGTGTTT
Found at i:42637283 original size:13 final size:13
Alignment explanation
Indices: 42637246--42637286 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
42637236 CACCAATAAA
42637246 ATATTTTTGAAAT
1 ATATTTTTGAAAT
42637259 AT-TTTTAT-AAAT
1 ATATTTT-TGAAAT
42637271 ATATTTTTGAAAT
1 ATATTTTTGAAAT
42637284 ATA
1 ATA
42637287 AAATATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (13 bp):
ATATTTTTGAAAT
Found at i:42641832 original size:7 final size:7
Alignment explanation
Indices: 42641820--42641857 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
42641810 TCTTGGCATA
42641820 CATGATC
1 CATGATC
42641827 CATGATC
1 CATGATC
42641834 CATGATC
1 CATGATC
42641841 CATGATC
1 CATGATC
42641848 CATGATC
1 CATGATC
42641855 CAT
1 CAT
42641858 CTCTATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (7 bp):
CATGATC
Found at i:42645892 original size:17 final size:17
Alignment explanation
Indices: 42645870--42645909 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
42645860 GTCGTCATCC
42645870 AAATTTGTCATAT-ATT
1 AAATTTGTCATATCATT
*
42645886 GAAATTTGTGATATCATT
1 -AAATTTGTCATATCATT
42645904 AAATTT
1 AAATTT
42645910 TATCAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (17 bp):
AAATTTGTCATATCATT
Found at i:42646362 original size:25 final size:25
Alignment explanation
Indices: 42646314--42646362 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
42646304 CTACACTAAT
* *
42646314 TAGAGTTTAAGTGGGAAACTAAAAA
1 TAGAGTTTAACTGGGAAACAAAAAA
*
42646339 TAGAGTTTAACTGGGAGA-AAAAAA
1 TAGAGTTTAACTGGGAAACAAAAAA
42646363 GTCGAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.49, C:0.04, G:0.24, T:0.22
Consensus pattern (25 bp):
TAGAGTTTAACTGGGAAACAAAAAA
Found at i:42649008 original size:46 final size:46
Alignment explanation
Indices: 42648955--42649093 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 46
42648945 ACAAGGCTAT
* *
42648955 AACTCAGTATGGTTTTCTTCACGGGAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
42649001 AACTCAGTAAGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
42649047 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
42649093 A
1 A
42649094 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:42650356 original size:16 final size:16
Alignment explanation
Indices: 42650317--42650357 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
42650307 TTTTAAACCA
42650317 AAAAATTCAATAAATC
1 AAAAATTCAATAAATC
* *
42650333 ACAAAATTCACTAATTC
1 A-AAAATTCAATAAATC
42650350 AAAAATTC
1 AAAAATTC
42650358 TTCTAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATTCAATAAATC
Found at i:42651920 original size:30 final size:31
Alignment explanation
Indices: 42651880--42651941 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
42651870 AATACAACTT
42651880 AACAAGCAAATGCCTCTAAAATAATAACAAA
1 AACAAGCAAATGCCTCTAAAATAATAACAAA
* *
42651911 AACAA-CAAATGTCTTTAAAATAATAACAAA
1 AACAAGCAAATGCCTCTAAAATAATAACAAA
42651941 A
1 A
42651942 TTAACAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (31 bp):
AACAAGCAAATGCCTCTAAAATAATAACAAA
Found at i:42652003 original size:22 final size:22
Alignment explanation
Indices: 42651978--42652020 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42651968 TATCCAAATA
42651978 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
42652000 ATAATAGTAAAATTGTAGCAA
1 ATAACAATAAAATAGTAGCAA
42652021 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:42652274 original size:15 final size:15
Alignment explanation
Indices: 42652254--42652284 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42652244 GGGTGGAATA
42652254 TAATATTTTCCTCAT
1 TAATATTTTCCTCAT
42652269 TAATATTTTCCTCAT
1 TAATATTTTCCTCAT
42652284 T
1 T
42652285 CACAATCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATATTTTCCTCAT
Found at i:42654142 original size:43 final size:43
Alignment explanation
Indices: 42654076--42654163 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
42654066 TTGTAACTTC
* * *
42654076 ATGCTTTACTTGTGCATCCATCTTTTGTTGATGTTTACATTTG
1 ATGCTTTACTTGTGCATCAATCTTTTGTTGATCTTTAAATTTG
42654119 ATGCTTTACTTGTGCATCAATCTTTTGTTGATCTTTAAATTTG
1 ATGCTTTACTTGTGCATCAATCTTTTGTTGATCTTTAAATTTG
42654162 AT
1 AT
42654164 ATGTGGTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (43 bp):
ATGCTTTACTTGTGCATCAATCTTTTGTTGATCTTTAAATTTG
Found at i:42660421 original size:24 final size:24
Alignment explanation
Indices: 42660394--42660441 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
42660384 CGTTCATAGT
* *
42660394 ATAACTTACCTCAATCTTAAGTAA
1 ATAACTTACCTCAACCCTAAGTAA
42660418 ATAACTTACCTCAACCCTAAGTAA
1 ATAACTTACCTCAACCCTAAGTAA
42660442 GTTGAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (24 bp):
ATAACTTACCTCAACCCTAAGTAA
Found at i:42669022 original size:15 final size:15
Alignment explanation
Indices: 42669002--42669050 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
42668992 ATTTCAAATT
42669002 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
* *
42669017 TTAAAACTA-ATTAAA
1 TTAAAAATATA-AAAA
42669032 TT-AAAATATAAAAA
1 TTAAAAATATAAAAA
42669046 TTAAA
1 TTAAA
42669051 TCTACAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:42669048 original size:14 final size:14
Alignment explanation
Indices: 42669005--42669050 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
42668995 TCAAATTTTA
42669005 AAAATATAAAAATT
1 AAAATATAAAAATT
*
42669019 AAAACTA-ATTAAATT
1 AAAA-TATA-AAAATT
42669034 AAAATATAAAAATT
1 AAAATATAAAAATT
42669048 AAA
1 AAA
42669051 TCTACAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:42669062 original size:29 final size:29
Alignment explanation
Indices: 42669005--42669065 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
42668995 TCAAATTTTA
*
42669005 AAAATATAAAAATTAAAACTAATTAAATT
1 AAAATATAAAAATTAAAACTAAATAAATT
* *
42669034 AAAATATAAAAATTAAATCTACAATAATTT
1 AAAATATAAAAATTAAAACTA-AATAAATT
42669064 AA
1 AA
42669066 GGAAAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (29 bp):
AAAATATAAAAATTAAAACTAAATAAATT
Found at i:42670257 original size:22 final size:23
Alignment explanation
Indices: 42670213--42670264 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
42670203 GAGGCGCTAA
42670213 TAAATAAAAAATTATTAAATTTTTT
1 TAAATAAAAAATTATT--ATTTTTT
*
42670238 TAAATAAAATATTATT-TTTTTT
1 TAAATAAAAAATTATTATTTTTT
*
42670260 AAAAT
1 TAAAT
42670265 TTAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
25 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAATAAAAAATTATTATTTTTT
Found at i:42670345 original size:27 final size:27
Alignment explanation
Indices: 42670314--42670382 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
42670304 GTCGGGTGGC
42670314 GCCTCATAGGGAGGCACCATCAAAAGT
1 GCCTCATAGGGAGGCACCATCAAAAGT
* * *
42670341 GCCTCATAAGGAGGCGCCATTAAAAGT
1 GCCTCATAGGGAGGCACCATCAAAAGT
*
42670368 GACTCATAGGGAGGC
1 GCCTCATAGGGAGGC
42670383 GTCAATGAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (27 bp):
GCCTCATAGGGAGGCACCATCAAAAGT
Found at i:42670440 original size:19 final size:19
Alignment explanation
Indices: 42670392--42670455 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
42670382 CGTCAATGAG
* * *
42670392 TAATTTTGTGTGTATATTG
1 TAATTTTGTATGAATATTA
42670411 TAACTTTTTGTATGAATATTA
1 TAA--TTTTGTATGAATATTA
42670432 TAATTTTGTATGAATATTA
1 TAATTTTGTATGAATATTA
42670451 TAATT
1 TAATT
42670456 ATTTTATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 24 0.60
21 16 0.40
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATGAATATTA
Found at i:42670536 original size:21 final size:21
Alignment explanation
Indices: 42670395--42670542 Score: 85
Period size: 21 Copynumber: 7.2 Consensus size: 21
42670385 CAATGAGTAA
* * *
42670395 TTTTGTGTGTATATTGTAACT
1 TTTTGTATGAATATTGTAATT
*
42670416 TTTTGTATGAATATTATAA--
1 TTTTGTATGAATATTGTAATT
*
42670435 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGTAATT
* * *
42670456 ATTTTATAATTAATTTTGT-ATT
1 -TTTTGT-ATGAATATTGTAATT
* * * *
42670478 TATTGTTTTGGAT-TAGT-A--
1 TTTTG-TATGAATATTGTAATT
* *
42670496 TTTTGTATGAATAGTATAATT
1 TTTTGTATGAATATTGTAATT
42670517 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
42670538 ATTTT
1 -TTTT
42670543 ATAATTAATT
Statistics
Matches: 96, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
17 5 0.05
18 5 0.05
19 20 0.21
20 4 0.04
21 41 0.43
22 13 0.14
23 8 0.08
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:42670601 original size:19 final size:19
Alignment explanation
Indices: 42670577--42670622 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
42670567 TTTGATTAAT
42670577 ATTTTGTATAAATATTGTA
1 ATTTTGTATAAATATTGTA
* *
42670596 ATTTTGTATGAATGTTGTA
1 ATTTTGTATAAATATTGTA
42670615 ATTTTGTA
1 ATTTTGTA
42670623 ATTATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
ATTTTGTATAAATATTGTA
Found at i:42670648 original size:88 final size:85
Alignment explanation
Indices: 42670416--42670771 Score: 461
Period size: 80 Copynumber: 4.3 Consensus size: 85
42670406 TATTGTAACT
*
42670416 TTTTGTATGAATATTATAATTTTGTATGAA---T-A-TTATAATTATTTTATAATTAATTTTGTA
1 TTTTGTATGAATATTATAATTTTGTATGAATTGTAATTTGTAATTATTTTATAATTAATTTTGTA
*
42670476 TTTATTGTTTTGGATTAGTA
66 TTTATAGTTTTGGATTAGTA
* * *
42670496 TTTTGTATGAATAGTATAATTTT-T-TGTA-TG-AATATTGTAATTATTTTATAATTAATTTTAT
1 TTTTGTATGAATATTATAATTTTGTATGAATTGTAAT-TTGTAATTATTTTATAATTAATTTTGT
* *
42670557 ATTTATAGTTTTTGATTAATA
65 ATTTATAGTTTTGGATTAGTA
* *
42670578 TTTTGTATAAATATTGTAATTTTGTATGAATGTTGTAATTTTGTAATTATTTTATAATTAATTTT
1 TTTTGTATGAATATTATAATTTTGTATGAA--TTGTAA-TTTGTAATTATTTTATAATTAATTTT
**
42670643 GTATTTATAGTTTTTTATTAGTA
63 GTATTTATAGTTTTGGATTAGTA
*
42670666 TTTTGTATGAATATTATAATGTTGTATGAA---T-A-TTGTAATTATTTTATAATTAATTTTGTA
1 TTTTGTATGAATATTATAATTTTGTATGAATTGTAATTTGTAATTATTTTATAATTAATTTTGTA
42670726 TTTATAGTTTTGGATTAGTA
66 TTTATAGTTTTGGATTAGTA
*
42670746 TTTTGTATGAATATTGTAATTTTGTA
1 TTTTGTATGAATATTATAATTTTGTA
42670772 ATTTTGTATG
Statistics
Matches: 243, Mismatches: 21, Indels: 24
0.84 0.07 0.08
Matches are distributed among these distances:
78 3 0.01
79 1 0.00
80 93 0.38
82 64 0.26
83 2 0.01
84 3 0.01
87 2 0.01
88 74 0.30
89 1 0.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (85 bp):
TTTTGTATGAATATTATAATTTTGTATGAATTGTAATTTGTAATTATTTTATAATTAATTTTGTA
TTTATAGTTTTGGATTAGTA
Found at i:42670690 original size:19 final size:19
Alignment explanation
Indices: 42670668--42670704 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42670658 TATTAGTATT
42670668 TTGTATGAATATTATAATG
1 TTGTATGAATATTATAATG
*
42670687 TTGTATGAATATTGTAAT
1 TTGTATGAATATTATAAT
42670705 TATTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGTATGAATATTATAATG
Found at i:42670750 original size:168 final size:169
Alignment explanation
Indices: 42670451--42670771 Score: 545
Period size: 168 Copynumber: 1.9 Consensus size: 169
42670441 ATGAATATTA
*
42670451 TAATTATTTTATAATTAATTTTGTATTTATTGTTTTGGATTAGTATTTTGTATGAATAGTATAAT
1 TAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATAGTATAA-
* *
42670516 TTTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGATTAATATTT
65 TTGTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAATATTT
42670581 TGTATAAATATTGTAATTTTGTATGAATGTTGTAATTTTG
130 TGTATAAATATTGTAATTTTGTATGAATGTTGTAATTTTG
** *
42670621 TAATTATTTTATAATTAATTTTGTATTTATAGTTTTTTATTAGTATTTTGTATGAATATTATAA-
1 TAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATAGTATAAT
* *
42670685 TGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTT
66 TGTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAATATTTT
*
42670750 GTATGAATATTGTAATTTTGTA
131 GTATAAATATTGTAATTTTGTA
42670772 ATTTTGTATG
Statistics
Matches: 142, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
168 82 0.58
170 60 0.42
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (169 bp):
TAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATAGTATAAT
TGTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAATATTTT
GTATAAATATTGTAATTTTGTATGAATGTTGTAATTTTG
Found at i:42670769 original size:19 final size:19
Alignment explanation
Indices: 42670767--42670835 Score: 102
Period size: 19 Copynumber: 3.4 Consensus size: 19
42670757 TATTGTAATT
42670767 TTGTAATTTTGTATGAATA
1 TTGTAATTTTGTATGAATA
42670786 TTGTAATATTGTTTGTATGAATA
1 TTGT-A-A-T-TTTGTATGAATA
42670809 TTGTAATTTTGTATGAATA
1 TTGTAATTTTGTATGAATA
42670828 TTGTAATT
1 TTGTAATT
42670836 ATTTTATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
19 24 0.52
20 2 0.04
21 2 0.04
22 2 0.04
23 16 0.35
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (19 bp):
TTGTAATTTTGTATGAATA
Found at i:42670775 original size:27 final size:27
Alignment explanation
Indices: 42670745--42670821 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
42670735 TTGGATTAGT
42670745 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
42670772 ATTTTGTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
42670797 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
42670822 TGAATATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 22 0.48
27 24 0.52
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:42670779 original size:88 final size:85
Alignment explanation
Indices: 42670432--42670792 Score: 454
Period size: 88 Copynumber: 4.3 Consensus size: 85
42670422 ATGAATATTA
* *
42670432 TAATTTTGTATGAATATTATAATTATTTTATAATTAATTTTGTATTTATTGTTTTGGATTAGTAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
**
42670497 TTTGTATGAATA-GTATAAT
66 TTTGTATGAATATGTATTTT
* * *
42670516 T--TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGATTAATAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
*
42670579 TTTGTATAAATATTGTAATTTT
66 TTTGTATGAATA-TGT-ATTTT
** * **
42670601 GT-ATGAATGT-TGTAATTTTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTTATTAG
1 -TAAT-TTTGTATG-AATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
42670664 TATTTTGTATGAATAT-TA----
63 TATTTTGTATGAATATGTATTTT
*
42670682 TAATGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
42670747 TTTGTATGAATATTGTAATTTT
66 TTTGTATGAATA-TGT-ATTTT
42670769 GTAATTTTGTATGAATATTGTAAT
1 -TAATTTTGTATGAATATTGTAAT
42670793 ATTGTTTGTA
Statistics
Matches: 239, Mismatches: 21, Indels: 30
0.82 0.07 0.10
Matches are distributed among these distances:
80 66 0.28
81 5 0.02
82 69 0.29
83 1 0.00
84 3 0.01
85 4 0.02
86 2 0.01
87 4 0.02
88 85 0.36
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (85 bp):
TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
TTTGTATGAATATGTATTTT
Found at i:42670898 original size:60 final size:60
Alignment explanation
Indices: 42670828--42670949 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
42670818 TGTATGAATA
* * * * *
42670828 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
42670888 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
42670948 TT
1 TT
42670950 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 50 0.89
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:42671100 original size:15 final size:16
Alignment explanation
Indices: 42671064--42671100 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42671054 CTCATTTAAT
42671064 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
42671080 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
42671095 TTTTAT
1 TTTTAT
42671101 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:42680349 original size:18 final size:18
Alignment explanation
Indices: 42680317--42680364 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
42680307 AGGTACATGT
* * *
42680317 TTAATTATTTTTATTTAA
1 TTAATTATATATATTCAA
*
42680335 TTAATTATATATATTCAT
1 TTAATTATATATATTCAA
42680353 TTAATT-TATATA
1 TTAATTATATATA
42680365 AGTACTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTATATATATTCAA
Found at i:42684738 original size:6 final size:6
Alignment explanation
Indices: 42684729--42684767 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
42684719 TTATTTTCTA
* **
42684729 TTTTCC TTTTTC TTTTCC TTTTCC TTTTTT TTTTCC TTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTT
42684768 ATAATGTCTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTCC
Found at i:42684752 original size:18 final size:18
Alignment explanation
Indices: 42684729--42684767 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
42684719 TTATTTTCTA
42684729 TTTTCCTTTTTCTTTTCC
1 TTTTCCTTTTTCTTTTCC
*
42684747 TTTTCCTTTTTTTTTTCC
1 TTTTCCTTTTTCTTTTCC
42684765 TTT
1 TTT
42684768 ATAATGTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCCTTTTTCTTTTCC
Found at i:42692769 original size:28 final size:28
Alignment explanation
Indices: 42692737--42692791 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
42692727 GACAATGATC
*
42692737 AGATTCAGGGTCAAGATGAATGCCTACA
1 AGATTCAGGGTCAAGATGAATGACTACA
* *
42692765 AGATTTAGGTTCAAGATGAATGACTAC
1 AGATTCAGGGTCAAGATGAATGACTAC
42692792 TTGTAGGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (28 bp):
AGATTCAGGGTCAAGATGAATGACTACA
Done.