Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 46 of 51
Found at i:9450289 original size:20 final size:20
Alignment explanation
Indices: 9450264--9450318 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
9450254 GACCATCCGA
9450264 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
9450284 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
9450304 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
9450319 CGAGCTATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.36, G:0.27, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:9450308 original size:10 final size:10
Alignment explanation
Indices: 9450271--9450351 Score: 58
Period size: 10 Copynumber: 7.8 Consensus size: 10
9450261 CGACCGAGGC
*
9450271 CATCCGAAAG
1 CATCCGAGAG
9450281 CATCCGAG-G
1 CATCCGAGAG
9450290 CCATCCGAGAG
1 -CATCCGAGAG
9450301 CATCCGAG-G
1 CATCCGAGAG
9450310 CCATCCGAACGAG
1 -CATCCG-A-GAG
* *
9450323 CTATGCGAGGG
1 C-ATCCGAGAG
*
9450334 CATCCGAGGG
1 CATCCGAGAG
*
9450344 CAACCGAG
1 CATCCGAG
9450352 CGAGCTATGC
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
9 2 0.03
10 44 0.75
11 5 0.08
12 3 0.05
13 5 0.08
ACGTcount: A:0.27, C:0.32, G:0.31, T:0.10
Consensus pattern (10 bp):
CATCCGAGAG
Found at i:9450339 original size:33 final size:33
Alignment explanation
Indices: 9450295--9450388 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
9450285 CGAGGCCATC
* *
9450295 CGAGAGCATCCGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
* *
9450328 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
* * *
9450361 CGAGGGAATCCGAGGGCAACCGAGCGAG
1 CGAGGGCATCCGAGGCCAACCGAACGAG
9450389 GGTAGGTCGC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.27, C:0.28, G:0.37, T:0.09
Consensus pattern (33 bp):
CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
Found at i:9453142 original size:19 final size:19
Alignment explanation
Indices: 9453114--9453159 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
9453104 TGGTAATGAA
9453114 TTTGGATGTTTATGAGGTAT
1 TTTGG-TGTTTATGAGGTAT
9453134 TTTGGTGTTTATGAGGTAT
1 TTTGGTGTTTATGAGGTAT
9453153 TTTGGTG
1 TTTGGTG
9453160 GTTAGATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (19 bp):
TTTGGTGTTTATGAGGTAT
Found at i:9457258 original size:13 final size:13
Alignment explanation
Indices: 9457219--9457262 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
9457209 TTTCCGCTTG
*
9457219 TTTTTAACTTTAT
1 TTTTTAAATTTAT
*
9457232 TTTATCATAATTTAT
1 TTT-TTA-AATTTAT
9457247 TTTTTAAATTTAT
1 TTTTTAAATTTAT
9457260 TTT
1 TTT
9457263 ATCTCCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 13 0.50
14 4 0.15
15 9 0.35
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTAAATTTAT
Found at i:9457294 original size:19 final size:19
Alignment explanation
Indices: 9457270--9457319 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
9457260 TTTATCTCCA
9457270 TTTTAATCTT-TAAAATTCT
1 TTTTAAT-TTCTAAAATTCT
9457289 TTTTAATTTCCTAAAATTCTT
1 TTTTAATTT-CTAAAATTC-T
9457310 GTTTTAATTT
1 -TTTTAATTT
9457320 GAATGAGGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.07
19 7 0.26
20 8 0.30
21 1 0.04
22 9 0.33
ACGTcount: A:0.28, C:0.10, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTAATTTCTAAAATTCT
Found at i:9457305 original size:20 final size:22
Alignment explanation
Indices: 9457280--9457319 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9457270 TTTTAATCTT
9457280 TAAAATTC-T-TTTTAATTTCC
1 TAAAATTCTTGTTTTAATTTCC
9457300 TAAAATTCTTGTTTTAATTT
1 TAAAATTCTTGTTTTAATTT
9457320 GAATGAGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (22 bp):
TAAAATTCTTGTTTTAATTTCC
Found at i:9457891 original size:259 final size:263
Alignment explanation
Indices: 9457428--9457950 Score: 1009
Period size: 259 Copynumber: 2.0 Consensus size: 263
9457418 TAATCTTATT
9457428 TTCTTTTTACGTTAATTCTTTTTTACTTTAATTTTTCATTTTTTCATTTTTTATTTATGTTATAT
1 TTCTTTTTACGTTAATTCTTTTTTACTTTAATTTTTCATTTTTTCATTTTTTATTTATGTTATAT
9457493 TTATTTAGTTTTGAGCATCTATATCGCATGTTTCATATTTCTTTTTATTATTACTTTATTCATAT
66 TTATTTAGTTTTGAGCATCTATATCGCA-GTTTCATATTTCTTTTTATTATTACTTTATTCATAT
9457558 GAATTGTATCATTAATTATATATTAGTATTCGTGACCCTTTTACTTTGTTCATGCAACTTGCATC
130 GAATTGTATCATTAATTATATATTAGTATTCGTGACCCTTTTACTTTGTTCATGCAACTTGCATC
9457623 ATTTCTTTAAATTTTGGTCTAAATTTCAAA-TTCGCAATTAAGACAATCGAGTAATCGTGTTGGT
195 ATTTCTTTAAATTTTGGTCTAAATTTCAAATTTCGCAATTAAGACAATCGAGTAATCGTGTTGGT
9457687 ACCG
260 ACCG
9457691 TTCTTTTTACGTTAATTCTTTTTTACTTTAA-TTTTCATTTTTTCATTTTTTA-TTATGTTATAT
1 TTCTTTTTACGTTAATTCTTTTTTACTTTAATTTTTCATTTTTTCATTTTTTATTTATGTTATAT
9457754 TTATTTAGTTTTGAGCATCTATATCGCA-TTTCATATTTCTTTTTATTATTACTTTATTCATATG
66 TTATTTAGTTTTGAGCATCTATATCGCAGTTTCATATTTCTTTTTATTATTACTTTATTCATATG
9457818 AATTGTATCATTAATTATATATTAGTATTCGTGACCCTTTTACTTTGTTCATGCAACTTGCATCA
131 AATTGTATCATTAATTATATATTAGTATTCGTGACCCTTTTACTTTGTTCATGCAACTTGCATCA
9457883 TTTCTTTAAATTTTGGTCTAAATTTCAAATTTCGCAATTAAGACAATCGAGTAATCGTGTTGGTA
196 TTTCTTTAAATTTTGGTCTAAATTTCAAATTTCGCAATTAAGACAATCGAGTAATCGTGTTGGTA
9457948 CCG
261 CCG
9457951 AAAGAGCAAT
Statistics
Matches: 259, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
259 130 0.50
260 38 0.15
261 39 0.15
262 21 0.08
263 31 0.12
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (263 bp):
TTCTTTTTACGTTAATTCTTTTTTACTTTAATTTTTCATTTTTTCATTTTTTATTTATGTTATAT
TTATTTAGTTTTGAGCATCTATATCGCAGTTTCATATTTCTTTTTATTATTACTTTATTCATATG
AATTGTATCATTAATTATATATTAGTATTCGTGACCCTTTTACTTTGTTCATGCAACTTGCATCA
TTTCTTTAAATTTTGGTCTAAATTTCAAATTTCGCAATTAAGACAATCGAGTAATCGTGTTGGTA
CCG
Found at i:9465127 original size:20 final size:22
Alignment explanation
Indices: 9465104--9465144 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
9465094 ATTTCAATCT
9465104 TTAAAATTC-T-TTTTAATTTC
1 TTAAAATTCTTGTTTTAATTTC
9465124 TTAAAATTCTTGTTTTAATTT
1 TTAAAATTCTTGTTTTAATTT
9465145 GCATGATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (22 bp):
TTAAAATTCTTGTTTTAATTTC
Found at i:9465236 original size:26 final size:27
Alignment explanation
Indices: 9465190--9465247 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
9465180 ATTCATATAT
* *
9465190 TTTTAAATTTTATTAGGTTTAAT-TGA
1 TTTTAAATTTTATAAGGTTTAATCTAA
*
9465216 TTTTAGATTTT-TAAGGTTTTAATCTAA
1 TTTTAAATTTTATAAGG-TTTAATCTAA
9465243 TTTTA
1 TTTTA
9465248 TTTTCTACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.15
26 16 0.59
27 7 0.26
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (27 bp):
TTTTAAATTTTATAAGGTTTAATCTAA
Found at i:9466385 original size:24 final size:27
Alignment explanation
Indices: 9466325--9466385 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
9466315 AAGATATTCG
*
9466325 TTTATATAAATTTATTTTCAAAATATTA
1 TTTA-ATAAATTTAATTTCAAAATATTA
*
9466353 TTTAATAAA-TTAATTTGAAAATA-T-
1 TTTAATAAATTTAATTTCAAAATATTA
9466377 TTTAATAAA
1 TTTAATAAA
9466386 AATAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.29
25 1 0.03
26 12 0.39
27 5 0.16
28 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTAATAAATTTAATTTCAAAATATTA
Found at i:9467133 original size:13 final size:14
Alignment explanation
Indices: 9467101--9467138 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
9467091 TAGTTTTTGT
9467101 ATTTTTTAATAGTA
1 ATTTTTTAATAGTA
* *
9467115 ATTTTTTATTATTA
1 ATTTTTTAATAGTA
9467129 A-TTTTTAATA
1 ATTTTTTAATA
9467139 ATATATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
ATTTTTTAATAGTA
Found at i:9467160 original size:13 final size:12
Alignment explanation
Indices: 9467119--9467167 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
9467109 ATAGTAATTT
9467119 TTTATT-ATTAA
1 TTTATTAATTAA
9467130 TTT-TTAA-TAA
1 TTTATTAATTAA
*
9467140 TATATTAATTAAA
1 TTTATTAATT-AA
9467153 TTTATTAATATAA
1 TTTATTAAT-TAA
9467166 TT
1 TT
9467168 AAAATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 7 0.23
11 8 0.26
12 1 0.03
13 14 0.45
14 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTATTAATTAA
Found at i:9471161 original size:45 final size:45
Alignment explanation
Indices: 9471105--9471197 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 45
9471095 ATAATTTCTT
* *
9471105 TGAGATGCACACATAGTGTCGATACGGTCATTCATAAACATATTA
1 TGAGATGCACACATAGTGCCGATACGGTCATTCATAAACATATGA
* * * *
9471150 TGAGTTGCACACTTAGTGCCGATACGGTCGTTCATTAACATATGA
1 TGAGATGCACACATAGTGCCGATACGGTCATTCATAAACATATGA
9471195 TGA
1 TGA
9471198 ATTTCATGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (45 bp):
TGAGATGCACACATAGTGCCGATACGGTCATTCATAAACATATGA
Found at i:9471222 original size:54 final size:54
Alignment explanation
Indices: 9471153--9471335 Score: 276
Period size: 54 Copynumber: 3.4 Consensus size: 54
9471143 CATATTATGA
* * *
9471153 GTTGCACACTTAGTGCCGATACGGTCGTTCATTAACATATGATGAATTTCATGG
1 GTTGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCATGG
* * **
9471207 GTTGAACACTTAGTGCCTATACTGTCGTTCACCAACATATGATGAATTCCATGG
1 GTTGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCATGG
* * *
9471261 GTTGCACACTTAGTGCTTATACGGTCGTTCATAAACATATTATGAATTCCGTGG
1 GTTGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCATGG
9471315 GTTGCACACTTAGTGCCTATA
1 GTTGCACACTTAGTGCCTATA
9471336 GTACACATAG
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 115 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (54 bp):
GTTGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCATGG
Found at i:9493413 original size:12 final size:12
Alignment explanation
Indices: 9493392--9493433 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
9493382 GTGGAGCAAA
9493392 GAAAGAGAAAAG
1 GAAAGAGAAAAG
*
9493404 GAAAGTGAAAAG
1 GAAAGAGAAAAG
9493416 AGAAAAGAGAAAAG
1 -G-AAAGAGAAAAG
9493430 GAAA
1 GAAA
9493434 AGGTAAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 14 0.54
13 2 0.08
14 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (12 bp):
GAAAGAGAAAAG
Found at i:9493436 original size:6 final size:7
Alignment explanation
Indices: 9493393--9493435 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
9493383 TGGAGCAAAG
9493393 AAAGAGA
1 AAAGAGA
9493400 AAAG-G-
1 AAAGAGA
*
9493405 AAAGTGA
1 AAAGAGA
9493412 AAAGAGA
1 AAAGAGA
9493419 AAAGAGA
1 AAAGAGA
9493426 AAAG-GA
1 AAAGAGA
9493432 AAAG
1 AAAG
9493436 GTAAAGTGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
5 4 0.12
6 8 0.24
7 21 0.64
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (7 bp):
AAAGAGA
Found at i:9515248 original size:46 final size:43
Alignment explanation
Indices: 9515144--9515269 Score: 137
Period size: 46 Copynumber: 2.8 Consensus size: 43
9515134 CTTTTTTCTC
* * * *
9515144 CCATGTGAACATGATGGTTCATCTATCTTCATGAACTTGGTTT
1 CCATGTGAACATGATGGTTCAGCTACCTTCATGAACTTGGATA
* *
9515187 CCATGTGAACGTGATGGTTC-GACTACCTTCTTTGAACTTGGATA
1 CCATGTGAACATGATGGTTCAG-CTACCTTC-ATGAACTTGGATA
*
9515231 CGTCGTGTGAACATGATGGTTCAGCTACCTTCCATGAAC
1 C--CATGTGAACATGATGGTTCAGCTACCTT-CATGAAC
9515270 ATGCATAAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
43 26 0.38
44 11 0.16
46 29 0.43
47 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (43 bp):
CCATGTGAACATGATGGTTCAGCTACCTTCATGAACTTGGATA
Found at i:9516259 original size:24 final size:23
Alignment explanation
Indices: 9516211--9516275 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
9516201 TTCAAACGTC
*
9516211 AAAGAGCACATCTTTTAGAATTTTA
1 AAAGA-CACATCCTTT-GAATTTTA
* *
9516236 AATGTCACATCCTTTGAATCTTTA
1 AAAGACACATCCTTTGAAT-TTTA
*
9516260 AAAGACAAATCCTTTG
1 AAAGACACATCCTTTG
9516276 GAACTTCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 4 0.12
24 26 0.79
25 3 0.09
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (23 bp):
AAAGACACATCCTTTGAATTTTA
Found at i:9518402 original size:20 final size:21
Alignment explanation
Indices: 9518374--9518412 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
9518364 CAAGTTCTTG
*
9518374 AATATGTAACATT-TAATAAA
1 AATAAGTAACATTCTAATAAA
9518394 AATAAGTAACATTCTAATA
1 AATAAGTAACATTCTAATA
9518413 CAACACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (21 bp):
AATAAGTAACATTCTAATAAA
Found at i:9522959 original size:2 final size:2
Alignment explanation
Indices: 9522952--9523006 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
9522942 TAGCTTTCAC
9522952 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
9522994 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
9523007 ATGAATGTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9524249 original size:14 final size:15
Alignment explanation
Indices: 9524219--9524253 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
9524209 ATCTCATTAA
*
9524219 TCTTTTATTTCTTTT
1 TCTTTTATTTCTCTT
9524234 TCTTTT-TTTCTCTT
1 TCTTTTATTTCTCTT
9524248 TCTTTT
1 TCTTTT
9524254 CTCTCCACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTATTTCTCTT
Found at i:9524255 original size:11 final size:11
Alignment explanation
Indices: 9524226--9524257 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
9524216 TAATCTTTTA
9524226 TTTCTTTT-TC
1 TTTCTTTTCTC
9524236 TTT-TTTTCTC
1 TTTCTTTTCTC
9524246 TTTCTTTTCTC
1 TTTCTTTTCTC
9524257 T
1 T
9524258 CCACCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 4 0.20
10 8 0.40
11 8 0.40
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTC
Found at i:9526928 original size:3 final size:3
Alignment explanation
Indices: 9526920--9526972 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
9526910 TTTCGTCCTG
9526920 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9526968 TAT TA
1 TAT TA
9526973 CAGGGCTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9531491 original size:245 final size:247
Alignment explanation
Indices: 9531006--9531498 Score: 803
Period size: 245 Copynumber: 2.0 Consensus size: 247
9530996 AGAAGGACGC
* * * *
9531006 GTAAGTTTGCATGTGCATTGACTATAGAGATCTTAATCGGGGCCAGCCTTAAAGATAATTTCTCA
1 GTAAGTTTGCATGTGCATTGACTACAAAGATCTTAATCGGAGCCAGCCTGAAAGATAATTTCTCA
* * *
9531071 TTGCCTCACATAGACACCCTGGTGGACAATACTGCTGGAAACTCCCTATTTTTATTCATGGATGG
66 TTGCCTCACATAAACACCCTGGTGGACAATACTGCTGGAAACTCCCTATTTTCATTCATGAATGG
* * *
9531136 GCTTTCAGGTTACAATCAAATAAAGATGCATCCAGAAGATATGGAAAAGACTATATTTGTCACCA
131 GATTTCAGGTTACAATCAAAAAAAGATGCATCCAGAAGATATGGAAAAGACTATATTTATCACCA
* *
9531201 TGTGGGGTACGTTTTGCTACAAGGTGATGTTGATTAGGCTATAGAATATAGG
196 TGTGGGGTACGTTTTCCTACAAGGTGATGTTGATTAGGCTATAGAATACAGG
*
9531253 GTAAGTTTGCATGTGCGTTGACTACAAAGATCTTAATC-GAGCCAGCCTGAAAGATAATTTC-CA
1 GTAAGTTTGCATGTGCATTGACTACAAAGATCTTAATCGGAGCCAGCCTGAAAGATAATTTCTCA
* *
9531316 TTTGCCTCACATAAACACTCTGGTGGACAATTCTGCTGGAAACTCCCTATTTTCATTCATGAATG
66 -TTGCCTCACATAAACACCCTGGTGGACAATACTGCTGGAAACTCCCTATTTTCATTCATGAATG
*
9531381 GGATTTCGGGTTACAAT-AAAAAAAGATGCATCCAGAAGATATGGAAAAGACTATATTTATCACC
130 GGATTTCAGGTTACAATCAAAAAAAGATGCATCCAGAAGATATGGAAAAGACTATATTTATCACC
*
9531445 ATGTGGGGTGCGTTTTCCTACAAGGTGATGTTGATTAGGCTATAGAATACAGG
195 ATGTGGGGTACGTTTTCCTACAAGGTGATGTTGATTAGGCTATAGAATACAGG
9531498 G
1 G
9531499 GTAACCTACC
Statistics
Matches: 228, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
245 98 0.43
246 95 0.42
247 35 0.15
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (247 bp):
GTAAGTTTGCATGTGCATTGACTACAAAGATCTTAATCGGAGCCAGCCTGAAAGATAATTTCTCA
TTGCCTCACATAAACACCCTGGTGGACAATACTGCTGGAAACTCCCTATTTTCATTCATGAATGG
GATTTCAGGTTACAATCAAAAAAAGATGCATCCAGAAGATATGGAAAAGACTATATTTATCACCA
TGTGGGGTACGTTTTCCTACAAGGTGATGTTGATTAGGCTATAGAATACAGG
Found at i:9538988 original size:20 final size:20
Alignment explanation
Indices: 9538963--9539000 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9538953 AGGATCTGCC
*
9538963 TGATCTTCCATGTTGTTGCT
1 TGATCTCCCATGTTGTTGCT
9538983 TGATCTCCCATGTTGTTG
1 TGATCTCCCATGTTGTTG
9539001 TTGCCTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (20 bp):
TGATCTCCCATGTTGTTGCT
Found at i:9539736 original size:50 final size:50
Alignment explanation
Indices: 9539679--9539781 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
9539669 ATTAGAGTTA
*
9539679 AGACATGTTTAGTTTGTTATTATATTT-TTCATTAGTTGTTTAGGACCTTT
1 AGACATGTTTAGTTTGTTATTAT-TTTATTCATTAGTTATTTAGGACCTTT
9539729 AGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACCTTT
1 AGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACCTTT
9539779 AGA
1 AGA
9539782 ACTCACTCCC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 3 0.06
50 48 0.94
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (50 bp):
AGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACCTTT
Found at i:9543558 original size:50 final size:50
Alignment explanation
Indices: 9543497--9543602 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
9543487 GGATTTAGAG
* *
9543497 TTTAGACATGTTTAGTTTGTTATTATTTTATTTATTAGTTATTTAGGACC
1 TTTAGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACA
9543547 TTTAGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACA
1 TTTAGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACA
9543597 TTTAGA
1 TTTAGA
9543603 ACTCACCCCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.55
Consensus pattern (50 bp):
TTTAGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACA
Found at i:9548056 original size:44 final size:43
Alignment explanation
Indices: 9547929--9548207 Score: 355
Period size: 44 Copynumber: 6.4 Consensus size: 43
9547919 AAGGTATTAT
* * * * *
9547929 CCTTGCACATAACAAAAGAGCCTGGGGAAACTGTAATGCTTAC
1 CCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
* *
9547972 CCTTGCACACAGTAAAGGAACCT-GGGAAATTGTAAGGCTTAC
1 CCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
* *
9548014 CCTTGCACACAACAAATGG-GCCTCGGGGAAACTGTAAGGCTTAC
1 CCTTGCACACAGCAAA-GGAACCT-GGGGAAACTGTAAGGCTTAC
* *
9548058 CCTTGCACATAGCAAAAGAACCTAGGGGAAACTGTAAGGCTTAC
1 CCTTGCACACAGCAAAGGAACCT-GGGGAAACTGTAAGGCTTAC
* *
9548102 CCTTGCACACAGCAAAGGAACCTAAGGGAAACTGTAAGACTTAC
1 CCTTGCACACAGCAAAGGAACCT-GGGGAAACTGTAAGGCTTAC
* * *
9548146 CCTTGCACAGAGCAAAGGAACCTGGGGAAACTGTAACGATTAC
1 CCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
*
9548189 CATTGCACACAGCAAAGGA
1 CCTTGCACACAGCAAAGGA
9548208 GCCTACTGTA
Statistics
Matches: 205, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
42 34 0.17
43 54 0.26
44 117 0.57
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (43 bp):
CCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
Found at i:9552154 original size:25 final size:24
Alignment explanation
Indices: 9552099--9552165 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
9552089 TATAAAGGGG
*
9552099 TAATATTTTTC-AAATTTTTTATT
1 TAATATTTTTCAAAATTTTTTAAT
*
9552122 TAACATTTTTCAAAATTCTTTTAAT
1 TAATATTTTTCAAAATT-TTTTAAT
*
9552147 TGATATTTTTC-AAATTTTT
1 TAATATTTTTCAAAATTTTT
9552166 GAAAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.34
24 10 0.26
25 15 0.39
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.60
Consensus pattern (24 bp):
TAATATTTTTCAAAATTTTTTAAT
Found at i:9553280 original size:223 final size:223
Alignment explanation
Indices: 9552892--9553339 Score: 860
Period size: 223 Copynumber: 2.0 Consensus size: 223
9552882 ATGTTCCAAC
9552892 TATCATCCTTGGCATAGATTTGTCTCATGGTTCTCTGGGGAAGTCTAATATTCCATCAATTGCTA
1 TATCATCCTTGGCATAGATTTGTCTCATGGTTCTCTGGGGAAGTCTAATATTCCATCAATTGCTA
* * *
9552957 TGGTGGCCAGCTCCAGGCAGTGGTCTTTGATTTCCTATTACAGGACAAATGTGCGTACACAATCT
66 CGGTGGCCAGCTCCAGACAGTGGTCTTTGATTTCCTATTACAGGACAAATGTACGTACACAATCT
9553022 CTGAAGCTTGAAATTATAGATTCTCTTTCCAAAACCATCTGGCAGGGATGATGATGGTATCATGA
131 CTGAAGCTTGAAATTATAGATTCTCTTTCCAAAACCATCTGGCAGGGATGATGATGGTATCATGA
9553087 GATAAGTTCTACTGGATTTTTATACAAG
196 GATAAGTTCTACTGGATTTTTATACAAG
*
9553115 TATCATCCTTGGCATATATTTGTCTCATGGTTCTCTGGGGAAGTCTAATATTCCATCAATTGCTA
1 TATCATCCTTGGCATAGATTTGTCTCATGGTTCTCTGGGGAAGTCTAATATTCCATCAATTGCTA
9553180 CGGTGGCCAGCTCCAGACAGTGGTCTTTGATTTCCTATTACAGGACAAATGTACGTACACAATCT
66 CGGTGGCCAGCTCCAGACAGTGGTCTTTGATTTCCTATTACAGGACAAATGTACGTACACAATCT
9553245 CTGAAGCTTGAAATTATAGATTCTCTTTCCAAAACCATCTGGCAGGGATGATGATGGTATCATGA
131 CTGAAGCTTGAAATTATAGATTCTCTTTCCAAAACCATCTGGCAGGGATGATGATGGTATCATGA
9553310 GATAAGTTCTACTGGATTTTTATACAAG
196 GATAAGTTCTACTGGATTTTTATACAAG
9553338 TA
1 TA
9553340 CAAAAAAGAA
Statistics
Matches: 221, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
223 221 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (223 bp):
TATCATCCTTGGCATAGATTTGTCTCATGGTTCTCTGGGGAAGTCTAATATTCCATCAATTGCTA
CGGTGGCCAGCTCCAGACAGTGGTCTTTGATTTCCTATTACAGGACAAATGTACGTACACAATCT
CTGAAGCTTGAAATTATAGATTCTCTTTCCAAAACCATCTGGCAGGGATGATGATGGTATCATGA
GATAAGTTCTACTGGATTTTTATACAAG
Found at i:9553993 original size:35 final size:36
Alignment explanation
Indices: 9553930--9554047 Score: 112
Period size: 35 Copynumber: 3.3 Consensus size: 36
9553920 CAAATTTTTG
* ** *
9553930 TCTCACTAGAGACAGTTTTTCTTGAAACAAAATTGA
1 TCTCACTTGAGACAGTTTTTCTCAAAACAAAATTCA
** * **
9553966 TCTCACTTGAGATTG-TTTTCTCAAAACAAATTTTT
1 TCTCACTTGAGACAGTTTTTCTCAAAACAAAATTCA
* * *
9554001 TCTCTCTTGAGACAGTTTTTCTTAAAAAACAAATTCA
1 TCTCACTTGAGACAGTTTTTCTCAAAACA-AAATTCA
9554038 TCTCACTTGA
1 TCTCACTTGA
9554048 TATAATCTTC
Statistics
Matches: 63, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
35 27 0.43
36 23 0.37
37 13 0.21
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (36 bp):
TCTCACTTGAGACAGTTTTTCTCAAAACAAAATTCA
Found at i:9553999 original size:72 final size:73
Alignment explanation
Indices: 9553899--9554047 Score: 212
Period size: 72 Copynumber: 2.1 Consensus size: 73
9553889 TTTGTTTCCT
* * *
9553899 TTGAGAATGTTTCTCTCGAAACAAATTTTTGTCTCACTAGAGACAGTTTTTCTTGAAACA-AAAT
1 TTGAGAATGTTTCTCTCAAAACAAATTTTT-TCTCACTAGAGACAGTTTTTCTTAAAAAACAAAT
*
9553963 TGATCTCAC
65 TCATCTCAC
* * *
9553972 TTGAGATTGTTT-TCTCAAAACAAATTTTTTCTCTCTTGAGACAGTTTTTCTTAAAAAACAAATT
1 TTGAGAATGTTTCTCTCAAAACAAATTTTTTCTCACTAGAGACAGTTTTTCTTAAAAAACAAATT
9554036 CATCTCAC
66 CATCTCAC
9554044 TTGA
1 TTGA
9554048 TATAATCTTC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 25 0.37
72 32 0.47
73 11 0.16
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (73 bp):
TTGAGAATGTTTCTCTCAAAACAAATTTTTTCTCACTAGAGACAGTTTTTCTTAAAAAACAAATT
CATCTCAC
Found at i:9554356 original size:66 final size:66
Alignment explanation
Indices: 9554279--9554403 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
9554269 TGATAAAACT
*
9554279 TTGAGATTGTTTCTC-TTGAAACAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGAGATTGTTTC-CATTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
9554343 AA
65 AA
* *
9554345 TTGAGATTGTTTCCATTGAAACAAATTTTGTCTTGCTTGAGATAGTTTCTCTTGAAACA
1 TTGAGATTGTTTCCATTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
9554404 AATTATCCCT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 1 0.02
66 54 0.98
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (66 bp):
TTGAGATTGTTTCCATTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACA
A
Found at i:9554755 original size:140 final size:140
Alignment explanation
Indices: 9554402--9555035 Score: 925
Period size: 139 Copynumber: 4.5 Consensus size: 140
9554392 TCTCTTGAAA
* ** *
9554402 CAAATTATCCCTAAAGATGGCTACATATCCTCATCACGTAGGAACAATGTCATCCAACGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
* * * * * *
9554467 TCTCCTCATCATGTAGGAGCATCGTCATCCTTATATAACCAGACTTCCTCATCACCTAGGAATCA
66 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
9554532 TGTTGTCTCC
131 TGTTGTCTCC
* *
9554542 C-AATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCCACTGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
* * *
9554606 TCTCCTCATCACGTAGGAGCAACGTCATCCATAGATAACCAGACTTCCTCATCACGTAGAAACCG
66 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
*
9554671 TGTTATCTCC
131 TGTTGTCTCC
* * * * * *
9554681 CAAATTACCCCTAAAGATGGCTAGACATCCTCATTATGTACGAACAATTTCATCCACCGA-CTCG
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCT-G
** *
9554745 ATCTCCTCATCACGTAGGAGCAGTATCATCCTTAGATAACCAGACTTCCTCATCAAGTAGGAACC
65 ATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACC
9554810 GTGTTGTCTCC
130 GTGTTGTCTCC
* * * *
9554821 CAAATTATCCCTAAAAATGGCTATATGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTAA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
* *
9554886 TCTCCTCATCACGTAGGA-CTAGTGTCATCCTTAGAT-ACCAGACTTCCTCATCACGTAGGAATC
66 TCTCCTCATCACGTAGGAGC-AGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACC
9554949 GTGTTGTCTCC
130 GTGTTGTCTCC
* *
9554960 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAATAATGTCATCCACCGACCAGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
9555025 TCTCCTCATCA
66 TCTCCTCATCA
9555036 TGGAGGACTA
Statistics
Matches: 442, Mismatches: 48, Indels: 9
0.89 0.10 0.02
Matches are distributed among these distances:
139 233 0.53
140 207 0.47
141 2 0.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (140 bp):
CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
TGTTGTCTCC
Found at i:9555096 original size:279 final size:279
Alignment explanation
Indices: 9554402--9555114 Score: 947
Period size: 279 Copynumber: 2.6 Consensus size: 279
9554392 TCTCTTGAAA
* * *
9554402 CAAATTATCCCTAAAGATGGCTACATATCCTCATCACGTAGGAACAATGTCATCCAACGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTCATCCACCGACC-GA
** * * *
9554467 TCTCCTCATCATGTAGGAGCATCGTCATCCTTATATAACCAGACTTCCTCATCACCTAGGAATCA
65 TCTCCTCATCATGTAGGAGCAGAGTCATCCTTAAATAACCAGACTTCCTCATCACATAGGAAACA
*
9554532 TGTTGTCTCCC-AATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCC
130 TGTTGTCTCCCAAATTATCCCTAAAAATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCC
* *
9554596 ACTGACCTGATCTCCTCATCACGTAGGAGCAACGTCATCCATAGATAACCAGACTTCCTCATCAC
195 ACCGACCTAATCTCCTCATCACGTAGGAGCAACGTCATCCATAGATAACCAGACTTCCTCATCAC
9554661 GTAGAAACCGTGTTATCTCC
260 GTAGAAACCGTGTTATCTCC
* * * * *
9554681 CAAATTACCCCTAAAGATGGCTAGACATCCTCATTATGTACGAACAATTTCATCCACCGACTCGA
1 CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTCATCCACCGAC-CGA
* * *
9554746 TCTCCTCATCACGTAGGAGCAGTA-TCATCCTTAGATAACCAGACTTCCTCATCA-AGTAGGAAC
65 TCTCCTCATCATGTAGGAGCAG-AGTCATCCTTAAATAACCAGACTTCCTCATCACA-TAGGAAA
* * * *
9554809 CGTGTTGTCTCCCAAATTATCCCTAAAAATGGCTATATGTCCTCATCACGTAGGAACAATGTCAT
128 CATGTTGTCTCCCAAATTATCCCTAAAAATGGCTAGACGTCCTCATCACGTAAGAACAATGTCAT
** *
9554874 CCACCGACCTAATCTCCTCATCACGTAGGA-CTAGTGTCATCCTTAGAT-ACCAGACTTCCTCAT
193 CCACCGACCTAATCTCCTCATCACGTAGGAGC-AACGTCATCCATAGATAACCAGACTTCCTCAT
* * *
9554937 CACGTAGGAATCGTGTTGTCTCC
257 CACGTAGAAACCGTGTTATCTCC
* *
9554960 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAATAATGTCATCCACCGACCAGA
1 CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTCATCCACCGACC-GA
* * ** * * * *
9555025 TCTCCTCATCATGGAGGA-CTAGAGCCATAATCAAATAACTAGGCTTCTTCATCACATAGGAAAC
65 TCTCCTCATCATGTAGGAGC-AGAGTCATCCTTAAATAACCAGACTTCCTCATCACATAGGAAAC
*
9555089 ATGTTGTCT-CCAAATT-TACCTAAAAA
129 ATGTTGTCTCCCAAATTATCCCTAAAAA
9555115 CGACCAGAAC
Statistics
Matches: 378, Mismatches: 47, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
277 9 0.02
278 10 0.03
279 269 0.71
280 90 0.24
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (279 bp):
CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTCATCCACCGACCGAT
CTCCTCATCATGTAGGAGCAGAGTCATCCTTAAATAACCAGACTTCCTCATCACATAGGAAACAT
GTTGTCTCCCAAATTATCCCTAAAAATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCCA
CCGACCTAATCTCCTCATCACGTAGGAGCAACGTCATCCATAGATAACCAGACTTCCTCATCACG
TAGAAACCGTGTTATCTCC
Found at i:9555102 original size:139 final size:140
Alignment explanation
Indices: 9554402--9555112 Score: 870
Period size: 139 Copynumber: 5.1 Consensus size: 140
9554392 TCTCTTGAAA
* ** * *
9554402 CAAATTATCCCTAAAGATGGCTACATATCCTCATCACGTAGGAACAATGTCATCCAACGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* ** * * * *
9554467 TCTCCTCATCATGTAGGAGCATCGTCATCCTTATATAACCAGACTTCCTCATCACCTAGGAATCA
66 TCTCCTCATCACGTAGGAGCAGAGTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAACG
9554532 TGTTGTCTCC
131 TGTTGTCTCC
* * *
9554542 C-AATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCCACTGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* *
9554606 TCTCCTCATCACGTAGGAGCA-ACGTCATCCATAGATAACCAGACTTCCTCATCACGTA-GAAAC
66 TCTCCTCATCACGTAGGAGCAGA-GTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAA-
*
9554669 CGTGTTATCTCC
129 CGTGTTGTCTCC
* * * * * *
9554681 CAAATTACCCCTAAAGATGGCTAGACATCCTCATTATGTACGAACAATTTCATCCACCGACTC-G
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGAC-CAG
9554745 ATCTCCTCATCACGTAGGAGCAGTA-TCATCCTTAGATAACCAGACTTCCTCATCA-AGTAGGAA
65 ATCTCCTCATCACGTAGGAGCAG-AGTCATCCTTAGATAACCAGACTTCCTCATCACA-TAGGAA
*
9554808 CCGTGTTGTCTCC
128 ACGTGTTGTCTCC
* * *
9554821 CAAATTATCCCTAAAAATGGCTATATGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTA-
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACC-AG
* * *
9554885 ATCTCCTCATCACGTAGGA-CTAGTGTCATCCTTAGAT-ACCAGACTTCCTCATCACGTAGGAAT
65 ATCTCCTCATCACGTAGGAGC-AGAGTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAA
9554948 CGTGTTGTCTCC
129 CGTGTTGTCTCC
*
9554960 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAATAATGTCATCCACCGACCAGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * * ** * * * * *
9555025 TCTCCTCATCATGGAGGA-CTAGAGCCATAATCAAATAACTAGGCTTCTTCATCACATAGGAAAC
66 TCTCCTCATCACGTAGGAGC-AGAGTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAAC
*
9555089 ATGTTGTCT-C
130 GTGTTGTCTCC
*
9555099 CAAATT-TACCTAAA
1 CAAATTATCCCTAAA
9555113 AACGACCAGA
Statistics
Matches: 500, Mismatches: 56, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
138 11 0.02
139 251 0.50
140 233 0.47
141 4 0.01
142 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (140 bp):
CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
TCTCCTCATCACGTAGGAGCAGAGTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAACG
TGTTGTCTCC
Found at i:9555366 original size:3 final size:3
Alignment explanation
Indices: 9555358--9555394 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
9555348 TTTTATTAAC
9555358 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9555395 GTATTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9556509 original size:2 final size:2
Alignment explanation
Indices: 9556502--9556540 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9556492 TGTTGTACCT
9556502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9556541 CATCCCTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9556730 original size:28 final size:28
Alignment explanation
Indices: 9556676--9556731 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
9556666 TCCATCATTC
* * *
9556676 TTTTATTCAACAGTGTTTAACATTTCAT
1 TTTTACTCAACAATGTTTAACAGTTCAT
*
9556704 TTTTACTCAACAATGTTTAACCGTTCAT
1 TTTTACTCAACAATGTTTAACAGTTCAT
9556732 CTAACTGACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (28 bp):
TTTTACTCAACAATGTTTAACAGTTCAT
Found at i:9556940 original size:81 final size:81
Alignment explanation
Indices: 9556705--9557092 Score: 512
Period size: 81 Copynumber: 4.8 Consensus size: 81
9556695 ACATTTCATT
* * *
9556705 TTTACTCAACAATGTTTAACCGTTCATCTAACTGACATAATTGGCACCTTTCTACCAATTGCACA
1 TTTACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
*
9556770 TTTAGGCCATTATTCC
66 GTTAGGCCATTATTCC
* * *
9556786 TTTACTCAACGGTA-TTAAACGTTCATCTAACTGGA-ATAATTGGTACCTTTATACCAATTGCAC
1 TTTACTCAACAGTATTTAACCGTTCATCTAACT-GACATAATTGGTACCTTTCTACCAATTGCAC
*
9556849 ATTTAGGCCATTATTCC
65 AGTTAGGCCATTATTCC
* * * *
9556866 TTTACTCAACAATATTTAACCGTTCATCTGACTGACATAATTGGTACTTTTCTACCAATTGTACA
1 TTTACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
*
9556931 GTTAGGCCATTATTCT
66 GTTAGGCCATTATTCC
* * * * * * *
9556947 TTTACTTAACGGTGTTTAATCGTTCATCTAACTGACATAATTGATACATTTCTACCAATTGCGCA
1 TTTACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
* *
9557012 GTTAGGTCATTATTCT
66 GTTAGGCCATTATTCC
* * **
9557028 TTTACTCAACAGTATTTAATCGTTCATCTAACTGGCATAATTGGTACC-TAATACCAATTGCACA
1 TTTACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
9557092 G
66 G
9557093 CCTTATGCCT
Statistics
Matches: 269, Mismatches: 35, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
80 88 0.33
81 181 0.67
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (81 bp):
TTTACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
GTTAGGCCATTATTCC
Found at i:9557046 original size:162 final size:161
Alignment explanation
Indices: 9556704--9557092 Score: 548
Period size: 161 Copynumber: 2.4 Consensus size: 161
9556694 AACATTTCAT
* *
9556704 TTTTACTCAACAATGTTTAACCGTTCATCTAACTGACATAATTGGCACCTTTCTACCAATTGCAC
1 TTTTACTCAACAATATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCAC
* * *
9556769 ATTTAGGCCATTATTCCTTTACTCAACGGTATTAAACGTTCATCTAACTGGAATAATTGGTACCT
66 AGTTAGGCCATTATTCCTTTACTCAACGGTATTAAACGTTCATCTAACTGGAATAATTGATACAT
*
9556834 TTATACCAATTGCACATTTAGGCCATTATTC
131 TTATACCAATTGCACAGTTAGGCCATTATTC
* * * *
9556865 CTTTACTCAACAATATTTAACCGTTCATCTGACTGACATAATTGGTACTTTTCTACCAATTGTAC
1 TTTTACTCAACAATATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCAC
* * * *
9556930 AGTTAGGCCATTATTCTTTTACTTAACGGTGTTTAATCGTTCATCTAACT-GACATAATTGATAC
66 AGTTAGGCCATTATTCCTTTACTCAACGGT-ATTAAACGTTCATCTAACTGGA-ATAATTGATAC
* * *
9556994 ATTTCTACCAATTGCGCAGTTAGGTCATTATTC
129 ATTTATACCAATTGCACAGTTAGGCCATTATTC
* * * **
9557027 TTTTACTCAACAGTATTTAATCGTTCATCTAACTGGCATAATTGGTACC-TAATACCAATTGCAC
1 TTTTACTCAACAATATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCAC
9557091 AG
66 AG
9557093 CCTTATGCCT
Statistics
Matches: 200, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
161 102 0.51
162 98 0.49
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (161 bp):
TTTTACTCAACAATATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCAC
AGTTAGGCCATTATTCCTTTACTCAACGGTATTAAACGTTCATCTAACTGGAATAATTGATACAT
TTATACCAATTGCACAGTTAGGCCATTATTC
Found at i:9557489 original size:53 final size:54
Alignment explanation
Indices: 9557420--9557566 Score: 201
Period size: 56 Copynumber: 2.7 Consensus size: 54
9557410 ACATATATTT
*
9557420 TCCCATAC-GAATATTCATACACTTGGTATGAATTTCTTA-GTTCGCACA-CATAG
1 TCCCATACAGAA-ATTCATACACTTAGTATGAATTTCTTATGTTCGCACACCA-AG
* *
9557473 TCCCATACAGAAATTCATACACTTAGTATGAATTTCCTTATTTTTGCACACCAAG
1 TCCCATACAGAAATTCATACACTTAGTATGAATTT-CTTATGTTCGCACACCAAG
*
9557528 TGCCCATACAGAAATTCATACACTTAGTATGAATATCTT
1 T-CCCATACAGAAATTCATACACTTAGTATGAATTTCTT
9557567 GCAATTTTGG
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
53 30 0.35
54 7 0.08
55 13 0.15
56 35 0.41
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (54 bp):
TCCCATACAGAAATTCATACACTTAGTATGAATTTCTTATGTTCGCACACCAAG
Found at i:9563288 original size:15 final size:15
Alignment explanation
Indices: 9563270--9563298 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9563260 TTCATTTCAA
9563270 AATTTTATAAAATAC
1 AATTTTATAAAATAC
9563285 AATTTTATAAAATA
1 AATTTTATAAAATA
9563299 ACTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:9563331 original size:26 final size:25
Alignment explanation
Indices: 9563294--9563342 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
9563284 CAATTTTATA
* *
9563294 AAATAACTTAAAAAAATTAAAATGT
1 AAATAACATAAAAAAATAAAAATGT
*
9563319 AAATAACAATAAAAATATAAAAAT
1 AAATAAC-ATAAAAAAATAAAAAT
9563343 ATATACATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (25 bp):
AAATAACATAAAAAAATAAAAATGT
Found at i:9567774 original size:13 final size:13
Alignment explanation
Indices: 9567756--9567784 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9567746 CAAAATCATA
9567756 TCTAGTATTATAT
1 TCTAGTATTATAT
9567769 TCTAGTATTATAT
1 TCTAGTATTATAT
9567782 TCT
1 TCT
9567785 GTTTATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (13 bp):
TCTAGTATTATAT
Found at i:9569204 original size:20 final size:18
Alignment explanation
Indices: 9569171--9569210 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
9569161 TATTGATAAT
9569171 ATATTTTTTTTAAAAACA
1 ATATTTTTTTTAAAAACA
* *
9569189 ATATTTTATTTATAAA-A
1 ATATTTTTTTTAAAAACA
9569206 ATATT
1 ATATT
9569211 ATTAATGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTTTTTTAAAAACA
Found at i:9570488 original size:39 final size:39
Alignment explanation
Indices: 9570407--9570530 Score: 154
Period size: 39 Copynumber: 3.3 Consensus size: 39
9570397 AAATTAAAAC
*
9570407 AACTATA-ATATATATATAT--A-TATATATATATATATA
1 AACTATATATATATATATATGAACTATATAT-TATGTATA
*
9570443 TA-TATATATATATATATATGAACTATATATTATGTATA
1 AACTATATATATATATATATGAACTATATATTATGTATA
9570481 AAC--TATATATATATATATGAACTATATATATTATGTATA
1 AACTATATATATATATATATGAAC--TATATATTATGTATA
9570520 AACTATATATA
1 AACTATATATA
9570531 CCATGTATAA
Statistics
Matches: 76, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
35 4 0.05
36 13 0.17
37 19 0.25
38 9 0.12
39 25 0.33
41 6 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (39 bp):
AACTATATATATATATATATGAACTATATATTATGTATA
Found at i:9570536 original size:20 final size:19
Alignment explanation
Indices: 9570407--9570548 Score: 155
Period size: 18 Copynumber: 7.5 Consensus size: 19
9570397 AAATTAAAAC
*
9570407 AACTATAATATATATATATA
1 AACTAT-ATATATATGTATA
* *
9570427 TA-TATATATATATATATA
1 AACTATATATATATGTATA
* * *
9570445 TA-TATATATATATATATG
1 AACTATATATATATGTATA
9570463 AACTATATAT-TATGTATA
1 AACTATATATATATGTATA
* *
9570481 AACTATATATATATATATG
1 AACTATATATATATGTATA
9570500 AACTATATATATTATGTATA
1 AACTATATATA-TATGTATA
*
9570520 AACTATATATACCATGTATA
1 AACTATATATA-TATGTATA
9570540 AACTATATA
1 AACTATATA
9570549 GTTTATATAT
Statistics
Matches: 108, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
18 47 0.44
19 27 0.25
20 34 0.31
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (19 bp):
AACTATATATATATGTATA
Found at i:9570548 original size:2 final size:2
Alignment explanation
Indices: 9570410--9570530 Score: 117
Period size: 2 Copynumber: 60.0 Consensus size: 2
9570400 TTAAAACAAC
9570410 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
9570451 TA TA TA TA TA TGA -A CTA TA TA T- TA TG TA TA AA CTA TA TA TA
1 TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
9570492 TA TA TA TGA -A CTA TA TA TA T- TA TG TA TA AA CTA TA TA TA
1 TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
9570531 CCATGTATAA
Statistics
Matches: 100, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
1 5 0.05
2 89 0.89
3 6 0.06
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:9570563 original size:20 final size:19
Alignment explanation
Indices: 9570407--9570767 Score: 161
Period size: 20 Copynumber: 18.5 Consensus size: 19
9570397 AAATTAAAAC
*
9570407 AACTATAATATATATATATA
1 AACTAT-ATATTTATATATA
* *
9570427 TA-TATATATATATATATA
1 AACTATATATTTATATATA
* * *
9570445 TA-TATATATATATATATG
1 AACTATATATTTATATATA
*
9570463 AACTATATA-TTATGTATA
1 AACTATATATTTATATATA
* *
9570481 AACTATATATATATATATG
1 AACTATATATTTATATATA
*
9570500 AACTATATATATTATGTATA
1 AACTATATAT-TTATATATA
** *
9570520 AACTATATATACCATGTATA
1 AACTATATAT-TTATATATA
*
9570540 AACTATATAGTTTATATATG
1 AACTATATA-TTTATATATA
**
9570560 AACTAT-TGAACTATATATA
1 AACTATAT-ATTTATATATA
*
9570579 AACTACATAGTTTATTAATATA
1 AACTATATA-TTTA-T-ATATA
* *
9570601 AATTATATAGTTTATATATG
1 AACTATATA-TTTATATATA
* *
9570621 AA-T-TATATATAAACTATA
1 AACTATATATTTATA-TATA
* *
9570639 CAA-TTTATA-TTATGTAT-
1 -AACTATATATTTATATATA
* * * *
9570656 TA-TGTATAATTATAAATA
1 AACTATATATTTATATATA
*
9570674 ATA-TATACTATGTATAATTATA
1 A-ACTATA-TATTTAT-A-TATA
*
9570696 AA-TAATATATATTATGTATA
1 AACT-ATATAT-TTATATATA
*
9570716 AATTATATAATTTATTAATATA
1 AACTATAT-ATTTA-T-ATATA
9570738 AACTATATAGTTTATATATA
1 AACTATATA-TTTATATATA
* *
9570758 TAGTATATAT
1 AACTATATAT
9570768 GGTTTAGGGT
Statistics
Matches: 268, Mismatches: 48, Indels: 51
0.73 0.13 0.14
Matches are distributed among these distances:
16 6 0.02
17 10 0.04
18 56 0.21
19 50 0.19
20 89 0.33
21 15 0.06
22 42 0.16
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (19 bp):
AACTATATATTTATATATA
Found at i:9570600 original size:22 final size:22
Alignment explanation
Indices: 9570574--9570615 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9570564 ATTGAACTAT
9570574 ATATAAACTACATAGTTTATTA
1 ATATAAACTACATAGTTTATTA
* *
9570596 ATATAAATTATATAGTTTAT
1 ATATAAACTACATAGTTTAT
9570616 ATATGAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATAAACTACATAGTTTATTA
Found at i:9570631 original size:31 final size:32
Alignment explanation
Indices: 9570592--9570669 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
9570582 TACATAGTTT
* *
9570592 ATTA-ATATAAATTATATAGTTTATA-TATGA
1 ATTATATATAAATTATACAATTTATATTATGA
* *
9570622 ATTATATATAAACTATACAATTTATATTATGT
1 ATTATATATAAATTATACAATTTATATTATGA
*
9570654 ATTATGTAT-AATTATA
1 ATTATATATAAATTATA
9570670 AATAATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.10
31 24 0.60
32 12 0.30
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (32 bp):
ATTATATATAAATTATACAATTTATATTATGA
Found at i:9570685 original size:26 final size:26
Alignment explanation
Indices: 9570656--9570722 Score: 116
Period size: 26 Copynumber: 2.5 Consensus size: 26
9570646 TATTATGTAT
9570656 TATGTATAATTATAAATAATATATAC
1 TATGTATAATTATAAATAATATATAC
*
9570682 TATGTATAATTATAAATAATATATAT
1 TATGTATAATTATAAATAATATATAC
9570708 TATGTATAAATTATA
1 TATGTAT-AATTATA
9570723 TAATTTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 32 0.82
27 7 0.18
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (26 bp):
TATGTATAATTATAAATAATATATAC
Found at i:9570948 original size:22 final size:22
Alignment explanation
Indices: 9570886--9570962 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
9570876 GTCAACTATA
*
9570886 TATATTATATAGTTTACATATGAAC
1 TATA-TATATAGTTT--ATATAAAC
* **
9570911 TATATGTATAAATTATATAAAC
1 TATATATATAGTTTATATAAAC
*
9570933 TATATATATAGTTTATTAACAAAC
1 TATATATATAGTTTA-T-ATAAAC
9570957 TATATA
1 TATATA
9570963 AACTACTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
22 19 0.45
23 1 0.02
24 18 0.43
25 4 0.10
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (22 bp):
TATATATATAGTTTATATAAAC
Found at i:9571068 original size:14 final size:13
Alignment explanation
Indices: 9571028--9571164 Score: 60
Period size: 14 Copynumber: 9.8 Consensus size: 13
9571018 ATATGAACTA
*
9571028 TATATATATATAA
1 TATATATATATAG
*
9571041 CATATATTATATAG
1 TATATA-TATATAG
9571055 TATATAGTATATAG
1 TATATA-TATATAG
*
9571069 TATAATTTACATATGAG
1 TAT-A--TATATAT-AG
* * *
9571086 TTATATATAAAAAC
1 -TATATATATATAG
*
9571100 TATATAAACTATAG
1 TATATATA-TATAG
* * *
9571114 TTTATATATAAAC
1 TATATATATATAG
9571127 TATATAT-TATAG
1 TATATATATATAG
* *
9571139 TTGATATTTATATAC
1 -T-ATATATATATAG
9571154 TATATACTATA
1 TATATA-TATA
9571165 GTTGATATTT
Statistics
Matches: 90, Mismatches: 23, Indels: 21
0.67 0.17 0.16
Matches are distributed among these distances:
12 3 0.03
13 26 0.29
14 40 0.44
15 9 0.10
16 4 0.04
17 5 0.06
18 3 0.03
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (13 bp):
TATATATATATAG
Found at i:9571150 original size:27 final size:27
Alignment explanation
Indices: 9571098--9571213 Score: 121
Period size: 27 Copynumber: 4.3 Consensus size: 27
9571088 ATATATAAAA
* *
9571098 ACTATATAAACTATAGTT--TATATATAA
1 ACTATAT-AA-TATAGTTGATATTTATAT
*
9571125 ACTATATATTATAGTTGATATTTATAT
1 ACTATATAATATAGTTGATATTTATAT
*
9571152 ACTATATACTATAGTTGATATTTATAT
1 ACTATATAATATAGTTGATATTTATAT
* *
9571179 TCTATATAATATAATT-ATATTTATAT
1 ACTATATAATATAGTTGATATTTATAT
**
9571205 TTTATATAA
1 ACTATATAA
9571214 AATTCAAAGT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
25 7 0.09
26 19 0.24
27 53 0.67
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.49
Consensus pattern (27 bp):
ACTATATAATATAGTTGATATTTATAT
Found at i:9571315 original size:16 final size:16
Alignment explanation
Indices: 9571277--9571327 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
9571267 AATAAACTAT
*
9571277 TTATATAGTATATACTA
1 TTATATAGTTTATA-TA
*
9571294 CATATATAGTTTATATA
1 -TTATATAGTTTATATA
*
9571311 TTATATAGTTTACATA
1 TTATATAGTTTATATA
9571327 T
1 T
9571328 GAACTATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 15 0.52
17 2 0.07
18 12 0.41
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (16 bp):
TTATATAGTTTATATA
Found at i:9571316 original size:18 final size:19
Alignment explanation
Indices: 9571272--9571317 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
9571262 TAATTAATAA
9571272 ACTATT-TATATAGTATAT
1 ACTATTATATATAGTATAT
* *
9571290 ACTA-CATATATAGTTTAT
1 ACTATTATATATAGTATAT
9571308 A-TATTATATA
1 ACTATTATATA
9571318 GTTTACATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (19 bp):
ACTATTATATATAGTATAT
Found at i:9571369 original size:18 final size:18
Alignment explanation
Indices: 9571346--9571457 Score: 94
Period size: 18 Copynumber: 6.5 Consensus size: 18
9571336 TATAAAAACT
*
9571346 ATATATATAAAGTATATG
1 ATATATATAAACTATATG
9571364 ATATATATAAAC--TATG
1 ATATATATAAACTATATG
* * * *
9571380 -TAT-TATATAGTTTATT
1 ATATATATAAACTATATG
*
9571396 AGTATGTATAAACTATAT-
1 A-TATATATAAACTATATG
9571414 AGTATATATAAACTATATG
1 A-TATATATAAACTATATG
*
9571433 GTATATATAAACTATAT-
1 ATATATATAAACTATATG
9571450 AT-TATATA
1 ATATATATA
9571458 GTTTATTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 5 0.06
15 3 0.04
16 13 0.17
17 1 0.01
18 47 0.60
19 9 0.12
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATATG
Found at i:9571474 original size:5 final size:5
Alignment explanation
Indices: 9571466--9571832 Score: 581
Period size: 5 Copynumber: 73.2 Consensus size: 5
9571456 TAGTTTATTT
9571466 TTATA TTATA TTATA TTATA TTAT- TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
9571515 TTATA TTATA TTATA TTATA -TATA TTATA TTAT- TATATA TATATA TTATATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA T-TATA -T-TATA
9571567 TTATA TTATA TTATA TTATA TTATATA TTATA TTATA TTATA -TATA TTATA
1 TTATA TTATA TTATA TTATA -T-TATA TTATA TTATA TTATA TTATA TTATA
9571618 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
9571668 TTATA TTATA TTATA TTATA TTATA TTATA TT-TA -TATA TATATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTATA
9571717 TTATA TTATA TTATATA TTATA TTATA TATATA TTATA TTATA TTATA
1 TTATA TTATA -T-TATA TTATA TTATA T-TATA TTATA TTATA TTATA
9571765 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -T-TA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
9571813 TTATA TTATA TTA-A TTATA T
1 TTATA TTATA TTATA TTATA T
9571833 AGTTCATTAG
Statistics
Matches: 345, Mismatches: 0, Indels: 34
0.91 0.00 0.09
Matches are distributed among these distances:
3 3 0.01
4 23 0.07
5 284 0.82
6 21 0.06
7 14 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:9571989 original size:61 final size:60
Alignment explanation
Indices: 9571923--9572049 Score: 209
Period size: 61 Copynumber: 2.1 Consensus size: 60
9571913 AGGAACAAAT
9571923 TTTAAATATGAAGCTTAAATTAACAAATTGTAACATTAAATTTGGACTAAATTGAAAAAAA
1 TTTAAATATGAAGCTTAAATTAACAAATTGTAACATTAAATTTGGACTAAATTG-AAAAAA
* * * *
9571984 TTTAAATATGAAGCTTAAATTAATATATTGTATCATTAAATTTGGACTAAATTGAACAAA
1 TTTAAATATGAAGCTTAAATTAACAAATTGTAACATTAAATTTGGACTAAATTGAAAAAA
9572044 TTTAAA
1 TTTAAA
9572050 ACTAGGAGAC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 11 0.18
61 51 0.82
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (60 bp):
TTTAAATATGAAGCTTAAATTAACAAATTGTAACATTAAATTTGGACTAAATTGAAAAAA
Found at i:9572445 original size:103 final size:103
Alignment explanation
Indices: 9572277--9572590 Score: 360
Period size: 103 Copynumber: 2.9 Consensus size: 103
9572267 TCATCTGTGT
* *
9572277 TCATCCCGAAAACCCTACTTTGATCTTCATAAACACCAAAACCCAAACCATTTCGTATTTTTTCG
1 TCATCCCAAAAACCCTACTTTGATCTTCACAAACACCAAAACCCAAACCATTTCGTATTTTTTCG
**
9572342 ATCAAACACCCAAACTTTCAACCCTTGTTCATTTATGC
66 ATCAAACACCCAAAAATTCAACCCTTGTTCATTTATGC
*
9572380 TCATCCCAAAAACCCTACTTTGATCTTCACAAACACCAAAACCCAAACCATTTCGTGTTTTTTCG
1 TCATCCCAAAAACCCTACTTTGATCTTCACAAACACCAAAACCCAAACCATTTCGTATTTTTTCG
*** *
9572445 ATCAAACACCCAAAAATTCAACCCTTGTTCATCCGTGT
66 ATCAAACACCCAAAAATTCAACCCTTGTTCATTTATGC
* * * *
9572483 TCATCACAATTTTTCCCCAAACCATTA-TTTGATCTTCACAAACACCAAAACCTAAACCCATTCC
1 TCATCCCAA---------AAACC-CTACTTTGATCTTCACAAACACCAAAACCCAAA-CCATTTC
* * * *
9572547 TTTTTTTCTTCGATCAAACACCCAATAATTAAACCCTTGTTCAT
55 GTATTTT-TTCGATCAAACACCCAAAAATTCAACCCTTGTTCAT
9572591 CCATGTTCTT
Statistics
Matches: 182, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
103 102 0.56
112 33 0.18
113 13 0.07
114 34 0.19
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (103 bp):
TCATCCCAAAAACCCTACTTTGATCTTCACAAACACCAAAACCCAAACCATTTCGTATTTTTTCG
ATCAAACACCCAAAAATTCAACCCTTGTTCATTTATGC
Found at i:9572790 original size:6 final size:6
Alignment explanation
Indices: 9572781--9572892 Score: 91
Period size: 6 Copynumber: 18.7 Consensus size: 6
9572771 CATATTCTCT
* * *
9572781 AACCCG AACCCA AACCCA AACTCA AACCCA AACCTGA AA-CCA AACCCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACC-CA AACCCA AACCCA
* ** * * * * * *
9572829 AACCCG AACCTG ATCCCA AACCCA AACCCG AATCTA AATCCA AACCCG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
*
9572877 AATCCA AACCCA AACC
1 AACCCA AACCCA AACC
9572893 TAAATCTGAT
Statistics
Matches: 83, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
5 3 0.04
6 77 0.93
7 3 0.04
ACGTcount: A:0.45, C:0.43, G:0.05, T:0.07
Consensus pattern (6 bp):
AACCCA
Found at i:9572871 original size:18 final size:18
Alignment explanation
Indices: 9572844--9572938 Score: 82
Period size: 18 Copynumber: 5.3 Consensus size: 18
9572834 GAACCTGATC
*
9572844 CCAAACCCAAACCCGAAT
1 CCAAATCCAAACCCGAAT
*
9572862 CTAAATCCAAACCCGAAT
1 CCAAATCCAAACCCGAAT
* **
9572880 CCAAACCCAAACCTAAAT
1 CCAAATCCAAACCCGAAT
** * * * *
9572898 CTGATTCTAAACCCCAAC
1 CCAAATCCAAACCCGAAT
*
9572916 CCAAATACAAACCCGAAT
1 CCAAATCCAAACCCGAAT
9572934 CCAAA
1 CCAAA
9572939 CTATTTGAAA
Statistics
Matches: 56, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.45, C:0.38, G:0.04, T:0.13
Consensus pattern (18 bp):
CCAAATCCAAACCCGAAT
Found at i:9572884 original size:36 final size:36
Alignment explanation
Indices: 9572843--9572934 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 36
9572833 CGAACCTGAT
*
9572843 CCCAAACCCAAACCCGAATCTAAATCCAAACCCGAA
1 CCCAAACCCAAACCCGAATCTAAATCCAAACCCCAA
* ** * * *
9572879 TCCAAACCCAAACCTAAATCTGATTCTAAACCCCAA
1 CCCAAACCCAAACCCGAATCTAAATCCAAACCCCAA
**
9572915 CCCAAATACAAACCCGAATC
1 CCCAAACCCAAACCCGAATC
9572935 CAAACTATTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.43, C:0.39, G:0.04, T:0.13
Consensus pattern (36 bp):
CCCAAACCCAAACCCGAATCTAAATCCAAACCCCAA
Found at i:9574676 original size:16 final size:16
Alignment explanation
Indices: 9574651--9574684 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9574641 AGTTTAGAGA
9574651 TAAAAATTATAAATTT
1 TAAAAATTATAAATTT
* *
9574667 TAAAATTTATATATTT
1 TAAAAATTATAAATTT
9574683 TA
1 TA
9574685 GCCTGTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAAATTATAAATTT
Found at i:9579249 original size:189 final size:190
Alignment explanation
Indices: 9578917--9579298 Score: 703
Period size: 189 Copynumber: 2.0 Consensus size: 190
9578907 AACATCAAAA
* *
9578917 CTAATAAGGACCGTGACGACCCAGAGATCATAGTAGGTACTTTCTATCTTTATGATGAGCCTGTA
1 CTAATAAGGACCGTGACGACCCAGAGATCATAGCAGGTACTTTCTATCTTTATGATGAGCCTATA
*
9578982 TTTGTTTTTGATTGATTCGAGTTCTACGTATTCCTATGTTAGTTTGAAATTAGTTAAAAATAAGA
66 TTTGTTTTTGATTGATTCAAGTTCTACGTATTCCTATGTTAGTTTGAAATTAGTTAAAAATAAGA
*
9579047 ATATTTCGTTAGAACCCATCAATAGTGATATGATAGCTATAAATCCACTGGGTCATAGTG
131 ATATTCCGTTAGAACCCATCAATAGTGATATGATAGCTATAAATCCACTGGGTCATAGTG
* *
9579107 CTAATGAGGATCGTGACGACCCAGAGATCATAGCAGGTACTTTCTATCTTTATGATGAGCCTATA
1 CTAATAAGGACCGTGACGACCCAGAGATCATAGCAGGTACTTTCTATCTTTATGATGAGCCTATA
9579172 TTTG-TTTTGATTGATTCAAGTTCTACGTATTCCTATGTTAGTTTGAAATTAGTTAAAAATAAGA
66 TTTGTTTTTGATTGATTCAAGTTCTACGTATTCCTATGTTAGTTTGAAATTAGTTAAAAATAAGA
9579236 ATATTCCGTTAGAACCCATCAATAGTGATATGATAGCTATAAATCCACTGGGTCATAGTG
131 ATATTCCGTTAGAACCCATCAATAGTGATATGATAGCTATAAATCCACTGGGTCATAGTG
9579296 CTA
1 CTA
9579299 GAGTTACACG
Statistics
Matches: 186, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
189 121 0.65
190 65 0.35
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (190 bp):
CTAATAAGGACCGTGACGACCCAGAGATCATAGCAGGTACTTTCTATCTTTATGATGAGCCTATA
TTTGTTTTTGATTGATTCAAGTTCTACGTATTCCTATGTTAGTTTGAAATTAGTTAAAAATAAGA
ATATTCCGTTAGAACCCATCAATAGTGATATGATAGCTATAAATCCACTGGGTCATAGTG
Found at i:9581261 original size:22 final size:21
Alignment explanation
Indices: 9581236--9581280 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 21
9581226 TCTCAAGGGG
*
9581236 CACTGCATATTTCCCGAAGGAC
1 CACTGC-TATGTCCCGAAGGAC
9581258 CA---CTATGTCCCGAAGGAC
1 CACTGCTATGTCCCGAAGGAC
9581276 CACTG
1 CACTG
9581281 ATTGTTCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 7
0.70 0.04 0.26
Matches are distributed among these distances:
18 16 0.84
19 1 0.05
22 2 0.11
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (21 bp):
CACTGCTATGTCCCGAAGGAC
Found at i:9581292 original size:20 final size:18
Alignment explanation
Indices: 9581247--9581316 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
9581237 ACTGCATATT
9581247 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
9581265 TCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACT-A-TG
* *
9581285 TTCCGAAGAACCCACTATG
1 TCCCGAAGGA-CCACTATG
**
9581304 TCATGAAGGACCA
1 TCCCGAAGGACCA
9581317 TGATAATCCC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 18 0.42
19 9 0.21
20 11 0.26
21 5 0.12
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:9584744 original size:65 final size:63
Alignment explanation
Indices: 9584625--9584834 Score: 212
Period size: 65 Copynumber: 3.3 Consensus size: 63
9584615 TTTTTTAGAG
* * *
9584625 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
9584687 ATT
61 ATT
* *
9584690 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
9584754 T
63 T
* * * * *
9584755 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
*
9584819 TGATGCAACGATGCAC
1 TGATGCATCGATGCAC
9584835 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 46 0.37
65 69 0.56
66 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:9589209 original size:35 final size:33
Alignment explanation
Indices: 9589163--9589253 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 33
9589153 GATTTAACAA
9589163 AAAAGGGGAGAAATGTTAAGT-GTTAAAAATGTTTTT
1 AAAA-GGGAGAAATGTTAA-TAG-T-AAAATGTTTTT
*
9589199 AAAAGGGAGAAATGTT-ATAGTAAAATTTTTTT
1 AAAAGGGAGAAATGTTAATAGTAAAATGTTTTT
*
9589231 AAAAGGGAGAAGTGTT-ATAGTAA
1 AAAAGGGAGAAATGTTAATAGTAA
9589254 GGGGGAGTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
32 32 0.62
33 2 0.04
34 2 0.04
35 12 0.23
36 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (33 bp):
AAAAGGGAGAAATGTTAATAGTAAAATGTTTTT
Found at i:9589230 original size:32 final size:32
Alignment explanation
Indices: 9589188--9589253 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
9589178 TTAAGTGTTA
9589188 AAAATGTTTTTAAAAGGGAGAAATGTTATAGT
1 AAAATGTTTTTAAAAGGGAGAAATGTTATAGT
* *
9589220 AAAATTTTTTTAAAAGGGAGAAGTGTTATAGT
1 AAAATGTTTTTAAAAGGGAGAAATGTTATAGT
9589252 AA
1 AA
9589254 GGGGGAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (32 bp):
AAAATGTTTTTAAAAGGGAGAAATGTTATAGT
Found at i:9589704 original size:65 final size:63
Alignment explanation
Indices: 9589635--9589794 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 63
9589625 AATTAAATTG
* *
9589635 AACATCGAATGCATTTCATGCATCGATGCACA-TACCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACAGT--CATGCACCGATGCACTCAGGATATTT-TG
9589698 AA
63 -A
* * *
9589700 AACATCGAATGCATTTGATGCATCGATGCACCAGTCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAGTCATGCACCGATGCACTCAGGATATTTTGA
*
9589764 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
9589795 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 49 0.57
66 5 0.06
67 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAGTCATGCACCGATGCACTCAGGATATTTTGA
Found at i:9593071 original size:2 final size:2
Alignment explanation
Indices: 9593064--9593114 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
9593054 TACACTAGTG
9593064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9593106 TA TA TA TA T
1 TA TA TA TA T
9593115 TCTAATTTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9594925 original size:20 final size:20
Alignment explanation
Indices: 9594909--9594977 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
9594899 TTTGATTATG
* *
9594909 CTTGATATTGCTTGATTTTG
1 CTTGATATTGCTTGATTCTA
* * * *
9594929 TTTTATATTGTTTGCTTCTA
1 CTTGATATTGCTTGATTCTA
*
9594949 TTTGATATTGCTTGATTCTA
1 CTTGATATTGCTTGATTCTA
9594969 CTTGATATT
1 CTTGATATT
9594978 TGTAAGGGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.58
Consensus pattern (20 bp):
CTTGATATTGCTTGATTCTA
Found at i:9595097 original size:23 final size:23
Alignment explanation
Indices: 9595082--9595188 Score: 169
Period size: 23 Copynumber: 4.7 Consensus size: 23
9595072 TGCTTGTTGT
9595082 ATTGATGCAATGATGCTTGCTAA
1 ATTGATGCAATGATGCTTGCTAA
*
9595105 ACTGATGCAATGATGCTTGCTAA
1 ATTGATGCAATGATGCTTGCTAA
*
9595128 ATTGATGCAATGATGCTTGATAA
1 ATTGATGCAATGATGCTTGCTAA
*
9595151 ATTGATGCAATGATGCTTGCTGA
1 ATTGATGCAATGATGCTTGCTAA
**
9595174 ATTGAAACAATGATG
1 ATTGATGCAATGATG
9595189 GTTGTCGGTT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 77 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTGATGCAATGATGCTTGCTAA
Found at i:9595790 original size:13 final size:13
Alignment explanation
Indices: 9595771--9595808 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
9595761 TTAATTTATG
9595771 ATTATAAATAA-A
1 ATTATAAATAAGA
9595783 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
9595798 ATTATAAATAA
1 ATTATAAATAA
9595809 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:9595850 original size:20 final size:19
Alignment explanation
Indices: 9595824--9595881 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
9595814 AGAATTGGAA
9595824 TTAATATAAAAACTAAATT
1 TTAATATAAAAACTAAATT
* *
9595843 TATAATATATAAATTATAA--
1 T-TAATATAAAAACTA-AATT
9595862 TTAATATAAAAACTAAATT
1 TTAATATAAAAACTAAATT
9595881 T
1 T
9595882 CAAAAAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
17 2 0.06
18 12 0.39
19 3 0.10
20 12 0.39
21 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATATAAAAACTAAATT
Found at i:9595868 original size:18 final size:19
Alignment explanation
Indices: 9595788--9595871 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
9595778 ATAAAATTTA
*
9595788 TAATAT-AAGAATTATAAA
1 TAATATAAAGAATTATAAT
**
9595806 TAATATAAAGAATTGGAAT
1 TAATATAAAGAATTATAAT
*
9595825 TAATATAAA-AACTA-AATTT
1 TAATATAAAGAATTATAA--T
*
9595844 ATAATATATA-AATTATAAT
1 -TAATATAAAGAATTATAAT
9595863 TAATATAAA
1 TAATATAAA
9595872 AACTAAATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 2 0.04
18 17 0.32
19 20 0.38
20 12 0.23
21 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (19 bp):
TAATATAAAGAATTATAAT
Found at i:9596788 original size:21 final size:22
Alignment explanation
Indices: 9596763--9596834 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 22
9596753 GCCTGACCCG
9596763 AATATATTAATATT-TTAAAAT
1 AATATATTAATATTATTAAAAT
* *
9596784 AATATATTTATAATTATT--TAT
1 AATATATTAAT-ATTATTAAAAT
* *
9596805 TATATTTTAA-ATTATTAAAAT
1 AATATATTAATATTATTAAAAT
9596826 AATATATTA
1 AATATATTA
9596835 TATAATAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 6 0.15
21 28 0.72
22 3 0.08
23 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATATTAATATTATTAAAAT
Found at i:9596825 original size:42 final size:43
Alignment explanation
Indices: 9596764--9596860 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 43
9596754 CCTGACCCGA
* *
9596764 ATATATTAATATTTTAAAATAATATATT-TATAATTAT-TTATT
1 ATATTTTAATATTTTAAAATAATATATTATATAATAATGTT-TT
9596806 ATATTTTAA-ATTATTAAAATAATATATTATATAATAATGTTTT
1 ATATTTTAATATT-TTAAAATAATATATTATATAATAATGTTTT
9596849 ATATTTTTAATA
1 ATA-TTTTAATA
9596861 ATATAAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
41 3 0.06
42 23 0.48
43 13 0.27
44 8 0.17
45 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (43 bp):
ATATTTTAATATTTTAAAATAATATATTATATAATAATGTTTT
Found at i:9613179 original size:19 final size:19
Alignment explanation
Indices: 9613137--9613190 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
9613127 TATCTAGTTT
*
9613137 AGAAATA-AAAAAGGAAAAAG
1 AGAAATAGAAAAA--AAAAAA
9613157 AGAAA-AGCAAAAAAAAAAA
1 AGAAATAG-AAAAAAAAAAA
9613176 AGAAATAGAAAAAAA
1 AGAAATAGAAAAAAA
9613191 GAATACATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 18 0.60
20 7 0.23
21 5 0.17
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.04
Consensus pattern (19 bp):
AGAAATAGAAAAAAAAAAA
Found at i:9615076 original size:36 final size:36
Alignment explanation
Indices: 9615036--9615225 Score: 263
Period size: 36 Copynumber: 5.2 Consensus size: 36
9615026 TTCGACCTTC
* **
9615036 GAAGCAAATCATTTTAAGCCTTCACAAAAGAGTAGT
1 GAAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGT
* *
9615072 GAAGCAAATCATCTTAAGCCTTTACGAAAGAGTAGT
1 GAAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGT
* *
9615108 GAAGCAAATCAATCTTAAGCATTCACGGATGAGTAGT
1 GAAGCAAATC-ATCTTAAGCCTTCACGGAAGAGTAGT
* * *
9615145 GAAGCAGATCATCTTCAGCCTTCACGGAATAGTAGT
1 GAAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGT
* *
9615181 GAAACAAATCATCTTAAGCCTTCACAGAAGAGTAGT
1 GAAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGT
9615217 GAAGCAAAT
1 GAAGCAAAT
9615226 TAATATCGAG
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
36 104 0.77
37 31 0.23
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (36 bp):
GAAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGT
Found at i:9615133 original size:73 final size:72
Alignment explanation
Indices: 9615036--9615225 Score: 272
Period size: 73 Copynumber: 2.6 Consensus size: 72
9615026 TTCGACCTTC
* * *
9615036 GAAGCAAATCATTTTAAGCCTTCACAAAAGAGTAGTGAAGCAAATCATCTTAAGCCTTTACGAAA
1 GAAGCAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCATCTTAAGCCTTCACGAAA
9615101 GAGTAGT
66 GAGTAGT
* * * * * *
9615108 GAAGCAAATCAATCTTAAGCATTCACGGATGAGTAGTGAAGCAGATCATCTTCAGCCTTCACGGA
1 GAAGCAAATC-ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCATCTTAAGCCTTCACGAA
*
9615173 ATAGTAGT
65 AGAGTAGT
*
9615181 GAAACAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
1 GAAGCAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
9615226 TAATATCGAG
Statistics
Matches: 102, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
72 41 0.40
73 61 0.60
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (72 bp):
GAAGCAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCATCTTAAGCCTTCACGAAA
GAGTAGT
Found at i:9615305 original size:55 final size:55
Alignment explanation
Indices: 9615245--9615809 Score: 631
Period size: 55 Copynumber: 10.3 Consensus size: 55
9615235 GTCTGATCCC
* * * *
9615245 CCCTGAAAGAATAGGGAGC-ATACACATTTAT-TGAAGATTGTTCGAG-TCTTATACT
1 CCCTGAAAGAATAGGGAGCGA-ACCCGTTT-TCAGAAGATTGCTCGAGTTC-TATACT
* * ** * ** *
9615300 CCCTGAAAGAATAAGGAGAAGAA-ATGTTTGCTCAAGATTGTTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAG-CGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * * *
9615355 CCCTGGAGGAATAAGGAGCGAACCCGTTTTCAGAATATTGCTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
* *
9615410 CCCT-AAAGAAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCAAGTTCTATACT
1 CCCTGAAAG-AATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
* *
9615465 CCCTGAAGGAATAGGGAGCGAACCCATTTTCAGAAGATTGCTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
* ** * *
9615520 CCCTGAAGGAATAGGGAGTAAACCCGTTTTCAGAATATTGCTCAAGTTCTATACT
1 CCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
* *
9615575 CCCTG-AAGCAATAGGGAGCGAACCAGTTTTCAAAAGATTGCTCGAGTTCTATACT
1 CCCTGAAAG-AATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * * *
9615630 CCCTGAAAGAATATGGAGCGAACCGGTTTTCAAAAGATTGTTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * * ** *
9615685 TCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTTTTCGAGTTATATACT
1 CCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * * * * *
9615740 CCCTGAAAAAATAGGGAGTGGACCCGTTTTCAGAAAACTGTTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
9615795 CCCTG-AAGCAATAGG
1 CCCTGAAAG-AATAGG
9615810 TATCAGACCT
Statistics
Matches: 440, Mismatches: 60, Indels: 20
0.85 0.12 0.04
Matches are distributed among these distances:
54 9 0.02
55 421 0.96
56 9 0.02
57 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (55 bp):
CCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACT
Found at i:9615532 original size:165 final size:165
Alignment explanation
Indices: 9615333--9615809 Score: 695
Period size: 165 Copynumber: 2.9 Consensus size: 165
9615323 ATGTTTGCTC
* * *
9615333 AAGATTGTTCGAGTTCTATACTCCCTGGAGGAATAAGGAGCGAACCCGTTTTCAGAATATTGCTC
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAATATTGCTC
*
9615398 GAGTTCTATACTCCCTAAAGAAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCAAGTTCTATA
66 GAGTTCTATACTCCCTAAAGAAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTATA
*
9615463 CTCCCTGAAGGAATAGGGAGCGAACCCATTTTCAG
131 CTCCCTGAAGGAATAGGGAGCGAACCCATTTTCAA
* *
9615498 AAGATTGCTCGAGTTCTATACTCCCTGAAGGAATAGGGAGTAAACCCGTTTTCAGAATATTGCTC
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAATATTGCTC
* * * *
9615563 AAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCAGTTTTCAAAAGATTGCTCGAGTTCTATA
66 GAGTTCTATACTCCCTAAAGAAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTATA
* * **
9615628 CTCCCTGAAAGAATATGGAGCGAACCGGTTTTCAA
131 CTCCCTGAAGGAATAGGGAGCGAACCCATTTTCAA
* * **
9615663 AAGATTGTTCGAGTTCTATACTTCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTTTTC
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAATATTGCTC
* * * * * * *
9615728 GAGTTATATACTCCCTGAAA-AAATAGGGAGTGGACCCGTTTTCAGAAAACTGTTCGAGTTCTAT
66 GAGTTCTATACTCCCT-AAAGAAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTAT
*
9615792 ACTCCCTGAAGCAATAGG
130 ACTCCCTGAAGGAATAGG
9615810 TATCAGACCT
Statistics
Matches: 276, Mismatches: 35, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
165 274 0.99
166 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (165 bp):
AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAATATTGCTC
GAGTTCTATACTCCCTAAAGAAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTATA
CTCCCTGAAGGAATAGGGAGCGAACCCATTTTCAA
Found at i:9615848 original size:110 final size:108
Alignment explanation
Indices: 9615336--9615863 Score: 512
Period size: 110 Copynumber: 4.8 Consensus size: 108
9615326 TTTGCTCAAG
* * * * * *
9615336 ATTGTTCGAGTTCTATACTCCCTGGAGGAATAAGGAGC-GAACCCGTTTTCAGAATATTGCTCGA
1 ATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCAG-ACCAGTTTTCAGAAGATT--TTGA
* * *
9615400 GTTCTATACTCCCT-AAAGAAATAGGGAGCGAACCAGTTTTCAGAAG
63 GTTCTATACTCCCTGAAAG-AATAGGGAGTGAACCCGTTTTCAGAAA
* * * *
9615446 ATTGCTCAAGTTCTATACTCCCTGAAGGAATAGGGAGC-GAACCCA-TTTTCAGAAGATTGCTCG
1 ATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCAG-A-CCAGTTTTCAGAAGATT--TTG
* * *
9615509 AGTTCTATACTCCCTGAAGGAATAGGGAGTAAACCCGTTTTCAGAAT
62 AGTTCTATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCAGAAA
* * * *
9615556 ATTGCTCAAGTTCTATACTCCCTGAAGCAATAGGGAGC-GAACCAGTTTTCAAAAGATTGCTCGA
1 ATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCAG-ACCAGTTTTCAGAAGATT--TTGA
* * *
9615620 GTTCTATACTCCCTGAAAGAATATGGAGCGAACCGGTTTTCA-AAA
63 GTTCTATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCAGAAA
* * * *
9615665 GATTGTTCGAGTTCTATACTTCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTTTTCGA
1 -ATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCAGACCAGTTTTCAGAAGA-TTTT-GA
* * *
9615730 GTTATATACTCCCTGAAAAAATAGGGAGTGGACCCGTTTTCAGAAA
63 GTTCTATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCAGAAA
* * * * *
9615776 ACTGTTCGAGTTCTATACTCCCTGAAGCAATAGGTATCAGACCTGTTTGTC-GAATATTTTGAAA
1 ATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCAGACCAGTTT-TCAGAAGATTTTG--A
* * *
9615840 ATCCTATACTCTCTGAAAGAATAG
63 GTTCTATACTCCCTGAAAGAATAG
9615864 AGAAAATATG
Statistics
Matches: 361, Mismatches: 46, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
108 1 0.00
109 10 0.03
110 338 0.94
111 12 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (108 bp):
ATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCAGACCAGTTTTCAGAAGATTTTGAGTT
CTATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCAGAAA
Found at i:9616077 original size:2 final size:2
Alignment explanation
Indices: 9616070--9616109 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9616060 TACTCCAATT
9616070 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9616110 CTAATTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9616188 original size:17 final size:16
Alignment explanation
Indices: 9616162--9616196 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
9616152 TTATATTATC
9616162 ATGTGTGTGTTTAATT
1 ATGTGTGTGTTTAATT
9616178 ATGTAGTGTGTTTAATT
1 ATGT-GTGTGTTTAATT
9616195 AT
1 AT
9616197 CTATGTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (16 bp):
ATGTGTGTGTTTAATT
Found at i:9616201 original size:21 final size:21
Alignment explanation
Indices: 9616151--9616205 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 21
9616141 TGATTATCTA
9616151 TTTATATTATC-ATGT-GTGTG
1 TTTA-ATTATCTATGTAGTGTG
9616171 TTT-A--AT-TATGTAGTGTG
1 TTTAATTATCTATGTAGTGTG
9616188 TTTAATTATCTATGTAGT
1 TTTAATTATCTATGTAGT
9616206 TATGCTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
16 6 0.21
17 8 0.28
18 2 0.07
20 5 0.17
21 8 0.28
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.55
Consensus pattern (21 bp):
TTTAATTATCTATGTAGTGTG
Found at i:9616226 original size:2 final size:2
Alignment explanation
Indices: 9616219--9616262 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
9616209 GCTTGTGATC
**
9616219 AT AT AT AT AT GC 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
9616261 AT
1 AT
9616263 GTTATGATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9621071 original size:16 final size:16
Alignment explanation
Indices: 9621047--9621081 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9621037 AGATATGAGA
9621047 AAATCAATTTAAATTT
1 AAATCAATTTAAATTT
* *
9621063 AAATTAATTTAATTTT
1 AAATCAATTTAAATTT
9621079 AAA
1 AAA
9621082 ATAACGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATCAATTTAAATTT
Found at i:9631975 original size:16 final size:15
Alignment explanation
Indices: 9631956--9631985 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9631946 TATTTAATAA
9631956 ATAAATATTATTTTTT
1 ATAAATATT-TTTTTT
9631972 ATAAATATTTTTTT
1 ATAAATATTTTTTT
9631986 AAAATACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATAAATATTTTTTTT
Found at i:9632596 original size:31 final size:31
Alignment explanation
Indices: 9632561--9632632 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
9632551 TTATTTTTTT
*
9632561 TATTAAATAAAAAATATTAACT-CATACATCA
1 TATTAAATAAAAAACATTAACTCCA-ACATCA
* * * *
9632592 TATTAGATTAGAAACATTAACTCCAACATTA
1 TATTAAATAAAAAACATTAACTCCAACATCA
9632623 TATTACAATA
1 TATTA-AATA
9632633 CAATAGAAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (31 bp):
TATTAAATAAAAAACATTAACTCCAACATCA
Found at i:9633394 original size:21 final size:21
Alignment explanation
Indices: 9633362--9633409 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
9633352 TTGGCCAAAA
9633362 ATATCA-TTCAATGATATGAT
1 ATATCACTTCAATGATATGAT
9633382 ATATCACTTCAATGATATGAT
1 ATATCACTTCAATGATATGAT
9633403 ATATCAC
1 ATATCAC
9633410 CGAATTGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATCACTTCAATGATATGAT
Found at i:9633539 original size:136 final size:135
Alignment explanation
Indices: 9633367--9633613 Score: 381
Period size: 136 Copynumber: 1.8 Consensus size: 135
9633357 CAAAAATATC
*
9633367 ATTCAATGATATGATATATCACTTCAATGATATGATATATCACCGAATTGAAGTGATATATCACT
1 ATTCAATGATATGATATATCACTTCAATGATATGATATATCACCGAATTGAAGTGATAGATCACT
* *
9633432 AAAAAGTTTCATGTCATTGTGCATTAAATGGTCTCTTAGATAAAAGACATATTTCAATAAAAAAA
66 AAAAAGTTTC-TGTCATTGTGCATTAAATGGTCTCTGAGAAAAAAGACATATTTCAATAAAAAAA
9633497 TAGGTT
130 TAGGTT
* * *
9633503 ATTCAATGGTATGATATATCAC-TGAATTGA-AGTGATATATCACTGAATTGAAGTGATAGATCA
1 ATTCAATGATATGATATATCACTTCAA-TGATA-TGATATATCACCGAATTGAAGTGATAGATCA
* *
9633566 CTGAAAAGTTTCTGTCATTGTGCATTAAATTGTCTCTGAGAAAAAAGA
64 CTAAAAAGTTTCTGTCATTGTGCATTAAATGGTCTCTGAGAAAAAAGA
9633614 TGTTTTTCAT
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
135 37 0.37
136 64 0.63
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (135 bp):
ATTCAATGATATGATATATCACTTCAATGATATGATATATCACCGAATTGAAGTGATAGATCACT
AAAAAGTTTCTGTCATTGTGCATTAAATGGTCTCTGAGAAAAAAGACATATTTCAATAAAAAAAT
AGGTT
Found at i:9633540 original size:21 final size:21
Alignment explanation
Indices: 9633514--9633570 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
9633504 TTCAATGGTA
9633514 TGATATATCACTGAATTGAAG
1 TGATATATCACTGAATTGAAG
9633535 TGATATATCACTGAATTGAAG
1 TGATATATCACTGAATTGAAG
*
9633556 TGATAGATCACTGAA
1 TGATATATCACTGAA
9633571 AAGTTTCTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (21 bp):
TGATATATCACTGAATTGAAG
Found at i:9634552 original size:28 final size:28
Alignment explanation
Indices: 9634514--9634579 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
9634504 TGAATTTAAG
9634514 ATGACGCGCAACTGTGCGTCATAAATTT
1 ATGACGCGCAACTGTGCGTCATAAATTT
* *
9634542 ATGACGTGCAACTGTGCGTCATAAGTTT
1 ATGACGCGCAACTGTGCGTCATAAATTT
9634570 ATGACGCGCA
1 ATGACGCGCA
9634580 TTTATGACGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (28 bp):
ATGACGCGCAACTGTGCGTCATAAATTT
Found at i:9643128 original size:22 final size:21
Alignment explanation
Indices: 9643103--9643144 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9643093 ATTTTATGGT
*
9643103 TTTTTTAATCTAAATTATATTA
1 TTTTATAATC-AAATTATATTA
*
9643125 TTTTATAATCAACTTATATT
1 TTTTATAATCAAATTATATT
9643145 TTTACGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATAATCAAATTATATTA
Found at i:9646411 original size:35 final size:35
Alignment explanation
Indices: 9646372--9646439 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
9646362 CTTAATCTCA
*
9646372 AAAATATAAAATAGTAATACGGAAAGTAAGGGTCG
1 AAAATATAAAATAGTAATAAGGAAAGTAAGGGTCG
9646407 AAAATATAAAATAGTAATAAGGAAAGTAAGGGT
1 AAAATATAAAATAGTAATAAGGAAAGTAAGGGT
9646440 TAATCCATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.21
Consensus pattern (35 bp):
AAAATATAAAATAGTAATAAGGAAAGTAAGGGTCG
Found at i:9659229 original size:32 final size:32
Alignment explanation
Indices: 9659183--9659261 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
9659173 AGCAGTTTTG
9659183 CATTCAGATAATGCACAACAGAATCAATGTTA
1 CATTCAGATAATGCACAACAGAATCAATGTTA
* * *
9659215 CATTTAGATAATGCACAACAGAATCAGTGTTG
1 CATTCAGATAATGCACAACAGAATCAATGTTA
*
9659247 TATTCAGATAATGCA
1 CATTCAGATAATGCA
9659262 TACGAGTGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (32 bp):
CATTCAGATAATGCACAACAGAATCAATGTTA
Found at i:9672872 original size:3 final size:3
Alignment explanation
Indices: 9672866--9672931 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
9672856 TTTACCCATT
* * * *
9672866 TTA TTA TTG TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9672914 -TA TATA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA
9672932 AAATAATAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:9674414 original size:24 final size:23
Alignment explanation
Indices: 9674369--9674415 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
9674359 TATTTTAAAA
*
9674369 TTAAATATTATATATAATTTTAT
1 TTAAATATTAAATATAATTTTAT
9674392 TTAAATTATTAAAT-TAATATTTAT
1 TTAAA-TATTAAATATAAT-TTTAT
9674416 CAAAGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAATATTAAATATAATTTTAT
Found at i:9678344 original size:16 final size:16
Alignment explanation
Indices: 9678325--9678358 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
9678315 TTTGGGATCA
*
9678325 ATACCTTTTTGCATAC
1 ATACATTTTTGCATAC
9678341 ATACATTTTTGCATAC
1 ATACATTTTTGCATAC
9678357 AT
1 AT
9678359 TAATTATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (16 bp):
ATACATTTTTGCATAC
Found at i:9686808 original size:93 final size:93
Alignment explanation
Indices: 9686650--9687239 Score: 747
Period size: 93 Copynumber: 6.1 Consensus size: 93
9686640 ACAAGTGTCG
9686650 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
*
9686715 AACCCCATCATTGGACTTGAAAGATGAG
66 AACCCCATCATTGGACTTGAAAGATGAA
* *
9686743 TGTGCTCATAGGATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
9686808 AACCCCATCATTGGACTTGAAAGATGAA
66 AACCCCATCATTGGACTTGAAAGATGAA
9686836 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
*
9686901 AACCCCATCATTAGACTTGAAAGATGAA
66 AACCCCATCATTGGACTTGAAAGATGAA
* *
9686929 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-ACTAC
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA-
* * *
9686993 AGA-CCAATCATTGGATTTGAAAGATGAA
65 AAACCCCATCATTGGACTTGAAAGATGAA
* * * ** *
9687021 TGTACTCATAGTACAAATAAAAAGAC-CCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTG
1 TGTGCTCATAG--C--AT-------CTTC--T-GGA-AGTG--------TTCTTTGAGTTATCTG
9687085 ATCTGGTTTGGTATGAACCCCAAAACCCCATCATTGGACTTGAAAGATGAA
43 ATCTGGTTTGGTATGAACCCCAAAACCCCATCATTGGACTTGAAAGATGAA
**
9687136 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACTACA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG-AACCCCA
* * *
9687201 GAA-CCAATCATTGGATTTGAAAGATGAA
65 AAACCCCATCATTGGACTTGAAAGATGAA
9687229 TGTGCTCATAG
1 TGTGCTCATAG
9687240 TACAAATAAA
Statistics
Matches: 435, Mismatches: 34, Indels: 56
0.83 0.06 0.11
Matches are distributed among these distances:
92 34 0.08
93 306 0.70
94 8 0.02
96 2 0.00
101 1 0.00
102 3 0.01
103 2 0.00
104 2 0.00
105 3 0.01
106 1 0.00
111 2 0.00
113 1 0.00
114 35 0.08
115 35 0.08
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (93 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
AACCCCATCATTGGACTTGAAAGATGAA
Found at i:9687198 original size:207 final size:208
Alignment explanation
Indices: 9686843--9687342 Score: 887
Period size: 207 Copynumber: 2.4 Consensus size: 208
9686833 GAATGTGCTC
9686843 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCA
*
9686908 TCATTAGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
66 TCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
9686973 CTGGTTTGGTATGAAACTACAG-ACCAATCATTGGATTTGAAAGATGAATGTACTCATAGTACAA
131 CTGGTTTGGTATGAAACTACAGAACCAATCATTGGATTTGAAAGATGAATGTACTCATAGTACAA
9687037 ATAAAAAGACCCA
196 ATAAAAAGACCCA
*
9687050 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCA
9687115 TCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
66 TCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
*
9687180 CTGGTTTGGTATGAAACTACAGAACCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTACAA
131 CTGGTTTGGTATGAAACTACAGAACCAATCATTGGATTTGAAAGATGAATGTACTCATAGTACAA
*
9687245 ATAAAGAGACCCA
196 ATAAAAAGACCCA
* * * * *
9687258 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCACAGAA-CCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCA
* *
9687322 TCATTGGAATTAAAAGATGAA
66 TCATTGGACTTGAAAGATGAA
9687343 CTGCATGATC
Statistics
Matches: 280, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
207 172 0.61
208 108 0.39
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (208 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCA
TCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
CTGGTTTGGTATGAAACTACAGAACCAATCATTGGATTTGAAAGATGAATGTACTCATAGTACAA
ATAAAAAGACCCA
Found at i:9688483 original size:113 final size:113
Alignment explanation
Indices: 9688028--9688712 Score: 792
Period size: 112 Copynumber: 6.0 Consensus size: 113
9688018 TAGCAAAGTT
* * *
9688028 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
* * *
9688093 AGAAGGAAGAAGAAATTAATAATGAGAAGAATTTATTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
9688141 TCAAATCCATCATTTGA-AGATCAGA-TTTTCCAGAAAAAGTTCATAATGAGAAAAACTCATCTG
1 TCAAATCCATCATTTGATGGATCA-ACTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTG
*
9688204 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
9688253 TTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAGATAGAGTTCATAATGAGAAGAA--C-TCATC
* *
9688318 TGAAAAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
9688369 TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
*
9688434 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ** *
9688482 TCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
* ** *
9688546 AGAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
9688590 AT-AATTCTATCACAGAAGCAGATAGATTAGTATCAACCTTTCCAGATAAAGTTCATAATGAGAA
1 -TCAA----ATC-C---ATCA-TTTGA-T-GGATCAACTTTTCCAGATAGAGTTCATAATGAGAA
* * ** *
9688654 GAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
9688713 AATGACTCTA
Statistics
Matches: 493, Mismatches: 56, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
108 33 0.07
109 3 0.01
110 1 0.00
111 1 0.00
112 133 0.27
113 131 0.27
114 1 0.00
115 1 0.00
116 104 0.21
117 3 0.01
118 1 0.00
119 14 0.03
120 30 0.06
122 1 0.00
123 2 0.00
124 34 0.07
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAACTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:9688661 original size:120 final size:119
Alignment explanation
Indices: 9688509--9688791 Score: 365
Period size: 124 Copynumber: 2.3 Consensus size: 119
9688499 TGGATCAGTT
*
9688509 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGC
1 TTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGC
* * * * **
9688574 TTATTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGTATCAACC
66 TTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACC
* *
9688628 TTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTG-A--AG-AAGAAAAAGTTCACAATGAGA
* * * *
9688693 AGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCC
61 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACC
9688752 ---CCAGCGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 TTTCCA--GAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
9688792 AGAGAAGAAT
Statistics
Matches: 144, Mismatches: 13, Indels: 15
0.84 0.08 0.09
Matches are distributed among these distances:
118 2 0.01
119 10 0.07
120 27 0.19
121 5 0.03
122 28 0.19
123 4 0.03
124 68 0.47
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (119 bp):
TTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGC
TTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACC
Found at i:9688955 original size:12 final size:12
Alignment explanation
Indices: 9688940--9689000 Score: 70
Period size: 12 Copynumber: 4.8 Consensus size: 12
9688930 TACCCATTTT
*
9688940 ATTATTGTTATA
1 ATTATTATTATA
9688952 ATTATTATTATA
1 ATTATTATTATA
9688964 ATTATTATTCTTATA
1 ATTATTA---TTATA
9688979 ATTATTA-TATA
1 ATTATTATTATA
9688990 TATTATTATTA
1 -ATTATTATTA
9689001 AATAATAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
11 4 0.09
12 25 0.58
13 2 0.05
15 12 0.28
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTATTATTATA
Found at i:9688977 original size:27 final size:27
Alignment explanation
Indices: 9688938--9688999 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
9688928 TTTACCCATT
*
9688938 TTATTATTGTTATAATTATTAT-TATAA
1 TTATTATTCTTATAATTATTATATAT-A
9688965 TTATTATTCTTATAATTATTATATATA
1 TTATTATTCTTATAATTATTATATATA
9688992 TTATTATT
1 TTATTATT
9689000 AAATAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
27 30 0.91
28 3 0.09
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATTATTCTTATAATTATTATATATA
Found at i:9691983 original size:13 final size:13
Alignment explanation
Indices: 9691934--9691984 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
9691924 TCATAAATCC
*
9691934 ATGACGCGCATTT
1 ATGATGCGCATTT
* *
9691947 ATGATACGTATTT
1 ATGATGCGCATTT
*
9691960 ATGACGCGCATTT
1 ATGATGCGCATTT
*
9691973 ATGATGTGCATT
1 ATGATGCGCATT
9691985 GCGCATCATT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (13 bp):
ATGATGCGCATTT
Found at i:9692062 original size:2 final size:2
Alignment explanation
Indices: 9692055--9692097 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
9692045 TGACGTAAAT
9692055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9692097 T
1 T
9692098 TGTAGATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9697198 original size:4 final size:4
Alignment explanation
Indices: 9697191--9697318 Score: 73
Period size: 4 Copynumber: 30.8 Consensus size: 4
9697181 ATAGTAAGTA
* * * * *
9697191 AAAT AAAT ATAAA AAAT AAAT AAAT AAAT AAAA AGAAG AAAA AAAT ATAT
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
* *
9697241 AAAT AAAAC AAAT AAAT AAA- ATAAT -AAT AAA- AAAGT AAAA ATAAT
1 AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAA-T AAAT A-AAT
* * *
9697286 ATAT ATAT ATAT ATAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT AAA
9697319 AAAGAGTAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 22
0.73 0.10 0.16
Matches are distributed among these distances:
3 7 0.07
4 70 0.71
5 22 0.22
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:9697208 original size:13 final size:13
Alignment explanation
Indices: 9697190--9697318 Score: 59
Period size: 13 Copynumber: 9.6 Consensus size: 13
9697180 AATAGTAAGT
9697190 AAAATAAATATAA
1 AAAATAAATATAA
9697203 AAAATAAATA-AA
1 AAAATAAATATAA
* * *
9697215 TAAATAAAAAGAA
1 AAAATAAATATAA
*
9697228 GAAAAAAATATATAAA
1 -AAAATAA-ATAT-AA
*
9697244 TAAAACAAATA-AA
1 -AAAATAAATATAA
9697257 TAAAAT-AATAATAA
1 -AAAATAAAT-ATAA
*
9697271 AAAAGTAAAAATAA
1 AAAA-TAAATATAA
* * * *
9697285 TATATATATATAT
1 AAAATAAATATAA
*
9697298 ATAATAAATA-AA
1 AAAATAAATATAA
9697310 TAAAATAAA
1 -AAAATAAA
9697319 AAAGAGTAAA
Statistics
Matches: 86, Mismatches: 21, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
12 14 0.16
13 43 0.50
14 14 0.16
15 7 0.08
16 8 0.09
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (13 bp):
AAAATAAATATAA
Found at i:9697211 original size:17 final size:17
Alignment explanation
Indices: 9697191--9697321 Score: 71
Period size: 17 Copynumber: 7.9 Consensus size: 17
9697181 ATAGTAAGTA
9697191 AAATAAATATAAAAAAT
1 AAATAAATATAAAAAAT
*
9697208 AAAT-AA-ATAAATAA-
1 AAATAAATATAAAAAAT
* *
9697222 AAA-GAAGA-AAAAAAT
1 AAATAAATATAAAAAAT
*
9697237 ATATAAATA-AAACAAAT
1 AAATAAATATAAA-AAAT
9697254 AAATAAAATAATAATAAAA-
1 AAAT-AAAT-ATAA-AAAAT
* * * *
9697273 AAGTAAAAATAATATAT
1 AAATAAATATAAAAAAT
* * *
9697290 ATATATATATAATAAAT
1 AAATAAATATAAAAAAT
9697307 AAATAAA-ATAAAAAA
1 AAATAAATATAAAAAA
9697322 GAGTAAATAT
Statistics
Matches: 86, Mismatches: 18, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
14 10 0.12
15 10 0.12
16 17 0.20
17 32 0.37
18 7 0.08
19 4 0.05
20 5 0.06
21 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATAAATATAAAAAAT
Found at i:9697219 original size:25 final size:24
Alignment explanation
Indices: 9697191--9697330 Score: 89
Period size: 21 Copynumber: 5.9 Consensus size: 24
9697181 ATAGTAAGTA
9697191 AAATAAATATAAAAAATAAATAAAT
1 AAATAAATA-AAAAAATAAATAAAT
* *
9697216 AAATAAA-AAGAAGA-AAA-AAAT
1 AAATAAATAAAAAAATAAATAAAT
*
9697237 ATATAAATAAAACAAATAAATAAA-
1 AAATAAATAAAA-AAATAAATAAAT
*
9697261 ATAAT-AATAAAAAAGT-AA-AAAT
1 A-AATAAATAAAAAAATAAATAAAT
* * * *
9697283 -AATATATATATATATATAATAAAT
1 AAATAAATAAAAAAATA-AATAAAT
9697307 AAATAAAATAAAAAAGAGTAAATA
1 AAAT-AAATAAAAAA-A-TAAATA
9697331 TATATATATA
Statistics
Matches: 85, Mismatches: 16, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
20 3 0.04
21 19 0.22
22 8 0.09
23 11 0.13
24 16 0.19
25 15 0.18
26 6 0.07
27 5 0.06
28 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.23
Consensus pattern (24 bp):
AAATAAATAAAAAAATAAATAAAT
Found at i:9697369 original size:2 final size:2
Alignment explanation
Indices: 9697362--9697388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9697352 GATAATAAAA
9697362 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9697389 ATCTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9698660 original size:36 final size:36
Alignment explanation
Indices: 9698611--9698844 Score: 195
Period size: 36 Copynumber: 6.6 Consensus size: 36
9698601 AGGGTTTTTA
*
9698611 TGTTT-AAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAA-AGAAACTGTCTCAAGAGAGACAAAATT
9698647 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
9698684 AG-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATT
* *
9698720 TGTTTCAAGGAA-AAGA-TAT-TC-A-A-AG----ATTT
1 TGTTTCAA--AAGAA-ACTGTCTCAAGAGAGACAAAATT
** *
9698749 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
** *
9698785 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAA-AATT
**
9698822 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAAAGAAACTGTCTCAA
9698845 AACTCGTTTT
Statistics
Matches: 167, Mismatches: 13, Indels: 35
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.01
28 5 0.03
29 13 0.08
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 1 0.01
36 73 0.44
37 65 0.39
38 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:9698703 original size:37 final size:35
Alignment explanation
Indices: 9698612--9698724 Score: 145
Period size: 37 Copynumber: 3.1 Consensus size: 35
9698602 GGGTTTTTAT
* *
9698612 GTTTAAAGAGAAACTGTCTCAAGAGGGACAAAATTT
1 GTTTAAA-AGAAACTGTCTCAAGAGAGACAAAATTA
9698648 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTA
1 GTTT-AAAAGAAACTGTCTCAAGAGAGACAAAA-TTA
* * *
9698685 GTTCTAAAAGAAACTGTCTCAAGGGAGACGAAATTT
1 GTT-TAAAAGAAACTGTCTCAAGAGAGACAAAATTA
9698721 GTTT
1 GTTT
9698725 CAAGGAAAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
35 1 0.01
36 33 0.48
37 34 0.49
38 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (35 bp):
GTTTAAAAGAAACTGTCTCAAGAGAGACAAAATTA
Done.