Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 7 of 29
Found at i:2346198 original size:26 final size:26
Alignment explanation
Indices: 2346161--2346222 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
2346151 TGGTTTCTTA
2346161 AAAAAACAAAAATAAATAAA-ATAAAT
1 AAAAAACAAAAATAAATAAAGA-AAAT
* *
2346187 AAAAAACCAAAATAAGTAAAGAAAAT
1 AAAAAACAAAAATAAATAAAGAAAAT
2346213 -AAAAACAAAA
1 AAAAAACAAAA
2346223 GGAAAGAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.28
26 22 0.69
27 1 0.03
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.11
Consensus pattern (26 bp):
AAAAAACAAAAATAAATAAAGAAAAT
Found at i:2351885 original size:27 final size:25
Alignment explanation
Indices: 2351829--2351886 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
2351819 TATATCACTT
*
2351829 ATGGCCTAGCCATATATATCAATCC
1 ATGGCCTAGCCATATATATCAAACC
* * *
2351854 GTGGCCTTGCCATGTATATCACAGACC
1 ATGGCCTAGCCATATATATCA-A-ACC
2351881 ATGGCC
1 ATGGCC
2351887 CCAGCCATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 18 0.69
26 1 0.04
27 7 0.27
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (25 bp):
ATGGCCTAGCCATATATATCAAACC
Found at i:2366209 original size:8 final size:8
Alignment explanation
Indices: 2366196--2366250 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
2366186 ATTGGTTTCT
2366196 TAAAAAAA
1 TAAAAAAA
2366204 T--AAAAA
1 TAAAAAAA
*
2366210 TAAATAAA
1 TAAAAAAA
*
2366218 TAAATAAA
1 TAAAAAAA
*
2366226 TAAAATAAG
1 TAAAA-AAA
2366235 TAAAAAAAA
1 T-AAAAAAA
2366244 TAAAAAA
1 TAAAAAA
2366251 GAAAAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 6 0.15
8 23 0.59
9 6 0.15
10 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:2366233 original size:13 final size:13
Alignment explanation
Indices: 2366207--2366247 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2366197 AAAAAAATAA
2366207 AAATAAAT-AAAT
1 AAATAAATAAAAT
2366219 AAATAAATAAAAT
1 AAATAAATAAAAT
* *
2366232 AAGTAAAAAAAAT
1 AAATAAATAAAAT
2366245 AAA
1 AAA
2366248 AAAGAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:2366249 original size:9 final size:9
Alignment explanation
Indices: 2366197--2366250 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
2366187 TTGGTTTCTT
2366197 AAAAAAATA
1 AAAAAAATA
2366206 AAAATAAATAA
1 AAAA-AAAT-A
2366217 ATAAATAAATA
1 A-AAA-AAATA
* *
2366228 AAATAAGTA
1 AAAAAAATA
2366237 AAAAAAATA
1 AAAAAAATA
2366246 AAAAA
1 AAAAA
2366251 GAAAAGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 20 0.53
10 6 0.16
11 4 0.11
12 8 0.21
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAAAAATA
Found at i:2373936 original size:74 final size:74
Alignment explanation
Indices: 2373851--2374054 Score: 230
Period size: 74 Copynumber: 2.8 Consensus size: 74
2373841 AGACTGAGTC
* * * * * *
2373851 CTCTTAGTTGACTAACCATACTTCTTAGTCCATTAAGTGTTCTCTATCTTGTACTTAAATTATTT
1 CTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTATCTTATAATTAAAGTATTT
*
2373916 -GATAGTGAG
66 AG-GAGTGAG
* * * * * * * *
2373925 CTCTTAATTGACTAATCATGTTTCTTAGTTGATTAAATTTTCTCTATCTTATAATTGAAGTCTTT
1 CTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTATCTTATAATTAAAGTATTT
2373990 AGGAGTGAG
66 AGGAGTGAG
* * *
2373999 CTCTTAGTTGAGTAACCATGCTTCTTAGTCGACTAAGTCTTCTCTATCTCATAATT
1 CTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTATCTTATAATT
2374055 TGCTTTACTC
Statistics
Matches: 106, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
74 105 0.99
75 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (74 bp):
CTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTATCTTATAATTAAAGTATTT
AGGAGTGAG
Found at i:2377053 original size:15 final size:15
Alignment explanation
Indices: 2377033--2377066 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2377023 TCTTTAAATA
2377033 TATTATAT-TATTATT
1 TATTATATATATT-TT
2377048 TATTATATATATTTT
1 TATTATATATATTTT
2377063 TATT
1 TATT
2377067 TCAATTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTATATATATTTT
Found at i:2381349 original size:23 final size:24
Alignment explanation
Indices: 2381318--2381367 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
2381308 AAAGCAATGT
2381318 TTTTCTTTCTTTCTTTTGCTT-TTC
1 TTTTCTTTCTTT-TTTTGCTTCTTC
*
2381342 TTTT-TTTCTTTTTTTTCTTCTTC
1 TTTTCTTTCTTTTTTTGCTTCTTC
2381365 TTT
1 TTT
2381368 AAGCTCCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 13 0.54
24 4 0.17
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTCTTTCTTTTTTTGCTTCTTC
Found at i:2382935 original size:74 final size:74
Alignment explanation
Indices: 2382846--2383117 Score: 359
Period size: 74 Copynumber: 3.7 Consensus size: 74
2382836 CAAACAGAGT
** * * * * * * *
2382846 GCTCTTAGTTGACTAACCAAACTTCTTAATCCATTAAGTTTTTTATGTCTTGTAATTGAATTCTC
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAACTTCTCTCTGTCTTGTAATTGAAATCTC
* *
2382911 TAGCAGTGA
66 TGGTAGTGA
*
2382920 GGTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAACTTCTCTCTGTCTTGTAATTGAAATCTC
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAACTTCTCTCTGTCTTGTAATTGAAATCTC
2382985 TGGTAGTGA
66 TGGTAGTGA
* * *
2382994 GCTCTTAGTTGATTAA-CAGTGCTTCTTAGTTGATTAACTTCTCTCTGTCTTGTAATTGAAGTCT
1 GCTCTTAGTTGACTAACCA-TGCTTCTTAGTCGATTAACTTCTCTCTGTCTTGTAATTGAAATCT
2383058 CTGGTAGTGA
65 CTGGTAGTGA
* *
2383068 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGACTAA-GTCTTCTCTGTCT
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAACTTC-TCTCTGTCT
2383118 CACAATCTGC
Statistics
Matches: 175, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
73 4 0.02
74 169 0.97
75 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (74 bp):
GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAACTTCTCTCTGTCTTGTAATTGAAATCTC
TGGTAGTGA
Found at i:2387262 original size:21 final size:22
Alignment explanation
Indices: 2387232--2387272 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2387222 TGAAATAGAG
2387232 AGCACTTAGTCGACCAAGAGAC
1 AGCACTTAGTCGACCAAGAGAC
*
2387254 AGCA-TTAGTCGACTAAGAG
1 AGCACTTAGTCGACCAAGAG
2387273 CTTACTGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (22 bp):
AGCACTTAGTCGACCAAGAGAC
Found at i:2387394 original size:73 final size:73
Alignment explanation
Indices: 2387258--2387395 Score: 159
Period size: 73 Copynumber: 1.9 Consensus size: 73
2387248 AGAGACAGCA
* * * * * * *
2387258 TTAGTCGACTAAGAGCTTACTGTCAGAAACTAAGTTCAGAGACAAAAATGACTTAATCTACTAAG
1 TTAGTCGACTAAAAGCCTACTGCCAGAAACTAAGTTCAAAGACAAAAACGACTTAACCGACTAAG
2387323 AAGTTTTG
66 AAGTTTTG
* ** * * *
2387331 TTAGTCGACTAAAAGCCTACTGCCAGAAGCTGGGTTCAAAGACAGAGACGACTTAGCCGACTAAG
1 TTAGTCGACTAAAAGCCTACTGCCAGAAACTAAGTTCAAAGACAAAAACGACTTAACCGACTAAG
2387396 TGATAATGTT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
73 52 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (73 bp):
TTAGTCGACTAAAAGCCTACTGCCAGAAACTAAGTTCAAAGACAAAAACGACTTAACCGACTAAG
AAGTTTTG
Found at i:2388644 original size:80 final size:80
Alignment explanation
Indices: 2388511--2388671 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
2388501 TTAGCATAGT
*
2388511 AGGATCTGGGAGTAAAAGTGTAAAACCATTAAAAATCTCTAGTAATTGAAAAAGCCTTGAAAAGT
1 AGGATCTGGGAGTAAAAGTGTAAAACCATTAAAAATCTCTAGCAATTGAAAAAGCCTTGAAAAGT
2388576 CTAAAGAACCATCCA
66 CTAAAGAACCATCCA
*
2388591 AGGATCTGGGAGTAAAAGTGTAAAACCCTTAAAAATCTCTAGCAATTGAAAAAGCCTTGAAAAGT
1 AGGATCTGGGAGTAAAAGTGTAAAACCATTAAAAATCTCTAGCAATTGAAAAAGCCTTGAAAAGT
2388656 CTAAAGAACCATCCA
66 CTAAAGAACCATCCA
2388671 A
1 A
2388672 TATCAACACA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (80 bp):
AGGATCTGGGAGTAAAAGTGTAAAACCATTAAAAATCTCTAGCAATTGAAAAAGCCTTGAAAAGT
CTAAAGAACCATCCA
Found at i:2390327 original size:17 final size:16
Alignment explanation
Indices: 2390298--2390340 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
2390288 GAACAAAAAT
*
2390298 AAATAAAATAAGTAAA
1 AAATAAAACAAGTAAA
2390314 AAATCAAAACAAGTAAAGA
1 AAAT-AAAACAAGT-AA-A
2390333 AAATAAAA
1 AAATAAAA
2390341 AAAAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
18 6 0.26
19 5 0.22
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.14
Consensus pattern (16 bp):
AAATAAAACAAGTAAA
Found at i:2396613 original size:30 final size:32
Alignment explanation
Indices: 2396574--2396632 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
2396564 TGTGCATTAA
2396574 GAAAAATAAAAATATTCAAT-AT-AAAAGCAT
1 GAAAAATAAAAATATTCAATCATGAAAAGCAT
* **
2396604 GAAATATAAATGTATTCAATCATGAAAAG
1 GAAAAATAAAAATATTCAATCATGAAAAG
2396633 ATATATGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.71
31 2 0.08
32 5 0.21
ACGTcount: A:0.58, C:0.07, G:0.10, T:0.25
Consensus pattern (32 bp):
GAAAAATAAAAATATTCAATCATGAAAAGCAT
Found at i:2399797 original size:21 final size:20
Alignment explanation
Indices: 2399770--2399823 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2399760 TTTCTGTTTC
*
2399770 AAATGTATCGATATATGTAGA
1 AAATGTATCGATACAT-TAGA
* * *
2399791 CAATGTATCAATACATTTGA
1 AAATGTATCGATACATTAGA
2399811 AAATGTATCGATA
1 AAATGTATCGATA
2399824 AAACATTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (20 bp):
AAATGTATCGATACATTAGA
Found at i:2406091 original size:35 final size:35
Alignment explanation
Indices: 2406052--2406118 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
2406042 TTACTCACAT
*
2406052 GCTGAAGCAATAGTCAGAGAACAAATCACGCATGA
1 GCTGAAGCAATAGGCAGAGAACAAATCACGCATGA
* * *
2406087 GCTGAAGCAATAGGCGGAGAATAGATCACGCA
1 GCTGAAGCAATAGGCAGAGAACAAATCACGCA
2406119 CAATGTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (35 bp):
GCTGAAGCAATAGGCAGAGAACAAATCACGCATGA
Found at i:2408239 original size:37 final size:37
Alignment explanation
Indices: 2408182--2408258 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
2408172 CTCTATAAAA
**
2408182 CTTGGCTGAGTACTTTTTACTTTATGCAATTTCTTTG
1 CTTGGCTGAGTACTCCTTACTTTATGCAATTTCTTTG
* *
2408219 CTTGGCTGAGTGCTCCTTACTTTATGCATTTTCTTTG
1 CTTGGCTGAGTACTCCTTACTTTATGCAATTTCTTTG
2408256 CTT
1 CTT
2408259 AGTTTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.51
Consensus pattern (37 bp):
CTTGGCTGAGTACTCCTTACTTTATGCAATTTCTTTG
Found at i:2410978 original size:27 final size:27
Alignment explanation
Indices: 2410948--2411042 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 27
2410938 TATTATCTTT
*
2410948 TAAAAAATTAAAATAAAATATATAATA
1 TAAAAAATTAAAATAAAATATAAAATA
* * *
2410975 TAAAAAATTATATTAAAAAATAAAATA
1 TAAAAAATTAAAATAAAATATAAAATA
* * *
2411002 TATAAAATTAAATTAAAAATAAAAAATA
1 TAAAAAATTAAAAT-AAAATATAAAATA
* *
2411030 TATAATATTAAAA
1 TAAAAAATTAAAA
2411043 ATATATTTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 35 0.61
28 22 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAAAAATTAAAATAAAATATAAAATA
Found at i:2410998 original size:34 final size:34
Alignment explanation
Indices: 2410957--2411058 Score: 110
Period size: 34 Copynumber: 3.2 Consensus size: 34
2410947 TTAAAAAATT
2410957 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAATATATAATATAAAAAATTATATTAA
**
2410991 AAAATAAAATATATAA-A-ATTAAATTA-A--AA
1 AAAATAAAATATATAATATAAAAAATTATATTAA
* * *
2411020 ATAA-AAAATATATAATATTAAAAA-TATATTTA
1 AAAATAAAATATATAATATAAAAAATTATATTAA
2411052 AAAATAA
1 AAAATAA
2411059 TATTGTATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
28 11 0.20
29 8 0.15
30 4 0.07
31 1 0.02
32 11 0.20
33 3 0.06
34 16 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAATAAAATATATAATATAAAAAATTATATTAA
Found at i:2411044 original size:35 final size:33
Alignment explanation
Indices: 2410957--2411058 Score: 84
Period size: 35 Copynumber: 3.0 Consensus size: 33
2410947 TTAAAAAATT
* * * *
2410957 AAAATAAAATATATAATATAAAAAATT-ATATTAA
1 AAAATAAAATATATAA-A-ATATAATTAAAAATAA
2410991 AAAATAAAATATATAAAAT-TAAATTAAAAATAA
1 AAAATAAAATATATAAAATAT-AATTAAAAATAA
*
2411024 AAAATATATAATAT-TAAAAATATATTTAAAAATAA
1 AAAATA-A-AATATAT-AAAATATAATTAAAAATAA
2411059 TATTGTATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
32 5 0.09
33 12 0.21
34 18 0.32
35 21 0.37
36 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (33 bp):
AAAATAAAATATATAAAATATAATTAAAAATAA
Found at i:2411061 original size:13 final size:13
Alignment explanation
Indices: 2411031--2411062 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2411021 TAAAAAATAT
2411031 ATAATA-TTAAAA
1 ATAATATTTAAAA
2411043 AT-ATATTTAAAA
1 ATAATATTTAAAA
2411055 ATAATATT
1 ATAATATT
2411063 GTATAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 10 0.56
13 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAATATTTAAAA
Found at i:2411068 original size:62 final size:64
Alignment explanation
Indices: 2410962--2411084 Score: 171
Period size: 62 Copynumber: 2.0 Consensus size: 64
2410952 AAATTAAAAT
*
2410962 AAAATATATAATATAAAAAATTATATTAAAAAATAAAATATATAAA-ATTAA-ATTAAAAATAA
1 AAAATATATAATATAAAAAATTATATTAAAAAATAAAATATATAAAGATTAACAGTAAAAATAA
* * * *
2411024 AAAATATATAATATTAAAAA-TATATTTAAAAATAATATTGTATAAAGATTAACAGTAAAAA
1 AAAATATATAATATAAAAAATTATATTAAAAAATAA-AATATATAAAGATTAACAGTAAAAA
2411085 ATACAATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
61 14 0.26
62 27 0.51
63 5 0.09
64 7 0.13
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (64 bp):
AAAATATATAATATAAAAAATTATATTAAAAAATAAAATATATAAAGATTAACAGTAAAAATAA
Found at i:2417087 original size:36 final size:36
Alignment explanation
Indices: 2416994--2417112 Score: 125
Period size: 37 Copynumber: 3.3 Consensus size: 36
2416984 TGAAATAATA
* **
2416994 CTTCACTTGTTTTAGTTGTT-TTTTATGAAGTAGTATG
1 CTTCACTTGTTTTAATTGTTCTTACATGAAGTA-T-TG
*
2417031 TTTCACTTGTTTTAATTGTTC-TACATGAAGTATTG
1 CTTCACTTGTTTTAATTGTTCTTACATGAAGTATTG
* * *
2417066 CTTCACTTATTTTTAATTGTTCTTACGTGAAGTAGTG
1 CTTCACTT-GTTTTAATTGTTCTTACATGAAGTATTG
*
2417103 CTTCATTTGT
1 CTTCACTTGT
2417113 AAAGGTTGTT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
35 9 0.13
36 14 0.20
37 46 0.67
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (36 bp):
CTTCACTTGTTTTAATTGTTCTTACATGAAGTATTG
Found at i:2417626 original size:17 final size:17
Alignment explanation
Indices: 2417606--2417638 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2417596 CAAAGTACAG
2417606 CAAAATTCAAAACAAAA
1 CAAAATTCAAAACAAAA
*
2417623 CAAAATTCAAAGCAAA
1 CAAAATTCAAAACAAA
2417639 GTTGATTTTT
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:0.67, C:0.18, G:0.03, T:0.12
Consensus pattern (17 bp):
CAAAATTCAAAACAAAA
Found at i:2425779 original size:22 final size:22
Alignment explanation
Indices: 2425745--2425794 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2425735 GACAACCGAA
2425745 AGAGAATAAAAA-GAGAATAAG
1 AGAGAATAAAAAGGAGAATAAG
** *
2425766 TAGAGAATGTAAAGGAGAATTAG
1 -AGAGAATAAAAAGGAGAATAAG
2425789 AGAGAA
1 AGAGAA
2425795 AAGTTAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (22 bp):
AGAGAATAAAAAGGAGAATAAG
Found at i:2426423 original size:35 final size:34
Alignment explanation
Indices: 2426379--2426448 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
2426369 TATAAGGTAG
*
2426379 TACTCTATTTATTTTAGTTCCTCTGCATGAAGTAA
1 TACTCTATTT-GTTTAGTTCCTCTGCATGAAGTAA
* ** *
2426414 TACTTTATTTGTTTAGTTGTTTTGCATGAAGTAA
1 TACTCTATTTGTTTAGTTCCTCTGCATGAAGTAA
2426448 T
1 T
2426449 GCATTTTACT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 21 0.70
35 9 0.30
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.50
Consensus pattern (34 bp):
TACTCTATTTGTTTAGTTCCTCTGCATGAAGTAA
Found at i:2428950 original size:51 final size:51
Alignment explanation
Indices: 2428852--2428950 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
2428842 ATATGTAATT
* * * * * *
2428852 TATAACAAGATGTGATGAGGCACGTAACTAGACATGCTAATGCATGTAGTA
1 TATAACAAGACGTGATGAAGCACGTAACAAGACATCCTAAAGAATGTAGTA
*
2428903 TATACCAAGACGTGATGAAGCACGTAACAAGACATCCTAAAGAATGTA
1 TATAACAAGACGTGATGAAGCACGTAACAAGACATCCTAAAGAATGTA
2428951 ATCCATTATG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.22
Consensus pattern (51 bp):
TATAACAAGACGTGATGAAGCACGTAACAAGACATCCTAAAGAATGTAGTA
Found at i:2441674 original size:18 final size:19
Alignment explanation
Indices: 2441651--2441689 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2441641 AGGTGACAAG
2441651 AATA-TTTGGAAATAAAAT
1 AATATTTTGGAAATAAAAT
**
2441669 AATATTTTTTAAATAAAAT
1 AATATTTTGGAAATAAAAT
2441688 AA
1 AA
2441690 CATTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AATATTTTGGAAATAAAAT
Found at i:2455190 original size:4 final size:4
Alignment explanation
Indices: 2455181--2455210 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2455171 TTATAATTTA
*
2455181 TATG TATG TATG TATG CATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
2455211 AGAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:2457338 original size:3 final size:3
Alignment explanation
Indices: 2457330--2457364 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2457320 AGCAAATTTC
2457330 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2457365 AAAGTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2461143 original size:31 final size:30
Alignment explanation
Indices: 2461072--2461176 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 30
2461062 AAGTTGACTT
* *
2461072 GGGCAGGGGGAATCGAGACTCGTGGGAGGG
1 GGGCAAGGGGAATCGGGACTCGTGGGAGGG
*
2461102 GGGCAGGGGGAATCGGGACTCGTGGGAAGGG
1 GGGCAAGGGGAATCGGGACTCGTGGG-AGGG
* * ***
2461133 GGTCAAGGGGAATCGGTAAGAGTGGGAGGG
1 GGGCAAGGGGAATCGGGACTCGTGGGAGGG
*
2461163 GGGCGAGGGGAATC
1 GGGCAAGGGGAATC
2461177 AAGTCTGGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
30 41 0.63
31 24 0.37
ACGTcount: A:0.22, C:0.11, G:0.56, T:0.10
Consensus pattern (30 bp):
GGGCAAGGGGAATCGGGACTCGTGGGAGGG
Found at i:2461163 original size:30 final size:30
Alignment explanation
Indices: 2461093--2461176 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 30
2461083 ATCGAGACTC
* ***
2461093 GTGGGAGGGGGGCAGGGGGAATCGGGACTC
1 GTGGGAGGGGGGCAAGGGGAATCGGGAAGA
* *
2461123 GTGGGAAGGGGGTCAAGGGGAATCGGTAAGA
1 GTGGG-AGGGGGGCAAGGGGAATCGGGAAGA
*
2461154 GTGGGAGGGGGGCGAGGGGAATC
1 GTGGGAGGGGGGCAAGGGGAATC
2461177 AAGTCTGGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
30 21 0.47
31 24 0.53
ACGTcount: A:0.21, C:0.10, G:0.58, T:0.11
Consensus pattern (30 bp):
GTGGGAGGGGGGCAAGGGGAATCGGGAAGA
Found at i:2479413 original size:16 final size:16
Alignment explanation
Indices: 2479388--2479418 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2479378 TATATATATT
2479388 TATTAGAATAAATTAC
1 TATTAGAATAAATTAC
*
2479404 TATTATAATAAATTA
1 TATTAGAATAAATTA
2479419 TTACATCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TATTAGAATAAATTAC
Found at i:2479906 original size:17 final size:17
Alignment explanation
Indices: 2479872--2479918 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2479862 AAAGTAGAAA
*
2479872 AAAAAGAACAATAGAAAAT
1 AAAAAGAA-AA-ACAAAAT
*
2479891 AAAATGAAAAACAAAAT
1 AAAAAGAAAAACAAAAT
2479908 AAAAAGAAAAA
1 AAAAAGAAAAA
2479919 GAAGAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 16 0.64
18 2 0.08
19 7 0.28
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAAACAAAAT
Found at i:2480903 original size:40 final size:39
Alignment explanation
Indices: 2480825--2480902 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
2480815 ACTCCCATTC
*
2480825 GGACTCACTTTTAATATATACAGAATAGATTTGATTTTTT
1 GGACTCACTTTTAATATATA-AGAACAGATTTGATTTTTT
* *
2480865 GGACTCACTTTTAATATAT-AGTACATATTTGATTTTTT
1 GGACTCACTTTTAATATATAAGAACAGATTTGATTTTTT
2480903 TGAGTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 16 0.46
40 19 0.54
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (39 bp):
GGACTCACTTTTAATATATAAGAACAGATTTGATTTTTT
Found at i:2490902 original size:13 final size:14
Alignment explanation
Indices: 2490884--2490924 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
2490874 TAAATTAATT
2490884 AATTAA-TAATTTA
1 AATTAACTAATTTA
2490897 AATTAACTAATTT-
1 AATTAACTAATTTA
*
2490910 AATTAATTAATTTA
1 AATTAACTAATTTA
2490924 A
1 A
2490925 CTCTCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTAACTAATTTA
Found at i:2490917 original size:17 final size:16
Alignment explanation
Indices: 2490871--2490920 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2490861 TTATAGTAAC
*
2490871 TAATAAATTAATTAAT
1 TAATAATTTAATTAAT
2490887 TAATAATTT-A--AAT
1 TAATAATTTAATTAAT
2490900 TAACTAATTTAATTAAT
1 TAA-TAATTTAATTAAT
2490917 TAAT
1 TAAT
2490921 TTAACTCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 2 0.07
16 9 0.31
17 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATAATTTAATTAAT
Found at i:2490924 original size:5 final size:4
Alignment explanation
Indices: 2490829--2490921 Score: 55
Period size: 4 Copynumber: 22.5 Consensus size: 4
2490819 TTAAACTACT
* * * * * * *
2490829 TTAA TTAA CT-A TATAA TTAA CTAA TTAG TTGA TTATA GTAA CTAA TAAA
1 TTAA TTAA TTAA T-TAA TTAA TTAA TTAA TTAA TTA-A TTAA TTAA TTAA
*
2490878 TTAA TTAA TTAA -TAA TTTAAA TTAA CTAA TTTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA -TT-AA TTAA TTAA -TTAA TTAA TTAA TT
2490922 TAACTCTCTA
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
3 4 0.06
4 50 0.75
5 11 0.16
6 2 0.03
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (4 bp):
TTAA
Found at i:2493817 original size:330 final size:328
Alignment explanation
Indices: 2493165--2493824 Score: 947
Period size: 330 Copynumber: 2.0 Consensus size: 328
2493155 TCGTTAACTA
*
2493165 CTCATTTTTTTCCAAAAAAAAAAAAAAACTACTCATTTTTTTTTAATTTTTCAAAACTACTATTT
1 CTCATTTTTTTCC--AAAAAAAAAAAAACTACCCATTTTTTTTTAATTTTTCAAAACTACTATTT
* * * *
2493230 TTCATTTGATTAAAAAACGAAACTCACTTATAGCTTCAATTTTTTTTTTCTCGCTCACTTATTGC
64 CTCATTTAATT-AAAAACGAAACTCACTTATAGCTTCAA-TTTTTTTTTCTCACTCACTTAGTGC
*
2493295 TACAAGATCTAGTTAGTCTTTTGTATACTACTTTATTAATTTAGTTTAGTCTTGGTATGTTTTTT
127 TACAAGATCTAGTTAGTCATTTGTATACTACTTTATTAATTTAGTTTAGTCTTGGTATGTTTTTT
* *
2493360 CTTTCGCTCTATCAGTTTAGTCTTGATGTTGGTGGTATTATGGTAGTTTTTTTTCTTTTGTATTG
192 CTTTCGCTCAATCAGTTTAGTCTTGATGTTGGTGGTATTACGGTAGTTTTTTTTCTTTTGTATTG
*
2493425 TTGAAATGAGCTTGATGGTGGTCTATTGGGTCTAGTTAATTATTAAGGACCTTATTTGTCTTACT
257 TTGAAATGAGCTTGATGGTGGTCTATTGGGTCTAGTTAATTATTAAGGACCTTATATGTCTTACT
2493490 TTACCTG
322 TTACCTG
* * *
2493497 CTCATTTTTTTCC-AAAACAGAAAAACTACCCATTTTGTTTTTCAATTTTTCGAAACTACTATTT
1 CTCATTTTTTTCCAAAAAAAAAAAAACTACCCATTTT-TTTTT-AATTTTTCAAAACTACTATTT
* *
2493561 CTCATTTAATT-AAAACTGAAACTCTCTTATTGCTTCAA-TTTTTTTTCTCACTCA-TAGTGAGT
64 CTCATTTAATTAAAAAC-GAAACTCACTTATAGCTTCAATTTTTTTTTCTCACTCACT--T-AGT
* * * * *
2493623 GTTACAAGATCTAGTTAGTCATTTGTGTATTACTTTATTGATTTAGTTTAGTCTTGGTGTG-TTT
125 GCTACAAGATCTAGTTAGTCATTTGTATACTACTTTATTAATTTAGTTTAGTCTTGGTATGTTTT
*
2493687 TT-TTT-GCTCAATCAGTTTAGTCTTGTTGTTGGTGGTATTACGGTAGTTTTTTTTTTTCTTTTG
190 TTCTTTCGCTCAATCAGTTTAGTCTTGATGTTGGTGGTATTACGGTAG---TTTTTTTTCTTTTG
* * *
2493750 TATTGTTGAAATGAGCTTGATGGTGGTTTATTGGGTCTAGTTAATTATTAAGGACTTTGTATGTC
252 TATTGTTGAAATGAGCTTGATGGTGGTCTATTGGGTCTAGTTAATTATTAAGGACCTTATATGTC
2493815 TTACTTTACC
317 TTACTTTACC
2493825 CGAGTTAAGT
Statistics
Matches: 296, Mismatches: 23, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
327 39 0.13
328 18 0.06
329 31 0.10
330 166 0.56
331 29 0.10
332 13 0.04
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.48
Consensus pattern (328 bp):
CTCATTTTTTTCCAAAAAAAAAAAAACTACCCATTTTTTTTTAATTTTTCAAAACTACTATTTCT
CATTTAATTAAAAACGAAACTCACTTATAGCTTCAATTTTTTTTTCTCACTCACTTAGTGCTACA
AGATCTAGTTAGTCATTTGTATACTACTTTATTAATTTAGTTTAGTCTTGGTATGTTTTTTCTTT
CGCTCAATCAGTTTAGTCTTGATGTTGGTGGTATTACGGTAGTTTTTTTTCTTTTGTATTGTTGA
AATGAGCTTGATGGTGGTCTATTGGGTCTAGTTAATTATTAAGGACCTTATATGTCTTACTTTAC
CTG
Found at i:2496803 original size:17 final size:17
Alignment explanation
Indices: 2496766--2496819 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
2496756 AGACTAAAAC
*
2496766 AGCCCTAAACATACA-A
1 AGCCCTAAACCTACATA
2496782 TAGCCCTAAACCTACATA
1 -AGCCCTAAACCTACATA
*
2496800 AGCCAT-AACCTACATA
1 AGCCCTAAACCTACATA
2496816 AGCC
1 AGCC
2496820 ATAATAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 14 0.41
17 19 0.56
18 1 0.03
ACGTcount: A:0.43, C:0.33, G:0.07, T:0.17
Consensus pattern (17 bp):
AGCCCTAAACCTACATA
Found at i:2496811 original size:16 final size:16
Alignment explanation
Indices: 2496790--2496823 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2496780 AATAGCCCTA
2496790 AACCTACATAAGCCAT
1 AACCTACATAAGCCAT
2496806 AACCTACATAAGCCAT
1 AACCTACATAAGCCAT
2496822 AA
1 AA
2496824 TAATGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.29, G:0.06, T:0.18
Consensus pattern (16 bp):
AACCTACATAAGCCAT
Found at i:2514368 original size:35 final size:35
Alignment explanation
Indices: 2514342--2514527 Score: 198
Period size: 35 Copynumber: 5.3 Consensus size: 35
2514332 CTTAATTGTT
*
2514342 CAATTTAATCAATTAAGCCTAATAACTTAATTAAA
1 CAATTTAATCAATTAGGCCTAATAACTTAATTAAA
* *
2514377 CAATTTAATCAATTAGGCATAATAACATAATTAAA
1 CAATTTAATCAATTAGGCCTAATAACTTAATTAAA
* ***
2514412 CAAATTTAATGAATTAGGCCTAATAACTTAATTGTT
1 C-AATTTAATCAATTAGGCCTAATAACTTAATTAAA
* * * *
2514448 TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
1 CAATTTAATCAATTAGGCCTAATAACTTAATTAAA
* * * *
2514483 TAATTTAATGAATTAGG-C--ACAACTTAAATAAA
1 CAATTTAATCAATTAGGCCTAATAACTTAATTAAA
2514515 CAATCTTAATCAA
1 CAAT-TTAATCAA
2514528 GTACTTAAGA
Statistics
Matches: 127, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
32 14 0.11
33 7 0.06
34 1 0.01
35 77 0.61
36 28 0.22
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (35 bp):
CAATTTAATCAATTAGGCCTAATAACTTAATTAAA
Found at i:2514421 original size:71 final size:70
Alignment explanation
Indices: 2514343--2514527 Score: 196
Period size: 71 Copynumber: 2.7 Consensus size: 70
2514333 TTAATTGTTC
* *
2514343 AATTTAATCAATTAAGCCTAATAACTTAATTAAACAATTTAATCAATTAGGCATAATAACATAAT
1 AATTTAATGAATTAAGCCTAATAACTTAATTAAACAATTTAATCAATTAGGCACAATAACATAAT
2514408 TAAACA
66 TAAA-A
* **** * * * *
2514414 AATTTAATGAATTAGGCCTAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAAT
1 AATTTAATGAATTAAGCCTAATAACTTAATTAAACAATTTAATCAATTAGGCACAATAACATAAT
*
2514479 TAAAT
66 TAAAA
* * *
2514484 AATTTAATGAATT-AGGC--ACAACTTAAATAAACAATCTTAATCAA
1 AATTTAATGAATTAAGCCTAATAACTTAATTAAACAAT-TTAATCAA
2514528 GTACTTAAGA
Statistics
Matches: 92, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
67 12 0.13
68 7 0.08
69 2 0.02
70 13 0.14
71 58 0.63
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (70 bp):
AATTTAATGAATTAAGCCTAATAACTTAATTAAACAATTTAATCAATTAGGCACAATAACATAAT
TAAAA
Found at i:2515452 original size:167 final size:167
Alignment explanation
Indices: 2515163--2515664 Score: 698
Period size: 167 Copynumber: 3.0 Consensus size: 167
2515153 AATCAAAGCA
* *
2515163 TAGCACTCCACATATAAGACAACTTGGTGTCTCAAGTCTAGGGAGTATTTGCATAACTGACACAT
1 TAGCACTCCACACATAAGACAACCTGGTGTCTCAAGTCTAGGGAGTATTTGCATAACTGACACAT
* *
2515228 GAGAAGTATTGCATAGACACTTGAATGAAATACCAAATGCACTTCTCACGATGGGTCATGTTCAG
66 GAGAAGTATTGCATAGACACTTGAGTGAAATACCAAATGCACTTCTCACGGTGGGTCATGTTCAG
2515293 TGAACTTGCTCTCCTAGGTAAGCACCTATATTCTAAT
131 TGAACTTGCTCTCCTAGGTAAGCACCTATATTCTAAT
* *
2515330 TAGCACTCCACACATAAGACAACCTGGCGTCTCAAGTCTAAGGAGTATTTGCATAACTGACACAT
1 TAGCACTCCACACATAAGACAACCTGGTGTCTCAAGTCTAGGGAGTATTTGCATAACTGACACAT
********** * *
2515395 GAGAAGTATTGCANNNNNNNNNNAGTGAAATACCAAATGCACTTTTCACGGTGGGTCATATTCAG
66 GAGAAGTATTGCATAGACACTTGAGTGAAATACCAAATGCACTTCTCACGGTGGGTCATGTTCAG
**********
2515460 TGAACTTGCTCTCCTAGGTAAGCANNNNNNNNNNAAT
131 TGAACTTGCTCTCCTAGGTAAGCACCTATATTCTAAT
* *
2515497 TAGCACTCCACACATAAGACAACCTAGTGTCTCAAGTCTAGGGAGTATTTACATAACTGACACAT
1 TAGCACTCCACACATAAGACAACCTGGTGTCTCAAGTCTAGGGAGTATTTGCATAACTGACACAT
* *
2515562 GAGAAGTATTGCATAGACACTTGAGTGAAATACCAAATGCACTTCTCACGGCGGGTCATGTTTAG
66 GAGAAGTATTGCATAGACACTTGAGTGAAATACCAAATGCACTTCTCACGGTGGGTCATGTTCAG
* *
2515627 TAAACTTGCTCTCCTAGGTAAGCTCCTATATTCTAAT
131 TGAACTTGCTCTCCTAGGTAAGCACCTATATTCTAAT
2515664 T
1 T
2515665 CCAAGTATCT
Statistics
Matches: 277, Mismatches: 58, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
167 277 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.27
Consensus pattern (167 bp):
TAGCACTCCACACATAAGACAACCTGGTGTCTCAAGTCTAGGGAGTATTTGCATAACTGACACAT
GAGAAGTATTGCATAGACACTTGAGTGAAATACCAAATGCACTTCTCACGGTGGGTCATGTTCAG
TGAACTTGCTCTCCTAGGTAAGCACCTATATTCTAAT
Found at i:2515764 original size:24 final size:25
Alignment explanation
Indices: 2515728--2515777 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
2515718 GAAACATAGA
*
2515728 ATGTACCAATCTCTATGA-ATCATTG
1 ATGTACCAATCTCAATGATA-CATTG
*
2515753 ATGT-CCAGTCTCAATGATACATTG
1 ATGTACCAATCTCAATGATACATTG
2515777 A
1 A
2515778 CTAGGAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (25 bp):
ATGTACCAATCTCAATGATACATTG
Found at i:2516946 original size:73 final size:73
Alignment explanation
Indices: 2516862--2516999 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 73
2516852 AACATTGCTA
* *
2516862 CTTAGTCGATTAAGTCGTCTCTATCTCTGAAC-CTAGA-TTTTGATAGTAAGATCTTAGTTGGCT
1 CTTAGTCGATTAAGTCATCTCTATCTCTGAACTC-A-ATTTTTGATAGTAAGATCTTAGTTGACT
2516925 AATAAAACTT
64 AATAAAACTT
* * * * *
2516935 CTTAGTTGATTAAGTCATTTCTGTCTCTGAACTCAATTTTTGGTAGTAAGCTCTTAGTTGACTAA
1 CTTAGTCGATTAAGTCATCTCTATCTCTGAACTCAATTTTTGATAGTAAGATCTTAGTTGACTAA
2517000 CACTGTCTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 1 0.02
73 54 0.96
74 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (73 bp):
CTTAGTCGATTAAGTCATCTCTATCTCTGAACTCAATTTTTGATAGTAAGATCTTAGTTGACTAA
TAAAACTT
Found at i:2527257 original size:12 final size:12
Alignment explanation
Indices: 2527242--2527269 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2527232 AAGCGGATGG
2527242 TGATAATAATAA
1 TGATAATAATAA
2527254 TGATAATAATAA
1 TGATAATAATAA
2527266 TGAT
1 TGAT
2527270 GATGATGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.36
Consensus pattern (12 bp):
TGATAATAATAA
Found at i:2532360 original size:2 final size:2
Alignment explanation
Indices: 2532353--2532377 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2532343 TACGTTCGTC
2532353 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2532378 AGCTGCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2534437 original size:15 final size:15
Alignment explanation
Indices: 2534402--2534442 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2534392 TGTGTTGTAC
* *
2534402 TATAACACCTTATAT
1 TATAACACTTTATAA
2534417 TATAACACTTTATAA
1 TATAACACTTTATAA
*
2534432 TGTAACACTTT
1 TATAACACTTT
2534443 GTGTTGTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (15 bp):
TATAACACTTTATAA
Found at i:2534482 original size:15 final size:15
Alignment explanation
Indices: 2534464--2534528 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
2534454 ACTTGTACTA
2534464 TAACACTTTAAGTAG
1 TAACACTTTAAGTAG
* *
2534479 TAACGCTTT-AGACAG
1 TAACACTTTAAG-TAG
** *
2534494 TAATGCTTTACGTAG
1 TAACACTTTAAGTAG
*
2534509 TAACACTTTAGGTAG
1 TAACACTTTAAGTAG
2534524 TAACA
1 TAACA
2534529 TGCTACTGTC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 2 0.05
15 37 0.93
16 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (15 bp):
TAACACTTTAAGTAG
Found at i:2539440 original size:3 final size:3
Alignment explanation
Indices: 2539432--2539470 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2539422 CTCATTTTTT
2539432 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2539471 TATGTATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2542057 original size:35 final size:34
Alignment explanation
Indices: 2541976--2542059 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 34
2541966 CATTAAAAGG
* *
2541976 CATTGTTGAAGGTTTTGGTTGAGCTTGTGAAAAAC
1 CATTG-TGAGGGTTTTGGTTAAGCTTGTGAAAAAC
** * * *
2542011 CATCATAAGGGTTGTTGGTTAATCTTGTGAAAAAT
1 CATTGTGAGGGTT-TTGGTTAAGCTTGTGAAAAAC
2542046 CATTGTGAGGGTTT
1 CATTGTGAGGGTTT
2542060 AACGCTTGAT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
34 7 0.18
35 31 0.82
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.38
Consensus pattern (34 bp):
CATTGTGAGGGTTTTGGTTAAGCTTGTGAAAAAC
Found at i:2547089 original size:13 final size:12
Alignment explanation
Indices: 2547060--2547092 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2547050 TAAAGTTGAA
*
2547060 ATTTTTGAAAAT
1 ATTTTTGAAAAC
2547072 ATTTTTGAAAAC
1 ATTTTTGAAAAC
2547084 ATTTTTGAA
1 ATTTTTGAA
2547093 CTTCATGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:2548396 original size:35 final size:35
Alignment explanation
Indices: 2548335--2548401 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
2548325 GGCATTGTTG
*
2548335 AGAGTTTTGGTTGAGCTTGTGCAAAAC-CATTGCA
1 AGAGTTTTGGTTAAGCTTGTGCAAAACACATTGCA
*
2548369 AGAGTTGTTGGTTAATCTTGT-CAAAAACACATT
1 AGAGTT-TTGGTTAAGCTTGTGC-AAAACACATT
2548402 TCCTTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 7 0.25
35 17 0.61
36 4 0.14
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (35 bp):
AGAGTTTTGGTTAAGCTTGTGCAAAACACATTGCA
Found at i:2552628 original size:3 final size:3
Alignment explanation
Indices: 2552620--2552655 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2552610 ATTTATTTAT
2552620 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2552656 AAACAATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2558540 original size:2 final size:2
Alignment explanation
Indices: 2558533--2558565 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2558523 GTCGCTCCTT
*
2558533 TA TA TA TA CA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2558566 GAGTTAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2559395 original size:29 final size:26
Alignment explanation
Indices: 2559329--2559395 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 26
2559319 TTCAATATAA
2559329 TTTTTTA-ATTTAAATATTAATTTTT
1 TTTTTTATATTTAAATATTAATTTTT
2559354 TTGATATTT-TATTTAAAATATTAATATGTTT
1 TT--T-TTTATATTT-AAATATTAAT-T-TTT
2559385 TTTTTTATATT
1 TTTTTTATATT
2559396 AATTTCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
25 2 0.06
27 1 0.03
28 10 0.29
29 15 0.44
30 1 0.03
31 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTTTTATATTTAAATATTAATTTTT
Found at i:2561120 original size:2 final size:2
Alignment explanation
Indices: 2561060--2561107 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2561050 AATTTAATAA
2561060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2561102 AT AT AT
1 AT AT AT
2561108 GCACACATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2562015 original size:17 final size:18
Alignment explanation
Indices: 2561993--2562026 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2561983 AATATGTACA
*
2561993 TAAAAA-GAAATAAAAAG
1 TAAAAATGAAAGAAAAAG
2562010 TAAAAATGAAAGAAAAA
1 TAAAAATGAAAGAAAAA
2562027 AGAAAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (18 bp):
TAAAAATGAAAGAAAAAG
Found at i:2562154 original size:19 final size:19
Alignment explanation
Indices: 2562116--2562155 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2562106 TCCCAACTAC
*
2562116 AATTCAAAATTCAAATTTG
1 AATTCAAAATTCAAAGTTG
2562135 AATTCAAAA-TCAAGAGTTG
1 AATTCAAAATTCAA-AGTTG
2562154 AA
1 AA
2562156 AAAGGAGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (19 bp):
AATTCAAAATTCAAAGTTG
Found at i:2562657 original size:15 final size:15
Alignment explanation
Indices: 2562637--2562666 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2562627 GTTTGGATAA
2562637 GAGTCTTTTAAATTT
1 GAGTCTTTTAAATTT
2562652 GAGTCTTTTAAATTT
1 GAGTCTTTTAAATTT
2562667 AGAATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
GAGTCTTTTAAATTT
Found at i:2564908 original size:19 final size:20
Alignment explanation
Indices: 2564884--2564928 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2564874 CCCATTCTCA
*
2564884 ATTTTTCTGATTTTTTTG-T
1 ATTTTTCTGATATTTTTGTT
* *
2564903 ATTTTTTTTATATTTTTGTT
1 ATTTTTCTGATATTTTTGTT
2564923 ATTTTT
1 ATTTTT
2564929 AAATTTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.13, C:0.02, G:0.07, T:0.78
Consensus pattern (20 bp):
ATTTTTCTGATATTTTTGTT
Found at i:2564929 original size:17 final size:16
Alignment explanation
Indices: 2564907--2564944 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2564897 TTTTGTATTT
*
2564907 TTTTTATATTTTTGTTA
1 TTTTTAAATTTTTG-TA
2564924 TTTTTAAATTTTTGTA
1 TTTTTAAATTTTTGTA
2564940 TTTTT
1 TTTTT
2564945 GTACATTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTTAAATTTTTGTA
Found at i:2565184 original size:42 final size:43
Alignment explanation
Indices: 2565136--2565302 Score: 180
Period size: 43 Copynumber: 3.9 Consensus size: 43
2565126 GTTTTGTAAT
* *
2565136 TTTAAAAGAATTGAAAAATACTCCTTGTATGAGGCTCCTTAAC
1 TTTAAAAGAATTGAAAAATACTCCTTCTATGAGGCTCCATAAC
* * * *
2565179 -TTAAAA-ATTTTGTAAAATACT-CTTCCTATGAGGTTTCATAAC
1 TTTAAAAGA-ATTGAAAAATACTCCTT-CTATGAGGCTCCATAAC
* **
2565221 TTTAAAAGAATTGAAAAATACTCCTCCTACAAGGCTCCAT-AC
1 TTTAAAAGAATTGAAAAATACTCCTTCTATGAGGCTCCATAAC
* *
2565263 GTTTAAAAGAATTGAAAACTACTCGTTCTATGAGGCTCCA
1 -TTTAAAAGAATTGAAAAATACTCCTTCTATGAGGCTCCA
2565303 CAATTTTCAA
Statistics
Matches: 100, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
41 4 0.04
42 32 0.32
43 61 0.61
44 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (43 bp):
TTTAAAAGAATTGAAAAATACTCCTTCTATGAGGCTCCATAAC
Found at i:2566611 original size:22 final size:22
Alignment explanation
Indices: 2566570--2566611 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2566560 AATGTATGGA
**
2566570 TTACAAGCCTTAGCTTGTTTGG
1 TTACAAGCCTTAGCACGTTTGG
*
2566592 TTACATGCCTTAGCACGTTT
1 TTACAAGCCTTAGCACGTTT
2566612 AGCTATACAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
TTACAAGCCTTAGCACGTTTGG
Found at i:2567738 original size:23 final size:23
Alignment explanation
Indices: 2567666--2567789 Score: 76
Period size: 23 Copynumber: 5.5 Consensus size: 23
2567656 TGTTCCAAAC
* *
2567666 ATGC-AAAGTATGTAAACCAAAT
1 ATGCTAAAGCATGTAAACTAAAT
* * * * *
2567688 AAGCTAAGGCATAT-AACTACAC
1 ATGCTAAAGCATGTAAACTAAAT
*
2567710 ACGCTAAAGCATGTAAACTAAAT
1 ATGCTAAAGCATGTAAACTAAAT
* * *
2567733 ATGCTAAGGCATATAAAC--ATT
1 ATGCTAAAGCATGTAAACTAAAT
* * *
2567754 CAAGCTAAGGCATGTAAACAAAAT
1 -ATGCTAAAGCATGTAAACTAAAT
*
2567778 ATGCTCAAGCAT
1 ATGCTAAAGCAT
2567790 ATAATCACAC
Statistics
Matches: 75, Mismatches: 22, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
21 2 0.03
22 35 0.47
23 36 0.48
24 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.22
Consensus pattern (23 bp):
ATGCTAAAGCATGTAAACTAAAT
Found at i:2567739 original size:45 final size:44
Alignment explanation
Indices: 2567670--2567817 Score: 156
Period size: 45 Copynumber: 3.3 Consensus size: 44
2567660 CCAAACATGC
* * * *
2567670 AAAGTATGTAAACCAAATAAGCTAAGGCATATAACTACACACGCT
1 AAAGCATGTAAACAAAATATGCTAAGGCATATAA-TACACAAGCT
*
2567715 AAAGCATGTAAACTAAATATGCTAAGGCATATAA-ACATTCAAGCT
1 AAAGCATGTAAACAAAATATGCTAAGGCATATAATACA--CAAGCT
* *
2567760 AAGGCATGTAAACAAAATATGCTCAA-GCATATAATCACACATGCT
1 AAAGCATGTAAACAAAATATGCT-AAGGCATATAAT-ACACAAGCT
* *
2567805 AAGGCATGCAAAC
1 AAAGCATGTAAAC
2567818 CAAAGACATT
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
43 3 0.03
45 82 0.91
46 2 0.02
47 3 0.03
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (44 bp):
AAAGCATGTAAACAAAATATGCTAAGGCATATAATACACAAGCT
Found at i:2567811 original size:22 final size:23
Alignment explanation
Indices: 2567690--2567811 Score: 90
Period size: 22 Copynumber: 5.4 Consensus size: 23
2567680 AACCAAATAA
* *
2567690 GCTAAGGCATAT-AACTACACAC
1 GCTAAGGCATATAAACTAAACAT
* * *
2567712 GCTAAAGCATGTAAACTAAATAT
1 GCTAAGGCATATAAACTAAACAT
** *
2567735 GCTAAGGCATATAAAC-ATTCAA
1 GCTAAGGCATATAAACTAAACAT
* * *
2567757 GCTAAGGCATGTAAACAAAATAT
1 GCTAAGGCATATAAACTAAACAT
* *
2567780 GCTCAA-GCATATAATC-ACACAT
1 GCT-AAGGCATATAAACTAAACAT
2567802 GCTAAGGCAT
1 GCTAAGGCAT
2567812 GCAAACCAAA
Statistics
Matches: 76, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
21 2 0.03
22 38 0.50
23 34 0.45
24 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (23 bp):
GCTAAGGCATATAAACTAAACAT
Found at i:2568964 original size:21 final size:21
Alignment explanation
Indices: 2568924--2568964 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2568914 TCAAAACTTC
*
2568924 ATGTATTGATACTTTGTCAAA
1 ATGTATTGATAATTTGTCAAA
2568945 ATGTATTGATAGATTT-TCAA
1 ATGTATTGATA-ATTTGTCAA
2568965 CAGAATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATTGATAATTTGTCAAA
Found at i:2577013 original size:62 final size:62
Alignment explanation
Indices: 2576909--2577029 Score: 224
Period size: 62 Copynumber: 2.0 Consensus size: 62
2576899 TATAGTTGCC
*
2576909 ATTTTCAAATTGTTAATGGGGTAATGCTATGCCCTTTCAACTTTCTCGAGGTATAAGCTACT
1 ATTTCCAAATTGTTAATGGGGTAATGCTATGCCCTTTCAACTTTCTCGAGGTATAAGCTACT
*
2576971 ATTTCCAAATTGTTAATGGGGTAATGCTATGCCCTTTTAACTTTCTCGAGGTATAAGCT
1 ATTTCCAAATTGTTAATGGGGTAATGCTATGCCCTTTCAACTTTCTCGAGGTATAAGCT
2577030 GTCACTTTGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (62 bp):
ATTTCCAAATTGTTAATGGGGTAATGCTATGCCCTTTCAACTTTCTCGAGGTATAAGCTACT
Found at i:2580486 original size:119 final size:119
Alignment explanation
Indices: 2580275--2580502 Score: 350
Period size: 119 Copynumber: 1.9 Consensus size: 119
2580265 TGAGTGTATA
* * *
2580275 GGTTCTAACTCAGCCTAGAAAAGTTAGTTTTTGGGTTTTGGTTGCTCCCGGAAAAAACCATTGTT
1 GGTTCTAACTCAGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGGAAAAAACCATTGCT
* ** *
2580340 GAAGGTTGTGGTTGAACTTGTGAAAAGCCATTGTAAAAGCTTGGTGAAAGCTTG
66 GAAGGTTATGACTGAACTTGGGAAAAGCCATTGTAAAAGCTTGGTGAAAGCTTG
*
2580394 GGTTCTAACTTAGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGGAAAAAACCATTGCT
1 GGTTCTAACTCAGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGGAAAAAACCATTGCT
* *
2580459 GAAGGTTATGACTGAGGC-TGGGAAAAGCCATTGTAAAAGTTTGG
66 GAAGGTTATGACTGA-ACTTGGGAAAAGCCATTGTAAAAGCTTGG
2580503 GAATTTTATC
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
119 97 0.99
120 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (119 bp):
GGTTCTAACTCAGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGGAAAAAACCATTGCT
GAAGGTTATGACTGAACTTGGGAAAAGCCATTGTAAAAGCTTGGTGAAAGCTTG
Found at i:2589104 original size:119 final size:119
Alignment explanation
Indices: 2588893--2589131 Score: 345
Period size: 119 Copynumber: 2.0 Consensus size: 119
2588883 ATTGAGTGTA
* * * * *
2588893 TAGGTTCTAACTTAGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGAAAAAAATCGTTA
1 TAGGTTCTAACTCAACCTAGAAAAGTTAATTTTTGAGTTTTGGTTGATCCCGAAAAAAACCATTA
* *
2588958 TTAAAGGTTGTGGCTGAGCCTATGAAAAACCATCATAAAAGCTTGGTGAAAGCT
66 TTAAAGGTTATGGCTAAGCCTATGAAAAACCATCATAAAAGCTTGGTGAAAGCT
2589012 TAGGTTCTAACTCAACCTAGAAAAGTTAATTTTTG-GATTTTGGTTGATCCCGAAAAAAACCATT
1 TAGGTTCTAACTCAACCTAGAAAAGTTAATTTTTGAG-TTTTGGTTGATCCCGAAAAAAACCATT
* * * * **
2589076 GTTGAAGGTTATGGCTAAGCCTGTGAAAAGCCATTGTAAAAGCTTGGTGAAAGCT
65 ATTAAAGGTTATGGCTAAGCCTATGAAAAACCATCATAAAAGCTTGGTGAAAGCT
2589131 T
1 T
2589132 GCGAATTTCA
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
118 1 0.01
119 105 0.99
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.32
Consensus pattern (119 bp):
TAGGTTCTAACTCAACCTAGAAAAGTTAATTTTTGAGTTTTGGTTGATCCCGAAAAAAACCATTA
TTAAAGGTTATGGCTAAGCCTATGAAAAACCATCATAAAAGCTTGGTGAAAGCT
Found at i:2591520 original size:75 final size:74
Alignment explanation
Indices: 2591424--2591577 Score: 177
Period size: 75 Copynumber: 2.1 Consensus size: 74
2591414 ATAAGGGACT
* * * * * *
2591424 CTTTAATGAAAGAAGGGTCAAT-CTTTTCAACATAGAACACTATTCTTAAACATTCTATTTTAAA
1 CTTTAATGAAAGAAGAGTCAATCCTTTT-AACATAAAAAACAATTCTTAAACACTCCATTTTAAA
2591488 AGGATCAACC
65 AGGATCAACC
*
2591498 CTTTAATGAAA-AGAGAAGTCAATCCTTTTAACATAAAAAACAATTCTTAAGCACTCCATTTTAA
1 CTTTAATGAAAGA-AG-AGTCAATCCTTTTAACATAAAAAACAATTCTTAAACACTCCATTTTAA
* * *
2591562 AGGGATCGATC
64 AAGGATCAACC
2591573 CTTTA
1 CTTTA
2591578 TCTCTTAAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
73 1 0.01
74 13 0.19
75 48 0.72
76 5 0.07
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (74 bp):
CTTTAATGAAAGAAGAGTCAATCCTTTTAACATAAAAAACAATTCTTAAACACTCCATTTTAAAA
GGATCAACC
Found at i:2592011 original size:23 final size:22
Alignment explanation
Indices: 2591981--2592092 Score: 98
Period size: 23 Copynumber: 5.0 Consensus size: 22
2591971 TAAATGATAT
2591981 ATGCTAAGGCATGTCAACCAAAC
1 ATGCTAAGGCATGT-AACCAAAC
* **
2592004 ATGCTAAGGCATATAACCATTC
1 ATGCTAAGGCATGTAACCAAAC
* *
2592026 ACGCTAAGGCATGTAACCCAAAT
1 ATGCTAAGGCATGTAA-CCAAAC
* * * *
2592049 ATGCTAAAGCATATAATCACAC
1 ATGCTAAGGCATGTAACCAAAC
* *
2592071 ATGCTAGGGCATGCAAACCAAA
1 ATGCTAAGGCATG-TAACCAAA
2592093 TACATTAAGG
Statistics
Matches: 67, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
22 33 0.49
23 34 0.51
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (22 bp):
ATGCTAAGGCATGTAACCAAAC
Found at i:2592031 original size:22 final size:22
Alignment explanation
Indices: 2591983--2592043 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
2591973 AATGATATAT
*
2591983 GCTAAGGCATGTCAACCAAACAT
1 GCTAAGGCATGT-AACCAAACAC
* **
2592006 GCTAAGGCATATAACCATTCAC
1 GCTAAGGCATGTAACCAAACAC
2592028 GCTAAGGCATGTAACC
1 GCTAAGGCATGTAACC
2592044 CAAATATGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 22 0.67
23 11 0.33
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (22 bp):
GCTAAGGCATGTAACCAAACAC
Found at i:2592082 original size:45 final size:44
Alignment explanation
Indices: 2591981--2592094 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 44
2591971 TAAATGATAT
* * **
2591981 ATGCTAAGGCATGTCAACCAAACATGCTAAGGCATATAACCATTC
1 ATGCTAAGGCATGT-AACCAAATATGCTAAAGCATATAACCACAC
* *
2592026 ACGCTAAGGCATGTAACCCAAATATGCTAAAGCATATAATCACAC
1 ATGCTAAGGCATGTAA-CCAAATATGCTAAAGCATATAACCACAC
* *
2592071 ATGCTAGGGCATGCAAACCAAATA
1 ATGCTAAGGCATG-TAACCAAATA
2592095 CATTAAGGCA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
44 2 0.03
45 54 0.93
46 2 0.03
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (44 bp):
ATGCTAAGGCATGTAACCAAATATGCTAAAGCATATAACCACAC
Found at i:2614549 original size:49 final size:47
Alignment explanation
Indices: 2614470--2614570 Score: 132
Period size: 49 Copynumber: 2.1 Consensus size: 47
2614460 AGTAGAAATA
**
2614470 TTTTTAAATTTTGAAAAAAATCTATGAATTTTAAAAAACATAAAAATAAT
1 TTTTTAAATTTT-AAAAAAATCTAAAAATTTTAAAAAAC--AAAAATAAT
*
2614520 TTTTTAAATTTT-AAAAATTCTAAAAAATTTTAAAAAACAAAAATAAT
1 TTTTTAAATTTTAAAAAAATCT-AAAAATTTTAAAAAACAAAAATAAT
2614567 TTTT
1 TTTT
2614571 AATTATTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
47 13 0.28
48 8 0.17
49 14 0.30
50 12 0.26
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (47 bp):
TTTTTAAATTTTAAAAAAATCTAAAAATTTTAAAAAACAAAAATAAT
Found at i:2614567 original size:19 final size:19
Alignment explanation
Indices: 2614525--2614569 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2614515 ATAATTTTTT
* *
2614525 AAATTTTAAAAATTCTAAA
1 AAATTTTAAAAATACAAAA
2614544 AAATTTTAAAAA-ACAAAA
1 AAATTTTAAAAATACAAAA
2614562 ATAATTTT
1 A-AATTTT
2614570 TAATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTTTAAAAATACAAAA
Found at i:2630492 original size:58 final size:58
Alignment explanation
Indices: 2630428--2630541 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
2630418 AGCACAACCC
* * *
2630428 ATGCCTTTTCACA-GATCAAGCATAACCTCAA-TCTTTTCAAGGATCAAGCAGAACTTAT
1 ATGCCTTTTCA-AGGAGCAAACATAACCTCAACT-TTTTCAAGGATCAAGCAAAACTTAT
* *
2630486 ATGCCTTTTGAAGGAGCAAACATAACTTCAACTTTTTCAAGGATCAAGCAAAACTT
1 ATGCCTTTTCAAGGAGCAAACATAACCTCAACTTTTTCAAGGATCAAGCAAAACTT
2630542 TTACAATACT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 1 0.02
58 47 0.96
59 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (58 bp):
ATGCCTTTTCAAGGAGCAAACATAACCTCAACTTTTTCAAGGATCAAGCAAAACTTAT
Found at i:2630540 original size:28 final size:28
Alignment explanation
Indices: 2630433--2630541 Score: 89
Period size: 28 Copynumber: 3.8 Consensus size: 28
2630423 AACCCATGCC
*
2630433 TTTTCACA-GATCAAGCATAACCTCAA-T
1 TTTTCA-AGGATCAAGCATAACTTCAACT
* *
2630460 CTTTTCAAGGATCAAGCAGAACTT-ATATGCC
1 -TTTTCAAGGATCAAGCATAACTTCA-A--CT
* * *
2630491 TTTTGAAGGAGCAAACATAACTTCAACT
1 TTTTCAAGGATCAAGCATAACTTCAACT
*
2630519 TTTTCAAGGATCAAGCAAAACTT
1 TTTTCAAGGATCAAGCATAACTT
2630542 TTACAATACT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
27 2 0.03
28 40 0.63
30 20 0.32
31 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (28 bp):
TTTTCAAGGATCAAGCATAACTTCAACT
Found at i:2631037 original size:20 final size:22
Alignment explanation
Indices: 2631014--2631057 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2631004 GCCTGGAACT
*
2631014 TTTTTC-TTTTTGAGA-ATTGA
1 TTTTTCATTCTTGAGATATTGA
2631034 TTTTTCATTCTTGAGATATTGA
1 TTTTTCATTCTTGAGATATTGA
2631056 TT
1 TT
2631058 CTTTTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.20, C:0.07, G:0.14, T:0.59
Consensus pattern (22 bp):
TTTTTCATTCTTGAGATATTGA
Found at i:2634483 original size:12 final size:12
Alignment explanation
Indices: 2634466--2634490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2634456 TCATTTATTT
2634466 TGTACATATGTA
1 TGTACATATGTA
2634478 TGTACATATGTA
1 TGTACATATGTA
2634490 T
1 T
2634491 ATTATTATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TGTACATATGTA
Found at i:2659785 original size:21 final size:21
Alignment explanation
Indices: 2659761--2659800 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2659751 CTAGAGAGCA
2659761 ATTGCCAAAGTATCGAGACTT
1 ATTGCCAAAGTATCGAGACTT
* *
2659782 ATTGTCAATGTATCGAGAC
1 ATTGCCAAAGTATCGAGAC
2659801 CTTGTCTTCG
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:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (21 bp):
ATTGCCAAAGTATCGAGACTT
Found at i:2659850 original size:71 final size:72
Alignment explanation
Indices: 2659729--2659890 Score: 236
Period size: 71 Copynumber: 2.3 Consensus size: 72
2659719 TTGTGGATAT
* * * *
2659729 CTCATCTTCAAAACTTCAATTTCTAGAGAGCAATTGCCAAAGTATCGAGACTTATTGTCAATGTA
1 CTCATCTTCAGAACTTCAATTTCTAGAGAACAAGTGCCAAAATATCGAGACTTATTGTCAATGTA
*
2659794 TCGAGAC
66 TCGAAAC
** * *
2659801 CTTGTCTTCGGAACTTCAATTT-TAGAGAACAAGTGCCAAAATATCGAGACTTGTTGTCAATGTA
1 CTCATCTTCAGAACTTCAATTTCTAGAGAACAAGTGCCAAAATATCGAGACTTATTGTCAATGTA
2659865 TCGAAAC
66 TCGAAAC
2659872 CTCATCTTCAGAACTTCAA
1 CTCATCTTCAGAACTTCAA
2659891 ATTCCAAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
71 60 0.77
72 18 0.23
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (72 bp):
CTCATCTTCAGAACTTCAATTTCTAGAGAACAAGTGCCAAAATATCGAGACTTATTGTCAATGTA
TCGAAAC
Found at i:2672828 original size:21 final size:20
Alignment explanation
Indices: 2672800--2672838 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2672790 CAATGAGCAG
*
2672800 GTTTCCAAGTATTGAGACTT
1 GTTTCCAAGTATCGAGACTT
2672820 GTTTGCCAAGTATCGAGAC
1 GTTT-CCAAGTATCGAGAC
2672839 AATCTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
GTTTCCAAGTATCGAGACTT
Found at i:2675352 original size:21 final size:22
Alignment explanation
Indices: 2675323--2675366 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2675313 AAGTGATTAA
2675323 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
2675344 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2675366 T
1 T
2675367 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2677006 original size:14 final size:14
Alignment explanation
Indices: 2676969--2677000 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2676959 ATATATACTA
2676969 TATATATTTGTTAC
1 TATATATTTGTTAC
*
2676983 TATATATTTGTTAT
1 TATATATTTGTTAC
2676997 TATA
1 TATA
2677001 CTTTTGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (14 bp):
TATATATTTGTTAC
Found at i:2679650 original size:22 final size:25
Alignment explanation
Indices: 2679614--2679659 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
2679604 ATAATTATAA
*
2679614 ACCAAATGTTGTAAT-GTTATTTTT
1 ACCAAATGTTGTAATCATTATTTTT
2679638 ACCAAAT-TT-TAATCATTATTTT
1 ACCAAATGTTGTAATCATTATTTT
2679660 GCTTATACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (25 bp):
ACCAAATGTTGTAATCATTATTTTT
Found at i:2683297 original size:72 final size:72
Alignment explanation
Indices: 2683175--2683313 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 72
2683165 TTTCACATAA
*** * *
2683175 AAAACCACCTACAATCCCATAGTCACACTATGTTGTATAATTTTTGAATTGATATGACTTTCAAA
1 AAAACCACCTACAATCCCATAGTCACACTATGTCACATAACTTTTGAATTGATAAGACTTTCAAA
2683240 TAGTATG
66 TAGTATG
* ** *
2683247 AAAACCACCTACAATTCTTTGGTCACACTATGTCACATAACCTTTT-AATTGATAAGACTTTCAA
1 AAAACCACCTACAATCCCATAGTCACACTATGTCACATAA-CTTTTGAATTGATAAGACTTTCAA
2683311 ATA
65 ATA
2683314 ATCATAACTT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 53 0.93
73 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (72 bp):
AAAACCACCTACAATCCCATAGTCACACTATGTCACATAACTTTTGAATTGATAAGACTTTCAAA
TAGTATG
Found at i:2687701 original size:15 final size:16
Alignment explanation
Indices: 2687677--2687718 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2687667 CAACCATCTA
*
2687677 CTTCATCTCCA-GACT
1 CTTCACCTCCACGACT
2687692 CTTCACCTCCACGACT
1 CTTCACCTCCACGACT
* *
2687708 CATCCCCTCCA
1 CTTCACCTCCA
2687719 AATCTGCTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.19, C:0.50, G:0.05, T:0.26
Consensus pattern (16 bp):
CTTCACCTCCACGACT
Found at i:2716612 original size:29 final size:28
Alignment explanation
Indices: 2716565--2716727 Score: 139
Period size: 29 Copynumber: 5.6 Consensus size: 28
2716555 TGAGAACTTT
2716565 AACATGTTTGTCTTAATTTAGATAAA-AA
1 AACATGTTTGTCTTAATTTAGA-AAAGAA
2716593 AACATGTTTGGTCTTAATTTAGAAAAGAA
1 AACATGTTT-GTCTTAATTTAGAAAAGAA
* *
2716622 AAAATGTTTGTCTTAATTTAAAACAAGAAA
1 AACATGTTTGTCTTAATTTAGAA-AAG-AA
* * * **
2716652 AATATTTTTTGTCTTAATCTAGGCAAGAA
1 AACA-TGTTTGTCTTAATTTAGAAAAGAA
* * * *
2716681 AACATATTTGTCTCAATTTTGACAAGATA
1 AACATGTTTGTCTTAATTTAGAAAAGA-A
* * *
2716710 AATATTTTTATCTTAATT
1 AACATGTTTGTCTTAATT
2716728 AAAGACAAGA
Statistics
Matches: 111, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
28 43 0.39
29 46 0.41
30 8 0.07
31 14 0.13
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGAAAAGAA
Found at i:2716736 original size:88 final size:88
Alignment explanation
Indices: 2716571--2716737 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
2716561 CTTTAACATG
* * * * *
2716571 TTTGTCTTAATTTAGATAAAAAAACATGTTTGGTCTTAATTTAGAAAAGAAAAAATGTTTGTCTT
1 TTTGTCTTAATCTAGACAAAAAAACATATTTGGTCTCAATTTAGAAAAGAAAAAATGTTTATCTT
2716636 AATTTAAAACAAGAAAAATATTT
66 AATTTAAAACAAGAAAAATATTT
* * * * * *
2716659 TTTGTCTTAATCTAGGCAAGAAAACATATTT-GTCTCAATTTTGACAAGATAAATATTTTTATCT
1 TTTGTCTTAATCTAGACAAAAAAACATATTTGGTCTCAATTTAGAAAAGA-AAAAATGTTTATCT
2716723 TAA-TTAAAGACAAGA
65 TAATTTAAA-ACAAGA
2716738 GTTGTCTTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 20 0.30
88 46 0.70
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.38
Consensus pattern (88 bp):
TTTGTCTTAATCTAGACAAAAAAACATATTTGGTCTCAATTTAGAAAAGAAAAAATGTTTATCTT
AATTTAAAACAAGAAAAATATTT
Found at i:2716901 original size:17 final size:17
Alignment explanation
Indices: 2716879--2716911 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2716869 ATAATAATAA
2716879 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
2716896 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
2716912 TTATTAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:2721808 original size:50 final size:50
Alignment explanation
Indices: 2721747--2721845 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
2721737 TCCATTATCA
* *
2721747 GGGATTTTTGCTTTTTAATGGGAAGCGATAACCCTTACACAATCCATAAT
1 GGGATTCTTGCTTTTTAATGGGAAACGATAACCCTTACACAATCCATAAT
* * *
2721797 GGGATTCTTGCTTTTTAATGGGAAATGATAACCTTTACATAATCCATAA
1 GGGATTCTTGCTTTTTAATGGGAAACGATAACCCTTACACAATCCATAA
2721846 ATAAGTCTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (50 bp):
GGGATTCTTGCTTTTTAATGGGAAACGATAACCCTTACACAATCCATAAT
Found at i:2728570 original size:50 final size:49
Alignment explanation
Indices: 2728504--2728620 Score: 135
Period size: 50 Copynumber: 2.4 Consensus size: 49
2728494 CACAATCAAG
* * *
2728504 GATTCTTACTTTTTAATGGAAAGTGATAACCCTCACATAATCCACAAAGA
1 GATTCTTGCTTTTTAATGGAAAGCGATAACCCTCACACAATCCA-AAAGA
* * * * * * *
2728554 GATTTTTTCTTTTTAATGGGAAGCGATAATCCTTACACAATCCATAAGG
1 GATTCTTGCTTTTTAATGGAAAGCGATAACCCTCACACAATCCAAAAGA
2728603 GATTCTTGCTTTTTAATG
1 GATTCTTGCTTTTTAATG
2728621 AGATCAACTA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
49 19 0.34
50 37 0.66
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (49 bp):
GATTCTTGCTTTTTAATGGAAAGCGATAACCCTCACACAATCCAAAAGA
Found at i:2729230 original size:15 final size:15
Alignment explanation
Indices: 2729206--2729237 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2729196 AAATCTGGCC
2729206 TGCTACAGTCAACTA
1 TGCTACAGTCAACTA
*
2729221 TGCTATAGTCAACTA
1 TGCTACAGTCAACTA
2729236 TG
1 TG
2729238 GTTGTGCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (15 bp):
TGCTACAGTCAACTA
Found at i:2737800 original size:22 final size:22
Alignment explanation
Indices: 2737751--2737800 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2737741 TTTTGAGTTT
*
2737751 TCTTTTTATTTATTTGCATTTA
1 TCTTTTTAGTTATTTGCATTTA
* *
2737773 TGTTTTTAGTTATTTATCATTTA
1 TCTTTTTAGTTATTT-GCATTTA
2737796 -CTTTT
1 TCTTTT
2737801 CTTTATGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (22 bp):
TCTTTTTAGTTATTTGCATTTA
Found at i:2740928 original size:14 final size:14
Alignment explanation
Indices: 2740909--2740937 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2740899 AGATAAGTCG
2740909 AAAGACTTTTATAA
1 AAAGACTTTTATAA
2740923 AAAGACTTTTATAA
1 AAAGACTTTTATAA
2740937 A
1 A
2740938 TAATTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (14 bp):
AAAGACTTTTATAA
Found at i:2744181 original size:20 final size:19
Alignment explanation
Indices: 2744140--2744181 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2744130 TATTAGTTGA
* *
2744140 GTTTATTTTATGTTTAAAT
1 GTTTATTTTAAGTTAAAAT
2744159 GTTTATTTTAAGTTAATAAT
1 GTTTATTTTAAGTTAA-AAT
2744179 GTT
1 GTT
2744182 AGTTTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (19 bp):
GTTTATTTTAAGTTAAAAT
Found at i:2752649 original size:2 final size:2
Alignment explanation
Indices: 2752642--2752670 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2752632 TCAATAATTG
2752642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2752671 GACATACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2753959 original size:10 final size:10
Alignment explanation
Indices: 2753946--2753983 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
2753936 TTTATTATAT
2753946 TTAATTATTA
1 TTAATTATTA
2753956 TTAA-TAGTTA
1 TTAATTA-TTA
2753966 GTTAATTATTA
1 -TTAATTATTA
2753977 TTAATTA
1 TTAATTA
2753984 AAATATCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.08
10 14 0.56
11 7 0.28
12 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (10 bp):
TTAATTATTA
Found at i:2755146 original size:2 final size:2
Alignment explanation
Indices: 2755141--2755167 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2755131 TGTGTGTGTG
2755141 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2755168 GAACTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2756120 original size:21 final size:21
Alignment explanation
Indices: 2756094--2756137 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2756084 ATTGATCAAA
*
2756094 TTTTGTATATAGATAGTAATT
1 TTTTGTACATAGATAGTAATT
2756115 TTTTGTACATAGATAGTAATT
1 TTTTGTACATAGATAGTAATT
2756136 TT
1 TT
2756138 AAGGTCCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTTGTACATAGATAGTAATT
Found at i:2756761 original size:19 final size:19
Alignment explanation
Indices: 2756733--2756775 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
2756723 GGTTTCATTA
* *
2756733 AAATAATATTTTTTAATTT
1 AAATAATATTGTATAATTT
* *
2756752 TAATAGTATTGTATAATTT
1 AAATAATATTGTATAATTT
2756771 AAATA
1 AAATA
2756776 TTAATATTTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
AAATAATATTGTATAATTT
Found at i:2760077 original size:211 final size:211
Alignment explanation
Indices: 2759705--2760126 Score: 745
Period size: 211 Copynumber: 2.0 Consensus size: 211
2759695 CCTAGATAAC
*
2759705 TTGCCAATAGAAAACCCCCACTTTGGGAAGAGCAAGATTGGACCACACCATCTTCCAAGTATTAT
1 TTGCCAACAGAAAACCCCCACTTTGGGAAGAGCAAGATTGGACCACACCATCTTCCAAGTATTAT
* * *
2759770 CAAAACTAACATGATAACCAAAAATAGTTCTACAAAAAGACTTAGCAAAATAGTTACCACTAGTA
66 CAAAACTAACATGATAACAAAAAATAATGCTACAAAAAGACTTAGCAAAATAGTTACCACTAGTA
*
2759835 CTTCCTTTCCATATAAAGCTATCCGGCATATCCCTATCAAGAGAGAAGTTATAAACAATACCAAA
131 CTTCCTTTCCATATAAAGCTATCCAGCATATCCCTATCAAGAGAGAAGTTATAAACAATACCAAA
2759900 TAGTTGGTTCCATTGG
196 TAGTTGGTTCCATTGG
*
2759916 TTGCCAACAGAAAACCCCCACTTTGGGAAGAGCAAGATTGGACCACGCCATCTTCCAAGTATTAT
1 TTGCCAACAGAAAACCCCCACTTTGGGAAGAGCAAGATTGGACCACACCATCTTCCAAGTATTAT
* *
2759981 CAAAACTACCATGATAACAAAAAATAATGCTACAAAAAGACTTAGCAGAATAGTTACCACTAGTA
66 CAAAACTAACATGATAACAAAAAATAATGCTACAAAAAGACTTAGCAAAATAGTTACCACTAGTA
***
2760046 CTTCCTTTCCATATAACTTTATCCAGCATATCCCTATCAAGAGAGAAGTTATAAACAATACCAAA
131 CTTCCTTTCCATATAAAGCTATCCAGCATATCCCTATCAAGAGAGAAGTTATAAACAATACCAAA
2760111 TAGTTGGTTCCATTGG
196 TAGTTGGTTCCATTGG
2760127 ACTCTTTCCT
Statistics
Matches: 200, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
211 200 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (211 bp):
TTGCCAACAGAAAACCCCCACTTTGGGAAGAGCAAGATTGGACCACACCATCTTCCAAGTATTAT
CAAAACTAACATGATAACAAAAAATAATGCTACAAAAAGACTTAGCAAAATAGTTACCACTAGTA
CTTCCTTTCCATATAAAGCTATCCAGCATATCCCTATCAAGAGAGAAGTTATAAACAATACCAAA
TAGTTGGTTCCATTGG
Found at i:2764554 original size:19 final size:19
Alignment explanation
Indices: 2764532--2764575 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2764522 ATAAAATTTC
2764532 TTCTCTCCCCCTAAATACT
1 TTCTCTCCCCCTAAATACT
* * *
2764551 TTCTTTCTCTCTAAATACT
1 TTCTCTCCCCCTAAATACT
2764570 TTCTCT
1 TTCTCT
2764576 TATATTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.34, G:0.00, T:0.48
Consensus pattern (19 bp):
TTCTCTCCCCCTAAATACT
Found at i:2769328 original size:24 final size:24
Alignment explanation
Indices: 2769285--2769330 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2769275 AAGATTTTTA
**
2769285 AATTTTAATTTATTTTTATAAACT
1 AATTTTAATTTATTAATATAAACT
2769309 AATTTTAATTTATTAATATAAA
1 AATTTTAATTTATTAATATAAA
2769331 TTTCATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTTTAATTTATTAATATAAACT
Found at i:2770755 original size:61 final size:61
Alignment explanation
Indices: 2770660--2770797 Score: 267
Period size: 61 Copynumber: 2.3 Consensus size: 61
2770650 GCCCTACCCT
2770660 TTTCTTTTTTTTTTTTTTTTCGCCATATATTCTTATACAGTAGCCATTCCACACCATCTAG
1 TTTCTTTTTTTTTTTTTTTTCGCCATATATTCTTATACAGTAGCCATTCCACACCATCTAG
*
2770721 TTTCTTTTTTTTTTTTTTTTTGCCATATATTCTTATACAGTAGCCATTCCACACCATCTAG
1 TTTCTTTTTTTTTTTTTTTTCGCCATATATTCTTATACAGTAGCCATTCCACACCATCTAG
2770782 TTTCTTTTTTTTTTTT
1 TTTCTTTTTTTTTTTT
2770798 AAAAAAAATT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 76 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (61 bp):
TTTCTTTTTTTTTTTTTTTTCGCCATATATTCTTATACAGTAGCCATTCCACACCATCTAG
Found at i:2772047 original size:20 final size:20
Alignment explanation
Indices: 2771989--2772047 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
2771979 CATACCTATT
*
2771989 ATTATTTTTTAAT-TATTAA
1 ATTATTTTTAAATATATTAA
* *
2772008 AAT-TTTTTAAACATGA-TAA
1 ATTATTTTTAAATAT-ATTAA
*
2772027 ATTATTTTTGAATATATTAA
1 ATTATTTTTAAATATATTAA
2772047 A
1 A
2772048 AAAATATCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 7 0.23
19 9 0.30
20 14 0.47
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTATTTTTAAATATATTAA
Found at i:2774852 original size:18 final size:18
Alignment explanation
Indices: 2774784--2774852 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 18
2774774 GTTATTTTTT
* *
2774784 AACATAATTATTTGAATA
1 AACATAATTATTTAAACA
* * *
2774802 AACTTAATTATGTGAACA
1 AACATAATTATTTAAACA
*
2774820 AACATAACT-TTTAAACA
1 AACATAATTATTTAAACA
*
2774837 ATCATAATTATTTAAA
1 AACATAATTATTTAAA
2774853 AGATTTCTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
17 13 0.32
18 28 0.68
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.36
Consensus pattern (18 bp):
AACATAATTATTTAAACA
Found at i:2776930 original size:38 final size:38
Alignment explanation
Indices: 2776899--2776983 Score: 170
Period size: 38 Copynumber: 2.2 Consensus size: 38
2776889 GTCAAATTAG
2776899 TATATCATATCATCATTAATTATGATATGTCAACATGT
1 TATATCATATCATCATTAATTATGATATGTCAACATGT
2776937 TATATCATATCATCATTAATTATGATATGTCAACATGT
1 TATATCATATCATCATTAATTATGATATGTCAACATGT
2776975 TATATCATA
1 TATATCATA
2776984 ATCAATTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (38 bp):
TATATCATATCATCATTAATTATGATATGTCAACATGT
Found at i:2776939 original size:18 final size:18
Alignment explanation
Indices: 2776918--2776977 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
2776908 TCATCATTAA
2776918 TTATGATATGTCAACATG
1 TTATGATATGTCAACATG
* * *
2776936 TTAT-ATCATATCATCATTAA
1 TTATGAT-ATGTCAACA-T-G
2776956 TTATGATATGTCAACATG
1 TTATGATATGTCAACATG
2776974 TTAT
1 TTAT
2776978 ATCATAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 2 0.06
18 15 0.47
19 2 0.06
20 11 0.34
21 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (18 bp):
TTATGATATGTCAACATG
Found at i:2776959 original size:20 final size:20
Alignment explanation
Indices: 2776899--2776959 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
2776889 GTCAAATTAG
2776899 TATATCATATCATCATTAAT
1 TATATCATATCATCATTAAT
* * *
2776919 TATGAT-ATGTCAACA-T-GT
1 TAT-ATCATATCATCATTAAT
2776937 TATATCATATCATCATTAAT
1 TATATCATATCATCATTAAT
2776957 TAT
1 TAT
2776960 GATATGTCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 2 0.06
18 11 0.35
19 2 0.06
20 14 0.45
21 2 0.06
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATCATATCATCATTAAT
Found at i:2776991 original size:33 final size:33
Alignment explanation
Indices: 2776905--2776997 Score: 114
Period size: 38 Copynumber: 2.7 Consensus size: 33
2776895 TTAGTATATC
* *
2776905 ATATCATCATTAATTATGATATGTCAACATGTT
1 ATATCATAATCAATTATGATATGTCAACATGTT
2776938 ATATCATATCATCATTAATTATGATATGTCAACATGTT
1 ATATCATA--ATC---AATTATGATATGTCAACATGTT
*
2776976 ATATCATAATCAATTATAATAT
1 ATATCATAATCAATTATGATAT
2776998 TTAACATATC
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
33 17 0.33
35 2 0.04
36 3 0.06
38 30 0.58
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (33 bp):
ATATCATAATCAATTATGATATGTCAACATGTT
Found at i:2777102 original size:30 final size:30
Alignment explanation
Indices: 2777066--2777143 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
2777056 CAATCATTAG
2777066 TTATAAGGGTTTATTTGATTCAAAATAAAA
1 TTATAAGGGTTTATTTGATTCAAAATAAAA
*
2777096 TTATAAGGGTTTATTTGGTTCAAAATAAAA
1 TTATAAGGGTTTATTTGATTCAAAATAAAA
* *
2777126 TTATAATGGCTTATTTGA
1 TTATAAGGGTTTATTTGA
2777144 ATTTTCTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.42
Consensus pattern (30 bp):
TTATAAGGGTTTATTTGATTCAAAATAAAA
Found at i:2777572 original size:64 final size:64
Alignment explanation
Indices: 2777489--2777783 Score: 283
Period size: 64 Copynumber: 4.6 Consensus size: 64
2777479 GCCACGTGGC
* * * * **
2777489 CTTGATCAAGACTTAATCCATTCAAAAATGGATTCAATTTTTGACAAATTTGAAAACTGGTTAA
1 CTTGATCAAGGCTTGATCCATTCAAAAATGGATTCAATTTTTGAAAAATATGAAAACTACTTAA
* ** ** * *
2777553 CTTGATCAAGGATCAATCCATTCAAAAATGGATTTGA-TTTTG-AAAATATGAAAACTCCTTGA
1 CTTGATCAAGGCTTGATCCATTCAAAAATGGATTCAATTTTTGAAAAATATGAAAACTACTTAA
* * * * * * * * *
2777615 TTTGATTAAGGCTTGATTCATTTAAAATTGGATTCATTTTTTGAAAAATATAAAAACTATTTGA
1 CTTGATCAAGGCTTGATCCATTCAAAAATGGATTCAATTTTTGAAAAATATGAAAACTACTTAA
* * * * *
2777679 CTTGATCGAGGCTCGATCCATTCAAAAATGGATTCGA-TTTT-AAAAATCTTGAAAATTACTTAA
1 CTTGATCAAGGCTTGATCCATTCAAAAATGGATTCAATTTTTGAAAAAT-ATGAAAACTACTTAA
*
2777742 CTTGATCAAGGCTTGATCCATTCAGAAAAGGGATTCTAATTT
1 CTTGATCAAGGCTTGATCCATTCA-AAAATGGATTC-AATTT
2777784 GATGATGATG
Statistics
Matches: 183, Mismatches: 42, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
62 47 0.26
63 46 0.25
64 87 0.48
65 1 0.01
66 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (64 bp):
CTTGATCAAGGCTTGATCCATTCAAAAATGGATTCAATTTTTGAAAAATATGAAAACTACTTAA
Found at i:2777718 original size:126 final size:127
Alignment explanation
Indices: 2777489--2777783 Score: 349
Period size: 126 Copynumber: 2.3 Consensus size: 127
2777479 GCCACGTGGC
* * * * * *
2777489 CTTGATCAAGACTTAATCCATTCAAAAATGGATTCAATTTTTGACAAATTTGAAAACTGGTTAAC
1 CTTGATCAAGGCTTGATCCATTCAAAAATGGATTCAATTTTTGAAAAATATAAAAACTAGTTAAC
* * * *
2777554 TTGATCAAGGATCAATCCATTCAAAAATGGATTTGATTTTGAAAAT-ATGAAAACTCCTTGA
66 TTGATCAAGGATCAATCCATTCAAAAATGGATTCGATTTTAAAAATCATGAAAACTACTTAA
* * * * * * * *
2777615 TTTGATTAAGGCTTGATTCATTTAAAATTGGATTCATTTTTTGAAAAATATAAAAACTATTTGAC
1 CTTGATCAAGGCTTGATCCATTCAAAAATGGATTCAATTTTTGAAAAATATAAAAACTAGTTAAC
* * * * *
2777680 TTGATCGAGGCTCGATCCATTCAAAAATGGATTCGATTTTAAAAATCTTGAAAATTACTTAA
66 TTGATCAAGGATCAATCCATTCAAAAATGGATTCGATTTTAAAAATCATGAAAACTACTTAA
*
2777742 CTTGATCAAGGCTTGATCCATTCAGAAAAGGGATTCTAATTT
1 CTTGATCAAGGCTTGATCCATTCA-AAAATGGATTC-AATTT
2777784 GATGATGATG
Statistics
Matches: 136, Mismatches: 30, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
126 92 0.68
127 31 0.23
128 9 0.07
129 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (127 bp):
CTTGATCAAGGCTTGATCCATTCAAAAATGGATTCAATTTTTGAAAAATATAAAAACTAGTTAAC
TTGATCAAGGATCAATCCATTCAAAAATGGATTCGATTTTAAAAATCATGAAAACTACTTAA
Found at i:2778258 original size:2 final size:2
Alignment explanation
Indices: 2778251--2778275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2778241 AGCTAAGTTC
2778251 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2778276 ATTCAGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2779423 original size:22 final size:22
Alignment explanation
Indices: 2779398--2779440 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2779388 ACATAATATT
2779398 TAAAAACAAGTCACGCAATGCC
1 TAAAAACAAGTCACGCAATGCC
* *
2779420 TAAAAACTAGTCACGTAATGC
1 TAAAAACAAGTCACGCAATGC
2779441 AATATCGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (22 bp):
TAAAAACAAGTCACGCAATGCC
Found at i:2781254 original size:17 final size:16
Alignment explanation
Indices: 2781228--2781259 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2781218 ACATAGTGAC
2781228 AAAAATCAAATACATT
1 AAAAATCAAATACATT
2781244 AAAACATCAAATACAT
1 AAAA-ATCAAATACAT
2781260 CTTAAATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATCAAATACATT
Done.