Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 65
Found at i:1208425 original size:18 final size:18
Alignment explanation
Indices: 1208398--1208483 Score: 75
Period size: 19 Copynumber: 4.6 Consensus size: 18
1208388 TGAAATTTAG
1208398 TTTTTATATTAATTATAA
1 TTTTTATATTAATTATAA
* **
1208416 TTTGTATATTATAAATT-TGG
1 TTT-T-TA-TATTAATTATAA
*
1208436 TTTTTATATTAATTCTAA
1 TTTTTATATTAATTATAA
* *
1208454 TTATTAATATTATTTATAA
1 TT-TTTATATTAATTATAA
1208473 TTTTTATATTA
1 TTTTTATATTA
1208484 TAATTTTTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
17 7 0.13
18 16 0.30
19 17 0.32
20 6 0.11
21 7 0.13
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTTATATTAATTATAA
Found at i:1208479 original size:13 final size:13
Alignment explanation
Indices: 1208463--1208500 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
1208453 ATTATTAATA
1208463 TTATTTATAATTT
1 TTATTTATAATTT
1208476 TTATATTATAATTT
1 TTAT-TTATAATTT
1208490 TTATTTATAAT
1 TTATTTATAAT
1208501 CATTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTTATAATTT
Found at i:1208484 original size:18 final size:18
Alignment explanation
Indices: 1208398--1208484 Score: 68
Period size: 18 Copynumber: 4.7 Consensus size: 18
1208388 TGAAATTTAG
*
1208398 TTTTTATATTAATTATAA
1 TTTTTATATTATTTATAA
* **
1208416 TTTGTATATTATAAATT-TGG
1 TTTTTATATTAT---TTATAA
* *
1208436 TTTTTATATTAATTCTAA
1 TTTTTATATTATTTATAA
*
1208454 TTATTAATATTATTTATAA
1 TT-TTTATATTATTTATAA
1208473 TTTTTATATTAT
1 TTTTTATATTAT
1208485 AATTTTTATT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
17 2 0.04
18 22 0.42
19 15 0.29
20 11 0.21
21 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTTATATTATTTATAA
Found at i:1208510 original size:27 final size:26
Alignment explanation
Indices: 1208463--1208515 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1208453 ATTATTAATA
** *
1208463 TTATTTATAATTTTTATATTATAATTT
1 TTATTTATAATCATTAAATTA-AATTT
1208490 TTATTTATAATCATTAAATTAAATTT
1 TTATTTATAATCATTAAATTAAATTT
1208516 AGTTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATTTATAATCATTAAATTAAATTT
Found at i:1209132 original size:23 final size:23
Alignment explanation
Indices: 1209106--1209189 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
1209096 GCAGGAACCG
* *
1209106 GCAAGTATCACTGTATCAATTCA
1 GCAAGCATCACTGCATCAATTCA
1209129 GCAAGCATCACTGCATCAATTCA
1 GCAAGCATCACTGCATCAATTCA
*
1209152 GCAAGCATCATTGCATCAATTCA
1 GCAAGCATCACTGCATCAATTCA
1209175 GCAAGCATC-CTGCAT
1 GCAAGCATCACTGCAT
1209190 TCAGAAAGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 5 0.09
23 52 0.91
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (23 bp):
GCAAGCATCACTGCATCAATTCA
Found at i:1209301 original size:20 final size:20
Alignment explanation
Indices: 1209276--1209356 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
1209266 AACACTTACA
**
1209276 AATATCAAGTAGAATCAAGC
1 AATATCAAACAGAATCAAGC
* *
1209296 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAATCAAGC
* *
1209316 AATATAAAATAGAATCAAG-
1 AATATCAAACAGAATCAAGC
*
1209335 ATATATCAAGCAGAATCAAGC
1 A-ATATCAAACAGAATCAAGC
1209356 A
1 A
1209357 CCAACTATTG
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.17
Consensus pattern (20 bp):
AATATCAAACAGAATCAAGC
Found at i:1211957 original size:18 final size:18
Alignment explanation
Indices: 1211929--1212168 Score: 218
Period size: 18 Copynumber: 13.5 Consensus size: 18
1211919 GTTTCAAATA
*
1211929 GTTTGGATTCGGGTTTGG
1 GTTTGGGTTCGGGTTTGG
*
1211947 ATTTGGGTTCGGGTTT-G
1 GTTTGGGTTCGGGTTTGG
*
1211964 GATTGGGTTCGGGTTT--
1 GTTTGGGTTCGGGTTTGG
**
1211980 GTATTGGGTTCGGGTTCAG
1 GT-TTGGGTTCGGGTTTGG
* *
1211999 GTTTGGATT-GGGTTCGG
1 GTTTGGGTTCGGGTTTGG
*** **
1212016 GTTCAAGTTTAGGTTTGG
1 GTTTGGGTTCGGGTTTGG
*
1212034 GTTCGGGTTCGGGTTTGG
1 GTTTGGGTTCGGGTTTGG
* * * **
1212052 ATTAGGGATCCAGTTTGG
1 GTTTGGGTTCGGGTTTGG
* * *
1212070 GTTTGGTTTCAGGTTCGG
1 GTTTGGGTTCGGGTTTGG
* *
1212088 GTTCGGGTTCGAGTTTGG
1 GTTTGGGTTCGGGTTTGG
*
1212106 GTTTGGGTTCGAGTTTGG
1 GTTTGGGTTCGGGTTTGG
1212124 GTTTGGGTTCGGGTTTGG
1 GTTTGGGTTCGGGTTTGG
*
1212142 GTTTGGGTTCAGGTTTGG
1 GTTTGGGTTCGGGTTTGG
1212160 GTTTGGGTT
1 GTTTGGGTT
1212169 AGAGAAGATG
Statistics
Matches: 180, Mismatches: 38, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
16 1 0.01
17 40 0.22
18 137 0.76
19 2 0.01
ACGTcount: A:0.07, C:0.07, G:0.43, T:0.42
Consensus pattern (18 bp):
GTTTGGGTTCGGGTTTGG
Found at i:1211960 original size:6 final size:6
Alignment explanation
Indices: 1211929--1212168 Score: 130
Period size: 6 Copynumber: 40.5 Consensus size: 6
1211919 GTTTCAAATA
* * * * * *
1211929 GTTTGG ATTCGG GTTTGG ATTTGG GTTCGG GTTT-G GATTGG GTTCGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* ** * * ***
1211976 GTTT-- GTATTGG GTTCGG GTTCAG GTTT-G GATTGG GTTCGG GTTCAA
1 GTTTGG GT-TTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * * * ***
1212022 GTTTAG GTTTGG GTTCGG GTTCGG GTTTGG ATTAGG GATCCA GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * * * *
1212070 GTTT-G GTTTCAG GTTCGG GTTCGG GTTCGA GTTTGG GTTTGG GTTCGA
1 GTTTGG GTTT-GG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* **
1212118 GTTTGG GTTTGG GTTCGG GTTTGG GTTTGG GTTCAG GTTTGG GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
1212166 GTT
1 GTT
1212169 AGAGAAGATG
Statistics
Matches: 176, Mismatches: 51, Indels: 14
0.73 0.21 0.06
Matches are distributed among these distances:
4 2 0.01
5 15 0.09
6 153 0.87
7 6 0.03
ACGTcount: A:0.07, C:0.07, G:0.43, T:0.42
Consensus pattern (6 bp):
GTTTGG
Found at i:1212038 original size:24 final size:23
Alignment explanation
Indices: 1211976--1212054 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
1211966 TTGGGTTCGG
* *
1211976 GTTTGTATTGGGTTCGGGTTCAG
1 GTTTGGATTGGGTTCGGGTTCAA
1211999 GTTTGGATTGGGTTCGGGTTCAA
1 GTTTGGATTGGGTTCGGGTTCAA
* **
1212022 GTTTAGGTTTGGGTTCGGGTTCGG
1 GTTT-GGATTGGGTTCGGGTTCAA
1212046 GTTTGGATT
1 GTTTGGATT
1212055 AGGGATCCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 29 0.59
24 20 0.41
ACGTcount: A:0.09, C:0.08, G:0.41, T:0.43
Consensus pattern (23 bp):
GTTTGGATTGGGTTCGGGTTCAA
Found at i:1212095 original size:24 final size:23
Alignment explanation
Indices: 1211958--1212147 Score: 177
Period size: 24 Copynumber: 8.1 Consensus size: 23
1211948 TTTGGGTTCG
*
1211958 GGTTTGGATT-GGGTTCGGGTTT
1 GGTTTGGGTTCGGGTTCGGGTTT
*
1211980 -GTATTGGGTTCGGGTTCAGGTTT
1 GGT-TTGGGTTCGGGTTCGGGTTT
* **
1212003 GGATTGGGTTCGGGTTCAAGTTT
1 GGTTTGGGTTCGGGTTCGGGTTT
1212026 AGGTTTGGGTTCGGGTTCGGGTTT
1 -GGTTTGGGTTCGGGTTCGGGTTT
* * ** *
1212050 GGATTAGGGATCCAGTTTGGGTTT
1 GG-TTTGGGTTCGGGTTCGGGTTT
* *
1212074 GGTTTCAGGTTCGGGTTCGGGTTC
1 GGTTT-GGGTTCGGGTTCGGGTTT
* *
1212098 GAGTTTGGGTTTGGGTTCGAGTTT
1 G-GTTTGGGTTCGGGTTCGGGTTT
*
1212122 GGGTTTGGGTTCGGGTTTGGGTTT
1 -GGTTTGGGTTCGGGTTCGGGTTT
1212146 GG
1 GG
1212148 GTTCAGGTTT
Statistics
Matches: 134, Mismatches: 26, Indels: 15
0.77 0.15 0.09
Matches are distributed among these distances:
21 2 0.01
22 6 0.04
23 36 0.27
24 85 0.63
25 5 0.04
ACGTcount: A:0.07, C:0.08, G:0.43, T:0.42
Consensus pattern (23 bp):
GGTTTGGGTTCGGGTTCGGGTTT
Found at i:1212148 original size:24 final size:24
Alignment explanation
Indices: 1211951--1212168 Score: 176
Period size: 24 Copynumber: 9.2 Consensus size: 24
1211941 GTTTGGATTT
* *
1211951 GGGTTCGGGTTTGGATT-GGGTTC
1 GGGTTTGGGTTTGGGTTCGGGTTC
1211974 GGGTTT--GTATTGGGTTCGGGTTC
1 GGGTTTGGGT-TTGGGTTCGGGTTC
* *
1211997 AGGTTT-GGATTGGGTTCGGGTTC
1 GGGTTTGGGTTTGGGTTCGGGTTC
** *
1212020 AAGTTTAGGTTTGGGTTCGGGTTC
1 GGGTTTGGGTTTGGGTTCGGGTTC
* * * ** *
1212044 GGGTTTGGATTAGGGATCCAGTTT
1 GGGTTTGGGTTTGGGTTCGGGTTC
*
1212068 GGGTTT-GGTTTCAGGTTCGGGTTC
1 GGGTTTGGGTTT-GGGTTCGGGTTC
* * *
1212092 GGGTTCGAGTTTGGGTTTGGGTTC
1 GGGTTTGGGTTTGGGTTCGGGTTC
* *
1212116 GAGTTTGGGTTTGGGTTCGGGTTT
1 GGGTTTGGGTTTGGGTTCGGGTTC
** * *
1212140 GGGTTTGGGTTCAGGTTTGGGTTT
1 GGGTTTGGGTTTGGGTTCGGGTTC
1212164 GGGTT
1 GGGTT
1212169 AGAGAAGATG
Statistics
Matches: 154, Mismatches: 35, Indels: 11
0.77 0.17 0.05
Matches are distributed among these distances:
21 2 0.01
22 6 0.04
23 38 0.25
24 104 0.68
25 4 0.03
ACGTcount: A:0.07, C:0.08, G:0.44, T:0.42
Consensus pattern (24 bp):
GGGTTTGGGTTTGGGTTCGGGTTC
Found at i:1212585 original size:116 final size:113
Alignment explanation
Indices: 1212354--1212683 Score: 385
Period size: 105 Copynumber: 3.0 Consensus size: 113
1212344 TTTGGGGAAT
* * * **
1212354 AACACGGATGAACAAGGGTTTAACT-TTTGGGTGTTTGAGTGAAAGAAAAAAACAGGAATGGGTT
1 AACACGGATGAACAAGGGTTGAA-TATTTGGGTGTTTGA-T-CAAGAAAAAAACACGAAACGGTT
* * * * *
1212418 TAGGTTTTGG-TGTTGTGAAGATCAAATAATGGTTTGGGGAAGAACTGGGATG
63 TGGGTTTTGGTTTTTGTGAAGATCAAATGATGGTTTTGGGATGAAC--GGATG
*
1212470 AACACGGATGAACAAGGGTTGAATATTTGGGTGTTTGATCAAGAAAAAAACATGAAACGGTTTGG
1 AACACGGATGAACAAGGGTTGAATATTTGGGTGTTTGATCAAGAAAAAAACACGAAACGGTTTGG
*
1212535 GTTTTGGTTTTTGTGAAGATCAAATGAGGGTTTT----TG---GGATG
66 GTTTTGGTTTTTGTGAAGATCAAATGATGGTTTTGGGATGAACGGATG
* *
1212576 AACACGGATGAACAAGGGTTGAA-ATTTTGGGTGTTTGATC-GGAAAAAAACACGAAATGGTTTG
1 AACACGGATGAACAAGGGTTGAATA-TTTGGGTGTTTGATCAAGAAAAAAACACGAAACGGTTTG
*
1212639 GGTTTTGGTGTTTGTGAAGATCAAATGATGGTTTTTGGGATGAAC
65 GGTTTTGGTTTTTGTGAAGATCAAATGATGG-TTTTGGGATGAAC
1212684 ACGGAAGAAA
Statistics
Matches: 187, Mismatches: 16, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
105 50 0.27
106 47 0.25
110 2 0.01
111 1 0.01
114 28 0.15
115 24 0.13
116 35 0.19
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.31
Consensus pattern (113 bp):
AACACGGATGAACAAGGGTTGAATATTTGGGTGTTTGATCAAGAAAAAAACACGAAACGGTTTGG
GTTTTGGTTTTTGTGAAGATCAAATGATGGTTTTGGGATGAACGGATG
Found at i:1212987 original size:61 final size:61
Alignment explanation
Indices: 1212918--1213059 Score: 230
Period size: 61 Copynumber: 2.3 Consensus size: 61
1212908 TCCTAGTTTT
* *
1212918 AAATTTGTTCAATTTAATCCAAATTTAATGATGCAATATATTAATTTAAGCTTTATATTTA
1 AAATTTGTTCAATTTAATCCAAATTTAATGATACAATATATTAATTTAAGCTTCATATTTA
* * *
1212979 AAATTTGTTCAATTTAGTCCAAATTTAATGTTACAATTTATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAATCCAAATTTAATGATACAATATATTAATTTAAGCTTCATATTTA
*
1213040 AAATTTGTTCAATTTGATCC
1 AAATTTGTTCAATTTAATCC
1213060 TTATATATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 74 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (61 bp):
AAATTTGTTCAATTTAATCCAAATTTAATGATACAATATATTAATTTAAGCTTCATATTTA
Found at i:1213114 original size:26 final size:27
Alignment explanation
Indices: 1213082--1213163 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 27
1213072 CAATTCTTTC
1213082 AATTAATATATATGTTTATAT-TAAT-A
1 AATTAATATATA-GTTTATATATAATGA
1213108 AATTAATATATAGGTTATATATAGTAATGA
1 AATTAATATATA-GTT-TATATA-TAATGA
1213138 ACTATATAATATATAGTTTATATATA
1 A--AT-TAATATATAGTTTATATATA
1213164 CTATATAGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
26 15 0.31
27 5 0.10
29 4 0.08
30 4 0.08
31 6 0.12
32 5 0.10
33 9 0.19
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (27 bp):
AATTAATATATAGTTTATATATAATGA
Found at i:1213148 original size:33 final size:33
Alignment explanation
Indices: 1213111--1213329 Score: 177
Period size: 33 Copynumber: 6.6 Consensus size: 33
1213101 ATTAATAAAT
* *
1213111 TAATATATAGGTTATATATAGTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
* *
1213144 TAATATATAGTTTATATATACT-AT-ATAGTTTA
1 TAATATATAGTTTATATATACTAATGA-ACTATA
* * *
1213176 T-ATATACTAG-TGA-ACTAT-GTAATGTATAGTTTATA
1 TAATATA-TAGTTTATA-TATACTAATG-A-A--CTATA
*
1213211 TATACCATATAGTTTATATATACTAATGAACTATA
1 TA-A-TATATAGTTTATATATACTAATGAACTATA
*
1213246 TAATATATAGTTTATATATATTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
* *
1213279 TAATATATAGTTTATATATAC-CAT-ATACTTTA
1 TAATATATAGTTTATATATACTAATGA-ACTATA
*
1213311 T-ATATATAGTTTTTATATA
1 TAATATATAGTTTATATATA
1213330 TAGTTCATAT
Statistics
Matches: 153, Mismatches: 18, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
30 2 0.01
31 31 0.20
32 18 0.12
33 71 0.46
34 1 0.01
35 10 0.07
37 5 0.03
38 9 0.06
39 6 0.04
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (33 bp):
TAATATATAGTTTATATATACTAATGAACTATA
Found at i:1213170 original size:51 final size:51
Alignment explanation
Indices: 1213114--1213265 Score: 250
Period size: 51 Copynumber: 3.0 Consensus size: 51
1213104 AATAAATTAA
* *
1213114 TATATAGGTTATATATAGTAATGAACTATATAATATATAGTTTATATATAC
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
* * *
1213165 TATATAGTTTATATATACTAGTGAACTATGTAATGTATAGTTTATATATAC
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
*
1213216 CATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATA
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATA
1213266 TTAATGAACT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 92 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.44
Consensus pattern (51 bp):
TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
Found at i:1213331 original size:84 final size:82
Alignment explanation
Indices: 1213111--1213329 Score: 260
Period size: 84 Copynumber: 2.6 Consensus size: 82
1213101 ATTAATAAAT
* ** * *
1213111 TAATATATAGGTTATATATAGTA-ATGAACTATATAATATATAGTTTATATATACTATATAGTTT
1 TAATATATAGTTTATATATACCATAT--ACTTTAT-ATATATAGTTTATATATAATATATAGTTT
* *
1213175 ATATATACTAGTGAACTATG
63 ATATATACTAATGAACTATA
* * * **
1213195 TAATGTATAGTTTATATATACCATATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
1 TAATATATAGTTTATATATACCATATACTTTATATATA-TAGTTTA-TATATAATATATAGTTTA
*
1213260 TATATATTAATGAACTATA
64 TATATACTAATGAACTATA
*
1213279 TAATATATAGTTTATATATACCATATACTTTATATATATAGTTTTTATATA
1 TAATATATAGTTTATATATACCATATACTTTATATATATAGTTTATATATA
1213330 TAGTTCATAT
Statistics
Matches: 113, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
82 11 0.10
83 12 0.11
84 88 0.78
85 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (82 bp):
TAATATATAGTTTATATATACCATATACTTTATATATATAGTTTATATATAATATATAGTTTATA
TATACTAATGAACTATA
Found at i:1213332 original size:13 final size:13
Alignment explanation
Indices: 1213301--1213339 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1213291 TATATATACC
*
1213301 ATATACTTTATAT
1 ATATAGTTTATAT
*
1213314 ATATAGTTTTTAT
1 ATATAGTTTATAT
*
1213327 ATATAGTTCATAT
1 ATATAGTTTATAT
1213340 GTAAACTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (13 bp):
ATATAGTTTATAT
Found at i:1213353 original size:64 final size:65
Alignment explanation
Indices: 1213111--1213330 Score: 214
Period size: 69 Copynumber: 3.3 Consensus size: 65
1213101 ATTAATAAAT
* * * *
1213111 TAATATATAGGTTATATATAGTAATGAACTATATAATATATAGTTTATATATACTATATAGTTTA
1 TAATATATAGTTTATATATATTAATGAACTATATAATATATAGTTTATATATACTATATACTATA
** * ** **
1213176 T-ATATACTAGTGAACTATGTAATGTATAGTTTA-TATATACCATATAGTTTATATATACTA-AT
1 TAATATA-TAGTTTA-TATAT-AT-TA-A-TGAACTATATAATATATAGTTTATATATACTATAT
1213238 GAACTATA
60 --ACTATA
* *
1213246 TAATATATAGTTTATATATATTAATGAACTATATAATATATAGTTTATATATACCATATACTTTA
1 TAATATATAGTTTATATATATTAATGAACTATATAATATATAGTTTATATATACTATATACTATA
*
1213311 T-ATATATAGTTTTTATATAT
1 TAATATATAGTTTATATATAT
1213331 AGTTCATATG
Statistics
Matches: 123, Mismatches: 21, Indels: 23
0.74 0.13 0.14
Matches are distributed among these distances:
64 23 0.19
65 13 0.11
66 29 0.24
67 5 0.04
68 6 0.05
69 30 0.24
70 12 0.10
71 5 0.04
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.45
Consensus pattern (65 bp):
TAATATATAGTTTATATATATTAATGAACTATATAATATATAGTTTATATATACTATATACTATA
Found at i:1213383 original size:18 final size:17
Alignment explanation
Indices: 1213140--1213387 Score: 66
Period size: 18 Copynumber: 14.8 Consensus size: 17
1213130 AGTAATGAAC
*
1213140 TATATAA-TATATAGTT
1 TATATAACTATATAGTA
*
1213156 TATATATACTATATAGTT
1 TATATA-ACTATATAGTA
* *
1213174 TATATATACTA-GT-GAA
1 TATATA-ACTATATAGTA
* * *
1213190 CTATGTAA-TGTATAGTT
1 -TATATAACTATATAGTA
* *
1213207 TATATATACCATATAGTT
1 TATATA-ACTATATAGTA
*
1213225 TATATATACTA-AT-GAA
1 TATATA-ACTATATAGTA
*
1213241 CTATATAA-TATATAGTT
1 -TATATAACTATATAGTA
* *
1213258 TATATATATTA-AT-GAA
1 TATATA-ACTATATAGTA
*
1213274 CTATATAA-TATATAGTT
1 -TATATAACTATATAGTA
* *
1213291 TATATATACCATATACT-
1 TATATA-ACTATATAGTA
1213308 T-TAT-A-TATATAGT-
1 TATATAACTATATAGTA
*
1213321 T-T-TTA-TATATAGTTCA
1 TATATAACTATATAG-T-A
*
1213337 TATGTAAACTATATAGTA
1 TATAT-AACTATATAGTA
1213355 TATATAAACTATATATGTA
1 TATAT-AACTATATA-GTA
1213374 GTATAT-ACTATATA
1 -TATATAACTATATA
1213388 AATAGTTTAT
Statistics
Matches: 179, Mismatches: 26, Indels: 52
0.70 0.10 0.20
Matches are distributed among these distances:
12 1 0.01
13 16 0.09
14 2 0.01
15 5 0.03
16 38 0.21
17 31 0.17
18 69 0.39
19 5 0.03
20 12 0.07
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (17 bp):
TATATAACTATATAGTA
Found at i:1213393 original size:18 final size:18
Alignment explanation
Indices: 1213341--1213393 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1213331 AGTTCATATG
1213341 TAAACTATATAGTATA-TA
1 TAAACTATATA-TATAGTA
*
1213359 TAAACTATATATGTAGTA
1 TAAACTATATATATAGTA
* *
1213377 TATACTATATAAATAGT
1 TAAACTATATATATAGT
1213394 TTATTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 3 0.10
18 27 0.90
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (18 bp):
TAAACTATATATATAGTA
Found at i:1213544 original size:47 final size:46
Alignment explanation
Indices: 1213488--1213691 Score: 116
Period size: 47 Copynumber: 4.2 Consensus size: 46
1213478 AATTATATTA
*
1213488 TATAATATATAAATATCAACTATAGTATATAGTATATAAATATCAAC
1 TATAGTATATAAATATCAACTATAGTATATAGTATATAAATAT-AAC
* * * ***
1213535 TATAGTATATAGTTTATATATAAACTATAGTTTATA-T-TGTTTTTAT-A-
1 TATAGTATATA----A-ATATCAACTATAGTATATAGTATATAAATATAAC
*
1213582 TATAGT-TCATAAGTA--AACTATAGTATATAGTATATATAGTTTATATATAATC
1 TATAGTAT-ATAAATATCAACTATAGTATATAG--TATATA----A-ATATAA-C
* *
1213634 TATAGTATATAAATATCAACTATAGTATGTAGTGTATAAATATAAAC
1 TATAGTATATAAATATCAACTATAGTATATAGTATATAAATAT-AAC
*
1213681 TATAGTTTATA
1 TATAGTATATA
1213692 TGTATAGTAT
Statistics
Matches: 118, Mismatches: 17, Indels: 44
0.66 0.09 0.25
Matches are distributed among these distances:
40 13 0.11
42 2 0.02
43 2 0.02
44 2 0.02
46 1 0.01
47 34 0.29
48 4 0.03
49 3 0.03
50 6 0.05
51 2 0.02
52 34 0.29
53 1 0.01
54 14 0.12
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (46 bp):
TATAGTATATAAATATCAACTATAGTATATAGTATATAAATATAAC
Found at i:1213570 original size:25 final size:27
Alignment explanation
Indices: 1213466--1213570 Score: 124
Period size: 27 Copynumber: 4.0 Consensus size: 27
1213456 TAGTATGAAT
* * * * *
1213466 TATATAAGTATAAATTATATTATATAA
1 TATATAAATATCAACTATAGTATATAG
1213493 TATATAAATATCAACTATAGTATATAG
1 TATATAAATATCAACTATAGTATATAG
1213520 TATATAAATATCAACTATAGTATATAG
1 TATATAAATATCAACTATAGTATATAG
* * *
1213547 T-T-TATATATAAACTATAGTTTATA
1 TATATAAATATCAACTATAGTATATA
1213571 TTGTTTTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
25 19 0.27
26 1 0.01
27 50 0.71
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (27 bp):
TATATAAATATCAACTATAGTATATAG
Found at i:1213576 original size:27 final size:26
Alignment explanation
Indices: 1213500--1213583 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
1213490 TAATATATAA
* * *
1213500 ATATCAACTATAG-TATATAGTATATAA
1 ATATAAACTATAGTTATATTGT-T-TAT
* *
1213527 ATATCAACTATAG-TATATAGTTTAT
1 ATATAAACTATAGTTATATTGTTTAT
*
1213552 ATATAAACTATAGTTTATATTGTTTTT
1 ATATAAACTATAG-TTATATTGTTTAT
1213579 ATATA
1 ATATA
1213584 TAGTTCATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.27
26 1 0.02
27 36 0.71
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (26 bp):
ATATAAACTATAGTTATATTGTTTAT
Found at i:1213621 original size:34 final size:34
Alignment explanation
Indices: 1213540--1213644 Score: 104
Period size: 34 Copynumber: 2.9 Consensus size: 34
1213530 TCAACTATAG
* *
1213540 TATATAGTTTATATATAAACTATAGTTTATATTGTTTTTA
1 TATATAGTTCATATATAAACTATAG--TATATAG----TA
1213580 TATATAGTTCATA-AGTAAACTATAGTATATAGTA
1 TATATAGTTCATATA-TAAACTATAGTATATAGTA
* *
1213614 TATATAGTTTATATATAATCTATAGTATATA
1 TATATAGTTCATATATAAACTATAGTATATA
1213645 AATATCAACT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
34 29 0.49
35 1 0.02
38 6 0.10
39 1 0.02
40 22 0.37
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.48
Consensus pattern (34 bp):
TATATAGTTCATATATAAACTATAGTATATAGTA
Found at i:1213702 original size:31 final size:31
Alignment explanation
Indices: 1213659--1213723 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
1213649 TCAACTATAG
1213659 TATGTAGTGTATA-AATATA-AACTATAGTTTA
1 TATGTAGTGTATATAATATATAA--ATAGTTTA
*
1213690 TATGTA-TAGTATATACTATATAAATAGTTTA
1 TATGTAGT-GTATATAATATATAAATAGTTTA
1213721 TAT
1 TAT
1213724 AGTTCACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
30 1 0.03
31 22 0.73
32 5 0.17
33 2 0.07
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (31 bp):
TATGTAGTGTATATAATATATAAATAGTTTA
Found at i:1213703 original size:27 final size:27
Alignment explanation
Indices: 1213595--1213722 Score: 93
Period size: 27 Copynumber: 4.9 Consensus size: 27
1213585 AGTTCATAAG
* * *
1213595 TAAACTATAGTATATAGTATATATAGTT
1 TAAACTATAGTATATAGTGTATA-AATA
* * * *
1213623 TATA-TATAATCTATAGTATATAAATA
1 TAAACTATAGTATATAGTGTATAAATA
* *
1213649 TCAACTATAGTATGTAGTGTATAAATA
1 TAAACTATAGTATATAGTGTATAAATA
* *
1213676 TAAACTATAGTTTATA-TGTAT-AGTA
1 TAAACTATAGTATATAGTGTATAAATA
* * *
1213701 TATACTATA-TAAATAGTTTATA
1 TAAACTATAGTATATAGTGTATA
1213723 TAGTTCACTA
Statistics
Matches: 78, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
24 4 0.05
25 15 0.19
26 9 0.12
27 47 0.60
28 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (27 bp):
TAAACTATAGTATATAGTGTATAAATA
Found at i:1213820 original size:2 final size:2
Alignment explanation
Indices: 1213813--1214005 Score: 76
Period size: 2 Copynumber: 93.5 Consensus size: 2
1213803 TAATGTAAAC
* *
1213813 TA TA TA TA TCA TA TA -A TA TA TA AA TA TCA -A CTA TA -A CA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA
* * *
1213853 TA GTT TA TA TA TA AA T- TA TA GTT 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
* * * *
1213896 TA TA TA TA TA GTT TT TA TA TA TA GT- TCA TA TG TA -A AA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA
* * * *
1213937 TA GTA TA TA TA GTT TT TA TA TA TA TA GTT TA TA TA TG TA CTA TA
1 TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * *
1213981 TG GA -A TA TA TA TA TA GTT TA TA TA T
1 TA TA TA TA TA TA TA TA -TA TA TA TA T
1214006 GTACTATATG
Statistics
Matches: 146, Mismatches: 25, Indels: 40
0.69 0.12 0.19
Matches are distributed among these distances:
1 7 0.05
2 123 0.84
3 16 0.11
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1213872 original size:18 final size:17
Alignment explanation
Indices: 1213850--1214005 Score: 124
Period size: 17 Copynumber: 8.9 Consensus size: 17
1213840 CAACTATAAC
*
1213850 ATATAGTTTATATATAA
1 ATATAGTTTATATATAT
1213867 ATTATAGTTTATATATAT
1 A-TATAGTTTATATATAT
*
1213885 ATATA-TATATATATAT
1 ATATAGTTTATATATAT
*
1213901 ATATAGTTTTTATATAT
1 ATATAGTTTATATATAT
*
1213918 AGTTCATATGTAAAATATATAGTAT
1 A--T-ATA-GT---TTATATA-TAT
1213943 ATATAGTTT-T-TATAT
1 ATATAGTTTATATATAT
*
1213958 ATATAGTTTATATATGT
1 ATATAGTTTATATATAT
**
1213975 ACTATA-TGGA-ATATAT
1 A-TATAGTTTATATATAT
1213991 ATATAGTTTATATAT
1 ATATAGTTTATATAT
1214006 GTACTATATG
Statistics
Matches: 111, Mismatches: 13, Indels: 30
0.72 0.08 0.19
Matches are distributed among these distances:
15 16 0.14
16 26 0.23
17 27 0.24
18 21 0.19
19 1 0.01
20 3 0.03
21 4 0.04
22 3 0.03
23 1 0.01
24 5 0.05
25 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (17 bp):
ATATAGTTTATATATAT
Found at i:1213914 original size:42 final size:42
Alignment explanation
Indices: 1213881--1213960 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
1213871 TAGTTTATAT
*
1213881 ATATATATATATATATA-TATATATAGTTTTTATATATAGTTC
1 ATATATA-AAATATATAGTATATATAGTTTTTATATATAGTTC
*
1213923 ATATGTAAAATATATAGTATATATAGTTTTTATATATA
1 ATATATAAAATATATAGTATATATAGTTTTTATATATA
1213961 TAGTTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 8 0.23
42 27 0.77
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (42 bp):
ATATATAAAATATATAGTATATATAGTTTTTATATATAGTTC
Found at i:1213981 original size:44 final size:41
Alignment explanation
Indices: 1213882--1213991 Score: 123
Period size: 44 Copynumber: 2.6 Consensus size: 41
1213872 AGTTTATATA
1213882 TATATATATATATATA-TATATATAGTTTTTATATATAGTT
1 TATATATATATATATAGTATATATAGTTTTTATATATAGTT
* * *
1213922 CATATGTAAAATATATAGTATATATAGTTTTTATATATATAGTT
1 TATATAT-ATATATATAGTATATATAG-TTTT-TATATATAGTT
* * *
1213966 TATATATGTACTATATGGAATATATA
1 TATATATATA-TATATAGTATATATA
1213992 TATAGTTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
40 5 0.09
41 8 0.14
42 9 0.16
43 5 0.09
44 29 0.52
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (41 bp):
TATATATATATATATAGTATATATAGTTTTTATATATAGTT
Found at i:1213990 original size:33 final size:33
Alignment explanation
Indices: 1213953--1214015 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
1213943 ATATAGTTTT
1213953 TATATATATAGTTTATATATGTACTATATGGAA
1 TATATATATAGTTTATATATGTACTATATGGAA
1213986 TATATATATAGTTTATATATGTACTATATG
1 TATATATATAGTTTATATATGTACTATATG
1214016 CTATAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (33 bp):
TATATATATAGTTTATATATGTACTATATGGAA
Found at i:1213992 original size:31 final size:33
Alignment explanation
Indices: 1213953--1214035 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
1213943 ATATAGTTTT
*
1213953 TATATATATAGTTTATATATGTACTATATGGAA
1 TATATATATAGTTTATATATGTACTATATGCAA
1213986 TATATATATAGTTTATATATGTACTATATGC--
1 TATATATATAGTTTATATATGTACTATATGCAA
* *
1214017 TATAAAAATAGTTTATATA
1 TATATATATAGTTTATATA
1214036 GTTTGTTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 17 0.36
33 30 0.64
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.46
Consensus pattern (33 bp):
TATATATATAGTTTATATATGTACTATATGCAA
Found at i:1214082 original size:79 final size:79
Alignment explanation
Indices: 1213999--1214145 Score: 172
Period size: 79 Copynumber: 1.9 Consensus size: 79
1213989 ATATATAGTT
****
1213999 TATATA-TGTACTATATGCTATAAAAATAGTTTATATAGTTTGTTAATAAACTATATATA-TATA
1 TATATAGTGTA-TATATGCTATAAAAATAGTTTATAT-GTAAACTAATAAACTATATATATTATA
1214062 TAGTTGATACGTAAAC
64 TAGTTGATACGTAAAC
* ** * * *
1214078 TATATAGTTTATATATTTTATATATATAGTTTATATGTAAACTACTAAACTATATATATTATATA
1 TATATAGTGTATATATGCTATAAAAATAGTTTATATGTAAACTAATAAACTATATATATTATATA
1214143 GTT
66 GTT
1214146 TACATAGTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
78 17 0.30
79 36 0.64
80 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (79 bp):
TATATAGTGTATATATGCTATAAAAATAGTTTATATGTAAACTAATAAACTATATATATTATATA
GTTGATACGTAAAC
Found at i:1214100 original size:42 final size:41
Alignment explanation
Indices: 1214054--1214226 Score: 144
Period size: 42 Copynumber: 4.2 Consensus size: 41
1214044 ATAAACTATA
* * *
1214054 TATATATATAGTTGATACGTAAACTATATAGTTTATATATTT
1 TATATATATAGTT-ATATGTAAACTATATAGTATATATAGTT
* *
1214096 TATATATATAGTTTATATGTAAACTACTAAACTATATATA-TT
1 TATATATATAG-TTATATGTAAACTA-TATAGTATATATAGTT
* *
1214138 ATATAGTTTACATAGTT-T-T-T--A-TATATAGTTTATATAGTT
1 -TATA---TATATAGTTATATGTAAACTATATAGTATATATAGTT
*
1214177 TATACATATAGTTCATATGTAAACTATATAGTATATATAGTT
1 TATATATATAGTT-ATATGTAAACTATATAGTATATATAGTT
*
1214219 TACATATA
1 TATATATA
1214227 GTATAAGTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
35 7 0.07
37 1 0.01
38 15 0.14
39 5 0.05
40 1 0.01
41 1 0.01
42 48 0.46
43 17 0.16
44 1 0.01
45 2 0.02
46 6 0.06
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (41 bp):
TATATATATAGTTATATGTAAACTATATAGTATATATAGTT
Found at i:1214165 original size:22 final size:22
Alignment explanation
Indices: 1214132--1214189 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1214122 CTAAACTATA
1214132 TATATTATATAGTTTACATAGTT
1 TATA-TATATAGTTTACATAGTT
* *
1214155 TTTATATATAGTTTATATAGTT
1 TATATATATAGTTTACATAGTT
*
1214177 TATACATATAGTT
1 TATATATATAGTT
1214190 CATATGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.53
Consensus pattern (22 bp):
TATATATATAGTTTACATAGTT
Found at i:1214167 original size:13 final size:13
Alignment explanation
Indices: 1214149--1214297 Score: 53
Period size: 13 Copynumber: 11.1 Consensus size: 13
1214139 TATAGTTTAC
*
1214149 ATAGTTTTTATAT
1 ATAGTTTATATAT
1214162 ATAG--T-T-TAT
1 ATAGTTTATATAT
*
1214171 ATAGTTTATACAT
1 ATAGTTTATATAT
* *
1214184 ATAGTTCATATGT
1 ATAGTTTATATAT
* *
1214197 AAACTATATAGTATAT
1 ATAGT-T-TA-TATAT
1214213 ATAGTTTACATATAGT
1 ATAGTTT--ATATA-T
1214229 ATAAG-TTAGTATAT
1 AT-AGTTTA-TATAT
*
1214243 ATTG-TT-TATAT
1 ATAGTTTATATAT
*
1214254 ATAGTTTAAATACT
1 ATAGTTTATATA-T
1214268 ACTA-TTTATAAACTAT
1 A-TAGTTTAT--A-TAT
1214284 ATAGTTTATATAT
1 ATAGTTTATATAT
1214297 A
1 A
1214298 ATTCCATAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 40
0.65 0.09 0.26
Matches are distributed among these distances:
9 7 0.07
10 1 0.01
11 10 0.10
12 3 0.03
13 29 0.28
14 13 0.13
15 14 0.14
16 21 0.21
17 4 0.04
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (13 bp):
ATAGTTTATATAT
Found at i:1214194 original size:22 final size:22
Alignment explanation
Indices: 1214138--1214228 Score: 84
Period size: 22 Copynumber: 4.3 Consensus size: 22
1214128 TATATATATT
* * *
1214138 ATATAGTTTACATAGTTTTTAT
1 ATATAGTTTATATAGTTTATAC
1214160 ATATAGTTTATATAGTTTATAC
1 ATATAGTTTATATAGTTTATAC
* *
1214182 ATATAGTTCATAT-G--TAAAC
1 ATATAGTTTATATAGTTTATAC
*
1214201 TATATAGTATATATAG-TT-TAC
1 -ATATAGTTTATATAGTTTATAC
1214222 ATATAGT
1 ATATAGT
1214229 ATAAGTTAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.07
20 18 0.31
21 4 0.07
22 32 0.55
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (22 bp):
ATATAGTTTATATAGTTTATAC
Found at i:1214242 original size:81 final size:80
Alignment explanation
Indices: 1214045--1214254 Score: 209
Period size: 81 Copynumber: 2.6 Consensus size: 80
1214035 AGTTTGTTAA
* * * *
1214045 TAAACTATATATA-TATATAGTT-GATACG-TA-AACTATATAGTTTATATATTTTATATATATA
1 TAAACTATATATATTATATAGTTACATA-GTTAGTA-TATATAGTTTATATAGTTTATACATATA
*
1214106 GTTTATATGTAAACTAC
64 GTTCATATGTAAACTAC
**
1214123 TAAACTATATATATTATATAGTTTACATAGTTTTTATATATAGTTTATATAGTTTATACATATAG
1 TAAACTATATATATTATATAG-TTACATAGTTAGTATATATAGTTTATATAGTTTATACATATAG
1214188 TTCATATGTAAACTA-
65 TTCATATGTAAACTAC
* * * *
1214203 TATAGTATATATAGTTTACATATAG-TATA-AGTTAGTATATATTGTTTATATA
1 TAAACTATATATA--TT--ATATAGTTACATAGTTAGTATATATAGTTTATATA
1214255 TAGTTTAAAT
Statistics
Matches: 111, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
78 13 0.12
79 7 0.06
80 14 0.13
81 65 0.59
82 6 0.05
84 6 0.05
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (80 bp):
TAAACTATATATATTATATAGTTACATAGTTAGTATATATAGTTTATATAGTTTATACATATAGT
TCATATGTAAACTAC
Found at i:1214363 original size:24 final size:22
Alignment explanation
Indices: 1214329--1214702 Score: 117
Period size: 22 Copynumber: 17.8 Consensus size: 22
1214319 CTCTAAACCA
* * *
1214329 TATATACTATATATATAAAAAC
1 TATATAATTTATATATATAAAC
* *
1214351 TATGTAGTTTATACTA-ATAAAC
1 TATATAATTTATA-TATATAAAC
1214373 TATATAATTTATATATAGT--A-
1 TATATAATTTATATATA-TAAAC
*
1214393 TATATTATTTATA-AT-T--A-
1 TATATAATTTATATATATAAAC
* * * *
1214410 TACATAATATATAAATATAAAT
1 TATATAATTTATATATATAAAC
* * **
1214432 TGTATAGTTTATATATA-ATTC
1 TATATAATTTATATATATAAAC
1214453 ATATATAA-TT-TATATATAAAC
1 -TATATAATTTATATATATAAAC
1214474 TATATAATTTATAT-TAATAAAC
1 TATATAATTTATATAT-ATAAAC
* * *
1214496 TATGTAGTTTATATATAGT--TC
1 TATATAATTTATATATA-TAAAC
* *
1214517 -A-AT-AGTT-CATATATAAAC
1 TATATAATTTATATATATAAAC
* * *
1214535 TATATAGTTTATACATGGT--A-
1 TATATAATTTATATAT-ATAAAC
* *
1214555 TATATAGTTT-TATACATAATA-
1 TATATAATTTATATATATAA-AC
*
1214576 TATATATAGTTTATATATAGTATA-
1 TATATA-A-TTTATATATA-TAAAC
*
1214600 TA-ATAA--TATAAATATAAAC
1 TATATAATTTATATATATAAAC
* *
1214619 TATATAGTTTATATATATATA-
1 TATATAATTTATATATATAAAC
* *
1214640 TATATATATATATATATATATA-
1 TATATA-ATTTATATATATAAAC
* *
1214662 TATATATATATATATATATATA-
1 TATATA-ATTTATATATATAAAC
*
1214684 TATATATATATATATATAT
1 TATATA-ATTTATATATAT
1214703 TATAGTTGTT
Statistics
Matches: 270, Mismatches: 48, Indels: 68
0.70 0.12 0.18
Matches are distributed among these distances:
16 1 0.00
17 17 0.06
18 9 0.03
19 17 0.06
20 41 0.15
21 29 0.11
22 134 0.50
23 12 0.04
24 8 0.03
25 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATAATTTATATATATAAAC
Found at i:1214466 original size:9 final size:10
Alignment explanation
Indices: 1214373--1214487 Score: 59
Period size: 9 Copynumber: 11.5 Consensus size: 10
1214363 ACTAATAAAC
1214373 TATATAATT-
1 TATATAATTA
1214382 TATAT-A-TA
1 TATATAATTA
1214390 GTATAT-ATTA
1 -TATATAATTA
*
1214400 TTTATAATTA
1 TATATAATTA
*
1214410 TACATAATATA
1 TATATAAT-TA
*
1214421 TAAATATAAATTG
1 T--ATAT-AATTA
1214434 TATAGT--TTA
1 TATA-TAATTA
1214443 TATATAATTCA
1 TATATAATT-A
1214454 TATATAATTTA
1 TATATAA-TTA
1214465 TATATAA--A
1 TATATAATTA
1214473 CTATATAATT-
1 -TATATAATTA
1214483 TATAT
1 TATAT
1214488 TAATAAACTA
Statistics
Matches: 84, Mismatches: 6, Indels: 32
0.69 0.05 0.26
Matches are distributed among these distances:
7 1 0.01
8 3 0.04
9 33 0.39
10 14 0.17
11 22 0.26
12 3 0.04
13 5 0.06
14 3 0.04
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (10 bp):
TATATAATTA
Found at i:1214469 original size:13 final size:11
Alignment explanation
Indices: 1214434--1214695 Score: 70
Period size: 11 Copynumber: 24.4 Consensus size: 11
1214424 ATATAAATTG
*
1214434 TATAGTTTATA
1 TATAATTTATA
*
1214445 TATAATTCATA
1 TATAATTTATA
1214456 TATAATTTATA
1 TATAATTTATA
1214467 TATAA---ACTA
1 TATAATTTA-TA
1214476 TATAATTTATA
1 TATAATTTATA
**
1214487 T-TAATAAACTA
1 TATAATTTA-TA
* *
1214498 TGTAGTTTATA
1 TATAATTTATA
* *
1214509 TAT-AGTT-CA
1 TATAATTTATA
* *
1214518 -ATAGTTCATA
1 TATAATTTATA
1214528 TATAA---ACTA
1 TATAATTTA-TA
*
1214537 TATAGTTTATA
1 TATAATTTATA
* **
1214548 CAT--GGTATA
1 TATAATTTATA
*
1214557 TATAGTTTTATA
1 TATA-ATTTATA
* *
1214569 CATAATATATA
1 TATAATTTATA
*
1214580 TATAGTTTATA
1 TATAATTTATA
* *
1214591 TATAGTATATA
1 TATAATTTATA
* *
1214602 -ATAATATAAA
1 TATAATTTATA
1214612 TATAA---ACTA
1 TATAATTTA-TA
*
1214621 TATAGTTTATA
1 TATAATTTATA
*
1214632 TATATATATATA
1 TATA-ATTTATA
*
1214644 TATATATATATA
1 TATA-ATTTATA
*
1214656 TATATATATATA
1 TATA-ATTTATA
*
1214668 TATATATATATA
1 TATA-ATTTATA
*
1214680 TATATATATATA
1 TATA-ATTTATA
1214692 TATA
1 TATA
1214696 TATATATTAT
Statistics
Matches: 192, Mismatches: 37, Indels: 43
0.71 0.14 0.16
Matches are distributed among these distances:
8 5 0.03
9 26 0.14
10 16 0.08
11 74 0.39
12 71 0.37
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (11 bp):
TATAATTTATA
Found at i:1214578 original size:2 final size:2
Alignment explanation
Indices: 1214573--1214706 Score: 175
Period size: 2 Copynumber: 66.5 Consensus size: 2
1214563 TTTATACATA
* *
1214573 AT AT AT AT AT AGT TT AT AT AT AGT AT AT A- AT A- AT AT AA AT AT
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* *
1214615 AA ACT AT AT AGT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1214659 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
1214701 AT -T AT A
1 AT AT AT A
1214707 GTTGTTTCAA
Statistics
Matches: 117, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
1 3 0.03
2 109 0.93
3 5 0.04
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1214636 original size:22 final size:22
Alignment explanation
Indices: 1214329--1214697 Score: 147
Period size: 20 Copynumber: 17.9 Consensus size: 22
1214319 CTCTAAACCA
* * *
1214329 TATATACTATATATATAAAAAC
1 TATATAGTTTATATATATAAAC
*
1214351 TATGTAGTTTATACTA-ATAAAC
1 TATATAGTTTATA-TATATAAAC
* *
1214373 TATATAATTTATATATAGTATA-
1 TATATAGTTTATATATA-TAAAC
*
1214395 TAT-TA-TTTATA-AT-TATAC
1 TATATAGTTTATATATATAAAC
* * *
1214413 -ATA-A-TATATAAATATAAAT
1 TATATAGTTTATATATATAAAC
* **
1214432 TGTATAGTTTATATATA-ATTC
1 TATATAGTTTATATATATAAAC
*
1214453 ATATATA-ATT-TATATATAAAC
1 -TATATAGTTTATATATATAAAC
*
1214474 TATATAATTTATAT-TAATAAAC
1 TATATAGTTTATATAT-ATAAAC
* *
1214496 TATGTAGTTTATATATAGT--TC
1 TATATAGTTTATATATA-TAAAC
*
1214517 -A-ATAG-TT-CATATATAAAC
1 TATATAGTTTATATATATAAAC
* *
1214535 TATATAGTTTATACATGGT--A-
1 TATATAGTTTATATAT-ATAAAC
* *
1214555 TATATAGTTT-TATACATAATATA
1 TATATAGTTTATATATATAA-A-C
*
1214578 TATATAGTTTATATATAGTATA-
1 TATATAGTTTATATATA-TAAAC
* *
1214600 TA-ATA--ATATAAATATAAAC
1 TATATAGTTTATATATATAAAC
*
1214619 TATATAGTTTATATATATATA-
1 TATATAGTTTATATATATAAAC
* *
1214640 TATATA-TATATATATATATA-
1 TATATAGTTTATATATATAAAC
* *
1214660 TATATA-TATATATATATATA-
1 TATATAGTTTATATATATAAAC
*
1214680 TATATA-TATATATATATA
1 TATATAGTTTATATATATA
1214698 TATATTATAG
Statistics
Matches: 270, Mismatches: 42, Indels: 72
0.70 0.11 0.19
Matches are distributed among these distances:
16 1 0.00
17 17 0.06
18 9 0.03
19 21 0.08
20 89 0.33
21 27 0.10
22 80 0.30
23 18 0.07
24 6 0.02
25 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATAGTTTATATATATAAAC
Found at i:1224276 original size:32 final size:32
Alignment explanation
Indices: 1224230--1224296 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
1224220 TTGGCCTTAA
*
1224230 TCTCCTCAGTCAAAGTGGGTTTAAACTGCAAT
1 TCTCCTCAGCCAAAGTGGGTTTAAACTGCAAT
*
1224262 TCTCCTCAGCCAAAGTGGGTTTAAACTGTAAT
1 TCTCCTCAGCCAAAGTGGGTTTAAACTGCAAT
1224294 TCT
1 TCT
1224297 GCTAACAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (32 bp):
TCTCCTCAGCCAAAGTGGGTTTAAACTGCAAT
Found at i:1228016 original size:31 final size:31
Alignment explanation
Indices: 1227918--1228008 Score: 152
Period size: 31 Copynumber: 3.0 Consensus size: 31
1227908 CAATTTAAGG
1227918 CAAAATGGTTTTT-GTACTTGAATTGAATTTA
1 CAAAATGGTTTTTAG-ACTTGAATTGAATTTA
1227949 CAAAATGGTTTTTAGACTTGAATTGAATTTA
1 CAAAATGGTTTTTAGACTTGAATTGAATTTA
1227980 CAAAAT-GTTTTTAGACTT-AATTGAATTTA
1 CAAAATGGTTTTTAGACTTGAATTGAATTTA
1228009 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.19
30 12 0.20
31 35 0.59
32 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (31 bp):
CAAAATGGTTTTTAGACTTGAATTGAATTTA
Found at i:1228201 original size:21 final size:21
Alignment explanation
Indices: 1228175--1228216 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1228165 ATTTGAATAT
*
1228175 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1228196 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1228217 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1228538 original size:34 final size:32
Alignment explanation
Indices: 1228499--1228568 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1228489 TTTTGTAAAG
*
1228499 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1228533 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1228565 GGGA
1 GGGA
1228569 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1229118 original size:31 final size:31
Alignment explanation
Indices: 1229080--1229143 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1229070 ACCGTCAAGT
1229080 CCAGTAAGGCCCTGAGCACAAAGTCGAGGAG
1 CCAGTAAGGCCCTGAGCACAAAGTCGAGGAG
1229111 CCAGTAAGGCCCTGAGCACAAAGTCGAGGAG
1 CCAGTAAGGCCCTGAGCACAAAGTCGAGGAG
1229142 CC
1 CC
1229144 TTCAAGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.31, T:0.09
Consensus pattern (31 bp):
CCAGTAAGGCCCTGAGCACAAAGTCGAGGAG
Found at i:1230040 original size:7 final size:7
Alignment explanation
Indices: 1230013--1230075 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
1230003 TTTGGTCAAA
1230013 GTCAAC-
1 GTCAACG
*
1230019 GTCAATG
1 GTCAACG
*
1230026 GTCGACG
1 GTCAACG
1230033 GTCAACG
1 GTCAACG
1230040 GT---CG
1 GTCAACG
*
1230044 GTCGACG
1 GTCAACG
1230051 GTCAACG
1 GTCAACG
*
1230058 GTCAATG
1 GTCAACG
1230065 GTCAACAG
1 GTCAAC-G
1230073 GTC
1 GTC
1230076 GGGTCGGGTC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
4 4 0.09
6 5 0.11
7 32 0.71
8 4 0.09
ACGTcount: A:0.24, C:0.25, G:0.32, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:1230048 original size:18 final size:18
Alignment explanation
Indices: 1230025--1230060 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1230015 CAACGTCAAT
1230025 GGTCGACGGTCAACGGTC
1 GGTCGACGGTCAACGGTC
1230043 GGTCGACGGTCAACGGTC
1 GGTCGACGGTCAACGGTC
1230061 AATGGTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.39, T:0.17
Consensus pattern (18 bp):
GGTCGACGGTCAACGGTC
Found at i:1231240 original size:18 final size:18
Alignment explanation
Indices: 1231219--1231276 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
1231209 CAAAACATTC
1231219 TTTTTCAAAACTTTCAAT
1 TTTTTCAAAACTTTCAAT
* * *
1231237 TTTTTTAAAGCTTTAAAT
1 TTTTTCAAAACTTTCAAT
1231255 CATTTTTCAAAA-TTTC-AT
1 --TTTTTCAAAACTTTCAAT
1231273 TTTT
1 TTTT
1231277 GTTTTTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 4 0.12
18 17 0.53
19 3 0.09
20 8 0.25
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTTCAAAACTTTCAAT
Found at i:1231293 original size:20 final size:20
Alignment explanation
Indices: 1231257--1231307 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1231247 CTTTAAATCA
*
1231257 TTTTTCAAAATTTCATTTTT
1 TTTTTCAAAATTCCATTTTT
1231277 GTTTTTCAAAA-TCCATTTTT
1 -TTTTTCAAAATTCCATTTTT
1231297 TTCTTTCAAAA
1 TT-TTTCAAAA
1231308 GAAAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.57
21 10 0.36
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTTCAAAATTCCATTTTT
Found at i:1232884 original size:2 final size:2
Alignment explanation
Indices: 1232877--1232912 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1232867 TGAAACCGAT
1232877 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
1232913 AAGTAGATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1233583 original size:2 final size:2
Alignment explanation
Indices: 1233576--1233603 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1233566 TTTCTATCAA
1233576 AT 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 AT
1233604 CTTTAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1236000 original size:2 final size:2
Alignment explanation
Indices: 1235934--1235985 Score: 65
Period size: 2 Copynumber: 26.5 Consensus size: 2
1235924 AGTACATTTT
1235934 TA TA T- TA TA TA GTA TA TA TGA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
1235976 TA TA TA -A TA T
1 TA TA TA TA TA T
1235986 TTTAAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.07
2 38 0.84
3 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1236014 original size:26 final size:26
Alignment explanation
Indices: 1235967--1236031 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
1235957 ATATATATAT
1235967 ATATATATATATATAATATTTTAAAAA
1 ATATATA-ATATATAATATTTTAAAAA
1235994 ATATATAATATATACAGT-TTTT-AAAA
1 ATATATAATATATA-A-TATTTTAAAAA
1236020 ATATATAATATA
1 ATATATAATATA
1236032 GTTTTTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 23 0.64
27 12 0.33
28 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATATATAATATATAATATTTTAAAAA
Found at i:1236023 original size:24 final size:23
Alignment explanation
Indices: 1235969--1236089 Score: 102
Period size: 22 Copynumber: 4.9 Consensus size: 23
1235959 ATATATATAT
*
1235969 ATATATATATATAATATTTTAAAAA
1 ATATATATATATAGT-TTTT-AAAA
1235994 ATATATAATATATACAGTTTTTAAAA
1 ATATAT-ATATAT--AGTTTTTAAAA
*
1236020 ATATATA-ATATAGTTTTTGAAA
1 ATATATATATATAGTTTTTAAAA
* *
1236042 ACATAT-TATATTGTTTTTGAAATATA
1 ATATATATATATAGTTTTT--AA-A-A
1236068 ATATATATTATATAGTTTTTAA
1 ATATATA-TATATAGTTTTTAA
1236090 TATATACATA
Statistics
Matches: 79, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
22 25 0.32
24 5 0.06
25 8 0.10
26 24 0.30
27 4 0.05
28 13 0.16
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (23 bp):
ATATATATATATAGTTTTTAAAA
Found at i:1236076 original size:28 final size:29
Alignment explanation
Indices: 1236044--1236118 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
1236034 TTTTGAAAAC
*
1236044 ATATTATATTGTTTTTGAA-ATATA-ATAT
1 ATATTATATAGTTTTT-AATATATACATAT
1236072 ATATTATATAGTTTTTAATATATACATAT
1 ATATTATATAGTTTTTAATATATACATAT
*
1236101 -TATTATATA-TTATTAATA
1 ATATTATATAGTTTTTAATA
1236119 GTATTTTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 10 0.23
28 29 0.67
29 4 0.09
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (29 bp):
ATATTATATAGTTTTTAATATATACATAT
Found at i:1246053 original size:20 final size:22
Alignment explanation
Indices: 1246013--1246054 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1246003 GAGCTGGAAA
*
1246013 TAAAAAAGAAGGAATTCGAAGC
1 TAAAAAAGAAGGAACTCGAAGC
1246035 TAAAAAAGAA-GAACT-GAAGC
1 TAAAAAAGAAGGAACTCGAAGC
1246055 AAAGATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.57, C:0.10, G:0.21, T:0.12
Consensus pattern (22 bp):
TAAAAAAGAAGGAACTCGAAGC
Found at i:1257607 original size:34 final size:37
Alignment explanation
Indices: 1257541--1257609 Score: 108
Period size: 34 Copynumber: 1.9 Consensus size: 37
1257531 AACCATTCAG
1257541 GGGGAATCGATACCCCCTTGGGAGGGAATCTGTTCTC
1 GGGGAATCGATACCCCCTTGGGAGGGAATCTGTTCTC
*
1257578 GGGGAATCGGTA-CCCC-TGGG-GGGAATCTGTTC
1 GGGGAATCGATACCCCCTTGGGAGGGAATCTGTTC
1257610 CCTCTGGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 12 0.39
35 4 0.13
36 4 0.13
37 11 0.35
ACGTcount: A:0.17, C:0.23, G:0.36, T:0.23
Consensus pattern (37 bp):
GGGGAATCGATACCCCCTTGGGAGGGAATCTGTTCTC
Found at i:1260952 original size:21 final size:21
Alignment explanation
Indices: 1260928--1260967 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1260918 TAACTTTTTA
* *
1260928 TTTTGATTACATTTAATATAT
1 TTTTGAATAAATTTAATATAT
1260949 TTTTGAATAAATTTAATAT
1 TTTTGAATAAATTTAATAT
1260968 GTTATTGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTGAATAAATTTAATATAT
Found at i:1262074 original size:20 final size:19
Alignment explanation
Indices: 1262033--1262075 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1262023 TTCAATTGAT
*
1262033 AAAAACAAACAGATACATG
1 AAAAACAAACAGATACAAG
1262052 AAAAACAAGATCAGAT-CAAG
1 AAAAACAA-A-CAGATACAAG
1262072 AAAA
1 AAAA
1262076 GTTACCACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 8 0.38
21 5 0.24
ACGTcount: A:0.65, C:0.14, G:0.12, T:0.09
Consensus pattern (19 bp):
AAAAACAAACAGATACAAG
Found at i:1264128 original size:17 final size:17
Alignment explanation
Indices: 1264081--1264133 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
1264071 AAGTAAAAAC
*
1264081 AAATAAATTT-CTTTAA
1 AAATCAATTTCCTTTAA
* *
1264097 AAACCAGTTTCCCTTTAA
1 AAATCAATTT-CCTTTAA
1264115 AAATCAATTTCCTTTAA
1 AAATCAATTTCCTTTAA
1264132 AA
1 AA
1264134 TAAAATTGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 7 0.23
17 9 0.30
18 14 0.47
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATCAATTTCCTTTAA
Found at i:1264951 original size:2 final size:2
Alignment explanation
Indices: 1264944--1264968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1264934 GTCGTTTAAT
1264944 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 T
1264969 TATCAGAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1265276 original size:25 final size:25
Alignment explanation
Indices: 1265242--1265289 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1265232 TAAAATATAT
1265242 AACTAAAAAATAATTAATTACAAAA
1 AACTAAAAAATAATTAATTACAAAA
*
1265267 AACTTAAAAATAATTAATTACAA
1 AACTAAAAAATAATTAATTACAA
1265290 TATATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (25 bp):
AACTAAAAAATAATTAATTACAAAA
Found at i:1266049 original size:181 final size:179
Alignment explanation
Indices: 1265539--1266049 Score: 391
Period size: 181 Copynumber: 2.8 Consensus size: 179
1265529 ATATATGCTA
* ** * * * * * * *
1265539 TCACTATAGTTAAAATTTATAACTACAAATATAATTTGTCAC-AAAAACGTGAATATCATTATTT
1 TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACTAAAAACTTAAATCTAATTA-TT
* **
1265603 TTTTGTGGA-AATATTTTTTGTA--ATAATTATTAACACTTATAGTTACAAAATTTGTCACTATA
65 TGTTGT-GACAAT-TTTTTTGTACGATAATTA-T-A-ACTTATAGTTACAAAACATGTCACTATA
* * * * *
1265665 TGACATT---TTTGGCACAAAACAATATGGAGGGA-AATCTTTGTGACAATATATTTTG
125 TGACCTTCAATTTGGTACCAAA-AAT-T-GA-AGATAATCTTTGTGACAATACATTTTG
*** * * * *
1265720 TCACTATAATTAAAACATATAACGACAAACATTGTTTTTTACTAAAAACTTGAATCTCATTATTT
1 TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACTAAAAACTTAAATCTAATTATTT
* * **
1265785 GTTGTGATAATTTTTTTGTAACGATAATTATAGCTTATAGTTACAAAACATGTCACTATATGATT
66 GTTGTGACAATTTTTTTGT-ACGATAATTATAACTTATAGTTACAAAACATGTCACTATATGACC
*** * *
1265850 TTGTTTTTTGTACCAAAAATTGAAGATAATCATTTGTGACTATACATTTTG
130 TTCAATTTGGTACCAAAAATTGAAGATAATC-TTTGTGACAATACATTTTG
* **
1265901 TCACTATAATTAAAATATATAATTACAAACAAAATTTGTCAC-AACAAA-TCTAAATCTAATTAT
1 TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACTAA-AAACT-TAAATCTAATTAT
* * **
1265964 TTGTTGTGACAATTTTTTCTGT-C-ATAGTTACTAAAACTTTTAGTTACAAAAGTTGTCACTATA
64 TTGTTGTGACAATTTTTT-TGTACGATAATTA-T--AACTTATAGTTACAAAACATGTCACTATA
*
1266027 TG-CCTTCAATTTGGTGCCAAAAA
125 TGACCTTCAATTTGGTACCAAAAA
1266050 ATTGGAGGGA
Statistics
Matches: 268, Mismatches: 46, Indels: 32
0.77 0.13 0.09
Matches are distributed among these distances:
179 8 0.03
180 51 0.19
181 142 0.53
182 51 0.19
183 16 0.06
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (179 bp):
TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACTAAAAACTTAAATCTAATTATTT
GTTGTGACAATTTTTTTGTACGATAATTATAACTTATAGTTACAAAACATGTCACTATATGACCT
TCAATTTGGTACCAAAAATTGAAGATAATCTTTGTGACAATACATTTTG
Found at i:1266247 original size:15 final size:15
Alignment explanation
Indices: 1266229--1266260 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1266219 CTACTAATAG
*
1266229 TGACAAAATTAATTT
1 TGACAAAATTAAATT
1266244 TGACAAAATTAAATT
1 TGACAAAATTAAATT
1266259 TG
1 TG
1266261 TCATAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (15 bp):
TGACAAAATTAAATT
Found at i:1266391 original size:20 final size:22
Alignment explanation
Indices: 1266366--1266405 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1266356 AGTCATATCT
1266366 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1266386 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1266406 TATGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1266649 original size:35 final size:36
Alignment explanation
Indices: 1266579--1266649 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1266569 ACCATTCAGG
*
1266579 GGGGAATCGGTACCCCTTGGGGGTGAATCTGTTCCC
1 GGGGAATCGGTACCCCCTGGGGGTGAATCTGTTCCC
1266615 GGGGAATCGGTACCCCCTGGGGG-GAATCTGTTCCC
1 GGGGAATCGGTACCCCCTGGGGGTGAATCTGTTCCC
1266650 TCTGGGCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 12 0.35
36 22 0.65
ACGTcount: A:0.14, C:0.27, G:0.37, T:0.23
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGTGAATCTGTTCCC
Found at i:1266655 original size:20 final size:20
Alignment explanation
Indices: 1266577--1266642 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1266567 AAACCATTCA
*
1266577 GGGGGGAATCGGTACCCCTT
1 GGGGGGAATCGGTACCCCCT
* *
1266597 GGGGGTGAATCTGT--TCCC-
1 GGGGG-GAATCGGTACCCCCT
1266615 --GGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
1266633 GGGGGGAATC
1 GGGGGGAATC
1266643 TGTTCCCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
15 7 0.20
16 3 0.09
17 3 0.09
19 2 0.06
20 13 0.37
21 7 0.20
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.20
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:1267125 original size:22 final size:22
Alignment explanation
Indices: 1267092--1267153 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1267082 GTGAAATTTT
*
1267092 TCCCGAATGACCTATGTATATA
1 TCCCGAAGGACCTATGTATATA
* * *
1267114 TCCTGAAGGACCTCTGTATATG
1 TCCCGAAGGACCTATGTATATA
*
1267136 TCCCGAATGACCTATGTA
1 TCCCGAAGGACCTATGTA
1267154 ACCCTCTACT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (22 bp):
TCCCGAAGGACCTATGTATATA
Found at i:1273224 original size:24 final size:24
Alignment explanation
Indices: 1273159--1273226 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
1273149 GTTGGGGCAG
*
1273159 TTGACCCGGTTTGACCCAACCCGT
1 TTGACCCGGTTTGACCCGACCCGT
*
1273183 TTGACCCGGTTTAACCCGACCCGT
1 TTGACCCGGTTTGACCCGACCCGT
*
1273207 TTGACTCGGTTTGACCCGAC
1 TTGACCCGGTTTGACCCGAC
1273227 AATTGACCCG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.16, C:0.35, G:0.22, T:0.26
Consensus pattern (24 bp):
TTGACCCGGTTTGACCCGACCCGT
Found at i:1273289 original size:13 final size:13
Alignment explanation
Indices: 1273271--1273296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1273261 TGACCATTTA
1273271 GTTGACTTTGACC
1 GTTGACTTTGACC
1273284 GTTGACTTTGACC
1 GTTGACTTTGACC
1273297 AAAAAGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
GTTGACTTTGACC
Found at i:1275809 original size:24 final size:24
Alignment explanation
Indices: 1275725--1275809 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
1275715 GAATGTTTTA
*
1275725 TCTGATTT-TCGATTTGAATTATGT
1 TCTGATTTCT-GATCTGAATTATGT
* *
1275749 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTATGT
* *
1275773 TCTGATATATGATCTGAATTATGT
1 TCTGATTTCTGATCTGAATTATGT
*
1275797 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1275810 ATCTCCGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
24 49 0.98
25 1 0.02
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTATGT
Found at i:1278173 original size:22 final size:22
Alignment explanation
Indices: 1278143--1278206 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
1278133 ATGTGAAATT
*
1278143 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAGGACCTCTGTATA
*
1278165 TGTCACGAAGGACCTCTGTATA
1 TGTCCCGAAGGACCTCTGTATA
1278187 TGTCCCGAAGGACCTCTGTA
1 TGTCCCGAAGGACCTCTGTA
1278207 ACCCTCTACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
TGTCCCGAAGGACCTCTGTATA
Found at i:1283393 original size:21 final size:21
Alignment explanation
Indices: 1283345--1283407 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1283335 AATATATAGT
* * *
1283345 TTTTGAAAATATACAATATAGT
1 TTTTGAAAACATATAATATA-A
*
1283367 TTTTGAAAACATATTATATAA
1 TTTTGAAAACATATAATATAA
*
1283388 TTTTGAAAACGTATAATATA
1 TTTTGAAAACATATAATATA
1283408 TAGTTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (21 bp):
TTTTGAAAACATATAATATAA
Found at i:1283422 original size:24 final size:23
Alignment explanation
Indices: 1283335--1283421 Score: 101
Period size: 22 Copynumber: 3.9 Consensus size: 23
1283325 AAATATATAC
1283335 AATATATAGTTTTTGAAAA-TAT
1 AATATATAGTTTTTGAAAACTAT
1283357 ACA-ATATAGTTTTTGAAAAC-AT
1 A-ATATATAGTTTTTGAAAACTAT
* *
1283379 ATTATATA-ATTTTGAAAACGTAT
1 AATATATAGTTTTTGAAAAC-TAT
*
1283402 AATATATAGTTTTTTAAAAC
1 AATATATAGTTTTTGAAAAC
1283422 GGTTTTTGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
21 10 0.19
22 25 0.46
23 10 0.19
24 9 0.17
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (23 bp):
AATATATAGTTTTTGAAAACTAT
Found at i:1283574 original size:15 final size:15
Alignment explanation
Indices: 1283551--1283589 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1283541 CTTATATATT
* *
1283551 TTTATTTTTATTTAC
1 TTTAATTTTATTTAA
1283566 TTTAATTTTATTTAA
1 TTTAATTTTATTTAA
1283581 TTT-ATTTTA
1 TTTAATTTTA
1283590 GGTCCAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTAATTTTATTTAA
Found at i:1286080 original size:15 final size:15
Alignment explanation
Indices: 1286060--1286101 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1286050 ACAGGAATGG
* *
1286060 GAAGAGAGTGACGGC
1 GAAGAGAGGGAAGGC
*
1286075 GAAGAGAGGGAAGGG
1 GAAGAGAGGGAAGGC
1286090 GAAGAGAGGGAA
1 GAAGAGAGGGAA
1286102 AATGGTTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.52, T:0.02
Consensus pattern (15 bp):
GAAGAGAGGGAAGGC
Found at i:1287438 original size:25 final size:25
Alignment explanation
Indices: 1287408--1287495 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 25
1287398 TTAAATTTAT
1287408 AATATTTTATATATAATAACTTAAA
1 AATATTTTATATATAATAACTTAAA
*
1287433 AATATTTT-T-TATATTAACTTATTAA
1 AATATTTTATATATAATAACTTA--AA
*
1287458 ATATATTTTATA-ATTAACTTAATTTAAA
1 A-ATATTTTATATA-TAA--TAACTTAAA
1287486 AATATTTTAT
1 AATATTTTAT
1287496 TTTCATTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
23 11 0.21
24 1 0.02
25 11 0.21
26 7 0.13
27 11 0.21
28 5 0.10
30 6 0.12
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (25 bp):
AATATTTTATATATAATAACTTAAA
Found at i:1287491 original size:27 final size:26
Alignment explanation
Indices: 1287408--1287495 Score: 94
Period size: 26 Copynumber: 3.4 Consensus size: 26
1287398 TTAAATTTAT
1287408 AATATTTTAT-ATATAA--TAACTTAAA
1 AATATTTTATAAT-TAACTTAA-TTAAA
*
1287433 AATATTTTTTATATTAACTT-ATTAAA
1 AATATTTTATA-ATTAACTTAATTAAA
*
1287459 TATATTTTATAATTAACTTAATTTAAA
1 AATATTTTATAATTAACTTAA-TTAAA
1287486 AATATTTTAT
1 AATATTTTAT
1287496 TTTCATTTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
25 17 0.32
26 18 0.34
27 17 0.32
28 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
AATATTTTATAATTAACTTAATTAAA
Found at i:1287714 original size:31 final size:31
Alignment explanation
Indices: 1287651--1287718 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1287641 TGATGGCTAC
* * * *
1287651 ATCTTAATTAAATAAAAATGAAAGTGATCAT
1 ATCTTAATTAAATAAAAATCAAAATAAACAT
1287682 ATCTTAATTAAATAAAAA-CAAATATAAACAT
1 ATCTTAATTAAATAAAAATCAAA-ATAAACAT
1287713 ATCTTA
1 ATCTTA
1287719 TGTTTTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAATCAAAATAAACAT
Found at i:1289174 original size:266 final size:261
Alignment explanation
Indices: 1288671--1289189 Score: 887
Period size: 266 Copynumber: 2.0 Consensus size: 261
1288661 TTATATCCCG
* *
1288671 TTCAAATATTAATGTTAAGTTTTGAAAAGATCGAAAGTTTAGGTATTAAAACATACAAAGTTATA
1 TTCAAATATTAATGTTAAGTTTTGAAAAGATCGAAAGTTTAGGTATTAAAACATACAAAATGATA
* *
1288736 GTTTAAGTACTAAATGTGTTAAGTTTTTAATGATAGGATACTAAAATGAAATAAAAACTAAAAGT
66 GTTTAAGTACTAAACGCGTTAAGTTTTTAATGATAGGATACTAAAATGAAATAAAAACTAAAAGT
* *
1288801 TACACATAATTTTGATTTTTTTTAAAGTTTAGGTACTAAAGCATATCAAAACTGATAATTTATGT
131 TACACATAATTTTGATTTTTTTTAAAGTTTAGGTACTAAAGCATATCAAAACAGATAATTTAAGT
1288866 ATTAAATGCGTAGTTTACCCTTAAAACAATTAATCTGCATCAGACTTGCGAATAATTTTAGTACC
196 ATTAAATGCGTAGTTTACCCTTAAAACAATTAATCTGCATCAGACTTGCGAATAATTTTAGTACC
1288931 A
261 A
*
1288932 TTCAAATATTAATGTTAAGTTTTGAAAAGATTGAAAGTTTAGGTATTAAAACATACAAAAATGAT
1 TTCAAATATTAATGTTAAGTTTTGAAAAGATCGAAAGTTTAGGTATTAAAACATAC-AAAATGAT
*
1288997 AGTTTAGGTACTAAACGCGTTAAGTTTTTAATGATAGCG-TACTAAAATGAAATAAAAACTAAAA
65 AGTTTAAGTACTAAACGCGTTAAGTTTTTAATGATAG-GATACTAAAATGAAATAAAAACTAAAA
*
1289061 GTTACACATAATTTTGATTTTGTTTTTTGAAAGTTTAGGTACTAAAGGATATCAAAACAGATAAT
129 GTTACACATAATTTTGA--TT-TTTTTT-AAAGTTTAGGTACTAAAGCATATCAAAACAGATAAT
*
1289126 TTAAGTATTAAATGGGTAGTTTACCCTTAAAACAATTAATCTGCATCAGACTTGCGAATAATTT
190 TTAAGTATTAAATGCGTAGTTTACCCTTAAAACAATTAATCTGCATCAGACTTGCGAATAATTT
1289190 AGGATTCCCA
Statistics
Matches: 242, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
261 55 0.23
262 82 0.34
263 1 0.00
264 2 0.01
265 6 0.02
266 96 0.40
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (261 bp):
TTCAAATATTAATGTTAAGTTTTGAAAAGATCGAAAGTTTAGGTATTAAAACATACAAAATGATA
GTTTAAGTACTAAACGCGTTAAGTTTTTAATGATAGGATACTAAAATGAAATAAAAACTAAAAGT
TACACATAATTTTGATTTTTTTTAAAGTTTAGGTACTAAAGCATATCAAAACAGATAATTTAAGT
ATTAAATGCGTAGTTTACCCTTAAAACAATTAATCTGCATCAGACTTGCGAATAATTTTAGTACC
A
Found at i:1291806 original size:268 final size:260
Alignment explanation
Indices: 1291109--1291900 Score: 1189
Period size: 268 Copynumber: 3.0 Consensus size: 260
1291099 TTCGGCTTCG
1291109 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCAGGTTCGGGTTTAGGGTGAAAAA
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC--G---GGTTCGGGTTTAGGGTGAAAAA
*
1291174 TACCCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAACA
61 TACCCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATA
*
1291239 CCCCTCTATATATAAATTTTTTT-TATTAAGTCACT-TTTTTATTGAATAAAAATA-TTTTTTTA
126 CCCCTCTATATAT-AATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTTA
**
1291301 TTATTTCGGGTCGGGTC-G--GGTTTCTAATTCATATATTCGGGTCAAGTCGGGTGAAACTTTA-
190 TTATTTCGGGTCGGGTCGGTCGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTAT
1291362 TTT--T
255 TTTGGT
* *
1291366 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTAGGGTTTAGGATGAAAAATACCC
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCC
* *
1291431 GACCCGACCCGAAAATATATATAATTTTACCTTATATATTTATGAATAATTACAATAATACCCCT
66 GACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCT
*
1291496 CTATATATAA-TTTTTTCAATTAAGTCACTGTTTTTGTTGAATAAAAATATTTTTTTTATTATTT
131 CTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTTATTATTT
1291560 CGGGTCGGGTCGGGTCAGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTG
196 CGGGTCGGGTC-GGTC-GGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTG
1291625 GT
259 GT
* *
1291627 CAGGTCGGGTCGGTTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGCGAAAAATAC
1 --GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAT--
*
1291692 CCGACCCGACCCGACCCGAAAAAATATATAATTTTACCTTACATATTTAGGAATAATTACAAT-A
62 ---ACCCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAA
* *
1291756 TATCCCTCTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATGTTTTTT
124 TACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTT
**
1291821 ATTATTTCGGGTTAGGTC-G--GGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTA
189 ATTATTTCGGGTCGGGTCGGTCGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTA
1291883 TTTTGGTT
254 TTTTGG-T
1291891 GGGTCGGGTC
1 -GGTCGGGTC
1291901 TCGGATGGAG
Statistics
Matches: 493, Mismatches: 22, Indels: 34
0.90 0.04 0.06
Matches are distributed among these distances:
250 6 0.01
251 13 0.03
252 113 0.23
253 25 0.05
255 2 0.00
257 37 0.08
258 41 0.08
259 3 0.01
261 1 0.00
263 115 0.23
264 1 0.00
266 1 0.00
267 17 0.03
268 118 0.24
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.39
Consensus pattern (260 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCC
GACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCT
CTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTTATTATTT
CGGGTCGGGTCGGTCGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGT
Found at i:1292800 original size:9 final size:9
Alignment explanation
Indices: 1292786--1292838 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
1292776 CCAGTAGAAA
1292786 ACCGGTTTG
1 ACCGGTTTG
*
1292795 ACCGGTCTG
1 ACCGGTTTG
1292804 AACCGGTTTG
1 -ACCGGTTTG
*
1292814 ACCGGTATG
1 ACCGGTTTG
*
1292823 AACCGGTTTT
1 -ACCGGTTTG
1292833 ACCGGT
1 ACCGGT
1292839 CCGACCTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 22 0.59
10 15 0.41
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1292809 original size:19 final size:19
Alignment explanation
Indices: 1292785--1292839 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
1292775 GCCAGTAGAA
1292785 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
1292804 AACCGGTTTGACCGGTATG
1 AACCGGTTTGACCGGTCTG
*
1292823 AACCGGTTTTACCGGTC
1 AACCGGTTTGACCGGTC
1292840 CGACCTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:1292810 original size:10 final size:10
Alignment explanation
Indices: 1292785--1292831 Score: 62
Period size: 9 Copynumber: 4.9 Consensus size: 10
1292775 GCCAGTAGAA
1292785 AACCGGTTTG
1 AACCGGTTTG
*
1292795 -ACCGGTCTG
1 AACCGGTTTG
1292804 AACCGGTTTG
1 AACCGGTTTG
*
1292814 -ACCGGTATG
1 AACCGGTTTG
1292823 AACCGGTTT
1 AACCGGTTT
1292832 TACCGGTCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 16 0.52
10 15 0.48
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:1292872 original size:18 final size:18
Alignment explanation
Indices: 1292849--1292900 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
1292839 CCGACCTGTT
1292849 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
1292867 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
1292885 GACCCGA-CCGTTGACC
1 GACCCGACCCGTTGACC
1292901 GTTGACCGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 9 0.26
18 25 0.74
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:1292890 original size:13 final size:13
Alignment explanation
Indices: 1292839--1292872 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1292829 TTTTACCGGT
*
1292839 CCGACCTGTTGAC
1 CCGACCCGTTGAC
1292852 CCGACCCGTTGAC
1 CCGACCCGTTGAC
1292865 CCGACCCG
1 CCGACCCG
1292873 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.47, G:0.24, T:0.15
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:1292952 original size:29 final size:29
Alignment explanation
Indices: 1292908--1292995 Score: 133
Period size: 29 Copynumber: 3.0 Consensus size: 29
1292898 ACCGTTGACC
*
1292908 GGTGCTATTCTGGGAATTAATTGGATTTT
1 GGTGCTATTCTGGGAATTAATTAGATTTT
*
1292937 GGTGCTATTCTTGGAATTAATTCA-ATTTT
1 GGTGCTATTCTGGGAATTAATT-AGATTTT
*
1292966 GGTGCTATTATGGGAATTAATTAGATTTT
1 GGTGCTATTCTGGGAATTAATTAGATTTT
1292995 G
1 G
1292996 TTCTATTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.02
29 52 0.98
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTAGATTTT
Found at i:1293038 original size:58 final size:58
Alignment explanation
Indices: 1292908--1293098 Score: 176
Period size: 58 Copynumber: 3.3 Consensus size: 58
1292898 ACCGTTGACC
* ****
1292908 GGTGCTATTCTGGGAATTAATTGGATTTTGGTGCTATTCTTGGAATTAATTCAATTTT
1 GGTGCTATTCTGGGAATTAATTAGATTTTGGTGCTATTCTTGGAATTAATTCAAAAAG
* * * *
1292966 GGTGCTATTATGGGAATTAATTAGATTTT-GTTCTATT-TTAGTAATTTATTCGAAAAAG
1 GGTGCTATTCTGGGAATTAATTAGATTTTGGTGCTATTCTT-GGAATTAATTC-AAAAAG
* * ** *
1293024 GGTGATATTCTGGGAATTAATTCGA-AATGGTGCTATT-TTGGGATTTAATTCAAAAA-
1 GGTGCTATTCTGGGAATTAATTAGATTTTGGTGCTATTCTT-GGAATTAATTCAAAAAG
* *
1293080 GGTGCTATTTTGGAAATTA
1 GGTGCTATTCTGGGAATTA
1293099 TTTCGAAAAG
Statistics
Matches: 108, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
56 18 0.17
57 22 0.20
58 68 0.63
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (58 bp):
GGTGCTATTCTGGGAATTAATTAGATTTTGGTGCTATTCTTGGAATTAATTCAAAAAG
Found at i:1293060 original size:28 final size:28
Alignment explanation
Indices: 1292908--1293106 Score: 130
Period size: 28 Copynumber: 7.0 Consensus size: 28
1292898 ACCGTTGACC
* **
1292908 GGTGCTATTCTGGGAATTAATTGGATTTT
1 GGTGCTATTCTGGGAATTAATTCGA-AAT
* *
1292937 GGTGCTATTCTTGGAATTAATTC-AATTTT
1 GGTGCTATTCTGGGAATTAATTCGAA--AT
* * **
1292966 GGTGCTATTATGGGAATTAATTAGATTT
1 GGTGCTATTCTGGGAATTAATTCGAAAT
* * * * * * *
1292994 TGTTCTATTTTAGTAATTTATTCGAAAAAG
1 GGTGCTATTCTGGGAATTAATTCG--AAAT
*
1293024 GGTGATATTCTGGGAATTAATTCGAAAT
1 GGTGCTATTCTGGGAATTAATTCGAAAT
* * * *
1293052 GGTGCTATTTTGGGATTTAATTCAAAAA
1 GGTGCTATTCTGGGAATTAATTCGAAAT
* * *
1293080 GGTGCTATTTTGGAAATTATTTCGAAA
1 GGTGCTATTCTGGGAATTAATTCGAAA
1293107 AGGGTACTAT
Statistics
Matches: 131, Mismatches: 34, Indels: 11
0.74 0.19 0.06
Matches are distributed among these distances:
28 69 0.53
29 43 0.33
30 19 0.15
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.43
Consensus pattern (28 bp):
GGTGCTATTCTGGGAATTAATTCGAAAT
Found at i:1293107 original size:28 final size:29
Alignment explanation
Indices: 1292998--1293127 Score: 120
Period size: 28 Copynumber: 4.5 Consensus size: 29
1292988 AGATTTTGTT
* * *
1292998 CTATTTTAGTAATTTATTCGAAAAAGGGTG
1 CTATTTTGGGAATTAATTCG-AAAAGGGTG
* * *
1293028 ATATTCTGGGAATTAATTCG-AAATGGTG
1 CTATTTTGGGAATTAATTCGAAAAGGGTG
* *
1293056 CTATTTTGGGATTTAATTC-AAAAAGGTG
1 CTATTTTGGGAATTAATTCGAAAAGGGTG
* * *
1293084 CTATTTTGGAAATTATTTCGAAAAGGGTA
1 CTATTTTGGGAATTAATTCGAAAAGGGTG
* *
1293113 CTATCTTGGTAATTA
1 CTATTTTGGGAATTA
1293128 TTTTAAAAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
28 46 0.57
29 20 0.25
30 15 0.19
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (29 bp):
CTATTTTGGGAATTAATTCGAAAAGGGTG
Found at i:1293121 original size:29 final size:29
Alignment explanation
Indices: 1293075--1293139 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1293065 GATTTAATTC
* *
1293075 AAAAAGGTGCTATTTTGGAAATTATTTCG
1 AAAAAGGTACTATCTTGGAAATTATTTCG
* * **
1293104 AAAAGGGTACTATCTTGGTAATTATTTTA
1 AAAAAGGTACTATCTTGGAAATTATTTCG
1293133 AAAAAGG
1 AAAAAGG
1293140 GTGTTATTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.35
Consensus pattern (29 bp):
AAAAAGGTACTATCTTGGAAATTATTTCG
Found at i:1294432 original size:17 final size:19
Alignment explanation
Indices: 1294405--1294443 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1294395 ATATCTGTAT
1294405 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
1294423 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
1294442 TA
1 TA
1294444 AGTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:1300158 original size:19 final size:19
Alignment explanation
Indices: 1300134--1300171 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1300124 GCCAGCAGAA
*
1300134 AACCGGTTTGACTGGTCCG
1 AACCGGTTTGACCGGTCCG
1300153 AACCGGTTTGACCGGTCCG
1 AACCGGTTTGACCGGTCCG
1300172 TTGACCCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.29, G:0.32, T:0.24
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCCG
Found at i:1300209 original size:7 final size:7
Alignment explanation
Indices: 1300197--1300222 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1300187 GACTCGACCC
1300197 GACCGTT
1 GACCGTT
1300204 GACCGTT
1 GACCGTT
1300211 GACCGTT
1 GACCGTT
1300218 GACCG
1 GACCG
1300223 GTGCTACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:1300311 original size:29 final size:29
Alignment explanation
Indices: 1300279--1300432 Score: 175
Period size: 29 Copynumber: 5.3 Consensus size: 29
1300269 ATTAGATTTT
* *
1300279 GGTGTTATTTTGGTAATTTATTCGAAAAG
1 GGTGCTATTTTGGTAATTAATTCGAAAAG
* * * *
1300308 GGTGATATTCTGGGAATTAATTCG-AAAT
1 GGTGCTATTTTGGTAATTAATTCGAAAAG
* *
1300336 GGTGCTATTTTGGGAATTAATTCAAAAAG
1 GGTGCTATTTTGGTAATTAATTCGAAAAG
*
1300365 GGTGCTATTTTGGTAATTATTTCGAAAAG
1 GGTGCTATTTTGGTAATTAATTCGAAAAG
* * **
1300394 GGTTCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGTAATTAATTCGAAAAG
*
1300423 GGTGATATTT
1 GGTGCTATTT
1300433 GTGTAAAATG
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 24 0.22
29 83 0.78
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTCGAAAAG
Found at i:1300364 original size:57 final size:57
Alignment explanation
Indices: 1300255--1300431 Score: 192
Period size: 58 Copynumber: 3.1 Consensus size: 57
1300245 GATTTGGTAC
* * ** * * *
1300255 TATTCTAGGAATTAATTAGATTTTGGTGTTATTTTGGTAATTTATTCGAAAAGGGTGA
1 TATTCTGGGAATTAATTCGA-AATGGTGCTATTTTGGTAATTAATTCAAAAAGGGTGA
* *
1300313 TATTCTGGGAATTAATTCGAAATGGTGCTATTTTGGGAATTAATTCAAAAAGGGTGC
1 TATTCTGGGAATTAATTCGAAATGGTGCTATTTTGGTAATTAATTCAAAAAGGGTGA
* * * * * * *
1300370 TATTTTGGTAATTATTTCGAAAAGGGTTCTATTTTGGTAATTATTTTAAAAAGGGTGA
1 TATTCTGGGAATTAATTCG-AAATGGTGCTATTTTGGTAATTAATTCAAAAAGGGTGA
1300428 TATT
1 TATT
1300432 TGTGTAAAAT
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
57 46 0.46
58 54 0.54
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.42
Consensus pattern (57 bp):
TATTCTGGGAATTAATTCGAAATGGTGCTATTTTGGTAATTAATTCAAAAAGGGTGA
Found at i:1302040 original size:17 final size:17
Alignment explanation
Indices: 1302015--1302059 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1302005 ATGGAATTGA
*
1302015 ATTCCAATTCCTGACAG
1 ATTCCAATTCCTCACAG
*
1302032 ATTCTAATTCCTCACAG
1 ATTCCAATTCCTCACAG
1302049 ATTCCAATTCC
1 ATTCCAATTCC
1302060 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (17 bp):
ATTCCAATTCCTCACAG
Found at i:1304778 original size:8 final size:8
Alignment explanation
Indices: 1304767--1304791 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1304757 AAGCAAAGAC
1304767 ACAGATGA
1 ACAGATGA
1304775 ACAGATGA
1 ACAGATGA
1304783 ACAGATGA
1 ACAGATGA
1304791 A
1 A
1304792 AGGATACGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.24, T:0.12
Consensus pattern (8 bp):
ACAGATGA
Found at i:1304858 original size:16 final size:16
Alignment explanation
Indices: 1304837--1304870 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1304827 CTGAGTTGAG
1304837 TTCGAGTTCAAAGTAT
1 TTCGAGTTCAAAGTAT
1304853 TTCGAGTTCAAAGTAT
1 TTCGAGTTCAAAGTAT
1304869 TT
1 TT
1304871 TCATAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (16 bp):
TTCGAGTTCAAAGTAT
Found at i:1307127 original size:38 final size:37
Alignment explanation
Indices: 1307077--1307151 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 37
1307067 CAGGTCGTTG
* *
1307077 TTACAAAAACAAAACGACATGCATGTCGTATTTTAAA
1 TTACAAAAACAAAACGACATGCAAGTCATATTTTAAA
*
1307114 TTACAATAAACAAAATGACATGCAAGTCATATTTTAAA
1 TTACAA-AAACAAAACGACATGCAAGTCATATTTTAAA
1307152 AATATACAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 6 0.18
38 28 0.82
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (37 bp):
TTACAAAAACAAAACGACATGCAAGTCATATTTTAAA
Found at i:1316279 original size:20 final size:20
Alignment explanation
Indices: 1316256--1316294 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1316246 TTGCTACTTT
* *
1316256 ATGAATAATATCGATACTAC
1 ATGAAAAATATCAATACTAC
1316276 ATGAAAAATATCAATACTA
1 ATGAAAAATATCAATACTA
1316295 TCCTTGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (20 bp):
ATGAAAAATATCAATACTAC
Found at i:1318152 original size:87 final size:87
Alignment explanation
Indices: 1318006--1318168 Score: 283
Period size: 87 Copynumber: 1.9 Consensus size: 87
1317996 TTATGTAAGT
* * *
1318006 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATATGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGGT
1318071 AG-TCCTTATATAATAAAATAGG
66 AGCT-CTTATATAATAAAATAGG
1318093 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGGT
1318158 AGCTCTTATAT
66 AGCTCTTATAT
1318169 TGACCTATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
87 71 0.99
88 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGGT
AGCTCTTATATAATAAAATAGG
Found at i:1318851 original size:200 final size:197
Alignment explanation
Indices: 1318163--1318886 Score: 1015
Period size: 200 Copynumber: 3.6 Consensus size: 197
1318153 TAGGTAGCTC
* * * * *
1318163 TTATATTGACCTATTTTCTAACT-AAACTGGTATATTTATACCGGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTCA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* *
1318227 TTACATTATAATTATCGGTTTCGATATTTTTGGGATCGGTACAATTTTAAATGTATCGACACTTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC--TTTTAAATGTATCGACACTTT
* *
1318292 ATGCGTGCACCTCGTTTGGACATTCATTCTGGACAATAAGTATCGACACAAATTTATCAAGTGTC
128 ATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTTA-AAAGTGTC
1318357 GATACA
192 GATACA
* * * *
1318363 TTATGTAGACCTATTTTCTCATAAAACCGGTAAATTTGTACAGGTTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
*
1318428 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAAAATTTTAAATGTATCGACACTTTA
66 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGAT--ACTTTTAAATGTATCGACACTTTA
*
1318493 TGCGTGCACCTCGTTT-GGCATTCATTCTGGACAA-ATGTATCGACACAAATTTAAAAAGTGTCG
129 TGCGTGCACCTCGTTTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTT-AAAAGTGTCG
*
1318556 ATACT
193 ATACA
* * *
1318561 TTATGTTGACCTATTCTCTCATAAAACCGATATATTTCTACCGGTTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* * *
1318626 TACATTATAATTATCGGTCTCGATGTTTTTGGGATCGGTACTTTTAAAAAACGTATCGACACTTT
66 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTT---AAATGTATCGACACTTT
1318691 ATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTCTAAAAGTGTC
128 ATGCGTGCACCTCGTTTGGGCATTCATTCTGGACAATAAGTATCGACACAAATT-TAAAAGTGTC
1318756 GATACA
192 GATACA
* * * * * *
1318762 TTATGTTGACCTATTTTATGAT-TAACTGGTATATGTATACCGGTTACATTGTTAATTTACCTAT
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
** *
1318826 TACATTATAATTATTTGTTTCGATGTTTTTGGGGTCGATACTTTTAGAAAATGTATCGACA
66 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTT---AAATGTATCGACA
1318887 TATATGTTTA
Statistics
Matches: 470, Mismatches: 44, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
196 5 0.01
198 125 0.27
199 52 0.11
200 237 0.50
201 49 0.10
202 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (197 bp):
TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAAATGTATCGACACTTTATG
CGTGCACCTCGTTTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTTAAAAGTGTCGATA
CA
Found at i:1322346 original size:21 final size:22
Alignment explanation
Indices: 1322316--1322357 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1322306 AAACACGCGT
1322316 AATTTAAAAAAGTATCGATACG
1 AATTTAAAAAAGTATCGATACG
*
1322338 AATTT-AAAAAGTGTCGATAC
1 AATTTAAAAAAGTATCGATAC
1322358 ATTATGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (22 bp):
AATTTAAAAAAGTATCGATACG
Found at i:1322851 original size:199 final size:200
Alignment explanation
Indices: 1322322--1323490 Score: 1636
Period size: 201 Copynumber: 5.8 Consensus size: 200
1322312 GCGTAATTTA
* * * * * * *
1322322 AAAAAGTATCGATACGAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTATTTACACA
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTATTAAAACC
* * ** * * *
1322387 GGTAAAATCA-AATGATTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTT
66 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAAGTCTCGATGTTT
* *
1322451 TTGGGATCGATAC-TTTTATAAATGTATCGAAACTTTATGCGTGCACCTAGTTAGGCATTCATTC
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
*
1322515 TAGAC
196 TGGAC
*
1322520 AAAAATGTATCGACACAAATATAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCA-TAAAA
1 -AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCT-ATTAAAA
* * *
1322584 CCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTATATTATAATTTTAAGTCTCGATGT
64 CCGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAAGTCTCGATGT
*
1322649 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTACACCTAGTTTGGCATTCAT
129 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCAT
1322714 TCTGGAC
194 TCTGGAC
*
1322721 AAAATGTATCGACACAAATTTATAAAGTGTCGATACATTATGTAGACCTA-TTTCTCA-TAAAAC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCT-ATTAAAAC
* * **
1322784 TGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTT
65 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAAGTCTCGATGTT
*
1322849 TTTGTGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATT
1322914 CTGGAC
195 CTGGAC
* * *
1322920 AAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAGATCTATTTTCTCA-TAAAAT
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCT-ATTAAAAC
* * * ** *
1322984 CGGTATATTTATACTGGTTACATTGTTAATTTACCTATTACATTATAATTATTTGTTTCGATGTT
65 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAAGTCTCGATGTT
* * * *
1323049 TTTGGGGTCGATAC-TTTTAGAAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGACATTCA
130 TTTGGGATCGATACTTTTTA-TAAATGTATCGACACTTTATGCGTGCACCTAGTTTGG-CATTCA
1323113 TTCTGGAC
193 TTCTGGAC
* * * *
1323121 AATAA-GTATTGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTATTTACAC
1 AA-AATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTATTAAAAC
* * * * *
1323185 CGGTAAATATCTACCGGTTACATTGTAAATTTACATATTACATTATAATTTTAAGTATCGATGTT
65 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAAGTCTCGATGTT
* * *
1323250 TTTGGGATCGATACTTTTAATAAATGCATCGACACTTTATGCGTGCACCTCGTTTGGACATTCAT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGG-CATTCAT
*
1323315 TCTGGAT
194 TCTGGAC
* * * * *
1323322 AATAA-GTATCTACACAAATTTAAAAAGTGTAGATACATTATGTTGACCTATTTTCTATTTACAC
1 AA-AATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTATTAAAAC
* *
1323386 CGGTAAATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTCTCGATGTT
65 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAAGTCTCGATGTT
*
1323451 TTTGGGATCGATACTTTTTATAAACGTATCGACACTTTAT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTAT
1323491 ACGTTTTCTC
Statistics
Matches: 882, Mismatches: 79, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
199 257 0.29
200 227 0.26
201 392 0.44
202 6 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (200 bp):
AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTATTAAAACC
GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAAGTCTCGATGTTT
TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
TGGAC
Found at i:1323065 original size:399 final size:400
Alignment explanation
Indices: 1322323--1323490 Score: 1706
Period size: 399 Copynumber: 2.9 Consensus size: 400
1322313 CGTAATTTAA
* *
1322323 AAAAGTATCGATACGAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTATTTACACAG
1 AAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTATTTACACAG
* * ** * *
1322388 GTAAAATCA-AATGATTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTT
66 GTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTATCGATGTTTT
* *
1322452 TGGGATCGATAC-TTTTATAAATGTATCGAAACTTTATGCGTGCACCTAGTTAGGCATTCATTCT
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
* *
1322516 AGACAAAAATGTATCGACACAAATATAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATA
196 GGAC-AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATA
*
1322581 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTATATTATAATT-TTAAGTCTCG
260 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATT-AGTCTCG
1322645 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTACACCTAGTTTGG-CA
324 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTACACCTAGTTTGGACA
1322709 TTCATTCTGGAC
389 TTCATTCTGGAC
* * * *
1322721 AAAATGTATCGACACAAATTTATAAAGTGTCGATACATTATGTAGACCTA-TTTCTCA-TAAAAC
1 AAAA-GTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCT-ATTTACAC
* * * *
1322784 TGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTT
64 AGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTATCGATGTT
*
1322849 TTTGTGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATT
129 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATT
* *
1322914 CTGGACAAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAGATCTATTTTCTCAT
194 CTGGACAAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCAT
* * * * *
1322979 AAAATCGGTATATTTATACTGGTTACATTGTTAATTTACCTATTACATTATAATTATTTGTTTCG
259 AAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTAGTCTCG
* * * * *
1323044 ATGTTTTTGGGGTCGATAC-TTTTAGAAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGAC
324 ATGTTTTTGGGATCGATACTTTTTA-TAAATGTATCGACACTTTATGCGTACACCTAGTTTGGAC
1323108 ATTCATTCTGGAC
388 ATTCATTCTGGAC
* *
1323121 AATAAGTATTGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTATTTACACC
1 AA-AAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTATTTACACA
* * * * *
1323186 GGTAAATATCTACCGGTTACATTGTAAATTTACATATTACATTATAATTTTAAGTATCGATGTTT
65 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTATCGATGTTT
* * *
1323251 TTGGGATCGATACTTTTAATAAATGCATCGACACTTTATGCGTGCACCTCGTTTGGACATTCATT
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGG-CATTCATT
* * * *
1323316 CTGGATAATAA-GTATCTACACAAATTTAAAAAGTGTAGATACATTATGTTGACCTATTTTCT-A
194 CTGGACAA-AATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCA
* * * * *
1323379 TTTACACCGGTAAATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTCT
258 -TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTAGTCT
*
1323444 CGATGTTTTTGGGATCGATACTTTTTATAAACGTATCGACACTTTAT
322 CGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTAT
1323491 ACGTTTTCTC
Statistics
Matches: 686, Mismatches: 70, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
398 25 0.04
399 266 0.39
400 114 0.17
401 121 0.18
402 153 0.22
403 7 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (400 bp):
AAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTATTTACACAG
GTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTATCGATGTTTT
TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
GGACAAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAA
AACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTAGTCTCGAT
GTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTACACCTAGTTTGGACATT
CATTCTGGAC
Found at i:1324834 original size:18 final size:18
Alignment explanation
Indices: 1324811--1324847 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1324801 CGAAATTTAC
1324811 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1324829 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1324847 A
1 A
1324848 CTCCTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1324866 original size:24 final size:24
Alignment explanation
Indices: 1324813--1324866 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1324803 AAATTTACAT
* *
1324813 TGAAATTCAAACTCAAATTGAAAT
1 TGAAATTCAAACTCAAATTAAAAA
* **
1324837 TTAAATTCAAACTCCTATTAAAAA
1 TGAAATTCAAACTCAAATTAAAAA
1324861 TGAAAT
1 TGAAAT
1324867 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (24 bp):
TGAAATTCAAACTCAAATTAAAAA
Found at i:1326274 original size:3 final size:3
Alignment explanation
Indices: 1326266--1326318 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1326256 ACTTGTTTGG
* *
1326266 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC AT- ATTC ATC GTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A-TC ATC ATC
*
1326311 ATC TTC AT
1 ATC ATC AT
1326319 TGCGCGTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.95
4 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.40
Consensus pattern (3 bp):
ATC
Found at i:1327502 original size:15 final size:15
Alignment explanation
Indices: 1327461--1327506 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1327451 GAAGAAACGA
*
1327461 TTGGTTGAGAAGGAGG
1 TTGGTTGAGAA-GAGC
1327477 TTGTCGTTGAGAAGAGC
1 TTG--GTTGAGAAGAGC
1327494 TTGGTTGAGAAGA
1 TTGGTTGAGAAGA
1327507 ACTTTGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 6 0.22
18 8 0.30
ACGTcount: A:0.26, C:0.04, G:0.41, T:0.28
Consensus pattern (15 bp):
TTGGTTGAGAAGAGC
Found at i:1328151 original size:200 final size:200
Alignment explanation
Indices: 1327797--1328760 Score: 1515
Period size: 200 Copynumber: 4.8 Consensus size: 200
1327787 GCAAAATTTA
* * *
1327797 AAAAAGTATCAACACAAATTTAAAAAGTGTCGATATATTATGTAGACCTATTTTCTCATAAAACC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
*
1327862 GATATATTTATACCGGTTACATTGTAATTTTACCTATTACATTATAATTTTAAGTCTCGATGTTT
66 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAGTCTCGATGTTT
*
1327927 TTGGGATCGATAATTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
*
1327992 TAGAC
196 TGGAC
* * * * *
1327997 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGCATACTTAGTTTCTCATAAAACT
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
*
1328062 GATAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAGTCTCGATGTTT
66 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAGTCTCGATGTTT
* * *
1328127 TTGAGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTACACCTAGTTTGGCATTCATTC
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
1328192 TGGAC
196 TGGAC
*
1328197 AAAATATATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTAGTTTT-TCATAAAAC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTA-TTTTCTCATAAAAC
*
1328261 CAATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAGTCTCTG-TGT
65 CGATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAGTCTC-GATGT
1328325 TTTTGGGATCGATAC-TTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCAT
129 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCAT
*
1328389 TCTGGAA
194 TCTGGAC
*
1328396 AAAATGTATCGACACAAATTTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
1328461 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAGTCTCGATGTTT
66 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAGTCTCGATGTTT
* * *
1328526 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTACGCGTGCACCTCGTTTGTACATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTG-GCATTCATT
1328591 CTGGAC
195 CTGGAC
** * *
1328597 AATAA-GTATCGACACAAATTTATCAAGTGTCGATACATTATGCAAACCTATTTTCTCATAAAAC
1 AA-AATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC
* * * * * * * *
1328661 CGATAAATTTCTACTGGTTATATTGTAAATTTACCTATTACATTAAAATTAT-CGTTCTCAATGT
65 CGATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAG-TCTCGATGT
* * *
1328725 TTTTGGGATCAATACTTTTTATAAACGAATCGACAC
129 TTTTGGGATCGATACTTTTTATAAATGTATCGACAC
1328761 ATCTATTTAC
Statistics
Matches: 708, Mismatches: 48, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
198 5 0.01
199 186 0.26
200 353 0.50
201 162 0.23
202 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (200 bp):
AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTAAGTCTCGATGTTT
TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
TGGAC
Found at i:1329182 original size:19 final size:20
Alignment explanation
Indices: 1329141--1329190 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1329131 TTACATTCAC
*
1329141 ATACAAAATTACAAAATCGT
1 ATACAAAATTACAAAAGCGT
*
1329161 ATACAAAATTA-TAAAGCGT
1 ATACAAAATTACAAAAGCGT
1329180 ATACAAAATTA
1 ATACAAAATTA
1329191 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (20 bp):
ATACAAAATTACAAAAGCGT
Found at i:1330675 original size:18 final size:18
Alignment explanation
Indices: 1330652--1330688 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1330642 TTCCTCCTCG
*
1330652 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATATTTTCTT
1330670 CTTCCTCCATATTTTCTT
1 CTTCCTCCATATTTTCTT
1330688 C
1 C
1330689 ATATTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (18 bp):
CTTCCTCCATATTTTCTT
Found at i:1331061 original size:15 final size:15
Alignment explanation
Indices: 1331041--1331073 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1331031 ACTCTGTTTT
1331041 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
1331056 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
1331071 CCC
1 CCC
1331074 ACTAGTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.64, G:0.06, T:0.18
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:1331128 original size:9 final size:9
Alignment explanation
Indices: 1331105--1331160 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
1331095 TTCTCCTCTT
*
1331105 CCTCAACTG
1 CCTCCACTG
*
1331114 CATCCACTG
1 CCTCCACTG
*
1331123 CCTCCACTT
1 CCTCCACTG
*
1331132 CCTCCACTA
1 CCTCCACTG
*
1331141 CCTCCACTT
1 CCTCCACTG
*
1331150 CCTCCTCTG
1 CCTCCACTG
1331159 CC
1 CC
1331161 GCCTCTACCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.14, C:0.54, G:0.05, T:0.27
Consensus pattern (9 bp):
CCTCCACTG
Found at i:1331134 original size:27 final size:27
Alignment explanation
Indices: 1331097--1331154 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1331087 CTTCTTCCTT
* *
1331097 CTCCTCTTCCTCAACTGCATCCACTGC
1 CTCCACTTCCTCAACTACATCCACTGC
* * *
1331124 CTCCACTTCCTCCACTACCTCCACTTC
1 CTCCACTTCCTCAACTACATCCACTGC
1331151 CTCC
1 CTCC
1331155 TCTGCCGCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.14, C:0.53, G:0.03, T:0.29
Consensus pattern (27 bp):
CTCCACTTCCTCAACTACATCCACTGC
Done.