Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 91 of 199
Found at i:31473357 original size:11 final size:11
Alignment explanation
Indices: 31473316--31473373 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
31473306 ATTGAACCCC
*
31473316 TTCTTCTTCTT
1 TTCTTTTTCTT
31473327 TT-TTTCTT-TT
1 TTCTTT-TTCTT
31473337 TTCTTTTTTCTT
1 TTC-TTTTTCTT
31473349 TTCTTTTTCTT
1 TTCTTTTTCTT
* *
31473360 TCCCTTTT-TT
1 TTCTTTTTCTT
31473370 TTCT
1 TTCT
31473374 GTTGGGCTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
10 10 0.26
11 20 0.53
12 8 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:31473424 original size:18 final size:19
Alignment explanation
Indices: 31473401--31473436 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31473391 TGGGTCTGGC
31473401 CTGCTGGG-TGCGCTGGGT
1 CTGCTGGGTTGCGCTGGGT
31473419 CTGCTGGGTTGCGCTGGG
1 CTGCTGGGTTGCGCTGGG
31473437 CCTGGCCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.00, C:0.22, G:0.50, T:0.28
Consensus pattern (19 bp):
CTGCTGGGTTGCGCTGGGT
Found at i:31473446 original size:24 final size:24
Alignment explanation
Indices: 31473391--31473488 Score: 118
Period size: 24 Copynumber: 4.3 Consensus size: 24
31473381 TGCTTGCGTG
*
31473391 TGGGTCTGGCCTGCTGGG-TGCGC
1 TGGGCCTGGCCTGCTGGGCTGCGC
*
31473414 TGGG--T---CTGCTGGGTTGCGC
1 TGGGCCTGGCCTGCTGGGCTGCGC
31473433 TGGGCCTGGCCTGCTGGGCTGCGC
1 TGGGCCTGGCCTGCTGGGCTGCGC
* *
31473457 TGGGCCTGCCCTACTGGGCTGCGC
1 TGGGCCTGGCCTGCTGGGCTGCGC
31473481 TGGGCCTG
1 TGGGCCTG
31473489 CTGAAAATGG
Statistics
Matches: 66, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.12
19 9 0.14
21 2 0.03
23 4 0.06
24 43 0.65
ACGTcount: A:0.01, C:0.30, G:0.45, T:0.24
Consensus pattern (24 bp):
TGGGCCTGGCCTGCTGGGCTGCGC
Found at i:31473677 original size:10 final size:10
Alignment explanation
Indices: 31473661--31473745 Score: 86
Period size: 10 Copynumber: 8.5 Consensus size: 10
31473651 ACAAAATATT
31473661 TTCTTTTTT-
1 TTCTTTTTTC
31473670 TTCTTTTTTTC
1 TTC-TTTTTTC
*
31473681 TGTCTTTCTTC
1 T-TCTTTTTTC
* *
31473692 TTCTTCTTCC
1 TTCTTTTTTC
31473702 TTCTTTCTTTC
1 TTCTTT-TTTC
*
31473713 -TCTTCTTTC
1 TTCTTTTTTC
31473722 TTCTTTTTTC
1 TTCTTTTTTC
31473732 TTC-TTTTTC
1 TTCTTTTTTC
31473741 TTCTT
1 TTCTT
31473746 CTCCGTTCGG
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
9 16 0.26
10 33 0.53
11 11 0.18
12 2 0.03
ACGTcount: A:0.00, C:0.25, G:0.01, T:0.74
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:31473681 original size:17 final size:19
Alignment explanation
Indices: 31473659--31473745 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 19
31473649 TTACAAAATA
31473659 TTTTCTT-TTTTTTCTT-T
1 TTTTCTTCTTTTTTCTTCT
*
31473676 TTTTCTGTCTTTCTTCTTCT
1 TTTTCT-TCTTTTTTCTTCT
*
31473696 TCTTCCTTCTTTCTTTC-TCT
1 T-TTTCTTCTTT-TTTCTTCT
31473716 TCTTTCTTCTTTTTTCTTCT
1 T-TTTCTTCTTTTTTCTTCT
31473736 TTTTCTTCTT
1 TTTTCTTCTT
31473746 CTCCGTTCGG
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.10
18 1 0.02
19 21 0.35
20 25 0.42
21 7 0.12
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTCTTCTTTTTTCTTCT
Found at i:31473692 original size:3 final size:3
Alignment explanation
Indices: 31473686--31473747 Score: 58
Period size: 3 Copynumber: 20.3 Consensus size: 3
31473676 TTTTCTGTCT
31473686 TTC TTC TTC TTC TTCC TTC TTTC TT- TCTC TTC TTTC TTC TT- TT- TTC
1 TTC TTC TTC TTC TT-C TTC -TTC TTC T-TC TTC -TTC TTC TTC TTC TTC
*
31473732 TTC TTT TTC TTC TTC T
1 TTC TTC TTC TTC TTC T
31473748 CCGTTCGGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
2 5 0.10
3 36 0.71
4 10 0.20
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:31474270 original size:30 final size:30
Alignment explanation
Indices: 31474099--31474267 Score: 146
Period size: 30 Copynumber: 5.7 Consensus size: 30
31474089 AAATGCAGCA
* * ** *
31474099 AAAGTTTTGGGGCCAAAACATAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTAAG
* * *
31474129 AAAGCTTAAGGGTCCAAATGTAATTTTAAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTAAG
*
31474159 AAAGTTTAGGGGTCAAAATATAA-TTTATA-
1 AAAGTTTAGGGGTCAAAATGTAATTTTA-AG
** *
31474188 AAAGTTTAGGGGTTGAACTGTAATTTTAAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTAAG
** * *
31474218 AAAGTTTATAGGTTAAAATGCAATTTT-AG
1 AAAGTTTAGGGGTCAAAATGTAATTTTAAG
*
31474247 AAAAGTTTAGTGGTCAAAATG
1 -AAAGTTTAGGGGTCAAAATG
31474268 CAAAAAAATT
Statistics
Matches: 111, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
29 26 0.23
30 85 0.77
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTAAG
Found at i:31474673 original size:76 final size:77
Alignment explanation
Indices: 31474550--31475057 Score: 760
Period size: 77 Copynumber: 6.6 Consensus size: 77
31474540 CGACATGTGC
* * ** *
31474550 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTCAAAAAACATAAATTTAAAAGAAA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAA
*
31474615 TACCTCGGCATGG
65 TACCTCGGCATGA
* * *
31474628 TCTGAGGCTCAACTCACATCTGTATTATGAGTTGA-TTTTTGAAAAAC-GAAAATTTAAAAGAAA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACAG-AAATTTAAAAGAAA
31474691 TACCTCGGCATGA
65 TACCTCGGCATGA
*
31474704 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACGGAAATTTAAAAGAAAT
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAAT
31474769 ACCTCGGCATGA
66 ACCTCGGCATGA
*
31474781 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAACGGAAATTTAAAAGAAAT
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAAT
*
31474845 ACCTTGGCATGA
66 ACCTCGGCATGA
31474857 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAA-TTAAAA-AA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG--AAAAACAGAAATTTAAAAGAA
* *
31474920 ATACCTCAGCGTGA
64 ATACCTCGGCATGA
*
31474934 CCGGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAA-TTAAAA-AA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAA-CAGAAATTTAAAAGAA
* *
31474997 ATACCTCAGCGTGA
64 ATACCTCGGCATGA
31475011 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
31475058 AAACAGAATT
Statistics
Matches: 404, Mismatches: 19, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
76 154 0.38
77 215 0.53
78 25 0.06
79 10 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (77 bp):
CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAAT
ACCTCGGCATGA
Found at i:31474740 original size:153 final size:153
Alignment explanation
Indices: 31474477--31475073 Score: 769
Period size: 153 Copynumber: 3.9 Consensus size: 153
31474467 GCGTGAAACA
* * * * * *
31474477 CGAGGCTCAACTCACCTCTTGGATTATGATTTGATCTTCGAAAAAC-AAAAATT--GA-AAATAC
1 CGAGGCTCAACTCACCTC-TGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAATAC
* * * * * * *
31474538 CCCGACATGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTCAAAAAACATAA
65 CTCGGCA--TGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAACAGAA
**
31474603 ATTTAAAAGAAATACCTCGGCATGGTC
127 ATTTAAAAGAAATACCTCGGCATGACC
* *
31474630 TGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAATACC
1 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAATACC
** *
31474695 TCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACGGAAATTT
66 TCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAACAGAAATTT
31474760 AAAAGAAATACCTCGGCATGACC
131 AAAAGAAATACCTCGGCATGACC
*
31474783 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAATACC
1 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAATACC
*
31474848 TTGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAA-
66 TCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTT-AAAAAAACAGAAAT
* *
31474912 TTAAAA-AAATACCTCAGCGTGACC
129 TTAAAAGAAATACCTCGGCATGACC
* *
31474936 GGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAA-TTAAAA-AAAT
1 CGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAACG-A-AAATTTAAAAGAAAT
* *
31474999 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACAG
63 ACCTCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTT--AAAAAAACAG
*
31475064 AATTTTAAAA
125 AAATTTAAAA
31475074 ATATTTCTTG
Statistics
Matches: 397, Mismatches: 36, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
152 23 0.06
153 225 0.57
154 100 0.25
155 29 0.07
156 20 0.05
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (153 bp):
CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAATACC
TCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAACAGAAATTT
AAAAGAAATACCTCGGCATGACC
Found at i:31475949 original size:16 final size:16
Alignment explanation
Indices: 31475930--31476002 Score: 53
Period size: 16 Copynumber: 4.3 Consensus size: 16
31475920 TTGATTTTTC
31475930 TTTTTCTTTTCTTTGT
1 TTTTTCTTTTCTTTGT
31475946 TTTTTCTTTTTTCTTT-T
1 TTTTTC--TTTTCTTTGT
31475963 TTTGTT-TTGTT-TTTGT
1 TTT-TTCTT-TTCTTTGT
*
31475979 TTTGTTCCTTTTTTGTTGT
1 TTT-TT-CTTTTCT-TTGT
31475998 TTTTT
1 TTTTT
31476003 TTAAGCATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
15 5 0.10
16 15 0.31
17 6 0.12
18 15 0.31
19 7 0.15
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTCTTTGT
Found at i:31475952 original size:22 final size:22
Alignment explanation
Indices: 31475925--31475970 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
31475915 TCATCTTGAT
31475925 TTTTC-TTTTTCTTTTCTTTGTT
1 TTTTCTTTTTTCTTTT-TTTGTT
31475947 TTTTCTTTTTTCTTTTTTTGTT
1 TTTTCTTTTTTCTTTTTTTGTT
31475969 TT
1 TT
31475971 GTTTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (22 bp):
TTTTCTTTTTTCTTTTTTTGTT
Found at i:31475981 original size:19 final size:18
Alignment explanation
Indices: 31475924--31476003 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
31475914 TTCATCTTGA
*
31475924 TTTTTCTTTTTCTTTTCTT
1 TTTTTCTTTTT-TTTTGTT
* *
31475943 TGTTTT-TTCTTTTTTCTT
1 T-TTTTCTTTTTTTTTGTT
*
31475961 TTTTTGTTTTGTTTTTGTT
1 TTTTTCTTTT-TTTTTGTT
* *
31475980 TTGTTCCTTTTTTGTTGTT
1 TT-TTTCTTTTTTTTTGTT
31475999 TTTTT
1 TTTTT
31476004 TAAGCATAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
17 4 0.08
18 13 0.26
19 23 0.46
20 10 0.20
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTGTT
Found at i:31475990 original size:27 final size:27
Alignment explanation
Indices: 31475941--31476004 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
31475931 TTTTCTTTTC
* *
31475941 TTTGTTTTTTCTTTTTTCTTTTTTTGT
1 TTTGTTTTTTCTTTGTTCCTTTTTTGT
31475968 TTTGTTTTTGT-TTTGTTCCTTTTTTGT
1 TTTGTTTTT-TCTTTGTTCCTTTTTTGT
31475995 TGTT-TTTTTT
1 T-TTGTTTTTT
31476005 AAGCATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 1 0.03
27 29 0.88
28 3 0.09
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (27 bp):
TTTGTTTTTTCTTTGTTCCTTTTTTGT
Found at i:31476001 original size:11 final size:10
Alignment explanation
Indices: 31475924--31476003 Score: 54
Period size: 11 Copynumber: 7.5 Consensus size: 10
31475914 TTCATCTTGA
*
31475924 TTTTTCTTTT
1 TTTTTGTTTT
*
31475934 TCTTTTCTTTGT
1 T-TTTTGTTT-T
*
31475946 TTTTTCTTTT
1 TTTTTGTTTT
31475956 TTCTTT-TTTT
1 TT-TTTGTTTT
*
31475966 GTTTTGTTTT
1 TTTTTGTTTT
*
31475976 TGTTTTGTTCCT
1 T-TTTTGTT-TT
31475988 TTTTTGTTGTT
1 TTTTTGTT-TT
31475999 TTTTT
1 TTTTT
31476004 TAAGCATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
9 3 0.05
10 13 0.22
11 39 0.66
12 4 0.07
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:31487173 original size:16 final size:17
Alignment explanation
Indices: 31487055--31487416 Score: 196
Period size: 17 Copynumber: 20.5 Consensus size: 17
31487045 AAAAAATTTG
*
31487055 AAACACGAGAATTTTTTA
1 AAACACGA-AAATTTTTA
* *
31487073 AAACACGAAGATTTTTG
1 AAACACGAAAATTTTTA
* *
31487090 GAACACGCAAAATTTTGA
1 AAACACG-AAAATTTTTA
* *
31487108 AAACATGAAAATTTTTG
1 AAACACGAAAATTTTTA
* *
31487125 AAATATGAAAA-TTTTA
1 AAACACGAAAATTTTTA
31487141 GAAACACGAAAATTTTTA
1 -AAACACGAAAATTTTTA
* *
31487159 AAACACG-ACATTTTTG
1 AAACACGAAAATTTTTA
* **
31487175 AAACATGGTCAATTTTTGA
1 AAACA-CGAAAATTTTT-A
* * *
31487194 AAATACGACAATTTTTG
1 AAACACGAAAATTTTTA
* * *
31487211 AAATATGAGAATTTTTTTTTA
1 AAACACGA-AA---ATTTTTA
*
31487232 AAACACGGAAATTTTTTTGA
1 AAACAC-GAAA-ATTTTT-A
* *
31487252 AAACAAGAAAATTTTCA
1 AAACACGAAAATTTTTA
* *
31487269 AAATAC-AGGAATTTTTGA
1 AAACACGA-AAATTTTT-A
*
31487287 AAACACGGGAAATTTTTTTAA
1 AAACAC--GAAA-ATTTTT-A
*
31487308 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTA
*
31487325 AAACACTG-GAATTTTTA
1 AAACAC-GAAAATTTTTA
* *
31487342 AAACACGAAGATTTTTG
1 AAACACGAAAATTTTTA
31487359 AAACACGAAAA-TTTTA
1 AAACACGAAAATTTTTA
**
31487375 GAAACGTGAAAATTTTTA
1 -AAACACGAAAATTTTTA
* *
31487393 AAACACGACAA-TTTTG
1 AAACACGAAAATTTTTA
31487409 AAACACGA
1 AAACACGA
31487417 TTTTTTTAAA
Statistics
Matches: 265, Mismatches: 57, Indels: 46
0.72 0.15 0.12
Matches are distributed among these distances:
16 34 0.13
17 117 0.44
18 62 0.23
19 19 0.07
20 7 0.03
21 24 0.09
22 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (17 bp):
AAACACGAAAATTTTTA
Found at i:31487246 original size:19 final size:19
Alignment explanation
Indices: 31487224--31487323 Score: 82
Period size: 20 Copynumber: 5.3 Consensus size: 19
31487214 TATGAGAATT
31487224 TTTTTTTAAAACACGGAAA
1 TTTTTTTAAAACACGGAAA
*
31487243 TTTTTTTGAAAACA-AGAAA
1 TTTTTTT-AAAACACGGAAA
* * *
31487262 -ATTTTCAAAATACAGG-AA
1 TTTTTTTAAAACAC-GGAAA
*
31487280 -TTTTTGAAAACACGGGAAA
1 TTTTTTTAAAACAC-GGAAA
*
31487299 TTTTTTTAAAAACACGAAAA
1 TTTTTTT-AAAACACGGAAA
31487319 TTTTT
1 TTTTT
31487324 GAAACACTGG
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
17 5 0.08
18 18 0.28
19 14 0.22
20 20 0.31
21 7 0.11
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (19 bp):
TTTTTTTAAAACACGGAAA
Found at i:31487310 original size:21 final size:20
Alignment explanation
Indices: 31487280--31487323 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
31487270 AATACAGGAA
* *
31487280 TTTTTGAAAACACGGGAAATT
1 TTTTTAAAAACAC-GAAAATT
31487301 TTTTTAAAAACACGAAAATT
1 TTTTTAAAAACACGAAAATT
31487321 TTT
1 TTT
31487324 GAAACACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTTAAAAACACGAAAATT
Found at i:31487718 original size:5 final size:5
Alignment explanation
Indices: 31487708--31487732 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31487698 TAAAATTATT
31487708 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
31487733 ATTGAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:31487922 original size:7 final size:7
Alignment explanation
Indices: 31487910--31487934 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31487900 TCTTCTTCTT
31487910 TTTTTTC
1 TTTTTTC
31487917 TTTTTTC
1 TTTTTTC
31487924 TTTTTTC
1 TTTTTTC
31487931 TTTT
1 TTTT
31487935 CTTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:31487934 original size:19 final size:17
Alignment explanation
Indices: 31487902--31487944 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
31487892 GAACCCCTTC
31487902 TTCTTCTTTTTTTTCTTTT
1 TTCTT-TTTTTTTTC-TTT
31487921 TTCTTTTTTCTTTTCTTT
1 TTCTTTTTT-TTTTCTTT
31487939 TTCTTT
1 TTCTTT
31487945 CCCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTCTTTTTTTTTTCTTT
Found at i:31488030 original size:24 final size:24
Alignment explanation
Indices: 31488003--31488073 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
31487993 TGCGCTGGGT
* *
31488003 CTGCTGGGCTGTGCTGGGCCTGGC
1 CTGCTGGGCTGCGCTGGGCCTGCC
31488027 CTGCTGGGCTGCGCTGGGCCTGCC
1 CTGCTGGGCTGCGCTGGGCCTGCC
* *
31488051 CTACTGGGCTGCGTTGGGCCTGC
1 CTGCTGGGCTGCGCTGGGCCTGC
31488074 TGAAAATGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.01, C:0.32, G:0.42, T:0.24
Consensus pattern (24 bp):
CTGCTGGGCTGCGCTGGGCCTGCC
Found at i:31488046 original size:19 final size:19
Alignment explanation
Indices: 31487982--31488049 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 19
31487972 GTGTGGGTCT
31487982 GGCCTGCTGGG-TGCGCTG
1 GGCCTGCTGGGCTGCGCTG
* *
31488000 GGTCTGCTGGGCTGTGCTGGG
1 GGCCTGCTGGGCTGCGCT--G
31488021 CCTGGCCTGCTGGGCTGCGCTG
1 ---GGCCTGCTGGGCTGCGCTG
31488043 GGCCTGC
1 GGCCTGC
31488050 CCTACTGGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 10 0.25
19 12 0.30
21 1 0.03
22 1 0.03
24 16 0.40
ACGTcount: A:0.00, C:0.29, G:0.47, T:0.24
Consensus pattern (19 bp):
GGCCTGCTGGGCTGCGCTG
Found at i:31488275 original size:3 final size:3
Alignment explanation
Indices: 31488269--31488317 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
31488259 TTTTCTATCT
31488269 TTC TTC TTC TTC TTCC TTC TTTC TTC TT- TT- TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TT-C TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
31488314 TTC T
1 TTC T
31488318 CAGTTCGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:31488330 original size:36 final size:38
Alignment explanation
Indices: 31488257--31488331 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 38
31488247 CTTTTTTTCT
**
31488257 TTTTTTCTATCTTTCTTCTTCTTCTTCCTTCTTTCTTC
1 TTTTTTCTATCTTTCTTCTTCTTCTTCCTTCGGTCTTC
*
31488295 TTTTTTCT-TC-TTCTTCTTCTTC-TCAGTTCGGTCTTC
1 TTTTTTCTATCTTTCTTCTTCTTCTTC-CTTCGGTCTTC
31488331 T
1 T
31488332 ATGCTGCCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 2 0.06
36 21 0.64
37 2 0.06
38 8 0.24
ACGTcount: A:0.03, C:0.28, G:0.04, T:0.65
Consensus pattern (38 bp):
TTTTTTCTATCTTTCTTCTTCTTCTTCCTTCGGTCTTC
Found at i:31488719 original size:30 final size:30
Alignment explanation
Indices: 31488668--31488836 Score: 189
Period size: 30 Copynumber: 5.7 Consensus size: 30
31488658 AAATGCAGCA
* *
31488668 AAAGTTTTGGGGCCAAAATGTAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
* * * *
31488698 AAAGCTTAAGGGTCCAAATGTAATTTTAAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
*
31488728 AAAGTTTAGGGGTCAAAATGTAATTTAGA-
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
** * * *
31488757 AAAGTTTAGGGGTTGAACTATAATTTTGAA
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
* *
31488787 AAAGTTTATGGGTTAAAATGTAATTTT-AG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
31488816 AAAAGTTTAGGGGTCAAAATG
1 -AAAGTTTAGGGGTCAAAATG
31488837 CAAAAAAAAA
Statistics
Matches: 114, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
29 25 0.22
30 89 0.78
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTGAG
Found at i:31488745 original size:60 final size:60
Alignment explanation
Indices: 31488667--31488836 Score: 193
Period size: 59 Copynumber: 2.9 Consensus size: 60
31488657 TAAATGCAGC
* * * * *
31488667 AAAAGTTTTGGGGCCAAAATGTAATTTTGAGAAAGCTTAAGGGTCCAAATGTAATTTT-A
1 AAAAGTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGTAATTTTGA
* ** * *
31488726 AGAAAGTTTAGGGGTCAAAATGTAATTTAGA-AAAGTTTAGGGGTTGAACTATAATTTTGA
1 A-AAAGTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGTAATTTTGA
* *
31488786 AAAAGTTTATGGGTTAAAATGTAATTTT-AGAAAAGTTTAGGGGTCAAAATG
1 AAAAGTTTAGGGGTCAAAATGTAATTTTGAG-AAAGTTTAGGGGTCAAAATG
31488837 CAAAAAAAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
58 1 0.01
59 46 0.51
60 44 0.48
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
AAAAGTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGTAATTTTGA
Found at i:31489319 original size:44 final size:44
Alignment explanation
Indices: 31489231--31489817 Score: 594
Period size: 44 Copynumber: 13.3 Consensus size: 44
31489221 AATTTCAGGG
* *
31489231 AGATAAGA-CTTG-TATCTTCGATCTTCTTC-TGCCAATACAGGA
1 AGATAAGATC-TGCTATCTTCGATCTACTTCATGCCAATACATGA
* * *
31489273 AGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGA
1 AGATAAGATCTGCTATCTTCGATCTACTTCATGCCAATACATGA
* * *
31489317 AGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACATGA
1 AGATAAGATCTGCTATCTTCGATCTACTTCATGCCAATACATGA
* * * ** * *
31489361 AGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATGA-GA
1 AGATAAGATCTGCTATCTTCGATCTACTTCA-TGCCAATA-CATGA
* * *
31489406 AGATAAGATCTGCTATCTTCGATCTAATTCACGCCAATATATGA
1 AGATAAGATCTGCTATCTTCGATCTACTTCATGCCAATACATGA
* * *
31489450 AGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGA
1 AGATAAGATCTGCTATCTTCGATCTACTTCATGCCAATACATGA
* *** * *
31489494 AGATAAGACCCATTATCTTCGATCTACTTCATGTCAAAACATGA
1 AGATAAGATCTGCTATCTTCGATCTACTTCATGCCAATACATGA
*
31489538 AGATAAGATCTGCTATC-TCTGATCTACTTCATGTCAATACATGA
1 AGATAAGATCTGCTATCTTC-GATCTACTTCATGCCAATACATGA
* *** ** * ***
31489582 AGACAAGATCCATTATCTTCGATCTACTTCACCACCAGTATGGGA
1 AGATAAGATCTGCTATCTTCGATCTACTTCA-TGCCAATACATGA
* * *
31489627 AGATAAGATCTACTATC-TCTGATCTACTTCATGTCAATACATAA
1 AGATAAGATCTGCTATCTTC-GATCTACTTCATGCCAATACATGA
*** *
31489671 AGATAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGA
1 AGATAAGATCTGCTATCTTCGATCTACTTCATGCCAATACATGA
* *
31489715 AGATAAGATCTTCTATC-TCTGATCTACTTCATGTCAATACATGA
1 AGATAAGATCTGCTATCTTC-GATCTACTTCATGCCAATACATGA
* *** *
31489759 AGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGA
1 AGATAAGATCTGCTATCTTCGATCTACTTCATGCCAATACATGA
31489803 AGATAAGATCTGCTA
1 AGATAAGATCTGCTA
31489818 CTTTTCAACC
Statistics
Matches: 458, Mismatches: 74, Indels: 24
0.82 0.13 0.04
Matches are distributed among these distances:
42 9 0.02
43 21 0.05
44 355 0.78
45 72 0.16
46 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (44 bp):
AGATAAGATCTGCTATCTTCGATCTACTTCATGCCAATACATGA
Found at i:31489462 original size:177 final size:175
Alignment explanation
Indices: 31489231--31489821 Score: 681
Period size: 177 Copynumber: 3.4 Consensus size: 175
31489221 AATTTCAGGG
* * *
31489231 AGATAAGA-CTTGTATCTTCGATCTTCTTC-TGCCAATACAGGAAGACAAGATCTGCTATCTTTG
1 AGATAAGATC-TGTATCTTCGATCTACTTCACGCCAATATAGGAAGACAAGATCTGCTATCTTTG
* ** * *
31489294 ATCTACTTCACGCCAATACATGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACAT
65 ATCTACTTCACGCCAATACATGAAGATAAGATCCATTATCTTCGATCTACTTCATGTCAATACAT
* * * * *
31489359 GAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATGA-GA
130 GAAGATAAGATCTGCTATCTCTGATCTACTTCA-CACCAATA-CATGA
* * * *
31489406 AGATAAGATCTGCTATCTTCGATCTAATTCACGCCAATATATGAAGACAAGATCTGCTTTCTTCG
1 AGATAAGATCTG-TATCTTCGATCTACTTCACGCCAATATAGGAAGACAAGATCTGCTATCTTTG
* *
31489471 ATCTACTTCACGCCAATACATGAAGATAAGACCCATTATCTTCGATCTACTTCATGTCAAAACAT
65 ATCTACTTCACGCCAATACATGAAGATAAGATCCATTATCTTCGATCTACTTCATGTCAATACAT
***
31489536 GAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGA
130 GAAGATAAGATCTGCTATCTCTGATCTACTTCACACCAATACATGA
* * * * * * *
31489582 AGACAAGATCCAT-TATCTTCGATCTACTTCACCACCAGTATGGGAAGATAAGATCTACTATCTC
1 AGATAAGAT-C-TGTATCTTCGATCTACTTCA-CGCCAATATAGGAAGACAAGATCTGCTATCTT
* * *
31489646 TGATCTACTTCATGTCAATACATAAAGATAAGATCCATTATCTTCGATCTACTTCATGTCAATAC
63 TGATCTACTTCACGCCAATACATGAAGATAAGATCCATTATCTTCGATCTACTTCATGTCAATAC
* ***
31489711 ATGAAGATAAGATCTTCTATCTCTGATCTACTTCATGTCAATACATGA
128 ATGAAGATAAGATCTGCTATCTCTGATCTACTTCACACCAATACATGA
* * * * * *
31489759 AGACAAGATCCAT-TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTA-CTTT
1 AGATAAGAT-C-TGTATCTTCGATCTACTTCACGCCAATATAGGAAGACAAGATCTGCTATCTTT
31489822 TCAACCTGCT
Statistics
Matches: 361, Mismatches: 48, Indels: 14
0.85 0.11 0.03
Matches are distributed among these distances:
175 14 0.04
176 67 0.19
177 279 0.77
178 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (175 bp):
AGATAAGATCTGTATCTTCGATCTACTTCACGCCAATATAGGAAGACAAGATCTGCTATCTTTGA
TCTACTTCACGCCAATACATGAAGATAAGATCCATTATCTTCGATCTACTTCATGTCAATACATG
AAGATAAGATCTGCTATCTCTGATCTACTTCACACCAATACATGA
Found at i:31489692 original size:221 final size:219
Alignment explanation
Indices: 31489243--31489812 Score: 724
Period size: 221 Copynumber: 2.6 Consensus size: 219
31489233 ATAAGACTTG
* * * * * *
31489243 TATCTTCGATCTTCTTC-TGCCAATACAGGAAGACAAGATC-TGCTATCTTTGATCTACTTCACG
1 TATCTTCGATCTACTTCATGCCAATACATGAAGATAAGACCAT--TATCTTCGATCTACTTCATG
* * *
31489306 CCAATACATGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
64 TCAATACATGAAGACAAGATCTGTTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
* *
31489371 TGCTTTCTTTGATCTACTTCACCACCAGTATGAGAAGATAAGATCTGCTATCTTCGATCTAATTC
129 -GCTTTCTTCGATCTACTTCACCACCAGTATGAGAAGATAAGATCTACTATCTTCGATCTAATTC
* *
31489436 ACGCCAATATATGAAGACAAGATCTGCT
193 ACGCCAATACATAAAGACAAGATC-GCT
*
31489464 T-TCTTCGATCTACTTCACGCCAATACATGAAGATAAGACCCATTATCTTCGATCTACTTCATGT
1 TATCTTCGATCTACTTCATGCCAATACATGAAGATAAGA-CCATTATCTTCGATCTACTTCATGT
* * *
31489528 CAAAACATGAAGATAAGATCTGCTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATC
65 CAATACATGAAGACAAGATCTGTTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATC
* *
31489592 -CATTATCTTCGATCTACTTCACCACCAGTATGGGAAGATAAGATCTACTATC-TCTGATCTACT
129 GC-TT-TCTTCGATCTACTTCACCACCAGTATGAGAAGATAAGATCTACTATCTTC-GATCTAAT
* * *
31489655 TCATGTCAATACATAAAGATAAGATC-CAT
191 TCACGCCAATACATAAAGACAAGATCGC-T
* * *
31489684 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTTCTATC-TCTGATCTACTTCATG
1 TATCTTCGATCTACTTCATGCCAATACATGAAGATAAGACCAT-TATCTTC-GATCTACTTCATG
** *
31489748 TCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATC
64 TCAATACATGAAGACAAGATCTGTTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
31489813 TGCTACTTTT
Statistics
Matches: 305, Mismatches: 32, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
219 2 0.01
220 26 0.09
221 273 0.90
222 3 0.01
223 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (219 bp):
TATCTTCGATCTACTTCATGCCAATACATGAAGATAAGACCATTATCTTCGATCTACTTCATGTC
AATACATGAAGACAAGATCTGTTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCGC
TTTCTTCGATCTACTTCACCACCAGTATGAGAAGATAAGATCTACTATCTTCGATCTAATTCACG
CCAATACATAAAGACAAGATCGCT
Found at i:31491139 original size:22 final size:23
Alignment explanation
Indices: 31491108--31491155 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
31491098 AGCCTCTCCA
31491108 TTTTATTTTTCCAT-TTTTCATTT
1 TTTTATTTTT-CATCTTTTCATTT
31491131 TTTTA-TTTTCATCTTTTCATTT
1 TTTTATTTTTCATCTTTTCATTT
31491153 TTT
1 TTT
31491156 CACATCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 3 0.12
22 16 0.67
23 5 0.21
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTCATCTTTTCATTT
Found at i:31496009 original size:3 final size:3
Alignment explanation
Indices: 31496001--31496037 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
31495991 ATTACCAGAT
*
31496001 TAA TAA TAA TAA CAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
31496038 CAGTAAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:31498673 original size:27 final size:26
Alignment explanation
Indices: 31498633--31498706 Score: 112
Period size: 27 Copynumber: 2.8 Consensus size: 26
31498623 ACACACCGCA
*
31498633 GCTCTTTATGAGCTTCCCGTTTAAAG
1 GCTCTTTATGAGCTTCCCGATTAAAG
*
31498659 GCTCTTTCATGAGCTTCCTGATTAAAG
1 GCTCTTT-ATGAGCTTCCCGATTAAAG
*
31498686 GCTCTTTATGAGCTTTCCGAT
1 GCTCTTTATGAGCTTCCCGAT
31498707 ATGGCTAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.44
27 24 0.56
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (26 bp):
GCTCTTTATGAGCTTCCCGATTAAAG
Found at i:31502499 original size:5 final size:5
Alignment explanation
Indices: 31502484--31502513 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
31502474 CAATCCGGGC
31502484 CCAAA -CAAA CCAAA CCAAA CCAAA CCAAA C
1 CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA C
31502514 AAAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:31503920 original size:3 final size:3
Alignment explanation
Indices: 31503914--31503947 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
31503904 TTTTCTGCCT
31503914 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
31503948 CTTTTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31508582 original size:44 final size:44
Alignment explanation
Indices: 31508519--31509283 Score: 744
Period size: 44 Copynumber: 17.2 Consensus size: 44
31508509 ACAAGATACG
* * * *
31508519 AATCTTATCTCCTTAAAGTTGCAGTGGGGTAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* *
31508563 AATCTTATTTCTCTGAAGTTGCAGTGG-GACAGATTAAAGCTACAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAAGCTAC-----A
* * * *
31508612 CAAGTCTTATCTCCCTGAACTTGCAGTGGAGTAGATTAAAACCACA
1 -AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * *
31508658 GATCTTCTCTCACTGAAGTTGCAGTGGAGTAGATTAAAACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
** * * * * *
31508702 GGTCTTCTCTCACTGAAGTTGCAGTGGACCAGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
31508746 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * *
31508790 AATCTTATCTCCTTGATGTTGCAATAGAGAAAATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
31508834 AATCTTATTTCCCTAAAGTTGTAGTGGAACAGATTAAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * *
31508878 AATCTTATCTCTCTGAAGGTGTAGTGGAGCAGAATAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* *
31508922 AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * *
31508966 AATCTTATTTCCTTAAAGTTGTAGTGGAGCAGATTGAAA-TTGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTACA
* * * *
31509010 AGTCTTATCTCCTTGAAGTTGTAGTGGAGTAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * * * * *
31509054 TATCTTCTCTCCATAAAGTTACAGTGGAGCAGACTGAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * *
31509098 AATTTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
31509142 AATCTTATCTCCCTAAAGTTACAGTGGAGTAGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * *
31509186 AATCTTATCTCTCTGAAGTTGCAGTGGAGC-GATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * *
31509229 AATCTCATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCGACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* *
31509273 AGTCTAATCTC
1 AATCTTATCTC
31509284 TTTAAAGTTG
Statistics
Matches: 603, Mismatches: 106, Indels: 24
0.82 0.14 0.03
Matches are distributed among these distances:
43 44 0.07
44 517 0.86
45 4 0.01
46 1 0.00
49 1 0.00
50 2 0.00
51 33 0.05
52 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
Found at i:31513491 original size:3 final size:3
Alignment explanation
Indices: 31513444--31513522 Score: 52
Period size: 3 Copynumber: 25.3 Consensus size: 3
31513434 TATTTTTTGC
* * * * * *
31513444 TAT TAT TGT TAT TTT TAA TAT TAC TAT TAC TAT TAT T-G TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
31513489 TAT TAT TACT TACCT TAT TAT TAT TAT AAT TAT T
1 TAT TAT TA-T TA--T TAT TAT TAT TAT TAT TAT T
31513523 TATTCATTCA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
2 1 0.02
3 48 0.83
4 5 0.09
5 4 0.07
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:31513508 original size:30 final size:29
Alignment explanation
Indices: 31513443--31513515 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
31513433 TTATTTTTTG
31513443 CTATTATTGTTATTTTTAATATTACTATTA
1 CTATTATTGTTATTTTTAATATTAC-ATTA
*
31513473 CTATTATTG-TATTTATTATTATTAC-TTA
1 CTATTATTGTTATTT-TTAATATTACATTA
*
31513501 CCTTATTATTATTAT
1 -C-TATTATTGTTAT
31513516 AATTATTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 3 0.08
29 6 0.16
30 25 0.68
31 3 0.08
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (29 bp):
CTATTATTGTTATTTTTAATATTACATTA
Found at i:31513608 original size:27 final size:27
Alignment explanation
Indices: 31513570--31513623 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
31513560 TATATACATG
*
31513570 CATACTAGATGTGTCCATGGGCCGGGC
1 CATACCAGATGTGTCCATGGGCCGGGC
31513597 CATACCAGATGTGTCCATGGGCCGGGC
1 CATACCAGATGTGTCCATGGGCCGGGC
31513624 GGCCCGGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.20
Consensus pattern (27 bp):
CATACCAGATGTGTCCATGGGCCGGGC
Found at i:31514104 original size:11 final size:12
Alignment explanation
Indices: 31514085--31514137 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
31514075 ACATACGTAC
31514085 TTATATATATAT
1 TTATATATATAT
31514097 TT-TATATAT-T
1 TTATATATATAT
*
31514107 TTATATACATAT
1 TTATATATATAT
* *
31514119 CTATTTATATAT
1 TTATATATATAT
*
31514131 CTATATA
1 TTATATA
31514138 CTTTTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 3 0.09
11 13 0.38
12 18 0.53
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATATATATAT
Found at i:31516160 original size:2 final size:2
Alignment explanation
Indices: 31516153--31516177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31516143 CGACTTATAG
31516153 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
31516178 GATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31524164 original size:26 final size:26
Alignment explanation
Indices: 31524129--31524180 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
31524119 AATGTGAAAG
*
31524129 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
31524155 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
31524181 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:31524191 original size:103 final size:102
Alignment explanation
Indices: 31524051--31524415 Score: 610
Period size: 102 Copynumber: 3.6 Consensus size: 102
31524041 TGTATATAAA
** * * *
31524051 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
31524115 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAA--TGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
31524154 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
31524219 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
31524256 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
31524321 TGAAATAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
31524358 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCG-GATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
31524416 ATAACGGTTA
Statistics
Matches: 252, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
101 34 0.13
102 154 0.61
103 63 0.25
104 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:31531343 original size:104 final size:104
Alignment explanation
Indices: 31531163--31531386 Score: 369
Period size: 104 Copynumber: 2.2 Consensus size: 104
31531153 TGTATATAAA
** * *
31531163 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
31531228 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
31531267 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
31531331 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
31531371 AGGGGTTTCTAAGTGC
1 AGGGGTTGCTAAGTGC
31531387 GATATCCATT
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
104 111 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:31531434 original size:70 final size:71
Alignment explanation
Indices: 31531305--31531455 Score: 232
Period size: 70 Copynumber: 2.1 Consensus size: 71
31531295 TCATTGGTGG
* *
31531305 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAA-GTGAAAAGGGGTTGCTATGTGCTGATTCCCCC
31531370 GAGGGGT
65 GAGGGGT
* ***
31531377 TTCTAAGTGCGATATCCATTGTATATTTGAAA-TGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
31531441 AGGGGT
66 AGGGGT
31531447 TGCTAAGTG
1 TGCTAAGTG
31531456 ATGATTCCCC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
70 45 0.62
72 27 0.38
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:31531460 original size:27 final size:27
Alignment explanation
Indices: 31531414--31531465 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
31531404 TGAAATGAAA
* *
31531414 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGATGATTCCCCCG
31531441 AGGGGTTGCTAAGTGATGATTCCCC
1 AGGGGTTGCTAAGTGATGATTCCCC
31531466 GATTCAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGATGATTCCCCCG
Found at i:31566514 original size:3 final size:3
Alignment explanation
Indices: 31566506--31566574 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
31566496 TTTCGTTTGC
31566506 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31566554 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
31566575 CAGCTATAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:31570642 original size:20 final size:20
Alignment explanation
Indices: 31570617--31570655 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31570607 TCAAAAATCT
31570617 GAATAAAAATGAATG-TAATG
1 GAATAAAAAT-AATGATAATG
*
31570637 GAATAACAATAATGATAAT
1 GAATAAAAATAATGATAAT
31570656 CAAACAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (20 bp):
GAATAAAAATAATGATAATG
Found at i:31571241 original size:3 final size:3
Alignment explanation
Indices: 31571235--31571266 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
31571225 ATAATAATAA
31571235 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
31571267 CATTAAACCA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:31571934 original size:17 final size:18
Alignment explanation
Indices: 31571903--31571936 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31571893 GGATTTATAA
31571903 AAAAATGGAAACAAAAAT
1 AAAAATGGAAACAAAAAT
*
31571921 AAAAAT-GAATCAAAAA
1 AAAAATGGAAACAAAAA
31571937 ATAACACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (18 bp):
AAAAATGGAAACAAAAAT
Found at i:31573616 original size:15 final size:15
Alignment explanation
Indices: 31573596--31573625 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31573586 CAATTGCTAA
31573596 CCTAAAATTGGATTT
1 CCTAAAATTGGATTT
31573611 CCTAAAATTGGATTT
1 CCTAAAATTGGATTT
31573626 TCCAATTTTG
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:0.13, T:0.40
Consensus pattern (15 bp):
CCTAAAATTGGATTT
Found at i:31575021 original size:150 final size:148
Alignment explanation
Indices: 31574790--31575596 Score: 1052
Period size: 150 Copynumber: 5.3 Consensus size: 148
31574780 GCACCAACAT
* * * * *
31574790 CCTTATTTTGGCCCTTTATTCGTATTTTTTTCCAAATTTTATTACTTTAAAAAATATACTATTTT
1 CCTTATTTCGGCCC-TTGTTCGTATTTTTTCCCAGATTTTATTACTTTAAAAAATATATTATTTT
*
31574855 CTAATTTTATTATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
65 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTA-TGTGTTTT
31574920 TTAAATAAA-TT-AAAAAAC
129 TTAAATAAATTTAAAAAAAC
*
31574938 CCTTATTTCGGCCCTTGTTCGTATTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATT
1 CCTTATTTCGGCCCTTGTTCGTATTTTTTCCCAGATTTTATTACTTT--A-AAAAATATATTATT
* *
31575003 TTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTGT
63 TTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTA-TGTGT
31575067 TTTTTAAATAAATTTAAAAAAAAC
126 TTTTTAAATAAATTT-AAAAAAAC
* * * * * *
31575091 TCTTATTTCGGCCATTTGTTTGTATTTTTTTCCCCGATTTTATTGC-TTAAAAAA-ATACTATTT
1 CCTTATTTCGGCC-CTTGTTCGTA-TTTTTTCCCAGATTTTATTACTTTAAAAAATATATTATTT
* *
31575154 TCTAATTTCATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCCATTTA-GTGTTTT
64 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATGTGTTTT
**
31575218 TTAAATAAATTTTTTTAAAAAC
129 TTAAATAAA--TTTAAAAAAAC
* *
31575240 CCTTATTTCGGCTCTTTGTTCGTATTTTTCTCCCAAATTTTATTACTTTCAATAAAAATATATTA
1 CCTTATTTCGGC-CCTTGTTCGTATTTTT-TCCCAGATTTTATTACTTT--A-AAAAATATATTA
* *
31575305 TTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTGT
61 TTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTA-TGT
31575369 GTTTTTTAAATAAATTTAGTAAAAAAAC
124 GTTTTTTAAATAAA-TT--TAAAAAAAC
* *
31575397 CCTTATTTCGGCTCTTTGTTCGTATTTTTCCCCAGATTTTATTACTTTAAAAAATATATTATTTT
1 CCTTATTTCGGC-CCTTGTTCGTATTTTTTCCCAGATTTTATTACTTTAAAAAATATATTATTTT
31575462 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTTTT
65 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTT-ATGTGTTTT
*
31575527 TTAAATAAATTTAAAAAAAA
129 TTAAATAAATTTAAAAAAAC
* * * * *
31575547 ACTTATTTCGGCCCTTTATTCGTATTTTTTTCTCAAATTTTATTATTTTA
1 CCTTATTTCGGCCC-TTGTTCGTA-TTTTTTCCCAGATTTTATTACTTTA
31575597 CATTATTTTA
Statistics
Matches: 585, Mismatches: 46, Indels: 53
0.86 0.07 0.08
Matches are distributed among these distances:
147 29 0.05
148 34 0.06
149 42 0.07
150 175 0.30
151 29 0.05
152 5 0.01
153 108 0.18
154 71 0.12
155 23 0.04
156 33 0.06
157 36 0.06
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (148 bp):
CCTTATTTCGGCCCTTGTTCGTATTTTTTCCCAGATTTTATTACTTTAAAAAATATATTATTTTC
TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATGTGTTTTTT
AAATAAATTTAAAAAAAC
Found at i:31575342 original size:304 final size:303
Alignment explanation
Indices: 31574790--31575591 Score: 1217
Period size: 304 Copynumber: 2.6 Consensus size: 303
31574780 GCACCAACAT
* * **
31574790 CCTTATTTTGGCCCTTTATTCGTATTTTTTT-CCAAATTTTATTACTTTAAAAAATATACTATTT
1 CCTTATTTCGG-CCTTTGTTCGTATTTTTTTCCCCGATTTTATTACTTTAAAAAATATACTATTT
*
31574854 TCTAATTTTATTATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
65 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTA-TGTGTTT
* **
31574919 TTTAAATAAA--TTAAAAAACCCTTATTTCGGCCCTTGTTCGTATTTTTTCCCGGATTTTATTAC
129 TTTAAATAAATTTTAAAAAACCCTTATTTCGGCCTTTGTTCGTATTTTTTCCCAAATTTTATTAC
31574982 TTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGA
194 TTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGA
*
31575047 AATATATTAATTTACTGTGTTTTTTAAATAAATTTA-AAAAAAAC
259 AATATATTAATTAACTGTGTTTTTTAAATAAATTTAGAAAAAAAC
* * *
31575091 TCTTATTTCGGCCATTTGTTTGTATTTTTTTCCCCGATTTTATTGC-TTAAAAAA-ATACTATTT
1 CCTTATTTCGGCC-TTTGTTCGTATTTTTTTCCCCGATTTTATTACTTTAAAAAATATACTATTT
* *
31575154 TCTAATTTCATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCCATTTA-GTGTTTT
65 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATGTGTTTT
*
31575218 TTAAATAAATTTTTTTAAAAACCCTTATTTCGGCTCTTTGTTCGTATTTTTCTCCCAAATTTTAT
130 TTAAATAAA--TTTTAAAAAACCCTTATTTCGGC-CTTTGTTCGTATTTTT-TCCCAAATTTTAT
31575283 TACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTT
191 TACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTT
* *
31575348 TGAAATGTATTAATTAATTGTGTTTTTTAAATAAATTTAGTAAAAAAAC
256 TGAAATATATTAATTAACTGTGTTTTTTAAATAAATTTAG-AAAAAAAC
*
31575397 CCTTATTTCGGCTCTTTGTTCGTA--TTTTTCCCCAGATTTTATTACTTTAAAAAATATATTATT
1 CCTTATTTCGGC-CTTTGTTCGTATTTTTTTCCCC-GATTTTATTACTTTAAAAAATATACTATT
31575460 TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTT
64 TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTT-ATGTGTT
* ** * *
31575525 TTTTAAATAAATTTAAAAAAAAACTTATTTCGGCCCTTTATTCGTATTTTTTTCTCAAATTTTAT
128 TTTTAAATAAATTTTAAAAAACCCTTATTTCGG-CCTTTGTTCGTA-TTTTTTCCCAAATTTTAT
31575590 TA
191 TA
31575592 TTTTACATTA
Statistics
Matches: 454, Mismatches: 29, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
298 16 0.04
300 65 0.14
301 32 0.07
302 31 0.07
303 15 0.03
304 121 0.27
305 10 0.02
306 36 0.08
307 105 0.23
308 7 0.02
309 16 0.04
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (303 bp):
CCTTATTTCGGCCTTTGTTCGTATTTTTTTCCCCGATTTTATTACTTTAAAAAATATACTATTTT
CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATGTGTTTTT
TAAATAAATTTTAAAAAACCCTTATTTCGGCCTTTGTTCGTATTTTTTCCCAAATTTTATTACTT
TCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
TATATTAATTAACTGTGTTTTTTAAATAAATTTAGAAAAAAAC
Found at i:31575696 original size:118 final size:118
Alignment explanation
Indices: 31575464--31575695 Score: 369
Period size: 118 Copynumber: 2.0 Consensus size: 118
31575454 ATTATTTTCT
* *
31575464 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTTTTTT
1 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCAATTAATATGTTTTTT
*
31575529 AAATAAATTTAAAAAAAAACTTATTTCGGCCCTTTATTCGTATTTTTTTCTCA
66 AAATAAATTTAAAAAAAAACTTACTTCGGCCCTTTATTCGTATTTTTTTCTCA
31575582 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATT-AATTAATTATG-TTTT
1 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCAATTAA-TATGTTTTT
** *
31575645 TAAATAAATTTAGTAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTT
65 TAAATAAATTTA--AAAAAAAACTTACTTCGGCCCTTTATTCGTATTTTTT
31575696 CCCCGGATTT
Statistics
Matches: 105, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
117 21 0.20
118 51 0.49
119 33 0.31
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.51
Consensus pattern (118 bp):
AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCAATTAATATGTTTTTT
AAATAAATTTAAAAAAAAACTTACTTCGGCCCTTTATTCGTATTTTTTTCTCA
Found at i:31575740 original size:151 final size:153
Alignment explanation
Indices: 31575582--31575866 Score: 432
Period size: 151 Copynumber: 1.9 Consensus size: 153
31575572 TTTTTTCTCA
*
31575582 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTATG-TTTTT
1 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAAGTATGTTTTTT
* *
31575646 -AAATAAATTTAGTAAAAAA-CCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCGGATTTTAT
66 AAAATAAATTTA-AAAAAAACCCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTAT
31575709 TACTTAAAAAAAATACTATTTTCT
130 TACTTAAAAAAAATACTATTTTCT
* * * *
31575733 AATTTTATTATTTTACATTATTTTAGTACGTTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
1 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAAGTATGTTTTTT
*** * *
31575798 AAAATTTTTTTAAAAAAAACCCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCAGATTTTATT
66 AAAATAAATTTAAAAAAAACCCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATT
31575863 ACTT
131 ACTT
31575867 TCAATAAAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
151 54 0.45
152 11 0.09
153 54 0.45
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.51
Consensus pattern (153 bp):
AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAAGTATGTTTTTT
AAAATAAATTTAAAAAAAACCCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATT
ACTTAAAAAAAATACTATTTTCT
Found at i:31575794 original size:269 final size:273
Alignment explanation
Indices: 31575312--31575863 Score: 916
Period size: 269 Copynumber: 2.0 Consensus size: 273
31575302 TTATTTTCGT
*
31575312 ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTGTGTTTTTTA
1 ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTATGTTTTTTA
* *
31575377 AATAAATTTAGTAAAAAAACCCTTATTTCGGCTCTTTGTTCGTATTTTTCCCCAGATTTTATTAC
66 AATAAATTTAGTAAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTCCCCAGATTTTATTAC
* *
31575442 TTTAAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
131 TTTAAAAAAAATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
31575507 GTATTCATTTAATGTGTTTTTT-AAATAAATTTAAAAAAAA-ACTTATTTCGGCCCTTTATTCGT
196 GTATTCATTTAATGTGTTTTTTAAAATAAATTTAAAAAAAACACTTATTTCGGCCCTTTATTCGT
*
31575570 ATTTTTTTCTCAA
261 ATTTTTTTCCCAA
31575583 ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTATG-TTTTTA
1 ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTATGTTTTTTA
*
31575647 AATAAATTTAGT-AAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCGGATTTTATTA
66 AATAAATTTAGTAAAAAAACCCTTACTTCGGCCCTTTGTTCGTA-TTTTTCCCCAGATTTTATTA
*
31575711 C-TTAAAAAAAATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACGTTATGTTTGAAA
130 CTTTAAAAAAAATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
* *** * *
31575775 TGTATTCATTTAGTGTGTTTTTTAAAATTTTTTTAAAAAAAACCCCTTATTTCGGCCCTTTGTTC
195 TGTATTCATTTAATGTGTTTTTTAAAATAAATTTAAAAAAAA-CACTTATTTCGGCCCTTTATTC
*
31575840 GTATTTTTTTCCCAG
259 GTATTTTTTTCCCAA
31575855 ATTTTATTA
1 ATTTTATTA
31575864 CTTTCAATAA
Statistics
Matches: 262, Mismatches: 15, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
269 111 0.42
270 53 0.20
271 57 0.22
272 41 0.16
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (273 bp):
ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTATGTTTTTTA
AATAAATTTAGTAAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTCCCCAGATTTTATTAC
TTTAAAAAAAATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
GTATTCATTTAATGTGTTTTTTAAAATAAATTTAAAAAAAACACTTATTTCGGCCCTTTATTCGT
ATTTTTTTCCCAA
Found at i:31583857 original size:61 final size:60
Alignment explanation
Indices: 31583774--31583919 Score: 141
Period size: 61 Copynumber: 2.4 Consensus size: 60
31583764 ATACACTTTT
* * * * * * * *
31583774 TCAATTTGATCCTAAATATAAAAAATTTAACAAATTTAGCCTTCAATATTTACAAAATTTG
1 TCAATTTAATTCTAATTCTAAAAAA-TCAACAAACTTAGCCCTCAACATTTACAAAATTTG
* * * * *
31583835 AT-ATTTTAGTTCTAATTCTAAAATCATCAACTAACTTCGCCCTCAACATTTACAAAATTTG
1 -TCAATTTAATTCTAATTCTAAAA-AATCAACAAACTTAGCCCTCAACATTTACAAAATTTG
31583896 TCAATTTAATTCTAATTCTAAAAA
1 TCAATTTAATTCTAATTCTAAAAA
31583920 TTTCAAAAAG
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
60 1 0.02
61 63 0.95
62 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.38
Consensus pattern (60 bp):
TCAATTTAATTCTAATTCTAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTG
Found at i:31585249 original size:107 final size:107
Alignment explanation
Indices: 31585060--31585272 Score: 286
Period size: 107 Copynumber: 2.0 Consensus size: 107
31585050 ATTCATCACC
* *
31585060 CCTTCACCTACATGATGACCATAAAATATCTTTCTATCGTCCGTGGGACAAAATTGAGTATCCAC
1 CCTTCACCTACATGATGACCATAAAATATATTTCTATCGTCCATGGGACAAAATTGAGTATCCAC
* * *
31585125 GTTGTGTACGCGAGAATTCAATATGAAAGCATCTAATCTTCA
66 ATTGTGTACGCGAGAATTCAATACGAAACCATCTAATCTTCA
* * * *
31585167 CCTTCACCTGCATGAAT-AGCATACAATATATTTCT-TTGATCCATGGGACAAAATTGAGTATCC
1 CCTTCACCTACATG-ATGACCATAAAATATATTTCTATCG-TCCATGGGACAAAATTGAGTATCC
** *
31585230 ACATTGTGTTGGCGTGAATTCAATACGAAACCATCTAATCTTC
64 ACATTGTGTACGCGAGAATTCAATACGAAACCATCTAATCTTC
31585273 CTAACCTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 2 0.02
107 88 0.96
108 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (107 bp):
CCTTCACCTACATGATGACCATAAAATATATTTCTATCGTCCATGGGACAAAATTGAGTATCCAC
ATTGTGTACGCGAGAATTCAATACGAAACCATCTAATCTTCA
Found at i:31595950 original size:20 final size:20
Alignment explanation
Indices: 31595925--31595971 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31595915 ATATCTTGAT
31595925 TTGATTTGATTTCAATCAAA
1 TTGATTTGATTTCAATCAAA
* * *
31595945 TTGATTTTATTTTATTCAAA
1 TTGATTTGATTTCAATCAAA
31595965 TTGATTT
1 TTGATTT
31595972 AAAGACTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (20 bp):
TTGATTTGATTTCAATCAAA
Found at i:31600621 original size:63 final size:62
Alignment explanation
Indices: 31600522--31600662 Score: 160
Period size: 63 Copynumber: 2.3 Consensus size: 62
31600512 TTTTAAGCCT
* * *** * **
31600522 AAACAGTGAGTTACACGGCCTGGATACATGTTCATGTCCCT-ACCCGTGTGG-CTTTTATACCAC
1 AAACAGTGAGTTACACAGCCTGGACACATACCCATGTCCCTGA-CCGTATGGTCTCGT-T-CCAC
*
31600585 AAACAGTGAGTTACACAGCCTGGGCACATACCCATGTCCCTGACCGTATGGTCTCGTTCCAC
1 AAACAGTGAGTTACACAGCCTGGACACATACCCATGTCCCTGACCGTATGGTCTCGTTCCAC
31600647 AAACAGTGAGTTACAC
1 AAACAGTGAGTTACAC
31600663 GACCCAAACA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
62 20 0.30
63 43 0.64
64 4 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (62 bp):
AAACAGTGAGTTACACAGCCTGGACACATACCCATGTCCCTGACCGTATGGTCTCGTTCCAC
Found at i:31602100 original size:91 final size:91
Alignment explanation
Indices: 31601945--31602129 Score: 361
Period size: 91 Copynumber: 2.0 Consensus size: 91
31601935 CATGTCATAA
*
31601945 TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACTTGTAATTAATATATATTTCC
1 TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACCTGTAATTAATATATATTTCC
31602010 AACTTTCTTTGAAAATTCACTCATCT
66 AACTTTCTTTGAAAATTCACTCATCT
31602036 TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACCTGTAATTAATATATATTTCC
1 TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACCTGTAATTAATATATATTTCC
31602101 AACTTTCTTTGAAAATTCACTCATCT
66 AACTTTCTTTGAAAATTCACTCATCT
31602127 TTG
1 TTG
31602130 TACGTTGTGG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (91 bp):
TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACCTGTAATTAATATATATTTCC
AACTTTCTTTGAAAATTCACTCATCT
Found at i:31605305 original size:27 final size:27
Alignment explanation
Indices: 31605258--31605310 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
31605248 AACGTGTTAT
*
31605258 AAAAAAAAGATGGAGAGAATAAAGAAC
1 AAAAAAAAGATGGAAAGAATAAAGAAC
* *
31605285 AAAAAAAATAT-GAAAGCAATAGAGAA
1 AAAAAAAAGATGGAAAG-AATAAAGAA
31605311 TGTACTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.68, C:0.04, G:0.19, T:0.09
Consensus pattern (27 bp):
AAAAAAAAGATGGAAAGAATAAAGAAC
Found at i:31605562 original size:17 final size:18
Alignment explanation
Indices: 31605540--31605583 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
31605530 GGGATTTAAA
*
31605540 TAATTAATTAAA-AATTT
1 TAATTAAGTAAATAATTT
31605557 TAATTATAGTAAATAATTT
1 TAATTA-AGTAAATAATTT
31605576 TCAATTAA
1 T-AATTAA
31605584 AATACCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 7 0.30
20 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TAATTAAGTAAATAATTT
Found at i:31608695 original size:3 final size:3
Alignment explanation
Indices: 31608689--31608715 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31608679 AATAGTATAG
31608689 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
31608716 TGTGGGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:31611009 original size:10 final size:11
Alignment explanation
Indices: 31610981--31611014 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
31610971 GATCTATCTC
31610981 TCAACAAAAATT
1 TCAA-AAAAATT
31610993 TCAAAAAAATT
1 TCAAAAAAATT
*
31611004 TCAAAATAATT
1 TCAAAAAAATT
31611015 ATTTAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (11 bp):
TCAAAAAAATT
Found at i:31611041 original size:19 final size:19
Alignment explanation
Indices: 31610997--31611051 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
31610987 AAAATTTCAA
31610997 AAAAATTTCAAAATAATTAT
1 AAAAA-TTCAAAATAATTAT
**
31611017 TTAAATTCAAAAT-ATTAAT
1 AAAAATTCAAAATAATT-AT
*
31611036 AAAAATTTAAAA-AATT
1 AAAAATTCAAAATAATT
31611052 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.11
19 22 0.79
20 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAATAATTAT
Found at i:31617404 original size:15 final size:16
Alignment explanation
Indices: 31617384--31617413 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31617374 ATTTTCAAAT
31617384 TTAAAA-TTATTATTG
1 TTAAAATTTATTATTG
31617399 TTAAAATTTATTATT
1 TTAAAATTTATTATT
31617414 AAAAAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTAAAATTTATTATTG
Found at i:31617420 original size:16 final size:16
Alignment explanation
Indices: 31617401--31617442 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
31617391 TATTATTGTT
31617401 AAAATTTATTATTAAA
1 AAAATTTATTATTAAA
* *
31617417 AAAATGTAATATTAAA
1 AAAATTTATTATTAAA
*
31617433 TAAA-TTATTA
1 AAAATTTATTA
31617443 AAATAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATTTATTATTAAA
Found at i:31617433 original size:28 final size:28
Alignment explanation
Indices: 31617402--31617463 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
31617392 ATTATTGTTA
31617402 AAATTTATTATTAAAAAAATGTA-ATATT
1 AAATTTATTATTAAAAAAAT-TATATATT
** * *
31617430 AAATAAATTATTAAAATAATTATTTATT
1 AAATTTATTATTAAAAAAATTATATATT
31617458 AAATTT
1 AAATTT
31617464 TTTAATAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATTTATTATTAAAAAAATTATATATT
Found at i:31617520 original size:16 final size:16
Alignment explanation
Indices: 31617464--31617521 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
31617454 TATTAAATTT
*
31617464 TTTAATAATTATTTATA
1 TTTAATAA-TATATATA
*
31617481 TTTAATAATATAAATA
1 TTTAATAATATATATA
* *
31617497 ATT-A-AATATATATG
1 TTTAATAATATATATA
31617511 TTTAATAATAT
1 TTTAATAATAT
31617522 TGAACACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
14 10 0.30
15 2 0.06
16 13 0.39
17 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTAATAATATATATA
Found at i:31617596 original size:17 final size:17
Alignment explanation
Indices: 31617576--31617610 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31617566 TGTTTTAAAA
31617576 ATTAAAATAAAAATATT
1 ATTAAAATAAAAATATT
* *
31617593 ATTAATATAATAATATT
1 ATTAAAATAAAAATATT
31617610 A
1 A
31617611 GGCTTAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAAATAAAAATATT
Found at i:31621892 original size:18 final size:17
Alignment explanation
Indices: 31621864--31621898 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31621854 ATTATTAAGA
*
31621864 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31621881 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31621899 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31622047 original size:157 final size:157
Alignment explanation
Indices: 31621852--31622168 Score: 607
Period size: 157 Copynumber: 2.0 Consensus size: 157
31621842 ATAAGAATAT
31621852 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
31621917 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
31621982 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
31622009 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
31622074 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
31622139 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
31622166 TAA
1 TAA
31622169 GGGTATTCTA
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:31622049 original size:18 final size:17
Alignment explanation
Indices: 31622021--31622055 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31622011 ATTATTAAGA
*
31622021 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31622038 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31622056 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31622089 original size:75 final size:75
Alignment explanation
Indices: 31621853--31622091 Score: 200
Period size: 75 Copynumber: 3.1 Consensus size: 75
31621843 TAAGAATATT
31621853 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
31621918 AATATGATTA
66 AATATGATTA
* ** * * * * *
31621928 AATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATA-A--CAATAATAATT
1 AATTATTAAGAATT-TTATT-A-AA--TTA-TATATTTTAATTAA-AATATATTTAATAATAATT
**** * * *
31621990 -TACCAAAACAAAT-TTCTGCT
59 AT-GTTTAA-ATATGAT-T--A
31622010 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
31622075 AATATGATTA
66 AATATGATTA
31622085 AATTATT
1 AATTATT
31622092 TATTATTGAT
Statistics
Matches: 117, Mismatches: 30, Indels: 34
0.65 0.17 0.19
Matches are distributed among these distances:
75 22 0.19
76 16 0.14
77 8 0.07
78 16 0.14
79 16 0.14
80 8 0.07
81 16 0.14
82 15 0.13
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:31622301 original size:45 final size:44
Alignment explanation
Indices: 31622201--31622310 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
31622191 TTTTCCATTA
31622201 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
31622240 TACTATTACGCCTCTATTCCATTACATTCAACCAAACATTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
*
31622285 TGCTATTACACCTCTATTCTATTACA
1 TGCTATTACACCTCTATTCCATTACA
31622311 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 24 0.42
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:31622308 original size:16 final size:16
Alignment explanation
Indices: 31622289--31622358 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
31622279 TTGATTTGCT
* *
31622289 ATTACACCTCTATTCT
1 ATTACACCTCTAATCC
31622305 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
31622321 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
31622337 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
31622353 AATACA
1 ATTACA
31622359 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:31628909 original size:21 final size:20
Alignment explanation
Indices: 31628871--31628910 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31628861 AATTTTAAAA
*
31628871 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTT
31628891 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAAT-AATTTTT
31628911 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTT
Found at i:31638488 original size:22 final size:22
Alignment explanation
Indices: 31638445--31638488 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
31638435 TTACCCTTAC
*
31638445 ATGCATTACATGCATTTCATAG
1 ATGCATTACATGCAATTCATAG
*
31638467 ATGCATTACCATGGAATT-ATAG
1 ATGCATTA-CATGCAATTCATAG
31638489 CTAATTCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (22 bp):
ATGCATTACATGCAATTCATAG
Found at i:31641523 original size:14 final size:15
Alignment explanation
Indices: 31641504--31641544 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
31641494 GTTGTAAAGT
31641504 TTTATTTTTATTTA-
1 TTTATTTTTATTTAG
*
31641518 TTTATTTTTACTTAG
1 TTTATTTTTATTTAG
31641533 TTTAATTTTTAT
1 TTT-ATTTTTAT
31641545 GTAAATATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATTTAG
Found at i:31645230 original size:14 final size:15
Alignment explanation
Indices: 31645211--31645251 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
31645201 AAGTTTTATT
31645211 TTTATTTTTATTTA-
1 TTTATTTTTATTTAG
*
31645225 TTTATTTTTACTTAG
1 TTTATTTTTATTTAG
31645240 TTTAATTTTTAT
1 TTT-ATTTTTAT
31645252 GTAAATATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATTTAG
Found at i:31665788 original size:2 final size:2
Alignment explanation
Indices: 31665781--31665809 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31665771 CATTTTAGAT
31665781 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31665810 AATCGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:31671355 original size:15 final size:15
Alignment explanation
Indices: 31671335--31671365 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31671325 TAGTTCAAAG
31671335 ACCAAATTAGTAATT
1 ACCAAATTAGTAATT
31671350 ACCAAATTAGTAATT
1 ACCAAATTAGTAATT
31671365 A
1 A
31671366 ATCATTTAAA
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:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (15 bp):
ACCAAATTAGTAATT
Found at i:31672288 original size:30 final size:30
Alignment explanation
Indices: 31672248--31672309 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
31672238 TTTTATAAAT
*
31672248 AATTAATA-TTTAT-TACTTAAAAATATTTAC
1 AATTAATATTTTATATA-TT-AAAATATTAAC
*
31672278 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATATTTTATATATTAAAATATTAAC
31672308 AA
1 AA
31672310 CAAATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 7 0.25
32 2 0.07
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTAATATTTTATATATTAAAATATTAAC
Found at i:31674359 original size:80 final size:82
Alignment explanation
Indices: 31674268--31674426 Score: 200
Period size: 82 Copynumber: 2.0 Consensus size: 82
31674258 GCATAAGCAA
** * * *
31674268 TTTTCAAAATATAACATA-AGCGGTCGCTCTCATAT-G-TGATCTTTAGAATTGCCTTTCGCC-A
1 TTTTCAAAATATAACATAGA-CGACCGCTCTCAGATAGCTGATCCTTAGAATTGCCTTTCACCAA
31674329 AACATTTAAACATAGGAGT
65 AACA-TTAAACATAGGAGT
* * *
31674348 TTTTTAAAATATAACATAGATGACCGTTCTCAGATAGCTGATCCTTAGAATTGCCTTTCACCAAA
1 TTTTCAAAATATAACATAGACGACCGCTCTCAGATAGCTGATCCTTAGAATTGCCTTTCACCAAA
31674413 ACATTAAACATAGG
66 ACATTAAACATAGG
31674427 TGATCTTCAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 27 0.40
81 2 0.03
82 33 0.49
83 5 0.07
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (82 bp):
TTTTCAAAATATAACATAGACGACCGCTCTCAGATAGCTGATCCTTAGAATTGCCTTTCACCAAA
ACATTAAACATAGGAGT
Found at i:31678311 original size:243 final size:244
Alignment explanation
Indices: 31677676--31678406 Score: 1428
Period size: 243 Copynumber: 3.0 Consensus size: 244
31677666 GTGAAATAGG
*
31677676 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCTAGAATTTTTAAAAATTATATATAGACAAGA
1 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
31677741 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
66 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
31677806 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
131 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
31677871 TTAACATGCTGGATGCTGGGGTCCTTGCAGAGAGATGATTGTTCTAGCT
196 TTAACATGCTGGATGCTGGGGTCCTTGCAGAGAGATGATTGTTCTAGCT
31677920 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
1 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
31677985 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
66 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
31678050 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
131 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
31678115 TTAACATGCTGGATGCT-GGGTCCTTGCAGAGAGATGATTGTTCTAGCT
196 TTAACATGCTGGATGCTGGGGTCCTTGCAGAGAGATGATTGTTCTAGCT
31678163 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
1 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
31678228 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
66 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
31678293 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
131 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
* *
31678358 TTAACATGCTGGATGCTGGGGTCCATGCAAAGAGATGATTGTTCTAGCT
196 TTAACATGCTGGATGCTGGGGTCCTTGCAGAGAGATGATTGTTCTAGCT
31678407 GAACCTTTAC
Statistics
Matches: 483, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
243 243 0.50
244 240 0.50
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (244 bp):
AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
TTAACATGCTGGATGCTGGGGTCCTTGCAGAGAGATGATTGTTCTAGCT
Found at i:31685977 original size:12 final size:12
Alignment explanation
Indices: 31685962--31686009 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
31685952 ATTTACAAAT
*
31685962 AATTATAATTAT
1 AATTATAATTAC
31685974 AATT-TAAATTAC
1 AATTAT-AATTAC
*
31685986 AATTACAATTAC
1 AATTATAATTAC
31685998 AATTATTAATTA
1 AATTA-TAATTA
31686010 AAAGTGTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 1 0.03
12 24 0.80
13 5 0.17
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTATAATTAC
Found at i:31685983 original size:18 final size:18
Alignment explanation
Indices: 31685962--31686009 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
31685952 ATTTACAAAT
*
31685962 AATTATAATTATAATTTA-
1 AATTATAATTACAA-TTAC
*
31685980 AATTACAATTACAATTAC
1 AATTATAATTACAATTAC
31685998 AATTATTAATTA
1 AATTA-TAATTA
31686010 AAAGTGTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 17 0.68
19 5 0.20
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTATAATTACAATTAC
Found at i:31691284 original size:26 final size:26
Alignment explanation
Indices: 31691255--31691307 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
31691245 TGATAAATAG
31691255 TCCAATTAAGACTAAAATGAGTTCAT
1 TCCAATTAAGACTAAAATGAGTTCAT
31691281 TCCAATTAAGACTAAAATGAGTTCAT
1 TCCAATTAAGACTAAAATGAGTTCAT
31691307 T
1 T
31691308 TAGATGGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (26 bp):
TCCAATTAAGACTAAAATGAGTTCAT
Found at i:31695311 original size:21 final size:21
Alignment explanation
Indices: 31695255--31695318 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
31695245 GCAATAATCA
31695255 AATTGCTGCTCCTGGTCAAAAT
1 AATT-CTGCTCCTGGTCAAAAT
* * *
31695277 TATTTTG-TGGCTGGTCAAAAT
1 AATTCTGCT-CCTGGTCAAAAT
*
31695298 AATTCTGCTTCTGGTCAAAAT
1 AATTCTGCTCCTGGTCAAAAT
31695319 GTGTGTGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.85
22 4 0.12
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (21 bp):
AATTCTGCTCCTGGTCAAAAT
Found at i:31695919 original size:33 final size:33
Alignment explanation
Indices: 31695877--31695945 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
31695867 AACGGGTGAT
31695877 GGTACGCCTGCTATGATATCATCTGTTGGTCAA
1 GGTACGCCTGCTATGATATCATCTGTTGGTCAA
31695910 GGTACGCCTGCTATGATATCATCTGTTGGTCAA
1 GGTACGCCTGCTATGATATCATCTGTTGGTCAA
31695943 GGT
1 GGT
31695946 GTGTTGCCGA
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:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (33 bp):
GGTACGCCTGCTATGATATCATCTGTTGGTCAA
Found at i:31698901 original size:7 final size:7
Alignment explanation
Indices: 31698878--31698974 Score: 83
Period size: 7 Copynumber: 14.0 Consensus size: 7
31698868 AATCAAAGTC
*
31698878 TAAATTT
1 TAAATCT
*
31698885 TAAA-CC
1 TAAATCT
*
31698891 TAAATAT
1 TAAATCT
31698898 TAAATCT
1 TAAATCT
*
31698905 TAAA-CAA
1 TAAATC-T
31698912 TAAAT-T
1 TAAATCT
31698918 ATAAATCT
1 -TAAATCT
*
31698926 TAAATAT
1 TAAATCT
*
31698933 TAAATCG
1 TAAATCT
31698940 TAAATCT
1 TAAATCT
*
31698947 TAAATAT
1 TAAATCT
*
31698954 TAAATTT
1 TAAATCT
31698961 TAAATCT
1 TAAATCT
31698968 TAAATCT
1 TAAATCT
31698975 ATTACTGTTG
Statistics
Matches: 71, Mismatches: 14, Indels: 10
0.75 0.15 0.11
Matches are distributed among these distances:
6 5 0.07
7 65 0.92
8 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.40
Consensus pattern (7 bp):
TAAATCT
Found at i:31698922 original size:21 final size:21
Alignment explanation
Indices: 31698898--31698972 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
31698888 ACCTAAATAT
* *
31698898 TAAATCTTAAACAATAAATTA
1 TAAATCTTAAATATTAAATTA
**
31698919 TAAATCTTAAATATTAAATCG
1 TAAATCTTAAATATTAAATTA
*
31698940 TAAATCTTAAATATTAAATTT
1 TAAATCTTAAATATTAAATTA
31698961 TAAATCTTAAAT
1 TAAATCTTAAAT
31698973 CTATTACTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (21 bp):
TAAATCTTAAATATTAAATTA
Found at i:31699730 original size:34 final size:35
Alignment explanation
Indices: 31699686--31699752 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
31699676 CAGTAAAAAA
31699686 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
31699720 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
31699753 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:31700783 original size:9 final size:9
Alignment explanation
Indices: 31700769--31700798 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
31700759 GACTCAATCT
31700769 ATTATTTGA
1 ATTATTTGA
31700778 ATTATTTGA
1 ATTATTTGA
*
31700787 GTTATTTGA
1 ATTATTTGA
31700796 ATT
1 ATT
31700799 GTAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (9 bp):
ATTATTTGA
Found at i:31705060 original size:29 final size:29
Alignment explanation
Indices: 31704995--31705051 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
31704985 CATGTATAAT
* **
31704995 TAATAAAAATTTAATAAATTTTAAAAAAC
1 TAATAAAAATTCAATAAATTAAAAAAAAC
31705024 TAATAAAAATTCAATAAATTAAAAAAAA
1 TAATAAAAATTCAATAAATTAAAAAAAA
31705052 TTAGAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (29 bp):
TAATAAAAATTCAATAAATTAAAAAAAAC
Found at i:31708600 original size:14 final size:14
Alignment explanation
Indices: 31708583--31708612 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31708573 TGAAAACGGA
31708583 TTTTAAAAAATGAT
1 TTTTAAAAAATGAT
*
31708597 TTTTGAAAAATGAT
1 TTTTAAAAAATGAT
31708611 TT
1 TT
31708613 ATTTTTCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTTAAAAAATGAT
Found at i:31716043 original size:16 final size:17
Alignment explanation
Indices: 31716015--31716046 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31716005 ATATAAAAAG
31716015 AAAATTGTAGTTAAATT
1 AAAATTGTAGTTAAATT
31716032 AAAATT-TAGTTAAAT
1 AAAATTGTAGTTAAAT
31716047 GTTTAGAAAA
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:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
AAAATTGTAGTTAAATT
Found at i:31716344 original size:12 final size:12
Alignment explanation
Indices: 31716310--31716348 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
31716300 TAAAATATAT
31716310 TAAATTTATTT-
1 TAAATTTATTTA
31716321 TATAATTT-TTTA
1 TA-AATTTATTTA
31716333 TAAATTTATTTA
1 TAAATTTATTTA
31716345 TAAA
1 TAAA
31716349 CAACATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAAATTTATTTA
Found at i:31721364 original size:15 final size:15
Alignment explanation
Indices: 31721344--31721374 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31721334 TTTTCAAATG
*
31721344 AACAACAATGAACAA
1 AACAACAAAGAACAA
31721359 AACAACAAAGAACAA
1 AACAACAAAGAACAA
31721374 A
1 A
31721375 GGCCCTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.19, G:0.06, T:0.03
Consensus pattern (15 bp):
AACAACAAAGAACAA
Found at i:31725282 original size:17 final size:17
Alignment explanation
Indices: 31725238--31725294 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
31725228 TATATTATTT
* *
31725238 TAATTTAATATTTAATA
1 TAATTAAATATTTTATA
*
31725255 -AATTTATATATTTT-TA
1 TAA-TTAAATATTTTATA
31725271 TTAATTAAATATTTTATA
1 -TAATTAAATATTTTATA
31725289 TAATTA
1 TAATTA
31725295 TCTTTAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 4 0.12
17 24 0.75
18 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTAAATATTTTATA
Found at i:31725282 original size:34 final size:34
Alignment explanation
Indices: 31725228--31725293 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
31725218 AAACTATATT
*
31725228 TATATTATTTTAATTTAATATTTAATA-AATTTA
1 TATATTATTTTAATTAAATATTTAATATAATTTA
* *
31725261 TATATTTTTATTAATTAAATATTTTATATAATT
1 TATATTATT-TTAATTAAATATTTAATATAATT
31725294 ATCTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 8 0.29
34 16 0.57
35 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATTATTTTAATTAAATATTTAATATAATTTA
Found at i:31725499 original size:23 final size:24
Alignment explanation
Indices: 31725455--31725500 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
31725445 TTCAAACTCG
31725455 AGCCTAACCCATATTTTTAAACAA
1 AGCCTAACCCATATTTTTAAACAA
31725479 AGCCTAACCCATA-TTTTAAACA
1 AGCCTAACCCATATTTTTAAACA
31725501 TACATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.28
Consensus pattern (24 bp):
AGCCTAACCCATATTTTTAAACAA
Found at i:31728086 original size:6 final size:6
Alignment explanation
Indices: 31728075--31728106 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
31728065 CATATAAATC
31728075 TAGATA TAGATA TAGATA TAGATA TAGATA TA
1 TAGATA TAGATA TAGATA TAGATA TAGATA TA
31728107 ATTATAAAAT
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:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
TAGATA
Found at i:31728087 original size:18 final size:18
Alignment explanation
Indices: 31728066--31728112 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
31728056 TTGGATAAAC
*
31728066 ATATAAATCTAGATATAG
1 ATATAAATATAGATATAG
*
31728084 ATATAGATATAGATATAG
1 ATATAAATATAGATATAG
*
31728102 ATATAATTATA
1 ATATAAATATA
31728113 AAATATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (18 bp):
ATATAAATATAGATATAG
Found at i:31729150 original size:17 final size:16
Alignment explanation
Indices: 31729119--31729161 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
31729109 ATGTCACTTC
*
31729119 AATTAAAAATTATAAAA
1 AATTAAAAA-AATAAAA
*
31729136 CATTTAAAAAAATAAAA
1 -AATTAAAAAAATAAAA
31729153 AATTAAAAA
1 AATTAAAAA
31729162 CATATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 6 0.27
18 8 0.36
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AATTAAAAAAATAAAA
Found at i:31730692 original size:14 final size:16
Alignment explanation
Indices: 31730658--31730694 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31730648 TTTCTAATAT
*
31730658 AAATTTAGCACTTATA
1 AAATTTAGCACGTATA
31730674 AAATTTAGCA-GTA-A
1 AAATTTAGCACGTATA
31730688 AAATTTA
1 AAATTTA
31730695 ATATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (16 bp):
AAATTTAGCACGTATA
Found at i:31732759 original size:27 final size:27
Alignment explanation
Indices: 31732728--31732792 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
31732718 GTAGGTAGTG
31732728 CCTATCT-AGTAGGCGCCACTA-GTGACT
1 CCTATCTGA-TAGGCGCCA-TAGGTGACT
31732755 CCTATCTGATAGGCGCCATAGGTGACT
1 CCTATCTGATAGGCGCCATAGGTGACT
31732782 CCTATCTGATA
1 CCTATCTGATA
31732793 TGTGCCACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 2 0.06
27 33 0.92
28 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (27 bp):
CCTATCTGATAGGCGCCATAGGTGACT
Found at i:31733182 original size:102 final size:102
Alignment explanation
Indices: 31732956--31733287 Score: 402
Period size: 102 Copynumber: 3.1 Consensus size: 102
31732946 GTTAAATTTA
* ** *
31732956 AAAAAATTACAAAATACTAAACTAAACACTAACAACTTATATAACCTAATCATAAATTACTAAC-
1 AAAAAATAACAAAACCCTAAACTAAACACTAACAA-TT-TGTAACC----CATAAATTACTAACA
* * *
31733020 --A-AAATAACTATAAAATTATTTTAAAAAAAAATTACATTACT
60 AAATAAATAACTATAACATT-TTTTTAAAAGAAATTACATTACT
*
31733061 AAAAAATCACAAAACCCTAAACTAAACACTAACAATTTGTAACCCATAAATTACTAACAAAATAA
1 AAAAAATAACAAAACCCTAAACTAAACACTAACAATTTGTAACCCATAAATTACTAACAAAATAA
*
31733126 ATAACTATAACATTTTTTTAAAAGAAATTACATCACT
66 ATAACTATAACATTTTTTTAAAAGAAATTACATTACT
*
31733163 AAAAAATAACAAAGCCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTACTAACA
1 AAAAAATAACAAAACCCTAAACTAAACACTAACAATTTG-----TAA-CCCATAAATTACTAACA
31733228 AAATAAATAACTATAACACTTTTTTTTAAAAGAAATTACATTACT
60 AAATAAATAACTATAACA--TTTTTTTAAAAGAAATTACATTACT
*
31733273 AAAAAATAGCAAAAC
1 AAAAAATAACAAAAC
31733288 ACAAAACACT
Statistics
Matches: 202, Mismatches: 13, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
99 14 0.07
102 58 0.29
103 21 0.10
104 2 0.01
105 32 0.16
107 3 0.01
108 35 0.17
110 37 0.18
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.27
Consensus pattern (102 bp):
AAAAAATAACAAAACCCTAAACTAAACACTAACAATTTGTAACCCATAAATTACTAACAAAATAA
ATAACTATAACATTTTTTTAAAAGAAATTACATTACT
Found at i:31733392 original size:38 final size:37
Alignment explanation
Indices: 31733350--31733467 Score: 93
Period size: 38 Copynumber: 3.2 Consensus size: 37
31733340 TTAAATTTAC
31733350 ATTACTAAAGACTCACAAAATACAACAATTTATAATAA
1 ATTACTAAA-ACTCACAAAATACAACAATTTATAATAA
** * * ** *
31733388 ATTACT--AA--CA-AAATATTTAACAAAATAATTTTAC
1 ATTACTAAAACTCACAAA-ATACAAC-AATTTATAATAA
*
31733422 ATTACTAAAAACTCACAAAACACAACAATTTATAATAA
1 ATTACT-AAAACTCACAAAATACAACAATTTATAATAA
31733460 ATTACTAA
1 ATTACTAA
31733468 CAAAATATTT
Statistics
Matches: 57, Mismatches: 15, Indels: 17
0.64 0.17 0.19
Matches are distributed among these distances:
32 3 0.05
33 7 0.12
34 13 0.23
35 1 0.02
36 1 0.02
37 4 0.07
38 19 0.33
39 6 0.11
40 3 0.05
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (37 bp):
ATTACTAAAACTCACAAAATACAACAATTTATAATAA
Found at i:31733400 original size:31 final size:31
Alignment explanation
Indices: 31733364--31733474 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 31
31733354 CTAAAGACTC
31733364 ACAAAATACAACAATTTATAATAAATTACTA
1 ACAAAATACAACAATTTATAATAAATTACTA
* * ** *
31733395 ACAAAATATTTAACAAAATAATTTTACATTACTAAAAACTC
1 ACAAAATA--CAAC--AAT--TTATA-A-TA--AATTACTA
*
31733436 ACAAAACACAACAATTTATAATAAATTACTA
1 ACAAAATACAACAATTTATAATAAATTACTA
31733467 ACAAAATA
1 ACAAAATA
31733475 TTTAACACAA
Statistics
Matches: 58, Mismatches: 12, Indels: 20
0.64 0.13 0.22
Matches are distributed among these distances:
31 20 0.34
33 5 0.09
34 1 0.02
35 7 0.12
37 7 0.12
38 1 0.02
39 5 0.09
41 12 0.21
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (31 bp):
ACAAAATACAACAATTTATAATAAATTACTA
Found at i:31733436 original size:72 final size:72
Alignment explanation
Indices: 31733345--31733481 Score: 256
Period size: 72 Copynumber: 1.9 Consensus size: 72
31733335 TATTTTTAAA
* *
31733345 TTTACATTACTAAAGACTCACAAAATACAACAATTTATAATAAATTACTAACAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
31733410 AAATAAT
66 AAATAAT
31733417 TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
31733482 CAACCAGTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (72 bp):
TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
AAATAAT
Found at i:31733452 original size:34 final size:34
Alignment explanation
Indices: 31733345--31733452 Score: 83
Period size: 34 Copynumber: 3.1 Consensus size: 34
31733335 TATTTTTAAA
* *
31733345 TTTACATTACTAAAGACTCACAAAATACAACAATT
1 TTTACATTACTAAAAACTCACAAAACACAACAA-T
* * *** * *
31733380 TATAATAAATTACTAACAAAAT-ATTTAACAAAATAAT
1 T-T--TACATTACTAA-AAACTCACAAAACACAACAAT
31733417 TTTACATTACTAAAAACTCACAAAACACAACAAT
1 TTTACATTACTAAAAACTCACAAAACACAACAAT
31733451 TT
1 TT
31733453 ATAATAAATT
Statistics
Matches: 52, Mismatches: 16, Indels: 11
0.66 0.20 0.14
Matches are distributed among these distances:
33 4 0.08
34 22 0.42
35 1 0.02
36 2 0.04
37 2 0.04
38 18 0.35
39 3 0.06
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.30
Consensus pattern (34 bp):
TTTACATTACTAAAAACTCACAAAACACAACAAT
Found at i:31733482 original size:38 final size:38
Alignment explanation
Indices: 31733371--31733485 Score: 123
Period size: 38 Copynumber: 3.1 Consensus size: 38
31733361 CTCACAAAAT
31733371 ACAACAATTTATAATAAATTACTAACAAAATATTTAAC
1 ACAACAATTTATAATAAATTACTAACAAAATATTTAAC
* * * * ***
31733409 AAAATAA-TT-T--TACATTACTAA-AAACTCACAAAAC
1 ACAACAATTTATAATAAATTACTAACAAAAT-ATTTAAC
31733443 ACAACAATTTATAATAAATTACTAACAAAATATTTAAC
1 ACAACAATTTATAATAAATTACTAACAAAATATTTAAC
31733481 ACAAC
1 ACAAC
31733486 CAGTGACGCC
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
33 4 0.07
34 19 0.33
35 2 0.04
36 2 0.04
37 2 0.04
38 24 0.42
39 4 0.07
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.29
Consensus pattern (38 bp):
ACAACAATTTATAATAAATTACTAACAAAATATTTAAC
Found at i:31733540 original size:27 final size:27
Alignment explanation
Indices: 31733484--31733541 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
31733474 ATTTAACACA
* *
31733484 ACCAGTGACGCCTATCAAATAGGAGTC
1 ACCAGTGACGCCTACCAAATAGGAGCC
*
31733511 ACCAGTGGCGCCTACCAAATAGGCA-CC
1 ACCAGTGACGCCTACCAAATAGG-AGCC
31733538 ACCA
1 ACCA
31733542 ACCCCATACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.33, G:0.21, T:0.14
Consensus pattern (27 bp):
ACCAGTGACGCCTACCAAATAGGAGCC
Found at i:31734151 original size:23 final size:22
Alignment explanation
Indices: 31734123--31734178 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
31734113 CCACCACTTT
* * *
31734123 TTTTAATAATATTTTTTTTTTA
1 TTTTAAAAATATTGTTATTTTA
31734145 CTTTTAAAAAATATTGTTATTTTA
1 -TTTT-AAAAATATTGTTATTTTA
31734169 TTTTATAAAA
1 TTTTA-AAAA
31734179 AATATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.04
23 12 0.43
24 15 0.54
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAAAATATTGTTATTTTA
Found at i:31734157 original size:24 final size:25
Alignment explanation
Indices: 31734130--31734185 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
31734120 TTTTTTTAAT
*
31734130 AATATTTTTTTTTTACTTT-TAAAA
1 AATATTTTTATTTTACTTTATAAAA
* *
31734154 AATATTGTTATTTTATTTTATAAAA
1 AATATTTTTATTTTACTTTATAAAA
31734179 AATATTT
1 AATATTT
31734186 AAATAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
AATATTTTTATTTTACTTTATAAAA
Found at i:31734356 original size:7 final size:7
Alignment explanation
Indices: 31734344--31734380 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
31734334 CACAGCCCCT
31734344 CCCTCTG
1 CCCTCTG
31734351 CCCTCTG
1 CCCTCTG
31734358 CCCTCTG
1 CCCTCTG
31734365 CCCTCTG
1 CCCTCTG
31734372 CCCTCTG
1 CCCTCTG
31734379 CC
1 CC
31734381 GTGGACTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.59, G:0.14, T:0.27
Consensus pattern (7 bp):
CCCTCTG
Found at i:31734769 original size:57 final size:57
Alignment explanation
Indices: 31734681--31734793 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
31734671 TTTTTTGTTT
*
31734681 TTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTGTG
1 TTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTG
31734738 TTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGT
1 TTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGT
31734794 TGTGTTTAGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (57 bp):
TTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTG
Found at i:31734895 original size:72 final size:72
Alignment explanation
Indices: 31734814--31734978 Score: 285
Period size: 72 Copynumber: 2.3 Consensus size: 72
31734804 TTAATATTTG
*
31734814 GTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAATATTTTGATGGTAAATCATTATAAATTGTT
1 GTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAATATTTTGATAGTAAATCATTATAAATTGTT
31734879 GTGTTTT
66 GTGTTTT
* * *
31734886 GTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAATATTTTGTTAGTAATTTATTATAAATTGTT
1 GTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAATATTTTGATAGTAAATCATTATAAATTGTT
31734951 GTGTTTT
66 GTGTTTT
*
31734958 GTTAGTTTTTAGTAATGTAAA
1 GTGAGTTTTTAGTAATGTAAA
31734979 TTTTTTTAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 88 1.00
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.53
Consensus pattern (72 bp):
GTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAATATTTTGATAGTAAATCATTATAAATTGTT
GTGTTTT
Found at i:31734909 original size:34 final size:33
Alignment explanation
Indices: 31734871--31734978 Score: 90
Period size: 34 Copynumber: 3.1 Consensus size: 33
31734861 AAATCATTAT
31734871 AAATTGTTGTGTTTTGTGAGTTTTTAGTAATGTA
1 AAATTGTTGTGTTTTGT-AGTTTTTAGTAATGTA
* * *** * *
31734905 AAATTATTTTGTTAAATATTTTGTTAGTAATTTATTA
1 AAATTGTTGTGTTTTGTAGTTT-TTAGTAA--T-GTA
31734942 TAAATTGTTGTGTTTTGTTAGTTTTTAGTAATGTA
1 -AAATTGTTGTGTTTTG-TAGTTTTTAGTAATGTA
31734977 AA
1 AA
31734979 TTTTTTTAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
33 4 0.07
34 21 0.39
35 2 0.04
36 2 0.04
37 2 0.04
38 18 0.33
39 5 0.09
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.55
Consensus pattern (33 bp):
AAATTGTTGTGTTTTGTAGTTTTTAGTAATGTA
Done.