Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2427979 original size:15 final size:15
Alignment explanation
Indices: 2427961--2427993 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2427951 AAATTCTAAA
2427961 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
2427976 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
2427991 TAT
1 TAT
2427994 ATCTGTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:2429993 original size:17 final size:17
Alignment explanation
Indices: 2429971--2430003 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2429961 GCAGACAAGG
2429971 TTTTTGGAATCATAATA
1 TTTTTGGAATCATAATA
2429988 TTTTTGGAATCATAAT
1 TTTTTGGAATCATAAT
2430004 CTGAAGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTTTGGAATCATAATA
Found at i:2431203 original size:13 final size:13
Alignment explanation
Indices: 2431175--2431209 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2431165 ATGAGTGTTA
*
2431175 TTTATTTATTTTTC
1 TTTATTT-TATTTC
2431189 TTTATTTTATTTC
1 TTTATTTTATTTC
2431202 TTTATTTT
1 TTTATTTT
2431210 TAATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTATTTC
Found at i:2431211 original size:19 final size:20
Alignment explanation
Indices: 2431175--2431217 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2431165 ATGAGTGTTA
2431175 TTTATTTATTTTTCTTT-AT
1 TTTATTTATTTTTCTTTAAT
*
2431194 TTTATTTCTTTATT-TTTAAT
1 TTTATTTATTT-TTCTTTAAT
2431214 TTTA
1 TTTA
2431218 ATATTAGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTTATTTTTCTTTAAT
Found at i:2433515 original size:24 final size:24
Alignment explanation
Indices: 2433484--2433532 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2433474 TAGCGGAGAA
2433484 AAAGAAAAAAGAAGCAGTTAAAGG
1 AAAGAAAAAAGAAGCAGTTAAAGG
*
2433508 AAAGAAAAAAGAAGTAGTTAAAGG
1 AAAGAAAAAAGAAGCAGTTAAAGG
2433532 A
1 A
2433533 GTTGGCTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.63, C:0.02, G:0.24, T:0.10
Consensus pattern (24 bp):
AAAGAAAAAAGAAGCAGTTAAAGG
Found at i:2437941 original size:12 final size:12
Alignment explanation
Indices: 2437911--2437943 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2437901 GAGCTAGGGC
2437911 CATT-AGTTTTA
1 CATTAAGTTTTA
2437922 CA-TAAGTTTTA
1 CATTAAGTTTTA
2437933 CATTAAGTTTT
1 CATTAAGTTTT
2437944 CTTTATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 11 0.55
12 8 0.40
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (12 bp):
CATTAAGTTTTA
Found at i:2443960 original size:12 final size:12
Alignment explanation
Indices: 2443943--2443972 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2443933 TAAGGCCATT
2443943 AGTTTTACATCA
1 AGTTTTACATCA
*
2443955 AGTTTTACATTA
1 AGTTTTACATCA
2443967 AGTTTT
1 AGTTTT
2443973 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:2455560 original size:23 final size:24
Alignment explanation
Indices: 2455523--2455569 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2455513 TAAAATGATC
* *
2455523 AGTTTATCGATTAATTTTTATTTA
1 AGTTTATCGATTAATATTGATTTA
*
2455547 AGTTTA-CTATTAATATTGATTTA
1 AGTTTATCGATTAATATTGATTTA
2455570 GTAGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (24 bp):
AGTTTATCGATTAATATTGATTTA
Found at i:2455973 original size:65 final size:63
Alignment explanation
Indices: 2455873--2455997 Score: 164
Period size: 65 Copynumber: 2.0 Consensus size: 63
2455863 AATTATTTAT
* *
2455873 TATCTATTTAACTTTGAATATTAAAAGATAATTATATCCTTTTTAAATATTTTAAATTAAAATAA
1 TATCTATTTAACTTTGAATATTAAAAGATAATTATAT--ATTTTAAATATTTGAAATTAAAATAA
* *
2455938 TATCTATTTAAGTTTGAATATTAAAA-A-AAGTTTATATATTTTGAATATTTGAAATTAAAA
1 TATCTATTTAACTTTGAATATTAAAAGATAA--TTATATATTTTAAATATTTGAAATTAAAA
2455998 GATATTATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
63 22 0.41
64 1 0.02
65 31 0.57
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (63 bp):
TATCTATTTAACTTTGAATATTAAAAGATAATTATATATTTTAAATATTTGAAATTAAAATAA
Found at i:2458248 original size:15 final size:15
Alignment explanation
Indices: 2458228--2458278 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
2458218 TGCTACCTGA
2458228 TCTACTATTATCTGG
1 TCTACTATTATCTGG
*
2458243 TCTACTTTTATCTGG
1 TCTACTATTATCTGG
* *
2458258 TCTATTATTATTTGG
1 TCTACTATTATCTGG
2458273 TCTACT
1 TCTACT
2458279 GAAATGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (15 bp):
TCTACTATTATCTGG
Found at i:2477868 original size:42 final size:42
Alignment explanation
Indices: 2477809--2477928 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
2477799 TTTTCCCGAA
*
2477809 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
2477851 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
2477893 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
2477929 TGTAATTCAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:2478149 original size:29 final size:30
Alignment explanation
Indices: 2478123--2478182 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2478113 TTAAAATATT
2478123 TAAA-ATAAT-TTATTAATATTTATAATAA
1 TAAATATAATATTATTAATATTTATAATAA
2478151 TAAATATAATATT-TTAATATTATATAA-AA
1 TAAATATAATATTATTAATATT-TATAATAA
2478180 TAA
1 TAA
2478183 TCATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 4 0.14
29 18 0.62
30 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAATATAATATTATTAATATTTATAATAA
Found at i:2478191 original size:25 final size:24
Alignment explanation
Indices: 2478138--2478276 Score: 81
Period size: 24 Copynumber: 5.5 Consensus size: 24
2478128 TAATTTATTA
2478138 ATATTT-ATAATAATAAATATAAT
1 ATATTTAATAATAATAAATATAAT
*
2478161 AT-TTTAATATTATATAAA-ATAAT
1 ATATTTAATAATA-ATAAATATAAT
2478184 CATATTT-ATAATAATATAAGATATTATATTT
1 -ATATTTAATAAT-A-ATAA-ATA-TA-A--T
* * * **
2478215 TTTTTTAATAATAATAAATTTTTT
1 ATATTTAATAATAATAAATATAAT
*
2478239 ATATTTAATAATGAAT-AATATTAT
1 ATATTTAATAAT-AATAAATATAAT
2478263 ATATTTCAATAATA
1 ATATTT-AATAATA
2478277 TTTTAGTAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 27
0.71 0.09 0.21
Matches are distributed among these distances:
22 3 0.03
23 12 0.13
24 35 0.38
25 18 0.20
26 1 0.01
27 2 0.02
28 4 0.04
29 5 0.05
30 5 0.05
31 6 0.07
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
ATATTTAATAATAATAAATATAAT
Found at i:2478517 original size:20 final size:20
Alignment explanation
Indices: 2478439--2478508 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
2478429 TTTCTAGATG
2478439 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2478459 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
2478479 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2478499 TTTTCCAGAA
1 TTTTCCAGAA
2478509 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:2478517 original size:40 final size:40
Alignment explanation
Indices: 2478439--2478517 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
2478429 TTTCTAGATG
* **
2478439 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
2478479 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
2478518 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:2478527 original size:15 final size:15
Alignment explanation
Indices: 2478491--2478557 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
2478481 TTACAGAAAT
**
2478491 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2478506 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
2478520 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2478535 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
2478550 GTAATTCA
1 GTAATTCA
2478558 TTTTCTGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:2478533 original size:29 final size:30
Alignment explanation
Indices: 2478491--2478562 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
2478481 TTACAGAAAT
2478491 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
2478520 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
2478550 GTAATTCATTTTC
1 GTAATTCATTTTC
2478563 TGGAAAACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:2479560 original size:139 final size:138
Alignment explanation
Indices: 2479173--2479562 Score: 394
Period size: 139 Copynumber: 2.8 Consensus size: 138
2479163 GACCTAAGTA
* * * *
2479173 ATTTTTAATTTGGTTCTCGCTTTTATGGTTGAGGTTCCATATTAATTA-TCTGATCCAACAATTT
1 ATTTTTAATTTGGTTCTCGCTTTTATGCTCGAGGTTCCATATTAATTATTC-GATCCAATAAATT
* * * * * * *
2479237 GTTAAATTTGGTTAGGATTAATACTAAAGCCTTCATTTT-AGATTAATTTCATATTTAGTCCTTT
65 GTAAAATTTGGTTAGG-TTAATAATAGAGTCTTCATTTTAAGTTTAATTTCATAGTTAGTCCATT
2479301 AATTTAGGAG
129 AATTTAGGAG
* * * * *
2479311 ATATTTTAATTTGGTCCTCACTTTTATGCCCGAGGTTCCATATTAATTATTTGATCCGATAAATT
1 AT-TTTTAATTTGGTTCTCGCTTTTATGCTCGAGGTTCCATATTAATTATTCGATCCAATAAATT
* ** ** * *
2479376 GTTAAAA-TGGGTTACATTTAATAATAGAGTCTTCACCTTAGGTTTAATTTCA-CGTTAGTCCAT
65 G-TAAAATTTGGTTA-GGTTAATAATAGAGTCTTCATTTTAAGTTTAATTTCATAGTTAGTCCAT
2479439 TAATTTA-GATG
128 TAATTTAGGA-G
* * * *
2479450 ACTTTTTAATTTGGTTCTTGCTTTTATGCTCGAGGTTCCATTTTAATTATTCGATTCAATAACTT
1 A-TTTTTAATTTGGTTCTCGCTTTTATGCTCGAGGTTCCATATTAATTATTCGATCCAATAAATT
* * * *
2479515 ATAAAAATTTGATTAGGTTAATATTAGAGTCTACATTTTAAGTTTAAT
65 GT-AAAATTTGGTTAGGTTAATAATAGAGTCTTCATTTTAAGTTTAAT
2479563 ACTTTAGGTC
Statistics
Matches: 201, Mismatches: 42, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
138 5 0.02
139 175 0.87
140 21 0.10
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (138 bp):
ATTTTTAATTTGGTTCTCGCTTTTATGCTCGAGGTTCCATATTAATTATTCGATCCAATAAATTG
TAAAATTTGGTTAGGTTAATAATAGAGTCTTCATTTTAAGTTTAATTTCATAGTTAGTCCATTAA
TTTAGGAG
Found at i:2485671 original size:19 final size:19
Alignment explanation
Indices: 2485647--2485692 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
2485637 AAAATCCTTA
2485647 GTGCATCGGTGTATGGTAT
1 GTGCATCGGTGTATGGTAT
2485666 GTGCATCGGTGTATGGTAT
1 GTGCATCGGTGTATGGTAT
2485685 GTGCATCG
1 GTGCATCG
2485693 ATGCATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.13, G:0.37, T:0.35
Consensus pattern (19 bp):
GTGCATCGGTGTATGGTAT
Found at i:2488496 original size:44 final size:44
Alignment explanation
Indices: 2488407--2488503 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
2488397 GCTCTTGTGC
* * *
2488407 ATCGATGCACATTCAAGGGCGTGCATCGGTGTATCAGCTGATGT
1 ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
* *
2488451 ATCGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCGGTGCATCAGCTAA-TGT
2488495 ATCGATGCA
1 ATCGATGCA
2488504 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.09
44 37 0.80
45 5 0.11
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
Found at i:2492000 original size:15 final size:15
Alignment explanation
Indices: 2491995--2492061 Score: 98
Period size: 15 Copynumber: 4.5 Consensus size: 15
2491985 GTCGTTCAGA
* *
2491995 ACGTAGTCCTTCAGA
1 ACGTAGTCCTTCGGG
*
2492010 ATGTAGTCCTTCGGG
1 ACGTAGTCCTTCGGG
*
2492025 ACGTAGTCTTTCGGG
1 ACGTAGTCCTTCGGG
2492040 ACGTAGTCCTTCGGG
1 ACGTAGTCCTTCGGG
2492055 ACGTAGT
1 ACGTAGT
2492062 GGTCTTACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (15 bp):
ACGTAGTCCTTCGGG
Found at i:2503416 original size:65 final size:65
Alignment explanation
Indices: 2503249--2503434 Score: 200
Period size: 65 Copynumber: 2.9 Consensus size: 65
2503239 TGACCGTTGG
* ** *
2503249 ATCCTTAGTGCATCGGTGCACT-AAAAGTGCATCGATGCATCAAGTGCATTCGATG-TTCCAAAA
1 ATCCTCAGTGCATCGGTGCA-TGGTAAGTGCATCGATGCATCAAATGCATTCGATGTTTCCAAAA
2503312 T
65 T
* ** * * * *
2503313 AGCCAGAGTGCATCGATGCATGGCT-GGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAA
1 ATCCTCAGTGCATCGGTGCATGG-TAAGTGCATCGATGCATCAAATGCATTCGATGTTTCCA-AA
2503377 A-
64 AT
* *
2503378 ATCCTCAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 ATCCTCAGTGCATCGGTGCATGGTAAGTGCATCGATGCATCAAATGCATTCGATGTT
2503435 CAATTTAATT
Statistics
Matches: 100, Mismatches: 17, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
63 1 0.01
64 44 0.44
65 52 0.52
66 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (65 bp):
ATCCTCAGTGCATCGGTGCATGGTAAGTGCATCGATGCATCAAATGCATTCGATGTTTCCAAAAT
Found at i:2503473 original size:65 final size:62
Alignment explanation
Indices: 2503274--2503484 Score: 203
Period size: 65 Copynumber: 3.3 Consensus size: 62
2503264 GTGCACTAAA
* * **
2503274 AGTGCATCGATGCATCAAGTGCATTCGATGTTCCAAAAT-AGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTT-CAATATAATTCAG-GTGCATCGATGCATGG-T
* * * *
2503338 GGTGCATCGATGCATCAAATGCATTTGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGG
1 AGTGCATCGATGCATCAAATGCATTCGATG--TTCAATATAAT--TCAGGTGCATCGATGCATGG
2503401 T
62 T
* *
2503402 ATGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATGGTGCATCGATGCATGGAT
1 A-GTGCATCGATGCATCAAATGCATTCGATGTTCAATATAATTCA-GGTGCATCGATGCATGG--
2503467 T
62 T
*
2503468 AGTGCATCGGTGCATCA
1 AGTGCATCGATGCATCA
2503485 CTCTGAAAAA
Statistics
Matches: 120, Mismatches: 16, Indels: 21
0.76 0.10 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 50 0.42
65 58 0.48
66 4 0.03
67 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (62 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTCAATATAATTCAGGTGCATCGATGCATGGT
Found at i:2509480 original size:10 final size:9
Alignment explanation
Indices: 2509458--2509518 Score: 59
Period size: 10 Copynumber: 6.4 Consensus size: 9
2509448 AGTGAGATGC
2509458 ACCGGTTTG
1 ACCGGTTTG
2509467 ACCGGTTCTG
1 ACCGGTT-TG
*
2509477 ACCGGTTCG
1 ACCGGTTTG
2509486 AACCGGTTTG
1 -ACCGGTTTG
** *
2509496 ACCACTCTG
1 ACCGGTTTG
2509505 AACCGGTTTG
1 -ACCGGTTTG
2509515 ACCG
1 ACCG
2509519 ACAGACCCGA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
9 18 0.44
10 23 0.56
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2509482 original size:19 final size:19
Alignment explanation
Indices: 2509458--2509518 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
2509448 AGTGAGATGC
*
2509458 ACCGGTTTG-ACCGGTTCTG
1 ACCGGTTCGAACCGGTT-TG
2509477 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
**
2509496 ACC-ACTCTGAACCGGTTTG
1 ACCGGTTC-GAACCGGTTTG
2509515 ACCG
1 ACCG
2509519 ACAGACCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.06
19 27 0.75
20 7 0.19
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (19 bp):
ACCGGTTCGAACCGGTTTG
Found at i:2509539 original size:14 final size:14
Alignment explanation
Indices: 2509516--2509548 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2509506 ACCGGTTTGA
2509516 CCGACAGACCCGAC
1 CCGACAGACCCGAC
*
2509530 CCGACTGACCCGAC
1 CCGACAGACCCGAC
2509544 CCGAC
1 CCGAC
2509549 CGTTGACCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.52, G:0.21, T:0.03
Consensus pattern (14 bp):
CCGACAGACCCGAC
Found at i:2509558 original size:7 final size:7
Alignment explanation
Indices: 2509546--2509589 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
2509536 GACCCGACCC
2509546 GACCGTT
1 GACCGTT
2509553 GACCGTT
1 GACCGTT
2509560 GACCGTT
1 GACCGTT
2509567 GACC-TT
1 GACCGTT
2509573 GACCGTT
1 GACCGTT
*
2509580 GATCGTT
1 GACCGTT
2509587 GAC
1 GAC
2509590 TTCCTTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (7 bp):
GACCGTT
Found at i:2509576 original size:20 final size:21
Alignment explanation
Indices: 2509546--2509589 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
2509536 GACCCGACCC
2509546 GACCGTTGACCGTTGACCGTT
1 GACCGTTGACCGTTGACCGTT
*
2509567 GACC-TTGACCGTTGATCGTT
1 GACCGTTGACCGTTGACCGTT
2509587 GAC
1 GAC
2509590 TTCCTTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
GACCGTTGACCGTTGACCGTT
Found at i:2512187 original size:11 final size:11
Alignment explanation
Indices: 2512149--2512181 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2512139 CTCCCACATC
2512149 TTTA-CTTA-G
1 TTTATCTTATG
2512158 TTTATCTTATG
1 TTTATCTTATG
2512169 TTTATCTTATG
1 TTTATCTTATG
2512180 TT
1 TT
2512182 ATTCTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.18
10 4 0.18
11 14 0.64
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (11 bp):
TTTATCTTATG
Found at i:2512444 original size:32 final size:32
Alignment explanation
Indices: 2512408--2512483 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
2512398 GCATAAAGAC
* *
2512408 ACTAGCTCGG-GAGTAGCTGAACGAGAGTTGAA
1 ACTAG-TCGGAGAATAGCTAAACGAGAGTTGAA
* * *
2512440 ACTAGTTGGAGAATAGCTAAATGGGAGTTGAA
1 ACTAGTCGGAGAATAGCTAAACGAGAGTTGAA
*
2512472 ACTAGTTGGAGA
1 ACTAGTCGGAGA
2512484 GTAGTTGAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 3 0.08
32 35 0.92
ACGTcount: A:0.34, C:0.11, G:0.33, T:0.22
Consensus pattern (32 bp):
ACTAGTCGGAGAATAGCTAAACGAGAGTTGAA
Found at i:2512988 original size:24 final size:25
Alignment explanation
Indices: 2512948--2512999 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
2512938 CAAACCAACA
2512948 CATAGGAAAAAAGGGCATACATATT
1 CATAGGAAAAAAGGGCATACATATT
* **
2512973 CATATGAAAAAA-GGCATATGTATT
1 CATAGGAAAAAAGGGCATACATATT
2512997 CAT
1 CAT
2513000 TAAATGGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (25 bp):
CATAGGAAAAAAGGGCATACATATT
Found at i:2524661 original size:4 final size:4
Alignment explanation
Indices: 2524652--2524686 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2524642 CAATGCATGT
*
2524652 ATAA ATAA ATAA ATAA ATAA ATAA TTAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
2524687 CATAGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:2526145 original size:40 final size:40
Alignment explanation
Indices: 2526090--2526288 Score: 371
Period size: 40 Copynumber: 5.0 Consensus size: 40
2526080 AGGTTTATAG
*
2526090 TACACTTTGGTGTATATGGTGGGCACGACCTTATGTGTAA
1 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
*
2526130 TACACTTTGGTGTATATGGTGGGCACGACCTTATGTGTAA
1 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
2526170 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
1 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
2526210 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
1 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
*
2526250 TACACTTCGGTGTATATGGTGGGAACGACCTTATGTGTA
1 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTA
2526289 GCACTATGGT
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 157 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.34
Consensus pattern (40 bp):
TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
Found at i:2526568 original size:46 final size:44
Alignment explanation
Indices: 2526392--2526553 Score: 279
Period size: 44 Copynumber: 3.6 Consensus size: 44
2526382 GGTAAGTATG
2526392 AAAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGT
2526436 AAAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGT
* *
2526480 AAAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGGAA-T-AATGGCAAGTATATTGGT
*
2526526 AAAATAAGCTTACGAGCTTATGGGATAA
1 AAAATAAGCTTACGAGCTTATGGAATAA
2526554 ATGGTAAGAG
Statistics
Matches: 113, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
44 71 0.63
45 2 0.02
46 40 0.35
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (44 bp):
AAAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGT
Found at i:2526989 original size:21 final size:21
Alignment explanation
Indices: 2526963--2527002 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2526953 TGTAGCAATT
*
2526963 ACTGTAGTAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
2526984 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
2527003 ACACAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:2527103 original size:26 final size:26
Alignment explanation
Indices: 2527067--2527137 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
2527057 CAGTGCATCG
2527067 GTACATTGTTCACTGTTCACGGTACT
1 GTACATTGTTCACTGTTCACGGTACT
2527093 GTACATTGTTCACTGTTCACGGTACT
1 GTACATTGTTCACTGTTCACGGTACT
* * *
2527119 GTTCATTGTTTACTATTCA
1 GTACATTGTTCACTGTTCA
2527138 TAAAAAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (26 bp):
GTACATTGTTCACTGTTCACGGTACT
Found at i:2536544 original size:23 final size:24
Alignment explanation
Indices: 2536518--2536573 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
2536508 TTGAAATGAC
*
2536518 TAATCCCTTTTTGTTGTT-ATGGA
1 TAATCCCTTTTTATTGTTCATGGA
* *
2536541 TAAT-CTTTTTTATTGTTCATGGC
1 TAATCCCTTTTTATTGTTCATGGA
2536564 TAATCCCTTT
1 TAATCCCTTT
2536574 CTGCTAGAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 11 0.41
23 12 0.44
24 4 0.15
ACGTcount: A:0.18, C:0.16, G:0.12, T:0.54
Consensus pattern (24 bp):
TAATCCCTTTTTATTGTTCATGGA
Found at i:2536556 original size:22 final size:23
Alignment explanation
Indices: 2536525--2536568 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2536515 GACTAATCCC
*
2536525 TTTTTGTTGTT-ATGGATAATCT
1 TTTTTATTGTTCATGGATAATCT
*
2536547 TTTTTATTGTTCATGGCTAATC
1 TTTTTATTGTTCATGGATAATC
2536569 CCTTTCTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.57
Consensus pattern (23 bp):
TTTTTATTGTTCATGGATAATCT
Found at i:2536863 original size:11 final size:11
Alignment explanation
Indices: 2536849--2536902 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
2536839 CATTAAATTT
2536849 ATATTAATAAA
1 ATATTAATAAA
2536860 ATATTAATAAA
1 ATATTAATAAA
*
2536871 A-ATCATATAAA
1 ATATTA-ATAAA
2536882 A-ATTCAA-AAA
1 ATATT-AATAAA
*
2536892 ATAATAATAAA
1 ATATTAATAAA
2536903 TGATATGCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
11 26 0.72
12 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (11 bp):
ATATTAATAAA
Found at i:2539704 original size:32 final size:32
Alignment explanation
Indices: 2539653--2539727 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
2539643 TTATTTTATA
* *
2539653 AAAAACTAGTCTCATATGCAAATCCAATGGTAT
1 AAAAATTA-TCTCACATGCAAATCCAATGGTAT
2539686 AAAAATTATCTCACATGCAAATCCAATGGTAT
1 AAAAATTATCTCACATGCAAATCCAATGGTAT
2539718 AAAAATTATC
1 AAAAATTATC
2539728 CTCTAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 33 0.82
33 7 0.17
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.28
Consensus pattern (32 bp):
AAAAATTATCTCACATGCAAATCCAATGGTAT
Found at i:2552578 original size:8 final size:7
Alignment explanation
Indices: 2552564--2552633 Score: 59
Period size: 8 Copynumber: 8.9 Consensus size: 7
2552554 AGTATTATTA
2552564 TTATTTT
1 TTATTTT
2552571 TCTATTTT
1 T-TATTTT
2552579 TCTATTTT
1 T-TATTTT
2552587 ACTTATTTT
1 --TTATTTT
2552596 TGTATATTT
1 T-TAT-TTT
2552605 TTACTTTT
1 TTA-TTTT
*
2552613 TTATATT
1 TTATTTT
2552620 TTATTTAT
1 TTATTT-T
2552628 TTATTT
1 TTATTT
2552634 ATTTCCTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
7 10 0.19
8 32 0.59
9 11 0.20
10 1 0.02
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (7 bp):
TTATTTT
Found at i:2552586 original size:16 final size:14
Alignment explanation
Indices: 2552564--2552633 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 14
2552554 AGTATTATTA
2552564 TTATTTTTCTATTTT
1 TTATTTTT-TATTTT
2552579 TCTATTTTACTTATTTT
1 T-TATTTT--TTATTTT
2552596 TGTATATTTTTACTTTT
1 T-TAT-TTTTTA-TTTT
*
2552613 TTATATTTTATTTAT
1 TTATTTTTTATTT-T
2552628 TTATTT
1 TTATTT
2552634 ATTTCCTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.07
15 12 0.26
16 12 0.26
17 15 0.33
18 4 0.09
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (14 bp):
TTATTTTTTATTTT
Found at i:2552592 original size:25 final size:26
Alignment explanation
Indices: 2552556--2552605 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
2552546 TTATTGTTAG
2552556 TATTATTATTATTTTTCTAT-TTTTC
1 TATTATTATTATTTTTCTATATTTTC
*
2552581 TATT-TTACTTATTTTTGTATATTTT
1 TATTATTA-TTATTTTTCTATATTTT
2552606 TACTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 15 0.68
26 4 0.18
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (26 bp):
TATTATTATTATTTTTCTATATTTTC
Found at i:2552630 original size:15 final size:15
Alignment explanation
Indices: 2552589--2552660 Score: 58
Period size: 16 Copynumber: 4.5 Consensus size: 15
2552579 TCTATTTTAC
2552589 TTATTTTTGTATATTT
1 TTATTTTT-TATATTT
2552605 TTACTTTTTTATA-TT
1 TTA-TTTTTTATATTT
2552620 TTATTTATTTAT-TTAT
1 TTATTT-TTTATATT-T
* *
2552636 TTCCTTTTATTTTATTT
1 TT-ATTTT-TTATATTT
2552653 TTATTTTT
1 TTATTTTT
2552661 ATTCATTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.07
15 12 0.26
16 15 0.33
17 14 0.30
18 2 0.04
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (15 bp):
TTATTTTTTATATTT
Found at i:2552661 original size:27 final size:27
Alignment explanation
Indices: 2552600--2552663 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
2552590 TATTTTTGTA
2552600 TATTTTTACTTTTTTATATTTTATTTAT
1 TATTTTTA-TTTTTTATATTTTATTTAT
*
2552628 T-TATTTATTTCCTTT-TATTTTATTT-T
1 TATTTTTATTT--TTTATATTTTATTTAT
2552654 TATTTTTATT
1 TATTTTTATT
2552664 CATTATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
26 5 0.16
27 22 0.71
28 4 0.13
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (27 bp):
TATTTTTATTTTTTATATTTTATTTAT
Found at i:2552662 original size:17 final size:17
Alignment explanation
Indices: 2552640--2552825 Score: 60
Period size: 17 Copynumber: 10.2 Consensus size: 17
2552630 ATTTATTTCC
2552640 TTTTATTTTATTTTTAT
1 TTTTATTTTATTTTTAT
2552657 TTTTATTCATTA-TTTTAT
1 TTTTATT--TTATTTTTAT
*
2552675 CCTTTTATCTCCTTTATATTTGTTT
1 --TTTTA--T--TTTAT-TTT-TAT
2552700 TATTTA-TTTATTTAGTTAT
1 T-TTTATTTTATTT--TTAT
* *
2552719 TTTTACTTTCTTTTTAT
1 TTTTATTTTATTTTTAT
2552736 TTTTA-TTTATTTTTTAT
1 TTTTATTTTA-TTTTTAT
* * * *
2552753 GTATATATTATTGTTAT
1 TTTTATTTTATTTTTAT
*
2552770 TACTTT-TTTCA-TTTTAT
1 T--TTTATTTTATTTTTAT
*
2552787 TTATT-TTATTCATTTTCAT
1 TT-TTATT-TT-ATTTTTAT
* *
2552806 CTTTACTTTATTTTTAT
1 TTTTATTTTATTTTTAT
2552823 TTT
1 TTT
2552826 ATGCATCTTT
Statistics
Matches: 126, Mismatches: 19, Indels: 48
0.65 0.10 0.25
Matches are distributed among these distances:
15 1 0.01
16 7 0.06
17 48 0.38
18 23 0.18
19 26 0.21
20 6 0.05
22 4 0.03
23 1 0.01
24 8 0.06
25 2 0.02
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTATTTTATTTTTAT
Found at i:2552802 original size:26 final size:26
Alignment explanation
Indices: 2552760--2552819 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2552750 TATGTATATA
2552760 TTATTGTTATTACTTTTTTCAT-TTTA-T
1 TTATT-TTATTAC--TTTTCATCTTTACT
2552787 TTATTTTATT-CATTTTCATCTTTACT
1 TTATTTTATTAC-TTTTCATCTTTACT
2552813 TTATTTT
1 TTATTTT
2552820 TATTTTATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 7 0.23
25 5 0.17
26 13 0.43
27 5 0.17
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.70
Consensus pattern (26 bp):
TTATTTTATTACTTTTCATCTTTACT
Found at i:2552822 original size:32 final size:31
Alignment explanation
Indices: 2552786--2552849 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
2552776 TTTCATTTTA
*
2552786 TTTATTTTATTCAT-TTTCATCTTTACTTTATT
1 TTTATTTTATGCATCTTTCAT-TTT-CTTTATT
*
2552818 TTTATTTTATGCATCTTTTATTTTCTTTATT
1 TTTATTTTATGCATCTTTCATTTTCTTTATT
2552849 T
1 T
2552850 CATTCGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 8 0.28
32 16 0.55
33 5 0.17
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (31 bp):
TTTATTTTATGCATCTTTCATTTTCTTTATT
Found at i:2553544 original size:65 final size:63
Alignment explanation
Indices: 2553430--2553576 Score: 249
Period size: 65 Copynumber: 2.3 Consensus size: 63
2553420 AAAGAGACAC
*
2553430 CTTCGTGTGAATTTATTCACCGTAGGCCTAGCAAGTAGCCTTCGAGATTCATATACCTTATGT
1 CTTCGTGTGAATTTATTCACCGCAGGCCTAGCAAGTAGCCTTCGAGATTCATATACCTTATGT
* *
2553493 CTTCGTGTGAATTTATTCACCATGCAGGCCTAGCAAGTAGCCTTTGGGATTCATATACCTTATGT
1 CTTCGTGTGAATTTATTCACC--GCAGGCCTAGCAAGTAGCCTTCGAGATTCATATACCTTATGT
2553558 CTTCGTGTGAATTTATTCA
1 CTTCGTGTGAATTTATTCA
2553577 TAGTGCAGGC
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
63 21 0.27
65 58 0.73
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (63 bp):
CTTCGTGTGAATTTATTCACCGCAGGCCTAGCAAGTAGCCTTCGAGATTCATATACCTTATGT
Found at i:2561439 original size:20 final size:20
Alignment explanation
Indices: 2561414--2561456 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2561404 TTTAAGAGCT
*
2561414 CATTTAGGAGCATATAGATG
1 CATTTAGAAGCATATAGATG
* *
2561434 CATTTAGAAGCATTTAGTTG
1 CATTTAGAAGCATATAGATG
2561454 CAT
1 CAT
2561457 GTGGTGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGAAGCATATAGATG
Found at i:2564333 original size:96 final size:96
Alignment explanation
Indices: 2564169--2564432 Score: 370
Period size: 96 Copynumber: 2.7 Consensus size: 96
2564159 AGATTATAAT
* * * *
2564169 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAACTCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTA
2564234 TGGATAAGATTCAACTAGCCTGATAAAGGTG
66 TGGATAAGATTCAACTAGCCTGATAAAGGTG
* * *
2564265 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGATCAATTGGTTAAACACCCCGGATTTA
1 ATTATATATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTA
*
2564330 TGGATAATATTCAACTAGCCTGATAAAGGTG
66 TGGATAAGATTCAACTAGCCTGATAAAGGTG
* * * *
2564361 ATTATAATATCTATACAATGATA--TTAAGATGTCTCTCTAGAGCAATTGGTTAAACCCCCCGGC
1 ATTAT-ATA--TATACAAT-AAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACACCCCGGC
2564424 TTTATGGAT
62 TTTATGGAT
2564433 CCAGCTAGCC
Statistics
Matches: 150, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
96 94 0.63
97 3 0.02
98 43 0.29
99 8 0.05
100 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (96 bp):
ATTATATATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTA
TGGATAAGATTCAACTAGCCTGATAAAGGTG
Found at i:2565359 original size:80 final size:80
Alignment explanation
Indices: 2565223--2566108 Score: 1140
Period size: 80 Copynumber: 11.0 Consensus size: 80
2565213 GCACCTTCTA
* *
2565223 CAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGAA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
*
2565288 AGAAGGGCTATATGC
66 AGAAGGGCTATCTGC
* * ** * *
2565303 CAAAGACCTTCAAGTTCAATTACACTCAGCTCAAAGGTGCACCATTTGCAGTATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
2565368 AGAA-GGCTATCTGTTAAC
66 AGAAGGGCTATCTG----C
* *
2565386 CAAAGACCATCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTTCAGCATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
*
2565451 AGAAGAGG-TACCTGC
66 AGAAG-GGCTATCTGC
2565466 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
* * *
2565531 AGAAGGGTTACCTAC
66 AGAAGGGCTATCTGC
*
2565546 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
*
2565611 AGAAGGGTTATCTGC
66 AGAAGGGCTATCTGC
* * * * *
2565626 CAAAGACCTTCGAGTT--ATTACACTAAGCTCAAAGACACATCATTTGTATCATAGCTCGAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
*
2565689 AGAAGCGCTATCTGC
66 AGAAGGGCTATCTGC
* * * * *
2565704 CAAAGACCTTCAAGTTCGATTACACTTAGCTCAAAGGTACATCATTTGCAGTATAGCTCAAGGAA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
*
2565769 AGAAGGGCTATAT-C
66 AGAAGGGCTATCTGC
* * *
2565783 CAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATAATTTGCAGTATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
2565848 AGAAGGGCTATCTGCC
66 AGAAGGGCTATCTG-C
* * * *
2565864 AACAAAATACCTTCGAGTTTGATTACATTTAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAG
1 --C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAG
* *
2565929 GAAAGAAGGGCTATCTAC
63 GCAAGAAGGGCTATCTGC
* * *
2565947 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCG
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
* *
2566012 ATAAGGGATATCTGC
66 AGAAGGGCTATCTGC
* * * *
2566027 CAAAAAGAGACCTTCGAGTTTGATTACACTAAACTCAAAGGAACATCAAATTT--AGCATAGCTC
1 C---AA-AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTC
* *
2566090 AA-GCGAGAAGGGTTATCTG
60 AAGGCAAGAAGGGCTATCTG
2566109 TCAACAAGAA
Statistics
Matches: 712, Mismatches: 74, Indels: 37
0.87 0.09 0.04
Matches are distributed among these distances:
78 70 0.10
79 84 0.12
80 348 0.49
81 2 0.00
83 81 0.11
84 121 0.17
85 2 0.00
86 4 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (80 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
AGAAGGGCTATCTGC
Found at i:2565992 original size:243 final size:244
Alignment explanation
Indices: 2565219--2566145 Score: 1164
Period size: 243 Copynumber: 3.8 Consensus size: 244
2565209 AAAAGCACCT
*
2565219 TCTA-CAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
1 TCTACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
* ** **
2565283 AGGAAAGAAGGGCTATATGCCAAAGACCTTCAAGTTCAATTACACTCAGCTCAAAGGTGCACCAT
66 AGGAAAGAAGGGCTATATGCCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATAAT
* * * *
2565348 TTGCAGTATAGCTCAAGGCAAGAA-GGCTATCTGTTAACCAAAGACCATCGAGTTCGATTACACT
131 TTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACT
* *
2565412 CAGCTCAAAGGCACATCATTTTCAGCATAGCTCAAGGCAAGAAGAGG-TA
196 TAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG-GGCTA
* *
2565461 CCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
1 TCTACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
* * ** * * *
2565526 AGGCAAGAAGGGTTACCTACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAT
66 AGGAAAGAAGGGCTATATGCCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATAAT
* *
2565591 TTGCAACATAGCTCAAGGCAAGAAGGGTTATCTG-C--C-AAAGACCTTCGAGTT--ATTACACT
131 TTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACT
* * * * * *
2565650 AAGCTCAAAGACACATCATTTGTATCATAGCTCGAGGCAAGAAGCGCTA
196 TAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA
* * * * *
2565699 TCTGCCAAAGACCTTCAAGTTCGATTACACTTAGCTCAAAGGTACATCATTTGCAGTATAGCTCA
1 TCTACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
2565764 AGGAAAGAAGGGCTATAT-CCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATAAT
66 AGGAAAGAAGGGCTATATGCCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATAAT
* * * * *
2565828 TTGCAGTATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAATACCTTCGAGTTTGATTACATT
131 TTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACT
*
2565893 TAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTA
196 TAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA
* *
2565942 TCTACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCA
1 TCTACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
** * * * * * * * *
2566007 AGGCGATAAGGGATATCTGCCAAAAAGAGACCTTCGAGTTTGATTACACTAAACTCAAAGGAACA
66 AGGAAAGAAGGGCTATATGCC---AA-AGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACA
* *
2566072 TCAAATTT--AGCATAGCTCAA-GCGAGAAGGGTTATCTGTCAACAAGAA-A-CTGTCGAGTTCG
127 T--AATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAA-AAGACCT-TCGAGTTCG
* *
2566132 ATTCCATTTAGCTC
188 ATTACACTTAGCTC
2566146 GACGACACAT
Statistics
Matches: 596, Mismatches: 71, Indels: 31
0.85 0.10 0.04
Matches are distributed among these distances:
237 76 0.13
238 123 0.21
240 15 0.03
241 15 0.03
242 2 0.00
243 256 0.43
244 10 0.02
246 2 0.00
247 45 0.08
248 47 0.08
250 5 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (244 bp):
TCTACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
AGGAAAGAAGGGCTATATGCCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATAAT
TTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACT
TAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA
Found at i:2565993 original size:401 final size:398
Alignment explanation
Indices: 2565223--2566092 Score: 1230
Period size: 401 Copynumber: 2.2 Consensus size: 398
2565213 GCACCTTCTA
* * *
2565223 CAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGAA
1 CAAAGACCTTCGAGTT-GATTACACTAAGCTCAAAGACACATCATTTGCAGCATAGCTCAAGGAA
* *
2565288 AGAAGGGCTATATGCCAAAGACCTTCAAGTTCAATTACACTCAGCTCAAAGGTGCACCATTTGCA
65 AGAAGCGCTATATGCCAAAGACCTTCAAGTTCAATTACACTCAGCTCAAAGGTACACCATTTGCA
* *
2565353 GTATAGCTCAAGGCAAGAAGGCTATCTGTTAACCAAAGACCATCGAGTTCGATTACACTCAGCTC
130 GTATAGCTCAAGGAAAGAAGGCTA----TTAACCAAAGACCATCAAGTTCGATTACACTCAGCTC
* *
2565418 AAAGGCACATCATTTTCAGCATAGCTCAAGGCAAGAAGAGGTACCTGCCAAAGACCTTCGAGTTC
191 AAAGGCACATAATTTGCAGCATAGCTCAAGGCAAGAAGAGGTACCTGCCAAAGACCTTCGAGTTC
* *
2565483 GATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTACCTACCA
256 GATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTACCTACCA
*
2565548 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAG
321 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAG
*
2565613 AAGGGTTATCTGC
386 AAGGGATATCTGC
* * * *
2565626 CAAAGACCTTCGAGTT-ATTACACTAAGCTCAAAGACACATCATTTGTATCATAGCTCGAGGCAA
1 CAAAGACCTTCGAGTTGATTACACTAAGCTCAAAGACACATCATTTGCAGCATAGCTCAAGGAAA
* * * *
2565690 GAAGCGCTATCTGCCAAAGACCTTCAAGTTCGATTACACTTAGCTCAAAGGTACATCATTTGCAG
66 GAAGCGCTATATGCCAAAGACCTTCAAGTTCAATTACACTCAGCTCAAAGGTACACCATTTGCAG
* *
2565755 TATAGCTCAAGGAAAGAAGGGCTA-TATCCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAG
131 TATAGCTCAAGGAAAGAA-GGCTATTAACCAAAGACCATCAAGTTCGATTACACTCAGCTCAAAG
* * *
2565819 GCACATAATTTGCAGTATAGCTCAAGGCAAGAAG-GGCTATCTGCCAACAAAATACCTTCGAGTT
195 GCACATAATTTGCAGCATAGCTCAAGGCAAGAAGAGG-TACCTG-C--C-AAAGACCTTCGAGTT
* * * *
2565883 TGATTACATTTAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTATCTACC
255 CGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTACCTACC
*
2565948 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCGA
320 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAA
*
2566013 TAAGGGATATCTGC
385 GAAGGGATATCTGC
*
2566027 CAAAAAGAGACCTTCGAGTTTGATTACACTAAACTCAAAGGA-ACATCAAATTT--AGCATAGCT
1 C---AA-AGACCTTCGAG-TTGATTACACTAAGCTCAAA-GACACATC--ATTTGCAGCATAGCT
2566089 CAAG
58 CAAG
2566093 CGAGAAGGGT
Statistics
Matches: 417, Mismatches: 35, Indels: 26
0.87 0.07 0.05
Matches are distributed among these distances:
396 2 0.00
397 73 0.18
398 1 0.00
400 1 0.00
401 266 0.64
402 5 0.01
403 16 0.04
404 2 0.00
405 11 0.03
406 2 0.00
407 32 0.08
408 2 0.00
409 4 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (398 bp):
CAAAGACCTTCGAGTTGATTACACTAAGCTCAAAGACACATCATTTGCAGCATAGCTCAAGGAAA
GAAGCGCTATATGCCAAAGACCTTCAAGTTCAATTACACTCAGCTCAAAGGTACACCATTTGCAG
TATAGCTCAAGGAAAGAAGGCTATTAACCAAAGACCATCAAGTTCGATTACACTCAGCTCAAAGG
CACATAATTTGCAGCATAGCTCAAGGCAAGAAGAGGTACCTGCCAAAGACCTTCGAGTTCGATTA
CACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTACCTACCAAAGAC
CTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGG
ATATCTGC
Found at i:2568010 original size:21 final size:24
Alignment explanation
Indices: 2567985--2568032 Score: 75
Period size: 21 Copynumber: 2.1 Consensus size: 24
2567975 TACATTTAAT
2567985 TATATTTC-TTA-TTTTA-TTTTC
1 TATATTTCTTTATTTTTAGTTTTC
2568006 TATATTTCTTTATTTTTAGTTTTC
1 TATATTTCTTTATTTTTAGTTTTC
2568030 TAT
1 TAT
2568033 TAATTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 5 0.21
24 8 0.33
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (24 bp):
TATATTTCTTTATTTTTAGTTTTC
Found at i:2568071 original size:3 final size:3
Alignment explanation
Indices: 2568040--2568090 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
2568030 TATTAATTTA
* * * *
2568040 TAT TA- TAT TAC TAT TTT TAT TAT TGT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2568087 TAT T
1 TAT T
2568091 TTTCTATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2568100 original size:8 final size:7
Alignment explanation
Indices: 2568086--2568393 Score: 58
Period size: 8 Copynumber: 40.0 Consensus size: 7
2568076 ATTATTACTA
2568086 TTATTTT
1 TTATTTT
2568093 TCTATTTT
1 T-TATTTT
2568101 AATTATTTT
1 --TTATTTT
2568110 TGTATTTTT
1 T-TA-TTTT
2568119 TTACTTTT
1 TTA-TTTT
* *
2568127 GTATATT
1 TTATTTT
2568134 TTATTTAT
1 TTATTT-T
2568142 TTATTTT
1 TTATTTT
2568149 CCTT-TTATT
1 --TTATT-TT
2568158 TTATTTTAT
1 TTA-TTT-T
*
2568167 TTTTCTTT
1 TTAT-TTT
*
2568175 TTATTCT
1 TTATTTT
2568182 TTA--TT
1 TTATTTT
*
2568187 TTATCCTT
1 TTAT-TTT
2568195 TTATCTTT
1 TTAT-TTT
*
2568203 GTT-TTAT
1 -TTATTTT
2568210 TTATTTAT
1 TTATTT-T
2568218 TTA-TTT
1 TTATTTT
*
2568224 GTACTTTCT
1 TTA-TTT-T
2568233 TCT-TATTT
1 T-TAT-TTT
2568241 TTATTTAT
1 TTATTT-T
* *
2568249 TTGTTAT
1 TTATTTT
* * *
2568256 GTATATA
1 TTATTTT
2568263 TTATTGTT
1 TTATT-TT
2568271 ATTATTTT
1 -TTATTTT
2568279 TTATTTTT
1 TTA-TTTT
*
2568287 TTCATTTA
1 TT-ATTTT
2568295 TTATTTT
1 TTATTTT
*
2568302 ATTAATTT
1 -TTATTTT
2568310 TTATCTTT
1 TTAT-TTT
2568318 ACTT-TGTTT
1 --TTAT-TTT
2568327 TTATTTT
1 TTATTTT
*
2568334 ATGTATCCTT
1 -T-TAT-TTT
2568344 TTATTTT
1 TTATTTT
*
2568351 CTT-TATT
1 -TTATTTT
*
2568358 TCATTTGT
1 TTATTT-T
2568366 TT-TTTT
1 TTATTTT
2568372 TTACTTTT
1 TTA-TTTT
*
2568380 TTATTAT
1 TTATTTT
2568387 TTATTTT
1 TTATTTT
2568394 CATTTTTCCC
Statistics
Matches: 221, Mismatches: 37, Indels: 86
0.64 0.11 0.25
Matches are distributed among these distances:
5 4 0.02
6 9 0.04
7 66 0.30
8 95 0.43
9 41 0.19
10 6 0.03
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.73
Consensus pattern (7 bp):
TTATTTT
Found at i:2568105 original size:17 final size:17
Alignment explanation
Indices: 2568085--2568117 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2568075 TATTATTACT
2568085 ATTATTTTTCTATTTTA
1 ATTATTTTTCTATTTTA
*
2568102 ATTATTTTTGTATTTT
1 ATTATTTTTCTATTTT
2568118 TTTACTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (17 bp):
ATTATTTTTCTATTTTA
Found at i:2568161 original size:5 final size:5
Alignment explanation
Indices: 2568130--2568399 Score: 57
Period size: 5 Copynumber: 51.2 Consensus size: 5
2568120 TACTTTTGTA
* *
2568130 TATTT TA-TT TA-TT TATTT TCCTTT TATTT TATTT TATTTT TCTTTT
1 TATTT TATTT TATTT TATTT T-ATTT TATTT TATTT TA-TTT T-ATTT
*
2568176 TATTCTT TATTT TATCCTTT TATCTT TGTTT TA-TT TA-TT TA-TT TATTT
1 TA-T-TT TATTT TA---TTT TAT-TT TATTT TATTT TATTT TATTT TATTT
* * * *
2568224 GTACTT TCTTCT TATTT T-TATT TATTTGT TATGTA TATAT TATTGT TATTAT
1 -TATTT TATT-T TATTT TAT-TT TA-TT-T TAT-TT TATTT TATT-T TATT-T
* *
2568276 T-TTT TATTT T-TTT CATTTAT TATTT TA-TT AATTTT TATCTT TACTTT
1 TATTT TATTT TATTT TA-TT-T TATTT TATTT TA-TTT TAT-TT TA-TTT
** * *
2568323 GT-TTT TATTT TATGTAT CCTTT TATTT T-CTT TATTT CATTT GT-TTT
1 -TATTT TATTT TAT-T-T TATTT TATTT TATTT TATTT TATTT -TATTT
2568369 T-TTT TACTTT T-TTAT TA-TT TATTT TCATTT T
1 TATTT TA-TTT TATT-T TATTT TATTT T-ATTT T
2568400 TCCCCTATCT
Statistics
Matches: 199, Mismatches: 27, Indels: 77
0.66 0.09 0.25
Matches are distributed among these distances:
4 43 0.22
5 74 0.37
6 62 0.31
7 15 0.08
8 5 0.03
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:2568162 original size:20 final size:20
Alignment explanation
Indices: 2568132--2568198 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
2568122 CTTTTGTATA
2568132 TTTTA-TTTATTTATTTTCC
1 TTTTATTTTATTTATTTTCC
*
2568151 TTTTATTTTATTTTATTTTTC
1 TTTTATTTTA-TTTATTTTCC
* *
2568172 TTTT-TATTCTTTATTTTATCC
1 TTTTATTTTATTTA-TTT-TCC
2568193 TTTTAT
1 TTTTAT
2568199 CTTTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.23
20 10 0.26
21 19 0.49
22 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTATTTTATTTATTTTCC
Found at i:2568201 original size:19 final size:19
Alignment explanation
Indices: 2568156--2568209 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2568146 TTTCCTTTTA
*
2568156 TTTTAT-TTTATTTT-TCT
1 TTTTATCTTTATTTTATCC
2568173 TTTTATTCTTTATTTTATCC
1 TTTTA-TCTTTATTTTATCC
*
2568193 TTTTATCTTTGTTTTAT
1 TTTTATCTTTATTTTAT
2568210 TTATTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 5 0.16
18 1 0.03
19 19 0.59
20 7 0.22
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATCTTTATTTTATCC
Found at i:2568296 original size:23 final size:22
Alignment explanation
Indices: 2568269--2568333 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 22
2568259 TATATTATTG
*
2568269 TTATTATTTTTTATTTTTTTCAT
1 TTATTATTTTTTATTTTTATC-T
2568292 TTATTATTTTATTAATTTTTATCT
1 TTATTATTTT-TT-ATTTTTATCT
2568316 TTACTT-TGTTTTTATTTT
1 TTA-TTAT-TTTTTATTTT
2568334 ATGTATCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 15 0.41
24 9 0.24
25 13 0.35
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (22 bp):
TTATTATTTTTTATTTTTATCT
Found at i:2573571 original size:17 final size:18
Alignment explanation
Indices: 2573545--2573578 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2573535 ATATATCATT
2573545 TTATTATTTAT-TTTAAA
1 TTATTATTTATATTTAAA
*
2573562 TTATTTTTTATATTTAA
1 TTATTATTTATATTTAA
2573579 TAATATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTATTTATATTTAAA
Found at i:2575712 original size:21 final size:21
Alignment explanation
Indices: 2575674--2575713 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2575664 TATCGATACT
* *
2575674 AAGGGCTTGGTGTTGAGACCA
1 AAGGGCTTGGTATAGAGACCA
2575695 AAGGGCTTGGTATAGAGAC
1 AAGGGCTTGGTATAGAGAC
2575714 TGGTATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.38, T:0.23
Consensus pattern (21 bp):
AAGGGCTTGGTATAGAGACCA
Found at i:2577238 original size:22 final size:23
Alignment explanation
Indices: 2577211--2577253 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2577201 AAATAAAGCA
2577211 AAATAAAGA-AGAGAAAATAAGT
1 AAATAAAGACAGAGAAAATAAGT
* *
2577233 AAATAACGACAGATAAAATAA
1 AAATAAAGACAGAGAAAATAA
2577254 AGACAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.67, C:0.05, G:0.14, T:0.14
Consensus pattern (23 bp):
AAATAAAGACAGAGAAAATAAGT
Found at i:2577560 original size:23 final size:23
Alignment explanation
Indices: 2577533--2577588 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2577523 GATAATCATA
2577533 ATATACATATAATA-CTAATAAAT
1 ATATACATATAATATCTAA-AAAT
* * * *
2577556 TTATAAATAAAATATTTAAAAAT
1 ATATACATATAATATCTAAAAAT
2577579 ATATACATAT
1 ATATACATAT
2577589 GTAAACTGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATACATATAATATCTAAAAAT
Found at i:2580898 original size:45 final size:44
Alignment explanation
Indices: 2580819--2580939 Score: 156
Period size: 45 Copynumber: 2.7 Consensus size: 44
2580809 ATATCCAAAT
* *
2580819 CGCCTTTT-CGGGTTTTCAACTTGGACCCATCCTTGGTTGCAAGA
1 CGCCTTTTGCGGGTTTTCATCTT-GACCCACCCTTGGTTGCAAGA
*
2580863 CGCCTTTTGTGGGTTTTCATCTTGATCCCACCCTTGGTTGCAAGA
1 CGCCTTTTGCGGGTTTTCATCTTGA-CCCACCCTTGGTTGCAAGA
*
2580908 CGTCC-TTTGCGGGTTTTCATCTTTAACCCACC
1 CG-CCTTTTGCGGGTTTTCATC-TTGACCCACC
2580940 TTATTTTTCT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
44 10 0.15
45 53 0.78
46 5 0.07
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (44 bp):
CGCCTTTTGCGGGTTTTCATCTTGACCCACCCTTGGTTGCAAGA
Found at i:2584671 original size:28 final size:28
Alignment explanation
Indices: 2584634--2584704 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
2584624 TATTTGAAAG
2584634 AAAATGGAAATGAAGTGCTGAAATGAGA
1 AAAATGGAAATGAAGTGCTGAAATGAGA
2584662 AAAATGGAAATGAAGTGCTGAAATGAGA
1 AAAATGGAAATGAAGTGCTGAAATGAGA
*
2584690 AAAATAGACAATGAA
1 AAAATGGA-AATGAA
2584705 TAATGAAAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 35 0.85
29 6 0.15
ACGTcount: A:0.54, C:0.04, G:0.25, T:0.17
Consensus pattern (28 bp):
AAAATGGAAATGAAGTGCTGAAATGAGA
Found at i:2584711 original size:28 final size:28
Alignment explanation
Indices: 2584634--2584712 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
2584624 TATTTGAAAG
* **
2584634 AAAATGGAAATGAAGTGCTGAAATGAGA
1 AAAATAGAAATGAAGTAATGAAATGAGA
* **
2584662 AAAATGGAAATGAAGTGCTGAAATGAGA
1 AAAATAGAAATGAAGTAATGAAATGAGA
2584690 AAAATAGACAATGAA-TAATGAAA
1 AAAATAGA-AATGAAGTAATGAAA
2584713 GAAAATTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 41 0.87
29 6 0.13
ACGTcount: A:0.54, C:0.04, G:0.24, T:0.18
Consensus pattern (28 bp):
AAAATAGAAATGAAGTAATGAAATGAGA
Found at i:2588634 original size:16 final size:17
Alignment explanation
Indices: 2588613--2588650 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
2588603 AAAAAACAAT
2588613 TAATAGA-TATAAATAA
1 TAATAGACTATAAATAA
2588629 TAATAGACGTATAAATAA
1 TAATAGAC-TATAAATAA
2588647 -AATA
1 TAATA
2588651 TTAATAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (17 bp):
TAATAGACTATAAATAA
Found at i:2588743 original size:23 final size:23
Alignment explanation
Indices: 2588716--2588771 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2588706 GATAATTATA
2588716 ATATACATATAATA-CTAATAAAT
1 ATATACATATAATATCTAA-AAAT
* * * *
2588739 TTATAAATAAAATATTTAAAAAT
1 ATATACATATAATATCTAAAAAT
2588762 ATATACATAT
1 ATATACATAT
2588772 GTAAACTGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATACATATAATATCTAAAAAT
Found at i:2590021 original size:21 final size:19
Alignment explanation
Indices: 2589995--2590033 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
2589985 AATGACAATA
2589995 TTTATACAATATATATATAAT
1 TTTATA-AATA-ATATATAAT
*
2590016 TTTATATATAATATATAA
1 TTTATAAATAATATATAA
2590034 ATATATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTATAAATAATATATAAT
Found at i:2590028 original size:23 final size:24
Alignment explanation
Indices: 2589997--2590041 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2589987 TGACAATATT
*
2589997 TATACAATATATATATA-ATTTTA
1 TATACAATATATAAATATATTTTA
*
2590020 TATATAATATATAAATATATTT
1 TATACAATATATAAATATATTT
2590042 CGGTCGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TATACAATATATAAATATATTTTA
Found at i:2592307 original size:16 final size:16
Alignment explanation
Indices: 2592271--2592306 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
2592261 TTCAGGTTGG
2592271 ATTTTGGGTCGGGTCA
1 ATTTTGGGTCGGGTCA
2592287 ATTTTGGGT-GGGTCA
1 ATTTTGGGTCGGGTCA
2592302 ATTTT
1 ATTTT
2592307 TTGGATCGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.14, C:0.08, G:0.33, T:0.44
Consensus pattern (16 bp):
ATTTTGGGTCGGGTCA
Found at i:2594122 original size:99 final size:99
Alignment explanation
Indices: 2594016--2594213 Score: 396
Period size: 99 Copynumber: 2.0 Consensus size: 99
2594006 GTGCCTGATC
2594016 GAAAACAAAATACTATCATGAATGGTGTCCAAAAAGGTGCTTGCAATACCGAAAGAAAATAGCCC
1 GAAAACAAAATACTATCATGAATGGTGTCCAAAAAGGTGCTTGCAATACCGAAAGAAAATAGCCC
2594081 GGTCTTCCTTGCATTCAATTTGAGACGACATGGT
66 GGTCTTCCTTGCATTCAATTTGAGACGACATGGT
2594115 GAAAACAAAATACTATCATGAATGGTGTCCAAAAAGGTGCTTGCAATACCGAAAGAAAATAGCCC
1 GAAAACAAAATACTATCATGAATGGTGTCCAAAAAGGTGCTTGCAATACCGAAAGAAAATAGCCC
2594180 GGTCTTCCTTGCATTCAATTTGAGACGACATGGT
66 GGTCTTCCTTGCATTCAATTTGAGACGACATGGT
2594214 CTAAAATTAC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (99 bp):
GAAAACAAAATACTATCATGAATGGTGTCCAAAAAGGTGCTTGCAATACCGAAAGAAAATAGCCC
GGTCTTCCTTGCATTCAATTTGAGACGACATGGT
Found at i:2595994 original size:15 final size:14
Alignment explanation
Indices: 2595974--2596049 Score: 70
Period size: 15 Copynumber: 5.5 Consensus size: 14
2595964 ATTTTACTTA
2595974 ATTATTATTAAAATT
1 ATTATTATT-AAATT
*
2595989 ATTATTATTATAAAT
1 ATTATTATTA-AATT
*
2596004 ATTATTATTATATT
1 ATTATTATTAAATT
2596018 A-TATATATT--A-T
1 ATTAT-TATTAAATT
*
2596029 ATTATTATTAAATA
1 ATTATTATTAAATT
2596043 ATTATTA
1 ATTATTA
2596050 CAAGTCCAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
11 6 0.12
12 4 0.08
13 4 0.08
14 15 0.29
15 22 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATTATTAAATT
Found at i:2595997 original size:18 final size:19
Alignment explanation
Indices: 2595974--2596049 Score: 97
Period size: 18 Copynumber: 4.1 Consensus size: 19
2595964 ATTTTACTTA
2595974 ATTATTATTAAA-ATTATT
1 ATTATTATTAAATATTATT
2595992 ATTATTA-TAAATATTATT
1 ATTATTATTAAATATTATT
2596010 ATTA-TATTATATATATTA-T
1 ATTATTATTA-A-ATATTATT
2596029 ATTATTATTAAATAATTATT
1 ATTATTATTAAAT-ATTATT
2596049 A
1 A
2596050 CAAGTCCAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.12
18 21 0.41
19 11 0.22
20 13 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATTATTAAATATTATT
Found at i:2596019 original size:20 final size:21
Alignment explanation
Indices: 2595986--2596038 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
2595976 TATTATTAAA
2595986 ATTATTATTATTATAAATATT
1 ATTATTATTATTATAAATATT
*
2596007 ATTATTA-TATTATATATATT
1 ATTATTATTATTATAAATATT
2596027 A-TATTATTATTA
1 ATTATTATTATTA
2596039 AATAATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.17
20 18 0.60
21 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTATTATTATAAATATT
Found at i:2596049 original size:3 final size:3
Alignment explanation
Indices: 2595974--2596038 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
2595964 ATTTTACTTA
** * *
2595974 ATT ATT ATT AAA ATT ATT ATT ATT ATA AAT ATT ATT ATT A-T ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2596020 ATAT ATT A-T ATT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A
2596039 AATAATTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.12
3 41 0.82
4 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:2596795 original size:18 final size:18
Alignment explanation
Indices: 2596774--2596812 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2596764 GAAGACGACT
2596774 GTCGACCGGTGGACGGCC
1 GTCGACCGGTGGACGGCC
2596792 GTCGACCGGTGGACGGCC
1 GTCGACCGGTGGACGGCC
2596810 GTC
1 GTC
2596813 CTCCGGTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.33, G:0.44, T:0.13
Consensus pattern (18 bp):
GTCGACCGGTGGACGGCC
Found at i:2596818 original size:18 final size:18
Alignment explanation
Indices: 2596778--2596819 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2596768 ACGACTGTCG
*
2596778 ACCGGTGGACGGCCGTCG
1 ACCGGTGGACGGCCGTCC
2596796 ACCGGTGGACGGCCGTCC
1 ACCGGTGGACGGCCGTCC
*
2596814 TCCGGT
1 ACCGGT
2596820 TGGAGGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.36, G:0.40, T:0.14
Consensus pattern (18 bp):
ACCGGTGGACGGCCGTCC
Found at i:2597124 original size:2 final size:2
Alignment explanation
Indices: 2597112--2597156 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
2597102 TCCTTTACTA
2597112 AT AT A- AT AT AT AT AT AT AT AT AT A- AT -T 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
2597151 AT AT AT
1 AT AT AT
2597157 TTAGGATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2597546 original size:22 final size:24
Alignment explanation
Indices: 2597520--2597566 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2597510 ATATTAGTCA
2597520 TAAATA-TAA-ATCTATATATTTT
1 TAAATATTAATATCTATATATTTT
* *
2597542 TAAATATTAATATTTATTTATTTT
1 TAAATATTAATATCTATATATTTT
2597566 T
1 T
2597567 TCGAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 12 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TAAATATTAATATCTATATATTTT
Found at i:2597967 original size:16 final size:17
Alignment explanation
Indices: 2597913--2597967 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
2597903 ATATCTTATT
*
2597913 TATATT-TAAAATTAATA
1 TATATTATAAAA-TAACA
*
2597930 TATTTTCATAAAATAACA
1 TATATT-ATAAAATAACA
2597948 -ATATTATAAAATAA-A
1 TATATTATAAAATAACA
2597963 TATAT
1 TATAT
2597968 CTTTGAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.03
16 13 0.41
17 9 0.28
18 4 0.12
19 5 0.16
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATTATAAAATAACA
Found at i:2598430 original size:25 final size:24
Alignment explanation
Indices: 2598402--2598454 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
2598392 TAATTCTTTC
*
2598402 TTTTCAAAATTTTTATATATATTTA
1 TTTTCAAAATATTTATATATA-TTA
* *
2598427 TTTTCATAGTATTTATATATATTA
1 TTTTCAAAATATTTATATATATTA
2598451 TTTT
1 TTTT
2598455 ATTAATTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTCAAAATATTTATATATATTA
Found at i:2600265 original size:716 final size:716
Alignment explanation
Indices: 2598870--2600302 Score: 2664
Period size: 716 Copynumber: 2.0 Consensus size: 716
2598860 AATCTAAGAC
2598870 AATACTGAAACCATGTCCATAGGTGTACACAAAGGAGAAATAAGTTTTAGCTTTTAATTTATTTA
1 AATACTGAAACCATGTCCATAGGTGTACACAAAGGAGAAATAAGTTTTAGCTTTTAATTTATTTA
2598935 ATTTATTATTATTTTTCTCTCTGAATAAATGCATGTGAACTAGAAATCATGCAGTTAGGTTAATT
66 ATTTATTATTATTTTTCTCTCTGAATAAATGCATGTGAACTAGAAATCATGCAGTTAGGTTAATT
*
2599000 TTTCCAAACAAGCATGGAACTAGAAAACATGAGGTTAGGATTTATACTTTGATAAATAGGATCTT
131 TTTCCAAACAAGCATGGAACTAGAAAACATAAGGTTAGGATTTATACTTTGATAAATAGGATCTT
2599065 TTCTTTCCATTAATTGGTACTAACCAATTTCTTTTTTCACTTCTCATTTTTTTCATACATATTGT
196 TTCTTTCCATTAATTGGTACTAACCAATTTCTTTTTTCACTTCTCATTTTTTTCATACATATTGT
2599130 TTGCTCTAAACTTGTTTATATTTGATTTCTTTTGTTTGCATTGCATGATCATGACATAATCAAAA
261 TTGCTCTAAACTTGTTTATATTTGATTTCTTTTGTTTGCATTGCATGATCATGACATAATCAAAA
*
2599195 GGTGTTGACTTGAAAGATGTTCATCAAATTGGAAAGAAATCGTAAATGGACAAAAAGTTTTATGA
326 GGTGTCGACTTGAAAGATGTTCATCAAATTGGAAAGAAATCGTAAATGGACAAAAAGTTTTATGA
2599260 TCAAACAAAATATGATGCGGCCAAGGAAAATATCCTGAAGAAACTACGAGATCGAGGGAAGTTTG
391 TCAAACAAAATATGATGCGGCCAAGGAAAATATCCTGAAGAAACTACGAGATCGAGGGAAGTTTG
*
2599325 TACATAGAGAACCGGTATATTAATACCAAAAGTGTTACACAAAGATCCTTCCAGATTGATACCAA
456 TACATAGAGAACCGGTATATTAATACCAAAAGTGTTACACAAAGATCCTACCAGATTGATACCAA
*
2599390 AAGCAGTCTATGGTAAGAATAACAGTCAGGGCATTCAGAGTAGTGGAGGTTTTTATGAAGCTCAA
521 AAGCAGTCTATGGTAAGAACAACAGTCAGGGCATTCAGAGTAGTGGAGGTTTTTATGAAGCTCAA
2599455 GCATGTTATTTGAAGGACTTGAACGACCAAAACAAGAAATTGAGCACGAAATGAAAACCATGCAT
586 GCATGTTATTTGAAGGACTTGAACGACCAAAACAAGAAATTGAGCACGAAATGAAAACCATGCAT
2599520 GAAGATTTTCAGAAGATCAGTCAAGCCTTTCGAAATGCTGGCATAGGAAACA-CCCAGAAGAGTG
651 GAAGATTTTCAGAAGATCAGTCAAGCCTTTCGAAATGCTGGCATAGGAAACACCCCAGAAGAGTG
2599584 G
716 G
2599585 AATACTGAAACCATGTCCATAGGTGTACACAAAGGAGAAATAAGTTTTAGCTTTTAATTTATTTA
1 AATACTGAAACCATGTCCATAGGTGTACACAAAGGAGAAATAAGTTTTAGCTTTTAATTTATTTA
*
2599650 ATTTATTATTTTTTTTCTCTCTGAATAAATGCATGTGAACTAGAAATCATGCAGTTAGGTTAATT
66 ATTTATTATTATTTTTCTCTCTGAATAAATGCATGTGAACTAGAAATCATGCAGTTAGGTTAATT
*
2599715 TTTCCAAACAAAGTATGGAACTAGAAAACATAAGGTTAGGATTTATACTTTGATAAATAGGATCT
131 TTTCCAAAC-AAGCATGGAACTAGAAAACATAAGGTTAGGATTTATACTTTGATAAATAGGATCT
2599780 TTTCTTTCCATTAATTGGTACTAACCAATTTCTTTTTTCACTTCTCATTTTTTTCATACATATTG
195 TTTCTTTCCATTAATTGGTACTAACCAATTTCTTTTTTCACTTCTCATTTTTTTCATACATATTG
*
2599845 TTTGCTCTAAACTTGTTTATATTTGATTTCTTTTGTTTGCATTGCATGATCATGGCATAATCAAA
260 TTTGCTCTAAACTTGTTTATATTTGATTTCTTTTGTTTGCATTGCATGATCATGACATAATCAAA
2599910 AGGTGTCGACTTGAAAGACTGTTCATCAAATTGGAAAGAAATCGTAAATGGACAAAAAGTTTTAT
325 AGGTGTCGACTTGAAAGA-TGTTCATCAAATTGGAAAGAAATCGTAAATGGACAAAAAGTTTTAT
2599975 GATCAAACAAAATATGATGCGGCCAAGGAAAAATATCCTGAAGAAACTACGAGGATCGAGGGAAG
389 GATCAAACAAAATATGATGCGGCCAAGG-AAAATATCCTGAAGAAACTACGA-GATCGAGGGAAG
*
2600040 TTCTGTACATAGAGAA-CGTTTATATT-ATACC-AAAGTGTTACAC-AA-ATCCTACCAGATTGA
452 TT-TGTACATAGAGAACCG-GTATATTAATACCAAAAGTGTTACACAAAGATCCTACCAGATTGA
*
2600100 TACCAAAAGCAGTGTATGGTAAGAACAACAGTCAGGGCATTCAGAGTAGTGGAGGTTTTTATGAA
515 TACCAAAAGCAGTCTATGGTAAGAACAACAGTCAGGGCATTCAGAGTAGTGGAGGTTTTTATGAA
2600165 GCTCAAGCATGTTATTTGAAGGACTTGAACGACCAAAACAAGAAATTGAGCACAGAAATGAAAAC
580 GCTCAAGCATGTTATTTGAAGGACTTGAACGACCAAAACAAGAAATTGAGCAC-GAAATGAAAAC
2600230 CATGCATGAAGATTTTCAGAAGATCAGTC-AGCCTTTCGAAATGCTGGCATAGGAAACACCCCAG
644 CATGCATGAAGATTTTCAGAAGATCAGTCAAGCCTTTCGAAATGCTGGCATAGGAAACACCCCAG
*
2600294 AATAGTGG
709 AAGAGTGG
2600302 A
1 A
2600303 TCACAGGGGT
Statistics
Matches: 700, Mismatches: 10, Indels: 14
0.97 0.01 0.02
Matches are distributed among these distances:
715 138 0.20
716 358 0.51
717 129 0.18
718 35 0.05
719 21 0.03
720 19 0.03
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (716 bp):
AATACTGAAACCATGTCCATAGGTGTACACAAAGGAGAAATAAGTTTTAGCTTTTAATTTATTTA
ATTTATTATTATTTTTCTCTCTGAATAAATGCATGTGAACTAGAAATCATGCAGTTAGGTTAATT
TTTCCAAACAAGCATGGAACTAGAAAACATAAGGTTAGGATTTATACTTTGATAAATAGGATCTT
TTCTTTCCATTAATTGGTACTAACCAATTTCTTTTTTCACTTCTCATTTTTTTCATACATATTGT
TTGCTCTAAACTTGTTTATATTTGATTTCTTTTGTTTGCATTGCATGATCATGACATAATCAAAA
GGTGTCGACTTGAAAGATGTTCATCAAATTGGAAAGAAATCGTAAATGGACAAAAAGTTTTATGA
TCAAACAAAATATGATGCGGCCAAGGAAAATATCCTGAAGAAACTACGAGATCGAGGGAAGTTTG
TACATAGAGAACCGGTATATTAATACCAAAAGTGTTACACAAAGATCCTACCAGATTGATACCAA
AAGCAGTCTATGGTAAGAACAACAGTCAGGGCATTCAGAGTAGTGGAGGTTTTTATGAAGCTCAA
GCATGTTATTTGAAGGACTTGAACGACCAAAACAAGAAATTGAGCACGAAATGAAAACCATGCAT
GAAGATTTTCAGAAGATCAGTCAAGCCTTTCGAAATGCTGGCATAGGAAACACCCCAGAAGAGTG
G
Found at i:2603279 original size:9 final size:8
Alignment explanation
Indices: 2603259--2603301 Score: 68
Period size: 8 Copynumber: 5.1 Consensus size: 8
2603249 TGAAAAAAAC
2603259 AAAGGAAA
1 AAAGGAAA
2603267 AAAGGAGAA
1 AAAGGA-AA
2603276 AAAGGAAAA
1 AAAGG-AAA
2603285 AAAGGAAA
1 AAAGGAAA
2603293 AAAGGAAA
1 AAAGGAAA
2603301 A
1 A
2603302 TTGAACCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 18 0.55
9 14 0.42
10 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AAAGGAAA
Found at i:2603281 original size:17 final size:16
Alignment explanation
Indices: 2603259--2603301 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
2603249 TGAAAAAAAC
2603259 AAAGGAAAAAAGGAGAA
1 AAAGGAAAAAAGGA-AA
2603276 AAAGGAAAAAAAGGAAA
1 AAAGG-AAAAAAGGAAA
2603293 AAAGGAAAA
1 AAAGGAAAA
2603302 TTGAACCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.16
17 12 0.48
18 9 0.36
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGGAAAAAAGGAAA
Found at i:2606538 original size:113 final size:113
Alignment explanation
Indices: 2606239--2606860 Score: 869
Period size: 113 Copynumber: 5.7 Consensus size: 113
2606229 TTCCAGAAAG
2606239 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* *
2606304 AACCTTTTGCTCAAATCCATCACTTGATGGATCAAC-TTTCCATAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAAAGAA
2606351 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
2606416 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAAAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAAAGAA
2606464 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
** * *
2606529 AATATTTTGCTCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAAAGAA
* *
2606577 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAG-A-AA--TGA-AA-GA-AAGAACTT-TT-
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * * * *
2606632 ----TGTTTGAATTC--AT-CACTCGA-TGGAT-CA-A--CTTTTCCAGAGAA
66 AACCT-TTTG--CTCAAATCCA-TC-ACTTGATGGATCAGCTTTTCCAAAGAA
2606673 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* *
2606738 AACCTTTTGCTCAAACCCATCACTTGATGGATCAGCTTTTCC-AGGAAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAAAG-AA
*
2606786 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
*
2606851 GACCTTTTGC
66 AACCTTTTGC
2606861 ATGACCCTAT
Statistics
Matches: 457, Mismatches: 24, Indels: 57
0.85 0.04 0.11
Matches are distributed among these distances:
96 43 0.09
97 4 0.01
98 1 0.00
99 6 0.01
100 12 0.03
101 3 0.01
102 4 0.01
103 2 0.00
104 9 0.02
105 9 0.02
106 2 0.00
107 4 0.01
108 3 0.01
109 11 0.02
110 6 0.01
111 1 0.00
112 105 0.23
113 232 0.51
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAAAGAA
Found at i:2606793 original size:209 final size:216
Alignment explanation
Indices: 2606217--2606850 Score: 903
Period size: 209 Copynumber: 2.9 Consensus size: 216
2606207 ATCCATCACA
* *
2606217 ATGGATTAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
2606281 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAAC-TTTCC
65 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
* *
2606345 ATAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
130 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-A-AAG-TCATAATGAGAAGAAC
*
2606410 TTGTTCAACCTTTTGCTCAAATCCATCACTTG
192 TTGTT----CTTTTG--C-AATCCATCACTCG
* *
2606442 ATGGATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
** *
2606507 TCATAATGAGAAGAGCTTGTTCAATATTTTGCTCAAATCCATCACTTGATGGATCAGTTTTTCCA
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCA
*
2606572 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAA-TGA-AA-GA-AAGAACTT-T
131 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAGTCATAATGAGAAGAACTTGT
*
2606631 T-TGTTTG-AATTCATCACTCG
196 TCT-TTTGCAATCCATCACTCG
2606651 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
2606716 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAACCCATCACTTGATGGATCAGCTTTTCCA
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCA
* *
2606781 G-GAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAGC
131 GAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-A-AAG-TCATAATGAGAAGAAC
2606845 TTGTTC
192 TTGTTC
2606851 GACCTTTTGC
Statistics
Matches: 373, Mismatches: 22, Indels: 34
0.87 0.05 0.08
Matches are distributed among these distances:
208 1 0.00
209 169 0.45
210 4 0.01
211 1 0.00
212 3 0.01
213 4 0.01
214 2 0.01
215 2 0.01
216 1 0.00
217 9 0.02
218 9 0.02
219 2 0.01
220 2 0.01
221 2 0.01
223 2 0.01
224 1 0.00
225 116 0.31
226 43 0.12
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (216 bp):
ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCA
GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAGTCATAATGAGAAGAACTTGT
TCTTTTGCAATCCATCACTCG
Found at i:2607603 original size:162 final size:164
Alignment explanation
Indices: 2607317--2607618 Score: 457
Period size: 162 Copynumber: 1.8 Consensus size: 164
2607307 AAAATGAGCA
* *
2607317 TTATATTGAGATTGGGGCATGTTACCCAAACAACATGTTATTTCAAAAAATAATGAGAAAACGAT
1 TTATATTGAGATTGGGGCATGTTACCCAAACAACATGTTATTT-AAAAAATAATGACAAAACAAT
* **
2607382 TTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAATAAGAAAACGATTTCCA
65 TTCCATAGTTTATCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAATAAGAAAACGATTTCCA
2607447 TAGTTTTTTTACTTAGTAAACTATTTCCAACCGCC
130 TAGTTTTTTTACTTAGTAAACTATTTCCAACCGCC
* * *
2607482 TTATCTTGAGATTGGGG-ATGTTACCCAATC-ACATGTTATTT-GAAAATAATGACAAAACAATT
1 TTATATTGAGATTGGGGCATGTTACCCAAACAACATGTTATTTAAAAAATAATGACAAAACAATT
* * * *
2607544 TTCATAGTTTATTATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCA
66 TCCATAGTTTATCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAATAAGAAAACGATTTCCA
2607609 TAGTTTTTTT
130 TAGTTTTTTT
2607619 TAAAACTATC
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
161 40 0.32
162 45 0.36
163 11 0.09
164 12 0.10
165 16 0.13
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (164 bp):
TTATATTGAGATTGGGGCATGTTACCCAAACAACATGTTATTTAAAAAATAATGACAAAACAATT
TCCATAGTTTATCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAATAAGAAAACGATTTCCAT
AGTTTTTTTACTTAGTAAACTATTTCCAACCGCC
Found at i:2607681 original size:45 final size:45
Alignment explanation
Indices: 2607632--2608297 Score: 964
Period size: 45 Copynumber: 14.8 Consensus size: 45
2607622 AACTATCCCA
* * *
2607632 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAACCCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
2607677 CATCTGTAAGCCCTTCTGTGGTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
2607722 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
2607767 CATCTGTAAGCCCTT-ATGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCA-GTGCTTGATGTTTTCAAAACCTTCGGGT
2607812 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACC-TCTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTC-GGGT
* *
2607857 CATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
2607902 CATCTGTAAGCCCTTCAGTGCTTGATGTTTT-AAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAA-CCTTCGGGT
*
2607947 CATCTGTAAG-CCTTCAGTGCTTGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
2607991 CATCTGTAAGCCCTTCAGTG-TATGATGTTATTCAAAACCTCCGAGT
1 CATCTGTAAGCCCTTCAGTGCT-TGATGTT-TTCAAAACCTTCGGGT
* *
2608037 CATATGTAAGCCCTTCAGTGCTTGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* * *
2608082 AATCTGTAAGCCCTTCAGTGCCTGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* * *
2608127 CCTCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* * * * *
2608172 TATCTGTAAGCCCTTTAGTGCATGATGTTATTCAAAACCGTCCGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTT-TTCAAAACCTTCGGGT
* * * * *
2608218 AATCTGTAAGTCCTTCAGTGCATAATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
2608263 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAA
2608298 CATTTCCATC
Statistics
Matches: 564, Mismatches: 46, Indels: 22
0.89 0.07 0.03
Matches are distributed among these distances:
44 45 0.08
45 436 0.77
46 82 0.15
47 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
Found at i:2608418 original size:3 final size:3
Alignment explanation
Indices: 2608410--2608470 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
2608400 ATTTTACTTA
** *
2608410 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATA ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2608457 ATT AAAT ATT ATT A
1 ATT -ATT ATT ATT A
2608471 CAAGCCTAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.92
4 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:2608863 original size:18 final size:19
Alignment explanation
Indices: 2608840--2608918 Score: 85
Period size: 18 Copynumber: 4.2 Consensus size: 19
2608830 ATTTTACTTA
2608840 ATTATTATTA-AAATTATT
1 ATTATTATTATAAATTATT
2608858 ATTATTATTATAAA-TATT
1 ATTATTATTATAAATTATT
*
2608876 ATTATTA-TATTATATATATT
1 ATTATTATTA-TAAAT-TATT
*
2608896 A-TATTATTATTAAATAATT
1 ATTATTATTA-TAAATTATT
2608915 ATTA
1 ATTA
2608919 CAAGCCTAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
17 2 0.04
18 24 0.46
19 12 0.23
20 14 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATTATTATAAATTATT
Found at i:2608918 original size:3 final size:3
Alignment explanation
Indices: 2608840--2608907 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
2608830 ATTTTACTTA
** * *
2608840 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2608887 A-T ATAT ATT A-T ATT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT A
2608908 AATAATTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
2 6 0.11
3 44 0.83
4 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:2610027 original size:29 final size:30
Alignment explanation
Indices: 2609994--2610052 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2609984 AGGGCTGTAA
2609994 ATTTTAATATTT-TATATTTTAATC-CTATT
1 ATTTTAAT-TTTATATATTTTAATCACTATT
* *
2610023 ATTTTAATTTTATATGTTTTAGTCACTATT
1 ATTTTAATTTTATATATTTTAATCACTATT
2610053 TAATTGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (30 bp):
ATTTTAATTTTATATATTTTAATCACTATT
Found at i:2611232 original size:28 final size:27
Alignment explanation
Indices: 2611181--2611234 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2611171 ATATTAATAA
*
2611181 AATAATATATATAAATACTATGAAAAT
1 AATAATATATATAAAAACTATGAAAAT
* *
2611208 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAACTATGAAAA
2611235 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (27 bp):
AATAATATATATAAAAACTATGAAAAT
Found at i:2614131 original size:3 final size:3
Alignment explanation
Indices: 2614123--2614156 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2614113 TTTCGTCCCG
2614123 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2614157 CAAATAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2621583 original size:16 final size:16
Alignment explanation
Indices: 2621562--2621596 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2621552 TTTCCTAGAA
2621562 TCAATTTTTGACTTTC
1 TCAATTTTTGACTTTC
2621578 TCAATTTTTGACTTTC
1 TCAATTTTTGACTTTC
2621594 TCA
1 TCA
2621597 TAAAGAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (16 bp):
TCAATTTTTGACTTTC
Found at i:2621727 original size:62 final size:62
Alignment explanation
Indices: 2621585--2621734 Score: 176
Period size: 62 Copynumber: 2.4 Consensus size: 62
2621575 TTCTCAATTT
* * * * **
2621585 TTGACTTTCTCATAAAGAGAAGTCAACCTTTATTATTCCTGACTCCCTAGTAGAGTCATTTT
1 TTGACTTTATCATAAAGAGAAGTCAACATGTATTATTCCTGACTCCCTAGTAGAGTCAATCC
* * * * *
2621647 TTGACTTCATCGTGAAGAGAAGTCAACATGTATTATTTCTGACTCCCTA-TAGGAGTTAATCC
1 TTGACTTTATCATAAAGAGAAGTCAACATGTATTATTCCTGACTCCCTAGTA-GAGTCAATCC
*
2621709 TTGATTTTATCATAAAGAGAAGTCAA
1 TTGACTTTATCATAAAGAGAAGTCAA
2621735 TCTTTTTAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 2 0.03
62 70 0.97
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (62 bp):
TTGACTTTATCATAAAGAGAAGTCAACATGTATTATTCCTGACTCCCTAGTAGAGTCAATCC
Found at i:2621986 original size:47 final size:47
Alignment explanation
Indices: 2621917--2622018 Score: 177
Period size: 47 Copynumber: 2.2 Consensus size: 47
2621907 CACGGAAAAA
2621917 TAGTGGAACAAATTCTTCTTATTTCAGATTTGGTCTCTACAAAAGAG
1 TAGTGGAACAAATTCTTCTTATTTCAGATTTGGTCTCTACAAAAGAG
* **
2621964 TAGTGGAACAAATTCTTCTTATTTCAGATTTGGTCTCTGCGGAAGAG
1 TAGTGGAACAAATTCTTCTTATTTCAGATTTGGTCTCTACAAAAGAG
2622011 TAGTGGAA
1 TAGTGGAA
2622019 GTGAAACAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (47 bp):
TAGTGGAACAAATTCTTCTTATTTCAGATTTGGTCTCTACAAAAGAG
Found at i:2622129 original size:36 final size:36
Alignment explanation
Indices: 2622082--2622399 Score: 424
Period size: 36 Copynumber: 8.8 Consensus size: 36
2622072 TATTTCAAAT
*
2622082 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTTATC
1 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTCATC
*
2622118 TTAGCATTCACGGAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTCATC
*
2622154 TTAGCCTTCACGAAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTCATC
* * *
2622190 TTAGCCTCCATGGAAGAGTAGTGAAACAAAGTCATC
1 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTCATC
*
2622226 TTAGCCTCCACGGAAGAGTAGTGAAGCAAA-TCCATC
1 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGT-CATC
* * * *
2622262 TTATCCTTCACAGAAGAGTAGTGAAGGAAAGCCATC
1 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTCATC
* * *
2622298 ATAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATC
1 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTCATC
* * *
2622334 TTAGCCTCCACGGAAAAGTAGTGAAGCAAAGCCATC
1 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTCATC
**
2622370 ATT-GCCTTCACAAAAAGAGTAGTGAAGCAA
1 -TTAGCCTTCAC-GGAAGAGTAGTGAAGCAA
2622400 GAACAAATCA
Statistics
Matches: 252, Mismatches: 26, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
35 1 0.00
36 234 0.93
37 17 0.07
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (36 bp):
TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGTCATC
Found at i:2623814 original size:22 final size:22
Alignment explanation
Indices: 2623788--2623829 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2623778 CGACCACCGT
* *
2623788 GAATAGTGATCGACGGTGGCTG
1 GAATAGTGACCAACGGTGGCTG
2623810 GAATAGTGACCAACGGTGGC
1 GAATAGTGACCAACGGTGGC
2623830 CGAAAAATGG
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:0.26, C:0.17, G:0.38, T:0.19
Consensus pattern (22 bp):
GAATAGTGACCAACGGTGGCTG
Found at i:2633828 original size:43 final size:43
Alignment explanation
Indices: 2633765--2633883 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
2633755 CTAAATTAAG
* *
2633765 AATCCACAAATACACTAAACTAGCATATTAAAACTA-ACGTAAC
1 AATCCACAAATACACCAAACTAACATATTAAAACTAGA-GTAAC
*
2633808 AATCCACAAATTCACCAAACTAACATATTAAAACTAGAGTAAC
1 AATCCACAAATACACCAAACTAACATATTAAAACTAGAGTAAC
* * * *
2633851 AATCCACAAATACATCAAATTAAAATATCAAAA
1 AATCCACAAATACACCAAACTAACATATTAAAA
2633884 GCATTTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 66 0.99
44 1 0.01
ACGTcount: A:0.54, C:0.22, G:0.03, T:0.21
Consensus pattern (43 bp):
AATCCACAAATACACCAAACTAACATATTAAAACTAGAGTAAC
Found at i:2635953 original size:3 final size:3
Alignment explanation
Indices: 2635933--2635974 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2635923 TTACCCATTT
* *
2635933 TTA TTT TTA TTA TAA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
2635975 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2635989 original size:11 final size:11
Alignment explanation
Indices: 2635973--2636015 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 11
2635963 TTATTATTAT
2635973 TAAATAAAAAA
1 TAAATAAAAAA
2635984 TAAATAAAAAAA
1 TAAAT-AAAAAA
2635996 TAATATAAAAAA
1 TAA-ATAAAAAA
2636008 TATAATAA
1 TA-AATAA
2636016 TAATTACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.17
12 21 0.72
13 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
TAAATAAAAAA
Found at i:2636015 original size:12 final size:12
Alignment explanation
Indices: 2635975--2636015 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
2635965 ATTATTATTA
2635975 AATAAAAAATA-
1 AATAAAAAATAT
2635986 AATAAAAAA-AT
1 AATAAAAAATAT
2635997 AATATAAAAAATAT
1 -A-ATAAAAAATAT
2636011 AATAA
1 AATAA
2636016 TAATTACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.04
11 9 0.35
12 5 0.19
13 9 0.35
14 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AATAAAAAATAT
Found at i:2637306 original size:28 final size:26
Alignment explanation
Indices: 2637262--2637316 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
2637252 ATTTTAAATA
*
2637262 ATTAATTAAATTAAGTATTTAATTTT
1 ATTAATTAAATTAAGTAATTAATTTT
*
2637288 ATTAGATTATAATTTAGTAATTAATTTT
1 ATTA-ATTA-AATTAAGTAATTAATTTT
2637316 A
1 A
2637317 AATATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 17 0.68
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (26 bp):
ATTAATTAAATTAAGTAATTAATTTT
Found at i:2637571 original size:24 final size:23
Alignment explanation
Indices: 2637535--2637580 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2637525 TTATAAAAAA
2637535 AAATTATAATTTAAT-TTTATTT
1 AAATTATAATTTAATATTTATTT
2637557 AAATTATATAGTTTAATATTTATT
1 AAATTATA-A-TTTAATATTTATT
2637581 AATATCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 1 0.05
24 6 0.29
25 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATTATAATTTAATATTTATTT
Found at i:2638478 original size:44 final size:43
Alignment explanation
Indices: 2638391--2638532 Score: 178
Period size: 44 Copynumber: 3.2 Consensus size: 43
2638381 ATTAAAAAAT
*
2638391 ATTATTAATTAATAATATTTTATTATTTATTAAAAACATTAATAA
1 ATTATTAATTTATAAT-TTTTATTATTTATTAAAAA-ATTAATAA
* * *
2638436 ATTAGTTAATTTATCATTTTTATTATTTAATAAAAAATTAATAC
1 ATTA-TTAATTTATAATTTTTATTATTTATTAAAAAATTAATAA
* * *
2638480 ATTAATTAATTTATTATTTTTATTATCTATTAATAAATTAAT-A
1 ATT-ATTAATTTATAATTTTTATTATTTATTAAAAAATTAATAA
2638523 ATTATTAATT
1 ATTATTAATT
2638533 AGATTTATTT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
42 7 0.08
43 3 0.03
44 43 0.50
45 23 0.27
46 10 0.12
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (43 bp):
ATTATTAATTTATAATTTTTATTATTTATTAAAAAATTAATAA
Found at i:2644484 original size:26 final size:22
Alignment explanation
Indices: 2644425--2644484 Score: 57
Period size: 26 Copynumber: 2.5 Consensus size: 22
2644415 ATTTAAAAAT
2644425 AATAAATATTATTATTTAATTC
1 AATAAATATTATTATTTAATTC
* *
2644447 AATAAGAAATTATTACATTGTATTTC
1 AATAA-ATATTATT--ATT-TAATTC
2644473 ATATAAATATTA
1 A-ATAAATATTA
2644485 GTGAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 5 0.17
23 7 0.23
25 3 0.10
26 11 0.37
27 4 0.13
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (22 bp):
AATAAATATTATTATTTAATTC
Found at i:2646228 original size:137 final size:137
Alignment explanation
Indices: 2646069--2646537 Score: 621
Period size: 137 Copynumber: 3.4 Consensus size: 137
2646059 CTATCAAAAA
* * * *
2646069 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCATCCTCAGATGAGTTCTTCTCATTGTGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* *
2646134 CTCCTT-T-TGGAAATGCTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATTAAT
66 CT--TTCTCTGAAAATGCTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAAT
2646197 TAAGGCAAG
129 TAAGGCAAG
* *
2646206 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCACATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
2646271 CTTTCTCTGAAAATGCTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAATTA
66 CTTTCTCTGAAAATGCTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAATTA
*
2646336 AGGTAAG
131 AGGCAAG
*
2646343 GTTGAATAAGTTCTTCTCATTATGAACTTCTTCTT--T-TTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
** * * * * * *
2646405 CTTTCTCTGAAAATATTGATCCTCAATAGAGGTTCTTCTTTCATTCAACTCCATAGGTGATGAAT
66 CTTTCTCTGAAAATGCTGATCCTCAAAAGAGG-T-GTCGTTGATTCAACTTCATATGTGATGAAT
*
2646470 CAA-GCTAAG
129 TAAGGC-AAG
* * * * *
2646479 GTCGAACAAGTTATTCT--TTATGAACTTCTTCTTCCTCTTCTGATAAGTTCTTCTTATTA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
2646538 CGAAATCCTT
Statistics
Matches: 296, Mismatches: 28, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
134 69 0.23
135 5 0.02
136 46 0.16
137 176 0.59
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (137 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGAAAATGCTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAATTA
AGGCAAG
Found at i:2646652 original size:39 final size:39
Alignment explanation
Indices: 2646607--2646706 Score: 191
Period size: 39 Copynumber: 2.6 Consensus size: 39
2646597 AAGGTTGAAC
2646607 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
*
2646646 AAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGAT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
2646685 AAGTTCTTCTCATTATGAACTT
1 AAGTTCTTCTCATTATGAACTT
2646707 TCTCTGAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.22, C:0.23, G:0.08, T:0.47
Consensus pattern (39 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
Found at i:2646654 original size:22 final size:22
Alignment explanation
Indices: 2646627--2646694 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
2646617 CATTATGAAC
2646627 TTCTTCTTCCTCTTCAGATAAG
1 TTCTTCTTCCTCTTCAGATAAG
* *
2646649 TTCTTC-T--TATT---ATGAAC
1 TTCTTCTTCCTCTTCAGAT-AAG
2646666 TTCTTCTTCCTCTTCAGATAAG
1 TTCTTCTTCCTCTTCAGATAAG
2646688 TTCTTCT
1 TTCTTCT
2646695 CATTATGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
16 2 0.06
17 8 0.23
18 1 0.03
19 3 0.09
20 3 0.09
21 1 0.03
22 15 0.43
23 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.07, T:0.50
Consensus pattern (22 bp):
TTCTTCTTCCTCTTCAGATAAG
Found at i:2646679 original size:162 final size:162
Alignment explanation
Indices: 2646496--2646830 Score: 512
Period size: 162 Copynumber: 2.1 Consensus size: 162
2646486 AAGTTATTCT
* * *
2646496 TTATGAACTTCTTCTTCCTCTTCTGATAAGTTCTTCTTATTACGAAATC-CTTCTGGAAATATT-
1 TTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTACGAAATCTC-TCTGAAAATATTA
* * *
2646559 GATGCTGATCTATATTCTTCTGTGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
65 G-TGCTGATCTATATCCTTCTGGGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
2646624 AACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTA
129 AACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTA
* * * *
2646658 TTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGAAAATGTTAG
1 TTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTACGAAATCTCTCTGAAAATATTAG
* * *
2646723 TGCTGATCTATCTCCTTTTGGGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
66 TGCTGATCTATATCCTTCTGGGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
*
2646788 CTTCTTCTTCCTCTTCAGATGAGTTCTTCTTA
131 CTTCTTCTTCCTCTTCAGATAAGTTCTTCTTA
2646820 TTATGAACTTC
1 TTATGAACTTC
2646831 CTCTGGAAAT
Statistics
Matches: 157, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
162 155 0.99
163 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (162 bp):
TTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTACGAAATCTCTCTGAAAATATTAG
TGCTGATCTATATCCTTCTGGGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
CTTCTTCTTCCTCTTCAGATAAGTTCTTCTTA
Found at i:2646778 original size:123 final size:123
Alignment explanation
Indices: 2646646--2646951 Score: 524
Period size: 123 Copynumber: 2.5 Consensus size: 123
2646636 CTCTTCAGAT
* *
2646646 AAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
1 AAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTC
2646711 TGAAAATGTTAGTGCTGATCTATCTCCTTTTGGGATAGAATCGAGCAAAAGGTTGAAC
66 TGAAAATGTTAGTGCTGATCTATCTCCTTTTGGGATAGAATCGAGCAAAAGGTTGAAC
* *
2646769 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTATGAACTTCCTC
1 AAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTC
* * *
2646834 TGGAAATGTTGGTGTTGATCTATCTCCTTTTGGGATAGAATCGAGCAAAAGGTTGAAC
66 TGAAAATGTTAGTGCTGATCTATCTCCTTTTGGGATAGAATCGAGCAAAAGGTTGAAC
*
2646892 AAGTTCTTATTATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 AAGTTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACT
2646952 CTTTTTGGAA
Statistics
Matches: 172, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
122 3 0.02
123 169 0.98
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (123 bp):
AAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTC
TGAAAATGTTAGTGCTGATCTATCTCCTTTTGGGATAGAATCGAGCAAAAGGTTGAAC
Found at i:2647822 original size:22 final size:22
Alignment explanation
Indices: 2647792--2647936 Score: 245
Period size: 22 Copynumber: 6.6 Consensus size: 22
2647782 AATAAAGCTT
2647792 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
2647814 TCATATTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
2647836 TCATCTTTAAAGAGAAAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
2647858 TCATCTTTGAAGAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
*
2647880 TCATCTTTAAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2647902 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2647924 TCATCTTTGAAGA
1 TCATCTTTGAAGA
2647937 ACGTAGATGT
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 113 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:2648391 original size:53 final size:54
Alignment explanation
Indices: 2648297--2648455 Score: 191
Period size: 53 Copynumber: 3.0 Consensus size: 54
2648287 ATAATCATTG
* ** *
2648297 GTTCATAAAACA-TTGACAACACATTCATTATTTCCTATGGC-TCTGC-CTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTATGGCTTCTGCAC-AGAT
* * * *
2648349 GTTTGTAAAACATTTGATAACACATTCATCCTTTTCTGTGGCTTTTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTATGGCTTCTGCACAGAT
* *
2648403 GTTCGTAAAACATTTGACAA-ACGTTCATCCTTTTCTATGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTATGGCTTCTGCACAGAT
2648456 TTCTGGTCAG
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
52 10 0.11
53 53 0.59
54 26 0.29
55 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTATGGCTTCTGCACAGAT
Found at i:2651881 original size:21 final size:22
Alignment explanation
Indices: 2651840--2651890 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
2651830 CTTGATTCAA
*
2651840 TTTTTTCCTTTTTTTCATCTT-
1 TTTTTTTCTTTTTTTCATCTTC
2651861 TTTTTTTCTTTTTTT-ATTCTTC
1 TTTTTTTCTTTTTTTCA-TCTTC
2651883 TTCTTTTT
1 TT-TTTTT
2651891 TGATGAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 18 0.69
22 2 0.08
23 5 0.19
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTCTTTTTTTCATCTTC
Found at i:2651990 original size:151 final size:151
Alignment explanation
Indices: 2651814--2652116 Score: 597
Period size: 151 Copynumber: 2.0 Consensus size: 151
2651804 ATCTTGAATC
2651814 TCAATGAGTAACCCATCTTGATTCAATTTTTTCCTTTTTTTCATCTTTTTTTTTCTTTTTTTATT
1 TCAATGAGTAACCCATCTTGATTCAATTTTTTCCTTTTTTTCATCTTTTTTTTTCTTTTTTTATT
2651879 CTTCTTCTTTTTTGATGAATGAGTATAGGATTTCAATTGCTTTGAGCACCTCCTTTTTCTCTTGC
66 CTTCTTCTTTTTTGATGAATGAGTATAGGATTTCAATTGCTTTGAGCACCTCCTTTTTCTCTTGC
2651944 ATTTCAGAAATTCTTTAGTTA
131 ATTTCAGAAATTCTTTAGTTA
2651965 TCAATGAGTAACCCATCTTGATTCAATTTTTTCCTTTTTTTCATCTTTTTTTTTCTTTTTTTATT
1 TCAATGAGTAACCCATCTTGATTCAATTTTTTCCTTTTTTTCATCTTTTTTTTTCTTTTTTTATT
*
2652030 CTTCTTCTTTTTTGATGAATGAGTATAGGATTTCAATTGTTTTGAGCACCTCCTTTTTCTCTTGC
66 CTTCTTCTTTTTTGATGAATGAGTATAGGATTTCAATTGCTTTGAGCACCTCCTTTTTCTCTTGC
2652095 ATTTCAGAAATTCTTTAGTTA
131 ATTTCAGAAATTCTTTAGTTA
2652116 T
1 T
2652117 TCTTGACTGG
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 151 1.00
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (151 bp):
TCAATGAGTAACCCATCTTGATTCAATTTTTTCCTTTTTTTCATCTTTTTTTTTCTTTTTTTATT
CTTCTTCTTTTTTGATGAATGAGTATAGGATTTCAATTGCTTTGAGCACCTCCTTTTTCTCTTGC
ATTTCAGAAATTCTTTAGTTA
Done.