Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_pilon, whole genome shotgun sequence
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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 23
Found at i:2729006 original size:21 final size:21
Alignment explanation
Indices: 2728982--2729042 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2728972 TTCAAAGAAA
2728982 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
2729003 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
2729017 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
2729038 CATTT
1 CATTT
2729043 TTTCATAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:2731795 original size:18 final size:18
Alignment explanation
Indices: 2731772--2731818 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2731762 CTGATTTCGG
**
2731772 TTGGGTTAGAACTGGGGC
1 TTGGGTTAGAACTAAGGC
2731790 TTGGGTTAGAACTAAGGC
1 TTGGGTTAGAACTAAGGC
2731808 TTGGGTTAGAA
1 TTGGGTTAGAA
2731819 TAGCTTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.23, C:0.09, G:0.38, T:0.30
Consensus pattern (18 bp):
TTGGGTTAGAACTAAGGC
Found at i:2741104 original size:20 final size:21
Alignment explanation
Indices: 2741052--2741112 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
2741042 TTCCCCTGTG
2741052 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
2741075 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
2741095 GGGGGCATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2741113 TGTACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2749191 original size:20 final size:21
Alignment explanation
Indices: 2749157--2749206 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
2749147 AATGATTTTC
* *
2749157 TTTTG-AAAGCAAAAAT-AGA
1 TTTTGAAAAACAAAAATGAAA
2749176 TTTTGAAAAACAAAAATGAAA
1 TTTTGAAAAACAAAAATGAAA
*
2749197 TTTTAAAAAA
1 TTTTGAAAAA
2749207 TGATTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 5 0.19
20 10 0.38
21 11 0.42
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.28
Consensus pattern (21 bp):
TTTTGAAAAACAAAAATGAAA
Found at i:2752460 original size:19 final size:19
Alignment explanation
Indices: 2752436--2752482 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2752426 AACTCAGACC
2752436 GAGTCAACCAAACCGAACT
1 GAGTCAACCAAACCGAACT
*
2752455 GAGTCAACCAAACTGAACT
1 GAGTCAACCAAACCGAACT
2752474 GAGTCAACC
1 GAGTCAACC
2752483 CGAGCCATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.30, G:0.17, T:0.13
Consensus pattern (19 bp):
GAGTCAACCAAACCGAACT
Found at i:2757292 original size:20 final size:21
Alignment explanation
Indices: 2757267--2757317 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2757257 AAGTTTTTCC
*
2757267 ATTAAAAATGTTC-CAAAAAA
1 ATTAAAAAAGTTCTCAAAAAA
*
2757287 ATTAAAAAAGTTCTTGAAAAAA
1 ATTAAAAAAGTTC-TCAAAAAA
2757309 ATTAAAAAA
1 ATTAAAAAA
2757318 AAGAAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 12 0.44
22 15 0.56
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (21 bp):
ATTAAAAAAGTTCTCAAAAAA
Found at i:2757341 original size:11 final size:11
Alignment explanation
Indices: 2757327--2757351 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2757317 AAAGAAAAAG
2757327 AAAAATGAGAA
1 AAAAATGAGAA
2757338 AAAAATGAGAA
1 AAAAATGAGAA
2757349 AAA
1 AAA
2757352 GGAGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAAATGAGAA
Found at i:2757371 original size:29 final size:28
Alignment explanation
Indices: 2757325--2757380 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
2757315 AAAAAGAAAA
*
2757325 AGAAAAATGAGAAAAAAATGAGAAAAAGG
1 AGAAAAATGAGAAAAAAAAGA-AAAAAGG
* *
2757354 AGAAAAATGTGAAGAAAAAGAAAAAAG
1 AGAAAAATGAGAAAAAAAAGAAAAAAG
2757381 TGGTTGAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (28 bp):
AGAAAAATGAGAAAAAAAAGAAAAAAGG
Found at i:2757379 original size:20 final size:20
Alignment explanation
Indices: 2757324--2757379 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
2757314 AAAAAAGAAA
*
2757324 AAGAAAAATGAGAAAAAAATG
1 AAGAAAAAGGA-AAAAAAATG
**
2757345 -AGAAAAAGGAGAAAAATGTG
1 AAGAAAAAGGA-AAAAAAATG
2757365 AAGAAAAA-GAAAAAA
1 AAGAAAAAGGAAAAAA
2757380 GTGGTTGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 5 0.16
20 19 0.61
21 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (20 bp):
AAGAAAAAGGAAAAAAAATG
Found at i:2759217 original size:24 final size:24
Alignment explanation
Indices: 2759190--2759272 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
2759180 AAACGGAGAT
* *
2759190 ATCAAAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
2759214 ATCAGATATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
2759238 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
2759262 ATCAGAAATCA
1 ATCAGAAATCA
2759273 GATAAAATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:2761777 original size:29 final size:29
Alignment explanation
Indices: 2761727--2761941 Score: 268
Period size: 29 Copynumber: 7.4 Consensus size: 29
2761717 TATTTTACAC
* * * *
2761727 AAATAGCACCCAAACAGAAATTAATTCCCA
1 AAATAGCACCAAAACCG-AATTATTTACCA
*
2761757 GAATAGCACCAAAACCGAATTATTTACCA
1 AAATAGCACCAAAACCGAATTATTTACCA
2761786 AAATAGCACCAAAACCGAATTATTTACCA
1 AAATAGCACCAAAACCGAATTATTTACCA
*
2761815 TAATAGCACCAAAACCGAATTATTTACCA
1 AAATAGCACCAAAACCGAATTATTTACCA
*
2761844 AAATAGCACCAAAATCGAATTATTTACCA
1 AAATAGCACCAAAACCGAATTATTTACCA
* * *
2761873 GAATAGTACCAAAACCGAATTATTTATCA
1 AAATAGCACCAAAACCGAATTATTTACCA
* * *** *
2761902 GAATAACACCAATTTCGAATTATTTCCCA
1 AAATAGCACCAAAACCGAATTATTTACCA
*
2761931 AAATATCACCA
1 AAATAGCACCA
2761942 CGAATTATTT
Statistics
Matches: 163, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
29 149 0.91
30 14 0.09
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.23
Consensus pattern (29 bp):
AAATAGCACCAAAACCGAATTATTTACCA
Found at i:2775285 original size:23 final size:23
Alignment explanation
Indices: 2775255--2775310 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2775245 CGTATAAATG
2775255 CACCGAAGTGCCACATAGAATTA
1 CACCGAAGTGCCACATAGAATTA
* * *
2775278 CACCGAAGAGCCGCATAGAATTG
1 CACCGAAGTGCCACATAGAATTA
2775301 CACCGAAGTG
1 CACCGAAGTG
2775311 TCATATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (23 bp):
CACCGAAGTGCCACATAGAATTA
Found at i:2780164 original size:23 final size:23
Alignment explanation
Indices: 2780134--2780194 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
2780124 CTCATATAAA
*
2780134 TGCACCGAAGTGCTACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2780157 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
2780180 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
2780195 TATAAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2781738 original size:20 final size:23
Alignment explanation
Indices: 2781712--2781768 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 23
2781702 TCCCCTTAAA
2781712 GTGCATCGATGCATTC-T-ACAT
1 GTGCATCGATGCATTCTTAACAT
*
2781733 -TGCATCGATGCTTTCTTTAACAT
1 GTGCATCGATGCATTC-TTAACAT
2781756 GTGCATCGATGCA
1 GTGCATCGATGCA
2781769 CTACCCATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 14 0.47
22 1 0.03
23 4 0.13
24 11 0.37
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (23 bp):
GTGCATCGATGCATTCTTAACAT
Found at i:2788287 original size:12 final size:12
Alignment explanation
Indices: 2788270--2788302 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2788260 AGTGGTCATG
2788270 GATGACTTGTTT
1 GATGACTTGTTT
2788282 GATGACTTGTTT
1 GATGACTTGTTT
2788294 GATGACTTG
1 GATGACTTG
2788303 ACTCTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.09, G:0.27, T:0.45
Consensus pattern (12 bp):
GATGACTTGTTT
Found at i:2789634 original size:31 final size:31
Alignment explanation
Indices: 2789599--2789659 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2789589 AAAATATAAG
*
2789599 ATATGATCACTTTTGTTTTTATTTAATTAAT
1 ATATGATCACTTTCGTTTTTATTTAATTAAT
*
2789630 ATATGGTCACTTTCGTTTTTATTTAATTAA
1 ATATGATCACTTTCGTTTTTATTTAATTAA
2789660 GATGTAGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (31 bp):
ATATGATCACTTTCGTTTTTATTTAATTAAT
Found at i:2789862 original size:27 final size:27
Alignment explanation
Indices: 2789827--2789898 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
2789817 GAAAAATAAA
2789827 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
2789854 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
2789879 -ATAAAATATTTTTAAGTTAA
1 AATAAAATATTTTTAAATTAA
2789899 TATATATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
24 12 0.30
25 10 0.25
26 5 0.12
27 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
AATAAAATATTTTTAAATTAAGTTAAT
Found at i:2789869 original size:22 final size:23
Alignment explanation
Indices: 2789844--2789900 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 23
2789834 TATTTTTAAA
2789844 TTAAGTTAATAATAAAATATATT
1 TTAAGTTAATAATAAAATATATT
2789867 TAATAAGTTAAT-ATAAAATAT-TT
1 T--TAAGTTAATAATAAAATATATT
2789890 TTAAGTTAATA
1 TTAAGTTAATA
2789901 TATATATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 9 0.29
23 4 0.13
24 9 0.29
25 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (23 bp):
TTAAGTTAATAATAAAATATATT
Found at i:2789907 original size:27 final size:25
Alignment explanation
Indices: 2789828--2789915 Score: 99
Period size: 27 Copynumber: 3.4 Consensus size: 25
2789818 AAAAATAAAA
2789828 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATATTTTT-AATTAAGTTAAT
*
2789854 AATAAAATATATTTAA-TAAGTTAAT
1 -ATAAAATATTTTTAATTAAGTTAAT
2789879 ATAAAATATTTTTAAGTTAA-TATATAT
1 ATAAAATATTTTTAA-TTAAGT-TA-AT
2789906 ATAAATATAT
1 ATAAA-ATAT
2789916 ACAACATGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
24 14 0.26
25 10 0.19
26 7 0.13
27 19 0.35
28 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (25 bp):
ATAAAATATTTTTAATTAAGTTAAT
Found at i:2790979 original size:26 final size:26
Alignment explanation
Indices: 2790945--2791011 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
2790935 TATCAAGTTC
*
2790945 AACTCGAACTCGAAATATAATATTAA
1 AACTTGAACTCGAAATATAATATTAA
*
2790971 AACTTGAACTCAAAATATAATATTAA
1 AACTTGAACTCGAAATATAATATTAA
2790997 AACTTGAACTCGAAA
1 AACTTGAACTCGAAA
2791012 AGGCTCGAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (26 bp):
AACTTGAACTCGAAATATAATATTAA
Found at i:2791071 original size:24 final size:25
Alignment explanation
Indices: 2791029--2791075 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2791019 AACTCAAAAA
*
2791029 AAAATTAGAAGCTCGATTGAAGCTT
1 AAAATTAGAAGCTCAATTGAAGCTT
*
2791054 AAAATTTG-AGCTCAATTGAAGC
1 AAAATTAGAAGCTCAATTGAAGC
2791076 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (25 bp):
AAAATTAGAAGCTCAATTGAAGCTT
Found at i:2797511 original size:23 final size:23
Alignment explanation
Indices: 2797471--2797514 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2797461 TCACCCAGCA
*
2797471 GAGAGAAGAGGGAGGGGGAAGGG
1 GAGAGAAGAGGGAAGGGGAAGGG
2797494 GAGAGAA-AGGGTAAGGGGAAG
1 GAGAGAAGAGGG-AAGGGGAAG
2797515 CAAATTGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.59, T:0.02
Consensus pattern (23 bp):
GAGAGAAGAGGGAAGGGGAAGGG
Found at i:2804072 original size:12 final size:13
Alignment explanation
Indices: 2804048--2804076 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2804038 TCGATGTGTC
2804048 TACAAATAGTATA
1 TACAAATAGTATA
2804061 TACAAA-AGTATA
1 TACAAATAGTATA
2804073 TACA
1 TACA
2804077 TGTAGTCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (13 bp):
TACAAATAGTATA
Found at i:2809206 original size:23 final size:23
Alignment explanation
Indices: 2809158--2809211 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2809148 AATATATATT
* *
2809158 ATACTTATTACATTTTTTAGATC
1 ATACATATTACATTTTTTAGAAC
2809181 ATACATATTACATTGTTTTA-AAC
1 ATACATATTACATT-TTTTAGAAC
2809204 ATA-ATATT
1 ATACATATT
2809212 GTTTCACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 5 0.18
23 18 0.64
24 5 0.18
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (23 bp):
ATACATATTACATTTTTTAGAAC
Found at i:2809226 original size:14 final size:13
Alignment explanation
Indices: 2809207--2809246 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
2809197 TTTAAACATA
2809207 ATATTGTTTCACAC
1 ATATTG-TTCACAC
2809221 ATATTGTTCACA-
1 ATATTGTTCACAC
2809233 ATATTGTTCACAC
1 ATATTGTTCACAC
2809246 A
1 A
2809247 AGAAACACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.48
13 7 0.28
14 6 0.24
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (13 bp):
ATATTGTTCACAC
Found at i:2809247 original size:14 final size:14
Alignment explanation
Indices: 2809206--2809247 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2809196 TTTTAAACAT
2809206 AATATTGTTTCACAC
1 AATATTG-TTCACAC
2809221 -ATATTGTT--CAC
1 AATATTGTTCACAC
2809232 AATATTGTTCACAC
1 AATATTGTTCACAC
2809246 AA
1 AA
2809248 GAAACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.12
12 8 0.33
13 2 0.08
14 11 0.46
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (14 bp):
AATATTGTTCACAC
Found at i:2809396 original size:23 final size:23
Alignment explanation
Indices: 2809369--2809428 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
2809359 CAACTCGTAT
2809369 AATTGCACCAAAGTGCCAAGTAG
1 AATTGCACCAAAGTGCCAAGTAG
* * ** *
2809392 AATTGTATCGTAGTGCCACGTAG
1 AATTGCACCAAAGTGCCAAGTAG
*
2809415 AAATGCACCAAAGT
1 AATTGCACCAAAGT
2809429 ACCATATAAG
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (23 bp):
AATTGCACCAAAGTGCCAAGTAG
Found at i:2813369 original size:21 final size:20
Alignment explanation
Indices: 2813296--2813394 Score: 117
Period size: 21 Copynumber: 4.8 Consensus size: 20
2813286 CGGAGTTTGA
*
2813296 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
* * *
2813316 GTGCATCGATGCACTACTGTAG
1 GTGCATGGATGCACTGCAG--G
*
2813338 GTGCATAGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
2813358 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
2813380 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2813395 TTGACACCCT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
20 17 0.25
21 30 0.45
22 20 0.30
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:2813495 original size:29 final size:29
Alignment explanation
Indices: 2813474--2813531 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
2813464 AAACTTTGAA
2813474 TAAATTCAATT-AAATCCAAAAACATTTTG
1 TAAATTCAATTGAAATCCAAAAACA-TTTG
*
2813503 TAAATTCAATTGAAGTCCAAAAACCATTT
1 TAAATTCAATTGAAATCCAAAAA-CATTT
2813532 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTGAAATCCAAAAACATTTG
Found at i:2813524 original size:30 final size:30
Alignment explanation
Indices: 2813474--2813533 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
2813464 AAACTTTGAA
2813474 TAAATTCAATTAAATCCAAAAA-CATTTTG
1 TAAATTCAATTAAATCCAAAAACCATTTTG
*
2813503 TAAATTCAATTGAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAATCCAAAAACCATTTTG
2813534 CCTTAAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAATCCAAAAACCATTTTG
Found at i:2814800 original size:19 final size:20
Alignment explanation
Indices: 2814770--2814807 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2814760 CAAAATTTCA
2814770 TTTTGACTTTCAAAATCAAC
1 TTTTGACTTTCAAAATCAAC
2814790 TTTTG-CTTTCAAAATCAA
1 TTTTGACTTTCAAAATCAA
2814808 ATTATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTGACTTTCAAAATCAAC
Found at i:2816755 original size:20 final size:20
Alignment explanation
Indices: 2816730--2816804 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
2816720 TACAGCCTTT
*
2816730 ATGCATGGATGCACATCAGG
1 ATGCATCGATGCACATCAGG
* **
2816750 ATGCATCGATGTACATCCTTG
1 ATGCATCGATGCACAT-CAGG
**
2816771 ATGCATCGATGCACAGAAGG
1 ATGCATCGATGCACATCAGG
2816791 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2816805 TAATTGCATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (20 bp):
ATGCATCGATGCACATCAGG
Found at i:2816792 original size:41 final size:41
Alignment explanation
Indices: 2816720--2816801 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
2816710 AACTAGCCGT
* * **
2816720 TACAGCCTTTATGCATGGATGCACATCAGGATGCATCGATG
1 TACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATG
*
2816761 TACATCCTTGATGCATCGATGCACAGAAGGATGCATCGATG
1 TACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATG
2816802 CACTAATTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (41 bp):
TACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATG
Found at i:2816872 original size:22 final size:23
Alignment explanation
Indices: 2816839--2816881 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2816829 ATGGATGCAC
2816839 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
2816862 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
2816882 GCAGGTATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:2816894 original size:21 final size:19
Alignment explanation
Indices: 2816825--2816923 Score: 99
Period size: 21 Copynumber: 4.8 Consensus size: 19
2816815 CGGTGTTTGA
2816825 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCA-G
*
2816845 GTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCAC---TGCAG
2816867 GTGCATGGATGCACTGCAG
1 GTGCATGGATGCACTGCAG
*
2816886 GTATGCATGGATACACTGCAGGG
1 G--TGCATGGATGCACTGCA--G
*
2816909 GTGCATTGATGCACT
1 GTGCATGGATGCACT
2816924 TTGACACCCT
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.09
20 13 0.19
21 28 0.42
22 14 0.21
23 6 0.09
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (19 bp):
GTGCATGGATGCACTGCAG
Found at i:2817024 original size:29 final size:29
Alignment explanation
Indices: 2817003--2817060 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
2816993 AAACTTTGAA
2817003 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
2817032 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
2817061 TGCGTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:2817050 original size:30 final size:30
Alignment explanation
Indices: 2817003--2817062 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
2816993 AAACTTTGAA
2817003 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
2817032 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
2817063 CGTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:2818968 original size:23 final size:23
Alignment explanation
Indices: 2818942--2819005 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
2818932 CAGCTCGTAT
2818942 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * * *
2818965 AATTACACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
* *
2818988 AAATGCACCAAAGTGCCA
1 AATTGCACCGAAGTGCCA
2819006 TATAAGATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:2825041 original size:2 final size:2
Alignment explanation
Indices: 2825001--2825026 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2824991 TAATACGAAG
2825001 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2825027 TTGTATTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2825308 original size:22 final size:23
Alignment explanation
Indices: 2825280--2825325 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2825270 AGAATATTAA
2825280 TTTTTAGAAT-TAGAATGGTTAG
1 TTTTTAGAATCTAGAATGGTTAG
2825302 TTTTTAGAATCTAGAATGGTTAG
1 TTTTTAGAATCTAGAATGGTTAG
2825325 T
1 T
2825326 GAACCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (23 bp):
TTTTTAGAATCTAGAATGGTTAG
Found at i:2830903 original size:67 final size:67
Alignment explanation
Indices: 2830707--2830910 Score: 270
Period size: 67 Copynumber: 3.1 Consensus size: 67
2830697 GTTGGATAAG
* * * *
2830707 ATTT-ATCTCACTCA-AGATAGTTTCCCTTGAAACACAAACCTTTGAGATCGCTTCTTTTGAAAT
1 ATTTCATCTCACT-AGAGATAGTTTCACTTGAAACACAAACCTTTGAGATCGTTTCTCTTGAAAC
2830770 AAA
65 AAA
* * * *
2830773 ATTTCATCTCGCTCGAGATAGTTTTCA-TTGAAACACAAACCTTTAAGATAGTTTCTCTTGAAAC
1 ATTTCATCTCACTAGAGATAG-TTTCACTTGAAACACAAACCTTTGAGATCGTTTCTCTTGAAAC
2830837 AAA
65 AAA
* * *
2830840 ATTTCATCTCACTAGAGATAGTTTCACTTGAAGCACAAACATTTGAGATCGTTTCTCTTGAAACG
1 ATTTCATCTCACTAGAGATAGTTTCACTTGAAACACAAACCTTTGAGATCGTTTCTCTTGAAACA
2830905 AA
66 AA
2830907 ATTT
1 ATTT
2830911 GCCTCGCCTG
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
66 9 0.08
67 106 0.89
68 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (67 bp):
ATTTCATCTCACTAGAGATAGTTTCACTTGAAACACAAACCTTTGAGATCGTTTCTCTTGAAACA
AA
Found at i:2831531 original size:2 final size:2
Alignment explanation
Indices: 2831524--2831562 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2831514 TATCTAAGAT
2831524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2831563 TTTTTTATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2832859 original size:42 final size:42
Alignment explanation
Indices: 2832795--2832889 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
2832785 TCCAATACAC
2832795 CACCCGCCCACCACCCACGATGGGT-AAAAAATTTCAAATCCA
1 CACCCGCCCACCACCCACGATGGGTAAAAAAATTT-AAATCCA
** *
2832837 CACCCGCCCACCAGTCATGATGGGTAAAAAAATTTAAATCCA
1 CACCCGCCCACCACCCACGATGGGTAAAAAAATTTAAATCCA
2832879 CACCCGCCCAC
1 CACCCGCCCAC
2832890 GCGGGTACAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 40 0.82
43 9 0.18
ACGTcount: A:0.35, C:0.38, G:0.13, T:0.15
Consensus pattern (42 bp):
CACCCGCCCACCACCCACGATGGGTAAAAAAATTTAAATCCA
Found at i:2834265 original size:12 final size:11
Alignment explanation
Indices: 2834248--2834273 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2834238 CATCTCTTTA
2834248 TTTTTTTTTTG
1 TTTTTTTTTTG
2834259 TTTTTTTTTTG
1 TTTTTTTTTTG
2834270 TTTT
1 TTTT
2834274 ATTGCATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:2842161 original size:175 final size:178
Alignment explanation
Indices: 2841857--2842209 Score: 685
Period size: 175 Copynumber: 2.0 Consensus size: 178
2841847 ATTAAATAGA
2841857 TTTCTCAATTAATTTTACATAAATTGATAACTGTTTATCTAATAAAACTGTCCAATGTATATCCA
1 TTTCTCAATTAATTTTACATAAATTGATAACTGTTTATCTAATAAAACTGTCCAATGTATATCCA
2841922 CAATAGAAAATATTTCTTGTAACTTTAGTTTTTCTTGTTACTTCCCATTAATAACTAACTGGTCA
66 CAATAGAAAATATTTCTTGTAACTTTAGTTTTTCTTGTTACTTCCCATTAATAACTAACTGGTCA
2841987 CACAAGCATGGCCCCTATATACATATAT-GTAGAATATA-CGTAAGAT
131 CACAAGCATGGCCCCTATATACATATATGGTAGAATATATCGTAAGAT
2842033 TTTCTCAATTAA-TTTACATAAATTGATAACTGTTTATCTAATAAAACTGTCCAATGTATATCCA
1 TTTCTCAATTAATTTTACATAAATTGATAACTGTTTATCTAATAAAACTGTCCAATGTATATCCA
2842097 CAATAGAAAATATTTCTTGTAACTTTAGTTTTTCTTGTTACTTCCCATTAATAACTAACTGGTCA
66 CAATAGAAAATATTTCTTGTAACTTTAGTTTTTCTTGTTACTTCCCATTAATAACTAACTGGTCA
2842162 CACAAGCATGGCCCCTATATACATATATGGTAGAATATATCGTAAGAT
131 CACAAGCATGGCCCCTATATACATATATGGTAGAATATATCGTAAGAT
2842210 GCAAAGGCAC
Statistics
Matches: 175, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
175 145 0.83
176 22 0.13
177 8 0.05
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (178 bp):
TTTCTCAATTAATTTTACATAAATTGATAACTGTTTATCTAATAAAACTGTCCAATGTATATCCA
CAATAGAAAATATTTCTTGTAACTTTAGTTTTTCTTGTTACTTCCCATTAATAACTAACTGGTCA
CACAAGCATGGCCCCTATATACATATATGGTAGAATATATCGTAAGAT
Found at i:2842695 original size:30 final size:30
Alignment explanation
Indices: 2842659--2842719 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2842649 TTTAAGGTCG
2842659 GTAGCTTCTGTTGTCCTCGAATACAAACCA
1 GTAGCTTCTGTTGTCCTCGAATACAAACCA
2842689 GTAGCTTCTGTTGTCCTCGAATACAAACCA
1 GTAGCTTCTGTTGTCCTCGAATACAAACCA
2842719 G
1 G
2842720 GAAAAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (30 bp):
GTAGCTTCTGTTGTCCTCGAATACAAACCA
Found at i:2844148 original size:4 final size:4
Alignment explanation
Indices: 2844134--2844187 Score: 99
Period size: 4 Copynumber: 13.5 Consensus size: 4
2844124 TAATTTCTCT
*
2844134 TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2844182 TATG TA
1 TATG TA
2844188 AATGACTAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:2844214 original size:26 final size:26
Alignment explanation
Indices: 2844178--2844239 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
2844168 TGTATGTATG
*
2844178 TATGTATGTAAATGACTAACTATATC
1 TATGTATGTAAATGACTAACTATATA
* *
2844204 TATGTATGTAAATGGCTAATTATATA
1 TATGTATGTAAATGACTAACTATATA
*
2844230 TATGGATGTA
1 TATGTATGTA
2844240 TGTAGGAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.40
Consensus pattern (26 bp):
TATGTATGTAAATGACTAACTATATA
Found at i:2853532 original size:37 final size:38
Alignment explanation
Indices: 2853456--2853529 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 38
2853446 TAATAATGTA
* *
2853456 ATATTATCGATGAATTTTTATATAATTTTTATTTAAAT
1 ATATTATCAATGAATTTTTATATAATTTTTATCTAAAT
2853494 ATATT-TCAATGAATTTTT-TATAAATTTTTTATCTAA
1 ATATTATCAATGAATTTTTATAT-AA-TTTTTATCTAA
2853530 TATTAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 3 0.09
37 14 0.44
38 15 0.47
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (38 bp):
ATATTATCAATGAATTTTTATATAATTTTTATCTAAAT
Found at i:2855710 original size:18 final size:19
Alignment explanation
Indices: 2855675--2855711 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2855665 CACGGAATGT
2855675 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2855695 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2855712 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2859671 original size:21 final size:21
Alignment explanation
Indices: 2859645--2859691 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2859635 ATTTACCGTG
**
2859645 ATTGCGGCCGTAGCGGGCGCT
1 ATTGCGGCCGTAGCGGAAGCT
* *
2859666 ATTGCGGTCGTCGCGGAAGCT
1 ATTGCGGCCGTAGCGGAAGCT
2859687 ATTGC
1 ATTGC
2859692 AGCTGTCGCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.26, G:0.38, T:0.23
Consensus pattern (21 bp):
ATTGCGGCCGTAGCGGAAGCT
Found at i:2861487 original size:19 final size:19
Alignment explanation
Indices: 2861445--2861487 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2861435 TAAGATAATA
2861445 TTATTACTAAATTTACTTT
1 TTATTACTAAATTTACTTT
* *
2861464 ATATTACTAAATTTAGTTT
1 TTATTACTAAATTTACTTT
2861483 TTATT
1 TTATT
2861488 TATTTTGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATTACTAAATTTACTTT
Found at i:2862977 original size:2 final size:2
Alignment explanation
Indices: 2862970--2863017 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2862960 AAGTGCAGAT
2862970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2863012 TA TA TA
1 TA TA TA
2863018 AAAGACAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2864539 original size:37 final size:37
Alignment explanation
Indices: 2864472--2864587 Score: 128
Period size: 37 Copynumber: 3.1 Consensus size: 37
2864462 TTAGAACAAA
* * *
2864472 AAATAAAAATAAAAAAACAATAATAAAAAACAGAAAT
1 AAATAAAAATAAAAAAACCATAATATAAAACAAAAAT
*
2864509 GAAA-ACAGAATAAAAAAACCA-AATATAAAACAAAAAT
1 -AAATA-AAAATAAAAAAACCATAATATAAAACAAAAAT
* *
2864546 AAATAAAAACAAAAAAAACATAATATAAAACATAAACAT
1 AAATAAAAATAAAAAAACCATAATATAAAACA-AAA-AT
2864585 AAA
1 AAA
2864588 AACAGAAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
36 15 0.23
37 27 0.41
38 19 0.29
39 5 0.08
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.13
Consensus pattern (37 bp):
AAATAAAAATAAAAAAACCATAATATAAAACAAAAAT
Found at i:2864556 original size:16 final size:17
Alignment explanation
Indices: 2864529--2864615 Score: 70
Period size: 16 Copynumber: 5.1 Consensus size: 17
2864519 TAAAAAAACC
2864529 AAATATAAAACAAAAAT
1 AAATATAAAACAAAAAT
2864546 AAATA-AAAACAAAAA-
1 AAATATAAAACAAAAAT
* * *
2864561 AAACATAATATAAAACAT
1 AAATATAAAACAAAA-AT
* *
2864579 AAACATAAAAACAGAAAT
1 AAATAT-AAAACAAAAAT
* * *
2864597 CAACATAATACAAAAAT
1 AAATATAAAACAAAAAT
2864614 AA
1 AA
2864616 GAGATTTGCA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
15 4 0.07
16 17 0.30
17 16 0.29
18 13 0.23
19 6 0.11
ACGTcount: A:0.74, C:0.10, G:0.01, T:0.15
Consensus pattern (17 bp):
AAATATAAAACAAAAAT
Found at i:2864559 original size:21 final size:21
Alignment explanation
Indices: 2864535--2864588 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
2864525 AACCAAATAT
2864535 AAAACAAAAATAA-ATAAAAAC
1 AAAACAAAAATAATAT-AAAAC
2864556 AAAA-AAAACATAATATAAAAC
1 AAAACAAAA-ATAATATAAAAC
2864577 ATAAACATAAAA
1 A-AAACA-AAAA
2864589 ACAGAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 4 0.14
21 14 0.50
22 5 0.18
23 2 0.07
24 3 0.11
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (21 bp):
AAAACAAAAATAATATAAAAC
Found at i:2864809 original size:27 final size:27
Alignment explanation
Indices: 2864778--2864877 Score: 67
Period size: 27 Copynumber: 3.4 Consensus size: 27
2864768 TTGCATGGTC
2864778 TATAAAACAAAAATATAAAAAATAGAA
1 TATAAAACAAAAATATAAAAAATAGAA
* *
2864805 TATAAACCAAATATAAATAAATTAAAATAGAAA
1 TATAAAACAAA-A-ATAT-AA--AAAATAG-AA
* * * *
2864838 TCGAAAAAACATAAATA-AAATACTAGAA
1 T--ATAAAACAAAAATATAAAAAATAGAA
2864866 TATAAAACAAAA
1 TATAAAACAAAA
2864878 TATTTAAGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 17
0.67 0.12 0.21
Matches are distributed among these distances:
26 9 0.16
27 10 0.18
28 4 0.07
29 8 0.15
30 2 0.04
31 2 0.04
32 7 0.13
33 5 0.09
34 1 0.02
35 7 0.13
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (27 bp):
TATAAAACAAAAATATAAAAAATAGAA
Found at i:2865492 original size:103 final size:102
Alignment explanation
Indices: 2865188--2865690 Score: 601
Period size: 103 Copynumber: 5.0 Consensus size: 102
2865178 AGAAAAGTTT
* * *
2865188 GAATGGTTTATTTAGGGATGAATAGATGAAGAATATGGGTTAGAGTTTGTGTTTTGATC--GAAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAAT-TGGGTTAGGGTTTGTGTTTTGATCGAGAAA
* * *
2865251 AACAAAAATTGAAGGAAAATTTGTGTTTATTTTGGATC
65 AACAGAAATCGAAGGAAGATTTGTGTTTATTTTGGATC
* * *
2865289 GAATGGGTTATTTAGGGAATAATAGATGAAGAATAAGAGTTA-GGTTTGTGTTTTGATCGAGAAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAAT-TGGGTTAGGGTTTGTGTTTTGATCGAGAAA
* * *
2865353 AAAAGAACTCGAAGGAAGATTTGTGTTTGTTTTGGATC
65 AACAGAAATCGAAGGAAGATTTGTGTTTATTTTGGATC
* * *
2865391 GAATGAGTTATTTAGGGAAGAATAGATAAAGAATTGGGGTTAGGGTTTGTGTTTTGATCAAGAAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAATT-GGGTTAGGGTTTGTGTTTTGATCGAGAAA
*
2865456 AACATAAATCGAAGGAAGATTTGTGTTTATTTTGGATC
65 AACAGAAATCGAAGGAAGATTTGTGTTTATTTTGGATC
* * * *
2865494 GAATGGGTTATTTATGGAAGAATAAATGAAGAA-TGAGATTTAGGGTTTATGTTTTGATCGAGAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAATTG-G-GTTAGGGTTTGTGTTTTGATCGAGAA
* *
2865558 AAATAGAAATCGAAGGAATG-TTTGAGTTTATTTTGGATC
64 AAACAGAAATCGAAGGAA-GATTTGTGTTTATTTTGGATC
* *
2865597 AAAT-GGTTATTTAGGGAAG---A-A--CA-AA---GGTTAGGGTTTGTGTTTTGATCGA-AAAA
1 GAATGGGTTATTTAGGGAAGAATAGATGAAGAATTGGGTTAGGGTTTGTGTTTTGATCGAGAAAA
2865650 ACAGAAATCGAAGGAATG-TTTGTGTTTATTTTGGATC
66 ACAGAAATCGAAGGAA-GATTTGTGTTTATTTTGGATC
2865687 GAAT
1 GAAT
2865691 ACTTTTGATG
Statistics
Matches: 355, Mismatches: 40, Indels: 25
0.85 0.10 0.06
Matches are distributed among these distances:
90 42 0.12
91 21 0.06
92 1 0.00
95 2 0.01
96 1 0.00
98 1 0.00
99 1 0.00
100 15 0.04
101 38 0.11
102 88 0.25
103 144 0.41
104 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (102 bp):
GAATGGGTTATTTAGGGAAGAATAGATGAAGAATTGGGTTAGGGTTTGTGTTTTGATCGAGAAAA
ACAGAAATCGAAGGAAGATTTGTGTTTATTTTGGATC
Found at i:2865608 original size:205 final size:201
Alignment explanation
Indices: 2865189--2865690 Score: 652
Period size: 205 Copynumber: 2.5 Consensus size: 201
2865179 GAAAAGTTTG
* *
2865189 AATGGTTTATTTAGGGATGAATAGATGAAGAATATGGGTTAGAGTTTGTGTTTTGATC-GAAAAA
1 AATGG-TTATTTAGGGA-GAATAGATAAAGAAT-TGGGTTAGGGTTTGTGTTTTGATCAGAAAAA
* * * *
2865253 CAAAAATTGAAGGAAAATTTGTGTTTATTTTGGATCGAATGGGTTATTTAGGGAATAATAGATGA
63 CAAAAATCGAAGGAAGATTTGTGTTTATTTTGGATCGAATGGGTTATTTAGGGAAGAATAAATGA
* * * *
2865318 AGAATAAGAGTTAGGTTTGTGTTTTGATCGAGAAAAAAAGAACTCGAAGGAAGATTTGTGTTTGT
128 AGAATAAGAGTTAGGTTTATGTTTTGATCGAGAAAAAAAGAAATCGAAGGAAGATTTGAGTTTAT
*
2865383 TTTGGATCG
193 TTTGGATCA
2865392 AATGAGTTATTTAGGGAAGAATAGATAAAGAATTGGGGTTAGGGTTTGTGTTTTGATCAAGAAAA
1 AATG-GTTATTTAGGG-AGAATAGATAAAGAATT-GGGTTAGGGTTTGTGTTTTGATC-AGAAAA
* *
2865457 ACATAAATCGAAGGAAGATTTGTGTTTATTTTGGATCGAATGGGTTATTTATGGAAGAATAAATG
62 ACAAAAATCGAAGGAAGATTTGTGTTTATTTTGGATCGAATGGGTTATTTAGGGAAGAATAAATG
* * *
2865522 AAGAATGAGATTTAGGGTTTATGTTTTGATCGAGAAAAATAGAAATCGAAGGAATG-TTTGAGTT
127 AAGAATAAGAGTTA-GGTTTATGTTTTGATCGAGAAAAAAAGAAATCGAAGGAA-GATTTGAGTT
2865586 TATTTTGGATCA
190 TATTTTGGATCA
*
2865598 AATGGTTATTTA-GG-G-A-AGA-ACA-AA---GGTTAGGGTTTGTGTTTTGATC-GAAAAAACA
1 AATGGTTATTTAGGGAGAATAGATAAAGAATTGGGTTAGGGTTTGTGTTTTGATCAG-AAAAACA
*
2865653 GAAATCGAAGGAATG-TTTGTGTTTATTTTGGATCGAAT
65 AAAATCGAAGGAA-GATTTGTGTTTATTTTGGATCGAAT
2865691 ACTTTTGATG
Statistics
Matches: 272, Mismatches: 18, Indels: 28
0.86 0.06 0.09
Matches are distributed among these distances:
192 1 0.00
193 42 0.15
194 23 0.08
198 2 0.01
199 2 0.01
200 3 0.01
201 1 0.00
202 2 0.01
203 50 0.18
204 4 0.01
205 84 0.31
206 57 0.21
207 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (201 bp):
AATGGTTATTTAGGGAGAATAGATAAAGAATTGGGTTAGGGTTTGTGTTTTGATCAGAAAAACAA
AAATCGAAGGAAGATTTGTGTTTATTTTGGATCGAATGGGTTATTTAGGGAAGAATAAATGAAGA
ATAAGAGTTAGGTTTATGTTTTGATCGAGAAAAAAAGAAATCGAAGGAAGATTTGAGTTTATTTT
GGATCA
Found at i:2866189 original size:17 final size:18
Alignment explanation
Indices: 2866167--2866231 Score: 75
Period size: 17 Copynumber: 3.8 Consensus size: 18
2866157 CATATATTTA
2866167 TATATTATA-ATTAAACT
1 TATATTATATATTAAACT
*
2866184 TATATTATATACTATAA--
1 TATATTATATATTA-AACT
*
2866201 TACATTATA-ATTAAACT
1 TATATTATATATTAAACT
2866218 TATATTATATATTA
1 TATATTATATATTA
2866232 TATATTATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 2 0.05
16 3 0.08
17 25 0.64
18 7 0.18
19 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTATATATTAAACT
Found at i:2866250 original size:17 final size:17
Alignment explanation
Indices: 2866164--2866250 Score: 51
Period size: 17 Copynumber: 5.3 Consensus size: 17
2866154 ATACATATAT
2866164 TTATATATTATAATTAAA
1 TTATATATTATAA-TAAA
* *
2866182 CT-TATATTAT-ATACTA
1 TTATATATTATAATA-AA
* *
2866198 TAATACATTATAATTAAA
1 TTATATATTATAA-TAAA
*
2866216 CT-TATATTAT-AT--A
1 TTATATATTATAATAAA
*
2866229 TTATATATTATAATACA
1 TTATATATTATAATAAA
2866246 TTATA
1 TTATA
2866251 GTCTTATAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 17
0.65 0.13 0.22
Matches are distributed among these distances:
13 2 0.04
14 8 0.16
15 5 0.10
16 3 0.06
17 28 0.55
18 3 0.06
19 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATATATTATAATAAA
Found at i:2866299 original size:18 final size:18
Alignment explanation
Indices: 2866276--2866310 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2866266 TAATATAGTT
2866276 TATATACACAGTTTATAG
1 TATATACACAGTTTATAG
* *
2866294 TATATATATAGTTTATA
1 TATATACACAGTTTATA
2866311 TAAGAGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (18 bp):
TATATACACAGTTTATAG
Found at i:2866508 original size:21 final size:21
Alignment explanation
Indices: 2866479--2866531 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2866469 ATTCTGAGTA
2866479 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
2866500 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
* *
2866521 TTGCAATGCGA
1 TCGCATTGCGA
2866532 ATACGTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2866546 original size:20 final size:20
Alignment explanation
Indices: 2866523--2866613 Score: 155
Period size: 20 Copynumber: 4.5 Consensus size: 20
2866513 TTCCTAATTT
*
2866523 GCAATGCGAATACGTAATTC
1 GCAATGCGAATACGTAAATC
2866543 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
2866563 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
2866583 GCATTGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
2866603 GCAACGCGAAT
1 GCAATGCGAAT
2866614 CTGACTATCG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:2866623 original size:20 final size:20
Alignment explanation
Indices: 2866600--2866706 Score: 160
Period size: 20 Copynumber: 5.3 Consensus size: 20
2866590 GAATACGTAA
*
2866600 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
2866620 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
2866640 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
2866660 ATCGTAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2866680 ATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2866700 ATCGCAA
1 ATCGCAA
2866707 TACTGAATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2869956 original size:20 final size:20
Alignment explanation
Indices: 2869931--2870003 Score: 121
Period size: 20 Copynumber: 3.6 Consensus size: 20
2869921 GAAATTCATT
*
2869931 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACACGGAA-A
2869951 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
2869971 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
2869991 TGACTATCGCAAC
1 TGACTATCGCAAC
2870004 GAGAGAATCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 48 0.94
21 3 0.06
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:2870064 original size:34 final size:33
Alignment explanation
Indices: 2869987--2870071 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
2869977 TCGCAACACG
**
2869987 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
2870020 GAAATGAAAATCGCAATGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
2870053 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
2870072 CGAATTTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 31 0.66
34 16 0.34
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:2870067 original size:20 final size:19
Alignment explanation
Indices: 2870009--2870075 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
2869999 GCAACGAGAG
2870009 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2870028 AATCGCAAT--G--A-GAG
1 AATCGCAATGCGAAATGAA
2870042 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2870062 AATCGCAACGCGAA
1 AATCGCAATGCGAA
2870076 TTTTGTTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 11 0.28
15 1 0.03
16 1 0.03
17 1 0.03
19 12 0.31
20 13 0.33
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2870129 original size:34 final size:34
Alignment explanation
Indices: 2870086--2870181 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
2870076 TTTTGTTTCG
2870086 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
2870120 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
2870153 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
2870182 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:2870160 original size:14 final size:14
Alignment explanation
Indices: 2870108--2870161 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
2870098 CATTTTCGCA
2870108 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2870122 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2870139 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
2870155 TTGCGAT
1 TTGCGAT
2870162 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2870306 original size:14 final size:14
Alignment explanation
Indices: 2870287--2870323 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2870277 CATCAATTAA
2870287 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2870301 ACAAATCATCTTTT
1 ACAAATCAACATTT
2870315 ACAAATCAA
1 ACAAATCAA
2870324 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2871771 original size:42 final size:42
Alignment explanation
Indices: 2871692--2871771 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
2871682 TGATTACAGT
* * **
2871692 GGCCTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGG
1 GGCCTCTTGAACGATGGGAGAGGACTCTTGAACGATGATAGG
*
2871734 GGCCTCTTGAACGATAGGG-GAGGTCTCTTGAACGATGA
1 GGCCTCTTGAACGAT-GGGAGAGGACTCTTGAACGATGA
2871772 CAGGTGAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 29 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (42 bp):
GGCCTCTTGAACGATGGGAGAGGACTCTTGAACGATGATAGG
Found at i:2872283 original size:20 final size:20
Alignment explanation
Indices: 2872255--2872343 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
2872245 GAAACTTAAA
* *
2872255 ATCGTAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
2872275 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
2872295 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** **
2872315 ATCGCAATACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2872335 ATCGCAACG
1 ATCGCAACG
2872344 AGATAATCGC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2872407 original size:34 final size:34
Alignment explanation
Indices: 2872366--2872521 Score: 154
Period size: 34 Copynumber: 4.4 Consensus size: 34
2872356 TGCGATTTTC
2872366 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
2872400 AATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCA
1 ATTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCA
* * * **
2872440 TTTTCGCGTTGCGATT-TTGTTGTTGCGATTTTC-
1 ATTTCGCATTGCGATTCTT-TCGTTGCGATAGTCA
*
2872473 ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
* *
2872507 TTTTCGCGTTGCGAT
1 ATTTCGCATTGCGAT
2872522 AGTCATTTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
33 25 0.26
34 37 0.38
35 2 0.02
36 4 0.04
38 6 0.06
40 24 0.24
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
Found at i:2872413 original size:20 final size:20
Alignment explanation
Indices: 2872388--2872544 Score: 135
Period size: 20 Copynumber: 8.5 Consensus size: 20
2872378 GATTCTTTCG
**
2872388 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
2872408 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2872428 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2872448 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
2872462 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2872481 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
2872495 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2872515 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2872535 TTGAGATAGT
1 TTGCGATAGT
2872545 AAACTATTCT
Statistics
Matches: 116, Mismatches: 7, Indels: 28
0.77 0.05 0.19
Matches are distributed among these distances:
14 14 0.12
16 12 0.10
17 6 0.05
18 5 0.04
19 7 0.06
20 72 0.62
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2874500 original size:34 final size:34
Alignment explanation
Indices: 2874457--2874576 Score: 125
Period size: 34 Copynumber: 3.4 Consensus size: 34
2874447 GAAAATGACT
2874457 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
* ** *
2874491 ATCGCAACGCGAA-ATGAAAATCGCAACACGAAAATGACA
1 ATCGCAACGCGAATTTGACTATCGC-A-ACG-CAA-G--A
* *
2874530 ATCGCAACGCGAATTTGACTATCGCAATGCAATA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
2874564 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2874577 ATGAAAATCG
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
33 8 0.12
34 28 0.41
35 3 0.04
36 2 0.03
37 3 0.04
38 2 0.03
39 15 0.22
40 8 0.12
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
Found at i:2874517 original size:53 final size:54
Alignment explanation
Indices: 2874436--2874539 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 54
2874426 CGAAAATGAA
** * ** *
2874436 AATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCAAG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACAATCGCAACGCAAG
*
2874490 AATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACAATCGCAACGC
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACAATCGCAACGC
2874540 GAATTTGACT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 32 0.74
54 11 0.26
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.13
Consensus pattern (54 bp):
AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACAATCGCAACGCAAG
Found at i:2874536 original size:73 final size:73
Alignment explanation
Indices: 2874416--2874590 Score: 305
Period size: 73 Copynumber: 2.4 Consensus size: 73
2874406 TGAAACTTAA
* *
2874416 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
1 AATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCG
2874481 CAACGCAAG
65 CAACGCAAG
2874490 AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCGC
1 AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCGC
* *
2874555 AATGCAAT
66 AACGCAAG
2874563 AATCGCAACGCGAAATGAAAATCGCAAC
1 AATCGCAACGCGAAATGAAAATCGCAAC
2874591 GACAGAATCA
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 86 0.89
74 11 0.11
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (73 bp):
AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCGC
AACGCAAG
Found at i:2874548 original size:20 final size:20
Alignment explanation
Indices: 2874416--2874591 Score: 128
Period size: 20 Copynumber: 9.5 Consensus size: 20
2874406 TGAAACTTAA
* *
2874416 AATCGCAACACGAAAATGAA
1 AATCGCAACGCGAAAATGAC
*
2874436 AATCGCAACACGAAAATGAC
1 AATCGCAACGCGAAAATGAC
* **
2874456 TATCGCAACGCGAATTTGAC
1 AATCGCAACGCGAAAATGAC
*
2874476 TATCGCAACGC---AA-G--
1 AATCGCAACGCGAAAATGAC
*
2874490 AATCGCAACGCG-AAATGAA
1 AATCGCAACGCGAAAATGAC
*
2874509 AATCGCAACACGAAAATGAC
1 AATCGCAACGCGAAAATGAC
**
2874529 AATCGCAACGCGAATTTGAC
1 AATCGCAACGCGAAAATGAC
* *
2874549 TATCGCAATGC---AAT---
1 AATCGCAACGCGAAAATGAC
*
2874563 AATCGCAACGCG-AAATGAA
1 AATCGCAACGCGAAAATGAC
2874582 AATCGCAACG
1 AATCGCAACG
2874592 ACAGAATCAC
Statistics
Matches: 126, Mismatches: 19, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
14 19 0.15
16 6 0.05
17 2 0.02
19 21 0.17
20 78 0.62
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAAAATGAC
Found at i:2874989 original size:22 final size:22
Alignment explanation
Indices: 2874927--2874992 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
2874917 TGACTGTGAA
* *
2874927 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
2874949 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2874971 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
2874993 AGATGTCACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:2875214 original size:20 final size:20
Alignment explanation
Indices: 2875191--2875263 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
2875181 TGATAGTCAG
*
2875191 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
2875211 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2875231 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2875251 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2875264 ATTAAGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2875284 original size:21 final size:21
Alignment explanation
Indices: 2875260--2875305 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2875250 TATTCGCATT
2875260 GCGAATTAAGAAAATCGCAAC
1 GCGAATTAAGAAAATCGCAAC
** *
2875281 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAAGAAAATCGCAAC
2875302 GCGA
1 GCGA
2875306 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAAGAAAATCGCAAC
Found at i:2877825 original size:7 final size:7
Alignment explanation
Indices: 2877815--2878083 Score: 100
Period size: 7 Copynumber: 40.9 Consensus size: 7
2877805 ATATAGATTA
2877815 TATATAG
1 TATATAG
2877822 TATA-A-
1 TATATAG
*
2877827 TTTATAG
1 TATATAG
*
2877834 TTTATAG
1 TATATAG
2877841 T-T-TA-
1 TATATAG
2877845 TATATAG
1 TATATAG
2877852 TATATAG
1 TATATAG
*
2877859 TATATAT
1 TATATAG
*
2877866 TATTTAG
1 TATATAG
** *
2877873 GGTTTAG
1 TATATAG
2877880 TATATA-
1 TATATAG
*
2877886 -ATTTA-
1 TATATAG
2877891 TATATAG
1 TATATAG
2877898 TATATAG
1 TATATAG
2877905 T-T-TA-
1 TATATAG
*
2877909 TATATAT
1 TATATAG
*
2877916 TATATAAA
1 TATAT-AG
*
2877924 TAAACTA-
1 TATA-TAG
2877931 TATATAG
1 TATATAG
2877938 T-T-TA-
1 TATATAG
2877942 TATATAG
1 TATATAG
*
2877949 TATAAAG
1 TATATAG
2877956 TATATAG
1 TATATAG
*
2877963 TTTATA-
1 TATATAG
2877969 TATATAG
1 TATATAG
*
2877976 TTTATATG
1 TATATA-G
2877984 TA-A-AG
1 TATATAG
2877989 TATATAG
1 TATATAG
*
2877996 AATATAAAG
1 --TATATAG
2878005 T-T-TA-
1 TATATAG
*
2878009 TCTATAG
1 TATATAG
2878016 TATATA-
1 TATATAG
2878022 TATATA-
1 TATATAG
*
2878028 TATATATA
1 TATATA-G
*
2878036 TATATAA
1 TATATAG
* *
2878043 TTTATAT
1 TATATAG
* *
2878050 TAATAAAA
1 T-ATATAG
2878058 TATATAG
1 TATATAG
*
2878065 TTTATA-
1 TATATAG
2878071 TATATAG
1 TATATAG
2878078 TATATA
1 TATATA
2878084 TGTTTTATAT
Statistics
Matches: 201, Mismatches: 32, Indels: 58
0.69 0.11 0.20
Matches are distributed among these distances:
4 4 0.02
5 21 0.10
6 44 0.22
7 108 0.54
8 17 0.08
9 7 0.03
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.48
Consensus pattern (7 bp):
TATATAG
Found at i:2877825 original size:9 final size:9
Alignment explanation
Indices: 2877813--2878212 Score: 76
Period size: 9 Copynumber: 44.7 Consensus size: 9
2877803 CAATATAGAT
2877813 TATATATAG
1 TATATATAG
2877822 TATAATTTATAG
1 TAT-A--TATAG
2877834 T-T-TATAG
1 TATATATAG
*
2877841 TTTATATA-
1 TATATATAG
2877849 TAGTATATAG
1 TA-TATATAG
2877859 TATATAT--
1 TATATATAG
2877866 TAT-T-TAG
1 TATATATAG
**
2877873 GGT-T-TAG
1 TATATATAG
2877880 TATATA-A-
1 TATATATAG
*
2877887 TTTATATA-
1 TATATATAG
2877895 TAGTATATAG
1 TA-TATATAG
*
2877905 TTTATATA-
1 TATATATAG
2877913 TAT-TATA-
1 TATATATAG
* * *
2877920 TAAATAAAC
1 TATATATAG
2877929 TATATATAG
1 TATATATAG
2877938 TTTATATATAG
1 --TATATATAG
2877949 TATA-A-AG
1 TATATATAG
2877956 TATATAGTTTA-
1 TATATA---TAG
2877967 TATATATAG
1 TATATATAG
*
2877976 TTTATAT-G
1 TATATATAG
2877984 TAAAGTATATAG
1 T--A-TATATAG
* *
2877996 AATATAAAG
1 TATATATAG
*
2878005 TTTATCTATAG
1 --TATATATAG
2878016 TATATATA-
1 TATATATAG
2878024 TATATATA-
1 TATATATAG
2878032 TATATATA-
1 TATATATAG
* *
2878040 TAATTTATAT
1 T-ATATATAG
*
2878050 TAATAAAATA-
1 T-AT-ATATAG
*
2878060 TATAGTTTA-
1 TATA-TATAG
2878069 TATATATAG
1 TATATATAG
2878078 TATATAT-G
1 TATATATAG
*
2878086 TTTTATATATTG
1 ---TATATATAG
* *
2878098 TTTATATAAT
1 TATATAT-AG
2878108 TATATATAG
1 TATATATAG
2878117 TTCATATATAG
1 -T-ATATATAG
*
2878128 TTCATACATAG
1 -T-ATATATAG
2878139 TATATA-A-
1 TATATATAG
2878146 -ATATA-A-
1 TATATATAG
2878152 -ACTATATAG
1 TA-TATATAG
*
2878161 TTTATATA-
1 TATATATAG
2878169 TATATATA-
1 TATATATAG
2878177 TATTATATAG
1 TA-TATATAG
2878187 TTTATATATAG
1 --TATATATAG
*
2878198 T-TCATATAT
1 TAT-ATATAG
2878207 TATATA
1 TATATA
2878213 CTGTTGAAAA
Statistics
Matches: 301, Mismatches: 38, Indels: 104
0.68 0.09 0.23
Matches are distributed among these distances:
5 1 0.00
6 8 0.03
7 36 0.12
8 51 0.17
9 113 0.38
10 19 0.06
11 62 0.21
12 11 0.04
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (9 bp):
TATATATAG
Found at i:2877852 original size:18 final size:18
Alignment explanation
Indices: 2877817--2878212 Score: 111
Period size: 18 Copynumber: 21.8 Consensus size: 18
2877807 ATAGATTATA
*
2877817 TATAGTATAATTTATAGTT
1 TATAGTAT-ATATATAGTT
* *
2877836 TATAGTTTATATATAGTA
1 TATAGTATATATATAGTT
2877854 TATAGTATATAT-TA-TT
1 TATAGTATATATATAGTT
** * *
2877870 TAGGGTTTAGTATATAATT
1 TATAGTATA-TATATAGTT
2877889 TATA-TATAGTATATAGTT
1 TATAGTATA-TATATAGTT
*
2877907 TATA-TATAT-TATA-TA
1 TATAGTATATATATAGTT
* *
2877922 AATA-AACTATATATAGTT
1 TATAGTA-TATATATAGTT
* *
2877940 TATA-TATAGTATAAAGTA
1 TATAGTATA-TATATAGTT
2877958 TATAGTTTATATATATAGTT
1 TATAG--TATATATATAGTT
*
2877978 TATATGTAAAGTATATAG--
1 TATA-GTATA-TATATAGTT
* * *
2877996 -A-A-TATAAAGTTTA-TC
1 TATAGTATATA-TATAGTT
*
2878011 TATAGTATATATATA-TA
1 TATAGTATATATATAGTT
*
2878028 TATA-TATATATATAATT
1 TATAGTATATATATAGTT
* * *
2878045 TATA-T-TA-ATAAAATA
1 TATAGTATATATATAGTT
*
2878060 TATAGTTTATATATATAGTA
1 TATAG--TATATATATAGTT
* *
2878080 TATATGTTTTATATATTGTT
1 TATA-G-TATATATATAGTT
2878100 TATA-TAATTATATATAGTT
1 TATAGT-A-TATATATAGTT
* *
2878119 CATATA-TAGTTCATACATAGTA
1 --TATAGTA--T-ATATATAGTT
*
2878141 TATAAATATAAACTATATAGTT
1 TAT-AGTAT--A-TATATAGTT
*
2878163 TATA-TATATATATATATT
1 TATAGTATATATATA-GTT
*
2878181 ATATAGTTTATATATAGTT
1 -TATAGTATATATATAGTT
*
2878200 CATA-TAT-TATATA
1 TATAGTATATATATA
2878213 CTGTTGAAAA
Statistics
Matches: 290, Mismatches: 49, Indels: 79
0.69 0.12 0.19
Matches are distributed among these distances:
13 1 0.00
14 6 0.02
15 15 0.05
16 34 0.12
17 37 0.13
18 69 0.24
19 32 0.11
20 60 0.21
21 16 0.06
22 20 0.07
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (18 bp):
TATAGTATATATATAGTT
Found at i:2877981 original size:11 final size:11
Alignment explanation
Indices: 2877836--2878206 Score: 133
Period size: 11 Copynumber: 34.3 Consensus size: 11
2877826 ATTTATAGTT
2877836 TATAGTTTATA
1 TATAGTTTATA
*
2877847 TATAGTATATA
1 TATAGTTTATA
*
2877858 GTATA-TATTATT
1 -TATAGT-TTATA
**
2877870 TAGGGTTTAGTA
1 TATAGTTTA-TA
*
2877882 TATAATTTATA
1 TATAGTTTATA
2877893 TATAG----TA
1 TATAGTTTATA
2877900 TATAGTTTATA
1 TATAGTTTATA
2877911 TATA-TTATATA
1 TATAGTT-TATA
* ***
2877922 AATAAACTATA
1 TATAGTTTATA
2877933 TATAGTTTATA
1 TATAGTTTATA
*
2877944 TATAGTATAAAGTA
1 TATAGT-T-TA-TA
2877958 TATAGTTTATA
1 TATAGTTTATA
2877969 TATA-TAGTT-TA
1 TATAGT--TTATA
**
2877980 TAT-GTAAAGTA
1 TATAGTTTA-TA
*
2877991 TATAG--AATA
1 TATAGTTTATA
* *
2878000 TAAAGTTTATC
1 TATAGTTTATA
2878011 TATAG--TATA
1 TATAGTTTATA
2878020 TATA---TATA
1 TATAGTTTATA
*
2878028 TATA-TATATA
1 TATAGTTTATA
*
2878038 TATAATTTATA
1 TATAGTTTATA
* **
2878049 T-TAATAAAATA
1 TATAGT-TTATA
2878060 TATAGTTTATA
1 TATAGTTTATA
*
2878071 TATA-TAGTATA
1 TATAGT-TTATA
2878082 TAT-GTTTTATA
1 TATAG-TTTATA
*
2878093 TATTGTTTATA
1 TATAGTTTATA
2878104 TA-A--TTATA
1 TATAGTTTATA
*
2878112 TATAGTTCATA
1 TATAGTTTATA
*
2878123 TATAGTTCATA
1 TATAGTTTATA
* *
2878134 CATAGTATATA
1 TATAGTTTATA
* **
2878145 AATA-TAAACTA
1 TATAGTTTA-TA
2878156 TATAGTTTATA
1 TATAGTTTATA
*
2878167 TATATATATATATTA
1 TATA-GT-T-TA-TA
2878182 TATAGTTTATA
1 TATAGTTTATA
*
2878193 TATAGTTCATA
1 TATAGTTTATA
2878204 TAT
1 TAT
2878207 TATATACTGT
Statistics
Matches: 274, Mismatches: 47, Indels: 78
0.69 0.12 0.20
Matches are distributed among these distances:
7 7 0.03
8 15 0.05
9 14 0.05
10 21 0.08
11 166 0.61
12 30 0.11
13 4 0.01
14 11 0.04
15 6 0.02
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (11 bp):
TATAGTTTATA
Found at i:2878212 original size:2 final size:2
Alignment explanation
Indices: 2877880--2878196 Score: 113
Period size: 2 Copynumber: 155.0 Consensus size: 2
2877870 TAGGGTTTAG
* *
2877880 TA TA TA -A TT TA TA TA TA GTA TA TA GTT TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
2877922 AA TA AA CTA TA TA TA GTT TA TA TA TA GTA TA AA GTA TA TA GTT TA
1 TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA -TA TA
* * * * * *
2877967 TA TA TA TA GTT TA TA TG TA AA GTA TA TA GA -A TA TA AA GTT TA
1 TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* *
2878009 TC TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA -A TT TA TA T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2878050 TA -A TA -A AA TA TA TA GTT TA TA TA TA TA GTA TA TA TG T- TT TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
2878091 TA TA T- TG TT TA TA TA -A T- TA TA TA TA GT- TCA TA TA TA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA -TA
* * * *
2878129 TCA TA CA TA GTA TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA
1 T-A TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
*
2878173 TA TA TA T- TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA
2878197 GTTCATATAT
Statistics
Matches: 234, Mismatches: 46, Indels: 70
0.67 0.13 0.20
Matches are distributed among these distances:
1 14 0.06
2 195 0.83
3 25 0.11
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2878480 original size:64 final size:65
Alignment explanation
Indices: 2878395--2878548 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 65
2878385 ACCCTATTTT
* * *
2878395 GAATGCATTTTGTGTATCGATGCACA-ACCATGCATCGATGCACTCTTGAAT-TTATTAAAACAT
1 GAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCATGAATCTT-TTAAAACAT
2878458 C
65 C
** *
2878459 GAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCATGGCTCTTTTGAAACATC
1 GAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCATGAATCTTTTAAAACATC
* *
2878524 GAATGTA-ATTAGTGTACCGATGCAC
1 GAATGCATTTTA-TGTACCGATGCAC
2878549 CCCTAGTGTA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 27 0.34
65 50 0.63
66 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (65 bp):
GAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCATGAATCTTTTAAAACATC
Found at i:2879738 original size:38 final size:38
Alignment explanation
Indices: 2879647--2879757 Score: 143
Period size: 39 Copynumber: 2.9 Consensus size: 38
2879637 TTCACCCTAA
* *
2879647 ACCTGAACCCGACCCGAATATCACACTTAAAAAAACCCG
1 ACCTG-ACCCGACCCAAATATCAAACTTAAAAAAACCCG
*
2879686 ACCCGACCCCGACCCAAATATCAAACTTAAAAAAACCCG
1 ACCTGA-CCCGACCCAAATATCAAACTTAAAAAAACCCG
* * *
2879725 ACCTGACCTGACCCAAA-ACCAAAATTAAAAAAA
1 ACCTGACCCGACCCAAATATCAAACTTAAAAAAA
2879758 AAAATCTGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
37 14 0.22
38 11 0.17
39 39 0.61
ACGTcount: A:0.46, C:0.34, G:0.08, T:0.12
Consensus pattern (38 bp):
ACCTGACCCGACCCAAATATCAAACTTAAAAAAACCCG
Found at i:2889449 original size:38 final size:38
Alignment explanation
Indices: 2889394--2889491 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
2889384 TATAAGACAT
* * * *
2889394 ATGATAGGTCCTACGGGACACATATTACATCCTTCAGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCAGG
* *
2889432 ATGACAGGTCTTTCGGGACACAGATGACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCAGG
*
2889470 ATGATAGGTCCTTCGGGACACA
1 ATGACAGGTCCTTCGGGACACA
2889492 ATTTATACGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATGACATCCTTCAGG
Found at i:2892894 original size:12 final size:12
Alignment explanation
Indices: 2892877--2892902 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2892867 AGATAATTTC
2892877 AAGATGACATCT
1 AAGATGACATCT
2892889 AAGATGACATCT
1 AAGATGACATCT
2892901 AA
1 AA
2892903 TCGACAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (12 bp):
AAGATGACATCT
Found at i:2895663 original size:38 final size:38
Alignment explanation
Indices: 2895607--2895704 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
2895597 TATAAGACAT
* * * *
2895607 ATGATAGGTCCTACGGGACACAGATTACATCTTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
2895645 ATGACAGGTCTTTCGGGACACAGATGACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
* *
2895683 ATGATAGTTCCTTCGGGACACA
1 ATGACAGGTCCTTCGGGACACA
2895705 ATTTATACGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:2897374 original size:21 final size:22
Alignment explanation
Indices: 2897324--2897376 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2897314 GTATGAACAA
2897324 TATCGATACCATATAGTAGAGG
1 TATCGATACCATATAGTAGAGG
* *
2897346 TGTCGATACC-TAT-GTGGAGGG
1 TATCGATACCATATAGTAGA-GG
2897367 TATCGATACC
1 TATCGATACC
2897377 CAGGGAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 14 0.52
22 9 0.33
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (22 bp):
TATCGATACCATATAGTAGAGG
Found at i:2897444 original size:22 final size:22
Alignment explanation
Indices: 2897419--2897499 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 22
2897409 ACCTAGATAG
2897419 GGTATCAGTACCCTAACTTAGA
1 GGTATCAGTACCCTAACTTAGA
2897441 GGTATC-GATACCCTAA---AG-
1 GGTATCAG-TACCCTAACTTAGA
2897459 GTAGTACTCAGTACCCTAACTTAGA
1 G--GTA-TCAGTACCCTAACTTAGA
*
2897484 GGTATCGGTACCCTAA
1 GGTATCAGTACCCTAA
2897500 GGGTAGTACC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 3 0.06
21 11 0.22
22 26 0.53
23 3 0.06
24 2 0.04
25 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (22 bp):
GGTATCAGTACCCTAACTTAGA
Found at i:2897477 original size:43 final size:43
Alignment explanation
Indices: 2897400--2897508 Score: 154
Period size: 43 Copynumber: 2.6 Consensus size: 43
2897390 AGCTAATTTT
2897400 GGTATCGATA-CCTAGATAGG--GTA-TCAGTACCCTAACTTAGA
1 GGTATCGATACCCTA-A-AGGTAGTACTCAGTACCCTAACTTAGA
2897441 GGTATCGATACCCTAAAGGTAGTACTCAGTACCCTAACTTAGA
1 GGTATCGATACCCTAAAGGTAGTACTCAGTACCCTAACTTAGA
* *
2897484 GGTATCGGTACCCTAAGGGTAGTAC
1 GGTATCGATACCCTAAAGGTAGTAC
2897509 CGATACTACT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
40 3 0.05
41 11 0.18
42 7 0.11
43 41 0.66
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
GGTATCGATACCCTAAAGGTAGTACTCAGTACCCTAACTTAGA
Found at i:2898296 original size:18 final size:18
Alignment explanation
Indices: 2898273--2898307 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2898263 GTTCTTAAGG
*
2898273 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
2898291 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGAGACA
2898308 AATTCTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:2901345 original size:21 final size:23
Alignment explanation
Indices: 2901254--2901352 Score: 118
Period size: 23 Copynumber: 4.5 Consensus size: 23
2901244 TGTTGCAAGG
* * *
2901254 GGTATCGATACCTGTAT-GAACA
1 GGTATCGATACCTATATGGTAGA
2901276 -GTATCGATACC-ATATGGTAGA
1 GGTATCGATACCTATATGGTAGA
*
2901297 GGTATCAATACCTATATGGTAGA
1 GGTATCGATACCTATATGGTAGA
*
2901320 GGTATAGATACCTATATGG-A-A
1 GGTATCGATACCTATATGGTAGA
2901341 GGTATCGATACC
1 GGTATCGATACC
2901353 CGGGGAACTT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.04
21 26 0.39
22 11 0.16
23 27 0.40
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (23 bp):
GGTATCGATACCTATATGGTAGA
Found at i:2909479 original size:27 final size:27
Alignment explanation
Indices: 2909442--2909505 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
2909432 TATAGGTGAA
2909442 AAATGATCATTAATCGATGTCTGAGAG
1 AAATGATCATTAATCGATGTCTGAGAG
* *
2909469 AAATGATCATTAATTGATGTTTGAGAG
1 AAATGATCATTAATCGATGTCTGAGAG
2909496 AAATGATCAT
1 AAATGATCAT
2909506 AAAAGTTCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (27 bp):
AAATGATCATTAATCGATGTCTGAGAG
Found at i:2909746 original size:30 final size:30
Alignment explanation
Indices: 2909711--2909768 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2909701 AACTTAAAAG
*
2909711 AGTTTTGCAATAAT-GAGATTTAAATAATTT
1 AGTTTTACAATAATGGA-ATTTAAATAATTT
* *
2909741 AGTTTTATAATACTGGAATTTAAATAAT
1 AGTTTTACAATAATGGAATTTAAATAAT
2909769 CCATACAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.43
Consensus pattern (30 bp):
AGTTTTACAATAATGGAATTTAAATAATTT
Found at i:2909819 original size:22 final size:22
Alignment explanation
Indices: 2909793--2909835 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2909783 TAATAAATTA
*
2909793 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
2909815 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2909836 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2909844 original size:22 final size:22
Alignment explanation
Indices: 2909795--2909843 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2909785 ATAAATTATT
* **
2909795 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
2909817 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2909840 TAAA
1 TAAA
2909844 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2909847 original size:54 final size:54
Alignment explanation
Indices: 2909783--2910304 Score: 490
Period size: 54 Copynumber: 9.4 Consensus size: 54
2909773 ACAACTACAA
*
2909783 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
2909837 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
2909891 TAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATTAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
2909945 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
2909999 TAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATT
1 TAATAAATTATTTAAAATAAATCAATC----C--AT--A-T-TTTAAAATAAATCAATCCATA--
*
2910064 T
54 C
* * * * *
2910065 TAAAATAAATCAATTCATACT-AAT-AA-AC-TA-TTTAAAATAAATCAATCCATA-
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
** * ** * ** **
2910116 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
* * ** **
2910171 -AACTATAA-TAATAAATCAATTCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAA-TA-AATTATTTAA--AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
2910229 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
2910283 GAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
2910305 TATTTTAAAA
Statistics
Matches: 398, Mismatches: 38, Indels: 64
0.80 0.08 0.13
Matches are distributed among these distances:
47 2 0.01
48 3 0.01
49 4 0.01
51 3 0.01
52 1 0.00
53 1 0.00
54 271 0.68
55 7 0.02
56 7 0.02
57 3 0.01
58 48 0.12
59 3 0.01
60 2 0.01
62 2 0.01
63 1 0.00
64 21 0.05
66 1 0.00
67 2 0.01
68 10 0.03
69 6 0.02
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:2909853 original size:32 final size:32
Alignment explanation
Indices: 2909815--2910304 Score: 374
Period size: 32 Copynumber: 16.4 Consensus size: 32
2909805 CAATTCATAT
2909815 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2909847 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2909869 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
2909901 TTTAAAATAAATTAATCCATATTTTAAAATAAATTAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAATT-A
* * ** * * *
2909938 TTCATACTAATAAAT-TATTTAAAATAAATCAATCCATA
1 TT--TA-AAATAAATCAATCCATACT-AATAAAT---TA
2909976 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
*
2910009 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2910041 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
2910063 TTTAAAATAAATCAATTCATACTAATAAACTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2910095 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2910117 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2910149 TTTAAAATAAATCAATCCATAC-AACT--A-TA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* *
2910178 ---ATAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2910207 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2910239 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
2910261 TTTAAAATAAATCAATACATACGAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2910293 TTTAAAATAAAT
1 TTTAAAATAAAT
2910305 TATTTTAAAA
Statistics
Matches: 375, Mismatches: 22, Indels: 122
0.72 0.04 0.24
Matches are distributed among these distances:
22 64 0.17
23 8 0.02
24 4 0.01
26 30 0.08
27 2 0.01
28 13 0.03
29 4 0.01
30 5 0.01
31 9 0.02
32 177 0.47
33 2 0.01
34 1 0.00
36 28 0.07
37 11 0.03
38 1 0.00
39 9 0.02
40 7 0.02
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:2909873 original size:22 final size:22
Alignment explanation
Indices: 2909847--2909889 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2909837 TAATAAATTA
2909847 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2909869 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2909890 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2909898 original size:22 final size:22
Alignment explanation
Indices: 2909849--2909897 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2909839 ATAAATTATT
**
2909849 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2909871 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2909894 TAAA
1 TAAA
2909898 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2909916 original size:22 final size:22
Alignment explanation
Indices: 2909891--2909938 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2909881 CAATCCATAC
2909891 TAATAAAT-TATTTAAAATAAAT
1 TAATAAATAT-TTTAAAATAAAT
**
2909913 TAATCCATATTTTAAAATAAAT
1 TAATAAATATTTTAAAATAAAT
2909935 TAAT
1 TAAT
2909939 TCATACTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAAATATTTTAAAATAAAT
Found at i:2909943 original size:22 final size:22
Alignment explanation
Indices: 2909901--2909943 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2909891 TAATAAATTA
2909901 TTTAAAATAAATTAATCCATAT
1 TTTAAAATAAATTAATCCATAT
*
2909923 TTTAAAATAAATTAATTCATA
1 TTTAAAATAAATTAATCCATA
2909944 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATAAATTAATCCATAT
Found at i:2909952 original size:22 final size:22
Alignment explanation
Indices: 2909903--2909951 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2909893 ATAAATTATT
**
2909903 TAAAATAAATTAATCCATATTT
1 TAAAATAAATTAATCCATATAA
*
2909925 TAAAATAAATTAATTCATACTAA
1 TAAAATAAATTAATCCATA-TAA
2909948 TAAA
1 TAAA
2909952 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATTAATCCATATAA
Found at i:2909980 original size:22 final size:22
Alignment explanation
Indices: 2909955--2909997 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2909945 TAATAAATTA
2909955 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2909977 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2909998 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2910006 original size:22 final size:22
Alignment explanation
Indices: 2909957--2910005 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2909947 ATAAATTATT
**
2909957 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2909979 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2910002 TAAA
1 TAAA
2910006 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2910019 original size:14 final size:14
Alignment explanation
Indices: 2910000--2910052 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
2909990 AATCCATACT
2910000 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
2910014 AATAAATCAATCTATACT
1 AATAAAT-TAT-T-TA-A
2910032 AATAAATTATTTAA
1 AATAAATTATTTAA
2910046 AATAAAT
1 AATAAAT
2910053 CAATCCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 4 0.13
16 2 0.06
17 4 0.13
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:2910067 original size:22 final size:22
Alignment explanation
Indices: 2910041--2910083 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2910031 TAATAAATTA
2910041 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
2910063 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
2910084 CTAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2910121 original size:22 final size:22
Alignment explanation
Indices: 2910095--2910137 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2910085 TAATAAACTA
2910095 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2910117 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2910138 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2910146 original size:22 final size:22
Alignment explanation
Indices: 2910097--2910145 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2910087 ATAAACTATT
**
2910097 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2910119 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2910142 TAAA
1 TAAA
2910146 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2910202 original size:18 final size:18
Alignment explanation
Indices: 2910179--2910236 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
2910169 ACAACTATAA
2910179 TAATAAATCAATTCATAC
1 TAATAAATCAATTCATAC
*
2910197 TAATAAAT-TATT--TA-
1 TAATAAATCAATTCATAC
* *
2910211 AAATAAATCAATCCATAC
1 TAATAAATCAATTCATAC
2910229 TAATAAAT
1 TAATAAAT
2910237 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
17 5 0.16
18 15 0.48
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATAAATCAATTCATAC
Found at i:2910265 original size:22 final size:22
Alignment explanation
Indices: 2910239--2910281 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2910229 TAATAAATTA
*
2910239 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
2910261 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATACATA
2910282 CGAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:2910313 original size:15 final size:15
Alignment explanation
Indices: 2910284--2910431 Score: 172
Period size: 15 Copynumber: 9.5 Consensus size: 15
2910274 AATACATACG
2910284 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
2910298 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2910313 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
2910335 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
2910350 AATAATTTATTTTAT
1 AATAAATTATTTTAA
*
2910365 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
2910380 AATAAATTATTTTAT
1 AATAAATTATTTTAA
2910395 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2910410 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2910425 AATAAAT
1 AATAAAT
2910432 AACCTTATTA
Statistics
Matches: 120, Mismatches: 6, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.08
15 94 0.78
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:2910416 original size:198 final size:194
Alignment explanation
Indices: 2909815--2910328 Score: 763
Period size: 194 Copynumber: 2.6 Consensus size: 194
2909805 CAATTCATAT
2909815 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * * * * * *
2909880 TCAATCCATACTAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATTAATTCATAC
66 TCAATACATACGAATAAACTATTTAAAAT-AA-CAAT-C-TATTTTAAAATAAATCAATCCATAA
* * *
2909945 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATACTAATAAA
127 TAATAAATTATTTAAAATAAATCAATCCATAAAACTATAATAATAAATCAATTCATACTAATAAA
2910006 TTA
192 TTA
*
2910009 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * *
2910074 TCAATTCATACTAATAAACTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
66 TCAATACATACGAATAAACTATTTAAAAT-AA-CAAT-C-TATTTTAAAATAAATCAATCCATAA
*
2910139 TAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAATAAATCAATTCATACTAATAAA
127 TAATAAATTATTTAAAATAAATCAATCCATAAAACTATAATAATAAATCAATTCATACTAATAAA
2910204 TTA
192 TTA
2910207 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
*
2910272 TCAATACATACGAATAAATTATTTAAAAT-A-AAT-TATTTTAAAATAAATCAATCCATA
66 TCAATACATACGAATAAACTATTTAAAATAACAATCTATTTTAAAATAAATCAATCCATA
2910329 TTTTATAATA
Statistics
Matches: 303, Mismatches: 13, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
191 24 0.08
194 157 0.52
196 1 0.00
197 5 0.02
198 116 0.38
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (194 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATACATACGAATAAACTATTTAAAATAACAATCTATTTTAAAATAAATCAATCCATAATAAT
AAATTATTTAAAATAAATCAATCCATAAAACTATAATAATAAATCAATTCATACTAATAAATTA
Found at i:2912914 original size:17 final size:18
Alignment explanation
Indices: 2912877--2912915 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2912867 TTATTATGTA
2912877 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
2912895 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
2912912 TTTA
1 TTTA
2912916 CTAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:2913173 original size:111 final size:111
Alignment explanation
Indices: 2912979--2913311 Score: 621
Period size: 111 Copynumber: 3.0 Consensus size: 111
2912969 TGAAAATCAT
* * *
2912979 ATATCTCTATACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
2913044 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAATAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
2913090 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
2913155 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
2913201 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTCAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
2913266 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
2913312 TTTTTGTAAT
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 217 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Done.